Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: CP032248.1 Gossypioides kirkii chromosome KI_06
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: 60359545
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 900 characters in sequence are not A, C, G, or T
File 184 of 193
Found at i:57378585 original size:20 final size:20
Alignment explanation
Indices: 57378544--57378585 Score: 59
Period size: 20 Copynumber: 2.1 Consensus size: 20
57378534 TTTGTTATTA
*
57378544 TTTTTATTGTTTTGTTGTTG
1 TTTTTATTGTTTTGTTGCTG
57378564 TTTTTATTGTTGTT-TTGCTG
1 TTTTTATTGTT-TTGTTGCTG
57378584 TT
1 TT
57378586 ATTTTTGCTA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
20 18 0.90
21 2 0.10
ACGTcount: A:0.05, C:0.02, G:0.19, T:0.74
Consensus pattern (20 bp):
TTTTTATTGTTTTGTTGCTG
Found at i:57395087 original size:24 final size:23
Alignment explanation
Indices: 57395060--57395104 Score: 63
Period size: 24 Copynumber: 1.9 Consensus size: 23
57395050 TATATTATAT
* *
57395060 TATAATTTAATAATTATAAAAAAG
1 TATAAATTAATAA-AATAAAAAAG
57395084 TATAAATTAATAAAATAAAAA
1 TATAAATTAATAAAATAAAAA
57395105 GTTATTAAAA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
23 7 0.37
24 12 0.63
ACGTcount: A:0.64, C:0.00, G:0.02, T:0.33
Consensus pattern (23 bp):
TATAAATTAATAAAATAAAAAAG
Found at i:57395733 original size:25 final size:25
Alignment explanation
Indices: 57395714--57395763 Score: 100
Period size: 25 Copynumber: 2.0 Consensus size: 25
57395704 CCTAAATCCT
57395714 TTAATGTGCTCTTTTTCTAAAAAAA
1 TTAATGTGCTCTTTTTCTAAAAAAA
57395739 TTAATGTGCTCTTTTTCTAAAAAAA
1 TTAATGTGCTCTTTTTCTAAAAAAA
57395764 CAAAACAATC
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 25 1.00
ACGTcount: A:0.36, C:0.12, G:0.08, T:0.44
Consensus pattern (25 bp):
TTAATGTGCTCTTTTTCTAAAAAAA
Found at i:57396615 original size:2 final size:2
Alignment explanation
Indices: 57396608--57396649 Score: 84
Period size: 2 Copynumber: 21.0 Consensus size: 2
57396598 GTATCAATTA
57396608 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
57396650 ATATATATAT
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 40 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
CT
Found at i:57396654 original size:2 final size:2
Alignment explanation
Indices: 57396649--57396681 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
57396639 TCTCTCTCTC
57396649 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
57396682 CAATCTCTTA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:57402350 original size:13 final size:13
Alignment explanation
Indices: 57402332--57402379 Score: 60
Period size: 13 Copynumber: 3.6 Consensus size: 13
57402322 ACCTAACCTG
57402332 ATAATAAATCAAT
1 ATAATAAATCAAT
***
57402345 ATAATAAATTTGT
1 ATAATAAATCAAT
57402358 ATAATAAATCAAT
1 ATAATAAATCAAT
57402371 ATACATAAA
1 ATA-ATAAA
57402380 ATAATAATAA
Statistics
Matches: 28, Mismatches: 6, Indels: 1
0.80 0.17 0.03
Matches are distributed among these distances:
13 23 0.82
14 5 0.18
ACGTcount: A:0.58, C:0.06, G:0.02, T:0.33
Consensus pattern (13 bp):
ATAATAAATCAAT
Found at i:57403066 original size:3 final size:3
Alignment explanation
Indices: 57403058--57403093 Score: 72
Period size: 3 Copynumber: 12.0 Consensus size: 3
57403048 TATTTTTGTT
57403058 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
57403094 ATAAAAAGCC
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 33 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TTA
Found at i:57404320 original size:6 final size:7
Alignment explanation
Indices: 57404302--57404326 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
57404292 AATAGATTGG
57404302 ATTTTTT
1 ATTTTTT
57404309 ATTTTTT
1 ATTTTTT
57404316 ATTTTTT
1 ATTTTTT
57404323 ATTT
1 ATTT
57404327 AACATGCTGA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.16, C:0.00, G:0.00, T:0.84
Consensus pattern (7 bp):
ATTTTTT
Found at i:57405083 original size:21 final size:23
Alignment explanation
Indices: 57405041--57405083 Score: 63
Period size: 21 Copynumber: 2.0 Consensus size: 23
57405031 AAAAAAATAG
*
57405041 TTTTATATTAATATTTATATAAT
1 TTTTATATTAATATTTAAATAAT
57405064 TTTTA-ATTAA-ATTTAAATAA
1 TTTTATATTAATATTTAAATAA
57405084 AAATATTTAA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
21 9 0.47
22 5 0.26
23 5 0.26
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (23 bp):
TTTTATATTAATATTTAAATAAT
Found at i:57416034 original size:31 final size:32
Alignment explanation
Indices: 57415999--57416084 Score: 88
Period size: 32 Copynumber: 2.8 Consensus size: 32
57415989 ATATATGTTG
* *
57415999 TTTTC-AATTTGATAC-TCAAATTTGATATTTT
1 TTTTCTAATTTGATACAT-AAACTTGACATTTT
*
57416030 TTTTCTAATTTGGTACATAAACTTGACATTTT
1 TTTTCTAATTTGATACATAAACTTGACATTTT
* * *
57416062 TTTT-TAAGTTGGTACTTAAACTT
1 TTTTCTAATTTGATACATAAACTT
57416085 TTTGGGATCC
Statistics
Matches: 48, Mismatches: 5, Indels: 4
0.84 0.09 0.07
Matches are distributed among these distances:
31 22 0.46
32 25 0.52
33 1 0.02
ACGTcount: A:0.28, C:0.10, G:0.09, T:0.52
Consensus pattern (32 bp):
TTTTCTAATTTGATACATAAACTTGACATTTT
Found at i:57420109 original size:35 final size:36
Alignment explanation
Indices: 57420070--57420139 Score: 106
Period size: 35 Copynumber: 1.9 Consensus size: 36
57420060 CTCAAATGCT
*
57420070 CTCTTCAAGTTTCCCAGT-AATTTAGCTCATACGAG
1 CTCTTCAAGTTTCCCAGTAAATTTAACTCATACGAG
*
57420105 CTCTTCAAGTTTCCTAGTAAAATTTAACTCATACG
1 CTCTTCAAGTTTCCCAGT-AAATTTAACTCATACG
57420140 CGCCCGGTCA
Statistics
Matches: 31, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
35 17 0.55
37 14 0.45
ACGTcount: A:0.29, C:0.24, G:0.11, T:0.36
Consensus pattern (36 bp):
CTCTTCAAGTTTCCCAGTAAATTTAACTCATACGAG
Found at i:57420233 original size:26 final size:26
Alignment explanation
Indices: 57420172--57420234 Score: 108
Period size: 26 Copynumber: 2.4 Consensus size: 26
57420162 TACGAGCTAG
* *
57420172 TATCGCTCTCACGAGCCAATTCAGTA
1 TATCGCTCTTACGAGCCAATTCAATA
57420198 TATCGCTCTTACGAGCCAATTCAATA
1 TATCGCTCTTACGAGCCAATTCAATA
57420224 TATCGCTCTTA
1 TATCGCTCTTA
57420235 GTACAGTATA
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
26 35 1.00
ACGTcount: A:0.27, C:0.29, G:0.13, T:0.32
Consensus pattern (26 bp):
TATCGCTCTTACGAGCCAATTCAATA
Found at i:57420421 original size:17 final size:17
Alignment explanation
Indices: 57420381--57420446 Score: 73
Period size: 17 Copynumber: 3.9 Consensus size: 17
57420371 GCCCAGTGAG
*
57420381 ATAAATTTAGATTTATT
1 ATAAATTTAAATTTATT
* *
57420398 TTGAATTTAAATTTGCA-T
1 ATAAATTTAAATTT--ATT
57420416 A-AAATTTAAATTTATT
1 ATAAATTTAAATTTATT
57420432 ATAAATTTAAATTTA
1 ATAAATTTAAATTTA
57420447 AAATTAAATG
Statistics
Matches: 40, Mismatches: 5, Indels: 8
0.75 0.09 0.15
Matches are distributed among these distances:
15 1 0.03
16 2 0.05
17 35 0.88
18 1 0.03
19 1 0.03
ACGTcount: A:0.44, C:0.02, G:0.05, T:0.50
Consensus pattern (17 bp):
ATAAATTTAAATTTATT
Found at i:57421291 original size:10 final size:10
Alignment explanation
Indices: 57421272--57421303 Score: 55
Period size: 10 Copynumber: 3.2 Consensus size: 10
57421262 AAAACGGTAG
57421272 AAATAATATT
1 AAATAATATT
*
57421282 AAATATTATT
1 AAATAATATT
57421292 AAATAATATT
1 AAATAATATT
57421302 AA
1 AA
57421304 TTTTTAATCA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
10 20 1.00
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (10 bp):
AAATAATATT
Found at i:57422586 original size:119 final size:119
Alignment explanation
Indices: 57422361--57422730 Score: 480
Period size: 119 Copynumber: 3.1 Consensus size: 119
57422351 TTGAACTTTT
* * *
57422361 CAAAAATTA-TATTTGACCCCCGAACTTTCCAAAAT-TC-TATTTTCAA-CTCCGATTTCACCAA
1 CAAAAATTACCATTTTACCCCCGAACTTTCCAAAATCTCAT-TTTTTAACCT-CGATTTCACCAA
* * * *
57422422 AAATCACCATTTTACCCTCAAACTTTCTAAAATCTCATTTTTAACCCCGATTTCAC
64 AAATTACCATTTTACCCCCAAACTTTCCAAAATCCCATTTTTAACCCCGATTTCAC
57422478 CAAAAATTACCATTTTACCCCCGAACTTTCCAAAATCTCATTTTTTAACCTCGATTTCACCAAAA
1 CAAAAATTACCATTTTACCCCCGAACTTTCCAAAATCTCATTTTTTAACCTCGATTTCACCAAAA
* * *
57422543 ATTACCATTTTACCCCCAAACTCTCCAAAATCCCCTATTTAACCCCGATTTCAC
66 ATTACCATTTTACCCCCAAACTTTCCAAAATCCCATTTTTAACCCCGATTTCAC
** ** * * *
57422597 CAAAAACCACCATTTTACCCCTAAACTTTCCAAAATCCCATTTTCTAACC-CTTATTTCACCAAA
1 CAAAAATTACCATTTTACCCCCGAACTTTCCAAAATCTCATTTTTTAACCTC-GATTTCACCAAA
* * * * *
57422661 AATTATCATTTTACCCCCTAACTTTCCAAAATTCCATTTTTAACCCTGATTTTAC
65 AATTACCATTTTACCCCCAAACTTTCCAAAATCCCATTTTTAACCCCGATTTCAC
57422716 CAAAAATTACCATTT
1 CAAAAATTACCATTT
57422731 CAACCCCGGG
Statistics
Matches: 221, Mismatches: 27, Indels: 8
0.86 0.11 0.03
Matches are distributed among these distances:
117 9 0.04
118 25 0.11
119 184 0.83
120 3 0.01
ACGTcount: A:0.34, C:0.31, G:0.02, T:0.34
Consensus pattern (119 bp):
CAAAAATTACCATTTTACCCCCGAACTTTCCAAAATCTCATTTTTTAACCTCGATTTCACCAAAA
ATTACCATTTTACCCCCAAACTTTCCAAAATCCCATTTTTAACCCCGATTTCAC
Found at i:57422718 original size:29 final size:31
Alignment explanation
Indices: 57422634--57422730 Score: 94
Period size: 31 Copynumber: 3.2 Consensus size: 31
57422624 TTCCAAAATC
* *
57422634 CCATTTTCTAACCCTTATTTCACCAAAAATTA
1 CCATTTT-TAACCCTAATTTTACCAAAAATTA
* * *
57422666 TCA-TTTTACCCCCTAACTTT-CC-AAAATT-
1 CCATTTTTA-ACCCTAATTTTACCAAAAATTA
*
57422694 CCATTTTTAACCCTGATTTTACCAAAAATTA
1 CCATTTTTAACCCTAATTTTACCAAAAATTA
57422725 CCATTT
1 CCATTT
57422731 CAACCCCGGG
Statistics
Matches: 51, Mismatches: 9, Indels: 11
0.72 0.13 0.15
Matches are distributed among these distances:
28 10 0.20
29 13 0.25
30 10 0.20
31 16 0.31
32 2 0.04
ACGTcount: A:0.32, C:0.28, G:0.01, T:0.39
Consensus pattern (31 bp):
CCATTTTTAACCCTAATTTTACCAAAAATTA
Found at i:57422737 original size:60 final size:59
Alignment explanation
Indices: 57422361--57422730 Score: 444
Period size: 59 Copynumber: 6.3 Consensus size: 59
57422351 TTGAACTTTT
* * * * *
57422361 CAAAAATTA-TATTTGACCCCCGAACTTTCCAAAATTCTATTTTCAACTCC-GATTTCAC
1 CAAAAATTACCATTTTACCCCCAAACTTTCCAAAATTCCATTTTTAAC-CCTGATTTCAC
