Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_018397266.1 Herrania umbratica cultivar Fairchild unplaced genomic scaffold, ASM216827v2 scaffold_20.0, whole genome shotgun sequence
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: 7441454
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 92215 characters in sequence are not A, C, G, or T
File 4 of 18
Found at i:1428428 original size:51 final size:51
Alignment explanation
Indices: 1428368--1428469 Score: 186
Period size: 51 Copynumber: 2.0 Consensus size: 51
1428358 AGGTGACCCC
*
1428368 ACATCCGGCATTACATTATATTAAACATGATTTACTTGCAATTTAAGGCTT
1 ACATCCGGCATTACATTATATTAAACATGACTTACTTGCAATTTAAGGCTT
*
1428419 ACATCCGGCATTGCATTATATTAAACATGACTTACTTGCAATTTAAGGCTT
1 ACATCCGGCATTACATTATATTAAACATGACTTACTTGCAATTTAAGGCTT
1428470 TTCAACACCA
Statistics
Matches: 49, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
51 49 1.00
ACGTcount: A:0.32, C:0.19, G:0.13, T:0.36
Consensus pattern (51 bp):
ACATCCGGCATTACATTATATTAAACATGACTTACTTGCAATTTAAGGCTT
Found at i:1432218 original size:60 final size:60
Alignment explanation
Indices: 1432093--1432224 Score: 142
Period size: 60 Copynumber: 2.2 Consensus size: 60
1432083 AAGGTAAACT
* * *
1432093 CGTAACGCTTAAGTCACGTAATGCCTAAAATCCAGTCACGCAATACTTACAACCCAATCA
1 CGTAATGCTTAAGTCACGTAATGCCTAAAATCCAGTCACGCAATACTTAAAAACCAATCA
* * * * * * *
1432153 TGTAATGCTTCAGTCATGTAGTGCCTAAAA-CCGAGTCATGCAATA-TCTAAAAACTAGTCA
1 CGTAATGCTTAAGTCACGTAATGCCTAAAATCC-AGTCACGCAATACT-TAAAAACCAATCA
1432213 CGTAATGCTTAA
1 CGTAATGCTTAA
1432225 AAATTAATCA
Statistics
Matches: 58, Mismatches: 12, Indels: 4
0.78 0.16 0.05
Matches are distributed among these distances:
59 3 0.05
60 55 0.95
ACGTcount: A:0.36, C:0.24, G:0.14, T:0.26
Consensus pattern (60 bp):
CGTAATGCTTAAGTCACGTAATGCCTAAAATCCAGTCACGCAATACTTAAAAACCAATCA
Found at i:1432225 original size:22 final size:22
Alignment explanation
Indices: 1432200--1432242 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 22
1432190 ATGCAATATC
* *
1432200 TAAAAACTAGTCACGTAATGCT
1 TAAAAACTAATCACATAATGCT
*
1432222 TAAAAATTAATCACATAATGC
1 TAAAAACTAATCACATAATGC
1432243 CTAAGTCATG
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.47, C:0.16, G:0.09, T:0.28
Consensus pattern (22 bp):
TAAAAACTAATCACATAATGCT
Found at i:1448043 original size:25 final size:27
Alignment explanation
Indices: 1447994--1448047 Score: 76
Period size: 26 Copynumber: 2.1 Consensus size: 27
1447984 TCAATTATAA
* *
1447994 AATATAAAAATTTATTTGACTCAAAAT
1 AATATAAAAATTTAATTGACACAAAAT
1448021 AATA-AAAAATTTAATTGA-ACAAAAT
1 AATATAAAAATTTAATTGACACAAAAT
1448046 AA
1 AA
1448048 AAGAATAAAA
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
25 8 0.32
26 13 0.52
27 4 0.16
ACGTcount: A:0.59, C:0.06, G:0.04, T:0.31
Consensus pattern (27 bp):
AATATAAAAATTTAATTGACACAAAAT
Found at i:1448671 original size:2 final size:2
Alignment explanation
Indices: 1448659--1448697 Score: 60
Period size: 2 Copynumber: 19.5 Consensus size: 2
1448649 GAATTGGGTC
* *
1448659 TA TA CA TA TA TA TA TA TA TA TA TA TA TA TA GA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1448698 TTGTGGGGTC
Statistics
Matches: 33, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.49, C:0.03, G:0.03, T:0.46
Consensus pattern (2 bp):
TA
Found at i:1457441 original size:29 final size:29
Alignment explanation
Indices: 1457400--1457483 Score: 87
Period size: 31 Copynumber: 2.8 Consensus size: 29
1457390 TACCAAATTG
* * *
1457400 TTTTTGAATATGATGTGTAATAATAATAT
1 TTTTTCAACATGACGTGTAATAATAATAT
* *
1457429 TTTTTCAACATGACGTGTAATAGTAGTATTT
1 TTTTTCAACATGACGTGTAATAATA--ATAT
* *
1457460 TTTTTTAACATGGCGTGTAATAAT
1 TTTTTCAACATGACGTGTAATAAT
1457484 CTTTTTTAAC
Statistics
Matches: 45, Mismatches: 8, Indels: 2
0.82 0.15 0.04
Matches are distributed among these distances:
29 21 0.47
31 24 0.53
ACGTcount: A:0.32, C:0.06, G:0.15, T:0.46
Consensus pattern (29 bp):
TTTTTCAACATGACGTGTAATAATAATAT
Found at i:1457489 original size:29 final size:29
Alignment explanation
Indices: 1457400--1457490 Score: 85
Period size: 29 Copynumber: 3.1 Consensus size: 29
1457390 TACCAAATTG
* * * * *
1457400 TTTTTGAATATGATGTGTAATAATAATAT
1 TTTTTCAACATGACGTGTAATAATATTTT
1457429 TTTTTCAACATGACGTGTAATAGTAGTATTTT
1 TTTTTCAACATGACGTGTAATA--A-TATTTT
* *
1457461 TTTTT-AACATGGCGTGTAATAATCTTTT
1 TTTTTCAACATGACGTGTAATAATATTTT
1457489 TT
1 TT
1457491 AACTATGGCA
Statistics
Matches: 52, Mismatches: 7, Indels: 7
0.79 0.11 0.11
Matches are distributed among these distances:
28 7 0.13
29 20 0.38
31 16 0.31
32 9 0.17
ACGTcount: A:0.30, C:0.07, G:0.14, T:0.49
Consensus pattern (29 bp):
TTTTTCAACATGACGTGTAATAATATTTT
Found at i:1457489 original size:57 final size:56
Alignment explanation
Indices: 1457420--1457527 Score: 137
Period size: 57 Copynumber: 1.9 Consensus size: 56
1457410 TGATGTGTAA
* * * *
1457420 TAATAATATTTTTTCAAC-ATGACGTGTAATAGTAGTATTTTTTTTTAACATGGCGTG
1 TAATAATATTTTTT-AACTATGACATGTAACA-AAATATTTTTTTTTAACATGGCGTG
* *
1457477 TAATAATCTTTTTTAACTATGGCATGTAACAAAATATTTTTTTTTAACATG
1 TAATAATATTTTTTAACTATGACATGTAACAAAATATTTTTTTTTAACATG
1457528 ACATGTAACA
Statistics
Matches: 44, Mismatches: 6, Indels: 3
0.83 0.11 0.06
Matches are distributed among these distances:
56 21 0.48
57 23 0.52
ACGTcount: A:0.32, C:0.09, G:0.12, T:0.46
Consensus pattern (56 bp):
TAATAATATTTTTTAACTATGACATGTAACAAAATATTTTTTTTTAACATGGCGTG
Found at i:1457582 original size:45 final size:45
Alignment explanation
Indices: 1457533--1457653 Score: 147
Period size: 45 Copynumber: 2.7 Consensus size: 45
1457523 ACATGACATG
* *
1457533 TAACAACCTAACTATAGCGTGTAACATATTTTTATATATGGTGTA
1 TAACAACCTAACTATAGCGTGTAACATATTTTTATAAATGGCGTA
* *
1457578 TAACAACCTAACTAT-GACGTGTCAA-ATATTTTTGTAAATGGCGTG
1 TAACAACCTAACTATAG-CGTGT-AACATATTTTTATAAATGGCGTA
* * *
1457623 TAATAACCTAACCATAGCATGTAACATATTT
1 TAACAACCTAACTATAGCGTGTAACATATTT
1457654 CTGTACATGT
Statistics
Matches: 65, Mismatches: 7, Indels: 8
0.81 0.09 0.10
Matches are distributed among these distances:
44 3 0.05
45 59 0.91
46 3 0.05
ACGTcount: A:0.36, C:0.16, G:0.13, T:0.35
Consensus pattern (45 bp):
TAACAACCTAACTATAGCGTGTAACATATTTTTATAAATGGCGTA
Found at i:1460261 original size:20 final size:18
Alignment explanation
Indices: 1460224--1460259 Score: 54
Period size: 18 Copynumber: 1.9 Consensus size: 18
1460214 TGTTTAATAA
*
1460224 AAAATATTTTTTTGAAAT
1 AAAATATTTTTTTAAAAT
1460242 AAAATATTTATTTTAAAA
1 AAAATATTT-TTTTAAAA
1460260 ATTAATAAAT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 9 0.56
19 7 0.44
ACGTcount: A:0.50, C:0.00, G:0.03, T:0.47
Consensus pattern (18 bp):
AAAATATTTTTTTAAAAT
Found at i:1461816 original size:39 final size:41
Alignment explanation
Indices: 1461738--1461817 Score: 119
Period size: 41 Copynumber: 2.0 Consensus size: 41
1461728 GTCACGACGT
* * *
1461738 CATTATCCTCTCTCCCATAAATGAGTTTATTAGTGGGTGTG
1 CATTACCCTCTCTCCCATAAATGAGCTTATTAGTAGGTGTG
1461779 CATTACCCTCTCTCCCATAAATGAGCTTA-TAG-AGGTGTG
1 CATTACCCTCTCTCCCATAAATGAGCTTATTAGTAGGTGTG
1461818 TAGCACACCC
Statistics
Matches: 36, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
39 6 0.17
40 3 0.08
41 27 0.75
ACGTcount: A:0.24, C:0.23, G:0.19, T:0.35
Consensus pattern (41 bp):
CATTACCCTCTCTCCCATAAATGAGCTTATTAGTAGGTGTG
Found at i:1461979 original size:57 final size:57
Alignment explanation
Indices: 1461891--1462002 Score: 197
Period size: 57 Copynumber: 2.0 Consensus size: 57
1461881 TTTTTGTGAC
**
1461891 ACTTTCTCACCAGATTTCGATAACGCTCTCGTTGTTGTCGGCCACCCTGCCTACCCA
1 ACTTTCTCACCAGATTTCGATAACGCTCTCGTTGCCGTCGGCCACCCTGCCTACCCA
*
1461948 ACTTTCTCACCCGATTTCGATAACGCTCTCGTTGCCGTCGGCCACCCTGCCTACC
1 ACTTTCTCACCAGATTTCGATAACGCTCTCGTTGCCGTCGGCCACCCTGCCTACC
1462003 TAACGGATAT
Statistics
Matches: 52, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
57 52 1.00
ACGTcount: A:0.16, C:0.39, G:0.16, T:0.29
Consensus pattern (57 bp):
ACTTTCTCACCAGATTTCGATAACGCTCTCGTTGCCGTCGGCCACCCTGCCTACCCA
Found at i:1462212 original size:130 final size:130
Alignment explanation
Indices: 1461979--1462239 Score: 452
Period size: 130 Copynumber: 2.0 Consensus size: 130
1461969 AACGCTCTCG
* *
1461979 TTGCCGTCGGCCACCCTGCCTACCTAACGGATATGTCATGGGGTCATTATCCTCTTCCCCATAAA
1 TTGCCGTCGGCCACCCTGCCTACCCAACGGATATGTCACGGGGTCATTATCCTCTTCCCCATAAA
*
1462044 CACGCTTATAGGGGTGTGCAGCACACCCACTTATAAGGAGCCTAAGACCTCCCGTTCCTGTCCGA
66 CACGCTTATAAGGGTGTGCAGCACACCCACTTATAAGGAGCCTAAGACCTCCCGTTCCTGTCCGA
*
1462109 TTGCCGTCGGCCACCCTGCCTACCCAACGGATATGTCACGGGGTCATTATCCT-GTCTCCCATAA
1 TTGCCGTCGGCCACCCTGCCTACCCAACGGATATGTCACGGGGTCATTATCCTCTTC-CCCATAA
* *
1462173 ACGCGCTTATAAGGGTGTGCAGCACACCCACTTATAAGGAGCCTAAGACCTCCCGTTCTTGTCCG
65 ACACGCTTATAAGGGTGTGCAGCACACCCACTTATAAGGAGCCTAAGACCTCCCGTTCCTGTCCG
1462238 A
130 A
1462239 T
1 T
1462240 GTGGGATAGA
Statistics
Matches: 124, Mismatches: 6, Indels: 2
0.94 0.05 0.02
Matches are distributed among these distances:
129 2 0.02
130 122 0.98
ACGTcount: A:0.21, C:0.33, G:0.21, T:0.25
Consensus pattern (130 bp):
TTGCCGTCGGCCACCCTGCCTACCCAACGGATATGTCACGGGGTCATTATCCTCTTCCCCATAAA
CACGCTTATAAGGGTGTGCAGCACACCCACTTATAAGGAGCCTAAGACCTCCCGTTCCTGTCCGA
Found at i:1462373 original size:21 final size:21
Alignment explanation
Indices: 1462347--1462389 Score: 86
Period size: 21 Copynumber: 2.0 Consensus size: 21
1462337 AAATAATCAG
1462347 CAACCTATTAATCAGTAAGAA
1 CAACCTATTAATCAGTAAGAA
1462368 CAACCTATTAATCAGTAAGAA
1 CAACCTATTAATCAGTAAGAA
1462389 C
1 C
1462390 CTATGTCACG
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.47, C:0.21, G:0.09, T:0.23
Consensus pattern (21 bp):
CAACCTATTAATCAGTAAGAA
Found at i:1462422 original size:22 final size:22
Alignment explanation
Indices: 1462397--1462440 Score: 88
Period size: 22 Copynumber: 2.0 Consensus size: 22
1462387 AACCTATGTC
1462397 ACGGGATCATTACTCTCTTTTT
1 ACGGGATCATTACTCTCTTTTT
1462419 ACGGGATCATTACTCTCTTTTT
1 ACGGGATCATTACTCTCTTTTT
1462441 CATAAACGTG
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.18, C:0.23, G:0.14, T:0.45
Consensus pattern (22 bp):
ACGGGATCATTACTCTCTTTTT
Found at i:1462726 original size:156 final size:155
Alignment explanation
Indices: 1462442--1462750 Score: 370
Period size: 156 Copynumber: 2.0 Consensus size: 155
1462432 TCTCTTTTTC
* * * * * * * * * * *
1462442 ATAAACGTGTTTATAGGGGTGTGTAGCACACTCATTTATAAGGAGCCTAGGACTTCCCGTTCTTG
1 ATAAACGCGCTTATAGGGGTGTGCAACACACTCACTTATAAGAAACCTAAGACCTCCCATTCCTG
* * * * * * * *
1462507 TCCGATGTGGGATAGAGACACTCTTTGTGACACTCTCTGACTCGATTTAGGCAAAGCTCTCGTTG
66 TCCGATATGGGATAGAGACACTCTTTGTGACACTCTCTCACCCAATTCAGACAAAACCCTCGTTG
* *
1462572 TCGTCGGCCACCCTGTCTGACCCCCT
131 CCGTCGGCCACCCTGCCT-ACCCCCT
1462598 ATAAACGCGCTTATAGGGGTGTGCAACACA-TCTACTTATAAGAAACCTAAGACCTCCCATTCCT
1 ATAAACGCGCTTATAGGGGTGTGCAACACACTC-ACTTATAAGAAACCTAAGACCTCCCATTCCT
* *
1462662 GTCCGATATGGGATAGAGGCACTCTTTGTGACACTCT-TCCACCCAATTCCGACAAAACCCTCGT
65 GTCCGATATGGGATAGAGACACTCTTTGTGACACTCTCT-CACCCAATTCAGACAAAACCCTCGT
1462726 TGCCGTCGGCCACCCTGCCTACCCC
129 TGCCGTCGGCCACCCTGCCTACCCC
1462751 GATATGTTGG
Statistics
Matches: 128, Mismatches: 23, Indels: 5
