Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: CP032245.1 Gossypioides kirkii chromosome KI_2_4
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: 41238926
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 6100 characters in sequence are not A, C, G, or T
File 132 of 132
Found at i:41137341 original size:23 final size:23
Alignment explanation
Indices: 41137285--41137390 Score: 149
Period size: 23 Copynumber: 4.6 Consensus size: 23
41137275 TCATTAACAT
*
41137285 TGTTCGTGAACATGTTCAATTATA
1 TGTTCGTGAACATGTTCGATTA-A
* *
41137309 TGTTCATGAACATGTTCGTTTAA
1 TGTTCGTGAACATGTTCGATTAA
*
41137332 TGTTCGTGAACGTGTTCGATTAA
1 TGTTCGTGAACATGTTCGATTAA
* *
41137355 TGTTCGTGAACGTATTCGATTAA
1 TGTTCGTGAACATGTTCGATTAA
41137378 TGTTCGTGAACAT
1 TGTTCGTGAACAT
41137391 TAAACAAACG
Statistics
Matches: 74, Mismatches: 8, Indels: 1
0.89 0.10 0.01
Matches are distributed among these distances:
23 55 0.74
24 19 0.26
ACGTcount: A:0.25, C:0.13, G:0.21, T:0.41
Consensus pattern (23 bp):
TGTTCGTGAACATGTTCGATTAA
Found at i:41139289 original size:20 final size:20
Alignment explanation
Indices: 41139253--41139290 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
41139243 TATTTTTATT
*
41139253 TTTATTTTTTCTCTATTTTA
1 TTTATTTTTTATCTATTTTA
41139273 TTTATTTATTTAT-TATTT
1 TTTATTT-TTTATCTATTT
41139291 GTCCAGGAAA
Statistics
Matches: 16, Mismatches: 1, Indels: 2
0.84 0.05 0.11
Matches are distributed among these distances:
20 12 0.75
21 4 0.25
ACGTcount: A:0.18, C:0.05, G:0.00, T:0.76
Consensus pattern (20 bp):
TTTATTTTTTATCTATTTTA
Found at i:41141583 original size:31 final size:29
Alignment explanation
Indices: 41141547--41141617 Score: 76
Period size: 28 Copynumber: 2.4 Consensus size: 29
41141537 TTATTTTATG
*
41141547 CTATTTATTTTTA-CTTCGACTTCCCTATTTT
1 CTATTTATTTTTATCTT-GAATT--CTATTTT
*
41141578 CTATTT-TTTTTATCTTTAATTCTATTTT
1 CTATTTATTTTTATCTTGAATTCTATTTT
41141606 CT-TTTATTTTTA
1 CTATTTATTTTTA
41141618 ATTCAGTTTA
Statistics
Matches: 36, Mismatches: 2, Indels: 7
0.80 0.04 0.16
Matches are distributed among these distances:
27 3 0.08
28 15 0.42
30 9 0.25
31 9 0.25
ACGTcount: A:0.17, C:0.15, G:0.01, T:0.66
Consensus pattern (29 bp):
CTATTTATTTTTATCTTGAATTCTATTTT
Found at i:41141602 original size:21 final size:22
Alignment explanation
Indices: 41141576--41141621 Score: 76
Period size: 22 Copynumber: 2.1 Consensus size: 22
41141566 CTTCCCTATT
41141576 TTCTATTTT-TTTTATCTTTAA
1 TTCTATTTTCTTTTATCTTTAA
*
41141597 TTCTATTTTCTTTTATTTTTAA
1 TTCTATTTTCTTTTATCTTTAA
41141619 TTC
1 TTC
41141622 AGTTTATTTT
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
21 9 0.39
22 14 0.61
ACGTcount: A:0.17, C:0.11, G:0.00, T:0.72
Consensus pattern (22 bp):
TTCTATTTTCTTTTATCTTTAA
Found at i:41141617 original size:22 final size:21
Alignment explanation
Indices: 41141576--41141637 Score: 81
Period size: 21 Copynumber: 2.9 Consensus size: 21
41141566 CTTCCCTATT
*
41141576 TTCTATTTTTTTTATCTTTAA
1 TTCTATTTTTTTTATTTTTAA
41141597 TTCTATTTTCTTTTATTTTTAA
1 TTCTATTTT-TTTTATTTTTAA
*
41141619 TTC-AGTTTATTTTATTTTT
1 TTCTA-TTTTTTTTATTTTT
41141638 CCTCATATCG
Statistics
Matches: 37, Mismatches: 2, Indels: 4
0.86 0.05 0.09
Matches are distributed among these distances:
21 20 0.54
22 17 0.46
ACGTcount: A:0.18, C:0.08, G:0.02, T:0.73
Consensus pattern (21 bp):
TTCTATTTTTTTTATTTTTAA
Found at i:41145222 original size:10 final size:11
Alignment explanation
Indices: 41145205--41145233 Score: 51
Period size: 10 Copynumber: 2.7 Consensus size: 11
41145195 TTTCTTTTAA
41145205 AATATTAATTT
1 AATATTAATTT
41145216 AAT-TTAATTT
1 AATATTAATTT
41145226 AATATTAA
1 AATATTAA
41145234 ATAAATTTAT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
10 10 0.59
11 7 0.41
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (11 bp):
AATATTAATTT
Found at i:41145421 original size:11 final size:10
Alignment explanation
Indices: 41145393--41145428 Score: 54
Period size: 10 Copynumber: 3.5 Consensus size: 10
41145383 TTCAATTAAG
41145393 TCAAATATTT
1 TCAAATATTT
41145403 TCAAATATGTT
1 TCAAATAT-TT
*
41145414 TTAAATATTT
1 TCAAATATTT
41145424 TCAAA
1 TCAAA
41145429 CAAGTTAGAA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
10 14 0.61
11 9 0.39
ACGTcount: A:0.42, C:0.08, G:0.03, T:0.47
Consensus pattern (10 bp):
TCAAATATTT
Found at i:41145608 original size:20 final size:21
