Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01013489.1 Corchorus olitorius cultivar O-4 contig13522, 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: 82859
ACGTcount: A:0.31, C:0.17, G:0.18, T:0.33
Found at i:1697 original size:31 final size:31
Alignment explanation
Indices: 1640--1700 Score: 79
Period size: 31 Copynumber: 2.0 Consensus size: 31
1630 ATTCAACGGG
* *
1640 CCTATTTACGTGTAAACTCAGGTCCAAATTA
1 CCTATTCACGTGTAAACTCAGATCCAAATTA
*
1671 CCTATTCACGTGTAAA-TCCATATCCAAATT
1 CCTATTCACGTGTAAACT-CAGATCCAAATT
1701 TTAAAAAAAT
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
30 1 0.04
31 25 0.96
ACGTcount: A:0.33, C:0.25, G:0.10, T:0.33
Consensus pattern (31 bp):
CCTATTCACGTGTAAACTCAGATCCAAATTA
Found at i:2568 original size:22 final size:22
Alignment explanation
Indices: 2523--2869 Score: 168
Period size: 22 Copynumber: 16.1 Consensus size: 22
2513 TGTGAAATTT
*
2523 TTTCATAGCA-AGGTTATCATAA
1 TTTCATAG-AGAGGTTATCAAAA
* * *
2545 TTTCATAGAGTGATTATCGAAA
1 TTTCATAGAGAGGTTATCAAAA
* * *
2567 TTTTATA-AGGGGTTATTAAAA
1 TTTCATAGAGAGGTTATCAAAA
* **
2588 TTTCATAGTAAAATAAATTATCAAAA
1 TTTCATAG----AGAGGTTATCAAAA
*
2614 TTTCAT---GAGGTTACCAAAA
1 TTTCATAGAGAGGTTATCAAAA
* * *
2633 TTCCATAGTGTGGTTATCAAAA
1 TTTCATAGAGAGGTTATCAAAA
*
2655 -TTCATAAAGAGGTTATCAAAA
1 TTTCATAGAGAGGTTATCAAAA
* * *
2676 TTTTATAGTGAGGTTATCGAAA
1 TTTCATAGAGAGGTTATCAAAA
* * *
2698 TTTCATAGGGAGCTTATCGAAA
1 TTTCATAGAGAGGTTATCAAAA
* *
2720 TTT--T-----TGTTATCGAAA
1 TTTCATAGAGAGGTTATCAAAA
*
2735 TTTCATAGGGAGGTTATCAAAA
1 TTTCATAGAGAGGTTATCAAAA
* * *
2757 TTACATAGTGTA-GTTATCAAAG
1 TTTCATAGAG-AGGTTATCAAAA
* * * *
2779 TTTCATTGTGTGGTTATCAAAT
1 TTTCATAGAGAGGTTATCAAAA
* **
2801 TTTCATAGGGAGGTTATTGAAA
1 TTTCATAGAGAGGTTATCAAAA
* *
2823 CTTCATTTG-GAGGTTATCAAAA
1 TTTCA-TAGAGAGGTTATCAAAA
* *
2845 TTTCATA-ATGAGGTTACCGAAA
1 TTTCATAGA-GAGGTTATCAAAA
2867 TTT
1 TTT
2870 TGAAAATTTT
Statistics
Matches: 245, Mismatches: 58, Indels: 44
0.71 0.17 0.13
Matches are distributed among these distances:
15 12 0.05
17 1 0.00
19 14 0.06
20 1 0.00
21 35 0.14
22 164 0.67
23 3 0.01
26 15 0.06
ACGTcount: A:0.35, C:0.10, G:0.18, T:0.37
Consensus pattern (22 bp):
TTTCATAGAGAGGTTATCAAAA
Found at i:2721 original size:44 final size:44
Alignment explanation
Indices: 2605--2869 Score: 198
Period size: 44 Copynumber: 6.3 Consensus size: 44
2595 GTAAAATAAA
* * ** *
2605 TTATCAAAATTTCAT---GAGGTTACCAAAATTCCATAGTGTGG
1 TTATCGAAATTTCATAGGGAGGTTATCAAAATTTTATAGTGAGG
* **
2646 TTATC-AAAATTCATAAAGAGGTTATCAAAATTTTATAGTGAGG
1 TTATCGAAATTTCATAGGGAGGTTATCAAAATTTTATAGTGAGG
* *
2689 TTATCGAAATTTCATAGGGAGCTTATCGAAA-TTT-T--T---G
1 TTATCGAAATTTCATAGGGAGGTTATCAAAATTTTATAGTGAGG
**
2726 TTATCGAAATTTCATAGGGAGGTTATCAAAATTACATAGTGTA-G
1 TTATCGAAATTTCATAGGGAGGTTATCAAAATTTTATAGTG-AGG
