Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Gbar_D12
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: 58873029
ACGTcount: A:0.33, C:0.17, G:0.16, T:0.33
Warning! 639818 characters in sequence are not A, C, G, or T
File 18 of 196
Found at i:5089751 original size:20 final size:20
Alignment explanation
Indices: 5089726--5089770 Score: 72
Period size: 20 Copynumber: 2.2 Consensus size: 20
5089716 TTCAGCTCTT
5089726 ATGCAGCAGGCAAGGTGGCC
1 ATGCAGCAGGCAAGGTGGCC
* *
5089746 ATGCAGGAGTCAAGGTGGCC
1 ATGCAGCAGGCAAGGTGGCC
5089766 ATGCA
1 ATGCA
5089771 AGGAACGTGC
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.27, C:0.22, G:0.38, T:0.13
Consensus pattern (20 bp):
ATGCAGCAGGCAAGGTGGCC
Found at i:5093828 original size:20 final size:20
Alignment explanation
Indices: 5093803--5093847 Score: 81
Period size: 20 Copynumber: 2.2 Consensus size: 20
5093793 GTCAGCTCCT
5093803 ATGCAGCAGTCAAGGTGGCC
1 ATGCAGCAGTCAAGGTGGCC
*
5093823 ATGCAGGAGTCAAGGTGGCC
1 ATGCAGCAGTCAAGGTGGCC
5093843 ATGCA
1 ATGCA
5093848 AGGAACGTGC
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 24 1.00
ACGTcount: A:0.27, C:0.22, G:0.36, T:0.16
Consensus pattern (20 bp):
ATGCAGCAGTCAAGGTGGCC
Found at i:5100651 original size:33 final size:33
Alignment explanation
Indices: 5100614--5100709 Score: 174
Period size: 33 Copynumber: 2.9 Consensus size: 33
5100604 TTTATTTTAT
5100614 TTTAGTTTGTTTACTTATATGTTTTAGTTTTTG
1 TTTAGTTTGTTTACTTATATGTTTTAGTTTTTG
*
5100647 TTTAGTTTGTTTACTTATATGTTGTAGTTTTTG
1 TTTAGTTTGTTTACTTATATGTTTTAGTTTTTG
*
5100680 TTTAGTTTGTTTACTTATGTGTTTTAGTTT
1 TTTAGTTTGTTTACTTATATGTTTTAGTTT
5100710 AGTACTATGT
Statistics
Matches: 60, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
33 60 1.00
ACGTcount: A:0.15, C:0.03, G:0.17, T:0.66
Consensus pattern (33 bp):
TTTAGTTTGTTTACTTATATGTTTTAGTTTTTG
Found at i:5105503 original size:12 final size:12
Alignment explanation
Indices: 5105486--5105519 Score: 59
Period size: 12 Copynumber: 2.8 Consensus size: 12
5105476 ATAGATTAAA
5105486 TTAGACTTTGAT
1 TTAGACTTTGAT
5105498 TTAGACTTTGAT
1 TTAGACTTTGAT
*
5105510 TTAGATTTTG
1 TTAGACTTTG
5105520 GTTTTTTTTT
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
12 21 1.00
ACGTcount: A:0.24, C:0.06, G:0.18, T:0.53
Consensus pattern (12 bp):
TTAGACTTTGAT
Found at i:5116762 original size:19 final size:21
Alignment explanation
Indices: 5116727--5116767 Score: 52
Period size: 20 Copynumber: 2.0 Consensus size: 21
5116717 GTGTGCATAG
5116727 CTTTTTGCATTTAATTG-CAT
1 CTTTTTGCATTTAATTGTCAT
5116747 CTTTTTG-ATATT-ATTGTCAT
1 CTTTTTGCAT-TTAATTGTCAT
5116767 C
1 C
5116768 CCATTCACTC
Statistics
Matches: 19, Mismatches: 0, Indels: 4
0.83 0.00 0.17
Matches are distributed among these distances:
19 6 0.32
20 13 0.68
ACGTcount: A:0.20, C:0.15, G:0.10, T:0.56
Consensus pattern (21 bp):
CTTTTTGCATTTAATTGTCAT
Found at i:5122336 original size:71 final size:71
Alignment explanation
Indices: 5122198--5122346 Score: 185
Period size: 71 Copynumber: 2.1 Consensus size: 71
5122188 AGAGTATTGG
* * * * **
5122198 TAGAAGTGCAGGGAATGTTGAACTTTGGCTACTCACTTGACTTGTTTCGTTAGAAGTCCTCAAGG
1 TAGAAGTGCAGGGAATGCTAAACTTTAGCTACTCACTTGACTTGTTTCGGTAGAAGGACTCAAGG
5122263 TATCAA
66 TATCAA
* *
5122269 TAGAAGTGCA-GGAGATGCTAAACTTTAGCTACTGACTTGACTTGTTTCGGTAGAAGGGAC-CAG
1 TAGAAGTGCAGGGA-ATGCTAAACTTTAGCTACTCACTTGACTTGTTTCGGTAGAA-GGACTCAA
*
5122332 GGTATCGA
64 GGTATCAA
5122340 TAGAAGT
1 TAGAAGT
5122347 CTCAGGCCAA
Statistics
Matches: 67, Mismatches: 9, Indels: 4
0.84 0.11 0.05
Matches are distributed among these distances:
70 3 0.04
71 62 0.93
72 2 0.03
ACGTcount: A:0.28, C:0.15, G:0.27, T:0.30
Consensus pattern (71 bp):
TAGAAGTGCAGGGAATGCTAAACTTTAGCTACTCACTTGACTTGTTTCGGTAGAAGGACTCAAGG
TATCAA
Found at i:5124369 original size:4 final size:4
Alignment explanation
Indices: 5124360--5124406 Score: 94
Period size: 4 Copynumber: 11.8 Consensus size: 4
5124350 ATTTCATTTA
5124360 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TAT
1 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TAT
5124407 ATTTGATTTC
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 43 1.00
ACGTcount: A:0.26, C:0.00, G:0.23, T:0.51
Consensus pattern (4 bp):
TATG
Found at i:5127382 original size:23 final size:23
Alignment explanation
Indices: 5127355--5127430 Score: 134
Period size: 23 Copynumber: 3.3 Consensus size: 23
5127345 AGTGTTATTG
5127355 ATCAGTGGTAGCTTCGGCTACAT
1 ATCAGTGGTAGCTTCGGCTACAT
*
5127378 TTCAGTGGTAGCTTCGGCTACAT
1 ATCAGTGGTAGCTTCGGCTACAT
*
5127401 AACAGTGGTAGCTTCGGCTACAT
1 ATCAGTGGTAGCTTCGGCTACAT
5127424 ATCAGTG
1 ATCAGTG
5127431 TTGCACTTAT
Statistics
Matches: 49, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
23 49 1.00
ACGTcount: A:0.22, C:0.21, G:0.26, T:0.30
Consensus pattern (23 bp):
ATCAGTGGTAGCTTCGGCTACAT
Found at i:5154932 original size:122 final size:122
Alignment explanation
Indices: 5154773--5155079 Score: 463
Period size: 122 Copynumber: 2.5 Consensus size: 122
5154763 AATTATTCAC
* * * *
5154773 AATATTAACTCAAAACTCAAGGCT-TGACCACTCTTGGTTCCACTAACCCAATCCTTCTAGCCCA
1 AATATTAACTCAAAAATC-AGGGTGTGACCACTATTGGTTCCACTAACCCAATCCTTCTAACCCA
*
5154837 GTTTTTGGGATGTGACAATAAGGATTTTAATTAGAAAGAAAGTTCAATTAATCAACCT
65 GTTTTTAGGATGTGACAATAAGGATTTTAATTAGAAAGAAAGTTCAATTAATCAACCT
** *
5154895 AATATTAACTCAAAAATCAGGGTGTGACCACTATTGGTTCCACTAACCCAATCCTTCTAATTCGG
1 AATATTAACTCAAAAATCAGGGTGTGACCACTATTGGTTCCACTAACCCAATCCTTCTAACCCAG
* *
5154960 TTTTTAGGATGTGACAATAGGGGTTTTAATTAGAAAGAAAGTTCAATTAATCAACCT
66 TTTTTAGGATGTGACAATAAGGATTTTAATTAGAAAGAAAGTTCAATTAATCAACCT
* ** * *
5155017 AATATTAACTCAAAAATCATGGTGTGACCGTTGTTGGTTCCACTAACCCAATCCTTTTAACCC
1 AATATTAACTCAAAAATCAGGGTGTGACCACTATTGGTTCCACTAACCCAATCCTTCTAACCC
5155080 GATTTAGGGT
Statistics
Matches: 167, Mismatches: 17, Indels: 2
0.90 0.09 0.01
Matches are distributed among these distances:
121 4 0.02
122 163 0.98
ACGTcount: A:0.34, C:0.21, G:0.15, T:0.31
Consensus pattern (122 bp):
AATATTAACTCAAAAATCAGGGTGTGACCACTATTGGTTCCACTAACCCAATCCTTCTAACCCAG
TTTTTAGGATGTGACAATAAGGATTTTAATTAGAAAGAAAGTTCAATTAATCAACCT
Found at i:5155378 original size:15 final size:15
Alignment explanation
Indices: 5155360--5155407 Score: 51
Period size: 16 Copynumber: 3.1 Consensus size: 15
5155350 AAATTAAATT
5155360 AATTAACTAGATGCA
1 AATTAACTAGATGCA
*
5155375 AATTAACCTAAATGCA
1 AATTAA-CTAGATGCA
* *
5155391 AATAAAATGAGATGCA
1 AATTAACT-AGATGCA
5155407 A
1 A
5155408 GGTGATGGTT
Statistics
Matches: 27, Mismatches: 4, Indels: 3
0.79 0.12 0.09
Matches are distributed among these distances:
15 7 0.26
16 20 0.74
ACGTcount: A:0.52, C:0.12, G:0.12, T:0.23
Consensus pattern (15 bp):
AATTAACTAGATGCA
Found at i:5156111 original size:49 final size:49
Alignment explanation
Indices: 5156026--5156161 Score: 152
Period size: 49 Copynumber: 2.8 Consensus size: 49
5156016 TCAAACATGT
** * *
5156026 TAAAA-CCATCATTGTCAGGCCACTC-AGGATGATAGAATATGCAAATAT
1 TAAAAGCCATCATTGTTTGGCCACTCGA-GATGGTAGAATATGCAAATAG
* *
5156074 TGAAAGCCATCATTGTTTGGCCATTCGAGATGGTAGAATATGCAAATAG
1 TAAAAGCCATCATTGTTTGGCCACTCGAGATGGTAGAATATGCAAATAG
* * *
5156123 TAAAAGTCATC-TTTTTTGGGCCACCCGAGATGGTAGAAT
1 TAAAAGCCATCATTGTTT-GGCCACTCGAGATGGTAGAAT
5156162 GTACAAGTTC
Statistics
Matches: 74, Mismatches: 11, Indels: 5
0.82 0.12 0.06
Matches are distributed among these distances:
48 9 0.12
49 64 0.86
50 1 0.01
ACGTcount: A:0.34, C:0.17, G:0.21, T:0.28
Consensus pattern (49 bp):
TAAAAGCCATCATTGTTTGGCCACTCGAGATGGTAGAATATGCAAATAG
Found at i:5160107 original size:20 final size:21
Alignment explanation
Indices: 5160074--5160112 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 21
5160064 GTTCTATAGA
* *
5160074 TAGAAGTCCGAGTT-TACCGG
1 TAGAACTCCCAGTTCTACCGG
5160094 TAGAACTCCCAGTTCTACC
1 TAGAACTCCCAGTTCTACC
5160113 AGCAGAATTT
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
20 12 0.75
21 4 0.25
ACGTcount: A:0.26, C:0.28, G:0.21, T:0.26
Consensus pattern (21 bp):
TAGAACTCCCAGTTCTACCGG
Found at i:5163329 original size:21 final size:21
Alignment explanation
Indices: 5163297--5163337 Score: 50
Period size: 21 Copynumber: 2.0 Consensus size: 21
5163287 AGGCTCGAGG
5163297 GGCCTGTTTTAGGCC-ATACAA
1 GGCCTGTTTTA-GCCTATACAA
5163318 GGCCT-TTCTTAGCCTATACA
1 GGCCTGTT-TTAGCCTATACA
5163338 CCAAATGTTC
Statistics
Matches: 18, Mismatches: 0, Indels: 4
0.82 0.00 0.18
Matches are distributed among these distances:
20 5 0.28
21 13 0.72
ACGTcount: A:0.22, C:0.27, G:0.20, T:0.32
Consensus pattern (21 bp):
GGCCTGTTTTAGCCTATACAA
Found at i:5166969 original size:4 final size:4
Alignment explanation
Indices: 5166960--5166994 Score: 70
Period size: 4 Copynumber: 8.8 Consensus size: 4
5166950 AATTGATTTA
5166960 TATG TATG TATG TATG TATG TATG TATG TATG TAT
1 TATG TATG TATG TATG TATG TATG TATG TATG TAT
5166995 ATTTGATTTC
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 31 1.00
ACGTcount: A:0.26, C:0.00, G:0.23, T:0.51
Consensus pattern (4 bp):
TATG
Found at i:5172653 original size:13 final size:13
Alignment explanation
Indices: 5172637--5172662 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
5172627 CTTTGCATAT
5172637 TGTCTTCAACAGG
1 TGTCTTCAACAGG
5172650 TGTCTTCAACAGG
1 TGTCTTCAACAGG
5172663 CTCTCACTTT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.23, C:0.23, G:0.23, T:0.31
Consensus pattern (13 bp):
TGTCTTCAACAGG
Found at i:5186469 original size:121 final size:120
Alignment explanation
Indices: 5186207--5186572 Score: 561
Period size: 121 Copynumber: 3.0 Consensus size: 120
5186197 AAATATTCAC
* * *
5186207 AATATTAACTCAAAAATCAAGGCTTAACCACTCTTGGTTCCACTAACCCAATCCTTCTAACCTAG
1 AATATTAACTCAAAAATCAGGGCGTGACCACTCTTGGTTCCACTAACCCAATCCTTCTAACCTAG
* * *
5186272 TTTTTGCGATGTGACAATAAGGATTTTAATTAGAAAGAAAGTTTAATTAATCAACCT
66 TTTTTG-GATGTGATAAT-AGGGTTTTAATTAGAAAGAAAGTTCAATTAATCAACCT
* *
5186329 AATATTAACTCAAAAATCAGGGCGTGACCACTCTTGGTTCCTCTAACCCAATCCTTCTAAACTAG
1 AATATTAACTCAAAAATCAGGGCGTGACCACTCTTGGTTCCACTAACCCAATCCTTCTAACCTAG
*
5186394 TTTTTAGGATGTGATAATAGGGTTTTAATTAGAAAGAAAGTTCAATTAATTAACCT
66 TTTTT-GGATGTGATAATAGGGTTTTAATTAGAAAGAAAGTTCAATTAATCAACCT
* * *
5186450 AATATTAACTCAAAAATCAGGGCGTGACCGCTCTTGGTTCCACTAACCCAATCCTTCTAACCCAA
1 AATATTAACTCAAAAATCAGGGCGTGACCACTCTTGGTTCCACTAACCCAATCCTTCTAACCTAG
* *
5186515 TTTTTCGGATGTGATAATAGGAGTTTTAATTAGAAAAAAAGTTGAATTAATCAACCT
66 TTTTT-GGATGTGATAATAGG-GTTTTAATTAGAAAGAAAGTTCAATTAATCAACCT
5186572 A
1 A
5186573 GAGTCAGTTG
Statistics
Matches: 224, Mismatches: 18, Indels: 4
0.91 0.07 0.02
Matches are distributed among these distances:
121 115 0.51
122 108 0.48
123 1 0.00
ACGTcount: A:0.36, C:0.19, G:0.14, T:0.32
Consensus pattern (120 bp):
AATATTAACTCAAAAATCAGGGCGTGACCACTCTTGGTTCCACTAACCCAATCCTTCTAACCTAG
TTTTTGGATGTGATAATAGGGTTTTAATTAGAAAGAAAGTTCAATTAATCAACCT
Found at i:5189170 original size:71 final size:71
Alignment explanation
Indices: 5189076--5189216 Score: 214
Period size: 71 Copynumber: 2.0 Consensus size: 71
5189066 AGAGTATTGG
* **
5189076 TAGAAGTGCAGGGAATGTTGAACTTTTTCTACTGACTTAACTTGTTTC-GATAGAAGTCCTCAAG
1 TAGAAGTGCAGGGAATGCTGAACTTTGGCTACTGACTTAACTTGTTTCTG-TAGAAGTCCTCAAG
5189140 GTATCGA
65 GTATCGA
*
5189147 TAGAAGTGCA-GGAGATGCTGAACTTTGGCTACTGACTTGACTTGTTTCTGTAGAAGTCCTCAAG
1 TAGAAGTGCAGGGA-ATGCTGAACTTTGGCTACTGACTTAACTTGTTTCTGTAGAAGTCCTCAAG
5189211 GTATCG
65 GTATCG
5189217 GTAACACCTT
Statistics
Matches: 64, Mismatches: 4, Indels: 4
0.89 0.06 0.06
Matches are distributed among these distances:
70 3 0.05
71 60 0.94
72 1 0.02
ACGTcount: A:0.26, C:0.16, G:0.25, T:0.33
Consensus pattern (71 bp):
TAGAAGTGCAGGGAATGCTGAACTTTGGCTACTGACTTAACTTGTTTCTGTAGAAGTCCTCAAGG
TATCGA
Found at i:5205490 original size:122 final size:121
Alignment explanation
Indices: 5205273--5205640 Score: 601
Period size: 122 Copynumber: 3.0 Consensus size: 121
5205263 AAAATATTCA
* * * *
5205273 TAATATTAACACAAAAATCAAGGCTTAACCACTCTTGGTTCCACTAACCCAATCCTTCTAACCCA
1 TAATATTAACTCAAAAATCAGGGCGTGACCACTCTTGGTTCCACTAACCCAATCCTTCTAACCCA
* * *
5205338 GTTTTTGCGATGTGACAATAAGAATTTTAATTAGAAAGAAAGTTCAATTAATCAACC
66 ATTTTTG-GATGTGACAATAGGAGTTTTAATTAGAAAGAAAGTTCAATTAATCAACC
5205395 TAATATTAACTCAAAAATCAGGGCGTGACCACTCTTGGTTCCACTAACCCAATCCTTCTAACCCA
1 TAATATTAACTCAAAAATCAGGGCGTGACCACTCTTGGTTCCACTAACCCAATCCTTCTAACCCA
*
5205460 ATTTTTAGGATGTGACAATAGGGGTTTTAATTAGAAAGAAAGTTCAATTAATCAACC
66 ATTTTT-GGATGTGACAATAGGAGTTTTAATTAGAAAGAAAGTTCAATTAATCAACC
* *
5205517 TAATATTAACTCAAAATTCAGGGCGTGACCGCTCTTGGTTCCACTAACCCAATCCTTCTAACCCA
1 TAATATTAACTCAAAAATCAGGGCGTGACCACTCTTGGTTCCACTAACCCAATCCTTCTAACCCA