0.82 0.15 0.03
Matches are distributed among these distances:
155 8 0.06
156 120 0.94
ACGTcount: A:0.23, C:0.29, G:0.21, T:0.27
Consensus pattern (155 bp):
ATAAACGCGCTTATAGGGGTGTGCAACACACTCACTTATAAGAAACCTAAGACCTCCCATTCCTG
TCCGATATGGGATAGAGACACTCTTTGTGACACTCTCTCACCCAATTCAGACAAAACCCTCGTTG
CCGTCGGCCACCCTGCCTACCCCCT
Found at i:1477718 original size:2 final size:2
Alignment explanation
Indices: 1477713--1477753 Score: 68
Period size: 2 Copynumber: 21.5 Consensus size: 2
1477703 TCTCTCCCAC
1477713 AT AT AT AT AT AT -T AT AT AT AT AT AT AT A- 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 AT AT AT
1477753 A
1 A
1477754 ATTCCCCACT
Statistics
Matches: 37, Mismatches: 0, Indels: 4
0.90 0.00 0.10
Matches are distributed among these distances:
1 2 0.05
2 35 0.95
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:1477733 original size:15 final size:15
Alignment explanation
Indices: 1477713--1477753 Score: 73
Period size: 15 Copynumber: 2.7 Consensus size: 15
1477703 TCTCTCCCAC
*
1477713 ATATATATATATTAT
1 ATATATATATATAAT
1477728 ATATATATATATAAT
1 ATATATATATATAAT
1477743 ATATATATATA
1 ATATATATATA
1477754 ATTCCCCACT
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
15 25 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (15 bp):
ATATATATATATAAT
Found at i:1477754 original size:13 final size:13
Alignment explanation
Indices: 1477713--1477755 Score: 68
Period size: 13 Copynumber: 3.2 Consensus size: 13
1477703 TCTCTCCCAC
1477713 ATATATATATATTA
1 ATATATATATA-TA
1477727 TATATATATATATA
1 -ATATATATATATA
1477741 ATATATATATATA
1 ATATATATATATA
1477754 AT
1 AT
1477756 TCCCCACTTC
Statistics
Matches: 28, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
13 15 0.54
14 2 0.07
15 11 0.39
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (13 bp):
ATATATATATATA
Found at i:1478185 original size:2 final size:2
Alignment explanation
Indices: 1478178--1478220 Score: 61
Period size: 2 Copynumber: 22.0 Consensus size: 2
1478168 CACATCTAAC
* *
1478178 AT AT AT AT AT AT AT AT AT AT AT AT AT TT TT A- AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1478219 AT
1 AT
1478221 GATCCAATGC
Statistics
Matches: 38, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
1 1 0.03
2 37 0.97
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (2 bp):
AT
Found at i:1491079 original size:69 final size:67
Alignment explanation
Indices: 1490948--1491086 Score: 215
Period size: 69 Copynumber: 2.0 Consensus size: 67
1490938 AAAATATAAT
* * **
1490948 GTTAAAAAACAAATAGATAAAATTAAAAGAAAATAGATAGCATTGTTTGAAATTGCTACACTATT
1 GTTAAAAAACAAACAGATAAAATTAAAAAAAAATAGATAGCATTACTTGAAATTGCTACACTATT
1491013 AA
66 AA
*
1491015 GTTAAAAAACAAACAGATAAAATTAAAAAAAAAAATAGATAGCATTACTTGAGATTGCTACACTA
1 GTTAAAAAACAAACAGATAAAATT--AAAAAAAAATAGATAGCATTACTTGAAATTGCTACACTA
1491080 TTAA
64 TTAA
1491084 GTT
1 GTT
1491087 TGTGAGTTGT
Statistics
Matches: 65, Mismatches: 5, Indels: 2
0.90 0.07 0.03
Matches are distributed among these distances:
67 23 0.35
69 42 0.65
ACGTcount: A:0.53, C:0.09, G:0.12, T:0.27
Consensus pattern (67 bp):
GTTAAAAAACAAACAGATAAAATTAAAAAAAAATAGATAGCATTACTTGAAATTGCTACACTATT
AA
Found at i:1492350 original size:21 final size:20
Alignment explanation
Indices: 1492313--1492352 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 20
1492303 TCATAATCTT
**
1492313 ATAAAAGATAATGTTAAAAA
1 ATAAAAGATAAAATTAAAAA
1492333 ATAAACAGATAAAATTAAAA
1 ATAAA-AGATAAAATTAAAA
1492353 GAAAATAGAT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 5 0.29
21 12 0.71
ACGTcount: A:0.68, C:0.03, G:0.07, T:0.23
Consensus pattern (20 bp):
ATAAAAGATAAAATTAAAAA
Found at i:1492480 original size:25 final size:24
Alignment explanation
Indices: 1492447--1492496 Score: 73
Period size: 25 Copynumber: 2.0 Consensus size: 24
1492437 CCAACATGAA
1492447 AAACCAAATAACCACTAAATAGAAG
1 AAACCAAATAACCAC-AAATAGAAG
* *
1492472 AAACTAAATAACCACAAGTAGAAG
1 AAACCAAATAACCACAAATAGAAG
1492496 A
1 A
1492497 CATGTAATTA
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
24 9 0.39
25 14 0.61
ACGTcount: A:0.60, C:0.18, G:0.10, T:0.12
Consensus pattern (24 bp):
AAACCAAATAACCACAAATAGAAG
Found at i:1501936 original size:151 final size:151
Alignment explanation
Indices: 1501644--1501939 Score: 348
Period size: 151 Copynumber: 2.0 Consensus size: 151
1501634 CTCCATAATT
* * * * *
1501644 ATTCAATTTTTTTTTCCATTTTTCTTTATTAAAAATAGAGATCCAAATTTGCTTTTTTTTTTAGT
1 ATTCAATTTTTGTTTACATTTTTCTTAATTAAAAATAAAGATCCAAATTTGC-TTTTTTTTAAGT
* *** **
1501709 AAAGAAATACATATTTTACGGCGTAGACAAATTGGTAATTATTATATCTTTTTTGTCGTGAGAAA
65 AAAGAAATACATATTTTACGGCGTAGACAAATTGATAATTATTATATCTTTTCAATCACGAGAAA
1501774 AAATGTATTATTTAAAGTTGTA
130 AAATGTATTATTTAAAGTTGTA
**
1501796 ATTCGAATTTTTGTTTAC-TTTTT-TTAATTAAAAATAAAGATTTAAATTTAGC-TTTTTTTAAG
1 ATTC-AATTTTTGTTTACATTTTTCTTAATTAAAAATAAAGATCCAAATTT-GCTTTTTTTTAAG
* * *
1501858 TAAAGAAATACATATTCTTACTG-TTGAGACAAATTGATAATTATTATATCTTTTCAATCACGGG
64 TAAAGAAATACATATT-TTACGGCGT-AGACAAATTGATAATTATTATATCTTTTCAATCACGAG
* * *
1501922 AAAAGATTTTTTATTTAA
127 AAAAAATGTATTATTTAA
1501940 GCTTTGTAGG
Statistics
Matches: 121, Mismatches: 19, Indels: 9
0.81 0.13 0.06
Matches are distributed among these distances:
150 26 0.21
151 73 0.60
152 11 0.09
153 11 0.09
ACGTcount: A:0.35, C:0.08, G:0.11, T:0.46
Consensus pattern (151 bp):
ATTCAATTTTTGTTTACATTTTTCTTAATTAAAAATAAAGATCCAAATTTGCTTTTTTTTAAGTA
AAGAAATACATATTTTACGGCGTAGACAAATTGATAATTATTATATCTTTTCAATCACGAGAAAA
AATGTATTATTTAAAGTTGTA
Found at i:1515934 original size:30 final size:30
Alignment explanation
Indices: 1515900--1515961 Score: 124
Period size: 30 Copynumber: 2.1 Consensus size: 30
1515890 AATTTCTGGG
1515900 TGTAAAGGAATTTAGCCTCTTTCAAATCTA
1 TGTAAAGGAATTTAGCCTCTTTCAAATCTA
1515930 TGTAAAGGAATTTAGCCTCTTTCAAATCTA
1 TGTAAAGGAATTTAGCCTCTTTCAAATCTA
1515960 TG
1 TG
1515962 GTCCTTAATA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 32 1.00
ACGTcount: A:0.32, C:0.16, G:0.15, T:0.37
Consensus pattern (30 bp):
TGTAAAGGAATTTAGCCTCTTTCAAATCTA
Found at i:1532460 original size:72 final size:72
Alignment explanation
Indices: 1532340--1532486 Score: 267
Period size: 72 Copynumber: 2.0 Consensus size: 72
1532330 ACGATACAAC
*
1532340 ATCTTAGAAGAAGTGTAACTAATTTAAGTAATGAAATCAGGTCAAGCACAGCAAACATACTCCCA
1 ATCTTAGAAGAAGTGTAACTAATTTAAGTAAAGAAATCAGGTCAAGCACAGCAAACATACTCCCA
1532405 CCAGCAA
66 CCAGCAA
* *
1532412 ATCTTAGAAGAAGTGTAACTAATTTAAGTAAAGAAATCAGTTCCAGCACAGCAAACATACTCCCA
1 ATCTTAGAAGAAGTGTAACTAATTTAAGTAAAGAAATCAGGTCAAGCACAGCAAACATACTCCCA
1532477 CCAGCAA
66 CCAGCAA
1532484 ATC
1 ATC
1532487 AGTTAGTAAC
Statistics
Matches: 72, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
72 72 1.00
ACGTcount: A:0.43, C:0.22, G:0.14, T:0.21
Consensus pattern (72 bp):
ATCTTAGAAGAAGTGTAACTAATTTAAGTAAAGAAATCAGGTCAAGCACAGCAAACATACTCCCA
CCAGCAA
Found at i:1535425 original size:4 final size:4
Alignment explanation
Indices: 1535416--1535454 Score: 60
Period size: 4 Copynumber: 9.8 Consensus size: 4
1535406 CTCACACTAT
* *
1535416 ATAC ATAC ATAT ATAC ATAC ATAC AAAC ATAC ATAC ATA
1 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATA
1535455 TGTATCTTCT
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
4 31 1.00
ACGTcount: A:0.54, C:0.21, G:0.00, T:0.26
Consensus pattern (4 bp):
ATAC
Found at i:1538118 original size:19 final size:19
Alignment explanation
Indices: 1538096--1538134 Score: 51
Period size: 19 Copynumber: 2.1 Consensus size: 19
1538086 TTTGTAACAC
**
1538096 ATTTATCATCATCATTCAT
1 ATTTATCAAAATCATTCAT
*
1538115 ATTTATGAAAATCATTCAT
1 ATTTATCAAAATCATTCAT
1538134 A
1 A
1538135 AGCAATAGTC
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.38, C:0.15, G:0.03, T:0.44
Consensus pattern (19 bp):
ATTTATCAAAATCATTCAT
Found at i:1541245 original size:45 final size:45
Alignment explanation
Indices: 1541151--1541238 Score: 131
Period size: 45 Copynumber: 2.0 Consensus size: 45
1541141 TGCTATTTAT
* *
1541151 AAAAATATGTTACACGTTATGATTAAGTTGTTACACGCCATGTAC
1 AAAAATATATTACACGTTATGATTAAGTTGTTACACACCATGTAC
* * *
1541196 AAAAATATATTACGCGTTATGGTTAGGTTGTTACACACCATGT
1 AAAAATATATTACACGTTATGATTAAGTTGTTACACACCATGT
1541239 TGAAAAAAAA
Statistics
Matches: 38, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
45 38 1.00
ACGTcount: A:0.34, C:0.15, G:0.17, T:0.34
Consensus pattern (45 bp):
AAAAATATATTACACGTTATGATTAAGTTGTTACACACCATGTAC
Found at i:1541321 original size:76 final size:76
Alignment explanation
Indices: 1541178--1541321 Score: 180
Period size: 76 Copynumber: 1.9 Consensus size: 76
1541168 TATGATTAAG
* * ** * **
1541178 TTGTTACACGCCATGTACAAAAATATATTACGCGTTATGGTTAGGTTGTTACACACCATGTTGAA
1 TTGTTACACGCCATGTACAAAAACATATTACACGCCATGGTTAGATTGTTACACACCATGTACAA
1541243 AAAAAATACTA
66 AAAAAATACTA
* * * **
1541254 TTGTTACATGCCATGTATAAAAACATGTTACACGCCATGGTTAGATTGTTACACTTCATGTACAA
1 TTGTTACACGCCATGTACAAAAACATATTACACGCCATGGTTAGATTGTTACACACCATGTACAA
1541319 AAA
66 AAA
1541322 CATGTTACAC
Statistics
Matches: 56, Mismatches: 12, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
76 56 1.00
ACGTcount: A:0.36, C:0.17, G:0.15, T:0.32
Consensus pattern (76 bp):
TTGTTACACGCCATGTACAAAAACATATTACACGCCATGGTTAGATTGTTACACACCATGTACAA
AAAAAATACTA
Found at i:1541344 original size:24 final size:23
Alignment explanation
Indices: 1541255--1541345 Score: 71
Period size: 24 Copynumber: 3.9 Consensus size: 23
1541245 AAAATACTAT
*
1541255 TGTTACATGCCATGTATAAAAACA
1 TGTTACACGCCATGT-TAAAAACA
* *
1541279 TGTTACACGCCATGGTT--AGA-T
1 TGTTACACGCCAT-GTTAAAAACA
** *
1541300 TGTTACACTTCATGTACAAAAACA
1 TGTTACACGCCATGT-TAAAAACA
1541324 TGTTACACGCCATGTTGAAAAA
1 TGTTACACGCCATGTT-AAAAA
1541346 AAAATATTGT
Statistics
Matches: 50, Mismatches: 11, Indels: 12
0.68 0.15 0.16
Matches are distributed among these distances:
20 2 0.04
21 11 0.22
22 2 0.04
23 2 0.04
24 31 0.62
25 2 0.04
ACGTcount: A:0.36, C:0.19, G:0.15, T:0.30
Consensus pattern (23 bp):
TGTTACACGCCATGTTAAAAACA
Found at i:1542293 original size:134 final size:132
Alignment explanation
Indices: 1542032--1542302 Score: 332
Period size: 134 Copynumber: 2.0 Consensus size: 132
1542022 TGATTAATGG
* * * *
1542032 TTTAATTTATTTGAAATAGTTTTAATAGCATTTTTATTAAGTCAAGGCTAAATATGTCTAAAATA
1 TTTAATTTATTTGAAATAGTTTTAAGAGCATTTTTATCAAGTCAAGACTAAATATGGCTAAAATA
* * * * * * *
1542097 AGTAAATTTATTTTGATAGTTATTTTTGAAATACCTTTGTCAAGGAAAGTTATTCTTGATAATTT
66 AGTAAATATATTTTAATAGTTATCTTTAAAATACCTTTATCAAGGAAAGCTATTCTTCATAA-TT
1542162 TCT
130 TCT
* *
1542165 CTTTAATTTATTTGAAATAGTTTTAAGGGTATTTTTATCAAGTCATA-ACTAAATATGGCTAAAA
1 -TTTAATTTATTTGAAATAGTTTTAAGAGCATTTTTATCAAGTCA-AGACTAAATATGGCTAAAA
* * *
1542229 -ATAGTTAAATATATTTTAATTGTTATCTTTAAAATGCCTTTATCAAGGAAGGCTATTC-TCATA
64 TA-AG-TAAATATATTTTAATAGTTATCTTTAAAATACCTTTATCAAGGAAAGCTATTCTTCATA
1542292 ATTTCT
127 ATTTCT
1542298 TTTAA
1 TTTAA
1542303 AAATATTTAC
Statistics
Matches: 118, Mismatches: 16, Indels: 8
0.83 0.11 0.06
Matches are distributed among these distances:
132 5 0.04
133 6 0.05
134 62 0.53
135 45 0.38
ACGTcount: A:0.35, C:0.08, G:0.11, T:0.45