* * * *
2770 TTATC-AAAGTTTCATTGTGTGGTTATC-AAATTTTCATAGGGAGG
1 TTATCGAAA-TTTCATAGGGAGGTTATCAAAATTTT-ATAGTGAGG
* * ** * *
2814 TTATTGAAACTTCATTTGGAGGTTATCAAAATTTCATAATGAGG
1 TTATCGAAATTTCATAGGGAGGTTATCAAAATTTTATAGTGAGG
*
2858 TTACCGAAATTT
1 TTATCGAAATTT
2870 TGAAAATTTT
Statistics
Matches: 177, Mismatches: 31, Indels: 29
0.75 0.13 0.12
Matches are distributed among these distances:
37 30 0.17
38 1 0.01
39 1 0.01
40 9 0.05
41 6 0.03
42 1 0.01
43 39 0.22
44 81 0.46
45 9 0.05
ACGTcount: A:0.34, C:0.10, G:0.18, T:0.37
Consensus pattern (44 bp):
TTATCGAAATTTCATAGGGAGGTTATCAAAATTTTATAGTGAGG
Found at i:2738 original size:37 final size:37
Alignment explanation
Indices: 2688--2758 Score: 124
Period size: 37 Copynumber: 1.9 Consensus size: 37
2678 TTATAGTGAG
*
2688 GTTATCGAAATTTCATAGGGAGCTTATCGAAATTTTT
1 GTTATCGAAATTTCATAGGGAGCTTATCAAAATTTTT
*
2725 GTTATCGAAATTTCATAGGGAGGTTATCAAAATT
1 GTTATCGAAATTTCATAGGGAGCTTATCAAAATT
2759 ACATAGTGTA
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
37 32 1.00
ACGTcount: A:0.32, C:0.10, G:0.20, T:0.38
Consensus pattern (37 bp):
GTTATCGAAATTTCATAGGGAGCTTATCAAAATTTTT
Found at i:2796 original size:81 final size:79
Alignment explanation
Indices: 2645--2803 Score: 187
Period size: 81 Copynumber: 2.0 Consensus size: 79
2635 CCATAGTGTG
**
2645 GTTATCAAAATTCATAAAGAGGTTATCAAAATTTTATAGTGAGGTTATCGAAATTTCATAGGGAG
1 GTTATCAAAATTCATAAAGAGGTTATCAAAATTACATAGTGAGGTTATCGAAATTTCATAGGGAG
2710 CTTATCGAAATTTTT
66 CTTATC-AAATTTTT
* ** * *
2725 GTTATCGAAATTTCATAGGGAGGTTATCAAAATTACATAGTGTA-GTTATC-AAAGTTTCATTGT
1 GTTATC-AAAATTCATAAAGAGGTTATCAAAATTACATAGTG-AGGTTATCGAAA-TTTCATAGG
* *
2788 GTGGTTATCAAATTTT
63 GAGCTTATCAAATTTT
2804 CATAGGGAGG
Statistics
Matches: 67, Mismatches: 9, Indels: 6
0.82 0.11 0.07
Matches are distributed among these distances:
80 16 0.24
81 50 0.75
82 1 0.01
ACGTcount: A:0.34, C:0.09, G:0.18, T:0.39
Consensus pattern (79 bp):
GTTATCAAAATTCATAAAGAGGTTATCAAAATTACATAGTGAGGTTATCGAAATTTCATAGGGAG
CTTATCAAATTTTT
Found at i:6548 original size:13 final size:13
Alignment explanation
Indices: 6532--6572 Score: 61
Period size: 13 Copynumber: 3.4 Consensus size: 13
6522 TTTGTGTTAC
6532 TTTTTTGTTTTGT
1 TTTTTTGTTTTGT
6545 TTTTTTGTTTTG-
1 TTTTTTGTTTTGT
6557 -TTTTTGTTTT-T
1 TTTTTTGTTTTGT
6568 TTTTT
1 TTTTT
6573 GAGAACAATT
Statistics
Matches: 26, Mismatches: 0, Indels: 5
0.84 0.00 0.16
Matches are distributed among these distances:
11 10 0.38
12 4 0.15
13 12 0.46
ACGTcount: A:0.00, C:0.00, G:0.12, T:0.88
Consensus pattern (13 bp):
TTTTTTGTTTTGT
Found at i:6561 original size:19 final size:18
Alignment explanation
Indices: 6534--6569 Score: 63
Period size: 19 Copynumber: 1.9 Consensus size: 18
6524 TGTGTTACTT
6534 TTTTGTTTTGTTTTTTTG
