Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01013563.1 Corchorus olitorius cultivar O-4 contig13596, 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: 30924
ACGTcount: A:0.31, C:0.18, G:0.18, T:0.33
Found at i:1030 original size:15 final size:15
Alignment explanation
Indices: 1000--1041 Score: 75
Period size: 15 Copynumber: 2.7 Consensus size: 15
990 TTACTTTGTT
1000 TTGTTTTCTAGTTTAA
1 TTGTTTTCT-GTTTAA
1016 TTGTTTTCTGTTTAA
1 TTGTTTTCTGTTTAA
1031 TTGTTTTCTGT
1 TTGTTTTCTGT
1042 CAACCTCTGT
Statistics
Matches: 26, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
15 17 0.65
16 9 0.35
ACGTcount: A:0.12, C:0.07, G:0.14, T:0.67
Consensus pattern (15 bp):
TTGTTTTCTGTTTAA
Found at i:4122 original size:25 final size:26
Alignment explanation
Indices: 4094--4142 Score: 66
Period size: 25 Copynumber: 1.9 Consensus size: 26
4084 AAGGTTGGGG
4094 AATTGATATCT-AAATA-AGAAATTGC
1 AATTG-TATCTAAAATAGAGAAATTGC
*
4119 AATTGTTTCTAAAATAGAGAAATT
1 AATTGTATCTAAAATAGAGAAATT
4143 TTTTAAGAAC
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
24 4 0.19
25 10 0.48
26 7 0.33
ACGTcount: A:0.47, C:0.06, G:0.12, T:0.35
Consensus pattern (26 bp):
AATTGTATCTAAAATAGAGAAATTGC
Found at i:6382 original size:25 final size:25
Alignment explanation
Indices: 6352--6417 Score: 105
Period size: 25 Copynumber: 2.6 Consensus size: 25
6342 TTGCTGCAGG
*
6352 AAGTGGCGCAGGGCCTGATAGAAGA
1 AAGTGGCGCAGGGCCTGAGAGAAGA
* *
6377 AAGTGGCGCAGGACCTGAGAGAGGA
1 AAGTGGCGCAGGGCCTGAGAGAAGA
6402 AAGTGGCGCAGGGCCT
1 AAGTGGCGCAGGGCCT
6418 AAAAGAAAAT
Statistics
Matches: 37, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
25 37 1.00
ACGTcount: A:0.29, C:0.18, G:0.42, T:0.11
Consensus pattern (25 bp):
AAGTGGCGCAGGGCCTGAGAGAAGA
Found at i:18585 original size:25 final size:25
Alignment explanation
Indices: 18555--18627 Score: 110
Period size: 25 Copynumber: 2.9 Consensus size: 25
18545 TTACTGCAGG
*
18555 AAGTGGCGCAGGGCCTGATAGAAGA
1 AAGTGGCGCAGGGCCTGAGAGAAGA
**
18580 AAGTGGCGCAGGGCCTGAGAGCGGA
1 AAGTGGCGCAGGGCCTGAGAGAAGA
*
18605 AAGTGGCGCAGGGCCTAAGAGAA
1 AAGTGGCGCAGGGCCTGAGAGAA
18628 AATAAGCACG
Statistics
Matches: 42, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
25 42 1.00
ACGTcount: A:0.30, C:0.18, G:0.42, T:0.10
Consensus pattern (25 bp):
AAGTGGCGCAGGGCCTGAGAGAAGA
Found at i:20341 original size:25 final size:25
Alignment explanation
Indices: 20307--20355 Score: 98
Period size: 25 Copynumber: 2.0 Consensus size: 25
20297 CCAAATAATC
20307 TTGAGCACTCTCGCTCGGTCTCTAT
