Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008120.1 Hibiscus syriacus cultivar Beakdansim tig00110670_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: 639723
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 2 of 3
Found at i:205071 original size:102 final size:102
Alignment explanation
Indices: 204895--205140 Score: 384
Period size: 102 Copynumber: 2.4 Consensus size: 102
204885 TAAAAAGAAG
* * * *
204895 ATTTTATCTCGCTTGAGATAGTTTCCCTTAAAACAAAATATTGTCTCCCTTGAGACAGTTTCTCT
1 ATTTTGTCTCTCTTGAGATAGTTTCCCTTGAAACAAAATATTGTATCCCTTGAGACAGTTTCTCT
* *
204960 TGAAACATAAATATTGAAAACATTTCCCTTGAAACGA
66 TGAAACATAAACATTGAAAACATTTCCCTTGAAACAA
** *
204997 ATTTTGTCTCTCTTGAGATAGTTTCCCTTGAAATGAAATTTTGTATCCCTTGAGACAGTTTCTCT
1 ATTTTGTCTCTCTTGAGATAGTTTCCCTTGAAACAAAATATTGTATCCCTTGAGACAGTTTCTCT
*
205062 TGAAACATAAACATTGAAAACATTTCCCTTGAAATAA
66 TGAAACATAAACATTGAAAACATTTCCCTTGAAACAA
* *
205099 ATTTTGTCTCTCTTGAGACAGTTTCCCTTGAAACAAATTATT
1 ATTTTGTCTCTCTTGAGATAGTTTCCCTTGAAACAAAATATT
205141 TGAATATGTT
Statistics
Matches: 129, Mismatches: 15, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
102 129 1.00
ACGTcount: A:0.31, C:0.19, G:0.12, T:0.38
Consensus pattern (102 bp):
ATTTTGTCTCTCTTGAGATAGTTTCCCTTGAAACAAAATATTGTATCCCTTGAGACAGTTTCTCT
TGAAACATAAACATTGAAAACATTTCCCTTGAAACAA
Found at i:205123 original size:65 final size:65
Alignment explanation
Indices: 205018--205403 Score: 273
Period size: 65 Copynumber: 5.8 Consensus size: 65
205008 CTTGAGATAG
* *
205018 TTTCCCTTGAAATGAAATTTTGTATCCCTTGAGACAGTTTCTCTTGAAACATAAA-CATTGAAAA
1 TTTCCCTTGAAAT-AAATTTTGTCTCCCTTGAGACAGTTTCTCTTGAAACA-AAATCATTGAATA
205082 CA
64 CA
* * * *
205084 TTTCCCTTGAAATAAATTTTGTCTCTCTTGAGACAGTTTCCCTTGAAAC-AAATTATTTGAATAT
1 TTTCCCTTGAAATAAATTTTGTCTCCCTTGAGACAGTTTCTCTTGAAACAAAATCA-TTGAATAC
*
205148 G
65 A
*** * * * * *
205149 TTTTATTTGAAACAAA-TTTGTCTCCCTTGAGACAGTTTCTTTTGGAACTAAGTTTTATCTCTCT
1 TTTCCCTTGAAATAAATTTTGTCTCCCTTGAGACAGTTTCTCTTGAAAC-AA-----A-ATC-AT
*
205213 TG-AGACA
58 TGAATACA
* * * * * *
205220 GTTTCTCTTGAAA-CAATTTTCGTCTCTCTTGAGACAGTTTCCCTTGAAACAAAATCTTTGAATT
1 -TTTCCCTTGAAATAAATTTT-GTCTCCCTTGAGACAGTTTCTCTTGAAACAAAATCATTGAATA
*
205284 TA
64 CA
* * *
205286 TTTCCCCTAAAATAAATTTTGTCTCCCTTGAGACAGTTTCTCTTGAAACACAAAATC-TTCAAAT
1 TTTCCCTTGAAATAAATTTTGTCTCCCTTGAGACAGTTTCTCTTG-AA-ACAAAATCATT-GAAT
**
205350 TTA
63 ACA
* * * * *
205353 TTTCCCTTAAAACAAAATTTTGTTTCCCTTGAGACCGTTT-TCATGAAACAA
1 TTTCCCTTGAAA-TAAATTTTGTCTCCCTTGAGACAGTTTCTCTTGAAACAA
205404 CAGATATCTT
Statistics
Matches: 254, Mismatches: 46, Indels: 41
0.74 0.13 0.12
Matches are distributed among these distances:
63 3 0.01
64 29 0.11
65 90 0.35
66 30 0.12
67 30 0.12
68 24 0.09
71 5 0.02
72 18 0.07
73 25 0.10
ACGTcount: A:0.30, C:0.19, G:0.11, T:0.39
Consensus pattern (65 bp):
TTTCCCTTGAAATAAATTTTGTCTCCCTTGAGACAGTTTCTCTTGAAACAAAATCATTGAATACA
Found at i:205131 original size:36 final size:36
Alignment explanation
Indices: 205084--205272 Score: 164
Period size: 36 Copynumber: 5.4 Consensus size: 36
205074 ATTGAAAACA
*
205084 TTTCCCTTGAAATAAATTTTGTCTCTCTTGAGACAG
1 TTTCCCTTGAAACAAATTTTGTCTCTCTTGAGACAG
* *
205120 TTTCCCTTGAAACAAA-----T-TAT-TTGA-ATATG
1 TTTCCCTTGAAACAAATTTTGTCTCTCTTGAGACA-G
*** *
205149 TTTTATTTGAAACAAA-TTTGTCTCCCTTGAGACAG
1 TTTCCCTTGAAACAAATTTTGTCTCTCTTGAGACAG
** * * *
205184 TTTCTTTTGGAACTAAGTTTTATCTCTCTTGAGACAG
1 TTTCCCTTGAAAC-AAATTTTGTCTCTCTTGAGACAG
*
205221 TTTCTCTTGAAAC-AATTTTCGTCTCTCTTGAGACAG
1 TTTCCCTTGAAACAAATTTT-GTCTCTCTTGAGACAG
205257 TTTCCCTTGAAACAAA
1 TTTCCCTTGAAACAAA
205273 ATCTTTGAAT
Statistics
Matches: 121, Mismatches: 20, Indels: 23
0.74 0.12 0.14
Matches are distributed among these distances:
28 2 0.02
29 18 0.15
30 2 0.02
31 1 0.01
33 1 0.01
34 1 0.01
35 20 0.17
36 46 0.38
37 30 0.25
ACGTcount: A:0.27, C:0.19, G:0.13, T:0.41
Consensus pattern (36 bp):
TTTCCCTTGAAACAAATTTTGTCTCTCTTGAGACAG
Found at i:205353 original size:67 final size:68
Alignment explanation
Indices: 205234--205402 Score: 220
Period size: 67 Copynumber: 2.5 Consensus size: 68
205224 CTCTTGAAAC
* * **
205234 AATTTTCGTCTCTCTTGAGACAGTTTCCCTTG-AA-ACAAAATCTTTGAATTTATTTCCCCTAAA
1 AATTTT-GTCTCCCTTGAGACAGTTTCTCTTGAAACACAAAATCTTCAAATTTATTTCCCCTAAA
*
205297 A-TA
65 ACAA
*
205300 AATTTTGTCTCCCTTGAGACAGTTTCTCTTGAAACACAAAATCTTCAAATTTATTTCCCTTAAAA
1 AATTTTGTCTCCCTTGAGACAGTTTCTCTTGAAACACAAAATCTTCAAATTTATTTCCCCTAAAA
205365 CAA
66 CAA
* * *
205368 AATTTTGTTTCCCTTGAGACCGTTT-TCATGAAACA
1 AATTTTGTCTCCCTTGAGACAGTTTCTCTTGAAACA
205403 ACAGATATCT
Statistics
Matches: 91, Mismatches: 9, Indels: 5
0.87 0.09 0.05
Matches are distributed among these distances:
65 23 0.25
66 8 0.09
67 36 0.40
68 24 0.26
ACGTcount: A:0.31, C:0.21, G:0.09, T:0.38
Consensus pattern (68 bp):
AATTTTGTCTCCCTTGAGACAGTTTCTCTTGAAACACAAAATCTTCAAATTTATTTCCCCTAAAA
CAA
Found at i:206234 original size:106 final size:105
Alignment explanation
Indices: 206076--206595 Score: 526
Period size: 106 Copynumber: 5.0 Consensus size: 105
206066 ATATCGTGCC
** * * * ** *
206076 ACTCGAGACAACACAATTTCAACTTCACAACGAATGGATGGTTGGTTGTCAACAAACAATTTCCC
1 ACTCGAGACAACACAAGCTCAACTTCACAACGAAGGGACGGCTGACTGTCAACAAACAACTTCCC
*
206141 AGTTTCAGAACCAATTTCAACTTCACAGCGAAGGATATTGG
66 A-TTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGG
* * * * * *
206182 ATTCGAGACAACACAAGTTCAACTTCTCAACGAAGGGACGACTGGCTATCAACAAACAACTTCCC
1 ACTCGAGACAACACAAGCTCAACTTCACAACGAAGGGACGGCTGACTGTCAACAAACAACTTCCC
* ** *
206247 AATTTCATAGTTAATTTCAACTTCACAGCGAAAGATATTGG
66 -ATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGG
* * * * *
206288 ACTCAAGACAACACAAGCTCGACCTCACAACGAAGGGGCGGCTGACTGTCAACAAATAACTTCCC
1 ACTCGAGACAACACAAGCTCAACTTCACAACGAAGGGACGGCTGACTGTCAACAAACAACTTCCC
* *
206353 AATTTCAGGGCCAATTTCAACTTCCCAGCGAAGGATATTGG
66 -ATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGG
* * * * * * *
206394 ACCCAAGATAACACAAGCTCAACTTCACGACGAAGGGGA-GGCTGATTGTCAA-TAA-AA-TT-T
1 ACTCGAGACAACACAAGCTCAACTTCACAACGAA-GGGACGGCTGACTGTCAACAAACAACTTCC
* * * *
206454 CA-TTCAGAGTCAATTTCAACTTCACAACGAAAGATATTAG
65 CATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGG
* * * * *
206494 ACTCGAGACAGCACAAGCTCAACTTCACAATGAAGGGGCGGCTAACTATCAACAAACAA--T---
1 ACTCGAGACAACACAAGCTCAACTTCACAACGAAGGGACGGCTGACTGTCAACAAACAACTTCCC
206554 -TTTCAGAGCCAATTTCAACTTCAC-GACGAAGGATATTGG
66 ATTTCAGAGCCAATTTCAACTTCACAG-CGAAGGATATTGG
206593 ACT
1 ACT
206596 TGGAACAATA
Statistics
Matches: 345, Mismatches: 62, Indels: 21
0.81 0.14 0.05
Matches are distributed among these distances:
99 39 0.11
100 70 0.20
101 4 0.01
102 3 0.01
103 2 0.01
104 2 0.01
105 2 0.01
106 219 0.63
107 4 0.01
ACGTcount: A:0.36, C:0.24, G:0.17, T:0.23
Consensus pattern (105 bp):
ACTCGAGACAACACAAGCTCAACTTCACAACGAAGGGACGGCTGACTGTCAACAAACAACTTCCC
ATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGG
Found at i:208620 original size:23 final size:23
Alignment explanation
Indices: 208594--208662 Score: 93
Period size: 23 Copynumber: 3.0 Consensus size: 23
208584 CACCACAGCT
*
208594 CGTATAATTGCACCGAAGTGCCA
1 CGTAGAATTGCACCGAAGTGCCA
* * *
208617 CGTAGAATTACACCGGAGTGCCG
1 CGTAGAATTGCACCGAAGTGCCA
*
208640 CGTAGAATTGCACCGTAGTGCCA
1 CGTAGAATTGCACCGAAGTGCCA
208663 TATAATAATG
Statistics
Matches: 39, Mismatches: 7, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
23 39 1.00
ACGTcount: A:0.28, C:0.26, G:0.26, T:0.20
Consensus pattern (23 bp):
CGTAGAATTGCACCGAAGTGCCA
Found at i:208854 original size:103 final size:103
Alignment explanation
Indices: 208678--208995 Score: 555
Period size: 103 Copynumber: 3.1 Consensus size: 103
208668 TAATGTCCAT
* * * *
208678 AAGGACTACATATCATTACTTAAGAATCATATACATATACTAGGGATCAAGTATGTGTCTCACCA
1 AAGGACCACATATCATTCCTTAAGAATCATATACATATACCAAGGATCAAGTATGTGTCTCACCA
208743 GACTTCACACATGTTCCAAAGAATACATATATGTCCCG
66 GACTTCACACATGTTCCAAAGAATACATATATGTCCCG
*
208781 AAGGACCACATATCATTCCTTAAGAATCATATACATATGCCAAGGATCAAGTATGTGTCTCACCA
1 AAGGACCACATATCATTCCTTAAGAATCATATACATATACCAAGGATCAAGTATGTGTCTCACCA
*
208846 GACATCACACATGTTCCAAAGAATACATATATGTCCCG
66 GACTTCACACATGTTCCAAAGAATACATATATGTCCCG
208884 AAGGACCACATATCATTCCTTAAGAATCATATACATATACCAAGGATCAAGTATGTGTCTCACCA
1 AAGGACCACATATCATTCCTTAAGAATCATATACATATACCAAGGATCAAGTATGTGTCTCACCA
*
208949 GACTTCACACATGTTCCAAAGAATATATATATATGTCCCG
66 GACTTCACACATGTTCCAAAG-A-ATACATATATGTCCCG
208989 AAGGACC
1 AAGGACC
208996 GCGTAGACCC
Statistics
Matches: 204, Mismatches: 9, Indels: 2
0.95 0.04 0.01
Matches are distributed among these distances:
103 181 0.89
104 1 0.00
105 22 0.11
ACGTcount: A:0.37, C:0.23, G:0.14, T:0.26
Consensus pattern (103 bp):
AAGGACCACATATCATTCCTTAAGAATCATATACATATACCAAGGATCAAGTATGTGTCTCACCA
GACTTCACACATGTTCCAAAGAATACATATATGTCCCG
Found at i:210706 original size:21 final size:21
Alignment explanation
Indices: 210681--210726 Score: 56
Period size: 21 Copynumber: 2.2 Consensus size: 21
210671 TTCTGGTTCG
* * *
210681 CTTGAGGGGGTATCGGTTCCC
1 CTTGAAGGGGTACCGATTCCC
*
210702 CTTGAATGGGTACCGATTCCC
1 CTTGAAGGGGTACCGATTCCC
210723 CTTG
1 CTTG
210727 CCCAGAAATC
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.13, C:0.26, G:0.30, T:0.30
Consensus pattern (21 bp):
CTTGAAGGGGTACCGATTCCC
Found at i:211585 original size:31 final size:31
Alignment explanation
Indices: 211527--211591 Score: 76
Period size: 31 Copynumber: 2.1 Consensus size: 31
211517 AGAGTCGAGG
* *
211527 GTTTACCTATGTTCTAAGGAACATATGGATA
1 GTTTACCTAGGTTCTAAGGAACATATGGACA
** * *
211558 GTTTACCTAGGTTCTTCGGGACCTATGGACA
1 GTTTACCTAGGTTCTAAGGAACATATGGACA
211589 GTT
1 GTT
211592 ACCGAGGATC
Statistics
Matches: 28, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
31 28 1.00
ACGTcount: A:0.25, C:0.17, G:0.23, T:0.35
Consensus pattern (31 bp):
GTTTACCTAGGTTCTAAGGAACATATGGACA
Found at i:211647 original size:30 final size:30
Alignment explanation
Indices: 211577--211649 Score: 119
Period size: 30 Copynumber: 2.4 Consensus size: 30
211567 GGTTCTTCGG
* * *
211577 GACCTATGGACAGTTACCGAGGATCTTTAT
1 GACCTCTGGATAGTTACCAAGGATCTTTAT
211607 GACCTCTGGATAGTTACCAAGGATCTTTAT
1 GACCTCTGGATAGTTACCAAGGATCTTTAT
211637 GACCTCTGGATAG
1 GACCTCTGGATAG
211650 GTCCTTCGGG
Statistics
Matches: 40, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
30 40 1.00
ACGTcount: A:0.26, C:0.21, G:0.23, T:0.30
Consensus pattern (30 bp):
GACCTCTGGATAGTTACCAAGGATCTTTAT
Found at i:213254 original size:9 final size:9
Alignment explanation
Indices: 213213--213268 Score: 53
Period size: 9 Copynumber: 6.2 Consensus size: 9