Alignment explanation
Indices: 41145579--41145617 Score: 62
Period size: 20 Copynumber: 1.9 Consensus size: 21
41145569 ATATCAATAC
41145579 TTTTCTTAAGGTATCGATATA
1 TTTTCTTAAGGTATCGATATA
*
41145600 TTTTC-TAAGGTATTGATA
1 TTTTCTTAAGGTATCGATA
41145618 AATCTGCTCC
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 12 0.71
21 5 0.29
ACGTcount: A:0.28, C:0.08, G:0.15, T:0.49
Consensus pattern (21 bp):
TTTTCTTAAGGTATCGATATA
Found at i:41149846 original size:93 final size:94
Alignment explanation
Indices: 41149686--41149879 Score: 354
Period size: 93 Copynumber: 2.1 Consensus size: 94
41149676 TCATGTATAC
*
41149686 AAACCTAGATGTTGCAGCCAAAAGAATGACCGACAAGCCTTCTAAATTGTCTCCCCCTGCTACGG
1 AAACCTAGATGATGCAGCCAAAAGAATGACCGACAAGCCTTCTAAATTGTCTCCCCCTGCTACGG
41149751 CAGCTGGGGATGGAAAGTCCAAGGACGAG
66 CAGCTGGGGATGGAAAGTCCAAGGACGAG
* *
41149780 -AACCTAGATGATGCAGCTAAAAGAATGACCGACAAGGCTTCTAAATTGTCTCCCCCTGCTACGG
1 AAACCTAGATGATGCAGCCAAAAGAATGACCGACAAGCCTTCTAAATTGTCTCCCCCTGCTACGG
41149844 CAGCTGGGGATGGAAAGTCCAAGGACGAG
66 CAGCTGGGGATGGAAAGTCCAAGGACGAG
41149873 AAACCTA
1 AAACCTA
41149880 AGAGTTTCGA
Statistics
Matches: 96, Mismatches: 3, Indels: 2
0.95 0.03 0.02
Matches are distributed among these distances:
93 90 0.94
94 6 0.06
ACGTcount: A:0.32, C:0.25, G:0.25, T:0.18
Consensus pattern (94 bp):
AAACCTAGATGATGCAGCCAAAAGAATGACCGACAAGCCTTCTAAATTGTCTCCCCCTGCTACGG
CAGCTGGGGATGGAAAGTCCAAGGACGAG
Found at i:41152152 original size:20 final size:22
Alignment explanation
Indices: 41152127--41152167 Score: 59
Period size: 22 Copynumber: 1.9 Consensus size: 22
41152117 ACTTCTTTCG
41152127 TTCAC-TATTTTT-TCATTTAC
1 TTCACTTATTTTTCTCATTTAC
41152147 TTCACTTTATTTTTCTCATTT
1 TTCAC-TTATTTTTCTCATTT
41152168 TTATTCTTTG
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
20 5 0.28
22 7 0.39
23 6 0.33
ACGTcount: A:0.17, C:0.20, G:0.00, T:0.63
Consensus pattern (22 bp):
TTCACTTATTTTTCTCATTTAC
Found at i:41152198 original size:24 final size:25
Alignment explanation
Indices: 41152156--41152205 Score: 66
Period size: 25 Copynumber: 2.0 Consensus size: 25
41152146 CTTCACTTTA
* *
41152156 TTTTTCTCATTTTTATTCTTTGTCT
1 TTTTTCTCATTCTTATTCTCTGTCT
*
41152181 TTTTTCTGATTCTT-TTCTCTGTCT
1 TTTTTCTCATTCTTATTCTCTGTCT
41152205 T
1 T
41152206 CACCCTTTCT
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
24 10 0.45
25 12 0.55
ACGTcount: A:0.06, C:0.18, G:0.06, T:0.70
Consensus pattern (25 bp):
TTTTTCTCATTCTTATTCTCTGTCT
Found at i:41154170 original size:26 final size:24
Alignment explanation
Indices: 41154128--41154187 Score: 68
Period size: 24 Copynumber: 2.4 Consensus size: 24
41154118 TATAATTTTA
41154128 AATTTTTTTTAAGATTTAAATAATAT
1 AATTTTTTTTAAGATTT--ATAATAT
* *
41154154 AGTTTTTTTT-AGAATTTATGATAT
1 AATTTTTTTTAAG-ATTTATAATAT
41154178 AATTTTTTTT
1 AATTTTTTTT
41154188 TTTACCATAA
Statistics
Matches: 30, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
24 15 0.50
25 2 0.07
26 13 0.43
ACGTcount: A:0.33, C:0.00, G:0.07, T:0.60
Consensus pattern (24 bp):
AATTTTTTTTAAGATTTATAATAT
Found at i:41156839 original size:24 final size:24
Alignment explanation
Indices: 41156803--41156848 Score: 60
Period size: 24 Copynumber: 1.9 Consensus size: 24
41156793 ACGAAAAGAA
41156803 AAGGAGAAGAGAATAG-AGGAGGAG
1 AAGGAGAAGAGAA-AGCAGGAGGAG
41156827 AAGGAG-AGAAGAAAGCAGGAGG
1 AAGGAGAAG-AGAAAGCAGGAGG
41156849 CTAAGAGAAT
Statistics
Matches: 20, Mismatches: 0, Indels: 4
0.83 0.00 0.17
Matches are distributed among these distances:
23 4 0.20
24 16 0.80
ACGTcount: A:0.50, C:0.02, G:0.46, T:0.02
Consensus pattern (24 bp):
AAGGAGAAGAGAAAGCAGGAGGAG
Found at i:41164966 original size:21 final size:21
Alignment explanation
Indices: 41164933--41164979 Score: 58
Period size: 21 Copynumber: 2.2 Consensus size: 21
41164923 ATCTTCGTTG
* * *
41164933 TTTTCCTTTTCTTTCTTTCGC
1 TTTTTCTTGTCTTTCTTGCGC
*
41164954 TTTTTCTTGTCTTTCTTGCTC
1 TTTTTCTTGTCTTTCTTGCGC
41164975 TTTTT
1 TTTTT
41164980 TAGCTCAGTT
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.00, C:0.23, G:0.06, T:0.70
Consensus pattern (21 bp):
TTTTTCTTGTCTTTCTTGCGC
Found at i:41165899 original size:18 final size:17
Alignment explanation
Indices: 41165867--41165910 Score: 52
Period size: 18 Copynumber: 2.5 Consensus size: 17
41165857 TTTGACCTTT
41165867 TAAAATTTATAAAAAAAA
1 TAAAA-TTATAAAAAAAA
* *
41165885 TATAAATTATTAAAAAGA
1 TA-AAATTATAAAAAAAA
