Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold412
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: 4645160
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.34
File 27 of 32
Found at i:3850243 original size:51 final size:52
Alignment explanation
Indices: 3850180--3850297 Score: 186
Period size: 51 Copynumber: 2.3 Consensus size: 52
3850170 TCATTTTCGA
*
3850180 GGGGATACTCCAACCCCAG-TTTTATTTCTAAAACACTAATTTTTCACAATC
1 GGGGATACTCCAACCCCAGATTTTATTTCCAAAACACTAATTTTTCACAATC
* * *
3850231 GGGGATACTCCAA-CTCTGATTTTATTTCCAAAACACTAATTTTTTACAATC
1 GGGGATACTCCAACCCCAGATTTTATTTCCAAAACACTAATTTTTCACAATC
3850282 GGGGATACTCCAACCC
1 GGGGATACTCCAACCC
3850298 TGTTATTTCA
Statistics
Matches: 60, Mismatches: 5, Indels: 3
0.88 0.07 0.04
Matches are distributed among these distances:
50 3 0.05
51 56 0.93
52 1 0.02
ACGTcount: A:0.31, C:0.25, G:0.12, T:0.32
Consensus pattern (52 bp):
GGGGATACTCCAACCCCAGATTTTATTTCCAAAACACTAATTTTTCACAATC
Found at i:3850318 original size:27 final size:28
Alignment explanation
Indices: 3850283--3850354 Score: 110
Period size: 28 Copynumber: 2.6 Consensus size: 28
3850273 TTTACAATCG
* *
3850283 GGGATACTCCAACCCTGTTA-TTTCATC
1 GGGATACTCCAACCCCGTTATTTTCAAC
*
3850310 GGGATACTCCAACCCCGTTATTTTCAAG
1 GGGATACTCCAACCCCGTTATTTTCAAC
3850338 GGGATACTCCAACCCCG
1 GGGATACTCCAACCCCG
3850355 GCTTTATTTC
Statistics
Matches: 41, Mismatches: 3, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
27 19 0.46
28 22 0.54
ACGTcount: A:0.24, C:0.32, G:0.18, T:0.26
Consensus pattern (28 bp):
GGGATACTCCAACCCCGTTATTTTCAAC
Found at i:3850353 original size:157 final size:156
Alignment explanation
Indices: 3850152--3850484 Score: 409
Period size: 157 Copynumber: 2.1 Consensus size: 156
3850142 TTTCACAATT
* * *
3850152 AGGGATACTCCAACCCCGTCATTTTCGAGGGGATACTCCAACCCCAGTTTTATTTCTAAAACACT
1 AGGGATACTCCAACCCCGTCATTTTCAAGGGGATACTCCAACCCCAGCTTTATTTCCAAAACACT
* * ** *
3850217 AATTTTTCACAATCGGGGATACTCCAACTCTGATTTTATTTCCAAAACA-CTAATTTTTTACAAT
66 AATTTCTCACAATCGGGGATACTCCAACCCTGACCTTATTTCCAAAACATC-AATTTTTCACAAT
* **
3850281 CGGGGATACTCCAACCCTGTTA-TTTC
130 CGGAGATACTCCAACCCCATTATTTTC
* * *
3850307 ATCGGGATACTCCAACCCCGTTATTTTCAAGGGGATACTCCAACCCCGGCTTTATTTCCAAAATA
1 A--GGGATACTCCAACCCCGTCATTTTCAAGGGGATACTCCAACCCCAGCTTTATTTCCAAAACA
* * * * * * * *
3850372 TTGATTTCTCACAATCGGGGATACTTCAACCCTGGCCTTATTTCTAAATCATCGATTTTTCATAA
64 CTAATTTCTCACAATCGGGGATACTCCAACCCTGACCTTATTTCCAAAACATCAATTTTTCACAA
3850437 TCGGAGATACTCCAACCCCATTATTTTC
129 TCGGAGATACTCCAACCCCATTATTTTC
3850465 GAGGGAATACTCCAACCCCG
1 -AGGG-ATACTCCAACCCCG
3850485 ATTTTATTTT
Statistics
Matches: 150, Mismatches: 22, Indels: 9
0.83 0.12 0.05
Matches are distributed among these distances:
155 1 0.01
157 129 0.86
158 19 0.13
159 1 0.01
ACGTcount: A:0.28, C:0.27, G:0.14, T:0.32
Consensus pattern (156 bp):
AGGGATACTCCAACCCCGTCATTTTCAAGGGGATACTCCAACCCCAGCTTTATTTCCAAAACACT
AATTTCTCACAATCGGGGATACTCCAACCCTGACCTTATTTCCAAAACATCAATTTTTCACAATC
GGAGATACTCCAACCCCATTATTTTC
Found at i:3850413 original size:51 final size:51
Alignment explanation
Indices: 3850337--3850455 Score: 150
Period size: 51 Copynumber: 2.3 Consensus size: 51
3850327 TTATTTTCAA
* *
3850337 GGGGATACTCCAACCCCGGCTTTATTTCCAAAAT-ATTGATTTCTCACAATC
1 GGGGATACTCCAACCCCGGCCTTATTT-CAAAATCATCGATTTCTCACAATC
* * * * *
3850388 GGGGATACTTCAACCCTGGCCTTATTTCTAAATCATCGATTTTTCATAATC
1 GGGGATACTCCAACCCCGGCCTTATTTCAAAATCATCGATTTCTCACAATC
*
3850439 GGAGATACTCCAACCCC
1 GGGGATACTCCAACCCC
3850456 ATTATTTTCG
Statistics
Matches: 57, Mismatches: 10, Indels: 2
0.83 0.14 0.03
Matches are distributed among these distances:
50 5 0.09
51 52 0.91
ACGTcount: A:0.27, C:0.28, G:0.14, T:0.31
Consensus pattern (51 bp):
GGGGATACTCCAACCCCGGCCTTATTTCAAAATCATCGATTTCTCACAATC
Found at i:3850493 original size:79 final size:78
Alignment explanation
Indices: 3850409--3850616 Score: 215
Period size: 79 Copynumber: 2.6 Consensus size: 78
3850399 AACCCTGGCC
*
3850409 TTATTTCTAAATCATCGATTTTTCATAATCGGAGATACTCCAACCCCATTATTTTCG-AGGGAAT
1 TTATTTCAAAATCA-CGATTTTTCATAATCGGAGATACTCCAACCCCATTATTTTCGAAGGG-AT
*
3850473 ACTCCAACCCCGATT
64 ACTCCAACCCCAATT
* * ** ** *
3850488 TTATTTTCAAAAT-ACCAATTTTCTATAATCAAAGATACTCCAACCCTGTTATTTTCGAAGGGGT
1 TTA-TTTCAAAATCACGATTTTTC-ATAATCGGAGATACTCCAACCCCATTATTTTCGAAGGGAT
*
3850552 ACTCTAACCCCAATT
64 ACTCCAACCCCAATT
* * * *
3850567 TTCTTTCCAAAA-CGCCGATTTTTCATAATCGGGGATACTCCAGCCCCATT
1 TTATTT-CAAAATC-ACGATTTTTCATAATCGGAGATACTCCAACCCCATT
3850617 GTTATCTCTA
Statistics
Matches: 103, Mismatches: 20, Indels: 12
0.76 0.15 0.09
Matches are distributed among these distances:
78 10 0.10
79 74 0.72
80 19 0.18
ACGTcount: A:0.29, C:0.25, G:0.11, T:0.34
Consensus pattern (78 bp):
TTATTTCAAAATCACGATTTTTCATAATCGGAGATACTCCAACCCCATTATTTTCGAAGGGATAC
TCCAACCCCAATT
Found at i:3858534 original size:26 final size:27
Alignment explanation
Indices: 3858505--3858561 Score: 107
Period size: 27 Copynumber: 2.1 Consensus size: 27
3858495 TTTTGAAAAT
3858505 AAATTTTTT-ATTCATCTAGAGGGAGA
1 AAATTTTTTAATTCATCTAGAGGGAGA
3858531 AAATTTTTTAATTCATCTAGAGGGAGA
1 AAATTTTTTAATTCATCTAGAGGGAGA
3858558 AAAT
1 AAAT
3858562 CCGATTACCA
Statistics
Matches: 30, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
26 9 0.30
27 21 0.70
ACGTcount: A:0.39, C:0.07, G:0.18, T:0.37
Consensus pattern (27 bp):
AAATTTTTTAATTCATCTAGAGGGAGA
Found at i:3859192 original size:13 final size:13
Alignment explanation
Indices: 3859174--3859200 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
3859164 ACATTATGCT
3859174 TTGTATCGATACA
1 TTGTATCGATACA
3859187 TTGTATCGATACA
1 TTGTATCGATACA
3859200 T
1 T
3859201 GTTCATTGTA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.30, C:0.15, G:0.15, T:0.41
Consensus pattern (13 bp):
TTGTATCGATACA
Found at i:3859197 original size:33 final size:32
Alignment explanation
Indices: 3859155--3859216 Score: 90
Period size: 33 Copynumber: 1.9 Consensus size: 32
3859145 CACACCCAGA
*
3859155 TGTATCGATACAT-TATGCTTTGTATCGATACAT
1 TGTATCGATACATGT-T-CATTGTATCGATACAT
3859188 TGTATCGATACATGTTCATTGTATCGATA
1 TGTATCGATACATGTTCATTGTATCGATA
3859217 AATTACTTAT
Statistics
Matches: 27, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
32 12 0.44
33 14 0.52
34 1 0.04
ACGTcount: A:0.27, C:0.15, G:0.16, T:0.42
Consensus pattern (32 bp):
TGTATCGATACATGTTCATTGTATCGATACAT
Found at i:3860207 original size:31 final size:31
Alignment explanation
Indices: 3860172--3860233 Score: 124
Period size: 31 Copynumber: 2.0 Consensus size: 31
3860162 TAGCAGTTTT
3860172 TCCTGCAAATTGAAAATGAGGAAATGACCAA
1 TCCTGCAAATTGAAAATGAGGAAATGACCAA
3860203 TCCTGCAAATTGAAAATGAGGAAATGACCAA
1 TCCTGCAAATTGAAAATGAGGAAATGACCAA
3860234 AACACCACCC
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
31 31 1.00
ACGTcount: A:0.45, C:0.16, G:0.19, T:0.19
Consensus pattern (31 bp):
TCCTGCAAATTGAAAATGAGGAAATGACCAA
Found at i:3861718 original size:21 final size:23
Alignment explanation
Indices: 3861692--3861739 Score: 66
Period size: 23 Copynumber: 2.2 Consensus size: 23
3861682 CTACTAGATG
3861692 ATTTTTCC-AAA-TTTTT-TGAA
1 ATTTTTCCTAAACTTTTTATGAA
3861712 CATTTTTCCTAAACTTTTTATGAA
1 -ATTTTTCCTAAACTTTTTATGAA
3861736 ATTT
1 ATTT
3861740 CCTTTTTGGA
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
21 8 0.33
22 3 0.12
23 9 0.38
24 4 0.17
ACGTcount: A:0.29, C:0.12, G:0.04, T:0.54
Consensus pattern (23 bp):
ATTTTTCCTAAACTTTTTATGAA
Found at i:3863222 original size:46 final size:46
Alignment explanation
Indices: 3863166--3863323 Score: 149
Period size: 46 Copynumber: 3.4 Consensus size: 46
3863156 TGATGATTCA
* * *
3863166 GCCCTAGTCGAACTCTTTTCATACCTCGTTTAACTATATCTGTGTT
1 GCCCTGGTCGAACTTTTTTCATACCTCGTTTGACTATATCTGTGTT
* * *
3863212 GCCCTGGTCGAACTTTTTTC-TTCCTTCATTTGACTGTAT-TAGTGTT
1 GCCCTGGTCGAACTTTTTTCATACC-TCGTTTGACTATATCT-GTGTT
* * * * * *
3863258 AACCCTTGTCAAACTTTTTTCATACCTTGTTTGACTATATCGGAGTT
1 -GCCCTGGTCGAACTTTTTTCATACCTCGTTTGACTATATCTGTGTT
* *
3863305 GCCCTGATCAAACTTTTTT
1 GCCCTGGTCGAACTTTTTT
3863324 TACCCTTGTT
Statistics
Matches: 89, Mismatches: 18, Indels: 10
0.76 0.15 0.09
Matches are distributed among these distances:
45 4 0.04
46 50 0.56
47 32 0.36
48 3 0.03
ACGTcount: A:0.19, C:0.23, G:0.14, T:0.44
Consensus pattern (46 bp):
GCCCTGGTCGAACTTTTTTCATACCTCGTTTGACTATATCTGTGTT
Found at i:3863469 original size:45 final size:46
Alignment explanation
Indices: 3863367--3863489 Score: 155
Period size: 45 Copynumber: 2.8 Consensus size: 46
3863357 GGTTAAATTC
* *
3863367 TTTCCACCTTTGTTTGACTGTATTGACATTAGGACCTAGTCAAACT
1 TTTCCACCTTCGTTTGACTGTATTGACATTAGGACCGAGTCAAACT
* * * * *
3863413 CTT---CCTTCGTTTGGCTGTATTGGCGTTA-GTCCGAGTCAAACT
1 TTTCCACCTTCGTTTGACTGTATTGACATTAGGACCGAGTCAAACT
3863455 TTTCCACCTTCGTTTGACTGTATTGACATTAGGAC
1 TTTCCACCTTCGTTTGACTGTATTGACATTAGGAC
3863490 TTGGTCAAAC
Statistics
Matches: 61, Mismatches: 12, Indels: 8
0.75 0.15 0.10
Matches are distributed among these distances:
42 14 0.23
43 21 0.34
45 22 0.36
46 4 0.07
ACGTcount: A:0.20, C:0.23, G:0.19, T:0.39
Consensus pattern (46 bp):
TTTCCACCTTCGTTTGACTGTATTGACATTAGGACCGAGTCAAACT
Found at i:3863534 original size:47 final size:47
Alignment explanation
Indices: 3863481--3863691 Score: 151
Period size: 47 Copynumber: 4.5 Consensus size: 47
3863471 ACTGTATTGA
*
3863481 CATTAGGACTTGGTCAAACTCTTTTAATCCTCATTTGACTATAATAG
1 CATTAGGACTTGGTCAAACTCTTTTAACCCTCATTTGACTATAATAG
* * * * * * * *
3863528 CGTTAGGACCTGGTCAAAATCTCTTT-ACCCTCGTTTGATTGTATTGG
1 CATTAGGACTTGGTCAAACTCT-TTTAACCCTCATTTGACTATAATAG
* * * * * * *
3863575 CATTAGGACATGGTCAAACTCTTTTTACCCTCGTCTAACTGTATTAG
1 CATTAGGACTTGGTCAAACTCTTTTAACCCTCATTTGACTATAATAG
* * ** * * *
3863622 CATTAGGGCTTAGTCAAACTCCGCTTAA-CCTGATTTGACTA-CATGG
1 CATTAGGACTTGGTCAAACT-CTTTTAACCCTCATTTGACTATAATAG
* *
3863668 CGTTA-GTCTTGGTCAAACTCTTTT
1 CATTAGGACTTGGTCAAACTCTTTT
3863692 CACTGTTATT
Statistics
Matches: 126, Mismatches: 35, Indels: 9
0.74 0.21 0.05
Matches are distributed among these distances:
44 3 0.02
45 12 0.10
46 9 0.07
47 95 0.75
48 7 0.06
ACGTcount: A:0.24, C:0.22, G:0.17, T:0.37
Consensus pattern (47 bp):
CATTAGGACTTGGTCAAACTCTTTTAACCCTCATTTGACTATAATAG
Found at i:3863638 original size:94 final size:94
Alignment explanation
Indices: 3863464--3863639 Score: 226
Period size: 94 Copynumber: 1.9 Consensus size: 94
3863454 TTTTCCACCT
* * * *
3863464 TCGTTTGACTGTATTGACATTAGGACTTGGTCAAACTCTTTTAATCCTCATTTGACTATAATAGC
1 TCGTTTGACTGTATTGACATTAGGACATGGTCAAACTCTTTTAACCCTCATCTAACTATAATAGC
* *
3863529 GTTAGGACCTGGTCAAAATCTCTTTACCC
66 ATTAGGACCTAGTCAAAATCTCTTTACCC
* * * * * *
3863558 TCGTTTGATTGTATTGGCATTAGGACATGGTCAAACTCTTTTTACCCTCGTCTAACTGTATTAGC
1 TCGTTTGACTGTATTGACATTAGGACATGGTCAAACTCTTTTAACCCTCATCTAACTATAATAGC
* *
3863623 ATTAGGGCTTAGTCAAA
66 ATTAGGACCTAGTCAAA
3863640 CTCCGCTTAA
Statistics
Matches: 68, Mismatches: 14, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
94 68 1.00
ACGTcount: A:0.25, C:0.20, G:0.18, T:0.38
Consensus pattern (94 bp):
TCGTTTGACTGTATTGACATTAGGACATGGTCAAACTCTTTTAACCCTCATCTAACTATAATAGC
ATTAGGACCTAGTCAAAATCTCTTTACCC
Found at i:3863659 original size:94 final size:94
Alignment explanation
Indices: 3863464--3863661 Score: 211
Period size: 94 Copynumber: 2.1 Consensus size: 94
3863454 TTTTCCACCT
* * * *
3863464 TCGTTTGACTGTATTGACATTAGGACTTGGTCAAACTCTTTTAATCCTCATTTGACTATAATAGC
1 TCGTTTGACTGTATTGACATTAGGACATGGTCAAACTCTTTTAACCCTCATCTAACTATAATAGC
* * * *
3863529 GTTAGGACCTGGTCAAAATCTCTTTACCC
66 ATTAGGACCTAGTCAAAATCTCCTTAACC
* * * * * *
3863558 TCGTTTGATTGTATTGGCATTAGGACATGGTCAAACTCTTTTTACCCTCGTCTAACTGTATTAGC
1 TCGTTTGACTGTATTGACATTAGGACATGGTCAAACTCTTTTAACCCTCATCTAACTATAATAGC
* * *
3863623 ATTAGGGCTTAGTCAAACTC-CGCTTAACC
66 ATTAGGACCTAGTCAAAATCTC-CTTAACC
3863652 T-GATTTGACT
1 TCG-TTTGACT
3863662 ACATGGCGTT
Statistics
Matches: 84, Mismatches: 18, Indels: 4
0.79 0.17 0.04
Matches are distributed among these distances:
93 2 0.02
94 82 0.98
ACGTcount: A:0.24, C:0.21, G:0.17, T:0.37
Consensus pattern (94 bp):
TCGTTTGACTGTATTGACATTAGGACATGGTCAAACTCTTTTAACCCTCATCTAACTATAATAGC
ATTAGGACCTAGTCAAAATCTCCTTAACC
Found at i:3863808 original size:45 final size:44
Alignment explanation
Indices: 3863726--3863868 Score: 144
