Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_019167914.1 Durio zibethinus cultivar Musang King isolate D1 unplaced genomic scaffold, Duzib1.0 scaffold_179, 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: 57263
ACGTcount: A:0.37, C:0.13, G:0.12, T:0.38
Found at i:1401 original size:3 final size:3
Alignment explanation
Indices: 1395--1432 Score: 53
Period size: 3 Copynumber: 13.0 Consensus size: 3
1385 TATTTAATAA
1395 TAT TAT TAT TAT TAT TA- TAT TAT TATT TAT T-T TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TA-T TAT TAT TAT TAT
1433 CATCATACAA
Statistics
Matches: 32, Mismatches: 0, Indels: 6
0.84 0.00 0.16
Matches are distributed among these distances:
2 4 0.12
3 25 0.78
4 3 0.09
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TAT
Found at i:1420 original size:20 final size:20
Alignment explanation
Indices: 1395--1432 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
1385 TATTTAATAA
1395 TATTA-TTATTATTATTATAT
1 TATTATTTATT-TTATTATAT
1415 TATTATTTATTTTATTAT
1 TATTATTTATTTTATTAT
1433 CATCATACAA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
20 12 0.71
21 5 0.29
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (20 bp):
TATTATTTATTTTATTATAT
Found at i:1490 original size:17 final size:17
Alignment explanation
Indices: 1465--1505 Score: 55
Period size: 17 Copynumber: 2.4 Consensus size: 17
1455 GTAGATAAAT
* *
1465 AAATCAAATAATATATA
1 AAATAAAATAAAATATA
1482 AAATAAAATAAAATATA
1 AAATAAAATAAAATATA
*
1499 TAATAAA
1 AAATAAA
1506 TTTTATTATT
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 21 1.00
ACGTcount: A:0.71, C:0.02, G:0.00, T:0.27
Consensus pattern (17 bp):
AAATAAAATAAAATATA
Found at i:1526 original size:13 final size:14
Alignment explanation
Indices: 1508--1538 Score: 55
Period size: 13 Copynumber: 2.3 Consensus size: 14
1498 ATAATAAATT
1508 TTATTATTTTA-TA
1 TTATTATTTTATTA
1521 TTATTATTTTATTA
1 TTATTATTTTATTA
1535 TTAT
1 TTAT
1539 ATGATAGAGA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 11 0.65
14 6 0.35
ACGTcount: A:0.29, C:0.00, G:0.00, T:0.71
Consensus pattern (14 bp):
TTATTATTTTATTA
Found at i:2459 original size:15 final size:16
Alignment explanation
Indices: 2439--2477 Score: 53
Period size: 17 Copynumber: 2.4 Consensus size: 16
2429 TAAAATTGAA
2439 TTATAAA-TTATTATT
1 TTATAAACTTATTATT
*
2454 TTATAAACTTTATTGTT
1 TTATAAAC-TTATTATT
2471 TTATAAA
1 TTATAAA
2478 AAATTAATTA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
15 7 0.33
17 14 0.67
ACGTcount: A:0.38, C:0.03, G:0.03, T:0.56
Consensus pattern (16 bp):
TTATAAACTTATTATT
Found at i:2633 original size:18 final size:19
Alignment explanation
Indices: 2612--2647 Score: 56
Period size: 18 Copynumber: 1.9 Consensus size: 19
2602 TTAGTTTTTA
2612 ATTATTTATCA-AAAAATT
1 ATTATTTATCATAAAAATT
*
2630 ATTATTTGTCATAAAAAT
1 ATTATTTATCATAAAAAT
2648 AATTTACTGA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 10 0.62
19 6 0.38
ACGTcount: A:0.47, C:0.06, G:0.03, T:0.44
Consensus pattern (19 bp):
ATTATTTATCATAAAAATT
Found at i:6702 original size:22 final size:23
Alignment explanation
Indices: 6677--6732 Score: 57
Period size: 22 Copynumber: 2.6 Consensus size: 23
6667 CATAAAAAAT
*
6677 TATTTTTTAATTAATT-ATTTTA
1 TATTTTATAATTAATTAATTTTA
* *
6699 TA-TTTATATTTATTTAATTTTA
1 TATTTTATAATTAATTAATTTTA
6721 TA-TTTAT-ATTAA
1 TATTTTATAATTAA
6733 AAATAATATT
Statistics
Matches: 28, Mismatches: 5, Indels: 3
0.78 0.14 0.08
Matches are distributed among these distances:
21 13 0.46
22 15 0.54
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (23 bp):
TATTTTATAATTAATTAATTTTA
Found at i:6706 original size:6 final size:6
Alignment explanation
Indices: 6691--6730 Score: 50
Period size: 6 Copynumber: 7.2 Consensus size: 6
6681 TTTTAATTAA
*
6691 TTAT-T TTATAT TTATAT TTAT-T TAAT-T TTATAT TTATAT T
1 TTATAT TTATAT TTATAT TTATAT TTATAT TTATAT TTATAT T
6731 AAAAATAATA
Statistics
Matches: 31, Mismatches: 2, Indels: 3
0.86 0.06 0.08
Matches are distributed among these distances:
5 12 0.39
6 19 0.61
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (6 bp):
TTATAT
Found at i:6720 original size:16 final size:17
Alignment explanation
Indices: 6691--6732 Score: 59
Period size: 17 Copynumber: 2.5 Consensus size: 17
6681 TTTTAATTAA
*
6691 TTATTTTATATTTATAT
1 TTATTTAATATTTATAT
6708 TTATTTAAT-TTTATAT
1 TTATTTAATATTTATAT
6724 TTATATTAA
1 TTAT-TTAA
6733 AAATAATATT
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
16 11 0.48
17 12 0.52
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (17 bp):
TTATTTAATATTTATAT
Found at i:6741 original size:18 final size:18
Alignment explanation
Indices: 6720--6770 Score: 68
Period size: 21 Copynumber: 2.7 Consensus size: 18