213203 TTTGATAACA
*
213213 TTTCTTTTC
1 TTTCATTTC
213222 ATTTCATTTC
1 -TTTCATTTC
*
213232 TTATCA-AT-
1 TT-TCATTTC
213240 TTTCATTTC
1 TTTCATTTC
213249 TTTCATTTC
1 TTTCATTTC
*
213258 TTTTATTTC
1 TTTCATTTC
213267 TT
1 TT
213269 CCTTTATATT
Statistics
Matches: 39, Mismatches: 4, Indels: 7
0.78 0.08 0.14
Matches are distributed among these distances:
7 3 0.08
8 3 0.08
9 22 0.56
10 11 0.28
ACGTcount: A:0.14, C:0.18, G:0.00, T:0.68
Consensus pattern (9 bp):
TTTCATTTC
Found at i:222104 original size:8 final size:8
Alignment explanation
Indices: 222091--222131 Score: 57
Period size: 8 Copynumber: 5.2 Consensus size: 8
222081 CTCATTTTTA
222091 GAGAATTT
1 GAGAATTT
222099 GAGAATTT
1 GAGAATTT
*
222107 -AGAGTTT
1 GAGAATTT
*
222114 GGGAATTT
1 GAGAATTT
222122 GAGAATTT
1 GAGAATTT
222130 GA
1 GA
222132 AAGATTATGA
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
7 6 0.21
8 22 0.79
ACGTcount: A:0.34, C:0.00, G:0.29, T:0.37
Consensus pattern (8 bp):
GAGAATTT
Found at i:222426 original size:126 final size:127
Alignment explanation
Indices: 222202--222815 Score: 1050
Period size: 126 Copynumber: 4.9 Consensus size: 127
222192 TAATCGGAGT
* * **
222202 ACTATTCACATGAAGGCGCGTTCCCGGGGGTGCGCTTTCCATTATTTTATCA-AGAATATGTTAT
1 ACTATTCACATGAAGGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTCGTCAGAGAATATGTTAT
222266 CATTG-CCTATTATGTCACTCATGTCCCTCGGGGACACTAGATATATCA-TACCTATTATTTC
66 CATTGCCCTATTATGTCACTCATGTCCCTC-GGGACACTAGATATATCAGTACCTATTATTTC
*
222327 ACTATTCACATGAAGGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTTGTCAGAGAATATGTTAT
1 ACTATTCACATGAAGGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTCGTCAGAGAATATGTTAT
*
222392 CATT-CCCTATTATGCCACTCATGTCCCTCGGGGACACTAGATATATCAGTACCTATTATTTC
66 CATTGCCCTATTATGTCACTCATGTCCCTC-GGGACACTAGATATATCAGTACCTATTATTTC
*
222454 ACTATTCACATGAAGGCGCGTTCCC-GGGGCGTGCCTTCCATTATTTCGTCAGAGAATATGTTAT
1 ACTATTCACATGAAGGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTCGTCAGAGAATATGTTAT
222518 CATTGCCCTATTATGTCACTCATGTCCCTCGGGACACTAG--ATATCAGTACCTATTATTTC
66 CATTGCCCTATTATGTCACTCATGTCCCTCGGGACACTAGATATATCAGTACCTATTATTTC
*
222578 ACTATTCACATGAAGGCGCGTTCCC-GGGG-GCGCCTTCCATTATTTCGTCATAGAATATGTTAT
1 ACTATTCACATGAAGGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTCGTCAGAGAATATGTTAT
222641 CATTGCCCTATTATGTCACTCATGTCCCTCGGGACACTAGATATATCAGTACCTATTATTTC
66 CATTGCCCTATTATGTCACTCATGTCCCTCGGGACACTAGATATATCAGTACCTATTATTTC
* *
222703 ACTATTCACATTAAGGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTCGTCATAGAATATGTTAT
1 ACTATTCACATGAAGGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTCGTCAGAGAATATGTTAT
222768 CATTGCCCTATTATG-CACTCATGTCCCTCGGGACACTAGATATATCAG
66 CATTGCCCTATTATGTCACTCATGTCCCTCGGGACACTAGATATATCAG
222816 AAAATCAGGT
Statistics
Matches: 471, Mismatches: 10, Indels: 15
0.95 0.02 0.03
Matches are distributed among these distances:
123 72 0.15
124 49 0.10
125 93 0.20
126 146 0.31
127 111 0.24
ACGTcount: A:0.23, C:0.25, G:0.18, T:0.33
Consensus pattern (127 bp):
ACTATTCACATGAAGGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTCGTCAGAGAATATGTTAT
CATTGCCCTATTATGTCACTCATGTCCCTCGGGACACTAGATATATCAGTACCTATTATTTC
Found at i:223307 original size:33 final size:33
Alignment explanation
Indices: 223214--223311 Score: 117
Period size: 32 Copynumber: 3.0 Consensus size: 33
223204 AAATTTAATG
*
223214 TTAAATTTTGAATACTATAATTTATATTTTAAAT
1 TTAAA-TTTGAATAATATAATTTATATTTTAAAT
* * * *
223248 TTAAATTTGAATAATAT-TTTTTTATTTTTATT
1 TTAAATTTGAATAATATAATTTATATTTTAAAT
* *
223280 TTAAATTTCAATAATATAATTTGTATTTTAAA
1 TTAAATTTGAATAATATAATTTATATTTTAAA
223312 AACATTTATC
Statistics
Matches: 53, Mismatches: 10, Indels: 3
0.80 0.15 0.05
Matches are distributed among these distances:
32 27 0.51
33 21 0.40
34 5 0.09
ACGTcount: A:0.39, C:0.02, G:0.03, T:0.56
Consensus pattern (33 bp):
TTAAATTTGAATAATATAATTTATATTTTAAAT
Found at i:223857 original size:21 final size:20
Alignment explanation
Indices: 223830--223899 Score: 95
Period size: 21 Copynumber: 3.4 Consensus size: 20
223820 GGTATAAAAC
*
223830 CCTGCGGGCTAGGCATGTAA
1 CCTGCGGGCTAGGAATGTAA
223850 CCTGGCGGGCTAGGAATGTAA
1 CCT-GCGGGCTAGGAATGTAA
*
223871 CCCTGCGGGCTCGGAATGTAA
1 -CCTGCGGGCTAGGAATGTAA
223892 CCCTGCGG
1 -CCTGCGG
223900 AGATGGCATA
Statistics
Matches: 46, Mismatches: 2, Indels: 3
0.90 0.04 0.06
Matches are distributed among these distances:
20 3 0.07
21 40 0.87
22 3 0.07
ACGTcount: A:0.19, C:0.27, G:0.36, T:0.19
Consensus pattern (20 bp):
CCTGCGGGCTAGGAATGTAA
Found at i:223929 original size:21 final size:21
Alignment explanation
Indices: 223903--223950 Score: 60
Period size: 21 Copynumber: 2.3 Consensus size: 21
223893 CCTGCGGAGA
*
223903 TGGCATATAAACTGGTGGGCT
1 TGGCATATAAACTGGAGGGCT
* *
223924 TGGCATATGAAGTGGAGGGCT
1 TGGCATATAAACTGGAGGGCT
*
223945 GGGCAT
1 TGGCAT
223951 GTACCCCTGC
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.23, C:0.12, G:0.40, T:0.25
Consensus pattern (21 bp):
TGGCATATAAACTGGAGGGCT
Found at i:229050 original size:18 final size:19
Alignment explanation
Indices: 229027--229063 Score: 58
Period size: 19 Copynumber: 2.0 Consensus size: 19
229017 ATATGCAAAA
229027 GGGTTTT-TTGATCTTTTG
1 GGGTTTTATTGATCTTTTG
*
229045 GGGTTTTATTTATCTTTTG
1 GGGTTTTATTGATCTTTTG
229064 ATGTTTTCCT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
18 7 0.41
19 10 0.59
ACGTcount: A:0.08, C:0.05, G:0.24, T:0.62
Consensus pattern (19 bp):
GGGTTTTATTGATCTTTTG
Found at i:240330 original size:43 final size:43
Alignment explanation
Indices: 240282--240443 Score: 261
Period size: 43 Copynumber: 3.8 Consensus size: 43
240272 CAGACCACCC
* * *
240282 AACTATTTAAATATATTCAATCAGGTCACTTACATTTAAAGCA
1 AACTATTTAAATACATTCAATCAGGCCACTTGCATTTAAAGCA
* *
240325 AACTATTTAAATACATTCAATTAGGTCACTTGCATTTAAAGCA
1 AACTATTTAAATACATTCAATCAGGCCACTTGCATTTAAAGCA
*
240368 AACTATTTAAATACATTCAATCAGACCACTTGCATTTAAAGCA
1 AACTATTTAAATACATTCAATCAGGCCACTTGCATTTAAAGCA
*
240411 AACTATTTAAATACATTCAATTAGGCCACTTGC
1 AACTATTTAAATACATTCAATCAGGCCACTTGC
240444 CGTTAACATT
Statistics
Matches: 111, Mismatches: 8, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
43 111 1.00
ACGTcount: A:0.40, C:0.19, G:0.08, T:0.33
Consensus pattern (43 bp):
AACTATTTAAATACATTCAATCAGGCCACTTGCATTTAAAGCA
Found at i:240634 original size:31 final size:28
Alignment explanation
Indices: 240596--240658 Score: 81
Period size: 31 Copynumber: 2.1 Consensus size: 28
240586 ATGTGTCACT
*
240596 ATTAGATTGGAATATATTTTTATTAATTTTA
1 ATTAGATTGG-AGATA-TTTTATTAA-TTTA
*
240627 ATTAGATTGGGGATATTTTATTAATTTA
1 ATTAGATTGGAGATATTTTATTAATTTA
240655 ATTA
1 ATTA
240659 TTTAATACTT
Statistics
Matches: 30, Mismatches: 2, Indels: 3
0.86 0.06 0.09
Matches are distributed among these distances:
28 8 0.27
29 9 0.30
30 3 0.10
31 10 0.33
ACGTcount: A:0.35, C:0.00, G:0.13, T:0.52
Consensus pattern (28 bp):
ATTAGATTGGAGATATTTTATTAATTTA
Found at i:242398 original size:11 final size:12
Alignment explanation
Indices: 242368--242398 Score: 62
Period size: 12 Copynumber: 2.6 Consensus size: 12
242358 ATTAATATTT
242368 TAATTTTTTCAA
1 TAATTTTTTCAA
242380 TAATTTTTTCAA
1 TAATTTTTTCAA
242392 TAATTTT
1 TAATTTT
242399 ATTTACTATA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 19 1.00
ACGTcount: A:0.32, C:0.06, G:0.00, T:0.61
Consensus pattern (12 bp):
TAATTTTTTCAA
Found at i:245502 original size:16 final size:16
Alignment explanation
Indices: 245481--245513 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 16
245471 TAATAAATAA
245481 ACGAACATAAACGAAC
1 ACGAACATAAACGAAC
*
245497 ACGAACATAAATGAAC
1 ACGAACATAAACGAAC
245513 A
1 A
245514 AATTTTTTTT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.58, C:0.21, G:0.12, T:0.09
Consensus pattern (16 bp):
ACGAACATAAACGAAC
Found at i:245606 original size:6 final size:6
Alignment explanation
Indices: 245595--245654 Score: 51
Period size: 6 Copynumber: 11.0 Consensus size: 6
245585 GAACATAAAC
* *
245595 GAACAT GAACAT -AA-AT GAACAC GAACAT -AA-AT GAACAC GAACAT
1 GAACAT GAACAT GAACAT GAACAT GAACAT GAACAT GAACAT GAACAT
*
245639 -AA-AT GAACAC GAACAT
1 GAACAT GAACAT GAACAT
245655 AAACGTTGGA
Statistics
Matches: 42, Mismatches: 6, Indels: 12
0.70 0.10 0.20
Matches are distributed among these distances:
4 6 0.14
5 12 0.29
6 24 0.57
ACGTcount: A:0.55, C:0.18, G:0.13, T:0.13
Consensus pattern (6 bp):
GAACAT
Found at i:245606 original size:16 final size:16
Alignment explanation
Indices: 245575--245657 Score: 134
Period size: 16 Copynumber: 5.3 Consensus size: 16
245565 CGTTCATTTA
245575 ATAAAT-AA-ACGAAC
1 ATAAATGAACACGAAC
* *
245589 ATAAACGAACATGAAC
1 ATAAATGAACACGAAC
245605 ATAAATGAACACGAAC
1 ATAAATGAACACGAAC
245621 ATAAATGAACACGAAC
1 ATAAATGAACACGAAC
245637 ATAAATGAACACGAAC
1 ATAAATGAACACGAAC
245653 ATAAA
1 ATAAA
245658 CGTTGGAGAC
Statistics
Matches: 63, Mismatches: 4, Indels: 2
0.91 0.06 0.03
Matches are distributed among these distances:
14 5 0.08
15 2 0.03
16 56 0.89
ACGTcount: A:0.59, C:0.17, G:0.11, T:0.13
Consensus pattern (16 bp):
ATAAATGAACACGAAC
Found at i:258374 original size:31 final size:29
Alignment explanation
Indices: 258305--258394 Score: 117
Period size: 31 Copynumber: 2.9 Consensus size: 29
258295 TAAAAATTTA
258305 GGTACTAAAATGAAAAAAAAAGTTAACCATGG
1 GGTACTAAAATGAAAAAAAAAG-TAA--ATGG
*
258337 GGTACTAAAATGAAACAAAAAGTAAATGCCG
1 GGTACTAAAATGAAAAAAAAAGTAAATG--G
*
258368 GGTACTAAAATGAAATAAAAAGTAAAT
1 GGTACTAAAATGAAAAAAAAAGTAAAT
258395 ATTATGTGTG
Statistics
Matches: 54, Mismatches: 2, Indels: 5
0.89 0.03 0.08
Matches are distributed among these distances:
29 3 0.06
31 30 0.56
32 21 0.39
ACGTcount: A:0.54, C:0.09, G:0.18, T:0.19
Consensus pattern (29 bp):
GGTACTAAAATGAAAAAAAAAGTAAATGG
Found at i:259505 original size:28 final size:29
Alignment explanation
Indices: 259449--259504 Score: 71
Period size: 29 Copynumber: 1.9 Consensus size: 29
259439 GTAATACCCT
*
259449 ATAGTAAGGGGACTATTTTGTAACTTTTA
1 ATAGTAAGGGGACCATTTTGTAACTTTTA
259478 ATAGTCAA-GGGACCATTTGTGT-ACTTT
1 ATAGT-AAGGGGACCATTT-TGTAACTTT
259505 ACCCTTATTA
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
29 19 0.79
30 5 0.21
ACGTcount: A:0.29, C:0.11, G:0.21, T:0.39
Consensus pattern (29 bp):
ATAGTAAGGGGACCATTTTGTAACTTTTA
Found at i:260962 original size:15 final size:15
Alignment explanation
Indices: 260942--260971 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
260932 AACAAATGAC
260942 ATTCATACTCATATA
1 ATTCATACTCATATA
260957 ATTCATACTCATATA