1 TTTTGTTTTGTTTTTTTG
6552 TTTTGTTTTTGTTTTTTT
1 TTTTG-TTTTGTTTTTTT
6570 TTTGAGAACA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
18 5 0.29
19 12 0.71
ACGTcount: A:0.00, C:0.00, G:0.14, T:0.86
Consensus pattern (18 bp):
TTTTGTTTTGTTTTTTTG
Found at i:9142 original size:27 final size:27
Alignment explanation
Indices: 9112--9165 Score: 108
Period size: 27 Copynumber: 2.0 Consensus size: 27
9102 GCTGCCCCGT
9112 TGATGGATAAAGGACTAAAGAAAGTAG
1 TGATGGATAAAGGACTAAAGAAAGTAG
9139 TGATGGATAAAGGACTAAAGAAAGTAG
1 TGATGGATAAAGGACTAAAGAAAGTAG
9166 GGATCTCTGG
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 27 1.00
ACGTcount: A:0.48, C:0.04, G:0.30, T:0.19
Consensus pattern (27 bp):
TGATGGATAAAGGACTAAAGAAAGTAG
Found at i:20464 original size:18 final size:18
Alignment explanation
Indices: 20443--20481 Score: 53
Period size: 17 Copynumber: 2.2 Consensus size: 18
20433 TATATTTATA
20443 TAATTAATTAATATAGT-T
1 TAATT-ATTAATATAGTAT
*
20461 TAATTCTTAATATAGTAT
1 TAATTATTAATATAGTAT
20479 TAA
1 TAA
20482 AAAAATATTA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
17 10 0.53
18 9 0.47
ACGTcount: A:0.44, C:0.03, G:0.05, T:0.49
Consensus pattern (18 bp):
TAATTATTAATATAGTAT
Found at i:21975 original size:4 final size:4
Alignment explanation
Indices: 21968--22036 Score: 129
Period size: 4 Copynumber: 17.2 Consensus size: 4
21958 TTCATTCATA
*
21968 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATA
1 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
22016 TATG TATG TATG TATG TATG T
1 TATG TATG TATG TATG TATG T
22037 TCATGCTGTC
Statistics
Matches: 63, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
4 63 1.00
ACGTcount: A:0.26, C:0.00, G:0.23, T:0.51
Consensus pattern (4 bp):
TATG
Found at i:22616 original size:30 final size:31
Alignment explanation
Indices: 22580--22637 Score: 91
Period size: 30 Copynumber: 1.9 Consensus size: 31
22570 ATTGGCTTAA
* *
22580 GACTTGATGGGTTGGGCTGCACG-GGGAAGG
1 GACTTGACGGGTTGAGCTGCACGAGGGAAGG
22610 GACTTGACGGGTTGAGCTGCACGAGGGA
1 GACTTGACGGGTTGAGCTGCACGAGGGA
22638 GAGATGAGGA
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
30 21 0.84
31 4 0.16
ACGTcount: A:0.19, C:0.16, G:0.47, T:0.19
Consensus pattern (31 bp):
GACTTGACGGGTTGAGCTGCACGAGGGAAGG
Found at i:25161 original size:18 final size:20
Alignment explanation
Indices: 25117--25163 Score: 62
Period size: 21 Copynumber: 2.4 Consensus size: 20
25107 GCATATATGG
*
25117 GAAATAATAATTATTATTTT
1 GAAATAATAATTATTATATT
25137 GAAAATAATAATTATT-TATT
1 G-AAATAATAATTATTATATT
25157 G-AATAAT
1 GAAATAAT
25164 TCTCGCCAAT
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
18 6 0.24
20 5 0.20
21 14 0.56
ACGTcount: A:0.49, C:0.00, G:0.06, T:0.45
Consensus pattern (20 bp):
GAAATAATAATTATTATATT
