Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01018438.1 Corchorus olitorius cultivar O-4 contig18471, 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: 66546
ACGTcount: A:0.31, C:0.19, G:0.19, T:0.31
Found at i:506 original size:30 final size:30
Alignment explanation
Indices: 472--542 Score: 115
Period size: 32 Copynumber: 2.3 Consensus size: 30
462 CCAACCTGCT
472 CAGGCCCGCGCTAGCTGGCCCAGCGCGCAC
1 CAGGCCCGCGCTAGCTGGCCCAGCGCGCAC
*
502 CAGGCCTGCGCGCTAGCTGGCCCAGCGCGCGC
1 CAGGCC--CGCGCTAGCTGGCCCAGCGCGCAC
534 CAGGCCCGC
1 CAGGCCCGC
543 TAGGCTGGCT
Statistics
Matches: 38, Mismatches: 1, Indels: 4
0.88 0.02 0.09
Matches are distributed among these distances:
30 9 0.24
32 29 0.76
ACGTcount: A:0.11, C:0.46, G:0.35, T:0.07
Consensus pattern (30 bp):
CAGGCCCGCGCTAGCTGGCCCAGCGCGCAC
Found at i:529 original size:17 final size:17
Alignment explanation
Indices: 478--531 Score: 67
Period size: 17 Copynumber: 3.3 Consensus size: 17
468 TGCTCAGGCC
478 CGCGCTAGCTGGCCCAG
1 CGCGCTAGCTGGCCCAG
* * *
495 CGCGC-ACCAGG-CCTG
1 CGCGCTAGCTGGCCCAG
510 CGCGCTAGCTGGCCCAG
1 CGCGCTAGCTGGCCCAG
527 CGCGC
1 CGCGC
532 GCCAGGCCCG
Statistics
Matches: 29, Mismatches: 6, Indels: 4
0.74 0.15 0.10
Matches are distributed among these distances:
15 8 0.28
16 8 0.28
17 13 0.45
ACGTcount: A:0.11, C:0.44, G:0.35, T:0.09
Consensus pattern (17 bp):
CGCGCTAGCTGGCCCAG
Found at i:4653 original size:30 final size:30
Alignment explanation
Indices: 4619--4689 Score: 115
Period size: 32 Copynumber: 2.3 Consensus size: 30
4609 CCAACCTGCT
4619 CAGGCCCGCGCTAGCTGGCCCAGCGCGCAC
1 CAGGCCCGCGCTAGCTGGCCCAGCGCGCAC
*
4649 CAGGCCTGCGCGCTAGCTGGCCCAGCGCGCGC
1 CAGGCC--CGCGCTAGCTGGCCCAGCGCGCAC
4681 CAGGCCCGC
1 CAGGCCCGC
4690 TAGGCTGGCT
Statistics
Matches: 38, Mismatches: 1, Indels: 4
0.88 0.02 0.09
Matches are distributed among these distances:
30 9 0.24
32 29 0.76
ACGTcount: A:0.11, C:0.46, G:0.35, T:0.07
Consensus pattern (30 bp):
CAGGCCCGCGCTAGCTGGCCCAGCGCGCAC
Found at i:4676 original size:17 final size:17
Alignment explanation
Indices: 4625--4678 Score: 67
Period size: 17 Copynumber: 3.3 Consensus size: 17
4615 TGCTCAGGCC
4625 CGCGCTAGCTGGCCCAG
1 CGCGCTAGCTGGCCCAG
* * *
4642 CGCGC-ACCAGG-CCTG
1 CGCGCTAGCTGGCCCAG
4657 CGCGCTAGCTGGCCCAG
1 CGCGCTAGCTGGCCCAG
4674 CGCGC
1 CGCGC
4679 GCCAGGCCCG
Statistics
Matches: 29, Mismatches: 6, Indels: 4
0.74 0.15 0.10
Matches are distributed among these distances:
15 8 0.28
16 8 0.28
17 13 0.45
ACGTcount: A:0.11, C:0.44, G:0.35, T:0.09
Consensus pattern (17 bp):
CGCGCTAGCTGGCCCAG
Found at i:5844 original size:24 final size:24
Alignment explanation
Indices: 5815--5874 Score: 102
Period size: 24 Copynumber: 2.5 Consensus size: 24
5805 AAATATTTCT
*
5815 AAATTGTCATTATTTTTTCCTTAA
1 AAATTGTCACTATTTTTTCCTTAA
*
5839 AAATTGTCACTATTTTTTCTTTAA
1 AAATTGTCACTATTTTTTCCTTAA
