Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008387.1 Hibiscus syriacus cultivar Beakdansim tig00111151_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: 2491990
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 8 of 12
Found at i:1539879 original size:2 final size:2
Alignment explanation
Indices: 1539872--1539932 Score: 122
Period size: 2 Copynumber: 30.5 Consensus size: 2
1539862 ATTAAGGGGC
1539872 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
1539914 AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT A
1539933 ATAATGACTA
Statistics
Matches: 59, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 59 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:1540001 original size:28 final size:29
Alignment explanation
Indices: 1539963--1540059 Score: 74
Period size: 28 Copynumber: 3.3 Consensus size: 29
1539953 AAAATGAAAT
*
1539963 GAAATATAATAATT-AAATTATAATAATA
1 GAAATAAAATAATTAAAATTATAATAATA
**
1539991 GAAATAAAATAAATTTGCAATTAGATAATAAT-
1 GAAATAAAAT-AA-TTAAAATT--ATAATAATA
* * *
1540023 CAAATCAAATAATTAAAATTATAACAATA
1 GAAATAAAATAATTAAAATTATAATAATA
*
1540052 -AATTAAAA
1 GAAATAAAA
1540060 AAAAAATAAA
Statistics
Matches: 54, Mismatches: 9, Indels: 12
0.72 0.12 0.16
Matches are distributed among these distances:
28 22 0.41
29 2 0.04
30 8 0.15
31 6 0.11
32 8 0.15
33 8 0.15
ACGTcount: A:0.61, C:0.04, G:0.04, T:0.31
Consensus pattern (29 bp):
GAAATAAAATAATTAAAATTATAATAATA
Found at i:1541438 original size:3 final size:3
Alignment explanation
Indices: 1541406--1541476 Score: 61
Period size: 3 Copynumber: 23.0 Consensus size: 3
1541396 TTGTAATATT
* * * **
1541406 TAA TAAA TAA TATA TAT TAT TAA TAT TAA TAA TAA TTT TAA TAA TAA
1 TAA T-AA TAA TA-A TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
**
1541453 TAA TAA TTT TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA
1541477 ATTTAAATTT
Statistics
Matches: 54, Mismatches: 12, Indels: 4
0.77 0.17 0.06
Matches are distributed among these distances:
3 48 0.89
4 6 0.11
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (3 bp):
TAA
Found at i:1541448 original size:18 final size:18
Alignment explanation
Indices: 1541399--1541482 Score: 107
Period size: 18 Copynumber: 4.5 Consensus size: 18
1541389 TTTGGGCTTG
1541399 TAATATTTAATAAATAAT-A
1 TAAT-TTTAAT-AATAATAA
*
1541418 TATATTATTAATATTAATAA
1 TA-ATT-TTAATAATAATAA
1541438 TAATTTTAATAATAATAA
1 TAATTTTAATAATAATAA
1541456 TAATTTTAATAATAATAA
1 TAATTTTAATAATAATAA
*
1541474 TAAATTTAA
1 TAATTTTAA
1541483 ATTTAAAATG
Statistics
Matches: 59, Mismatches: 3, Indels: 7
0.86 0.04 0.10
Matches are distributed among these distances:
18 38 0.64
19 11 0.19
20 10 0.17
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (18 bp):
TAATTTTAATAATAATAA
Found at i:1541467 original size:9 final size:9
Alignment explanation
Indices: 1541435--1541482 Score: 51
Period size: 9 Copynumber: 5.3 Consensus size: 9
1541425 TTAATATTAA
1541435 TAATAATTT
1 TAATAATTT
**
1541444 TAATAATAA
1 TAATAATTT
1541453 TAATAATTT
1 TAATAATTT
**
1541462 TAATAATAA
1 TAATAATTT
*
1541471 TAATAAATT
1 TAATAATTT
1541480 TAA
1 TAA
1541483 ATTTAAAATG
Statistics
Matches: 30, Mismatches: 9, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
9 30 1.00
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (9 bp):
TAATAATTT
Found at i:1541664 original size:45 final size:45
Alignment explanation
Indices: 1541613--1541714 Score: 161
Period size: 45 Copynumber: 2.3 Consensus size: 45
1541603 GATGGAAATG
*
1541613 TTGAAAACATCATGAACTGAAAGG-CTTACAGATGACCCGAAGGTT
1 TTGAAAACATCATGAACTG-AAGGACTTACAGATGACCCGAAGGCT
* *
1541658 TTGAAAACATCATGCACTGAAGGACTTACAGATGACCCTAAGGCT
1 TTGAAAACATCATGAACTGAAGGACTTACAGATGACCCGAAGGCT
1541703 TTGAAAACATCA
1 TTGAAAACATCA
1541715 AAAAGCTCCC
Statistics
Matches: 53, Mismatches: 3, Indels: 2
0.91 0.05 0.03
Matches are distributed among these distances:
44 4 0.08
45 49 0.92
ACGTcount: A:0.38, C:0.20, G:0.20, T:0.23
Consensus pattern (45 bp):
TTGAAAACATCATGAACTGAAGGACTTACAGATGACCCGAAGGCT
Found at i:1541758 original size:76 final size:76
Alignment explanation
Indices: 1541648--1542366 Score: 1253
Period size: 76 Copynumber: 9.6 Consensus size: 76
1541638 TTACAGATGA
* *
1541648 CCCGAAGG--TTTTGAAAACATCATGCACTGAAGGACTTACAGATGACCCTAAGGCTTTGAAAAC
1 CCCGAAGGCTTTTTGGAAACATCATGCACTGCAGGACTTACAGATGACCCTAAGGCTTTGAAAAC
1541711 ATCAAAAAGCT
66 ATCAAAAAGCT
*
1541722 CCCGAAGGCTTTTTGGAAACATCATGCACTGTAGGAC-TACAGATGACCCTAAGG-TTTGAAAAC
1 CCCGAAGGCTTTTTGGAAACATCATGCACTGCAGGACTTACAGATGACCCTAAGGCTTTGAAAAC
1541785 ATC-AAAAGCT
66 ATCAAAAAGCT
* *
1541795 CCCGAAGGC-TTTTGGAAACATCATGCACTGTAGGACTTACAGATGACCCAAAGG-TTTGAAAAC
1 CCCGAAGGCTTTTTGGAAACATCATGCACTGCAGGACTTACAGATGACCCTAAGGCTTTGAAAAC
1541858 ATCAAAAAGCT
66 ATCAAAAAGCT
* *
1541869 CCCGAAGGCTTTTTGGAAACATCATGCACTGTAGGACTTACAGATGACCCTAAGGTTTTGAAAAC
1 CCCGAAGGCTTTTTGGAAACATCATGCACTGCAGGACTTACAGATGACCCTAAGGCTTTGAAAAC
1541934 ATCAAAAAGCT
66 ATCAAAAAGCT
*
1541945 CCCGAAGGCTTTTTGGAAACATCATGCACTGCAGGACTTACAGATGACTCTAAGGCTTTGAAAAC
1 CCCGAAGGCTTTTTGGAAACATCATGCACTGCAGGACTTACAGATGACCCTAAGGCTTTGAAAAC
1542010 ATCAAAAAGCT
66 ATCAAAAAGCT
*
1542021 CCCAAAGGCTTTTTGGAAACATCATGCACTGCAGGACTTACAGATGACCCTAAGGCTTTGAAAAC
1 CCCGAAGGCTTTTTGGAAACATCATGCACTGCAGGACTTACAGATGACCCTAAGGCTTTGAAAAC
1542086 ATCAAAAAGCT
66 ATCAAAAAGCT
* *
1542097 CCCGAAGGCTTTTTGGAAACATCATGCACTGCAGGACTTATAGATGACCCTAAGGTTTTGAAAAC
1 CCCGAAGGCTTTTTGGAAACATCATGCACTGCAGGACTTACAGATGACCCTAAGGCTTTGAAAAC
1542162 ATC-AAAAGCT
66 ATCAAAAAGCT
*
1542172 CCCGAAGGCTTTTTGGAAACATCATGCACTGCAGGACTTACAGATGACCCTAAGGTTTTGAAAAC
1 CCCGAAGGCTTTTTGGAAACATCATGCACTGCAGGACTTACAGATGACCCTAAGGCTTTGAAAAC
1542237 ATCAAAAAGCT
66 ATCAAAAAGCT
1542248 CCCGAAGGCTTTTTGGAAACATCATGCACTGCAGGACTTACAGATGACCCTAAGGCTTTGAAAAC
1 CCCGAAGGCTTTTTGGAAACATCATGCACTGCAGGACTTACAGATGACCCTAAGGCTTTGAAAAC
1542313 ATC-AAAAGCT
66 ATCAAAAAGCT
1542323 -CCGAAGGC-TTTTGGAAACATCATGCACTGCAGGACTTACAGATG
1 CCCGAAGGCTTTTTGGAAACATCATGCACTGCAGGACTTACAGATG
1542367 TGGGAAATAG
Statistics
Matches: 624, Mismatches: 14, Indels: 15
0.96 0.02 0.02
Matches are distributed among these distances:
72 27 0.04
73 80 0.13
74 44 0.07
75 142 0.23
76 331 0.53
ACGTcount: A:0.34, C:0.22, G:0.20, T:0.23
Consensus pattern (76 bp):
CCCGAAGGCTTTTTGGAAACATCATGCACTGCAGGACTTACAGATGACCCTAAGGCTTTGAAAAC
ATCAAAAAGCT
Found at i:1542199 original size:227 final size:226
Alignment explanation
Indices: 1541648--1542366 Score: 1256
Period size: 227 Copynumber: 3.2 Consensus size: 226
1541638 TTACAGATGA
* * *
1541648 CCCGAAGG-TTTTGAAAACATCATGCACTGAAGGACTTACAGATGACCCTAAGGCTTTGAAAACA
1 CCCGAAGGCTTTTGGAAACATCATGCACTGCAGGACTTACAGATGACCCTAAGGTTTTGAAAACA
*
1541712 TCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTGTAGGAC-TACAGATGACCCTAAGG
66 TCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTGCAGGACTTACAGATGACCCTAAGG
*
1541776 TTTGAAAACATC-AAAAGCTCCCGAAGGC-TTTTGGAAACATCATGCACTGTAGGACTTACAGAT
131 TTTGAAAACATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTGCAGGACTTACAGAT
*
1541839 GACCCAAAGG-TTTGAAAACATCAAAAAGCT
196 GACCCTAAGGCTTTGAAAACATCAAAAAGCT
*
1541869 CCCGAAGGCTTTTTGGAAACATCATGCACTGTAGGACTTACAGATGACCCTAAGGTTTTGAAAAC
1 CCCGAAGGC-TTTTGGAAACATCATGCACTGCAGGACTTACAGATGACCCTAAGGTTTTGAAAAC
*
1541934 ATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTGCAGGACTTACAGATGACTCTAAG
65 ATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTGCAGGACTTACAGATGACCCTAAG
*
1541999 GCTTTGAAAACATCAAAAAGCTCCCAAAGGCTTTTTGGAAACATCATGCACTGCAGGACTTACAG
130 G-TTTGAAAACATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTGCAGGACTTACAG
1542064 ATGACCCTAAGGCTTTGAAAACATCAAAAAGCT
194 ATGACCCTAAGGCTTTGAAAACATCAAAAAGCT
*
1542097 CCCGAAGGCTTTTTGGAAACATCATGCACTGCAGGACTTATAGATGACCCTAAGGTTTTGAAAAC
1 CCCGAAGGC-TTTTGGAAACATCATGCACTGCAGGACTTACAGATGACCCTAAGGTTTTGAAAAC
1542162 ATC-AAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTGCAGGACTTACAGATGACCCTAAG
65 ATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTGCAGGACTTACAGATGACCCTAAG
1542226 GTTTTGAAAACATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTGCAGGACTTACAG
130 G-TTTGAAAACATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTGCAGGACTTACAG
1542291 ATGACCCTAAGGCTTTGAAAACATC-AAAAGCT
194 ATGACCCTAAGGCTTTGAAAACATCAAAAAGCT
1542323 -CCGAAGGCTTTTGGAAACATCATGCACTGCAGGACTTACAGATG
1 CCCGAAGGCTTTTGGAAACATCATGCACTGCAGGACTTACAGATG
1542367 TGGGAAATAG
Statistics
Matches: 477, Mismatches: 14, Indels: 11
0.95 0.03 0.02
Matches are distributed among these distances:
221 8 0.02
223 99 0.21
224 51 0.11
225 20 0.04
226 22 0.05
227 191 0.40
228 86 0.18
ACGTcount: A:0.34, C:0.22, G:0.20, T:0.23
Consensus pattern (226 bp):
CCCGAAGGCTTTTGGAAACATCATGCACTGCAGGACTTACAGATGACCCTAAGGTTTTGAAAACA
TCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTGCAGGACTTACAGATGACCCTAAGG
TTTGAAAACATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTGCAGGACTTACAGAT
GACCCTAAGGCTTTGAAAACATCAAAAAGCT
Found at i:1542255 original size:151 final size:152
Alignment explanation
Indices: 1541648--1542366 Score: 1262
Period size: 151 Copynumber: 4.8 Consensus size: 152
1541638 TTACAGATGA
* *
1541648 CCCGAAGG--TTTTGAAAACATCATGCACTGAAGGACTTACAGATGACCCTAAGGCTTTGAAAAC
1 CCCGAAGGCTTTTTGGAAACATCATGCACTGCAGGACTTACAGATGACCCTAAGGCTTTGAAAAC
*
1541711 ATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTGTAGGAC-TACAGATGACCCTAAG
66 ATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTGCAGGACTTACAGATGACCCTAAG
1541775 G-TTTGAAAACATC-AAAAGCT
131 GTTTTGAAAACATCAAAAAGCT
* *
1541795 CCCGAAGGC-TTTTGGAAACATCATGCACTGTAGGACTTACAGATGACCCAAAGG-TTTGAAAAC
1 CCCGAAGGCTTTTTGGAAACATCATGCACTGCAGGACTTACAGATGACCCTAAGGCTTTGAAAAC
*
1541858 ATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTGTAGGACTTACAGATGACCCTAAG
66 ATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTGCAGGACTTACAGATGACCCTAAG
1541923 GTTTTGAAAACATCAAAAAGCT
131 GTTTTGAAAACATCAAAAAGCT
*
1541945 CCCGAAGGCTTTTTGGAAACATCATGCACTGCAGGACTTACAGATGACTCTAAGGCTTTGAAAAC
1 CCCGAAGGCTTTTTGGAAACATCATGCACTGCAGGACTTACAGATGACCCTAAGGCTTTGAAAAC
*
1542010 ATCAAAAAGCTCCCAAAGGCTTTTTGGAAACATCATGCACTGCAGGACTTACAGATGACCCTAAG
66 ATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTGCAGGACTTACAGATGACCCTAAG
*
1542075 GCTTTGAAAACATCAAAAAGCT
131 GTTTTGAAAACATCAAAAAGCT
* *
1542097 CCCGAAGGCTTTTTGGAAACATCATGCACTGCAGGACTTATAGATGACCCTAAGGTTTTGAAAAC
1 CCCGAAGGCTTTTTGGAAACATCATGCACTGCAGGACTTACAGATGACCCTAAGGCTTTGAAAAC
1542162 ATC-AAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTGCAGGACTTACAGATGACCCTAAG
66 ATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTGCAGGACTTACAGATGACCCTAAG
1542226 GTTTTGAAAACATCAAAAAGCT
131 GTTTTGAAAACATCAAAAAGCT
1542248 CCCGAAGGCTTTTTGGAAACATCATGCACTGCAGGACTTACAGATGACCCTAAGGCTTTGAAAAC
1 CCCGAAGGCTTTTTGGAAACATCATGCACTGCAGGACTTACAGATGACCCTAAGGCTTTGAAAAC
1542313 ATC-AAAAGCT-CCGAAGGC-TTTTGGAAACATCATGCACTGCAGGACTTACAGATG
66 ATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTGCAGGACTTACAGATG
1542367 TGGGAAATAG
Statistics
Matches: 550, Mismatches: 16, Indels: 10
0.95 0.03 0.02
Matches are distributed among these distances:
147 65 0.12
148 59 0.11
149 48 0.09
150 24 0.04
151 196 0.36
152 158 0.29
ACGTcount: A:0.34, C:0.22, G:0.20, T:0.23
Consensus pattern (152 bp):
CCCGAAGGCTTTTTGGAAACATCATGCACTGCAGGACTTACAGATGACCCTAAGGCTTTGAAAAC
ATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTGCAGGACTTACAGATGACCCTAAG
GTTTTGAAAACATCAAAAAGCT
Found at i:1543653 original size:54 final size:54
Alignment explanation
Indices: 1543589--1543744 Score: 249
Period size: 54 Copynumber: 2.9 Consensus size: 54
1543579 AGAATAGCAG
* *** *
1543589 GTTCGTAAAACATTTGGCAGTGCATTGATCCTTTCCTGTGGCTTCTGCTCAGAT
1 GTTCGTAAAACATTTGACAACACATTCATCCTTTCCTGTGGCTTCTGCTCAGAT
* *
1543643 GTTCGTAAAACATTTGACAACACATTCATCCTTTCCTGTGGTTTCTGTTCAGAT
1 GTTCGTAAAACATTTGACAACACATTCATCCTTTCCTGTGGCTTCTGCTCAGAT
1543697 GTTCGTAAAACATTTGACAACACATTCATCCTTTCCTGTGGCTTCTGC
1 GTTCGTAAAACATTTGACAACACATTCATCCTTTCCTGTGGCTTCTGC
1543745 CAAGATTTCT
Statistics
Matches: 93, Mismatches: 9, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
54 93 1.00
ACGTcount: A:0.22, C:0.24, G:0.17, T:0.37
Consensus pattern (54 bp):
GTTCGTAAAACATTTGACAACACATTCATCCTTTCCTGTGGCTTCTGCTCAGAT
Found at i:1545936 original size:114 final size:114
Alignment explanation
Indices: 1545736--1546069 Score: 542
