Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr10
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: 48586650
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.32
Warning! 2183483 characters in sequence are not A, C, G, or T
File 51 of 145
Found at i:16649905 original size:132 final size:132
Alignment explanation
Indices: 16649668--16650006 Score: 520
Period size: 132 Copynumber: 2.6 Consensus size: 132
16649658 TACAGTGGGG
*
16649668 AGTGGAGTACATTGAAGCCAGTAATTCTACTTCCCTGGGCATCAGCAGAATAGATTGAAGATTTC
1 AGTGGAGTACATTGAAGCCAGTAATTCTACTTCCCTGGGCATCAGCGGAATAGATTGAAGATTTC
* * * * *
16649733 AGATCTTGTCCCCTTGAGCAGTAGTGGGGCAGATCAAAGATGGCAGATTTTACCTCCCTGTGGTT
66 AAATCTTGTCCCCCTAAGCAGTAGTGGAGCAGATCAAAGATGGCAGATTTTACCTCCCCGTGGTT
*
16649798 AT
131 AC
16649800 AGTGGAGTACATTGAAGCCAGTAATTCTACTTCCCTGGGCATCAGCGGAATAGATTGAAGATTTC
1 AGTGGAGTACATTGAAGCCAGTAATTCTACTTCCCTGGGCATCAGCGGAATAGATTGAAGATTTC
*
16649865 AAATCTT-TCCTCCCTAAGCAGTAGTGGAGCAGATCAAAGATGGCGGATTTTACCTCCCCGTGGT
66 AAATCTTGTCC-CCCTAAGCAGTAGTGGAGCAGATCAAAGATGGCAGATTTTACCTCCCCGTGGT
16649929 TAC
130 TAC
* * * *
16649932 AGTGGAGTACATTGAAGCCAGTAATTCTA-TCTCCCTGGGCAGCAGTGGAATAGATTGTAGACTT
1 AGTGGAGTACATTGAAGCCAGTAATTCTACT-TCCCTGGGCATCAGCGGAATAGATTGAAGATTT
* *
16649996 CAGATTTTGTC
65 CAAATCTTGTC
16650007 TTCATGTACT
Statistics
Matches: 190, Mismatches: 14, Indels: 5
0.91 0.07 0.02
Matches are distributed among these distances:
131 4 0.02
132 184 0.97
133 2 0.01
ACGTcount: A:0.27, C:0.20, G:0.24, T:0.29
Consensus pattern (132 bp):
AGTGGAGTACATTGAAGCCAGTAATTCTACTTCCCTGGGCATCAGCGGAATAGATTGAAGATTTC
AAATCTTGTCCCCCTAAGCAGTAGTGGAGCAGATCAAAGATGGCAGATTTTACCTCCCCGTGGTT
AC
Found at i:16650051 original size:44 final size:44
Alignment explanation
Indices: 16649997--16650186 Score: 182
Period size: 44 Copynumber: 4.3 Consensus size: 44
16649987 TGTAGACTTC
* *
16649997 AGATTTTGTCTTCATGTACTGGCGTGAAGTAGATTAAAGATAGT
1 AGATCTTGTCTTCATGTACTGGCGTGAAGTAGATCAAAGATAGT
*** * * * * *
16650041 AGATCTTGTCTTCCCATACTGGTGGCGAAGTAGATCGAAGAGAGC
1 AGATCTTGTCTTCATGTACTGG-CGTGAAGTAGATCAAAGATAGT
* * * ** * *
16650086 AAATCTTATCTTCATGTATTGGCGTGAAGTAGATTGAAGAAAAT
1 AGATCTTGTCTTCATGTACTGGCGTGAAGTAGATCAAAGATAGT
* *
16650130 GGATCGTGTCTTCATGTACTGGCGTGAAGTAGATCAAAGATAGT
1 AGATCTTGTCTTCATGTACTGGCGTGAAGTAGATCAAAGATAGT
* *
16650174 AGGTCCTGTCTTC
1 AGATCTTGTCTTC
16650187 CTATATTGGT
Statistics
Matches: 111, Mismatches: 34, Indels: 2
0.76 0.23 0.01
Matches are distributed among these distances:
44 79 0.71
45 32 0.29
ACGTcount: A:0.28, C:0.14, G:0.26, T:0.32
Consensus pattern (44 bp):
AGATCTTGTCTTCATGTACTGGCGTGAAGTAGATCAAAGATAGT
Found at i:16650150 original size:89 final size:88
Alignment explanation
Indices: 16650005--16650169 Score: 213
Period size: 89 Copynumber: 1.9 Consensus size: 88
16649995 TCAGATTTTG
* * * * *
16650005 TCTTCATGTACTGGCGTGAAGTAGATTAAAGATAGTAGATCTTGTCTTCCCATACTGGTGGCGAA
1 TCTTCATGTACTGGCGTGAAGTAGATTAAAGAAAATAGATCGTGTCTTCACATACTGG-CGCGAA
*
16650070 GTAGATCGAAGAGAGCAAATCTTA
65 GTAGATCAAAGAGAGCAAATCTTA
* * * ** *
16650094 TCTTCATGTATTGGCGTGAAGTAGATTGAAGAAAATGGATCGTGTCTTCATGTACTGGCGTGAAG
1 TCTTCATGTACTGGCGTGAAGTAGATTAAAGAAAATAGATCGTGTCTTCACATACTGGCGCGAAG
16650159 TAGATCAAAGA
66 TAGATCAAAGA
16650170 TAGTAGGTCC
Statistics
Matches: 64, Mismatches: 12, Indels: 1
0.83 0.16 0.01
Matches are distributed among these distances:
88 15 0.23
89 49 0.77
ACGTcount: A:0.30, C:0.14, G:0.26, T:0.30
Consensus pattern (88 bp):
TCTTCATGTACTGGCGTGAAGTAGATTAAAGAAAATAGATCGTGTCTTCACATACTGGCGCGAAG
TAGATCAAAGAGAGCAAATCTTA
Found at i:16650248 original size:133 final size:133
Alignment explanation
Indices: 16650003--16650258 Score: 334
Period size: 133 Copynumber: 1.9 Consensus size: 133
16649993 CTTCAGATTT
* * *
16650003 TGTCTTCATGTACTGGCGTGAAGTAGATTAAAGATAGTAGATCTTGTCTTCCCATACTGGTGGCG
1 TGTCTTCATGTACTGGCGTGAAGTAGATCAAAGATAGTAGATCCTGTCTTCCCATACTGGTAGCG
** ** * *
16650068 AAGTAGATCGAAGAGAGCAAATCTTATCTTCATGTATTGGCGTGAAGTAGATTGAAGAAAATGGA
66 AAGTAGATCGAAGAGAGCAAATCTTATCTTCACATACCGGCGCGAAGTAGATTCAAGAAAATGGA
16650133 TCG
131 TCG
* * *
16650136 TGTCTTCATGTACTGGCGTGAAGTAGATCAAAGATAGTAGGTCCTGTCTTCCTATATTGGTAGCG
1 TGTCTTCATGTACTGGCGTGAAGTAGATCAAAGATAGTAGATCCTGTCTTCCCATACTGGTAGCG
* * * * * *
16650201 AAGTGGATCGAATATA-CATATTTTATCTTCCCATACCGGCGGCGAAGTAGATTCAAGA
66 AAGTAGATCGAAGAGAGCAAATCTTATCTTCACATACCGGC-GCGAAGTAGATTCAAGA
16650259 TTACAGATCT
Statistics
Matches: 104, Mismatches: 18, Indels: 2
0.84 0.15 0.02
Matches are distributed among these distances:
132 17 0.16
133 87 0.84
ACGTcount: A:0.29, C:0.16, G:0.25, T:0.30
Consensus pattern (133 bp):
TGTCTTCATGTACTGGCGTGAAGTAGATCAAAGATAGTAGATCCTGTCTTCCCATACTGGTAGCG
AAGTAGATCGAAGAGAGCAAATCTTATCTTCACATACCGGCGCGAAGTAGATTCAAGAAAATGGA
TCG
Found at i:16651943 original size:3 final size:3
Alignment explanation
Indices: 16651937--16652009 Score: 121
Period size: 3 Copynumber: 24.3 Consensus size: 3
16651927 TTTTAATTTT
*
16651937 TTA TTA TTA TTA TTA TTA TTA TTG TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
16651985 TTA TTA TTA TTA -TA CTTA TTA TTA T
1 TTA TTA TTA TTA TTA -TTA TTA TTA T
16652010 ACTTACATAT
Statistics
Matches: 66, Mismatches: 2, Indels: 4
0.92 0.03 0.06
Matches are distributed among these distances:
2 2 0.03
3 62 0.94
4 2 0.03
ACGTcount: A:0.32, C:0.01, G:0.01, T:0.66
Consensus pattern (3 bp):
TTA
Found at i:16654757 original size:17 final size:17
Alignment explanation
Indices: 16654735--16654776 Score: 52
Period size: 16 Copynumber: 2.6 Consensus size: 17
16654725 TGTTTATTAA
*
16654735 TATAATAATTTTTATTT
1 TATAATAATTTTTAATT
*
16654752 TATAAT-TTTTTTAATT
1 TATAATAATTTTTAATT
16654768 TATAA-AATT
1 TATAATAATT
16654777 CCAATAATTA
Statistics
Matches: 21, Mismatches: 3, Indels: 3
0.78 0.11 0.11
Matches are distributed among these distances:
16 15 0.71
17 6 0.29
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (17 bp):
TATAATAATTTTTAATT
Found at i:16659284 original size:49 final size:49
Alignment explanation
Indices: 16659226--16659349 Score: 185
Period size: 49 Copynumber: 2.5 Consensus size: 49
16659216 ATGATGGTCC
* *
16659226 ACTGGTAGGGCAAGTTAGTTGCTAACCAGATTGGCATATGTGTTGGACT
1 ACTGGTAGGGCATGTTAGTTGCTAACCAGATTGACATATGTGTTGGACT
* * **
16659275 ACTGGTAGGGCATGTTAGTTGCTAGCCAGATTGACGTATGTGTTGGGTT
1 ACTGGTAGGGCATGTTAGTTGCTAACCAGATTGACATATGTGTTGGACT
*
16659324 ACTGGTAGGGCATGTTAATTGCTAAC
1 ACTGGTAGGGCATGTTAGTTGCTAAC
16659350 TAGTCTGGAA
Statistics
Matches: 67, Mismatches: 8, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
49 67 1.00
ACGTcount: A:0.23, C:0.14, G:0.31, T:0.32
Consensus pattern (49 bp):
ACTGGTAGGGCATGTTAGTTGCTAACCAGATTGACATATGTGTTGGACT
Found at i:16664957 original size:31 final size:31
Alignment explanation
Indices: 16664913--16664990 Score: 102
Period size: 31 Copynumber: 2.5 Consensus size: 31
16664903 TATAGAATGA
* * * *
16664913 TCACTGAATTATTCGAAAGATTTTGTTTAAG
1 TCACTAAACTATTCAAAAGATTTTATTTAAG
*
16664944 TCACTAAACTATTCAAAAGTTTTTATTTAAG
1 TCACTAAACTATTCAAAAGATTTTATTTAAG
*
16664975 TCACTAGACTATTCAA
1 TCACTAAACTATTCAA
16664991 TAATCGGTAT
Statistics
Matches: 41, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
31 41 1.00
ACGTcount: A:0.36, C:0.14, G:0.10, T:0.40
Consensus pattern (31 bp):
TCACTAAACTATTCAAAAGATTTTATTTAAG
Found at i:16665564 original size:2 final size:2
Alignment explanation
Indices: 16665559--16665583 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
16665549 AATTATTAAC
16665559 TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA T
16665584 TAGATGCTTC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:16666646 original size:25 final size:25
Alignment explanation
Indices: 16666597--16666646 Score: 66
Period size: 25 Copynumber: 2.0 Consensus size: 25
16666587 TTCATACTAT
* *
16666597 TTTTTGAAATTTTTTATAATTTTTA
1 TTTTTAAAATTTTTTATAATGTTTA
16666622 TTTTTAAAATATTTTTATAA-GTTTA
1 TTTTTAAAAT-TTTTTATAATGTTTA
16666647 ATATTTTTTG
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
25 13 0.59
26 9 0.41
ACGTcount: A:0.32, C:0.00, G:0.04, T:0.64
Consensus pattern (25 bp):
TTTTTAAAATTTTTTATAATGTTTA
Found at i:16668798 original size:25 final size:25
Alignment explanation
Indices: 16668749--16668798 Score: 66
Period size: 25 Copynumber: 2.0 Consensus size: 25
16668739 TTCATACTAT
* *
16668749 TTTTTGAAATTTTTTATAATTTTTA
1 TTTTTAAAATTTTTTATAATGTTTA
16668774 TTTTTAAAATATTTTTATAA-GTTTA
1 TTTTTAAAAT-TTTTTATAATGTTTA
16668799 ATATTTTTTG
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
25 13 0.59
26 9 0.41
ACGTcount: A:0.32, C:0.00, G:0.04, T:0.64
Consensus pattern (25 bp):
TTTTTAAAATTTTTTATAATGTTTA
Found at i:16669563 original size:18 final size:18
Alignment explanation
Indices: 16669527--16669568 Score: 50
Period size: 18 Copynumber: 2.3 Consensus size: 18
16669517 TGTATAATTT
*
16669527 TAAAAAATATATAATACA
1 TAAAAAATATATAAAACA
16669545 TAAAAAATACTA-AAAACA
1 TAAAAAATA-TATAAAACA
16669563 TCAAAA
1 T-AAAA
16669569 TAAATATTTC
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
18 15 0.71
19 6 0.29
ACGTcount: A:0.69, C:0.10, G:0.00, T:0.21
Consensus pattern (18 bp):
TAAAAAATATATAAAACA
Found at i:16669659 original size:29 final size:29
Alignment explanation
Indices: 16669618--16669677 Score: 102
Period size: 29 Copynumber: 2.1 Consensus size: 29
16669608 ATGTATACTT
16669618 AAATAACACTAAGATAGATGCAACTTAAC
1 AAATAACACTAAGATAGATGCAACTTAAC
* *
16669647 AAATAATATTAAGATAGATGCAACTTAAC
1 AAATAACACTAAGATAGATGCAACTTAAC
16669676 AA
1 AA
16669678 GCAAATGCCT
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
29 29 1.00
ACGTcount: A:0.53, C:0.13, G:0.10, T:0.23
Consensus pattern (29 bp):
AAATAACACTAAGATAGATGCAACTTAAC
Found at i:16669714 original size:30 final size:30
Alignment explanation
Indices: 16669680--16669738 Score: 91
Period size: 30 Copynumber: 2.0 Consensus size: 30
16669670 CTTAACAAGC
16669680 AAATGCCTCAAAAATAATAACAAAATTAAT
1 AAATGCCTCAAAAATAATAACAAAATTAAT
** *
16669710 AAATGCCTTTAAAATAATAATAAAATTAA
1 AAATGCCTCAAAAATAATAACAAAATTAA
16669739 CAATAAAATA
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
30 26 1.00
ACGTcount: A:0.59, C:0.10, G:0.03, T:0.27
Consensus pattern (30 bp):
AAATGCCTCAAAAATAATAACAAAATTAAT
Found at i:16669806 original size:112 final size:113
Alignment explanation
Indices: 16669670--16669894 Score: 416
Period size: 112 Copynumber: 2.0 Consensus size: 113
16669660 ATAGATGCAA
*
16669670 CTTAACAAGCAAATGCCTCAAAAATAATAACAAAATTAATAAATGCCTTTAAAATAATAATAAAA
1 CTTAACAAGAAAATGCCTCAAAAATAATAACAAAATTAATAAATGCCTTTAAAATAATAATAAAA
16669735 TTAACAATAAAATAGTAGCAACATAATAGTAAAATGG-AGCAAAATAG
66 TTAACAATAAAATAGTAGCAACATAATAGTAAAATGGTAGCAAAATAG
* *
16669782 CTTAACAAGAAAATGTCTCTAAAATAATAACAAAATTAATAAATGCCTTTAAAATAATAATAAAA
1 CTTAACAAGAAAATGCCTCAAAAATAATAACAAAATTAATAAATGCCTTTAAAATAATAATAAAA
16669847 TTAACAATAAAATAGTAGCAACATAATAGTAAAATGGTAGCAAAATAG
66 TTAACAATAAAATAGTAGCAACATAATAGTAAAATGGTAGCAAAATAG
16669895 GGAGAAAAAA
Statistics
Matches: 109, Mismatches: 3, Indels: 1
0.96 0.03 0.01
