Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr08 129432109
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: 129432109
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32
Warning! 350 characters in sequence are not A, C, G, or T
File 390 of 425
Found at i:119704449 original size:16 final size:16
Alignment explanation
Indices: 119704428--119704465 Score: 58
Period size: 16 Copynumber: 2.4 Consensus size: 16
119704418 TTAGGGTAGC
*
119704428 TGTAATTGAATAGAGA
1 TGTAATGGAATAGAGA
*
119704444 TGTAATGGAATAGAGC
1 TGTAATGGAATAGAGA
119704460 TGTAAT
1 TGTAAT
119704466 CAGTAATTCA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
16 20 1.00
ACGTcount: A:0.39, C:0.03, G:0.26, T:0.32
Consensus pattern (16 bp):
TGTAATGGAATAGAGA
Found at i:119704721 original size:58 final size:58
Alignment explanation
Indices: 119704650--119704763 Score: 167
Period size: 58 Copynumber: 2.0 Consensus size: 58
119704640 AGATTATTAT
* *
119704650 TAAAAATAATTTAATAAAAATAATAAATAATTTAATCATATT-TTAACATAATTATTGC
1 TAAAAATAATTTAAT-AAAATAATAAATAATTTAATAAAATTCTTAACATAATTATTGC
* * *
119704708 TAAATATAATTTAATAAAATAATATATAATTTAATAAAATTCTTAATATAATTATT
1 TAAAAATAATTTAATAAAATAATAAATAATTTAATAAAATTCTTAACATAATTATT
119704764 ATTATATGAA
Statistics
Matches: 50, Mismatches: 5, Indels: 2
0.88 0.09 0.04
Matches are distributed among these distances:
57 23 0.46
58 27 0.54
ACGTcount: A:0.54, C:0.04, G:0.01, T:0.42
Consensus pattern (58 bp):
TAAAAATAATTTAATAAAATAATAAATAATTTAATAAAATTCTTAACATAATTATTGC
Found at i:119705656 original size:26 final size:26
Alignment explanation
Indices: 119705620--119705729 Score: 166
Period size: 26 Copynumber: 4.2 Consensus size: 26
119705610 TGATACAAAT
*
119705620 TGATAAAAGGTTAGGTAAATGTTCCA
1 TGATAATAGGTTAGGTAAATGTTCCA
119705646 TGATAATAGGTTAGGTAAATGTTCCA
1 TGATAATAGGTTAGGTAAATGTTCCA
* *
119705672 TGATAATGGGTTAGGTAAATGTTTCA
1 TGATAATAGGTTAGGTAAATGTTCCA
* * *
119705698 TAATAATGGGTTAGGTAAATGTTTCA
1 TGATAATAGGTTAGGTAAATGTTCCA
119705724 TGATAA
1 TGATAA
119705730 GAATTTCATG
Statistics
Matches: 79, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
26 79 1.00
ACGTcount: A:0.35, C:0.05, G:0.24, T:0.35
Consensus pattern (26 bp):
TGATAATAGGTTAGGTAAATGTTCCA
Found at i:119711182 original size:50 final size:50
Alignment explanation
Indices: 119711107--119711205 Score: 153
Period size: 50 Copynumber: 2.0 Consensus size: 50
119711097 ACCTTATTCT
* * * *
119711107 AATCAATATCAAATAGAAGAAGAGTAGTTCTATATTGATTCTACTTGTGC
1 AATCAATATCAAATAAAAGAAGAGTAATTCTAGATGGATTCTACTTGTGC
*
119711157 AATCAATGTCAAATAAAAGAAGAGTAATTCTAGATGGATTCTACTTGTG
1 AATCAATATCAAATAAAAGAAGAGTAATTCTAGATGGATTCTACTTGTG
119711206 TAGCCTGGTC
Statistics
Matches: 44, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
50 44 1.00
ACGTcount: A:0.39, C:0.11, G:0.17, T:0.32
Consensus pattern (50 bp):
AATCAATATCAAATAAAAGAAGAGTAATTCTAGATGGATTCTACTTGTGC
Found at i:119717555 original size:26 final size:26
Alignment explanation
Indices: 119717519--119717602 Score: 141
Period size: 26 Copynumber: 3.2 Consensus size: 26
119717509 TGATACAAAT
* *
119717519 TGATAATAGGTTAGGTAAATATTCCA
1 TGATAATAGGTTAGGTAAATGTTTCA
119717545 TGATAATAGGTTAGGTAAATGTTTCA
1 TGATAATAGGTTAGGTAAATGTTTCA
*
119717571 TGATAATGGGTTAGGTAAATGTTTCA
1 TGATAATAGGTTAGGTAAATGTTTCA
119717597 TGATAA
1 TGATAA
119717603 GAATTTCATG
Statistics
Matches: 55, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
26 55 1.00
ACGTcount: A:0.36, C:0.05, G:0.23, T:0.37
Consensus pattern (26 bp):
TGATAATAGGTTAGGTAAATGTTTCA
Found at i:119721652 original size:26 final size:26
Alignment explanation
Indices: 119721616--119721725 Score: 175
Period size: 26 Copynumber: 4.2 Consensus size: 26
119721606 TGATACAAAT
*
119721616 TGATAATAGGTTAGGTAAATATTCCA
1 TGATAATAGGTTAGGTAAATGTTCCA
119721642 TGATAATAGGTTAGGTAAATGTTCCA
1 TGATAATAGGTTAGGTAAATGTTCCA
* *
119721668 TGATAATGGGTTAGGTAAATGTTTCA
1 TGATAATAGGTTAGGTAAATGTTCCA
* *
119721694 TGATAATGGGTTAGGTAAATGTTTCA
1 TGATAATAGGTTAGGTAAATGTTCCA
119721720 TGATAA
1 TGATAA
119721726 GAATTTCATG
Statistics
Matches: 81, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
26 81 1.00
ACGTcount: A:0.35, C:0.05, G:0.24, T:0.36
Consensus pattern (26 bp):
TGATAATAGGTTAGGTAAATGTTCCA
Found at i:119725737 original size:44 final size:44
Alignment explanation
Indices: 119725688--119725775 Score: 158
Period size: 44 Copynumber: 2.0 Consensus size: 44
119725678 GCAATTCATG
*
119725688 CATATACATGTATTCATAATCAAATGGAAAAACTTACGCTGAAT
1 CATATACATGTATTCATAATCAAATAGAAAAACTTACGCTGAAT
*
119725732 CATATACATGTGTTCATAATCAAATAGAAAAACTTACGCTGAAT
1 CATATACATGTATTCATAATCAAATAGAAAAACTTACGCTGAAT
119725776 TTACCATGTA
Statistics
Matches: 42, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
44 42 1.00
ACGTcount: A:0.43, C:0.16, G:0.11, T:0.30
Consensus pattern (44 bp):
CATATACATGTATTCATAATCAAATAGAAAAACTTACGCTGAAT
Found at i:119726063 original size:3 final size:3
Alignment explanation
Indices: 119726055--119726089 Score: 70
Period size: 3 Copynumber: 11.7 Consensus size: 3
119726045 AACCATAACA
119726055 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
119726090 CTTCAATGAT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 32 1.00
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (3 bp):
AAT
Found at i:119727309 original size:38 final size:38
Alignment explanation
Indices: 119727258--119727335 Score: 138
Period size: 38 Copynumber: 2.1 Consensus size: 38
119727248 GATCTTAGGG
119727258 ATTTAATCTTCCAAATTAGCACACAAGAAATTCAGAGA
1 ATTTAATCTTCCAAATTAGCACACAAGAAATTCAGAGA
* *
119727296 ATTTAATCTTCCAAATTAGCACATAAGAAATTTAGAGA
1 ATTTAATCTTCCAAATTAGCACACAAGAAATTCAGAGA
119727334 AT
1 AT
119727336 ATCTACTCTC
Statistics
Matches: 38, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
38 38 1.00
ACGTcount: A:0.45, C:0.15, G:0.10, T:0.29
Consensus pattern (38 bp):
ATTTAATCTTCCAAATTAGCACACAAGAAATTCAGAGA
Found at i:119732667 original size:37 final size:37
Alignment explanation
Indices: 119732592--119732683 Score: 132
Period size: 37 Copynumber: 2.5 Consensus size: 37
119732582 TAAATATAAA
* *
119732592 AATAATTATATTAAGAATGTTATTAAATTATATGTAAT
1 AATAATTATATTAA-AATATGATTAAATTATATGTAAT
*
119732630 AATAATTATATTAAAATATGATTAAATTATATTTAAT
1 AATAATTATATTAAAATATGATTAAATTATATGTAAT
119732667 AATAATCT-TATTAAAAT
1 AATAAT-TATATTAAAAT
119732684 TTAATAACAA
Statistics
Matches: 50, Mismatches: 3, Indels: 3
0.89 0.05 0.05
Matches are distributed among these distances:
37 35 0.70
38 15 0.30
ACGTcount: A:0.50, C:0.01, G:0.04, T:0.45
Consensus pattern (37 bp):
AATAATTATATTAAAATATGATTAAATTATATGTAAT
Found at i:119736284 original size:25 final size:25
Alignment explanation
Indices: 119736256--119736322 Score: 82
Period size: 25 Copynumber: 2.7 Consensus size: 25
119736246 AGAATATTAA
* *
119736256 TAAGCTCCTACGAGCTGA-ATAACGG
1 TAAGCTCATACGAGCTGAGA-AACAG
* *
119736281 TAAGCTCTTACGAGCTGAGAATCAG
1 TAAGCTCATACGAGCTGAGAAACAG
119736306 TAAGCTCATACGAGCTG
1 TAAGCTCATACGAGCTG
119736323 CGGTGAGCCT
Statistics
Matches: 37, Mismatches: 4, Indels: 2
0.86 0.09 0.05
Matches are distributed among these distances:
25 36 0.97
26 1 0.03
ACGTcount: A:0.31, C:0.22, G:0.24, T:0.22
Consensus pattern (25 bp):
TAAGCTCATACGAGCTGAGAAACAG
Found at i:119737432 original size:11 final size:11
Alignment explanation
Indices: 119737416--119737440 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
119737406 ATACAAACGG
119737416 TAATATTAAAA
1 TAATATTAAAA
119737427 TAATATTAAAA
1 TAATATTAAAA
119737438 TAA
1 TAA
119737441 ATTTTATGAC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (11 bp):
TAATATTAAAA
Found at i:119738000 original size:11 final size:11
Alignment explanation
Indices: 119737984--119738008 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
119737974 ATATGATATT
119737984 TTATTATTTTA
1 TTATTATTTTA
119737995 TTATTATTTTA
1 TTATTATTTTA
119738006 TTA
1 TTA
119738009 GTATATATAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.28, C:0.00, G:0.00, T:0.72
Consensus pattern (11 bp):
TTATTATTTTA
Found at i:119743397 original size:26 final size:26
Alignment explanation
Indices: 119743366--119743473 Score: 189
Period size: 26 Copynumber: 4.2 Consensus size: 26
119743356 TGAAATTCCC
*
119743366 ATCATGGAACATTTACCTAAACCATT
1 ATCATGGAACATTTACCTAACCCATT
119743392 ATCATGGAACATTTACCTAACCCATT
1 ATCATGGAACATTTACCTAACCCATT
* *
119743418 ATCATGGAATATTTACCTAATCCATT
1 ATCATGGAACATTTACCTAACCCATT
119743444 ATCATGGAACATTTACCTAACCCATT
1 ATCATGGAACATTTACCTAACCCATT
119743470 ATCA
1 ATCA
119743474 ATTTGTACCA
Statistics
Matches: 77, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
26 77 1.00
ACGTcount: A:0.36, C:0.24, G:0.07, T:0.32
Consensus pattern (26 bp):
ATCATGGAACATTTACCTAACCCATT
Found at i:119748978 original size:27 final size:27
Alignment explanation
Indices: 119748948--119749000 Score: 97
Period size: 27 Copynumber: 2.0 Consensus size: 27
119748938 AAACACTACT
119748948 ATGAGTCATAATAAAAAAACATCATCA
