Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr12
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: 24583705
ACGTcount: A:0.31, C:0.16, G:0.16, T:0.31
Warning! 1509421 characters in sequence are not A, C, G, or T
File 6 of 75
Found at i:1572386 original size:39 final size:39
Alignment explanation
Indices: 1572274--1572409 Score: 123
Period size: 40 Copynumber: 3.4 Consensus size: 39
1572264 CGTTTGTATA
* * *
1572274 AAAAACGCCGCTAAAAATCAAGCATTAGCGGCG-CTTTT
1 AAAAACGCCGCTAAAAATCGAGAATTAGCGGCGTTTTTT
* * * *
1572312 AAAATACCGCCACTAAAGATCGGGTATTAGCGGCGTTTTTT
1 AAAA-A-CGCCGCTAAAAATCGAGAATTAGCGGCGTTTTTT
* **
1572353 AGAAAACGCCGCTAAAAAT-GAGAATTAGTGGCGTTTTCC
1 A-AAAACGCCGCTAAAAATCGAGAATTAGCGGCGTTTTTT
*
1572392 AAAAAGCGCCGCAAAAAA
1 AAAAA-CGCCGCTAAAAA
1572410 CCTAAGCCCA
Statistics
Matches: 79, Mismatches: 14, Indels: 9
0.77 0.14 0.09
Matches are distributed among these distances:
38 8 0.10
39 28 0.35
40 34 0.43
41 6 0.08
42 3 0.04
ACGTcount: A:0.38, C:0.21, G:0.21, T:0.21
Consensus pattern (39 bp):
AAAAACGCCGCTAAAAATCGAGAATTAGCGGCGTTTTTT
Found at i:1572552 original size:41 final size:41
Alignment explanation
Indices: 1572449--1572801 Score: 498
Period size: 41 Copynumber: 8.7 Consensus size: 41
1572439 TTTCGGGGCC
* ** * * *
1572449 TTAGTGGCGTTTTTCAAAAAGCGCCACTAAAGATCTGGTCT
1 TTAGCGGCGTTTTTGGAAAAGCGCCGCTAATGCTCTGGTCT
1572490 TTAGC-GCGTTTTTGGAAAAGCGCCGCTAATGCTCTGGTCT
1 TTAGCGGCGTTTTTGGAAAAGCGCCGCTAATGCTCTGGTCT
1572530 TTAGCGGCGTTTTTGGAAAAGCGCCGCTAATGCTCTGGTCT
1 TTAGCGGCGTTTTTGGAAAAGCGCCGCTAATGCTCTGGTCT
1572571 TTAGCGGCGTTTTTGGAAAAGCGCCGCTAATGCTCTGGTCT
1 TTAGCGGCGTTTTTGGAAAAGCGCCGCTAATGCTCTGGTCT
*
1572612 TTAGCGGCGTTTTT-GAGAAAGCGCCGCTAATGGTCTGGTCT
1 TTAGCGGCGTTTTTGGA-AAAGCGCCGCTAATGCTCTGGTCT
* **
1572653 TTAGCGGCGTTTTTGGGAAAGCGCCGCTAATGCTCTATTCT
1 TTAGCGGCGTTTTTGGAAAAGCGCCGCTAATGCTCTGGTCT
*
1572694 TTAGCGGCGCTTTTGTGAAAA-CGCCGCTAATGCTCTGGTCT
1 TTAGCGGCGTTTTTG-GAAAAGCGCCGCTAATGCTCTGGTCT
* * * * * *
1572735 TTAGCGACGTTTTTGTAGAAGTGCCGCTATTACTCT-GTCT
1 TTAGCGGCGTTTTTGGAAAAGCGCCGCTAATGCTCTGGTCT
*
1572775 TTAGCGGCGTTTTTGGGAAAGCGCCGC
1 TTAGCGGCGTTTTTGGAAAAGCGCCGC
1572802 AAAATGTATT
Statistics
Matches: 280, Mismatches: 27, Indels: 11
0.88 0.08 0.03
Matches are distributed among these distances:
40 66 0.24
41 209 0.75
42 5 0.02
ACGTcount: A:0.18, C:0.22, G:0.28, T:0.33
Consensus pattern (41 bp):
TTAGCGGCGTTTTTGGAAAAGCGCCGCTAATGCTCTGGTCT
Found at i:1573327 original size:21 final size:20
Alignment explanation
Indices: 1573295--1573335 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 20
1573285 TTAAGGACTA
*
1573295 GGGATTATGGTTTAAGGGTT
1 GGGATTAAGGTTTAAGGGTT
*
1573315 GGGATTTAAGGTTTAGGGGTT
1 GGGA-TTAAGGTTTAAGGGTT
1573336 AGGGGTTAGA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
20 4 0.22
21 14 0.78
ACGTcount: A:0.20, C:0.00, G:0.41, T:0.39
Consensus pattern (20 bp):
GGGATTAAGGTTTAAGGGTT
Found at i:1578094 original size:14 final size:14
Alignment explanation
Indices: 1578075--1578104 Score: 60
Period size: 14 Copynumber: 2.1 Consensus size: 14
1578065 AGTTGCACTA
1578075 TTTGAACTTGAAAT
1 TTTGAACTTGAAAT
1578089 TTTGAACTTGAAAT
1 TTTGAACTTGAAAT
1578103 TT
1 TT
1578105 AACATGATTT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.33, C:0.07, G:0.13, T:0.47
Consensus pattern (14 bp):
TTTGAACTTGAAAT
Found at i:1578417 original size:86 final size:85
Alignment explanation
Indices: 1578286--1578489 Score: 293
Period size: 86 Copynumber: 2.4 Consensus size: 85
1578276 ATTTGTAATC
* * * *
1578286 AAAGCGTCGCTAAATGTCTTGAGCTATAGCGGCGTTTGTGAAAAAAGAGCCGCTAAAGGTCTTGA
1 AAAGCGTCGCTAAAGGTCCTGATCTATAGCGGCGTTTGTGAAAAAAGAGCCGCTAAAGGTCCTGA
*
1578351 GCTATAGCGGCGTTTGT-GA
66 ACTATAGCGGCGTTTGTGGA
* * *
1578370 AAGATGCGTCGCTAAAGGTCCTGATCTATAGCGGCGTTTTTGTAAAAAGCGCCGCTAAAGGTCCT
1 AA-A-GCGTCGCTAAAGGTCCTGATCTATAGCGGCGTTTGTGAAAAAAGAGCCGCTAAAGGTCCT
*
1578435 GAACTATAGCGGCGTTTTTGGA
64 GAACTATAGCGGCGTTTGTGGA
*
1578457 AAAGCGCCGCTAAAGGTCCTGATCTATAGCGGC
1 AAAGCGTCGCTAAAGGTCCTGATCTATAGCGGC
1578490 ATGACAATAG
Statistics
Matches: 107, Mismatches: 10, Indels: 5
0.88 0.08 0.04
Matches are distributed among these distances:
84 2 0.02
85 30 0.28
86 71 0.66
87 4 0.04
ACGTcount: A:0.26, C:0.20, G:0.28, T:0.25
Consensus pattern (85 bp):
AAAGCGTCGCTAAAGGTCCTGATCTATAGCGGCGTTTGTGAAAAAAGAGCCGCTAAAGGTCCTGA
ACTATAGCGGCGTTTGTGGA
Found at i:1578473 original size:42 final size:43
Alignment explanation
Indices: 1578269--1578489 Score: 266
Period size: 43 Copynumber: 5.2 Consensus size: 43
1578259 ATGGTACTTT
* * * * *
1578269 TAGCGGCATTTGT-AATCAAAGCGTCGCTAAATGTCTTGAGCTA
1 TAGCGGCGTTTGTGAA-AAAAGCGCCGCTAAAGGTCCTGAGCTA
* *
1578312 TAGCGGCGTTTGTGAAAAAAGAGCCGCTAAAGGTCTTGAGCTA
1 TAGCGGCGTTTGTGAAAAAAGCGCCGCTAAAGGTCCTGAGCTA
* * * *
1578355 TAGCGGCGTTTGTGAAAGATGCGTCGCTAAAGGTCCTGATCTA
1 TAGCGGCGTTTGTGAAAAAAGCGCCGCTAAAGGTCCTGAGCTA
* * *
1578398 TAGCGGCGTTTTTGTAAAAAGCGCCGCTAAAGGTCCTGAACTA
1 TAGCGGCGTTTGTGAAAAAAGCGCCGCTAAAGGTCCTGAGCTA
* * *
1578441 TAGCGGCGTTTTTG-GAAAAGCGCCGCTAAAGGTCCTGATCTA
1 TAGCGGCGTTTGTGAAAAAAGCGCCGCTAAAGGTCCTGAGCTA
1578483 TAGCGGC
1 TAGCGGC
1578490 ATGACAATAG
Statistics
Matches: 158, Mismatches: 19, Indels: 3
0.88 0.11 0.02
Matches are distributed among these distances:
42 33 0.21
43 123 0.78
44 2 0.01
ACGTcount: A:0.26, C:0.19, G:0.28, T:0.26
Consensus pattern (43 bp):
TAGCGGCGTTTGTGAAAAAAGCGCCGCTAAAGGTCCTGAGCTA
Found at i:1581661 original size:24 final size:24
Alignment explanation
Indices: 1581628--1581686 Score: 77
Period size: 24 Copynumber: 2.5 Consensus size: 24
1581618 TCTGTGGTTA
1581628 AATGACTGATTTGT-TTGTG-TTTGG
1 AATGACTGATTTGTCTT-TGATTT-G
*
1581652 TATGACTGATTTGTCTTTGATTTG
1 AATGACTGATTTGTCTTTGATTTG
1581676 AATGACTGATT
1 AATGACTGATT
1581687 CTGAGTATGG
Statistics
Matches: 31, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
24 26 0.84
25 5 0.16
ACGTcount: A:0.20, C:0.07, G:0.24, T:0.49
Consensus pattern (24 bp):
AATGACTGATTTGTCTTTGATTTG
Found at i:1581843 original size:26 final size:27
Alignment explanation
Indices: 1581802--1581856 Score: 76
Period size: 26 Copynumber: 2.1 Consensus size: 27
1581792 GTGGCCACAT
* *
1581802 ATACTAATTACTGGCAGCTTTGCTGCG
1 ATACTAATTACTGGCAACTTTGCTACG
*
1581829 ATACT-ATTGCTGGCAACTTTGCTACG
1 ATACTAATTACTGGCAACTTTGCTACG
1581855 AT
1 AT
1581857 GCTACTGATG
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
26 20 0.80
27 5 0.20
ACGTcount: A:0.24, C:0.22, G:0.20, T:0.35
Consensus pattern (27 bp):
ATACTAATTACTGGCAACTTTGCTACG
Found at i:1581904 original size:32 final size:32
Alignment explanation
Indices: 1581859--1582105 Score: 234
Period size: 32 Copynumber: 7.7 Consensus size: 32
1581849 GCTACGATGC
*
1581859 TACTGATGACTTTGTGCCGATCATAGTACCGT
1 TACTGATGGCTTTGTGCCGATCATAGTACCGT
*
1581891 TACTGATGGCTTTGTGCCGATCATAGTACCAT
1 TACTGATGGCTTTGTGCCGATCATAGTACCGT
* * *
1581923 TACTGATAGCTTTGTACCGATCATATTACCGT
1 TACTGATGGCTTTGTGCCGATCATAGTACCGT
* * * * ** *
1581955 TACCGAT-GATTGTATGCCGATCGTTTTACTGT
1 TACTGATGGCTT-TGTGCCGATCATAGTACCGT
* * **
1581987 TACTGATGGCTGTGTGCCAATCATA-TCATTGT
1 TACTGATGGCTTTGTGCCGATCATAGT-ACCGT
1582019 TACTGATGGCTTTGTGCCGATCAT-GTTACCGT
1 TACTGATGGCTTTGTGCCGATCATAG-TACCGT
* * *
1582051 TACTGATGG-TTGTATGCCGATCATA-TCACTGC
1 TACTGATGGCTT-TGTGCCGATCATAGT-ACCGT
*
1582083 TACTGATGGCTTTGTGCCAATCA
1 TACTGATGGCTTTGTGCCGATCA
1582106 CATTATTGTA
Statistics
Matches: 176, Mismatches: 30, Indels: 18
0.79 0.13 0.08
Matches are distributed among these distances:
31 7 0.04
32 164 0.93
33 5 0.03
ACGTcount: A:0.21, C:0.21, G:0.21, T:0.36
Consensus pattern (32 bp):
TACTGATGGCTTTGTGCCGATCATAGTACCGT
Found at i:1582031 original size:96 final size:95
Alignment explanation
Indices: 1581873--1582125 Score: 303
Period size: 96 Copynumber: 2.6 Consensus size: 95
1581863 GATGACTTTG
* * *** *
1581873 TGCCGATCATAGT-ACCGTTACTGATGGCTTTGTGCCGATCATAGTACCATTACTGATAGCTTTG
1 TGCCGATCATA-TCACTGTTACTGATGGCTTTGTGCCAATCATA-TATTGTTACTGATGGCTTTG
1581937 TACCGATCATATTACCGTTACCGATGATTGTA
64 TACCGATCATATTACCGTTACCGATGATTGTA
* * * *
1581969 TGCCGATCGTTTTACTGTTACTGATGGCTGTGTGCCAATCATATCATTGTTACTGATGGCTTTGT
1 TGCCGATCATATCACTGTTACTGATGGCTTTGTGCCAATCATAT-ATTGTTACTGATGGCTTTGT
* * * *
1582034 GCCGATCATGTTACCGTTACTGATGGTTGTA
65 ACCGATCATATTACCGTTACCGATGATTGTA
* * *
1582065 TGCCGATCATATCACTGCTACTGATGGCTTTGTGCCAATCACATTATTG-TACTTATGGCTT
1 TGCCGATCATATCACTGTTACTGATGGCTTTGTGCCAATCATA-TATTGTTACTGATGGCTT
1582126 GTAGCCATTC
Statistics
Matches: 134, Mismatches: 20, Indels: 7
0.83 0.12 0.04
Matches are distributed among these distances:
95 13 0.10
96 120 0.90
97 1 0.01
ACGTcount: A:0.21, C:0.21, G:0.21, T:0.37
Consensus pattern (95 bp):
TGCCGATCATATCACTGTTACTGATGGCTTTGTGCCAATCATATATTGTTACTGATGGCTTTGTA
CCGATCATATTACCGTTACCGATGATTGTA
Found at i:1582128 original size:64 final size:65
Alignment explanation
Indices: 1581980--1582132 Score: 179
Period size: 64 Copynumber: 2.4 Consensus size: 65
1581970 GCCGATCGTT
* * * * * **
1581980 TTACTGTTACTGATGGC-TGTGTGCCAATCATATCATTGTTACTGATGGCTTTGTGCCGATCATG
1 TTACCGTTACTGATGGCTTGTATGCCAATCATATCACTGCTACTGATGGCTTTGTGCCAATCACA
*
1582044 TTACCGTTACTGATGG-TTGTATGCCGATCATATCACTGCTACTGATGGCTTTGTGCCAATCACA
1 TTACCGTTACTGATGGCTTGTATGCCAATCATATCACTGCTACTGATGGCTTTGTGCCAATCACA
** *
1582108 TTATTG-TACTTATGGCTTGTA-GCCA
1 TTACCGTTACTGATGGCTTGTATGCCA
1582133 TTCTGTTTAT
Statistics
Matches: 75, Mismatches: 12, Indels: 5
0.82 0.13 0.05
Matches are distributed among these distances:
63 11 0.15
64 64 0.85
ACGTcount: A:0.20, C:0.20, G:0.22, T:0.38
Consensus pattern (65 bp):
TTACCGTTACTGATGGCTTGTATGCCAATCATATCACTGCTACTGATGGCTTTGTGCCAATCACA
Found at i:1591747 original size:5 final size:5
Alignment explanation
Indices: 1591732--1591765 Score: 61
Period size: 5 Copynumber: 7.0 Consensus size: 5
1591722 AAAATAAATG
1591732 GGAAA -GAAA GGAAA GGAAA GGAAA GGAAA GGAAA
1 GGAAA GGAAA GGAAA GGAAA GGAAA GGAAA GGAAA