Period size: 114 Copynumber: 2.9 Consensus size: 114
1545726 GATCATGTAG
* * * * * *
1545736 TTCATCTTTCAATTTCAATGATTGGTTATGGGATTCCTACCGAACCAGATCAGATAACTCAAAGA
1 TTCATCTTTCAAATCCAATGATTGGTTTTGGGGTTCATACCAAACCAGATCAGATAACTCAAAGA
1545801 ACACTTCCAGAAGATGCTATTGGGTCTTCTTATTTCTACTATGAACAAA
66 ACACTTCCAGAAGATGCTATTGGGTCTTCTTATTTCTACTATGAACAAA
* * *
1545850 TTCATCTTTTAAATCTAATGATTGGTTTTGGGGTTCATACCAAACCAGATCAAATAACTCAAAGA
1 TTCATCTTTCAAATCCAATGATTGGTTTTGGGGTTCATACCAAACCAGATCAGATAACTCAAAGA
*
1545915 ACACTTCCAGAAGATGCTATTGGGTCTTCTTATTTCTAATATGAACAAA
66 ACACTTCCAGAAGATGCTATTGGGTCTTCTTATTTCTACTATGAACAAA
*
1545964 TTCATCTTTCAAATCCAATTATTGGTTTTGGGGTTCATACCAAACCAGATCAGATAACTCAAAGA
1 TTCATCTTTCAAATCCAATGATTGGTTTTGGGGTTCATACCAAACCAGATCAGATAACTCAAAGA
* * *
1546029 GCACTTCCAGAAGATGCTATTGGGGCTCCTTATTTCTACTA
66 ACACTTCCAGAAGATGCTATTGGGTCTTCTTATTTCTACTA
1546070 CGAGAATGTG
Statistics
Matches: 202, Mismatches: 18, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
114 202 1.00
ACGTcount: A:0.32, C:0.20, G:0.15, T:0.34
Consensus pattern (114 bp):
TTCATCTTTCAAATCCAATGATTGGTTTTGGGGTTCATACCAAACCAGATCAGATAACTCAAAGA
ACACTTCCAGAAGATGCTATTGGGTCTTCTTATTTCTACTATGAACAAA
Found at i:1552848 original size:46 final size:49
Alignment explanation
Indices: 1552796--1552887 Score: 118
Period size: 48 Copynumber: 1.9 Consensus size: 49
1552786 GAAATTGTCT
1552796 CTATTATTAGAA-ATTAAAAAT-TCAAAAATATAT-TTAATTTATAATC
1 CTATTATTAGAAGATTAAAAATATCAAAAATATATATTAATTTATAATC
** * * *
1552842 CTATTATTTTAAGATTATAATTATGAAAAATATATATTAATTTATA
1 CTATTATTAGAAGATTAAAAATATCAAAAATATATATTAATTTATA
1552888 TATATTTATA
Statistics
Matches: 38, Mismatches: 5, Indels: 3
0.83 0.11 0.07
Matches are distributed among these distances:
46 10 0.26
47 7 0.18
48 11 0.29
49 10 0.26
ACGTcount: A:0.48, C:0.04, G:0.03, T:0.45
Consensus pattern (49 bp):
CTATTATTAGAAGATTAAAAATATCAAAAATATATATTAATTTATAATC
Found at i:1553010 original size:20 final size:19
Alignment explanation
Indices: 1552971--1553022 Score: 59
Period size: 20 Copynumber: 2.6 Consensus size: 19
1552961 TTTCTTTGAT
1552971 ATTAAAAAATAAATAAATA
1 ATTAAAAAATAAATAAATA
* *
1552990 ATTAAAACAATTAATATATA
1 ATTAAAA-AATAAATAAATA
*
1553010 ATTTATAAAATAA
1 A-TTAAAAAATAA
1553023 GATATTTATT
Statistics
Matches: 27, Mismatches: 4, Indels: 3
0.79 0.12 0.09
Matches are distributed among these distances:
19 7 0.26
20 15 0.56
21 5 0.19
ACGTcount: A:0.65, C:0.02, G:0.00, T:0.33
Consensus pattern (19 bp):
ATTAAAAAATAAATAAATA
Found at i:1554960 original size:20 final size:20
Alignment explanation
Indices: 1554930--1555030 Score: 100
Period size: 20 Copynumber: 5.2 Consensus size: 20
1554920 TTTTGGTTGA
1554930 AATGAAAATCGCAACGAGAG
1 AATGAAAATCGCAACGAGAG
** *
1554950 AATGACTATCGCAACGCG-G
1 AATGAAAATCGCAACGAGAG
** *
1554969 AAATGACTATCGCAACGCGA-
1 -AATGAAAATCGCAACGAGAG
*
1554989 AATAAAAATCGCAACGAGA-
1 AATGAAAATCGCAACGAGAG
*
1555008 AATTAAAATCGCAACGAGAG
1 AATGAAAATCGCAACGAGAG
1555028 AAT
1 AAT
1555031 CGCAACGCGA
Statistics
Matches: 70, Mismatches: 8, Indels: 6
0.83 0.10 0.07
Matches are distributed among these distances:
19 34 0.49
20 36 0.51
ACGTcount: A:0.47, C:0.19, G:0.21, T:0.14
Consensus pattern (20 bp):
AATGAAAATCGCAACGAGAG
Found at i:1554999 original size:19 final size:19
Alignment explanation
Indices: 1554928--1555059 Score: 121
Period size: 19 Copynumber: 7.1 Consensus size: 19
1554918 TCTTTTGGTT
*
1554928 GAAATGAAAATCGCAACGA
1 GAAATGAAAATCGCAACGC
**
1554947 GAGAATGACTATCGCAACGC
1 GA-AATGAAAATCGCAACGC
**
1554967 GGAAATGACTATCGCAACGC
1 -GAAATGAAAATCGCAACGC
* *
1554987 GAAATAAAAATCGCAACGA
1 GAAATGAAAATCGCAACGC
*
1555006 GAAATTAAAATCGCAA--C
1 GAAATGAAAATCGCAACGC
*
1555023 G--A-GAGAATCGCAACGC
1 GAAATGAAAATCGCAACGC
*
1555039 GAAATGAAAATCGCAATGC
1 GAAATGAAAATCGCAACGC
1555058 GA
1 GA
1555060 TTTTGGTTTC
Statistics
Matches: 93, Mismatches: 13, Indels: 14
0.77 0.11 0.12
Matches are distributed among these distances:
14 9 0.10
15 1 0.01
16 2 0.02
17 1 0.01
18 1 0.01
19 46 0.49
20 31 0.33
21 2 0.02
ACGTcount: A:0.45, C:0.20, G:0.22, T:0.13
Consensus pattern (19 bp):
GAAATGAAAATCGCAACGC
Found at i:1555092 original size:19 final size:19
Alignment explanation
Indices: 1555055--1555162 Score: 92
Period size: 19 Copynumber: 5.5 Consensus size: 19
1555045 AAAATCGCAA
** *
1555055 TGCGATTTTGGTTTCGCGT
1 TGCGATTTTCATTTTGCGT
1555074 TGCGATTTTCATTTTGCGT
1 TGCGATTTTCATTTTGCGT
* *
1555093 TGTGATTTTCATTTCTCTCGT
1 TGCGATTTTCATTT-T-GCGT
** *
1555114 TGCGATAGTCATTTTCGTGT
1 TGCGATTTTCATTTT-GCGT
1555134 TGCGATTTTCATTTT-CATGT
1 TGCGATTTTCATTTTGC--GT
1555154 TGCGATTTT
1 TGCGATTTT
1555163 AAGTTTAGAA
Statistics
Matches: 72, Mismatches: 13, Indels: 7
0.78 0.14 0.08
Matches are distributed among these distances:
19 29 0.40
20 29 0.40
21 14 0.19
ACGTcount: A:0.11, C:0.16, G:0.21, T:0.52
Consensus pattern (19 bp):
TGCGATTTTCATTTTGCGT
Found at i:1555116 original size:40 final size:41
Alignment explanation
Indices: 1555071--1555162 Score: 118
Period size: 40 Copynumber: 2.3 Consensus size: 41
1555061 TTTGGTTTCG
*
1555071 CGTTGCGATTTTCATTTT-GCGTTGTGATTTTCATTTCTC-T
1 CGTTGCGATTTTCATTTTCGCGTTGCGATTTTCATTT-TCAT
** *
1555111 CGTTGCGATAGTCATTTTCGTGTTGCGATTTTCATTTTCAT
1 CGTTGCGATTTTCATTTTCGCGTTGCGATTTTCATTTTCAT
1555152 -GTTGCGATTTT
1 CGTTGCGATTTT
1555163 AAGTTTAGAA
Statistics
Matches: 44, Mismatches: 6, Indels: 4
0.81 0.11 0.07
Matches are distributed among these distances:
40 27 0.61
41 17 0.39
ACGTcount: A:0.12, C:0.16, G:0.20, T:0.52
Consensus pattern (41 bp):
CGTTGCGATTTTCATTTTCGCGTTGCGATTTTCATTTTCAT
Found at i:1555160 original size:20 final size:19
Alignment explanation
Indices: 1555072--1555162 Score: 103
Period size: 20 Copynumber: 4.6 Consensus size: 19
1555062 TTGGTTTCGC
1555072 GTTGCGATTTTCATTTTGC-
1 GTTGCGATTTTCATTTT-CT
*
1555091 GTTGTGATTTTCATTTCTCT
1 GTTGCGATTTTCATTT-TCT
**
1555111 CGTTGCGATAGTCATTTTCGT
1 -GTTGCGATTTTCATTTTC-T
1555132 GTTGCGATTTTCATTTTCAT
1 GTTGCGATTTTCATTTTC-T
1555152 GTTGCGATTTT
1 GTTGCGATTTT
1555163 AAGTTTAGAA
Statistics
Matches: 61, Mismatches: 7, Indels: 7
0.81 0.09 0.09
Matches are distributed among these distances:
19 16 0.26
20 31 0.51
21 14 0.23
ACGTcount: A:0.12, C:0.15, G:0.20, T:0.53
Consensus pattern (19 bp):
GTTGCGATTTTCATTTTCT
Found at i:1555722 original size:20 final size:19
Alignment explanation
Indices: 1555697--1555869 Score: 141
Period size: 20 Copynumber: 8.6 Consensus size: 19
1555687 CTTTAAAAAT
1555697 CGCGTTGCGATTTACTGATA
1 CGCGTTGCGATTTAC-GATA
*
1555717 CGCGTTGCGATTTTACGTATT
1 CGCGTTGCGA-TTTACG-ATA
**
1555738 TTCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTAC-GATA
* *
1555758 CGCATTGCGATTTACGTATT
1 CGCGTTGCGATTTACG-ATA
* *
1555778 CTCGTTGCGATTTACGTATT
1 CGCGTTGCGATTTACG-ATA
* *
1555798 CTCATTGCGATTTACGGATA
1 CGCGTTGCGATTTAC-GATA
1555818 CGCGTTGCGATTTTACG-TA
1 CGCGTTGCGA-TTTACGATA
*
1555837 TTGTCGTTGCGATTTACGGATA
1 -CG-CGTTGCGATTTAC-GATA
*
1555859 CTCGTTGCGAT
1 CGCGTTGCGAT
1555870 AGTCAGAATC
Statistics
Matches: 126, Mismatches: 17, Indels: 20
0.77 0.10 0.12
Matches are distributed among these distances:
19 3 0.02
20 90 0.71
21 31 0.25
22 2 0.02
ACGTcount: A:0.18, C:0.19, G:0.24, T:0.39
Consensus pattern (19 bp):
CGCGTTGCGATTTACGATA
Found at i:1555758 original size:41 final size:40
Alignment explanation
Indices: 1555699--1555869 Score: 182
Period size: 41 Copynumber: 4.2 Consensus size: 40
1555689 TTAAAAATCG
* * *
1555699 CGTTGCGATTTACTGATACGCGTTGCGATTTTACGTATTTT
1 CGTTGCGATTTACGGATACGCATTGCGA-TTTACGTATTCT
1555740 CGTTGCGATTTACGGATACGCATTGCGATTTACGTATTCT
1 CGTTGCGATTTACGGATACGCATTGCGATTTACGTATTCT
* * * * * *
1555780 CGTTGCGATTTACGTATTCTCATTGCGATTTACGGATACG
1 CGTTGCGATTTACGGATACGCATTGCGATTTACGTATTCT
* * * * *
1555820 CGTTGCGATTTTACGTAT-TGTCGTTGCGATTTACGGATACT
1 CGTTGCGA-TTTACGGATACG-CATTGCGATTTACGTATTCT
1555861 CGTTGCGAT
1 CGTTGCGAT
1555870 AGTCAGAATC
Statistics
Matches: 115, Mismatches: 13, Indels: 5
0.86 0.10 0.04
Matches are distributed among these distances:
40 54 0.47
41 61 0.53
ACGTcount: A:0.18, C:0.19, G:0.23, T:0.40
Consensus pattern (40 bp):
CGTTGCGATTTACGGATACGCATTGCGATTTACGTATTCT
Found at i:1555883 original size:61 final size:61
Alignment explanation
Indices: 1555697--1555891 Score: 184
Period size: 61 Copynumber: 3.2 Consensus size: 61
1555687 CTTTAAAAAT
* * * ** * * *
1555697 CGCGTTGCGA-TTTAC-TGATACGCGTTGCGATTTTACGTATTTTCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTTACGT-ATTCTCGTTGCGA-TTTACGGATACTCATTGCGATTCACGAATA
* * * * *
1555758 CGCATTGCGA-TTTACGTATTCTCGTTGCGATTTACGTATTCTCATTGCGATTTACGGATA
1 CGCGTTGCGATTTTACGTATTCTCGTTGCGATTTACGGATACTCATTGCGATTCACGAATA
* *
1555818 CGCGTTGCGATTTTACGTATTGTCGTTGCGATTTACGGATACTCGTTGCGATAGTCA-GAAT-
1 CGCGTTGCGATTTTACGTATTCTCGTTGCGATTTACGGATACTCATTGCGAT--TCACGAATA
1555879 CGCGTTGCGATTT
1 CGCGTTGCGATTT
1555892 ATATGTTCGC
Statistics
Matches: 118, Mismatches: 12, Indels: 8
0.86 0.09 0.06
Matches are distributed among these distances:
60 37 0.31
61 75 0.64
62 4 0.03
63 2 0.02
ACGTcount: A:0.18, C:0.19, G:0.24, T:0.38
Consensus pattern (61 bp):
CGCGTTGCGATTTTACGTATTCTCGTTGCGATTTACGGATACTCATTGCGATTCACGAATA
Found at i:1555885 original size:101 final size:101
Alignment explanation
Indices: 1555701--1555892 Score: 289
Period size: 101 Copynumber: 1.9 Consensus size: 101
1555691 AAAAATCGCG
* *
1555701 TTGCGATTTACTGATACGCGTTGCGATTTTACGTATTTTCGTTGCGATTTACGGATACGCATTGC
1 TTGCGATTTACGGATACGCGTTGCGATTTTACGTATTGTCGTTGCGATTTACGGATACGCATTGC
* * *
1555766 GATTTACGTATTCTCGTTGCGATTTACGTATTCTCA
66 GATTCACGTAATCGCGTTGCGATTTACGTATTCTCA
* *
1555802 TTGCGATTTACGGATACGCGTTGCGATTTTACGTATTGTCGTTGCGATTTACGGATACTCGTTGC
1 TTGCGATTTACGGATACGCGTTGCGATTTTACGTATTGTCGTTGCGATTTACGGATACGCATTGC
1555867 GATAGTCA-G-AATCGCGTTGCGATTTA
66 GAT--TCACGTAATCGCGTTGCGATTTA
1555893 TATGTTCGCG
Statistics
Matches: 82, Mismatches: 7, Indels: 4
0.88 0.08 0.04
Matches are distributed among these distances:
101 79 0.96
102 1 0.01
103 2 0.02
ACGTcount: A:0.19, C:0.18, G:0.23, T:0.39
Consensus pattern (101 bp):
TTGCGATTTACGGATACGCGTTGCGATTTTACGTATTGTCGTTGCGATTTACGGATACGCATTGC
GATTCACGTAATCGCGTTGCGATTTACGTATTCTCA
Found at i:1555922 original size:21 final size:21
Alignment explanation
Indices: 1555877--1555950 Score: 57
Period size: 21 Copynumber: 3.6 Consensus size: 21
1555867 GATAGTCAGA
1555877 ATCGCGTTGCG-ATTTATATG
1 ATCGCGTTGCGAATTTATATG
* *
1555897 TTCGCGTTGCGAATTTGTACT-
1 ATCGCGTTGCGAATTTATA-TG
* *
1555918 ATCGCATTGCG-ATTCT-TCATA
1 ATCGCGTTGCGAATT-TAT-ATG
1555939 ATCGCGTTGCGA
1 ATCGCGTTGCGA
1555951 TTCTGGTAAC
Statistics
Matches: 43, Mismatches: 5, Indels: 10
0.74 0.09 0.17
Matches are distributed among these distances:
20 15 0.35
21 27 0.63
22 1 0.02
ACGTcount: A:0.19, C:0.20, G:0.23, T:0.38
Consensus pattern (21 bp):
ATCGCGTTGCGAATTTATATG
Found at i:1555988 original size:20 final size:20
Alignment explanation
Indices: 1555942--1555992 Score: 59
Period size: 20 Copynumber: 2.5 Consensus size: 20
1555932 CTTCATAATC
1555942 GCGTTGCGATTCTGGTAACT
1 GCGTTGCGATTCTGGTAACT
** *
1555962 GATTTGCGATTCTGG-AGATT
1 GCGTTGCGATTCTGGTA-ACT
1555982 GCGTTGCGATT
1 GCGTTGCGATT
1555993 TTTATTTCGC
Statistics
Matches: 25, Mismatches: 5, Indels: 2
0.78 0.16 0.06
Matches are distributed among these distances:
19 1 0.04
20 24 0.96
ACGTcount: A:0.16, C:0.16, G:0.31, T:0.37
Consensus pattern (20 bp):
GCGTTGCGATTCTGGTAACT
Found at i:1561284 original size:19 final size:19
Alignment explanation
Indices: 1561256--1561292 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
1561246 CCTTTCCTTC
*
1561256 AATATTTAAAAAATAAATA
1 AATATCTAAAAAATAAATA
*
1561275 AATATCTAAAATATAAAT
1 AATATCTAAAAAATAAAT
1561293 TAAACATTTC
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 16 1.00
ACGTcount: A:0.65, C:0.03, G:0.00, T:0.32
Consensus pattern (19 bp):
AATATCTAAAAAATAAATA
Found at i:1561496 original size:19 final size:19
Alignment explanation
Indices: 1561459--1561497 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 19
1561449 AAATAGGGAC
*
1561459 TAAAATATATTAAAATAAA
1 TAAAATATATAAAAATAAA
1561478 TAAAATAT-TAAAAATTAAA
1 TAAAATATATAAAAA-TAAA
1561497 T
1 T
1561498 TTACAGCCCT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
18 5 0.28
19 13 0.72
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (19 bp):
TAAAATATATAAAAATAAA
Found at i:1562368 original size:19 final size:19
Alignment explanation
