Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01013595.1 Kokia drynarioides strain JFW-HI SEQ_128622, 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: 326202
ACGTcount: A:0.33, C:0.16, G:0.17, T:0.33
Warning! 121 characters in sequence are not A, C, G, or T
Found at i:812 original size:12 final size:12
Alignment explanation
Indices: 795--823 Score: 58
Period size: 12 Copynumber: 2.4 Consensus size: 12
785 CCCAACATCT
795 ACAACCAATAGC
1 ACAACCAATAGC
807 ACAACCAATAGC
1 ACAACCAATAGC
819 ACAAC
1 ACAAC
824 AAGAAGCAGA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 17 1.00
ACGTcount: A:0.52, C:0.34, G:0.07, T:0.07
Consensus pattern (12 bp):
ACAACCAATAGC
Found at i:1127 original size:61 final size:62
Alignment explanation
Indices: 936--1165 Score: 369
Period size: 62 Copynumber: 3.8 Consensus size: 62
926 ATTGATTTAT
* * *
936 TTTGAATATTTTTGTAAACATTA-TTTT--TATATTGTTTTATTTAATAAAATCGAAGTTCA
1 TTTGAATATTTTTGTACACATTAGTTTTGGCATATTGTTTCATTTAATAAAATCGAAGTTCA
*
995 TTTGAATATTTTTGTACATATTAGTTTTGGCATATTGTTTCATTTAATAAAATCGAAGTTCA
1 TTTGAATATTTTTGTACACATTAGTTTTGGCATATTGTTTCATTTAATAAAATCGAAGTTCA
*
1057 TTTGAATATTTTTGTACACATTAGTTTTGGCA-ATTATTTCATTTAATAAAATCGAAGTTCA
1 TTTGAATATTTTTGTACACATTAGTTTTGGCATATTGTTTCATTTAATAAAATCGAAGTTCA
* *
1118 TTTGAATATTTCTGTACACATTAGTTTTGGCATGTTGTTTCATTTAAT
1 TTTGAATATTTTTGTACACATTAGTTTTGGCATATTGTTTCATTTAAT
1166 TGTGAACCAA
Statistics
Matches: 158, Mismatches: 9, Indels: 5
0.92 0.05 0.03
Matches are distributed among these distances:
59 21 0.13
60 4 0.03
61 59 0.37
62 74 0.47
ACGTcount: A:0.30, C:0.08, G:0.12, T:0.50
Consensus pattern (62 bp):
TTTGAATATTTTTGTACACATTAGTTTTGGCATATTGTTTCATTTAATAAAATCGAAGTTCA
Found at i:1156 original size:123 final size:121
Alignment explanation
Indices: 936--1165 Score: 363
Period size: 123 Copynumber: 1.9 Consensus size: 121
926 ATTGATTTAT
* * *
936 TTTGAATATTTTTGTAAACATTATTTTTATATTGTTTTATTTAATAAAATCGAAGTTCATTTGAA
1 TTTGAATATTTTTGTAAACATTATTTTCATATTATTTCATTTAATAAAATCGAAGTTCATTTGAA
* *
1001 TATTTTTGTACATATTAGTTTTGGCATATTGTTTCATTTAATAAAATCGAAGTTCA
66 TATTTCTGTACACATTAGTTTTGGCATATTGTTTCATTTAATAAAATCGAAGTTCA
*
1057 TTTGAATATTTTTGTACACATTAGTTTTGGCA-ATTATTTCATTTAATAAAATCGAAGTTCATTT
1 TTTGAATATTTTTGTAAACATTA-TTTT--CATATTATTTCATTTAATAAAATCGAAGTTCATTT
*
1121 GAATATTTCTGTACACATTAGTTTTGGCATGTTGTTTCATTTAAT
63 GAATATTTCTGTACACATTAGTTTTGGCATATTGTTTCATTTAAT
1166 TGTGAACCAA
Statistics
Matches: 99, Mismatches: 7, Indels: 4
0.90 0.06 0.04
Matches are distributed among these distances:
121 22 0.22
122 4 0.04
123 72 0.73
124 1 0.01
ACGTcount: A:0.30, C:0.08, G:0.12, T:0.50
Consensus pattern (121 bp):
TTTGAATATTTTTGTAAACATTATTTTCATATTATTTCATTTAATAAAATCGAAGTTCATTTGAA
TATTTCTGTACACATTAGTTTTGGCATATTGTTTCATTTAATAAAATCGAAGTTCA
Found at i:5068 original size:22 final size:22
Alignment explanation
Indices: 5022--5109 Score: 101
Period size: 22 Copynumber: 4.1 Consensus size: 22
5012 AAAACTCTTC
* *
5022 ATTTAAACTACCTT-AACCCTT
1 ATTTAAAATACCTTAAACCCTA
*
5043 ATTTAAAATATCTTAAACCCTA
1 ATTTAAAATACCTTAAACCCTA
* *
5065 ATTTAAATTACCATAAACCCTA
1 ATTTAAAATACCTTAAACCCTA
*
5087 TTTTAAAA-ACC-TAAACCCTA
1 ATTTAAAATACCTTAAACCCTA
5107 ATT
1 ATT
5110 AAACAAAAAA
Statistics
Matches: 57, Mismatches: 9, Indels: 3
0.83 0.13 0.04
Matches are distributed among these distances:
20 11 0.19
21 15 0.26
22 31 0.54
ACGTcount: A:0.42, C:0.23, G:0.00, T:0.35
Consensus pattern (22 bp):
ATTTAAAATACCTTAAACCCTA
Found at i:5089 original size:43 final size:42
Alignment explanation
Indices: 5022--5113 Score: 109
Period size: 43 Copynumber: 2.2 Consensus size: 42
5012 AAAACTCTTC
* *
5022 ATTTAAACTACCTTAACCCTTA-TTTAAAATATCTTAAACCCTA
1 ATTTAAACTACCTAAACCCTTATTTTAAAA-A-CCTAAACCCTA
*
5065 ATTTAAATTACCATAAACCC-TATTTTAAAAACCTAAACCCTA
1 ATTTAAACTACC-TAAACCCTTATTTTAAAAACCTAAACCCTA
5107 A-TTAAAC
1 ATTTAAAC
5114 AAAAAACACC
Statistics
Matches: 43, Mismatches: 4, Indels: 6
0.81 0.08 0.11
Matches are distributed among these distances:
41 5 0.12
42 11 0.26
43 14 0.33
44 13 0.30
ACGTcount: A:0.43, C:0.23, G:0.00, T:0.34
Consensus pattern (42 bp):
ATTTAAACTACCTAAACCCTTATTTTAAAAACCTAAACCCTA
Found at i:12652 original size:31 final size:33
Alignment explanation
Indices: 12586--12660 Score: 100
Period size: 35 Copynumber: 2.3 Consensus size: 33
12576 TATGATGGGT
*
12586 TTTTTTATTTCATTATTAAATACAACTTTTTTATG
1 TTTTTTATTTAATTATTAAATACAA--TTTTTATG
12621 TTTTTTATTTAATTATTAAATA-AA-TTTTATG
1 TTTTTTATTTAATTATTAAATACAATTTTTATG
*
12652 TTTTATATT
1 TTTTTTATT
12661 GGTCTAAGAA
Statistics
Matches: 38, Mismatches: 2, Indels: 4
0.86 0.05 0.09
Matches are distributed among these distances:
31 15 0.39
34 2 0.05
35 21 0.55
ACGTcount: A:0.31, C:0.04, G:0.03, T:0.63
Consensus pattern (33 bp):
TTTTTTATTTAATTATTAAATACAATTTTTATG
Found at i:15375 original size:39 final size:40
Alignment explanation
Indices: 15307--15388 Score: 148
Period size: 39 Copynumber: 2.1 Consensus size: 40
15297 GTTAGATCAC
*
15307 TAGATGATATGAGAAAAACTTCAGGCTATTACTTCACGTT
1 TAGATAATATGAGAAAAACTTCAGGCTATTACTTCACGTT
15347 TAGATAATATGAG-AAAACTTCAGGCTATTACTTCACGTT
1 TAGATAATATGAGAAAAACTTCAGGCTATTACTTCACGTT
15386 TAG
1 TAG
15389 GTCAGGATGC
Statistics
Matches: 41, Mismatches: 1, Indels: 1
0.95 0.02 0.02
Matches are distributed among these distances:
39 29 0.71
40 12 0.29
ACGTcount: A:0.35, C:0.15, G:0.17, T:0.33
Consensus pattern (40 bp):
TAGATAATATGAGAAAAACTTCAGGCTATTACTTCACGTT
Found at i:18182 original size:21 final size:22
Alignment explanation
Indices: 18151--18191 Score: 75
Period size: 21 Copynumber: 1.9 Consensus size: 22
18141 CTAAGTCCTA
18151 AGGAGATTGTTAGGTTGTTAGT
1 AGGAGATTGTTAGGTTGTTAGT
18173 AGGAG-TTGTTAGGTTGTTA
1 AGGAGATTGTTAGGTTGTTA
18192 AGTTGTTACG
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
21 14 0.74
22 5 0.26
ACGTcount: A:0.22, C:0.00, G:0.37, T:0.41
Consensus pattern (22 bp):
AGGAGATTGTTAGGTTGTTAGT
Found at i:18536 original size:13 final size:13
Alignment explanation
Indices: 18518--18549 Score: 64
Period size: 13 Copynumber: 2.5 Consensus size: 13
18508 CTTGATTTAA
18518 GTTTTAGTTTAGG
1 GTTTTAGTTTAGG
18531 GTTTTAGTTTAGG
1 GTTTTAGTTTAGG
18544 GTTTTA
1 GTTTTA
18550 AAGTTGATTT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 19 1.00
ACGTcount: A:0.16, C:0.00, G:0.28, T:0.56
Consensus pattern (13 bp):
GTTTTAGTTTAGG
Found at i:20544 original size:9 final size:9
Alignment explanation
Indices: 20530--20561 Score: 64
Period size: 9 Copynumber: 3.6 Consensus size: 9
20520 CAGCTTACAT
20530 AAATTGTAG
1 AAATTGTAG
20539 AAATTGTAG
1 AAATTGTAG
20548 AAATTGTAG
1 AAATTGTAG
20557 AAATT
1 AAATT
20562 ATAAAGAAAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 23 1.00
ACGTcount: A:0.47, C:0.00, G:0.19, T:0.34
Consensus pattern (9 bp):
AAATTGTAG
Found at i:22660 original size:35 final size:35
Alignment explanation
Indices: 22621--22689 Score: 120
Period size: 35 Copynumber: 2.0 Consensus size: 35
22611 ATGATTATGA
*
22621 ATAAATTTGATTCTGTTTCACATGTTAAGCATGCC
1 ATAAATTTGATTCTATTTCACATGTTAAGCATGCC
*
22656 ATAAATTTGATTCTATTTCGCATGTTAAGCATGC
1 ATAAATTTGATTCTATTTCACATGTTAAGCATGC
22690 AATATTCTGA
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
35 32 1.00
ACGTcount: A:0.29, C:0.16, G:0.14, T:0.41
Consensus pattern (35 bp):
ATAAATTTGATTCTATTTCACATGTTAAGCATGCC
Found at i:23409 original size:13 final size:14
Alignment explanation
Indices: 23378--23412 Score: 54
Period size: 13 Copynumber: 2.6 Consensus size: 14
23368 TTTATTTCTG
23378 TGGACTTTTGGTTT
1 TGGACTTTTGGTTT
*
23392 AGGACTTTT-GTTT
1 TGGACTTTTGGTTT
23405 TGGACTTT
1 TGGACTTT
23413 GGATTATTTT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
13 11 0.58
14 8 0.42
ACGTcount: A:0.11, C:0.09, G:0.26, T:0.54
Consensus pattern (14 bp):
TGGACTTTTGGTTT
Found at i:27406 original size:20 final size:20
Alignment explanation
Indices: 27381--27420 Score: 62
Period size: 20 Copynumber: 2.0 Consensus size: 20
27371 CTTGAAGATA
27381 AAAATTTTAAAAATAAAAAT
1 AAAATTTTAAAAATAAAAAT
**
27401 AAAATTTTATCAATAAAAAT
1 AAAATTTTAAAAATAAAAAT
27421 GAGAGGATCC
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:0.65, C:0.03, G:0.00, T:0.33
Consensus pattern (20 bp):
AAAATTTTAAAAATAAAAAT
Found at i:27605 original size:28 final size:29
Alignment explanation
Indices: 27570--27636 Score: 93
Period size: 29 Copynumber: 2.3 Consensus size: 29
27560 AAAAATTTTT
27570 AATTTTTATATT-TTAATAATTTTTT-TAG
1 AATTTTTATATTATTAATAATTTTTTAT-G
**
27598 AATTTTTATATTATTTGTAATTTTTTATG
1 AATTTTTATATTATTAATAATTTTTTATG
27627 AATTTTTATA
1 AATTTTTATA
27637 AGTTTTTATA
Statistics
Matches: 35, Mismatches: 2, Indels: 3
0.88 0.05 0.08
Matches are distributed among these distances:
28 12 0.34
29 22 0.63
30 1 0.03
ACGTcount: A:0.31, C:0.00, G:0.04, T:0.64
Consensus pattern (29 bp):
AATTTTTATATTATTAATAATTTTTTATG
Found at i:27646 original size:10 final size:9
Alignment explanation
Indices: 27565--27997 Score: 73
Period size: 10 Copynumber: 46.6 Consensus size: 9
27555 CTTTTAAAAA
27565 TTTT-TAAT
1 TTTTATAAT
27573 TTTTAT-AT
1 TTTTATAAT
*
27581 TTTAATAATTT
1 TTTTATAA--T
*
27592 TTTTAGAAT
1 TTTTATAAT
27601 TTTTAT-AT
1 TTTTATAAT
*
27609 TATTTGTAATT
1 T-TTTATAA-T
27620 TTTTATGAAT
1 TTTTAT-AAT
27630 TTTTATAAGT
1 TTTTATAA-T
*
27640 TTTTATAAAA
1 TTTTAT-AAT
*
27650 TTTTACATAT
1 TTTTATA-AT
**
27660 AGTTATTAA-
1 TTTTA-TAAT
*
27669 TTTTAAATAT
1 TTTTATA-AT
27679 TTTTAATAAT
1 TTTT-ATAAT
*
27689 TTATTAAAAT
1 TT-TTATAAT
*
27699 TTATTA-GAT
1 TT-TTATAAT
27708 TTATTATAAT
1 TT-TTATAAT
**
27718 TTTTATGGTTT
1 TTTTAT--AAT
27729 TTTTATAA-
1 TTTTATAAT
**
27737 ACTTATAAGT
1 TTTTATAA-T
* *
27747 TTATATCAAA
1 TTTTAT-AAT
*
27757 TTTAAT-AT
1 TTTTATAAT
*
27765 TTTTATGAT
1 TTTTATAAT
* **
27774 TTTAATGGT
1 TTTTATAAT
*
27783 TTTTAATTAT
1 TTTT-ATAAT
27793 TTTTA-ATAT
1 TTTTATA-AT
*
27802 TTTTATGAT
1 TTTTATAAT
*
27811 TTTTATAGGT
1 TTTTATA-AT
* *
27821 TTTAAAGAAT
1 TTT-TATAAT
**
27831 TTTTATTCGT
1 TTTTA-TAAT
27841 TTTTATAAAT
1 TTTTAT-AAT
*
27851 TATTA-AAT
1 TTTTATAAT
27859 ATTTTA-ACAT
1 -TTTTATA-AT
27869 GTTTTATTAA-
1 -TTTTA-TAAT
27879 TTTTATAATTT
1 TTTTATAA--T
27890 TTTTATAA-
1 TTTTATAAT
27898 -TTTACTAGAT
1 TTTTA-TA-AT
27908 TTTTAT-AT
1 TTTTATAAT
*
27916 TTTT-TTAT
1 TTTTATAAT
*
27924 GTTTATAAGT
1 TTTTATAA-T
* *
27934 TTATATCA-
1 TTTTATAAT
27942 TTTTAT--T
1 TTTTATAAT
*
27949 TTCTA-AAT
1 TTTTATAAT
27957 ATTTT-T-AT
1 -TTTTATAAT
27965 TTTTAATAA-
1 TTTT-ATAAT
27974 TTTTATAAT
1 TTTTATAAT
*
27983 ATTTTCTAAT
1 -TTTTATAAT
27993 TTTTA
1 TTTTA
27998 GAAAATTACT