Period size: 45 Copynumber: 3.2 Consensus size: 44
3863716 TTAGTCCTAA
* * *
3863726 TCAAACTCCTTTCATATCTCATTT-AACATGATAGTTTAGCCCTAG
1 TCAAACTCTTTTCATAT-TCATTTGAA-ATGATGGTTTAGCCCTGG
* * ** * *
3863771 TCAAACTCTTTTACATCTTTATTTGATGTGATGGTTTAGTCTTGG
1 TCAAACTCTTTT-CATATTCATTTGAAATGATGGTTTAGCCCTGG
* *
3863816 TCAAACTACTTTTCATATTCATTTGAAATAAAGGTTTAGCCCTGG
1 TCAAACT-CTTTTCATATTCATTTGAAATGATGGTTTAGCCCTGG
3863861 TCAAACTC
1 TCAAACTC
3863869 GGTATATCTA
Statistics
Matches: 78, Mismatches: 17, Indels: 7
0.76 0.17 0.07
Matches are distributed among these distances:
44 1 0.01
45 67 0.86
46 10 0.13
ACGTcount: A:0.27, C:0.20, G:0.13, T:0.41
Consensus pattern (44 bp):
TCAAACTCTTTTCATATTCATTTGAAATGATGGTTTAGCCCTGG
Found at i:3864029 original size:43 final size:43
Alignment explanation
Indices: 3863896--3864033 Score: 111
Period size: 43 Copynumber: 3.2 Consensus size: 43
3863886 AATTCAACCC
* * * * *
3863896 TTTTATCCTTTGTTTACCTTTCAGTTTAGTCCTAGGTAAGTCT
1 TTTTATCCTTTGTTTACCTATCAGATTAGTCCCAGGTAAATCA
* * * * * * * *
3863939 TTTTATCGTTTGTTGACTTCTC-GATTCAATCGCA-GTCAACCA
1 TTTTATCCTTTGTTTACCTATCAGATT-AGTCCCAGGTAAATCA
*
3863981 TTTTATCCTTTGTTTACCTATCAGCTTAGTCCCAGGTAAAT-A
1 TTTTATCCTTTGTTTACCTATCAGATTAGTCCCAGGTAAATCA
3864023 CTTTTATCCTT
1 -TTTTATCCTT
3864034 GTTGACTTGT
Statistics
Matches: 70, Mismatches: 21, Indels: 8
0.71 0.21 0.08
Matches are distributed among these distances:
42 31 0.44
43 39 0.56
ACGTcount: A:0.20, C:0.22, G:0.12, T:0.46
Consensus pattern (43 bp):
TTTTATCCTTTGTTTACCTATCAGATTAGTCCCAGGTAAATCA
Found at i:3865442 original size:155 final size:154
Alignment explanation
Indices: 3865176--3865708 Score: 576
Period size: 155 Copynumber: 3.4 Consensus size: 154
3865166 TACTTTTGAT
* *
3865176 GTAAAAGTACCCGATACCCCTAAAAGACTTAAAAAGAATTTTAAAAGGGATGAACCTATCCTAAA
1 GTAAAAGTACCTGATACCCCTAAAAGACTTAAAAAGGATTTTAAAAGGGATGAACCTATCCTAAA
* * * * * *
3865241 TATCCATC-TTCGACATAAAAGCAAACCC-ATTAACAACTTAGGAGTTGGTT-TTAAAAACATAC
66 TATCCACCTTTAGA-ATAAAAGC-AACCCTAGTGACAACCTAGGAGTTGGTTCTTAAAAA-TTAC
*
3865303 GAAAATGCCCTTAGAAGATACCTTCGAC
128 GAAAATGCCCTTA-AAGATACCTTCAAC
* * * *
3865331 GTAAAAGTACCTAATACCCCTAAAAAACTTAAAAAGGATTTTAAAAGGGATAAACATATCCTAAA
1 GTAAAAGTACCTGATACCCCTAAAAGACTTAAAAAGGATTTTAAAAGGGATGAACCTATCCTAAA
* * * *
3865396 TATCCACCTTTGGAATAAAAACAGACCCTA-TGACGACCTAGCAGTTGGTTCTGT-AAAATTACG
66 TATCCACCTTTAGAATAAAAGCA-ACCCTAGTGACAACCTAGGAGTTGGTTCT-TAAAAATTACG
*
3865459 AAAATACTCC-TAAATGATACCTTCAAC
129 AAAATGC-CCTTAAA-GATACCTTCAAC
* * * * *
3865486 ATAAAAGTACCTGATATCCTTAAAAGACTTAAAAAAAGATTTTAAAAGGGATGAACCTATCTTAA
1 GTAAAAGTACCTGATACCCCTAAAAGACTT-AAAAAGGATTTTAAAAGGGATGAACCTATCCTAA
* * * * *
3865551 ATATCCACCTTTAGCATAAAAGCAAACCTAGTGACAACCTAGGAGTGGGTTCTGAAAAATTATGA
65 ATATCCACCTTTAGAATAAAAGCAACCCTAGTGACAACCTAGGAGTTGGTTCTTAAAAATTACGA
*
3865616 AAATGCCCTTAAAAGGTA-CTTCCAAC
130 AAATGCCCTT-AAAGATACCTT-CAAC
* ** * * * ***
3865642 GTAAAAGTACGTGGCACCCCTAAAGGACCTAAAAAGGATTATAAATCAGATGAACCTATCCTAAA
1 GTAAAAGTACCTGATACCCCTAAAAGACTTAAAAAGGATTTTAAAAGGGATGAACCTATCCTAAA
3865707 TA
66 TA
3865709 CGCATCTTCA
Statistics
Matches: 315, Mismatches: 50, Indels: 26
0.81 0.13 0.07
Matches are distributed among these distances:
154 3 0.01
155 182 0.58
156 126 0.40
157 4 0.01
ACGTcount: A:0.42, C:0.19, G:0.14, T:0.24
Consensus pattern (154 bp):
GTAAAAGTACCTGATACCCCTAAAAGACTTAAAAAGGATTTTAAAAGGGATGAACCTATCCTAAA
TATCCACCTTTAGAATAAAAGCAACCCTAGTGACAACCTAGGAGTTGGTTCTTAAAAATTACGAA
AATGCCCTTAAAGATACCTTCAAC
Found at i:3865776 original size:311 final size:310
Alignment explanation
Indices: 3865177--3865812 Score: 681
Period size: 311 Copynumber: 2.0 Consensus size: 310
3865167 ACTTTTGATG
*
3865177 TAAAAGTACCCGATACCCCTAAAAGACTTAAAAAGAATTTTAAAAGGGATGAACCTATCCTAAAT
1 TAAAAGTACCCGATACCCCTAAAAGACTTAAAAAAAATTTTAAAAGGGATGAACCTATCCTAAAT
* * * * * *
3865242 ATCCATCTTCGACATAAAAGCAAACCCATTAACAACTTAGGAGTTGGTTTTAAAAACATACGAAA
66 ATCCACCTTAGACATAAAAGCAAACCCAGTAACAACCTAGGAGTGGGTTTGAAAAACATACGAAA
* * * * *
3865307 ATGCCCTTAGAAGATACCTTCGACGTAAAAGTACCTAATACCCCTAAAAAACTTAAAAAGGATTT
131 ATGCCCTTAAAAGATACCTTCAACGTAAAAGTACCTAACACCCCTAAAAAACCTAAAAAGGATTA
** ** * *
3865372 TAAAAGGGATAAACATATCCTAAATATCCACCTTTGGAATAAAAACAGACCCTATGACGACCTAG
196 TAAAACAGATAAACATATCCTAAATATCCACCTTCAGAATAAAAACAGACCCGATGACAACCTAG
* ** * *
3865437 CAGTTGGTTCTGTAAAATTACGAAAATACTCCTAAATGATACCTTCAACA
261 CACTCAGCTCTGTAAAATTACGAAAATACCCCTAAATGATACCTTCAACA
* * * *
3865487 TAAAAGTACCTGATATCCTTAAAAGACTTAAAAAAAGATTTTAAAAGGGATGAACCTATCTTAAA
1 TAAAAGTACCCGATACCCCTAAAAGACTTAAAAAAA-ATTTTAAAAGGGATGAACCTATCCTAAA
* * * *
3865552 TATCCACCTTTAG-CATAAAAGCAAACCTAGTGACAACCTAGGAGTGGGTTCTGAAAAA-TTATG
65 TATCCACC-TTAGACATAAAAGCAAACCCAGTAACAACCTAGGAGTGGGTT-TGAAAAACATACG
* * ** **
3865615 AAAATGCCCTTAAAAGGTA-CTTCCAACGTAAAAGTACGTGGCACCCCTAAAGGACCTAAAAAGG
128 AAAATGCCCTTAAAAGATACCTT-CAACGTAAAAGTACCTAACACCCCTAAAAAACCTAAAAAGG
* * * * * **** *
3865679 ATTATAAATCAGATGAACCTATCCTAAATA-CGCATCTTCAGCATAAAGGTTGACCCGGTGACAA
192 ATTATAAAACAGATAAACATATCCTAAATATC-CACCTTCAGAATAAAAACAGACCCGATGACAA
* ** * ** *
3865743 CCTAAG-ACTCAGCTCTAG-AAAATTATGAAAATACCCCTAAGGGATACTTTTGACG
256 CCT-AGCACTCAGCTCT-GTAAAATTACGAAAATACCCCTAAATGATACCTTCAACA
3865798 TAAAAGTACCCGATA
1 TAAAAGTACCCGATA
3865813 ATCTTAGTGG
Statistics
Matches: 264, Mismatches: 55, Indels: 13
0.80 0.17 0.04
Matches are distributed among these distances:
310 36 0.14
311 216 0.82
312 12 0.05
ACGTcount: A:0.41, C:0.20, G:0.14, T:0.24
Consensus pattern (310 bp):
TAAAAGTACCCGATACCCCTAAAAGACTTAAAAAAAATTTTAAAAGGGATGAACCTATCCTAAAT
ATCCACCTTAGACATAAAAGCAAACCCAGTAACAACCTAGGAGTGGGTTTGAAAAACATACGAAA
ATGCCCTTAAAAGATACCTTCAACGTAAAAGTACCTAACACCCCTAAAAAACCTAAAAAGGATTA
TAAAACAGATAAACATATCCTAAATATCCACCTTCAGAATAAAAACAGACCCGATGACAACCTAG
CACTCAGCTCTGTAAAATTACGAAAATACCCCTAAATGATACCTTCAACA
Found at i:3872355 original size:5 final size:6
Alignment explanation
Indices: 3872314--3872354 Score: 57
Period size: 6 Copynumber: 6.7 Consensus size: 6
3872304 CATGCTATGG
3872314 TTTTTA TCTCTTTA TTTTTA TTTTTA TTTTTA -TTTTA TTTT
1 TTTTTA T-T-TTTA TTTTTA TTTTTA TTTTTA TTTTTA TTTT
3872355 AGCAAACATA
Statistics
Matches: 32, Mismatches: 0, Indels: 6
0.84 0.00 0.16
Matches are distributed among these distances:
5 5 0.16
6 20 0.62
7 2 0.06
8 5 0.16
ACGTcount: A:0.15, C:0.05, G:0.00, T:0.80
Consensus pattern (6 bp):
TTTTTA
Found at i:3875768 original size:15 final size:15
Alignment explanation
Indices: 3875744--3875774 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
3875734 TTTAAATTTA
*
3875744 TCATTTCATAACTTT
1 TCATTACATAACTTT
3875759 TCATTACATAACTTT
1 TCATTACATAACTTT
3875774 T
1 T
3875775 AAATAAAAAT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.29, C:0.19, G:0.00, T:0.52
Consensus pattern (15 bp):
TCATTACATAACTTT
Found at i:3876100 original size:73 final size:73
Alignment explanation
Indices: 3875954--3877477 Score: 219
Period size: 73 Copynumber: 20.9 Consensus size: 73
3875944 ATTATATCGT
* * * *
3875954 AAAATATTAAACTCATATAATCATACTCAAAAAACAACTTTAAATTTTTACAAATAAAAAAAATA
1 AAAAAATTAAACTCATATAATCATACTCAAAAAACAAATTTAAAGTTCTACAAATAAAAAAAATA
*
3876019 TTCTTTAA
66 TTCATTAA
* * **
3876027 AAAAAATTAAACTCATATAATTA-ACT-AAAAAACAAATTTAAAGTTCTATAAATAGAAGTAAAT
1 AAAAAATTAAACTCATATAATCATACTCAAAAAACAAATTTAAAGTTCTACAAATA-AAAAAAAT
3876090 CATAT-ATT--
65 -AT-TCATTAA
* ** * * * * * *
3876098 AAAAATTTAAACTCGCATACTTATACCTGAAAAAATAAATTTAAACTTTTACAAATAAAATTAAA
1 AAAAAATTAAACTCATATAATCATA-CTCAAAAAACAAATTTAAAGTTCTACAAATAAAA--AAA
* ** **
3876163 TTAAACCCT--
63 ATATTCATTAA
* ** * ** * *
3876172 AAAAATTTAAACTGGTATAATCATACTAAAAAACACATAAAACACATAAACTTTTACAAATAAAA
1 AAAAAATTAAACTCATATAATCATACTCAAAAA-AC----AA-ATTTAAAGTTCTACAAATAAAA
3876237 ATAAATGATAT-ATT--
60 A-AAAT-AT-TCATTAA
** * * * * * * *
3876251 AAAATTTTAAATTCGTAAAATCATACCCAAAAATCAAATTTAAA-TGACTACAAATAAAGATAAA
1 AAAAAATTAAACTCATATAATCATACTCAAAAAACAAATTTAAAGT-TCTACAAATAAA-AAAAA
* *
3876315 TAATACCTT--
64 T-ATTCATTAA
** * * * * * *
3876324 AAAATTTTAAACTCGTATAATCATA-TCTTAAAAATAAATTTAAATTTTTACATATAAAAATAAA
1 AAAAAATTAAACTCATATAATCATACTC-AAAAAACAAATTTAAAGTTCTACAAATAAAAA-AAA
*
3876388 TTATATC-TT-C
64 -TAT-TCATTAA
* ** * * * * * * *
3876398 AAAAATTTAAACTTGTATAATCTTAAACCCCAAAAAATAAATTTTAACTTCTACAAATAGAAATA
1 AAAAAATTAAACTCATATAATC--ATA-CTCAAAAAACAAATTTAAAGTTCTACAAATAAAAAAA
*
3876463 A-ATT-A-TACCC
63 ATATTCATTA--A
* * * * * * * *
3876473 CACAATTTAAACTTATATAATCATACCCAAAAAACAAATATAAAGTTCTACAACTAAAGATAAAT
1 AAAAAATTAAACTCATATAATCATACTCAAAAAACAAATTTAAAGTTCTACAAATAAA-AAAAAT
* *
3876538 AATGC-TT-T
65 -ATTCATTAA
* * * * * * * *
3876546 AAAAATTTAAACTGATATAATTA-ACCCAAAAAATAAATTTAAACTTATACAAA-AAAATAAATT
1 AAAAAATTAAACTCATATAATCATACTCAAAAAACAAATTTAAAGTTCTACAAATAAAA-AAAAT
* * *
3876609 ATACCTT-C
65 ATTCATTAA
* * * * * * * *
3876617 AAAAATTTAAACTCGA-AT-ATTAAACCTCAAAAAATATATTTTAACTCCTACAAA-AAAATAAA
1 AAAAAATTAAACTC-ATATAATCATA-CTCAAAAAACAAATTTAAAGTTCTACAAATAAAA-AAA
* *
3876679 TTATATC-CT--
63 ATAT-TCATTAA
* * * * *
3876688 AAAAATTTAAACT-AGTATAATCATAC-CAAAAAAATAAATTTAAACTTTTACAAATAAAGATAA
1 AAAAAATTAAACTCA-TATAATCATACTC-AAAAAACAAATTTAAAGTTCTACAAATAAA-AAAA
* ****
3876751 ATAAT-AGGCT
63 ATATTCATTAA
* * ** * * **
3876761 AAAAATTTAAACTTATATAATCA-A-TCCAAAAAGTAAATTTAAACTTCTAAAAATAAAAGTAA-
1 AAAAAATTAAACTCATATAATCATACT-CAAAAAACAAATTTAAAGTTCTACAAATAAAAAAAAT
3876823 ATT-A-TACCA
65 ATTCATTA--A
* * * * ** * *
3876832 CCAAAAATTTAAACTTATTTAATAATA-TCTAAAAAGTATATTTAAACTTCTACAAATAAAATAA
1 --AAAAAATTAAACTCATATAATCATACTC-AAAAAACAAATTTAAAGTTCTACAAATAAAA-AA
* *
3876896 ATTATATC-CT--
62 AATAT-TCATTAA
* * ** * * * *
3876906 AAAAATTTAGACTTGTATAATTATACT-AAAAAATAAATTTAAATTTCTACAAATAAAGATAAAT
1 AAAAAATTAAACTCATATAATCATACTCAAAAAACAAATTTAAAGTTCTACAAATAAA-AAAAAT
* *
3876970 AAT-ACCT--
65 ATTCA-TTAA
* * * * * * *
3876977 AAAAATTTAAACTCAAATAGTCA-ACCTC-AAAAATAAATTTAAATTTTTATAAATAAAAATAAA
1 AAAAAATTAAACTCATATAATCATA-CTCAAAAAACAAATTTAAAGTTCTACAAATAAAAA-AAA
* * *
3877040 TTATACCTT-T
64 -TATTCATTAA
* * * * *
3877050 AAAAATTTAAACTCGTATAATCATAC-CTAAAAAGCATATTTAAACTTCTACAAATTAAAATAAA
1 AAAAAATTAAACTCATATAATCATACTC-AAAAAACAAATTTAAAGTTCTACAAA-TAAAA-AAA
* * **
3877114 TTATACCCT--
63 ATATTCATTAA
** *** * * * * *
3877123 AAAACTTTAAACTTGCATAATCA-A-ACAAAAAATAAATTTAAAGTTCTACAAACAAAAATAA-C
1 AAAAAATTAAACTCATATAATCATACTCAAAAAACAAATTTAAAGTTCTACAAATAAAAAAAATA
3877185 TT-ATATAA
66 TTCAT-TAA
* * **** * * *
3877193 TCAAAAATTTAAACTCGTATAATCATA-TCCAAAAAGTGTATTTAAACTTTTATAAATAAAAATA
1 --AAAAAATTAAACTCATATAATCATACT-CAAAAAACAAATTTAAAGTTCTACAAATAAAAA-A
* *
3877257 AATTATACCTT--
62 AA-TATTCATTAA
* * * * * * * *
3877268 AAAAATTTAAACTCGTATAATCATAC-CCAAAAATAAGTTTAAACTTCTACCAATAAAGATAAAT
1 AAAAAATTAAACTCATATAATCATACTCAAAAAACAAATTTAAAGTTCTACAAATAAA-AAAAAT
* * *
3877332 AATAACCT--
65 ATTCA-TTAA
*** * * *
3877340 AAACCTTTAAACTCATATAATCGA-AC-CAAAAAATAAATTTACACTTCTACAAATAAAAATAAA
1 AAAAAATTAAACTCATATAATC-ATACTCAAAAAACAAATTTAAAGTTCTACAAATAAAAA-AAA
* **
3877403 TTATAC-TTTC
64 -TATTCATTAA
* * * * * *
3877413 AAAAAATTAAACTCGTATAATTATACAT-AAAAAACACATTTAAACTTTTACAAATTAAAATAAA
1 AAAAAATTAAACTCATATAATCATAC-TCAAAAAACAAATTTAAAGTTCTACAAA-TAAAAAAAA
3877477 T
64 T
3877478 TATACTTAAA
Statistics
Matches: 1108, Mismatches: 235, Indels: 216
0.71 0.15 0.14
Matches are distributed among these distances:
68 2 0.00
69 3 0.00
70 19 0.02
71 217 0.20
72 270 0.24
73 274 0.25
74 187 0.17
75 40 0.04
76 8 0.01
77 30 0.03
78 9 0.01
79 49 0.04
ACGTcount: A:0.53, C:0.13, G:0.03, T:0.31
Consensus pattern (73 bp):
AAAAAATTAAACTCATATAATCATACTCAAAAAACAAATTTAAAGTTCTACAAATAAAAAAAATA
TTCATTAA
Found at i:3876182 original size:145 final size:142
Alignment explanation
Indices: 3875914--3877605 Score: 1185
Period size: 145 Copynumber: 11.7 Consensus size: 142
3875904 TAATTACAAT
* * * *
3875914 ATAATTTTAAACTTC-ATAAATAAAAAATAAATTATATCGT-AAAATATTAAACTCATATAATCA
1 ATAAATTTAAACTTCTACAAAT-AAAAATAAATTATATCTTAAAAAT-TTAAACTCGTATAATCA
* * * * * ** ** *
3875977 TACTCAAAAAACAACTTTAAATTTTTACAAATAAAA-AAAATATTCTTTAAAAAAAATTAAACTC
64 TAC-CAAAAAATAAATTTAAACTTCTACAAATAAAATAAATTAAACCCT--AAAAATTTAAACTC
*
3876041 ATATAATTAACTAAAAA
126 GTATAATTAACTAAAAA
* * * * * * * * * *
3876058 ACAAATTTAAAGTTCTATAAATAGAAGTAAATCATATATTAAAAATTTAAACTCGCATACTTATA
