Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01009437.1 Hibiscus syriacus cultivar Beakdansim tig00113495_pilon, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 392309
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 1 of 2
Found at i:5641 original size:21 final size:22
Alignment explanation
Indices: 5617--5661 Score: 74
Period size: 22 Copynumber: 2.1 Consensus size: 22
5607 ATAAGGGAGA
5617 TATTGATACT-CTTAGCCTAGG
1 TATTGATACTCCTTAGCCTAGG
*
5638 TATTGATACTCCTTAGTCTAGG
1 TATTGATACTCCTTAGCCTAGG
5660 TA
1 TA
5662 GTTTATTTTG
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
21 10 0.45
22 12 0.55
ACGTcount: A:0.24, C:0.18, G:0.18, T:0.40
Consensus pattern (22 bp):
TATTGATACTCCTTAGCCTAGG
Found at i:16730 original size:22 final size:21
Alignment explanation
Indices: 16690--16730 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
16680 TTCTTTAGTC
* *
16690 TCTGACTGTTAAAAGTTATCA
1 TCTGACTATTAAAAATTATCA
16711 TCTGACTATTAAAAAATTAT
1 TCTGACTATT-AAAAATTAT
16731 AAAATGATCA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 9 0.53
22 8 0.47
ACGTcount: A:0.39, C:0.12, G:0.10, T:0.39
Consensus pattern (21 bp):
TCTGACTATTAAAAATTATCA
Found at i:18100 original size:2 final size:2
Alignment explanation
Indices: 18093--18123 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
18083 AACCGTATGA
18093 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
18124 AACAAAGATA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:20096 original size:3 final size:3
Alignment explanation
Indices: 20090--20125 Score: 65
Period size: 3 Copynumber: 12.3 Consensus size: 3
20080 TATGTAACAT
20090 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA T-A TAA T
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA T
20126 TTTAATATAA
Statistics
Matches: 32, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
2 2 0.06
3 30 0.94
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (3 bp):
TAA
Found at i:20543 original size:55 final size:55
Alignment explanation
Indices: 20428--20620 Score: 284
Period size: 55 Copynumber: 3.5 Consensus size: 55
20418 CCCTTTTTCT
* * * *
20428 TTCAGGGAGTAT-AGAACTCAAAC-ATCTTCAACACTCGTGTCGT-TCCCTATTCC
1 TTCAGAGAGTATAAG-ACTCGAACAATCTTCAACAATCGTGTCTTCTCCCTATTCC
*
20481 TTCAGAGAGTATAAGACTTGAACAATCTTCAACAATCGTGTCTTCTCCCTATTCC
1 TTCAGAGAGTATAAGACTCGAACAATCTTCAACAATCGTGTCTTCTCCCTATTCC
* * *
20536 TTTAGAGAGTATAAGACTCGAACAATCTTCAACTATCGTGTCTGCTCCCTATTCC
1 TTCAGAGAGTATAAGACTCGAACAATCTTCAACAATCGTGTCTTCTCCCTATTCC
20591 TTCAGAGAGTATAAGACTCGAACAATCTTC
1 TTCAGAGAGTATAAGACTCGAACAATCTTC
20621 TTCTTATGGG
Statistics
Matches: 127, Mismatches: 10, Indels: 4
0.90 0.07 0.03
Matches are distributed among these distances:
53 17 0.13
54 20 0.16
55 90 0.71
ACGTcount: A:0.29, C:0.25, G:0.15, T:0.31
Consensus pattern (55 bp):
TTCAGAGAGTATAAGACTCGAACAATCTTCAACAATCGTGTCTTCTCCCTATTCC
Found at i:20638 original size:55 final size:53
Alignment explanation
Indices: 20387--20785 Score: 231
Period size: 54 Copynumber: 7.3 Consensus size: 53
20377 GAAGTATGGA
* * * * * *
20387 ACTCGAACAGTCTTCTGCCAATGGGTTCGTTCCCTTTTTCTTTCAGGGAGTAT-AG
1 ACTCGAACAATCTTCT-TCAAT-GGTTCGCTCCC-TATTCCTTCAGAGAGTATAAG
* ** * * *
20442 AACTCAAAC-ATCTTCAACACTCGTGTCGTTCCCTATTCCTTCAGAGAGTATAAG
1 -ACTCGAACAATCTTCTTCAATGGT-TCGCTCCCTATTCCTTCAGAGAGTATAAG
* ** * * *
20496 ACTTGAACAATCTTCAACAATCGTGTCTTCTCCCTATTCCTTTAGAGAGTATAAG
1 ACTCGAACAATCTTCTTCAATGGT-TC-GCTCCCTATTCCTTCAGAGAGTATAAG
** * *
20551 ACTCGAACAATCTTCAACTATCGTGTCTGCTCCCTATTCCTTCAGAGAGTATAAG
1 ACTCGAACAATCTTCTTCAATGGT-TC-GCTCCCTATTCCTTCAGAGAGTATAAG
* * *
20606 ACTCGAACAATCTTCTTCTTATGGGTTCGCTCCCTCTTTCTTCAGAGAGTAT-AG
1 ACTCGAACAATCTTCTTC-AAT-GGTTCGCTCCCTATTCCTTCAGAGAGTATAAG
* * * * * * *
20660 AACTCGAA-TATCTTCTTCAAACAGGTTTGCTCCCTCTTTC-TCTAGGGAGTATAAA
1 -ACTCGAACAATCTTCTTC-AA-TGGTTCGCTCCCTATTCCTTC-AGAGAGTATAAG
* * * * *
20715 ACTCGGAC-ATCTTCTTCAAACGGGTTCGCTCCCTCTTTC-TCTAGGGAGTAT-AG
1 ACTCGAACAATCTTCTTC-AA-TGGTTCGCTCCCTATTCCTTC-AGAGAGTATAAG
20768 AACTCGAAC-ATCTTCTTC
1 -ACTCGAACAATCTTCTTC
20786 TGCACTACTT
Statistics
Matches: 295, Mismatches: 36, Indels: 26
0.83 0.10 0.07
Matches are distributed among these distances:
53 26 0.09
54 129 0.44
55 126 0.43
56 12 0.04
57 2 0.01
ACGTcount: A:0.25, C:0.26, G:0.16, T:0.34
Consensus pattern (53 bp):
ACTCGAACAATCTTCTTCAATGGTTCGCTCCCTATTCCTTCAGAGAGTATAAG
Found at i:20697 original size:54 final size:54
Alignment explanation
Indices: 20594--20785 Score: 253
Period size: 54 Copynumber: 3.5 Consensus size: 54
20584 CTATTCCTTC
** *
20594 AGAGAGTATA-AGACTCGAACAATCTTCTTCTTATGGGTTCGCTCCCTCTTTCT-T
1 AGAGAGTATAGA-ACTCGAAC-ATCTTCTTCAAACGGGTTCGCTCCCTCTTTCTCT
* * *
20648 CAGAGAGTATAGAACTCGAATATCTTCTTCAAACAGGTTTGCTCCCTCTTTCTCT
1 -AGAGAGTATAGAACTCGAACATCTTCTTCAAACGGGTTCGCTCCCTCTTTCTCT
* * *
20703 AGGGAGTATAAAACTCGGACATCTTCTTCAAACGGGTTCGCTCCCTCTTTCTCT
1 AGAGAGTATAGAACTCGAACATCTTCTTCAAACGGGTTCGCTCCCTCTTTCTCT
*
20757 AGGGAGTATAGAACTCGAACATCTTCTTC
1 AGAGAGTATAGAACTCGAACATCTTCTTC
20786 TGCACTACTT
Statistics
Matches: 121, Mismatches: 14, Indels: 5
0.86 0.10 0.04
Matches are distributed among these distances:
54 102 0.84
55 18 0.15
56 1 0.01
ACGTcount: A:0.24, C:0.25, G:0.17, T:0.33
Consensus pattern (54 bp):
AGAGAGTATAGAACTCGAACATCTTCTTCAAACGGGTTCGCTCCCTCTTTCTCT
Found at i:33204 original size:2 final size:2
Alignment explanation
Indices: 33197--33226 Score: 51
Period size: 2 Copynumber: 14.5 Consensus size: 2
33187 AACCGTATGA
33197 AT AT AT AT AT AT AT AT AT AT AT AT CAT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT -AT AT A
33227 AACAAAAGAT
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
2 25 0.93
3 2 0.07
ACGTcount: A:0.50, C:0.03, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:35207 original size:3 final size:3
Alignment explanation
Indices: 35201--35230 Score: 53
Period size: 3 Copynumber: 10.3 Consensus size: 3
35191 TATGTAACAT
35201 TAA TAA TAA TAA TAA TAA TAA TAA T-A TAA T
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA T
35231 TTTAATATAA
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
2 2 0.08
3 24 0.92
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (3 bp):
TAA
Found at i:36023 original size:2 final size:2
Alignment explanation
Indices: 36016--36040 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
36006 TTTTGTTAAT
36016 TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA T
36041 CCTTTTTAAA
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:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:36449 original size:18 final size:19
Alignment explanation
Indices: 36428--36468 Score: 75
Period size: 18 Copynumber: 2.2 Consensus size: 19
36418 CTACAAGATA
36428 ACAAACTATTCTAGAACT-
1 ACAAACTATTCTAGAACTC
36446 ACAAACTATTCTAGAACTC
1 ACAAACTATTCTAGAACTC
36465 ACAA
1 ACAA
36469 CATATCCATA
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
18 18 0.82
19 4 0.18
ACGTcount: A:0.46, C:0.24, G:0.05, T:0.24
Consensus pattern (19 bp):
ACAAACTATTCTAGAACTC
Found at i:38340 original size:45 final size:45
Alignment explanation
Indices: 38251--38352 Score: 107
Period size: 45 Copynumber: 2.3 Consensus size: 45
38241 GTCATGGACA
* * ** **
38251 GCCATTGCTCCAAAAGGCGTGGCTCCAAGAACATTGTCGTGGTCG
1 GCCATAGCTCCAAAAGCCGTGGCTCCAAGAACATCATCACGGTCG
*
38296 GCCATAGCTCCAAAAGCCGTGG-TCCCAAGCACATCATCACGGTCG
1 GCCATAGCTCCAAAAGCCGTGGCT-CCAAGAACATCATCACGGTCG
* *
38341 GGCATAACTCCA
1 GCCATAGCTCCA
38353 TGGACCGATG
Statistics
Matches: 47, Mismatches: 9, Indels: 2
0.81 0.16 0.03
Matches are distributed among these distances:
44 1 0.02
45 46 0.98
ACGTcount: A:0.25, C:0.31, G:0.25, T:0.19
Consensus pattern (45 bp):
GCCATAGCTCCAAAAGCCGTGGCTCCAAGAACATCATCACGGTCG
Found at i:39022 original size:15 final size:15
Alignment explanation
Indices: 38981--39022 Score: 66
Period size: 15 Copynumber: 2.8 Consensus size: 15
38971 GGAACACACG
*
38981 TTGATGGAGCAAATA
1 TTGATGGAGCATATA
*
38996 CTGATGGAGCATATA
1 TTGATGGAGCATATA
39011 TTGATGGAGCAT
1 TTGATGGAGCAT
39023 GCACTGGTGG
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
15 24 1.00
ACGTcount: A:0.33, C:0.10, G:0.29, T:0.29
Consensus pattern (15 bp):
TTGATGGAGCATATA
Found at i:39034 original size:30 final size:30
Alignment explanation
Indices: 38981--39037 Score: 78
Period size: 30 Copynumber: 1.9 Consensus size: 30
38971 GGAACACACG
*
38981 TTGATGGAGCAAATACTGATGGAGCATATA
1 TTGATGGAGCAAACACTGATGGAGCATATA
** *
39011 TTGATGGAGCATGCACTGGTGGAGCAT
1 TTGATGGAGCAAACACTGATGGAGCAT
39038 GTGTTGTCTG
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
30 23 1.00
ACGTcount: A:0.30, C:0.12, G:0.32, T:0.26
Consensus pattern (30 bp):
TTGATGGAGCAAACACTGATGGAGCATATA
Found at i:41328 original size:20 final size:20
Alignment explanation
Indices: 41288--41330 Score: 61
Period size: 20 Copynumber: 2.1 Consensus size: 20
41278 GGACCACCAT
*
41288 ATGCAACTATATGAGTCTAA
1 ATGCAACTATATGAATCTAA
41308 ATGCAACTATATGCAAT-TAA
1 ATGCAACTATATG-AATCTAA
41328 ATG
1 ATG
41331 AGCTTTAAAA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
20 19 0.90
21 2 0.10
ACGTcount: A:0.42, C:0.14, G:0.14, T:0.30
Consensus pattern (20 bp):
ATGCAACTATATGAATCTAA
Found at i:43858 original size:15 final size:15
Alignment explanation
Indices: 43838--43873 Score: 63
Period size: 15 Copynumber: 2.4 Consensus size: 15
43828 ATGATAAACG
43838 TTAGTTAAAATGATT
1 TTAGTTAAAATGATT
43853 TTAGTTAAAATGATT
1 TTAGTTAAAATGATT
*
43868 GTAGTT
1 TTAGTT
43874 GAGTTGGGTG
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
15 20 1.00
ACGTcount: A:0.36, C:0.00, G:0.17, T:0.47
Consensus pattern (15 bp):
TTAGTTAAAATGATT
Found at i:44784 original size:23 final size:23
Alignment explanation
Indices: 44742--44793 Score: 68
Period size: 23 Copynumber: 2.3 Consensus size: 23
44732 TCTTATATGG
* *
44742 CACTTCGGTGTATTTTTACGCGA
1 CACTTCGGTGTAATTCTACGCGA
* *
44765 CACTTCGGTGTAATTCTACGTGT
1 CACTTCGGTGTAATTCTACGCGA
44788 CACTTC
1 CACTTC
44794 AGTGCATTTA
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 25 1.00
ACGTcount: A:0.17, C:0.25, G:0.19, T:0.38
Consensus pattern (23 bp):
CACTTCGGTGTAATTCTACGCGA
Found at i:51674 original size:23 final size:23
Alignment explanation
Indices: 51641--51703 Score: 74
Period size: 23 Copynumber: 2.7 Consensus size: 23
51631 CTTATATGGT
* *
51641 ACTTCGGTGCATTTCTACGCT-GC
1 ACTTCGGTGCATTTATAAG-TGGC
* *
51664 ACTTCGATGCAATTATAAGTGGC
1 ACTTCGGTGCATTTATAAGTGGC
51687 ACTTCGGTGCATTTATA