Statistics
Matches: 307, Mismatches: 64, Indels: 107
0.64 0.13 0.22
Matches are distributed among these distances:
7 13 0.04
8 58 0.19
9 86 0.28
10 107 0.35
11 42 0.14
12 1 0.00
ACGTcount: A:0.32, C:0.02, G:0.05, T:0.61
Consensus pattern (9 bp):
TTTTATAAT
Found at i:27793 original size:28 final size:27
Alignment explanation
Indices: 27757--27815 Score: 75
Period size: 28 Copynumber: 2.1 Consensus size: 27
27747 TTATATCAAA
*
27757 TTTAATATTTTT-ATGATTTTAATGGTT
1 TTTAATATTTTTAAT-ATTTTAATGATT
*
27784 TTTAATTATTTTTAATATTTTTATGATT
1 TTTAA-TATTTTTAATATTTTAATGATT
27812 TTTA
1 TTTA
27816 TAGGTTTTAA
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
27 5 0.18
28 21 0.75
29 2 0.07
ACGTcount: A:0.27, C:0.00, G:0.07, T:0.66
Consensus pattern (27 bp):
TTTAATATTTTTAATATTTTAATGATT
Found at i:27977 original size:15 final size:17
Alignment explanation
Indices: 27941--27979 Score: 55
Period size: 15 Copynumber: 2.4 Consensus size: 17
27931 AGTTTATATC
27941 ATTTTATTTTCTAAATA
1 ATTTTATTTTCTAAATA
*
27958 TTTTTATTTT-T-AATA
1 ATTTTATTTTCTAAATA
27973 ATTTTAT
1 ATTTTAT
27980 AATATTTTCT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
15 10 0.50
16 1 0.05
17 9 0.45
ACGTcount: A:0.31, C:0.03, G:0.00, T:0.67
Consensus pattern (17 bp):
ATTTTATTTTCTAAATA
Found at i:30610 original size:21 final size:22
Alignment explanation
Indices: 30584--30624 Score: 66
Period size: 22 Copynumber: 1.9 Consensus size: 22
30574 TGAATTGAAT
30584 TGAATT-TATTTTTATTTAAAA
1 TGAATTATATTTTTATTTAAAA
*
30605 TGAATTATTTTTTTATTTAA
1 TGAATTATATTTTTATTTAA
30625 TTAAAAATAC
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 6 0.33
22 12 0.67
ACGTcount: A:0.34, C:0.00, G:0.05, T:0.61
Consensus pattern (22 bp):
TGAATTATATTTTTATTTAAAA
Found at i:34037 original size:2 final size:2
Alignment explanation
Indices: 34030--34076 Score: 80
Period size: 2 Copynumber: 24.5 Consensus size: 2
34020 GCTTCACTAC
34030 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA G- GA GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
34071 GA -A GA G
1 GA GA GA G
34077 TTGAATACGA
Statistics
Matches: 43, Mismatches: 0, Indels: 4
0.91 0.00 0.09
Matches are distributed among these distances:
1 2 0.05
2 41 0.95
ACGTcount: A:0.49, C:0.00, G:0.51, T:0.00
Consensus pattern (2 bp):
GA
Found at i:36578 original size:16 final size:18
Alignment explanation
Indices: 36544--36580 Score: 51
Period size: 16 Copynumber: 2.2 Consensus size: 18
36534 ATATTAACAT
36544 AATATATATATAATATAA
1 AATATATATATAATATAA
*
36562 AATAT-TATA-AATTTAA
1 AATATATATATAATATAA
36578 AAT
1 AAT
36581 GAGTCAGGTT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
16 9 0.50
17 4 0.22
18 5 0.28
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (18 bp):
AATATATATATAATATAA
Found at i:39608 original size:20 final size:20
Alignment explanation
Indices: 39583--39623 Score: 66
Period size: 20 Copynumber: 2.0 Consensus size: 20
39573 AAAAATACAT
39583 AAAAATAAC-ACCTAAACAAC
1 AAAAATAACAACC-AAACAAC
39603 AAAAATAACAACCAAACAAC
1 AAAAATAACAACCAAACAAC
39623 A
1 A
39624 GTAAAAATAG
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
20 17 0.85
21 3 0.15
ACGTcount: A:0.68, C:0.24, G:0.00, T:0.07
Consensus pattern (20 bp):
AAAAATAACAACCAAACAAC
Found at i:39631 original size:43 final size:42
Alignment explanation
Indices: 39581--39751 Score: 122
Period size: 43 Copynumber: 4.1 Consensus size: 42
39571 GTAAAAATAC
*
39581 ATAAAAATAACACCTAAACAAC-AAAAATAACAACCAAACAACA
1 ATAAAAATAACACCAAAACAACAAAAAATAACAA-CAAA-AACA
* * * * *
39624 GTAAAAATAGCAGCAAAATAACAAAAAATAGCAACAAAAACA
1 ATAAAAATAACACCAAAACAACAAAAAATAACAACAAAAACA
* *
39666 ATAAAAATAACATCAAAAGCAACACAAAACAGTAA-AA-AAAAGCA
1 ATAAAAATAACACCAAAA-CAACA-AAAA-A-TAACAACAAAAACA
* * * **
39710 CT-AAAACAACAACAAAACAGTAAAAAA-AAC--CAAAAACA
1 ATAAAAATAACACCAAAACAACAAAAAATAACAACAAAAACA
39748 ATAA
1 ATAA
39752 TATATTTTTT
Statistics
Matches: 101, Mismatches: 19, Indels: 20
0.72 0.14 0.14
Matches are distributed among these distances:
38 9 0.09
39 1 0.01
40 1 0.01
41 4 0.04
42 22 0.22
43 38 0.38
44 21 0.21
45 3 0.03
46 2 0.02
ACGTcount: A:0.68, C:0.18, G:0.05, T:0.09
Consensus pattern (42 bp):
ATAAAAATAACACCAAAACAACAAAAAATAACAACAAAAACA
Found at i:39671 original size:21 final size:21
Alignment explanation
Indices: 39581--39751 Score: 77
Period size: 21 Copynumber: 8.2 Consensus size: 21
39571 GTAAAAATAC
**
39581 ATAAAAATAAC-ACCTAAACA
1 ATAAAAATAACAACAAAAACA
*
39601 ACAAAAATAACAACCAAACAACA
1 ATAAAAATAACAA-CAAA-AACA
* * *
39624 GTAAAAATAGCAGCAAAATA-A
1 ATAAAAATAACAACAAAA-ACA
*
39645 CA-AAAAATAGCAACAAAAACA
1 -ATAAAAATAACAACAAAAACA
* *
39666 ATAAAAATAACATCAAAAGCA
1 ATAAAAATAACAACAAAAACA
* * ** *
39687 ACACAAAACAGTAAAAAAAAGCA
1 ATA-AAAATAACAACAAAAA-CA
* *
39710 CT-AAAACAACAAC-AAAACA
1 ATAAAAATAACAACAAAAACA
* *
39729 GTAAAAA-AA-ACCAAAAACA
1 ATAAAAATAACAACAAAAACA
39748 ATAA
1 ATAA
39752 TATATTTTTT
Statistics
Matches: 113, Mismatches: 27, Indels: 23
0.69 0.17 0.14
Matches are distributed among these distances:
18 2 0.02
19 14 0.12
20 20 0.18
21 45 0.40
22 17 0.15
23 15 0.13
ACGTcount: A:0.68, C:0.18, G:0.05, T:0.09
Consensus pattern (21 bp):
ATAAAAATAACAACAAAAACA
Found at i:39676 original size:31 final size:31
Alignment explanation
Indices: 39638--39745 Score: 94
Period size: 31 Copynumber: 3.5 Consensus size: 31
39628 AAATAGCAGC
39638 AAAATAACAAAAAATAGCAACA-AAAACAATA
1 AAAATAACAAAAAA-AGCAACACAAAACAATA
** *
39669 AAAATAACATCAAAAGCAACACAAAACAGTA
1 AAAATAACAAAAAAAGCAACACAAAACAATA
* ** *
39700 AAAAAAAGCACTAAAA-CAACAACAAAACAGTA
1 AAAATAA-CAAAAAAAGCAAC-ACAAAACAATA
* *
39732 AAAAAAACCAAAAA
1 AAAATAACAAAAAA
39746 CAATAATATA
Statistics
Matches: 65, Mismatches: 9, Indels: 6
0.81 0.11 0.08
Matches are distributed among these distances:
30 7 0.11
31 34 0.52
32 24 0.37
ACGTcount: A:0.71, C:0.17, G:0.05, T:0.07
Consensus pattern (31 bp):
AAAATAACAAAAAAAGCAACACAAAACAATA
Found at i:39704 original size:32 final size:31
Alignment explanation
Indices: 39638--39744 Score: 100
Period size: 32 Copynumber: 3.5 Consensus size: 31
39628 AAATAGCAGC
* *
39638 AAAATAACAAAAAATAGCAACA-AAAACAAT-A
1 AAAATAAC-ACAAA-AGCAACACAAAACAGTAA
39669 AAAATAACATCAAAAGCAACACAAAACAGTAA
1 AAAATAACA-CAAAAGCAACACAAAACAGTAA
39701 AAAA-AAGCACTAAAA-CAACAACAAAACAGTAA
1 AAAATAA-CAC-AAAAGCAAC-ACAAAACAGTAA
39733 AAAA-AAC-CAAAA
1 AAAATAACACAAAA
39745 ACAATAATAT
Statistics
Matches: 68, Mismatches: 2, Indels: 14
0.81 0.02 0.17
Matches are distributed among these distances:
29 4 0.06
30 9 0.13
31 26 0.38
32 29 0.43
ACGTcount: A:0.71, C:0.17, G:0.05, T:0.07
Consensus pattern (31 bp):
AAAATAACACAAAAGCAACACAAAACAGTAA
Found at i:75833 original size:49 final size:49
Alignment explanation
Indices: 75761--75861 Score: 202
Period size: 49 Copynumber: 2.1 Consensus size: 49
75751 TTGTTTTGGT
75761 AAGTTTATTTTCCCTACTGACTTTGTCATTTTAGACTTTGAAGTAGATA
1 AAGTTTATTTTCCCTACTGACTTTGTCATTTTAGACTTTGAAGTAGATA
75810 AAGTTTATTTTCCCTACTGACTTTGTCATTTTAGACTTTGAAGTAGATA
1 AAGTTTATTTTCCCTACTGACTTTGTCATTTTAGACTTTGAAGTAGATA
75859 AAG
1 AAG
75862 AAGTGTCAAT
Statistics
Matches: 52, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
49 52 1.00
ACGTcount: A:0.28, C:0.14, G:0.15, T:0.44
Consensus pattern (49 bp):
AAGTTTATTTTCCCTACTGACTTTGTCATTTTAGACTTTGAAGTAGATA
Found at i:78408 original size:11 final size:11
Alignment explanation
Indices: 78392--78416 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
78382 AGAAATTTAA
78392 TTGCGACATTG
1 TTGCGACATTG
78403 TTGCGACATTG
1 TTGCGACATTG
78414 TTG
1 TTG
78417 GACGTAATCT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.16, C:0.16, G:0.28, T:0.40
Consensus pattern (11 bp):
TTGCGACATTG
Found at i:85198 original size:15 final size:14
Alignment explanation
Indices: 85180--85210 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 14
85170 AAATAGAAAT
85180 GAAAAAGAAAAAGAA
1 GAAAAAGAAAAA-AA
85195 GAAAAAGAAAAAAA
1 GAAAAAGAAAAAAA
85209 GA
1 GA
85211 GCATATGTAC
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:0.81, C:0.00, G:0.19, T:0.00
Consensus pattern (14 bp):
GAAAAAGAAAAAAA
Found at i:85820 original size:16 final size:18
Alignment explanation
Indices: 85776--85817 Score: 50
Period size: 20 Copynumber: 2.2 Consensus size: 18
85766 ATTAATGTTG
85776 AAAAATATAATTTATTTAT
1 AAAAAT-TAATTTATTTAT
85795 AAAATAATTAATTTATTT-T
1 -AAA-AATTAATTTATTTAT
85814 AAAA
1 AAAA
85818 TTACCAAAAT
Statistics
Matches: 21, Mismatches: 0, Indels: 5
0.81 0.00 0.19
Matches are distributed among these distances:
17 1 0.05
18 3 0.14
19 1 0.05
20 13 0.62
21 3 0.14
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (18 bp):
AAAAATTAATTTATTTAT
Found at i:86705 original size:12 final size:12
Alignment explanation
Indices: 86688--86712 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
86678 TGTTATCATG
86688 ATGAATGCTATT
1 ATGAATGCTATT
86700 ATGAATGCTATT
1 ATGAATGCTATT
86712 A
1 A
86713 ATTCTTTAAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.36, C:0.08, G:0.16, T:0.40
Consensus pattern (12 bp):
ATGAATGCTATT
Found at i:93173 original size:18 final size:18
Alignment explanation
Indices: 93150--93200 Score: 59
Period size: 18 Copynumber: 2.8 Consensus size: 18
93140 GCAACCTGAT
93150 CAGATGC-GATCACAGAAC
1 CAGATGCAG-TCACAGAAC
* *
93168 CAGATGCAGTCATATAAC
1 CAGATGCAGTCACAGAAC
*
93186 CAGATGCAGCCACAG
1 CAGATGCAGTCACAG
93201 GTTCGAATGC
Statistics
Matches: 27, Mismatches: 5, Indels: 2
0.79 0.15 0.06
Matches are distributed among these distances:
18 26 0.96
19 1 0.04
ACGTcount: A:0.37, C:0.27, G:0.22, T:0.14
Consensus pattern (18 bp):
CAGATGCAGTCACAGAAC
Found at i:99242 original size:3 final size:3
Alignment explanation
Indices: 99219--99276 Score: 52
Period size: 3 Copynumber: 20.0 Consensus size: 3
99209 GTATTAAGGT
*
99219 AGA AGA AGG AGAA AGA A-A AGA AGA AGA AGA AGA AG- AGA AGGA AGA
1 AGA AGA AGA AG-A AGA AGA AGA AGA AGA AGA AGA AGA AGA A-GA AGA
*
99264 A-A A-A AAA AGA AGA
1 AGA AGA AGA AGA AGA
99277 TATTACCTTG
Statistics
Matches: 47, Mismatches: 3, Indels: 10
0.78 0.05 0.17
Matches are distributed among these distances:
2 8 0.17
3 34 0.72
4 5 0.11
ACGTcount: A:0.69, C:0.00, G:0.31, T:0.00
Consensus pattern (3 bp):
AGA
Found at i:99262 original size:21 final size:21
Alignment explanation
Indices: 99214--99264 Score: 59
Period size: 21 Copynumber: 2.4 Consensus size: 21
99204 TGTGGGTATT
* *
99214 AAGGTAGAAGAAGGAGAAAGA
1 AAGGAAGAAGAAGAAGAAAGA
*
99235 AAAGAAGAAGAAGAAG-AAGA
1 AAGGAAGAAGAAGAAGAAAGA