1 ATAAATTTAAACTTCTACAAATAAAAATAAATTATATCTTAAAAATTTAAACTCGTATAATCATA
* *
3876123 CCTGAAAAAATAAATTTAAACTTTTACAAATAAAATTAAATTAAACCCTAAAAATTTAAACTGGT
66 CC--AAAAAATAAATTTAAACTTCTACAAATAAAA-TAAATTAAACCCTAAAAATTTAAACTCGT
*
3876188 ATAATCATACTAAAAAACA
128 ATAATTA-ACT--AAAA-A
** * * * * * *
3876207 CATAAAACACATAAACTTTTACAAATAAAAATAAATGATATATTAAAATTTTAAATTCGTAAAAT
1 -AT--AA-ATTTAAACTTCTACAAATAAAAATAAATTATATCTTAAAAATTTAAACTCGTATAAT
* * * *
3876272 CATACCCAAAAATCAAATTTAAA-TGACTACAAATAAAGATAAA-TAATACCTTAAAATTTTAAA
62 CATACCAAAAAAT-AAATTTAAACT-TCTACAAATAAA-ATAAATTAA-ACCCTAAAAATTTAAA
* *
3876335 CTCGTATAATCATATCTTAAAA
123 CTCGTATAAT--TAACTAAAAA
* * * *
3876357 ATAAATTTAAATTTTTACATATAAAAATAAATTATATCTTCAAAAATTTAAACTTGTATAATCTT
1 ATAAATTTAAACTTCTACAAATAAAAATAAATTATATCTT-AAAAATTTAAACTCGTATAATC--
* * * * *
3876422 AAACCCCAAAAAATAAATTTTAACTTCTACAAATAGAAATAAATTATACCC-CACAATTTAAACT
63 ATA--CCAAAAAATAAATTTAAACTTCTACAAATA-AAATAAATTAAACCCTAAAAATTTAAACT
** * *
3876486 TATATAATCATACCCAAAAA
125 CGTATAAT--TAACTAAAAA
* * * * * *
3876506 ACAAATATAAAGTTCTACAACTAAAGATAAA-TA-ATGCTTTAAAAATTTAAACT-GATATAATT
1 ATAAATTTAAACTTCTACAAATAAAAATAAATTATAT-C-TTAAAAATTTAAACTCG-TATAATC
* * *
3876568 A-ACCCAAAAAATAAATTTAAACTTATACAAA-AAAATAAATTATACCTTCAAAAATTTAAACTC
63 ATA-CCAAAAAATAAATTTAAACTTCTACAAATAAAATAAATTAAACCCT-AAAAATTTAAACTC
*
3876631 GAAT-ATTAAACCTCAAAAA
126 GTATAATT-AA-CT-AAAAA
* * * * *
3876650 ATATATTTTAACTCCTAC-AA-AAAAATAAATTATATCCTAAAAATTTAAACTAGTATAATCATA
1 ATAAATTTAAACTTCTACAAATAAAAATAAATTATATCTTAAAAATTTAAACTCGTATAATCATA
* ** **
3876713 CCAAAAAAATAAATTTAAACTTTTACAAATAAAGATAAA-TAATAGGCTAAAAATTTAAACTTAT
66 CC-AAAAAATAAATTTAAACTTCTACAAATAAA-ATAAATTAA-ACCCTAAAAATTTAAACTCGT
* *
3876777 ATAATCAATCCAAAAA
128 ATAATTAA-CTAAAAA
* * * * ** ** * *
3876793 GTAAATTTAAACTTCTAAAAATAAAAGTAAATTATACCACCAAAAATTTAAACTTATTTAATAAT
1 ATAAATTTAAACTTCTACAAATAAAAATAAATTATATC-TTAAAAATTTAAACTCGTATAATCAT
* * * * * * *
3876858 ATCTAAAAAGTATATTTAAACTTCTACAAATAAAATAAATTATATCCTAAAAATTTAGACTTGTA
65 A-CCAAAAAATAAATTTAAACTTCTACAAATAAAATAAATTAAACCCTAAAAATTTAAACTCGTA
3876923 TAATTATACTAAAAA
129 TAATTA-ACTAAAAA
* * * * ** *
3876938 ATAAATTTAAATTTCTACAAATAAAGATAAATAATA-CCTAAAAATTTAAACTCAAATAGTCA-A
1 ATAAATTTAAACTTCTACAAATAAAAATAAATTATATCTTAAAAATTTAAACTCGTATAATCATA
* * * * * *
3877001 CCTCAAAAATAAATTTAAATTTTTATAAATAAAAATAAATTATACCTTTAAAAATTTAAACTCGT
66 CC-AAAAAATAAATTTAAACTTCTACAAAT-AAAATAAATTAAACC-CTAAAAATTTAAACTCGT
*
3877066 ATAATCATACCTAAAAA
128 ATAAT--TAACTAAAAA
** * * * * * * *
3877083 GCATATTTAAACTTCTACAAATTAAAATAAATTATACCCTAAAACTTTAAACTTGCATAATCA-A
1 ATAAATTTAAACTTCTACAAATAAAAATAAATTATATCTTAAAAATTTAAACTCGTATAATCATA
* * * * **
3877147 ACAAAAAATAAATTTAAAGTTCTACAAACAAAAATAACTTATATAATC-AAAAATTTAAACTCGT
66 CCAAAAAATAAATTTAAACTTCTACAAA-TAAAATAAATTA-A-ACCCTAAAAATTTAAACTCGT
* *
3877211 ATAATCATATCCAAAAA
128 ATAAT--TAACTAAAAA
* ** * * *
3877228 GTGTATTTAAACTTTTATAAATAAAAATAAATTATACCTTAAAAATTTAAACTCGTATAATCATA
1 ATAAATTTAAACTTCTACAAATAAAAATAAATTATATCTTAAAAATTTAAACTCGTATAATCATA
* * * * ** *
3877293 CCCAAAAATAAGTTTAAACTTCTACCAATAAAGATAAA-TAATAACCTAAACCTTTAAACTCATA
66 CCAAAAAATAAATTTAAACTTCTACAAATAAA-ATAAATTAA-ACCCTAAAAATTTAAACTCGTA
* *
3877357 TAATCGAACCAAAAA
129 TAAT-TAACTAAAAA
* * *
3877372 ATAAATTTACACTTCTACAAATAAAAATAAATTATA-CTTTCAAAAAATTAAACTCGTATAATTA
1 ATAAATTTAAACTTCTACAAATAAAAATAAATTATATC-TT-AAAAATTTAAACTCGTATAATCA
* * * * * *
3877436 TACATAAAAAACACATTTAAACTTTTACAAATTAAAATAAATTATA-CTTAAAAATTTAAACTCG
64 TAC-CAAAAAATAAATTTAAACTTCTACAAA-TAAAATAAATTAAACCCTAAAAATTTAAACTCG
*
3877500 CATAA-T--C---AAA
127 TATAATTAACTAAAAA
* * * * *
3877510 A-AAATTTAAACTTCTATAAATAAAAATAAATTATACCTTCAAAATTTAAATTCATATAATCATA
1 ATAAATTTAAACTTCTACAAATAAAAATAAATTATATCTTAAAAATTTAAACTCGTATAATCATA
* * *
3877574 CCTTACAAATAAATTTATACTT-TACAAATAAA
66 CC-AAAAAATAAATTTAAACTTCTACAAATAAA
3877606 TTTAAATTTT
Statistics
Matches: 1237, Mismatches: 241, Indels: 150
0.76 0.15 0.09
Matches are distributed among these distances:
134 4 0.00
135 6 0.00
136 35 0.03
137 34 0.03
138 5 0.00
141 3 0.00
142 68 0.05
143 88 0.07
144 191 0.15
145 364 0.29
146 165 0.13
147 38 0.03
148 26 0.02
149 56 0.05
150 27 0.02
151 26 0.02
152 48 0.04
153 52 0.04
154 1 0.00
ACGTcount: A:0.53, C:0.13, G:0.03, T:0.32
Consensus pattern (142 bp):
ATAAATTTAAACTTCTACAAATAAAAATAAATTATATCTTAAAAATTTAAACTCGTATAATCATA
CCAAAAAATAAATTTAAACTTCTACAAATAAAATAAATTAAACCCTAAAAATTTAAACTCGTATA
ATTAACTAAAAA
Found at i:3876536 original size:72 final size:72
Alignment explanation
Indices: 3875914--3877605 Score: 1187
Period size: 72 Copynumber: 23.3 Consensus size: 72
3875904 TAATTACAAT
* * * *
3875914 ATAATTTTAAACTTC-ATAAATAAAAAATAAATTATATCGT-AAAATATTAAACTCATATAATCA
1 ATAAATTTAAACTTCTACAAAT-AAAAATAAATTATA-CCTAAAAAT-TTAAACTTATATAATCA
*
3875977 TACTCAAAAA
63 TACCCAAAAA
* * * * * * * *
3875987 ACAACTTTAAATTTTTACAAATAAAAA-AAA-TATTCTTTAAAAAAAATTAAACTCATATAAT--
1 ATAAATTTAAACTTCTACAAATAAAAATAAATTATAC-CT--AAAAATTTAAACTTATATAATCA
* *
3876048 TAACTAAAAA
63 TACCCAAAAA
* * * * * * *** * *
3876058 ACAAATTTAAAGTTCTATAAATAGAAGTAAATCATATA-TTAAAAATTTAAACTCGCATACTTAT
1 ATAAATTTAAACTTCTACAAATAAAAATAAAT--TATACCTAAAAATTTAAACTTATATAATCAT
*
3876122 ACCTGAAAAA
64 ACC-CAAAAA
* * * **
3876132 ATAAATTTAAACTTTTACAAATAAAATTAAATTAAACCCTAAAAATTTAAACTGGTATAATCATA
1 ATAAATTTAAACTTCTACAAATAAAAATAAATTATA-CCTAAAAATTTAAACTTATATAATCATA
**
3876197 CTAAAAAACA
65 C-CCAAAA-A
** * * * * *
3876207 CATAAAACACATAAACTTTTACAAATAAAAATAAATGATATA-TTAAAATTTTAAA-TTCGTAAA
1 -AT--AA-ATTTAAACTTCTACAAATAAAAATAAAT--TATACCTAAAAATTTAAACTT-ATATA
3876270 ATCATACCC-AAAA
59 ATCATACCCAAAAA
* * * * **
3876283 ATCAAATTTAAA-TGACTACAAATAAAGATAAATAATACCTTAAAATTTTAAACTCGTATAATCA
1 AT-AAATTTAAACT-TCTACAAATAAAAATAAATTATACC-TAAAAATTTAAACTTATATAATCA
* **
3876347 TATCTTAAAA
63 TACCCAAAAA
* * * * *
3876357 ATAAATTTAAATTTTTACATATAAAAATAAATTATATCTTCAAAAATTTAAACTTGTATAATCTT
1 ATAAATTTAAACTTCTACAAATAAAAATAAATTATA-CCT-AAAAATTTAAACTTATATAATC--
*
3876422 AAACCCCAAAAA
62 ATA-CCCAAAAA
* * ** *
3876434 ATAAATTTTAACTTCTACAAATAGAAATAAATTATACCCCACAATTTAAACTTATATAATCATAC
1 ATAAATTTAAACTTCTACAAATAAAAATAAATTATACCTAAAAATTTAAACTTATATAATCATAC
3876499 CCAAAAA
66 CCAAAAA
* * * * * * * * * *
3876506 ACAAATATAAAGTTCTACAACTAAAGATAAATAATGCTTTAAAAATTTAAACTGATATAATTA-A
1 ATAAATTTAAACTTCTACAAATAAAAATAAATTATAC-CTAAAAATTTAAACTTATATAATCATA
3876570 CCCAAAAA
65 CCCAAAAA
* * *
3876578 ATAAATTTAAACTTATAC-AA-AAAAATAAATTATACCTTCAAAAATTTAAACTCGA-AT-ATTA
1 ATAAATTTAAACTTCTACAAATAAAAATAAATTATACC-T-AAAAATTTAAACT-TATATAATCA
*
3876639 AACCTCAAAAA
63 TACC-CAAAAA
* * *
3876650 ATATATTTTAACTCCTAC-AA-AAAAATAAATTATATCCTAAAAATTTAAAC-TAGTATAATCAT
1 ATAAATTTAAACTTCTACAAATAAAAATAAATTATA-CCTAAAAATTTAAACTTA-TATAATCAT
*
3876712 ACCAAAAAA
64 ACCCAAAAA
* * * *
3876721 ATAAATTTAAACTTTTACAAATAAAGATAAATAATAGGCTAAAAATTTAAACTTATATAATCA-A
1 ATAAATTTAAACTTCTACAAATAAAAATAAATTATA-CCTAAAAATTTAAACTTATATAATCATA
*
3876785 TCCAAAAA
65 CCCAAAAA
* * * * * *
3876793 GTAAATTTAAACTTCTAAAAATAAAAGTAAATTATACCACCAAAAATTTAAACTTATTTAATAAT
1 ATAAATTTAAACTTCTACAAATAAAAATAAATTATA-C-CTAAAAATTTAAACTTATATAATCAT
* *
3876858 ATCTAAAAA
64 ACCCAAAAA
* * * * *
3876867 GTATATTTAAACTTCTACAAAT-AAAATAAATTATATCCTAAAAATTTAGACTTGTATAATTATA
1 ATAAATTTAAACTTCTACAAATAAAAATAAATTATA-CCTAAAAATTTAAACTTATATAATCATA
*
3876931 -CTAAAAA
65 CCCAAAAA
* * * * * *
3876938 ATAAATTTAAATTTCTACAAATAAAGATAAATAATACCTAAAAATTTAAACTCAAATAGTCA-AC
1 ATAAATTTAAACTTCTACAAATAAAAATAAATTATACCTAAAAATTTAAACTTATATAATCATAC
3877002 CTC-AAAA
66 C-CAAAAA
* * * **
3877009 ATAAATTTAAATTTTTATAAATAAAAATAAATTATACCTTTAAAAATTTAAACTCGTATAATCAT
1 ATAAATTTAAACTTCTACAAATAAAAATAAATTATACC--TAAAAATTTAAACTTATATAATCAT
*
3877074 ACCTAAAAA
64 ACCCAAAAA
** * * * **
3877083 GCATATTTAAACTTCTACAAATTAAAATAAATTATACCCTAAAACTTTAAACTTGCATAATCA-A
1 ATAAATTTAAACTTCTACAAATAAAAATAAATTATA-CCTAAAAATTTAAACTTATATAATCATA
*
3877147 -ACAAAAA
65 CCCAAAAA
* * * ** **
3877154 ATAAATTTAAAGTTCTACAAACAAAAATAACTTATATAATCAAAAATTTAAACTCGTATAATCAT
1 ATAAATTTAAACTTCTACAAATAAAAATAAATTATA-CCT-AAAAATTTAAACTTATATAATCAT
*
3877219 ATCCAAAAA
64 ACCCAAAAA
* ** * * **
3877228 GTGTATTTAAACTTTTATAAATAAAAATAAATTATACCTTAAAAATTTAAACTCGTATAATCATA
1 ATAAATTTAAACTTCTACAAATAAAAATAAATTATACC-TAAAAATTTAAACTTATATAATCATA
3877293 CCC-AAAA
65 CCCAAAAA
* * * * ** *
3877300 ATAAGTTTAAACTTCTACCAATAAAGATAAATAATAACCTAAACCTTTAAACTCATATAATCGA-
1 ATAAATTTAAACTTCTACAAATAAAAATAAATTAT-ACCTAAAAATTTAAACTTATATAATC-AT
3877364 A-CCAAAAA
64 ACCCAAAAA
* * * ** *
3877372 ATAAATTTACACTTCTACAAATAAAAATAAATTATACTTTCAAAAAATTAAACTCGTATAATTAT
1 ATAAATTTAAACTTCTACAAATAAAAATAAATTATAC-CT-AAAAATTTAAACTTATATAATCAT
**
3877437 ACATAAAAA
64 ACCCAAAAA
* * * * * ***
3877446 ACACATTTAAACTTTTACAAATTAAAATAAATTATACTTAAAAATTTAAACTCGCAT-A--AT--
1 ATAAATTTAAACTTCTACAAATAAAAATAAATTATACCTAAAAATTTAAACTTATATAATCATAC
3877506 -C--AAA
66 CCAAAAA
* *
3877510 A-AAATTTAAACTTCTATAAATAAAAATAAATTATACCTTCAAAATTTAAA-TTCATATAATCAT
1 ATAAATTTAAACTTCTACAAATAAAAATAAATTATACC-TAAAAATTTAAACTT-ATATAATCAT
** *
3877573 ACCTTACAA
64 ACCCAAAAA
*
3877582 ATAAATTTATACTT-TACAAATAAA
1 ATAAATTTAAACTTCTACAAATAAA
3877606 TTTAAATTTT
Statistics
Matches: 1291, Mismatches: 249, Indels: 159
0.76 0.15 0.09
Matches are distributed among these distances:
63 32 0.02
64 17 0.01
65 1 0.00
67 2 0.00
69 3 0.00
70 19 0.01
71 229 0.18
72 322 0.25
73 305 0.24
74 236 0.18
75 27 0.02
76 6 0.00
77 39 0.03
78 3 0.00
79 47 0.04
81 3 0.00
ACGTcount: A:0.53, C:0.13, G:0.03, T:0.32
Consensus pattern (72 bp):
ATAAATTTAAACTTCTACAAATAAAAATAAATTATACCTAAAAATTTAAACTTATATAATCATAC
CCAAAAA
Found at i:3876914 original size:39 final size:37
Alignment explanation
Indices: 3876871--3876989 Score: 95
Period size: 39 Copynumber: 3.2 Consensus size: 37
3876861 TAAAAAGTAT
3876871 ATTTAAACTTCTACAAATAAAATAAATTATATCCTAAAA
1 ATTTAAACTTCTACAAATAAAATAAA-TATA-CCTAAAA
* * * * * * *
3876910 ATTTAGACTTGTATAATTATACTAAA-A-A---ATAA
1 ATTTAAACTTCTACAAATAAAATAAATATACCTAAAA
*
3876942 ATTTAAATTTCTACAAATAAAGATAAATAATACCTAAAA
1 ATTTAAACTTCTACAAATAAA-ATAAAT-ATACCTAAAA
3876981 ATTTAAACT
1 ATTTAAACT
3876990 CAAATAGTCA
Statistics
Matches: 57, Mismatches: 16, Indels: 14
0.66 0.18 0.16
Matches are distributed among these distances:
32 18 0.32
33 4 0.07
35 1 0.02
36 2 0.04
37 1 0.02
39 31 0.54
ACGTcount: A:0.53, C:0.10, G:0.03, T:0.34
Consensus pattern (37 bp):
ATTTAAACTTCTACAAATAAAATAAATATACCTAAAA
Found at i:3877419 original size:26 final size:26
Alignment explanation
Indices: 3877368--3877419 Score: 61
Period size: 26 Copynumber: 2.0 Consensus size: 26
3877358 AATCGAACCA
* *
3877368 AAAAATAAATTTACACTTCTACAAAT
1 AAAAATAAATTTACACTTCAAAAAAT
*
3877394 AAAAATAAATTATAC-TTTCAAAAAAT
1 AAAAATAAATT-TACACTTCAAAAAAT
3877420 TAAACTCGTA
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
26 19 0.86
27 3 0.14
ACGTcount: A:0.58, C:0.12, G:0.00, T:0.31
Consensus pattern (26 bp):
AAAAATAAATTTACACTTCAAAAAAT
Found at i:3877598 original size:19 final size:19
Alignment explanation
Indices: 3877571--3877625 Score: 74
Period size: 19 Copynumber: 2.8 Consensus size: 19
3877561 TCATATAATC
*
3877571 ATACCTTACAAATAAATTT
1 ATACTTTACAAATAAATTT
3877590 ATACTTTACAAATAAATTT
1 ATACTTTACAAATAAATTT
* *
3877609 AAATTTTTACAAATAAA
1 ATA-CTTTACAAATAAA
3877626 AATAATACCT
Statistics
Matches: 32, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
19 20 0.62
20 12 0.38
ACGTcount: A:0.51, C:0.11, G:0.00, T:0.38
Consensus pattern (19 bp):
ATACTTTACAAATAAATTT
Found at i:3878016 original size:18 final size:16
Alignment explanation
Indices: 3877969--3878017 Score: 55
Period size: 18 Copynumber: 2.9 Consensus size: 16
3877959 CATTTATCAC
3877969 TTTATTTT-TTAAAAT
1 TTTATTTTATTAAAAT
3877984 TTTATTTTAATTTAAAATT
1 TTTATTTT-A-TTAAAA-T
3878003 TTGTATTTTATTAAA
1 TT-TATTTTATTAAA
3878018 TAATTAATAT
Statistics
Matches: 29, Mismatches: 0, Indels: 7
0.81 0.00 0.19
Matches are distributed among these distances:
15 8 0.28
18 11 0.38
19 4 0.14
20 6 0.21
ACGTcount: A:0.35, C:0.00, G:0.02, T:0.63
Consensus pattern (16 bp):
TTTATTTTATTAAAAT
Found at i:3878153 original size:76 final size:76
Alignment explanation
Indices: 3878017--3878171 Score: 181
Period size: 76 Copynumber: 2.0 Consensus size: 76
