Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01009001.1 Hibiscus syriacus cultivar Beakdansim tig00112383_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: 4740655
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 8 of 24
Found at i:1600039 original size:20 final size:20
Alignment explanation
Indices: 1600011--1600240 Score: 203
Period size: 20 Copynumber: 11.5 Consensus size: 20
1600001 AAATTTCAGT
* *
1600011 GTTGTGATTTACAGATTCTC
1 GTTGCGATTTACGGATTCTC
*
1600031 GTTGCGATTTACGGATTATC
1 GTTGCGATTTACGGATTCTC
*
1600051 GTTGCGATTTACAGATTCTC
1 GTTGCGATTTACGGATTCTC
*
1600071 GTTGCGATTTACGGATTATC
1 GTTGCGATTTACGGATTCTC
*
1600091 GTTGCGATTTACGGATACGT-
1 GTTGCGATTTACGGATTC-TC
* * *
1600111 GTTGCGATATACGGATACAC
1 GTTGCGATTTACGGATTCTC
* ** * *
1600131 ATTGCGATTTACCCATACGC
1 GTTGCGATTTACGGATTCTC
* *
1600151 GTTGCGATTTACGGATACAC
1 GTTGCGATTTACGGATTCTC
* **
1600171 GTTGCGATTTACGGATACGA
1 GTTGCGATTTACGGATTCTC
* *
1600191 GTTGCGATTTATGTG-TTCGC
1 GTTGCGATTTACG-GATTCTC
* ** *
1600211 GTTGCGATTTTCATATTCGC
1 GTTGCGATTTACGGATTCTC
1600231 GTTGCGATTT
1 GTTGCGATTT
1600241 TGGAAAATCG
Statistics
Matches: 177, Mismatches: 29, Indels: 8
0.83 0.14 0.04
Matches are distributed among these distances:
20 175 0.99
21 2 0.01
ACGTcount: A:0.20, C:0.18, G:0.24, T:0.37
Consensus pattern (20 bp):
GTTGCGATTTACGGATTCTC
Found at i:1600257 original size:21 final size:21
Alignment explanation
Indices: 1600227--1600309 Score: 78
Period size: 21 Copynumber: 4.0 Consensus size: 21
1600217 ATTTTCATAT
*
1600227 TCGCGTTGCGATTTTGGAAAA
1 TCGCATTGCGATTTTGGAAAA
* * * **
1600248 TCGCAATGCGAATTTGTACTA
1 TCGCATTGCGATTTTGGAAAA
*
1600269 TCGCATTGCGATTTT-CAAGAA
1 TCGCATTGCGATTTTGGAA-AA
*
1600290 TCGCGTTGCGATTTTGGAAA
1 TCGCATTGCGATTTTGGAAA
1600310 CTGATTTGCG
Statistics
Matches: 47, Mismatches: 13, Indels: 4
0.73 0.20 0.06
Matches are distributed among these distances:
20 1 0.02
21 44 0.94
22 2 0.04
ACGTcount: A:0.25, C:0.17, G:0.24, T:0.34
Consensus pattern (21 bp):
TCGCATTGCGATTTTGGAAAA
Found at i:1600300 original size:42 final size:43
Alignment explanation
Indices: 1600207--1600305 Score: 100
Period size: 42 Copynumber: 2.4 Consensus size: 43
1600197 ATTTATGTGT
* *
1600207 TCGCGTTGCG-ATTT-TCATATTCGCGTTGCGATTTTGGAAAA
1 TCGCGTTGCGAATTTGTCATATTCGCATTGCGATTTTGCAAAA
**
1600248 TCGCAATGCGAATTTGT-ACTA-TCGCATTGCGATTTT-CAAGAA
1 TCGCGTTGCGAATTTGTCA-TATTCGCATTGCGATTTTGCAA-AA
*
1600290 TCGCGTTGCGATTTTG
1 TCGCGTTGCGAATTTG
1600306 GAAACTGATT
Statistics
Matches: 47, Mismatches: 7, Indels: 7
0.77 0.11 0.11
Matches are distributed among these distances:
41 10 0.21
42 34 0.72
43 3 0.06
ACGTcount: A:0.21, C:0.18, G:0.23, T:0.37
Consensus pattern (43 bp):
TCGCGTTGCGAATTTGTCATATTCGCATTGCGATTTTGCAAAA
Found at i:1601069 original size:14 final size:14
Alignment explanation
Indices: 1601046--1601084 Score: 60
Period size: 14 Copynumber: 2.7 Consensus size: 14
1601036 ACGCGACATA
1601046 TTTAAGGTTTTGAG
1 TTTAAGGTTTTGAG
*
1601060 TTTAATGTTTTGAG
1 TTTAAGGTTTTGAG
1601074 TTTTAAGGTTT
1 -TTTAAGGTTT
1601085 AAAATCTATA
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
14 13 0.59
15 9 0.41
ACGTcount: A:0.21, C:0.00, G:0.23, T:0.56
Consensus pattern (14 bp):
TTTAAGGTTTTGAG
Found at i:1605386 original size:2 final size:2
Alignment explanation
Indices: 1605379--1605405 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
1605369 AGTAAAGTAA
1605379 AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT A
1605406 AAAGTTATTA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:1607072 original size:3 final size:3
Alignment explanation
Indices: 1607064--1607101 Score: 60
Period size: 3 Copynumber: 13.0 Consensus size: 3
1607054 AAAATGTATT
*
1607064 TAA TAA TAA TAA TAA T-A TAT TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1607102 CAAAAGTAAA
Statistics
Matches: 32, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
2 2 0.06
3 30 0.94
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (3 bp):
TAA
Found at i:1607088 original size:20 final size:20
Alignment explanation
Indices: 1607063--1607100 Score: 76
Period size: 20 Copynumber: 1.9 Consensus size: 20
1607053 TAAAATGTAT
1607063 TTAATAATAATAATAATATA
1 TTAATAATAATAATAATATA
1607083 TTAATAATAATAATAATA
1 TTAATAATAATAATAATA
1607101 ACAAAAGTAA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (20 bp):
TTAATAATAATAATAATATA
Found at i:1607454 original size:116 final size:116
Alignment explanation
Indices: 1607250--1607776 Score: 757
Period size: 116 Copynumber: 4.5 Consensus size: 116
1607240 TTCTGCCTAG
* * *
1607250 AGGTCTTATGAATGGCCCTGAGGTCTTATCATCTTGCACCGAAGGTCTTACAGATGACCCAGAGG
1 AGGTCTTATGGATGGCCCTGAGGTCTTATCATCTTGCACTGTAGGTCTTACAGATGACCCAGAGG
* ** *
1607315 TTTTAAATATCAAAAACCTCCCGAAGGCTTTTTTTACACATCCTGCACTGT
66 TTTTAAATATCAAAAAGCTCCCGAAGGCTTTTTGAAAACATCCTGCACTGT
* * *
1607366 AGGTCTTATGGATGGCCATGAGGTCTTATCATCTTGCACTGTAGATCTTACAGATGACCCGGAGG
1 AGGTCTTATGGATGGCCCTGAGGTCTTATCATCTTGCACTGTAGGTCTTACAGATGACCCAGAGG
* * *
1607431 TTTTAAATATCAAAAAGCTCCCGAAGGATTTTTGAAAACATTCTACACTGT
66 TTTTAAATATCAAAAAGCTCCCGAAGGCTTTTTGAAAACATCCTGCACTGT
* *
1607482 AGGTGTTATGGATAGCCCTGAGGTCTTATCATCTTGCACTGTAGGTCTTACAGATGACCCAGAGG
1 AGGTCTTATGGATGGCCCTGAGGTCTTATCATCTTGCACTGTAGGTCTTACAGATGACCCAGAGG
* * *
1607547 CTTTAAATATCAAAAAGCTCCTGAAGGCTTTTTTGAAAACATCCTGAACTGT
66 TTTTAAATATCAAAAAGCTCCCGAAGGC-TTTTTGAAAACATCCTGCACTGT
1607599 AGGTCTTATGGATGGCCCTGAGGTCTTATCATCTTGCACTGTAGGTCTTACAGATGACCCAGAGG
1 AGGTCTTATGGATGGCCCTGAGGTCTTATCATCTTGCACTGTAGGTCTTACAGATGACCCAGAGG
* * * * * * *
1607664 CTTTAAAATATCAAAAAACTGCAGAAGGCCTTTTGAAAATATTCTGCACTGT
66 -TTTTAAATATCAAAAAGCTCCCGAAGGCTTTTTGAAAACATCCTGCACTGT
* * * *
1607716 AGGTCTTATGGATGGCCCTGAGGATTTTAAACATCCTGCACTGGAGGTCTTACAGATGACC
1 AGGTCTTATGGATGGCCCTGAGG-TCTT-ATCATCTTGCACTGTAGGTCTTACAGATGACC
1607777 TGAAGGATTT
Statistics
Matches: 368, Mismatches: 39, Indels: 5
0.89 0.09 0.01
Matches are distributed among these distances:
116 188 0.51
117 125 0.34
118 26 0.07
119 29 0.08
ACGTcount: A:0.28, C:0.21, G:0.21, T:0.30
Consensus pattern (116 bp):
AGGTCTTATGGATGGCCCTGAGGTCTTATCATCTTGCACTGTAGGTCTTACAGATGACCCAGAGG
TTTTAAATATCAAAAAGCTCCCGAAGGCTTTTTGAAAACATCCTGCACTGT
Found at i:1607784 original size:44 final size:43
Alignment explanation
Indices: 1607707--1607817 Score: 168
Period size: 44 Copynumber: 2.5 Consensus size: 43
1607697 TGAAAATATT
* ** *
1607707 CTGCACTGTAGGTCTTATGGATGGCCCTGAGGATTTTAAACATC
1 CTGCACTGGAGGTCTTACAGAT-GACCTGAGGATTTTAAACATC
1607751 CTGCACTGGAGGTCTTACAGATGACCTGAAGGATTTTAAACATC
1 CTGCACTGGAGGTCTTACAGATGACCTG-AGGATTTTAAACATC
1607795 CTGCACTGGAGGTCTTACAGATG
1 CTGCACTGGAGGTCTTACAGATG
1607818 CGGGAAATAG
Statistics
Matches: 62, Mismatches: 4, Indels: 2
0.91 0.06 0.03
Matches are distributed among these distances:
43 5 0.08
44 57 0.92
ACGTcount: A:0.25, C:0.21, G:0.25, T:0.29
Consensus pattern (43 bp):
CTGCACTGGAGGTCTTACAGATGACCTGAGGATTTTAAACATC
Found at i:1608506 original size:22 final size:22
Alignment explanation
Indices: 1608481--1608557 Score: 106
Period size: 22 Copynumber: 3.5 Consensus size: 22
1608471 AATAAAGCTT
1608481 TCATCTTTGAAAAGATAATATA
1 TCATCTTTGAAAAGATAATATA
1608503 TCATCTTT-AAAGAGATAATATA
1 TCATCTTTGAAA-AGATAATATA
1608525 TCATCTTTGAAGAATGA-AA-ATA
1 TCATCTTTGAA-AA-GATAATATA
1608547 TCATCTTTGAA
1 TCATCTTTGAA
1608558 GAATGTAGAT
Statistics
Matches: 51, Mismatches: 0, Indels: 8
0.86 0.00 0.14
Matches are distributed among these distances:
21 3 0.06
22 40 0.78
23 5 0.10
24 3 0.06
ACGTcount: A:0.43, C:0.10, G:0.10, T:0.36
Consensus pattern (22 bp):
TCATCTTTGAAAAGATAATATA
Found at i:1615998 original size:2 final size:2
Alignment explanation
Indices: 1615993--1616017 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
1615983 AATATAAAAG
1615993 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 T
1616018 TTAAGTTATT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:1616178 original size:2 final size:2
Alignment explanation
Indices: 1616171--1616211 Score: 73
Period size: 2 Copynumber: 20.5 Consensus size: 2
1616161 AATGAAGTAA
*
1616171 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT TT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1616212 AATAAGATAT
Statistics
Matches: 37, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
AT
Found at i:1617676 original size:3 final size:3
Alignment explanation
Indices: 1617668--1617708 Score: 57
Period size: 3 Copynumber: 14.0 Consensus size: 3
1617658 GAAATGTATT
* *
1617668 TAA TAA TAA TAA TAA TAA TAA T-A TAT TAT TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1617709 AAAAAGTAAA
Statistics
Matches: 35, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
2 2 0.06
3 33 0.94
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (3 bp):
TAA
Found at i:1625505 original size:33 final size:33
Alignment explanation
Indices: 1625452--1625549 Score: 164
Period size: 32 Copynumber: 3.0 Consensus size: 33
1625442 TTTGTTTCAA
1625452 TTATCGAACTT-GAAGTTTTTAAGTATTTGAAT
1 TTATCGAACTTGGAAGTTTTTAAGTATTTGAAT
1625484 TTATCGAACTTGGAAGTTTTTAAGTATTTGAAT
1 TTATCGAACTTGGAAGTTTTTAAGTATTTGAAT
* *
1625517 TTATC-AACTTGGAAGTATTTAAGTATTTCAAT
1 TTATCGAACTTGGAAGTTTTTAAGTATTTGAAT
1625549 T
1 T
1625550 ATTGAGTTAA
Statistics
Matches: 63, Mismatches: 2, Indels: 2
0.94 0.03 0.03
Matches are distributed among these distances:
32 37 0.59
33 26 0.41
ACGTcount: A:0.32, C:0.07, G:0.15, T:0.46
Consensus pattern (33 bp):
TTATCGAACTTGGAAGTTTTTAAGTATTTGAAT
Found at i:1625576 original size:13 final size:13
Alignment explanation
Indices: 1625535--1625587 Score: 56
Period size: 13 Copynumber: 4.2 Consensus size: 13
1625525 TTGGAAGTAT
1625535 TTAAGTATTTCAA
1 TTAAGTATTTCAA
* *
1625548 TT-ATTGAGTT-AA
1 TTAAGT-ATTTCAA
1625560 TTAAGTATTTCAA
1 TTAAGTATTTCAA
*
1625573 TTAAGTATTTGAA
1 TTAAGTATTTCAA
1625586 TT
1 TT
1625588 TATCGAACTT
Statistics
Matches: 32, Mismatches: 5, Indels: 6
0.74 0.12 0.14
Matches are distributed among these distances:
12 9 0.28
13 23 0.72
ACGTcount: A:0.36, C:0.04, G:0.11, T:0.49
Consensus pattern (13 bp):
TTAAGTATTTCAA
Found at i:1626034 original size:15 final size:15
Alignment explanation
Indices: 1625994--1626037 Score: 52
Period size: 17 Copynumber: 2.8 Consensus size: 15
1625984 AAAATCGGAA
*
1625994 TTTTTATAACCGGTT
1 TTTTTAAAACCGGTT
*
1626009 TTTTAAAAAAACCGGTT
1 TTTT--TAAAACCGGTT
1626026 TTTTTAAAACCG
1 TTTTTAAAACCG
1626038 AAACCGGTTA
Statistics
Matches: 24, Mismatches: 3, Indels: 4
0.77 0.10 0.13
Matches are distributed among these distances:
15 11 0.46
17 13 0.54
ACGTcount: A:0.32, C:0.14, G:0.11, T:0.43
Consensus pattern (15 bp):
TTTTTAAAACCGGTT
Found at i:1626046 original size:21 final size:18
Alignment explanation
Indices: 1626001--1626034 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
1625991 GAATTTTTAT
1626001 AACCGG-TTTTTTAAAAA
1 AACCGGTTTTTTTAAAAA
1626018 AACCGGTTTTTTTAAAA
1 AACCGGTTTTTTTAAAA
1626035 CCGAAACCGG
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 6 0.38
18 10 0.62
ACGTcount: A:0.38, C:0.12, G:0.12, T:0.38
Consensus pattern (18 bp):
AACCGGTTTTTTTAAAAA
Found at i:1626154 original size:15 final size:17