1 ACTTCGGTGCATTTATA
51704 CAACATGTGG
Statistics
Matches: 33, Mismatches: 6, Indels: 2
0.80 0.15 0.05
Matches are distributed among these distances:
22 1 0.03
23 32 0.97
ACGTcount: A:0.22, C:0.22, G:0.21, T:0.35
Consensus pattern (23 bp):
ACTTCGGTGCATTTATAAGTGGC
Found at i:60414 original size:36 final size:36
Alignment explanation
Indices: 60323--60541 Score: 246
Period size: 37 Copynumber: 6.0 Consensus size: 36
60313 AAAATATATA
* * * **
60323 TATAATATATTGTTTTTGAAAA-ATTATTTAAAAAATA
1 TATAATATATAGTTTTTTAAAATATT-TTT-GAAAACG
60360 TATAATATATAGTTTTTTTTAAAATATTTTTGAAAACG
1 TATAATATATAG--TTTTTTAAAATATTTTTGAAAACG
* *
60398 TATAATATATAGTTTTTTAAAAATAGTTTTCAAAACG
1 TATAATATATAGTTTTTT-AAAATATTTTTGAAAACG
**
60435 TATAATATATAG-TTTTTAAAATAGTTTTT-AAAATA
1 TATAATATATAGTTTTTTAAAATA-TTTTTGAAAACG
*
60470 TATAATATATAGTTTTTTAAAATAATTTTGAAAACG
1 TATAATATATAGTTTTTTAAAATATTTTTGAAAACG
* *
60506 TATAATATATAATTTTTTTAAAATAGTTTTGAAAAC
1 TATAATATAT-AGTTTTTTAAAATATTTTTGAAAAC
60542 ATATTTGAAA
Statistics
Matches: 159, Mismatches: 15, Indels: 16
0.84 0.08 0.08
Matches are distributed among these distances:
35 26 0.16
36 40 0.25
37 62 0.39
38 16 0.10
39 12 0.08
40 3 0.02
ACGTcount: A:0.44, C:0.02, G:0.07, T:0.47
Consensus pattern (36 bp):
TATAATATATAGTTTTTTAAAATATTTTTGAAAACG
Found at i:60460 original size:12 final size:12
Alignment explanation
Indices: 60443--60469 Score: 54
Period size: 12 Copynumber: 2.2 Consensus size: 12
60433 CGTATAATAT
60443 ATAGTTTTTAAA
1 ATAGTTTTTAAA
60455 ATAGTTTTTAAA
1 ATAGTTTTTAAA
60467 ATA
1 ATA
60470 TATAATATAT
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:0.44, C:0.00, G:0.07, T:0.48
Consensus pattern (12 bp):
ATAGTTTTTAAA
Found at i:60505 original size:108 final size:110
Alignment explanation
Indices: 60323--60541 Score: 329
Period size: 108 Copynumber: 2.0 Consensus size: 110
60313 AAAATATATA
* *
60323 TATAATATATTGTTTTTGAAAAATTATTTAAAAAATATATAATATATAGTTTTTTTTAAAATATT
1 TATAATATATAGTTTTTGAAAAATTATTT-AAAAATATATAATATATAG-TTTTTTTAAAATAAT
*
60388 TTTGAAAACGTATAATATATAGTTTTTTAAAAATAGTTTTCAAAACG
64 TTTGAAAACGTATAATATATAATTTTTTAAAAATAGTTTTCAAAACG
60435 TATAATATATAGTTTTT-AAAATAGTT-TTT-AAAATATATAATATATAG-TTTTTTAAAATAAT
1 TATAATATATAGTTTTTGAAAA-A-TTATTTAAAAATATATAATATATAGTTTTTTTAAAATAAT
* *
60496 TTTGAAAACGTATAATATATAATTTTTTTAAAATAGTTTTGAAAAC
64 TTTGAAAACGTATAATATATAATTTTTTAAAAATAGTTTTCAAAAC
60542 ATATTTGAAA
Statistics
Matches: 100, Mismatches: 5, Indels: 8
0.88 0.04 0.07
Matches are distributed among these distances:
108 56 0.56
110 18 0.18
111 4 0.04
112 20 0.20
113 2 0.02
ACGTcount: A:0.44, C:0.02, G:0.07, T:0.47
Consensus pattern (110 bp):
TATAATATATAGTTTTTGAAAAATTATTTAAAAATATATAATATATAGTTTTTTTAAAATAATTT
TGAAAACGTATAATATATAATTTTTTAAAAATAGTTTTCAAAACG
Found at i:60621 original size:9 final size:9
Alignment explanation
Indices: 60609--60671 Score: 60
Period size: 9 Copynumber: 7.0 Consensus size: 9
60599 TCGTTATTAT
60609 TATTATTTA
1 TATTATTTA
60618 TATTATTTA
1 TATTATTTA
60627 TTATT-TTTA
1 -TATTATTTA
*
60636 T-TTAATTA
1 TATTATTTA
60644 TTATGTATTTA
1 -TAT-TATTTA
*
60655 TTTTATTTA
1 TATTATTTA
60664 T-TTATTTA
1 TATTATTTA
60672 ACCATTTCAG
Statistics
Matches: 46, Mismatches: 3, Indels: 11
0.77 0.05 0.18
Matches are distributed among these distances:
7 2 0.04
8 11 0.24
9 21 0.46
10 7 0.15
11 5 0.11
ACGTcount: A:0.29, C:0.00, G:0.02, T:0.70
Consensus pattern (9 bp):
TATTATTTA
Found at i:60627 original size:4 final size:4
Alignment explanation
Indices: 60611--60671 Score: 61
Period size: 4 Copynumber: 14.8 Consensus size: 4
60601 GTTATTATTA
* * *
60611 TTAT TTAT ATTAT TTAT TATTT TTAT TTAA TTA- TTAT GTAT TTATT TTAT
1 TTAT TTAT -TTAT TTAT T-TAT TTAT TTAT TTAT TTAT TTAT TTA-T TTAT
60661 TTAT TTAT TTA
1 TTAT TTAT TTA
60672 ACCATTTCAG
Statistics
Matches: 48, Mismatches: 5, Indels: 8
0.79 0.08 0.13
Matches are distributed among these distances:
3 3 0.06
4 34 0.71
5 11 0.23
ACGTcount: A:0.28, C:0.00, G:0.02, T:0.70
Consensus pattern (4 bp):
TTAT
Found at i:60652 original size:24 final size:24
Alignment explanation
Indices: 60603--60669 Score: 77
Period size: 24 Copynumber: 2.9 Consensus size: 24
60593 AGTTTTTCGT
* *
60603 TATTATTATTATTT-A-TATTATT
1 TATTATTTTTATTTAATTATTATG
60625 TATTATTTTTATTTAATTATTATG
1 TATTATTTTTATTTAATTATTATG
*
60649 TATT-TATTTTATTTATTTATT
1 TATTAT-TTTTATTTAATTATT
60670 TAACCATTTC
Statistics
Matches: 39, Mismatches: 3, Indels: 4
0.85 0.07 0.09
Matches are distributed among these distances:
22 13 0.33
23 2 0.05
24 24 0.62
ACGTcount: A:0.28, C:0.00, G:0.01, T:0.70
Consensus pattern (24 bp):
TATTATTTTTATTTAATTATTATG
Found at i:71684 original size:47 final size:49
Alignment explanation
Indices: 71630--71745 Score: 173
Period size: 50 Copynumber: 2.4 Consensus size: 49
71620 TGGAGAGAAC
**
71630 ACCCGAAAGGATACTCTAAGTAGTAGT-AAAAAAGT-TTTAGGGTGAAA
1 ACCCGAAAGGGCACTCTAAGTAGTAGTAAAAAAAGTATTTAGGGTGAAA
*
71677 ACCCGAAAGGGCACTCTAAGTAGTAGTAAAAAAATTAATTTAGGGTGAAA
1 ACCCGAAAGGGCACTCTAAGTAGTAGTAAAAAAAGT-ATTTAGGGTGAAA
*
71727 ACCTGAAAGGGCACTCTAA
1 ACCCGAAAGGGCACTCTAA
71746 ATTGGAAAAT
Statistics
Matches: 62, Mismatches: 4, Indels: 3
0.90 0.06 0.04
Matches are distributed among these distances:
47 25 0.40
48 7 0.11
50 30 0.48
ACGTcount: A:0.42, C:0.14, G:0.22, T:0.22
Consensus pattern (49 bp):
ACCCGAAAGGGCACTCTAAGTAGTAGTAAAAAAAGTATTTAGGGTGAAA
Found at i:71760 original size:50 final size:50
Alignment explanation
Indices: 71665--71760 Score: 131
Period size: 50 Copynumber: 1.9 Consensus size: 50
71655 GTAAAAAAGT
* * *
71665 TTTAGGGTGAAAACCCGAAAGGGCACTCTAAGTAGTAGTAAAAAAATTAA
1 TTTAGGGTGAAAACCCGAAAGGGCACTCTAAATAGGAGAAAAAAAATTAA
* *
71715 TTTAGGGTGAAAACCTGAAAGGGCACTCTAAATTGGA-AAATAAAAA
1 TTTAGGGTGAAAACCCGAAAGGGCACTCTAAATAGGAGAAA-AAAAA
71761 CAAATAAAGC
Statistics
Matches: 40, Mismatches: 5, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
49 2 0.05
50 38 0.95
ACGTcount: A:0.45, C:0.11, G:0.22, T:0.22
Consensus pattern (50 bp):
TTTAGGGTGAAAACCCGAAAGGGCACTCTAAATAGGAGAAAAAAAATTAA
Found at i:73435 original size:36 final size:37
Alignment explanation
Indices: 73384--73453 Score: 115
Period size: 36 Copynumber: 1.9 Consensus size: 37
73374 TGAAAACTTA
73384 TTTTAAAAAAACATATAATATATAGTTCTTAAAACGG
1 TTTTAAAAAAACATATAATATATAGTTCTTAAAACGG
* *
73421 TTTT-AAAAAACATATAGTATATAGTTTTTAAAA
1 TTTTAAAAAAACATATAATATATAGTTCTTAAAA
73454 AATATTTTTG
Statistics
Matches: 31, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
36 27 0.87
37 4 0.13
ACGTcount: A:0.49, C:0.06, G:0.07, T:0.39
Consensus pattern (37 bp):
TTTTAAAAAAACATATAATATATAGTTCTTAAAACGG
Found at i:73539 original size:38 final size:37
Alignment explanation
Indices: 73391--73565 Score: 208
Period size: 37 Copynumber: 4.7 Consensus size: 37
73381 TTATTTTAAA
* * *** **
73391 AAAACATATAATATATAGTTCTT-AAAACGGTTTTAA
1 AAAACGTATAATATATAGTTTTTAAAAAATATTTTTG
* *
73427 AAAACATATAGTATATAGTTTTTAAAAAATATTTTTG
1 AAAACGTATAATATATAGTTTTTAAAAAATATTTTTG
* *
73464 AAAATGTATAATATATAGTTTTTTAAAAATATTTTTG
1 AAAACGTATAATATATAGTTTTTAAAAAATATTTTTG
* *
73501 AAAACGTATAATATATACTTTTCTAAAAAATAGTTTTG
1 AAAACGTATAATATATAGTTTT-TAAAAAATATTTTTG
*
73539 AAAGCGTATAATATATAGTTTTTAAAA
1 AAAACGTATAATATATAGTTTTTAAAA
73566 TGTATAATAT
Statistics
Matches: 120, Mismatches: 17, Indels: 3
0.86 0.12 0.02
Matches are distributed among these distances:
36 21 0.17
37 66 0.55
38 33 0.28
ACGTcount: A:0.46, C:0.05, G:0.09, T:0.41
Consensus pattern (37 bp):
AAAACGTATAATATATAGTTTTTAAAAAATATTTTTG
Found at i:73585 original size:25 final size:23
Alignment explanation
Indices: 73530--73590 Score: 86
Period size: 23 Copynumber: 2.6 Consensus size: 23
73520 TTTCTAAAAA
* **
73530 ATAGTTTTGAAAGCGTATAATAT
1 ATAGTTTTTAAAATGTATAATAT
73553 ATAGTTTTTAAAATGTATAATAT
1 ATAGTTTTTAAAATGTATAATAT
73576 ATAGTTTTTTAAAAT
1 ATAG-TTTTTAAAAT
73591 AATTTTGAAA
Statistics
Matches: 34, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
23 24 0.71
24 10 0.29
ACGTcount: A:0.41, C:0.02, G:0.11, T:0.46
Consensus pattern (23 bp):
ATAGTTTTTAAAATGTATAATAT
Found at i:73598 original size:59 final size:62
Alignment explanation
Indices: 73495--73626 Score: 171
Period size: 59 Copynumber: 2.2 Consensus size: 62
73485 TTTAAAAATA
* * * * *
73495 TTTTTGAAAACGTATAATATATACTTTTCTAAAAAATAGTTTTGAAAGCGTATAATATATAG
1 TTTTTTAAAATGTATAATATATACTTTTCTAAAAAATAATTTTGAAAACGTAAAATATATAG
* * *
73557 -TTTTTAAAATGTATAATATATAGTTTT-T-TAAAATAATTTTGAAAACTTAAAATATATAG
1 TTTTTTAAAATGTATAATATATACTTTTCTAAAAAATAATTTTGAAAACGTAAAATATATAG
73616 TTTTTTAAAAT
1 TTTTTTAAAAT
73627 AGTTTTGAAA
Statistics
Matches: 61, Mismatches: 8, Indels: 4
0.84 0.11 0.05
Matches are distributed among these distances:
59 26 0.43
60 11 0.18
61 24 0.39
ACGTcount: A:0.43, C:0.04, G:0.08, T:0.45
Consensus pattern (62 bp):
TTTTTTAAAATGTATAATATATACTTTTCTAAAAAATAATTTTGAAAACGTAAAATATATAG
Found at i:73650 original size:36 final size:36
Alignment explanation
Indices: 73571--73650 Score: 124
Period size: 36 Copynumber: 2.2 Consensus size: 36
73561 TAAAATGTAT
*
73571 AATATATAGTTTTTTAAAATAATTTTGAAAACTTAA
1 AATATATAGTTTTTTAAAATAATTTTGAAAACATAA
*
73607 AATATATAGTTTTTTAAAATAGTTTTGAAAACATATA
1 AATATATAGTTTTTTAAAATAATTTTGAAAACATA-A
73644 TAATATA
1 -AATATA
73651 ATGATTTTGA
Statistics
Matches: 40, Mismatches: 2, Indels: 2
0.91 0.05 0.05
Matches are distributed among these distances:
36 33 0.82
37 1 0.03
38 6 0.15
ACGTcount: A:0.47, C:0.03, G:0.06, T:0.44
Consensus pattern (36 bp):
AATATATAGTTTTTTAAAATAATTTTGAAAACATAA
Found at i:73740 original size:15 final size:15
Alignment explanation
Indices: 73720--73772 Score: 63
Period size: 15 Copynumber: 3.5 Consensus size: 15
73710 ATATATTTTT
*
73720 TATTATTATTGTTTA
1 TATTATTATTATTTA
73735 TATTATTTATTATTTA
1 TATTA-TTATTATTTA
73751 -ATTATTATGTATTTA
1 TATTATTAT-TATTTA
*
73766 TTTTATT
1 TATTATT
73773 TATTTAACCA
Statistics
Matches: 33, Mismatches: 2, Indels: 5
0.82 0.05 0.12
Matches are distributed among these distances:
14 4 0.12
15 15 0.45
16 14 0.42
ACGTcount: A:0.28, C:0.00, G:0.04, T:0.68
Consensus pattern (15 bp):
TATTATTATTATTTA
Found at i:75889 original size:24 final size:25
Alignment explanation
Indices: 75848--75905 Score: 66
Period size: 23 Copynumber: 2.4 Consensus size: 25
75838 TTTTATACAT
* *
75848 AAAATATATATAATATATAGTTTTTA
1 AAAACATATATAATATATA-ATTTTA
*
75874 AAAAGATATAT-A-ATATAATTTTA
1 AAAACATATATAATATATAATTTTA
75897 AAAACATAT
1 AAAACATAT
75906 TATTTTATAT
Statistics
Matches: 29, Mismatches: 3, Indels: 3