1 ATGAGTCATAATAAAAAAACATCATCA
*
119748975 ATGAGTCATAATAAAACAACATCATC
1 ATGAGTCATAATAAAAAAACATCATC
119749001 CATCTCCATT
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
27 25 1.00
ACGTcount: A:0.53, C:0.17, G:0.08, T:0.23
Consensus pattern (27 bp):
ATGAGTCATAATAAAAAAACATCATCA
Found at i:119758268 original size:64 final size:64
Alignment explanation
Indices: 119758197--119758317 Score: 233
Period size: 64 Copynumber: 1.9 Consensus size: 64
119758187 TCATTTCATT
*
119758197 ATTTATTTAATTATTTTATATTATTTGGATAAAAATTCTAATACTTTACTTTTTTTTTTAAAGA
1 ATTTATTTAATTATTTTATATTATTTAGATAAAAATTCTAATACTTTACTTTTTTTTTTAAAGA
119758261 ATTTATTTAATTATTTTATATTATTTAGATAAAAATTCTAATACTTTACTTTTTTTT
1 ATTTATTTAATTATTTTATATTATTTAGATAAAAATTCTAATACTTTACTTTTTTTT
119758318 AAAAAAAGAA
Statistics
Matches: 56, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
64 56 1.00
ACGTcount: A:0.34, C:0.05, G:0.03, T:0.58
Consensus pattern (64 bp):
ATTTATTTAATTATTTTATATTATTTAGATAAAAATTCTAATACTTTACTTTTTTTTTTAAAGA
Found at i:119765608 original size:21 final size:21
Alignment explanation
Indices: 119765582--119765622 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
119765572 ATCTGCTCAA
* *
119765582 ACTCCACCTGTTTTGGAGTAC
1 ACTCCACCTGCTGTGGAGTAC
119765603 ACTCCACCTGCTGTGGAGTA
1 ACTCCACCTGCTGTGGAGTA
119765623 TCGCTCGTCT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.20, C:0.29, G:0.22, T:0.29
Consensus pattern (21 bp):
ACTCCACCTGCTGTGGAGTAC
Found at i:119770264 original size:13 final size:13
Alignment explanation
Indices: 119770246--119770270 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
119770236 TCACTCAACG
119770246 TAATCAAATTTGT
1 TAATCAAATTTGT
119770259 TAATCAAATTTG
1 TAATCAAATTTG
119770271 CTATTAACTT
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:0.40, C:0.08, G:0.08, T:0.44
Consensus pattern (13 bp):
TAATCAAATTTGT
Found at i:119770579 original size:18 final size:17
Alignment explanation
Indices: 119770556--119770590 Score: 52
Period size: 18 Copynumber: 2.0 Consensus size: 17
119770546 ATTTATAAAG
*
119770556 ATTCAATAGTATTAAATA
1 ATTCAATAATA-TAAATA
119770574 ATTCAATAATATAAATA
1 ATTCAATAATATAAATA
119770591 GTGTAAAATG
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 6 0.38
18 10 0.62
ACGTcount: A:0.54, C:0.06, G:0.03, T:0.37
Consensus pattern (17 bp):
ATTCAATAATATAAATA
Found at i:119770826 original size:20 final size:21
Alignment explanation
Indices: 119770801--119770847 Score: 62
Period size: 20 Copynumber: 2.3 Consensus size: 21
119770791 GGGGGTGGGA
*
119770801 TGGGAGGAGAA-TAAA-AGTTT
1 TGGGAGGA-AAGTAAATAGGTT
119770821 TGGGAGGAAAGTAAATAGGTT
1 TGGGAGGAAAGTAAATAGGTT
119770842 TGGGAG
1 TGGGAG
119770848 TTTGGGGTAA
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
19 2 0.08
20 12 0.50
21 10 0.42
ACGTcount: A:0.36, C:0.00, G:0.40, T:0.23
Consensus pattern (21 bp):
TGGGAGGAAAGTAAATAGGTT
Found at i:119770985 original size:18 final size:18
Alignment explanation
Indices: 119770962--119770997 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
119770952 AAGTTGACTC
*
119770962 GAATAATTCGATTAATTT
1 GAATAACTCGATTAATTT
*
119770980 GAATAACTCGATTCATTT
1 GAATAACTCGATTAATTT
119770998 AATTCAAAAT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.36, C:0.11, G:0.11, T:0.42
Consensus pattern (18 bp):
GAATAACTCGATTAATTT
Found at i:119774777 original size:3 final size:3
Alignment explanation
Indices: 119774769--119774812 Score: 58
Period size: 3 Copynumber: 15.7 Consensus size: 3
119774759 ACAATATTCA
*
119774769 AAT AAT AAT AAC AAT -AT AAT AAT AA- AAT AAT AAT AA- AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
119774813 GAAAACAATA
Statistics
Matches: 36, Mismatches: 2, Indels: 6
0.82 0.05 0.14
Matches are distributed among these distances:
2 6 0.17
3 30 0.83
ACGTcount: A:0.70, C:0.02, G:0.00, T:0.27
Consensus pattern (3 bp):
AAT
Found at i:119774778 original size:14 final size:12
Alignment explanation
Indices: 119774767--119774812 Score: 60
Period size: 11 Copynumber: 3.8 Consensus size: 12
119774757 ATACAATATT
119774767 CAAATAATAATAA
1 CAAATAATAAT-A
119774780 CAATATAATAATA
1 CAA-ATAATAATA
119774793 -AAATAATAATA
1 CAAATAATAATA
119774804 -AAATAATAA
1 CAAATAATAA
119774813 GAAAACAATA
Statistics
Matches: 32, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
11 18 0.56
12 2 0.06
13 4 0.12
14 8 0.25
ACGTcount: A:0.70, C:0.04, G:0.00, T:0.26
Consensus pattern (12 bp):
CAAATAATAATA
Found at i:119774787 original size:11 final size:11
Alignment explanation
Indices: 119774772--119774822 Score: 66
Period size: 11 Copynumber: 4.6 Consensus size: 11
119774762 ATATTCAAAT
*
119774772 AATAATAACAA
1 AATAATAATAA
*
119774783 TATAATAATAA
1 AATAATAATAA
119774794 AATAATAATAA
1 AATAATAATAA
*
119774805 AATAATAAGAA
1 AATAATAATAA
*
119774816 AACAATA
1 AATAATA
119774823 GCAAAACAGT
Statistics
Matches: 35, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
11 35 1.00
ACGTcount: A:0.71, C:0.04, G:0.02, T:0.24
Consensus pattern (11 bp):
AATAATAATAA
Found at i:119774800 original size:22 final size:22
Alignment explanation
Indices: 119774727--119774822 Score: 67
Period size: 22 Copynumber: 4.5 Consensus size: 22
119774717 TAAATGTATC
*
119774727 TAAAATAGTAACAATATTAA-AA
1 TAAAATAATAACAATA-TAATAA
*
119774749 TAAAAGTTAT-ACAATAT--TCAA
1 TAAAA-TAATAACAATATAAT-AA
*
119774770 -ATAATAATAACAATATAATAA
1 TAAAATAATAACAATATAATAA
* *
119774791 TAAAATAATAATAAAATAATAA
1 TAAAATAATAACAATATAATAA
* *
119774813 GAAAACAATA
1 TAAAATAATA
119774823 GCAAAACAGT
Statistics
Matches: 58, Mismatches: 9, Indels: 14
0.72 0.11 0.17
Matches are distributed among these distances:
19 3 0.05
20 10 0.17
21 5 0.09
22 38 0.66
23 2 0.03
ACGTcount: A:0.65, C:0.05, G:0.03, T:0.27
Consensus pattern (22 bp):
TAAAATAATAACAATATAATAA
Found at i:119774828 original size:22 final size:22
Alignment explanation
Indices: 119774775--119774828 Score: 63
Period size: 22 Copynumber: 2.5 Consensus size: 22
119774765 TTCAAATAAT
* * *
119774775 AATAACAATATAATAATAAAAT
1 AATAACAAAATAATAAGAAAAC
*
119774797 AATAATAAAATAATAAGAAAAC
1 AATAACAAAATAATAAGAAAAC
*
119774819 AATAGCAAAA
1 AATAACAAAA
119774829 CAGTGAGGAA
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:0.70, C:0.06, G:0.04, T:0.20
Consensus pattern (22 bp):
AATAACAAAATAATAAGAAAAC
Found at i:119776937 original size:9 final size:9
Alignment explanation
Indices: 119776923--119776947 Score: 50
Period size: 9 Copynumber: 2.8 Consensus size: 9
119776913 CAAGTATAAG
119776923 AATTAAAAA
1 AATTAAAAA
119776932 AATTAAAAA
1 AATTAAAAA
119776941 AATTAAA
1 AATTAAA
119776948 TAAAGAAGTA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 16 1.00
ACGTcount: A:0.76, C:0.00, G:0.00, T:0.24
Consensus pattern (9 bp):
AATTAAAAA
Found at i:119778107 original size:21 final size:20
Alignment explanation
Indices: 119778071--119778109 Score: 60
Period size: 21 Copynumber: 1.9 Consensus size: 20
119778061 CCAAAACAAA
*
119778071 AAGAAAATAGAAGAAAGAAC
1 AAGAAAATAAAAGAAAGAAC
119778091 AAGAAAAGTAAAAGAAAGA
1 AAGAAAA-TAAAAGAAAGA
119778110 CGAAACAGAG
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 7 0.41
21 10 0.59
ACGTcount: A:0.72, C:0.03, G:0.21, T:0.05
Consensus pattern (20 bp):
AAGAAAATAAAAGAAAGAAC
Found at i:119789663 original size:14 final size:14
Alignment explanation
Indices: 119789640--119789673 Score: 50
Period size: 14 Copynumber: 2.4 Consensus size: 14
119789630 GGTTTCTTTC
*
119789640 TCTAATGATACTAT
1 TCTAACGATACTAT
*
119789654 TCTAACGATATTAT
1 TCTAACGATACTAT
119789668 TCTAAC
1 TCTAAC
119789674 ATGTAATTTG
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.35, C:0.18, G:0.06, T:0.41
Consensus pattern (14 bp):
TCTAACGATACTAT
Found at i:119792179 original size:14 final size:15
Alignment explanation
Indices: 119792147--119792192 Score: 51
Period size: 14 Copynumber: 3.1 Consensus size: 15
119792137 TGTATTTACT
*
119792147 TATTATTTA-AGTAAA
1 TATTATTTATA-TTAA
119792162 TATTA-TTATATTAA
1 TATTATTTATATTAA
119792176 TATTATTTTATATTAA
1 TATTA-TTTATATTAA
119792192 T
1 T
119792193 TAAATAAAGT
Statistics
Matches: 27, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
14 11 0.41
15 6 0.22
16 10 0.37
ACGTcount: A:0.41, C:0.00, G:0.02, T:0.57
Consensus pattern (15 bp):
TATTATTTATATTAA
Found at i:119793631 original size:44 final size:44
Alignment explanation
Indices: 119793582--119793673 Score: 114
Period size: 44 Copynumber: 2.1 Consensus size: 44
119793572 TGTTCAAGGA
* * *
119793582 TACTTCGACCTTGAGTTGATGAGGCA-CTATAAGTGTCGTACTGT
1 TACTTCGACCTTAAGTCGATGAGGCATCT-TAAGTGTCGTACTAT
* **
119793626 TACTTCGACTTTAAGTCGATGAGGCATCTTGTGTGTCGTACTAT
1 TACTTCGACCTTAAGTCGATGAGGCATCTTAAGTGTCGTACTAT
119793670 TACT
1 TACT
119793674 ATTACTTTGG
Statistics
Matches: 41, Mismatches: 6, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
44 39 0.95
45 2 0.05
ACGTcount: A:0.22, C:0.18, G:0.23, T:0.37
Consensus pattern (44 bp):
TACTTCGACCTTAAGTCGATGAGGCATCTTAAGTGTCGTACTAT