1 ATTCATACTCATATA
260972 TACATATTCC
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.40, C:0.20, G:0.00, T:0.40
Consensus pattern (15 bp):
ATTCATACTCATATA
Found at i:264916 original size:12 final size:12
Alignment explanation
Indices: 264899--264930 Score: 55
Period size: 12 Copynumber: 2.7 Consensus size: 12
264889 AAACCCTTTT
*
264899 CAGCAGCACTAC
1 CAGCAGCACCAC
264911 CAGCAGCACCAC
1 CAGCAGCACCAC
264923 CAGCAGCA
1 CAGCAGCA
264931 TCAGGTTTCT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
12 19 1.00
ACGTcount: A:0.34, C:0.44, G:0.19, T:0.03
Consensus pattern (12 bp):
CAGCAGCACCAC
Found at i:269386 original size:31 final size:32
Alignment explanation
Indices: 269343--269423 Score: 119
Period size: 33 Copynumber: 2.5 Consensus size: 32
269333 CTAGCAAATG
* *
269343 ATCTCTTAATGTCAAGA-GATTTGTGGTTTTT
1 ATCTATTAATGTCAAGAGGATTTGTGGCTTTT
*
269374 ATCTATTAATGTCAGGTAGGATTTGTGGCTTTT
1 ATCTATTAATGTCAAG-AGGATTTGTGGCTTTT
269407 ATCTATTAATGTCAAGA
1 ATCTATTAATGTCAAGA
269424 AAAATGTCTT
Statistics
Matches: 44, Mismatches: 4, Indels: 3
0.86 0.08 0.06
Matches are distributed among these distances:
31 14 0.32
32 2 0.05
33 28 0.64
ACGTcount: A:0.26, C:0.10, G:0.20, T:0.44
Consensus pattern (32 bp):
ATCTATTAATGTCAAGAGGATTTGTGGCTTTT
Found at i:270399 original size:16 final size:16
Alignment explanation
Indices: 270371--270420 Score: 75
Period size: 16 Copynumber: 3.1 Consensus size: 16
270361 AATAATTAAG
270371 ATAC-TAAACATGTAAT
1 ATACTTAAA-ATGTAAT
*
270387 TTACTTAAAATGTAAT
1 ATACTTAAAATGTAAT
270403 ATACTTAAAATGTAAT
1 ATACTTAAAATGTAAT
270419 AT
1 AT
270421 CCAAAATTTG
Statistics
Matches: 31, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
16 27 0.87
17 4 0.13
ACGTcount: A:0.48, C:0.08, G:0.06, T:0.38
Consensus pattern (16 bp):
ATACTTAAAATGTAAT
Found at i:284098 original size:21 final size:21
Alignment explanation
Indices: 284073--284131 Score: 73
Period size: 21 Copynumber: 2.8 Consensus size: 21
284063 GTCCGAGTTA
*
284073 CCCGCGACGGCCGCAATAACG
1 CCCGCGACAGCCGCAATAACG
* *
284094 TCCGCGACAGCCGCAATAGCG
1 CCCGCGACAGCCGCAATAACG
* *
284115 CCCGGGACTGCCGCAAT
1 CCCGCGACAGCCGCAAT
284132 CACGGTAAAT
Statistics
Matches: 32, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 32 1.00
ACGTcount: A:0.22, C:0.41, G:0.29, T:0.08
Consensus pattern (21 bp):
CCCGCGACAGCCGCAATAACG
Found at i:292733 original size:13 final size:13
Alignment explanation
Indices: 292703--292757 Score: 92
Period size: 13 Copynumber: 4.2 Consensus size: 13
292693 TCACGTTCAG
*
292703 ATTTTTAAAATAAA
1 ATTTTTAAAA-AAT
292717 ATTTTTAAAAAAT
1 ATTTTTAAAAAAT
292730 ATTTTTAAAAAAT
1 ATTTTTAAAAAAT
292743 ATTTTTAAAAAAT
1 ATTTTTAAAAAAT
292756 AT
1 AT
292758 ATAAACATAA
Statistics
Matches: 40, Mismatches: 1, Indels: 1
0.95 0.02 0.02
Matches are distributed among these distances:
13 30 0.75
14 10 0.25
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (13 bp):
ATTTTTAAAAAAT
Found at i:296990 original size:15 final size:15
Alignment explanation
Indices: 296972--297002 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
296962 AAATTCTAAA
296972 TATTTAAATAAAAAT
1 TATTTAAATAAAAAT
*
296987 TATTTATATAAAAAT
1 TATTTAAATAAAAAT
297002 T
1 T
297003 CTATCTGTTG
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (15 bp):
TATTTAAATAAAAAT
Found at i:302941 original size:23 final size:23
Alignment explanation
Indices: 302915--302983 Score: 93
Period size: 23 Copynumber: 3.0 Consensus size: 23
302905 CACCACAACT
*
302915 CGTATAATTGCACCGAAGTGCCA
1 CGTAGAATTGCACCGAAGTGCCA
* * *
302938 CGTAGAATTGTACCGGAGTGCCG
1 CGTAGAATTGCACCGAAGTGCCA
*
302961 CGTAGAATTGCACCGTAGTGCCA
1 CGTAGAATTGCACCGAAGTGCCA
302984 TATAATAATG
Statistics
Matches: 39, Mismatches: 7, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
23 39 1.00
ACGTcount: A:0.26, C:0.25, G:0.28, T:0.22
Consensus pattern (23 bp):
CGTAGAATTGCACCGAAGTGCCA
Found at i:303172 original size:103 final size:104
Alignment explanation
Indices: 302999--303218 Score: 352
Period size: 103 Copynumber: 2.1 Consensus size: 104
302989 TAATGTCCAT
* * * *
302999 AAGGACTACATATCATTCCTTAAGAATCATATATATATATACTAGGGATCAAGTATGTGTCTCAC
1 AAGGACCACATATCATTCCTTAAGAATCA-ATATACATATACCAAGGATCAAGTATGTGTCTCAC
303064 CAGACTTCACACATGTTCCAAAGAATACATATATGTCCCG
65 CAGACTTCACACATGTTCCAAAGAATACATATATGTCCCG
* *
303104 AAGGACCATATATCATTCCTTAAGAATC-ATATACATATGCCAAGGATCAAGTATGTGTCTCACC
1 AAGGACCACATATCATTCCTTAAGAATCAATATACATATACCAAGGATCAAGTATGTGTCTCACC
303168 AGACTTCACACATGTTCCAAAGAATACATATATGTCCCG
66 AGACTTCACACATGTTCCAAAGAATACATATATGTCCCG
* *
303207 AAAGACCGCATA
1 AAGGACCACATA
303219 GACCCTCAAC
Statistics
Matches: 106, Mismatches: 9, Indels: 2
0.91 0.08 0.02
Matches are distributed among these distances:
103 80 0.75
105 26 0.25
ACGTcount: A:0.37, C:0.22, G:0.14, T:0.27
Consensus pattern (104 bp):
AAGGACCACATATCATTCCTTAAGAATCAATATACATATACCAAGGATCAAGTATGTGTCTCACC
AGACTTCACACATGTTCCAAAGAATACATATATGTCCCG
Found at i:304923 original size:21 final size:21
Alignment explanation
Indices: 304899--304943 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
304889 TTTTGTTCGT
* *
304899 TTGAAGGGGTATCGGTTCCCC
1 TTGAAGGGGTACCGATTCCCC
*
304920 TTGAATGGGTACCGATTCCCC
1 TTGAAGGGGTACCGATTCCCC
304941 TTG
1 TTG
304944 CCCAGAAATC
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.16, C:0.24, G:0.29, T:0.31
Consensus pattern (21 bp):
TTGAAGGGGTACCGATTCCCC
Found at i:305812 original size:2 final size:2
Alignment explanation
Indices: 305805--305831 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
305795 CTTTTTCCTT
305805 TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA T
305832 GTCACTTATC
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:308167 original size:23 final size:23
Alignment explanation
Indices: 308141--308204 Score: 83
Period size: 23 Copynumber: 2.8 Consensus size: 23
308131 CAGCTCGTAT
*
308141 AATTGCACCGAAGTTCCACATAG
1 AATTGCACCGAAGTGCCACATAG
* * *
308164 AATTGCACCGGAGTGCCGCGTAG
1 AATTGCACCGAAGTGCCACATAG
*
308187 AATTGCACCGTAGTGCCA
1 AATTGCACCGAAGTGCCA
308205 TATAATAATG
Statistics
Matches: 35, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
23 35 1.00
ACGTcount: A:0.28, C:0.27, G:0.25, T:0.20
Consensus pattern (23 bp):
AATTGCACCGAAGTGCCACATAG
Found at i:308391 original size:103 final size:103
Alignment explanation
Indices: 308220--308432 Score: 372
Period size: 103 Copynumber: 2.1 Consensus size: 103
308210 TAATGTCCAT
* * * *
308220 AAGGACTACATATAATTCCTTAAGAATCATATATATATACTAGGGATCAAGTATGTGTCTCACCA
1 AAGGACCACATATAATTCCTTAAGAATCATATACATATACCAAGGATCAAGTATGTGTCTCACCA
308285 GACTTCACACATGTTCCAAAGAATACATATATGTCCCG
66 GACTTCACACATGTTCCAAAGAATACATATATGTCCCG
*
308323 AAGGACCACATATAATTCCTTAAGAATCATATACATATGCCAAGGATCAAGTATGTGTCTCACCA
1 AAGGACCACATATAATTCCTTAAGAATCATATACATATACCAAGGATCAAGTATGTGTCTCACCA
308388 GACTTCACACATGTTCCAAAGAATACATATATGTCCCG
66 GACTTCACACATGTTCCAAAGAATACATATATGTCCCG
*
308426 AAAGACC
1 AAGGACC
308433 GCGTAGACCC
Statistics
Matches: 104, Mismatches: 6, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
103 104 1.00
ACGTcount: A:0.38, C:0.22, G:0.14, T:0.27
Consensus pattern (103 bp):
AAGGACCACATATAATTCCTTAAGAATCATATACATATACCAAGGATCAAGTATGTGTCTCACCA
GACTTCACACATGTTCCAAAGAATACATATATGTCCCG
Found at i:311743 original size:21 final size:21
Alignment explanation
Indices: 311719--311796 Score: 84
Period size: 21 Copynumber: 3.7 Consensus size: 21
311709 CATTCGGGAT
*
311719 ATATATGTAATCCTTTGGAAC
1 ATATATGTGATCCTTTGGAAC
* * *
311740 ATATATGTGGTTCTTTGGGAC
1 ATATATGTGATCCTTTGGAAC
* * * *
311761 ACATATTTGGTCCTTTGGAAT
1 ATATATGTGATCCTTTGGAAC
311782 ATATATGTGATCCTT
1 ATATATGTGATCCTT
311797 AAGGAGTTGT
Statistics
Matches: 45, Mismatches: 12, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
21 45 1.00
ACGTcount: A:0.26, C:0.13, G:0.19, T:0.42
Consensus pattern (21 bp):
ATATATGTGATCCTTTGGAAC
Found at i:311877 original size:23 final size:21
Alignment explanation
Indices: 311809--311882 Score: 94
Period size: 21 Copynumber: 3.4 Consensus size: 21
311799 GGAGTTGTCT
311809 TTCGGGACATCTATGTGGTCC
1 TTCGGGACATCTATGTGGTCC
* * *
311830 TTCAGGACATATATATGGTCC
1 TTCGGGACATCTATGTGGTCC
*
311851 TTCGGGACATTTCTATGTGGTCA
1 TTCGGGACA--TCTATGTGGTCC
311874 TTCGGGACA
1 TTCGGGACA
311883 AAATTTTATA
Statistics
Matches: 44, Mismatches: 7, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
21 26 0.59
23 18 0.41
ACGTcount: A:0.20, C:0.20, G:0.26, T:0.34
Consensus pattern (21 bp):
TTCGGGACATCTATGTGGTCC
Found at i:320917 original size:10 final size:11
Alignment explanation
Indices: 320893--320921 Score: 51
Period size: 10 Copynumber: 2.7 Consensus size: 11
320883 ACATCATACC
320893 AAAATAATAAT
1 AAAATAATAAT
320904 AAAATAAT-AT
1 AAAATAATAAT
320914 AAAATAAT
1 AAAATAAT
320922 CAAACATGAA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
10 10 0.56
11 8 0.44
ACGTcount: A:0.72, C:0.00, G:0.00, T:0.28
Consensus pattern (11 bp):
AAAATAATAAT
Found at i:328084 original size:46 final size:45
Alignment explanation
Indices: 328034--328129 Score: 106
Period size: 46 Copynumber: 2.1 Consensus size: 45
328024 ATATAATTTT
*
328034 AATTTTAAATAAAAT-TTTAAAAAATAGTTTAAGTATCTATTCGATG
1 AATTTTAAATAAAATAGTT-AAAAATAGTTTAAGTATCTATTCGA-G
* ***
328080 AA-TTTAGATTGGATGAGTTAAAAATAGTTTAAGTATCTATTCGAG
1 AATTTTAAATAAAAT-AGTTAAAAATAGTTTAAGTATCTATTCGAG
328125 AATTT
1 AATTT
328130 AGATATAGTT
Statistics
Matches: 42, Mismatches: 5, Indels: 6
0.79 0.09 0.11
Matches are distributed among these distances:
45 11 0.26
46 29 0.69
47 2 0.05
ACGTcount: A:0.42, C:0.04, G:0.14, T:0.41
Consensus pattern (45 bp):
AATTTTAAATAAAATAGTTAAAAATAGTTTAAGTATCTATTCGAG
Found at i:328783 original size:13 final size:14
Alignment explanation
Indices: 328754--328786 Score: 50
Period size: 13 Copynumber: 2.4 Consensus size: 14
328744 ATTAACTTCA
328754 TAAAATTAAAATAT
1 TAAAATTAAAATAT
*
328768 TAAAATT-AAATTT
1 TAAAATTAAAATAT
328781 TAAAAT
1 TAAAAT
328787 AATATGACAA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
13 11 0.61
14 7 0.39
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (14 bp):
TAAAATTAAAATAT
Found at i:328961 original size:2 final size:2
Alignment explanation
Indices: 328954--328979 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
328944 ACCCAATACA
328954 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
328980 TAAATAAATA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:332552 original size:58 final size:59
Alignment explanation