Indices: 1562336--1562376 Score: 75
Period size: 18 Copynumber: 2.2 Consensus size: 19
1562326 TGCTGTGTTC
1562336 TCTTTCTCTGTTTTTTTTT
1 TCTTTCTCTGTTTTTTTTT
1562355 TCTTT-TCTGTTTTTTTTT
1 TCTTTCTCTGTTTTTTTTT
1562373 TCTT
1 TCTT
1562377 GTCGTTCTCT
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
18 17 0.77
19 5 0.23
ACGTcount: A:0.00, C:0.15, G:0.05, T:0.80
Consensus pattern (19 bp):
TCTTTCTCTGTTTTTTTTT
Found at i:1562771 original size:3 final size:3
Alignment explanation
Indices: 1562763--1562868 Score: 140
Period size: 3 Copynumber: 34.7 Consensus size: 3
1562753 TTATTTATTA
* *
1562763 AAT AAT AAT AAT ATAT AAT ATT AAT AAT AAT AAT AAT AAAT AAT GAT
1 AAT AAT AAT AAT A-AT AAT AAT AAT AAT AAT AAT AAT -AAT AAT AAT
* * **
1562810 AAT AAT AAT AAT AAT AAT GAT ACT AAT AAT AAT AAT AAT AAT TTT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1562858 AAT AAT AAT AA
1 AAT AAT AAT AA
1562869 ATTTAAATGA
Statistics
Matches: 89, Mismatches: 12, Indels: 4
0.85 0.11 0.04
Matches are distributed among these distances:
3 83 0.93
4 6 0.07
ACGTcount: A:0.61, C:0.01, G:0.02, T:0.36
Consensus pattern (3 bp):
AAT
Found at i:1564631 original size:21 final size:22
Alignment explanation
Indices: 1564600--1564642 Score: 63
Period size: 21 Copynumber: 2.0 Consensus size: 22
1564590 GAAACCCCAC
1564600 TTTCTTCTCTTTCCAT-TTTCTT
1 TTTCTTCTCTTT-CATCTTTCTT
1564622 TTTC-TCTCTTTCATCTTTCTT
1 TTTCTTCTCTTTCATCTTTCTT
1564643 CTCCAAGATT
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
20 3 0.15
21 13 0.65
22 4 0.20
ACGTcount: A:0.05, C:0.28, G:0.00, T:0.67
Consensus pattern (22 bp):
TTTCTTCTCTTTCATCTTTCTT
Found at i:1565403 original size:17 final size:18
Alignment explanation
Indices: 1565381--1565422 Score: 68
Period size: 17 Copynumber: 2.4 Consensus size: 18
1565371 TTTTAATTTG
1565381 TTTATTTAATTATTAT-T
1 TTTATTTAATTATTATCT
*
1565398 TTTATTTAATTTTTATCT
1 TTTATTTAATTATTATCT
1565416 TTTATTT
1 TTTATTT
1565423 TTTTTAAAAA
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
17 15 0.65
18 8 0.35
ACGTcount: A:0.24, C:0.02, G:0.00, T:0.74
Consensus pattern (18 bp):
TTTATTTAATTATTATCT
Found at i:1565989 original size:12 final size:12
Alignment explanation
Indices: 1565972--1565999 Score: 56
Period size: 12 Copynumber: 2.3 Consensus size: 12
1565962 AAATACCTAA
1565972 AAATAATATTCT
1 AAATAATATTCT
1565984 AAATAATATTCT
1 AAATAATATTCT
1565996 AAAT
1 AAAT
1566000 CCTAATTAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 16 1.00
ACGTcount: A:0.54, C:0.07, G:0.00, T:0.39
Consensus pattern (12 bp):
AAATAATATTCT
Found at i:1566052 original size:24 final size:23
Alignment explanation
Indices: 1566008--1566052 Score: 54
Period size: 24 Copynumber: 1.9 Consensus size: 23
1565998 ATCCTAATTA
* **
1566008 AAATACTAAAACATATTTAAACT
1 AAATACTAAAACAAAGATAAACT
1566031 AAATACCTAAAACAAAGATAAA
1 AAATA-CTAAAACAAAGATAAA
1566053 ATATAAAAAT
Statistics
Matches: 18, Mismatches: 3, Indels: 1
0.82 0.14 0.05
Matches are distributed among these distances:
23 5 0.28
24 13 0.72
ACGTcount: A:0.62, C:0.13, G:0.02, T:0.22
Consensus pattern (23 bp):
AAATACTAAAACAAAGATAAACT
Found at i:1568011 original size:12 final size:12
Alignment explanation
Indices: 1567994--1568023 Score: 60
Period size: 12 Copynumber: 2.5 Consensus size: 12
1567984 CATTCTTGAG
1567994 TGTTCTTTTCTT
1 TGTTCTTTTCTT
1568006 TGTTCTTTTCTT
1 TGTTCTTTTCTT
1568018 TGTTCT
1 TGTTCT
1568024 AGAATTGTAC
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 18 1.00
ACGTcount: A:0.00, C:0.17, G:0.10, T:0.73
Consensus pattern (12 bp):
TGTTCTTTTCTT
Found at i:1573461 original size:22 final size:22
Alignment explanation
Indices: 1573435--1573518 Score: 91
Period size: 22 Copynumber: 3.8 Consensus size: 22
1573425 ATAGGGCAGA
1573435 GGGAATCGATACCCCCTTGAAG
1 GGGAATCGATACCCCCTTGAAG
*
1573457 GGGAA-CTGATTCCCCCTTTGAAG
1 GGGAATC-GATACCCCC-TTGAAG
* * *
1573480 GGGAACCGATTCCTCCC-TGTAG
1 GGGAATCGATACC-CCCTTGAAG
1573502 GGGAATCGATACCCCCT
1 GGGAATCGATACCCCCT
1573519 GGGGTTTCTG
Statistics
Matches: 53, Mismatches: 4, Indels: 10
0.79 0.06 0.15
Matches are distributed among these distances:
21 4 0.08
22 28 0.53
23 17 0.32
24 4 0.08
ACGTcount: A:0.23, C:0.30, G:0.26, T:0.21
Consensus pattern (22 bp):
GGGAATCGATACCCCCTTGAAG
Found at i:1573951 original size:15 final size:16
Alignment explanation
Indices: 1573928--1573960 Score: 50
Period size: 15 Copynumber: 2.1 Consensus size: 16
1573918 AAAAATTTAT
1573928 TTTTAAATT-ATTGTG
1 TTTTAAATTAATTGTG
*
1573943 TTTTGAATTAATTGTG
1 TTTTAAATTAATTGTG
1573959 TT
1 TT
1573961 ATTTACATGT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
15 8 0.50
16 8 0.50
ACGTcount: A:0.24, C:0.00, G:0.15, T:0.61
Consensus pattern (16 bp):
TTTTAAATTAATTGTG
Found at i:1575756 original size:23 final size:22
Alignment explanation
Indices: 1575730--1575811 Score: 83
Period size: 23 Copynumber: 3.6 Consensus size: 22
1575720 TCTTTTTGAT
*
1575730 TTAACAAAAATGGGGAGAAAGTG
1 TTAA-AAAAAGGGGGAGAAAGTG
**
1575753 TTAAAGTAAGGGGGAGAAAGTG
1 TTAAAAAAAGGGGGAGAAAGTG
* *
1575775 TTAAAATAAGGGGGGGGAAAGTG
1 TTAAAA-AAAGGGGGAGAAAGTG
*
1575798 TTAAAGTAAAGGGG
1 TTAAA-AAAAGGGG
1575812 AGTAGTATTT
Statistics
Matches: 48, Mismatches: 9, Indels: 4
0.79 0.15 0.07
Matches are distributed among these distances:
22 20 0.42
23 28 0.58
ACGTcount: A:0.43, C:0.01, G:0.38, T:0.18
Consensus pattern (22 bp):
TTAAAAAAAGGGGGAGAAAGTG
Found at i:1575766 original size:22 final size:22
Alignment explanation
Indices: 1575741--1575813 Score: 110
Period size: 22 Copynumber: 3.3 Consensus size: 22
1575731 TAACAAAAAT
1575741 GGGGAGAAAGTGTTAAAGTAAG
1 GGGGAGAAAGTGTTAAAGTAAG
*
1575763 GGGGAGAAAGTGTTAAAATAAGG
1 GGGGAGAAAGTGTTAAAGTAA-G
* *
1575786 GGGGGGAAAGTGTTAAAGTAAA
1 GGGGAGAAAGTGTTAAAGTAAG
1575808 GGGGAG
1 GGGGAG
1575814 TAGTATTTTT
Statistics
Matches: 45, Mismatches: 5, Indels: 2
0.87 0.10 0.04
Matches are distributed among these distances:
22 25 0.56
23 20 0.44
ACGTcount: A:0.40, C:0.00, G:0.44, T:0.16
Consensus pattern (22 bp):
GGGGAGAAAGTGTTAAAGTAAG
Found at i:1595828 original size:2 final size:2
Alignment explanation
Indices: 1595821--1595861 Score: 82
Period size: 2 Copynumber: 20.5 Consensus size: 2
1595811 TTGGTTTCTT
1595821 TA TA TA TA TA TA TA 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 TA TA TA TA TA TA TA T
1595862 CAATCATCAA
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:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:1600511 original size:41 final size:42
Alignment explanation
Indices: 1600434--1600526 Score: 125
Period size: 41 Copynumber: 2.2 Consensus size: 42
1600424 GAGGTATAGA
*
1600434 ACTTTCGATTCTCATCTAAAGTAGAACAGAAGGAAGCATCGC
1 ACTTTCGATTCTCATCTAAAGTAGAACAGAAGGAAGCATCAC
* * ** *
1600476 ACTTTCGATTCTCGTCT-ATGTAGAATGGAATGAAGCATCAC
1 ACTTTCGATTCTCATCTAAAGTAGAACAGAAGGAAGCATCAC
1600517 ACTTTCGATT
1 ACTTTCGATT
1600527 GCATCATACT
Statistics
Matches: 45, Mismatches: 6, Indels: 1
0.87 0.12 0.02
Matches are distributed among these distances:
41 29 0.64
42 16 0.36
ACGTcount: A:0.31, C:0.20, G:0.18, T:0.30
Consensus pattern (42 bp):
ACTTTCGATTCTCATCTAAAGTAGAACAGAAGGAAGCATCAC
Found at i:1600532 original size:17 final size:17
Alignment explanation
Indices: 1600510--1600543 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
1600500 ATGGAATGAA
1600510 GCATCACACTTTCGATT
1 GCATCACACTTTCGATT
*
1600527 GCATCATACTTTCGATT
1 GCATCACACTTTCGATT
1600544 CATACGGAAT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.24, C:0.26, G:0.12, T:0.38
Consensus pattern (17 bp):
GCATCACACTTTCGATT
Found at i:1604521 original size:51 final size:52
Alignment explanation
Indices: 1604408--1604523 Score: 144
Period size: 51 Copynumber: 2.2 Consensus size: 52
1604398 GTAATTATTG
* * * * * * *
1604408 AATAAAATAATAATAAATTGAAGATAATATTTTTGATTCTATCCTAATTCTT
1 AATAAAATAATAATAAACTAAAAATAATAGTTTTAACTCTATCCTAATTCCT
* *
1604460 AATAAAATAATAATAAACTAAAAATAAT-GTTTTAACTCTATCTTACTTCCT
1 AATAAAATAATAATAAACTAAAAATAATAGTTTTAACTCTATCCTAATTCCT
1604511 AATAAAATAATAA
1 AATAAAATAATAA
1604524 ATCTAATATT
Statistics
Matches: 55, Mismatches: 9, Indels: 1
0.85 0.14 0.02
Matches are distributed among these distances:
51 30 0.55
52 25 0.45
ACGTcount: A:0.49, C:0.09, G:0.03, T:0.38
Consensus pattern (52 bp):
AATAAAATAATAATAAACTAAAAATAATAGTTTTAACTCTATCCTAATTCCT
Found at i:1607379 original size:29 final size:30
Alignment explanation
Indices: 1607337--1607400 Score: 121
Period size: 29 Copynumber: 2.2 Consensus size: 30
1607327 TTAATGTATG
1607337 TATTTCGTTTTAATTTAGTGTCTAACG-TT
1 TATTTCGTTTTAATTTAGTGTCTAACGTTT
1607366 TATTTCGTTTTAATTTAGTGTCTAACGTTT
1 TATTTCGTTTTAATTTAGTGTCTAACGTTT
1607396 TATTT
1 TATTT
1607401 TATTGCTTAT
Statistics
Matches: 34, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
29 27 0.79
30 7 0.21
ACGTcount: A:0.20, C:0.09, G:0.12, T:0.58
Consensus pattern (30 bp):
TATTTCGTTTTAATTTAGTGTCTAACGTTT
Found at i:1612303 original size:43 final size:43
Alignment explanation
Indices: 1612255--1612339 Score: 161
Period size: 43 Copynumber: 2.0 Consensus size: 43
1612245 AAAATTTACC
1612255 AAAATTCTTCATTTCTTAGAGAACTTCCACATAAAACAAACAG
1 AAAATTCTTCATTTCTTAGAGAACTTCCACATAAAACAAACAG
*
1612298 AAAATTCTTCATTTCTTAGAGAACTTCCACATAAAACTAACA
1 AAAATTCTTCATTTCTTAGAGAACTTCCACATAAAACAAACA
1612340 TGAACAACAG
Statistics
Matches: 41, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
43 41 1.00
ACGTcount: A:0.44, C:0.21, G:0.06, T:0.29
Consensus pattern (43 bp):
AAAATTCTTCATTTCTTAGAGAACTTCCACATAAAACAAACAG
Found at i:1615185 original size:24 final size:22
Alignment explanation
Indices: 1615158--1615219 Score: 61
Period size: 24 Copynumber: 2.6 Consensus size: 22
1615148 CCGCTGGGAA
1615158 TTAATTTTTTTAAATAATAAATTT
1 TTAATTTTTTTAAATAATAAA--T
* *
1615182 TTAATATTTTTGAAGATGATAAAT
1 TTAAT-TTTTTTAA-ATAATAAAT
*
1615206 TAAATTTTTTTAAA
1 TTAATTTTTTTAAA
1615220 AAATTAATAA
Statistics
Matches: 32, Mismatches: 4, Indels: 6
0.76 0.10 0.14
Matches are distributed among these distances:
22 1 0.03
23 7 0.22
24 10 0.31
25 7 0.22
26 7 0.22
ACGTcount: A:0.42, C:0.00, G:0.05, T:0.53
Consensus pattern (22 bp):
TTAATTTTTTTAAATAATAAAT
Found at i:1620239 original size:15 final size:15
Alignment explanation
Indices: 1620216--1620245 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
1620206 CTAAATCATT
1620216 TTCCCTCTCTTCCCC
1 TTCCCTCTCTTCCCC
*
1620231 TTCCTTCTCTTCCCC
1 TTCCCTCTCTTCCCC
1620246 GTCAGTTTCT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.00, C:0.57, G:0.00, T:0.43
Consensus pattern (15 bp):
TTCCCTCTCTTCCCC
Found at i:1620672 original size:16 final size:16
Alignment explanation
Indices: 1620645--1620688 Score: 70
Period size: 16 Copynumber: 2.8 Consensus size: 16
1620635 TCAGATCAGT
*
1620645 TCAATAACAAGTTGAA
1 TCAATTACAAGTTGAA
*
1620661 TCATTTACAAGTTGAA
1 TCAATTACAAGTTGAA
1620677 TCAATTACAAGT
1 TCAATTACAAGT
1620689 CAAGTTCATA
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 25 1.00
ACGTcount: A:0.43, C:0.14, G:0.11, T:0.32
Consensus pattern (16 bp):
TCAATTACAAGTTGAA
Found at i:1622546 original size:23 final size:24
Alignment explanation
Indices: 1622509--1622559 Score: 68
Period size: 23 Copynumber: 2.2 Consensus size: 24
1622499 CATTTTCAGG
* *
1622509 TTTAATTTCAATTTCTTTATTTTA
1 TTTAATATCAATTTCTTCATTTTA
*
1622533 TTTAATAT-AATTTCTTCATTTTC
1 TTTAATATCAATTTCTTCATTTTA
1622556 TTTA
1 TTTA
1622560 TAATCTTTAT
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
23 17 0.71
24 7 0.29
ACGTcount: A:0.25, C:0.10, G:0.00, T:0.65
Consensus pattern (24 bp):
TTTAATATCAATTTCTTCATTTTA
Found at i:1626773 original size:191 final size:191
Alignment explanation
Indices: 1626433--1626807 Score: 540
Period size: 191 Copynumber: 2.0 Consensus size: 191
1626423 TTATCGCCAT
* * * **
1626433 TGAATTTAATAAACGGCACAGAATCGGTTTCGAGTATTTTTAATAAACAGCATAGAAACATCATT
1 TGAATTTAATAAACGGCACAGAATCGGTTTCGACTATTTATAATAAACAGCACAGAAACATCACG
* * *
1626498 CATGATGTTGTTGCAGAGAATTATATTCCATGGATGTATGTCACCACTTGTGTGTCCTTTGGCAT
66 CATGATGTTGTAGCACAGAATTATATTCCATAGATGTATGTCACCACTTGTGTGTCCTTTGGCAT
* * *
1626563 CTACTCTGCAATTACTTTGTTTCACTTAACTGAAAGATTTGCCTGTATTTGTTCTTTTAAG
131 CTACTCTACAATCACTTTGTTTCACTTAACTGAAAGATTTGACTGTATTTGTTCTTTTAAG
*
1626624 TGAATTTTAATAAACGGCACAGAATCGGTTTCGACTATTTATAATCAAC-GCACAGAAACATCAC
1 TGAA-TTTAATAAACGGCACAGAATCGGTTTCGACTATTTATAATAAACAGCACAGAAACATCAC
