Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01013931.1 Corchorus capsularis cultivar CVL-1 contig13952, 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: 54536
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.34
Found at i:2542 original size:1 final size:1
Alignment explanation
Indices: 2536--2564 Score: 58
Period size: 1 Copynumber: 29.0 Consensus size: 1
2526 CTTCTTCTTC
2536 TTTTTTTTTTTTTTTTTTTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTT
2565 GATTTCATTT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 28 1.00
ACGTcount: A:0.00, C:0.00, G:0.00, T:1.00
Consensus pattern (1 bp):
T
Found at i:3008 original size:3 final size:3
Alignment explanation
Indices: 3002--3033 Score: 64
Period size: 3 Copynumber: 10.7 Consensus size: 3
2992 TGTTATTATC
3002 TGT TGT TGT TGT TGT TGT TGT TGT TGT TGT TG
1 TGT TGT TGT TGT TGT TGT TGT TGT TGT TGT TG
3034 GGTTTGGACA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 29 1.00
ACGTcount: A:0.00, C:0.00, G:0.34, T:0.66
Consensus pattern (3 bp):
TGT
Found at i:6218 original size:126 final size:126
Alignment explanation
Indices: 5993--6366 Score: 658
Period size: 126 Copynumber: 3.0 Consensus size: 126
5983 TCAAAAGCTA
5993 CTGCCGAACAATGTAATGATAGTGATAACTCATTAAAGGCTGAACTTGAAGCCATGATTCATCGA
1 CTGCCGAACAATGTAATGATAGTGATAACTCATTAAAGGCTGAACTTGAAGCCATGATTCATCGA
* * *
6058 ACAGCGGAACTTGAAGTGAAACTGGAGATGATTGAACTTGAGAAGGCTGAACTAGAGCGAT
66 ACAGCGGAACTTGAAGAGAAATTGGAGAAGATTGAACTTGAGAAGGCTGAACTAGAGCGAT
*
6119 CTGCCAAACAATGTAATGATAGTGATAACTCATTAAAGGCTGAACTTGAAGCCATGATTCATCGA
1 CTGCCGAACAATGTAATGATAGTGATAACTCATTAAAGGCTGAACTTGAAGCCATGATTCATCGA
*
6184 ACAGCGGAACTTGAAGAGAAATTGGAGAAGATTGAATTTGAGAAGGCTGAACTAGAGCGAT
66 ACAGCGGAACTTGAAGAGAAATTGGAGAAGATTGAACTTGAGAAGGCTGAACTAGAGCGAT
* * *
6245 CTGCCGAACAATCTAATGATAGTGACAACTCATTAAAGGCTGAACTCGAAGCCATGATTCATCGA
1 CTGCCGAACAATGTAATGATAGTGATAACTCATTAAAGGCTGAACTTGAAGCCATGATTCATCGA
* *
6310 ACAGCGGAAATTGAAGAGAAATTGGAGAAGATTGAACTTGTGAAGGCTGAACTAGAG
66 ACAGCGGAACTTGAAGAGAAATTGGAGAAGATTGAACTTGAGAAGGCTGAACTAGAG
6367 ATCGCTCTCA
Statistics
Matches: 236, Mismatches: 12, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
126 236 1.00
ACGTcount: A:0.37, C:0.16, G:0.25, T:0.22
Consensus pattern (126 bp):
CTGCCGAACAATGTAATGATAGTGATAACTCATTAAAGGCTGAACTTGAAGCCATGATTCATCGA
ACAGCGGAACTTGAAGAGAAATTGGAGAAGATTGAACTTGAGAAGGCTGAACTAGAGCGAT
Found at i:9754 original size:3 final size:3
Alignment explanation
Indices: 9746--9785 Score: 80
Period size: 3 Copynumber: 13.3 Consensus size: 3
9736 TTTTAAGTTA
9746 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T
9786 TTTAGTGAAA
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 37 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TAT
Found at i:11901 original size:33 final size:33
Alignment explanation
Indices: 11850--11938 Score: 121
Period size: 33 Copynumber: 2.8 Consensus size: 33
11840 AAAAATAATT
*
11850 TATTATATAT-T-TTTTATATATATCATAAATA
1 TATTATATATATATTATATATATATCATAAATA
11881 TATTATATATATATTATATATATATCATAAATA
1 TATTATATATATATTATATATATATCATAAATA
* *
11914 TATT-TATCATATATCATAAATATAT
1 TATTATAT-ATATATTATATATATAT
11939 TTTATATATA
Statistics
Matches: 52, Mismatches: 3, Indels: 4
0.88 0.05 0.07
Matches are distributed among these distances:
31 10 0.19
32 4 0.08
33 38 0.73
ACGTcount: A:0.45, C:0.04, G:0.00, T:0.51
Consensus pattern (33 bp):
TATTATATATATATTATATATATATCATAAATA
Found at i:11902 original size:11 final size:11
Alignment explanation
Indices: 11850--11948 Score: 96
Period size: 11 Copynumber: 9.2 Consensus size: 11
11840 AAAAATAATT
11850 TATTATATAT-
1 TATTATATATA
*
11860 T-TTTTATATA
1 TATTATATATA
* *
11870 TATCATAAATA
1 TATTATATATA
11881 TATTATATATA
1 TATTATATATA
11892 TATTATATATA
1 TATTATATATA