Indices: 332444--332593 Score: 160
Period size: 58 Copynumber: 2.6 Consensus size: 59
332434 GTCAGATGAT
* * ***
332444 CATTTTGTAACTTTTACTAGTTGA-AGGACTCAATAAAGCATTGCCAATAGTTGA-AGAC
1 CATTTTATAACTTTTAATAGTTGAGA-GACTCAATAAAGCACCACCAATAGTTGAGAGAC
* * *
332502 CATTTTATAACTTTTAATAGTTGAGAGACTCAATAAAGTACCACCTATAGTTGAGGGAC
1 CATTTTATAACTTTTAATAGTTGAGAGACTCAATAAAGCACCACCAATAGTTGAGAGAC
* * * * *
332561 TATTCTATAATTTTTAATAGTTAAGATACTCAA
1 CATTTTATAACTTTTAATAGTTGAGAGACTCAA
332594 CAAAATAATA
Statistics
Matches: 77, Mismatches: 13, Indels: 3
0.83 0.14 0.03
Matches are distributed among these distances:
58 45 0.58
59 32 0.42
ACGTcount: A:0.36, C:0.14, G:0.15, T:0.35
Consensus pattern (59 bp):
CATTTTATAACTTTTAATAGTTGAGAGACTCAATAAAGCACCACCAATAGTTGAGAGAC
Found at i:335742 original size:258 final size:258
Alignment explanation
Indices: 335444--335979 Score: 844
Period size: 258 Copynumber: 2.1 Consensus size: 258
335434 TTTTAATTAT
*
335444 TTCGGGTCGGGTCGGGTGAAACTTTATTTTGGTCGGGTCGGGTCGGTTTTTTTAAGTGTGATATT
1 TTCGGGTCGGGTCGGGTGAAACTTTATTTTGGTCGGGTCGGATCGGTTTTTTTAAGTGTGATATT
* * *
335509 CGGGTCGGGTCAAGTTCGGGTTTAGGGTGAAAAATACACGACCCG-TATATATATATAATTTTAC
66 CGGGTCGGGTCAAGTTCGGGTTTAGGGTGAAAAATACACGACCCGCAAAAAATATATAATTTTAC
*
335573 CTTATATATTTAGGAATAATTACAATAATACCCCTCTCTATATATTTTTTT-TAATTAAGTCACT
131 CTTATATATTTAGGAATAATTACAATAATACCCCTCTCTATATATTTTTTTCCAATTAAGTCACT
**
335637 ATTTTTATTGAATAAAAATATTTTTTTTTATTATTTCAGGTCGGGTCGA-ATTTCTAATTCATAT
196 ATTTTTATTGAAT--AAATATAATTTTTTATTATTTCAGGTCGGGT-GAGATTTCTAATTCATAT
335701 A
258 A
*
335702 TTCGGGTCGGGTCGGGTGAAACTTTATTTTGGTCGGGTCGGATCGGTTTTTTTAAGTGTGGTATT
1 TTCGGGTCGGGTCGGGTGAAACTTTATTTTGGTCGGGTCGGATCGGTTTTTTTAAGTGTGATATT
** *
335767 CGGGTCGGGTCGGGTTCGGGTTTAGGGTGAAAAATACCCGACCCGACCCAAAAAATATATAATTT
66 CGGGTCGGGTCAAGTTCGGGTTTAGGGTGAAAAATACACGACCCG---CAAAAAATATATAATTT
*
335832 TACCTTATATATTTAGGAATAATTACAATAATACCCCTCTCTATTTATTTTTTTCCAATTAAGTC
128 TACCTTATATATTTAGGAATAATTACAATAATACCCCTCTCTATATATTTTTTTCCAATTAAGTC
* ** * *
335897 ATTATTTTTATTGAATAAATATAATTTTTTATTATTTTGGGTCGGGTTAGGTTTCTAATTCATAT
193 ACTATTTTTATTGAATAAATATAATTTTTTATTATTTCAGGTCGGGTGAGATTTCTAATTCATAT
335962 A
258 A
335963 TTCGGGTCGGGTCGGGT
1 TTCGGGTCGGGTCGGGT
335980 CTCGGATGGA
Statistics
Matches: 255, Mismatches: 17, Indels: 9
0.91 0.06 0.03
Matches are distributed among these distances:
258 105 0.41
260 1 0.00
261 59 0.23
262 66 0.26
263 24 0.09
ACGTcount: A:0.25, C:0.13, G:0.21, T:0.41
Consensus pattern (258 bp):
TTCGGGTCGGGTCGGGTGAAACTTTATTTTGGTCGGGTCGGATCGGTTTTTTTAAGTGTGATATT
CGGGTCGGGTCAAGTTCGGGTTTAGGGTGAAAAATACACGACCCGCAAAAAATATATAATTTTAC
CTTATATATTTAGGAATAATTACAATAATACCCCTCTCTATATATTTTTTTCCAATTAAGTCACT
ATTTTTATTGAATAAATATAATTTTTTATTATTTCAGGTCGGGTGAGATTTCTAATTCATATA
Found at i:336659 original size:75 final size:74
Alignment explanation
Indices: 336545--336723 Score: 277
Period size: 75 Copynumber: 2.4 Consensus size: 74
336535 GTATGGTATT
*
336545 GATACCCCCATATAAGGTACCGATACCCCTATGAACATTTTGGTTCCGAGAAATAACAGAATACT
1 GATACCCCC-TAT-AGGTATCGATACCCCTATGAACATTTTGGTTCCGAGAAATAACAGAATACT
*
336610 CGGATGGTACC
64 CAGATGGTACC
* * *
336621 TATACCCCCTATAGGGTATCGATACCCCTATGAACATTTTGGTTCTGAGAAATAACAGAATGCTC
1 GATACCCCCTATA-GGTATCGATACCCCTATGAACATTTTGGTTCCGAGAAATAACAGAATACTC
336686 AGATGGTACC
65 AGATGGTACC
336696 GATACCCCCTAGTAGGTATCGATACCCC
1 GATACCCCCTA-TAGGTATCGATACCCC
336724 CATTATATGG
Statistics
Matches: 95, Mismatches: 6, Indels: 5
0.90 0.06 0.05
Matches are distributed among these distances:
74 1 0.01
75 84 0.88
76 10 0.11
ACGTcount: A:0.31, C:0.26, G:0.18, T:0.25
Consensus pattern (74 bp):
GATACCCCCTATAGGTATCGATACCCCTATGAACATTTTGGTTCCGAGAAATAACAGAATACTCA
GATGGTACC
Found at i:336738 original size:22 final size:21
Alignment explanation
Indices: 336688--336765 Score: 81
Period size: 20 Copynumber: 3.7 Consensus size: 21
336678 GAATGCTCAG
*
336688 ATGGTACCGATACCCCCTAGT
1 ATGGTATCGATACCCCCTAGT
336709 A-GGTATCGATACCCCCATTA-T
1 ATGGTATCGATACCCCC--TAGT
*
336730 ATGGTATCGATACCCCCTACT
1 ATGGTATCGATACCCCCTAGT
*
336751 -TAGGTACCGATACCC
1 AT-GGTATCGATACCC
336766 TCAGGCATTT
Statistics
Matches: 50, Mismatches: 2, Indels: 10
0.81 0.03 0.16
Matches are distributed among these distances:
20 17 0.34
21 16 0.32
22 17 0.34
ACGTcount: A:0.26, C:0.32, G:0.17, T:0.26
Consensus pattern (21 bp):
ATGGTATCGATACCCCCTAGT
Found at i:336756 original size:21 final size:20
Alignment explanation
Indices: 336690--336765 Score: 82
Period size: 22 Copynumber: 3.6 Consensus size: 20
336680 ATGCTCAGAT
*
336690 GGTACCGATACCCCCTAGTA
1 GGTACCGATACCCCCTATTA
*
336710 GGTATCGATACCCCC-ATTATA
1 GGTACCGATACCCCCTA-T-TA
*
336731 TGGTATCGATACCCCCTACTTA
1 -GGTACCGATACCCCCTA-TTA
336753 GGTACCGATACCC
1 GGTACCGATACCC
336766 TCAGGCATTT
Statistics
Matches: 48, Mismatches: 4, Indels: 7
0.81 0.07 0.12
Matches are distributed among these distances:
19 1 0.02
20 14 0.29
21 14 0.29
22 17 0.35
23 2 0.04
ACGTcount: A:0.25, C:0.33, G:0.17, T:0.25
Consensus pattern (20 bp):
GGTACCGATACCCCCTATTA
Found at i:342328 original size:21 final size:20
Alignment explanation
Indices: 342297--342402 Score: 97
Period size: 23 Copynumber: 4.8 Consensus size: 20
342287 ATTTATGTGC
342297 ATAGAGTATCGATACCCCTGAA
1 ATAG-GTATCGATACCCCTG-A
*
342319 ACAGGTATCGATACCCCCTTTGA
1 ATAGGTATCGATA-CCCC--TGA
*
342342 ATAGGTATCGATACCCTTTGA
1 ATAGGTATCGATACCC-CTGA
342363 ATAGGTATCGATACCCTCTTTGA
1 ATAGGTATCGATACCC-C--TGA
342386 AT-GAGTATCGATACCCC
1 ATAG-GTATCGATACCCC
342403 CCCTGATGGT
Statistics
Matches: 73, Mismatches: 4, Indels: 14
0.80 0.04 0.15
Matches are distributed among these distances:
21 29 0.40
22 12 0.16
23 30 0.41
24 2 0.03
ACGTcount: A:0.29, C:0.25, G:0.18, T:0.28
Consensus pattern (20 bp):
ATAGGTATCGATACCCCTGA
Found at i:342351 original size:23 final size:23
Alignment explanation
Indices: 342297--342425 Score: 130
Period size: 21 Copynumber: 5.8 Consensus size: 23
342287 ATTTATGTGC
342297 ATAGAGTATCGATA-CCCC--TGAA
1 ATAG-GTATCGATACCCCCTTTG-A
*
342319 ACAGGTATCGATACCCCCTTTGA
1 ATAGGTATCGATACCCCCTTTGA
342342 ATAGGTATCGATA--CCCTTTGA
1 ATAGGTATCGATACCCCCTTTGA
*
342363 ATAGGTATCGATACCCTCTTTGA
1 ATAGGTATCGATACCCCCTTTGA
**
342386 AT-GAGTATCGATACCCCCCCTG-
1 ATAG-GTATCGATACCCCCTTTGA
*
342408 AT-GGTATCAATACCCCCT
1 ATAGGTATCGATACCCCCT
342426 ATCGGGTTTA
Statistics
Matches: 93, Mismatches: 8, Indels: 13
0.82 0.07 0.11
Matches are distributed among these distances:
21 43 0.46
22 11 0.12
23 37 0.40
24 2 0.02
ACGTcount: A:0.28, C:0.27, G:0.17, T:0.28
Consensus pattern (23 bp):
ATAGGTATCGATACCCCCTTTGA
Found at i:342369 original size:44 final size:45
Alignment explanation
Indices: 342297--342402 Score: 155
Period size: 44 Copynumber: 2.4 Consensus size: 45
342287 ATTTATGTGC
342297 ATAGAGTATCGATACCCCTGAAACAGGTATCGATACCCCCTTTGA
1 ATAGAGTATCGATACCCCTGAAACAGGTATCGATACCCCCTTTGA
* * *
342342 ATAG-GTATCGATACCCTTTG-AATAGGTATCGATACCCTCTTTGA
1 ATAGAGTATCGATACCC-CTGAAACAGGTATCGATACCCCCTTTGA
342386 AT-GAGTATCGATACCCC
1 ATAGAGTATCGATACCCC
342403 CCCTGATGGT
Statistics
Matches: 55, Mismatches: 4, Indels: 6
0.85 0.06 0.09
Matches are distributed among these distances:
43 1 0.02
44 48 0.87
45 6 0.11
ACGTcount: A:0.29, C:0.25, G:0.18, T:0.28
Consensus pattern (45 bp):
ATAGAGTATCGATACCCCTGAAACAGGTATCGATACCCCCTTTGA
Found at i:342414 original size:44 final size:44
Alignment explanation
Indices: 342297--342425 Score: 140
Period size: 44 Copynumber: 2.9 Consensus size: 44
342287 ATTTATGTGC
*
342297 ATAGAGTATCGATA-CCCCTGAAACAGGTATCGATACCCCCTTTGA
1 ATAG-GTATCGATACCCCCTG-AATAGGTATCGATACCCCCTTTGA
** *
342342 ATAGGTATCGATACCCTTTGAATAGGTATCGATACCCTCTTTGA
1 ATAGGTATCGATACCCCCTGAATAGGTATCGATACCCCCTTTGA
*
342386 AT-GAGTATCGATACCCCCCCTG-AT-GGTATCAATACCCCCT
1 ATAG-GTATCGATA--CCCCCTGAATAGGTATCGATACCCCCT
342426 ATCGGGTTTA
Statistics
Matches: 72, Mismatches: 8, Indels: 9
0.81 0.09 0.10
Matches are distributed among these distances:
43 1 0.01
44 56 0.78
45 10 0.14
46 5 0.07
ACGTcount: A:0.28, C:0.27, G:0.17, T:0.28
Consensus pattern (44 bp):
ATAGGTATCGATACCCCCTGAATAGGTATCGATACCCCCTTTGA
Found at i:345116 original size:75 final size:75
Alignment explanation
Indices: 345002--345188 Score: 304
Period size: 75 Copynumber: 2.5 Consensus size: 75
344992 TTTATTTAGT
* *
345002 ATGGTATCGATACCCCCATATAGGGTACCGATACCCCTATGAACATTTTAGTTCCGAGAAATAAT
1 ATGGTACCGATACCCCC-TATAGGGTACCGATACCCCTATGAACATTTTAGTTCCGAGAAATAAC
345067 AGAATGCTCGG
65 AGAATGCTCGG
*
345078 ATGGTACCGATACCCCCTATAGGGTACCGATACCCCTATGAACATTTTGGTTCCGAGAAATAACA
1 ATGGTACCGATACCCCCTATAGGGTACCGATACCCCTATGAACATTTTAGTTCCGAGAAATAACA
345143 GAATGCTCGG
66 GAATGCTCGG
* *
345153 ATGGTACCGATACCACCTAGTA-GGTATCGATACCCC
1 ATGGTACCGATACCCCCTA-TAGGGTACCGATACCCC
345189 CCATGATATA
Statistics
Matches: 105, Mismatches: 5, Indels: 3
0.93 0.04 0.03
Matches are distributed among these distances:
75 87 0.83
76 18 0.17
ACGTcount: A:0.30, C:0.25, G:0.20, T:0.25
Consensus pattern (75 bp):
ATGGTACCGATACCCCCTATAGGGTACCGATACCCCTATGAACATTTTAGTTCCGAGAAATAACA
GAATGCTCGG
Found at i:346236 original size:62 final size:62
Alignment explanation
Indices: 346138--346258 Score: 181
Period size: 62 Copynumber: 2.0 Consensus size: 62
346128 GGAATTTATC
* * *
346138 CACGCTGTAAGATGGGCACTCCCTGAACTCCGATTACCTATATCGGTAATTAGTCGAACTCA
1 CACGCTGTAAGATGGGCACTCCCTGAACTCCAATTACCTATAACGGTAATCAGTCGAACTCA
* *
346200 CACGCTGTAAG-TTGGCTACTCTCTGAACTCCAATTACCTATAACGGTAATCAGTCGAAC
1 CACGCTGTAAGATGGGC-ACTCCCTGAACTCCAATTACCTATAACGGTAATCAGTCGAAC
346259 CCAAAGTCGA
Statistics
Matches: 53, Mismatches: 5, Indels: 2
0.88 0.08 0.03
Matches are distributed among these distances:
61 4 0.08
62 49 0.92
ACGTcount: A:0.28, C:0.27, G:0.18, T:0.26
Consensus pattern (62 bp):
CACGCTGTAAGATGGGCACTCCCTGAACTCCAATTACCTATAACGGTAATCAGTCGAACTCA
Found at i:359782 original size:42 final size:41
Alignment explanation
Indices: 359704--359811 Score: 108
Period size: 42 Copynumber: 2.6 Consensus size: 41
359694 ACAATTTAAG
* * ** *
359704 TCCTTCGGGACATCAATAAGTCTTTCGAGCATGATGATGAAA
1 TCCTTCGGGTCATCAATAAGCCTTTAAAGCAAGATGAT-AAA
** *
359746 TCCTTCGGGTCATCTGTAAGCCTTTAAAGCAAGATGATAAG
1 TCCTTCGGGTCATCAATAAGCCTTTAAAGCAAGATGATAAA
* *
359787 TCATTCGGGTCATCCATAAGACCTT
1 TCCTTCGGGTCATCAATAAG-CCTT
359812 CGGGTAGGAT
Statistics
Matches: 54, Mismatches: 11, Indels: 2
0.81 0.16 0.03
Matches are distributed among these distances:
41 19 0.35
42 35 0.65
ACGTcount: A:0.29, C:0.21, G:0.20, T:0.30
Consensus pattern (41 bp):