41165903 TAAAATTA
1 TAAAATTA
41165911 AATTTTTACT
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
17 6 0.26
18 14 0.61
19 3 0.13
ACGTcount: A:0.66, C:0.00, G:0.02, T:0.32
Consensus pattern (17 bp):
TAAAATTATAAAAAAAA
Found at i:41166712 original size:15 final size:16
Alignment explanation
Indices: 41166694--41166733 Score: 55
Period size: 16 Copynumber: 2.6 Consensus size: 16
41166684 AATACCACCT
*
41166694 AAATTAAAAATA-AAA
1 AAATTAAAAACACAAA
*
41166709 AAATTAAAAGCACAAA
1 AAATTAAAAACACAAA
41166725 AAATTAAAA
1 AAATTAAAA
41166734 TAATTAATTA
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
15 10 0.45
16 12 0.55
ACGTcount: A:0.75, C:0.05, G:0.03, T:0.17
Consensus pattern (16 bp):
AAATTAAAAACACAAA
Found at i:41168077 original size:2 final size:2
Alignment explanation
Indices: 41168066--41168109 Score: 79
Period size: 2 Copynumber: 22.0 Consensus size: 2
41168056 TGAAACACAC
*
41168066 AG AG AA AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
41168108 AG
1 AG
41168110 TATGAATCGC
Statistics
Matches: 40, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 40 1.00
ACGTcount: A:0.52, C:0.00, G:0.48, T:0.00
Consensus pattern (2 bp):
AG
Found at i:41172305 original size:60 final size:61
Alignment explanation
Indices: 41172195--41172313 Score: 168
Period size: 60 Copynumber: 2.0 Consensus size: 61
41172185 AACTAAAAGC
* * *
41172195 TAAAATATTATTATGGTGCAGATATATTTGGATGGACGGGAAGATTAAAAATAATGGTAGT
1 TAAAATACTATTATAGTGCAGATATATTTGGATGCACGGGAAGATTAAAAATAATGGTAGT
* * * *
41172256 TAAAATACTATTATAGTGCATATCTA-TTGGATGCATGGTAAGATTAAAAATAATGGTA
1 TAAAATACTATTATAGTGCAGATATATTTGGATGCACGGGAAGATTAAAAATAATGGTA
41172314 ATGGAAAGAT
Statistics
Matches: 51, Mismatches: 7, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
60 29 0.57
61 22 0.43
ACGTcount: A:0.40, C:0.05, G:0.21, T:0.34
Consensus pattern (61 bp):
TAAAATACTATTATAGTGCAGATATATTTGGATGCACGGGAAGATTAAAAATAATGGTAGT
Found at i:41174537 original size:12 final size:12
Alignment explanation
Indices: 41174520--41174546 Score: 54
Period size: 12 Copynumber: 2.2 Consensus size: 12
41174510 AGTTTTCTAC
41174520 AGAACTAGCAAG
1 AGAACTAGCAAG
41174532 AGAACTAGCAAG
1 AGAACTAGCAAG
41174544 AGA
1 AGA
41174547 GGTGGCAGCA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 15 1.00
ACGTcount: A:0.52, C:0.15, G:0.26, T:0.07
Consensus pattern (12 bp):
AGAACTAGCAAG
Found at i:41184760 original size:73 final size:73
Alignment explanation
Indices: 41184672--41184957 Score: 423
Period size: 73 Copynumber: 3.9 Consensus size: 73
41184662 CTTCTAGCGA
* * * * *
41184672 TTGTTGAGGCAAAATGAATGTTGCCCCCACACC-ATCAAAGACAGACAGAATAAAATTGGAATTC
1 TTGTTGAGGCAAAATGAATGTTGCCCCCACCCCGTTAAAAG-CAGACCGAATAAAATTGGTATTC
***
41184736 CACTGAAAG
65 CACTGGTGG
* *
41184745 TTGTTGAGGCAAAATGAATGTTGCCCCCACCCCGTTAAAAGCAGACCGAATAAATTTGGTATTTC
1 TTGTTGAGGCAAAATGAATGTTGCCCCCACCCCGTTAAAAGCAGACCGAATAAAATTGGTATTCC
41184810 ACTGGTGG
66 ACTGGTGG
* *
41184818 TTGTTGAGGCAAAATGAATGTTGCCCCCACCCCGTTAAAAGCAGACCGAATAAATTTGGTATTTC
1 TTGTTGAGGCAAAATGAATGTTGCCCCCACCCCGTTAAAAGCAGACCGAATAAAATTGGTATTCC
41184883 ACTGGTGG
66 ACTGGTGG
*
41184891 TTGTTGAGGCAAAATGAATGTTGCCCCCACCCCGTT-AAAGACAGACCGAACAAAATTGGTATTC
1 TTGTTGAGGCAAAATGAATGTTGCCCCCACCCCGTTAAAAG-CAGACCGAATAAAATTGGTATTC
41184955 CAC
65 CAC
41184958 CCGCCCCCAT
Statistics
Matches: 198, Mismatches: 13, Indels: 4
0.92 0.06 0.02
Matches are distributed among these distances:
72 4 0.02
73 189 0.95
74 5 0.03
ACGTcount: A:0.33, C:0.22, G:0.21, T:0.24
Consensus pattern (73 bp):
TTGTTGAGGCAAAATGAATGTTGCCCCCACCCCGTTAAAAGCAGACCGAATAAAATTGGTATTCC
ACTGGTGG
Found at i:41185191 original size:29 final size:30
Alignment explanation
Indices: 41185151--41185211 Score: 81
Period size: 29 Copynumber: 2.1 Consensus size: 30
41185141 TAATAAAAGT
*
41185151 AAAATTATATTTTATTC-TTAAAAATGATA
1 AAAATTATATTTAATTCTTTAAAAATGATA
*
41185180 AAAATT-TGATTTAATTCTTTAAAAATTATA
1 AAAATTAT-ATTTAATTCTTTAAAAATGATA
41185210 AA
1 AA
41185212 GATATAGATA
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
28 1 0.04
29 14 0.50
30 13 0.46
ACGTcount: A:0.49, C:0.03, G:0.03, T:0.44
Consensus pattern (30 bp):
AAAATTATATTTAATTCTTTAAAAATGATA
Found at i:41185600 original size:22 final size:22
Alignment explanation
Indices: 41185556--41185600 Score: 56
Period size: 22 Copynumber: 2.0 Consensus size: 22
41185546 ATAAATTTTT
* *