3878007 ATTTTATTAA
* * *
3878017 ATAATTAATATTTTGATATTTTAATATAATTTTTTTAATTTTAGTTAAATTGTACTTTTTTCAAT
1 ATAATTAATATATTGA-ATTTCAATATAATTTTTTAAATTTTA-TTAAATTGTACTTTTTTCAAT
3878082 TTTATAAAAATTG
64 TTTATAAAAATTG
* *
3878095 ATAATTAATATATTG-ATTTCAATATAAATTTTTTAAAAATTTT-TTAAATTTTA-TTTTTTTAA
1 ATAATTAATATATTGAATTTCAATAT-AATTTTTT--AAATTTTATTAAATTGTACTTTTTTCAA
**
3878157 TTTTATCTAAATTG
63 TTTTATAAAAATTG
3878171 A
1 A
3878172 GAAATAATCA
Statistics
Matches: 67, Mismatches: 7, Indels: 8
0.82 0.09 0.10
Matches are distributed among these distances:
76 30 0.45
77 17 0.25
78 14 0.21
79 6 0.09
ACGTcount: A:0.37, C:0.03, G:0.04, T:0.56
Consensus pattern (76 bp):
ATAATTAATATATTGAATTTCAATATAATTTTTTAAATTTTATTAAATTGTACTTTTTTCAATTT
TATAAAAATTG
Found at i:3878154 original size:15 final size:14
Alignment explanation
Indices: 3878133--3878162 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
3878123 TTTTTTAAAA
*
3878133 ATTTTTTAAATTTT
1 ATTTTTTTAATTTT
3878147 ATTTTTTTAATTTT
1 ATTTTTTTAATTTT
3878161 AT
1 AT
3878163 CTAAATTGAG
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.27, C:0.00, G:0.00, T:0.73
Consensus pattern (14 bp):
ATTTTTTTAATTTT
Found at i:3878564 original size:12 final size:11
Alignment explanation
Indices: 3878536--3878578 Score: 50
Period size: 11 Copynumber: 3.7 Consensus size: 11
3878526 TTAAAATTTT
*
3878536 TATTTAAAATA
1 TATTTAAATTA
3878547 TAATTTAGAATTA
1 T-ATTTA-AATTA
*
3878560 TATTTAAATAA
1 TATTTAAATTA
3878571 TATTTAAA
1 TATTTAAA
3878579 AAATACTATT
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
11 13 0.46
12 10 0.36
13 5 0.18
ACGTcount: A:0.51, C:0.00, G:0.02, T:0.47
Consensus pattern (11 bp):
TATTTAAATTA
Found at i:3882525 original size:8 final size:8
Alignment explanation
Indices: 3882512--3882698 Score: 73
Period size: 8 Copynumber: 22.6 Consensus size: 8
3882502 AAAATTTAAG
3882512 AAAAATAT
1 AAAAATAT
3882520 AAAAATATT
1 AAAAATA-T
*
3882529 AAAACTAT
1 AAAAATAT
3882537 -AAAAT-T
1 AAAAATAT
3882543 AAAAATTTAT
1 AAAAA--TAT
*
3882553 AAAAAAATTT
1 --AAAAATAT
3882563 AAAAATA-
1 AAAAATAT
** *
3882570 AAATTTGAG
1 AAAAAT-AT
3882579 AAAAATATT
1 AAAAATA-T
3882588 AAAAATAT
1 AAAAATAT
*
3882596 AAAATTCCA-
1 AAAAAT--AT
3882605 AAAAATTATT
1 AAAAA-TA-T
*
3882615 AAAAATTT
1 AAAAATAT
3882623 AAAAA-AT
1 AAAAATAT
* * *
3882630 ATATATAC
1 AAAAATAT
*
3882638 AAAATTAT
1 AAAAATAT
*
3882646 AAAAATCT
1 AAAAATAT
3882654 ATAAAAT-T
1 A-AAAATAT
3882662 AAAAA-AT
1 AAAAATAT
**
3882669 AAAAATGC
1 AAAAATAT
3882677 AAAAACTAT
1 AAAAA-TAT
*
3882686 AAAATTAT
1 AAAAATAT
3882694 AAAAA
1 AAAAA
3882699 AATTCAAAAT
Statistics
Matches: 131, Mismatches: 28, Indels: 40
0.66 0.14 0.20
Matches are distributed among these distances:
6 1 0.01
7 26 0.20
8 55 0.42
9 34 0.26
10 10 0.08
12 5 0.04
ACGTcount: A:0.66, C:0.04, G:0.02, T:0.28
Consensus pattern (8 bp):
AAAAATAT
Found at i:3882565 original size:26 final size:27
Alignment explanation
Indices: 3882536--3882599 Score: 69
Period size: 26 Copynumber: 2.4 Consensus size: 27
3882526 ATTAAAACTA
*
3882536 TAAAATTAAAAATTT-ATAAAAAAATT
1 TAAAATTAAAAATTTGAGAAAAAAATT
* *
3882562 TAAAAAT-AAAATTTGAGAAAAATATT
1 TAAAATTAAAAATTTGAGAAAAAAATT
*
3882588 AAAAATATAAAA
1 TAAAAT-TAAAA
3882600 TTCCAAAAAA
Statistics
Matches: 30, Mismatches: 5, Indels: 4
0.77 0.13 0.10
Matches are distributed among these distances:
25 7 0.23
26 19 0.63
27 1 0.03
28 3 0.10
ACGTcount: A:0.67, C:0.00, G:0.03, T:0.30
Consensus pattern (27 bp):
TAAAATTAAAAATTTGAGAAAAAAATT
Found at i:3882588 original size:59 final size:57
Alignment explanation
Indices: 3882484--3882668 Score: 166
Period size: 59 Copynumber: 3.2 Consensus size: 57
3882474 AAAATTTCAA
* * *
3882484 AAAATT-AAAAATAAAAATAAAATTT-AAGAA-AAATAT--AAAAATATTAAAACTAT
1 AAAATTAAAAAATTATAA-AAAATTTAAAAAATAAATATACAAAAATATTAAAACTAT
* * * *
3882537 AAAATTAAAAATTTATAAAAAAATTT-AAAAATAAAATTTGAGAAAAATATTAAAAATAT
1 AAAATTAAAAAATTAT-AAAAAATTTAAAAAAT-AAATAT-ACAAAAATATTAAAACTAT
* * * *
3882596 AAAATTCCAAAAAATTATTAAAAATTTAAAAAATATATATACAAAATTATAAAAATCTAT
1 AAAATT--AAAAAATTATAAAAAATTTAAAAAATAAATATACAAAAATATTAAAA-CTAT
3882656 AAAATTAAAAAAT
1 AAAATTAAAAAAT
3882669 AAAAATGCAA
Statistics
Matches: 107, Mismatches: 14, Indels: 17
0.78 0.10 0.12
Matches are distributed among these distances:
53 6 0.06
54 17 0.16
55 2 0.02
56 5 0.05
58 7 0.07
59 34 0.32
60 21 0.20
61 15 0.14
ACGTcount: A:0.66, C:0.03, G:0.02, T:0.29
Consensus pattern (57 bp):
AAAATTAAAAAATTATAAAAAATTTAAAAAATAAATATACAAAAATATTAAAACTAT
Found at i:3882621 original size:20 final size:22
Alignment explanation
Indices: 3882596--3882656 Score: 58
Period size: 22 Copynumber: 2.9 Consensus size: 22
3882586 TTAAAAATAT
3882596 AAAATTCCAAAAAAT-TAT-TA-
1 AAAATT-CAAAAAATATATATAC
*
3882616 AAAATTTAAAAAATATATATAC
1 AAAATTCAAAAAATATATATAC
*
3882638 AAAATT-ATAAAAATCTATA
1 AAAATTCA-AAAAATATATA
3882657 AAATTAAAAA
Statistics
Matches: 35, Mismatches: 2, Indels: 6
0.81 0.05 0.14
Matches are distributed among these distances:
19 7 0.20
20 9 0.26
21 3 0.09
22 16 0.46
ACGTcount: A:0.62, C:0.07, G:0.00, T:0.31
Consensus pattern (22 bp):
AAAATTCAAAAAATATATATAC
Found at i:3882656 original size:10 final size:9
Alignment explanation
Indices: 3882512--3882821 Score: 74
Period size: 9 Copynumber: 34.6 Consensus size: 9
3882502 AAAATTTAAG
3882512 AAAAA-TAT
1 AAAAATTAT
3882520 AAAAA-TAT
1 AAAAATTAT
* *
3882528 TAAAACTAT
1 AAAAATTAT
3882537 -AAAATTA-
1 AAAAATTAT
*
3882544 AAAATTTAT
1 AAAAATTAT
3882553 AAAAAAATT-T
1 --AAAAATTAT
3882563 -AAAA--AT
1 AAAAATTAT
* *
3882569 AAAATTTGAG
1 AAAAATT-AT
3882579 AAAAA-TATT
1 AAAAATTA-T
3882588 AAAAA-TAT
1 AAAAATTAT
3882596 -AAAATTCCA-
1 AAAAATT--AT
3882605 AAAAATTATT
1 AAAAATTA-T
*
3882615 AAAAATTTAA
1 AAAAA-TTAT
3882625 AAAATATATAT
1 AAAA-AT-TAT
3882636 ACAAAATTAT
1 A-AAAATTAT
3882646 AAAAATCTAT
1 AAAAAT-TAT
3882656 -AAAA-T-T
1 AAAAATTAT
3882662 AAAAA--AT
1 AAAAATTAT
**
3882669 AAAAA-TGC
1 AAAAATTAT
*
3882677 AAAAACTAT
1 AAAAATTAT
3882686 -AAAATTAT
1 AAAAATTAT
*
3882694 AAAAA-AATT
1 AAAAATTA-T
*
3882703 CAAAATTCAT
1 AAAAATT-AT
*
3882713 AAAAGTTAT
1 AAAAATTAT
3882722 AAAAATTGAAT
1 AAAAATT--AT
*
3882733 ATAAAA--GT
1 A-AAAATTAT
*
3882741 ACAAATTCA-
1 AAAAATT-AT
*
3882750 AAAAAATAT
1 AAAAATTAT
3882759 AAAAATTAT
1 AAAAATTAT
*
3882768 ATAAAATTCAA
1 A-AAAATT-AT
3882779 ATAAAATTAT
1 A-AAAATTAT
*
3882789 AAAAAAT-T
1 AAAAATTAT
* *
3882797 AAAAATAAAA
1 AAAAAT-TAT
3882807 ATAAAATTAT
1 A-AAAATTAT
3882817 AAAAA
1 AAAAA
3882822 AATAAAAAAT
Statistics
Matches: 225, Mismatches: 35, Indels: 83
0.66 0.10 0.24
Matches are distributed among these distances:
6 2 0.01
7 25 0.11
8 50 0.22
9 61 0.27
10 47 0.21
11 33 0.15
12 7 0.03
ACGTcount: A:0.66, C:0.04, G:0.02, T:0.28
Consensus pattern (9 bp):
AAAAATTAT
Found at i:3882656 original size:22 final size:20
Alignment explanation
Indices: 3882604--3882650 Score: 60
Period size: 19 Copynumber: 2.2 Consensus size: 20
3882594 ATAAAATTCC
3882604 AAAAAATTAT-TAAAAATTT
1 AAAAAATTATATAAAAATTT
3882623 AAAAAATATATATACAAAATTAT
1 AAAAAAT-TATATA-AAAATT-T
3882646 AAAAA
1 AAAAA
3882651 TCTATAAAAT
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
19 7 0.29
20 3 0.12
21 2 0.08
22 6 0.25
23 6 0.25
ACGTcount: A:0.68, C:0.02, G:0.00, T:0.30
Consensus pattern (20 bp):
AAAAAATTATATAAAAATTT
Found at i:3882680 original size:39 final size:39
Alignment explanation
Indices: 3882606--3882697 Score: 98
Period size: 39 Copynumber: 2.3 Consensus size: 39
3882596 AAAATTCCAA
* * *
3882606 AAAATTATTAAAAATTTAAAAAATATATATAC-AAAATTAT
1 AAAATTA-T-AAAATTTAAAAAATAAAAATACAAAAACTAT
*
3882646 AAAAATCTATAAAA-TTAAAAAATAAAAATGCAAAAACTAT
1 -AAAAT-TATAAAATTTAAAAAATAAAAATACAAAAACTAT
3882686 AAAATTATAAAA
1 AAAATTATAAAA
3882698 AAATTCAAAA
Statistics
Matches: 45, Mismatches: 4, Indels: 7
0.80 0.07 0.12
Matches are distributed among these distances:
38 7 0.16
39 19 0.42
40 11 0.24
41 6 0.13
42 2 0.04
ACGTcount: A:0.66, C:0.04, G:0.01, T:0.28
Consensus pattern (39 bp):
AAAATTATAAAATTTAAAAAATAAAAATACAAAAACTAT
Found at i:3882769 original size:11 final size:10
Alignment explanation
Indices: 3882751--3882797 Score: 51
Period size: 10 Copynumber: 4.7 Consensus size: 10
3882741 ACAAATTCAA
*
3882751 AAAAATATA-
1 AAAATTATAT
3882760 AAAATTATAT
1 AAAATTATAT
*
3882770 AAAATTCAAAT
1 AAAATT-ATAT
*
3882781 AAAATTATAA
1 AAAATTATAT
3882791 AAAATTA
1 AAAATTA
3882798 AAAATAAAAA
Statistics
Matches: 32, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
9 8 0.25
10 15 0.47
11 9 0.28
ACGTcount: A:0.68, C:0.02, G:0.00, T:0.30
Consensus pattern (10 bp):
AAAATTATAT
Found at i:3882784 original size:21 final size:22
Alignment explanation
Indices: 3882760--3882806 Score: 69
Period size: 21 Copynumber: 2.2 Consensus size: 22
3882750 AAAAAATATA
* *
3882760 AAAATTATATAAAATT-CAAAT
1 AAAATTATAAAAAATTAAAAAT
3882781 AAAATTATAAAAAATTAAAAAT
1 AAAATTATAAAAAATTAAAAAT
3882803 AAAA
1 AAAA
3882807 ATAAAATTAT
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
21 15 0.65
22 8 0.35
ACGTcount: A:0.70, C:0.02, G:0.00, T:0.28
Consensus pattern (22 bp):
AAAATTATAAAAAATTAAAAAT
Found at i:3882801 original size:28 final size:28
Alignment explanation
Indices: 3882743--3882829 Score: 106
Period size: 28 Copynumber: 3.1 Consensus size: 28
3882733 ATAAAAGTAC
*
3882743 AAATTCAAA-AAAA-TATAAAAATTATATA
1 AAATTCAAATAAAATTATAAAAAAT-TA-A
3882771 AAATTCAAATAAAATTATAAAAAATTAA
1 AAATTCAAATAAAATTATAAAAAATTAA
** *
3882799 AAATAAAAATAAAATTATAAAAAAATAA
1 AAATTCAAATAAAATTATAAAAAATTAA
3882827 AAA
1 AAA
3882830 ATCTATATAT
Statistics
Matches: 53, Mismatches: 4, Indels: 4
0.87 0.07 0.07
Matches are distributed among these distances:
28 38 0.72
29 6 0.11
30 9 0.17
ACGTcount: A:0.72, C:0.02, G:0.00, T:0.25
Consensus pattern (28 bp):
AAATTCAAATAAAATTATAAAAAATTAA
Found at i:3882801 original size:46 final size:46
Alignment explanation
Indices: 3882683--3882807 Score: 114
Period size: 46 Copynumber: 2.7 Consensus size: 46
3882673 ATGCAAAAAC
* * *
3882683 TATAAAATTATAAAAAAATTCAAAATTCATAAAAGTTATAAAAATTGAA
1 TATAAAATTAT-AAAAAATT-AAAAAT-ATAAAAATTATAAAAATTCAA
* * *
3882732 TATAAAAGTACAAATTCAA--AAAAATATAAAAATTATATAAAATTCAA
1 TATAAAATTATAAA--AAATTAAAAATATAAAAATTATA-AAAATTCAA
3882779 -ATAAAATTATAAAAAATTAAAAATA-AAAA
1 TATAAAATTATAAAAAATTAAAAATATAAAA
3882808 TAAAATTATA
Statistics
Matches: 62, Mismatches: 9, Indels: 14
0.73 0.11 0.16
Matches are distributed among these distances:
44 2 0.03
45 4 0.06
46 29 0.47
47 13 0.21
48 3 0.05
49 9 0.15
50 2 0.03
ACGTcount: A:0.66, C:0.04, G:0.02, T:0.28
Consensus pattern (46 bp):
TATAAAATTATAAAAAATTAAAAATATAAAAATTATAAAAATTCAA
Found at i:3882821 original size:68 final size:66
Alignment explanation
Indices: 3882704--3882838 Score: 168
Period size: 68 Copynumber: 2.0 Consensus size: 66
3882694 AAAAAAATTC
* * *
3882704 AAAATTCATAAAAGTTATAAAAATTGAATATAAAAGTACAAATTCAAAAAAATATAAAAAT-TAT
1 AAAATTCATAAAAGTTATAAAAATTAAAAATAAAAATACAAATTCAAAAAAATA-AAAAATCTAT
3882768 AT
65 AT
*
3882770 AAAATTCAAATAAAA-TTATAAAAAATTAAAAATAAAAATA-AAATTATAAAAAAATAAAAAATC
1 AAAATTC--ATAAAAGTTAT-AAAAATTAAAAATAAAAATACAAATT-CAAAAAAATAAAAAATC
3882833 TATAT
62 TATAT
3882838 A
1 A
3882839 TTTTTATATT
Statistics
Matches: 60, Mismatches: 4, Indels: 8
0.83 0.06 0.11
Matches are distributed among these distances:
66 7 0.12
67 15 0.25
68 38 0.63
ACGTcount: A:0.67, C:0.04, G:0.02, T:0.27
Consensus pattern (66 bp):
AAAATTCATAAAAGTTATAAAAATTAAAAATAAAAATACAAATTCAAAAAAATAAAAAATCTATA
T
Found at i:3882823 original size:11 final size:10
Alignment explanation
Indices: 3882759--3882830 Score: 51
Period size: 10 Copynumber: 7.3 Consensus size: 10
3882749 AAAAAAATAT
*
3882759 AAAAATTATA
1 AAAAATTAAA
*
3882769 TAAAATTCAAA
1 AAAAATT-AAA
* *
3882780 TAAAATTATA
1 AAAAATTAAA
3882790 AAAAATTAAA
1 AAAAATTAAA
*
3882800 AATAA--AAA
1 AAAAATTAAA
*
3882808 TAAAATTATAA
1 AAAAATTA-AA
3882819 AAAAA-TAAA
1 AAAAATTAAA
3882828 AAA
1 AAA
3882831 TCTATATATT
Statistics
Matches: 49, Mismatches: 9, Indels: 9
0.73 0.13 0.13
Matches are distributed among these distances:
8 6 0.12
9 5 0.10
10 23 0.47
11 15 0.31
ACGTcount: A:0.74, C:0.01, G:0.00, T:0.25
Consensus pattern (10 bp):
AAAAATTAAA
Found at i:3882895 original size:22 final size:22