Alignment explanation
Indices: 1626128--1626159 Score: 50
Period size: 16 Copynumber: 2.0 Consensus size: 17
1626118 TTCTATGAGA
1626128 AAAAACCGGAT-CGGAT
1 AAAAACCGGATCCGGAT
1626144 AAAAACC-GATCCGGAT
1 AAAAACCGGATCCGGAT
1626160 CGGATTGAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
15 3 0.20
16 12 0.80
ACGTcount: A:0.44, C:0.22, G:0.22, T:0.12
Consensus pattern (17 bp):
AAAAACCGGATCCGGAT
Found at i:1627414 original size:57 final size:57
Alignment explanation
Indices: 1627345--1627458 Score: 228
Period size: 57 Copynumber: 2.0 Consensus size: 57
1627335 TCGCGATAAA
1627345 TGAACTCTCTGATATGGGTGAGTGCCTCATACCATAGGAATAAAAAATGACTTTAAC
1 TGAACTCTCTGATATGGGTGAGTGCCTCATACCATAGGAATAAAAAATGACTTTAAC
1627402 TGAACTCTCTGATATGGGTGAGTGCCTCATACCATAGGAATAAAAAATGACTTTAAC
1 TGAACTCTCTGATATGGGTGAGTGCCTCATACCATAGGAATAAAAAATGACTTTAAC
1627459 GACAAGTCGG
Statistics
Matches: 57, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
57 57 1.00
ACGTcount: A:0.35, C:0.18, G:0.19, T:0.28
Consensus pattern (57 bp):
TGAACTCTCTGATATGGGTGAGTGCCTCATACCATAGGAATAAAAAATGACTTTAAC
Found at i:1630867 original size:7 final size:7
Alignment explanation
Indices: 1630855--1630987 Score: 77
Period size: 7 Copynumber: 19.3 Consensus size: 7
1630845 CGGACACATT
1630855 TAGTATA
1 TAGTATA
1630862 TAGTATA
1 TAGTATA
1630869 TAGTATA
1 TAGTATA
*
1630876 TTATGGTACA
1 -TA--GTATA
1630886 TAGTATA
1 TAGTATA
1630893 T--TATA
1 TAGTATA
1630898 T--TATA
1 TAGTATA
1630903 TA-TATA
1 TAGTATA
*
1630909 TATTATA
1 TAGTATA
*
1630916 TAGTAAAA
1 TAGT-ATA
*
1630924 TATTATA
1 TAGTATA
*
1630931 T-TTATA
1 TAGTATA
1630937 TA-T-TA
1 TAGTATA
1630942 T-GTATA
1 TAGTATA
*
1630948 TATTATA
1 TAGTATA
1630955 TTAGCTATA
1 -TAG-TATA
*
1630964 TACTATA
1 TAGTATA
1630971 TAGTATA
1 TAGTATA
1630978 TATGTATA
1 TA-GTATA
1630986 TA
1 TA
1630988 TTTAGTACAT
Statistics
Matches: 103, Mismatches: 10, Indels: 25
0.75 0.07 0.18
Matches are distributed among these distances:
5 14 0.14
6 16 0.16
7 45 0.44
8 18 0.17
9 6 0.06
10 4 0.04
ACGTcount: A:0.41, C:0.02, G:0.08, T:0.48
Consensus pattern (7 bp):
TAGTATA
Found at i:1630870 original size:2 final size:2
Alignment explanation
Indices: 1630858--1631104 Score: 98
Period size: 2 Copynumber: 133.0 Consensus size: 2
1630848 ACACATTTAG
* *
1630858 TA TA TA GTA TA TA GTA TA T- TA TGG TA CA TA GTA TA T- TA TA T-
1 TA TA TA -TA TA TA -TA TA TA TA T-A TA TA TA -TA TA TA TA TA TA
* *
1630899 TA TA TA TA TA TA T- TA TA TA GTA -A AA TA T- TA TA TT 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
* **
1630939 T- TA TG TA TA TA T- TA TA T- TA GC TA TA TA CTA TA TA GTA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA -TA TA TA -TA TA TA
* * * *
1630980 TG TA TA TA TT TA GTA CA TA T- TA TA T- TA TA T- TA TA TT TA TA
1 TA TA TA TA TA TA -TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
* * *
1631020 -A TA T- TA T- TA TG T- TA TA TA TA GA TA -A TA T- TA TT TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
*
1631056 T- TA TA TA TA -A TA T- TA T- TA TG T- TA TA TA TA TA -A TA T-
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1631091 TA T- TA TA T- TA TA TA
1 TA TA TA TA TA TA TA TA
1631105 CTTATTATAT
Statistics
Matches: 183, Mismatches: 27, Indels: 70
0.65 0.10 0.25
Matches are distributed among these distances:
1 27 0.15
2 141 0.77
3 15 0.08
ACGTcount: A:0.41, C:0.02, G:0.06, T:0.51
Consensus pattern (2 bp):
TA
Found at i:1630926 original size:15 final size:13
Alignment explanation
Indices: 1630895--1630955 Score: 54
Period size: 13 Copynumber: 4.7 Consensus size: 13
1630885 ATAGTATATT
*
1630895 ATATTATATATAT
1 ATATTATATATAA
1630908 ATATTATATAGTAAA
1 ATATTATATA-T-AA
* *
1630923 ATATTATATTTAT
1 ATATTATATATAA
*
1630936 ATATTATGTAT--
1 ATATTATATATAA
1630947 ATATTATAT
1 ATATTATAT
1630956 TAGCTATATA
Statistics
Matches: 40, Mismatches: 6, Indels: 6
0.77 0.12 0.12
Matches are distributed among these distances:
11 8 0.20
13 20 0.50
14 2 0.05
15 10 0.25
ACGTcount: A:0.44, C:0.00, G:0.03, T:0.52
Consensus pattern (13 bp):
ATATTATATATAA
Found at i:1631073 original size:45 final size:45
Alignment explanation
Indices: 1630960--1631104 Score: 172
Period size: 45 Copynumber: 3.1 Consensus size: 45
1630950 TTATATTAGC
* *
1630960 TATATACTATATAGTATATATGTATATATTTAG-TACATATTATATTATAT
1 TATATA-TA-ATATTAT-TATGT-TATATATAGATA-ATATTAT-TTATAT
1631010 TATATTTATAATATTATTATGTTATATATAGATAATATTATTTATAT
1 TATA--TATAATATTATTATGTTATATATAGATAATATTATTTATAT
1631057 TATATATAATATTATTATGTTATATAT--ATAATATTA-TTATAT
1 TATATATAATATTATTATGTTATATATAGATAATATTATTTATAT
1631099 TATATA
1 TATATA
1631105 CTTATTATAT
Statistics
Matches: 90, Mismatches: 2, Indels: 14
0.85 0.02 0.13
Matches are distributed among these distances:
42 12 0.13
43 9 0.10
45 23 0.26
47 10 0.11
48 15 0.17
49 7 0.08
50 10 0.11
51 2 0.02
52 2 0.02
ACGTcount: A:0.41, C:0.01, G:0.04, T:0.53
Consensus pattern (45 bp):
TATATATAATATTATTATGTTATATATAGATAATATTATTTATAT
Found at i:1631115 original size:5 final size:5
Alignment explanation
Indices: 1630889--1631116 Score: 115
Period size: 5 Copynumber: 45.4 Consensus size: 5
1630879 TGGTACATAG
* *
1630889 TATAT TATAT TATA- TATA- TATAT TATA- TAGTAA AATAT TATAT T-TA-
1 TATAT TATAT TATAT TATAT TATAT TATAT TA-TAT TATAT TATAT TATAT
* *
1630935 TATAT TATGT ATATAT TATAT TAGCTA- TATAC TATA- TAGTA- TATAT
1 TATAT TATAT -TATAT TATAT TA--TAT TATAT TATAT TA-TAT TATAT
* *
1630981 GTATA- TAT-T TAGTA- CATAT TATAT TATAT TATATT TATAA TATTAT
1 -TATAT TATAT TA-TAT TATAT TATAT TATAT TATA-T TATAT TA-TAT
* * * * *
1631027 TATGT TATAT ATAGAT AATAT TAT-T TATAT TATA- TATAA TATTAT TATGT
1 TATAT TATAT -TATAT TATAT TATAT TATAT TATAT TATAT TA-TAT TATAT
*
1631077 TATAT ATATAA TATTAT TATAT TATA- TACTTAT TATAT TA
1 TATAT -TATAT TA-TAT TATAT TATAT TA--TAT TATAT TA
1631117 ATTTATTTAA
Statistics
Matches: 176, Mismatches: 20, Indels: 54
0.70 0.08 0.22
Matches are distributed among these distances:
3 1 0.01
4 37 0.21
5 96 0.55
6 38 0.22
7 4 0.02
ACGTcount: A:0.41, C:0.02, G:0.04, T:0.53
Consensus pattern (5 bp):
TATAT
Found at i:1631115 original size:24 final size:23
Alignment explanation
Indices: 1630889--1631116 Score: 161
Period size: 22 Copynumber: 9.7 Consensus size: 23
1630879 TGGTACATAG
*
1630889 TATATTATATTATATATATATATTA
1 TATATTATAATAT-TAT-TATATTA
* *
1630914 TATAGTAAAATATTA-TAT-TTA
1 TATATTATAATATTATTATATTA
*
1630935 TATATTAT-GTATATATTATATTA
1 TATATTATAATAT-TATTATATTA
*
1630958 GCTATA-TACTATATAGTA-TATATGTA
1 --TATATTA-TA-ATATTATTATAT-TA
1630984 TATATTTAGTACATATTATATTATATTA
1 TATA-TTA-TA-ATA-T-TATTATATTA
*
1631012 TAT-TTATAATATTATTATGTTA
1 TATATTATAATATTATTATATTA
*
1631034 TATATAGATAATATTATT-TA-TA
1 TATAT-TATAATATTATTATATTA
*
1631056 T-TATATATAATATTATTATGTTA
1 TATAT-TATAATATTATTATATTA
1631079 TATA-TATAATATTATTATATTA
1 TATATTATAATATTATTATATTA
*
1631101 TATACTTATTATATTA
1 TATA-TTATAATATTA
1631117 ATTTATTTAA
Statistics
Matches: 164, Mismatches: 18, Indels: 43
0.73 0.08 0.19
Matches are distributed among these distances:
20 3 0.02
21 26 0.16
22 43 0.26
23 9 0.05
24 33 0.20
25 22 0.13
26 14 0.09
27 2 0.01
28 7 0.04
29 5 0.03
ACGTcount: A:0.41, C:0.02, G:0.04, T:0.53
Consensus pattern (23 bp):
TATATTATAATATTATTATATTA
Found at i:1635621 original size:18 final size:17
Alignment explanation
Indices: 1635598--1635634 Score: 65
Period size: 17 Copynumber: 2.1 Consensus size: 17
1635588 TCTTTATCTA
1635598 AATAAATAAAAATAAAAT
1 AATAAAT-AAAATAAAAT
1635616 AATAAATAAAATAAAAT
1 AATAAATAAAATAAAAT
1635633 AA
1 AA
1635635 AAAACATACC
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
17 12 0.63
18 7 0.37
ACGTcount: A:0.78, C:0.00, G:0.00, T:0.22
Consensus pattern (17 bp):
AATAAATAAAATAAAAT
Found at i:1638577 original size:35 final size:37
Alignment explanation
Indices: 1638508--1638578 Score: 103
Period size: 36 Copynumber: 1.9 Consensus size: 37
1638498 CTGATCTTGC
1638508 TTCACTACTCTTTTTTGTGAATGTTGGATATGCATTGT
1 TTCACTAC-CTTTTTTGTGAATGTTGGATATGCATTGT
1638546 TTCACTA-CTTTTTTGTGAATGCTT-GAT-TGCATT
1 TTCACTACCTTTTTTGTGAATG-TTGGATATGCATT
1638579 TCTTGTTTCC
Statistics
Matches: 32, Mismatches: 0, Indels: 5
0.86 0.00 0.14
Matches are distributed among these distances:
35 6 0.19
36 17 0.53
37 2 0.06
38 7 0.22
ACGTcount: A:0.18, C:0.14, G:0.17, T:0.51
Consensus pattern (37 bp):
TTCACTACCTTTTTTGTGAATGTTGGATATGCATTGT
Found at i:1647777 original size:14 final size:15
Alignment explanation
Indices: 1647752--1647780 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
1647742 CATGATATGA
1647752 AAATGAAAAATGAAG
1 AAATGAAAAATGAAG
1647767 AAATG-AAAATGAAG
1 AAATGAAAAATGAAG
1647781 CATAAAAATT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 9 0.64
15 5 0.36
ACGTcount: A:0.66, C:0.00, G:0.21, T:0.14
Consensus pattern (15 bp):
AAATGAAAAATGAAG
Found at i:1650318 original size:21 final size:21
Alignment explanation
Indices: 1650292--1650331 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
1650282 TGTAACAAGT
1650292 AATAATAATAA-TATAATATAA
1 AATAAT-ATAATTATAATATAA
*
1650313 AATAATGTAATTATAATAT
1 AATAATATAATTATAATAT
1650332 TATATTGAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 3 0.18
21 14 0.82
ACGTcount: A:0.60, C:0.00, G:0.03, T:0.38
Consensus pattern (21 bp):
AATAATATAATTATAATATAA
Found at i:1650936 original size:16 final size:17
Alignment explanation
Indices: 1650899--1650942 Score: 54
Period size: 16 Copynumber: 2.6 Consensus size: 17
1650889 ATGATAAAAA
* *
1650899 TTAAAGAAATTATTTGT
1 TTAAATAAATTATTTAT
1650916 TTAAATAAATTA-TTAT
1 TTAAATAAATTATTTAT
*
1650932 TTAAATTAATT
1 TTAAATAAATT
1650943 GTAAATTGTT
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
16 13 0.54
17 11 0.46
ACGTcount: A:0.45, C:0.00, G:0.05, T:0.50
Consensus pattern (17 bp):
TTAAATAAATTATTTAT
Found at i:1651303 original size:29 final size:27
Alignment explanation
Indices: 1651271--1651343 Score: 101
Period size: 29 Copynumber: 2.6 Consensus size: 27
1651261 CCAAAATTTA
*
1651271 TTTGAAATTTATTAACTGAACCGAATTAT
1 TTTGAAAATTATTAACT-AACCGAA-TAT
1651300 TTTGAAAATTATTAACCTAACCGAATAT
1 TTTGAAAATTATTAA-CTAACCGAATAT
*
1651328 ATTGAAAATTATTAAC
1 TTTGAAAATTATTAAC
1651344 CGAATTAATC
Statistics
Matches: 41, Mismatches: 2, Indels: 4
0.87 0.04 0.09
Matches are distributed among these distances:
27 1 0.02
28 17 0.41
29 21 0.51
30 2 0.05
ACGTcount: A:0.42, C:0.11, G:0.08, T:0.38
Consensus pattern (27 bp):
TTTGAAAATTATTAACTAACCGAATAT
Found at i:1651344 original size:28 final size:30
Alignment explanation
Indices: 1651268--1651344 Score: 108
Period size: 28 Copynumber: 2.7 Consensus size: 30
1651258 GAACCAAAAT
*
1651268 TTAT-TTGAAATTTATTAA-CTGAACCGAA
1 TTATATTGAAAATTATTAACCTGAACCGAA
*
1651296 TTATTTTGAAAATTATTAACCT-AACCGAA
1 TTATATTGAAAATTATTAACCTGAACCGAA
1651325 -TATATTGAAAATTATTAACC
1 TTATATTGAAAATTATTAACC
1651345 GAATTAATCG
Statistics
Matches: 45, Mismatches: 2, Indels: 4
0.88 0.04 0.08
Matches are distributed among these distances:
28 23 0.51
29 20 0.44
30 2 0.04
ACGTcount: A:0.42, C:0.12, G:0.08, T:0.39
Consensus pattern (30 bp):
TTATATTGAAAATTATTAACCTGAACCGAA
Found at i:1651362 original size:131 final size:130
