Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr6
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: 47432654
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.32
Warning! 2298022 characters in sequence are not A, C, G, or T
File 125 of 136
Found at i:42649768 original size:90 final size:90
Alignment explanation
Indices: 42649615--42649815 Score: 375
Period size: 90 Copynumber: 2.2 Consensus size: 90
42649605 NNNNNNNNNN
*
42649615 TACTGTTACTGTTACTGTTACCGATTCGGCACTTTGTGTGTCGAATACTGTTACCGTTACTGTTA
1 TACTGTTACTGTTACTGTTACCGACTCGGCACTTTGTGTGTCGAATACTGTTACCGTTACTGTTA
42649680 CAGATTCAGCACTTTGTGTGTTGAA
66 CAGATTCAGCACTTTGTGTGTTGAA
42649705 TACTGTTACTGTTACTGTTACCGACTCGGCACTTTGTGTGTCGAATACTGTTACCGTTACTGTTA
1 TACTGTTACTGTTACTGTTACCGACTCGGCACTTTGTGTGTCGAATACTGTTACCGTTACTGTTA
42649770 CAGATTCAGCACTTTGTGTGTTGAA
66 CAGATTCAGCACTTTGTGTGTTGAA
* *
42649795 TACTGTTACTGCTACCGTTAC
1 TACTGTTACTGTTACTGTTAC
42649816 TGATTACTGT
Statistics
Matches: 108, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
90 108 1.00
ACGTcount: A:0.20, C:0.20, G:0.20, T:0.39
Consensus pattern (90 bp):
TACTGTTACTGTTACTGTTACCGACTCGGCACTTTGTGTGTCGAATACTGTTACCGTTACTGTTA
CAGATTCAGCACTTTGTGTGTTGAA
Found at i:42649815 original size:45 final size:45
Alignment explanation
Indices: 42649615--42649820 Score: 304
Period size: 45 Copynumber: 4.6 Consensus size: 45
42649605 NNNNNNNNNN
* *
42649615 TACTGTTACTGTTACTGTTACCGATTCGGCACTTTGTGTGTCGAA
1 TACTGTTACTGTTACTGTTACAGATTCAGCACTTTGTGTGTCGAA
* *
42649660 TACTGTTACCGTTACTGTTACAGATTCAGCACTTTGTGTGTTGAA
1 TACTGTTACTGTTACTGTTACAGATTCAGCACTTTGTGTGTCGAA
* * *
42649705 TACTGTTACTGTTACTGTTACCGACTCGGCACTTTGTGTGTCGAA
1 TACTGTTACTGTTACTGTTACAGATTCAGCACTTTGTGTGTCGAA
* *
42649750 TACTGTTACCGTTACTGTTACAGATTCAGCACTTTGTGTGTTGAA
1 TACTGTTACTGTTACTGTTACAGATTCAGCACTTTGTGTGTCGAA
* * *
42649795 TACTGTTACTGCTACCGTTACTGATT
1 TACTGTTACTGTTACTGTTACAGATT
42649821 ACTGTATACT
Statistics
Matches: 143, Mismatches: 18, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
45 143 1.00
ACGTcount: A:0.20, C:0.20, G:0.20, T:0.40
Consensus pattern (45 bp):
TACTGTTACTGTTACTGTTACAGATTCAGCACTTTGTGTGTCGAA
Found at i:42653474 original size:24 final size:24
Alignment explanation
Indices: 42653446--42653497 Score: 77
Period size: 24 Copynumber: 2.2 Consensus size: 24
42653436 TTAGTAAGTC
*
42653446 AAATAAACTATGCTAATAAATACT
1 AAATAAACTATACTAATAAATACT
* *
42653470 AAATATATTATACTAATAAATACT
1 AAATAAACTATACTAATAAATACT
42653494 AAAT
1 AAAT
42653498 CTTTTAGAAA
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.56, C:0.10, G:0.02, T:0.33
Consensus pattern (24 bp):
AAATAAACTATACTAATAAATACT
Found at i:42660257 original size:8 final size:8
Alignment explanation
Indices: 42660244--42660274 Score: 62
Period size: 8 Copynumber: 3.9 Consensus size: 8
42660234 GAAATGGACC
42660244 AATTATTT
1 AATTATTT
42660252 AATTATTT
1 AATTATTT
42660260 AATTATTT
1 AATTATTT
42660268 AATTATT
1 AATTATT
42660275 GAAATCGCGT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 23 1.00
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (8 bp):
AATTATTT
Found at i:42661803 original size:16 final size:18
Alignment explanation
Indices: 42661749--42661803 Score: 55
Period size: 19 Copynumber: 3.1 Consensus size: 18
42661739 TGCAATATTC
42661749 TTTTATTTTA--TAAATAA
1 TTTTATTTTATTTAAAT-A
42661766 CTTTCTATTTTATTTAAATA
1 -TTT-TATTTTATTTAAATA
42661786 TTTTATTTT-TTT-AATA
1 TTTTATTTTATTTAAATA
42661802 TT
1 TT
42661804 ATACTATACC
Statistics
Matches: 34, Mismatches: 0, Indels: 8
0.81 0.00 0.19
Matches are distributed among these distances:
16 6 0.18
17 3 0.09
18 9 0.26
19 10 0.29
20 1 0.03
21 5 0.15
ACGTcount: A:0.31, C:0.04, G:0.00, T:0.65
Consensus pattern (18 bp):
TTTTATTTTATTTAAATA
Found at i:42664680 original size:6 final size:6
Alignment explanation
Indices: 42664671--42664708 Score: 76
Period size: 6 Copynumber: 6.3 Consensus size: 6
42664661 TTTCAATTTA
42664671 TAATCC TAATCC TAATCC TAATCC TAATCC TAATCC TA
1 TAATCC TAATCC TAATCC TAATCC TAATCC TAATCC TA
42664709 CTCATTTTAT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 32 1.00
ACGTcount: A:0.34, C:0.32, G:0.00, T:0.34
Consensus pattern (6 bp):
TAATCC
Found at i:42666393 original size:51 final size:51
Alignment explanation
Indices: 42666317--42666415 Score: 189
Period size: 51 Copynumber: 1.9 Consensus size: 51
42666307 AAAGTACAAC
42666317 CTTGCAAATGTGATAATCACAGTTTGGAACCAAAAAACTATTAGGGATGTA
1 CTTGCAAATGTGATAATCACAGTTTGGAACCAAAAAACTATTAGGGATGTA
*
42666368 CTTGCAAATGTGATAATCACAGTTTGGAACCAAAAAATTATTAGGGAT
1 CTTGCAAATGTGATAATCACAGTTTGGAACCAAAAAACTATTAGGGAT
42666416 TAGAAGTTTT
Statistics
Matches: 47, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
51 47 1.00
ACGTcount: A:0.39, C:0.13, G:0.19, T:0.28
Consensus pattern (51 bp):
CTTGCAAATGTGATAATCACAGTTTGGAACCAAAAAACTATTAGGGATGTA
Found at i:42670386 original size:21 final size:21
Alignment explanation
Indices: 42670362--42670409 Score: 53
Period size: 21 Copynumber: 2.3 Consensus size: 21
42670352 GCTTTTTAGG
* *
42670362 TTTTTAA-ATTTTTTTTCTTTA
1 TTTTTAATATTCTTTTT-TTGA
*
42670383 TTTTCAATATTCTTTTTTTGA
1 TTTTTAATATTCTTTTTTTGA
42670404 TTTTTA
1 TTTTTA
42670410 TTTTTTATAC
Statistics
Matches: 22, Mismatches: 4, Indels: 2
0.79 0.14 0.07
Matches are distributed among these distances:
21 14 0.64
22 8 0.36
ACGTcount: A:0.19, C:0.06, G:0.02, T:0.73
Consensus pattern (21 bp):
TTTTTAATATTCTTTTTTTGA
Found at i:42671588 original size:13 final size:13
Alignment explanation
Indices: 42671566--42671595 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
42671556 CTAATTTATT
*
42671566 AAATTTTATATAA
1 AAATTATATATAA
42671579 AAATTATATATAA
1 AAATTATATATAA
42671592 AAAT
1 AAAT
42671596 GGTCAAATTT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (13 bp):
AAATTATATATAA
Found at i:42679031 original size:18 final size:19
Alignment explanation
Indices: 42678999--42679034 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
42678989 TAGCTAATAC
*
42678999 ATTAAAAAATTAATTAAAA
1 ATTAAAAAATAAATTAAAA
42679018 ATTAAAAAA-AAATTAAA
1 ATTAAAAAATAAATTAAA
42679035 TCAAAATAAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 7 0.44
19 9 0.56
ACGTcount: A:0.72, C:0.00, G:0.00, T:0.28
Consensus pattern (19 bp):
ATTAAAAAATAAATTAAAA
Found at i:42679040 original size:11 final size:11
Alignment explanation
Indices: 42679003--42679051 Score: 55
Period size: 11 Copynumber: 4.5 Consensus size: 11
42678993 TAATACATTA
*
42679003 AAAAATTAATT
1 AAAAATTAAAT
*
42679014 AAAAATTAAAA
1 AAAAATTAAAT
42679025 AAAAATTAAAT
1 AAAAATTAAAT
*
42679036 CAAAA-TAAACT
1 AAAAATTAAA-T
42679047 AAAAA
1 AAAAA
42679052 ATACAAATGT
Statistics
Matches: 32, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
10 4 0.12
11 28 0.88
ACGTcount: A:0.73, C:0.04, G:0.00, T:0.22
Consensus pattern (11 bp):
AAAAATTAAAT
Found at i:42679050 original size:23 final size:23
Alignment explanation
Indices: 42679001--42679053 Score: 65
Period size: 22 Copynumber: 2.3 Consensus size: 23
42678991 GCTAATACAT
*
42679001 TAAAAAATTAATTAAAAATTAAA
1 TAAAAAATTAAATAAAAATTAAA
*
42679024 -AAAAAATTAAATCAAAA-TAAA
1 TAAAAAATTAAATAAAAATTAAA
42679045 CTAAAAAAT
1 -TAAAAAAT
42679054 ACAAATGTGA
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
21 4 0.15
22 15 0.58
23 7 0.27
ACGTcount: A:0.72, C:0.04, G:0.00, T:0.25
Consensus pattern (23 bp):
TAAAAAATTAAATAAAAATTAAA
Found at i:42688342 original size:23 final size:22
Alignment explanation
Indices: 42688294--42688350 Score: 64
Period size: 22 Copynumber: 2.6 Consensus size: 22
42688284 CCTCGGGTAA
*
42688294 ATTTTT-TTATTAAATATATAT
1 ATTTTTATTTTTAAATATATAT
42688315 ATTTTTATTTTTAAA-ATATACT
1 ATTTTTATTTTTAAATATATA-T
* *
42688337 ACTTTTAGTTTTAA
1 ATTTTTATTTTTAA
42688351 GTTTTATGTT
Statistics
Matches: 31, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
21 11 0.35
22 20 0.65
ACGTcount: A:0.35, C:0.04, G:0.02, T:0.60
Consensus pattern (22 bp):
ATTTTTATTTTTAAATATATAT
Found at i:42689080 original size:23 final size:22
Alignment explanation
Indices: 42689023--42689080 Score: 73
Period size: 23 Copynumber: 2.6 Consensus size: 22
42689013 TTTTAATTTA
*
42689023 CTTAATTTT-CGTTGTATTTTG
1 CTTAATTTTGCGTCGTATTTTG
*
42689044 CTTAATTGTAGCGTCGTATTTTG
1 CTTAATT-TTGCGTCGTATTTTG
42689067 CTTAATTTTCGCGT
1 CTTAATTTT-GCGT
42689081 TTGAATCTTT
Statistics
Matches: 31, Mismatches: 3, Indels: 4
0.82 0.08 0.11
Matches are distributed among these distances:
21 7 0.23
22 2 0.06
23 22 0.71
ACGTcount: A:0.16, C:0.14, G:0.17, T:0.53
Consensus pattern (22 bp):
CTTAATTTTGCGTCGTATTTTG
Found at i:42699026 original size:21 final size:22
Alignment explanation
Indices: 42699002--42699054 Score: 72
Period size: 23 Copynumber: 2.4 Consensus size: 22
42698992 TTTTAATTTA
42699002 CTTAATTTTCG-TTGTATTTTG
1 CTTAATTTTCGATTGTATTTTG
*
42699023 CTTAATTGTCGCATTGTATTTTG
1 CTTAATTTTCG-ATTGTATTTTG
*
42699046 ATTAATTTT
1 CTTAATTTT
42699055 TGCGTTTGAA
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
21 10 0.37
23 17 0.63
ACGTcount: A:0.19, C:0.09, G:0.13, T:0.58
Consensus pattern (22 bp):
CTTAATTTTCGATTGTATTTTG
Found at i:42699473 original size:5 final size:5
Alignment explanation
Indices: 42699465--42699499 Score: 70
Period size: 5 Copynumber: 7.0 Consensus size: 5
42699455 TTCTTTTTAG
42699465 AATTT AATTT AATTT AATTT AATTT AATTT AATTT
1 AATTT AATTT AATTT AATTT AATTT AATTT AATTT
42699500 TACTTTGTAC
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 30 1.00
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (5 bp):
AATTT
Found at i:42714683 original size:14 final size:14
Alignment explanation
Indices: 42714660--42714699 Score: 53
Period size: 14 Copynumber: 2.9 Consensus size: 14
42714650 ACAGAAAAGT
*
42714660 AAAACATTTTCCAG
1 AAAACATTTTACAG
* *
42714674 AAATCATTTTACGG
1 AAAACATTTTACAG
42714688 AAAACATTTTAC
1 AAAACATTTTAC
42714700 TGGTAATCAA
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
14 22 1.00
ACGTcount: A:0.42, C:0.17, G:0.07, T:0.33
Consensus pattern (14 bp):
AAAACATTTTACAG
Found at i:42714684 original size:34 final size:35
Alignment explanation
Indices: 42714625--42714691 Score: 91
Period size: 34 Copynumber: 1.9 Consensus size: 35
42714615 CAAACAGCAG
* * *
42714625 AAAATATTTTCTAGTAAATTATTTTACAGAAAAGT
1 AAAACATTTTCCAGTAAATCATTTTACAGAAAAGT
*
42714660 AAAACATTTTCCAG-AAATCATTTTACGGAAAA
1 AAAACATTTTCCAGTAAATCATTTTACAGAAAA
42714692 CATTTTACTG
Statistics
Matches: 28, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
34 16 0.57
35 12 0.43
ACGTcount: A:0.46, C:0.10, G:0.09, T:0.34
Consensus pattern (35 bp):
AAAACATTTTCCAGTAAATCATTTTACAGAAAAGT
Found at i:42715197 original size:41 final size:40
Alignment explanation
Indices: 42715152--42715254 Score: 143
Period size: 41 Copynumber: 2.5 Consensus size: 40
42715142 CAACTTCAAG
*
42715152 TCGATGAGGCACTGGGTGCCAATTTACTACTTCGGATTTAT
1 TCGATGAGGCACTGGGTGCCAATTTACTACTTC-GAATTAT