0.83 0.09 0.09
Matches are distributed among these distances:
23 13 0.45
24 5 0.17
25 1 0.03
26 10 0.34
ACGTcount: A:0.55, C:0.02, G:0.03, T:0.40
Consensus pattern (25 bp):
AAAACATATATAATATATAATTTTA
Found at i:75914 original size:24 final size:23
Alignment explanation
Indices: 75848--75905 Score: 71
Period size: 26 Copynumber: 2.4 Consensus size: 23
75838 TTTTATACAT
*
75848 AAAATATATATAATATATAGTTTTTA
1 AAAACATATATAATATA-A--TTTTA
*
75874 AAAAGATATATAATATAATTTTA
1 AAAACATATATAATATAATTTTA
75897 AAAACATAT
1 AAAACATAT
75906 TATTTTATAT
Statistics
Matches: 30, Mismatches: 2, Indels: 3
0.86 0.06 0.09
Matches are distributed among these distances:
23 13 0.43
25 1 0.03
26 16 0.53
ACGTcount: A:0.55, C:0.02, G:0.03, T:0.40
Consensus pattern (23 bp):
AAAACATATATAATATAATTTTA
Found at i:75952 original size:15 final size:15
Alignment explanation
Indices: 75934--75966 Score: 50
Period size: 15 Copynumber: 2.2 Consensus size: 15
75924 TGTAGTATTA
75934 TTTA-TATTATTTTAT
1 TTTATTATT-TTTTAT
75949 TTTATTATTTTTTAT
1 TTTATTATTTTTTAT
75964 TTT
1 TTT
75967 TAATTTTAGG
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 13 0.76
16 4 0.24
ACGTcount: A:0.21, C:0.00, G:0.00, T:0.79
Consensus pattern (15 bp):
TTTATTATTTTTTAT
Found at i:75956 original size:13 final size:14
Alignment explanation
Indices: 75931--75959 Score: 51
Period size: 13 Copynumber: 2.1 Consensus size: 14
75921 ATATGTAGTA
75931 TTATTTATATTATT
1 TTATTTATATTATT
75945 TTATTT-TATTATT
1 TTATTTATATTATT
75958 TT
1 TT
75960 TTATTTTTAA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 9 0.60
14 6 0.40
ACGTcount: A:0.24, C:0.00, G:0.00, T:0.76
Consensus pattern (14 bp):
TTATTTATATTATT
Found at i:83051 original size:44 final size:44
Alignment explanation
Indices: 82950--83102 Score: 261
Period size: 44 Copynumber: 3.5 Consensus size: 44
82940 CATTTATCGT
82950 ATAAGCTCGTAAGCTTATTTTACCAATATACTTACCATTTATTCC
1 ATAAGCTCGTAAGCTTATTTTACCAATATACTTACCA-TTATTCC
* *
82995 ATAATCTCGTAAGCTTATTTTACCAAAATACTTACCATTATTCC
1 ATAAGCTCGTAAGCTTATTTTACCAATATACTTACCATTATTCC
*
83039 ATAAGCTCGTAAGCTTATTTTACCAATATACTTGCCATTATTCC
1 ATAAGCTCGTAAGCTTATTTTACCAATATACTTACCATTATTCC
*
83083 ATAAGCTCGTAAACTTATTT
1 ATAAGCTCGTAAGCTTATTT
83103 GCATGGTTAC
Statistics
Matches: 102, Mismatches: 6, Indels: 1
0.94 0.06 0.01
Matches are distributed among these distances:
44 67 0.66
45 35 0.34
ACGTcount: A:0.32, C:0.22, G:0.07, T:0.39
Consensus pattern (44 bp):
ATAAGCTCGTAAGCTTATTTTACCAATATACTTACCATTATTCC
Found at i:83292 original size:40 final size:40
Alignment explanation
Indices: 83234--83395 Score: 261
Period size: 40 Copynumber: 4.0 Consensus size: 40
83224 ACCGTAGTGC
*
83234 TACACATAAGGTCATGCCCACCATATACATCGAAGTGTAT
1 TACACATAAGGTCATGCCCACCATATACACCGAAGTGTAT
* * * *
83274 TACACATAAGGTCGTGCCCACCATATACAGCAAAGTATAT
1 TACACATAAGGTCATGCCCACCATATACACCGAAGTGTAT
**
83314 TACACATAAGGTTGTGCCCACCATATACACCGAAGTGTAT
1 TACACATAAGGTCATGCCCACCATATACACCGAAGTGTAT
83354 TACACATAAGGTCATGCCCACCATATACACCGAAGTGTAT
1 TACACATAAGGTCATGCCCACCATATACACCGAAGTGTAT
83394 TA
1 TA
83396 TAAACCTGCA
Statistics
Matches: 112, Mismatches: 10, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
40 112 1.00
ACGTcount: A:0.35, C:0.25, G:0.15, T:0.24
Consensus pattern (40 bp):
TACACATAAGGTCATGCCCACCATATACACCGAAGTGTAT
Found at i:84383 original size:30 final size:29
Alignment explanation
Indices: 84341--84416 Score: 89
Period size: 30 Copynumber: 2.5 Consensus size: 29
84331 ATACAACCAG
*
84341 CCCCAACTTTTTCCAAAATTATGAATTGGT
1 CCCCAAC-TTTTCCAAAATTATAAATTGGT
*
84371 CCCCTAACTTTTCAAAAATTATAAATTGGT
1 CCCC-AACTTTTCCAAAATTATAAATTGGT
* *
84401 CCTCAAATTTTTCCAA
1 CC-CCAACTTTTCCAA
84417 GGCCTGTAGA
Statistics
Matches: 39, Mismatches: 5, Indels: 4
0.81 0.10 0.08
Matches are distributed among these distances:
30 35 0.90
31 4 0.10
ACGTcount: A:0.33, C:0.24, G:0.07, T:0.37
Consensus pattern (29 bp):
CCCCAACTTTTCCAAAATTATAAATTGGT
Found at i:85401 original size:30 final size:30
Alignment explanation
Indices: 85365--85423 Score: 84
Period size: 30 Copynumber: 2.0 Consensus size: 30
85355 TTTAGTCCCT
* *
85365 AAACTTT-TCAAAGTTTATACTTTGGTCACC
1 AAACTTTACCAAA-TTTATAATTTGGTCACC
85395 AAACTTTACCAAATTTATAATTTGGTCAC
1 AAACTTTACCAAATTTATAATTTGGTCAC
85424 TAAATAAATC
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
30 22 0.85
31 4 0.15
ACGTcount: A:0.34, C:0.19, G:0.08, T:0.39
Consensus pattern (30 bp):
AAACTTTACCAAATTTATAATTTGGTCACC
Found at i:87402 original size:6 final size:6
Alignment explanation
Indices: 87385--87538 Score: 109
Period size: 6 Copynumber: 24.8 Consensus size: 6
87375 ATGAAATATT
* *
87385 TTTTTC TCTTTC TTTTTC TTTTTA TGTTTT- TTTCTTC TTTTTC -TTTTC
1 TTTTTC TTTTTC TTTTTC TTTTTC T-TTTTC TTT-TTC TTTTTC TTTTTC
* *
87433 ATGTTTT- TTTCTTC TTTTTC TTTTTC TTCTTC TTATTTT TTTTTC -TTTTC
1 -T-TTTTC TTT-TTC TTTTTC TTTTTC TTTTTC TT-TTTC TTTTTC TTTTTC
* * * * * *
87483 TTTTTA TTTTTC TTCTTAC TTTTTG TTTTCTT TTTTTC TATTTA TTTTTC
1 TTTTTC TTTTTC TT-TTTC TTTTTC TTTT-TC TTTTTC TTTTTC TTTTTC
87533 GTTTTT
1 -TTTTT
87539 AGCTCATATG
Statistics
Matches: 117, Mismatches: 18, Indels: 25
0.73 0.11 0.16
Matches are distributed among these distances:
5 14 0.12
6 70 0.60
7 29 0.25
8 4 0.03
ACGTcount: A:0.05, C:0.14, G:0.03, T:0.79
Consensus pattern (6 bp):
TTTTTC
Found at i:87414 original size:25 final size:25
Alignment explanation
Indices: 87384--87457 Score: 121
Period size: 25 Copynumber: 2.9 Consensus size: 25
87374 AATGAAATAT
87384 TTTTTTCTCTTTCTTTTTCTTTTTATG
1 TTTTTT-TC-TTCTTTTTCTTTTTATG
*
87411 TTTTTTTCTTCTTTTTCTTTTCATG
1 TTTTTTTCTTCTTTTTCTTTTTATG
87436 TTTTTTTCTTCTTTTTCTTTTT
1 TTTTTTTCTTCTTTTTCTTTTT
87458 CTTCTTCTTA
Statistics
Matches: 45, Mismatches: 2, Indels: 2
0.92 0.04 0.04
Matches are distributed among these distances:
25 37 0.82
26 2 0.04
27 6 0.13
ACGTcount: A:0.03, C:0.15, G:0.03, T:0.80
Consensus pattern (25 bp):
TTTTTTTCTTCTTTTTCTTTTTATG
Found at i:87511 original size:5 final size:5
Alignment explanation
Indices: 87386--87486 Score: 52
Period size: 5 Copynumber: 19.8 Consensus size: 5
87376 TGAAATATTT
* *
87386 TTTTC TCTTTC TTTTTC TTTT- TATGTTT TTTTC TTCT- TTTTC TTTTC
1 TTTTC T-TTTC -TTTTC TTTTC T-T-TTC TTTTC TTTTC TTTTC TTTTC
* *
87433 ATGTTT- TTTTC TTCT- TTTTC TTTTTC TTCTTC TTAT- TTTT- TTTTC
1 -T-TTTC TTTTC TTTTC TTTTC -TTTTC TT-TTC TTTTC TTTTC TTTTC
87478 TTTTC TTTT
1 TTTTC TTTT
87487 TATTTTTCTT
Statistics
Matches: 76, Mismatches: 7, Indels: 26
0.70 0.06 0.24
Matches are distributed among these distances:
4 17 0.22
5 32 0.42
6 22 0.29
7 5 0.07
ACGTcount: A:0.03, C:0.16, G:0.02, T:0.79
Consensus pattern (5 bp):
TTTTC
Found at i:90334 original size:44 final size:44
Alignment explanation
Indices: 90233--90385 Score: 216
Period size: 44 Copynumber: 3.5 Consensus size: 44
90223 CATTTATCCT
* * * * **
90233 ATAAGCTCGTAAGCTTTTTTTGCCATATTTTTTACCATTTATTCC
1 ATAAGCTCGTAAGCTTATTTTACCAAAATACTTACCA-TTATTCC
90278 ATAAGCTCGTAAGCTTATTTTACCAAAATACTTACCATTATTCC
1 ATAAGCTCGTAAGCTTATTTTACCAAAATACTTACCATTATTCC
* *
90322 ATAAGCTCGTAAGCTTATTTTACCAATATACTTGCCATTATTCC
1 ATAAGCTCGTAAGCTTATTTTACCAAAATACTTACCATTATTCC
*
90366 ATAAGTTCGTAAGCTTATTT
1 ATAAGCTCGTAAGCTTATTT
90386 GCATGGTTAC
Statistics
Matches: 99, Mismatches: 9, Indels: 1
0.91 0.08 0.01
Matches are distributed among these distances:
44 68 0.69
45 31 0.31
ACGTcount: A:0.29, C:0.20, G:0.09, T:0.42
Consensus pattern (44 bp):
ATAAGCTCGTAAGCTTATTTTACCAAAATACTTACCATTATTCC
Found at i:90441 original size:13 final size:14
Alignment explanation
Indices: 90407--90452 Score: 60
Period size: 13 Copynumber: 3.4 Consensus size: 14
90397 ATTTATTAAC
90407 CAATAAACCATA-A
1 CAATAAACCATAGA
90420 CAATAAACCATAGA
1 CAATAAACCATAGA
*
90434 CCAT-AACCAATAGA
1 CAATAAACC-ATAGA
90448 CAATA
1 CAATA
90453 TTATGTAGCC
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
13 16 0.57
14 12 0.43
ACGTcount: A:0.57, C:0.24, G:0.04, T:0.15
Consensus pattern (14 bp):
CAATAAACCATAGA
Found at i:90637 original size:40 final size:40
Alignment explanation
Indices: 90517--90638 Score: 199
Period size: 40 Copynumber: 3.0 Consensus size: 40
90507 ACCGTAGTGC
* *
90517 TACACATAAGGTCGTGCCCACCATATACACTGAAGTGTAC
1 TACACATAAGGTCGTGCCCACCATATACACCGAAGTGTAT
*
90557 TACACATAAGGTCGTGCCCACCATATACACCGAAGGGTAT
1 TACACATAAGGTCGTGCCCACCATATACACCGAAGTGTAT
* *
90597 TACACATAAGGTCGTGCCCACTATATACACCGAACTGTAT
1 TACACATAAGGTCGTGCCCACCATATACACCGAAGTGTAT
90637 TA
1 TA
90639 TAAACATGTA
Statistics
Matches: 76, Mismatches: 6, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
40 76 1.00
ACGTcount: A:0.33, C:0.27, G:0.17, T:0.23
Consensus pattern (40 bp):
TACACATAAGGTCGTGCCCACCATATACACCGAAGTGTAT
Found at i:91615 original size:29 final size:29
Alignment explanation
Indices: 91583--91656 Score: 78
Period size: 30 Copynumber: 2.5 Consensus size: 29
91573 TATACAACCA
* *
91583 GTCCCAACTTTTTCTAAAATTACAAATTG
1 GTCCCAACTTTTTCAAAAATTACAAAATG
*
91612 GTCCCCTAAC-TTTTCAAAAATTATAAAATG
1 GT-CCC-AACTTTTTCAAAAATTACAAAATG
*
91642 GTCCTCAAATTTTTC
1 GTCC-CAACTTTTTC
91657 CAAGGCATGT
Statistics
Matches: 37, Mismatches: 4, Indels: 7
0.77 0.08 0.15
Matches are distributed among these distances:
29 6 0.16
30 28 0.76
31 3 0.08
ACGTcount: A:0.34, C:0.22, G:0.07, T:0.38
Consensus pattern (29 bp):
GTCCCAACTTTTTCAAAAATTACAAAATG
Found at i:94656 original size:6 final size:6
Alignment explanation
Indices: 94639--94776 Score: 115
Period size: 6 Copynumber: 22.8 Consensus size: 6
94629 ATGAAATACT
* * *
94639 TTTTTC TCTTTC TTTTTC -TTTTC TTTTTA TTTTT- TTTCTTA TTTTTC
1 TTTTTC TTTTTC TTTTTC TTTTTC TTTTTC TTTTTC TTT-TTC TTTTTC
* * *
94686 TTATTTT TTTCTTA TTTTTC TTTTTC TTTTTC TTCTTTC TCTTTT- TTCTTC
1 TT-TTTC TTT-TTC TTTTTC TTTTTC TTTTTC TT-TTTC T-TTTTC TTTTTC
* *
94737 -TTTTC TTTTTA TTTTTC TTCTTAC TTTTTC -TTTTC TTTTT
1 TTTTTC TTTTTC TTTTTC TT-TTTC TTTTTC TTTTTC TTTTT
94777 TTAGCTCGTA
Statistics
Matches: 108, Mismatches: 13, Indels: 22
0.76 0.09 0.15
Matches are distributed among these distances:
5 20 0.19
6 61 0.56
7 26 0.24
8 1 0.01
ACGTcount: A:0.04, C:0.16, G:0.00, T:0.80
Consensus pattern (6 bp):
TTTTTC
Found at i:94676 original size:20 final size:20
Alignment explanation
Indices: 94651--94758 Score: 93
Period size: 20 Copynumber: 5.4 Consensus size: 20
94641 TTTCTCTTTC
94651 TTTTTCTTTTCTTTTTATTT
1 TTTTTCTTTTCTTTTTATTT
94671 TTTTTCTTATT-TTTCTTA-TT
1 TTTTTCTT-TTCTTT-TTATTT
94691 TTTTTCTTATT-TTTCTT-TTT
1 TTTTTCTT-TTCTTT-TTATTT
* *
94711 CTTTTTC--TTCTTTCTCTTT