Alignment explanation
Indices: 3882870--3882911 Score: 66
Period size: 22 Copynumber: 1.9 Consensus size: 22
3882860 TTAATTACAC
*
3882870 ATTTTTAGTTTTTCATTTTTAT
1 ATTTTTACTTTTTCATTTTTAT
*
3882892 ATTTTTACTTTTTGATTTTT
1 ATTTTTACTTTTTCATTTTT
3882912 TGAATTTTTT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.17, C:0.05, G:0.05, T:0.74
Consensus pattern (22 bp):
ATTTTTACTTTTTCATTTTTAT
Found at i:3882919 original size:22 final size:22
Alignment explanation
Indices: 3882872--3882919 Score: 53
Period size: 22 Copynumber: 2.2 Consensus size: 22
3882862 AATTACACAT
* *
3882872 TTTTAGTTTTTCATTTTTATAT
1 TTTTACTTTTTCATTTTTATAA
*
3882894 TTTTACTTTTTGATTTTT-TGAA
1 TTTTACTTTTTCATTTTTAT-AA
3882916 TTTT
1 TTTT
3882920 TTATAATTTT
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
21 1 0.05
22 21 0.95
ACGTcount: A:0.17, C:0.04, G:0.06, T:0.73
Consensus pattern (22 bp):
TTTTACTTTTTCATTTTTATAA
Found at i:3882927 original size:10 final size:10
Alignment explanation
Indices: 3882914--3882959 Score: 51
Period size: 10 Copynumber: 4.8 Consensus size: 10
3882904 TGATTTTTTG
3882914 AATTTTTTAT
1 AATTTTTTAT
*
3882924 AATTTTTT-G
1 AATTTTTTAT
* *
3882933 AATTTTTAAC
1 AATTTTTTAT
3882943 AA-TTTTTAT
1 AATTTTTTAT
3882952 AATTTTTT
1 AATTTTTT
3882960 GAGTTTGTAT
Statistics
Matches: 29, Mismatches: 5, Indels: 4
0.76 0.13 0.11
Matches are distributed among these distances:
9 14 0.48
10 15 0.52
ACGTcount: A:0.30, C:0.02, G:0.02, T:0.65
Consensus pattern (10 bp):
AATTTTTTAT
Found at i:3882930 original size:19 final size:19
Alignment explanation
Indices: 3882906--3882959 Score: 74
Period size: 19 Copynumber: 2.8 Consensus size: 19
3882896 TTACTTTTTG
*
3882906 ATTTTTTGAATTTTTTATA
1 ATTTTTTGAATTTTTTACA
*
3882925 ATTTTTTGAATTTTTAACA
1 ATTTTTTGAATTTTTTACA
3882944 ATTTTTAT-AATTTTTT
1 ATTTTT-TGAATTTTTT
3882960 GAGTTTGTAT
Statistics
Matches: 31, Mismatches: 3, Indels: 2
0.86 0.08 0.06
Matches are distributed among these distances:
19 30 0.97
20 1 0.03
ACGTcount: A:0.28, C:0.02, G:0.04, T:0.67
Consensus pattern (19 bp):
ATTTTTTGAATTTTTTACA
Found at i:3882936 original size:9 final size:9
Alignment explanation
Indices: 3882900--3882961 Score: 56
Period size: 9 Copynumber: 6.8 Consensus size: 9
3882890 ATATTTTTAC
3882900 TTTTTG-AT
1 TTTTTGAAT
3882908 TTTTTGAAT
1 TTTTTGAAT
*
3882917 TTTTTATAAT
1 TTTTT-GAAT
3882927 TTTTTGAAT
1 TTTTTGAAT
**
3882936 TTTTAACAAT
1 TTTT-TGAAT
3882946 TTTTAT-AAT
1 TTTT-TGAAT
3882955 TTTTTGA
1 TTTTTGA
3882962 GTTTGTATAG
Statistics
Matches: 45, Mismatches: 5, Indels: 7
0.79 0.09 0.12
Matches are distributed among these distances:
8 7 0.16
9 22 0.49
10 16 0.36
ACGTcount: A:0.26, C:0.02, G:0.06, T:0.66
Consensus pattern (9 bp):
TTTTTGAAT
Found at i:3882937 original size:28 final size:28
Alignment explanation
Indices: 3882900--3882961 Score: 90
Period size: 28 Copynumber: 2.2 Consensus size: 28
3882890 ATATTTTTAC
* * *
3882900 TTTTTGATTTTTTGA-ATTTTTTATAAT
1 TTTTTGAATTTTTAACAATTTTTATAAT
3882927 TTTTTGAATTTTTAACAATTTTTATAAT
1 TTTTTGAATTTTTAACAATTTTTATAAT
3882955 TTTTTGA
1 TTTTTGA
3882962 GTTTGTATAG
Statistics
Matches: 31, Mismatches: 3, Indels: 1
0.89 0.09 0.03
Matches are distributed among these distances:
27 13 0.42
28 18 0.58
ACGTcount: A:0.26, C:0.02, G:0.06, T:0.66
Consensus pattern (28 bp):
TTTTTGAATTTTTAACAATTTTTATAAT
Found at i:3883038 original size:15 final size:16
Alignment explanation
Indices: 3883011--3883040 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
3883001 TTTTAGCTTT
3883011 TTATTTATTATAATTA
1 TTATTTATTATAATTA
3883027 TTATTT-TTATAATT
1 TTATTTATTATAATT
3883041 TTTAAAATTT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 8 0.57
16 6 0.43
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (16 bp):
TTATTTATTATAATTA
Found at i:3883049 original size:9 final size:9
Alignment explanation
Indices: 3883029--3883082 Score: 54
Period size: 9 Copynumber: 5.8 Consensus size: 9
3883019 TATAATTATT
*
3883029 ATTTTTATA
1 ATTTTTAAA
3883038 ATTTTTAAA
1 ATTTTTAAA
3883047 ATTTTTAATA
1 ATTTTTAA-A
* *
3883057 ATCTTTGATA
1 AT-TTTTAAA
*
3883067 ATTTTTTAA
1 ATTTTTAAA
3883076 ATTTTTA
1 ATTTTTA
3883083 TTTTTAATTA
Statistics
Matches: 36, Mismatches: 7, Indels: 4
0.77 0.15 0.09
Matches are distributed among these distances:
9 26 0.72
10 6 0.17
11 4 0.11
ACGTcount: A:0.35, C:0.02, G:0.02, T:0.61
Consensus pattern (9 bp):
ATTTTTAAA
Found at i:3884726 original size:28 final size:27
Alignment explanation
Indices: 3884661--3884757 Score: 81
Period size: 27 Copynumber: 3.6 Consensus size: 27
3884651 TTAAATTTTG
* * * *
3884661 AAATTTTCAATTTAACCTTCACATGA-A
1 AAATTTTTAATTAAACTTTCA-AAGATA
* *
3884688 AAATTTGTAATTAAACTTTCAACCA-ATG
1 AAATTTTTAATTAAACTTTCAA--AGATA
* *
3884716 AAATTTTTAATTAAATTTTTAAAGATA
1 AAATTTTTAATTAAACTTTCAAAGATA
3884743 AAATTTTTAATTAAA
1 AAATTTTTAATTAAA
3884758 TTCCCACGGA
Statistics
Matches: 56, Mismatches: 10, Indels: 8
0.76 0.14 0.11
Matches are distributed among these distances:
26 2 0.04
27 35 0.62
28 19 0.34
ACGTcount: A:0.45, C:0.09, G:0.04, T:0.41
Consensus pattern (27 bp):
AAATTTTTAATTAAACTTTCAAAGATA
Found at i:3884733 original size:12 final size:12
Alignment explanation
Indices: 3884716--3884759 Score: 52
Period size: 12 Copynumber: 3.4 Consensus size: 12
3884706 TCAACCAATG
3884716 AAATTTTTAATT
1 AAATTTTTAATT
*
3884728 AAATTTTTAAAGATA
1 AAATTTTT--A-ATT
3884743 AAATTTTTAATT
1 AAATTTTTAATT
3884755 AAATT
1 AAATT
3884760 CCCACGGATG
Statistics
Matches: 27, Mismatches: 2, Indels: 6
0.77 0.06 0.17
Matches are distributed among these distances:
12 15 0.56
13 1 0.04
14 1 0.04
15 10 0.37
ACGTcount: A:0.48, C:0.00, G:0.02, T:0.50
Consensus pattern (12 bp):
AAATTTTTAATT
Found at i:3885388 original size:15 final size:15
Alignment explanation
Indices: 3885365--3885394 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
3885355 AAAGAAAAAG
3885365 AATAAAAAAATTTAA
1 AATAAAAAAATTTAA
*
3885380 AATATAAAAATTTAA
1 AATAAAAAAATTTAA
3885395 TGCAGGTGTG
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (15 bp):
AATAAAAAAATTTAA
Found at i:3886622 original size:15 final size:15
Alignment explanation
Indices: 3886585--3886625 Score: 57
Period size: 15 Copynumber: 2.7 Consensus size: 15
3886575 CAAACTTTTA
*
3886585 TTTATATTT-ATTAG
1 TTTATTTTTAATTAG
3886599 TTTATTTTTTAATTAG
1 TTTA-TTTTTAATTAG
3886615 TTTATTTTTAA
1 TTTATTTTTAA
3886626 AAAATATTTA
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
14 4 0.17
15 11 0.46
16 9 0.38
ACGTcount: A:0.27, C:0.00, G:0.05, T:0.68
Consensus pattern (15 bp):
TTTATTTTTAATTAG
Found at i:3886930 original size:11 final size:11
Alignment explanation
Indices: 3886906--3886963 Score: 55
Period size: 11 Copynumber: 5.1 Consensus size: 11
3886896 AATAATTGAA
*
3886906 TATAAATAAAT
1 TATAAATAATT
3886917 TATAAATAATT
1 TATAAATAATT
3886928 TATTAAATAAATT
1 TA-TAAAT-AATT
* *
3886941 T-TAAATGACT
1 TATAAATAATT
3886951 TATAAATTAATT
1 TATAAA-TAATT
3886963 T
1 T
3886964 TTTTAGACAT
Statistics
Matches: 38, Mismatches: 5, Indels: 7
0.76 0.10 0.14
Matches are distributed among these distances:
10 3 0.08
11 21 0.55
12 9 0.24
13 5 0.13
ACGTcount: A:0.52, C:0.02, G:0.02, T:0.45
Consensus pattern (11 bp):
TATAAATAATT
Found at i:3886937 original size:23 final size:25
Alignment explanation
Indices: 3886888--3886946 Score: 77
Period size: 23 Copynumber: 2.4 Consensus size: 25
3886878 TAATATTATT
3886888 AATTATATAATAATTGAATATAAATA
1 AATTATA-AATAATTGAATATAAATA
*
3886914 AATTATAAATAATT-TAT-TAAATA
1 AATTATAAATAATTGAATATAAATA
*
3886937 AATTTTAAAT
1 AATTATAAAT
3886947 GACTTATAAA
Statistics
Matches: 31, Mismatches: 2, Indels: 3
0.86 0.06 0.08
Matches are distributed among these distances:
23 15 0.48
24 2 0.06
25 7 0.23
26 7 0.23
ACGTcount: A:0.56, C:0.00, G:0.02, T:0.42
Consensus pattern (25 bp):
AATTATAAATAATTGAATATAAATA
Found at i:3886953 original size:23 final size:22
Alignment explanation
Indices: 3886906--3886964 Score: 73
Period size: 23 Copynumber: 2.6 Consensus size: 22
3886896 AATAATTGAA
* *
3886906 TATAAATAAATTATAAATAATT
1 TATAAATAAATTTTAAATAACT
*
3886928 TATTAAATAAATTTTAAATGACT
1 TA-TAAATAAATTTTAAATAACT
*
3886951 TATAAATTAATTTT
1 TATAAATAAATTTT
3886965 TTTAGACATC
Statistics
Matches: 32, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
22 13 0.41
23 19 0.59
ACGTcount: A:0.51, C:0.02, G:0.02, T:0.46
Consensus pattern (22 bp):
TATAAATAAATTTTAAATAACT
Found at i:3887642 original size:18 final size:17
Alignment explanation
Indices: 3887618--3887662 Score: 58
Period size: 17 Copynumber: 2.7 Consensus size: 17
3887608 TTAAATTATT
3887618 ATAATAAAATATTTTAA
1 ATAATAAAATATTTTAA
*
3887635 ATTAATAATA-ATTTTAA
1 A-TAATAAAATATTTTAA
3887652 A-AATAAAATAT
1 ATAATAAAATAT
3887663 AAATATAAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 5
0.77 0.06 0.16
Matches are distributed among these distances:
15 6 0.25
16 2 0.08
17 9 0.38
18 7 0.29
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (17 bp):
ATAATAAAATATTTTAA
Found at i:3887686 original size:65 final size:63
Alignment explanation
Indices: 3887562--3887707 Score: 152
Period size: 65 Copynumber: 2.3 Consensus size: 63
3887552 ATACGTTAAT
* * * *
3887562 AATATATTAAATATAATTATAATATAAAAATAATATAAATTTAAAATTAAATTATTATAATAA
1 AATATATTAAATATAATAATAATATAAAAATAATATAAATATAAAATTAAATAAATATAATAA
* *
3887625 AATATTTTAAAT-TAATAATAATTTTAAAAATAAAATATAAATATAAAA-TAATATAAATATAAT
1 AATATATTAAATATAATAATAA-TATAAAAAT--AATATAAATATAAAATTAA-ATAAATATAAT
*
3887688 ATG
62 A-A
* *
3887691 AACATATTATATATAAT
1 AATATATTAAATATAAT
3887708 TTACTTTATG
Statistics
Matches: 67, Mismatches: 10, Indels: 8
0.79 0.12 0.09
Matches are distributed among these distances:
62 8 0.12
63 19 0.28
64 3 0.04
65 24 0.36
66 9 0.13
67 4 0.06
ACGTcount: A:0.60, C:0.01, G:0.01, T:0.39
Consensus pattern (63 bp):
AATATATTAAATATAATAATAATATAAAAATAATATAAATATAAAATTAAATAAATATAATAA
Found at i:3887687 original size:11 final size:11
Alignment explanation
Indices: 3887571--3887703 Score: 65
Period size: 11 Copynumber: 11.5 Consensus size: 11
3887561 TAATATATTA
*
3887571 AATATAATTAT
1 AATATAAATAT
*
3887582 AATATAAAAAT
1 AATATAAATAT
*
3887593 AATATAAATTT
1 AATATAAATAT
*
3887604 AAAATTAAATTAT
1 AATA-TAAA-TAT
*
3887617 TATAATAAA-AT
1 AAT-ATAAATAT
* *
3887628 ATTTTAAAT-T
1 AATATAAATAT
* *
3887638 AATAATAATTTT
1 AAT-ATAAATAT
*
3887650 AAAAATAAAATAT
1 -AATAT-AAATAT
3887663 AAATATAAA-AT
1 -AATATAAATAT
3887674 AATATAAATAT
1 AATATAAATAT
3887685 AATATGAACATAT
1 AATAT-AA-ATAT
*
3887698 TATATA
1 AATATA
3887704 TAATTTACTT
Statistics
Matches: 92, Mismatches: 19, Indels: 21
0.70 0.14 0.16
Matches are distributed among these distances:
10 15 0.16
11 37 0.40
12 13 0.14
13 26 0.28
14 1 0.01
ACGTcount: A:0.60, C:0.01, G:0.01, T:0.38
Consensus pattern (11 bp):
AATATAAATAT
Found at i:3887798 original size:19 final size:18
Alignment explanation
Indices: 3887757--3887803 Score: 51
Period size: 19 Copynumber: 2.6 Consensus size: 18
3887747 TAAAATTTAA
3887757 TTTATTTA-AATTATATT
1 TTTATTTATAATTATATT
**
3887774 AATATTTATAATTTATATT
1 TTTATTTATAA-TTATATT
*
3887793 TTTATTAATAA
1 TTTATTTATAA
3887804 ATAAAAAATA
Statistics
Matches: 23, Mismatches: 5, Indels: 2
0.77 0.17 0.07
Matches are distributed among these distances:
17 6 0.26
18 2 0.09
19 15 0.65
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (18 bp):
TTTATTTATAATTATATT
Found at i:3888674 original size:27 final size:24
Alignment explanation
Indices: 3888615--3888684 Score: 74
Period size: 27 Copynumber: 2.9 Consensus size: 24
3888605 ATAATTTTTT
3888615 ATAATAT--ATATAATATAAAAAA
1 ATAATATAAATATAATATAAAAAA
3888637 ATAAT-TAAAATATAATATGATATAAAA
1 ATAATAT-AAATATAATAT-A-A-AAAA
*
3888664 ATAATATAAATATTATATAAA
1 ATAATATAAATATAATATAAA
3888685 TATATCAACA
Statistics
Matches: 40, Mismatches: 1, Indels: 12
0.75 0.02 0.23
Matches are distributed among these distances:
21 1 0.03
22 5 0.12
24 10 0.25
25 2 0.05
26 2 0.05
27 19 0.47
28 1 0.03
ACGTcount: A:0.64, C:0.00, G:0.01, T:0.34
Consensus pattern (24 bp):
ATAATATAAATATAATATAAAAAA
Found at i:3888685 original size:11 final size:11
Alignment explanation
Indices: 3888614--3888688 Score: 63
Period size: 11 Copynumber: 7.4 Consensus size: 11
3888604 AATAATTTTT