* *
11903 TATCATAAATA
1 TATTATATATA
11914 TATT-TATCATA
1 TATTATAT-ATA
* *
11925 TATCATAAATA
1 TATTATATATA
*
11936 TATTTTATATA
1 TATTATATATA
11947 TA
1 TA
11949 ATGCCATAAT
Statistics
Matches: 70, Mismatches: 15, Indels: 7
0.76 0.16 0.08
Matches are distributed among these distances:
9 7 0.10
10 4 0.06
11 57 0.81
12 2 0.03
ACGTcount: A:0.44, C:0.04, G:0.00, T:0.52
Consensus pattern (11 bp):
TATTATATATA
Found at i:12449 original size:12 final size:12
Alignment explanation
Indices: 12434--12464 Score: 62
Period size: 12 Copynumber: 2.6 Consensus size: 12
12424 CCCGCACGAA
12434 AATCCGAACCCG
1 AATCCGAACCCG
12446 AATCCGAACCCG
1 AATCCGAACCCG
12458 AATCCGA
1 AATCCGA
12465 CCTGAAGCCG
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 19 1.00
ACGTcount: A:0.35, C:0.39, G:0.16, T:0.10
Consensus pattern (12 bp):
AATCCGAACCCG
Found at i:12552 original size:16 final size:16
Alignment explanation
Indices: 12511--12553 Score: 50
Period size: 16 Copynumber: 2.7 Consensus size: 16
12501 AACTTGCCTG
* *
12511 AACCCGAATCCGAAAA
1 AACCCGAACCCAAAAA
* *
12527 AACTCAAACCCAAAAA
1 AACCCGAACCCAAAAA
12543 AACCCGAACCC
1 AACCCGAACCC
12554 GAATCCGAAA
Statistics
Matches: 21, Mismatches: 6, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
16 21 1.00
ACGTcount: A:0.51, C:0.37, G:0.07, T:0.05
Consensus pattern (16 bp):
AACCCGAACCCAAAAA
Found at i:16211 original size:32 final size:33
Alignment explanation
Indices: 16170--16242 Score: 121
Period size: 33 Copynumber: 2.2 Consensus size: 33
16160 ACAAAGTTTA
* *
16170 TTTAACATGCATAATCT-CTTCTTCTACCTTTC
1 TTTATCATGCATAATCTCCTCCTTCTACCTTTC
16202 TTTATCATGCATAATCTCCTCCTTCTACCTTTC
1 TTTATCATGCATAATCTCCTCCTTCTACCTTTC
16235 TTTATCAT
1 TTTATCAT
16243 TAAAAATTAT
Statistics
Matches: 38, Mismatches: 2, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
32 16 0.42
33 22 0.58
ACGTcount: A:0.21, C:0.29, G:0.03, T:0.48
Consensus pattern (33 bp):
TTTATCATGCATAATCTCCTCCTTCTACCTTTC
Found at i:16322 original size:33 final size:33
Alignment explanation
Indices: 16273--16371 Score: 171
Period size: 33 Copynumber: 3.0 Consensus size: 33
16263 ATACTACCTT
*
16273 GTATATTAGTGACACCTGAAGTTGTCACATCAA
1 GTATATTAGTGGCACCTGAAGTTGTCACATCAA
*
16306 GTATATAAGTGGCACCTGAAGTTGTCACATCAA
1 GTATATTAGTGGCACCTGAAGTTGTCACATCAA
*
16339 GTATATTAGTGGCACCTGAAGTTGTCGCATCAA
1 GTATATTAGTGGCACCTGAAGTTGTCACATCAA
16372 AAATATAATA
Statistics
Matches: 62, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
33 62 1.00
ACGTcount: A:0.31, C:0.18, G:0.21, T:0.29
Consensus pattern (33 bp):
GTATATTAGTGGCACCTGAAGTTGTCACATCAA
Found at i:17263 original size:6 final size:6
Alignment explanation
Indices: 17248--17286 Score: 60
Period size: 6 Copynumber: 6.5 Consensus size: 6
17238 ACTATAATTA
* *
17248 TGGACG TGGACA TGGACG TGGACG TGGACG TGGCCG TGG
1 TGGACG TGGACG TGGACG TGGACG TGGACG TGGACG TGG
17287 TCGCGGGTTT
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
6 30 1.00
ACGTcount: A:0.15, C:0.18, G:0.49, T:0.18
Consensus pattern (6 bp):
TGGACG
Found at i:17372 original size:42 final size:42
Alignment explanation
Indices: 17311--17392 Score: 128
Period size: 42 Copynumber: 2.0 Consensus size: 42
17301 ATGGTCGCGG
* *
17311 TCGTGATCGTAGCTCTGGATATAATGGTCATCATTTGAAATA
1 TCGTGATCGTAGCTATGGATATAATGGTCATCATTCGAAATA
* *
17353 TCGTGGTCGTAGCTATGGATATAATGGTGATCATTCGAAA
1 TCGTGATCGTAGCTATGGATATAATGGTCATCATTCGAAA
17393 AACATATCTT
Statistics
Matches: 36, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
42 36 1.00
ACGTcount: A:0.28, C:0.13, G:0.24, T:0.34
Consensus pattern (42 bp):
TCGTGATCGTAGCTATGGATATAATGGTCATCATTCGAAATA
Found at i:22999 original size:12 final size:12
Alignment explanation
Indices: 22967--23005 Score: 50
Period size: 12 Copynumber: 3.6 Consensus size: 12