Alignment explanation
Indices: 1651202--1651446 Score: 411
Period size: 131 Copynumber: 1.9 Consensus size: 130
1651192 AATTTTTTTT
* *
1651202 AAATTAATAACCGAATTAATTGAAGCAAAAATTTGGTTAATTC-GATTCGGTTAATCGAACCAAA
1 AAATTAATAACCGAATTAATCGAAGCAAAAATTTGGTTAATTCAG-TTCGGTTAATCAAACCAAA
* *
1651266 ATTTATTTGAAATTTATTAACTGAACCGAATTATTTTGAAAATTATTAACCTAACCGAATATATT
65 ATTTATTTGAAA-TTATTAACCGAACCGAATTAATTTGAAAATTATTAACCTAACCGAATATATT
1651331 GA
129 GA
* *
1651333 AAATTATTAACCGAATTAATCGAAGCAAAAATTTGGTTAATTCAGTTCGGTTAATCAAACCAAGA
1 AAATTAATAACCGAATTAATCGAAGCAAAAATTTGGTTAATTCAGTTCGGTTAATCAAACCAAAA
1651398 TTTATTTGAAATTATTAACCGAACCGAATTAATTTGAAAATTATTAACC
66 TTTATTTGAAATTATTAACCGAACCGAATTAATTTGAAAATTATTAACC
1651447 GAATTTTCTC
Statistics
Matches: 107, Mismatches: 6, Indels: 3
0.92 0.05 0.03
Matches are distributed among these distances:
130 36 0.34
131 70 0.65
132 1 0.01
ACGTcount: A:0.42, C:0.12, G:0.11, T:0.34
Consensus pattern (130 bp):
AAATTAATAACCGAATTAATCGAAGCAAAAATTTGGTTAATTCAGTTCGGTTAATCAAACCAAAA
TTTATTTGAAATTATTAACCGAACCGAATTAATTTGAAAATTATTAACCTAACCGAATATATTGA
Found at i:1652440 original size:5 final size:5
Alignment explanation
Indices: 1652432--1652458 Score: 54
Period size: 5 Copynumber: 5.4 Consensus size: 5
1652422 GAAACACGGT
1652432 GGAGG GGAGG GGAGG GGAGG GGAGG GG
1 GGAGG GGAGG GGAGG GGAGG GGAGG GG
1652459 CATTGTTGGT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 22 1.00
ACGTcount: A:0.19, C:0.00, G:0.81, T:0.00
Consensus pattern (5 bp):
GGAGG
Found at i:1652873 original size:48 final size:47
Alignment explanation
Indices: 1652774--1652904 Score: 158
Period size: 48 Copynumber: 2.8 Consensus size: 47
1652764 AAACTTATCA
* **
1652774 TAACATGTAACTTTCATGTTAAAAACTTATATCATAAATTCATAATT
1 TAACATATAACTTTCATGACAAAAACTTATATCATAAATTCATAATT
*
1652821 TAACATATAACTTTCATGACAAGAACTTGCA-ATCATAAATTCATAATT
1 TAACATATAACTTTCATGACAAAAACTT--ATATCATAAATTCATAATT
* * *
1652869 TAACATATAAATTTCATTG-CAATAACTTTTATCATA
1 TAACATATAACTTTCA-TGACAAAAACTTATATCATA
1652905 TATTAGCTTA
Statistics
Matches: 73, Mismatches: 7, Indels: 8
0.83 0.08 0.09
Matches are distributed among these distances:
47 30 0.41
48 40 0.55
49 3 0.04
ACGTcount: A:0.43, C:0.15, G:0.05, T:0.38
Consensus pattern (47 bp):
TAACATATAACTTTCATGACAAAAACTTATATCATAAATTCATAATT
Found at i:1661300 original size:20 final size:20
Alignment explanation
Indices: 1661275--1661321 Score: 76
Period size: 20 Copynumber: 2.4 Consensus size: 20
1661265 AGGGATATAC
1661275 CGATACCTTAAGGATGATAT
1 CGATACCTTAAGGATGATAT
*
1661295 CGATACCTTAAGGATGGTAT
1 CGATACCTTAAGGATGATAT
*
1661315 CAATACC
1 CGATACC
1661322 CTCTTGAAAC
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
20 25 1.00
ACGTcount: A:0.34, C:0.19, G:0.19, T:0.28
Consensus pattern (20 bp):
CGATACCTTAAGGATGATAT
Found at i:1662090 original size:22 final size:22
Alignment explanation
Indices: 1662027--1662092 Score: 105
Period size: 22 Copynumber: 3.0 Consensus size: 22
1662017 CGAGGGTTTC
* *
1662027 ATAGGTCCTTCGGGACATAATC
1 ATAGGTCCTTCGGGACATATTT
1662049 ATAGGTCCTTCGGGACATATTT
1 ATAGGTCCTTCGGGACATATTT
*
1662071 ATAGGTCATTCGGGACATATTT
1 ATAGGTCCTTCGGGACATATTT
1662093 CACATGCCAC
Statistics
Matches: 41, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
22 41 1.00
ACGTcount: A:0.26, C:0.18, G:0.23, T:0.33
Consensus pattern (22 bp):
ATAGGTCCTTCGGGACATATTT
Found at i:1662407 original size:2 final size:2
Alignment explanation
Indices: 1662400--1662425 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
1662390 ACTGTATAAG
1662400 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
1662426 AGTAATGAGT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:1663222 original size:2 final size:2
Alignment explanation
Indices: 1663215--1663246 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
1663205 GTATTAAGTG
1663215 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
1663247 GTTGGCATGT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:1666788 original size:22 final size:22
Alignment explanation
Indices: 1666722--1666789 Score: 127
Period size: 22 Copynumber: 3.1 Consensus size: 22
1666712 AGTCAAGGGT
1666722 TTCATAGGTCCTTCGGGACATA
1 TTCATAGGTCCTTCGGGACATA
*
1666744 ATCATAGGTCCTTCGGGACATA
1 TTCATAGGTCCTTCGGGACATA
1666766 TTCATAGGTCCTTCGGGACATA
1 TTCATAGGTCCTTCGGGACATA
1666788 TT
1 TT
1666790 TCACATGCCA
Statistics
Matches: 44, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
22 44 1.00
ACGTcount: A:0.24, C:0.22, G:0.22, T:0.32
Consensus pattern (22 bp):
TTCATAGGTCCTTCGGGACATA
Found at i:1668299 original size:26 final size:26
Alignment explanation
Indices: 1668270--1668329 Score: 102
Period size: 26 Copynumber: 2.3 Consensus size: 26
1668260 TTTAAGTACG
*
1668270 ATTGACACTCTAAAGGCATGTACTTT
1 ATTGACACTCTAAAGGCATGTACTTC
1668296 ATTGACACTCTAAAGGCATGTACTTC
1 ATTGACACTCTAAAGGCATGTACTTC
*
1668322 ATTAACAC
1 ATTGACAC
1668330 CAAATGACTC
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
26 32 1.00
ACGTcount: A:0.33, C:0.22, G:0.13, T:0.32
Consensus pattern (26 bp):
ATTGACACTCTAAAGGCATGTACTTC
Found at i:1671549 original size:17 final size:16
Alignment explanation
Indices: 1671512--1671580 Score: 50
Period size: 17 Copynumber: 3.9 Consensus size: 16
1671502 TTTTCTGATT
* *
1671512 TCTGATTTGAATTTTGT
1 TCTGA-TTGAATTCTGA
1671529 TCTGATATGAATTCTGA
1 TCTGAT-TGAATTCTGA
1671546 TCTGGATT-ATATTCTGATA
1 TCT-GATTGA-ATTCTG--A
1671565 TCTGATCTGAATTCTG
1 TCTGAT-TGAATTCTG
1671581 TTTTGATTTC
Statistics
Matches: 43, Mismatches: 2, Indels: 12
0.75 0.04 0.21
Matches are distributed among these distances:
16 2 0.05
17 23 0.53
18 6 0.14
19 11 0.26
20 1 0.02
ACGTcount: A:0.23, C:0.12, G:0.17, T:0.48
Consensus pattern (16 bp):
TCTGATTGAATTCTGA
Found at i:1673093 original size:3 final size:3
Alignment explanation
Indices: 1673085--1673116 Score: 64
Period size: 3 Copynumber: 10.7 Consensus size: 3
1673075 TGTGAAGTTG
1673085 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT AT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT AT
1673117 ATAGAAAATA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 29 1.00
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
ATT
Found at i:1676429 original size:24 final size:24
Alignment explanation
Indices: 1676402--1676477 Score: 75
Period size: 24 Copynumber: 3.2 Consensus size: 24
1676392 AATTATGTTC
*
1676402 TGATCTGAATTTTGTTCTTATTTT
1 TGATCTGAATTCTGTTCTTATTTT
* * *
1676426 TGATCTGGATTCTGTTCTGATATCT
1 TGATCTGAATTCTGTTCTTAT-TTT
*
1676451 T-ATTTGAATTCTGTT-TTGATTTT
1 TGATCTGAATTCTGTTCTT-ATTTT
1676474 TGAT
1 TGAT
1676478 ATCTCTGTTT
Statistics
Matches: 41, Mismatches: 8, Indels: 6
0.75 0.15 0.11
Matches are distributed among these distances:
23 4 0.10
24 34 0.83
25 3 0.07
ACGTcount: A:0.17, C:0.09, G:0.16, T:0.58
Consensus pattern (24 bp):
TGATCTGAATTCTGTTCTTATTTT
Found at i:1677672 original size:26 final size:26
Alignment explanation
Indices: 1677643--1677717 Score: 132
Period size: 26 Copynumber: 2.9 Consensus size: 26
1677633 GCTCAGTGCC
1677643 ACATATGAGCATGCTACATGCATTCA
1 ACATATGAGCATGCTACATGCATTCA
*
1677669 ACATATGAGCATGCTACATGTATTCA
1 ACATATGAGCATGCTACATGCATTCA
*
1677695 ACATATGAGTATGCTACATGCAT
1 ACATATGAGCATGCTACATGCAT
1677718 AGTTTGAATC
Statistics
Matches: 46, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
26 46 1.00
ACGTcount: A:0.35, C:0.20, G:0.16, T:0.29
Consensus pattern (26 bp):
ACATATGAGCATGCTACATGCATTCA
Found at i:1682507 original size:6 final size:6
Alignment explanation
Indices: 1682496--1682528 Score: 66
Period size: 6 Copynumber: 5.5 Consensus size: 6
1682486 TTAGTCGACA
1682496 GGATTT GGATTT GGATTT GGATTT GGATTT GGA
1 GGATTT GGATTT GGATTT GGATTT GGATTT GGA
1682529 AGGTTACAGC
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 27 1.00
ACGTcount: A:0.18, C:0.00, G:0.36, T:0.45
Consensus pattern (6 bp):
GGATTT
Found at i:1682683 original size:29 final size:29
Alignment explanation
Indices: 1682637--1682695 Score: 73
Period size: 29 Copynumber: 2.0 Consensus size: 29
1682627 AACATTTCCG
* * * * *
1682637 AAACTTGCATTTAGGTCCCTAAACTTTTA
1 AAACTTGCAATAAAGTCCCCAAACATTTA
1682666 AAACTTGCAATAAAGTCCCCAAACATTTA
1 AAACTTGCAATAAAGTCCCCAAACATTTA
1682695 A
1 A
1682696 TCCGTTTACA
Statistics
Matches: 25, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
29 25 1.00
ACGTcount: A:0.39, C:0.22, G:0.08, T:0.31
Consensus pattern (29 bp):
AAACTTGCAATAAAGTCCCCAAACATTTA
Found at i:1682859 original size:35 final size:34
Alignment explanation
Indices: 1682815--1682927 Score: 163
Period size: 35 Copynumber: 3.2 Consensus size: 34
1682805 AAAACAATTC
*
1682815 TCAATTTCATTCTAAACCACAAATTCTAAAGTAAT
1 TCAATTTCATTCTAAACC-CAAATTCTAAAATAAT
*
1682850 TCAATTTCATTCTAAACCCTAAATTCCAAAATAAT
1 TCAATTTCATTCTAAACCC-AAATTCTAAAATAAT
* *
1682885 TCAATTACATTCTAAAACCCAAATTCTAAAATACT
1 TCAATTTCATTCT-AAACCCAAATTCTAAAATAAT
1682920 TCAATTTC
1 TCAATTTC
1682928 TGTCTTTTTA
Statistics
Matches: 70, Mismatches: 6, Indels: 4
0.88 0.08 0.05
Matches are distributed among these distances:
34 1 0.01
35 63 0.90
36 6 0.09
ACGTcount: A:0.42, C:0.22, G:0.01, T:0.35
Consensus pattern (34 bp):
TCAATTTCATTCTAAACCCAAATTCTAAAATAAT
Found at i:1683992 original size:35 final size:35
Alignment explanation
Indices: 1683939--1684012 Score: 105
Period size: 35 Copynumber: 2.1 Consensus size: 35
1683929 ATCTATTACT
* *
1683939 TTGAATTATTTTGGAATTTAGGG-TTTAGAATGAAA
1 TTGAATTACTTTGAAATTT-GGGATTTAGAATGAAA
*
1683974 TTGAATTACTTTGAAATTTGGGATTTATAATGAAA
1 TTGAATTACTTTGAAATTTGGGATTTAGAATGAAA
1684009 TTGA
1 TTGA
1684013 GGAATGTTTT
Statistics
Matches: 35, Mismatches: 3, Indels: 2
0.88 0.08 0.05
Matches are distributed among these distances:
34 3 0.09
35 32 0.91
ACGTcount: A:0.35, C:0.01, G:0.20, T:0.43
Consensus pattern (35 bp):
TTGAATTACTTTGAAATTTGGGATTTAGAATGAAA
Found at i:1684482 original size:20 final size:20
Alignment explanation
Indices: 1684459--1684535 Score: 100
Period size: 20 Copynumber: 3.9 Consensus size: 20
1684449 TGCGATTTTC
1684459 CAAATTCGCAACGCGAAAGT
1 CAAATTCGCAACGCGAAAGT
*
1684479 CAAATTCGCAACGCGATAGT
1 CAAATTCGCAACGCGAAAGT
* * * * *
1684499 TAAATTCGCGACACAAAATT
1 CAAATTCGCAACGCGAAAGT
1684519 CAAATTCGCAACGCGAA
1 CAAATTCGCAACGCGAA
1684536 TTTAATTTCG
Statistics
Matches: 46, Mismatches: 11, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
20 46 1.00
ACGTcount: A:0.40, C:0.25, G:0.17, T:0.18
Consensus pattern (20 bp):
CAAATTCGCAACGCGAAAGT
Found at i:1684495 original size:41 final size:42
Alignment explanation
Indices: 1684414--1684538 Score: 109
Period size: 40 Copynumber: 3.1 Consensus size: 42
1684404 TGCAAACCAG
* * **
1684414 TTTCCAATTTCGCAACGCGAATCTGT-AAA-TCGCATTGCGAT-
1 TTTCCAAATTCGCAACGCGAA--AGTCAAATTCGCAACGCGATA
1684455 TTTCCAAATTCGCAACGCGAAAGTCAAATTCGCAACGCGATA
1 TTTCCAAATTCGCAACGCGAAAGTCAAATTCGCAACGCGATA
* * * * *
1684497 GTT--AAATTCGCGACACAAAATTCAAATTCGCAACGCGA-A
1 TTTCCAAATTCGCAACGCGAAAGTCAAATTCGCAACGCGATA
1684536 TTT
1 TTT
1684539 AATTTCGCGA
Statistics
Matches: 71, Mismatches: 10, Indels: 8
0.80 0.11 0.09
Matches are distributed among these distances:
39 5 0.07
40 34 0.48
41 30 0.42
42 2 0.03