* *
1626688 GCATGATGTTGTAGCACAGAATTTTATGT-CATAGATGTATGTCTCCACTTGTGTGTCCTTTGGC
65 GCATGATGTTGTAGCACAGAATTATAT-TCCATAGATGTATGTCACCACTTGTGTGTCCTTTGGC
* * * *
1626752 ATCTAAGT-TACAATCACTTTGTTTCACTTAGCTGGAAGATTTGATTGTATTTGTTC
129 ATCT-ACTCTACAATCACTTTGTTTCACTTAACTGAAAGATTTGACTGTATTTGTTC
1626808 ATTTCAAGAA
Statistics
Matches: 163, Mismatches: 18, Indels: 6
0.87 0.10 0.03
Matches are distributed among these distances:
191 119 0.73
192 44 0.27
ACGTcount: A:0.28, C:0.17, G:0.18, T:0.37
Consensus pattern (191 bp):
TGAATTTAATAAACGGCACAGAATCGGTTTCGACTATTTATAATAAACAGCACAGAAACATCACG
CATGATGTTGTAGCACAGAATTATATTCCATAGATGTATGTCACCACTTGTGTGTCCTTTGGCAT
CTACTCTACAATCACTTTGTTTCACTTAACTGAAAGATTTGACTGTATTTGTTCTTTTAAG
Found at i:1627018 original size:213 final size:215
Alignment explanation
Indices: 1626624--1627060 Score: 630
Period size: 213 Copynumber: 2.0 Consensus size: 215
1626614 TTCTTTTAAG
* * *
1626624 TGAATTTTAATAAACGGCACAGAATCGGTTTCGACTATTTATAATCAACGCACAGAAACATCACG
1 TGAATTTTAATAAACGGCACAGAATCAGTTTCAACTATTTATAATAAACGCACAGAAACATCACG
*
1626689 CATGATGTTGTAGCACAGAATTTTATGTCATAGATGTATGTCTCCACTTGTGTGTCCTTTGGCAT
66 CATGACGTTGTAGCACAGAATTTTATGTCATAGATGTATGTCTCCACTTGTGTGTCCTTTGGCAT
* * * * *
1626754 CTAAGTTACAATCACTTTGTTTCACTTAGCTGGAAGATTTGATTGTATTTGTTCATTTCAAGAAC
131 CTAAGTTACAATCACTTTGTTTCACTAAGCCGAAAGATCTGATTATATTTGTTCATTTCAAGAAC
*
1626819 TTTTGGCTCTTCATTTCTGT
196 TTTTGGCTCTTCATTCCTGT
* * * *
1626839 TGAATTTTAATAAA-GGACACAGAATCAGTTTCAAGTATTTTTAATAAATGGTACAGAAACATCA
1 TGAATTTTAATAAACGG-CACAGAATCAGTTTCAACTATTTATAATAAA-CGCACAGAAACATCA
* * * *
1626903 TGCATGACG-T-T-GCAGAGAATTTTATGTCATAGATGTATGTCTCCACTTGTTTTTCCTTTGGC
64 CGCATGACGTTGTAGCACAGAATTTTATGTCATAGATGTATGTCTCCACTTGTGTGTCCTTTGGC
* * * *
1626965 ATCTAAGTTGCATTCACTTTGTTTCCCTAAGCCGAAAGATCTGCTTATATTTGTTCATTTCAAGA
129 ATCTAAGTTACAATCACTTTGTTTCACTAAGCCGAAAGATCTGATTATATTTGTTCATTTCAAGA
1627030 ACTTTTGGCTCTTCATTCCTGT
194 ACTTTTGGCTCTTCATTCCTGT
1627052 TGAATTTTA
1 TGAATTTTA
1627061 GCTAGTTCGG
Statistics
Matches: 198, Mismatches: 22, Indels: 6
0.88 0.10 0.03
Matches are distributed among these distances:
213 134 0.68
214 3 0.02
215 41 0.21
216 20 0.10
ACGTcount: A:0.27, C:0.17, G:0.16, T:0.39
Consensus pattern (215 bp):
TGAATTTTAATAAACGGCACAGAATCAGTTTCAACTATTTATAATAAACGCACAGAAACATCACG
CATGACGTTGTAGCACAGAATTTTATGTCATAGATGTATGTCTCCACTTGTGTGTCCTTTGGCAT
CTAAGTTACAATCACTTTGTTTCACTAAGCCGAAAGATCTGATTATATTTGTTCATTTCAAGAAC
TTTTGGCTCTTCATTCCTGT
Found at i:1628563 original size:51 final size:51
Alignment explanation
Indices: 1628486--1628758 Score: 282
Period size: 51 Copynumber: 5.6 Consensus size: 51
1628476 CTAGTCAACA
* * *
1628486 ATGAAACTCTGGTCGAAGTACTCAAGGAGAGCAAACACCATACCATTGGTG
1 ATGAAACTCTGGTCGAAGTACCCAAGGAGAGCAAACACAATACCATTGGCG
* * * *
1628537 ATGAAACTCTGGTCGAAGTACCCAAGGAGAGC-AA-GC-AT---ATCGACA
1 ATGAAACTCTGGTCGAAGTACCCAAGGAGAGCAAACACAATACCATTGGCG
* * *
1628582 ATGAAACTCTGGTTGAAGTACCCAAGGACAGCAAACACAATACCATTGGTG
1 ATGAAACTCTGGTCGAAGTACCCAAGGAGAGCAAACACAATACCATTGGCG
* * * * * *
1628633 ATGAAAATCCGGTCGAAGTACCCAAGGAGAGC-AA-GC-AT---ATAGACA
1 ATGAAACTCTGGTCGAAGTACCCAAGGAGAGCAAACACAATACCATTGGCG
*
1628678 ATGAAACTCTAGTCGAAGTACCCAAGGAGAGCAAACACAATACCATTGGCG
1 ATGAAACTCTGGTCGAAGTACCCAAGGAGAGCAAACACAATACCATTGGCG
* **
1628729 ATGAAACACCAGTCGAAGTACCCAAGGAGA
1 ATGAAACTCTGGTCGAAGTACCCAAGGAGA
1628759 TCAAGCATAT
Statistics
Matches: 179, Mismatches: 31, Indels: 24
0.76 0.13 0.10
Matches are distributed among these distances:
45 65 0.36
46 4 0.02
47 2 0.01
48 8 0.04
49 2 0.01
50 4 0.02
51 94 0.53
ACGTcount: A:0.39, C:0.22, G:0.23, T:0.16
Consensus pattern (51 bp):
ATGAAACTCTGGTCGAAGTACCCAAGGAGAGCAAACACAATACCATTGGCG
Found at i:1628647 original size:96 final size:96
Alignment explanation
Indices: 1628483--1628768 Score: 457
Period size: 96 Copynumber: 3.0 Consensus size: 96
1628473 TCGCTAGTCA
* * * *
1628483 ACAATGAAACTCTGGTCGAAGTACTCAAGGAGAGCAAACACCATACCATTGGTGATGAAACTCTG
1 ACAATGAAACTCTGGTCGAAGTACCCAAGGAGAGCAAACACAATACCATTGGTGATGAAAATCCG
*
1628548 GTCGAAGTACCCAAGGAGAGCAAGCATATCG
66 GTCGAAGTACCCAAGGAGAGCAAGCATATAG
* *
1628579 ACAATGAAACTCTGGTTGAAGTACCCAAGGACAGCAAACACAATACCATTGGTGATGAAAATCCG
1 ACAATGAAACTCTGGTCGAAGTACCCAAGGAGAGCAAACACAATACCATTGGTGATGAAAATCCG
1628644 GTCGAAGTACCCAAGGAGAGCAAGCATATAG
66 GTCGAAGTACCCAAGGAGAGCAAGCATATAG
* *
1628675 ACAATGAAACTCTAGTCGAAGTACCCAAGGAGAGCAAACACAATACCATTGGCGATGAAACA-CC
1 ACAATGAAACTCTGGTCGAAGTACCCAAGGAGAGCAAACACAATACCATTGGTGATGAAA-ATCC
* *
1628739 AGTCGAAGTACCCAAGGAGATCAAGCATAT
65 GGTCGAAGTACCCAAGGAGAGCAAGCATAT
1628769 TGCCATCGAC
Statistics
Matches: 176, Mismatches: 13, Indels: 2
0.92 0.07 0.01
Matches are distributed among these distances:
96 175 0.99
97 1 0.01
ACGTcount: A:0.39, C:0.22, G:0.22, T:0.16
Consensus pattern (96 bp):
ACAATGAAACTCTGGTCGAAGTACCCAAGGAGAGCAAACACAATACCATTGGTGATGAAAATCCG
GTCGAAGTACCCAAGGAGAGCAAGCATATAG
Found at i:1630528 original size:32 final size:32
Alignment explanation
Indices: 1630471--1630533 Score: 90
Period size: 32 Copynumber: 2.0 Consensus size: 32
1630461 GATCAATATC
*
1630471 GGGTCGGGTTAATACCATATAGGTTGATTTTT
1 GGGTCGGGTTAATACCAGATAGGTTGATTTTT
* * *
1630503 GGGTCGGGTTAATATCGGATCGGTTGATTTT
1 GGGTCGGGTTAATACCAGATAGGTTGATTTT
1630534 CGGTTTAGGT
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
32 27 1.00
ACGTcount: A:0.19, C:0.10, G:0.32, T:0.40
Consensus pattern (32 bp):
GGGTCGGGTTAATACCAGATAGGTTGATTTTT
Found at i:1630804 original size:25 final size:25
Alignment explanation
Indices: 1630770--1630822 Score: 106
Period size: 25 Copynumber: 2.1 Consensus size: 25
1630760 ATACGTGTTA
1630770 GATTTTGTTATCAAAATTTTATATT
1 GATTTTGTTATCAAAATTTTATATT
1630795 GATTTTGTTATCAAAATTTTATATT
1 GATTTTGTTATCAAAATTTTATATT
1630820 GAT
1 GAT
1630823 CTCGTACAAA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 28 1.00
ACGTcount: A:0.32, C:0.04, G:0.09, T:0.55
Consensus pattern (25 bp):
GATTTTGTTATCAAAATTTTATATT
Found at i:1630838 original size:23 final size:25
Alignment explanation
Indices: 1630776--1630840 Score: 89
Period size: 25 Copynumber: 2.7 Consensus size: 25
1630766 GTTAGATTTT
* *
1630776 GTTATCAAAATTTTATATTGATTTT
1 GTTATCAAAATTTTATATTGATCTC
1630801 GTTATCAAAATTTTATATTGATCTC
1 GTTATCAAAATTTTATATTGATCTC
*
1630826 G-TA-CAAAAATTTATA
1 GTTATCAAAATTTTATA
1630841 ACGAGAACTA
Statistics
Matches: 37, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
23 11 0.30
24 2 0.05
25 24 0.65
ACGTcount: A:0.37, C:0.08, G:0.08, T:0.48
Consensus pattern (25 bp):
GTTATCAAAATTTTATATTGATCTC
Found at i:1631166 original size:19 final size:19
Alignment explanation
Indices: 1631139--1631198 Score: 56
Period size: 18 Copynumber: 3.3 Consensus size: 19
1631129 TCTTAAACTT
*
1631139 TATATTATTTTATTATAAA
1 TATAATATTTTATTATAAA
*
1631158 TATAATATTTT-TAATAAA
1 TATAATATTTTATTATAAA
*
1631176 TTATCA-ATTTTATT-TAAA
1 -TATAATATTTTATTATAAA
1631194 T-TAAT
1 TATAAT
1631199 TTATTATTGA
Statistics
Matches: 33, Mismatches: 5, Indels: 8
0.72 0.11 0.17
Matches are distributed among these distances:
16 2 0.06
17 1 0.03
18 15 0.45
19 15 0.45
ACGTcount: A:0.43, C:0.02, G:0.00, T:0.55
Consensus pattern (19 bp):
TATAATATTTTATTATAAA
Found at i:1631298 original size:16 final size:15
Alignment explanation
Indices: 1631279--1631322 Score: 52
Period size: 16 Copynumber: 2.8 Consensus size: 15
1631269 TCGGATTAAA
1631279 TTCGGTTCAGGTTGCT
1 TTCGGTTC-GGTTGCT
**
1631295 TTCGGATGGGGTTGCT
1 TTCGG-TTCGGTTGCT
1631311 TTCGGTTCGGTT
1 TTCGGTTCGGTT
1631323 TAATTTCGAT
Statistics
Matches: 23, Mismatches: 4, Indels: 3
0.77 0.13 0.10
Matches are distributed among these distances:
15 5 0.22
16 17 0.74
17 1 0.04
ACGTcount: A:0.05, C:0.16, G:0.36, T:0.43
Consensus pattern (15 bp):
TTCGGTTCGGTTGCT
Found at i:1632009 original size:23 final size:23
Alignment explanation
Indices: 1631983--1632030 Score: 69
Period size: 23 Copynumber: 2.1 Consensus size: 23
1631973 ATAAAGTACA
*
1631983 ATAACATACTAGGTAGCGCTTAT
1 ATAACATAATAGGTAGCGCTTAT
**
1632006 ATAATGTAATAGGTAGCGCTTAT
1 ATAACATAATAGGTAGCGCTTAT
1632029 AT
1 AT
1632031 TTACCTATTT
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
23 22 1.00
ACGTcount: A:0.35, C:0.12, G:0.19, T:0.33
Consensus pattern (23 bp):
ATAACATAATAGGTAGCGCTTAT
Found at i:1632436 original size:21 final size:22
Alignment explanation
Indices: 1632411--1632462 Score: 77
Period size: 23 Copynumber: 2.3 Consensus size: 22
1632401 ACACTTTACA
*
1632411 ATATAACCACTACCTATTACATT
1 ATATAAACA-TACCTATTACATT
1632434 ATATAAACGATACCTATTACATT
1 ATATAAAC-ATACCTATTACATT
1632457 ATATAA
1 ATATAA
1632463 GGGCTATATA
Statistics
Matches: 27, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
23 26 0.96
24 1 0.04
ACGTcount: A:0.44, C:0.19, G:0.02, T:0.35
Consensus pattern (22 bp):
ATATAAACATACCTATTACATT
Found at i:1632935 original size:39 final size:39
Alignment explanation
Indices: 1632881--1633006 Score: 234
Period size: 39 Copynumber: 3.2 Consensus size: 39
1632871 TCAAGTTGTA
1632881 GATTTTGATTTCCTTTTGCTTGGCATCATATGAGATTTG
1 GATTTTGATTTCCTTTTGCTTGGCATCATATGAGATTTG
1632920 GATTTTGATTTCCTTTTGCTTGGCATCATATGAGATTTG
1 GATTTTGATTTCCTTTTGCTTGGCATCATATGAGATTTG
* *
1632959 GATTTTGATTTCCTTTTGCTTGGCACCATATGAGCTTTG
1 GATTTTGATTTCCTTTTGCTTGGCATCATATGAGATTTG
1632998 GATTTTGAT
1 GATTTTGAT
1633007 GAGCATCGGA
Statistics
Matches: 85, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
39 85 1.00
ACGTcount: A:0.17, C:0.13, G:0.21, T:0.48
Consensus pattern (39 bp):
GATTTTGATTTCCTTTTGCTTGGCATCATATGAGATTTG
Found at i:1633286 original size:18 final size:18
Alignment explanation
Indices: 1633263--1633299 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
1633253 GCCGAAATAT
1633263 ATTGAAATTCAAACTCAA
1 ATTGAAATTCAAACTCAA
* *
1633281 ATTGAAATTTAAATTCAA
1 ATTGAAATTCAAACTCAA
1633299 A
1 A
1633300 CTCCAATTAC
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.51, C:0.11, G:0.05, T:0.32
Consensus pattern (18 bp):
ATTGAAATTCAAACTCAA
Found at i:1633577 original size:25 final size:25
Alignment explanation
Indices: 1633548--1633598 Score: 84
Period size: 25 Copynumber: 2.0 Consensus size: 25
1633538 TTAATCCAAA
*
1633548 TAATGTACCCATAACAATGTTCAAT
1 TAATGTACCCACAACAATGTTCAAT
*
1633573 TAATGTACCCACAACAATGTTTAAT
1 TAATGTACCCACAACAATGTTCAAT
1633598 T
1 T
1633599 GATTTGTTGT
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
25 24 1.00
ACGTcount: A:0.39, C:0.20, G:0.08, T:0.33
Consensus pattern (25 bp):
TAATGTACCCACAACAATGTTCAAT
Found at i:1633903 original size:23 final size:23
Alignment explanation
Indices: 1633877--1633939 Score: 90
Period size: 23 Copynumber: 2.7 Consensus size: 23
1633867 ATATAACCAC
1633877 TACCTATTACATTATATAAACGA
1 TACCTATTACATTATATAAACGA
** *
1633900 TACCTATTACATTATATAAGGGC
1 TACCTATTACATTATATAAACGA
*
1633923 TACCTATTACATCATAT
1 TACCTATTACATTATAT
1633940 GTTTACCTAT
Statistics
Matches: 36, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
23 36 1.00
ACGTcount: A:0.38, C:0.19, G:0.06, T:0.37
Consensus pattern (23 bp):
TACCTATTACATTATATAAACGA
Found at i:1634320 original size:21 final size:22
Alignment explanation
Indices: 1634295--1634346 Score: 77
Period size: 23 Copynumber: 2.3 Consensus size: 22
1634285 ACACTTTACA
*
1634295 ATATAACCACTACCTATTACATT
1 ATATAAACA-TACCTATTACATT
1634318 ATATAAACGATACCTATTACATT
1 ATATAAAC-ATACCTATTACATT
1634341 ATATAA
1 ATATAA
1634347 GGGCTACCTA
Statistics
Matches: 27, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
23 26 0.96
24 1 0.04
ACGTcount: A:0.44, C:0.19, G:0.02, T:0.35
Consensus pattern (22 bp):
ATATAAACATACCTATTACATT
Found at i:1634331 original size:23 final size:23
Alignment explanation
Indices: 1634305--1634367 Score: 90
Period size: 23 Copynumber: 2.7 Consensus size: 23
1634295 ATATAACCAC
1634305 TACCTATTACATTATATAAACGA
1 TACCTATTACATTATATAAACGA
** *
1634328 TACCTATTACATTATATAAGGGC
1 TACCTATTACATTATATAAACGA
*
1634351 TACCTATTACATCATAT
1 TACCTATTACATTATAT
1634368 GTTTACCTAT
Statistics
Matches: 36, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
23 36 1.00
ACGTcount: A:0.38, C:0.19, G:0.06, T:0.37
Consensus pattern (23 bp):
TACCTATTACATTATATAAACGA
Found at i:1634436 original size:428 final size:429
Alignment explanation
Indices: 1633630--1634464 Score: 1602
Period size: 428 Copynumber: 1.9 Consensus size: 429
1633620 TTTGAATTAT
1633630 TTGATTTAATAATTTCATTTGCACAAAAAATTATTTGATTGTTTTGATATTTTATAAAATAATAT
