Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01004507.1 Hibiscus syriacus cultivar Beakdansim tig00009942_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: 1776135
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 8 of 8
Found at i:1590128 original size:23 final size:23
Alignment explanation
Indices: 1590112--1590161 Score: 82
Period size: 23 Copynumber: 2.2 Consensus size: 23
1590102 TTATGTTTGT
1590112 CTTTATGGCACATTTATCTCTGA
1 CTTTATGGCACATTTATCTCTGA
* *
1590135 CTTTGTGGCACATTTTTCTCTGA
1 CTTTATGGCACATTTATCTCTGA
1590158 CTTT
1 CTTT
1590162 TGGTAGCTTA
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
23 25 1.00
ACGTcount: A:0.16, C:0.22, G:0.14, T:0.48
Consensus pattern (23 bp):
CTTTATGGCACATTTATCTCTGA
Found at i:1599145 original size:21 final size:17
Alignment explanation
Indices: 1599103--1599137 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 17
1599093 TTAATTTTTA
1599103 TAATTTTTTAATTAAAT
1 TAATTTTTTAATTAAAT
1599120 TAATTTATTTAAGTTAAA
1 TAATTT-TTTAA-TTAAA
1599138 ATTTAATTAG
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 6 0.38
18 5 0.31
19 5 0.31
ACGTcount: A:0.43, C:0.00, G:0.03, T:0.54
Consensus pattern (17 bp):
TAATTTTTTAATTAAAT
Found at i:1599244 original size:18 final size:19
Alignment explanation
Indices: 1599216--1599272 Score: 62
Period size: 18 Copynumber: 3.0 Consensus size: 19
1599206 GATTTTGAAC
*
1599216 TTAAATTATATAATTAATA
1 TTAAATAATATAATTAATA
*
1599235 -TAAATAATATATTTAATA
1 TTAAATAATATAATTAATA
* *
1599253 TTTAATAATTTACATTAATA
1 TTAAATAATATA-ATTAATA
1599273 AGATTAATTA
Statistics
Matches: 31, Mismatches: 5, Indels: 3
0.79 0.13 0.08
Matches are distributed among these distances:
18 16 0.52
19 9 0.29
20 6 0.19
ACGTcount: A:0.51, C:0.02, G:0.00, T:0.47
Consensus pattern (19 bp):
TTAAATAATATAATTAATA
Found at i:1605346 original size:23 final size:24
Alignment explanation
Indices: 1605314--1605358 Score: 74
Period size: 23 Copynumber: 1.9 Consensus size: 24
1605304 TTTATTAGTT
*
1605314 TAATTTAATATATAA-ATTATTAA
1 TAATTAAATATATAATATTATTAA
1605337 TAATTAAATATATAATATTATT
1 TAATTAAATATATAATATTATT
1605359 TTATATATAA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
23 14 0.70
24 6 0.30
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (24 bp):
TAATTAAATATATAATATTATTAA
Found at i:1605691 original size:5 final size:6
Alignment explanation
Indices: 1605663--1605688 Score: 52
Period size: 6 Copynumber: 4.3 Consensus size: 6
1605653 TTAATTTATT
1605663 AAATTA AAATTA AAATTA AAATTA AA
1 AAATTA AAATTA AAATTA AAATTA AA
1605689 TTAGTAGAAT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 20 1.00
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (6 bp):
AAATTA
Found at i:1606022 original size:60 final size:55
Alignment explanation
Indices: 1605929--1606099 Score: 155
Period size: 58 Copynumber: 2.9 Consensus size: 55
1605919 CATCATACGT
* *
1605929 ATAATTTGGGATAAAATTAGAGTGTTCAAAAAGTTTAGAGACTAATTTAAAATAAATGTC
1 ATAATTTGGGATAAAATTA-AATGTT-TAAAAGTTTAGAGACTAATTTAAAAT-AA--TC
* * *
1605989 ATAATTTGGGGATAAAATTGAAATGTTTAAAAG-TTAAAGGATTAATTTAATGATAATC
1 ATAATTT-GGGATAAAATT-AAATGTTTAAAAGTTTAGA-GACTAATTTAA-AATAATC
* ** *
1606047 ATAATTTAGGGATGAAATTAAAACATTTAAAAGTTTAGAAACTAATTTAAAAT
1 ATAATTT-GGGATAAAATT-AAATGTTTAAAAGTTTAGAGACTAATTTAAAAT
1606100 GAGGAATATA
Statistics
Matches: 92, Mismatches: 14, Indels: 13
0.77 0.12 0.11
Matches are distributed among these distances:
57 2 0.02
58 39 0.42
59 8 0.09
60 24 0.26
61 18 0.20
62 1 0.01
ACGTcount: A:0.47, C:0.04, G:0.15, T:0.35
Consensus pattern (55 bp):
ATAATTTGGGATAAAATTAAATGTTTAAAAGTTTAGAGACTAATTTAAAATAATC
Found at i:1613041 original size:30 final size:31
Alignment explanation
Indices: 1612981--1613041 Score: 97
Period size: 31 Copynumber: 2.0 Consensus size: 31
1612971 TCTTTTTGAA
* *
1612981 ATAACTATTAGTACTTCGGCTTTTTGATACT
1 ATAACTATTAGTACTTCGACTTTTTCATACT
1613012 ATAACTATTAGTACTT-GACTTTTTCATACT
1 ATAACTATTAGTACTTCGACTTTTTCATACT
1613042 TTAGATTGAT
Statistics
Matches: 28, Mismatches: 2, Indels: 1
0.90 0.06 0.03
Matches are distributed among these distances:
30 12 0.43
31 16 0.57
ACGTcount: A:0.28, C:0.16, G:0.10, T:0.46
Consensus pattern (31 bp):
ATAACTATTAGTACTTCGACTTTTTCATACT
Found at i:1615991 original size:17 final size:17
Alignment explanation
Indices: 1615969--1616001 Score: 66
Period size: 17 Copynumber: 1.9 Consensus size: 17
1615959 TTCTTATTTT
1615969 TATAAAGCATGAATATC
1 TATAAAGCATGAATATC
1615986 TATAAAGCATGAATAT
1 TATAAAGCATGAATAT
1616002 ATTTATAAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.48, C:0.09, G:0.12, T:0.30
Consensus pattern (17 bp):
TATAAAGCATGAATATC
Found at i:1622729 original size:24 final size:24
Alignment explanation
Indices: 1622702--1622749 Score: 96
Period size: 24 Copynumber: 2.0 Consensus size: 24
1622692 TATAAAGAGT
1622702 AAAATTATATCGTTCCTCATTGAA
1 AAAATTATATCGTTCCTCATTGAA
1622726 AAAATTATATCGTTCCTCATTGAA
1 AAAATTATATCGTTCCTCATTGAA
1622750 TTTTACCCTT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.38, C:0.17, G:0.08, T:0.38
Consensus pattern (24 bp):
AAAATTATATCGTTCCTCATTGAA
Found at i:1645307 original size:13 final size:13
Alignment explanation
Indices: 1645289--1645313 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1645279 AAATTCAATG
1645289 AAGACTAAAAAGC
1 AAGACTAAAAAGC
1645302 AAGACTAAAAAG
1 AAGACTAAAAAG
1645314 GTCTAACACA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.64, C:0.12, G:0.16, T:0.08
Consensus pattern (13 bp):
AAGACTAAAAAGC
Found at i:1645483 original size:3 final size:3
Alignment explanation
Indices: 1645475--1645521 Score: 94
Period size: 3 Copynumber: 15.7 Consensus size: 3
1645465 TTTTTACCCA
1645475 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA
1645522 AATATATATT
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 44 1.00
