Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01012497.1 Corchorus olitorius cultivar O-4 contig12530, 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: 90948
ACGTcount: A:0.33, C:0.19, G:0.17, T:0.31
Found at i:1180 original size:13 final size:13
Alignment explanation
Indices: 1158--1189 Score: 57
Period size: 13 Copynumber: 2.5 Consensus size: 13
1148 AAGACATTGA
1158 AATAGT-ATTAAT
1 AATAGTAATTAAT
1170 AATAGTAATTAAT
1 AATAGTAATTAAT
1183 AATAGTA
1 AATAGTA
1190 TTATTACTTT
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
12 6 0.32
13 13 0.68
ACGTcount: A:0.53, C:0.00, G:0.09, T:0.38
Consensus pattern (13 bp):
AATAGTAATTAAT
Found at i:2909 original size:36 final size:35
Alignment explanation
Indices: 2811--2914 Score: 84
Period size: 36 Copynumber: 2.8 Consensus size: 35
2801 AAAAAGGCTT
*
2811 ATATGGGGAGGCGTCACACCCCACCTATCCCAATTCA
1 ATATGGGGAGGCGTCACACCCC-CCT-TACCAATTCA
* * * *
2848 AT-TGGGTTGGGAGGCATGACGCCCCCCTTACCAATTTA
1 ATAT--G--GGGAGGCGTCACACCCCCCTTACCAATTCA
2886 GATATGGGGAGGCGTCACACCCCCACTTA
1 -ATATGGGGAGGCGTCACACCCCC-CTTA
2915 TCCCAACTTA
Statistics
Matches: 52, Mismatches: 8, Indels: 14
0.70 0.11 0.19
Matches are distributed among these distances:
36 16 0.31
37 6 0.12
38 10 0.19
39 5 0.10
40 15 0.29
ACGTcount: A:0.24, C:0.31, G:0.24, T:0.21
Consensus pattern (35 bp):
ATATGGGGAGGCGTCACACCCCCCTTACCAATTCA
Found at i:3598 original size:24 final size:25
Alignment explanation
Indices: 3554--3601 Score: 80
Period size: 24 Copynumber: 2.0 Consensus size: 25
3544 CATGAATACT
*
3554 CATCAAAGGGTATACCGTAAACACC
1 CATCAAAGGGTATACCATAAACACC
3579 CATCAAA-GGTATACCATAAACAC
1 CATCAAAGGGTATACCATAAACAC
3602 ACCAACCAAA
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
24 15 0.68
25 7 0.32
ACGTcount: A:0.44, C:0.27, G:0.12, T:0.17
Consensus pattern (25 bp):
CATCAAAGGGTATACCATAAACACC
Found at i:3611 original size:26 final size:25
Alignment explanation
Indices: 3557--3611 Score: 67
Period size: 24 Copynumber: 2.2 Consensus size: 25
3547 GAATACTCAT
* *
3557 CAAAGGGTATACCGTAAACACCCAT
1 CAAAGGGTATACCATAAACACCCAC
3582 CAAA-GGTATACCATAAACACACCAAC
1 CAAAGGGTATACCATAAACAC-CC-AC
3608 CAAA
1 CAAA
3612 TATTATACCC
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
24 15 0.58
25 6 0.23
26 5 0.19
ACGTcount: A:0.47, C:0.29, G:0.11, T:0.13
Consensus pattern (25 bp):
CAAAGGGTATACCATAAACACCCAC
Found at i:12005 original size:29 final size:30
Alignment explanation
Indices: 11959--12033 Score: 98
Period size: 29 Copynumber: 2.5 Consensus size: 30
11949 TACCGTACAT
*
11959 GTCCCTCTACTTACAAAAAAAATCAATTTG
1 GTCCCTCTACTTATAAAAAAAATCAATTTG
* ***
11989 GTCTCTCTAC-TATAAAAACTGTCAATTTG
1 GTCCCTCTACTTATAAAAAAAATCAATTTG
12018 GTCCCTCTACTTATAA
1 GTCCCTCTACTTATAA
12034 TTTGGTGTCG
Statistics
Matches: 38, Mismatches: 6, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
29 24 0.63
30 14 0.37
ACGTcount: A:0.33, C:0.24, G:0.08, T:0.35