1 -TTTTTCTTTTCTTTTTATTT
94730 TTTCTTCTTTTCTTTTTATTT
1 TTT-TTCTTTTCTTTTTATTT
*
94751 TTCTTCTT
1 TTTTTCTT
94759 ACTTTTTCTT
Statistics
Matches: 75, Mismatches: 4, Indels: 18
0.77 0.04 0.19
Matches are distributed among these distances:
18 6 0.08
19 9 0.12
20 37 0.49
21 23 0.31
ACGTcount: A:0.05, C:0.15, G:0.00, T:0.81
Consensus pattern (20 bp):
TTTTTCTTTTCTTTTTATTT
Found at i:94683 original size:9 final size:9
Alignment explanation
Indices: 94671--94755 Score: 57
Period size: 9 Copynumber: 8.9 Consensus size: 9
94661 CTTTTTATTT
94671 TTTTTCTTA
1 TTTTTCTTA
94680 TTTTTCTTA
1 TTTTTCTTA
94689 TTTTTTTCTTA
1 --TTTTTCTTA
94700 TTTTTCTT-
1 TTTTTCTTA
* *
94708 TTTCTTTTTC
1 TTT-TTCTTA
94718 TTCTTTCTCT-
1 TT-TTTCT-TA
*
94728 TTTTTCTTCT
1 TTTTTCTT-A
*
94738 TTTCTTTTTA
1 TTT-TTCTTA
94748 TTTTTCTT
1 TTTTTCTT
94756 CTTACTTTTT
Statistics
Matches: 62, Mismatches: 5, Indels: 18
0.73 0.06 0.21
Matches are distributed among these distances:
8 4 0.06
9 30 0.48
10 13 0.21
11 15 0.24
ACGTcount: A:0.05, C:0.15, G:0.00, T:0.80
Consensus pattern (9 bp):
TTTTTCTTA
Found at i:97558 original size:44 final size:44
Alignment explanation
Indices: 97442--97609 Score: 246
Period size: 44 Copynumber: 3.8 Consensus size: 44
97432 TATAAAATTT
* * *
97442 CTTATCATTTTTCCTATAAGCTCGTAATCTTATTTTACCAATATA
1 CTTACCATTATTCC-ATAAGCTCGTAAGCTTATTTTACCAATATA
* * *
97487 CTTACCATTTATTTCATAATCTCGTAAGCTTATTTTACCAAAATA
1 CTTACCA-TTATTCCATAAGCTCGTAAGCTTATTTTACCAATATA
97532 CTTACCATTATTCCATAAGCTCGTAAGCTTATTTTACCAATATA
1 CTTACCATTATTCCATAAGCTCGTAAGCTTATTTTACCAATATA
* *
97576 CTTGCCATTATTCCATAAGCTCGTAAACTTATTT
1 CTTACCATTATTCCATAAGCTCGTAAGCTTATTT
97610 GCATGGTTAC
Statistics
Matches: 111, Mismatches: 11, Indels: 3
0.89 0.09 0.02
Matches are distributed among these distances:
44 66 0.59
45 40 0.36
46 5 0.05
ACGTcount: A:0.30, C:0.21, G:0.06, T:0.42
Consensus pattern (44 bp):
CTTACCATTATTCCATAAGCTCGTAAGCTTATTTTACCAATATA
Found at i:97859 original size:40 final size:40
Alignment explanation
Indices: 97741--97861 Score: 206
Period size: 40 Copynumber: 3.0 Consensus size: 40
97731 CCGTAGTGTG
*
97741 ACACATAAGGTCGTGCCCACCATATACACCGAAGTGTACT
1 ACACATAAGGTCGTGCCCACCATATACACCGAAGTGTATT
97781 ACACATAAGGTCGTGCCCACCATATACACCGAAGTGTATT
1 ACACATAAGGTCGTGCCCACCATATACACCGAAGTGTATT
* * *
97821 ACACATAAGGTCGTTCCCACTATATACATCGAAGTGTATT
1 ACACATAAGGTCGTGCCCACCATATACACCGAAGTGTATT
97861 A
1 A
97862 TAAACCTGCA
Statistics
Matches: 77, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
40 77 1.00
ACGTcount: A:0.33, C:0.26, G:0.17, T:0.24
Consensus pattern (40 bp):
ACACATAAGGTCGTGCCCACCATATACACCGAAGTGTATT
Found at i:102247 original size:36 final size:36
Alignment explanation
Indices: 102202--102271 Score: 113
Period size: 36 Copynumber: 1.9 Consensus size: 36
102192 TAACCATTGT
* *
102202 TGCCCAACATCTTTCTAAATTCTATATTGTCATTAC
1 TGCCCAACATCTTTCTAAACTCTAGATTGTCATTAC
*
102238 TGCCTAACATCTTTCTAAACTCTAGATTGTCATT
1 TGCCCAACATCTTTCTAAACTCTAGATTGTCATT
102272 GTTGCACATC
Statistics
Matches: 31, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
36 31 1.00
ACGTcount: A:0.27, C:0.24, G:0.07, T:0.41
Consensus pattern (36 bp):
TGCCCAACATCTTTCTAAACTCTAGATTGTCATTAC
Found at i:106860 original size:34 final size:33
Alignment explanation
Indices: 106813--106876 Score: 92
Period size: 34 Copynumber: 1.9 Consensus size: 33
106803 TTTTCATCCA
*
106813 TTCTTTATTTCTTTGTGTATATACATATATTAT
1 TTCTTTATTTCTTTATGTATATACATATATTAT
* *
106846 TTCTTTCTATTCTTTATGTATATATATATAT
1 TTCTTTAT-TTCTTTATGTATATACATATAT
106877 ATATATATAT
Statistics
Matches: 27, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
33 7 0.26
34 20 0.74
ACGTcount: A:0.25, C:0.09, G:0.05, T:0.61
Consensus pattern (33 bp):
TTCTTTATTTCTTTATGTATATACATATATTAT
Found at i:106871 original size:2 final size:2
Alignment explanation
Indices: 106864--106910 Score: 94
Period size: 2 Copynumber: 23.5 Consensus size: 2
106854 ATTCTTTATG
106864 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
106906 TA TA T
1 TA TA T
106911 TCCCTCCACA
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 45 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:114169 original size:16 final size:16
Alignment explanation
Indices: 114148--114180 Score: 66
Period size: 16 Copynumber: 2.1 Consensus size: 16
114138 TGATACTCTC
114148 TTGATAACTATTATTA
1 TTGATAACTATTATTA
114164 TTGATAACTATTATTA
1 TTGATAACTATTATTA
114180 T
1 T
114181 GCGAACTCCA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.36, C:0.06, G:0.06, T:0.52
Consensus pattern (16 bp):
TTGATAACTATTATTA
Found at i:120063 original size:14 final size:14
Alignment explanation
Indices: 120044--120071 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
120034 TCAAATCATA
120044 TATCATTCATTTAT
1 TATCATTCATTTAT
120058 TATCATTCATTTAT
1 TATCATTCATTTAT
120072 AAATAGTATC
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:0.29, C:0.14, G:0.00, T:0.57
Consensus pattern (14 bp):
TATCATTCATTTAT
Found at i:124437 original size:15 final size:15
Alignment explanation
Indices: 124401--124447 Score: 51
Period size: 15 Copynumber: 3.1 Consensus size: 15
124391 ATCATATTTG
124401 TATATA-TATAATAT
1 TATATAGTATAATAT
* *
124415 ACATTATAGTATTATAT
1 -TA-TATAGTATAATAT
124432 TATATAGTATAATAT
1 TATATAGTATAATAT
124447 T
1 T
124448 TTACACATAA
Statistics
Matches: 26, Mismatches: 4, Indels: 4
0.76 0.12 0.12
Matches are distributed among these distances:
15 14 0.54
16 5 0.19
17 7 0.27
ACGTcount: A:0.45, C:0.02, G:0.04, T:0.49
Consensus pattern (15 bp):
TATATAGTATAATAT
Found at i:124518 original size:23 final size:22
Alignment explanation
Indices: 124486--124528 Score: 59
Period size: 22 Copynumber: 1.9 Consensus size: 22
124476 TTTTTGAAAA
* *
124486 AATATTATATAATATATTTTTTT
1 AATATAATAT-ATATAGTTTTTT
124509 AATATAATATATATAGTTTT
1 AATATAATATATATAGTTTT
124529 GAAAATGTAT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
22 9 0.50
23 9 0.50
ACGTcount: A:0.42, C:0.00, G:0.02, T:0.56
Consensus pattern (22 bp):
AATATAATATATATAGTTTTTT
Found at i:124523 original size:29 final size:28
Alignment explanation
Indices: 124456--124525 Score: 81
Period size: 27 Copynumber: 2.5 Consensus size: 28
124446 TTTTACACAT
124456 AAAATATATATAGTATATAGTTTTTGAA
1 AAAATATATATAGTATATAGTTTTTGAA
* *
124484 AAAATAT-TATA-TAATATATTTTTTTAA
1 AAAATATATATAGT-ATATAGTTTTTGAA
*
124511 TATAATATATATAGT
1 -AAAATATATATAGT
124526 TTTGAAAATG
Statistics
Matches: 35, Mismatches: 3, Indels: 6
0.80 0.07 0.14
Matches are distributed among these distances:
26 1 0.03
27 16 0.46
28 13 0.37
29 4 0.11
30 1 0.03
ACGTcount: A:0.47, C:0.00, G:0.06, T:0.47
Consensus pattern (28 bp):
AAAATATATATAGTATATAGTTTTTGAA
Found at i:124628 original size:9 final size:9
Alignment explanation
Indices: 124614--124653 Score: 50
Period size: 9 Copynumber: 4.8 Consensus size: 9
124604 TTTTGAAAAC
124614 ATATTATAT
1 ATATTATAT
124623 ATATTATAT
1 ATATTATAT
*
124632 GTATTAT-T
1 ATATTATAT
124640 AT-TTATAT
1 ATATTATAT
124648 -TATTAT
1 ATATTAT
124654 TTTATTTGTT
Statistics
Matches: 27, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
7 5 0.19
8 7 0.26
9 15 0.56
ACGTcount: A:0.38, C:0.00, G:0.03, T:0.60
Consensus pattern (9 bp):
ATATTATAT
Found at i:124654 original size:12 final size:12
Alignment explanation
Indices: 124617--124659 Score: 52
Period size: 12 Copynumber: 3.6 Consensus size: 12
124607 TGAAAACATA
124617 TTATATATATTAT
1 TTATAT-TATTAT
* *
124630 ATGTATTATTAT
1 TTATATTATTAT
124642 TTATATTATTAT
1 TTATATTATTAT
124654 TT-TATT
1 TTATATT
124660 TGTTATTAAT
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
11 4 0.15
12 18 0.69
13 4 0.15
ACGTcount: A:0.33, C:0.00, G:0.02, T:0.65
Consensus pattern (12 bp):
TTATATTATTAT
Found at i:125911 original size:20 final size:19
Alignment explanation
Indices: 125883--125945 Score: 58
Period size: 20 Copynumber: 3.2 Consensus size: 19
125873 GTTTTACAAC
*
125883 ATTTATATTATTGTTATTTA
1 ATTTTTATTATT-TTATTTA
*
125903 ATTTTTATTA-TTTATTTC
1 ATTTTTATTATTTTATTTA
125921 A-TTTTATTATTATTAACTTTA
1 ATTTTTATTATT-TT-A-TTTA
125942 ATTT
1 ATTT
125946 CCTTTTTTTC
Statistics
Matches: 35, Mismatches: 3, Indels: 8
0.76 0.07 0.17
Matches are distributed among these distances:
17 8 0.23
18 8 0.23
19 3 0.09
20 10 0.29
21 4 0.11
22 2 0.06
ACGTcount: A:0.29, C:0.03, G:0.02, T:0.67
Consensus pattern (19 bp):
ATTTTTATTATTTTATTTA
Found at i:125925 original size:17 final size:17
Alignment explanation
Indices: 125882--125931 Score: 55
Period size: 17 Copynumber: 2.7 Consensus size: 17
125872 TGTTTTACAA
125882 CATTTATATTATTGTTATTT
1 CATTT-TATTA-T-TTATTT
*
125902 AATTTTTATTATTTATTT
1 CA-TTTTATTATTTATTT
125920 CATTTTATTATT
1 CATTTTATTATT
125932 ATTAACTTTA
Statistics
Matches: 27, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
17 10 0.37
18 7 0.26
19 1 0.04
20 6 0.22
21 3 0.11
ACGTcount: A:0.26, C:0.04, G:0.02, T:0.68
Consensus pattern (17 bp):
CATTTTATTATTTATTT
Found at i:127212 original size:27 final size:27
Alignment explanation
Indices: 127150--127209 Score: 75
Period size: 27 Copynumber: 2.2 Consensus size: 27
127140 AGGCAATAAC
* * *
127150 ATAAAATATCATAATTACTTCAAGACA
1 ATAAAATGTCATAAATACTTCAAAACA
*
127177 TTAAAATGTCATAAATACTTCAAAAACA
1 ATAAAATGTCATAAATACTTC-AAAACA
127205 ATAAA
1 ATAAA
127210 TGTAACTCAA
Statistics
Matches: 27, Mismatches: 5, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
27 18 0.67
28 9 0.33
ACGTcount: A:0.55, C:0.13, G:0.03, T:0.28
Consensus pattern (27 bp):
ATAAAATGTCATAAATACTTCAAAACA
Found at i:127458 original size:21 final size:21
Alignment explanation
Indices: 127432--127480 Score: 98
Period size: 21 Copynumber: 2.3 Consensus size: 21
127422 TTTCATAGTC
127432 CAATGTATATGTAAGAGAATG
1 CAATGTATATGTAAGAGAATG
127453 CAATGTATATGTAAGAGAATG
1 CAATGTATATGTAAGAGAATG
127474 CAATGTA
1 CAATGTA
127481 CATGAGTAGA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 28 1.00
ACGTcount: A:0.43, C:0.06, G:0.22, T:0.29
Consensus pattern (21 bp):
CAATGTATATGTAAGAGAATG
Found at i:127596 original size:29 final size:29
Alignment explanation
Indices: 127563--127675 Score: 154
Period size: 29 Copynumber: 3.9 Consensus size: 29
127553 ACATTCATAG
* *
127563 AATTTGCACCAACAGTGTCTTTCTTTGAT
1 AATTTGCACCAACGGTGCCTTTCTTTGAT
*
127592 AATTTGCACAAACGGTGCCTTTCTTTGAT
1 AATTTGCACCAACGGTGCCTTTCTTTGAT
* * *
127621 CATTTGCACCAACGGTGTCTTTCTATGAT
1 AATTTGCACCAACGGTGCCTTTCTTTGAT
* *
127650 CATTTACACCAACGGTGCCTTTCTTT