1591766 AAATGAAGAA
Statistics
Matches: 28, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
4 4 0.14
5 24 0.86
ACGTcount: A:0.62, C:0.00, G:0.38, T:0.00
Consensus pattern (5 bp):
GGAAA
Found at i:1594242 original size:9 final size:9
Alignment explanation
Indices: 1594228--1594252 Score: 50
Period size: 9 Copynumber: 2.8 Consensus size: 9
1594218 TGCAAATGCT
1594228 ATAATAACA
1 ATAATAACA
1594237 ATAATAACA
1 ATAATAACA
1594246 ATAATAA
1 ATAATAA
1594253 ATACATCATC
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:0.68, C:0.08, G:0.00, T:0.24
Consensus pattern (9 bp):
ATAATAACA
Found at i:1595303 original size:19 final size:19
Alignment explanation
Indices: 1595279--1595351 Score: 119
Period size: 19 Copynumber: 3.8 Consensus size: 19
1595269 AAATTAAATC
*
1595279 TCTAAGATTACATATCATA
1 TCTAAGATTGCATATCATA
1595298 TCTAAGATTGCATATCATA
1 TCTAAGATTGCATATCATA
*
1595317 TCTAGGATTGCATATCATA
1 TCTAAGATTGCATATCATA
*
1595336 TCTAAGATTGCGTATC
1 TCTAAGATTGCATATC
1595352 CTCAGAAATT
Statistics
Matches: 50, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
19 50 1.00
ACGTcount: A:0.34, C:0.16, G:0.12, T:0.37
Consensus pattern (19 bp):
TCTAAGATTGCATATCATA
Found at i:1600726 original size:14 final size:14
Alignment explanation
Indices: 1600707--1600745 Score: 51
Period size: 14 Copynumber: 2.8 Consensus size: 14
1600697 TAAGCAAGTA
*
1600707 TAATAATATTAAAC
1 TAATAATAATAAAC
* *
1600721 TAATAATAATACAG
1 TAATAATAATAAAC
1600735 TAATAATAATA
1 TAATAATAATA
1600746 TAAATAAACA
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
14 22 1.00
ACGTcount: A:0.59, C:0.05, G:0.03, T:0.33
Consensus pattern (14 bp):
TAATAATAATAAAC
Found at i:1600756 original size:22 final size:21
Alignment explanation
Indices: 1600723--1600774 Score: 68
Period size: 22 Copynumber: 2.4 Consensus size: 21
1600713 TATTAAACTA
*
1600723 ATAATAATACAGTAATAATAAT
1 ATAATAA-ACAGTAATAACAAT
*
1600745 ATAAATAAACAGTATTAACAAT
1 AT-AATAAACAGTAATAACAAT
1600767 ATAATAAA
1 ATAATAAA
1600775 AAACTAAAAA
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
21 6 0.22
22 16 0.59
23 5 0.19
ACGTcount: A:0.62, C:0.06, G:0.04, T:0.29
Consensus pattern (21 bp):
ATAATAAACAGTAATAACAAT
Found at i:1602169 original size:2 final size:2
Alignment explanation
Indices: 1602162--1602186 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
1602152 AGCAATGGCG
1602162 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 A
1602187 AATCAAAACA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:1604590 original size:17 final size:17
Alignment explanation
Indices: 1604568--1604604 Score: 74
Period size: 17 Copynumber: 2.2 Consensus size: 17
1604558 AGAAATTGTT
1604568 ATTAATTTCTGAGACCC
1 ATTAATTTCTGAGACCC
1604585 ATTAATTTCTGAGACCC
1 ATTAATTTCTGAGACCC
1604602 ATT
1 ATT
1604605 TTGTAGTTAT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 20 1.00
ACGTcount: A:0.30, C:0.22, G:0.11, T:0.38
Consensus pattern (17 bp):
ATTAATTTCTGAGACCC
Found at i:1608002 original size:30 final size:30
Alignment explanation
Indices: 1607967--1608026 Score: 84
Period size: 30 Copynumber: 2.0 Consensus size: 30
1607957 TGGGTAACGA
* **
1607967 AAAAAAGGAATTTGTTAATAGTTAGGTGAC
1 AAAAAAGAAATTTACTAATAGTTAGGTGAC
*
1607997 AAAAAAGAAATTTACTAATAGTTGGGTGAC
1 AAAAAAGAAATTTACTAATAGTTAGGTGAC
1608027 TATTTGTGCA
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
30 26 1.00
ACGTcount: A:0.45, C:0.05, G:0.22, T:0.28
Consensus pattern (30 bp):
AAAAAAGAAATTTACTAATAGTTAGGTGAC
Found at i:1610126 original size:17 final size:17
Alignment explanation
Indices: 1610104--1610137 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
1610094 ACTTGGGTTA
1610104 ATTTTTTGCAAATATAG
1 ATTTTTTGCAAATATAG
*
1610121 ATTTTTTGTAAATATAG
1 ATTTTTTGCAAATATAG
1610138 GTGGGTTTGG
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.35, C:0.03, G:0.12, T:0.50
Consensus pattern (17 bp):
ATTTTTTGCAAATATAG
Found at i:1611650 original size:25 final size:26
Alignment explanation
Indices: 1611599--1611651 Score: 63
Period size: 29 Copynumber: 2.0 Consensus size: 26
1611589 ATACGATACT
1611599 TATAAATCTTATCTCATTGATCAATCGTA
1 TATAAATCTTATCTC--T-ATCAATCGTA
*
1611628 TATAAATCTTATCTC-ATCCATCGT
1 TATAAATCTTATCTCTATCAATCGT
1611652 GCTTTTAAAG
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
25 8 0.35
29 15 0.65
ACGTcount: A:0.32, C:0.21, G:0.06, T:0.42
Consensus pattern (26 bp):
TATAAATCTTATCTCTATCAATCGTA
Found at i:1617467 original size:6 final size:5
Alignment explanation
Indices: 1617451--1617489 Score: 51
Period size: 5 Copynumber: 7.4 Consensus size: 5
1617441 GAATAGGAAG
*
1617451 TTAGT TTAGT TTAAGT TTAGTT TTAGT TTAAT TTAGT TT
1 TTAGT TTAGT TT-AGT TTAG-T TTAGT TTAGT TTAGT TT
1617490 TATGGTATCT
Statistics
Matches: 30, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
5 20 0.67
6 10 0.33
ACGTcount: A:0.23, C:0.00, G:0.15, T:0.62
Consensus pattern (5 bp):
TTAGT
Found at i:1617469 original size:11 final size:10
Alignment explanation
Indices: 1617451--1617489 Score: 51
Period size: 11 Copynumber: 3.7 Consensus size: 10
1617441 GAATAGGAAG
1617451 TTAGTTTAGT
1 TTAGTTTAGT
1617461 TTAAGTTTAGTT
1 TT-AGTTTAG-T
*
1617473 TTAGTTTAAT
1 TTAGTTTAGT
1617483 TTAGTTT
1 TTAGTTT
1617490 TATGGTATCT
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
10 10 0.38
11 13 0.50
12 3 0.12
ACGTcount: A:0.23, C:0.00, G:0.15, T:0.62
Consensus pattern (10 bp):
TTAGTTTAGT
Found at i:1617472 original size:16 final size:15
Alignment explanation
Indices: 1617451--1617489 Score: 60
Period size: 17 Copynumber: 2.5 Consensus size: 15
1617441 GAATAGGAAG
1617451 TTAGTTTAGTTTAAGT
1 TTAGTTTAGTTTAA-T
1617467 TTAGTTTTAGTTTAAT
1 TTAG-TTTAGTTTAAT
1617483 TTAGTTT
1 TTAGTTT
1617490 TATGGTATCT
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
15 3 0.14
16 9 0.41
17 10 0.45
ACGTcount: A:0.23, C:0.00, G:0.15, T:0.62
Consensus pattern (15 bp):
TTAGTTTAGTTTAAT
Found at i:1617490 original size:16 final size:17
Alignment explanation
Indices: 1617451--1617491 Score: 68
Period size: 16 Copynumber: 2.5 Consensus size: 17
1617441 GAATAGGAAG
1617451 TTAG-TTTAGTTTAAGT
1 TTAGTTTTAGTTTAAGT
1617467 TTAGTTTTAGTTTAA-T
1 TTAGTTTTAGTTTAAGT
1617483 TTAGTTTTA
1 TTAGTTTTA
1617492 TGGTATCTTA
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
16 14 0.58
17 10 0.42
ACGTcount: A:0.24, C:0.00, G:0.15, T:0.61
Consensus pattern (17 bp):
TTAGTTTTAGTTTAAGT
Found at i:1634824 original size:14 final size:14
Alignment explanation
Indices: 1634805--1634834 Score: 60
Period size: 14 Copynumber: 2.1 Consensus size: 14
1634795 TCGCTTGATT
1634805 ATTGGTTGAGAACA
1 ATTGGTTGAGAACA
1634819 ATTGGTTGAGAACA
1 ATTGGTTGAGAACA
1634833 AT
1 AT
1634835 GAAGTATGGC
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.37, C:0.07, G:0.27, T:0.30
Consensus pattern (14 bp):
ATTGGTTGAGAACA
Found at i:1662193 original size:31 final size:31
Alignment explanation
Indices: 1662132--1662193 Score: 88
Period size: 31 Copynumber: 2.0 Consensus size: 31
1662122 TAAACTTGAC
* *
1662132 TCAACTCAGAATTTAATCGGGATACGATGTG
1 TCAACTCAGAATTTAATCAGGATACAATGTG
* *
1662163 TCAACTTAGAATTTAATCAGGATCCAATGTG
1 TCAACTCAGAATTTAATCAGGATACAATGTG
1662194 ACTACTTAAT
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
31 27 1.00
ACGTcount: A:0.34, C:0.16, G:0.19, T:0.31
Consensus pattern (31 bp):
TCAACTCAGAATTTAATCAGGATACAATGTG
Found at i:1662201 original size:31 final size:31
Alignment explanation
Indices: 1662133--1662201 Score: 84
Period size: 31 Copynumber: 2.2 Consensus size: 31
1662123 AAACTTGACT
* * * *
1662133 CAACTCAGAATTTAATCGGGATACGATGTGT
1 CAACTTAGAATTTAATCAGGATACAATGTGA
*
1662164 CAACTTAGAATTTAATCAGGATCCAATGTGA
1 CAACTTAGAATTTAATCAGGATACAATGTGA
*
1662195 CTACTTA
1 CAACTTA
1662202 ATACGGTAGG
Statistics
Matches: 32, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
31 32 1.00
ACGTcount: A:0.35, C:0.17, G:0.17, T:0.30
Consensus pattern (31 bp):
CAACTTAGAATTTAATCAGGATACAATGTGA
Found at i:1667310 original size:16 final size:16
Alignment explanation
Indices: 1667289--1667319 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
1667279 TATGTTAGAT
1667289 CATATAAATTTGAAAC
1 CATATAAATTTGAAAC
*
1667305 CATATATATTTGAAA
1 CATATAAATTTGAAA
1667320 AAAAATAAGA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.48, C:0.10, G:0.06, T:0.35
Consensus pattern (16 bp):
CATATAAATTTGAAAC
Found at i:1667492 original size:18 final size:18
Alignment explanation
Indices: 1667469--1667512 Score: 54
Period size: 18 Copynumber: 2.4 Consensus size: 18
1667459 TTTTTAAAAA
*
1667469 TATAAATTTTGAAATTTT
1 TATAAATTTTGAAAATTT
*
1667487 TATAAATATTTTAAAATTT
1 TATAAAT-TTTGAAAATTT
1667506 TA-AAATT
1 TATAAATT
1667513 ACTTTAATTT
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
17 1 0.04
18 11 0.48
19 11 0.48
ACGTcount: A:0.45, C:0.00, G:0.02, T:0.52
Consensus pattern (18 bp):
TATAAATTTTGAAAATTT
Found at i:1667524 original size:18 final size:19
Alignment explanation
Indices: 1667480--1667530 Score: 50
Period size: 19 Copynumber: 2.6 Consensus size: 19
1667470 ATAAATTTTG
*
1667480 AAATTTTTATAAATATTTT
1 AAATTTTTATAAATACTTT
*
1667499 AAAATTTTA-AAATTACTTT
1 AAATTTTTATAAA-TACTTT
*
1667518 AATTTTTTTATAA
1 AA-ATTTTTATAA
1667531 TTATTGTTGG
Statistics
Matches: 25, Mismatches: 4, Indels: 4
0.76 0.12 0.12
Matches are distributed among these distances:
18 3 0.12
19 15 0.60
20 5 0.20
21 2 0.08
ACGTcount: A:0.43, C:0.02, G:0.00, T:0.55
Consensus pattern (19 bp):
AAATTTTTATAAATACTTT
Found at i:1669274 original size:25 final size:25
Alignment explanation
Indices: 1669230--1669364 Score: 139
Period size: 25 Copynumber: 5.3 Consensus size: 25
1669220 TGGCTCGTAT
*
1669230 GAGCTTCCTGA-TAATTGGCTCTCTG
1 GAGCTTCCTGATTAA-TGGCTCTCTA
* *
1669255 GAGCTTCCTGATTAAAGGCTCTTTCA
1 GAGCTTCCTGATTAATGGCTCTCT-A
*
1669281 TGAGCTTCTTGATTAATGGCTCTCTA
1 -GAGCTTCCTGATTAATGGCTCTCTA
* * *