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
TAT
Found at i:1646055 original size:19 final size:17
Alignment explanation
Indices: 1646019--1646051 Score: 66
Period size: 17 Copynumber: 1.9 Consensus size: 17
1646009 ACAAAACCGG
1646019 AGAGAAAGAAAAAAAAC
1 AGAGAAAGAAAAAAAAC
1646036 AGAGAAAGAAAAAAAA
1 AGAGAAAGAAAAAAAA
1646052 AACAACTAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.79, C:0.03, G:0.18, T:0.00
Consensus pattern (17 bp):
AGAGAAAGAAAAAAAAC
Found at i:1658309 original size:1 final size:1
Alignment explanation
Indices: 1658299--1658372 Score: 67
Period size: 1 Copynumber: 74.0 Consensus size: 1
1658289 ATGCTTGAAG
* * * * * * * *
1658299 AAAAAGAAAAAAAAAGAGAAAAGAAAAAAAAAAGAGAAAAAAAAAGAAAAAAAAAAGAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
*
1658364 AGAAAAAAA
1 AAAAAAAAA
1658373 GGGGGTCAAG
Statistics
Matches: 55, Mismatches: 18, Indels: 0
0.75 0.25 0.00
Matches are distributed among these distances:
1 55 1.00
ACGTcount: A:0.88, C:0.00, G:0.12, T:0.00
Consensus pattern (1 bp):
A
Found at i:1658314 original size:10 final size:10
Alignment explanation
Indices: 1658299--1658372 Score: 105
Period size: 10 Copynumber: 7.3 Consensus size: 10
1658289 ATGCTTGAAG
1658299 AAAAAGAAAA
1 AAAAAGAAAA
1658309 AAAAAGAGAAA
1 AAAAAGA-AAA
*
1658320 AGAAA-AAAA
1 AAAAAGAAAA
*
1658329 AAAGAGAAAA
1 AAAAAGAAAA
1658339 AAAAAGAAAAA
1 AAAAAG-AAAA
1658350 AAAAAGAAAA
1 AAAAAGAAAA
1658360 AAAAAGAAAA
1 AAAAAGAAAA
1658370 AAA
1 AAA
1658373 GGGGGTCAAG
Statistics
Matches: 57, Mismatches: 4, Indels: 6
0.85 0.06 0.09
Matches are distributed among these distances:
9 6 0.11
10 34 0.60
11 17 0.30
ACGTcount: A:0.88, C:0.00, G:0.12, T:0.00
Consensus pattern (10 bp):
AAAAAGAAAA
Found at i:1658320 original size:18 final size:18
Alignment explanation
Indices: 1658297--1658373 Score: 99
Period size: 18 Copynumber: 4.4 Consensus size: 18
1658287 TTATGCTTGA
1658297 AGAAAAAGAAAAAAAAAG
1 AGAAAAAGAAAAAAAAAG
1658315 AG-AAAAGAAAAAAAAAAG
1 AGAAAAAG-AAAAAAAAAG
*
1658333 AGAAAAA-AAAAGAAAA-
1 AGAAAAAGAAAAAAAAAG
1658349 A-AAAAAGAAAAAAAAAG
1 AGAAAAAGAAAAAAAAAG
*
1658366 AAAAAAAG
1 AGAAAAAG
1658374 GGGGTCAAGG
Statistics
Matches: 52, Mismatches: 2, Indels: 10
0.81 0.03 0.16
Matches are distributed among these distances:
15 5 0.10
16 9 0.17
17 14 0.27
18 20 0.38
19 4 0.08
ACGTcount: A:0.86, C:0.00, G:0.14, T:0.00
Consensus pattern (18 bp):
AGAAAAAGAAAAAAAAAG
Found at i:1659615 original size:83 final size:83
Alignment explanation
Indices: 1659424--1660208 Score: 1244
Period size: 83 Copynumber: 9.5 Consensus size: 83
1659414 GAATTTGCCA
* ** *
1659424 ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGACCTGGTTTAACAGAA-CAATCATTGAGTT
1 ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGCAGAACCAATCATTGAATT
* *
1659488 TAGAAGATGAATTTG-CC
66 TAGAAGATGAATGTGTTC
* * * *
1659505 AATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCT-GATTGGACAGAATCAAGCATTGAG
1 -ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGG-CAGAACCAATCATTGAA
* *
1659569 TTTAGAAGATGAATTTG-CC
64 TTTAGAAGATGAATGTGTTC
* * *
1659588 AATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGACCTGGTTTAGCAGAA-CAATCATTGAGT
1 -ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGCAGAACCAATCATTGAAT
* *
1659652 TTAGAAGATGAATTTG-CC
65 TTAGAAGATGAATGTGTTC
* * *
1659670 AATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCT-GATTGGACAGAATCAAGCATTGAA
1 -ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGG-CAGAACCAATCATTGAA
1659734 TTTAGAAGATGAATGTGTTC
64 TTTAGAAGATGAATGTGTTC
1659754 ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGCAGAACCAATCATTGAATT
1 ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGCAGAACCAATCATTGAATT
1659819 TAGAAGATGAATGTGTTC
66 TAGAAGATGAATGTGTTC
1659837 ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGCAGAACCAATCATTGAATT
1 ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGCAGAACCAATCATTGAATT
1659902 TAGAAGATGAATGTGTTC
66 TAGAAGATGAATGTGTTC
1659920 ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGCAGAACCAATCATTGAATT
1 ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGCAGAACCAATCATTGAATT
1659985 TAGAAGATGAATGTGTTC
66 TAGAAGATGAATGTGTTC
1660003 ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGCAGAACCAATCATTGAATT
1 ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGCAGAACCAATCATTGAATT
*
1660068 TGGAAGAT-AGATGTGTTC
66 TAGAAGATGA-ATGTGTTC
1660086 ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGCAGAACCAATCATTGAATT
1 ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGCAGAACCAATCATTGAATT
** *
1660151 CGGAAAATGAATGTGTTC
66 TAGAAGATGAATGTGTTC
1660169 ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTG
1 ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTG
1660209 ATTCAGTAGG
Statistics
Matches: 672, Mismatches: 22, Indels: 17
0.95 0.03 0.02
Matches are distributed among these distances:
81 7 0.01
82 117 0.17
83 537 0.80
84 11 0.02
ACGTcount: A:0.27, C:0.14, G:0.23, T:0.37
Consensus pattern (83 bp):
ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGCAGAACCAATCATTGAATT
TAGAAGATGAATGTGTTC
Found at i:1661280 original size:113 final size:112
Alignment explanation
Indices: 1660940--1661281 Score: 603
Period size: 112 Copynumber: 3.0 Consensus size: 112
1660930 GATTCAAATC
1660940 CATCACTTGATGGATCAACATTGCCAGAGAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAA
1 CATCACTTGATGGATCAACATTGCCAGAGAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAA
1661005 GAAGAAGTTCATAATGAGAAGAACTTGTTCAACTTTTTGTTTGAATT
66 GAAGAAGTTCATAATGAGAAGAACTTGTTCAACTTTTTGTTTGAATT
*
1661052 CATCATTTGATGGATCAACATTGCCAGAGAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAA
1 CATCACTTGATGGATCAACATTGCCAGAGAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAA
1661117 GAAGAAGTTCATAATGAGAAGAACTTGTTCAACTTTTTGTTTGAATT
66 GAAGAAGTTCATAATGAGAAGAACTTGTTCAACTTTTTGTTTGAATT
* ***
1661164 CATCACTTGATGGATTATTTTTGCCAGAGAAGGTTCATAATGAGAAGAACTCATCTGAAGAAGGA
1 CATCACTTGATGGATCAACATTGCCAGAGAA-GTTCATAATGAGAAGAACTCATCTGAAGAAGGA
* * *
1661229 AGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTGTCTGAATT
65 AGAAGAAGTTCATAATGAGAAGAACTTGTTCAACTTTTTGTTTGAATT
1661277 CATCA
1 CATCA
1661282 TCTGAAGAAG
Statistics
Matches: 220, Mismatches: 9, Indels: 1
0.96 0.04 0.00
Matches are distributed among these distances:
112 137 0.62
113 83 0.38
ACGTcount: A:0.37, C:0.13, G:0.20, T:0.30
Consensus pattern (112 bp):
CATCACTTGATGGATCAACATTGCCAGAGAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAA
GAAGAAGTTCATAATGAGAAGAACTTGTTCAACTTTTTGTTTGAATT
Found at i:1661295 original size:65 final size:65
Alignment explanation
Indices: 1661214--1661346 Score: 230
Period size: 65 Copynumber: 2.0 Consensus size: 65
1661204 TGAGAAGAAC
* *
1661214 TCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTGTCTGAATTCA
1 TCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACCTTTTGTCTAAATTCA
* *
1661279 TCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACTTTTTGTTTAAATTCA
1 TCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACCTTTTGTCTAAATTCA
1661344 TCA
1 TCA
1661347 CTTGATGGAT
Statistics
Matches: 64, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
65 64 1.00
ACGTcount: A:0.38, C:0.12, G:0.19, T:0.32
Consensus pattern (65 bp):
TCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACCTTTTGTCTAAATTCA
Found at i:1661317 original size:178 final size:178
Alignment explanation
Indices: 1661101--1661976 Score: 1571
Period size: 178 Copynumber: 4.9 Consensus size: 178
1661091 TGAGAAGAAC
* *
1661101 TCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACTTTTTGTTTGAATTCA
1 TCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACTTTTTGTCTGAATTCA
*
1661166 TCACTTGATGGATTATTTTTGCCAGAGAAGGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAG
66 TCACTTGATGGATTATTTTTGCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAG
1661231 AAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTGTCTGAATTCA
131 AAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTGTCTGAATTCA
* * *
1661279 TCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACTTTTTGTTTAAATTCA
1 TCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACTTTTTGTCTGAATTCA
*
1661344 TCACTTGATGGATTATTTTTGCCAGAGAAGGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAG
66 TCACTTGATGGATTATTTTTGCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAG
1661409 AAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTGTCTGAATTCA
131 AAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTGTCTGAATTCA
* *
1661457 TCATCTGAAGAAGGAAGAAGAAATTCATAATGAGAAGAATTTGTTCAACCTTTTGTCTGAATTCA
1 TCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACTTTTTGTCTGAATTCA
1661522 TCACTTGATGGATTATTTTTGCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAG
66 TCACTTGATGGATTATTTTTGCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAG
1661587 AAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTGTCTGAATTCA
131 AAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTGTCTGAATTCA
* *
1661635 TCATCTGAAGAAGGAAGAAGAAATTCATAATGAGAAGAATTTGTTCAACCTTTTGTCTGAATTCA
1 TCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACTTTTTGTCTGAATTCA
* *
1661700 TCACTTGATGGATGATTTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAG
66 TCACTTGATGGATTATTTTTGCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAG
*
1661765 AAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTGTCTAAATTCA
131 AAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTGTCTGAATTCA
*
1661813 TCATCTGAAG-A--ATGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTT-TCTGAATTC
1 TCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAA-CTTTTTGTCTGAATTC
1661874 ATCACTTGATGGATTATTTTTGCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAA
65 ATCACTTGATGGATTATTTTTGCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAA
*
1661939 GAAGAAGTTCATAATGAGAAAAATTTGTTCAACCTTTT
130 GAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTT
1661977 TGATCAAATC
Statistics
Matches: 681, Mismatches: 16, Indels: 5
0.97 0.02 0.01
Matches are distributed among these distances:
175 141 0.21
176 5 0.01
177 1 0.00
178 534 0.78
ACGTcount: A:0.37, C:0.12, G:0.20, T:0.31
Consensus pattern (178 bp):
TCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACTTTTTGTCTGAATTCA
TCACTTGATGGATTATTTTTGCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAG
AAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTGTCTGAATTCA
Found at i:1661473 original size:65 final size:65
Alignment explanation
Indices: 1661392--1661524 Score: 257
Period size: 65 Copynumber: 2.0 Consensus size: 65
1661382 TGAGAAGAAC
*
1661392 TCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTGTCTGAATTCA
1 TCATCTGAAGAAGGAAGAAGAAATTCATAATGAGAAGAATTTGTTCAACCTTTTGTCTGAATTCA
1661457 TCATCTGAAGAAGGAAGAAGAAATTCATAATGAGAAGAATTTGTTCAACCTTTTGTCTGAATTCA
1 TCATCTGAAGAAGGAAGAAGAAATTCATAATGAGAAGAATTTGTTCAACCTTTTGTCTGAATTCA
1661522 TCA
1 TCA
1661525 CTTGATGGAT
Statistics
Matches: 67, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
65 67 1.00
ACGTcount: A:0.38, C:0.13, G:0.19, T:0.31
Consensus pattern (65 bp):
TCATCTGAAGAAGGAAGAAGAAATTCATAATGAGAAGAATTTGTTCAACCTTTTGTCTGAATTCA
Found at i:1661651 original size:65 final size:65
Alignment explanation
Indices: 1661570--1661702 Score: 257
Period size: 65 Copynumber: 2.0 Consensus size: 65
1661560 TGAGAAGAAC
*
1661570 TCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTGTCTGAATTCA
1 TCATCTGAAGAAGGAAGAAGAAATTCATAATGAGAAGAATTTGTTCAACCTTTTGTCTGAATTCA
1661635 TCATCTGAAGAAGGAAGAAGAAATTCATAATGAGAAGAATTTGTTCAACCTTTTGTCTGAATTCA