ACGTcount: A:0.34, C:0.24, G:0.16, T:0.26
Consensus pattern (42 bp):
TTTCCAAATTCGCAACGCGAAAGTCAAATTCGCAACGCGATA
Found at i:1684522 original size:40 final size:39
Alignment explanation
Indices: 1684460--1684550 Score: 119
Period size: 40 Copynumber: 2.3 Consensus size: 39
1684450 GCGATTTTCC
* * *
1684460 AAATTCGCAACGCGAAAGTCAAATTCGCAACGCGATAGTT
1 AAATTCGCGACACAAAAGTCAAATTCGCAACGCGA-AGTT
* *
1684500 AAATTCGCGACACAAAATTCAAATTCGCAACGCGAATTT
1 AAATTCGCGACACAAAAGTCAAATTCGCAACGCGAAGTT
*
1684539 AATTTCGCGACA
1 AAATTCGCGACA
1684551 GGCTTTAGTT
Statistics
Matches: 45, Mismatches: 6, Indels: 1
0.87 0.12 0.02
Matches are distributed among these distances:
39 14 0.31
40 31 0.69
ACGTcount: A:0.38, C:0.23, G:0.16, T:0.22
Consensus pattern (39 bp):
AAATTCGCGACACAAAAGTCAAATTCGCAACGCGAAGTT
Found at i:1685316 original size:12 final size:12
Alignment explanation
Indices: 1685295--1685328 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
1685285 ACCACATTTT
*
1685295 CAATACCAAACA
1 CAATATCAAACA
1685307 CAATATCAAACA
1 CAATATCAAACA
*
1685319 CAATCTCAAA
1 CAATATCAAA
1685329 ACCCACAACA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
12 20 1.00
ACGTcount: A:0.56, C:0.29, G:0.00, T:0.15
Consensus pattern (12 bp):
CAATATCAAACA
Found at i:1685505 original size:24 final size:24
Alignment explanation
Indices: 1685440--1685507 Score: 91
Period size: 24 Copynumber: 2.8 Consensus size: 24
1685430 GTGAGTACTA
*
1685440 GTCAATACTCAAAATTTGATCTTG
1 GTCAATACTCAGAATTTGATCTTG
* *
1685464 GTCAATACCCAGACTTTGATCTTG
1 GTCAATACTCAGAATTTGATCTTG
* *
1685488 GTCAATACTCGGATTTTGAT
1 GTCAATACTCAGAATTTGAT
1685508 GATGTGATGG
Statistics
Matches: 38, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
24 38 1.00
ACGTcount: A:0.28, C:0.19, G:0.16, T:0.37
Consensus pattern (24 bp):
GTCAATACTCAGAATTTGATCTTG
Found at i:1687865 original size:20 final size:20
Alignment explanation
Indices: 1687837--1687882 Score: 74
Period size: 20 Copynumber: 2.3 Consensus size: 20
1687827 ATGTTGCGAT
* *
1687837 CAACACGAAAGTTAAATTCG
1 CAACGCGAAAGTCAAATTCG
1687857 CAACGCGAAAGTCAAATTCG
1 CAACGCGAAAGTCAAATTCG
1687877 CAACGC
1 CAACGC
1687883 AAAATAAGTG
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
20 24 1.00
ACGTcount: A:0.41, C:0.26, G:0.17, T:0.15
Consensus pattern (20 bp):
CAACGCGAAAGTCAAATTCG
Found at i:1688066 original size:25 final size:25
Alignment explanation
Indices: 1688021--1688070 Score: 73
Period size: 25 Copynumber: 2.0 Consensus size: 25
1688011 AAATCAATTA
* * *
1688021 AACATTGTTGTGGGTACATTATTTG
1 AACATTGTTATGAGTAAATTATTTG
1688046 AACATTGTTATGAGTAAATTATTTG
1 AACATTGTTATGAGTAAATTATTTG
1688071 GAAAAATAAT
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
25 22 1.00
ACGTcount: A:0.30, C:0.06, G:0.20, T:0.44
Consensus pattern (25 bp):
AACATTGTTATGAGTAAATTATTTG
Found at i:1688478 original size:18 final size:18
Alignment explanation
Indices: 1688457--1688493 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
1688447 GTAATTGGAG
1688457 TTTGAATTTAAATTTCAA
1 TTTGAATTTAAATTTCAA
* *
1688475 TTTGAGTTTGAATTTCAA
1 TTTGAATTTAAATTTCAA
1688493 T
1 T
1688494 ATAAATTTCG
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:0.32, C:0.05, G:0.11, T:0.51
Consensus pattern (18 bp):
TTTGAATTTAAATTTCAA
Found at i:1688500 original size:24 final size:24
Alignment explanation
Indices: 1688449--1688501 Score: 70
Period size: 24 Copynumber: 2.2 Consensus size: 24
1688439 TTTCATATGT
* * *
1688449 AATTGGAGTTTGAATTTAAATTTC
1 AATTTGAGTTTGAATTTAAATATA
*
1688473 AATTTGAGTTTGAATTTCAATATA
1 AATTTGAGTTTGAATTTAAATATA
1688497 AATTT
1 AATTT
1688502 CGGCTCCACT
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.36, C:0.04, G:0.13, T:0.47
Consensus pattern (24 bp):
AATTTGAGTTTGAATTTAAATATA
Found at i:1688847 original size:39 final size:39
Alignment explanation
Indices: 1688804--1688890 Score: 156
Period size: 39 Copynumber: 2.2 Consensus size: 39
1688794 TCCGATGCTC
*
1688804 ATCAAAATCCAAAGCTCATATGGTGCCAAGCAAAAGGAA
1 ATCAAAATCCAAAGCTAATATGGTGCCAAGCAAAAGGAA
*
1688843 ATCAAAATCCAAATCTAATATGGTGCCAAGCAAAAGGAA
1 ATCAAAATCCAAAGCTAATATGGTGCCAAGCAAAAGGAA
1688882 ATCAAAATC
1 ATCAAAATC
1688891 TACAACTTGA
Statistics
Matches: 46, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
39 46 1.00
ACGTcount: A:0.48, C:0.20, G:0.15, T:0.17
Consensus pattern (39 bp):
ATCAAAATCCAAAGCTAATATGGTGCCAAGCAAAAGGAA
Found at i:1689095 original size:20 final size:20
Alignment explanation
Indices: 1689066--1689115 Score: 66
Period size: 20 Copynumber: 2.5 Consensus size: 20
1689056 ATGTTACGAT
* *
1689066 CAACGTGAAAGTTAAAT-TCG
1 CAACGCGAAAGTCAAATCT-G
1689086 CAACGCGAAAGTCAAATCTG
1 CAACGCGAAAGTCAAATCTG
1689106 CAACGCGAAA
1 CAACGCGAAA
1689116 TAAGCGTTGC
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
20 26 0.96
21 1 0.04
ACGTcount: A:0.42, C:0.22, G:0.20, T:0.16
Consensus pattern (20 bp):
CAACGCGAAAGTCAAATCTG
Found at i:1689179 original size:20 final size:20
Alignment explanation
Indices: 1689154--1689206 Score: 88
Period size: 20 Copynumber: 2.6 Consensus size: 20
1689144 TCGAAAATCG
*
1689154 CGTTGCTAATTTGACTTTCA
1 CGTTGCGAATTTGACTTTCA
*
1689174 CGTTGCGAATTTGACTTTTA
1 CGTTGCGAATTTGACTTTCA
1689194 CGTTGCGAATTTG
1 CGTTGCGAATTTG
1689207 TACCTTCAAC
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 31 1.00
ACGTcount: A:0.19, C:0.17, G:0.21, T:0.43
Consensus pattern (20 bp):
CGTTGCGAATTTGACTTTCA
Found at i:1689347 original size:14 final size:14
Alignment explanation
Indices: 1689313--1689366 Score: 72
Period size: 14 Copynumber: 3.9 Consensus size: 14
1689303 ATAATTCTTA
*
1689313 TTTACAAATCAAAT
1 TTTACAAATCAACT
**
1689327 TAAACAAATCAACT
1 TTTACAAATCAACT
*
1689341 TTTACAAATCATCT
1 TTTACAAATCAACT
1689355 TTTACAAATCAA
1 TTTACAAATCAA
1689367 TTAATCAAAG
Statistics
Matches: 33, Mismatches: 7, Indels: 0
0.82 0.17 0.00
Matches are distributed among these distances:
14 33 1.00
ACGTcount: A:0.48, C:0.19, G:0.00, T:0.33
Consensus pattern (14 bp):
TTTACAAATCAACT
Found at i:1690820 original size:21 final size:21
Alignment explanation
Indices: 1690796--1690891 Score: 79
Period size: 21 Copynumber: 4.6 Consensus size: 21
1690786 AACGGGACCA
*
1690796 CTTGAACGATGACAGGGGCCT
1 CTTGAACGATGAGAGGGGCCT
* * *
1690817 CTTGAACGGTGGGAGGGGCTT
1 CTTGAACGATGAGAGGGGCCT
* * *
1690838 CTTCG-ATGATGAAAGGGACCT
1 CTT-GAACGATGAGAGGGGCCT
*
1690859 CTTGAACGAT-AGGAGGCGCCT
1 CTTGAACGATGA-GAGGGGCCT
*
1690880 CTTGAATGATGA
1 CTTGAACGATGA
1690892 TAGGTGCATC
Statistics
Matches: 56, Mismatches: 15, Indels: 7
0.72 0.19 0.09
Matches are distributed among these distances:
20 2 0.04
21 52 0.93
22 2 0.04
ACGTcount: A:0.24, C:0.19, G:0.34, T:0.23
Consensus pattern (21 bp):
CTTGAACGATGAGAGGGGCCT
Found at i:1690874 original size:42 final size:42
Alignment explanation
Indices: 1690796--1690891 Score: 113
Period size: 42 Copynumber: 2.3 Consensus size: 42
1690786 AACGGGACCA
* * * * * * *
1690796 CTTGAACGATGACAGGGGCCTCTTGAACGGTGGGAGGGGCTT
1 CTTGAATGATGAAAGGGACCTCTTGAACGATAGGAGGCGCCT
1690838 CTTCG-ATGATGAAAGGGACCTCTTGAACGATAGGAGGCGCCT
1 CTT-GAATGATGAAAGGGACCTCTTGAACGATAGGAGGCGCCT
1690880 CTTGAATGATGA
1 CTTGAATGATGA
1690892 TAGGTGCATC
Statistics
Matches: 45, Mismatches: 7, Indels: 4
0.80 0.12 0.07
Matches are distributed among these distances:
41 1 0.02
42 43 0.96
43 1 0.02
ACGTcount: A:0.24, C:0.19, G:0.34, T:0.23
Consensus pattern (42 bp):
CTTGAATGATGAAAGGGACCTCTTGAACGATAGGAGGCGCCT
Found at i:1693144 original size:13 final size:13
Alignment explanation
Indices: 1693126--1693153 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
1693116 TGGTTACTTT
1693126 AACAAAAAGACAA
1 AACAAAAAGACAA
1693139 AACAAAAAGACAA
1 AACAAAAAGACAA
1693152 AA
1 AA
1693154 TAAAGACAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.79, C:0.14, G:0.07, T:0.00
Consensus pattern (13 bp):
AACAAAAAGACAA
Found at i:1693383 original size:22 final size:22
Alignment explanation
Indices: 1693353--1693400 Score: 78
Period size: 22 Copynumber: 2.2 Consensus size: 22
1693343 GATGGAGATA
*
1693353 GACGGATTTCGTCGGAAATGGG
1 GACGAATTTCGTCGGAAATGGG
*
1693375 GACGAATTTCGTCGGAGATGGG
1 GACGAATTTCGTCGGAAATGGG
1693397 GACG
1 GACG
1693401 GATGTCGCCG
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
22 24 1.00
ACGTcount: A:0.23, C:0.15, G:0.42, T:0.21
Consensus pattern (22 bp):
GACGAATTTCGTCGGAAATGGG
Found at i:1693556 original size:20 final size:20
Alignment explanation
Indices: 1693531--1693655 Score: 137
Period size: 20 Copynumber: 6.2 Consensus size: 20
1693521 GCGTAAAAAC
*
1693531 ATTTGACTTTCACGTTGCGA
1 ATTTGACTTTCGCGTTGCGA
* *
1693551 ATTTGACTATCGCATTGCGA
1 ATTTGACTTTCGCGTTGCGA
* *
1693571 ATTTGACTTTTGTGTTGCG-
1 ATTTGACTTTCGCGTTGCGA
*
1693590 ATTT-ACAAATTCGCGTTGCGA
1 ATTTGAC--TTTCGCGTTGCGA
**
1693611 ATTTGACTTTCATGTTGCGA
1 ATTTGACTTTCGCGTTGCGA
*
1693631 ATTTGACTTTCGCGTTGCTA
1 ATTTGACTTTCGCGTTGCGA
1693651 ATTTG
1 ATTTG
1693656 GAAAATTGCA
Statistics
Matches: 85, Mismatches: 16, Indels: 8
0.78 0.15 0.07
Matches are distributed among these distances:
18 2 0.02
19 4 0.05
20 73 0.86
21 4 0.05
22 2 0.02
ACGTcount: A:0.20, C:0.17, G:0.21, T:0.42
Consensus pattern (20 bp):
ATTTGACTTTCGCGTTGCGA
Found at i:1693588 original size:40 final size:40
Alignment explanation
Indices: 1693531--1693655 Score: 155
Period size: 40 Copynumber: 3.1 Consensus size: 40
1693521 GCGTAAAAAC
* *
1693531 ATTTGACTTTCACGTTGCGAATTTGACTATCGCATTGCGA
1 ATTTGACTTTCATGTTGCGAATTTGACTATCGCGTTGCGA
** *
1693571 ATTTGACTTTTGTGTTGCG-ATTT-ACAAATTCGCGTTGCGA
1 ATTTGACTTTCATGTTGCGAATTTGAC-TA-TCGCGTTGCGA
* *
1693611 ATTTGACTTTCATGTTGCGAATTTGACTTTCGCGTTGCTA
1 ATTTGACTTTCATGTTGCGAATTTGACTATCGCGTTGCGA
1693651 ATTTG
1 ATTTG
1693656 GAAAATTGCA
Statistics
Matches: 71, Mismatches: 10, Indels: 8
0.80 0.11 0.09
Matches are distributed among these distances:
38 2 0.03
39 5 0.07
40 58 0.82
41 4 0.06
42 2 0.03
ACGTcount: A:0.20, C:0.17, G:0.21, T:0.42
Consensus pattern (40 bp):
ATTTGACTTTCATGTTGCGAATTTGACTATCGCGTTGCGA
Found at i:1693683 original size:20 final size:20
Alignment explanation
Indices: 1693645--1693716 Score: 69
Period size: 20 Copynumber: 3.5 Consensus size: 20
1693635 GACTTTCGCG
*
1693645 TTGCTAATTTGGAAAATTGCA
1 TTGCGAATTTGG-AAATTGCA
1693666 TTGCGAATTTGGAAATTG-A
1 TTGCGAATTTGGAAATTGCA
*
1693685 GTTGCGAGA-TTGG-AATTCGCG
1 -TTGCGA-ATTTGGAAATT-GCA
1693706 TTGCGAATTTG
1 TTGCGAATTTG
1693717 TTGGTCATTT
Statistics
Matches: 44, Mismatches: 2, Indels: 11
0.77 0.04 0.19
Matches are distributed among these distances:
19 6 0.14
20 26 0.59
21 12 0.27
ACGTcount: A:0.26, C:0.10, G:0.28, T:0.36
Consensus pattern (20 bp):
TTGCGAATTTGGAAATTGCA
Found at i:1695917 original size:10 final size:10
Alignment explanation
Indices: 1695878--1695917 Score: 53
Period size: 10 Copynumber: 4.0 Consensus size: 10
1695868 TTCATCAATC
1695878 CAAATTCTCT
1 CAAATTCTCT
*
1695888 CAATTTCTCT
1 CAAATTCTCT
*
1695898 CAACTTCTCT
1 CAAATTCTCT
*
1695908 CAAATACTCT
1 CAAATTCTCT
1695918 TATAATCTCT
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
10 26 1.00
ACGTcount: A:0.28, C:0.33, G:0.00, T:0.40
Consensus pattern (10 bp):
CAAATTCTCT
Found at i:1695976 original size:9 final size:9