* **
42715193 TCGATGAGACACTGGGTGTTAATTTACTACTTCGAATTAT
1 TCGATGAGGCACTGGGTGCCAATTTACTACTTCGAATTAT
* *
42715233 CCAATGAGGCACTGGGTGCCAA
1 TCGATGAGGCACTGGGTGCCAA
42715255 ATTGGTGTGT
Statistics
Matches: 53, Mismatches: 9, Indels: 1
0.84 0.14 0.02
Matches are distributed among these distances:
40 23 0.43
41 30 0.57
ACGTcount: A:0.25, C:0.19, G:0.24, T:0.31
Consensus pattern (40 bp):
TCGATGAGGCACTGGGTGCCAATTTACTACTTCGAATTAT
Found at i:42728840 original size:15 final size:15
Alignment explanation
Indices: 42728820--42728850 Score: 62
Period size: 15 Copynumber: 2.1 Consensus size: 15
42728810 AGGTTTTTGC
42728820 ATCTCAGAGGTCTAT
1 ATCTCAGAGGTCTAT
42728835 ATCTCAGAGGTCTAT
1 ATCTCAGAGGTCTAT
42728850 A
1 A
42728851 GCTTGTACAG
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.29, C:0.19, G:0.19, T:0.32
Consensus pattern (15 bp):
ATCTCAGAGGTCTAT
Found at i:42739695 original size:243 final size:244
Alignment explanation
Indices: 42739255--42739744 Score: 973
Period size: 243 Copynumber: 2.0 Consensus size: 244
42739245 TTTATGATGT
42739255 AAAAATAAATATTTTATATTTAAAATAGTAAAAAAAACTTAAATTATTTTGTATAAAAATATTTT
1 AAAAATAAATATTTTATATTTAAAATAGTAAAAAAAACTTAAATTATTTTGTATAAAAATATTTT
42739320 TCAAAAAAATATTTACTTGAATTAATATTGTTTTTTAAGAAATATTTATGAACAAGATTTTAAAA
66 TCAAAAAAATATTTACTTGAATTAATATTGTTTTTTAAGAAATATTTATGAACAAGATTTTAAAA
42739385 CTTTACCAAATAATTTCATACGCTATAATTTGTCAAAATAAGTGTAAAATTTCAAAGACAAAAAT
131 CTTTACCAAATAATTTCATACGCTATAATTTGTCAAAATAAGTGTAAAATTTCAAAGACAAAAAT
42739450 TAATATGAAAAAATCGAAAACTAAATTGAACCAAACTTCAACAGTTTGA
196 TAATATGAAAAAATCGAAAACTAAATTGAACCAAACTTCAACAGTTTGA
42739499 AAAAATAAATA-TTTATATTTAAAATAGTAAAAAAAACTTAAATTATTTTGTATAAAAATATTTT
1 AAAAATAAATATTTTATATTTAAAATAGTAAAAAAAACTTAAATTATTTTGTATAAAAATATTTT
42739563 TCAAAAAAATATTTACTTGAATTAATATTGTTTTTTAAGAAATATTTATGAACAAGATTTTAAAA
66 TCAAAAAAATATTTACTTGAATTAATATTGTTTTTTAAGAAATATTTATGAACAAGATTTTAAAA
42739628 CTTTACCAAATAATTTCATACGCTATAATTTGTCAAAATAAGTGTAAAATTTCAAAGACAAAAAT
131 CTTTACCAAATAATTTCATACGCTATAATTTGTCAAAATAAGTGTAAAATTTCAAAGACAAAAAT
42739693 TAATATGAAAAAATCGAAAACTAAATTGAACCAAACTTCAACAGTTTGA
196 TAATATGAAAAAATCGAAAACTAAATTGAACCAAACTTCAACAGTTTGA
42739742 AAA
1 AAA
42739745 CTACAAAAAA
Statistics
Matches: 246, Mismatches: 0, Indels: 1
1.00 0.00 0.00
Matches are distributed among these distances:
243 235 0.96
244 11 0.04
ACGTcount: A:0.50, C:0.08, G:0.07, T:0.35
Consensus pattern (244 bp):
AAAAATAAATATTTTATATTTAAAATAGTAAAAAAAACTTAAATTATTTTGTATAAAAATATTTT
TCAAAAAAATATTTACTTGAATTAATATTGTTTTTTAAGAAATATTTATGAACAAGATTTTAAAA
CTTTACCAAATAATTTCATACGCTATAATTTGTCAAAATAAGTGTAAAATTTCAAAGACAAAAAT
TAATATGAAAAAATCGAAAACTAAATTGAACCAAACTTCAACAGTTTGA
Found at i:42756992 original size:86 final size:87
Alignment explanation
Indices: 42756846--42757184 Score: 383
Period size: 86 Copynumber: 3.7 Consensus size: 87
42756836 TTAAAAAGAG
* * * * *
42756846 GTAAAGTAGTTTTATTTAATACCTAACAAGTTTTTTTTATGTTTGGAAACGTATTTTATTATTAA
1 GTAACGTAATTTTATTTAATACCTAAAAAGTTTTTTTTATGTTTGGAAATGTATTCTATTATTAA
42756911 TGACACTATTAAAAAAAGTGAA
66 TGACACTATTAAAAAAAGTGAA
* * *
42756933 GTAACGTAGTTTTATTTAATAACTAAAAAG-TTTTTGTATGTTTGGAAATGTATTCTATTATTAA
1 GTAACGTAATTTTATTTAATACCTAAAAAGTTTTTTTTATGTTTGGAAATGTATTCTATTATTAA
* *
42756997 TGACACTGTTAAGAAAAAAAAGGTAAA
66 TGACACTATT----AAAAAAA-GTGAA
42757024 GTAACGTAATTTTATTTAATACCTAAAAAGTTTTTTTTTTTTTTTTATGTTTGGAAATGTATTCT
1 GTAACGTAATTTTATTTAATACCTAAAAAG--------TTTTTTTTATGTTTGGAAATGTATTCT
* * * * *
42757089 ATTATTAATCACATTAATAAAAAATGGTGGA
58 ATTATTAATGACACTATTAAAAAA-AGTGAA
* * *
42757120 GTAACGTAATTTTATTTAATACCTACAATGTTTTTTTTATGTTTGGAAATGTATTTTATTATTAA
1 GTAACGTAATTTTATTTAATACCTAAAAAGTTTTTTTTATGTTTGGAAATGTATTCTATTATTAA
42757185 AAAAAGTGAA
Statistics
Matches: 216, Mismatches: 21, Indels: 29
0.81 0.08 0.11
Matches are distributed among these distances:
86 40 0.19
87 27 0.12
88 34 0.16
90 7 0.03
91 32 0.15
96 37 0.17
100 39 0.18
ACGTcount: A:0.36, C:0.06, G:0.13, T:0.45
Consensus pattern (87 bp):
GTAACGTAATTTTATTTAATACCTAAAAAGTTTTTTTTATGTTTGGAAATGTATTCTATTATTAA
TGACACTATTAAAAAAAGTGAA
Found at i:42757141 original size:96 final size:99
Alignment explanation
Indices: 42756963--42757157 Score: 288
Period size: 96 Copynumber: 2.0 Consensus size: 99
42756953 AACTAAAAAG
*
42756963 TTTTTGTATGTTTGGAAATGTATTCTATTATTAATGACACTGTTAAGAAAAAAAAGGTAAAGTAA
1 TTTTTGTATGTTTGGAAATGTATTCTATTATTAAT-ACACTATTAAGAAAAAAAAGGTAAAGTAA
42757028 CGTAATTTTATTTAATACCTAAAAAGTTTTTTTTT
65 CGTAATTTTATTTAATACCTAAAAAGTTTTTTTTT
* * * **
42757063 TTTTTTTATGTTTGGAAATGTATTCTATTATTAAT-CAC-ATTAA-TAAAAAATGGTGGAGTAAC
1 TTTTTGTATGTTTGGAAATGTATTCTATTATTAATACACTATTAAGAAAAAAAAGGTAAAGTAAC
* *
42757125 GTAATTTTATTTAATACCTACAATGTTTTTTTT
66 GTAATTTTATTTAATACCTAAAAAGTTTTTTTT
42757158 ATGTTTGGAA
Statistics
Matches: 87, Mismatches: 8, Indels: 4
0.88 0.08 0.04
Matches are distributed among these distances:
96 46 0.53
97 4 0.05
98 3 0.03
100 34 0.39
ACGTcount: A:0.35, C:0.07, G:0.12, T:0.46
Consensus pattern (99 bp):
TTTTTGTATGTTTGGAAATGTATTCTATTATTAATACACTATTAAGAAAAAAAAGGTAAAGTAAC
GTAATTTTATTTAATACCTAAAAAGTTTTTTTTT
Found at i:42757200 original size:75 final size:75
Alignment explanation
Indices: 42757100--42757303 Score: 263
Period size: 71 Copynumber: 2.8 Consensus size: 75
42757090 TTATTAATCA
* * * * *
42757100 CATTAATAAAAAATGGTGGAGTAACGTAATTTTATTTAATACCTACAATGTTTTTTTTATGTTTG
1 CATTATTAAAAAA-AGTGAAGTAACGTAGTTTTATTTAATACCTACAATGTTTTTTTTATCTTTG
*
42757165 GAAATGTATTT
65 GAAATGTATTC
* * *
42757176 TATTATTAAAAAAAGTGAAGTAACGTAGTTTTATTTAATA-CT-C-TTTTTTTTTTTATCTTTGG
1 CATTATTAAAAAAAGTGAAGTAACGTAGTTTTATTTAATACCTACAATGTTTTTTTTATCTTTGG
42757238 AAATGTATTC
66 AAATGTATTC
* * *
42757248 CATTATT-AAAAAAGTGAAGTAACGTAGTTTTATTTAATACTTAAAAAGTTTTTTTT
1 CATTATTAAAAAAAGTGAAGTAACGTAGTTTTATTTAATACCTACAATGTTTTTTTT
42757304 TTAAATATAA
Statistics
Matches: 110, Mismatches: 15, Indels: 8
0.83 0.11 0.06
Matches are distributed among these distances:
71 32 0.29
72 32 0.29
73 1 0.01
74 10 0.09
75 24 0.22
76 11 0.10
ACGTcount: A:0.35, C:0.06, G:0.12, T:0.47
Consensus pattern (75 bp):
CATTATTAAAAAAAGTGAAGTAACGTAGTTTTATTTAATACCTACAATGTTTTTTTTATCTTTGG
AAATGTATTC
Found at i:42764950 original size:4 final size:4
Alignment explanation
Indices: 42764941--42765045 Score: 60
Period size: 4 Copynumber: 25.8 Consensus size: 4
42764931 GGGAAAGGAG
*
42764941 AAGA AAGA AAGA AAG- AA-A AAGA AAGAA AAGGA AAGGA AAGGA GAGGA
1 AAGA AAGA AAGA AAGA AAGA AAGA AAG-A AA-GA AA-GA AA-GA -AAGA
* *
42764988 AAGA AAG- AA-A AAGA AGGA AAGAA AAGGA AGGA GAAGA AA-A AA-A AAGA
1 AAGA AAGA AAGA AAGA AAGA AAG-A AA-GA AAGA -AAGA AAGA AAGA AAGA
*
42765035 AAGA AAAA AAG
1 AAGA AAGA AAG
42765046 GTGATCTTTT
Statistics
Matches: 82, Mismatches: 8, Indels: 22
0.73 0.07 0.20
Matches are distributed among these distances:
3 14 0.17
4 41 0.50
5 24 0.29
6 3 0.04
ACGTcount: A:0.71, C:0.00, G:0.29, T:0.00
Consensus pattern (4 bp):
AAGA
Found at i:42764961 original size:10 final size:10
Alignment explanation
Indices: 42764948--42765042 Score: 68
Period size: 10 Copynumber: 9.3 Consensus size: 10
42764938 GAGAAGAAAG
42764948 AAAGAAAGAA
1 AAAGAAAGAA
42764958 AAAGAAAGAA
1 AAAGAAAGAA
* *
42764968 AAGGAAAGGA
1 AAAGAAAGAA
* * *
42764978 AAGGAGAG-G
1 AAAGAAAGAA
42764987 AAAGAAAGAA
1 AAAGAAAGAA
*
42764997 AAAGAAGGAA
1 AAAGAAAGAA
*
42765007 AGAA-AAGGAA
1 A-AAGAAAGAA
*
42765017 GGAGAAGAAAAAA
1 --A-AAGAAAGAA
42765030 AAAGAAAGAA
1 AAAGAAAGAA
42765040 AAA
1 AAA
42765043 AAGGTGATCT
Statistics
Matches: 69, Mismatches: 11, Indels: 10
0.77 0.12 0.11
Matches are distributed among these distances:
9 6 0.09
10 52 0.75
11 3 0.04
12 4 0.06
13 4 0.06
ACGTcount: A:0.72, C:0.00, G:0.28, T:0.00
Consensus pattern (10 bp):
AAAGAAAGAA
Found at i:42764980 original size:33 final size:33
Alignment explanation
Indices: 42764934--42765041 Score: 94
Period size: 33 Copynumber: 3.1 Consensus size: 33
42764924 AAGGAGAGGG
42764934 AAAGGAGAA-GAAAGAAAGAAAGAAAAAGAAAGA
1 AAAGGA-AAGGAAAGAAAGAAAGAAAAAGAAAGA
*
42764967 AAAGGAAAGGAAAGGAGAGGAAAGAAAGAAAAAG-AAGG
1 AAAGGAAAGG--A--A-A-GAAAGAAAGAAAAAGAAAGA
* * *
42765005 AAAGAAAAGGAAGGAGAAGAAAAAAAAAGAAAGA
1 AAAGGAAAGGAAAGA-AAGAAAGAAAAAGAAAGA
42765039 AAA
1 AAA
42765042 AAAGGTGATC
Statistics
Matches: 61, Mismatches: 5, Indels: 17
0.73 0.06 0.20
Matches are distributed among these distances:
32 4 0.07
33 19 0.31
34 7 0.11
35 1 0.02
36 1 0.02
37 1 0.02
38 13 0.21
39 15 0.25
ACGTcount: A:0.70, C:0.00, G:0.30, T:0.00
Consensus pattern (33 bp):
AAAGGAAAGGAAAGAAAGAAAGAAAAAGAAAGA
Found at i:42764990 original size:43 final size:43
Alignment explanation
Indices: 42764932--42765042 Score: 145
Period size: 43 Copynumber: 2.6 Consensus size: 43
42764922 AGAAGGAGAG
42764932 GGAAAGGAGAAGAAAGAAAGAAAGAA-AAAGAAAGAAAAGGAAA
1 GGAAAGGAGAAGAAAGAAAGAAA-AAGAAAGAAAGAAAAGGAAA
* *
42764975 GGAAAGGAGAGGAAAGAAAGAAAAAGAAGGAAAGAAAAGG-AA
1 GGAAAGGAGAAGAAAGAAAGAAAAAGAAAGAAAGAAAAGGAAA
* * *
42765017 GGAGAAGAAAAAAAAAGAAAGAAAAA
1 GGA-AAGGAGAAGAAAGAAAGAAAAA
42765043 AAGGTGATCT
Statistics
Matches: 60, Mismatches: 6, Indels: 4
0.86 0.09 0.06
Matches are distributed among these distances:
42 7 0.12
43 53 0.88
ACGTcount: A:0.69, C:0.00, G:0.31, T:0.00
Consensus pattern (43 bp):
GGAAAGGAGAAGAAAGAAAGAAAAAGAAAGAAAGAAAAGGAAA
Found at i:42765043 original size:14 final size:14
Alignment explanation
Indices: 42764944--42765044 Score: 76
Period size: 14 Copynumber: 7.1 Consensus size: 14
42764934 AAAGGAGAAG
*
42764944 AAAGAAAGAAAGAA
1 AAAGAAAGAAAAAA
*
42764958 AAAGAAAGAAAAGGA
1 AAAGAAAGAAAA-AA
* * * **
42764973 AAGGAAAGGAGAGG
1 AAAGAAAGAAAAAA
*
42764987 AAAGAAAGAAAAAG
1 AAAGAAAGAAAAAA
* **
42765001 AAGGAAAGAAAAGG
1 AAAGAAAGAAAAAA
*
42765015 AAGGAGAAGAAAAAA
1 AAAGA-AAGAAAAAA
42765030 AAAGAAAGAAAAAA
1 AAAGAAAGAAAAAA
42765044 A
1 A
42765045 GGTGATCTTT
Statistics
Matches: 70, Mismatches: 15, Indels: 4
0.79 0.17 0.04
Matches are distributed among these distances:
14 49 0.70
15 21 0.30
ACGTcount: A:0.72, C:0.00, G:0.28, T:0.00
Consensus pattern (14 bp):
AAAGAAAGAAAAAA
Found at i:42765565 original size:158 final size:152
Alignment explanation
Indices: 42765373--42765846 Score: 526
Period size: 158 Copynumber: 3.0 Consensus size: 152
42765363 AAATGGTATA
* * * *
42765373 TTTAAAAAACACACTAAATTAATAAATTTCAAACATAATGTTCTAAAATAATATAAAATAATAAA
1 TTTAAAAAACAAAATAAATTAATAAATTTCAAACATAATGTACTGAAATAATATAAAATAATAAA
*
42765438 ATTAGAAAATATGATATTTTTT-AAAGTAATAAAATGCGGAGAAAAAAATACGAGCAAAGGGCCG
66 ATTAGAAAATAT-ATATTTTTTGAAAGTAATAAAATTCGGAGAAAAAAATACGAGCAAAGGGCCG
* *
42765502 AAGTAAGAGTTTTTTACTAAATTT
130 AAATAAG-GTTTTTTATTAAATTT
* *
42765526 TTTAAAAATTCAGAAAT-AATTAATACAAATATTTCAAACAAAATGTACTGAAATAATATAAAAT
1 TTTAAAAA-ACA-AAATAAATTAAT---AA-ATTTCAAACATAATGTACTGAAATAATATAAAAT
*
42765590 AATAAAA-TACGAAAATAATATATTTTTATCGAAAGTAATAAAATTC-GAAAAAAATAATACGAG
60 AATAAAATTA-GAAAAT-ATATATTTTT-T-GAAAGTAATAAAATTCGGAGAAAAA-AATACGAG
* *
