Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold928
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: 62206
ACGTcount: A:0.34, C:0.15, G:0.15, T:0.35
Found at i:519 original size:17 final size:17
Alignment explanation
Indices: 499--531 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
489 ATTATTTAAA
499 TAATATTAAAATTTATT
1 TAATATTAAAATTTATT
*
516 TAATATTAATATTTAT
1 TAATATTAAAATTTAT
532 ATTTTATAAT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (17 bp):
TAATATTAAAATTTATT
Found at i:1430 original size:8 final size:8
Alignment explanation
Indices: 1409--1498 Score: 55
Period size: 8 Copynumber: 11.1 Consensus size: 8
1399 ATGTATAATC
*
1409 TATTTAAA
1 TATTTATA
1417 TA-TTATA
1 TATTTATA
1424 TATTTATA
1 TATTTATA
*
1432 TAATTATA
1 TATTTATA
1440 TA-TTACTA
1 TATTTA-TA
1448 -ATTT-T-
1 TATTTATA
1453 TATTATATA
1 TATT-TATA
*
1462 AATTTTAATA
1 TA-TTT-ATA
1472 TATTTATA
1 TATTTATA
*
1480 TATTCATA
1 TATTTATA
1488 TTATATTATA
1 -TAT-TTATA
1498 T
1 T
1499 TAATTTTATA
Statistics
Matches: 65, Mismatches: 6, Indels: 21
0.71 0.07 0.23
Matches are distributed among these distances:
6 4 0.06
7 11 0.17
8 31 0.48
9 9 0.14
10 10 0.15
ACGTcount: A:0.41, C:0.02, G:0.00, T:0.57
Consensus pattern (8 bp):
TATTTATA
Found at i:1731 original size:4 final size:4
Alignment explanation
Indices: 1711--1846 Score: 85
Period size: 4 Copynumber: 34.2 Consensus size: 4
1701 CTTACTGCAA
* * * * * * *
1711 ATAT -TAT ATAT ACAT ATAT ATAT ACAT GTGT ACAT ACAT ATAT ATAC
1 ATAT ATAT ATAT ATAT ATAT ATAT ATAT ATAT ATAT ATAT ATAT ATAT
* * * * * * * * * * *
1758 ATAC ATAT ATAC ATGT ATAC ATAC ACAT GTAT ACAT ACAT ACAT ACAT
1 ATAT ATAT ATAT ATAT ATAT ATAT ATAT ATAT ATAT ATAT ATAT ATAT
* *
1806 ACAT ACAT ATAT ATAT ATAT ATAT ATAT ATAT ATAT ATAT A
1 ATAT ATAT ATAT ATAT ATAT ATAT ATAT ATAT ATAT ATAT A
1847 ACTCCAGCAT
Statistics
Matches: 107, Mismatches: 24, Indels: 2
0.80 0.18 0.02
Matches are distributed among these distances:
3 3 0.03
4 104 0.97
ACGTcount: A:0.47, C:0.12, G:0.03, T:0.38
Consensus pattern (4 bp):
ATAT
Found at i:1757 original size:34 final size:34
Alignment explanation
Indices: 1715--1836 Score: 154
Period size: 34 Copynumber: 3.6 Consensus size: 34
1705 CTGCAAATAT
* *
1715 TATATATACATATATATATACATGTGTACATACA
1 TATATATACATACATATATACATGTATACATACA
1749 TATATATACATACATATATACATGTATACATACA
1 TATATATACATACATATATACATGTATACATACA
* * * ** *
1783 CATGTATACATACATACATACATACATACATATA
1 TATATATACATACATATATACATGTATACATACA
* *
1817 TATATATATATATATATATA
1 TATATATACATACATATATA
1837 TATATATATA
Statistics
Matches: 75, Mismatches: 13, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
34 75 1.00
ACGTcount: A:0.47, C:0.13, G:0.03, T:0.37
Consensus pattern (34 bp):
TATATATACATACATATATACATGTATACATACA
Found at i:1846 original size:12 final size:12
Alignment explanation
Indices: 1715--1842 Score: 107
Period size: 12 Copynumber: 10.7 Consensus size: 12
1705 CTGCAAATAT
1715 TATATATACATA
1 TATATATACATA
*
1727 TATATATACATG
1 TATATATACATA
* *
1739 TGTACATAC--A
1 TATATATACATA
1749 TATATATACATA
1 TATATATACATA
*
1761 CATATATACATGTA
1 TATATATACA--TA
* * *
1775 TACATACACATG
1 TATATATACATA
*
1787 TATACATACATA
1 TATATATACATA
* *
1799 CATACATACATA
1 TATATATACATA
* *
1811 CATATATATATA
1 TATATATACATA
*
1823 TATATATATATA
1 TATATATACATA
1835 TATATATA
1 TATATATA
1843 TATAACTCCA
Statistics
Matches: 93, Mismatches: 19, Indels: 8
0.77 0.16 0.07
Matches are distributed among these distances:
10 7 0.08
12 77 0.83
14 9 0.10
ACGTcount: A:0.47, C:0.12, G:0.03, T:0.38
Consensus pattern (12 bp):
TATATATACATA
Found at i:2291 original size:16 final size:15
Alignment explanation
Indices: 2266--2301 Score: 54
Period size: 16 Copynumber: 2.3 Consensus size: 15
2256 CTCGAGTAAG
2266 TATTTAATATAAATA
1 TATTTAATATAAATA
*
2281 TATTATAATATAATTA
1 TATT-TAATATAAATA
2297 TATTT
1 TATTT
2302 TATTTTTTAA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
15 5 0.26
16 14 0.74
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (15 bp):
TATTTAATATAAATA
Found at i:2907 original size:20 final size:19
Alignment explanation
Indices: 2878--2929 Score: 68
Period size: 20 Copynumber: 2.7 Consensus size: 19
2868 TTCTTTTTAC
*
2878 ATTTTAAAAAATATCTTAT
1 ATTTTTAAAAATATCTTAT
* *
2897 GCTTTTTAAAAATATTTTAT
1 -ATTTTTAAAAATATCTTAT
2917 ATTTTTAAAAATA
1 ATTTTTAAAAATA
2930 ATTAATTTTT
Statistics
Matches: 28, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
19 12 0.43
20 16 0.57
ACGTcount: A:0.44, C:0.04, G:0.02, T:0.50
Consensus pattern (19 bp):
ATTTTTAAAAATATCTTAT
Found at i:2921 original size:19 final size:19
Alignment explanation
Indices: 2872--2929 Score: 71
Period size: 19 Copynumber: 3.0 Consensus size: 19
2862 CTCAAATTCT
* *
2872 TTTTACATTTTAAAAAATA
1 TTTTATATTTTTAAAAATA
* *
2891 TCTTATGCTTTTTAAAAATA
1 TTTTAT-ATTTTTAAAAATA
2911 TTTTATATTTTTAAAAATA
1 TTTTATATTTTTAAAAATA
2930 ATTAATTTTT
Statistics
Matches: 32, Mismatches: 6, Indels: 2
0.80 0.15 0.05
Matches are distributed among these distances:
19 16 0.50
20 16 0.50
ACGTcount: A:0.41, C:0.05, G:0.02, T:0.52
Consensus pattern (19 bp):
TTTTATATTTTTAAAAATA
Found at i:2940 original size:19 final size:19
Alignment explanation
Indices: 2899--2941 Score: 61
Period size: 19 Copynumber: 2.3 Consensus size: 19
2889 TATCTTATGC
* *
2899 TTTTTAAAAATATTTTATA
1 TTTTTAAAAATAATTAATA
2918 TTTTTAAAAATAATTAAT-
1 TTTTTAAAAATAATTAATA