22957 ATGGAATTAA
22967 ATATCCGTCG--
1 ATATCCGTCGAT
22977 ATA-CC-TCGAT
1 ATATCCGTCGAT
22987 ATATCCGTCGAT
1 ATATCCGTCGAT
22999 ATATCCG
1 ATATCCG
23006 ATATCTGTAC
Statistics
Matches: 25, Mismatches: 0, Indels: 6
0.81 0.00 0.19
Matches are distributed among these distances:
8 3 0.12
9 2 0.08
10 6 0.24
11 2 0.08
12 12 0.48
ACGTcount: A:0.26, C:0.28, G:0.15, T:0.31
Consensus pattern (12 bp):
ATATCCGTCGAT
Found at i:24579 original size:12 final size:13
Alignment explanation
Indices: 24562--24597 Score: 56
Period size: 12 Copynumber: 2.8 Consensus size: 13
24552 CATCGATACC
24562 TCGATATATCCG-
1 TCGATATATCCGT
*
24574 TCGATATATCTGT
1 TCGATATATCCGT
24587 TCGATATATCC
1 TCGATATATCC
24598 ATCAATACCT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
12 11 0.52
13 10 0.48
ACGTcount: A:0.25, C:0.22, G:0.14, T:0.39
Consensus pattern (13 bp):
TCGATATATCCGT
Found at i:24609 original size:23 final size:25
Alignment explanation
Indices: 24562--24609 Score: 64
Period size: 25 Copynumber: 2.0 Consensus size: 25
24552 CATCGATACC
* *
24562 TCGATATATCCGTCGATATATCTGT
1 TCGATATATCCATCGATATACCTGT
24587 TCGATATATCCATC-A-ATACCTGT
1 TCGATATATCCATCGATATACCTGT
24610 ATTAAACTCC
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
23 7 0.33
24 1 0.05
25 13 0.62
ACGTcount: A:0.27, C:0.23, G:0.12, T:0.38
Consensus pattern (25 bp):
TCGATATATCCATCGATATACCTGT
Found at i:24918 original size:2 final size:2
Alignment explanation
Indices: 24911--24937 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
24901 ATCAAATACT
24911 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 T
24938 TCTAGTTTCA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:25084 original size:22 final size:22
Alignment explanation
Indices: 25059--25658 Score: 178
Period size: 22 Copynumber: 27.6 Consensus size: 22
25049 ATGATCCCAT
25059 TATGAAATTTTGATAACCTTCC
1 TATGAAATTTTGATAACCTTCC
* ** *
25081 TATGAAATTTTAATAACGATAC
1 TATGAAATTTTGATAACCTTCC
* * * * **
25103 TACGGAATTTTGAGAATCTTTT
1 TATGAAATTTTGATAACCTTCC
** *
25125 TAT-AAATTTTTTTTAACCTTCT
1 TATGAAA-TTTTGATAACCTTCC
* * *
25147 TATGAAATTTGGTTAACCTCCC
1 TATGAAATTTTGATAACCTTCC
* * *
25169 TAAGGAATTTTGA-AGA-CTTCAA
1 TATGAAATTTTGATA-ACCTTC-C
25191 TATGAAATTTTGATAA-CTTCC
1 TATGAAATTTTGATAACCTTCC
**
25212 TAATGAAATTTTGATAACCAACAC
1 T-ATGAAATTTTGATAACCTTC-C
* * *
25236 TATGAGATGTTGAGAACC-TCC
1 TATGAAATTTTGATAACCTTCC
* * * *
25257 ATATGATATATTGATAACC-ACGT
1 -TATGAAATTTTGATAACCTTC-C
* * *
25280 TATGAAAATTTAAAAACC-TCC
1 TATGAAATTTTGATAACCTTCC
* ***
25301 ATATG-AATTGTT-AGTAAACAAAC
1 -TATGAAATT-TTGA-TAACCTTCC
* * *
25324 TCTAAAATTTTGATAA--TTACAA
1 TATGAAATTTTGATAACCTT-C-C
* * *
25346 TATGAAATTGTGATAATC-TCGT
1 TATGAAATTTTGATAACCTTC-C
*
25368 TATGAAATTTTGATAAATCTTCC
1 TATGAAATTTTGAT-AACCTTCC
*
25391 TATAAAATTTTGATAAACC-TCTC
1 TATGAAATTTTGAT-AACCTTC-C
* * *
25414 TATAAAATTTTGATAACTTTCT
1 TATGAAATTTTGATAACCTTCC
* * *
25436 TGTGAAATCTTGAGAA-----C
1 TATGAAATTTTGATAACCTTCC
*
25453 TA-CAAATTTTGATAACC-TCC
1 TATGAAATTTTGATAACCTTCC
** **
25473 ATATGATTTTTTGATAACCTTAT
1 -TATGAAATTTTGATAACCTTCC
* * *
25496 TATGAAATTTTGTTAATCTCCC
1 TATGAAATTTTGATAACCTTCC
* *
25518 TATGAAATTTTGATCTACAC--AC
1 TATGAAATTTTGAT-AAC-CTTCC
*
25540 TATGAAATTTTGATAATCC-TCT
1 TATGAAATTTTGATAA-CCTTCC
* * **
25562 TGTGAAATTTTGA-AAACTAAAC
1 TATGAAATTTTGATAACCT-TCC
*
25584 TATGAAATTTTGATAACCTTCA
1 TATGAAATTTTGATAACCTTCC
* *
25606 TATGAAATTGTGATATCC-TCC
1 TATGAAATTTTGATAACCTTCC
* *
25627 -CTG-AATTTTGATATCC-T-C
1 TATGAAATTTTGATAACCTTCC
*
25645 TTTGAAATTTTGAT
1 TATGAAATTTTGAT
25659 TACTCCATAA
Statistics
Matches: 421, Mismatches: 117, Indels: 82
0.68 0.19 0.13
Matches are distributed among these distances:
16 10 0.02
17 1 0.00
18 1 0.00
19 15 0.04
20 13 0.03
21 20 0.05
22 285 0.68
23 71 0.17
