Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01018026.1 Corchorus olitorius cultivar O-4 contig18059, 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: 67372
ACGTcount: A:0.32, C:0.19, G:0.18, T:0.31
Found at i:2597 original size:27 final size:28
Alignment explanation
Indices: 2560--2635 Score: 102
Period size: 27 Copynumber: 2.8 Consensus size: 28
2550 CTGTGACCCA
* *
2560 TTTTCATGATCTATTGTAAGA-GCATCT
1 TTTTCATGATCTATTGTAAGATGCACCG
*
2587 TTTTCATGATCTATTGTAA-ATGTACCG
1 TTTTCATGATCTATTGTAAGATGCACCG
*
2614 TTTTAATGATCTATTGTAAGAT
1 TTTTCATGATCTATTGTAAGAT
2636 TGCTTTAGGA
Statistics
Matches: 43, Mismatches: 4, Indels: 3
0.86 0.08 0.06
Matches are distributed among these distances:
26 1 0.02
27 40 0.93
28 2 0.05
ACGTcount: A:0.28, C:0.12, G:0.14, T:0.46
Consensus pattern (28 bp):
TTTTCATGATCTATTGTAAGATGCACCG
Found at i:16428 original size:31 final size:31
Alignment explanation
Indices: 16387--16556 Score: 205
Period size: 31 Copynumber: 5.5 Consensus size: 31
16377 TCCTTTTGTG
* * **
16387 CACGAGGCATGCCACGTGTCACTTTTTGAAA
1 CACGTGGCATGCCACATGTCACTTTTTGGTA
* *
16418 CACATGGCATGCCACATGTCATTTTTTGGTA
1 CACGTGGCATGCCACATGTCACTTTTTGGTA
* ** *
16449 CACATGGCATGATATATGTCACTTTTTGGTA
1 CACGTGGCATGCCACATGTCACTTTTTGGTA
* * *
16480 CACGTGGCGTGTCACATGTCGCTTTTTGGTA
1 CACGTGGCATGCCACATGTCACTTTTTGGTA
* *
16511 CACGTGGCGTGCCACATGTCGCTTTTTGGTA
1 CACGTGGCATGCCACATGTCACTTTTTGGTA
16542 CACGTGGCATGCCAC
1 CACGTGGCATGCCAC
16557 GTCGGACACC
Statistics
Matches: 121, Mismatches: 18, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
31 121 1.00
ACGTcount: A:0.20, C:0.24, G:0.24, T:0.32
Consensus pattern (31 bp):
CACGTGGCATGCCACATGTCACTTTTTGGTA
Found at i:21918 original size:19 final size:19
Alignment explanation
Indices: 21898--21934 Score: 58
Period size: 19 Copynumber: 2.0 Consensus size: 19
21888 AATTAATTAT
21898 TTTA-ATATTAAATTTTTA
1 TTTATATATTAAATTTTTA
*
21916 TTTATATATTATATTTTTA
1 TTTATATATTAAATTTTTA
21935 CTTAAAAATT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
18 4 0.24
19 13 0.76
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (19 bp):
TTTATATATTAAATTTTTA
Found at i:21945 original size:19 final size:19
Alignment explanation
Indices: 21904--21946 Score: 50
Period size: 19 Copynumber: 2.3 Consensus size: 19
21894 TTATTTTAAT
* * * *
21904 ATTAAATTTTTATTTATAT
1 ATTATATTTTTACTTAAAA
21923 ATTATATTTTTACTTAAAA
1 ATTATATTTTTACTTAAAA
21942 ATTAT
1 ATTAT
21947 TCCTAATTAA
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.40, C:0.02, G:0.00, T:0.58
Consensus pattern (19 bp):
ATTATATTTTTACTTAAAA
Found at i:23122 original size:28 final size:28
Alignment explanation
Indices: 23089--23170 Score: 119
Period size: 28 Copynumber: 2.9 Consensus size: 28
23079 GCTTAAAGAG
* *
23089 AACAAGTGCCAAACCACTTAAACCAACA
1 AACAAGTGTCAAACCACTTGAACCAACA
*
23117 AACAAGTGTCAAGCCACTTGAACCAACA
1 AACAAGTGTCAAACCACTTGAACCAACA