42765653 CAAAGGGCAGAAATAAGGTTTTTTTTTTTAAATTT
120 CAAAGGGCCGAAATAAGG--TTTTTTATTAAATTT
* * * *
42765688 ATTTAAAAAACACACTAAATTAATAAATTTCAAACATAATGTACTGAAATAATGTAAACTAATAA
1 -TTTAAAAAACAAAATAAATTAATAAATTTCAAACATAATGTACTGAAATAATATAAAATAATAA
* * ** *
42765753 AATTAGAAAATATAATATTTTTATTGAAAGTAATAAAATTCGG-GAAAATAGTACGAATAAATGG
65 AATTAGAAAATAT-ATA-TTTT-TTGAAAGTAATAAAATTCGGAGAAAAAAATACGAGCAAAGGG
* *
42765817 ACGAAATAAGGGTTTTTTATTAATTTT
127 CCGAAATAA-GGTTTTTTATTAAATTT
42765844 TTT
1 TTT
42765847 TGAACTTGCA
Statistics
Matches: 271, Mismatches: 28, Indels: 42
0.79 0.08 0.12
Matches are distributed among these distances:
153 8 0.03
154 9 0.03
155 5 0.02
156 13 0.05
157 24 0.09
158 121 0.45
159 13 0.05
160 9 0.03
161 39 0.14
162 22 0.08
163 8 0.03
ACGTcount: A:0.50, C:0.07, G:0.10, T:0.32
Consensus pattern (152 bp):
TTTAAAAAACAAAATAAATTAATAAATTTCAAACATAATGTACTGAAATAATATAAAATAATAAA
ATTAGAAAATATATATTTTTTGAAAGTAATAAAATTCGGAGAAAAAAATACGAGCAAAGGGCCGA
AATAAGGTTTTTTATTAAATTT
Found at i:42767927 original size:11 final size:11
Alignment explanation
Indices: 42767908--42767977 Score: 65
Period size: 10 Copynumber: 6.5 Consensus size: 11
42767898 AAAAATTAAA
42767908 AAAAGTATTTTT
1 AAAA-TATTTTT
42767920 AAAATATTTTT
1 AAAATATTTTT
42767931 AAAATA-TTTT
1 AAAATATTTTT
***
42767941 AAAAT-TTAAA
1 AAAATATTTTT
*
42767951 AAAAGTATTTTA
1 AAAA-TATTTTT
42767963 AAAATA-TTTT
1 AAAATATTTTT
42767973 AAAAT
1 AAAAT
42767978 TAAAAAAATT
Statistics
Matches: 49, Mismatches: 6, Indels: 8
0.78 0.10 0.13
Matches are distributed among these distances:
10 22 0.45
11 16 0.33
12 11 0.22
ACGTcount: A:0.53, C:0.00, G:0.03, T:0.44
Consensus pattern (11 bp):
AAAATATTTTT
Found at i:42767933 original size:43 final size:42
Alignment explanation
Indices: 42767882--42767994 Score: 160
Period size: 43 Copynumber: 2.7 Consensus size: 42
42767872 GGCCCATTTT
*
42767882 TATTTTAAAAATTTTAAAAAATTAAAAAAAGTATTTTTAAAA
1 TATTTTAAAAATTTTAAAAAATTAAAAAAAGTATTTTAAAAA
*
42767924 TATTTTTAAAATATTTT-AAAATTTAAAAAAAGTATTTTAAAAA
1 TA-TTTTAAAA-ATTTTAAAAAATTAAAAAAAGTATTTTAAAAA
*
42767967 TATTTT-AAAA-TTAAAAAAATTAAAAAAA
1 TATTTTAAAAATTTTAAAAAATTAAAAAAA
42767995 TAAAAATATT
Statistics
Matches: 64, Mismatches: 4, Indels: 8
0.84 0.05 0.11
Matches are distributed among these distances:
39 2 0.03
40 14 0.22
41 3 0.05
42 6 0.09
43 34 0.53
44 5 0.08
ACGTcount: A:0.58, C:0.00, G:0.02, T:0.40
Consensus pattern (42 bp):
TATTTTAAAAATTTTAAAAAATTAAAAAAAGTATTTTAAAAA
Found at i:42767965 original size:31 final size:31
Alignment explanation
Indices: 42767920--42767985 Score: 107
Period size: 32 Copynumber: 2.1 Consensus size: 31
42767910 AAGTATTTTT
*
42767920 AAAA-TATTTTTAAAATATTTTAAAATTTAAA
1 AAAAGTATTTTAAAAATATTTTAAAA-TTAAA
42767951 AAAAGTATTTTAAAAATATTTTAAAATTAAA
1 AAAAGTATTTTAAAAATATTTTAAAATTAAA
42767982 AAAA
1 AAAA
42767986 TTAAAAAAAT
Statistics
Matches: 33, Mismatches: 1, Indels: 2
0.92 0.03 0.06
Matches are distributed among these distances:
31 13 0.39
32 20 0.61
ACGTcount: A:0.59, C:0.00, G:0.02, T:0.39
Consensus pattern (31 bp):
AAAAGTATTTTAAAAATATTTTAAAATTAAA
Found at i:42767982 original size:17 final size:17
Alignment explanation
Indices: 42767960--42768006 Score: 58
Period size: 17 Copynumber: 2.8 Consensus size: 17
42767950 AAAAAGTATT
**
42767960 TTAAAAATATTTTAAAA
1 TTAAAAATATTAAAAAA
*
42767977 TTAAAAAAATTAAAAAA
1 TTAAAAATATTAAAAAA
*
42767994 ATAAAAATATTAA
1 TTAAAAATATTAA
42768007 TTATATTCGG
Statistics
Matches: 25, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
17 25 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (17 bp):
TTAAAAATATTAAAAAA
Found at i:42767987 original size:9 final size:9
Alignment explanation
Indices: 42767973--42768006 Score: 52
Period size: 9 Copynumber: 3.9 Consensus size: 9
42767963 AAAATATTTT
42767973 AAAATTAAA
1 AAAATTAAA
42767982 AAAATTAAA
1 AAAATTAAA
42767991 AAAA-TAAA
1 AAAATTAAA
*
42767999 AATATTAA
1 AAAATTAA
42768007 TTATATTCGG
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
8 7 0.30
9 16 0.70
ACGTcount: A:0.76, C:0.00, G:0.00, T:0.24
Consensus pattern (9 bp):
AAAATTAAA
Found at i:42768285 original size:59 final size:59
Alignment explanation
Indices: 42768188--42768310 Score: 237
Period size: 59 Copynumber: 2.1 Consensus size: 59
42768178 CCTCTAGTTG
*
42768188 CGAACATCTAGAACGTGACTGTCGACCTCCGAATAGGTATACCCCTATGACCACACCAT
1 CGAACATCTAGAACGTGACTGTCGACCTCCGAAAAGGTATACCCCTATGACCACACCAT
42768247 CGAACATCTAGAACGTGACTGTCGACCTCCGAAAAGGTATACCCCTATGACCACACCAT
1 CGAACATCTAGAACGTGACTGTCGACCTCCGAAAAGGTATACCCCTATGACCACACCAT
42768306 CGAAC
1 CGAAC
42768311 CATCAATTTT
Statistics
Matches: 63, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
59 63 1.00
ACGTcount: A:0.32, C:0.33, G:0.17, T:0.19
Consensus pattern (59 bp):
CGAACATCTAGAACGTGACTGTCGACCTCCGAAAAGGTATACCCCTATGACCACACCAT
Found at i:42776288 original size:3 final size:3
Alignment explanation
Indices: 42776280--42776304 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
42776270 CTCCCCTTTC
42776280 TCT TCT TCT TCT TCT TCT TCT TCT T
1 TCT TCT TCT TCT TCT TCT TCT TCT T
42776305 ATTTTTATCC
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.00, C:0.32, G:0.00, T:0.68
Consensus pattern (3 bp):
TCT
Found at i:42781203 original size:15 final size:15
Alignment explanation
Indices: 42781154--42781204 Score: 52
Period size: 15 Copynumber: 3.5 Consensus size: 15
42781144 TTATTTCAAA
42781154 TTATATTTTAGTCAT
1 TTATATTTTAGTCAT
* **
42781169 TTAT-GTTT-GAAAT
1 TTATATTTTAGTCAT
42781182 GTTATATTTTAGTCAT
1 -TTATATTTTAGTCAT
42781198 TTATATT
1 TTATATT
42781205 ATCGTATTGT
Statistics
Matches: 27, Mismatches: 6, Indels: 6
0.69 0.15 0.15
Matches are distributed among these distances:
13 3 0.11
14 7 0.26
15 14 0.52
16 3 0.11
ACGTcount: A:0.27, C:0.04, G:0.10, T:0.59
Consensus pattern (15 bp):
TTATATTTTAGTCAT
Found at i:42782159 original size:19 final size:19
Alignment explanation
Indices: 42782121--42782169 Score: 53
Period size: 19 Copynumber: 2.5 Consensus size: 19
42782111 ACATTGGATG
**
42782121 AAATAAAAATTATTTGTAA
1 AAATAAAAATTATTAATAA
*
42782140 AAATAATAATTATTAATAA
1 AAATAAAAATTATTAATAA
*
42782159 AGAATTAAAAT
1 A-AATAAAAAT
42782170 ATAAACAATC
Statistics
Matches: 24, Mismatches: 5, Indels: 1
0.80 0.17 0.03
Matches are distributed among these distances:
19 17 0.71
20 7 0.29
ACGTcount: A:0.61, C:0.00, G:0.04, T:0.35
Consensus pattern (19 bp):
AAATAAAAATTATTAATAA
Found at i:42784899 original size:21 final size:22
Alignment explanation
Indices: 42784853--42784910 Score: 59
Period size: 22 Copynumber: 2.8 Consensus size: 22
42784843 GCTGTGCTTA
*
42784853 CTTA-ATTTTCTTTTTTTAAAT
1 CTTATATTCTCTTTTTTTAAAT
* *
42784874 ATTATATTCTCTTTTTTT-CAT
1 CTTATATTCTCTTTTTTTAAAT
*
42784895 CTTAT-TTCCCTTTTTT
1 CTTATATTCTCTTTTTT
42784911 AGCAAACTGC
Statistics
Matches: 31, Mismatches: 5, Indels: 3
0.79 0.13 0.08
Matches are distributed among these distances:
20 10 0.32
21 9 0.29
22 12 0.39
ACGTcount: A:0.17, C:0.16, G:0.00, T:0.67
Consensus pattern (22 bp):
CTTATATTCTCTTTTTTTAAAT
Found at i:42798132 original size:22 final size:20
Alignment explanation
Indices: 42798101--42798162 Score: 63
Period size: 21 Copynumber: 3.0 Consensus size: 20
42798091 TCCAAAAAAC
*
42798101 AAAAATATTTTTATATTTTTT
1 AAAAATAATTTTATA-TTTTT
*
42798122 TAAAATAATTTTA-ATTTTT
1 AAAAATAATTTTATATTTTT
*
42798141 AAAAATAAATTTCATAATTTTT
1 AAAAAT-AATTTTAT-ATTTTT
42798163 GAGCATTAAA
Statistics
Matches: 34, Mismatches: 4, Indels: 5
0.79 0.09 0.12
Matches are distributed among these distances:
19 10 0.29
20 7 0.21
21 11 0.32
22 6 0.18
ACGTcount: A:0.44, C:0.02, G:0.00, T:0.55
Consensus pattern (20 bp):
AAAAATAATTTTATATTTTT
Found at i:42798910 original size:2 final size:2
Alignment explanation
Indices: 42798905--42798929 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
42798895 TTATTTAATA
42798905 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
42798930 GGTAAAATGA
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:42805480 original size:17 final size:17
Alignment explanation
Indices: 42805460--42805494 Score: 70
Period size: 17 Copynumber: 2.1 Consensus size: 17
42805450 CAGATTATAT
42805460 AGAAGGATTAAAATTAC
1 AGAAGGATTAAAATTAC
42805477 AGAAGGATTAAAATTAC
1 AGAAGGATTAAAATTAC
42805494 A
1 A
42805495 TAAACCAAAC
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.54, C:0.06, G:0.17, T:0.23
Consensus pattern (17 bp):
AGAAGGATTAAAATTAC
Found at i:42812923 original size:69 final size:69
Alignment explanation
Indices: 42812845--42812999 Score: 188
Period size: 69 Copynumber: 2.2 Consensus size: 69
42812835 GAAATTATAA
* * * *
42812845 ACGTAAGACCATAGTGAGACTATGGCCGTTGTTCGGATA-TAAGACCATGGTTGGACCATGGCAA
1 ACGTAAGACCATAGCGAGACTATGGCAGTTATT--GATACAAAGACCATGGTTGGACCATGGCAA
42812909 TG-TAT
64 TGATAT
* * *
42812914 ACGTAAGACCATAGCGAGGCTATGGTAGTTATTTATACGAAAGACCATGGTTGGACCATGGCAAT
1 ACGTAAGACCATAGCGAGACTATGGCAGTTATTGATAC-AAAGACCATGGTTGGACCATGGCAAT
42812979 GTATAT
65 G-ATAT
*
42812985 ATGTAAGACCATAGC
1 ACGTAAGACCATAGC
42813000 TGGGCTATGG
Statistics
Matches: 74, Mismatches: 8, Indels: 6
0.84 0.09 0.07
Matches are distributed among these distances:
67 3 0.04
69 54 0.73
71 17 0.23
ACGTcount: A:0.32, C:0.17, G:0.26, T:0.26
Consensus pattern (69 bp):
ACGTAAGACCATAGCGAGACTATGGCAGTTATTGATACAAAGACCATGGTTGGACCATGGCAATG
ATAT
Found at i:42823211 original size:50 final size:50
Alignment explanation
Indices: 42823091--42823337 Score: 246
Period size: 50 Copynumber: 4.8 Consensus size: 50
42823081 GATAATAACA
* * ** * *
42823091 TGCCAAAGCCATGTCCCAGACATAGTCTTACATGGGATGTTTCATGTAC--
1 TGCCAACGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCT-CGG
* * **
42823140 TACCAATGCCATGTCCCAGACATGGTCTTACGGGGGACCTCTCATCTCGG
1 TGCCAACGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCGG
* * *
42823190 TGCCAACGCCATGTCCCAGACATGGTATTACATGGGACCTCTCGTCTTGG
1 TGCCAACGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCGG
*
42823240 TGCCAACGCCATGTCCCAGACATGGTCTTACATGAGACCTCTCATGATCTCAAGG
1 TGCCAACGCCATGTCCCAGACATGGTCTTACATGGGACCTCTC---ATCTC--GG
* ** * *
42823295 ATGCCAATGCCATGTCATATACATGGTCTTACATGGGATCTCT
1 -TGCCAACGCCATGTCCCAGACATGGTCTTACATGGGACCTCT
42823338 TTACCCAAAT
Statistics
Matches: 164, Mismatches: 26, Indels: 9
0.82 0.13 0.05
Matches are distributed among these distances:
48 1 0.01
49 38 0.23
50 84 0.51
53 3 0.02
55 2 0.01
56 36 0.22
ACGTcount: A:0.23, C:0.28, G:0.21, T:0.27
Consensus pattern (50 bp):
TGCCAACGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCGG
Found at i:42823708 original size:30 final size:30
Alignment explanation
Indices: 42823674--42823731 Score: 73
Period size: 30 Copynumber: 1.9 Consensus size: 30
42823664 CCTCGACTCT
42823674 AACTTTGGA-AAAATTACAATTTTTCCCCTA
1 AACTTT-GACAAAATTACAATTTTTCCCCTA
* * *
42823704 AACTTTTACATAATTACACTTTTTCCCC
1 AACTTTGACAAAATTACAATTTTTCCCC
42823732 AAAGCTCGGA
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
