Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01012119.1 Corchorus olitorius cultivar O-4 contig12152, 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: 91367
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32
Found at i:3392 original size:26 final size:26
Alignment explanation
Indices: 3363--3415 Score: 97
Period size: 26 Copynumber: 2.0 Consensus size: 26
3353 CCTAAACTCT
3363 TAATTTTGGTCAAATAAACCATTTTC
1 TAATTTTGGTCAAATAAACCATTTTC
*
3389 TAATTTTGGTCAAATAAATCATTTTC
1 TAATTTTGGTCAAATAAACCATTTTC
3415 T
1 T
3416 GTAACGGCAC
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
26 26 1.00
ACGTcount: A:0.34, C:0.13, G:0.08, T:0.45
Consensus pattern (26 bp):
TAATTTTGGTCAAATAAACCATTTTC
Found at i:4143 original size:83 final size:83
Alignment explanation
Indices: 4044--4209 Score: 287
Period size: 83 Copynumber: 2.0 Consensus size: 83
4034 CTTATTACAC
*
4044 TACAGAACTAGAAATCAAAATAATAAATCTACTGAATTCATTCCCAAATCAATAAATAGGAAACT
1 TACAGAACTAGAAATCAAAATAATAAATCTACTGAATTCATTCCCAAATCAATAAATAGGAAACC
* *
4109 AGCTTCTCTCTCAGCCGA
66 AGATTCTCTCTCAACCGA
* *
4127 TACAGAACTAGGAATCAAAATAATAAATCTACTGAATTCATTCCCGAATCAATAAATAGGAAACC
1 TACAGAACTAGAAATCAAAATAATAAATCTACTGAATTCATTCCCAAATCAATAAATAGGAAACC
4192 AGATTCTCTCTCAACCGA
66 AGATTCTCTCTCAACCGA
4210 CTGCTGACCT
Statistics
Matches: 78, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
83 78 1.00
ACGTcount: A:0.43, C:0.22, G:0.10, T:0.25
Consensus pattern (83 bp):
TACAGAACTAGAAATCAAAATAATAAATCTACTGAATTCATTCCCAAATCAATAAATAGGAAACC
AGATTCTCTCTCAACCGA
Found at i:4863 original size:2 final size:2
Alignment explanation
Indices: 4856--4896 Score: 73
Period size: 2 Copynumber: 20.5 Consensus size: 2
4846 GGTAGTTGGA
*
4856 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT TT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
4897 CTAAATATTA
Statistics
Matches: 37, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
AT
Found at i:8358 original size:24 final size:24
Alignment explanation
Indices: 8324--8396 Score: 101
Period size: 24 Copynumber: 3.0 Consensus size: 24
8314 AAGTGTGATT
* * *
8324 GTGCTGCCATGACTGCTTCTTCCG
1 GTGCTGACATGACTGTTTCTTCCA
*
8348 GTGCTGACATGACTGTTTCTGCCA
1 GTGCTGACATGACTGTTTCTTCCA
*
8372 GTGCTGACATGACTATTTCTTCCA
1 GTGCTGACATGACTGTTTCTTCCA
8396 G
1 G
8397 ATGAGTCGTT
Statistics
Matches: 43, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
24 43 1.00
ACGTcount: A:0.15, C:0.27, G:0.23, T:0.34
Consensus pattern (24 bp):
GTGCTGACATGACTGTTTCTTCCA
Found at i:12165 original size:7 final size:7
Alignment explanation
Indices: 12143--12178 Score: 54
Period size: 7 Copynumber: 5.0 Consensus size: 7
12133 TTAATGTCTT
12143 TAAAAAA
1 TAAAAAA
12150 TAAATAAA
1 TAAA-AAA
12158 TAAAAAA
1 TAAAAAA
*
12165 TAGAAAA
1 TAAAAAA
12172 TAAAAAA
1 TAAAAAA
12179 ATCAGTAATG