2936 TTTTTA
1 TTTTTA
2942 TTAATCAAAT
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
18 6 0.27
19 16 0.73
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (19 bp):
TTTTTAAAAATAATTAATA
Found at i:3251 original size:50 final size:48
Alignment explanation
Indices: 3149--3259 Score: 122
Period size: 48 Copynumber: 2.3 Consensus size: 48
3139 AATCTACGAG
3149 TTTAA-ATTTATTTTTTAAATATATTAAAATAATAAAAAAATATTTTT
1 TTTAATATTTATTTTTTAAATATATTAAAATAATAAAAAAATATTTTT
* *
3196 ATTAATATTTATATATTTATAATTATATT-AAAT-A-AAAAAAATATTTTAAT
1 TTTAATATTTAT-T-TTT-TAAATATATTAAAATAATAAAAAAATATTTT--T
*
3246 TTTAATATTAATTT
1 TTTAATATTTATTT
3260 AAATTAAATT
Statistics
Matches: 54, Mismatches: 4, Indels: 11
0.78 0.06 0.16
Matches are distributed among these distances:
47 4 0.07
48 20 0.37
49 3 0.06
50 18 0.33
51 9 0.17
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (48 bp):
TTTAATATTTATTTTTTAAATATATTAAAATAATAAAAAAATATTTTT
Found at i:3864 original size:9 final size:9
Alignment explanation
Indices: 3850--3899 Score: 59
Period size: 9 Copynumber: 5.6 Consensus size: 9
3840 TCGTACAAAT
3850 TTTATTATA
1 TTTATTATA
3859 TTTATTAT-
1 TTTATTATA
3867 TTATATTATA
1 TT-TATTATA
*
3877 TATATT-TA
1 TTTATTATA
3885 TATTATTATA
1 T-TTATTATA
3895 TTTAT
1 TTTAT
3900 GTTATGTGAG
Statistics
Matches: 35, Mismatches: 2, Indels: 8
0.78 0.04 0.18
Matches are distributed among these distances:
8 5 0.14
9 26 0.74
10 4 0.11
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (9 bp):
TTTATTATA
Found at i:5758 original size:7 final size:7
Alignment explanation
Indices: 5741--5770 Score: 53
Period size: 7 Copynumber: 4.4 Consensus size: 7
5731 AGATATATAC
5741 TTTTA-T
1 TTTTATT
5747 TTTTATT
1 TTTTATT
5754 TTTTATT
1 TTTTATT
5761 TTTTATT
1 TTTTATT
5768 TTT
1 TTT
5771 GGACTTGTAA
Statistics
Matches: 23, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
6 5 0.22
7 18 0.78
ACGTcount: A:0.13, C:0.00, G:0.00, T:0.87
Consensus pattern (7 bp):
TTTTATT
Found at i:9539 original size:17 final size:17
Alignment explanation
Indices: 9529--9563 Score: 61
Period size: 17 Copynumber: 2.1 Consensus size: 17
9519 TATATGTTTT
9529 ATATAAATATATATTAA
1 ATATAAATATATATTAA
*
9546 ATATAAATATATTTTAA
1 ATATAAATATATATTAA
9563 A
1 A
9564 ATATTTAATT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (17 bp):
ATATAAATATATATTAA
Found at i:9567 original size:25 final size:25
Alignment explanation
Indices: 9539--9594 Score: 60
Period size: 25 Copynumber: 2.2 Consensus size: 25
9529 ATATAAATAT
9539 ATATTAAATATAAATATAT-TTTAAA
1 ATATTAAAT-TAAATATATATTTAAA
* ***
9564 ATATTTAATTTTTTATATATTTAAA
1 ATATTAAATTAAATATATATTTAAA
9589 ATATTA
1 ATATTA
9595 TATTTTAGAT
Statistics
Matches: 25, Mismatches: 5, Indels: 2
0.78 0.16 0.06
Matches are distributed among these distances:
24 6 0.24
25 19 0.76
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (25 bp):
ATATTAAATTAAATATATATTTAAA
Found at i:9645 original size:21 final size:21
Alignment explanation
Indices: 9606--9653 Score: 62
Period size: 21 Copynumber: 2.3 Consensus size: 21
9596 ATTTTAGATT
***
9606 TATATTTAAATATGTATTAAA
1 TATATTTAAATAAAAATTAAA
9627 TATATTTAAATAAAAATTAAA
1 TATATTTAAATAAAAATTAAA
9648 T-TATTT
1 TATATTT
9654 TTAGTTGGAT
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
20 5 0.21
21 19 0.79
ACGTcount: A:0.50, C:0.00, G:0.02, T:0.48
Consensus pattern (21 bp):
TATATTTAAATAAAAATTAAA
Found at i:9748 original size:33 final size:33
Alignment explanation
Indices: 9711--9773 Score: 110
Period size: 33 Copynumber: 1.9 Consensus size: 33
9701 TTAAATTTTT
9711 TAATTTTAAATTAATTGATTT-AATTATTTTGAA
1 TAATTTTAAATTAATT-ATTTGAATTATTTTGAA
9744 TAATTTTAAATTAATTATTTGAATTATTTT
1 TAATTTTAAATTAATTATTTGAATTATTTT
9774 TTATTTAAGT
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
32 4 0.14
33 25 0.86
ACGTcount: A:0.38, C:0.00, G:0.05, T:0.57
Consensus pattern (33 bp):
TAATTTTAAATTAATTATTTGAATTATTTTGAA
Found at i:9781 original size:24 final size:24
Alignment explanation
Indices: 9728--9773 Score: 67
Period size: 23 Copynumber: 2.0 Consensus size: 24
9718 AAATTAATTG
9728 ATTTAATTATTTTGAATAATTTTA
1 ATTTAATTATTTTGAATAATTTTA
* *
9752 AATTAATTA-TTTGAATTATTTT
1 ATTTAATTATTTTGAATAATTTT
9774 TTATTTAAGT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
23 12 0.60
24 8 0.40
ACGTcount: A:0.37, C:0.00, G:0.04, T:0.59
Consensus pattern (24 bp):
ATTTAATTATTTTGAATAATTTTA
Found at i:9809 original size:15 final size:16
Alignment explanation
Indices: 9753--9815 Score: 60
Period size: 15 Copynumber: 4.1 Consensus size: 16
9743 ATAATTTTAA
*
9753 ATTAATTATTTGAATT
1 ATTAATTATTTAAATT
** *
9769 ATTTTTTATTTAAGTT
1 ATTAATTATTTAAATT
9785 AATTAA-T-TTTAAATT
1 -ATTAATTATTTAAATT
9800 ATTAATT-TTTAAATT
1 ATTAATTATTTAAATT
9815 A
1 A
9816 AATTAAATTT
Statistics
Matches: 38, Mismatches: 7, Indels: 5
0.76 0.14 0.10
Matches are distributed among these distances:
14 5 0.13
15 17 0.45
16 13 0.34
17 3 0.08
ACGTcount: A:0.38, C:0.00, G:0.03, T:0.59
Consensus pattern (16 bp):
ATTAATTATTTAAATT
Found at i:9820 original size:31 final size:29
Alignment explanation
Indices: 9698--9838 Score: 99
Period size: 31 Copynumber: 4.6 Consensus size: 29
9688 TATATTTTTA
*
9698 AATTTAAATTTTTTAA-TTTTAAATTAATT
1 AATTTAAA-TTATTAATTTTTAAATTAATT
*
9727 GATTT-AATTATTTTGAATAATTTTAAATTAATT
1 AATTTAAATTA--TT-AAT--TTTTAAATTAATT
* ** *
9760 -ATTTGAATTATTTTTTATTTAAGTTAATT