6710 ATTTAATTTT
6720 ATATTTATATTAAAAATA
1 ATATTTATATTAAAAATA
6738 ATATTTTATATTTAAAAAATA
1 ATA-TTTATA-TT-AAAAATA
6759 ATATTT-TATTAA
1 ATATTTATATTAA
6771 TTTCGGGTTG
Statistics
Matches: 30, Mismatches: 0, Indels: 7
0.81 0.00 0.19
Matches are distributed among these distances:
17 2 0.07
18 5 0.17
19 8 0.27
20 5 0.17
21 10 0.33
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (18 bp):
ATATTTATATTAAAAATA
Found at i:6749 original size:25 final size:21
Alignment explanation
Indices: 6723--6767 Score: 76
Period size: 21 Copynumber: 2.2 Consensus size: 21
6713 TAATTTTATA
6723 TTTATA-TT-AAAAATAATAT
1 TTTATATTTAAAAAATAATAT
6742 TTTATATTTAAAAAATAATAT
1 TTTATATTTAAAAAATAATAT
6763 TTTAT
1 TTTAT
6768 TAATTTCGGG
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
19 6 0.25
20 2 0.08
21 16 0.67
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (21 bp):
TTTATATTTAAAAAATAATAT
Found at i:6980 original size:18 final size:18
Alignment explanation
Indices: 6957--6991 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
6947 GATGATAGAG
*
6957 TTTTTAAAAATTTATTAA
1 TTTTTAAAAATATATTAA
6975 TTTTTAAAAATATATTA
1 TTTTTAAAAATATATTA
6992 TAAAATAAAT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (18 bp):
TTTTTAAAAATATATTAA
Found at i:9814 original size:102 final size:102
Alignment explanation
Indices: 9696--9903 Score: 362
Period size: 102 Copynumber: 2.0 Consensus size: 102
9686 TTAAATGTTT
9696 ATTACATAAAGAAATAAATATAGTACTATTGTTTTTTCAATTAAACATTTTTTTAATTCTTGAAA
1 ATTACATAAAGAAATAAATATAGTACTATTGTTTTTTCAATTAAACATTTTTTTAATTCTTGAAA
* *
9761 TTTTTTTTACAATTTAATTAGCCAATATATATTATTA
66 ATTTTTTTACAATTTAATTAGCCAATATATAGTATTA
* * *
9798 ATTACATAAAGAAATAAATATATTCCTATTGTTTTTTCAATTAAACATTTTTTTAATTGTTGAAA
1 ATTACATAAAGAAATAAATATAGTACTATTGTTTTTTCAATTAAACATTTTTTTAATTCTTGAAA
*
9863 ATTTTTTTACAATTTAATTAGTCAATATATAGTATTA
66 ATTTTTTTACAATTTAATTAGCCAATATATAGTATTA
9900 ATTA
1 ATTA
9904 AAAATAAAAA
Statistics
Matches: 100, Mismatches: 6, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
102 100 1.00
ACGTcount: A:0.39, C:0.07, G:0.05, T:0.48
Consensus pattern (102 bp):
ATTACATAAAGAAATAAATATAGTACTATTGTTTTTTCAATTAAACATTTTTTTAATTCTTGAAA
ATTTTTTTACAATTTAATTAGCCAATATATAGTATTA
Found at i:10793 original size:23 final size:26
Alignment explanation
Indices: 10738--10793 Score: 73
Period size: 27 Copynumber: 2.2 Consensus size: 26
10728 TCTTTTTTTT
10738 ATTTTTTAATTAATATATTATGAATAA
1 ATTTTTTAATTAATATA-TATGAATAA
10765 ATTTTTTAATTTAATATA-AT-AA-AA
1 ATTTTTTAA-TTAATATATATGAATAA
10789 ATTTT
1 ATTTT
10794 GTTATATAAT
Statistics
Matches: 28, Mismatches: 0, Indels: 5
0.85 0.00 0.15
Matches are distributed among these distances:
24 7 0.25
25 2 0.07
26 2 0.07
27 9 0.32
28 8 0.29
ACGTcount: A:0.45, C:0.00, G:0.02, T:0.54
Consensus pattern (26 bp):
ATTTTTTAATTAATATATATGAATAA
Found at i:10888 original size:28 final size:24
Alignment explanation
Indices: 10860--10919 Score: 68
Period size: 25 Copynumber: 2.4 Consensus size: 24
10850 ATTATTTTAT
10860 TATTATA-TAAAAAATAATAACTAAA
1 TATTATATTAAAAAATAA-AA-TAAA
* *
10885 TATTATATTATAAACTAAAATAAA
1 TATTATATTAAAAAATAAAATAAA
10909 TATTAGTATTA
1 TATTA-TATTA
10920 TGTTATTATT
Statistics
Matches: 31, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
24 9 0.29
25 14 0.45
26 8 0.26
ACGTcount: A:0.57, C:0.03, G:0.02, T:0.38
Consensus pattern (24 bp):
TATTATATTAAAAAATAAAATAAA
Found at i:13553 original size:21 final size:21
Alignment explanation
Indices: 13528--13571 Score: 61
Period size: 21 Copynumber: 2.1 Consensus size: 21
13518 GAATGTTTTT
13528 AATATAGAAAATCACTGTTTG
1 AATATAGAAAATCACTGTTTG
* **
13549 AATATATAATGTCACTGTTTG
1 AATATAGAAAATCACTGTTTG
13570 AA
1 AA
13572 AATTAAAAAA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.41, C:0.09, G:0.14, T:0.36
Consensus pattern (21 bp):
AATATAGAAAATCACTGTTTG
Found at i:14209 original size:22 final size:24
Alignment explanation
Indices: 14174--14217 Score: 65
Period size: 22 Copynumber: 1.9 Consensus size: 24
14164 TATAAATAAA
14174 TAAAATTATAATTATCTTATTAAC
1 TAAAATTATAATTATCTTATTAAC
*
14198 TAAAATT-T-ATTATTTTATTA
1 TAAAATTATAATTATCTTATTA
14218 TTATATAAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
22 11 0.58
23 1 0.05
24 7 0.37
ACGTcount: A:0.43, C:0.05, G:0.00, T:0.52
Consensus pattern (24 bp):
TAAAATTATAATTATCTTATTAAC
Found at i:14226 original size:25 final size:23
Alignment explanation
Indices: 14172--14227 Score: 58
Period size: 25 Copynumber: 2.3 Consensus size: 23
14162 CTTATAAATA
*
14172 AATAAAATTATAATTATCTTATT
1 AATAAAATTATAATTATATTATT
* *
14195 AACTAAAATTTATTATTTTATTATT
1 AA-TAAAA-TTATAATTATATTATT
14220 ATATAAAA
1 A-ATAAAA
14228 ATAATAACTA