Consensus pattern (132 bp):
TTTAATTTATTTGAAATAGTTTTAAGAGCATTTTTATCAAGTCAAGACTAAATATGGCTAAAATA
AGTAAATATATTTTAATAGTTATCTTTAAAATACCTTTATCAAGGAAAGCTATTCTTCATAATTT
CT
Found at i:1555280 original size:2 final size:2
Alignment explanation
Indices: 1555273--1555315 Score: 77
Period size: 2 Copynumber: 21.5 Consensus size: 2
1555263 AGCGCAGTTT
*
1555273 AG AG AG AG AG AG AG AG AG AG AG AG AG GG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1555315 A
1 A
1555316 AGGAAAGGAG
Statistics
Matches: 39, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 39 1.00
ACGTcount: A:0.49, C:0.00, G:0.51, T:0.00
Consensus pattern (2 bp):
AG
Found at i:1575620 original size:27 final size:27
Alignment explanation
Indices: 1575589--1575640 Score: 86
Period size: 27 Copynumber: 1.9 Consensus size: 27
1575579 ATTTTGTTTT
*
1575589 TTTAAAATATTAATAATTTATAATTTA
1 TTTAAAATATTAATAATTAATAATTTA
*
1575616 TTTAAAATATTAATACTTAATAATT
1 TTTAAAATATTAATAATTAATAATT
1575641 AATAATGTAA
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
27 23 1.00
ACGTcount: A:0.48, C:0.02, G:0.00, T:0.50
Consensus pattern (27 bp):
TTTAAAATATTAATAATTAATAATTTA
Found at i:1575753 original size:29 final size:29
Alignment explanation
Indices: 1575721--1575778 Score: 75
Period size: 29 Copynumber: 2.0 Consensus size: 29
1575711 ATTCTCAAAT
1575721 TTAAAATA-TTAAA-TTTTTATAATATATAA
1 TTAAAA-ACTTAAACTTTTTATAATA-ATAA
*
1575750 TTAAAAACTTAAACTTTTTATTATAATAA
1 TTAAAAACTTAAACTTTTTATAATAATAA
1575779 GATTTATTTT
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
28 1 0.04
29 15 0.58
30 10 0.38
ACGTcount: A:0.50, C:0.03, G:0.00, T:0.47
Consensus pattern (29 bp):
TTAAAAACTTAAACTTTTTATAATAATAA
Found at i:1581936 original size:39 final size:38
Alignment explanation
Indices: 1581881--1582017 Score: 123
Period size: 39 Copynumber: 3.5 Consensus size: 38
1581871 AATTATTTTT
*
1581881 TGCTTTGGATTTATTCATATGAGGAATATTGATTTATGAA
1 TGCTTT-GATTTATTCATATGAAGAA-ATTGATTTATGAA
* * **
1581921 TGCTTTGATTTATTCATGTGACAGAAATTGATTCACAAA
1 TGCTTTGATTTATTCATATGA-AGAAATTGATTTATGAA
* * *
1581960 TGATTTGGTTTATTCATATGATA-AACATTAATTTATGAA
1 TGCTTTGATTTATTCATATGA-AGAA-ATTGATTTATGAA
* * *
1581999 TGTTTTGGTTTATTTATAT
1 TGCTTTGATTTATTCATAT
1582018 AATGAGTATC
Statistics
Matches: 80, Mismatches: 15, Indels: 5
0.80 0.15 0.05
Matches are distributed among these distances:
38 2 0.03
39 69 0.86
40 9 0.11
ACGTcount: A:0.31, C:0.07, G:0.16, T:0.47
Consensus pattern (38 bp):
TGCTTTGATTTATTCATATGAAGAAATTGATTTATGAA
Found at i:1592940 original size:2 final size:2
Alignment explanation
Indices: 1592933--1592972 Score: 66
Period size: 2 Copynumber: 21.0 Consensus size: 2
1592923 ATTTGGACTA
1592933 AT AT AT AT AT AT AT AT AT AT AT AT AT -T AT AT AT AT -T AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1592973 TTAAATTCAA
Statistics
Matches: 36, Mismatches: 0, Indels: 4
0.90 0.00 0.10
Matches are distributed among these distances:
1 2 0.06
2 34 0.94
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (2 bp):
AT
Found at i:1594306 original size:20 final size:21
Alignment explanation
Indices: 1594273--1594313 Score: 59
Period size: 20 Copynumber: 2.0 Consensus size: 21
1594263 AAAGACTTAT
1594273 TTAACTTAAAATAA-AAAAAA
1 TTAACTTAAAATAATAAAAAA
1594293 TTAA-TTAAATATAATAAAAAA
1 TTAACTTAAA-ATAATAAAAAA
1594314 ATAAAAATTT
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
19 5 0.26
20 8 0.42
21 6 0.32
ACGTcount: A:0.68, C:0.02, G:0.00, T:0.29
Consensus pattern (21 bp):
TTAACTTAAAATAATAAAAAA
Found at i:1601111 original size:23 final size:23
Alignment explanation
Indices: 1601077--1601122 Score: 83
Period size: 23 Copynumber: 2.0 Consensus size: 23
1601067 TCTGTATTCT
*
1601077 GTAAAGCTAAAACATGATGTGCA
1 GTAAAGCCAAAACATGATGTGCA
1601100 GTAAAGCCAAAACATGATGTGCA
1 GTAAAGCCAAAACATGATGTGCA
1601123 ATAACGATAA
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
23 22 1.00
ACGTcount: A:0.43, C:0.15, G:0.22, T:0.20
Consensus pattern (23 bp):
GTAAAGCCAAAACATGATGTGCA
Found at i:1605085 original size:25 final size:25
Alignment explanation
Indices: 1605015--1605078 Score: 101
Period size: 25 Copynumber: 2.6 Consensus size: 25
1605005 ACTTCCATAT
*
1605015 AGATAATAGTCACGCAATGCCTTAC
1 AGATAATAGTCACGAAATGCCTTAC
* *
1605040 AGATAACAGTCACGAAATGCCTTTC
1 AGATAATAGTCACGAAATGCCTTAC
1605065 AGATAATAGTCACG
1 AGATAATAGTCACG
1605079 TATTGCCCTT
Statistics
Matches: 35, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
25 35 1.00
ACGTcount: A:0.38, C:0.22, G:0.17, T:0.23
Consensus pattern (25 bp):
AGATAATAGTCACGAAATGCCTTAC
Found at i:1605150 original size:23 final size:23
Alignment explanation
Indices: 1605122--1605165 Score: 63
Period size: 23 Copynumber: 1.9 Consensus size: 23
1605112 TACAATTAAT
1605122 AGTCATACAATGC-CTAATCAAAC
1 AGTCATACAATGCTC-AATCAAAC
*
1605145 AGTCATGCAATGCTCAATCAA
1 AGTCATACAATGCTCAATCAA
1605166 GAGTCACGCA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
23 18 0.95
24 1 0.05
ACGTcount: A:0.41, C:0.25, G:0.11, T:0.23
Consensus pattern (23 bp):
AGTCATACAATGCTCAATCAAAC
Found at i:1626143 original size:15 final size:15
Alignment explanation
Indices: 1626123--1626157 Score: 54
Period size: 15 Copynumber: 2.3 Consensus size: 15
1626113 ATGGGGTAGG
1626123 AAAAAGCAAAAAAA-A
1 AAAAAG-AAAAAAAGA
1626138 AAAAAGAAAAAAAGA
1 AAAAAGAAAAAAAGA
1626153 AAAAA
1 AAAAA
1626158 AAACCAACAA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
14 7 0.37
15 12 0.63
ACGTcount: A:0.89, C:0.03, G:0.09, T:0.00
Consensus pattern (15 bp):
AAAAAGAAAAAAAGA
Found at i:1626169 original size:22 final size:23
Alignment explanation
Indices: 1626123--1626171 Score: 64
Period size: 22 Copynumber: 2.2 Consensus size: 23
1626113 ATGGGGTAGG
*
1626123 AAAAAGCAAAAAAAAAAAAAGAA
1 AAAAAGCAAAAAAAAAAAAACAA
**
1626146 AAAAAG-AAAAAAAAACCAACAA
1 AAAAAGCAAAAAAAAAAAAACAA
1626168 AAAA
1 AAAA
1626172 GTCAAGCAAA
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
22 17 0.74
23 6 0.26
ACGTcount: A:0.86, C:0.08, G:0.06, T:0.00
Consensus pattern (23 bp):
AAAAAGCAAAAAAAAAAAAACAA
Found at i:1627143 original size:19 final size:18
Alignment explanation
Indices: 1627112--1627155 Score: 54
Period size: 19 Copynumber: 2.4 Consensus size: 18
1627102 AACTTTTAGA
*
1627112 TATAATATTTTTACAAATT
1 TATAA-ATTTTTAAAAATT
1627131 TATAAATTATTTAAAAATT
1 TATAAATT-TTTAAAAATT
1627150 T-TAAAT
1 TATAAAT
1627156 AAATTTTATT
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
18 8 0.35
19 15 0.65
ACGTcount: A:0.48, C:0.02, G:0.00, T:0.50
Consensus pattern (18 bp):
TATAAATTTTTAAAAATT
Found at i:1627191 original size:29 final size:30
Alignment explanation
Indices: 1627149--1627206 Score: 75
Period size: 30 Copynumber: 2.0 Consensus size: 30
1627139 ATTTAAAAAT
1627149 TTTAAATAAA-TTTTAT-TTTTTATATTTTA
1 TTTAAATAAATTTTTATATTTTTAT-TTTTA
* *
1627178 TTTAATTAAGTTTTTATATTTTTATTTTT
1 TTTAAATAAATTTTTATATTTTTATTTTT
1627207 GATCAAATAG
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
29 8 0.32
30 10 0.40
31 7 0.28
ACGTcount: A:0.29, C:0.00, G:0.02, T:0.69
Consensus pattern (30 bp):
TTTAAATAAATTTTTATATTTTTATTTTTA
Found at i:1627521 original size:20 final size:19
Alignment explanation
Indices: 1627494--1627531 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 19
1627484 ATAAAAATTT
1627494 ATTTAAAACTTTTTAAATA
1 ATTTAAAACTTTTTAAATA
1627513 ATTTAAAAACTTTTTAAAT
1 ATTT-AAAACTTTTTAAAT
1627532 CCTTATATAA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
19 4 0.22
20 14 0.78
ACGTcount: A:0.47, C:0.05, G:0.00, T:0.47
Consensus pattern (19 bp):
ATTTAAAACTTTTTAAATA
Found at i:1628741 original size:5 final size:5
Alignment explanation
Indices: 1628723--1628759 Score: 56
Period size: 5 Copynumber: 7.2 Consensus size: 5
1628713 AAAACCCAAG
*
1628723 AAGAA AAGGAA AAGAA AAGAA AAGGA AAGAA AAGAA A
1 AAGAA AA-GAA AAGAA AAGAA AAGAA AAGAA AAGAA A
1628760 GGAACTTTTA
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
5 24 0.83
6 5 0.17
ACGTcount: A:0.76, C:0.00, G:0.24, T:0.00
Consensus pattern (5 bp):
AAGAA
Found at i:1628744 original size:16 final size:16
Alignment explanation
Indices: 1628723--1628763 Score: 68
Period size: 15 Copynumber: 2.7 Consensus size: 16
1628713 AAAACCCAAG
1628723 AAGAAAAGGAAAAGAA
1 AAGAAAAGGAAAAGAA
1628739 AAGAAAAGG-AAAGAA
1 AAGAAAAGGAAAAGAA
1628754 AAG-AAAGGAA
1 AAGAAAAGGAA
1628764 CTTTTATTCT
Statistics
Matches: 24, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
14 5 0.21
15 10 0.42
16 9 0.38
ACGTcount: A:0.73, C:0.00, G:0.27, T:0.00
Consensus pattern (16 bp):
AAGAAAAGGAAAAGAA
Found at i:1636675 original size:30 final size:30
Alignment explanation
Indices: 1636639--1636706 Score: 136
Period size: 30 Copynumber: 2.3 Consensus size: 30
1636629 TGGGCATGGG
1636639 CATGACCACCACCACCATCATCACCATGAT
1 CATGACCACCACCACCATCATCACCATGAT
1636669 CATGACCACCACCACCATCATCACCATGAT
1 CATGACCACCACCACCATCATCACCATGAT
1636699 CATGACCA
1 CATGACCA
1636707 TCATCAGCAC
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 38 1.00
ACGTcount: A:0.34, C:0.43, G:0.07, T:0.16
Consensus pattern (30 bp):
CATGACCACCACCACCATCATCACCATGAT
Found at i:1652896 original size:4 final size:4
Alignment explanation
Indices: 1652887--1652914 Score: 56
Period size: 4 Copynumber: 7.0 Consensus size: 4
1652877 AATCATATGT
1652887 ATAC ATAC ATAC ATAC ATAC ATAC ATAC
1 ATAC ATAC ATAC ATAC ATAC ATAC ATAC
1652915 TGAATTTGAA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 24 1.00
ACGTcount: A:0.50, C:0.25, G:0.00, T:0.25
Consensus pattern (4 bp):
ATAC
Found at i:1653583 original size:2 final size:2
Alignment explanation
Indices: 1653576--1653625 Score: 75
Period size: 2 Copynumber: 25.0 Consensus size: 2
1653566 TCTCTGTAAG
*
1653576 TC TC TC TC TC -C ATC TC AC TC TC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC -TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1653618 TC TC TC TC
1 TC TC TC TC
1653626 AAGTGCAGGG
Statistics
Matches: 44, Mismatches: 2, Indels: 4
0.88 0.04 0.08
Matches are distributed among these distances:
1 1 0.02
2 42 0.95
3 1 0.02
ACGTcount: A:0.04, C:0.50, G:0.00, T:0.46
Consensus pattern (2 bp):
TC
Found at i:1659379 original size:16 final size:16
Alignment explanation
Indices: 1659358--1659389 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
1659348 TTAAATAAAT
*
1659358 TTTTTGTCTAAAATAA
1 TTTTTGTATAAAATAA
1659374 TTTTTGTATAAAATAA
1 TTTTTGTATAAAATAA
1659390 CATACTATAA
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:0.41, C:0.03, G:0.06, T:0.50
Consensus pattern (16 bp):
TTTTTGTATAAAATAA
Found at i:1668708 original size:2 final size:2
Alignment explanation
Indices: 1668701--1668765 Score: 53
Period size: 2 Copynumber: 33.0 Consensus size: 2
1668691 GCCCTTTCTG
* * **
1668701 GA GA GA GA AA GA GA GA GA GA GA GA GA GA GA AA CCT GA GA GA -A
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA -GA GA GA GA GA
* *
1668743 AA GA GA GA G- GA GA GA GA AA GA GA
1 GA GA GA GA GA GA GA GA GA GA GA GA
1668766 AAAAAAAAAC
Statistics
Matches: 50, Mismatches: 10, Indels: 6
0.76 0.15 0.09