Found at i:29820 original size:3 final size:3
Alignment explanation
Indices: 29812--29837 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
29802 CTTAACCTGC
29812 TGA TGA TGA TGA TGA TGA TGA TGA TG
1 TGA TGA TGA TGA TGA TGA TGA TGA TG
29838 GTAGGCTTCA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.31, C:0.00, G:0.35, T:0.35
Consensus pattern (3 bp):
TGA
Found at i:32380 original size:25 final size:25
Alignment explanation
Indices: 32352--32403 Score: 95
Period size: 25 Copynumber: 2.1 Consensus size: 25
32342 TGAGTACTAT
32352 TATTTAATACAAATCTTAGTATGTA
1 TATTTAATACAAATCTTAGTATGTA
*
32377 TATTTAGTACAAATCTTAGTATGTA
1 TATTTAATACAAATCTTAGTATGTA
32402 TA
1 TA
32404 GTTTTTCCCT
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
25 26 1.00
ACGTcount: A:0.38, C:0.08, G:0.10, T:0.44
Consensus pattern (25 bp):
TATTTAATACAAATCTTAGTATGTA
Found at i:34598 original size:8 final size:8
Alignment explanation
Indices: 34570--34608 Score: 53
Period size: 8 Copynumber: 4.9 Consensus size: 8
34560 TTAACGCAAT
*
34570 TCCCTCCC
1 TCCCCCCC
34578 TCTCCCCCC
1 TC-CCCCCC
34587 -CCCCCCC
1 TCCCCCCC
34594 TCCCCCCC
1 TCCCCCCC
34602 TCCCCCC
1 TCCCCCC
34609 AAATATCACA
Statistics
Matches: 28, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
7 6 0.21
8 17 0.61
9 5 0.18
ACGTcount: A:0.00, C:0.85, G:0.00, T:0.15
Consensus pattern (8 bp):
TCCCCCCC
Found at i:34598 original size:14 final size:15
Alignment explanation
Indices: 34579--34608 Score: 53
Period size: 14 Copynumber: 2.1 Consensus size: 15
34569 TTCCCTCCCT
34579 CTCCCCCCC-CCCCC
1 CTCCCCCCCTCCCCC
34593 CTCCCCCCCTCCCCC
1 CTCCCCCCCTCCCCC
34608 C
1 C
34609 AAATATCACA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 9 0.60
15 6 0.40
ACGTcount: A:0.00, C:0.90, G:0.00, T:0.10
Consensus pattern (15 bp):
CTCCCCCCCTCCCCC
Found at i:35680 original size:6 final size:6
Alignment explanation
Indices: 35669--35693 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
35659 AATTTTCTTG
35669 TTTAAA TTTAAA TTTAAA TTTAAA T
1 TTTAAA TTTAAA TTTAAA TTTAAA T
35694 CAAATTAAAG
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:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (6 bp):
TTTAAA
Found at i:39841 original size:2 final size:2
Alignment explanation
Indices: 39830--39867 Score: 69
Period size: 2 Copynumber: 19.5 Consensus size: 2
39820 TAACATTATG
39830 TA TA -A TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
39868 GAGTTTTGGT
Statistics
Matches: 35, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
1 1 0.03
2 34 0.97
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:40389 original size:19 final size:20
Alignment explanation
Indices: 40360--40401 Score: 68
Period size: 19 Copynumber: 2.1 Consensus size: 20
40350 TTAATCACAA