Statistics
Matches: 27, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
23 2 0.07
24 5 0.19
25 19 0.70
26 1 0.04
ACGTcount: A:0.48, C:0.04, G:0.00, T:0.48
Consensus pattern (23 bp):
AATAAAATTATAATTATATTATT
Found at i:16065 original size:22 final size:23
Alignment explanation
Indices: 16041--16083 Score: 63
Period size: 21 Copynumber: 2.0 Consensus size: 23
16031 GCCCAAAAAA
16041 AAAATTTCAA-TTTA-TTAATTT
1 AAAATTTCAATTTTATTTAATTT
*
16062 AAAATTTTAATTTTATTTAATT
1 AAAATTTCAATTTTATTTAATT
16084 ATTTTAATAA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
21 9 0.47
22 4 0.21
23 6 0.32
ACGTcount: A:0.42, C:0.02, G:0.00, T:0.56
Consensus pattern (23 bp):
AAAATTTCAATTTTATTTAATTT
Found at i:16623 original size:15 final size:16
Alignment explanation
Indices: 16592--16624 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
16582 GATGTATTAG
*
16592 ATAATTTTCATTTAAA
1 ATAATTATCATTTAAA
16608 ATAATTATCA-TTAAA
1 ATAATTATCATTTAAA
16623 AT
1 AT
16625 TTTTTAACCT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
15 7 0.44
16 9 0.56
ACGTcount: A:0.48, C:0.06, G:0.00, T:0.45
Consensus pattern (16 bp):
ATAATTATCATTTAAA
Found at i:19184 original size:25 final size:25
Alignment explanation
Indices: 19155--19208 Score: 74
Period size: 25 Copynumber: 2.2 Consensus size: 25
19145 ATAAATAAAT
*
19155 AAAATTATTATTATCTTATTGAT-TA
1 AAAATTATTATTATATTATT-ATATA
*
19180 AAAATTATTATTTTATTATTATATA
1 AAAATTATTATTATATTATTATATA
19205 AAAA
1 AAAA
19209 ATTAATAACT
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
24 2 0.08
25 24 0.92
ACGTcount: A:0.46, C:0.02, G:0.02, T:0.50
Consensus pattern (25 bp):
AAAATTATTATTATATTATTATATA
Found at i:20081 original size:26 final size:22
Alignment explanation
Indices: 20048--20100 Score: 63
Period size: 23 Copynumber: 2.3 Consensus size: 22
20038 CTACTCACAT
20048 TATT-ATTTTTATTATATCTTTAAA
1 TATTAATTTTTA--ATAT-TTTAAA
20072 TAATTAATTTTTAATATTTTAAA
1 T-ATTAATTTTTAATATTTTAAA
20095 TATTAA
1 TATTAA
20101 ATAAAATTAA
Statistics
Matches: 27, Mismatches: 0, Indels: 6
0.82 0.00 0.18
Matches are distributed among these distances:
22 5 0.19
23 7 0.26
24 5 0.19
25 3 0.11
26 7 0.26
ACGTcount: A:0.40, C:0.02, G:0.00, T:0.58
Consensus pattern (22 bp):
TATTAATTTTTAATATTTTAAA
Found at i:21984 original size:72 final size:72
Alignment explanation
Indices: 21893--22036 Score: 225
Period size: 72 Copynumber: 2.0 Consensus size: 72
21883 AATCGGAAGG
* * * * *
21893 TTGACCAGCTTATCTACTCTCTACCTTCATCTAACTATGTTTTCTGGTTCAATCCCTGCTTCCAT
1 TTGACCAGCTTATCTACTCTCGACCTTCATCAAAATATGTTCTCTGGTTCAATCCCTGCTTCAAT
21958 AGGAAAC
66 AGGAAAC
*
21965 TTGACCAGCTTATCTACTCTCGACCTTTATCAAAATATGTTCTCTGGTTCAATCCCTGCTTCAAT
1 TTGACCAGCTTATCTACTCTCGACCTTCATCAAAATATGTTCTCTGGTTCAATCCCTGCTTCAAT
*
22030 TGGAAAC
66 AGGAAAC
22037 ATGAGGAAGC
Statistics
Matches: 65, Mismatches: 7, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
72 65 1.00
ACGTcount: A:0.24, C:0.28, G:0.12, T:0.37
Consensus pattern (72 bp):
TTGACCAGCTTATCTACTCTCGACCTTCATCAAAATATGTTCTCTGGTTCAATCCCTGCTTCAAT
AGGAAAC
Found at i:28004 original size:13 final size:13
Alignment explanation
Indices: 27986--28012 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
27976 GAACTCTCCT
27986 TTTTTCATCAATA
1 TTTTTCATCAATA
27999 TTTTTCATCAATA
1 TTTTTCATCAATA
28012 T
1 T
28013 AAACTCCAGA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.30, C:0.15, G:0.00, T:0.56
Consensus pattern (13 bp):
TTTTTCATCAATA
Found at i:31007 original size:161 final size:162
Alignment explanation
Indices: 30742--31070 Score: 597
Period size: 161 Copynumber: 2.0 Consensus size: 162
30732 ATATTGTGAT
*
30742 TTTATTGTATTGATCAAACTTAATATAAGTAAATTAAATTGTTCTATTTTATTATTCTTTTTCAT
1 TTTATTGTATTGATAAAACTTAATATAAGTAAATTAAATTGTTCTATTTTATTATTCTTTTTCAT
*
30807 AATCTATCCATGATTGTATGTTATGAAAGTGGATTTAGGTGAATGTATATTCT-TAATGAATATG
66 AATCTATCCATGAATGTATGTTATGAAAGTGGATTTAGGTGAATGTATATTCTATAATGAATATG
30871 ATTTTTTATTCATTTTCATCATACTAACTTGC
131 ATTTTTTATTCATTTTCATCATACTAACTTGC
*
30903 TTTATTGTATTGATAAAACTTAATATAAGTAAATTAAATTGTTCTATTTTATTCTTCTTTTTCAT
1 TTTATTGTATTGATAAAACTTAATATAAGTAAATTAAATTGTTCTATTTTATTATTCTTTTTCAT
***
30968 AATCTATTTGTGAATGTATGTTATGAAAGTGGATTTAGGTGAATGTATATTCTATAATGAATATG
66 AATCTATCCATGAATGTATGTTATGAAAGTGGATTTAGGTGAATGTATATTCTATAATGAATATG
31033 ATTTTTTATTCATTTTCATCATACTAACTTGC
131 ATTTTTTATTCATTTTCATCATACTAACTTGC
31065 TTTATT
1 TTTATT
31071 TTCCATTTCA
Statistics
Matches: 161, Mismatches: 6, Indels: 1
0.96 0.04 0.01
Matches are distributed among these distances:
161 112 0.70
162 49 0.30
ACGTcount: A:0.31, C:0.09, G:0.11, T:0.49
Consensus pattern (162 bp):
TTTATTGTATTGATAAAACTTAATATAAGTAAATTAAATTGTTCTATTTTATTATTCTTTTTCAT