Alignment explanation
Indices: 1695964--1695997 Score: 52
Period size: 9 Copynumber: 3.9 Consensus size: 9
1695954 TAATATTTTG
1695964 TATTTAATT
1 TATTTAATT
*
1695973 TATTTAA-G
1 TATTTAATT
1695981 TATTTAATT
1 TATTTAATT
1695990 TATTTAAT
1 TATTTAAT
1695998 ATTTTACTTA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
8 7 0.32
9 15 0.68
ACGTcount: A:0.35, C:0.00, G:0.03, T:0.62
Consensus pattern (9 bp):
TATTTAATT
Found at i:1696003 original size:17 final size:17
Alignment explanation
Indices: 1695963--1696001 Score: 71
Period size: 17 Copynumber: 2.4 Consensus size: 17
1695953 TTAATATTTT
1695963 GTATTTAATTTATTTAA
1 GTATTTAATTTATTTAA
1695980 GTATTTAATTTATTTAA
1 GTATTTAATTTATTTAA
1695997 -TATTT
1 GTATTT
1696002 TACTTAATTA
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
16 5 0.23
17 17 0.77
ACGTcount: A:0.33, C:0.00, G:0.05, T:0.62
Consensus pattern (17 bp):
GTATTTAATTTATTTAA
Found at i:1698093 original size:9 final size:9
Alignment explanation
Indices: 1698079--1698124 Score: 60
Period size: 9 Copynumber: 5.1 Consensus size: 9
1698069 TTAGCTGCTC
1698079 AGGACGACG
1 AGGACGACG
1698088 AGGACGA-G
1 AGGACGACG
1698096 AAGGACGACG
1 -AGGACGACG
1698106 AGGACGA-G
1 AGGACGACG
1698114 AAGGACGACG
1 -AGGACGACG
1698124 A
1 A
1698125 CGATGATGAT
Statistics
Matches: 33, Mismatches: 0, Indels: 8
0.80 0.00 0.20
Matches are distributed among these distances:
8 2 0.06
9 29 0.88
10 2 0.06
ACGTcount: A:0.39, C:0.17, G:0.43, T:0.00
Consensus pattern (9 bp):
AGGACGACG
Found at i:1698102 original size:18 final size:18
Alignment explanation
Indices: 1698079--1698124 Score: 92
Period size: 18 Copynumber: 2.6 Consensus size: 18
1698069 TTAGCTGCTC
1698079 AGGACGACGAGGACGAGA
1 AGGACGACGAGGACGAGA
1698097 AGGACGACGAGGACGAGA
1 AGGACGACGAGGACGAGA
1698115 AGGACGACGA
1 AGGACGACGA
1698125 CGATGATGAT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 28 1.00
ACGTcount: A:0.39, C:0.17, G:0.43, T:0.00
Consensus pattern (18 bp):
AGGACGACGAGGACGAGA
Found at i:1698280 original size:13 final size:13
Alignment explanation
Indices: 1698260--1698306 Score: 58
Period size: 13 Copynumber: 3.6 Consensus size: 13
1698250 TATTTAGTAC
*
1698260 TTTTTATTGTAGT
1 TTTTTATTGTAAT
* * *
1698273 TGTTTATTGGACT
1 TTTTTATTGTAAT
1698286 TTTTTATTGTAAT
1 TTTTTATTGTAAT
1698299 TTTTTATT
1 TTTTTATT
1698307 ATTTATCATT
Statistics
Matches: 28, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
13 28 1.00
ACGTcount: A:0.17, C:0.02, G:0.13, T:0.68
Consensus pattern (13 bp):
TTTTTATTGTAAT
Found at i:1698369 original size:33 final size:34
Alignment explanation
Indices: 1698327--1698402 Score: 86
Period size: 33 Copynumber: 2.3 Consensus size: 34
1698317 TAATACTTAC
*
1698327 TTTAATTTGTT-AATATGGTTGGA-TTTATT-TTAA
1 TTTATTTTGTTAAAT-TGGTTGGACTTT-TTGTTAA
*
1698360 TTTATTTTGTTAAATTTGTTGGACTTTTTGTTAA
1 TTTATTTTGTTAAATTGGTTGGACTTTTTGTTAA
*
1698394 TTAATTTTG
1 TTTATTTTG
1698403 CTTTATTTTA
Statistics
Matches: 37, Mismatches: 3, Indels: 5
0.82 0.07 0.11
Matches are distributed among these distances:
33 19 0.51
34 18 0.49
ACGTcount: A:0.24, C:0.01, G:0.14, T:0.61
Consensus pattern (34 bp):
TTTATTTTGTTAAATTGGTTGGACTTTTTGTTAA
Found at i:1704455 original size:20 final size:20
Alignment explanation
Indices: 1704432--1704473 Score: 59
Period size: 20 Copynumber: 2.1 Consensus size: 20
1704422 ACATCAAATA
1704432 TAAT-AAATAATATTATTTAT
1 TAATAAAATAATATTA-TTAT
*
1704452 TAATAAAATATTATTATTAT
1 TAATAAAATAATATTATTAT
1704472 TA
1 TA
1704474 TTTTTAAAAT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
20 10 0.50
21 10 0.50
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (20 bp):
TAATAAAATAATATTATTAT
Found at i:1704474 original size:23 final size:24
Alignment explanation
Indices: 1704442--1704504 Score: 74
Period size: 23 Copynumber: 2.6 Consensus size: 24
1704432 TAATAAATAA
1704442 TATTATTTATTAATAAAATATTAT
1 TATTATTTATTAATAAAATATTAT
**
1704466 TATTA-TTATTTTTAAAATATTAT
1 TATTATTTATTAATAAAATATTAT
* *
1704489 AATAATTTATTTAATA
1 TATTATTTA-TTAATA
1704505 TTATTTATGT
Statistics
Matches: 31, Mismatches: 6, Indels: 3
0.77 0.15 0.08
Matches are distributed among these distances:
23 19 0.61
24 8 0.26
25 4 0.13
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (24 bp):
TATTATTTATTAATAAAATATTAT
Found at i:1704509 original size:23 final size:21
Alignment explanation
Indices: 1704458--1704509 Score: 52
Period size: 20 Copynumber: 2.4 Consensus size: 21
1704448 TTATTAATAA
* *
1704458 AATATTATTATTATTATTTTT
1 AATATTATTATAATAATTTTT
*
1704479 AA-AATATTATAATAATTTATTT
1 AATATTATTATAATAA-TT-TTT
1704501 AATATTATT
1 AATATTATT
1704510 TATGTAAATA
Statistics
Matches: 24, Mismatches: 4, Indels: 4
0.75 0.12 0.12
Matches are distributed among these distances:
20 10 0.42
21 4 0.17
22 5 0.21
23 5 0.21
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (21 bp):
AATATTATTATAATAATTTTT
Found at i:1704606 original size:37 final size:38
Alignment explanation
Indices: 1704556--1704656 Score: 127
Period size: 41 Copynumber: 2.6 Consensus size: 38
1704546 TAAAATTTCA
*
1704556 TATTTATCAAAATAAGAT-TATTA-TAAATTATATTAAT
1 TATTTATTAAAATAAGATATATTATTAAA-TATATTAAT
1704593 TATTTATTAAAATAAAAAGATATATTATTAAATATATTAAT
1 TATTTATTAAAAT---AAGATATATTATTAAATATATTAAT
*
1704634 TATTTATTAAAATAATA-ATATTA
1 TATTTATTAAAATAAGATATATTA
1704657 AAATATTGAA
Statistics
Matches: 57, Mismatches: 2, Indels: 10
0.83 0.03 0.14
Matches are distributed among these distances:
37 18 0.32
38 3 0.05
40 5 0.09
41 27 0.47
42 4 0.07
ACGTcount: A:0.51, C:0.01, G:0.02, T:0.46
Consensus pattern (38 bp):
TATTTATTAAAATAAGATATATTATTAAATATATTAAT
Found at i:1704631 original size:41 final size:40
Alignment explanation
Indices: 1704569--1704648 Score: 135
Period size: 41 Copynumber: 2.0 Consensus size: 40
1704559 TTATCAAAAT
1704569 AAGATTATTATAAATTATATTAATTATTTATTAAAATAAA
1 AAGATTATTATAAATTATATTAATTATTTATTAAAATAAA
1704609 AAGATATATTATTAAA-TATATTAATTATTTATTAAAATAA
1 AAGAT-TATTA-TAAATTATATTAATTATTTATTAAAATAA
1704649 TAATATTAAA
Statistics
Matches: 38, Mismatches: 0, Indels: 3
0.93 0.00 0.07
Matches are distributed among these distances:
40 5 0.13
41 29 0.76
42 4 0.11
ACGTcount: A:0.53, C:0.00, G:0.03, T:0.45
Consensus pattern (40 bp):
AAGATTATTATAAATTATATTAATTATTTATTAAAATAAA
Found at i:1704673 original size:45 final size:41
Alignment explanation
Indices: 1704579--1704672 Score: 116
Period size: 41 Copynumber: 2.2 Consensus size: 41
1704569 AAGATTATTA
* *
1704579 TAAATTATATTAATTATTTATTAAAATAAAAAGATATATTAT
1 TAAA-TATATTAATTATTTATTAAAATAAAAAGATAAAATAT
* *
1704621 TAAATATATTAATTATTTATTAAAATAATAATATTAAAATAT
1 TAAATATATTAATTATTTATTAAAATAAAAAGA-TAAAATAT
*
1704663 TGAAAAATAT
1 T-AAATATAT
1704673 AATAAATAAA
Statistics
Matches: 45, Mismatches: 5, Indels: 3
0.85 0.09 0.06
Matches are distributed among these distances:
41 27 0.60
42 11 0.24
43 7 0.16
ACGTcount: A:0.54, C:0.00, G:0.02, T:0.44
Consensus pattern (41 bp):
TAAATATATTAATTATTTATTAAAATAAAAAGATAAAATAT
Found at i:1705725 original size:256 final size:255
Alignment explanation
Indices: 1705271--1705785 Score: 985
Period size: 256 Copynumber: 2.0 Consensus size: 255
1705261 TCAAAAAACC
1705271 AATTACTAGGAAATAAACGGACCCTAATTAATTCATGCACTTAAAAGTTTTTTTAATTAATCATT
1 AATTACTAGGAAATAAACGGACCCTAATTAATTCATGCACTTAAAAGTTTTTTTAATTAATCATT
* * * *
1705336 AATATTCGATTTATTAATAAACTAATACATATTAAATACTATAAAGACGAAAACGACGATCCTCC
66 AATATTCGATTTATTAATAAACTAATACAGATTAAATACTATAAAAACAAAAACGACGACCCTCC
1705401 TAATCTAATTTATTCTATTCACAATTCTCACGAACTTAAAAGCCTTTTAAATAATGCTTTAATTC
131 TAATCTAATTTATTCTATTCACAATTCTCACGAACTTAAAAGCCTTTTAAATAATGCTTTAATTC
1705466 AGTAATATAATATGTTAACAAATATTTATTCTTTTTCATGGTAAACAATAAAACAAATAG
196 AGTAATATAATATGTTAACAAATATTTATTCTTTTTCATGGTAAACAATAAAACAAATAG
1705526 AATTACTAGGAAATAAACGGACCCTAATTAATTCATGCACTTAAAAGTTTTTTTTAATTAATCAT
1 AATTACTAGGAAATAAACGGACCCTAATTAATTCATGCACTTAAAAG-TTTTTTTAATTAATCAT
1705591 TAATATTCGATTTATTAATAAACTAATACAGATTAAATACTATAAAAACAAAAACGACGACCCTC
65 TAATATTCGATTTATTAATAAACTAATACAGATTAAATACTATAAAAACAAAAACGACGACCCTC
1705656 CTAATCTAATTTATTCTATTCACAATTCTCACGAACTTAAAAGCCTTTTAAATAATGCTTTAATT
130 CTAATCTAATTTATTCTATTCACAATTCTCACGAACTTAAAAGCCTTTTAAATAATGCTTTAATT
1705721 CAGTAATATAATATGTTAACAAATATTTATTCTTTTTCATGGTAAACAATAAAACAAATAG
195 CAGTAATATAATATGTTAACAAATATTTATTCTTTTTCATGGTAAACAATAAAACAAATAG
1705782 AATT
1 AATT
1705786 TATTTATTAA
Statistics
Matches: 255, Mismatches: 4, Indels: 1
0.98 0.02 0.00
Matches are distributed among these distances:
255 47 0.18
256 208 0.82
ACGTcount: A:0.42, C:0.15, G:0.07, T:0.36
Consensus pattern (255 bp):
AATTACTAGGAAATAAACGGACCCTAATTAATTCATGCACTTAAAAGTTTTTTTAATTAATCATT
AATATTCGATTTATTAATAAACTAATACAGATTAAATACTATAAAAACAAAAACGACGACCCTCC
TAATCTAATTTATTCTATTCACAATTCTCACGAACTTAAAAGCCTTTTAAATAATGCTTTAATTC
AGTAATATAATATGTTAACAAATATTTATTCTTTTTCATGGTAAACAATAAAACAAATAG
Found at i:1706034 original size:24 final size:23
Alignment explanation
Indices: 1705988--1706038 Score: 59
Period size: 24 Copynumber: 2.2 Consensus size: 23
1705978 TCCCGCCACT
*
1705988 TCCTCGCTCTCTCCGTCCTCTTCC
1 TCCTCCCTCTCTCCGTCCTCTT-C
*
1706012 TCCTCCCTCTCTCC-TTCTCCTTC
1 TCCTCCCTCTCTCCGTCCT-CTTC
1706035 TCCT
1 TCCT
1706039 TCTCCGCCTA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
23 8 0.33
24 16 0.67
ACGTcount: A:0.00, C:0.55, G:0.04, T:0.41
Consensus pattern (23 bp):
TCCTCCCTCTCTCCGTCCTCTTC
Found at i:1707054 original size:35 final size:34
Alignment explanation
Indices: 1706995--1707106 Score: 127
Period size: 35 Copynumber: 3.2 Consensus size: 34
1706985 AAAACATTCC
* * *
1706995 TCAATTTCATTATAAATCCCAAATTTCAAAGTAAT
1 TCAATTTCATTCTAAA-CCTAAATTTCAAAATAAT
*
1707030 TCAATTTCATTCTAAACCTTAAATTCCAAAATAAT
1 TCAATTTCATTCTAAACC-TAAATTTCAAAATAAT
* *
1707065 TCAATTACATTCTAAACCCTAAA-TTCTAAAATACT
1 TCAATTTCATTCTAAA-CCTAAATTTC-AAAATAAT
1707100 TCAATTT
1 TCAATTT
1707107 AAGGAGAAAT
Statistics
Matches: 66, Mismatches: 8, Indels: 6
0.82 0.10 0.08
Matches are distributed among these distances:
34 4 0.06
35 60 0.91
36 2 0.03
ACGTcount: A:0.42, C:0.20, G:0.01, T:0.38
Consensus pattern (34 bp):
TCAATTTCATTCTAAACCTAAATTTCAAAATAAT
Found at i:1708174 original size:35 final size:34
Alignment explanation
Indices: 1708125--1708237 Score: 163
Period size: 35 Copynumber: 3.2 Consensus size: 34
1708115 TAAAAAGACA
* *
1708125 GAAATTGAAGTATTTTAGAATTTGGGTTTTAGAAT
1 GAAATTGAATTATTTTGGAATTTGGG-TTTAGAAT
*
1708160 GTAATTGAATTATTTTGGAATTTAGGGTTTAGAAT
1 GAAATTGAATTATTTTGGAATTT-GGGTTTAGAAT
*
1708195 GAAATTGAATTACTTTGGAATTTGTGGTTTAGAAT
1 GAAATTGAATTATTTTGGAATTTG-GGTTTAGAAT
1708230 GAAATTGA
1 GAAATTGA
1708238 GAATTGTTTT
Statistics
Matches: 71, Mismatches: 5, Indels: 4
0.89 0.06 0.05
Matches are distributed among these distances:
34 1 0.01
35 67 0.94
36 3 0.04
ACGTcount: A:0.34, C:0.01, G:0.23, T:0.42
Consensus pattern (34 bp):
GAAATTGAATTATTTTGGAATTTGGGTTTAGAAT
Found at i:1708901 original size:2 final size:2
Alignment explanation
Indices: 1708896--1708944 Score: 68
Period size: 2 Copynumber: 26.0 Consensus size: 2
1708886 CAAAACATAC
*
1708896 AT AT AT AT AT AT AT GT AT -T AT AT -T 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