Found at i:119795028 original size:29 final size:28
Alignment explanation
Indices: 119794971--119795056 Score: 118
Period size: 28 Copynumber: 3.0 Consensus size: 28
119794961 TACCTGTATC
* *
119794971 TGGCCCATTAAGCCCAATCATATTCATA
1 TGGCCCATTAGGCCCAATCACATTCATA
*
119794999 TGGCCCATTAGGCCCAAATCACATTTATA
1 TGGCCCATTAGGCCC-AATCACATTCATA
* *
119795028 TGGCCCGTTAGGCCCAGTCACATTCATA
1 TGGCCCATTAGGCCCAATCACATTCATA
119795056 T
1 T
119795057 TCATGCTCAC
Statistics
Matches: 51, Mismatches: 6, Indels: 2
0.86 0.10 0.03
Matches are distributed among these distances:
28 26 0.51
29 25 0.49
ACGTcount: A:0.28, C:0.29, G:0.15, T:0.28
Consensus pattern (28 bp):
TGGCCCATTAGGCCCAATCACATTCATA
Found at i:119796483 original size:16 final size:16
Alignment explanation
Indices: 119796462--119796493 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
119796452 AAAAATTCAA
*
119796462 GATTTCGGGATTTTTG
1 GATTTCGAGATTTTTG
119796478 GATTTCGAGATTTTTG
1 GATTTCGAGATTTTTG
119796494 AGGCGTTATA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.16, C:0.06, G:0.28, T:0.50
Consensus pattern (16 bp):
GATTTCGAGATTTTTG
Found at i:119796558 original size:18 final size:18
Alignment explanation
Indices: 119796521--119796632 Score: 98
Period size: 18 Copynumber: 6.2 Consensus size: 18
119796511 TAAATAAAAG
* *
119796521 TACTGAATGACTGACTGT
1 TACTGAATAACTGATTGT
* *
119796539 TACTGAATAATTGATCGT
1 TACTGAATAACTGATTGT
* * *
119796557 TATTGCATAACTGATTGC
1 TACTGAATAACTGATTGT
** *
119796575 TACTGAGCAAATGATTGT
1 TACTGAATAACTGATTGT
* *
119796593 TACTGAATAACTAATTGC
1 TACTGAATAACTGATTGT
* *
119796611 TACTGAATAATTGAATGT
1 TACTGAATAACTGATTGT
119796629 TACT
1 TACT
119796633 AAATGAAACT
Statistics
Matches: 70, Mismatches: 24, Indels: 0
0.74 0.26 0.00
Matches are distributed among these distances:
18 70 1.00
ACGTcount: A:0.33, C:0.13, G:0.17, T:0.37
Consensus pattern (18 bp):
TACTGAATAACTGATTGT
Found at i:119796579 original size:36 final size:36
Alignment explanation
Indices: 119796521--119796632 Score: 118
Period size: 36 Copynumber: 3.1 Consensus size: 36
119796511 TAAATAAAAG
* * *
119796521 TACTGAATGACTGACTGTTACTGAATAATTGATCGT
1 TACTGAATAACTGATTGCTACTGAATAATTGATCGT
* * ** * *
119796557 TATTGCATAACTGATTGCTACTGAGCAAATGATTGT
1 TACTGAATAACTGATTGCTACTGAATAATTGATCGT
*
119796593 TACTGAATAACTAATTGCTACTGAATAATTGAAT-GT
1 TACTGAATAACTGATTGCTACTGAATAATTG-ATCGT
119796629 TACT
1 TACT
119796633 AAATGAAACT
Statistics
Matches: 60, Mismatches: 15, Indels: 2
0.78 0.19 0.03
Matches are distributed among these distances:
36 58 0.97
37 2 0.03
ACGTcount: A:0.33, C:0.13, G:0.17, T:0.37
Consensus pattern (36 bp):
TACTGAATAACTGATTGCTACTGAATAATTGATCGT
Found at i:119803349 original size:18 final size:18
Alignment explanation
Indices: 119803300--119803350 Score: 75
Period size: 19 Copynumber: 2.8 Consensus size: 18
119803290 AAAATTGTGC
*
119803300 GCAATTTTATTTCTTTAT
1 GCAATTTTATTTCTTTAG
*
119803318 GTAATTTATATTTCTTTAG
1 GCAATTT-TATTTCTTTAG
119803337 GCAATTTTATTTCT
1 GCAATTTTATTTCT
119803351 CTGTCATTAA
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
18 13 0.45
19 16 0.55
ACGTcount: A:0.24, C:0.10, G:0.08, T:0.59
Consensus pattern (18 bp):
GCAATTTTATTTCTTTAG
Found at i:119812321 original size:26 final size:26
Alignment explanation
Indices: 119812284--119812367 Score: 150
Period size: 26 Copynumber: 3.2 Consensus size: 26
119812274 TGATACAAAT
* *
119812284 TGATAATAGGTTAGGTAAATGTTCCA
1 TGATAATGGGTTAGGTAAATGTTTCA
119812310 TGATAATGGGTTAGGTAAATGTTTCA
1 TGATAATGGGTTAGGTAAATGTTTCA
119812336 TGATAATGGGTTAGGTAAATGTTTCA
1 TGATAATGGGTTAGGTAAATGTTTCA
119812362 TGATAA
1 TGATAA
119812368 GAATTTCATG
Statistics
Matches: 56, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
26 56 1.00
ACGTcount: A:0.33, C:0.05, G:0.25, T:0.37
Consensus pattern (26 bp):
TGATAATGGGTTAGGTAAATGTTTCA
Found at i:119822106 original size:14 final size:13
Alignment explanation
Indices: 119822087--119822117 Score: 53
Period size: 14 Copynumber: 2.3 Consensus size: 13
119822077 ATATTTCTTA
119822087 TTTTTTAAATGAAT
1 TTTTTTAAAT-AAT
119822101 TTTTTTAAATAAT
1 TTTTTTAAATAAT
119822114 TTTT
1 TTTT
119822118 CAATTGAGTT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 7 0.41
14 10 0.59
ACGTcount: A:0.32, C:0.00, G:0.03, T:0.65
Consensus pattern (13 bp):
TTTTTTAAATAAT
Found at i:119822178 original size:14 final size:15
Alignment explanation
Indices: 119822159--119822192 Score: 52
Period size: 15 Copynumber: 2.3 Consensus size: 15
119822149 CTAATTCTAT
119822159 TAATAACT-TAAATA
1 TAATAACTATAAATA
*
119822173 TAATAACTATAGATA
1 TAATAACTATAAATA
119822188 TAATA
1 TAATA
119822193 TTTTAAATTA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
14 8 0.44
15 10 0.56
ACGTcount: A:0.56, C:0.06, G:0.03, T:0.35
Consensus pattern (15 bp):
TAATAACTATAAATA
Found at i:119833150 original size:49 final size:49
Alignment explanation
Indices: 119833095--119833192 Score: 187
Period size: 49 Copynumber: 2.0 Consensus size: 49
119833085 ACCTCTTTAT
119833095 TGAAAAACAAGTAAAGTAATCCTTATACATTTAGAAATATACAAATTAA
1 TGAAAAACAAGTAAAGTAATCCTTATACATTTAGAAATATACAAATTAA
*
119833144 TGAAAAACAAGTAAAGTAATCCTTATACATTTAGAAATATGCAAATTAA
1 TGAAAAACAAGTAAAGTAATCCTTATACATTTAGAAATATACAAATTAA
119833193 CCTTTCCCTT
Statistics
Matches: 48, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
49 48 1.00
ACGTcount: A:0.52, C:0.10, G:0.09, T:0.29
Consensus pattern (49 bp):
TGAAAAACAAGTAAAGTAATCCTTATACATTTAGAAATATACAAATTAA
Found at i:119835037 original size:21 final size:21
Alignment explanation
Indices: 119835013--119835052 Score: 80
Period size: 21 Copynumber: 1.9 Consensus size: 21
119835003 ATTAATAAAT
119835013 AATGAAATTACATTTTGACCC
1 AATGAAATTACATTTTGACCC
119835034 AATGAAATTACATTTTGAC
1 AATGAAATTACATTTTGAC
119835053 ACATTTAAAT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.40, C:0.15, G:0.10, T:0.35
Consensus pattern (21 bp):
AATGAAATTACATTTTGACCC
Found at i:119835186 original size:23 final size:24
Alignment explanation
Indices: 119835153--119835212 Score: 61
Period size: 23 Copynumber: 2.5 Consensus size: 24
119835143 TCCCTTCAAA
119835153 ATAATCAAATTATA-AAATTAATAT
1 ATAAT-AAATTATATAAATTAATAT
** *
119835177 ATAATAAATT-TATATTTTAATTT
1 ATAATAAATTATATAAATTAATAT
*
119835200 ATAAAAAATTATA
1 ATAATAAATTATA
119835213 GTTAAATTTC
Statistics
Matches: 30, Mismatches: 4, Indels: 4
0.79 0.11 0.11
Matches are distributed among these distances:
22 2 0.07
23 21 0.70
24 7 0.23
ACGTcount: A:0.55, C:0.02, G:0.00, T:0.43
Consensus pattern (24 bp):
ATAATAAATTATATAAATTAATAT
Found at i:119835220 original size:22 final size:23
Alignment explanation
Indices: 119835176--119835221 Score: 58
Period size: 22 Copynumber: 2.0 Consensus size: 23
119835166 AAAATTAATA
* * *
119835176 TATAATAAATTTATATTTTAATT
1 TATAATAAAATTATAGTTAAATT
119835199 TATAA-AAAATTATAGTTAAATT
1 TATAATAAAATTATAGTTAAATT
119835221 T
1 T
119835222 CGACTCTGTA
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
22 15 0.75
23 5 0.25
ACGTcount: A:0.48, C:0.00, G:0.02, T:0.50
Consensus pattern (23 bp):
TATAATAAAATTATAGTTAAATT
Found at i:119839741 original size:2 final size:2
Alignment explanation
Indices: 119839734--119839774 Score: 64
Period size: 2 Copynumber: 20.5 Consensus size: 2
119839724 ATAAAAACTA
* *
119839734 AT AT AT AT AT AT AT AT AT AT AT AT TT AT AT AT AT AT GT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
119839775 ATGAATAAAA
Statistics
Matches: 35, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.46, C:0.00, G:0.02, T:0.51
Consensus pattern (2 bp):
AT
Found at i:119841189 original size:18 final size:18
Alignment explanation
Indices: 119841128--119841199 Score: 60
Period size: 18 Copynumber: 4.1 Consensus size: 18
119841118 CCTTAATAGT
*
119841128 TCAC-ACTTTA-ATGTGC
1 TCACAACTTTAGATGAGC
* * *
119841144 TCGCAACTTCAGTTGAGC
1 TCACAACTTTAGATGAGC
**
119841162 TCACGTCTTTATG-TGAGC
1 TCACAACTTTA-GATGAGC
119841180 TCACAACTTTAGATGAGC
1 TCACAACTTTAGATGAGC
119841198 TC
1 TC
119841200 GTAGCTTCAA
Statistics
Matches: 42, Mismatches: 10, Indels: 6
0.72 0.17 0.10
Matches are distributed among these distances:
16 3 0.07
17 6 0.14
18 32 0.76
19 1 0.02
ACGTcount: A:0.24, C:0.25, G:0.18, T:0.33
Consensus pattern (18 bp):
TCACAACTTTAGATGAGC
Found at i:119844018 original size:6 final size:6
Alignment explanation
Indices: 119844001--119844040 Score: 55
Period size: 6 Copynumber: 6.8 Consensus size: 6
119843991 TCAGTCTCTA
* *
119844001 TCAGTT TTAGTT TCAGTT TCAGTT TCA-CT TCAGTT TCAGT
1 TCAGTT TCAGTT TCAGTT TCAGTT TCAGTT TCAGTT TCAGT
119844041 ATACATTAAC
Statistics
Matches: 29, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
5 4 0.14
6 25 0.86
ACGTcount: A:0.17, C:0.17, G:0.15, T:0.50
Consensus pattern (6 bp):
TCAGTT
Found at i:119849514 original size:2 final size:2
Alignment explanation
Indices: 119849507--119849542 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
119849497 AAAGGCCATT
