Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01018601.1 Corchorus olitorius cultivar O-4 contig18634, 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: 72717
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.33
Found at i:5639 original size:19 final size:19
Alignment explanation
Indices: 5617--5674 Score: 64
Period size: 19 Copynumber: 3.1 Consensus size: 19
5607 TTATTGGCTT
*
5617 TTATAGATTTTATATCATA
1 TTATATATTTTATATCATA
*
5636 TTATATATTATATAT-ATA
1 TTATATATTTTATATCATA
* *
5654 TATATATATATCATATCATA
1 T-TATATATTTTATATCATA
5674 T
1 T
5675 CAAATAAAAG
Statistics
Matches: 32, Mismatches: 5, Indels: 3
0.80 0.12 0.08
Matches are distributed among these distances:
18 4 0.12
19 24 0.75
20 4 0.12
ACGTcount: A:0.41, C:0.05, G:0.02, T:0.52
Consensus pattern (19 bp):
TTATATATTTTATATCATA
Found at i:5649 original size:2 final size:2
Alignment explanation
Indices: 5627--5674 Score: 55
Period size: 2 Copynumber: 23.5 Consensus size: 2
5617 TTATAGATTT
5627 TA TA TCA TA T- TA TA TA T- TA TA TA TA TA TA TA TA TA TA TCA TA
1 TA TA T-A TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T-A TA
5669 TCA TA T
1 T-A TA T
5675 CAAATAAAAG
Statistics
Matches: 41, Mismatches: 0, Indels: 10
0.80 0.00 0.20
Matches are distributed among these distances:
1 2 0.05
2 33 0.80
3 6 0.15
ACGTcount: A:0.44, C:0.06, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:5980 original size:2 final size:2
Alignment explanation
Indices: 5968--5997 Score: 51
Period size: 2 Copynumber: 15.0 Consensus size: 2
5958 ATTGCTTGTC
*
5968 TA TA TA AA 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
5998 ACTTCTTCAA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (2 bp):
TA
Found at i:12853 original size:16 final size:16
Alignment explanation
Indices: 12832--12862 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
12822 TTCTTCTGCA
12832 GGGCAAAAGGGCAAAT
1 GGGCAAAAGGGCAAAT
*
12848 GGGCAAATGGGCAAA
1 GGGCAAAAGGGCAAA
12863 ATGGATTAGA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.42, C:0.13, G:0.39, T:0.06
Consensus pattern (16 bp):
GGGCAAAAGGGCAAAT
Found at i:20306 original size:108 final size:108
Alignment explanation
Indices: 20117--20336 Score: 386
Period size: 108 Copynumber: 2.0 Consensus size: 108
20107 GGAATGTGAG
* * *
20117 TTTAGTTTGTTATTTGCTTATTTGTGTATTTGGTAGGTAGATGGTTCATTTATGTTAGTTTTTTA
1 TTTAGTTTGTTATTTGCTTATTTGTGTATTCGGTAGGTAGATGGTTCATTTATGGTAGTTTCTTA
*
20182 GTTTGAGTTGATTTCTCCATTTAGATGTTTGTGCATATAGAGA
66 CTTTGAGTTGATTTCTCCATTTAGATGTTTGTGCATATAGAGA
*
20225 TTTAGTTTGTTATTTGTTTATTTGTGTATTCGGTAGGTAGATGGTTCATTTATGGTAGTTTCTTA
1 TTTAGTTTGTTATTTGCTTATTTGTGTATTCGGTAGGTAGATGGTTCATTTATGGTAGTTTCTTA
*
20290 CTTTTAGTTGATTTCTCCATTTAGATGTTTGTGCATATAGAGA
