Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007993.1 Hibiscus syriacus cultivar Beakdansim tig00110443_pilon, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 2245901
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 9 of 12
Found at i:1617621 original size:102 final size:102
Alignment explanation
Indices: 1617445--1617836 Score: 651
Period size: 102 Copynumber: 3.9 Consensus size: 102
1617435 CTTGAGACAG
** * * *
1617445 TTTCCCTTGAAACAAACTTTGTCTCTCTTGAGACAGTTTCCCTTGAAACAAATTTTTTTCTCCCT
1 TTTCCCTTGAAATGAATTTTGTCTCTCTTGAGATAGTTTCCCTTGAAACAAAATTTTTTCTCCCT
1617510 TGAGACAGTTTCTCTTGAAACATAAACATTGAAAACA
66 TGAGACAGTTTCTCTTGAAACATAAACATTGAAAACA
*
1617547 TTTCCCTTGAAATGAGTTTTGTCTCTCTTGAGATAGTTTCCCTTGAAACAAAATTTTTTCTCCCT
1 TTTCCCTTGAAATGAATTTTGTCTCTCTTGAGATAGTTTCCCTTGAAACAAAATTTTTTCTCCCT
*
1617612 TGAGACAGTTTCTCTTGAAACATAAACATTGGAAACA
66 TGAGACAGTTTCTCTTGAAACATAAACATTGAAAACA
* *
1617649 TTTCCCTTGAAATGAATTTTGTCTCTCTTGAGATAGTTTACCTTGAAACAAAATTTTATCTCCCT
1 TTTCCCTTGAAATGAATTTTGTCTCTCTTGAGATAGTTTCCCTTGAAACAAAATTTTTTCTCCCT
* *
1617714 TGAGACTGTTTCTCCTGAAACATAAACATTGAAAACA
66 TGAGACAGTTTCTCTTGAAACATAAACATTGAAAACA
* * *
1617751 TTTCCCTTGAAATGAATTTTGTTTCTCTTGAGATAATTTCCCTTGAAAC-AAATTTTGTCTCCCT
1 TTTCCCTTGAAATGAATTTTGTCTCTCTTGAGATAGTTTCCCTTGAAACAAAATTTTTTCTCCCT
1617815 TGAGACAGTTTCTCTTGAAACA
66 TGAGACAGTTTCTCTTGAAACA
1617837 CAAAACCTTT
Statistics
Matches: 271, Mismatches: 19, Indels: 1
0.93 0.07 0.00
Matches are distributed among these distances:
101 34 0.13
102 237 0.87
ACGTcount: A:0.29, C:0.20, G:0.12, T:0.38
Consensus pattern (102 bp):
TTTCCCTTGAAATGAATTTTGTCTCTCTTGAGATAGTTTCCCTTGAAACAAAATTTTTTCTCCCT
TGAGACAGTTTCTCTTGAAACATAAACATTGAAAACA
Found at i:1617622 original size:37 final size:37
Alignment explanation
Indices: 1617563--1617633 Score: 106
Period size: 37 Copynumber: 1.9 Consensus size: 37
1617553 TTGAAATGAG
* *
1617563 TTTTGTCTCTCTTGAGATAGTTTCCCTTGAAACAAAA
1 TTTTGTCTCCCTTGAGACAGTTTCCCTTGAAACAAAA
* *
1617600 TTTTTTCTCCCTTGAGACAGTTTCTCTTGAAACA
1 TTTTGTCTCCCTTGAGACAGTTTCCCTTGAAACA
1617634 TAAACATTGG
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
37 30 1.00
ACGTcount: A:0.24, C:0.21, G:0.13, T:0.42
Consensus pattern (37 bp):
TTTTGTCTCCCTTGAGACAGTTTCCCTTGAAACAAAA
Found at i:1617775 original size:21 final size:20
Alignment explanation
Indices: 1617751--1617789 Score: 51
Period size: 21 Copynumber: 1.9 Consensus size: 20
1617741 ATTGAAAACA
1617751 TTTCCCTTGAAATGAATTTTG
1 TTTCCCTTGAAAT-AATTTTG
* *
1617772 TTTCTCTTGAGATAATTT
1 TTTCCCTTGAAATAATTT
1617790 CCCTTGAAAC
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
20 5 0.31
21 11 0.69
ACGTcount: A:0.23, C:0.13, G:0.13, T:0.51
Consensus pattern (20 bp):
TTTCCCTTGAAATAATTTTG
Found at i:1617795 original size:204 final size:203
Alignment explanation
Indices: 1617445--1617903 Score: 659
Period size: 204 Copynumber: 2.2 Consensus size: 203
1617435 CTTGAGACAG
* * *
1617445 TTTCCCTTGAAACAAACTTTGTCTCTCTTGAGACAGTTTCCCTTGAAACAAATTTTTTTCTCCCT
1 TTTCCCTTGAAACAAACTTTGTCTCTCTTGAGACAGTTTACCTTGAAACAAAATTTTATCTCCCT
* *
1617510 TGAGACAGTTTCTCTTGAAACATAAACATTGAAAACATTTCCCTTGAAATGAGTTTTGTCTCTCT
66 TGAGACAGTTTCTCCTGAAACATAAACATTGAAAACATTTCCCTTGAAATGAATTTTGTCTCTCT
* *
1617575 TGAGATAGTTTCCCTTGAAACAAAATTTTTTCTCCCTTGAGACAGTTTCTCTTGAAACATAAACA
131 TGAGATAATTTCCCTTGAAAC-AAATTTTGTCTCCCTTGAGACAGTTTCTCTTGAAACATAAACA
1617640 TTGGAAACA
195 TTGGAAACA
** * *
1617649 TTTCCCTTGAAATGAATTTTGTCTCTCTTGAGATAGTTTACCTTGAAACAAAATTTTATCTCCCT
1 TTTCCCTTGAAACAAACTTTGTCTCTCTTGAGACAGTTTACCTTGAAACAAAATTTTATCTCCCT
* *
1617714 TGAGACTGTTTCTCCTGAAACATAAACATTGAAAACATTTCCCTTGAAATGAATTTTGTTTCTCT
66 TGAGACAGTTTCTCCTGAAACATAAACATTGAAAACATTTCCCTTGAAATGAATTTTGTCTCTCT
* *
1617779 TGAGATAATTTCCCTTGAAACAAATTTTGTCTCCCTTGAGACAGTTTCTCTTGAAACACAAAACC
131 TGAGATAATTTCCCTTGAAACAAATTTTGTCTCCCTTGAGACAGTTTCTCTTGAAACA-TAAACA
* ***
1617844 TTTGAGATTG
195 TTGGA-AACA
* * * * *
1617854 TTTCCCTCGAAAAAAATTTTGTCTCCCATGAGACAGTTT-CTCTTGAAACA
1 TTTCCCTTGAAACAAACTTTGTCTCTCTTGAGACAGTTTAC-CTTGAAACA
1617904 CAAAATCTTT
Statistics
Matches: 227, Mismatches: 25, Indels: 5
0.88 0.10 0.02
Matches are distributed among these distances:
203 36 0.16
204 148 0.65
205 43 0.19
ACGTcount: A:0.29, C:0.21, G:0.12, T:0.37
Consensus pattern (203 bp):
TTTCCCTTGAAACAAACTTTGTCTCTCTTGAGACAGTTTACCTTGAAACAAAATTTTATCTCCCT
TGAGACAGTTTCTCCTGAAACATAAACATTGAAAACATTTCCCTTGAAATGAATTTTGTCTCTCT
TGAGATAATTTCCCTTGAAACAAATTTTGTCTCCCTTGAGACAGTTTCTCTTGAAACATAAACAT
TGGAAACA
Found at i:1617797 original size:36 final size:36
Alignment explanation
Indices: 1617750--1617836 Score: 111
Period size: 36 Copynumber: 2.4 Consensus size: 36
1617740 CATTGAAAAC
** * * *
1617750 ATTTCCCTTGAAATGAATTTTGTTTCTCTTGAGATA
1 ATTTCCCTTGAAACAAATTTTGTCTCCCTTGAGACA
1617786 ATTTCCCTTGAAACAAATTTTGTCTCCCTTGAGACA
1 ATTTCCCTTGAAACAAATTTTGTCTCCCTTGAGACA
* *
1617822 GTTTCTCTTGAAACA
1 ATTTCCCTTGAAACA
1617837 CAAAACCTTT
Statistics
Matches: 44, Mismatches: 7, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
36 44 1.00
ACGTcount: A:0.26, C:0.20, G:0.13, T:0.41
Consensus pattern (36 bp):
ATTTCCCTTGAAACAAATTTTGTCTCCCTTGAGACA
Found at i:1617927 original size:67 final size:67
Alignment explanation
Indices: 1617778--1617915 Score: 222
Period size: 67 Copynumber: 2.1 Consensus size: 67
1617768 TTTGTTTCTC
** * * *
1617778 TTGAGATAATTTCCCTTGAAACAAATTTTGTCTCCCTTGAGACAGTTTCTCTTGAAACACAAAAC
1 TTGAGATTGTTTCCCTCGAAAAAAATTTTGTCTCCCATGAGACAGTTTCTCTTGAAACACAAAAC
1617843 CT
66 CT
*
1617845 TTGAGATTGTTTCCCTCGAAAAAAATTTTGTCTCCCATGAGACAGTTTCTCTTGAAACACAAAAT
1 TTGAGATTGTTTCCCTCGAAAAAAATTTTGTCTCCCATGAGACAGTTTCTCTTGAAACACAAAAC
1617910 CT
66 CT
1617912 TTGA
1 TTGA
1617916 ATTTATCTCC
Statistics
Matches: 65, Mismatches: 6, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
67 65 1.00
ACGTcount: A:0.31, C:0.21, G:0.13, T:0.35
Consensus pattern (67 bp):
TTGAGATTGTTTCCCTCGAAAAAAATTTTGTCTCCCATGAGACAGTTTCTCTTGAAACACAAAAC
CT
Found at i:1618710 original size:108 final size:109
Alignment explanation
Indices: 1618521--1618987 Score: 561
Period size: 108 Copynumber: 4.3 Consensus size: 109
1618511 TAGAGTCAAA
* * * * *
1618521 TTCAACTTCACAACGAAAGGACGGCTGGTTGCCAAC-AATAATTTCCCAATTTCGGAACCGATTT
1 TTCAACTTCACAACGAAGGGACGGCTGGTTGTCAACGAACAACTTCCCAATTTCAGAACCGATTT
1618585 CAACTCCACGACGGAGGATATCGTGCTACCCGAGACAACACAAG
66 CAACTCCACGACGGAGGATATCGTGCTACCCGAGACAACACAAG
* *
1618629 TTCAACTTCACAGCGAAGGGACGGCTGGTTGTCAACGAACAACTTCCCAA-TCCAGAACCGATTT
1 TTCAACTTCACAACGAAGGGACGGCTGGTTGTCAACGAACAACTTCCCAATTTCAGAACCGATTT
*
1618693 CAACTCCACGACGGAGGATATCGTGCTACCCGAGAAAACACAAG
66 CAACTCCACGACGGAGGATATCGTGCTACCCGAGACAACACAAG
* * * * ** * **
1618737 TCCAACTTCACAACGAAGGGACAGCTAGTTGTCAATGAACAACTTTTCAGTTTCA-TCCGCGATT
1 TTCAACTTCACAACGAAGGGACGGCTGGTTGTCAACGAACAACTTCCCAATTTCAGAAC-CGATT
* *
1618801 TCAACTCCACGACGGAGGATATCGTGCCACTCGAGACAACACAAG
65 TCAACTCCACGACGGAGGATATCGTGCTACCCGAGACAACACAAG
* ** * ** * * * *
1618846 TTCAACTTCACAATGAAGGGACAACTGGTTGTCAACAAACATTTTTCAAATTTCAGAGCCAATTT
1 TTCAACTTCACAACGAAGGGACGGCTGGTTGTCAACGAACAACTTCCCAATTTCAGAACCGATTT
* * * *
1618911 CAACTTCAC-AGCGAAGGATAT--TG-GACTCGAGACAACACAAG
66 CAACTCCACGA-CGGAGGATATCGTGCTACCCGAGACAACACAAG
*
1618952 TTCAACTTCACAACGAAGGGACGGCTGATTGTCAAC
1 TTCAACTTCACAACGAAGGGACGGCTGGTTGTCAAC
1618988 AAGATTTCGT
Statistics
Matches: 311, Mismatches: 43, Indels: 12
0.85 0.12 0.03
Matches are distributed among these distances:
106 49 0.16
107 2 0.01
108 132 0.42
109 127 0.41
110 1 0.00
ACGTcount: A:0.33, C:0.26, G:0.19, T:0.21
Consensus pattern (109 bp):
TTCAACTTCACAACGAAGGGACGGCTGGTTGTCAACGAACAACTTCCCAATTTCAGAACCGATTT
CAACTCCACGACGGAGGATATCGTGCTACCCGAGACAACACAAG
Found at i:1619050 original size:100 final size:102
Alignment explanation
Indices: 1618521--1619145 Score: 445
Period size: 108 Copynumber: 5.9 Consensus size: 102
1618511 TAGAGTCAAA
* * * * * * * *
1618521 TTCAACTTCACAACGAAAGGACGGCTGGTTGCCAACAATAATTTCCCAATTTCGGAACCGATTTC
1 TTCAACTTCACAACGAAGGGACGGCTGATTGTCAACAAAAATTT--C-AGTTCAGAGCCAATTTC
* * * *
1618586 AACTCCAC-GACGGAGGATATCGTGCTACCCGAGACAACACAAG
63 AACTTCACAG-CGAAGGATAT--TG-GACTCGAGACAACACAAG
* * * * * * * *
1618629 TTCAACTTCACAGCGAAGGGACGGCTGGTTGTCAACGAACAACTTCCCAATCCAGAACCGATTTC
1 TTCAACTTCACAACGAAGGGACGGCTGATTGTCAAC-AA-AAATT-TCAGTTCAGAGCCAATTTC
* * * * *
1618694 AACTCCAC-GACGGAGGATATCGTGCTACCCGAGAAAACACAAG
63 AACTTCACAG-CGAAGGATAT--TG-GACTCGAGACAACACAAG
* * * * ** *
1618737 TCCAACTTCACAACGAAGGGACAGCT-AGTTGTCAATGAACAACTTTTCAGTTTCA-TCCGCGAT
1 TTCAACTTCACAACGAAGGGACGGCTGA-TTGTCAA-CAA-AA-ATTTCAG-TTCAGAGC-CAAT
* * *
1618800 TTCAACTCCAC-GACGGAGGATATCGTGCCACTCGAGACAACACAAG
60 TTCAACTTCACAG-CGAAGGATAT--TG-GACTCGAGACAACACAAG
* ** * * *
1618846 TTCAACTTCACAATGAAGGGACAACTGGTTGTCAACAAACATTTTTCAAATTTCAGAGCCAATTT
1 TTCAACTTCACAACGAAGGGACGGCTGATTGTCAACAAA-A-ATTTC--AGTTCAGAGCCAATTT
1618911 CAACTTCACAGCGAAGGATATTGGACTCGAGACAACACAAG
62 CAACTTCACAGCGAAGGATATTGGACTCGAGACAACACAAG
* *
1618952 TTCAACTTCACAACGAAGGGACGGCTGATTGTCAAC-AAGATTTC-GTTCAGAGTCAATTTCAAC
1 TTCAACTTCACAACGAAGGGACGGCTGATTGTCAACAAAAATTTCAGTTCAGAGCCAATTTCAAC
* *
1619015 TTCACAGCGAAGGATATTAGACTCGAGACAGCACAAG
66 TTCACAGCGAAGGATATTGGACTCGAGACAACACAAG
* * * * * *
1619052 CTCAACTTCACAGCGAAGGGGCGGCTGACTGTCAACAAATAATTTCCCGGTTCCAGAACCAATTT
1 TTCAACTTCACAACGAAGGGACGGCTGATTGTCAACAAA-AATTT--CAGTT-CAGAGCCAATTT
*
1619117 CAACTTCACAGCGGAGGATATTGGACTCG
62 CAACTTCACAGCGAAGGATATTGGACTCG
1619146 GAACAATATT
Statistics
Matches: 441, Mismatches: 56, Indels: 42
0.82 0.10 0.08
Matches are distributed among these distances:
100 84 0.19
101 2 0.00
102 4 0.01
103 4 0.01
104 1 0.00
105 5 0.01
106 86 0.20
107 3 0.01
108 135 0.31
109 111 0.25
110 6 0.01
ACGTcount: A:0.33, C:0.26, G:0.20, T:0.22
Consensus pattern (102 bp):
TTCAACTTCACAACGAAGGGACGGCTGATTGTCAACAAAAATTTCAGTTCAGAGCCAATTTCAAC
TTCACAGCGAAGGATATTGGACTCGAGACAACACAAG
Found at i:1619116 original size:206 final size:209
Alignment explanation
Indices: 1618581--1619145 Score: 590
Period size: 206 Copynumber: 2.7 Consensus size: 209
1618571 TTCGGAACCG
* *
1618581 ATTTCAACTCCACGACGGAGGATATCGTGCTACCCGAGACAACACAAGTTCAACTTCACAGCGAA
1 ATTTCAACTCCACGACGAAGGATATC-TGC-ACTCGAGACAACACAAGTTCAACTTCACAGCGAA
* * * * *
1618646 GGGACGGCTGGTTGTCAACGAACAACTTCCCAATCCAGAACCGATTTCAACTCCAC-GACGGAGG
64 GGGACGGCTGGTTGTCAACAAACAATTTCCCATTCCAGAACCAATTTCAACTTCACAG-CGGAGG
* *
1618710 ATATCGTGCTACCCGAGAAAACACAAGTCCAACTTCACAACGAAGGGACAGCTAGTTGTCAATGA
128 ATAT--TG-GACTCGAGAAAACACAAGTCCAACTTCACAACGAAGGGACAGCTAGTTGTC-A--A
* * *
1618775 ACAACTTTTCAGTTTCATCCGCG
187 ACAACATTTCAGTTTCATCAGCA
* **
1618798 ATTTCAACTCCACGACGGAGGATATCGTGCCACTCGAGACAACACAAGTTCAACTTCACAATGAA
1 ATTTCAACTCCACGACGAAGGATATC-TG-CACTCGAGACAACACAAGTTCAACTTCACAGCGAA
** * ** * * *
1618863 GGGACAACTGGTTGTCAACAAACATTTTTCAAATTTCAGAGCCAATTTCAACTTCACAGCGAAGG
64 GGGACGGCTGGTTGTCAACAAACA-ATTTCCCATTCCAGAACCAATTTCAACTTCACAGCGGAGG
* * * *
1618928 ATATTGGACTCGAGACAACACAAGTTCAACTTCACAACGAAGGGACGGCT-GATTGTC-AACAAG
128 ATATTGGACTCGAGAAAACACAAGTCCAACTTCACAACGAAGGGACAGCTAG-TTGTCAAACAAC
*
1618991 ATTTC-G-TTCA-GAGTCA
192 ATTTCAGTTTCATCAG-CA
* * *
1619007 ATTTCAACTTCAC-AGCGAAGGATAT-TAG-ACTCGAGACAGCACAAGCTCAACTTCACAGCGAA
1 ATTTCAACTCCACGA-CGAAGGATATCT-GCACTCGAGACAACACAAGTTCAACTTCACAGCGAA
* ** * *
1619069 GGGGCGGCTGACTGTCAACAAATAATTTCCCGGTTCCAGAACCAATTTCAACTTCACAGCGGAGG
64 GGGACGGCTGGTTGTCAACAAACAATTTCCC-ATTCCAGAACCAATTTCAACTTCACAGCGGAGG
1619134 ATATTGGACTCG
128 ATATTGGACTCG
1619146 GAACAATATT
Statistics
Matches: 295, Mismatches: 45, Indels: 27
0.80 0.12 0.07
Matches are distributed among these distances:
205 4 0.01
206 89 0.30
207 1 0.00
208 3 0.01
209 26 0.09
210 1 0.00
211 9 0.03
214 1 0.00
215 44 0.15
216 2 0.01
217 81 0.27
218 33 0.11
219 1 0.00
ACGTcount: A:0.33, C:0.26, G:0.20, T:0.21
Consensus pattern (209 bp):
ATTTCAACTCCACGACGAAGGATATCTGCACTCGAGACAACACAAGTTCAACTTCACAGCGAAGG
GACGGCTGGTTGTCAACAAACAATTTCCCATTCCAGAACCAATTTCAACTTCACAGCGGAGGATA
TTGGACTCGAGAAAACACAAGTCCAACTTCACAACGAAGGGACAGCTAGTTGTCAAACAACATTT
CAGTTTCATCAGCA
Found at i:1619704 original size:37 final size:36
Alignment explanation
Indices: 1619610--1619706 Score: 115
Period size: 36 Copynumber: 2.6 Consensus size: 36
1619600 GTCCTACTAG
1619610 GATTCAAACT-CTCAAAAATAGGATAGAATTCTGCTAT
1 GATT-AAACTCCT-AAAAATAGGATAGAATTCTGCTAT
* * *
1619647 GATTCAACTCCTAAAAATAGGATAGAATTTTTCTAT
1 GATTAAACTCCTAAAAATAGGATAGAATTCTGCTAT
* *
1619683 GTTTTAAACTCCTAAAGATAGGAT
1 G-ATTAAACTCCTAAAAATAGGAT
1619707 CCACAAGCAC
Statistics
Matches: 52, Mismatches: 6, Indels: 4
0.84 0.10 0.06
Matches are distributed among these distances:
36 27 0.52
37 25 0.48
ACGTcount: A:0.39, C:0.14, G:0.13, T:0.33
Consensus pattern (36 bp):
GATTAAACTCCTAAAAATAGGATAGAATTCTGCTAT
Found at i:1620171 original size:11 final size:11
Alignment explanation
Indices: 1620151--1620234 Score: 55
Period size: 11 Copynumber: 7.3 Consensus size: 11
1620141 TTAATTATTT
*
1620151 TTATTCTAATA
1 TTATTTTAATA
*
1620162 TTATTTTAATG
1 TTATTTTAATA
1620173 TT-TTTTAA-A
1 TTATTTTAATA
*
1620182 GTTATTATATATA
1 -TTATTTTA-ATA
1620195 TATATTTATAACTA
1 T-TATTT-TAA-TA
*
1620209 TTATATTTATTA
1 TTAT-TTTAATA
*
1620221 TTATTTTACTA
1 TTATTTTAATA
1620232 TTA
1 TTA
1620235 ACGTATATAA
Statistics
Matches: 58, Mismatches: 7, Indels: 16
0.72 0.09 0.20
Matches are distributed among these distances:
10 8 0.14
11 24 0.41
12 8 0.14
13 11 0.19
14 7 0.12
ACGTcount: A:0.35, C:0.04, G:0.02, T:0.60
Consensus pattern (11 bp):
TTATTTTAATA
Found at i:1620225 original size:15 final size:15
Alignment explanation
Indices: 1620183--1620225 Score: 50
Period size: 15 Copynumber: 2.7 Consensus size: 15
1620173 TTTTTTAAAG
1620183 TTATTATATATATATAT
1 TTATTAT-TAT-TATAT
* *
1620200 TTATAACTATTATAT
1 TTATTATTATTATAT
1620215 TTATTATTATT
1 TTATTATTATT
1620226 TTACTATTAA
Statistics
Matches: 22, Mismatches: 4, Indels: 2
0.79 0.14 0.07
Matches are distributed among these distances:
15 14 0.64
16 3 0.14
17 5 0.23
ACGTcount: A:0.37, C:0.02, G:0.00, T:0.60
Consensus pattern (15 bp):
TTATTATTATTATAT
Found at i:1620436 original size:21 final size:22
Alignment explanation
Indices: 1620403--1620460 Score: 64
Period size: 21 Copynumber: 2.7 Consensus size: 22
1620393 CATGTATTTA
* *
1620403 TATTATTATTATTATTTTACTT
1 TATTATAATTATTATTTTACGT
* *
1620425 TATTA-AATTATTTTTTTTCGT
1 TATTATAATTATTATTTTACGT
*
1620446 TATTATATTTATTAT
1 TATTATAATTATTAT
1620461 ATATATATAT
Statistics
Matches: 29, Mismatches: 6, Indels: 2
0.78 0.16 0.05
Matches are distributed among these distances:
21 17 0.59
22 12 0.41
ACGTcount: A:0.28, C:0.03, G:0.02, T:0.67