99255 GAAGGAAGAA
1 -AAGGAAGAA
99265 AAAAAAAGAA
Statistics
Matches: 25, Mismatches: 4, Indels: 2
0.81 0.13 0.06
Matches are distributed among these distances:
20 4 0.16
21 21 0.84
ACGTcount: A:0.63, C:0.00, G:0.35, T:0.02
Consensus pattern (21 bp):
AAGGAAGAAGAAGAAGAAAGA
Found at i:100327 original size:2 final size:2
Alignment explanation
Indices: 100320--100383 Score: 74
Period size: 2 Copynumber: 32.0 Consensus size: 2
100310 TAAAAGAAGA
* * * *
100320 AT AT AT AT AT AT AT AC AT AT AT AC AT AT AT GT AT AT AT GT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
* *
100362 AT AT GT TT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT
100384 GTATGTATGT
Statistics
Matches: 51, Mismatches: 11, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
2 51 1.00
ACGTcount: A:0.44, C:0.03, G:0.05, T:0.48
Consensus pattern (2 bp):
AT
Found at i:100399 original size:8 final size:8
Alignment explanation
Indices: 100320--100395 Score: 71
Period size: 8 Copynumber: 9.2 Consensus size: 8
100310 TAAAAGAAGA
*
100320 ATATATAT
1 ATATATGT
**
100328 ATATATAC
1 ATATATGT
**
100336 ATATATAC
1 ATATATGT
100344 ATATATGT
1 ATATATGT
100352 ATATATGT
1 ATATATGT
100360 ATATATGTTT
1 ATATATG--T
*
100370 ATATATAT
1 ATATATGT
100378 ATATATGT
1 ATATATGT
*
100386 ATGTATGT
1 ATATATGT
100394 AT
1 AT
100396 GTATATTATT
Statistics
Matches: 60, Mismatches: 6, Indels: 4
0.86 0.09 0.06
Matches are distributed among these distances:
8 53 0.88
10 7 0.12
ACGTcount: A:0.41, C:0.03, G:0.08, T:0.49
Consensus pattern (8 bp):
ATATATGT
Found at i:100400 original size:26 final size:26
Alignment explanation
Indices: 100320--100401 Score: 92
Period size: 26 Copynumber: 3.2 Consensus size: 26
100310 TAAAAGAAGA
* * * *
100320 ATATATATATATATACATATATACAT
1 ATATATATATATGTATATATGTATAT
* *
100346 ATATGTATATATGTATATATGTTTAT
1 ATATATATATATGTATATATGTATAT
* *
100372 ATATATATATATGTATGTATGTATGT
1 ATATATATATATGTATATATGTATAT
100398 ATAT
1 ATAT
100402 TATTATACAA
Statistics
Matches: 46, Mismatches: 10, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
26 46 1.00
ACGTcount: A:0.40, C:0.02, G:0.09, T:0.49
Consensus pattern (26 bp):
ATATATATATATGTATATATGTATAT
Found at i:100408 original size:26 final size:25
Alignment explanation
Indices: 100344--100408 Score: 69
Period size: 26 Copynumber: 2.5 Consensus size: 25
100334 ACATATATAC
*
100344 ATATATGTATATATGTATATATGTTT
1 ATATATAT-TATATGTATATATGTTT
*
100370 ATATATATATATATGTATGTATGTATGT
1 ATATATAT-TATATGTATATATGT-T-T
100398 ATAT-TATTATA
1 ATATATATTATA
100409 CAATAAATGT
Statistics
Matches: 35, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
26 26 0.74
27 4 0.11
28 5 0.14
ACGTcount: A:0.37, C:0.00, G:0.11, T:0.52
Consensus pattern (25 bp):
ATATATATTATATGTATATATGTTT
Found at i:107839 original size:12 final size:12
Alignment explanation
Indices: 107818--107860 Score: 50
Period size: 12 Copynumber: 3.6 Consensus size: 12
107808 GGAGGAGAAG
107818 GAAGAAGAAAAA
1 GAAGAAGAAAAA
* *
107830 GAAGACGAAAGA
1 GAAGAAGAAAAA
*
107842 GAAGAAGAGAAA
1 GAAGAAGAAAAA
*
107854 GAGGAAG
1 GAAGAAG
107861 TTCCTATCGT
Statistics
Matches: 25, Mismatches: 6, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
12 25 1.00
ACGTcount: A:0.63, C:0.02, G:0.35, T:0.00
Consensus pattern (12 bp):
GAAGAAGAAAAA
Found at i:107860 original size:15 final size:15
Alignment explanation
Indices: 107828--107856 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
107818 GAAGAAGAAA
107828 AAGAAGACGAAAGAG
1 AAGAAGACGAAAGAG
107843 AAGAAGA-GAAAGAG
1 AAGAAGACGAAAGAG
107857 GAAGTTCCTA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 7 0.50
15 7 0.50
ACGTcount: A:0.62, C:0.03, G:0.34, T:0.00
Consensus pattern (15 bp):
AAGAAGACGAAAGAG
Found at i:118146 original size:26 final size:26
Alignment explanation
Indices: 118117--118170 Score: 108
Period size: 26 Copynumber: 2.1 Consensus size: 26
118107 TGTTACCCCA
118117 ACGGGTAATGCAATTATACCAATAGT
1 ACGGGTAATGCAATTATACCAATAGT
118143 ACGGGTAATGCAATTATACCAATAGT
1 ACGGGTAATGCAATTATACCAATAGT
118169 AC
1 AC
118171 AAGAATTTTA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 28 1.00
ACGTcount: A:0.39, C:0.17, G:0.19, T:0.26
Consensus pattern (26 bp):
ACGGGTAATGCAATTATACCAATAGT
Found at i:143886 original size:27 final size:27
Alignment explanation
Indices: 143856--143912 Score: 78
Period size: 27 Copynumber: 2.1 Consensus size: 27
143846 ATCAATAGAG
* *
143856 AGTCCACTAGGATAGTAAACATGGGGT
1 AGTCCACTAGGACAGTAAACACGGGGT
* *
143883 AGTCCATTGGGACAGTAAACACGGGGT
1 AGTCCACTAGGACAGTAAACACGGGGT
143910 AGT
1 AGT
143913 TTGTCAGGAT
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
27 26 1.00
ACGTcount: A:0.32, C:0.16, G:0.32, T:0.21
Consensus pattern (27 bp):
AGTCCACTAGGACAGTAAACACGGGGT
Found at i:143928 original size:27 final size:27
Alignment explanation
Indices: 143898--143960 Score: 126
Period size: 27 Copynumber: 2.3 Consensus size: 27
143888 ATTGGGACAG
143898 TAAACACGGGGTAGTTTGTCAGGATAT
1 TAAACACGGGGTAGTTTGTCAGGATAT
143925 TAAACACGGGGTAGTTTGTCAGGATAT
1 TAAACACGGGGTAGTTTGTCAGGATAT
143952 TAAACACGG
1 TAAACACGG
143961 CGAAGTCTTC
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 36 1.00
ACGTcount: A:0.32, C:0.13, G:0.29, T:0.27
Consensus pattern (27 bp):
TAAACACGGGGTAGTTTGTCAGGATAT
Found at i:147460 original size:15 final size:15
Alignment explanation
Indices: 147440--147470 Score: 62
Period size: 15 Copynumber: 2.1 Consensus size: 15
147430 GTGAAATCAC
147440 AATATCCATCACAAG
1 AATATCCATCACAAG
147455 AATATCCATCACAAG
1 AATATCCATCACAAG
147470 A
1 A
147471 TATTGCGACA
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:0.48, C:0.26, G:0.06, T:0.19
Consensus pattern (15 bp):
AATATCCATCACAAG
Found at i:152938 original size:50 final size:51
Alignment explanation
Indices: 152807--152964 Score: 223
Period size: 51 Copynumber: 3.1 Consensus size: 51
152797 TTATAAATGA
* *
152807 ATCGTGGGTAAACGAATCCTCTACGGATTAAAGGT-TCGATGACGAAGTGTC
1 ATCGTGAGTAAACGAATCCTCTACGGATTAAAGGTCT-GATGACGTAGTGTC
152858 ATCGTGAGTAAACGAATCCTCTACGGATTAAAGGTCTGATGAC-TAGTGTC
1 ATCGTGAGTAAACGAATCCTCTACGGATTAAAGGTCTGATGACGTAGTGTC
* * * *
152908 ATCGTGAGTAAATGAATCCAT-AACGAATTAAAGGTCTGATGACTTAGTGTC
1 ATCGTGAGTAAACGAATCC-TCTACGGATTAAAGGTCTGATGACGTAGTGTC
152959 ATCGTG
1 ATCGTG
152965 GGTATATGAA
Statistics
Matches: 99, Mismatches: 5, Indels: 6
0.90 0.05 0.05
Matches are distributed among these distances:
50 44 0.44
51 54 0.55
52 1 0.01
ACGTcount: A:0.31, C:0.16, G:0.25, T:0.28
Consensus pattern (51 bp):
ATCGTGAGTAAACGAATCCTCTACGGATTAAAGGTCTGATGACGTAGTGTC
Found at i:157020 original size:95 final size:94
Alignment explanation
Indices: 156857--157046 Score: 362
Period size: 95 Copynumber: 2.0 Consensus size: 94
156847 GTTGATAGAA
156857 GCTCCGGTAGTGACACAACCTGAAACGAGTAAATAGTTTGTTGTATATAGTGATGCATCCCTAAA
1 GCTCCGGTAGTGACACAACCTGAAACGAGTAAATAGTTTGTTGTATATAGTGATGCATCCCTAAA
*
156922 TGTCCTGGGTCGTGTATTAATGCAAACAG
66 TGTCCAGGGTCGTGTATTAATGCAAACAG
156951 NGCTCCGGTAGTGACACAACCTGAAACGAGTAAATAGTTTGTTGTATATAGTGATGCATCCCTAA
1 -GCTCCGGTAGTGACACAACCTGAAACGAGTAAATAGTTTGTTGTATATAGTGATGCATCCCTAA
157016 ATGTCCAGGGTCGTGTATTAATGCAAACAG
65 ATGTCCAGGGTCGTGTATTAATGCAAACAG
157046 G
1 G
157047 ACAGGTAATA
Statistics
Matches: 94, Mismatches: 1, Indels: 1
0.98 0.01 0.01
Matches are distributed among these distances:
94 1 0.01
95 93 0.99
ACGTcount: A:0.30, C:0.18, G:0.24, T:0.28
Consensus pattern (94 bp):
GCTCCGGTAGTGACACAACCTGAAACGAGTAAATAGTTTGTTGTATATAGTGATGCATCCCTAAA
TGTCCAGGGTCGTGTATTAATGCAAACAG
Found at i:160102 original size:51 final size:51
Alignment explanation
Indices: 160040--160236 Score: 342
Period size: 51 Copynumber: 3.9 Consensus size: 51
160030 CTATAAATGA
*
160040 AAAGGTCCGATGACTAAGTGTCATTGTGAGTAAACGAATCCTCTACGGATT
1 AAAGGTCCGATGACTAAGTGTCATCGTGAGTAAACGAATCCTCTACGGATT
* *
160091 AAAGGTTCGATGACTAAGTGTCATCGTGAGTAAATGAATCCTCTACGGATT
1 AAAGGTCCGATGACTAAGTGTCATCGTGAGTAAACGAATCCTCTACGGATT
160142 AAAGGTCCGATGACTAAGTGTCATCGTGAGTAAACGAATCCTCTACGGATT
1 AAAGGTCCGATGACTAAGTGTCATCGTGAGTAAACGAATCCTCTACGGATT
* *
160193 AAAGGTCCGATGACT-AGTGTCATTGTGAGTAAACAAATCCTCTA
1 AAAGGTCCGATGACTAAGTGTCATCGTGAGTAAACGAATCCTCTA
160237 TAGATTAAGC
Statistics
Matches: 139, Mismatches: 7, Indels: 1
0.95 0.05 0.01
Matches are distributed among these distances:
50 27 0.19
51 112 0.81
ACGTcount: A:0.32, C:0.18, G:0.23, T:0.27
Consensus pattern (51 bp):
AAAGGTCCGATGACTAAGTGTCATCGTGAGTAAACGAATCCTCTACGGATT
Found at i:166239 original size:17 final size:17
Alignment explanation
Indices: 166200--166237 Score: 51
Period size: 17 Copynumber: 2.3 Consensus size: 17
166190 AACTCCTAAC
* *
166200 CTTTACTATTTTTTTTA
1 CTTTTCTATTTGTTTTA
166217 CTTTTCTATTTGTTTT-
1 CTTTTCTATTTGTTTTA
166233 CTTTT
1 CTTTT
166238 TCAATTTGTA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
16 5 0.26
17 14 0.74
ACGTcount: A:0.11, C:0.13, G:0.03, T:0.74
Consensus pattern (17 bp):
CTTTTCTATTTGTTTTA
Found at i:174734 original size:19 final size:19
Alignment explanation
Indices: 174718--174761 Score: 56
Period size: 19 Copynumber: 2.3 Consensus size: 19
174708 AAGGAAAATG
174718 AGAAAA-AGAAAGAAAAAA
1 AGAAAAGAGAAAGAAAAAA
174736 AGAAAAGAGAAA-ACAAAAGA
1 AGAAAAGAGAAAGA-AAAA-A
174756 AGAAAA
1 AGAAAA
174762 AAATGTTTGC
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
18 7 0.30
19 9 0.39
20 7 0.30
ACGTcount: A:0.80, C:0.02, G:0.18, T:0.00
Consensus pattern (19 bp):
AGAAAAGAGAAAGAAAAAA
Found at i:174742 original size:13 final size:13
Alignment explanation
Indices: 174705--174764 Score: 52
Period size: 14 Copynumber: 4.5 Consensus size: 13
174695 CAGTCACTTG
*
174705 AAAAAGGAAAATGA
1 AAAAAAGAAAA-GA
*
174719 GAAAAAG-AAAGA
1 AAAAAAGAAAAGA
174731 AAAAAAGAAAAGA
1 AAAAAAGAAAAGA
174744 GAAAACAA-AAGAAGA
1 -AAAA-AAGAA-AAGA
174759 AAAAAA
1 AAAAAA
174765 TGTTTGCTAT
Statistics
Matches: 39, Mismatches: 3, Indels: 9
0.76 0.06 0.18
Matches are distributed among these distances:
12 8 0.21
13 10 0.26
14 15 0.38
15 6 0.15
ACGTcount: A:0.78, C:0.02, G:0.18, T:0.02
Consensus pattern (13 bp):
AAAAAAGAAAAGA
Found at i:174745 original size:25 final size:26
Alignment explanation
Indices: 174705--174762 Score: 75
Period size: 26 Copynumber: 2.2 Consensus size: 26
174695 CAGTCACTTG
*
174705 AAAAAGGAAAATGAGAAAA-AGAAAGA
1 AAAAAAGAAAATGAGAAAACA-AAAGA
174731 AAAAAAGAAAA-GAGAAAACAAAAGA
1 AAAAAAGAAAATGAGAAAACAAAAGA
174756 AGAAAAA
1 A-AAAAA
174763 AATGTTTGCT
Statistics
Matches: 29, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
25 13 0.45