Matches are distributed among these distances:
112 99 0.91
113 10 0.09
ACGTcount: A:0.56, C:0.11, G:0.09, T:0.24
Consensus pattern (113 bp):
CTTAACAAGAAAATGCCTCAAAAATAATAACAAAATTAATAAATGCCTTTAAAATAATAATAAAA
TTAACAATAAAATAGTAGCAACATAATAGTAAAATGGTAGCAAAATAG
Found at i:16669835 original size:30 final size:30
Alignment explanation
Indices: 16669792--16669850 Score: 91
Period size: 30 Copynumber: 2.0 Consensus size: 30
16669782 CTTAACAAGA
*
16669792 AAATGTCTCTAAAATAATAACAAAATTAAT
1 AAATGCCTCTAAAATAATAACAAAATTAAT
* *
16669822 AAATGCCTTTAAAATAATAATAAAATTAA
1 AAATGCCTCTAAAATAATAACAAAATTAA
16669851 CAATAAAATA
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
30 26 1.00
ACGTcount: A:0.58, C:0.08, G:0.03, T:0.31
Consensus pattern (30 bp):
AAATGCCTCTAAAATAATAACAAAATTAAT
Found at i:16671318 original size:23 final size:24
Alignment explanation
Indices: 16671277--16671323 Score: 69
Period size: 23 Copynumber: 2.0 Consensus size: 24
16671267 ATACTTTTAC
**
16671277 ATATTCATATTTTTTAATT-TTTT
1 ATATTCATATTTTGCAATTATTTT
16671300 ATATTCATATTTTGCAATTATTTT
1 ATATTCATATTTTGCAATTATTTT
16671324 TAACCTATAA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
23 17 0.81
24 4 0.19
ACGTcount: A:0.28, C:0.06, G:0.02, T:0.64
Consensus pattern (24 bp):
ATATTCATATTTTGCAATTATTTT
Found at i:16674003 original size:21 final size:21
Alignment explanation
Indices: 16673977--16674020 Score: 79
Period size: 21 Copynumber: 2.1 Consensus size: 21
16673967 TTGACCAATC
*
16673977 AAGGAGACAAGACATGAAGAG
1 AAGGAGACAAAACATGAAGAG
16673998 AAGGAGACAAAACATGAAGAG
1 AAGGAGACAAAACATGAAGAG
16674019 AA
1 AA
16674021 TGTTTGCTCT
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.57, C:0.09, G:0.30, T:0.05
Consensus pattern (21 bp):
AAGGAGACAAAACATGAAGAG
Found at i:16686202 original size:156 final size:156
Alignment explanation
Indices: 16685975--16686286 Score: 401
Period size: 156 Copynumber: 2.0 Consensus size: 156
16685965 AGCTACAGTC
* * **
16685975 ACTAAATTATTTTTATCTGGAGATATAGAACTCAAAATTAAGTTCCATTAATTTGACCTGAAACT
1 ACTAAATCATTTTTATCTGGAGATACAGAACTCAAAATTAAGTTCCATTAATTTGACCCAAAACT
* * * *
16686040 AGACTCACATATATTATTATCATAAAATTTTCAGAATTTTTGGCTTAGCCAATTTGTACAGTTTT
66 AGACTCACATATATTATTACCATAAAATTTTCAGAATTTTTGACTTAGCCAATTAGTACAGTTTA
*
16686105 TTCTTTAAATTCACCCCTGTTTCACT
131 TTCTTTAAAGTCACCCCTGTTTCACT
* * * * **
16686131 ACTAAATCATTTTTATCTGGAGCTACAGAGCTCCAAATTAA-TATCCGTTAATTTTTCCCAAAAC
1 ACTAAATCATTTTTATCTGGAGATACAGAACTCAAAATTAAGT-TCCATTAATTTGACCCAAAAC
* * * * * * *
16686195 TATACTCATATATCTTCTTACCATAAAATTTTCAGAATTTTTTACTTGGCCAATTAGTATAGTTT
65 TAGACTCACATATATTATTACCATAAAATTTTCAGAATTTTTGACTTAGCCAATTAGTACAGTTT
*
16686260 ATTCTTTAAAGTCACTCCTGTTTCACT
130 ATTCTTTAAAGTCACCCCTGTTTCACT
16686287 GCTCAACATC
Statistics
Matches: 132, Mismatches: 23, Indels: 2
0.84 0.15 0.01
Matches are distributed among these distances:
155 1 0.01
156 131 0.99
ACGTcount: A:0.32, C:0.18, G:0.09, T:0.41
Consensus pattern (156 bp):
ACTAAATCATTTTTATCTGGAGATACAGAACTCAAAATTAAGTTCCATTAATTTGACCCAAAACT
AGACTCACATATATTATTACCATAAAATTTTCAGAATTTTTGACTTAGCCAATTAGTACAGTTTA
TTCTTTAAAGTCACCCCTGTTTCACT
Found at i:16687022 original size:51 final size:51
Alignment explanation
Indices: 16686964--16687151 Score: 252
Period size: 51 Copynumber: 3.7 Consensus size: 51
16686954 TCGGTTCACA
*
16686964 TAGTAGCCTGCACATAGTACTACACATATGACCATTACCATCCGATACATG
1 TAGTAGCCTGCACATAGTACTACACACATGACCATTACCATCCGATACATG
* * * * * * * *
16687015 TAGTAGCCTGCGCATAGTACTACACACGTGATCGA-AACTATCCGGTACGTA
1 TAGTAGCCTGCACATAGTACTACACACATGA-CCATTACCATCCGATACATG
*
16687066 TAGTAGCCTGCACATAGTACTACACATATGACCATTACCATCCGATACATG
1 TAGTAGCCTGCACATAGTACTACACACATGACCATTACCATCCGATACATG
* *
16687117 TAGTAGCCTGCGCATAGTACTACACACGTGACCAT
1 TAGTAGCCTGCACATAGTACTACACACATGACCAT
16687152 CACTTTCACT
Statistics
Matches: 114, Mismatches: 21, Indels: 4
0.82 0.15 0.03
Matches are distributed among these distances:
50 2 0.02
51 110 0.96
52 2 0.02
ACGTcount: A:0.31, C:0.27, G:0.17, T:0.24
Consensus pattern (51 bp):
TAGTAGCCTGCACATAGTACTACACACATGACCATTACCATCCGATACATG
Found at i:16687089 original size:102 final size:102
Alignment explanation
Indices: 16686963--16687147 Score: 370
Period size: 102 Copynumber: 1.8 Consensus size: 102
16686953 TTCGGTTCAC
16686963 ATAGTAGCCTGCACATAGTACTACACATATGACCATTACCATCCGATACATGTAGTAGCCTGCGC
1 ATAGTAGCCTGCACATAGTACTACACATATGACCATTACCATCCGATACATGTAGTAGCCTGCGC
16687028 ATAGTACTACACACGTGATCGAAACTATCCGGTACGT
66 ATAGTACTACACACGTGATCGAAACTATCCGGTACGT
16687065 ATAGTAGCCTGCACATAGTACTACACATATGACCATTACCATCCGATACATGTAGTAGCCTGCGC
1 ATAGTAGCCTGCACATAGTACTACACATATGACCATTACCATCCGATACATGTAGTAGCCTGCGC
16687130 ATAGTACTACACACGTGA
66 ATAGTACTACACACGTGA
16687148 CCATCACTTT
Statistics
Matches: 83, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
102 83 1.00
ACGTcount: A:0.32, C:0.26, G:0.17, T:0.24
Consensus pattern (102 bp):
ATAGTAGCCTGCACATAGTACTACACATATGACCATTACCATCCGATACATGTAGTAGCCTGCGC
ATAGTACTACACACGTGATCGAAACTATCCGGTACGT
Found at i:16699830 original size:138 final size:138
Alignment explanation
Indices: 16699582--16699853 Score: 517
Period size: 138 Copynumber: 2.0 Consensus size: 138
16699572 AGGTTTGGGA
*
16699582 GTGTGATAACTCTTGAAAAGAGTTATATTTTAGGATATTATATTAGTATTTTAGGACATTGCATC
1 GTGTGATAACTCTTGAAAAGAGTTAAATTTTAGGATATTATATTAGTATTTTAGGACATTGCATC
* *
16699647 ATGAACTTGGATTGTGCTTAAATGTTATTATGTTACTTTTACTTGTGGGTGGAAAAGATTTTTTT
66 ATGAACTTGGACTGTGCTTAAATGTTATTATGTTACTTTTACTTGTGGGTGGAAAAGATTTGTTT
16699712 GGATAGGG
131 GGATAGGG
16699720 GTGTGATAACTCTTGAAAAGAGTTAAATTTTAGGATATTATATTAGTATTTTAGGACATTGCATC
1 GTGTGATAACTCTTGAAAAGAGTTAAATTTTAGGATATTATATTAGTATTTTAGGACATTGCATC
16699785 ATGAACTTGGACTGTGCTTAAATGTTATTATGTTACTTTTACTTGTGGGTGGAAAAGATTTGTTT
66 ATGAACTTGGACTGTGCTTAAATGTTATTATGTTACTTTTACTTGTGGGTGGAAAAGATTTGTTT
16699850 GGAT
131 GGAT
16699854 GACAAGTGTA
Statistics
Matches: 131, Mismatches: 3, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
138 131 1.00
ACGTcount: A:0.29, C:0.07, G:0.22, T:0.42
Consensus pattern (138 bp):
GTGTGATAACTCTTGAAAAGAGTTAAATTTTAGGATATTATATTAGTATTTTAGGACATTGCATC
ATGAACTTGGACTGTGCTTAAATGTTATTATGTTACTTTTACTTGTGGGTGGAAAAGATTTGTTT
GGATAGGG
Found at i:16701174 original size:3 final size:3
Alignment explanation
Indices: 16701166--16701195 Score: 60
Period size: 3 Copynumber: 10.0 Consensus size: 3
16701156 CGAGGAGATA
16701166 GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT
1 GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT
16701196 TAGAACTTAA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 27 1.00
ACGTcount: A:0.33, C:0.00, G:0.33, T:0.33
Consensus pattern (3 bp):
GAT
Found at i:16728756 original size:25 final size:24
Alignment explanation
Indices: 16728706--16728756 Score: 57
Period size: 25 Copynumber: 2.1 Consensus size: 24
16728696 GGGTATCAAC
*
16728706 AAAAAAAATATCAAATTAAAATAT
1 AAAAAAAATATCAAATTAAAACAT
* **
16728730 AAAAATAAATATTAAATTTTAACAT
1 AAAAA-AAATATCAAATTAAAACAT
16728755 AA
1 AA
16728757 TCCACTAATA
Statistics
Matches: 22, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
24 5 0.23
25 17 0.77
ACGTcount: A:0.67, C:0.04, G:0.00, T:0.29
Consensus pattern (24 bp):
AAAAAAAATATCAAATTAAAACAT
Found at i:16728848 original size:71 final size:70
Alignment explanation
Indices: 16728713--16728848 Score: 218
Period size: 71 Copynumber: 1.9 Consensus size: 70
16728703 AACAAAAAAA
* * * **
16728713 ATATCAAATTAAAATATAAAAATAAATATTAAATTTTAACATAATCCACTAATAATTAGTCAAAA
1 ATATCAAAATAAAATATAAAAATAAATATTAAAATTTAACATAATCCACTAATAATAACCCAAAA
16728778 TATAT
66 TATAT
16728783 ATATCAAAATAAAATATAAAAAATAAATATTAAAATTTAACATAATCCACTAATAATAACCCAAA
1 ATATCAAAATAAAATAT-AAAAATAAATATTAAAATTTAACATAATCCACTAATAATAACCCAAA
16728848 A
65 A
16728849 GCTAATCTTT
Statistics
Matches: 60, Mismatches: 5, Indels: 1
0.91 0.08 0.02
Matches are distributed among these distances:
70 16 0.27
71 44 0.73
ACGTcount: A:0.59, C:0.10, G:0.01, T:0.30
Consensus pattern (70 bp):
ATATCAAAATAAAATATAAAAATAAATATTAAAATTTAACATAATCCACTAATAATAACCCAAAA
TATAT
Found at i:16737258 original size:3 final size:3
Alignment explanation
Indices: 16737252--16737297 Score: 92
Period size: 3 Copynumber: 15.3 Consensus size: 3
16737242 CCCCCCGCCA
16737252 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T
16737298 TCTTTACTCT
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:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TAT
Found at i:16739919 original size:19 final size:17
Alignment explanation
Indices: 16739892--16739945 Score: 54
Period size: 19 Copynumber: 3.0 Consensus size: 17
16739882 AGAATTTAAC
16739892 AAAAGAAAACTGTGAAAA
1 AAAAGAAAA-TGTGAAAA
* * *
16739910 GAAAACAAAAGAGAGAAAA
1 -AAAAGAAAA-TGTGAAAA
16739929 AAAAGAAAATGTGAAAA
1 AAAAGAAAATGTGAAAA
16739946 CTAATGGGGA
Statistics
Matches: 28, Mismatches: 7, Indels: 2
0.76 0.19 0.05
Matches are distributed among these distances:
17 6 0.21
18 8 0.29
19 14 0.50
ACGTcount: A:0.70, C:0.04, G:0.19, T:0.07
Consensus pattern (17 bp):
AAAAGAAAATGTGAAAA
Found at i:16748608 original size:39 final size:39
Alignment explanation
Indices: 16748527--16748812 Score: 302
Period size: 39 Copynumber: 7.5 Consensus size: 39
16748517 CACAGCACAA
* * * *
16748527 AAGTGCTATTAGGAGTATCGAAGTACAACCA--GGCACGT
1 AAGTGCGATCAGGGGTATCCAAGTACAA-CAGGGGCACGT
* *
16748565 AAGTGCGATCAGGGGTA-CCAAGGTACAACAAGGGCACAT
1 AAGTGCGATCAGGGGTATCCAA-GTACAACAGGGGCACGT
* * **
16748604 AAGTGCAATTAGGGGTATTGAAGTACAACAGGGGCACGT
1 AAGTGCGATCAGGGGTATCCAAGTACAACAGGGGCACGT
* *
16748643 AAGAGCGATCAGGGGTATCGAAGTACAACAGGGGCACGT
1 AAGTGCGATCAGGGGTATCCAAGTACAACAGGGGCACGT
* *
16748682 AAGTACGATCAGGGGTA-CCGAAGTACAATAGGGGCACGT
1 AAGTGCGATCAGGGGTATCC-AAGTACAACAGGGGCACGT
* *
16748721 AAGTGCG-TCAGGGGTATCGAAGTACAACAGGGGCACAT
1 AAGTGCGATCAGGGGTATCCAAGTACAACAGGGGCACGT
* *
16748759 TAGTGCGATCAAGGGTA-CCAAAGTAC-A-A-GGGCACGT
1 AAGTGCGATCAGGGGTATCC-AAGTACAACAGGGGCACGT
*
16748795 AAGTGCCATCAGGGGTAT
1 AAGTGCGATCAGGGGTAT
16748813 AATTATAGAA
Statistics
Matches: 209, Mismatches: 30, Indels: 19
0.81 0.12 0.07
Matches are distributed among these distances:
36 21 0.10
37 6 0.03
38 55 0.26
39 125 0.60
40 2 0.01
ACGTcount: A:0.33, C:0.18, G:0.32, T:0.17
Consensus pattern (39 bp):
AAGTGCGATCAGGGGTATCCAAGTACAACAGGGGCACGT
Found at i:16748657 original size:20 final size:20
Alignment explanation
Indices: 16748632--16748756 Score: 95
Period size: 19 Copynumber: 6.5 Consensus size: 20
16748622 TGAAGTACAA
16748632 CAGGGGCACGTAAG-AGCGAT
1 CAGGGGCACGTAAGTA-CGAT
* *
16748652 CAGGGGTATCG-AAGTAC-AA
1 CAGGGGCA-CGTAAGTACGAT
16748671 CAGGGGCACGTAAGTACGAT
1 CAGGGGCACGTAAGTACGAT
* *
16748691 CAGGGGTACCG-AAGTACAAT
1 CAGGGGCA-CGTAAGTACGAT
*
16748711 -AGGGGCACGTAAGTGCG-T
1 CAGGGGCACGTAAGTACGAT
* *
16748729 CAGGGGTATCG-AAGTAC-AA
1 CAGGGGCA-CGTAAGTACGAT
16748748 CAGGGGCAC
1 CAGGGGCAC
16748757 ATTAGTGCGA
Statistics
Matches: 83, Mismatches: 13, Indels: 20
0.72 0.11 0.17
Matches are distributed among these distances:
18 6 0.07
19 43 0.52
20 29 0.35
21 5 0.06
ACGTcount: A:0.31, C:0.19, G:0.36, T:0.14