Matches are distributed among these distances:
1 2 0.04
2 48 0.96
ACGTcount: A:0.54, C:0.03, G:0.42, T:0.02
Consensus pattern (2 bp):
GA
Found at i:1668756 original size:35 final size:35
Alignment explanation
Indices: 1668701--1668767 Score: 109
Period size: 35 Copynumber: 1.9 Consensus size: 35
1668691 GCCCTTTCTG
*
1668701 GAGAGAGAAAGAGAGAGAGAGAGAGAGAGAAACCT
1 GAGAGAGAAAGAGAGAGAGAGAGAAAGAGAAACCT
1668736 GAGAGA-AAAGAGAGAGGAGAGAGAAAGAGAAA
1 GAGAGAGAAAGAGAGA-GAGAGAGAAAGAGAAA
1668768 AAAAAAACCT
Statistics
Matches: 30, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
34 9 0.30
35 21 0.70
ACGTcount: A:0.55, C:0.03, G:0.40, T:0.01
Consensus pattern (35 bp):
GAGAGAGAAAGAGAGAGAGAGAGAAAGAGAAACCT
Found at i:1677007 original size:21 final size:23
Alignment explanation
Indices: 1676978--1677019 Score: 61
Period size: 21 Copynumber: 1.9 Consensus size: 23
1676968 TCCCTAACAA
1676978 TTTTGTCTTACTTTA-TTTTTAC
1 TTTTGTCTTACTTTAGTTTTTAC
*
1677000 TTTT-TCTTGCTTTAGTTTTT
1 TTTTGTCTTACTTTAGTTTTT
1677020 GCACATCTAC
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
21 9 0.50
22 9 0.50
ACGTcount: A:0.10, C:0.12, G:0.07, T:0.71
Consensus pattern (23 bp):
TTTTGTCTTACTTTAGTTTTTAC
Found at i:1679791 original size:33 final size:33
Alignment explanation
Indices: 1679725--1679808 Score: 96
Period size: 33 Copynumber: 2.5 Consensus size: 33
1679715 AATGATATTA
* * **
1679725 TAATATATCATAATTGATAATGATGTGGTATGT
1 TAATATATTATAATTGATAATGATATGACATGT
*
1679758 TAATATATTATAATTGATTATGATATGACATGT
1 TAATATATTATAATTGATAATGATATGACATGT
1679791 TAATTTGATATTATAATT
1 TAA--T-ATATTATAATT
1679809 TAACCATATA
Statistics
Matches: 43, Mismatches: 5, Indels: 3
0.84 0.10 0.06
Matches are distributed among these distances:
33 31 0.72
35 1 0.02
36 11 0.26
ACGTcount: A:0.38, C:0.02, G:0.13, T:0.46
Consensus pattern (33 bp):
TAATATATTATAATTGATAATGATATGACATGT
Found at i:1680038 original size:3 final size:3
Alignment explanation
Indices: 1680030--1680078 Score: 89
Period size: 3 Copynumber: 16.3 Consensus size: 3
1680020 TACTTCTCTT
*
1680030 TTA TTA TTA TTA GTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1680078 T
1 T
1680079 ATTGTAATTA
Statistics
Matches: 44, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
3 44 1.00
ACGTcount: A:0.33, C:0.00, G:0.02, T:0.65
Consensus pattern (3 bp):
TTA
Found at i:1681234 original size:519 final size:519
Alignment explanation
Indices: 1680253--1681293 Score: 1570
Period size: 519 Copynumber: 2.0 Consensus size: 519
1680243 TGTTCTCTTT
*
1680253 GTTTTGCTAGGTTAATGCGGTATATAGACCTATGACAATTAAGGAAAGATCATTTGATCTCAAAC
1 GTTTTGCTAGGTTAATGCGGTATATAGACCTAGGACAATTAAGGAAAGATCATTTGATCTCAAAC
*
1680318 CTGCAAGGTCATCCTCACTCGTAAAGAAAGAGGGTAACCCCACTTTGACAAGAGAGTTTATTATT
66 CTGCAAGGTCATCCTCACTCGTAAAGAAAGAGGGTAACCCCACTTTGACAAGAGAGCTTATTATT
* * * *
1680383 GTCAATAGATTTTAACATAAACACATATGTTATCGGTATATTTTCAAAATCAAAAGTTATATTAC
131 GTCAATAGATTTTAACATAAACACATATATTATCGGTATATTTTCAAAATAAAAAATTATATCAC
* * * *
1680448 ATGATAAAAAACTATTTTAACTCAAAAGTTACGTCGCATAAAGTGACATAGTGTGTTTATTGAAT
196 ATGATAAAAAACTATCTTAACTCAAAAGTTACGTCACATAAAGTGACATAGTATGTCTATTGAAT
* * * *
1680513 TATAAGTAAGTTTTCATATGAATGGTTATGTCTTTTGGTAAAATGACATCTAAAAGTTATGAGAT
261 TATAAGTAAGTTTTCATATGAATGGTTATGTCTTTTGATAAAATAACATCTAAAAGTTATGAAAC
* * * *
1680578 ATATTGAAAAGATACTATAACTCAAAAATTAAATATAAAAGTTATTATTTCAAATTATAACTTAA
326 ATATTGAAAAGACACCATAACTCAAAAATTAAATATAAAAGTTATTATTTCAAAGTATAACTCAA
** * *
1680643 AGATTATAATTTATGGAATGAATAATTATCTTTTCATAAGATGATTATTAAAACAATACTTTTAT
391 AGATTATAATTTATAAAATGAATAATTATATTTTCATAAGATGATTATTAAAACAATACCTTTAT
1680708 CCAAAAGTTATATTTGGCAAAATGAAAAGATA-TCTCTTAGACAAAATGGTACCTTAATGAAAGG
456 CCAAAAGTTATATTTGGCAAAATGAAAAGATACT-TCTTAGACAAAATGGTACCTTAATGAAAGG
* *
1680772 GTTTTGCTAGGTTAATGGGGTATATAGACTTAGGACAATTAAGGAAAGATCATTTGATCTCAAAC
1 GTTTTGCTAGGTTAATGCGGTATATAGACCTAGGACAATTAAGGAAAGATCATTTGATCTCAAAC
* * *
1680837 CTGTAAGGTCATCCTCATTCGTAAAGAAAGAGGGTAACCCCACTTTGACAAGATAGCTTATTATT
66 CTGCAAGGTCATCCTCACTCGTAAAGAAAGAGGGTAACCCCACTTTGACAAGAGAGCTTATTATT
* * *
1680902 GTCAATAGATTTTAACATAAACACATATATTGTTGGTGTATTTTCAAAATAAAAAATTATATCAC
131 GTCAATAGATTTTAACATAAACACATATATTATCGGTATATTTTCAAAATAAAAAATTATATCAC
* * ** * *
1680967 ATGATGAAAAGCTATCTTAGTTTAAAAGTTACGTCACATAAAGTGACATAGTATGTCTATTGGAT
196 ATGATAAAAAACTATCTTAACTCAAAAGTTACGTCACATAAAGTGACATAGTATGTCTATTGAAT
*
1681032 TAT-AG-ACAGGTTTGT-ATATGAATGGTTATGT-TTCTTGATAAAATAACATTTAAAAGTTATG
261 TATAAGTA-A-GTTT-TCATATGAATGGTTATGTCTT-TTGATAAAATAACATCTAAAAGTTATG
*
1681093 AAACATATTGAAAAGACACCATAACTCAAAAGTTAAATATAAAAGTTATTATTTCAAAGTATAAC
322 AAACATATTGAAAAGACACCATAACTCAAAAATTAAATATAAAAGTTATTATTTCAAAGTATAAC
* * * *
1681158 TCAAAGATTATAATTTATAAAATGAATAGTTGTATTTTCATAATATGATTATTGAAACAATACCT
387 TCAAAGATTATAATTTATAAAATGAATAATTATATTTTCATAAGATGATTATTAAAACAATACCT
* * * * * *
1681223 TTATTCAAAAGTTGTATTTGGTAAAATGAAAAGATACTTTTTAGATAAAATGGTGCCTTAATGAA
452 TTATCCAAAAGTTATATTTGGCAAAATGAAAAGATACTTCTTAGACAAAATGGTACCTTAATGAA
1681288 AGG
517 AGG
1681291 GTT
1 GTT
1681294 GTATCCTTAA
Statistics
Matches: 469, Mismatches: 48, Indels: 10
0.89 0.09 0.02
Matches are distributed among these distances:
517 1 0.00
518 5 0.01
519 461 0.98
520 2 0.00
ACGTcount: A:0.40, C:0.11, G:0.15, T:0.34
Consensus pattern (519 bp):
GTTTTGCTAGGTTAATGCGGTATATAGACCTAGGACAATTAAGGAAAGATCATTTGATCTCAAAC
CTGCAAGGTCATCCTCACTCGTAAAGAAAGAGGGTAACCCCACTTTGACAAGAGAGCTTATTATT
GTCAATAGATTTTAACATAAACACATATATTATCGGTATATTTTCAAAATAAAAAATTATATCAC
ATGATAAAAAACTATCTTAACTCAAAAGTTACGTCACATAAAGTGACATAGTATGTCTATTGAAT
TATAAGTAAGTTTTCATATGAATGGTTATGTCTTTTGATAAAATAACATCTAAAAGTTATGAAAC
ATATTGAAAAGACACCATAACTCAAAAATTAAATATAAAAGTTATTATTTCAAAGTATAACTCAA
AGATTATAATTTATAAAATGAATAATTATATTTTCATAAGATGATTATTAAAACAATACCTTTAT
CCAAAAGTTATATTTGGCAAAATGAAAAGATACTTCTTAGACAAAATGGTACCTTAATGAAAGG
Found at i:1689099 original size:2 final size:2
Alignment explanation
Indices: 1689094--1689119 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
1689084 GGGGGAGTCT
1689094 AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG
1689120 GGAGGAAAAG
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:0.50, T:0.00
Consensus pattern (2 bp):
AG
Found at i:1689634 original size:6 final size:6
Alignment explanation
Indices: 1689625--1689660 Score: 63
Period size: 6 Copynumber: 6.0 Consensus size: 6
1689615 TTCCTTTCTT
*
1689625 TTTTTT TTTTTG TTTTTG TTTTTG TTTTTG TTTTTG
1 TTTTTG TTTTTG TTTTTG TTTTTG TTTTTG TTTTTG
1689661 GTTTGGCAGT
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
6 29 1.00
ACGTcount: A:0.00, C:0.00, G:0.14, T:0.86
Consensus pattern (6 bp):
TTTTTG
Found at i:1692814 original size:20 final size:20
Alignment explanation
Indices: 1692789--1692845 Score: 105
Period size: 20 Copynumber: 2.9 Consensus size: 20
1692779 ATACCTAGTG
*
1692789 ATGTATCAATACATGTGGGA
1 ATGTATCGATACATGTGGGA
1692809 ATGTATCGATACATGTGGGA
1 ATGTATCGATACATGTGGGA
1692829 ATGTATCGATACATGTG
1 ATGTATCGATACATGTG
1692846 TATAGATTTT
Statistics
Matches: 36, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 36 1.00
ACGTcount: A:0.32, C:0.11, G:0.26, T:0.32
Consensus pattern (20 bp):
ATGTATCGATACATGTGGGA
Found at i:1693127 original size:20 final size:20
Alignment explanation
Indices: 1693102--1693139 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
1693092 CATTTTGTCA
1693102 AGAATGTATCGATACATTCG
1 AGAATGTATCGATACATTCG
*
1693122 AGAATGTATTGATACATT
1 AGAATGTATCGATACATT
1693140 TTCCCTTGTT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.37, C:0.11, G:0.18, T:0.34
Consensus pattern (20 bp):
AGAATGTATCGATACATTCG
Found at i:1698759 original size:16 final size:16
Alignment explanation
Indices: 1698738--1698770 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 16
1698728 CTCCAAATAA
*
1698738 CCTAATTTCTAAAATC
1 CCTAATTTCCAAAATC
1698754 CCTAATTTCCAAAATC
1 CCTAATTTCCAAAATC
1698770 C
1 C
1698771 TATCAAGTTC
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:0.30, G:0.00, T:0.33
Consensus pattern (16 bp):
CCTAATTTCCAAAATC
Found at i:1701376 original size:33 final size:33
Alignment explanation
Indices: 1701339--1701416 Score: 147
Period size: 33 Copynumber: 2.4 Consensus size: 33
1701329 TATGGGAATG
1701339 TATCAATACATTTGCATAGATTTCGTCTAAATC
1 TATCAATACATTTGCATAGATTTCGTCTAAATC
1701372 TATCAATACATTTGCATAGATTTCGTCTAAATC
1 TATCAATACATTTGCATAGATTTCGTCTAAATC
*
1701405 TATCAACACATT
1 TATCAATACATT
1701417 AAGCGATGCA
Statistics
Matches: 44, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
33 44 1.00
ACGTcount: A:0.35, C:0.19, G:0.08, T:0.38
Consensus pattern (33 bp):
TATCAATACATTTGCATAGATTTCGTCTAAATC
Found at i:1702047 original size:83 final size:83
Alignment explanation
Indices: 1701894--1702064 Score: 270
Period size: 83 Copynumber: 2.1 Consensus size: 83
1701884 TGATATTTTG
* * * *
1701894 ACCACAACTTTCTCTAAAGAAGTTCAAATGAGATGATTTTTAAACCAATGGAAAGATAAGAGGAA
1 ACCATAACTTTCTCTAAAGAAGTTCAAATGAGATGATTCTTAAACCAATAGAAAGATAAGAAGAA
* *
1701959 GGGCTACAACATTTGTTT
66 AGGCTACAACATGTGTTT
* *
1701977 ACCATAACTTTCTTTAAAGAAGTTCAAATGAGGTGATTCTTAAACCAATAGAAAGATAAGAAGAA
1 ACCATAACTTTCTCTAAAGAAGTTCAAATGAGATGATTCTTAAACCAATAGAAAGATAAGAAGAA
1702042 AGGCTACAACATGTGTTT
66 AGGCTACAACATGTGTTT
1702060 ACCAT
1 ACCAT
1702065 TTTGTCTAGT
Statistics
Matches: 80, Mismatches: 8, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
83 80 1.00
ACGTcount: A:0.41, C:0.15, G:0.17, T:0.27
Consensus pattern (83 bp):
ACCATAACTTTCTCTAAAGAAGTTCAAATGAGATGATTCTTAAACCAATAGAAAGATAAGAAGAA
AGGCTACAACATGTGTTT
Found at i:1711389 original size:2 final size:2
Alignment explanation
Indices: 1711384--1711412 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
1711374 TTACCTTTGA
1711384 AT 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 AT A
1711413 GCATAAGAGA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:1717497 original size:143 final size:142
Alignment explanation
Indices: 1717271--1717684 Score: 439
Period size: 143 Copynumber: 2.9 Consensus size: 142
1717261 GCCATTAAAA
*
1717271 AAAGTTTTATATTGTTAC-GCGC-CAAGCTTGTTAGATGTCGTTTACA--TCTTGTGACATGCCA
1 AAAGTTTTATATTGTTACTGC-CACAA-CTTGTTAGATGTCATTTACATTTCTTGTGACATGCCA
** * * * * * *
1717332 TTTCATCGATGTCTTACATTGTTATACGTCACGCTTGTTAAATGTCATTGACATCTTCTTGTTAC
64 TTTCATCGAACTATTATATTGTTACACGCCACACTTGTTAAATGTCATTGACATCTTCTTGTGAC
*
1717397 ACCCTATGTCGTT-
129 ACCCTATGTCATTG
*
1717410 AAAGTTTTATATTGTTACATGCCACAACTTGTTAAATGTCATTTACATGTTCTTGTGACATGCCA
1 AAAGTTTTATATTGTTAC-TGCCACAACTTGTTAGATGTCATTTACAT-TTCTTGTGACATGCCA
* * * * *
1717475 TTT-AGTTGAACTATTATATTGTTACACGCCATACTTGTTAGATGTCGTTGACATCTTTTTGTGA
64 TTTCA-TCGAACTATTATATTGTTACACGCCACACTTGTTAAATGTCATTGACATCTTCTTGTGA
**
1717539 CATGCTATGTCATTG
128 CACCCTATGTCATTG
* * * **
1717554 AAA-TATTATATTGTTACTGCCCACAACTGGTTGGATGTCATTTACATCTTCTTGTGACACACCA
1 AAAGTTTTATATTGTTACTG-CCACAACTTGTTAGATGTCATTTACAT-TTCTTGTGACATGCCA
* * * * * *
1717618 TTTCATCGAACTGTTATATTGTTACATGCCATATTTGTTAAATGTCGTTTACATCTAT-TTGTGA
64 TTTCATCGAACTATTATATTGTTACACGCCACACTTGTTAAATGTCATTGACATCT-TCTTGTGA
1717682 CAC
128 CAC