1 TCATCTGAAGAAGGAAGAAGAAATTCATAATGAGAAGAATTTGTTCAACCTTTTGTCTGAATTCA
1661700 TCA
1 TCA
1661703 CTTGATGGAT
Statistics
Matches: 67, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
65 67 1.00
ACGTcount: A:0.38, C:0.13, G:0.19, T:0.31
Consensus pattern (65 bp):
TCATCTGAAGAAGGAAGAAGAAATTCATAATGAGAAGAATTTGTTCAACCTTTTGTCTGAATTCA
Found at i:1661830 original size:65 final size:62
Alignment explanation
Indices: 1661748--1661877 Score: 206
Period size: 62 Copynumber: 2.0 Consensus size: 62
1661738 TGAGAAGAAC
1661748 TCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTGTCTAAATTCA
1 TCATCTGAAGAA-G--GAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTGTCTAAATTCA
* * *
1661813 TCATCTGAAGAATGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTTTCTGAATTCA
1 TCATCTGAAGAAGGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTGTCTAAATTCA
1661875 TCA
1 TCA
1661878 CTTGATGGAT
Statistics
Matches: 62, Mismatches: 3, Indels: 3
0.91 0.04 0.04
Matches are distributed among these distances:
62 50 0.81
65 12 0.19
ACGTcount: A:0.37, C:0.13, G:0.17, T:0.33
Consensus pattern (62 bp):
TCATCTGAAGAAGGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTGTCTAAATTCA
Found at i:1661952 original size:113 final size:114
Alignment explanation
Indices: 1661820--1662075 Score: 381
Period size: 114 Copynumber: 2.2 Consensus size: 114
1661810 TCATCATCTG
** * *
1661820 AAGAATGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTTTCTGAATTC-ATCACTTGAT
1 AAGAA-GAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTTGATCAAATCTATCACTTGAT
*
1661884 GGATTATTTTTGCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGA
65 GGATTATTTTTGCCAGAGAAAGTTCATAATGAGAAGAAATCATCTGAAGA
* * *
1661934 AGGAAGAAGAAGTTCATAATGAGAAAAATTTGTTCAACCTTTTTGATCAAATCTATTACTTGATG
1 AAGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTTGATCAAATCTATCACTTGATG
* **
1661999 GGTTATTTTTTTCAGAGAAAGTTCATAATGAGAAGAAATCATCTGAAGA
66 GATTATTTTTGCCAGAGAAAGTTCATAATGAGAAGAAATCATCTGAAGA
1662048 AAGAAG-AGAAAGTTCATAATGAGAAGAA
1 AAGAAGAAG-AAGTTCATAATGAGAAGAA
1662076 CTCATCAAAA
Statistics
Matches: 127, Mismatches: 13, Indels: 4
0.88 0.09 0.03
Matches are distributed among these distances:
113 45 0.35
114 82 0.65
ACGTcount: A:0.40, C:0.10, G:0.19, T:0.31
Consensus pattern (114 bp):
AAGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTTGATCAAATCTATCACTTGATG
GATTATTTTTGCCAGAGAAAGTTCATAATGAGAAGAAATCATCTGAAGA
Found at i:1662334 original size:3 final size:3
Alignment explanation
Indices: 1662326--1662393 Score: 127
Period size: 3 Copynumber: 22.7 Consensus size: 3
1662316 TTTTTACCCA
1662326 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
*
1662374 TAT CAT TAT TAT TAT TAT TA
1 TAT TAT TAT TAT TAT TAT TA
1662394 AATATATATT
Statistics
Matches: 63, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
3 63 1.00
ACGTcount: A:0.34, C:0.01, G:0.00, T:0.65
Consensus pattern (3 bp):
TAT
Found at i:1662926 original size:18 final size:17
Alignment explanation
Indices: 1662891--1662923 Score: 66
Period size: 17 Copynumber: 1.9 Consensus size: 17
1662881 ACAGAACCGG
1662891 AGAGAAAGAAAAAAAAC
1 AGAGAAAGAAAAAAAAC
1662908 AGAGAAAGAAAAAAAA
1 AGAGAAAGAAAAAAAA
1662924 ACAACTAAAC
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.79, C:0.03, G:0.18, T:0.00
Consensus pattern (17 bp):
AGAGAAAGAAAAAAAAC
Found at i:1670388 original size:46 final size:45
Alignment explanation
Indices: 1670290--1670393 Score: 138
Period size: 45 Copynumber: 2.3 Consensus size: 45
1670280 GCACTAAGAG
* * *
1670290 TGCATCGATGCATCAAGTGCATTCGATGTTTCAAAATAGCCAGAG
1 TGCATCGATGCATCAAATGCATTCGATGTTTCAAAATAGCCACAA
* *
1670335 TGCATCGATGCATCAAATGCATTCGATGTTTTCATAAA-ATCCTCAA
1 TGCATCGATGCATCAAATGCATTCGATG-TTTCA-AAATAGCCACAA
1670381 TGCATCGATGCAT
1 TGCATCGATGCAT
1670394 GGTATGTGCA
Statistics
Matches: 52, Mismatches: 5, Indels: 3
0.87 0.08 0.05
Matches are distributed among these distances:
45 27 0.52
46 22 0.42
47 3 0.06
ACGTcount: A:0.31, C:0.21, G:0.18, T:0.30
Consensus pattern (45 bp):
TGCATCGATGCATCAAATGCATTCGATGTTTCAAAATAGCCACAA
Found at i:1670405 original size:19 final size:19
Alignment explanation
Indices: 1670381--1670432 Score: 95
Period size: 19 Copynumber: 2.7 Consensus size: 19
1670371 AAATCCTCAA
1670381 TGCATCGATGCATGGTATG
1 TGCATCGATGCATGGTATG
1670400 TGCATCGATGCATGGTATG
1 TGCATCGATGCATGGTATG
*
1670419 TGCATCAATGCATG
1 TGCATCGATGCATG
1670433 AAATGCATTT
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
19 32 1.00
ACGTcount: A:0.23, C:0.17, G:0.29, T:0.31
Consensus pattern (19 bp):
TGCATCGATGCATGGTATG
Found at i:1672013 original size:27 final size:28
Alignment explanation
Indices: 1671983--1672053 Score: 83
Period size: 30 Copynumber: 2.5 Consensus size: 28
1671973 TAAAGAGAAA
1671983 ATAAATCATA-TTT-TAGTAAAAAATTAT
1 ATAAATCA-AGTTTATAGTAAAAAATTAT
*
1672010 ATAAATTAAGTTTACATAGTAAAAAATTAT
1 ATAAATCAAGTTT--ATAGTAAAAAATTAT
*
1672040 ATAAATTAAGTTTA
1 ATAAATCAAGTTTA
1672054 CATAGTACAA
Statistics
Matches: 39, Mismatches: 1, Indels: 7
0.83 0.02 0.15
Matches are distributed among these distances:
26 1 0.03
27 10 0.26
28 1 0.03
30 27 0.69
ACGTcount: A:0.52, C:0.03, G:0.06, T:0.39
Consensus pattern (28 bp):
ATAAATCAAGTTTATAGTAAAAAATTAT
Found at i:1672031 original size:30 final size:30
Alignment explanation
Indices: 1671996--1672060 Score: 130
Period size: 30 Copynumber: 2.2 Consensus size: 30
1671986 AATCATATTT
1671996 TAGTAAAAAATTATATAAATTAAGTTTACA
1 TAGTAAAAAATTATATAAATTAAGTTTACA
1672026 TAGTAAAAAATTATATAAATTAAGTTTACA
1 TAGTAAAAAATTATATAAATTAAGTTTACA
1672056 TAGTA
1 TAGTA
1672061 CAACCTCCGG
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 35 1.00
ACGTcount: A:0.52, C:0.03, G:0.08, T:0.37
Consensus pattern (30 bp):
TAGTAAAAAATTATATAAATTAAGTTTACA
Found at i:1672552 original size:555 final size:554