29 1 0.04
30 23 0.96
ACGTcount: A:0.33, C:0.24, G:0.03, T:0.40
Consensus pattern (30 bp):
AACTTTGACAAAATTACAATTTTTCCCCTA
Found at i:42834960 original size:15 final size:14
Alignment explanation
Indices: 42834942--42834988 Score: 53
Period size: 14 Copynumber: 3.4 Consensus size: 14
42834932 ATAATAATTA
42834942 AAATAATAAGAAAAT
1 AAATAATAA-AAAAT
*
42834957 AAATAA-AAACAA-
1 AAATAATAAAAAAT
*
42834969 AAATAATAAAAATT
1 AAATAATAAAAAAT
42834983 AAATAA
1 AAATAA
42834989 AATGAAATGA
Statistics
Matches: 27, Mismatches: 3, Indels: 5
0.77 0.09 0.14
Matches are distributed among these distances:
12 6 0.22
13 7 0.26
14 8 0.30
15 6 0.22
ACGTcount: A:0.77, C:0.02, G:0.02, T:0.19
Consensus pattern (14 bp):
AAATAATAAAAAAT
Found at i:42836642 original size:17 final size:17
Alignment explanation
Indices: 42836620--42836652 Score: 66
Period size: 17 Copynumber: 1.9 Consensus size: 17
42836610 TTTGAATTAG
42836620 TGAATTTTGTGATTTAT
1 TGAATTTTGTGATTTAT
42836637 TGAATTTTGTGATTTA
1 TGAATTTTGTGATTTA
42836653 AAAAGAATTT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.24, C:0.00, G:0.18, T:0.58
Consensus pattern (17 bp):
TGAATTTTGTGATTTAT
Found at i:42837955 original size:46 final size:46
Alignment explanation
Indices: 42837885--42838023 Score: 242
Period size: 46 Copynumber: 3.0 Consensus size: 46
42837875 CATGGCAAAG
*
42837885 TGTGAAACGTAGGTATGGTATTTCAGTGAAGAAAACCATACTGAGT
1 TGTGAAAAGTAGGTATGGTATTTCAGTGAAGAAAACCATACTGAGT
*
42837931 TGTGAAAAGTAGGTATGGTGTTTCAGTGAAGAAAACCATACTGAGT
1 TGTGAAAAGTAGGTATGGTATTTCAGTGAAGAAAACCATACTGAGT
* *
42837977 TGTGAAAAGTAGGTATGGTATTTCTGTGAAGAAAACCATATTGAGT
1 TGTGAAAAGTAGGTATGGTATTTCAGTGAAGAAAACCATACTGAGT
42838023 T
1 T
42838024 ATAGCAATGT
Statistics
Matches: 88, Mismatches: 5, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
46 88 1.00
ACGTcount: A:0.35, C:0.09, G:0.27, T:0.30
Consensus pattern (46 bp):
TGTGAAAAGTAGGTATGGTATTTCAGTGAAGAAAACCATACTGAGT
Found at i:42843526 original size:13 final size:13
Alignment explanation
Indices: 42843503--42843536 Score: 52
Period size: 13 Copynumber: 2.6 Consensus size: 13
42843493 AAAACCATAT
42843503 ATTTT-AATTTAA
1 ATTTTAAATTTAA
42843515 ATTTTAAATTTAA
1 ATTTTAAATTTAA
42843528 ATTGTTAAA
1 ATT-TTAAA
42843537 AGATTAAGCT
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
12 5 0.25
13 10 0.50
14 5 0.25
ACGTcount: A:0.44, C:0.00, G:0.03, T:0.53
Consensus pattern (13 bp):
ATTTTAAATTTAA
Found at i:42847685 original size:24 final size:24
Alignment explanation
Indices: 42847648--42847734 Score: 72
Period size: 24 Copynumber: 3.6 Consensus size: 24
42847638 GGACACACCA
*
42847648 CAACTCGTATGAGCTTATCGATTT
1 CAACTCGTATGAGCTTACCGATTT
42847672 CAACTCGTGA-GAGCTTACCGA-TT
1 CAACTCGT-ATGAGCTTACCGATTT
* * *
42847695 CATAGCTCGGAGGAGCTTACCGTTTAT
1 CA-A-CTCGTATGAGCTTACCGATT-T
*
42847722 C-ACTTGTATGAGC
1 CAACTCGTATGAGC
42847735 ATACATTTAC
Statistics
Matches: 51, Mismatches: 6, Indels: 12
0.74 0.09 0.17
Matches are distributed among these distances:
23 4 0.08
24 28 0.55
25 16 0.31
26 1 0.02
27 2 0.04
ACGTcount: A:0.24, C:0.23, G:0.22, T:0.31
Consensus pattern (24 bp):
CAACTCGTATGAGCTTACCGATTT
Found at i:42850424 original size:26 final size:29
Alignment explanation
Indices: 42850402--42850456 Score: 87
Period size: 28 Copynumber: 2.0 Consensus size: 29
42850392 ATATTATGTT
42850402 TTAAA-AATAATTATATTAATTATATATG
1 TTAAATAATAATTATATTAATTATATATG
*
42850430 TTAAATAATAATTATA-TATTTATATAT
1 TTAAATAATAATTATATTAATTATATAT
42850457 ATTGAATTAC
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
28 15 0.60
29 10 0.40
ACGTcount: A:0.49, C:0.00, G:0.02, T:0.49
Consensus pattern (29 bp):
TTAAATAATAATTATATTAATTATATATG
Found at i:42869549 original size:91 final size:86
Alignment explanation
Indices: 42869441--42869602 Score: 252
Period size: 91 Copynumber: 1.8 Consensus size: 86
42869431 GCAAAGACAG
*
42869441 AAATTTTCGTTTATTTTTTACACATGTTCTAGTATATAGGAAAATTTTTCATTTTAGTATATAGG
1 AAATTTTCATTTATTTTTTACACATGTTCTAGTATATAGGAAAA----T-ATTTTAGTATATAGG
42869506 TTAGCAATAAACTAATTCAATTGGTA
61 TTAGCAATAAACTAATTCAATTGGTA
* *
42869532 AAATTTTCATTTATTTTTTACGCATGTTTTAGTATATAGGAAAATATTTTAGTATATAGGTTAGC
1 AAATTTTCATTTATTTTTTACACATGTTCTAGTATATAGGAAAATATTTTAGTATATAGGTTAGC
42869597 AATAAA
66 AATAAA
42869603 TAGGCTTTTT
Statistics
Matches: 68, Mismatches: 3, Indels: 5
0.89 0.04 0.07
Matches are distributed among these distances:
86 26 0.38
87 1 0.01
91 41 0.60
ACGTcount: A:0.35, C:0.07, G:0.12, T:0.45
Consensus pattern (86 bp):
AAATTTTCATTTATTTTTTACACATGTTCTAGTATATAGGAAAATATTTTAGTATATAGGTTAGC
AATAAACTAATTCAATTGGTA
Found at i:42876864 original size:25 final size:25
Alignment explanation
Indices: 42876823--42877001 Score: 75
Period size: 25 Copynumber: 7.2 Consensus size: 25
42876813 ACAAACCGCA
*
42876823 GCTCTTTTG-AGCGTCCCGATATATG
1 GCTC-TTTGAAGCTTCCCGATATATG
* * **
42876848 GCTCTTTGAAGCTTCCCAATAAAAA
1 GCTCTTTGAAGCTTCCCGATATATG
* * *
42876873 TCTCTTTCATGAGCTTCCCGAT-TAAAG
1 GCTCTTTGA--AGCTTCCCGATAT-ATG
* * *
42876900 ACTCTCTGGAGCTTCCCGATAT-TG
1 GCTCTTTGAAGCTTCCCGATATATG
* *
42876924 GCTCGCTTGAACCTTCCCG-TCAT-TG
1 GCTC-TTTGAAGCTTCCCGAT-ATATG
* *
42876949 GCTCGTATG-AGCTTCCCGTTA-ATG
1 GCTC-TTTGAAGCTTCCCGATATATG
* * * *
42876973 GCTCTTTGGAGCTTTCCGTTACATG
1 GCTCTTTGAAGCTTCCCGATATATG
42876998 GCTC
1 GCTC
42877002 ACATGGGCTT
Statistics
Matches: 118, Mismatches: 25, Indels: 22
0.72 0.15 0.13
Matches are distributed among these distances:
23 3 0.03
24 35 0.30
25 62 0.53
26 1 0.01
27 17 0.14
ACGTcount: A:0.18, C:0.27, G:0.20, T:0.34
Consensus pattern (25 bp):
GCTCTTTGAAGCTTCCCGATATATG
Found at i:42876974 original size:24 final size:23
Alignment explanation
Indices: 42876881--42877001 Score: 73
Period size: 24 Copynumber: 5.0 Consensus size: 23
42876871 AATCTCTTTC
* *
42876881 ATGAGCTTCCCGATTAAAGACTCT
1 ATGAGCTTCCCG-TTAATGGCTCT
* * *
42876905 CTGGAGCTTCCCGATATTGGCTCGCT
1 AT-GAGCTTCCCGTTAATGGCT--CT
* * *
42876931 -TGAACCTTCCCGTCATTGGCTCGT
1 ATG-AGCTTCCCGTTAATGGCTC-T
42876955 ATGAGCTTCCCGTTAATGGCTCT
1 ATGAGCTTCCCGTTAATGGCTCT
* *
42876978 TTGGAGCTTTCCGTTACATGGCTC
1 AT-GAGCTTCCCGTTA-ATGGCTC
42877002 ACATGGGCTT
Statistics
Matches: 76, Mismatches: 13, Indels: 15
0.73 0.12 0.14
Matches are distributed among these distances:
23 3 0.04
24 36 0.47
25 35 0.46
26 2 0.03
ACGTcount: A:0.17, C:0.28, G:0.22, T:0.33
Consensus pattern (23 bp):
ATGAGCTTCCCGTTAATGGCTCT
Found at i:42879340 original size:28 final size:28
Alignment explanation
Indices: 42879275--42879346 Score: 83
Period size: 28 Copynumber: 2.5 Consensus size: 28
42879265 GAGCCCTATA
*
42879275 CAATATCAGT-ACAATGTGGGCCTTAGCC
1 CAATA-CAGTAACAGTGTGGGCCTTAGCC
* * *
42879303 TATTATAGTAACAGTGTGGGCCTTAGCC
1 CAATACAGTAACAGTGTGGGCCTTAGCC
42879331 CAATACAGTAATCAGT
1 CAATACAGTAA-CAGT
42879347 ACAATGCAGT
Statistics
Matches: 35, Mismatches: 7, Indels: 3
0.78 0.16 0.07
Matches are distributed among these distances:
27 3 0.09
28 28 0.80
29 4 0.11
ACGTcount: A:0.31, C:0.21, G:0.21, T:0.28
Consensus pattern (28 bp):
CAATACAGTAACAGTGTGGGCCTTAGCC
Found at i:42879517 original size:25 final size:25
Alignment explanation
Indices: 42879457--42879527 Score: 90
Period size: 26 Copynumber: 2.8 Consensus size: 25
42879447 AATATCACAG
*
42879457 CAAAGCTGCCAGTAATAATAACGTA
1 CAAAGCTGCCAGTAATAGTAACGTA
* *
42879482 GCAAAGATGCCAGTAACAGTAACGCT-
1 -CAAAGCTGCCAGTAATAGTAACG-TA
42879508 CAAAGCTGCCAGTAATAGTA
1 CAAAGCTGCCAGTAATAGTA
42879528 TATGTGGCAT
Statistics
Matches: 39, Mismatches: 5, Indels: 3
0.83 0.11 0.06
Matches are distributed among these distances:
25 18 0.46
26 20 0.51
27 1 0.03
ACGTcount: A:0.41, C:0.21, G:0.20, T:0.18
Consensus pattern (25 bp):
CAAAGCTGCCAGTAATAGTAACGTA
Found at i:42879735 original size:27 final size:27
Alignment explanation
Indices: 42879685--42879755 Score: 79
Period size: 27 Copynumber: 2.6 Consensus size: 27
42879675 GCATAATACC
* * *
42879685 ATAACAGTCATTTCATCTCCTAGGGGT
1 ATAACAGTCATTTTACCTCATAGGGGT
*
42879712 ATAACAGTCATTTTACCTTATAGGGGT
1 ATAACAGTCATTTTACCTCATAGGGGT
***
42879739 ATTTTAGTCATTTTACC
1 ATAACAGTCATTTTACC
42879756 CTTCAAAGGT
Statistics
Matches: 37, Mismatches: 7, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
27 37 1.00
ACGTcount: A:0.27, C:0.18, G:0.15, T:0.39
Consensus pattern (27 bp):
ATAACAGTCATTTTACCTCATAGGGGT
Found at i:42879766 original size:27 final size:27
Alignment explanation
Indices: 42879735--42880148 Score: 380
Period size: 27 Copynumber: 15.3 Consensus size: 27
42879725 TACCTTATAG
* * *
42879735 GGGTATTTTAGTCATTTTACCCTTCAA
1 GGGTATTTTGGTAATTTTACCCTTCGA
* * * * * *
42879762 AGGTATTTCGATTATTTTACCTTTCAA
1 GGGTATTTTGGTAATTTTACCCTTCGA
* *
42879789 GGGTATTTTGGTAATTTTACCTTTCAA
1 GGGTATTTTGGTAATTTTACCCTTCGA
* * * *
42879816 TGGTATTTTGGTTATTTTACCATTCAGG
1 GGGTATTTTGGTAATTTTACCCTTC-GA
* * *
42879844 GGGAATTTCGGTAATTTTACCCTTTGA
1 GGGTATTTTGGTAATTTTACCCTTCGA
* * *
42879871 AGGTATTTCGATAATTTTACCCTTCGA
1 GGGTATTTTGGTAATTTTACCCTTCGA
* *
42879898 GGGTTTTTTGGTCATTTTACCCTTCGA
1 GGGTATTTTGGTAATTTTACCCTTCGA
*** * *
42879925 GGGTATTTCAATCATTTTACCATTCGA
1 GGGTATTTTGGTAATTTTACCCTTCGA
* * *
42879952 GGGTATTTCGGTTATTTTACCCTT-TA
1 GGGTATTTTGGTAATTTTACCCTTCGA
* *
42879978 GGGGTATTTTGGTTATTTTACCCTTTGA
1 -GGGTATTTTGGTAATTTTACCCTTCGA
* *
42880006 GGGTATTTCGGTTATTTTACCCTTCGA
1 GGGTATTTTGGTAATTTTACCCTTCGA
* * *
42880033 AGGTATTTTGATAATTTTAACCTTCGA
1 GGGTATTTTGGTAATTTTACCCTTCGA
* * * * **
42880060 GGGTATTTCGATAATTTTTCCTTTTAA
1 GGGTATTTTGGTAATTTTACCCTTCGA
* *
42880087 GGGTATTTCGGTAATTTTACCCTTCAA
1 GGGTATTTTGGTAATTTTACCCTTCGA
*
42880114 GGGTATTTTGATAATTTTACCCTTCGA
1 GGGTATTTTGGTAATTTTACCCTTCGA
42880141 GGGTATTT
1 GGGTATTT
42880149 CGGTCCCATT
Statistics
Matches: 320, Mismatches: 64, Indels: 6
0.82 0.16 0.02
Matches are distributed among these distances:
26 1 0.00
27 299 0.93
28 20 0.06
ACGTcount: A:0.21, C:0.15, G:0.19, T:0.46
Consensus pattern (27 bp):
GGGTATTTTGGTAATTTTACCCTTCGA
Found at i:42879969 original size:81 final size:81
Alignment explanation
Indices: 42879735--42880153 Score: 444
Period size: 81 Copynumber: 5.2 Consensus size: 81
42879725 TACCTTATAG
* * * * * * * *
42879735 GGGTATTTTAGTCATTTTACCCTTCAAAGGTATTTCGATTATTTTACCTTTCAAGGGTATTTTGG
1 GGGTATTTTGGTCATTTTACCCTTCGAGGGTATTTCGGTAATTTTACCCTTCGAGGGTATTTTGA
* *
42879800 TAATTTTACCTTTCAA
66 TAATTTTACCCTTCGA
* * * * * * * *
42879816 TGGTATTTTGGTTATTTTACCATTCAGGGGGAATTTCGGTAATTTTACCCTTTGAAGGTATTTCG
1 GGGTATTTTGGTCATTTTACCCTTC-GAGGGTATTTCGGTAATTTTACCCTTCGAGGGTATTTTG
42879881 ATAATTTTACCCTTCGA
65 ATAATTTTACCCTTCGA
* ** * * * *
42879898 GGGTTTTTTGGTCATTTTACCCTTCGAGGGTATTTCAATCATTTTACCATTCGAGGGTATTTCGG
1 GGGTATTTTGGTCATTTTACCCTTCGAGGGTATTTCGGTAATTTTACCCTTCGAGGGTATTTTGA
* *
42879963 TTATTTTACCCTT-TA
66 TAATTTTACCCTTCGA
* * * *
42879978 GGGGTATTTTGGTTATTTTACCCTTTGAGGGTATTTCGGTTATTTTACCCTTCGAAGGTATTTTG
1 -GGGTATTTTGGTCATTTTACCCTTCGAGGGTATTTCGGTAATTTTACCCTTCGAGGGTATTTTG