1 TTGAGCACTCTCGCTCGGTCTCTAT
20332 TTGAGCACTCTCGCTCGGTCTCTA
1 TTGAGCACTCTCGCTCGGTCTCTA
20356 CAAACCAATC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 24 1.00
ACGTcount: A:0.12, C:0.33, G:0.20, T:0.35
Consensus pattern (25 bp):
TTGAGCACTCTCGCTCGGTCTCTAT
Found at i:20381 original size:21 final size:21
Alignment explanation
Indices: 20352--20393 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
20342 TCGCTCGGTC
*
20352 TCTACAAACCAATC-ATCACA
1 TCTACAAACCAAACAATCACA
20372 TCTACCAAACCAAACAATCACA
1 TCTA-CAAACCAAACAATCACA
20394 CACACACATC
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
20 4 0.21
21 9 0.47
22 6 0.32
ACGTcount: A:0.48, C:0.36, G:0.00, T:0.17
Consensus pattern (21 bp):
TCTACAAACCAAACAATCACA
Found at i:20884 original size:30 final size:31
Alignment explanation
Indices: 20850--20927 Score: 106
Period size: 30 Copynumber: 2.6 Consensus size: 31
20840 ACTTGTAGCG
*
20850 TTTGGACGTTTTGCCCCTCTGAACTTCAAT-
1 TTTGGACGTTTTACCCCTCTGAACTTCAATA
*
20880 TTTGGACATTTTACCCC-CTGAACTTCAATA
1 TTTGGACGTTTTACCCCTCTGAACTTCAATA
* *
20910 TTGGGACGATTTACCCCT
1 TTTGGACGTTTTACCCCT
20928 TAAGCCTAAC
Statistics
Matches: 41, Mismatches: 5, Indels: 3
0.84 0.10 0.06
Matches are distributed among these distances:
29 12 0.29
30 29 0.71
ACGTcount: A:0.21, C:0.27, G:0.15, T:0.37
Consensus pattern (31 bp):
TTTGGACGTTTTACCCCTCTGAACTTCAATA
Found at i:21403 original size:65 final size:65
Alignment explanation
Indices: 21238--21436 Score: 290
Period size: 66 Copynumber: 3.0 Consensus size: 65
21228 CACCAAAGCC
* *
21238 CCAACAATATTAAAGCAAAATTGTTACTAGTTTCATTCCATTCTAGCCATACCAGCCGAAACATG
1 CCAACAATATTAAAGCAAAATTGTTACTAGTTTCGTTCCGTTCTAGCCATACCAGCCGAAACATG
* *
21303 TCAACCAATATTAAAGCAAAATTGTTACTAGTTTCGTTCCGTTTTAGCCATACCAGCCGAAACAT
1 CCAA-CAATATTAAAGCAAAATTGTTACTAGTTTCGTTCCGTTCTAGCCATACCAGCCGAAACAT
21368 G
65 G
* ** * * * *
21369 CCAATAATATTAAATTAATATTGTTACTAGTTTCGTTCCGATCTAGCCATACCAGCCAAAACAAG
1 CCAACAATATTAAAGCAAAATTGTTACTAGTTTCGTTCCGTTCTAGCCATACCAGCCGAAACATG
21434 CCA
1 CCA
21437 TTTTGGCTTG
Statistics
Matches: 120, Mismatches: 13, Indels: 2
0.89 0.10 0.01
Matches are distributed among these distances:
65 59 0.49
66 61 0.51
ACGTcount: A:0.36, C:0.24, G:0.12, T:0.29
Consensus pattern (65 bp):
CCAACAATATTAAAGCAAAATTGTTACTAGTTTCGTTCCGTTCTAGCCATACCAGCCGAAACATG
Found at i:21796 original size:43 final size:44
Alignment explanation
Indices: 21682--21816 Score: 236
Period size: 43 Copynumber: 3.0 Consensus size: 44