24 5 0.01
ACGTcount: A:0.35, C:0.14, G:0.11, T:0.40
Consensus pattern (22 bp):
TATGAAATTTTGATAACCTTCC
Found at i:25398 original size:23 final size:23
Alignment explanation
Indices: 25372--25429 Score: 91
Period size: 23 Copynumber: 2.5 Consensus size: 23
25362 TCTCGTTATG
*
25372 AAATTTTGATAAATCT-TCCTATA
1 AAATTTTGATAAACCTCT-CTATA
25395 AAATTTTGATAAACCTCTCTATA
1 AAATTTTGATAAACCTCTCTATA
25418 AAATTTTGATAA
1 AAATTTTGATAA
25430 CTTTCTTGTG
Statistics
Matches: 33, Mismatches: 1, Indels: 2
0.92 0.03 0.06
Matches are distributed among these distances:
23 32 0.97
24 1 0.03
ACGTcount: A:0.41, C:0.12, G:0.05, T:0.41
Consensus pattern (23 bp):
AAATTTTGATAAACCTCTCTATA
Found at i:25638 original size:19 final size:20
Alignment explanation
Indices: 25608--25658 Score: 68
Period size: 19 Copynumber: 2.6 Consensus size: 20
25598 AACCTTCATA
*
25608 TGAAATTGTGATATCCTCCC
1 TGAAATTTTGATATCCTCCC
**
25628 TG-AATTTTGATATCCTCTT
1 TGAAATTTTGATATCCTCCC
25647 TGAAATTTTGAT
1 TGAAATTTTGAT
25659 TACTCCATAA
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
19 16 0.59
20 11 0.41
ACGTcount: A:0.25, C:0.16, G:0.14, T:0.45
Consensus pattern (20 bp):
TGAAATTTTGATATCCTCCC
Found at i:25784 original size:22 final size:22
Alignment explanation
Indices: 25753--25968 Score: 131
Period size: 22 Copynumber: 9.8 Consensus size: 22
25743 AATCACATTT
*
25753 TGAAAATTTGATAACCTCTTTA
1 TGAAATTTTGATAACCTCTTTA
25775 TGAAATTTTGATAACCTCTTTA
1 TGAAATTTTGATAACCTCTTTA
* * * *
25797 TAAAATTTTGTTGACC-CGTCTA
1 TGAAATTTTGATAACCTC-TTTA
* * * *
25819 TGAAATTCTGATAATCACATTA
1 TGAAATTTTGATAACCTCTTTA
* *
25841 TGTAATTTTGATAACCTCACTTCA
1 TGAAATTTTGATAACCT--CTTTA
*
25865 --AAATTTTGATAACAATAC--TA
1 TGAAATTTTGATAAC-CT-CTTTA
* *
25885 TGAAATTTTGATAATCTTTTTA
1 TGAAATTTTGATAACCTCTTTA
*
25907 T-AAATTTTGATAATCCGATCTCTA
1 TGAAATTTTGATAA-CC--TCTTTA
* * * *
25931 TGAAATTTCGATAATCACTCTA
1 TGAAATTTTGATAACCTCTTTA
*
25953 TGAGA-TTTGATAACCT
1 TGAAATTTTGATAACCT
25969 TCTATCAAAT
Statistics
Matches: 147, Mismatches: 34, Indels: 27
0.71 0.16 0.13
Matches are distributed among these distances:
20 1 0.01
21 22 0.15
22 102 0.69
23 2 0.01
24 9 0.06
25 11 0.07
ACGTcount: A:0.35, C:0.14, G:0.10, T:0.41
Consensus pattern (22 bp):
TGAAATTTTGATAACCTCTTTA
Found at i:25823 original size:66 final size:66
Alignment explanation
Indices: 25753--25919 Score: 171
Period size: 66 Copynumber: 2.5 Consensus size: 66
25743 AATCACATTT
* * * * * **
25753 TGAAAATTTGATAACCTCTTTATGAAATTTTGATAACCTC-TTTATAAAATTTTGTTGACCCGT-
1 TGAAAATTTGATAATCTCTTTATGAAATTTTGATAACCTCACTT-CAAAATTTTGAT-AACAATA
25816 CTA
64 CTA
* * *
25819 TG-AAATTCTGATAATCACATTATGTAATTTTGATAACCTCACTTCAAAATTTTGATAACAATAC
1 TGAAAATT-TGATAATCTCTTTATGAAATTTTGATAACCTCACTTCAAAATTTTGATAACAATAC
25883 TA
65 TA
* *
25885 TGAAATTTTGATAATCTTTTTAT-AAATTTTGATAA
1 TGAAAATTTGATAATCTCTTTATGAAATTTTGATAA
25920 TCCGATCTCT
Statistics
Matches: 82, Mismatches: 15, Indels: 9
0.77 0.14 0.08
Matches are distributed among these distances:
65 19 0.23
66 57 0.70
67 6 0.07
ACGTcount: A:0.36, C:0.13, G:0.09, T:0.43
Consensus pattern (66 bp):
TGAAAATTTGATAATCTCTTTATGAAATTTTGATAACCTCACTTCAAAATTTTGATAACAATACT
A
Found at i:26034 original size:22 final size:21
Alignment explanation
Indices: 26005--26060 Score: 60
Period size: 22 Copynumber: 2.6 Consensus size: 21
25995 AAATTGAGAC
26005 TTTT-ATAACCTTCATATGAAA
1 TTTTGATAACC-TCATATGAAA
* *
26026 TTTTGATAACCACATTATAAAA
1 TTTTGATAACCTCA-TATGAAA
*
26048 CTTTGATAACCTC
1 TTTTGATAACCTC
26061 CCCATGAAAT
Statistics
Matches: 29, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
21 6 0.21
22 23 0.79
ACGTcount: A:0.38, C:0.18, G:0.05, T:0.39
Consensus pattern (21 bp):
TTTTGATAACCTCATATGAAA
Found at i:26202 original size:22 final size:22
Alignment explanation