Consensus pattern (20 bp):
CAGGGGCACGTAAGTACGAT
Found at i:16748669 original size:78 final size:77
Alignment explanation
Indices: 16748521--16748812 Score: 342
Period size: 77 Copynumber: 3.8 Consensus size: 77
16748511 CGTAACCACA
* * * * * *
16748521 GCACAAAAGTGCTATTAGGAGTATCGAAGTACAACCA-GGCACGTAAGTGCGATCAGGGGTA-CC
1 GCACATAAGTGCGATCAGGGGTACCGAAGTACAA-CAGGGCACGTAAGTGCGATCAGGGGTATCG
*
16748584 AAGGTACAACAAGG
65 AA-GTACAACAGGG
* * ** *
16748598 GCACATAAGTGCAATTAGGGGTATTGAAGTACAACAGGGGCACGTAAGAGCGATCAGGGGTATCG
1 GCACATAAGTGCGATCAGGGGTACCGAAGTACAACA-GGGCACGTAAGTGCGATCAGGGGTATCG
16748663 AAGTACAACAGGG
65 AAGTACAACAGGG
* * *
16748676 GCACGTAAGTACGATCAGGGGTACCGAAGTACAATAGGGGCACGTAAGTGCG-TCAGGGGTATCG
1 GCACATAAGTGCGATCAGGGGTACCGAAGTACAACA-GGGCACGTAAGTGCGATCAGGGGTATCG
16748740 AAGTACAACAGGG
65 AAGTACAACAGGG
* * * *
16748753 GCACATTAGTGCGATCAAGGGTACCAAAGTAC-A-AGGGCACGTAAGTGCCATCAGGGGTAT
1 GCACATAAGTGCGATCAGGGGTACCGAAGTACAACAGGGCACGTAAGTGCGATCAGGGGTAT
16748813 AATTATAGAA
Statistics
Matches: 190, Mismatches: 21, Indels: 10
0.86 0.10 0.05
Matches are distributed among these distances:
74 14 0.07
75 11 0.06
76 3 0.02
77 82 0.43
78 77 0.41
79 3 0.02
ACGTcount: A:0.34, C:0.18, G:0.32, T:0.16
Consensus pattern (77 bp):
GCACATAAGTGCGATCAGGGGTACCGAAGTACAACAGGGCACGTAAGTGCGATCAGGGGTATCGA
AGTACAACAGGG
Found at i:16754754 original size:16 final size:15
Alignment explanation
Indices: 16754729--16754762 Score: 50
Period size: 16 Copynumber: 2.2 Consensus size: 15
16754719 AAAGTTTATA
*
16754729 ATAATTAATATATATT
1 ATAATAAATATA-ATT
16754745 ATAATAAATATAATT
1 ATAATAAATATAATT
16754760 ATA
1 ATA
16754763 TACTATTTAT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
15 6 0.35
16 11 0.65
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (15 bp):
ATAATAAATATAATT
Found at i:16756432 original size:295 final size:295
Alignment explanation
Indices: 16755902--16756791 Score: 1762
Period size: 295 Copynumber: 3.0 Consensus size: 295
16755892 GAAGTTTGAC
* *
16755902 AACTCCGTATGGATAAACTTGGTGAATCATAAATGGACCGGACCAACATGATTTTAACTTACCTA
1 AACTCCGTATGGATAAACTTGGTGAATCGTAAATGGACCGAACCAACATGATTTTAACTTACCTA
16755967 GAAAGAACCTTAATCTGGAATTGAATAATAAGACTTGGTGACCTACTTCAAATTCTCGAACTCGA
66 GAAAGAACCTTAATCTGGAATTGAATAATAAGACTTGGTGACCTACTTCAAATTCTCGAACTCGA
16756032 ATGTGCTTGTCATGCCATCTTTTTAGTCTTTCCTTGAGTAATTTGGCATTCTCGTATGAGAACAT
131 ATGTGCTTGTCATGCCATCTTTTTAGTCTTTCCTTGAGTAATTTGGCATTCTCGTATGAGAACAT
16756097 TCGAAACTCTTCTAACTCATTGATTTGAAGCATCTGTTTCTCTTTAGCAAGCTTAAGATCCAAGT
196 TCGAAACTCTTCTAACTCATTGATTTGAAGCATCTGTTTCTCTTTAGCAAGCTTAAGATCCAAGT
16756162 TTAGATGTTGGAGAGCCTAGTAAACTTTGTCCTCT
261 TTAGATGTTGGAGAGCCTAGTAAACTTTGTCCTCT
16756197 AACTCCGTATGGATAAACTTGGTGAATCGTAAATGGACCGAACCAACATGATTTTAACTTACCTA
1 AACTCCGTATGGATAAACTTGGTGAATCGTAAATGGACCGAACCAACATGATTTTAACTTACCTA
16756262 GAAAGAACCTTAATCTGGAATTGAATAATAAGACTTGGTGACCTACTTCAAATTCTCGAACTCGA
66 GAAAGAACCTTAATCTGGAATTGAATAATAAGACTTGGTGACCTACTTCAAATTCTCGAACTCGA
16756327 ATGTGCTTGTCATGCCATCTTTTTAGTCTTTCCTTGAGTAATTTGGCATTCTCGTATGAGAACAT
131 ATGTGCTTGTCATGCCATCTTTTTAGTCTTTCCTTGAGTAATTTGGCATTCTCGTATGAGAACAT
16756392 TCGAAACTCTTCTAACTCATTGATTTGAAGCATCTGTTTCTCTTTAGCAAGCTTAAGATCCAAGT
196 TCGAAACTCTTCTAACTCATTGATTTGAAGCATCTGTTTCTCTTTAGCAAGCTTAAGATCCAAGT
16756457 TTAGATGTTGGAGAGCCTAGTAAACTTTGTCCTCT
261 TTAGATGTTGGAGAGCCTAGTAAACTTTGTCCTCT
16756492 AACTCCGTATGGATAAACTTGGTGAATCGTAAATGGACCGAACCAACATGATTTTAACTTACCTA
1 AACTCCGTATGGATAAACTTGGTGAATCGTAAATGGACCGAACCAACATGATTTTAACTTACCTA
16756557 GAAAGAACCTTAATCTGGAATTGAATAATAAGACTTGGTGACCTACTTCAAATTCTCGAACTCGA
66 GAAAGAACCTTAATCTGGAATTGAATAATAAGACTTGGTGACCTACTTCAAATTCTCGAACTCGA
16756622 ATGTGCTTGTCATGCCATCTTTTTAGTCTTTCCTTGAGTAATTTGGCATTCTCGTATGAGAACAT
131 ATGTGCTTGTCATGCCATCTTTTTAGTCTTTCCTTGAGTAATTTGGCATTCTCGTATGAGAACAT
16756687 TCGAAACTCTTCTAACTCATTGATTTGAAGCATCTGTTTCTCTTTAGCAAGCTTAAGATCCAAGT
196 TCGAAACTCTTCTAACTCATTGATTTGAAGCATCTGTTTCTCTTTAGCAAGCTTAAGATCCAAGT
16756752 TTAGATGTTGGAGAGCCTAGTAAACTTTGTCCTCT
261 TTAGATGTTGGAGAGCCTAGTAAACTTTGTCCTCT
16756787 AACTC
1 AACTC
16756792 TAAGGGCAGA
Statistics
Matches: 593, Mismatches: 2, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
295 593 1.00
ACGTcount: A:0.29, C:0.19, G:0.17, T:0.34
Consensus pattern (295 bp):
AACTCCGTATGGATAAACTTGGTGAATCGTAAATGGACCGAACCAACATGATTTTAACTTACCTA
GAAAGAACCTTAATCTGGAATTGAATAATAAGACTTGGTGACCTACTTCAAATTCTCGAACTCGA
ATGTGCTTGTCATGCCATCTTTTTAGTCTTTCCTTGAGTAATTTGGCATTCTCGTATGAGAACAT
TCGAAACTCTTCTAACTCATTGATTTGAAGCATCTGTTTCTCTTTAGCAAGCTTAAGATCCAAGT
TTAGATGTTGGAGAGCCTAGTAAACTTTGTCCTCT
Found at i:16763720 original size:11 final size:10
Alignment explanation
Indices: 16763690--16763737 Score: 51
Period size: 10 Copynumber: 4.6 Consensus size: 10
16763680 GAATTTGTCG
* *
16763690 AAAATAAATC
1 AAAATTAATA
16763700 AAAATTAATA
1 AAAATTAATA
16763710 AAAATTTAATA
1 AAAA-TTAATA
*
16763721 TAAAATTAATT
1 -AAAATTAATA
16763732 AAAATT
1 AAAATT
16763738 CAACATGTTA
Statistics
Matches: 33, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
10 18 0.55
11 11 0.33
12 4 0.12
ACGTcount: A:0.65, C:0.02, G:0.00, T:0.33
Consensus pattern (10 bp):
AAAATTAATA
Found at i:16767098 original size:47 final size:46
Alignment explanation
Indices: 16767030--16767118 Score: 151
Period size: 47 Copynumber: 1.9 Consensus size: 46
16767020 TTGTAATGGT
*
16767030 ATGTCGTTGGGAGAGCTCAATCACAATATTATAGTGGAATGATTTG
1 ATGTCGTTGGGAGAGCTCAATCACAATACTATAGTGGAATGATTTG
*
16767076 ATGTCGTTGGGGAGAGCTCAATCACAATGCTATAGTGGAATGA
1 ATGTCGTT-GGGAGAGCTCAATCACAATACTATAGTGGAATGA
16767119 CTTGGTGACT
Statistics
Matches: 40, Mismatches: 2, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
46 8 0.20
47 32 0.80
ACGTcount: A:0.30, C:0.12, G:0.28, T:0.29
Consensus pattern (46 bp):
ATGTCGTTGGGAGAGCTCAATCACAATACTATAGTGGAATGATTTG
Found at i:16767558 original size:26 final size:26
Alignment explanation
Indices: 16767512--16767575 Score: 74
Period size: 26 Copynumber: 2.5 Consensus size: 26
16767502 ATGAATTTTC
*
16767512 TCAAAATTTTATCAAGGGTAAAATCA
1 TCAAAATTTTACCAAGGGTAAAATCA
* * **
16767538 TCAAAATTTTACCATGTGTAAAATTG
1 TCAAAATTTTACCAAGGGTAAAATCA
*
16767564 TCGAAATTTTAC
1 TCAAAATTTTAC
16767576 TGGGTAACAT
Statistics
Matches: 32, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
26 32 1.00
ACGTcount: A:0.41, C:0.12, G:0.11, T:0.36
Consensus pattern (26 bp):
TCAAAATTTTACCAAGGGTAAAATCA
Found at i:16768625 original size:25 final size:25
Alignment explanation
Indices: 16768581--16768655 Score: 123
Period size: 25 Copynumber: 3.0 Consensus size: 25
16768571 GGACATAAAT
*
16768581 TAATTTTTCCAAAAAAGATTCCATG
1 TAATTTTTCCAAAAAGGATTCCATG
* *
16768606 TAATTTTTCTAGAAAGGATTCCATG
1 TAATTTTTCCAAAAAGGATTCCATG
16768631 TAATTTTTCCAAAAAGGATTCCATG
1 TAATTTTTCCAAAAAGGATTCCATG
16768656 GCAAGGAGAA
Statistics
Matches: 45, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
25 45 1.00
ACGTcount: A:0.36, C:0.15, G:0.12, T:0.37
Consensus pattern (25 bp):
TAATTTTTCCAAAAAGGATTCCATG
Found at i:16772648 original size:24 final size:25
Alignment explanation
Indices: 16772621--16772677 Score: 71
Period size: 25 Copynumber: 2.3 Consensus size: 25
16772611 CTCCTCGAAG
* *
16772621 GAGCTTACCG-TTTACAGCTCGTAA
1 GAGCATACCGATTCACAGCTCGTAA
* *
16772645 GAGCATACCGATTCAGAGCTCGTAT
1 GAGCATACCGATTCACAGCTCGTAA
16772670 GAGCATAC
1 GAGCATAC
16772678 ATGTACAGGA
Statistics
Matches: 28, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
24 9 0.32
25 19 0.68
ACGTcount: A:0.28, C:0.25, G:0.23, T:0.25
Consensus pattern (25 bp):
GAGCATACCGATTCACAGCTCGTAA
Found at i:16778092 original size:26 final size:26
Alignment explanation
Indices: 16778063--16778136 Score: 89
Period size: 26 Copynumber: 2.9 Consensus size: 26
16778053 AATTTTCTTG
16778063 AAATTTTA-TCGAGGGTAAAATTGTCA
1 AAATTTTACT-GAGGGTAAAATTGTCA
* *
16778089 AAATTTTACTGTGTGTAAAATTGTCA
1 AAATTTTACTGAGGGTAAAATTGTCA
* *
16778115 AAATTTAACTG-GGGTAACATTG
1 AAATTTTACTGAGGGTAAAATTG
16778137 GGGTGAGAAA
Statistics
Matches: 42, Mismatches: 5, Indels: 3
0.84 0.10 0.06
Matches are distributed among these distances:
25 9 0.21
26 32 0.76
27 1 0.02
ACGTcount: A:0.36, C:0.08, G:0.19, T:0.36
Consensus pattern (26 bp):
AAATTTTACTGAGGGTAAAATTGTCA
Found at i:16778131 original size:25 final size:26
Alignment explanation
Indices: 16778075--16778136 Score: 90
Period size: 26 Copynumber: 2.4 Consensus size: 26
16778065 ATTTTATCGA
*
16778075 GGGTAAAATTGTCAAAATTTTACTGT
1 GGGTAAAATTGTCAAAATTTAACTGT
*
16778101 GTGTAAAATTGTCAAAATTTAACTG-
1 GGGTAAAATTGTCAAAATTTAACTGT
*
16778126 GGGTAACATTG
1 GGGTAAAATTG
16778137 GGGTGAGAAA
Statistics
Matches: 32, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
25 9 0.28
26 23 0.72
ACGTcount: A:0.35, C:0.08, G:0.21, T:0.35
Consensus pattern (26 bp):
GGGTAAAATTGTCAAAATTTAACTGT
Found at i:16782443 original size:15 final size:15
Alignment explanation
Indices: 16782423--16782451 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
16782413 GTGAAATAAA
16782423 CTGAAATAATAAAAG
1 CTGAAATAATAAAAG
16782438 CTGAAATAATAAAA
1 CTGAAATAATAAAA
16782452 TATTGTGAAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.62, C:0.07, G:0.10, T:0.21
Consensus pattern (15 bp):
CTGAAATAATAAAAG
Found at i:16783944 original size:22 final size:18
Alignment explanation
Indices: 16783900--16783941 Score: 84
Period size: 18 Copynumber: 2.3 Consensus size: 18
16783890 AATTTTAGGT
16783900 CAATTATACATACACCAA
1 CAATTATACATACACCAA
16783918 CAATTATACATACACCAA
1 CAATTATACATACACCAA
16783936 CAATTA
1 CAATTA
16783942 ATTTTAGGGT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 24 1.00
ACGTcount: A:0.50, C:0.26, G:0.00, T:0.24
Consensus pattern (18 bp):
CAATTATACATACACCAA
Found at i:16783968 original size:51 final size:51
Alignment explanation
Indices: 16783874--16783974 Score: 132
Period size: 51 Copynumber: 2.0 Consensus size: 51
16783864 CTTGAAGTAC
* * * * *
16783874 ACATATACCAACAATTAATTTTAGGTCAATTATACATACACCAACAATTAT
1 ACATACACCAACAATTAATTTTAGGTCAAATAAAAATAAACCAACAATTAT
*
16783925 ACATACACCAACAATTAATTTTAGGGT-AAATAAAAATAAACCAAGAATTA
1 ACATACACCAACAATTAATTTTA-GGTCAAATAAAAATAAACCAACAATTA
16783975 ATTTTAGGTC
Statistics
Matches: 43, Mismatches: 6, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
51 40 0.93
52 3 0.07
ACGTcount: A:0.50, C:0.17, G:0.06, T:0.28
Consensus pattern (51 bp):
ACATACACCAACAATTAATTTTAGGTCAAATAAAAATAAACCAACAATTAT
Found at i:16784020 original size:33 final size:33
Alignment explanation
Indices: 16783918--16784027 Score: 159
Period size: 33 Copynumber: 3.3 Consensus size: 33
16783908 CATACACCAA
16783918 CAATTATACATACACCAACAATTAATTTTAGGGT
1 CAATTATACATACACCAACAATTAATTTTA-GGT
* * * * *
16783952 -AAATAAAAATAAACCAAGAATTAATTTTAGGT
1 CAATTATACATACACCAACAATTAATTTTAGGT
16783984 CAATTATACATACACCAACAATTAATTTTAGGT
1 CAATTATACATACACCAACAATTAATTTTAGGT
16784017 CAATTATACAT
1 CAATTATACAT
16784028 GCTTTATAAT
Statistics
Matches: 65, Mismatches: 10, Indels: 3
0.83 0.13 0.04
Matches are distributed among these distances:
32 3 0.05
33 62 0.95
ACGTcount: A:0.46, C:0.15, G:0.07, T:0.32
Consensus pattern (33 bp):
CAATTATACATACACCAACAATTAATTTTAGGT
Found at i:16788183 original size:45 final size:44
Alignment explanation
Indices: 16788092--16788183 Score: 112
Period size: 45 Copynumber: 2.1 Consensus size: 44
16788082 ACCTCTATTC
* * *
16788092 CATTCAACCAAACACAAGATTACTATTACGCCTCTATTCCATTA
1 CATTCAACCAAACACAAGATTACTATTACACCTCTAATCCAATA
*** *
16788136 CATTCAACCAAACAGTTGATTTGCTATTACACCTCTAATCCAATA
1 CATTCAACCAAACACAAGA-TTACTATTACACCTCTAATCCAATA
16788181 CAT
1 CAT
16788184 CTCTAATCCA
Statistics
Matches: 40, Mismatches: 7, Indels: 1
0.83 0.15 0.02
Matches are distributed among these distances:
44 16 0.40
45 24 0.60
ACGTcount: A:0.36, C:0.28, G:0.05, T:0.30
Consensus pattern (44 bp):
CATTCAACCAAACACAAGATTACTATTACACCTCTAATCCAATA
Found at i:16788187 original size:16 final size:16
Alignment explanation
Indices: 16788163--16788214 Score: 86
Period size: 16 Copynumber: 3.2 Consensus size: 16
16788153 GATTTGCTAT
16788163 TACACCTCTAATCCAA
1 TACACCTCTAATCCAA
*
16788179 TACATCTCTAATCCAA
1 TACACCTCTAATCCAA
*
16788195 TACACCTCTAATACAA
1 TACACCTCTAATCCAA
16788211 TACA
1 TACA
16788215 GCGAACCAAA
Statistics
Matches: 33, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
16 33 1.00
ACGTcount: A:0.40, C:0.33, G:0.00, T:0.27
Consensus pattern (16 bp):
TACACCTCTAATCCAA
Found at i:16800851 original size:27 final size:25
Alignment explanation
Indices: 16800796--16800853 Score: 80
Period size: 25 Copynumber: 2.2 Consensus size: 25
16800786 TATATATAAT
* *
16800796 ATATATATTTGATTACAAATAAAAT
1 ATATATATTTGATTAAAAATAAAAA
16800821 ATATATATTTGATTAAAAATTTAAAAA
1 ATATATATTTGATTAAAAA--TAAAAA
16800848 ATATAT
1 ATATAT
16800854 TTAATATATA
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
25 18 0.62
27 11 0.38
ACGTcount: A:0.53, C:0.02, G:0.03, T:0.41
Consensus pattern (25 bp):
ATATATATTTGATTAAAAATAAAAA
Found at i:16800855 original size:25 final size:25
Alignment explanation
Indices: 16800793--16800840 Score: 87
Period size: 25 Copynumber: 1.9 Consensus size: 25
16800783 TAATATATAT
*
16800793 AATATATATATTTGATTACAAATAA
1 AATATATATATTTGATTAAAAATAA
16800818 AATATATATATTTGATTAAAAAT
1 AATATATATATTTGATTAAAAAT
16800841 TTAAAAAATA
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
25 22 1.00
ACGTcount: A:0.52, C:0.02, G:0.04, T:0.42
Consensus pattern (25 bp):
AATATATATATTTGATTAAAAATAA
Found at i:16811051 original size:41 final size:41
Alignment explanation
Indices: 16811006--16811328 Score: 571
Period size: 41 Copynumber: 7.9 Consensus size: 41
16810996 CTTCTTTTTC
16811006 TTTCTTT-TTTTTCTCTTCTCCTTTCCTTTTCTTTCCT-TCTT
1 TTTCTTTCTTTTT-TCTTCTCCTTTCCTTTTCTTTCCTCT-TT
16811047 TTTCTTTCTTTTTTCTTCTCCTTTCCTTTTCTTTCCTCTTT
1 TTTCTTTCTTTTTTCTTCTCCTTTCCTTTTCTTTCCTCTTT
16811088 TTTCTTTCTTTTTTCTTCTCCTTTCCTTTTCTTTCCTCTTT
1 TTTCTTTCTTTTTTCTTCTCCTTTCCTTTTCTTTCCTCTTT
16811129 TTTCTTTCTTTTTTCTTCTCCTTTCCTTTTCTTTCCTCTTT
1 TTTCTTTCTTTTTTCTTCTCCTTTCCTTTTCTTTCCTCTTT
16811170 TTTCTTTCTTTTTTCTTCTCCTTTCCTTTTCTTTCCTCTTT
1 TTTCTTTCTTTTTTCTTCTCCTTTCCTTTTCTTTCCTCTTT
16811211 TTTCTTTCTTTTTTCTTCTCCTTTCCTTTTCTTTCCTCTTT
1 TTTCTTTCTTTTTTCTTCTCCTTTCCTTTTCTTTCCTCTTT
*
16811252 TTTCTTTCTTTTTTCTTCTCCTTTCCTTTTCTTTCCTC-CT
1 TTTCTTTCTTTTTTCTTCTCCTTTCCTTTTCTTTCCTCTTT
*
16811292 TTTCTTTCTTTTTTTTCTTCTCATTTCCTTTTCTTTC
1 TTTCTTTC--TTTTTTCTTCTCCTTTCCTTTTCTTTC
16811329 TTTTCCTTCC
Statistics
Matches: 276, Mismatches: 2, Indels: 7
0.97 0.01 0.02
Matches are distributed among these distances:
40 9 0.03
41 235 0.85
42 32 0.12
ACGTcount: A:0.00, C:0.29, G:0.00, T:0.71
Consensus pattern (41 bp):
TTTCTTTCTTTTTTCTTCTCCTTTCCTTTTCTTTCCTCTTT
Found at i:16811369 original size:26 final size:27
Alignment explanation
Indices: 16811233--16811357 Score: 91
Period size: 29 Copynumber: 4.6 Consensus size: 27
16811223 TTCTTCTCCT
*
16811233 TTCCTTTTCTTTCCTCTTT--TTTCTTTC
1 TTCCTTTTCTTT-CT-TTTCCTTCCTTTC
* *
16811260 TT--TTTTCTTCTCCTTTCCTTTTCTTTC
1 TTCCTTTTCTT-TCTTTTCC-TTCCTTTC
* * *
16811287 CTCCTTTTCTTTCTTTT-TTTTCTTCTC
1 TTCCTTTTCTTTCTTTTCCTTCCTT-TC
16811314 ATTTCCTTTTCTTTCTTTTCCTTCCTTTC
1 --TTCCTTTTCTTTCTTTTCCTTCCTTTC
16811343 TTCC-TTTCTTTCTTT
1 TTCCTTTTCTTTCTTT
16811358 CTCTCTCCTT
Statistics
Matches: 81, Mismatches: 7, Indels: 21
0.74 0.06 0.19
Matches are distributed among these distances:
24 3 0.04
25 8 0.10
26 18 0.22
27 17 0.21
28 5 0.06
29 25 0.31
30 5 0.06
ACGTcount: A:0.01, C:0.30, G:0.00, T:0.70
Consensus pattern (27 bp):
TTCCTTTTCTTTCTTTTCCTTCCTTTC
Found at i:16811446 original size:27 final size:27
Alignment explanation
Indices: 16811404--16811474 Score: 115
Period size: 27 Copynumber: 2.6 Consensus size: 27
16811394 TATAACACTA
16811404 GTGCCGCCAATGACTTTGGCACCATCG
1 GTGCCGCCAATGACTTTGGCACCATCG
* * *
16811431 GTGCCGCCAATCACTTTGGCACCTTTG
1 GTGCCGCCAATGACTTTGGCACCATCG
16811458 GTGCCGCCAATGACTTT
1 GTGCCGCCAATGACTTT
16811475 CCCTCCACCA
Statistics
Matches: 40, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
27 40 1.00
ACGTcount: A:0.17, C:0.32, G:0.24, T:0.27
Consensus pattern (27 bp):
GTGCCGCCAATGACTTTGGCACCATCG
Found at i:16813098 original size:30 final size:28
Alignment explanation
Indices: 16813017--16813100 Score: 86
Period size: 30 Copynumber: 3.0 Consensus size: 28
16813007 CATTTTACAT
16813017 TCAATATTTATATATTTTATTAATTTAA-TC
1 TCAATATTTATATATTTTA--AA-TTAATTC
*
16813047 TCAAT-TTTA-ATA-ATTAAATTAATTC
1 TCAATATTTATATATTTTAAATTAATTC
16813072 TCAATATTTATATATTTGTCAAATTAATT
1 TCAATATTTATATATTT-T-AAATTAATT
16813101 TTAATTTTAA
Statistics
Matches: 46, Mismatches: 2, Indels: 12
0.77 0.03 0.20
Matches are distributed among these distances:
24 4 0.09
25 9 0.20
26 4 0.09
27 6 0.13
28 4 0.09
29 5 0.11
30 14 0.30
ACGTcount: A:0.39, C:0.07, G:0.01, T:0.52
Consensus pattern (28 bp):
TCAATATTTATATATTTTAAATTAATTC
Found at i:16813169 original size:7 final size:7
Alignment explanation
Indices: 16813157--16813187 Score: 55
Period size: 7 Copynumber: 4.6 Consensus size: 7
16813147 TTAAATCTAA
16813157 AAAAATT
1 AAAAATT
16813164 AAAAATT
1 AAAAATT
16813171 AAAAATT
1 AAAAATT
16813178 AAAAA-T
1 AAAAATT
16813184 AAAA
1 AAAA
16813188 TAATTTGAAC
Statistics
Matches: 24, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
6 5 0.21
7 19 0.79
ACGTcount: A:0.77, C:0.00, G:0.00, T:0.23
Consensus pattern (7 bp):
AAAAATT
Found at i:16813174 original size:15 final size:14
Alignment explanation
Indices: 16813156--16813192 Score: 56
Period size: 14 Copynumber: 2.6 Consensus size: 14
16813146 TTTAAATCTA
16813156 AAAAAATTAAAAAT
1 AAAAAATTAAAAAT
*
16813170 TAAAAATTAAAAAT
1 AAAAAATTAAAAAT
16813184 AAAATAATT
1 AAAA-AATT
16813193 TGAACTTTAT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
14 16 0.80
15 4 0.20
ACGTcount: A:0.73, C:0.00, G:0.00, T:0.27
Consensus pattern (14 bp):
AAAAAATTAAAAAT
Found at i:16815809 original size:21 final size:22
Alignment explanation
Indices: 16815785--16815828 Score: 63
Period size: 21 Copynumber: 2.0 Consensus size: 22
16815775 AAAAATTCAA
*
16815785 TAAATAAAAATTAT-TAAATAT
1 TAAATAAAAATAATATAAATAT
*
16815806 TAAATTAAAATAATATAAATAT
1 TAAATAAAAATAATATAAATAT
16815828 T
1 T
16815829 TTAAAAAAAT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
21 12 0.60
22 8 0.40
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (22 bp):
TAAATAAAAATAATATAAATAT
Found at i:16826580 original size:9 final size:9
Alignment explanation
Indices: 16826566--16826590 Score: 50
Period size: 9 Copynumber: 2.8 Consensus size: 9
16826556 AAAATATTTA
16826566 TTTTAATAT
1 TTTTAATAT
16826575 TTTTAATAT
1 TTTTAATAT
16826584 TTTTAAT
1 TTTTAAT
16826591 GTATTATATA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 16 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (9 bp):
TTTTAATAT
Found at i:16826628 original size:51 final size:49
Alignment explanation
Indices: 16826529--16826632 Score: 111
Period size: 51 Copynumber: 2.1 Consensus size: 49
16826519 TTAAGTATGC
* * * * *
16826529 ATATTTTTAATTTTTTAAATATTTTGGAAAATATTTATTTTAATATTTTTA
1 ATATTTTTAATTTTATAAATATTTT-GAAAAAATTTA-TATAAAAATTTTA
*
16826580 ATATTTTTAATGTATTATATATATTTT-AAAAAATTTATATAAAAATTTTA
1 ATATTTTTAAT-T-TTATAAATATTTTGAAAAAATTTATATAAAAATTTTA
16826630 ATA
1 ATA
16826633 CGGGCAGCCA
Statistics
Matches: 45, Mismatches: 6, Indels: 5
0.80 0.11 0.09
Matches are distributed among these distances:
50 13 0.29
51 20 0.44
52 1 0.02
53 11 0.24
ACGTcount: A:0.41, C:0.00, G:0.03, T:0.56
Consensus pattern (49 bp):
ATATTTTTAATTTTATAAATATTTTGAAAAAATTTATATAAAAATTTTA
Found at i:16829915 original size:23 final size:23
Alignment explanation
Indices: 16829875--16829927 Score: 74
Period size: 23 Copynumber: 2.3 Consensus size: 23
16829865 ATAGAAAAAG
*
16829875 ATATA-TATGCAACGATATATATT
1 ATATATTATGAAACGATATATA-T
16829898 ATATATTATGAAAC-ATATATAT
1 ATATATTATGAAACGATATATAT
16829920 ATATATTA
1 ATATATTA
16829928 ACATTGTTTT
Statistics
Matches: 28, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
22 9 0.32
23 12 0.43
24 7 0.25
ACGTcount: A:0.47, C:0.06, G:0.06, T:0.42
Consensus pattern (23 bp):
ATATATTATGAAACGATATATAT
Found at i:16830919 original size:23 final size:23
Alignment explanation
Indices: 16830879--16830931 Score: 74
Period size: 23 Copynumber: 2.3 Consensus size: 23
16830869 ATAGAAAAAG
*
16830879 ATATA-TATGCAACGATATATATT
1 ATATATTATGAAACGATATATA-T
16830902 ATATATTATGAAAC-ATATATAT
1 ATATATTATGAAACGATATATAT
16830924 ATATATTA
1 ATATATTA
16830932 ACATTGTTTT
Statistics
Matches: 28, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
22 9 0.32
23 12 0.43
24 7 0.25
ACGTcount: A:0.47, C:0.06, G:0.06, T:0.42
Consensus pattern (23 bp):
ATATATTATGAAACGATATATAT
Found at i:16832559 original size:14 final size:14
Alignment explanation
Indices: 16832540--16832566 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
16832530 GCTGCCTTTA
16832540 GCTTCTATTTTCCG
1 GCTTCTATTTTCCG
16832554 GCTTCTATTTTCC
1 GCTTCTATTTTCC
16832567 AGTCAAAACG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.07, C:0.30, G:0.11, T:0.52
Consensus pattern (14 bp):
GCTTCTATTTTCCG
Found at i:16832990 original size:92 final size:92
Alignment explanation
Indices: 16832889--16833823 Score: 1834
Period size: 92 Copynumber: 10.1 Consensus size: 92
16832879 CCTCTCCACG
16832889 AATAATAAATTTATAACTTAAATAAGTATTACTATTTTTTTAATATTATACATATATTCATTTAC
1 AATAATAAATTTATAACTTAAATAAGTATTACTATTTTTTTAATATTATACATATATTCATTTAC
16832954 GTATGTAAGCTATATTTAAATTTTATT
66 GTATGTAAGCTATATTTAAATTTTATT
16832981 AATAATAAATTTATAACTTAAATAAGTATTACTATTTTTTTAATATTATACATATATTCATTTAC
1 AATAATAAATTTATAACTTAAATAAGTATTACTATTTTTTTAATATTATACATATATTCATTTAC
16833046 GTATGTAAGCTATATTTAAATTTTATT
66 GTATGTAAGCTATATTTAAATTTTATT
16833073 AATAATAAATTTATAACTTAAATAAGTATTACTATTTTTTTAATATTATACATATATTCATTTAC
1 AATAATAAATTTATAACTTAAATAAGTATTACTATTTTTTTAATATTATACATATATTCATTTAC
16833138 GTATGTAAGCTATATTTAAATTTTATT
66 GTATGTAAGCTATATTTAAATTTTATT
16833165 AATAATAAATTTATAACTTAAATAAGTATTACTATTTTTTTAATATTATACATATATTCATTTAC
1 AATAATAAATTTATAACTTAAATAAGTATTACTATTTTTTTAATATTATACATATATTCATTTAC