21672 TCTAACTTTG
21682 CAATAAGTGCAGAGGCCTAACTTGATTATAAGGCACCTAGGGAT
1 CAATAAGTGCAGAGGCCTAACTTGATTATAAGGCACCTAGGGAT
21726 CAATAAGTGGTGCAGAGGCCTAACTTGATTAT-AGGCACCTAGGGAT
1 CAATAA---GTGCAGAGGCCTAACTTGATTATAAGGCACCTAGGGAT
21772 CAATAAGTGCAGAGGCCTAACTTGATTATAAGGCACCTAGGGAT
1 CAATAAGTGCAGAGGCCTAACTTGATTATAAGGCACCTAGGGAT
21816 C
1 C
21817 GGATAGTGGA
Statistics
Matches: 87, Mismatches: 0, Indels: 8
0.92 0.00 0.08
Matches are distributed among these distances:
43 23 0.26
44 21 0.24
46 20 0.23
47 23 0.26
ACGTcount: A:0.33, C:0.19, G:0.26, T:0.23
Consensus pattern (44 bp):
CAATAAGTGCAGAGGCCTAACTTGATTATAAGGCACCTAGGGAT
Found at i:22821 original size:65 final size:65
Alignment explanation
Indices: 22713--22845 Score: 187
Period size: 65 Copynumber: 2.0 Consensus size: 65
22703 CACCAAAGCC
**
22713 CCAACAATATTAAAACAAAATTGTTACCAGTCTCGTCCTGTTCTAGCCATATGAGCCGAAAAATG
1 CCAACAATATTAAAACAAAATTGTTACCAGTCTCGTCCTGTTCTAGCCATACCAGCCGAAAAATG
* * * * *
22778 CCAACAATATTAAAGCAAAATTGTTACTAGTTTCATTCC-GTTCTAGCCATACCAGCCGAAACAT
1 CCAACAATATTAAAACAAAATTGTTACCAGTCTC-GTCCTGTTCTAGCCATACCAGCCGAAAAAT
22842 G
65 G
22843 CCA
1 CCA
22846 TTTTGGCTTA
Statistics
Matches: 60, Mismatches: 7, Indels: 2
0.87 0.10 0.03
Matches are distributed among these distances:
65 57 0.95
66 3 0.05
ACGTcount: A:0.36, C:0.25, G:0.13, T:0.26
Consensus pattern (65 bp):
CCAACAATATTAAAACAAAATTGTTACCAGTCTCGTCCTGTTCTAGCCATACCAGCCGAAAAATG
Found at i:23139 original size:101 final size:101
Alignment explanation
Indices: 22964--23167 Score: 390
Period size: 101 Copynumber: 2.0 Consensus size: 101
22954 ATAGGCGGAG
*
22964 AGACCTAGCTTGAACATAAGGCATGCATCTAGTCATGTCATATAGGGATATATTACAACTCTAGG
1 AGACCTAGCTTGAACATAAGGCATGCATCTAGTCATGTCATATAGGGATATATTACAACTCTAGA
*
23029 GGCTTGAGTTATAATAACAGCACATGTTATTTGTGT
66 GGCTTGAGTTATAATAACAACACATGTTATTTGTGT
23065 AGACCTAGCTTGAACATAAGGCATGCATCTAGTCATGTCATATAGGGATATATTACAACTCTAGA
1 AGACCTAGCTTGAACATAAGGCATGCATCTAGTCATGTCATATAGGGATATATTACAACTCTAGA
23130 GGCTTGAGTTATAATAACAACACATGTTATTTGTGT
66 GGCTTGAGTTATAATAACAACACATGTTATTTGTGT
23166 AG
1 AG
23168 CAGATCCAGG
Statistics
Matches: 101, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
101 101 1.00
ACGTcount: A:0.33, C:0.16, G:0.20, T:0.31
Consensus pattern (101 bp):
AGACCTAGCTTGAACATAAGGCATGCATCTAGTCATGTCATATAGGGATATATTACAACTCTAGA
GGCTTGAGTTATAATAACAACACATGTTATTTGTGT
Found at i:23449 original size:16 final size:15
Alignment explanation
Indices: 23422--23451 Score: 51
Period size: 16 Copynumber: 1.9 Consensus size: 15