AATCTATCCATGAATGTATGTTATGAAAGTGGATTTAGGTGAATGTATATTCTATAATGAATATG
ATTTTTTATTCATTTTCATCATACTAACTTGC
Found at i:32870 original size:5 final size:5
Alignment explanation
Indices: 32851--32886 Score: 63
Period size: 5 Copynumber: 7.0 Consensus size: 5
32841 AGAAAAAAAT
32851 ATAAA ATAAA TATAAA ATAAA ATAAA ATAAA ATAAA
1 ATAAA ATAAA -ATAAA ATAAA ATAAA ATAAA ATAAA
32887 TTTTTGTTGA
Statistics
Matches: 30, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
5 25 0.83
6 5 0.17
ACGTcount: A:0.78, C:0.00, G:0.00, T:0.22
Consensus pattern (5 bp):
ATAAA
Found at i:35549 original size:5 final size:5
Alignment explanation
Indices: 35524--35567 Score: 61
Period size: 5 Copynumber: 8.6 Consensus size: 5
35514 GCTCGGATCG
* *
35524 CGGCT CCGGCT TGGTT CGGCT CGGCT CGGCT CGGCT CGGCT CGG
1 CGGCT -CGGCT CGGCT CGGCT CGGCT CGGCT CGGCT CGGCT CGG
35568 AGGGGCTGAA
Statistics
Matches: 34, Mismatches: 4, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
5 29 0.85
6 5 0.15
ACGTcount: A:0.00, C:0.36, G:0.41, T:0.23
Consensus pattern (5 bp):
CGGCT
Found at i:35833 original size:11 final size:11
Alignment explanation
Indices: 35817--35852 Score: 54
Period size: 11 Copynumber: 3.3 Consensus size: 11
35807 CCGGAATCTG
*
35817 GGAAATTCGCC
1 GGAAATTGGCC
35828 GGAAATTGGCC
1 GGAAATTGGCC
*
35839 GGAAGTTGGCC
1 GGAAATTGGCC
35850 GGA
1 GGA
35853 TGGTCGCCGG
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
11 23 1.00
ACGTcount: A:0.25, C:0.19, G:0.39, T:0.17
Consensus pattern (11 bp):
GGAAATTGGCC
Found at i:35941 original size:31 final size:32
Alignment explanation
Indices: 35900--35965 Score: 100
Period size: 31 Copynumber: 2.1 Consensus size: 32
35890 GTCTGTCACC
*
35900 GAAAACTTC-AAAGTTCGTCGGAATTTTCGCCG
1 GAAAACTTCAAAAG-TCGCCGGAATTTTCGCCG
35932 GAAAA-TTCAAAAGTCGCCGGAATTTTCGCCG
1 GAAAACTTCAAAAGTCGCCGGAATTTTCGCCG
35963 GAA
1 GAA
35966 TCTGGAAATT
Statistics
Matches: 32, Mismatches: 1, Indels: 3
0.89 0.03 0.08
Matches are distributed among these distances:
31 23 0.72
32 9 0.28
ACGTcount: A:0.32, C:0.21, G:0.23, T:0.24
Consensus pattern (32 bp):
GAAAACTTCAAAAGTCGCCGGAATTTTCGCCG
Found at i:36374 original size:30 final size:29
Alignment explanation
Indices: 36325--36394 Score: 99
Period size: 30 Copynumber: 2.4 Consensus size: 29
36315 TAATTAGAAC
*
36325 AGATAAAT-AAAAAAACAGATATATTA-T
1 AGATAAATAAAAAAAACAGATATATAATT
36352 AGGATAAATAAAAAATAACAGATATATAATT
1 A-GATAAATAAAAAA-AACAGATATATAATT
36383 AGATAAATAAAA
1 AGATAAATAAAA
36395 TACAACAATA
Statistics
Matches: 38, Mismatches: 1, Indels: 5
0.86 0.02 0.11
Matches are distributed among these distances:
27 1 0.03
28 7 0.18
29 5 0.13
30 23 0.61
31 2 0.05
ACGTcount: A:0.64, C:0.03, G:0.09, T:0.24
Consensus pattern (29 bp):
AGATAAATAAAAAAAACAGATATATAATT
Found at i:36395 original size:28 final size:27
Alignment explanation
Indices: 36292--36396 Score: 95
Period size: 28 Copynumber: 3.7 Consensus size: 27
36282 AAAAAATCAA
* *
36292 ATAATATATAAA-AAAATAATAGATAATT
1 ATAATAGATAAATAAAATAACAGAT-A-T
* * *
36320 AGAACAGATAAATAAAAAAACAGATAT
1 ATAATAGATAAATAAAATAACAGATAT
*
36347 ATTATAGGATAAATAAAAAATAACAGATAT
1 ATAATA-GATAAAT--AAAATAACAGATAT
36377 ATAATTAGATAAATAAAATA
1 ATAA-TAGATAAATAAAATA
36397 CAACAATAAA
Statistics
Matches: 62, Mismatches: 10, Indels: 10
0.76 0.12 0.12
Matches are distributed among these distances:
27 4 0.06
28 23 0.37
29 10 0.16
30 23 0.37
31 2 0.03
ACGTcount: A:0.64, C:0.03, G:0.08, T:0.26
Consensus pattern (27 bp):
ATAATAGATAAATAAAATAACAGATAT
Found at i:36421 original size:17 final size:17
Alignment explanation
Indices: 36375--36434 Score: 61
Period size: 17 Copynumber: 3.5 Consensus size: 17
36365 AATAACAGAT
36375 ATATAATTAGATAAATAAA
1 ATATAA-TA-ATAAATAAA
* *
36394 ATACAACAATAAATAAA
1 ATATAATAATAAATAAA
*
36411 ATATAATAAT-AATAAT
1 ATATAATAATAAATAAA
36427 A-ATAATAA
1 ATATAATAA
36435 ATATATAACT
Statistics
Matches: 36, Mismatches: 5, Indels: 4
0.80 0.11 0.09
Matches are distributed among these distances:
15 7 0.19
16 6 0.17
17 17 0.47
18 1 0.03
19 5 0.14
ACGTcount: A:0.67, C:0.03, G:0.02, T:0.28
Consensus pattern (17 bp):
ATATAATAATAAATAAA
Found at i:36442 original size:23 final size:25
Alignment explanation
Indices: 36405--36485 Score: 68
Period size: 25 Copynumber: 3.4 Consensus size: 25
36395 TACAACAATA
36405 AATA-AAATATAATAA-TA-AT-AAT
1 AATATAAATAT-ATAACTATATAAAT
36427 AATAATAAATATATAACTATATAAAT
1 AAT-ATAAATATATAACTATATAAAT
*
36453 AATATACATATA-AATCTATA-AAA-
1 AATATAAATATATAA-CTATATAAAT
*
36476 AAAATAAATA
1 AATATAAATA
36486 AATACAGATA
Statistics
Matches: 50, Mismatches: 3, Indels: 11
0.78 0.05 0.17
Matches are distributed among these distances:
22 3 0.06
23 13 0.26
24 13 0.26
25 15 0.30
26 6 0.12