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
7 19 0.73
8 7 0.27
ACGTcount: A:0.81, C:0.00, G:0.03, T:0.17
Consensus pattern (7 bp):
TAAAAAA
Found at i:18828 original size:24 final size:24
Alignment explanation
Indices: 18801--18852 Score: 86
Period size: 24 Copynumber: 2.2 Consensus size: 24
18791 CGTTTATTGA
18801 ATTTATTTGAATTAATAAGTTTTG
1 ATTTATTTGAATTAATAAGTTTTG
* *
18825 ATTTATTTGGATTAATAGGTTTTG
1 ATTTATTTGAATTAATAAGTTTTG
18849 ATTT
1 ATTT
18853 CTAACTTAAT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
24 26 1.00
ACGTcount: A:0.29, C:0.00, G:0.15, T:0.56
Consensus pattern (24 bp):
ATTTATTTGAATTAATAAGTTTTG
Found at i:19110 original size:2 final size:2
Alignment explanation
Indices: 19103--19140 Score: 67
Period size: 2 Copynumber: 19.0 Consensus size: 2
19093 TTACTAAGCA
*
19103 AT AT AT AT AT AT AT AT AT AT GT 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
19141 GATTACCATG
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.50
Consensus pattern (2 bp):
AT
Found at i:20894 original size:2 final size:2
Alignment explanation
Indices: 20887--20921 Score: 54
Period size: 2 Copynumber: 18.0 Consensus size: 2
20877 GAACATGCAG
*
20887 TA TA TA TA -A TA TA TA TA TA TA TA TA AA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
20922 CACTTACACT
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
1 1 0.03
2 29 0.97
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (2 bp):
TA
Found at i:22463 original size:15 final size:16
Alignment explanation
Indices: 22437--22470 Score: 52
Period size: 15 Copynumber: 2.2 Consensus size: 16
22427 AATTCTCCCA
22437 AGAAGAAAGAGAAAAT
1 AGAAGAAAGAGAAAAT
*
22453 AGAAG-AAGAGAAGAT
1 AGAAGAAAGAGAAAAT
22468 AGA
1 AGA
22471 TTTAAAATAC
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
15 12 0.71
16 5 0.29
ACGTcount: A:0.65, C:0.00, G:0.29, T:0.06
Consensus pattern (16 bp):
AGAAGAAAGAGAAAAT
Found at i:23557 original size:21 final size:21
Alignment explanation
Indices: 23519--23559 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
23509 CCACGGTTGG
*
23519 GACCGTCGAGGGTGCCGTTTC
1 GACCGTCGAGGGTCCCGTTTC
**
23540 GACCGTCGTTGGTCCCGTTT
1 GACCGTCGAGGGTCCCGTTT
23560 AGGAGAGATT
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.07, C:0.29, G:0.34, T:0.29
Consensus pattern (21 bp):
GACCGTCGAGGGTCCCGTTTC
Found at i:26127 original size:16 final size:16
Alignment explanation
Indices: 26106--26138 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 16
26096 CAAGGCAGTC
*
26106 ATTCAAAGTGGAACGG
1 ATTCAAAATGGAACGG
26122 ATTCAAAATGGAACGG
1 ATTCAAAATGGAACGG
26138 A
1 A
26139 GGGAGTACAT
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:0.42, C:0.12, G:0.27, T:0.18
Consensus pattern (16 bp):
ATTCAAAATGGAACGG
Found at i:27590 original size:43 final size:44