Consensus pattern (30 bp):
GTCCCTCTACTTATAAAAAAAATCAATTTG
Found at i:12387 original size:30 final size:30
Alignment explanation
Indices: 12326--12402 Score: 86
Period size: 29 Copynumber: 2.6 Consensus size: 30
12316 TGACACCAAA
*
12326 TTGTAAGTAGAGAGACCAAATTGACAGTTT
1 TTGTAAGTAGAGAGACCAAATTGACACTTT
*
12356 TTGT-AGTAG-GAGGACCAAATTGATCCCTTT
1 TTGTAAGTAGAGA-GACCAAATTGA-CACTTT
* *
12386 TTATAAGTAGAGGGACC
1 TTGTAAGTAGAGAGACC
12403 TGTACAGTAT
Statistics
Matches: 39, Mismatches: 4, Indels: 7
0.78 0.08 0.14
Matches are distributed among these distances:
28 2 0.05
29 16 0.41
30 11 0.28
31 9 0.23
32 1 0.03
ACGTcount: A:0.32, C:0.13, G:0.25, T:0.30
Consensus pattern (30 bp):
TTGTAAGTAGAGAGACCAAATTGACACTTT
Found at i:13001 original size:1 final size:1
Alignment explanation
Indices: 12995--13022 Score: 56
Period size: 1 Copynumber: 28.0 Consensus size: 1
12985 AAGAGCTAGC
12995 TTTTTTTTTTTTTTTTTTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTT
13023 GGGCAAGAAC
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 27 1.00
ACGTcount: A:0.00, C:0.00, G:0.00, T:1.00
Consensus pattern (1 bp):
T
Found at i:17445 original size:13 final size:13
Alignment explanation
Indices: 17414--17458 Score: 56
Period size: 14 Copynumber: 3.5 Consensus size: 13
17404 ATTTTATTGC
*
17414 TGTTTTATTAAAT
1 TGTTTTAATAAAT
17427 TG-TTTAATAAAT
1 TGTTTTAATAAAT
*
17439 GGTTTTAAATAAAT
1 TGTTTT-AATAAAT
17453 TGTTTT
1 TGTTTT
17459 GGGTGCATTA
Statistics
Matches: 27, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
12 10 0.37
13 5 0.19
14 12 0.44
ACGTcount: A:0.33, C:0.00, G:0.11, T:0.56
Consensus pattern (13 bp):
TGTTTTAATAAAT
Found at i:22889 original size:24 final size:24
Alignment explanation
Indices: 22857--22914 Score: 116
Period size: 24 Copynumber: 2.4 Consensus size: 24
22847 CTATAAGGTA
22857 AAGGCCAAGGTATGGTATGCCATT
1 AAGGCCAAGGTATGGTATGCCATT
22881 AAGGCCAAGGTATGGTATGCCATT
1 AAGGCCAAGGTATGGTATGCCATT
22905 AAGGCCAAGG
1 AAGGCCAAGG
22915 AATTCTATTG
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 34 1.00
ACGTcount: A:0.31, C:0.17, G:0.31, T:0.21
Consensus pattern (24 bp):
AAGGCCAAGGTATGGTATGCCATT
Found at i:25035 original size:16 final size:16
Alignment explanation
Indices: 25004--25085 Score: 60
Period size: 16 Copynumber: 5.2 Consensus size: 16
24994 CCGTTTGTTA
* *
25004 CTTTCTAAGGAAAGTG
1 CTTTCCAAGGAGAGTG
*
25020 CTTTCCAAGTAGAGTG
1 CTTTCCAAGGAGAGTG
* *
25036 ATTTTC-AGGAGAGTG
1 CTTTCCAAGGAGAGTG
* * *
25051 CCTTCCATGGAGAAT-
1 CTTTCCAAGGAGAGTG
* *
25066 CATTCCAAGGAGAGTA
1 CTTTCCAAGGAGAGTG
25082 CTTT
1 CTTT
25086 ACATGAAAAG
Statistics
Matches: 49, Mismatches: 15, Indels: 4
0.72 0.22 0.06
Matches are distributed among these distances:
15 23 0.47
16 26 0.53
ACGTcount: A:0.28, C:0.17, G:0.24, T:0.30
Consensus pattern (16 bp):
CTTTCCAAGGAGAGTG
Found at i:28460 original size:19 final size:18
Alignment explanation