1 AATTTAAATTATTAATT-TTTAAATTAATT
9789 AATTTTAAATTATTAATTTTTAAATTAAATT
1 AA-TTTAAATTATTAATTTTTAAATT-AATT
* *
9820 AAATTTAAATAAATAATTT
1 -AATTTAAATTATTAATTT
9839 ATATTTTTAA
Statistics
Matches: 89, Mismatches: 11, Indels: 22
0.73 0.09 0.18
Matches are distributed among these distances:
27 2 0.02
28 3 0.03
29 17 0.19
30 11 0.12
31 32 0.36
32 6 0.07
33 18 0.20
ACGTcount: A:0.42, C:0.00, G:0.03, T:0.55
Consensus pattern (29 bp):
AATTTAAATTATTAATTTTTAAATTAATT
Found at i:9832 original size:15 final size:15
Alignment explanation
Indices: 9785--9838 Score: 58
Period size: 15 Copynumber: 3.6 Consensus size: 15
9775 TATTTAAGTT
9785 AATTAATTTTAAAT-
1 AATTAATTTTAAATA
*
9799 TATTAATTTTTAAATTA
1 AATTAA-TTTTAAA-TA
*
9816 AATTAAATTTAAATA
1 AATTAATTTTAAATA
9831 AA-TAATTT
1 AATTAATTT
9839 ATATTTTTAA
Statistics
Matches: 33, Mismatches: 4, Indels: 6
0.77 0.09 0.14
Matches are distributed among these distances:
14 10 0.30
15 11 0.33
16 7 0.21
17 5 0.15
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (15 bp):
AATTAATTTTAAATA
Found at i:10846 original size:30 final size:30
Alignment explanation
Indices: 10812--10868 Score: 71
Period size: 30 Copynumber: 1.9 Consensus size: 30
10802 ATATATAAAA
*
10812 GAAAAGTTTAAGAATAAATT-GATTAATGAT
1 GAAAAATTT-AGAATAAATTCGATTAATGAT
* *
10842 GAAAAATTTTGATTAAATTCGATTAAT
1 GAAAAATTTAGAATAAATTCGATTAAT
10869 TAAATTTATT
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
29 8 0.35
30 15 0.65
ACGTcount: A:0.47, C:0.02, G:0.14, T:0.37
Consensus pattern (30 bp):
GAAAAATTTAGAATAAATTCGATTAATGAT
Found at i:10977 original size:5 final size:6
Alignment explanation
Indices: 10960--10984 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
10950 AGTTTAATAG
10960 ATAAAA ATAAAA ATAAAA ATAAAA A
1 ATAAAA ATAAAA ATAAAA ATAAAA A
10985 ACCAAAGAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.84, C:0.00, G:0.00, T:0.16
Consensus pattern (6 bp):
ATAAAA
Found at i:11280 original size:2 final size:2
Alignment explanation
Indices: 11275--11312 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
11265 CCCCACACAC
11275 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
11313 GCCCTCAAGT
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:11404 original size:14 final size:13
Alignment explanation
Indices: 11366--11419 Score: 54
Period size: 14 Copynumber: 3.9 Consensus size: 13
11356 TATCTAATAT
*
11366 ATTATTATTTCATA
1 ATTAATATTT-ATA
* *
11380 ATTTAAAATTTTTA
1 A-TTAATATTTATA
11394 ATTATATATTTATA
1 ATTA-ATATTTATA
11408 ATTAATATTTAT
1 ATTAATATTTAT
11420 CATATTACTG
Statistics
Matches: 33, Mismatches: 5, Indels: 5
0.77 0.12 0.12
Matches are distributed among these distances:
13 11 0.33
14 15 0.45
15 7 0.21
ACGTcount: A:0.41, C:0.02, G:0.00, T:0.57
Consensus pattern (13 bp):
ATTAATATTTATA
Found at i:11587 original size:12 final size:12
Alignment explanation
Indices: 11570--11594 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
11560 GATCTATGTC
11570 ACTTACTTAGCA
1 ACTTACTTAGCA
11582 ACTTACTTAGCA
1 ACTTACTTAGCA
11594 A
1 A
11595 GGACAAAGAA
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:0.24, G:0.08, T:0.32
Consensus pattern (12 bp):
ACTTACTTAGCA
Found at i:11740 original size:17 final size:17
Alignment explanation
Indices: 11703--11740 Score: 53
Period size: 16 Copynumber: 2.3 Consensus size: 17
11693 ATATTTTAAA
11703 AATTTTTATTTAAATTT
1 AATTTTTATTTAAATTT
11720 -ATTTTTGATTT-AATTT
1 AATTTTT-ATTTAAATTT
11736 AATTT
1 AATTT
11741 ATAAATTTAT
Statistics
Matches: 19, Mismatches: 0, Indels: 4
0.83 0.00 0.17
Matches are distributed among these distances:
16 11 0.58
17 8 0.42
ACGTcount: A:0.32, C:0.00, G:0.03, T:0.66
Consensus pattern (17 bp):
AATTTTTATTTAAATTT
Found at i:12664 original size:182 final size:179
Alignment explanation
Indices: 12360--12722 Score: 656
Period size: 182 Copynumber: 2.0 Consensus size: 179
12350 CATCTCCGAT
*
12360 TAATTAATATGCTGAGATTGATGGGTTTTAGCTGGGGAATTTTTTGTTTTGTTTTTTTTATAGTT
1 TAATTAATATGCTGAGATTGATGCGTTTTAGCTGGGGAATTTTTTGTTTTGTTTTTTTTATAGTT
*
12425 TGTAGGTTGTTCTCAATTTTGTAGAATAAAACTAGATTTTTCCGGCAATTCCATGTCAAAAAGAG
66 TGCAGGTTGTTCTCAATTTTGTAGAATAAAACTAGATTTTTCCGGCAATTCCATGTCAAAAAGAG
12490 AATTTCATTGATGATTGTTTATCTGGGGTCTGCCGCTAAATCTAAATCA
131 AATTTCATTGATGATTGTTTATCTGGGGTCTGCCGCTAAATCTAAATCA
12539 TAATTAATATGCTGAGATTGATGCGTTTTAGCTGGGGAATTTTTT-TTTTGTTTTTTTTTTTTAT
1 TAATTAATATGCTGAGATTGATGCGTTTTAGCTGGGGAATTTTTTGTTTTG----TTTTTTTTAT
*
12603 AGTTTGCAGGTTGTTCTCAATTTTGTAGAATAAAACTAGATTTTTTCGGCAATTCCATGTCAAAA
62 AGTTTGCAGGTTGTTCTCAATTTTGTAGAATAAAACTAGATTTTTCCGGCAATTCCATGTCAAAA
12668 AGAGAATTTCATTGATGATTGTTTATCTGGGGTCTGCCGCTAAATCTAAATCA
127 AGAGAATTTCATTGATGATTGTTTATCTGGGGTCTGCCGCTAAATCTAAATCA
12721 TA
1 TA
12723 GTCTCGAATT
Statistics
Matches: 177, Mismatches: 3, Indels: 5
0.96 0.02 0.03
Matches are distributed among these distances:
178 5 0.03
179 44 0.25
182 128 0.72
ACGTcount: A:0.26, C:0.11, G:0.19, T:0.44
Consensus pattern (179 bp):
TAATTAATATGCTGAGATTGATGCGTTTTAGCTGGGGAATTTTTTGTTTTGTTTTTTTTATAGTT
TGCAGGTTGTTCTCAATTTTGTAGAATAAAACTAGATTTTTCCGGCAATTCCATGTCAAAAAGAG
AATTTCATTGATGATTGTTTATCTGGGGTCTGCCGCTAAATCTAAATCA
Found at i:17296 original size:23 final size:24
Alignment explanation
Indices: 17250--17307 Score: 73
Period size: 23 Copynumber: 2.4 Consensus size: 24
17240 TCAGTTTTGA
*
17250 AAAAAAATGATAAATATATAATTTT
1 AAAAAAAT-AAAAATATATAATTTT