Consensus pattern (22 bp):
TATTATAATTATTATTTTACGT
Found at i:1629239 original size:20 final size:19
Alignment explanation
Indices: 1629185--1629230 Score: 56
Period size: 20 Copynumber: 2.3 Consensus size: 19
1629175 CTGGTAGCGC
*
1629185 TTTACCGGTTTTATCATTT
1 TTTACCAGTTTTATCATTT
*
1629204 TGATACCAGTTTTATCATATT
1 T-TTACCAGTTTTATCAT-TT
1629225 TTTACC
1 TTTACC
1629231 TGTTATATCG
Statistics
Matches: 22, Mismatches: 3, Indels: 3
0.79 0.11 0.11
Matches are distributed among these distances:
19 1 0.05
20 18 0.82
21 3 0.14
ACGTcount: A:0.22, C:0.17, G:0.09, T:0.52
Consensus pattern (19 bp):
TTTACCAGTTTTATCATTT
Found at i:1631315 original size:2 final size:2
Alignment explanation
Indices: 1631286--1631456 Score: 112
Period size: 2 Copynumber: 94.0 Consensus size: 2
1631276 TTAAATAAAA
* *
1631286 AT AT A- AT AA AT A- AT AT AT A- AC AT A- AT AT AT A- AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
*
1631323 AT A- AT AT AT AT AT AT -T AT ACC AT A- AT AT A- AT AT A- AT AT
1 AT AT AT AT AT AT AT AT AT AT A-T AT AT AT AT AT AT AT AT AT AT
*
1631361 A- AT AT AT AT AT A- AT ACT AT AT ACT AT A- AT AT A- AT AT GT AT
1 AT AT AT AT AT AT AT AT A-T AT AT A-T AT AT AT AT AT AT AT AT AT
* * *
1631401 AC A- AT A- AA AT AT AT A- AT AT AT A- AT AT AC AT AT A- AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1631438 AT AT AT AT AT AT AT -T AT AT
1 AT AT AT AT AT AT AT AT AT AT
1631457 TTTCAAAAAT
Statistics
Matches: 135, Mismatches: 11, Indels: 46
0.70 0.06 0.24
Matches are distributed among these distances:
1 20 0.15
2 110 0.81
3 5 0.04
ACGTcount: A:0.54, C:0.04, G:0.01, T:0.41
Consensus pattern (2 bp):
AT
Found at i:1631317 original size:7 final size:7
Alignment explanation
Indices: 1631286--1631456 Score: 94
Period size: 7 Copynumber: 24.6 Consensus size: 7
1631276 TTAAATAAAA
1631286 ATATAAT
1 ATATAAT
*
1631293 AAATAAT
1 ATATAAT
1631300 ATAT-A-
1 ATATAAT
*
1631305 ACATAAT
1 ATATAAT
1631312 ATATAAT
1 ATATAAT
1631319 ATAT-AT
1 ATATAAT
1631325 A-ATATAT
1 ATATA-AT
*
1631332 ATATATT
1 ATATAAT
**
1631339 ATACCAT
1 ATATAAT
1631346 A-AT-AT
1 ATATAAT
1631351 AATATAAT
1 -ATATAAT
1631359 ATAATATAT
1 AT-ATA-AT
1631368 ATATAAT
1 ATATAAT
1631375 ACTAT-AT
1 A-TATAAT
1631382 ACTATAAT
1 A-TATAAT
1631390 ATA-ATAT
1 ATATA-AT
*
1631397 GTATACA-
1 ATATA-AT
*
1631404 ATAAAAT
1 ATATAAT
1631411 ATATAAT
1 ATATAAT
1631418 ATATAAT
1 ATATAAT
*
1631425 ATA-CAT
1 ATATAAT
1631431 ATA-ATAT
1 ATATA-AT
1631438 ATATATAT
1 ATATA-AT
*
1631446 ATATATT
1 ATATAAT
1631453 ATAT
1 ATAT
1631457 TTTCAAAAAT
Statistics
Matches: 130, Mismatches: 17, Indels: 34
0.72 0.09 0.19
Matches are distributed among these distances:
5 7 0.05
6 14 0.11
7 77 0.59
8 28 0.22
9 4 0.03
ACGTcount: A:0.54, C:0.04, G:0.01, T:0.41
Consensus pattern (7 bp):
ATATAAT
Found at i:1631470 original size:22 final size:22
Alignment explanation
Indices: 1631445--1631512 Score: 75
Period size: 22 Copynumber: 3.0 Consensus size: 22
1631435 TATATATATA
1631445 TATATATTATATTTTCAAAAAT
1 TATATATTATATTTTCAAAAAT
* * *
1631467 TATATAATATGTTTTC-AAAAC
1 TATATATTATATTTTCAAAAAT
*
1631488 TATATTATATACATTTTCAAAAAT
1 TATA-TAT-TATATTTTCAAAAAT
1631512 T
1 T
1631513 GTTTTTTTAA
Statistics
Matches: 36, Mismatches: 7, Indels: 4
0.77 0.15 0.09
Matches are distributed among these distances:
21 8 0.22
22 16 0.44
23 7 0.19
24 5 0.14
ACGTcount: A:0.44, C:0.07, G:0.01, T:0.47
Consensus pattern (22 bp):
TATATATTATATTTTCAAAAAT
Found at i:1631476 original size:5 final size:5
Alignment explanation
Indices: 1631285--1631455 Score: 120
Period size: 5 Copynumber: 33.2 Consensus size: 5
1631275 GTTAAATAAA
*
1631285 AATAT AATA- AATA- ATATAT AACAT AATAT -ATAAT ATATAT AATAT
1 AATAT AATAT AATAT A-ATAT AATAT AATAT AAT-AT A-ATAT AATAT
* **
1631330 ATATAT ATTAT ACCAT AATAT AATAT AATAT AATAT ATATAT AATACT
1 A-ATAT AATAT AATAT AATAT AATAT AATAT AATAT A-ATAT AATA-T
* * * *
1631378 -ATAT ACTAT AATAT AATAT GTATAC AATAA AATAT -ATA- ATATAT AATAT
1 AATAT AATAT AATAT AATAT -AATAT AATAT AATAT AATAT A-ATAT AATAT
*
1631427 ACATAT AATAT ATATAT ATATAT ATTAT A
1 A-ATAT AATAT A-ATAT A-ATAT AATAT A
1631456 TTTTCAAAAA
Statistics
Matches: 136, Mismatches: 15, Indels: 30
0.75 0.08 0.17
Matches are distributed among these distances:
4 11 0.08
5 88 0.65
6 35 0.26
7 2 0.01
ACGTcount: A:0.55, C:0.04, G:0.01, T:0.40
Consensus pattern (5 bp):
AATAT
Found at i:1631548 original size:37 final size:38
Alignment explanation
Indices: 1631488--1631569 Score: 112
Period size: 37 Copynumber: 2.2 Consensus size: 38
1631478 TTTTCAAAAC
**
1631488 TATATTATATACATTTTCAAAAATTGTTTTTTTAAACAA
1 TATATTATATACA-TTTCAAAAATTGTTTTTAAAAACAA
* *
1631527 TATATTATATGC-TTTCAAAAATTGTTTTTAAAAACTA
1 TATATTATATACATTTCAAAAATTGTTTTTAAAAACAA
1631564 TATATT
1 TATATT
1631570 CGATGTTTTA
Statistics
Matches: 39, Mismatches: 4, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
37 28 0.72
39 11 0.28
ACGTcount: A:0.40, C:0.07, G:0.04, T:0.49
Consensus pattern (38 bp):
TATATTATATACATTTCAAAAATTGTTTTTAAAAACAA
Found at i:1631594 original size:37 final size:34
Alignment explanation
Indices: 1631521--1631692 Score: 130
Period size: 37 Copynumber: 4.8 Consensus size: 34
1631511 TTGTTTTTTT
* * **
1631521 AAACAATATATTATATGCTTTCAAAAATTGTTTTTAA
1 AAACTATATATTATATG-TTTTAAAAA-T-CATTTAA
** *
1631558 AAACTATATATTCGATGTTTTAAAAATCGTCCTTTAA
1 AAACTATATATTATATGTTTTAAAAA---TCATTTAA
* *
1631595 AATA-TATATATGATATGTTTTCAAAATCATTTAA
1 AA-ACTATATATTATATGTTTTAAAAATCATTTAA
*
1631629 AAACTATATATTATATGTTTTAAAAAACACGTTTTAA
1 AAACTATATATTATATGTTTTAAAAATCA---TTTAA
* * *
1631666 AAACTGTATATTATATGATTTCAAAAT
1 AAACTATATATTATATGTTTTAAAAAT
1631693 ATATTTTCGA
Statistics
Matches: 109, Mismatches: 19, Indels: 14
0.77 0.13 0.10
Matches are distributed among these distances:
33 1 0.01
34 31 0.28
36 8 0.07
37 67 0.61
38 2 0.02
ACGTcount: A:0.43, C:0.09, G:0.06, T:0.42
Consensus pattern (34 bp):
AAACTATATATTATATGTTTTAAAAATCATTTAA
Found at i:1631665 original size:71 final size:70
Alignment explanation
Indices: 1631553--1631692 Score: 176
Period size: 71 Copynumber: 2.0 Consensus size: 70
1631543 AAAAATTGTT
* * *
1631553 TTTAAAAACTATATATTCGATGTTTTAAAAATCGTCCTTTAAAATA-TATATATGATATGTTTTC
1 TTTAAAAACTATATATTAGATGTTTTAAAAAACGT-CTTTAAAA-ACTATATATGATATGATTTC
1631617 AAAATCA
64 AAAATCA
* * *
1631624 TTTAAAAACTATATATTATATGTTTTAAAAAACACGT-TTTAAAAACTGTATATTATATGATTTC
1 TTTAAAAACTATATATTAGATGTTTT-AAAAA-ACGTCTTTAAAAACTATATATGATATGATTTC
1631688 AAAAT
64 AAAAT
1631693 ATATTTTCGA
Statistics
Matches: 60, Mismatches: 6, Indels: 6
0.83 0.08 0.08
Matches are distributed among these distances:
70 1 0.02
71 51 0.85
72 5 0.08
73 3 0.05
ACGTcount: A:0.43, C:0.09, G:0.06, T:0.42
Consensus pattern (70 bp):
TTTAAAAACTATATATTAGATGTTTTAAAAAACGTCTTTAAAAACTATATATGATATGATTTCAA
AATCA
Found at i:1631734 original size:24 final size:21
Alignment explanation
Indices: 1631691--1631737 Score: 67
Period size: 22 Copynumber: 2.2 Consensus size: 21
1631681 TGATTTCAAA
* *
1631691 ATATATTTTCGAAAACTATACT
1 ATATATCTTCAAAAACTATA-T
1631713 ATATATCTTCAAAAACTATAT
1 ATATATCTTCAAAAACTATAT
1631734 ATAT
1 ATAT
1631738 CATATATACT
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
21 5 0.22
22 18 0.78
ACGTcount: A:0.45, C:0.13, G:0.02, T:0.40
Consensus pattern (21 bp):
ATATATCTTCAAAAACTATAT
Found at i:1633243 original size:29 final size:29
Alignment explanation
Indices: 1633192--1633390 Score: 246
Period size: 29 Copynumber: 7.0 Consensus size: 29
1633182 CACAATTATT
*
1633192 ACCCTTTTAAGAAATATTTACAAAAATATC
1 ACCCTTTTAA-AAATAATTACAAAAATATC
1633222 ACCCTTTTAAAAATAATTACAAAAATATC
1 ACCCTTTTAAAAATAATTACAAAAATATC
* *
1633251 A--CTTTTAAAAA-AATTACGAAATTATC
1 ACCCTTTTAAAAATAATTACAAAAATATC
* *
1633277 ACCCTTTTAAAAAAAATTACAAAATTATC
1 ACCCTTTTAAAAATAATTACAAAAATATC
* *
1633306 ACCCTTTTAAAAA-AATTACGAAAATAGC
1 ACCCTTTTAAAAATAATTACAAAAATATC
* * * *
1633334 ACCATTTTCAAAATAATTACCAAAATAAC
1 ACCCTTTTAAAAATAATTACAAAAATATC
*
1633363 ACCATTTT-AAAATAATTACAAAAATATC
1 ACCCTTTTAAAAATAATTACAAAAATATC
1633391 TCCCGGTCAA
Statistics
Matches: 152, Mismatches: 13, Indels: 10
0.87 0.07 0.06
Matches are distributed among these distances:
26 14 0.09
27 10 0.07
28 51 0.34
29 67 0.44
30 10 0.07
ACGTcount: A:0.51, C:0.17, G:0.02, T:0.31
Consensus pattern (29 bp):
ACCCTTTTAAAAATAATTACAAAAATATC
Found at i:1633314 original size:57 final size:57
Alignment explanation
Indices: 1633179--1633390 Score: 250
Period size: 57 Copynumber: 3.7 Consensus size: 57
1633169 ATCAACTATT
* * *
1633179 TTACACAATTATTACCCTTTTAAGAAATATTTACAAAAATATCACCCTTTTAAAAATAA
1 TTACAAAATTATCACCCTTTTAA-AAA-AATTACAAAAATATCACCCTTTTAAAAATAA
* * * *
1633238 TTACAAAAATATCA--CTTTTAAAAAAATTACGAAATTATCACCCTTTTAAAAAAAA
1 TTACAAAATTATCACCCTTTTAAAAAAATTACAAAAATATCACCCTTTTAAAAATAA
* * * *
1633293 TTACAAAATTATCACCCTTTTAAAAAAATTACGAAAATAGCACCATTTTCAAAATAA
1 TTACAAAATTATCACCCTTTTAAAAAAATTACAAAAATATCACCCTTTTAAAAATAA
* * *
1633350 TTACCAAAA-TAACACCATTTTAAAATAATTACAAAAATATC
1 TTA-CAAAATTATCACCCTTTTAAAAAAATTACAAAAATATC
1633391 TCCCGGTCAA
Statistics
Matches: 132, Mismatches: 18, Indels: 8
0.84 0.11 0.05
Matches are distributed among these distances:
55 40 0.30
56 3 0.02
57 73 0.55
58 5 0.04
59 11 0.08
ACGTcount: A:0.50, C:0.17, G:0.02, T:0.32
Consensus pattern (57 bp):
TTACAAAATTATCACCCTTTTAAAAAAATTACAAAAATATCACCCTTTTAAAAATAA
Found at i:1633520 original size:19 final size:19
Alignment explanation
Indices: 1633465--1633521 Score: 69
Period size: 19 Copynumber: 2.9 Consensus size: 19
1633455 GGTCGGGTAG
* *
1633465 AACCGGTTCAAACCGGTCTG
1 AACCGG-TCAAACCGGTTTA
*
1633485 AACCGGTCAACCCGGTTTA
1 AACCGGTCAAACCGGTTTA
*
1633504 AACCGGTCAAATCGGTTT
1 AACCGGTCAAACCGGTTT
1633522 TCAAGCAGTC
Statistics
Matches: 32, Mismatches: 5, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
19 26 0.81
20 6 0.19
ACGTcount: A:0.26, C:0.28, G:0.23, T:0.23
Consensus pattern (19 bp):
AACCGGTCAAACCGGTTTA
Found at i:1640630 original size:28 final size:28
Alignment explanation
Indices: 1640562--1640769 Score: 213
Period size: 29 Copynumber: 7.2 Consensus size: 28
1640552 TTTACACAAT
* *
1640562 TATCACCTTTTTAAAAAATATATACAAAAA
1 TATCACCATTTTAAAAAA-AT-TACGAAAA
*
1640592 TATCACCCTTTTAAAAATAATTACGAAAA
1 TATCACCATTTTAAAAA-AATTACGAAAA
1640621 TATCACC-TTTTAAAAAAAATTAC-AAAA
1 TATCACCATTTT-AAAAAAATTACGAAAA
*
1640648 TTATCACCATTTTAAAAAATATTACGAAAT
1 -TATCACCATTTTAAAAAA-ATTACGAAAA
* *
1640678 TATCACCCTTTTAAAAAAATTATGAAAA
1 TATCACCATTTTAAAAAAATTACGAAAA
* * * *
1640706 TAACACCATTTTTAAAATAATAACCAAAA
1 TATCACCA-TTTTAAAAAAATTACGAAAA
* **
1640735 TAGCACCATTTTAAAAATAATTAAAAAAA
1 TATCACCATTTTAAAAA-AATTACGAAAA
1640764 TATCAC
1 TATCAC
1640770 ACGGTCAACG
Statistics
Matches: 152, Mismatches: 18, Indels: 17
0.81 0.10 0.09
Matches are distributed among these distances:
27 4 0.03
28 45 0.30
29 81 0.53
30 21 0.14
31 1 0.01
ACGTcount: A:0.52, C:0.15, G:0.02, T:0.31
Consensus pattern (28 bp):
TATCACCATTTTAAAAAAATTACGAAAA
Found at i:1640653 original size:57 final size:58
Alignment explanation
Indices: 1640562--1640769 Score: 242
Period size: 57 Copynumber: 3.6 Consensus size: 58
1640552 TTTACACAAT
* * *
1640562 TATCACCTTTTTAAAAAATATATACAAAAATATCACCCTTTTAAAAATAATTACGAAAA
1 TATCACCATTTTAAAAAAAAT-TACAAAAATATCACCATTTTAAAAATAATTACGAAAA
* *
1640621 TATCACC-TTTTAAAAAAAATTACAAAATTATCACCATTTTAAAAA-ATATTACGAAAT
1 TATCACCATTTTAAAAAAAATTACAAAAATATCACCATTTTAAAAATA-ATTACGAAAA
* ** * * * *
1640678 TATCACCCTTTT-AAAAAAATTATGAAAATAACACCATTTTTAAAATAATAACCAAAA
1 TATCACCATTTTAAAAAAAATTACAAAAATATCACCATTTTAAAAATAATTACGAAAA
* * *
1640735 TAGCACCATTTTAAAAATAATTAAAAAAATATCAC
1 TATCACCATTTTAAAAAAAATTACAAAAATATCAC
1640770 ACGGTCAACG
Statistics
Matches: 127, Mismatches: 18, Indels: 9
0.82 0.12 0.06
Matches are distributed among these distances:
56 1 0.01
57 84 0.66
58 35 0.28
59 7 0.06
ACGTcount: A:0.52, C:0.15, G:0.02, T:0.31
Consensus pattern (58 bp):
TATCACCATTTTAAAAAAAATTACAAAAATATCACCATTTTAAAAATAATTACGAAAA
Found at i:1640782 original size:7 final size:7
Alignment explanation
Indices: 1640770--1640802 Score: 50
Period size: 7 Copynumber: 4.9 Consensus size: 7
1640760 AAAATATCAC
1640770 ACGGTCA
1 ACGGTCA
1640777 ACGGTCA
1 ACGGTCA
*
1640784 ACAGTCA
1 ACGGTCA
1640791 ACGGTCA
1 ACGGTCA
1640798 A-GGTC
1 ACGGTC
1640803 GGATCAACGG
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
6 4 0.17
7 20 0.83
ACGTcount: A:0.30, C:0.27, G:0.27, T:0.15
Consensus pattern (7 bp):
ACGGTCA
Found at i:1642814 original size:17 final size:17
Alignment explanation
Indices: 1642788--1642825 Score: 69
Period size: 17 Copynumber: 2.3 Consensus size: 17
1642778 AGCACACGAC
1642788 AACA-GGCAGTGGCATG
1 AACACGGCAGTGGCATG
1642804 AACACGGCAGTGGCATG
1 AACACGGCAGTGGCATG
1642821 AACAC
1 AACAC
1642826 AACATCAGCA
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
16 4 0.19
17 17 0.81
ACGTcount: A:0.34, C:0.24, G:0.32, T:0.11
Consensus pattern (17 bp):
AACACGGCAGTGGCATG
Found at i:1643513 original size:16 final size:18
Alignment explanation
Indices: 1643471--1643513 Score: 54
Period size: 18 Copynumber: 2.5 Consensus size: 18
1643461 ATATTTTACG
1643471 TATATTTTAAGTTCCATA
1 TATATTTTAAGTTCCATA
* *
1643489 GAAATTTTAAGTTCC-T-
1 TATATTTTAAGTTCCATA
1643505 TATATTTTA
1 TATATTTTA
1643514 CGTATTTTTG
Statistics
Matches: 21, Mismatches: 4, Indels: 2
0.78 0.15 0.07
Matches are distributed among these distances:
16 7 0.33
17 1 0.05
18 13 0.62
ACGTcount: A:0.33, C:0.09, G:0.07, T:0.51
Consensus pattern (18 bp):
TATATTTTAAGTTCCATA
Found at i:1644860 original size:423 final size:424
Alignment explanation
Indices: 1644062--1644894 Score: 1178
Period size: 423 Copynumber: 2.0 Consensus size: 424
1644052 GAAAAATGGT
* * * * * * *
1644062 TGATCTCCCGCATTTATGCTAGGGGACGAATGTTATTGGCTTTAATAAATGAATACTCTTTTCAA
1 TGATCTCCCGCATTCATACTAGGGGACAAATGCTATTGGCTTTAATAAATCAATACACTTCTCAA
* * * *
1644127 CTTTGCATCCGTGATGATTTTTAAATTAGGTAAAGTTCGAATTCAAAATTTCCAATTTTAAATAT
66 CTTTGCATCCATAATGATTTTTAAATTAGATAAAGTTCGAACTCAAAATTTCCAATTTTAAATAT
* * * * *
1644192 AGGGTAATCAACTATGTACCAATTTTTTGGTGCTGTAGGGGTGCTAATCCTTCTCCACGCGTAGC
131 AGAGTAATCAACTAGGTACCAATTTTTTAGTGCTGTAGGGGTGCTAATCCTTCCCCACACGTAGC
* * *
1644257 TGACTCCCGAACTTGATTTATGGATTTTCGCAGACCCTAAAACTTAATATTTTGATAAAAATAAA
196 TGACTCCCGAACCTGATTTATGGATTTTCGCAAACCCTAAAACTTAATATTTTAATAAAAATAAA
* * *
1644322 ATATTTTATTAAAATCACTCAATTTTTATGGTGTCCCAATCGTATCTTAAAATGATTGGTGGCAA
261 ATATTTTATTAAAATCACCCAATTTTTATGGTGTCCCAATCGCACCTTAAAATGATTGGTGGCAA
* * *
1644387 CTCCTCACATTTTAAAACATTTTCAAAGAAAACCCACTAAGTTGGTACTTGTTTTCCCCCGCCCG