Indices: 28419--28454 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
28409 TTTCTCTTCA
28419 TCTA-TTTTTCTTATAGT
1 TCTAGTTTTTCTTATAGT
*
28436 TCTAGTTTTTCTTCTAGT
1 TCTAGTTTTTCTTATAGT
28454 T
1 T
28455 TTTAGTCTAG
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
17 4 0.24
18 13 0.76
ACGTcount: A:0.14, C:0.14, G:0.08, T:0.64
Consensus pattern (18 bp):
TCTAGTTTTTCTTATAGT
Found at i:33879 original size:41 final size:41
Alignment explanation
Indices: 33785--34029 Score: 189
Period size: 41 Copynumber: 6.0 Consensus size: 41
33775 GTTTTCAGCA
* * * *
33785 TGGTCCTTGATTTAGGATATTATTTGCTTTTTG-TGCGATT
1 TGGTCCCTGATTTAGGATATTATTTACTATTTGATGCAATT
* * *
33825 TGATCCCTGATTTAGGATCTTATTTACTATTTGATTCAATT
1 TGGTCCCTGATTTAGGATATTATTTACTATTTGATGCAATT
* * *
33866 TGGTCCCTGATTTAGGGTAATATTTA-TTTTCTGATGCAATT
1 TGGTCCCTGATTTAGGATATTATTTACTATT-TGATGCAATT
* * * *
33907 TTGTCCCTGATTTAGGATTTTACTTT--TGATTT-ATGC-GTCC
1 TGGTCCCTGATTTAGGATATTA-TTTACT-ATTTGATGCAAT-T
* * * * **
33947 TAGTCCCTGGTTTAAGAT-TTATTTCCTGATTAAATGCAATT
1 TGGTCCCTGATTTAGGATATTATTTACT-ATTTGATGCAATT
* * *
33988 TGGTCCCTGCTTTAGGATGTTGTTTACTATTTGATGCAATT
1 TGGTCCCTGATTTAGGATATTATTTACTATTTGATGCAATT
34029 T
1 T
34030 AATCCGTGAT
Statistics
Matches: 162, Mismatches: 33, Indels: 19
0.76 0.15 0.09
Matches are distributed among these distances:
38 3 0.02
39 4 0.02
40 55 0.34
41 87 0.54
42 13 0.08
ACGTcount: A:0.20, C:0.14, G:0.18, T:0.48
Consensus pattern (41 bp):
TGGTCCCTGATTTAGGATATTATTTACTATTTGATGCAATT
Found at i:36134 original size:17 final size:18
Alignment explanation
Indices: 36112--36147 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
36102 AAAGGGTAGT
*
36112 TAAAAA-AATTGTTTTCA
1 TAAAAAGAAGTGTTTTCA
36129 TAAAAAGAAGTGTTTTCA
1 TAAAAAGAAGTGTTTTCA
36147 T
1 T
36148 GCTAGAGGAG
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
17 6 0.35
18 11 0.65
ACGTcount: A:0.44, C:0.06, G:0.11, T:0.39
Consensus pattern (18 bp):
TAAAAAGAAGTGTTTTCA
Found at i:37893 original size:18 final size:17
Alignment explanation
Indices: 37866--37901 Score: 54
Period size: 18 Copynumber: 2.1 Consensus size: 17
37856 TTTCTCTTCA
37866 TCTATTTTTCATCTAGT
1 TCTATTTTTCATCTAGT
*
37883 TCTAGTTTTTCTTCTAGT
1 TCTA-TTTTTCATCTAGT
37901 T
1 T
37902 TTTAGGCTAG
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
17 4 0.24
18 13 0.76
ACGTcount: A:0.14, C:0.17, G:0.08, T:0.61
Consensus pattern (17 bp):
TCTATTTTTCATCTAGT
Found at i:48608 original size:21 final size:21
Alignment explanation
Indices: 48579--48635 Score: 62
Period size: 21 Copynumber: 2.7 Consensus size: 21
48569 GGCTTGGAAT
* *
48579 GGTGATGGCACGG-GCATGGCC
1 GGTGGTGGCACGGTG-ATGACC
* *
48600 GGTGGTGGCATGGTGGTGACC
1 GGTGGTGGCACGGTGATGACC
48621 GGTGGTGGCACGGTG
1 GGTGGTGGCACGGTG
48636 GAAACATGGA
Statistics
Matches: 30, Mismatches: 5, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
21 29 0.97
22 1 0.03