119849507 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
119849543 CACACACACA
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:119863441 original size:25 final size:25
Alignment explanation
Indices: 119863368--119863444 Score: 70
Period size: 25 Copynumber: 3.2 Consensus size: 25
119863358 CTCTCCCATC
*
119863368 CCTCACCCTCTTCCCCACCATCCCT
1 CCTCCCCCTCTTCCCCACCATCCCT
* **** *
119863393 CC-CCCACTCTGATTC-CC-TCTCT
1 CCTCCCCCTCTTCCCCACCATCCCT
119863415 CCTCCCCCTCTTCCCCACCATCCCT
1 CCTCCCCCTCTTCCCCACCATCCCT
119863440 CCTCC
1 CCTCC
119863445 TACTCTGATT
Statistics
Matches: 36, Mismatches: 13, Indels: 6
0.65 0.24 0.11
Matches are distributed among these distances:
22 6 0.17
23 10 0.28
24 9 0.25
25 11 0.31
ACGTcount: A:0.09, C:0.64, G:0.01, T:0.26
Consensus pattern (25 bp):
CCTCCCCCTCTTCCCCACCATCCCT
Found at i:119863467 original size:47 final size:47
Alignment explanation
Indices: 119863368--119863469 Score: 134
Period size: 47 Copynumber: 2.2 Consensus size: 47
119863358 CTCTCCCATC
* * *
119863368 CCTCACCCTCTTCCCCACCATCCCTCCCCCACTCTGATTCCCTCTCT
1 CCTCCCCCTCTTCCCCACCATCCCTCCCCCACTCTGATTACCTCCCT
* **
119863415 CCTCCCCCTCTTCCCCACCATCCCTCCTCCTACTCTGATTATTTCCCT
1 CCTCCCCCTCTTCCCCACCATCCCTCC-CCCACTCTGATTACCTCCCT
119863463 -CTCCCCC
1 CCTCCCCC
119863470 ACCATCCCTC
Statistics
Matches: 48, Mismatches: 6, Indels: 2
0.86 0.11 0.04
Matches are distributed among these distances:
47 33 0.69
48 15 0.31
ACGTcount: A:0.10, C:0.59, G:0.02, T:0.29
Consensus pattern (47 bp):
CCTCCCCCTCTTCCCCACCATCCCTCCCCCACTCTGATTACCTCCCT
Found at i:119872073 original size:16 final size:18
Alignment explanation
Indices: 119872052--119872093 Score: 54
Period size: 16 Copynumber: 2.5 Consensus size: 18
119872042 TTTTTTACTT
119872052 TTTTGTCTTTC-T-TTTA
1 TTTTGTCTTTCATATTTA
*
119872068 TTTTGTTTTTCATATTTA
1 TTTTGTCTTTCATATTTA
119872086 TTTT-TCTT
1 TTTTGTCTT
119872094 ATTTTTTTAT
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
16 10 0.45
17 4 0.18
18 8 0.36
ACGTcount: A:0.10, C:0.10, G:0.05, T:0.76
Consensus pattern (18 bp):
TTTTGTCTTTCATATTTA
Found at i:119872108 original size:20 final size:20
Alignment explanation
Indices: 119872083--119872138 Score: 60
Period size: 20 Copynumber: 2.7 Consensus size: 20
119872073 TTTTTCATAT
119872083 TTATTTTTCTTATTTT-TTTA
1 TTATTTTT-TTATTTTGTTTA
119872103 TTATTTTTATTATATTTGTTTA
1 TTATTTTT-TTAT-TTTGTTTA
* *
119872125 CTATTGTTTTATTT
1 TTATTTTTTTATTT
119872139 AATTTAGTTA
Statistics
Matches: 31, Mismatches: 3, Indels: 4
0.82 0.08 0.11
Matches are distributed among these distances:
20 14 0.45
21 7 0.23
22 10 0.32
ACGTcount: A:0.18, C:0.04, G:0.04, T:0.75
Consensus pattern (20 bp):
TTATTTTTTTATTTTGTTTA
Found at i:119874248 original size:2 final size:2
Alignment explanation
Indices: 119874243--119874304 Score: 124
Period size: 2 Copynumber: 31.0 Consensus size: 2
119874233 TATATATATA
119874243 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG
1 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG
119874285 TG TG TG TG TG TG TG TG TG TG
1 TG TG TG TG TG TG TG TG TG TG
119874305 AATGAGATAT
Statistics
Matches: 60, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 60 1.00
ACGTcount: A:0.00, C:0.00, G:0.50, T:0.50
Consensus pattern (2 bp):
TG
Found at i:119874478 original size:15 final size:15
Alignment explanation
Indices: 119874460--119874516 Score: 89
Period size: 15 Copynumber: 3.9 Consensus size: 15
119874450 TATCTGTTTT
119874460 ATTGAATTTATATTG
1 ATTGAATTTATATTG
* *
119874475 ATTGAAATTATTTTG
1 ATTGAATTTATATTG
119874490 ATTGAATTTATATTG
1 ATTGAATTTATATTG
119874505 ATTGAA-TTATAT
1 ATTGAATTTATAT
119874517 AATATATATG
Statistics
Matches: 38, Mismatches: 4, Indels: 1
0.88 0.09 0.02
Matches are distributed among these distances:
14 6 0.16
15 32 0.84
ACGTcount: A:0.35, C:0.00, G:0.12, T:0.53
Consensus pattern (15 bp):
ATTGAATTTATATTG
Found at i:119874495 original size:30 final size:28
Alignment explanation
Indices: 119874456--119874514 Score: 100
Period size: 30 Copynumber: 2.0 Consensus size: 28
119874446 TGAATATCTG
119874456 TTTTATTGAATTTATATTGATTGAAATTA
1 TTTTATTGAATTTATATTGATTG-AATTA
119874485 TTTTGATTGAATTTATATTGATTGAATTA
1 TTTT-ATTGAATTTATATTGATTGAATTA
119874514 T
1 T
119874515 ATAATATATA
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
29 10 0.34
30 19 0.66
ACGTcount: A:0.32, C:0.00, G:0.12, T:0.56
Consensus pattern (28 bp):
TTTTATTGAATTTATATTGATTGAATTA
Found at i:119874946 original size:21 final size:23
Alignment explanation
Indices: 119874890--119874952 Score: 85
Period size: 21 Copynumber: 2.8 Consensus size: 23
119874880 TTATCGATCT
119874890 GGCACTTTATGTGTCGTATTTCA
1 GGCACTTTATGTGTCGTATTTCA
* **
119874913 GGCACCTCGTGTGTCGT-TTT-A
1 GGCACTTTATGTGTCGTATTTCA
119874934 GGCACTTTATGTGTCGTAT
1 GGCACTTTATGTGTCGTAT
119874953 ACTGATCAGG
Statistics
Matches: 33, Mismatches: 6, Indels: 3
0.79 0.14 0.07
Matches are distributed among these distances:
21 15 0.45
22 4 0.12
23 14 0.42
ACGTcount: A:0.14, C:0.19, G:0.25, T:0.41
Consensus pattern (23 bp):
GGCACTTTATGTGTCGTATTTCA
Found at i:119875135 original size:18 final size:19
Alignment explanation
Indices: 119875114--119875154 Score: 59
Period size: 19 Copynumber: 2.2 Consensus size: 19
119875104 AATGAAATGA
119875114 GAAATTGA-AT-TGAGAATT
1 GAAATTGAGATATGAG-ATT
119875132 GAAATTGAGATATGAGATT
1 GAAATTGAGATATGAGATT
119875151 GAAA
1 GAAA
119875155 ACATGAATCA
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
18 8 0.38
19 9 0.43
20 4 0.19
ACGTcount: A:0.46, C:0.00, G:0.24, T:0.29
Consensus pattern (19 bp):
GAAATTGAGATATGAGATT
Found at i:119877394 original size:14 final size:15
Alignment explanation
Indices: 119877373--119877402 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
119877363 ATTCTTTTCT
119877373 CTTTTTTTTTCTTAA
1 CTTTTTTTTTCTTAA
119877388 CTTTTTTTTTCTTAA
1 CTTTTTTTTTCTTAA
119877403 GAATGTATTG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.13, C:0.13, G:0.00, T:0.73
Consensus pattern (15 bp):
CTTTTTTTTTCTTAA
Found at i:119877501 original size:106 final size:107
Alignment explanation
Indices: 119877390--119877593 Score: 266
Period size: 106 Copynumber: 1.9 Consensus size: 107
119877380 TTTCTTAACT
* * * * * *
119877390 TTTTTTTTCTTAAGAATGTATTGGCCCTTTTGACGCAAAGAGGGATGATAACCCAAGCACCCTAC
1 TTTTTTTGCTTAAGAATATATTGGCCCTATTGACGCAAAGAGGAATGACAACCCAAGCACCCCAC
* ** *
119877455 CCTGGTTACTCAGCTTAACACGCTCTT-ATTTTATTATTATA
66 CCCGGTTACTCAGCCCAACACACTCTTAATTTTATTATTATA
* * * * *
119877496 TTTTTTTGGTTCAGAATATTTTGGCCCTATTGACGTAAAGTGGAATGACAACCCAAGCACCCCAC
1 TTTTTTTGCTTAAGAATATATTGGCCCTATTGACGCAAAGAGGAATGACAACCCAAGCACCCCAC
119877561 CCCGGTTACTCAGCCCAACACACTCTTAATTTT
66 CCCGGTTACTCAGCCCAACACACTCTTAATTTT
119877594 TTTGTTTAAT
Statistics
Matches: 82, Mismatches: 15, Indels: 1
0.84 0.15 0.01
Matches are distributed among these distances:
106 77 0.94
107 5 0.06
ACGTcount: A:0.26, C:0.25, G:0.15, T:0.34
Consensus pattern (107 bp):
TTTTTTTGCTTAAGAATATATTGGCCCTATTGACGCAAAGAGGAATGACAACCCAAGCACCCCAC
CCCGGTTACTCAGCCCAACACACTCTTAATTTTATTATTATA
Found at i:119883510 original size:25 final size:24
Alignment explanation
Indices: 119883440--119883511 Score: 72
Period size: 25 Copynumber: 2.9 Consensus size: 24
119883430 AGCTCATATT
* *
119883440 AGCTTACCAATTTGTAACTCGTATG
1 AGCTTACTAA-TTCTAACTCGTATG
* * *
119883465 AGTTTACTGATTCTCATCTCGTATG
1 AGCTTACTAATTCT-AACTCGTATG
119883490 AGCTTACTAATTCATAACTCGT
1 AGCTTACTAATTC-TAACTCGT
119883512 GAAAGCATGC
Statistics
Matches: 37, Mismatches: 8, Indels: 4
0.76 0.16 0.08
Matches are distributed among these distances:
24 3 0.08
25 33 0.89
26 1 0.03
ACGTcount: A:0.26, C:0.21, G:0.14, T:0.39
Consensus pattern (24 bp):
AGCTTACTAATTCTAACTCGTATG
Found at i:119883733 original size:30 final size:30
Alignment explanation
Indices: 119883694--119883755 Score: 76
Period size: 31 Copynumber: 2.1 Consensus size: 30
119883684 TACATGAAAT
119883694 ACATGGAAAT-GAT-ATTACATGATATATTGAA
1 ACATGGAAATGGATGA-TACATG-TATA-TGAA
119883725 ACAT-GAAATGGATGATACATGTATATGAA
1 ACATGGAAATGGATGATACATGTATATGAA
119883754 AC
1 AC
119883756 TTGCTTAGTG
Statistics
Matches: 29, Mismatches: 0, Indels: 6
0.83 0.00 0.17
Matches are distributed among these distances:
29 6 0.21
30 9 0.31
31 13 0.45
32 1 0.03
ACGTcount: A:0.45, C:0.08, G:0.18, T:0.29
Consensus pattern (30 bp):
ACATGGAAATGGATGATACATGTATATGAA
Found at i:119886126 original size:25 final size:25
Alignment explanation
Indices: 119886078--119886127 Score: 64
Period size: 25 Copynumber: 2.0 Consensus size: 25
119886068 ACCCTTATAA
* * * *
119886078 TAAAAATGACCGTTTTGCCTCTAGG
1 TAAAAATGACCATTATACCCCTAGG
119886103 TAAAAATGACCATTATACCCCTAGG
1 TAAAAATGACCATTATACCCCTAGG
119886128 GTTTATATAT
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
25 21 1.00
ACGTcount: A:0.34, C:0.22, G:0.16, T:0.28
Consensus pattern (25 bp):
TAAAAATGACCATTATACCCCTAGG
Found at i:119886194 original size:20 final size:20
Alignment explanation