326 CTCCTCACATTTCAAAACATTTTCAAAAAAAACCCACTAAGTTGGTACTTGTTTTCCCACGCCC-
*
1644452 A-GCGAAAAATGATGTCGACATTGGGCACAATAGC
390 ATGCAAAAAATGATGTCGACATTGGGCACAATAGC
*
1644486 TGATCTCCTGCATTCATACTAGGAGG-CAAATGCTATTGGCTTTAATAAA-CAATACACTTCTCA
1 TGATCTCCCGCATTCATACTAGG-GGACAAATGCTATTGGCTTTAATAAATCAATACACTTCTCA
* *
1644549 ACTTTGCATCCATAATGATTTTTAAATTAGATAAAGTTCGAACTCAAAATTTTCGATTTTAAATA
65 ACTTTGCATCCATAATGATTTTTAAATTAGATAAAGTTCGAACTCAAAATTTCCAATTTTAAATA
* *
1644614 TAGAGTAATCAACTAGGTACCAATTTTTTAGTGTTGTGGGGGGTGCTAATCCTTCCCCACACGTC
130 TAGAGTAATCAACTAGGTACCAATTTTTTAGTGCTGT-AGGGGTGCTAATCCTTCCCCACACGT-
* * *
1644679 A-CTGACTCCCGAACCT-ATTTTCTGG-TTTTTGTAAACCCTAAAACTTAATATTTTAATAAAAA
193 AGCTGACTCCCGAACCTGA-TTTATGGATTTTCGCAAACCCTAAAACTTAATATTTTAATAAAAA
* *
1644741 TAAAATATTTTATTAAAATCACCCGATTTTTATGGTGTCTCAATCGCACCTTAAAATGATTGGTG
257 TAAAATATTTTATTAAAATCACCCAATTTTTATGGTGTCCCAATCGCACCTTAAAATGATTGGTG
* * * *
1644806 GCGACTCCTCACATTTCAAAACCTTTTCAGAAAAAAACCC-CTACGTCT-GTACTTGTTTTTCCA
322 GCAACTCCTCACATTTCAAAACATTTTCA-AAAAAAACCCACTAAGT-TGGTACTTGTTTTCCCA
*
1644869 CGCCCATGCAAAAAATGGTGTCGACA
385 CGCCCATGCAAAAAATGATGTCGACA
1644895 AGCTCCTTTC
Statistics
Matches: 361, Mismatches: 41, Indels: 15
0.87 0.10 0.04
Matches are distributed among these distances:
422 1 0.00
423 263 0.73
424 94 0.26
425 3 0.01
ACGTcount: A:0.31, C:0.20, G:0.15, T:0.34
Consensus pattern (424 bp):
TGATCTCCCGCATTCATACTAGGGGACAAATGCTATTGGCTTTAATAAATCAATACACTTCTCAA
CTTTGCATCCATAATGATTTTTAAATTAGATAAAGTTCGAACTCAAAATTTCCAATTTTAAATAT
AGAGTAATCAACTAGGTACCAATTTTTTAGTGCTGTAGGGGTGCTAATCCTTCCCCACACGTAGC
TGACTCCCGAACCTGATTTATGGATTTTCGCAAACCCTAAAACTTAATATTTTAATAAAAATAAA
ATATTTTATTAAAATCACCCAATTTTTATGGTGTCCCAATCGCACCTTAAAATGATTGGTGGCAA
CTCCTCACATTTCAAAACATTTTCAAAAAAAACCCACTAAGTTGGTACTTGTTTTCCCACGCCCA
TGCAAAAAATGATGTCGACATTGGGCACAATAGC
Found at i:1645825 original size:25 final size:25
Alignment explanation
Indices: 1645791--1645840 Score: 100
Period size: 25 Copynumber: 2.0 Consensus size: 25
1645781 AACGATATAT
1645791 TTTTTTATTAAATATGAAAAAAGAA
1 TTTTTTATTAAATATGAAAAAAGAA
1645816 TTTTTTATTAAATATGAAAAAAGAA
1 TTTTTTATTAAATATGAAAAAAGAA
1645841 ATCTTAACTC
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.08, T:0.40
Consensus pattern (25 bp):
TTTTTTATTAAATATGAAAAAAGAA
Found at i:1649790 original size:29 final size:30
Alignment explanation
Indices: 1649738--1649822 Score: 93
Period size: 29 Copynumber: 2.8 Consensus size: 30
1649728 TAGAACAATT
* *
1649738 AATAAACATAATAAAAATAATAAAAACAAGA
1 AATAAA-ATAATAAAAACAATAAAAACAACA
*
1649769 AATAAAA-AATAAAAACAGTAAAAACAACA
1 AATAAAATAATAAAAACAATAAAAACAACA
*
1649798 ACATAAAATAA-AAATAAAAATAAAA
1 A-ATAAAATAATAAA-AACAATAAAA
1649823 TATAAGGACC
Statistics
Matches: 46, Mismatches: 5, Indels: 6
0.81 0.09 0.11
Matches are distributed among these distances:
29 20 0.43
30 10 0.22
31 16 0.35
ACGTcount: A:0.76, C:0.07, G:0.02, T:0.14
Consensus pattern (30 bp):
AATAAAATAATAAAAACAATAAAAACAACA
Found at i:1652528 original size:54 final size:54
Alignment explanation
Indices: 1652461--1652631 Score: 170
Period size: 54 Copynumber: 3.4 Consensus size: 54
1652451 TTGGTGCTAT
1652461 TCCAACTCCGTATGTGATGGAATCGAGCAAAAATGACAATATTGATGATGTTTA
1 TCCAACTCCGTATGTGATGGAATCGAGCAAAAATGACAATATTGATGATGTTTA
*
1652515 TCCAACTCCGTATGTGATGG-AT-GAGC--CAA-G----TATTG--G-TGTTGT-
1 TCCAACTCCGTATGTGATGGAATCGAGCAAAAATGACAATATTGATGATGTT-TA
* * * * * *
1652557 TCCAACTCCGTATATGATGGAATCGAGCAAGAATAACAATGTTGATGATGCTGA
1 TCCAACTCCGTATGTGATGGAATCGAGCAAAAATGACAATATTGATGATGTTTA
*
1652611 TCCAACTCCATATGTGATGGA
1 TCCAACTCCGTATGTGATGGA
1652632 TTAGCCAAGT
Statistics
Matches: 94, Mismatches: 9, Indels: 28
0.72 0.07 0.21
Matches are distributed among these distances:
42 23 0.24
43 4 0.04
44 4 0.04
45 5 0.05
46 2 0.02
49 1 0.01
50 2 0.02
51 4 0.04
52 4 0.04
53 3 0.03
54 42 0.45
ACGTcount: A:0.31, C:0.17, G:0.23, T:0.29
Consensus pattern (54 bp):
TCCAACTCCGTATGTGATGGAATCGAGCAAAAATGACAATATTGATGATGTTTA
Found at i:1652562 original size:42 final size:42
Alignment explanation
Indices: 1652515--1652769 Score: 127
Period size: 42 Copynumber: 5.5 Consensus size: 42
1652505 ATGATGTTTA
1652515 TCCAACTCCGTATGTGATGGATGAGCCAAGTATTGGTGTTGT
1 TCCAACTCCGTATGTGATGGATGAGCCAAGTATTGGTGTTGT
* * *
1652557 TCCAACTCCGTATATGATGGAATCGAG-CAAGAATAACAATGTTGATGATGCTGA
1 TCCAACTCCGTATGTGATGG-AT-GAGCCAAG--T----A--TTG--G-TGTTGT
* * *
1652611 TCCAACTCCATATGTGATGGATTAGCCAAGTATTGGTGCTGT
1 TCCAACTCCGTATGTGATGGATGAGCCAAGTATTGGTGTTGT
* * * *
1652653 TCCAACTCCGCAAGTGATGGAATCGATAATAATGACAATGT-TTGAAGATGTTGA
1 TCCAACTCCGTATGTGATGG-AT-G------A-GCCAA-GTATTG--G-TGTTGT
* ** *
1652707 TCCAACTCCGTATGCGATGGATGAGCCAAGTATAAGTGTTTT
1 TCCAACTCCGTATGTGATGGATGAGCCAAGTATTGGTGTTGT
*
1652749 TCCAACTCTGTATGTGATGGA
1 TCCAACTCCGTATGTGATGGA
1652770 ATCGAGCAAG
Statistics
Matches: 161, Mismatches: 24, Indels: 56
0.67 0.10 0.23
Matches are distributed among these distances:
42 64 0.40
43 10 0.06
44 5 0.03
45 9 0.06
46 1 0.01
47 1 0.01
49 1 0.01
50 1 0.01
51 11 0.07
52 5 0.03
53 10 0.06
54 43 0.27
ACGTcount: A:0.29, C:0.17, G:0.24, T:0.30
Consensus pattern (42 bp):
TCCAACTCCGTATGTGATGGATGAGCCAAGTATTGGTGTTGT
Found at i:1652837 original size:96 final size:96
Alignment explanation
Indices: 1652272--1652835 Score: 774
Period size: 96 Copynumber: 5.9 Consensus size: 96
1652262 GTTGCTGATT
* * * *
1652272 CAACTCTGTATGTGAT-GAATCAAGCAAGAATGACAATATTGATGATGCTGATCCAACTCCATAT
1 CAACTCCGTATGTGATGGAATCGAGCAAGAATGACAATGTTGATGATGCTGATCCAACTCCGTAT
*
1652336 GCGATGGATGAGCCAAGTATTGGT-TCTGTTT
66 GCGATGGATGAGCCAAGTATTGGTGT-TGTTC
* * *
1652367 CAACTCCGTATGTGATGGAATCGAGCAAGAATGACAATGCTAATGATGTTGATCCAACTCCGTAT
1 CAACTCCGTATGTGATGGAATCGAGCAAGAATGACAATGTTGATGATGCTGATCCAACTCCGTAT
* * *
1652432 GCGATGGATGAGCTAAGTATTGGTGCTATTC
66 GCGATGGATGAGCCAAGTATTGGTGTTGTTC
* * * *
1652463 CAACTCCGTATGTGATGGAATCGAGCAAAAATGACAATATTGATGATGTTTATCCAACTCCGTAT
1 CAACTCCGTATGTGATGGAATCGAGCAAGAATGACAATGTTGATGATGCTGATCCAACTCCGTAT
*
1652528 GTGATGGATGAGCCAAGTATTGGTGTTGTTC
66 GCGATGGATGAGCCAAGTATTGGTGTTGTTC
* * *
1652559 CAACTCCGTATATGATGGAATCGAGCAAGAATAACAATGTTGATGATGCTGATCCAACTCCATAT
1 CAACTCCGTATGTGATGGAATCGAGCAAGAATGACAATGTTGATGATGCTGATCCAACTCCGTAT
* * *
1652624 GTGATGGATTAGCCAAGTATTGGTGCTGTTC
66 GCGATGGATGAGCCAAGTATTGGTGTTGTTC
* * * * * *
1652655 CAACTCCGCAAGTGATGGAATCGA-TAATAATGACAATGTTTGAAGATGTTGATCCAACTCCGTA
1 CAACTCCGTATGTGATGGAATCGAGCAAGAATGACAATG-TTGATGATGCTGATCCAACTCCGTA
** *
1652719 TGCGATGGATGAGCCAAGTATAAGTGTTTTTC
65 TGCGATGGATGAGCCAAGTATTGGTGTTGTTC
* * *
1652751 CAACTCTGTATGTGATGGAATCGAGCAAGAATGACAATGTTGATGATACTGATCCAACTTCGTAT
1 CAACTCCGTATGTGATGGAATCGAGCAAGAATGACAATGTTGATGATGCTGATCCAACTCCGTAT
*
1652816 ACGATGGATGAGCCAAGTAT
66 GCGATGGATGAGCCAAGTAT
1652836 AAACAAGTTC
Statistics
Matches: 411, Mismatches: 54, Indels: 7
0.87 0.11 0.01
Matches are distributed among these distances:
95 26 0.06
96 373 0.91
97 12 0.03
ACGTcount: A:0.30, C:0.17, G:0.23, T:0.29
Consensus pattern (96 bp):
CAACTCCGTATGTGATGGAATCGAGCAAGAATGACAATGTTGATGATGCTGATCCAACTCCGTAT
GCGATGGATGAGCCAAGTATTGGTGTTGTTC
Found at i:1653121 original size:117 final size:117
Alignment explanation
Indices: 1652837--1653507 Score: 912
Period size: 117 Copynumber: 5.7 Consensus size: 117
1652827 GCCAAGTATA
*
1652837 AACAAGTTCTTCTCATTATTAACTTATTCTCCCTCATCGGATGAGTTCTTCTCATTATGAACTCT
1 AACAAGTTCTTCTCATTATGAACTTATTCTCCCTCATCGGATGAGTTCTTCTCATTATGAACTCT
* *
1652902 CCACTGGAAAATGTTGATCCACGTCCTTCTGTGATGGAATCAACCCAAGGTTG
66 CCACTGGAAAATGTTGATCCACCTCCTTCTGTGATGGAATCGA-CCAAGGTTG
* * *
1652955 AACAAGTTCTTCTCATTATGAACTTCTTCTCCCTCATCAGATGACTTCTTCTCATTATGAACTCT
1 AACAAGTTCTTCTCATTATGAACTTATTCTCCCTCATCGGATGAGTTCTTCTCATTATGAACTCT
* * * * * *
1653020 CCACTGAAAAATATTGATCCGCCTCCTTTTGTGATAGAATCGAGCAAGGTTG
66 CCACTGGAAAATGTTGATCCACCTCCTTCTGTGATGGAATCGACCAAGGTTG
* * * * *
1653072 AACAAGTTCTTCTTACTATGAACTTCTTCTCCCTCATCGGACGAGTTCTTCTCATTATAAACTCT
1 AACAAGTTCTTCTCATTATGAACTTATTCTCCCTCATCGGATGAGTTCTTCTCATTATGAACTCT
* * * * *
1653137 CCACTGAAAAATGTTGATCCAACTCCTTTTGTGATGGAATCAAACAAGGTTG
66 CCACTGGAAAATGTTGATCCACCTCCTTCTGTGATGGAATCGACCAAGGTTG
* * * * * **
1653189 AAAAATTTCTTCTCATTATGAACTTTTTTTCCCTCATCGGATGAGTTTTTCTCATTATGATTTCT
1 AACAAGTTCTTCTCATTATGAACTTATTCTCCCTCATCGGATGAGTTCTTCTCATTATGAACTCT
* *
1653254 CCACTGGAAAATGTTGATCCAACTCCTTCTGTGATGGAATCGAGCAAGGTTG
66 CCACTGGAAAATGTTGATCCACCTCCTTCTGTGATGGAATCGACCAAGGTTG
* * * * *
1653306 AACAAGTTCTTCTCATTATGAAATTTTTCTCCCTTATTGGATGAGTTCTTCTTATTATGAACTCT
1 AACAAGTTCTTCTCATTATGAACTTATTCTCCCTCATCGGATGAGTTCTTCTCATTATGAACTCT
* * *
1653371 CCACTGGAAAATGTTGATCCACCTCCTTCTATGATAGAATCGAACCAATGTTG
66 CCACTGGAAAATGTTGATCCACCTCCTTCTGTGATGGAATCG-ACCAAGGTTG
* * *
1653424 AACAACTTCTTCTCATTATGAACTTATTCTGCCTCTGTCGGATGAGTTCTTCTCATTATGAACTC
1 AACAAGTTCTTCTCATTATGAACTTATTCTCCCTC-ATCGGATGAGTTCTTCTCATTATGAACTC
* *
1653489 TTCATTGG-AAATGTTGATC
65 TCCACTGGAAAATGTTGATC
1653508 GATTTATCTT
Statistics
Matches: 487, Mismatches: 64, Indels: 4
0.88 0.12 0.01
Matches are distributed among these distances:
117 309 0.63
118 146 0.30
119 32 0.07
ACGTcount: A:0.26, C:0.23, G:0.14, T:0.37
Consensus pattern (117 bp):
AACAAGTTCTTCTCATTATGAACTTATTCTCCCTCATCGGATGAGTTCTTCTCATTATGAACTCT
CCACTGGAAAATGTTGATCCACCTCCTTCTGTGATGGAATCGACCAAGGTTG
Found at i:1653996 original size:36 final size:36
Alignment explanation
Indices: 1653951--1654072 Score: 121
Period size: 36 Copynumber: 3.5 Consensus size: 36
1653941 CTTTAGAGAT
1653951 AATTTGTTTCAAGAGAAACTGTCTCAAGAGAGACAA
1 AATTTGTTTCAAGAGAAACTGTCTCAAGAGAGACAA
* ** * *
1653987 AATTTGTTTCAAGGGAAACAATCTC-----A-ATAT
1 AATTTGTTTCAAGAGAAACTGTCTCAAGAGAGACAA
**
1654017 TTTTATGTTTCAAGAGAAACTGTCTCAAGAGAGACAA
1 AATT-TGTTTCAAGAGAAACTGTCTCAAGAGAGACAA
*
1654054 AATTTGTTTCAAGAAAAAC
1 AATTTGTTTCAAGAGAAAC
1654073 CATCCCAAGT
Statistics
Matches: 64, Mismatches: 15, Indels: 14
0.69 0.16 0.15
Matches are distributed among these distances:
30 4 0.06
31 19 0.30
36 37 0.58
37 4 0.06
ACGTcount: A:0.41, C:0.13, G:0.16, T:0.30
Consensus pattern (36 bp):
AATTTGTTTCAAGAGAAACTGTCTCAAGAGAGACAA
Found at i:1654262 original size:40 final size:38
Alignment explanation
Indices: 1654201--1654312 Score: 111
Period size: 40 Copynumber: 2.9 Consensus size: 38
1654191 AAGGTTTTGC
* *
1654201 GTTTCAAGAGAAATTGA-CTCAAG-GAAGACAAAATTCTTCT
1 GTTTCAAG-GAAACT-ATCTCAAGCG-AGACAAAA-TCTTAT
*
1654241 GTTTCAAGTGAAACTATCTCAAGCGAGATAAAATCTTAT
1 GTTTCAAG-GAAACTATCTCAAGCGAGACAAAATCTTAT
* * *
1654280 TTTTTAAGGAAACTATCTCAAGCGAGATAAAAT
1 GTTTCAAGGAAACTATCTCAAGCGAGACAAAAT
1654313 ATTCTATTTT
Statistics
Matches: 64, Mismatches: 6, Indels: 6
0.84 0.08 0.08
Matches are distributed among these distances:
38 25 0.39
39 12 0.19
40 26 0.41
41 1 0.02
ACGTcount: A:0.40, C:0.14, G:0.16, T:0.29
Consensus pattern (38 bp):
GTTTCAAGGAAACTATCTCAAGCGAGACAAAATCTTAT
Found at i:1654298 original size:38 final size:39
Alignment explanation
Indices: 1654250--1654353 Score: 131
Period size: 38 Copynumber: 2.7 Consensus size: 39
1654240 TGTTTCAAGT
*
1654250 GAAACTATCTCAAGCGAGATAAAATCTTAT-TTTTTAAG
1 GAAACTATCTCAAGCGAGATAAAATCTTATATTTTGAAG
* * *
1654288 GAAACTATCTCAAGCGAGATAAAATATTCTATTTTGAGG
1 GAAACTATCTCAAGCGAGATAAAATCTTATATTTTGAAG
* **
1654327 GAAGCTATCTCAAGAAAGAT-AAATCTT
1 GAAACTATCTCAAGCGAGATAAAATCTT
1654354 CTTTAACACA
Statistics
Matches: 57, Mismatches: 8, Indels: 2
0.85 0.12 0.03
Matches are distributed among these distances:
38 34 0.60
39 23 0.40
ACGTcount: A:0.40, C:0.13, G:0.15, T:0.31
Consensus pattern (39 bp):
GAAACTATCTCAAGCGAGATAAAATCTTATATTTTGAAG
Found at i:1654470 original size:76 final size:75
Alignment explanation
Indices: 1654361--1654568 Score: 260
Period size: 76 Copynumber: 2.7 Consensus size: 75
1654351 CTTCTTTAAC
* * * * *
1654361 ACAATCTTGAGTGAAATGAAATGTCTTATTTCGAGTAAAACCCGTCTCAAGC-AGGACAAATCTT
1 ACAATCTT-AGTGAAATAAAATATCTTGTTTCGAGTAAAAACTGTCTCAAGCGA-GACAAATCTT
1654425 GCTTTAAGAAAA
64 GCTTTAAGAAAA
* *
1654437 ACAATCTTAAGTTAAAT-AAATCTTCTTGTTTCGAGTAAAAACTGTCTCAAGCGAGACAAATCTT
1 ACAATCTT-AGTGAAATAAAAT-ATCTTGTTTCGAGTAAAAACTGTCTCAAGCGAGACAAATCTT
*
1654501 GTTTTAAGAAAA
64 GCTTTAAGAAAA
*
1654513 ACAA-CATGTAGTGAAATAAAATATCTTGTTTTGAGTAAAAACTGTCTCAAGCGAGA
1 ACAATC-T-TAGTGAAATAAAATATCTTGTTTCGAGTAAAAACTGTCTCAAGCGAGA
1654569 AAAAAACAAT
Statistics
Matches: 117, Mismatches: 10, Indels: 10
0.85 0.07 0.07
Matches are distributed among these distances:
75 5 0.04
76 106 0.91
77 6 0.05
ACGTcount: A:0.39, C:0.15, G:0.16, T:0.30
Consensus pattern (75 bp):
ACAATCTTAGTGAAATAAAATATCTTGTTTCGAGTAAAAACTGTCTCAAGCGAGACAAATCTTGC
TTTAAGAAAA
Found at i:1654576 original size:61 final size:61
Alignment explanation
Indices: 1654509--1654629 Score: 154
Period size: 61 Copynumber: 2.0 Consensus size: 61
1654499 TTGTTTTAAG
* * * *
1654509 AAAAACAA-CATGTAGTGAAATAAAATATCTTGTTTTGAGTAAAAACTGTCTCAAGCGAGAA
1 AAAAACAATCATG-AGTGAAATAAAATATATTCTTTTGAGTAAAAAATGTCTCAAGAGAGAA
* * * *
1654570 AAAAACAATCTTGAGTGAAATGAAATGTATTCTTTTGAGTAAAAAATGTCTTAAGAGAGA
1 AAAAACAATCATGAGTGAAATAAAATATATTCTTTTGAGTAAAAAATGTCTCAAGAGAGA
1654630 TAAATATTGT
Statistics
Matches: 51, Mismatches: 8, Indels: 2
0.84 0.13 0.03
Matches are distributed among these distances:
61 48 0.94
62 3 0.06
ACGTcount: A:0.45, C:0.09, G:0.17, T:0.28
Consensus pattern (61 bp):
AAAAACAATCATGAGTGAAATAAAATATATTCTTTTGAGTAAAAAATGTCTCAAGAGAGAA
Found at i:1654650 original size:76 final size:75
Alignment explanation
Indices: 1654570--1654731 Score: 209
Period size: 75 Copynumber: 2.1 Consensus size: 75
1654560 CAAGCGAGAA
* * *
1654570 AAAAACAATCTTGAGTGAAATGAAATGTATTCTTTTGAGTAAAAAATGTCTTAAGAGAGATAAA-
1 AAAAACAATCTTGAGTCAAATGAAATGTATTCTTTTGAGT-AAAAATGTCTCAAGAGAGACAAAG
*
1654634 TATTGTTTTAAG
65 T-CTGTTTTAAG
* * * * * *
1654646 AAAAATAATATTGAGTCAAATGAAATTTCTTCTTTTGAGTAAAATTGTCTCAAGCGAGACAAAGT
1 AAAAACAATCTTGAGTCAAATGAAATGTATTCTTTTGAGTAAAAATGTCTCAAGAGAGACAAAGT
1654711 CTGTTTTAAG
66 CTGTTTTAAG
1654721 AAAAACAATCT
1 AAAAACAATCT
1654732 CAAGTGAGAT
Statistics
Matches: 73, Mismatches: 12, Indels: 3
0.83 0.14 0.03
Matches are distributed among these distances:
75 37 0.51
76 36 0.49
ACGTcount: A:0.43, C:0.09, G:0.15, T:0.33
Consensus pattern (75 bp):
AAAAACAATCTTGAGTCAAATGAAATGTATTCTTTTGAGTAAAAATGTCTCAAGAGAGACAAAGT
CTGTTTTAAG
Found at i:1654682 original size:137 final size:136
Alignment explanation
Indices: 1654433--1654704 Score: 341
Period size: 137 Copynumber: 2.0 Consensus size: 136
1654423 TTGCTTTAAG
* * * * * *
1654433 AAAAACAATCTTAAGTTAAATAAATCTTCTTGTTTCGAGTAAAAACTGTCTCAAGCGAGACAAAT
1 AAAAACAATCTTAAGTGAAATAAATCGTATTCTTTCGAGTAAAAAATGTCTCAAGAGAGACAAAT
* * *