41185556 AAAAAAATTATAATGTTGCTTC
1 AAAAAAAATATAATGTTGATTC
41185578 AAAAAAACATATAATG-TGATTC
1 AAAAAAA-ATATAATGTTGATTC
41185600 A
1 A
41185601 TATACTTTAA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
22 13 0.65
23 7 0.35
ACGTcount: A:0.51, C:0.09, G:0.09, T:0.31
Consensus pattern (22 bp):
AAAAAAAATATAATGTTGATTC
Found at i:41187111 original size:30 final size:26
Alignment explanation
Indices: 41187075--41187136 Score: 70
Period size: 26 Copynumber: 2.2 Consensus size: 26
41187065 TATATATGCC
*
41187075 TTATTTTCTTAGTAATAATTACATTGTTAA
1 TTATTTT-TTAG-AATAA-TACATAG-TAA
*
41187105 TTATTTTTTTGAATAATACATAGTAA
1 TTATTTTTTAGAATAATACATAGTAA
41187131 TTATTT
1 TTATTT
41187137 GAATGGACTG
Statistics
Matches: 30, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
26 9 0.30
27 6 0.20
28 5 0.17
29 3 0.10
30 7 0.23
ACGTcount: A:0.34, C:0.05, G:0.06, T:0.55
Consensus pattern (26 bp):
TTATTTTTTAGAATAATACATAGTAA
Found at i:41198062 original size:30 final size:28
Alignment explanation
Indices: 41198028--41198094 Score: 80
Period size: 30 Copynumber: 2.3 Consensus size: 28
41198018 GTGGTTTTGA
41198028 AAAAGTTTAGATGTTAAAAAGTAATTTCAG
1 AAAAGTTTAGA-GTTAAAAAGTAATTT-AG
* * *
41198058 AAAAGTTCGAGAGTTAAAATGTAATTTTG
1 AAAAGTT-TAGAGTTAAAAAGTAATTTAG
41198087 AAAAGTTT
1 AAAAGTTT
41198095 GAGGGTCAAA
Statistics
Matches: 32, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
29 8 0.25
30 21 0.66
31 3 0.09
ACGTcount: A:0.45, C:0.03, G:0.18, T:0.34
Consensus pattern (28 bp):
AAAAGTTTAGAGTTAAAAAGTAATTTAG
Found at i:41198090 original size:89 final size:89
Alignment explanation
Indices: 41197915--41198124 Score: 246
Period size: 89 Copynumber: 2.4 Consensus size: 89
41197905 TTTTGAGACT
* * * * * * * * **
41197915 TTTGGGGGTAAAAATGTAAATTTGGAAAGGTTTA-AGGTTAAAAGGTAATTTTGGAAAAGTTCGA
1 TTTGAGGGTCAAAATATAATTTTGAAAAAGTTTAGATGTTAAAAAGTAATTTCAGAAAAGTTCGA
41197979 GGATAAAATGCAATTTTGGAAAAG
66 GGATAAAATGCAATTTTGGAAAAG
* **
41198003 TTT-AGGGGTCAAAATGTGGTTTTGAAAAAGTTTAGATGTTAAAAAGTAATTTCAGAAAAGTTCG
1 TTTGA-GGGTCAAAATATAATTTTGAAAAAGTTTAGATGTTAAAAAGTAATTTCAGAAAAGTTCG
* *
41198067 AGAGTTAAAATGTAATTTT-GAAAAG
65 AG-GATAAAATGCAATTTTGGAAAAG
41198092 TTTGAGGGTCAAAATATAATTTTGAAAAAGTTT
1 TTTGAGGGTCAAAATATAATTTTGAAAAAGTTT
41198125 GGTGGCCAAA
Statistics
Matches: 102, Mismatches: 16, Indels: 7
0.82 0.13 0.06
Matches are distributed among these distances:
88 26 0.25
89 61 0.60
90 15 0.15
ACGTcount: A:0.40, C:0.03, G:0.24, T:0.33
Consensus pattern (89 bp):
TTTGAGGGTCAAAATATAATTTTGAAAAAGTTTAGATGTTAAAAAGTAATTTCAGAAAAGTTCGA
GGATAAAATGCAATTTTGGAAAAG
Found at i:41198123 original size:30 final size:30
Alignment explanation
Indices: 41197915--41198162 Score: 152
Period size: 29 Copynumber: 8.4 Consensus size: 30
41197905 TTTTGAGACT
* * * * *
41197915 TTTGGGGGTAAAAATGTAAATTTGGAAAGG
1 TTTGAGGGTCAAAATGTAATTTTGAAAAAG
* * * *
41197945 TTT-AAGGTTAAAAGGTAATTTTGGAAAAG
1 TTTGAGGGTCAAAATGTAATTTTGAAAAAG
* * * *
41197974 TTCGAGGAT-AAAATGCAATTTTGGAAAAG
1 TTTGAGGGTCAAAATGTAATTTTGAAAAAG
**
41198003 TTT-AGGGGTCAAAATGTGGTTTTGAAAAAG
1 TTTGA-GGGTCAAAATGTAATTTTGAAAAAG
* * * *
41198033 TTT-AGATGTTAAAAAGTAA-TTTCAGAAAAG
1 TTTGAG-GGTCAAAATGTAATTTTGA-AAAAG
* * *
41198063 TTCGAGAGTTAAAATGTAATTTTG-AAAAG
1 TTTGAGGGTCAAAATGTAATTTTGAAAAAG
*
41198092 TTTGAGGGTCAAAATATAATTTTGAAAAAG
1 TTTGAGGGTCAAAATGTAATTTTGAAAAAG
* * * *
41198122 TTTG-GTGGCCAAAATGCAATATTGGAAAA-
1 TTTGAG-GGTCAAAATGTAATTTTGAAAAAG
*
41198151 TTTAAGGGTCAA
1 TTTGAGGGTCAA
41198163 TTTTAAAATA
Statistics
Matches: 170, Mismatches: 38, Indels: 21
0.74 0.17 0.09
Matches are distributed among these distances:
28 1 0.01
29 84 0.49
30 80 0.47
31 5 0.03
ACGTcount: A:0.40, C:0.04, G:0.24, T:0.32
Consensus pattern (30 bp):
TTTGAGGGTCAAAATGTAATTTTGAAAAAG
Found at i:41198150 original size:89 final size:88
Alignment explanation
Indices: 41197964--41198150 Score: 209
Period size: 89 Copynumber: 2.1 Consensus size: 88
41197954 AAAAGGTAAT
* **
41197964 TTTGGAAAAGTTCGAGGATAAAATGCAATTTTGGAAAAGTTTAGGGGTCAAAATGTGGTTTTGAA
1 TTTGGAAAAGTTCGAGGATAAAATGCAATTTTGGAAAAGTTTAGGGGTCAAAATATAATTTTGAA
** *
41198029 AAAGTTTAGATGTTAAAAAGTAA
66 AAAGTTTAGATGCCAAAAAGCAA
* * *
41198052 TTTCAGAAAAGTTCGAGAGTTAAAATGTAATTTT-GAAAAGTTT-GAGGGTCAAAATATAATTTT
1 TTT-GGAAAAGTTCGAG-GATAAAATGCAATTTTGGAAAAGTTTAG-GGGTCAAAATATAATTTT
* *
41198115 GAAAAAGTTT-GGTGGCCAAAATGCAA