ACGTcount: A:0.11, C:0.18, G:0.53, T:0.19
Consensus pattern (21 bp):
GGTGGTGGCACGGTGATGACC
Found at i:48614 original size:11 final size:11
Alignment explanation
Indices: 48595--48636 Score: 52
Period size: 11 Copynumber: 4.0 Consensus size: 11
48585 GGCACGGGCA
48595 TGGC-CGGTGG
1 TGGCACGGTGG
*
48605 TGGCATGGTGG
1 TGGCACGGTGG
*
48616 TGAC-CGGTGG
1 TGGCACGGTGG
48626 TGGCACGGTGG
1 TGGCACGGTGG
48637 AAACATGGAC
Statistics
Matches: 26, Mismatches: 4, Indels: 3
0.79 0.12 0.09
Matches are distributed among these distances:
10 12 0.46
11 14 0.54
ACGTcount: A:0.07, C:0.17, G:0.55, T:0.21
Consensus pattern (11 bp):
TGGCACGGTGG
Found at i:48687 original size:21 final size:21
Alignment explanation
Indices: 48657--48698 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
48647 TGGAGCAAGC
* *
48657 ATGGCCGGTCTTGGCTCGGTG
1 ATGGCCGGTCGTGGCCCGGTG
*
48678 ATGGCTGGTCGTGGCCCGGTG
1 ATGGCCGGTCGTGGCCCGGTG
48699 GAATCACAAG
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.05, C:0.24, G:0.45, T:0.26
Consensus pattern (21 bp):
ATGGCCGGTCGTGGCCCGGTG
Found at i:56412 original size:65 final size:65
Alignment explanation
Indices: 56308--56439 Score: 237
Period size: 65 Copynumber: 2.0 Consensus size: 65
56298 CTGGTGAAGA
56308 AGAGAAATTGAGAGGAACGGCGCTGCCTTCAAAAGAAAATGACAGTGATAGGGTTAAAATTAAGG
1 AGAGAAATTGAGAGGAACGGCGCTGCCTTCAAAAGAAAATGACAGTGATAGGGTTAAAATTAAGG
* * *
56373 AGAGAAATTGAGAGGAATGGCGCTGCCTTCAAAAGAAAATGACGGTGCTAGGGTTAAAATTAAGG
1 AGAGAAATTGAGAGGAACGGCGCTGCCTTCAAAAGAAAATGACAGTGATAGGGTTAAAATTAAGG
56438 AG
1 AG
56440 TTTAGATTCA
Statistics
Matches: 64, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
65 64 1.00
ACGTcount: A:0.40, C:0.11, G:0.30, T:0.19
Consensus pattern (65 bp):
AGAGAAATTGAGAGGAACGGCGCTGCCTTCAAAAGAAAATGACAGTGATAGGGTTAAAATTAAGG
Found at i:64225 original size:24 final size:23
Alignment explanation
Indices: 64177--64225 Score: 64
Period size: 24 Copynumber: 2.1 Consensus size: 23
64167 TTTAGCTGTA
*
64177 TCCTCCTCCTTTTTCTAACAGAT
1 TCCTCCTCCTTTTTCTAACAAAT
64200 TCCTCC-CCTTTTTAGCTAACAAAT
1 TCCTCCTCCTTTTT--CTAACAAAT
64224 TC
1 TC
64226 TTGGTTGTCT
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
22 7 0.30
23 6 0.26
24 10 0.43
ACGTcount: A:0.20, C:0.35, G:0.04, T:0.41
Consensus pattern (23 bp):
TCCTCCTCCTTTTTCTAACAAAT
Found at i:65646 original size:18 final size:18
Alignment explanation
Indices: 65602--65647 Score: 56
Period size: 19 Copynumber: 2.5 Consensus size: 18
65592 GCTAAAGTGC
* *
65602 CTAAATGCAAGCCCAATG
1 CTAAGTGCAAGCCCAAAG
*
65620 CGCAAGTGCAAGCCCAAAG
1 C-TAAGTGCAAGCCCAAAG
65639 CTAAGTGCA
1 CTAAGTGCA
65648 TCTAATACAA
Statistics
Matches: 23, Mismatches: 4, Indels: 2
0.79 0.14 0.07
Matches are distributed among these distances:
18 8 0.35
19 15 0.65
ACGTcount: A:0.37, C:0.28, G:0.22, T:0.13
Consensus pattern (18 bp):
CTAAGTGCAAGCCCAAAG
Found at i:66059 original size:27 final size:27
Alignment explanation