* *
23145 AACAAATGTCAAATCACTTGAACCAA
1 AACAAGTGTCAAACCACTTGAACCAA
23171 TCACTTGTAG
Statistics
Matches: 48, Mismatches: 6, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
28 48 1.00
ACGTcount: A:0.48, C:0.28, G:0.10, T:0.15
Consensus pattern (28 bp):
AACAAGTGTCAAACCACTTGAACCAACA
Found at i:23948 original size:178 final size:178
Alignment explanation
Indices: 23635--23967 Score: 521
Period size: 178 Copynumber: 1.9 Consensus size: 178
23625 TTTCCACCAT
* * *
23635 AAGCACAAATTATGTAATATTAAGTAGACCGTCTATTTCCGTTAACCGAAACAACTAATTCTTTG
1 AAGCACAAATTATATAATATTAAGTAGACCGTCTATTCCCGTTAACCGAAACAACAAATTCTTTG
* *
23700 GAAGCATTGTTTATACCTTGAACCATAAATTTAGTTTTCGAGTCCTTCATGAAAGTTGTAGATCA
66 GAAGCATTGTTTATACCTTGAAACATAAATTTAGTTTTCGAGTCCTTCATGAAAGTTATAGATCA
23765 TGGAACAAACTTTCAAGAGACACTTGAATCATCTCAATTAGAGAACTG
131 TGGAACAAACTTTCAAGAGACACTTGAATCATCTCAATTAGAGAACTG
*
23813 AAGCA-AAAGTTATATAATATTAAGTGGACCGTCTATTCCCGTTAACCGAAACAACAAATT-TTT
1 AAGCACAAA-TTATATAATATTAAGTAGACCGTCTATTCCCGTTAACCGAAACAACAAATTCTTT
23876 CGGAAGCATT-TTTGATA-CTTGAAACATTAAATTTAGTTTTCGAGTCCTTCATGAAAGTTATAG
65 -GGAAGCATTGTTT-ATACCTTGAAACA-TAAATTTAGTTTTCGAGTCCTTCATGAAAGTTATAG
* * *
23939 ATCATGGAACAATCTTTTAATAGACACTT
127 ATCATGGAACAAACTTTCAAGAGACACTT
23968 AAAGCACCTT
Statistics
Matches: 142, Mismatches: 9, Indels: 8
0.89 0.06 0.05
Matches are distributed among these distances:
177 17 0.12
178 125 0.88
ACGTcount: A:0.36, C:0.17, G:0.15, T:0.33
Consensus pattern (178 bp):
AAGCACAAATTATATAATATTAAGTAGACCGTCTATTCCCGTTAACCGAAACAACAAATTCTTTG
GAAGCATTGTTTATACCTTGAAACATAAATTTAGTTTTCGAGTCCTTCATGAAAGTTATAGATCA
TGGAACAAACTTTCAAGAGACACTTGAATCATCTCAATTAGAGAACTG
Found at i:24006 original size:178 final size:177
Alignment explanation
Indices: 23635--24023 Score: 507
Period size: 178 Copynumber: 2.2 Consensus size: 177
23625 TTTCCACCAT
* * *
23635 AAGCACAAATTATGTAATATTAAGTAGACCGTCTATTTCCGTTAACCGAAACAACTAATTCTTTG
1 AAGCA-AAATTATATAATATTAAGTAGACCGTCTATTCCCGTTAACCGAAACAACAAATTCTTTG
* *
23700 GAAGCATTGTTTATACCTTGAACCATAAATTTAGTTTTCGAGTCCTTCATGAAAGTTGTAGATCA
65 GAAGCATTGTTTATACCTTGAAACATAAATTTAGTTTTCGAGTCCTTCATGAAAGTTATAGATCA
* * * * *
23765 TGGAACAAACTTTCAAGAGACACTTGAATCATCTCAATTAGAGAACTG
130 TGGAACAAACTTTCAAGAGACACTTAAAGCACCTCAATCAGAGAACGG
*
23813 AAGCAAAAGTTATATAATATTAAGTGGACCGTCTATTCCCGTTAACCGAAACAACAAATT-TTTC
1 AAGCAAAA-TTATATAATATTAAGTAGACCGTCTATTCCCGTTAACCGAAACAACAAATTCTTT-
23877 GGAAGCATT-TTTGATA-CTTGAAACATTAAATTTAGTTTTCGAGTCCTTCATGAAAGTTATAGA
64 GGAAGCATTGTTT-ATACCTTGAAACA-TAAATTTAGTTTTCGAGTCCTTCATGAAAGTTATAGA
* * * * * *
23940 TCATGGAACAATCTTTTAATAGACACTTAAAGCACCTTAATCGGATAACCGG
127 TCATGGAACAAACTTTCAAGAGACACTTAAAGCACCTCAATCAGAGAA-CGG
* *
23992 AGAG-AAAATTATATAATGTTAAAATAGACCGT
1 A-AGCAAAATTATATAATATT-AAGTAGACCGT
24024 TTAGTCAAAT
Statistics
Matches: 184, Mismatches: 20, Indels: 13
0.85 0.09 0.06
Matches are distributed among these distances:
177 17 0.09
178 149 0.81
179 16 0.09
180 2 0.01
ACGTcount: A:0.37, C:0.16, G:0.15, T:0.32
Consensus pattern (177 bp):
AAGCAAAATTATATAATATTAAGTAGACCGTCTATTCCCGTTAACCGAAACAACAAATTCTTTGG
AAGCATTGTTTATACCTTGAAACATAAATTTAGTTTTCGAGTCCTTCATGAAAGTTATAGATCAT
GGAACAAACTTTCAAGAGACACTTAAAGCACCTCAATCAGAGAACGG
Found at i:24801 original size:2 final size:2
Alignment explanation
Indices: 24796--24826 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
24786 ATATATTTAA
24796 AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC A
1 AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC A
24827 TATATATATA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.52, C:0.48, G:0.00, T:0.00
Consensus pattern (2 bp):
AC
Found at i:27357 original size:40 final size:40
Alignment explanation
Indices: 27295--27414 Score: 152
Period size: 41 Copynumber: 3.0 Consensus size: 40
27285 ATCAGAACAG
*
27295 GTATGCAATATTCTTATTAACTACCAGCAAGCAAAACCAA
1 GTATGCAATATTCATATTAACTACCAGCAAGCAAAACCAA
* * * *
27335 GTATGCAATATTCATATAAACTACGAGCAAAGCAAAAACAC
1 GTATGCAATATTCATATTAACTACCAGC-AAGCAAAACCAA
* * *
27376 GTATACAACATTCCTATTAACTACCAGCAAGC-AAACCAA
1 GTATGCAATATTCATATTAACTACCAGCAAGCAAAACCAA
27415 TAACATTCTT
Statistics
Matches: 67, Mismatches: 12, Indels: 3
0.82 0.15 0.04
Matches are distributed among these distances:
39 5 0.07
40 29 0.43
41 33 0.49
ACGTcount: A:0.45, C:0.23, G:0.10, T:0.22
Consensus pattern (40 bp):
GTATGCAATATTCATATTAACTACCAGCAAGCAAAACCAA
Found at i:27398 original size:41 final size:40
Alignment explanation
Indices: 27290--27410 Score: 152
Period size: 40 Copynumber: 3.0 Consensus size: 40
27280 ATTCAATCAG
* *
27290 AACAGGTATGCAATATTCTTATTAACTACCAGCAAGCAAA
1 AACAAGTATGCAATATTCATATTAACTACCAGCAAGCAAA
* * *
27330 ACCAAGTATGCAATATTCATATAAACTACGAGCAAAGCAAA
1 AACAAGTATGCAATATTCATATTAACTACCAGC-AAGCAAA
* * * *
27371 AACACGTATACAACATTCCTATTAACTACCAGCAAGCAAA
1 AACAAGTATGCAATATTCATATTAACTACCAGCAAGCAAA
27411 CCAATAACAT
Statistics
Matches: 68, Mismatches: 12, Indels: 2
0.83 0.15 0.02
Matches are distributed among these distances:
40 35 0.51
41 33 0.49
ACGTcount: A:0.45, C:0.22, G:0.11, T:0.21
Consensus pattern (40 bp):
AACAAGTATGCAATATTCATATTAACTACCAGCAAGCAAA
Found at i:27702 original size:11 final size:11
Alignment explanation
Indices: 27688--27712 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
27678 CTCAAAATCC
27688 TTTTAAAACTA
1 TTTTAAAACTA
27699 TTTTAAAACTA
1 TTTTAAAACTA
27710 TTT
1 TTT
27713 ACATAAAAGA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.40, C:0.08, G:0.00, T:0.52
Consensus pattern (11 bp):
TTTTAAAACTA
Found at i:27751 original size:66 final size:66
Alignment explanation
Indices: 27645--27794 Score: 300
Period size: 66 Copynumber: 2.3 Consensus size: 66
27635 TAACCCGACC
27645 TTACATAAAAGAAGCAAACCCGAGAGTAGTATTCTCAAAATCCTTTTAAAACTATTTTAAAACTA