Alignment explanation
Indices: 27517--27620 Score: 122
Period size: 43 Copynumber: 2.4 Consensus size: 44
27507 TGAATATTTT
* * * * *
27517 TATGAAATTGTGATTACTATCCTATTAAATTTTGATAATCACGC-
1 TATGAAATTTTGATAACTATCCTATGAAATTGTGATAAACAC-CA
* *
27561 TATGAAATTTTGATAATTA-CCTATGAAATTGTGATAAACTCCA
1 TATGAAATTTTGATAACTATCCTATGAAATTGTGATAAACACCA
27604 TATGAAATTTTGATAAC
1 TATGAAATTTTGATAAC
27621 CTAACTATAA
Statistics
Matches: 51, Mismatches: 8, Indels: 3
0.82 0.13 0.05
Matches are distributed among these distances:
42 1 0.02
43 34 0.67
44 16 0.31
ACGTcount: A:0.38, C:0.12, G:0.12, T:0.39
Consensus pattern (44 bp):
TATGAAATTTTGATAACTATCCTATGAAATTGTGATAAACACCA
Found at i:27633 original size:22 final size:22
Alignment explanation
Indices: 27517--27702 Score: 141
Period size: 22 Copynumber: 8.5 Consensus size: 22
27507 TGAATATTTT
* *
27517 TATGAAATTGTGATTA-CTATCC
1 TATGAAATTTTGATAACCTA-CC
* *
27539 TATTAAATTTTGATAATC-ACGC
1 TATGAAATTTTGATAACCTAC-C
*
27561 TATGAAATTTTGATAA-TTACC
1 TATGAAATTTTGATAACCTACC
* *
27582 TATGAAATTGTGATAAACT-CC
1 TATGAAATTTTGATAACCTACC
*
27603 ATATGAAATTTTGATAACCTAAC
1 -TATGAAATTTTGATAACCTACC
* * * *
27626 TATAAAATTTTAATAAACCTTCA
1 TATGAAATTTTGAT-AACCTACC
* *
27649 TATAAAATTTTG-TAACCTTCC
1 TATGAAATTTTGATAACCTACC
* *
27670 TATG-ATTTTTGATAACCTCCC
1 TATGAAATTTTGATAACCTACC
*
27691 TATGAGATTTTG
1 TATGAAATTTTG
27703 TTAATCTCCC
Statistics
Matches: 133, Mismatches: 22, Indels: 18
0.77 0.13 0.10
Matches are distributed among these distances:
20 6 0.05
21 41 0.31
22 68 0.51
23 18 0.14
ACGTcount: A:0.36, C:0.14, G:0.10, T:0.40
Consensus pattern (22 bp):
TATGAAATTTTGATAACCTACC
Found at i:27634 original size:65 final size:64
Alignment explanation
Indices: 27517--27641 Score: 146
Period size: 65 Copynumber: 1.9 Consensus size: 64
27507 TGAATATTTT
* * * * * *
27517 TATGAAATTGTGATTACTATCCTATTAAATTTTGATAATCACGCTATGAAATTTTGATAATTACC
1 TATGAAATTGTGATAAC-ATCCTATGAAATTTTGATAACCACACTATAAAATTTTAATAATTACC
27582 TATGAAATTGTGATAA-ACTCCATATGAAATTTTGATAACCTA-ACTATAAAATTTTAATAA
1 TATGAAATTGTGATAACA-TCC-TATGAAATTTTGATAACC-ACACTATAAAATTTTAATAA
27642 ACCTTCATAT
Statistics
Matches: 51, Mismatches: 6, Indels: 6
0.81 0.10 0.10
Matches are distributed among these distances:
63 1 0.02
64 3 0.06
65 46 0.90
66 1 0.02
ACGTcount: A:0.40, C:0.11, G:0.10, T:0.39
Consensus pattern (64 bp):
TATGAAATTGTGATAACATCCTATGAAATTTTGATAACCACACTATAAAATTTTAATAATTACC
Found at i:27667 original size:21 final size:21
Alignment explanation
Indices: 27602--27668 Score: 64
Period size: 23 Copynumber: 3.0 Consensus size: 21
27592 TGATAAACTC
*
27602 CATATGAAATTTTGATAACC-T
1 CATATAAAATTTTG-TAACCTT
* *
27623 AACTATAAAATTTTAATAAACCTT
1 CA-TATAAAATTTT-GT-AACCTT
27647 CATATAAAATTTTGTAACCTT
1 CATATAAAATTTTGTAACCTT
27668 C
1 C
27669 CTATGATTTT
Statistics