1654498 CTTGTTTTAAGAAAAACAACATGTAGTGAAATAAAATATCTTGTTTTGAGTAAAAACTGTCTCAA
66 ATTGTTTTAAGAAAAACAACATGTAGTCAAATAAAATATCTTCTTTTGAGT-AAAACTGTCTCAA
1654563 GCGAGAA
130 GCGAGAA
* * * *
1654570 AAAAACAATCTTGAGTGAAATGAAAT-GTATTCTTTTGAGTAAAAAATGTCTTAAGAGAGATAAA
1 AAAAACAATCTTAAGTGAAAT-AAATCGTATTCTTTCGAGTAAAAAATGTCTCAAGAGAGACAAA
* * * * *
1654634 TATTGTTTTAAGAAAAATAATAT-TGAGTCAAATGAAATTTCTTCTTTTGAGTAAAATTGTCTCA
65 TATTGTTTTAAGAAAAACAACATGT-AGTCAAATAAAATATCTTCTTTTGAGTAAAACTGTCTCA
1654698 AGCGAGA
129 AGCGAGA
1654705 CAAAGTCTGT
Statistics
Matches: 115, Mismatches: 18, Indels: 5
0.83 0.13 0.04
Matches are distributed among these distances:
136 19 0.17
137 92 0.80
138 4 0.03
ACGTcount: A:0.42, C:0.10, G:0.15, T:0.32
Consensus pattern (136 bp):
AAAAACAATCTTAAGTGAAATAAATCGTATTCTTTCGAGTAAAAAATGTCTCAAGAGAGACAAAT
ATTGTTTTAAGAAAAACAACATGTAGTCAAATAAAATATCTTCTTTTGAGTAAAACTGTCTCAAG
CGAGAA
Found at i:1654806 original size:37 final size:36
Alignment explanation
Indices: 1654677--1654855 Score: 139
Period size: 37 Copynumber: 4.8 Consensus size: 36
1654667 GAAATTTCTT
* * * *
1654677 CTTTTGAGTAAAATTGTCTCAAGCGAGACAAAGTCTG
1 CTTTTAAG-AAAACTGTCTCAAGCGAGACAAAATTTG
** * * *
1654714 -TTTTAAGAAAAACAATCTCAAGTGAGATAAATCCTTTG
1 CTTTTAAG-AAAACTGTCTCAAGCGAGACAAA--ATTTG
*
1654752 -TATTAA-ATAAGACTGTCTCAAGCGAGACAAAATTTG
1 CTTTTAAGA-AA-ACTGTCTCAAGCGAGACAAAATTTG
* * *
1654788 TTTTTAGCGAAAACTGTCTCAAGCAAGACAAAATTTG
1 CTTTTA-AGAAAACTGTCTCAAGCGAGACAAAATTTG
*
1654825 CTTTTAAGAAAACTCGTCTCGAGCGAGACAA
1 CTTTTAAGAAAACT-GTCTCAAGCGAGACAA
1654856 CCCTTTGTTT
Statistics
Matches: 112, Mismatches: 22, Indels: 16
0.75 0.15 0.11
Matches are distributed among these distances:
36 36 0.32
37 49 0.44
38 26 0.23
39 1 0.01
ACGTcount: A:0.38, C:0.16, G:0.17, T:0.28
Consensus pattern (36 bp):
CTTTTAAGAAAACTGTCTCAAGCGAGACAAAATTTG
Found at i:1655157 original size:25 final size:25
Alignment explanation
Indices: 1655129--1655176 Score: 62
Period size: 25 Copynumber: 1.9 Consensus size: 25
1655119 GTCTGAAAAT
1655129 ATCAACAAGTTTTGA-AAAATGTTTA
1 ATCAACAA-TTTTGAGAAAATGTTTA
**
1655154 ATCAATGATTTTGAGAAAATGTT
1 ATCAACAATTTTGAGAAAATGTT
1655177 GCCCTTTTCT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
24 6 0.30
25 14 0.70
ACGTcount: A:0.42, C:0.06, G:0.15, T:0.38
Consensus pattern (25 bp):
ATCAACAATTTTGAGAAAATGTTTA
Found at i:1656031 original size:16 final size:13
Alignment explanation
Indices: 1656000--1656060 Score: 52
Period size: 13 Copynumber: 4.3 Consensus size: 13
1655990 GTGCTTCTTG
1656000 TTTTTTTCTTTTC
1 TTTTTTTCTTTTC
1656013 TTTTTCTTCTATTTAC
1 TTTTT-TTCT-TTT-C
*
1656029 TTTTTTCTTTTTTTC
1 -TTTTT-TTCTTTTC
1656044 TTTGTTTT-TTTTC
1 TTT-TTTTCTTTTC
1656057 TTTT
1 TTTT
1656061 ATCCTCACCT
Statistics
Matches: 42, Mismatches: 1, Indels: 11
0.78 0.02 0.20
Matches are distributed among these distances:
12 1 0.02
13 13 0.31
14 9 0.21
15 6 0.14
16 4 0.10
17 9 0.21
ACGTcount: A:0.03, C:0.13, G:0.02, T:0.82
Consensus pattern (13 bp):
TTTTTTTCTTTTC
Found at i:1656055 original size:21 final size:22
Alignment explanation
Indices: 1656001--1656060 Score: 70
Period size: 21 Copynumber: 2.7 Consensus size: 22
1655991 TGCTTCTTGT
1656001 TTTTTTCTTTTCTTTTTCTTCTA
1 TTTTTT-TTTTCTTTTTCTTCTA
*
1656024 TTTACTTTTTTCTTTTT-TTCT-
1 TTT-TTTTTTTCTTTTTCTTCTA
1656045 TTGTTTTTTTTCTTTT
1 TT-TTTTTTTTCTTTT
1656061 ATCCTCACCT
Statistics
Matches: 33, Mismatches: 2, Indels: 6
0.80 0.05 0.15
Matches are distributed among these distances:
21 13 0.39
22 5 0.15
23 13 0.39
24 2 0.06
ACGTcount: A:0.03, C:0.13, G:0.02, T:0.82
Consensus pattern (22 bp):
TTTTTTTTTTCTTTTTCTTCTA
Found at i:1659912 original size:29 final size:29
Alignment explanation
Indices: 1659853--1659921 Score: 81
Period size: 30 Copynumber: 2.4 Consensus size: 29
1659843 TAATAAACAT
*
1659853 AATAAAAATAATAAAAGACAAGAAATAAAA
1 AATAAAAATAATAAAAGACAACAAAT-AAA
1659883 AATAAAAACT-ATAAAA-ACAACAACAT-AA
1 AATAAAAA-TAATAAAAGACAACAA-ATAAA
1659911 AATAAAAATAA
1 AATAAAAATAA
1659922 AATATGAGGA
Statistics
Matches: 35, Mismatches: 1, Indels: 8
0.80 0.02 0.18
Matches are distributed among these distances:
27 1 0.03
28 11 0.31
29 6 0.17
30 16 0.46
31 1 0.03
ACGTcount: A:0.75, C:0.07, G:0.03, T:0.14
Consensus pattern (29 bp):
AATAAAAATAATAAAAGACAACAAATAAA
Found at i:1670302 original size:36 final size:36
Alignment explanation
Indices: 1670262--1670380 Score: 94
Period size: 36 Copynumber: 3.2 Consensus size: 36
1670252 TATTTTGAGT
*
1670262 AAAAACCGTCTCAAGAGAGACAAATCTTGTTTTAAG
1 AAAAACAGTCTCAAGAGAGACAAATCTTGTTTTAAG
* ** * * * **
1670298 AAAAACAATCTTGAGTGAAATAAATCTTCTTGTTTCGAG
1 AAAAACAGTCTCAAGAGAGACAAA---TCTTGTTTTAAG
** *
1670337 TAAAAATTGTCTCAAGCGAGACAAATCTTGTTTTAAG
1 -AAAAACAGTCTCAAGAGAGACAAATCTTGTTTTAAG
1670374 AAAAACA
1 AAAAACA
1670381 TGTAGTGAAA
Statistics
Matches: 58, Mismatches: 21, Indels: 8
0.67 0.24 0.09
Matches are distributed among these distances:
36 22 0.38
37 10 0.17
39 10 0.17
40 16 0.28
ACGTcount: A:0.42, C:0.14, G:0.15, T:0.29
Consensus pattern (36 bp):
AAAAACAGTCTCAAGAGAGACAAATCTTGTTTTAAG
Found at i:1670313 original size:76 final size:76
Alignment explanation
Indices: 1670223--1670434 Score: 324
Period size: 76 Copynumber: 2.8 Consensus size: 76
1670213 AATCTTCTTT
* * *
1670223 AAAACAATCTTGAGTGAAATGAAATGTCTTATTTTGAGTAAAAACCGTCTCAAGAGAGACAAATC
1 AAAACAATCTTGAGTGAAATGAAATGTCTTGTTTTGAGTAAAAACTGTCTCAAGCGAGACAAATC
1670288 TTGTTTTAAGA
66 TTGTTTTAAGA
* * *
1670299 AAAACAATCTTGAGTGAAAT-AAATCTTCTTGTTTCGAGTAAAAATTGTCTCAAGCGAGACAAAT
1 AAAACAATCTTGAGTGAAATGAAAT-GTCTTGTTTTGAGTAAAAACTGTCTCAAGCGAGACAAAT
1670363 CTTGTTTTAAGA
65 CTTGTTTTAAGA
*
1670375 AAAAC-AT-GT-AGTGAAATGAAATGTCTTGTTTTGAGTAAAAACTGTCTCAAGCGAGACAAA
1 AAAACAATCTTGAGTGAAATGAAATGTCTTGTTTTGAGTAAAAACTGTCTCAAGCGAGACAAA
1670435 AACAATCTTG
Statistics
Matches: 124, Mismatches: 10, Indels: 7
0.88 0.07 0.05
Matches are distributed among these distances:
73 43 0.35
74 5 0.04
75 6 0.05
76 70 0.56
ACGTcount: A:0.40, C:0.12, G:0.17, T:0.30
Consensus pattern (76 bp):
AAAACAATCTTGAGTGAAATGAAATGTCTTGTTTTGAGTAAAAACTGTCTCAAGCGAGACAAATC
TTGTTTTAAGA
Found at i:1670541 original size:134 final size:134
Alignment explanation
Indices: 1670298--1670544 Score: 365
Period size: 134 Copynumber: 1.8 Consensus size: 134
1670288 TTGTTTTAAG
* * * *
1670298 AAAAACAATCTTGAGTGAAATAAATCTTCTTGTTTCGAGTAAAAATTGTCTCAAGCGAGACAAAT
1 AAAAACAATCTTGAGTGAAATAAATCGTATTCTTTCGAGTAAAAATTGTCTCAAGAGAGACAAAT
* * *
1670363 CTTGTTTTAAGAAAAACATGTAGTGAAATGAAATGTCTTGTTTTGAGTAAAAACTGTCTCAAGCG
66 CTTGTTTAAAGAAAAACATGTAGTCAAATGAAATGTCTTATTTTGAGTAAAAACTGTCTCAAGCG
1670428 AGAC
131 AGAC
*
1670432 AAAAACAATCTTGAGTGAAATAAAAT-GTATTCTTTCGAGTAAAAA-TGTCTTAAGAGAGACAAA
1 AAAAACAATCTTGAGTGAAAT-AAATCGTATTCTTTCGAGTAAAAATTGTCTCAAGAGAGACAAA
*
1670495 TCTTGTTTAAAGAAAAA-ATCTTGAGTCAAATGAAATGTCTTATTTTGAGT
65 TCTTGTTTAAAGAAAAACAT-GT-AGTCAAATGAAATGTCTTATTTTGAGT
1670545 TAAATTGTCT
Statistics
Matches: 101, Mismatches: 9, Indels: 6
0.87 0.08 0.05
Matches are distributed among these distances:
132 2 0.02
133 33 0.33
134 62 0.61
135 4 0.04
ACGTcount: A:0.40, C:0.11, G:0.17, T:0.32
Consensus pattern (134 bp):
AAAAACAATCTTGAGTGAAATAAATCGTATTCTTTCGAGTAAAAATTGTCTCAAGAGAGACAAAT
CTTGTTTAAAGAAAAACATGTAGTCAAATGAAATGTCTTATTTTGAGTAAAAACTGTCTCAAGCG
AGAC
Found at i:1670707 original size:37 final size:36
Alignment explanation
Indices: 1670617--1670707 Score: 112
Period size: 37 Copynumber: 2.5 Consensus size: 36
1670607 ATTAAATAAG
*
1670617 ACTGTCTCAAGCGAGACAAAATTTGTTTTTAGCAAAA
1 ACTGTCTCAAGCGAGACAAAATTTATTTTTAG-AAAA
* *
1670654 ACTGACTCAAGAGAGACAAAATTTATTTTTA-AGAAA
1 ACTGTCTCAAGCGAGACAAAATTTATTTTTAGA-AAA
*
1670690 ACTCGTCTCGAGCGAGAC
1 ACT-GTCTCAAGCGAGAC
1670708 GACCCTTTGT
Statistics
Matches: 46, Mismatches: 6, Indels: 4
0.82 0.11 0.07
Matches are distributed among these distances:
35 1 0.02
36 6 0.13
37 39 0.85
ACGTcount: A:0.38, C:0.18, G:0.18, T:0.26
Consensus pattern (36 bp):
ACTGTCTCAAGCGAGACAAAATTTATTTTTAGAAAA
Found at i:1671010 original size:25 final size:25
Alignment explanation
Indices: 1670982--1671029 Score: 62
Period size: 25 Copynumber: 1.9 Consensus size: 25
1670972 GTCTGAAAAT
1670982 ATCAACAAGTTTTGA-AAAATGTTTA
1 ATCAACAA-TTTTGAGAAAATGTTTA
**
1671007 ATCAATGATTTTGAGAAAATGTT
1 ATCAACAATTTTGAGAAAATGTT
1671030 GCCCCTTTCT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
24 6 0.30
25 14 0.70
ACGTcount: A:0.42, C:0.06, G:0.15, T:0.38
Consensus pattern (25 bp):
ATCAACAATTTTGAGAAAATGTTTA
Found at i:1671581 original size:18 final size:17
Alignment explanation
Indices: 1671550--1671583 Score: 50
Period size: 18 Copynumber: 1.9 Consensus size: 17
1671540 ATGAAAATAG
*
1671550 TCTATTATGTTTAGAAA
1 TCTATTATGATTAGAAA
1671567 TCTATGTATGATTAGAA
1 TCTAT-TATGATTAGAA
1671584 GGGACTTTTA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 5 0.33
18 10 0.67
ACGTcount: A:0.35, C:0.06, G:0.15, T:0.44
Consensus pattern (17 bp):
TCTATTATGATTAGAAA
Found at i:1671881 original size:21 final size:20
Alignment explanation
Indices: 1671840--1671899 Score: 61
Period size: 21 Copynumber: 2.9 Consensus size: 20
1671830 ACTCTTTGCT
*
1671840 TTTTTCTTTGTTTT-TTCTTC
1 TTTTTCTTT-TTTTCTTTTTC
1671860 TATTTTCTTTTTTTCTTTTTC
1 T-TTTTCTTTTTTTCTTTTTC
1671881 TTTGTT-TTTTTTTGCTTTT
1 TTT-TTCTTTTTTT-CTTTT
1671900 ATCCTCGGCT
Statistics
Matches: 35, Mismatches: 1, Indels: 7
0.81 0.02 0.16
Matches are distributed among these distances:
20 14 0.40
21 21 0.60
ACGTcount: A:0.02, C:0.12, G:0.05, T:0.82
Consensus pattern (20 bp):
TTTTTCTTTTTTTCTTTTTC
Found at i:1671898 original size:29 final size:30
Alignment explanation
Indices: 1671834--1671899 Score: 75
Period size: 29 Copynumber: 2.3 Consensus size: 30
1671824 CGAGAGACTC
*
1671834 TTTGC-TTTTTTCTTTGTTTTTTCTTCTAT
1 TTTGCTTTTTTTCTTTGTTCTTTCTTCTAT
* * *
1671863 TTT-CTTTTTTTCTTT-TTCTTTGTTTTTT
1 TTTGCTTTTTTTCTTTGTTCTTTCTTCTAT
1671891 TTTGCTTTT
1 TTTGCTTTT
1671900 ATCCTCGGCT
Statistics
Matches: 31, Mismatches: 4, Indels: 4
0.79 0.10 0.10
Matches are distributed among these distances:
28 13 0.42
29 18 0.58
ACGTcount: A:0.02, C:0.12, G:0.06, T:0.80
Consensus pattern (30 bp):
TTTGCTTTTTTTCTTTGTTCTTTCTTCTAT
Found at i:1673573 original size:149 final size:148
Alignment explanation
Indices: 1673287--1673563 Score: 412
Period size: 149 Copynumber: 1.9 Consensus size: 148
1673277 CATCTCCTAC
* **
1673287 TTTCATAAGTCTTTCAACCTAGTTCGTGATCTTCAACTATTGGCTTTGGCATCGAATCATATCGA
1 TTTCATAAATCTTTCAACCTAGTTCGTGATCTTCAACTATTGGCTTCAGCATCGAATCATATCGA
* * *
1673352 GTCTAACTTTTTACCTCAGCATGCAAATGTCTGGATCGTCTCCTTGGTAGATAGACTCCCTCTAG
66 GTCCAACTTGTTACCTCAGCAGGCAAATGTCTGGATCGTCTCCTTGGTAGATAGACTCCCTCTAG
1673417 CTCCTACTTCATCACTTA
131 CTCCTACTTCATCACTTA
* * * * * *
1673435 TTTCTATAAATCTTTCAAGCTTGTAT-GTGATCTTCAATTATTGGCTTCAGCGTCGAATCGTCTC
1 TTTC-ATAAATCTTTCAACCTAGT-TCGTGATCTTCAACTATTGGCTTCAGCATCGAATCATATC
*
1673499 GAGTCCAACTTGTTACCTCAGCAGGCAAATGTCTGGATCGTCTCCTTGGTAGGTAGACTCCCTCT
64 GAGTCCAACTTGTTACCTCAGCAGGCAAATGTCTGGATCGTCTCCTTGGTAGATAGACTCCCTCT
1673564 TGACTCTACT
Statistics
Matches: 114, Mismatches: 13, Indels: 3
0.88 0.10 0.02
Matches are distributed among these distances:
148 4 0.04
149 109 0.96
150 1 0.01
ACGTcount: A:0.22, C:0.25, G:0.17, T:0.36
Consensus pattern (148 bp):
TTTCATAAATCTTTCAACCTAGTTCGTGATCTTCAACTATTGGCTTCAGCATCGAATCATATCGA
GTCCAACTTGTTACCTCAGCAGGCAAATGTCTGGATCGTCTCCTTGGTAGATAGACTCCCTCTAG
CTCCTACTTCATCACTTA
Found at i:1681456 original size:42 final size:42
Alignment explanation
Indices: 1681397--1681747 Score: 155
Period size: 42 Copynumber: 7.5 Consensus size: 42
1681387 ATGATGCTGA
* *
1681397 TCCAACTCCATATGTGATGGATGAGCCAAGTATTGGTGTTGT
1 TCCAACTCCGTATGTGATGGATGAGCCAAGTATTGGTGATGT
**
1681439 TCCAACTCCGTATGTGATGGAATCGAG-CAAGAATGACAATGCTAATGATGTT
1 TCCAACTCCGTATGTGATGG-AT-GAGCCAAG--T----AT--TGGTGATG-T
* * *
1681491 GATCCAACTCCGTATGCGATGGATAAGCCAAGTATTGGTGCTGT
1 --TCCAACTCCGTATGTGATGGATGAGCCAAGTATTGGTGATGT
* * *
1681535 TCCAACTCCGTATATGATGGAATCGAGCAAGAATGACAATATTGATGATGATGA
1 TCCAACTCCGTATGTGATGG-AT-GAGC--CAA-G----TATTG--G-TGATGT
** *
1681589 TCCAACTCCGTATACGATGGATGAGTCAAGTATTGGTGATGT
1 TCCAACTCCGTATGTGATGGATGAGCCAAGTATTGGTGATGT
* * * * **
1681631 TCTAACTCTGTATGTGATGGAATCGAGCAGGAATGACAATGTTAATGATGATAA
1 TCCAACTCCGTATGTGATGG-AT-GAGC--------CAA-G-TATTGGTGATGT
* * * *
1681685 TCCAACTTCTTATGCGATGGATGAGCCAAGTATTGGTGTTGT
1 TCCAACTCCGTATGTGATGGATGAGCCAAGTATTGGTGATGT
1681727 TCCAACTCCGTATGTGATGGA
1 TCCAACTCCGTATGTGATGGA
1681748 ATTGAGTAAG
Statistics
Matches: 230, Mismatches: 41, Indels: 76
0.66 0.12 0.22
Matches are distributed among these distances:
42 83 0.36
43 12 0.05
44 13 0.06
45 11 0.05
46 2 0.01
47 3 0.01
49 3 0.01
50 2 0.01
51 11 0.05
52 13 0.06
53 12 0.05
54 65 0.28
ACGTcount: A:0.29, C:0.17, G:0.25, T:0.30
Consensus pattern (42 bp):
TCCAACTCCGTATGTGATGGATGAGCCAAGTATTGGTGATGT
Found at i:1681512 original size:96 final size:96
Alignment explanation
Indices: 1681346--1681909 Score: 765
Period size: 96 Copynumber: 5.9 Consensus size: 96
1681336 GTTACTGATT
* * * * *
1681346 CAACTCCGTATGTGAT-GAATCGAGCAAGAATAACAATGCTGATGATGCTGATCCAACTCCATAT
1 CAACTCCGTATGTGATGGAATCGAGCAAGAATGACAATGTTAATGATGATGATCCAACTCCGTAT
*
1681410 GTGATGGATGAGCCAAGTATTGGTGTTGTTC
66 GCGATGGATGAGCCAAGTATTGGTGTTGTTC
* *
1681441 CAACTCCGTATGTGATGGAATCGAGCAAGAATGACAATGCTAATGATGTTGATCCAACTCCGTAT
1 CAACTCCGTATGTGATGGAATCGAGCAAGAATGACAATGTTAATGATGATGATCCAACTCCGTAT
* *
1681506 GCGATGGATAAGCCAAGTATTGGTGCTGTTC
66 GCGATGGATGAGCCAAGTATTGGTGTTGTTC
* * *
1681537 CAACTCCGTATATGATGGAATCGAGCAAGAATGACAATATTGATGATGATGATCCAACTCCGTAT
1 CAACTCCGTATGTGATGGAATCGAGCAAGAATGACAATGTTAATGATGATGATCCAACTCCGTAT
* * *
1681602 ACGATGGATGAGTCAAGTATTGGTGATGTTC
66 GCGATGGATGAGCCAAGTATTGGTGTTGTTC
* * * * * *
1681633 TAACTCTGTATGTGATGGAATCGAGCAGGAATGACAATGTTAATGATGATAATCCAACTTCTTAT
1 CAACTCCGTATGTGATGGAATCGAGCAAGAATGACAATGTTAATGATGATGATCCAACTCCGTAT
1681698 GCGATGGATGAGCCAAGTATTGGTGTTGTTC
66 GCGATGGATGAGCCAAGTATTGGTGTTGTTC
* * ** * **
1681729 CAACTCCGTATGTGATGGAATTGAGTAAGAATGACAATGTTGAA-GATTTTGATCCAAATTTGTA
1 CAACTCCGTATGTGATGGAATCGAGCAAGAATGACAATGTT-AATGATGATGATCCAACTCCGTA
**
1681793 TGCGATGGATGAGCCAAGTATAAGTGCTT-TTC
65 TGCGATGGATGAGCCAAGTATTGGTG-TTGTTC
* * * *
1681825 CAACTCCGTATGTGATGGAATTGAGCAAGAATGACAATGTTGATGATGCTGATCCAACTCTGTAT
1 CAACTCCGTATGTGATGGAATCGAGCAAGAATGACAATGTTAATGATGATGATCCAACTCCGTAT
*
1681890 GCGATGGATGAGACAAGTAT
66 GCGATGGATGAGCCAAGTAT
1681910 AAACAAGTTC
Statistics
Matches: 417, Mismatches: 48, Indels: 7
0.88 0.10 0.01
Matches are distributed among these distances:
95 17 0.04
96 396 0.95
97 4 0.01
ACGTcount: A:0.30, C:0.16, G:0.25, T:0.29