26 16 0.55
ACGTcount: A:0.78, C:0.02, G:0.19, T:0.02
Consensus pattern (26 bp):
AAAAAAGAAAATGAGAAAACAAAAGA
Found at i:176683 original size:21 final size:21
Alignment explanation
Indices: 176659--176724 Score: 54
Period size: 21 Copynumber: 3.4 Consensus size: 21
176649 AGCCTAATAA
176659 GCACAAAGCCCGATTACACCG
1 GCACAAAGCCCGATTACACCG
*
176680 GCACGAAG-CC---TACTA--G
1 GCACAAAGCCCGATTAC-ACCG
*
176696 GCACAAACCCCGATTACACCG
1 GCACAAAGCCCGATTACACCG
*
176717 ACACAAAG
1 GCACAAAG
176725 TCTACTAGGC
Statistics
Matches: 33, Mismatches: 5, Indels: 14
0.63 0.10 0.27
Matches are distributed among these distances:
16 7 0.21
17 5 0.15
18 1 0.03
19 1 0.03
20 5 0.15
21 14 0.42
ACGTcount: A:0.36, C:0.36, G:0.18, T:0.09
Consensus pattern (21 bp):
GCACAAAGCCCGATTACACCG
Found at i:176689 original size:37 final size:37
Alignment explanation
Indices: 176639--176894 Score: 257
Period size: 37 Copynumber: 6.9 Consensus size: 37
176629 TTCTTTGGTA
** * * *
176639 ACCAGCAAAAAGCCTAATAAGCACAAAGCCCGATTAC
1 ACCAGCACGAAGCCTACTAGGCACAAAGCCCGAATAC
* * *
176676 ACCGGCACGAAGCCTACTAGGCACAAACCCCGATTAC
1 ACCAGCACGAAGCCTACTAGGCACAAAGCCCGAATAC
* *
176713 ACC-GACACAAAGTCTACTAGGCACAAAG-CCGAATAC
1 ACCAG-CACGAAGCCTACTAGGCACAAAGCCCGAATAC
* * * *
176749 ATCAACACGAAGCCTACTAGGCATATAGCCCGAATAC
1 ACCAGCACGAAGCCTACTAGGCACAAAGCCCGAATAC
* * * *
176786 ACCAGCATGAAGCTTACTAGGCACATAGCCCGAAAAC
1 ACCAGCACGAAGCCTACTAGGCACAAAGCCCGAATAC
* * * * *
176823 ACCAGCACAAAGCCTATTAAGCACATAGCTCGAATAC
1 ACCAGCACGAAGCCTACTAGGCACAAAGCCCGAATAC
*
176860 ACCGGCACGAAGCCTACTAGGCACACAA-CCCGAAT
1 ACCAGCACGAAGCCTACTAGGCACA-AAGCCCGAAT
176895 TTTTAGATGC
Statistics
Matches: 180, Mismatches: 35, Indels: 8
0.81 0.16 0.04
Matches are distributed among these distances:
36 29 0.16
37 150 0.83
38 1 0.01
ACGTcount: A:0.39, C:0.32, G:0.17, T:0.12
Consensus pattern (37 bp):
ACCAGCACGAAGCCTACTAGGCACAAAGCCCGAATAC
Found at i:176847 original size:110 final size:111
Alignment explanation
Indices: 176665--176882 Score: 278
Period size: 110 Copynumber: 2.0 Consensus size: 111
176655 ATAAGCACAA
* * ** *
176665 AGCCCGATTACACCGGCACGAAGCCTACTAGGCACAAACCCCGATTACACCGACACAAAGTCTAC
1 AGCCCGAATACACCAGCACGAAGCCTACTAGGCACAAACCCCGAAAACACCGACACAAAGCCTAC
* *
176730 TAGGCACAAAGC-CGAATACATCAACACGAAGCCTACTAGGCATAT
66 TAAGCACAAAGCTCGAATACACCAACACGAAGCCTACTAGGCATAT
* * * *
176775 AGCCCGAATACACCAGCATGAAGCTTACTAGGCACATAGCCCGAAAACACC-AGCACAAAGCCTA
1 AGCCCGAATACACCAGCACGAAGCCTACTAGGCACAAACCCCGAAAACACCGA-CACAAAGCCTA
* * **
176839 TTAAGCACATAGCTCGAATACACCGGCACGAAGCCTACTAGGCA
65 CTAAGCACAAAGCTCGAATACACCAACACGAAGCCTACTAGGCA
176883 CACAACCCGA
Statistics
Matches: 91, Mismatches: 15, Indels: 3
0.83 0.14 0.03
Matches are distributed among these distances:
109 1 0.01
110 63 0.69
111 27 0.30
ACGTcount: A:0.37, C:0.32, G:0.18, T:0.13
Consensus pattern (111 bp):
AGCCCGAATACACCAGCACGAAGCCTACTAGGCACAAACCCCGAAAACACCGACACAAAGCCTAC
TAAGCACAAAGCTCGAATACACCAACACGAAGCCTACTAGGCATAT
Found at i:180264 original size:137 final size:138
Alignment explanation
Indices: 179904--180457 Score: 884
Period size: 137 Copynumber: 4.0 Consensus size: 138
179894 AACATAGATC
* *
179904 TAATTAATATATGAATTTGATTCATACAAAATATTAATTATATATATTTTACCAAATTTATTAAT
1 TAATTAATATATGAATTTGATTCATACAAAATATTAATTGTATATATTTTACCGAATTTATTAAT
* * * *
179969 ATAAACAGTTATATTAATTAATTTTGGTCAAAATATAAAATATATGAAAATTAATATTCTTTTGA
66 ATAAACAGTTATATTAATTAATTTCGGTCAAAATATAAAAGACATGAAAATTAATATTCTTTTGG
180034 AAAGAATA
131 AAAGAATA
180042 TAATTAATATATGAATTTGATTCATACAAAATATTAAATTGTATATATTTTACCGAATTTATTAA
1 TAATTAATATATGAATTTGATTCATACAAAATATT-AATTGTATATATTTTACCGAATTTATTAA
* * *
180107 TATAAACAGTTCTATTAATTAATTTCGATCAAAATATAAAACACATGAAAATTAATATTC-TTTG
65 TATAAACAGTTATATTAATTAATTTCGGTCAAAATATAAAAGACATGAAAATTAATATTCTTTTG
180171 GAAAGAATA
130 GAAAGAATA
* *
180180 TAATTAATATATGAATTTGATTCATATAAAATATTAATTGTATATAATTTACCGAATTTATTAAT
1 TAATTAATATATGAATTTGATTCATACAAAATATTAATTGTATATATTTTACCGAATTTATTAAT
* *
180245 ATAAACAATTATATTAATTAATTTCGGTCAAAATATAAAAGACAT-AGAAATTAATATTATTTT-
66 ATAAACAGTTATATTAATTAATTTCGGTCAAAATATAAAAGACATGA-AAATTAATATTCTTTTG
180308 GAAAGAATA
130 GAAAGAATA
* * *
180317 TAATTAATATATAAATTTGATTCATAAAAAATATTAATTGTATATATTTTACCTAATTTATTAAT
1 TAATTAATATATGAATTTGATTCATACAAAATATTAATTGTATATATTTTACCGAATTTATTAAT
* * *
180382 AT--ATAGTTATATTAATTAATTTCGGTCAAAATATAAAAGACATAAAAATTAATATTCTTTTAG
66 ATAAACAGTTATATTAATTAATTTCGGTCAAAATATAAAAGACATGAAAATTAATATTCTTTTGG
180445 AAAGAATA
131 AAAGAATA
180453 TAATT
1 TAATT
180458 CATTTTCTAA
Statistics
Matches: 389, Mismatches: 22, Indels: 12
0.92 0.05 0.03
Matches are distributed among these distances:
135 54 0.14
136 16 0.04
137 153 0.39
138 84 0.22
139 82 0.21
ACGTcount: A:0.47, C:0.06, G:0.06, T:0.41
Consensus pattern (138 bp):
TAATTAATATATGAATTTGATTCATACAAAATATTAATTGTATATATTTTACCGAATTTATTAAT
ATAAACAGTTATATTAATTAATTTCGGTCAAAATATAAAAGACATGAAAATTAATATTCTTTTGG
AAAGAATA
Found at i:180402 original size:276 final size:274
Alignment explanation
Indices: 179904--180457 Score: 857
Period size: 276 Copynumber: 2.0 Consensus size: 274
179894 AACATAGATC
*
179904 TAATTAATATATGAATTTGATTCATACAAAATATTAATTATATATATTTTACCAAATTTATTAAT
1 TAATTAATATATGAATTTGATTCATACAAAATATTAATTATATATAATTTACCAAATTTATTAAT
* * * * *
179969 ATAAACAGTTATATTAATTAATTTTGGTCAAAATATAAAATATATGAAAATTAATATTCTTTTGA
66 ATAAACAATTATATTAATTAATTTCGGTCAAAATATAAAAGACATGAAAATTAATATTATTTTGA
* *
180034 AAAGAATATAATTAATATATGAATTTGATTCATACAAAATATTAAATTGTATATATTTTACCGAA
131 AAAGAATATAATTAATATATAAATTTGATTCATAAAAAATATTAAATTGTATATATTTTACCGAA
*
180099 TTTATTAATATAAACAGTTCTATTAATTAATTTCGATCAAAATATAAAACACATGAAAATTAATA
196 TTTATTAATAT-AACAG-TC-ATTAATTAATTTCGATCAAAATATAAAACACATAAAAATTAATA
*
180164 TTC-TTTGGAAAGAATA
258 TTCTTTTAGAAAGAATA
* * *
180180 TAATTAATATATGAATTTGATTCATATAAAATATTAATTGTATATAATTTACCGAATTTATTAAT
1 TAATTAATATATGAATTTGATTCATACAAAATATTAATTATATATAATTTACCAAATTTATTAAT
180245 ATAAACAATTATATTAATTAATTTCGGTCAAAATATAAAAGACAT-AGAAATTAATATTATTTTG
66 ATAAACAATTATATTAATTAATTTCGGTCAAAATATAAAAGACATGA-AAATTAATATTATTTTG
*
180309 -AAAGAATATAATTAATATATAAATTTGATTCATAAAAAATATT-AATTGTATATATTTTACCTA
130 AAAAGAATATAATTAATATATAAATTTGATTCATAAAAAATATTAAATTGTATATATTTTACCGA
* * * *
180372 ATTTATTAATAT-ATAGTTATATTAATTAATTTCGGTCAAAATATAAAAGACATAAAAATTAATA
195 ATTTATTAATATAACAG-T-CATTAATTAATTTCGATCAAAATATAAAACACATAAAAATTAATA
180436 TTCTTTTAGAAAGAATA
258 TTCTTTTAGAAAGAATA
180453 TAATT
1 TAATT
180458 CATTTTCTAA
Statistics
Matches: 257, Mismatches: 18, Indels: 9
0.90 0.06 0.03
Matches are distributed among these distances:
272 49 0.19
273 17 0.07
274 31 0.12
275 42 0.16
276 118 0.46
ACGTcount: A:0.47, C:0.06, G:0.06, T:0.41
Consensus pattern (274 bp):
TAATTAATATATGAATTTGATTCATACAAAATATTAATTATATATAATTTACCAAATTTATTAAT
ATAAACAATTATATTAATTAATTTCGGTCAAAATATAAAAGACATGAAAATTAATATTATTTTGA
AAAGAATATAATTAATATATAAATTTGATTCATAAAAAATATTAAATTGTATATATTTTACCGAA
TTTATTAATATAACAGTCATTAATTAATTTCGATCAAAATATAAAACACATAAAAATTAATATTC
TTTTAGAAAGAATA
Found at i:183901 original size:23 final size:23
Alignment explanation
Indices: 183869--184143 Score: 300
Period size: 23 Copynumber: 12.0 Consensus size: 23
183859 GTTCTTATAC
*
183869 TTATACTTAAATATTAATAG-GAT
1 TTATGCTTAAATATTAAT-GTGAT
* *
183892 TTATGATTAAATAATAATGTGAT
1 TTATGCTTAAATATTAATGTGAT
* **
183915 TTGTGCTTAAGCATTAATGTGAT
1 TTATGCTTAAATATTAATGTGAT
*
183938 TTATGCTTAAATATTAATATGAT
1 TTATGCTTAAATATTAATGTGAT
* * *
183961 TTGTGCTCAAGTATTAATGTGAT
1 TTATGCTTAAATATTAATGTGAT
* *
183984 TTATGTTTAAATATTAACGTGAT
1 TTATGCTTAAATATTAATGTGAT
* *
184007 TTATGTTTAAATATTAATATGAT
1 TTATGCTTAAATATTAATGTGAT
* * *
184030 CTGTGCTCAAATATTAATGTGAT
1 TTATGCTTAAATATTAATGTGAT
* *
184053 TTATACTTAAATATTAATATGAT
1 TTATGCTTAAATATTAATGTGAT
* *
184076 TTGTGCTTAAATATAAATGTGAT
1 TTATGCTTAAATATTAATGTGAT
* * * *
184099 TTGTGCTTAAAAATGAATATGAT
1 TTATGCTTAAATATTAATGTGAT
*
184122 TTATGATTAAATATTAATGTGA
1 TTATGCTTAAATATTAATGTGA
184144 AATTGTGAAT
Statistics
Matches: 206, Mismatches: 45, Indels: 2
0.81 0.18 0.01
Matches are distributed among these distances:
22 1 0.00
23 205 1.00
ACGTcount: A:0.37, C:0.05, G:0.14, T:0.45
Consensus pattern (23 bp):
TTATGCTTAAATATTAATGTGAT
Found at i:183985 original size:69 final size:69
Alignment explanation
Indices: 183869--184143 Score: 334
Period size: 69 Copynumber: 4.0 Consensus size: 69
183859 GTTCTTATAC
* * * * * * * **
183869 TTATACTTAAATATTAATAGGATTTATGATTAAATAATAATGTGATTTGTGCTTAAGCATTAATG
1 TTATGCTTAAATATTAATATGATTTGTGCTCAAATATTAATGTGATTTATGCTTAAATATTAATG
183934 TGAT
66 TGAT
* * *
183938 TTATGCTTAAATATTAATATGATTTGTGCTCAAGTATTAATGTGATTTATGTTTAAATATTAACG
1 TTATGCTTAAATATTAATATGATTTGTGCTCAAATATTAATGTGATTTATGCTTAAATATTAATG
184003 TGAT
66 TGAT
* * * *
184007 TTATGTTTAAATATTAATATGATCTGTGCTCAAATATTAATGTGATTTATACTTAAATATTAATA
1 TTATGCTTAAATATTAATATGATTTGTGCTCAAATATTAATGTGATTTATGCTTAAATATTAATG
184072 TGAT
66 TGAT
* * * * * * * *
184076 TTGTGCTTAAATATAAATGTGATTTGTGCTTAAAAATGAATATGATTTATGATTAAATATTAATG
1 TTATGCTTAAATATTAATATGATTTGTGCTCAAATATTAATGTGATTTATGCTTAAATATTAATG
184141 TGA
66 TGA
184144 AATTGTGAAT
Statistics
Matches: 175, Mismatches: 31, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
69 175 1.00
ACGTcount: A:0.37, C:0.05, G:0.14, T:0.45
Consensus pattern (69 bp):
TTATGCTTAAATATTAATATGATTTGTGCTCAAATATTAATGTGATTTATGCTTAAATATTAATG
TGAT
Found at i:187230 original size:18 final size:18
Alignment explanation
Indices: 187204--187238 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
187194 TATTTTGATC
*
187204 TTTTTATTATAATTTTTA
1 TTTTCATTATAATTTTTA
*
187222 TTTTCATTATTATTTTT
1 TTTTCATTATAATTTTT
187239 TAGGTTTAAT
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.23, C:0.03, G:0.00, T:0.74
Consensus pattern (18 bp):
TTTTCATTATAATTTTTA
Found at i:190186 original size:18 final size:19
Alignment explanation
Indices: 190146--190186 Score: 50
Period size: 19 Copynumber: 2.2 Consensus size: 19
190136 TAAGCCCCTT
*
190146 TTTATTTTTTTCTTCAAAT
1 TTTATTTTTTTCTTCAAAC
190165 TTTATTTTTGTT-TT-AAAC
1 TTTATTTTT-TTCTTCAAAC
190183 TTTA
1 TTTA
190187 CCCTCTGATT
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
18 7 0.35
19 11 0.55
20 2 0.10
ACGTcount: A:0.22, C:0.07, G:0.02, T:0.68
Consensus pattern (19 bp):
TTTATTTTTTTCTTCAAAC
Found at i:196036 original size:52 final size:52
Alignment explanation
Indices: 195973--196077 Score: 201
Period size: 52 Copynumber: 2.0 Consensus size: 52
195963 TATGGAATTG
*
195973 AACATTCTCTACTCATCAAATTAATTGTTCAAATCATGATTTGTTAACATTT