Matches: 37, Mismatches: 5, Indels: 8
0.74 0.10 0.16
Matches are distributed among these distances:
21 8 0.22
22 12 0.32
23 15 0.41
24 2 0.05
ACGTcount: A:0.42, C:0.15, G:0.04, T:0.39
Consensus pattern (21 bp):
CATATAAAATTTTGTAACCTT
Found at i:27685 original size:21 final size:22
Alignment explanation
Indices: 27656--27727 Score: 76
Period size: 22 Copynumber: 3.4 Consensus size: 22
27646 TCATATAAAA
*
27656 TTTTG-TAACCTTCCTATGA-T
1 TTTTGATAACCTCCCTATGAGT
*
27676 TTTTGATAACCTCCCTATGAGA
1 TTTTGATAACCTCCCTATGAGT
* * * *
27698 TTTTGTTAATCTCCCTATAATT
1 TTTTGATAACCTCCCTATGAGT
27720 TTTTGATA
1 TTTTGATA
27728 TTATAGTATG
Statistics
Matches: 42, Mismatches: 8, Indels: 2
0.81 0.15 0.04
Matches are distributed among these distances:
20 5 0.12
21 13 0.31
22 24 0.57
ACGTcount: A:0.24, C:0.18, G:0.10, T:0.49
Consensus pattern (22 bp):
TTTTGATAACCTCCCTATGAGT
Found at i:27723 original size:22 final size:22
Alignment explanation
Indices: 27611--27727 Score: 67
Period size: 22 Copynumber: 5.4 Consensus size: 22
27601 CCATATGAAA
** **
27611 TTTTGATAACCTAACTATAAAA
1 TTTTGATAACCTCCCTATAAGT
* * * **
27633 TTTTAATAAACCTTCATATAAAA
1 TTTTGAT-AACCTCCCTATAAGT
* *
27656 TTTTG-TAACCTTCCTATGA-T
1 TTTTGATAACCTCCCTATAAGT
* *
27676 TTTTGATAACCTCCCTATGAGA
1 TTTTGATAACCTCCCTATAAGT
* * *
27698 TTTTGTTAATCTCCCTATAATT
1 TTTTGATAACCTCCCTATAAGT
27720 TTTTGATA
1 TTTTGATA
27728 TTATAGTATG
Statistics
Matches: 76, Mismatches: 16, Indels: 6
0.78 0.16 0.06
Matches are distributed among these distances:
20 5 0.07
21 24 0.32
22 31 0.41
23 16 0.21
ACGTcount: A:0.32, C:0.16, G:0.07, T:0.44
Consensus pattern (22 bp):
TTTTGATAACCTCCCTATAAGT
Found at i:28410 original size:10 final size:10
Alignment explanation
Indices: 28397--28475 Score: 55
Period size: 10 Copynumber: 8.5 Consensus size: 10
28387 TTTTATTTTT
28397 TTAATTATTA
1 TTAATTATTA
28407 TTAATTA-T-
1 TTAATTATTA
28415 TT-A--ATTA
1 TTAATTATTA
28422 TTAATTATTA
1 TTAATTATTA
*
28432 TTAATT-TAAA
1 TTAATTAT-TA
*
28442 TT-GTTATTA
1 TTAATTATTA
*
28451 TTAATTATAA
1 TTAATTATTA
* *
28461 TTAATAATAA
1 TTAATTATTA
28471 TTAAT
1 TTAAT
28476 AAAAAAAAAC
Statistics
Matches: 55, Mismatches: 6, Indels: 16
0.71 0.08 0.21
Matches are distributed among these distances:
5 1 0.02
6 1 0.02
7 3 0.05
8 3 0.05
9 7 0.13
10 40 0.73
ACGTcount: A:0.43, C:0.00, G:0.01, T:0.56
Consensus pattern (10 bp):
TTAATTATTA
Found at i:28413 original size:7 final size:7
Alignment explanation
Indices: 28403--28475 Score: 62
Period size: 7 Copynumber: 10.3 Consensus size: 7
28393 TTTTTTAATT
28403 ATTATTA
1 ATTATTA
28410 ATTATTTA
1 ATTA-TTA
28418 ATTATTA
1 ATTATTA
28425 ATTATT-
1 ATTATTA
28431 ATTAATTTAA
1 ATT-A-TT-A
*
28441 ATTGTT-
1 ATTATTA
28447 ATTATTA
1 ATTATTA
28454 ATTA-TA
1 ATTATTA
*
28460 ATTAATA
1 ATTATTA
*
28467 ATAATTA
1 ATTATTA
28474 AT
1 AT