1669307 GAGCTACCCGA-TATATGGCTCTCTT
1 GAGCTTCCTGATTA-ATGGCTCTCTA
*
1669332 GAGCTTCCCGATTAATGGCTCTCTA
1 GAGCTTCCTGATTAATGGCTCTCTA
*
1669357 AAGCTTCC
1 GAGCTTCC
1669365 CTGGATATTG
Statistics
Matches: 92, Mismatches: 13, Indels: 10
0.80 0.11 0.09
Matches are distributed among these distances:
24 2 0.02
25 63 0.68
26 6 0.07
27 21 0.23
ACGTcount: A:0.20, C:0.25, G:0.20, T:0.35
Consensus pattern (25 bp):
GAGCTTCCTGATTAATGGCTCTCTA
Found at i:1669327 original size:52 final size:50
Alignment explanation
Indices: 1669208--1669452 Score: 182
Period size: 50 Copynumber: 4.9 Consensus size: 50
1669198 GTTCTCATGG
* *
1669208 GCTTCCC-ATTTATGGCTCGT-ATGAGCTTCCTGA-TAATTGGCTCTCTGGA
1 GCTTCCCGATATATGGCTC-TCATGAGCTTCCTGATTAA-TGGCTCTCTAGA
* * *
1669257 GCTTCCTGAT-TAAAGGCTCTTTCATGAGCTTCTTGATTAATGGCTCTCTAGA
1 GCTTCCCGATAT-ATGGCTC--TCATGAGCTTCCTGATTAATGGCTCTCTAGA
* * * *
1669309 GCTACCCGATATATGGCTCTCTTGAGCTTCCCGATTAATGGCTCTCTAAA
1 GCTTCCCGATATATGGCTCTCATGAGCTTCCTGATTAATGGCTCTCTAGA
* * * *
1669359 GCTTCCCTGGATAT-TGGCTCGCATGAGTTTCCTAATT-ACGGCTCTC-ATGA
1 GCTTCCC--GATATATGGCTCTCATGAGCTTCCTGATTAATGGCTCTCTA-GA
** * * * *
1669409 GCTTTTCGTTACATGGCTCACATGTGCTTCCTG-TTATATGGCTC
1 GCTTCCCGATATATGGCTCTCATGAGCTTCCTGATTA-ATGGCTC
1669453 GAAAGAGCTA
Statistics
Matches: 155, Mismatches: 29, Indels: 23
0.75 0.14 0.11
Matches are distributed among these distances:
48 5 0.03
49 24 0.15
50 61 0.39
51 19 0.12
52 42 0.27
53 4 0.03
ACGTcount: A:0.18, C:0.25, G:0.20, T:0.36
Consensus pattern (50 bp):
GCTTCCCGATATATGGCTCTCATGAGCTTCCTGATTAATGGCTCTCTAGA
Found at i:1669365 original size:25 final size:25
Alignment explanation
Indices: 1669208--1669365 Score: 135
Period size: 25 Copynumber: 6.3 Consensus size: 25
1669198 GTTCTCATGG
* *
1669208 GCTTCCC-ATTTATGGCTC-GTATGA
1 GCTTCCCGATTAATGGCTCTCTA-GA
* *
1669232 GCTTCCTGA-TAATTGGCTCTCTGGA
1 GCTTCCCGATTAA-TGGCTCTCTAGA
* * *
1669257 GCTTCCTGATTAAAGGCTCTTTCATGA
1 GCTTCCCGATTAATGGCTCTCT-A-GA
**
1669284 GCTTCTTGATTAATGGCTCTCTAGA
1 GCTTCCCGATTAATGGCTCTCTAGA
* *
1669309 GCTACCCGA-TATATGGCTCTCTTGA
1 GCTTCCCGATTA-ATGGCTCTCTAGA
*
1669334 GCTTCCCGATTAATGGCTCTCTAAA
1 GCTTCCCGATTAATGGCTCTCTAGA
1669359 GCTTCCC
1 GCTTCCC
1669366 TGGATATTGG
Statistics
Matches: 109, Mismatches: 17, Indels: 15
0.77 0.12 0.11
Matches are distributed among these distances:
24 10 0.09
25 71 0.65
26 7 0.06
27 21 0.19
ACGTcount: A:0.19, C:0.26, G:0.20, T:0.35
Consensus pattern (25 bp):
GCTTCCCGATTAATGGCTCTCTAGA
Found at i:1676917 original size:8 final size:8
Alignment explanation
Indices: 1676904--1676928 Score: 50
Period size: 8 Copynumber: 3.1 Consensus size: 8
1676894 TTTTGCCTCA
1676904 AATACATC
1 AATACATC
1676912 AATACATC
1 AATACATC
1676920 AATACATC
1 AATACATC
1676928 A
1 A
1676929 GTACGCTAAT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 17 1.00
ACGTcount: A:0.52, C:0.24, G:0.00, T:0.24
Consensus pattern (8 bp):
AATACATC
Found at i:1677880 original size:21 final size:23
Alignment explanation
Indices: 1677855--1677902 Score: 57
Period size: 21 Copynumber: 2.2 Consensus size: 23
1677845 GCCAAAAAAT
*
1677855 ATTTTTA-TCATTTCAAT-TAAA
1 ATTTTTATTAATTTCAATATAAA
*
1677876 A-TTTTATTAATTTTAATATAAA
1 ATTTTTATTAATTTCAATATAAA
1677898 ATTTT
1 ATTTT
1677903 AATAAATACA
Statistics
Matches: 22, Mismatches: 2, Indels: 4
0.79 0.07 0.14
Matches are distributed among these distances:
20 5 0.23
21 9 0.41
22 5 0.23
23 3 0.14
ACGTcount: A:0.40, C:0.04, G:0.00, T:0.56
Consensus pattern (23 bp):
ATTTTTATTAATTTCAATATAAA
Found at i:1686922 original size:8 final size:8
Alignment explanation
Indices: 1686909--1686933 Score: 50
Period size: 8 Copynumber: 3.1 Consensus size: 8
1686899 TTTTGCCTCA
1686909 AATACATC
1 AATACATC
1686917 AATACATC
1 AATACATC
1686925 AATACATC
1 AATACATC
1686933 A
1 A
1686934 GTACGCTAAT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 17 1.00
ACGTcount: A:0.52, C:0.24, G:0.00, T:0.24
Consensus pattern (8 bp):
AATACATC
Found at i:1687821 original size:10 final size:10
Alignment explanation
Indices: 1687806--1687830 Score: 50
Period size: 10 Copynumber: 2.5 Consensus size: 10
1687796 TAAAATATTT
1687806 TATATTTATA
1 TATATTTATA
1687816 TATATTTATA
1 TATATTTATA
1687826 TATAT
1 TATAT
1687831 ATAAAACATA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 15 1.00
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (10 bp):
TATATTTATA
Found at i:1688153 original size:21 final size:23
Alignment explanation
Indices: 1688128--1688175 Score: 57
Period size: 21 Copynumber: 2.2 Consensus size: 23
1688118 GCCAAAAAAT
*
1688128 ATTTTTA-TCATTTCAAT-TAAA
1 ATTTTTATTAATTTCAATATAAA
*
1688149 A-TTTTATTAATTTTAATATAAA
1 ATTTTTATTAATTTCAATATAAA
1688171 ATTTT
1 ATTTT
1688176 AATAAATACA
Statistics
Matches: 22, Mismatches: 2, Indels: 4
0.79 0.07 0.14
Matches are distributed among these distances:
20 5 0.23
21 9 0.41
22 5 0.23
23 3 0.14
ACGTcount: A:0.40, C:0.04, G:0.00, T:0.56
Consensus pattern (23 bp):
ATTTTTATTAATTTCAATATAAA
Found at i:1691177 original size:13 final size:13
Alignment explanation
Indices: 1691158--1691199 Score: 66
Period size: 13 Copynumber: 3.2 Consensus size: 13
1691148 GGTGCAAAAG
*
1691158 AAGCACTTTTCCA
1 AAGCACTTTTCAA
*
1691171 CAGCACTTTTCAA
1 AAGCACTTTTCAA
1691184 AAGCACTTTTCAA
1 AAGCACTTTTCAA
1691197 AAG
1 AAG
1691200 TAATGAAGAA
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
13 26 1.00
ACGTcount: A:0.36, C:0.26, G:0.10, T:0.29
Consensus pattern (13 bp):
AAGCACTTTTCAA
Found at i:1691470 original size:15 final size:15
Alignment explanation
Indices: 1691450--1691487 Score: 51
Period size: 15 Copynumber: 2.5 Consensus size: 15
1691440 CACAATGTAA
1691450 ATAAAAAATCAT-TAT
1 ATAAAAAAT-ATATAT
*
1691465 ATAAAAAATATATTT
1 ATAAAAAATATATAT
1691480 ATAAAAAA
1 ATAAAAAA
1691488 AATTAATACA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
14 2 0.10
15 19 0.90
ACGTcount: A:0.66, C:0.03, G:0.00, T:0.32
Consensus pattern (15 bp):
ATAAAAAATATATAT
Found at i:1694418 original size:4 final size:4
Alignment explanation
Indices: 1694409--1694433 Score: 50
Period size: 4 Copynumber: 6.2 Consensus size: 4
1694399 TACTAAATTT
1694409 ATAA ATAA ATAA ATAA ATAA ATAA A
1 ATAA ATAA ATAA ATAA ATAA ATAA A
1694434 AATCTTTGCT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 21 1.00
ACGTcount: A:0.76, C:0.00, G:0.00, T:0.24
Consensus pattern (4 bp):
ATAA
Found at i:1695691 original size:16 final size:17
Alignment explanation
Indices: 1695654--1695691 Score: 53
Period size: 17 Copynumber: 2.3 Consensus size: 17
1695644 TTTTTTAAAA
1695654 ATTAAAAAATATAAATT
1 ATTAAAAAATATAAATT
1695671 ATTAAAATAATA-AAATT
1 ATTAAAA-AATATAAATT
1695688 -TTAA
1 ATTAA
1695692 CTTATATAAA
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
16 4 0.20
17 12 0.60
18 4 0.20
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (17 bp):
ATTAAAAAATATAAATT
Found at i:1696788 original size:29 final size:29
Alignment explanation
Indices: 1696755--1696812 Score: 82
Period size: 29 Copynumber: 2.0 Consensus size: 29
1696745 TTTTAATTTA
*
1696755 ATGTGTAATTTGATACAT-AAACTTTGATT
1 ATGTGCAATTT-ATACATGAAACTTTGATT
*
1696784 ATGTGCAATTTATATATGAAACTTTGATT
1 ATGTGCAATTTATACATGAAACTTTGATT
1696813 GTGATTCTAT
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
28 5 0.19
29 21 0.81
ACGTcount: A:0.34, C:0.07, G:0.14, T:0.45
Consensus pattern (29 bp):
ATGTGCAATTTATACATGAAACTTTGATT
Found at i:1701763 original size:77 final size:78
Alignment explanation
Indices: 1701633--1701791 Score: 266
Period size: 77 Copynumber: 2.0 Consensus size: 78
1701623 TCCCATCTTA
*
1701633 ATTATTACTAAAATGGCTTAAAAGACTCTTCTGATATCAGTATCCTACCCAAATCTCAACTCACC
1 ATTATTACAAAAATGGCTTAAAAGAC-CTTCTGATATCAGTATCCTACCCAAATCTCAACTCACC
1701698 CAATCTTCATAAAC
65 CAATCTTCATAAAC
* *
1701712 ATTATTACAAAAATGGCTTAAAAGA-CTTCTTATATCAGTATCCTACCCAAATCTCAACTCACCT
1 ATTATTACAAAAATGGCTTAAAAGACCTTCTGATATCAGTATCCTACCCAAATCTCAACTCACCC
*
1701776 GATCTTCATAAAC
66 AATCTTCATAAAC
1701789 ATT
1 ATT
1701792 GCTAGTGGCT
Statistics
Matches: 76, Mismatches: 4, Indels: 2
0.93 0.05 0.02
Matches are distributed among these distances:
77 52 0.68
79 24 0.32
ACGTcount: A:0.37, C:0.25, G:0.06, T:0.31
Consensus pattern (78 bp):
ATTATTACAAAAATGGCTTAAAAGACCTTCTGATATCAGTATCCTACCCAAATCTCAACTCACCC
AATCTTCATAAAC
Found at i:1704209 original size:46 final size:46
Alignment explanation
Indices: 1704134--1704235 Score: 136
Period size: 46 Copynumber: 2.2 Consensus size: 46
1704124 AGAAAAAGTT
* * * *
1704134 CGCTAAAAAGGAGCCTCCCCTTCTCATTAAGGGGTTACTCTCGTGC
1 CGCTAAAAAGGACCCTCCCCTCCTCATTAAGGGGTCACCCTCGTGC
1704180 CGCTAAAAAGGACCCTCCCCCTCCT-ATTAAGGGGTCACCCTCGTGC
1 CGCTAAAAAGGACCCT-CCCCTCCTCATTAAGGGGTCACCCTCGTGC
*
1704226 CAC-AAAAAGG
1 CGCTAAAAAGG
1704236 GGTCGCCTTG
Statistics
Matches: 50, Mismatches: 5, Indels: 3
0.86 0.09 0.05
Matches are distributed among these distances:
45 7 0.14
46 36 0.72
47 7 0.14
ACGTcount: A:0.25, C:0.33, G:0.21, T:0.21
Consensus pattern (46 bp):
CGCTAAAAAGGACCCTCCCCTCCTCATTAAGGGGTCACCCTCGTGC
Found at i:1704956 original size:12 final size:12
Alignment explanation
Indices: 1704939--1704965 Score: 54
Period size: 12 Copynumber: 2.2 Consensus size: 12
1704929 AGAGATACAA
1704939 CCCCTCTTGATG
1 CCCCTCTTGATG
1704951 CCCCTCTTGATG
1 CCCCTCTTGATG
1704963 CCC
1 CCC
1704966 TAAAAGGGAT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 15 1.00
ACGTcount: A:0.07, C:0.48, G:0.15, T:0.30
Consensus pattern (12 bp):
CCCCTCTTGATG
Found at i:1705350 original size:98 final size:96
Alignment explanation
Indices: 1705248--1705436 Score: 211
Period size: 98 Copynumber: 1.9 Consensus size: 96
1705238 TCTTAGGCGT
** * *
1705248 CTTATTTTGTCTCTTCAAGCTCGCTTCG-CAAGTTCGCCT-CTAAGGCATCTCATTTTGCCTCTT
1 CTTATTTTACCTCTTCAAGCTCGCTTCGCCAAATTCGCATAC-AA-GCATCTCATTTTGCCTC-T
* * *
1705311 TATAAGTCTGCTTCACCAGATTCATCTCTAAATTG
63 T-CAAGTCTGCTTCACCAGAATCACCTCTAAATTG