Indices: 26170--26218 Score: 62
Period size: 22 Copynumber: 2.2 Consensus size: 22
26160 TTGTGATGAT
* *
26170 TAACCACCCTATGAAATTTCAA
1 TAACCAACCTAAGAAATTTCAA
* *
26192 TAACCAACCTAAGAGATTTTAA
1 TAACCAACCTAAGAAATTTCAA
26214 TAACC
1 TAACC
26219 TGATCCTATA
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
22 23 1.00
ACGTcount: A:0.43, C:0.24, G:0.06, T:0.27
Consensus pattern (22 bp):
TAACCAACCTAAGAAATTTCAA
Found at i:26297 original size:22 final size:22
Alignment explanation
Indices: 26247--26308 Score: 81
Period size: 22 Copynumber: 2.9 Consensus size: 22
26237 GTAATCACAC
*
26247 TATGAAATTTTGATAA-CTTCT
1 TATGAAATTTTGATAACCATCT
* * *
26268 CATGAAATTATAATAACCATCT
1 TATGAAATTTTGATAACCATCT
26290 TATGAAATTTTGATAACCA
1 TATGAAATTTTGATAACCA
26309 CATAGAGACA
Statistics
Matches: 33, Mismatches: 7, Indels: 1
0.80 0.17 0.02
Matches are distributed among these distances:
21 13 0.39
22 20 0.61
ACGTcount: A:0.40, C:0.13, G:0.08, T:0.39
Consensus pattern (22 bp):
TATGAAATTTTGATAACCATCT
Found at i:26505 original size:19 final size:20
Alignment explanation
Indices: 26474--26511 Score: 53
Period size: 19 Copynumber: 1.9 Consensus size: 20
26464 TATTGACATT
26474 TAAAAATTGAAATT-AAAAG
1 TAAAAATTGAAATTCAAAAG
26493 TAAAATATT-AAATTCAAAA
1 TAAAA-ATTGAAATTCAAAA
26512 AATAATAGTA
Statistics
Matches: 17, Mismatches: 0, Indels: 3
0.85 0.00 0.15
Matches are distributed among these distances:
19 10 0.59
20 7 0.41
ACGTcount: A:0.63, C:0.03, G:0.05, T:0.29
Consensus pattern (20 bp):
TAAAAATTGAAATTCAAAAG
Found at i:26889 original size:31 final size:31
Alignment explanation
Indices: 26831--26896 Score: 91
Period size: 31 Copynumber: 2.1 Consensus size: 31
26821 ATTTACTTTA
*
26831 GAAATATGTTTTAAAGAAAATGGTACAATTG
1 GAAATATGTTTTAAAGAAAATGGTACAATCG
26862 GAAATATGTTTTAAA-AATAA-GGATACAATCG
1 GAAATATGTTTTAAAGAA-AATGG-TACAATCG
26893 GAAA
1 GAAA
26897 ACATAAAATT
Statistics
Matches: 32, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
30 4 0.12
31 28 0.88
ACGTcount: A:0.48, C:0.05, G:0.18, T:0.29
Consensus pattern (31 bp):
GAAATATGTTTTAAAGAAAATGGTACAATCG
Found at i:33061 original size:31 final size:31
Alignment explanation
Indices: 33026--33085 Score: 86
Period size: 31 Copynumber: 1.9 Consensus size: 31
33016 ATGTTTTCTG
*
33026 ATTGTACCCTTAAT-TTTAAAATATATTTCCA
1 ATTGTACCCTT-ATCTTTAAAACATATTTCCA
*
33057 ATTGTACCCTTTTCTTTAAAACATATTTC
1 ATTGTACCCTTATCTTTAAAACATATTTC
33086 GAAATTGCCA
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
30 1 0.04
31 25 0.96
ACGTcount: A:0.32, C:0.18, G:0.03, T:0.47
Consensus pattern (31 bp):
ATTGTACCCTTATCTTTAAAACATATTTCCA
Found at i:33418 original size:19 final size:20
Alignment explanation
Indices: 33391--33428 Score: 53
Period size: 19 Copynumber: 1.9 Consensus size: 20
33381 TACTATTATT
33391 TTTTGAATTT-AATATTTTAC
1 TTTTGAATTTCAA-ATTTTAC
33411 TTTT-AATTTCAAATTTTA
1 TTTTGAATTTCAAATTTTA
33429 AATGTCAATA
Statistics
Matches: 17, Mismatches: 0, Indels: 3
0.85 0.00 0.15
Matches are distributed among these distances:
19 11 0.65
20 6 0.35
ACGTcount: A:0.32, C:0.05, G:0.03, T:0.61
Consensus pattern (20 bp):
TTTTGAATTTCAAATTTTAC
Found at i:33699 original size:42 final size:42
Alignment explanation
Indices: 33639--33721 Score: 139
Period size: 42 Copynumber: 2.0 Consensus size: 42
33629 TTCATGAGGA
* *
33639 GGTTATCAAAATTCCATAGTGTGGTTACCAAAATTTCATAGT
1 GGTTACCAAAATTCCATAGTATGGTTACCAAAATTTCATAGT
*
33681 GGTTACCAAAATTTCATAGTATGGTTACCAAAATTTCATAG
1 GGTTACCAAAATTCCATAGTATGGTTACCAAAATTTCATAG
33722 GATCAGGTTA
Statistics
Matches: 38, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
42 38 1.00
ACGTcount: A:0.35, C:0.14, G:0.16, T:0.35
Consensus pattern (42 bp):
GGTTACCAAAATTCCATAGTATGGTTACCAAAATTTCATAGT
Found at i:33707 original size:64 final size:66