1 TTGATTTAATAATTTCATTTGCACAAAAAATTATTTGATTGTTTTGATATTTTATAAAATAATAT
* *
1633695 TTAGAATTTTTAATTTAATAATAATATATATCGTAACGTAAAAAATAAATCATTATACGCCTATA
66 TTAGAATTTTTAATTTAATAATAATATATACCGTAACGTAAAAAATAAATCATTAGACGCCTATA
1633760 ATTACTAAATTAATATCTTAAAACTCACTCAAAAGATAACCTTAAATTAATGTTTTCCACAGTGA
131 ATTACTAAATTAATATCTTAAAACTCACTCAAAAGATAACCTTAAATTAATGTTTTCCACAGTGA
1633825 AAAAAGTATGGACACTTTTATAAAAAGGATAGACACCTTACAATATAACCACTACCTATTACATT
196 AAAAAGTATGGACACTTTTATAAAAAGGATAGACACCTTACAATATAACCACTACCTATTACATT
1633890 ATATAAACGATACCTATTACATTATATAAGGGCTACCTATTACATCATATGTTTACCTATTATAT
261 ATATAAACGATACCTATTACATTATATAAGGGCTACCTATTACATCATATGTTTACCTATTATAT
1633955 TGAAAGTGTCCATACTTTTATAAAAAGGATCGATACTTTTTTTAAAACTTATGTAATTTATGTTT
326 TGAAAGTGTCCATACTTTTATAAAAAGGATCGATACTTTTTTTAAAACTTATGTAATTTATGTTT
1634020 CAATTTTTTTAACAGTGTTTCATGTTTTCCACCTACAATA
391 CAA-TTTTTTAACAGTGTTTCATGTTTTCCACCTACAATA
* *
1634060 TTGATTT-ATAATTTCATTTGCACAAAAAATTATTTGATTGTTTTTATATTTTATAAAATATTAT
1 TTGATTTAATAATTTCATTTGCACAAAAAATTATTTGATTGTTTTGATATTTTATAAAATAATAT
1634124 TTAGAATTTTTAATTTAATAATAATATATACCGTAACGT-AAAAATAAATCATTAGACGCCTATA
66 TTAGAATTTTTAATTTAATAATAATATATACCGTAACGTAAAAAATAAATCATTAGACGCCTATA
1634188 ATTACTAAATTAATATCTTAAAACTCACTCAAAAGATAACCTTAAATTAATGTTTTCCACAGTGA
131 ATTACTAAATTAATATCTTAAAACTCACTCAAAAGATAACCTTAAATTAATGTTTTCCACAGTGA
*
1634253 AAAAAGTATGGACACTTTTATAAAAAGGATAGACACTTTACAATATAACCACTACCTATTACATT
196 AAAAAGTATGGACACTTTTATAAAAAGGATAGACACCTTACAATATAACCACTACCTATTACATT
1634318 ATATAAACGATACCTATTACATTATATAAGGGCTACCTATTACATCATATGTTTACCTATTATAT
261 ATATAAACGATACCTATTACATTATATAAGGGCTACCTATTACATCATATGTTTACCTATTATAT
1634383 TGAAAGTGTCCATACTTTTATAAAAAGGATCGATACTTTTTTTAAAACTTATGTAATTTATGTTT
326 TGAAAGTGTCCATACTTTTATAAAAAGGATCGATACTTTTTTTAAAACTTATGTAATTTATGTTT
1634448 CAATTTTTTAACAGTGT
391 CAATTTTTTAACAGTGT
1634465 ACTGCGAATT
Statistics
Matches: 400, Mismatches: 5, Indels: 3
0.98 0.01 0.01
Matches are distributed among these distances:
427 14 0.04
428 286 0.71
429 93 0.23
430 7 0.02
ACGTcount: A:0.39, C:0.13, G:0.08, T:0.39
Consensus pattern (429 bp):
TTGATTTAATAATTTCATTTGCACAAAAAATTATTTGATTGTTTTGATATTTTATAAAATAATAT
TTAGAATTTTTAATTTAATAATAATATATACCGTAACGTAAAAAATAAATCATTAGACGCCTATA
ATTACTAAATTAATATCTTAAAACTCACTCAAAAGATAACCTTAAATTAATGTTTTCCACAGTGA
AAAAAGTATGGACACTTTTATAAAAAGGATAGACACCTTACAATATAACCACTACCTATTACATT
ATATAAACGATACCTATTACATTATATAAGGGCTACCTATTACATCATATGTTTACCTATTATAT
TGAAAGTGTCCATACTTTTATAAAAAGGATCGATACTTTTTTTAAAACTTATGTAATTTATGTTT
CAATTTTTTAACAGTGTTTCATGTTTTCCACCTACAATA
Found at i:1637366 original size:22 final size:23
Alignment explanation
Indices: 1637335--1637377 Score: 70
Period size: 22 Copynumber: 1.9 Consensus size: 23
1637325 TTCCACAGTG
1637335 AAAAAAGTATCGACAC-TTTTAT
1 AAAAAAGTATCGACACATTTTAT
*
1637357 AAAAAGGTATCGACACATTTT
1 AAAAAAGTATCGACACATTTT
1637378 TATACCGGTT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
22 15 0.79
23 4 0.21
ACGTcount: A:0.44, C:0.14, G:0.12, T:0.30
Consensus pattern (23 bp):
AAAAAAGTATCGACACATTTTAT
Found at i:1637873 original size:183 final size:183
Alignment explanation
Indices: 1637373--1638066 Score: 1232
Period size: 183 Copynumber: 3.8 Consensus size: 183
1637363 GTATCGACAC
1637373 ATTTTTATACCGGTTATATTACAAAATTATCTATTACATTATAAATCTGGGTTCCGATGTGTAAA
1 ATTTTTATACCGGTTATATTACAAAATTATCTATTACATTATAAATCTGGGTTCCGATGTGTAAA
1637438 TGTCGACACTTTTTTAAATGGTATCGACACATTTTTCTTCCAATCTGAACATAAAGTACCGACAC
66 TGTCGACACTTTTTTAAATGGTATCGACACATTTTTCTTCCAATCTGAACATAAAGTACCGACAC
1637503 AATATTAGAAAGTGTCGATAAAGGTTGTAGACCTATTCGCTCATAAAACCGGT
131 AATATTAGAAAGTGTCGATAAAGGTTGTAGACCTATTCGCTCATAAAACCGGT
*
1637556 ATTTTTATA-CGGTTATATTACAAAATTATCTATTACATTATAAATTTGGGTTCCGATGTGTAAA
1 ATTTTTATACCGGTTATATTACAAAATTATCTATTACATTATAAATCTGGGTTCCGATGTGTAAA
1637620 TGTCGACACTTTTTTAAATGGTATCGACACATTTTTCTTCCAATCTGAACATAAAGTACCGACAC
66 TGTCGACACTTTTTTAAATGGTATCGACACATTTTTCTTCCAATCTGAACATAAAGTACCGACAC
1637685 AATATTAGAAAGTGTCGATAAAGGTTGTAGACCTATTCGCTCATAAAACCGGT
131 AATATTAGAAAGTGTCGATAAAGGTTGTAGACCTATTCGCTCATAAAACCGGT
*
1637738 ATTTTTATACCGGTTATATTACAAAATTATCTATTACATTATAAATATGGGTTCCGATGTGTAAA
1 ATTTTTATACCGGTTATATTACAAAATTATCTATTACATTATAAATCTGGGTTCCGATGTGTAAA
*
1637803 TGTCGACACTTTTTTAAATGGTATCGACACATTTTTCTTCCAATCTGGACATAAAGTACCGACAC
66 TGTCGACACTTTTTTAAATGGTATCGACACATTTTTCTTCCAATCTGAACATAAAGTACCGACAC
*
1637868 AATATTAGAAAGTGTCGATATAGGTTGTAGACCTATTCGCTCATAAAACCGGT
131 AATATTAGAAAGTGTCGATAAAGGTTGTAGACCTATTCGCTCATAAAACCGGT
* *
1637921 ATATTTATACCGGTTATATTACAAAATTATCTATTACATTATAAATCTGGGTTCCGATGTTTTTT
1 ATTTTTATACCGGTTATATTACAAAATTATCTATTACATTATAAATCTGGGTTCCGATG---TGT
* * * * *
1637986 CAA--TCGACACTTTTTTAAATGGTATCGACACATTTTTCTTTCATTCTGGACATAAAGTACAGA
63 AAATGTCGACACTTTTTTAAATGGTATCGACACATTTTTCTTCCAATCTGAACATAAAGTACCGA
*
1638049 CACAATATTAAAAAGTGT
128 CACAATATTAGAAAGTGT
1638067 GAAAACTTTG
Statistics
Matches: 495, Mismatches: 12, Indels: 7
0.96 0.02 0.01
Matches are distributed among these distances:
182 181 0.37
183 236 0.48
184 74 0.15
186 4 0.01
ACGTcount: A:0.33, C:0.16, G:0.14, T:0.36
Consensus pattern (183 bp):
ATTTTTATACCGGTTATATTACAAAATTATCTATTACATTATAAATCTGGGTTCCGATGTGTAAA
TGTCGACACTTTTTTAAATGGTATCGACACATTTTTCTTCCAATCTGAACATAAAGTACCGACAC
AATATTAGAAAGTGTCGATAAAGGTTGTAGACCTATTCGCTCATAAAACCGGT
Found at i:1639271 original size:3 final size:3
Alignment explanation
Indices: 1639263--1639334 Score: 63
Period size: 3 Copynumber: 24.0 Consensus size: 3
1639253 ACTTGTTTGG
* * * * **
1639263 ATC ATC ATC TTC ATC ATC ATC ATC ATC ATC GTA ATC ATC TTC ATC GCC
1 ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC
* * *
1639311 AGC TTC ATC GTC ATC ATC ATC ATC
1 ATC ATC ATC ATC ATC ATC ATC ATC
1639335 GTCGTCAGCT
Statistics
Matches: 52, Mismatches: 17, Indels: 0
0.75 0.25 0.00
Matches are distributed among these distances:
3 52 1.00
ACGTcount: A:0.26, C:0.33, G:0.06, T:0.35
Consensus pattern (3 bp):
ATC
Found at i:1639348 original size:15 final size:15
Alignment explanation
Indices: 1639264--1639349 Score: 70
Period size: 15 Copynumber: 5.9 Consensus size: 15
1639254 CTTGTTTGGA
* *
1639264 TCATCATCTTCATCA
1 TCATCAGCTTCATCG
* *
1639279 TCATCATCATCATCG
1 TCATCAGCTTCATCG
* *
1639294 TAATCATCTTCATCG
1 TCATCAGCTTCATCG
1639309 -C--CAGCTTCATCG
1 TCATCAGCTTCATCG
* *
1639321 TCATCATCATCATCG
1 TCATCAGCTTCATCG
*
1639336 TCGTCAGCTTCATC
1 TCATCAGCTTCATC
1639350 TTCTGCGACC
Statistics
Matches: 57, Mismatches: 11, Indels: 6
0.77 0.15 0.08
Matches are distributed among these distances:
12 10 0.18
13 1 0.02
15 46 0.81
ACGTcount: A:0.23, C:0.34, G:0.08, T:0.35
Consensus pattern (15 bp):
TCATCAGCTTCATCG
Found at i:1641822 original size:198 final size:199
Alignment explanation
Indices: 1640807--1641968 Score: 2211
Period size: 198 Copynumber: 5.9 Consensus size: 199
1640797 TATTTAAATT
1640807 AGTATCGACACAAACTATATTAGTGTCGACACATTATTTAGACATATTCTCTCATAAAACCGGTA
1 AGTATCGACACAAACTATATTAGTGTCGACACATTATTTAGACATATTCTCTCATAAAACCGGTA
1640872 TAATTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGA-TTTGGG
66 TAATTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGG
1640936 ATCGACACTTTTTATATATGGATCGACACTTTATGGGTGCACCTTGTTTTCCATTCATTCTGGGA
131 ATCGACACTTTTTATATATGGATCGACACTTTATGGGTGCACCTTGTTTTCCATTCATTCTGGGA
1641001 AAAA
196 AAAA
1641005 AGTATCGACACAAACTATATTAGTGTCGACACATTATTTAGACATATTCTCTCATAAAACCGGTA
1 AGTATCGACACAAACTATATTAGTGTCGACACATTATTTAGACATATTCTCTCATAAAACCGGTA
1641070 TAATTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGG
66 TAATTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGG
1641135 ATCGACACTTTTTATATATGGATCGACACTTTATGGGTGCACCTTGTTTTCCATTCATTCTGGGA
131 ATCGACACTTTTTATATATGGATCGACACTTTATGGGTGCACCTTGTTTTCCATTCATTCTGGGA
1641200 AAAA
196 AAAA
*
1641204 AGTATCGACGCAAACTATATTAGTGTCGACACATTATTTAGACATATTCTCTCATAAAACCGGTA
1 AGTATCGACACAAACTATATTAGTGTCGACACATTATTTAGACATATTCTCTCATAAAACCGGTA
1641269 TAATTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGG
66 TAATTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGG
1641334 ATCGACACTTTTTATATATGGATCGACACTTTATGGGTGCACCTTG-TTTCCATTCATTCTGGGA
131 ATCGACACTTTTTATATATGGATCGACACTTTATGGGTGCACCTTGTTTTCCATTCATTCTGGGA
1641398 AAAA
196 AAAA
1641402 AGTATCGACACAAACTATATTAGTGTCG--ACATTATTTAGACATATTCTCTCATAAAA-CGGTA
1 AGTATCGACACAAACTATATTAGTGTCGACACATTATTTAGACATATTCTCTCATAAAACCGGTA
1641464 TAATTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGA-TTTGGG
66 TAATTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGG
1641528 ATCGACAC-TTTTATATATGGATCGACAC-TTATGGGTGCACCTTGTTTTCCATTCATTCTGGGA
131 ATCGACACTTTTTATATATGGATCGACACTTTATGGGTGCACCTTGTTTTCCATTCATTCTGGGA
1641591 AAAA
196 AAAA
1641595 AGTATCGACACAAACTATATTAGTGTCGACACATTATTTAGACATATTCTCTCATAAAACCGGTA
1 AGTATCGACACAAACTATATTAGTGTCGACACATTATTTAGACATATTCTCTCATAAAACCGGTA
1641660 TAATTGTACCGGTTAGATTGAAAAATTACATATTACATTATAC-TTTGGGTTCGATGATTTTGGG
66 TAATTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGG
1641724 ATCGACACTTTTTATATATGGATCGACACTTTATGGGTGCACCTTGTTTTCCATTCATTCTGGGA
131 ATCGACACTTTTTATATATGGATCGACACTTTATGGGTGCACCTTGTTTTCCATTCATTCTGGGA
1641789 AAAA
196 AAAA
*
1641793 AGTATCGACACAAACTATATTAGTGTCGACACATTATTTAGA-ATATTCTCTTATAAAACCGGTA
1 AGTATCGACACAAACTATATTAGTGTCGACACATTATTTAGACATATTCTCTCATAAAACCGGTA
1641857 TAATTGTACCGGTTAGATTGAAAAATTACATATTACATTATAC-TTTGGGTTCGATGATTTTGGG
66 TAATTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGG
* *
1641921 ATTGACACTTTTTATATATGGATCGACACTTTATGGGTGCACCCTGTT
131 ATCGACACTTTTTATATATGGATCGACACTTTATGGGTGCACCTTGTT
1641969 GGCCATATTG
Statistics
Matches: 951, Mismatches: 5, Indels: 17
0.98 0.01 0.02
Matches are distributed among these distances:
192 16 0.02
193 70 0.07
194 14 0.01
195 106 0.11
196 91 0.10
197 151 0.16
198 253 0.27
199 250 0.26
ACGTcount: A:0.31, C:0.16, G:0.17, T:0.37
Consensus pattern (199 bp):
AGTATCGACACAAACTATATTAGTGTCGACACATTATTTAGACATATTCTCTCATAAAACCGGTA
TAATTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGG
ATCGACACTTTTTATATATGGATCGACACTTTATGGGTGCACCTTGTTTTCCATTCATTCTGGGA
AAAA
Found at i:1642113 original size:18 final size:18
Alignment explanation
Indices: 1642087--1642134 Score: 69
Period size: 18 Copynumber: 2.6 Consensus size: 18
1642077 TTATATTCAC
*
1642087 ATACAAAAATATAAATCGT
1 ATACAAAATTAT-AATCGT
*
1642106 ATACAAAATTATAATCTT
1 ATACAAAATTATAATCGT
1642124 ATACAAAATTA
1 ATACAAAATTA
1642135 ACTCGACATT
Statistics
Matches: 27, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
18 16 0.59
19 11 0.41
ACGTcount: A:0.56, C:0.10, G:0.02, T:0.31
Consensus pattern (18 bp):
ATACAAAATTATAATCGT
Found at i:1643950 original size:33 final size:33
Alignment explanation
Indices: 1643913--1643978 Score: 105
Period size: 33 Copynumber: 2.0 Consensus size: 33
1643903 CATCTTAATA
*
1643913 TCACCCCTTAACACCCCAACTTCTTTCACCACT
1 TCACCCCTCAACACCCCAACTTCTTTCACCACT
* *
1643946 TCACCCCTCAACACCTCTACTTCTTTCACCACT
1 TCACCCCTCAACACCCCAACTTCTTTCACCACT
1643979 CCATCTATTT
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
33 30 1.00
ACGTcount: A:0.23, C:0.48, G:0.00, T:0.29
Consensus pattern (33 bp):
TCACCCCTCAACACCCCAACTTCTTTCACCACT
Found at i:1644051 original size:21 final size:21
Alignment explanation
Indices: 1644011--1644075 Score: 69
Period size: 21 Copynumber: 3.1 Consensus size: 21
1644001 CCCCTTATTC
* *
1644011 CTCTCGAGTGTATCTTCGACT
1 CTCTCGAGTTTCTCTTCGACT
*
1644032 CTCTCGAGTTTCTCTACGACT
1 CTCTCGAGTTTCTCTTCGACT
* *
1644053 -TGATCAAGTTTCTCTTCGACT
1 CT-CTCGAGTTTCTCTTCGACT
1644074 CT
1 CT
1644076 TGATTGTCTT
Statistics
Matches: 36, Mismatches: 6, Indels: 3
0.80 0.13 0.07
Matches are distributed among these distances:
20 1 0.03
21 34 0.94
22 1 0.03
ACGTcount: A:0.15, C:0.29, G:0.15, T:0.40
Consensus pattern (21 bp):
CTCTCGAGTTTCTCTTCGACT
Found at i:1646321 original size:20 final size:20
Alignment explanation
Indices: 1646294--1646340 Score: 69
Period size: 20 Copynumber: 2.4 Consensus size: 20
1646284 TCCGGTATCA
1646294 TTTTACCGATTTTATCAT-T
1 TTTTACCGATTTTATCATAT
*
1646313 TTGTTACCGGTTTTATCATAT
1 TT-TTACCGATTTTATCATAT
1646334 TTTTACC
1 TTTTACC
1646341 TGTTATATCG
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
19 2 0.08
20 20 0.80
21 3 0.12
ACGTcount: A:0.19, C:0.17, G:0.09, T:0.55
Consensus pattern (20 bp):
TTTTACCGATTTTATCATAT
Found at i:1646349 original size:20 final size:20
Alignment explanation