5863 AAATTGTCACTA
1 AAATTGTCACTA
5875 CTTAAAGTCA
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
24 34 1.00
ACGTcount: A:0.32, C:0.13, G:0.05, T:0.50
Consensus pattern (24 bp):
AAATTGTCACTATTTTTTCCTTAA
Found at i:6725 original size:22 final size:22
Alignment explanation
Indices: 6700--6770 Score: 65
Period size: 22 Copynumber: 3.2 Consensus size: 22
6690 TAAAAAACTT
6700 ATAGGG-AGATTAACAAAATCTC
1 ATAGGGAAGATT-ACAAAATCTC
* *
6722 ATAGGGAAGGTTACAAAATTTC
1 ATAGGGAAGATTACAAAATCTC
* *
6744 ATA-GGAAGGATTATTAAAATTTC
1 ATAGGGAA-GATTA-CAAAATCTC
6767 ATAG
1 ATAG
6771 TTAGGTTATC
Statistics
Matches: 41, Mismatches: 4, Indels: 6
0.80 0.08 0.12
Matches are distributed among these distances:
21 4 0.10
22 22 0.54
23 15 0.37
ACGTcount: A:0.44, C:0.08, G:0.20, T:0.28
Consensus pattern (22 bp):
ATAGGGAAGATTACAAAATCTC
Found at i:6765 original size:23 final size:21
Alignment explanation
Indices: 6712--6797 Score: 73
Period size: 22 Copynumber: 3.8 Consensus size: 21
6702 AGGGAGATTA
*
6712 ACAAAATCTCATAGGGAAGGTT
1 ACAAAATTTCATA-GGAAGGTT
6734 ACAAAATTTCATAGGAAGGATT
1 ACAAAATTTCATAGGAAGG-TT
* **
6756 ATTAAAATTTCATAGTTAGGTT
1 A-CAAAATTTCATAGGAAGGTT
*
6778 ATCAAAGGTTTCATATGGAA
1 A-CAAA-ATTTCATA-GGAA
6798 TTTATCACAA
Statistics
Matches: 52, Mismatches: 8, Indels: 6
0.79 0.12 0.09
Matches are distributed among these distances:
21 6 0.12
22 22 0.42
23 22 0.42
24 2 0.04
ACGTcount: A:0.41, C:0.09, G:0.19, T:0.31
Consensus pattern (21 bp):
ACAAAATTTCATAGGAAGGTT
Found at i:6833 original size:22 final size:21
Alignment explanation
Indices: 6799--6881 Score: 85
Period size: 22 Copynumber: 3.8 Consensus size: 21
6789 CATATGGAAT
*
6799 TTATCACAATTTTATAGGTAA
1 TTATCAAAATTTTATAGGTAA
***
6820 TTATCAAAATTTTTTATAGCGCGG
1 TTATCAAAA--TTTTATAG-GTAA
*
6844 TTATCAAAATTTAATAGGGTAA
1 TTATCAAAATTTTATA-GGTAA
6866 TTATCAAAATTTTATA
1 TTATCAAAATTTTATA
6882 AAAATATTCA
Statistics
Matches: 49, Mismatches: 9, Indels: 7
0.75 0.14 0.11
Matches are distributed among these distances:
21 8 0.16
22 22 0.45
23 9 0.18
24 10 0.20
ACGTcount: A:0.39, C:0.08, G:0.11, T:0.42
Consensus pattern (21 bp):
TTATCAAAATTTTATAGGTAA
Found at i:6931 original size:54 final size:54
Alignment explanation
Indices: 6867--6977 Score: 195
Period size: 54 Copynumber: 2.1 Consensus size: 54
6857 ATAGGGTAAT
* *
6867 TATCAAAATTTTATAAAAATATTCATTCGAAATATTTTGGGCCATATATATATA
1 TATCAAAATTTTATAAAAATATTCATTCGAAACATTTTGGGACATATATATATA
*
6921 TATCAAAATTTTATAAAAATATTCATTCGAAACATTTTGGGATATATATATATA
1 TATCAAAATTTTATAAAAATATTCATTCGAAACATTTTGGGACATATATATATA
6975 TAT
1 TAT
6978 ATATATTGTA
Statistics
Matches: 54, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
54 54 1.00
ACGTcount: A:0.43, C:0.08, G:0.07, T:0.41
Consensus pattern (54 bp):
TATCAAAATTTTATAAAAATATTCATTCGAAACATTTTGGGACATATATATATA
Found at i:6990 original size:52 final size:53