40360 ATAATCAGTATTTACAGATT
1 ATAATCAGTATTTACAGATT
*
40380 ATAA-CAGTATTTACCGATT
1 ATAATCAGTATTTACAGATT
40399 ATA
1 ATA
40402 TTCACGAATA
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
19 17 0.81
20 4 0.19
ACGTcount: A:0.40, C:0.12, G:0.10, T:0.38
Consensus pattern (20 bp):
ATAATCAGTATTTACAGATT
Found at i:51555 original size:12 final size:12
Alignment explanation
Indices: 51538--51562 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
51528 GCTACAGATT
51538 GAGGAAGAAGAG
1 GAGGAAGAAGAG
51550 GAGGAAGAAGAG
1 GAGGAAGAAGAG
51562 G
1 G
51563 TTAAACTGAT
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:0.48, C:0.00, G:0.52, T:0.00
Consensus pattern (12 bp):
GAGGAAGAAGAG
Found at i:53884 original size:30 final size:30
Alignment explanation
Indices: 53850--53911 Score: 88
Period size: 30 Copynumber: 2.1 Consensus size: 30
53840 ACCTCCAATA
*
53850 CCTGGTGCCCCACCACCACCACCTCCTCCT
1 CCTGGTGCACCACCACCACCACCTCCTCCT
* * *
53880 CCTGGTGCACCTCCACCTCCGCCTCCTCCT
1 CCTGGTGCACCACCACCACCACCTCCTCCT
53910 CC
1 CC
53912 AGGAAGCCTA
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
30 28 1.00
ACGTcount: A:0.10, C:0.60, G:0.11, T:0.19
Consensus pattern (30 bp):
CCTGGTGCACCACCACCACCACCTCCTCCT
Found at i:61055 original size:15 final size:16
Alignment explanation
Indices: 61035--61074 Score: 55
Period size: 15 Copynumber: 2.5 Consensus size: 16
61025 AAATACCATA
*
61035 TATTAATTTAT-TTTT
1 TATTAATTTATATATT
61050 TATTAATTTATATATT
1 TATTAATTTATATATT
61066 TATATAATT
1 TAT-TAATT
61075 ATGAATTAAT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
15 11 0.50
16 6 0.27
17 5 0.23
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (16 bp):
TATTAATTTATATATT
Found at i:63655 original size:40 final size:38
Alignment explanation
Indices: 63542--63673 Score: 155
Period size: 36 Copynumber: 3.5 Consensus size: 38
63532 GAGAACCCGA
* *
63542 ATATATATTTTATTATAAATATTAAATTATTTAAG-AT
1 ATATATATTATATTATTAATATTAAATTATTTAAGTAT
* * *
63579 ATATATATTATA-TATTAATAATAAGTT-TTT-ATTAT
1 ATATATATTATATTATTAATATTAAATTATTTAAGTAT
*
63614 ATATATATTTTATTATTAATATTAAATATATTTAAGATAT
1 ATATATATTATATTATTAATATTAAAT-TATTTAAG-TAT
*
63654 ATATATATTATATTAGTAAT
1 ATATATATTATATTATTAAT
63674 CAGTTTTTAT
Statistics
Matches: 78, Mismatches: 11, Indels: 9
0.80 0.11 0.09
Matches are distributed among these distances:
34 1 0.01
35 16 0.21
36 24 0.31
37 12 0.15
38 3 0.04
39 1 0.01
40 21 0.27
ACGTcount: A:0.45, C:0.00, G:0.03, T:0.52
Consensus pattern (38 bp):
ATATATATTATATTATTAATATTAAATTATTTAAGTAT
Found at i:63679 original size:73 final size:72
Alignment explanation
Indices: 63542--63695 Score: 256
Period size: 73 Copynumber: 2.1 Consensus size: 72
63532 GAGAACCCGA
63542 ATATATATTTTATTATAAATATTAAATTATTTAAGATATATATATTATATATTAATAATAAGTTT