1 AATTTGCACCAACGGTGCCTTTCTTT
127676 AATGTACACG
Statistics
Matches: 74, Mismatches: 10, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
29 74 1.00
ACGTcount: A:0.22, C:0.24, G:0.15, T:0.39
Consensus pattern (29 bp):
AATTTGCACCAACGGTGCCTTTCTTTGAT
Found at i:127631 original size:58 final size:58
Alignment explanation
Indices: 127564--127675 Score: 179
Period size: 58 Copynumber: 1.9 Consensus size: 58
127554 CATTCATAGA
* *
127564 ATTTGCACCAACAGTGTCTTTCTTTGATAATTTGCACAAACGGTGCCTTTCTTTGATC
1 ATTTGCACCAACAGTGTCTTTCTATGATAATTTACACAAACGGTGCCTTTCTTTGATC
* * *
127622 ATTTGCACCAACGGTGTCTTTCTATGATCATTTACACCAACGGTGCCTTTCTTT
1 ATTTGCACCAACAGTGTCTTTCTATGATAATTTACACAAACGGTGCCTTTCTTT
127676 AATGTACACG
Statistics
Matches: 49, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
58 49 1.00
ACGTcount: A:0.21, C:0.24, G:0.15, T:0.39
Consensus pattern (58 bp):
ATTTGCACCAACAGTGTCTTTCTATGATAATTTACACAAACGGTGCCTTTCTTTGATC
Found at i:129510 original size:11 final size:11
Alignment explanation
Indices: 129490--129518 Score: 51
Period size: 11 Copynumber: 2.7 Consensus size: 11
129480 GCTTTATAAA
129490 ATTT-AAATTC
1 ATTTAAAATTC
129500 ATTTAAAATTC
1 ATTTAAAATTC
129511 ATTTAAAA
1 ATTTAAAA
129519 GAAATTCCAA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
10 4 0.22
11 14 0.78
ACGTcount: A:0.48, C:0.07, G:0.00, T:0.45
Consensus pattern (11 bp):
ATTTAAAATTC
Found at i:135408 original size:13 final size:14
Alignment explanation
Indices: 135390--135419 Score: 53
Period size: 13 Copynumber: 2.2 Consensus size: 14
135380 AGTTGGACAA
135390 TCTTCATATGCA-G
1 TCTTCATATGCACG
135403 TCTTCATATGCACG
1 TCTTCATATGCACG
135417 TCT
1 TCT
135420 GTAATGGGAA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 12 0.75
14 4 0.25
ACGTcount: A:0.20, C:0.27, G:0.13, T:0.40
Consensus pattern (14 bp):
TCTTCATATGCACG
Found at i:154718 original size:39 final size:39
Alignment explanation
Indices: 154675--154750 Score: 152
Period size: 39 Copynumber: 1.9 Consensus size: 39
154665 CTTATCTTTT
154675 TGTGCTTGTGAAAGTAGCATAAAACGTGAGATGTCAGAC
1 TGTGCTTGTGAAAGTAGCATAAAACGTGAGATGTCAGAC
154714 TGTGCTTGTGAAAGTAGCATAAAACGTGAGATGTCAG
1 TGTGCTTGTGAAAGTAGCATAAAACGTGAGATGTCAG
154751 CCTCCACTTC
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
39 37 1.00
ACGTcount: A:0.33, C:0.12, G:0.29, T:0.26
Consensus pattern (39 bp):
TGTGCTTGTGAAAGTAGCATAAAACGTGAGATGTCAGAC
Found at i:157126 original size:2 final size:2
Alignment explanation
Indices: 157119--157201 Score: 166
Period size: 2 Copynumber: 41.5 Consensus size: 2
157109 TCTTTATTAG
157119 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
157161 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
157202 CCTTATTTCA
Statistics
Matches: 81, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 81 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:163251 original size:18 final size:18
Alignment explanation
Indices: 163225--163265 Score: 73
Period size: 18 Copynumber: 2.3 Consensus size: 18
163215 GTTCTATGAA
163225 GAAAGGATGATAGAGAGT
1 GAAAGGATGATAGAGAGT
*
163243 GAAATGATGATAGAGAGT
1 GAAAGGATGATAGAGAGT
163261 GAAAG
1 GAAAG
163266 AAATATCTGC
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
18 21 1.00
ACGTcount: A:0.46, C:0.00, G:0.37, T:0.17
Consensus pattern (18 bp):
GAAAGGATGATAGAGAGT
Found at i:169845 original size:46 final size:45
Alignment explanation
Indices: 169664--169848 Score: 118
Period size: 46 Copynumber: 4.2 Consensus size: 45
169654 CCAGACGTCC
*
169664 TCATCACGTAGGAACCGTGTTATCATCTTTAGATGGCCAAAACTCT
1 TCATCACGTAGGAACCGTGTTATCATCTTTA-ATGGCCAGAACTCT
* * ** * * * * *
169710 TCATCACATATGAGTCGTATCATCATC--TAA---CCTGATCTCC
1 TCATCACGTAGGAACCGTGTTATCATCTTTAATGGCCAGAACTCT
* * ** * *
169750 TCATCACGCA-GAAGCCGTGTTA--ACCTTTAATAACCAGCCATTC-
1 TCATCACGTAGGAA-CCGTGTTATCATCTTTAATGGCCAG-AACTCT
*
169793 TCATCACGTAGGAAACGTGTTATCATCTTTAGATGGCCAGAACTCT
1 TCATCACGTAGGAACCGTGTTATCATCTTTA-ATGGCCAGAACTCT
169839 TCATCACGTA
1 TCATCACGTA
169849 TGAGTTGTGT
Statistics
Matches: 99, Mismatches: 28, Indels: 24
0.66 0.19 0.16
Matches are distributed among these distances:
38 2 0.02
39 2 0.02
40 22 0.22
43 20 0.20
44 7 0.07
45 9 0.09
46 37 0.37
ACGTcount: A:0.29, C:0.26, G:0.15, T:0.30
Consensus pattern (45 bp):
TCATCACGTAGGAACCGTGTTATCATCTTTAATGGCCAGAACTCT
Found at i:169880 original size:129 final size:129
Alignment explanation
Indices: 169479--169906 Score: 552
Period size: 129 Copynumber: 3.3 Consensus size: 129
169469 TCATCAACTA
* * * *
169479 TGACCAGATCTCCTCATTATGTAGGAGCCATGTCAACCTTTGATAACCAGACGTCCTCATCACGT
1 TGACCAGATCTCCTCATCACGTAGGAGCCGTGTTAACCTTTGATAACCAGACGTCCTCATCACGT
* * *
169544 GGGAACCGTGTTATCATCTTTAGATGGCTATAACTCTTCATCACGTATGAGTCGTGTCATCATC
66 AGGAACCGTGTTATCATCTTTAGATGGCCAAAACTCTTCATCACGTATGAGTCGTGTCATCATC
* * **
169608 TGA-CATGATATCCTCGTCACGTAGGAGTTGTGTTAACCTTTGATAACCAGACGTCCTCATCACG
1 TGACCA-GATCTCCTCATCACGTAGGAGCCGTGTTAACCTTTGATAACCAGACGTCCTCATCACG
* *
169672 TAGGAACCGTGTTATCATCTTTAGATGGCCAAAACTCTTCATCACATATGAGTCGTATCATCATC
65 TAGGAACCGTGTTATCATCTTTAGATGGCCAAAACTCTTCATCACGTATGAGTCGTGTCATCATC
* * * * * * * *
169737 TAACCTGATCTCCTCATCACGCAGAAGCCGTGTTAACCTTTAATAACCAGCCATTCTCATCACGT
1 TGACCAGATCTCCTCATCACGTAGGAGCCGTGTTAACCTTTGATAACCAGACGTCCTCATCACGT
* * * *
169802 AGGAAACGTGTTATCATCTTTAGATGGCCAGAACTCTTCATCACGTATGAGTTGTGTCATCACC
66 AGGAACCGTGTTATCATCTTTAGATGGCCAAAACTCTTCATCACGTATGAGTCGTGTCATCATC
* * * * * * *
169866 CGACCAGATTTCCTCATTATGAAGGAGCCATGTTAATCTTT
1 TGACCAGATCTCCTCATCACGTAGGAGCCGTGTTAACCTTT
169907 AAACGACTAG
Statistics
Matches: 256, Mismatches: 41, Indels: 4
0.85 0.14 0.01
Matches are distributed among these distances:
128 2 0.01
129 253 0.99
130 1 0.00
ACGTcount: A:0.26, C:0.25, G:0.18, T:0.31
Consensus pattern (129 bp):
TGACCAGATCTCCTCATCACGTAGGAGCCGTGTTAACCTTTGATAACCAGACGTCCTCATCACGT
AGGAACCGTGTTATCATCTTTAGATGGCCAAAACTCTTCATCACGTATGAGTCGTGTCATCATC
Found at i:170601 original size:15 final size:15
Alignment explanation
Indices: 170578--170624 Score: 76
Period size: 15 Copynumber: 3.1 Consensus size: 15
170568 ATGATTTCAC
* *
170578 CTAATTGGTCTGTAT
1 CTAACTGGTCAGTAT
170593 CTAACTGGTCAGTAT
1 CTAACTGGTCAGTAT
170608 CTAACTGGTCAGTAT
1 CTAACTGGTCAGTAT
170623 CT
1 CT
170625 TACCAAACAT
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 30 1.00
ACGTcount: A:0.23, C:0.19, G:0.19, T:0.38
Consensus pattern (15 bp):
CTAACTGGTCAGTAT
Found at i:187069 original size:51 final size:56
Alignment explanation
Indices: 186955--187072 Score: 140
Period size: 51 Copynumber: 2.2 Consensus size: 56
186945 ATTATTTTCT
* *
186955 TGTACTTTATTTATTTATTTCGTTTTTCCTGTCTATTTTTCTTTCATTTTCATTTTA
1 TGTATTTTATTTATTTATTTCGTTTTT-CTGTCTATTTTTCTTTCATTGTCATTTTA
*
187012 TGTATTTTATTTATTTATTT-GTTTTT-T-TAC-A-TTTTC-TTCATTGTCATTTTG
1 TGTATTTTATTTATTTATTTCGTTTTTCTGT-CTATTTTTCTTTCATTGTCATTTTA
*
187063 TTTATTTTAT
1 TGTATTTTAT
187073 ACACTGTTTA
Statistics
Matches: 56, Mismatches: 4, Indels: 8
0.82 0.06 0.12
Matches are distributed among these distances:
51 22 0.39
52 5 0.09
53 2 0.04
54 2 0.04
56 6 0.11
57 19 0.34
ACGTcount: A:0.15, C:0.10, G:0.06, T:0.69
Consensus pattern (56 bp):
TGTATTTTATTTATTTATTTCGTTTTTCTGTCTATTTTTCTTTCATTGTCATTTTA
Found at i:190823 original size:39 final size:39
Alignment explanation
Indices: 190752--190829 Score: 95
Period size: 39 Copynumber: 2.0 Consensus size: 39
190742 CCCGGAATAT
* *
190752 TACCCGGGGACGCATCTGCTACTAAAGGGAAAGCCGCAC
1 TACCCGGGGACGCATCTGCTACCAAAGCGAAAGCCGCAC
* * *
190791 TACCCGGGGACTCAT-TCGTTACCAAAGCGAAAGTCGCAC
1 TACCCGGGGACGCATCT-GCTACCAAAGCGAAAGCCGCAC
190830 CTGCTGCGAA
Statistics
Matches: 33, Mismatches: 5, Indels: 2
0.82 0.12 0.05
Matches are distributed among these distances:
38 1 0.03
39 32 0.97
ACGTcount: A:0.28, C:0.31, G:0.26, T:0.15
Consensus pattern (39 bp):
TACCCGGGGACGCATCTGCTACCAAAGCGAAAGCCGCAC
Found at i:198579 original size:105 final size:105
Alignment explanation
Indices: 198393--199173 Score: 1307
Period size: 105 Copynumber: 7.4 Consensus size: 105
198383 GGTTTTACCC
*
198393 AGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTCGAGACAACGCAAGTTCAACTTCACGA
1 AGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGA
* *
198458 CGAAGGGACCGTTGGTTGTCACCAAACATTTCTCAAATTT
66 CGAAGGGACCGCTGGTTGTCAACAAACATTTCTCAAATTT
198498 AGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGA
1 AGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGA
198563 CGAAGGGACCGCTGGTTGTCAACAAACATTTCTCAAATTT
66 CGAAGGGACCGCTGGTTGTCAACAAACATTTCTCAAATTT
*
198603 AGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTCCAGACAATGCAAGTTCAACTTCACGA
1 AGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGA
198668 CGAAGGGACCGCTGGTTGTCAACAAACATTTCTCAAATTT
66 CGAAGGGACCGCTGGTTGTCAACAAACATTTCTCAAATTT
198708 AGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGA
1 AGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGA
198773 CGAAGGGACCGCTGGTTGTCAACAAACATTTCTCAAATTT
66 CGAAGGGACCGCTGGTTGTCAACAAACATTTCTCAAATTT
* *
198813 AGAGTCAATTTCAACTTCACAGCGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCAAGA
1 AGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGA
198878 CGAAGGGACCGCTGGTTGTCAACAAACATTTCTC-AATTT
66 CGAAGGGACCGCTGGTTGTCAACAAACATTTCTCAAATTT
*
198917 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACG
1 -AGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACG
*
198982 ACGAAGGGACTGCTGGTTGTCAACAAACATTTCTC-AATTT
65 ACGAAGGGACCGCTGGTTGTCAACAAACATTTCTCAAATTT
* * * * ***
199022 CAGAGCCAATTTCAACTTTACAACGAAGGATATTGGACTCAAGATAGTACAAGTTCAACTTCACG
1 -AGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACG
** * *
199087 ACGAAGGGACCGCTGACTGTCAACAAACAACTTCTC-AATGTC
65 ACGAAGGGACCGCTGGTTGTCAACAAAC-ATTTCTCAAAT-TT
* * *
199129 AGAGCCAATTTCAACTTCACAGCAAAGGATATTGAACTCAAGACA
1 AGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTCCAGACA
199174 GCACAAGCTC
Statistics
Matches: 646, Mismatches: 27, Indels: 5
0.95 0.04 0.01
Matches are distributed among these distances:
104 5 0.01
105 591 0.91
106 49 0.08
107 1 0.00
ACGTcount: A:0.34, C:0.24, G:0.19, T:0.23
Consensus pattern (105 bp):
AGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGA
CGAAGGGACCGCTGGTTGTCAACAAACATTTCTCAAATTT
Found at i:200808 original size:2 final size:2
Alignment explanation
Indices: 200803--200828 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
200793 TATTTTTTTA
200803 AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT
200829 TATCTATTTA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:201754 original size:28 final size:28
Alignment explanation
Indices: 201721--201776 Score: 87
Period size: 28 Copynumber: 2.0 Consensus size: 28
201711 AAATTATCTC
*
201721 TTTATTTTTGTT-TTAATTTATTAAATAT
1 TTTATTTTT-TTCTTAATTTAATAAATAT
201749 TTTATTTTTTTCTTAATTTAATAAATAT
1 TTTATTTTTTTCTTAATTTAATAAATAT
201777 ATTTTTATTT
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
27 2 0.08
28 24 0.92
ACGTcount: A:0.30, C:0.02, G:0.02, T:0.66
Consensus pattern (28 bp):
TTTATTTTTTTCTTAATTTAATAAATAT
Found at i:201781 original size:24 final size:22
Alignment explanation
Indices: 201754--201807 Score: 63
Period size: 24 Copynumber: 2.3 Consensus size: 22
201744 AATATTTTAT
*
201754 TTTTTTCTTAATTTAATAAATATA
1 TTTTTT-TTAATGTAA-AAATATA
201778 TTTTTATTTAATGTAAAAATATA
1 TTTTT-TTTAATGTAAAAATATA
*
201801 TATTTTT
1 TTTTTTT
201808 AAATATCTTA
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
22 2 0.07
23 11 0.41
24 13 0.48
25 1 0.04
ACGTcount: A:0.37, C:0.02, G:0.02, T:0.59
Consensus pattern (22 bp):
TTTTTTTTAATGTAAAAATATA
Found at i:201808 original size:25 final size:25
Alignment explanation
Indices: 201751--201808 Score: 73
Period size: 25 Copynumber: 2.3 Consensus size: 25
201741 TTAAATATTT
* * *
201751 TATTTTTTTCTTAATTTAATAAATA
1 TATTTTTATCTTAATGTAAAAAATA
201776 TATTTTTAT-TTAATGTAAAAATATA
1 TATTTTTATCTTAATGTAAAAA-ATA
201801 TATTTTTA
1 TATTTTTA
201809 AATATCTTAA
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
24 10 0.34
25 19 0.66
ACGTcount: A:0.38, C:0.02, G:0.02, T:0.59
Consensus pattern (25 bp):
TATTTTTATCTTAATGTAAAAAATA
Found at i:201873 original size:31 final size:31
Alignment explanation
Indices: 201835--201899 Score: 87
Period size: 31 Copynumber: 2.1 Consensus size: 31
201825 ATATATTTAA
*
201835 ATATTTTATTATTAATTT-AATATAAAAATAT
1 ATATTTTACTATTAATTTAAAT-TAAAAATAT
* *
201866 ATATTTTACTCTTATTTTAAATTAAAAATAT
1 ATATTTTACTATTAATTTAAATTAAAAATAT
201897 ATA
1 ATA
201900 ATATTTTATT
Statistics
Matches: 30, Mismatches: 3, Indels: 2
0.86 0.09 0.06
Matches are distributed among these distances:
31 27 0.90
32 3 0.10
ACGTcount: A:0.46, C:0.03, G:0.00, T:0.51
Consensus pattern (31 bp):
ATATTTTACTATTAATTTAAATTAAAAATAT
Found at i:203771 original size:23 final size:24
Alignment explanation
Indices: 203718--203771 Score: 60
Period size: 23 Copynumber: 2.4 Consensus size: 24
203708 TCAATTGCCT
203718 TTATTTT-ATCAGAGATTTATATA
1 TTATTTTAATCAGAGATTTATATA
* * *
203741 TT-TATTAATCCGAGA-TTATCTA
1 TTATTTTAATCAGAGATTTATATA
203763 TTATTTTAA
1 TTATTTTAA
203772 ATTTTATAAT
Statistics
Matches: 25, Mismatches: 4, Indels: 4
0.76 0.12 0.12
Matches are distributed among these distances:
22 11 0.44
23 14 0.56
ACGTcount: A:0.33, C:0.07, G:0.07, T:0.52
Consensus pattern (24 bp):
TTATTTTAATCAGAGATTTATATA
Found at i:204512 original size:7 final size:7
Alignment explanation
Indices: 204500--204524 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
204490 AGACCTATAT
204500 GGAGATG
1 GGAGATG
204507 GGAGATG
1 GGAGATG
204514 GGAGATG
1 GGAGATG
204521 GGAG
1 GGAG
204525 CCGGATAATG
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.28, C:0.00, G:0.60, T:0.12
Consensus pattern (7 bp):
GGAGATG
Found at i:205824 original size:20 final size:21
Alignment explanation
Indices: 205801--205851 Score: 70
Period size: 20 Copynumber: 2.5 Consensus size: 21
205791 TAGTCGGTAG
205801 TTGACAAAACCA-GTTGAAAT
1 TTGACAAAACCATGTTGAAAT
**
205821 TTGACAAAA-CATGTTTTAAT
1 TTGACAAAACCATGTTGAAAT
205841 TTGACAAAACC
1 TTGACAAAACC
205852 GGTAAAAAGC
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
19 2 0.07
20 24 0.89
21 1 0.04
ACGTcount: A:0.43, C:0.16, G:0.12, T:0.29
Consensus pattern (21 bp):
TTGACAAAACCATGTTGAAAT
Found at i:206204 original size:20 final size:20
Alignment explanation
Indices: 206179--206216 Score: 76
Period size: 20 Copynumber: 1.9 Consensus size: 20
206169 AATATAACAT
206179 GTTTCAATTTGACAAAACCG
1 GTTTCAATTTGACAAAACCG
206199 GTTTCAATTTGACAAAAC
1 GTTTCAATTTGACAAAAC
206217 TGGTAAAGCG
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.37, C:0.18, G:0.13, T:0.32
Consensus pattern (20 bp):
GTTTCAATTTGACAAAACCG
Found at i:207017 original size:21 final size:21
Alignment explanation
Indices: 206993--207056 Score: 92
Period size: 21 Copynumber: 3.0 Consensus size: 21
206983 CCTCGAATAG
* *
206993 ATGTCCCCAATGACAACATAT
1 ATGTCCCGAATGACCACATAT
*
207014 ATGTCCCGAAGGACCACATAT
1 ATGTCCCGAATGACCACATAT
*
207035 ATATCCCGAATGACCACATAT
1 ATGTCCCGAATGACCACATAT
207056 A
1 A
207057 ACCCTCGACT
Statistics
Matches: 38, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 38 1.00
ACGTcount: A:0.38, C:0.28, G:0.12, T:0.22
Consensus pattern (21 bp):
ATGTCCCGAATGACCACATAT
Found at i:207972 original size:23 final size:23
Alignment explanation
Indices: 207904--207972 Score: 63
Period size: 23 Copynumber: 3.0 Consensus size: 23
207894 ATCTCACTTT
* * *
207904 TCATTTAATCACTTA-ATTCTAA
1 TCATATAATTACTTATATTCTTA
*
207926 TTCATATAATT--TATATATTGTTA
1 -TCATATAATTACT-TATATTCTTA
207949 TCATATAATTACTTATATTCTTA
1 TCATATAATTACTTATATTCTTA
207972 T
1 T
207973 TACACAAAAT
Statistics
Matches: 37, Mismatches: 5, Indels: 8
0.74 0.10 0.16
Matches are distributed among these distances:
21 1 0.03
22 12 0.32
23 23 0.62
24 1 0.03
ACGTcount: A:0.35, C:0.12, G:0.01, T:0.52
Consensus pattern (23 bp):
TCATATAATTACTTATATTCTTA
Found at i:212141 original size:20 final size:21
Alignment explanation
Indices: 212087--212149 Score: 65
Period size: 20 Copynumber: 2.9 Consensus size: 21
212077 TATTCCCCTG
212087 TGGGGGGAATCGGTTCCCCTTCAA
1 TGGGGGG-ATCGGTT-CCC-TCAA
* *
212111 AGGGGGAATCGGTTCCCTC-A
1 TGGGGGGATCGGTTCCCTCAA
*
212131 TGGGGGGATCGATTCCCTC
1 TGGGGGGATCGGTTCCCTC
212150 TGCACCAAAA
Statistics
Matches: 34, Mismatches: 5, Indels: 4
0.79 0.12 0.09
Matches are distributed among these distances:
20 17 0.50
21 2 0.06
22 3 0.09
23 7 0.21
24 5 0.15
ACGTcount: A:0.16, C:0.25, G:0.35, T:0.24
Consensus pattern (21 bp):
TGGGGGGATCGGTTCCCTCAA
Found at i:219352 original size:46 final size:45
Alignment explanation
Indices: 219266--219352 Score: 113
Period size: 46 Copynumber: 1.9 Consensus size: 45
219256 GCATTTTATA
* * * *
219266 CATCGATGCACATACCATGCATCGATTCACTTAGTGTATTTGATG
1 CATCGATGCACAGACCATGCATCGATGCACTCAGTCTATTTGATG
219311 CATCGATGCACAAGACCATGCATCGATGCACTCA-TACTATTT
1 CATCGATGCAC-AGACCATGCATCGATGCACTCAGT-CTATTT
219353 CAAAACATCG
Statistics
Matches: 36, Mismatches: 4, Indels: 3
0.84 0.09 0.07
Matches are distributed among these distances:
45 12 0.33
46 24 0.67
ACGTcount: A:0.29, C:0.25, G:0.16, T:0.30
Consensus pattern (45 bp):
CATCGATGCACAGACCATGCATCGATGCACTCAGTCTATTTGATG
Found at i:227150 original size:12 final size:13
Alignment explanation
Indices: 227133--227167 Score: 54
Period size: 12 Copynumber: 2.8 Consensus size: 13
227123 TAAGGGGGAG
227133 TAATTTCAAAA-T
1 TAATTTCAAAACT
227145 TAATTTCAAAACT
1 TAATTTCAAAACT
*
227158 TATTTTCAAA
1 TAATTTCAAA
227168 GAAAATCTTA
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
12 11 0.52
13 10 0.48
ACGTcount: A:0.46, C:0.11, G:0.00, T:0.43
Consensus pattern (13 bp):
TAATTTCAAAACT
Found at i:230081 original size:45 final size:45
Alignment explanation
Indices: 230032--230165 Score: 139
Period size: 45 Copynumber: 3.0 Consensus size: 45
230022 GAACATCGAA
* *
230032 TGCATTTTATACATCGATGCACATATCATGCATCGATGCACTTAG
1 TGCATTTAATACATCGATGCACATATCATGCATCGATGCACTCAG
* * * *
230077 TGCATTTGATGCATCGATCCACAATACCATGCATCGATGCACTCAG
1 TGCATTTAATACATCGATGCAC-ATATCATGCATCGATGCACTCAG
* *
230123 -GCTATTTCAAAACATCGAATG--CATTTCATGCATCGATGCACTC
1 TGC-ATTT-AATACATCG-ATGCACATATCATGCATCGATGCACTC
230166 TTAGTTCACC
Statistics
Matches: 74, Mismatches: 11, Indels: 8
0.80 0.12 0.09
Matches are distributed among these distances:
45 40 0.54
46 26 0.35
47 6 0.08
48 2 0.03
ACGTcount: A:0.29, C:0.25, G:0.16, T:0.30
Consensus pattern (45 bp):
TGCATTTAATACATCGATGCACATATCATGCATCGATGCACTCAG
Found at i:232535 original size:20 final size:20
Alignment explanation
Indices: 232510--232554 Score: 81
Period size: 20 Copynumber: 2.2 Consensus size: 20
232500 ATCATATATT
232510 TATACTTATGTTTTTGTATC
1 TATACTTATGTTTTTGTATC
232530 TATACTTATGTTTTTGTATC
1 TATACTTATGTTTTTGTATC
*
232550 GATAC
1 TATAC
232555 ACATACTATA
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 24 1.00
ACGTcount: A:0.22, C:0.11, G:0.11, T:0.56
Consensus pattern (20 bp):
TATACTTATGTTTTTGTATC
Found at i:232782 original size:74 final size:74
Alignment explanation
Indices: 232700--232859 Score: 232
Period size: 74 Copynumber: 2.2 Consensus size: 74
232690 CTTAACCGGT
* * * * * * *
232700 TAAAATAAAATATGTGCTACCTATTATGTTAATCACCTATCGGTTTGT-TTAAAGGTTATTAATA
1 TAAAATAAAATAAGCGCTACCTATTACGTT-ATAACCTACCGGTTTGTATAAAAGGTTACTAATA
232764 ATGTAAACGG
65 ATGTAAACGG
*
232774 TAAAATAAAATAAGCGCTACCTATTACGTTATAATCTACCGGTTTGTATAAAAGGTTACTAATAA
1 TAAAATAAAATAAGCGCTACCTATTACGTTATAACCTACCGGTTTGTATAAAAGGTTACTAATAA
232839 TGTAAACGG
66 TGTAAACGG
232848 TAAAATAAAATA
1 TAAAATAAAATA
232860 GACGTAAATG
Statistics
Matches: 77, Mismatches: 8, Indels: 2
0.89 0.09 0.02
Matches are distributed among these distances:
73 14 0.18
74 63 0.82
ACGTcount: A:0.41, C:0.11, G:0.14, T:0.34
Consensus pattern (74 bp):
TAAAATAAAATAAGCGCTACCTATTACGTTATAACCTACCGGTTTGTATAAAAGGTTACTAATAA
TGTAAACGG
Found at i:233184 original size:197 final size:197
Alignment explanation
Indices: 232896--233657 Score: 777
Period size: 197 Copynumber: 3.9 Consensus size: 197
232886 TATCATGACC
* * * * * * *
232896 GTATAGATACTTTTATTCCAGTATGGTTCTCAAATAATTTGCCCGCAACAAAGAATCGATACCCA
1 GTATCGATACTTTTATTACAGTATGCTTCTCAAACAATTTGCACGCAACAAAGTATCGATACACA
*
232961 TATATAAAGTATCAATACTGGGAATTTCAAAACCTATTACTTTAAAGTAATAGGTAAATTTACAA
66 TATATAAAGTATCAATACTTGGAATTTC-AAA--TATTACTTTAAAGTAATAGGTAAATTTACAA
*
233026 TGAAAACGGTAAAAGTCTATCGGTAT-A-ATAATAGACGTAAACATCAAGTATCGATATTTTTTA
128 TGAAAACGGTAAAAGTCTACCGGTATAAGATAATAGACGTAAACATCAAGTATCGATATTTTTTA
*
233089 TCTCG
193 TATCG
** * * *
233094 GTATCGATACTTTTATTACAACATGCTTATCAAACAATTTGAACGCAA-AAAGTATCGATACACT
1 GTATCGATACTTTTATTACAGTATGCTTCTCAAACAATTTGCACGCAACAAAGTATCGATACACA
* * * *
233158 TATATAAAGTACCGATACTTGG-------AAT-TT-C-------TAA-ACGTAAATTTACAATGT
66 TATATAAAGTATCAATACTTGGAATTTCAAATATTACTTTAAAGTAATAGGTAAATTTACAATGA
* * * * ** * *
233206 AAACGGTAAAAGTCTACCGATATAATGATAATA-AGTGTAAACATAAATTATTTATCTTGTTTAT
131 AAACGGTAAAAGTCTACCGGTATAA-GATAATAGA-CGTAAACATCAAGTATCGATATTTTTTAT
233270 ATCG