* *
5205582 ATTTTTTGGATGTGATAATAGGAGTTTTAATTAGAAAGAAAGTTGAATTAATCAACC
66 A-TTTTTGGATGTGACAATAGGAGTTTTAATTAGAAAGAAAGTTCAATTAATCAACC
5205639 TA
1 TA
5205641 GAGTCAGTTG
Statistics
Matches: 231, Mismatches: 13, Indels: 4
0.93 0.05 0.02
Matches are distributed among these distances:
122 225 0.97
123 6 0.03
ACGTcount: A:0.36, C:0.20, G:0.14, T:0.30
Consensus pattern (121 bp):
TAATATTAACTCAAAAATCAGGGCGTGACCACTCTTGGTTCCACTAACCCAATCCTTCTAACCCA
ATTTTTGGATGTGACAATAGGAGTTTTAATTAGAAAGAAAGTTCAATTAATCAACC
Found at i:5205943 original size:34 final size:34
Alignment explanation
Indices: 5205905--5205969 Score: 112
Period size: 34 Copynumber: 1.9 Consensus size: 34
5205895 ATAGATTTTA
* *
5205905 AAATTGAATTAATTAACTAGATGCAAATTAACCG
1 AAATTAAATTAATTAACTAGATGAAAATTAACCG
5205939 AAATTAAATTAATTAACTAGATGAAAATTAA
1 AAATTAAATTAATTAACTAGATGAAAATTAA
5205970 TCAGCTTTTA
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
34 29 1.00
ACGTcount: A:0.52, C:0.08, G:0.09, T:0.31
Consensus pattern (34 bp):
AAATTAAATTAATTAACTAGATGAAAATTAACCG
Found at i:5208935 original size:122 final size:122
Alignment explanation
Indices: 5208718--5209084 Score: 581
Period size: 122 Copynumber: 3.0 Consensus size: 122
5208708 AAATATTCAC
* * *
5208718 AATATTAACTCAAAAATCAAGGCTTGACCACTCTTGGTTCCACTAACCCAATCCTTCTAACCCAG
1 AATATTAACTCAAAAATCAGGGCGTGACCACTCTTGGTTCCACTAACCCAATCCTTCTAACCCAA
* * *
5208783 TTTTTGGGATGTGACAATAAGGATTTTAATTAGAAAGAAAGTTCAATTAATCAACCT
66 TTTTTAGGATGTGACAATAGGGGTTTTAATTAGAAAGAAAGTTCAATTAATCAACCT
5208840 AATATTAACTCAAAAATCAGGGCGTGACCACTCTTGGTTCCACTAACCCAATCCTTCTAACCCAA
1 AATATTAACTCAAAAATCAGGGCGTGACCACTCTTGGTTCCACTAACCCAATCCTTCTAACCCAA
5208905 TTTTTAGGATGTGACAATAGGGGTTTTAATTAGAAAGAAAGTTCAATTAATCAACCT
66 TTTTTAGGATGTGACAATAGGGGTTTTAATTAGAAAGAAAGTTCAATTAATCAACCT
** * ***
5208962 AATATTAACTCAAAAATCAGGGCGTGACTGCTCTTGGATCCACTAACCCAATCCTTCTAACTTGA
1 AATATTAACTCAAAAATCAGGGCGTGACCACTCTTGGTTCCACTAACCCAATCCTTCTAACCCAA
* * * * *
5209027 TTTTTCGGATGTGATAATAGGAGTTTTAATTAGAAATAAAGTTGAATTAATCAACCT
66 TTTTTAGGATGTGACAATAGGGGTTTTAATTAGAAAGAAAGTTCAATTAATCAACCT
5209084 A
1 A
5209085 GAGTCAGTTG
Statistics
Matches: 228, Mismatches: 17, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
122 228 1.00
ACGTcount: A:0.35, C:0.19, G:0.14, T:0.31
Consensus pattern (122 bp):
AATATTAACTCAAAAATCAGGGCGTGACCACTCTTGGTTCCACTAACCCAATCCTTCTAACCCAA
TTTTTAGGATGTGACAATAGGGGTTTTAATTAGAAAGAAAGTTCAATTAATCAACCT
Found at i:5211692 original size:71 final size:71
Alignment explanation
Indices: 5211598--5211734 Score: 215
Period size: 71 Copynumber: 1.9 Consensus size: 71
5211588 AGAGTATTGG
5211598 TAGAAGTGCAAGGAATGTTGAACTTT-TGCTACTGACTTGACTTCTTTCAATAGAAGTCCTCAAG
1 TAGAAGTGCAAGGAATGTTGAACTTTAT-CTACTGACTTGACTTCTTTCAATAGAAGTCCTCAAG
5211662 GTGTCGA
65 GTGTCGA
* **
5211669 TAGAAGTGCAA-GAGATGTTGAACTTTATCTACTGACTTGACTTGTTTCTGTAGAAGTCCTCAAG
1 TAGAAGTGCAAGGA-ATGTTGAACTTTATCTACTGACTTGACTTCTTTCAATAGAAGTCCTCAAG
5211733 GT
65 GT
5211735 ATCGGTAACA
Statistics
Matches: 61, Mismatches: 3, Indels: 4
0.90 0.04 0.06
Matches are distributed among these distances:
70 2 0.03
71 58 0.95
72 1 0.02
ACGTcount: A:0.28, C:0.16, G:0.23, T:0.34
Consensus pattern (71 bp):
TAGAAGTGCAAGGAATGTTGAACTTTATCTACTGACTTGACTTCTTTCAATAGAAGTCCTCAAGG
TGTCGA
Found at i:5213888 original size:105 final size:107
Alignment explanation
Indices: 5213767--5213964 Score: 283
Period size: 108 Copynumber: 1.9 Consensus size: 107
5213757 TGAAATTCAA
*
5213767 AAGGATATTTGACTATTTGGTTAAACGAG-AAATCGAAACACAACACATTAGGGAACG-TTCCTC
1 AAGGATATTCGACTATTTGGTTAAACGAGAAAATCGAAACACAACACATTAGGGAACGTTTCCTC
* *
5213830 GAATTTCCAAACGTAAAACATTGCCTTATTTGAAATTTTTTG
66 GAATTTCCAAACGCAAAACATTACCTTATTTGAAATTTTTTG
* * * * * *
5213872 AAGGATATTCGGCTATTTGGTTGAACGAGACAAATCGAAACCCAGCACATTAGGGCACGTTTTCT
1 AAGGATATTCGACTATTTGGTTAAACGAGA-AAATCGAAACACAACACATTAGGGAACGTTTCCT
*
5213937 CGAATTTCCAAACGCAAAATATTACCTT
65 CGAATTTCCAAACGCAAAACATTACCTT
5213965 TATTATTTTT
Statistics
Matches: 80, Mismatches: 10, Indels: 3
0.86 0.11 0.03
Matches are distributed among these distances:
105 26 0.32
107 25 0.31
108 29 0.36
ACGTcount: A:0.35, C:0.19, G:0.17, T:0.29
Consensus pattern (107 bp):
AAGGATATTCGACTATTTGGTTAAACGAGAAAATCGAAACACAACACATTAGGGAACGTTTCCTC
GAATTTCCAAACGCAAAACATTACCTTATTTGAAATTTTTTG
Found at i:5216209 original size:174 final size:174
Alignment explanation
Indices: 5215897--5216520 Score: 415
Period size: 174 Copynumber: 3.6 Consensus size: 174
5215887 CTGTAATCTT
* * *
5215897 AGGGAGATAAGACCTGATGCGATCTACTCTACTGTAACTTCAGAGAGATAAGATCCTTTATTTTA
1 AGGGAGATAAGACCTGATACGATCTACTCTACTGTAACTTCAGAGAGATAAGATCCTTGATCTTA
* * * * * * * * * *
5215962 ATCCGCTCCATTGTAATCTCAGGGAGATAGGATTACTGCTTTATGTTTGTTCCGCTGTAATCTCA
66 ATCCACTCCACTGCAACCTCAGGAAGATAGGATTACTGCTTTATGTCTGCTCCACTGCAACCTCA
5216027 AAGAGATAAGGCTGAAGTTCTTCGGTCCACTCCACTGTACCCTC
131 AAGAGATAAGGCTGAAGTTCTTCGGTCCACTCCACTGTACCCTC
* * *
5216071 AGGGAGATAAGGCTTGATACGATCTACTCTACTGTAACTTCAGAGAGATAAGAT-CTGTGGTCTT
1 AGGGAGATAAGACCTGATACGATCTACTCTACTGTAACTTCAGAGAGATAAGATCCT-TGATCTT
* ** * *
5216135 AGTCCACTCCACTGCAACCTCAAGGAAG-TAGGATTGGT-TTCTTCTGTCTGCTCCACTGCAACC
65 AATCCACTCCACTGCAACCTC-AGGAAGATAGGATTACTGCT-TTATGTCTGCTCCACTGCAACC
* * * * * ** * * * *
5216198 TCAAGGAGATAAGACTG--G--ATACGATCTGCTCTACTGCAACTTC
128 TCAAAGAGATAAGGCTGAAGTTCTTCGGTCCACTCCACTGTACCCTC
* * * ** ** * * * * * *
5216241 AGAGAGATAAGATCTGTGGTTTTGATCCGCTCCACTGCAACTTCAGGGAGATAGGATTAC-T-AG
1 AGGGAGATAAGA-C-CT-GATACGATCTACTCTACTGTAACTTCAGAGAGATAAGA-TCCTTGAT
*** * * * * ** * * *
5216304 CTTCAATTTGCTCCGCTGTAATCTCAGGGAA-ATAAGATCCCTGGCTTCA-ATCTGCTCCACTGT
62 CTT-AATCCACTCCACTGCAACCTCA-GGAAGATAGGATTACT-GCTTTATGTCTGCTCCACTGC
** * * * * * *
5216367 AACCTCAGGGAGATAAGATCTGAAATTCTTCGATCTACTCCATTGTAACCTC
124 AACCTCAAAGAGATAAG-GCTGAAGTTCTTCGGTCCACTCCACTGTACCCTC
* * * * *
5216419 AGGGAGATAAGACCTGATGCGATCTACTCTGCTGTAACTTCAGAGAGATAAAATCTTTGATTTTA
1 AGGGAGATAAGACCTGATACGATCTACTCTACTGTAACTTCAGAGAGATAAGATCCTTGATCTTA
* * *
5216484 ATCCACTCCACTGTAATCTCAGGGAGATAGGATTACT
66 ATCCACTCCACTGCAACCTCAGGAAGATAGGATTACT
5216521 ATCTTCAATC
Statistics
Matches: 332, Mismatches: 97, Indels: 41
0.71 0.21 0.09
Matches are distributed among these distances:
170 26 0.08
171 1 0.00
172 6 0.02
173 85 0.26
174 119 0.36
175 61 0.18
176 4 0.01
177 1 0.00
178 29 0.09
ACGTcount: A:0.28, C:0.22, G:0.21, T:0.29
Consensus pattern (174 bp):
AGGGAGATAAGACCTGATACGATCTACTCTACTGTAACTTCAGAGAGATAAGATCCTTGATCTTA
ATCCACTCCACTGCAACCTCAGGAAGATAGGATTACTGCTTTATGTCTGCTCCACTGCAACCTCA
AAGAGATAAGGCTGAAGTTCTTCGGTCCACTCCACTGTACCCTC
Found at i:5216282 original size:44 final size:44
Alignment explanation
Indices: 5216101--5216293 Score: 127
Period size: 44 Copynumber: 4.5 Consensus size: 44
5216091 GATCTACTCT
* * *
5216101 ACTGTAACTTCAGAGAGATAAGATCTGTGGTCTT-AGTCCACTCC
1 ACTGCAACTTCAGAGAGATAAGATCTGTGGTTTTGA-TCCGCTCC
* * * *
5216145 ACTGCAACCTCA-AG-GAAGTAGGAT-TG-GTTTCTTCTG-TCTGCTCC
1 ACTGCAACTTCAGAGAG-A-TAAGATCTGTG-GT-TT-TGATCCGCTCC
* * ** * *
5216189 ACTGCAACCTCA-AGGAGATAAGA-C--TGGATACGATCTGCTCT
1 ACTGCAACTTCAGA-GAGATAAGATCTGTGGTTTTGATCCGCTCC
5216230 ACTGCAACTTCAGAGAGATAAGATCTGTGGTTTTGATCCGCTCC
1 ACTGCAACTTCAGAGAGATAAGATCTGTGGTTTTGATCCGCTCC
*
5216274 ACTGCAACTTCAGGGAGATA
1 ACTGCAACTTCAGAGAGATA
5216294 GGATTACTAG
Statistics
Matches: 114, Mismatches: 20, Indels: 30
0.70 0.12 0.18
Matches are distributed among these distances:
40 1 0.01
41 28 0.25
42 4 0.04
43 7 0.06
44 70 0.61
45 3 0.03
46 1 0.01
ACGTcount: A:0.27, C:0.23, G:0.22, T:0.27
Consensus pattern (44 bp):
ACTGCAACTTCAGAGAGATAAGATCTGTGGTTTTGATCCGCTCC
Found at i:5216316 original size:129 final size:129
Alignment explanation
Indices: 5216056--5216388 Score: 364
Period size: 129 Copynumber: 2.6 Consensus size: 129
5216046 CTTCGGTCCA
* * * *
5216056 CTCCACTGTACCCTCAGGGAGATAAGGCTTGATACGATCTACTCTACTGTAACTTCAGAGAGATA
1 CTCCACTGTAACCTCAGGGAGATAAGACTGGATACGATCTGCTCTACTGTAACTTCAGAGAGATA
** ** **
5216121 AGATCTGTGGTCTTAGTCCACTCCACTGCAACCTCAAGGAAGTAGGATTGGTTTCTTCTGTCTG
66 AGATCTGTGGTCTTAGTCCACTCCACTGCAACCTCAAGGAAGTAGGATTACTAGCTTCAATCTG
* * *
5216185 CTCCACTGCAACCTCAAGGAGATAAGACTGGATACGATCTGCTCTACTGCAACTTCAGAGAGATA
1 CTCCACTGTAACCTCAGGGAGATAAGACTGGATACGATCTGCTCTACTGTAACTTCAGAGAGATA
* * * * *
5216250 AGATCTGTGGT-TTTGATCCGCTCCACTGCAACTTC-AGGGAGATAGGATTACTAGCTTCAATTT
66 AGATCTGTGGTCTTAG-TCCACTCCACTGCAACCTCAAGGAAG-TAGGATTACTAGCTTCAATCT
5216313 G
129 G
* * * * * * * * *
5216314 CTCCGCTGTAATCTCAGGGAAATAAGATCCCTGGCTTCAATCTGCTCCACTGTAACCTCAGGGAG
1 CTCCACTGTAACCTCAGGGAGATAAGA---CTGGATACGATCTGCTCTACTGTAACTTCAGAGAG
5216379 ATAAGATCTG
63 ATAAGATCTG
5216389 AAATTCTTCG
Statistics
Matches: 169, Mismatches: 30, Indels: 7
0.82 0.15 0.03
Matches are distributed among these distances:
128 8 0.05
129 123 0.73
132 38 0.22
ACGTcount: A:0.26, C:0.24, G:0.22, T:0.28
Consensus pattern (129 bp):
CTCCACTGTAACCTCAGGGAGATAAGACTGGATACGATCTGCTCTACTGTAACTTCAGAGAGATA
AGATCTGTGGTCTTAGTCCACTCCACTGCAACCTCAAGGAAGTAGGATTACTAGCTTCAATCTG
Found at i:5216317 original size:44 final size:44
Alignment explanation
Indices: 5216221--5217527 Score: 568
Period size: 44 Copynumber: 29.8 Consensus size: 44
5216211 ACTGGATACG
* * * ** * * **
5216221 ATCTGCTCTACTGCAACTTCAGAGAGATAAGATCTGTGGTTTTG
1 ATCTGCTCCACTGTAACTTCAGGGAGATAAGATCACTAGCTTCA
* * * *
5216265 ATCCGCTCCACTGCAACTTCAGGGAGATAGGATTACTAGCTTCA
1 ATCTGCTCCACTGTAACTTCAGGGAGATAAGATCACTAGCTTCA
* * * * *
5216309 ATTTGCTCCGCTGTAA-TCTCAGGGAAATAAGATCCCTGGCTTCA
1 ATCTGCTCCACTGTAACT-TCAGGGAGATAAGATCACTAGCTTCA
* * * *
5216353 ATCTGCTCCACTGTAACCTCAGGGAGATAAGATCTGA-AATTCTTCG
1 ATCTGCTCCACTGTAACTTCAGGGAGATAAGATC--ACTA-GCTTCA
* * * * * *
5216399 ATCTACTCCATTGTAACCTCAGGGAGATAAGA-C-CT-GATGCG
1 ATCTGCTCCACTGTAACTTCAGGGAGATAAGATCACTAGCTTCA
* ** * * * * * *
5216440 ATCTACTCTGCTGTAACTTCAGAGAGATAAAATC-TTTGATTTTA
1 ATCTGCTCCACTGTAACTTCAGGGAGATAAGATCACTAG-CTTCA
** * * *
5216484 ATCCACTCCACTGTAA-TCTCAGGGAGATAGGATTACTATCTTCA
1 ATCTGCTCCACTGTAACT-TCAGGGAGATAAGATCACTAGCTTCA
* * * *
5216528 ATCTGCTCCGCTGTAA-TCTCAGGGAGATAAGATCTCTGGCTTTA
1 ATCTGCTCCACTGTAACT-TCAGGGAGATAAGATCACTAGCTTCA
* * * *
5216572 ATCTGCTCCACTGTAACCTCAGGGAGATAAGATCTCTGGCTTTA
1 ATCTGCTCCACTGTAACTTCAGGGAGATAAGATCACTAGCTTCA
* * * * *
5216616 ATCTGCTCCACTGTAACCTCAAGGAGATAAGA-C-CT-GATGCG
1 ATCTGCTCCACTGTAACTTCAGGGAGATAAGATCACTAGCTTCA
* ** * * * *
5216657 ATCTACTCTGCTGTAACTTCAGAGAGATAAGATC-CTTGATTTTA
1 ATCTGCTCCACTGTAACTTCAGGGAGATAAGATCACTAG-CTTCA
** * * * *
5216701 ATCCACTCCACTATAA-TCTCAGGGAGATAGGATTACTATCTTCA
1 ATCTGCTCCACTGTAACT-TCAGGGAGATAAGATCACTAGCTTCA
* * * *
5216745 ATCTGCTCCGCTGTAA-TCTCACGGAGATAAGATCTCTGGCTTCA
1 ATCTGCTCCACTGTAACT-TCAGGGAGATAAGATCACTAGCTTCA
* * * * *
5216789 ATCTGCTCCACTGTAACCTCAGGGAGATAAAATCTGA-AATTCTTCG
1 ATCTGCTCCACTGTAACTTCAGGGAGATAAGATC--ACTA-GCTTCA
* * * * * * * *
5216835 GTCTACTCCACTGTAACCTCAGGGAGATAAGGTTTGA-AATTCTTCG
1 ATCTGCTCCACTGTAACTTCAGGGAGATAA-G-ATCACTA-GCTTCA
* * * * * *
5216881 GTCTACTCCACTGTAACCTCAGGGAGATAAGA-C-CT-GATGCG
1 ATCTGCTCCACTGTAACTTCAGGGAGATAAGATCACTAGCTTCA
* ** * * * *
5216922 ATCTACTCTGCTGTAACTTCAGAGAGATAAGATC-CTTGATTTTA
1 ATCTGCTCCACTGTAACTTCAGGGAGATAAGATCACTAG-CTTCA
* * * *
5216966 ATCCGCTCCACTGTAA-TGTCAGGGAGATAGGATTACTATCTTCA
1 ATCTGCTCCACTGTAACT-TCAGGGAGATAAGATCACTAGCTTCA
* *
5217010 ATCTGCTCCGA-TGTAA-TCTCAGGGAGATAAGATCTCTGGCTTCA
1 ATCTGCTCC-ACTGTAACT-TCAGGGAGATAAGATCACTAGCTTCA
* * * *
5217054 ATCTGCTCCACTGTAACCTCAGGGAGATAAGATCTGA-AATTCTTCG
1 ATCTGCTCCACTGTAACTTCAGGGAGATAAGATC--ACTA-GCTTCA
* * * * * * *
5217100 GTCTACTCCACTGTAACCTCAGGGAGATAAGGTTTGA-AATTCTTCA
1 ATCTGCTCCACTGTAACTTCAGGGAGATAA-G-ATCACTA-GCTTCA
* * * * * *
5217146 GTCTACTCCACTGTAACCTCAGGGAGATAAGA-C-CT-GATGCG
1 ATCTGCTCCACTGTAACTTCAGGGAGATAAGATCACTAGCTTCA
* ** * ** * *
5217187 ATCTACTCTGCTGTAACTTCAGAGAGATAAGATCTGT-GATTTTA
1 ATCTGCTCCACTGTAACTTCAGGGAGATAAGATCACTAG-CTTCA
* * *
5217231 AT-TCGCTCCACTGTAA-TCTCAGGGAGATAGGATTACTATCTTCA
1 ATCT-GCTCCACTGTAACT-TCAGGGAGATAAGATCACTAGCTTCA
* * *
5217275 ATCTGCTCCGCTGTAA-TCTCAGGGAGATAAGATCTCTGGCTTCA
1 ATCTGCTCCACTGTAACT-TCAGGGAGATAAGATCACTAGCTTCA
* * * *
5217319 ATCTGCTCCACTGTAACCTCAGGGAGATAAGATCTGA-AATTCTTCG
1 ATCTGCTCCACTGTAACTTCAGGGAGATAAGATC--ACTA-GCTTCA
* * * * * * *
5217365 GTCTACTCCACTGTAACCTCAGGGAGATAA-AAC-CT-GATGCG
1 ATCTGCTCCACTGTAACTTCAGGGAGATAAGATCACTAGCTTCA
* ** ** * * *
5217406 ATCTACTCTGCTGTAACTTCAAAGAGATAAGATC-CTTGATTTTA
1 ATCTGCTCCACTGTAACTTCAGGGAGATAAGATCACTAG-CTTCA
* * * * *
5217450 ATCCGCTCCACTGTAA-TCTCAGGGAGATAGGATTATTATCTTCA