* * * * *
1705346 CTTATTTTACCTCTTTAGGCTCGCTTTGCCAAATTTGCATACAAGCATCTCATTTTGTCTCTTCA
1 CTTATTTTACCTCTTCAAGCTCGCTTCGCCAAATTCGCATACAAGCATCTCATTTTGCCTCTTCA
*
1705411 AGTCTGCTTCACTAGAATCACCTCTA
66 AGTCTGCTTCACCAGAATCACCTCTA
1705437 CATGCATCTA
Statistics
Matches: 76, Mismatches: 13, Indels: 6
0.80 0.14 0.06
Matches are distributed among these distances:
96 24 0.32
97 2 0.03
98 39 0.51
99 10 0.13
100 1 0.01
ACGTcount: A:0.21, C:0.28, G:0.12, T:0.40
Consensus pattern (96 bp):
CTTATTTTACCTCTTCAAGCTCGCTTCGCCAAATTCGCATACAAGCATCTCATTTTGCCTCTTCA
AGTCTGCTTCACCAGAATCACCTCTAAATTG
Found at i:1714149 original size:41 final size:42
Alignment explanation
Indices: 1714088--1714170 Score: 132
Period size: 41 Copynumber: 2.0 Consensus size: 42
1714078 AATTTAACAC
* *
1714088 TATTATTAAGTCATGATTGAAATTTTAAAA-TTTGAAAAAGT
1 TATTATTAAGACATAATTGAAATTTTAAAATTTTGAAAAAGT
*
1714129 TATTGTTAAGACATAATTGAAATTTTAAAATTTTGAAAAAGT
1 TATTATTAAGACATAATTGAAATTTTAAAATTTTGAAAAAGT
1714171 ATGAGAAATA
Statistics
Matches: 38, Mismatches: 3, Indels: 1
0.90 0.07 0.02
Matches are distributed among these distances:
41 27 0.71
42 11 0.29
ACGTcount: A:0.45, C:0.02, G:0.12, T:0.41
Consensus pattern (42 bp):
TATTATTAAGACATAATTGAAATTTTAAAATTTTGAAAAAGT
Found at i:1715884 original size:31 final size:31
Alignment explanation
Indices: 1715822--1715884 Score: 81
Period size: 31 Copynumber: 2.0 Consensus size: 31
1715812 CAACCTAGTG
* *
1715822 ACTTAAATAAAAACTTTTAAATAATTCAGTA
1 ACTTAAATAAAAACTTTCAAATAATTAAGTA
* * *
1715853 ACTTAAATGAAAACTTTCGAATAGTTAAGTA
1 ACTTAAATAAAAACTTTCAAATAATTAAGTA
1715884 A
1 A
1715885 TCATTTTGTA
Statistics
Matches: 27, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
31 27 1.00
ACGTcount: A:0.49, C:0.10, G:0.08, T:0.33
Consensus pattern (31 bp):
ACTTAAATAAAAACTTTCAAATAATTAAGTA
Found at i:1717393 original size:12 final size:12
Alignment explanation
Indices: 1717376--1717400 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
1717366 TGCAAATGCA
1717376 AAAAAAAAAAAG
1 AAAAAAAAAAAG
1717388 AAAAAAAAAAAG
1 AAAAAAAAAAAG
1717400 A
1 A
1717401 GTTAGAATTC
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.92, C:0.00, G:0.08, T:0.00
Consensus pattern (12 bp):
AAAAAAAAAAAG
Found at i:1718135 original size:30 final size:30
Alignment explanation
Indices: 1718099--1718171 Score: 92
Period size: 30 Copynumber: 2.4 Consensus size: 30
1718089 GGAGCATAAG
* * *
1718099 GAGGAGGGTATCCCTGAGCAGGGTATCCTT
1 GAGGAGGATATCCCTGAGCAGGATAACCTT
* * *
1718129 GAGGAGGATAACCTTGAGGAGGATAACCTT
1 GAGGAGGATATCCCTGAGCAGGATAACCTT
1718159 GAGGAGGATATCC
1 GAGGAGGATATCC
1718172 TGGCGGTGGA
Statistics
Matches: 36, Mismatches: 7, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
30 36 1.00
ACGTcount: A:0.27, C:0.16, G:0.36, T:0.21
Consensus pattern (30 bp):
GAGGAGGATATCCCTGAGCAGGATAACCTT
Found at i:1718165 original size:18 final size:15
Alignment explanation
Indices: 1718125--1718168 Score: 88
Period size: 15 Copynumber: 2.9 Consensus size: 15
1718115 AGCAGGGTAT
1718125 CCTTGAGGAGGATAA
1 CCTTGAGGAGGATAA
1718140 CCTTGAGGAGGATAA
1 CCTTGAGGAGGATAA
1718155 CCTTGAGGAGGATA
1 CCTTGAGGAGGATA
1718169 TCCTGGCGGT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 29 1.00
ACGTcount: A:0.32, C:0.14, G:0.34, T:0.20
Consensus pattern (15 bp):
CCTTGAGGAGGATAA
Found at i:1718183 original size:30 final size:30
Alignment explanation
Indices: 1718125--1718183 Score: 82
Period size: 30 Copynumber: 2.0 Consensus size: 30
1718115 AGCAGGGTAT
*
1718125 CCTTGAGGAGGATAACCTTGAGGAGGATAA
1 CCTTGAGGAGGATAACCTGGAGGAGGATAA
* * *
1718155 CCTTGAGGAGGATATCCTGGCGGTGGATA
1 CCTTGAGGAGGATAACCTGGAGGAGGATA
1718184 CGCTGCTGGT
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
30 25 1.00
ACGTcount: A:0.27, C:0.15, G:0.36, T:0.22
Consensus pattern (30 bp):
CCTTGAGGAGGATAACCTGGAGGAGGATAA
Found at i:1724585 original size:21 final size:22
Alignment explanation
Indices: 1724556--1724633 Score: 63
Period size: 23 Copynumber: 3.5 Consensus size: 22
1724546 ACATTAAAAA
*
1724556 ATATGAAAAAT-GGAAATAAAT
1 ATATAAAAAATAGGAAATAAAT
1724577 ATATAAAAAATTCA-GAAA-AATAT
1 ATATAAAAAA-T-AGGAAATAA-AT
**
1724600 ATATAAAATCTAGGAAATAAAT
1 ATATAAAAAATAGGAAATAAAT
*
1724622 AAATAAATAAAT
1 ATATAAA-AAAT
1724634 TATAAAAATA
Statistics
Matches: 44, Mismatches: 6, Indels: 12
0.71 0.10 0.19
Matches are distributed among these distances:
21 10 0.23
22 16 0.36
23 18 0.41
ACGTcount: A:0.64, C:0.03, G:0.08, T:0.26
Consensus pattern (22 bp):
ATATAAAAAATAGGAAATAAAT
Found at i:1734267 original size:25 final size:26
Alignment explanation
Indices: 1734239--1734287 Score: 66
Period size: 25 Copynumber: 1.9 Consensus size: 26
1734229 ATAAAATAAA
*
1734239 ATAAAATATAACATAA-TT-ATATATG
1 ATAAAAT-TAAAATAAGTTAATATATG
1734264 ATAAAATTAAAATAAGTTAATATA
1 ATAAAATTAAAATAAGTTAATATA
1734288 AATATACCAA
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
24 7 0.33
25 9 0.43
26 5 0.24
ACGTcount: A:0.59, C:0.02, G:0.04, T:0.35
Consensus pattern (26 bp):
ATAAAATTAAAATAAGTTAATATATG
Found at i:1738187 original size:33 final size:33
Alignment explanation
Indices: 1738145--1738300 Score: 108
Period size: 33 Copynumber: 4.6 Consensus size: 33
1738135 AAGATACGGT
1738145 GGAATCAGCACTTAGCAACCACCAATGAATCGG
1 GGAATCAGCACTTAGCAACCACCAATGAATCGG
* * *
1738178 GGAATCAGCACTTAGTAATC-CC--T---TGGG
1 GGAATCAGCACTTAGCAACCACCAATGAATCGG
* *
1738205 GGAATCAGCACTTAGCAACCCCCTTTATATTTAAAGATACGG
1 GGAATCAGCACTTAGCAACCACC---A-A--T-GA-AT-CGG
* * *
1738247 TGGAATCAGCACTTAGCAACCACCATTGAGTCGA
1 -GGAATCAGCACTTAGCAACCACCAATGAATCGG
1738281 GGAATCAGCACTTAGCAACC
1 GGAATCAGCACTTAGCAACC
1738301 CCTTCATATT
Statistics
Matches: 96, Mismatches: 11, Indels: 32
0.69 0.08 0.23
Matches are distributed among these distances:
27 21 0.22
28 2 0.02
30 1 0.01
32 2 0.02
33 38 0.40
34 2 0.02
35 1 0.01
36 2 0.02
37 1 0.01
40 1 0.01
41 1 0.01
42 2 0.02
43 22 0.23
ACGTcount: A:0.33, C:0.26, G:0.21, T:0.21
Consensus pattern (33 bp):
GGAATCAGCACTTAGCAACCACCAATGAATCGG
Found at i:1738285 original size:103 final size:103
Alignment explanation
Indices: 1738100--1738304 Score: 365
Period size: 103 Copynumber: 2.0 Consensus size: 103
1738090 NNNNNNNNNN
1738100 GGGGAATCAGCACTTAGCAACCCCCTTTATATTTAAAGATACGGTGGAATCAGCACTTAGCAACC
1 GGGGAATCAGCACTTAGCAACCCCCTTTATATTTAAAGATACGGTGGAATCAGCACTTAGCAACC
* * *
1738165 ACCAATGAATCGGGGAATCAGCACTTAGTAATCCCTTG
66 ACCAATGAATCGAGGAATCAGCACTTAGCAACCCCTTG
1738203 GGGGAATCAGCACTTAGCAACCCCCTTTATATTTAAAGATACGGTGGAATCAGCACTTAGCAACC
1 GGGGAATCAGCACTTAGCAACCCCCTTTATATTTAAAGATACGGTGGAATCAGCACTTAGCAACC
* *
1738268 ACCATTGAGTCGAGGAATCAGCACTTAGCAACCCCTT
66 ACCAATGAATCGAGGAATCAGCACTTAGCAACCCCTT
1738305 CATATTCCAT
Statistics
Matches: 97, Mismatches: 5, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
103 97 1.00
ACGTcount: A:0.32, C:0.25, G:0.20, T:0.23
Consensus pattern (103 bp):
GGGGAATCAGCACTTAGCAACCCCCTTTATATTTAAAGATACGGTGGAATCAGCACTTAGCAACC
ACCAATGAATCGAGGAATCAGCACTTAGCAACCCCTTG
Found at i:1739348 original size:35 final size:36
Alignment explanation
Indices: 1739309--1739379 Score: 135
Period size: 35 Copynumber: 2.0 Consensus size: 36
1739299 ATTGACACTT
1739309 CTAACATGTAGAACTCAACTTTTGT-CTTTTTACAA
1 CTAACATGTAGAACTCAACTTTTGTACTTTTTACAA
1739344 CTAACATGTAGAACTCAACTTTTGTACTTTTTACAA
1 CTAACATGTAGAACTCAACTTTTGTACTTTTTACAA
1739380 TTTAGTCCTT
Statistics
Matches: 35, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
35 25 0.71
36 10 0.29
ACGTcount: A:0.32, C:0.20, G:0.08, T:0.39
Consensus pattern (36 bp):
CTAACATGTAGAACTCAACTTTTGTACTTTTTACAA
Found at i:1739443 original size:11 final size:12
Alignment explanation
Indices: 1739415--1739448 Score: 52
Period size: 11 Copynumber: 2.8 Consensus size: 12
1739405 GCCCAAACGT
1739415 CGAAATTTTTGAA
1 CGAAATTTTT-AA
1739428 CGAAATTTTT-A
1 CGAAATTTTTAA
1739439 CGAAATTTTT
1 CGAAATTTTT
1739449 CCGTAAAATT
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
11 11 0.52
13 10 0.48
ACGTcount: A:0.35, C:0.09, G:0.12, T:0.44
Consensus pattern (12 bp):
CGAAATTTTTAA
Found at i:1743289 original size:10 final size:10
Alignment explanation
Indices: 1743274--1743308 Score: 54
Period size: 10 Copynumber: 3.6 Consensus size: 10
1743264 AAAAAATATG
1743274 TATATAGATA
1 TATATAGATA
1743284 TATATAGATA
1 TATATAGATA
*
1743294 TGTATA-ATA
1 TATATAGATA
1743303 TATATA
1 TATATA
1743309 AATTATAAAA
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
9 8 0.35
10 15 0.65
ACGTcount: A:0.49, C:0.00, G:0.09, T:0.43
Consensus pattern (10 bp):
TATATAGATA
Found at i:1743321 original size:19 final size:20
Alignment explanation
Indices: 1743299--1743341 Score: 52
Period size: 21 Copynumber: 2.1 Consensus size: 20
1743289 AGATATGTAT
1743299 AATATATA-TAAATTATAAA
1 AATATATACTAAATTATAAA
* *
1743318 AATATGTACGTATATTATAAA
1 AATATATAC-TAAATTATAAA
1743339 AAT
1 AAT
1743342 GTATGCATGT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
19 7 0.35
21 13 0.65
ACGTcount: A:0.56, C:0.02, G:0.05, T:0.37
Consensus pattern (20 bp):
AATATATACTAAATTATAAA
Found at i:1743346 original size:23 final size:21
Alignment explanation
Indices: 1743310--1743361 Score: 59
Period size: 23 Copynumber: 2.3 Consensus size: 21
1743300 ATATATATAA
*
1743310 ATTATAAAAATATGTACGTAT
1 ATTATAAAAATATGCACGTAT
*
1743331 ATTATAAAAATGTATGCATGTAT
1 ATTATAAAAA--TATGCACGTAT
1743354 ATATATAA
1 AT-TATAA
1743362 TAAAATTTAA
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
21 10 0.38
23 11 0.42
24 5 0.19
ACGTcount: A:0.48, C:0.04, G:0.10, T:0.38
Consensus pattern (21 bp):
ATTATAAAAATATGCACGTAT
Found at i:1747056 original size:27 final size:27
Alignment explanation
Indices: 1747014--1747074 Score: 106
Period size: 27 Copynumber: 2.3 Consensus size: 27
1747004 GGGCAATAGC
1747014 TTCACATTGGTCGCGTATTGAGGAGGG
1 TTCACATTGGTCGCGTATTGAGGAGGG
*
1747041 TTCACATTGGTTGCGTATTGAGGAGGG
1 TTCACATTGGTCGCGTATTGAGGAGGG
1747068 TT-ACATT