66 CTTTGAGTTGATTTCTCCATTTAGATGTTTGTGCATATAGAGA
20333 TTTA
1 TTTA
20337 TTCTGATTGT
Statistics
Matches: 106, Mismatches: 6, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
108 106 1.00
ACGTcount: A:0.20, C:0.06, G:0.21, T:0.53
Consensus pattern (108 bp):
TTTAGTTTGTTATTTGCTTATTTGTGTATTCGGTAGGTAGATGGTTCATTTATGGTAGTTTCTTA
CTTTGAGTTGATTTCTCCATTTAGATGTTTGTGCATATAGAGA
Found at i:20364 original size:49 final size:49
Alignment explanation
Indices: 20308--20407 Score: 173
Period size: 49 Copynumber: 2.0 Consensus size: 49
20298 TGATTTCTCC
*
20308 ATTTAGATGTTTGTGCATATAGAGATTTATTCTGATTGTTAATACCTAG
1 ATTTAGATGTTTGGGCATATAGAGATTTATTCTGATTGTTAATACCTAG
* *
20357 ATTTAGATGTTTGGGCATATAGAGATTTATTTTGATTGTTAATGCCTAG
1 ATTTAGATGTTTGGGCATATAGAGATTTATTCTGATTGTTAATACCTAG
20406 AT
1 AT
20408 AGGGATGCAT
Statistics
Matches: 48, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
49 48 1.00
ACGTcount: A:0.28, C:0.07, G:0.20, T:0.45
Consensus pattern (49 bp):
ATTTAGATGTTTGGGCATATAGAGATTTATTCTGATTGTTAATACCTAG
Found at i:20646 original size:183 final size:183
Alignment explanation
Indices: 20338--20704 Score: 716
Period size: 183 Copynumber: 2.0 Consensus size: 183
20328 AGAGATTTAT
20338 TCTGATTGTTAATACCTAGATTTAGATGTTTGGGCATATAGAGATTTATTTTGATTGTTAATGCC
1 TCTGATTGTTAATACCTAGATTTAGATGTTTGGGCATATAGAGATTTATTTTGATTGTTAATGCC
20403 TAGATAGGGATGCATGTGGGTAGTAAATGATAGGGTACTCGGCACTATATAATCGGGTTAGAATA
66 TAGATAGGGATGCATGTGGGTAGTAAATGATAGGGTACTCGGCACTATATAATCGGGTTAGAATA
*
20468 AGGTACAAGTAGTTAGGGTATTATATAATTGAGTTAGGATAAGGTACAAGTAG
131 AGGTACAAGTAGTTAGGGTATTATATAATTGAGTTAGGATAAGGTAAAAGTAG
20521 TCTGATTGTTAATACCTAGATTTAGATGTTTGGGCATATAGAGATTTATTTTGATTGTTAATGCC
1 TCTGATTGTTAATACCTAGATTTAGATGTTTGGGCATATAGAGATTTATTTTGATTGTTAATGCC
*
20586 TAGATAGGGATGCATGTGGGTAGTAAATGATAGGGTACTCGGCACTATATAATCGGGTTAGGATA
66 TAGATAGGGATGCATGTGGGTAGTAAATGATAGGGTACTCGGCACTATATAATCGGGTTAGAATA
20651 AGGTACAAGTAGTTAGGGTATTATATAATTGAGTTAGGATAAGGTAAAAGTAG
131 AGGTACAAGTAGTTAGGGTATTATATAATTGAGTTAGGATAAGGTAAAAGTAG
20704 T
1 T
20705 AGTTTTAGTA
Statistics
Matches: 182, Mismatches: 2, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
183 182 1.00
ACGTcount: A:0.32, C:0.07, G:0.26, T:0.35
Consensus pattern (183 bp):
TCTGATTGTTAATACCTAGATTTAGATGTTTGGGCATATAGAGATTTATTTTGATTGTTAATGCC
TAGATAGGGATGCATGTGGGTAGTAAATGATAGGGTACTCGGCACTATATAATCGGGTTAGAATA
AGGTACAAGTAGTTAGGGTATTATATAATTGAGTTAGGATAAGGTAAAAGTAG
Found at i:20667 original size:20 final size:20
Alignment explanation
Indices: 20642--20704 Score: 54
Period size: 20 Copynumber: 3.1 Consensus size: 20
20632 ATATAATCGG
*
20642 GTTAGGATAAGGTACAAGTA
1 GTTAGGATAAGGTAAAAGTA
* *** * *
20662 GTTAGGGTATTATATAATTGA
1 GTTAGGATAAGGTAAAAGT-A
20683 GTTAGGATAAGGTAAAAGTA
1 GTTAGGATAAGGTAAAAGTA