* *
17275 TAAAAAATAAAAAT-TATCATTTT
1 AAAAAAATAAAAATATATAATTTT
17298 AAAAAAATAA
1 AAAAAAATAA
17308 TATTTAATAA
Statistics
Matches: 29, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
23 17 0.59
24 5 0.17
25 7 0.24
ACGTcount: A:0.64, C:0.02, G:0.02, T:0.33
Consensus pattern (24 bp):
AAAAAAATAAAAATATATAATTTT
Found at i:17340 original size:10 final size:10
Alignment explanation
Indices: 17327--17370 Score: 63
Period size: 10 Copynumber: 4.4 Consensus size: 10
17317 ATATTTATAA
17327 TTAAATTGAT
1 TTAAATTGAT
17337 TTAAATTGAAT
1 TTAAATTG-AT
*
17348 TT-AATTAAT
1 TTAAATTGAT
17357 TTAAATTGAT
1 TTAAATTGAT
17367 TTAA
1 TTAA
17371 TTTATTAATT
Statistics
Matches: 30, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
9 4 0.13
10 22 0.73
11 4 0.13
ACGTcount: A:0.43, C:0.00, G:0.07, T:0.50
Consensus pattern (10 bp):
TTAAATTGAT
Found at i:17348 original size:15 final size:15
Alignment explanation
Indices: 17319--17370 Score: 59
Period size: 15 Copynumber: 3.4 Consensus size: 15
17309 ATTTAATAAT
17319 ATTTATAATTAAATTG
1 ATTTA-AATTAAATTG
* *
17335 ATTTAAATTGAATTT
1 ATTTAAATTAAATTG
* *
17350 AATTAATTTAAATTG
1 ATTTAAATTAAATTG
17365 ATTTAA
1 ATTTAA
17371 TTTATTAATT
Statistics
Matches: 29, Mismatches: 7, Indels: 1
0.78 0.19 0.03
Matches are distributed among these distances:
15 24 0.83
16 5 0.17
ACGTcount: A:0.44, C:0.00, G:0.06, T:0.50
Consensus pattern (15 bp):
ATTTAAATTAAATTG
Found at i:17353 original size:20 final size:20
Alignment explanation
Indices: 17325--17372 Score: 71
Period size: 20 Copynumber: 2.5 Consensus size: 20
17315 TAATATTTAT
* *
17325 AATTAAATTGATTTAAATTG
1 AATTTAATTAATTTAAATTG
17345 AATTTAATTAATTTAAATTG
1 AATTTAATTAATTTAAATTG
17365 -ATTTAATT
1 AATTTAATT
17373 TATTAATTTT
Statistics
Matches: 26, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
19 8 0.31
20 18 0.69
ACGTcount: A:0.44, C:0.00, G:0.06, T:0.50
Consensus pattern (20 bp):
AATTTAATTAATTTAAATTG
Found at i:17371 original size:15 final size:15
Alignment explanation
Indices: 17327--17374 Score: 60
Period size: 15 Copynumber: 3.2 Consensus size: 15
17317 ATATTTATAA
*
17327 TTAAATTGATTTAAA
1 TTAAATTGATTTAAT
* * *
17342 TTGAATTTAATTAAT
1 TTAAATTGATTTAAT
17357 TTAAATTGATTTAAT
1 TTAAATTGATTTAAT
17372 TTA
1 TTA
17375 TTAATTTTAA
Statistics
Matches: 26, Mismatches: 7, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
15 26 1.00
ACGTcount: A:0.42, C:0.00, G:0.06, T:0.52
Consensus pattern (15 bp):
TTAAATTGATTTAAT
Found at i:21272 original size:12 final size:12
Alignment explanation
Indices: 21252--21343 Score: 57
Period size: 12 Copynumber: 7.7 Consensus size: 12
21242 AATAATAATT
* *
21252 TTTATTTTTATA
1 TTTAATTTTAAA
21264 TTTAATTTTAAA
1 TTTAATTTTAAA
21276 TTTAATTATTTAAA
1 TTTAA-T-TTTAAA
* *
21290 TTAAAATTTAAA
1 TTTAATTTTAAA
* *
21302 TTTAA-ATTCAA
1 TTTAATTTTAAA
*
21313 TAATAATTGTTAAA
1 T-TTAATT-TTAAA
21327 --TAA-TTTAAA
1 TTTAATTTTAAA
21336 TTTAATTT
1 TTTAATTT
21344 AATAATAATT
Statistics
Matches: 62, Mismatches: 10, Indels: 16
0.70 0.11 0.18
Matches are distributed among these distances:
9 5 0.08
10 1 0.02
11 11 0.18
12 30 0.48
13 1 0.02
14 14 0.23
ACGTcount: A:0.43, C:0.01, G:0.01, T:0.54
Consensus pattern (12 bp):
TTTAATTTTAAA
Found at i:21277 original size:26 final size:27
Alignment explanation
Indices: 21248--21309 Score: 65
Period size: 26 Copynumber: 2.4 Consensus size: 27
21238 TAATAATAAT
* * * *
21248 AATTTTTATT-TTTATATTTAATTTTA
1 AATTTTAATTATTTAAATTAAAATTTA
21274 AA-TTTAATTATTTAAATTAAAATTTA
1 AATTTTAATTATTTAAATTAAAATTTA
*
21300 AATTTAAATT
1 AATTTTAATT
21310 CAATAATAAT
Statistics
Matches: 29, Mismatches: 5, Indels: 3
0.78 0.14 0.08
Matches are distributed among these distances:
25 6 0.21
26 17 0.59
27 6 0.21
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (27 bp):
AATTTTAATTATTTAAATTAAAATTTA
Found at i:21285 original size:20 final size:20
Alignment explanation
Indices: 21262--21309 Score: 64
Period size: 20 Copynumber: 2.5 Consensus size: 20
21252 TTTATTTTTA
* *
21262 TATTTAATTTTAAATTTAAT
1 TATTTAAATTAAAATTTAAT
21282 TATTTAAATTAAAATTTAA-
1 TATTTAAATTAAAATTTAAT
21301 -ATTTAAATT
1 TATTTAAATT
21310 CAATAATAAT
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
18 9 0.35
20 17 0.65
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (20 bp):
TATTTAAATTAAAATTTAAT
Found at i:21296 original size:6 final size:6
Alignment explanation
Indices: 21258--21309 Score: 59
Period size: 6 Copynumber: 8.3 Consensus size: 6
21248 AATTTTTATT
* * *
21258 TTTATA TTTAAT TTTAAA TTTAATTA TTTAAA TTAAAA TTTAAA TTTAAA
1 TTTAAA TTTAAA TTTAAA TTTAA--A TTTAAA TTTAAA TTTAAA TTTAAA
21308 TT
1 TT
21310 CAATAATAAT
Statistics
Matches: 39, Mismatches: 5, Indels: 4
0.81 0.10 0.08
Matches are distributed among these distances:
6 33 0.85
8 6 0.15
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (6 bp):
TTTAAA
Found at i:21306 original size:13 final size:13
Alignment explanation
Indices: 21270--21307 Score: 51
Period size: 13 Copynumber: 2.9 Consensus size: 13
21260 TATATTTAAT
*
21270 TTTAAATTTAATTA
1 TTTAAATTTAA-AA
21284 TTTAAA-TTAAAA
1 TTTAAATTTAAAA
21296 TTTAAATTTAAA
1 TTTAAATTTAAA
21308 TTCAATAATA
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
12 7 0.32
13 9 0.41
14 6 0.27
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (13 bp):
TTTAAATTTAAAA
Found at i:22210 original size:23 final size:23
Alignment explanation