1 AACATACTCTACTCATCAAATTAATTGTTCAAATCATGATTTGTTAACATTT
196025 AACATACTCTACTCATCAAATTAATTGTTCAAATCATGATTTGTTAACATTT
1 AACATACTCTACTCATCAAATTAATTGTTCAAATCATGATTTGTTAACATTT
196077 A
1 A
196078 CGCACTTGAA
Statistics
Matches: 52, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
52 52 1.00
ACGTcount: A:0.36, C:0.17, G:0.06, T:0.41
Consensus pattern (52 bp):
AACATACTCTACTCATCAAATTAATTGTTCAAATCATGATTTGTTAACATTT
Found at i:198633 original size:232 final size:229
Alignment explanation
Indices: 198128--198585 Score: 659
Period size: 232 Copynumber: 2.0 Consensus size: 229
198118 GTAGATCTGT
* * * * * * * *
198128 ACACTAAGACAGACAAAATTGTCAATGTAATTATAAAAGTTAATTGTCAAATCAATTGAAAGTAA
1 ACACTAAGATAGTCAAAATCGACAATGTAATCACAAAA-TTAATTGTAAAATCAACTGAAAGTAA
*
198193 ATCAAATTATTGTTAAATTGTTAAGAATTTAAATGCATGAAAGTAAAGTATGATCAAGTGTGAAG
65 ATCAAATTATTGTTAAATTGTTAAGAATTTAAATGCATGAAAGTAAAGTATGATCAAGTGCGAAG
* *
198258 AATTGGAGTGGATCATTGATTTTACTAAGTAGCAATGCTAGATAAGTCGACAAGGTATTGTATAG
130 AATTGGAATGGATCATTGA--TTA-TAAGTAGCAACGCTAGATAAGTCGACAAGGTATTGTATAG
*
198323 ACGAATTGTTGCAGCACTAAAGCTCCAATGAAATCTGC
192 ACGAATTGTTGCAGCACTAAAGCTCCAATGAAATCTCC
* * * *
198361 ACACTAAGATAGTCAAAATTGTCAATGTAATTATAAAATTAATTGTAAAATCAACTGAAAGTAAA
1 ACACTAAGATAGTCAAAATCGACAATGTAATCACAAAATTAATTGTAAAATCAACTGAAAGTAAA
* * *
198426 TCAATTTGTTGTTGAATTGTTAAGAATTTAAATGCATGAAAGTAAAGTATGATCAAGTGCGAAGA
66 TCAAATTATTGTTAAATTGTTAAGAATTTAAATGCATGAAAGTAAAGTATGATCAAGTGCGAAGA
*** *
198491 ATTGGAATGGATCATTGA-T-TAAGTAGCAACGCTAGATGCTTCGACAAGGTATTGTATAGAGGA
131 ATTGGAATGGATCATTGATTATAAGTAGCAACGCTAGATAAGTCGACAAGGTATTGTATAGACGA
198554 ATTGTTGCAGCACTAAAGCTCCAATGAAATCT
196 ATTGTTGCAGCACTAAAGCTCCAATGAAATCT
198586 TACCAATTAC
Statistics
Matches: 211, Mismatches: 14, Indels: 6
0.91 0.06 0.03
Matches are distributed among these distances:
227 71 0.34
229 1 0.00
232 103 0.49
233 36 0.17
ACGTcount: A:0.40, C:0.11, G:0.19, T:0.30
Consensus pattern (229 bp):
ACACTAAGATAGTCAAAATCGACAATGTAATCACAAAATTAATTGTAAAATCAACTGAAAGTAAA
TCAAATTATTGTTAAATTGTTAAGAATTTAAATGCATGAAAGTAAAGTATGATCAAGTGCGAAGA
ATTGGAATGGATCATTGATTATAAGTAGCAACGCTAGATAAGTCGACAAGGTATTGTATAGACGA
ATTGTTGCAGCACTAAAGCTCCAATGAAATCTCC
Found at i:199650 original size:17 final size:17
Alignment explanation
Indices: 199625--199666 Score: 57
Period size: 17 Copynumber: 2.4 Consensus size: 17
199615 ATGCAACTAT
*
199625 AATGCAAATGTATTAACA
1 AATG-AAATGTAGTAACA
*
199643 AATGAAATGTAGTGACA
1 AATGAAATGTAGTAACA
199660 AATGAAA
1 AATGAAA
199667 ATGCAATGAC
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
17 18 0.82
18 4 0.18
ACGTcount: A:0.52, C:0.07, G:0.17, T:0.24
Consensus pattern (17 bp):
AATGAAATGTAGTAACA
Found at i:199676 original size:18 final size:17
Alignment explanation
Indices: 199640--199678 Score: 51
Period size: 18 Copynumber: 2.2 Consensus size: 17
199630 AAATGTATTA
* *
199640 ACAAATGAAATGTAGTG
1 ACAAATGAAATGCAATG
199657 ACAAATGAAAATGCAATG
1 ACAAATG-AAATGCAATG
199675 ACAA
1 ACAA
199679 CTAAATAAAA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
17 7 0.37
18 12 0.63
ACGTcount: A:0.54, C:0.10, G:0.18, T:0.18
Consensus pattern (17 bp):
ACAAATGAAATGCAATG
Found at i:199821 original size:21 final size:19
Alignment explanation
Indices: 199788--199833 Score: 58
Period size: 21 Copynumber: 2.3 Consensus size: 19
199778 AGGGGCTCAC
199788 CTTCTTTTTTGCGC-TTCTT
1 CTTCTTTTTTGCGCTTTC-T
199807 CTTCTTATCTTTGCGCTTTCT
1 CTTCTT-T-TTTGCGCTTTCT
199828 CTTCTT
1 CTTCTT
199834 GTCCTTCGAA
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
19 6 0.25
20 1 0.04
21 14 0.58
22 3 0.12
ACGTcount: A:0.02, C:0.28, G:0.09, T:0.61
Consensus pattern (19 bp):
CTTCTTTTTTGCGCTTTCT
Found at i:202032 original size:14 final size:14
Alignment explanation
Indices: 202013--202051 Score: 53
Period size: 14 Copynumber: 2.8 Consensus size: 14
202003 GCATACAATT
202013 TAAAAGGAAACAAA
1 TAAAAGGAAACAAA
*
202027 TAAAAGTGAAA-AGA
1 TAAAAG-GAAACAAA
202041 TAAAAGGAAAC
1 TAAAAGGAAAC
202052 GCAAAAATGC
Statistics
Matches: 22, Mismatches: 1, Indels: 4
0.81 0.04 0.15
Matches are distributed among these distances:
13 4 0.18
14 14 0.64
15 4 0.18
ACGTcount: A:0.67, C:0.05, G:0.18, T:0.10
Consensus pattern (14 bp):
TAAAAGGAAACAAA
Found at i:208350 original size:20 final size:20
Alignment explanation
Indices: 208325--208373 Score: 55
Period size: 20 Copynumber: 2.5 Consensus size: 20
208315 AATGATTTAC
208325 CAAAATTTCTAACACTTCAA
1 CAAAATTTCTAACACTTCAA
* * *
208345 CTAAATCTT-TAAGACTTTAA
1 CAAAAT-TTCTAACACTTCAA
208365 CAAAATTTC
1 CAAAATTTC
208374 AAAGGATTTA
Statistics
Matches: 23, Mismatches: 4, Indels: 4
0.74 0.13 0.13
Matches are distributed among these distances:
19 2 0.09
20 19 0.83
21 2 0.09
ACGTcount: A:0.43, C:0.20, G:0.02, T:0.35
Consensus pattern (20 bp):
CAAAATTTCTAACACTTCAA
Found at i:208401 original size:20 final size:19
Alignment explanation
Indices: 208367--208481 Score: 79
Period size: 20 Copynumber: 5.8 Consensus size: 19
208357 GACTTTAACA
* * *
208367 AAATTTCAAAGGATTTATC
1 AAATTTCTAACGATTTACC
208386 AAATTATCTAACGATTTACC
1 AAATT-TCTAACGATTTACC
*
208406 ATAATTTTTAACGATTTACC
1 A-AATTTCTAACGATTTACC
* **
208426 AATATTTCTAA-TACTTCCCC
1 AA-ATTTCTAACGA-TTTACC
* *
208446 AATATTTCTAATGATTTACA
1 AA-ATTTCTAACGATTTACC
* *
208466 AAATTTTTAACAATTT
1 AAATTTCTAACGATTT
208482 TCTTTTATTT
Statistics
Matches: 76, Mismatches: 15, Indels: 10
0.75 0.15 0.10
Matches are distributed among these distances:
19 18 0.24
20 53 0.70
21 5 0.07
ACGTcount: A:0.38, C:0.16, G:0.04, T:0.42
Consensus pattern (19 bp):
AAATTTCTAACGATTTACC
Found at i:208561 original size:20 final size:19
Alignment explanation
Indices: 208539--208660 Score: 91
Period size: 20 Copynumber: 6.2 Consensus size: 19
208529 GTTTAACATT
208539 TTTACCAAAATATCTAAAA
1 TTTACCAAAATATCTAAAA
*
208558 TTTTACCAAAATATTTAACAA
1 -TTTACCAAAATATCTAA-AA
* **
208579 ATTATTAAAATATCTAAAA
1 TTTACCAAAATATCTAAAA
* *
208598 CTTTACCAATATATTTATAAA
1 -TTTACCAAAATATCTA-AAA
* ** * *
208619 TTTATCAATTTTTATATAAA
1 TTTACCAAAATATCTA-AAA
*
208639 TTTACCAAAATATCTAATA
1 TTTACCAAAATATCTAAAA
208658 TTT
1 TTT
208661 TAGTAAAATT
Statistics
Matches: 79, Mismatches: 20, Indels: 7
0.75 0.19 0.07
Matches are distributed among these distances:
19 7 0.09
20 67 0.85
21 5 0.06
ACGTcount: A:0.47, C:0.11, G:0.00, T:0.42
Consensus pattern (19 bp):
TTTACCAAAATATCTAAAA
Found at i:208563 original size:40 final size:39
Alignment explanation
Indices: 208517--208614 Score: 115
Period size: 40 Copynumber: 2.4 Consensus size: 39
208507 ATTTTCCAAG
* **
208517 ACTTTACCAAATGTTTAACATTTTTACCAAAATATCTAAA
1 ACTTTACCAAATATTTAACA-AATTACCAAAATATCTAAA
* **
208557 ATTTTACCAAAATATTTAACAAATTATTAAAATATCTAAA
1 ACTTTACC-AAATATTTAACAAATTACCAAAATATCTAAA
208597 ACTTTACCAATATATTTA
1 ACTTTACCAA-ATATTTA
208615 TAAATTTATC
Statistics
Matches: 49, Mismatches: 7, Indels: 4
0.82 0.12 0.07
Matches are distributed among these distances:
39 2 0.04
40 36 0.73
41 11 0.22
ACGTcount: A:0.46, C:0.14, G:0.01, T:0.39
Consensus pattern (39 bp):
ACTTTACCAAATATTTAACAAATTACCAAAATATCTAAA
Found at i:209427 original size:3 final size:3
Alignment explanation
Indices: 209419--209458 Score: 55
Period size: 3 Copynumber: 13.3 Consensus size: 3
209409 TTACCTCCGC
*
209419 CTT CTT CTT CTT CTT CTT CTT CTT CTC CTT CGTT -TT CTT C
1 CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT C-TT CTT CTT C
209459 ACATTGTTTT
Statistics
Matches: 33, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
2 2 0.06
3 29 0.88
4 2 0.06
ACGTcount: A:0.00, C:0.35, G:0.03, T:0.62
Consensus pattern (3 bp):
CTT
Found at i:219201 original size:73 final size:73
Alignment explanation
Indices: 219078--219215 Score: 206
Period size: 73 Copynumber: 1.9 Consensus size: 73
219068 GGAGGAATTA
*
219078 TATGAAATTGTGATTTCACGTTATTCATATCACTTATCAATAAGAGAATGACAAATCAGATTTTT
1 TATGAAATTGTGATTTCACGTTATTCATATCACTTATCAATAAGAAAATGACAAATCAGATTTTT
219143 TCGGATTG
66 TCGGATTG
* * * * *
219151 TATGAAATTGTGATTTTACGTTATTCATAT-ATTTTTTCAATATGAAAATGACAAATTAGATTTT
1 TATGAAATTGTGATTTCACGTTATTCATATCA-CTTATCAATAAGAAAATGACAAATCAGATTTT
219215 T
65 T
219216 CCTTTTGATT
Statistics
Matches: 58, Mismatches: 6, Indels: 2
0.88 0.09 0.03
Matches are distributed among these distances:
72 1 0.02
73 57 0.98
ACGTcount: A:0.35, C:0.09, G:0.13, T:0.43
Consensus pattern (73 bp):
TATGAAATTGTGATTTCACGTTATTCATATCACTTATCAATAAGAAAATGACAAATCAGATTTTT
TCGGATTG
Found at i:222099 original size:57 final size:58
Alignment explanation
Indices: 222009--222127 Score: 195
Period size: 57 Copynumber: 2.1 Consensus size: 58
221999 AAAATGAGTT
* *
222009 GTTTATGAGTGTTATTTAGGAATAAAATTATATTTGGGTTTAAAAATATTTGGGTTTA
1 GTTTATGAGTGTTATTTAAGAATAAAATTATATTTGGATTTAAAAATATTTGGGTTTA
* *
222067 GTTTATGAGT-TTTTTTAAGAATGAAATTATATTTGGATTTAAAAATATTTGGGTTTA
1 GTTTATGAGTGTTATTTAAGAATAAAATTATATTTGGATTTAAAAATATTTGGGTTTA
222124 GTTT
1 GTTT
222128 GTTGATGGTT
Statistics
Matches: 57, Mismatches: 4, Indels: 1
0.92 0.06 0.02
Matches are distributed among these distances:
57 47 0.82
58 10 0.18
ACGTcount: A:0.32, C:0.00, G:0.19, T:0.49
Consensus pattern (58 bp):
GTTTATGAGTGTTATTTAAGAATAAAATTATATTTGGATTTAAAAATATTTGGGTTTA
Found at i:222140 original size:57 final size:57
Alignment explanation
Indices: 222009--222141 Score: 178
Period size: 57 Copynumber: 2.3 Consensus size: 57
221999 AAAATGAGTT
* * *
222009 GTTTATGAGTGTTATTTAGGAATAAAATTATATTTGGGTTTAAAAATATTTGGGTTTA
1 GTTTATGAGTGGT-TTTAAGAATAAAATTATATTTGGATTTAAAAATATTTGGGTTTA
** *
222067 GTTTATGAGTTTTTTTAAGAATGAAATTATATTTGGATTTAAAAATATTTGGGTTTA
1 GTTTATGAGTGGTTTTAAGAATAAAATTATATTTGGATTTAAAAATATTTGGGTTTA
*
222124 GTTTGTTGA-TGGTTTTAA
1 GTTT-ATGAGTGGTTTTAA
222142 ATATTAGGGA
Statistics
Matches: 67, Mismatches: 7, Indels: 3
0.87 0.09 0.04
Matches are distributed among these distances:
57 52 0.78
58 15 0.22
ACGTcount: A:0.31, C:0.00, G:0.20, T:0.49
Consensus pattern (57 bp):
GTTTATGAGTGGTTTTAAGAATAAAATTATATTTGGATTTAAAAATATTTGGGTTTA
Found at i:222851 original size:15 final size:15
Alignment explanation
Indices: 222833--222902 Score: 68
Period size: 15 Copynumber: 4.7 Consensus size: 15
222823 TTGCAATGTG
*
222833 AGTGCTTGCAACATT
1 AGTGCTCGCAACATT
* * *
222848 AGTGCTCACAGCTTT
1 AGTGCTCGCAACATT
* * *
222863 AGTGTTCGCAGCATG
1 AGTGCTCGCAACATT
*
222878 AGTGCTCGCAACACT
1 AGTGCTCGCAACATT
222893 AGTGCTCGCA
1 AGTGCTCGCA
222903 TCTTCCATGC
Statistics
Matches: 43, Mismatches: 12, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
15 43 1.00
ACGTcount: A:0.23, C:0.26, G:0.24, T:0.27