Consensus pattern (96 bp):
CAACTCCGTATGTGATGGAATCGAGCAAGAATGACAATGTTAATGATGATGATCCAACTCCGTAT
GCGATGGATGAGCCAAGTATTGGTGTTGTTC
Found at i:1681880 original size:288 final size:287
Alignment explanation
Indices: 1681347--1681909 Score: 849
Period size: 288 Copynumber: 2.0 Consensus size: 287
1681337 TTACTGATTC
* * * *
1681347 AACTCCGTATGTGATGAATCGAGCAAGAATAACAATGCTGATGATGCTGATCCAACTCCATATGT
1 AACTCCGTATGTGATGAATCGAGCAAGAATAACAATGCTAATGATGATAATCCAACTCCATATGC
1681412 GATGGATGAGCCAAGTATTGGTGTTGTTCCAACTCCGTATGTGATGGAATCGAGCAAGAATGACA
66 GATGGATGAGCCAAGTATTGGTGTTGTTCCAACTCCGTATGTGATGGAATCGAGCAAGAATGACA
* **
1681477 ATGCTAATGATGTTGATCCAACTCCGTATGCGATGGATAAGCCAAGTATTGGTGCTGTTCCAACT
131 ATGCTAATGATGTTGATCCAAATCCGTATGCGATGGATAAGCCAAGTATAAGTGCTGTTCCAACT
1681542 CCGTATATGATGGAATCGAGCAAGAATGACAATATTGATGATGATGATCCAACTCCGTATACGAT
196 CCGTATATGATGGAATCGAGCAAGAATGACAATATTGATGATGATGATCCAACTCCGTATACGAT
*
1681607 GGATGAGTCAAGTATTGGTGATGTTCT
261 GGATGAGACAAGTATTGGTGATGTTCT
* * * * * *
1681634 AACTCTGTATGTGATGGAATCGAGCAGGAATGACAATGTTAATGATGATAATCCAACTTCTTATG
1 AACTCCGTATGTGAT-GAATCGAGCAAGAATAACAATGCTAATGATGATAATCCAACTCCATATG
* *
1681699 CGATGGATGAGCCAAGTATTGGTGTTGTTCCAACTCCGTATGTGATGGAATTGAGTAAGAATGAC
65 CGATGGATGAGCCAAGTATTGGTGTTGTTCCAACTCCGTATGTGATGGAATCGAGCAAGAATGAC
* * ** * *
1681764 AATGTTGAA-GATTTTGATCCAAATTTGTATGCGATGGATGAGCCAAGTATAAGTGCTTTTCCAA
130 AATGCT-AATGATGTTGATCCAAATCCGTATGCGATGGATAAGCCAAGTATAAGTGCTGTTCCAA
* * * * * *
1681828 CTCCGTATGTGATGGAATTGAGCAAGAATGACAATGTTGATGATGCTGATCCAACTCTGTATGCG
194 CTCCGTATATGATGGAATCGAGCAAGAATGACAATATTGATGATGATGATCCAACTCCGTATACG
1681893 ATGGATGAGACAAGTAT
259 ATGGATGAGACAAGTAT
1681910 AAACAAGTTC
Statistics
Matches: 246, Mismatches: 28, Indels: 3
0.89 0.10 0.01
Matches are distributed among these distances:
287 14 0.06
288 230 0.93
289 2 0.01
ACGTcount: A:0.31, C:0.15, G:0.25, T:0.29
Consensus pattern (287 bp):
AACTCCGTATGTGATGAATCGAGCAAGAATAACAATGCTAATGATGATAATCCAACTCCATATGC
GATGGATGAGCCAAGTATTGGTGTTGTTCCAACTCCGTATGTGATGGAATCGAGCAAGAATGACA
ATGCTAATGATGTTGATCCAAATCCGTATGCGATGGATAAGCCAAGTATAAGTGCTGTTCCAACT
CCGTATATGATGGAATCGAGCAAGAATGACAATATTGATGATGATGATCCAACTCCGTATACGAT
GGATGAGACAAGTATTGGTGATGTTCT
Found at i:1682201 original size:117 final size:117
Alignment explanation
Indices: 1681911--1682576 Score: 896
Period size: 117 Copynumber: 5.7 Consensus size: 117
1681901 GACAAGTATA
* *
1681911 AACAAGTTCTTCTCATTATGAACTTATTCTCCCTCATCGGATAAGTTCTTCTCATTATGAACTCT
1 AACAAGTTCTTCTCATTATGAACTTCTTCTCCCTCATCGGATGAGTTCTTCTCATTATGAACTCT
** * * * * * *
1681976 ATATTGGAAAATATTTATACACGTCCTTATGTGATGGAATCGAACCAAGGTTG
66 CCATTGGAAAATGTTGATCCACCTCCTTCTGTGATGGAATCG-AGCAAGGTTG
*
1682029 AACAAGTTCTTCTCATTATGAA---C--ATCCCTCATCGGATGAGTTCTTCTCATTATGAACTCT
1 AACAAGTTCTTCTCATTATGAACTTCTTCTCCCTCATCGGATGAGTTCTTCTCATTATGAACTCT
1682089 CCATTGGAAAATGTTGATCCACCTCCTTCTGTGATGGAATCGAGCAAGGTTG
66 CCATTGGAAAATGTTGATCCACCTCCTTCTGTGATGGAATCGAGCAAGGTTG
* *
1682141 AACAAGTTGTTCTCATTATGAACTTCTTCTCCCTCATCGGATGAGTTCTTCTCAATATGAACTCT
1 AACAAGTTCTTCTCATTATGAACTTCTTCTCCCTCATCGGATGAGTTCTTCTCATTATGAACTCT
* * * *
1682206 CCATTGAAAAATGTTGATCCAACTCCTTTTGTGATGGAATCGAGCAAGATTG
66 CCATTGGAAAATGTTGATCCACCTCCTTCTGTGATGGAATCGAGCAAGGTTG
* *
1682258 AACAAATTCTTCTCATTATGAACTTCTTCTCCCTCATCGGATGAGTTTTTCTCATTATGAACTCT
1 AACAAGTTCTTCTCATTATGAACTTCTTCTCCCTCATCGGATGAGTTCTTCTCATTATGAACTCT
* * ** *
1682323 CCACTGGAAAATGTTGATCCAACTTATTCTGTGATAGAATCGAGCAAGGTTG
66 CCATTGGAAAATGTTGATCCACCTCCTTCTGTGATGGAATCGAGCAAGGTTG
* * *
1682375 AACAAGTTCTTCTTATTATGGAA-TTTTTCTCCCTCATCGGATGAGTTCTTCTTATTATGAACTC
1 AACAAGTTCTTCTCATTAT-GAACTTCTTCTCCCTCATCGGATGAGTTCTTCTCATTATGAACTC
* * * * *
1682439 TCCACTGGAAAATATTGATTCACCTCCTTCTGTGATGGAATCAAACCAAGGTTG
65 TCCATTGGAAAATGTTGATCCACCTCCTTCTGTGATGGAATC-GAGCAAGGTTG
* * * * * * *
1682493 AACAAGTTCTTTTCATCATGAACTTCTTTTCCCTCTGTCGGACGTGTTCTTCTCATTAGGAACTC
1 AACAAGTTCTTCTCATTATGAACTTCTTCTCCCTC-ATCGGATGAGTTCTTCTCATTATGAACTC
1682558 TCCATTGG-AAATGTTGATC
65 TCCATTGGAAAATGTTGATC
1682577 GATTTATATT
Statistics
Matches: 484, Mismatches: 55, Indels: 18
0.87 0.10 0.03
Matches are distributed among these distances:
112 30 0.06
113 70 0.14
115 1 0.00
117 283 0.58
118 69 0.14
119 31 0.06
ACGTcount: A:0.27, C:0.22, G:0.16, T:0.36
Consensus pattern (117 bp):
AACAAGTTCTTCTCATTATGAACTTCTTCTCCCTCATCGGATGAGTTCTTCTCATTATGAACTCT
CCATTGGAAAATGTTGATCCACCTCCTTCTGTGATGGAATCGAGCAAGGTTG
Found at i:1683328 original size:40 final size:38
Alignment explanation
Indices: 1683268--1683405 Score: 150
Period size: 40 Copynumber: 3.5 Consensus size: 38
1683258 AAGATTTTGC
* * * *
1683268 GTTTCAAGAGAAATTGTCTCAAGGGAGACAAAATTCTTCT
1 GTTTCAAG-GAAACTATCTCAAGCGAGA-AAAAATCTTCT
*
1683308 GTTTCAAGTGAAACTATCTCAAGTGAGAAAAAAAATCTTCT
1 GTTTCAAG-GAAACTATCTCAAGCGAG--AAAAAATCTTCT
*
1683349 GTTTCAAGGAAACTATCTCAAGCGAGATAAAATCTTCT
1 GTTTCAAGGAAACTATCTCAAGCGAGAAAAAATCTTCT
* *
1683387 ATTTCGAGGGAAACTATCT
1 GTTTC-AAGGAAACTATCT
1683406 GAAGAAAGAT
Statistics
Matches: 86, Mismatches: 9, Indels: 7
0.84 0.09 0.07
Matches are distributed among these distances:
38 15 0.17
39 12 0.14
40 40 0.47
41 18 0.21
42 1 0.01
ACGTcount: A:0.37, C:0.16, G:0.17, T:0.30
Consensus pattern (38 bp):
GTTTCAAGGAAACTATCTCAAGCGAGAAAAAATCTTCT
Found at i:1683515 original size:76 final size:75
Alignment explanation
Indices: 1683427--1683641 Score: 306
Period size: 76 Copynumber: 2.8 Consensus size: 75
1683417 AATTTTCTTT
* * * *
1683427 AAAACAATCTTGAGTGAAATGAAATGTCTTATTTCGAGTAAAAACCGTCTCAAGCAAGACAAATC
1 AAAACAATCTTGAGTGAAAT-AAATATCTTGTTTCGAGTAAAAACTGTCTCAAGCGAGACAAATC
1683492 TTGTTTTAAGA
65 TTGTTTTAAGA
* * *
1683503 AAAACAATCTTGAGTGAAATAAATCTCCGTGTTTCGAGTAAAAATTGTCTCAAGCGAGACAAATC
1 AAAACAATCTTGAGTGAAATAAATAT-CTTGTTTCGAGTAAAAACTGTCTCAAGCGAGACAAATC
1683568 TTGTTTTAAGA
65 TTGTTTTAAGA
* *
1683579 AAAACAA-CATGTAGTGAAATAAAATATCTTGTTTTGAGTAAAAACTGTCTCAAGCGAGACAAA
1 AAAACAATCTTG-AGTGAAAT-AAATATCTTGTTTCGAGTAAAAACTGTCTCAAGCGAGACAAA
1683642 AACAATCTTG
Statistics
Matches: 125, Mismatches: 11, Indels: 6
0.88 0.08 0.04
Matches are distributed among these distances:
75 8 0.06
76 112 0.90
77 5 0.04
ACGTcount: A:0.41, C:0.14, G:0.16, T:0.28
Consensus pattern (75 bp):
AAAACAATCTTGAGTGAAATAAATATCTTGTTTCGAGTAAAAACTGTCTCAAGCGAGACAAATCT
TGTTTTAAGA
Found at i:1683727 original size:73 final size:72
Alignment explanation
Indices: 1683640--1683791 Score: 182
Period size: 73 Copynumber: 2.1 Consensus size: 72
1683630 AAGCGAGACA
* *
1683640 AAAACAATCTTGAGTGAAATGAAATGTATTATTTCAAGTAAAAATGTCTTC-AGAGAGACAAA-T
1 AAAA-AATCTTGAGTCAAATGAAATGTATTATTTCAAGTAAAAATGTC-ACAAGA-AGACAAAGT
1683703 CTTGTTTTAAG
63 C-TGTTTTAAG
* * ** *
1683714 AAAAAATCTTGAGTCAAATGAAATGTCTTCTTTTGAGTAAAATTGTCACAAGCAAGACAAAGTCT
1 AAAAAATCTTGAGTCAAATGAAATGTATTATTTCAAGTAAAAATGTCACAAG-AAGACAAAGTCT
1683779 GTTTTAAG
65 GTTTTAAG
1683787 AAAAA
1 AAAAA
1683792 TAATCTCGAG
Statistics
Matches: 68, Mismatches: 7, Indels: 7
0.83 0.09 0.09
Matches are distributed among these distances:
72 1 0.01
73 60 0.88
74 7 0.10
ACGTcount: A:0.43, C:0.11, G:0.16, T:0.31
Consensus pattern (72 bp):
AAAAAATCTTGAGTCAAATGAAATGTATTATTTCAAGTAAAAATGTCACAAGAAGACAAAGTCTG
TTTTAAG
Found at i:1684222 original size:25 final size:25
Alignment explanation
Indices: 1684194--1684241 Score: 62
Period size: 25 Copynumber: 1.9 Consensus size: 25
1684184 GTCTGAAAAT
1684194 ATCAACAAGTTTTGA-AAAATGTTTA
1 ATCAACAA-TTTTGAGAAAATGTTTA
**
1684219 ATCAATGATTTTGAGAAAATGTT
1 ATCAACAATTTTGAGAAAATGTT
1684242 ACCCATTTCT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
24 6 0.30
25 14 0.70
ACGTcount: A:0.42, C:0.06, G:0.15, T:0.38
Consensus pattern (25 bp):
ATCAACAATTTTGAGAAAATGTTTA
Found at i:1685112 original size:21 final size:21
Alignment explanation
Indices: 1685058--1685112 Score: 65
Period size: 21 Copynumber: 2.6 Consensus size: 21
1685048 ATGCATGTGC
*
1685058 TTCTTGTTTTTTTCTTTGCTTT
1 TTCTT-TTTTTCTCTTTGCTTT
* * *
1685080 TTCTTCTCTTCTCTTTTCTTT
1 TTCTTTTTTTCTCTTTGCTTT
1685101 TTCTTTTTTTCT
1 TTCTTTTTTTCT
1685113 TTGTTTTTAT
Statistics
Matches: 27, Mismatches: 6, Indels: 1
0.79 0.18 0.03
Matches are distributed among these distances:
21 22 0.81
22 5 0.19
ACGTcount: A:0.00, C:0.20, G:0.04, T:0.76
Consensus pattern (21 bp):
TTCTTTTTTTCTCTTTGCTTT
Found at i:1688667 original size:9 final size:8
Alignment explanation
Indices: 1688659--1688733 Score: 50
Period size: 9 Copynumber: 9.4 Consensus size: 8
1688649 AACAATTAAT
1688659 AAACATAA
1 AAACATAA
*
1688667 TAAAAATAA
1 -AAACATAA
*
1688676 TAAAAATAA
1 -AAACATAA
1688685 AAA-ATAA
1 AAACATAA
1688692 AAA-ATAA
1 AAACATAA
1688699 AAACAGTAA
1 AAACA-TAA
1688708 AAAC--AA
1 AAACATAA
*
1688714 CAACATAA
1 AAACATAA
*
1688722 AATAAATAA
1 AA-ACATAA
1688731 AAA
1 AAA
1688734 AATATAAGGA
Statistics
Matches: 57, Mismatches: 4, Indels: 11
0.79 0.06 0.15
Matches are distributed among these distances:
6 5 0.09
7 14 0.25
8 8 0.14
9 30 0.53
ACGTcount: A:0.77, C:0.07, G:0.01, T:0.15
Consensus pattern (8 bp):
AAACATAA
Found at i:1688674 original size:6 final size:7
Alignment explanation
Indices: 1688668--1688701 Score: 50
Period size: 7 Copynumber: 4.6 Consensus size: 7
1688658 TAAACATAAT
1688668 AAAAATA
1 AAAAATA
1688675 ATAAAAATA
1 A--AAAATA
1688684 AAAAATA
1 AAAAATA
1688691 AAAAATA
1 AAAAATA
1688698 AAAA
1 AAAA
1688702 CAGTAAAAAC
Statistics
Matches: 25, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
7 18 0.72
9 7 0.28
ACGTcount: A:0.85, C:0.00, G:0.00, T:0.15
Consensus pattern (7 bp):
AAAAATA
Found at i:1688674 original size:15 final size:13
Alignment explanation
Indices: 1688669--1688737 Score: 52
Period size: 14 Copynumber: 5.1 Consensus size: 13
1688659 AAACATAATA
1688669 AAAATAATAAAAAT
1 AAAA-AATAAAAAT
1688683 AAAAAATAAAAAAT
1 AAAAAAT-AAAAAT
*
1688697 AAAAACAGTAAAAAC
1 AAAAA-A-TAAAAAT
*
1688712 AACAACAT-AAAAT
1 AA-AAAATAAAAAT
*
1688725 AAATAA-AAAAAT
1 AAAAAATAAAAAT
1688737 A
1 A
1688738 TAAGGACCTA
Statistics
Matches: 45, Mismatches: 5, Indels: 12
0.73 0.08 0.19
Matches are distributed among these distances:
12 8 0.18
13 9 0.20
14 16 0.36
15 9 0.20
16 3 0.07
ACGTcount: A:0.78, C:0.06, G:0.01, T:0.14
Consensus pattern (13 bp):
AAAAAATAAAAAT
Found at i:1688740 original size:14 final size:15
Alignment explanation
Indices: 1688665--1688737 Score: 55
Period size: 15 Copynumber: 4.9 Consensus size: 15
1688655 TAATAAACAT
1688665 AATAAAAATAATAAA
1 AATAAAAATAATAAA
1688680 AAT-AAAA-AATAAAA
1 AATAAAAATAAT-AAA
* *
1688694 AATAAAAACAGTAAA
1 AATAAAAATAATAAA
*
1688709 AACAACAACATAA-AATA
1 AATAA-AA-ATAATAA-A
1688726 AATAAAAA-AATA
1 AATAAAAATAATA
1688738 TAAGGACCTA
Statistics
Matches: 46, Mismatches: 5, Indels: 14
0.71 0.08 0.22
Matches are distributed among these distances:
13 3 0.07
14 12 0.26
15 16 0.35
16 8 0.17
17 7 0.15
ACGTcount: A:0.78, C:0.05, G:0.01, T:0.15
Consensus pattern (15 bp):
AATAAAAATAATAAA
Found at i:1699268 original size:18 final size:18
Alignment explanation
Indices: 1699229--1699268 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 18
1699219 TTTGATTATT
*
1699229 GCAGGAGTTCTGACAGTT
1 GCAGGAGTTCTGACAGTG
* *
1699247 GCAGGAGTTCTGGCTGTG
1 GCAGGAGTTCTGACAGTG
1699265 GCAG
1 GCAG
1699269 AGGATGGCTT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.17, C:0.17, G:0.40, T:0.25
Consensus pattern (18 bp):
GCAGGAGTTCTGACAGTG
Found at i:1700309 original size:370 final size:366
Alignment explanation
Indices: 1699489--1700681 Score: 1739
Period size: 370 Copynumber: 3.2 Consensus size: 366
1699479 GGTGCTCACA
** *
1699489 TACATATATTACAGACAAAGAATGGTCTGTTGACATTTTTTCAACCACTCATTAAAGTCATAATC
1 TACATATATTACAGACAAAGAATGGTCCATTGACATTTTTTCAACCACTCATTAAAGTCACAATC
* * *
1699554 AAAGAGAATTTAGATTCAAAACTTACAGACAAATTACTG---AAAAAATTCATATATCATTTTCG
66 AAAGAGAATTTAGATTCAAAACTTAGAGACAAATTACTGAAAAAAAAAGTCATATATCATTTTCC
* * * *
1699616 TATTATTTCAATTTCCAAATATAGTAATATGAATACAAATCTGGACCTTAACGCTAAATCACTTT
131 CATTATTTCAATTTCCAAAGATAGTAATATGAATACAAATCTGGACCTTAATGTTAAATCACTTT
* * * *
1699681 TCCTTA-ATTCGTGGACCTGGATGTACAATGAATGGTGGAGGCTATAGGTCGCTAGTATTGAACA
196 TCCTTAGA-T-GTGGACCTAGACGTACAATGAATGGTGGAGGCTATAAGTCGCTAGTATTGAACG
* * * * * *
1699745 TTTCGACGACTCTTGAAGATAGAAATGAGTAAACATTAAAATGTTTTTTATAGTCTCAAATGATT
259 TTTCGACGACTCTTGAAGGTAGAAACGAGGAAACATTAAAAGGTTTTTTATAGTCTTAATTGATT
* ** * *
1699810 ATAAGTTAGTATTTACTTATAATTTTTTTAATCATTGACAAAG
324 ACAAGTTAGTATTTGTTTAAAATTTTTTTAATCATTGACAACG
* * *
1699853 TACATATATTACAGACAAAGAATGGTCCACTGACATTTTTTCAACCACTCATTAAAGTTAAAATC
1 TACATATATTACAGACAAAGAATGGTCCATTGACATTTTTTCAACCACTCATTAAAGTCACAATC
1699918 AAAGAGAATTTAGATTCAAAACTTAGAGACAAATTACTGGAAAAAAAAAGTCATATATCATTTTC
66 AAAGAGAATTTAGATTCAAAACTTAGAGACAAATTACT-GAAAAAAAAAGTCATATATCATTTTC
* * *
1699983 CCATTATTTCAATTTCGAAAGATAGTAGTATGAATACAAATCTGGACCTTAATATTAAATCACTT
130 CCATTATTTCAATTTCCAAAGATAGTAATATGAATACAAATCTGGACCTTAATGTTAAATCACTT
* *
1700048 TTCCTTGAGATGTGGACATAGACGTACAATGAATGATGGAGGCTATAAGTCGCTAGTATTGAACG
195 TTCCTT-AGATGTGGACCTAGACGTACAATGAATGGTGGAGGCTATAAGTCGCTAGTATTGAACG
* *
1700113 TTTTGACTACTC-TGTAAGGTAGAAACGAGGAAACATTAAAAGGCTTTTTTTATAGTCTTAATTG
259 TTTCGACGACTCTTG-AAGGTAGAAACGAGGAAACATTAAAAGG--TTTTTTATAGTCTTAATTG
****
1700177 ATTACAAGTTAGTATTTGTTTAAAAAAAATTTAATCATTGACAACG
321 ATTACAAGTTAGTATTTGTTTAAAATTTTTTTAATCATTGACAACG
* * *
1700223 TACATATATTACAAATAAAGAATGGTCCATTGACATTTTTTCAGCCACTCATTAAAGTCACAATC
1 TACATATATTACAGACAAAGAATGGTCCATTGACATTTTTTCAACCACTCATTAAAGTCACAATC
* *
1700288 AAAGAGAATTTATATTCAAAACTTAGCGACAAATTACTGAAGAAAAAAAGTCATATATCATTTTC
66 AAAGAGAATTTAGATTCAAAACTTAGAGACAAATTACTGAA-AAAAAAAGTCATATATCATTTTC
* *
1700353 CCATTATTTCAATTTCCAATGATAGTAATATGAATACAAATCTTGACCTTAATGTTAAATCACTT
130 CCATTATTTCAATTTCCAAAGATAGTAATATGAATACAAATCTGGACCTTAATGTTAAATCACTT
* * * *
1700418 TTCCTTAAGACGTGGACCTACACGTACAATGAATGGTGGAGGCTATAAGTCGTTGGTATTGAACG
195 TTCCTT-AGATGTGGACCTAGACGTACAATGAATGGTGGAGGCTATAAGTCGCTAGTATTGAACG
*
1700483 TTTCGACGACTCTTGAAGGTAGAAAGGAGGAAACATTAAAAGGATTTTTTATAGTCTTAATTGAT
259 TTTCGACGACTCTTGAAGGTAGAAACGAGGAAACATTAAAAGG-TTTTTTATAGTCTTAATTGAT
* *
1700548 TACAAGTTAGTATTTGTTTAGAATTTTTTTAGTCATTGACAACG
323 TACAAGTTAGTATTTGTTTAAAATTTTTTTAATCATTGACAACG
* * * *
1700592 TACATATATTACAGACAAAGAATGATCCATTGACATTTTTTTTAACCAATCATTAAGGTCACAAT
1 TACATATATTACAGACAAAGAATGGTCCATTGACA-TTTTTTCAACCACTCATTAAAGTCACAAT
1700657 CAAAGAGAATTTAGATTCAAAACTT
65 CAAAGAGAATTTAGATTCAAAACTT
1700682 TCAAGAGTCA
Statistics
Matches: 741, Mismatches: 76, Indels: 18
0.89 0.09 0.02
Matches are distributed among these distances:
364 97 0.13
365 1 0.00
367 2 0.00
368 166 0.22
369 96 0.13
370 377 0.51
371 2 0.00