23412 GTAGGCACTA
23422 TATAATTAATAATAC
1 TATAATTAATAATAC
23437 TATAATATAATAATA
1 TATAAT-TAATAATA
23452 AAAAACATTT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 6 0.43
16 8 0.57
ACGTcount: A:0.57, C:0.03, G:0.00, T:0.40
Consensus pattern (15 bp):
TATAATTAATAATAC
Found at i:23724 original size:21 final size:24
Alignment explanation
Indices: 23665--23745 Score: 75
Period size: 22 Copynumber: 3.5 Consensus size: 24
23655 TTTAGTAATT
*
23665 AAATATATATTATTTATTTATTTTG
1 AAATATATATTA-TTATTTATTTAG
*
23690 AACTCAT-TA-T-TTA-TTATTTA-
1 AAAT-ATATATTATTATTTATTTAG
23710 AAATATAT-TTATTATTTATTTAG
1 AAATATATATTATTATTTATTTAG
*
23733 TAATATATATTAT
1 AAATATATATTAT
23746 ATCTAAGATA
Statistics
Matches: 45, Mismatches: 4, Indels: 15
0.70 0.06 0.23
Matches are distributed among these distances:
19 2 0.04
20 5 0.11
21 9 0.20
22 10 0.22
23 7 0.16
24 5 0.11
25 5 0.11
26 2 0.04
ACGTcount: A:0.38, C:0.02, G:0.02, T:0.57
Consensus pattern (24 bp):
AAATATATATTATTATTTATTTAG
Found at i:23740 original size:25 final size:25
Alignment explanation
Indices: 23695--23743 Score: 64
Period size: 25 Copynumber: 2.0 Consensus size: 25
23685 TTTTGAACTC
*
23695 ATTATTTATTATTTAAAATATATTT
1 ATTATTTATTATGTAAAATATATTT
*
23720 ATTATTTATT-TAGTAATATATATT
1 ATTATTTATTAT-GTAAAATATATT
23744 ATATCTAAGA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
24 1 0.05
25 20 0.95
ACGTcount: A:0.39, C:0.00, G:0.02, T:0.59
Consensus pattern (25 bp):
ATTATTTATTATGTAAAATATATTT
Found at i:26079 original size:41 final size:41
Alignment explanation
Indices: 26017--26106 Score: 171
Period size: 41 Copynumber: 2.2 Consensus size: 41
26007 TTGTGTGATG
*
26017 ATTTTTGTTTTTATTCCTTGTCCATAATACAGATACAAGCC
1 ATTTATGTTTTTATTCCTTGTCCATAATACAGATACAAGCC
26058 ATTTATGTTTTTATTCCTTGTCCATAATACAGATACAAGCC
1 ATTTATGTTTTTATTCCTTGTCCATAATACAGATACAAGCC
26099 ATTTATGT
1 ATTTATGT
26107 CTGGTCTATT
Statistics
Matches: 48, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
41 48 1.00
ACGTcount: A:0.28, C:0.18, G:0.10, T:0.44
Consensus pattern (41 bp):
ATTTATGTTTTTATTCCTTGTCCATAATACAGATACAAGCC
Found at i:27854 original size:16 final size:16
Alignment explanation
Indices: 27835--27971 Score: 113
Period size: 16 Copynumber: 8.6 Consensus size: 16
27825 GAACCCGTCC
27835 GACCCGAGACCCGAAT
1 GACCCGAGACCCGAAT
27851 GACCCGCAG-CCC-AGAT
1 GACCCG-AGACCCGA-AT
27867 GACCCGAGACCCGAAT
1 GACCCGAGACCCGAAT
*
27883 GACCAGTA-ACCC-AGAT
1 GACCCG-AGACCCGA-AT
*
27899 GACCCGAAACCCGAAT
1 GACCCGAGACCCGAAT