TCCTTCGGGTCATCAATAAGCCTTTAAAGCAAGATGATAAA
Found at i:359977 original size:42 final size:42
Alignment explanation
Indices: 359918--360009 Score: 130
Period size: 42 Copynumber: 2.2 Consensus size: 42
359908 CGCACTTAGT
* *
359918 AAGTCCTTCGGGCCATCAATAATTCTTTTGAGCATGATGATG
1 AAGTCCTTCGGGCCATCAATAAGTCTTTCGAGCATGATGATG
* * *
359960 AAGTCTTTCGGGCCATCAGTAAGTCTTTCGAGCATGATGATT
1 AAGTCCTTCGGGCCATCAATAAGTCTTTCGAGCATGATGATG
*
360002 AAATCCTT
1 AAGTCCTT
360010 AGGGTAATTT
Statistics
Matches: 43, Mismatches: 7, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
42 43 1.00
ACGTcount: A:0.26, C:0.20, G:0.21, T:0.34
Consensus pattern (42 bp):
AAGTCCTTCGGGCCATCAATAAGTCTTTCGAGCATGATGATG
Found at i:359985 original size:20 final size:20
Alignment explanation
Indices: 359915--359989 Score: 62
Period size: 20 Copynumber: 3.6 Consensus size: 20
359905 TTCCGCACTT
*
359915 AGTAAGTCCTTCGGGCCATC
1 AGTAAGTCTTTCGGGCCATC
* * * * *
359935 AATAATTCTTTTGAG-CATG
1 AGTAAGTCTTTCGGGCCATC
359954 ATGATGAAGTCTTTCGGGCCATC
1 A-G-T-AAGTCTTTCGGGCCATC
359977 AGTAAGTCTTTCG
1 AGTAAGTCTTTCG
359990 AGCATGATGA
Statistics
Matches: 40, Mismatches: 11, Indels: 8
0.68 0.19 0.14
Matches are distributed among these distances:
19 4 0.10
20 20 0.50
21 2 0.05
22 10 0.25
23 4 0.10
ACGTcount: A:0.24, C:0.20, G:0.23, T:0.33
Consensus pattern (20 bp):
AGTAAGTCTTTCGGGCCATC
Found at i:360105 original size:42 final size:41
Alignment explanation
Indices: 360058--360144 Score: 113
Period size: 42 Copynumber: 2.1 Consensus size: 41
360048 AAATCCATCA
* * * *
360058 GTAAGTCTTTCTAGCATGATGATGAAATCCTTCGGGTCATTT
1 GTAAGTCTTTCGAGCAAGATGAT-AAATCCTACGGGCCATTT
*
360100 GTAAGTCTTTCGAGCAAGATGATAAGTCCTACGGGCCATTT
1 GTAAGTCTTTCGAGCAAGATGATAAATCCTACGGGCCATTT
360141 -TAAG
1 GTAAG
360145 CCTTCACGGA
Statistics
Matches: 40, Mismatches: 5, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
40 4 0.10
41 15 0.38
42 21 0.52
ACGTcount: A:0.26, C:0.17, G:0.23, T:0.33
Consensus pattern (41 bp):
GTAAGTCTTTCGAGCAAGATGATAAATCCTACGGGCCATTT
Found at i:360281 original size:53 final size:53
Alignment explanation
Indices: 360214--360385 Score: 256
Period size: 53 Copynumber: 3.2 Consensus size: 53
360204 AGAATCACAC
*
360214 CAGAAGATTGTTCGAGTTCTACTCCCTAAAGCAAGAGGGAGCGAACCCATAGG
1 CAGAAGATTGTTCGAGTTCTACTCCCTGAAGCAAGAGGGAGCGAACCCATAGG
* * * *
360267 CAGAAGATTATTCGAGTTCTACTCCTTGAAGCAATAGGGAGCGAACCCGTAGG
1 CAGAAGATTGTTCGAGTTCTACTCCCTGAAGCAAGAGGGAGCGAACCCATAGG
* * *
360320 CAGAAGACTGTTTGAGTTCTACTCCCTGAAGCAAGAGGGAGCGAACCCATTGG
1 CAGAAGATTGTTCGAGTTCTACTCCCTGAAGCAAGAGGGAGCGAACCCATAGG
360373 TC-GAAGATTGTTC
1 -CAGAAGATTGTTC
360386 AAATAAGAGA
Statistics
Matches: 104, Mismatches: 14, Indels: 2
0.87 0.12 0.02
Matches are distributed among these distances:
53 103 0.99
54 1 0.01
ACGTcount: A:0.30, C:0.22, G:0.27, T:0.22
Consensus pattern (53 bp):
CAGAAGATTGTTCGAGTTCTACTCCCTGAAGCAAGAGGGAGCGAACCCATAGG
Found at i:360552 original size:14 final size:15
Alignment explanation
Indices: 360533--360566 Score: 52
Period size: 14 Copynumber: 2.3 Consensus size: 15
360523 TTTATTCGGG
360533 TTATAAATATT-ATA
1 TTATAAATATTAATA
*
360547 TTATAATTATTAATA
1 TTATAAATATTAATA
360562 TTATA
1 TTATA
360567 TTATAACTAT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
14 10 0.56
15 8 0.44
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (15 bp):
TTATAAATATTAATA
Found at i:360577 original size:20 final size:20
Alignment explanation
Indices: 360538--360602 Score: 80
Period size: 20 Copynumber: 3.4 Consensus size: 20
360528 TCGGGTTATA
*
360538 AATATTATATTATAATTATT
1 AATATTATATTATAACTATT
360558 AATATTATATTATAACTATT
1 AATATTATATTATAACTATT
* *
360578 ATTA-T-TATTATAACAATT
1 AATATTATATTATAACTATT
*
360596 AAAATTA
1 AATATTA
360603 AAATTATTAT
Statistics
Matches: 38, Mismatches: 5, Indels: 4
0.81 0.11 0.09
Matches are distributed among these distances:
18 14 0.37
19 2 0.05
20 22 0.58
ACGTcount: A:0.48, C:0.03, G:0.00, T:0.49
Consensus pattern (20 bp):
AATATTATATTATAACTATT
Found at i:360582 original size:3 final size:3
Alignment explanation
Indices: 360540--360631 Score: 53
Period size: 3 Copynumber: 31.3 Consensus size: 3
360530 GGGTTATAAA
* * * *
360540 TAT TA- TAT TAT AAT TAT TAA TAT TA- TAT TAT AAC TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
* * * * * * * * *
360586 TAT AAC AAT TAA AAT TAA AAT TAT TAT TAG TAT TAT TAT TAA TAT T
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T
360632 GCTTATGTTT
Statistics
Matches: 63, Mismatches: 24, Indels: 4
0.69 0.26 0.04
Matches are distributed among these distances:
2 4 0.06
3 59 0.94
ACGTcount: A:0.45, C:0.02, G:0.01, T:0.52
Consensus pattern (3 bp):
TAT
Found at i:366086 original size:18 final size:19
Alignment explanation
Indices: 366047--366086 Score: 55
Period size: 20 Copynumber: 2.1 Consensus size: 19
366037 AAATAATAAT
*
366047 AAAATAATTTGAAGTGATCA
1 AAAATAATTT-AAGTGAGCA
366067 AAAATAATTT-AGTGAGCA
1 AAAATAATTTAAGTGAGCA
366085 AA
1 AA
366087 TTAGAAAAAC
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
18 9 0.47
20 10 0.53
ACGTcount: A:0.53, C:0.05, G:0.15, T:0.28
Consensus pattern (19 bp):
AAAATAATTTAAGTGAGCA
Found at i:368491 original size:12 final size:11
Alignment explanation
Indices: 368462--368501 Score: 53
Period size: 11 Copynumber: 3.5 Consensus size: 11
368452 CAATCAATAT
*
368462 ATAAATATAAA
1 ATAAAAATAAA
*
368473 CTAAAAATAACA
1 ATAAAAATAA-A
368485 ATAAAAATAAA
1 ATAAAAATAAA
368496 ATAAAA
1 ATAAAA
368502 GAATCCCAAG
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
11 15 0.60
12 10 0.40
ACGTcount: A:0.75, C:0.05, G:0.00, T:0.20
Consensus pattern (11 bp):
ATAAAAATAAA
Found at i:372654 original size:31 final size:32
Alignment explanation
Indices: 372601--372666 Score: 107
Period size: 31 Copynumber: 2.1 Consensus size: 32
372591 GTATAAGTCG
*
372601 CAACAGAGTTAGGATTACATTCAGATAATGCA
1 CAACACAGTTAGGATTACATTCAGATAATGCA
*
372633 CAACACAGTTAGTA-TACATTCAGATAATGCA
1 CAACACAGTTAGGATTACATTCAGATAATGCA
372664 CAA
1 CAA
372667 TAGAGCCAAT
Statistics
Matches: 32, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
31 20 0.62
32 12 0.38
ACGTcount: A:0.42, C:0.18, G:0.15, T:0.24
Consensus pattern (32 bp):
CAACACAGTTAGGATTACATTCAGATAATGCA
Found at i:374825 original size:20 final size:17
Alignment explanation
Indices: 374781--374867 Score: 61
Period size: 20 Copynumber: 4.8 Consensus size: 17
374771 ATTTGTATTA
374781 TTTATATCTTTTATTTTT
1 TTTATAT-TTTTATTTTT
374799 TCCTTATATATTTTACTATTTT
1 T--TTATAT-TTTTA-T-TTTT
374821 TTTATATTTTT-TCTTTT
1 TTTATATTTTTAT-TTTT
* **
374838 CTT-TATTTTTATCCTT
1 TTTATATTTTTATTTTT
374854 TTTATCATTTTTAT
1 TTTAT-ATTTTTAT
374868 CCTTTTACAT
Statistics
Matches: 56, Mismatches: 6, Indels: 14
0.74 0.08 0.18
Matches are distributed among these distances:
16 11 0.20
17 9 0.16
18 9 0.16
19 4 0.07
20 17 0.30
21 1 0.02
22 5 0.09
ACGTcount: A:0.17, C:0.10, G:0.00, T:0.72
Consensus pattern (17 bp):
TTTATATTTTTATTTTT
Found at i:374854 original size:18 final size:18
Alignment explanation
Indices: 374825--374884 Score: 63
Period size: 18 Copynumber: 3.3 Consensus size: 18
374815 TATTTTTTTA
374825 TATTTTT-T-CTTTTCTT
1 TATTTTTATCCTTTTCTT
374841 TATTTTTATCCTTTT-TAT
1 TATTTTTATCCTTTTCT-T
*
374859 CATTTTTATCCTTTTACATT
1 TATTTTTATCCTTTT-C-TT
374879 TATTTT
1 TATTTT
374885 ATTACTTTAT
Statistics
Matches: 36, Mismatches: 2, Indels: 8
0.78 0.04 0.17
Matches are distributed among these distances:
16 7 0.19
17 2 0.06
18 20 0.56
20 6 0.17
21 1 0.03
ACGTcount: A:0.15, C:0.13, G:0.00, T:0.72
Consensus pattern (18 bp):
TATTTTTATCCTTTTCTT
Found at i:374855 original size:9 final size:9
Alignment explanation
Indices: 374843--374873 Score: 53
Period size: 9 Copynumber: 3.4 Consensus size: 9
374833 CTTTTCTTTA
374843 TTTTTATCC
1 TTTTTATCC
*
374852 TTTTTATCA
1 TTTTTATCC
374861 TTTTTATCC
1 TTTTTATCC
374870 TTTT
1 TTTT
374874 ACATTTATTT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
9 20 1.00
ACGTcount: A:0.13, C:0.16, G:0.00, T:0.71
Consensus pattern (9 bp):
TTTTTATCC
Found at i:384607 original size:3 final size:3
Alignment explanation
Indices: 384599--384641 Score: 86
Period size: 3 Copynumber: 14.3 Consensus size: 3
384589 TAACCTTACT
384599 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A
384642 ATAGCAACAT
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 40 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:386214 original size:18 final size:19
Alignment explanation
Indices: 386179--386215 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 19
386169 CACGGAATGT
386179 AAGATTACCAGTGGGAATAA
1 AAGATTACCAG-GGGAATAA
386199 AAGATTACCA-GGGAATA
1 AAGATTACCAGGGGAATA
386216 GGATTACTGG
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 7 0.41
20 10 0.59
ACGTcount: A:0.46, C:0.11, G:0.24, T:0.19
Consensus pattern (19 bp):
AAGATTACCAGGGGAATAA
Found at i:387067 original size:19 final size:20
Alignment explanation
Indices: 387031--387072 Score: 59
Period size: 20 Copynumber: 2.1 Consensus size: 20
387021 ATACATTAAC
387031 ATAAAAAAAACATAGTTCAA
1 ATAAAAAAAACATAGTTCAA
* *
387051 ATAAAAGAAAGAT-GTTCAA
1 ATAAAAAAAACATAGTTCAA
387070 ATA
1 ATA
387073 CTTAACACCA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
19 9 0.45
20 11 0.55
ACGTcount: A:0.62, C:0.07, G:0.10, T:0.21
Consensus pattern (20 bp):
ATAAAAAAAACATAGTTCAA
Found at i:392091 original size:27 final size:27
Alignment explanation
Indices: 392010--392100 Score: 92
Period size: 27 Copynumber: 3.2 Consensus size: 27
392000 ATATTTTCAG
*
392010 TAAAATACTTAATAATAACAAAACCGA
1 TAAAATACCTAATAATAACAAAACCGA
* * *
392037 TAAAATTTTCTCGGACATGATAACAAAACCGA
1 TAAAA--TAC-C-TA-ATAATAACAAAACCGA
*
392069 TAAAATACCTAATAATAACAAAATCGA
1 TAAAATACCTAATAATAACAAAACCGA
392096 TAAAA
1 TAAAA
392101 ATAATAATGT
Statistics
Matches: 51, Mismatches: 8, Indels: 10
0.74 0.12 0.14
Matches are distributed among these distances:
27 24 0.47
28 1 0.02
29 3 0.06
30 2 0.04
31 1 0.02
32 20 0.39
ACGTcount: A:0.55, C:0.15, G:0.07, T:0.23
Consensus pattern (27 bp):
TAAAATACCTAATAATAACAAAACCGA
Found at i:397036 original size:14 final size:15
Alignment explanation
Indices: 397017--397045 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
397007 CCCCCTTTTT
397017 ATTATATAA-AAATA
1 ATTATATAATAAATA
397031 ATTATATAATAAATA
1 ATTATATAATAAATA
397046 GGAAAATTTT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 9 0.64
15 5 0.36
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (15 bp):
ATTATATAATAAATA