Consensus pattern (15 bp):
AGTGCTCGCAACATT
Found at i:222917 original size:45 final size:45
Alignment explanation
Indices: 222831--222917 Score: 104
Period size: 45 Copynumber: 1.9 Consensus size: 45
222821 GTTTGCAATG
* * * *
222831 TGAGTGCTTGCAACATTAGTGCTCACAGCTTTAGTGTTCGCAGCA
1 TGAGTGCTCGCAACACTAGTGCTCACAGCTTCAGTGCTCGCAGCA
* *
222876 TGAGTGCTCGCAACACTAGTGCTCGCATCTTCCA-TGCTCGCA
1 TGAGTGCTCGCAACACTAGTGCTCACAGCTT-CAGTGCTCGCA
222918 TCAGAAAGTT
Statistics
Matches: 35, Mismatches: 6, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
45 34 0.97
46 1 0.03
ACGTcount: A:0.21, C:0.28, G:0.23, T:0.29
Consensus pattern (45 bp):
TGAGTGCTCGCAACACTAGTGCTCACAGCTTCAGTGCTCGCAGCA
Found at i:227252 original size:50 final size:50
Alignment explanation
Indices: 227198--227315 Score: 182
Period size: 50 Copynumber: 2.4 Consensus size: 50
227188 AATTCGATCC
* * *
227198 TTGCAACTTCAGGGATATAAGATTTTGGGTTGTAGCTTCATCTTGCTCCA
1 TTGCAACTTTAGGGATATAAGATTTTGAGTTGTAACTTCATCTTGCTCCA
*
227248 TTGCAACTTTAAGGATATAAGATTTTGAGTTGTAACTTCATCTTGCTCCA
1 TTGCAACTTTAGGGATATAAGATTTTGAGTTGTAACTTCATCTTGCTCCA
* *
227298 CTGTAACTTTAGGGATAT
1 TTGCAACTTTAGGGATAT
227316 CATATTTGCC
Statistics
Matches: 61, Mismatches: 7, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
50 61 1.00
ACGTcount: A:0.25, C:0.16, G:0.19, T:0.39
Consensus pattern (50 bp):
TTGCAACTTTAGGGATATAAGATTTTGAGTTGTAACTTCATCTTGCTCCA
Found at i:227454 original size:98 final size:98
Alignment explanation
Indices: 227283--227821 Score: 445
Period size: 98 Copynumber: 5.5 Consensus size: 98
227273 TGAGTTGTAA
** * * * *
227283 CTTCATCTTGCTCCACTGTAACTT-TAGG-GATATCATATTTGCCAATATTAGTTTTAATCCGAT
1 CTTCATCTTGCTCCACTACAACTTCAAGGAGATA-AAGATTTGCCAATATTAGTTTTAATTCGAT
* ** * *
227346 CCCTATAACTTTAGGGATATAGGATTTGGTATGG
65 CACTGCAACTTCAGGGATATAGGATTTGGTGTGG
* ** * *
227380 CTTCATCTTGCTCTACTGTAACTTCAAGGAGATAAAGATTTTCCAATGTTAGTTTTAATTCGATC
1 CTTCATCTTGCTCCACTACAACTTCAAGGAGATAAAGATTTGCCAATATTAGTTTTAATTCGATC
*
227445 ACTGCAACTTCAGGGATATAAGATTTGGTGTCGTAG
66 ACTGCAACTTCAGGGATATAGGATTTGGTGT-G--G
* * *
227481 CTTCAGCATCTTGCTCTACTACAACTTCAAAGAGATAAAGATTTG-C--TACTA-TTTTAATTCG
1 CTT---CATCTTGCTCCACTACAACTTCAAGGAGATAAAGATTTGCCAATATTAGTTTTAATTCG
* * *
227542 TTTCA-TGGCAACTTCAGGAAGATAGGATTTGGTGTGG
63 -ATCACT-GCAACTTCAGGGATATAGGATTTGGTGTGG
* * * * *
227579 CTTCATCTTACTCCACTACAACTTCAGGGAGATAAAGATTTGCCAATGTTAGTTTTAATCCTATC
1 CTTCATCTTGCTCCACTACAACTTCAAGGAGATAAAGATTTGCCAATATTAGTTTTAATTCGATC
* * * * ** *
227644 CCTGTAACTTTAGAGATATAAAATTAGGTGTTGCAG
66 ACTGCAACTTCAGGGATATAGGATTTGGTG-TG--G
* * * * * *
227680 CTTCATCTTGCTTCACTACAACTTTAGGGAGATAAAGATTT---TATACT-GTTTTAA-TCTGCT
1 CTTCATCTTGCTCCACTACAACTTCAAGGAGATAAAGATTTGCCAATATTAGTTTTAATTC-G-A
* * *
227740 TCACTGCAACTTCAGGAAGATAGGTTTTGGTGTGG
64 TCACTGCAACTTCAGGGATATAGGATTTGGTGTGG
* * *
227775 CTTCATCTTGCTCCACTGCAACTTCAGGGAGATAAATATTTGCCAAT
1 CTTCATCTTGCTCCACTACAACTTCAAGGAGATAAAGATTTGCCAAT
227822 GAGACTTGTA
Statistics
Matches: 354, Mismatches: 65, Indels: 45
0.76 0.14 0.10
Matches are distributed among these distances:
95 73 0.21
96 2 0.01
97 32 0.09
98 109 0.31
99 16 0.05
100 12 0.03
101 74 0.21
103 1 0.00
104 35 0.10
ACGTcount: A:0.28, C:0.18, G:0.18, T:0.36
Consensus pattern (98 bp):
CTTCATCTTGCTCCACTACAACTTCAAGGAGATAAAGATTTGCCAATATTAGTTTTAATTCGATC
ACTGCAACTTCAGGGATATAGGATTTGGTGTGG
Found at i:227773 original size:196 final size:197
Alignment explanation
Indices: 227364--227822 Score: 611
Period size: 196 Copynumber: 2.3 Consensus size: 197
227354 CTTTAGGGAT
* * * * *
227364 ATAGGATTTGGTATGGCTTCATCTTGCTCTACTGTAACTTCAAGGAGATAAAGATTTTCCAATGT
1 ATAGGATTTGGTGTGGCTTCATCTTGCTCCACTGCAACTTCAGGGAGATAAAGATTTGCCAATGT
* * * * *
227429 TAGTTTTAATTCGATCACTGCAACTTCAGGGATATAAGATTTGGTGTCGTAGCTTCAGCATCTTG
66 TAGTTTTAATCCGATCACTGCAACTTCAGAGATATAAAATTAGGTGTCGCAGCTT-A-CATCTTG
* *
227494 CTCTACTACAACTTCAAAGAGATAAAGATTTGCTACTATTTTAATTCGTTTCATGGCAACTTCAG
129 CTCTACTACAACTTCAAAGAGATAAAGATTTGATACTATTTTAATTCGCTTCATGGCAACTTCAG
227559 GAAG
194 GAAG
* *
227563 ATAGGATTTGGTGTGGCTTCATCTTACTCCACTACAACTTCAGGGAGATAAAGATTTGCCAATGT
1 ATAGGATTTGGTGTGGCTTCATCTTGCTCCACTGCAACTTCAGGGAGATAAAGATTTGCCAATGT
* * * * *
227628 TAGTTTTAATCCTATCCCTGTAACTTTAGAGATATAAAATTAGGTGTTGCAGCTT-CATCTTGCT
66 TAGTTTTAATCCGATCACTGCAACTTCAGAGATATAAAATTAGGTGTCGCAGCTTACATCTTGCT
* ** * *
227692 -TCACTACAACTTTAGGGAGATAAAGATTTTATACTGTTTTAA-TCTGCTTCACT-GCAACTTCA
131 CT-ACTACAACTTCAAAGAGATAAAGATTTGATACTATTTTAATTC-GCTTCA-TGGCAACTTCA
227754 GGAAG
193 GGAAG
* *
227759 ATAGGTTTTGGTGTGGCTTCATCTTGCTCCACTGCAACTTCAGGGAGATAAATATTTGCCAATG
1 ATAGGATTTGGTGTGGCTTCATCTTGCTCCACTGCAACTTCAGGGAGATAAAGATTTGCCAATG
227823 AGACTTGTAG
Statistics
Matches: 229, Mismatches: 28, Indels: 9
0.86 0.11 0.03
Matches are distributed among these distances:
195 3 0.01
196 122 0.53
197 1 0.00
199 103 0.45
ACGTcount: A:0.28, C:0.18, G:0.19, T:0.36
Consensus pattern (197 bp):
ATAGGATTTGGTGTGGCTTCATCTTGCTCCACTGCAACTTCAGGGAGATAAAGATTTGCCAATGT
TAGTTTTAATCCGATCACTGCAACTTCAGAGATATAAAATTAGGTGTCGCAGCTTACATCTTGCT
CTACTACAACTTCAAAGAGATAAAGATTTGATACTATTTTAATTCGCTTCATGGCAACTTCAGGA
AG
Found at i:239774 original size:26 final size:26
Alignment explanation
Indices: 239745--239798 Score: 63
Period size: 26 Copynumber: 2.1 Consensus size: 26
239735 CACCCAGGAA
239745 TGTCACTGCATGAACATATCCAGAAT
1 TGTCACTGCATGAACATATCCAGAAT
** ** *
239771 TGTCGTTGCATGAATGTGTCCAGAAT
1 TGTCACTGCATGAACATATCCAGAAT
239797 TG
1 TG
239799 CACCCAAAAT
Statistics
Matches: 23, Mismatches: 5, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
26 23 1.00
ACGTcount: A:0.28, C:0.19, G:0.22, T:0.31
Consensus pattern (26 bp):
TGTCACTGCATGAACATATCCAGAAT
Found at i:240630 original size:16 final size:16
Alignment explanation
Indices: 240609--240639 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
240599 TTGTGGATCC
240609 CATTTTACCTTTATTA
1 CATTTTACCTTTATTA
*
240625 CATTTTATCTTTATT
1 CATTTTACCTTTATT
240640 TTTACATTAT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.23, C:0.16, G:0.00, T:0.61
Consensus pattern (16 bp):
CATTTTACCTTTATTA
Found at i:254647 original size:15 final size:15
Alignment explanation
Indices: 254627--254662 Score: 63
Period size: 15 Copynumber: 2.3 Consensus size: 15
254617 AATTTACGTG
254627 CAAGTAAAATCTTTC
1 CAAGTAAAATCTTTC
254642 CAAGTAAAATCTTTC
1 CAAGTAAAATCTTTC
254657 CTAAGT
1 C-AAGT
254663 CAAGTAGGGT
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
15 16 0.80
16 4 0.20
ACGTcount: A:0.39, C:0.19, G:0.08, T:0.33
Consensus pattern (15 bp):
CAAGTAAAATCTTTC
Found at i:255660 original size:50 final size:50
Alignment explanation
Indices: 255548--255776 Score: 209
Period size: 50 Copynumber: 4.7 Consensus size: 50
255538 CTACTAATCA
* * * * *
255548 AACCAATCTTGTGACCTAAGGTAGA--CT-TT-GTGTTTTATGTTTAACG
1 AACCAATCTTGCGACCTAAGGCAGACTCTGTTCATGTTTTCTGTTTAATG
* *
255594 AACCAATCTTGTGACCTAAGGCAGACTCTGTTCATGTTTTCTATTTAATG
1 AACCAATCTTGCGACCTAAGGCAGACTCTGTTCATGTTTTCTGTTTAATG
* * * * * *
255644 AACCAGTCTTACGACCTAAGGTAGA-TCCAGTTCGTGTTTTCTG-CTAATTG
1 AACCAATCTTGCGACCTAAGGCAGACT-CTGTTCATGTTTTCTGTTTAA-TG
* * *
255694 AACCAATCTTGCAACCTAAGGCAGAATCTGTTCATGTTTTTTGTTTAATG
1 AACCAATCTTGCGACCTAAGGCAGACTCTGTTCATGTTTTCTGTTTAATG
** * * *
255744 AACCAGCCTTGTGACTTAAGGTAGACTCTGTTC
1 AACCAATCTTGCGACCTAAGGCAGACTCTGTTC
255777 GTATGTGTGA
Statistics
Matches: 147, Mismatches: 28, Indels: 12
0.79 0.15 0.06
Matches are distributed among these distances:
46 24 0.16
48 2 0.01
49 6 0.04
50 111 0.76
51 4 0.03
ACGTcount: A:0.26, C:0.20, G:0.18, T:0.36
Consensus pattern (50 bp):
AACCAATCTTGCGACCTAAGGCAGACTCTGTTCATGTTTTCTGTTTAATG
Found at i:257303 original size:27 final size:26
Alignment explanation
Indices: 257265--257337 Score: 119
Period size: 26 Copynumber: 2.8 Consensus size: 26
257255 AAACACGCTA
*
257265 GAAATATGAAAGAGTAGTCTTTTTAGT
1 GAAATATGAAAGAGTAG-CCTTTTAGT
*
257292 GAAATATGAAAGAGTAGCCTTTTGGT
1 GAAATATGAAAGAGTAGCCTTTTAGT
257318 GAAATATGAAAGAGTAGCCT
1 GAAATATGAAAGAGTAGCCT
257338 CTGTGGAGAA
Statistics
Matches: 44, Mismatches: 2, Indels: 1
0.94 0.04 0.02
Matches are distributed among these distances:
26 27 0.61
27 17 0.39
ACGTcount: A:0.38, C:0.07, G:0.25, T:0.30
Consensus pattern (26 bp):
GAAATATGAAAGAGTAGCCTTTTAGT
Found at i:257321 original size:26 final size:26
Alignment explanation
Indices: 257265--257354 Score: 126
Period size: 27 Copynumber: 3.4 Consensus size: 26
257255 AAACACGCTA
* *
257265 GAAATATGAAAGAGTAGTCTTTTTAGT
1 GAAATATGAAAGAGTAG-CCTTTTGGT
257292 GAAATATGAAAGAGTAGCCTTTTGGT
1 GAAATATGAAAGAGTAGCCTTTTGGT
* *
257318 GAAATATGAAAGAGTAGCCTCTGTGGA
1 GAAATATGAAAGAGTAGCCT-TTTGGT
257345 GAAATATGAA
1 GAAATATGAA
257355 GGAATGTCTT
Statistics
Matches: 58, Mismatches: 4, Indels: 2
0.91 0.06 0.03
Matches are distributed among these distances:
26 27 0.47
27 31 0.53
ACGTcount: A:0.39, C:0.07, G:0.26, T:0.29
Consensus pattern (26 bp):
GAAATATGAAAGAGTAGCCTTTTGGT
Found at i:259852 original size:39 final size:41
Alignment explanation
Indices: 259765--259855 Score: 105
Period size: 41 Copynumber: 2.3 Consensus size: 41
259755 TGTAACGGGT
* * ** *
259765 CTTGAGCCTAGCAGGCTTTATGTTGGTGTATTGTATCGAGC
1 CTTGAGCCTAGCAAGCTTAATGCCGGTGTACTGTATCGAGC
*
259806 CTTGAGCCTAGCAAGCTTAATGCCGGTG-ACT-TATCGGGC
1 CTTGAGCCTAGCAAGCTTAATGCCGGTGTACTGTATCGAGC
*
259845 TTTGAGCCTAG
1 CTTGAGCCTAG
259856 TAGGCTTCGT
Statistics
Matches: 43, Mismatches: 7, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
39 17 0.40
40 2 0.05
41 24 0.56
ACGTcount: A:0.19, C:0.21, G:0.29, T:0.32
Consensus pattern (41 bp):
CTTGAGCCTAGCAAGCTTAATGCCGGTGTACTGTATCGAGC
Found at i:263984 original size:30 final size:30
Alignment explanation
Indices: 263878--264210 Score: 119
Period size: 30 Copynumber: 11.3 Consensus size: 30
263868 CAAAAATCAT
* *
263878 ATTTTAACC-CTTAAAATTCTCCAAAATTGT
1 ATTTTAACCAC-TAAACTTCTCCAAAATTGC
* * **
263908 ATTTTAACTACTAAACTTTTTGAAAATTGC
1 ATTTTAACCACTAAACTTCTCCAAAATTGC
263938 ATTTTAACCTA-TAAACTTCTCCAAAATTGC
1 ATTTTAACC-ACTAAACTTCTCCAAAATTGC
* * * * **
263968 ATTTTGACCCCCAAACTTCTCAAAAATCAC
1 ATTTTAACCACTAAACTTCTCCAAAATTGC
* * **
263998 A-TTGACCCA-TAAACCTT-TCCAAAATCCC
1 ATTTTAACCACTAAA-CTTCTCCAAAATTGC
* * **
264026 ATTTTCACC-CATAATA-TTTTCCAAAATCAC
1 ATTTTAACCAC-TAA-ACTTCTCCAAAATTGC
* * **
264056 ATTTTGACCTC-AAACTTC-CCTAAAATTAT
1 ATTTTAACCACTAAACTTCTCC-AAAATTGC
*
264085 GTTTTAACC-CTAAACCTTC-CCAAAATCT-C
1 ATTTTAACCACTAAA-CTTCTCCAAAAT-TGC
* * *
264114 ATTTTAACC-CCAAACTT-TCATAAAATTAC