Indices: 119886171--119886229 Score: 109
Period size: 20 Copynumber: 3.0 Consensus size: 20
119886161 TAAACATGGT
119886171 ATGTATGATATGCACATGAC
1 ATGTATGATATGCACATGAC
*
119886191 ATGTATGATATGCACATGAT
1 ATGTATGATATGCACATGAC
119886211 ATGTATGATATGCACATGA
1 ATGTATGATATGCACATGA
119886230 GGTATTCATA
Statistics
Matches: 38, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 38 1.00
ACGTcount: A:0.36, C:0.12, G:0.20, T:0.32
Consensus pattern (20 bp):
ATGTATGATATGCACATGAC
Found at i:119886211 original size:11 final size:11
Alignment explanation
Indices: 119886175--119886229 Score: 55
Period size: 11 Copynumber: 5.4 Consensus size: 11
119886165 CATGGTATGT
119886175 ATGATATGCAC
1 ATGATATGCAC
* *
119886186 ATGACATG--T
1 ATGATATGCAC
119886195 ATGATATGCAC
1 ATGATATGCAC
*
119886206 ATGATATG--T
1 ATGATATGCAC
119886215 ATGATATGCAC
1 ATGATATGCAC
119886226 ATGA
1 ATGA
119886230 GGTATTCATA
Statistics
Matches: 34, Mismatches: 6, Indels: 8
0.71 0.12 0.17
Matches are distributed among these distances:
9 15 0.44
11 19 0.56
ACGTcount: A:0.36, C:0.13, G:0.20, T:0.31
Consensus pattern (11 bp):
ATGATATGCAC
Found at i:119886311 original size:24 final size:24
Alignment explanation
Indices: 119886280--119886408 Score: 197
Period size: 24 Copynumber: 5.4 Consensus size: 24
119886270 GAGGAAGTGC
*
119886280 AAAAGGGCTTATGCCCCAGTTATC
1 AAAAGGGCTTATGCCCCAGTTATT
*
119886304 AAAAGGGCTTATGCTCCAGTTATT
1 AAAAGGGCTTATGCCCCAGTTATT
*
119886328 GAAAGGGCTTATGCCCCAGTTATT
1 AAAAGGGCTTATGCCCCAGTTATT
*
119886352 AAAAGGGTTTATGCCCCAGTTATT
1 AAAAGGGCTTATGCCCCAGTTATT
*
119886376 AAAAGGGCTT-TGCCCTAGTTATT
1 AAAAGGGCTTATGCCCCAGTTATT
119886399 AAAAGAGGCT
1 AAAAG-GGCT
119886409 AGGCCTCCAG
Statistics
Matches: 96, Mismatches: 8, Indels: 2
0.91 0.08 0.02
Matches are distributed among these distances:
23 17 0.18
24 79 0.82
ACGTcount: A:0.29, C:0.19, G:0.22, T:0.29
Consensus pattern (24 bp):
AAAAGGGCTTATGCCCCAGTTATT
Found at i:119894323 original size:20 final size:20
Alignment explanation
Indices: 119894300--119894358 Score: 109
Period size: 20 Copynumber: 3.0 Consensus size: 20
119894290 TAAACATGGT
119894300 ATGTATGATATGCACATGAC
1 ATGTATGATATGCACATGAC
*
119894320 ATGTATGATATGCACATGAT
1 ATGTATGATATGCACATGAC
119894340 ATGTATGATATGCACATGA
1 ATGTATGATATGCACATGA
119894359 GGTATTCATA
Statistics
Matches: 38, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 38 1.00
ACGTcount: A:0.36, C:0.12, G:0.20, T:0.32
Consensus pattern (20 bp):
ATGTATGATATGCACATGAC
Found at i:119894340 original size:11 final size:11
Alignment explanation
Indices: 119894304--119894358 Score: 55
Period size: 11 Copynumber: 5.4 Consensus size: 11
119894294 CATGGTATGT
119894304 ATGATATGCAC
1 ATGATATGCAC
* *
119894315 ATGACATG--T
1 ATGATATGCAC
119894324 ATGATATGCAC
1 ATGATATGCAC
*
119894335 ATGATATG--T
1 ATGATATGCAC
119894344 ATGATATGCAC
1 ATGATATGCAC
119894355 ATGA
1 ATGA
119894359 GGTATTCATA
Statistics
Matches: 34, Mismatches: 6, Indels: 8
0.71 0.12 0.17
Matches are distributed among these distances:
9 15 0.44
11 19 0.56
ACGTcount: A:0.36, C:0.13, G:0.20, T:0.31
Consensus pattern (11 bp):
ATGATATGCAC
Found at i:119894435 original size:24 final size:24
Alignment explanation
Indices: 119894409--119894578 Score: 270
Period size: 24 Copynumber: 7.1 Consensus size: 24
119894399 GACGAAGTGC
* *
119894409 AAAAGAGCTTATGCCCCAGTTATC
1 AAAAGGGCTTATGCCCCAGTTATT
119894433 AAAAGGGCTTATGCCCCAGTTATT
1 AAAAGGGCTTATGCCCCAGTTATT
* *
119894457 GAAAGGGCTTATGCCCCAGTTATC
1 AAAAGGGCTTATGCCCCAGTTATT
119894481 AAAAGGGCTTATGCCCCAGTTATT
1 AAAAGGGCTTATGCCCCAGTTATT
* *
119894505 GAAAGGGCTTATGCCCTAGTTATT
1 AAAAGGGCTTATGCCCCAGTTATT
119894529 AAAAGGGCTTATGCCCCAGTTATT
1 AAAAGGGCTTATGCCCCAGTTATT
*
119894553 AAAAGGGCTT-TGCCCTAGTTATT
1 AAAAGGGCTTATGCCCCAGTTATT
119894576 AAA
1 AAA
119894579 GAGGCTAGGC
Statistics
Matches: 135, Mismatches: 11, Indels: 1
0.92 0.07 0.01
Matches are distributed among these distances:
23 15 0.11
24 120 0.89
ACGTcount: A:0.29, C:0.21, G:0.21, T:0.29
Consensus pattern (24 bp):
AAAAGGGCTTATGCCCCAGTTATT
Found at i:119896348 original size:33 final size:33
Alignment explanation
Indices: 119896302--119896384 Score: 94
Period size: 33 Copynumber: 2.5 Consensus size: 33
119896292 GAAAATCCTC
* * * *
119896302 TATTTTCTTTTGGAAATCAACAATTTGTCGTTA
1 TATTTGCTGTTGGAAATCAACAATTTGCCATTA
* * * *
119896335 TATTTGTTGTTGGAAATCAATAGTTTGCCATTG
1 TATTTGCTGTTGGAAATCAACAATTTGCCATTA
119896368 TATTTGCTGTTGGAAAT
1 TATTTGCTGTTGGAAAT
119896385 TAAGCACATT
Statistics
Matches: 41, Mismatches: 9, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
33 41 1.00
ACGTcount: A:0.25, C:0.10, G:0.18, T:0.47
Consensus pattern (33 bp):
TATTTGCTGTTGGAAATCAACAATTTGCCATTA
Found at i:119903650 original size:19 final size:19
Alignment explanation
Indices: 119903623--119903681 Score: 70
Period size: 18 Copynumber: 3.2 Consensus size: 19
119903613 ATTTTATTTG
*
119903623 TTTTCTTTTTAGTTTTATT
1 TTTTATTTTTAGTTTTATT
119903642 TTTTATTTTTA-TGTTTA-T
1 TTTTATTTTTAGT-TTTATT
*
119903660 TTTTGTTTTTAGTTTT-TT
1 TTTTATTTTTAGTTTTATT
119903678 TTTT
1 TTTT
119903682 CTTAAACTTC
Statistics
Matches: 35, Mismatches: 2, Indels: 7
0.80 0.05 0.16
Matches are distributed among these distances:
18 20 0.57
19 15 0.43
ACGTcount: A:0.10, C:0.02, G:0.07, T:0.81
Consensus pattern (19 bp):
TTTTATTTTTAGTTTTATT
Found at i:119903681 original size:6 final size:6
Alignment explanation
Indices: 119903623--119903681 Score: 57
Period size: 6 Copynumber: 9.7 Consensus size: 6
119903613 ATTTTATTTG
* * * *
119903623 TTTTCT TTTTAG TTTTATT TTTTAT TTTTAT GTTTAT TTTTGT TTTTAGT
1 TTTTAT TTTTAT TTTTA-T TTTTAT TTTTAT TTTTAT TTTTAT TTTTA-T
119903673 TTTT-T TTTT
1 TTTTAT TTTT
119903682 CTTAAACTTC
Statistics
Matches: 44, Mismatches: 7, Indels: 5
0.79 0.12 0.09
Matches are distributed among these distances:
5 5 0.11
6 29 0.66
7 10 0.23
ACGTcount: A:0.10, C:0.02, G:0.07, T:0.81
Consensus pattern (6 bp):
TTTTAT
Found at i:119906095 original size:39 final size:39
Alignment explanation
Indices: 119906041--119906297 Score: 365
Period size: 39 Copynumber: 6.5 Consensus size: 39
119906031 TAATGGACAA
119906041 TTATATCCGGGCTAAGTCCCGAAGGCATTCGTGCTGGTG
1 TTATATCCGGGCTAAGTCCCGAAGGCATTCGTGCTGGTG
*
119906080 TTATATCCGGGCTAAGTCCTGAAGGCATTCGTGCTGGTG
1 TTATATCCGGGCTAAGTCCCGAAGGCATTCGTGCTGGTG
* * *
119906119 TTATTTTCGGGCTAAG-CTCCAAAGGCATTCGTGCTGGTG
1 TTATATCCGGGCTAAGTC-CCGAAGGCATTCGTGCTGGTG
119906158 TTATATCCGGGCTAAGTCCCGAAGGCATTCGTGCTGGTG
1 TTATATCCGGGCTAAGTCCCGAAGGCATTCGTGCTGGTG
* *
119906197 TTATATCCGGGCTAAGCCCCGAAGGTATTCGTGCTGGTG
1 TTATATCCGGGCTAAGTCCCGAAGGCATTCGTGCTGGTG
* * * *
119906236 TTATATCAGGGCTAAAGTCCCGTAGGC-TTTGTGCTGGTA
1 TTATATCCGGGCT-AAGTCCCGAAGGCATTCGTGCTGGTG
*
119906275 TTATATTCGGGCTTAAAGTCCCG
1 TTATATCCGGGC-T-AAGTCCCG
119906298 CATGCTTTGT
Statistics
Matches: 196, Mismatches: 18, Indels: 7
0.89 0.08 0.03
Matches are distributed among these distances:
38 1 0.01
39 174 0.89
40 21 0.11
ACGTcount: A:0.19, C:0.21, G:0.29, T:0.31
Consensus pattern (39 bp):
TTATATCCGGGCTAAGTCCCGAAGGCATTCGTGCTGGTG
Found at i:119912806 original size:2 final size:2
Alignment explanation
Indices: 119912801--119912826 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
119912791 AAAAAAAAAA
119912801 AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT
119912827 GTTGTATAAA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:119922605 original size:7 final size:7
Alignment explanation
Indices: 119922593--119922626 Score: 52
Period size: 7 Copynumber: 5.0 Consensus size: 7
119922583 TTCGATCGTG
119922593 ATTAAAA
1 ATTAAAA
119922600 ATTAAAA
1 ATTAAAA
*
119922607 ACTAAAA
1 ATTAAAA
119922614 ATT-AAA
1 ATTAAAA
119922620 ATTAAAA
1 ATTAAAA
119922627 TCAGAATAGG
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
6 6 0.25
7 18 0.75
ACGTcount: A:0.71, C:0.03, G:0.00, T:0.26
Consensus pattern (7 bp):
ATTAAAA
Found at i:119924367 original size:19 final size:17
Alignment explanation
Indices: 119924282--119924358 Score: 52
Period size: 19 Copynumber: 4.4 Consensus size: 17
119924272 TATTATTTAA
*
119924282 TAATTTTTTCATTTATG
1 TAATTTTTTAATTTATG
119924299 TAATTTTAATTAA-TT-T-
1 TAATTTT--TTAATTTATG
* *
119924315 TAATTTTTAAATATTATT
1 TAATTTTTTAAT-TTATG
*
119924333 TAATATTTTTCCATTTATG
1 TAAT-TTTTT-AATTTATG
119924352 TAATTTT
1 TAATTTT
119924359 AATTAATTTG
Statistics
Matches: 47, Mismatches: 5, Indels: 15
0.70 0.07 0.22
Matches are distributed among these distances:
14 3 0.06
16 9 0.19
17 9 0.19
18 9 0.19
19 15 0.32
20 2 0.04
ACGTcount: A:0.31, C:0.04, G:0.03, T:0.62
Consensus pattern (17 bp):
TAATTTTTTAATTTATG
Found at i:119924374 original size:53 final size:54
Alignment explanation
Indices: 119924254--119924367 Score: 203
Period size: 53 Copynumber: 2.1 Consensus size: 54
119924244 ATGGTAAGGG
* *
119924254 TTAATTTTAATTTTTGAATATTATTTAATAATTTTTTCATTTATGTAATTTTAA
1 TTAATTTTAATTTTTAAATATTATTTAATAATTTTTCCATTTATGTAATTTTAA