Indices: 1646296--1646349 Score: 56
Period size: 20 Copynumber: 2.7 Consensus size: 20
1646286 CGGTATCATT
* *
1646296 TTACCGATTTTATCATTTTG
1 TTACCGGTTATATCATTTTG
*
1646316 TTACCGGTTTTATCATATTT-
1 TTACCGGTTATATCAT-TTTG
*
1646336 TTACCTGTTATATC
1 TTACCGGTTATATC
1646350 GTTGTGGATC
Statistics
Matches: 30, Mismatches: 3, Indels: 2
0.86 0.09 0.06
Matches are distributed among these distances:
20 27 0.90
21 3 0.10
ACGTcount: A:0.20, C:0.17, G:0.09, T:0.54
Consensus pattern (20 bp):
TTACCGGTTATATCATTTTG
Found at i:1648247 original size:19 final size:20
Alignment explanation
Indices: 1648210--1648255 Score: 76
Period size: 19 Copynumber: 2.4 Consensus size: 20
1648200 TTTAGTTGTT
1648210 TGTTCTGGGTAATTTTTCTA
1 TGTTCTGGGTAATTTTTCTA
1648230 TGTTCTGGGTAA-TTTTCTA
1 TGTTCTGGGTAATTTTTCTA
*
1648249 GGTTCTG
1 TGTTCTG
1648256 AAGTTTATTT
Statistics
Matches: 25, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
19 13 0.52
20 12 0.48
ACGTcount: A:0.13, C:0.11, G:0.24, T:0.52
Consensus pattern (20 bp):
TGTTCTGGGTAATTTTTCTA
Found at i:1653282 original size:2 final size:2
Alignment explanation
Indices: 1653275--1653358 Score: 69
Period size: 2 Copynumber: 42.0 Consensus size: 2
1653265 TTACTAAAAG
* * * * * * *
1653275 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AC AC AC AC AC AC AC
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
* * * *
1653317 AC AC AC AC 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
1653359 TCCTTCTTAT
Statistics
Matches: 80, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
2 80 1.00
ACGTcount: A:0.50, C:0.13, G:0.00, T:0.37
Consensus pattern (2 bp):
AT
Found at i:1656245 original size:29 final size:29
Alignment explanation
Indices: 1656203--1656260 Score: 116
Period size: 29 Copynumber: 2.0 Consensus size: 29
1656193 CTCACGAGGC
1656203 GCCCTGAAAATGAACGATGACCAGGACGG
1 GCCCTGAAAATGAACGATGACCAGGACGG
1656232 GCCCTGAAAATGAACGATGACCAGGACGG
1 GCCCTGAAAATGAACGATGACCAGGACGG
1656261 AGCCGTTGTC
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 29 1.00
ACGTcount: A:0.34, C:0.24, G:0.31, T:0.10
Consensus pattern (29 bp):
GCCCTGAAAATGAACGATGACCAGGACGG
Found at i:1656755 original size:30 final size:29
Alignment explanation
Indices: 1656721--1656784 Score: 74
Period size: 29 Copynumber: 2.2 Consensus size: 29
1656711 AATAAATATT
* *
1656721 TAAAACATATTTATGTTTAAAATAGGTACC
1 TAAAACAT-TTTATGGTCAAAATAGGTACC
* * *
1656751 TAAAATATTTTTTGGTCAAAATAGGTACT
1 TAAAACATTTTATGGTCAAAATAGGTACC
1656780 TAAAA
1 TAAAA
1656785 TATTCAATGC
Statistics
Matches: 29, Mismatches: 5, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
29 22 0.76
30 7 0.24
ACGTcount: A:0.44, C:0.08, G:0.11, T:0.38
Consensus pattern (29 bp):
TAAAACATTTTATGGTCAAAATAGGTACC
Found at i:1657669 original size:20 final size:20
Alignment explanation
Indices: 1657644--1657699 Score: 103
Period size: 20 Copynumber: 2.8 Consensus size: 20
1657634 CATATTCCCT
1657644 GGTAATCTTACATTCCCACC
1 GGTAATCTTACATTCCCACC
*
1657664 GGTAATCTTACATTCCCACT
1 GGTAATCTTACATTCCCACC
1657684 GGTAATCTTACATTCC
1 GGTAATCTTACATTCC
1657700 GTAAACCAAA
Statistics
Matches: 35, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 35 1.00
ACGTcount: A:0.25, C:0.30, G:0.11, T:0.34
Consensus pattern (20 bp):
GGTAATCTTACATTCCCACC
Found at i:1657964 original size:12 final size:12
Alignment explanation
Indices: 1657947--1657971 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
1657937 ATCAATAAGT
1657947 ACTAGTAGGTGA
1 ACTAGTAGGTGA
1657959 ACTAGTAGGTGA
1 ACTAGTAGGTGA
1657971 A
1 A
1657972 GTTAGATGGA
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:0.36, C:0.08, G:0.32, T:0.24
Consensus pattern (12 bp):
ACTAGTAGGTGA
Found at i:1669548 original size:18 final size:19
Alignment explanation
Indices: 1669521--1669557 Score: 58
Period size: 18 Copynumber: 2.0 Consensus size: 19
1669511 AGCTATACAA
1669521 TTGTGACTATTCTA-ATAT
1 TTGTGACTATTCTAGATAT
*
1669539 TTGTGTCTATTCTAGATAT
1 TTGTGACTATTCTAGATAT
1669558 AAAGGAAAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
18 13 0.76
19 4 0.24
ACGTcount: A:0.24, C:0.11, G:0.14, T:0.51
Consensus pattern (19 bp):
TTGTGACTATTCTAGATAT
Found at i:1673097 original size:38 final size:38
Alignment explanation
Indices: 1673016--1673100 Score: 109
Period size: 38 Copynumber: 2.2 Consensus size: 38
1673006 TTCTTTTCGA
*
1673016 TTTCTTTTGGGTAATTTGACGAATTTGTTTATAAGGCT
1 TTTCATTTGGGTAATTTGACGAATTTGTTTATAAGGCT
* * * *
1673054 CTTCATTTGGGTACTTTGACGAATTTGTTTGT-AGGATT
1 TTTCATTTGGGTAATTTGACGAATTTGTTTATAAGG-CT
1673092 TTTCATTTG
1 TTTCATTTG
1673101 TGTATTTTAA
Statistics
Matches: 40, Mismatches: 6, Indels: 2
0.83 0.12 0.04
Matches are distributed among these distances:
37 3 0.08
38 37 0.93
ACGTcount: A:0.19, C:0.09, G:0.21, T:0.51
Consensus pattern (38 bp):
TTTCATTTGGGTAATTTGACGAATTTGTTTATAAGGCT
Found at i:1676152 original size:3 final size:3
Alignment explanation
Indices: 1676135--1676199 Score: 98
Period size: 3 Copynumber: 22.0 Consensus size: 3
1676125 TGAAATGTAT
*
1676135 TAA TAT TAA -AA TAA TAA TAA TGAA -AA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA T-AA TAA TAA TAA TAA TAA TAA TAA
1676179 TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA
1676200 AACCAAGAAA
Statistics
Matches: 57, Mismatches: 2, Indels: 6
0.88 0.03 0.09
Matches are distributed among these distances:
2 4 0.07
3 51 0.89
4 2 0.04
ACGTcount: A:0.66, C:0.00, G:0.02, T:0.32
Consensus pattern (3 bp):
TAA
Found at i:1678697 original size:30 final size:29
Alignment explanation
Indices: 1678663--1678720 Score: 71
Period size: 29 Copynumber: 2.0 Consensus size: 29
1678653 TATTTTTTGA
*
1678663 AAACTAGGTGGGAAGGTTTTTAATGTTTTT
1 AAACT-GGTGGGAAGATTTTTAATGTTTTT
** *
1678693 AAACTTTTGGGAAGATTTTTTATGTTTT
1 AAACTGGTGGGAAGATTTTTAATGTTTT
1678721 GAATTAGATC
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
29 19 0.79
30 5 0.21
ACGTcount: A:0.26, C:0.03, G:0.22, T:0.48
Consensus pattern (29 bp):
AAACTGGTGGGAAGATTTTTAATGTTTTT
Found at i:1678812 original size:12 final size:12
Alignment explanation
Indices: 1678795--1678823 Score: 58
Period size: 12 Copynumber: 2.4 Consensus size: 12
1678785 TTTTGAGCTG
1678795 TTTAGTTTTATT
1 TTTAGTTTTATT
1678807 TTTAGTTTTATT
1 TTTAGTTTTATT
1678819 TTTAG
1 TTTAG
1678824 AGAACATTTA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 17 1.00
ACGTcount: A:0.17, C:0.00, G:0.10, T:0.72
Consensus pattern (12 bp):
TTTAGTTTTATT
Found at i:1680885 original size:11 final size:11
Alignment explanation
Indices: 1680869--1680895 Score: 54
Period size: 11 Copynumber: 2.5 Consensus size: 11
1680859 TGTTCTAGGA
1680869 TTTTTATTTAT
1 TTTTTATTTAT
1680880 TTTTTATTTAT
1 TTTTTATTTAT
1680891 TTTTT
1 TTTTT
1680896 GATAGAAGTT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 16 1.00
ACGTcount: A:0.15, C:0.00, G:0.00, T:0.85
Consensus pattern (11 bp):
TTTTTATTTAT
Found at i:1696650 original size:31 final size:32
Alignment explanation
Indices: 1696615--1696686 Score: 87
Period size: 32 Copynumber: 2.3 Consensus size: 32
1696605 TTTTCAACAC
*
1696615 TTATTATTA-AGGGTT-AA-ATTTTTCATGATAT
1 TTATTATTATA-GGTTCAATATTTTTC-TAATAT
*
1696646 TTATTATTATAGGTTCAATTTTTTTCTAATAT
1 TTATTATTATAGGTTCAATATTTTTCTAATAT
1696678 TTATTATTA
1 TTATTATTA
1696687 GGGGCTTACT
Statistics
Matches: 36, Mismatches: 2, Indels: 5
0.84 0.05 0.12
Matches are distributed among these distances:
31 13 0.36
32 17 0.47
33 6 0.17
ACGTcount: A:0.31, C:0.04, G:0.08, T:0.57
Consensus pattern (32 bp):
TTATTATTATAGGTTCAATATTTTTCTAATAT
Found at i:1702359 original size:6 final size:7
Alignment explanation
Indices: 1702342--1702366 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
1702332 TGAAAATTTA
1702342 AAAAAAT
1 AAAAAAT
1702349 AAAAAAT
1 AAAAAAT
1702356 AAAAAAT
1 AAAAAAT
1702363 AAAA
1 AAAA
1702367 TTCATCTCCG
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.88, C:0.00, G:0.00, T:0.12
Consensus pattern (7 bp):
AAAAAAT
Found at i:1711899 original size:19 final size:20
Alignment explanation
Indices: 1711877--1711922 Score: 67
Period size: 19 Copynumber: 2.4 Consensus size: 20
1711867 CCTTTTGTTC
1711877 TTGCATTTAGCATTTGGAT-
1 TTGCATTTAGCATTTGGATG
* *
1711896 TTGCATTTTGCATTTGTATG
1 TTGCATTTAGCATTTGGATG
1711916 TTGCATT
1 TTGCATT
1711923 GCATGTATTT
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
19 17 0.71
20 7 0.29
ACGTcount: A:0.17, C:0.11, G:0.20, T:0.52
Consensus pattern (20 bp):
TTGCATTTAGCATTTGGATG
Found at i:1714387 original size:195 final size:195
Alignment explanation
Indices: 1714055--1714454 Score: 719
Period size: 195 Copynumber: 2.1 Consensus size: 195
1714045 AATATGTGTA
1714055 TACAATAAAGCTAAGCTATTCCACTAAGGCAATTAGTTATAGAGGAAACTCGAAAGCCCTGGCTT
1 TACAATAAAGCTAAGCTATTCCACTAAGGCAATTAGTTATAGAGGAAACTCGAAAGCCCTGGCTT
*
1714120 TATGAATAGATTATATTCAAACCATGACCTTGATCGAGTACTTGACAATTCGGTGTATGCTCCAC
66 TATGAATAGATTATATTCAAACCATGACCTTGATCGAGTACTCGACAATTCGGTGTATGCTCCAC
* * * *
1714185 TGTGATTGTCAAGTCAAAGACTTTGTGATGAGATGAATCCTTCAGTTAGTCCGATAAATGCAAAT
131 TGTGATTGTCAAGTCAAAGAATTTGTGATGAGATGAATCCTTCAGCTAGCCCGATAAAGGCAAAT
* *
1714250 TACAATAAAGCTGAGCTATTCCACTAAGGCAATTGGTTATAGAGGAAACTCGAAAGCCCTGGCTT
1 TACAATAAAGCTAAGCTATTCCACTAAGGCAATTAGTTATAGAGGAAACTCGAAAGCCCTGGCTT
* *
1714315 TATGAATAGATTATATTCAAACCATGACCTTGATCGGGTACTCGGCAATTCGGTGTATGCTCCAC
66 TATGAATAGATTATATTCAAACCATGACCTTGATCGAGTACTCGACAATTCGGTGTATGCTCCAC
1714380 TGTGATTGTCAAGTCAAAGAATTTGTGATGAGATGAATCCTTCAGCTAGCCCGATAAAGGCAAAT
131 TGTGATTGTCAAGTCAAAGAATTTGTGATGAGATGAATCCTTCAGCTAGCCCGATAAAGGCAAAT
1714445 TACAATAAAG
1 TACAATAAAG
1714455 TTGATTTCAG
Statistics
Matches: 196, Mismatches: 9, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
195 196 1.00
ACGTcount: A:0.33, C:0.18, G:0.20, T:0.28
Consensus pattern (195 bp):
TACAATAAAGCTAAGCTATTCCACTAAGGCAATTAGTTATAGAGGAAACTCGAAAGCCCTGGCTT
TATGAATAGATTATATTCAAACCATGACCTTGATCGAGTACTCGACAATTCGGTGTATGCTCCAC
TGTGATTGTCAAGTCAAAGAATTTGTGATGAGATGAATCCTTCAGCTAGCCCGATAAAGGCAAAT
Found at i:1714479 original size:40 final size:39
Alignment explanation
Indices: 1714420--1714495 Score: 107
Period size: 40 Copynumber: 1.9 Consensus size: 39
1714410 AGATGAATCC
* * *
1714420 TTCAGCTAGCCCGATAAAGGCAAATTACAATAAAGTTGAT
1 TTCAGCTAGCCAGACAAAGGAAAATTA-AATAAAGTTGAT
*
1714460 TTCAGCTAGCCAGACAAAGGAAAATTAAATCAAGTT
1 TTCAGCTAGCCAGACAAAGGAAAATTAAATAAAGTT
1714496 TATCTAAATA
Statistics
Matches: 32, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
39 8 0.25
40 24 0.75
ACGTcount: A:0.42, C:0.17, G:0.17, T:0.24
Consensus pattern (39 bp):
TTCAGCTAGCCAGACAAAGGAAAATTAAATAAAGTTGAT
Found at i:1715755 original size:124 final size:124
Alignment explanation
Indices: 1715417--1715785 Score: 416
Period size: 125 Copynumber: 3.0 Consensus size: 124
1715407 CACTCTGGGA
* *
1715417 CACGACTGAACCCACATCATGTTGAGATGACGAGATTCATACCAAGGAGGCATGAAGAATGAGCC
1 CACGACTGAACCCACATCATGTTGAGATGACAAAATTCATACCAA-GAGGCATGAAGAATGAGCC
* * * *
1715482 TTACAAATTGAGGTGATGGGGTATTTTGAAGGCCCGTACCAGTATGAGATAATGTCGGGG
65 TTACAAATTGAGGTGTTGGGGCATTTTGAAGGCCCGTACCAGTATAAGATAATGTCAGGG
* * * * * * *
1715542 CACGACTGAGCCCAAATCATGTTGATATGATAATATTCAGACCACGGAGGCATGAAGAATGAGCC
1 CACGACTGAACCCACATCATGTTGAGATGACAAAATTCATACCA-AGAGGCATGAAGAATGAGCC
* * *
1715607 TTACAAATTGTGGTGTTAGGGCATTTTGAAGGCCCGTACCCA-TATAAGATAATGTTAGGG
65 TTACAAATTGAGGTGTTGGGGCATTTTGAAGGCCCGTA-CCAGTATAAGATAATGTCAGGG
* * * * * * * * *
1715667 CATGATTGAACCCCCATAATGTGGAGATGACAAAATCCATACCAAAAGGCATGGAGAATAAGCCT
1 CACGACTGAACCCACATCATGTTGAGATGACAAAATTCATACCAAGAGGCATGAAGAATGAGCCT
* * ** * * *
1715732 TATAATTTGAGGTGTTGGGGCATTTTGAAGATCTGTACCAGTACAAGATGATGT
66 TACAAATTGAGGTGTTGGGGCATTTTGAAGGCCCGTACCAGTATAAGATAATGT
1715786 TGGGGCACTA
Statistics
Matches: 201, Mismatches: 40, Indels: 7
0.81 0.16 0.03
Matches are distributed among these distances:
123 3 0.01
124 58 0.29
125 137 0.68
126 3 0.01
ACGTcount: A:0.33, C:0.17, G:0.26, T:0.25
Consensus pattern (124 bp):
CACGACTGAACCCACATCATGTTGAGATGACAAAATTCATACCAAGAGGCATGAAGAATGAGCCT
TACAAATTGAGGTGTTGGGGCATTTTGAAGGCCCGTACCAGTATAAGATAATGTCAGGG
Found at i:1716896 original size:42 final size:42
Alignment explanation
Indices: 1716782--1716896 Score: 126
Period size: 42 Copynumber: 2.7 Consensus size: 42
1716772 TTTCCCAATT
* * *
1716782 TATAAGTCCTTCGGGCCAT-CAGTAAGTCTTTCGAGCATGATG
1 TATAAGTCCTTCGGGCCATCCA-TAAGCCTTTAGAGCAAGATG
* * * **