Alignment explanation
Indices: 6867--6992 Score: 175
Period size: 54 Copynumber: 2.4 Consensus size: 53
6857 ATAGGGTAAT
* *
6867 TATCAAAATTTTATAAAAATATTCATTCGAAATATTTTGGGCCATATATATATA
1 TATCAAAATATTATAAAAATATTCATTCGAAACATTTTGGG-CATATATATATA
*
6921 TATCAAAATTTTATAAAAATATTCATTCGAAACATTTTGGG-ATATATATATA
1 TATCAAAATATTATAAAAATATTCATTCGAAACATTTTGGGCATATATATATA
* *
6973 TAT-ATATATATTGTAAAAAT
1 TATCA-AAATATTATAAAAAT
6993 TGCAAGTGAT
Statistics
Matches: 67, Mismatches: 4, Indels: 4
0.89 0.05 0.05
Matches are distributed among these distances:
51 1 0.01
52 26 0.39
54 40 0.60
ACGTcount: A:0.44, C:0.07, G:0.07, T:0.41
Consensus pattern (53 bp):
TATCAAAATATTATAAAAATATTCATTCGAAACATTTTGGGCATATATATATA
Found at i:7783 original size:21 final size:21
Alignment explanation
Indices: 7748--7789 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
7738 TGGGTGTGTG
*
7748 TGTGATTGTTTGGTTTGGTAGA
1 TGTGATTGATTGGTTT-GTAGA
7770 TGTGA-TGATTGGTTTGTAGA
1 TGTGATTGATTGGTTTGTAGA
7790 GACCGAGCGA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
20 5 0.26
21 9 0.47
22 5 0.26
ACGTcount: A:0.17, C:0.00, G:0.36, T:0.48
Consensus pattern (21 bp):
TGTGATTGATTGGTTTGTAGA
Found at i:7820 original size:25 final size:25
Alignment explanation
Indices: 7786--7834 Score: 89
Period size: 25 Copynumber: 2.0 Consensus size: 25
7776 GATTGGTTTG
*
7786 TAGAGACCGAGCGAGAGTGCTCAAA
1 TAGAGACCGAGCGAGAGTACTCAAA
7811 TAGAGACCGAGCGAGAGTACTCAA
1 TAGAGACCGAGCGAGAGTACTCAA
7835 GATTGTTTGA
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
25 23 1.00
ACGTcount: A:0.37, C:0.20, G:0.31, T:0.12
Consensus pattern (25 bp):
TAGAGACCGAGCGAGAGTACTCAAA
Found at i:27482 original size:6 final size:7
Alignment explanation
Indices: 27464--27490 Score: 54
Period size: 7 Copynumber: 3.9 Consensus size: 7
27454 GACCCCTTCT
27464 CTTTTTC
1 CTTTTTC
27471 CTTTTTC
1 CTTTTTC
27478 CTTTTTC
1 CTTTTTC
27485 CTTTTT
1 CTTTTT
27491 TTTTTTTTCA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 20 1.00
ACGTcount: A:0.00, C:0.26, G:0.00, T:0.74
Consensus pattern (7 bp):
CTTTTTC
Found at i:29163 original size:96 final size:96
Alignment explanation
Indices: 28999--29192 Score: 388
Period size: 96 Copynumber: 2.0 Consensus size: 96
28989 AAAGTCGTAG
28999 ATCACACAATAACCTTTTAACCTACACTTGAACAACCTCAATCGGACAAGTTGTTGCGCCAAAAA
1 ATCACACAATAACCTTTTAACCTACACTTGAACAACCTCAATCGGACAAGTTGTTGCGCCAAAAA
29064 TCTTTGATAGAGTTTTTGCGAAAAAAACTAA
66 TCTTTGATAGAGTTTTTGCGAAAAAAACTAA
29095 ATCACACAATAACCTTTTAACCTACACTTGAACAACCTCAATCGGACAAGTTGTTGCGCCAAAAA
1 ATCACACAATAACCTTTTAACCTACACTTGAACAACCTCAATCGGACAAGTTGTTGCGCCAAAAA
29160 TCTTTGATAGAGTTTTTGCGAAAAAAACTAA
66 TCTTTGATAGAGTTTTTGCGAAAAAAACTAA
29191 AT
1 AT
29193 AACAGCGCGG
Statistics
Matches: 98, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
96 98 1.00
ACGTcount: A:0.39, C:0.22, G:0.12, T:0.27
Consensus pattern (96 bp):