3888614 TATAATAT--A
1 TATAATATAAA
3888623 TATAATATAAA
1 TATAATATAAA
*
3888634 -A-AA-ATAAT
1 TATAATATAAA
*
3888642 TAAAATAT-AA
1 TATAATATAAA
*
3888652 TATGATATAAA
1 TATAATATAAA
*
3888663 AATAATATAAA
1 TATAATATAAA
*
3888674 TATTATATAAA
1 TATAATATAAA
3888685 TATA
1 TATA
3888689 TCAACATATT
Statistics
Matches: 51, Mismatches: 9, Indels: 10
0.73 0.13 0.14
Matches are distributed among these distances:
8 4 0.08
9 11 0.22
10 10 0.20
11 26 0.51
ACGTcount: A:0.63, C:0.00, G:0.01, T:0.36
Consensus pattern (11 bp):
TATAATATAAA
Found at i:3888859 original size:2 final size:2
Alignment explanation
Indices: 3888854--3888883 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
3888844 AGGACAAAAA
3888854 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
3888884 TGTTATAAAA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:3893220 original size:22 final size:23
Alignment explanation
Indices: 3893188--3893234 Score: 60
Period size: 22 Copynumber: 2.1 Consensus size: 23
3893178 TTTATACATG
* *
3893188 ATACAATAAAAATATATAATTTT
1 ATACAATAAAAATAAATAATCTT
*
3893211 ATACAA-AAAATTAAATAATCTT
1 ATACAATAAAAATAAATAATCTT
3893233 AT
1 AT
3893235 TTCATTAAAA
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
22 15 0.71
23 6 0.29
ACGTcount: A:0.57, C:0.06, G:0.00, T:0.36
Consensus pattern (23 bp):
ATACAATAAAAATAAATAATCTT
Found at i:3893449 original size:14 final size:15
Alignment explanation
Indices: 3893426--3893501 Score: 66
Period size: 14 Copynumber: 4.9 Consensus size: 15
3893416 ATATTTTAAT
3893426 AATTTATATTATATA
1 AATTTATATTATATA
3893441 AATTT-TATTATATA
1 AATTTATATTATATA
*
3893455 TATTTATATTA-ATTA
1 AATTTATATTATA-TA
* * *
3893470 TTATTTTTATTTTTATTA
1 -AATTTATA-TTATA-TA
3893488 AATTTATATTATAT
1 AATTTATATTATAT
3893502 TTTAATTATT
Statistics
Matches: 50, Mismatches: 6, Indels: 10
0.76 0.09 0.15
Matches are distributed among these distances:
14 14 0.28
15 13 0.26
16 11 0.22
17 8 0.16
18 4 0.08
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (15 bp):
AATTTATATTATATA
Found at i:3893464 original size:15 final size:15
Alignment explanation
Indices: 3893402--3893501 Score: 73
Period size: 15 Copynumber: 6.5 Consensus size: 15
3893392 TATTTAAAAT
3893402 TATTATATAT-TTTAA
1 TATTATATATATTT-A
*
3893417 TATTTTA-ATAATTTA
1 TATTATATAT-ATTTA
*
3893432 TATTATATAAATTT-
1 TATTATATATATTTA
3893446 TATTATATATATTTA
1 TATTATATATATTTA
*
3893461 TATTA-ATTATTATTTT
1 TATTATA-TA-TATTTA
* *
3893477 TATTTTTATTAAATTTA
1 TA-TTATA-TATATTTA
3893494 TATTATAT
1 TATTATAT
3893502 TTTAATTATT
Statistics
Matches: 68, Mismatches: 9, Indels: 16
0.73 0.10 0.17
Matches are distributed among these distances:
14 16 0.24
15 25 0.37
16 15 0.22
17 8 0.12
18 4 0.06
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (15 bp):
TATTATATATATTTA
Found at i:3893494 original size:46 final size:44
Alignment explanation
Indices: 3893378--3893512 Score: 120
Period size: 44 Copynumber: 3.0 Consensus size: 44
3893368 GTTTTTGGTG
*
3893378 TTATT-TTTTTATATTATTTAAAATTATTATATAT-TTTAATATT
1 TTATTATTTTTATATTA-TTAAATTTATTATATATATTTAATATT
* *
3893421 TTAATA-ATTTATATTATATAAATTTTATTATATATATTT-ATATT
1 TTATTATTTTTATATTAT-TAAA-TTTATTATATATATTTAATATT
*
3893465 AATTATTATTTTTATTTTTATTAAATTTA-TAT-TATATTTTAATTATT
1 --TTATTATTTTTA-TATTATTAAATTTATTATATATA-TTTAA-TATT
3893512 T
1 T
3893513 AATAAATAAT
Statistics
Matches: 75, Mismatches: 6, Indels: 20
0.74 0.06 0.20
Matches are distributed among these distances:
42 1 0.01
43 17 0.23
44 20 0.27
45 10 0.13
46 10 0.13
47 12 0.16
48 5 0.07
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (44 bp):
TTATTATTTTTATATTATTAAATTTATTATATATATTTAATATT
Found at i:3893504 original size:22 final size:23
Alignment explanation
Indices: 3893446--3893509 Score: 71
Period size: 22 Copynumber: 2.9 Consensus size: 23
3893436 ATATAAATTT
* *
3893446 TATTATA-TATATTTATATTAAT
1 TATTATATTATATTTTTATTAAA
*
3893468 TATTAT-TTTTATTTTTATTAAA
1 TATTATATTATATTTTTATTAAA
*
3893490 T-TTATATTATATTTTAATTA
1 TATTATATTATATTTTTATTA
3893510 TTTAATAAAT
Statistics
Matches: 35, Mismatches: 5, Indels: 4
0.80 0.11 0.09
Matches are distributed among these distances:
21 4 0.11
22 31 0.89
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (23 bp):
TATTATATTATATTTTTATTAAA
Found at i:3893511 original size:62 final size:61
Alignment explanation
Indices: 3893386--3893501 Score: 148
Period size: 62 Copynumber: 1.9 Consensus size: 61
3893376 TGTTATTTTT
3893386 TTATATTATTTAAAATTATTATATATTTTAATATTTTAATAATTTATATTATATAAATTTTA
1 TTATATTATTTAAAATTATTATATATTTTAATATTTTAATAATTTATATTATATAAA-TTTA
* * *
3893448 TTATATATATTT-ATATTAATTAT-TATTTTTAT-TTTTATTAAATTTATATTATAT
1 TTATAT-TATTTAAAATT-ATTATATATTTTAATATTTTAAT-AATTTATATTATAT
3893502 TTTAATTATT
Statistics
Matches: 48, Mismatches: 3, Indels: 6
0.84 0.05 0.11
Matches are distributed among these distances:
61 6 0.12
62 32 0.67
63 10 0.21
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (61 bp):
TTATATTATTTAAAATTATTATATATTTTAATATTTTAATAATTTATATTATATAAATTTA
Found at i:3894146 original size:13 final size:13
Alignment explanation
Indices: 3894117--3894165 Score: 55
Period size: 13 Copynumber: 3.8 Consensus size: 13
3894107 AAATAAATAC
*
3894117 ATAAT-TATTTGT
1 ATAATATATTAGT
*
3894129 TTAATATATTAGT
1 ATAATATATTAGT
* *
3894142 ATAATATATAAAT
1 ATAATATATTAGT
3894155 ATAATATATTA
1 ATAATATATTA
3894166 AATAAATTTT
Statistics
Matches: 30, Mismatches: 6, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
12 4 0.13
13 26 0.87
ACGTcount: A:0.47, C:0.00, G:0.04, T:0.49
Consensus pattern (13 bp):
ATAATATATTAGT
Found at i:3895095 original size:33 final size:31
Alignment explanation
Indices: 3895057--3895123 Score: 80
Period size: 33 Copynumber: 2.1 Consensus size: 31
3895047 TTATGCATAG
3895057 AATAATTTAACATAAAAACTTATTTGAATTTAA
1 AATAATTTAACATAAAAA-TTATTT-AATTTAA
* ** *
3895090 AATAATTTGAGTTCAAAATTATTTAATTTAA
1 AATAATTTAACATAAAAATTATTTAATTTAA
3895121 AAT
1 AAT
3895124 TACTTAAATC
Statistics
Matches: 30, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
31 10 0.33
32 6 0.20
33 14 0.47
ACGTcount: A:0.49, C:0.04, G:0.04, T:0.42
Consensus pattern (31 bp):
AATAATTTAACATAAAAATTATTTAATTTAA
Found at i:3895124 original size:15 final size:16
Alignment explanation
Indices: 3895071--3895125 Score: 67
Period size: 16 Copynumber: 3.4 Consensus size: 16
3895061 ATTTAACATA
3895071 AAAACTTATTTGAATTT
1 AAAA-TTATTTGAATTT
* * *
3895088 AAAATAATTTGAGTTC
1 AAAATTATTTGAATTT
3895104 AAAATTATTT-AATTT
1 AAAATTATTTGAATTT
3895119 AAAATTA
1 AAAATTA
3895126 CTTAAATCTA
Statistics
Matches: 32, Mismatches: 6, Indels: 2
0.80 0.15 0.05
Matches are distributed among these distances:
15 10 0.31
16 18 0.56
17 4 0.12
ACGTcount: A:0.47, C:0.04, G:0.05, T:0.44
Consensus pattern (16 bp):
AAAATTATTTGAATTT
Found at i:3896795 original size:32 final size:32
Alignment explanation
Indices: 3896733--3896795 Score: 81
Period size: 32 Copynumber: 2.0 Consensus size: 32
3896723 AATTTCCATC
* * * * *
3896733 GAAATAATTATTTCTTATGGAATTTTCATTGG
1 GAAATAATTATTTATGATAGAATATACATTGG
3896765 GAAATAATTATTTATGATAGAATATACATTG
1 GAAATAATTATTTATGATAGAATATACATTG
3896796 AGAGATCAAC
Statistics
Matches: 26, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
32 26 1.00
ACGTcount: A:0.38, C:0.05, G:0.14, T:0.43
Consensus pattern (32 bp):
GAAATAATTATTTATGATAGAATATACATTGG
Found at i:3901391 original size:3 final size:3
Alignment explanation
Indices: 3901383--3901428 Score: 92
Period size: 3 Copynumber: 15.3 Consensus size: 3
3901373 CTATATCAAC
3901383 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT A
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT A
3901429 AAGCTTTTAA
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 43 1.00
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (3 bp):
ATT
Found at i:3901507 original size:18 final size:18
Alignment explanation
Indices: 3901486--3901525 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 18
3901476 ATTAAAAATT
3901486 ATTAAAAAATTAAATAAA
1 ATTAAAAAATTAAATAAA
* **
3901504 ATTATATTATTAAATAAA
1 ATTAAAAAATTAAATAAA
3901522 ATTA
1 ATTA
3901526 GGTATATTTA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (18 bp):
ATTAAAAAATTAAATAAA
Found at i:3901748 original size:14 final size:15
Alignment explanation
Indices: 3901712--3901741 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
3901702 ATTTAAAAAA
3901712 AGTAAATAGTTTTTT
1 AGTAAATAGTTTTTT
3901727 AGTAAATAGTTTTTT
1 AGTAAATAGTTTTTT
3901742 TTTAATAAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.33, C:0.00, G:0.13, T:0.53
Consensus pattern (15 bp):
AGTAAATAGTTTTTT
Found at i:3902528 original size:24 final size:23
Alignment explanation
Indices: 3902505--3902554 Score: 59
Period size: 21 Copynumber: 2.2 Consensus size: 23
3902495 TCAAAAATTA
*
3902505 ATAATATTTTTTTATA-TAATATT
1 ATAA-ATTATTTTATATTAATATT
3902528 A-AAATTATTTTATATTAATATTT
1 ATAAATTATTTTATATTAATA-TT
3902551 ATAA
1 ATAA
3902555 CTAAAAATAT
Statistics
Matches: 23, Mismatches: 1, Indels: 5
0.79 0.03 0.17
Matches are distributed among these distances:
21 10 0.43
22 7 0.30
23 4 0.17
24 2 0.09
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (23 bp):
ATAAATTATTTTATATTAATATT
Found at i:3905546 original size:16 final size:16
Alignment explanation
Indices: 3905525--3905556 Score: 64
Period size: 16 Copynumber: 2.0 Consensus size: 16
3905515 AAATGGCTAA
3905525 TCTATAAGCACAGGGC
1 TCTATAAGCACAGGGC
3905541 TCTATAAGCACAGGGC
1 TCTATAAGCACAGGGC
3905557 ACAATCTAAC
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.31, C:0.25, G:0.25, T:0.19
Consensus pattern (16 bp):
TCTATAAGCACAGGGC
Found at i:3914941 original size:8 final size:8
Alignment explanation
Indices: 3914930--3914959 Score: 51
Period size: 8 Copynumber: 3.6 Consensus size: 8
3914920 TTTCAAAATT
3914930 AATTAAAA
1 AATTAAAA
3914938 AATTAAAGA
1 AATTAAA-A
3914947 AATTAAAA
1 AATTAAAA
3914955 AATTA
1 AATTA
3914960 TAAGAAAATT
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
8 13 0.62
9 8 0.38
ACGTcount: A:0.70, C:0.00, G:0.03, T:0.27
Consensus pattern (8 bp):
AATTAAAA
Found at i:3914950 original size:17 final size:18
Alignment explanation
Indices: 3914930--3914966 Score: 67
Period size: 17 Copynumber: 2.1 Consensus size: 18
3914920 TTTCAAAATT
3914930 AATTAAAAAATTA-AAGA
1 AATTAAAAAATTATAAGA
3914947 AATTAAAAAATTATAAGA
1 AATTAAAAAATTATAAGA
3914965 AA
1 AA
3914967 ATTTTACAAT
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
17 13 0.68
18 6 0.32
ACGTcount: A:0.70, C:0.00, G:0.05, T:0.24
Consensus pattern (18 bp):
AATTAAAAAATTATAAGA
Found at i:3918770 original size:51 final size:50
Alignment explanation
Indices: 3918650--3918771 Score: 138
Period size: 50 Copynumber: 2.4 Consensus size: 50
3918640 TTGGAGATAA
* * *
3918650 AAACC-GGGTTGGAGTATCCCCAATGGTAGAAAATCGATGTTTTGGAAAC
1 AAACCAGGGTTGGAGTATCCCCAATGATAGAAAATCAATGTTTTAGAAAC
** * * * *
3918699 AAACTGGGGTTGGAGTATCCCCGATTATGGAAAATCAATGTTTTAGAAAT
1 AAACCAGGGTTGGAGTATCCCCAATGATAGAAAATCAATGTTTTAGAAAC
*
3918749 AAAGCCAGGGTTGAAGTATCCCC
1 AAA-CCAGGGTTGGAGTATCCCC
3918772 TTGAAAATAA
Statistics
Matches: 60, Mismatches: 11, Indels: 2
0.82 0.15 0.03
Matches are distributed among these distances:
49 4 0.07
50 40 0.67
51 16 0.27
ACGTcount: A:0.33, C:0.16, G:0.25, T:0.25
Consensus pattern (50 bp):
AAACCAGGGTTGGAGTATCCCCAATGATAGAAAATCAATGTTTTAGAAAC
Found at i:3918838 original size:79 final size:79
Alignment explanation
Indices: 3918703--3918900 Score: 254
Period size: 79 Copynumber: 2.5 Consensus size: 79
3918693 GGAAACAAAC
* * *
3918703 TGGGGTTGGAGTATCCCCGATTATGGAAAATCAATGTTTTAGAAATAAAGCCAGGGTTGAAGTAT
1 TGGGGTTGGAGTATCCCCGATTGTGGAAAATCAATATTTTAGAAATAAAACCAGGGTTGAAGTAT
3918768 CCCCTT-GAAAATAA
66 -CCCTTCGAAAATAA
* * * * * * *
3918782 TGGGGTTGGAGTATCCCCGATGGTAGAAAATTAGTATTTTGGAAATAAAACTAGGGTTGGAGTAT
1 TGGGGTTGGAGTATCCCCGATTGTGGAAAATCAATATTTTAGAAATAAAACCAGGGTTGAAGTAT
*
3918847 CTCTTCGAAAATAA
66 CCCTTCGAAAATAA
** *
3918861 CAGGGTTGGAGTATCCCCGATTGTGGAAAATCGATATTTT
1 TGGGGTTGGAGTATCCCCGATTGTGGAAAATCAATATTTT
3918901 TCTTTTGAAG
Statistics
Matches: 100, Mismatches: 18, Indels: 2
0.83 0.15 0.02
Matches are distributed among these distances:
78 4 0.04
79 96 0.96