*
42880043 ATAATTTTAACCTTCGA
65 ATAATTTTACCCTTCGA
* * * * * ** *
42880060 GGGTATTTCGATAATTTTTCCTTTTAAGGGTATTTCGGTAATTTTACCCTTCAAGGGTATTTTGA
1 GGGTATTTTGGTCATTTTACCCTTCGAGGGTATTTCGGTAATTTTACCCTTCGAGGGTATTTTGA
42880125 TAATTTTACCCTTCGA
66 TAATTTTACCCTTCGA
*
42880141 GGGTATTTCGGTC
1 GGGTATTTTGGTC
42880154 CCATTATGGC
Statistics
Matches: 277, Mismatches: 58, Indels: 6
0.81 0.17 0.02
Matches are distributed among these distances:
80 1 0.00
81 212 0.77
82 64 0.23
ACGTcount: A:0.21, C:0.15, G:0.19, T:0.46
Consensus pattern (81 bp):
GGGTATTTTGGTCATTTTACCCTTCGAGGGTATTTCGGTAATTTTACCCTTCGAGGGTATTTTGA
TAATTTTACCCTTCGA
Found at i:42884173 original size:79 final size:79
Alignment explanation
Indices: 42884083--42884240 Score: 307
Period size: 79 Copynumber: 2.0 Consensus size: 79
42884073 TTGTGTGCGT
*
42884083 TCTTTCTGTTGTTCTTTGTAGCTTCTTTTGGCATTGTTTGCTTCTGCTATACAAATTGGTGCCTT
1 TCTTTCTGTTGTTCTTTGTAGCTTCTTTTGGCATTGTTTGCTTCCGCTATACAAATTGGTGCCTT
42884148 GGAGGAGTTCTTTA
66 GGAGGAGTTCTTTA
42884162 TCTTTCTGTTGTTCTTTGTAGCTTCTTTTGGCATTGTTTGCTTCCGCTATACAAATTGGTGCCTT
1 TCTTTCTGTTGTTCTTTGTAGCTTCTTTTGGCATTGTTTGCTTCCGCTATACAAATTGGTGCCTT
42884227 GGAGGAGTTCTTTA
66 GGAGGAGTTCTTTA
42884241 AGAATCCTCA
Statistics
Matches: 78, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
79 78 1.00
ACGTcount: A:0.13, C:0.17, G:0.22, T:0.49
Consensus pattern (79 bp):
TCTTTCTGTTGTTCTTTGTAGCTTCTTTTGGCATTGTTTGCTTCCGCTATACAAATTGGTGCCTT
GGAGGAGTTCTTTA
Found at i:42907664 original size:703 final size:703
Alignment explanation
Indices: 42906319--42907724 Score: 2780
Period size: 703 Copynumber: 2.0 Consensus size: 703
42906309 AAACTATATT
42906319 TTAATAGGAGTGTAATGAGATTGAAACACCTTATTCTAATCAATATCAAATAGATGGAGTTTAAT
1 TTAATAGGAGTGTAATGAGATTGAAACACCTTATTCTAATCAATATCAAATAGATGGAGTTTAAT
42906384 ACGGTTTAAAAAATGTTATTCTAAAAAAAAAAAGAAGTGTACTTCTATAGGGATTTTACTTTTAT
66 ACGGTTTAAAAAATGTTATTCTAAAAAAAAAAAGAAGTGTACTTCTATAGGGATTTTACTTTTAT
42906449 TTTATTTTACCACTGTATTTTATTTAAATAAGGATTCGGGTCACTTAATTCTAGTAGAGCATATA
131 TTTATTTTACCACTGTATTTTATTTAAATAAGGATTCGGGTCACTTAATTCTAGTAGAGCATATA
42906514 AACAAATTAGCAAATAACAACTTCAGACGTGTATATACGTATACAAAATGTAAAGAGAATGTACC
196 AACAAATTAGCAAATAACAACTTCAGACGTGTATATACGTATACAAAATGTAAAGAGAATGTACC
42906579 ATAGGTACGAAGTGAAGAGCAAAGGCGAAATAAGTCATTTTACGATTTTCTTGCAGGAGCCGAAA
261 ATAGGTACGAAGTGAAGAGCAAAGGCGAAATAAGTCATTTTACGATTTTCTTGCAGGAGCCGAAA
42906644 CAACAGAGAAGCAACGACCTTTAAAACCTAAAGAAATGGTGGTTATTTATACTGACGTTGGATAA
326 CAACAGAGAAGCAACGACCTTTAAAACCTAAAGAAATGGTGGTTATTTATACTGACGTTGGATAA
42906709 TGGACGAGCTGGGGTTGTACCGATCCAATGAGTTAAGGTGAGTTTGGATGGGTGGTGCGTTTACC
391 TGGACGAGCTGGGGTTGTACCGATCCAATGAGTTAAGGTGAGTTTGGATGGGTGGTGCGTTTACC
42906774 TGCGGTTAGTGTAAAAACTGCGGTGGCGGTGAGATTAAACACTATAACGATACTGTAGCGTGAGA
456 TGCGGTTAGTGTAAAAACTGCGGTGGCGGTGAGATTAAACACTATAACGATACTGTAGCGTGAGA
42906839 CAAAAAGTAAACTAAACGCACCGCACCGCACCCAATCACCCATCCAAATCCACCTTTAGTGGGCC
521 CAAAAAGTAAACTAAACGCACCGCACCGCACCCAATCACCCATCCAAATCCACCTTTAGTGGGCC
42906904 ACATTCAACCCCATTCAATGTCCACTAATCTATAATTTATTTATTTAGACTAATTTATTT-ATTT
586 ACATTCAACCCCATTCAATGTCCACTAATCTATAATTTATTTATTTAGACTAATTTATTTAATTT
42906968 TTATTATAATATATATCCATGTCTATAATACATAATATATAAATATATAAATTA
651 TTATTA-AATATATATCCATGTCTATAATACATAATATATAAATATATAAATTA
42907022 TTAATAGGAGTGTAATGAGATTGAAACACCTTATTCTAATCAATATCAAATAGATGGAGTTTAAT
1 TTAATAGGAGTGTAATGAGATTGAAACACCTTATTCTAATCAATATCAAATAGATGGAGTTTAAT
42907087 ACGGTTTAAAAAATGTTATTCTAAAAAAAAAAAGAAGTGTACTTCTATAGGGATTTTACTTTTAT
66 ACGGTTTAAAAAATGTTATTCTAAAAAAAAAAAGAAGTGTACTTCTATAGGGATTTTACTTTTAT
42907152 TTTATTTTACCACTGTATTTTATTTAAATAAGGATTCGGGTCACTTAATTCTAGTAGAGCATATA
131 TTTATTTTACCACTGTATTTTATTTAAATAAGGATTCGGGTCACTTAATTCTAGTAGAGCATATA
42907217 AACAAATTAGCAAATAACAACTTCAGACGTGTATATACGTATACAAAATGTAAAGAGAATGTACC
196 AACAAATTAGCAAATAACAACTTCAGACGTGTATATACGTATACAAAATGTAAAGAGAATGTACC
42907282 ATAGGTACGAAGTGAAGAGCAAAGGCGAAATAAGTCATTTTACGATTTTCTTGCAGGAGCCGAAA
261 ATAGGTACGAAGTGAAGAGCAAAGGCGAAATAAGTCATTTTACGATTTTCTTGCAGGAGCCGAAA
42907347 CAACAGAGAAGCAACGACCTTTAAAACCTAAAGAAATGGTGGTTATTTATACTGACGTTGGATAA
326 CAACAGAGAAGCAACGACCTTTAAAACCTAAAGAAATGGTGGTTATTTATACTGACGTTGGATAA
42907412 TGGACGAGCT-GGGTTGTACCCGATCCAATGAGTTAAGGTGAGTTTGGATGGGTGGTGCGTTTAC
391 TGGACGAGCTGGGGTTGTA-CCGATCCAATGAGTTAAGGTGAGTTTGGATGGGTGGTGCGTTTAC
42907476 CTGCGGTTAGTGTAAAAACTGCGGTGGCGGTGAGATTAAACACTATAACGATACTGTAGCGTGAG
455 CTGCGGTTAGTGTAAAAACTGCGGTGGCGGTGAGATTAAACACTATAACGATACTGTAGCGTGAG
42907541 ACAAAAAGTAAACTAAACGCACCGCACCGCACCCAATCACCCATCCAAATCCACCTTTAGTGGGC
520 ACAAAAAGTAAACTAAACGCACCGCACCGCACCCAATCACCCATCCAAATCCACCTTTAGTGGGC
42907606 CACATTCAACCCCATTCAATGTCCACTAATCTATAATTTATTTATTTAGACTAATTTATTTAATT
585 CACATTCAACCCCATTCAATGTCCACTAATCTATAATTTATTTATTTAGACTAATTTATTTAATT
42907671 TTTATTAAATATATATCCATGTCTATAATACATAATATATAAATATATAAATTA
650 TTTATTAAATATATATCCATGTCTATAATACATAATATATAAATATATAAATTA
42907725 CGAGTTTTAA
Statistics
Matches: 701, Mismatches: 0, Indels: 4
0.99 0.00 0.01
Matches are distributed among these distances:
702 8 0.01
703 683 0.97
704 10 0.01
ACGTcount: A:0.36, C:0.15, G:0.18, T:0.31
Consensus pattern (703 bp):
TTAATAGGAGTGTAATGAGATTGAAACACCTTATTCTAATCAATATCAAATAGATGGAGTTTAAT
ACGGTTTAAAAAATGTTATTCTAAAAAAAAAAAGAAGTGTACTTCTATAGGGATTTTACTTTTAT
TTTATTTTACCACTGTATTTTATTTAAATAAGGATTCGGGTCACTTAATTCTAGTAGAGCATATA
AACAAATTAGCAAATAACAACTTCAGACGTGTATATACGTATACAAAATGTAAAGAGAATGTACC
ATAGGTACGAAGTGAAGAGCAAAGGCGAAATAAGTCATTTTACGATTTTCTTGCAGGAGCCGAAA
CAACAGAGAAGCAACGACCTTTAAAACCTAAAGAAATGGTGGTTATTTATACTGACGTTGGATAA
TGGACGAGCTGGGGTTGTACCGATCCAATGAGTTAAGGTGAGTTTGGATGGGTGGTGCGTTTACC
TGCGGTTAGTGTAAAAACTGCGGTGGCGGTGAGATTAAACACTATAACGATACTGTAGCGTGAGA
CAAAAAGTAAACTAAACGCACCGCACCGCACCCAATCACCCATCCAAATCCACCTTTAGTGGGCC
ACATTCAACCCCATTCAATGTCCACTAATCTATAATTTATTTATTTAGACTAATTTATTTAATTT
TTATTAAATATATATCCATGTCTATAATACATAATATATAAATATATAAATTA
Found at i:42909530 original size:21 final size:20
Alignment explanation
Indices: 42909483--42909531 Score: 53
Period size: 20 Copynumber: 2.4 Consensus size: 20
42909473 GGATCCCCCG
42909483 CACCACCAACTCCCTCGCAA
1 CACCACCAACTCCCTCGCAA
** * *
42909503 CGTCACCAACTTCTTCCGCAA
1 CACCACCAACTCCCT-CGCAA
42909524 CACCACCA
1 CACCACCA
42909532 CGTCTGTCTT
Statistics
Matches: 22, Mismatches: 6, Indels: 1
0.76 0.21 0.03
Matches are distributed among these distances:
20 11 0.50
21 11 0.50
ACGTcount: A:0.29, C:0.51, G:0.06, T:0.14
Consensus pattern (20 bp):
CACCACCAACTCCCTCGCAA
Found at i:42911929 original size:16 final size:16
Alignment explanation
Indices: 42911905--42911937 Score: 50
Period size: 17 Copynumber: 2.1 Consensus size: 16
42911895 TCTTGAAAAG
42911905 AAAAAAGAAT-TCTTT
1 AAAAAAGAATGTCTTT
42911920 AAAAATAGAATGTCTTT
1 AAAAA-AGAATGTCTTT
42911937 A
1 A
42911938 CAGTTTATAC
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 5 0.31
16 5 0.31
17 6 0.38
ACGTcount: A:0.52, C:0.06, G:0.09, T:0.33
Consensus pattern (16 bp):
AAAAAAGAATGTCTTT
Found at i:42934422 original size:6 final size:6
Alignment explanation
Indices: 42934411--42934444 Score: 54
Period size: 6 Copynumber: 6.0 Consensus size: 6
42934401 TATTCTGTTC
42934411 ATAAAT ATAAAT ATAAAT ATAAAT -TAAAT A-AAAT
1 ATAAAT ATAAAT ATAAAT ATAAAT ATAAAT ATAAAT
42934445 TATTTATTAT
Statistics
Matches: 27, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
5 9 0.33
6 18 0.67
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (6 bp):
ATAAAT
Found at i:42934453 original size:17 final size:18
Alignment explanation
Indices: 42934433--42934467 Score: 54
Period size: 17 Copynumber: 2.0 Consensus size: 18
42934423 ATAAATATAA
42934433 ATTAAATAAA-ATTATTT
1 ATTAAATAAACATTATTT
*
42934450 ATTATATAAACATTATTT
1 ATTAAATAAACATTATTT
42934468 CGAATCAAGA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 9 0.56
18 7 0.44
ACGTcount: A:0.49, C:0.03, G:0.00, T:0.49
Consensus pattern (18 bp):
ATTAAATAAACATTATTT
Found at i:42935499 original size:15 final size:14
Alignment explanation
Indices: 42935475--42935505 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 14
42935465 AATTAGTACA
42935475 TTTTTTAAATTGAT
1 TTTTTTAAATTGAT
42935489 TTTTCTTAAATTGAT
1 TTTT-TTAAATTGAT
42935504 TT
1 TT
42935506 ACACAATTCT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 4 0.25
15 12 0.75
ACGTcount: A:0.26, C:0.03, G:0.06, T:0.65
Consensus pattern (14 bp):
TTTTTTAAATTGAT
Found at i:42947527 original size:19 final size:20
Alignment explanation
Indices: 42947488--42947527 Score: 55
Period size: 19 Copynumber: 2.0 Consensus size: 20
42947478 AAATATTAAA
* *
42947488 TATTAAAATTGATATAAACT
1 TATTAAAAGTGATAAAAACT
42947508 TATTAAAAGT-ATAAAAACT
1 TATTAAAAGTGATAAAAACT
42947527 T
1 T
42947528 GTCAATATTG
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
19 9 0.50
20 9 0.50
ACGTcount: A:0.53, C:0.05, G:0.05, T:0.38
Consensus pattern (20 bp):
TATTAAAAGTGATAAAAACT
Found at i:42947597 original size:10 final size:9
Alignment explanation
Indices: 42947546--42947597 Score: 50
Period size: 10 Copynumber: 5.3 Consensus size: 9
42947536 TGTAAAAATA
*
42947546 TAAAAATTC
1 TAAAAATTT
42947555 TAATAAATTT
1 TAA-AAATTT
42947565 TAAAAATTT
1 TAAAAATTT
*
42947574 ATAAAACTTAT
1 -TAAAAATT-T
42947585 TAAAAATATT
1 TAAAAAT-TT
42947595 TAA
1 TAA
42947598 GATTAAAAAA
Statistics
Matches: 36, Mismatches: 3, Indels: 7
0.78 0.07 0.15
Matches are distributed among these distances:
9 9 0.25
10 25 0.69
11 2 0.06
ACGTcount: A:0.56, C:0.04, G:0.00, T:0.40
Consensus pattern (9 bp):
TAAAAATTT
Found at i:42948159 original size:9 final size:9
Alignment explanation
Indices: 42948118--42948319 Score: 56
Period size: 10 Copynumber: 21.2 Consensus size: 9
42948108 TTTTATTATT
42948118 TTTTTATAA
1 TTTTTATAA
*
42948127 GTTTATATCAA
1 -TTTTTAT-AA
*
42948138 TTTTGAT-A
1 TTTTTATAA
*
42948146 CTTTTATAA
1 TTTTTATAA
42948155 TTTTTATAGAA
1 TTTTTAT--AA
* *
42948166 TTTTAATACG
1 TTTTTATA-A
42948176 TTTTTATAAAA
1 TTTTTAT--AA
* *
42948187 TTTTAAATAT
1 TTTT-TATAA
42948197 TTTTTATTAA
1 TTTTTA-TAA
*
42948207 TTTATTAGAA
1 TTT-TTATAA
42948217 TTTATTAT--
1 TTT-TTATAA
* *
42948225 GTTTTATAT
1 TTTTTATAA
42948234 TTTTTATAA
1 TTTTTATAA
*
42948243 TATTTATAA
1 TTTTTATAA
*
42948252 GCTTTTTTTATAT
1 ----TTTTTATAA
*
42948265 TTTTTCTAA
1 TTTTTATAA
* *
42948274 GCTTATATCAA
1 -TTTTTAT-AA
*
42948285 TTTTCAT-A
1 TTTTTATAA
*
42948293 TTTTTTTAA
1 TTTTTATAA
42948302 TTTTTAT-A
1 TTTTTATAA
42948310 -TTTTATAA
1 TTTTTATAA
42948318 TT
1 TT
42948320 CCTTATGATT
Statistics
Matches: 138, Mismatches: 33, Indels: 43
0.64 0.15 0.20
Matches are distributed among these distances:
7 10 0.07
8 16 0.12
9 39 0.28
10 44 0.32
11 19 0.14
12 3 0.02
13 7 0.05
ACGTcount: A:0.31, C:0.04, G:0.04, T:0.61
Consensus pattern (9 bp):
TTTTTATAA
Found at i:42948167 original size:28 final size:29
Alignment explanation
Indices: 42948119--42948184 Score: 73
Period size: 28 Copynumber: 2.3 Consensus size: 29
42948109 TTTATTATTT
*
42948119 TTTTATAAGTTTATATCAATTTTGATAC-