ATCACACAATAACCTTTTAACCTACACTTGAACAACCTCAATCGGACAAGTTGTTGCGCCAAAAA
TCTTTGATAGAGTTTTTGCGAAAAAAACTAA
Found at i:29856 original size:15 final size:15
Alignment explanation
Indices: 29836--29866 Score: 62
Period size: 15 Copynumber: 2.1 Consensus size: 15
29826 CTTAAGCAGC
29836 GGTGAGAAAATATGT
1 GGTGAGAAAATATGT
29851 GGTGAGAAAATATGT
1 GGTGAGAAAATATGT
29866 G
1 G
29867 TTTGGTGAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.39, C:0.00, G:0.35, T:0.26
Consensus pattern (15 bp):
GGTGAGAAAATATGT
Found at i:29892 original size:18 final size:20
Alignment explanation
Indices: 29848--29894 Score: 57
Period size: 18 Copynumber: 2.5 Consensus size: 20
29838 TGAGAAAATA
29848 TGTGGTGAGAAAATATGTGT
1 TGTGGTGAGAAAATATGTGT
29868 T-TGGTGA-AAACA-ATG-GT
1 TGTGGTGAGAAA-ATATGTGT
29885 TGTGGTGAGA
1 TGTGGTGAGA
29895 TAAGAATGTA
Statistics
Matches: 24, Mismatches: 0, Indels: 7
0.77 0.00 0.23
Matches are distributed among these distances:
17 3 0.12
18 12 0.50
19 8 0.33
20 1 0.04
ACGTcount: A:0.30, C:0.02, G:0.36, T:0.32
Consensus pattern (20 bp):
TGTGGTGAGAAAATATGTGT
Found at i:35392 original size:67 final size:67
Alignment explanation
Indices: 35284--35413 Score: 233
Period size: 67 Copynumber: 1.9 Consensus size: 67
35274 GCGTCTGCGT
* *
35284 GGACGCTCTGTCTCACTGATGGACGAACGGGGGCGCCAGTCTAGGCGCTTAGCCGTTGATTGAAA
1 GGACGCTCTGCCTCACTGATGGACGAACGGGGGCGCCAGTCTAGGCGCTCAGCCGTTGATTGAAA
35349 GC
66 GC
*
35351 GGACGCTCTGCCTCACTGGTGGACGAACGGGGGCGCCAGTCTAGGCGCTCAGCCGTTGATTGA
1 GGACGCTCTGCCTCACTGATGGACGAACGGGGGCGCCAGTCTAGGCGCTCAGCCGTTGATTGA
35414 GTGGCGCCTG
Statistics
Matches: 60, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
67 60 1.00
ACGTcount: A:0.18, C:0.27, G:0.35, T:0.20
Consensus pattern (67 bp):
GGACGCTCTGCCTCACTGATGGACGAACGGGGGCGCCAGTCTAGGCGCTCAGCCGTTGATTGAAA
GC
Found at i:35481 original size:76 final size:76
Alignment explanation
Indices: 35351--35601 Score: 371
Period size: 76 Copynumber: 3.3 Consensus size: 76
35341 GATTGAAAGC
* * * *
35351 GGACGCTCTGCCTCACTGGTGGACGAACGGGGGCGCCAGTCTAGGCGCTCAGCCGTTGATTGAGT
1 GGACGCTCTGTCTCACTGATGGACGAACGGGGGCGCCAGTCTAGGCGCTCAGCCGTTGAGTGAGC
**
35416 GGCGCCTGCGT
66 GGCGTTTGCGT
* *
35427 GGGCGCTCTGTCTCACTGATGGACGAACGGGGGCGCCAGTCTAGGCGCTTAGCCGTTGAGTGAGC
1 GGACGCTCTGTCTCACTGATGGACGAACGGGGGCGCCAGTCTAGGCGCTCAGCCGTTGAGTGAGC
*
35492 GGCGTTTGCAT
66 GGCGTTTGCGT
* * * *
35503 AGACGCTCTGTCTCACTGATGTACGAACGGGGGCGTCAGTTTAGGCGCTCAGCCGTTGAGTGAGC
1 GGACGCTCTGTCTCACTGATGGACGAACGGGGGCGCCAGTCTAGGCGCTCAGCCGTTGAGTGAGC
35568 GGCGTTTGCGT
66 GGCGTTTGCGT
35579 GGACG--CTGTCTCACTGATGGACG
1 GGACGCTCTGTCTCACTGATGGACG
35602 TTCCAAATCT
Statistics
Matches: 157, Mismatches: 18, Indels: 2
0.89 0.10 0.01
Matches are distributed among these distances:
74 17 0.11
76 140 0.89
ACGTcount: A:0.15, C:0.26, G:0.37, T:0.22
Consensus pattern (76 bp):