* * * *
57422419 CAAAAATCACCATTTTACCCTCAAACTTTCTAAAA-TCTCATTTTTAACCCCGATTTCAC
1 CAAAAATTACCATTTTACCCCCAAACTTTCCAAAATTC-CATTTTTAACCCTGATTTCAC
*
57422478 CAAAAATTACCATTTTACCCCCGAACTTTCCAAAA-TCTCATTTTTTAA-CCTCGATTTCAC
1 CAAAAATTACCATTTTACCCCCAAACTTTCCAAAATTC-CA-TTTTTAACCCT-GATTTCAC
* * * * *
57422538 CAAAAATTACCATTTTACCCCCAAACTCTCCAAAATCCCCTATTTAACCCCGATTTCAC
1 CAAAAATTACCATTTTACCCCCAAACTTTCCAAAATTCCATTTTTAACCCTGATTTCAC
** * * *
57422597 CAAAAACCACCATTTTACCCCTAAACTTTCCAAAATCCCATTTTCTAACCCTTATTTCAC
1 CAAAAATTACCATTTTACCCCCAAACTTTCCAAAATTCCATTTT-TAACCCTGATTTCAC
* * *
57422657 CAAAAATTATCATTTTACCCCCTAACTTTCCAAAATTCCATTTTTAACCCTGATTTTAC
1 CAAAAATTACCATTTTACCCCCAAACTTTCCAAAATTCCATTTTTAACCCTGATTTCAC
57422716 CAAAAATTACCATTT
1 CAAAAATTACCATTT
57422731 CAACCCCGGG
Statistics
Matches: 268, Mismatches: 36, Indels: 15
0.84 0.11 0.05
Matches are distributed among these distances:
58 12 0.04
59 153 0.57
60 102 0.38
61 1 0.00
ACGTcount: A:0.34, C:0.31, G:0.02, T:0.34
Consensus pattern (59 bp):
CAAAAATTACCATTTTACCCCCAAACTTTCCAAAATTCCATTTTTAACCCTGATTTCAC
Found at i:57432800 original size:2 final size:2
Alignment explanation
Indices: 57432793--57432843 Score: 102
Period size: 2 Copynumber: 25.5 Consensus size: 2
57432783 AATCTTGTTT
57432793 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
57432835 TA TA TA TA T
1 TA TA TA TA T
57432844 CAAAAGTTTG
Statistics
Matches: 49, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 49 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:57447169 original size:7 final size:7
Alignment explanation
Indices: 57447157--57447198 Score: 84
Period size: 7 Copynumber: 6.0 Consensus size: 7
57447147 CGACAAAAAC
57447157 GGTTCAA
1 GGTTCAA
57447164 GGTTCAA
1 GGTTCAA
57447171 GGTTCAA
1 GGTTCAA
57447178 GGTTCAA
1 GGTTCAA
57447185 GGTTCAA
1 GGTTCAA
57447192 GGTTCAA
1 GGTTCAA
57447199 ATCTCGCCTC
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 35 1.00
ACGTcount: A:0.29, C:0.14, G:0.29, T:0.29
Consensus pattern (7 bp):
GGTTCAA
Found at i:57447767 original size:234 final size:235
Alignment explanation
Indices: 57447183--57447774 Score: 1096
Period size: 235 Copynumber: 2.5 Consensus size: 235
57447173 TTCAAGGTTC
*
57447183 AAGGTTCAAGGTTCAAATCTCGCCTCGTGTAGTTTGGTTCGTAGGATGTCGGTTACTTGAACTAT
1 AAGGTTCAAGGTTCGAATCTCGCCTCGTGTAGTTTGGTTCGTAGGATGTCGGTTACTTGAACTAT
* * *
57447248 TGAATGATATTTGAAATGCATCAGTATGAATCAACATCTTTATAATACTACTACATAAAAGTGCA
66 TGAATGATATTTGAAATGCATCAGTATGAATCAACATCTTTATAATACAACTACATGAAAGAGCA
57447313 CAATTTTTGGAAATGAGGGTAGTTAATAGTTTGCTTTGACTCCCTATATAAGTATTTGTGTTCGA
131 CAATTTTTGGAAATGAGGGTAGTTAATAGTTTGCTTTGACTCCCTATATAAGTATTTGTGTTCGA
*
57447378 TATTCGTGTTTTGATATTTGGCCTAATGTTCGACAAAAAA
196 TATTCGTGTTTTGACATTTGGCCTAATGTTCGACAAAAAA
* * *
57447418 AAGGTTCAAGATTTGAATCTCGCCTCGTGTAGTTTAGTTCGTAGGATGTCGGTTACTTGAACTAT
1 AAGGTTCAAGGTTCGAATCTCGCCTCGTGTAGTTTGGTTCGTAGGATGTCGGTTACTTGAACTAT
*
57447483 TGAATGATATTTGAAACGCATCAGTATGAATCAACATCTTTATAATACAACTACATGAAAGAGCA
66 TGAATGATATTTGAAATGCATCAGTATGAATCAACATCTTTATAATACAACTACATGAAAGAGCA
57447548 CAATTTTTGGAAATGAGGGTAGTTAATAGTTTGCTTTGACTCCCTATATAAGTATTTGTGTTCGA
131 CAATTTTTGGAAATGAGGGTAGTTAATAGTTTGCTTTGACTCCCTATATAAGTATTTGTGTTCGA
57447613 TATTCGTGTTTTGACATTTGGCCTAATGTTCGAC-AAAAA
196 TATTCGTGTTTTGACATTTGGCCTAATGTTCGACAAAAAA
57447652 AAGGTTCAAGGTTCGAATCTCGCCTCGTGTAGTTTGGTTCGTAGGATGTCGGTTACTTGAACTAT
1 AAGGTTCAAGGTTCGAATCTCGCCTCGTGTAGTTTGGTTCGTAGGATGTCGGTTACTTGAACTAT
57447717 TGAATGATATTTGAAATGCATCAGTATGAATCAACATCTTTATAATACAACTACATGA
66 TGAATGATATTTGAAATGCATCAGTATGAATCAACATCTTTATAATACAACTACATGA
57447775 TTAAGGATGT
Statistics
Matches: 344, Mismatches: 13, Indels: 1
0.96 0.04 0.00
Matches are distributed among these distances:
234 124 0.36
235 220 0.64
ACGTcount: A:0.30, C:0.14, G:0.20, T:0.36
Consensus pattern (235 bp):
AAGGTTCAAGGTTCGAATCTCGCCTCGTGTAGTTTGGTTCGTAGGATGTCGGTTACTTGAACTAT
TGAATGATATTTGAAATGCATCAGTATGAATCAACATCTTTATAATACAACTACATGAAAGAGCA
CAATTTTTGGAAATGAGGGTAGTTAATAGTTTGCTTTGACTCCCTATATAAGTATTTGTGTTCGA
TATTCGTGTTTTGACATTTGGCCTAATGTTCGACAAAAAA
Found at i:57451119 original size:28 final size:26
Alignment explanation
Indices: 57451078--57451130 Score: 63
Period size: 25 Copynumber: 2.0 Consensus size: 26
57451068 TTTTCATGTG
*
57451078 TTTTTCATGATAAAATGTGAAAAAATTAC
1 TTTTCCATGAT-AAAT-T-AAAAAATTAC
57451107 TTTTCCATG-TAAATTAAAAAATTA
1 TTTTCCATGATAAATTAAAAAATTA
57451131 AAAAATTATT
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
25 9 0.39
26 1 0.04
27 4 0.17
28 1 0.04
29 8 0.35
ACGTcount: A:0.45, C:0.08, G:0.08, T:0.40
Consensus pattern (26 bp):
TTTTCCATGATAAATTAAAAAATTAC
Found at i:57456829 original size:24 final size:24
Alignment explanation
Indices: 57456793--57456838 Score: 65
Period size: 24 Copynumber: 1.9 Consensus size: 24
57456783 TTTTAATTAT
*
57456793 ATTTTTGAGTTTTTTTTAATATCA
1 ATTTTTGAGTTTTTTTCAATATCA
**
57456817 ATTTTTGTTTTTTTTTCAATAT
1 ATTTTTGAGTTTTTTTCAATAT
57456839 GTTTTTTAAT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
24 19 1.00
ACGTcount: A:0.22, C:0.04, G:0.07, T:0.67
Consensus pattern (24 bp):
ATTTTTGAGTTTTTTTCAATATCA
Found at i:57458298 original size:44 final size:45
Alignment explanation
Indices: 57458236--57458352 Score: 173
Period size: 44 Copynumber: 2.6 Consensus size: 45
57458226 ATATAAATAA
57458236 ATAATAAATACTATATAATTTAATTAAAATTAATATGAATAA-TT
1 ATAATAAATACTATATAATTTAATTAAAATTAATATGAATAATTT
* * * * *
57458280 ATAACAAATACTACATAATTTAGTTAAAATTAATTTTAATAATTT
1 ATAATAAATACTATATAATTTAATTAAAATTAATATGAATAATTT
*
57458325 ATAATAGATACTATATAATTTAATTAAA
1 ATAATAAATACTATATAATTTAATTAAA
57458353 TATTTAGTAG
Statistics
Matches: 63, Mismatches: 9, Indels: 1
0.86 0.12 0.01
Matches are distributed among these distances:
44 37 0.59
45 26 0.41
ACGTcount: A:0.52, C:0.04, G:0.03, T:0.41
Consensus pattern (45 bp):
ATAATAAATACTATATAATTTAATTAAAATTAATATGAATAATTT
Found at i:57470969 original size:30 final size:31
Alignment explanation
Indices: 57470910--57470970 Score: 81
Period size: 31 Copynumber: 2.0 Consensus size: 31
57470900 AAATTGATAT
*
57470910 TTGAACTATTCAAAAGTTTTCATTTAAGTCA
1 TTGAACTATTCAAAAATTTTCATTTAAGTCA
*
57470941 TTGAACTATT-AGAAAATTTTTA-TTAAGTCA
1 TTGAACTATTCA-AAAATTTTCATTTAAGTCA
57470971 CTGGGTTTAT
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
30 9 0.33
31 18 0.67
ACGTcount: A:0.38, C:0.10, G:0.10, T:0.43
Consensus pattern (31 bp):
TTGAACTATTCAAAAATTTTCATTTAAGTCA
Found at i:57473849 original size:20 final size:21
Alignment explanation
Indices: 57473805--57473850 Score: 53
Period size: 20 Copynumber: 2.3 Consensus size: 21
57473795 TCATTAATGA
57473805 TAAA-AAAATATAATTTTTAT
1 TAAATAAAATATAATTTTTAT
*
57473825 GAAATAAAATAT-ATTTATT-T
1 TAAATAAAATATAATTT-TTAT
57473845 TAAATA
1 TAAATA
57473851 TAAAAATTTA
Statistics
Matches: 22, Mismatches: 2, Indels: 4
0.79 0.07 0.14
Matches are distributed among these distances:
20 13 0.59
21 9 0.41
ACGTcount: A:0.54, C:0.00, G:0.02, T:0.43
Consensus pattern (21 bp):
TAAATAAAATATAATTTTTAT
Found at i:57474748 original size:29 final size:31
Alignment explanation
Indices: 57474706--57474784 Score: 90
Period size: 29 Copynumber: 2.6 Consensus size: 31
57474696 GAAAATTCTT
* *
57474706 TTAAATTATAATTTT-TAAATTTTAAAAGA-
1 TTAAATTAAAATTTTATAAATTTTAAAAAAG
* *
57474735 TTAAATTAAAATTTTATCATTTTTAAAAAAG
1 TTAAATTAAAATTTTATAAATTTTAAAAAAG
*
57474766 TTCAAAATAAAATTTTATA
1 TT-AAATTAAAATTTTATA
57474785 TTTATTAATT
Statistics
Matches: 41, Mismatches: 6, Indels: 3
0.82 0.12 0.06
Matches are distributed among these distances:
29 14 0.34
30 11 0.27
31 2 0.05
32 14 0.34
ACGTcount: A:0.49, C:0.03, G:0.03, T:0.46
Consensus pattern (31 bp):
TTAAATTAAAATTTTATAAATTTTAAAAAAG
Found at i:57474777 original size:32 final size:29
Alignment explanation
Indices: 57474725--57474792 Score: 82
Period size: 32 Copynumber: 2.2 Consensus size: 29
57474715 AATTTTTAAA
* *
57474725 TTTTAAAAGATTAAATTAAAATTTTATCAT
1 TTTTAAAAAATTAAAATAAAATTTTAT-AT
57474755 TTTTAAAAAAGTTCAAAATAAAATTTTATAT
1 TTTTAAAAAA-TT-AAAATAAAATTTTATAT
57474786 TTATTAA
1 TT-TTAA
57474793 TTTAAATTTT
Statistics
Matches: 33, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
30 9 0.27
31 6 0.18
32 18 0.55
ACGTcount: A:0.49, C:0.03, G:0.03, T:0.46
Consensus pattern (29 bp):
TTTTAAAAAATTAAAATAAAATTTTATAT
Found at i:57478124 original size:14 final size:15
Alignment explanation
Indices: 57478100--57478134 Score: 54
Period size: 14 Copynumber: 2.4 Consensus size: 15
57478090 TTTTACATTG
*
57478100 AAAATCTTTTCGACA
1 AAAATCTTTTCGAAA
57478115 AAAATC-TTTCGAAA
1 AAAATCTTTTCGAAA
57478129 AAAATC
1 AAAATC
57478135 ATAGATAAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
14 13 0.68
15 6 0.32
ACGTcount: A:0.49, C:0.17, G:0.06, T:0.29
Consensus pattern (15 bp):
AAAATCTTTTCGAAA
Found at i:57480796 original size:20 final size:20
Alignment explanation
Indices: 57480773--57480824 Score: 54
Period size: 20 Copynumber: 2.6 Consensus size: 20
57480763 AAACATATTT
*
57480773 AAAATATTTAAAAAT-TTATA
1 AAAATATATAAAAATCTTA-A
* *
57480793 AAAATGTATAAAATTCTTAA
1 AAAATATATAAAAATCTTAA
57480813 AAAATATA-AAAA
1 AAAATATATAAAA
57480825 TAATAAAAAA
Statistics
Matches: 27, Mismatches: 4, Indels: 3
0.79 0.12 0.09
Matches are distributed among these distances:
19 4 0.15
20 20 0.74
21 3 0.11
ACGTcount: A:0.63, C:0.02, G:0.02, T:0.33
Consensus pattern (20 bp):
AAAATATATAAAAATCTTAA
Found at i:57480805 original size:19 final size:18
Alignment explanation
Indices: 57480783--57480840 Score: 55
Period size: 19 Copynumber: 3.1 Consensus size: 18
57480773 AAAATATTTA
*
57480783 AAAATTTATAAAAATGTAT
1 AAAATTTATAAAAA-ATAT
57480802 AAAATTCT-TAAAAAATAT
1 AAAATT-TATAAAAAATAT
* *
57480820 AAAAATAATAAAAAATTAT
1 AAAATTTATAAAAAA-TAT
57480839 AA
1 AA
57480841 TATTAAATTT
Statistics
Matches: 33, Mismatches: 3, Indels: 6
0.79 0.07 0.14
Matches are distributed among these distances:
18 15 0.45
19 17 0.52
20 1 0.03