ACGTcount: A:0.65, C:0.04, G:0.00, T:0.31
Consensus pattern (25 bp):
AATATAAATATATAACTATATAAAT
Found at i:36741 original size:1 final size:1
Alignment explanation
Indices: 36737--36894 Score: 109
Period size: 1 Copynumber: 158.0 Consensus size: 1
36727 CATTTTTTGA
* * ** * * * ** **
36737 TTTTTTTTTTTATCTTTTTGATTTTTTTATTTTTGTTTTTATTTTTTGATTTTTTTTGATTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
** * * * * * * * * *
36802 TGATTTTTTGTTTTTTTGTTTTTTGTTTTTTGTTTTTTTGTTTTTTGTTTTTTTGTTTGTTTTTG
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
*
36867 TTTTTTGTTTTTTTTTTTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTT
36895 GCCGAAGCTC
Statistics
Matches: 115, Mismatches: 42, Indels: 0
0.73 0.27 0.00
Matches are distributed among these distances:
1 115 1.00
ACGTcount: A:0.04, C:0.01, G:0.09, T:0.85
Consensus pattern (1 bp):
T
Found at i:36879 original size:7 final size:7
Alignment explanation
Indices: 36729--36891 Score: 139
Period size: 7 Copynumber: 23.9 Consensus size: 7
36719 CAACTCAACA
36729 TTTTTTG
1 TTTTTTG
*
36736 ATTTTT-
1 TTTTTTG
*
36742 TTTTTTA
1 TTTTTTG
36749 TCTTTTTG
1 T-TTTTTG
36757 ATTTTTT-
1 -TTTTTTG
36764 TATTTTTG
1 T-TTTTTG
*
36772 -TTTTTA
1 TTTTTTG
36778 TTTTTTG
1 TTTTTTG
*
36785 ATTTTT-
1 TTTTTTG
**
36791 TTTGAT-
1 TTTTTTG
36797 TTTTTTG
1 TTTTTTG
36804 ATTTTTTG
1 -TTTTTTG
36812 TTTTTTTG
1 -TTTTTTG
36820 TTTTTTG
1 TTTTTTG
36827 TTTTTTG
1 TTTTTTG
36834 TTTTTTTG
1 -TTTTTTG
36842 TTTTTTG
1 TTTTTTG
36849 -TTTTT-
1 TTTTTTG
*
36854 TTGTTTG
1 TTTTTTG
36861 -TTTTTG
1 TTTTTTG
36867 TTTTTTG
1 TTTTTTG
36874 TTTTTT-
1 TTTTTTG
36880 TTTTTT-
1 TTTTTTG
36886 TTTTTT
1 TTTTTT
36892 TTTGCCGAAG
Statistics
Matches: 130, Mismatches: 14, Indels: 25
0.77 0.08 0.15
Matches are distributed among these distances:
6 44 0.34
7 54 0.42
8 31 0.24
9 1 0.01
ACGTcount: A:0.05, C:0.01, G:0.10, T:0.85
Consensus pattern (7 bp):
TTTTTTG
Found at i:36880 original size:8 final size:8
Alignment explanation
Indices: 36737--36895 Score: 149
Period size: 8 Copynumber: 20.6 Consensus size: 8
36727 CATTTTTTGA
36737 TTTT-TTT
1 TTTTGTTT
* *
36744 TTTTATCT
1 TTTTGTTT
*
36752 TTTTGATT
1 TTTTGTTT
*
36760 TTTT-TAT
1 TTTTGTTT
36767 TTTTGTTT
1 TTTTGTTT
36775 TTATT-TTT
1 TT-TTGTTT
**
36783 TGAT-TTT
1 TTTTGTTT
36790 TTTTGATTT
1 TTTTG-TTT
*
36799 TTTTGATT
1 TTTTGTTT
36807 TTTTGTTT
1 TTTTGTTT
36815 TTTTG-TT
1 TTTTGTTT
36822 TTTTG-TT
1 TTTTGTTT
36829 TTTTGTTT
1 TTTTGTTT
36837 TTTTG-TT
1 TTTTGTTT
36844 TTTTGTTT
1 TTTTGTTT
36852 TTTTGTTT
1 TTTTGTTT
36860 GTTTT-TGTT
1 -TTTTGT-TT
36869 TTTTGTTT
1 TTTTGTTT
36877 TTTT-TTT
1 TTTTGTTT
36884 TTTT-TTT
1 TTTTGTTT
36891 TTTTG
1 TTTTG
36896 CCGAAGCTCC
Statistics
Matches: 128, Mismatches: 13, Indels: 21
0.79 0.08 0.13
Matches are distributed among these distances:
7 50 0.39
8 61 0.48
9 17 0.13
ACGTcount: A:0.04, C:0.01, G:0.10, T:0.85
Consensus pattern (8 bp):
TTTTGTTT
Found at i:36893 original size:47 final size:47
Alignment explanation
Indices: 36729--36895 Score: 168
Period size: 47 Copynumber: 3.6 Consensus size: 47
36719 CAACTCAACA
* * *
36729 TTTTTTGATTTTTTTTTTTATCTTTTTGATTT-TTTTATT-TTTGTTTTTA
1 TTTTTTG-TTTTTTTTTTT-T-TTTTT-TTTTGTTTTTTTGTTTGTTTTTG
* ** *
36778 TTTTTTG---ATTTTTTTTGATTTTTTTGATTTTTTG-TT-TTTTTG
1 TTTTTTGTTTTTTTTTTTTTTTTTTTTTGTTTTTTTGTTTGTTTTTG
* *
36820 TTTTTTGTTTTTTGTTTTTTTGTTTTTTGTTTTTTTGTTTGTTTTTG
1 TTTTTTGTTTTTTTTTTTTTTTTTTTTTGTTTTTTTGTTTGTTTTTG
36867 TTTTTTGTTTTTTTTTTTTTTTTTTTTTG
1 TTTTTTGTTTTTTTTTTTTTTTTTTTTTG
36896 CCGAAGCTCC
Statistics
Matches: 96, Mismatches: 15, Indels: 16
0.76 0.12 0.13
Matches are distributed among these distances:
42 15 0.16
43 10 0.10
44 1 0.01
45 28 0.29
46 2 0.02
47 33 0.34
49 7 0.07
ACGTcount: A:0.05, C:0.01, G:0.10, T:0.84
Consensus pattern (47 bp):
TTTTTTGTTTTTTTTTTTTTTTTTTTTTGTTTTTTTGTTTGTTTTTG
Found at i:36970 original size:42 final size:40
Alignment explanation
Indices: 36920--37480 Score: 524
Period size: 41 Copynumber: 13.7 Consensus size: 40
36910 AACGGAAACT
*
36920 CAACGACTTTTG-AAAGTAAATTGGCTCCTCTAAAACAGAGG
1 CAACGACTTTTGAAAAGTAAATT-GCTCCTCT-CAACAGAGG
*
36961 CAACGGAC-TTTG-GAAGTAAATTGCTCCCTCTCAACAGAGG
1 CAAC-GACTTTTGAAAAGTAAATTGCT-CCTCTCAACAGAGG
* * *
37001 CACCACGA-TTTGGAAAAATAAATTGCTTCTCTCAACAGAGG
1 CA--ACGACTTTTGAAAAGTAAATTGCTCCTCTCAACAGAGG
* *
37042 CACACGAC-TTTGAAAAAGTAAATTGCTCCTCTCAATAGAGA
1 CA-ACGACTTTTG-AAAAGTAAATTGCTCCTCTCAACAGAGG
*
37083 CACCACGA--TTTGAAAAGT-AATTGCTCCTCCCAACAGAGG
1 CA--ACGACTTTTGAAAAGTAAATTGCTCCTCTCAACAGAGG
* *
37122 ACCACGAC-TTTGAAAAGTAAATTGCT-CTCTAAACCAGAGG
1 -CAACGACTTTTGAAAAGTAAATTGCTCCTCTCAA-CAGAGG
* * *
37162 TACCACGA-TTTGGAAAAGTAAATTGCTCCTCTAAACAGAGG
1 --CAACGACTTTTGAAAAGTAAATTGCTCCTCTCAACAGAGG