ACGTcount: A:0.38, C:0.14, G:0.14, T:0.34
Consensus pattern (366 bp):
TACATATATTACAGACAAAGAATGGTCCATTGACATTTTTTCAACCACTCATTAAAGTCACAATC
AAAGAGAATTTAGATTCAAAACTTAGAGACAAATTACTGAAAAAAAAAGTCATATATCATTTTCC
CATTATTTCAATTTCCAAAGATAGTAATATGAATACAAATCTGGACCTTAATGTTAAATCACTTT
TCCTTAGATGTGGACCTAGACGTACAATGAATGGTGGAGGCTATAAGTCGCTAGTATTGAACGTT
TCGACGACTCTTGAAGGTAGAAACGAGGAAACATTAAAAGGTTTTTTATAGTCTTAATTGATTAC
AAGTTAGTATTTGTTTAAAATTTTTTTAATCATTGACAACG
Found at i:1703176 original size:367 final size:370
Alignment explanation
Indices: 1702501--1703344 Score: 1358
Period size: 367 Copynumber: 2.3 Consensus size: 370
1702491 AAATAATGGG
* *
1702501 CATTTTTTCAACCACTCATTAAAGTTAAAATCAAAGAGAATATAGATTTAAAACTTAGAGACAAA
1 CATTTTTTCAACCACTCATTAAAGTTAAAATCAAAGAGAATTTAGATTCAAAACTTAGAGACAAA
* *
1702566 TTACTGGAAAAAAAAAGTCATATATCAGTTTCCCATTAGTTCAATTTCGAAAGATAGTAGTATGA
66 TTACTGG-AAAAAAAAGTCATATATCATTTTCCCATTATTTCAATTTCGAAAGATAGTAGTATGA
* *
1702631 ATACAAATCTGGACCTTAATATTAAATCACTTTTCCTTGAGACGTGGGCGTGGACGTACAATGAA
130 ATACAAATCTGGACCTTAATATTAAATCACTTTTCCTTGAGACGTGGACCTGGACGTACAATGAA
* * * * * *
1702696 TGGTGGAGGCTATAAGTCGCTAGTATTGAACGTTTCAGCGACTTTTTATGGTAGAAATGAGGAAA
195 TGGTGCAGGCTATAAGTCGCTAGTATTAAACATTTCAGCGACTCTTAAAGGTAGAAATGAGGAAA
** * *
1702761 CATTAAAAGGTTTTTTTATAGTCTTAATTGACTACAAGTTATTATTTGTTTAG-AA-TTTTTTTA
260 CATTAAAAGGCCTTTTTATAGTCTTAACTGACTACAAGTTAGTATTTGTTTAGAAATTTTTTTTA
1702824 ATCATTGACAACGTACATATATTACAGACAAAG-AATGGTCCATTGA
325 ATCATTGACAACGTACATATATTACAGACAAAGAAAT-GTCCATTGA
1702870 CATTTTTTCAACCACTCATTAAAGTTAAAATCAAAGAGAATTTAGATTCAAAACTTAGAGACAAA
1 CATTTTTTCAACCACTCATTAAAGTTAAAATCAAAGAGAATTTAGATTCAAAACTTAGAGACAAA
*
1702935 TTACTGGGAAAAAAA-TCATATATCATTTTCCCATTATTTCAATTTCGAAAGATAGTAGTATGAA
66 TTACTGGAAAAAAAAGTCATATATCATTTTCCCATTATTTCAATTTCGAAAGATAGTAGTATGAA
*
1702999 TACAAATCTGGACCTTAATATTAAATCACTTTTCCTTGAGATGTGGACCTGGACGTACAATGAAT
131 TACAAATCTGGACCTTAATATTAAATCACTTTTCCTTGAGACGTGGACCTGGACGTACAATGAAT
1703064 GGTGCAGGCTATAAGTCGCTAGTATTAAACATTTC-GTCGACTCTTAAAGGTAGAAATGAGGAAA
196 GGTGCAGGCTATAAGTCGCTAGTATTAAACATTTCAG-CGACTCTTAAAGGTAGAAATGAGGAAA
*
1703128 CATTAAAAGGCCTTTTTATAGTCTTAACTGATTACAAGTTAGTATTTGTTTAGAAATTTTTTTTA
260 CATTAAAAGGCCTTTTTATAGTCTTAACTGACTACAAGTTAGTATTTGTTTAGAAATTTTTTTTA
* *
1703193 ATCATTGACAACGTACATATATTACTGACAAAGAAATGTTCATTGA
325 ATCATTGACAACGTACATATATTACAGACAAAGAAATGTCCATTGA
* * * * * *
1703239 CATTTTTTTCAACCACTTATTAAAGTCACAATCAAATAGAATTTAGGTTCAAAACTTAGAGAAAA
1 CA-TTTTTTCAACCACTCATTAAAGTTAAAATCAAAGAGAATTTAGATTCAAAACTTAGAGACAA
*
1703304 ATTACT-GAAAAAAAAGTCATACATCATTTTCCCATTATTTC
65 ATTACTGGAAAAAAAAGTCATATATCATTTTCCCATTATTTC
1703345 TGTAACACCC
Statistics
Matches: 440, Mismatches: 29, Indels: 11
0.92 0.06 0.02
Matches are distributed among these distances:
366 1 0.00
367 213 0.48
368 9 0.02
369 128 0.29
370 89 0.20
ACGTcount: A:0.37, C:0.14, G:0.15, T:0.34
Consensus pattern (370 bp):
CATTTTTTCAACCACTCATTAAAGTTAAAATCAAAGAGAATTTAGATTCAAAACTTAGAGACAAA
TTACTGGAAAAAAAAGTCATATATCATTTTCCCATTATTTCAATTTCGAAAGATAGTAGTATGAA
TACAAATCTGGACCTTAATATTAAATCACTTTTCCTTGAGACGTGGACCTGGACGTACAATGAAT
GGTGCAGGCTATAAGTCGCTAGTATTAAACATTTCAGCGACTCTTAAAGGTAGAAATGAGGAAAC
ATTAAAAGGCCTTTTTATAGTCTTAACTGACTACAAGTTAGTATTTGTTTAGAAATTTTTTTTAA
TCATTGACAACGTACATATATTACAGACAAAGAAATGTCCATTGA
Found at i:1704326 original size:40 final size:40
Alignment explanation
Indices: 1704282--1704401 Score: 213
Period size: 40 Copynumber: 3.0 Consensus size: 40
1704272 ACCGTAGTGC
*
1704282 TACACATAAGGTCGTGCTCACCATATACACCGAAGTGTAT
1 TACACATAAGGTCGTGCCCACCATATACACCGAAGTGTAT
*
1704322 TACACATAAGGTCGTGCCCACCATATATACCGAAGTGTAT
1 TACACATAAGGTCGTGCCCACCATATACACCGAAGTGTAT
*
1704362 TACACATAAGGTCGTGCCCACCATATACACCAAAGTGTAT
1 TACACATAAGGTCGTGCCCACCATATACACCGAAGTGTAT
1704402 ATAAACCTGC
Statistics
Matches: 76, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
40 76 1.00
ACGTcount: A:0.33, C:0.26, G:0.17, T:0.24
Consensus pattern (40 bp):
TACACATAAGGTCGTGCCCACCATATACACCGAAGTGTAT
Found at i:1708152 original size:843 final size:839
Alignment explanation
Indices: 1706528--1708396 Score: 2886
Period size: 841 Copynumber: 2.2 Consensus size: 839
1706518 GGGTATTACA
*
1706528 ATTTCAATTTCCAAAGATAGTAGTATGAATACAAATCTGAACCTTAATGTTAAATCACTTTTCCT
1 ATTTCAATTTCCAAAGATAGTAGTATGAATACAAATCTGGACCTTAATGTTAAATCACTTTTCCT
* * * * * *
1706593 TAAGACGTGGACCTGGATGTACAATGAATAGTGGAGGCTATAAGTTGTTGGTATTGAACGTTTCG
66 TAAGACGTGGACCTGGATGTACAAAGAATGGTGGAGGCTATAAGTCGCTAGTTTTGAACGTTTCG
* *
1706658 AAGA-TCCTTGAAGGTAGAAAGGAGGAAACATTAAAAGGTTTTTTTATAGTCTTAATTGATTATA
131 AAGACT-CTTGAAGGTAGAAAGGAGGAAACATTAAAAGGTTTTTTTATAATCTTAA-TGACTATA
* * * **
1706722 GAAAAAGCTTTTAATGTTTCCTCATTTTCTATTTTCAAGAGTCGTCAAAACATTCAATACTAACG
194 AAAAAACCTTTTAATGTTTCCTCACTTTCTACCTTCAAGAGTCGTCAAAACATTCAATACTAACG
*
1706787 ACTTATAGCCTCCACCATTCATTGTACGTCCAAGTCCACATCATATGGAAAAGGTATTTAACATT
259 ACTTATAGCCTCCACCATTCATTGTACGTCCAAGTCCACATCATAAGGAAAAGGTATTTAACATT
* * *
1706852 AAGGTCCAGAGTTGTATTCATCCTACTATCTTTGGAAATTGAAATAATGGAAAAATGATATACGA
324 AAGGACCAGAGTTGTATTCATACTACTATCTTTGGAAATTGAAATAATGGAAAAATAATATACGA
* * *
1706917 CTTTCTTTCAGTAATTTGTCTCTAAGTTTTGTATCCAAATTCTCTTTGATTGTGACTCTAATGAG
389 CTTTCTTTAAGTAATTTGTCTCTAAGTTTTGAATCCAAATTCTCTTTGATTATGACTCTAATGAG
* * *
1706982 TGGTTGAAAAAATGTCAAAGGACCATTCTTTGTCTGTAATTTATGTACGTTGTCAATGATTAAAG
454 TAGTTGAAAAAATGTCAAAGGACCATTCTTTGTCTGTAATATATGTACGTTGTCAATGATTAAAA
* *
1707047 AACTTCTAAACAAATACTAACTTGTAATCAATTAAGACTATAAAAAACCCTTTTAATGTTTCCTC
519 AACTTCTAAACAAATACTAACTTGTAATCAATTAAGACTATAAAAAAACCTTTTAACGTTTCCTC
* * *
1707112 CTTTCTACCTTCAAGAGTCGTTGAAACGATCAATACTAGTGTCTTATAGCCCCCACCATTCATTG
584 CCTTCTAACTTCAAGAGTCGTTGAAACGATCAATACTAGTGACTTATAGCCCCCACCATTCATTG
** *
1707177 TACGTCCAGGTCTTCTTCATAAGGAAAAATGATTAAAGATTAAGGTCTAGATTTGTATTCATACT
649 TACGTCCAGGTCCACTTCATAAGGAAAAATGATTAAACATTAAGGTCTAGATTTGTATTCATACT
*
1707242 ACTATCTTTGGAAATTGAAATAATGGGCCATTTTTTCAACCACTCATTAAAGTCACAATCAAAGA
714 ACTATCTTTGGAAATTGAAATAATGGGCCATTTTTCCAACCACTCATTAAAGTCACAATCAAAGA
* *
1707307 GAATTTAGATTCAAAACTTAGAGACAAATTACTGGAAAAAATGGCATATATCATTTTCCCATT
779 GAATATAGATTCAAAACTTAGAGACAAATTA-TAGAAAAAA-GGCATATATCATTTTCCCATT
*
1707370 ATTTCAATTTCCAAAGATAGTAGTATGAATACAAATCTGGACCTTAATGTTATATCACTTTTCCT
1 ATTTCAATTTCCAAAGATAGTAGTATGAATACAAATCTGGACCTTAATGTTAAATCACTTTTCCT
* * * *
1707435 TAAGACGTGGACCTGGACGTACAAAGAATGGTGCAGGCAATAAGTCGCTAGTTTTGAACGTTTTG
66 TAAGACGTGGACCTGGATGTACAAAGAATGGTGGAGGCTATAAGTCGCTAGTTTTGAACGTTTCG
* ** * *
1707500 ATGACTCTTGAAAATAGATATGAGGAAACATTAAAAGGTTTTTTTATAATCAATTAA-GACTATA
131 AAGACTCTTGAAGGTAGAAAGGAGGAAACATTAAAAGGTTTTTTTATAATC--TTAATGACTATA
* **
1707564 AAAAAACCTTTTAATGTTTCCTC-CTTTCTACCTTCAAGAGTCGTCAAAACGTTCAATACTAGTG
194 AAAAAACCTTTTAATGTTTCCTCACTTTCTACCTTCAAGAGTCGTCAAAACATTCAATACTAACG
* * * *
1707628 ACTTATAGCCTCCACCATTCATTGTACGTCCAGGTCCACGTCTTAAGGAAAA-ATGATTTAACAT
259 ACTTATAGCCTCCACCATTCATTGTACGTCCAAGTCCACATCATAAGGAAAAGGT-ATTTAACAT
* * * *
1707692 TAAGGACCAGATTTGTATTGATACTACTATCTTTGGAAATTGAAATAATGGGAAAATAATATATG
323 TAAGGACCAGAGTTGTATTCATACTACTATCTTTGGAAATTGAAATAATGGAAAAATAATATACG
* * * * *
1707757 ACTTTTTTTAAAGTAATTTGTCTCTAAGTTTTGAATCTAAATTCTTTTTTATTATGACTTTAATG
388 ACTTTCTTT-AAGTAATTTGTCTCTAAGTTTTGAATCCAAATTCTCTTTGATTATGACTCTAATG
* * *
1707822 AGTAGTTGAAAAAATGTCAATGG-CTCATTTTTTTGTCTGTAATATATGTACGTTGTCATTGATT
452 AGTAGTTGAAAAAATGTCAAAGGAC-CA-TTCTTTGTCTGTAATATATGTACGTTGTCAATGATT
1707886 AAAAAACTTCTAAACAAATACTAACTTGTAATCAATTAAGACTATAAAAAAACCTTTTAACGTTT
515 AAAAAACTTCTAAACAAATACTAACTTGTAATCAATTAAGACTATAAAAAAACCTTTTAACGTTT
* **
1707951 CCTCCCTTCTAACTTCAAGAGTCGTTGAAACGTTCAATACTAGTGACTTATAGCCTTCACCATTC
580 CCTCCCTTCTAACTTCAAGAGTCGTTGAAACGATCAATACTAGTGACTTATAGCCCCCACCATTC
* * *
1708016 ATTGTACGTCCATGTCCACTTCTTAAGGAAAAATGATTTAACATTAAGGTCTAGATTTGTATTCA
645 ATTGTACGTCCAGGTCCACTTCATAAGGAAAAATGATTAAACATTAAGGTCTAGATTTGTATTCA
1708081 TACTACTATCTTTGGAAATTGAAATAATGGGCCATTTTTCCAACCACTCATTAAAGTCACAATCA
710 TACTACTATCTTTGGAAATTGAAATAATGGGCCATTTTTCCAACCACTCATTAAAGTCACAATCA
* *
1708146 AAGAGAATATATATTCAAAACTTAGAGACAAATTATAGAAAAAAGTCATATATCATTTTCCCATT
775 AAGAGAATATAGATTCAAAACTTAGAGACAAATTATAGAAAAAAGGCATATATCATTTTCCCATT
**
1708211 ATTTCAATTTCCAAAGATAGTAGTATGAATACAAATCTGGACCTTAATGTTAAATCACTTTTTTT
1 ATTTCAATTTCCAAAGATAGTAGTATGAATACAAATCTGGACCTTAATGTTAAATCACTTTTCCT
*
1708276 TAAGAGGTGGACCTGGATGTA-AAATGAATGGTGGAGGCTATAAGTCGCTAGTTTTGAACGTTTC
66 TAAGACGTGGACCTGGATGTACAAA-GAATGGTGGAGGCTATAAGTCGCTAGTTTTGAACGTTTC
* * * *
1708340 GACGACTCTTGAAGGCAGAAAGGAGGAAACATTAAAAGGTTTTTTAATAGTCTTAAT
130 GAAGACTCTTGAAGGTAGAAAGGAGGAAACATTAAAAGGTTTTTTTATAATCTTAAT
1708397 TGATTACAAG
Statistics
Matches: 930, Mismatches: 88, Indels: 20
0.90 0.08 0.02
Matches are distributed among these distances:
839 4 0.00
840 4 0.00
841 340 0.37
842 267 0.29
843 311 0.33
844 4 0.00
ACGTcount: A:0.35, C:0.16, G:0.15, T:0.35
Consensus pattern (839 bp):
ATTTCAATTTCCAAAGATAGTAGTATGAATACAAATCTGGACCTTAATGTTAAATCACTTTTCCT
TAAGACGTGGACCTGGATGTACAAAGAATGGTGGAGGCTATAAGTCGCTAGTTTTGAACGTTTCG
AAGACTCTTGAAGGTAGAAAGGAGGAAACATTAAAAGGTTTTTTTATAATCTTAATGACTATAAA
AAAACCTTTTAATGTTTCCTCACTTTCTACCTTCAAGAGTCGTCAAAACATTCAATACTAACGAC
TTATAGCCTCCACCATTCATTGTACGTCCAAGTCCACATCATAAGGAAAAGGTATTTAACATTAA
GGACCAGAGTTGTATTCATACTACTATCTTTGGAAATTGAAATAATGGAAAAATAATATACGACT
TTCTTTAAGTAATTTGTCTCTAAGTTTTGAATCCAAATTCTCTTTGATTATGACTCTAATGAGTA
GTTGAAAAAATGTCAAAGGACCATTCTTTGTCTGTAATATATGTACGTTGTCAATGATTAAAAAA
CTTCTAAACAAATACTAACTTGTAATCAATTAAGACTATAAAAAAACCTTTTAACGTTTCCTCCC
TTCTAACTTCAAGAGTCGTTGAAACGATCAATACTAGTGACTTATAGCCCCCACCATTCATTGTA
CGTCCAGGTCCACTTCATAAGGAAAAATGATTAAACATTAAGGTCTAGATTTGTATTCATACTAC
TATCTTTGGAAATTGAAATAATGGGCCATTTTTCCAACCACTCATTAAAGTCACAATCAAAGAGA
ATATAGATTCAAAACTTAGAGACAAATTATAGAAAAAAGGCATATATCATTTTCCCATT
Found at i:1708817 original size:2 final size:2
Alignment explanation
Indices: 1708812--1708839 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
1708802 CATTGACAAC
1708812 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1708840 TACAGACAAA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1714512 original size:16 final size:16
Alignment explanation
Indices: 1714491--1714529 Score: 55
Period size: 16 Copynumber: 2.5 Consensus size: 16
1714481 AAGCAAAGCA
1714491 AATAAAATA-AAATAAT
1 AATAAAA-ACAAATAAT
1714507 AATAAAAACAAATAAT
1 AATAAAAACAAATAAT
1714523 AA-AAAAA
1 AATAAAAA
1714530 GAAGTTAATA
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
15 6 0.27
16 16 0.73
ACGTcount: A:0.79, C:0.03, G:0.00, T:0.18
Consensus pattern (16 bp):
AATAAAAACAAATAAT
Found at i:1714623 original size:86 final size:86
Alignment explanation
Indices: 1714516--1714798 Score: 256
Period size: 85 Copynumber: 3.2 Consensus size: 86
1714506 TAATAAAAAC
1714516 AAATAATAAAAAAAGAAGTTAATAAGTGACCAAAACATAAGATATACAAATATAAAACAAAATTC
1 AAATAATAAAAAAAGAAGTTAATAAGTGACCAAAACATAAGATATACAAATATAAAACAAAATTC
1714581 GAATATTAACAAAAAAATATG
66 GAATATTAACAAAAAAATATG
** * ** * *
1714602 AAAT-ATAAAAAAACGGGGTTAA-AATGTAATTAAATAAATTAA-TTAATTA-AAATAATAGAAT
1 AAATAATAAAAAAA-GAAGTTAATAA-GTGACCAAA-ACA-TAAGAT-A-TACAAAT-ATA-AA-
** * *
1714663 A-ATAAATAAGAA-ATCAAAGCAAATAAAATAATAAAAA
57 ACA-AAATTCGAATAT-TAA-CAAA-AAAAT-AT----G
1714700 AAATAATAAAAAAAGAAGTTAATAAGTGACCAAAACATAAGATATACAAATATAAAACAAAATTC
1 AAATAATAAAAAAAGAAGTTAATAAGTGACCAAAACATAAGATATACAAATATAAAACAAAATTC
1714765 GAATATTAACAAAAAAATATG
66 GAATATTAACAAAAAAATATG
1714786 AAAT-ATAAAAAAA
1 AAATAATAAAAAAA
1714799 CGGGGTTAAA
Statistics
Matches: 151, Mismatches: 22, Indels: 49
0.68 0.10 0.22
Matches are distributed among these distances:
85 20 0.13
86 20 0.13
87 3 0.02
88 8 0.05
89 5 0.03
90 7 0.05
91 15 0.10
92 8 0.05
93 15 0.10
94 7 0.05
95 5 0.03
96 8 0.05
97 3 0.02
98 16 0.11
99 11 0.07
ACGTcount: A:0.64, C:0.06, G:0.08, T:0.22
Consensus pattern (86 bp):
AAATAATAAAAAAAGAAGTTAATAAGTGACCAAAACATAAGATATACAAATATAAAACAAAATTC
GAATATTAACAAAAAAATATG
Found at i:1714704 original size:12 final size:12
Alignment explanation
Indices: 1714687--1714713 Score: 54
Period size: 12 Copynumber: 2.2 Consensus size: 12
1714677 CAAAGCAAAT
1714687 AAAATAATAAAA
1 AAAATAATAAAA
1714699 AAAATAATAAAA
1 AAAATAATAAAA
1714711 AAA
1 AAA
1714714 GAAGTTAATA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 15 1.00
ACGTcount: A:0.85, C:0.00, G:0.00, T:0.15
Consensus pattern (12 bp):
AAAATAATAAAA
Found at i:1724578 original size:15 final size:15
Alignment explanation
Indices: 1724558--1724586 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
1724548 CTTAATCATT
1724558 TGAATAACGAGGTTA
1 TGAATAACGAGGTTA
1724573 TGAATAACGAGGTT
1 TGAATAACGAGGTT
1724587 CAATGGGGAT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.38, C:0.07, G:0.28, T:0.28
Consensus pattern (15 bp):
TGAATAACGAGGTTA
Found at i:1726014 original size:21 final size:21
Alignment explanation
Indices: 1725990--1726031 Score: 75
Period size: 21 Copynumber: 2.0 Consensus size: 21
1725980 GATTTAGCTC
1725990 TCGAACGTGCAGATTCTACAT
1 TCGAACGTGCAGATTCTACAT
*
1726011 TCGAATGTGCAGATTCTACAT
1 TCGAACGTGCAGATTCTACAT
1726032 GCAATTATAT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.29, C:0.21, G:0.19, T:0.31
Consensus pattern (21 bp):
TCGAACGTGCAGATTCTACAT
Found at i:1726743 original size:18 final size:18
Alignment explanation
Indices: 1726693--1726743 Score: 84
Period size: 18 Copynumber: 2.8 Consensus size: 18
1726683 TGCGCTTATT
* *
1726693 TTTTCAAAATCAAAACAG
1 TTTTCAAAATCAAAGCAA
1726711 TTTTCAAAATCAAAGCAA
1 TTTTCAAAATCAAAGCAA
1726729 TTTTCAAAATCAAAG
1 TTTTCAAAATCAAAG
1726744 ATAGACTTTG
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 31 1.00
ACGTcount: A:0.49, C:0.16, G:0.06, T:0.29
Consensus pattern (18 bp):
TTTTCAAAATCAAAGCAA
Found at i:1729066 original size:21 final size:21
Alignment explanation
Indices: 1729040--1729083 Score: 79
Period size: 21 Copynumber: 2.1 Consensus size: 21
1729030 GTTTTTTAAT
*
1729040 AATCTTTGTACGACAAAAAGG
1 AATCTTTGTAAGACAAAAAGG
1729061 AATCTTTGTAAGACAAAAAGG
1 AATCTTTGTAAGACAAAAAGG
1729082 AA
1 AA
1729084 GCTTACAAGG
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.48, C:0.11, G:0.18, T:0.23
Consensus pattern (21 bp):
AATCTTTGTAAGACAAAAAGG
Found at i:1732736 original size:6 final size:6
Alignment explanation
Indices: 1732725--1732758 Score: 68
Period size: 6 Copynumber: 5.7 Consensus size: 6
1732715 AATTATGTTA
1732725 TATTTT TATTTT TATTTT TATTTT TATTTT TATT
1 TATTTT TATTTT TATTTT TATTTT TATTTT TATT
1732759 AAGCATGTTT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 28 1.00
ACGTcount: A:0.18, C:0.00, G:0.00, T:0.82
Consensus pattern (6 bp):
TATTTT