ACGTcount: A:0.66, C:0.02, G:0.02, T:0.31
Consensus pattern (18 bp):
AAAATTTATAAAAAATAT
Found at i:57481458 original size:9 final size:9
Alignment explanation
Indices: 57481441--57481707 Score: 71
Period size: 9 Copynumber: 28.1 Consensus size: 9
57481431 TTAAATTATT
57481441 TTTTTATAA
1 TTTTTATAA
*
57481450 TTCTTATAA
1 TTTTTATAA
57481459 GTTTTTATGAA
1 -TTTTTAT-AA
57481470 TTTTTATAA
1 TTTTTATAA
57481479 TTTTTA-AA
1 TTTTTATAA
**** *
57481487 AAAATAAATA
1 TTTTTATA-A
57481497 TATTTTACTAA
1 T-TTTTA-TAA
57481508 -TTTTATAA
1 TTTTTATAA
*
57481516 TATTTATAA
1 TTTTTATAA
*
57481525 -GTTTATACCA
1 TTTTTATA--A
57481535 TTTTTA-ATA
1 TTTTTATA-A
57481544 TTTTTAATAA
1 TTTTT-ATAA
*
57481554 CTTTTAT-A
1 TTTTTATAA
* *
57481562 TTTGTAAGAA
1 TTT-TTATAA
*
57481572 TTTTTGATAG
1 TTTTT-ATAA
* * *
57481582 CTTTAAGAA
1 TTTTTATAA
*
57481591 TTTTTATATG
1 TTTTTATA-A
*
57481601 TTTTTGTAAA
1 TTTTTAT-AA
* *
57481611 ATTTTAAATA
1 TTTTTATA-A
*
57481621 TGTTTTATTGA
1 T-TTTTA-TAA
*
57481632 TTTTATAAAA
1 TTTT-TATAA
*
57481642 GTTTTTATAG
1 -TTTTTATAA
*
57481652 TTTATTATAT
1 TTT-TTATAA
57481662 TTTTTATATA
1 TTTTTATA-A
57481672 TATTTTATAA
1 T-TTTTATAA
*
57481682 TATTTATAA
1 TTTTTATAA
*
57481691 -TTTT-TCA
1 TTTTTATAA
57481698 TTTTTATAA
1 TTTTTATAA
57481707 T
1 T
57481708 GTTAATATTA
Statistics
Matches: 183, Mismatches: 48, Indels: 54
0.64 0.17 0.19
Matches are distributed among these distances:
7 2 0.01
8 23 0.13
9 66 0.36
10 60 0.33
11 31 0.17
12 1 0.01
ACGTcount: A:0.35, C:0.03, G:0.05, T:0.57
Consensus pattern (9 bp):
TTTTTATAA
Found at i:57481463 original size:20 final size:20
Alignment explanation
Indices: 57481440--57481483 Score: 63
Period size: 20 Copynumber: 2.2 Consensus size: 20
57481430 TTTAAATTAT
57481440 TTTTTTAT-AATTCTTATAA
1 TTTTTTATGAATTCTTATAA
* *
57481459 GTTTTTATGAATTTTTATAA
1 TTTTTTATGAATTCTTATAA
57481479 TTTTT
1 TTTTT
57481484 AAAAAAATAA
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
19 7 0.33
20 14 0.67
ACGTcount: A:0.27, C:0.02, G:0.05, T:0.66
Consensus pattern (20 bp):
TTTTTTATGAATTCTTATAA
Found at i:57481576 original size:18 final size:18
Alignment explanation
Indices: 57481534--57481596 Score: 56
Period size: 19 Copynumber: 3.4 Consensus size: 18
57481524 AGTTTATACC
*
57481534 ATTTTTAATATTTTTAATA
1 ATTTTTAATA-TTTTAAGA
*
57481553 ACTTTT-ATATTTGTAAGA
1 ATTTTTAATATTT-TAAGA
* *
57481571 ATTTTTGATAGCTTTAAGA
1 ATTTTTAATA-TTTTAAGA
57481590 ATTTTTA
1 ATTTTTA
57481597 TATGTTTTTG
Statistics
Matches: 36, Mismatches: 5, Indels: 6
0.77 0.11 0.13
Matches are distributed among these distances:
17 3 0.08
18 12 0.33
19 19 0.53
20 2 0.06
ACGTcount: A:0.33, C:0.03, G:0.08, T:0.56
Consensus pattern (18 bp):
ATTTTTAATATTTTAAGA
Found at i:57483364 original size:34 final size:34
Alignment explanation
Indices: 57483325--57483393 Score: 138
Period size: 34 Copynumber: 2.0 Consensus size: 34
57483315 CATCAAATTT
57483325 ATCATATTTAACTTCTATCCAACAAATATTATCA
1 ATCATATTTAACTTCTATCCAACAAATATTATCA
57483359 ATCATATTTAACTTCTATCCAACAAATATTATCA
1 ATCATATTTAACTTCTATCCAACAAATATTATCA
57483393 A
1 A
57483394 CTTTTAAAAA
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
34 35 1.00
ACGTcount: A:0.42, C:0.20, G:0.00, T:0.38
Consensus pattern (34 bp):
ATCATATTTAACTTCTATCCAACAAATATTATCA
Found at i:57486839 original size:20 final size:19
Alignment explanation
Indices: 57486814--57486883 Score: 63
Period size: 19 Copynumber: 3.7 Consensus size: 19
57486804 TTAATTATAA
57486814 TTTAAAAATTTAAAAATATT
1 TTTAAAAATTT-AAAATATT
* * *
57486834 TTTAAAACTTTTATATATT
1 TTTAAAAATTTAAAATATT
* *
57486853 TTTAAAAA--TAATATATA
1 TTTAAAAATTTAAAATATT
*
57486870 TTTAAAATTTTAAA
1 TTTAAAAATTTAAA
57486884 TTCTAAAAAA
Statistics
Matches: 40, Mismatches: 8, Indels: 5
0.75 0.15 0.09
Matches are distributed among these distances:
17 14 0.35
19 16 0.40
20 10 0.25
ACGTcount: A:0.50, C:0.01, G:0.00, T:0.49
Consensus pattern (19 bp):
TTTAAAAATTTAAAATATT
Found at i:57495719 original size:23 final size:23
Alignment explanation
Indices: 57495676--57495719 Score: 54
Period size: 23 Copynumber: 1.9 Consensus size: 23
57495666 TATTTTTTAA
* *
57495676 TTCTATAATATAAAAATAAATAT
1 TTCTATAAAATAAAAAAAAATAT
57495699 TTCT-TAAAATAAAGAAAAAAT
1 TTCTATAAAATAAA-AAAAAAT
57495720 TAAATATTAT
Statistics
Matches: 18, Mismatches: 2, Indels: 2
0.82 0.09 0.09
Matches are distributed among these distances:
22 8 0.44
23 10 0.56
ACGTcount: A:0.59, C:0.05, G:0.02, T:0.34
Consensus pattern (23 bp):
TTCTATAAAATAAAAAAAAATAT
Found at i:57498719 original size:22 final size:23
Alignment explanation
Indices: 57498674--57498720 Score: 87
Period size: 23 Copynumber: 2.1 Consensus size: 23
57498664 GAAACAATAA
57498674 GCACACACAGTGCAATCCAGTAG
1 GCACACACAGTGCAATCCAGTAG
57498697 GCACACACAGTGCAAT-CAGTAG
1 GCACACACAGTGCAATCCAGTAG
57498719 GC
1 GC
57498721 GTAAATAGCG
Statistics
Matches: 24, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
22 8 0.33
23 16 0.67
ACGTcount: A:0.34, C:0.30, G:0.23, T:0.13
Consensus pattern (23 bp):
GCACACACAGTGCAATCCAGTAG
Found at i:57498772 original size:23 final size:23
Alignment explanation
Indices: 57498742--57498834 Score: 150
Period size: 23 Copynumber: 4.0 Consensus size: 23
57498732 AAATCAATAG
*
57498742 GCACACGAGGTGCGAAACAGTAA
1 GCACACGAAGTGCGAAACAGTAA
57498765 GCACACGAAGTGCGAAACAGTAA
1 GCACACGAAGTGCGAAACAGTAA
57498788 GCACACGAAGTGCGAAACAGTAA
1 GCACACGAAGTGCGAAACAGTAA
* * *
57498811 GCACACAAAGTGTGAAATAGTAA
1 GCACACGAAGTGCGAAACAGTAA
57498834 G
1 G
57498835 TGTGAAACAA
Statistics
Matches: 66, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
23 66 1.00
ACGTcount: A:0.43, C:0.19, G:0.27, T:0.11
Consensus pattern (23 bp):
GCACACGAAGTGCGAAACAGTAA
Found at i:57498795 original size:46 final size:46
Alignment explanation
Indices: 57498742--57498895 Score: 164
Period size: 46 Copynumber: 3.5 Consensus size: 46
57498732 AAATCAATAG
* *
57498742 GCACACGAGGTGCGAAACAGTAAGCACACGAAGTGCGAAACAGTAA
1 GCACACGAAGTGCGAAACAGTAAGCACACAAAGTGCGAAACAGTAA
*
57498788 GCACACGAAGTGCGAAACAGTAAGCACACAAAGTGTG-AA-A-T-A
1 GCACACGAAGTGCGAAACAGTAAGCACACAAAGTGCGAAACAGTAA
* * * *
57498830 G-----TAAGTGTGAAACAATAAGCACACAAAGTGCGAAGCAGTAA
1 GCACACGAAGTGCGAAACAGTAAGCACACAAAGTGCGAAACAGTAA
* *
57498871 GCACACAAAGTGCGAAATAGTAAGC
1 GCACACGAAGTGCGAAACAGTAAGC
57498896 GCGCTAGCGT
Statistics
Matches: 87, Mismatches: 12, Indels: 18
0.74 0.10 0.15
Matches are distributed among these distances:
37 27 0.31
38 1 0.01
39 1 0.01
40 1 0.01
41 2 0.02
42 2 0.02
43 1 0.01
44 1 0.01
45 2 0.02
46 49 0.56
ACGTcount: A:0.44, C:0.19, G:0.25, T:0.12
Consensus pattern (46 bp):
GCACACGAAGTGCGAAACAGTAAGCACACAAAGTGCGAAACAGTAA
Found at i:57498869 original size:60 final size:60
Alignment explanation
Indices: 57498772--57498894 Score: 201
Period size: 60 Copynumber: 2.0 Consensus size: 60
57498762 TAAGCACACG
* * *
57498772 AAGTGCGAAACAGTAAGCACACGAAGTGCGAAACAGTAAGCACACAAAGTGTGAAATAGT
1 AAGTGCGAAACAATAAGCACACAAAGTGCGAAACAGTAAGCACACAAAGTGCGAAATAGT
* *
57498832 AAGTGTGAAACAATAAGCACACAAAGTGCGAAGCAGTAAGCACACAAAGTGCGAAATAGT
1 AAGTGCGAAACAATAAGCACACAAAGTGCGAAACAGTAAGCACACAAAGTGCGAAATAGT
57498892 AAG
1 AAG
57498895 CGCGCTAGCG
Statistics
Matches: 58, Mismatches: 5, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
60 58 1.00
ACGTcount: A:0.46, C:0.16, G:0.24, T:0.13
Consensus pattern (60 bp):
AAGTGCGAAACAATAAGCACACAAAGTGCGAAACAGTAAGCACACAAAGTGCGAAATAGT
Found at i:57498870 original size:37 final size:37
Alignment explanation
Indices: 57498795--57498871 Score: 109
Period size: 37 Copynumber: 2.1 Consensus size: 37
57498785 TAAGCACACG
* * *
57498795 AAGTGCGAAACAGTAAGCACACAAAGTGTGAAATAGT
1 AAGTGCGAAACAATAAGCACACAAAGTGCGAAACAGT
* *
57498832 AAGTGTGAAACAATAAGCACACAAAGTGCGAAGCAGT
1 AAGTGCGAAACAATAAGCACACAAAGTGCGAAACAGT
57498869 AAG
1 AAG
57498872 CACACAAAGT
Statistics
Matches: 35, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
37 35 1.00
ACGTcount: A:0.47, C:0.14, G:0.25, T:0.14
Consensus pattern (37 bp):
AAGTGCGAAACAATAAGCACACAAAGTGCGAAACAGT
Found at i:57498892 original size:23 final size:23
Alignment explanation
Indices: 57498832--57498895 Score: 92
Period size: 23 Copynumber: 2.8 Consensus size: 23
57498822 GTGAAATAGT
* *
57498832 AAGTGTGAAACAATAAGCACACA
1 AAGTGCGAAACAGTAAGCACACA
*
57498855 AAGTGCGAAGCAGTAAGCACACA
1 AAGTGCGAAACAGTAAGCACACA
*
57498878 AAGTGCGAAATAGTAAGC
1 AAGTGCGAAACAGTAAGC
57498896 GCGCTAGCGT
Statistics
Matches: 36, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
23 36 1.00
ACGTcount: A:0.47, C:0.17, G:0.23, T:0.12
Consensus pattern (23 bp):
AAGTGCGAAACAGTAAGCACACA
Found at i:57502321 original size:59 final size:59
Alignment explanation
Indices: 57502216--57502327 Score: 172
Period size: 59 Copynumber: 1.9 Consensus size: 59
57502206 ATAGCCTAGT
* * *
57502216 TATGGTCTTACACATTATGAACCCATGTTTAATATCTTGGCGGACTCTATATGTAGCAC
1 TATGGTCTTACACATTATGAACCCATGTTTAATATCTTGACAGACTCCATATGTAGCAC
*
57502275 TATGGTCTTACACATTATGAACCCATGTTTAATCT-TCTGACAGACTCCATATG
1 TATGGTCTTACACATTATGAACCCATGTTTAATATCT-TGACAGACTCCATATG
57502328 ATTCCATAGC
Statistics
Matches: 48, Mismatches: 4, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
58 1 0.02
59 47 0.98
ACGTcount: A:0.28, C:0.21, G:0.15, T:0.36
Consensus pattern (59 bp):
TATGGTCTTACACATTATGAACCCATGTTTAATATCTTGACAGACTCCATATGTAGCAC
Found at i:57512487 original size:30 final size:31
Alignment explanation
Indices: 57512429--57512492 Score: 112
Period size: 31 Copynumber: 2.1 Consensus size: 31
57512419 TGACAGAAAA
*
57512429 GGATTGTTTTGTCACATTTTTAAAAGTTGAG
1 GGATTGTTGTGTCACATTTTTAAAAGTTGAG
57512460 GGATTGTTGTGTCACATTTTT-AAAGTTGAG
1 GGATTGTTGTGTCACATTTTTAAAAGTTGAG
57512490 GGA
1 GGA
57512493 CTGAAATATA
Statistics
Matches: 32, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
30 12 0.38
31 20 0.62
ACGTcount: A:0.25, C:0.06, G:0.27, T:0.42
Consensus pattern (31 bp):
GGATTGTTGTGTCACATTTTTAAAAGTTGAG