28476 AAAAAAAAAC
Statistics
Matches: 55, Mismatches: 4, Indels: 14
0.75 0.05 0.19
Matches are distributed among these distances:
6 14 0.25
7 27 0.49
8 11 0.20
10 3 0.05
ACGTcount: A:0.44, C:0.00, G:0.01, T:0.55
Consensus pattern (7 bp):
ATTATTA
Found at i:28425 original size:25 final size:27
Alignment explanation
Indices: 28397--28465 Score: 88
Period size: 29 Copynumber: 2.6 Consensus size: 27
28387 TTTTATTTTT
28397 TTAATTATTATTAATT-ATT-TAATTA
1 TTAATTATTATTAATTAATTGTAATTA
*
28422 TTAATTATTATTAATTTAAATTGTTATTA
1 TTAATTATTATTAA-TT-AATTGTAATTA
*
28451 TTAATTATAATTAAT
1 TTAATTATTATTAAT
28466 AATAATTAAT
Statistics
Matches: 38, Mismatches: 2, Indels: 5
0.84 0.04 0.11
Matches are distributed among these distances:
25 14 0.37
26 2 0.05
28 4 0.11
29 18 0.47
ACGTcount: A:0.41, C:0.00, G:0.01, T:0.58
Consensus pattern (27 bp):
TTAATTATTATTAATTAATTGTAATTA
Found at i:28540 original size:33 final size:33
Alignment explanation
Indices: 28503--28577 Score: 107
Period size: 33 Copynumber: 2.3 Consensus size: 33
28493 GCCCTCCTAG
*
28503 GGCGGCACTAACCATGGCATGCCGCCCT-AGGAA
1 GGCGGCACCAACCATGGCATGCCG-CCTAAGGAA
* *
28536 GGCGGCACCAACCATGGCGTGCCGCCTAAGGAG
1 GGCGGCACCAACCATGGCATGCCGCCTAAGGAA
28569 GGCGGCACC
1 GGCGGCACC
28578 GATTATTTTT
Statistics
Matches: 38, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
32 3 0.08
33 35 0.92
ACGTcount: A:0.21, C:0.35, G:0.35, T:0.09
Consensus pattern (33 bp):
GGCGGCACCAACCATGGCATGCCGCCTAAGGAA
Found at i:37338 original size:19 final size:19
Alignment explanation
Indices: 37310--37354 Score: 54
Period size: 19 Copynumber: 2.3 Consensus size: 19
37300 TGGTGAGACT
*
37310 TTTTTGTATTTTCAGTTTTC
1 TTTTT-TATTTTCACTTTTC
**
37330 TTTTTTATTTTTTCTTTTC
1 TTTTTTATTTTCACTTTTC
37349 TTTTTT
1 TTTTTT
37355 TTGGGCTTTT
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
19 17 0.77
20 5 0.23
ACGTcount: A:0.07, C:0.09, G:0.04, T:0.80
Consensus pattern (19 bp):
TTTTTTATTTTCACTTTTC
Found at i:39828 original size:20 final size:20
Alignment explanation
Indices: 39804--39842 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
39794 ATGAGAGAGG
*
39804 AAAAATAAAGAAAGATTTGCT
1 AAAAA-AAACAAAGATTTGCT
*
39825 AAAAAAAACAAATATTTG
1 AAAAAAAACAAAGATTTG
39843 GAAATTGTTT
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
20 11 0.69
21 5 0.31
ACGTcount: A:0.62, C:0.05, G:0.10, T:0.23
Consensus pattern (20 bp):
AAAAAAAACAAAGATTTGCT
Found at i:42318 original size:20 final size:18
Alignment explanation
Indices: 42259--42314 Score: 69
Period size: 19 Copynumber: 3.1 Consensus size: 18
42249 TTAAAAAACA
42259 ATTTTTATT-TTTAAATT
1 ATTTTTATTATTTAAATT
* *
42276 ACTTTTAATATTTTAAATT
1 ATTTTTATTA-TTTAAATT
42295 ATTATTTATTATTTAAATT
1 ATT-TTTATTATTTAAATT
42314 A
1 A
42315 ATTAAAATTC
Statistics
Matches: 32, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