Alignment explanation
Indices: 33592--33721 Score: 158
Period size: 64 Copynumber: 2.0 Consensus size: 66
33582 CTTGTCTCTA
* * ** * *
33592 TGTGGTTATCAAAATTTTATAAGATGGTTATTATAATTTCATGAGGAGGTTATCAAAATTCCATA
1 TGTGGTTACCAAAATTTCATAAGATGGTTACCAAAATTTCATGAGGAGGTTACCAAAATTCCATA
33657 G
66 G
* *
33658 TGTGGTTACCAAAATTTCAT-AG-TGGTTACCAAAATTTCAT-AGTATGGTTACCAAAATTTCAT
1 TGTGGTTACCAAAATTTCATAAGATGGTTACCAAAATTTCATGAGGA-GGTTACCAAAATTCCAT
33720 AG
65 AG
33722 GATCAGGTTA
Statistics
Matches: 55, Mismatches: 8, Indels: 4
0.82 0.12 0.06
Matches are distributed among these distances:
63 3 0.05
64 32 0.58
65 2 0.04
66 18 0.33
ACGTcount: A:0.35, C:0.11, G:0.17, T:0.38
Consensus pattern (66 bp):
TGTGGTTACCAAAATTTCATAAGATGGTTACCAAAATTTCATGAGGAGGTTACCAAAATTCCATA
G
Found at i:33737 original size:24 final size:22
Alignment explanation
Indices: 33594--33775 Score: 138
Period size: 22 Copynumber: 8.3 Consensus size: 22
33584 TGTCTCTATG
* * *
33594 TGGTTATCAAAATTTTATAAGA
1 TGGTTATTAAAATTTCATAGGA
*
33616 TGGTTATTATAATTTCATGAGGA
1 TGGTTATTAAAATTTCAT-AGGA
* *
33639 -GGTTATCAAAATTCCATAGTG-
1 TGGTTATTAAAATTTCATAG-GA
**
33660 TGGTTACCAAAATTTCATA-G-
1 TGGTTATTAAAATTTCATAGGA
** *
33680 TGGTTACCAAAATTTCATAGTA
1 TGGTTATTAAAATTTCATAGGA
**
33702 TGGTTACCAAAATTTCATAGGA
1 TGGTTATTAAAATTTCATAGGA
* * *
33724 TCAGGTTATTAAAATCTCTTAGGT
1 T--GGTTATTAAAATTTCATAGGA
* *
33748 TGGTTATTGAAATTTCATAGGG
1 TGGTTATTAAAATTTCATAGGA
33770 TGGTTA
1 TGGTTA
33776 ATTATAACAA
Statistics
Matches: 133, Mismatches: 20, Indels: 14
0.80 0.12 0.08
Matches are distributed among these distances:
20 20 0.15
21 2 0.02
22 91 0.68
23 3 0.02
24 17 0.13
ACGTcount: A:0.33, C:0.10, G:0.19, T:0.38
Consensus pattern (22 bp):
TGGTTATTAAAATTTCATAGGA
Found at i:33752 original size:46 final size:43
Alignment explanation
Indices: 33626--33775 Score: 126
Period size: 42 Copynumber: 3.4 Consensus size: 43
33616 TGGTTATTAT
* * *
33626 AATTTCATGAGGAGGTTATCAAAAT-TCCATAGTGTGGTTACCAA
1 AATTTCAT-AGGTGGTTACCAAAATCT-CATAGTATGGTTACCAA
*
33670 AATTTCATA-GTGGTTACCAAAATTTCATAGTATGGTTACCAA
1 AATTTCATAGGTGGTTACCAAAATCTCATAGTATGGTTACCAA
** * ***
33712 AATTTCATAGGATCAGGTTATTAAAATCTCTTAGGT-TGGTTATTGA
1 AATTTCATAGG-T--GGTTACCAAAATCTCATA-GTATGGTTACCAA
33758 AATTTCATAGGGTGGTTA
1 AATTTCATA-GGTGGTTA
33776 ATTATAACAA
Statistics
Matches: 89, Mismatches: 10, Indels: 14
0.79 0.09 0.12
Matches are distributed among these distances:
42 37 0.42
43 3 0.03
44 14 0.16
46 31 0.35
47 4 0.04
ACGTcount: A:0.33, C:0.11, G:0.19, T:0.37
Consensus pattern (43 bp):
AATTTCATAGGTGGTTACCAAAATCTCATAGTATGGTTACCAA
Found at i:34028 original size:22 final size:22
Alignment explanation
Indices: 33885--34051 Score: 76
Period size: 22 Copynumber: 7.6 Consensus size: 22
33875 ATTTCATGGG
33885 GAGGTTATC-AAAATTCCAT-AT
1 GAGGTTATCAAAAATT-CATAAT
* *
33906 GAAGGTTATCAAAATTTCATAGTT
1 G-AGGTTATCAAAAATTCATA-AT
* * *
33930 TA-GTTTTC-AAAATTACACAA-
1 GAGGTTATCAAAAATT-CATAAT
* *
33950 GAGAGTTATCAAAACTTCATAGT
1 GAG-GTTATCAAAAATTCATAAT
* * * **
33973 -ATGTAGATCAAAATTTCATAGG
1 GAGGT-TATCAAAAATTCATAAT
* *
33995 GAGATTAACAAAAATTCATAAT
1 GAGGTTATCAAAAATTCATAAT
* * **
34017 GAGGTTATCAAAAAATCGTAGG
1 GAGGTTATCAAAAATTCATAAT
34039 GAGGTTATCAAAA
1 GAGGTTATCAAAA
34052 TTTGTAGTTA
Statistics
Matches: 106, Mismatches: 29, Indels: 21
0.68 0.19 0.13
Matches are distributed among these distances:
20 1 0.01
21 8 0.08
22 83 0.78
23 13 0.12
24 1 0.01
ACGTcount: A:0.43, C:0.11, G:0.16, T:0.31
Consensus pattern (22 bp):
GAGGTTATCAAAAATTCATAAT
Found at i:34109 original size:23 final size:23
Alignment explanation
Indices: 34059--34184 Score: 107
Period size: 22 Copynumber: 5.6 Consensus size: 23
34049 AAATTTGTAG
* * * *
34059 TTATCAAGATTTCATAAGAAAG-
1 TTATCAAAATTTCATAGGGAGGA
* *