* *
37203 CACCACGAC-TTTGGAAAGT-AATTGCTCCTCTAAACAGAGG
1 CA--ACGACTTTTGAAAAGTAAATTGCTCCTCTCAACAGAGG
* * *
37243 TACCCACGACTTTGGAAAAATAAATTGCTCCTCTCAACAGAGG
1 ---CAACGACTTTTGAAAAGTAAATTGCTCCTCTCAACAGAGG
37286 CACCACGAC-TTTGAAAAGTAAATTGCTCCTCTCAACAGAGG
1 CA--ACGACTTTTGAAAAGTAAATTGCTCCTCTCAACAGAGG
* *
37327 TACCACGACTTTGGAAAAGTAAATTGCTCCTCTCAACAGAGG
1 --CAACGACTTTTGAAAAGTAAATTGCTCCTCTCAACAGAGG
* *
37369 CACCACGACTTTGGAAAAGTAAATTGCTCCTCTAAACAGAGG
1 CA--ACGACTTTTGAAAAGTAAATTGCTCCTCTCAACAGAGG
37411 CAACGAAC--TTGAAAAGTAAATTGCTCCTCTCAACAGAGG
1 CAACG-ACTTTTGAAAAGTAAATTGCTCCTCTCAACAGAGG
* * * *
37450 TACCACGACTTTGGAAAAATAAATTACTCCT
1 --CAACGACTTTTGAAAAGTAAATTGCTCCT
37481 TGACAATCAT
Statistics
Matches: 445, Mismatches: 39, Indels: 71
0.80 0.07 0.13
Matches are distributed among these distances:
38 4 0.01
39 63 0.14
40 69 0.16
41 160 0.36
42 127 0.29
43 22 0.05
ACGTcount: A:0.35, C:0.24, G:0.18, T:0.23
Consensus pattern (40 bp):
CAACGACTTTTGAAAAGTAAATTGCTCCTCTCAACAGAGG
Found at i:37061 original size:83 final size:82
Alignment explanation
Indices: 36932--37480 Score: 726
Period size: 83 Copynumber: 6.7 Consensus size: 82
36922 ACGACTTTTG
* * *
36932 AAAGTAAATTGGCTCCTCTAAAACAGAGGCA--ACGGACTTTG-GAAGTAAATTGCTCCCTCTCA
1 AAAGTAAATT-GCTCCTCT-CAACAGAGGCACCAC-GACTTTGAAAAGTAAATTGCT-CCTCTAA
36994 ACAGAGGCACCACGATTTGGA
62 ACAGAGGCACCACGATTTGGA
* * * *
37015 AAAATAAATTGCTTCTCTCAACAGAGGCA-CACGACTTTGAAAAAGTAAATTGCTCCTCTCAATA
1 AAAGTAAATTGCTCCTCTCAACAGAGGCACCACGACTTTG-AAAAGTAAATTGCTCCTCTAAACA
*
37079 GAGACACCACGATTT-GA
65 GAGGCACCACGATTTGGA
*
37096 AAAGT-AATTGCTCCTCCCAACAGAGG-ACCACGACTTTGAAAAGTAAATTGCT-CTCTAAACCA
1 AAAGTAAATTGCTCCTCTCAACAGAGGCACCACGACTTTGAAAAGTAAATTGCTCCTCTAAA-CA
*
37158 GAGGTACCACGATTTGGA
65 GAGGCACCACGATTTGGA
* *
37176 AAAGTAAATTGCTCCTCTAAACAGAGGCACCACGACTTTGGAAAGT-AATTGCTCCTCTAAACAG
1 AAAGTAAATTGCTCCTCTCAACAGAGGCACCACGACTTTGAAAAGTAAATTGCTCCTCTAAACAG
*
37240 AGGTACCCACGACTTTGGA
66 AGGCA-CCACGA-TTTGGA
* *
37259 AAAATAAATTGCTCCTCTCAACAGAGGCACCACGACTTTGAAAAGTAAATTGCTCCTCTCAACAG
1 AAAGTAAATTGCTCCTCTCAACAGAGGCACCACGACTTTGAAAAGTAAATTGCTCCTCTAAACAG
*
37324 AGGTACCACGACTTTGGA
66 AGGCACCACGA-TTTGGA
37342 AAAGTAAATTGCTCCTCTCAACAGAGGCACCACGACTTTGGAAAAGTAAATTGCTCCTCTAAACA
1 AAAGTAAATTGCTCCTCTCAACAGAGGCACCACGACTTT-GAAAAGTAAATTGCTCCTCTAAACA
*
37407 GAGGCA--ACGAACTT-GA
65 GAGGCACCACG-ATTTGGA
* * *
37423 AAAGTAAATTGCTCCTCTCAACAGAGGTACCACGACTTTGGAAAAATAAATTACTCCT
1 AAAGTAAATTGCTCCTCTCAACAGAGGCACCACGACTTT-GAAAAGTAAATTGCTCCT
37481 TGACAATCAT
Statistics
Matches: 425, Mismatches: 27, Indels: 30
0.88 0.06 0.06
Matches are distributed among these distances:
78 6 0.01
79 29 0.07
80 36 0.08
81 114 0.27
82 67 0.16
83 122 0.29
84 51 0.12
ACGTcount: A:0.36, C:0.23, G:0.18, T:0.23
Consensus pattern (82 bp):
AAAGTAAATTGCTCCTCTCAACAGAGGCACCACGACTTTGAAAAGTAAATTGCTCCTCTAAACAG
AGGCACCACGATTTGGA
Found at i:38762 original size:11 final size:10
Alignment explanation
Indices: 38736--38792 Score: 60
Period size: 12 Copynumber: 5.2 Consensus size: 10
38726 CATTTTCTCA
*
38736 TTTTTTCCTT
1 TTTTTTCTTT
38746 TTTTTTCTTT
1 TTTTTTCTTT
38756 TTCTTTTCTTTT
1 TT-TTTTC-TTT
38768 TTTTTTCATCTT
1 TTTTTTC-T-TT
38780 TTTTTTCATTT
1 TTTTTTC-TTT
38791 TT
1 TT
38793 CATCTATTAT
Statistics
Matches: 42, Mismatches: 2, Indels: 5
0.86 0.04 0.10
Matches are distributed among these distances:
10 11 0.26
11 15 0.36
12 16 0.38
ACGTcount: A:0.04, C:0.14, G:0.00, T:0.82
Consensus pattern (10 bp):
TTTTTTCTTT
Found at i:38762 original size:12 final size:12
Alignment explanation
Indices: 38744--38792 Score: 66
Period size: 11 Copynumber: 4.2 Consensus size: 12
38734 CATTTTTTCC
38744 TTTTTTTTC-TT
1 TTTTTTTTCATT
*
38755 TTTCTTTTC-TT
1 TTTTTTTTCATT
*
38766 TTTTTTTTCATC
1 TTTTTTTTCATT
38778 TTTTTTTTCATT
1 TTTTTTTTCATT
38790 TTT
1 TTT
38793 CATCTATTAT
Statistics
Matches: 33, Mismatches: 4, Indels: 1
0.87 0.11 0.03
Matches are distributed among these distances:
11 18 0.55
12 15 0.45
ACGTcount: A:0.04, C:0.12, G:0.00, T:0.84
Consensus pattern (12 bp):
TTTTTTTTCATT
Found at i:38791 original size:19 final size:18
Alignment explanation
Indices: 38743--38797 Score: 71
Period size: 17 Copynumber: 3.1 Consensus size: 18
38733 TCATTTTTTC
38743 CTTTTTTTTCTTTTTC-T
1 CTTTTTTTTCTTTTTCAT
38760 -TTTCTTTTT-TTTTTCAT
1 CTTT-TTTTTCTTTTTCAT
38777 CTTTTTTTTCATTTTTCAT
1 CTTTTTTTTC-TTTTTCAT
38796 CT
1 CT
38798 ATTATTGATA
Statistics
Matches: 33, Mismatches: 0, Indels: 8
0.80 0.00 0.20
Matches are distributed among these distances:
16 9 0.27
17 11 0.33
18 3 0.09
19 10 0.30
ACGTcount: A:0.05, C:0.16, G:0.00, T:0.78
Consensus pattern (18 bp):
CTTTTTTTTCTTTTTCAT
Found at i:42684 original size:5 final size:5