*
27915 GACCCGTA-ACCCGAGT
1 GACCCG-AGACCCGAAT
* *
27931 GACCTGAGACCCGTAT
1 GACCCGAGACCCGAAT
* * *
27947 GACTCGAAAGCCGAAT
1 GACCCGAGACCCGAAT
*
27963 GACTCGAGA
1 GACCCGAGA
27972 ATATTATAAA
Statistics
Matches: 99, Mismatches: 12, Indels: 20
0.76 0.09 0.15
Matches are distributed among these distances:
15 6 0.06
16 87 0.88
17 6 0.06
ACGTcount: A:0.31, C:0.34, G:0.24, T:0.10
Consensus pattern (16 bp):
GACCCGAGACCCGAAT
Found at i:27871 original size:32 final size:32
Alignment explanation
Indices: 27835--27949 Score: 160
Period size: 32 Copynumber: 3.6 Consensus size: 32
27825 GAACCCGTCC
* *
27835 GACCCGAGACCCGAATGACCCGCAGCCCAGAT
1 GACCCGAGACCCGAATGACCCGTAACCCAGAT
*
27867 GACCCGAGACCCGAATGACCAGTAACCCAGAT
1 GACCCGAGACCCGAATGACCCGTAACCCAGAT
*
27899 GACCCGAAACCCGAATGACCCGTAACCC-GAGT
1 GACCCGAGACCCGAATGACCCGTAACCCAGA-T
* *
27931 GACCTGAGACCCGTATGAC
1 GACCCGAGACCCGAATGAC
27950 TCGAAAGCCG
Statistics
Matches: 74, Mismatches: 8, Indels: 2
0.88 0.10 0.02
Matches are distributed among these distances:
31 2 0.03
32 72 0.97
ACGTcount: A:0.30, C:0.37, G:0.23, T:0.10
Consensus pattern (32 bp):
GACCCGAGACCCGAATGACCCGTAACCCAGAT
Found at i:27917 original size:48 final size:48
Alignment explanation
Indices: 27835--27971 Score: 129
Period size: 48 Copynumber: 2.9 Consensus size: 48
27825 GAACCCGTCC
* * * *
27835 GACCCGAGACCCGAATGACCCGCAGCCC-AGATGACCCGAGACCCGAAT
1 GACCAGAGACCCGTATGACCCGAAACCCGA-ATGACCCGAGACCCGAAT
*
27883 GACCAGTA-ACCCAG-ATGACCCGAAACCCGAATGACCCGTA-ACCCGAGT
1 GACCAG-AGACCC-GTATGACCCGAAACCCGAATGACCCG-AGACCCGAAT
* * * *
27931 GACCTGAGACCCGTATGACTCGAAAGCCGAATGACTCGAGA
1 GACCAGAGACCCGTATGACCCGAAACCCGAATGACCCGAGA
27972 ATATTATAAA
Statistics
Matches: 74, Mismatches: 8, Indels: 14
0.77 0.08 0.15
Matches are distributed among these distances:
47 3 0.04
48 67 0.91
49 4 0.05
ACGTcount: A:0.31, C:0.34, G:0.24, T:0.10
Consensus pattern (48 bp):
GACCAGAGACCCGTATGACCCGAAACCCGAATGACCCGAGACCCGAAT
Found at i:28501 original size:42 final size:42
Alignment explanation
Indices: 28454--28535 Score: 146
Period size: 42 Copynumber: 2.0 Consensus size: 42
28444 TGTTGACACA
*
28454 TACCCCACTTAATAATTAATTATGTATTTAATATTCAAAACT
1 TACCCCACCTAATAATTAATTATGTATTTAATATTCAAAACT
*
28496 TACCCCACCTGATAATTAATTATGTATTTAATATTCAAAA
1 TACCCCACCTAATAATTAATTATGTATTTAATATTCAAAA
28536 TTAATATCAA
Statistics
Matches: 38, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
42 38 1.00
ACGTcount: A:0.40, C:0.17, G:0.04, T:0.39
Consensus pattern (42 bp):