1 TTTTATAAGTTTATATCAATTTTAATACG
* *
42948147 TTTTATAA-TTTTTATAGAATTTTAATACG
1 TTTTATAAGTTTATAT-CAATTTTAATACG
42948176 TTTTTATAA
1 -TTTTATAA
42948185 AATTTTAAAT
Statistics
Matches: 32, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
27 6 0.19
28 18 0.56
30 8 0.25
ACGTcount: A:0.33, C:0.05, G:0.06, T:0.56
Consensus pattern (29 bp):
TTTTATAAGTTTATATCAATTTTAATACG
Found at i:42948260 original size:22 final size:22
Alignment explanation
Indices: 42948233--42948277 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 22
42948223 ATGTTTTATA
42948233 TTTTTTATAATATTTATAAGCT
1 TTTTTTATAATATTTATAAGCT
* * *
42948255 TTTTTTATATTTTTTCTAAGCT
1 TTTTTTATAATATTTATAAGCT
42948277 T
1 T
42948278 ATATCAATTT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.24, C:0.07, G:0.04, T:0.64
Consensus pattern (22 bp):
TTTTTTATAATATTTATAAGCT
Found at i:42948792 original size:19 final size:19
Alignment explanation
Indices: 42948768--42948822 Score: 56
Period size: 22 Copynumber: 2.7 Consensus size: 19
42948758 TTAAATCATA
42948768 ATTAAATTAATTGTATAAT
1 ATTAAATTAATTGTATAAT
* * *
42948787 ATTAAAAAAATATTTATATAAT
1 ATT---AAATTAATTGTATAAT
42948809 ATTAAATTAATTGT
1 ATTAAATTAATTGT
42948823 GTTGGATTTT
Statistics
Matches: 27, Mismatches: 6, Indels: 6
0.69 0.15 0.15
Matches are distributed among these distances:
19 11 0.41
22 16 0.59
ACGTcount: A:0.51, C:0.00, G:0.04, T:0.45
Consensus pattern (19 bp):
ATTAAATTAATTGTATAAT
Found at i:42949844 original size:19 final size:19
Alignment explanation
Indices: 42949820--42949874 Score: 56
Period size: 22 Copynumber: 2.7 Consensus size: 19
42949810 TTAAATCATA
42949820 ATTAAATTAATTGTATAAT
1 ATTAAATTAATTGTATAAT
* * *
42949839 ATTAAAAAAATATTTATATAAT
1 ATT---AAATTAATTGTATAAT
42949861 ATTAAATTAATTGT
1 ATTAAATTAATTGT
42949875 GTTGGATTTT
Statistics
Matches: 27, Mismatches: 6, Indels: 6
0.69 0.15 0.15
Matches are distributed among these distances:
19 11 0.41
22 16 0.59
ACGTcount: A:0.51, C:0.00, G:0.04, T:0.45
Consensus pattern (19 bp):
ATTAAATTAATTGTATAAT
Found at i:42950568 original size:59 final size:59
Alignment explanation
Indices: 42950504--42950691 Score: 156
Period size: 59 Copynumber: 3.2 Consensus size: 59
42950494 ATAATTTTTT
42950504 ATTAATATATTTTCTTGTATTTTTATAATTTTTGTAAATTAATTTATATTATACAAATG
1 ATTAATATATTTTCTTGTATTTTTATAATTTTTGTAAATTAATTTATATTATACAAATG
* * * * * ** * **** *
42950563 ATTAATGTATTTT-TTG---GTCTA-AA-ATTGGT-AATTGCTCTCGTCAAATATATATTTTTT
1 ATTAATATATTTTCTTGTATTTTTATAATTTTTGTAAATTAAT-T--T-ATAT-TATACAAATG
42950620 ATTAATATATTTTCTTGTATTTTTATAATTTTTGTAAATTAATTTATATTATACAAATG
1 ATTAATATATTTTCTTGTATTTTTATAATTTTTGTAAATTAATTTATATTATACAAATG
*
42950679 ATTAATGTATTTT
1 ATTAATATATTTT
42950692 TTGGTCTAAA
Statistics
Matches: 90, Mismatches: 27, Indels: 24
0.64 0.19 0.17
Matches are distributed among these distances:
52 5 0.06
53 5 0.06
54 2 0.02
55 4 0.04
56 3 0.03
57 17 0.19
58 6 0.07
59 29 0.32
60 3 0.03
61 4 0.04
62 2 0.02
63 5 0.06
64 5 0.06
ACGTcount: A:0.33, C:0.05, G:0.07, T:0.55
Consensus pattern (59 bp):
ATTAATATATTTTCTTGTATTTTTATAATTTTTGTAAATTAATTTATATTATACAAATG
Found at i:42950694 original size:116 final size:117
Alignment explanation
Indices: 42950487--42950719 Score: 459
Period size: 116 Copynumber: 2.0 Consensus size: 117
42950477 AACATGAGTC
42950487 CAAATATATAATTTTTTATTAATATATTTTCTTGTATTTTTATAATTTTTGTAAATTAATTTATA
1 CAAATATATAATTTTTTATTAATATATTTTCTTGTATTTTTATAATTTTTGTAAATTAATTTATA
42950552 TTATACAAATGATTAATGTATTTTTTGGTCTAAAATTGGTAATTGCTCTCGT
66 TTATACAAATGATTAATGTATTTTTTGGTCTAAAATTGGTAATTGCTCTCGT
42950604 CAAATATAT-ATTTTTTATTAATATATTTTCTTGTATTTTTATAATTTTTGTAAATTAATTTATA
1 CAAATATATAATTTTTTATTAATATATTTTCTTGTATTTTTATAATTTTTGTAAATTAATTTATA
42950668 TTATACAAATGATTAATGTATTTTTTGGTCTAAAATTGGTAATTGCTCTCGT
66 TTATACAAATGATTAATGTATTTTTTGGTCTAAAATTGGTAATTGCTCTCGT
42950720 ATTGAGATCT
Statistics
Matches: 116, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
116 107 0.92
117 9 0.08
ACGTcount: A:0.32, C:0.06, G:0.09, T:0.53
Consensus pattern (117 bp):
CAAATATATAATTTTTTATTAATATATTTTCTTGTATTTTTATAATTTTTGTAAATTAATTTATA
TTATACAAATGATTAATGTATTTTTTGGTCTAAAATTGGTAATTGCTCTCGT
Found at i:42964856 original size:41 final size:40
Alignment explanation
Indices: 42964763--42964860 Score: 101
Period size: 43 Copynumber: 2.4 Consensus size: 40
42964753 AACTAAAGTT
*
42964763 ATATTTATAATTAAAATTTATTAAATTAAATTAAATTATTAA
1 ATATTTAT-ATTAAAATTTATTAAATTAAATAAAATTA-TAA
* *
42964805 ATCATATATATTAAAA-TTAGGTTATATTAAATAATAATTA-AA
1 AT-ATTTATATTAAAATTTA--TTAAATTAAATAA-AATTATAA
42964847 ATATTTATATTAAA
1 ATATTTATATTAAA
42964861 TAATTAAAGA
Statistics
Matches: 48, Mismatches: 4, Indels: 9
0.79 0.07 0.15
Matches are distributed among these distances:
41 14 0.29
42 13 0.27
43 16 0.33
44 5 0.10
ACGTcount: A:0.52, C:0.01, G:0.02, T:0.45
Consensus pattern (40 bp):
ATATTTATATTAAAATTTATTAAATTAAATAAAATTATAA
Found at i:42964858 original size:25 final size:28
Alignment explanation
Indices: 42964799--42964864 Score: 84
Period size: 25 Copynumber: 2.4 Consensus size: 28
42964789 TAAATTAAAT
42964799 TATTAAATCATATATATTAAAATTAGGTTA
1 TATTAAAT-A-ATATATTAAAATTAGGTTA
*
42964829 TATTAAATAATA-ATTAAAA-TA-TTTA
1 TATTAAATAATATATTAAAATTAGGTTA
42964854 TATTAAATAAT
1 TATTAAATAAT
42964865 TAAAGAGTGA
Statistics
Matches: 35, Mismatches: 1, Indels: 5
0.85 0.02 0.12
Matches are distributed among these distances:
25 14 0.40
26 2 0.06
27 7 0.20
28 3 0.09
29 1 0.03
30 8 0.23
ACGTcount: A:0.52, C:0.02, G:0.03, T:0.44
Consensus pattern (28 bp):
TATTAAATAATATATTAAAATTAGGTTA
Found at i:42973140 original size:3 final size:3
Alignment explanation
Indices: 42973132--42973158 Score: 54
Period size: 3 Copynumber: 9.0 Consensus size: 3
42973122 ATAAAGAATG
42973132 AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT
42973159 GTAATTAAAA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 24 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:42973202 original size:5 final size:6
Alignment explanation
Indices: 42973183--42973229 Score: 67
Period size: 6 Copynumber: 7.5 Consensus size: 6
42973173 TTTGGAATTC
*
42973183 AAATAA AAATAA AAATAA AACATTAC AAATAA AAATAA AAATAA AAA
1 AAATAA AAATAA AAATAA AA-A-TAA AAATAA AAATAA AAATAA AAA
42973230 AATAAAGATA
Statistics
Matches: 37, Mismatches: 2, Indels: 4
0.86 0.05 0.09
Matches are distributed among these distances:
6 31 0.84
7 2 0.05
8 4 0.11
ACGTcount: A:0.79, C:0.04, G:0.00, T:0.17
Consensus pattern (6 bp):
AAATAA
Found at i:42973232 original size:20 final size:20
Alignment explanation
Indices: 42973187--42973241 Score: 67
Period size: 20 Copynumber: 2.8 Consensus size: 20
42973177 GAATTCAAAT
*
42973187 AAAAATAAAAATAAAACATT
1 AAAAATAAAAATAAAACATA
*
42973207 ACAAATAAAAATAAAA-ATAA
1 AAAAATAAAAATAAAACAT-A
*
42973227 AAAAATAAAGATAAA
1 AAAAATAAAAATAAA
42973242 CTAAATTGGT
Statistics
Matches: 30, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
19 2 0.07
20 28 0.93
ACGTcount: A:0.78, C:0.04, G:0.02, T:0.16
Consensus pattern (20 bp):
AAAAATAAAAATAAAACATA
Found at i:42973240 original size:26 final size:26
Alignment explanation
Indices: 42973182--42973241 Score: 86
Period size: 26 Copynumber: 2.3 Consensus size: 26
42973172 ATTTGGAATT
* *
42973182 CAAATAAAAATAAAAATAAAACATTA
1 CAAATAAAAATAAAAATAAAAAAATA
42973208 CAAATAAAAATAAAAATAAAAAAATA
1 CAAATAAAAATAAAAATAAAAAAATA
42973234 -AAGATAAA
1 CAA-ATAAA
42973242 CTAAATTGGT
Statistics
Matches: 31, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
25 2 0.06
26 29 0.94
ACGTcount: A:0.77, C:0.05, G:0.02, T:0.17
Consensus pattern (26 bp):
CAAATAAAAATAAAAATAAAAAAATA
Found at i:42976747 original size:10 final size:10
Alignment explanation
Indices: 42976732--42976756 Score: 50
Period size: 10 Copynumber: 2.5 Consensus size: 10
42976722 CCTGATATCA
42976732 CATACTTTCT
1 CATACTTTCT
42976742 CATACTTTCT
1 CATACTTTCT
42976752 CATAC
1 CATAC
42976757 AATATGTATT
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:0.24, C:0.32, G:0.00, T:0.44
Consensus pattern (10 bp):
CATACTTTCT
Found at i:42981728 original size:9 final size:9
Alignment explanation
Indices: 42981714--42981744 Score: 53
Period size: 9 Copynumber: 3.4 Consensus size: 9
42981704 GTTAAACGAA
42981714 TCGAGTTAT
1 TCGAGTTAT
*
42981723 TCGAGTTAA
1 TCGAGTTAT
42981732 TCGAGTTAT
1 TCGAGTTAT
42981741 TCGA
1 TCGA
42981745 ATCAACTCGA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
9 20 1.00
ACGTcount: A:0.26, C:0.13, G:0.23, T:0.39
Consensus pattern (9 bp):
TCGAGTTAT
Found at i:42983880 original size:40 final size:39
Alignment explanation
Indices: 42983825--42983956 Score: 119
Period size: 40 Copynumber: 3.4 Consensus size: 39
42983815 ACTACTTTGG
*
42983825 CACCCAGTGCCTCATCAGATAATTTGAAGTAGTAAATTGA
1 CACCCAGTGCCTCATC-GATAATCTGAAGTAGTAAATTGA
* * * * * *
42983865 CACCCAGTGTCTCATCGGTTAAACCG-A--AGTAAGTTGG
1 CACCCAGTGCCTCATC-GATAATCTGAAGTAGTAAATTGA
*
42983902 CACCCAGTGCCTCATCGAATAAATCTGAAGTAATAAATTGA
1 CACCCAGTGCCTCATCG-AT-AATCTGAAGTAGTAAATTGA
*
42983943 CA-CCAGTGTCTCAT
1 CACCCAGTGCCTCAT
42983957 TGACTCGAAG
Statistics
Matches: 71, Mismatches: 16, Indels: 10
0.73 0.16 0.10
Matches are distributed among these distances:
36 1 0.01
37 24 0.34
38 4 0.06
39 2 0.03
40 31 0.44
41 9 0.13
ACGTcount: A:0.33, C:0.23, G:0.18, T:0.26
Consensus pattern (39 bp):
CACCCAGTGCCTCATCGATAATCTGAAGTAGTAAATTGA
Found at i:42986807 original size:10 final size:11
Alignment explanation
Indices: 42986781--42986806 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
42986771 AAAAATAAAA
42986781 AAAAATATTTT
1 AAAAATATTTT
42986792 AAAAATATTTT
1 AAAAATATTTT
42986803 AAAA
1 AAAA
42986807 TTAAAAAATT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (11 bp):
AAAAATATTTT
Found at i:42986812 original size:16 final size:18
Alignment explanation
Indices: 42986789--42986834 Score: 71
Period size: 16 Copynumber: 2.7 Consensus size: 18
42986779 AAAAAAATAT
42986789 TTTAAAAATATTTTAAAA
1 TTTAAAAATATTTTAAAA
42986807 -TTAAAAA-A-TTTAAAA
1 TTTAAAAATATTTTAAAA
42986822 TTTAAAAATATTT
1 TTTAAAAATATTT
42986835 ATTATATCGG
Statistics
Matches: 25, Mismatches: 0, Indels: 6
0.81 0.00 0.19
Matches are distributed among these distances:
15 7 0.28
16 8 0.32
17 8 0.32
18 2 0.08
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (18 bp):
TTTAAAAATATTTTAAAA
Found at i:42986835 original size:17 final size:17
Alignment explanation
Indices: 42986789--42986835 Score: 71
Period size: 17 Copynumber: 2.8 Consensus size: 17
42986779 AAAAAAATAT
42986789 TTTAAAAATATTTTAAAA
1 TTTAAAAATA-TTTAAAA
42986807 -TTAAAAA-ATTTAAAA
1 TTTAAAAATATTTAAAA
42986822 TTTAAAAATATTTA
1 TTTAAAAATATTTA
42986836 TTATATCGGG
Statistics
Matches: 27, Mismatches: 0, Indels: 5
0.84 0.00 0.16
Matches are distributed among these distances:
15 7 0.26
16 8 0.30
17 12 0.44
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (17 bp):
TTTAAAAATATTTAAAA
Found at i:42988754 original size:15 final size:16