16833230 GTATGTAAGCTATATTTAAATTTTATT
66 GTATGTAAGCTATATTTAAATTTTATT
16833257 AATAATAAATTTATAACTTAAATAAGTATTACTATTTTTTTAATATTATACATATATTCATTTAC
1 AATAATAAATTTATAACTTAAATAAGTATTACTATTTTTTTAATATTATACATATATTCATTTAC
16833322 GTATGTAAGCTATATTTAAATTTTATT
66 GTATGTAAGCTATATTTAAATTTTATT
16833349 AATAATAAATTTATAACTTAAATAAGTATTACTATTTTTTTAATATTATACATATATTCATTTAC
1 AATAATAAATTTATAACTTAAATAAGTATTACTATTTTTTTAATATTATACATATATTCATTTAC
16833414 GTATGTAAGCTATATTTAAATTTTATT
66 GTATGTAAGCTATATTTAAATTTTATT
16833441 AATAATAAATTTATAACTTAAATAAGTATTACTATTTTTTTAATATTATACATATATTCATTTAC
1 AATAATAAATTTATAACTTAAATAAGTATTACTATTTTTTTAATATTATACATATATTCATTTAC
16833506 GTATGTAAGCTATATTTAAATTTTATT
66 GTATGTAAGCTATATTTAAATTTTATT
16833533 AATAATAAATTTATAACTTAAATAAGTATTACTATTTTTTTAATATTATACATATATTCATTTAC
1 AATAATAAATTTATAACTTAAATAAGTATTACTATTTTTTTAATATTATACATATATTCATTTAC
16833598 GTATGTAAGCTATATTTAAATTTTATT
66 GTATGTAAGCTATATTTAAATTTTATT
16833625 AATAATAAATTTATAACTTAAATAAGTATTACTATTTTTTTAATATTATACATATATTCATTTAC
1 AATAATAAATTTATAACTTAAATAAGTATTACTATTTTTTTAATATTATACATATATTCATTTAC
16833690 GTATGTAAGCTATATTTAAATTTTATT
66 GTATGTAAGCTATATTTAAATTTTATT
16833717 AATAATAAATTTATAACTTAAATAAGTATTACTATTTTTTTAATATTATACATATATATATTCAT
1 AATAATAAATTTATAACTTAAATAAGTATTACTATTTTTTTAATATTATAC----ATATATTCAT
16833782 TTACGTATGTAAGCTATATTTAAATTTTATT
62 TTACGTATGTAAGCTATATTTAAATTTTATT
16833813 AATAATAAATT
1 AATAATAAATT
16833824 NNNNNNNNNN
Statistics
Matches: 839, Mismatches: 0, Indels: 4
1.00 0.00 0.00
Matches are distributed among these distances:
92 787 0.94
96 52 0.06
ACGTcount: A:0.41, C:0.06, G:0.04, T:0.49
Consensus pattern (92 bp):
AATAATAAATTTATAACTTAAATAAGTATTACTATTTTTTTAATATTATACATATATTCATTTAC
GTATGTAAGCTATATTTAAATTTTATT
Found at i:16840220 original size:21 final size:21
Alignment explanation
Indices: 16840195--16840263 Score: 84
Period size: 21 Copynumber: 3.3 Consensus size: 21
16840185 CAGCAACTTA
* *
16840195 AAGCAGAGGCGGCAGCGAGGG
1 AAGCAGAGGCCGCAGCGAGAG
* **
16840216 AAGCAGAAGCTACAGCGAGAG
1 AAGCAGAGGCCGCAGCGAGAG
*
16840237 AAGCAGAGGCCGCAACGAGAG
1 AAGCAGAGGCCGCAGCGAGAG
16840258 AAGCAG
1 AAGCAG
16840264 CGAGAGAAGC
Statistics
Matches: 40, Mismatches: 8, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
21 40 1.00
ACGTcount: A:0.38, C:0.20, G:0.41, T:0.01
Consensus pattern (21 bp):
AAGCAGAGGCCGCAGCGAGAG
Found at i:16840269 original size:12 final size:12
Alignment explanation
Indices: 16840252--16840287 Score: 54
Period size: 12 Copynumber: 3.0 Consensus size: 12
16840242 GAGGCCGCAA
16840252 CGAGAGAAGCAG
1 CGAGAGAAGCAG
16840264 CGAGAGAAGCAG
1 CGAGAGAAGCAG
* *
16840276 CAATAGAAGCAG
1 CGAGAGAAGCAG
16840288 AGATTCAAAA
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
12 22 1.00
ACGTcount: A:0.44, C:0.17, G:0.36, T:0.03
Consensus pattern (12 bp):
CGAGAGAAGCAG
Found at i:16840510 original size:42 final size:42
Alignment explanation
Indices: 16840451--16840953 Score: 943
Period size: 42 Copynumber: 12.0 Consensus size: 42
16840441 TATGTTGCAT
16840451 TTTCTAAGTGCCGCTAAAGAACATGATCTTTAGCGGTGTTTG
1 TTTCTAAGTGCCGCTAAAGAACATGATCTTTAGCGGTGTTTG
16840493 TTTCTAAGTGCCGCTAAAGAACATGATCTTTAGCGGTGTTTG
1 TTTCTAAGTGCCGCTAAAGAACATGATCTTTAGCGGTGTTTG
16840535 TTTCTAAGTGCCGCTAAAGAACATGATCTTTAGCGGTGTTTG
1 TTTCTAAGTGCCGCTAAAGAACATGATCTTTAGCGGTGTTTG
16840577 TTTCTAAGTGCCGCTAAAGAACATGATCTTTAGCGGTGTTTG
1 TTTCTAAGTGCCGCTAAAGAACATGATCTTTAGCGGTGTTTG
16840619 TTTCTAAGTGCCGCTAAAGAACATGATCTTTAGCGGTGTTTG
1 TTTCTAAGTGCCGCTAAAGAACATGATCTTTAGCGGTGTTTG
16840661 TTTCTAAGTGCCGCTAAAGAACATGATCTTTAGCGGTGTTTG
1 TTTCTAAGTGCCGCTAAAGAACATGATCTTTAGCGGTGTTTG
16840703 TTTCTAAGTGCCGCTAAAGAACATGATCTTTAGCGGTGTTTG
1 TTTCTAAGTGCCGCTAAAGAACATGATCTTTAGCGGTGTTTG
16840745 TTTCTAAGTGCCGCTAAAGAACATGATCTTTAGCGGTGTTTG
1 TTTCTAAGTGCCGCTAAAGAACATGATCTTTAGCGGTGTTTG
* *
16840787 TTTCTAAGTGCCGCTAAAGAACATGATCTTTAGCGGCGTTTT
1 TTTCTAAGTGCCGCTAAAGAACATGATCTTTAGCGGTGTTTG
* **
16840829 TTTCTAAGCGCCGCTAAAGAACATGATCTTTAGCGACGTTTG
1 TTTCTAAGTGCCGCTAAAGAACATGATCTTTAGCGGTGTTTG
*
16840871 TTTCTAAGCGCCGCTAAAGAACATGATCTTTAGCGGTGTTTG
1 TTTCTAAGTGCCGCTAAAGAACATGATCTTTAGCGGTGTTTG
*
16840913 TTTCTAAGTGCCGCTAAAGAACATGATCTTTAGCGGCGTTT
1 TTTCTAAGTGCCGCTAAAGAACATGATCTTTAGCGGTGTTT
16840954 TTTTATGTAA
Statistics
Matches: 452, Mismatches: 9, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
42 452 1.00
ACGTcount: A:0.24, C:0.18, G:0.23, T:0.35
Consensus pattern (42 bp):
TTTCTAAGTGCCGCTAAAGAACATGATCTTTAGCGGTGTTTG
Found at i:16841078 original size:22 final size:22
Alignment explanation
Indices: 16841047--16841089 Score: 68
Period size: 22 Copynumber: 2.0 Consensus size: 22
16841037 TAGTGGCGTT
* *
16841047 AAAAAGCGCCGCTAAAGACCTA
1 AAAAAACGCCGCTAAAAACCTA
16841069 AAAAAACGCCGCTAAAAACCT
1 AAAAAACGCCGCTAAAAACCT
16841090 GTTCTGCTGT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.49, C:0.28, G:0.14, T:0.09
Consensus pattern (22 bp):
AAAAAACGCCGCTAAAAACCTA
Found at i:16841303 original size:18 final size:18
Alignment explanation
Indices: 16841247--16841303 Score: 51
Period size: 18 Copynumber: 3.1 Consensus size: 18
16841237 TGGCACCTCG
* *
16841247 GTTTTTACATATATCTCT
1 GTTTATACATATATCTGT
* *
16841265 GTGTATAGATATATCCATGT
1 GTTTATACATATAT-C-TGT
*
16841285 GTTTCTACATATATCTGT
1 GTTTATACATATATCTGT
16841303 G
1 G
16841304 CAATTATGTA
Statistics
Matches: 30, Mismatches: 7, Indels: 4
0.73 0.17 0.10
Matches are distributed among these distances:
18 15 0.50
19 2 0.07
20 13 0.43
ACGTcount: A:0.25, C:0.14, G:0.14, T:0.47
Consensus pattern (18 bp):
GTTTATACATATATCTGT
Found at i:16858571 original size:85 final size:85
Alignment explanation
Indices: 16858428--16858597 Score: 259
Period size: 85 Copynumber: 2.0 Consensus size: 85
16858418 TTAGAGTAGA
* * * *
16858428 GGTTTAGGCTATTTCTAAATTCCTAAATAACGTAATGAATCATGTCTACAAGCAGCGATTCCAAG
1 GGTTTAGGCTATTTCTAAATTCCCAAATAACGCAATGAATCATGTCTACAAGCAGCGATTACAAA
*
16858493 CAGTCACCAATTACTTTCGC
66 CACTCACCAATTACTTTCGC
* * *
16858513 GGTTTAGGCTATTTTTAAATTCCCAAATAACGCATTGAATCGTGTCTACAAGCAGCGATTACAAA
1 GGTTTAGGCTATTTCTAAATTCCCAAATAACGCAATGAATCATGTCTACAAGCAGCGATTACAAA
*
16858578 CACTCGCCAATTACTTTCGC
66 CACTCACCAATTACTTTCGC
16858598 CTAGACGCCG
Statistics
Matches: 76, Mismatches: 9, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
85 76 1.00
ACGTcount: A:0.31, C:0.23, G:0.15, T:0.31
Consensus pattern (85 bp):
GGTTTAGGCTATTTCTAAATTCCCAAATAACGCAATGAATCATGTCTACAAGCAGCGATTACAAA
CACTCACCAATTACTTTCGC
Found at i:16860935 original size:12 final size:12
Alignment explanation
Indices: 16860918--16860947 Score: 51
Period size: 12 Copynumber: 2.5 Consensus size: 12
16860908 TCGAAACCTG
*
16860918 AGATTTGCCTCT
1 AGATTTACCTCT
16860930 AGATTTACCTCT
1 AGATTTACCTCT
16860942 AGATTT
1 AGATTT
16860948 TGGGGTAAGT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
12 17 1.00
ACGTcount: A:0.23, C:0.20, G:0.13, T:0.43
Consensus pattern (12 bp):
AGATTTACCTCT
Found at i:16863346 original size:16 final size:16
Alignment explanation
Indices: 16863321--16863351 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
16863311 TTTAAGTGAA
16863321 TTGAAATACTATATGT
1 TTGAAATACTATATGT
*
16863337 TTGAATTACTATATG
1 TTGAAATACTATATG
16863352 ATATGGTTAT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.35, C:0.06, G:0.13, T:0.45
Consensus pattern (16 bp):
TTGAAATACTATATGT
Found at i:16866530 original size:25 final size:25
Alignment explanation
Indices: 16866502--16866549 Score: 62
Period size: 25 Copynumber: 1.9 Consensus size: 25
16866492 TTTAATGTTC
*
16866502 AATTTGATA-TATGTGTTTTTTTTCT
1 AATTTGATACT-TGAGTTTTTTTTCT
*
16866527 AATTTGGTACTTGAGTTTTTTTT
1 AATTTGATACTTGAGTTTTTTTT
16866550 TCTCAATTAA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
25 19 0.95
26 1 0.05
ACGTcount: A:0.19, C:0.04, G:0.15, T:0.62
Consensus pattern (25 bp):
AATTTGATACTTGAGTTTTTTTTCT
Found at i:16871026 original size:63 final size:63
Alignment explanation
Indices: 16870927--16871055 Score: 224
Period size: 63 Copynumber: 2.0 Consensus size: 63
16870917 CAACCTGATT
*
16870927 TATAACTTAAATTTTGTAATTCAAACTCTATTAAGATGCGCCTCATT-CTCGATGTGATAAGAA
1 TATAACTTAAATTTGGTAATTCAAACTCTATTAAGATGCGCCTCATTCCT-GATGTGATAAGAA
*
16870990 TATAACTTAAATTTGGTAATTCAAACTCTATTAAGATGTGCCTCATTCCTGATGTGATAAGAA
1 TATAACTTAAATTTGGTAATTCAAACTCTATTAAGATGCGCCTCATTCCTGATGTGATAAGAA
16871053 TAT
1 TAT
16871056 CTCTTTGTGA
Statistics
Matches: 63, Mismatches: 2, Indels: 2
0.94 0.03 0.03
Matches are distributed among these distances:
63 61 0.97
64 2 0.03
ACGTcount: A:0.35, C:0.15, G:0.13, T:0.37
Consensus pattern (63 bp):
TATAACTTAAATTTGGTAATTCAAACTCTATTAAGATGCGCCTCATTCCTGATGTGATAAGAA
Found at i:16875170 original size:16 final size:17
Alignment explanation
Indices: 16875138--16875171 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
16875128 TAATAGTGGT
*
16875138 TTGAAATGTTAACTTAA
1 TTGAAATATTAACTTAA
16875155 TTGAAATATT-ACTTAA
1 TTGAAATATTAACTTAA
16875171 T
1 T
16875172 GACTTATTTT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 7 0.44
17 9 0.56
ACGTcount: A:0.41, C:0.06, G:0.09, T:0.44
Consensus pattern (17 bp):
TTGAAATATTAACTTAA
Found at i:16878135 original size:24 final size:24
Alignment explanation
Indices: 16878088--16878135 Score: 60
Period size: 24 Copynumber: 2.0 Consensus size: 24
16878078 CATATTTAAA
** *
16878088 TTATAAATAAAATATTAATTAACC
1 TTATAAATAAAATAACAATCAACC
*
16878112 TTATAAATAAAATAACACTCAACC
1 TTATAAATAAAATAACAATCAACC
16878136 AGGCTTTTTT
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
24 20 1.00
ACGTcount: A:0.54, C:0.15, G:0.00, T:0.31
Consensus pattern (24 bp):
TTATAAATAAAATAACAATCAACC
Found at i:16880827 original size:14 final size:14
Alignment explanation
Indices: 16880808--16880834 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
16880798 TGGAAGATGG
16880808 TAATATATAAAATT
1 TAATATATAAAATT
16880822 TAATATATAAAAT
1 TAATATATAAAAT
16880835 AAGCTTTTAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (14 bp):
TAATATATAAAATT
Found at i:16881293 original size:20 final size:20
Alignment explanation
Indices: 16881256--16881311 Score: 98
Period size: 20 Copynumber: 2.9 Consensus size: 20
16881246 ATTATAATGC
16881256 TGTTGTTTACTT-CGACTCA
1 TGTTGTTTACTTGCGACTCA
16881275 TGTTGTTTACTTGCGACTCA
1 TGTTGTTTACTTGCGACTCA
16881295 TGTTGTTTACTTG-GACT
1 TGTTGTTTACTTGCGACT
16881312 TTTACTTATG
Statistics
Matches: 36, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
19 16 0.44
20 20 0.56
ACGTcount: A:0.14, C:0.18, G:0.20, T:0.48
Consensus pattern (20 bp):
TGTTGTTTACTTGCGACTCA
Found at i:16882845 original size:36 final size:36
Alignment explanation
Indices: 16882805--16882887 Score: 96
Period size: 35 Copynumber: 2.3 Consensus size: 36
16882795 AATCCCTCCA
* * *
16882805 AAACACACCAAGTACTCACAAGAGCTAGTCCAACCG
1 AAACACACCAAATACTCAAAAGAGCTAATCCAACCG
** *
16882841 AAACA-TGCAAATGCTCAAAAGAGCTAATCCAACCG
1 AAACACACCAAATACTCAAAAGAGCTAATCCAACCG
*
16882876 AAACACGCCAAA
1 AAACACACCAAA
16882888 CAGAAAGTAT
Statistics
Matches: 38, Mismatches: 8, Indels: 2