1717685 GCCATTTAGT
Statistics
Matches: 232, Mismatches: 32, Indels: 18
0.82 0.11 0.06
Matches are distributed among these distances:
139 18 0.08
140 19 0.08
141 5 0.02
142 3 0.01
143 182 0.78
144 5 0.02
ACGTcount: A:0.25, C:0.18, G:0.15, T:0.41
Consensus pattern (142 bp):
AAAGTTTTATATTGTTACTGCCACAACTTGTTAGATGTCATTTACATTTCTTGTGACATGCCATT
TCATCGAACTATTATATTGTTACACGCCACACTTGTTAAATGTCATTGACATCTTCTTGTGACAC
CCTATGTCATTG
Found at i:1717537 original size:71 final size:70
Alignment explanation
Indices: 1717244--1717709 Score: 323
Period size: 71 Copynumber: 6.6 Consensus size: 70
1717234 GATATTGTTA
* * * *** * * * *
1717244 ACATCTTTTTGTTACATGCCATTAAAAAAAGTTTTATATTGTTACGCGCCAAGCTTGTTAGATGT
1 ACATCTTCTTGTGACATGCCATTTATTGAAGTATTATATTGTTACACGCCAAACTTGTTAAATGT
*
1717309 CGTTT
66 CATTT
* * * * * * **
1717314 ACA---TCTTGTGACATGCCATTTCATCGATGTCTTACATTGTTATACGTCACGCTTGTTAAATG
1 ACATCTTCTTGTGACATGCCATTT-ATTGAAGTATTATATTGTTACACGCCAAACTTGTTAAATG
*
1717376 TCATTG
65 TCATTT
* * ** * * *
1717382 ACATCTTCTTGTTACA-CCCTATGTCGTTAAAGTTTTATATTGTTACATGCCACAACTTGTTAAA
1 ACATCTTCTTGTGACATGCC-AT-TTATTGAAGTATTATATTGTTACACGCCA-AACTTGTTAAA
1717446 TGTCATTT
63 TGTCATTT
* * * *
1717454 ACATGTTCTTGTGACATGCCATTTAGTTGAACTATTATATTGTTACACGCCATACTTGTTAGATG
1 ACATCTTCTTGTGACATGCCATTTA-TTGAAGTATTATATTGTTACACGCCAAACTTGTTAAATG
* *
1717519 TCGTTG
65 TCATTT
* * * * * * **
1717525 ACATCTTTTTGTGACATGCTATGTCATTGAAATATTATATTGTTAC-TGCCCACAACTGGTTGGA
1 ACATCTTCTTGTGACATGCCAT-TTATTGAAGTATTATATTGTTACACG-CCA-AACTTGTTAAA
1717589 TGTCATTT
63 TGTCATTT
** * * * * * *
1717597 ACATCTTCTTGTGACACACCATTTCATCGAACTGTTATATTGTTACATGCCATATTTGTTAAATG
1 ACATCTTCTTGTGACATGCCATTT-ATTGAAGTATTATATTGTTACACGCCAAACTTGTTAAATG
*
1717662 TCGTTT
65 TCATTT
* *
1717668 ACATCTAT-TTGTGACACGCCATTTAGTTGAAGTCTTATATTG
1 ACATCT-TCTTGTGACATGCCATTTA-TTGAAGTATTATATTG
1717710 AACATGCCAT
Statistics
Matches: 307, Mismatches: 73, Indels: 31
0.75 0.18 0.08
Matches are distributed among these distances:
67 15 0.05
68 36 0.12
70 7 0.02
71 134 0.44
72 111 0.36
73 4 0.01
ACGTcount: A:0.25, C:0.18, G:0.15, T:0.41
Consensus pattern (70 bp):
ACATCTTCTTGTGACATGCCATTTATTGAAGTATTATATTGTTACACGCCAAACTTGTTAAATGT
CATTT
Found at i:1717728 original size:71 final size:70
Alignment explanation
Indices: 1717365--1717719 Score: 313
Period size: 72 Copynumber: 5.0 Consensus size: 70
1717355 ATACGTCACG
* * ** * * *
1717365 CTTGTTAAATGTCATTGACATCTTCTTGTTACAC-CCTATGTCGTTAAAGTTTTATATTGTTACA
1 CTTGTTAAATGTCATTTACATCTTCTTGTGACACGCC-AT-TTATTGAACTATTATATTGTTACA
*
1717429 TGCCACAA
64 TGCCA-TA
* * *
1717437 CTTGTTAAATGTCATTTACATGTTCTTGTGACATGCCATTTAGTTGAACTATTATATTGTTACAC
1 CTTGTTAAATGTCATTTACATCTTCTTGTGACACGCCATTTA-TTGAACTATTATATTGTTACAT
1717502 GCCATA
65 GCCATA
* * * * * * * *
1717508 CTTGTTAGATGTCGTTGACATCTTTTTGTGACATGCTATGTCATTGAAATATTATATTGTTAC-T
1 CTTGTTAAATGTCATTTACATCTTCTTGTGACACGCCAT-TTATTGAACTATTATATTGTTACAT
*
1717572 GCCCACAA
65 G-CCA-TA
* ** * * *
1717580 CTGGTTGGATGTCATTTACATCTTCTTGTGACACACCATTTCATCGAACTGTTATATTGTTACAT
1 CTTGTTAAATGTCATTTACATCTTCTTGTGACACGCCATTT-ATTGAACTATTATATTGTTACAT
1717645 GCCATA
65 GCCATA
* * * * *
1717651 TTTGTTAAATGTCGTTTACATCTAT-TTGTGACACGCCATTTAGTTGAAGTCTTATATTG-AACA
1 CTTGTTAAATGTCATTTACATCT-TCTTGTGACACGCCATTTA-TTGAACTATTATATTGTTACA
1717714 TGCCAT
64 TGCCAT
1717720 GGATTGTTAG
Statistics
Matches: 230, Mismatches: 44, Indels: 20
0.78 0.15 0.07
Matches are distributed among these distances:
70 11 0.05
71 105 0.46
72 110 0.48
73 4 0.02
ACGTcount: A:0.26, C:0.18, G:0.15, T:0.41
Consensus pattern (70 bp):
CTTGTTAAATGTCATTTACATCTTCTTGTGACACGCCATTTATTGAACTATTATATTGTTACATG
CCATA
Found at i:1720917 original size:23 final size:23
Alignment explanation
Indices: 1720883--1721172 Score: 178
Period size: 23 Copynumber: 12.7 Consensus size: 23
1720873 GCTTGTTATT
1720883 TGTCACATATTCTCACTATGGCG
1 TGTCACATATTCTCACTATGGCG
* * *
1720906 TGTTACATATTCTC-TTCATGGTG
1 TGTCACATATTCTCACT-ATGGCG
* * * *
1720929 TGTCACATATTCCCTCTATGACA
1 TGTCACATATTCTCACTATGGCG
* *
1720952 TGTCACATATTCTCACCATGAC-
1 TGTCACATATTCTCACTATGGCG
**
1720974 TACCACATATTCTCAAC-ATGGCG
1 TGTCACATATTCTC-ACTATGGCG
* ** * *
1720997 TTTCACATATTCTGTCAATAGCG
1 TGTCACATATTCTCACTATGGCG
* * * *
1721020 TGTCACATATTCCCTCCATGGTG
1 TGTCACATATTCTCACTATGGCG
* **
1721043 TGTCACATATTCTTA-TCATAACG
1 TGTCACATATTCTCACT-ATGGCG
*
1721066 TGTCACATATTC-CATCTATGGCA
1 TGTCACATATTCTCA-CTATGGCG
* * * *
1721089 TGTTACATATTCTCACCATCGCC
1 TGTCACATATTCTCACTATGGCG
* * *
1721112 TGTCACTTATTCTCACCATGTCG
1 TGTCACATATTCTCACTATGGCG
* * *
1721135 TGTCACATATTC-CCCGCACGGCG
1 TGTCACATATTCTCAC-TATGGCG
*
1721158 TGTCACATAGTCTCA
1 TGTCACATATTCTCA
1721173 TCATGGCATG
Statistics
Matches: 204, Mismatches: 52, Indels: 21
0.74 0.19 0.08
Matches are distributed among these distances:
22 21 0.10
23 178 0.87
24 5 0.02
ACGTcount: A:0.23, C:0.28, G:0.13, T:0.35
Consensus pattern (23 bp):
TGTCACATATTCTCACTATGGCG
Found at i:1721047 original size:91 final size:91
Alignment explanation
Indices: 1720886--1721146 Score: 251
Period size: 91 Copynumber: 2.9 Consensus size: 91
1720876 TGTTATTTGT
* * * *
1720886 CACATATTCTCACTATGGCGTGTTACATATTCTCTTCATGGTGTGTCACATATTCCCTCTATGAC
1 CACATATTCTCACTATGGCGTGTTACATATTCTCGTCATAGCGTGTCACATATTCCCTCCATGAC
1720951 ATGTCACATATTCTCACCATGACTAC
66 ATGTCACATATTCTCACCATGACTAC
1720977 CACATATTCTCAAC-ATGGCGT-TTCACATATTCT-GTCAATAGCGTGTCACATATTCCCTCCAT
1 CACATATTCTC-ACTATGGCGTGTT-ACATATTCTCGTC-ATAGCGTGTCACATATTCCCTCCAT
*** * * * **
1721039 GGTGTGTCACATATTCTTATCATAACGTGT
63 GACATGTCACATATTCTCACCATGAC-TAC
* ** * * * * * *
1721069 CACATATTC-CATCTATGGCATGTTACATATTCTCACCATCGCCTGTCACTTATTCTCACCATGT
1 CACATATTCTCA-CTATGGCGTGTTACATATTCTCGTCATAGCGTGTCACATATTCCCTCCATGA
*
1721133 CGTGTCACATATTC
65 CATGTCACATATTC
1721147 CCCGCACGGC
Statistics
Matches: 140, Mismatches: 22, Indels: 15
0.79 0.12 0.08
Matches are distributed among these distances:
90 5 0.04
91 71 0.51
92 61 0.44
93 3 0.02
ACGTcount: A:0.24, C:0.28, G:0.12, T:0.36
Consensus pattern (91 bp):
CACATATTCTCACTATGGCGTGTTACATATTCTCGTCATAGCGTGTCACATATTCCCTCCATGAC
ATGTCACATATTCTCACCATGACTAC
Found at i:1721097 original size:69 final size:68
Alignment explanation
Indices: 1720883--1721147 Score: 233
Period size: 69 Copynumber: 3.9 Consensus size: 68
1720873 GCTTGTTATT
* * * ** ** *
1720883 TGTCACATATTCTCACTATGGCGTGTTACATATTCTCTTCATGGTGTGTCACATATTCCCTCTAT
1 TGTCACATATTCTCACCATGAC-TGTCACATATTCTCAACATGACGTGTCACATATTCCATCTAT
*
1720948 GACA
65 GGCA
** * * ** * *
1720952 TGTCACATATTCTCACCATGACTACCACATATTCTCAACATGGCGTTTCACATATTCTGTCAATA
1 TGTCACATATTCTCACCATGACTGTCACATATTCTCAACATGACGTGTCACATATTCCATCTATG
*
1721017 GCG
66 GCA
* * ** * * *
1721020 TGTCACATATTCCCTCCATGGTGTGTCACATATTCTTATCATAACGTGTCACATATTCCATCTAT
1 TGTCACATATTCTCACCAT-GACTGTCACATATTCTCAACATGACGTGTCACATATTCCATCTAT
1721085 GGCA
65 GGCA
* * * * *
1721089 TGTTACATATTCTCACCATCGCCTGTCACTTATTCTCACCATGTCGTGTCACATATTCC
1 TGTCACATATTCTCACCAT-GACTGTCACATATTCTCAACATGACGTGTCACATATTCC
1721148 CCGCACGGCG
Statistics
Matches: 153, Mismatches: 42, Indels: 2
0.78 0.21 0.01
Matches are distributed among these distances:
68 50 0.33
69 103 0.67
ACGTcount: A:0.24, C:0.28, G:0.12, T:0.36
Consensus pattern (68 bp):
TGTCACATATTCTCACCATGACTGTCACATATTCTCAACATGACGTGTCACATATTCCATCTATG
GCA
Found at i:1721166 original size:69 final size:68
Alignment explanation
Indices: 1720883--1721179 Score: 229
Period size: 69 Copynumber: 4.3 Consensus size: 68
1720873 GCTTGTTATT
* * * * *
1720883 TGTCACATATTCTCACTATGGCGTGTTACATATTCTCTTCATGGT-GTGTCACATATTCCCTCTA
1 TGTCACATATTCTCACCATGGCCTGTCACATATTCTCATCAT-GTCGTGTCACATATTCCC-CCA
*
1720947 TGACA
64 TGGCA
* ** * * * ** *
1720952 TGTCACATATTCTCACCAT-GACTACCACATATTCTCAACATGGCGTTTCACATATTCTGTCAAT
1 TGTCACATATTCTCACCATGGCCTGTCACATATTCTCATCATGTCGTGTCACATATTC-CCCCAT
* *
1721016 AGCG
65 GGCA
* * ** * ** * *
1721020 TGTCACATATTCCCTCCATGGTGTGTCACATATTCTTATCATAACGTGTCACATATTCCATCTAT
1 TGTCACATATTCTCACCATGGCCTGTCACATATTCTCATCATGTCGTGTCACATATTCC-CCCAT
1721085 GGCA
65 GGCA
* * * * *
1721089 TGTTACATATTCTCACCATCGCCTGTCACTTATTCTCACCATGTCGTGTCACATATTCCCCGCAC
1 TGTCACATATTCTCACCATGGCCTGTCACATATTCTCATCATGTCGTGTCACATATTCCCC-CAT
*
1721154 GGCG
65 GGCA
* *
1721158 TGTCACATAGTCTCATCATGGC
1 TGTCACATATTCTCACCATGGC
1721180 ATGTTACGTG
Statistics
Matches: 173, Mismatches: 50, Indels: 10
0.74 0.21 0.04
Matches are distributed among these distances:
67 1 0.01
68 49 0.28
69 123 0.71
ACGTcount: A:0.23, C:0.28, G:0.14, T:0.35
Consensus pattern (68 bp):
TGTCACATATTCTCACCATGGCCTGTCACATATTCTCATCATGTCGTGTCACATATTCCCCCATG
GCA
Found at i:1727253 original size:2 final size:2
Alignment explanation
Indices: 1727246--1727282 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
1727236 TGGTTAACAA
1727246 AT AT AT AT AT 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 AT AT AT AT AT A
1727283 AATGTATGTA
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:1733725 original size:13 final size:13
Alignment explanation
Indices: 1733707--1733735 Score: 51
Period size: 12 Copynumber: 2.3 Consensus size: 13
1733697 TTTTTAATTC
1733707 AATTTTTTTT-AA
1 AATTTTTTTTGAA
1733719 AATTTTTTTTGAA
1 AATTTTTTTTGAA
1733732 AATT
1 AATT
1733736 GGGATTTTTG
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 10 0.62
13 6 0.38
ACGTcount: A:0.34, C:0.00, G:0.03, T:0.62
Consensus pattern (13 bp):
AATTTTTTTTGAA
Found at i:1736811 original size:31 final size:30
Alignment explanation
Indices: 1736776--1736876 Score: 116
Period size: 29 Copynumber: 3.3 Consensus size: 30
1736766 TCACAAAGGC
1736776 TTATTTGATTCAAAATAAAATATATAAAAAT
1 TTATTTGATTCAAAATAAAA-ATATAAAAAT
*
1736807 TTATTTGACTCAAAATAAAAATATAAAAAT
1 TTATTTGATTCAAAATAAAAATATAAAAAT
* ** *
1736837 TTGA-TTGAAT-ATTATAAAAATATAAAGAT
1 TT-ATTTGATTCAAAATAAAAATATAAAAAT
1736866 TTATTTAGATT
1 TTATTT-GATT
1736877 TTTTTGAATA
Statistics
Matches: 61, Mismatches: 6, Indels: 7
0.82 0.08 0.09
Matches are distributed among these distances:
28 1 0.02
29 20 0.33
30 20 0.33
31 20 0.33
ACGTcount: A:0.51, C:0.03, G:0.06, T:0.40
Consensus pattern (30 bp):
TTATTTGATTCAAAATAAAAATATAAAAAT
Found at i:1746741 original size:2 final size:2
Alignment explanation
Indices: 1746736--1746761 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
1746726 TTTTTCTATT
1746736 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
1746762 CACACCTATA
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):
TA
Found at i:1747570 original size:13 final size:13
Alignment explanation
Indices: 1747552--1747576 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1747542 AAACCCCTTT
1747552 TTCACTTTCCCTC
1 TTCACTTTCCCTC
1747565 TTCACTTTCCCT
1 TTCACTTTCCCT
1747577 TCCCACTTTC
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:0.44, G:0.00, T:0.48
Consensus pattern (13 bp):
TTCACTTTCCCTC
Found at i:1748796 original size:31 final size:29
Alignment explanation
Indices: 1748711--1748796 Score: 73
Period size: 31 Copynumber: 2.8 Consensus size: 29
1748701 TAAACTCTAT
*
1748711 TATGCCAACATAACTGAACTTATACATTTTA