1 ATCTGCTCCACTGTAACT-TCAGGGAGATAAGATCACTAGCTTCA
* *
5217494 ATCTGCTCCGCTGTAA-TCTCAAGGAGATAAGATC
1 ATCTGCTCCACTGTAACT-TCAGGGAGATAAGATC
5217528 TCTAATATTC
Statistics
Matches: 968, Mismatches: 240, Indels: 110
0.73 0.18 0.08
Matches are distributed among these distances:
41 143 0.15
42 15 0.02
43 15 0.02
44 570 0.59
45 13 0.01
46 209 0.22
47 1 0.00
48 2 0.00
ACGTcount: A:0.28, C:0.23, G:0.20, T:0.30
Consensus pattern (44 bp):
ATCTGCTCCACTGTAACTTCAGGGAGATAAGATCACTAGCTTCA
Found at i:5216963 original size:265 final size:265
Alignment explanation
Indices: 5216489--5217394 Score: 1470
Period size: 265 Copynumber: 3.4 Consensus size: 265
5216479 TTTTAATCCA
* * ** * *
5216489 CTCCACTGTAATCTCAGGGAGATAGGAT-TACTATCTTCAATCTGCTCCGCTGTAATCTCAGGGA
1 CTCCGCTGTAATCTCAGGGAGATAAGATCT-CTGGCTTCAATCTGCTCCACTGTAACCTCAGGGA
* * *** * * *
5216553 GATAAGATCT---CTGGCTTTAATCTGCTCCACTGTAACCTCAGGGAGATAAGATCTCTG----G
65 GATAAGATCTGAAAT-TCTTCGGTCTACTCCACTGTAACCTCAGGGAGATAAGGT-T-TGAAATT
* * * *
5216611 CTTTAATCTGCTCCACTGTAACCTCAAGGAGATAAGACCTGATGCGATCTACTCTGCTGTAACTT
127 CTTCAGTCTACTCCACTGTAACCTCAGGGAGATAAGACCTGATGCGATCTACTCTGCTGTAACTT
* *
5216676 CAGAGAGATAAGATCCTTGATTTTAATCCACTCCACTATAATCTCAGGGAGATAGGATTACTATC
192 CAGAGAGATAAGATCCTTGATTTTAATCCGCTCCACTGTAATCTCAGGGAGATAGGATTACTATC
5216741 TTCAATCTG
257 TTCAATCTG
*
5216750 CTCCGCTGTAATCTCACGGAGATAAGATCTCTGGCTTCAATCTGCTCCACTGTAACCTCAGGGAG
1 CTCCGCTGTAATCTCAGGGAGATAAGATCTCTGGCTTCAATCTGCTCCACTGTAACCTCAGGGAG
*
5216815 ATAAAATCTGAAATTCTTCGGTCTACTCCACTGTAACCTCAGGGAGATAAGGTTTGAAATTCTTC
66 ATAAGATCTGAAATTCTTCGGTCTACTCCACTGTAACCTCAGGGAGATAAGGTTTGAAATTCTTC
*
5216880 GGTCTACTCCACTGTAACCTCAGGGAGATAAGACCTGATGCGATCTACTCTGCTGTAACTTCAGA
131 AGTCTACTCCACTGTAACCTCAGGGAGATAAGACCTGATGCGATCTACTCTGCTGTAACTTCAGA
*
5216945 GAGATAAGATCCTTGATTTTAATCCGCTCCACTGTAATGTCAGGGAGATAGGATTACTATCTTCA
196 GAGATAAGATCCTTGATTTTAATCCGCTCCACTGTAATCTCAGGGAGATAGGATTACTATCTTCA
5217010 ATCTG
261 ATCTG
*
5217015 CTCCGATGTAATCTCAGGGAGATAAGATCTCTGGCTTCAATCTGCTCCACTGTAACCTCAGGGAG
1 CTCCGCTGTAATCTCAGGGAGATAAGATCTCTGGCTTCAATCTGCTCCACTGTAACCTCAGGGAG
5217080 ATAAGATCTGAAATTCTTCGGTCTACTCCACTGTAACCTCAGGGAGATAAGGTTTGAAATTCTTC
66 ATAAGATCTGAAATTCTTCGGTCTACTCCACTGTAACCTCAGGGAGATAAGGTTTGAAATTCTTC
5217145 AGTCTACTCCACTGTAACCTCAGGGAGATAAGACCTGATGCGATCTACTCTGCTGTAACTTCAGA
131 AGTCTACTCCACTGTAACCTCAGGGAGATAAGACCTGATGCGATCTACTCTGCTGTAACTTCAGA
*
5217210 GAGATAAGAT-CTGTGATTTTAATTCGCTCCACTGTAATCTCAGGGAGATAGGATTACTATCTTC
196 GAGATAAGATCCT-TGATTTTAATCCGCTCCACTGTAATCTCAGGGAGATAGGATTACTATCTTC
5217274 AATCTG
260 AATCTG
5217280 CTCCGCTGTAATCTCAGGGAGATAAGATCTCTGGCTTCAATCTGCTCCACTGTAACCTCAGGGAG
1 CTCCGCTGTAATCTCAGGGAGATAAGATCTCTGGCTTCAATCTGCTCCACTGTAACCTCAGGGAG
5217345 ATAAGATCTGAAATTCTTCGGTCTACTCCACTGTAACCTCAGGGAGATAA
66 ATAAGATCTGAAATTCTTCGGTCTACTCCACTGTAACCTCAGGGAGATAA
5217395 AACCTGATGC
Statistics
Matches: 605, Mismatches: 31, Indels: 14
0.93 0.05 0.02
Matches are distributed among these distances:
261 66 0.11
262 2 0.00
263 33 0.05
264 3 0.00
265 501 0.83
ACGTcount: A:0.27, C:0.23, G:0.20, T:0.29
Consensus pattern (265 bp):
CTCCGCTGTAATCTCAGGGAGATAAGATCTCTGGCTTCAATCTGCTCCACTGTAACCTCAGGGAG
ATAAGATCTGAAATTCTTCGGTCTACTCCACTGTAACCTCAGGGAGATAAGGTTTGAAATTCTTC
AGTCTACTCCACTGTAACCTCAGGGAGATAAGACCTGATGCGATCTACTCTGCTGTAACTTCAGA
GAGATAAGATCCTTGATTTTAATCCGCTCCACTGTAATCTCAGGGAGATAGGATTACTATCTTCA
ATCTG
Found at i:5217330 original size:219 final size:218
Alignment explanation
Indices: 5217021--5217530 Score: 790
Period size: 219 Copynumber: 2.3 Consensus size: 218
5217011 TCTGCTCCGA
* ** * *
5217021 TGTAATCTCAGGGAGATAAGATCT-CTGGCTTCAATCTGCTCCACTGTAACCTCAGGGAGATAAG
1 TGTAATCTCAGGGAGATAGGAT-TACTATCTTCAATCTGCTCCGCTGTAATCTCAGGGAGATAAG
* * ** * *
5217085 ATCTGAAATTCTTCGGTCTACTCCACTGTAACCTCAGGGAGATAAGGTTTGAAATTCTTCAGTCT
65 ATCT---CTGCTTCAATCTACTCCACTGTAACCTCAGGGAGATAAGATCTGAAATTCTTCAGTCT
* *
5217150 ACTCCACTGTAACCTCAGGGAGATAAGACCTGATGCGATCTACTCTGCTGTAACTTCAGAGAGAT
127 ACTCCACTGTAACCTCAGGGAGATAAAACCTGATGCGATCTACTCTGCTGTAACTTCAAAGAGAT
*
5217215 AAGAT-CTGTGATTTTAATTCGCTCCAC
192 AAGATCCT-TGATTTTAATCCGCTCCAC
5217242 TGTAATCTCAGGGAGATAGGATTACTATCTTCAATCTGCTCCGCTGTAATCTCAGGGAGATAAGA
1 TGTAATCTCAGGGAGATAGGATTACTATCTTCAATCTGCTCCGCTGTAATCTCAGGGAGATAAGA
* *
5217307 TCTCTGGCTTCAATCTGCTCCACTGTAACCTCAGGGAGATAAGATCTGAAATTCTTCGGTCTACT
66 TCTCT-GCTTCAATCTACTCCACTGTAACCTCAGGGAGATAAGATCTGAAATTCTTCAGTCTACT
5217372 CCACTGTAACCTCAGGGAGATAAAACCTGATGCGATCTACTCTGCTGTAACTTCAAAGAGATAAG
130 CCACTGTAACCTCAGGGAGATAAAACCTGATGCGATCTACTCTGCTGTAACTTCAAAGAGATAAG
5217437 ATCCTTGATTTTAATCCGCTCCAC
195 ATCCTTGATTTTAATCCGCTCCAC
* *
5217461 TGTAATCTCAGGGAGATAGGATTATTATCTTCAATCTGCTCCGCTGTAATCTCAAGGAGATAAGA
1 TGTAATCTCAGGGAGATAGGATTACTATCTTCAATCTGCTCCGCTGTAATCTCAGGGAGATAAGA
5217526 TCTCT
66 TCTCT
5217531 AATATTCACT
Statistics
Matches: 268, Mismatches: 18, Indels: 8
0.91 0.06 0.03
Matches are distributed among these distances:
218 1 0.00
219 203 0.76
220 3 0.01
221 61 0.23
ACGTcount: A:0.28, C:0.23, G:0.20, T:0.30
Consensus pattern (218 bp):
TGTAATCTCAGGGAGATAGGATTACTATCTTCAATCTGCTCCGCTGTAATCTCAGGGAGATAAGA
TCTCTGCTTCAATCTACTCCACTGTAACCTCAGGGAGATAAGATCTGAAATTCTTCAGTCTACTC
CACTGTAACCTCAGGGAGATAAAACCTGATGCGATCTACTCTGCTGTAACTTCAAAGAGATAAGA
TCCTTGATTTTAATCCGCTCCAC
Found at i:5218778 original size:14 final size:14
Alignment explanation
Indices: 5218759--5218825 Score: 104
Period size: 13 Copynumber: 5.0 Consensus size: 14
5218749 TTAGCCTCTC
5218759 CATTTTTCATTTTT
1 CATTTTTCATTTTT
5218773 CATTTTTCATTTTT
1 CATTTTTCATTTTT
5218787 CA-TTTTCATTTTT
1 CATTTTTCATTTTT
*
5218800 CATTTTTCA-TTCT
1 CATTTTTCATTTTT
5218813 CATTTTTC-TTTTT
1 CATTTTTCATTTTT
5218826 TTTTTGACTC
Statistics
Matches: 49, Mismatches: 2, Indels: 5
0.88 0.04 0.09
Matches are distributed among these distances:
13 27 0.55
14 22 0.45
ACGTcount: A:0.13, C:0.16, G:0.00, T:0.70
Consensus pattern (14 bp):
CATTTTTCATTTTT
Found at i:5218819 original size:27 final size:28
Alignment explanation
Indices: 5218759--5218826 Score: 104
Period size: 27 Copynumber: 2.5 Consensus size: 28
5218749 TTAGCCTCTC
*
5218759 CATTTTTCATTTTTCATTTTTCATTTTT
1 CATTTTTCATTTTTCATTTTTCATTTCT
5218787 CA-TTTTCATTTTTCATTTTTCA-TTCT
1 CATTTTTCATTTTTCATTTTTCATTTCT
*
5218813 CATTTTTCTTTTTT
1 CATTTTTCATTTTT
5218827 TTTTGACTCA
Statistics
Matches: 37, Mismatches: 2, Indels: 3
0.88 0.05 0.07
Matches are distributed among these distances:
26 5 0.14
27 30 0.81
28 2 0.05
ACGTcount: A:0.13, C:0.16, G:0.00, T:0.71
Consensus pattern (28 bp):
CATTTTTCATTTTTCATTTTTCATTTCT
Found at i:5218826 original size:7 final size:7
Alignment explanation
Indices: 5218759--5218825 Score: 104
Period size: 7 Copynumber: 10.0 Consensus size: 7
5218749 TTAGCCTCTC
5218759 CATTTTT
1 CATTTTT
5218766 CATTTTT
1 CATTTTT
5218773 CATTTTT
1 CATTTTT
5218780 CATTTTT
1 CATTTTT
5218787 CA-TTTT
1 CATTTTT
5218793 CATTTTT
1 CATTTTT
5218800 CATTTTT
1 CATTTTT
*
5218807 CA-TTCT
1 CATTTTT
5218813 CATTTTT
1 CATTTTT
5218820 C-TTTTT
1 CATTTTT
5218826 TTTTTGACTC
Statistics
Matches: 56, Mismatches: 2, Indels: 5
0.89 0.03 0.08
Matches are distributed among these distances:
6 16 0.29
7 40 0.71
ACGTcount: A:0.13, C:0.16, G:0.00, T:0.70
Consensus pattern (7 bp):
CATTTTT
Found at i:5218826 original size:20 final size:20
Alignment explanation
Indices: 5218759--5218825 Score: 109
Period size: 20 Copynumber: 3.4 Consensus size: 20
5218749 TTAGCCTCTC
5218759 CATTTTTCATTTTTCATTTTT
1 CATTTTTCA-TTTTCATTTTT
5218780 CATTTTTCATTTTCATTTTT
1 CATTTTTCATTTTCATTTTT
*
5218800 CATTTTTCATTCTCATTTTT
1 CATTTTTCATTTTCATTTTT
5218820 C-TTTTT
1 CATTTTT
5218826 TTTTTGACTC
Statistics
Matches: 45, Mismatches: 1, Indels: 2
0.94 0.02 0.04
Matches are distributed among these distances:
19 5 0.11
20 31 0.69
21 9 0.20
ACGTcount: A:0.13, C:0.16, G:0.00, T:0.70
Consensus pattern (20 bp):
CATTTTTCATTTTCATTTTT
Found at i:5223386 original size:107 final size:106
Alignment explanation
Indices: 5223227--5223424 Score: 272
Period size: 108 Copynumber: 1.9 Consensus size: 106
5223217 TGAAATTCAA
*
5223227 AAGGATATTTGACTATTTGGTTAAACGAGAAATCGAAACACAACACATTAGGGAACG-TTCCTCG
1 AAGGATATTCGACTATTTGGTTAAACGAGAAATCGAAACACAACACATTAGGGAACGTTTCCTCG
* *
5223291 AATTTCCAAACGTAAAACATTGCCTTATTTGAAATTTTTGG
66 AATTTCCAAACGCAAAACATTACCTTATTTGAAATTTTTGG
* * * * * * *
5223332 AAGGATATTCGGCTATTTGGTTGAATGAGAAAAATCGAAACCCAGCACATTAGGGCACGTTTTCT
1 AAGGATATTCGACTATTTGGTTAAACGAG--AAATCGAAACACAACACATTAGGGAACGTTTCCT
*
5223397 CGAATTTCCAAACGCAAAATATTACCTT
64 CGAATTTCCAAACGCAAAACATTACCTT
5223425 TATTATTTTT
Statistics
Matches: 79, Mismatches: 11, Indels: 3
0.85 0.12 0.03
Matches are distributed among these distances:
105 25 0.32
107 25 0.32
108 29 0.37
ACGTcount: A:0.35, C:0.18, G:0.18, T:0.29
Consensus pattern (106 bp):
AAGGATATTCGACTATTTGGTTAAACGAGAAATCGAAACACAACACATTAGGGAACGTTTCCTCG
AATTTCCAAACGCAAAACATTACCTTATTTGAAATTTTTGG
Found at i:5223931 original size:7 final size:7
Alignment explanation
Indices: 5223919--5223948 Score: 60
Period size: 7 Copynumber: 4.3 Consensus size: 7
5223909 TCTATATATT
5223919 TAAATTA
1 TAAATTA
5223926 TAAATTA
1 TAAATTA
5223933 TAAATTA
1 TAAATTA
5223940 TAAATTA
1 TAAATTA
5223947 TA
1 TA
5223949 TGAATGTATA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 23 1.00
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (7 bp):
TAAATTA
Found at i:5224263 original size:3 final size:3
Alignment explanation
Indices: 5224219--5224243 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
5224209 CAAGATATAG
5224219 ATA ATA ATA ATA ATA ATA ATA ATA A
1 ATA ATA ATA ATA ATA ATA ATA ATA A
5224244 CTTATTAGTT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
ATA
Found at i:5224973 original size:13 final size:13
Alignment explanation
Indices: 5224955--5224979 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
5224945 AAGAAAGGGT
5224955 ATAAAACAAAATG
1 ATAAAACAAAATG
5224968 ATAAAACAAAAT
1 ATAAAACAAAAT
5224980 AAAATGAAAA
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:0.72, C:0.08, G:0.04, T:0.16
Consensus pattern (13 bp):
ATAAAACAAAATG
Found at i:5226822 original size:25 final size:25
Alignment explanation
Indices: 5226793--5226840 Score: 60
Period size: 25 Copynumber: 1.9 Consensus size: 25
5226783 TTTGCTATTC
*
5226793 ATATACACGCATATTTTTATATACA
1 ATATACACGCATATTTTAATATACA
***
5226818 ATATATGTGCATATTTTAATATA
1 ATATACACGCATATTTTAATATA
5226841 TACTTTTAAG
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
25 19 1.00
ACGTcount: A:0.40, C:0.10, G:0.06, T:0.44
Consensus pattern (25 bp):
ATATACACGCATATTTTAATATACA
Found at i:5226963 original size:33 final size:29
Alignment explanation
Indices: 5226926--5226996 Score: 88
Period size: 29 Copynumber: 2.3 Consensus size: 29
5226916 TTTATACTAT
5226926 ATATATACTTACACACTTTTTTTATTTTTGTAA
1 ATATATACTTACACA---TTTTTA-TTTTGTAA
* *
5226959 ATATATACATATACATTTTTATTTTGTAA
1 ATATATACTTACACATTTTTATTTTGTAA
5226988 ATATATACT
1 ATATATACT
5226997 GGTACATGCT
Statistics
Matches: 35, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
29 16 0.46
30 6 0.17
33 13 0.37
ACGTcount: A:0.35, C:0.10, G:0.03, T:0.52
Consensus pattern (29 bp):
ATATATACTTACACATTTTTATTTTGTAA
Found at i:5227267 original size:22 final size:22
Alignment explanation
Indices: 5227237--5227279 Score: 68
Period size: 22 Copynumber: 2.0 Consensus size: 22
5227227 GCACCAAAAC
*
5227237 AGGCTTTTAGCAGCGCTTTTTT
1 AGGCCTTTAGCAGCGCTTTTTT
*
5227259 AGGCCTTTAGCGGCGCTTTTT
1 AGGCCTTTAGCAGCGCTTTTT
5227280 AACGGCGCTA
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:0.12, C:0.21, G:0.26, T:0.42
Consensus pattern (22 bp):
AGGCCTTTAGCAGCGCTTTTTT
Found at i:5227440 original size:43 final size:43
Alignment explanation
Indices: 5227390--5227644 Score: 314
Period size: 43 Copynumber: 5.9 Consensus size: 43
5227380 GCTAAAAGTA
* *
5227390 ATGACCTTTAGCGGCGCTTTCCCCACAAACGCCGCTATAGACC
1 ATGACCTTTAGCGGCGCTTTTCCCACAAACGCCGCTAAAGACC
*
5227433 ATAACCTTTAGCGGCGCTTTTCCCACAAACGCCGCTAAAGACC
1 ATGACCTTTAGCGGCGCTTTTCCCACAAACGCCGCTAAAGACC
** * * *
5227476 ATGACCTTTAGCTACGTTTTTTCTACAAACGCCGCTAAAGACC
1 ATGACCTTTAGCGGCGCTTTTCCCACAAACGCCGCTAAAGACC
* * *
5227519 ACGAGCTTTAGCGGAGCTTTTCCCACAAACGCCGCTAAAGACC
1 ATGACCTTTAGCGGCGCTTTTCCCACAAACGCCGCTAAAGACC
* ** ** *
5227562 ATGACCTTTAGCGGCACTTTTTTGCACAAACGCTACTAAATACC
1 ATGACCTTTAGCGGCGC-TTTTCCCACAAACGCCGCTAAAGACC
* *
5227606 ATGACCTTTAGCGACGCTTTTCGCGA-AAACGCCGCTAAA
1 ATGACCTTTAGCGGCGCTTTTC-CCACAAACGCCGCTAAA
5227645 AACATATCAT
Statistics