Found at i:57518664 original size:11 final size:11
Alignment explanation
Indices: 57518627--57518665 Score: 51
Period size: 11 Copynumber: 3.5 Consensus size: 11
57518617 CGATAACAAC
57518627 AAAATAATAGT
1 AAAATAATAGT
*
57518638 AACATAATAGT
1 AAAATAATAGT
* *
57518649 GAAATGATAGT
1 AAAATAATAGT
57518660 AAAATA
1 AAAATA
57518666 GTAAGAAAAT
Statistics
Matches: 22, Mismatches: 6, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
11 22 1.00
ACGTcount: A:0.59, C:0.03, G:0.13, T:0.26
Consensus pattern (11 bp):
AAAATAATAGT
Found at i:57519046 original size:2 final size:2
Alignment explanation
Indices: 57519035--57519064 Score: 53
Period size: 2 Copynumber: 15.5 Consensus size: 2
57519025 TATAATGCCT
57519035 TA TA -A TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
57519065 TGATGGGTAA
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
1 1 0.04
2 26 0.96
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:57524602 original size:11 final size:10
Alignment explanation
Indices: 57524579--57524614 Score: 56
Period size: 11 Copynumber: 3.6 Consensus size: 10
57524569 ATAAAAATAA
57524579 AAAAATTA-T
1 AAAAATTATT
57524588 AAAAATTATT
1 AAAAATTATT
57524598 AAAAATTAATT
1 AAAAATT-ATT
57524609 AAAAAT
1 AAAAAT
57524615 CATAAAATTT
Statistics
Matches: 25, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
9 8 0.32
10 8 0.32
11 9 0.36
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (10 bp):
AAAAATTATT
Found at i:57524630 original size:19 final size:18
Alignment explanation
Indices: 57524567--57524631 Score: 60
Period size: 20 Copynumber: 3.4 Consensus size: 18
57524557 TATTATGGAA
*
57524567 TTATAAAAATA-AAAAAA
1 TTATAAAAATATAAAAAT
57524584 TTATAAAAATTATTAAAAAT
1 TTATAAAAA-TA-TAAAAAT
* *
57524604 TAATTAAAAATCATAAAATT
1 TTA-TAAAAAT-ATAAAAAT
57524624 TTATAAAA
1 TTATAAAA
57524632 TTTAATTTAT
Statistics
Matches: 39, Mismatches: 4, Indels: 8
0.76 0.08 0.16
Matches are distributed among these distances:
17 9 0.23
18 2 0.05
19 5 0.13
20 16 0.41
21 7 0.18
ACGTcount: A:0.65, C:0.02, G:0.00, T:0.34
Consensus pattern (18 bp):
TTATAAAAATATAAAAAT
Found at i:57524635 original size:9 final size:9
Alignment explanation
Indices: 57524565--57524631 Score: 64
Period size: 9 Copynumber: 7.1 Consensus size: 9
57524555 AATATTATGG
57524565 AATTATAAA
1 AATTATAAA
*
57524574 AA-TAAAAA
1 AATTATAAA
57524582 AATTATAAA
1 AATTATAAA
57524591 AATTATTAAA
1 AATTA-TAAA
57524601 AATTAATTAAA
1 AATT-A-TAAA
*
57524612 AATCATAAA
1 AATTATAAA
*
57524621 ATTTTATAAA
1 A-ATTATAAA
57524631 A
1 A
57524632 TTTAATTTAT
Statistics
Matches: 49, Mismatches: 5, Indels: 7
0.80 0.08 0.11
Matches are distributed among these distances:
8 7 0.14
9 17 0.35
10 16 0.33
11 9 0.18
ACGTcount: A:0.66, C:0.01, G:0.00, T:0.33
Consensus pattern (9 bp):
AATTATAAA
Found at i:57528786 original size:20 final size:20
Alignment explanation
Indices: 57528763--57528801 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 20
57528753 ATTGATCTTG
57528763 CTTGTGGGGTGTTG-AGAAAC
1 CTTGT-GGGTGTTGAAGAAAC
*
57528783 CTTGTTGGTGTTGAAGAAA
1 CTTGTGGGTGTTGAAGAAA
57528802 TTAAGAGGTT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 7 0.41
20 10 0.59
ACGTcount: A:0.23, C:0.08, G:0.36, T:0.33
Consensus pattern (20 bp):
CTTGTGGGTGTTGAAGAAAC
Found at i:57531880 original size:21 final size:21
Alignment explanation
Indices: 57531856--57531895 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
57531846 TAAAATTTTC
57531856 TAAA-ATTTTAAAACAAAATCA
1 TAAATATTTTAAAA-AAAATCA
*
57531877 TAAATATTTTGAAAAAAAT
1 TAAATATTTTAAAAAAAAT
57531896 TATTCACATA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
21 9 0.53
22 8 0.47
ACGTcount: A:0.60, C:0.05, G:0.03, T:0.33
Consensus pattern (21 bp):
TAAATATTTTAAAAAAAATCA
Found at i:57532470 original size:19 final size:16
Alignment explanation
Indices: 57532435--57532493 Score: 61
Period size: 17 Copynumber: 3.7 Consensus size: 16
57532425 ATTTTATAAT
57532435 ATTTATAAAAAATTAA
1 ATTTATAAAAAATTAA
57532451 ATTTATTAAAAACCATTAA
1 ATTTA-TAAAAA--ATTAA
*
57532470 AATTA-AAAAAA-T-A
1 ATTTATAAAAAATTAA
57532483 ATTTATAAAAA
1 ATTTATAAAAA
57532494 TTGTTAGAAA
Statistics
Matches: 37, Mismatches: 2, Indels: 10
0.76 0.04 0.20
Matches are distributed among these distances:
13 5 0.14
14 6 0.16
15 1 0.03
16 5 0.14
17 11 0.30
19 9 0.24
ACGTcount: A:0.63, C:0.03, G:0.00, T:0.34
Consensus pattern (16 bp):
ATTTATAAAAAATTAA
Found at i:57532805 original size:10 final size:10
Alignment explanation
Indices: 57532762--57532825 Score: 53
Period size: 10 Copynumber: 6.5 Consensus size: 10
57532752 ATTTTATGGT
57532762 TTTTAATTAA
1 TTTTAATTAA
57532772 TTTCTAA-TAA
1 TTT-TAATTAA
* *
57532782 GTGTT-ATAAA
1 -TTTTAATTAA
57532792 TTTTAATTAA
1 TTTTAATTAA
* *
57532802 TTTTAATGAT
1 TTTTAATTAA
57532812 TTTTAA-TAA
1 TTTTAATTAA
57532821 TTTTA
1 TTTTA
57532826 TAAGTTTTTT
Statistics
Matches: 42, Mismatches: 8, Indels: 9
0.71 0.14 0.15
Matches are distributed among these distances:
9 10 0.24
10 27 0.64
11 5 0.12
ACGTcount: A:0.38, C:0.02, G:0.05, T:0.56
Consensus pattern (10 bp):
TTTTAATTAA
Found at i:57532835 original size:20 final size:20
Alignment explanation
Indices: 57532792--57532834 Score: 54
Period size: 19 Copynumber: 2.2 Consensus size: 20
57532782 GTGTTATAAA
*
57532792 TTTTAATTAATTTTAATGAT
1 TTTTAATTAATTTTAAAGAT
57532812 TTTTAA-TAATTTTATAAG-T
1 TTTTAATTAATTTTA-AAGAT
57532831 TTTT
1 TTTT
57532835 TTATGTTTTT
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
19 13 0.62
20 8 0.38
ACGTcount: A:0.33, C:0.00, G:0.05, T:0.63
Consensus pattern (20 bp):
TTTTAATTAATTTTAAAGAT
Found at i:57533238 original size:88 final size:88
Alignment explanation
Indices: 57533089--57533262 Score: 312
Period size: 88 Copynumber: 2.0 Consensus size: 88
57533079 TTTACAGATC
*
57533089 TAAGTCAAGTGTTTAAAACTCAAGTGTCATTGTCGCACCTCTCTCAATGTCTCTAAGTAGTTTAA
1 TAAGTCAAGTGTTTAAAACTCAAGTGTCATTGTCGCACCTCTCTCAATGTCTCTAAATAGTTTAA
*
57533154 TAATTTATCAACTTCACATAATT
66 TAATTTACCAACTTCACATAATT
* *
57533177 TAAGTCAAGTGTTTAAAACTCAAGTGTCATTGTCGTACCTTTCTCAATGTCTCTAAATAGTTTAA
1 TAAGTCAAGTGTTTAAAACTCAAGTGTCATTGTCGCACCTCTCTCAATGTCTCTAAATAGTTTAA
57533242 TAATTTACCAACTTCACATAA
66 TAATTTACCAACTTCACATAA
57533263 GTGCAATGTA
Statistics
Matches: 82, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
88 82 1.00
ACGTcount: A:0.33, C:0.19, G:0.11, T:0.37
Consensus pattern (88 bp):
TAAGTCAAGTGTTTAAAACTCAAGTGTCATTGTCGCACCTCTCTCAATGTCTCTAAATAGTTTAA
TAATTTACCAACTTCACATAATT
Found at i:57536420 original size:21 final size:22
Alignment explanation
Indices: 57536395--57536436 Score: 68
Period size: 21 Copynumber: 2.0 Consensus size: 22
57536385 AGAACAGAAT
*
57536395 AAAAATAAAC-TAAACCTAAAA
1 AAAAATAAACAAAAACCTAAAA
57536416 AAAAATAAACAAAAACCTAAA
1 AAAAATAAACAAAAACCTAAA
57536437 TCTACGAAAG
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 10 0.53
22 9 0.47
ACGTcount: A:0.74, C:0.14, G:0.00, T:0.12
Consensus pattern (22 bp):
AAAAATAAACAAAAACCTAAAA
Found at i:57537338 original size:26 final size:26
Alignment explanation
Indices: 57537302--57537368 Score: 80
Period size: 26 Copynumber: 2.6 Consensus size: 26
57537292 TGTTATATGT
* * *
57537302 GAGCCTTTGTGGTTGATTCTGTTAAA
1 GAGCCTTTGTGGCTAATTCTGCTAAA
*
57537328 GAGCCTTTGTGACTAATTCTGCTAAA
1 GAGCCTTTGTGGCTAATTCTGCTAAA
* *
57537354 AAGCATTTGTGGCTA
1 GAGCCTTTGTGGCTA
57537369 TCATTATTAT
Statistics
Matches: 34, Mismatches: 7, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
26 34 1.00
ACGTcount: A:0.24, C:0.15, G:0.24, T:0.37
Consensus pattern (26 bp):
GAGCCTTTGTGGCTAATTCTGCTAAA
Found at i:57537662 original size:18 final size:18
Alignment explanation
Indices: 57537639--57537676 Score: 60
Period size: 18 Copynumber: 2.1 Consensus size: 18
57537629 TTTTTTTTCG
57537639 AATTCGAAT-AACTCGAAT
1 AATTCGAATAAAC-CGAAT
57537657 AATTCGAATAAACCGAAT
1 AATTCGAATAAACCGAAT
57537675 AA
1 AA
57537677 AACTATATTA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
18 16 0.84
19 3 0.16
ACGTcount: A:0.50, C:0.16, G:0.11, T:0.24
Consensus pattern (18 bp):
AATTCGAATAAACCGAAT
Found at i:57540701 original size:9 final size:9
Alignment explanation
Indices: 57540687--57540716 Score: 51
Period size: 9 Copynumber: 3.3 Consensus size: 9
57540677 CACCATCTTC
57540687 AATGAAGAT
1 AATGAAGAT
57540696 AATGAAGAT
1 AATGAAGAT
*
57540705 GATGAAGAT
1 AATGAAGAT
57540714 AAT
1 AAT
57540717 AGCTTGTTAC
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
9 19 1.00
ACGTcount: A:0.53, C:0.00, G:0.23, T:0.23
Consensus pattern (9 bp):
AATGAAGAT
Found at i:57540817 original size:29 final size:28
Alignment explanation
Indices: 57540755--57540819 Score: 71
Period size: 29 Copynumber: 2.3 Consensus size: 28
57540745 CATTTTTTTA
*
57540755 TTTTAT-TTTATTATATATATTTAGAAT
1 TTTTATATTTATTAAATATATTTAGAAT
*
57540782 TTATTATATTT-TTAAATAATATTTATGTAT
1 TT-TTATATTTATTAAAT-ATATTTA-GAAT
57540812 TTTTATAT
1 TTTTATAT
57540820 GTTGCTTTAA
Statistics
Matches: 32, Mismatches: 2, Indels: 6
0.80 0.05 0.15
Matches are distributed among these distances:
27 2 0.06
28 9 0.28
29 16 0.50
30 5 0.16
ACGTcount: A:0.34, C:0.00, G:0.03, T:0.63
Consensus pattern (28 bp):
TTTTATATTTATTAAATATATTTAGAAT
Found at i:57545378 original size:7 final size:7
Alignment explanation
Indices: 57545368--57545393 Score: 52
Period size: 7 Copynumber: 3.7 Consensus size: 7
57545358 TTTTATTTTT
57545368 ATTTTAA
1 ATTTTAA
57545375 ATTTTAA
1 ATTTTAA
57545382 ATTTTAA
1 ATTTTAA
57545389 ATTTT
1 ATTTT
57545394 TAGTAATGTT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 19 1.00
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (7 bp):
ATTTTAA
Found at i:57547233 original size:59 final size:59
Alignment explanation
Indices: 57547166--57547595 Score: 643
Period size: 59 Copynumber: 7.3 Consensus size: 59
57547156 GTGCGGCGGC
* * *
57547166 AAAATGGTAATTTTTGGTTAAACCGGGGTTAAAAAGGGAATTTTGGAAAGTTTAGGGGT
1 AAAATGGTAATTTTTGGTGAAATCGGGGTTAAAAATGGAATTTTGGAAAGTTTAGGGGT