34081 TTATCAAAATTTTATAGGGAGGT
1 TTATCAAAATTTCATAGGGAGGA
* *
34104 TTATCAAAATTTTATA-GGAAGA
1 TTATCAAAATTTCATAGGGAGGA
*
34126 TTTATCAAAATTTCATAGCGA-GA
1 -TTATCAAAATTTCATAGGGAGGA
* * *
34149 TTATCATAATTTCATAGTG-TGA
1 TTATCAAAATTTCATAGGGAGGA
34171 TTATCAAAATTTCA
1 TTATCAAAATTTCA
34185 GAGTGTGATT
Statistics
Matches: 88, Mismatches: 12, Indels: 8
0.81 0.11 0.07
Matches are distributed among these distances:
22 53 0.60
23 33 0.38
24 2 0.02
ACGTcount: A:0.40, C:0.09, G:0.13, T:0.38
Consensus pattern (23 bp):
TTATCAAAATTTCATAGGGAGGA
Found at i:34153 original size:45 final size:45
Alignment explanation
Indices: 34059--34184 Score: 132
Period size: 45 Copynumber: 2.8 Consensus size: 45
34049 AAATTTGTAG
* * * * *
34059 TTATCAAGATTTCATAAGAA-AGTTATCAAAATTTTATAGGGAGGT
1 TTATCAAAATTTCATAGGAAGA-TTATCAAAATTTCATAGCGAGGA
*
34104 TTATCAAAATTTTATAGGAAGATTTATCAAAATTTCATAGCGA-GA
1 TTATCAAAATTTCATAGGAAGA-TTATCAAAATTTCATAGCGAGGA
* *
34149 TTATCATAATTTCATAGTG-TGATTATCAAAATTTCA
1 TTATCAAAATTTCATAG-GAAGATTATCAAAATTTCA
34185 GAGTGTGATT
Statistics
Matches: 69, Mismatches: 10, Indels: 5
0.82 0.12 0.06
Matches are distributed among these distances:
44 14 0.20
45 35 0.51
46 20 0.29
ACGTcount: A:0.40, C:0.09, G:0.13, T:0.38
Consensus pattern (45 bp):
TTATCAAAATTTCATAGGAAGATTATCAAAATTTCATAGCGAGGA
Found at i:34206 original size:22 final size:22
Alignment explanation
Indices: 34127--34195 Score: 93
Period size: 22 Copynumber: 3.1 Consensus size: 22
34117 ATAGGAAGAT
* * *
34127 TTATCAAAATTTCATAGCGAGA
1 TTATCAAAATTTCAGAGTGTGA
* *
34149 TTATCATAATTTCATAGTGTGA
1 TTATCAAAATTTCAGAGTGTGA
34171 TTATCAAAATTTCAGAGTGTGA
1 TTATCAAAATTTCAGAGTGTGA
34193 TTA
1 TTA
34196 CTAACAATTC
Statistics
Matches: 42, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
22 42 1.00
ACGTcount: A:0.36, C:0.10, G:0.14, T:0.39
Consensus pattern (22 bp):
TTATCAAAATTTCAGAGTGTGA
Found at i:34251 original size:22 final size:23
Alignment explanation
Indices: 34226--34274 Score: 57
Period size: 22 Copynumber: 2.2 Consensus size: 23
34216 TTTTAAATTT
*
34226 TCATAACGTA-GTTATCAATATA
1 TCATAACGGAGGTTATCAATATA
* *
34248 TCAT-ATGGAGGTTATCAATATC
1 TCATAACGGAGGTTATCAATATA
34270 TCATA
1 TCATA
34275 GTGTTGGTTA
Statistics
Matches: 22, Mismatches: 3, Indels: 3
0.79 0.11 0.11
Matches are distributed among these distances:
21 3 0.14
22 19 0.86
ACGTcount: A:0.37, C:0.14, G:0.12, T:0.37
Consensus pattern (23 bp):
TCATAACGGAGGTTATCAATATA
Found at i:34287 original size:23 final size:22
Alignment explanation
Indices: 34236--34288 Score: 70
Period size: 22 Copynumber: 2.4 Consensus size: 22
34226 TCATAACGTA
34236 GTTATCAATATATCATATGGAG
1 GTTATCAATATATCATATGGAG
* **
34258 GTTATCAATATCTCATAGTGTTG
1 GTTATCAATATATCATA-TGGAG
34281 GTTATCAA
1 GTTATCAA
34289 AAATTTCATT
Statistics
Matches: 27, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
22 16 0.59
23 11 0.41
ACGTcount: A:0.32, C:0.11, G:0.17, T:0.40
Consensus pattern (22 bp):
GTTATCAATATATCATATGGAG
Found at i:38137 original size:18 final size:16
Alignment explanation
Indices: 38108--38142 Score: 52
Period size: 18 Copynumber: 2.1 Consensus size: 16
38098 TAAATCATAG
38108 TATAATTCTATATATT
1 TATAATTCTATATATT
38124 TATATATTCATATATATT
1 TATA-ATTC-TATATATT
38142 T
1 T
38143 TAGATTTTAT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 4 0.24
17 4 0.24
18 9 0.53
ACGTcount: A:0.37, C:0.06, G:0.00, T:0.57
Consensus pattern (16 bp):
TATAATTCTATATATT
Found at i:39447 original size:14 final size:14
Alignment explanation
Indices: 39428--39459 Score: 64
Period size: 14 Copynumber: 2.3 Consensus size: 14
39418 TAACAATTGC
39428 GACTGTAACAAAAA
1 GACTGTAACAAAAA
39442 GACTGTAACAAAAA
1 GACTGTAACAAAAA
39456 GACT
1 GACT
39460 ATATAAACTT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.53, C:0.16, G:0.16, T:0.16