Alignment explanation
Indices: 42662--42704 Score: 68
Period size: 5 Copynumber: 8.6 Consensus size: 5
42652 GCTCGGATCG
* *
42662 CGGCT CGGCT TGGTT CGGCT CGGCT CGGCT CGGCT CGGCT CGG
1 CGGCT CGGCT CGGCT CGGCT CGGCT CGGCT CGGCT CGGCT CGG
42705 AGGGGCTGAA
Statistics
Matches: 34, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
5 34 1.00
ACGTcount: A:0.00, C:0.35, G:0.42, T:0.23
Consensus pattern (5 bp):
CGGCT
Found at i:42711 original size:15 final size:15
Alignment explanation
Indices: 42650--42711 Score: 52
Period size: 15 Copynumber: 4.0 Consensus size: 15
42640 AAACCTGGAG
42650 CGGCTCGGATCGCGGCT
1 CGGCTCGGA--GCGGCT
* **
42667 CGGCTTGGTTCGGCT
1 CGGCTCGGAGCGGCT
**
42682 CGGCTCGGCTCGGCT
1 CGGCTCGGAGCGGCT
*
42697 CGGCTCGGAGGGGCT
1 CGGCTCGGAGCGGCT
42712 GAAACGCGCG
Statistics
Matches: 37, Mismatches: 8, Indels: 2
0.79 0.17 0.04
Matches are distributed among these distances:
15 30 0.81
17 7 0.19
ACGTcount: A:0.03, C:0.32, G:0.44, T:0.21
Consensus pattern (15 bp):
CGGCTCGGAGCGGCT
Found at i:42946 original size:19 final size:20
Alignment explanation
Indices: 42922--42959 Score: 60
Period size: 19 Copynumber: 1.9 Consensus size: 20
42912 AGAACGCCGG
*
42922 TGCCGGATTCT-GGAAATTT
1 TGCCGGAATCTGGGAAATTT
42941 TGCCGGAATCTGGGAAATT
1 TGCCGGAATCTGGGAAATT
42960 CGTCGGAAAT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 10 0.59
20 7 0.41
ACGTcount: A:0.24, C:0.16, G:0.29, T:0.32
Consensus pattern (20 bp):
TGCCGGAATCTGGGAAATTT
Found at i:43071 original size:31 final size:31
Alignment explanation
Indices: 43031--43101 Score: 99
Period size: 31 Copynumber: 2.3 Consensus size: 31
43021 ACTGGGTCTG
*
43031 TCGCCGGAAACTTC-AAAGTTCACCGGAATTT
1 TCGCCGGAAAATTCAAAAG-TCACCGGAATTT
* *
43062 TTGCCGGAAAATTCAAAAGTCGCCGGAATTT
1 TCGCCGGAAAATTCAAAAGTCACCGGAATTT
43093 TCGCCGGAA
1 TCGCCGGAA
43102 TCTGGAAATT
Statistics
Matches: 35, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
31 31 0.89
32 4 0.11
ACGTcount: A:0.30, C:0.24, G:0.23, T:0.24
Consensus pattern (31 bp):
TCGCCGGAAAATTCAAAAGTCACCGGAATTT
Found at i:43500 original size:28 final size:29
Alignment explanation
Indices: 43463--43535 Score: 105
Period size: 30 Copynumber: 2.5 Consensus size: 29
43453 TAATTAGAAC
*
43463 AGATAAATAAAAA-AACAGATATATTA-T
1 AGATAAATAAAAATAACAGATATATAATT
43490 AGGATAAATAAAAAATAACAGATATATAATT
1 A-GATAAAT-AAAAATAACAGATATATAATT
43521 AGATAAATAAAAATA
1 AGATAAATAAAAATA
43536 CAACAATAAA
Statistics
Matches: 41, Mismatches: 1, Indels: 6
0.85 0.02 0.12
Matches are distributed among these distances:
27 1 0.02
28 7 0.17
29 12 0.29
30 19 0.46
31 2 0.05
ACGTcount: A:0.64, C:0.03, G:0.08, T:0.25
Consensus pattern (29 bp):
AGATAAATAAAAATAACAGATATATAATT
Found at i:43558 original size:3 final size:3
Alignment explanation
Indices: 43544--43576 Score: 52
Period size: 3 Copynumber: 11.7 Consensus size: 3
43534 TACAACAATA
43544 AAT AA- AAT -AT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
43577 ATATATAACT
Statistics
Matches: 28, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
2 4 0.14
3 24 0.86
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (3 bp):
AAT
Found at i:43597 original size:23 final size:23
Alignment explanation
Indices: 43564--43627 Score: 67
Period size: 25 Copynumber: 2.7 Consensus size: 23
43554 AATAATAATA
*
43564 ATAATAATAATAAATATATAA-CT
1 ATAAAAATAATAAATATA-AATCT
*
43587 ATATAAATAATATACATATAAATCT
1 ATAAAAATAATA-A-ATATAAATCT
*
43612 ATAAAAAAAATAAATA
1 ATAAAAATAATAAATA
43628 AATACAGATA
Statistics
Matches: 34, Mismatches: 4, Indels: 6
0.77 0.09 0.14
Matches are distributed among these distances:
23 13 0.38
24 4 0.12
25 17 0.50
ACGTcount: A:0.64, C:0.05, G:0.00, T:0.31
Consensus pattern (23 bp):
ATAAAAATAATAAATATAAATCT
Found at i:46618 original size:3 final size:3
Alignment explanation
Indices: 46610--46654 Score: 90
Period size: 3 Copynumber: 15.0 Consensus size: 3
46600 TATCTTCACT
46610 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
46655 CATTGTTATT
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 42 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
TAA
Found at i:47781 original size:22 final size:23
Alignment explanation
Indices: 47742--47791 Score: 59
Period size: 22 Copynumber: 2.2 Consensus size: 23
47732 AACTTATAAA
47742 GAAATAAAATTATAATTATATTAT
1 GAAATAAAA-TATAATTATATTAT
* *
47766 GAAATAAAA-ATTATTATTTTAT
1 GAAATAAAATATAATTATATTAT
47788 -AAAT
1 GAAAT
47792 TTTATTATCA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
21 4 0.17
22 11 0.46
24 9 0.38
ACGTcount: A:0.54, C:0.00, G:0.04, T:0.42
Consensus pattern (23 bp):
GAAATAAAATATAATTATATTAT
Found at i:47789 original size:17 final size:17
Alignment explanation