1 TATGCCAATATAACTGAACTTA-A-ATTTTA
* * *** *
1748742 TATGCCAATATGATTGGGTTTAAATTCTTT
1 TATGCCAATATAACTGAACTTAAATT-TTA
1748772 TCATGCCAATATAACTGAACTTAAA
1 T-ATGCCAATATAACTGAACTTAAA
1748797 CATCTTAGAT
Statistics
Matches: 41, Mismatches: 12, Indels: 4
0.72 0.21 0.07
Matches are distributed among these distances:
29 3 0.07
30 4 0.10
31 34 0.83
ACGTcount: A:0.36, C:0.16, G:0.10, T:0.37
Consensus pattern (29 bp):
TATGCCAATATAACTGAACTTAAATTTTA
Found at i:1750221 original size:22 final size:23
Alignment explanation
Indices: 1750187--1750231 Score: 56
Period size: 22 Copynumber: 2.0 Consensus size: 23
1750177 TGCAATGCCT
*
1750187 AAGTCACACAATG-CTTATCAAC
1 AAGTCACACAATGCCCTATCAAC
**
1750209 AAGTCACGTAATGCCCTATCAAC
1 AAGTCACACAATGCCCTATCAAC
1750232 TTGCCACGCA
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
22 11 0.58
23 8 0.42
ACGTcount: A:0.38, C:0.29, G:0.11, T:0.22
Consensus pattern (23 bp):
AAGTCACACAATGCCCTATCAAC
Found at i:1750565 original size:22 final size:23
Alignment explanation
Indices: 1750540--1750601 Score: 72
Period size: 23 Copynumber: 2.7 Consensus size: 23
1750530 AGTATATAAA
1750540 AACTAGTCAAGCAATGCC-TACC
1 AACTAGTCAAGCAATGCCTTACC
* * *
1750562 AACTAGTCACGCAATACCTTATC
1 AACTAGTCAAGCAATGCCTTACC
* *
1750585 AACTTGTCATGCAATGC
1 AACTAGTCAAGCAATGC
1750602 TTATAAAATT
Statistics
Matches: 33, Mismatches: 6, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
22 16 0.48
23 17 0.52
ACGTcount: A:0.34, C:0.29, G:0.13, T:0.24
Consensus pattern (23 bp):
AACTAGTCAAGCAATGCCTTACC
Found at i:1752040 original size:36 final size:37
Alignment explanation
Indices: 1752000--1752098 Score: 114
Period size: 36 Copynumber: 2.8 Consensus size: 37
1751990 TTGAGCATGC
*
1752000 TATAGGGCCTTAAG-AAGAGTTGGGCTACGAGCAAGA
1 TATAGGGCCTTAAGTAAGAGTTGAGCTACGAGCAAGA
* **
1752036 TATAGGGCC-TCAGTCGGAGTTGAGCTACGAGCAAGA
1 TATAGGGCCTTAAGTAAGAGTTGAGCTACGAGCAAGA
* **
1752072 TATAGGGCC-TCAGTCGGAGTTGAGCTA
1 TATAGGGCCTTAAGTAAGAGTTGAGCTA
1752099 TAAAGAGGAG
Statistics
Matches: 58, Mismatches: 4, Indels: 2
0.91 0.06 0.03
Matches are distributed among these distances:
35 3 0.05
36 55 0.95
ACGTcount: A:0.28, C:0.17, G:0.33, T:0.21
Consensus pattern (37 bp):
TATAGGGCCTTAAGTAAGAGTTGAGCTACGAGCAAGA
Found at i:1754023 original size:215 final size:214
Alignment explanation
Indices: 1753640--1754060 Score: 589
Period size: 215 Copynumber: 2.0 Consensus size: 214
1753630 GCAAATGAAG
* * * *
1753640 TGTGAGCCATTAACTTGCAGGGACTAAAGATGATACATCAAGATGGAGCAAAGCTGCTGTAAAGA
1 TGTGAGCCATTAACTTGCAGGGACTAAAGATAATACATCAAGATAGAGCAAAACTACTGTAAAGA
* *
1753705 TAAGGATTGAAGCAATGATGGTAAAGCTAGAGAAAGATAAAAATGAGAGATGACGGAGAACGAAG
66 TAAGGATTGAAGCAATGATGGTAAAGCTAAAGAAAGATAAAAATGAGAGATGACGGAGAACAAAG
*
1753770 GAAATAAAGAGGTAGAAGTGAATAAGGAACGACAATGAAAAAGAGAGATAGTAGAAGGAGAGGAT
131 GAAATAAAGAGGTAGAAGTGAAGAAGGAACGACAATG-AAAAGAGAGATAGTAGAAGGAGAGGAT
1753835 CAA-GAATGCTAATAAGGAGC
195 -AAGGAATGCTAATAAGGAGC
* * * * *
1753855 TGTGAGCC-TTCAGCTTGCAGGGACTAGAGATAATGCGTCAAGATAGAGCAAAACTACTGTAAGG
1 TGTGAGCCATT-AACTTGCAGGGACTAAAGATAATACATCAAGATAGAGCAAAACTACTGTAAAG
* * * *
1753919 GTAAGGATTGAAGCAATTATGGTAAAG-TCAAAGAAAGGTAAAAATGAGAGATGATGGAGAACAA
65 ATAAGGATTGAAGCAATGATGGTAAAGCT-AAAGAAAGATAAAAATGAGAGATGACGGAGAACAA
* * * *
1753983 AGGAAATAAAGAGGTAGGAGTGAAGGAGGAAC-AGCAATGAAAAGGGAGATTGTAGAAGGAGAGG
129 AGGAAATAAAGAGGTAGAAGTGAAGAAGGAACGA-CAATGAAAAGAGAGATAGTAGAAGGAGAGG
1754047 ATAAGGAATGCTAA
193 ATAAGGAATGCTAA
1754061 CAAGAAATCT
Statistics
Matches: 182, Mismatches: 20, Indels: 9
0.86 0.09 0.04
Matches are distributed among these distances:
213 2 0.01
214 38 0.21
215 142 0.78
ACGTcount: A:0.44, C:0.09, G:0.30, T:0.17
Consensus pattern (214 bp):
TGTGAGCCATTAACTTGCAGGGACTAAAGATAATACATCAAGATAGAGCAAAACTACTGTAAAGA
TAAGGATTGAAGCAATGATGGTAAAGCTAAAGAAAGATAAAAATGAGAGATGACGGAGAACAAAG
GAAATAAAGAGGTAGAAGTGAAGAAGGAACGACAATGAAAAGAGAGATAGTAGAAGGAGAGGATA
AGGAATGCTAATAAGGAGC
Found at i:1756695 original size:2 final size:2
Alignment explanation
Indices: 1756688--1756728 Score: 82
Period size: 2 Copynumber: 20.5 Consensus size: 2
1756678 TTTGACAGAG
1756688 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1756729 TAATTGATGT
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 39 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:1764639 original size:47 final size:47
Alignment explanation
Indices: 1764521--1764732 Score: 302
Period size: 47 Copynumber: 4.6 Consensus size: 47
1764511 TTTTGCATAC
* * * * *
1764521 AATTTTACTTATCAAATAAGTTAAATAATTGCATCATGCATTTTGTA
1 AATTTTACCTAACAAATAAGTAAAATAATTACATCATGCATTTTATA
* * **
1764568 AA-TTTACCTAACAAATAGGAAAAATAATTACATCATGCATTTTGCA
1 AATTTTACCTAACAAATAAGTAAAATAATTACATCATGCATTTTATA
1764614 AATTTTACCTAACAAATAAGTAAAATAATTACATCATGCATTTTATA
1 AATTTTACCTAACAAATAAGTAAAATAATTACATCATGCATTTTATA
* *
1764661 AATTTTACCTAAAAAATAAGTAATATAATTACATCATG-ATTTTATA
1 AATTTTACCTAACAAATAAGTAAAATAATTACATCATGCATTTTATA
*
1764707 AATTTTACCTAACAAATAAGCAAAAT
1 AATTTTACCTAACAAATAAGTAAAAT
1764733 CATTCAAAAT
Statistics
Matches: 148, Mismatches: 16, Indels: 3
0.89 0.10 0.02
Matches are distributed among these distances:
46 70 0.47
47 78 0.53
ACGTcount: A:0.46, C:0.12, G:0.06, T:0.36
Consensus pattern (47 bp):
AATTTTACCTAACAAATAAGTAAAATAATTACATCATGCATTTTATA
Found at i:1764703 original size:93 final size:93
Alignment explanation
Indices: 1764521--1764732 Score: 300
Period size: 93 Copynumber: 2.3 Consensus size: 93
1764511 TTTTGCATAC
* * * * * * *
1764521 AATTTTACTTATCAAATAAGTTAAATAATTGCATCATGCATTTTGTAAATTTACCTAACAAATAG
1 AATTTTACCTAACAAATAAGTAAAATAATTACATCATGCATTTTATAAATTTACCTAAAAAATAA
*
1764586 GAAAAATAATTACATCATGCATTTTGCA
66 GAAAAATAATTACATCATGCATTTTACA
1764614 AATTTTACCTAACAAATAAGTAAAATAATTACATCATGCATTTTATAAATTTTACCTAAAAAATA
1 AATTTTACCTAACAAATAAGTAAAATAATTACATCATGCATTTTATAAA-TTTACCTAAAAAATA
* * *
1764679 AGTAATATAATTACATCATG-ATTTTATA
65 AGAAAAATAATTACATCATGCATTTTACA
*
1764707 AATTTTACCTAACAAATAAGCAAAAT
1 AATTTTACCTAACAAATAAGTAAAAT
1764733 CATTCAAAAT
Statistics
Matches: 106, Mismatches: 12, Indels: 2
0.88 0.10 0.02
Matches are distributed among these distances:
93 75 0.71
94 31 0.29
ACGTcount: A:0.46, C:0.12, G:0.06, T:0.36
Consensus pattern (93 bp):
AATTTTACCTAACAAATAAGTAAAATAATTACATCATGCATTTTATAAATTTACCTAAAAAATAA
GAAAAATAATTACATCATGCATTTTACA
Found at i:1767574 original size:20 final size:18
Alignment explanation
Indices: 1767541--1767577 Score: 56
Period size: 20 Copynumber: 1.9 Consensus size: 18
1767531 TGAGATCATA
1767541 AAAATTTATTAATTAATC
1 AAAATTTATTAATTAATC
1767559 AAAATATTATTTAATTAAT
1 AAAAT-TTA-TTAATTAAT
1767578 AAATTAATAA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 5 0.29
19 3 0.18
20 9 0.53
ACGTcount: A:0.51, C:0.03, G:0.00, T:0.46
Consensus pattern (18 bp):
AAAATTTATTAATTAATC
Found at i:1767590 original size:20 final size:20
Alignment explanation
Indices: 1767549--1767596 Score: 55
Period size: 20 Copynumber: 2.5 Consensus size: 20
1767539 TAAAAATTTA
*
1767549 TTAATTAATCAAAATATTAT
1 TTAATTAATCAAAATATAAT
*
1767569 TTAATTAAT-AAATTAATAAT
1 TTAATTAATCAAAAT-ATAAT
1767589 TT-ATTAAT
1 TTAATTAAT
1767597 TTATACATTA
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
19 10 0.40
20 15 0.60
ACGTcount: A:0.50, C:0.02, G:0.00, T:0.48
Consensus pattern (20 bp):
TTAATTAATCAAAATATAAT
Found at i:1767612 original size:16 final size:15
Alignment explanation
Indices: 1767570--1767612 Score: 50
Period size: 15 Copynumber: 2.8 Consensus size: 15
1767560 AAATATTATT
*
1767570 TAATTAATAAATTAA
1 TAATTAATTAATTAA
* *
1767585 TAATTTATTAATTTA
1 TAATTAATTAATTAA
1767600 TACATTAATTAAT
1 TA-ATTAATTAAT
1767613 AAAAAAATTA
Statistics
Matches: 23, Mismatches: 4, Indels: 1
0.82 0.14 0.04
Matches are distributed among these distances:
15 14 0.61
16 9 0.39
ACGTcount: A:0.49, C:0.02, G:0.00, T:0.49
Consensus pattern (15 bp):
TAATTAATTAATTAA
Found at i:1768986 original size:15 final size:15
Alignment explanation
Indices: 1768966--1768995 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
1768956 TAATCAAGAT
1768966 TATTAATTTATTGAG
1 TATTAATTTATTGAG
1768981 TATTAATTTATTGAG
1 TATTAATTTATTGAG
1768996 ATGTTACTAT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.33, C:0.00, G:0.13, T:0.53
Consensus pattern (15 bp):
TATTAATTTATTGAG
Found at i:1778040 original size:144 final size:144
Alignment explanation
Indices: 1777873--1778148 Score: 482
Period size: 144 Copynumber: 1.9 Consensus size: 144
1777863 GTGGAACGAG
* *
1777873 AGTGAGTTTGATAGTATTTTTTTAAGATTATACAATGAATGAGAGAGAAAATATATAAAAAAA-G
1 AGTGAGTTTGAGAGTATTTTTTTAAGATTACACAATGAATGAGAGAGAAAATATATAAAAAAAGG
* *
1777937 TTTTGAATTTGTTTGTGAATAGAGATTATATATTTTTTTAATTTTTTAATAATGAAAGCTCTGTT
66 TTTTGAATTTGTTTGTAAATAGAGATTATAT-TTTTTTTAATTTTTTAATAATAAAAGCTCTGTT
1778002 TCAAGGTGGAGTGAC
130 TCAAGGTGGAGTGAC
*
1778017 AGTGAGTTTGAGAGTATTTTTTTAAGATTACACAATGAATGAGAGAGATAATATATAAAAAAAGG
1 AGTGAGTTTGAGAGTATTTTTTTAAGATTACACAATGAATGAGAGAGAAAATATATAAAAAAAGG
*
1778082 TTTTGAATTTGTTTGTAAATAGAGATTATATTTTTTTTAATTTTTTAATAATAAAAGGTCTGTTT
66 TTTTGAATTTGTTTGTAAATAGAGATTATATTTTTTTTAATTTTTTAATAATAAAAGCTCTGTTT
1778147 CA
131 CA
1778149 TTTCGTAGAC
Statistics
Matches: 125, Mismatches: 6, Indels: 2
0.94 0.05 0.02
Matches are distributed among these distances:
144 94 0.75
145 31 0.25
ACGTcount: A:0.37, C:0.03, G:0.18, T:0.42
Consensus pattern (144 bp):
AGTGAGTTTGAGAGTATTTTTTTAAGATTACACAATGAATGAGAGAGAAAATATATAAAAAAAGG
TTTTGAATTTGTTTGTAAATAGAGATTATATTTTTTTTAATTTTTTAATAATAAAAGCTCTGTTT
CAAGGTGGAGTGAC
Found at i:1799193 original size:29 final size:29
Alignment explanation
Indices: 1799145--1799225 Score: 101
Period size: 29 Copynumber: 2.8 Consensus size: 29
1799135 TTAGAGGTAA
* * *
1799145 AAGAGAA-AAGGTATACGTGAACAAGCAT
1 AAGAGAAGAAGTTGTACGTGAACAAGCAC
* *
1799173 AAGAGAAGAAGTTGTACGTGAACAGGTAC
1 AAGAGAAGAAGTTGTACGTGAACAAGCAC
*
1799202 AAGAGAAGAAGTTGTAAGTGAACA
1 AAGAGAAGAAGTTGTACGTGAACA
1799226 GGTACATGAA
Statistics
Matches: 46, Mismatches: 6, Indels: 1
0.87 0.11 0.02
Matches are distributed among these distances:
28 7 0.15
29 39 0.85
ACGTcount: A:0.47, C:0.09, G:0.28, T:0.16
Consensus pattern (29 bp):
AAGAGAAGAAGTTGTACGTGAACAAGCAC
Found at i:1799226 original size:29 final size:29
Alignment explanation
Indices: 1799173--1799231 Score: 109
Period size: 29 Copynumber: 2.0 Consensus size: 29
1799163 GAACAAGCAT
*
1799173 AAGAGAAGAAGTTGTACGTGAACAGGTAC
1 AAGAGAAGAAGTTGTAAGTGAACAGGTAC
1799202 AAGAGAAGAAGTTGTAAGTGAACAGGTAC
1 AAGAGAAGAAGTTGTAAGTGAACAGGTAC
1799231 A
1 A
1799232 TGAAAACAAG
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
29 29 1.00
ACGTcount: A:0.44, C:0.08, G:0.31, T:0.17
Consensus pattern (29 bp):
AAGAGAAGAAGTTGTAAGTGAACAGGTAC
Found at i:1799743 original size:15 final size:15
Alignment explanation
Indices: 1799723--1799759 Score: 56
Period size: 15 Copynumber: 2.5 Consensus size: 15
1799713 GCCTGTAGAG
1799723 AGTAACACCTTAAGT
1 AGTAACACCTTAAGT
*
1799738 AGTAACGCCTTAAGT
1 AGTAACACCTTAAGT
*
1799753 AATAACA
1 AGTAACA
1799760 TGTTACTATT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
15 19 1.00