Indices: 22184--22252 Score: 77
Period size: 23 Copynumber: 2.9 Consensus size: 23
22174 AAATGTTATG
22184 TTAATTAA-TTTAAAAATATAAAA
1 TTAA-TAATTTTAAAAATATAAAA
* *
22207 TTAATAATTTTTAAAATTTAAAA
1 TTAATAATTTTAAAAATATAAAA
*
22230 TTTATAATTATTAAATAATATAA
1 TTAATAATT-TTAAA-AATATAA
22253 TTATATTTAA
Statistics
Matches: 38, Mismatches: 5, Indels: 4
0.81 0.11 0.09
Matches are distributed among these distances:
22 3 0.08
23 25 0.66
24 4 0.11
25 6 0.16
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (23 bp):
TTAATAATTTTAAAAATATAAAA
Found at i:25548 original size:3 final size:3
Alignment explanation
Indices: 25540--25564 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
25530 AATGGTTCCT
25540 TTC TTC TTC TTC TTC TTC TTC TTC T
1 TTC TTC TTC TTC TTC TTC TTC TTC T
25565 CGTACCAAAC
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.00, C:0.32, G:0.00, T:0.68
Consensus pattern (3 bp):
TTC
Found at i:29527 original size:13 final size:13
Alignment explanation
Indices: 29509--29533 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
29499 GTGACCTTGT
29509 AACATCAGAACCG
1 AACATCAGAACCG
29522 AACATCAGAACC
1 AACATCAGAACC
29534 AAATAAACGA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.48, C:0.32, G:0.12, T:0.08
Consensus pattern (13 bp):
AACATCAGAACCG
Found at i:32692 original size:20 final size:19
Alignment explanation
Indices: 32646--32715 Score: 56
Period size: 20 Copynumber: 3.6 Consensus size: 19
32636 ATATAATATG
*
32646 AATTATAAATATTTTAAAA
1 AATTATAAATATTTAAAAA
**
32665 TTTATATAAATATTTAAATAA
1 AAT-TATAAATATTTAAA-AA
32686 AATTAT-AATA--TAATAAA
1 AATTATAAATATTTAA-AAA
32703 AATATATAAATAT
1 AAT-TATAAATAT
32716 AATATTTATA
Statistics
Matches: 40, Mismatches: 5, Indels: 11
0.71 0.09 0.20
Matches are distributed among these distances:
17 8 0.20
18 4 0.10
19 9 0.22
20 16 0.40
21 3 0.08
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (19 bp):
AATTATAAATATTTAAAAA
Found at i:32695 original size:19 final size:20
Alignment explanation
Indices: 32673--32743 Score: 63
Period size: 20 Copynumber: 3.4 Consensus size: 20
32663 AATTTATATA
32673 AATATTTAAATA-AAATTAT
1 AATATTTAAATATAAATTAT
* *
32692 AATATAATAAAAATATATAAATAT
1 AATAT--T-TAAATATA-AATTAT
*
32716 AATATTTATATATAAATTAT
1 AATATTTAAATATAAATTAT
*
32736 TATATTTA
1 AATATTTA
32744 CTTTCCTACG
Statistics
Matches: 41, Mismatches: 6, Indels: 9
0.73 0.11 0.16
Matches are distributed among these distances:
19 5 0.12
20 12 0.29
21 7 0.17
22 6 0.15
23 1 0.02
24 10 0.24
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (20 bp):
AATATTTAAATATAAATTAT
Found at i:32702 original size:16 final size:18
Alignment explanation
Indices: 32636--32719 Score: 57
Period size: 19 Copynumber: 4.4 Consensus size: 18
32626 ATAAAGCCTT
*
32636 ATATAATATGAAT-TATAA
1 ATATAATA-AAATATATAA
**
32654 ATATTTTAAAATTTATATAA
1 ATATAATAAAA--TATATAA
32674 ATATTTAAATAAAAT-TAT-A
1 ATA--T-AATAAAATATATAA
32693 ATATAATAAAAATATATAA
1 ATATAAT-AAAATATATAA
32712 ATATAATA
1 ATATAATA
32720 TTTATATATA
Statistics
Matches: 52, Mismatches: 5, Indels: 18
0.69 0.07 0.24
Matches are distributed among these distances:
16 3 0.06
17 8 0.15
18 10 0.19
19 13 0.25
20 11 0.21
21 1 0.02
22 1 0.02
23 5 0.10
ACGTcount: A:0.58, C:0.00, G:0.01, T:0.40
Consensus pattern (18 bp):
ATATAATAAAATATATAA
Found at i:32727 original size:30 final size:29
Alignment explanation
Indices: 32667--32731 Score: 71
Period size: 30 Copynumber: 2.2 Consensus size: 29
32657 TTTTAAAATT
* *
32667 TATATAAATATTTAAATAAAATTATAATA
1 TATAAAAATATATAAATAAAATTATAATA
32696 TAATAAAAATATATAAATATAATATT-T-ATA
1 T-ATAAAAATATATAAATA-AA-ATTATAATA
32726 TATAAA
1 TATAAA
32732 TTATTATATT
Statistics
Matches: 31, Mismatches: 2, Indels: 6
0.79 0.05 0.15
Matches are distributed among these distances:
29 6 0.19
30 19 0.61
31 3 0.10
32 3 0.10
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (29 bp):
TATAAAAATATATAAATAAAATTATAATA
Found at i:32919 original size:22 final size:21
Alignment explanation
Indices: 32875--32920 Score: 58
Period size: 22 Copynumber: 2.1 Consensus size: 21
32865 TATTTTATTA
*
32875 TTATAATAATTAATCTTACAT
1 TTATAATAATTAATATTACAT
32896 TTATAATCAATTAAATATTA-AT
1 TTATAAT-AATT-AATATTACAT
32918 TTA
1 TTA
32921 ATCGGCATAA
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
21 7 0.32
22 9 0.41
23 6 0.27
ACGTcount: A:0.46, C:0.07, G:0.00, T:0.48
Consensus pattern (21 bp):
TTATAATAATTAATATTACAT
Found at i:33047 original size:18 final size:18
Alignment explanation
Indices: 33004--33048 Score: 58
Period size: 18 Copynumber: 2.5 Consensus size: 18
32994 AATTAATTAA
33004 ATAAAAATTATAAAATAT
1 ATAAAAATTATAAAATAT
33022 A-AATAAATTA-AAAATAT
1 ATAA-AAATTATAAAATAT
33039 ATTAAAAATT
1 A-TAAAAATT
33049 TTCATTATAA
Statistics
Matches: 24, Mismatches: 0, Indels: 6
0.80 0.00 0.20
Matches are distributed among these distances:
17 10 0.42
18 12 0.50
19 2 0.08
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (18 bp):
ATAAAAATTATAAAATAT
Found at i:33097 original size:22 final size:20
Alignment explanation
Indices: 33045--33102 Score: 62
Period size: 22 Copynumber: 2.7 Consensus size: 20
33035 ATATATTAAA
33045 AATTTTCATTATAAATTATTTT
1 AATTTT-ATTA-AAATTATTTT
33067 AATTTTATTAAAATTAATTTT
1 AATTTTATTAAAATT-ATTTT
* *
33088 ATTATTTATTCAAAT
1 AAT-TTTATTAAAAT
33103 AAATCTAACA
Statistics
Matches: 32, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