Alignment explanation
Indices: 1671503--1672588 Score: 2050
Period size: 555 Copynumber: 2.0 Consensus size: 554
1671493 TATTTGTGCC
1671503 AGTACAACCTCCGGTAATGTATTATCCTAACCAATGATATTATATTTCATATCCGAAAAGAGTTG
1 AGTACAACCTCCGGTAATGTATTATCCTAACCAATGATATTATATTTCATATCCGAAAAGAGTTG
1671568 TACACCAATTTTCGATGACACCTTTAGTAAGCCAACTGCAGTGGTCACAAGATCCAAATTCAATA
66 TACACCAATTTTCGATGACACCTTTAGTAAGCCAACTGCAGTGGTCACAAGATCCAAATTCAATA
*
1671633 TATCAAAAAAGCTATGCTGAAATTATAAAAAATTGAAATATTGTTGAAACCACAACAGACAGAAA
131 TATCAAAAAAGCTATGCTGAAATTATAAAAAATTGAAATACTGTTGAAACCACAACAGACAGAAA
*
1671698 CAAAAAAAAAGAAATAAAAGATTTTTATAATCATGGTTTAGAAAAAAATATATAATTTGATTAAT
196 CAAAAAAAAAGAAATAAAAGATTCTTATAATCATGGTTTAGAAAAAAATATATAATTTGATTAAT
1671763 GAGGTATGAAAAAACCATTTAACTAATCAAAAGAACAATTTTGAAAAATCTCGTACTACACTTTC
261 GAGGTATGAAAAAACCATTTAACTAATCAAAAGAACAATTTTGAAAAATCTCGTACTACACTTTC
1671828 AAAAACTTAAGTTGAAAAAATAACTAAGTTGAAGAATTATTATTAAGGTCTAACATATACAGTGA
326 AAAAACTTAAGTTGAAAAAATAACTAAGTTGAAGAATTATTATTAAGGTCTAACATATACAGTGA
1671893 TTGATTTATCCTAAAAATATATTTTTTTAATAATAGATGAGATAAATAATCTTTTTGATAAATGT
391 TTGATTTATCCTAAAAATATATTTTTTTAATAATAGATGAGATAAATAATCTTTTTGATAAATGT
1671958 CAATATTTTTTTTGATAAAGAGAAAATAAATCATATTTTAGTAAAAAATTATATAAATTAAGTTT
456 CAATATTTTTTTTGATAAAGAGAAAATAAATCATATTTTAGTAAAAAATTATATAAATTAAGTTT
1672023 ACATAGTAAAAAATTATATAAATTAAGTTTACAT
521 ACATAGTAAAAAATTATATAAATTAAGTTTACAT
*
1672057 AGTACAACCTCCGGTAATGTATTATCCTAATCAATGATATTATATTTCATATCCGAAAAGAGTTG
1 AGTACAACCTCCGGTAATGTATTATCCTAACCAATGATATTATATTTCATATCCGAAAAGAGTTG
1672122 TACACCAATTTTCGATGACACCTTTAGTAAGCCAACTGCAGTGGTCACAAGATCCAAATTCAATA
66 TACACCAATTTTCGATGACACCTTTAGTAAGCCAACTGCAGTGGTCACAAGATCCAAATTCAATA
*
1672187 TATCAAAAAAGCTATGCTGAAATTATAAAAAAATTGAATTACTGTTGAAACCACAACAGACAGAA
131 TATCAAAAAAGCTATGCTGAAATTAT-AAAAAATTGAAATACTGTTGAAACCACAACAGACAGAA
1672252 ACAAAAAAAAAAGAAATAAAAGATTCTTATAATCATGGTTTAG-AAAAAATATATAATTTGATTA
195 AC-AAAAAAAAAGAAATAAAAGATTCTTATAATCATGGTTTAGAAAAAAATATATAATTTGATTA
* * **
1672316 ATGAGGTATGGAAAAACCATTTCACTAATCAAAAGAACAATTTTGAAAAATCTTTTACTACACTT
259 ATGAGGTATGAAAAAACCATTTAACTAATCAAAAGAACAATTTTGAAAAATCTCGTACTACACTT
1672381 TCAAAAACTTAAGTTGAAAAAATAACTGAAGTTGAAGAATTATTATTAAGGTCTAACATATACAG
324 TCAAAAACTTAAGTTGAAAAAATAACT-AAGTTGAAGAATTATTATTAAGGTCTAACATATACAG
1672446 TGATTGATTTATCCTAAAAATATA-TTTTTTAATAATAGATGAGATAAATAATCTTTTTGATAAA
388 TGATTGATTTATCCTAAAAATATATTTTTTTAATAATAGATGAGATAAATAATCTTTTTGATAAA
*
1672510 TGTCAATATTTTTTTTGATAAAGAGAAAATAACTCATATTTTAGTAAAAAATTATATAAATTAAG
453 TGTCAATATTTTTTTTGATAAAGAGAAAATAAATCATATTTTAGTAAAAAATTATATAAATTAAG
1672575 TTTACATAGTAAAA
518 TTTACATAGTAAAA
1672589 CTTATTAGGT
Statistics
Matches: 520, Mismatches: 9, Indels: 5
0.97 0.02 0.01
Matches are distributed among these distances:
554 155 0.30
555 265 0.51
556 100 0.19
ACGTcount: A:0.45, C:0.11, G:0.11, T:0.32
Consensus pattern (554 bp):
AGTACAACCTCCGGTAATGTATTATCCTAACCAATGATATTATATTTCATATCCGAAAAGAGTTG
TACACCAATTTTCGATGACACCTTTAGTAAGCCAACTGCAGTGGTCACAAGATCCAAATTCAATA
TATCAAAAAAGCTATGCTGAAATTATAAAAAATTGAAATACTGTTGAAACCACAACAGACAGAAA
CAAAAAAAAAGAAATAAAAGATTCTTATAATCATGGTTTAGAAAAAAATATATAATTTGATTAAT
GAGGTATGAAAAAACCATTTAACTAATCAAAAGAACAATTTTGAAAAATCTCGTACTACACTTTC
AAAAACTTAAGTTGAAAAAATAACTAAGTTGAAGAATTATTATTAAGGTCTAACATATACAGTGA
TTGATTTATCCTAAAAATATATTTTTTTAATAATAGATGAGATAAATAATCTTTTTGATAAATGT
CAATATTTTTTTTGATAAAGAGAAAATAAATCATATTTTAGTAAAAAATTATATAAATTAAGTTT
ACATAGTAAAAAATTATATAAATTAAGTTTACAT
Found at i:1676017 original size:24 final size:24
Alignment explanation
Indices: 1675985--1676034 Score: 100
Period size: 24 Copynumber: 2.1 Consensus size: 24
1675975 GAACCATTCA
1675985 TGCTCTAGTACCTTTTCAAGTTAT
1 TGCTCTAGTACCTTTTCAAGTTAT
1676009 TGCTCTAGTACCTTTTCAAGTTAT
1 TGCTCTAGTACCTTTTCAAGTTAT
1676033 TG
1 TG
1676035 ATGATTTTGC
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 26 1.00
ACGTcount: A:0.20, C:0.20, G:0.14, T:0.46
Consensus pattern (24 bp):
TGCTCTAGTACCTTTTCAAGTTAT
Found at i:1676288 original size:20 final size:20
Alignment explanation
Indices: 1676263--1676300 Score: 76
Period size: 20 Copynumber: 1.9 Consensus size: 20
1676253 CCATGTTGTA
1676263 ATCTCAATGGTTAAAAAAAC
1 ATCTCAATGGTTAAAAAAAC
1676283 ATCTCAATGGTTAAAAAA
1 ATCTCAATGGTTAAAAAA
1676301 GAGATTTGGA
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:0.50, C:0.13, G:0.11, T:0.26
Consensus pattern (20 bp):
ATCTCAATGGTTAAAAAAAC
Found at i:1680408 original size:34 final size:34
Alignment explanation
Indices: 1680365--1680434 Score: 131
Period size: 34 Copynumber: 2.1 Consensus size: 34
1680355 TTCTTCTATG
*
1680365 AAACCAGCAGTTTGAGTCGAGAGTCTCACAATTC
1 AAACCAGCAGTTCGAGTCGAGAGTCTCACAATTC
1680399 AAACCAGCAGTTCGAGTCGAGAGTCTCACAATTC
1 AAACCAGCAGTTCGAGTCGAGAGTCTCACAATTC
1680433 AA
1 AA
1680435 CTAGCTTTAC
Statistics
Matches: 35, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
34 35 1.00
ACGTcount: A:0.34, C:0.24, G:0.20, T:0.21
Consensus pattern (34 bp):
AAACCAGCAGTTCGAGTCGAGAGTCTCACAATTC
Found at i:1693073 original size:20 final size:20
Alignment explanation
Indices: 1693048--1693088 Score: 82
Period size: 20 Copynumber: 2.0 Consensus size: 20
1693038 GACTGCAAAA
1693048 TGGATTTTTCAACTATTTTG
1 TGGATTTTTCAACTATTTTG
1693068 TGGATTTTTCAACTATTTTG
1 TGGATTTTTCAACTATTTTG
1693088 T
1 T
1693089 CGGCCCGTAG
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.20, C:0.10, G:0.15, T:0.56
Consensus pattern (20 bp):
TGGATTTTTCAACTATTTTG
Found at i:1700892 original size:14 final size:14
Alignment explanation
Indices: 1700883--1700915 Score: 57
Period size: 14 Copynumber: 2.4 Consensus size: 14
1700873 AATGAATTAT
1700883 ATTTTCTGAAAAAC
1 ATTTTCTGAAAAAC
*
1700897 ATTTTCTGAAAAAT
1 ATTTTCTGAAAAAC
1700911 ATTTT
1 ATTTT
1700916 ACGATATTTG