Found at i:400014 original size:20 final size:21
Alignment explanation
Indices: 399991--400029 Score: 62
Period size: 20 Copynumber: 1.9 Consensus size: 21
399981 TTGAGATAAT
399991 ATTAAAATCTTA-AAAATTAA
1 ATTAAAATCTTATAAAATTAA
*
400011 ATTAAAATGTTATAAAATT
1 ATTAAAATCTTATAAAATT
400030 CTAAAATTTA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 11 0.65
21 6 0.35
ACGTcount: A:0.56, C:0.03, G:0.03, T:0.38
Consensus pattern (21 bp):
ATTAAAATCTTATAAAATTAA
Found at i:405998 original size:32 final size:31
Alignment explanation
Indices: 405949--406051 Score: 118
Period size: 33 Copynumber: 3.2 Consensus size: 31
405939 TTTTTAACCG
405949 CTAACTTTGCTAACTTTTA-TTTATTTGTTCATA
1 CTAAC-TT-CTAACTTTTATTTTA-TTGTTCATA
405982 CTAACATTCTAACTTTTATTTTATTGTTCATA
1 CTAAC-TTCTAACTTTTATTTTATTGTTCATA
* * *
406014 CTAACTCACTAACATTTTATTTTATTGCTCAAA
1 CTAACT-TCTAAC-TTTTATTTTATTGTTCATA
406047 CTAAC
1 CTAAC
406052 CCGCTAATTC
Statistics
Matches: 63, Mismatches: 4, Indels: 6
0.86 0.05 0.08
Matches are distributed among these distances:
31 1 0.02
32 29 0.46
33 33 0.52
ACGTcount: A:0.29, C:0.18, G:0.04, T:0.49
Consensus pattern (31 bp):
CTAACTTCTAACTTTTATTTTATTGTTCATA
Found at i:406032 original size:33 final size:32
Alignment explanation
Indices: 405958--406051 Score: 120
Period size: 32 Copynumber: 2.9 Consensus size: 32
405948 GCTAACTTTG
*
405958 CTAACTTTTA-TTTATTTGTTCATACTAACATT
1 CTAACTTTTATTTTA-TTGTTCATACTAACATA
405990 CTAACTTTTATTTTATTGTTCATACTAAC-TCA
1 CTAACTTTTATTTTATTGTTCATACTAACAT-A
* *
406022 CTAACATTTTATTTTATTGCTCAAACTAAC
1 CTAAC-TTTTATTTTATTGTTCATACTAAC
406052 CCGCTAATTC
Statistics
Matches: 56, Mismatches: 3, Indels: 5
0.88 0.05 0.08
Matches are distributed among these distances:
31 1 0.02
32 29 0.52
33 26 0.46
ACGTcount: A:0.30, C:0.18, G:0.03, T:0.49
Consensus pattern (32 bp):
CTAACTTTTATTTTATTGTTCATACTAACATA
Found at i:407300 original size:41 final size:41
Alignment explanation
Indices: 407238--407330 Score: 168
Period size: 41 Copynumber: 2.3 Consensus size: 41
407228 ACTGATTAAG
*
407238 ATGACACTTATTTGTTATCATGTTAATCTTCCCTGGTGATA
1 ATGAGACTTATTTGTTATCATGTTAATCTTCCCTGGTGATA
*
407279 ATGAGACTTATTTGTTATCATGTTAATCTTCCCTTGTGATA
1 ATGAGACTTATTTGTTATCATGTTAATCTTCCCTGGTGATA
407320 ATGAGACTTAT
1 ATGAGACTTAT
407331 CTCATGGTTT
Statistics
Matches: 50, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
41 50 1.00
ACGTcount: A:0.26, C:0.15, G:0.15, T:0.44
Consensus pattern (41 bp):
ATGAGACTTATTTGTTATCATGTTAATCTTCCCTGGTGATA
Found at i:407315 original size:22 final size:22
Alignment explanation
Indices: 407249--407315 Score: 52
Period size: 22 Copynumber: 3.2 Consensus size: 22
407239 TGACACTTAT
407249 TTGTTATCATGTTAATCTTCCC
1 TTGTTATCATGTTAATCTTCCC
* * * **
407271 TGGTGATAATG--AGA-CTT-AT
1 TTGTTATCATGTTA-ATCTTCCC
407290 TTGTTATCATGTTAATCTTCCC
1 TTGTTATCATGTTAATCTTCCC
407312 TTGT
1 TTGT
407316 GATAATGAGA
Statistics
Matches: 30, Mismatches: 10, Indels: 10
0.60 0.20 0.20
Matches are distributed among these distances:
19 8 0.27
20 5 0.17
21 5 0.17
22 12 0.40
ACGTcount: A:0.21, C:0.16, G:0.15, T:0.48
Consensus pattern (22 bp):
TTGTTATCATGTTAATCTTCCC
Found at i:410307 original size:2 final size:2
Alignment explanation
Indices: 410300--410326 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
410290 TTCCTATGCT
410300 TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA T
410327 TTCGGGTACT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:410561 original size:27 final size:27
Alignment explanation
Indices: 410528--410619 Score: 85
Period size: 27 Copynumber: 3.2 Consensus size: 27
410518 AATATTTTTA
410528 ATAAAATACTTAATAATAACAAAACCG
1 ATAAAATACTTAATAATAACAAAACCG
* * * *
410555 ATAAAATTTTCTCGGACATGATAACAAAACTG
1 ATAAAA--TACT--TA-ATAATAACAAAACCG
* *
410587 ATAAAATACCTAATAATAACAAAATCG
1 ATAAAATACTTAATAATAACAAAACCG
410614 ATAAAA
1 ATAAAA
410620 ATAATAATGT
Statistics
Matches: 50, Mismatches: 10, Indels: 10
0.71 0.14 0.14
Matches are distributed among these distances:
27 24 0.48
28 1 0.02
29 3 0.06
30 2 0.04
31 1 0.02
32 19 0.38
ACGTcount: A:0.55, C:0.14, G:0.07, T:0.24
Consensus pattern (27 bp):
ATAAAATACTTAATAATAACAAAACCG
Found at i:415595 original size:14 final size:15
Alignment explanation
Indices: 415576--415604 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
415566 CCCCCTTTTT
415576 ATTATATAA-AAATA
1 ATTATATAATAAATA
415590 ATTATATAATAAATA
1 ATTATATAATAAATA
415605 GGAAAATTTT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 9 0.64
15 5 0.36
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (15 bp):
ATTATATAATAAATA
Found at i:418576 original size:20 final size:21
Alignment explanation
Indices: 418553--418591 Score: 62
Period size: 20 Copynumber: 1.9 Consensus size: 21
418543 TTGAGATAAT
418553 ATTAAAATCTTA-AAAATTAA
1 ATTAAAATCTTATAAAATTAA
*
418573 ATTAAAATGTTATAAAATT
1 ATTAAAATCTTATAAAATT
418592 CTAAAATTTA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 11 0.65
21 6 0.35
ACGTcount: A:0.56, C:0.03, G:0.03, T:0.38
Consensus pattern (21 bp):
ATTAAAATCTTATAAAATTAA
Found at i:424522 original size:32 final size:31
Alignment explanation
Indices: 424477--424579 Score: 118
Period size: 33 Copynumber: 3.2 Consensus size: 31
424467 CTACTAATTT
424477 CTAACTTTGCTAACTTTTA-TTTATTTGTTCATA
1 CTAAC-TT-CTAACTTTTATTTTA-TTGTTCATA
424510 CTAACATTCTAACTTTTATTTTATTGTTCATA
1 CTAAC-TTCTAACTTTTATTTTATTGTTCATA
* * *
424542 CTAACTCACTAACATTTTATTTTATTGCTCAAA
1 CTAACT-TCTAAC-TTTTATTTTATTGTTCATA
424575 CTAAC
1 CTAAC
424580 CCGCTAATTC
Statistics
Matches: 63, Mismatches: 4, Indels: 6
0.86 0.05 0.08
Matches are distributed among these distances:
31 1 0.02
32 29 0.46
33 33 0.52
ACGTcount: A:0.29, C:0.18, G:0.04, T:0.49
Consensus pattern (31 bp):
CTAACTTCTAACTTTTATTTTATTGTTCATA
Found at i:424568 original size:33 final size:32
Alignment explanation
Indices: 424486--424579 Score: 120
Period size: 32 Copynumber: 2.9 Consensus size: 32
424476 TCTAACTTTG
*
424486 CTAACTTTTA-TTTATTTGTTCATACTAACATT
1 CTAACTTTTATTTTA-TTGTTCATACTAACATA
424518 CTAACTTTTATTTTATTGTTCATACTAAC-TCA
1 CTAACTTTTATTTTATTGTTCATACTAACAT-A
* *
424550 CTAACATTTTATTTTATTGCTCAAACTAAC
1 CTAAC-TTTTATTTTATTGTTCATACTAAC
424580 CCGCTAATTC
Statistics
Matches: 56, Mismatches: 3, Indels: 5
0.88 0.05 0.08
Matches are distributed among these distances:
31 1 0.02
32 29 0.52
33 26 0.46
ACGTcount: A:0.30, C:0.18, G:0.03, T:0.49
Consensus pattern (32 bp):
CTAACTTTTATTTTATTGTTCATACTAACATA
Found at i:427868 original size:14 final size:15
Alignment explanation
Indices: 427849--427877 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
427839 CCCCCTTTTT
427849 ATTATATAA-AAATA
1 ATTATATAATAAATA
427863 ATTATATAATAAATA
1 ATTATATAATAAATA
427878 GGAAAATTTT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 9 0.64
15 5 0.36
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (15 bp):
ATTATATAATAAATA
Found at i:430842 original size:20 final size:21
Alignment explanation
Indices: 430819--430857 Score: 62
Period size: 20 Copynumber: 1.9 Consensus size: 21
430809 TTGAGATAAT
430819 ATTAAAATCTTA-AAAATTAA
1 ATTAAAATCTTATAAAATTAA
*
430839 ATTAAAATGTTATAAAATT
1 ATTAAAATCTTATAAAATT
430858 CTAAAATTTA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 11 0.65
21 6 0.35
ACGTcount: A:0.56, C:0.03, G:0.03, T:0.38
Consensus pattern (21 bp):
ATTAAAATCTTATAAAATTAA
Found at i:431586 original size:103 final size:103
Alignment explanation
Indices: 431407--431619 Score: 417
Period size: 103 Copynumber: 2.1 Consensus size: 103
431397 GTACATCTGC
*
431407 AAATCAAACACAAACATATTTAGGAATTAGGGTTGAGTCATGATTATATAATATGATACAGATAT
1 AAATCAAACACAAACATATTTAGAAATTAGGGTTGAGTCATGATTATATAATATGATACAGATAT
431472 TCACAAAAGACTGGGATTTTATTTGTGTAAACTCGACT
66 TCACAAAAGACTGGGATTTTATTTGTGTAAACTCGACT
431510 AAATCAAACACAAACATATTTAGAAATTAGGGTTGAGTCATGATTATATAATATGATACAGATAT
1 AAATCAAACACAAACATATTTAGAAATTAGGGTTGAGTCATGATTATATAATATGATACAGATAT
431575 TCACAAAAGACTGGGATTTTATTTGTGTAAACTCGACT
66 TCACAAAAGACTGGGATTTTATTTGTGTAAACTCGACT
431613 AAATCAA
1 AAATCAA
431620 TTTAGAACTT
Statistics
Matches: 109, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
103 109 1.00
ACGTcount: A:0.41, C:0.12, G:0.15, T:0.31
Consensus pattern (103 bp):
AAATCAAACACAAACATATTTAGAAATTAGGGTTGAGTCATGATTATATAATATGATACAGATAT
TCACAAAAGACTGGGATTTTATTTGTGTAAACTCGACT
Found at i:436969 original size:33 final size:32
Alignment explanation
Indices: 436895--436988 Score: 111
Period size: 32 Copynumber: 2.9 Consensus size: 32
436885 GCTAACTTTG
* *
436895 CTAACTTTTA-TTTATTTGTTCATATTAACATT
1 CTAACTTTTATTTTA-TTGTTCATACTAACATA
436927 CTAACTTTTATTTTATTGTTCATACTAAC-TCA
1 CTAACTTTTATTTTATTGTTCATACTAACAT-A
* *
436959 CTAACATTTTATTTTATTGCTCAAACTAAC
1 CTAAC-TTTTATTTTATTGTTCATACTAAC
436989 CCGCTAATTC
Statistics
Matches: 55, Mismatches: 4, Indels: 5
0.86 0.06 0.08
Matches are distributed among these distances:
31 1 0.02
32 28 0.51
33 26 0.47
ACGTcount: A:0.30, C:0.17, G:0.03, T:0.50
Consensus pattern (32 bp):
CTAACTTTTATTTTATTGTTCATACTAACATA
Found at i:441278 original size:9 final size:9
Alignment explanation
Indices: 441264--441358 Score: 66
Period size: 9 Copynumber: 9.7 Consensus size: 9
441254 ACGGTTCAAA
441264 CCGGTTTTG
1 CCGGTTTTG
441273 CCGGTTTTCAG
1 CCGGTTTT--G
*
441284 CCGGTTTTA
1 CCGGTTTTG
441293 CCGGTTTTCAG
1 CCGGTTTT--G
* *
441304 CCGATTTTA
1 CCGGTTTTG
441313 CCGGTTTTCAG
1 CCGGTTTT--G
*
441324 CCGGTTTTC
1 CCGGTTTTG
441333 CCGGTTTTCAG
1 CCGGTTTT--G
441344 CCGGTTATT-
1 CCGGTT-TTG
441353 CCGGTT
1 CCGGTT
441359 CTTTACCGAT
Statistics
Matches: 69, Mismatches: 8, Indels: 18
0.73 0.08 0.19
Matches are distributed among these distances:
9 37 0.54
11 30 0.43
12 2 0.03
ACGTcount: A:0.08, C:0.26, G:0.25, T:0.40
Consensus pattern (9 bp):
CCGGTTTTG
Found at i:441289 original size:20 final size:20
Alignment explanation
Indices: 441264--441358 Score: 147
Period size: 20 Copynumber: 4.8 Consensus size: 20
441254 ACGGTTCAAA
*
441264 CCGGTTTTGCCGGTTTTCAG
1 CCGGTTTTACCGGTTTTCAG
441284 CCGGTTTTACCGGTTTTCAG
1 CCGGTTTTACCGGTTTTCAG
*
441304 CCGATTTTACCGGTTTTCAG
1 CCGGTTTTACCGGTTTTCAG
*
441324 CCGGTTTTCCCGGTTTTCAG
1 CCGGTTTTACCGGTTTTCAG
441344 CCGGTTATT-CCGGTT
1 CCGGTT-TTACCGGTT
441359 CTTTACCGAT
Statistics
Matches: 70, Mismatches: 4, Indels: 2
0.92 0.05 0.03
Matches are distributed among these distances:
20 68 0.97
21 2 0.03
ACGTcount: A:0.08, C:0.26, G:0.25, T:0.40
Consensus pattern (20 bp):
CCGGTTTTACCGGTTTTCAG