17 7 0.22
19 19 0.59
20 6 0.19
ACGTcount: A:0.36, C:0.02, G:0.00, T:0.62
Consensus pattern (18 bp):
ATTTTTATTATTTAAATT
Found at i:42332 original size:19 final size:20
Alignment explanation
Indices: 42310--42348 Score: 53
Period size: 19 Copynumber: 2.0 Consensus size: 20
42300 TTATTATTTA
42310 AATTAATTAAAATTC-AAAT
1 AATTAATTAAAATTCGAAAT
* *
42329 AATTTATTTAAATTCGAAAT
1 AATTAATTAAAATTCGAAAT
42349 TAGGGTGTCA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
19 13 0.76
20 4 0.24
ACGTcount: A:0.51, C:0.05, G:0.03, T:0.41
Consensus pattern (20 bp):
AATTAATTAAAATTCGAAAT
Found at i:45601 original size:36 final size:36
Alignment explanation
Indices: 45552--45624 Score: 128
Period size: 36 Copynumber: 2.0 Consensus size: 36
45542 TGCATTCATT
45552 TCGGCGATCTAAATTTTGGACTTCACAAGCGAATCG
1 TCGGCGATCTAAATTTTGGACTTCACAAGCGAATCG
* *
45588 TCGGCGATGTAAATTTTGGACTTCACAAGCGGATCG
1 TCGGCGATCTAAATTTTGGACTTCACAAGCGAATCG
45624 T
1 T
45625 GGAGTTGATA
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
36 35 1.00
ACGTcount: A:0.26, C:0.21, G:0.25, T:0.29
Consensus pattern (36 bp):
TCGGCGATCTAAATTTTGGACTTCACAAGCGAATCG
Found at i:47811 original size:23 final size:24
Alignment explanation
Indices: 47785--47829 Score: 65
Period size: 24 Copynumber: 1.9 Consensus size: 24
47775 GCGCCACCTC
*
47785 CTTC-TCCTTGTATGGAGTTTTCT
1 CTTCTTCCTTGTAAGGAGTTTTCT
*
47808 CTTCTTTCTTGTAAGGAGTTTT
1 CTTCTTCCTTGTAAGGAGTTTT
47830 TCATGAGCTA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
23 4 0.21
24 15 0.79
ACGTcount: A:0.11, C:0.18, G:0.18, T:0.53
Consensus pattern (24 bp):
CTTCTTCCTTGTAAGGAGTTTTCT
Found at i:51513 original size:22 final size:20
Alignment explanation
Indices: 51473--51513 Score: 55
Period size: 22 Copynumber: 1.9 Consensus size: 20
51463 AAAAAAAAAG
51473 ATTTTTTTTTTACGTTTTTA
1 ATTTTTTTTTTACGTTTTTA
*
51493 ATTTTTGTTTCTTGCGTTTTT
1 ATTTTT-TTT-TTACGTTTTT
51514 GAAAAAAAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 6 0.33
21 3 0.17
22 9 0.50
ACGTcount: A:0.10, C:0.07, G:0.10, T:0.73
Consensus pattern (20 bp):
ATTTTTTTTTTACGTTTTTA
Found at i:55650 original size:18 final size:18
Alignment explanation
Indices: 55627--55663 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
55617 AAGGGTAGTT
*
55627 TAAAAAAAATTGTTTTCA
1 TAAAAAAAAGTGTTTTCA
*
55645 TAAAAAGAAGTGTTTTCA
1 TAAAAAAAAGTGTTTTCA
55663 T
1 T
55664 GCAAGAGGAG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.46, C:0.05, G:0.11, T:0.38
Consensus pattern (18 bp):
TAAAAAAAAGTGTTTTCA
Found at i:57901 original size:17 final size:19
Alignment explanation
Indices: 57879--57913 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
57869 AGAAGAAGTA
57879 TGTTTT-TTT-TTAATTAT
1 TGTTTTCTTTCTTAATTAT
57896 TGTTTTCTTTCTTAATTA
1 TGTTTTCTTTCTTAATTA