20 5 0.16
21 11 0.34
22 16 0.50
ACGTcount: A:0.40, C:0.03, G:0.00, T:0.57
Consensus pattern (20 bp):
AATTTTATTAAAATTATTTT
Found at i:33723 original size:22 final size:22
Alignment explanation
Indices: 33689--33736 Score: 62
Period size: 22 Copynumber: 2.2 Consensus size: 22
33679 TAAAAATAAA
*
33689 ATTT-TTTATATTTATATTATT
1 ATTTATTTAAATTTATATTATT
* *
33710 TTTTATTTAAATTTATTTTATT
1 ATTTATTTAAATTTATATTATT
33732 ATTTA
1 ATTTA
33737 AAAATATTAA
Statistics
Matches: 22, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
21 3 0.14
22 19 0.86
ACGTcount: A:0.29, C:0.00, G:0.00, T:0.71
Consensus pattern (22 bp):
ATTTATTTAAATTTATATTATT
Found at i:33733 original size:18 final size:17
Alignment explanation
Indices: 33687--33738 Score: 65
Period size: 16 Copynumber: 3.2 Consensus size: 17
33677 AATAAAAATA
33687 AAATT-TTTTA-TATTT
1 AAATTATTTTATTATTT
*
33702 ATATTATTTT-TTATTT
1 AAATTATTTTATTATTT
33718 AAATTTATTTTATTATTT
1 AAA-TTATTTTATTATTT
33736 AAA
1 AAA
33739 AATATTAAAA
Statistics
Matches: 31, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
15 4 0.13
16 11 0.35
17 7 0.23
18 9 0.29
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (17 bp):
AAATTATTTTATTATTT
Found at i:33744 original size:18 final size:17
Alignment explanation
Indices: 33706--33744 Score: 51
Period size: 18 Copynumber: 2.2 Consensus size: 17
33696 ATATTTATAT
**
33706 TATTTTTTATTTAAATT
1 TATTTTTTATTTAAAAA
33723 TATTTTATTATTTAAAAA
1 TATTTT-TTATTTAAAAA
33741 TATT
1 TATT
33745 AAAAATTAAT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
17 6 0.32
18 13 0.68
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (17 bp):
TATTTTTTATTTAAAAA
Found at i:33802 original size:18 final size:19
Alignment explanation
Indices: 33779--33816 Score: 60
Period size: 18 Copynumber: 2.1 Consensus size: 19
33769 TTATAATTAA
33779 ATTTAAATAAAAAT-ATTT
1 ATTTAAATAAAAATAATTT
*
33797 ATTTAAATAATAATAATTT
1 ATTTAAATAAAAATAATTT
33816 A
1 A
33817 AATCAATTCA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
18 13 0.72
19 5 0.28
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (19 bp):
ATTTAAATAAAAATAATTT
Found at i:33845 original size:21 final size:20
Alignment explanation
Indices: 33821--33865 Score: 56
Period size: 21 Copynumber: 2.2 Consensus size: 20
33811 AATTTAAATC
33821 AATTC-ATATTAATTTTATTTA
1 AATTCAATA-TAATTTTA-TTA
*
33842 AATTTAATATAATTTTATTA
1 AATTCAATATAATTTTATTA
33862 AATT
1 AATT
33866 AAACAAATAG
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
20 7 0.32
21 12 0.55
22 3 0.14
ACGTcount: A:0.42, C:0.02, G:0.00, T:0.56
Consensus pattern (20 bp):
AATTCAATATAATTTTATTA
Found at i:34199 original size:2 final size:2
Alignment explanation
Indices: 34192--34219 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
34182 GGAGGCTAGA
34192 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
34220 TCACTATGAT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:36243 original size:15 final size:15
Alignment explanation
Indices: 36223--36251 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
36213 TAAATATGAA
36223 ATATTTATATTTAAT
1 ATATTTATATTTAAT
36238 ATATTTATATTTAA
1 ATATTTATATTTAA
36252 ACACAATCAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (15 bp):
ATATTTATATTTAAT
Found at i:36344 original size:84 final size:84
Alignment explanation
Indices: 36201--36357 Score: 269
Period size: 84 Copynumber: 1.9 Consensus size: 84
36191 GGACTCCTCA
* *
36201 TTAATATATAATTAAATATGAAATATTTATATTTAATATATTTATATTTAAACACAATCAAATAG
1 TTAATATATAATTAAATATAAAATATTTATAATTAATATATTTATATTTAAACACAATCAAATAG
36266 AAAAAATATATGTTCGTAT
66 AAAAAATATATGTTCGTAT
* * *
36285 TTAATATATAATTAAATATAAAATTTTTATAATTAATATATTTATATTTAAATATAATCAAATAG
1 TTAATATATAATTAAATATAAAATATTTATAATTAATATATTTATATTTAAACACAATCAAATAG
36350 AAAAAATA
66 AAAAAATA
36358 AATATATTTA
Statistics
Matches: 68, Mismatches: 5, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
84 68 1.00
ACGTcount: A:0.52, C:0.03, G:0.03, T:0.42
Consensus pattern (84 bp):
TTAATATATAATTAAATATAAAATATTTATAATTAATATATTTATATTTAAACACAATCAAATAG
AAAAAATATATGTTCGTAT
Found at i:36871 original size:183 final size:183
Alignment explanation
Indices: 36553--36911 Score: 596
Period size: 183 Copynumber: 2.0 Consensus size: 183
36543 CAATAACCAT
*
36553 AAGATGCCTTTCAATAGACAAGCAAAAGGCATCAACTGCCCATGGACTAAGCTAAGGCACTCAAC
1 AAGATGCCTTTCAATAGACAAGCAAAAGGCATCAACTGCCCAGGGACTAAGCTAAGGCACTCAAC
* * *
36618 AATATATCAGCAGTAACAATATATATATATATATTTCCTCGCTTTTCGAAGATTTATGGACTCGT
66 AATATATCAGCAGTAACAATATATATATATATATTTCCTCGCTTTTCCAAGATTTACGGACTCCT
*
36683 GAGAGTTAGCATAACATCTGTTCTCCATTGATCCAACTAAATGAAGTACCCAG
131 GAGAGTTAGCATAACATCTATTCTCCATTGATCCAACTAAATGAAGTACCCAG
* * *
36736 AAGATGCCTTTCAATAGAGAAGCAAACGGCATCAACTGCCCAGGGACTAAGCTAAGGCAGTCAAC
1 AAGATGCCTTTCAATAGACAAGCAAAAGGCATCAACTGCCCAGGGACTAAGCTAAGGCACTCAAC
* *
36801 -A-ATGTCAGCAGTAACTATATATATATATATATATTTCCTTGCTTTTCCAAGATTTACGGACTC
66 AATATATCAGCAGTAAC-A-ATATATATATATATATTTCCTCGCTTTTCCAAGATTTACGGACTC
36864 CTGAGAGTTAGCATAACATCTATTCTCCATTGATCCAACTAAATGAAG
129 CTGAGAGTTAGCATAACATCTATTCTCCATTGATCCAACTAAATGAAG
36912 AACTCAAATA
Statistics
Matches: 164, Mismatches: 10, Indels: 4
0.92 0.06 0.02
Matches are distributed among these distances:
181 13 0.08
182 2 0.01
183 149 0.91
ACGTcount: A:0.35, C:0.21, G:0.16, T:0.28
Consensus pattern (183 bp):
AAGATGCCTTTCAATAGACAAGCAAAAGGCATCAACTGCCCAGGGACTAAGCTAAGGCACTCAAC