Found at i:456703 original size:21 final size:19
Alignment explanation
Indices: 456668--456706 Score: 60
Period size: 19 Copynumber: 1.9 Consensus size: 19
456658 ATAACTGTAG
456668 ACAAAAAAAAATAATTAAC
1 ACAAAAAAAAATAATTAAC
456687 ACAAAAAAATAATTAATTAA
1 ACAAAAAAA-AA-TAATTAA
456707 TAAATTTAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
19 9 0.50
20 2 0.11
21 7 0.39
ACGTcount: A:0.72, C:0.08, G:0.00, T:0.21
Consensus pattern (19 bp):
ACAAAAAAAAATAATTAAC
Found at i:456730 original size:16 final size:16
Alignment explanation
Indices: 456704--456758 Score: 58
Period size: 16 Copynumber: 3.4 Consensus size: 16
456694 AATAATTAAT
456704 TAATAAATTTAAATAAA
1 TAAT-AATTTAAATAAA
*
456721 TAATAATTTATATAAA
1 TAATAATTTAAATAAA
* *
456737 T-ATTATTTTAATAAA
1 TAATAATTTAAATAAA
*
456752 AAATAAT
1 TAATAAT
456759 ATTTATATAA
Statistics
Matches: 31, Mismatches: 6, Indels: 3
0.77 0.15 0.08
Matches are distributed among these distances:
15 11 0.35
16 16 0.52
17 4 0.13
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (16 bp):
TAATAATTTAAATAAA
Found at i:456790 original size:32 final size:32
Alignment explanation
Indices: 456713--456791 Score: 90
Period size: 30 Copynumber: 2.4 Consensus size: 32
456703 TTAATAAATT
*
456713 TAAATAAATAATAATTTATATAAATATTATTTTAA
1 TAAA-AAATAAT-ATTTATAT-AATATTATATTAA
456748 TAAAAAATAATATTTATAT-A-ATTATATTAA
1 TAAAAAATAATATTTATATAATATTATATTAA
456778 TATAAAATATAATA
1 TA-AAAA-ATAATA
456792 ACTATGTAAA
Statistics
Matches: 41, Mismatches: 1, Indels: 7
0.84 0.02 0.14
Matches are distributed among these distances:
30 11 0.27
31 5 0.12
32 6 0.15
33 8 0.20
34 7 0.17
35 4 0.10
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (32 bp):
TAAAAAATAATATTTATATAATATTATATTAA
Found at i:458765 original size:2 final size:2
Alignment explanation
Indices: 458758--458815 Score: 116
Period size: 2 Copynumber: 29.0 Consensus size: 2
458748 GAGTTCATCA
458758 AT AT AT AT AT AT AT 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 AT AT AT AT AT AT AT
458800 AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT
458816 TCTTTTCAGA
Statistics
Matches: 56, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 56 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:472093 original size:33 final size:30
Alignment explanation
Indices: 472056--472120 Score: 76
Period size: 30 Copynumber: 2.1 Consensus size: 30
472046 AAAAACTACT
472056 AAATAAATCAAAAGAGAGAAAAAAAAATAAAAA
1 AAATAAATC-AAAG-GA-AAAAAAAAATAAAAA
* * *
472089 AAATAAGTCAAAGGAAAAATAAAATAAGAA
1 AAATAAATCAAAGGAAAAAAAAAATAAAAA
472119 AA
1 AA
472121 GAAAAAAATG
Statistics
Matches: 29, Mismatches: 3, Indels: 3
0.83 0.09 0.09
Matches are distributed among these distances:
30 15 0.52
31 2 0.07
32 4 0.14
33 8 0.28
ACGTcount: A:0.75, C:0.03, G:0.11, T:0.11
Consensus pattern (30 bp):
AAATAAATCAAAGGAAAAAAAAAATAAAAA
Found at i:472248 original size:13 final size:13
Alignment explanation
Indices: 472230--472264 Score: 52
Period size: 13 Copynumber: 2.7 Consensus size: 13
472220 GAAAAATACA
472230 AAATAAATAAAAT
1 AAATAAATAAAAT
**
472243 AAATAAATGTAAT
1 AAATAAATAAAAT
472256 AAATAAATA
1 AAATAAATA
472265 GGAAATGTAT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
13 19 1.00
ACGTcount: A:0.71, C:0.00, G:0.03, T:0.26
Consensus pattern (13 bp):
AAATAAATAAAAT
Found at i:472395 original size:14 final size:14
Alignment explanation
Indices: 472311--472458 Score: 68
Period size: 14 Copynumber: 9.9 Consensus size: 14
472301 AATAAATCAA
472311 AATAATAATAATAAT
1 AATAATAA-AATAAT
*
472326 AATAATAAACTAAAT
1 AATAATAAAAT-AAT
472341 ATATATATATAAAT-AT
1 A-ATA-ATA-AAATAAT
472357 GAAGGTAAATAAAA-AAT
1 -AA--T-AATAAAATAAT
*
472374 ATTAAATAAAATAAT
1 AAT-AATAAAATAAT
*
472389 AATAATAACAA-AGT
1 AATAATAA-AATAAT
* * *
472403 AATAAAGAAAAGGAAA
1 AAT-AATAAAA-TAAT
* * *
472419 AATAAGAAAAAAAC
1 AATAATAAAATAAT
*
472433 AATAATATAATAAT
1 AATAATAAAATAAT
472447 AATAATAAAATA
1 AATAATAAAATA
472459 TGCATGAGTG
Statistics
Matches: 104, Mismatches: 15, Indels: 29
0.70 0.10 0.20
Matches are distributed among these distances:
14 46 0.44
15 30 0.29
16 11 0.11
17 9 0.09
18 7 0.07
19 1 0.01
ACGTcount: A:0.68, C:0.02, G:0.05, T:0.25
Consensus pattern (14 bp):
AATAATAAAATAAT
Found at i:473732 original size:4 final size:4
Alignment explanation
Indices: 473719--473771 Score: 79
Period size: 4 Copynumber: 13.0 Consensus size: 4
473709 AAAAAAAAGA
* *
473719 AAAT AGAT AAAT AAAT AAAT GAAAT AAAT AAAT AAAT AAAT AGAT AAAT
1 AAAT AAAT AAAT AAAT AAAT -AAAT AAAT AAAT AAAT AAAT AAAT AAAT
473768 AAAT
1 AAAT
473772 TAAAAACATT
Statistics
Matches: 44, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
4 40 0.91
5 4 0.09
ACGTcount: A:0.70, C:0.00, G:0.06, T:0.25
Consensus pattern (4 bp):
AAAT
Found at i:473744 original size:21 final size:21
Alignment explanation
Indices: 473719--473771 Score: 81
Period size: 21 Copynumber: 2.6 Consensus size: 21
473709 AAAAAAAAGA
*
473719 AAATAGATAAATAAATAAATG
1 AAATAAATAAATAAATAAATG
473740 AAATAAATAAATAAATAAAT-
1 AAATAAATAAATAAATAAATG
*
473760 AGATAAATAAAT
1 AAATAAATAAAT
473772 TAAAAACATT
Statistics
Matches: 30, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
20 11 0.37
21 19 0.63
ACGTcount: A:0.70, C:0.00, G:0.06, T:0.25
Consensus pattern (21 bp):
AAATAAATAAATAAATAAATG
Found at i:473826 original size:36 final size:36
Alignment explanation
Indices: 473781--474111 Score: 258
Period size: 36 Copynumber: 8.7 Consensus size: 36
473771 TTAAAAACAT
* ** *
473781 TTTTTAAAACTATGCAATATATGTTTTAAAAAATAA
1 TTTTCAAAACTATATAATATATATTTTAAAAAATAA
* *
473817 TTTTCAAAACCATATAATATATATTTTAAAAACTAA
1 TTTTCAAAACTATATAATATATATTTTAAAAAATAA
473853 TTTTCAAAACTATATAATATATATATATATATATATTTAAA-AGCTA
1 TTTTCAAAACTATATAATATATAT-T-T-TA-A-A---AAATA---A
* ** *
473899 ATTTTCAAA--ACTATATAATATATATATTTAAAAACTAA
1 TTTTCAAAACTA-TAT--AATATATAT-TTTAAAAAATAA
* * *
473937 TTTTCAAAACTATATAATATATATGTTTTTCAAAAGT-G
1 TTTTCAAAACTATATAATATATA---TTTTAAAAAATAA
*
473975 TTTTCAAAACTATATAATATATATATTTAAAAACTAA
1 TTTTCAAAACTATATAATATATAT-TTTAAAAAATAA
* *
474012 TTTTCAAAACTATATAATATATATGTTTTTCAAAAAT-G
1 TTTTCAAAACTATATAATATATA---TTTTAAAAAATAA
*
474050 TTTTCAAAACTATATAATATATATTTTTAAAAACTAA
1 TTTTCAAAACTATATAATATATA-TTTTAAAAAATAA
474087 TTTTCAAAACTATATATATATATAT
1 TTTTCAAAACTATATA-ATATATAT
474112 ATTATAGTTT
Statistics
Matches: 241, Mismatches: 27, Indels: 53
0.75 0.08 0.17
Matches are distributed among these distances:
35 1 0.00
36 71 0.29
37 49 0.20
38 61 0.25
39 21 0.09
40 6 0.02
41 2 0.01
43 2 0.01
44 4 0.02
45 5 0.02
46 8 0.03
47 11 0.05
ACGTcount: A:0.47, C:0.08, G:0.02, T:0.43
Consensus pattern (36 bp):
TTTTCAAAACTATATAATATATATTTTAAAAAATAA
Found at i:473885 original size:84 final size:84
Alignment explanation
Indices: 473797--473960 Score: 278
Period size: 84 Copynumber: 2.0 Consensus size: 84
473787 AAACTATGCA
*
473797 ATATATGT-TTTAAAAAATAATTTTCAAAACCATATAATATATAT-TTTAAAAACTAATTTTCAA
1 ATATATATATTTAAAAAATAATTTTCAAAACCATATAATATATATATTTAAAAACTAATTTTCAA
473860 AACTATATAATATATATAT
66 AACTATATAATATATATAT
** *
473879 ATATATATATTTAAAAGCTAATTTTCAAAACTATATAATATATATATTTAAAAACTAATTTTCAA
1 ATATATATATTTAAAAAATAATTTTCAAAACCATATAATATATATATTTAAAAACTAATTTTCAA
473944 AACTATATAATATATAT
66 AACTATATAATATATAT
473961 GTTTTTCAAA
Statistics
Matches: 76, Mismatches: 4, Indels: 2
0.93 0.05 0.02
Matches are distributed among these distances:
82 7 0.09
83 33 0.43
84 36 0.47
ACGTcount: A:0.50, C:0.07, G:0.01, T:0.41
Consensus pattern (84 bp):
ATATATATATTTAAAAAATAATTTTCAAAACCATATAATATATATATTTAAAAACTAATTTTCAA
AACTATATAATATATATAT
Found at i:473893 original size:47 final size:46
Alignment explanation
Indices: 473828--473925 Score: 171
Period size: 47 Copynumber: 2.1 Consensus size: 46
473818 TTTCAAAACC
473828 ATATA-ATATATATTTTAAAAACTAATTTTCAAAACTATATAATAT
1 ATATATATATATATTTTAAAAACTAATTTTCAAAACTATATAATAT
*
473873 ATATATATATATATATTTAAAAGCTAATTTTCAAAACTATATAATAT
1 ATATATATATATAT-TTTAAAAACTAATTTTCAAAACTATATAATAT
473920 ATATAT
1 ATATAT
473926 TTAAAAACTA
Statistics
Matches: 50, Mismatches: 1, Indels: 2
0.94 0.02 0.04
Matches are distributed among these distances:
45 5 0.10
46 8 0.16
47 37 0.74
ACGTcount: A:0.50, C:0.06, G:0.01, T:0.43
Consensus pattern (46 bp):
ATATATATATATATTTTAAAAACTAATTTTCAAAACTATATAATAT
Found at i:473923 original size:37 final size:37
Alignment explanation
Indices: 473872--474114 Score: 330
Period size: 37 Copynumber: 6.5 Consensus size: 37
473862 CTATATAATA
*
473872 TATATATATATATATATTTAAAAGCTAATTTTCAAAAC
1 TATATA-ATATATATATTTAAAAACTAATTTTCAAAAC
473910 TATATAATATATATATTTAAAAACTAATTTTCAAAAC
1 TATATAATATATATATTTAAAAACTAATTTTCAAAAC
* * * *
473947 TATATAATATATATGTTTTTCAAAAGT-GTTTTCAAAAC
1 TATATAATATATA--TATTTAAAAACTAATTTTCAAAAC
473985 TATATAATATATATATTTAAAAACTAATTTTCAAAAC
1 TATATAATATATATATTTAAAAACTAATTTTCAAAAC
* *
474022 TATATAATATATATGTTTTTCAAAAA-T-GTTTTCAAAAC
1 TATATAATATATA--TATTT-AAAAACTAATTTTCAAAAC
*
474060 TATATAATATATATTTTTAAAAACTAATTTTCAAAAC
1 TATATAATATATATATTTAAAAACTAATTTTCAAAAC
474097 TATATATATATATATATT
1 TATATA-ATATATATATT
474115 ATAGTTTGAA
Statistics
Matches: 183, Mismatches: 13, Indels: 18
0.86 0.06 0.08
Matches are distributed among these distances:
35 5 0.03
36 15 0.08
37 82 0.45
38 62 0.34
39 14 0.08
40 5 0.03
ACGTcount: A:0.47, C:0.07, G:0.02, T:0.44
Consensus pattern (37 bp):
TATATAATATATATATTTAAAAACTAATTTTCAAAAC
Found at i:473982 original size:75 final size:75
Alignment explanation
Indices: 473900--474111 Score: 397
Period size: 75 Copynumber: 2.8 Consensus size: 75
473890 TAAAAGCTAA
473900 TTTTCAAAACTATATAATATATATATTTAAAAACTAATTTTCAAAACTATATAATATATATGTTT
1 TTTTCAAAACTATATAATATATATATTTAAAAACTAATTTTCAAAACTATATAATATATATGTTT
*
473965 TTCAAAAGTG
66 TTCAAAAATG
473975 TTTTCAAAACTATATAATATATATATTTAAAAACTAATTTTCAAAACTATATAATATATATGTTT
1 TTTTCAAAACTATATAATATATATATTTAAAAACTAATTTTCAAAACTATATAATATATATGTTT
474040 TTCAAAAATG
66 TTCAAAAATG
*
474050 TTTTCAAAACTATATAATATATATTTTTAAAAACTAATTTTCAAAACTATATATATATATAT
1 TTTTCAAAACTATATAATATATATATTTAAAAACTAATTTTCAAAACTATATA-ATATATAT
474112 ATTATAGTTT
Statistics
Matches: 134, Mismatches: 2, Indels: 1
0.98 0.01 0.01
Matches are distributed among these distances:
75 126 0.94
76 8 0.06
ACGTcount: A:0.46, C:0.08, G:0.02, T:0.43
Consensus pattern (75 bp):
TTTTCAAAACTATATAATATATATATTTAAAAACTAATTTTCAAAACTATATAATATATATGTTT
TTCAAAAATG
Found at i:474145 original size:75 final size:74
Alignment explanation
Indices: 473869--474114 Score: 339