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.39, C:0.09, G:0.06, T:0.45
Consensus pattern (14 bp):
ATTTTCTGAAAAAC
Found at i:1701090 original size:17 final size:20
Alignment explanation
Indices: 1701051--1701090 Score: 59
Period size: 20 Copynumber: 2.1 Consensus size: 20
1701041 ATTTTTAAAA
1701051 TATTAAAATGATTTATTTAT
1 TATTAAAATGATTTATTTAT
1701071 TATTAAAAT-A-TTATTT-T
1 TATTAAAATGATTTATTTAT
1701088 TAT
1 TAT
1701091 AAATTTATTA
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
17 4 0.20
18 6 0.30
19 1 0.05
20 9 0.45
ACGTcount: A:0.40, C:0.00, G:0.03, T:0.57
Consensus pattern (20 bp):
TATTAAAATGATTTATTTAT
Found at i:1701206 original size:19 final size:20
Alignment explanation
Indices: 1701182--1701252 Score: 67
Period size: 19 Copynumber: 3.6 Consensus size: 20
1701172 TTAAATATAT
*
1701182 TTATTAA-AATATTATTAGA
1 TTATTAATAATATTATTAAA
* *
1701201 TTATT-ATATTACTATTAAA
1 TTATTAATAATATTATTAAA
* *
1701220 TATATAAATAATATTATT-CA
1 T-TATTAATAATATTATTAAA
1701240 TTATTAATAATAT
1 TTATTAATAATAT
1701253 AATAATATTA
Statistics
Matches: 41, Mismatches: 8, Indels: 6
0.75 0.15 0.11
Matches are distributed among these distances:
18 1 0.02
19 26 0.63
20 5 0.12
21 9 0.22
ACGTcount: A:0.46, C:0.03, G:0.01, T:0.49
Consensus pattern (20 bp):
TTATTAATAATATTATTAAA
Found at i:1701233 original size:24 final size:26
Alignment explanation
Indices: 1701206--1701262 Score: 66
Period size: 27 Copynumber: 2.2 Consensus size: 26
1701196 TTAGATTATT
1701206 ATATTACT-ATTA-AAT-ATATAAATA
1 ATATTACTCATTATAATAATAT-AATA
*
1701230 ATATTATTCATTATTAATAATATAATA
1 ATATTACTCATTA-TAATAATATAATA
1701257 ATATTA
1 ATATTA
1701263 TTTCTATGAA
Statistics
Matches: 28, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
24 7 0.25
25 4 0.14
27 13 0.46
28 4 0.14
ACGTcount: A:0.51, C:0.04, G:0.00, T:0.46
Consensus pattern (26 bp):
ATATTACTCATTATAATAATATAATA
Found at i:1701399 original size:22 final size:23
Alignment explanation
Indices: 1701371--1701417 Score: 69
Period size: 22 Copynumber: 2.1 Consensus size: 23
1701361 TTGATTATTT
1701371 TATTATAATATTAAAAATA-TAA
1 TATTATAATATTAAAAATATTAA
* *
1701393 TATTATATTATTAGAAATATTAA
1 TATTATAATATTAAAAATATTAA
1701416 TA
1 TA
1701418 AATATATTTT
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
22 17 0.77
23 5 0.23
ACGTcount: A:0.53, C:0.00, G:0.02, T:0.45
Consensus pattern (23 bp):
TATTATAATATTAAAAATATTAA
Found at i:1701422 original size:22 final size:22
Alignment explanation
Indices: 1701379--1701422 Score: 54
Period size: 22 Copynumber: 2.0 Consensus size: 22
1701369 TTTATTATAA
*
1701379 TATTAAAAATATAATATTATAT
1 TATTAAAAATATAATATAATAT
*
1701401 TATTAGAAATATTAATA-AATAT
1 TATTAAAAATA-TAATATAATAT
1701423 ATTTTAAATA
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
22 14 0.74
23 5 0.26
ACGTcount: A:0.55, C:0.00, G:0.02, T:0.43
Consensus pattern (22 bp):
TATTAAAAATATAATATAATAT
Found at i:1701447 original size:53 final size:54
Alignment explanation
Indices: 1701339--1701483 Score: 133
Period size: 53 Copynumber: 2.7 Consensus size: 54
1701329 ATAATATCTT
* ** *
1701339 ATATTATATTATTATAATATAATTGAT-TATTTTATTATAATATTAAAAATATA
1 ATATTATATTATTAAAATATAATAAATATATTTTATAATAATATTAAAAATATA
* *
1701392 ATATTATATTATTAGAAATATTAATAAATATATTTTA-AAT-ATTTTAATAAT-TA
1 ATATTATATTATTA-AAATA-TAATAAATATATTTTATAATAATATTAAAAATATA
* *
1701445 ATATT-T-TGATTAAAATAATATTAAA-ATATTTTATTAATA
1 ATATTATATTATTAAAAT-ATAATAAATATATTTTA-TAATA
1701484 TTGAATTCAT
Statistics
Matches: 77, Mismatches: 8, Indels: 15
0.77 0.08 0.15
Matches are distributed among these distances:
49 8 0.10
50 10 0.13
51 9 0.12
52 1 0.01
53 21 0.27
54 13 0.17
55 8 0.10
56 7 0.09
ACGTcount: A:0.48, C:0.00, G:0.02, T:0.50
Consensus pattern (54 bp):
ATATTATATTATTAAAATATAATAAATATATTTTATAATAATATTAAAAATATA
Found at i:1701463 original size:24 final size:23
Alignment explanation
Indices: 1701436--1701481 Score: 58
Period size: 24 Copynumber: 1.9 Consensus size: 23
1701426 TTAAATATTT
1701436 TAATAATT-AATATTTTGATTAAAA
1 TAAT-ATTAAATATTTT-ATTAAAA
1701460 TAATATTAAAATATTTTATTAA
1 TAATATT-AAATATTTTATTAA
1701482 TATTGAATTC
Statistics
Matches: 20, Mismatches: 0, Indels: 4
0.83 0.00 0.17
Matches are distributed among these distances:
23 3 0.15
24 9 0.45
25 8 0.40
ACGTcount: A:0.50, C:0.00, G:0.02, T:0.48
Consensus pattern (23 bp):
TAATATTAAATATTTTATTAAAA
Found at i:1708730 original size:15 final size:15
Alignment explanation
Indices: 1708678--1708718 Score: 73
Period size: 15 Copynumber: 2.7 Consensus size: 15
1708668 AGCACCAAAG
*
1708678 CTTTCATCCTCCTCA
1 CTTTCTTCCTCCTCA
1708693 CTTTCTTCCTCCTCA
1 CTTTCTTCCTCCTCA
1708708 CTTTCTTCCTC
1 CTTTCTTCCTC
1708719 TTCCTCTTCT
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
15 25 1.00
ACGTcount: A:0.07, C:0.46, G:0.00, T:0.46
Consensus pattern (15 bp):
CTTTCTTCCTCCTCA
Found at i:1713944 original size:2 final size:2
Alignment explanation
Indices: 1713937--1713971 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
1713927 TTATACAGCG
1713937 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1713972 AGTAAAAGAA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:1716388 original size:12 final size:12
Alignment explanation
Indices: 1716373--1716418 Score: 56
Period size: 12 Copynumber: 3.6 Consensus size: 12
1716363 CGGTTTTTTT
*
1716373 ACCGGATAAAAA
1 ACCGGTTAAAAA
1716385 ACCGGTTTGAAAAAA
1 ACCGG-TT--AAAAA
1716400 ACCGGTTAAAAA
1 ACCGGTTAAAAA
1716412 ACCGGTT
1 ACCGGTT
1716419 TTTATCCGAA
Statistics
Matches: 30, Mismatches: 1, Indels: 6
0.81 0.03 0.16
Matches are distributed among these distances:
12 17 0.57
13 1 0.03
14 2 0.07
15 10 0.33
ACGTcount: A:0.46, C:0.17, G:0.20, T:0.17
Consensus pattern (12 bp):
ACCGGTTAAAAA
Found at i:1716400 original size:15 final size:13
Alignment explanation
Indices: 1716379--1716419 Score: 57