1 ATATATATTTTATTATAAATATTAAATTATTTAAGATATATATATTATATATTAATAATAAGTTT
63607 TTATTAT
66 TTATTAT
* * *
63614 ATATATATTTTATTATTAATATTAAATATATTTAAGATATATATA-TATTATATTAGTAATCAGT
1 ATATATATTTTATTATAAATATTAAAT-TATTTAAGATATATATATTA-TATATTAATAATAAGT
63678 TTTTATTAT
64 TTTTATTAT
63687 ATATATATT
1 ATATATATT
63696 AAAGATAACT
Statistics
Matches: 77, Mismatches: 3, Indels: 3
0.93 0.04 0.04
Matches are distributed among these distances:
72 28 0.36
73 49 0.64
ACGTcount: A:0.43, C:0.01, G:0.03, T:0.53
Consensus pattern (72 bp):
ATATATATTTTATTATAAATATTAAATTATTTAAGATATATATATTATATATTAATAATAAGTTT
TTATTAT
Found at i:63980 original size:15 final size:15
Alignment explanation
Indices: 63960--63989 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
63950 TTTTGTGTAT
63960 CTTATATATATATTA
1 CTTATATATATATTA
63975 CTTATATATATATTA
1 CTTATATATATATTA
63990 AATGTGTAAG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.40, C:0.07, G:0.00, T:0.53
Consensus pattern (15 bp):
CTTATATATATATTA
Found at i:65634 original size:286 final size:291
Alignment explanation
Indices: 65110--65689 Score: 884
Period size: 286 Copynumber: 2.0 Consensus size: 291
65100 TTTTTAGTGA
*
65110 CTATGGAAATTACTTAAATGCCAAATTGAGGATTAATGTGGTGCCTCATTTTGGCTTTTTTTGGT
1 CTATGGAAATTACTTAAAGGCCAAATTGAGGATTAATGTGGTGCCTCATTTT-G-TTTTTTTGGT
* * * * *
65175 TTTTTCTCACTTTTCGGATGACTAAAAAGGCCCTTGATAAATTTCTTTCCTTACTTTTCCTACTA
64 CTTTTCTCACTTTTCGGATGACTAAAAAAGCCCTCGATAAATTTCCTTCCTTACTTCTCCTACTA
* * * *
65240 TCCTTTTTTGTAATTTACTATTTTTGTATTTATGATTAAGTGTGTTTTAATTACGTATTAATTGT
129 CCCTTTTTTGTAATTTACTATTTTTATATTAATGATTAAGTGTGTTTTAATTACATATTAATTGT
* * *
65305 GTGTGGATATTAGGATTTACCGGTTCAATTCCTCTACCGGAATTCTAAAGGATTGGTGCTATAAA
194 GTGTGGATATTAGGATTTACCGGTTCAACTCCTCTACCGGAATTCCAAAGGATTAGTGCTATAAA
65370 TGTATCTACCCGAGTTCATTAATTTAACAATTG
259 TGTATCTACCCGAGTTCATTAATTTAACAATTG
65403 CTATGGAAATTACTTAAAAGGCCAAATTG-GGATTAATGTGGTG-C-C-TTTT-TTTTTTT-GTC
1 CTATGGAAATTACTT-AAAGGCCAAATTGAGGATTAATGTGGTGCCTCATTTTGTTTTTTTGGTC
* * * * *
65462 TTTTCTCACTTTTCGGGTGACTAAAAAAGCCCTCGTTGAATTTCCTTCCTTACTTCTCCTGCTGC
65 TTTTCTCACTTTTCGGATGACTAAAAAAGCCCTCGATAAATTTCCTTCCTTACTTCTCCTACTAC
*
65527 CCTTTTTTGTAATTTACTATTTTTATATTAATGATTAAGTGTGTTTTAATTACATATTGATTGTG
130 CCTTTTTTGTAATTTACTATTTTTATATTAATGATTAAGTGTGTTTTAATTACATATTAATTGTG
** *
65592 TGTGGATATTAGGATTTACCGGTTCAACTCCTCTGTCGGAATTCCAAAGGATTAGTGCTGTAAAT
195 TGTGGATATTAGGATTTACCGGTTCAACTCCTCTACCGGAATTCCAAAGGATTAGTGCTATAAAT
*
65657 GTGTCTACCCGAGTTCATTAATTTAACAATTG
260 GTATCTACCCGAGTTCATTAATTTAACAATTG
65689 C
1 C
65690 AATCAAGATT
Statistics
Matches: 263, Mismatches: 23, Indels: 9
0.89 0.08 0.03
Matches are distributed among these distances:
286 209 0.79
287 7 0.03
290 4 0.02
291 1 0.00
292 1 0.00
293 29 0.11
294 12 0.05