* * * *
57547225 AAAATGGTAATTTTTGGTGAAACCGGGATTAAAAATGGAATTTTGGAAGGTTTAAGGGT
1 AAAATGGTAATTTTTGGTGAAATCGGGGTTAAAAATGGAATTTTGGAAAGTTTAGGGGT
* *
57547284 AAAATGGTAATTTTTGGTGAAATCGAGGTTAAAAAATGGAATTTTGGAAAG-TTCGGAGGT
1 AAAATGGTAATTTTTGGTGAAATCGGGGTT-AAAAATGGAATTTTGGAAAGTTTAGG-GGT
* *
57547344 AAAATGGTAATTTTTGGTGAAATCGGGGTTAAAAATGGAATTTTGGAAGGTTCA-GGGT
1 AAAATGGTAATTTTTGGTGAAATCGGGGTTAAAAATGGAATTTTGGAAAGTTTAGGGGT
*
57547402 AAAATGGTAATTTTTTGGTGAAATCGGGGTT-AAAATGGAATTTT-GAAAGGTTTGGGGGT
1 AAAATGGTAA-TTTTTGGTGAAATCGGGGTTAAAAATGGAATTTTGGAAA-GTTTAGGGGT
* **
57547461 AAAATGGTAATTTTTGGTGAAATCGGGGTTAAAAATGGAATTTTGGAAGGTTCGGGGGT
1 AAAATGGTAATTTTTGGTGAAATCGGGGTTAAAAATGGAATTTTGGAAAGTTTAGGGGT
* *
57547520 AAAATGGTGATTTTTGGTGAAATCGGGATTAAAAATGGAATTTTGGAAAGTTTAGGGGT
1 AAAATGGTAATTTTTGGTGAAATCGGGGTTAAAAATGGAATTTTGGAAAGTTTAGGGGT
57547579 AAAATGGTAATTTTTGG
1 AAAATGGTAATTTTTGG
57547596 ATAGTCCAGG
Statistics
Matches: 337, Mismatches: 26, Indels: 16
0.89 0.07 0.04
Matches are distributed among these distances:
57 3 0.01
58 49 0.15
59 230 0.68
60 55 0.16
ACGTcount: A:0.33, C:0.03, G:0.30, T:0.33
Consensus pattern (59 bp):
AAAATGGTAATTTTTGGTGAAATCGGGGTTAAAAATGGAATTTTGGAAAGTTTAGGGGT
Found at i:57547343 original size:31 final size:30
Alignment explanation
Indices: 57547253--57547571 Score: 127
Period size: 30 Copynumber: 10.8 Consensus size: 30
57547243 GAAACCGGGA
* **
57547253 TTAAAAATGGAATTTTGGAAGGTT-TAAGG
1 TTAAAAATGGAATTTTGGAAAGTTCGGAGG
*
57547282 GT-AAAATGGTAATTTTTGGTGAAA--TC-GAGG
1 TTAAAAATGG-AA-TTTT-G-GAAAGTTCGGAGG
57547312 TTAAAAAATGGAATTTTGGAAAGTTCGGAGG
1 TT-AAAAATGGAATTTTGGAAAGTTCGGAGG
57547343 -T-AAAATGGTAATTTTTGGTGAAA--TCGG-GG
1 TTAAAAATGG-AA-TTTT-G-GAAAGTTCGGAGG
*
57547372 TTAAAAATGGAATTTTGGAAGGTTC--AGG
1 TTAAAAATGGAATTTTGGAAAGTTCGGAGG
*
57547400 GT-AAAATGGTAATTTTTTGGTGAAA--TCGG-GG
1 TTAAAAATGG-AA--TTTT-G-GAAAGTTCGGAGG
*
57547431 TT-AAAATGGAATTTT-GAAAGGTTTGG-GG
1 TTAAAAATGGAATTTTGGAAA-GTTCGGAGG
*
57547459 GT-AAAATGGTAATTTTTGGTGAAA--TCGG-GG
1 TTAAAAATGG-AA-TTTT-G-GAAAGTTCGGAGG
*
57547489 TTAAAAATGGAATTTTGGAAGGTTCGG-GG
1 TTAAAAATGGAATTTTGGAAAGTTCGGAGG
* * *
57547518 GT-AAAATGGTGATTTTTGGTGAAA--TCGG-GA
1 TTAAAAAT-G-GAATTTT-G-GAAAGTTCGGAGG
57547548 TTAAAAATGGAATTTTGGAAAGTT
1 TTAAAAATGGAATTTTGGAAAGTT
57547572 TAGGGGTAAA
Statistics
Matches: 227, Mismatches: 19, Indels: 88
0.68 0.06 0.26
Matches are distributed among these distances:
25 4 0.02
27 17 0.07
28 48 0.21
29 35 0.15
30 60 0.26
31 39 0.17
32 20 0.09
33 4 0.02
ACGTcount: A:0.34, C:0.03, G:0.30, T:0.34
Consensus pattern (30 bp):
TTAAAAATGGAATTTTGGAAAGTTCGGAGG
Found at i:57548742 original size:3 final size:3
Alignment explanation
Indices: 57548734--57548775 Score: 84
Period size: 3 Copynumber: 14.0 Consensus size: 3
57548724 TAATGCTGTA
57548734 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
57548776 GTCATTAATG
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 39 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
ATT
Found at i:57549514 original size:11 final size:12
Alignment explanation
Indices: 57549491--57549524 Score: 52
Period size: 11 Copynumber: 2.8 Consensus size: 12
57549481 TTATTTGGAC
57549491 TTTTAATTTAAA
1 TTTTAATTTAAA
57549503 TTTTAA-TTAAA
1 TTTTAATTTAAA
57549514 TTTTAAATTTA
1 TTTT-AATTTA
57549525 TTTCAAATAT
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
11 9 0.45
12 8 0.40
13 3 0.15
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (12 bp):
TTTTAATTTAAA
Found at i:57549524 original size:17 final size:17
Alignment explanation
Indices: 57549497--57549564 Score: 57
Period size: 17 Copynumber: 3.7 Consensus size: 17
57549487 GGACTTTTAA
57549497 TTTAAATTTTAATTAAAT
1 TTTAAA-TTTAATTAAAT
*
57549515 TTTAAATTTATTTCAAATATT
1 TTTAAATTTAATT--AA-A-T
*
57549536 TTTAAATTTAAAATAAA-
1 TTTAAATTT-AATTAAAT
57549553 TTTAAATTTAAT
1 TTTAAATTTAAT
57549565 AATGAATTTA
Statistics
Matches: 41, Mismatches: 4, Indels: 12
0.72 0.07 0.21
Matches are distributed among these distances:
16 2 0.05
17 15 0.37
18 6 0.15
19 3 0.07
20 3 0.07
21 10 0.24
22 2 0.05
ACGTcount: A:0.46, C:0.01, G:0.00, T:0.53
Consensus pattern (17 bp):
TTTAAATTTAATTAAAT
Found at i:57549574 original size:18 final size:17
Alignment explanation
Indices: 57549495--57549576 Score: 65
Period size: 18 Copynumber: 4.5 Consensus size: 17
57549485 TTGGACTTTT
* *
57549495 AATTTAAATTTTAATTA
1 AATTTAAATTTAAAATA
57549512 AATTTTAAATTTATTTCAAATA
1 AA-TTTAAATTTA----AAATA
**
57549534 TTTTTAAATTTAAAATA
1 AATTTAAATTTAAAATA
*
57549551 AATTTAAATTTAATAATG
1 AATTTAAATTTAA-AATA
57549569 AATTTAAA
1 AATTTAAA
57549577 CCTAAAGATC
Statistics
Matches: 52, Mismatches: 7, Indels: 11
0.74 0.10 0.16
Matches are distributed among these distances:
17 18 0.35
18 20 0.38
21 10 0.19
22 4 0.08
ACGTcount: A:0.49, C:0.01, G:0.01, T:0.49
Consensus pattern (17 bp):
AATTTAAATTTAAAATA
Found at i:57564510 original size:31 final size:29
Alignment explanation
Indices: 57564441--57564514 Score: 80
Period size: 29 Copynumber: 2.5 Consensus size: 29
57564431 ACAAAATACT
*
57564441 AACATAAGTGACTAAAACGTAACATTACA
1 AACAAAAGTGACTAAAACGTAACATTACA
*
57564470 AA-AATAAGTGACTAAAATGTAAC-TTGAGACA
1 AACAA-AAGTGACTAAAACGTAACATT---ACA
57564501 AACAAAAGTGACTA
1 AACAAAAGTGACTA
57564515 TTTTTATAGT
Statistics
Matches: 38, Mismatches: 2, Indels: 8
0.79 0.04 0.17
Matches are distributed among these distances:
28 3 0.08
29 19 0.50
31 14 0.37
32 2 0.05
ACGTcount: A:0.53, C:0.14, G:0.14, T:0.20
Consensus pattern (29 bp):
AACAAAAGTGACTAAAACGTAACATTACA
Found at i:57567948 original size:15 final size:14
Alignment explanation
Indices: 57567925--57567970 Score: 56
Period size: 15 Copynumber: 3.1 Consensus size: 14
57567915 TTTTTATAGG
57567925 ATAATATAATATTAAA
1 ATAA-ATAA-ATTAAA
57567941 ATAAATAAATTAAA
1 ATAAATAAATTAAA
*
57567955 ATTGAATAAATTAAA
1 A-TAAATAAATTAAA
57567970 A
1 A
57567971 ATATTTTCCA
Statistics
Matches: 28, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
14 7 0.25
15 17 0.61
16 4 0.14
ACGTcount: A:0.65, C:0.00, G:0.02, T:0.33
Consensus pattern (14 bp):
ATAAATAAATTAAA
Found at i:57568744 original size:3 final size:3
Alignment explanation
Indices: 57568736--57568765 Score: 60
Period size: 3 Copynumber: 10.0 Consensus size: 3
57568726 TTGCTTAGAG
57568736 GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA
1 GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA
57568766 TCCTTGAGAG
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 27 1.00
ACGTcount: A:0.67, C:0.00, G:0.33, T:0.00
Consensus pattern (3 bp):
GAA
Found at i:57569195 original size:30 final size:30
Alignment explanation
Indices: 57569153--57569220 Score: 86
Period size: 30 Copynumber: 2.3 Consensus size: 30
57569143 AAAATTTTAA
*
57569153 TTAATAAA-GATAAAATTAT-ATTTTGATCTT
1 TTAA-AAATGATAAAATTATAATTTAG-TCTT
*
57569183 TTAAAAATGATAAAATTTTAATTTAGTCTT
1 TTAAAAATGATAAAATTATAATTTAGTCTT
57569213 TTAAAAAT
1 TTAAAAAT
57569221 TGTACTTTTA
Statistics
Matches: 34, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
29 3 0.09
30 26 0.76
31 5 0.15
ACGTcount: A:0.46, C:0.03, G:0.06, T:0.46
Consensus pattern (30 bp):
TTAAAAATGATAAAATTATAATTTAGTCTT
Found at i:57569967 original size:25 final size:25
Alignment explanation
Indices: 57569913--57569960 Score: 78
Period size: 25 Copynumber: 1.9 Consensus size: 25
57569903 TAACGCATAA
57569913 ATTATATCCATAACATTACAAATAT
1 ATTATATCCATAACATTACAAATAT
* *
57569938 ATTATATTCATAATATTACAAAT
1 ATTATATCCATAACATTACAAAT
57569961 TAGTTATTGT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
25 21 1.00
ACGTcount: A:0.48, C:0.12, G:0.00, T:0.40
Consensus pattern (25 bp):
ATTATATCCATAACATTACAAATAT
Found at i:57570061 original size:17 final size:18
Alignment explanation
Indices: 57570018--57570066 Score: 66
Period size: 18 Copynumber: 2.8 Consensus size: 18
57570008 GTTTCATCAG
57570018 CAATTTTAAATAATATAT
1 CAATTTTAAATAATATAT
*
57570036 CAATATTAACATAATA-A-
1 CAATTTTAA-ATAATATAT
57570053 CAATTTTAAATAAT
1 CAATTTTAAATAAT
57570067 TCATGCATCG
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
16 5 0.18
17 8 0.29
18 9 0.32
19 6 0.21
ACGTcount: A:0.53, C:0.08, G:0.00, T:0.39
Consensus pattern (18 bp):
CAATTTTAAATAATATAT
Found at i:57579618 original size:22 final size:23
Alignment explanation
Indices: 57579586--57579645 Score: 61
Period size: 25 Copynumber: 2.5 Consensus size: 23
57579576 TTAATATGTT
57579586 AAAAACATTAATAA-AAAAT-ATAA
1 AAAAAC-TTAA-AACAAAATAATAA
57579609 AAAAACTTAAAACAAAATGAAATAA
1 AAAAACTTAAAACAAAAT--AATAA
57579634 AAAAACTATAAA
1 AAAAACT-TAAA
57579646 TGTGGGTGGG
Statistics
Matches: 32, Mismatches: 0, Indels: 7
0.82 0.00 0.18
Matches are distributed among these distances:
21 2 0.06
22 9 0.28
23 6 0.19
25 11 0.34
26 4 0.12
ACGTcount: A:0.73, C:0.07, G:0.02, T:0.18
Consensus pattern (23 bp):
AAAAACTTAAAACAAAATAATAA
Found at i:57579841 original size:29 final size:30
Alignment explanation
Indices: 57579809--57579868 Score: 88
Period size: 29 Copynumber: 2.0 Consensus size: 30
57579799 CTTATTTTCT
57579809 TAATTAATT-TTAAAAAT-GACCTAAAAACC
1 TAATTAATTATT-AAAATCGACCTAAAAACC
*
57579838 TAATTAATTATTAAAATCGGCCTAAAAACC
1 TAATTAATTATTAAAATCGACCTAAAAACC
57579868 T
1 T
57579869 TTTTTAACCG
Statistics
Matches: 28, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
29 14 0.50
30 14 0.50
ACGTcount: A:0.48, C:0.15, G:0.05, T:0.32
Consensus pattern (30 bp):
TAATTAATTATTAAAATCGACCTAAAAACC
Found at i:57583779 original size:17 final size:18
Alignment explanation
Indices: 57583757--57583793 Score: 51
Period size: 17 Copynumber: 2.1 Consensus size: 18
57583747 ATCGAAAAAT
57583757 ATAAATT-TATTATTT-TA
1 ATAAATTATA-TATTTATA
57583774 ATAAATTATATATTTATA
1 ATAAATTATATATTTATA
57583792 AT
1 AT
57583794 TTTAAAAGAA
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
17 12 0.67
18 6 0.33
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (18 bp):