Period size: 12 Copynumber: 3.1 Consensus size: 13
1716369 TTTTACCGGA
1716379 TAAAAAACCGGTT
1 TAAAAAACCGGTT
1716392 TGAAAAAAACCGG-T
1 T--AAAAAACCGGTT
1716406 TAAAAAACCGGTT
1 TAAAAAACCGGTT
1716419 T
1 T
1716420 TTATCCGAAA
Statistics
Matches: 25, Mismatches: 0, Indels: 6
0.81 0.00 0.19
Matches are distributed among these distances:
12 10 0.40
13 3 0.12
14 2 0.08
15 10 0.40
ACGTcount: A:0.46, C:0.15, G:0.17, T:0.22
Consensus pattern (13 bp):
TAAAAAACCGGTT
Found at i:1718722 original size:21 final size:21
Alignment explanation
Indices: 1718698--1718737 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
1718688 TTTATTTTAT
1718698 AACTTTATTTCAATTATCGTA
1 AACTTTATTTCAATTATCGTA
*
1718719 AACTTTGTTTCAATTATCG
1 AACTTTATTTCAATTATCG
1718738 AACTTGAAGT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.30, C:0.15, G:0.07, T:0.47
Consensus pattern (21 bp):
AACTTTATTTCAATTATCGTA
Found at i:1718785 original size:33 final size:33
Alignment explanation
Indices: 1718732--1718830 Score: 164
Period size: 33 Copynumber: 3.0 Consensus size: 33
1718722 TTTGTTTCAA
1718732 TTATCGAACTT-GAAGTTTTTAAGTATTTGAAT
1 TTATCGAACTTGGAAGTTTTTAAGTATTTGAAT
1718764 TTATCGAACTTGGAAGTTTTTAAGTATTTGAAT
1 TTATCGAACTTGGAAGTTTTTAAGTATTTGAAT
* * *
1718797 TTATCAAACTTGGAAGTATTTAAGTATTTCAAT
1 TTATCGAACTTGGAAGTTTTTAAGTATTTGAAT
1718830 T
1 T
1718831 ATTTTGAGTT
Statistics
Matches: 63, Mismatches: 3, Indels: 1
0.94 0.04 0.01
Matches are distributed among these distances:
32 11 0.17
33 52 0.83
ACGTcount: A:0.32, C:0.07, G:0.15, T:0.45
Consensus pattern (33 bp):
TTATCGAACTTGGAAGTTTTTAAGTATTTGAAT
Found at i:1718859 original size:13 final size:13
Alignment explanation
Indices: 1718841--1718870 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
1718831 ATTTTGAGTT
*
1718841 AATTAAGTATTTC
1 AATTAAGTATTTA
1718854 AATTAAGTATTTA
1 AATTAAGTATTTA
1718867 AATT
1 AATT
1718871 TATCGAACTT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.43, C:0.03, G:0.07, T:0.47
Consensus pattern (13 bp):
AATTAAGTATTTA
Found at i:1719295 original size:14 final size:15
Alignment explanation
Indices: 1719265--1719318 Score: 90
Period size: 15 Copynumber: 3.6 Consensus size: 15
1719255 ATCTGGAATA
*
1719265 TTAAAATCGGTTTTT
1 TTAAAACCGGTTTTT
*
1719280 TTATAACCGGTTTTT
1 TTAAAACCGGTTTTT
1719295 TTAAAACCGGTTTTT
1 TTAAAACCGGTTTTT
1719310 TTAAAACCG
1 TTAAAACCG
1719319 AAACCGGTTA
Statistics
Matches: 36, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
15 36 1.00
ACGTcount: A:0.28, C:0.13, G:0.13, T:0.46
Consensus pattern (15 bp):
TTAAAACCGGTTTTT
Found at i:1719435 original size:15 final size:17
Alignment explanation
Indices: 1719409--1719440 Score: 50
Period size: 16 Copynumber: 2.0 Consensus size: 17
1719399 TTCTATGAGA
1719409 AAAAACCGGAT-CGGAT
1 AAAAACCGGATCCGGAT
1719425 AAAAACC-GATCCGGAT
1 AAAAACCGGATCCGGAT
1719441 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:1723244 original size:27 final size:27
Alignment explanation
Indices: 1723204--1723260 Score: 105
Period size: 27 Copynumber: 2.1 Consensus size: 27
1723194 GCCAACGAAG
1723204 AATGTTATTAACTTGAAAGGAAATACT
1 AATGTTATTAACTTGAAAGGAAATACT
*
1723231 AATGTTATTCACTTGAAAGGAAATACT
1 AATGTTATTAACTTGAAAGGAAATACT
1723258 AAT
1 AAT
1723261 TTAAAAGATG
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
27 29 1.00
ACGTcount: A:0.44, C:0.09, G:0.14, T:0.33
Consensus pattern (27 bp):
AATGTTATTAACTTGAAAGGAAATACT
Found at i:1728341 original size:15 final size:15
Alignment explanation
Indices: 1728323--1728353 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
1728313 AAATTCTAAA
1728323 TATTTAAATAAAAAT
1 TATTTAAATAAAAAT
*
1728338 TATTTATATAAAAAT
1 TATTTAAATAAAAAT
1728353 T
1 T
1728354 CATCGATAAT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (15 bp):
TATTTAAATAAAAAT
Found at i:1746826 original size:13 final size:13
Alignment explanation
Indices: 1746788--1746828 Score: 50
Period size: 13 Copynumber: 3.2 Consensus size: 13
1746778 GCTGAACATG
1746788 TATCATATAA-ACA
1 TATCAT-TAACACA
*
1746801 TAT-ATTCACACA
1 TATCATTAACACA
1746813 TATCATTAACACA
1 TATCATTAACACA
1746826 TAT
1 TAT
1746829 ATAACATATC
Statistics
Matches: 24, Mismatches: 2, Indels: 4
0.80 0.07 0.13
Matches are distributed among these distances:
11 2 0.08
12 8 0.33
13 14 0.58
ACGTcount: A:0.46, C:0.20, G:0.00, T:0.34
Consensus pattern (13 bp):
TATCATTAACACA
Found at i:1747195 original size:24 final size:20
Alignment explanation
Indices: 1747140--1747177 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
1747130 TTTCCTTTGA
*
1747140 AGTGCATCGATACATTCTAC
1 AGTGCATCGATGCATTCTAC
1747160 AGTGCATCGATGCATTCT
1 AGTGCATCGATGCATTCT
1747178 TTAACATGTG
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.26, C:0.24, G:0.18, T:0.32
Consensus pattern (20 bp):
AGTGCATCGATGCATTCTAC
Found at i:1747272 original size:64 final size:63
Alignment explanation
Indices: 1747185--1747345 Score: 189
Period size: 64 Copynumber: 2.5 Consensus size: 63
1747175 TCTTTAACAT
* * *
1747185 GTGCATCGATGAACTACCTATGCATCGATACACCAATCACCTTCGATATTTTCA-TTTTAAGGGG
1 GTGCATCGATGCACT-CCTATGCATCGATACACCAATCACATTCGATATTTCCATTTTTAA-GGG
* * ** * *
1747249 GTGCATCGATGCACTCCTTATGCATCGATGCACTAATTGCATTCGATGTTTCCATTTTTAATGG
1 GTGCATCGATGCACTCC-TATGCATCGATACACCAATCACATTCGATATTTCCATTTTTAAGGG
*
1747313 GTGCATCGATGCACTTCCTGTGCATCGATACAC
1 GTGCATCGATGCAC-TCCTATGCATCGATACAC
1747346 ACTGAACAAT
Statistics
Matches: 83, Mismatches: 11, Indels: 6
0.83 0.11 0.06
Matches are distributed among these distances:
63 2 0.02
64 72 0.87
65 9 0.11
ACGTcount: A:0.24, C:0.24, G:0.19, T:0.33
Consensus pattern (63 bp):
GTGCATCGATGCACTCCTATGCATCGATACACCAATCACATTCGATATTTCCATTTTTAAGGG
Found at i:1755072 original size:6 final size:6
Alignment explanation
Indices: 1755063--1755092 Score: 60
Period size: 6 Copynumber: 5.0 Consensus size: 6