1716824 TTTAAATCCTTCGGGTCATCTGTAAGCCTTTAGAGCAAGATG
1 TATAAGTCCTTCGGGCCATCCATAAGCCTTTAGAGCAAGATG
1716866 -ATAAGTCCTTCGGGCCATCCATAAGACCTTT
1 TATAAGTCCTTCGGGCCATCCATAAG-CCTTT
1716897 GGGTAGGATG
Statistics
Matches: 58, Mismatches: 13, Indels: 4
0.77 0.17 0.05
Matches are distributed among these distances:
41 20 0.34
42 38 0.66
ACGTcount: A:0.25, C:0.23, G:0.21, T:0.31
Consensus pattern (42 bp):
TATAAGTCCTTCGGGCCATCCATAAGCCTTTAGAGCAAGATG
Found at i:1717261 original size:214 final size:215
Alignment explanation
Indices: 1716675--1717555 Score: 1345
Period size: 214 Copynumber: 4.1 Consensus size: 215
1716665 GCAAATCCAA
* * *
1716675 ACCTTCGGGTAAGATGTTTTCAAATGAATTTGAAAAATGAAAAAATGATGTTTTAAGTAGATGTA
1 ACCTTCGGGTAGGATGTTTTCAAATGAATTTG-AAAATGAAAAAATGATGTTTTAAGAAGATGGA
* *
1716740 ATTTTTGAAAACGAAGAATGTGATTTTCAAAATTTCC-CAATTTATAAGTCCTTCGGGCCATCAG
65 ATTTTTGAAAACGAAGAATGCGATTTTCAAAA-TCCCACAATTTATAAGTCCTTCGGGCCATCAG
1716804 TAAGTCTTTCGAGCATGATGTTTAAATCCTTCGGGTCATCTGTAAGCCTTTAGAGCAAGATGATA
129 TAAGTCTTTCGAGCATGATGTTTAAATCCTTCGGGTCATCTGTAAGCCTTTAGAGCAAGATGATA
1716869 AGTCCTTCGGGCCATCCATAAG
194 AGTCCTTCGGGCCATCCATAAG
* * * *
1716891 ACCTTTGGGTAGGATGTTCTCAAATGAATTTGACAATGAAAAAAATGATGTTTTAAGAAGATGAA
1 ACCTTCGGGTAGGATGTTTTCAAATGAATTTGAAAATG-AAAAAATGATGTTTTAAGAAGATGGA
* ** *
1716956 ATTTTTGAAAACAAAGAATGCGATTTTCAAAATTTCACAATTTATAAGTTCTTCGGGCCATCAGT
65 ATTTTTGAAAACGAAGAATGCGATTTTCAAAATCCCACAATTTATAAGTCCTTCGGGCCATCAGT
* * *
1717021 AAGTCTTTCGAGCATGATGCTTAAATCCTTCGGGTCATCTGTAAGTCTTTAGAGAAAGATGATAA
130 AAGTCTTTCGAGCATGATGTTTAAATCCTTCGGGTCATCTGTAAGCCTTTAGAGCAAGATGATAA
1717086 GTCCTTCGGGCCATCCATAAG
195 GTCCTTCGGGCCATCCATAAG
* * *
1717107 ACCTTCAGGTAGGATGTTTTCACATTAATTTGAAAATG-AAAAATGATGTTTTAAGAAGATGGAA
1 ACCTTCGGGTAGGATGTTTTCAAATGAATTTGAAAATGAAAAAATGATGTTTTAAGAAGATGGAA
* *
1717171 TTTTTGAAAACGAAGAATGCGATTTTCAAAATCCCACAATTTATAAGTCTTTCGGGCCATCAATA
66 TTTTTGAAAACGAAGAATGCGATTTTCAAAATCCCACAATTTATAAGTCCTTCGGGCCATCAGTA
1717236 AGTCTTTCGAGCATGATGTTTAAATCCTTCGGGTCATCTGTAAGCCTTTAGAGCAAGATGATAAG
131 AGTCTTTCGAGCATGATGTTTAAATCCTTCGGGTCATCTGTAAGCCTTTAGAGCAAGATGATAAG
*
1717301 TCATTCGGGCCATCCATAAG
196 TCCTTCGGGCCATCCATAAG
*
1717321 ACCTTCGGGTAGGATGTTTTCAAATAAATTTGAAAATG-AAAAATGATGTTTTAAGAAGATGGAA
1 ACCTTCGGGTAGGATGTTTTCAAATGAATTTGAAAATGAAAAAATGATGTTTTAAGAAGATGGAA
1717385 TTTTTGAAAACGAAGAATGCGATTTTCAAAATCCCACAATTTATAAGTCCTTCGGGCCATCAGTA
66 TTTTTGAAAACGAAGAATGCGATTTTCAAAATCCCACAATTTATAAGTCCTTCGGGCCATCAGTA
* * * * ** * * *
1717450 AGTCTTTCGATCATGATGTTTAAATCTTTCAGGTCATCAGTAAATCTTTCGAGCATGATGCTTAA
131 AGTCTTTCGAGCATGATGTTTAAATCCTTCGGGTCATCTGTAAGCCTTTAGAGCAAGATG-ATAA
* ** * * *
1717515 ATCCTTTAGGTCATCTATAAA
195 GTCCTTCGGGCCATCCATAAG
* *
1717536 ACCTTCGGGCATGATGTTTT
1 ACCTTCGGGTAGGATGTTTT
1717556 TCACCAGGAT
Statistics
Matches: 609, Mismatches: 53, Indels: 7
0.91 0.08 0.01
Matches are distributed among these distances:
214 341 0.56
215 43 0.07
216 225 0.37
ACGTcount: A:0.33, C:0.15, G:0.19, T:0.33
Consensus pattern (215 bp):
ACCTTCGGGTAGGATGTTTTCAAATGAATTTGAAAATGAAAAAATGATGTTTTAAGAAGATGGAA
TTTTTGAAAACGAAGAATGCGATTTTCAAAATCCCACAATTTATAAGTCCTTCGGGCCATCAGTA
AGTCTTTCGAGCATGATGTTTAAATCCTTCGGGTCATCTGTAAGCCTTTAGAGCAAGATGATAAG
TCCTTCGGGCCATCCATAAG
Found at i:1717477 original size:22 final size:21
Alignment explanation
Indices: 1717452--1717517 Score: 64
Period size: 22 Copynumber: 3.1 Consensus size: 21
1717442 CATCAGTAAG
1717452 TCTTTCGATCATGATGTTTAAA
1 TCTTTCGATCATGATG-TTAAA
* *
1717474 TCTTTCAGGTCATCA-G-TAAA
1 TCTTTC-GATCATGATGTTAAA
*
1717494 TCTTTCGAGCATGATGCTTAAA
1 TCTTTCGATCATGATG-TTAAA
1717516 TC
1 TC
1717518 CTTTAGGTCA
Statistics
Matches: 35, Mismatches: 5, Indels: 8
0.73 0.10 0.17
Matches are distributed among these distances:
19 5 0.14
20 11 0.31
22 13 0.37
23 6 0.17
ACGTcount: A:0.27, C:0.18, G:0.15, T:0.39
Consensus pattern (21 bp):
TCTTTCGATCATGATGTTAAA
Found at i:1717501 original size:42 final size:42
Alignment explanation
Indices: 1717442--1717551 Score: 134
Period size: 42 Copynumber: 2.6 Consensus size: 42
1717432 TCCTTCGGGC
* * *
1717442 CATCAGTAAGTCTTTCGATCATGATGTTTAAAT-CTTTCAGGT
1 CATCAGTAAATCTTTCGAGCATGATGCTTAAATCCTTT-AGGT
1717484 CATCAGTAAATCTTTCGAGCATGATGCTTAAATCCTTTAGGT
1 CATCAGTAAATCTTTCGAGCATGATGCTTAAATCCTTTAGGT
* * *
1717526 CATCTA-TAAAACCTTCGGGCATGATG
1 CATC-AGTAAATCTTTCGAGCATGATG
1717552 TTTTTCACCA
Statistics
Matches: 60, Mismatches: 6, Indels: 4
0.86 0.09 0.06
Matches are distributed among these distances:
42 55 0.92
43 5 0.08
ACGTcount: A:0.28, C:0.19, G:0.17, T:0.35
Consensus pattern (42 bp):
CATCAGTAAATCTTTCGAGCATGATGCTTAAATCCTTTAGGT
Found at i:1717559 original size:430 final size:431
Alignment explanation
Indices: 1716673--1717555 Score: 1369
Period size: 430 Copynumber: 2.1 Consensus size: 431
1716663 AAGCAAATCC
* *
1716673 AAACCTTCGGGTAAGATGTTTTCAAATGAATTTGAAAAATGAAAAAATGATGTTTTAAGTAGATG
1 AAACCTTCGGGTAAGATGTTTTCACATGAATTTGAAAAATGAAAAAATGATGTTTTAAGAAGATG
* * *
1716738 TAATTTTTGAAAACGAAGAATGTGATTTTCAAAATTTCCCAATTTATAAGTCCTTCGGGCCATCA
66 GAATTTTTGAAAACGAAGAATGCGATTTTCAAAATTCCCCAATTTATAAGTCCTTCGGGCCATCA
*
1716803 GTAAGTCTTTCGAGCATGATGTTTAAATCCTTCGGGTCATCTGTAAGCCTTTAGAGCAAGATGAT
131 ATAAGTCTTTCGAGCATGATGTTTAAATCCTTCGGGTCATCTGTAAGCCTTTAGAGCAAGATGAT
* * * *
1716868 AAGTCCTTCGGGCCATCCATAAGACCTTTGGGTAGGATGTTCTCAAATGAATTTGACAATGAAAA
196 AAGTCATTCGGGCCATCCATAAGACCTTCGGGTAGGATGTTCTCAAATAAATTTGAAAATG-AAA
**
1716933 AAATGATGTTTTAAGAAGATGAAATTTTTGAAAACAAAGAATGCGATTTTCAAAATTTCACAATT
260 AAATGATGTTTTAAGAAGATGAAATTTTTGAAAACAAAGAATGCGATTTTCAAAATCCCACAATT
* * *
1716998 TATAAGTTCTTCGGGCCATCAGTAAGTCTTTCGAGCATGATGCTTAAATCCTTCGGGTCATCTGT
325 TATAAGTCCTTCGGGCCATCAGTAAGTCTTTCGAGCATGATGCTTAAATCCTTCAGGTCATCAGT
* * *
1717063 AAGTCTTTAGAGAAAGATGATAAGTCCTTCGGGCCATCCATA
390 AAATCTTTAGAGAAAGATGATAAATCCTTCAGGCCATCCATA
* * * *
1717105 AGACCTTCAGGTAGGATGTTTTCACATTAATTTG-AAAATG-AAAAATGATGTTTTAAGAAGATG
1 AAACCTTCGGGTAAGATGTTTTCACATGAATTTGAAAAATGAAAAAATGATGTTTTAAGAAGATG
*
1717168 GAATTTTTGAAAACGAAGAATGCGATTTTCAAAA-TCCCACAATTTATAAGTCTTTCGGGCCATC
66 GAATTTTTGAAAACGAAGAATGCGATTTTCAAAATTCCC-CAATTTATAAGTCCTTCGGGCCATC
1717232 AATAAGTCTTTCGAGCATGATGTTTAAATCCTTCGGGTCATCTGTAAGCCTTTAGAGCAAGATGA
130 AATAAGTCTTTCGAGCATGATGTTTAAATCCTTCGGGTCATCTGTAAGCCTTTAGAGCAAGATGA
*
1717297 TAAGTCATTCGGGCCATCCATAAGACCTTCGGGTAGGATGTTTTCAAATAAATTTGAAAATG-AA
195 TAAGTCATTCGGGCCATCCATAAGACCTTCGGGTAGGATGTTCTCAAATAAATTTGAAAATGAAA
* *
1717361 AAATGATGTTTTAAGAAGATGGAATTTTTGAAAACGAAGAATGCGATTTTCAAAATCCCACAATT
260 AAATGATGTTTTAAGAAGATGAAATTTTTGAAAACAAAGAATGCGATTTTCAAAATCCCACAATT
* * *
1717426 TATAAGTCCTTCGGGCCATCAGTAAGTCTTTCGATCATGATGTTTAAATCTTTCAGGTCATCAGT
325 TATAAGTCCTTCGGGCCATCAGTAAGTCTTTCGAGCATGATGCTTAAATCCTTCAGGTCATCAGT
* * * * * * *
1717491 AAATCTTTCGAGCATGATGCTTAAATCCTTTAGGTCATCTATA
390 AAATCTTTAGAGAAAGATG-ATAAATCCTTCAGGCCATCCATA
* *
1717534 AAACCTTCGGGCATGATGTTTT
1 AAACCTTCGGGTAAGATGTTTT
1717556 TCACCAGGAT
Statistics
Matches: 409, Mismatches: 40, Indels: 7
0.90 0.09 0.02
Matches are distributed among these distances:
428 137 0.33
429 38 0.09
430 199 0.49
431 6 0.01
432 29 0.07
ACGTcount: A:0.33, C:0.15, G:0.19, T:0.33
Consensus pattern (431 bp):
AAACCTTCGGGTAAGATGTTTTCACATGAATTTGAAAAATGAAAAAATGATGTTTTAAGAAGATG
GAATTTTTGAAAACGAAGAATGCGATTTTCAAAATTCCCCAATTTATAAGTCCTTCGGGCCATCA
ATAAGTCTTTCGAGCATGATGTTTAAATCCTTCGGGTCATCTGTAAGCCTTTAGAGCAAGATGAT
AAGTCATTCGGGCCATCCATAAGACCTTCGGGTAGGATGTTCTCAAATAAATTTGAAAATGAAAA
AATGATGTTTTAAGAAGATGAAATTTTTGAAAACAAAGAATGCGATTTTCAAAATCCCACAATTT
ATAAGTCCTTCGGGCCATCAGTAAGTCTTTCGAGCATGATGCTTAAATCCTTCAGGTCATCAGTA
AATCTTTAGAGAAAGATGATAAATCCTTCAGGCCATCCATA
Found at i:1721377 original size:21 final size:21
Alignment explanation
Indices: 1721335--1721383 Score: 62
Period size: 21 Copynumber: 2.3 Consensus size: 21
1721325 TTATTAAAAA
*
1721335 TATTATTATTTTTATCGGTTT
1 TATTATTATTTTTATCGATTT
* *
1721356 TATTATTTTTTTTATTGATTT
1 TATTATTATTTTTATCGATTT
*
1721377 TGTTATT
1 TATTATT
1721384 GTTGAGCACT
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 24 1.00
ACGTcount: A:0.18, C:0.02, G:0.08, T:0.71
Consensus pattern (21 bp):
TATTATTATTTTTATCGATTT
Found at i:1721780 original size:2 final size:2
Alignment explanation
Indices: 1721775--1721820 Score: 92
Period size: 2 Copynumber: 23.0 Consensus size: 2
1721765 AAATGAAAAT
1721775 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
1721817 TA TA
1 TA TA
1721821 ATTTATATTA
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 44 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:1737913 original size:103 final size:103
Alignment explanation
Indices: 1737734--1737930 Score: 272
Period size: 103 Copynumber: 1.9 Consensus size: 103
1737724 TATAGTATCA
* *
1737734 ATACACTAAAGGTATAGATACATTGGATGTAACTAGTAAAACAATGGTATATGCTAATATCGATA
1 ATACACTAAAGGTATAGATACATTGGATGTAACCAGTAAAACAATAGTATATGCTAATATCGATA
* *
1737799 CTTCTTGTGTACCGATACACCTTAGCTTCAAGGTATTG
66 CTTCTGGTGTACCGATACAACTTAGCTTCAAGGTATTG
* * * * *
1737837 ATACACTAAAGGTATCA-ATACATTGGATGTAACCCGTTATACAATATTATATGAC-ATTATCGA
1 ATACACTAAAGGTAT-AGATACATTGGATGTAACCAGTAAAACAATAGTATATG-CTAATATCGA
*
1737900 TACTTCTGGTGTACCGGTACAACTTAGCTTC
64 TACTTCTGGTGTACCGATACAACTTAGCTTC
1737931 TATTAGGTCT
Statistics
Matches: 82, Mismatches: 10, Indels: 4
0.85 0.10 0.04
Matches are distributed among these distances:
103 80 0.98
104 2 0.02
ACGTcount: A:0.34, C:0.17, G:0.16, T:0.32
Consensus pattern (103 bp):
ATACACTAAAGGTATAGATACATTGGATGTAACCAGTAAAACAATAGTATATGCTAATATCGATA
CTTCTGGTGTACCGATACAACTTAGCTTCAAGGTATTG
Found at i:1739228 original size:5 final size:5
Alignment explanation
Indices: 1739218--1739253 Score: 63
Period size: 5 Copynumber: 7.0 Consensus size: 5
1739208 ATATGAGAAA
1739218 AATTT AATTT AAATTT AATTT AATTT AATTT AATTT
1 AATTT AATTT -AATTT AATTT AATTT AATTT AATTT
1739254 TAAAATAACC
Statistics
Matches: 30, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
5 25 0.83
6 5 0.17
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (5 bp):
AATTT
Found at i:1739233 original size:11 final size:11
Alignment explanation
Indices: 1739217--1739256 Score: 64
Period size: 11 Copynumber: 3.7 Consensus size: 11
1739207 TATATGAGAA
1739217 AAATTTAATTT
1 AAATTTAATTT
1739228 AAATTTAATTT
1 AAATTTAATTT
1739239 -AATTTAATTT
1 AAATTTAATTT
*
1739249 AATTTTAA
1 AAATTTAA
1739257 AATAACCTTA
Statistics
Matches: 27, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
10 10 0.37
11 17 0.63
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (11 bp):
AAATTTAATTT
Found at i:1751864 original size:35 final size:35
Alignment explanation
Indices: 1751818--1751956 Score: 215
Period size: 35 Copynumber: 3.9 Consensus size: 35
1751808 TGAATAAAAA
*
1751818 GAACGAAAGGAAGCATCGGCACTTTCGATTCAAGT
1 GAACGAAAGGAAGCATCAGCACTTTCGATTCAAGT
* *
1751853 GAACGGAAGGAAGCATCAGCACTTTCGATTCAAGAA
1 GAACGAAAGGAAGCATCAGCACTTTCGATTCAAG-T
* *
1751889 GAACGAAAGGAAGCACCGGCACTTTCGATTCAAGT
1 GAACGAAAGGAAGCATCAGCACTTTCGATTCAAGT
*
1751924 GAACGGAAGGAAGCATCAGCACTTTCGATTCAA
1 GAACGAAAGGAAGCATCAGCACTTTCGATTCAA
1751957 TTGTTCATCT
Statistics
Matches: 93, Mismatches: 10, Indels: 2
0.89 0.10 0.02
Matches are distributed among these distances:
35 62 0.67
36 31 0.33
ACGTcount: A:0.36, C:0.21, G:0.25, T:0.18
Consensus pattern (35 bp):
GAACGAAAGGAAGCATCAGCACTTTCGATTCAAGT
Found at i:1751932 original size:71 final size:71
Alignment explanation
Indices: 1751816--1751956 Score: 273
Period size: 71 Copynumber: 2.0 Consensus size: 71
1751806 GGTGAATAAA
*
1751816 AAGAACGAAAGGAAGCATCGGCACTTTCGATTCAAGTGAACGGAAGGAAGCATCAGCACTTTCGA
1 AAGAACGAAAGGAAGCACCGGCACTTTCGATTCAAGTGAACGGAAGGAAGCATCAGCACTTTCGA
1751881 TTCAAG
66 TTCAAG
1751887 AAGAACGAAAGGAAGCACCGGCACTTTCGATTCAAGTGAACGGAAGGAAGCATCAGCACTTTCGA
1 AAGAACGAAAGGAAGCACCGGCACTTTCGATTCAAGTGAACGGAAGGAAGCATCAGCACTTTCGA
1751952 TTCAA
66 TTCAA
1751957 TTGTTCATCT
Statistics
Matches: 69, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
71 69 1.00
ACGTcount: A:0.37, C:0.21, G:0.25, T:0.18
Consensus pattern (71 bp):
AAGAACGAAAGGAAGCACCGGCACTTTCGATTCAAGTGAACGGAAGGAAGCATCAGCACTTTCGA
TTCAAG
Found at i:1757727 original size:72 final size:72
Alignment explanation
Indices: 1757605--1757743 Score: 251
Period size: 72 Copynumber: 1.9 Consensus size: 72
1757595 TTCTGGTCCT
* *
1757605 ATTCCACTGTCGATATGGGAGTTATCATCTTTGAAGGTCTTTGATGTTTCAGAAAATCAATTAAA