63 GAAAAAGTTTAGAT-GCCAAAAAGCAA
41198141 TATTGGAAAA
1 T-TTGGAAAA
41198151 TTTAAGGGTC
Statistics
Matches: 82, Mismatches: 12, Indels: 9
0.80 0.12 0.09
Matches are distributed among these distances:
88 6 0.07
89 60 0.73
90 16 0.20
ACGTcount: A:0.41, C:0.05, G:0.23, T:0.32
Consensus pattern (88 bp):
TTTGGAAAAGTTCGAGGATAAAATGCAATTTTGGAAAAGTTTAGGGGTCAAAATATAATTTTGAA
AAAGTTTAGATGCCAAAAAGCAA
Found at i:41200015 original size:39 final size:38
Alignment explanation
Indices: 41199971--41200157 Score: 151
Period size: 39 Copynumber: 4.8 Consensus size: 38
41199961 CCCATGGTTA
* *
41199971 GGGTAAGAGATCGGATGGCTGCAATCTGTCCCATGATC
1 GGGTAAGAGATCGGATGGTTGCAATCTGCCCCATGATC
* * **
41200009 GAGGTAAGAGATTGTATGGTTGTGATCTGCCCCATGATC
1 G-GGTAAGAGATCGGATGGTTGCAATCTGCCCCATGATC
* * **
41200048 GGGTAAAAGATCAGATGGTTGCAATCTGCCCC-TAGCGC
1 GGGTAAGAGATCGGATGGTTGCAATCTGCCCCAT-GATC
* * * * ** *
41200086 GGGGTAAGAGATTGGCTGATGGTGATTTGCCCCATGATC
1 -GGGTAAGAGATCGGATGGTTGCAATCTGCCCCATGATC
* * *
41200125 GGGGTAAAAGATCGGATGCTTACAATCTGCCCC
1 -GGGTAAGAGATCGGATGGTTGCAATCTGCCCC
41200158 TGGCGCGAGG
Statistics
Matches: 111, Mismatches: 34, Indels: 7
0.73 0.22 0.05
Matches are distributed among these distances:
37 1 0.01
38 28 0.25
39 81 0.73
40 1 0.01
ACGTcount: A:0.24, C:0.20, G:0.31, T:0.25
Consensus pattern (38 bp):
GGGTAAGAGATCGGATGGTTGCAATCTGCCCCATGATC
Found at i:41200071 original size:77 final size:78
Alignment explanation
Indices: 41199956--41200344 Score: 364
Period size: 78 Copynumber: 5.0 Consensus size: 78
41199946 GATTGGTTTT
* ** * * * **
41199956 TTTGCCCCATGGTTAGGGTAAGAGATCGGATGGCTGCAATCTGTCCC-ATGATCGAGGTAAGAGA
1 TTTGCCCCATGATCGGGGTAAAAGATCGGATGGTTGCAATCTGCCCCTA-GCGCGAGGTAAGAGA
** * *
41200020 TTGTATGGTTGTGA
65 TTGGCTGATGGTGA
* * *
41200034 TCTGCCCCATGATC-GGGTAAAAGATCAGATGGTTGCAATCTGCCCCTAGCGCGGGGTAAGAGAT
1 TTTGCCCCATGATCGGGGTAAAAGATCGGATGGTTGCAATCTGCCCCTAGCGCGAGGTAAGAGAT
41200098 TGGCTGATGGTGA
66 TGGCTGATGGTGA
* * *
41200111 TTTGCCCCATGATCGGGGTAAAAGATCGGATGCTTACAATCTGCCCCTGGCGCGAGGTAAGAGAT
1 TTTGCCCCATGATCGGGGTAAAAGATCGGATGGTTGCAATCTGCCCCTAGCGCGAGGTAAGAGAT
41200176 TGGCTGATGGTGA
66 TGGCTGATGGTGA
* * **
41200189 TTTGCCCCATGATCGGGGTAAAAGATCGGTCACGGGGTAAG-AGATC-G-GTC-A-CG-G-GGTA
1 TTTGCCCCATGATCGGGGTAAAAGATCGG--A--TGGT-TGCA-ATCTGCCCCTAGCGCGAGGTA
* *
41200247 AGAGATAGGCTGACGGTGA
60 AGAGATTGGCTGATGGTGA
* * * * * * *
41200266 TCTGCCTCATGATCGAGGTGAAAGATCGGATGGTTTCAATCTGCCCCTATCGCGGGGTAAGAGAT
1 TTTGCCCCATGATCGGGGTAAAAGATCGGATGGTTGCAATCTGCCCCTAGCGCGAGGTAAGAGAT
*
41200331 TGGCTGATAGTGA
66 TGGCTGATGGTGA
41200344 T
1 T
41200345 GTAACTTCTC
Statistics
Matches: 255, Mismatches: 41, Indels: 30
0.78 0.13 0.09
Matches are distributed among these distances:
72 3 0.01
73 5 0.02
74 1 0.00
75 2 0.01
76 2 0.01
77 110 0.43
78 121 0.47
79 2 0.01
80 1 0.00
81 1 0.00
82 4 0.02
83 3 0.01
ACGTcount: A:0.24, C:0.19, G:0.33, T:0.25
Consensus pattern (78 bp):
TTTGCCCCATGATCGGGGTAAAAGATCGGATGGTTGCAATCTGCCCCTAGCGCGAGGTAAGAGAT
TGGCTGATGGTGA
Found at i:41200209 original size:39 final size:39
Alignment explanation
Indices: 41199994--41200214 Score: 141
Period size: 39 Copynumber: 5.7 Consensus size: 39
41199984 GATGGCTGCA
* * * ** * *
41199994 ATCTGTCCCATGATCGAGGTAAGAGATTGTATGGTTGTG
1 ATCTGCCCCATGATCGGGGTAAAAGATTGGCTGATGGTG
*
41200033 ATCTGCCCCATGATC-GGGTAAAAGA-T--CAGATGGTTG
1 ATCTGCCCCATGATCGGGGTAAAAGATTGGCTGATGG-TG
** *
41200069 CAATCTGCCCC-TAGCGCGGGGTAAGAGATTGGCTGATGGTG
1 --ATCTGCCCCAT-GATCGGGGTAAAAGATTGGCTGATGGTG
* * * * ****
41200110 ATTTGCCCCATGATCGGGGTAAAAGATCGGATGCTTACA
1 ATCTGCCCCATGATCGGGGTAAAAGATTGGCTGATGGTG
* *
41200149 ATCTGCCCC-TG-GCGCGAGGTAAGAGATTGGCTGATGGTG
1 ATCTGCCCCATGATCG-G-GGTAAAAGATTGGCTGATGGTG
*
41200188 ATTTGCCCCATGATCGGGGTAAAAGAT
1 ATCTGCCCCATGATCGGGGTAAAAGAT
41200215 CGGTCACGGG
Statistics
Matches: 134, Mismatches: 35, Indels: 26
0.69 0.18 0.13
Matches are distributed among these distances:
35 3 0.02
36 2 0.01
37 4 0.03
38 22 0.16
39 88 0.66
40 5 0.04
41 4 0.03
42 6 0.04
ACGTcount: A:0.24, C:0.19, G:0.31, T:0.26
Consensus pattern (39 bp):
ATCTGCCCCATGATCGGGGTAAAAGATTGGCTGATGGTG
Found at i:41200226 original size:19 final size:19
Alignment explanation
Indices: 41200202--41200252 Score: 93
Period size: 19 Copynumber: 2.7 Consensus size: 19
41200192 GCCCCATGAT
*
41200202 CGGGGTAAAAGATCGGTCA
1 CGGGGTAAGAGATCGGTCA
41200221 CGGGGTAAGAGATCGGTCA