194 ATCG
* * * *
233274 GTATCGATACTTTTATTTCAGTATGTTTCTCAAACAATTTGTACGCAACAAAGTTTCGATAC-CA
1 GTATCGATACTTTTATTACAGTATGCTTCTCAAACAATTTGCACGCAACAAAGTATCGATACAC-
* *
233338 ATATATAAAGTAT-AGATACTTGTAATTTCGAA-ATTACTTTAAAGTAATAGGTAAATTTACAAT
65 ATATATAAAGTATCA-ATACTTGGAATTTCAAATATTACTTTAAAGTAATAGGTAAATTTACAAT
* * *
233401 GTAAACGGTAAAAGTCTACCGGTATAATGATAATAGACGTAAATTAT-AAGTATCGATATGTTTT
129 GAAAACGGTAAAAGTCTACCGGTATAA-GATAATAGACGTAAA-CATCAAGTATCGATATTTTTT
233465 ATATCG
192 ATATCG
* *
233471 GTATCGATACTTTTATTATAGTATGCTT-TCAAACAATTTGCACGCAA-AACGTATCGATACACA
1 GTATCGATACTTTTATTACAGTATGCTTCTCAAACAATTTGCACGCAACAAAGTATCGATACACA
* ** * * *
233534 TATGTAAAGTATCAATACTTATATTTTGAAACCTATTACTTTAAAGTAATAGGTTAATTTACAAT
66 TATATAAAGTATCAATACTTGGAATTTCAAA--TATTACTTTAAAGTAATAGGTAAATTTACAAT
* * * ** *
233599 GAAAACAGTAAAAGTCTATCGGTATAGTGATAATAGGTGTAAACATCAAGTACCGATAT
129 GAAAACGGTAAAAGTCTACCGGTATA-AGATAATAGACGTAAACATCAAGTATCGATAT
233658 ACATGTATAA
Statistics
Matches: 463, Mismatches: 68, Indels: 66
0.78 0.11 0.11
Matches are distributed among these distances:
177 36 0.08
178 4 0.01
179 1 0.00
180 74 0.16
181 30 0.06
185 1 0.00
186 2 0.00
187 1 0.00
188 4 0.01
189 3 0.01
195 36 0.08
196 23 0.05
197 129 0.28
198 119 0.26
ACGTcount: A:0.39, C:0.14, G:0.14, T:0.34
Consensus pattern (197 bp):
GTATCGATACTTTTATTACAGTATGCTTCTCAAACAATTTGCACGCAACAAAGTATCGATACACA
TATATAAAGTATCAATACTTGGAATTTCAAATATTACTTTAAAGTAATAGGTAAATTTACAATGA
AAACGGTAAAAGTCTACCGGTATAAGATAATAGACGTAAACATCAAGTATCGATATTTTTTATAT
CG
Found at i:233313 original size:180 final size:178
Alignment explanation
Indices: 233014--233366 Score: 442
Period size: 180 Copynumber: 2.0 Consensus size: 178
233004 AAAGTAATAG
* * *
233014 GTAAATTTACAATGAAAACGGTAAAAGTCTATCGGTATAATAATAGACGTAAACATCAAGTATCG
1 GTAAATTTACAATGAAAACGGTAAAAGTCTACCGATATAATAATAGACGTAAACATAAAGTATCG
* *
233079 ATATTTTTTATCTCGGTATCGATACTTTTATTACAACATGCTTATCAAACAATTTGAACGCAA-A
66 ATATTGTTTATATCGGTATCGATACTTTTATTACAACATGCTTATCAAACAATTTGAACGCAACA
* *
233143 AAGTATCGATA-CACTTATATAAAGTACCGATACTTGGAATTTCTAAAC
131 AAGTATCGATACCA-ATATATAAAGTACAGATACTTGGAATTTCTAAAC
* * *
233191 GTAAATTTACAATGTAAACGGTAAAAGTCTACCGATATAATGATAATA-AGTGTAAACATAAATT
1 GTAAATTTACAATGAAAACGGTAAAAGTCTACCGATAT-A--ATAATAGA-CGTAAACATAAAGT
** * * ** * * *
233255 ATTTATCTTGTTTATATCGGTATCGATACTTTTATTTCAGTATGTTTCTCAAACAATTTGTACGC
62 ATCGATATTGTTTATATCGGTATCGATACTTTTATTACAACATGCTTATCAAACAATTTGAACGC
* * *
233320 AACAAAGTTTCGATACCAATATATAAAGTATAGATACTTGTAATTTC
127 AACAAAGTATCGATACCAATATATAAAGTACAGATACTTGGAATTTC
233367 GAAATTACTT
Statistics
Matches: 148, Mismatches: 22, Indels: 8
0.83 0.12 0.04
Matches are distributed among these distances:
177 35 0.24
178 1 0.01
179 1 0.01
180 73 0.49
181 36 0.24
182 2 0.01
ACGTcount: A:0.39, C:0.14, G:0.13, T:0.35
Consensus pattern (178 bp):
GTAAATTTACAATGAAAACGGTAAAAGTCTACCGATATAATAATAGACGTAAACATAAAGTATCG
ATATTGTTTATATCGGTATCGATACTTTTATTACAACATGCTTATCAAACAATTTGAACGCAACA
AAGTATCGATACCAATATATAAAGTACAGATACTTGGAATTTCTAAAC
Found at i:233675 original size:198 final size:197
Alignment explanation
Indices: 233191--233678 Score: 496
Period size: 198 Copynumber: 2.5 Consensus size: 197
233181 ATTTCTAAAC
* * * * *
233191 GTAAATTTACAATGTAAACGGTAAAAGTCTACCGATATAATGATAATA-AGTGTAAA-CATAAAT
1 GTAAATTTACAATGAAAACAGTAAAAGTCTACCGGTATAATGATAATAGA-CGTAAATCAT-AAG
** * ** * *
233254 TA--TTTATCTTGTTTATATCGGTATCGATACTTTTATTTCAGTATGTTTCTCAAACAATTTGTA
64 TACCGATATCATG--TATATAAGTATCGATACTTTTATTTCAGTATGCTTCTCAAACAATTTGCA
* *
233317 CGCAACAAAGTTTCGATACCAATATATAAAGTATAGATACTTGTAATTTCGAAATTACTTTAAAG
127 CGCAACAAAGTATCGATACCAATATATAAAGTATAGATACTTATAATTTCGAAATTACTTTAAAG
233382 TAATAG
192 TAATAG
* * *
233388 GTAAATTTACAATGTAAACGGTAAAAGTCTACCGGTATAATGATAATAGACGTAAATTATAAGTA
1 GTAAATTTACAATGAAAACAGTAAAAGTCTACCGGTATAATGATAATAGACGTAAATCATAAGTA
* ** * **
233453 TCGATATGTTTTATATCGGTATCGATACTTTTATTAT-AGTATGCTT-TCAAACAATTTGCACGC
66 CCGATATCATGTATATAAGTATCGATACTTTTATT-TCAGTATGCTTCTCAAACAATTTGCACGC
* * *
233516 AA-AACGTATCGATA-CACATATGTAAAGTATCA-ATACTTAT-ATTTTGAAACCTATTACTTTA
130 AACAAAGTATCGATACCA-ATATATAAAGTAT-AGATACTTATAATTTCG-AA---ATTACTTTA
233577 AAGTAATAG
189 AAGTAATAG
* * * **
233586 GTTAATTTACAATGAAAACAGTAAAAGTCTATCGGTATAGTGATAATAGGTGTAAA-CATCAAGT
1 GTAAATTTACAATGAAAACAGTAAAAGTCTACCGGTATAATGATAATAGACGTAAATCAT-AAGT
233650 ACCGATATACATGTATA-AAGTATCGATAC
65 ACCGATAT-CATGTATATAAGTATCGATAC
233679 GTGGAATTTT
Statistics
Matches: 249, Mismatches: 29, Indels: 25
0.82 0.10 0.08
Matches are distributed among these distances:
194 7 0.03
195 31 0.12
196 19 0.08
197 90 0.36
198 92 0.37
199 10 0.04
ACGTcount: A:0.39, C:0.12, G:0.14, T:0.35
Consensus pattern (197 bp):
GTAAATTTACAATGAAAACAGTAAAAGTCTACCGGTATAATGATAATAGACGTAAATCATAAGTA
CCGATATCATGTATATAAGTATCGATACTTTTATTTCAGTATGCTTCTCAAACAATTTGCACGCA
ACAAAGTATCGATACCAATATATAAAGTATAGATACTTATAATTTCGAAATTACTTTAAAGTAAT
AG
Found at i:234363 original size:216 final size:217
Alignment explanation
Indices: 233805--234394 Score: 796
Period size: 224 Copynumber: 2.7 Consensus size: 217
233795 GGTAATATAT
* * *
233805 TAATAATATTGAAAACAAATCAAGTAATTAACCTATTTTGTTATCGTCGGATTTCTAAGGTCTTA
1 TAATAATATTGATAACAAATCAAGTAATTAACCTATTTTGTTATCGTCGGATTTCTAAGGCCTCA
* * *
233870 TCACTTTAAACAGACGCTACCTATTACATTAAATAAGCGCTACTTGTTATGTTATTATGGTTGAT
66 TAACTTTAAACAGGCGCTACCTATTACATTAAATAAGTGCTACTTGTTATGTTATTATGGTTGAT
*
233935 AATATTTCCAGTAATTAATCTATTTTGTTATCGTCAGATTTCTAAGGCTCTATAGCTTAAACTTT
131 AATATTTCCAGTAATTAATCTATTTTGTTATCGTCAGATTTCTAAGGCTCAATAGCTTAAACTTT
* *
234000 GGTAACATTTTATGCGCTACCTAA
196 AGTAACATTTTAGGCGCTACC--A
* * *
234024 TATGTTGATAATATTTATAACTAATCAAGTAATTAACCTATTTTTTTATCGTCGGATTTCTAAGG
1 TA-----ATAATATTGATAACAAATCAAGTAATTAACCTATTTTGTTATCGTCGGATTTCTAAGG
* * * **
234089 CC-CATAAGCTTTAAACATGTGCAACCTATTACATTAAATAAGTTTTACTTGTTATGTTATTATG
61 CCTCATAA-CTTTAAACAGGCGCTACCTATTACATTAAATAAGTGCTACTTGTTATGTTATTATG
* * **
234153 GTTGATAATGTTTCCAGTAATTAA-CTTATTTTGTTA-CTGTCTGATTTCTAAGGCTCAATCATT
125 GTTGATAATATTTCCAGTAATTAATC-TATTTTGTTATC-GTCAGATTTCTAAGGCTCAAT-AGC
234216 TTAAACTTTAGTAACATTTTAGGCGCTACC-
187 TTAAACTTTAGTAACATTTTAGGCGCTACCA
*
234246 TAAT-ATATTGATAACAAATCAAGTAATTAACCTATTTTGTTATCGTTGGATTTCTAAGGCCTCA
1 TAATAATATTGATAACAAATCAAGTAATTAACCTATTTTGTTATCGTCGGATTTCTAAGGCCTCA
* * * *
234310 TTAACTTTAAA-AGGCGCTACCTATTACGTTATATAAGTGCTACTTGTTATGTTATTATGTTTAA
66 -TAACTTTAAACAGGCGCTACCTATTACATTAAATAAGTGCTACTTGTTATGTTATTATGGTTGA
234374 TAATATTTCCAGTAATTAATC
130 TAATATTTCCAGTAATTAATC
234395 AGTTATGTTA
Statistics
Matches: 324, Mismatches: 35, Indels: 26
0.84 0.09 0.07
Matches are distributed among these distances:
216 115 0.35
217 12 0.04
218 3 0.01
219 2 0.01
222 2 0.01
223 5 0.02
224 156 0.48
225 29 0.09
ACGTcount: A:0.32, C:0.15, G:0.13, T:0.41
Consensus pattern (217 bp):
TAATAATATTGATAACAAATCAAGTAATTAACCTATTTTGTTATCGTCGGATTTCTAAGGCCTCA
TAACTTTAAACAGGCGCTACCTATTACATTAAATAAGTGCTACTTGTTATGTTATTATGGTTGAT
AATATTTCCAGTAATTAATCTATTTTGTTATCGTCAGATTTCTAAGGCTCAATAGCTTAAACTTT
AGTAACATTTTAGGCGCTACCA
Found at i:234550 original size:15 final size:15
Alignment explanation
Indices: 234526--234560 Score: 54
Period size: 15 Copynumber: 2.4 Consensus size: 15
234516 TAACTAATCA
234526 CGTA-AATTTTTAAC
1 CGTATAATTTTTAAC
234540 CGTATAATTTTTAAC
1 CGTATAATTTTTAAC
*
234555 AGTATA
1 CGTATA
234561 TTAATCTAAC
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
14 4 0.21
15 15 0.79
ACGTcount: A:0.37, C:0.11, G:0.09, T:0.43
Consensus pattern (15 bp):
CGTATAATTTTTAAC
Found at i:241019 original size:20 final size:20
Alignment explanation
Indices: 240973--241068 Score: 79
Period size: 20 Copynumber: 4.8 Consensus size: 20
240963 CGATTTTCCA
* *
240973 ACTATCGCAATGTGAATATG
1 ACTATCGCAATGCGATTATG
* *
240993 TA-AATCGCAATGCGAGTATG
1 -ACTATCGCAATGCGATTATG
* *
241013 ACTATCGCAACGCGATTCTG
1 ACTATCGCAATGCGATTATG
** * *
241033 ACTAT-AAAACGCGATTCTG
1 ACTATCGCAATGCGATTATG
241052 ACTATCGCAATGCGATT
1 ACTATCGCAATGCGATT
241069 TTTAAAGCGC
Statistics
Matches: 61, Mismatches: 12, Indels: 5
0.78 0.15 0.06
Matches are distributed among these distances:
19 18 0.30
20 42 0.69
21 1 0.02
ACGTcount: A:0.32, C:0.21, G:0.20, T:0.27
Consensus pattern (20 bp):
ACTATCGCAATGCGATTATG
Found at i:241283 original size:22 final size:22
Alignment explanation
Indices: 241242--241284 Score: 68
Period size: 22 Copynumber: 2.0 Consensus size: 22
241232 GCCGACATCC
*
241242 GTCCCCATCTCCGACGAAATCA
1 GTCCCCATCTCCGACAAAATCA
*
241264 GTCCCCATCTCCGGCAAAATC
1 GTCCCCATCTCCGACAAAATC
241285 CGTCTATCTC
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.26, C:0.42, G:0.14, T:0.19
Consensus pattern (22 bp):
GTCCCCATCTCCGACAAAATCA
Found at i:241692 original size:19 final size:19
Alignment explanation
Indices: 241670--241714 Score: 65
Period size: 19 Copynumber: 2.4 Consensus size: 19
241660 AGAATCGCAA
241670 TGCGATTTT-AGTTTCGCGT
1 TGCGATTTTCA-TTTCGCGT
241689 TGCGATTTTCATTTCGCGT
1 TGCGATTTTCATTTCGCGT
*
241708 TGTGATT
1 TGCGATT
241715 CTCGCATTGC
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
19 23 0.96
20 1 0.04
ACGTcount: A:0.11, C:0.16, G:0.24, T:0.49
Consensus pattern (19 bp):
TGCGATTTTCATTTCGCGT
Found at i:243217 original size:31 final size:31
Alignment explanation
Indices: 243179--243369 Score: 328
Period size: 31 Copynumber: 6.2 Consensus size: 31
243169 ATAGTCGAGG
243179 GTTTACATATGTTTAAAGGCACATATGAACA
1 GTTTACATATGTTTAAAGGCACATATGAACA
243210 GTTTACATATGTTTAAAGGCACATATGAACA
1 GTTTACATATGTTTAAAGGCACATATGAACA
* * *
243241 ATTTACATATGTTTAAAGGCTCATATGAAAA
1 GTTTACATATGTTTAAAGGCACATATGAACA
243272 GTTTACATATGTTTAAAGGCACATATGAACA
1 GTTTACATATGTTTAAAGGCACATATGAACA
*
243303 GTTTATATATGTTTAAAGGCACATATGAACA
1 GTTTACATATGTTTAAAGGCACATATGAACA
* *
243334 GTTTACATATGTTTAAAGGCATATATGAATA
1 GTTTACATATGTTTAAAGGCACATATGAACA
243365 GTTTA
1 GTTTA
243370 TATTGTGACA
Statistics
Matches: 150, Mismatches: 10, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
31 150 1.00
ACGTcount: A:0.39, C:0.10, G:0.16, T:0.35
Consensus pattern (31 bp):
GTTTACATATGTTTAAAGGCACATATGAACA
Found at i:247119 original size:31 final size:31
Alignment explanation
Indices: 247081--247297 Score: 398
Period size: 31 Copynumber: 7.0 Consensus size: 31
247071 ATAGTCGAGG
247081 GTTTACATATGTTTAAAGGCACATATGAACA
1 GTTTACATATGTTTAAAGGCACATATGAACA
247112 GTTTACATATGTTTAAAGGCACATATGAACA
1 GTTTACATATGTTTAAAGGCACATATGAACA
*
247143 GTTTGCATATGTTTAAAGGCACATATGAACA
1 GTTTACATATGTTTAAAGGCACATATGAACA