119924308 TTAATTTTAATTTTTAAATATTATTTAAT-ATTTTTCCATTTATGTAATTTTAA
1 TTAATTTTAATTTTTAAATATTATTTAATAATTTTTCCATTTATGTAATTTTAA
119924361 TTAATTT
1 TTAATTT
119924368 GTATTTTATA
Statistics
Matches: 58, Mismatches: 2, Indels: 1
0.95 0.03 0.02
Matches are distributed among these distances:
53 30 0.52
54 28 0.48
ACGTcount: A:0.33, C:0.03, G:0.03, T:0.61
Consensus pattern (54 bp):
TTAATTTTAATTTTTAAATATTATTTAATAATTTTTCCATTTATGTAATTTTAA
Found at i:119927758 original size:7 final size:7
Alignment explanation
Indices: 119927748--119927779 Score: 55
Period size: 7 Copynumber: 4.6 Consensus size: 7
119927738 AGTCATTTCA
119927748 TATTTAG
1 TATTTAG
119927755 TATTTAG
1 TATTTAG
119927762 TATTTAG
1 TATTTAG
*
119927769 TATATAG
1 TATTTAG
119927776 TATT
1 TATT
119927780 ATGTATATAA
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
7 23 1.00
ACGTcount: A:0.31, C:0.00, G:0.12, T:0.56
Consensus pattern (7 bp):
TATTTAG
Found at i:119927765 original size:14 final size:14
Alignment explanation
Indices: 119927748--119927788 Score: 57
Period size: 14 Copynumber: 2.9 Consensus size: 14
119927738 AGTCATTTCA
*
119927748 TATTTAGTATTTAG
1 TATTTAGTATATAG
119927762 TATTTAGTATATAG
1 TATTTAGTATATAG
119927776 TA-TTATGTATATA
1 TATTTA-GTATATA
119927789 ACTAATATTT
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
13 3 0.12
14 22 0.88
ACGTcount: A:0.34, C:0.00, G:0.12, T:0.54
Consensus pattern (14 bp):
TATTTAGTATATAG
Found at i:119928421 original size:18 final size:18
Alignment explanation
Indices: 119928398--119928439 Score: 66
Period size: 18 Copynumber: 2.3 Consensus size: 18
119928388 GCTAGGTGCA
*
119928398 TATCCTAGCCCTTATATG
1 TATCCTAACCCTTATATG
119928416 TATCCTAACCCTTATATG
1 TATCCTAACCCTTATATG
*
119928434 TTTCCT
1 TATCCT
119928440 TTTCCCAGTC
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
18 22 1.00
ACGTcount: A:0.21, C:0.29, G:0.07, T:0.43
Consensus pattern (18 bp):
TATCCTAACCCTTATATG
Found at i:119930273 original size:18 final size:17
Alignment explanation
Indices: 119930230--119930274 Score: 54
Period size: 18 Copynumber: 2.5 Consensus size: 17
119930220 TAAAAAAATG
119930230 AAAGTAATAGTAATAAT
1 AAAGTAATAGTAATAAT
* *
119930247 AATATTAATGGTAATAAT
1 AA-AGTAATAGTAATAAT
119930265 ATAAGTAATA
1 A-AAGTAATA
119930275 AATATTTAAA
Statistics
Matches: 22, Mismatches: 4, Indels: 3
0.76 0.14 0.10
Matches are distributed among these distances:
17 2 0.09
18 19 0.86
19 1 0.05
ACGTcount: A:0.56, C:0.00, G:0.11, T:0.33
Consensus pattern (17 bp):
AAAGTAATAGTAATAAT
Found at i:119930414 original size:3 final size:3
Alignment explanation
Indices: 119930406--119930544 Score: 192
Period size: 3 Copynumber: 47.0 Consensus size: 3
119930396 TAGATATATG
* * * *
119930406 TAA TAA TAA T-A TAA TAG TAA TGA TAA TAA T-A TAA TAA TAA TAG TAG
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
* *
119930452 TAA TAG TAA TAA AAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
* *
119930500 TAA TAA TAA TAA TAA TAA TAA TAA TAG TAA TAA TAG TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
119930545 GACCGTAAAG
Statistics
Matches: 120, Mismatches: 14, Indels: 4
0.87 0.10 0.03
Matches are distributed among these distances:
2 4 0.03
3 116 0.97
ACGTcount: A:0.62, C:0.00, G:0.05, T:0.33
Consensus pattern (3 bp):
TAA
Found at i:119930639 original size:10 final size:9
Alignment explanation
Indices: 119930624--119930660 Score: 51
Period size: 8 Copynumber: 4.2 Consensus size: 9
119930614 TAGTAATGAC
119930624 AATAATAGAA
1 AATAATA-AA
119930634 AATAATAAA
1 AATAATAAA
119930643 AATAA-AAA
1 AATAATAAA
119930651 AATAA-AAA
1 AATAATAAA
119930659 AA
1 AA
119930661 CTATGTCAAT
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
8 13 0.48
9 7 0.26
10 7 0.26
ACGTcount: A:0.81, C:0.00, G:0.03, T:0.16
Consensus pattern (9 bp):
AATAATAAA
Found at i:119930654 original size:14 final size:16
Alignment explanation
Indices: 119930627--119930658 Score: 50
Period size: 14 Copynumber: 2.1 Consensus size: 16
119930617 TAATGACAAT
119930627 AATAGAAAATAATAAA
1 AATAGAAAATAATAAA
119930643 AATA-AAAA-AATAAA
1 AATAGAAAATAATAAA
119930657 AA
1 AA
119930659 AACTATGTCA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
14 8 0.50
15 4 0.25
16 4 0.25
ACGTcount: A:0.81, C:0.00, G:0.03, T:0.16
Consensus pattern (16 bp):
AATAGAAAATAATAAA
Found at i:119930717 original size:12 final size:11
Alignment explanation
Indices: 119930691--119930743 Score: 52
Period size: 12 Copynumber: 4.4 Consensus size: 11
119930681 GAAATAACAG
*
119930691 TAATAAAAACAA
1 TAATAATAA-AA
119930703 TAATAATAAATA
1 TAATAATAAA-A
119930715 TAATAATAGAAAA
1 TAATAAT--AAAA
119930728 TAATAATGAAAA
1 TAATAAT-AAAA
119930740 TAAT
1 TAAT
119930744 TAATTTGAGA
Statistics
Matches: 37, Mismatches: 1, Indels: 6
0.84 0.02 0.14
Matches are distributed among these distances:
11 1 0.03
12 25 0.68
13 8 0.22
14 3 0.08
ACGTcount: A:0.68, C:0.02, G:0.04, T:0.26
Consensus pattern (11 bp):
TAATAATAAAA
Found at i:119933218 original size:126 final size:127
Alignment explanation
Indices: 119932853--119933218 Score: 538
Period size: 126 Copynumber: 2.9 Consensus size: 127
119932843 AGTTCACATT
* * * *
119932853 GGAGCATTTTTCAGAAATTTTGCTAACATTACATCCTGCTTGAAGTGTTTCTGATACTATTTGTT
1 GGAGCTTTTTTCAGAAATTTTGCTGACATTACATCCTGCTTGAAGTGTTTTTGACACTATTTGTT
*
119932918 CAGAAACATCTTCTCAAAATTATTTTTTCAGGAATTACTGTAGAAAAA-GAGCTTCTACGTA
66 CAGAAACATCTTCTCAAAATTATTTTTTCAGGAATTACTGTAGAAAAATGAGCATCTACGTA
* * * *
119932979 GGAGCTTTTTTCAGAAATTTTGATGACATTGCATCCTGCTTGAAGCGTTGTTGACACTATTTGTT
1 GGAGCTTTTTTCAGAAATTTTGCTGACATTACATCCTGCTTGAAGTGTTTTTGACACTATTTGTT
* * * * * *
119933044 CAAAAACGTCTTCTCAAAATTATTTTTTCAAGAATTATTGTAGAAAAATGA-CATCTATGTG
66 CAGAAACATCTTCTCAAAATTATTTTTTCAGGAATTACTGTAGAAAAATGAGCATCTACGTA
* * *
119933105 GGAGCTTTTTTCAGAAATTTTGCTGACATTACATCTTCCTTGAGGTGTTTTTGACACTATTTGTT
1 GGAGCTTTTTTCAGAAATTTTGCTGACATTACATCCTGCTTGAAGTGTTTTTGACACTATTTGTT
* *
119933170 CAGAAACATCTTCTCAAAATTATTTTTTCAGGAACTACTGCAGAAAAAT
66 CAGAAACATCTTCTCAAAATTATTTTTTCAGGAATTACTGTAGAAAAAT
119933219 CATAAACCTT
Statistics
Matches: 211, Mismatches: 28, Indels: 2
0.88 0.12 0.01
Matches are distributed among these distances:
126 209 0.99
127 2 0.01
ACGTcount: A:0.30, C:0.16, G:0.16, T:0.39
Consensus pattern (127 bp):
GGAGCTTTTTTCAGAAATTTTGCTGACATTACATCCTGCTTGAAGTGTTTTTGACACTATTTGTT
CAGAAACATCTTCTCAAAATTATTTTTTCAGGAATTACTGTAGAAAAATGAGCATCTACGTA
Found at i:119933759 original size:19 final size:21
Alignment explanation
Indices: 119933737--119933775 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 21
119933727 TAAATTCTTA
119933737 AATAAA-ATTATAAA-AATAG
1 AATAAATATTATAAATAATAG
*
119933756 AATAAATTTTATAAATAATA
1 AATAAATATTATAAATAATA
119933776 AAAACCCTCA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 6 0.35
20 7 0.41
21 4 0.24
ACGTcount: A:0.64, C:0.00, G:0.03, T:0.33
Consensus pattern (21 bp):
AATAAATATTATAAATAATAG
Found at i:119937439 original size:2 final size:2
Alignment explanation
Indices: 119937432--119937465 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
119937422 TGTTTTACTT
119937432 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
119937466 ATGTAATAAC
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:119944766 original size:3 final size:3
Alignment explanation
Indices: 119944752--119944784 Score: 50
Period size: 3 Copynumber: 11.0 Consensus size: 3
119944742 TATTCTAAAT
119944752 TAA TAA -AA TAA TAA TAA TAA TAA TAAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA T-AA TAA TAA
119944785 AACTAAATAA
Statistics
Matches: 28, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
2 2 0.07
3 23 0.82
4 3 0.11
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (3 bp):
TAA
Found at i:119944782 original size:13 final size:13
Alignment explanation
Indices: 119944753--119944794 Score: 54
Period size: 13 Copynumber: 3.4 Consensus size: 13
119944743 ATTCTAAATT
119944753 AATAA-AATAAT-
1 AATAATAATAATA
119944764 AATAATAATAATA
1 AATAATAATAATA
119944777 AATAATAA-AACTA
1 AATAATAATAA-TA
119944790 AATAA
1 AATAA
119944795 AACAAAATAA
Statistics
Matches: 28, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
11 5 0.18
12 8 0.29
13 15 0.54
ACGTcount: A:0.71, C:0.02, G:0.00, T:0.26
Consensus pattern (13 bp):
AATAATAATAATA
Found at i:119957009 original size:18 final size:18
Alignment explanation
Indices: 119956988--119957025 Score: 58
Period size: 18 Copynumber: 2.1 Consensus size: 18
119956978 TAGAATGTAT
* *
119956988 TTTATTTGTATAAATTTA
1 TTTATTTGAATAAATATA
119957006 TTTATTTGAATAAATATA
1 TTTATTTGAATAAATATA
119957024 TT
1 TT
119957026 GGACAAATTT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.37, C:0.00, G:0.05, T:0.58
Consensus pattern (18 bp):
TTTATTTGAATAAATATA
Found at i:119957466 original size:17 final size:16
Alignment explanation
Indices: 119957446--119957488 Score: 50
Period size: 17 Copynumber: 2.6 Consensus size: 16
119957436 TTTATATTCT
119957446 TTTTTGTTAATTATTTA
1 TTTTT-TTAATTATTTA
* *