ATAAATTATATATTTATA
Found at i:57586742 original size:16 final size:16
Alignment explanation
Indices: 57586723--57586756 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
57586713 CATCTCTCTA
57586723 TTTCTTCTCCTTTTCT
1 TTTCTTCTCCTTTTCT
* *
57586739 TTTCTTTTTCTTTTCT
1 TTTCTTCTCCTTTTCT
57586755 TT
1 TT
57586757 ACACCAAAAT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.00, C:0.24, G:0.00, T:0.76
Consensus pattern (16 bp):
TTTCTTCTCCTTTTCT
Found at i:57586751 original size:11 final size:11
Alignment explanation
Indices: 57586723--57586756 Score: 50
Period size: 11 Copynumber: 3.1 Consensus size: 11
57586713 CATCTCTCTA
* *
57586723 TTTCTTCTCCT
1 TTTCTTTTCTT
57586734 TTTCTTTTCTT
1 TTTCTTTTCTT
57586745 TTTCTTTTCTT
1 TTTCTTTTCTT
57586756 T
1 T
57586757 ACACCAAAAT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
11 21 1.00
ACGTcount: A:0.00, C:0.24, G:0.00, T:0.76
Consensus pattern (11 bp):
TTTCTTTTCTT
Found at i:57590007 original size:25 final size:24
Alignment explanation
Indices: 57589978--57590032 Score: 58
Period size: 25 Copynumber: 2.2 Consensus size: 24
57589968 TTATGTTTAC
*
57589978 TAAATTAAATTAATTCGA-AAAAAA
1 TAAATTAAAGTAATTC-ACAAAAAA
* *
57590002 TTAAATGAAAGTATTTCACAAAAAA
1 -TAAATTAAAGTAATTCACAAAAAA
57590027 TAAATT
1 TAAATT
57590033 TCAAATAAAA
Statistics
Matches: 25, Mismatches: 4, Indels: 3
0.78 0.12 0.09
Matches are distributed among these distances:
24 6 0.24
25 19 0.76
ACGTcount: A:0.58, C:0.05, G:0.05, T:0.31
Consensus pattern (24 bp):
TAAATTAAAGTAATTCACAAAAAA
Found at i:57590475 original size:13 final size:13
Alignment explanation
Indices: 57590457--57590482 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
57590447 GCCCAAACAT
57590457 TCCAATCCCTGCA
1 TCCAATCCCTGCA
57590470 TCCAATCCCTGCA
1 TCCAATCCCTGCA
57590483 CTTTCAACTC
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.23, C:0.46, G:0.08, T:0.23
Consensus pattern (13 bp):
TCCAATCCCTGCA
Found at i:57594631 original size:9 final size:9
Alignment explanation
Indices: 57594617--57594761 Score: 73
Period size: 9 Copynumber: 15.6 Consensus size: 9
57594607 ACATGTAGTA
57594617 AAAAATTAT
1 AAAAATTAT
57594626 AAAAA-TA-
1 AAAAATTAT
57594633 AAAAA-TAGT
1 AAAAATTA-T
*
57594642 AAAAGTTAT
1 AAAAATTAT
57594651 AAAAATTATT
1 AAAAATTA-T
**
57594661 AAACTTTAAT
1 AAAAATT-AT
*
57594671 AAAAAATAT
1 AAAAATTAT
*
57594680 AATAAATATTT
1 AA-AAAT-TAT
**
57594691 AAATTTTATT
1 AAAAATTA-T
57594701 AAAAA-TAT
1 AAAAATTAT
* *
57594709 AAAATTTTT
1 AAAAATTAT
57594718 AAAAATATAT
1 AAAAAT-TAT
*
57594728 AAAAAATTGT
1 -AAAAATTAT
*
57594738 AATAATTTAT
1 AA-AAATTAT
*
57594748 AAAAATCAT
1 AAAAATTAT
57594757 AAAAA
1 AAAAA
57594762 AATATAAATG
Statistics
Matches: 101, Mismatches: 23, Indels: 24
0.68 0.16 0.16
Matches are distributed among these distances:
7 7 0.07
8 7 0.07
9 43 0.43
10 33 0.33
11 11 0.11
ACGTcount: A:0.62, C:0.01, G:0.02, T:0.34
Consensus pattern (9 bp):
AAAAATTAT
Found at i:57594654 original size:19 final size:20
Alignment explanation
Indices: 57594629--57594678 Score: 57
Period size: 19 Copynumber: 2.5 Consensus size: 20
57594619 AAATTATAAA
57594629 AATAAAAAATAGTAAAAGTT
1 AATAAAAAATAGTAAAAGTT
* * **
57594649 -ATAAAAATTATTAAACTTT
1 AATAAAAAATAGTAAAAGTT
57594668 AATAAAAAATA
1 AATAAAAAATA
57594679 TAATAAATAT
Statistics
Matches: 24, Mismatches: 5, Indels: 2
0.77 0.16 0.06
Matches are distributed among these distances:
19 15 0.62
20 9 0.38
ACGTcount: A:0.64, C:0.02, G:0.04, T:0.30
Consensus pattern (20 bp):
AATAAAAAATAGTAAAAGTT
Found at i:57594680 original size:29 final size:28
Alignment explanation
Indices: 57594648--57594734 Score: 79
Period size: 29 Copynumber: 3.0 Consensus size: 28
57594638 TAGTAAAAGT
57594648 TATAAAAATTATTAAACTTTAATAAAAAA
1 TATAAAAATTATTAAA-TTTAATAAAAAA
* *
57594677 TATAATAAA-TATTTAAATTTTATTAAAAA
1 TATAA-AAATTA-TTAAATTTAATAAAAAA
* **
57594706 TAT-AAAATTTTTAAAAATATATAAAAAA
1 TATAAAAATTATTAAATTTA-ATAAAAAA
57594734 T
1 T
57594735 TGTAATAATT
Statistics
Matches: 47, Mismatches: 7, Indels: 9
0.75 0.11 0.14
Matches are distributed among these distances:
27 9 0.19
28 10 0.21
29 20 0.43
30 8 0.17
ACGTcount: A:0.60, C:0.01, G:0.00, T:0.39
Consensus pattern (28 bp):
TATAAAAATTATTAAATTTAATAAAAAA
Found at i:57594727 original size:19 final size:19
Alignment explanation
Indices: 57594677--57594731 Score: 58
Period size: 19 Copynumber: 2.8 Consensus size: 19
57594667 TAATAAAAAA
* *
57594677 TATAATAAATATTTAAATTT
1 TATAAAAAATA-TAAAATTT
*
57594697 TATTAAAAATATAAAATTT
1 TATAAAAAATATAAAATTT
57594716 T-TAAAAATATATAAAA
1 TATAAAAA-ATATAAAA
57594732 AATTGTAATA
Statistics
Matches: 30, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
18 5 0.17
19 16 0.53
20 9 0.30
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (19 bp):
TATAAAAAATATAAAATTT
Found at i:57594732 original size:20 final size:20
Alignment explanation
Indices: 57594691--57594753 Score: 58
Period size: 20 Copynumber: 3.2 Consensus size: 20
57594681 ATAAATATTT
*
57594691 AAATTTTATTAAAA-ATAT-A
1 AAATTTT-TAAAAATATATAA
57594710 AAATTTTTAAAAATATATAA
1 AAATTTTTAAAAATATATAA
* * * *
57594730 AAAATTGTAATAATTTATAA
1 AAATTTTTAAAAATATATAA
57594750 AAAT
1 AAAT
57594754 CATAAAAAAA
Statistics
Matches: 36, Mismatches: 6, Indels: 3
0.80 0.13 0.07
Matches are distributed among these distances:
18 5 0.14
19 11 0.31
20 20 0.56
ACGTcount: A:0.59, C:0.00, G:0.02, T:0.40
Consensus pattern (20 bp):
AAATTTTTAAAAATATATAA
Found at i:57594753 original size:19 final size:19
Alignment explanation
Indices: 57594701--57594769 Score: 59
Period size: 19 Copynumber: 3.6 Consensus size: 19
57594691 AAATTTTATT
* *
57594701 AAAA-ATATAAAATTTTTA
1 AAAATATATAAAAATTGTA
57594719 AAAATATATAAAAAATTGTA
1 AAAATATAT-AAAAATTGTA
* * **
57594739 ATAATTTATAAAAATCATA
1 AAAATATATAAAAATTGTA
*
57594758 AAAAAATATAAA
1 AAAATATATAAA
57594770 TGCATCAAAA
Statistics
Matches: 40, Mismatches: 9, Indels: 3
0.77 0.17 0.06
Matches are distributed among these distances:
18 4 0.10
19 21 0.52
20 15 0.38
ACGTcount: A:0.65, C:0.01, G:0.01, T:0.32
Consensus pattern (19 bp):
AAAATATATAAAAATTGTA
Found at i:57594759 original size:48 final size:46
Alignment explanation
Indices: 57594626--57594760 Score: 132
Period size: 48 Copynumber: 2.8 Consensus size: 46
57594616 AAAAAATTAT
* * *
57594626 AAAA-ATAAAAAATAGTAAAAGTTATAAAAATTATTAAACTTTAATAA
1 AAAATATAAAAAATTGTAAAATTTATAAAAA-TA-TAAAATTTAATAA
* *
57594673 AAAATATAATAAATATT-TAAATTTTATTAAAAATATAAAATTT-TTAA
1 AAAATATAA-AAA-ATTGTAAAATTTA-TAAAAATATAAAATTTAATAA
57594720 AAATATATAAAAAATTGTAATAATTTATAAAAATCATAAAA
1 AAA-ATATAAAAAATTGTAA-AATTTATAAAAAT-ATAAAA
57594761 AAATATAAAT
Statistics
Matches: 74, Mismatches: 6, Indels: 15
0.78 0.06 0.16
Matches are distributed among these distances:
46 3 0.04
47 23 0.31
48 28 0.38
49 12 0.16
50 8 0.11
ACGTcount: A:0.61, C:0.01, G:0.02, T:0.35
Consensus pattern (46 bp):
AAAATATAAAAAATTGTAAAATTTATAAAAATATAAAATTTAATAA
Found at i:57595090 original size:26 final size:24
Alignment explanation
Indices: 57595055--57595106 Score: 68
Period size: 24 Copynumber: 2.1 Consensus size: 24
57595045 TATAATTTTT
57595055 TTATAATTTTCAATAAAATTTTAATA
1 TTATAATTTT-AATAAAA-TTTAATA
* *
57595081 TTATATTTTTATTAAAATTTAATA
1 TTATAATTTTAATAAAATTTAATA
57595105 TT
1 TT
57595107 TTTATAACTT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
24 9 0.38
25 6 0.25
26 9 0.38
ACGTcount: A:0.42, C:0.02, G:0.00, T:0.56
Consensus pattern (24 bp):
TTATAATTTTAATAAAATTTAATA
Found at i:57595757 original size:21 final size:21
Alignment explanation
Indices: 57595733--57595778 Score: 53
Period size: 20 Copynumber: 2.3 Consensus size: 21
57595723 AATTTAAAAA
57595733 ATATTTATTTT-ATTATATTTT
1 ATATTTATTTTAATTAT-TTTT
*
57595754 ATA-TAATTTTAATTATTTTT
1 ATATTTATTTTAATTATTTTT
57595774 A-ATTT
1 ATATTT
57595779 TTTAAAAATA
Statistics
Matches: 21, Mismatches: 2, Indels: 5
0.75 0.07 0.18
Matches are distributed among these distances:
19 1 0.05
20 12 0.57
21 8 0.38
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (21 bp):
ATATTTATTTTAATTATTTTT
Found at i:57596421 original size:23 final size:23
Alignment explanation
Indices: 57596395--57596444 Score: 66
Period size: 22 Copynumber: 2.2 Consensus size: 23
57596385 AAGGTAGAGG
* *
57596395 AAAAACGTGCTATAAA-GCAAAA
1 AAAAACATGCTACAAAGGCAAAA
*
57596417 AAAAACATGCTACAAAGGCAAAT
1 AAAAACATGCTACAAAGGCAAAA
57596440 AAAAA
1 AAAAA
57596445 TTAAAAAAAA
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
22 14 0.58
23 10 0.42
ACGTcount: A:0.62, C:0.14, G:0.12, T:0.12
Consensus pattern (23 bp):
AAAAACATGCTACAAAGGCAAAA
Found at i:57597801 original size:23 final size:23
Alignment explanation
Indices: 57597767--57597838 Score: 81
Period size: 23 Copynumber: 3.1 Consensus size: 23
57597757 TTTGCAGGGT
*
57597767 TTTTTTGTTGTTGATTTGGTGTTG
1 TTTTTTG-TGTTGTTTTGGTGTTG
** *
57597791 TTTTTTGTGTTGTTTTGGTACTA
1 TTTTTTGTGTTGTTTTGGTGTTG
* *
57597814 TTTTTTATGTTGTTTTGTTGTTG
1 TTTTTTGTGTTGTTTTGGTGTTG
57597837 TT
1 TT
57597839 CTGCAGCTGT
Statistics
Matches: 39, Mismatches: 9, Indels: 1
0.80 0.18 0.02
Matches are distributed among these distances:
23 32 0.82
24 7 0.18
ACGTcount: A:0.06, C:0.01, G:0.24, T:0.69
Consensus pattern (23 bp):
TTTTTTGTGTTGTTTTGGTGTTG
Found at i:57597802 original size:12 final size:12
Alignment explanation
Indices: 57597765--57597806 Score: 50
Period size: 12 Copynumber: 3.4 Consensus size: 12
57597755 ATTTTGCAGG
57597765 GTTTTTT-TGTT
1 GTTTTTTGTGTT
*
57597776 GTTGATTTGGTGTT
1 GTT--TTTTGTGTT
57597790 GTTTTTTGTGTT
1 GTTTTTTGTGTT
57597802 GTTTT
1 GTTTT
57597807 GGTACTATTT
Statistics
Matches: 26, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
11 3 0.12
12 13 0.50
13 3 0.12
14 7 0.27
ACGTcount: A:0.02, C:0.00, G:0.26, T:0.71
Consensus pattern (12 bp):
GTTTTTTGTGTT
Found at i:57597827 original size:26 final size:23
Alignment explanation
Indices: 57597766--57597827 Score: 63