1755053 GGGATGAGGA
1755063 TCTGCC TCTGCC TCTGCC TCTGCC TCTGCC
1 TCTGCC TCTGCC TCTGCC TCTGCC TCTGCC
1755093 ATCACTACTA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 24 1.00
ACGTcount: A:0.00, C:0.50, G:0.17, T:0.33
Consensus pattern (6 bp):
TCTGCC
Found at i:1755165 original size:36 final size:36
Alignment explanation
Indices: 1755118--1755191 Score: 139
Period size: 36 Copynumber: 2.1 Consensus size: 36
1755108 CACCATATTA
1755118 TGTGTTTTGGAAAAGCCCCCTCTCCTCCTGGGCTAT
1 TGTGTTTTGGAAAAGCCCCCTCTCCTCCTGGGCTAT
*
1755154 TGTGTTTTGGAAAAGCCCTCTCTCCTCCTGGGCTAT
1 TGTGTTTTGGAAAAGCCCCCTCTCCTCCTGGGCTAT
1755190 TG
1 TG
1755192 GGCTTCTAAT
Statistics
Matches: 37, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
36 37 1.00
ACGTcount: A:0.14, C:0.28, G:0.23, T:0.35
Consensus pattern (36 bp):
TGTGTTTTGGAAAAGCCCCCTCTCCTCCTGGGCTAT
Found at i:1761250 original size:31 final size:31
Alignment explanation
Indices: 1761214--1761272 Score: 91
Period size: 31 Copynumber: 1.9 Consensus size: 31
1761204 AACTTAAAAG
*
1761214 AGTTTTGCAATAATGAAATTTAAATAATTTT
1 AGTTTTACAATAATGAAATTTAAATAATTTT
* *
1761245 AGTTTTATAATACTGAAATTTAAATAAT
1 AGTTTTACAATAATGAAATTTAAATAAT
1761273 CCATACAACT
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
31 25 1.00
ACGTcount: A:0.44, C:0.03, G:0.08, T:0.44
Consensus pattern (31 bp):
AGTTTTACAATAATGAAATTTAAATAATTTT
Found at i:1761323 original size:22 final size:22
Alignment explanation
Indices: 1761298--1761943 Score: 942
Period size: 22 Copynumber: 29.5 Consensus size: 22
1761288 AATAAATTTG
1761298 TTAAAATAAATCAATCCATATT
1 TTAAAATAAATCAATCCATATT
1761320 TTAAAATAAATCAATCCATATT
1 TTAAAATAAATCAATCCATATT
* *** *
1761342 TTAAAATAATTTTTTCTATATT
1 TTAAAATAAATCAATCCATATT
1761364 TTAAAATAAATCAATCCATATT
1 TTAAAATAAATCAATCCATATT
* ** *
1761386 TTAAAACAAAAT-TTTTCATATT
1 TTAAAA-TAAATCAATCCATATT
**
1761408 TTAAAATAAAT-TTTCCATATT
1 TTAAAATAAATCAATCCATATT
1761429 TTAAAATAAATCAATCCATATT
1 TTAAAATAAATCAATCCATATT
*
1761451 TTAAAATAAATCAATCTATATT
1 TTAAAATAAATCAATCCATATT
*
1761473 TTAAAATAAATCAATCTATATT
1 TTAAAATAAATCAATCCATATT
1761495 TTAAAATAAATCAATCCATATT
1 TTAAAATAAATCAATCCATATT
*
1761517 TTAAAATAAATCAATCTATATT
1 TTAAAATAAATCAATCCATATT
*
1761539 TTAAAATAAGTCAATCCATATT
1 TTAAAATAAATCAATCCATATT
1761561 TTAAAATAAATCAATCCATATT
1 TTAAAATAAATCAATCCATATT
** *
1761583 TTAAAATAAAT-TTTTCATATT
1 TTAAAATAAATCAATCCATATT
1761604 TTAAAATAAATCAATCCATATT
1 TTAAAATAAATCAATCCATATT
*
1761626 TTAAAATAAATCAATCTATATT
1 TTAAAATAAATCAATCCATATT
**
1761648 TTAAAATAAAAT-TTTCCATATT
1 TTAAAAT-AAATCAATCCATATT
1761670 TTAAAATAAATCAATCCATATT
1 TTAAAATAAATCAATCCATATT
**
1761692 TTAAAATAAAAT-TTTCCATATT
1 TTAAAAT-AAATCAATCCATATT
1761714 TTAAAATAAATCAATCCATATT
1 TTAAAATAAATCAATCCATATT
* *
1761736 TTAAAATAAACCAATCTATATT
1 TTAAAATAAATCAATCCATATT
1761758 TTAAAATAAATCAATCCATATT
1 TTAAAATAAATCAATCCATATT
*
1761780 TTAAAATAAATCAATCTATATT
1 TTAAAATAAATCAATCCATATT
***
1761802 TTAAAATAAATTTTTCCATATT
1 TTAAAATAAATCAATCCATATT
* *
1761824 TTAAAATAAATAAATCTATATT
1 TTAAAATAAATCAATCCATATT
*
1761846 TTAAAATAAATCAATCGATATT
1 TTAAAATAAATCAATCCATATT
1761868 TTAAAATAAATCAATCCATATT
1 TTAAAATAAATCAATCCATATT
1761890 TTAAAATAAATCAATCCATATT
1 TTAAAATAAATCAATCCATATT
1761912 TTAAAATAAATCAATCCATATT
1 TTAAAATAAATCAATCCATATT
1761934 TTAAAATAAA
1 TTAAAATAAA
1761944 ATTTAAAATA
Statistics
Matches: 561, Mismatches: 56, Indels: 14
0.89 0.09 0.02
Matches are distributed among these distances:
21 50 0.09
22 499 0.89
23 12 0.02
ACGTcount: A:0.49, C:0.11, G:0.00, T:0.40
Consensus pattern (22 bp):
TTAAAATAAATCAATCCATATT
Found at i:1762323 original size:3 final size:3
Alignment explanation
Indices: 1762315--1762372 Score: 71
Period size: 3 Copynumber: 19.3 Consensus size: 3
1762305 ATATTAATTA
* * * * *
1762315 ATT ATT ATT ATT ATA ATA ATA ATA ATT ATT ATT ATC ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
1762363 ATT ATT ATT A
1 ATT ATT ATT A
1762373 AATATATTAA
Statistics
Matches: 51, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 51 1.00
ACGTcount: A:0.41, C:0.02, G:0.00, T:0.57
Consensus pattern (3 bp):
ATT
Found at i:1764555 original size:18 final size:18
Alignment explanation
Indices: 1764506--1764556 Score: 59
Period size: 18 Copynumber: 2.8 Consensus size: 18
1764496 TTCTTTTCAA
*
1764506 ATTTTTTTATTATTTATT
1 ATTTTTATATTATTTATT
*
1764524 ATTTTTATAATATTTA-T
1 ATTTTTATATTATTTATT
*
1764541 ATGTTTTATTTTATTT
1 AT-TTTTATATTATTT
1764557 GCAAGTATTT
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
17 3 0.11
18 25 0.89
ACGTcount: A:0.25, C:0.00, G:0.02, T:0.73
Consensus pattern (18 bp):
ATTTTTATATTATTTATT
Found at i:1775191 original size:1 final size:1
Alignment explanation
Indices: 1775180--1775243 Score: 56
Period size: 1 Copynumber: 64.0 Consensus size: 1
1775170 GCTTGAAGAG
* * * * * * * *
1775180 AAAAAAGAAAAAAAAAAGAAAAGAAAAAGAAAAAACAAAGAAAAAGAAAAAAAAGAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
1775244 GGAAAAGGGG
Statistics
Matches: 47, Mismatches: 16, Indels: 0
0.75 0.25 0.00
Matches are distributed among these distances:
1 47 1.00
ACGTcount: A:0.88, C:0.02, G:0.11, T:0.00
Consensus pattern (1 bp):
A
Found at i:1775243 original size:11 final size:11
Alignment explanation
Indices: 1775180--1775241 Score: 81
Period size: 11 Copynumber: 5.5 Consensus size: 11
1775170 GCTTGAAGAG
1775180 AAAAAAGAAAA
1 AAAAAAGAAAA
1775191 AAAAAAGAAAA
1 AAAAAAGAAAA
*
1775202 GAAAAAGAAAA
1 AAAAAAGAAAA
*
1775213 AACAAAGAAAA
1 AAAAAAGAAAA
1775224 AGAAAAA-AAAGA
1 A-AAAAAGAAA-A
1775236 AAAAAA
1 AAAAAA
1775242 AAGGAAAAGG
Statistics
Matches: 45, Mismatches: 4, Indels: 4
0.85 0.08 0.08
Matches are distributed among these distances:
11 39 0.87
12 6 0.13
ACGTcount: A:0.87, C:0.02, G:0.11, T:0.00
Consensus pattern (11 bp):
AAAAAAGAAAA
Done.