ACGTcount: A:0.43, C:0.19, G:0.14, T:0.24
Consensus pattern (15 bp):
AGTAACACCTTAAGT
Found at i:1805062 original size:29 final size:29
Alignment explanation
Indices: 1805019--1805133 Score: 131
Period size: 29 Copynumber: 4.0 Consensus size: 29
1805009 ATATATCAAA
* * * * *
1805019 AGGTACAAAAAAAGAAACCGTACATGAAT
1 AGGTACAAGAGAAGAAGCTGTACGTGAAT
* *
1805048 AGGTACAAGAGAAGAAGCTGTACGTAAAC
1 AGGTACAAGAGAAGAAGCTGTACGTGAAT
* *
1805077 AGATATAAGAGAAGAAGCTGTACGTGAAT
1 AGGTACAAGAGAAGAAGCTGTACGTGAAT
* *
1805106 AGGTACAAGAGAAGAAGGTGTATGTGAA
1 AGGTACAAGAGAAGAAGCTGTACGTGAA
1805134 CAAGTAGACA
Statistics
Matches: 71, Mismatches: 15, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
29 71 1.00
ACGTcount: A:0.47, C:0.10, G:0.27, T:0.17
Consensus pattern (29 bp):
AGGTACAAGAGAAGAAGCTGTACGTGAAT
Found at i:1805532 original size:13 final size:13
Alignment explanation
Indices: 1805514--1805541 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
1805504 TCTATAGTGA
1805514 GCTACCCTTTTGC
1 GCTACCCTTTTGC
1805527 GCTACCCTTTTGC
1 GCTACCCTTTTGC
1805540 GC
1 GC
1805542 AAGCAGTATG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.07, C:0.39, G:0.18, T:0.36
Consensus pattern (13 bp):
GCTACCCTTTTGC
Found at i:1807374 original size:21 final size:21
Alignment explanation
Indices: 1807323--1807374 Score: 52
Period size: 21 Copynumber: 2.5 Consensus size: 21
1807313 CTTTTATGAT
* *
1807323 ATTAAAAAAAAGTAAAATAAA
1 ATTAAGAATAAGTAAAATAAA
* *
1807344 ATTAATAATAAGTATAA-AAA
1 ATTAAGAATAAGTAAAATAAA
1807364 ATATAAGAATA
1 AT-TAAGAATA
1807375 TTAAATATTG
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
20 5 0.19
21 21 0.81
ACGTcount: A:0.69, C:0.00, G:0.06, T:0.25
Consensus pattern (21 bp):
ATTAAGAATAAGTAAAATAAA
Found at i:1808689 original size:16 final size:15
Alignment explanation
Indices: 1808663--1808693 Score: 53
Period size: 16 Copynumber: 2.0 Consensus size: 15
1808653 TTATAATTTT
1808663 TAATTTAAAAATAAA
1 TAATTTAAAAATAAA
1808678 TAATTATAAAAATAAA
1 TAATT-TAAAAATAAA
1808694 AATAATAATT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 5 0.33
16 10 0.67
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (15 bp):
TAATTTAAAAATAAA
Found at i:1808700 original size:21 final size:22
Alignment explanation
Indices: 1808668--1808710 Score: 70
Period size: 21 Copynumber: 2.0 Consensus size: 22
1808658 ATTTTTAATT
1808668 TAAAAATAAATAATTATAAAAA
1 TAAAAATAAATAATTATAAAAA
*
1808690 TAAAAAT-AATAATTATTAAAA
1 TAAAAATAAATAATTATAAAAA
1808711 GTTATTATTG
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
21 13 0.65
22 7 0.35
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (22 bp):
TAAAAATAAATAATTATAAAAA
Found at i:1808711 original size:251 final size:251
Alignment explanation
Indices: 1807858--1809291 Score: 1266
Period size: 251 Copynumber: 5.7 Consensus size: 251
1807848 ATTTTTGTAA
* * * * *
1807858 AAAATAAATATTTAAATTTATATTCTTGAGTTAAAAGTAGTTAA-ACGATTTACAAAATTTAATT
1 AAAATAAACATTTAAATTTATATTTTTGAGTTAAAAGTATTTAATA--ATTTATAAATTTTAATT
* * * * *
1807922 TAAAAATAAATAATAATAAGAATAAAAATAATTATTATTAAAAGTTGTTATTGAAAAA-CCTTGA
64 TAAAAATAAATAATAATAAAAATAAAAATAATTATTATTAAAAGTTATCATT-AAAAAGCTTTAA
* * * * * * *
1807986 CTTAAAGTTATAAGAATTGACATAGAAACTTATAAAAGTGGAACAAGTACT-TTTAAAATCTTAA
128 CGTAAAATTATAAGAATTGACGTAAAAACTTATAAATGTAGAACAAGTA-TATTTAAAATTTTAA
* * * ** * * * *
1808050 CCTAAATGTGCGAAAGTTAACATAATAAGTCAATTAAAACACAAAAATCTAATTTTAATG
192 CATAAATGTGTGAGAGTTAATGTAACAAGTCAATTAAATCACAAAATTATAATTTTAATG
* * * *
1808110 AAAAACAAACA-TTAAATTTATATTTTTGAGCTAAAACTATTTAACAATTTATAAATTTTAATTT
1 -AAAATAAACATTTAAATTTATATTTTTGAGTTAAAAGTATTTAATAATTTATAAATTTTAATTT
* * * *
1808174 AAAAATAAATAATAAT-AAAAT-----TAATTATTTTTAAAAATTACCATTGAAAAGCTTTAACG
65 AAAAATAAATAATAATAAAAATAAAAATAATTATTATTAAAAGTTATCATTAAAAAGCTTTAACG
* * * * * * *
1808233 TAAAGTTATACGAATTGATGTAAAAA-TTCATAAATGGAGAACGAGTATATTTAAAATTCTAACG
130 TAAAATTATAAGAATTGACGTAAAAACTT-ATAAATGTAGAACAAGTATATTTAAAATTTTAACA
* * * ** * * * *
1808297 TAAATGTGTGAGAGTTAATATAA-AAATGAATTACCTTA-ATAACTTTTAATTTTAATA
194 TAAATGTGTGAGAGTTAATGTAACAAGTCAATTAAATCACA-AAATTATAATTTTAATG
* ** * * ** * * * *
1808354 AAAACAAATGTTTGAATTTATATTCTCAAGGTAAAAGTATTTAATAATATAAAAATTTTAATTTT
1 AAAATAAACATTTAAATTTATATTTTTGAGTTAAAAGTATTTAATAATTTATAAATTTTAATTTA
* * * * *
1808419 AAAATAAAAAATAATAAAGATAAAAATAATTA-TAGTTAAAAGTTACCATTAAAAAGGTTTAATG
66 AAAATAAATAATAATAAAAATAAAAATAATTATTA-TTAAAAGTTATCATTAAAAAGCTTTAACG
* * * *
1808483 GAAAACTATAAGAATTGACGTAAAAACTTATAAATGTAGAATAAATATATTTAAAATTTTAACAT
130 TAAAATTATAAGAATTGACGTAAAAACTTATAAATGTAGAACAAGTATATTTAAAATTTTAACAT
* * * * *
1808548 AAGTGTGTGAGAGGTAATGTAATAAATTAATTAAATCACAAAATTATAATTTTAATG
195 AAATGTGTGAGAGTTAATGTAACAAGTCAATTAAATCACAAAATTATAATTTTAATG
* * *
1808605 AAAAGAAACATTTAAATTTATATTTTTG-GACTAAAAGTATTTAATAATTTATAATTTTTAATTT
1 AAAATAAACATTTAAATTTATATTTTTGAG-TTAAAAGTATTTAATAATTTATAAATTTTAATTT
* * * * *
1808669 AAAAATAAATAATTATAAAAATAAAAATAATAATTATTAAAAGTTATTATTGAAAAAAC-TTGAC
65 AAAAATAAATAATAATAAAAATAAAAATAATTATTATTAAAAGTTATCATT-AAAAAGCTTTAAC
** * * * **
1808733 GTAAAATTATAAGAATTGGGGTAAAAACTCATAAAGGT-GAAAGAAACATATTTAAAATTTTAAC
129 GTAAAATTATAAGAATTGACGTAAAAACTTATAAATGTAG-AACAAGTATATTTAAAATTTTAAC
* * * * * * *
1808797 ATAAATGTGTGAGAGGTAACGTGACAGGTCAATTAAGTCACAAAAATATAATTTTAGTG
193 ATAAATGTGTGAGAGTTAATGTAACAAGTCAATTAAATCACAAAATTATAATTTTAATG
1808856 AAAAATAAACATTTAAATTTATATTTTT-AGATTAAAAGTATTTAATTAATGATTTATAAATTTT
1 -AAAATAAACATTTAAATTTATATTTTTGAG-TTAAAAGTATTTAA-T-A--ATTTATAAATTTT
* * * *
1808920 AATTTAAAAAT-AATAATAATAAAGATAAAAATAATTATTGTT-AAAGTTGTCATTAAAAAGTTT
60 AATTTAAAAATAAATAATAATAAAAATAAAAATAATTATTATTAAAAGTTATCATTAAAAAGCTT
* * * * * *
1808983 TAACATAAAAATATAAAAATTGACGTAAAAACTCGTAAAAATG-A-AATAAGTATATTTAAAATC
125 TAACGTAAAATTATAAGAATTGACGTAAAAACT--TATAAATGTAGAACAAGTATATTTAAAATT
* * * * * * * * * *
1809046 TGAACGTAAATATATGAGAATTAATGTAACAAGTCAAGTAAGTCATAAAATTTTAATTGTAATG
188 TTAACATAAATGTGTGAGAGTTAATGTAACAAGTCAATTAAATCACAAAATTATAATTTTAATG
* * * *
1809110 AAAGATAAATATTTAAATTTATATTTTTAAGTTAAAAGTATTTAATGATTTATAAATTTTAGTTT
1 AAA-ATAAACATTTAAATTTATATTTTTGAGTTAAAAGTATTTAATAATTTATAAATTTTAATTT
* * * * * *
1809175 AAAAATAAGTAAT-A-AAAAATAAAAATAATTATAATTAAAAATCATCATCTAAAAA-CTTTGAT
65 AAAAATAAATAATAATAAAAATAAAAATAATTATTATTAAAAGTTATCAT-TAAAAAGCTTTAAC
* ** * * * * *
1809237 ATAAAGCTATAA-AAAT-AAGTAAAAAACTCATAAAAGTAGAACAAATATATTTAAA
129 GTAAAATTATAAGAATTGACGT-AAAAACTTATAAATGTAGAACAAGTATATTTAAA
1809292 TTCTAATAAA
Statistics
Matches: 960, Mismatches: 183, Indels: 80
0.78 0.15 0.07
Matches are distributed among these distances:
243 9 0.01
244 87 0.09
245 96 0.10
247 5 0.01
248 4 0.00
249 44 0.05
250 153 0.16
251 268 0.28
252 78 0.08
253 19 0.02
254 140 0.15
255 29 0.03
256 28 0.03
ACGTcount: A:0.50, C:0.06, G:0.09, T:0.35
Consensus pattern (251 bp):
AAAATAAACATTTAAATTTATATTTTTGAGTTAAAAGTATTTAATAATTTATAAATTTTAATTTA
AAAATAAATAATAATAAAAATAAAAATAATTATTATTAAAAGTTATCATTAAAAAGCTTTAACGT
AAAATTATAAGAATTGACGTAAAAACTTATAAATGTAGAACAAGTATATTTAAAATTTTAACATA
AATGTGTGAGAGTTAATGTAACAAGTCAATTAAATCACAAAATTATAATTTTAATG
Found at i:1808841 original size:746 final size:750
Alignment explanation
Indices: 1807858--1809214 Score: 1686
Period size: 746 Copynumber: 1.8 Consensus size: 750
1807848 ATTTTTGTAA
* * *
1807858 AAAATAAATATTTAAATTTATATTCTTGAGTTAAAAGTAGTTAAACGATTTACAAAATTTAATTT
1 AAAAGAAACATTTAAATTTATATTCTTGAGCTAAAAGTAGTTAAAC-ATTTACAAAATTTAATTT
* * * * *
1807923 AAAAATAAATAATAATAAGAATAAAAATAATTATTATTAAAAGTTGTTATTGAAAAACCTTGACT
65 AAAAATAAATAATAATAAAAATAAAAATAATAATTATTAAAAGTTATTATTGAAAAAACTTGACG
* * * * *
1807988 TAAAGTTATAAGAATTGACATAGAAACTTATAAAAGTGGAACAAGTACTTTTAAAATCTTAACCT
130 TAAAATTATAAGAATTGACATAAAAACTCATAAAAGTGAAACAAG-ACTTTTAAAATCTTAACAT
* * *
1808053 AAATGTGCGAAAGTTAACATAATAAGTCAATTAAAACACAAAAATCTAATTTTAATGAAAAACAA
194 AAATGTGCGAAAGGTAACATAACAAGTCAATTAAAACACAAAAATATAATTTTAATGAAAAACAA
*
1808118 ACA-TTAAATTTATATTTTT-GAGCTAAAACTATTTAA-CA-ATTTATAAATTTTAATTTAAAAA
259 ACATTTAAATTTATATTTTTAGA-CTAAAACTATTTAATAAGATTTATAAATTTTAATTTAAAAA
* * * * **
1808179 T-A-AATAAT-A-ATAAAATTAATTATTTTTAAAAATTACCATTGAAAAGCTTTAACGTAAAGTT
323 TAATAATAATAAGATAAAAATAATTATTGTT-AAAATTACCATTAAAAAGCTTTAACATAAAAAT
** * * * * *
1808240 ATACGAATTGATGTAAAAATTC-ATAAATGGAGAACGAGTATATTTAAAATTCT-AACGTAAATG
387 ATAAAAATTGACGTAAAAACTCGAAAAAT-GA-AACAAGTATATTTAAAA-TCTGAACGTAAATA
* * * * * * *
1808303 TGTGAGAGTTAATATAA-AAATGAA-TTA-CCTTAATAACTTTTAATTTTAAT-AAAAACAAATG
449 TATGAGAATTAATATAACAAATCAAGTAAGCCATAA-AA-TTTTAATTGTAATGAAAAACAAATA
* *
1808364 TTTGAATTTATATTCTCAAGGTAAAAGTATTTAATAATATAAAAATTTTAATTTTAAAATAAAAA
512 TTTAAATTTATATTCTCAAGGTAAAAGTATTTAATAATATAAAAATTTTAATTTAAAAATAAAAA
*
1808429 ATAATAAAGATAAAAATAATTATAGTTAAAAGTTACCATTAAAAAGGTTTAATGGAAAACTATAA
577 ATAA-AAA-ATAAAAATAATTATAATTAAAAGTTACCATTAAAAAGGTTTAATGGAAAACTATAA
1808494 GAATTGACGTAAAAACTTATAAATGTAGAATAAATATATTTAAAATTTTAACATAAGTGTGTGAG
640 GAATTGACGTAAAAACTTATAAATGTAGAATAAATATATTTAAAATTTTAACATAAGTGTGTGAG
1808559 AGGTAATGTAATAAATTAATTAAATCACAAAATTATAATTTTAATG
705 AGGTAATGTAATAAATTAATTAAATCACAAAATTATAATTTTAATG
* * * **
1808605 AAAAGAAACATTTAAATTTATATTTTTG-GACTAAAAGTATTTAATA-ATTTATAATTTTTAATT
1 AAAAGAAACATTTAAATTTATATTCTTGAG-CTAAAAGTAGTTAA-ACATTTACAAAATTTAATT
*
1808668 TAAAAATAAATAATTATAAAAATAAAAATAATAATTATTAAAAGTTATTATTGAAAAAACTTGAC
64 TAAAAATAAATAATAATAAAAATAAAAATAATAATTATTAAAAGTTATTATTGAAAAAACTTGAC
*** * * *
1808733 GTAAAATTATAAGAATTGGGGTAAAAACTCATAAAGGTGAAAGAA-ACATATTTAAAATTTTAAC
129 GTAAAATTATAAGAATTGACATAAAAACTCATAAAAGTGAAACAAGAC-T-TTTAAAATCTTAAC
* * * * * ** * *
1808797 ATAAATGTGTGAGAGGTAACGTGACAGGTCAATTAAGTCACAAAAATATAATTTTAGTGAAAAAT
192 ATAAATGTGCGAAAGGTAACATAACAAGTCAATTAAAACACAAAAATATAATTTTAATGAAAAAC
* *
1808862 AAACATTTAAATTTATATTTTTAGATTAAAAGTATTTAATTAATGATTTATAAATTTTAATTTAA
257 AAACATTTAAATTTATATTTTTAGACTAAAACTATTTAA-TAA-GATTTATAAATTTTAATTTAA
* ** *
1808927 AAATAATAATAATAAAGATAAAAATAATTATTGTTAAAGTTGTCATTAAAAAGTTTTAACATAAA
320 AAATAATAATAAT-AAGATAAAAATAATTATTGTTAAAATTACCATTAAAAAGCTTTAACATAAA
*
1808992 AATATAAAAATTGACGTAAAAACTCGTAAAAATGAAATAAGTATATTTAAAATCTGAACGTAAAT
384 AATATAAAAATTGACGTAAAAACTCG-AAAAATGAAACAAGTATATTTAAAATCTGAACGTAAAT
* * * * *
1809057 ATATGAGAATTAATGTAACAAGTCAAGTAAGTCATAAAATTTTAATTGTAATGAAAGATAAATAT
448 ATATGAGAATTAATATAACAAATCAAGTAAGCCATAAAATTTTAATTGTAATGAAAAACAAATAT
* * * * * * * **
1809122 TTAAATTTATATTTTTAAGTTAAAAGTATTTAATGATTTATAAATTTTAGTTTAAAAATAAGTAA
513 TTAAATTTATATTCTCAAGGTAAAAGTATTTAATAATATAAAAATTTTAATTTAAAAATAAAAAA
1809187 TAAAAAATAAAAATAATTATAATTAAAA
578 TAAAAAATAAAAATAATTATAATTAAAA
1809215 ATCATCATCT
Statistics
Matches: 506, Mismatches: 82, Indels: 36
0.81 0.13 0.06
Matches are distributed among these distances:
744 2 0.00
745 1 0.00
746 180 0.36
747 65 0.13
748 3 0.01
749 1 0.00
751 24 0.05
752 1 0.00
753 6 0.01
754 3 0.01
755 103 0.20
756 38 0.08
757 75 0.15
758 4 0.01
ACGTcount: A:0.50, C:0.05, G:0.10, T:0.35
Consensus pattern (750 bp):
AAAAGAAACATTTAAATTTATATTCTTGAGCTAAAAGTAGTTAAACATTTACAAAATTTAATTTA
AAAATAAATAATAATAAAAATAAAAATAATAATTATTAAAAGTTATTATTGAAAAAACTTGACGT