ACGTcount: A:0.32, C:0.13, G:0.26, T:0.30
Consensus pattern (79 bp):
TGGGGTTGGAGTATCCCCGATTGTGGAAAATCAATATTTTAGAAATAAAACCAGGGTTGAAGTAT
CCCTTCGAAAATAA
Found at i:3921319 original size:9 final size:9
Alignment explanation
Indices: 3921307--3921353 Score: 69
Period size: 9 Copynumber: 5.3 Consensus size: 9
3921297 ATTATTATTA
3921307 TTTTTGATT
1 TTTTTGATT
3921316 TTTTTGATT
1 TTTTTGATT
*
3921325 TTTTTGA-A
1 TTTTTGATT
3921333 TTTTTGATT
1 TTTTTGATT
*
3921342 TCTTTGATT
1 TTTTTGATT
3921351 TTT
1 TTT
3921354 AATTTTCTTG
Statistics
Matches: 33, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
8 7 0.21
9 26 0.79
ACGTcount: A:0.13, C:0.02, G:0.11, T:0.74
Consensus pattern (9 bp):
TTTTTGATT
Found at i:3921360 original size:17 final size:18
Alignment explanation
Indices: 3921316--3921362 Score: 64
Period size: 17 Copynumber: 2.8 Consensus size: 18
3921306 ATTTTTGATT
3921316 TTTTTGATTTT-TTTGAA
1 TTTTTGATTTTCTTTGAA
3921333 TTTTTGA-TTTCTTTG-A
1 TTTTTGATTTTCTTTGAA
*
3921349 TTTTTAATTTTCTT
1 TTTTTGATTTTCTT
3921363 GTGTCGAAAA
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
16 10 0.37
17 17 0.63
ACGTcount: A:0.15, C:0.04, G:0.09, T:0.72
Consensus pattern (18 bp):
TTTTTGATTTTCTTTGAA
Found at i:3922336 original size:13 final size:13
Alignment explanation
Indices: 3922318--3922343 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
3922308 TACAGCAAGT
3922318 ATGTATCGATACA
1 ATGTATCGATACA
3922331 ATGTATCGATACA
1 ATGTATCGATACA
3922344 CAAAAAATTG
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:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:3924595 original size:21 final size:21
Alignment explanation
Indices: 3924562--3924606 Score: 56
Period size: 21 Copynumber: 2.1 Consensus size: 21
3924552 TTGCAAGTTG
*
3924562 AAATAAAGAAGTTGGCTAATGA
1 AAATAAAGAAGTTAGCTAA-GA
*
3924584 AAATAATG-AGTTAGCTAAGA
1 AAATAAAGAAGTTAGCTAAGA
3924604 AAA
1 AAA
3924607 ATGAAAACTT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
20 5 0.24
21 9 0.43
22 7 0.33
ACGTcount: A:0.53, C:0.04, G:0.20, T:0.22
Consensus pattern (21 bp):
AAATAAAGAAGTTAGCTAAGA
Found at i:3926430 original size:15 final size:15
Alignment explanation
Indices: 3926410--3926440 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
3926400 TAAAAATGTC
*
3926410 CAAAATGAGGAAGCT
1 CAAAATGAAGAAGCT
3926425 CAAAATGAAGAAGCT
1 CAAAATGAAGAAGCT
3926440 C
1 C
3926441 CAAACGAAAT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.48, C:0.16, G:0.23, T:0.13
Consensus pattern (15 bp):
CAAAATGAAGAAGCT
Found at i:3928515 original size:13 final size:13
Alignment explanation
Indices: 3928497--3928521 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
3928487 GGAAATTCAA
3928497 TGTATCGATACAT
1 TGTATCGATACAT
3928510 TGTATCGATACA
1 TGTATCGATACA
3928522 GGGTGATTAT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:3932076 original size:52 final size:52
Alignment explanation
Indices: 3931983--3932335 Score: 207
Period size: 52 Copynumber: 6.8 Consensus size: 52
3931973 ATAAAGGTGC
* * * *
3931983 CAATATGCTGATTCAAGGCCAGTGATATTAGGCTTAGAGGTGCGAAGAATGA
1 CAATATGCTGATTCAAGGCCAGCGACATTAGACTTAGAGGTGAGAAGAATGA
* *
3932035 CAATGTGCTGATTCACGGCCAGCGACATTAGACTT-GAAGGTGAGAAGAATGA
1 CAATATGCTGATTCAAGGCCAGCGACATTAGACTTAG-AGGTGAGAAGAATGA
* * * * * * ** ** *
3932087 CAACATACTAATTCAAGGCCAGTGACATTGGGCTTAG-GGATGTTAA-TTTGC
1 CAATATGCTGATTCAAGGCCAGCGACATTAGACTTAGAGG-TGAGAAGAATGA
* ** * * * *
3932138 CAATATGCTGATTCAAGGCTAGCGACATTAGACTTTA-ACATGATAGGGATGC
1 CAATATGCTGATTCAAGGCCAGCGACATTAGAC-TTAGAGGTGAGAAGAATGA
* * * * * * *
3932190 CAATTTGCTAATTCAAGGCCAACGACATTAGACTTAAAGATG-GCAA-AGGTGC
1 CAATATGCTGATTCAAGGCCAGCGACATTAGACTTAGAGGTGAG-AAGA-ATGA
* * * * ** ** *
3932242 CAATATGCTGATTCAAGGCCAGCGATATTGGACTTAAAAGTGCCAA-AGGGG
1 CAATATGCTGATTCAAGGCCAGCGACATTAGACTTAGAGGTGAGAAGAATGA
* * * *
3932293 CTAATATGTTGATTCAAGGCCAGCGATATTGGACTTAAAGGTG
1 C-AATATGCTGATTCAAGGCCAGCGACATTAGACTTAGAGGTG
3932336 TCAATGTGCT
Statistics
Matches: 237, Mismatches: 53, Indels: 22
0.76 0.17 0.07
Matches are distributed among these distances:
51 41 0.17
52 195 0.82
53 1 0.00
ACGTcount: A:0.33, C:0.17, G:0.25, T:0.25
Consensus pattern (52 bp):
CAATATGCTGATTCAAGGCCAGCGACATTAGACTTAGAGGTGAGAAGAATGA
Found at i:3932201 original size:103 final size:103
Alignment explanation
Indices: 3931980--3932276 Score: 281
Period size: 103 Copynumber: 2.9 Consensus size: 103
3931970 ATGATAAAGG
* * * * *
3931980 TGCCAATATGCTGATTCAAGGCCAGTGATATTAGGCTTAGAGG-TGCGAAGAATGACAATGTGCT
1 TGCCAATATGCTAATTCAAGGCCAGTGACATTAGGCTTAG-GGATGC-AAAAATGCCAATATGCT
* **
3932044 GATTCACGGCCAGCGACATTAGACTTGAAGGTGAGAAGAA
64 GATTCAAGGCCAGCGACATTAGACTTGAACATGAGAAGAA
* * * * ** **
3932084 TGACAACATACTAATTCAAGGCCAGTGACATTGGGCTTAGGGATGTTAATTTGCCAATATGCTGA
1 TGCCAATATGCTAATTCAAGGCCAGTGACATTAGGCTTAGGGATGCAAAAATGCCAATATGCTGA
* * * * *
3932149 TTCAAGGCTAGCGACATTAGACTTTAACATGATAGGGA
66 TTCAAGGCCAGCGACATTAGACTTGAACATGAGAAGAA
* ** * ** **
3932187 TGCCAATTTGCTAATTCAAGGCCAACGACATTAGACTTAAAGATGGCAAAGGTGCCAATATGCTG
1 TGCCAATATGCTAATTCAAGGCCAGTGACATTAGGCTTAGGGAT-GCAAAAATGCCAATATGCTG
* *
3932252 ATTCAAGGCCAGCGATATTGGACTT
65 ATTCAAGGCCAGCGACATTAGACTT
3932277 AAAAGTGCCA
Statistics
Matches: 153, Mismatches: 38, Indels: 4
0.78 0.19 0.02
Matches are distributed among these distances:
103 79 0.52
104 74 0.48
ACGTcount: A:0.32, C:0.18, G:0.25, T:0.26
Consensus pattern (103 bp):
TGCCAATATGCTAATTCAAGGCCAGTGACATTAGGCTTAGGGATGCAAAAATGCCAATATGCTGA
TTCAAGGCCAGCGACATTAGACTTGAACATGAGAAGAA
Found at i:3932308 original size:104 final size:103
Alignment explanation
Indices: 3932135--3932332 Score: 238
Period size: 104 Copynumber: 1.9 Consensus size: 103
3932125 GATGTTAATT
* * * *
3932135 TGCCAATATGCTGATTCAAGGCTAGCGACATTAGACTTTAACATGATAGGGATGCCAATTTGCTA
1 TGCCAATATGCTGATTCAAGGCCAGCGACATTAGACTTTAAAATGAAAGGGA-GCCAATATGCTA
3932200 ATTCAAGGCCAACGACATTAGACTTAAAGATGGCAAAGG
65 ATTCAAGGCCAACGACATTAGACTTAAAGATGGCAAAGG
* * * *
3932239 TGCCAATATGCTGATTCAAGGCCAGCGATATTGGAC-TTAAAAGTGCCAAAGGG-GCTAATATGT
1 TGCCAATATGCTGATTCAAGGCCAGCGACATTAGACTTTAAAA-TG--AAAGGGAGCCAATATGC
* * * *
3932302 TGATTCAAGGCCAGCGATATTGGACTTAAAG
63 TAATTCAAGGCCAACGACATTAGACTTAAAG
3932333 GTGTCAATGT
Statistics
Matches: 79, Mismatches: 12, Indels: 6
0.81 0.12 0.06
Matches are distributed among these distances:
103 5 0.06
104 69 0.87
106 5 0.06
ACGTcount: A:0.33, C:0.18, G:0.24, T:0.25
Consensus pattern (103 bp):
TGCCAATATGCTGATTCAAGGCCAGCGACATTAGACTTTAAAATGAAAGGGAGCCAATATGCTAA
TTCAAGGCCAACGACATTAGACTTAAAGATGGCAAAGG
Found at i:3932425 original size:32 final size:32
Alignment explanation
Indices: 3932381--3932627 Score: 297
Period size: 32 Copynumber: 7.7 Consensus size: 32
3932371 TAGAAGGAAA
3932381 TGCCACCAACTTGTGTGGGCTTTTGAAAGGGT
1 TGCCACCAACTTGTGTGGGCTTTTGAAAGGGT
* *
3932413 TACCACCCACTTGTGTGGGC-TTT-AAAGAAGGT
1 TGCCACCAACTTGTGTGGGCTTTTGAAAG--GGT
* *
3932445 TGCTACCAACTTGTGTGGGCTTTAGAAAGGGT
1 TGCCACCAACTTGTGTGGGCTTTTGAAAGGGT
3932477 TGCCACCAACTTGTGTGGGCTTTTG-AAGAGGT
1 TGCCACCAACTTGTGTGGGCTTTTGAAAG-GGT
* * *
3932509 TGCCACCAACTTGTGTGGACCTTAGAAAGGGT
1 TGCCACCAACTTGTGTGGGCTTTTGAAAGGGT
* * *
3932541 TGCCACCAA-TTGGTGTGGACCTTAGAAAGGGT
1 TGCCACCAACTT-GTGTGGGCTTTTGAAAGGGT
* *
3932573 TGCTACCAACTTGTGTGGACTTTTG-AAGAGGT
1 TGCCACCAACTTGTGTGGGCTTTTGAAAG-GGT
*
3932605 TGCCACTAACTTGTGTGGGCTTT
1 TGCCACCAACTTGTGTGGGCTTT
3932628 GAAGAAGGTT
Statistics
Matches: 189, Mismatches: 17, Indels: 18
0.84 0.08 0.08
Matches are distributed among these distances:
30 4 0.02
31 11 0.06
32 163 0.86
33 7 0.04
34 4 0.02
ACGTcount: A:0.21, C:0.19, G:0.29, T:0.30
Consensus pattern (32 bp):
TGCCACCAACTTGTGTGGGCTTTTGAAAGGGT
Found at i:3932542 original size:96 final size:96
Alignment explanation
Indices: 3932381--3932637 Score: 340
Period size: 96 Copynumber: 2.7 Consensus size: 96
3932371 TAGAAGGAAA
* * * *
3932381 TGCCACCAACTTGTGTGGGCTTTTGAA-AGGGTTACCACCCACTTGTGTGGGCTTTAAAGAAGGT
1 TGCCACCAACTTGTGTGGGCTTTTGAAGA-GGTTGCCACCAACTTGTGTGGACCTTAAAGAAGGT
* * *
3932445 TGCTACCAACTT-GTGTGGGCTTTAGAAAGGGT
65 TGCCACCAA-TTGGTGTGGACCTTAGAAAGGGT
*
3932477 TGCCACCAACTTGTGTGGGCTTTTGAAGAGGTTGCCACCAACTTGTGTGGACCTTAGAA-AGGGT
1 TGCCACCAACTTGTGTGGGCTTTTGAAGAGGTTGCCACCAACTTGTGTGGACCTTA-AAGAAGGT
3932541 TGCCACCAATTGGTGTGGACCTTAGAAAGGGT
65 TGCCACCAATTGGTGTGGACCTTAGAAAGGGT
* * * * * *
3932573 TGCTACCAACTTGTGTGGACTTTTGAAGAGGTTGCCACTAACTTGTGTGGGCTTTGAAGAAGGTT
1 TGCCACCAACTTGTGTGGGCTTTTGAAGAGGTTGCCACCAACTTGTGTGGACCTTAAAGAAGGTT
3932638 TCTCCACTGC
Statistics
Matches: 142, Mismatches: 15, Indels: 8
0.86 0.09 0.05
Matches are distributed among these distances:
95 4 0.03
96 135 0.95
97 3 0.02
ACGTcount: A:0.22, C:0.18, G:0.30, T:0.30
Consensus pattern (96 bp):
TGCCACCAACTTGTGTGGGCTTTTGAAGAGGTTGCCACCAACTTGTGTGGACCTTAAAGAAGGTT
GCCACCAATTGGTGTGGACCTTAGAAAGGGT
Found at i:3932881 original size:28 final size:28
Alignment explanation
Indices: 3932811--3932887 Score: 111
Period size: 28 Copynumber: 2.8 Consensus size: 28
3932801 TATAGCATGC
* * *
3932811 GCCACT-AATAGTGGACTTCGAAGAGGT
1 GCCACTGACTAGTGGGCTTTGAAGAGGT
3932838 GCCACTGACTAGTGGGCTTTGAAGAGGT
1 GCCACTGACTAGTGGGCTTTGAAGAGGT
*
3932866 GCCATTGACTAGTGGGCTTTGA
1 GCCACTGACTAGTGGGCTTTGA
3932888 GAAGGGATTC
Statistics
Matches: 45, Mismatches: 4, Indels: 1
0.90 0.08 0.02
Matches are distributed among these distances:
27 6 0.13
28 39 0.87
ACGTcount: A:0.23, C:0.18, G:0.32, T:0.26
Consensus pattern (28 bp):
GCCACTGACTAGTGGGCTTTGAAGAGGT
Found at i:3934100 original size:12 final size:12
Alignment explanation
Indices: 3934085--3934141 Score: 62
Period size: 12 Copynumber: 4.7 Consensus size: 12
3934075 CCCCATTTTC
3934085 TTTTTTTATTT-
1 TTTTTTTATTTG
* *
3934096 ATTTTTTGTTTG
1 TTTTTTTATTTG
3934108 TTTTTTTATTTG
1 TTTTTTTATTTG
*
3934120 TTTTTTTGTTTTGG
1 TTTTTTT-ATTT-G
3934134 TTTTTTTA
1 TTTTTTTA
3934142 CGAAAGACGT
Statistics
Matches: 37, Mismatches: 6, Indels: 4
0.79 0.13 0.09
Matches are distributed among these distances:
11 9 0.24
12 17 0.46
13 3 0.08
14 8 0.22
ACGTcount: A:0.07, C:0.00, G:0.11, T:0.82
Consensus pattern (12 bp):
TTTTTTTATTTG
Found at i:3934115 original size:23 final size:26
Alignment explanation
Indices: 3934085--3934141 Score: 84
Period size: 23 Copynumber: 2.3 Consensus size: 26
3934075 CCCCATTTTC
3934085 TTTTTTTATTT-ATTTTTTG-TTT-G
1 TTTTTTTATTTGATTTTTTGTTTTGG
*
3934108 TTTTTTTATTTGTTTTTTTGTTTTGG
1 TTTTTTTATTTGATTTTTTGTTTTGG
3934134 TTTTTTTA
1 TTTTTTTA
3934142 CGAAAGACGT
Statistics
Matches: 30, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
23 11 0.37
24 7 0.23
25 3 0.10
26 9 0.30
ACGTcount: A:0.07, C:0.00, G:0.11, T:0.82
Consensus pattern (26 bp):
TTTTTTTATTTGATTTTTTGTTTTGG
Found at i:3944226 original size:68 final size:68
Alignment explanation
Indices: 3944117--3944252 Score: 245
Period size: 68 Copynumber: 2.0 Consensus size: 68
3944107 CTGGAAAAAC
* *
3944117 CCAGATGTATCGATACAATATTTTAAGTATTGATATATTATATCGATACATTGTATTGATACAGG
1 CCAGATGTATCGATACAATATTTTAAGTATTGATACATTATACCGATACATTGTATTGATACAGG
3944182 GTT
66 GTT
*
3944185 CCAGATGTATCGATATAATATTTTAAGTATTGATACATTATACCGATACATTGTATTGATACAGG
1 CCAGATGTATCGATACAATATTTTAAGTATTGATACATTATACCGATACATTGTATTGATACAGG
3944250 GTT
66 GTT
3944253 ACTATTTAGA
Statistics
Matches: 65, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
68 65 1.00
ACGTcount: A:0.34, C:0.11, G:0.16, T:0.39
Consensus pattern (68 bp):
CCAGATGTATCGATACAATATTTTAAGTATTGATACATTATACCGATACATTGTATTGATACAGG
GTT
Found at i:3946885 original size:20 final size:19
Alignment explanation
Indices: 3946837--3946890 Score: 81
Period size: 19 Copynumber: 2.8 Consensus size: 19
3946827 TGTATTGATA
*
3946837 CATTGTATCGATACATGCT
1 CATTGTATCGATACATACT
3946856 CATTGTATCGATACATACT
1 CATTGTATCGATACATACT
*
3946875 CAATTGCATCGATACA
1 C-ATTGTATCGATACA
3946891 CAAAATTAGC
Statistics
Matches: 32, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
19 19 0.59
20 13 0.41
ACGTcount: A:0.31, C:0.22, G:0.13, T:0.33
Consensus pattern (19 bp):
CATTGTATCGATACATACT
Found at i:3946965 original size:20 final size:20
Alignment explanation
Indices: 3946922--3946973 Score: 68
Period size: 20 Copynumber: 2.6 Consensus size: 20
3946912 TAAGTGAAAT
* **
3946922 GTATCGATACATGGGACATT