1 ATTTTAACCACTAAACTTCTC-CAAAATTGC
* **
264143 CTTTTAACTC-CTAAA-TTCTTCCAAAATTAA
1 ATTTTAAC-CACTAAACTTC-TCCAAAATTGC
* *
264173 ATTTTAACC-CCAAA-TTCTCTAAAAGTT-C
1 ATTTTAACCACTAAACTTCTCCAAAA-TTGC
264201 ATTTTTAACC
1 A-TTTTAACC
264211 CCATTTTTTT
Statistics
Matches: 235, Mismatches: 45, Indels: 47
0.72 0.14 0.14
Matches are distributed among these distances:
28 29 0.12
29 83 0.35
30 117 0.50
31 6 0.03
ACGTcount: A:0.36, C:0.26, G:0.03, T:0.36
Consensus pattern (30 bp):
ATTTTAACCACTAAACTTCTCCAAAATTGC
Found at i:263994 original size:60 final size:60
Alignment explanation
Indices: 263837--264000 Score: 177
Period size: 60 Copynumber: 2.7 Consensus size: 60
263827 CCTATTTTGT
* * * *
263837 TCCAAAATTTCATTTTGACTCTTGAACTTTTCAAAAATCATATTTTAACCCTTAAAATTC
1 TCCAAAATTGCATTTTGACTCCTAAACTTTTCAAAAATCACATTTTAACCCTTAAAATTC
* * * ** ** *
263897 TCCAAAATTGTATTTTAACTACTAAACTTTTTGAAAATTGCATTTTAA-CCTATAAACTTC
1 TCCAAAATTGCATTTTGACTCCTAAACTTTTCAAAAATCACATTTTAACCCT-TAAAATTC
* * *
263957 TCCAAAATTGCATTTTGACCCCCAAACTTCTCAAAAATCACATT
1 TCCAAAATTGCATTTTGACTCCTAAACTTTTCAAAAATCACATT
264001 GACCCATAAA
Statistics
Matches: 81, Mismatches: 22, Indels: 2
0.77 0.21 0.02
Matches are distributed among these distances:
59 3 0.04
60 78 0.96
ACGTcount: A:0.36, C:0.21, G:0.04, T:0.38
Consensus pattern (60 bp):
TCCAAAATTGCATTTTGACTCCTAAACTTTTCAAAAATCACATTTTAACCCTTAAAATTC
Found at i:264011 original size:28 final size:28
Alignment explanation
Indices: 263948--264028 Score: 65
Period size: 28 Copynumber: 2.8 Consensus size: 28
263938 ATTTTAACCT
* **
263948 ATAAACTTCTCCAAAATTGCATTTTGACCC
1 ATAAACTTCT-CAAAAAT-CACATTGACCC
**
263978 CCAAACTTCTCAAAAATCACATTGACCC
1 ATAAACTTCTCAAAAATCACATTGACCC
* *
264006 ATAAACCTT-TCCAAAATCCCATT
1 ATAAA-CTTCTCAAAAATCACATT
264029 TTCACCCATA
Statistics
Matches: 41, Mismatches: 9, Indels: 4
0.76 0.17 0.07
Matches are distributed among these distances:
28 24 0.59
29 9 0.22
30 8 0.20
ACGTcount: A:0.37, C:0.31, G:0.04, T:0.28
Consensus pattern (28 bp):
ATAAACTTCTCAAAAATCACATTGACCC
Found at i:264108 original size:58 final size:57
Alignment explanation
Indices: 264044--264211 Score: 178
Period size: 58 Copynumber: 2.9 Consensus size: 57
264034 CCATAATATT
* *
264044 TTCCAAAATCACATTTTGACCTCAAACTTCCCTAAAATTATGTTTTAACCCTAAA-CC
1 TTCCAAAATCACATTTTAACCCCAAACTTCCCTAAAATTAT-TTTTAACCCTAAATCC
* * * * *
264101 TTCCCAAAATCTCATTTTAACCCCAAACTTTCATAAAATTACCTTTTAACTCCTAAATTC
1 TT-CCAAAATCACATTTTAACCCCAAACTTCCCTAAAATTA-TTTTTAAC-CCTAAATCC
* * *
264161 TTCCAAAATTAAATTTTAACCCCAAA-TTCTCTAAAAGTTCATTTTTAACCC
1 TTCCAAAATCACATTTTAACCCCAAACTTCCCTAAAA-TT-ATTTTTAACCC
264212 CATTTTTTTT
Statistics
Matches: 91, Mismatches: 14, Indels: 11
0.78 0.12 0.09
Matches are distributed among these distances:
57 2 0.02
58 49 0.54
59 36 0.40
60 4 0.04
ACGTcount: A:0.36, C:0.27, G:0.02, T:0.36
Consensus pattern (57 bp):
TTCCAAAATCACATTTTAACCCCAAACTTCCCTAAAATTATTTTTAACCCTAAATCC
Found at i:264147 original size:29 final size:29
Alignment explanation
Indices: 264046--264186 Score: 108
Period size: 29 Copynumber: 4.8 Consensus size: 29
264036 ATAATATTTT
* * *
264046 CCAAAATCACATTTTGACCTCAAAC-TTC
1 CCAAAATTACATTTTAACCCCAAACTTTC
** * *
264074 CCTAAAATTATGTTTTAACCCTAAACCTTC
1 CC-AAAATTACATTTTAACCCCAAACTTTC
264104 CCAAAATCT-CATTTTAACCCCAAACTTTC
1 CCAAAAT-TACATTTTAACCCCAAACTTTC
** * * *
264133 ATAAAATTACCTTTTAACTCCTAAA-TTCTT
1 CCAAAATTACATTTTAAC-CCCAAACTT-TC
*
264163 CCAAAATTAAATTTTAACCCCAAA
1 CCAAAATTACATTTTAACCCCAAA
264187 TTCTCTAAAA
Statistics
Matches: 87, Mismatches: 20, Indels: 11
0.74 0.17 0.09
Matches are distributed among these distances:
28 3 0.03
29 58 0.67
30 26 0.30
ACGTcount: A:0.38, C:0.28, G:0.01, T:0.33
Consensus pattern (29 bp):
CCAAAATTACATTTTAACCCCAAACTTTC
Found at i:264206 original size:29 final size:27
Alignment explanation
Indices: 264056--264213 Score: 86
Period size: 29 Copynumber: 5.4 Consensus size: 27
264046 CCAAAATCAC
* * *
264056 ATTTTGACCTCAAACTTCCCTAAAATTA
1 ATTTTAACCCCAAA-TTCTCTAAAATTA
* * * *
264084 TGTTTTAACCCTAAACCTTC-CCAAAATCTC
1 -ATTTTAACCCCAAA--TTCTCTAAAAT-TA
264114 ATTTTAACCCCAAACTT-TCATAAAATTA
1 ATTTTAACCCCAAA-TTCTC-TAAAATTA
* * *
264142 CCTTTTAACTCCTAAATTCTTCCAAAATTAA
1 -ATTTTAAC-CCCAAATTC-TCTAAAATT-A
264173 ATTTTAACCCCAAATTCTCTAAAAGTTCA
1 ATTTTAACCCCAAATTCTCTAAAA-TT-A
*
264202 TTTTTAACCCCA
1 ATTTTAACCCCA
264214 TTTTTTTTAT
Statistics
Matches: 101, Mismatches: 18, Indels: 20
0.73 0.13 0.14
Matches are distributed among these distances:
28 11 0.11
29 64 0.63
30 23 0.23
31 3 0.03
ACGTcount: A:0.35, C:0.27, G:0.02, T:0.36
Consensus pattern (27 bp):
ATTTTAACCCCAAATTCTCTAAAATTA
Found at i:274784 original size:30 final size:30
Alignment explanation
Indices: 274748--274851 Score: 190
Period size: 30 Copynumber: 3.5 Consensus size: 30
274738 ACATGTATGT
*
274748 CACATGGGCGTGTGTCACTCACGGCTAACC
1 CACATGGGCATGTGTCACTCACGGCTAACC
274778 CACATGGGCATGTGTCACTCACGGCTAACC
1 CACATGGGCATGTGTCACTCACGGCTAACC
274808 CACATGGGCATGTGTCACTCACGGCTAACC
1 CACATGGGCATGTGTCACTCACGGCTAACC
*
274838 CACATGGGCGTGTG
1 CACATGGGCATGTG
274852 CCCTGAGCGT
Statistics
Matches: 72, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
30 72 1.00
ACGTcount: A:0.21, C:0.32, G:0.27, T:0.20
Consensus pattern (30 bp):
CACATGGGCATGTGTCACTCACGGCTAACC
Found at i:287111 original size:51 final size:51
Alignment explanation
Indices: 287040--287168 Score: 159
Period size: 51 Copynumber: 2.5 Consensus size: 51
287030 GGATCCAATA
* * * *
287040 ACTAAGTGTCATCGTAAGTAAATGAATGCTTTATGGATTAAAGGTCCGATG
1 ACTAAGTGTCATCGTGAGTAAATGAATCCATGATGGATTAAAGGTCCGATG
* * **
287091 ACTAAGTTTCATCATGAGTAAATGAATCCATGATGGATTAAAGGTTTGATG
1 ACTAAGTGTCATCGTGAGTAAATGAATCCATGATGGATTAAAGGTCCGATG
* * *
287142 ACTCAGTGTCATTGTGAGTATATGAAT
1 ACTAAGTGTCATCGTGAGTAAATGAAT
287169 TCCTATACGG
Statistics
Matches: 65, Mismatches: 13, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
51 65 1.00
ACGTcount: A:0.33, C:0.11, G:0.22, T:0.33
Consensus pattern (51 bp):
ACTAAGTGTCATCGTGAGTAAATGAATCCATGATGGATTAAAGGTCCGATG
Found at i:287243 original size:61 final size:61
Alignment explanation
Indices: 287163--287341 Score: 236
Period size: 61 Copynumber: 3.0 Consensus size: 61
287153 TTGTGAGTAT
* *
287163 ATGAATTCCTATACGGAACAAGAGGTCTGATTACTATATGTCATCGTGAGTATTAAATGAA
1 ATGAGTTCCTATACGGAACAAGAGGTCTGATGACTATATGTCATCGTGAGTATTAAATGAA
* *
287224 ATGAGTTCCTATACGGAACAATAGGTTTGATGACTATATGTCATCGTGAGTATTAAATGAA
1 ATGAGTTCCTATACGGAACAAGAGGTCTGATGACTATATGTCATCGTGAGTATTAAATGAA
* * * * * * * *
287285 ATGAGTTCCAATGC-AAACAAG-GGTCCGATGACTTTGTGTCATCATGAGTAATAAATG
1 ATGAGTTCCTATACGGAACAAGAGGTCTGATGACTATATGTCATCGTGAGTATTAAATG
287342 CGAGTGAAAC
Statistics
Matches: 104, Mismatches: 14, Indels: 2
0.87 0.12 0.02
Matches are distributed among these distances:
59 30 0.29
60 5 0.05
61 69 0.66
ACGTcount: A:0.35, C:0.13, G:0.21, T:0.31
Consensus pattern (61 bp):
ATGAGTTCCTATACGGAACAAGAGGTCTGATGACTATATGTCATCGTGAGTATTAAATGAA
Found at i:291016 original size:59 final size:61
Alignment explanation
Indices: 290839--291017 Score: 238
Period size: 61 Copynumber: 3.0 Consensus size: 61
290829 TCGTGAGTGT
* * * * *
290839 ATGAATTCCTATACGGAATAAGAGGTCTGATGACTATATGTCATCGTGAGTATTAAATGAA
1 ATGAGTTCCTATATGGAACAAGAGGTCCGATGACTATATGTCATCGTGAGTATTAAATAAA
* *
290900 ATGAGTTCCTATATGGAACAAGAGGTCCGATGACTACATGTCATCGTGAATATTAAATAAA
1 ATGAGTTCCTATATGGAACAAGAGGTCCGATGACTATATGTCATCGTGAGTATTAAATAAA
* * *
290961 ATGAGTTCC-A-ATGCGAACAAG-GGTCCGATGACTTTGTGTCATCGTGAGTAATAAATA
1 ATGAGTTCCTATATG-GAACAAGAGGTCCGATGACTATATGTCATCGTGAGTATTAAATA
291018 CGAGTGAAAC
Statistics
Matches: 105, Mismatches: 12, Indels: 4
0.87 0.10 0.03
Matches are distributed among these distances:
59 34 0.32
60 8 0.08
61 63 0.60
ACGTcount: A:0.35, C:0.14, G:0.22, T:0.29
Consensus pattern (61 bp):
ATGAGTTCCTATATGGAACAAGAGGTCCGATGACTATATGTCATCGTGAGTATTAAATAAA
Found at i:291487 original size:21 final size:21
Alignment explanation
Indices: 291461--291515 Score: 101
Period size: 21 Copynumber: 2.6 Consensus size: 21
291451 TTAGCTTACT
*
291461 TGTTTCGGTAGAACTCATGTG
1 TGTTTCGGTAGAACCCATGTG
291482 TGTTTCGGTAGAACCCATGTG
1 TGTTTCGGTAGAACCCATGTG
291503 TGTTTCGGTAGAA
1 TGTTTCGGTAGAA
291516 GTGCAAGATA
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
21 33 1.00
ACGTcount: A:0.20, C:0.15, G:0.29, T:0.36
Consensus pattern (21 bp):
TGTTTCGGTAGAACCCATGTG
Found at i:291596 original size:22 final size:24
Alignment explanation
Indices: 291554--291611 Score: 59
Period size: 22 Copynumber: 2.5 Consensus size: 24
291544 AACTTGAGTT
291554 GTATCGGTAGTTAAAATTAT-G-A
1 GTATCGGTAGTTAAAATTATGGAA
**
291576 GTATCGGTAGTT-GTATGTATGGAA
1 GTATCGGTAGTTAAAAT-TATGGAA
*
291600 ATATCGGTAGTT
1 GTATCGGTAGTT
291612 TGCATGCTTA
Statistics
Matches: 30, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
21 2 0.07
22 15 0.50
23 1 0.03
24 12 0.40
ACGTcount: A:0.29, C:0.05, G:0.28, T:0.38
Consensus pattern (24 bp):
GTATCGGTAGTTAAAATTATGGAA
Found at i:291713 original size:21 final size:21
Alignment explanation
Indices: 291689--291745 Score: 87
Period size: 21 Copynumber: 2.7 Consensus size: 21
291679 ATGAATGACA
*
291689 TGTATCAATAGAACTTATACT
1 TGTATCAGTAGAACTTATACT
*
291710 TGTATCGGTAGAACTTATACT
1 TGTATCAGTAGAACTTATACT
*
291731 TGTATCTGTAGAACT
1 TGTATCAGTAGAACT
291746 AGTACAGGTA
Statistics
Matches: 33, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
21 33 1.00
ACGTcount: A:0.32, C:0.14, G:0.16, T:0.39
Consensus pattern (21 bp):
TGTATCAGTAGAACTTATACT
Found at i:296945 original size:10 final size:10
Alignment explanation
Indices: 296916--296950 Score: 52
Period size: 10 Copynumber: 3.3 Consensus size: 10
296906 ACTCGATTTT
296916 AAATTTCAAG
1 AAATTTCAAG
296926 AAATTCTTCAAG
1 AAA-T-TTCAAG
296938 AAATTTCAAG
1 AAATTTCAAG
296948 AAA
1 AAA
296951 AGGCATGGAT
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
10 12 0.52
11 2 0.09
12 9 0.39
ACGTcount: A:0.51, C:0.11, G:0.09, T:0.29
Consensus pattern (10 bp):
AAATTTCAAG
Found at i:298989 original size:2 final size:2
Alignment explanation
Indices: 298984--299022 Score: 69
Period size: 2 Copynumber: 19.5 Consensus size: 2
298974 CAAACACACC
*
298984 CT CT CT CT CT CT CT CT CT CT TT CT CT CT CT CT CT CT CT C
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT C
299023 CACATGCACA
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.00, C:0.49, G:0.00, T:0.51
Consensus pattern (2 bp):
CT
Found at i:300978 original size:20 final size:20
Alignment explanation