Found at i:1738935 original size:65 final size:64
Alignment explanation
Indices: 1738816--1738948 Score: 230
Period size: 65 Copynumber: 2.1 Consensus size: 64
1738806 TGTAGATATA
1738816 ATTTAAAGTTTTGTATTTACATCTAGGCCCCCTTATAAATAGCCCATAAACCCCATCTTATTTC
1 ATTTAAAGTTTTGTATTTACATCTAGGCCCCCTTATAAATAGCCCATAAACCCCATCTTATTTC
* * *
1738880 ATTTATAGTTTTGTATTTACATCTAGGTCTCCCTTATAAATAGCCCATAAACCCCATTTTATTTC
1 ATTTAAAGTTTTGTATTTACATCTAGG-CCCCCTTATAAATAGCCCATAAACCCCATCTTATTTC
1738945 ATTT
1 ATTT
1738949 CAAACCATTT
Statistics
Matches: 65, Mismatches: 3, Indels: 1
0.94 0.04 0.01
Matches are distributed among these distances:
64 26 0.40
65 39 0.60
ACGTcount: A:0.29, C:0.23, G:0.08, T:0.41
Consensus pattern (64 bp):
ATTTAAAGTTTTGTATTTACATCTAGGCCCCCTTATAAATAGCCCATAAACCCCATCTTATTTC
Found at i:1739758 original size:14 final size:15
Alignment explanation
Indices: 1739739--1739772 Score: 52
Period size: 15 Copynumber: 2.3 Consensus size: 15
1739729 GGACCTTACA
*
1739739 GGCTTGC-TGGGTTG
1 GGCTTGCTTCGGTTG
1739753 GGCTTGCTTCGGTTG
1 GGCTTGCTTCGGTTG
1739768 GGCTT
1 GGCTT
1739773 TGTCGGGCTT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
14 7 0.39
15 11 0.61
ACGTcount: A:0.00, C:0.18, G:0.44, T:0.38
Consensus pattern (15 bp):
GGCTTGCTTCGGTTG
Found at i:1739956 original size:7 final size:7
Alignment explanation
Indices: 1739866--1740213 Score: 287
Period size: 7 Copynumber: 49.4 Consensus size: 7
1739856 AAAACCGAAA
1739866 ATAATAT
1 ATAATAT
1739873 -TAATA-
1 ATAATAT
1739878 ATAATAT
1 ATAATAT
1739885 AGT-ATA-
1 A-TAATAT
1739891 ATAAATAT
1 AT-AATAT
1739899 ATAATA-
1 ATAATAT
1739905 ATAAATAT
1 AT-AATAT
1739913 ATAATAT
1 ATAATAT
1739920 A-AATAT
1 ATAATAT
1739926 ATAATAT
1 ATAATAT
1739933 A-AATAT
1 ATAATAT
* *
1739939 GCT-A-CT
1 -ATAATAT
1739945 ATAATAT
1 ATAATAT
1739952 ATAATA-
1 ATAATAT
*
1739958 AGTATATGCT
1 A-TA-AT-AT
1739968 ATAATAT
1 ATAATAT
1739975 ATAATAT
1 ATAATAT
*
1739982 ATACATGT
1 ATA-ATAT
1739990 GAT-ATAT
1 -ATAATAT
1739997 A-ATATAT
1 ATA-ATAT
1740004 ATAAATAT
1 AT-AATAT
*
1740012 ATACTAT
1 ATAATAT
1740019 AATAATAAT
1 -ATAAT-AT
*
1740028 ATAATGT
1 ATAATAT
1740035 ATAATAT
1 ATAATAT
*
1740042 ATAATGT
1 ATAATAT
1740049 ATAATAT
1 ATAATAT
1740056 ATAATAT
1 ATAATAT
1740063 ATAATAT
1 ATAATAT
1740070 ATAATAT
1 ATAATAT
1740077 AT-ATAT
1 ATAATAT
1740083 ATAATAT
1 ATAATAT
*
1740090 AT-A-CT
1 ATAATAT
*
1740095 ATAACAT
1 ATAATAT
1740102 ATAATAT
1 ATAATAT
1740109 ATAATAT
1 ATAATAT
1740116 ATAATAT
1 ATAATAT
1740123 ATAATAT
1 ATAATAT
1740130 ATAATAT
1 ATAATAT
1740137 ATATACTAT
1 ATA-A-TAT
1740146 ATAATAT
1 ATAATAT
1740153 AT-ATAT
1 ATAATAT
1740159 ATAATACCAT
1 ATAAT---AT
*
1740169 AAAATAT
1 ATAATAT
*
1740176 ATACTAT
1 ATAATAT
* *
1740183 ATTATTT
1 ATAATAT
*
1740190 ATTATAT
1 ATAATAT
*
1740197 ATACTAT
1 ATAATAT
1740204 ATAATAT
1 ATAATAT
1740211 ATA
1 ATA
1740214 TATTATCCCA
Statistics
Matches: 280, Mismatches: 27, Indels: 68
0.75 0.07 0.18
Matches are distributed among these distances:
5 5 0.02
6 42 0.15
7 184 0.66
8 29 0.10
9 13 0.05
10 7 0.03
ACGTcount: A:0.53, C:0.03, G:0.02, T:0.41
Consensus pattern (7 bp):
ATAATAT
Found at i:1740044 original size:67 final size:65
Alignment explanation
Indices: 1739866--1740216 Score: 215
Period size: 67 Copynumber: 5.5 Consensus size: 65
1739856 AAAACCGAAA
* * *
1739866 ATAATAT-TAATAATAATATAGT-ATAATAAATATATA-ATAATA-AATATAT-A-ATATAAATA
1 ATAATATATAATAATAATATA-TAATATTATATATATATATAATATAACATATAATATATAAATA
1739925 T
65 T
** ** *
1739926 ATAATATA-AAT-ATGCTACTATAATA-TATA-ATAAGTATATGCTATAATATATAATATAT--A
1 ATAATATATAATAATAATA-TATAATATTATATAT-A-TATATAATATAACATATAATATATAAA
*
1739985 CAT
63 TAT
* * **
1739988 GTGATATATAAT-AT-ATATA-AATA-TATACTATA-ATAATAATATAATGTATAATATAT-AAT
1 ATAATATATAATAATAATATATAATATTATA-TATATAT-ATAATATAACATATAATATATAAAT
*
1740047 GT
64 AT
*
1740049 ATAATATATAATATATAATATATAATATATATATATAATATATACTATAACATATAATATAT-AA
1 ATAATATATAATA-ATAATATATAATAT-TATATAT-ATATATAATATAACATATAATATATAAA
1740113 TAT
63 TAT
* * *
1740116 ATAATATATAATATATAATATAT-ATACTATATAATATATATATATAATACCATAAAATATAT-A
1 ATAATATATAATA-ATAATATATAATATTATAT-ATATATATA-AT-ATAACATATAATATATAA
*
1740179 CTAT
62 ATAT
* * * *
1740183 ATTATTTATTATATATACTATATAATA-TATATAT
1 ATAATATATAATA-ATAATATATAATATTATATAT
1740217 TATCCCAGAC
Statistics
Matches: 236, Mismatches: 29, Indels: 46
0.76 0.09 0.15
Matches are distributed among these distances:
58 2 0.01
59 11 0.05
60 43 0.18
61 19 0.08
62 20 0.08
63 8 0.03
64 9 0.04
65 16 0.07
66 11 0.05
67 92 0.39
68 5 0.02
ACGTcount: A:0.53, C:0.03, G:0.02, T:0.41
Consensus pattern (65 bp):
ATAATATATAATAATAATATATAATATTATATATATATATAATATAACATATAATATATAAATAT
Found at i:1740175 original size:60 final size:58
Alignment explanation
Indices: 1739875--1740216 Score: 290
Period size: 60 Copynumber: 6.0 Consensus size: 58
1739865 AATAATATTA
*
1739875 ATAATAATATAGTATAATAAATATATAATA-ATAA-ATATATAATATA-AATATATA-AT
1 ATAATAATATAATAT-AT-AATATATAATATATAATATATATAATATATAATATATATAT
** * *
1739931 AT-A-AATATGCTACTATAATATATAATA-AGT-ATATGCTATAATATATAATATATACATGT
1 ATAATAATATAATA-TATAATATATAATATA-TAATAT-ATATAATATATAATATAT--ATAT
* * *
1739990 GATATATAATAT-ATATA-AATATATACTATAATAATA-ATATAATGTATAATATATAATGT
1 -ATA-ATAATATAATATATAATATATAATAT-ATAATATATATAATATATAATATAT-ATAT
* *
1740049 ATAAT-ATATAATATATAATATAT-A-ATAT-ATATATATAATATATACTATA-ACAT
1 ATAATAATATAATATATAATATATAATATATAATATATATAATATATAATATATATAT
*
1740102 ATAAT-ATATAATATATAATATATAATATATAATATATATACTATATAATATATATAT
1 ATAATAATATAATATATAATATATAATATATAATATATATAATATATAATATATATAT
* * * * *
1740159 ATAATACCATAAAATATATACTATAT--TATTTATTATATATACTATATAATATATATAT
1 ATAATA--ATATAATATATAATATATAATATATAATATATATAATATATAATATATATAT
1740217 TATCCCAGAC
Statistics
Matches: 240, Mismatches: 21, Indels: 48
0.78 0.07 0.16
Matches are distributed among these distances:
53 38 0.16
54 16 0.07
55 32 0.13
56 34 0.14
57 15 0.06
58 41 0.17
59 5 0.02
60 44 0.18
61 3 0.01
62 7 0.03
63 5 0.02
ACGTcount: A:0.53, C:0.04, G:0.02, T:0.41
Consensus pattern (58 bp):
ATAATAATATAATATATAATATATAATATATAATATATATAATATATAATATATATAT
Found at i:1748898 original size:22 final size:22
Alignment explanation
Indices: 1748850--1748927 Score: 108
Period size: 22 Copynumber: 3.7 Consensus size: 22
1748840 AATGCAAAAA
*
1748850 TAGTATCGATACCATA-T-CAG
1 TAGTATCGATACCATAGTATAG
*
1748870 -AGTATCGGTACCATAGTATAG
1 TAGTATCGATACCATAGTATAG
*
1748891 TAGTATCGGTACCATAGTATAG
1 TAGTATCGATACCATAGTATAG
1748913 TAGTATCGATACCAT
1 TAGTATCGATACCAT
1748928 GGTAAGGGTA
Statistics
Matches: 52, Mismatches: 3, Indels: 4
0.88 0.05 0.07
Matches are distributed among these distances:
19 14 0.27
20 1 0.02
21 2 0.04
22 35 0.67
ACGTcount: A:0.33, C:0.17, G:0.19, T:0.31
Consensus pattern (22 bp):
TAGTATCGATACCATAGTATAG
Found at i:1749330 original size:54 final size:54
Alignment explanation
Indices: 1749271--1749500 Score: 309
Period size: 54 Copynumber: 4.3 Consensus size: 54
1749261 TTATCAAATA
* ** * *
1749271 GGCACTAAATGTGCATTTCATGGAATTCATCATATGTTGATGAATAACCGTTTC
1 GGCACTAAGTGTGCATTTCACAGAATTCATCCTATGTGGATGAATAACCGTTTC
* * *
1749325 GGCACTAAGTATGCATTTCAAAGAATTCATCCTATGTGGATGAATAAACGTTTC
1 GGCACTAAGTGTGCATTTCACAGAATTCATCCTATGTGGATGAATAACCGTTTC
* *
1749379 GGCACTAAGTGTGCATTTCACAGAATTTATCCTATGTGGATGAATAACCGTTTT
1 GGCACTAAGTGTGCATTTCACAGAATTCATCCTATGTGGATGAATAACCGTTTC
* * *
1749433 GGCACTAAGTGGGCATTTCAC-GAAATTCATCCTATGTGGATAAATAACCATTTC
1 GGCACTAAGTGTGCATTTCACAG-AATTCATCCTATGTGGATGAATAACCGTTTC
* *
1749487 GACACTATGTGTGC
1 GGCACTAAGTGTGC
1749501 TAAACACTGA
Statistics
Matches: 155, Mismatches: 20, Indels: 2
0.88 0.11 0.01
Matches are distributed among these distances:
53 1 0.01
54 154 0.99
ACGTcount: A:0.30, C:0.18, G:0.20, T:0.33
Consensus pattern (54 bp):
GGCACTAAGTGTGCATTTCACAGAATTCATCCTATGTGGATGAATAACCGTTTC
Found at i:1749513 original size:108 final size:108
Alignment explanation
Indices: 1749293--1749547 Score: 289
Period size: 108 Copynumber: 2.4 Consensus size: 108
1749283 GCATTTCATG
* *
1749293 GAATTCATCATATGTTGATGAATAACCGTTTCGGCACTAAGTATGCATTTCAAAGAATTCATCCT
1 GAATTCATCATATGTGGATGAATAACCGTTTCGGCACTAAGTAGGCATTTCAAAGAATTCATCCT
* * * **
1749358 ATGTGGATGAATAAACGTTTCGGCACTAAGTGTGCATTTCACA
66 ATGTGGATAAATAAACATTTCGACACTAAGTGTGCATAACACA
* * * * *
1749401 GAATTTATCCTATGTGGATGAATAACCGTTTTGGCACTAAGTGGGCATTTC-ACGAAATTCATCC
1 GAATTCATCATATGTGGATGAATAACCGTTTCGGCACTAAGTAGGCATTTCAAAG-AATTCATCC
* * *
1749465 TATGTGGATAAATAACCATTTCGACACTATGTGTGC-TAAACACT
65 TATGTGGATAAATAAACATTTCGACACTAAGTGTGCAT-AACACA
* ** * * *
1749509 GAATTCATAATATGTTTATGAATGATCGTTTGGGCACTA
1 GAATTCATCATATGTGGATGAATAACCGTTTCGGCACTA
1749548 CTGGTGCATT
Statistics
Matches: 122, Mismatches: 23, Indels: 4
0.82 0.15 0.03
Matches are distributed among these distances:
107 3 0.02
108 119 0.98
ACGTcount: A:0.31, C:0.17, G:0.19, T:0.33
Consensus pattern (108 bp):
GAATTCATCATATGTGGATGAATAACCGTTTCGGCACTAAGTAGGCATTTCAAAGAATTCATCCT
ATGTGGATAAATAAACATTTCGACACTAAGTGTGCATAACACA
Found at i:1754244 original size:39 final size:39
Alignment explanation
Indices: 1754197--1754280 Score: 114
Period size: 39 Copynumber: 2.2 Consensus size: 39
1754187 GTAGACAGGC
* * *
1754197 TTGGGCCTTACCAGGCTTGCTAGGTCAGCCTTGCTTTGG
1 TTGGGCCTTACAAGGCTTGCTAGGTCAGCCTTACTTCGG
* * *
1754236 TTGGGCCTTGCAAGGCTTGCTGGGTCAGGCTTACTTCGG
1 TTGGGCCTTACAAGGCTTGCTAGGTCAGCCTTACTTCGG
1754275 TTGGGC
1 TTGGGC
1754281 TTCATTGTTG
Statistics
Matches: 39, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
39 39 1.00
ACGTcount: A:0.10, C:0.24, G:0.35, T:0.32
Consensus pattern (39 bp):
TTGGGCCTTACAAGGCTTGCTAGGTCAGCCTTACTTCGG
Found at i:1754343 original size:5 final size:5
Alignment explanation
Indices: 1754328--1754471 Score: 101
Period size: 5 Copynumber: 29.6 Consensus size: 5
1754318 TTGGACCTAA
* ** *
1754328 ATAAT AAAAT ATAAT AT--T ATAAT ATGCT ACAAT ATAAT AT-AT AATAAT
1 ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT -ATAAT
*
1754376 ATAAT AT-AT ATAAT AT-AT AT-AT ACTACT ATAAT AT-AT ATAAT ATAAT
1 ATAAT ATAAT ATAAT ATAAT ATAAT A-TAAT ATAAT ATAAT ATAAT ATAAT
* *
1754423 ACT-AT CATAAA AT-AT ATAATAT ATAAT ATAAT ATAAT AT-AT ATACT
1 A-TAAT -ATAAT ATAAT AT-A-AT ATAAT ATAAT ATAAT ATAAT ATAAT
1754469 ATA
1 ATA
1754472 TACTTATACT
Statistics
Matches: 111, Mismatches: 13, Indels: 30
0.72 0.08 0.19
Matches are distributed among these distances:
3 3 0.03
4 24 0.22
5 72 0.65
6 8 0.07
7 4 0.04
ACGTcount: A:0.55, C:0.05, G:0.01, T:0.40
Consensus pattern (5 bp):
ATAAT
Found at i:1754384 original size:2 final size:2
Alignment explanation
Indices: 1754359--1754493 Score: 93
Period size: 2 Copynumber: 71.5 Consensus size: 2
1754349 ATATGCTACA
1754359 AT AT A- AT AT AT A- AT A- AT AT A- AT AT AT AT A- AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
*
1754396 AT ACT ACT AT A- AT AT AT AT A- AT AT A- AT ACT AT CAT A- AA AT
1 AT A-T A-T AT AT AT AT AT AT AT AT AT AT AT A-T AT -AT AT AT AT
1754436 AT AT A- AT AT AT A- AT AT A- AT AT A- AT AT AT AT ACT AT AT ACT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A-T AT AT A-T
1754476 -T AT ACT AT AT A- AT AT AT A
1 AT AT A-T AT AT AT AT AT AT A
1754494 CTATTATGGA
Statistics
Matches: 111, Mismatches: 1, Indels: 42
0.72 0.01 0.27
Matches are distributed among these distances:
1 15 0.14
2 82 0.74
3 14 0.13
ACGTcount: A:0.53, C:0.05, G:0.00, T:0.41
Consensus pattern (2 bp):
AT
Found at i:1754463 original size:7 final size:7
Alignment explanation
Indices: 1754327--1754493 Score: 113
Period size: 7 Copynumber: 24.1 Consensus size: 7
1754317 TTTGGACCTA
1754327 AATA-AT
1 AATATAT
*
1754333 AAAATAT
1 AATATAT
1754340 AATATTAT
1 AATA-TAT
*
1754348 AATATGCT
1 AATAT-AT
1754356 ACA-ATAT
1 A-ATATAT
1754363 AATATAT
1 AATATAT
1754370 AATAATAT
1 AAT-ATAT
1754378 AATATAT
1 AATATAT
1754385 -ATA-AT
1 AATATAT
1754390 ATATATAT
1 A-ATATAT
*
1754398 ACTACTAT
1 AATA-TAT
1754406 AATATAT
1 AATATAT
1754413 -ATAATAT
1 AAT-ATAT
1754420 AATACTAT
1 AATA-TAT
*
1754428 CATA-A-
1 AATATAT
1754433 AATATAT
1 AATATAT
1754440 AATATAT
1 AATATAT
1754447 -A-ATAT
1 AATATAT
1754452 AATATA-
1 AATATAT
1754458 ATATATAT
1 A-ATATAT
*
1754466 ACTATAT
1 AATATAT
*
1754473 ACT-TAT
1 AATATAT
*
1754479 ACTATAT
1 AATATAT
1754486 AATATAT
1 AATATAT
1754493 A
1 A
1754494 CTATTATGGA
Statistics
Matches: 131, Mismatches: 10, Indels: 39
0.73 0.06 0.22
Matches are distributed among these distances:
5 9 0.07
6 20 0.15
7 65 0.50
8 36 0.27
9 1 0.01
ACGTcount: A:0.54, C:0.05, G:0.01, T:0.40
Consensus pattern (7 bp):
AATATAT
Found at i:1754583 original size:20 final size:20
Alignment explanation
Indices: 1754558--1754606 Score: 98
Period size: 20 Copynumber: 2.5 Consensus size: 20
1754548 ACATGCCTCT
1754558 ACAGTTTCGAGTTCTGTTCC
1 ACAGTTTCGAGTTCTGTTCC
1754578 ACAGTTTCGAGTTCTGTTCC
1 ACAGTTTCGAGTTCTGTTCC
1754598 ACAGTTTCG
1 ACAGTTTCG
1754607 TTGCCTCCTG
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 29 1.00
ACGTcount: A:0.16, C:0.24, G:0.20, T:0.39
Consensus pattern (20 bp):
ACAGTTTCGAGTTCTGTTCC
Found at i:1755149 original size:2 final size:2
Alignment explanation
Indices: 1755142--1755182 Score: 82
Period size: 2 Copynumber: 20.5 Consensus size: 2
1755132 ATAGTTTCAC
1755142 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1755183 CTTATACATT
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 39 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:1755541 original size:23 final size:23
Alignment explanation
Indices: 1755515--1755558 Score: 79
Period size: 23 Copynumber: 1.9 Consensus size: 23
1755505 TTATTTTTTA
*
1755515 TTTTATTTTATTTTAGTTTAATT
1 TTTTATTTTATTTTAATTTAATT
1755538 TTTTATTTTATTTTAATTTAA
1 TTTTATTTTATTTTAATTTAA
1755559 GTATTGAAAA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
23 20 1.00
ACGTcount: A:0.25, C:0.00, G:0.02, T:0.73
Consensus pattern (23 bp):
TTTTATTTTATTTTAATTTAATT
Found at i:1755558 original size:5 final size:5
Alignment explanation
Indices: 1755498--1755557 Score: 56
Period size: 5 Copynumber: 12.6 Consensus size: 5
1755488 TATTTTCAAA
* *
1755498 TTATT TT-TT ATT-TT TTATT TTATT TTATT TTAGT TTA-A TT-TT TTATT
1 TTATT TTATT -TTATT TTATT TTATT TTATT TTATT TTATT TTATT TTATT
*
1755545 TTATT TTAAT TTA
1 TTATT TTATT TTA
1755558 AGTATTGAAA
Statistics
Matches: 47, Mismatches: 4, Indels: 8
0.80 0.07 0.14
Matches are distributed among these distances:
4 8 0.17
5 39 0.83
ACGTcount: A:0.22, C:0.00, G:0.02, T:0.77
Consensus pattern (5 bp):
TTATT
Found at i:1757655 original size:2 final size:2
Alignment explanation
Indices: 1757601--1757643 Score: 61
Period size: 2 Copynumber: 21.5 Consensus size: 2
1757591 ACAAACACAC
*