Indices: 47769--47812 Score: 52
Period size: 17 Copynumber: 2.6 Consensus size: 17
47759 ATATTATGAA
**
47769 ATAAAAATTATTATTTT
1 ATAAAAATTATTATCAT
**
47786 ATAAATTTTATTATCAT
1 ATAAAAATTATTATCAT
47803 ATAAAAATTA
1 ATAAAAATTA
47813 ATTAACTAAA
Statistics
Matches: 21, Mismatches: 6, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
17 21 1.00
ACGTcount: A:0.50, C:0.02, G:0.00, T:0.48
Consensus pattern (17 bp):
ATAAAAATTATTATCAT
Found at i:48003 original size:19 final size:20
Alignment explanation
Indices: 47967--48004 Score: 51
Period size: 19 Copynumber: 1.9 Consensus size: 20
47957 ATTTGACATA
*
47967 AAAATAATTTACTGATTTTT
1 AAAATAATTTACTAATTTTT
*
47987 AAAAT-ATTTATTAATTTT
1 AAAATAATTTACTAATTTT
48005 ATAGAATTTT
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
19 11 0.69
20 5 0.31
ACGTcount: A:0.42, C:0.03, G:0.03, T:0.53
Consensus pattern (20 bp):
AAAATAATTTACTAATTTTT
Found at i:49061 original size:15 final size:17
Alignment explanation
Indices: 49029--49060 Score: 57
Period size: 16 Copynumber: 1.9 Consensus size: 17
49019 TTAAATATCA
49029 ATATTGACAATTTTTTT
1 ATATTGACAATTTTTTT
49046 ATATTG-CAATTTTTT
1 ATATTGACAATTTTTT
49061 AATAAAAAAT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 9 0.60
17 6 0.40
ACGTcount: A:0.28, C:0.06, G:0.06, T:0.59
Consensus pattern (17 bp):
ATATTGACAATTTTTTT
Found at i:49556 original size:17 final size:19
Alignment explanation
Indices: 49534--49568 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
49524 AAATTATAAC
49534 TATTATT-T-TAAAAATTT
1 TATTATTATATAAAAATTT
49551 TATTATTATATAAAAATT
1 TATTATTATATAAAAATT
49569 AATTAACTAA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 7 0.44
18 1 0.06
19 8 0.50
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (19 bp):
TATTATTATATAAAAATTT
Found at i:50288 original size:2 final size:2
Alignment explanation
Indices: 50281--50306 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
50271 AAATAAATAA
50281 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
50307 TAGAATTGTT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:52177 original size:3 final size:3
Alignment explanation
Indices: 52171--52207 Score: 74
Period size: 3 Copynumber: 12.3 Consensus size: 3
52161 AATAACATTG
52171 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
52208 ATGACAGAGA
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 34 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:53293 original size:22 final size:23
Alignment explanation
Indices: 53254--53303 Score: 59
Period size: 22 Copynumber: 2.2 Consensus size: 23
53244 AACTTATAAA
53254 GAAATAAAATTATAATTATATTAT
1 GAAATAAAA-TATAATTATATTAT
* *
53278 GAAATAAAA-ATTATTATTTTAT
1 GAAATAAAATATAATTATATTAT
53300 -AAAT
1 GAAAT
53304 TTTATTATCA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
21 4 0.17
22 11 0.46
24 9 0.38
ACGTcount: A:0.54, C:0.00, G:0.04, T:0.42
Consensus pattern (23 bp):
GAAATAAAATATAATTATATTAT
Found at i:53301 original size:17 final size:17
Alignment explanation
Indices: 53281--53324 Score: 52
Period size: 17 Copynumber: 2.6 Consensus size: 17
53271 ATATTATGAA
**
53281 ATAAAAATTATTATTTT
1 ATAAAAATTATTATCAT
**
53298 ATAAATTTTATTATCAT
1 ATAAAAATTATTATCAT
53315 ATAAAAATTA
1 ATAAAAATTA
53325 ATTGACTAAA
Statistics
Matches: 21, Mismatches: 6, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
17 21 1.00
ACGTcount: A:0.50, C:0.02, G:0.00, T:0.48
Consensus pattern (17 bp):
ATAAAAATTATTATCAT
Found at i:53515 original size:19 final size:20
Alignment explanation
Indices: 53479--53516 Score: 51
Period size: 19 Copynumber: 1.9 Consensus size: 20
53469 ATTTGACATA
*
53479 AAAATAATTTACTGATTTTT
1 AAAATAATTTACTAATTTTT
*
53499 AAAAT-ATTTATTAATTTT
1 AAAATAATTTACTAATTTT
53517 ATAGAATTTT
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
19 11 0.69
20 5 0.31
ACGTcount: A:0.42, C:0.03, G:0.03, T:0.53
Consensus pattern (20 bp):
AAAATAATTTACTAATTTTT
Found at i:54546 original size:16 final size:17
Alignment explanation
Indices: 54518--54553 Score: 65
Period size: 16 Copynumber: 2.2 Consensus size: 17
54508 TTAAATATCA
54518 ATATTGACAATTTTTTT
1 ATATTGACAATTTTTTT
54535 ATATTG-CAATTTTTTT
1 ATATTGACAATTTTTTT
54551 ATA
1 ATA
54554 AAAAAATCCA
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
16 13 0.68
17 6 0.32
ACGTcount: A:0.31, C:0.06, G:0.06, T:0.58
Consensus pattern (17 bp):
ATATTGACAATTTTTTT
Found at i:55783 original size:2 final size:2
Alignment explanation
Indices: 55776--55803 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
55766 TATTAAATAA
55776 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
55804 TAGAATTGTT
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
Done.