AATATATCAGCAGTAACAATATATATATATATATTTCCTCGCTTTTCCAAGATTTACGGACTCCT
GAGAGTTAGCATAACATCTATTCTCCATTGATCCAACTAAATGAAGTACCCAG
Found at i:39235 original size:30 final size:30
Alignment explanation
Indices: 39177--39258 Score: 96
Period size: 30 Copynumber: 2.7 Consensus size: 30
39167 TGCTATTATA
* *
39177 AAAATTTAATTAATTATAATTA-AATTTAAAT
1 AAAATTT-ATTTATTA-AATAATAATTTAAAT
39208 AAAATTTATTTATTAAATAATAATTTAAAT
1 AAAATTTATTTATTAAATAATAATTTAAAT
* *
39238 TAAATTAATTT-TTAAATAATA
1 AAAATTTATTTATTAAATAATA
39259 TTTTTTAATA
Statistics
Matches: 46, Mismatches: 4, Indels: 4
0.85 0.07 0.07
Matches are distributed among these distances:
29 14 0.30
30 25 0.54
31 7 0.15
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (30 bp):
AAAATTTATTTATTAAATAATAATTTAAAT
Found at i:39254 original size:47 final size:45
Alignment explanation
Indices: 39188--39275 Score: 115
Period size: 47 Copynumber: 1.9 Consensus size: 45
39178 AAATTTAATT
*
39188 AATTATAATTAAATTTAAATAAAATTTATTTATTAAATAATAATTTA
1 AATTATAATTAAATTTAAATAAAATTT-TTTAAT-AATAATAATTTA
* *
39235 AATTA-AATTAATTTTTAAATAATATTTTTTAATAATAATAA
1 AATTATAATTAA-ATTTAAATAAAATTTTTTAATAATAATAA
39276 ATAAATCACT
Statistics
Matches: 37, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
45 8 0.22
46 11 0.30
47 18 0.49
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (45 bp):
AATTATAATTAAATTTAAATAAAATTTTTTAATAATAATAATTTA
Found at i:46958 original size:20 final size:21
Alignment explanation
Indices: 46917--46958 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
46907 TATGATTGAA
*
46917 TAAAATTTAAACTCTAAATAT
1 TAAAATTAAAACTCTAAATAT
*
46938 TAAAATTAAAACT-TAATTAT
1 TAAAATTAAAACTCTAAATAT
46958 T
1 T
46959 TTTTAAATAA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
20 7 0.37
21 12 0.63
ACGTcount: A:0.52, C:0.07, G:0.00, T:0.40
Consensus pattern (21 bp):
TAAAATTAAAACTCTAAATAT
Found at i:48590 original size:17 final size:18
Alignment explanation
Indices: 48561--48604 Score: 56
Period size: 17 Copynumber: 2.6 Consensus size: 18
48551 ATTTATTAGA
* *
48561 TATTTTAAATTTTATA-T
1 TATTATAAATTTTTTACT
48578 TATTA-AAATTTTTTACT
1 TATTATAAATTTTTTACT
48595 TATTATAAAT
1 TATTATAAAT
48605 ATATTTTTTA
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
16 9 0.39
17 10 0.43
18 4 0.17
ACGTcount: A:0.39, C:0.02, G:0.00, T:0.59
Consensus pattern (18 bp):
TATTATAAATTTTTTACT
Found at i:48732 original size:15 final size:15
Alignment explanation
Indices: 48703--48735 Score: 50
Period size: 15 Copynumber: 2.2 Consensus size: 15
48693 AAATATAAAC
48703 AATTAAAATCTAATT
1 AATTAAAATCTAATT
48718 AATTAAAAT-TGAATT
1 AATTAAAATCT-AATT
48733 AAT
1 AAT
48736 CGAAATAATT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
14 1 0.06
15 16 0.94
ACGTcount: A:0.55, C:0.03, G:0.03, T:0.39
Consensus pattern (15 bp):
AATTAAAATCTAATT
Found at i:49307 original size:6 final size:6
Alignment explanation
Indices: 49292--49327 Score: 51
Period size: 6 Copynumber: 6.5 Consensus size: 6
49282 TTCTTTCTCT
49292 CTTT-C CTTTCC CTTTCC CTTTCC C-TTCC C-TTCC CTT
1 CTTTCC CTTTCC CTTTCC CTTTCC CTTTCC CTTTCC CTT
49328 CCGTTCATTT
Statistics
Matches: 29, Mismatches: 0, Indels: 3
0.91 0.00 0.09
Matches are distributed among these distances:
5 14 0.48
6 15 0.52
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (6 bp):
CTTTCC
Found at i:53039 original size:17 final size:17
Alignment explanation
Indices: 53017--53107 Score: 64
Period size: 17 Copynumber: 5.2 Consensus size: 17
53007 TATGCATTCC
53017 TATTATATTAATATATT
1 TATTATATTAATATATT
53034 TATTATATTATAATTATAATTT
1 TATTATA-T-TAA-TAT-A-TT
53056 TATTATATTAATA-ATT
1 TATTATATTAATATATT
53072 GATATTATA-TAA-AT-TT
1 --TATTATATTAATATATT
** *
53088 TAAAATATTTATATATT
1 TATTATATTAATATATT
53105 TAT
1 TAT
53108 ATTATAGATA
Statistics
Matches: 59, Mismatches: 4, Indels: 22
0.69 0.05 0.26
Matches are distributed among these distances:
14 5 0.08
15 2 0.03
16 7 0.12
17 15 0.25
18 8 0.14
19 5 0.08
20 6 0.10
21 2 0.03
22 9 0.15
ACGTcount: A:0.43, C:0.00, G:0.01, T:0.56
Consensus pattern (17 bp):
TATTATATTAATATATT
Found at i:53096 original size:32 final size:33
Alignment explanation
Indices: 53034--53113 Score: 83
Period size: 32 Copynumber: 2.4 Consensus size: 33
53024 TTAATATATT
**
53034 TATT-ATATTATAATTATAATTTTATTATATTAATA
1 TATTGATATTAT-A-TA-AATTTTAAAATATTAATA
*
53069 -ATTGATATTATATAAATTTTAAAATATTTATA
1 TATTGATATTATATAAATTTTAAAATATTAATA
*
53101 TATTTATATTATA
1 TATTGATATTATA
53114 GATATATATA
Statistics
Matches: 39, Mismatches: 4, Indels: 6
0.80 0.08 0.12
Matches are distributed among these distances:
32 15 0.38
33 13 0.33
34 4 0.10
35 7 0.18
ACGTcount: A:0.44, C:0.00, G:0.01, T:0.55
Consensus pattern (33 bp):
TATTGATATTATATAAATTTTAAAATATTAATA
Found at i:54619 original size:25 final size:26
Alignment explanation
Indices: 54574--54628 Score: 60
Period size: 25 Copynumber: 2.2 Consensus size: 26
54564 AAAATATTTT
* *
54574 TAAATATAAATTTAATTATAA-AATA
1 TAAAAATAAATTTAATAATAATAATA
*
54599 TAAAAATAAA-TTAATGAATAATAATT
1 TAAAAATAAATTTAAT-AATAATAATA
54625 TAAA
1 TAAA
54629 CTTTAAAATC
Statistics
Matches: 25, Mismatches: 3, Indels: 3
0.81 0.10 0.10
Matches are distributed among these distances:
24 5 0.20
25 13 0.52
26 7 0.28
ACGTcount: A:0.62, C:0.00, G:0.02, T:0.36
Consensus pattern (26 bp):
TAAAAATAAATTTAATAATAATAATA
Found at i:55026 original size:21 final size:21