1757601 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA AA TA CT- TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA -TA TA TA TA
1757643 T
1 T
1757644 TAAAGGTATA
Statistics
Matches: 37, Mismatches: 2, Indels: 4
0.86 0.05 0.09
Matches are distributed among these distances:
1 1 0.03
2 35 0.95
3 1 0.03
ACGTcount: A:0.49, C:0.02, G:0.00, T:0.49
Consensus pattern (2 bp):
TA
Found at i:1763244 original size:21 final size:21
Alignment explanation
Indices: 1763220--1763261 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
1763210 TAGATCTTTG
1763220 CATTAGCAT-ATATACATTGTA
1 CATTA-CATGATATACATTGTA
*
1763241 CATTACATGGTATACATTGTA
1 CATTACATGATATACATTGTA
1763262 TCTCAACATG
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
20 3 0.16
21 16 0.84
ACGTcount: A:0.36, C:0.14, G:0.12, T:0.38
Consensus pattern (21 bp):
CATTACATGATATACATTGTA
Found at i:1764304 original size:2 final size:2
Alignment explanation
Indices: 1764297--1764331 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
1764287 CTTTCAAATA
1764297 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG T
1 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG T
1764332 ATATATCACT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.00, C:0.00, G:0.49, T:0.51
Consensus pattern (2 bp):
TG
Found at i:1764664 original size:59 final size:58
Alignment explanation
Indices: 1764589--1764713 Score: 139
Period size: 59 Copynumber: 2.1 Consensus size: 58
1764579 GAAAAGATGT
* ** * *
1764589 AGAAAAAAAGATAGAAAA-AAGGAGA-AAAAGGAGGAAAAAATGAGAAATAAGAGAGAAA
1 AGAAAAAAAGATAGAAAAGAA--AGATAAAAGAAACAAAAAAAGAGAAAAAAGAGAGAAA
*
1764647 GAGAAAAAGAAGA-AGAAAAGAAAGATAAAAGAAACAAAAAAAGAGAAAAAAGAGGGAAA
1 -AGAAAAA-AAGATAGAAAAGAAAGATAAAAGAAACAAAAAAAGAGAAAAAAGAGAGAAA
1764706 AGAAAAAA
1 AGAAAAAA
1764714 GAAAAAAGAA
Statistics
Matches: 57, Mismatches: 6, Indels: 8
0.80 0.08 0.11
Matches are distributed among these distances:
57 1 0.02
58 10 0.18
59 40 0.70
60 6 0.11
ACGTcount: A:0.72, C:0.01, G:0.24, T:0.03
Consensus pattern (58 bp):
AGAAAAAAAGATAGAAAAGAAAGATAAAAGAAACAAAAAAAGAGAAAAAAGAGAGAAA
Found at i:1764705 original size:25 final size:23
Alignment explanation
Indices: 1764677--1764722 Score: 65
Period size: 23 Copynumber: 1.9 Consensus size: 23
1764667 AAAGATAAAA
1764677 GAAACAAAAAAAGAGAAAAAAGAGG
1 GAAA-AAAAAAA-AGAAAAAAGAGG
*
1764702 GAAAAGAAAAAAGAAAAAAGA
1 GAAAAAAAAAAAGAAAAAAGA
1764723 AGAAAGAAGA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
23 10 0.50
24 6 0.30
25 4 0.20
ACGTcount: A:0.76, C:0.02, G:0.22, T:0.00
Consensus pattern (23 bp):
GAAAAAAAAAAAGAAAAAAGAGG
Found at i:1764707 original size:30 final size:28
Alignment explanation
Indices: 1764591--1764734 Score: 85
Period size: 30 Copynumber: 4.9 Consensus size: 28
1764581 AAAGATGTAG
* * *
1764591 AAAAAAAGATAGAAAAAAGGAGAAAAAGGA
1 AAAAAAAAAGAGAAAAAA-GAGGAAAA-GA
** * *
1764621 GGAAAAAATGAGAAATAAGAGAGAAAGAGA
1 AAAAAAAAAGAGAAAAAAGAG-GAAA-AGA
* *
1764651 AAAAGAAGAAGA-AAAGAAAGA-TAAAAGA
1 AAAA-AAAAAGAGAAA-AAAGAGGAAAAGA
1764679 AACAAAAAAAGAGAAAAAAGAGGGAAAAGA
1 AA-AAAAAAAGAGAAAAAAGA-GGAAAAGA
* * *
1764709 AAAAAGAAAAAAGAAGAAAGAAGAAA
1 AAAAA-AAAAGAGAAAAAAGAGGAAA
1764735 GAAGAAAGAA
Statistics
Matches: 87, Mismatches: 18, Indels: 19
0.70 0.15 0.15
Matches are distributed among these distances:
28 16 0.18
29 18 0.21
30 43 0.49
31 10 0.11
ACGTcount: A:0.73, C:0.01, G:0.24, T:0.03
Consensus pattern (28 bp):
AAAAAAAAAGAGAAAAAAGAGGAAAAGA
Found at i:1764713 original size:7 final size:7
Alignment explanation
Indices: 1764644--1764749 Score: 72
Period size: 7 Copynumber: 14.4 Consensus size: 7
1764634 AATAAGAGAG
1764644 AAAGAGAA
1 AAAGA-AA
1764652 AAAGAAGA
1 AAAGAA-A
*
1764660 AGAA-AAG
1 A-AAGAAA
*
1764667 AAAGATA
1 AAAGAAA
1764674 AAAGAAA
1 AAAGAAA
1764681 CAAA-AAA
1 -AAAGAAA
*
1764688 AGAGAAA
1 AAAGAAA
*
1764695 AAAGAGGGA
1 AAAGA--AA
1764704 AAAGAAA
1 AAAGAAA
1764711 AAAGAAA
1 AAAGAAA
*
1764718 AAAGAAG
1 AAAGAAA
*
1764725 AAAGAAG
1 AAAGAAA
*
1764732 AAAGAAG
1 AAAGAAA
1764739 AAAGAAGA
1 AAAGAA-A
1764747 AAA
1 AAA
1764750 TAAATAGATT
Statistics
Matches: 80, Mismatches: 10, Indels: 16
0.75 0.09 0.15
Matches are distributed among these distances:
6 4 0.05
7 53 0.66
8 15 0.19
9 8 0.10
ACGTcount: A:0.75, C:0.01, G:0.23, T:0.01
Consensus pattern (7 bp):
AAAGAAA
Found at i:1764714 original size:59 final size:58
Alignment explanation
Indices: 1764623--1764737 Score: 146
Period size: 59 Copynumber: 2.0 Consensus size: 58
1764613 AAAAAGGAGG
* *
1764623 AAAAAATGAGAAATAAGAGAGAAAGAGAAAAAGAAGAAGAA-AAGAAAGATA-AAAGAAAC
1 AAAAAAAGAGAAAAAAGAGAGAAAGAGAAAAAGAA-AA-AAGAAGAAAGA-AGAAAGAAAC
*
1764682 AAAAAAAGAGAAAAAAGAGGGAAA-AGAAAAAAGAAAAAAGAAGAAAGAAGAAAGAA
1 AAAAAAAGAGAAAAAAGAGAGAAAGAG-AAAAAGAAAAAAGAAGAAAGAAGAAAGAA
1764738 GAAAGAAGAA
Statistics
Matches: 50, Mismatches: 3, Indels: 7
0.83 0.05 0.12
Matches are distributed among these distances:
57 3 0.06
58 18 0.36
59 29 0.58
ACGTcount: A:0.74, C:0.01, G:0.23, T:0.03
Consensus pattern (58 bp):
AAAAAAAGAGAAAAAAGAGAGAAAGAGAAAAAGAAAAAAGAAGAAAGAAGAAAGAAAC
Found at i:1764728 original size:21 final size:21
Alignment explanation
Indices: 1764644--1764748 Score: 90
Period size: 21 Copynumber: 4.8 Consensus size: 21
1764634 AATAAGAGAG
1764644 AAAGAGAAAAAGAAG-AAGAAAA
1 AAAGA-AAAAAGAAGAAAG-AAA
*
1764666 GAAAGATAAAAGAA-ACAA-AAA
1 -AAAGAAAAAAGAAGA-AAGAAA
*
1764687 AAGAGAAAAAAGAGGGAAAAGAAA
1 AA-AGAAAAAAGA-AG-AAAGAAA
*
1764711 AAAGAAAAAAGAAGAAAGAAG
1 AAAGAAAAAAGAAGAAAGAAA
*
1764732 AAAGAAGAAAGAAGAAA
1 AAAGAAAAAAGAAGAAA
1764749 ATAAATAGAT
Statistics
Matches: 69, Mismatches: 6, Indels: 16
0.76 0.07 0.18
Matches are distributed among these distances:
20 2 0.03
21 34 0.49
22 8 0.12
23 19 0.28
24 6 0.09
ACGTcount: A:0.75, C:0.01, G:0.23, T:0.01
Consensus pattern (21 bp):
AAAGAAAAAAGAAGAAAGAAA
Found at i:1769566 original size:18 final size:19
Alignment explanation
Indices: 1769512--1769576 Score: 62
Period size: 18 Copynumber: 3.3 Consensus size: 19
1769502 CTCTATATAT
1769512 TTATTTTTCAATGAAATAACTA
1 TTATTTTTCAAT-AAA-AA-TA
*
1769534 TT-TTTATTGAATAAAAATA
1 TTATTT-TTCAATAAAAATA
*
1769553 TTATTTTT-AATAAATATA
1 TTATTTTTCAATAAAAATA
1769571 TTATTT
1 TTATTT
1769577 CGGGCCGTGT
Statistics
Matches: 39, Mismatches: 2, Indels: 8
0.80 0.04 0.16
Matches are distributed among these distances:
18 15 0.38
19 6 0.15
20 5 0.13
21 6 0.15
22 7 0.18
ACGTcount: A:0.42, C:0.03, G:0.03, T:0.52
Consensus pattern (19 bp):
TTATTTTTCAATAAAAATA
Found at i:1772353 original size:30 final size:31
Alignment explanation
Indices: 1772291--1772353 Score: 74
Period size: 30 Copynumber: 2.1 Consensus size: 31
1772281 TTAACGGCTG
* ** *
1772291 AGGGACTAAAATCAAACGGATTGGTAATGTT
1 AGGGACTAAAATCAAACGGATCGACAACGTT
*
1772322 AGGGACT-AAATCGAACGGATCGACAACGTT
1 AGGGACTAAAATCAAACGGATCGACAACGTT
1772352 AG
1 AG
1772354 TGACCATGTA
Statistics
Matches: 27, Mismatches: 5, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
30 20 0.74
31 7 0.26
ACGTcount: A:0.38, C:0.14, G:0.27, T:0.21
Consensus pattern (31 bp):
AGGGACTAAAATCAAACGGATCGACAACGTT
Found at i:1773290 original size:3 final size:3
Alignment explanation
Indices: 1773282--1773491 Score: 149
Period size: 3 Copynumber: 68.0 Consensus size: 3
1773272 GTATTTTGTT
*
1773282 TAA TAA TAA TAG TAA -ATA TAA TAA TAA TAA TAA TAA TAA T-A TAA
1 TAA TAA TAA TAA TAA TA-A TAA TAA TAA TAA TAA TAA TAA TAA TAA
* * * * *
1773326 TAA TAA TAA TAA TAA TAA TAC T-A TAA TGA CAA TATT TAA TAGA TAG
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TA-A TAA TA-A TAA
* * * * **
1773372 TAA TAA TAA TAG TAAA TCA TCA TAG TAGA TAA TCGT TAA TAA TAAA TAA
1 TAA TAA TAA TAA T-AA TAA TAA TAA TA-A TAA T-AA TAA TAA T-AA TAA
* * * *
1773421 TAA TAG TAA TAA AAA TAA TAC TAA TAA TAA TAT TAA T-A TAA CGTCAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA --T-AA
*
1773468 AAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA
1773492 GAGAAAATCG
Statistics
Matches: 161, Mismatches: 32, Indels: 28
0.73 0.14 0.13
Matches are distributed among these distances:
2 6 0.04
3 138 0.86
4 14 0.09
5 1 0.01
6 2 0.01
ACGTcount: A:0.59, C:0.04, G:0.05, T:0.33
Consensus pattern (3 bp):
TAA
Found at i:1773682 original size:21 final size:21
Alignment explanation
Indices: 1773632--1773710 Score: 70
Period size: 21 Copynumber: 3.8 Consensus size: 21
1773622 AATCAGTTTC
**
1773632 CAAAATCGCAATGCGATTCTTA
1 CAAAATCGCAATGCGA-TAGTA
1773654 -AAAATCGCAATGCGATAGTA
1 CAAAATCGCAATGCGATAGTA
* * ** *
1773674 CAAATTCGCATTGCGATTTTC
1 CAAAATCGCAATGCGATAGTA
*
1773695 CAAAATCGCAACGCGA
1 CAAAATCGCAATGCGA
1773711 ATATGAAAAT
Statistics
Matches: 46, Mismatches: 10, Indels: 3
0.78 0.17 0.05
Matches are distributed among these distances:
20 3 0.07
21 43 0.93
ACGTcount: A:0.37, C:0.23, G:0.16, T:0.24
Consensus pattern (21 bp):
CAAAATCGCAATGCGATAGTA
Found at i:1773759 original size:20 final size:20
Alignment explanation
Indices: 1773697--1773926 Score: 232
Period size: 20 Copynumber: 11.5 Consensus size: 20
1773687 CGATTTTCCA
* ** *
1773697 AAATCGCAACGCGAATATGA
1 AAATCGCAACGCGTATCCGT
* *
1773717 AAATCGCAACGCG-AACACAT
1 AAATCGCAACGCGTATC-CGT
1773737 AAATCGCAACGCGTATCCGT
1 AAATCGCAACGCGTATCCGT
*
1773757 AAATCGCAACGTGTATCCGT
1 AAATCGCAACGCGTATCCGT
**
1773777 AAATCGCAACGCGTATGGGT
1 AAATCGCAACGCGTATCCGT
*
1773797 AAATCGCAATGCGTATCCGT
1 AAATCGCAACGCGTATCCGT
*
1773817 ATATCGCAACGCGTATCCGT
1 AAATCGCAACGCGTATCCGT
*
1773837 AAATCGCAACG-ATAATCCGT
1 AAATCGCAACGCGT-ATCCGT
* * *
1773857 AAATCGCAACGAGAATCTGT
1 AAATCGCAACGCGTATCCGT
*
1773877 AAATCGCAACG-ATAATCCGT
1 AAATCGCAACGCGT-ATCCGT
* * *
1773897 AAATCGCAACGAGAATCTGT
1 AAATCGCAACGCGTATCCGT
*
1773917 AAATCACAAC
1 AAATCGCAAC
1773927 ACTGAAATTT
Statistics
Matches: 176, Mismatches: 28, Indels: 12
0.81 0.13 0.06
Matches are distributed among these distances:
19 2 0.01
20 172 0.98
21 2 0.01
ACGTcount: A:0.37, C:0.25, G:0.19, T:0.20
Consensus pattern (20 bp):
AAATCGCAACGCGTATCCGT
Found at i:1774648 original size:24 final size:24
Alignment explanation
Indices: 1774609--1774655 Score: 69
Period size: 24 Copynumber: 2.0 Consensus size: 24
1774599 AAATTTGGTC
1774609 TTGGTCAATATCCGGACTTTGATA
1 TTGGTCAATATCCGGACTTTGATA
*
1774633 TTGGTCAATA-CACGGATTTTGAT
1 TTGGTCAATATC-CGGACTTTGAT
1774656 GATGTTTCAG
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
23 1 0.05
24 20 0.95
ACGTcount: A:0.26, C:0.15, G:0.21, T:0.38
Consensus pattern (24 bp):
TTGGTCAATATCCGGACTTTGATA
Found at i:1774847 original size:12 final size:12
Alignment explanation
Indices: 1774830--1774854 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
1774820 ATATAATCCT
1774830 GAAGAAGAAAAA
1 GAAGAAGAAAAA
1774842 GAAGAAGAAAAA
1 GAAGAAGAAAAA
1774854 G
1 G
1774855 TCCCCGAAGA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.72, C:0.00, G:0.28, T:0.00
Consensus pattern (12 bp):
GAAGAAGAAAAA
Found at i:1777242 original size:19 final size:19
Alignment explanation
Indices: 1777151--1777410 Score: 317
Period size: 19 Copynumber: 14.7 Consensus size: 19
1777141 GCAACGAGAG
1777151 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
*
1777170 AATCCCAA--C---ATGAA
1 AATCGCAATGCGAAATGAA
1777184 AATCGCAATGCGGAAATGAA
1 AATCGCAATGC-GAAATGAA
*
1777204 AATCGCAA--CG--A-GAG
1 AATCGCAATGCGAAATGAA
1777218 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
1777237 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
*
1777256 AATCGCAA--CG--A-GAG
1 AATCGCAATGCGAAATGAA
1777270 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
1777289 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
1777308 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
1777327 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
1777346 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
*
1777365 AATCGCAA--CG--A-GAG
1 AATCGCAATGCGAAATGAA
*
1777379 AATCGCAATGCGAAATTAA
1 AATCGCAATGCGAAATGAA
*
1777398 AATCGCATTGCGA
1 AATCGCAATGCGA
1777411 TTCTCTCGTT
Statistics
Matches: 210, Mismatches: 10, Indels: 42
0.80 0.04 0.16
Matches are distributed among these distances:
14 42 0.20
15 3 0.01
16 7 0.03
17 6 0.03
18 4 0.02
19 135 0.64
20 13 0.06
ACGTcount: A:0.46, C:0.18, G:0.22, T:0.15
Consensus pattern (19 bp):
AATCGCAATGCGAAATGAA
Found at i:1777264 original size:52 final size:52
Alignment explanation
Indices: 1777179--1777410 Score: 383
Period size: 52 Copynumber: 4.3 Consensus size: 52
1777169 AAATCCCAAC
1777179 ATGAAAATCGCAATGCGGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAA
1 ATGAAAATCGCAATGC-GAAATGAAAATCGCAACGAGAGAATCGCAATGCGAA
1777232 ATGAAAATCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAA
1 ATGAAAATCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAA
*
1777284 ATGAAAATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAAAATCGCAATGCGAA
1 ATGAAAATCGCAATGCGAAATGAAAATCGCAA--CG--A-GAGAATCGCAATGCGAA
1777341 ATGAAAATCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAA
1 ATGAAAATCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAA
* *
1777393 ATTAAAATCGCATTGCGA
1 ATGAAAATCGCAATGCGA
1777411 TTCTCTCGTT
Statistics
Matches: 170, Mismatches: 4, Indels: 11
0.92 0.02 0.06
Matches are distributed among these distances:
52 100 0.59
53 17 0.10
54 2 0.01
55 2 0.01
56 1 0.01
57 48 0.28
ACGTcount: A:0.46, C:0.17, G:0.22, T:0.15
Consensus pattern (52 bp):
ATGAAAATCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAA
Found at i:1777351 original size:109 final size:104
Alignment explanation
Indices: 1777179--1777410 Score: 383
Period size: 109 Copynumber: 2.2 Consensus size: 104
1777169 AAATCCCAAC
*
1777179 ATGAAAATCGCAATGCGGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAAATGAAAATCGCA
1 ATGAAAATCGCAATGC-GAAATGAAAATCGCAACGAGAAAATCGCAATGCGAAATGAAAATCGCA
1777244 ATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAA
65 ATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAA
1777284 ATGAAAATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAAAAT
1 ATGAAAATCGCAATGCGAAATGAAAATCGCAA--CG--A-GAAAATCGCAATGCGAAATGAAAAT
1777349 CGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAA
61 CGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAA
* *
1777393 ATTAAAATCGCATTGCGA
1 ATGAAAATCGCAATGCGA
1777411 TTCTCTCGTT
Statistics
Matches: 119, Mismatches: 3, Indels: 6
0.93 0.02 0.05
Matches are distributed among these distances:
104 16 0.13
105 16 0.13
106 2 0.02
108 1 0.01
109 84 0.71
ACGTcount: A:0.46, C:0.17, G:0.22, T:0.15
Consensus pattern (104 bp):
ATGAAAATCGCAATGCGAAATGAAAATCGCAACGAGAAAATCGCAATGCGAAATGAAAATCGCAA
TGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAA
Done.