1 CGGGGTAAGAGATCGGTCA
41200240 CGGGGTAAGAGAT
1 CGGGGTAAGAGAT
41200253 AGGCTGACGG
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
19 31 1.00
ACGTcount: A:0.29, C:0.14, G:0.41, T:0.16
Consensus pattern (19 bp):
CGGGGTAAGAGATCGGTCA
Found at i:41201071 original size:39 final size:39
Alignment explanation
Indices: 41200998--41201222 Score: 159
Period size: 39 Copynumber: 5.8 Consensus size: 39
41200988 ACGATATGCA
* * * * * *
41200998 ATCTGTCCCATGATCGAGGTAAGAGATTGTATGGTTGTG
1 ATCTGCCCCATGATCGGGGTAAAAGATCGGATGATTGTG
* * **
41201037 ATCTGCCCCATGATCGGGGTAAAAGATCAGATGGTTGCA
1 ATCTGCCCCATGATCGGGGTAAAAGATCGGATGATTGTG
** * * * *
41201076 ATCTGCCCC-TAGCGCGGGGTAAGAGATTGGCTGATGGTG
1 ATCTGCCCCAT-GATCGGGGTAAAAGATCGGATGATTGTG
* * ***
41201115 ATTTGCCCCATGATCGGGGTAAAAGATCGGATGCTTACA
1 ATCTGCCCCATGATCGGGGTAAAAGATCGGATGATTGTG
* * * * *
41201154 ATCTGCCCC-TG-GCGCGAGGTAAGAGATTGGCTGATGGTG
1 ATCTGCCCCATGATCG-G-GGTAAAAGATCGGATGATTGTG
*
41201193 ATTTGCCCCATGATCGGGGTAAAAGATCGG
1 ATCTGCCCCATGATCGGGGTAAAAGATCGG
41201223 TCACGGGGTA
Statistics
Matches: 137, Mismatches: 43, Indels: 12
0.71 0.22 0.06
Matches are distributed among these distances:
37 2 0.01
38 4 0.03
39 125 0.91
40 4 0.03
41 2 0.01
ACGTcount: A:0.24, C:0.19, G:0.32, T:0.25
Consensus pattern (39 bp):
ATCTGCCCCATGATCGGGGTAAAAGATCGGATGATTGTG
Found at i:41201123 original size:78 final size:78
Alignment explanation
Indices: 41201015--41201349 Score: 363
Period size: 78 Copynumber: 4.3 Consensus size: 78
41201005 CCATGATCGA
** * * *
41201015 GGTAAGAGATTGTATGGTTGTGATCTGCCCCATGATCGGGGTAAAAGATCAGATGGTTGCAATCT
1 GGTAAGAGATTGGCTGATGGTGATCTGCCCCATGATCGGGGTAAAAGATCGGATGGTTGCAATCT
41201080 GCCCCTAGCGCGG
66 GCCCCTAGCGCGG
* * *
41201093 GGTAAGAGATTGGCTGATGGTGATTTGCCCCATGATCGGGGTAAAAGATCGGATGCTTACAATCT
1 GGTAAGAGATTGGCTGATGGTGATCTGCCCCATGATCGGGGTAAAAGATCGGATGGTTGCAATCT
* *
41201158 GCCCCTGGCGCGA
66 GCCCCTAGCGCGG
* * * *
41201171 GGTAAGAGATTGGCTGATGGTGATTTGCCCCATGATCGGGGTAAAAGATCGGTCACGG-GGTAA-
1 GGTAAGAGATTGGCTGATGGTGATCTGCCCCATGATCGGGGTAAAAGATCGG--ATGGTTGCAAT
** ** * *
41201234 GAG-ATC-GGTCACGG
64 CTGCCCCTAG-CGCGG
* * * * * *
41201248 GGTAAGAGATAGGCTGACGGTGATCTGCCTCATGATCGAGGTGAAAGATCGGATGGTTTCAATCT
1 GGTAAGAGATTGGCTGATGGTGATCTGCCCCATGATCGGGGTAAAAGATCGGATGGTTGCAATCT
*
41201313 GCCCCTATCGCGG
66 GCCCCTAGCGCGG
*
41201326 GGTAAGAGATTGGCTGATAGTGAT
1 GGTAAGAGATTGGCTGATGGTGAT
41201350 GTAACTTCTC
Statistics
Matches: 209, Mismatches: 41, Indels: 14
0.79 0.16 0.05
Matches are distributed among these distances:
75 3 0.01
76 4 0.02
77 51 0.24
78 147 0.70
79 2 0.01
80 2 0.01
ACGTcount: A:0.24, C:0.18, G:0.34, T:0.24
Consensus pattern (78 bp):
GGTAAGAGATTGGCTGATGGTGATCTGCCCCATGATCGGGGTAAAAGATCGGATGGTTGCAATCT
GCCCCTAGCGCGG
Found at i:41201231 original size:19 final size:19
Alignment explanation
Indices: 41201207--41201257 Score: 93
Period size: 19 Copynumber: 2.7 Consensus size: 19
41201197 GCCCCATGAT
*
41201207 CGGGGTAAAAGATCGGTCA
1 CGGGGTAAGAGATCGGTCA
41201226 CGGGGTAAGAGATCGGTCA
1 CGGGGTAAGAGATCGGTCA
41201245 CGGGGTAAGAGAT
1 CGGGGTAAGAGAT
41201258 AGGCTGACGG
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
19 31 1.00
ACGTcount: A:0.29, C:0.14, G:0.41, T:0.16
Consensus pattern (19 bp):
CGGGGTAAGAGATCGGTCA
Found at i:41202557 original size:6 final size:6
Alignment explanation
Indices: 41202546--41202616 Score: 56
Period size: 6 Copynumber: 11.7 Consensus size: 6
41202536 TTTCGACCTC
* * *
41202546 TCTTTT TCTTTT TCTTGTT TTTGTTT TCGTTTG T-TTTT TCTTCT T-TTTT
1 TCTTTT TCTTTT TCTT-TT TCT-TTT TC-TTTT TCTTTT TCTTTT TCTTTT
* *
41202595 TCCTTA TCTTTT TCTTTT TCTT
1 TCTTTT TCTTTT TCTTTT TCTT
41202617 CTTGAGCGGA
Statistics
Matches: 50, Mismatches: 10, Indels: 10
0.71 0.14 0.14
Matches are distributed among these distances:
5 8 0.16
6 30 0.60
7 10 0.20
8 2 0.04
ACGTcount: A:0.01, C:0.15, G:0.06, T:0.77
Consensus pattern (6 bp):
TCTTTT
Found at i:41202612 original size:29 final size:26
Alignment explanation
Indices: 41202546--41202619 Score: 78
Period size: 26 Copynumber: 2.7 Consensus size: 26
41202536 TTTCGACCTC
*
41202546 TCTTTTTCTTTTTCTTGTTTTTGTTT
1 TCTTTTTCTTTTTCTTCTTTTTGTTT
* *
41202572 TCGTTTGT-TTTTTCTTCTTTTTTTCCTT
1 TC-TTTTTCTTTTTCTTCTTTTTGT--TT
41202600 ATCTTTTTCTTTTTCTTCTT
1 -TCTTTTTCTTTTTCTTCTT
41202620 GAGCGGAGTC
Statistics
Matches: 39, Mismatches: 4, Indels: 7
0.78 0.08 0.14