ACGTcount: A:0.25, C:0.16, G:0.17, T:0.43
Consensus pattern (291 bp):
CTATGGAAATTACTTAAAGGCCAAATTGAGGATTAATGTGGTGCCTCATTTTGTTTTTTTGGTCT
TTTCTCACTTTTCGGATGACTAAAAAAGCCCTCGATAAATTTCCTTCCTTACTTCTCCTACTACC
CTTTTTTGTAATTTACTATTTTTATATTAATGATTAAGTGTGTTTTAATTACATATTAATTGTGT
GTGGATATTAGGATTTACCGGTTCAACTCCTCTACCGGAATTCCAAAGGATTAGTGCTATAAATG
TATCTACCCGAGTTCATTAATTTAACAATTG
Found at i:71715 original size:2 final size:2
Alignment explanation
Indices: 71708--71737 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
71698 TACTCCCTGC
71708 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
71738 TTTTCTTTTT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
CT
Found at i:73739 original size:3 final size:3
Alignment explanation
Indices: 73733--73783 Score: 60
Period size: 3 Copynumber: 19.0 Consensus size: 3
73723 ATTATTATAT
73733 ATA ATA ATA ATA AT- ATA AT- ATA AT- ATA AT- ATA AT- ATA ATA AT-
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
73775 ATA ATA ATA
1 ATA ATA ATA
73784 TAGTAATATA
Statistics
Matches: 42, Mismatches: 0, Indels: 12
0.78 0.00 0.22
Matches are distributed among these distances:
2 12 0.29
3 30 0.71
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (3 bp):
ATA
Found at i:73752 original size:5 final size:5
Alignment explanation
Indices: 73736--73793 Score: 68
Period size: 5 Copynumber: 11.6 Consensus size: 5
73726 ATTATATATA
73736 ATAAT AATAAT ATAAT ATAAT ATAAT ATAAT AT-A- ATAAT ATAAT A-ATAT
1 ATAAT -ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT ATA-AT
73785 AGTAAT ATA
1 A-TAAT ATA
73794 TAGAGTTCTT
Statistics
Matches: 47, Mismatches: 0, Indels: 11
0.81 0.00 0.19
Matches are distributed among these distances:
3 2 0.04
4 3 0.06
5 33 0.70
6 8 0.17
7 1 0.02
ACGTcount: A:0.60, C:0.00, G:0.02, T:0.38
Consensus pattern (5 bp):
ATAAT
Found at i:73764 original size:31 final size:30
Alignment explanation
Indices: 73728--73795 Score: 88
Period size: 28 Copynumber: 2.3 Consensus size: 30
73718 TTATTATTAT
73728 TATATATAATAATAATAATATAAT-ATA-A-
1 TATATATAAT-ATAATAATATAATAATATAG
73756 TATAATATAATATAATAATATAATAATATAG
1 TAT-ATATAATATAATAATATAATAATATAG
73787 TAATATATA
1 T-ATATATA
73796 GAGTTCTTAG
Statistics
Matches: 35, Mismatches: 0, Indels: 7
0.83 0.00 0.17
Matches are distributed among these distances:
28 16 0.46
29 10 0.29
30 1 0.03
31 6 0.17
32 2 0.06
ACGTcount: A:0.59, C:0.00, G:0.01, T:0.40
Consensus pattern (30 bp):
TATATATAATATAATAATATAATAATATAG
Found at i:73796 original size:10 final size:9
Alignment explanation
Indices: 73728--73795 Score: 72
Period size: 8 Copynumber: 7.7 Consensus size: 9
73718 TTATTATTAT
73728 TATATATAA
1 TATATATAA
73737 TA-ATAATAA
1 TATAT-ATAA
73746 TATAATATAA
1 TAT-ATATAA
73756 TATAATATAA
1 TAT-ATATAA
73766 TATA-ATAA
1 TATATATAA