1708936 A- AT AT AT AT
1 AT AT AT AT AT
1708945 TATTATTTTT
Statistics
Matches: 42, Mismatches: 2, Indels: 6
0.84 0.04 0.12
Matches are distributed among these distances:
1 3 0.07
2 39 0.93
ACGTcount: A:0.47, C:0.00, G:0.02, T:0.51
Consensus pattern (2 bp):
AT
Found at i:1708928 original size:24 final size:26
Alignment explanation
Indices: 1708896--1708947 Score: 79
Period size: 26 Copynumber: 2.0 Consensus size: 26
1708886 CAAAACATAC
*
1708896 ATATATATATATAT-GTATTATATTAT
1 ATATATATATATATAATA-TATATTAT
1708922 ATATATATATATATAATATATATTAT
1 ATATATATATATATAATATATATTAT
1708948 TATTTTTTTA
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
26 22 0.92
27 2 0.08
ACGTcount: A:0.46, C:0.00, G:0.02, T:0.52
Consensus pattern (26 bp):
ATATATATATATATAATATATATTAT
Found at i:1708943 original size:26 final size:24
Alignment explanation
Indices: 1708896--1708947 Score: 77
Period size: 24 Copynumber: 2.1 Consensus size: 24
1708886 CAAAACATAC
*
1708896 ATATATATATATATGTATTATATT
1 ATATATATATATATATATTATATT
1708920 ATATATATATATATATAATATATATT
1 ATATATATATATATAT-AT-TATATT
1708946 AT
1 AT
1708948 TATTTTTTTA
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
24 15 0.60
25 2 0.08
26 8 0.32
ACGTcount: A:0.46, C:0.00, G:0.02, T:0.52
Consensus pattern (24 bp):
ATATATATATATATATATTATATT
Found at i:1709938 original size:19 final size:19
Alignment explanation
Indices: 1709914--1709978 Score: 64
Period size: 19 Copynumber: 3.5 Consensus size: 19
1709904 TTATGTTTTG
1709914 TTTTTATTATATTTTTATC
1 TTTTTATTATATTTTTATC
* *
1709933 TTTTTATTAT-TTCTAATC
1 TTTTTATTATATTTTTATC
*
1709951 ACTTTTATT-TATTTTTAT-
1 -TTTTTATTATATTTTTATC
*
1709969 TTATTATTAT
1 TTTTTATTAT
1709979 TATTATTATA
Statistics
Matches: 36, Mismatches: 7, Indels: 7
0.72 0.14 0.14
Matches are distributed among these distances:
17 6 0.17
18 8 0.22
19 22 0.61
ACGTcount: A:0.23, C:0.06, G:0.00, T:0.71
Consensus pattern (19 bp):
TTTTTATTATATTTTTATC
Found at i:1709969 original size:6 final size:6
Alignment explanation
Indices: 1709958--1710040 Score: 62
Period size: 6 Copynumber: 13.7 Consensus size: 6
1709948 ATCACTTTTA
* * * * * *
1709958 TTTATT TTTATT TATTATT ATTATT ATTATA TTAATG ATT-TT TTTATT
1 TTTATT TTTATT T-TTATT TTTATT TTTATT TTTATT TTTATT TTTATT
*
1710006 ATTATT CATTT-TT TTTATT TTTATT TTTATT TTTA
1 TTTATT --TTTATT TTTATT TTTATT TTTATT TTTA
1710041 CAATCTAACC
Statistics
Matches: 61, Mismatches: 11, Indels: 10
0.74 0.13 0.12
Matches are distributed among these distances:
5 6 0.10
6 46 0.75
7 7 0.11
8 2 0.03
ACGTcount: A:0.24, C:0.01, G:0.01, T:0.73
Consensus pattern (6 bp):
TTTATT
Found at i:1709977 original size:3 final size:3
Alignment explanation
Indices: 1709959--1710036 Score: 52
Period size: 3 Copynumber: 25.7 Consensus size: 3
1709949 TCACTTTTAT
* * *
1709959 TTA TTT TTA TTTA TTA TTA TTA TTA TTA -TA TTAA TGA TT- TTT TTA
1 TTA TTA TTA -TTA TTA TTA TTA TTA TTA TTA TT-A TTA TTA TTA TTA
* * * *
1710004 TTA TTA TTCA TTT TTT TTA TTT TTA TTT TTA TT
1 TTA TTA TT-A TTA TTA TTA TTA TTA TTA TTA TT
1710037 TTTACAATCT
Statistics
Matches: 59, Mismatches: 11, Indels: 10
0.74 0.14 0.12
Matches are distributed among these distances:
2 4 0.07
3 47 0.80
4 8 0.14
ACGTcount: A:0.24, C:0.01, G:0.01, T:0.73
Consensus pattern (3 bp):
TTA
Found at i:1710039 original size:19 final size:19
Alignment explanation
Indices: 1709957--1710030 Score: 64
Period size: 19 Copynumber: 3.9 Consensus size: 19
1709947 AATCACTTTT
1709957 ATTTATTTTTATTTATTATT-
1 ATTT-TTTTTA-TTATTATTC
* * * *
1709977 ATTATTATTA-TATTAATG
1 ATTTTTTTTATTATTATTC
1709995 A-TTTTTTTATTATTATTC
1 ATTTTTTTTATTATTATTC
*
1710013 ATTTTTTTTATTTTTATT
1 ATTTTTTTTATTATTATT
1710031 TTTATTTTTA
Statistics
Matches: 43, Mismatches: 8, Indels: 7
0.74 0.14 0.12
Matches are distributed among these distances:
17 12 0.28
18 8 0.19
19 20 0.47
20 3 0.07
ACGTcount: A:0.26, C:0.01, G:0.01, T:0.72
Consensus pattern (19 bp):
ATTTTTTTTATTATTATTC
Found at i:1713940 original size:106 final size:106
Alignment explanation
Indices: 1713753--1714936 Score: 1956
Period size: 106 Copynumber: 11.2 Consensus size: 106
1713743 AACCATGAGC
* * * *
1713753 ACGAAGAAAATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTAGTTGTTA
1 ACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCA
* * *
1713818 ATAAACAATTTTCCAA-TACTAGAGCCAATTTCAACTTCACA
66 ATAAACAACTTCCCAATTTC-AGAGCCAATTTCAACTTCACA
* * * * *
1713859 GCGAAGGATAGTGGACTCCATACAACACAAGTTCAACTTCACGATGAAGGGACCGCTGGTTGTCA
1 ACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCA
* *
1713924 ATAAACGACTTCCCAATTTCAGAGTCAATTTCAACTTCACA
66 ATAAACAACTTCCCAATTTCAGAGCCAATTTCAACTTCACA
* *
1713965 ACAAAGGATATTGGACTCCAGACAACGCATGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCA
1 ACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCA
* *
1714030 ACAAACAACTTCTCAATTTCAGAGCCAATTTCAACTTCACA
66 ATAAACAACTTCCCAATTTCAGAGCCAATTTCAACTTCACA
1714071 ACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCA
1 ACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCA
1714136 ATAAACAACTTCCCAATTTCAGAGCCAATTTCAACTTCACA
66 ATAAACAACTTCCCAATTTCAGAGCCAATTTCAACTTCACA
* *
1714177 GCGAAGGATATTGGACTCCAGACAACACAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCA
1 ACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCA
*
1714242 ACAAACAACTTCCCAATTTCAGAGCCAATTTCAACTTCACA
66 ATAAACAACTTCCCAATTTCAGAGCCAATTTCAACTTCACA
** * *
1714283 ACGAAGGATATTGGACTCCAGACAACATAAGTTCAACTTTACGACGAAGGGACCACTGGTTGTCA
1 ACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCA
* *
1714348 ACAAACAACTTCTCAATTTCAGAGCCAATTTCAACTTCACA
66 ATAAACAACTTCCCAATTTCAGAGCCAATTTCAACTTCACA
1714389 ACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCA
1 ACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCA
1714454 ATAAACAACTTCCCAATTTCAGAGCCAATTTCAACTTCACA
66 ATAAACAACTTCCCAATTTCAGAGCCAATTTCAACTTCACA
* * * *
1714495 GCGAAGGATATTGGACTCCAGACAACGTAAGATCAACTTTACGACGAAGGGACCGCTGGTTGTCA
1 ACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCA
* * *
1714560 ACAAACAACTTCTCAATTTCAGAGTCAATTTCAACTTCACA
66 ATAAACAACTTCCCAATTTCAGAGCCAATTTCAACTTCACA
1714601 ACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCA
1 ACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCA
* *
1714666 ATAAATAAATTCCCAATTTCAGAGCCAATTTCAACTTCACA
66 ATAAACAACTTCCCAATTTCAGAGCCAATTTCAACTTCACA
1714707 ACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCA
1 ACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCA
* *
1714772 ACAAACAACTTCTCAATTTCAGAGCCAATTTCAACTTCACA
66 ATAAACAACTTCCCAATTTCAGAGCCAATTTCAACTTCACA
*
1714813 ACGAATGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCA
1 ACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCA
* * *
1714878 ATAAACAATTTCCCAATTTCAGAGTCAATTTCAACTTCACG
66 ATAAACAACTTCCCAATTTCAGAGCCAATTTCAACTTCACA
* *
1714919 GCGGAGGATATTGGACTC
1 ACGAAGGATATTGGACTC
1714937 GGAAGGGGCC
Statistics
Matches: 1005, Mismatches: 72, Indels: 2
0.93 0.07 0.00
Matches are distributed among these distances:
106 1003 1.00
107 2 0.00
ACGTcount: A:0.34, C:0.25, G:0.18, T:0.23
Consensus pattern (106 bp):
ACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCA
ATAAACAACTTCCCAATTTCAGAGCCAATTTCAACTTCACA
Found at i:1715058 original size:264 final size:264
Alignment explanation
Indices: 1714721--1715204 Score: 745
Period size: 264 Copynumber: 1.8 Consensus size: 264
1714711 AGGATATTGG
* * * *
1714721 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCTC
1 ACTCAAGACAACACAAGTTCAACTTCACAACGAAGGGACCGCTGGTTGTCAACAAACAACTTCCC
* *
1714786 AATTTCAGAGCCAATTTCAACTTCACAACGAATGATATTGGACTCCAGACAACGCAAGTTCAACT
66 AATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACACAAGTTCAACT
* * * **
1714851 TCACGACGAAGGGACCG-CTGGTTGTCAATAAACAATTTCCCAATTTCAGAGTCAATTTCAACTT
131 TCACAACGAAGGGA-CGACTGGTTGTCAACAAACAATTTCCCAATTCCAGAACCAATTTCAACTT
1714915 CACGGCGGAGGATATTGGACTCGGAAGGGGCCATCTGCAATTTTAACTCCACGACGGAGGATATC
195 CACGGCGGAGGATATTGGACTCGGAAGGGGCCATCTGCAATTTTAACTCCACGACGGAGGATATC
1714980 GTGCC
260 GTGCC
* * * *
1714985 ACTCAAGACAACACAAGTTCAACTTCACAACGAATGGACGGCTGGTTGTTAACAAACAATTTCCC
1 ACTCAAGACAACACAAGTTCAACTTCACAACGAAGGGACCGCTGGTTGTCAACAAACAACTTCCC
* ** *
1715050 AATTTCAGAGCCAATTTTAACTTCACAGTGAAGGATATTGGACTCGAGACAACACAAGTTCAACT
66 AATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACACAAGTTCAACT
* *
1715115 TCACAACGAAGGGACGACTGGTTGTCAACAAATAATTTCCCAGTTCCAGAACCAATTTCAACTTC
131 TCACAACGAAGGGACGACTGGTTGTCAACAAACAATTTCCCAATTCCAGAACCAATTTCAACTTC
* *
1715180 GCGGCGGATGATATTGGACTCGGAA
196 ACGGCGGAGGATATTGGACTCGGAA
1715205 CAATACAACT
Statistics
Matches: 196, Mismatches: 23, Indels: 2
0.89 0.10 0.01
Matches are distributed among these distances:
263 2 0.01
264 194 0.99
ACGTcount: A:0.33, C:0.25, G:0.20, T:0.23
Consensus pattern (264 bp):
ACTCAAGACAACACAAGTTCAACTTCACAACGAAGGGACCGCTGGTTGTCAACAAACAACTTCCC
AATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACACAAGTTCAACT
TCACAACGAAGGGACGACTGGTTGTCAACAAACAATTTCCCAATTCCAGAACCAATTTCAACTTC
ACGGCGGAGGATATTGGACTCGGAAGGGGCCATCTGCAATTTTAACTCCACGACGGAGGATATCG
TGCC
Found at i:1715114 original size:106 final size:106
Alignment explanation
Indices: 1714985--1715179 Score: 309
Period size: 106 Copynumber: 1.8 Consensus size: 106
1714975 ATATCGTGCC
* * *
1714985 ACTCAAGACAACACAAGTTCAACTTCACAACGAATGGACGGCTGGTTGTTAACAAACAATTTCCC
1 ACTCAAGACAACACAAGTTCAACTTCACAACGAAGGGACGACTGGTTGTCAACAAACAATTTCCC
* * *
1715050 AATTTCAGAGCCAATTTTAACTTCACAGTGAAGGATATTGG
66 AATTCCAGAACCAATTTCAACTTCACAGTGAAGGATATTGG
* *
1715091 ACTCGAGACAACACAAGTTCAACTTCACAACGAAGGGACGACTGGTTGTCAACAAATAATTTCCC
1 ACTCAAGACAACACAAGTTCAACTTCACAACGAAGGGACGACTGGTTGTCAACAAACAATTTCCC
*
1715156 AGTTCCAGAACCAATTTCAACTTC
66 AATTCCAGAACCAATTTCAACTTC
1715180 GCGGCGGATG
Statistics
Matches: 80, Mismatches: 9, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
106 80 1.00
ACGTcount: A:0.36, C:0.24, G:0.16, T:0.24
Consensus pattern (106 bp):
ACTCAAGACAACACAAGTTCAACTTCACAACGAAGGGACGACTGGTTGTCAACAAACAATTTCCC
AATTCCAGAACCAATTTCAACTTCACAGTGAAGGATATTGG
Found at i:1715193 original size:106 final size:106
Alignment explanation
Indices: 1714985--1715201 Score: 308
Period size: 106 Copynumber: 2.0 Consensus size: 106
1714975 ATATCGTGCC
* * * *
1714985 ACTCAAGACAACACAAGTTCAACTTCACAACGAATGGACGGCTGGTTGTTAACAAACAATTTCCC
1 ACTCGAGACAACACAAGTTCAACTTCACAACGAAGGGACGACTGGTTGTCAACAAACAATTTCCC
* * * *
1715050 AATTTCAGAGCCAATTTTAACTTCACAGTGAAGGATATTGG
66 AATTCCAGAACCAATTTCAACTTCACAGCGAAGGATATTGG
*
1715091 ACTCGAGACAACACAAGTTCAACTTCACAACGAAGGGACGACTGGTTGTCAACAAATAATTTCCC
1 ACTCGAGACAACACAAGTTCAACTTCACAACGAAGGGACGACTGGTTGTCAACAAACAATTTCCC
* * * * *
1715156 AGTTCCAGAACCAATTTCAACTTCGCGGCGGATGATATTGG
66 AATTCCAGAACCAATTTCAACTTCACAGCGAAGGATATTGG
1715197 ACTCG
1 ACTCG
1715202 GAACAATACA
Statistics
Matches: 97, Mismatches: 14, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
106 97 1.00
ACGTcount: A:0.34, C:0.24, G:0.18, T:0.24
Consensus pattern (106 bp):
ACTCGAGACAACACAAGTTCAACTTCACAACGAAGGGACGACTGGTTGTCAACAAACAATTTCCC
AATTCCAGAACCAATTTCAACTTCACAGCGAAGGATATTGG
Found at i:1715956 original size:2 final size:2