Matches are distributed among these distances:
26 16 0.41
27 4 0.10
28 6 0.15
29 13 0.33
ACGTcount: A:0.01, C:0.16, G:0.05, T:0.77
Consensus pattern (26 bp):
TCTTTTTCTTTTTCTTCTTTTTGTTT
Found at i:41206905 original size:20 final size:20
Alignment explanation
Indices: 41206868--41206906 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
41206858 AAATTTTATG
** *
41206868 TACAAAAAATCAATTTAAAA
1 TACAAAAAAAAAAATTAAAA
41206888 TACAAAAAAAAAAATTAAA
1 TACAAAAAAAAAAATTAAA
41206907 TTTTATGTAC
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.72, C:0.08, G:0.00, T:0.21
Consensus pattern (20 bp):
TACAAAAAAAAAAATTAAAA
Found at i:41208381 original size:18 final size:18
Alignment explanation
Indices: 41208358--41208394 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
41208348 ACAATTCATA
41208358 TCACTTTCAATTCCAATT
1 TCACTTTCAATTCCAATT
* *
41208376 TCACTTTCACTTTCAATT
1 TCACTTTCAATTCCAATT
41208394 T
1 T
41208395 TGATCACAAA
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:0.24, C:0.27, G:0.00, T:0.49
Consensus pattern (18 bp):
TCACTTTCAATTCCAATT
Found at i:41210837 original size:51 final size:52
Alignment explanation
Indices: 41210769--41210900 Score: 180
Period size: 50 Copynumber: 2.6 Consensus size: 52
41210759 TTAATAAGGT
* * * *
41210769 CATGCATTATGTAACTCTCATGATTAGTTAAGTTTGCATTATAAATAAT-AA
1 CATGCATTATGTAACTCTCATGATTCGTTAAGATTGCATAAAAAATAATGAA
* *
41210820 CATGCATTATGTAACTCTCATG-TTCGTTAAGATTGCATAAAAAATTATGTA
1 CATGCATTATGTAACTCTCATGATTCGTTAAGATTGCATAAAAAATAATGAA
*
41210871 C-TGCATTATGTAACTCTCATTATTCGTTAA
1 CATGCATTATGTAACTCTCATGATTCGTTAA
41210901 AATTTGTATC
Statistics
Matches: 72, Mismatches: 7, Indels: 4
0.87 0.08 0.05
Matches are distributed among these distances:
50 40 0.56
51 32 0.44
ACGTcount: A:0.34, C:0.14, G:0.12, T:0.39
Consensus pattern (52 bp):
CATGCATTATGTAACTCTCATGATTCGTTAAGATTGCATAAAAAATAATGAA
Found at i:41210939 original size:53 final size:50
Alignment explanation
Indices: 41210767--41210939 Score: 158
Period size: 50 Copynumber: 3.4 Consensus size: 50
41210757 ATTTAATAAG
* **
41210767 GTCATGCATTATGTAACTCTCATGATTAGTTAAGTTTGCATTATAAATAA-TAA
1 GTCATGCATTATGTAACTCTCAT-ATTCGTTAAAATTGCA-TA-AAA-AATTAA
* * *
41210820 --CATGCATTATGTAACTCTCATGTTCGTTAAGATTGCATAAAAAATTAT
1 GTCATGCATTATGTAACTCTCATATTCGTTAAAATTGCATAAAAAATTAA
* *
41210868 GT-ACTGCATTATGTAACTCTCATTATTCGTTAAAATTTGTATCAATAAATTAA
1 GTCA-TGCATTATGTAACTCTCA-TATTCGTTAAAA-TTGCAT-AAAAAATTAA
41210921 GTCATGCATT-TAGTAACTC
1 GTCATGCATTAT-GTAACTC
41210940 ATATTCATTT
Statistics
Matches: 102, Mismatches: 9, Indels: 18
0.79 0.07 0.14
Matches are distributed among these distances:
47 2 0.02
48 5 0.05
49 3 0.03
50 31 0.30
51 31 0.30
52 6 0.06
53 23 0.23
54 1 0.01
ACGTcount: A:0.35, C:0.14, G:0.12, T:0.39
Consensus pattern (50 bp):
GTCATGCATTATGTAACTCTCATATTCGTTAAAATTGCATAAAAAATTAA
Found at i:41210957 original size:101 final size:99
Alignment explanation
Indices: 41210771--41210958 Score: 211
Period size: 101 Copynumber: 1.9 Consensus size: 99
41210761 AATAAGGTCA
* *
41210771 TGCATTATGTAACTCTCATGATTAGTTAAGTTTGCATTATAAATAATAACATGCATTATGTAACT
1 TGCATTATGTAACTCTCATGATTAGTTAAATTTGCATAATAAATAAT-ACATGCATTATGTAAC-
* *
41210836 CTCATGTTCGTTAAGATTGCATAAAAAATTATGTAC
64 CTCATATTCATTAAGATTGCATAAAAAATTATGTAC
* * *
41210872 TGCATTATGTAACTCTCATTATTCGTTAAAATTTGTATCAATAAATTAAGT-CATGCATT-TAGT
1 TGCATTATGTAACTCTCATGATTAGTT-AAATTTGCAT-AATAAA-TAA-TACATGCATTAT-GT
* *
41210935 AA-CTCATATTCATTTAGTTTGCAT
61 AACCTCATATTCATTAAGATTGCAT
41210959 CTTTAATCAT
Statistics
Matches: 73, Mismatches: 9, Indels: 10
0.79 0.10 0.11
Matches are distributed among these distances:
101 43 0.59
102 9 0.12
103 17 0.23
104 3 0.04
105 1 0.01
ACGTcount: A:0.34, C:0.13, G:0.12, T:0.41
Consensus pattern (99 bp):
TGCATTATGTAACTCTCATGATTAGTTAAATTTGCATAATAAATAATACATGCATTATGTAACCT
CATATTCATTAAGATTGCATAAAAAATTATGTAC
Found at i:41212445 original size:12 final size:12
Alignment explanation
Indices: 41212428--41212473 Score: 58
Period size: 12 Copynumber: 3.9 Consensus size: 12
41212418 TTGTTTAATA
41212428 TTCACGAACATG
1 TTCACGAACATG
41212440 TTCACGAACAT-
1 TTCACGAACATG
**
41212451 TAAACGAACATG
1 TTCACGAACATG
*
41212463 TTCATGAACAT
1 TTCACGAACAT
41212474 ATAATTGAAC
Statistics
Matches: 28, Mismatches: 5, Indels: 2
0.80 0.14 0.06
Matches are distributed among these distances:
11 9 0.32
12 19 0.68