Matches: 177, Mismatches: 33, Indels: 4
0.83 0.15 0.02
Matches are distributed among these distances:
43 140 0.79
44 37 0.21
ACGTcount: A:0.27, C:0.31, G:0.17, T:0.24
Consensus pattern (43 bp):
ATGACCTTTAGCGGCGCTTTTCCCACAAACGCCGCTAAAGACC
Found at i:5227531 original size:129 final size:130
Alignment explanation
Indices: 5227395--5227644 Score: 351
Period size: 129 Copynumber: 1.9 Consensus size: 130
5227385 AAGTAATGAC
* * *
5227395 CTTTAGCGGCGCTTTCCCCACAAACGCCGCTATAGACCATAACCTTTAGCGGCGC-TTTTCCCAC
1 CTTTAGCGGAGCTTTCCCCACAAACGCCGCTAAAGACCATAACCTTTAGCGGCACTTTTTCCCAC
* * ** *
5227459 AAACGCCGCTAAAGACCATGACCTTTAGCTACG-TTTTTTCTACAAACGCCGCTAAAGACCACGA
66 AAACGCCACTAAAGACCATGACCTTTAGCGACGCTTTTCGCGA-AAACGCCGCTAAAGACCACGA
5227523 G
130 G
* * **
5227524 CTTTAGCGGAGCTTTTCCCACAAACGCCGCTAAAGACCATGACCTTTAGCGGCACTTTTTTGCAC
1 CTTTAGCGGAGCTTTCCCCACAAACGCCGCTAAAGACCATAACCTTTAGCGGCACTTTTTCCCAC
* *
5227589 AAACGCTACTAAATACCATGACCTTTAGCGACGCTTTTCGCGAAAACGCCGCTAAA
66 AAACGCCACTAAAGACCATGACCTTTAGCGACGCTTTTCGCGAAAACGCCGCTAAA
5227645 AACATATCAT
Statistics
Matches: 105, Mismatches: 14, Indels: 3
0.86 0.11 0.02
Matches are distributed among these distances:
129 50 0.48
130 49 0.47
131 6 0.06
ACGTcount: A:0.27, C:0.32, G:0.17, T:0.24
Consensus pattern (130 bp):
CTTTAGCGGAGCTTTCCCCACAAACGCCGCTAAAGACCATAACCTTTAGCGGCACTTTTTCCCAC
AAACGCCACTAAAGACCATGACCTTTAGCGACGCTTTTCGCGAAAACGCCGCTAAAGACCACGAG
Found at i:5232235 original size:19 final size:17
Alignment explanation
Indices: 5232181--5232238 Score: 62
Period size: 19 Copynumber: 3.1 Consensus size: 17
5232171 TATTAATTTT
*
5232181 AAATAAATAAATTTTGAA
1 AAATTAATAAATTTT-AA
5232199 AAATTAAGTAATATTTTAA
1 AAATTAA-TAA-ATTTTAA
5232218 AGAATTAGATAAATTTTAA
1 A-AATTA-ATAAATTTTAA
5232237 AA
1 AA
5232239 TTTTTATATA
Statistics
Matches: 35, Mismatches: 1, Indels: 8
0.80 0.02 0.18
Matches are distributed among these distances:
18 7 0.20
19 14 0.40
20 13 0.37
21 1 0.03
ACGTcount: A:0.57, C:0.00, G:0.07, T:0.36
Consensus pattern (17 bp):
AAATTAATAAATTTTAA
Found at i:5232549 original size:12 final size:12
Alignment explanation
Indices: 5232521--5232553 Score: 52
Period size: 12 Copynumber: 2.9 Consensus size: 12
5232511 TATTTAAAAA
5232521 ATTTTAAAA-TC
1 ATTTTAAAATTC
5232532 -TTTTAAAATTC
1 ATTTTAAAATTC
5232543 ATTTTAAAATT
1 ATTTTAAAATT
5232554 TTAAATCACG
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
10 8 0.40
11 2 0.10
12 10 0.50
ACGTcount: A:0.42, C:0.06, G:0.00, T:0.52
Consensus pattern (12 bp):
ATTTTAAAATTC
Found at i:5233353 original size:14 final size:14
Alignment explanation
Indices: 5233312--5233375 Score: 69
Period size: 14 Copynumber: 4.5 Consensus size: 14
5233302 CCCTAACTCG
5233312 ACCCTAAATCTCTAA
1 ACCCTAAATCTCT-A
5233327 ACCCTAAATCTCTA
1 ACCCTAAATCTCTA
* *
5233341 ACTCTAAACCTCTA
1 ACCCTAAATCTCTA
5233355 ATCCC-AAA-CTCATA
1 A-CCCTAAATCTC-TA
5233369 ACCCTAA
1 ACCCTAA
5233376 TTACCCCAAT
Statistics
Matches: 43, Mismatches: 3, Indels: 7
0.81 0.06 0.13
Matches are distributed among these distances:
13 6 0.14
14 22 0.51
15 15 0.35
ACGTcount: A:0.39, C:0.36, G:0.00, T:0.25
Consensus pattern (14 bp):
ACCCTAAATCTCTA
Found at i:5233364 original size:21 final size:21
Alignment explanation
Indices: 5233321--5233375 Score: 60
Period size: 21 Copynumber: 2.6 Consensus size: 21
5233311 GACCCTAAAT
* *
5233321 CTCTAAACCCTAAATCTCTAA
1 CTCTAAACCCTAAATCCCAAA
5233342 CTCTAAACCTCT-AATCCCAAA
1 CTCTAAACC-CTAAATCCCAAA
5233363 CTC-ATAACCCTAA
1 CTCTA-AACCCTAA
5233376 TTACCCCAAT
Statistics
Matches: 29, Mismatches: 2, Indels: 6
0.78 0.05 0.16
Matches are distributed among these distances:
20 3 0.10
21 24 0.83
22 2 0.07
ACGTcount: A:0.38, C:0.36, G:0.00, T:0.25
Consensus pattern (21 bp):
CTCTAAACCCTAAATCCCAAA
Found at i:5234230 original size:42 final size:42
Alignment explanation
Indices: 5234180--5234276 Score: 167
Period size: 42 Copynumber: 2.3 Consensus size: 42
5234170 CTTTACCAAT
*
5234180 AACGCCGCTAAAGGTCTGCGCATTAGCGGCGCTTCATGAAAA
1 AACGCCGCTAAAGGTCTGCACATTAGCGGCGCTTCATGAAAA
*
5234222 AACGCCGCTAAAGGTCTGCACATTAGCGGCGCTTCTTGAAAA
1 AACGCCGCTAAAGGTCTGCACATTAGCGGCGCTTCATGAAAA
*
5234264 AATGCCGCTAAAG
1 AACGCCGCTAAAG
5234277 ACCCACAAGG
Statistics
Matches: 52, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
42 52 1.00
ACGTcount: A:0.30, C:0.26, G:0.25, T:0.20
Consensus pattern (42 bp):
AACGCCGCTAAAGGTCTGCACATTAGCGGCGCTTCATGAAAA
Found at i:5253689 original size:25 final size:25
Alignment explanation
Indices: 5253661--5253856 Score: 139
Period size: 25 Copynumber: 7.9 Consensus size: 25
5253651 CGTTATTTAT
* *
5253661 CTCTTATGAGCATCCTATTATATGG
1 CTCTTATGAGCTTCCCATTATATGG
* * * *
5253686 CTCTCACGAGCTTCCCAATATTTGG
1 CTCTTATGAGCTTCCCATTATATGG
*
5253711 CTCTCATGAGCTTCCCAATTA-ATGG
1 CTCTTATGAGCTTCCC-ATTATATGG
*
5253736 CTCTCT-TGAGCTTCCCGTT-TATGG
1 CTCT-TATGAGCTTCCCATTATATGG
*
5253760 CTCTTATGAGCTTCCCGATAAT-TGG
1 CTCTTATGAGCTTCCC-ATTATATGG
* * **
5253785 CTCGTAAGAGCTTCCCATTATACAG
1 CTCTTATGAGCTTCCCATTATATGG
** * * **
5253810 CTCGCATGAGTTTCCCGTTATACAG
1 CTCTTATGAGCTTCCCATTATATGG
** *
5253835 CTCACATGAGCTTCCCGTTATA
1 CTCTTATGAGCTTCCCATTATA
5253857 CAGCTCACAT
Statistics
Matches: 140, Mismatches: 24, Indels: 14
0.79 0.13 0.08
Matches are distributed among these distances:
23 1 0.01
24 24 0.17
25 111 0.79
26 4 0.03
ACGTcount: A:0.21, C:0.28, G:0.17, T:0.34
Consensus pattern (25 bp):
CTCTTATGAGCTTCCCATTATATGG
Found at i:5253775 original size:49 final size:51
Alignment explanation
Indices: 5253661--5253801 Score: 141
Period size: 49 Copynumber: 2.8 Consensus size: 51
5253651 CGTTATTTAT
* *
5253661 CTCTTATGAGCAT-CCTATTATATGGCTCTCACGAGCTTCCCAATATTTGG
1 CTCTTATGAGCTTCCCAATTATATGGCTCTCACGAGCTTCCCAATATTTGG
* ** *
5253711 CTCTCATGAGCTTCCCAATTA-ATGGCTCTCTTGAGCTTCCC-GT-TTATGG
1 CTCTTATGAGCTTCCCAATTATATGGCTCTCACGAGCTTCCCAATATT-TGG
* * *
5253760 CTCTTATGAGCTTCCCGATAAT-TGGCTCGT-AAGAGCTTCCCA
1 CTCTTATGAGCTTCCCAATTATATGGCTC-TCACGAGCTTCCCA
5253802 TTATACAGCT
Statistics
Matches: 75, Mismatches: 11, Indels: 10
0.78 0.11 0.10
Matches are distributed among these distances:
48 2 0.03
49 37 0.49
50 30 0.40
51 6 0.08
ACGTcount: A:0.20, C:0.28, G:0.18, T:0.35
Consensus pattern (51 bp):
CTCTTATGAGCTTCCCAATTATATGGCTCTCACGAGCTTCCCAATATTTGG
Found at i:5253825 original size:74 final size:75
Alignment explanation
Indices: 5253678--5253851 Score: 192
Period size: 74 Copynumber: 2.3 Consensus size: 75
5253668 GAGCATCCTA
* * * * ** * *
5253678 TTATATGGCTCTCACGAGCTTCCCAATATTTGGCTCTCATGAGCTTCCCAATTAATGGCTCTCTT
1 TTATATGGCTCTCATGAGCTTCCCGATAATTGGCTCTCAAGAGCTTCCCAATTAACAGCTCGCAT
5253743 GAGCTTCCCG
66 GAGCTTCCCG
*
5253753 TT-TATGGCTCTTATGAGCTTCCCGATAATTGGCTCGT-AAGAGCTTCCC-ATTATACAGCTCGC
1 TTATATGGCTCTCATGAGCTTCCCGATAATTGGCTC-TCAAGAGCTTCCCAATTA-ACAGCTCGC
*
5253815 ATGAGTTTCCCG
64 ATGAGCTTCCCG
** *
5253827 TTATACAGCTCACATGAGCTTCCCG
1 TTATATGGCTCTCATGAGCTTCCCG
5253852 TTATACAGCT
Statistics
Matches: 82, Mismatches: 14, Indels: 6
0.80 0.14 0.06
Matches are distributed among these distances:
73 4 0.05
74 57 0.70
75 21 0.26
ACGTcount: A:0.20, C:0.28, G:0.18, T:0.33
Consensus pattern (75 bp):
TTATATGGCTCTCATGAGCTTCCCGATAATTGGCTCTCAAGAGCTTCCCAATTAACAGCTCGCAT
GAGCTTCCCG
Found at i:5253857 original size:25 final size:25
Alignment explanation
Indices: 5253792--5253879 Score: 140
Period size: 25 Copynumber: 3.5 Consensus size: 25
5253782 TGGCTCGTAA
* *
5253792 GAGCTTCCCATTATACAGCTCGCAT
1 GAGCTTCCCGTTATACAGCTCACAT
*
5253817 GAGTTTCCCGTTATACAGCTCACAT
1 GAGCTTCCCGTTATACAGCTCACAT
5253842 GAGCTTCCCGTTATACAGCTCACAT
1 GAGCTTCCCGTTATACAGCTCACAT
*
5253867 AAGCTTCCCGTTA
1 GAGCTTCCCGTTA
5253880 CATGACTCAG
Statistics
Matches: 58, Mismatches: 5, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
25 58 1.00
ACGTcount: A:0.24, C:0.31, G:0.16, T:0.30
Consensus pattern (25 bp):
GAGCTTCCCGTTATACAGCTCACAT
Found at i:5253888 original size:25 final size:25
Alignment explanation
Indices: 5253821--5253913 Score: 86
Period size: 25 Copynumber: 3.7 Consensus size: 25
5253811 TCGCATGAGT
* *
5253821 TTCCCGTTATACA-GCTCACATGAGC
1 TTCCCGAT-TACATGCTCACATAAGC
*
5253846 TTCCCGTTATACA-GCTCACATAAGC
1 TTCCCGAT-TACATGCTCACATAAGC
*
5253871 TTCCCG-TTACATGACTCAGA-AGAGC
1 TTCCCGATTACATG-CTCACATA-AGC
5253896 TTCCCGATTACATGCTCA
1 TTCCCGATTACATGCTCA
5253914 TATGGGCATA
Statistics
Matches: 62, Mismatches: 2, Indels: 8
0.86 0.03 0.11
Matches are distributed among these distances:
23 4 0.06
24 3 0.05
25 48 0.77
26 7 0.11
ACGTcount: A:0.26, C:0.31, G:0.15, T:0.28
Consensus pattern (25 bp):
TTCCCGATTACATGCTCACATAAGC
Found at i:5253896 original size:50 final size:50
Alignment explanation
Indices: 5253790--5253901 Score: 138
Period size: 50 Copynumber: 2.2 Consensus size: 50
5253780 ATTGGCTCGT
* * * *
5253790 AAGAGCTTCCCATTATACAGCTCGCATGAGTTTCCCGTTATACAGCTCAC
1 AAGAGCTTCCCGTTATACAGCTCACATAAGCTTCCCGTTATACAGCTCAC
* *
5253840 ATGAGCTTCCCGTTATACAGCTCACATAAGCTTCCCG-T-TACATGACTCAG
1 AAGAGCTTCCCGTTATACAGCTCACATAAGCTTCCCGTTATACA-G-CTCAC
5253890 AAGAGCTTCCCG
1 AAGAGCTTCCCG
5253902 ATTACATGCT
Statistics
Matches: 53, Mismatches: 7, Indels: 4
0.83 0.11 0.06
Matches are distributed among these distances:
48 4 0.08
49 2 0.04
50 47 0.89
ACGTcount: A:0.26, C:0.30, G:0.17, T:0.27
Consensus pattern (50 bp):
AAGAGCTTCCCGTTATACAGCTCACATAAGCTTCCCGTTATACAGCTCAC
Found at i:5258754 original size:35 final size:35
Alignment explanation
Indices: 5258714--5258788 Score: 114
Period size: 35 Copynumber: 2.1 Consensus size: 35
5258704 CTCTAACAAT
**
5258714 CATTTCCATGATGCTGCTACGTAGAGCCAGTACAC
1 CATTTCCATGATGCCACTACGTAGAGCCAGTACAC
* *
5258749 CATTTCCATGATGCCACTCCGTAGAGCCAGTAGAC
1 CATTTCCATGATGCCACTACGTAGAGCCAGTACAC
5258784 CATTT
1 CATTT
5258789 TCGACCAAAC
Statistics
Matches: 36, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
35 36 1.00
ACGTcount: A:0.25, C:0.29, G:0.19, T:0.27
Consensus pattern (35 bp):
CATTTCCATGATGCCACTACGTAGAGCCAGTACAC
Found at i:5262503 original size:86 final size:83
Alignment explanation
Indices: 5262322--5262630 Score: 298
Period size: 87 Copynumber: 3.6 Consensus size: 83
5262312 TCTAAAAGTG
* ** * * * *
5262322 AATAAAATATGTTTTGGGATTTATTCCAGCCATTCAATAGATTTTATTCCAATTTGATTTTATTT
1 AATAAAATCTGTTTCAGGATTTATTCC-GCCGTTCAACAGATTTTATT-CATTTTAATTTTATTT
5262387 CCAAAACGAGAATTTAAATTAA
64 CCAAAACGAGAA-TTAAATT-A
* * * *
5262409 AATAAAATCTATTTCAGGATTTATTCACGCCGTTCAACATATTTTATTCTTTTTTATTTTATTTC
1 AATAAAATCTGTTTCAGGATTTATTC-CGCCGTTCAACAGATTTTATTCATTTTAATTTTATTTC
5262474 CAAAACGAGAAATTAAAATTA
65 CAAAACGAG-AATT-AAATTA
* *
5262495 AATAAAATCTGTTTCAGGATTTATTCCCGCCGATT-AACAAGATTCTATTCGATTTTAATTTTGT
1 AATAAAATCTGTTTCAGGATTTATT-CCGCCG-TTCAAC-AGATTTTATTC-ATTTTAATTTTAT
* **
5262559 TT-CTAAATTAGAATTAAATTA
62 TTCCAAAACGAGAATTAAATTA
* * * * *
5262580 AATAAAATCTGTTACGGGATTTATTCTCGTCATTTAACAAGATTTTATTCA
1 AATAAAATCTGTTTCAGGATTTATTC-CGCCGTTCAAC-AGATTTTATTCA
5262631 ATATCAATTT
Statistics
Matches: 189, Mismatches: 24, Indels: 21
0.81 0.10 0.09
Matches are distributed among these distances:
84 4 0.02
85 46 0.24
86 62 0.33
87 64 0.34
88 13 0.07
ACGTcount: A:0.35, C:0.13, G:0.10, T:0.42
Consensus pattern (83 bp):
AATAAAATCTGTTTCAGGATTTATTCCGCCGTTCAACAGATTTTATTCATTTTAATTTTATTTCC
AAAACGAGAATTAAATTA
Found at i:5262603 original size:85 final size:85
Alignment explanation
Indices: 5262322--5262630 Score: 299
Period size: 86 Copynumber: 3.6 Consensus size: 85
5262312 TCTAAAAGTG
* ** * * *
5262322 AATAAAATATGTTTTGGGATTTATTC-CAGCC-ATTCAA-TAGATTTTATTCCAATTTGATTTTA
1 AATAAAATCTGTTTCAGGATTTATTCAC-GCCGATT-AACAAGATTTTATT-CATTTTAATTTTA
5262384 TTTCCAAAACGAGAATTTAAATTAA
63 TTTCCAAAACGAGAA-TTAAATT-A
* * * *
5262409 AATAAAATCTATTTCAGGATTTATTCACGCCG-TTCAAC-ATATTTTATTCTTTTTTATTTTATT
1 AATAAAATCTGTTTCAGGATTTATTCACGCCGATT-AACAAGATTTTATTCATTTTAATTTTATT
5262472 TCCAAAACGAGAAATTAAAATTA
65 TCCAAAACGAG-AATT-AAATTA
* * *
5262495 AATAAAATCTGTTTCAGGATTTATTCCCGCCGATTAACAAGATTCTATTCGATTTTAATTTTGTT
1 AATAAAATCTGTTTCAGGATTTATTCACGCCGATTAACAAGATTTTATTC-ATTTTAATTTTATT
* **
5262560 T-CTAAATTAGAATTAAATTA
65 TCCAAAACGAGAATTAAATTA
* * * *
5262580 AATAAAATCTGTTACGGGATTTATTCTCGTC-ATTTAACAAGATTTTATTCA
1 AATAAAATCTGTTTCAGGATTTATTCACGCCGA-TTAACAAGATTTTATTCA
5262631 ATATCAATTT
Statistics
Matches: 190, Mismatches: 23, Indels: 21
0.81 0.10 0.09
Matches are distributed among these distances:
84 2 0.01
85 49 0.26
86 63 0.33
87 63 0.33
88 13 0.07
ACGTcount: A:0.35, C:0.13, G:0.10, T:0.42
Consensus pattern (85 bp):
AATAAAATCTGTTTCAGGATTTATTCACGCCGATTAACAAGATTTTATTCATTTTAATTTTATTT