1 TTCACATT
1747075 AAACTTAATA
Statistics
Matches: 33, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
26 5 0.15
27 28 0.85
ACGTcount: A:0.20, C:0.13, G:0.33, T:0.34
Consensus pattern (27 bp):
TTCACATTGGTCGCGTATTGAGGAGGG
Found at i:1747185 original size:19 final size:19
Alignment explanation
Indices: 1747163--1747201 Score: 78
Period size: 19 Copynumber: 2.1 Consensus size: 19
1747153 GACTGACGAC
1747163 GTGGTTTTACAATGACAAT
1 GTGGTTTTACAATGACAAT
1747182 GTGGTTTTACAATGACAAT
1 GTGGTTTTACAATGACAAT
1747201 G
1 G
1747202 GGAGAGGGTA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.31, C:0.10, G:0.23, T:0.36
Consensus pattern (19 bp):
GTGGTTTTACAATGACAAT
Found at i:1747674 original size:9 final size:8
Alignment explanation
Indices: 1747652--1747686 Score: 52
Period size: 8 Copynumber: 4.2 Consensus size: 8
1747642 CATCAGTTTG
*
1747652 TTAAAAAC
1 TTAAAAAA
1747660 TTAAAAGAA
1 TTAAAA-AA
1747669 TTAAAAAA
1 TTAAAAAA
1747677 TTAAAAAA
1 TTAAAAAA
1747685 TT
1 TT
1747687 CTGTTTCAAT
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
8 18 0.72
9 7 0.28
ACGTcount: A:0.66, C:0.03, G:0.03, T:0.29
Consensus pattern (8 bp):
TTAAAAAA
Found at i:1747674 original size:17 final size:16
Alignment explanation
Indices: 1747652--1747686 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 16
1747642 CATCAGTTTG
*
1747652 TTAAAAACTTAAAAGAA
1 TTAAAAAATTAAAA-AA
1747669 TTAAAAAATTAAAAAA
1 TTAAAAAATTAAAAAA
1747685 TT
1 TT
1747687 CTGTTTCAAT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
16 4 0.24
17 13 0.76
ACGTcount: A:0.66, C:0.03, G:0.03, T:0.29
Consensus pattern (16 bp):
TTAAAAAATTAAAAAA
Found at i:1754804 original size:395 final size:396
Alignment explanation
Indices: 1754074--1754865 Score: 1577
Period size: 395 Copynumber: 2.0 Consensus size: 396
1754064 TAAAAATGGT
1754074 TTACCAGTAGTTAGGATCAAGATAGGCCGAAGCCGACGAAGGAGGGTCGGTTTTTTTATGATCTG
1 TTACCAGTAGTTAGGATCAAGATAGGCCGAAGCCGACGAAGGAGGGTCGGTTTTTTTATGATCTG
1754139 AGTCTGGGTTTTGAGCCGTATCCATTTTTTTTTTCTTTTTGGTTATTAAGTTCTTCCCCTTGTGC
66 AGTCTGGGTTTTGAGCCGTATCCATTTTTTTTTTCTTTTTGGTTATTAAGTTCTTCCCCTTGTGC
1754204 TGCTTTATTCACCTCTGGGTTTCCTGGCCCTTAAACCCTAATCAAATCCTCAGTGTTAAAGAAAA
131 TGCTTTATTCACCTCTGGGTTTCCTGGCCCTTAAACCCTAATCAAATCCTCAGTGTTAAAGAAAA
1754269 AAAAAACGAAGATTTAGTCCCAAACTTACAATTTTTCACGTTTTGATTTCTAATTTTCGGTCAAA
196 AAAAAACGAAGATTTAGTCCCAAACTTACAATTTTTCACGTTTTGATTTCTAATTTTCGGTCAAA
1754334 AACTTGATATTATTTTCAATTTGATCCCTAAACTTAAATTCCCGAGCTCAAGAATTAAATTTTTC
261 AACTTGATATTATTTTCAATTTGATCCCTAAACTTAAATTCCCGAGCTCAAGAATTAAATTTTTC
1754399 TAAATCTTTTTCATCCATTGAAATTTGGTGTAGGGGCATATAATTCTCCAATCAATTGAATTT-T
326 TAAATCTTTTTCATCCATTGAAATTTGGTGTAGGGGCATATAATTCTCCAATCAATTGAATTTAT
1754463 TTATAA
391 TTATAA
1754469 TTACCAGTAGTTAGGATCAAGATAGGCCGAAGCCGACGAAGGAGGGTCGGTTTTTTTATGATCTG
1 TTACCAGTAGTTAGGATCAAGATAGGCCGAAGCCGACGAAGGAGGGTCGGTTTTTTTATGATCTG
1754534 AGTCTGGGTTTTGAGCCGTATCCATTTTTTTTTTCTTTTTGGTTATTAAGTTCTTCCCCTTGTGC
66 AGTCTGGGTTTTGAGCCGTATCCATTTTTTTTTTCTTTTTGGTTATTAAGTTCTTCCCCTTGTGC
1754599 TGCTTTATTCACCTCTGGGTTTCCTGGCCCTTAAACCCTAATCAAATCCTCAGTGTTAAAGAAAA
131 TGCTTTATTCACCTCTGGGTTTCCTGGCCCTTAAACCCTAATCAAATCCTCAGTGTTAAAGAAAA
1754664 AAAAAACGAAGATTTAGTCCCAAACTTACAATTTTTCACGTTTTGATTTCTAATTTTCGGTCAAA
196 AAAAAACGAAGATTTAGTCCCAAACTTACAATTTTTCACGTTTTGATTTCTAATTTTCGGTCAAA
1754729 AACTTGATATTATTTTCAATTTGATCCCTAAACTTAAATTCCCGAGCTCAAGAATTAAATTTTTC
261 AACTTGATATTATTTTCAATTTGATCCCTAAACTTAAATTCCCGAGCTCAAGAATTAAATTTTTC
1754794 TAAATCTTTTTCATCCATTGAAATTTGGTGTAGGGGCATATAATTCTCCAATCAATTGAATTTAT
326 TAAATCTTTTTCATCCATTGAAATTTGGTGTAGGGGCATATAATTCTCCAATCAATTGAATTTAT
1754859 TTATAA
391 TTATAA
1754865 T
1 T
1754866 ATTAATTTAA
Statistics
Matches: 396, Mismatches: 0, Indels: 1
1.00 0.00 0.00
Matches are distributed among these distances:
395 388 0.98
396 8 0.02
ACGTcount: A:0.28, C:0.18, G:0.16, T:0.39
Consensus pattern (396 bp):
TTACCAGTAGTTAGGATCAAGATAGGCCGAAGCCGACGAAGGAGGGTCGGTTTTTTTATGATCTG
AGTCTGGGTTTTGAGCCGTATCCATTTTTTTTTTCTTTTTGGTTATTAAGTTCTTCCCCTTGTGC
TGCTTTATTCACCTCTGGGTTTCCTGGCCCTTAAACCCTAATCAAATCCTCAGTGTTAAAGAAAA
AAAAAACGAAGATTTAGTCCCAAACTTACAATTTTTCACGTTTTGATTTCTAATTTTCGGTCAAA
AACTTGATATTATTTTCAATTTGATCCCTAAACTTAAATTCCCGAGCTCAAGAATTAAATTTTTC
TAAATCTTTTTCATCCATTGAAATTTGGTGTAGGGGCATATAATTCTCCAATCAATTGAATTTAT
TTATAA
Found at i:1764319 original size:67 final size:67
Alignment explanation
Indices: 1764211--1764346 Score: 263
Period size: 67 Copynumber: 2.0 Consensus size: 67
1764201 AATCAATGAA
*
1764211 AAAATGTGTCATCAAATTTTGCAATGTCATAGAGAATAGATGTACCTGATACTAGCTCTCCTGAA
1 AAAATGTGTCATCAAATTTTGCAATGTCATAGAGAATAGATGTACCTGAAACTAGCTCTCCTGAA
1764276 GG
66 GG
1764278 AAAATGTGTCATCAAATTTTGCAATGTCATAGAGAATAGATGTACCTGAAACTAGCTCTCCTGAA
1 AAAATGTGTCATCAAATTTTGCAATGTCATAGAGAATAGATGTACCTGAAACTAGCTCTCCTGAA
1764343 GG
66 GG
1764345 AA
1 AA
1764347 GCTTTATTAC
Statistics
Matches: 68, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
67 68 1.00
ACGTcount: A:0.36, C:0.16, G:0.19, T:0.29
Consensus pattern (67 bp):
AAAATGTGTCATCAAATTTTGCAATGTCATAGAGAATAGATGTACCTGAAACTAGCTCTCCTGAA
GG
Found at i:1772445 original size:16 final size:16
Alignment explanation
Indices: 1772424--1772466 Score: 52
Period size: 18 Copynumber: 2.6 Consensus size: 16
1772414 TTTAATGTAT
*
1772424 TATAAATTACATAATA
1 TATAAATAACATAATA
1772440 TATAAAAATAACATAATA
1 TAT--AAATAACATAATA
1772458 TA-AAATAAC
1 TATAAATAAC
1772467 TTAAAAACGA
Statistics
Matches: 24, Mismatches: 1, Indels: 5
0.80 0.03 0.17
Matches are distributed among these distances:
15 7 0.29
16 3 0.12
18 14 0.58
ACGTcount: A:0.63, C:0.07, G:0.00, T:0.30
Consensus pattern (16 bp):
TATAAATAACATAATA
Found at i:1791114 original size:12 final size:12
Alignment explanation
Indices: 1791097--1791121 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
1791087 AGTAATTTCG
1791097 GGTCGGTTAACC
1 GGTCGGTTAACC
1791109 GGTCGGTTAACC
1 GGTCGGTTAACC
1791121 G
1 G
1791122 AATGAACACC
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.16, C:0.24, G:0.36, T:0.24
Consensus pattern (12 bp):
GGTCGGTTAACC
Found at i:1811401 original size:2 final size:2
Alignment explanation
Indices: 1811394--1811435 Score: 84
Period size: 2 Copynumber: 21.0 Consensus size: 2
1811384 ACCACCACCT
1811394 AG AG AG AG AG AG AG AG 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 AG AG AG AG AG AG AG AG
1811436 CAACCTCTAT
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 40 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
AG
Found at i:1817575 original size:128 final size:127
Alignment explanation
Indices: 1817315--1817580 Score: 324
Period size: 128 Copynumber: 2.1 Consensus size: 127
1817305 TTTAAACTAT
1817315 AAAAATTAATTAATTGCTTACGTGACAATCTACTTGGATGGCATGTCAACAAATTTAAAAAATAT
1 AAAAATTAATTAATTGCTTACGTGACAATCTACTTGGATGGCATGTCAACAAATTTAAAAAATAT
*** * * * ******
1817380 TAACTTTTCCATCCATTTGAGTAATTTGTAATTTTAAAAATTTTATGAATTATTAATTTTTTT
66 TAACTTTTCCATCCATTTGAGTAATTTGTAATAAGAAAAAATTTAAGAACTA-TAATAGAGAC
1817443 AAAAATTAATTAATTGCTTACGTGACAATCTACTTGGATGGCATGTCAACAAATTTAAAAAATAT
1 AAAAATTAATTAATTGCTTACGTGACAATCTACTTGGATGGCATGTCAACAAATTTAAAAAATAT
*
1817508 TAACTTTTCCATCCATTTTAGAGTAATTTG-ACA-AAGAACATAAATTTAAGGACTA-AA-AGAG
66 TAACTTTTCCATCCA-TTT-GAGTAATTTGTA-ATAAGAA-A-AAATTTAAGAACTATAATAGAG
1817569 AC
126 AC
1817571 AAAAAGTTAA
1 AAAAA-TTAA
1817581 ATACATGACT
Statistics
Matches: 119, Mismatches: 13, Indels: 11
0.83 0.09 0.08
Matches are distributed among these distances:
128 85 0.71
129 12 0.10
130 12 0.10
131 10 0.08
ACGTcount: A:0.41, C:0.11, G:0.11, T:0.36
Consensus pattern (127 bp):
AAAAATTAATTAATTGCTTACGTGACAATCTACTTGGATGGCATGTCAACAAATTTAAAAAATAT
TAACTTTTCCATCCATTTGAGTAATTTGTAATAAGAAAAAATTTAAGAACTATAATAGAGAC
Found at i:1821114 original size:22 final size:22
Alignment explanation
Indices: 1821086--1821132 Score: 76
Period size: 22 Copynumber: 2.1 Consensus size: 22
1821076 TATTTGATTA
1821086 TTAGCACATTAGTGCTCTCCGT
1 TTAGCACATTAGTGCTCTCCGT
* *
1821108 TTAGCACATTTGTGCTCTCTGT
1 TTAGCACATTAGTGCTCTCCGT
1821130 TTA
1 TTA
1821133 ATAGTGCATA
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
22 23 1.00
ACGTcount: A:0.17, C:0.23, G:0.17, T:0.43
Consensus pattern (22 bp):
TTAGCACATTAGTGCTCTCCGT
Found at i:1827826 original size:14 final size:13
Alignment explanation
Indices: 1827808--1827832 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1827798 AAATTCTCTT
1827808 TTTTTTTAAATTA
1 TTTTTTTAAATTA
1827821 TTTTTTTAAATT
1 TTTTTTTAAATT
1827833 TAGAACTAAT
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:0.28, C:0.00, G:0.00, T:0.72
Consensus pattern (13 bp):
TTTTTTTAAATTA
Found at i:1827855 original size:89 final size:90
Alignment explanation
Indices: 1827762--1827941 Score: 353
Period size: 89 Copynumber: 2.0 Consensus size: 90
1827752 TTACCACCAA
1827762 AAGAATCACTAATTTATCTCTTCCTTTTTAAAAAAAAAATTCTCTTTTTTTTTAAATTATTTTTT
1 AAGAATCACTAATTTATCTCTTCCTTTTTAAAAAAAAAATTCTCTTTTTTTTTAAATTATTTTTT
1827827 TAAATTTAGAACT-AATTGATAACT
66 TAAATTTAGAACTAAATTGATAACT
1827851 AAGAATCACTAATTTATCTCTTCCTTTTTAAAAAAAAAATTCTCTTTTTTTTTAAATTATTTTTT
1 AAGAATCACTAATTTATCTCTTCCTTTTTAAAAAAAAAATTCTCTTTTTTTTTAAATTATTTTTT
1827916 TAAATTTAGAACTAAATTGATAACT
66 TAAATTTAGAACTAAATTGATAACT
1827941 A
1 A
1827942 TTATAAATGT
Statistics
Matches: 90, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
89 78 0.87
90 12 0.13
ACGTcount: A:0.38, C:0.11, G:0.03, T:0.48
Consensus pattern (90 bp):
AAGAATCACTAATTTATCTCTTCCTTTTTAAAAAAAAAATTCTCTTTTTTTTTAAATTATTTTTT
TAAATTTAGAACTAAATTGATAACT
Found at i:1827915 original size:14 final size:13
Alignment explanation
Indices: 1827897--1827921 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1827887 AAATTCTCTT
1827897 TTTTTTTAAATTA
1 TTTTTTTAAATTA
1827910 TTTTTTTAAATT
1 TTTTTTTAAATT
1827922 TAGAACTAAA
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:0.28, C:0.00, G:0.00, T:0.72