57914 GATTTAATTT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 6 0.38
18 3 0.19
19 7 0.44
ACGTcount: A:0.17, C:0.06, G:0.06, T:0.71
Consensus pattern (19 bp):
TGTTTTCTTTCTTAATTAT
Found at i:58481 original size:14 final size:15
Alignment explanation
Indices: 58462--58491 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
58452 AACTAGGAAA
58462 AATAAAT-AACAAGG
1 AATAAATAAACAAGG
58476 AATAAATAAACAAGG
1 AATAAATAAACAAGG
58491 A
1 A
58492 TTGGACTTAG
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 7 0.47
15 8 0.53
ACGTcount: A:0.67, C:0.07, G:0.13, T:0.13
Consensus pattern (15 bp):
AATAAATAAACAAGG
Found at i:60812 original size:19 final size:21
Alignment explanation
Indices: 60774--60819 Score: 62
Period size: 19 Copynumber: 2.3 Consensus size: 21
60764 TTTATTGCCT
60774 CTTTTTATTTTCTGATTTTTC
1 CTTTTTATTTTCTGATTTTTC
60795 ACTTTTT-TTTT-T-ATTTTTC
1 -CTTTTTATTTTCTGATTTTTC
60814 CTTTTT
1 CTTTTT
60820 CCATCTCTAG
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
18 6 0.25
19 7 0.29
20 1 0.04
21 4 0.17
22 6 0.25
ACGTcount: A:0.09, C:0.13, G:0.02, T:0.76
Consensus pattern (21 bp):
CTTTTTATTTTCTGATTTTTC
Found at i:72092 original size:27 final size:26
Alignment explanation
Indices: 72047--72123 Score: 75
Period size: 26 Copynumber: 2.9 Consensus size: 26
72037 GGGGTCACCT
* *
72047 AGGGGCATTTTAGTAATTTGCACA-TTC
1 AGGGGCATTTTGGTCATTT-CA-AGTTC
*
72074 AGGGGCATTTTGGTCATTTTAAGTTC
1 AGGGGCATTTTGGTCATTTCAAGTTC
** *
72100 AGGGGCACGTTGGTCATTTTAAGT
1 AGGGGCATTTTGGTCATTTCAAGT
72124 CCACTCTTAA
Statistics
Matches: 44, Mismatches: 5, Indels: 3
0.85 0.10 0.06
Matches are distributed among these distances:
25 1 0.02
26 26 0.59
27 17 0.39
ACGTcount: A:0.22, C:0.13, G:0.27, T:0.38
Consensus pattern (26 bp):
AGGGGCATTTTGGTCATTTCAAGTTC
Found at i:72112 original size:26 final size:26
Alignment explanation
Indices: 72071--72123 Score: 88
Period size: 26 Copynumber: 2.0 Consensus size: 26
72061 AATTTGCACA
**
72071 TTCAGGGGCATTTTGGTCATTTTAAG
1 TTCAGGGGCACGTTGGTCATTTTAAG
72097 TTCAGGGGCACGTTGGTCATTTTAAG
1 TTCAGGGGCACGTTGGTCATTTTAAG
72123 T
1 T
72124 CCACTCTTAA
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
26 25 1.00
ACGTcount: A:0.19, C:0.13, G:0.28, T:0.40
Consensus pattern (26 bp):
TTCAGGGGCACGTTGGTCATTTTAAG
Found at i:79207 original size:21 final size:21
Alignment explanation
Indices: 79163--79207 Score: 54
Period size: 21 Copynumber: 2.1 Consensus size: 21
79153 GGCGCCCACA
* * *
79163 TGGTTGGCTTGAGCAGCCATG
1 TGGTTGGCTTGAGAACCCAGG
*
79184 TGGTTTGCTTGAGAACCCAGG
1 TGGTTGGCTTGAGAACCCAGG
79205 TGG
1 TGG
79208 GCAGTGTTAC
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.16, C:0.18, G:0.38, T:0.29
Consensus pattern (21 bp):
TGGTTGGCTTGAGAACCCAGG
Found at i:80765 original size:15 final size:14
Alignment explanation