CCAAAACGAGAATTAAATTA
Found at i:5262640 original size:85 final size:85
Alignment explanation
Indices: 5262484--5262645 Score: 220
Period size: 85 Copynumber: 1.9 Consensus size: 85
5262474 CAAAACGAGA
* * *
5262484 AATTAAAATTAAATAAAATCTGTTTCAGGATTTATTCCCGCCGATTAACAAGATTCTATTCGATT
1 AATTAAAATTAAATAAAATCTGTTACAGGATTTATTCCCGCCGATTAACAAGATTCTATTCAATA
*
5262549 TTAATTTTGTTTCTAAATTAG
66 TCAA-TTTGTTTCTAAATTAG
* * * *
5262570 AATT-AAATTAAATAAAATCTGTTACGGGATTTATTCTCGTC-ATTTAACAAGATTTTATTCAAT
1 AATTAAAATTAAATAAAATCTGTTACAGGATTTATTCCCGCCGA-TTAACAAGATTCTATTCAAT
5262633 ATCAATTTGTTTC
65 ATCAATTTGTTTC
5262646 CAAACGAAAA
Statistics
Matches: 67, Mismatches: 8, Indels: 4
0.85 0.10 0.05
Matches are distributed among these distances:
84 9 0.13
85 54 0.81
86 4 0.06
ACGTcount: A:0.35, C:0.12, G:0.10, T:0.43
Consensus pattern (85 bp):
AATTAAAATTAAATAAAATCTGTTACAGGATTTATTCCCGCCGATTAACAAGATTCTATTCAATA
TCAATTTGTTTCTAAATTAG
Found at i:5267632 original size:14 final size:14
Alignment explanation
Indices: 5267613--5267642 Score: 60
Period size: 14 Copynumber: 2.1 Consensus size: 14
5267603 TATTATATAT
5267613 ATCCGGTCATGCAA
1 ATCCGGTCATGCAA
5267627 ATCCGGTCATGCAA
1 ATCCGGTCATGCAA
5267641 AT
1 AT
5267643 TAACTTCTAT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.30, C:0.27, G:0.20, T:0.23
Consensus pattern (14 bp):
ATCCGGTCATGCAA
Found at i:5269535 original size:41 final size:43
Alignment explanation
Indices: 5269434--5269545 Score: 138
Period size: 41 Copynumber: 2.7 Consensus size: 43
5269424 ATATCGAACA
* * * **
5269434 ATGCCAATGTCCCAGACGTGGTCTTACATGCTATCTCATATCG
1 ATGCCAATGTCCCAGACATGGTCTTACACGCAATCAAATATCG
* *
5269477 ATGCCACTGTCCCAGACAAGGTCTTACACG-AATCAAATA-CG
1 ATGCCAATGTCCCAGACATGGTCTTACACGCAATCAAATATCG
*
5269518 ATGCCAATGTCCTAGACATGGTCTTACA
1 ATGCCAATGTCCCAGACATGGTCTTACA
5269546 TGTAAACACA
Statistics
Matches: 59, Mismatches: 10, Indels: 2
0.83 0.14 0.03
Matches are distributed among these distances:
41 27 0.46
42 6 0.10
43 26 0.44
ACGTcount: A:0.29, C:0.28, G:0.18, T:0.26
Consensus pattern (43 bp):
ATGCCAATGTCCCAGACATGGTCTTACACGCAATCAAATATCG
Found at i:5269584 original size:84 final size:84
Alignment explanation
Indices: 5269434--5269592 Score: 198
Period size: 84 Copynumber: 1.9 Consensus size: 84
5269424 ATATCGAACA
* * *
5269434 ATGCCAATGTCCCAGACGTGGTCTTACATGCTATCTCATATCGATGCCACTGTCCCAGACAAGGT
1 ATGCCAATGTCCCAGACATGGTCTTACATGCTAACACATATCGATGCCACTGTCCCAGACAAGGT
5269499 CTTACACGAATCAAATACG
66 CTTACACGAATCAAATACG
* * * **
5269518 ATGCCAATGTCCTAGACATGGTCTTACATG-TAAACACA-AGTCGATGCTGAC-GTCCTAGACGT
1 ATGCCAATGTCCCAGACATGGTCTTACATGCT-AACACATA-TCGATGC-CACTGTCCCAGACAA
5269580 GGTCTTACACGAA
63 GGTCTTACACGAA
5269593 AACACATATC
Statistics
Matches: 64, Mismatches: 8, Indels: 6
0.82 0.10 0.08
Matches are distributed among these distances:
83 2 0.03
84 60 0.94
85 2 0.03
ACGTcount: A:0.29, C:0.26, G:0.19, T:0.25
Consensus pattern (84 bp):
ATGCCAATGTCCCAGACATGGTCTTACATGCTAACACATATCGATGCCACTGTCCCAGACAAGGT
CTTACACGAATCAAATACG
Found at i:5288131 original size:27 final size:27
Alignment explanation
Indices: 5288098--5288247 Score: 151
Period size: 27 Copynumber: 5.6 Consensus size: 27
5288088 AGACCCTAAA
*
5288098 ATAAGGTAAAATGACCAAAATACCCCT
1 ATAAGGTAAAATGACCGAAATACCCCT
* *
5288125 AGAAGGTAAAATGACTGAAATACCCCT
1 ATAAGGTAAAATGACCGAAATACCCCT
* * *
5288152 ATAGGGTAAAATAACCGAAATACCCCA
1 ATAAGGTAAAATGACCGAAATACCCCT
* * * *
5288179 ATAGGGTAAAATAATCGAAATACCCCC
1 ATAAGGTAAAATGACCGAAATACCCCT
**
5288206 AT-AGGATAAAATGACAAAAATA-CCCT
1 ATAAGG-TAAAATGACCGAAATACCCCT
*
5288232 CATATGGTAAAATGAC
1 -ATAAGGTAAAATGAC
5288248 TGTTATACCC
Statistics
Matches: 103, Mismatches: 17, Indels: 6
0.82 0.13 0.05
Matches are distributed among these distances:
26 5 0.05
27 96 0.93
28 2 0.02
ACGTcount: A:0.47, C:0.19, G:0.15, T:0.19
Consensus pattern (27 bp):
ATAAGGTAAAATGACCGAAATACCCCT
Found at i:5288176 original size:54 final size:54
Alignment explanation
Indices: 5288102--5288260 Score: 178
Period size: 54 Copynumber: 2.9 Consensus size: 54
5288092 CCTAAAATAA
*
5288102 GGTAAAATGACCAAAATACCCCTAGAAGGTAAAATGACTGAAATACCCCTATAG
1 GGTAAAATGACCAAAATACCCCTATAAGGTAAAATGACTGAAATACCCCTATAG
* * * * * *
5288156 GGTAAAATAACCGAAATACCCCAATAGGGTAAAAT-AATCGAAATACCCCCATAG
1 GGTAAAATGACCAAAATACCCCTATAAGGTAAAATGACT-GAAATACCCCTATAG
* * * **
5288210 GATAAAATGACAAAAATA-CCCTCATATGGTAAAATGACTGTTATACCCCTA
1 GGTAAAATGACCAAAATACCCCT-ATAAGGTAAAATGACTGAAATACCCCTA
5288261 GTATATGAAA
Statistics
Matches: 85, Mismatches: 17, Indels: 6
0.79 0.16 0.06
Matches are distributed among these distances:
53 5 0.06
54 78 0.92
55 2 0.02
ACGTcount: A:0.45, C:0.21, G:0.14, T:0.20
Consensus pattern (54 bp):
GGTAAAATGACCAAAATACCCCTATAAGGTAAAATGACTGAAATACCCCTATAG
Found at i:5291362 original size:39 final size:39
Alignment explanation
Indices: 5291308--5291747 Score: 637
Period size: 39 Copynumber: 11.2 Consensus size: 39
5291298 AAATCTTATA
5291308 CAGTATAATCAGTGGATAATGCTCGTTTGAGCAAGCATT
1 CAGTATAATCAGTGGATAATGCTCGTTTGAGCAAGCATT
*
5291347 CAGTATAATCAGTGGATAATGTTCGTTTGAGCAAGCATT
1 CAGTATAATCAGTGGATAATGCTCGTTTGAGCAAGCATT
* * *
5291386 CAGCATAATCAGTGGGTAATGCTCGTTTAAGCAAGCATT
1 CAGTATAATCAGTGGATAATGCTCGTTTGAGCAAGCATT
* * *
5291425 CAGCATAATCAGTGGGTAATGCTCGTTTAAGCAAGCATT
1 CAGTATAATCAGTGGATAATGCTCGTTTGAGCAAGCATT
** *
5291464 CAACATAATCAGTGGATATTGCTCGTTTGAGCAAGCATT
1 CAGTATAATCAGTGGATAATGCTCGTTTGAGCAAGCATT
* **
5291503 CAGCATAATCAGTGGATAATGCTTATTTGAGCAAGCATT
1 CAGTATAATCAGTGGATAATGCTCGTTTGAGCAAGCATT
* * *
5291542 CAGTATAATTAATGGATAATGCTAGTTTGAGCAAGCATT
1 CAGTATAATCAGTGGATAATGCTCGTTTGAGCAAGCATT
* *
5291581 CAGCATAATCAGTGGATAATGCTCATTTTGAGCAAGCATT
1 CAGTATAATCAGTGGATAATGCTC-GTTTGAGCAAGCATT
* *
5291621 CAATATAATCAGTGGATAATGCTCGTTTGAGCAAACATT
1 CAGTATAATCAGTGGATAATGCTCGTTTGAGCAAGCATT
*
5291660 CAGTATAATCAGTGGATAATGCTCGTTTGAGCAAACATT
1 CAGTATAATCAGTGGATAATGCTCGTTTGAGCAAGCATT
* * * *
5291699 CAATATAATCAGTGGATATTGCTCGTTTGAACAAATCATT
1 CAGTATAATCAGTGGATAATGCTCGTTTGAGC-AAGCATT
5291739 CAGTATAAT
1 CAGTATAAT
5291748 TAGTATTCTA
Statistics
Matches: 366, Mismatches: 33, Indels: 3
0.91 0.08 0.01
Matches are distributed among these distances:
39 316 0.86
40 50 0.14
ACGTcount: A:0.33, C:0.15, G:0.20, T:0.31
Consensus pattern (39 bp):
CAGTATAATCAGTGGATAATGCTCGTTTGAGCAAGCATT
Found at i:5299293 original size:63 final size:63
Alignment explanation
Indices: 5299216--5299358 Score: 180
Period size: 63 Copynumber: 2.3 Consensus size: 63
5299206 TGGTAGTCCA
* * * *
5299216 TGTAACTCACTGTTTTTGAATTGGAGGCACACGAGCTAGGGGCATGGGCATGTGTCTAAGCT-G
1 TGTAACTCACTGTTTTAGAATTAGAGGCACACGAGCTAGGGACATGGACATGTGTC-AAGCTCG
* * * * *
5299279 TGTAACTCACTGTTTTAGATTTAGAGTCACACGGGCTAGGGACATGGACATGTGTCCAGGTCG
1 TGTAACTCACTGTTTTAGAATTAGAGGCACACGAGCTAGGGACATGGACATGTGTCAAGCTCG
*
5299342 TGTAACTCACTATTTTA
1 TGTAACTCACTGTTTTA
5299359 AGCCACATGG
Statistics
Matches: 69, Mismatches: 10, Indels: 2
0.85 0.12 0.02
Matches are distributed among these distances:
62 3 0.04
63 66 0.96
ACGTcount: A:0.24, C:0.18, G:0.27, T:0.31
Consensus pattern (63 bp):
TGTAACTCACTGTTTTAGAATTAGAGGCACACGAGCTAGGGACATGGACATGTGTCAAGCTCG
Found at i:5300202 original size:22 final size:22
Alignment explanation
Indices: 5300177--5300230 Score: 63
Period size: 22 Copynumber: 2.5 Consensus size: 22
5300167 ATAGATATCT
5300177 TATTGTTTGTTTAATTTCAAAC
1 TATTGTTTGTTTAATTTCAAAC
* ** *
5300199 TATTGTATGTTTTGTTTCAGAC
1 TATTGTTTGTTTAATTTCAAAC
*
5300221 TATGGTTTGT
1 TATTGTTTGT
5300231 AAACTTGAAT
Statistics
Matches: 26, Mismatches: 6, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
22 26 1.00
ACGTcount: A:0.20, C:0.07, G:0.17, T:0.56
Consensus pattern (22 bp):
TATTGTTTGTTTAATTTCAAAC
Found at i:5302535 original size:22 final size:21
Alignment explanation
Indices: 5302488--5302537 Score: 55
Period size: 22 Copynumber: 2.3 Consensus size: 21
5302478 TTCCTAAAAT
* *
5302488 ATTATTTATTTAATCAATTAT
1 ATTATTTATTTAATCAACTAA
* *
5302509 TTTATTTAGTTTAATTAACTAA
1 ATTATTTA-TTTAATCAACTAA
5302531 ATTATTT
1 ATTATTT
5302538 TTTCAATTAA
Statistics
Matches: 23, Mismatches: 5, Indels: 1
0.79 0.17 0.03
Matches are distributed among these distances:
21 7 0.30
22 16 0.70
ACGTcount: A:0.36, C:0.04, G:0.02, T:0.58
Consensus pattern (21 bp):
ATTATTTATTTAATCAACTAA
Found at i:5302550 original size:17 final size:17
Alignment explanation
Indices: 5302528--5302560 Score: 66
Period size: 17 Copynumber: 1.9 Consensus size: 17
5302518 TTTAATTAAC
5302528 TAAATTATTTTTTCAAT
1 TAAATTATTTTTTCAAT
5302545 TAAATTATTTTTTCAA
1 TAAATTATTTTTTCAA
5302561 CCCAATTCTA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.36, C:0.06, G:0.00, T:0.58
Consensus pattern (17 bp):
TAAATTATTTTTTCAAT
Found at i:5302567 original size:17 final size:17
Alignment explanation
Indices: 5302529--5302567 Score: 51
Period size: 17 Copynumber: 2.3 Consensus size: 17
5302519 TTAATTAACT
**
5302529 AAATTATTTTTTCAATT
1 AAATTATTTTTTCAACC
5302546 AAATTATTTTTTCAACC
1 AAATTATTTTTTCAACC
*
5302563 CAATT
1 AAATT
5302568 CTAATTCTGT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.36, C:0.13, G:0.00, T:0.51
Consensus pattern (17 bp):
AAATTATTTTTTCAACC
Found at i:5305690 original size:14 final size:14
Alignment explanation
Indices: 5305671--5305702 Score: 55
Period size: 14 Copynumber: 2.3 Consensus size: 14
5305661 CCTTTCAAAT
*
5305671 ATTTTATTTTTAAC
1 ATTTTATTTTTAAA
5305685 ATTTTATTTTTAAA
1 ATTTTATTTTTAAA
5305699 ATTT
1 ATTT
5305703 ATAATCTTAC
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 17 1.00
ACGTcount: A:0.31, C:0.03, G:0.00, T:0.66
Consensus pattern (14 bp):
ATTTTATTTTTAAA
Found at i:5307338 original size:266 final size:266
Alignment explanation
Indices: 5306864--5307400 Score: 1074
Period size: 266 Copynumber: 2.0 Consensus size: 266
5306854 ATCAAGTCTT
5306864 CCCTGACAGTAGAGCAACCAGCCAAGTTGTATGTTTGCAGGACCCGTCCAACCCAACACTGAGCT
1 CCCTGACAGTAGAGCAACCAGCCAAGTTGTATGTTTGCAGGACCCGTCCAACCCAACACTGAGCT
5306929 CCATTTCTGAGAGGACAATAGACTGCCTAAACTGATCATCAGTTCCAAGGGATGCCATAGTCATT
66 CCATTTCTGAGAGGACAATAGACTGCCTAAACTGATCATCAGTTCCAAGGGATGCCATAGTCATT
5306994 TTGTTTTAGTGGGTCCTATGATACTGTCTCATGCTCTTCAGCAATCCTTTCTTTAACACGCTGCA
131 TTGTTTTAGTGGGTCCTATGATACTGTCTCATGCTCTTCAGCAATCCTTTCTTTAACACGCTGCA
5307059 AAAGTTCCTCATAGACTTTGGAGGACTCGGAACTGAAGTTTTCCATTGCCTCAAATATGCGTTGC
196 AAAGTTCCTCATAGACTTTGGAGGACTCGGAACTGAAGTTTTCCATTGCCTCAAATATGCGTTGC
5307124 AAGCCC
261 AAGCCC
5307130 CCCTGACAGTAGAGCAACCAGCCAAGTTGTATGTTTGCAGGACCCGTCCAACCCAACACTGAGCT
1 CCCTGACAGTAGAGCAACCAGCCAAGTTGTATGTTTGCAGGACCCGTCCAACCCAACACTGAGCT
5307195 CCATTTCTGAGAGGACAATAGACTGCCTAAACTGATCATCAGTTCCAAGGGATGCCATAGTCATT
66 CCATTTCTGAGAGGACAATAGACTGCCTAAACTGATCATCAGTTCCAAGGGATGCCATAGTCATT
5307260 TTGTTTTAGTGGGTCCTATGATACTGTCTCATGCTCTTCAGCAATCCTTTCTTTAACACGCTGCA
131 TTGTTTTAGTGGGTCCTATGATACTGTCTCATGCTCTTCAGCAATCCTTTCTTTAACACGCTGCA
5307325 AAAGTTCCTCATAGACTTTGGAGGACTCGGAACTGAAGTTTTCCATTGCCTCAAATATGCGTTGC
196 AAAGTTCCTCATAGACTTTGGAGGACTCGGAACTGAAGTTTTCCATTGCCTCAAATATGCGTTGC
5307390 AAGCCC
261 AAGCCC
5307396 CCCTG
1 CCCTG
5307401 CAAACTACTG
Statistics
Matches: 271, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
266 271 1.00
ACGTcount: A:0.26, C:0.26, G:0.20, T:0.28
Consensus pattern (266 bp):
CCCTGACAGTAGAGCAACCAGCCAAGTTGTATGTTTGCAGGACCCGTCCAACCCAACACTGAGCT
CCATTTCTGAGAGGACAATAGACTGCCTAAACTGATCATCAGTTCCAAGGGATGCCATAGTCATT
TTGTTTTAGTGGGTCCTATGATACTGTCTCATGCTCTTCAGCAATCCTTTCTTTAACACGCTGCA
AAAGTTCCTCATAGACTTTGGAGGACTCGGAACTGAAGTTTTCCATTGCCTCAAATATGCGTTGC
AAGCCC
Found at i:5312253 original size:31 final size:34
Alignment explanation
Indices: 5312218--5312287 Score: 101
Period size: 35 Copynumber: 2.1 Consensus size: 34
5312208 ACTAAACAAT
*
5312218 TTGATTTT-CTTTTA-AAAAC-ACATTCAAAGAA
1 TTGATTTTGCTTTAAGAAAACAACATTCAAAGAA
5312249 TTGATTTTGCTTTAAGAAAACAGACATTCAAAGAA
1 TTGATTTTGCTTTAAGAAAACA-ACATTCAAAGAA
5312284 TTGA
1 TTGA
5312288 CAAATTTTTT
Statistics
Matches: 34, Mismatches: 1, Indels: 4
0.87 0.03 0.10
Matches are distributed among these distances:
31 8 0.24
32 5 0.15
33 5 0.15
35 16 0.47
ACGTcount: A:0.41, C:0.11, G:0.11, T:0.36
Consensus pattern (34 bp):
TTGATTTTGCTTTAAGAAAACAACATTCAAAGAA
Found at i:5312814 original size:26 final size:26
Alignment explanation
Indices: 5312763--5312816 Score: 81
Period size: 26 Copynumber: 2.1 Consensus size: 26
5312753 ACATTCAATA
*
5312763 TAATCCATTATTCTTGTTAAATAATG
1 TAATCCATTATTCTTGTTAAAGAATG
* *
5312789 TAATTCATTATTCTTGTTAAGGAATG