Consensus pattern (13 bp):
TTTTTTTAAATTA
Found at i:1835582 original size:27 final size:27
Alignment explanation
Indices: 1835537--1835622 Score: 88
Period size: 27 Copynumber: 3.2 Consensus size: 27
1835527 AGTAAGTGTG
*
1835537 AAATTAGAAAATAGAAATATTAGTAATT
1 AAATTAG-AAATAAAAATATTAGTAATT
1835565 AAATTAGAAATAAAAATATTTAGTAA-T
1 AAATTAGAAATAAAAATA-TTAGTAATT
* * *
1835592 AAATT--AAATATAATTAATTAGTGATT
1 AAATTAGAAATAAAAAT-ATTAGTAATT
1835618 AAATT
1 AAATT
1835623 GATGAAGTTA
Statistics
Matches: 51, Mismatches: 4, Indels: 8
0.81 0.06 0.13
Matches are distributed among these distances:
25 14 0.27
26 7 0.14
27 16 0.31
28 14 0.27
ACGTcount: A:0.56, C:0.00, G:0.08, T:0.36
Consensus pattern (27 bp):
AAATTAGAAATAAAAATATTAGTAATT
Found at i:1842540 original size:43 final size:43
Alignment explanation
Indices: 1842427--1842554 Score: 168
Period size: 43 Copynumber: 3.0 Consensus size: 43
1842417 ATATCCCAAT
* * * * *
1842427 TTGGCAC-CATAGTGCATCATCGGATAAACTGAAGGAAATATA
1 TTGGCACACATAGTGCATCATCGGACAAGCCGAAGCAATTATA
*
1842469 TTGGCACACATAGTGCGTCATCGGACAAGCCGAAGCAATTATA
1 TTGGCACACATAGTGCATCATCGGACAAGCCGAAGCAATTATA
* * *
1842512 TTGGCACACACAGTGCATCATCGGACAAGCCAAATCAATTATA
1 TTGGCACACATAGTGCATCATCGGACAAGCCGAAGCAATTATA
1842555 CTAGCACATA
Statistics
Matches: 75, Mismatches: 10, Indels: 1
0.87 0.12 0.01
Matches are distributed among these distances:
42 7 0.09
43 68 0.91
ACGTcount: A:0.36, C:0.22, G:0.20, T:0.22
Consensus pattern (43 bp):
TTGGCACACATAGTGCATCATCGGACAAGCCGAAGCAATTATA
Found at i:1842575 original size:43 final size:43
Alignment explanation
Indices: 1842472--1842575 Score: 118
Period size: 43 Copynumber: 2.4 Consensus size: 43
1842462 AAATATATTG
* * * * * *
1842472 GCACACATAGTGCGTCATCGGACAAGCCGAAGCAATTATATTG
1 GCACACACACTGCATCATCGGACAAGCCAAAGCAATTATACTA
* *
1842515 GCACACACAGTGCATCATCGGACAAGCCAAATCAATTATACTA
1 GCACACACACTGCATCATCGGACAAGCCAAAGCAATTATACTA
* *
1842558 GCACATACACTGTATCAT
1 GCACACACACTGCATCAT
1842576 TGGATGAATC
Statistics
Matches: 52, Mismatches: 9, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
43 52 1.00
ACGTcount: A:0.36, C:0.26, G:0.17, T:0.21
Consensus pattern (43 bp):
GCACACACACTGCATCATCGGACAAGCCAAAGCAATTATACTA
Found at i:1855832 original size:16 final size:16
Alignment explanation
Indices: 1855811--1855846 Score: 54
Period size: 16 Copynumber: 2.2 Consensus size: 16
1855801 CTATAAAATG
*
1855811 ATTAAAAATAATAAAA
1 ATTAAAAAAAATAAAA
*
1855827 ATTAAAAAAAATTAAA
1 ATTAAAAAAAATAAAA
1855843 ATTA
1 ATTA
1855847 CATCAACTTA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.72, C:0.00, G:0.00, T:0.28
Consensus pattern (16 bp):
ATTAAAAAAAATAAAA
Found at i:1855902 original size:18 final size:17
Alignment explanation
Indices: 1855879--1855921 Score: 50
Period size: 17 Copynumber: 2.5 Consensus size: 17
1855869 AAAATTATAT
*
1855879 TAAAAAAATTATAAAATA
1 TAAAAAAATAAT-AAATA
**
1855897 TAAAAATCTAATAAATA
1 TAAAAAAATAATAAATA
1855914 TAAAAAAA
1 TAAAAAAA
1855922 GTTTTATAAC
Statistics
Matches: 20, Mismatches: 5, Indels: 1
0.77 0.19 0.04
Matches are distributed among these distances:
17 11 0.55
18 9 0.45
ACGTcount: A:0.72, C:0.02, G:0.00, T:0.26
Consensus pattern (17 bp):
TAAAAAAATAATAAATA
Found at i:1856028 original size:9 final size:9
Alignment explanation
Indices: 1856016--1856077 Score: 54
Period size: 9 Copynumber: 6.8 Consensus size: 9
1856006 NTTAAAAAGA
1856016 ATAAAAATT
1 ATAAAAATT
*
1856025 ATAAAAAAT
1 ATAAAAATT
*
1856034 ATTAAAA-T
1 ATAAAAATT
**
1856042 ATTAAAAACG
1 A-TAAAAATT
*
1856052 ATATAAAATA
1 ATA-AAAATT
1856062 ATAAAAATT
1 ATAAAAATT
1856071 ATAAAAA
1 ATAAAAA
1856078 AATCATAATA
Statistics
Matches: 43, Mismatches: 7, Indels: 6
0.77 0.12 0.11
Matches are distributed among these distances:
8 2 0.05
9 33 0.77
10 8 0.19
ACGTcount: A:0.69, C:0.02, G:0.02, T:0.27
Consensus pattern (9 bp):
ATAAAAATT
Found at i:1856047 original size:27 final size:26
Alignment explanation
Indices: 1856025--1856076 Score: 68
Period size: 27 Copynumber: 1.9 Consensus size: 26
1856015 AATAAAAATT
*
1856025 ATAAAAAATATTAAAATATTAAAAACG
1 ATAAAAAATAATAAAA-ATTAAAAACG
*
1856052 ATATAAAATAATAAAAATTATAAAA
1 ATAAAAAATAATAAAAATTA-AAAA
1856077 AAATCATAAT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
26 4 0.18
27 18 0.82
ACGTcount: A:0.69, C:0.02, G:0.02, T:0.27
Consensus pattern (26 bp):
ATAAAAAATAATAAAAATTAAAAACG
Found at i:1856058 original size:19 final size:18
Alignment explanation
Indices: 1856007--1856068 Score: 65
Period size: 19 Copynumber: 3.4 Consensus size: 18
1855997 NNNNNNNNNN
1856007 TTAAAAAGA-ATAAAA-A
1 TTAAAAAGATATAAAATA
*
1856023 TTATAAAAAATATTAAAATA
1 TTA-AAAAGATA-TAAAATA
1856043 TTAAAAACGATATAAAATA
1 TTAAAAA-GATATAAAATA
*
1856062 ATAAAAA
1 TTAAAAA
1856069 TTATAAAAAA
Statistics
Matches: 38, Mismatches: 3, Indels: 7
0.79 0.06 0.15
Matches are distributed among these distances:
16 3 0.08
17 5 0.13
18 1 0.03
19 22 0.58
20 7 0.18
ACGTcount: A:0.69, C:0.02, G:0.03, T:0.26
Consensus pattern (18 bp):
TTAAAAAGATATAAAATA
Found at i:1856078 original size:19 final size:19
Alignment explanation
Indices: 1856018--1856078 Score: 52
Period size: 19 Copynumber: 3.3 Consensus size: 19
1856008 TAAAAAGAAT
*
1856018 AAAAATTATAAAAAATAT-
1 AAAAATAATAAAAAATATA
* * **
1856036 TAAAATATTAAAAACGATA
1 AAAAATAATAAAAAATATA
* *
1856055 TAAAATAATAAAAATTATA
1 AAAAATAATAAAAAATATA
1856074 AAAAA
1 AAAAA
1856079 ATCATAATAA
Statistics
Matches: 33, Mismatches: 9, Indels: 1
0.77 0.21 0.02
Matches are distributed among these distances:
18 13 0.39
19 20 0.61
ACGTcount: A:0.70, C:0.02, G:0.02, T:0.26
Consensus pattern (19 bp):
AAAAATAATAAAAAATATA
Found at i:1856596 original size:8 final size:9
Alignment explanation
Indices: 1856573--1856598 Score: 52
Period size: 9 Copynumber: 2.9 Consensus size: 9
1856563 TAATATTTAA
1856573 TATTTTTTC
1 TATTTTTTC
1856582 TATTTTTTC
1 TATTTTTTC
1856591 TATTTTTT
1 TATTTTTT
1856599 ATAATCTTTT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 17 1.00
ACGTcount: A:0.12, C:0.08, G:0.00, T:0.81
Consensus pattern (9 bp):
TATTTTTTC
Found at i:1856987 original size:392 final size:393
Alignment explanation
Indices: 1856526--1857312 Score: 1567
Period size: 392 Copynumber: 2.0 Consensus size: 393
1856516 TAATTTTTAC
1856526 AAGTTTATATCAATTTTCATATATATTTTTTAATATTTAATATTTAATATTTTTTCTATTTTTTC
1 AAGTTTATATCAATTTTCATATATATTTTTTAATATTTAATATTTAATATTTTTTCTATTTTTTC
1856591 TATTTTTTATAATCTTTTATGATTTTTCAATCATTTTTATGAAAAATTATATTTTTAAAAGTTGT
66 TATTTTTTATAATCTTTTATGATTTTTCAATCATTTTTATGAAAAATTATATTTTTAAAAGTTGT
1856656 GTAATAGTAATTAATATTATTAATTTATTATATTATAGTCACTTATTTATTAATTATTGTTAAGG
131 GTAATAGTAATTAATATTATTAATTTATTATATTATAGTCACTTATTTATTAATTATTGTTAAGG
1856721 GAGTAATGACAAGTTTGTGGCATGTTAATTTTGCCACATTTTGGTTTATAGTTATGAGCAAGATA
196 GAGTAATGACAAGTTTGTGGCATGTTAATTTTGCCACATTTTGGTTTATAGTTATGAGCAAGATA
1856786 GTTAGAATTACATCGGTGGATACATCGTTTTCCTATTGAAACCGGTATATGTTAGTACCTTTTTG
261 GTTAGAATTACATCGGTGGATACATCGTTTTCCTATTGAAACCGGTATATGTTAGTACCTTTTTG
1856851 TGTATCATTTTAAATTTATTGATGTTTTTAAAAAATATTTAATATATATAAAATA-TTACAAATA
326 TGTATCATTTTAAATTTATTGATGTTTTTAAAAAATATTTAATATATATAAAATATTTACAAATA
1856915 TAA
391 TAA
1856918 AAGTTTATATCAATTTTCATATATATTTTTTAATATTTAATATTTAATATTTTTTCTATTTTTTC
1 AAGTTTATATCAATTTTCATATATATTTTTTAATATTTAATATTTAATATTTTTTCTATTTTTTC
1856983 TATTTTTTATAATCTTTTATGATTTTTCAATCATTTTTATGAAAAATTATATTTTTAAAAGTTGT
66 TATTTTTTATAATCTTTTATGATTTTTCAATCATTTTTATGAAAAATTATATTTTTAAAAGTTGT
1857048 GTAATAGTAATTAATATTATTAATTTATTATATTATAGTCACTTATTTATTAATTATTGTTAAGG
131 GTAATAGTAATTAATATTATTAATTTATTATATTATAGTCACTTATTTATTAATTATTGTTAAGG
1857113 GAGTAATGACAAGTTTGTGGCATGTTAATTTTGCCACATTTTGGTTTATAGTTATGAGCAAGATA
196 GAGTAATGACAAGTTTGTGGCATGTTAATTTTGCCACATTTTGGTTTATAGTTATGAGCAAGATA
1857178 GTTAGAATTACATCGGTGGATACATCGTTTTCCTATTGAAACCGGTATATGTTAGTACCTTTTTG
261 GTTAGAATTACATCGGTGGATACATCGTTTTCCTATTGAAACCGGTATATGTTAGTACCTTTTTG
1857243 TGTATCATTTTAAATTTATTGATGTTTTTAAAAAATATTTAATATATATAAAATATTTACAAATA
326 TGTATCATTTTAAATTTATTGATGTTTTTAAAAAATATTTAATATATATAAAATATTTACAAATA
1857308 TAA
391 TAA
1857311 AA
1 AA
1857313 TAAATGATGC
Statistics
Matches: 394, Mismatches: 0, Indels: 1
1.00 0.00 0.00
Matches are distributed among these distances:
392 380 0.96
393 14 0.04
ACGTcount: A:0.34, C:0.07, G:0.11, T:0.49
Consensus pattern (393 bp):
AAGTTTATATCAATTTTCATATATATTTTTTAATATTTAATATTTAATATTTTTTCTATTTTTTC
TATTTTTTATAATCTTTTATGATTTTTCAATCATTTTTATGAAAAATTATATTTTTAAAAGTTGT
GTAATAGTAATTAATATTATTAATTTATTATATTATAGTCACTTATTTATTAATTATTGTTAAGG
GAGTAATGACAAGTTTGTGGCATGTTAATTTTGCCACATTTTGGTTTATAGTTATGAGCAAGATA
GTTAGAATTACATCGGTGGATACATCGTTTTCCTATTGAAACCGGTATATGTTAGTACCTTTTTG
TGTATCATTTTAAATTTATTGATGTTTTTAAAAAATATTTAATATATATAAAATATTTACAAATA
TAA
Found at i:1856988 original size:8 final size:9
Alignment explanation
Indices: 1856965--1856990 Score: 52
Period size: 9 Copynumber: 2.9 Consensus size: 9
1856955 TAATATTTAA
1856965 TATTTTTTC
1 TATTTTTTC
1856974 TATTTTTTC
1 TATTTTTTC
1856983 TATTTTTT
1 TATTTTTT
1856991 ATAATCTTTT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 17 1.00
ACGTcount: A:0.12, C:0.08, G:0.00, T:0.81
Consensus pattern (9 bp):
TATTTTTTC
Found at i:1857310 original size:17 final size:18
Alignment explanation
Indices: 1857274--1857314 Score: 59
Period size: 18 Copynumber: 2.3 Consensus size: 18
1857264 ATGTTTTTAA
1857274 AAAATATTTAATATATAT
1 AAAATATTTAATATATAT
1857292 AAAATATTTACA-A-ATAT
1 AAAATATTTA-ATATATAT
1857309 AAAATA
1 AAAATA
1857315 AATGATGCTA
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
17 10 0.45
18 11 0.50
19 1 0.05
ACGTcount: A:0.61, C:0.02, G:0.00, T:0.37
Consensus pattern (18 bp):
AAAATATTTAATATATAT
Found at i:1858231 original size:18 final size:20
Alignment explanation
Indices: 1858191--1858239 Score: 61
Period size: 18 Copynumber: 2.6 Consensus size: 20
1858181 AATAAAGAAA
1858191 ATAAAAATAAA-AAGATGTT