Indices: 66000--66076 Score: 102
Period size: 27 Copynumber: 2.9 Consensus size: 27
65990 AATGAATAAA
* *
66000 AAATGACTAAAGTGCCCCT-GAAGTAC
1 AAATGACTAAAATGCCCCTGGATGTAC
* *
66026 AAATGACCAAAATGCCCCTGGATGTGC
1 AAATGACTAAAATGCCCCTGGATGTAC
*
66053 AAATGACTAAAATACCCCTGGATG
1 AAATGACTAAAATGCCCCTGGATG
66077 ACTTTAATGC
Statistics
Matches: 44, Mismatches: 6, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
26 17 0.39
27 27 0.61
ACGTcount: A:0.38, C:0.23, G:0.19, T:0.19
Consensus pattern (27 bp):
AAATGACTAAAATGCCCCTGGATGTAC
Found at i:67384 original size:25 final size:24
Alignment explanation
Indices: 67333--67384 Score: 70
Period size: 23 Copynumber: 2.2 Consensus size: 24
67323 TTCAAAAAGC
*
67333 AAAAAAAAATTTCTAAAAACGCAAA
1 AAAAAAAAAATTC-AAAAACGCAAA
*
67358 AAAAAAAAAATTC-AAAACGCAAG
1 AAAAAAAAAATTCAAAAACGCAAA
67381 AAAA
1 AAAA
67385 TAAGAATTTT
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
23 13 0.52
25 12 0.48
ACGTcount: A:0.71, C:0.12, G:0.06, T:0.12
Consensus pattern (24 bp):
AAAAAAAAAATTCAAAAACGCAAA
Found at i:67451 original size:18 final size:18
Alignment explanation
Indices: 67426--67469 Score: 70
Period size: 18 Copynumber: 2.4 Consensus size: 18
67416 ACCTAAGGAA
*
67426 TATTCCTTGAGATGAGTC
1 TATTCCTTCAGATGAGTC
*
67444 TTTTCCTTCAGATGAGTC
1 TATTCCTTCAGATGAGTC
67462 TATTCCTT
1 TATTCCTT
67470 ACTTCCCTGG
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 23 1.00
ACGTcount: A:0.18, C:0.20, G:0.16, T:0.45
Consensus pattern (18 bp):
TATTCCTTCAGATGAGTC
Found at i:69109 original size:19 final size:18
Alignment explanation
Indices: 69072--69111 Score: 53
Period size: 19 Copynumber: 2.2 Consensus size: 18
69062 CTCTTGAGAT
*
69072 AATTCTTCAATAGTCTTC
1 AATTCTTCAATACTCTTC
*
69090 AATTCTTCAAATTCTCTTC
1 AATTCTTC-AATACTCTTC
69109 AAT
1 AAT
69112 AAAACTTCAA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
18 8 0.42
19 11 0.58
ACGTcount: A:0.30, C:0.23, G:0.03, T:0.45
Consensus pattern (18 bp):
AATTCTTCAATACTCTTC
Found at i:73657 original size:10 final size:10
Alignment explanation
Indices: 73642--73666 Score: 50
Period size: 10 Copynumber: 2.5 Consensus size: 10
73632 ATATCAAAAC
73642 TTTTTTCTTT
1 TTTTTTCTTT
73652 TTTTTTCTTT
1 TTTTTTCTTT
73662 TTTTT
1 TTTTT
73667 AGAAGCAAGA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 15 1.00
ACGTcount: A:0.00, C:0.08, G:0.00, T:0.92
Consensus pattern (10 bp):
TTTTTTCTTT
Found at i:87255 original size:26 final size:23
Alignment explanation
Indices: 87225--87271 Score: 67
Period size: 26 Copynumber: 1.9 Consensus size: 23
87215 CTTGAAAATT
87225 TGAAAAACTTTGATGGATGAGATGGA
1 TGAAAAAC-TTGAT-GAT-AGATGGA
87251 TGAAAAACTTGATGATAGATG
1 TGAAAAACTTGATGATAGATG
87272 AATAGAAGGA
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
23 5 0.24
24 3 0.14
25 5 0.24
26 8 0.38
ACGTcount: A:0.40, C:0.04, G:0.28, T:0.28
Consensus pattern (23 bp):
TGAAAAACTTGATGATAGATGGA
Done.