1 TAATCCATTATTCTTGTTAAAGAATG
5312815 TA
1 TA
5312817 CTAGTATTTG
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
26 25 1.00
ACGTcount: A:0.33, C:0.09, G:0.11, T:0.46
Consensus pattern (26 bp):
TAATCCATTATTCTTGTTAAAGAATG
Found at i:5324734 original size:23 final size:23
Alignment explanation
Indices: 5324704--5324747 Score: 88
Period size: 23 Copynumber: 1.9 Consensus size: 23
5324694 GTTAATTCAC
5324704 ATGTTAGTTAATTTTTTTTCTAT
1 ATGTTAGTTAATTTTTTTTCTAT
5324727 ATGTTAGTTAATTTTTTTTCT
1 ATGTTAGTTAATTTTTTTTCT
5324748 TTTTTTCTTT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 21 1.00
ACGTcount: A:0.20, C:0.05, G:0.09, T:0.66
Consensus pattern (23 bp):
ATGTTAGTTAATTTTTTTTCTAT
Found at i:5328438 original size:18 final size:20
Alignment explanation
Indices: 5328400--5328439 Score: 57
Period size: 18 Copynumber: 2.1 Consensus size: 20
5328390 AATTTTACTA
5328400 TTGATATAATATTAAAAATT
1 TTGATATAATATTAAAAATT
*
5328420 TTGA-ATAAT-TTAAACATT
1 TTGATATAATATTAAAAATT
5328438 TT
1 TT
5328440 AGTAGATTTC
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
18 10 0.53
19 5 0.26
20 4 0.21
ACGTcount: A:0.45, C:0.03, G:0.05, T:0.47
Consensus pattern (20 bp):
TTGATATAATATTAAAAATT
Found at i:5330040 original size:18 final size:18
Alignment explanation
Indices: 5330019--5330054 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
5330009 AACTGATAAT
5330019 ACATATATAAATTCATTC
1 ACATATATAAATTCATTC
*
5330037 ACATATATATATTCATTC
1 ACATATATAAATTCATTC
5330055 CGAACACATC
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.42, C:0.17, G:0.00, T:0.42
Consensus pattern (18 bp):
ACATATATAAATTCATTC
Found at i:5330212 original size:28 final size:28
Alignment explanation
Indices: 5330141--5330239 Score: 128
Period size: 28 Copynumber: 3.6 Consensus size: 28
5330131 ACACGTGACC
* * * *
5330141 AATTTGCTCACACAACCTCTAATATTCG
1 AATTTGCTCACACAAGCTGTGATATTTG
*
5330169 AATTTGCTCACACAAGTTGTGATATTTG
1 AATTTGCTCACACAAGCTGTGATATTTG
5330197 AATTTGCTCACACAAGCTGTGATATTTG
1 AATTTGCTCACACAAGCTGTGATATTTG
**
5330225 -GGTTGCTCACACAAG
1 AATTTGCTCACACAAG
5330240 TGTAGGTTAG
Statistics
Matches: 63, Mismatches: 8, Indels: 1
0.88 0.11 0.01
Matches are distributed among these distances:
27 13 0.21
28 50 0.79
ACGTcount: A:0.29, C:0.21, G:0.16, T:0.33
Consensus pattern (28 bp):
AATTTGCTCACACAAGCTGTGATATTTG
Found at i:5331819 original size:4 final size:4
Alignment explanation
Indices: 5331798--5331837 Score: 53
Period size: 4 Copynumber: 10.0 Consensus size: 4
5331788 ATAGGCAAAT
* * *
5331798 GAAA CAAA GAAG GAAA GAAA GAAA GAAG GAAA GAAA GAAA
1 GAAA GAAA GAAA GAAA GAAA GAAA GAAA GAAA GAAA GAAA
5331838 AGGGAAAATT
Statistics
Matches: 30, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
4 30 1.00
ACGTcount: A:0.70, C:0.03, G:0.28, T:0.00
Consensus pattern (4 bp):
GAAA
Found at i:5331822 original size:16 final size:16
Alignment explanation
Indices: 5331798--5331837 Score: 71
Period size: 16 Copynumber: 2.5 Consensus size: 16
5331788 ATAGGCAAAT
*
5331798 GAAACAAAGAAGGAAA
1 GAAAGAAAGAAGGAAA
5331814 GAAAGAAAGAAGGAAA
1 GAAAGAAAGAAGGAAA
5331830 GAAAGAAA
1 GAAAGAAA
5331838 AGGGAAAATT
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
16 23 1.00
ACGTcount: A:0.70, C:0.03, G:0.28, T:0.00
Consensus pattern (16 bp):
GAAAGAAAGAAGGAAA
Found at i:5332981 original size:23 final size:21
Alignment explanation
Indices: 5332954--5333037 Score: 89
Period size: 23 Copynumber: 3.9 Consensus size: 21
5332944 TCTACCGATT
5332954 AGGCACTTTATGTGTCGTGTATC
1 AGGCACTTTATGTGTCGT-T-TC
5332977 AGGCACTTTATGTGTCGTATTTC
1 AGGCACTTTATGTGTCG--TTTC
* ** *
5333000 AGGCACCTCGTGTGTCGTTTT
1 AGGCACTTTATGTGTCGTTTC
5333021 AGGCAC-TTATGTGTCGT
1 AGGCACTTTATGTGTCGT
5333038 ATACTGATCA
Statistics
Matches: 53, Mismatches: 6, Indels: 7
0.80 0.09 0.11
Matches are distributed among these distances:
20 9 0.17
21 9 0.17
23 33 0.62
24 1 0.02
25 1 0.02
ACGTcount: A:0.15, C:0.19, G:0.26, T:0.39
Consensus pattern (21 bp):
AGGCACTTTATGTGTCGTTTC
Found at i:5334045 original size:19 final size:19
Alignment explanation
Indices: 5334021--5334061 Score: 55
Period size: 19 Copynumber: 2.2 Consensus size: 19
5334011 TTAACATAAA
*
5334021 TAACTAATCATAATTAACT
1 TAACTAAACATAATTAACT
* *
5334040 TAACTAAACCTTATTAACT
1 TAACTAAACATAATTAACT
5334059 TAA
1 TAA
5334062 TATAATGATG
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.46, C:0.17, G:0.00, T:0.37
Consensus pattern (19 bp):
TAACTAAACATAATTAACT
Found at i:5347016 original size:39 final size:39
Alignment explanation
Indices: 5346987--5347180 Score: 253
Period size: 39 Copynumber: 5.0 Consensus size: 39
5346977 ATCCTATTAC
*
5346987 ACATATAATCACCTAACATTCAAGCATATATCACAATAT
1 ACATATAATCACATAACATTCAAGCATATATCACAATAT
* * * * *
5347026 ATATTTAATCTCATAACATTTAAGCATATATCACAACAT
1 ACATATAATCACATAACATTCAAGCATATATCACAATAT
* *
5347065 TCATATAATCACATAATATTCAAGCATATATCACAATAT
1 ACATATAATCACATAACATTCAAGCATATATCACAATAT
* * *
5347104 ACATATAATCTCATAAAATTTAAGCATATATCACAATAT
1 ACATATAATCACATAACATTCAAGCATATATCACAATAT
** * *
5347143 ACATATAATCTTATAACATTTAAACATATATCACAATA
1 ACATATAATCACATAACATTCAAGCATATATCACAATA
5347181 ATAAAAAACA
Statistics
Matches: 135, Mismatches: 20, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
39 135 1.00
ACGTcount: A:0.47, C:0.18, G:0.02, T:0.33
Consensus pattern (39 bp):
ACATATAATCACATAACATTCAAGCATATATCACAATAT
Found at i:5347102 original size:78 final size:78
Alignment explanation
Indices: 5346987--5347180 Score: 289
Period size: 78 Copynumber: 2.5 Consensus size: 78
5346977 ATCCTATTAC
* * * *
5346987 ACATATAATCACCTAACATTCAAGCATATATCACAATATATATTTAATCTCATAACATTTAAGCA
1 ACATATAATCACATAACATTCAAGCATATATCACAATATACATATAATCTCATAAAATTTAAGCA
5347052 TATATCACAACAT
66 TATATCACAACAT
* *
5347065 TCATATAATCACATAATATTCAAGCATATATCACAATATACATATAATCTCATAAAATTTAAGCA
1 ACATATAATCACATAACATTCAAGCATATATCACAATATACATATAATCTCATAAAATTTAAGCA
*
5347130 TATATCACAATAT
66 TATATCACAACAT
** * *
5347143 ACATATAATCTTATAACATTTAAACATATATCACAATA
1 ACATATAATCACATAACATTCAAGCATATATCACAATA
5347181 ATAAAAAACA
Statistics
Matches: 103, Mismatches: 13, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
78 103 1.00
ACGTcount: A:0.47, C:0.18, G:0.02, T:0.33
Consensus pattern (78 bp):
ACATATAATCACATAACATTCAAGCATATATCACAATATACATATAATCTCATAAAATTTAAGCA
TATATCACAACAT
Found at i:5349422 original size:242 final size:241
Alignment explanation
Indices: 5348991--5349631 Score: 953
Period size: 242 Copynumber: 2.6 Consensus size: 241
5348981 ACATTTTTAA
* * * *
5348991 AAAAACCATAAAAAAAATTACTGATATAACATGTCGCAAAATTTCGAACGCACTAAGGCTAAAAT
1 AAAAACCATAAAAAACATTAC-GATATAACATGTCGCAAAA-TTCTAACACTCTAAGGCTAAAAT
* * *
5349056 TCTTAAAATACCCTAAAACTCCTAGGCCTTATTTTAGGGTGTTACATACACATTCAAGATTGTCT
64 TCCTAAAATACCCTAAAACTCCTAGGCCCTATTTTGGGGTGTTACATACACATTCAAGATTGTCT
* * *
5349121 CTTATTAAATATTTTCCCAAGAAACACTCTAAGGTTAAAATTCATAAAATATCCCTAAAACCAT-
129 CTTATTAAATATTTTCCCAAGAAACAATCTAAGGCTAAAATTCATAAAATACCCCTAAAACCATG
* *
5349185 AAAAAACCATAAATATTTTCCCTAAAACAATCTAAGGCTTAAATTCCT
194 AAAAAACCATAAATATTTTCCCTAAAACAATCGAAGGCTAAAATTCCT
* * *
5349233 AAAAAGCATAAAAAACATTATCGATATATCATATCGCAAAATTCTAAACACTCTAAGGCTAAAAT
1 AAAAACCATAAAAAACATTA-CGATATAACATGTCGCAAAATTCT-AACACTCTAAGGCTAAAAT
* *
5349298 TCCTAAAATACCTTTAAAACTCCTAGGCCCTATTTTGGGGTCTTACATACACATTCAAGATTGTC
64 TCCTAAAATACC-CTAAAACTCCTAGGCCCTATTTTGGGGTGTTACATACACATTCAAGATTGTC
* *
5349363 TCTTATT-AATATTTTCCCAAGAAACAATCTAAGGCTAAAATTCCTAAAGTACCCCTAAAACCAT
128 TCTTATTAAATATTTTCCCAAGAAACAATCTAAGGCTAAAATTCATAAAATACCCCTAAAACCAT
* *
5349427 GAAAAAACCATAAATATTTTCCCTAAAACACTCGAAGGCTAAAATTTCT
193 GAAAAAACCATAAATATTTTCCCTAAAACAATCGAAGGCTAAAATTCCT
* * *
5349476 AAAAACCATAAAAAAACATTACCAATATACCATGTCGCAAAATTCCTAATACTCTAAGGCTAAAA
1 AAAAACCAT-AAAAAACATTA-CGATATAACATGTCGCAAAATT-CTAACACTCTAAGGCTAAAA
*
5349541 TTCCTAAAATACCCCTAAAACTCTTAGGCCCTATTTTGGGGTGTTACATACACATTCAAGATTGT
63 TTCCTAAAATA-CCCTAAAACTCCTAGGCCCTATTTTGGGGTGTTACATACACATTCAAGATTGT
*
5349606 CTCTTATTAAATATTTTTCCAAGAAA
127 CTCTTATTAAATATTTTCCCAAGAAA
5349632 TGATATTTAA
Statistics
Matches: 360, Mismatches: 31, Indels: 13
0.89 0.08 0.03
Matches are distributed among these distances:
241 3 0.01
242 115 0.32
243 108 0.30
244 114 0.32
245 20 0.06
ACGTcount: A:0.41, C:0.21, G:0.09, T:0.29
Consensus pattern (241 bp):
AAAAACCATAAAAAACATTACGATATAACATGTCGCAAAATTCTAACACTCTAAGGCTAAAATTC
CTAAAATACCCTAAAACTCCTAGGCCCTATTTTGGGGTGTTACATACACATTCAAGATTGTCTCT
TATTAAATATTTTCCCAAGAAACAATCTAAGGCTAAAATTCATAAAATACCCCTAAAACCATGAA
AAAACCATAAATATTTTCCCTAAAACAATCGAAGGCTAAAATTCCT
Found at i:5349590 original size:244 final size:243
Alignment explanation
Indices: 5348991--5349631 Score: 966
Period size: 244 Copynumber: 2.6 Consensus size: 243
5348981 ACATTTTTAA
* * * *
5348991 AAAAACCATAAAAAAA-ATTACTGATATAACATGTCGCAAAATTTCGAACGCACTAAGGCTAAAA
1 AAAAACCATAAAAAAACATTACCGATATAACATGTCGCAAAA-TTCTAACACTCTAAGGCTAAAA
* * *
5349055 TTCTTAAAATA-CCCTAAAACTCCTAGGCCTTATTTTAGGGTGTTACATACACATTCAAGATTGT
65 TTCCTAAAATACCCCTAAAACTCCTAGGCCCTATTTTGGGGTGTTACATACACATTCAAGATTGT
* * *
5349119 CTCTTATTAAATATTTTCCCAAGAAACACTCTAAGGTTAAAATTCATAAAATATCCCTAAAACCA
130 CTCTTATTAAATATTTTCCCAAGAAACAATCTAAGGCTAAAATTCATAAAATACCCCTAAAACCA
* *
5349184 TAAAAAACCATAAATATTTTCCCTAAAACAATCTAAGGCTTAAATTCCT
195 TAAAAAACCATAAATATTTTCCCTAAAACAATCGAAGGCTAAAATTCCT
* * * *
5349233 AAAAAGCAT-AAAAAACATTATCGATATATCATATCGCAAAATTCTAAACACTCTAAGGCTAAAA
1 AAAAACCATAAAAAAACATTACCGATATAACATGTCGCAAAATTCT-AACACTCTAAGGCTAAAA
** *
5349297 TTCCTAAAATACCTTTAAAACTCCTAGGCCCTATTTTGGGGTCTTACATACACATTCAAGATTGT
65 TTCCTAAAATACCCCTAAAACTCCTAGGCCCTATTTTGGGGTGTTACATACACATTCAAGATTGT
* *
5349362 CTCTTATT-AATATTTTCCCAAGAAACAATCTAAGGCTAAAATTCCTAAAGTACCCCTAAAACCA
130 CTCTTATTAAATATTTTCCCAAGAAACAATCTAAGGCTAAAATTCATAAAATACCCCTAAAACCA
* *
5349426 TGAAAAAACCATAAATATTTTCCCTAAAACACTCGAAGGCTAAAATTTCT
195 T-AAAAAACCATAAATATTTTCCCTAAAACAATCGAAGGCTAAAATTCCT
* * *
5349476 AAAAACCATAAAAAAACATTACCAATATACCATGTCGCAAAATTCCTAATACTCTAAGGCTAAAA
1 AAAAACCATAAAAAAACATTACCGATATAACATGTCGCAAAATT-CTAACACTCTAAGGCTAAAA
*
5349541 TTCCTAAAATACCCCTAAAACTCTTAGGCCCTATTTTGGGGTGTTACATACACATTCAAGATTGT
65 TTCCTAAAATACCCCTAAAACTCCTAGGCCCTATTTTGGGGTGTTACATACACATTCAAGATTGT
*
5349606 CTCTTATTAAATATTTTTCCAAGAAA
130 CTCTTATTAAATATTTTCCCAAGAAA
5349632 TGATATTTAA
Statistics
Matches: 358, Mismatches: 34, Indels: 11
0.89 0.08 0.03
Matches are distributed among these distances:
241 9 0.03
242 107 0.30
243 108 0.30
244 116 0.32
245 18 0.05
ACGTcount: A:0.41, C:0.21, G:0.09, T:0.29
Consensus pattern (243 bp):
AAAAACCATAAAAAAACATTACCGATATAACATGTCGCAAAATTCTAACACTCTAAGGCTAAAAT
TCCTAAAATACCCCTAAAACTCCTAGGCCCTATTTTGGGGTGTTACATACACATTCAAGATTGTC
TCTTATTAAATATTTTCCCAAGAAACAATCTAAGGCTAAAATTCATAAAATACCCCTAAAACCAT
AAAAAACCATAAATATTTTCCCTAAAACAATCGAAGGCTAAAATTCCT
Found at i:5350577 original size:21 final size:21
Alignment explanation
Indices: 5350551--5350590 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
5350541 CTAAAAGACG
5350551 CATAATATGACATGTTTATGC
1 CATAATATGACATGTTTATGC
* *
5350572 CATAATTTGACTTGTTTAT
1 CATAATATGACATGTTTAT
5350591 TTGTTGTTCC
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.30, C:0.12, G:0.12, T:0.45
Consensus pattern (21 bp):
CATAATATGACATGTTTATGC
Found at i:5351126 original size:13 final size:13
Alignment explanation
Indices: 5351108--5351133 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
5351098 AGTAGATGAG
5351108 GTTTTATTTTTAT
1 GTTTTATTTTTAT
5351121 GTTTTATTTTTAT
1 GTTTTATTTTTAT
5351134 TTCGTGTGTG
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:0.15, C:0.00, G:0.08, T:0.77
Consensus pattern (13 bp):
GTTTTATTTTTAT
Found at i:5362399 original size:21 final size:20
Alignment explanation
Indices: 5362365--5362404 Score: 55
Period size: 20 Copynumber: 1.9 Consensus size: 20
5362355 TCTTGAATCA
5362365 TTTCTAAACGATTTTAAATTG
1 TTTCTAAACGA-TTTAAATTG
5362386 TTTCTAAA-GCATTTAAATT
1 TTTCTAAACG-ATTTAAATT
5362405 ATTTTTTATG
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
20 9 0.50
21 9 0.50
ACGTcount: A:0.35, C:0.10, G:0.07, T:0.47
Consensus pattern (20 bp):
TTTCTAAACGATTTAAATTG
Found at i:5362684 original size:32 final size:32
Alignment explanation
Indices: 5362617--5362683 Score: 98
Period size: 32 Copynumber: 2.1 Consensus size: 32
5362607 TCCAAAATTT
* * *
5362617 AAATTTTAGCAAAAAAAATAAATTTTTATTAA
1 AAATTTTAGCAAAAAAAATAAAATTTAAGTAA
5362649 AAATTTTAGCAAAAAAAATTAAAATTTAAGTAA
1 AAATTTTAGCAAAAAAAA-TAAAATTTAAGTAA
5362682 AA
1 AA