0.79 0.17 0.04
Matches are distributed among these distances:
35 29 0.76
36 9 0.24
ACGTcount: A:0.46, C:0.30, G:0.13, T:0.11
Consensus pattern (36 bp):
AAACACACCAAATACTCAAAAGAGCTAATCCAACCG
Found at i:16891252 original size:20 final size:19
Alignment explanation
Indices: 16891229--16891333 Score: 84
Period size: 20 Copynumber: 5.3 Consensus size: 19
16891219 TAAGTGCGTT
16891229 CAGGGGTACTGAAGTACAAA
1 CAGGGGTAC-GAAGTACAAA
* * ** *
16891249 CAGGGGCACGTATGTGTAAT
1 CAGGGGTACG-AAGTACAAA
16891269 CAGGGGTACGAAGTACAAA
1 CAGGGGTACGAAGTACAAA
* * * *
16891288 CAGGGGCACGTATGTGCAAT
1 CAGGGGTACG-AAGTACAAA
16891308 CAGGGGTACCGAAGTACAAA
1 CAGGGGTA-CGAAGTACAAA
*
16891328 TAGGGG
1 CAGGGG
16891334 CATGTATGTG
Statistics
Matches: 63, Mismatches: 19, Indels: 6
0.72 0.22 0.07
Matches are distributed among these distances:
19 15 0.24
20 46 0.73
21 2 0.03
ACGTcount: A:0.33, C:0.16, G:0.34, T:0.16
Consensus pattern (19 bp):
CAGGGGTACGAAGTACAAA
Found at i:16891341 original size:79 final size:81
Alignment explanation
Indices: 16891209--16891388 Score: 247
Period size: 79 Copynumber: 2.2 Consensus size: 81
16891199 AGAGTATAAT
* * ** * * *
16891209 CAGGGGCACTTAAGTGCGTTCAGGGGTACTGAAGTACAAACAGGGGCACGTATGTGTAA-TCAGG
1 CAGGGGCACGTATGTGCAATCAGGGGTACCGAAGTACAAACAGGGGCACGTATGTGCAATTCAAG
16891273 GGTAC-GAAGTACAAA
66 GGTACTGAAGTACAAA
* *
16891288 CAGGGGCACGTATGTGCAATCAGGGGTACCGAAGTACAAATAGGGGCATGTATGTGCAATTCAAG
1 CAGGGGCACGTATGTGCAATCAGGGGTACCGAAGTACAAACAGGGGCACGTATGTGCAATTCAAG
16891353 GGTACTGAAGTACAAA
66 GGTACTGAAGTACAAA
* *
16891369 TAGGGACACGTATGTGCAAT
1 CAGGGGCACGTATGTGCAAT
16891389 TCATGCAATA
Statistics
Matches: 88, Mismatches: 11, Indels: 2
0.87 0.11 0.02
Matches are distributed among these distances:
79 51 0.58
80 9 0.10
81 28 0.32
ACGTcount: A:0.32, C:0.16, G:0.32, T:0.20
Consensus pattern (81 bp):
CAGGGGCACGTATGTGCAATCAGGGGTACCGAAGTACAAACAGGGGCACGTATGTGCAATTCAAG
GGTACTGAAGTACAAA
Found at i:16891368 original size:41 final size:41
Alignment explanation
Indices: 16891209--16891391 Score: 248
Period size: 40 Copynumber: 4.6 Consensus size: 41
16891199 AGAGTATAAT
* * *
16891209 CAGGGGCACTTAAGTGC-GTTCAGGGGTACTGAAGTACAAA
1 CAGGGGCACGTATGTGCAATTCAGGGGTACTGAAGTACAAA
*
16891249 CAGGGGCACGTATGTGTAA-TCAGGGGTAC-GAAGTACAAA
1 CAGGGGCACGTATGTGCAATTCAGGGGTACTGAAGTACAAA
*
16891288 CAGGGGCACGTATGTGCAA-TCAGGGGTACCGAAGTACAAA
1 CAGGGGCACGTATGTGCAATTCAGGGGTACTGAAGTACAAA
* * *
16891328 TAGGGGCATGTATGTGCAATTCAAGGGTACTGAAGTACAAA
1 CAGGGGCACGTATGTGCAATTCAGGGGTACTGAAGTACAAA
* *
16891369 TAGGGACACGTATGTGCAATTCA
1 CAGGGGCACGTATGTGCAATTCA
16891392 TGCAATAATT
Statistics
Matches: 129, Mismatches: 11, Indels: 5
0.89 0.08 0.03
Matches are distributed among these distances:
39 38 0.29
40 51 0.40
41 40 0.31
ACGTcount: A:0.32, C:0.16, G:0.31, T:0.20
Consensus pattern (41 bp):
CAGGGGCACGTATGTGCAATTCAGGGGTACTGAAGTACAAA
Found at i:16891487 original size:22 final size:22
Alignment explanation
Indices: 16891459--16891503 Score: 90
Period size: 22 Copynumber: 2.0 Consensus size: 22
16891449 GAAATTCATT
16891459 TACATATTGAAATACTATGAAC
1 TACATATTGAAATACTATGAAC
16891481 TACATATTGAAATACTATGAAC
1 TACATATTGAAATACTATGAAC
16891503 T
1 T
16891504 TACTTGTCAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 23 1.00
ACGTcount: A:0.44, C:0.13, G:0.09, T:0.33
Consensus pattern (22 bp):
TACATATTGAAATACTATGAAC
Found at i:16894276 original size:34 final size:33
Alignment explanation
Indices: 16894160--16894271 Score: 107
Period size: 34 Copynumber: 3.3 Consensus size: 33
16894150 TTCTAATCTT
* * * *
16894160 ATATGAAATTCTAATCTGACATATGCTTCTAGAA
1 ATATGAAATTCTAATCTGATATATG-TTTTTGGA
* * *
16894194 ATATGACATTCTAATCCGATATAAGTTTTTGGA
1 ATATGAAATTCTAATCTGATATATGTTTTTGGA
* * *
16894227 ATTATGACATTTTGATCTGATATATGTTTTTGGTA
1 A-TATGAAATTCTAATCTGATATATGTTTTTGG-A
16894262 ATATGAAATT
1 ATATGAAATT
16894272 TTGATATTAT
Statistics
Matches: 64, Mismatches: 12, Indels: 4
0.80 0.15 0.05
Matches are distributed among these distances:
33 6 0.09
34 56 0.88
35 2 0.03
ACGTcount: A:0.34, C:0.10, G:0.14, T:0.42
Consensus pattern (33 bp):
ATATGAAATTCTAATCTGATATATGTTTTTGGA
Found at i:16897232 original size:12 final size:12
Alignment explanation
Indices: 16897212--16897247 Score: 63
Period size: 12 Copynumber: 3.0 Consensus size: 12
16897202 TAAACTATGC
*
16897212 CCAACATCATTT
1 CCAAGATCATTT
16897224 CCAAGATCATTT
1 CCAAGATCATTT
16897236 CCAAGATCATTT
1 CCAAGATCATTT
16897248 ATCATTGAAA
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
12 23 1.00
ACGTcount: A:0.33, C:0.28, G:0.06, T:0.33
Consensus pattern (12 bp):
CCAAGATCATTT
Found at i:16900583 original size:12 final size:12
Alignment explanation
Indices: 16900566--16900599 Score: 52
Period size: 12 Copynumber: 2.9 Consensus size: 12
16900556 CGGCCCGCCC
16900566 ATATTAATTTTT
1 ATATTAATTTTT
*
16900578 ATATTATTTTTT
1 ATATTAATTTTT
16900590 ATA-TAATTTT
1 ATATTAATTTT
16900600 AAAATATATA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
11 6 0.30
12 14 0.70
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (12 bp):
ATATTAATTTTT
Found at i:16900753 original size:30 final size:30
Alignment explanation
Indices: 16900719--16900787 Score: 129
Period size: 30 Copynumber: 2.3 Consensus size: 30
16900709 GATGCAACTT
*
16900719 AATTAACAAATATCTTTAAAATAATAACAA
1 AATTAACAAATATATTTAAAATAATAACAA
16900749 AATTAACAAATATATTTAAAATAATAACAA
1 AATTAACAAATATATTTAAAATAATAACAA
16900779 AATTAACAA
1 AATTAACAA
16900788 TAAAATAAGT
Statistics
Matches: 38, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
30 38 1.00
ACGTcount: A:0.62, C:0.09, G:0.00, T:0.29
Consensus pattern (30 bp):
AATTAACAAATATATTTAAAATAATAACAA
Found at i:16904264 original size:3 final size:3
Alignment explanation
Indices: 16904256--16904283 Score: 56
Period size: 3 Copynumber: 9.3 Consensus size: 3
16904246 TTGCTGGTAC
16904256 TCT TCT TCT TCT TCT TCT TCT TCT TCT T
1 TCT TCT TCT TCT TCT TCT TCT TCT TCT T
16904284 AACTACTCTG
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.00, C:0.32, G:0.00, T:0.68
Consensus pattern (3 bp):
TCT
Found at i:16904389 original size:4 final size:4
Alignment explanation
Indices: 16904380--16904405 Score: 52
Period size: 4 Copynumber: 6.5 Consensus size: 4
16904370 ATTTGTGCCG
16904380 ATTT ATTT ATTT ATTT ATTT ATTT AT
1 ATTT ATTT ATTT ATTT ATTT ATTT AT
16904406 GGCATCATTC
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 22 1.00
ACGTcount: A:0.27, C:0.00, G:0.00, T:0.73
Consensus pattern (4 bp):
ATTT
Found at i:16908749 original size:33 final size:33
Alignment explanation
Indices: 16908707--16908774 Score: 136
Period size: 33 Copynumber: 2.1 Consensus size: 33
16908697 CAGCGGAAGT
16908707 TATGGAAAGGCCAAGCGATAAAAGAATGGAAAC
1 TATGGAAAGGCCAAGCGATAAAAGAATGGAAAC
16908740 TATGGAAAGGCCAAGCGATAAAAGAATGGAAAC
1 TATGGAAAGGCCAAGCGATAAAAGAATGGAAAC
16908773 TA
1 TA
16908775 ACATTAAAAT
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
33 35 1.00
ACGTcount: A:0.49, C:0.12, G:0.26, T:0.13
Consensus pattern (33 bp):
TATGGAAAGGCCAAGCGATAAAAGAATGGAAAC
Found at i:16915138 original size:35 final size:30
Alignment explanation
Indices: 16915099--16915172 Score: 80
Period size: 29 Copynumber: 2.3 Consensus size: 30
16915089 TAATTTTAAT
16915099 AATTAAATTTACATTATTAAATCAAAAAATAGAAA-
1 AATTAAATTTAC-TTA--AAAT--AAAAATA-AAAG
16915134 AATTAAA-TTACTTAAAATAAAAATAAAAG
1 AATTAAATTTACTTAAAATAAAAATAAAAG
16915163 AATTAAATTT
1 AATTAAATTT
16915173 CAAATATACA
Statistics
Matches: 37, Mismatches: 0, Indels: 9
0.80 0.00 0.20
Matches are distributed among these distances:
28 3 0.08
29 14 0.38
30 2 0.05
31 4 0.11
33 3 0.08
34 4 0.11
35 7 0.19
ACGTcount: A:0.61, C:0.04, G:0.03, T:0.32
Consensus pattern (30 bp):
AATTAAATTTACTTAAAATAAAAATAAAAG
Found at i:16915185 original size:29 final size:28
Alignment explanation
Indices: 16915123--16915193 Score: 67
Period size: 29 Copynumber: 2.5 Consensus size: 28
16915113 TATTAAATCA
*
16915123 AAAAATAGAAAAATTAAATTACTTAAAAT
1 AAAAATAGAAAAATTAAATTA-TCAAAAT
16915152 AAAAATA-AAAGAATTAAATT-TCAAATAT
1 AAAAATAGAAA-AATTAAATTATCAAA-AT
16915180 ACAAAA-AGTAAAAA
1 A-AAAATAG-AAAAA
16915194 AGCGTATATT
Statistics
Matches: 36, Mismatches: 1, Indels: 10
0.77 0.02 0.21
Matches are distributed among these distances:
27 4 0.11
28 7 0.19
29 22 0.61
30 3 0.08
ACGTcount: A:0.68, C:0.04, G:0.04, T:0.24
Consensus pattern (28 bp):
AAAAATAGAAAAATTAAATTATCAAAAT
Found at i:16916177 original size:124 final size:123
Alignment explanation
Indices: 16915968--16916221 Score: 436
Period size: 124 Copynumber: 2.1 Consensus size: 123
16915958 AAATAGTGGG
** *
16915968 AAATCGCTTCTACCAGAATGCTATTTGAGAAGAAATTGTGAAATCGCGCCCTCGTGGACGCGATT
1 AAATCGCTGATACCAGAATGCTATATGAGAAGAAATTGTGAAATCGCGCCCTCGTGGACGCGATT
16916033 TCGCTACAGTTGGTCATGTAGGAAATAATTTTTTTGACGTTTTCTGAGCAAATAGTATA
66 TCGCTACAGTTGGTCATGTAGGAAATAATTTTTTTGACG-TTTCTGAGCAAATAGTATA
*
16916092 AAATCGCTGATACCAGGATGCTATATGAGAAGAAATTGTGAAATCGCGCCCTCGTGGACGCGATT
1 AAATCGCTGATACCAGAATGCTATATGAGAAGAAATTGTGAAATCGCGCCCTCGTGGACGCGATT
* * *
16916157 TCGCTACAGTTGGTCATGTAGGAAATAATTTTTTTGACGTTTCTGAGTAAATAGTGTC
66 TCGCTACAGTTGGTCATGTAGGAAATAATTTTTTTGACGTTTCTGAGCAAATAGTATA
16916215 AAATCGC
1 AAATCGC
16916222 GCCATCGTGG
Statistics
Matches: 123, Mismatches: 7, Indels: 1
0.94 0.05 0.01
Matches are distributed among these distances:
123 23 0.19
124 100 0.81
ACGTcount: A:0.29, C:0.17, G:0.23, T:0.31
Consensus pattern (123 bp):
AAATCGCTGATACCAGAATGCTATATGAGAAGAAATTGTGAAATCGCGCCCTCGTGGACGCGATT
TCGCTACAGTTGGTCATGTAGGAAATAATTTTTTTGACGTTTCTGAGCAAATAGTATA
Found at i:16921878 original size:15 final size:16
Alignment explanation
Indices: 16921860--16921891 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 16
16921850 AAAATATAAT
16921860 TTTAT-AATATAAAAA
1 TTTATCAATATAAAAA
16921875 TTTATCAATATAAAAA
1 TTTATCAATATAAAAA
16921891 T
1 T
16921892 CTTGATTAGG
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 5 0.31
16 11 0.69
ACGTcount: A:0.56, C:0.03, G:0.00, T:0.41
Consensus pattern (16 bp):
TTTATCAATATAAAAA
Found at i:16925429 original size:141 final size:142
Alignment explanation
Indices: 16925284--16925566 Score: 543
Period size: 141 Copynumber: 2.0 Consensus size: 142
16925274 ACAAAACCAT
16925284 TTTCGTTTTAAATTTCAAAGTTATCTTTATACTTATCTAAAAAAATATA-TAATGTAATATAAAA
1 TTTCGTTTTAAATTTCAAAGTTATCTTTATACTTATCTAAAAAAATATAGT-ATGTAATATAAAA
16925348 TTTTAAAATAATTTTTTATATCTAAATAATAAACAAATATTAATTTCCCAAATAGGATTACTTAG
65 TTTTAAAATAATTTTTTATATCTAAATAATAAACAAATATTAATTTCCCAAATAGGATTACTTAG
16925413 CA-TATATACTTG
130 CAGTATATACTTG
16925425 TTTCGTTTTAAATTTCAAAGTTATCTTTATACTTATCTAAAAAAATATAGTATGTAATATAAAAT
1 TTTCGTTTTAAATTTCAAAGTTATCTTTATACTTATCTAAAAAAATATAGTATGTAATATAAAAT
16925490 TTTAAAATAATTTTTTATATCTAAATAATAAACAAATATTAATTTCCCAAATAGGATTACTTAGC
66 TTTAAAATAATTTTTTATATCTAAATAATAAACAAATATTAATTTCCCAAATAGGATTACTTAGC
16925555 AGTATATACTTG
131 AGTATATACTTG
16925567 GTGAGTGTTG
Statistics
Matches: 140, Mismatches: 0, Indels: 3
0.98 0.00 0.02
Matches are distributed among these distances:
141 129 0.92
142 11 0.08
ACGTcount: A:0.43, C:0.09, G:0.06, T:0.42
Consensus pattern (142 bp):
TTTCGTTTTAAATTTCAAAGTTATCTTTATACTTATCTAAAAAAATATAGTATGTAATATAAAAT
TTTAAAATAATTTTTTATATCTAAATAATAAACAAATATTAATTTCCCAAATAGGATTACTTAGC
AGTATATACTTG
Found at i:16926143 original size:4 final size:4
Alignment explanation
Indices: 16926134--16926160 Score: 54
Period size: 4 Copynumber: 6.8 Consensus size: 4
16926124 ATGCGTATAC
16926134 ATGT ATGT ATGT ATGT ATGT ATGT ATG
1 ATGT ATGT ATGT ATGT ATGT ATGT ATG
16926161 AATGCCTATA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 23 1.00
ACGTcount: A:0.26, C:0.00, G:0.26, T:0.48
Consensus pattern (4 bp):
ATGT
Found at i:16927545 original size:76 final size:76
Alignment explanation
Indices: 16927419--16927564 Score: 258
Period size: 76 Copynumber: 1.9 Consensus size: 76
16927409 AAGTGGTTGG
* *
16927419 TAAGGTAGGATTAGCAATGGGTTTACTAATATCATCTGCAAATCTAAAGTAAAGCCAGTCCC-AA
1 TAAGGTAAGATTAACAATGGGTTTACTAATATCATCTGCAAATCTAAAGTAAAGCCAG-CCCTAA
16927483 GGTCATGGCTAT
65 GGTCATGGCTAT
16927495 TAAGGTAAGATTAACAATGGGTTTACTAATATCATCTGCAAATCTAAAGTAAAGCCAGCCCTAAG
1 TAAGGTAAGATTAACAATGGGTTTACTAATATCATCTGCAAATCTAAAGTAAAGCCAGCCCTAAG
16927560 GTCAT
66 GTCAT
16927565 TATTCTTGTC
Statistics
Matches: 67, Mismatches: 2, Indels: 2
0.94 0.03 0.03
Matches are distributed among these distances:
75 3 0.04
76 64 0.96
ACGTcount: A:0.36, C:0.17, G:0.19, T:0.27
Consensus pattern (76 bp):
TAAGGTAAGATTAACAATGGGTTTACTAATATCATCTGCAAATCTAAAGTAAAGCCAGCCCTAAG
GTCATGGCTAT
Found at i:16932086 original size:20 final size:19
Alignment explanation
Indices: 16932063--16932136 Score: 80
Period size: 20 Copynumber: 3.8 Consensus size: 19
16932053 AGTTTTAGTG
16932063 AAGTATCAATACTTTACCTT
1 AAGTATCAATACTTTA-CTT
*
16932083 AAGTATCAATA-TTT-TTT
1 AAGTATCAATACTTTACTT
*
16932100 AAAACTATCAATACTTTAGCTT
1 --AAGTATCAATACTTTA-CTT
16932122 AAGTATCAATACTTT
1 AAGTATCAATACTTT
16932137 TGTTAAAGTA
Statistics
Matches: 45, Mismatches: 4, Indels: 10
0.76 0.07 0.17
Matches are distributed among these distances:
17 2 0.04
19 13 0.29
20 28 0.62
22 2 0.04
ACGTcount: A:0.38, C:0.15, G:0.05, T:0.42
Consensus pattern (19 bp):
AAGTATCAATACTTTACTT
Found at i:16932109 original size:39 final size:41
Alignment explanation
Indices: 16932066--16932143 Score: 133
Period size: 39 Copynumber: 2.0 Consensus size: 41
16932056 TTTAGTGAAG
16932066 TATCAATACTTTACCTTAAGTATCAATA-TTTT-TTAAAAC
1 TATCAATACTTTACCTTAAGTATCAATACTTTTGTTAAAAC
*
16932105 TATCAATACTTTAGCTTAAGTATCAATACTTTTGTTAAA
1 TATCAATACTTTACCTTAAGTATCAATACTTTTGTTAAA
16932144 GTATCTTCAG
Statistics
Matches: 36, Mismatches: 1, Indels: 2
0.92 0.03 0.05
Matches are distributed among these distances:
39 27 0.75
40 4 0.11
41 5 0.14
ACGTcount: A:0.37, C:0.14, G:0.05, T:0.44
Consensus pattern (41 bp):
TATCAATACTTTACCTTAAGTATCAATACTTTTGTTAAAAC
Found at i:16932145 original size:20 final size:19
Alignment explanation
Indices: 16932063--16932148 Score: 77
Period size: 20 Copynumber: 4.4 Consensus size: 19
16932053 AGTTTTAGTG
**
16932063 AAGTATCAATACTTTACCTT
1 AAGTATCAATACTTT-TGTT
16932083 AAGTATCAATA-TTTT-TT
1 AAGTATCAATACTTTTGTT
* *
16932100 AAAACTATCAATACTTTAGCTT
1 --AAGTATCAATACTTTTG-TT
16932122 AAGTATCAATACTTTTGTT
1 AAGTATCAATACTTTTGTT
16932141 AAAGTATC
1 -AAGTATC
16932149 TTCAGCTACC
Statistics
Matches: 55, Mismatches: 5, Indels: 12
0.76 0.07 0.17
Matches are distributed among these distances:
17 2 0.04
19 15 0.27
20 36 0.65
22 2 0.04
ACGTcount: A:0.37, C:0.14, G:0.07, T:0.42
Consensus pattern (19 bp):
AAGTATCAATACTTTTGTT
Found at i:16940929 original size:19 final size:19
Alignment explanation
Indices: 16940905--16940947 Score: 59
Period size: 19 Copynumber: 2.3 Consensus size: 19
16940895 AAAACATCAT
* *
16940905 ATTAATTTTAATTAATTTG
1 ATTAATTTAAATTAACTTG
*
16940924 ATTAATTTAAATTTACTTG
1 ATTAATTTAAATTAACTTG
16940943 ATTAA
1 ATTAA
16940948 AATTAATTTT
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
19 21 1.00
ACGTcount: A:0.40, C:0.02, G:0.05, T:0.53
Consensus pattern (19 bp):
ATTAATTTAAATTAACTTG
Found at i:16942417 original size:22 final size:22
Alignment explanation
Indices: 16942383--16942446 Score: 74
Period size: 25 Copynumber: 2.8 Consensus size: 22
16942373 ATAAACTGAG
*
16942383 AGCACAAATGTGCTAATCAGAA
1 AGCACTAATGTGCTAATCAGAA
* *
16942405 AGCACTAACGTGCTAATAGTCAGAG
1 AGCACTAATGTGCT-A-A-TCAGAA
16942430 AGCACTAATGTGCTAAT
1 AGCACTAATGTGCTAAT
16942447 AATCAGAGCG
Statistics
Matches: 35, Mismatches: 4, Indels: 6
0.78 0.09 0.13
Matches are distributed among these distances:
22 13 0.37
23 2 0.06
24 2 0.06
25 18 0.51
ACGTcount: A:0.39, C:0.19, G:0.20, T:0.22
Consensus pattern (22 bp):
AGCACTAATGTGCTAATCAGAA
Found at i:16942433 original size:25 final size:25
Alignment explanation
Indices: 16942396--16942454 Score: 91
Period size: 25 Copynumber: 2.4 Consensus size: 25
16942386 ACAAATGTGC
*
16942396 TAATCAGAAAGCACTAACGTGCTAA
1 TAATCAGAGAGCACTAACGTGCTAA
* *
16942421 TAGTCAGAGAGCACTAATGTGCTAA
1 TAATCAGAGAGCACTAACGTGCTAA
16942446 TAATCAGAG
1 TAATCAGAG
16942455 CGCGCGCTAA
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
25 30 1.00
ACGTcount: A:0.41, C:0.17, G:0.20, T:0.22
Consensus pattern (25 bp):
TAATCAGAGAGCACTAACGTGCTAA
Found at i:16947810 original size:25 final size:25
Alignment explanation
Indices: 16947758--16947823 Score: 89
Period size: 25 Copynumber: 2.6 Consensus size: 25
16947748 ATAAAATACA
*
16947758 TCTTTGCATTCATTTTTGAGCTAATAT
1 TCTTT-CATTC-TTTTTGAACTAATAT
16947785 TCTTTCATTCTTTTTGAAC-AATTAT
1 TCTTTCATTCTTTTTGAACTAA-TAT
16947810 TCTTTCATTCTTTT
1 TCTTTCATTCTTTT
16947824 GGATTTTCTT
Statistics
Matches: 37, Mismatches: 1, Indels: 4
0.88 0.02 0.10
Matches are distributed among these distances:
24 2 0.05
25 25 0.68
26 5 0.14
27 5 0.14
ACGTcount: A:0.20, C:0.17, G:0.06, T:0.58
Consensus pattern (25 bp):
TCTTTCATTCTTTTTGAACTAATAT
Found at i:16948900 original size:12 final size:12
Alignment explanation
Indices: 16948885--16948931 Score: 53
Period size: 12 Copynumber: 3.9 Consensus size: 12
16948875 AATTTCATAA
16948885 AAAAAAAGAAAG
1 AAAAAAAGAAAG
16948897 AAAAGAAA-AAAG
1 AAAA-AAAGAAAG
*
16948909 AAAAAAACAAA-
1 AAAAAAAGAAAG
16948920 ATAAAAAAGAAA
1 A-AAAAAAGAAA
16948932 AATCAAAGTC
Statistics
Matches: 31, Mismatches: 1, Indels: 6
0.82 0.03 0.16
Matches are distributed among these distances:
11 4 0.13
12 24 0.77
13 3 0.10
ACGTcount: A:0.85, C:0.02, G:0.11, T:0.02
Consensus pattern (12 bp):
AAAAAAAGAAAG
Found at i:16948909 original size:7 final size:7
Alignment explanation
Indices: 16948886--16948933 Score: 53
Period size: 7 Copynumber: 6.7 Consensus size: 7
16948876 ATTTCATAAA
16948886 AAAAAAG
1 AAAAAAG
16948893 AAAGAAAAG
1 -AA-AAAAG
16948902 AAAAAAG
1 AAAAAAG
16948909 AAAAAA-
1 AAAAAAG
* *
16948915 ACAAAAT
1 AAAAAAG
16948922 AAAAAAG
1 AAAAAAG
16948929 AAAAA
1 AAAAA
16948934 TCAAAGTCAA
Statistics
Matches: 35, Mismatches: 3, Indels: 5
0.81 0.07 0.12
Matches are distributed among these distances:
6 5 0.14
7 21 0.60
8 4 0.11
9 5 0.14
ACGTcount: A:0.85, C:0.02, G:0.10, T:0.02
Consensus pattern (7 bp):
AAAAAAG
Found at i:16948913 original size:13 final size:13
Alignment explanation
Indices: 16948883--16948999 Score: 55
Period size: 13 Copynumber: 8.8 Consensus size: 13
16948873 TCAATTTCAT
16948883 AAAA-AAAAAGAAA
1 AAAAGAAAAAG-AA
16948896 GAAAAGAAAAAAGAA
1 -AAAAG-AAAAAGAA
*
16948911 AAAA-ACAAAATAA
1 AAAAGA-AAAAGAA
**
16948924 AAAAGAAAAATCA
1 AAAAGAAAAAGAA
*** *
16948937 AAGTCAAAATACAA
1 AAAAGAAAA-AGAA
*
16948951 AAAA-ATGAAAATAA
1 AAAAGA--AAAAGAA
*
16948965 AAAATAAAAAG--
1 AAAAGAAAAAGAA
16948976 AAAAGAAAAAGAA
1 AAAAGAAAAAGAA
16948989 AAAAGAAAAAG
1 AAAAGAAAAAG
16949000 GAGAGGCCAA
Statistics
Matches: 81, Mismatches: 12, Indels: 21
0.71 0.11 0.18
Matches are distributed among these distances:
11 10 0.12
12 1 0.01
13 38 0.47
14 20 0.25
15 6 0.07
16 6 0.07
ACGTcount: A:0.80, C:0.03, G:0.10, T:0.06
Consensus pattern (13 bp):
AAAAGAAAAAGAA
Found at i:16948945 original size:20 final size:20
Alignment explanation
Indices: 16948881--16948974 Score: 75
Period size: 20 Copynumber: 4.7 Consensus size: 20
16948871 ATTCAATTTC
* *
16948881 ATAAAAAA-AAAGAAAGAAA
1 ATAAAAAAGAAAAAAACAAA
*
16948900 AGAAAAAAGAAAAAAACAAA
1 ATAAAAAAGAAAAAAACAAA
*
16948920 ATAAAAAAG-AAAAATCAAA
1 ATAAAAAAGAAAAAAACAAA
* * * *
16948939 GTCAAAATACAAAAAAATGAAA
1 AT-AAAAAAGAAAAAAA-CAAA
*
16948961 ATAAAAAATAAAAA
1 ATAAAAAAGAAAAA
16948975 GAAAAGAAAA
Statistics
Matches: 58, Mismatches: 13, Indels: 6
0.75 0.17 0.08
Matches are distributed among these distances:
19 17 0.29
20 22 0.38
21 15 0.26
22 4 0.07
ACGTcount: A:0.80, C:0.04, G:0.07, T:0.09
Consensus pattern (20 bp):
ATAAAAAAGAAAAAAACAAA
Found at i:16949898 original size:61 final size:59
Alignment explanation
Indices: 16949826--16949940 Score: 160
Period size: 61 Copynumber: 1.9 Consensus size: 59
16949816 GAGAAAGGAT
** * *
16949826 CAAGGTGAAAACCTGCAAAGGGCGCTTTGATTCCTAAAAATAATAATAAT-AATAAAAAGAC
1 CAAGGTGAAAACCCACAAAGGGCACTTTGAGTCC-AAAAA-AATAA-AATAAATAAAAAGAC
16949887 CAAGGTGAAAACCCACAAAGGGCACTTTGAGTCCAAAAAAATAAAATAAATAAA
1 CAAGGTGAAAACCCACAAAGGGCACTTTGAGTCCAAAAAAATAAAATAAATAAA
16949941 TAAATAAAAA
Statistics
Matches: 49, Mismatches: 4, Indels: 4
0.86 0.07 0.07
Matches are distributed among these distances:
58 3 0.06
59 11 0.22
60 5 0.10
61 30 0.61
ACGTcount: A:0.50, C:0.16, G:0.16, T:0.18
Consensus pattern (59 bp):
CAAGGTGAAAACCCACAAAGGGCACTTTGAGTCCAAAAAAATAAAATAAATAAAAAGAC
Found at i:16951641 original size:44 final size:44
Alignment explanation
Indices: 16951546--16951645 Score: 121
Period size: 44 Copynumber: 2.3 Consensus size: 44
16951536 AAGCCACTAG
* ** **
16951546 TCTTATCTCCCTGGACAGCAGTGGAATATGTTGAAGGTTGTGAA
1 TCTTATCTCCCTGGACAGCAGTGGAATAGGTTGAAAATTCAGAA
* *
16951590 TCCTATCTCCCTGGTCAGCAGTGGAATAGGTTGAAAATTACAG-A
1 TCTTATCTCCCTGGACAGCAGTGGAATAGGTTGAAAATT-CAGAA
16951634 TCTTATCTCCCT
1 TCTTATCTCCCT
16951646 AAGCAATAGT
Statistics
Matches: 47, Mismatches: 8, Indels: 2
0.82 0.14 0.04
Matches are distributed among these distances:
44 46 0.98
45 1 0.02
ACGTcount: A:0.25, C:0.21, G:0.22, T:0.32
Consensus pattern (44 bp):
TCTTATCTCCCTGGACAGCAGTGGAATAGGTTGAAAATTCAGAA
Found at i:16951795 original size:44 final size:44
Alignment explanation
Indices: 16951747--16952009 Score: 168
Period size: 44 Copynumber: 6.0 Consensus size: 44
16951737 AACAGGGGAA
* *
16951747 TAGGTGGAAGATGGTAAGCCTTATCTCCCTAAGCAGTAGTGGAG
1 TAGGTTGAAGATGGTAAGTCTTATCTCCCTAAGCAGTAGTGGAG
* *
16951791 TAGGTTGAAAAT--TACAGATCTTATATCCCTAAGCAGTAGTGGAG
1 TAGGTTGAAGATGGTA-AG-TCTTATCTCCCTAAGCAGTAGTGGAG
* * * * *
16951835 TAGATTGAAGACAGCG-AA-TCTTATTTTCCC-CAGAAGTAG-GGAAG
1 TAGGTTGAAGA-TG-GTAAGTCTTA-TCTCCCTAAGCAGTAGTGG-AG
* * **** * * *
16951879 CAGGTTTAAGCCACT-AGTCTTATCTCCCT-GGACAGCAGTGGAA
1 TAGGTTGAAGATGGTAAGTCTTATCTCCCTAAG-CAGTAGTGGAG
* *
16951922 TAGGTTGAAGATTGTAAGCCTTATCTCCCTAAGCAGTAGTGGAG
1 TAGGTTGAAGATGGTAAGTCTTATCTCCCTAAGCAGTAGTGGAG
* * *
16951966 TAGGTT-AA-AAGTTACAGATCTTATCTCCCTAAACAGTAGTGGAG