1 GTATCGATACATGGGAAAAA
*
3946942 GTATCGATACATGGTAAAAA
1 GTATCGATACATGGGAAAAA
3946962 GTATCGATACAT
1 GTATCGATACAT
3946974 TGTGCTTAAC
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 28 1.00
ACGTcount: A:0.37, C:0.13, G:0.21, T:0.29
Consensus pattern (20 bp):
GTATCGATACATGGGAAAAA
Found at i:3949113 original size:20 final size:19
Alignment explanation
Indices: 3949067--3949115 Score: 62
Period size: 19 Copynumber: 2.5 Consensus size: 19
3949057 CATATCTAGA
**
3949067 TGTATCGATACATGTTCAT
1 TGTATCGATACATACTCAT
*
3949086 TGTGTCGATACATACTCAAT
1 TGTATCGATACATACTC-AT
3949106 TGTATCGATA
1 TGTATCGATA
3949116 AATGAAACTG
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
19 14 0.56
20 11 0.44
ACGTcount: A:0.29, C:0.16, G:0.16, T:0.39
Consensus pattern (19 bp):
TGTATCGATACATACTCAT
Found at i:3958861 original size:38 final size:38
Alignment explanation
Indices: 3958757--3958861 Score: 147
Period size: 38 Copynumber: 2.8 Consensus size: 38
3958747 TCAATTAATA
*
3958757 GCATGGTTCAAAACAAAAATTACTATTCTTATCAGGTG
1 GCATGGTTCAAAACAAAAACTACTATTCTTATCAGGTG
* *
3958795 GCATGATTCAAAACAAAAACTACGATTCTTATCAGGTG
1 GCATGGTTCAAAACAAAAACTACTATTCTTATCAGGTG
** * *
3958833 GCATGGTTTGAAACAAAAACCAATATTCT
1 GCATGGTTCAAAACAAAAACTACTATTCT
3958862 AAACTGGTTG
Statistics
Matches: 58, Mismatches: 9, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
38 58 1.00
ACGTcount: A:0.39, C:0.17, G:0.15, T:0.29
Consensus pattern (38 bp):
GCATGGTTCAAAACAAAAACTACTATTCTTATCAGGTG
Found at i:3960777 original size:2 final size:2
Alignment explanation
Indices: 3960772--3960802 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
3960762 ATTTTAGGCT
3960772 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 T
3960803 TCTTTGGACT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:3962005 original size:23 final size:23
Alignment explanation
Indices: 3961979--3962047 Score: 59
Period size: 24 Copynumber: 2.9 Consensus size: 23
3961969 TTTAACTAAC
*
3961979 ATTTTTATCTTTTCATTTTTTTT
1 ATTTTTATCTTTTCATTTTTTTA
* *
3962002 ATTTTTCTCCTTTTTGA-TTTTTTA
1 ATTTTTAT-C-TTTTCATTTTTTTA
* *
3962026 ATTTTCGATTTTTTCATTTTTT
1 ATTTT-TATCTTTTCATTTTTT
3962048 GACTCTTCTT
Statistics
Matches: 35, Mismatches: 7, Indels: 7
0.71 0.14 0.14
Matches are distributed among these distances:
23 12 0.34
24 17 0.49
25 6 0.17
ACGTcount: A:0.13, C:0.10, G:0.03, T:0.74
Consensus pattern (23 bp):
ATTTTTATCTTTTCATTTTTTTA
Found at i:3962030 original size:15 final size:15
Alignment explanation
Indices: 3962012--3962046 Score: 52
Period size: 15 Copynumber: 2.3 Consensus size: 15
3962002 ATTTTTCTCC
3962012 TTTTTGATTTTTTAA
1 TTTTTGATTTTTTAA
* *
3962027 TTTTCGATTTTTTCA
1 TTTTTGATTTTTTAA
3962042 TTTTT
1 TTTTT
3962047 TGACTCTTCT
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.14, C:0.06, G:0.06, T:0.74
Consensus pattern (15 bp):
TTTTTGATTTTTTAA
Found at i:3963674 original size:19 final size:20
Alignment explanation
Indices: 3963632--3963683 Score: 70
Period size: 19 Copynumber: 2.6 Consensus size: 20
3963622 ACACCTAGAA
* *
3963632 GTATCGATACATTATGCTTT
1 GTATCGATACATGATGCATT
3963652 GTATCGATACATGAT-CATT
1 GTATCGATACATGATGCATT
*
3963671 GTATCAATACATG
1 GTATCGATACATG
3963684 GACAAATGTA
Statistics
Matches: 29, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
19 15 0.52
20 14 0.48
ACGTcount: A:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (20 bp):
GTATCGATACATGATGCATT
Found at i:3963757 original size:20 final size:20
Alignment explanation
Indices: 3963732--3963785 Score: 74
Period size: 20 Copynumber: 2.7 Consensus size: 20
3963722 TTACCACTGT
*
3963732 TTGTATCGATACATGGT-ACA
1 TTGTATCGATACATGATGA-A
*
3963752 TTGTATTGATACATGATGAA
1 TTGTATCGATACATGATGAA
3963772 TTGTATCGATACAT
1 TTGTATCGATACAT
3963786 TGCTTGTAAC
Statistics
Matches: 30, Mismatches: 3, Indels: 2
0.86 0.09 0.06
Matches are distributed among these distances:
20 29 0.97
21 1 0.03
ACGTcount: A:0.31, C:0.11, G:0.19, T:0.39
Consensus pattern (20 bp):
TTGTATCGATACATGATGAA
Found at i:3970048 original size:20 final size:22
Alignment explanation
Indices: 3970014--3970054 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 22
3970004 ACAAATTTCC
*
3970014 TCATTTTTACTTC-AAATCACT
1 TCATTTTTACATCAAAATCACT
3970035 TCATTTTT-CATCAAAATCAC
1 TCATTTTTACATCAAAATCAC
3970055 CAACAAAAAT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 3 0.17
21 15 0.83
ACGTcount: A:0.32, C:0.24, G:0.00, T:0.44
Consensus pattern (22 bp):
TCATTTTTACATCAAAATCACT
Found at i:3972383 original size:20 final size:19
Alignment explanation
Indices: 3972360--3972432 Score: 85
Period size: 20 Copynumber: 3.7 Consensus size: 19
3972350 ACACTCAGAA
* *
3972360 GTATCGATACATTATGCTTT
1 GTATCGATACATGAT-CATT
*
3972380 GTATCAATACATGATCATT
1 GTATCGATACATGATCATT
3972399 GTATCGATACATGGA-CAATT
1 GTATCGATACAT-GATC-ATT
3972419 GTATCGATACATGA
1 GTATCGATACATGA
3972433 AACTGGCAGT
Statistics
Matches: 47, Mismatches: 4, Indels: 5
0.84 0.07 0.09
Matches are distributed among these distances:
19 17 0.36
20 30 0.64
ACGTcount: A:0.33, C:0.15, G:0.16, T:0.36
Consensus pattern (19 bp):
GTATCGATACATGATCATT
Found at i:3972494 original size:13 final size:13
Alignment explanation
Indices: 3972476--3972508 Score: 66
Period size: 13 Copynumber: 2.5 Consensus size: 13
3972466 CAATACATGG
3972476 TACATTGTATCGA
1 TACATTGTATCGA
3972489 TACATTGTATCGA
1 TACATTGTATCGA
3972502 TACATTG
1 TACATTG
3972509 CTTCTAACGG
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 20 1.00
ACGTcount: A:0.30, C:0.15, G:0.15, T:0.39
Consensus pattern (13 bp):
TACATTGTATCGA
Found at i:3973441 original size:146 final size:147
Alignment explanation
Indices: 3973211--3973475 Score: 419
Period size: 146 Copynumber: 1.8 Consensus size: 147
3973201 TGAGCTTTCA
* *
3973211 CATTAGTTTTTAAATTTTTTCTGTGAAATTTTCTTATTTCCAAAGTACGGAGTTTTTTACTCCGT
1 CATTAGTTTTTAAATTTTTTCTGTGAAATTCTCTTATTTCCAAAGTACGGAGTTTTCTACTCCGT
*
3973276 AAATTTTTTTAGGAGGATTTTTCTTGGTTTTTAATTTTTAAAATTCATCAAATAAATCAGTTTTC
66 AAATTTTTTCAGGAGGATTTTTCTTGGTTTTTAATTTTTAAAATTCATCAAATAAATCAGTTTTC
3973341 AAAAGTTCATTCAATTT
131 AAAAGTTCATTCAATTT
* * **
3973358 CATTAGTTTTTGAATTTTTTCT-TGAAATTCTCTTTTTTTTTAAA-TACGGAGTTTTCTACTCCG
1 CATTAGTTTTTAAATTTTTTCTGTGAAATTCTC-TTATTTCCAAAGTACGGAGTTTTCTACTCCG
*
3973421 TAAATTTTTTCAGG-GAGATTTTTCTTTGTTTTTAATTTTTAAAATTCATCAAATA
65 TAAATTTTTTCAGGAG-GATTTTTCTTGGTTTTTAATTTTTAAAATTCATCAAATA
3973476 TTATTATTTA
Statistics
Matches: 108, Mismatches: 8, Indels: 5
0.89 0.07 0.04
Matches are distributed among these distances:
145 1 0.01
146 78 0.72
147 29 0.27
ACGTcount: A:0.27, C:0.11, G:0.11, T:0.51
Consensus pattern (147 bp):
CATTAGTTTTTAAATTTTTTCTGTGAAATTCTCTTATTTCCAAAGTACGGAGTTTTCTACTCCGT
AAATTTTTTCAGGAGGATTTTTCTTGGTTTTTAATTTTTAAAATTCATCAAATAAATCAGTTTTC
AAAAGTTCATTCAATTT
Found at i:3973578 original size:165 final size:165
Alignment explanation
Indices: 3973328--3973706 Score: 432
Period size: 164 Copynumber: 2.3 Consensus size: 165
3973318 ATTCATCAAA
* * * *
3973328 TAAATCAGTTTTCAAAAGTTCATTCAATTTCATTAGTTTTTGAATTTTTTCTTGAAATTCTCTTT
1 TAAATCATTTTTCAAAAATTCATTCAATTTCATGAATTTTTGAATTTTTTCTTGAAATTCTCTTT
* * * * * * **
3973393 TTTTTTAAATACGGAGTTTTCTACTCCGTAAATTTTTTCAGGGAGATTTTTCTTTGTTTTTAATT
66 TTTTTTAAAAACGGAGTTTTCTACTCCATAAATATTTTCACGG-GATTCTTCTTGGTTTACAATT
* * *
3973458 TTTAAAATTCATCAAATATTATT-ATTTAATTCATAT
130 TTCAAAATTCATCAAATATT-TTCATTAAATTCACAT
* * *
3973494 TAAATCATTTTTCAAAAATTCATTCATTTTGATGAATTTTT-CATTTTTTCTTGAAATT-T-TTT
1 TAAATCATTTTTCAAAAATTCATTCAATTTCATGAATTTTTGAATTTTTTCTTGAAATTCTCTTT
* *
3973556 TATTTTTGAAAAATC-GAGTTTTCTACTCTATAAATATTTTGACGGGATTCTTCTTGGTTTACAA
66 T-TTTTT-AAAAA-CGGAGTTTTCTACTCCATAAATATTTTCACGGGATTCTTCTTGGTTTACAA
*
3973620 TTTTCAAAATTCATCTAATATTTTCATTAAATTCACAT
128 TTTTCAAAATTCATCAAATATTTTCATTAAATTCACAT
* *
3973658 TAAACCATTTTTAAAAAATTCAAATT--ATTTCATGAA-TTTTGAATTTTTT
1 TAAATCATTTTTCAAAAATTC--ATTCAATTTCATGAATTTTTGAATTTTTT
3973707 GTATATATTG
Statistics
Matches: 180, Mismatches: 26, Indels: 16
0.81 0.12 0.07
Matches are distributed among these distances:
163 10 0.06
164 86 0.48
165 45 0.25
166 39 0.22
ACGTcount: A:0.31, C:0.11, G:0.07, T:0.51
Consensus pattern (165 bp):
TAAATCATTTTTCAAAAATTCATTCAATTTCATGAATTTTTGAATTTTTTCTTGAAATTCTCTTT
TTTTTTAAAAACGGAGTTTTCTACTCCATAAATATTTTCACGGGATTCTTCTTGGTTTACAATTT
TCAAAATTCATCAAATATTTTCATTAAATTCACAT
Found at i:3976446 original size:20 final size:21
Alignment explanation
Indices: 3976410--3976450 Score: 66
Period size: 20 Copynumber: 2.0 Consensus size: 21
3976400 AGTATAGATA
3976410 TTTTTCAAGCATAAAAATAATG
1 TTTTTCAAG-ATAAAAATAATG
3976432 TTTTTCAAG-TAAAAATAAT
1 TTTTTCAAGATAAAAATAAT
3976451 TCAAAGTATC
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 10 0.53
22 9 0.47
ACGTcount: A:0.46, C:0.07, G:0.07, T:0.39
Consensus pattern (21 bp):
TTTTTCAAGATAAAAATAATG
Found at i:3976591 original size:19 final size:20
Alignment explanation
Indices: 3976547--3976618 Score: 85
Period size: 20 Copynumber: 3.6 Consensus size: 20
3976537 ATACCCAGAT
3976547 GTATCGATACATATTGCTTA
1 GTATCGATACATATTGCTTA
* *
3976567 GTATCGATACATGTT-CTTG
1 GTATCGATACATATTGCTTA
* *
3976586 GTATCGATATATATTGGATTA
1 GTATCGATACATATT-GCTTA
3976607 -TATCGATACATA
1 GTATCGATACATA
3976619 AAACGGGCAG
Statistics
Matches: 43, Mismatches: 7, Indels: 4
0.80 0.13 0.07
Matches are distributed among these distances:
19 16 0.37
20 25 0.58
21 2 0.05
ACGTcount: A:0.31, C:0.12, G:0.17, T:0.40
Consensus pattern (20 bp):
GTATCGATACATATTGCTTA
Found at i:3981135 original size:52 final size:52
Alignment explanation
Indices: 3980994--3981114 Score: 197
Period size: 52 Copynumber: 2.3 Consensus size: 52
3980984 GAAAATTTGT
*
3980994 CTGCATGTATCGATACATTTCATAGTGTATCGATACATCTGGGCAAATTTGC
1 CTGCATGTATCGATACATTTCATAGTGTATCGATACATCTGGGCAAATTTAC
* * * *
3981046 TTGTATGTATCAATATATTTCATAGTGTATCGATACATCTGGGCAAATTTAC
1 CTGCATGTATCGATACATTTCATAGTGTATCGATACATCTGGGCAAATTTAC
3981098 CTGCATGTATCGATACA
1 CTGCATGTATCGATACA
3981115 AAGATCAGTG
Statistics
Matches: 60, Mismatches: 9, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
52 60 1.00
ACGTcount: A:0.29, C:0.17, G:0.17, T:0.36
Consensus pattern (52 bp):
CTGCATGTATCGATACATTTCATAGTGTATCGATACATCTGGGCAAATTTAC
Found at i:3981197 original size:13 final size:13
Alignment explanation
Indices: 3981179--3981262 Score: 51
Period size: 13 Copynumber: 5.5 Consensus size: 13
3981169 AGCTTCGTAG
3981179 CGATACATTGTAT
1 CGATACATTGTAT
3981192 CGATACAAAACTTATGTAT
1 CGATAC---A-TT--GTAT
3981211 CGATACATTGTAT
1 CGATACATTGTAT
*
3981224 CGATACAACACTTATGTGT
1 CGAT---ACA--T-TGTAT
3981243 CGATACATTGTAT
1 CGATACATTGTAT
3981256 CGATACA
1 CGATACA
3981263 AACCGTTGAA
Statistics
Matches: 57, Mismatches: 2, Indels: 24
0.69 0.02 0.29
Matches are distributed among these distances:
13 25 0.44
14 1 0.02
15 2 0.04
16 8 0.14
17 2 0.04
18 1 0.02
19 18 0.32
ACGTcount: A:0.35, C:0.18, G:0.14, T:0.33
Consensus pattern (13 bp):
CGATACATTGTAT
Found at i:3981211 original size:19 final size:18
Alignment explanation
Indices: 3981187--3981249 Score: 64
Period size: 19 Copynumber: 3.7 Consensus size: 18
3981177 AGCGATACAT
3981187 TGTATCGATACAAAACTTA
1 TGTATCGATAC-AAACTTA
3981206 TGTATCGATAC--A--T-
1 TGTATCGATACAAACTTA
3981219 TGTATCGATACAACACTTA
1 TGTATCGATACAA-ACTTA
*
3981238 TGTGTCGATACA
1 TGTATCGATACA
3981250 TTGTATCGAT
Statistics
Matches: 37, Mismatches: 1, Indels: 12
0.74 0.02 0.24
Matches are distributed among these distances:
13 11 0.30
14 1 0.03
16 2 0.05
18 1 0.03
19 22 0.59
ACGTcount: A:0.35, C:0.17, G:0.14, T:0.33
Consensus pattern (18 bp):
TGTATCGATACAAACTTA
Found at i:3981220 original size:32 final size:32
Alignment explanation
Indices: 3981179--3981264 Score: 154
Period size: 32 Copynumber: 2.7 Consensus size: 32
3981169 AGCTTCGTAG
3981179 CGATACATTGTATCGATACAAAACTTATGTAT
1 CGATACATTGTATCGATACAAAACTTATGTAT
* *
3981211 CGATACATTGTATCGATACAACACTTATGTGT
1 CGATACATTGTATCGATACAAAACTTATGTAT
3981243 CGATACATTGTATCGATACAAA
1 CGATACATTGTATCGATACAAA
3981265 CCGTTGAAAT
Statistics
Matches: 51, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
32 51 1.00
ACGTcount: A:0.36, C:0.17, G:0.14, T:0.33
Consensus pattern (32 bp):
CGATACATTGTATCGATACAAAACTTATGTAT
Done.