5362684 TAAGGAAACT
Statistics
Matches: 31, Mismatches: 3, Indels: 1
0.89 0.09 0.03
Matches are distributed among these distances:
32 18 0.58
33 13 0.42
ACGTcount: A:0.60, C:0.03, G:0.04, T:0.33
Consensus pattern (32 bp):
AAATTTTAGCAAAAAAAATAAAATTTAAGTAA
Found at i:5377579 original size:16 final size:16
Alignment explanation
Indices: 5377558--5377588 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
5377548 ATAACCCTAG
5377558 TAATTATATTTTCATT
1 TAATTATATTTTCATT
*
5377574 TAATTATTTTTTCAT
1 TAATTATATTTTCAT
5377589 GTCCAAACAG
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:0.29, C:0.06, G:0.00, T:0.65
Consensus pattern (16 bp):
TAATTATATTTTCATT
Found at i:5377794 original size:16 final size:15
Alignment explanation
Indices: 5377764--5377793 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
5377754 GAAATAATTA
5377764 AACATAGTGATTTTT
1 AACATAGTGATTTTT
*
5377779 AACATCGTGATTTTT
1 AACATAGTGATTTTT
5377794 TTTATAATAT
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:0.30, C:0.10, G:0.13, T:0.47
Consensus pattern (15 bp):
AACATAGTGATTTTT
Found at i:5381920 original size:6 final size:6
Alignment explanation
Indices: 5381885--5381975 Score: 64
Period size: 6 Copynumber: 14.8 Consensus size: 6
5381875 TCTTTAACAT
*
5381885 TTTTTC TTTTATC TTCTTT- TGTTCTTC TTTTTC -TTTTC TTCTTTC TTTCGTC
1 TTTTTC TTTT-TC TT-TTTC T-TT-TTC TTTTTC TTTTTC TT-TTTC TTT-TTC
** *
5381937 TTTCAC -CTTTC -TTTTC TTTTTC TTTTTC TTTTTC TTTTT
1 TTTTTC TTTTTC TTTTTC TTTTTC TTTTTC TTTTTC TTTTT
5381976 GCTTGCTTCC
Statistics
Matches: 69, Mismatches: 7, Indels: 18
0.73 0.07 0.19
Matches are distributed among these distances:
5 11 0.16
6 34 0.49
7 21 0.30
8 3 0.04
ACGTcount: A:0.02, C:0.21, G:0.02, T:0.75
Consensus pattern (6 bp):
TTTTTC
Found at i:5381932 original size:18 final size:18
Alignment explanation
Indices: 5381898--5381974 Score: 72
Period size: 18 Copynumber: 4.4 Consensus size: 18
5381888 TTCTTTTATC
*
5381898 TTCTTTTGTTC-TTCTTT
1 TTCTTTTCTTCTTTCTTT
5381915 TTCTTTTCTTCTTTCTTT
1 TTCTTTTCTTCTTTCTTT
* **
5381933 CGTC-TTTCACCTTTC-TT
1 -TTCTTTTCTTCTTTCTTT
5381950 TTCTTTTTCTT-TTTCTTT
1 TTC-TTTTCTTCTTTCTTT
5381968 TTCTTTT
1 TTCTTTT
5381975 TGCTTGCTTC
Statistics
Matches: 48, Mismatches: 7, Indels: 10
0.74 0.11 0.15
Matches are distributed among these distances:
16 2 0.04
17 20 0.42
18 24 0.50
19 2 0.04
ACGTcount: A:0.01, C:0.22, G:0.03, T:0.74
Consensus pattern (18 bp):
TTCTTTTCTTCTTTCTTT
Found at i:5383929 original size:25 final size:25
Alignment explanation
Indices: 5383901--5383970 Score: 97
Period size: 25 Copynumber: 2.8 Consensus size: 25
5383891 AAAGCCATTA
5383901 ATCGGGAAGCTCATGAGAGC-AAATT
1 ATCGGGAAGCTCATGAGAGCTAAA-T
*
5383926 ATCGGGAAGCTCGTGAGAGCTAAAT
1 ATCGGGAAGCTCATGAGAGCTAAAT
* *
5383951 AACGGGAAGCTCAAGAGAGC
1 ATCGGGAAGCTCATGAGAGC
5383971 CATATATGCT
Statistics
Matches: 40, Mismatches: 4, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
25 37 0.93
26 3 0.08
ACGTcount: A:0.36, C:0.17, G:0.31, T:0.16
Consensus pattern (25 bp):
ATCGGGAAGCTCATGAGAGCTAAAT
Found at i:5390442 original size:12 final size:12
Alignment explanation
Indices: 5390422--5390460 Score: 53
Period size: 12 Copynumber: 3.2 Consensus size: 12
5390412 CGATACCAAT
5390422 AAATTTATTTTA
1 AAATTTATTTTA
*
5390434 AAATGTATTTT-
1 AAATTTATTTTA
5390445 AAATTTATATTTA
1 AAATTTAT-TTTA
5390458 AAA
1 AAA
5390461 ATTTTATTTG
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
11 7 0.30
12 13 0.57
13 3 0.13
ACGTcount: A:0.46, C:0.00, G:0.03, T:0.51
Consensus pattern (12 bp):
AAATTTATTTTA
Found at i:5390567 original size:58 final size:59
Alignment explanation
Indices: 5390463--5390586 Score: 162
Period size: 58 Copynumber: 2.1 Consensus size: 59
5390453 ATTTAAAAAT
*
5390463 TTTATTTGTACAAAAAAAATTAAAATATAATTTAAACTTAAATTTAAAATTTTTTGTTA
1 TTTATTTGTACAAAAAAAATTAAAATATAATTTAAACTTAAATTTAAAATTTTTTATTA
* * * ** *
5390522 TTTATTTGTACCAAAAAAA-T-AATTTTAATTTTAATTTTGAATTTAAAATTTTTTATTA
1 TTTATTTGTACAAAAAAAATTAAAATATAA-TTTAAACTTAAATTTAAAATTTTTTATTA
5390580 TTTATTT
1 TTTATTT
5390587 TGAATTATTA
Statistics
Matches: 57, Mismatches: 7, Indels: 3
0.85 0.10 0.04
Matches are distributed among these distances:
57 6 0.11
58 33 0.58
59 18 0.32
ACGTcount: A:0.42, C:0.03, G:0.03, T:0.52
Consensus pattern (59 bp):
TTTATTTGTACAAAAAAAATTAAAATATAATTTAAACTTAAATTTAAAATTTTTTATTA
Found at i:5403769 original size:31 final size:28
Alignment explanation
Indices: 5403722--5403791 Score: 86
Period size: 31 Copynumber: 2.4 Consensus size: 28
5403712 GTCATCCAAC
* * *
5403722 TTTTAAATCTTACAAAATTATCACTTACA
1 TTTTAAGTGTTACAAAATAATCACTTA-A
5403751 TTATTAAGGTGTTACAAAATAATCACTTAA
1 TT-TTAA-GTGTTACAAAATAATCACTTAA
5403781 TTTTAAGTGTT
1 TTTTAAGTGTT
5403792 GTTTATAGTG
Statistics
Matches: 36, Mismatches: 3, Indels: 5
0.82 0.07 0.11
Matches are distributed among these distances:
28 5 0.14
29 6 0.17
30 7 0.19
31 18 0.50
ACGTcount: A:0.39, C:0.11, G:0.07, T:0.43
Consensus pattern (28 bp):
TTTTAAGTGTTACAAAATAATCACTTAA
Found at i:5407344 original size:25 final size:25
Alignment explanation
Indices: 5407299--5407364 Score: 71
Period size: 25 Copynumber: 2.7 Consensus size: 25
5407289 GTCGTTAAGG
* *
5407299 TTACCGATTC-CAGCTCTTATGAGC
1 TTACCGATACTCAGCTCGTATGAGC
*
5407323 TTACCGATACTCAGCTCGTATGAGT
1 TTACCGATACTCAGCTCGTATGAGC
* * *
5407348 TTATCGTTATTCAGCTC
1 TTACCGATACTCAGCTC
5407365 AGAAGAGCTT
Statistics
Matches: 35, Mismatches: 6, Indels: 1
0.83 0.14 0.02
Matches are distributed among these distances:
24 9 0.26
25 26 0.74
ACGTcount: A:0.21, C:0.26, G:0.17, T:0.36
Consensus pattern (25 bp):
TTACCGATACTCAGCTCGTATGAGC
Found at i:5408259 original size:25 final size:25
Alignment explanation
Indices: 5408231--5408280 Score: 73
Period size: 25 Copynumber: 2.0 Consensus size: 25
5408221 CAGGTAAGGC
5408231 TCCTTCTCCTTCTTCCATTATTCAT
1 TCCTTCTCCTTCTTCCATTATTCAT
* * *
5408256 TCCTTTTCCTTCTTCCGTTCTTCAT
1 TCCTTCTCCTTCTTCCATTATTCAT
5408281 CTTCTCTTCG
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
25 22 1.00
ACGTcount: A:0.08, C:0.36, G:0.02, T:0.54
Consensus pattern (25 bp):
TCCTTCTCCTTCTTCCATTATTCAT
Found at i:5409701 original size:13 final size:13
Alignment explanation
Indices: 5409683--5409707 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
5409673 TATTTTAATA
5409683 TTATTTTGTGTGT
1 TTATTTTGTGTGT
5409696 TTATTTTGTGTG
1 TTATTTTGTGTG
5409708 CATTTGATTG
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:0.08, C:0.00, G:0.24, T:0.68
Consensus pattern (13 bp):
TTATTTTGTGTGT
Found at i:5411763 original size:41 final size:41
Alignment explanation
Indices: 5411718--5411892 Score: 216
Period size: 41 Copynumber: 4.3 Consensus size: 41
5411708 TAGCAGATGT
*
5411718 AGTGCCGGTGAAT-T-AATTCAGACTT-TAAGTCTAGCAGGCTA
1 AGTGCCGGTG-ATCTGAA-TCAG-CTTATAAGCCTAGCAGGCTA
* *
5411759 AGTGCCGGTGATCTGAACCAGGTTATGAA-CCTAGCAGGCTA
1 AGTGCCGGTGATCTGAATCAGCTTAT-AAGCCTAGCAGGCTA
* *
5411800 AGTGCCGGTGATCTGAATCAGGTTATAAACCTAGCAGGCTA
1 AGTGCCGGTGATCTGAATCAGCTTATAAGCCTAGCAGGCTA
*
5411841 CGTGCCGGTGATCTGAATCAGGC-TATAAGCCTAGCAGGCTA
1 AGTGCCGGTGATCTGAATCA-GCTTATAAGCCTAGCAGGCTA
5411882 AGTGCCGGTGA
1 AGTGCCGGTGA
5411893 ATATGTTAAA
Statistics
Matches: 120, Mismatches: 8, Indels: 12
0.86 0.06 0.09
Matches are distributed among these distances:
40 6 0.05
41 109 0.91
42 5 0.04
ACGTcount: A:0.27, C:0.21, G:0.29, T:0.24
Consensus pattern (41 bp):
AGTGCCGGTGATCTGAATCAGCTTATAAGCCTAGCAGGCTA
Found at i:5419635 original size:41 final size:40
Alignment explanation
Indices: 5419590--5419734 Score: 218
Period size: 41 Copynumber: 3.5 Consensus size: 40
5419580 GACTTTAAGT
*
5419590 CTAGCAGGCTAAGTGCCGGTGATCTGAACCAGGTTATGAAC
1 CTAGCAGGCTAAGTGCCGGTGATCTGAATCAGGTTAT-AAC
5419631 CTAGCAGGCTAAGTGCCGGTGATCTGAATCAGGTTATAAAC
1 CTAGCAGGCTAAGTGCCGGTGATCTGAATCAGGTTAT-AAC
* * *
5419672 CTAGCAAGCTACGTGCCGGTGATCTGAATCAGGCTATAAGC
1 CTAGCAGGCTAAGTGCCGGTGATCTGAATCAGGTTATAA-C
*
5419713 CTACCAGGCTAAGTGCCGGTGA
1 CTAGCAGGCTAAGTGCCGGTGA
5419735 ATATGTTAAA
Statistics
Matches: 95, Mismatches: 8, Indels: 2
0.90 0.08 0.02
Matches are distributed among these distances:
40 2 0.02
41 93 0.98
ACGTcount: A:0.27, C:0.23, G:0.28, T:0.22
Consensus pattern (40 bp):
CTAGCAGGCTAAGTGCCGGTGATCTGAATCAGGTTATAAC
Found at i:5421964 original size:20 final size:19
Alignment explanation
Indices: 5421919--5421956 Score: 76
Period size: 19 Copynumber: 2.0 Consensus size: 19
5421909 CATCCAAACA
5421919 CCAGAAAAGTAAATCATTT
1 CCAGAAAAGTAAATCATTT
5421938 CCAGAAAAGTAAATCATTT
1 CCAGAAAAGTAAATCATTT
5421957 TTCAGAAATT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.47, C:0.16, G:0.11, T:0.26
Consensus pattern (19 bp):
CCAGAAAAGTAAATCATTT
Found at i:5425801 original size:49 final size:48
Alignment explanation
Indices: 5425671--5425803 Score: 128
Period size: 49 Copynumber: 2.7 Consensus size: 48
5425661 AAAATTAGTT
* * * *
5425671 AATTTATATTTTATGTATCATTATATTAAATTATTTAAACATTTTATG
1 AATTTATATTTTATATATCATTATATTAAATTATTGAAAAATTTTATA
* * * *
5425719 TATCATTA-ATTTTACAAATAATTTATATT-AATTACTTGAAAAATATTTA-A
1 AAT--TTATATTTTATATATCA-TTATATTAAATTA-TTGAAAAAT-TTTATA
5425769 AATTTATATTTTATATATCATTATATTAAATTATT
1 AATTTATATTTTATATATCATTATATTAAATTATT
5425804 TAAATATCGT
Statistics
Matches: 66, Mismatches: 12, Indels: 14
0.72 0.13 0.15
Matches are distributed among these distances:
48 14 0.21
49 29 0.44
50 19 0.29
51 4 0.06
ACGTcount: A:0.41, C:0.05, G:0.02, T:0.52
Consensus pattern (48 bp):
AATTTATATTTTATATATCATTATATTAAATTATTGAAAAATTTTATA
Found at i:5430740 original size:36 final size:36
Alignment explanation
Indices: 5430684--5430757 Score: 103
Period size: 36 Copynumber: 2.1 Consensus size: 36
5430674 TTATTTGTGA
* * * *
5430684 TTGTTTTTTCCAACATTCAAAGGTTGAAACCTGCAT
1 TTGTTCTTTCCAACAATCAAAGGTTCAAACATGCAT
*
5430720 TTGTTCTTTCCGACAATCAAAGGTTCAAACATGCAT
1 TTGTTCTTTCCAACAATCAAAGGTTCAAACATGCAT
5430756 TT
1 TT
5430758 TCTTTGTTGA
Statistics
Matches: 33, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
36 33 1.00
ACGTcount: A:0.28, C:0.20, G:0.14, T:0.38
Consensus pattern (36 bp):
TTGTTCTTTCCAACAATCAAAGGTTCAAACATGCAT
Found at i:5431055 original size:16 final size:16
Alignment explanation
Indices: 5431034--5431066 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 16
5431024 TTCGCTGTAT
5431034 TGGAATAGAGGCGTAA
1 TGGAATAGAGGCGTAA
*
5431050 TGGAATAGAGGTGTAA
1 TGGAATAGAGGCGTAA
5431066 T
1 T
5431067 AACAAATCAA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.36, C:0.03, G:0.36, T:0.24
Consensus pattern (16 bp):
TGGAATAGAGGCGTAA
Found at i:5431545 original size:16 final size:16
Alignment explanation
Indices: 5431501--5431547 Score: 53
Period size: 16 Copynumber: 3.0 Consensus size: 16
5431491 TACTATAAAA
*
5431501 TATAATTTAACATA-AT
1 TATAA-TTAAAATATAT
*
5431517 TATTATT-AAATATAT
1 TATAATTAAAATATAT
5431532 TATAATTAAAATATAT
1 TATAATTAAAATATAT
5431548 AATTTAATAA
Statistics
Matches: 26, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
14 4 0.15
15 10 0.38
16 12 0.46
ACGTcount: A:0.51, C:0.02, G:0.00, T:0.47
Consensus pattern (16 bp):
TATAATTAAAATATAT
Found at i:5431581 original size:120 final size:120
Alignment explanation
Indices: 5431267--5431837 Score: 1013
Period size: 120 Copynumber: 4.8 Consensus size: 120
5431257 ATTTAATCAT
*
5431267 ATTTAAACATAATTTTTATTAAATATATTATAATTAAAATATATAATTTAATAAAATTCTTAATA
1 ATTT-AACATAATTATTATTAAATATATTATAATTAAAATATATAATTTAATAAAATTCTTAATA
* * * *
5431332 ATCAATATTCTTATATAAATTTTCTCAAATCATAATATATGATACTATAAAATATA
65 ATTAATATTCTTATATGAATTTACTCAAATCATAATATATGATACTATAAAAGATA
5431388 ATTTAACAT-A--ATTATTAAATATATTATAATTAAAATATATAATTTAATAAAATTCTTAATAA
1 ATTTAACATAATTATTATTAAATATATTATAATTAAAATATATAATTTAATAAAATTCTTAATAA
* * *
5431450 TCAATATTCTTATATGAATTTTCTCAAATCATAATATATGATACTATAAAATATA
66 TTAATATTCTTATATGAATTTACTCAAATCATAATATATGATACTATAAAAGATA
5431505 ATTTAACATAATTATTATTAAATATATTATAATTAAAATATATAATTTAATAAAATTCTTAATAA
1 ATTTAACATAATTATTATTAAATATATTATAATTAAAATATATAATTTAATAAAATTCTTAATAA
5431570 TTAATATTCTTATATGAATTTACTCAAATCATAATATATGATACTATAAAAGATA
66 TTAATATTCTTATATGAATTTACTCAAATCATAATATATGATACTATAAAAGATA
*
5431625 ATTTAACATAATTATTATTAAATATATTATAATTAAAATATATAATTTAATAAAATTATTAATAA
1 ATTTAACATAATTATTATTAAATATATTATAATTAAAATATATAATTTAATAAAATTCTTAATAA
*
5431690 ATAATATTCTTATATGAATTTACTCAAATCATAATATATGATACTATAAAAGATA
66 TTAATATTCTTATATGAATTTACTCAAATCATAATATATGATACTATAAAAGATA
*
5431745 ATTTAACATAATTATTATTAAATATATTATAATTAAAATATATGATTTAATAAAATTCTTAATAA
1 ATTTAACATAATTATTATTAAATATATTATAATTAAAATATATAATTTAATAAAATTCTTAATAA