Alignment explanation
Indices: 55002--55042 Score: 66
Period size: 21 Copynumber: 2.0 Consensus size: 21
54992 TATTTTTATT
55002 TAAA-TTTAATTATAAAATATA
1 TAAATTTTAA-TATAAAATATA
55023 TAAATTTTAATATAAAATAT
1 TAAATTTTAATATAAAATAT
55043 TTTTAATATT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
21 14 0.74
22 5 0.26
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (21 bp):
TAAATTTTAATATAAAATATA
Found at i:56071 original size:14 final size:14
Alignment explanation
Indices: 56052--56108 Score: 53
Period size: 14 Copynumber: 4.0 Consensus size: 14
56042 ATTTTTAATT
56052 TTATATTAAAAATA
1 TTATATTAAAAATA
**
56066 TTATATT-TTAATA
1 TTATATTAAAAATA
*
56079 TTTATATTAAATATAA
1 -TTATATTAAAAAT-A
*
56095 TTATTTTAAAAATA
1 TTATATTAAAAATA
56109 AAAAATTTAC
Statistics
Matches: 33, Mismatches: 7, Indels: 6
0.72 0.15 0.13
Matches are distributed among these distances:
13 4 0.12
14 15 0.45
15 13 0.39
16 1 0.03
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (14 bp):
TTATATTAAAAATA
Found at i:56102 original size:27 final size:27
Alignment explanation
Indices: 56020--56103 Score: 100
Period size: 28 Copynumber: 3.0 Consensus size: 27
56010 TAGTAAATAT
56020 ATATTTA-ATATAAATATATTTAATTTTTA
1 ATATTTATAT-TAAATATATTT-A-TTTTA
*
56049 AT-TTTATATTAAAAATATTATATTTTA
1 ATATTTATATTAAATATATT-TATTTTA
*
56076 ATATTTATATTAAATATAATTATTTTA
1 ATATTTATATTAAATATATTTATTTTA
56103 A
1 A
56104 AAATAAAAAA
Statistics
Matches: 49, Mismatches: 3, Indels: 8
0.82 0.05 0.13
Matches are distributed among these distances:
27 15 0.31
28 29 0.59
29 5 0.10
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (27 bp):
ATATTTATATTAAATATATTTATTTTA
Found at i:56181 original size:13 final size:14
Alignment explanation
Indices: 56138--56193 Score: 50
Period size: 13 Copynumber: 4.3 Consensus size: 14
56128 ATTTAAATAA
*
56138 TAATATAAT-TTTT
1 TAATATAATATATT
56151 TAATA-AAT-T-TT
1 TAATATAATATATT
*
56162 AAATAT-ATATATT
1 TAATATAATATATT
56175 TAATATAAATATATT
1 TAATAT-AATATATT
56190 TAAT
1 TAAT
56194 TTTTTAAAAA
Statistics
Matches: 36, Mismatches: 2, Indels: 8
0.78 0.04 0.17
Matches are distributed among these distances:
11 8 0.22
12 5 0.14
13 12 0.33
15 11 0.31
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (14 bp):
TAATATAATATATT
Found at i:56186 original size:15 final size:15
Alignment explanation
Indices: 56159--56193 Score: 54
Period size: 15 Copynumber: 2.4 Consensus size: 15
56149 TTTAATAAAT
*
56159 TTTAA-ATATATATA
1 TTTAATATAAATATA
56173 TTTAATATAAATATA
1 TTTAATATAAATATA
56188 TTTAAT
1 TTTAAT
56194 TTTTTAAAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
14 5 0.26
15 14 0.74
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (15 bp):
TTTAATATAAATATA
Found at i:56212 original size:44 final size:43
Alignment explanation
Indices: 56125--56215 Score: 105
Period size: 44 Copynumber: 2.1 Consensus size: 43
56115 TTACTGTTAT
**
56125 TATATTTAAATAATAATATAATTTTTTAATAAATTTTAAATATA
1 TATATTTAAATAATAATATAATTTTTTAATAAAAATT-AATATA
*
56169 TATATTTAATATAAATATATTTAATTTTTTAA-AAAAATT-ATATA
1 TATATTTAA-AT-AATA-ATATAATTTTTTAATAAAAATTAATATA
56213 TAT
1 TAT
56216 TAAAATATCA
Statistics
Matches: 41, Mismatches: 3, Indels: 6
0.82 0.06 0.12
Matches are distributed among these distances:
44 17 0.41
45 2 0.05
46 9 0.22
47 13 0.32
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (43 bp):
TATATTTAAATAATAATATAATTTTTTAATAAAAATTAATATA
Found at i:56385 original size:11 final size:11
Alignment explanation
Indices: 56357--56395 Score: 51
Period size: 11 Copynumber: 3.4 Consensus size: 11
56347 TACTGTCCAT
*
56357 AAAAAAATAAA
1 AAAAAAAGAAA
56368 AAGAAAAAGGAAA
1 AA-AAAAA-GAAA
56381 AAAAAAAGAAA
1 AAAAAAAGAAA
56392 AAAA
1 AAAA
56396 GGGTTAAATC
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
11 10 0.40
12 10 0.40
13 5 0.20
ACGTcount: A:0.87, C:0.00, G:0.10, T:0.03
Consensus pattern (11 bp):
AAAAAAAGAAA
Found at i:56394 original size:20 final size:21
Alignment explanation
Indices: 56357--56397 Score: 59
Period size: 20 Copynumber: 2.0 Consensus size: 21
56347 TACTGTCCAT
56357 AAAAAAATAAAAAGAAAAAGG
1 AAAAAAATAAAAAGAAAAAGG
56378 AAAAAAA-AAAGAA-AAAAAGG
1 AAAAAAATAAA-AAGAAAAAGG
56398 GTTAAATCAT
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
20 10 0.53
21 9 0.47
ACGTcount: A:0.83, C:0.00, G:0.15, T:0.02
Consensus pattern (21 bp):
AAAAAAATAAAAAGAAAAAGG
Found at i:61695 original size:15 final size:15
Alignment explanation
Indices: 61653--61704 Score: 52
Period size: 15 Copynumber: 3.5 Consensus size: 15
61643 TATCATCAAG
*
61653 TTAT-TTTAAAAGAT
1 TTATATTTAAAAAAT
**
61667 TTATAAAATAAAAAAT
1 TTAT-ATTTAAAAAAT
61683 TTATATTTAAAAAAT
1 TTATATTTAAAAAAT
*
61698 ATATATT
1 TTATATT
61705 ATATTATATT
Statistics
Matches: 30, Mismatches: 6, Indels: 3
0.77 0.15 0.08
Matches are distributed among these distances:
14 4 0.13
15 15 0.50
16 11 0.37
ACGTcount: A:0.54, C:0.00, G:0.02, T:0.44
Consensus pattern (15 bp):
TTATATTTAAAAAAT
Found at i:61727 original size:11 final size:11
Alignment explanation
Indices: 61711--61737 Score: 54
Period size: 11 Copynumber: 2.5 Consensus size: 11
61701 TATTATATTA
61711 TATTTTTAATT
1 TATTTTTAATT
61722 TATTTTTAATT
1 TATTTTTAATT
61733 TATTT
1 TATTT
61738 AAGATAATAT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 16 1.00
ACGTcount: A:0.26, C:0.00, G:0.00, T:0.74
Consensus pattern (11 bp):
TATTTTTAATT
Done.