Consensus pattern (14 bp):
GACTGTAACAAAAA
Found at i:46222 original size:2 final size:2
Alignment explanation
Indices: 46208--46245 Score: 60
Period size: 2 Copynumber: 19.0 Consensus size: 2
46198 CCCGTATTAC
46208 TA TA TA CTA -A TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA -TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
46246 AAATATTGTT
Statistics
Matches: 34, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
1 1 0.03
2 31 0.91
3 2 0.06
ACGTcount: A:0.50, C:0.03, G:0.00, T:0.47
Consensus pattern (2 bp):
TA
Found at i:47256 original size:42 final size:42
Alignment explanation
Indices: 47210--47307 Score: 151
Period size: 42 Copynumber: 2.3 Consensus size: 42
47200 AGCAACAATT
* * *
47210 AATATTAGTTTTATTTTGATGAATTATCTAGAGATGGAGTAG
1 AATATTAGCTTTATTTTGATGAATTACCTAGAGATGAAGTAG
47252 AATATTAGCTTTATTTTGATGAATTACCTAGAGATGAAGTAG
1 AATATTAGCTTTATTTTGATGAATTACCTAGAGATGAAGTAG
*
47294 AATTATTTGCTTTA
1 AA-TATTAGCTTTA
47308 AATATGCAAA
Statistics
Matches: 51, Mismatches: 4, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
42 41 0.80
43 10 0.20
ACGTcount: A:0.34, C:0.05, G:0.18, T:0.43
Consensus pattern (42 bp):
AATATTAGCTTTATTTTGATGAATTACCTAGAGATGAAGTAG
Found at i:53335 original size:6 final size:6
Alignment explanation
Indices: 53320--53359 Score: 55
Period size: 6 Copynumber: 6.8 Consensus size: 6
53310 CTGTATACTA
* *
53320 TATATC TATATT TATATC TATATA TATATC TATA-C TATAT
1 TATATC TATATC TATATC TATATC TATATC TATATC TATAT
53360 ATAAAAGTAC
Statistics
Matches: 29, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
5 5 0.17
6 24 0.83
ACGTcount: A:0.38, C:0.10, G:0.00, T:0.53
Consensus pattern (6 bp):
TATATC
Found at i:53337 original size:12 final size:12
Alignment explanation
Indices: 53313--53361 Score: 71
Period size: 12 Copynumber: 3.9 Consensus size: 12
53303 AGCCTTCCTG
53313 TATACTATATATC
1 TATA-TATATATC
*
53326 TATATTTATATC
1 TATATATATATC
53338 TATATATATATC
1 TATATATATATC
53350 TATACTATATAT
1 TATA-TATATAT
53362 AAAAGTACGA
Statistics
Matches: 33, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
12 22 0.67
13 11 0.33
ACGTcount: A:0.39, C:0.10, G:0.00, T:0.51
Consensus pattern (12 bp):
TATATATATATC
Found at i:53650 original size:109 final size:109
Alignment explanation
Indices: 53454--53749 Score: 457
Period size: 109 Copynumber: 2.7 Consensus size: 109
53444 ACTATTATAG
* * *
53454 TTTTATTCTATTAGAAACTCTATTTTTATTCAATTAAATTAAATCTAATATCTTTATAATTACTT
1 TTTTATTCTACTAAAAACTCTA---TT-TTC-ATTTAATTAAATCTAATATCTTTATAATTACTT
53519 TATTTTTACCAAAAAATTTGGATATACTAAAATTTTTTCTAATATACAA
61 TATTTTTACCAAAAAATTTGGATATACTAAAATTTTTTCTAATATACAA
53568 TTTTATTCTACTAAAAACTCTATTTTCATTTAATTAAATCTAATATCTTTATAATTACTTTATTT
1 TTTTATTCTACTAAAAACTCTATTTTCATTTAATTAAATCTAATATCTTTATAATTACTTTATTT
*
53633 TTACCAAAAAATTTGGATATATTAAAATTTTTTCTAATATACAA
66 TTACCAAAAAATTTGGATATACTAAAATTTTTTCTAATATACAA
* * **
53677 TTTTATTCTACTAAAAACTCTATTTTCATTTAATTAAATCCAATATTTTATATAATTTTTTTTAT
1 TTTTATTCTACTAAAAACTCTATTTTCATTTAATTAAATCTAATATCTT-TATAA-TTACTTTAT
53742 TTTTACCA
64 TTTTACCA
53750 TTTTAATTTA
Statistics
Matches: 172, Mismatches: 8, Indels: 7
0.92 0.04 0.04
Matches are distributed among these distances:
109 127 0.74
110 8 0.05
111 17 0.10
114 20 0.12
ACGTcount: A:0.37, C:0.11, G:0.02, T:0.50
Consensus pattern (109 bp):
TTTTATTCTACTAAAAACTCTATTTTCATTTAATTAAATCTAATATCTTTATAATTACTTTATTT
TTACCAAAAAATTTGGATATACTAAAATTTTTTCTAATATACAA
Found at i:54516 original size:2 final size:2
Alignment explanation
Indices: 54503--54536 Score: 59
Period size: 2 Copynumber: 17.0 Consensus size: 2
54493 CGAAGACTAG
*
54503 TA TA TC TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.47, C:0.03, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Done.