1 TTACATAAAAGAAGCAAACCCGAGAGTAGTATTCTCAAAATCCTTTTAAAACTATTTTAAAACTA
27710 T
66 T
27711 TTACATAAAAGAAGCAAACCCGAGAGTAGTATTCTCAAAATCCTTTTAAAACTATTTTAAAACTA
1 TTACATAAAAGAAGCAAACCCGAGAGTAGTATTCTCAAAATCCTTTTAAAACTATTTTAAAACTA
27776 T
66 T
27777 TTACATAAAAGAAGCAAA
1 TTACATAAAAGAAGCAAA
27795 GCCTATTTTA
Statistics
Matches: 84, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
66 84 1.00
ACGTcount: A:0.46, C:0.16, G:0.09, T:0.29
Consensus pattern (66 bp):
TTACATAAAAGAAGCAAACCCGAGAGTAGTATTCTCAAAATCCTTTTAAAACTATTTTAAAACTA
T
Found at i:27768 original size:11 final size:11
Alignment explanation
Indices: 27754--27778 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
27744 CTCAAAATCC
27754 TTTTAAAACTA
1 TTTTAAAACTA
27765 TTTTAAAACTA
1 TTTTAAAACTA
27776 TTT
1 TTT
27779 ACATAAAAGA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.40, C:0.08, G:0.00, T:0.52
Consensus pattern (11 bp):
TTTTAAAACTA
Found at i:32136 original size:17 final size:18
Alignment explanation
Indices: 32103--32139 Score: 58
Period size: 18 Copynumber: 2.1 Consensus size: 18
32093 CTTCGTGGTT
*
32103 TTTCTGTAAAAACTTATA
1 TTTCTCTAAAAACTTATA
32121 TTTCTCTAAAAA-TTATA
1 TTTCTCTAAAAACTTATA
32138 TT
1 TT
32140 ATATTTAGAC
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
17 7 0.39
18 11 0.61
ACGTcount: A:0.38, C:0.11, G:0.03, T:0.49
Consensus pattern (18 bp):
TTTCTCTAAAAACTTATA
Found at i:48399 original size:5 final size:5
Alignment explanation
Indices: 48389--48421 Score: 66
Period size: 5 Copynumber: 6.6 Consensus size: 5
48379 TTACTTTTTC
48389 TTGCT TTGCT TTGCT TTGCT TTGCT TTGCT TTG
1 TTGCT TTGCT TTGCT TTGCT TTGCT TTGCT TTG
48422 ATTGAATATT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 28 1.00
ACGTcount: A:0.00, C:0.18, G:0.21, T:0.61
Consensus pattern (5 bp):
TTGCT
Found at i:49091 original size:16 final size:16
Alignment explanation
Indices: 49072--49103 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
49062 GGGTAATTAC
*
49072 AAAAAAAAATTGTTTT
1 AAAAAAAAAGTGTTTT
49088 AAAAAAAAAGTGTTTT
1 AAAAAAAAAGTGTTTT
49104 CATGATAGAG
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.56, C:0.00, G:0.09, T:0.34
Consensus pattern (16 bp):
AAAAAAAAAGTGTTTT
Found at i:51311 original size:22 final size:23
Alignment explanation
Indices: 51261--51314 Score: 60
Period size: 22 Copynumber: 2.4 Consensus size: 23
51251 TGCTTTCTTA
*
51261 TTAATTGTTTTCTTTAATTCTCT
1 TTAATTGTTTTCTTTAATTATCT
*
51284 TT-ATTGTTTTC-TTAGTTAAT-T
1 TTAATTGTTTTCTTTAATT-ATCT
51305 TTAATTGTTT
1 TTAATTGTTT
51315 GTTTGATTTA
Statistics
Matches: 27, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
21 8 0.30
22 17 0.63
23 2 0.07
ACGTcount: A:0.19, C:0.07, G:0.07, T:0.67
Consensus pattern (23 bp):
TTAATTGTTTTCTTTAATTATCT
Found at i:55688 original size:41 final size:41
Alignment explanation
Indices: 55637--55742 Score: 160
Period size: 41 Copynumber: 2.6 Consensus size: 41