119957463 TTTTTATAGATTTTTTA
1 TTTTTTTA-ATTATTTA
119957480 TTTTTTTAA
1 TTTTTTTAA
119957489 AATTTATACT
Statistics
Matches: 22, Mismatches: 3, Indels: 3
0.79 0.11 0.11
Matches are distributed among these distances:
16 3 0.14
17 19 0.86
ACGTcount: A:0.23, C:0.00, G:0.05, T:0.72
Consensus pattern (16 bp):
TTTTTTTAATTATTTA
Found at i:119975295 original size:2 final size:2
Alignment explanation
Indices: 119975288--119975314 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
119975278 ATAACTGTAC
119975288 AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT A
119975315 AATGTCTACT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:119981755 original size:7 final size:7
Alignment explanation
Indices: 119981743--119981772 Score: 60
Period size: 7 Copynumber: 4.3 Consensus size: 7
119981733 AAAGTATAAA
119981743 AAATTTT
1 AAATTTT
119981750 AAATTTT
1 AAATTTT
119981757 AAATTTT
1 AAATTTT
119981764 AAATTTT
1 AAATTTT
119981771 AA
1 AA
119981773 CAAAAAATAA
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:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (7 bp):
AAATTTT
Found at i:119981795 original size:9 final size:9
Alignment explanation
Indices: 119981783--119981822 Score: 53
Period size: 9 Copynumber: 4.3 Consensus size: 9
119981773 CAAAAAATAA
*
119981783 AAAAATTGT
1 AAAAATTAT
119981792 AAAAATTAT
1 AAAAATTAT
*
119981801 AAAAATCAT
1 AAAAATTAT
119981810 AAAAAATTAT
1 -AAAAATTAT
119981820 AAA
1 AAA
119981823 TTGTATCAAA
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
9 19 0.70
10 8 0.30
ACGTcount: A:0.68, C:0.03, G:0.03, T:0.28
Consensus pattern (9 bp):
AAAAATTAT
Found at i:119981795 original size:10 final size:10
Alignment explanation
Indices: 119981774--119981822 Score: 52
Period size: 9 Copynumber: 5.3 Consensus size: 10
119981764 AAATTTTAAC
119981774 AAAAAA-TA-
1 AAAAAATTAT
*
119981782 AAAAAATTGT
1 AAAAAATTAT
119981792 -AAAAATTAT
1 AAAAAATTAT
*
119981801 -AAAAATCAT
1 AAAAAATTAT
119981810 AAAAAATTAT
1 AAAAAATTAT
119981820 AAA
1 AAA
119981823 TTGTATCAAA
Statistics
Matches: 34, Mismatches: 4, Indels: 4
0.81 0.10 0.10
Matches are distributed among these distances:
8 6 0.18
9 17 0.50
10 11 0.32
ACGTcount: A:0.71, C:0.02, G:0.02, T:0.24
Consensus pattern (10 bp):
AAAAAATTAT
Found at i:119983793 original size:25 final size:25
Alignment explanation
Indices: 119983740--119983793 Score: 63
Period size: 25 Copynumber: 2.2 Consensus size: 25
119983730 AAAATTTATA
* *
119983740 TGATAGGAAAATTGTATGAAAATAT
1 TGATAGGAAAATTGTATCAAAATAG
* **
119983765 TGATAGGAAAATTTTATCAATTTAG
1 TGATAGGAAAATTGTATCAAAATAG
119983790 TGAT
1 TGAT
119983794 TAGTTAGAAA
Statistics
Matches: 24, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
25 24 1.00
ACGTcount: A:0.43, C:0.02, G:0.19, T:0.37
Consensus pattern (25 bp):
TGATAGGAAAATTGTATCAAAATAG
Found at i:120001224 original size:40 final size:40
Alignment explanation
Indices: 120001165--120001248 Score: 161
Period size: 40 Copynumber: 2.1 Consensus size: 40
120001155 GGCCATCATA
120001165 AATA-GCCTAAAGTTCAACTTGTTCAGCACTACATCTTCT
1 AATATGCCTAAAGTTCAACTTGTTCAGCACTACATCTTCT
120001204 AATATGCCTAAAGTTCAACTTGTTCAGCACTACATCTTCT
1 AATATGCCTAAAGTTCAACTTGTTCAGCACTACATCTTCT
120001244 AATAT
1 AATAT
120001249 TTCTCTCAAT
Statistics
Matches: 44, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
39 4 0.09
40 40 0.91
ACGTcount: A:0.32, C:0.24, G:0.10, T:0.35
Consensus pattern (40 bp):
AATATGCCTAAAGTTCAACTTGTTCAGCACTACATCTTCT
Found at i:120004953 original size:51 final size:51
Alignment explanation
Indices: 120004882--120004989 Score: 198
Period size: 51 Copynumber: 2.1 Consensus size: 51
120004872 CTGATCACAT
120004882 TTATCACTTGTCACTGATCAGATAAGTGTAGCTAAAGCTACCACTTATCAC
1 TTATCACTTGTCACTGATCAGATAAGTGTAGCTAAAGCTACCACTTATCAC
*
120004933 TTATCACTTGTCACTGATCAGATAAGTGTAGCTAAATCTACCACTTATCAC
1 TTATCACTTGTCACTGATCAGATAAGTGTAGCTAAAGCTACCACTTATCAC
*
120004984 TGATCA
1 TTATCA
120004990 GATAAGTGTA
Statistics
Matches: 55, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
51 55 1.00
ACGTcount: A:0.31, C:0.23, G:0.13, T:0.32
Consensus pattern (51 bp):
TTATCACTTGTCACTGATCAGATAAGTGTAGCTAAAGCTACCACTTATCAC
Found at i:120004987 original size:37 final size:37
Alignment explanation
Indices: 120004937--120005021 Score: 134
Period size: 37 Copynumber: 2.3 Consensus size: 37
120004927 TATCACTTAT
* *
120004937 CACTTGTCACTGATCAGATAAGTGTAGCTAAATCTAC
1 CACTTATCACTGATCAGATAAGTGTAGCTAAAGCTAC
* *
120004974 CACTTATCACTGATCAGATAAGTGTAGCTGAGGCTAC
1 CACTTATCACTGATCAGATAAGTGTAGCTAAAGCTAC
120005011 CACTTATCACT
1 CACTTATCACT
120005022 TGTCACTGAT
Statistics
Matches: 44, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
37 44 1.00
ACGTcount: A:0.31, C:0.24, G:0.16, T:0.29
Consensus pattern (37 bp):
CACTTATCACTGATCAGATAAGTGTAGCTAAAGCTAC
Found at i:120013688 original size:3 final size:3
Alignment explanation
Indices: 120013675--120013718 Score: 52
Period size: 3 Copynumber: 14.3 Consensus size: 3
120013665 GGAATCCAAT
* * *
120013675 AAG AGG AAG AAG AAG AAG AAG CAAG ACG AGG AAG AAG AAG AAG A
1 AAG AAG AAG AAG AAG AAG AAG -AAG AAG AAG AAG AAG AAG AAG A
120013719 GCCGGAGGAA
Statistics
Matches: 35, Mismatches: 5, Indels: 2
0.83 0.12 0.05
Matches are distributed among these distances:
3 32 0.91
4 3 0.09
ACGTcount: A:0.59, C:0.05, G:0.36, T:0.00
Consensus pattern (3 bp):
AAG
Found at i:120018436 original size:21 final size:22
Alignment explanation
Indices: 120018395--120018441 Score: 53
Period size: 22 Copynumber: 2.2 Consensus size: 22
120018385 GTTCATCTAT
* *
120018395 TTTGTTTTTTTCT-CAATTTAA
1 TTTGTTTTTTTCTAAAATTAAA
120018416 TTTGTATTTTTT-TAAAATTAAA
1 TTTGT-TTTTTTCTAAAATTAAA
120018438 TTTG
1 TTTG
120018442 ATTATTAACT
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
21 6 0.27
22 16 0.73
ACGTcount: A:0.26, C:0.04, G:0.06, T:0.64
Consensus pattern (22 bp):
TTTGTTTTTTTCTAAAATTAAA
Found at i:120018893 original size:16 final size:18
Alignment explanation
Indices: 120018861--120018898 Score: 53
Period size: 17 Copynumber: 2.2 Consensus size: 18
120018851 GCGATGAACT
*
120018861 TTACTATTTTATTAAT-A
1 TTACTATTTTATAAATAA
120018878 TTACTA-TTTATAAATAA
1 TTACTATTTTATAAATAA
120018895 TTAC
1 TTAC
120018899 AAGGATATGT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
16 8 0.42
17 11 0.58
ACGTcount: A:0.39, C:0.08, G:0.00, T:0.53
Consensus pattern (18 bp):
TTACTATTTTATAAATAA
Found at i:120018951 original size:2 final size:2
Alignment explanation
Indices: 120018944--120018979 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
120018934 TGAGATAGTA
120018944 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
120018980 TGGACTTTGA
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:120019483 original size:20 final size:20
Alignment explanation
Indices: 120019458--120019496 Score: 62
Period size: 20 Copynumber: 1.9 Consensus size: 20
120019448 AATGATTCTG
120019458 CCATT-AATTTTAAAGTTTAT
1 CCATTAAATTTTAAA-TTTAT
120019478 CCATTAAATTTTAAATTTA
1 CCATTAAATTTTAAATTTA
120019497 GGTTCAAGAA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 9 0.50
21 9 0.50
ACGTcount: A:0.38, C:0.10, G:0.03, T:0.49
Consensus pattern (20 bp):
CCATTAAATTTTAAATTTAT
Found at i:120019691 original size:17 final size:16
Alignment explanation
Indices: 120019667--120019714 Score: 60
Period size: 17 Copynumber: 2.9 Consensus size: 16
120019657 TTAAATTATA
120019667 AAATTAAAGTTTAATTT
1 AAATTAAA-TTTAATTT
**
120019684 TTATTAAATTTTAATTT
1 AAATTAAA-TTTAATTT
120019701 AAATTAAATTTAAT
1 AAATTAAATTTAAT
120019715 AAAAATATTT
Statistics
Matches: 26, Mismatches: 5, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
16 6 0.23
17 20 0.77
ACGTcount: A:0.46, C:0.00, G:0.02, T:0.52
Consensus pattern (16 bp):
AAATTAAATTTAATTT
Found at i:120022138 original size:13 final size:13
Alignment explanation
Indices: 120022120--120022144 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
120022110 GTATCCGACC
120022120 AAAAGAGAAAAAA
1 AAAAGAGAAAAAA
120022133 AAAAGAGAAAAA
1 AAAAGAGAAAAA
120022145 GGCAAGCTAA
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:0.84, C:0.00, G:0.16, T:0.00
Consensus pattern (13 bp):
AAAAGAGAAAAAA
Found at i:120029401 original size:11 final size:11
Alignment explanation
Indices: 120029387--120029426 Score: 57
Period size: 10 Copynumber: 3.8 Consensus size: 11
120029377 ACTTCATGCT
120029387 AATTTTTTATG
1 AATTTTTTATG
120029398 AA-TTTTTATG
1 AATTTTTTATG
120029408 AATTTTTT-TG
1 AATTTTTTATG
*
120029418 AATATTTTA
1 AATTTTTTA
120029427 ATAAATTTTA
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
10 19 0.73
11 7 0.27
ACGTcount: A:0.30, C:0.00, G:0.07, T:0.62
Consensus pattern (11 bp):
AATTTTTTATG
Found at i:120029413 original size:21 final size:22
Alignment explanation
Indices: 120029387--120029435 Score: 66
Period size: 21 Copynumber: 2.3 Consensus size: 22
120029377 ACTTCATGCT
*
120029387 AATTTTTTATGAAT-TTTT-ATG
1 AATTTTTT-TGAATATTTTAATA