Period size: 24 Copynumber: 2.6 Consensus size: 23
57597756 TTTTGCAGGG
*
57597766 TTTTTTTGTTGTTGATTTGGTGT
1 TTTTTTTGTTGTTGATTTGGTCT
*
57597789 TGTTTTTTG-TGTTGTTTTGGTACT
1 T-TTTTTTGTTGTTGATTTGGT-CT
57597813 ATTTTTTATGTTGTT
1 -TTTTTT-TGTTGTT
57597828 TTGTTGTTGT
Statistics
Matches: 32, Mismatches: 2, Indels: 7
0.78 0.05 0.17
Matches are distributed among these distances:
23 12 0.38
24 13 0.41
25 3 0.09
26 4 0.12
ACGTcount: A:0.06, C:0.02, G:0.23, T:0.69
Consensus pattern (23 bp):
TTTTTTTGTTGTTGATTTGGTCT
Found at i:57597890 original size:23 final size:23
Alignment explanation
Indices: 57597864--57597908 Score: 72
Period size: 23 Copynumber: 2.0 Consensus size: 23
57597854 ATGTTGTTTC
57597864 GCTTCCATTTTTAATATTATTTA
1 GCTTCCATTTTTAATATTATTTA
**
57597887 GCTTTTATTTTTAATATTATTT
1 GCTTCCATTTTTAATATTATTT
57597909 GGATATTATA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
23 20 1.00
ACGTcount: A:0.24, C:0.09, G:0.04, T:0.62
Consensus pattern (23 bp):
GCTTCCATTTTTAATATTATTTA
Found at i:57597917 original size:23 final size:23
Alignment explanation
Indices: 57597870--57597917 Score: 69
Period size: 23 Copynumber: 2.1 Consensus size: 23
57597860 TTTCGCTTCC
* *
57597870 ATTTTTAATATTATTTAGCTTTT
1 ATTTTTAATATTATTTAGATATT
*
57597893 ATTTTTAATATTATTTGGATATT
1 ATTTTTAATATTATTTAGATATT
57597916 AT
1 AT
57597918 AAAATTTTTA
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
23 22 1.00
ACGTcount: A:0.29, C:0.02, G:0.06, T:0.62
Consensus pattern (23 bp):
ATTTTTAATATTATTTAGATATT
Found at i:57598402 original size:26 final size:26
Alignment explanation
Indices: 57598338--57598423 Score: 79
Period size: 24 Copynumber: 3.2 Consensus size: 26
57598328 AAAAATTGAT
* *
57598338 AAAAAAAATTTGTGCCCTTAAAAATTA
1 AAAAAAAATTT-TGACCTTAAAAAGTA
57598365 AAAAAAAA--TTGACCTGT-AAAAGTA
1 AAAAAAAATTTTGACCT-TAAAAAGTA
*
57598389 AAAAAAAATTTTGAGCCTCTTAAAAATTA
1 AAAAAAAATTTTGA--C-CTTAAAAAGTA
57598418 AAAAAA
1 AAAAAA
57598424 TAAAAATTTG
Statistics
Matches: 49, Mismatches: 3, Indels: 12
0.77 0.05 0.19
Matches are distributed among these distances:
24 19 0.39
25 2 0.04
26 4 0.08
27 8 0.16
28 2 0.04
29 14 0.29
ACGTcount: A:0.57, C:0.09, G:0.08, T:0.26
Consensus pattern (26 bp):
AAAAAAAATTTTGACCTTAAAAAGTA
Found at i:57598419 original size:29 final size:28
Alignment explanation
Indices: 57598307--57598423 Score: 118
Period size: 29 Copynumber: 4.2 Consensus size: 28
57598297 GAAGTTGGAG
* *
57598307 AAAAAAAATTTTAGGTCTCTTAAAAATTGA
1 AAAAAAAATTTGA-GCCTCTTAAAAATT-A
*
57598337 TAAAAAAAATTTGTGCC-CTTAAAAATTA
1 -AAAAAAAATTTGAGCCTCTTAAAAATTA
* *
57598365 AAAAAAAA-TTGA-CCT-GT-AAAAGTA
1 AAAAAAAATTTGAGCCTCTTAAAAATTA
57598389 AAAAAAAATTTTGAGCCTCTTAAAAATTA
1 AAAAAAAA-TTTGAGCCTCTTAAAAATTA
57598418 AAAAAA
1 AAAAAA
57598424 TAAAAATTTG
Statistics
Matches: 72, Mismatches: 8, Indels: 14
0.77 0.09 0.15
Matches are distributed among these distances:
24 14 0.19
25 3 0.04
26 7 0.10
27 11 0.15
28 2 0.03
29 22 0.31
30 2 0.03
31 11 0.15
ACGTcount: A:0.55, C:0.09, G:0.09, T:0.28
Consensus pattern (28 bp):
AAAAAAAATTTGAGCCTCTTAAAAATTA
Found at i:57599413 original size:39 final size:39
Alignment explanation
Indices: 57599370--57599457 Score: 115
Period size: 39 Copynumber: 2.3 Consensus size: 39
57599360 TAAAAAGTAT
** * *
57599370 TTATATTAAAAAACTAC-CATAAATATAATAAATGTTTTA
1 TTATATTAAAAAAAGACAAATAAATACAATAAAT-TTTTA
57599409 TTATATTAAAAAAAGACAAATAAATACAATAAATTTTTA
1 TTATATTAAAAAAAGACAAATAAATACAATAAATTTTTA
*
57599448 TTGTATTAAA
1 TTATATTAAA
57599458 TATAAATTTT
Statistics
Matches: 43, Mismatches: 5, Indels: 2
0.86 0.10 0.04
Matches are distributed among these distances:
39 29 0.67
40 14 0.33
ACGTcount: A:0.53, C:0.06, G:0.03, T:0.38
Consensus pattern (39 bp):
TTATATTAAAAAAAGACAAATAAATACAATAAATTTTTA
Found at i:57599554 original size:17 final size:18
Alignment explanation
Indices: 57599518--57599560 Score: 52
Period size: 17 Copynumber: 2.4 Consensus size: 18
57599508 TGAGCAATGA
* *
57599518 ATTTAATTGTTGTGAGAT
1 ATTTAATTGTTATGACAT
57599536 ATTT-ATTGTTATGACAT
1 ATTTAATTGTTATGACAT
*
57599553 ATATAATT
1 ATTTAATT
57599561 AATATAATAT
Statistics
Matches: 21, Mismatches: 3, Indels: 2
0.81 0.12 0.08
Matches are distributed among these distances:
17 14 0.67
18 7 0.33
ACGTcount: A:0.33, C:0.02, G:0.14, T:0.51
Consensus pattern (18 bp):
ATTTAATTGTTATGACAT
Found at i:57600846 original size:59 final size:59
Alignment explanation
Indices: 57600780--57600898 Score: 238
Period size: 59 Copynumber: 2.0 Consensus size: 59
57600770 CTTTCGACTT
57600780 TATTTTCACCCTTTCATTCCTTTCACGAAAAAATATAGTGAAAAAGAAATCTAAAACTC
1 TATTTTCACCCTTTCATTCCTTTCACGAAAAAATATAGTGAAAAAGAAATCTAAAACTC
57600839 TATTTTCACCCTTTCATTCCTTTCACGAAAAAATATAGTGAAAAAGAAATCTAAAACTC
1 TATTTTCACCCTTTCATTCCTTTCACGAAAAAATATAGTGAAAAAGAAATCTAAAACTC
57600898 T
1 T
57600899 GCTTCACCTT
Statistics
Matches: 60, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
59 60 1.00
ACGTcount: A:0.40, C:0.20, G:0.07, T:0.33
Consensus pattern (59 bp):
TATTTTCACCCTTTCATTCCTTTCACGAAAAAATATAGTGAAAAAGAAATCTAAAACTC
Found at i:57601850 original size:28 final size:28
Alignment explanation
Indices: 57601791--57601853 Score: 74
Period size: 28 Copynumber: 2.2 Consensus size: 28
57601781 ATTTTTTTCT
***
57601791 TTTTCTTATTCTCAAATTTCAATTCTTGA
1 TTTT-TTATTCTCAAATTTCAATTCCCAA
57601820 TTTTTTATTCT-AAATTCTCAATTCCCAA
1 TTTTTTATTCTCAAATT-TCAATTCCCAA
57601848 TTTTTT
1 TTTTTT
57601854 TTAAAAAAAA
Statistics
Matches: 30, Mismatches: 3, Indels: 3
0.83 0.08 0.08
Matches are distributed among these distances:
27 5 0.17
28 21 0.70
29 4 0.13
ACGTcount: A:0.24, C:0.17, G:0.02, T:0.57
Consensus pattern (28 bp):
TTTTTTATTCTCAAATTTCAATTCCCAA
Found at i:57602550 original size:6 final size:6
Alignment explanation
Indices: 57602532--57602589 Score: 77
Period size: 6 Copynumber: 10.2 Consensus size: 6
57602522 TTAAATTGAT
*
57602532 TTTAAA TTT--A TTTAAA TTTAAA TTT-AC TTTAAA TTTAAA TTTAAA
1 TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA
*
57602577 TTTAAA TTAAAA T
1 TTTAAA TTTAAA T
57602590 ACTAAACATT
Statistics
Matches: 46, Mismatches: 3, Indels: 6
0.84 0.05 0.11
Matches are distributed among these distances:
4 4 0.09
5 4 0.09
6 38 0.83
ACGTcount: A:0.47, C:0.02, G:0.00, T:0.52
Consensus pattern (6 bp):
TTTAAA
Found at i:57602556 original size:23 final size:23
Alignment explanation
Indices: 57602541--57602587 Score: 76
Period size: 23 Copynumber: 2.0 Consensus size: 23
57602531 TTTTAAATTT
*
57602541 ATTTAAATTTAAATTTACTTTAA
1 ATTTAAATTTAAATTTAATTTAA
*
57602564 ATTTAAATTTAAATTTAAATTAA
1 ATTTAAATTTAAATTTAATTTAA
57602587 A
1 A
57602588 ATACTAAACA
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
23 22 1.00
ACGTcount: A:0.49, C:0.02, G:0.00, T:0.49
Consensus pattern (23 bp):
ATTTAAATTTAAATTTAATTTAA
Found at i:57602562 original size:11 final size:11
Alignment explanation
Indices: 57602522--57602584 Score: 58
Period size: 12 Copynumber: 5.6 Consensus size: 11
57602512 TAATTTGGAG
* *
57602522 TTAAATTGATT
1 TTAAATTTAAT
57602533 TTAAATTT-AT
1 TTAAATTTAAT
57602543 TTAAATTTAAAT
1 TTAAATTT-AAT
*
57602555 TT-ACTTTAAAT
1 TTAAATTT-AAT
57602566 TTAAATTTAAAT
1 TTAAATTT-AAT
57602578 TTAAATT
1 TTAAATT
57602585 AAAATACTAA
Statistics
Matches: 45, Mismatches: 4, Indels: 5
0.83 0.07 0.09
Matches are distributed among these distances:
10 9 0.20
11 17 0.38
12 19 0.42
ACGTcount: A:0.43, C:0.02, G:0.02, T:0.54
Consensus pattern (11 bp):
TTAAATTTAAT
Found at i:57602562 original size:17 final size:16
Alignment explanation
Indices: 57602532--57602589 Score: 80
Period size: 17 Copynumber: 3.4 Consensus size: 16
57602522 TTAAATTGAT
57602532 TTTAAATTTATTTAAA
1 TTTAAATTTATTTAAA
57602548 TTTAAATTTACTTTAAA
1 TTTAAATTTA-TTTAAA
57602565 TTTAAATTTAAATTTAAA
1 TTTAAATTT--ATTTAAA
*
57602583 TTAAAAT
1 TTTAAAT
57602590 ACTAAACATT
Statistics
Matches: 38, Mismatches: 1, Indels: 4
0.88 0.02 0.09
Matches are distributed among these distances:
16 10 0.26
17 15 0.39
18 12 0.32
19 1 0.03
ACGTcount: A:0.47, C:0.02, G:0.00, T:0.52
Consensus pattern (16 bp):
TTTAAATTTATTTAAA
Found at i:57602586 original size:11 final size:11
Alignment explanation
Indices: 57602522--57602587 Score: 62
Period size: 11 Copynumber: 5.9 Consensus size: 11
57602512 TAATTTGGAG
* *
57602522 TTAAATTGATT
1 TTAAATTAAAT
*
57602533 TTAAATT-TAT
1 TTAAATTAAAT
57602543 TTAAATTTAAAT
1 TTAAA-TTAAAT
**
57602555 TTACTTTAAAT
1 TTAAATTAAAT
57602566 TTAAATTTAAAT
1 TTAAA-TTAAAT
57602578 TTAAATTAAA
1 TTAAATTAAA
57602588 ATACTAAACA
Statistics
Matches: 45, Mismatches: 7, Indels: 6
0.78 0.12 0.10
Matches are distributed among these distances:
10 6 0.13
11 23 0.51
12 16 0.36
ACGTcount: A:0.45, C:0.02, G:0.02, T:0.52
Consensus pattern (11 bp):
TTAAATTAAAT
Found at i:57604619 original size:120 final size:120
Alignment explanation
Indices: 57604479--57604844 Score: 560
Period size: 120 Copynumber: 3.1 Consensus size: 120
57604469 AAATTATCCG
* * *
57604479 AAAATTACATTTCGAACCTAAGACTTTTTGAAAATTATATTTTGACCCCAAAAATTTCTAAAAAT
1 AAAATTACATTTCGACCCTAAAACTTTTTAAAAATTATATTTTGACCCCAAAAATTTCTAAAAAT
* *
57604544 TACATTTTGACCCCTAAACTTTTTCAAAATTATTTTTTGACCCCAAAACTTTTCC
66 TACATTTTGACCCCTAAACTTTTCCAAAATTATATTTTGACCCCAAAACTTTTCC
* ** * *
57604599 AAAATTACATTTTGACCCTAAAACTTTTTAAAAATTATATTTTGACCTTAAAACTTTCTGAAAAT
1 AAAATTACATTTCGACCCTAAAACTTTTTAAAAATTATATTTTGACCCCAAAAATTTCTAAAAAT
*
57604664 TACATTTTGACTCCTAAACTTTTCCAAAATTATATTTTGACCCCAAAACTTTTCC
66 TACATTTTGACCCCTAAACTTTTCCAAAATTATATTTTGACCCCAAAACTTTTCC
*
57604719 AAAATTACATTTCGACCC-AAAACTTTCTAAAAAATTATATTTTGA-CCCAAAAACTTTCTAAAA
1 AAAATTACATTTCGACCCTAAAACTTT-TTAAAAATTATATTTTGACCCCAAAAA-TTTCTAAAA
*
57604782 ATTACATTTTGACCCCAAAAC-TTTCCTAAAATTATATTTTGA-CCCAAAACTTTTCC
64 ATTACATTTTGACCCCTAAACTTTTCC-AAAATTATATTTTGACCCCAAAACTTTTCC
57604838 AAAATTA
1 AAAATTA
57604845 TACTTTAACC
Statistics
Matches: 224, Mismatches: 19, Indels: 7
0.90 0.08 0.03
Matches are distributed among these distances:
119 39 0.17
120 185 0.83
ACGTcount: A:0.39, C:0.20, G:0.04, T:0.37
Consensus pattern (120 bp):
AAAATTACATTTCGACCCTAAAACTTTTTAAAAATTATATTTTGACCCCAAAAATTTCTAAAAAT
TACATTTTGACCCCTAAACTTTTCCAAAATTATATTTTGACCCCAAAACTTTTCC
Found at i:57604889 original size:30 final size:30
Alignment explanation
Indices: 57604509--57604873 Score: 402
Period size: 30 Copynumber: 12.2 Consensus size: 30
57604499 AGACTTTTTG
*
57604509 AAAATTATATTTTGACCCCAAAA-ATTTCTA
1 AAAATTATATTTTGACCCCAAAACTTTTC-A
* *
57604539 AAAATTACATTTTGACCCCTAAACTTTTTC-
1 AAAATTATATTTTGACCCCAAAAC-TTTTCA
* *
57604569 AAAATTATTTTTTGACCCCAAAACTTTTCC
1 AAAATTATATTTTGACCCCAAAACTTTTCA
* * *
57604599 AAAATTACATTTTGACCCTAAAACTTTTTA
1 AAAATTATATTTTGACCCCAAAACTTTTCA
** *
57604629 AAAATTATATTTTGACCTTAAAAC-TTTCTG
1 AAAATTATATTTTGACCCCAAAACTTTTC-A
* * * *
57604659 AAAATTACATTTTGACTCCTAAACTTTTCC
1 AAAATTATATTTTGACCCCAAAACTTTTCA
*
57604689 AAAATTATATTTTGACCCCAAAACTTTTCC
1 AAAATTATATTTTGACCCCAAAACTTTTCA
* * *
57604719 AAAATTACATTTCGA-CCCAAAACTTTCTAA
1 AAAATTATATTTTGACCCCAAAACTTT-TCA
*
57604749 AAAATTATATTTTGACCCAAAAAC-TTTCTA
1 AAAATTATATTTTGACCCCAAAACTTTTC-A
* * *
57604779 AAAATTACATTTTGACCCCAAAACTTTCCT
1 AAAATTATATTTTGACCCCAAAACTTTTCA
*
57604809 AAAATTATATTTTGA-CCCAAAACTTTTCC
1 AAAATTATATTTTGACCCCAAAACTTTTCA
* *
57604838 AAAATTATACTTTAACCCCAAAAC-TTTCA
1 AAAATTATATTTTGACCCCAAAACTTTTCA
57604867 AAAATTA
1 AAAATTA
57604874 CCATTTTACT
Statistics
Matches: 283, Mismatches: 42, Indels: 21
0.82 0.12 0.06
Matches are distributed among these distances:
29 56 0.20
30 209 0.74
31 14 0.05
32 4 0.01
ACGTcount: A:0.39, C:0.21, G:0.03, T:0.37
Consensus pattern (30 bp):
AAAATTATATTTTGACCCCAAAACTTTTCA
Found at i:57604928 original size:59 final size:56
Alignment explanation
Indices: 57604865--57605058 Score: 149
Period size: 59 Copynumber: 3.3 Consensus size: 56
57604855 CCAAAACTTT
57604865 CAAAAATTACCATTTTACTCCCAAACTTCCCTAAATCTCATTTTTAACCCCGATTTCAC
1 CAAAAATTACCATTTTACTCCCAAACTT-CC-AAAT-TCATTTTTAACCCCGATTTCAC
* * * * * * ** * **
57604924 CAAAACTTATCGTTTTGC-CTCCGAACTTCCAAAATTTCATTTTTGACCTTGTTTTTGC
1 CAAAAATTACCATTTTACTC-CCAAACTTCC-AAA-TTCATTTTTAACCCCGATTTCAC
* * * *
57604982 CAAAATTTACCATTTTATTCCCTAAACTTTTCAAATTCCATTTTCAACCCCGATTTTCA-
1 CAAAAATTACCATTTTACTCCC-AAAC-TTCCAAATT-CATTTTTAACCCCGA-TTTCAC
57605041 CAAAAATTACCATTTTAC
1 CAAAAATTACCATTTTAC
57605059 CCCTAAAAAC
Statistics
Matches: 100, Mismatches: 28, Indels: 14
0.70 0.20 0.10
Matches are distributed among these distances:
58 39 0.39
59 55 0.55
60 6 0.06
ACGTcount: A:0.30, C:0.27, G:0.04, T:0.39
Consensus pattern (56 bp):
CAAAAATTACCATTTTACTCCCAAACTTCCAAATTCATTTTTAACCCCGATTTCAC
Found at i:57605082 original size:117 final size:117
Alignment explanation
Indices: 57604865--57605083 Score: 248
Period size: 117 Copynumber: 1.9 Consensus size: 117
57604855 CCAAAACTTT
* *
57604865 CAAAAATTACCATTTTACTCCCAAACTTCCCTAAATCTCATTTTTAACCCCGATTTCACCAAAAC
1 CAAAAATTACCATTTTACTCCCAAACTTCCCTAAATCTCATTTTCAACCCCGATTTCACCAAAAA
* * * *** *
57604930 TTATCGTTTTGCCTCCGAACTTCCAAAATTTCATTTTTGACCTTGTTTTTGC
66 TTACCATTTTACCTCCGAAAAACCAAAATTCCATTTTTGACCTTGTTTTTGC
* * **
57604982 CAAAATTTACCATTTTATTCCCTAAACTTTTC-AAAT-TCCATTTTCAACCCCGATTTTCA-CAA
1 CAAAAATTACCATTTTACTCCC-AAACTTCCCTAAATCT-CATTTTCAACCCCGA-TTTCACCAA
*
57605044 AAATTACCATTTTACC-CCTAAAAACCAAAATTACCATTTT
63 AAATTACCATTTTACCTCCGAAAAACCAAAATT-CCATTTT
57605084 GCCACCGGGT
Statistics
Matches: 84, Mismatches: 14, Indels: 8
0.79 0.13 0.08
Matches are distributed among these distances:
116 13 0.15
117 59 0.70
118 12 0.14
ACGTcount: A:0.32, C:0.27, G:0.04, T:0.37
Consensus pattern (117 bp):
CAAAAATTACCATTTTACTCCCAAACTTCCCTAAATCTCATTTTCAACCCCGATTTCACCAAAAA
TTACCATTTTACCTCCGAAAAACCAAAATTCCATTTTTGACCTTGTTTTTGC
Found at i:57614104 original size:28 final size:29
Alignment explanation
Indices: 57614026--57614105 Score: 92
Period size: 28 Copynumber: 2.8 Consensus size: 29
57614016 GAAATGAACG
*
57614026 CCTTCGTGGCAAATCATGAGAAA-GGATAA
1 CCTTCGTGGCAAATTATGA-AAAGGGATAA
* * * *
57614055 CCTTCTTGGCAAGTTCTTAAAAGGGA-AA
1 CCTTCGTGGCAAATTATGAAAAGGGATAA
57614083 CCTTCGTGGCAAATTATGAAAAG
1 CCTTCGTGGCAAATTATGAAAAG
57614106 AATTGTTTTG
Statistics
Matches: 41, Mismatches: 9, Indels: 3
0.77 0.17 0.06
Matches are distributed among these distances:
28 24 0.59
29 17 0.41
ACGTcount: A:0.35, C:0.17, G:0.23, T:0.25
Consensus pattern (29 bp):
CCTTCGTGGCAAATTATGAAAAGGGATAA
Found at i:57619347 original size:20 final size:18
Alignment explanation
Indices: 57619315--57619372 Score: 62
Period size: 18 Copynumber: 3.1 Consensus size: 18
57619305 TTTAAAATTA
*
57619315 ATAAAATTATAAAAAAAT
1 ATAAAAATATAAAAAAAT
**
57619333 ATAAAAACTATTAAAAATTT
1 ATAAAAA-TA-TAAAAAAAT
*
57619353 ATAAAAATATAGAAAAAT
1 ATAAAAATATAAAAAAAT
57619371 AT
1 AT
57619373 TTAAATTTTA
Statistics
Matches: 32, Mismatches: 6, Indels: 4
0.76 0.14 0.10
Matches are distributed among these distances:
18 14 0.44
19 4 0.12
20 14 0.44
ACGTcount: A:0.67, C:0.02, G:0.02, T:0.29
Consensus pattern (18 bp):
ATAAAAATATAAAAAAAT
Found at i:57619350 original size:38 final size:36
Alignment explanation
Indices: 57619289--57619372 Score: 105
Period size: 38 Copynumber: 2.2 Consensus size: 36
57619279 GATACATGAT
* *
57619289 AAAAAATGATAAAAATTTTAAAATTAATAAAATTATA
1 AAAAAAT-ATAAAAATTTAAAAATTAATAAAAATATA
*
57619326 AAAAAATATAAAAACTATTAAAAATTTATAAAAATATA
1 AAAAAATATAAAAA-T-TTAAAAATTAATAAAAATATA
*
57619364 GAAAAATAT
1 AAAAAATAT
57619373 TTAAATTTTA
Statistics
Matches: 41, Mismatches: 4, Indels: 3
0.85 0.08 0.06
Matches are distributed among these distances:
36 7 0.17
37 8 0.20
38 26 0.63
ACGTcount: A:0.67, C:0.01, G:0.02, T:0.30
Consensus pattern (36 bp):
AAAAAATATAAAAATTTAAAAATTAATAAAAATATA
Found at i:57619396 original size:30 final size:30
Alignment explanation
Indices: 57619311--57619399 Score: 90
Period size: 30 Copynumber: 2.9 Consensus size: 30
57619301 AAATTTTAAA
* * *
57619311 ATTAATAAAATTATAAAAAAATATAAAAACT
1 ATTAA-AAATTTATAAAAATATAGAAAAACT
57619342 ATTAAAAATTTATAAAAATATAGAAAAA-T
1 ATTAAAAATTTATAAAAATATAGAAAAACT
* * * *
57619371 ATTTAAATTTTATTAAAATTTTAGAAAAA
1 ATTAAAAATTTA-TAAAAATATAGAAAAA
57619400 AAAAACCATA
Statistics
Matches: 50, Mismatches: 7, Indels: 3
0.83 0.12 0.05
Matches are distributed among these distances:
29 11 0.22
30 34 0.68
31 5 0.10
ACGTcount: A:0.62, C:0.01, G:0.02, T:0.35
Consensus pattern (30 bp):
ATTAAAAATTTATAAAAATATAGAAAAACT
Found at i:57624286 original size:6 final size:6
Alignment explanation
Indices: 57624275--57624321 Score: 58
Period size: 6 Copynumber: 7.8 Consensus size: 6
57624265 ACCATCGTCT
* * * *
57624275 TCATCG TCATCG TCATCG TCATCT TCCTCG TCGTCC TCATCG TCATC
1 TCATCG TCATCG TCATCG TCATCG TCATCG TCATCG TCATCG TCATC
57624322 ATCTTCTTCG
Statistics
Matches: 34, Mismatches: 7, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
6 34 1.00
ACGTcount: A:0.13, C:0.38, G:0.13, T:0.36
Consensus pattern (6 bp):
TCATCG
Found at i:57624305 original size:24 final size:24
Alignment explanation
Indices: 57624272--57624321 Score: 73
Period size: 24 Copynumber: 2.1 Consensus size: 24
57624262 TCCACCATCG
*
57624272 TCTTCATCGTCATCGTCATCGTCA
1 TCTTCATCGTCATCCTCATCGTCA
* *
57624296 TCTTCCTCGTCGTCCTCATCGTCA
1 TCTTCATCGTCATCCTCATCGTCA
57624320 TC
1 TC
57624322 ATCTTCTTCG
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
24 23 1.00
ACGTcount: A:0.12, C:0.38, G:0.12, T:0.38
Consensus pattern (24 bp):
TCTTCATCGTCATCCTCATCGTCA
Found at i:57624314 original size:18 final size:18
Alignment explanation
Indices: 57624269--57624321 Score: 61
Period size: 18 Copynumber: 2.9 Consensus size: 18
57624259 ATCTCCACCA
*
57624269 TCGTCTTCATCGTCATCG
1 TCGTCCTCATCGTCATCG
* * * *
57624287 TCATCGTCATCTTCCTCG
1 TCGTCCTCATCGTCATCG
57624305 TCGTCCTCATCGTCATC
1 TCGTCCTCATCGTCATC
57624322 ATCTTCTTCG
Statistics
Matches: 27, Mismatches: 8, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
18 27 1.00
ACGTcount: A:0.11, C:0.38, G:0.13, T:0.38
Consensus pattern (18 bp):
TCGTCCTCATCGTCATCG
Found at i:57635543 original size:17 final size:17
Alignment explanation
Indices: 57635517--57635557 Score: 55
Period size: 17 Copynumber: 2.4 Consensus size: 17
57635507 AAAAAAAAAA
*
57635517 TTAAACTTAATATAAAT
1 TTAAACTTAAAATAAAT
*
57635534 TTAAATTTAAAATAAAT
1 TTAAACTTAAAATAAAT
*
57635551 ATAAACT
1 TTAAACT
57635558 AATGTCCAAA
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
17 20 1.00
ACGTcount: A:0.56, C:0.05, G:0.00, T:0.39
Consensus pattern (17 bp):
TTAAACTTAAAATAAAT
Found at i:57635993 original size:26 final size:26
Alignment explanation
Indices: 57635953--57636041 Score: 81
Period size: 27 Copynumber: 3.3 Consensus size: 26
57635943 ATCCAAATGC
*
57635953 AAACCCAACTCTTGAAGATCAATAGAA
1 AAACCCATCT-TTGAAGATCAATAGAA
* * * *
57635980 AAACCCATCTTTGAAAACCCAATACAC
1 AAACCCATCTTTGAAGA-TCAATAGAA
57636007 AAA-CCATTCTTTGAAGATCAATAGACA
1 AAACCCA-TCTTTGAAGATCAATAGA-A
*
57636034 GAACCCAT
1 AAACCCAT
57636042 TCTGGAAAAT
Statistics
Matches: 48, Mismatches: 10, Indels: 8
0.73 0.15 0.12
Matches are distributed among these distances:
26 15 0.31
27 30 0.62
28 3 0.06
ACGTcount: A:0.45, C:0.26, G:0.09, T:0.20
Consensus pattern (26 bp):
AAACCCATCTTTGAAGATCAATAGAA
Found at i:57636038 original size:27 final size:27
Alignment explanation
Indices: 57635964--57636044 Score: 94
Period size: 27 Copynumber: 3.0 Consensus size: 27
57635954 AACCCAACTC
*
57635964 TTGAAGATCAATAGAAAAACCCA-TCT
1 TTGAAGATCAATAGACAAACCCATTCT
* * *
57635990 TTGAAAACCCAATACACAAA-CCATTCT
1 TTGAAGA-TCAATAGACAAACCCATTCT
57636017 TTGAAGATCAATAGACAGAACCCATTCT
1 TTGAAGATCAATAGACA-AACCCATTCT
57636045 GGAAAATCAA
Statistics
Matches: 44, Mismatches: 7, Indels: 6
0.77 0.12 0.11
Matches are distributed among these distances:
26 17 0.39
27 20 0.45
28 7 0.16
ACGTcount: A:0.43, C:0.23, G:0.10, T:0.23
Consensus pattern (27 bp):
TTGAAGATCAATAGACAAACCCATTCT
Done.