Alignment explanation
Indices: 1715951--1715992 Score: 61
Period size: 2 Copynumber: 22.0 Consensus size: 2
1715941 CAAAACATAC
*
1715951 AT AT AT AT AT GT AT -T AT AT AT AT AT AT AT AT AT AT AT A- AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1715991 AT
1 AT
1715993 TATTATTTTT
Statistics
Matches: 36, Mismatches: 2, Indels: 4
0.86 0.05 0.10
Matches are distributed among these distances:
1 2 0.06
2 34 0.94
ACGTcount: A:0.48, C:0.00, G:0.02, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1717050 original size:57 final size:57
Alignment explanation
Indices: 1716958--1717085 Score: 145
Period size: 57 Copynumber: 2.2 Consensus size: 57
1716948 TTTAACCCGC
* * * *
1716958 ATTTATGTTTTGTTTTTATTATATTTTTATCTTTTTATTATT-TTACTCACTTTTATT-T
1 ATTTAT-TTTTATTATTATTATATTATGATCTTTTT-TTATTATTACTCA-TTTTATTAT
* *
1717016 ATTTATTTTTATTATTATTATATTAATGAT-TTTTTTTATTATTATTCATTTTTTTAT
1 ATTTATTTTTATTATTATTATATT-ATGATCTTTTTTTATTATTACTCATTTTATTAT
1717073 ATTTATTTTTATT
1 ATTTATTTTTATT
1717086 TTTACAATCT
Statistics
Matches: 61, Mismatches: 6, Indels: 7
0.82 0.08 0.09
Matches are distributed among these distances:
56 11 0.18
57 41 0.67
58 9 0.15
ACGTcount: A:0.23, C:0.04, G:0.02, T:0.71
Consensus pattern (57 bp):
ATTTATTTTTATTATTATTATATTATGATCTTTTTTTATTATTACTCATTTTATTAT
Found at i:1717072 original size:15 final size:15
Alignment explanation
Indices: 1717048--1717085 Score: 51
Period size: 14 Copynumber: 2.5 Consensus size: 15
1717038 TTAATGATTT
1717048 TTTTTATTATTATTCA
1 TTTTTATTA-TATTCA
*
1717064 TTTTT-TTATATTTA
1 TTTTTATTATATTCA
1717078 TTTTTATT
1 TTTTTATT
1717086 TTTACAATCT
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
14 10 0.50
15 5 0.25
16 5 0.25
ACGTcount: A:0.21, C:0.03, G:0.00, T:0.76
Consensus pattern (15 bp):
TTTTTATTATATTCA
Found at i:1717084 original size:27 final size:27
Alignment explanation
Indices: 1717015--1717085 Score: 81
Period size: 27 Copynumber: 2.5 Consensus size: 27
1717005 CACTTTTATT
1717015 TATTTATTTTTATTATTATTATATTAA
1 TATTTATTTTTATTATTATTATATTAA
* *
1717042 TGATTT-TTTTTATTATTATTCATTTTTTTA
1 T-ATTTATTTTTATTATTATT-A--TATTAA
1717072 TATTTATTTTTATT
1 TATTTATTTTTATT
1717086 TTTACAATCT
Statistics
Matches: 37, Mismatches: 2, Indels: 7
0.80 0.04 0.15
Matches are distributed among these distances:
27 15 0.41
28 5 0.14
29 4 0.11
30 13 0.35
ACGTcount: A:0.25, C:0.01, G:0.01, T:0.72
Consensus pattern (27 bp):
TATTTATTTTTATTATTATTATATTAA
Found at i:1718528 original size:9 final size:10
Alignment explanation
Indices: 1718514--1718562 Score: 57
Period size: 9 Copynumber: 4.9 Consensus size: 10
1718504 TCTTTCGCTA
1718514 TATAAT-TAC
1 TATAATATAC
1718523 TATAATAAATAC
1 TATAAT--ATAC
1718535 TATAATATAC
1 TATAATATAC
1718545 TATAAT-TAC
1 TATAATATAC
*
1718554 TATACTATA
1 TATAATATA
1718563 TTTAGTACCA
Statistics
Matches: 35, Mismatches: 1, Indels: 7
0.81 0.02 0.16
Matches are distributed among these distances:
9 14 0.40
10 12 0.34
12 9 0.26
ACGTcount: A:0.49, C:0.10, G:0.00, T:0.41
Consensus pattern (10 bp):
TATAATATAC
Found at i:1718535 original size:12 final size:12
Alignment explanation
Indices: 1718511--1718550 Score: 50
Period size: 12 Copynumber: 3.6 Consensus size: 12
1718501 CACTCTTTCG
*
1718511 CTAT-ATAATTA
1 CTATAATAAATA
1718522 CTATAATAAATA
1 CTATAATAAATA
1718534 CTATAAT--ATA
1 CTATAATAAATA
1718544 CTATAAT
1 CTATAAT
1718551 TACTATACTA
Statistics
Matches: 27, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
10 10 0.37
11 4 0.15
12 13 0.48
ACGTcount: A:0.50, C:0.10, G:0.00, T:0.40
Consensus pattern (12 bp):
CTATAATAAATA
Found at i:1718554 original size:19 final size:20
Alignment explanation
Indices: 1718514--1718562 Score: 57
Period size: 19 Copynumber: 2.5 Consensus size: 20
1718504 TCTTTCGCTA
1718514 TATAAT-TACTATAATAAATAC
1 TATAATATACTATAAT--ATAC
1718535 TATAATATACTATAAT-TAC
1 TATAATATACTATAATATAC
*
1718554 TATACTATA
1 TATAATATA
1718563 TTTAGTACCA
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
19 11 0.42
21 6 0.23
22 9 0.35
ACGTcount: A:0.49, C:0.10, G:0.00, T:0.41
Consensus pattern (20 bp):
TATAATATACTATAATATAC
Found at i:1720401 original size:35 final size:34
Alignment explanation
Indices: 1720346--1720416 Score: 97
Period size: 35 Copynumber: 2.1 Consensus size: 34
1720336 TAAACAAAAA
* *
1720346 AATAAATCTTTCATCAAGTGACGTGACTTATTAT
1 AATAAATCTTTCACCAAGTGACATGACTTATTAT
* *
1720380 AATAAATTTATTCACCAAGTGATATGACTTATTAT
1 AATAAATCT-TTCACCAAGTGACATGACTTATTAT
1720415 AA
1 AA
1720417 AGAACATCAA
Statistics
Matches: 32, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
34 8 0.25
35 24 0.75
ACGTcount: A:0.39, C:0.13, G:0.10, T:0.38
Consensus pattern (34 bp):
AATAAATCTTTCACCAAGTGACATGACTTATTAT
Found at i:1722225 original size:20 final size:20
Alignment explanation
Indices: 1722200--1722250 Score: 102
Period size: 20 Copynumber: 2.5 Consensus size: 20
1722190 TACTGATGTG
1722200 GGTATCGATACTAAGAGAAA
1 GGTATCGATACTAAGAGAAA
1722220 GGTATCGATACTAAGAGAAA
1 GGTATCGATACTAAGAGAAA
1722240 GGTATCGATAC
1 GGTATCGATAC
1722251 CATGGATTCT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 31 1.00
ACGTcount: A:0.41, C:0.12, G:0.25, T:0.22
Consensus pattern (20 bp):
GGTATCGATACTAAGAGAAA
Found at i:1722749 original size:54 final size:53
Alignment explanation
Indices: 1722669--1723218 Score: 625
Period size: 54 Copynumber: 10.2 Consensus size: 53
1722659 AATATCATTG
* * *
1722669 TGTGTGCAACTTAAGAAATTCATAATAAGTTTATGAATTCCCTTATTGGCACTG
1 TGTGTGCAACCTAAGAAATTCATAATAAGTTTATGAATT-TCTTATTGGCACTA
* * * *
1722723 TGTGTGCAACTTAAGAAATTCATAATAAGTTTATGAATTTATGTATTGGCATTG
1 TGTGTGCAACCTAAGAAATTCATAATAAGTTTATGAATTTCT-TATTGGCACTA
* * * *
1722777 TGTGTGCAACTTAAGAAATTCATAATAAGTTTATGAATTTCCGTATTAGCACTG
1 TGTGTGCAACCTAAGAAATTCATAATAAGTTTATGAATTT-CTTATTGGCACTA
* * * *
1722831 TGTGTGCAGCTTAAGAAATTCATAATAAGTTTATCAATTTCCGTATTGGCACTA
1 TGTGTGCAACCTAAGAAATTCATAATAAGTTTATGAATTT-CTTATTGGCACTA
* * *
1722885 TATGTACAACCTAAGAAATTCATAATAAGTTTATGAATTTTTGTATTGGCACTA
1 TGTGTGCAACCTAAGAAATTCATAATAAGTTTATGAATTTCT-TATTGGCACTA
* * *
1722939 TATGTGCAACCTAAAAAATTCATAATTAGTTTATGAATTTCTGTATTGGCACTA
1 TGTGTGCAACCTAAGAAATTCATAATAAGTTTATGAATTTCT-TATTGGCACTA
* * * *
1722993 TGTGTACAACCTAAGAAATTCATAATTAGTTTATGAATTTTCATATTGCCACTA
1 TGTGTGCAACCTAAGAAATTCATAATAAGTTTATGAA-TTTCTTATTGGCACTA
* * *
1723047 TGTGTGCAACCTAAGAAATTCATAATTAGTTTATGAATTTATGTATTGGCACTG
1 TGTGTGCAACCTAAGAAATTCATAATAAGTTTATGAATTTCT-TATTGGCACTA
** * * *
1723101 TGTGTAAAACCTAAGAAATTCATAATTAGTTTATGAATTTCCGTAGTGGCACTA
1 TGTGTGCAACCTAAGAAATTCATAATAAGTTTATGAATTT-CTTATTGGCACTA
* * * * * * * *
1723155 TGTGTGC-ACCCATGTAATTCATAATGAGTTTGTGAATTATCGTATCGACACTA
1 TGTGTGCAACCTAAGAAATTCATAATAAGTTTATGAATT-TCTTATTGGCACTA
*
1723208 AGTGTGCAACC
1 TGTGTGCAACC
1723219 CACAGAATTT
Statistics
Matches: 439, Mismatches: 49, Indels: 16
0.87 0.10 0.03
Matches are distributed among these distances:
53 46 0.10
54 389 0.89
55 4 0.01
ACGTcount: A:0.33, C:0.13, G:0.16, T:0.37
Consensus pattern (53 bp):
TGTGTGCAACCTAAGAAATTCATAATAAGTTTATGAATTTCTTATTGGCACTA
Found at i:1722853 original size:108 final size:108
Alignment explanation
Indices: 1722667--1723192 Score: 703
Period size: 108 Copynumber: 4.9 Consensus size: 108
1722657 CGAATATCAT
* * * * *
1722667 TGTGTGTGCAACTTAAGAAATTCATAATAAGTTTATGAATTCCCTTATTGGCACTGTGTGTGCAA
1 TGTGTGTACAACCTAAGAAATTCATAATAAGTTTATGAATTTCCGTATTGGCACTATGTGTGCAA
* *
1722732 CTTAAGAAATTCATAATAAGTTTATGAATTTATGTATTGGCAT
66 CCTAAGAAATTCATAATAAGTTTATGAATTTATGTATTGGCAC
* * * * *
1722775 TGTGTGTGCAACTTAAGAAATTCATAATAAGTTTATGAATTTCCGTATTAGCACTGTGTGTGCAG
1 TGTGTGTACAACCTAAGAAATTCATAATAAGTTTATGAATTTCCGTATTGGCACTATGTGTGCAA
* * **
1722840 CTTAAGAAATTCATAATAAGTTTATCAATTTCCGTATTGGCAC
66 CCTAAGAAATTCATAATAAGTTTATGAATTTATGTATTGGCAC
* * ** *
1722883 TATATGTACAACCTAAGAAATTCATAATAAGTTTATGAATTTTTGTATTGGCACTATATGTGCAA
1 TGTGTGTACAACCTAAGAAATTCATAATAAGTTTATGAATTTCCGTATTGGCACTATGTGTGCAA
* * *
1722948 CCTAAAAAATTCATAATTAGTTTATGAATTTCTGTATTGGCAC
66 CCTAAGAAATTCATAATAAGTTTATGAATTTATGTATTGGCAC
* * * * *
1722991 TATGTGTACAACCTAAGAAATTCATAATTAGTTTATGAATTTTCATATTGCCACTATGTGTGCAA
1 TGTGTGTACAACCTAAGAAATTCATAATAAGTTTATGAATTTCCGTATTGGCACTATGTGTGCAA
*
1723056 CCTAAGAAATTCATAATTAGTTTATGAATTTATGTATTGGCAC
66 CCTAAGAAATTCATAATAAGTTTATGAATTTATGTATTGGCAC
* * *
1723099 TGTGTGTAAAACCTAAGAAATTCATAATTAGTTTATGAATTTCCGTAGTGGCACTATGTGTGC-A
1 TGTGTGTACAACCTAAGAAATTCATAATAAGTTTATGAATTTCCGTATTGGCACTATGTGTGCAA
* * * * *
1723163 CCCATGTAATTCATAATGAGTTTGTGAATT
66 CCTAAGAAATTCATAATAAGTTTATGAATT
1723193 ATCGTATCGA
Statistics
Matches: 376, Mismatches: 42, Indels: 1
0.90 0.10 0.00
Matches are distributed among these distances:
107 26 0.07
108 350 0.93
ACGTcount: A:0.33, C:0.13, G:0.16, T:0.38
Consensus pattern (108 bp):
TGTGTGTACAACCTAAGAAATTCATAATAAGTTTATGAATTTCCGTATTGGCACTATGTGTGCAA
CCTAAGAAATTCATAATAAGTTTATGAATTTATGTATTGGCAC
Found at i:1722934 original size:162 final size:162
Alignment explanation
Indices: 1722669--1723162 Score: 736
Period size: 162 Copynumber: 3.0 Consensus size: 162
1722659 AATATCATTG
* * * *
1722669 TGTGTGCAACTTAAGAAATTCATAATAAGTTTATGAATTCCCTTATTGGCACTGTGTGTGCAACT
1 TGTGTGCAACTTAAGAAATTCATAATAAGTTTATGAATTTCCATATTGGCACTATGTGTGCAACC
* *
1722734 TAAGAAATTCATAATAAGTTTATGAATTTATGTATTGGCATTGTGTGTGCAACTTAAGAAATTCA
66 TAAGAAATTCATAATAAGTTTATGAATTTATGTATTGGCACTGTGTGTGCAACCTAAGAAATTCA
* * *
1722799 TAATAAGTTTATGAATTTCCGTATTAGCACTG
131 TAATTAGTTTATGAATTTCCGTATTGGCACTA
* * * * *
1722831 TGTGTGCAGCTTAAGAAATTCATAATAAGTTTATCAATTTCCGTATTGGCACTATATGTACAACC
1 TGTGTGCAACTTAAGAAATTCATAATAAGTTTATGAATTTCCATATTGGCACTATGTGTGCAACC
* * * *
1722896 TAAGAAATTCATAATAAGTTTATGAATTTTTGTATTGGCACTATATGTGCAACCTAAAAAATTCA
66 TAAGAAATTCATAATAAGTTTATGAATTTATGTATTGGCACTGTGTGTGCAACCTAAGAAATTCA
*
1722961 TAATTAGTTTATGAATTTCTGTATTGGCACTA
131 TAATTAGTTTATGAATTTCCGTATTGGCACTA
* * * * *
1722993 TGTGTACAACCTAAGAAATTCATAATTAGTTTATGAATTTTCATATTGCCACTATGTGTGCAACC
1 TGTGTGCAACTTAAGAAATTCATAATAAGTTTATGAATTTCCATATTGGCACTATGTGTGCAACC
* **
1723058 TAAGAAATTCATAATTAGTTTATGAATTTATGTATTGGCACTGTGTGTAAAACCTAAGAAATTCA
66 TAAGAAATTCATAATAAGTTTATGAATTTATGTATTGGCACTGTGTGTGCAACCTAAGAAATTCA
*
1723123 TAATTAGTTTATGAATTTCCGTAGTGGCACTA
131 TAATTAGTTTATGAATTTCCGTATTGGCACTA
1723155 TGTGTGCA
1 TGTGTGCA
1723163 CCCATGTAAT
Statistics
Matches: 294, Mismatches: 38, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
162 294 1.00
ACGTcount: A:0.33, C:0.13, G:0.16, T:0.38
Consensus pattern (162 bp):
TGTGTGCAACTTAAGAAATTCATAATAAGTTTATGAATTTCCATATTGGCACTATGTGTGCAACC
TAAGAAATTCATAATAAGTTTATGAATTTATGTATTGGCACTGTGTGTGCAACCTAAGAAATTCA
TAATTAGTTTATGAATTTCCGTATTGGCACTA
Found at i:1728029 original size:54 final size:54
Alignment explanation
Indices: 1727947--1728443 Score: 564
Period size: 54 Copynumber: 9.2 Consensus size: 54
1727937 AATGTCATTG
* * * *
1727947 TGTGTGCAACTTAAGAAATTCATAATAAGTTTTTGAATTTCCGTATTGGCACTC
1 TGTGTGCAACCTAAGAAATTCATAATTAGTTTATGAATTTCCGTATTGGCACTA
* * * * * *
1728001 TGTGTGCAACTTAAGAAATTCATAATAAGTTTATGAATTTACGTATTGACTCTG
1 TGTGTGCAACCTAAGAAATTCATAATTAGTTTATGAATTTCCGTATTGGCACTA
* * ** * *
1728055 TGTGTGCAACTTAAGAAATTCATAATAAGTTTATGAATTTTTGTATTGACATTA