Indices: 80745--80782 Score: 58
Period size: 15 Copynumber: 2.6 Consensus size: 14
80735 AAATGGTTGC
80745 TTTGTTTTGTTTCGG
1 TTTGTTTTGTTTC-G
80760 TTTGTTTTGTTTCG
1 TTTGTTTTGTTTCG
*
80774 TTTGCTTTG
1 TTTGTTTTG
80783 ATGTTTTATT
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
14 9 0.41
15 13 0.59
ACGTcount: A:0.00, C:0.08, G:0.24, T:0.68
Consensus pattern (14 bp):
TTTGTTTTGTTTCG
Found at i:83871 original size:27 final size:27
Alignment explanation
Indices: 83799--83872 Score: 123
Period size: 27 Copynumber: 2.7 Consensus size: 27
83789 AGGGTCACCT
*
83799 AGGGGCATTTTGGTCATTAGTGCATCC
1 AGGGGCATTTTGGTCATTTGTGCATCC
83826 -GAGGGCATTTTGGTCATTTGTGCATCC
1 AG-GGGCATTTTGGTCATTTGTGCATCC
83853 AGGGGCATTTTGGTCATTTG
1 AGGGGCATTTTGGTCATTTG
83873 GTCCATTACC
Statistics
Matches: 44, Mismatches: 1, Indels: 4
0.90 0.02 0.08
Matches are distributed among these distances:
26 1 0.02
27 42 0.95
28 1 0.02
ACGTcount: A:0.16, C:0.16, G:0.31, T:0.36
Consensus pattern (27 bp):
AGGGGCATTTTGGTCATTTGTGCATCC
Found at i:83931 original size:17 final size:17
Alignment explanation
Indices: 83909--83941 Score: 66
Period size: 17 Copynumber: 1.9 Consensus size: 17
83899 TTCACATTAA
83909 CATTTAGTTTTAGTAGG
1 CATTTAGTTTTAGTAGG
83926 CATTTAGTTTTAGTAG
1 CATTTAGTTTTAGTAG
83942 ATTACCTTTA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.24, C:0.06, G:0.21, T:0.48
Consensus pattern (17 bp):
CATTTAGTTTTAGTAGG
Found at i:86771 original size:41 final size:40
Alignment explanation
Indices: 86726--86862 Score: 175
Period size: 41 Copynumber: 3.4 Consensus size: 40
86716 GTGTGATTTC
** **
86726 ATTCAATTGGGTCCCTAATTTAGGCTGTTATTTATTAATTG
1 ATTCAATTTTGTCCCTAATTTAGG-TAATATTTATTAATTG
* * *
86767 ATTCAATTTTGTCCCTGATCTAAGGTAATATTTGTTAATTG
1 ATTCAATTTTGTCCCTAAT-TTAGGTAATATTTATTAATTG
*
86808 ATTCAATTTTGTCCCTAATTTAGAGTAATATTTATTTATTG
1 ATTCAATTTTGTCCCTAATTTAG-GTAATATTTATTAATTG
86849 ATTCAATTTTGTCC
1 ATTCAATTTTGTCC
86863 TGGATTTTGA
Statistics
Matches: 83, Mismatches: 11, Indels: 4
0.85 0.11 0.04
Matches are distributed among these distances:
40 3 0.04
41 76 0.92
42 4 0.05
ACGTcount: A:0.26, C:0.12, G:0.13, T:0.48
Consensus pattern (40 bp):
ATTCAATTTTGTCCCTAATTTAGGTAATATTTATTAATTG
Found at i:88368 original size:32 final size:32
Alignment explanation
Indices: 88317--88405 Score: 142
Period size: 32 Copynumber: 2.8 Consensus size: 32
88307 AATAGCGGCA
* *
88317 TTTCTGTACTGAAACGCCGCTATTTACTGGCG
1 TTTCCGTACAGAAACGCCGCTATTTACTGGCG
*
88349 TTTCCGTACAGAAACGCCGCTATTTAGTGGCG
1 TTTCCGTACAGAAACGCCGCTATTTACTGGCG
*
88381 TTTTCGTACAGAAACGCCGCTATTT
1 TTTCCGTACAGAAACGCCGCTATTT
88406 TGGCTTCTTT
Statistics
Matches: 53, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
32 53 1.00
ACGTcount: A:0.21, C:0.25, G:0.21, T:0.33
Consensus pattern (32 bp):
TTTCCGTACAGAAACGCCGCTATTTACTGGCG
Done.