1 ATTCCACTGTCGATAGGGGAGTTATCATCTTTGAAGGTCTTTGATATTTCAGAAAATCAATTAAA
1757670 TGATCCC
66 TGATCCC
*
1757677 ATTCCACTGTCGATAGGGGAGTTATCATCTTTGAAGGTCTTTGATATTTCAGTAAATCAATTAAA
1 ATTCCACTGTCGATAGGGGAGTTATCATCTTTGAAGGTCTTTGATATTTCAGAAAATCAATTAAA
1757742 TG
66 TG
1757744 GTACTCTTCC
Statistics
Matches: 64, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
72 64 1.00
ACGTcount: A:0.29, C:0.15, G:0.19, T:0.37
Consensus pattern (72 bp):
ATTCCACTGTCGATAGGGGAGTTATCATCTTTGAAGGTCTTTGATATTTCAGAAAATCAATTAAA
TGATCCC
Found at i:1766649 original size:21 final size:21
Alignment explanation
Indices: 1766625--1766676 Score: 95
Period size: 21 Copynumber: 2.5 Consensus size: 21
1766615 TATACCAGCA
1766625 AATCATTTAAAATACTTTCCT
1 AATCATTTAAAATACTTTCCT
1766646 AATCATTTAAAATACTTTCCT
1 AATCATTTAAAATACTTTCCT
*
1766667 AATCAGTTAA
1 AATCATTTAA
1766677 GAAAATATTT
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
21 30 1.00
ACGTcount: A:0.40, C:0.17, G:0.02, T:0.40
Consensus pattern (21 bp):
AATCATTTAAAATACTTTCCT
Found at i:1767816 original size:17 final size:17
Alignment explanation
Indices: 1767791--1767839 Score: 62
Period size: 17 Copynumber: 2.9 Consensus size: 17
1767781 CGTCATTATT
* **
1767791 CCGGCCACTATTTGCCG
1 CCGGTCACTATTCACCG
1767808 CCGGTCACTATTCACCG
1 CCGGTCACTATTCACCG
*
1767825 CTGGTCACTATTCAC
1 CCGGTCACTATTCAC
1767840 GATGGCCGAA
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 28 1.00
ACGTcount: A:0.16, C:0.39, G:0.18, T:0.27
Consensus pattern (17 bp):
CCGGTCACTATTCACCG
Found at i:1768821 original size:137 final size:135
Alignment explanation
Indices: 1768569--1769222 Score: 699
Period size: 137 Copynumber: 4.8 Consensus size: 135
1768559 GAGATCCAAC
* ** *
1768569 TAGTGTATGACATTGTTACTTCATGATGAGGATGTCTGGCCATCTTTGAAGATATTTGAGATAAC
1 TAGTGGATGACATTGTTA-TTCATGATGAGGACATCTGGCCATCTTTAAAGATATTTGAGATAAC
* * *
1768634 ACGGTTCCTTCGTGATGAGAACGTCTGGTTATCTGAGGATGACTCGGCTCCTAT-GTGATGAGGA
65 ACGGTTCCTTCGTGATGAGGACGTCTGGTTATCTAAGGATGAAT-GGCTCCT-TCGTGATGAGGA
*
1768698 GTTCTGGT
128 GTTCTGAT
* * * *
1768706 CAGTGGATGACATTGTTATGTCATGATGAGGTCGTCTAGCCATCTTTAAAGATATTTGAGATAAC
1 TAGTGGATGACATTGTTAT-TCATGATGAGGACATCTGGCCATCTTTAAAGATATTTGAGATAAC
* ** * *
1768771 ATGGTTCCTTCGTGATGAGGATATATGGCTATCTAAGGAT-AATGTTGCTCCTTCGTGATGAGGA
65 ACGGTTCCTTCGTGATGAGGACGTCTGGTTATCTAAGGATGAATG--GCTCCTTCGTGATGAGGA
1768835 GATT-TGAT
128 G-TTCTGAT
* * * * ** *
1768843 TGGTGAATGAAATTGTTCCTTCATGATGAGGACATCTTCCCATCTTTAAAGATATTTGAGATAAT
1 TAGTGGATGACATTGTT-ATTCATGATGAGGACATCTGGCCATCTTTAAAGATATTTGAGATAAC
* * *
1768908 GCGGTTCCTTCGTGATGAGGACGTCTGGTTATCTAAGGATGACATGACTCCTTCATGATGAGGAG
65 ACGGTTCCTTCGTGATGAGGACGTCTGGTTATCTAAGGATGA-ATGGCTCCTTCGTGATGAGGAG
1768973 TTCTGAT
129 TTCTGAT
* ** * * * * *
1768980 TTGTATATGAAATTGTTCCTTCGTGATGAGGACATCTGGCCATCTTTGAAGAAATTTGAGATAAC
1 TAGTGGATGACATTGTT-ATTCATGATGAGGACATCTGGCCATCTTTAAAGATATTTGAGATAAC
*** * * * *
1769045 ATATTTCCTTCATGACGAGGATGTCTGGTTATCTAAGGATG-ACGCGACTCCTTCGTGATGAGGA
65 ACGGTTCCTTCGTGATGAGGACGTCTGGTTATCTAAGGATGAATG-G-CTCCTTCGTGATGAGGA
1769109 GTTCTGAT
128 GTTCTGAT
* * * * *
1769117 TGGTAGATGACATTG-TACCTTCGTGATGAGGACATCTGTCCACCTTT-AAGATATTTGAGATAA
1 TAGTGGATGACATTGTTA--TTCATGATGAGGACATCTGGCCATCTTTAAAGATATTTGAGATAA
* *
1769180 CACGGTTCCTTCGTGATGAGGACGTCTGGATATCTAAAGATGA
64 CACGGTTCCTTCGTGATGAGGACGTCTGGTTATCTAAGGATGA
1769223 TGTTAATGGA
Statistics
Matches: 436, Mismatches: 67, Indels: 28
0.82 0.13 0.05
Matches are distributed among these distances:
135 3 0.01
136 56 0.13
137 370 0.85
138 4 0.01
139 3 0.01
ACGTcount: A:0.25, C:0.15, G:0.25, T:0.34
Consensus pattern (135 bp):
TAGTGGATGACATTGTTATTCATGATGAGGACATCTGGCCATCTTTAAAGATATTTGAGATAACA
CGGTTCCTTCGTGATGAGGACGTCTGGTTATCTAAGGATGAATGGCTCCTTCGTGATGAGGAGTT
CTGAT
Found at i:1769080 original size:274 final size:272
Alignment explanation
Indices: 1768575--1769222 Score: 804
Period size: 274 Copynumber: 2.4 Consensus size: 272
1768565 CAACTAGTGT
* ** *
1768575 ATGACATTGTTACTTCATGATGAGGATGTCTGGCCATCTTTGAAGATATTTGAGATAACACGGTT
1 ATGACATTGTTCCTTCATGATGAGGACATCT-TCCATCTTT-AAGATATTTGAGATAACACGGTT
* * * * *
1768640 CCTTCGTGATGAGAACGTCTGGTTATCTGAGGATGACTCGGCTCCTATGTGATGAGGAGTTCTGG
64 CCTTCGTGATGAGGACGTCTGGTTATCTAAGGATGACTCGACTCCTATATGATGAGGAGTTCTGA
* * * * *
1768705 TCAGTGGATGACATTGTTATGTCATGATGAGGTCGTCTAGCCATCTTTAAAGATATTTGAGATAA
129 TCAGTAGATGAAATTGTTATGTCATGATGAGGACATCTAGCCATCTTTAAAGAAATTTGAGATAA
* * * * *
1768770 CATGGTTCCTTCGTGATGAGGATATATGGCTATCTAAGGATAATGTTG-CTCCTTCGTGATGAGG
194 CATAGTTCCTTCATGACGAGGATATATGGCTATCTAAGGATAACG-CGACTCCTTCGTGATGAGG
1768834 AGATT-TGATTGGT-G
258 AG-TTCTGATTGGTAG
* **
1768848 AATGAAATTGTTCCTTCATGATGAGGACATCTTCCCATCTTTAAAGATATTTGAGATAATGCGGT
1 -ATGACATTGTTCCTTCATGATGAGGACATCTT-CCATCTTT-AAGATATTTGAGATAACACGGT
1768913 TCCTTCGTGATGAGGACGTCTGGTTATCTAAGGATGACAT-GACTCCT-TCATGATGAGGAGTTC
63 TCCTTCGTGATGAGGACGTCTGGTTATCTAAGGATGAC-TCGACTCCTAT-ATGATGAGGAGTTC
** * * * * *
1768976 TGATTTGTATATGAAATTGTTCCT-TCGTGATGAGGACATCTGGCCATCTTTGAAGAAATTTGAG
126 TGATCAGTAGATGAAATTGTT-ATGTCATGATGAGGACATCTAGCCATCTTTAAAGAAATTTGAG
* * * * *
1769040 ATAACATATTTCCTTCATGACGAGGATGTCTGGTTATCTAAGGATGACGCGACTCCTTCGTGATG
190 ATAACATAGTTCCTTCATGACGAGGATATATGGCTATCTAAGGATAACGCGACTCCTTCGTGATG
1769105 AGGAGTTCTGATTGGTAG
255 AGGAGTTCTGATTGGTAG
* * *
1769123 ATGACATTGTACCTTCGTGATGAGGACATCTGTCCACCTTTAAGATATTTGAGATAACACGGTTC
1 ATGACATTGTTCCTTCATGATGAGGACATCT-TCCATCTTTAAGATATTTGAGATAACACGGTTC
* *
1769188 CTTCGTGATGAGGACGTCTGGATATCTAAAGATGA
65 CTTCGTGATGAGGACGTCTGGTTATCTAAGGATGA
1769223 TGTTAATGGA
Statistics
Matches: 323, Mismatches: 43, Indels: 17
0.84 0.11 0.04
Matches are distributed among these distances:
273 59 0.18
274 260 0.80
275 4 0.01
ACGTcount: A:0.25, C:0.16, G:0.25, T:0.34
Consensus pattern (272 bp):
ATGACATTGTTCCTTCATGATGAGGACATCTTCCATCTTTAAGATATTTGAGATAACACGGTTCC
TTCGTGATGAGGACGTCTGGTTATCTAAGGATGACTCGACTCCTATATGATGAGGAGTTCTGATC
AGTAGATGAAATTGTTATGTCATGATGAGGACATCTAGCCATCTTTAAAGAAATTTGAGATAACA
TAGTTCCTTCATGACGAGGATATATGGCTATCTAAGGATAACGCGACTCCTTCGTGATGAGGAGT
TCTGATTGGTAG
Found at i:1769420 original size:124 final size:124
Alignment explanation
Indices: 1769282--1769506 Score: 353
Period size: 124 Copynumber: 1.8 Consensus size: 124
1769272 TTGCTGCTGG
* * * * * *
1769282 TGGACACAATATCCTTCTTCGTGAATTTGATATCGTGAATGGCCTATTTGT-TGTGAAGTTGAGC
1 TGGACACAATATCCTTCCTCGTGAAGTTGAAATCGTGAATGACCCATTCGTCT-TGAAGTTGAGC
* *
1769346 CTCGAATTGGATATCCTTCGTTGTGAAGTTGAAATCCCATCTGAAGATGAATGTTACTGA
65 CTAGAATTGGATATCCTTCGTCGTGAAGTTGAAATCCCATCTGAAGATGAATGTTACTGA
*
1769406 TGGACACAATATCCTTCCTCGTGAAGTTGAAATCGTGGATGACCCATTCGTCTTGAAGTTGAGCC
1 TGGACACAATATCCTTCCTCGTGAAGTTGAAATCGTGAATGACCCATTCGTCTTGAAGTTGAGCC
1769471 TAGAATTGGATATCCTTCGTCGTGAAGTTGAAATCC
66 TAGAATTGGATATCCTTCGTCGTGAAGTTGAAATCC
1769507 AAGGGTTGCA
Statistics
Matches: 91, Mismatches: 9, Indels: 2
0.89 0.09 0.02
Matches are distributed among these distances:
124 90 0.99
125 1 0.01
ACGTcount: A:0.26, C:0.18, G:0.23, T:0.33
Consensus pattern (124 bp):
TGGACACAATATCCTTCCTCGTGAAGTTGAAATCGTGAATGACCCATTCGTCTTGAAGTTGAGCC
TAGAATTGGATATCCTTCGTCGTGAAGTTGAAATCCCATCTGAAGATGAATGTTACTGA
Found at i:1771066 original size:52 final size:50
Alignment explanation
Indices: 1770986--1771120 Score: 162
Period size: 51 Copynumber: 2.7 Consensus size: 50
1770976 ATATCTCAAC
* * * * *
1770986 CTTTTTATTCTGGTGTGAGCCTTCAAGATGCCTCATATGGATTACTTTTAT
1 CTTTTTATGCTGATGTGAGCCTTCAAGATGCC-CACATGGATAACTTATAT
* * *
1771037 CTTTTTCATGCTGATGTGAGCCTTTAAGATACCCACATGGATAACTTATGT
1 CTTTTT-ATGCTGATGTGAGCCTTCAAGATGCCCACATGGATAACTTATAT
* *
1771088 ATTTTTATGCTGATGTGAACCTTCAAGATGCCC
1 CTTTTTATGCTGATGTGAGCCTTCAAGATGCCC
1771121 CAGATAGATA
Statistics
Matches: 71, Mismatches: 12, Indels: 3
0.83 0.14 0.03
Matches are distributed among these distances:
50 24 0.34
51 25 0.35
52 22 0.31
ACGTcount: A:0.23, C:0.19, G:0.18, T:0.40
Consensus pattern (50 bp):
CTTTTTATGCTGATGTGAGCCTTCAAGATGCCCACATGGATAACTTATAT
Found at i:1772529 original size:5 final size:5
Alignment explanation
Indices: 1772521--1772568 Score: 55
Period size: 5 Copynumber: 10.0 Consensus size: 5
1772511 TTTAATTTAA
* * *
1772521 TTTCT TTTCT CTT-T TCTCT TTTCT TTT-T TTTCT TTTGT TTTCT TTTCT
1 TTTCT TTTCT TTTCT TTTCT TTTCT TTTCT TTTCT TTTCT TTTCT TTTCT
1772569 CTTTTTCTCT
Statistics
Matches: 35, Mismatches: 6, Indels: 4
0.78 0.13 0.09
Matches are distributed among these distances:
4 6 0.17
5 29 0.83
ACGTcount: A:0.00, C:0.19, G:0.02, T:0.79
Consensus pattern (5 bp):
TTTCT
Found at i:1772561 original size:14 final size:14
Alignment explanation
Indices: 1772521--1772568 Score: 60
Period size: 14 Copynumber: 3.4 Consensus size: 14
1772511 TTTAATTTAA
*
1772521 TTTCTTTTCTCTTT
1 TTTCTTTTCTTTTT
*
1772535 TCTCTTTTCTTTTT
1 TTTCTTTTCTTTTT
*
1772549 TTTCTTTTGTTTTCT
1 TTTCTTTTCTTTT-T
1772564 TTTCT
1 TTTCT
1772569 CTTTTTCTCT
Statistics
Matches: 29, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
14 23 0.79
15 6 0.21
ACGTcount: A:0.00, C:0.19, G:0.02, T:0.79
Consensus pattern (14 bp):
TTTCTTTTCTTTTT
Found at i:1772573 original size:7 final size:7
Alignment explanation
Indices: 1772523--1772556 Score: 50
Period size: 7 Copynumber: 4.9 Consensus size: 7
1772513 TAATTTAATT
1772523 TCTTTTC
1 TCTTTTC
1772530 TCTTTTC
1 TCTTTTC
1772537 TCTTTTC
1 TCTTTTC
* *
1772544 TTTTTTT
1 TCTTTTC
1772551 TCTTTT
1 TCTTTT
1772557 GTTTTCTTTT
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
7 24 1.00
ACGTcount: A:0.00, C:0.21, G:0.00, T:0.79
Consensus pattern (7 bp):
TCTTTTC
Found at i:1778043 original size:30 final size:30
Alignment explanation
Indices: 1778002--1778061 Score: 86
Period size: 29 Copynumber: 2.0 Consensus size: 30
1777992 CAATTTAAGG
1778002 CAAAATGGTTTTTGAAATTGAATTGAATTTA
1 CAAAATGGTTTTTGAAATT-AATTGAATTTA
* *
1778033 CAAAAT-GTTTTTGGACTTAATTGAATTTA
1 CAAAATGGTTTTTGAAATTAATTGAATTTA
1778062 TTCAAAGTTT
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
29 11 0.41
30 10 0.37
31 6 0.22
ACGTcount: A:0.37, C:0.05, G:0.15, T:0.43
Consensus pattern (30 bp):
CAAAATGGTTTTTGAAATTAATTGAATTTA
Found at i:1778270 original size:21 final size:21
Alignment explanation
Indices: 1778244--1778284 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
1778234 ATTTGAATTT
1778244 TATGAAGGGGTA-TCGATACCA
1 TATGAAGGGGTACT-GATACCA
*
1778265 TATGAATGGGTACTGATACC
1 TATGAAGGGGTACTGATACC
1778285 CCCTGTACGG
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
21 17 0.94
22 1 0.06
ACGTcount: A:0.32, C:0.15, G:0.27, T:0.27
Consensus pattern (21 bp):
TATGAAGGGGTACTGATACCA
Found at i:1778607 original size:34 final size:32
Alignment explanation
Indices: 1778568--1778637 Score: 95
Period size: 34 Copynumber: 2.1 Consensus size: 32
1778558 TTTTGTAAAG
* *
1778568 GGGAAAGGTTCTAGCTTAGCCCGTGTAAAAGCTA
1 GGGAAAAGTTCTAGCTTAGCCCG-G-AAAAACTA
*
1778602 GGGAAAAGTTCTAGTTTAGCCCGGAAAAACTA
1 GGGAAAAGTTCTAGCTTAGCCCGGAAAAACTA
1778634 GGGA
1 GGGA
1778638 GTTTGTAAGG
Statistics
Matches: 33, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
32 11 0.33
33 1 0.03
34 21 0.64
ACGTcount: A:0.33, C:0.16, G:0.30, T:0.21
Consensus pattern (32 bp):
GGGAAAAGTTCTAGCTTAGCCCGGAAAAACTA
Found at i:1781248 original size:30 final size:30
Alignment explanation
Indices: 1781214--1781276 Score: 108
Period size: 30 Copynumber: 2.1 Consensus size: 30
1781204 GTTATATGAG
* *
1781214 CTATGTGATAAAGGTATGTAAATGATATGT
1 CTATGTGATAAAGGTATGCAAATAATATGT
1781244 CTATGTGATAAAGGTATGCAAATAATATGT
1 CTATGTGATAAAGGTATGCAAATAATATGT
1781274 CTA
1 CTA
1781277 CGCGATATGA
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
30 31 1.00
ACGTcount: A:0.38, C:0.06, G:0.21, T:0.35
Consensus pattern (30 bp):
CTATGTGATAAAGGTATGCAAATAATATGT
Found at i:1781555 original size:23 final size:23
Alignment explanation
Indices: 1781529--1781603 Score: 82
Period size: 23 Copynumber: 3.2 Consensus size: 23
1781519 GGCATTACGA
1781529 TGCAATTCTACGTGGCACTTCGG
1 TGCAATTCTACGTGGCACTTCGG
* *
1781552 TGCAATTCTACGCGGTC-CTTTGG
1 TGCAATTCTACGTGG-CACTTCGG
*
1781575 -GACAAATTCTATGTGGCACTTCGG
1 TG-C-AATTCTACGTGGCACTTCGG
1781599 TGCAA
1 TGCAA
1781604 ATTTATATGA
Statistics
Matches: 42, Mismatches: 5, Indels: 10
0.74 0.09 0.18
Matches are distributed among these distances:
22 1 0.02
23 23 0.55
24 17 0.40
25 1 0.02
ACGTcount: A:0.20, C:0.24, G:0.25, T:0.31
Consensus pattern (23 bp):
TGCAATTCTACGTGGCACTTCGG
Done.