Indices: 300940--300979 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 20
300930 AGTTGAACAG
*
300940 ATCCAAGAAAGTGTATCAGA
1 ATCCAAGAAAGGGTATCAGA
300960 ATCCAAGAAAGAGGT-TCAGA
1 ATCCAAGAAAG-GGTATCAGA
300980 GAGAAGGAAT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 16 0.89
21 2 0.11
ACGTcount: A:0.45, C:0.15, G:0.23, T:0.17
Consensus pattern (20 bp):
ATCCAAGAAAGGGTATCAGA
Found at i:306780 original size:2 final size:2
Alignment explanation
Indices: 306773--306909 Score: 103
Period size: 2 Copynumber: 68.5 Consensus size: 2
306763 GTACATTTTC
* * * * * * * *
306773 AT AT AT AT AT AT AC AC AT AT AC AC AT AT AC AC AT AT AC AC AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
* * * *
306815 AT AT AC AT AC AT AT AT AC AT AC 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
* * * * * * *
306857 AT AT AC AT AT AC AC AT AT AC AC AT AT AC AT AT AT AC 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
306899 AT AT AT AT AT A
1 AT AT AT AT AT A
306910 CCAATTTGAT
Statistics
Matches: 109, Mismatches: 26, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
2 109 1.00
ACGTcount: A:0.50, C:0.14, G:0.00, T:0.36
Consensus pattern (2 bp):
AT
Found at i:306909 original size:8 final size:8
Alignment explanation
Indices: 306772--306907 Score: 137
Period size: 8 Copynumber: 17.0 Consensus size: 8
306762 GGTACATTTT
306772 CATATATA
1 CATATATA
* *
306780 TATATACA
1 CATATATA
*
306788 CATATACA
1 CATATATA
*
306796 CATATACA
1 CATATATA
*
306804 CATATACA
1 CATATATA
306812 CATATATA
1 CATATATA
*
306820 CATACATA
1 CATATATA
* *
306828 TATACATA
1 CATATATA
306836 CATATATA
1 CATATATA
*
306844 TATATATA
1 CATATATA
*
306852 TATATATA
1 CATATATA
* *
306860 TACATATA
1 CATATATA
*
306868 CACATATA
1 CATATATA
*
306876 CACATATA
1 CATATATA
306884 CATATATA
1 CATATATA
306892 CATATATA
1 CATATATA
*
306900 TATATATA
1 CATATATA
306908 TACCAATTTG
Statistics
Matches: 115, Mismatches: 13, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
8 115 1.00
ACGTcount: A:0.50, C:0.15, G:0.00, T:0.35
Consensus pattern (8 bp):
CATATATA
Found at i:310090 original size:15 final size:16
Alignment explanation
Indices: 310072--310109 Score: 51
Period size: 15 Copynumber: 2.4 Consensus size: 16
310062 TGTTTATTTC
310072 TTGTTTTCAATTGT-T
1 TTGTTTTCAATTGTAT
* *
310087 TTGTTTTCTATTTTAT
1 TTGTTTTCAATTGTAT
310103 TTGTTTT
1 TTGTTTT
310110 GTTTCTATTT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
15 12 0.60
16 8 0.40
ACGTcount: A:0.11, C:0.05, G:0.11, T:0.74
Consensus pattern (16 bp):
TTGTTTTCAATTGTAT
Found at i:310121 original size:21 final size:21
Alignment explanation
Indices: 310082--310120 Score: 71
Period size: 20 Copynumber: 1.9 Consensus size: 21
310072 TTGTTTTCAA
310082 TTGTTTTGTTTTCTATTTTAT
1 TTGTTTTGTTTTCTATTTTAT
310103 TTGTTTTG-TTTCTATTTT
1 TTGTTTTGTTTTCTATTTT
310121 TGTTTTAGTT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
20 10 0.56
21 8 0.44
ACGTcount: A:0.08, C:0.05, G:0.10, T:0.77
Consensus pattern (21 bp):
TTGTTTTGTTTTCTATTTTAT
Found at i:310273 original size:21 final size:20
Alignment explanation
Indices: 310233--310273 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 20
310223 TGTTTTTTAG
* *
310233 TCATTTTAGTATTTATTATT
1 TCATTTTAGTAGTTAGTATT
310253 TCATTTTCAGTAGTTAGTATT
1 TCATTTT-AGTAGTTAGTATT
310274 AAAAGATAAT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
20 7 0.39
21 11 0.61
ACGTcount: A:0.24, C:0.07, G:0.10, T:0.59
Consensus pattern (20 bp):
TCATTTTAGTAGTTAGTATT
Found at i:312201 original size:27 final size:27
Alignment explanation
Indices: 312154--312207 Score: 74
Period size: 27 Copynumber: 2.0 Consensus size: 27
312144 AGAGAATTAC
* *
312154 CCCATGTTTATTGTCTCGATGGACTCT
1 CCCATGTTTACTGTCTCGATGAACTCT
312181 CCCATGTTTACTGTC-CTGATGAACTCT
1 CCCATGTTTACTGTCTC-GATGAACTCT
312208 TTATGTTGCC
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
26 1 0.04
27 23 0.96
ACGTcount: A:0.17, C:0.28, G:0.17, T:0.39
Consensus pattern (27 bp):
CCCATGTTTACTGTCTCGATGAACTCT
Found at i:321100 original size:31 final size:31
Alignment explanation
Indices: 321038--321146 Score: 107
Period size: 31 Copynumber: 3.5 Consensus size: 31
321028 TATATAAAAA
* * *
321038 ATTAGATTATTGAAATATTTCATGTATCATTAT
1 ATTAAATTATTTAAATA--TCATTTATCATTAT
321071 ATTAAATTATTTAAATATCATTTATCATTAT
1 ATTAAATTATTTAAATATCATTTATCATTAT
* * *
321102 ATTAAAATT-TTTAAATCTTATTT-TTATTAT
1 ATT-AAATTATTTAAATATCATTTATCATTAT
321132 ATTTAAA-TATTTAAA
1 A-TTAAATTATTTAAA
321147 AATATTTTTT
Statistics
Matches: 67, Mismatches: 6, Indels: 9
0.82 0.07 0.11
Matches are distributed among these distances:
29 1 0.01
30 16 0.24
31 30 0.45
32 5 0.07
33 15 0.22
ACGTcount: A:0.40, C:0.05, G:0.03, T:0.52
Consensus pattern (31 bp):
ATTAAATTATTTAAATATCATTTATCATTAT
Found at i:321156 original size:30 final size:30
Alignment explanation
Indices: 321066--321164 Score: 87
Period size: 30 Copynumber: 3.3 Consensus size: 30
321056 TTCATGTATC
* *
321066 ATTATA-TTAAATTATTTAAATATCATTTATC
1 ATTATATTTAAA-TATTTAAATAT-ATTTTTT
* * *
321097 ATTATATTAAAATTTTTAAATCT-TATTTTT
1 ATTATATTTAAATATTTAAATATAT-TTTTT
*
321127 ATTATATTTAAATATTTAAAAATATTTTTT
1 ATTATATTTAAATATTTAAATATATTTTTT
*
321157 -TGATATTT
1 ATTATATTT
321165 TTATGTTTAT
Statistics
Matches: 55, Mismatches: 10, Indels: 8
0.75 0.14 0.11
Matches are distributed among these distances:
29 8 0.15
30 27 0.49
31 16 0.29
32 4 0.07
ACGTcount: A:0.39, C:0.03, G:0.01, T:0.57
Consensus pattern (30 bp):
ATTATATTTAAATATTTAAATATATTTTTT
Found at i:321157 original size:31 final size:30
Alignment explanation
Indices: 321066--321157 Score: 80
Period size: 31 Copynumber: 3.0 Consensus size: 30
321056 TTCATGTATC
* * *
321066 ATTATATTAAATTATTTAAATATCA-TTTATC
1 ATTATATTAAA-TATTTAAAAAT-ATTTTTTT
** *
321097 ATTATATTAAA-ATTTTTAAATCTTATTTTT
1 ATTATATTAAATATTTAAAAATATT-TTTTT
321127 ATTATATTTAAATATTTAAAAATATTTTTTT
1 ATTATA-TTAAATATTTAAAAATATTTTTTT
321158 GATATTTTTA
Statistics
Matches: 48, Mismatches: 9, Indels: 8
0.74 0.14 0.12
Matches are distributed among these distances:
29 8 0.17
30 9 0.19
31 21 0.44
32 10 0.21
ACGTcount: A:0.40, C:0.03, G:0.00, T:0.57
Consensus pattern (30 bp):
ATTATATTAAATATTTAAAAATATTTTTTT
Found at i:321357 original size:25 final size:25
Alignment explanation
Indices: 321311--321358 Score: 62
Period size: 25 Copynumber: 1.9 Consensus size: 25
321301 TTAAAATTTA
* *
321311 TATTTAATATATTATTATATTAAAT
1 TATTTAATATATCATTAAATTAAAT
321336 TATTTAA-ATATCATATAAATTAA
1 TATTTAATATATCAT-TAAATTAA
321359 TTAAACTTTT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
24 6 0.30
25 14 0.70
ACGTcount: A:0.48, C:0.02, G:0.00, T:0.50
Consensus pattern (25 bp):
TATTTAATATATCATTAAATTAAAT
Found at i:323110 original size:41 final size:41
Alignment explanation
Indices: 322952--323110 Score: 160
Period size: 41 Copynumber: 3.9 Consensus size: 41
322942 AAAAAAGTCA
* * **
322952 CTAAAGGTCAGAA-CATTAGAGGCGTTTATGA-AAAAGTGCCG
1 CTAAAGGTCA-AAGCAATAGCGGCGTTTATGAGAAAA-CACCG
* * * * *
322993 TTAAAGATCAGAGTAATAGCGGCGTTTATGAGAAAGCACCG
1 CTAAAGGTCAAAGCAATAGCGGCGTTTATGAGAAAACACCG
* *
323034 CTAAAGGTCAGAGTAATAGCGGCGTTTATGAGAAAACACCG
1 CTAAAGGTCAAAGCAATAGCGGCGTTTATGAGAAAACACCG
* * *
323075 CTAAATGTCAAAGCATTAGCGGCGTTTATGTGAAAA
1 CTAAAGGTCAAAGCAATAGCGGCGTTTATGAGAAAA
323111 ATGTCGCTAA
Statistics
Matches: 99, Mismatches: 17, Indels: 4
0.82 0.14 0.03
Matches are distributed among these distances:
40 1 0.01
41 95 0.96
42 3 0.03
ACGTcount: A:0.36, C:0.15, G:0.26, T:0.23
Consensus pattern (41 bp):
CTAAAGGTCAAAGCAATAGCGGCGTTTATGAGAAAACACCG
Found at i:323130 original size:41 final size:41
Alignment explanation
Indices: 323007--323136 Score: 147
Period size: 41 Copynumber: 3.2 Consensus size: 41
322997 AGATCAGAGT
* * * *
323007 AATAGCGGCGTTTATGAGAAAGCACCGCTAAAGGTCAGAGT
1 AATAGCGGCGTTTATGAGAAAACACCGCTAAAAGTCAAAGC
*
323048 AATAGCGGCGTTTATGAGAAAACACCGCTAAATGTCAAAGC
1 AATAGCGGCGTTTATGAGAAAACACCGCTAAAAGTCAAAGC
* * * *
323089 ATTAGCGGCGTTTATGTGAAAA-ATGTCGCTAAAAGT-TAAGC
1 AATAGCGGCGTTTATGAGAAAACA--CCGCTAAAAGTCAAAGC
323130 AATAGCG
1 AATAGCG
323137 ATGCTTTCCC
Statistics
Matches: 77, Mismatches: 10, Indels: 4
0.85 0.11 0.04
Matches are distributed among these distances:
40 1 0.01
41 67 0.87
42 9 0.12
ACGTcount: A:0.36, C:0.16, G:0.25, T:0.22
Consensus pattern (41 bp):
AATAGCGGCGTTTATGAGAAAACACCGCTAAAAGTCAAAGC
Found at i:325427 original size:27 final size:27
Alignment explanation
Indices: 325397--325474 Score: 86
Period size: 27 Copynumber: 2.9 Consensus size: 27
325387 ACATTTATTT
*
325397 TAAAACTTAAATAAACTAAAAAAATTC
1 TAAAATTTAAATAAACTAAAAAAATTC
* ** *
325424 TAAAATTTTAAA-AAATTTCAAAAATTT
1 TAAAA-TTTAAATAAACTAAAAAAATTC
*
325451 TAAAATTTATATAAACTAAAAAAA
1 TAAAATTTAAATAAACTAAAAAAA
325475 ATTATATTAT
Statistics
Matches: 40, Mismatches: 9, Indels: 4
0.75 0.17 0.08
Matches are distributed among these distances:
26 5 0.12
27 30 0.75
28 5 0.12
ACGTcount: A:0.62, C:0.06, G:0.00, T:0.32
Consensus pattern (27 bp):
TAAAATTTAAATAAACTAAAAAAATTC
Found at i:325435 original size:19 final size:19
Alignment explanation
Indices: 325413--325455 Score: 68
Period size: 19 Copynumber: 2.3 Consensus size: 19
325403 TTAAATAAAC
*
325413 TAAAAAAATTCTAAAATTT
1 TAAAAAAATTCAAAAATTT
*
325432 TAAAAAATTTCAAAAATTT
1 TAAAAAAATTCAAAAATTT
325451 TAAAA
1 TAAAA
325456 TTTATATAAA
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
19 22 1.00
ACGTcount: A:0.60, C:0.05, G:0.00, T:0.35
Consensus pattern (19 bp):
TAAAAAAATTCAAAAATTT
Found at i:325964 original size:8 final size:8
Alignment explanation
Indices: 325953--325989 Score: 56
Period size: 8 Copynumber: 4.5 Consensus size: 8
325943 TTAATATCAT
*
325953 TATTTAAT
1 TATTTAAA
325961 TATTTAAA
1 TATTTAAA
325969 TATTTAAA
1 TATTTAAA
325977 TATTTATAA
1 TATTTA-AA
325986 TATT
1 TATT
325990 ATAATTTAAA
Statistics
Matches: 27, Mismatches: 1, Indels: 1
0.93 0.03 0.03
Matches are distributed among these distances:
8 21 0.78
9 6 0.22
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (8 bp):
TATTTAAA
Found at i:325974 original size:16 final size:17
Alignment explanation
Indices: 325953--325995 Score: 61
Period size: 16 Copynumber: 2.5 Consensus size: 17
325943 TTAATATCAT
325953 TATTTAATTATTTA-AA
1 TATTTAATTATTTATAA
*
325969 TATTTAAATATTTATAA
1 TATTTAATTATTTATAA
325986 TATTATAATT
1 TATT-TAATT
325996 TAAATTTTGA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
16 13 0.57
17 6 0.26
18 4 0.17
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (17 bp):
TATTTAATTATTTATAA
Done.