55627 AGAAAAATTA
* * *
55637 GGACCAAATTGAATCAAATAGTAACCAGAATCCTAAATCAG
1 GGACTAAATTGTATCAAATAGTAAACAGAATCCTAAATCAG
*
55678 GGACTAAATTGTATCAAATAGTAAATAGAATCCTAAATCAG
1 GGACTAAATTGTATCAAATAGTAAACAGAATCCTAAATCAG
*
55719 GGACTAAACTGTATCAAATA-TAAA
1 GGACTAAATTGTATCAAATAGTAAA
55743 ATTAGACTCC
Statistics
Matches: 60, Mismatches: 5, Indels: 1
0.91 0.08 0.02
Matches are distributed among these distances:
40 4 0.07
41 56 0.93
ACGTcount: A:0.47, C:0.15, G:0.14, T:0.24
Consensus pattern (41 bp):
GGACTAAATTGTATCAAATAGTAAACAGAATCCTAAATCAG
Found at i:55757 original size:41 final size:41
Alignment explanation
Indices: 55649--55761 Score: 158
Period size: 41 Copynumber: 2.8 Consensus size: 41
55639 ACCAAATTGA
** *
55649 ATCAAATAGTAACCAGAATCCTAAATCAGGGACTAAATTGT
1 ATCAAATAGTAAATAGAATCCTAAATCAGGGACTAAACTGT
55690 ATCAAATAGTAAATAGAATCCTAAATCAGGGACTAAACTGT
1 ATCAAATAGTAAATAGAATCCTAAATCAGGGACTAAACTGT
*
55731 ATCAAATA-TAAAATTAGACTCC-AAATCAGGG
1 ATCAAATAGT-AAA-TAGAATCCTAAATCAGGG
55762 GTAACATTGA
Statistics
Matches: 66, Mismatches: 4, Indels: 4
0.89 0.05 0.05
Matches are distributed among these distances:
40 1 0.02
41 58 0.88
42 7 0.11
ACGTcount: A:0.46, C:0.16, G:0.14, T:0.24
Consensus pattern (41 bp):
ATCAAATAGTAAATAGAATCCTAAATCAGGGACTAAACTGT
Found at i:59278 original size:44 final size:44
Alignment explanation
Indices: 59223--59309 Score: 156
Period size: 44 Copynumber: 2.0 Consensus size: 44
59213 TGGTATACGA
*
59223 GATTGAAATCAACTTTATCATTTCAGGATTATTTTGTGGTAGGG
1 GATTGAAATCAACTTGATCATTTCAGGATTATTTTGTGGTAGGG
*
59267 GATTGAAATCAACTTGATCATTTTAGGATTATTTTGTGGTAGG
1 GATTGAAATCAACTTGATCATTTCAGGATTATTTTGTGGTAGG
59310 AGTATTTTCT
Statistics
Matches: 41, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
44 41 1.00
ACGTcount: A:0.28, C:0.08, G:0.23, T:0.41
Consensus pattern (44 bp):
GATTGAAATCAACTTGATCATTTCAGGATTATTTTGTGGTAGGG
Found at i:59575 original size:22 final size:20
Alignment explanation
Indices: 59525--59575 Score: 57
Period size: 22 Copynumber: 2.4 Consensus size: 20
59515 CATGTTTACT
59525 TTGCGACAAACAAATCCAAA
1 TTGCGACAAACAAATCCAAA
* *
59545 TATGCGACAAATATATTCCTAAA
1 T-TGCGACAAACA-AATCC-AAA
59568 TTGCGACA
1 TTGCGACA
59576 GGCACTAACA
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
20 1 0.04
21 10 0.38
22 11 0.42
23 4 0.15
ACGTcount: A:0.43, C:0.22, G:0.12, T:0.24
Consensus pattern (20 bp):
TTGCGACAAACAAATCCAAA
Found at i:66067 original size:15 final size:15
Alignment explanation
Indices: 66037--66078 Score: 66
Period size: 15 Copynumber: 2.7 Consensus size: 15
66027 TTACTTTGTT
*
66037 TTGTTCTCTAGTTTAA
1 TTGTTTTCT-GTTTAA
66053 TTGTTTTCTGTTTAA
1 TTGTTTTCTGTTTAA
66068 TTGTTTTCTGT
1 TTGTTTTCTGT
66079 CAACCTCTGT
Statistics
Matches: 25, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
15 17 0.68
16 8 0.32
ACGTcount: A:0.12, C:0.10, G:0.14, T:0.64
Consensus pattern (15 bp):
TTGTTTTCTGTTTAA
Done.