120029408 AATTTTTTTGAATATTTTAATA
1 AATTTTTTTGAATATTTTAATA
120029430 AATTTT
1 AATTTT
120029436 AAATTATTTG
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
20 5 0.20
21 12 0.48
22 8 0.32
ACGTcount: A:0.33, C:0.00, G:0.06, T:0.61
Consensus pattern (22 bp):
AATTTTTTTGAATATTTTAATA
Found at i:120029424 original size:22 final size:21
Alignment explanation
Indices: 120029387--120029435 Score: 55
Period size: 22 Copynumber: 2.3 Consensus size: 21
120029377 ACTTCATGCT
* *
120029387 AATTTTTTATGAATTTTTATG
1 AATTTTTTATGAATTTTAATA
120029408 AATTTTTT-TGAATATTTTAATA
1 AATTTTTTATG-A-ATTTTAATA
120029430 AATTTT
1 AATTTT
120029436 AAATTATTTG
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
20 2 0.08
21 9 0.38
22 13 0.54
ACGTcount: A:0.33, C:0.00, G:0.06, T:0.61
Consensus pattern (21 bp):
AATTTTTTATGAATTTTAATA
Found at i:120031235 original size:33 final size:33
Alignment explanation
Indices: 120031193--120031257 Score: 121
Period size: 33 Copynumber: 2.0 Consensus size: 33
120031183 GTATGATAGC
*
120031193 CTAGAATATTTAGATAAATTTTCAATTGAGAAG
1 CTAGAATATTTAGATAAATTTTCAATTAAGAAG
120031226 CTAGAATATTTAGATAAATTTTCAATTAAGAA
1 CTAGAATATTTAGATAAATTTTCAATTAAGAA
120031258 AATTAGTTCA
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
33 31 1.00
ACGTcount: A:0.45, C:0.06, G:0.12, T:0.37
Consensus pattern (33 bp):
CTAGAATATTTAGATAAATTTTCAATTAAGAAG
Found at i:120031811 original size:21 final size:21
Alignment explanation
Indices: 120031785--120031936 Score: 90
Period size: 21 Copynumber: 7.2 Consensus size: 21
120031775 ACTCATATAA
*
120031785 GTTTCCGTTCAACCCTAATGG
1 GTTTCCGTTCAACCCTTATGG
* * * *
120031806 GTTTCCGTTCAGCACTTTTGA
1 GTTTCCGTTCAACCCTTATGG
* * * *
120031827 GCTTCTGTTTAACCCTAATGG
1 GTTTCCGTTCAACCCTTATGG
* * * * *
120031848 GTCTCTGTTCAACTCTTTTGA
1 GTTTCCGTTCAACCCTTATGG
* * *
120031869 GCTTCTGTTTAACCCTTATGG
1 GTTTCCGTTCAACCCTTATGG
* * *
120031890 GTTTCCGTT-AAGCTCTCATGA
1 GTTTCCGTTCAA-CCCTTATGG
* *
120031911 GCTTCCATTCAACCCTTATGG
1 GTTTCCGTTCAACCCTTATGG
120031932 GTTTC
1 GTTTC
120031937 TGTTTAGCAC
Statistics
Matches: 92, Mismatches: 37, Indels: 4
0.69 0.28 0.03
Matches are distributed among these distances:
20 2 0.02
21 88 0.96
22 2 0.02
ACGTcount: A:0.16, C:0.26, G:0.18, T:0.40
Consensus pattern (21 bp):
GTTTCCGTTCAACCCTTATGG
Found at i:120031858 original size:42 final size:42
Alignment explanation
Indices: 120031795--120031961 Score: 181
Period size: 42 Copynumber: 4.0 Consensus size: 42
120031785 GTTTCCGTTC
*
120031795 AACCCTAATGGGTTTCCGTTCAGCACTTTTGAGCTTCTGTTT
1 AACCCTAATGGGTTTCCGTTCAGCACTTATGAGCTTCTGTTT
* * * * *
120031837 AACCCTAATGGGTCTCTGTTCAACTCTTTTGAGCTTCTGTTT
1 AACCCTAATGGGTTTCCGTTCAGCACTTATGAGCTTCTGTTT
* * * * ** *
120031879 AACCCTTATGGGTTTCCGTTAAGCTCTCATGAGCTTCCATTC
1 AACCCTAATGGGTTTCCGTTCAGCACTTATGAGCTTCTGTTT
* * * *
120031921 AACCCTTATGGGTTTCTGTTTAGCACTTATGTGCTTCTGTT
1 AACCCTAATGGGTTTCCGTTCAGCACTTATGAGCTTCTGTT
120031962 CAGCCTTCGG
Statistics
Matches: 104, Mismatches: 21, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
42 104 1.00
ACGTcount: A:0.17, C:0.24, G:0.18, T:0.41
Consensus pattern (42 bp):
AACCCTAATGGGTTTCCGTTCAGCACTTATGAGCTTCTGTTT
Found at i:120034377 original size:21 final size:21
Alignment explanation
Indices: 120034353--120034395 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
120034343 TAATTATCTT
* *
120034353 ATAATTGCGCATTGATTTGTA
1 ATAATTGCACATTAATTTGTA
*
120034374 ATAATTGCATATTAATTTGTA
1 ATAATTGCACATTAATTTGTA
120034395 A
1 A
120034396 ATTTTTGTGT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.35, C:0.07, G:0.14, T:0.44
Consensus pattern (21 bp):
ATAATTGCACATTAATTTGTA
Found at i:120035855 original size:32 final size:32
Alignment explanation
Indices: 120035818--120035899 Score: 119
Period size: 32 Copynumber: 2.6 Consensus size: 32
120035808 TTGAAATTAG
*
120035818 TTTGTTGGATTTTGAAATTATTATGTCTTAAA
1 TTTGTTGGATATTGAAATTATTATGTCTTAAA
* * *
120035850 TTTGTTAGATATTGAATTTATTATGTTTTAAA
1 TTTGTTGGATATTGAAATTATTATGTCTTAAA
*
120035882 CTTGTTGGATATTGAAAT
1 TTTGTTGGATATTGAAAT
120035900 GATTGACAAT
Statistics
Matches: 43, Mismatches: 7, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
32 43 1.00
ACGTcount: A:0.29, C:0.02, G:0.16, T:0.52
Consensus pattern (32 bp):
TTTGTTGGATATTGAAATTATTATGTCTTAAA
Found at i:120049128 original size:20 final size:20
Alignment explanation
Indices: 120049079--120049130 Score: 59
Period size: 20 Copynumber: 2.5 Consensus size: 20
120049069 TTATGCCACA
120049079 TCAGTATTCTTATCCTGAAGT
1 TCAGTATT-TTATCCTGAAGT
* * *
120049100 TCAGGATTTTATTCTGAATT
1 TCAGTATTTTATCCTGAAGT
*
120049120 TTAGTATTTTA
1 TCAGTATTTTA
120049131 ATTTGGATTT
Statistics
Matches: 26, Mismatches: 5, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
20 19 0.73
21 7 0.27
ACGTcount: A:0.25, C:0.12, G:0.13, T:0.50
Consensus pattern (20 bp):
TCAGTATTTTATCCTGAAGT
Found at i:120050694 original size:20 final size:21
Alignment explanation
Indices: 120050654--120050707 Score: 69
Period size: 21 Copynumber: 2.7 Consensus size: 21
120050644 ACAAATAAAG
*
120050654 TAAAAATTTTAAAAAGATTCA
1 TAAAAATTATAAAAAGATTCA
120050675 -AACAAATTATAAAAAG-TTCA
1 TAA-AAATTATAAAAAGATTCA
120050695 TAAAAATTA-AAAA
1 TAAAAATTATAAAA
120050708 TAATATGTAG
Statistics
Matches: 30, Mismatches: 1, Indels: 6
0.81 0.03 0.16
Matches are distributed among these distances:
19 4 0.13
20 12 0.40
21 14 0.47
ACGTcount: A:0.63, C:0.06, G:0.04, T:0.28
Consensus pattern (21 bp):
TAAAAATTATAAAAAGATTCA
Found at i:120052969 original size:21 final size:21
Alignment explanation
Indices: 120052935--120052974 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
120052925 AAACAGTATC
*
120052935 TCCTTTCTTCATTTGTTTACA
1 TCCTTTCTTCATTTATTTACA
120052956 TCCTTTCTGT-ATTTATTTA
1 TCCTTTCT-TCATTTATTTA
120052975 TTTTATTATT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
21 16 0.94
22 1 0.06
ACGTcount: A:0.15, C:0.20, G:0.05, T:0.60
Consensus pattern (21 bp):
TCCTTTCTTCATTTATTTACA
Found at i:120062430 original size:15 final size:16
Alignment explanation
Indices: 120062390--120062428 Score: 53
Period size: 15 Copynumber: 2.5 Consensus size: 16
120062380 TTTGGGAAAG
*
120062390 AAATTCAAATTTT-AA
1 AAATTAAAATTTTAAA
*
120062405 AATTTAAAATTTTAAA
1 AAATTAAAATTTTAAA
120062421 AAATTAAA
1 AAATTAAA
120062429 TTCTAAATTT
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
15 11 0.55
16 9 0.45
ACGTcount: A:0.59, C:0.03, G:0.00, T:0.38
Consensus pattern (16 bp):
AAATTAAAATTTTAAA
Found at i:120062774 original size:31 final size:30
Alignment explanation
Indices: 120062736--120062815 Score: 97
Period size: 31 Copynumber: 2.6 Consensus size: 30
120062726 GAATTATTTG
**
120062736 AAAGTTTTCATTTAAGTCATTGAACTATTCA
1 AAAGTTTT-ATTTAAGTCATCAAACTATTCA
* *
120062767 AAAGTTTTTATTTAACTTATCAAACTATTCA
1 AAAG-TTTTATTTAAGTCATCAAACTATTCA
*
120062798 AAAGTTTTATTCAAGTCA
1 AAAGTTTTATTTAAGTCA
120062816 CAAGATTGTT
Statistics
Matches: 41, Mismatches: 7, Indels: 3
0.80 0.14 0.06
Matches are distributed among these distances:
30 11 0.27
31 26 0.63
32 4 0.10
ACGTcount: A:0.38, C:0.12, G:0.07, T:0.42
Consensus pattern (30 bp):
AAAGTTTTATTTAAGTCATCAAACTATTCA
Found at i:120066104 original size:33 final size:33
Alignment explanation
Indices: 120065958--120066104 Score: 122
Period size: 33 Copynumber: 4.5 Consensus size: 33
120065948 CATTGACGGA
* *
120065958 TAAGACCATGGTTGGGCCATGGCAATATATGTG
1 TAAGACCATAGTTGGGCCATGGCAATACATGTG
* * * *
120065991 TAAGACCATAGCTAGGCTATGGC-AT-CCTGATG
1 TAAGACCATAGTTGGGCCATGGCAATACATG-TG
** **
120066023 ATAAGACCATA-TCTGGGATATGGCACCACGA-GTG
1 -TAAGACCATAGT-TGGGCCATGGCAATAC-ATGTG
*
120066057 TAAGACCATGGTTGGGCCATGGCAATACATGTG
1 TAAGACCATAGTTGGGCCATGGCAATACATGTG
*
120066090 TAAGACCGTAGTTGG
1 TAAGACCATAGTTGG
120066105 ACTATTGCAT
Statistics
Matches: 87, Mismatches: 19, Indels: 16
0.71 0.16 0.13
Matches are distributed among these distances:
31 2 0.02
32 5 0.06
33 75 0.86
34 3 0.03
35 2 0.02
ACGTcount: A:0.29, C:0.18, G:0.29, T:0.24
Consensus pattern (33 bp):
TAAGACCATAGTTGGGCCATGGCAATACATGTG
Found at i:120066177 original size:45 final size:45
Alignment explanation
Indices: 120066127--120066297 Score: 171
Period size: 45 Copynumber: 3.8 Consensus size: 45
120066117 TACCAGAAAT
*
120066127 GAGTAAGACTATAGCTGAAAGACGCTATGGCATCACGATTCAAAC
1 GAGTAAGACCATAGCTGAAAGACGCTATGGCATCACGATTCAAAC
* *
120066172 GAGTAAGACCATAGCTGAAAGACGCTATGGCATCGCGATTCAAAT
1 GAGTAAGACCATAGCTGAAAGACGCTATGGCATCACGATTCAAAC
* * * ** * * * *** *
120066217 GTGTAAGACCATGGTTGAAAGATACCATGGCAACATGACAGAAAGT
1 GAGTAAGACCATAGCTGAAAGACGCTATGGCATCACGATTCAAA-C
* * *
120066263 GAGTAAGACCATAGTTGAAAAACACTATGGCATCA
1 GAGTAAGACCATAGCTGAAAGACGCTATGGCATCA
120066298 TGTCGAAGAT
Statistics
Matches: 104, Mismatches: 21, Indels: 1
0.83 0.17 0.01
Matches are distributed among these distances:
45 74 0.71
46 30 0.29
ACGTcount: A:0.39, C:0.18, G:0.23, T:0.20
Consensus pattern (45 bp):
GAGTAAGACCATAGCTGAAAGACGCTATGGCATCACGATTCAAAC
Done.