73774 TATA-ATAA
1 TATATATAA
*
73782 TATA-GTAA
1 TATATATAA
73790 TATATA
1 TATATA
73796 GAGTTCTTAG
Statistics
Matches: 53, Mismatches: 2, Indels: 8
0.84 0.03 0.13
Matches are distributed among these distances:
8 25 0.47
9 9 0.17
10 17 0.32
11 2 0.04
ACGTcount: A:0.59, C:0.00, G:0.01, T:0.40
Consensus pattern (9 bp):
TATATATAA
Found at i:76189 original size:16 final size:16
Alignment explanation
Indices: 76168--76200 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 16
76158 TCAGGCAATA
*
76168 TATATGATTATATAGT
1 TATATGATTACATAGT
76184 TATATGATTACATAGT
1 TATATGATTACATAGT
76200 T
1 T
76201 TTTTCTTCGT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.36, C:0.03, G:0.12, T:0.48
Consensus pattern (16 bp):
TATATGATTACATAGT
Found at i:76229 original size:56 final size:58
Alignment explanation
Indices: 76143--76290 Score: 237
Period size: 56 Copynumber: 2.6 Consensus size: 58
76133 CGAGTCTACC
* **
76143 TTTTTTCTTCGTAGATCAGGCAATATATATGATTATATAGTTATATG-A-TTACATAG
1 TTTTTTCTTCGTAGATCAGGCAATATATATGATTACATAGTTATATGAACAGACATAG
*
76199 TTTTTTCTTCGTAGATCAGACAATATATATGATTACATAGTTATATGAAGCAGACATAG
1 TTTTTTCTTCGTAGATCAGGCAATATATATGATTACATAGTTATATGAA-CAGACATAG
76258 TTTTTTCTTCGTAGATCAGGCAATATATATGAT
1 TTTTTTCTTCGTAGATCAGGCAATATATATGAT
76291 ATTATGATTA
Statistics
Matches: 84, Mismatches: 5, Indels: 3
0.91 0.05 0.03
Matches are distributed among these distances:
56 45 0.54
57 1 0.01
59 38 0.45
ACGTcount: A:0.32, C:0.11, G:0.15, T:0.42
Consensus pattern (58 bp):
TTTTTTCTTCGTAGATCAGGCAATATATATGATTACATAGTTATATGAACAGACATAG
Found at i:76314 original size:16 final size:16
Alignment explanation
Indices: 76293--76323 Score: 62
Period size: 16 Copynumber: 1.9 Consensus size: 16
76283 TATATGATAT
76293 TATGATTACATAGTTA
1 TATGATTACATAGTTA
76309 TATGATTACATAGTT
1 TATGATTACATAGTT
76324 GTAATTTTGA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.35, C:0.06, G:0.13, T:0.45
Consensus pattern (16 bp):
TATGATTACATAGTTA
Found at i:78331 original size:21 final size:21
Alignment explanation
Indices: 78305--78345 Score: 73
Period size: 21 Copynumber: 2.0 Consensus size: 21
78295 AGATTTGAGC
78305 TAGGGTTTTGGTCTTGGGCAG
1 TAGGGTTTTGGTCTTGGGCAG
*
78326 TAGGGTTTTGTTCTTGGGCA
1 TAGGGTTTTGGTCTTGGGCA
78346 TTACCTTTTG
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.10, C:0.10, G:0.39, T:0.41
Consensus pattern (21 bp):
TAGGGTTTTGGTCTTGGGCAG
Found at i:79596 original size:6 final size:6
Alignment explanation
Indices: 79585--79609 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
79575 GGAGAAGATG
79585 ATGAAA ATGAAA ATGAAA ATGAAA A
1 ATGAAA ATGAAA ATGAAA ATGAAA A
79610 GAGCTTTTCC
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:0.68, C:0.00, G:0.16, T:0.16
Consensus pattern (6 bp):
ATGAAA
Done.