Alignment explanation
Indices: 42988736--42988772 Score: 58
Period size: 16 Copynumber: 2.4 Consensus size: 16
42988726 CTTATTATAA
*
42988736 AATAAATAA-ATAGAG
1 AATAAATAAGAAAGAG
42988751 AATAAATAAGAAAGAG
1 AATAAATAAGAAAGAG
42988767 AATAAA
1 AATAAA
42988773 GTTTTTATTT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
15 9 0.45
16 11 0.55
ACGTcount: A:0.70, C:0.00, G:0.14, T:0.16
Consensus pattern (16 bp):
AATAAATAAGAAAGAG
Found at i:42989234 original size:27 final size:27
Alignment explanation
Indices: 42989180--42989230 Score: 68
Period size: 26 Copynumber: 1.9 Consensus size: 27
42989170 TGTCTTTCTT
*
42989180 CTCCTCTTCCTATCCCACGCTTTCACC
1 CTCCTCCTCCTATCCCACGCTTTCACC
* *
42989207 CTCCTCCTCCT-TCCCTCTCTTTCA
1 CTCCTCCTCCTATCCCACGCTTTCA
42989231 ACCCCACTCC
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
26 11 0.52
27 10 0.48
ACGTcount: A:0.08, C:0.53, G:0.02, T:0.37
Consensus pattern (27 bp):
CTCCTCCTCCTATCCCACGCTTTCACC
Found at i:43001193 original size:21 final size:21
Alignment explanation
Indices: 43001154--43001200 Score: 60
Period size: 21 Copynumber: 2.2 Consensus size: 21
43001144 GTAATTTACT
*
43001154 CTTTTTTTTAAATCTTTGTTA
1 CTTTTTTTTAAATCATTGTTA
*
43001175 GTTTTTGTTTAAAT-ATTGTTA
1 CTTTTT-TTTAAATCATTGTTA
43001196 CTTTT
1 CTTTT
43001201 AATACAATAT
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
21 15 0.68
22 7 0.32
ACGTcount: A:0.19, C:0.06, G:0.09, T:0.66
Consensus pattern (21 bp):
CTTTTTTTTAAATCATTGTTA
Found at i:43002700 original size:32 final size:32
Alignment explanation
Indices: 43002659--43002722 Score: 128
Period size: 32 Copynumber: 2.0 Consensus size: 32
43002649 ATTCTCTGTC
43002659 CTATATCTAAGTTATGAATTTAGTCTTTGTAA
1 CTATATCTAAGTTATGAATTTAGTCTTTGTAA
43002691 CTATATCTAAGTTATGAATTTAGTCTTTGTAA
1 CTATATCTAAGTTATGAATTTAGTCTTTGTAA
43002723 TTTAATTTAG
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
32 32 1.00
ACGTcount: A:0.31, C:0.09, G:0.12, T:0.47
Consensus pattern (32 bp):
CTATATCTAAGTTATGAATTTAGTCTTTGTAA
Found at i:43011736 original size:34 final size:34
Alignment explanation
Indices: 43011693--43011813 Score: 86
Period size: 34 Copynumber: 3.3 Consensus size: 34
43011683 TTTCACTAGT
*
43011693 TTAATTATAAAACATTTATATATACAAATTAAAA
1 TTAAGTATAAAACATTTATATATACAAATTAAAA
* **
43011727 TTAAGTATAAATTAAACAATTGTAT-TA-ATTATTTTCACCAAA
1 TTAAGTAT--A--AAAC-ATT-TATATATA-CAAATT-A--AAA
43011769 TTTAA-TATAAAACATTTATATATACAAATTAAAA
1 -TTAAGTATAAAACATTTATATATACAAATTAAAA
43011803 TTAAGTATAAA
1 TTAAGTATAAA
43011814 TTAAACAAAA
Statistics
Matches: 66, Mismatches: 7, Indels: 28
0.65 0.07 0.28
Matches are distributed among these distances:
33 4 0.06
34 16 0.24
36 5 0.08
37 8 0.12
38 10 0.15
39 8 0.12
40 5 0.08
42 6 0.09
43 4 0.06
ACGTcount: A:0.52, C:0.07, G:0.02, T:0.39
Consensus pattern (34 bp):
TTAAGTATAAAACATTTATATATACAAATTAAAA
Found at i:43011789 original size:76 final size:77
Alignment explanation
Indices: 43011667--43011821 Score: 269
Period size: 76 Copynumber: 2.0 Consensus size: 77
43011657 TTTTTTTTTA
* *
43011667 AATTGTATTAATTTATTTTCACTAGTTTAATTATAAAACATTTATATATACAAATTAAAATTAAG
1 AATTGTATTAATTTATTTTCACAAATTTAATTATAAAACATTTATATATACAAATTAAAATTAAG
43011732 TATAAATTAAAC
66 TATAAATTAAAC
43011744 AATTGTATTAA-TTATTTTCACCAAATTTAA-TATAAAACATTTATATATACAAATTAAAATTAA
1 AATTGTATTAATTTATTTTCA-CAAATTTAATTATAAAACATTTATATATACAAATTAAAATTAA
43011807 GTATAAATTAAAC
65 GTATAAATTAAAC
43011820 AA
1 AA
43011822 AAATAAAATT
Statistics
Matches: 75, Mismatches: 2, Indels: 3
0.94 0.03 0.04
Matches are distributed among these distances:
76 57 0.76
77 18 0.24
ACGTcount: A:0.49, C:0.07, G:0.03, T:0.41
Consensus pattern (77 bp):
AATTGTATTAATTTATTTTCACAAATTTAATTATAAAACATTTATATATACAAATTAAAATTAAG
TATAAATTAAAC
Found at i:43018826 original size:20 final size:20
Alignment explanation
Indices: 43018789--43018826 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
43018779 AAGTTAGAAT
*
43018789 TATGATATTTATTTTTATTA
1 TATGATATTTATTCTTATTA
43018809 TATGATTATTT-TTCTTAT
1 TATGA-TATTTATTCTTAT
43018827 ATTCCAATTT
Statistics
Matches: 16, Mismatches: 1, Indels: 2
0.84 0.05 0.11
Matches are distributed among these distances:
20 11 0.69
21 5 0.31
ACGTcount: A:0.26, C:0.03, G:0.05, T:0.66
Consensus pattern (20 bp):
TATGATATTTATTCTTATTA
Found at i:43020608 original size:11 final size:11
Alignment explanation
Indices: 43020592--43020618 Score: 54
Period size: 11 Copynumber: 2.5 Consensus size: 11
43020582 ATACACGGAT
43020592 AGATTTACTGG
1 AGATTTACTGG
43020603 AGATTTACTGG
1 AGATTTACTGG
43020614 AGATT
1 AGATT
43020619 AGTGATAGGT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 16 1.00
ACGTcount: A:0.30, C:0.07, G:0.26, T:0.37
Consensus pattern (11 bp):
AGATTTACTGG
Found at i:43043616 original size:2 final size:2
Alignment explanation
Indices: 43043611--43043646 Score: 54
Period size: 2 Copynumber: 18.0 Consensus size: 2
43043601 CTCTCGCTCT
* *
43043611 CA CA CA CA CA CA CA CA CA CA CA CA AA CA CA AA CA CA
1 CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA
43043647 AACATATATA
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.56, C:0.44, G:0.00, T:0.00
Consensus pattern (2 bp):
CA
Found at i:43043647 original size:6 final size:6
Alignment explanation
Indices: 43043612--43043650 Score: 51
Period size: 6 Copynumber: 6.5 Consensus size: 6
43043602 TCTCGCTCTC
* * *
43043612 ACACAC ACACAC ACACAC ACACAA ACACAA ACACAA ACA
1 ACACAA ACACAA ACACAA ACACAA ACACAA ACACAA ACA
43043651 TATATAATAT
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
6 32 1.00
ACGTcount: A:0.59, C:0.41, G:0.00, T:0.00
Consensus pattern (6 bp):
ACACAA
Found at i:43043647 original size:12 final size:12
Alignment explanation
Indices: 43043612--43043650 Score: 60
Period size: 12 Copynumber: 3.2 Consensus size: 12
43043602 TCTCGCTCTC
*
43043612 ACACACACACAC
1 ACACACACACAA
43043624 ACACACACACAA
1 ACACACACACAA
*
43043636 ACACAAACACAA
1 ACACACACACAA
43043648 ACA
1 ACA
43043651 TATATAATAT
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
12 25 1.00
ACGTcount: A:0.59, C:0.41, G:0.00, T:0.00
Consensus pattern (12 bp):
ACACACACACAA
Found at i:43055332 original size:29 final size:31
Alignment explanation
Indices: 43055284--43055356 Score: 75
Period size: 30 Copynumber: 2.5 Consensus size: 31
43055274 TTAAATTATT
*
43055284 AATAAT-AAAATTATATTTTAA-CTCCTAAA
1 AATAATAAAAATTATATTTTAATCTCATAAA
*
43055313 AATAATAAAAATT-TGA-TTTAATCTTATAAA
1 AATAATAAAAATTAT-ATTTTAATCTCATAAA
43055343 AAT-ATAAAATATTA
1 AATAATAAAA-ATTA
43055357 AATAATTTAT
Statistics
Matches: 37, Mismatches: 2, Indels: 8
0.79 0.04 0.17
Matches are distributed among these distances:
29 18 0.49
30 19 0.51
ACGTcount: A:0.55, C:0.05, G:0.01, T:0.38
Consensus pattern (31 bp):
AATAATAAAAATTATATTTTAATCTCATAAA
Found at i:43067920 original size:14 final size:14
Alignment explanation
Indices: 43067903--43067930 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
43067893 TAATTATAAA
43067903 AATGTAAAAATATT
1 AATGTAAAAATATT
43067917 AATGTAAAAATATT
1 AATGTAAAAATATT
43067931 TATAATTTTT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.57, C:0.00, G:0.07, T:0.36
Consensus pattern (14 bp):
AATGTAAAAATATT
Found at i:43073592 original size:3 final size:3
Alignment explanation
Indices: 43073584--43073613 Score: 60
Period size: 3 Copynumber: 10.0 Consensus size: 3
43073574 ATCTGACCCC
43073584 ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG
1 ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG
43073614 CAAGAATTAG
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 27 1.00
ACGTcount: A:0.33, C:0.00, G:0.33, T:0.33
Consensus pattern (3 bp):
ATG
Found at i:43077520 original size:6 final size:6
Alignment explanation
Indices: 43077499--43077538 Score: 55
Period size: 6 Copynumber: 6.7 Consensus size: 6
43077489 AATTGGAGAG
*
43077499 AAAACA AAATAGA AAAAGA AAAA-A AAAAGA AAAAGA AAAA
1 AAAAGA AAA-AGA AAAAGA AAAAGA AAAAGA AAAAGA AAAA
43077539 TAATAAAAGG
Statistics
Matches: 31, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
5 5 0.16
6 21 0.68
7 5 0.16
ACGTcount: A:0.85, C:0.03, G:0.10, T:0.03
Consensus pattern (6 bp):
AAAAGA
Found at i:43077527 original size:11 final size:12
Alignment explanation
Indices: 43077499--43077538 Score: 55
Period size: 11 Copynumber: 3.3 Consensus size: 12
43077489 AATTGGAGAG
*
43077499 AAAACAAAATAGA
1 AAAAGAAAA-AGA
43077512 AAAAGAAAAA-A
1 AAAAGAAAAAGA
43077523 AAAAGAAAAAGA
1 AAAAGAAAAAGA
43077535 AAAA
1 AAAA
43077539 TAATAAAAGG
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
11 11 0.44
12 6 0.24
13 8 0.32
ACGTcount: A:0.85, C:0.03, G:0.10, T:0.03
Consensus pattern (12 bp):
AAAAGAAAAAGA
Found at i:43077529 original size:17 final size:17
Alignment explanation
Indices: 43077497--43077538 Score: 66
Period size: 17 Copynumber: 2.4 Consensus size: 17
43077487 ATAATTGGAG
*
43077497 AGAAAACAAAATAGAAAA
1 AGAAAA-AAAAAAGAAAA
43077515 AGAAAAAAAAAAGAAAA
1 AGAAAAAAAAAAGAAAA
43077532 AGAAAAA
1 AGAAAAA
43077539 TAATAAAAGG
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
17 17 0.74
18 6 0.26
ACGTcount: A:0.83, C:0.02, G:0.12, T:0.02
Consensus pattern (17 bp):
AGAAAAAAAAAAGAAAA
Found at i:43079260 original size:3 final size:3
Alignment explanation
Indices: 43079252--43079281 Score: 60
Period size: 3 Copynumber: 10.0 Consensus size: 3
43079242 ATCCGACCCC
43079252 ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG
1 ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG
43079282 CAAGAGTTAA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 27 1.00
ACGTcount: A:0.33, C:0.00, G:0.33, T:0.33
Consensus pattern (3 bp):
ATG
Found at i:43088482 original size:19 final size:19
Alignment explanation
Indices: 43088458--43088495 Score: 76
Period size: 19 Copynumber: 2.0 Consensus size: 19
43088448 ACATGCTCAG
43088458 TTAGTAAGCAATAAAGAAT
1 TTAGTAAGCAATAAAGAAT
43088477 TTAGTAAGCAATAAAGAAT
1 TTAGTAAGCAATAAAGAAT
43088496 ATTTTGCTTA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.53, C:0.05, G:0.16, T:0.26
Consensus pattern (19 bp):
TTAGTAAGCAATAAAGAAT
Found at i:43091187 original size:29 final size:31
Alignment explanation
Indices: 43091130--43091213 Score: 109
Period size: 31 Copynumber: 2.7 Consensus size: 31
43091120 ATTTTAAAAT
* *
43091130 TATACATAAATTTTAATTTAATCCATAATTA
1 TATACATGAATTTTAATTTAGTCCATAATTA
43091161 TATACATGAATTTTAATTTAGT-C-TAATTA
1 TATACATGAATTTTAATTTAGTCCATAATTA
*
43091190 TATACGTGAAATTTTAATTATAGT
1 TATACATG-AATTTTAATT-TAGT
43091214 TCAAATATAT
Statistics
Matches: 48, Mismatches: 3, Indels: 4
0.87 0.05 0.07
Matches are distributed among these distances:
29 13 0.27
30 11 0.23
31 24 0.50
ACGTcount: A:0.40, C:0.07, G:0.06, T:0.46
Consensus pattern (31 bp):
TATACATGAATTTTAATTTAGTCCATAATTA
Found at i:43091221 original size:29 final size:28
Alignment explanation
Indices: 43091130--43091223 Score: 89