1 TGTGTGCAACCTAAGAAATTCATAATTAGTTTATGAATTTCCGTATTGGCACTA
*
1728109 TGTGTGCAACCTAAGAAATTCATAATTAGTTTATGAATTTCCATATTGGCACTA
1 TGTGTGCAACCTAAGAAATTCATAATTAGTTTATGAATTTCCGTATTGGCACTA
* * *
1728163 TGTGTGCAACCTAAGAAATTCATAATTAGTTTATGAATTTTCATATTGCCACTA
1 TGTGTGCAACCTAAGAAATTCATAATTAGTTTATGAATTTCCGTATTGGCACTA
** *
1728217 TGTGTGCAACCTAAGAAATTCATAATTAGTTTATGAATTTATGTATTGGCACTG
1 TGTGTGCAACCTAAGAAATTCATAATTAGTTTATGAATTTCCGTATTGGCACTA
** *
1728271 TGTGTAAAACCTAAGAAATTCATAATTAGTTTATGAATTTCCGTAGTGGCACTA
1 TGTGTGCAACCTAAGAAATTCATAATTAGTTTATGAATTTCCGTATTGGCACTA
* * * * * * * *
1728325 TGTGTGCACCCCATGTAATTCATAATGAGTTTGTGAATTAT-CGTATCGACACTA
1 TGTGTGCAACCTAAGAAATTCATAATTAGTTTATGAATT-TCCGTATTGGCACTA
* * * * * * * ** * *
1728379 AGTGTGCAACCCACGAAATTTATTATGAGCTTATGAATGACTGTATCGGCACTA
1 TGTGTGCAACCTAAGAAATTCATAATTAGTTTATGAATTTCCGTATTGGCACTA
*
1728433 CGTGTGCAACC
1 TGTGTGCAACC
1728444 CAAAGAACTT
Statistics
Matches: 387, Mismatches: 54, Indels: 4
0.87 0.12 0.01
Matches are distributed among these distances:
54 386 1.00
55 1 0.00
ACGTcount: A:0.32, C:0.14, G:0.17, T:0.37
Consensus pattern (54 bp):
TGTGTGCAACCTAAGAAATTCATAATTAGTTTATGAATTTCCGTATTGGCACTA
Found at i:1728223 original size:162 final size:162
Alignment explanation
Indices: 1727942--1728416 Score: 626
Period size: 162 Copynumber: 2.9 Consensus size: 162
1727932 TACCAAATGT
* * * *
1727942 CATTGTGTGTGCAACTTAAGAAATTCATAATAAGTTTTTGAATTTCCGTATTGGCACTCTGTGTG
1 CATTGTGTGTGCAACCTAAGAAATTCATAATTAGTTTATGAATTTCCGTATTGGCACTATGTGTG
* * * * *
1728007 CAACTTAAGAAATTCATAATAAGTTTATGAATTTACGTATTGACTCTGTGTGTGCAACTTAAGAA
66 CAACCTAAGAAATTCATAATAAGTTTATGAATTTTCGTATTGACACTATGTGTGCAACCTAAGAA
*
1728072 ATTCATAATAAGTTTATGAATTTTTGTATTGA
131 ATTCATAATAAGTTTATGAATTTATGTATTGA
* *
1728104 CATTATGTGTGCAACCTAAGAAATTCATAATTAGTTTATGAATTTCCATATTGGCACTATGTGTG
1 CATTGTGTGTGCAACCTAAGAAATTCATAATTAGTTTATGAATTTCCGTATTGGCACTATGTGTG
* * *
1728169 CAACCTAAGAAATTCATAATTAGTTTATGAATTTTCATATTGCCACTATGTGTGCAACCTAAGAA
66 CAACCTAAGAAATTCATAATAAGTTTATGAATTTTCGTATTGACACTATGTGTGCAACCTAAGAA
* *
1728234 ATTCATAATTAGTTTATGAATTTATGTATTGG
131 ATTCATAATAAGTTTATGAATTTATGTATTGA
* ** *
1728266 CACTGTGTGTAAAACCTAAGAAATTCATAATTAGTTTATGAATTTCCGTAGTGGCACTATGTGTG
1 CATTGTGTGTGCAACCTAAGAAATTCATAATTAGTTTATGAATTTCCGTATTGGCACTATGTGTG
* * * * * * * * * * *
1728331 CACCCCATGTAATTCATAATGAGTTTGTGAATTATCGTATCGACACTAAGTGTGCAACCCACGAA
66 CAACCTAAGAAATTCATAATAAGTTTATGAATTTTCGTATTGACACTATGTGTGCAACCTAAGAA
* * * *
1728396 ATTTATTATGAGCTTATGAAT
131 ATTCATAATAAGTTTATGAAT
1728417 GACTGTATCG
Statistics
Matches: 273, Mismatches: 40, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
162 273 1.00
ACGTcount: A:0.32, C:0.13, G:0.16, T:0.38
Consensus pattern (162 bp):
CATTGTGTGTGCAACCTAAGAAATTCATAATTAGTTTATGAATTTCCGTATTGGCACTATGTGTG
CAACCTAAGAAATTCATAATAAGTTTATGAATTTTCGTATTGACACTATGTGTGCAACCTAAGAA
ATTCATAATAAGTTTATGAATTTATGTATTGA
Found at i:1731560 original size:22 final size:22
Alignment explanation
Indices: 1731501--1731572 Score: 65
Period size: 22 Copynumber: 3.1 Consensus size: 22
1731491 TTGAAATTTT
* *
1731501 TTATTATTTTAAAATTAATAATAA
1 TTATTATATT-AAA-TAATATTAA
* *
1731525 TTTTTTATAATAAATAATATTAA
1 -TTATTATATTAAATAATATTAA
1731548 TTATTATATTAAATAA-ATATAA
1 TTATTATATTAAATAATAT-TAA
1731570 TTA
1 TTA
1731573 ATCATTTTAT
Statistics
Matches: 40, Mismatches: 6, Indels: 5
0.78 0.12 0.10
Matches are distributed among these distances:
21 2 0.05
22 20 0.50
23 8 0.20
24 3 0.08
25 7 0.17
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (22 bp):
TTATTATATTAAATAATATTAA
Found at i:1731587 original size:26 final size:26
Alignment explanation
Indices: 1731512--1731587 Score: 68
Period size: 26 Copynumber: 3.0 Consensus size: 26
1731502 TATTATTTTA
* *
1731512 AAAT-TAA-TAATAATTTTTTATAAT
1 AAATATAATTAATAATTTTATAAAAT
* * *
1731536 AAATA-ATATTAATTATTATATTAAAT
1 AAATATA-ATTAATAATTTTATAAAAT
*
1731562 AAATATAATTAATCATTTTATAAAAT
1 AAATATAATTAATAATTTTATAAAAT
1731588 TACCAATAAA
Statistics
Matches: 40, Mismatches: 8, Indels: 6
0.74 0.15 0.11
Matches are distributed among these distances:
24 5 0.12
25 1 0.03
26 33 0.82
27 1 0.03
ACGTcount: A:0.53, C:0.01, G:0.00, T:0.46
Consensus pattern (26 bp):
AAATATAATTAATAATTTTATAAAAT
Found at i:1735031 original size:138 final size:138
Alignment explanation
Indices: 1734780--1735815 Score: 1572
Period size: 138 Copynumber: 7.5 Consensus size: 138
1734770 GGCGAGTTCT
* * * * *
1734780 CGGGGGTGCGCTTTTCATTATTTTATCAGAGAATATGTTATCATTGGCCTATTATGTCACTCATG
1 CGGGGGCGCGCCTTCCATTATTTTGTCAGAGAATATGTTATCATTGCCCTATTATGTCACTCATG
* * * *
1734845 TCCCCCGGGGAACTATTCATATCAGTACCTATTATTTATGAGGAGACTTGGCAAAGTGGTGAAAA
66 TCCCCCGGGGAACTATTCATGTCAGTACCTATTATTTCTGAGGGGACTTGGCAAAGTGGTGAAAG
1734910 CGTGTTTC
131 CGTGTTTC
* * * * *
1734918 CGGGGGCACGCCTTCCATTATTTTGTTAAAGAATATGTTATCATTGCTCTATTATGTCACTTATG
1 CGGGGGCGCGCCTTCCATTATTTTGTCAGAGAATATGTTATCATTGCCCTATTATGTCACTCATG
* *
1734983 TCCCCCGGAGAACTATTCATGTCAGTACCTATTATTTATGAGGGGACTTGGCAAAGTGGTGAAAG
66 TCCCCCGGGGAACTATTCATGTCAGTACCTATTATTTCTGAGGGGACTTGGCAAAGTGGTGAAAG
* *
1735048 CATATTTC
131 CGTGTTTC
* *
1735056 CGGGGGCGTGCCTTCCATTATTTTATCAGAGAATATGTTATCATTGCCCTATTATGTCACAT-AT
1 CGGGGGCGCGCCTTCCATTATTTTGTCAGAGAATATGTTATCATTGCCCTATTATGTCAC-TCAT
*
1735120 GTCCCCCAGGGAACTATTCATGTCAGTACCTATTATTTCTGAGGGGACTTGGCAAAGTGGTGAAA
65 GTCCCCCGGGGAACTATTCATGTCAGTACCTATTATTTCTGAGGGGACTTGGCAAAGTGGTGAAA
*
1735185 GCTTGTTTC
130 GCGTGTTTC
* * *
1735194 CGGGGGCACGCCTTCCATTATTTTGTAAAAGAATATGTTATCATTGCCCTATTATGTCACTCATG
1 CGGGGGCGCGCCTTCCATTATTTTGTCAGAGAATATGTTATCATTGCCCTATTATGTCACTCATG
* * * *
1735259 TCCCTCGGGGAACTATTAATGTAAGTACCTATTATTTCTTAGGGGACTTGGCAAAGTGGTGAAAG
66 TCCCCCGGGGAACTATTCATGTCAGTACCTATTATTTCTGAGGGGACTTGGCAAAGTGGTGAAAG
**
1735324 CACGTTTC
131 CGTGTTTC
* * * * *
1735332 CGAGGGTGCGCCTTCCATTATTTTGTTAGAGAATATGTTATCATTGCTCTATTATGTCACTTATG
1 CGGGGGCGCGCCTTCCATTATTTTGTCAGAGAATATGTTATCATTGCCCTATTATGTCACTCATG
* *
1735397 TCTCCCGGGAAACTATTCATGTCAGTACCTATTATTTCTGAGGGGACTTGGCAAAGTGGTGAAAG
66 TCCCCCGGGGAACTATTCATGTCAGTACCTATTATTTCTGAGGGGACTTGGCAAAGTGGTGAAAG
1735462 CGTGTTTC
131 CGTGTTTC
* * *
1735470 CGGAGGCGCGCCTTCCATTATTTTGTCAGAGAATATGTTATCATTGCACTATTATGTCACTTATG
1 CGGGGGCGCGCCTTCCATTATTTTGTCAGAGAATATGTTATCATTGCCCTATTATGTCACTCATG
* * * *
1735535 TCCCCTGGAGAACTATTCATGTCAGTACCTATTATTTTTTAGGGGACTTGGCAAAGTGGTGAAAG
66 TCCCCCGGGGAACTATTCATGTCAGTACCTATTATTTCTGAGGGGACTTGGCAAAGTGGTGAAAG
1735600 CGTG-TTC
131 CGTGTTTC
* *
1735607 TCGGGGGCGCGCCTTTCATTATTTTGTCAGAGAATATGTTATCATTGTCCTATTATGTCACTCAT
1 -CGGGGGCGCGCCTTCCATTATTTTGTCAGAGAATATGTTATCATTGCCCTATTATGTCACTCAT
*
1735672 GTCCCCCGGGGAACTATTCATATCAGTACCTATTATTTCTGAGGGGACTTGGCAAAGTGGTGAAA
65 GTCCCCCGGGGAACTATTCATGTCAGTACCTATTATTTCTGAGGGGACTTGGCAAAGTGGTGAAA
*
1735737 GCGTGTTCC
130 GCGTGTTTC
* * *
1735746 CAGGGGCGCGCCTTCCATTATTTTGTCAAAGAATATGTTTTCATTGCCCTATTATGTCACTCATG
1 CGGGGGCGCGCCTTCCATTATTTTGTCAGAGAATATGTTATCATTGCCCTATTATGTCACTCATG
1735811 TCCCC
66 TCCCC
1735816 AAGAGACACA
Statistics
Matches: 813, Mismatches: 81, Indels: 8
0.90 0.09 0.01
Matches are distributed among these distances:
137 4 0.00
138 806 0.99
139 3 0.00
ACGTcount: A:0.23, C:0.20, G:0.22, T:0.35
Consensus pattern (138 bp):
CGGGGGCGCGCCTTCCATTATTTTGTCAGAGAATATGTTATCATTGCCCTATTATGTCACTCATG
TCCCCCGGGGAACTATTCATGTCAGTACCTATTATTTCTGAGGGGACTTGGCAAAGTGGTGAAAG
CGTGTTTC
Found at i:1736090 original size:14 final size:14
Alignment explanation
Indices: 1736071--1736101 Score: 53
Period size: 14 Copynumber: 2.2 Consensus size: 14
1736061 TGATAAGTTG
*
1736071 GTTTTAATGTATAT
1 GTTTTAATATATAT
1736085 GTTTTAATATATAT
1 GTTTTAATATATAT
1736099 GTT
1 GTT
1736102 AAGGATAAAA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.29, C:0.00, G:0.13, T:0.58
Consensus pattern (14 bp):
GTTTTAATATATAT
Found at i:1736260 original size:34 final size:34
Alignment explanation
Indices: 1736222--1736294 Score: 128
Period size: 34 Copynumber: 2.1 Consensus size: 34
1736212 TAAAGTTGAA
1736222 TTTAATGTTAAATTTCGAATACTATAATTTATAT
1 TTTAATGTTAAATTTCGAATACTATAATTTATAT
* *
1736256 TTTAATTTTAAATTTCGAATACTATAATTTGTAT
1 TTTAATGTTAAATTTCGAATACTATAATTTATAT
1736290 TTTAA
1 TTTAA
1736295 AAACATTTAA
Statistics
Matches: 37, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
34 37 1.00
ACGTcount: A:0.37, C:0.05, G:0.05, T:0.52
Consensus pattern (34 bp):
TTTAATGTTAAATTTCGAATACTATAATTTATAT
Found at i:1736843 original size:21 final size:21
Alignment explanation
Indices: 1736817--1736877 Score: 86
Period size: 21 Copynumber: 2.9 Consensus size: 21
1736807 ATAAAACCCT
*
1736817 GAGGGCTAGGCATGTAACCTG
1 GAGGGCTAGGAATGTAACCTG
* *
1736838 GCGGGCTAGGAATGTAACCTT
1 GAGGGCTAGGAATGTAACCTG
*
1736859 GAGGGCTAGGAATATAACC
1 GAGGGCTAGGAATGTAACC
1736878 CTGCAGAGAT
Statistics
Matches: 35, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 35 1.00
ACGTcount: A:0.28, C:0.18, G:0.34, T:0.20
Consensus pattern (21 bp):
GAGGGCTAGGAATGTAACCTG
Found at i:1736955 original size:42 final size:42
Alignment explanation
Indices: 1736859--1736964 Score: 117
Period size: 42 Copynumber: 2.5 Consensus size: 42
1736849 ATGTAACCTT
* * * *
1736859 GAGGGCTAGGAATATAACCCTGCAGAGATGGCATATGAACTG
1 GAGGGTTAGGCATATACCCCTGCAGAGATGGCATATGAACTA
* *
1736901 GTGGGCTT-GGCATATACCCCTG-AGGAGATGGCATCTGAACTA
1 GAGGG-TTAGGCATATACCCCTGCA-GAGATGGCATATGAACTA
*
1736943 GAGGGTTAGGCATGTACCCCTG
1 GAGGGTTAGGCATATACCCCTG
1736965 TGGCATCATC
Statistics
Matches: 53, Mismatches: 8, Indels: 6
0.79 0.12 0.09
Matches are distributed among these distances:
41 3 0.06
42 49 0.92
43 1 0.02
ACGTcount: A:0.26, C:0.20, G:0.32, T:0.22
Consensus pattern (42 bp):
GAGGGTTAGGCATATACCCCTGCAGAGATGGCATATGAACTA
Found at i:1739013 original size:35 final size:34
Alignment explanation
Indices: 1738969--1739081 Score: 163
Period size: 35 Copynumber: 3.2 Consensus size: 34
1738959 AAAACAATTC
*
1738969 TCAATTTCATTCTAAACCACAAATTCCAAAGTAAT
1 TCAATTTCATTCTAAACC-CAAATTCCAAAATAAT
1739004 TCAATTTCATTCTAAACCCTAAATTCCAAAATAAT
1 TCAATTTCATTCTAAACCC-AAATTCCAAAATAAT
* * *
1739039 TCAATTACATTCTAAAACCCAAATTCTAAAATACT
1 TCAATTTCATTCT-AAACCCAAATTCCAAAATAAT
1739074 TCAATTTC
1 TCAATTTC
1739082 TGTCTTTTTA
Statistics
Matches: 71, Mismatches: 5, Indels: 4
0.89 0.06 0.05
Matches are distributed among these distances:
34 1 0.01
35 64 0.90
36 6 0.08
ACGTcount: A:0.42, C:0.23, G:0.01, T:0.34
Consensus pattern (34 bp):
TCAATTTCATTCTAAACCCAAATTCCAAAATAAT
Found at i:1740148 original size:35 final size:34
Alignment explanation
Indices: 1740100--1740211 Score: 145
Period size: 35 Copynumber: 3.2 Consensus size: 34
1740090 ATTTCTCCTT
*
1740100 AAATTGAAGTATTTTAGAATTTAGGGTTTAGAATG
1 AAATTGAATTATTTT-GAATTTAGGGTTTAGAATG
*
1740135 TAATTGAATTATTTTGGAATTTAGGGTTTAGAATG
1 AAATTGAATTATTTT-GAATTTAGGGTTTAGAATG
* *
1740170 AAATTGAATTACTTTGAAATTT-GGGATTTATAATG
1 AAATTGAATTATTTTG-AATTTAGGG-TTTAGAATG
1740205 AAATTGA
1 AAATTGA
1740212 GGAATGTTTT
Statistics
Matches: 69, Mismatches: 6, Indels: 4
0.87 0.08 0.05
Matches are distributed among these distances:
34 4 0.06
35 65 0.94
ACGTcount: A:0.37, C:0.01, G:0.21, T:0.42
Consensus pattern (34 bp):
AAATTGAATTATTTTGAATTTAGGGTTTAGAATG
Done.