ACGTcount: A:0.39, C:0.22, G:0.13, T:0.26
Consensus pattern (12 bp):
TTCACGAACATG
Found at i:41212488 original size:24 final size:23
Alignment explanation
Indices: 41212431--41212494 Score: 92
Period size: 23 Copynumber: 2.7 Consensus size: 23
41212421 TTTAATATTC
*
41212431 ACGAACATGTTCACGAACATTAA
1 ACGAACATGTTCATGAACATTAA
41212454 ACGAACATGTTCATGAACATATAA
1 ACGAACATGTTCATGAACAT-TAA
**
41212478 TTGAACATGTTCATGAA
1 ACGAACATGTTCATGAA
41212495 TAATGTTAAT
Statistics
Matches: 37, Mismatches: 3, Indels: 1
0.90 0.07 0.02
Matches are distributed among these distances:
23 19 0.51
24 18 0.49
ACGTcount: A:0.42, C:0.17, G:0.14, T:0.27
Consensus pattern (23 bp):
ACGAACATGTTCATGAACATTAA
Found at i:41215630 original size:16 final size:17
Alignment explanation
Indices: 41215609--41215644 Score: 56
Period size: 16 Copynumber: 2.1 Consensus size: 17
41215599 TGGACTTTTG
41215609 TTTATTTTTG-TTTGGT
1 TTTATTTTTGATTTGGT
41215625 TTTATTTTTGATTTTGGT
1 TTTATTTTTGA-TTTGGT
41215643 TT
1 TT
41215645 GTTTTATCCT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
16 10 0.56
18 8 0.44
ACGTcount: A:0.08, C:0.00, G:0.17, T:0.75
Consensus pattern (17 bp):
TTTATTTTTGATTTGGT
Found at i:41233387 original size:48 final size:48
Alignment explanation
Indices: 41233332--41233428 Score: 185
Period size: 48 Copynumber: 2.0 Consensus size: 48
41233322 ATCCATTGTC
41233332 TATAACTAATCAACTACTCTTTTAGTGTCATCCAACCTCTTCAAACAA
1 TATAACTAATCAACTACTCTTTTAGTGTCATCCAACCTCTTCAAACAA
*
41233380 TATAACTAATCAATTACTCTTTTAGTGTCATCCAACCTCTTCAAACAA
1 TATAACTAATCAACTACTCTTTTAGTGTCATCCAACCTCTTCAAACAA
41233428 T
1 T
41233429 CAGATAAGAT
Statistics
Matches: 48, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
48 48 1.00
ACGTcount: A:0.35, C:0.26, G:0.04, T:0.35
Consensus pattern (48 bp):
TATAACTAATCAACTACTCTTTTAGTGTCATCCAACCTCTTCAAACAA
Found at i:41237144 original size:29 final size:29
Alignment explanation
Indices: 41237110--41237174 Score: 85
Period size: 29 Copynumber: 2.2 Consensus size: 29
41237100 CGGAGTTTAA
* *
41237110 AAATTTAAAAGTTTAAAGTTTTTAATTTT
1 AAATTTAAAAGTTTAAAATTTTAAATTTT
* * *
41237139 AGATTTTAAGGTTTAAAATTTTAAATTTT
1 AAATTTAAAAGTTTAAAATTTTAAATTTT
41237168 AAATTTA
1 AAATTTA
41237175 GCGTTTAAGA
Statistics
Matches: 29, Mismatches: 7, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
29 29 1.00
ACGTcount: A:0.42, C:0.00, G:0.08, T:0.51
Consensus pattern (29 bp):
AAATTTAAAAGTTTAAAATTTTAAATTTT
Found at i:41237146 original size:22 final size:22
Alignment explanation
Indices: 41237103--41237174 Score: 74
Period size: 22 Copynumber: 3.3 Consensus size: 22
41237093 TAAAATTCGG
* *
41237103 AGTTTAAAAATTTAAAAGTTTAA
1 AGTTT-AAAATTTTAAATTTTAA
** *
41237126 AGTTTTTAATTTTAGATTTTAA
1 AGTTTAAAATTTTAAATTTTAA
*
41237148 GGTTTAAAATTTTAAATTTTAA
1 AGTTTAAAATTTTAAATTTTAA
41237170 A-TTTA
1 AGTTTA
41237175 GCGTTTAAGA
Statistics
Matches: 39, Mismatches: 10, Indels: 2
0.76 0.20 0.04
Matches are distributed among these distances:
21 4 0.10
22 30 0.77
23 5 0.13
ACGTcount: A:0.42, C:0.00, G:0.08, T:0.50
Consensus pattern (22 bp):
AGTTTAAAATTTTAAATTTTAA
Found at i:41237164 original size:7 final size:7
Alignment explanation
Indices: 41237110--41237173 Score: 56
Period size: 7 Copynumber: 8.9 Consensus size: 7
41237100 CGGAGTTTAA
*
41237110 AAATTTA
1 AAATTTT
*
41237117 AAAGTTT
1 AAATTTT
41237124 AAAGTTTT
1 AAA-TTTT
*
41237132 TAATTTT
1 AAATTTT
*
41237139 AGATTTT
1 AAATTTT
* *
41237146 AAGGTTTA
1 AA-ATTTT
41237154 AAATTTT
1 AAATTTT
41237161 AAATTTT
1 AAATTTT
41237168 AAATTT
1 AAATTT
41237174 AGCGTTTAAG
Statistics
Matches: 44, Mismatches: 11, Indels: 4
0.75 0.19 0.07
Matches are distributed among these distances:
7 34 0.77
8 10 0.23
ACGTcount: A:0.41, C:0.00, G:0.08, T:0.52
Consensus pattern (7 bp):
AAATTTT
Found at i:41237498 original size:21 final size:21
Alignment explanation
Indices: 41237468--41237518 Score: 84
Period size: 21 Copynumber: 2.4 Consensus size: 21
41237458 AATGGAAAAC
41237468 AAATATACAATTACAAACATTA
1 AAAT-TACAATTACAAACATTA
41237490 AAATTACAATTACAAACATTA
1 AAATTACAATTACAAACATTA
*
41237511 GAATTACA
1 AAATTACA
41237519 CCATTAATGA
Statistics
Matches: 28, Mismatches: 1, Indels: 1
0.93 0.03 0.03
Matches are distributed among these distances:
21 24 0.86
22 4 0.14
ACGTcount: A:0.57, C:0.14, G:0.02, T:0.27
Consensus pattern (21 bp):
AAATTACAATTACAAACATTA
Done.