AAAATTATAAGAATTGACATAAAAACTCATAAAAGTGAAACAAGACTTTTAAAATCTTAACATAA
ATGTGCGAAAGGTAACATAACAAGTCAATTAAAACACAAAAATATAATTTTAATGAAAAACAAAC
ATTTAAATTTATATTTTTAGACTAAAACTATTTAATAAGATTTATAAATTTTAATTTAAAAATAA
TAATAATAAGATAAAAATAATTATTGTTAAAATTACCATTAAAAAGCTTTAACATAAAAATATAA
AAATTGACGTAAAAACTCGAAAAATGAAACAAGTATATTTAAAATCTGAACGTAAATATATGAGA
ATTAATATAACAAATCAAGTAAGCCATAAAATTTTAATTGTAATGAAAAACAAATATTTAAATTT
ATATTCTCAAGGTAAAAGTATTTAATAATATAAAAATTTTAATTTAAAAATAAAAAATAAAAAAT
AAAAATAATTATAATTAAAAGTTACCATTAAAAAGGTTTAATGGAAAACTATAAGAATTGACGTA
AAAACTTATAAATGTAGAATAAATATATTTAAAATTTTAACATAAGTGTGTGAGAGGTAATGTAA
TAAATTAATTAAATCACAAAATTATAATTTTAATG
Found at i:1809792 original size:24 final size:24
Alignment explanation
Indices: 1809739--1809792 Score: 58
Period size: 24 Copynumber: 2.2 Consensus size: 24
1809729 CAGTCCTAAA
*
1809739 AGAAAAAAAAAGCCAGCGAATATT
1 AGAAAAAAAAAGCCAGAGAATATT
*
1809763 AAAAAAAAAAAGCAACAGAGAA-A-T
1 AGAAAAAAAAAGC--CAGAGAATATT
1809787 AGAAAA
1 AGAAAA
1809793 GATGGAGCGG
Statistics
Matches: 25, Mismatches: 3, Indels: 4
0.78 0.09 0.12
Matches are distributed among these distances:
24 18 0.72
25 1 0.04
26 6 0.24
ACGTcount: A:0.69, C:0.09, G:0.15, T:0.07
Consensus pattern (24 bp):
AGAAAAAAAAAGCCAGAGAATATT
Found at i:1835484 original size:33 final size:34
Alignment explanation
Indices: 1835444--1835507 Score: 103
Period size: 34 Copynumber: 1.9 Consensus size: 34
1835434 AAAGTTTTAC
1835444 AAAACAAAAAACAA-TCAAAAGTTTTTTTAAAAA
1 AAAACAAAAAACAATTCAAAAGTTTTTTTAAAAA
**
1835477 AAAACAAAAATTAATTCAAAAGTTTTTTTAA
1 AAAACAAAAAACAATTCAAAAGTTTTTTTAA
1835508 TTGAAAGCTA
Statistics
Matches: 28, Mismatches: 2, Indels: 1
0.90 0.06 0.03
Matches are distributed among these distances:
33 12 0.43
34 16 0.57
ACGTcount: A:0.59, C:0.08, G:0.03, T:0.30
Consensus pattern (34 bp):
AAAACAAAAAACAATTCAAAAGTTTTTTTAAAAA
Found at i:1839712 original size:14 final size:14
Alignment explanation
Indices: 1839688--1839725 Score: 58
Period size: 14 Copynumber: 2.6 Consensus size: 14
1839678 GTTCAATCTG
1839688 TTTAGTAAATTTACT
1 TTTA-TAAATTTACT
*
1839703 TTTATAAATTTTCT
1 TTTATAAATTTACT
1839717 TTTATAAAT
1 TTTATAAAT
1839726 AAGTTGTTTG
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
14 18 0.82
15 4 0.18
ACGTcount: A:0.34, C:0.05, G:0.03, T:0.58
Consensus pattern (14 bp):
TTTATAAATTTACT
Found at i:1840003 original size:18 final size:17
Alignment explanation
Indices: 1839980--1840022 Score: 52
Period size: 17 Copynumber: 2.5 Consensus size: 17
1839970 ATTTTTGAAA
1839980 TAAAAATAAAAAT-TTTCT
1 TAAAAA-AAAAATGTTT-T
*
1839998 TAAAAAAAACATGTTTT
1 TAAAAAAAAAATGTTTT
1840015 TAAAAAAA
1 TAAAAAAA
1840023 GATAAAAAAA
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
17 14 0.61
18 9 0.39
ACGTcount: A:0.60, C:0.05, G:0.02, T:0.33
Consensus pattern (17 bp):
TAAAAAAAAAATGTTTT
Found at i:1857052 original size:23 final size:23
Alignment explanation
Indices: 1857019--1857064 Score: 67
Period size: 23 Copynumber: 2.0 Consensus size: 23
1857009 GTGAGATAGA
1857019 CAAAAAAATTTCTTTTAT-TTTT
1 CAAAAAAATTTCTTTTATCTTTT
*
1857041 CAAAAAATATTTTTTTTATCTTTT
1 CAAAAAA-ATTTCTTTTATCTTTT
1857065 ATTTTTTACT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
22 7 0.33
23 10 0.48
24 4 0.19
ACGTcount: A:0.35, C:0.09, G:0.00, T:0.57
Consensus pattern (23 bp):
CAAAAAAATTTCTTTTATCTTTT
Found at i:1857791 original size:45 final size:45
Alignment explanation
Indices: 1857689--1857793 Score: 119
Period size: 45 Copynumber: 2.4 Consensus size: 45
1857679 ATATAACAAT
*
1857689 AATAGGAATATTATT-TTATATATGGATACTGAAATTTTTAAATA
1 AATAGAAATATTATTATTATATATGGATACTGAAATTTTTAAATA
** *
1857733 AATTATCAA-ATTATTATTTTATATGGATGA-TGAAATTTTTAAATTA
1 AA-TAGAAATATTATTATTATATATGGAT-ACTGAAATTTTTAAA-TA
1857779 AA-AGAAATATTATTA
1 AATAGAAATATTATTA
1857794 CCCGTTACAT
Statistics
Matches: 51, Mismatches: 5, Indels: 9
0.78 0.08 0.14
Matches are distributed among these distances:
44 11 0.22
45 35 0.69
46 5 0.10
ACGTcount: A:0.45, C:0.02, G:0.10, T:0.44
Consensus pattern (45 bp):
AATAGAAATATTATTATTATATATGGATACTGAAATTTTTAAATA
Found at i:1875878 original size:2 final size:2
Alignment explanation
Indices: 1875871--1875907 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
1875861 CGTTTGAAAT
1875871 AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC A
1 AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC A
1875908 TATATATATA
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.51, C:0.49, G:0.00, T:0.00
Consensus pattern (2 bp):
AC
Found at i:1875912 original size:2 final size:2
Alignment explanation
Indices: 1875907--1875936 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
1875897 ACACACACAC
1875907 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
1875937 TTTGCTTCCG
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1878984 original size:6 final size:6
Alignment explanation
Indices: 1878973--1879004 Score: 64
Period size: 6 Copynumber: 5.3 Consensus size: 6
1878963 GTTTTTTATT
1878973 ATTCAG ATTCAG ATTCAG ATTCAG ATTCAG AT
1 ATTCAG ATTCAG ATTCAG ATTCAG ATTCAG AT
1879005 GGGTAATAAA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 26 1.00
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.34
Consensus pattern (6 bp):
ATTCAG
Found at i:1882386 original size:22 final size:22
Alignment explanation
Indices: 1882360--1882408 Score: 64
Period size: 21 Copynumber: 2.3 Consensus size: 22
1882350 TGTTTCTGAA
*
1882360 TTTTAAGCATTGCGTAATTGAT
1 TTTTAAGCATTACGTAATTGAT
* *
1882382 TTTT-AGTATTACGTGATTGAT
1 TTTTAAGCATTACGTAATTGAT
1882403 TTTTAA
1 TTTTAA
1882409 ATATTGTGTG
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
21 18 0.78
22 5 0.22
ACGTcount: A:0.27, C:0.06, G:0.16, T:0.51
Consensus pattern (22 bp):
TTTTAAGCATTACGTAATTGAT
Found at i:1882522 original size:46 final size:46
Alignment explanation
Indices: 1882448--1882543 Score: 120
Period size: 46 Copynumber: 2.1 Consensus size: 46
1882438 CTAAGTCGTA
* * ** * *
1882448 CAATGCCTTATTAACTAGTCATGTAATACCTTGCTAACTAATCACG
1 CAATGCATGATTAACTAGTCATACAATACATTACTAACTAATCACG
* *
1882494 CAATGCATGATTAACTAGTTATACAATACATTACTAACTAGTCACG
1 CAATGCATGATTAACTAGTCATACAATACATTACTAACTAATCACG
1882540 CAAT
1 CAAT
1882544 ACTTAAAAAT
Statistics
Matches: 42, Mismatches: 8, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
46 42 1.00
ACGTcount: A:0.36, C:0.22, G:0.10, T:0.31
Consensus pattern (46 bp):
CAATGCATGATTAACTAGTCATACAATACATTACTAACTAATCACG
Found at i:1882543 original size:23 final size:23
Alignment explanation
Indices: 1882459--1882545 Score: 75
Period size: 23 Copynumber: 3.8 Consensus size: 23
1882449 AATGCCTTAT
* * * *
1882459 TAACTAGTCATGTAATACCTTGC
1 TAACTAGTCACGCAATACATTAC
* * * *
1882482 TAACTAATCACGCAATGCATGAT
1 TAACTAGTCACGCAATACATTAC
* **
1882505 TAACTAGTTATACAATACATTAC
1 TAACTAGTCACGCAATACATTAC
1882528 TAACTAGTCACGCAATAC
1 TAACTAGTCACGCAATAC
1882546 TTAAAAATTA
Statistics
Matches: 46, Mismatches: 18, Indels: 0
0.72 0.28 0.00
Matches are distributed among these distances:
23 46 1.00
ACGTcount: A:0.38, C:0.22, G:0.10, T:0.30
Consensus pattern (23 bp):
TAACTAGTCACGCAATACATTAC
Found at i:1882579 original size:22 final size:22
Alignment explanation
Indices: 1882529--1882579 Score: 59
Period size: 22 Copynumber: 2.3 Consensus size: 22
1882519 ATACATTACT
1882529 AACTAGTCACGCAATACTTAAA
1 AACTAGTCACGCAATACTTAAA
* *
1882551 AATTAGTCACGTAATAGC-TAAA
1 AACTAGTCACGCAATA-CTTAAA
*
1882573 AGCTAGT
1 AACTAGT
1882580 TACACAATGT
Statistics
Matches: 24, Mismatches: 4, Indels: 2
0.80 0.13 0.07
Matches are distributed among these distances:
22 23 0.96
23 1 0.04
ACGTcount: A:0.43, C:0.18, G:0.14, T:0.25
Consensus pattern (22 bp):
AACTAGTCACGCAATACTTAAA
Found at i:1882683 original size:22 final size:22
Alignment explanation
Indices: 1882605--1882688 Score: 80
Period size: 22 Copynumber: 3.8 Consensus size: 22
1882595 GATCAGTTAT
* ** *
1882605 GTAATGTCTAAAAATTATTAAC
1 GTAATGCCTAAAAACCATTTAC
* * *
1882627 GCAATGCCTAAAAACTAATTAC
1 GTAATGCCTAAAAACCATTTAC
*
1882649 GTAATATCC-AAAAACCATTTAC
1 GTAAT-GCCTAAAAACCATTTAC
1882671 GTAATGCCTAAAAACCAT
1 GTAATGCCTAAAAACCAT
1882689 CAAAACTACT
Statistics
Matches: 50, Mismatches: 10, Indels: 4
0.78 0.16 0.06
Matches are distributed among these distances:
21 2 0.04
22 46 0.92
23 2 0.04
ACGTcount: A:0.45, C:0.19, G:0.08, T:0.27
Consensus pattern (22 bp):
GTAATGCCTAAAAACCATTTAC
Found at i:1882900 original size:51 final size:50
Alignment explanation
Indices: 1882784--1882910 Score: 155
Period size: 52 Copynumber: 2.5 Consensus size: 50
1882774 TTTGATGAAG
* **
1882784 AATACTCAAAATGCTCAAAGGTTTTCTTCGTATATCAAAAATTACTCTAA
1 AATACTTAAAATGCTCAAAGGTTTTCTTCGTATATCAAAAACCACTCTAA
* * *
1882834 AATGCTTAAACATGCTCAAAGGCTTTTCTTCGTGTATCAAAAACCATTCTAA
1 AATACTTAAA-ATGCTCAAAGG-TTTTCTTCGTATATCAAAAACCACTCTAA
* * *
1882886 CATACTTAAAATGCTTAAAAGTTTT
1 AATACTTAAAATGCTCAAAGGTTTT
1882911 TTTTTTGTAA
Statistics
Matches: 65, Mismatches: 10, Indels: 4
0.82 0.13 0.05
Matches are distributed among these distances:
50 12 0.18
51 20 0.31
52 33 0.51
ACGTcount: A:0.38, C:0.18, G:0.09, T:0.35
Consensus pattern (50 bp):
AATACTTAAAATGCTCAAAGGTTTTCTTCGTATATCAAAAACCACTCTAA
Found at i:1885642 original size:18 final size:20
Alignment explanation
Indices: 1885610--1885652 Score: 72
Period size: 19 Copynumber: 2.2 Consensus size: 20
1885600 ATATAATATT
1885610 TTTTAAAAAATTTAAAT-TA
1 TTTTAAAAAATTTAAATGTA
1885629 TTTTAAAAAA-TTAAATGTA
1 TTTTAAAAAATTTAAATGTA
1885648 TTTTA
1 TTTTA
1885653 TTTTTTATTA
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
18 6 0.26
19 17 0.74
ACGTcount: A:0.49, C:0.00, G:0.02, T:0.49
Consensus pattern (20 bp):
TTTTAAAAAATTTAAATGTA
Found at i:1885870 original size:15 final size:15
Alignment explanation
Indices: 1885832--1885870 Score: 51
Period size: 15 Copynumber: 2.5 Consensus size: 15
1885822 TGTTAATACT
*
1885832 ATTTGATTAAAAAATT
1 ATTT-ATTAAAAAATA
*
1885848 ATTAATTAAAAAATA
1 ATTTATTAAAAAATA
1885863 ATTTATTA
1 ATTTATTA
1885871 TAAACAAAAA
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
15 17 0.85
16 3 0.15
ACGTcount: A:0.54, C:0.00, G:0.03, T:0.44
Consensus pattern (15 bp):
ATTTATTAAAAAATA
Found at i:1892181 original size:2 final size:2
Alignment explanation
Indices: 1892174--1892210 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
1892164 ATTTTAAGCT
1892174 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1892211 CTTGGTTCTT
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:1893875 original size:27 final size:27
Alignment explanation
Indices: 1893845--1893905 Score: 77
Period size: 27 Copynumber: 2.3 Consensus size: 27
1893835 CAATATATAT
** *
1893845 TAAAATATTAATATTTAAAATAAATTA
1 TAAAATATTAATACATAAAATAAAATA
*
1893872 TAAATTATTAATACATAAAATAAAATA
1 TAAAATATTAATACATAAAATAAAATA
*
1893899 AAAAATA
1 TAAAATA
1893906 AATAATCACA
Statistics
Matches: 28, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
27 28 1.00
ACGTcount: A:0.64, C:0.02, G:0.00, T:0.34
Consensus pattern (27 bp):
TAAAATATTAATACATAAAATAAAATA
Done.