1 ATAAAAATAAATAAGATGTT
1858210 -TAAAAATAAATAA-AT-TT
1 ATAAAAATAAATAAGATGTT
*
1858227 ATAAAAAGAAATA
1 ATAAAAATAAATA
1858240 TTAACCTAAT
Statistics
Matches: 27, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
17 2 0.07
18 23 0.85
19 2 0.07
ACGTcount: A:0.67, C:0.00, G:0.06, T:0.27
Consensus pattern (20 bp):
ATAAAAATAAATAAGATGTT
Found at i:1858760 original size:65 final size:66
Alignment explanation
Indices: 1858674--1858813 Score: 255
Period size: 65 Copynumber: 2.1 Consensus size: 66
1858664 AAATTAAGAT
*
1858674 ATTTTAATCTGATAAACTTGAATCATTAATTAACTTATTTAGGTTTCTAAAATTATTACTTTAG-
1 ATTTTAA-ATGATAAACTTGAATCATTAATTAACTTATTTAGGTTTCTAAAATTATTACTTTAGA
1858738 AC
65 AC
1858740 ATTTTAAATGATAAACTTGAATCATTAATTAACTTATTTAGGTTTCTAAAATTATTACTTTAGAA
1 ATTTTAAATGATAAACTTGAATCATTAATTAACTTATTTAGGTTTCTAAAATTATTACTTTAGAA
1858805 C
66 C
1858806 ATTTTAAA
1 ATTTTAAA
1858814 AATTTTAACT
Statistics
Matches: 72, Mismatches: 1, Indels: 2
0.96 0.01 0.03
Matches are distributed among these distances:
65 55 0.76
66 17 0.24
ACGTcount: A:0.39, C:0.09, G:0.07, T:0.45
Consensus pattern (66 bp):
ATTTTAAATGATAAACTTGAATCATTAATTAACTTATTTAGGTTTCTAAAATTATTACTTTAGAA
C
Found at i:1863407 original size:27 final size:27
Alignment explanation
Indices: 1863373--1863442 Score: 86
Period size: 27 Copynumber: 2.6 Consensus size: 27
1863363 GGAGGGCCTG
* *
1863373 CCACAGGCGGCACCAGAGGTGCCAGTG
1 CCACAGGCGGCACCAGAGGTGCCACTA
* * * *
1863400 GCAGAGGCGGCACCAAATGTGCCACTA
1 CCACAGGCGGCACCAGAGGTGCCACTA
1863427 CCACAGGCGGCACCAG
1 CCACAGGCGGCACCAG
1863443 CCTCTTATAT
Statistics
Matches: 34, Mismatches: 9, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
27 34 1.00
ACGTcount: A:0.26, C:0.34, G:0.33, T:0.07
Consensus pattern (27 bp):
CCACAGGCGGCACCAGAGGTGCCACTA
Found at i:1863490 original size:13 final size:13
Alignment explanation
Indices: 1863472--1863528 Score: 60
Period size: 13 Copynumber: 4.1 Consensus size: 13
1863462 CAATTCGGCT
1863472 GAAGGAGAAGAAA
1 GAAGGAGAAGAAA
1863485 GAAGGAGAAGAAA
1 GAAGGAGAAGAAA
**
1863498 GAAAAAGAAAGAAAA
1 GAAGGAG-AAG-AAA
1863513 GGAAAGGAGAAGAAA
1 -G-AAGGAGAAGAAA
1863528 G
1 G
1863529 GAAAGGAAAT
Statistics
Matches: 36, Mismatches: 4, Indels: 7
0.77 0.09 0.15
Matches are distributed among these distances:
13 18 0.50
14 4 0.11
15 6 0.17
16 4 0.11
17 4 0.11
ACGTcount: A:0.65, C:0.00, G:0.35, T:0.00
Consensus pattern (13 bp):
GAAGGAGAAGAAA
Found at i:1863517 original size:20 final size:21
Alignment explanation
Indices: 1863494--1863576 Score: 82
Period size: 20 Copynumber: 4.0 Consensus size: 21
1863484 AGAAGGAGAA
1863494 GAAA-GAAAAAGAAAGAAAAG
1 GAAAGGAAAAAGAAAGAAAAG
* *
1863514 GAAAGG-AGAAGAAAGGAAAG
1 GAAAGGAAAAAGAAAGAAAAG
**
1863534 GAAATGAGAAAAAG-AAGAGGGAG
1 GAAA-G-GAAAAAGAAAGA-AAAG
1863557 GAAAGGAAAAAGAAAGAAAA
1 GAAAGGAAAAAGAAAGAAAA
1863577 AATAAGGAAA
Statistics
Matches: 49, Mismatches: 8, Indels: 11
0.72 0.12 0.16
Matches are distributed among these distances:
20 20 0.41
21 10 0.20
22 9 0.18
23 10 0.20
ACGTcount: A:0.66, C:0.00, G:0.33, T:0.01
Consensus pattern (21 bp):
GAAAGGAAAAAGAAAGAAAAG
Found at i:1863586 original size:11 final size:11
Alignment explanation
Indices: 1863492--1863586 Score: 53
Period size: 10 Copynumber: 9.0 Consensus size: 11
1863482 AAAGAAGGAG
1863492 AAGAAA-GAAA
1 AAGAAAGGAAA
1863502 AAGAAA-GAAA
1 AAGAAAGGAAA
* *
1863512 AGGAAAGG-AG
1 AAGAAAGGAAA
1863522 AAGAAAGG-AA
1 AAGAAAGGAAA
*
1863532 AGGAAATGAGAAA
1 AAGAAA-G-GAAA
*
1863545 AAGAAGAGG--G
1 AAGAA-AGGAAA
*
1863555 AGGAAAGGAAA
1 AAGAAAGGAAA
1863566 AAGAAA-GAAA
1 AAGAAAGGAAA
1863576 AA-ATAAGGAAA
1 AAGA-AAGGAAA
1863587 TGTATTTTTT
Statistics
Matches: 66, Mismatches: 10, Indels: 17
0.71 0.11 0.18
Matches are distributed among these distances:
9 4 0.06
10 41 0.62
11 11 0.17
12 2 0.03
13 7 0.11
14 1 0.02
ACGTcount: A:0.67, C:0.00, G:0.31, T:0.02
Consensus pattern (11 bp):
AAGAAAGGAAA
Found at i:1864062 original size:153 final size:158
Alignment explanation
Indices: 1863839--1864360 Score: 727
Period size: 161 Copynumber: 3.3 Consensus size: 158
1863829 TGAAAATAAG
* * * * * * * *
1863839 AAAAATACGAATAAAGGGCCAAAATAAAGGTTTTTGTAGTAAATTTATATAAAACATATACTAAA
1 AAAAATACGAACAAATGGCCGAAATAAGGGTTTTT-TACTAAATTTATTTAAAACACACACTAAA
*
1863904 TTAATACATTTCAAACATAATGTACTAAAATAATGTAAAAT-AAT---AAAAT-ACGAAAATAAT
65 TTAATACATTTCAAACATAATGTACTAAAATAATGTAAAATAAATCAGAAAATCA-GAAAATAGT
1863964 ATATTTTTTGAAAGTAATAAAATCCGGGAA
129 ATATTTTTTGAAAGTAATAAAATCCGGGAA
1863994 AAAAATACGAACAAA-GGCCGAAATAAGGGTTTTTTACTAAATTTATTTAAAACACACACTAAAT
1 AAAAATACGAACAAATGGCCGAAATAAGGGTTTTTTACTAAATTTATTTAAAACACACACTAAAT
1864058 TAATACATTTCAAACATAATGTACTAAAATAATGTAAAATCAGAAAATCAGAAAATCAGAAAATA
66 TAATACATTTCAAACATAATGTACTAAAATAATGTAAAAT----AAATCAGAAAATCAGAAAATA
***
1864123 GTATATTTTTTGAAAGTAATAAAATTTTGG-A
127 GTATATTTTTTGAAAGTAATAAAATCCGGGAA
* * * *
1864154 AAAAATACGAACAAATGGCCGAAACTAA-AGTTTTTTACTAAATTTATTTAAAAAACACAATTAA
1 AAAAATACGAACAAATGGCCGAAA-TAAGGGTTTTTTACTAAATTTATTTAAAACACACACTAAA
1864218 TTAATACATTTCAAACATAATGTACTAAAATAATGTAAAATCAGAAAATCAGAAAATCAGAAAAT
65 TTAATACATTTCAAACATAATGTACTAAAATAATGTAAAAT----AAATCAGAAAATCAGAAAAT
1864283 AGTATATTTTTTGAAAGTAATAAAATCCGGGAA
126 AGTATATTTTTTGAAAGTAATAAAATCCGGGAA
* *
1864316 AAAAATATGAGCAAATGGCCGAAATAAGGGTTTTTTACTAAATTT
1 AAAAATACGAACAAATGGCCGAAATAAGGGTTTTTTACTAAATTT
1864361 GTTTTGAAGT
Statistics
Matches: 333, Mismatches: 21, Indels: 19
0.89 0.06 0.05
Matches are distributed among these distances:
153 66 0.20
154 17 0.05
155 14 0.04
158 3 0.01
160 16 0.05
161 174 0.52
162 43 0.13
ACGTcount: A:0.50, C:0.09, G:0.11, T:0.29
Consensus pattern (158 bp):
AAAAATACGAACAAATGGCCGAAATAAGGGTTTTTTACTAAATTTATTTAAAACACACACTAAAT
TAATACATTTCAAACATAATGTACTAAAATAATGTAAAATAAATCAGAAAATCAGAAAATAGTAT
ATTTTTTGAAAGTAATAAAATCCGGGAA
Found at i:1864106 original size:8 final size:8
Alignment explanation
Indices: 1864093--1864121 Score: 58
Period size: 8 Copynumber: 3.6 Consensus size: 8
1864083 AAAATAATGT
1864093 AAAATCAG
1 AAAATCAG
1864101 AAAATCAG
1 AAAATCAG
1864109 AAAATCAG
1 AAAATCAG
1864117 AAAAT
1 AAAAT
1864122 AGTATATTTT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 21 1.00
ACGTcount: A:0.66, C:0.10, G:0.10, T:0.14
Consensus pattern (8 bp):
AAAATCAG
Found at i:1864267 original size:8 final size:8
Alignment explanation
Indices: 1864254--1864282 Score: 58
Period size: 8 Copynumber: 3.6 Consensus size: 8
1864244 AAAATAATGT
1864254 AAAATCAG
1 AAAATCAG
1864262 AAAATCAG
1 AAAATCAG
1864270 AAAATCAG
1 AAAATCAG
1864278 AAAAT
1 AAAAT
1864283 AGTATATTTT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 21 1.00
ACGTcount: A:0.66, C:0.10, G:0.10, T:0.14
Consensus pattern (8 bp):
AAAATCAG
Found at i:1867591 original size:39 final size:40
Alignment explanation
Indices: 1867531--1867631 Score: 113
Period size: 40 Copynumber: 2.6 Consensus size: 40
1867521 CCACTAATCC
** *
1867531 TAATAACTAACACA-A-TAATAA-TAGTTTTTTACTCAAAA
1 TAATAACTAACA-ATAGTAATAATTAGGGTTTTACTAAAAA
1867569 TAAT-ACTAACTAATAGTAATAATTAGGGTTTTACTAAAAA
1 TAATAACTAAC-AATAGTAATAATTAGGGTTTTACTAAAAA
*
1867609 TAATAACTAACAATAAT-ATAATT
1 TAATAACTAACAATAGTAATAATT
1867632 TAAAAACTAA
Statistics
Matches: 54, Mismatches: 4, Indels: 9
0.81 0.06 0.13
Matches are distributed among these distances:
37 7 0.13
38 6 0.11
39 12 0.22
40 23 0.43
41 6 0.11
ACGTcount: A:0.50, C:0.10, G:0.05, T:0.35
Consensus pattern (40 bp):
TAATAACTAACAATAGTAATAATTAGGGTTTTACTAAAAA
Found at i:1867658 original size:23 final size:23
Alignment explanation
Indices: 1867613--1867659 Score: 60
Period size: 23 Copynumber: 2.0 Consensus size: 23
1867603 TAAAAATAAT
*
1867613 AACTAACAATAATATAATTTAAA
1 AACTAACAATAATATAATCTAAA
*
1867636 AACTAACAATCATACTAA-CTAAA
1 AACTAACAATAATA-TAATCTAAA
1867659 A
1 A
1867660 TAATAATTAG
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
23 18 0.86
24 3 0.14
ACGTcount: A:0.60, C:0.15, G:0.00, T:0.26
Consensus pattern (23 bp):
AACTAACAATAATATAATCTAAA
Found at i:1868007 original size:9 final size:9
Alignment explanation
Indices: 1867993--1868022 Score: 51
Period size: 9 Copynumber: 3.3 Consensus size: 9
1867983 CACCACCTTT
*
1867993 TTCTTCTTC
1 TTCTTCTCC
1868002 TTCTTCTCC
1 TTCTTCTCC
1868011 TTCTTCTCC
1 TTCTTCTCC
1868020 TTC
1 TTC
1868023 AGCTGAACTG
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
9 20 1.00
ACGTcount: A:0.00, C:0.40, G:0.00, T:0.60
Consensus pattern (9 bp):
TTCTTCTCC
Found at i:1869786 original size:42 final size:42
Alignment explanation
Indices: 1869727--1869808 Score: 164
Period size: 42 Copynumber: 2.0 Consensus size: 42
1869717 CAAAGACAGA
1869727 TACAAGAATTGCAGAGGCTTCAAATTCGGGATCAAGAACATC
1 TACAAGAATTGCAGAGGCTTCAAATTCGGGATCAAGAACATC
1869769 TACAAGAATTGCAGAGGCTTCAAATTCGGGATCAAGAACA
1 TACAAGAATTGCAGAGGCTTCAAATTCGGGATCAAGAACA
1869809 GCTCGCTATG
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
42 40 1.00
ACGTcount: A:0.39, C:0.18, G:0.22, T:0.21
Consensus pattern (42 bp):
TACAAGAATTGCAGAGGCTTCAAATTCGGGATCAAGAACATC
Found at i:1872168 original size:15 final size:15
Alignment explanation
Indices: 1872145--1872175 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
1872135 ACGTGTTGAC
1872145 ATATAAAAAATATAT
1 ATATAAAAAATATAT
*
1872160 ATATTAAAAATATAT
1 ATATAAAAAATATAT
1872175 A
1 A
1872176 ACAATGGCGA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (15 bp):
ATATAAAAAATATAT
Found at i:1874673 original size:21 final size:21
Alignment explanation
Indices: 1874647--1874687 Score: 66
Period size: 21 Copynumber: 2.0 Consensus size: 21
1874637 TTTTGTTCAG
1874647 TGTTGTTTACT-TCTATTTTGT
1 TGTTGTTTACTATC-ATTTTGT
1874668 TGTTGTTTACTATCATTTTG
1 TGTTGTTTACTATCATTTTG
1874688 CTATTATATT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
21 17 0.89
22 2 0.11
ACGTcount: A:0.12, C:0.10, G:0.15, T:0.63
Consensus pattern (21 bp):
TGTTGTTTACTATCATTTTGT
Found at i:1881522 original size:48 final size:48