GGACGCTCTGTCTCACTGATGGACGAACGGGGGCGCCAGTCTAGGCGCTCAGCCGTTGAGTGAGC
GGCGTTTGCGT
Found at i:39121 original size:25 final size:25
Alignment explanation
Indices: 39087--39138 Score: 95
Period size: 25 Copynumber: 2.1 Consensus size: 25
39077 TCACTGGCAT
39087 GCAAACCCAATTAACCCGCTGTCAA
1 GCAAACCCAATTAACCCGCTGTCAA
*
39112 GCAAACCCAATTAACCTGCTGTCAA
1 GCAAACCCAATTAACCCGCTGTCAA
39137 GC
1 GC
39139 GCGGCTAACT
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:0.35, C:0.35, G:0.13, T:0.17
Consensus pattern (25 bp):
GCAAACCCAATTAACCCGCTGTCAA
Found at i:45467 original size:31 final size:31
Alignment explanation
Indices: 45425--45511 Score: 165
Period size: 31 Copynumber: 2.8 Consensus size: 31
45415 ATCGGGCAAA
*
45425 ATGCTCAATTTGGGGCCAAACGTTTACCGCG
1 ATGCTCGATTTGGGGCCAAACGTTTACCGCG
45456 ATGCTCGATTTGGGGCCAAACGTTTACCGCG
1 ATGCTCGATTTGGGGCCAAACGTTTACCGCG
45487 ATGCTCGATTTGGGGCCAAACGTTT
1 ATGCTCGATTTGGGGCCAAACGTTT
45512 CAATTTGAAC
Statistics
Matches: 55, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
31 55 1.00
ACGTcount: A:0.21, C:0.24, G:0.28, T:0.28
Consensus pattern (31 bp):
ATGCTCGATTTGGGGCCAAACGTTTACCGCG
Found at i:51951 original size:21 final size:22
Alignment explanation
Indices: 51926--51969 Score: 72
Period size: 21 Copynumber: 2.0 Consensus size: 22
51916 GGGCCATGGC
51926 CTCGGCATGGCT-GGTGCCTGT
1 CTCGGCATGGCTCGGTGCCTGT
*
51947 CTCGGCATGGCTCGGTGCTTGT
1 CTCGGCATGGCTCGGTGCCTGT
51969 C
1 C
51970 GAGCTATGCC
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
21 12 0.57
22 9 0.43
ACGTcount: A:0.05, C:0.30, G:0.36, T:0.30
Consensus pattern (22 bp):
CTCGGCATGGCTCGGTGCCTGT
Found at i:52052 original size:22 final size:22
Alignment explanation
Indices: 52027--52068 Score: 57
Period size: 22 Copynumber: 1.9 Consensus size: 22
52017 GCGCGGGGCA
*
52027 TGGCCGGGTCATGACCGGGCTG
1 TGGCCGGGCCATGACCGGGCTG
* *
52049 TGGCCTGGCCATGTCCGGGC
1 TGGCCGGGCCATGACCGGGC
52069 CATGTCTTGG
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
22 17 1.00
ACGTcount: A:0.07, C:0.31, G:0.43, T:0.19
Consensus pattern (22 bp):
TGGCCGGGCCATGACCGGGCTG
Found at i:62385 original size:49 final size:49
Alignment explanation
Indices: 62267--62390 Score: 151
Period size: 50 Copynumber: 2.5 Consensus size: 49
62257 GATTTTGTCA
* * * * **
62267 AAAAATTGATAAAAAAATGCAA-TAAAAAGTAAAAGATCAATTTTGTCTT
1 AAAAATTGA-GAAAAAGTGCAAGAAAAAAATAAAAGATCAATTTTGTAGT
*
62316 AAAAATTGAGAAAAAGGTGCAAGAAAAAAATAAAAGTTCAATTTTGTAGT
1 AAAAATTGAGAAAAA-GTGCAAGAAAAAAATAAAAGATCAATTTTGTAGT
*
62366 AAAAATTGAGAAAAAGTGCAGGAAA
1 AAAAATTGAGAAAAAGTGCAAGAAA
62391 TGTAATAGAT
Statistics
Matches: 65, Mismatches: 8, Indels: 4
0.84 0.10 0.05
Matches are distributed among these distances:
48 5 0.08
49 23 0.35
50 37 0.57
ACGTcount: A:0.56, C:0.05, G:0.16, T:0.23
Consensus pattern (49 bp):
AAAAATTGAGAAAAAGTGCAAGAAAAAAATAAAAGATCAATTTTGTAGT
Done.