Period size: 75 Copynumber: 3.2 Consensus size: 74
473859 AAACTATATA
*
473869 ATATATATATATATATATATTTAAAAGCTAATTTTCAAAACTATATAATATATATATTTAAAAAC
1 ATATA-ATATATATAT-TTTTTAAAAG-T-ATTTTCAAAAC-ATATAATATATATATTTAAAAAC
473934 TAATTTTCAAAACT
61 TAATTTTCAAAACT
* * *
473948 ATATAATATATATGTTTTTCAAAAGTGTTTTCAAAACTATATAATATATATATTTAAAAACTAAT
1 ATATAATATATATATTTTTTAAAAGTATTTTCAAAAC-ATATAATATATATATTTAAAAACTAAT
474013 TTTCAAAACT
65 TTTCAAAACT
* * * * *
474023 ATATAATATATATGTTTTTCAAAAATGTTTTCAAAACTATATAATATATATTTTTAAAAACTAAT
1 ATATAATATATATATTTTTTAAAAGTATTTTCAAAAC-ATATAATATATATATTTAAAAACTAAT
474088 TTTCAAAACT
65 TTTCAAAACT
474098 ATATATATATATATATT
1 ATATA-ATATATATATT
474115 ATAGTTTGAA
Statistics
Matches: 159, Mismatches: 7, Indels: 5
0.93 0.04 0.03
Matches are distributed among these distances:
75 126 0.79
76 11 0.07
77 8 0.05
78 9 0.06
79 5 0.03
ACGTcount: A:0.47, C:0.07, G:0.02, T:0.43
Consensus pattern (74 bp):
ATATAATATATATATTTTTTAAAAGTATTTTCAAAACATATAATATATATATTTAAAAACTAATT
TTCAAAACT
Found at i:483209 original size:23 final size:21
Alignment explanation
Indices: 483179--483220 Score: 57
Period size: 22 Copynumber: 1.9 Consensus size: 21
483169 TTATGTTTAA
*
483179 ATAAATTAGATCAAAACCATGG
1 ATAAATTA-ACCAAAACCATGG
483201 ATAACATTAACCAAAACCAT
1 ATAA-ATTAACCAAAACCAT
483221 AATGAAAAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
22 14 0.78
23 4 0.22
ACGTcount: A:0.52, C:0.19, G:0.07, T:0.21
Consensus pattern (21 bp):
ATAAATTAACCAAAACCATGG
Found at i:500690 original size:23 final size:22
Alignment explanation
Indices: 500647--500693 Score: 60
Period size: 22 Copynumber: 2.1 Consensus size: 22
500637 ACCTTTATCC
500647 TTTTTTCAAATCTGTATCCTTT
1 TTTTTTCAAATCTGTATCCTTT
* *
500669 TTTTTTTAAAT-TCGTATCCCTT
1 TTTTTTCAAATCT-GTATCCTTT
500691 TTT
1 TTT
500694 CTATTTTCGG
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
21 1 0.05
22 21 0.95
ACGTcount: A:0.17, C:0.17, G:0.04, T:0.62
Consensus pattern (22 bp):
TTTTTTCAAATCTGTATCCTTT
Found at i:500920 original size:16 final size:17
Alignment explanation
Indices: 500895--500936 Score: 59
Period size: 16 Copynumber: 2.5 Consensus size: 17
500885 TGTGTTTGTT
*
500895 TTTATTTTATTAATTTA
1 TTTATCTTATTAATTTA
*
500912 -TTATCTTATTTATTTA
1 TTTATCTTATTAATTTA
500928 TTTATCTTA
1 TTTATCTTA
500937 GCTTTTTTTA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
16 14 0.64
17 8 0.36
ACGTcount: A:0.26, C:0.05, G:0.00, T:0.69
Consensus pattern (17 bp):
TTTATCTTATTAATTTA
Found at i:501810 original size:15 final size:16
Alignment explanation
Indices: 501790--501821 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 16
501780 AAAATACAAC
501790 ATTCCC-AGTAATCTT
1 ATTCCCTAGTAATCTT
501805 ATTCCCTAGTAATCTT
1 ATTCCCTAGTAATCTT
501821 A
1 A
501822 CACTCCCACT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 6 0.38
16 10 0.62
ACGTcount: A:0.28, C:0.25, G:0.06, T:0.41
Consensus pattern (16 bp):
ATTCCCTAGTAATCTT
Found at i:507956 original size:13 final size:13
Alignment explanation
Indices: 507938--507966 Score: 58
Period size: 13 Copynumber: 2.2 Consensus size: 13
507928 AATGCACACA
507938 AAATAAAGATTTT
1 AAATAAAGATTTT
507951 AAATAAAGATTTT
1 AAATAAAGATTTT
507964 AAA
1 AAA
507967 ACTTATTAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.59, C:0.00, G:0.07, T:0.34
Consensus pattern (13 bp):
AAATAAAGATTTT
Found at i:514033 original size:21 final size:21
Alignment explanation
Indices: 514003--514050 Score: 87
Period size: 21 Copynumber: 2.3 Consensus size: 21
513993 TAATTTTCAA
*
514003 ACATTATTGCACCTAATTTTG
1 ACATTGTTGCACCTAATTTTG
514024 ACATTGTTGCACCTAATTTTG
1 ACATTGTTGCACCTAATTTTG
514045 ACATTG
1 ACATTG
514051 CAATATTAGG
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
21 26 1.00
ACGTcount: A:0.27, C:0.19, G:0.12, T:0.42
Consensus pattern (21 bp):
ACATTGTTGCACCTAATTTTG
Found at i:524257 original size:35 final size:36
Alignment explanation
Indices: 524190--524291 Score: 152
Period size: 35 Copynumber: 2.8 Consensus size: 36
524180 TTCAACAAAC
524190 TACCAAACTTTGAAAAACTATTTTTCAAAGAAACATT
1 TACCAAACTTTG-AAAACTATTTTTCAAAGAAACATT
*
524227 TACCAAACTTTGAAAATTA-TTTTCAAAGAAACATT
1 TACCAAACTTTGAAAACTATTTTTCAAAGAAACATT
* *
524262 TTCCAAACTTTGAAAACCATTTTTTCAAAG
1 TACCAAACTTTGAAAACTA-TTTTTCAAAG
524292 TTAGTTACCA
Statistics
Matches: 59, Mismatches: 4, Indels: 4
0.88 0.06 0.06
Matches are distributed among these distances:
35 32 0.54
36 6 0.10
37 21 0.36
ACGTcount: A:0.43, C:0.17, G:0.06, T:0.34
Consensus pattern (36 bp):
TACCAAACTTTGAAAACTATTTTTCAAAGAAACATT
Found at i:531127 original size:20 final size:20
Alignment explanation
Indices: 531102--531161 Score: 120
Period size: 20 Copynumber: 3.0 Consensus size: 20
531092 AGAAAATAAA
531102 TATGTATAATGGTGTTGAAG
1 TATGTATAATGGTGTTGAAG
531122 TATGTATAATGGTGTTGAAG
1 TATGTATAATGGTGTTGAAG
531142 TATGTATAATGGTGTTGAAG
1 TATGTATAATGGTGTTGAAG
531162 ACTTGTAGTT
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 40 1.00
ACGTcount: A:0.30, C:0.00, G:0.30, T:0.40
Consensus pattern (20 bp):
TATGTATAATGGTGTTGAAG
Found at i:531671 original size:2 final size:2
Alignment explanation
Indices: 531664--531710 Score: 94
Period size: 2 Copynumber: 23.5 Consensus size: 2
531654 TATAAACTTC
531664 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA 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
531706 TA TA T
1 TA TA T
531711 GAGTTAGATC
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 45 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:534981 original size:18 final size:20
Alignment explanation
Indices: 534939--534982 Score: 56
Period size: 20 Copynumber: 2.3 Consensus size: 20
534929 TTTGGTTCAC
* *
534939 GGAATGTAAGATTACCAGTG
1 GGAATATAAGACTACCAGTG
534959 GGAATATAAGACTACC-G-G
1 GGAATATAAGACTACCAGTG
534977 GGAATA
1 GGAATA
534983 GGATTACTGG
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
18 7 0.32
19 1 0.05
20 14 0.64
ACGTcount: A:0.39, C:0.11, G:0.30, T:0.20
Consensus pattern (20 bp):
GGAATATAAGACTACCAGTG
Found at i:539325 original size:201 final size:199
Alignment explanation
Indices: 538932--539332 Score: 696
Period size: 201 Copynumber: 2.0 Consensus size: 199
538922 TTTGAACTTG
* * *
538932 AAAATTTAAAGCTTGCGAGTTTTCGAGCGGAGTCGAGATTCATTTTAGAGTTTTCGAGTCGTGCT
1 AAAATTTAAAGCTTGCGAGTTTTAGAGCGGAATCGAGATCCATTTTAGAGTTTTCGAGTCGTGCT
538997 CAACAATACTCAAGCTCAGCTCGACTCGTTTACAACCTCTCTCTCGAAATAATACTCAAAATTTT
66 CAACAATACTCAAGCTCAGCTCGACTCGTTTACAACCTCTCTCTCGAAATAATACTCAAAATTTT
539062 CAATATAATTATTACTTTTGAAATAAAATTTTCAGTATAATTCATTCGACAACGATCTTGAATTT
131 CAATATAATTATTACTTTTGAAATAAAATTTTCAGTATAATTCATTCGACAACGATCTTGAATTT
539127 ATTT
196 ATTT
* * *
539131 AAAATTTAAAGCTTGCGAGTTTTATAGTC-GAATCGAGCTCCATTTTAGAGTTTTCGAGTTGTGC
1 AAAATTTAAAGCTTGCGAGTTTTAGAG-CGGAATCGAGATCCATTTTAGAGTTTTCGAGTCGTGC
*
539195 TCAACAATACTCAAGCTCAGTTCGACTCGTTTACAACCTCTCTCTCTCGAAATAATACTCAAAAT
65 TCAACAATACTCAAGCTCAGCTCGACTCGTTTACAA-C-CTCTCTCTCGAAATAATACTCAAAAT
*
539260 TTTCAATATAATTATTACTTTTGAAATAAAATTTTCAGTATAATTCATTCGACAGCGATCTTGAA
128 TTTCAATATAATTATTACTTTTGAAATAAAATTTTCAGTATAATTCATTCGACAACGATCTTGAA
539325 TTTATTT
193 TTTATTT
539332 A
1 A
539333 TTCATTTATA
Statistics
Matches: 191, Mismatches: 8, Indels: 4
0.94 0.04 0.02
Matches are distributed among these distances:
199 91 0.48
200 2 0.01
201 98 0.51
ACGTcount: A:0.32, C:0.18, G:0.13, T:0.37
Consensus pattern (199 bp):
AAAATTTAAAGCTTGCGAGTTTTAGAGCGGAATCGAGATCCATTTTAGAGTTTTCGAGTCGTGCT
CAACAATACTCAAGCTCAGCTCGACTCGTTTACAACCTCTCTCTCGAAATAATACTCAAAATTTT
CAATATAATTATTACTTTTGAAATAAAATTTTCAGTATAATTCATTCGACAACGATCTTGAATTT
ATTT
Found at i:559246 original size:161 final size:161
Alignment explanation
Indices: 558944--559262 Score: 464
Period size: 161 Copynumber: 2.0 Consensus size: 161
558934 TTGATAAAAA
* *
558944 CAAAATTTTAAGTTAAACTATGGTTGGAACTAATTAAATATTTTGAAGAATTTGGGGATGGAATT
1 CAAAAATTTAAGTTAAACTATGGTTGGAACTAATTAAATATTTTGAAGAATTTGGGGAGGGAATT
559009 GGAATATTGTAATACCCCAAAATTTTGATAAGGGACCAAAATGTAAACTTGGATAATTTGGTGGC
66 GGAATATTGTAATACCCCAAAATTTTGATAAGGGACCAAAATGTAAACTTGGATAATTTGGTGGC
* *
559074 CAAAGTAGAAATTT-GGAAAAAGTTCAAGTAC
131 CAAAATAGAAATTTAAG-AAAAGTTCAAGTAC
* * *
559105 CAAAAATTTAGGTTAAACTATGGTTGGAGCTAATTACATATTTTGAAGAATTTGGGGAGGGAATT
1 CAAAAATTTAAGTTAAACTATGGTTGGAACTAATTAAATATTTTGAAGAATTTGGGGAGGGAATT
* * * * * *
559170 GGAATGTTGTGATACCCCAAAATTTTTATAAGTTG-CCAAAATGTAAATTTGGA-AAGTTTTGTG
66 GGAATATTGTAATACCCCAAAATTTTGATAAG-GGACCAAAATGTAAACTTGGATAA-TTTGGTG
*
559233 GTCAAAATAGAAATTTAAGAAAAGTTCAAG
129 GCCAAAATAGAAATTTAAGAAAAGTTCAAG
559263 GATCAAAGTG
Statistics
Matches: 141, Mismatches: 14, Indels: 6
0.88 0.09 0.04
Matches are distributed among these distances:
160 2 0.01
161 137 0.97
162 2 0.01
ACGTcount: A:0.39, C:0.08, G:0.21, T:0.32
Consensus pattern (161 bp):
CAAAAATTTAAGTTAAACTATGGTTGGAACTAATTAAATATTTTGAAGAATTTGGGGAGGGAATT
GGAATATTGTAATACCCCAAAATTTTGATAAGGGACCAAAATGTAAACTTGGATAATTTGGTGGC
CAAAATAGAAATTTAAGAAAAGTTCAAGTAC
Found at i:563321 original size:60 final size:59
Alignment explanation
Indices: 563161--563332 Score: 166
Period size: 60 Copynumber: 2.8 Consensus size: 59
563151 GGGTGTTACA
* * * *
563161 AATATTCAAAAGTTTAAGGATCAATTCAAAATGAATGTCATAGTTT-ACGATTCAAAGTAG
1 AATATTCAAAAGTTTAAGGAT-AATTCAAAATGAGTGTTATAGTTTGA-GAGTAAAAGTAG
* * * * * * * *
563221 AATGTTCAATAGTGTAAGGACTTATTCAGAATGAGGGTTATAATTTGAGAGTAAAATTAG
1 AATATTCAAAAGTTTAAGGA-TAATTCAAAATGAGTGTTATAGTTTGAGAGTAAAAGTAG
* *
563281 AATATTCAAAAGTTTAAGGATAAATTTAAAATTAGTGTTATAGTTTGGAGAG
1 AATATTCAAAAGTTTAAGGAT-AATTCAAAATGAGTGTTATAGTTT-GAGAG
563333 AGATGATACA
Statistics
Matches: 87, Mismatches: 21, Indels: 7
0.76 0.18 0.06
Matches are distributed among these distances:
59 1 0.01
60 79 0.91
61 7 0.08
ACGTcount: A:0.41, C:0.06, G:0.19, T:0.34
Consensus pattern (59 bp):
AATATTCAAAAGTTTAAGGATAATTCAAAATGAGTGTTATAGTTTGAGAGTAAAAGTAG
Found at i:564384 original size:28 final size:28
Alignment explanation
Indices: 564352--564424 Score: 96
Period size: 27 Copynumber: 2.6 Consensus size: 28
564342 CGTGGAAGAT
*
564352 GGGTTAAATTGATTTTTTTTAAGTTCGA
1 GGGTTAAATTGATTTTTTTTAAGTTCAA
*
564380 GGGTTAAATTGA-TTTTCTTAAGTTCAA
1 GGGTTAAATTGATTTTTTTTAAGTTCAA
*
564407 GGGCTT-ATTTGATTTTTT
1 GGG-TTAAATTGATTTTTT
564425 ATAAAAAATG
Statistics
Matches: 39, Mismatches: 4, Indels: 4
0.83 0.09 0.09
Matches are distributed among these distances:
27 21 0.54
28 18 0.46
ACGTcount: A:0.23, C:0.05, G:0.21, T:0.51
Consensus pattern (28 bp):
GGGTTAAATTGATTTTTTTTAAGTTCAA
Done.