Period size: 31 Copynumber: 3.1 Consensus size: 28
43091120 ATTTTAAAAT
* *
43091130 TATACATAAATTTTAATTTAATCCATAATTA
1 TATACATGAATTTTAATTTAGT-C-TAA-TA
43091161 TATACATGAATTTTAATTTAGTCTAATTA
1 TATACATGAATTTTAATTTAGTCTAA-TA
* *
43091190 TATACGTGAAATTTTAATTATAGTTCAAATA
1 TATACATG-AATTTTAATT-TAG-TCTAATA
43091221 TAT
1 TAT
43091224 GCTTGAAACT
Statistics
Matches: 56, Mismatches: 4, Indels: 6
0.85 0.06 0.09
Matches are distributed among these distances:
29 13 0.23
30 11 0.20
31 28 0.50
32 4 0.07
ACGTcount: A:0.41, C:0.07, G:0.05, T:0.46
Consensus pattern (28 bp):
TATACATGAATTTTAATTTAGTCTAATA
Found at i:43091617 original size:31 final size:29
Alignment explanation
Indices: 43091582--43091650 Score: 75
Period size: 31 Copynumber: 2.3 Consensus size: 29
43091572 TAATATTAAA
* *
43091582 TTTATATATAAACGTTATTTTAATGTGTAAT
1 TTTATATATAAACGTTAATTT-A-GTATAAT
* * *
43091613 TTTATGTATTAACTTTAATTTAGTATAAT
1 TTTATATATAAACGTTAATTTAGTATAAT
43091642 TTTATATAT
1 TTTATATAT
43091651 GAAATTTGAG
Statistics
Matches: 32, Mismatches: 6, Indels: 2
0.80 0.15 0.05
Matches are distributed among these distances:
29 14 0.44
30 1 0.03
31 17 0.53
ACGTcount: A:0.35, C:0.03, G:0.07, T:0.55
Consensus pattern (29 bp):
TTTATATATAAACGTTAATTTAGTATAAT
Found at i:43094797 original size:11 final size:11
Alignment explanation
Indices: 43094781--43094806 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
43094771 TATATATAAT
43094781 TAAATATTAAA
1 TAAATATTAAA
43094792 TAAATATTAAA
1 TAAATATTAAA
43094803 TAAA
1 TAAA
43094807 AGAATTATTT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (11 bp):
TAAATATTAAA
Found at i:43098467 original size:43 final size:43
Alignment explanation
Indices: 43098419--43098710 Score: 419
Period size: 43 Copynumber: 6.8 Consensus size: 43
43098409 GCGTCGCTAA
* **
43098419 CTTTAGCGGCGCTTTTCCCACAAACGCCGCTAAAGATTAGGAC
1 CTTTAGCGGCGCTTTTCCCGCAAACGCCGCTAAAGACCAGGAC
*
43098462 CTTTAGCGGCACTTTTCCCGCAAACGCCGCTAAAGACCAGGAC
1 CTTTAGCGGCGCTTTTCCCGCAAACGCCGCTAAAGACCAGGAC
43098505 CTTTAGCGGCGCTTCTT-CCGCAAACGCCGCTAAAGACCAGGAC
1 CTTTAGCGGCGCTT-TTCCCGCAAACGCCGCTAAAGACCAGGAC
43098548 CTTTAGCGGCGCTTCTT-CCGCAAACGCCGCTAAAGACCAGGAC
1 CTTTAGCGGCGCTT-TTCCCGCAAACGCCGCTAAAGACCAGGAC
* * * * *
43098591 CTTTAGCGGCACTTCTCCCGAAAATGCCGCTAAAGACCAAGAC
1 CTTTAGCGGCGCTTTTCCCGCAAACGCCGCTAAAGACCAGGAC
*
43098634 CTTTAGCGGCGC-TCTCCCGCAAACGCCGCTAAAGACCAGGAC
1 CTTTAGCGGCGCTTTTCCCGCAAACGCCGCTAAAGACCAGGAC
* ** *
43098676 CTTTAGCGGCACTTTTCCCAAAAACGCCACTAAAG
1 CTTTAGCGGCGCTTTTCCCGCAAACGCCGCTAAAG
43098711 GTCACGAAAA
Statistics
Matches: 227, Mismatches: 19, Indels: 6
0.90 0.08 0.02
Matches are distributed among these distances:
42 39 0.17
43 186 0.82
44 2 0.01
ACGTcount: A:0.26, C:0.34, G:0.21, T:0.19
Consensus pattern (43 bp):
CTTTAGCGGCGCTTTTCCCGCAAACGCCGCTAAAGACCAGGAC
Found at i:43106161 original size:41 final size:41
Alignment explanation
Indices: 43106065--43107004 Score: 1481
Period size: 41 Copynumber: 23.0 Consensus size: 41
43106055 GATAAATTTG
* * *** *
43106065 AGCATTAGCGGCGCTTCCTCATAAACGCCGCTAA--AAATAG
1 AGCATTAGCGGCGCTTCTTCAAAAACGCCGCTAATGCCCT-T
** * * *
43106105 AGCATTAGCGGCGCTTCTTCAAAAACGCTACTAAAGACCTG
1 AGCATTAGCGGCGCTTCTTCAAAAACGCCGCTAATGCCCTT
* * * *
43106146 AGCATTAGCGGCGCTTTTTCAAAAACGCCGCTAAAGACCTG
1 AGCATTAGCGGCGCTTCTTCAAAAACGCCGCTAATGCCCTT
* * * *
43106187 AGCATTAGCGGCGCTTTTTCAAAAACGCCGCTAAAGACCTG
1 AGCATTAGCGGCGCTTCTTCAAAAACGCCGCTAATGCCCTT
* * * *
43106228 AGCATTAGCGGCGCTTTTTCAAAAACGCCGCTAAAGACCTG
1 AGCATTAGCGGCGCTTCTTCAAAAACGCCGCTAATGCCCTT
* * * *
43106269 AGCATTAGCGGCGCTTTTTCAAAAACGCCGCTAAAGACCTG
1 AGCATTAGCGGCGCTTCTTCAAAAACGCCGCTAATGCCCTT
* * * *
43106310 AGCATTAGCGGCGCTTTTTCAAAAACGCCGCTAAAGACCTG
1 AGCATTAGCGGCGCTTCTTCAAAAACGCCGCTAATGCCCTT
* * *
43106351 AGCATTAGCGGCGCTTTTTCAAAAACGCCGCTAAAGCCCTA
1 AGCATTAGCGGCGCTTCTTCAAAAACGCCGCTAATGCCCTT
* * * * *
43106392 AGCATTAGCGGCCCTT-TTACAAAAACGCCACTAAAGACCTG
1 AGCATTAGCGGCGCTTCTT-CAAAAACGCCGCTAATGCCCTT
*
43106433 AGCTTTAGCGGCGCTTCTTCAAAAACGCCGCTAATGCCCTT
1 AGCATTAGCGGCGCTTCTTCAAAAACGCCGCTAATGCCCTT
43106474 AGCATTAGCGGCGCTTCTTCAAAAACGCCGCTAATGCCCTT
1 AGCATTAGCGGCGCTTCTTCAAAAACGCCGCTAATGCCCTT
43106515 AGCATTAGCGGCGCTTCTTCAAAAACGCCGCTAATGCCCTT
1 AGCATTAGCGGCGCTTCTTCAAAAACGCCGCTAATGCCCTT
43106556 AGCATTAGCGGCGCTTCTTCAAAAACGCCGCTAATGCCCTT
1 AGCATTAGCGGCGCTTCTTCAAAAACGCCGCTAATGCCCTT
43106597 AGCATTAGCGGCGCTTCTTCAAAAACGCCGCTAATGCCCTT
1 AGCATTAGCGGCGCTTCTTCAAAAACGCCGCTAATGCCCTT
43106638 AGCATTAGCGGCGCTTCTTCAAAAACGCCGCTAATGCCCTT
1 AGCATTAGCGGCGCTTCTTCAAAAACGCCGCTAATGCCCTT
43106679 AGCATTAGCGGCGCTTCTTCAAAAACGCCGCTAATGCCCTT
1 AGCATTAGCGGCGCTTCTTCAAAAACGCCGCTAATGCCCTT
43106720 AGCATTAGCGGCGCTTCTTCAAAAACGCCGCTAATGCCCTT
1 AGCATTAGCGGCGCTTCTTCAAAAACGCCGCTAATGCCCTT
43106761 AGCATTAGCGGCGCTTCTTCAAAAACGCCGCTAATGCCCTT
1 AGCATTAGCGGCGCTTCTTCAAAAACGCCGCTAATGCCCTT
43106802 AGCATTAGCGGCGCTTCTTCAAAAACGCCGCTAATGCCCTT
1 AGCATTAGCGGCGCTTCTTCAAAAACGCCGCTAATGCCCTT
43106843 AGCATTAGCGGCGCTTCTTCAAAAACGCCGCTAATGCCCTT
1 AGCATTAGCGGCGCTTCTTCAAAAACGCCGCTAATGCCCTT
43106884 AGCATTAGCGGCGCTTCTTCAAAAACGCCGCTAATGCCCTT
1 AGCATTAGCGGCGCTTCTTCAAAAACGCCGCTAATGCCCTT
43106925 AGCATTAGCGGCGCTTCTTCAAAAACGCCGCTAATGCCCTT
1 AGCATTAGCGGCGCTTCTTCAAAAACGCCGCTAATGCCCTT
43106966 AGCATTAGCGGCGCTTCTTCAAAAACGCCGCTAATGCCC
1 AGCATTAGCGGCGCTTCTTCAAAAACGCCGCTAATGCCC
43107005 CCAAAACTCA
Statistics
Matches: 874, Mismatches: 22, Indels: 7
0.97 0.02 0.01
Matches are distributed among these distances:
40 32 0.04
41 838 0.96
42 4 0.00
ACGTcount: A:0.27, C:0.30, G:0.20, T:0.23
Consensus pattern (41 bp):
AGCATTAGCGGCGCTTCTTCAAAAACGCCGCTAATGCCCTT
Found at i:43107125 original size:40 final size:40
Alignment explanation
Indices: 43107059--43107176 Score: 154
Period size: 40 Copynumber: 3.0 Consensus size: 40
43107049 CGCTTTATGG
43107059 AAAA-CGCCGCTAATGCTC-ATTTTTAGTGGCGTTTTTTA
1 AAAAGCGCCGCTAATGCTCTATTTTTAGTGGCGTTTTTTA
* * *
43107097 AAAAGCGCCGCCAATACTCTATATTTAGTGGCGTTTTATT-
1 AAAAGCGCCGCTAATGCTCTATTTTTAGTGGCGTTTT-TTA
*
43107137 AAAAGCGCCGCTAATGCT-TGATTTTTAGCGGCGTTTTTTA
1 AAAAGCGCCGCTAATGCTCT-ATTTTTAGTGGCGTTTTTTA
43107177 TCTAAACGCC
Statistics
Matches: 68, Mismatches: 7, Indels: 8
0.82 0.08 0.10
Matches are distributed among these distances:
38 4 0.06
39 15 0.22
40 47 0.69
41 2 0.03
ACGTcount: A:0.25, C:0.19, G:0.19, T:0.37
Consensus pattern (40 bp):
AAAAGCGCCGCTAATGCTCTATTTTTAGTGGCGTTTTTTA
Found at i:43109192 original size:89 final size:91
Alignment explanation
Indices: 43109038--43109203 Score: 221
Period size: 89 Copynumber: 1.8 Consensus size: 91
43109028 TCAGTAAATG
* * * *
43109038 TATTTTCATAAAATATCTAATATAATATTTATATTTTAAAAATGTTTAAGGTAGTATTTAAACTA
1 TATTTTCATAAAATATCTAATATAATACTTATACTTTAAAAATGTTCAAGGTAGTACTTAAACTA
43109103 TCAATATATATTTTATTTTTAATTTA
66 TCAATATATATTTTATTTTTAATTTA
* * * *
43109129 TATTTTCATAAAATATC-AAT-TAGTACTTGTACTTTGAAAATGTTCAATGT-GATACTTAAACT
1 TATTTTCATAAAATATCTAATATAATACTTATACTTTAAAAATGTTCAAGGTAG-TACTTAAACT
*
43109191 ATCAATATGTATT
65 ATCAATATATATT
43109204 AGTATTAATA
Statistics
Matches: 65, Mismatches: 9, Indels: 4
0.83 0.12 0.05
Matches are distributed among these distances:
88 1 0.02
89 44 0.68
90 3 0.05
91 17 0.26
ACGTcount: A:0.39, C:0.07, G:0.07, T:0.47
Consensus pattern (91 bp):
TATTTTCATAAAATATCTAATATAATACTTATACTTTAAAAATGTTCAAGGTAGTACTTAAACTA
TCAATATATATTTTATTTTTAATTTA
Found at i:43111234 original size:21 final size:21
Alignment explanation
Indices: 43111209--43111249 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
43111199 CAAAATATAT
43111209 CAAAAACAAAA-ACAAAAAAAC
1 CAAAAA-AAAACACAAAAAAAC
*
43111230 CAAAAAAAAACAGAAAAAAA
1 CAAAAAAAAACACAAAAAAA
43111250 ACCTGGACTG
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 4 0.22
21 14 0.78
ACGTcount: A:0.83, C:0.15, G:0.02, T:0.00
Consensus pattern (21 bp):
CAAAAAAAAACACAAAAAAAC
Found at i:43111319 original size:27 final size:27
Alignment explanation
Indices: 43111278--43111357 Score: 124
Period size: 27 Copynumber: 3.0 Consensus size: 27
43111268 ACTCCCTGGG
*
43111278 ACAAGGGAACACTGTTGGCGGCACCAA
1 ACAAGGGAACCCTGTTGGCGGCACCAA
43111305 ACAAGGGAACCCTGTTGGCGGCACCAA
1 ACAAGGGAACCCTGTTGGCGGCACCAA
** *
43111332 ACAAGGGTTCCTTGTTGGCGGCACCA
1 ACAAGGGAACCCTGTTGGCGGCACCA
43111358 CCCTTGAATT
Statistics
Matches: 49, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
27 49 1.00
ACGTcount: A:0.28, C:0.28, G:0.30, T:0.15
Consensus pattern (27 bp):
ACAAGGGAACCCTGTTGGCGGCACCAA
Found at i:43111422 original size:12 final size:12
Alignment explanation
Indices: 43111405--43111489 Score: 54
Period size: 12 Copynumber: 7.1 Consensus size: 12
43111395 AAAGAGAGGG
43111405 GAAG-AAGAAGAA
1 GAAGAAAGAA-AA
*
43111417 GAAGAAAGAAAG
1 GAAGAAAGAAAA
43111429 GAAGAAAG-AAA
1 GAAGAAAGAAAA
*
43111440 -AAGAAGGAAAA
1 GAAGAAAGAAAA
* *
43111451 G--GAAAGGAGAG
1 GAAGAAA-GAAAA
43111462 GAAAGAAAGAAAAA
1 G-AAGAAAG-AAAA
43111476 GAAGGAAAGAAAA
1 GAA-GAAAGAAAA
43111489 G
1 G
43111490 GAAAGGGGAG
Statistics
Matches: 56, Mismatches: 8, Indels: 17
0.69 0.10 0.21
Matches are distributed among these distances:
10 9 0.16
11 9 0.16
12 13 0.23
13 13 0.23
14 12 0.21
ACGTcount: A:0.67, C:0.00, G:0.33, T:0.00
Consensus pattern (12 bp):
GAAGAAAGAAAA
Found at i:43111425 original size:10 final size:10
Alignment explanation
Indices: 43111405--43111539 Score: 65
Period size: 10 Copynumber: 13.8 Consensus size: 10
43111395 AAAGAGAGGG
43111405 GAAGAAG-AA
1 GAAGAAGAAA
43111414 GAAGAAGAAA
1 GAAGAAGAAA
43111424 GAAAGGAAGAAA
1 G-AA-GAAGAAA
* *
43111436 GAAAAAGAAG
1 GAAGAAGAAA
43111446 GAA-AAGGAAA
1 GAAGAA-GAAA
* *
43111456 GGAGAGGAAA
1 GAAGAAGAAA
43111466 G-A-AAGAAA
1 GAAGAAGAAA
43111474 -AAGAAGGAAA
1 GAAGAA-GAAA
43111484 GAA-AAGGAAA
1 GAAGAA-GAAA
** *
43111494 GGGGAGGAAA
1 GAAGAAGAAA
43111504 G-A-AAGAAA
1 GAAGAAGAAA
*
43111512 -AATAAGGAAA
1 GAAGAA-GAAA
43111522 GAA-AAGGAAA
1 GAAGAA-GAAA
43111532 GAAGAAGA
1 GAAGAAGA
43111540 GAAATTTTTT
Statistics
Matches: 100, Mismatches: 11, Indels: 29
0.71 0.08 0.21
Matches are distributed among these distances:
8 12 0.12
9 14 0.14
10 54 0.54
11 12 0.12
12 8 0.08
ACGTcount: A:0.66, C:0.00, G:0.33, T:0.01
Consensus pattern (10 bp):
GAAGAAGAAA
Found at i:43111443 original size:28 final size:29
Alignment explanation
Indices: 43111392--43111492 Score: 89
Period size: 28 Copynumber: 3.3 Consensus size: 29
43111382 TGGTGGGGGG
* * *
43111392 AAGAAAGAGAGGGGAAGAAGAAGAAGAAGA
1 AAGAAAG-GAAGGAAAGAAAAAGAAGAAGA
43111422 AAGAAAGGAA-GAAAGAAAAAGAAGGAA-A
1 AAGAAAGGAAGGAAAGAAAAAGAA-GAAGA
* *
43111450 AGGAAAGGAGAGGAAAGAAAGAAAAAGAAGGA
1 AAGAAAGGA-AGGAAAGAAA-AAGAAGAA-GA
43111482 AAGAAAAGGAA
1 AAG-AAAGGAA
43111493 AGGGGAGGAA
Statistics
Matches: 58, Mismatches: 6, Indels: 12
0.76 0.08 0.16
Matches are distributed among these distances:
28 20 0.34
29 6 0.10
30 18 0.31
31 4 0.07
32 4 0.07
33 6 0.10
ACGTcount: A:0.65, C:0.00, G:0.35, T:0.00
Consensus pattern (29 bp):
AAGAAAGGAAGGAAAGAAAAAGAAGAAGA
Done.