247174 GTTTACATATGTTTAAAGGCACATATGAACA
1 GTTTACATATGTTTAAAGGCACATATGAACA
247205 GTTTACATATGTTTAAAGGCACATATGAACA
1 GTTTACATATGTTTAAAGGCACATATGAACA
* *
247236 GTTTATATATGTTTAAAGGAACATATGAACA
1 GTTTACATATGTTTAAAGGCACATATGAACA
*
247267 GTTTACATATGTTTAAAGGAACATATGAACA
1 GTTTACATATGTTTAAAGGCACATATGAACA
247298 TTTTCTATTG
Statistics
Matches: 181, Mismatches: 5, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
31 181 1.00
ACGTcount: A:0.39, C:0.12, G:0.17, T:0.33
Consensus pattern (31 bp):
GTTTACATATGTTTAAAGGCACATATGAACA
Found at i:247998 original size:20 final size:20
Alignment explanation
Indices: 247975--248015 Score: 73
Period size: 20 Copynumber: 2.0 Consensus size: 20
247965 ATAGCGATAG
*
247975 TCATTTTGGTGTTGCGATTT
1 TCATTTTCGTGTTGCGATTT
247995 TCATTTTCGTGTTGCGATTT
1 TCATTTTCGTGTTGCGATTT
248015 T
1 T
248016 AAGTTTCAGA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.10, C:0.12, G:0.22, T:0.56
Consensus pattern (20 bp):
TCATTTTCGTGTTGCGATTT
Found at i:248022 original size:20 final size:20
Alignment explanation
Indices: 247983--248022 Score: 62
Period size: 20 Copynumber: 2.0 Consensus size: 20
247973 AGTCATTTTG
* *
247983 GTGTTGCGATTTTCATTTTC
1 GTGTTGCGATTTTAAGTTTC
248003 GTGTTGCGATTTTAAGTTTC
1 GTGTTGCGATTTTAAGTTTC
248023 AGAAACTATT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.12, C:0.12, G:0.23, T:0.53
Consensus pattern (20 bp):
GTGTTGCGATTTTAAGTTTC
Found at i:249947 original size:20 final size:20
Alignment explanation
Indices: 249922--249969 Score: 69
Period size: 20 Copynumber: 2.4 Consensus size: 20
249912 TAGTTTACTT
*
249922 TCGCAACGTGAAAATGACTA
1 TCGCAACGCGAAAATGACTA
**
249942 TCGCAACGCGAATTTGACTA
1 TCGCAACGCGAAAATGACTA
249962 TCGCAACG
1 TCGCAACG
249970 AAATAATCAC
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 25 1.00
ACGTcount: A:0.33, C:0.25, G:0.21, T:0.21
Consensus pattern (20 bp):
TCGCAACGCGAAAATGACTA
Found at i:250625 original size:41 final size:41
Alignment explanation
Indices: 250526--250630 Score: 104
Period size: 41 Copynumber: 2.5 Consensus size: 41
250516 CCCGACTCAC
* * *
250526 CTGTCATCGTTCAAGAGGCCTCCCCTATCATTCAAGAGGCCC
1 CTGTCATCGTTCAAGAGTCC-CCCCTACCATTCAAGAGGCCA
* ** *
250568 CTATCATCCCTCAAGAGTCCCCTCC-ACCATTTAAGAGGCCA
1 CTGTCATCGTTCAAGAGTCCCC-CCTACCATTCAAGAGGCCA
*
250609 CTGTCATCGTTGAAGAGGTCCC
1 CTGTCATCGTTCAAGA-GTCCC
250631 TCCCAACATT
Statistics
Matches: 50, Mismatches: 11, Indels: 4
0.77 0.17 0.06
Matches are distributed among these distances:
41 27 0.54
42 23 0.46
ACGTcount: A:0.23, C:0.35, G:0.18, T:0.24
Consensus pattern (41 bp):
CTGTCATCGTTCAAGAGTCCCCCCTACCATTCAAGAGGCCA
Found at i:252071 original size:14 final size:14
Alignment explanation
Indices: 252034--252095 Score: 61
Period size: 14 Copynumber: 4.3 Consensus size: 14
252024 TTGCTTGTTT
*
252034 AATTGATTTATAAA
1 AATTGATTTGTAAA
252048 AATTGATTTGTAAA
1 AATTGATTTGTAAA
* *
252062 AGTTGATTTGTTTAA
1 AATTGATTTG-TAAA
* *
252077 TATTGATGTGTAAA
1 AATTGATTTGTAAA
252091 TAATT
1 -AATT
252096 CTTATTTGTG
Statistics
Matches: 38, Mismatches: 8, Indels: 3
0.78 0.16 0.06
Matches are distributed among these distances:
14 25 0.66
15 13 0.34
ACGTcount: A:0.39, C:0.00, G:0.15, T:0.47
Consensus pattern (14 bp):
AATTGATTTGTAAA
Found at i:252247 original size:20 final size:20
Alignment explanation
Indices: 252194--252247 Score: 72
Period size: 20 Copynumber: 2.7 Consensus size: 20
252184 AGGTACACTT
* **
252194 TCGCAACGCTAAACTCAAAA
1 TCGCAACGCGAAAGACAAAA
*
252214 TCGCAATGCGAAAGACAAAA
1 TCGCAACGCGAAAGACAAAA
252234 TCGCAACGCGAAAG
1 TCGCAACGCGAAAG
252248 TCAATTCGCG
Statistics
Matches: 29, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 29 1.00
ACGTcount: A:0.44, C:0.26, G:0.19, T:0.11
Consensus pattern (20 bp):
TCGCAACGCGAAAGACAAAA
Found at i:252462 original size:74 final size:74
Alignment explanation
Indices: 252289--252546 Score: 288
Period size: 74 Copynumber: 3.4 Consensus size: 74
252279 TGCGATTTTC
* * * *
252289 TCGTTGCAATAGTCAAATACCCGTTGCGATAATCAAATTCGCGTTGCGATACTCAAATTCGCGTT
1 TCGTTGCAATAGTCAAATTCGCGTTGCGATAGTCAAATTCGCGTTGCGAT--T----TTCTCGTT
*
252354 GCGATACTCAAATTCG
60 GCGATAGTCAAA-TCG
* *
252370 -CGTTGCAATACTCAAATTCGCGTTGCAATAGTCAAATTCGCGTTGCGATTTTCTCGTTGCGATA
1 TCGTTGCAATAGTCAAATTCGCGTTGCGATAGTCAAATTCGCGTTGCGATTTTCTCGTTGCGATA
*
252434 GTCAAATAG
66 GTCAAATCG
* *
252443 TCGTTGCGATAGTCAAATTCGCGTTGCGATAGACAAATTCGCGTTGCGATTTT-TGCGTTGCGAT
1 TCGTTGCAATAGTCAAATTCGCGTTGCGATAGTCAAATTCGCGTTGCGATTTTCT-CGTTGCGAT
*
252507 AGTCATATTCG
65 AGTCA-AATCG
* * *
252518 T-GTTACGATAATCAAATTCGCGTTGCGAT
1 TCGTTGCAATAGTCAAATTCGCGTTGCGAT
252547 TTTTGAGTTG
Statistics
Matches: 158, Mismatches: 16, Indels: 13
0.84 0.09 0.07
Matches are distributed among these distances:
73 3 0.02
74 106 0.67
75 4 0.03
78 1 0.01
80 44 0.28
ACGTcount: A:0.26, C:0.21, G:0.21, T:0.33
Consensus pattern (74 bp):
TCGTTGCAATAGTCAAATTCGCGTTGCGATAGTCAAATTCGCGTTGCGATTTTCTCGTTGCGATA
GTCAAATCG
Found at i:252481 original size:20 final size:20
Alignment explanation
Indices: 252241--252608 Score: 311
Period size: 20 Copynumber: 19.6 Consensus size: 20
252231 AAATCGCAAC
*
252241 GCGAAAGTC-AATTCGCGTT
1 GCGATAGTCAAATTCGCGTT
* * *
252260 GCGATAGTCTAATACGCTTT
1 GCGATAGTCAAATTCGCGTT
*
252280 GCGAT--T----TTCTCGTT
1 GCGATAGTCAAATTCGCGTT
* * *
252294 GCAATAGTCAAATACCCGTT
1 GCGATAGTCAAATTCGCGTT
*
252314 GCGATAATCAAATTCGCGTT
1 GCGATAGTCAAATTCGCGTT
*
252334 GCGATACTCAAATTCGCGTT
1 GCGATAGTCAAATTCGCGTT
*
252354 GCGATACTCAAATTCGCGTT
1 GCGATAGTCAAATTCGCGTT
* *
252374 GCAATACTCAAATTCGCGTT
1 GCGATAGTCAAATTCGCGTT
*
252394 GCAATAGTCAAATTCGCGTT
1 GCGATAGTCAAATTCGCGTT
*
252414 GCGAT--T----TTCTCGTT
1 GCGATAGTCAAATTCGCGTT
*
252428 GCGATAGTCAAA-TAGTCGTT
1 GCGATAGTCAAATTCG-CGTT
252448 GCGATAGTCAAATTCGCGTT
1 GCGATAGTCAAATTCGCGTT
*
252468 GCGATAGACAAATTCGCGTT
1 GCGATAGTCAAATTCGCGTT
*
252488 GCGAT--T----TTTGCGTT
1 GCGATAGTCAAATTCGCGTT
* *
252502 GCGATAGTCATATTCGTGTT
1 GCGATAGTCAAATTCGCGTT
* *
252522 ACGATAATCAAATTCGCGTT
1 GCGATAGTCAAATTCGCGTT
* *
252542 GCGAT--T----TTTGAGTT
1 GCGATAGTCAAATTCGCGTT
*
252556 GCGATAATCAAATTCGCGTT
1 GCGATAGTCAAATTCGCGTT
252576 GCGATAGTCAAATTCGCGTT
1 GCGATAGTCAAATTCGCGTT
*
252596 GCGATATTCAAAT
1 GCGATAGTCAAAT
252609 GAATGTGTAA
Statistics
Matches: 285, Mismatches: 37, Indels: 53
0.76 0.10 0.14
Matches are distributed among these distances:
14 44 0.15
16 4 0.01
18 3 0.01
19 9 0.03
20 223 0.78
21 2 0.01
ACGTcount: A:0.26, C:0.20, G:0.21, T:0.33
Consensus pattern (20 bp):
GCGATAGTCAAATTCGCGTT
Found at i:252502 original size:54 final size:54
Alignment explanation
Indices: 252444--252600 Score: 244
Period size: 54 Copynumber: 2.9 Consensus size: 54
252434 GTCAAATAGT
252444 CGTTGCGATAGTCAAATTCGCGTTGCGATAGACAAATTCGCGTTGCGATTTTTG
1 CGTTGCGATAGTCAAATTCGCGTTGCGATAGACAAATTCGCGTTGCGATTTTTG
* * *
252498 CGTTGCGATAGTCATATTCGTGTTACGATA-ATCAAATTCGCGTTGCGATTTTTG
1 CGTTGCGATAGTCAAATTCGCGTTGCGATAGA-CAAATTCGCGTTGCGATTTTTG
* * *
252552 AGTTGCGATAATCAAATTCGCGTTGCGATAGTCAAATTCGCGTTGCGAT
1 CGTTGCGATAGTCAAATTCGCGTTGCGATAGACAAATTCGCGTTGCGAT
252601 ATTCAAATGA
Statistics
Matches: 92, Mismatches: 9, Indels: 4
0.88 0.09 0.04
Matches are distributed among these distances:
53 1 0.01
54 91 0.99
ACGTcount: A:0.24, C:0.18, G:0.24, T:0.34
Consensus pattern (54 bp):
CGTTGCGATAGTCAAATTCGCGTTGCGATAGACAAATTCGCGTTGCGATTTTTG
Found at i:252811 original size:129 final size:129
Alignment explanation
Indices: 252579--252839 Score: 495
Period size: 129 Copynumber: 2.0 Consensus size: 129
252569 TCGCGTTGCG
*
252579 ATAGTCAAATTCGCGTTGCGATATTCAAATGAATGTGTAATAAGTGATAACAACTGAACATATCA
1 ATAGTCAAATTCGCGTTGCGATATTCAAATGAATGTGTAATAAGTGATAACAACTGAACAGATCA
* *
252644 TAGCAATGTTCAAACTCAAGTTACTAATACATGTCTAACTGAAAATGTTAAAAGTTTACACATA
66 TAGCAATATTCAAACTCAAGTTACTAATACATGCCTAACTGAAAATGTTAAAAGTTTACACATA
252708 ATAGTCAAATTCGCGTTGCGATATTCAAATGAATGTGTAATAAGTGATAACAACTGAACAGATCA
1 ATAGTCAAATTCGCGTTGCGATATTCAAATGAATGTGTAATAAGTGATAACAACTGAACAGATCA
252773 TAGCAATATTCAAACTCAAGTTACTAATACATGCCTAACTGAAAATGTTAAAAGTTTACACATA
66 TAGCAATATTCAAACTCAAGTTACTAATACATGCCTAACTGAAAATGTTAAAAGTTTACACATA
252837 ATA
1 ATA
252840 CAACGTTTGC
Statistics
Matches: 129, Mismatches: 3, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
129 129 1.00
ACGTcount: A:0.42, C:0.15, G:0.14, T:0.30
Consensus pattern (129 bp):
ATAGTCAAATTCGCGTTGCGATATTCAAATGAATGTGTAATAAGTGATAACAACTGAACAGATCA
TAGCAATATTCAAACTCAAGTTACTAATACATGCCTAACTGAAAATGTTAAAAGTTTACACATA
Found at i:252920 original size:18 final size:18
Alignment explanation
Indices: 252897--252931 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
252887 AAGCCGGTTG
*
252897 TGATTGGGATTTTGATTT
1 TGATTGCGATTTTGATTT
252915 TGATTGCGATTTTGATT
1 TGATTGCGATTTTGATT
252932 GCCTTTTTCT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.17, C:0.03, G:0.26, T:0.54
Consensus pattern (18 bp):
TGATTGCGATTTTGATTT
Found at i:254987 original size:14 final size:15
Alignment explanation
Indices: 254968--255000 Score: 50
Period size: 14 Copynumber: 2.3 Consensus size: 15
254958 GTGGCATTTC
254968 CTTCGGGGACTT-TT
1 CTTCGGGGACTTCTT
*
254982 CTTCGGGGATTTCTT
1 CTTCGGGGACTTCTT
254997 CTTC
1 CTTC
255001 TTCTTTTTCT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
14 11 0.65
15 6 0.35
ACGTcount: A:0.06, C:0.24, G:0.24, T:0.45
Consensus pattern (15 bp):
CTTCGGGGACTTCTT
Found at i:256107 original size:20 final size:20
Alignment explanation
Indices: 256061--256151 Score: 96
Period size: 20 Copynumber: 4.5 Consensus size: 20
256051 AAATTCAGTG
* * *
256061 TTGCGACAGTCAGAATCGCA
1 TTGCGATAGTCATATTCGCA
256081 TTGCGATAGTCATATTCGCA
1 TTGCGATAGTCATATTCGCA
* *
256101 TTGCGAT-TTACACATTCGCA
1 TTGCGATAGT-CATATTCGCA
*
256121 TTGCGAT-TTACATATTCGCA
1 TTGCGATAGT-CATATTCGCA
256141 TTGCGATAGTC
1 TTGCGATAGTC
256152 GGAAAATCGC
Statistics
Matches: 62, Mismatches: 7, Indels: 4
0.85 0.10 0.05
Matches are distributed among these distances:
19 1 0.02
20 60 0.97
21 1 0.02
ACGTcount: A:0.25, C:0.22, G:0.20, T:0.33
Consensus pattern (20 bp):
TTGCGATAGTCATATTCGCA
Found at i:256845 original size:19 final size:19
Alignment explanation
Indices: 256807--256845 Score: 51
Period size: 19 Copynumber: 2.1 Consensus size: 19
256797 AGTTTACATT
* *
256807 TATTTTTATTATATTGAAA
1 TATTTTTATTACATTAAAA
*
256826 TATTTTTATTGCATTAAAA
1 TATTTTTATTACATTAAAA
256845 T
1 T
256846 TTTATGTTTT
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.36, C:0.03, G:0.05, T:0.56
Consensus pattern (19 bp):
TATTTTTATTACATTAAAA
Done.