5431810 TTAATATTCTTATATGAATTTACTCAAA
66 TTAATATTCTTATATGAATTTACTCAAA
5431838 AATTGTTAGC
Statistics
Matches: 437, Mismatches: 10, Indels: 7
0.96 0.02 0.02
Matches are distributed among these distances:
117 114 0.26
118 1 0.00
119 1 0.00
120 317 0.73
121 4 0.01
ACGTcount: A:0.49, C:0.06, G:0.02, T:0.43
Consensus pattern (120 bp):
ATTTAACATAATTATTATTAAATATATTATAATTAAAATATATAATTTAATAAAATTCTTAATAA
TTAATATTCTTATATGAATTTACTCAAATCATAATATATGATACTATAAAAGATA
Found at i:5431665 original size:16 final size:16
Alignment explanation
Indices: 5431622--5431667 Score: 51
Period size: 16 Copynumber: 2.9 Consensus size: 16
5431612 ACTATAAAAG
*
5431622 ATAATTTAACATA-ATT
1 ATAA-TTAAAATATATT
*
5431638 ATTATT-AAATATATT
1 ATAATTAAAATATATT
5431653 ATAATTAAAATATAT
1 ATAATTAAAATATAT
5431668 AATTTAATAA
Statistics
Matches: 25, Mismatches: 3, Indels: 4
0.78 0.09 0.12
Matches are distributed among these distances:
14 4 0.16
15 10 0.40
16 11 0.44
ACGTcount: A:0.52, C:0.02, G:0.00, T:0.46
Consensus pattern (16 bp):
ATAATTAAAATATATT
Found at i:5431674 original size:14 final size:15
Alignment explanation
Indices: 5431622--5431676 Score: 53
Period size: 15 Copynumber: 3.7 Consensus size: 15
5431612 ACTATAAAAG
5431622 ATAATTTAACATA-ATT
1 ATAA-TTAA-ATATATT
*
5431638 ATTATTAAATATATT
1 ATAATTAAATATATT
5431653 ATAATTAAA-ATA-T
1 ATAATTAAATATATT
*
5431666 ATAATTTAATA
1 ATAATTAAATA
5431677 AAATTATTAA
Statistics
Matches: 34, Mismatches: 3, Indels: 6
0.79 0.07 0.14
Matches are distributed among these distances:
13 9 0.26
14 7 0.21
15 15 0.44
16 3 0.09
ACGTcount: A:0.53, C:0.02, G:0.00, T:0.45
Consensus pattern (15 bp):
ATAATTAAATATATT
Found at i:5431785 original size:16 final size:16
Alignment explanation
Indices: 5431742--5431787 Score: 51
Period size: 16 Copynumber: 2.9 Consensus size: 16
5431732 ACTATAAAAG
*
5431742 ATAATTTAACATA-ATT
1 ATAA-TTAAAATATATT
*
5431758 ATTATT-AAATATATT
1 ATAATTAAAATATATT
5431773 ATAATTAAAATATAT
1 ATAATTAAAATATAT
5431788 GATTTAATAA
Statistics
Matches: 25, Mismatches: 3, Indels: 4
0.78 0.09 0.12
Matches are distributed among these distances:
14 4 0.16
15 10 0.40
16 11 0.44
ACGTcount: A:0.52, C:0.02, G:0.00, T:0.46
Consensus pattern (16 bp):
ATAATTAAAATATATT
Found at i:5433836 original size:33 final size:34
Alignment explanation
Indices: 5433796--5433898 Score: 120
Period size: 33 Copynumber: 3.0 Consensus size: 34
5433786 AGAAAAGGTG
5433796 AAACAGAGGGAGCAAATCGGCAGAAAAGAAAAT-
1 AAACAGAGGGAGCAAATCGGCAGAAAAGAAAATA
* *
5433829 AAACAGAGAGAACAAATCGGCAGAAAAGAAAAGATAA
1 AAACAGAGGGAGCAAATCGGCAGAAAAG-AAA-AT-A
* *
5433866 GAAACAGAGGGAGAAAATCGGCAG-AGAGAAAAT
1 -AAACAGAGGGAGCAAATCGGCAGAAAAGAAAAT
5433899 CGGCAGAGGC
Statistics
Matches: 59, Mismatches: 6, Indels: 8
0.81 0.08 0.11
Matches are distributed among these distances:
33 26 0.44
34 3 0.05
35 4 0.07
36 3 0.05
37 3 0.05
38 20 0.34
ACGTcount: A:0.56, C:0.11, G:0.27, T:0.06
Consensus pattern (34 bp):
AAACAGAGGGAGCAAATCGGCAGAAAAGAAAATA
Found at i:5433860 original size:38 final size:38
Alignment explanation
Indices: 5433817--5433890 Score: 105
Period size: 38 Copynumber: 1.9 Consensus size: 38
5433807 GCAAATCGGC
*
5433817 AGAAAAGAAAATAAACAGAGAGA-ACAAATCGGCAGAAA
1 AGAAAAGAAAAGAAACAGAGAGAGA-AAATCGGCAGAAA
* *
5433855 AGAAAAGATAAGAAACAGAGGGAGAAAATCGGCAGA
1 AGAAAAGAAAAGAAACAGAGAGAGAAAATCGGCAGA
5433891 GAGAAAATCG
Statistics
Matches: 32, Mismatches: 3, Indels: 2
0.86 0.08 0.05
Matches are distributed among these distances:
38 31 0.97
39 1 0.03
ACGTcount: A:0.59, C:0.09, G:0.26, T:0.05
Consensus pattern (38 bp):
AGAAAAGAAAAGAAACAGAGAGAGAAAATCGGCAGAAA
Found at i:5433896 original size:15 final size:15
Alignment explanation
Indices: 5433876--5433906 Score: 62
Period size: 15 Copynumber: 2.1 Consensus size: 15
5433866 GAAACAGAGG
5433876 GAGAAAATCGGCAGA
1 GAGAAAATCGGCAGA
5433891 GAGAAAATCGGCAGA
1 GAGAAAATCGGCAGA
5433906 G
1 G
5433907 GCTAGAAGGA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.45, C:0.13, G:0.35, T:0.06
Consensus pattern (15 bp):
GAGAAAATCGGCAGA
Found at i:5440954 original size:16 final size:16
Alignment explanation
Indices: 5440933--5440965 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
5440923 ACAAACAAAG
5440933 AAAATATATAAAC-TAT
1 AAAATATA-AAACATAT
5440949 AAAATATAAAACATAT
1 AAAATATAAAACATAT
5440965 A
1 A
5440966 CATGAGTGTA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 4 0.25
16 12 0.75
ACGTcount: A:0.67, C:0.06, G:0.00, T:0.27
Consensus pattern (16 bp):
AAAATATAAAACATAT
Found at i:5442888 original size:41 final size:41
Alignment explanation
Indices: 5442826--5442974 Score: 106
Period size: 41 Copynumber: 3.6 Consensus size: 41
5442816 AGTCTATTCC
* *
5442826 ACTGTAA-TCTCAGGGAAATAAGACCTGACACGATCTACTCT
1 ACTGTAACT-TCAGAGAGATAAGACCTGACACGATCTACTCT
* * ** ** *
5442867 GCTGTAACTTCAGAGAGATAAGATCCT-TCATTTTAATCCGCTCC
1 ACTGTAACTTCAGAGAGATAAGA-CCTGACA---CGATCTACTCT
* * * *
5442911 ACTGTAA-TCTCAGGGAGATAGGATCTGAAACGATCTACTCT
1 ACTGTAACT-TCAGAGAGATAAGACCTGACACGATCTACTCT
5442952 ACTGTAACTTCAGAGAGATAAGA
1 ACTGTAACTTCAGAGAGATAAGA
5442975 TCCTTCGTTT
Statistics
Matches: 78, Mismatches: 22, Indels: 16
0.67 0.19 0.14
Matches are distributed among these distances:
41 45 0.58
42 5 0.06
43 3 0.04
44 25 0.32
ACGTcount: A:0.33, C:0.21, G:0.19, T:0.27
Consensus pattern (41 bp):
ACTGTAACTTCAGAGAGATAAGACCTGACACGATCTACTCT
Found at i:5442917 original size:44 final size:42
Alignment explanation
Indices: 5442868--5443355 Score: 247
Period size: 44 Copynumber: 11.6 Consensus size: 42
5442858 ATCTACTCTG
* *
5442868 CTGTAACTTCAGAGAGATAAGATCCTTCATTTTAATCCGCTCCA
1 CTGTAA-TTCAGGGAGATAAGAT-CTTCATTTCAATCCGCTCCA
* * ** * ** *
5442912 CTGTAATCTCAGGGAGATAGGATC-TGA-AACGATCTACTCTA
1 CTGTAAT-TCAGGGAGATAAGATCTTCATTTCAATCCGCTCCA
* * *
5442953 CTGTAACTTCAGAGAGATAAGATCCTTCGTTTTAATCCGCTCCA
1 CTGTAA-TTCAGGGAGATAAGAT-CTTCATTTCAATCCGCTCCA
* * * *
5442997 CTGTAATATCAGGGAGATAGGAT-TACTATCTTCAATCTGCTCCG
1 CTGTAAT-TCAGGGAGATAAGATCTTC-AT-TTCAATCCGCTCCA
* ** * ** *
5443041 CTGTAATCTCAGGGAGATAAGATC-TGA-AACGATCTACTCTA
1 CTGTAAT-TCAGGGAGATAAGATCTTCATTTCAATCCGCTCCA
* *
5443082 CTGTAACTTCAGAGAGATAAGATCCTTCATTTTAATCCGCTCCA
1 CTGTAA-TTCAGGGAGATAAGAT-CTTCATTTCAATCCGCTCCA
* * * *
5443126 CTGTAATTCAGGGAGATAGGAT-TACTATCTTCAATCTGCTCCG
1 CTGTAATTCAGGGAGATAAGATCTTC-AT-TTCAATCCGCTCCA
* **
5443169 CTGTAATCTCAGGGAGATAAGATCTGCCATCTTCAATGTGCTCCA
1 CTGTAAT-TCAGGGAGATAAGATCT-TCAT-TTCAATCCGCTCCA
* ** * ** *
5443214 C--T--TT--GGGAGATAAGATC-TGA-AACGATCTACTCTA
1 CTGTAATTCAGGGAGATAAGATCTTCATTTCAATCCGCTCCA
* * *
5443248 CTGTAACTTCAGAGAGATAAGATC--C-TTTTAATCCACTCCA
1 CTGTAA-TTCAGGGAGATAAGATCTTCATTTCAATCCGCTCCA
* * * *
5443288 CTGTAATCTCAGGGAGATAGGAT-TACTAGCTTCAATCTGCTCCA
1 CTGTAAT-TCAGGGAGATAAGATCTTC-A-TTTCAATCCGCTCCA
5443332 CTGTAATTCAGGGAGATAAGATCT
1 CTGTAATTCAGGGAGATAAGATCT
5443356 GAAATTCTTT
Statistics
Matches: 331, Mismatches: 80, Indels: 66
0.69 0.17 0.14
Matches are distributed among these distances:
34 9 0.03
36 2 0.01
38 13 0.04
39 3 0.01
40 28 0.08
41 70 0.21
42 10 0.03
43 55 0.17
44 123 0.37
45 17 0.05
46 1 0.00
ACGTcount: A:0.30, C:0.22, G:0.18, T:0.30
Consensus pattern (42 bp):
CTGTAATTCAGGGAGATAAGATCTTCATTTCAATCCGCTCCA
Found at i:5443012 original size:85 final size:85
Alignment explanation
Indices: 5442823--5443019 Score: 331
Period size: 85 Copynumber: 2.3 Consensus size: 85
5442813 TTCAGTCTAT
* * * * *
5442823 TCCACTGTAATCTCAGGGAAATAAGACCTGACACGATCTACTCTGCTGTAACTTCAGAGAGATAA
1 TCCACTGTAATCTCAGGGAGATAGGATCTGAAACGATCTACTCTACTGTAACTTCAGAGAGATAA
5442888 GATCCTTCATTTTAATCCGC
66 GATCCTTCATTTTAATCCGC
5442908 TCCACTGTAATCTCAGGGAGATAGGATCTGAAACGATCTACTCTACTGTAACTTCAGAGAGATAA
1 TCCACTGTAATCTCAGGGAGATAGGATCTGAAACGATCTACTCTACTGTAACTTCAGAGAGATAA
*
5442973 GATCCTTCGTTTTAATCCGC
66 GATCCTTCATTTTAATCCGC
*
5442993 TCCACTGTAATATCAGGGAGATAGGAT
1 TCCACTGTAATCTCAGGGAGATAGGAT
5443020 TACTATCTTC
Statistics
Matches: 105, Mismatches: 7, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
85 105 1.00
ACGTcount: A:0.30, C:0.22, G:0.19, T:0.28
Consensus pattern (85 bp):
TCCACTGTAATCTCAGGGAGATAGGATCTGAAACGATCTACTCTACTGTAACTTCAGAGAGATAA
GATCCTTCATTTTAATCCGC
Found at i:5443048 original size:129 final size:128
Alignment explanation
Indices: 5442901--5443194 Score: 543
Period size: 129 Copynumber: 2.3 Consensus size: 128
5442891 CCTTCATTTT
* * *
5442901 AATCCGCTCCACTGTAATCTCAGGGAGATAGGATCTGAAACGATCTACTCTACTGTAACTTCAGA
1 AATCTGCTCCGCTGTAATCTCAGGGAGATAAGATCTGAAACGATCTACTCTACTGTAACTTCAGA
*
5442966 GAGATAAGATCCTTCGTTTTAATCCGCTCCACTGTAATATCAGGGAGATAGGATTACTATCTTC
66 GAGATAAGATCCTTCATTTTAATCCGCTCCACTGTAAT-TCAGGGAGATAGGATTACTATCTTC
5443030 AATCTGCTCCGCTGTAATCTCAGGGAGATAAGATCTGAAACGATCTACTCTACTGTAACTTCAGA
1 AATCTGCTCCGCTGTAATCTCAGGGAGATAAGATCTGAAACGATCTACTCTACTGTAACTTCAGA
5443095 GAGATAAGATCCTTCATTTTAATCCGCTCCACTGTAATTCAGGGAGATAGGATTACTATCTTC
66 GAGATAAGATCCTTCATTTTAATCCGCTCCACTGTAATTCAGGGAGATAGGATTACTATCTTC
5443158 AATCTGCTCCGCTGTAATCTCAGGGAGATAAGATCTG
1 AATCTGCTCCGCTGTAATCTCAGGGAGATAAGATCTG
5443195 CCATCTTCAA
Statistics
Matches: 161, Mismatches: 4, Indels: 1
0.97 0.02 0.01
Matches are distributed among these distances:
128 62 0.39
129 99 0.61
ACGTcount: A:0.29, C:0.22, G:0.19, T:0.30
Consensus pattern (128 bp):
AATCTGCTCCGCTGTAATCTCAGGGAGATAAGATCTGAAACGATCTACTCTACTGTAACTTCAGA
GAGATAAGATCCTTCATTTTAATCCGCTCCACTGTAATTCAGGGAGATAGGATTACTATCTTC
Found at i:5443237 original size:166 final size:162
Alignment explanation
Indices: 5443052--5443356 Score: 531
Period size: 166 Copynumber: 1.9 Consensus size: 162
5443042 TGTAATCTCA
5443052 GGGAGATAAGATCTGAAACGATCTACTCTACTGTAACTTCAGAGAGATAAGATCCTTCATTTTAA
1 GGGAGATAAGATCTGAAACGATCTACTCTACTGTAACTTCAGAGAGATAAGAT-C--C-TTTTAA
* * *
5443117 TCCGCTCCACTGTAAT-TCAGGGAGATAGGATTACTATCTTCAATCTGCTCCGCTGTAATCTCAG
62 TCCACTCCACTGTAATCTCAGGGAGATAGGATTACTAGCTTCAATCTGCTCCACTGTAAT-TCAG
5443181 GGAGATAAGATCTGCCATCTTCAATGTGCTCCACTTT
126 GGAGATAAGATCTGCCATCTTCAATGTGCTCCACTTT
5443218 GGGAGATAAGATCTGAAACGATCTACTCTACTGTAACTTCAGAGAGATAAGATCCTTTTAATCCA
1 GGGAGATAAGATCTGAAACGATCTACTCTACTGTAACTTCAGAGAGATAAGATCCTTTTAATCCA
5443283 CTCCACTGTAATCTCAGGGAGATAGGATTACTAGCTTCAATCTGCTCCACTGTAATTCAGGGAGA
66 CTCCACTGTAATCTCAGGGAGATAGGATTACTAGCTTCAATCTGCTCCACTGTAATTCAGGGAGA
5443348 TAAGATCTG
131 TAAGATCTG
5443357 AAATTCTTTG
Statistics
Matches: 135, Mismatches: 3, Indels: 6
0.94 0.02 0.04
Matches are distributed among these distances:
162 39 0.29
163 42 0.31
165 1 0.01
166 53 0.39
ACGTcount: A:0.30, C:0.21, G:0.19, T:0.30
Consensus pattern (162 bp):
GGGAGATAAGATCTGAAACGATCTACTCTACTGTAACTTCAGAGAGATAAGATCCTTTTAATCCA
CTCCACTGTAATCTCAGGGAGATAGGATTACTAGCTTCAATCTGCTCCACTGTAATTCAGGGAGA
TAAGATCTGCCATCTTCAATGTGCTCCACTTT
Found at i:5443305 original size:40 final size:41
Alignment explanation
Indices: 5443242--5443354 Score: 106
Period size: 40 Copynumber: 2.7 Consensus size: 41
5443232 GAAACGATCT
* * *
5443242 ACTCTACTGTAA-CTTCAGAGAGATAAGATCCT-TTTAATCC
1 ACTCCACTGTAATC-TCAGGGAGATAAGATCCTATTCAATCC
* * *
5443282 ACTCCACTGTAATCTCAGGGAGATAGGATTACTAGCTTCAATCT
1 ACTCCACTGTAATCTCAGGGAGATAAGA-TCCTA--TTCAATCC
*
5443326 GCTCCACTGTAAT-TCAGGGAGATAAGATC
1 ACTCCACTGTAATCTCAGGGAGATAAGATC
5443355 TGAAATTCTT
Statistics
Matches: 59, Mismatches: 9, Indels: 8
0.78 0.12 0.11
Matches are distributed among these distances:
40 23 0.39
41 4 0.07
42 1 0.02
43 13 0.22
44 18 0.31
ACGTcount: A:0.31, C:0.22, G:0.18, T:0.29
Consensus pattern (41 bp):
ACTCCACTGTAATCTCAGGGAGATAAGATCCTATTCAATCC
Found at i:5457463 original size:40 final size:40
Alignment explanation
Indices: 5457419--5457588 Score: 252
Period size: 40 Copynumber: 4.2 Consensus size: 40
5457409 CTCCTCGTTT
* * * *
5457419 AAATGCCTTCGGGACATAGCCCGG-TTATAGTAATTTGCAC
1 AAATGCCTTCGGGACTTAACCCGGATT-TAGTAACTCGCAC
5457459 AAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCAC
1 AAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCAC
*
5457499 AAATGCCATCGGGACTTAACCCGGATTTAGTAACTCGCAC
1 AAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCAC
* * *
5457539 AAATGCCGTCGGGACTTAACCCGGAATTAGTATCTCGCAC
1 AAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCAC
5457579 AAATGCCTTC
1 AAATGCCTTC
5457589 AGATCTTAGT
Statistics
Matches: 120, Mismatches: 9, Indels: 2
0.92 0.07 0.02
Matches are distributed among these distances:
40 118 0.98
41 2 0.02
ACGTcount: A:0.28, C:0.26, G:0.21, T:0.25
Consensus pattern (40 bp):
AAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCAC
Done.