Alignment explanation
Indices: 1881466--1881619 Score: 254
Period size: 48 Copynumber: 3.2 Consensus size: 48
1881456 TCTGTCCCCC
* * * *
1881466 CTGATGGCCCTAATACGGTGGTTTCTCGTGCTCCTCTTCCTGTCGGTG
1 CTGATGGCCCTACTACGGTGGTTTATCGTGCTCCTCCTCATGTCGGTG
1881514 CTGATGGCCCTACTACGGTGGTTTATCGTGCTCCTCCTCATGTCGGTG
1 CTGATGGCCCTACTACGGTGGTTTATCGTGCTCCTCCTCATGTCGGTG
* *
1881562 CTGATGGCCCTACTACGTTGGTTTATCGCGCTCCTCCTCATGTCGGTG
1 CTGATGGCCCTACTACGGTGGTTTATCGTGCTCCTCCTCATGTCGGTG
1881610 CTGATGGCCC
1 CTGATGGCCC
1881620 GCATACCTTC
Statistics
Matches: 100, Mismatches: 6, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
48 100 1.00
ACGTcount: A:0.10, C:0.31, G:0.27, T:0.33
Consensus pattern (48 bp):
CTGATGGCCCTACTACGGTGGTTTATCGTGCTCCTCCTCATGTCGGTG
Found at i:1881646 original size:48 final size:48
Alignment explanation
Indices: 1881506--1881646 Score: 115
Period size: 48 Copynumber: 2.9 Consensus size: 48
1881496 CTCCTCTTCC
* ** * * ** *
1881506 TGTCGGTGCTGATGGCCCTACTACGGTGGTTTATCGTGCTCCTCCTCA
1 TGTCGGTGCTGATGGCCCCACTACCTTCGTTGATCGCCCCCCTCCTCA
* * * * * *
1881554 TGTCGGTGCTGATGGCCCTACTACGTTGGTTTATCGCGCTCCTCCTCA
1 TGTCGGTGCTGATGGCCCCACTACCTTCGTTGATCGCCCCCCTCCTCA
*
1881602 TGTCGGTGCTGATGGCCCGCA-TACCTTCGTTGCTC-CTCCCCCTCC
1 TGTCGGTGCTGATGGCCC-CACTACCTTCGTTGATCGC-CCCCCTCC
1881647 AGCGGCTCGA
Statistics
Matches: 82, Mismatches: 9, Indels: 4
0.86 0.09 0.04
Matches are distributed among these distances:
47 1 0.01
48 80 0.98
49 1 0.01
ACGTcount: A:0.09, C:0.34, G:0.25, T:0.32
Consensus pattern (48 bp):
TGTCGGTGCTGATGGCCCCACTACCTTCGTTGATCGCCCCCCTCCTCA
Found at i:1881646 original size:96 final size:96
Alignment explanation
Indices: 1881466--1881646 Score: 211
Period size: 96 Copynumber: 1.9 Consensus size: 96
1881456 TCTGTCCCCC
* * * * * *
1881466 CTGATGGCCCTAATACGGTGGTTTCTCGTGCTCCTCTTCCTGTCGGTGCTGATGGCCCTACTACG
1 CTGATGGCCCTAATACGGTGGTTTATCGCGCTCCTCCTCATGTCGGTGCTGATGGCCCCACTACC
* * * * *
1881531 GTGGTTTATCGTGCTCCTCCTCATGTCGGTG
66 GTCGTTGATCCTCCCCCTCCTCATGTCGGTG
* *
1881562 CTGATGGCCCTACTACGTTGGTTTATCGCGCTCCTCCTCATGTCGGTGCTGATGGCCCGCA-TAC
1 CTGATGGCCCTAATACGGTGGTTTATCGCGCTCCTCCTCATGTCGGTGCTGATGGCCC-CACTAC
* *
1881626 CTTCGTTGCTCCTCCCCCTCC
65 CGTCGTTGATCCTCCCCCTCC
1881647 AGCGGCTCGA
Statistics
Matches: 69, Mismatches: 15, Indels: 2
0.80 0.17 0.02
Matches are distributed among these distances:
96 68 0.99
97 1 0.01
ACGTcount: A:0.09, C:0.34, G:0.24, T:0.33
Consensus pattern (96 bp):
CTGATGGCCCTAATACGGTGGTTTATCGCGCTCCTCCTCATGTCGGTGCTGATGGCCCCACTACC
GTCGTTGATCCTCCCCCTCCTCATGTCGGTG
Found at i:1883478 original size:38 final size:39
Alignment explanation
Indices: 1883436--1883556 Score: 110
Period size: 38 Copynumber: 3.1 Consensus size: 39
1883426 ACTAACACAA
* *
1883436 TAACAATAATAATT-GTTTTATACTGAAATAAT-ACTAAC
1 TAACAATAATAATTAGGTTT-TACTAAAATAATAACTAAC
1883474 TAACAATAATAATTAGGGTTTTACTAAAATAATAACTAACC
1 TAACAATAATAATTA-GGTTTTACTAAAATAATAACTAA-C
* * *
1883515 ATAATAATAAT-ATTA-GTTTT-TTAACAATAAT-ACTAAG
1 -TAACAATAATAATTAGGTTTTACTAA-AATAATAACTAAC
1883552 TAACA
1 TAACA
1883557 TCTAAACCCT
Statistics
Matches: 71, Mismatches: 6, Indels: 14
0.78 0.07 0.15
Matches are distributed among these distances:
36 4 0.06
38 22 0.31
39 22 0.31
40 9 0.13
41 5 0.07
42 9 0.13
ACGTcount: A:0.49, C:0.10, G:0.06, T:0.36
Consensus pattern (39 bp):
TAACAATAATAATTAGGTTTTACTAAAATAATAACTAAC
Found at i:1884379 original size:52 final size:52
Alignment explanation
Indices: 1884301--1884402 Score: 204
Period size: 52 Copynumber: 2.0 Consensus size: 52
1884291 TTTGTCAAAG
1884301 GGAGAGATTATTGAAGCAATTTTTGAGTAACACCTGAATTAAGGATAACTGT
1 GGAGAGATTATTGAAGCAATTTTTGAGTAACACCTGAATTAAGGATAACTGT
1884353 GGAGAGATTATTGAAGCAATTTTTGAGTAACACCTGAATTAAGGATAACT
1 GGAGAGATTATTGAAGCAATTTTTGAGTAACACCTGAATTAAGGATAACT
1884403 AGTTGTGGCA
Statistics
Matches: 50, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
52 50 1.00
ACGTcount: A:0.37, C:0.10, G:0.23, T:0.30
Consensus pattern (52 bp):
GGAGAGATTATTGAAGCAATTTTTGAGTAACACCTGAATTAAGGATAACTGT
Found at i:1885537 original size:28 final size:28
Alignment explanation
Indices: 1885476--1885538 Score: 67
Period size: 29 Copynumber: 2.2 Consensus size: 28
1885466 TTTAAATTAA
* *
1885476 TAAAAATAAAATTATACTTTAATTTTTT
1 TAAAAATAAAATTATAATTTAATTCTTT
1885504 TAAAAATATAAAAATT-TAATTTAA-TCTTT
1 T-AAAA-AT-AAAATTATAATTTAATTCTTT
1885533 TAAAAA
1 TAAAAA
1885539 CCATAAAGAT
Statistics
Matches: 30, Mismatches: 2, Indels: 7
0.77 0.05 0.18
Matches are distributed among these distances:
27 1 0.03
28 5 0.17
29 9 0.30
30 9 0.30
31 6 0.20
ACGTcount: A:0.52, C:0.03, G:0.00, T:0.44
Consensus pattern (28 bp):
TAAAAATAAAATTATAATTTAATTCTTT
Found at i:1885545 original size:30 final size:31
Alignment explanation
Indices: 1885483--1885545 Score: 76
Period size: 30 Copynumber: 2.1 Consensus size: 31
1885473 TAATAAAAAT
* * *
1885483 AAAATTATACTTTAATTTTTTTAAAAATATA
1 AAAATTATAATTTAATTCTTTTAAAAACATA
1885514 AAAATT-TAATTTAA-TCTTTTAAAAACCATA
1 AAAATTATAATTTAATTCTTTTAAAAA-CATA
1885544 AA
1 AA
1885546 GATATAAATT
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
29 10 0.36
30 12 0.43
31 6 0.21
ACGTcount: A:0.51, C:0.06, G:0.00, T:0.43
Consensus pattern (31 bp):
AAAATTATAATTTAATTCTTTTAAAAACATA
Found at i:1890071 original size:8 final size:8
Alignment explanation
Indices: 1890060--1890098 Score: 62
Period size: 8 Copynumber: 4.9 Consensus size: 8
1890050 ATAAAATGAC
1890060 AATAATAT
1 AATAATAT
1890068 AATAATAT
1 AATAATAT
1890076 AATAAATAT
1 AAT-AATAT
1890085 AATAATA-
1 AATAATAT
1890092 AATAATA
1 AATAATA
1890099 ACAATTCAAT
Statistics
Matches: 30, Mismatches: 0, Indels: 3
0.91 0.00 0.09
Matches are distributed among these distances:
7 7 0.23
8 15 0.50
9 8 0.27
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (8 bp):
AATAATAT
Found at i:1890085 original size:17 final size:16
Alignment explanation
Indices: 1890063--1890096 Score: 59
Period size: 17 Copynumber: 2.1 Consensus size: 16
1890053 AAATGACAAT
1890063 AATATAATAATATAATA
1 AATATAATAATA-AATA
1890080 AATATAATAATAAATA
1 AATATAATAATAAATA
1890096 A
1 A
1890097 TAACAATTCA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 5 0.29
17 12 0.71
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (16 bp):
AATATAATAATAAATA
Found at i:1890099 original size:22 final size:21
Alignment explanation
Indices: 1890033--1890099 Score: 59
Period size: 22 Copynumber: 3.0 Consensus size: 21
1890023 TAACAAAATG
1890033 ATAACATAAATAATGAAATAA-A
1 ATAA-ATAAATAAT-AAATAATA
1890055 ATGACAATAATATAAT-AAT-ATA
1 AT-A-AATAA-ATAATAAATAATA
1890077 ATAAATATAATAATAAATAATA
1 ATAAATA-AATAATAAATAATA
1890099 A
1 A
1890100 CAATTCAATT
Statistics
Matches: 38, Mismatches: 0, Indels: 14
0.73 0.00 0.27
Matches are distributed among these distances:
20 9 0.24
21 6 0.16
22 12 0.32
23 5 0.13
24 6 0.16
ACGTcount: A:0.66, C:0.03, G:0.03, T:0.28
Consensus pattern (21 bp):
ATAAATAAATAATAAATAATA
Found at i:1890149 original size:3 final size:3
Alignment explanation
Indices: 1890060--1890138 Score: 56
Period size: 3 Copynumber: 25.3 Consensus size: 3
1890050 ATAAAATGAC
*
1890060 AAT AAT -AT AAT AAT -AT AAT AA- ATAT AAT AAT AAAT AAT AAC AATT
1 AAT AAT AAT AAT AAT AAT AAT AAT A-AT AAT AAT -AAT AAT AAT AA-T
* *
1890105 CAATT AAT AAT ACT ATAT AAT AAT GAT AAT AAT A
1 -AA-T AAT AAT AAT A-AT AAT AAT AAT AAT AAT A
1890139 GTGAAATAAT
Statistics
Matches: 62, Mismatches: 6, Indels: 16
0.74 0.07 0.19
Matches are distributed among these distances:
2 5 0.08
3 45 0.73
4 8 0.13
5 4 0.06
ACGTcount: A:0.61, C:0.04, G:0.01, T:0.34
Consensus pattern (3 bp):
AAT
Found at i:1890572 original size:29 final size:30
Alignment explanation
Indices: 1890523--1890582 Score: 79
Period size: 30 Copynumber: 2.0 Consensus size: 30
1890513 ATCTCAAAAC
*
1890523 TATACATAAACTTTGATTTTG-TGCAATTT
1 TATACATAAAATTTGATTTTGATGCAATTT
*
1890552 TATACATGAAAATTTGA-TTTGATTCAATTT
1 TATACAT-AAAATTTGATTTTGATGCAATTT
1890582 T
1 T
1890583 CACAAATTAT
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
29 11 0.41
30 16 0.59
ACGTcount: A:0.33, C:0.08, G:0.10, T:0.48
Consensus pattern (30 bp):
TATACATAAAATTTGATTTTGATGCAATTT
Found at i:1892986 original size:26 final size:25
Alignment explanation
Indices: 1892957--1893041 Score: 71
Period size: 26 Copynumber: 3.2 Consensus size: 25
1892947 AAAATTAAAA
*
1892957 TTATGCATATCTATAAAATTACATTT
1 TTAT-CATTTCTATAAAATTACATTT
* * *
1892983 TTATAACTTTTTATAAAACTACATTT
1 TTATCA-TTTCTATAAAATTACATTT
*
1893009 TTATAACTTTTTACTATAAAATTACATTT
1 TTAT--C-ATTT-CTATAAAATTACATTT
1893038 TTAT
1 TTAT
1893042 ATCTTTTTTA
Statistics
Matches: 46, Mismatches: 8, Indels: 7
0.75 0.13 0.11
Matches are distributed among these distances:
25 1 0.02
26 24 0.52
28 3 0.07
29 18 0.39
ACGTcount: A:0.38, C:0.11, G:0.01, T:0.51
Consensus pattern (25 bp):
TTATCATTTCTATAAAATTACATTT
Found at i:1893036 original size:29 final size:28
Alignment explanation
Indices: 1892966--1893049 Score: 127
Period size: 29 Copynumber: 3.0 Consensus size: 28
1892956 ATTATGCATA
1892966 TCTATAAAATTACATTTTTATAAC-TTT
1 TCTATAAAATTACATTTTTATAACTTTT
*
1892993 T-TATAAAACTACATTTTTATAACTTTT
1 TCTATAAAATTACATTTTTATAACTTTT
*
1893020 TACTATAAAATTACATTTTTATATCTTTT
1 T-CTATAAAATTACATTTTTATAACTTTT
1893049 T
1 T
1893050 TACGAATTAT
Statistics
Matches: 51, Mismatches: 3, Indels: 4
0.88 0.05 0.07
Matches are distributed among these distances:
26 21 0.41
27 5 0.10
29 25 0.49
ACGTcount: A:0.36, C:0.11, G:0.00, T:0.54
Consensus pattern (28 bp):
TCTATAAAATTACATTTTTATAACTTTT
Found at i:1895583 original size:14 final size:14
Alignment explanation
Indices: 1895564--1895590 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
1895554 ATATTAATTG
1895564 TTATTATTATTATA
1 TTATTATTATTATA
1895578 TTATTATTATTAT
1 TTATTATTATTAT
1895591 GAAATAAGTT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (14 bp):
TTATTATTATTATA
Done.