TACCCCACCTAATAATTAATTATGTATTTAATATTCAAAACT
Found at i:28754 original size:16 final size:15
Alignment explanation
Indices: 28735--28816 Score: 76
Period size: 16 Copynumber: 5.2 Consensus size: 15
28725 AACCTGCCCA
*
28735 ACCCGAGACCTGAATG
1 ACCCGAAACC-GAATG
*
28751 ACCCGAAACCCATATG
1 ACCCGAAACCGA-ATG
*
28767 ACCCGAAACCTGAATA
1 ACCCGAAACC-GAATG
*
28783 ACCC-AAACCCAGATG
1 ACCCGAAACCGA-ATG
28798 ACCCGAAACCCGAATG
1 ACCCGAAA-CCGAATG
28814 ACC
1 ACC
28817 TGAGAAAACT
Statistics
Matches: 54, Mismatches: 7, Indels: 10
0.76 0.10 0.14
Matches are distributed among these distances:
14 1 0.02
15 12 0.22
16 37 0.69
17 4 0.07
ACGTcount: A:0.38, C:0.37, G:0.16, T:0.10
Consensus pattern (15 bp):
ACCCGAAACCGAATG
Found at i:28799 original size:31 final size:32
Alignment explanation
Indices: 28735--28812 Score: 113
Period size: 31 Copynumber: 2.5 Consensus size: 32
28725 AACCTGCCCA
* * *
28735 ACCCGAGACCTGAATGACCCGAAACCCATATG
1 ACCCGAAACCTGAATAACCCGAAACCCAGATG
28767 ACCCGAAACCTGAATAACCC-AAACCCAGATG
1 ACCCGAAACCTGAATAACCCGAAACCCAGATG
*
28798 ACCCGAAACCCGAAT
1 ACCCGAAACCTGAAT
28813 GACCTGAGAA
Statistics
Matches: 42, Mismatches: 4, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
31 24 0.57
32 18 0.43
ACGTcount: A:0.38, C:0.36, G:0.15, T:0.10
Consensus pattern (32 bp):
ACCCGAAACCTGAATAACCCGAAACCCAGATG
Found at i:30008 original size:124 final size:123
Alignment explanation
Indices: 29766--30013 Score: 268
Period size: 124 Copynumber: 2.0 Consensus size: 123
29756 AATCTTTCAA
* **
29766 ATTAAAATGGTAAAAATAAAATAATTACAAAATATTGAATTTAATTAAATGAAAATAGATTTTTT
1 ATTAAAATGGTAAAAATAAAATAATTACAAAATATTGAATTTAATTAAATAAAAATAGAGCTTTT
* ** * * * *
29831 AGTAGAATAAAACTGTATATTAAAAAATTTTAATTTATCCAATTTTTTATTGAAAAAT
66 AGTAGAATAAAACTATATATTAAAAAATTGGAATTTATACAAATATATATTGAAAAAT
* * * * *
29889 ATTAAAATGGTAAAAATAAAGTAATTATAACGATATTGTATTTAATTGAATAAAAATAGAGCTTT
1 ATTAAAATGGTAAAAATAAAATAATTACAA-AATATTGAATTTAATTAAATAAAAATAGAGCTTT
** * *
29954 TAGTAGAATAAAACTATAATAGTTTAAGCAA-TGGCATTTA-AGAAATATAT-TTGAAAAAT
65 TAGTAGAATAAAACTAT-ATA--TTAAAAAATTGGAATTTATACAAATATATATTGAAAAAT
30013 A
1 A
30014 AGGGTATAAT
Statistics
Matches: 102, Mismatches: 19, Indels: 7
0.80 0.15 0.05
Matches are distributed among these distances:
123 28 0.27
124 54 0.53
125 8 0.08
126 6 0.06
127 6 0.06
ACGTcount: A:0.50, C:0.04, G:0.10, T:0.36
Consensus pattern (123 bp):
ATTAAAATGGTAAAAATAAAATAATTACAAAATATTGAATTTAATTAAATAAAAATAGAGCTTTT
AGTAGAATAAAACTATATATTAAAAAATTGGAATTTATACAAATATATATTGAAAAAT
Done.