1 TAGGTTGAAGATGGTA-AG-TCTTATCTCCCTAAGCAGTAGTGGAG
16952010 CAGATAAAAA
Statistics
Matches: 165, Mismatches: 37, Indels: 34
0.70 0.16 0.14
Matches are distributed among these distances:
42 12 0.07
43 27 0.16
44 118 0.72
45 6 0.04
46 1 0.01
47 1 0.01
ACGTcount: A:0.30, C:0.17, G:0.25, T:0.27
Consensus pattern (44 bp):
TAGGTTGAAGATGGTAAGTCTTATCTCCCTAAGCAGTAGTGGAG
Found at i:16952031 original size:175 final size:175
Alignment explanation
Indices: 16951257--16952014 Score: 1110
Period size: 175 Copynumber: 4.3 Consensus size: 175
16951247 TCCCTGGGTT
* * * *
16951257 GTAGTGGAGCAGGTTGAAAATAATAGATCTTATCTCCCTAAGAAGTAGTGGAGCAGATCGAAGAC
1 GTAGTGGAGTAGGTTGAAAATTACAGATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCGAAGAC
* *
16951322 GGCGAATCTTATCTTCCCCAGGAGTAGGGAAGCAGATTTAAGCCATTAGTCCTATCTCCCTGGAC
66 AGCGAATCTTATCTTCCCCAGGAGTAGGGAAGCAGATTTAAGCCACTAGTCCTATCTCCCTGGAC
* *
16951387 AGCAGGGGAATAGGTGGAAGATTGTAAGCCTTATCTCCCGAAGTA
131 AGCAGGGGAATAGGTGGAAGATTGTAAGCCTTATCTCCCTAAGCA
16951432 GTAGTGGAGTAGGTTGAAAATTACAGATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCGAAGAC
1 GTAGTGGAGTAGGTTGAAAATTACAGATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCGAAGAC
* * * *
16951497 -GACGAATCTTATCTTCCCCAGGAGTCGCGAAGTAGATTTAAGCCACTAGTCTTATCTCCCTGGA
66 AG-CGAATCTTATCTTCCCCAGGAGTAGGGAAGCAGATTTAAGCCACTAGTCCTATCTCCCTGGA
* * * * * *
16951561 CAGCAGTGGAATATGTTGAAGGTTGTGAATCC-TATCTCCCT-GGTCA
130 CAGCAGGGGAATAGGTGGAAGATTGT-AAGCCTTATCTCCCTAAG-CA
* * * * *
16951607 GCAGTGGAATAGGTTGAAAATTACAGATCTTATCTCCCTAAGCAATAGTGGAACAGATCGAAGAT
1 GTAGTGGAGTAGGTTGAAAATTACAGATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCGAAGAC
* * *
16951672 GGCGAATTTTATCTTCCCCAGGAGTAGGGAAGCAGATTTAAGTCACTAGTCCTATCTCCCTGGAC
66 AGCGAATCTTATCTTCCCCAGGAGTAGGGAAGCAGATTTAAGCCACTAGTCCTATCTCCCTGGAC
* *
16951737 AACAGGGGAATAGGTGGAAGATGGTAAGCCTTATCTCCCTAAGCA
131 AGCAGGGGAATAGGTGGAAGATTGTAAGCCTTATCTCCCTAAGCA
* * *
16951782 GTAGTGGAGTAGGTTGAAAATTACAGATCTTATATCCCTAAGCAGTAGTGGAGTAGATTGAAGAC
1 GTAGTGGAGTAGGTTGAAAATTACAGATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCGAAGAC
* * * *
16951847 AGCGAATCTTATTTTCCCCAGAAGTAGGGAAGCAGGTTTAAGCCACTAGTCTTATCTCCCTGGAC
66 AGCGAATCTTATCTTCCCCAGGAGTAGGGAAGCAGATTTAAGCCACTAGTCCTATCTCCCTGGAC
* *
16951912 AGCAGTGGAATAGGTTGAAGATTGTAAGCCTTATCTCCCTAAGCA
131 AGCAGGGGAATAGGTGGAAGATTGTAAGCCTTATCTCCCTAAGCA
*
16951957 GTAGTGGAGTAGGTT-AAAAGTTACAGATCTTATCTCCCTAAACAGTAGTGGAGCAGAT
1 GTAGTGGAGTAGGTTGAAAA-TTACAGATCTTATCTCCCTAAGCAGTAGTGGAGCAGAT
16952015 AAAAAATAGT
Statistics
Matches: 518, Mismatches: 58, Indels: 14
0.88 0.10 0.02
Matches are distributed among these distances:
174 10 0.02
175 502 0.97
176 6 0.01
ACGTcount: A:0.30, C:0.19, G:0.25, T:0.26
Consensus pattern (175 bp):
GTAGTGGAGTAGGTTGAAAATTACAGATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCGAAGAC
AGCGAATCTTATCTTCCCCAGGAGTAGGGAAGCAGATTTAAGCCACTAGTCCTATCTCCCTGGAC
AGCAGGGGAATAGGTGGAAGATTGTAAGCCTTATCTCCCTAAGCA
Found at i:16960063 original size:17 final size:17
Alignment explanation
Indices: 16960041--16960074 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
16960031 CTTAGAAGAA
16960041 CTTAGTCCAACAAACTT
1 CTTAGTCCAACAAACTT
*
16960058 CTTAGTCCAACATACTT
1 CTTAGTCCAACAAACTT
16960075 TTTAACATCC
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.32, C:0.29, G:0.06, T:0.32
Consensus pattern (17 bp):
CTTAGTCCAACAAACTT
Found at i:16969039 original size:28 final size:27
Alignment explanation
Indices: 16968974--16969039 Score: 71
Period size: 28 Copynumber: 2.4 Consensus size: 27
16968964 CATCTTTCAG
**
16968974 TTTTAAATTTTGTCTATTTATTCATTT
1 TTTTAAATTTTGAATATTTATTCATTT
*
16969001 TTTTATTATTTTGAATATTTATTC-TTAGT
1 TTTTA-AATTTTGAATATTTATTCATT--T
16969030 TTTTAAATTT
1 TTTTAAATTT
16969040 ATTCTTTTAG
Statistics
Matches: 32, Mismatches: 4, Indels: 5
0.78 0.10 0.12
Matches are distributed among these distances:
27 7 0.22
28 19 0.59
29 6 0.19
ACGTcount: A:0.24, C:0.05, G:0.05, T:0.67
Consensus pattern (27 bp):
TTTTAAATTTTGAATATTTATTCATTT
Found at i:16974260 original size:16 final size:16
Alignment explanation
Indices: 16974236--16974278 Score: 50
Period size: 16 Copynumber: 2.6 Consensus size: 16
16974226 AAGAGAGTGA
*
16974236 AAAAGAAATGGAAAAGG
1 AAAA-AAATGGAAAAAG
*
16974253 AAAAAAATAGAAAAAG
1 AAAAAAATGGAAAAAG
16974269 AAAAAGAATG
1 AAAAA-AATG
16974279 AGAGAGAAAA
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
16 15 0.68
17 7 0.32
ACGTcount: A:0.72, C:0.00, G:0.21, T:0.07
Consensus pattern (16 bp):
AAAAAAATGGAAAAAG
Found at i:16975134 original size:44 final size:44
Alignment explanation
Indices: 16975084--16975168 Score: 161
Period size: 44 Copynumber: 1.9 Consensus size: 44
16975074 AATTAATTAT
16975084 AGAAAATACTTACTAATCTAATCGAGTCACGAATTAGTAGTTAC
1 AGAAAATACTTACTAATCTAATCGAGTCACGAATTAGTAGTTAC
*
16975128 AGAAAATACTTACTAATCTAATCGAGTCATGAATTAGTAGT
1 AGAAAATACTTACTAATCTAATCGAGTCACGAATTAGTAGT
16975169 GTGAATCCAA
Statistics
Matches: 40, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
44 40 1.00
ACGTcount: A:0.41, C:0.14, G:0.14, T:0.31
Consensus pattern (44 bp):
AGAAAATACTTACTAATCTAATCGAGTCACGAATTAGTAGTTAC
Found at i:16977914 original size:102 final size:102
Alignment explanation
Indices: 16977788--16977992 Score: 401
Period size: 102 Copynumber: 2.0 Consensus size: 102
16977778 TAATGCCAAA
16977788 GAATGAAGGAGAAGTTACATTGAAGATAACTCCAAAGGACTTATTGAAGGTATTGGTTCTATAGG
1 GAATGAAGGAGAAGTTACATTGAAGATAACTCCAAAGGACTTATTGAAGGTATTGGTTCTATAGG
16977853 TATAAATTCTTCCACTCTCATTAAAAATATGCTTTAT
66 TATAAATTCTTCCACTCTCATTAAAAATATGCTTTAT
16977890 GAATGAAGGAGAAGTTACATTGAAGATAACTCCAAAGGACTTATTGAAGGTATTGGTTCTATAGG
1 GAATGAAGGAGAAGTTACATTGAAGATAACTCCAAAGGACTTATTGAAGGTATTGGTTCTATAGG
*
16977955 TATAAATTCTTCCACTCTCATTAAAAATGTGCTTTAT
66 TATAAATTCTTCCACTCTCATTAAAAATATGCTTTAT
16977992 G
1 G
16977993 TCTATGGTCT
Statistics
Matches: 102, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
102 102 1.00
ACGTcount: A:0.36, C:0.13, G:0.19, T:0.33
Consensus pattern (102 bp):
GAATGAAGGAGAAGTTACATTGAAGATAACTCCAAAGGACTTATTGAAGGTATTGGTTCTATAGG
TATAAATTCTTCCACTCTCATTAAAAATATGCTTTAT
Found at i:16982065 original size:41 final size:40
Alignment explanation
Indices: 16982009--16982154 Score: 138
Period size: 41 Copynumber: 3.6 Consensus size: 40
16981999 TGATTCGATA
16982009 CACCGGC-TTATAGCCTGCTAGACCTATAGTCCGAAATGTAT
1 CACCGGCATTA-AGCCTGCTAGACCTATAGTCCGAAAT-TAT
* * *
16982050 CACCGGCATTAAGCCTGCTAGACGTAAAGTCTG-AATTAATT
1 CACCGGCATTAAGCCTGCTAGACCTATAGTCCGAAATT-A-T
* *
16982091 CACCGGCATTAAGCCTGCTAGGCAC-ATAG-CCTGAATTATAT
1 CACCGGCATTAAGCCTGCTAGAC-CTATAGTCC-GAAAT-TAT
**
16982132 CACCGGCATCCAGCCTGCTAGAC
1 CACCGGCATTAAGCCTGCTAGAC
16982155 AATAAGTCTG
Statistics
Matches: 87, Mismatches: 11, Indels: 14
0.78 0.10 0.12
Matches are distributed among these distances:
39 1 0.01
40 5 0.06
41 74 0.85
42 6 0.07
43 1 0.01
ACGTcount: A:0.28, C:0.28, G:0.20, T:0.24
Consensus pattern (40 bp):
CACCGGCATTAAGCCTGCTAGACCTATAGTCCGAAATTAT
Found at i:16982162 original size:82 final size:83
Alignment explanation
Indices: 16982009--16982174 Score: 198
Period size: 82 Copynumber: 2.0 Consensus size: 83
16981999 TGATTCGATA
* * *
16982009 CACCGGCTTATAGCCTGCTAGACCTATAGTCCGAAATGTATCACCGGCATTAAGCCTGCTAGACG
1 CACCGGCTTATAGCCTGCTAGACCTATAGTCCGAAATATATCACCGGCATCAAGCCTGCTAGACA
16982074 TAAAGTCTGAATTA-ATT
66 TAAAGTCTGAATTACATT
* * *
16982091 CACCGGCATTA-AGCCTGCTAGGCAC-ATAG-CCTGAATTATATCACCGGCATCCAGCCTGCTAG
1 CACCGGC-TTATAGCCTGCTAGAC-CTATAGTCC-GAAATATATCACCGGCATCAAGCCTGCTAG
*
16982153 ACA-ATAAGTCTGATTTACATT
63 ACATA-AAGTCTGAATTACATT
16982174 C
1 C
16982175 GATCACTTTA
Statistics
Matches: 72, Mismatches: 7, Indels: 9
0.82 0.08 0.10
Matches are distributed among these distances:
81 3 0.04
82 61 0.85
83 8 0.11
ACGTcount: A:0.29, C:0.27, G:0.19, T:0.26
Consensus pattern (83 bp):
CACCGGCTTATAGCCTGCTAGACCTATAGTCCGAAATATATCACCGGCATCAAGCCTGCTAGACA
TAAAGTCTGAATTACATT
Found at i:16990332 original size:30 final size:30
Alignment explanation
Indices: 16990298--16990360 Score: 117
Period size: 30 Copynumber: 2.1 Consensus size: 30
16990288 TAGCAAAAAA
16990298 CTCAAATTTCTCCTTAAATTTCTCAAAGCT
1 CTCAAATTTCTCCTTAAATTTCTCAAAGCT
*
16990328 CTCAAATTTCTCCTTAATTTTCTCAAAGCT
1 CTCAAATTTCTCCTTAAATTTCTCAAAGCT
16990358 CTC
1 CTC
16990361 TTTAATTGAT
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
30 32 1.00
ACGTcount: A:0.27, C:0.29, G:0.03, T:0.41
Consensus pattern (30 bp):
CTCAAATTTCTCCTTAAATTTCTCAAAGCT
Found at i:16990360 original size:21 final size:21
Alignment explanation
Indices: 16990327--16990367 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
16990317 TTCTCAAAGC
**
16990327 TCTCAAATTTCTCCTTAATTT
1 TCTCAAAGCTCTCCTTAATTT
*
16990348 TCTCAAAGCTCTCTTTAATT
1 TCTCAAAGCTCTCCTTAATT
16990368 GATTATTTCC
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.24, C:0.24, G:0.02, T:0.49
Consensus pattern (21 bp):
TCTCAAAGCTCTCCTTAATTT
Found at i:16991846 original size:30 final size:30
Alignment explanation
Indices: 16991795--16991858 Score: 85
Period size: 30 Copynumber: 2.1 Consensus size: 30
16991785 TTAATTTCCG
*
16991795 AGTTTTGGGGAAAAAGTGTAATTATGTAAA
1 AGTTTAGGGGAAAAAGTGTAATTATGTAAA
* *
16991825 AGTTTAGGGGTAAAA-TCGTAATTTTGTAAA
1 AGTTTAGGGGAAAAAGT-GTAATTATGTAAA
16991855 AGTT
1 AGTT
16991859 AGAGTCGAGG
Statistics
Matches: 30, Mismatches: 3, Indels: 2
0.86 0.09 0.06
Matches are distributed among these distances:
29 1 0.03
30 29 0.97
ACGTcount: A:0.38, C:0.02, G:0.25, T:0.36
Consensus pattern (30 bp):
AGTTTAGGGGAAAAAGTGTAATTATGTAAA
Found at i:16992298 original size:46 final size:46
Alignment explanation
Indices: 16992248--16992359 Score: 116
Period size: 50 Copynumber: 2.3 Consensus size: 46
16992238 CATTGAGATT
* * *
16992248 ATGAGAGGTCCCATGTCCATGTTTGGGACATGGCGTTGGCACCGAG
1 ATGAGAGGTCCCATGTCCATGTATGGGACATGGCATGGGCACCGAG
* * *
16992294 ATGAGAGGTCCCCCGTAAGACCATGTATGGGACATGGCATGGGCACCGAT
1 ATGAGAGGT--CCC--ATGTCCATGTATGGGACATGGCATGGGCACCGAG
**
16992344 ATGAGAACTCCCATGT
1 ATGAGAGGTCCCATGT
16992360 AAGACCATAT
Statistics
Matches: 52, Mismatches: 10, Indels: 8
0.74 0.14 0.11
Matches are distributed among these distances:
46 11 0.21
48 6 0.12
50 35 0.67
ACGTcount: A:0.24, C:0.23, G:0.31, T:0.21
Consensus pattern (46 bp):
ATGAGAGGTCCCATGTCCATGTATGGGACATGGCATGGGCACCGAG
Found at i:16992331 original size:50 final size:50
Alignment explanation
Indices: 16992264--16992367 Score: 136
Period size: 50 Copynumber: 2.1 Consensus size: 50
16992254 GGTCCCATGT
* * * ** *
16992264 CCATGTTTGGGACATGGCGTTGGCACCGAGATGAGAGGTCCCCCGTAAGA
1 CCATGTATGGGACATGGCATGGGCACCGAGATGAGAACTCCCACGTAAGA
* *
16992314 CCATGTATGGGACATGGCATGGGCACCGATATGAGAACTCCCATGTAAGA
1 CCATGTATGGGACATGGCATGGGCACCGAGATGAGAACTCCCACGTAAGA
16992364 CCAT
1 CCAT
16992368 ATCTGGGATA
Statistics
Matches: 46, Mismatches: 8, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
50 46 1.00
ACGTcount: A:0.26, C:0.24, G:0.30, T:0.20
Consensus pattern (50 bp):
CCATGTATGGGACATGGCATGGGCACCGAGATGAGAACTCCCACGTAAGA
Done.