20703 GT
1 GT
20705 AGTTTTAGTA
Statistics
Matches: 30, Mismatches: 12, Indels: 2
0.68 0.27 0.05
Matches are distributed among these distances:
20 16 0.53
21 14 0.47
ACGTcount: A:0.38, C:0.02, G:0.29, T:0.32
Consensus pattern (20 bp):
GTTAGGATAAGGTAAAAGTA
Found at i:22378 original size:2 final size:2
Alignment explanation
Indices: 22371--22407 Score: 67
Period size: 2 Copynumber: 19.0 Consensus size: 2
22361 ACCGCCCTGC
22371 TA TA TA TA TA TA TA TA -A 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
22408 ATTAATCAGT
Statistics
Matches: 34, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 33 0.97
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
TA
Found at i:22936 original size:11 final size:11
Alignment explanation
Indices: 22893--22930 Score: 51
Period size: 11 Copynumber: 3.5 Consensus size: 11
22883 TTCCTATATA
*
22893 AAATAAATTATT
1 AAATTAATTA-T
22905 AAA-TAATTAT
1 AAATTAATTAT
22915 AAATTAATTAT
1 AAATTAATTAT
22926 AAATT
1 AAATT
22931 TGTTATGAAT
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
10 4 0.17
11 17 0.71
12 3 0.12
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (11 bp):
AAATTAATTAT
Found at i:24140 original size:28 final size:31
Alignment explanation
Indices: 24070--24142 Score: 89
Period size: 31 Copynumber: 2.5 Consensus size: 31
24060 GTTTAAATAC
* *
24070 CAAAAAAATCCCTTAGCCTTTTCATTTGGGA
1 CAAATAAATCCCTTAGCCTTTTCATTTAGGA
* *
24101 CAAATAAATCCCTTA-TCTTTT-TTTTAGGA
1 CAAATAAATCCCTTAGCCTTTTCATTTAGGA
24130 C-AATAAATCCCTT
1 CAAATAAATCCCTT
24143 TGCTTTCAAA
Statistics
Matches: 38, Mismatches: 4, Indels: 3
0.84 0.09 0.07
Matches are distributed among these distances:
28 12 0.32
29 7 0.18
30 5 0.13
31 14 0.37
ACGTcount: A:0.33, C:0.22, G:0.08, T:0.37
Consensus pattern (31 bp):
CAAATAAATCCCTTAGCCTTTTCATTTAGGA
Found at i:24148 original size:28 final size:30
Alignment explanation
Indices: 24070--24148 Score: 83
Period size: 28 Copynumber: 2.7 Consensus size: 30
24060 GTTTAAATAC
* * *
24070 CAAAAAAATCCCTTAGCCTTTTCATTTGGGA
1 CAAATAAATCCCTTTG-CTTTTCATTTAGGA
*
24101 CAAATAAATCCCTTAT-CTTTT-TTTTAGGA
1 CAAATAAATCCCTT-TGCTTTTCATTTAGGA
24130 C-AATAAATCCCTTTGCTTT
1 CAAATAAATCCCTTTGCTTT
24149 CAAAAGTGAG
Statistics
Matches: 42, Mismatches: 4, Indels: 7
0.79 0.08 0.13
Matches are distributed among these distances:
27 1 0.02
28 16 0.38
29 7 0.17
30 5 0.12
31 13 0.31
ACGTcount: A:0.30, C:0.22, G:0.09, T:0.39
Consensus pattern (30 bp):
CAAATAAATCCCTTTGCTTTTCATTTAGGA
Found at i:25149 original size:31 final size:28
Alignment explanation
Indices: 25082--25159 Score: 95
Period size: 31 Copynumber: 2.7 Consensus size: 28
25072 CTCACTTTTG
*
25082 AAAGCAAAGGGATTTA-TTGTCCCAAAA
1 AAAGCTAAGGGATTTATTTGTCCCAAAA
*
25109 AAAGATAAGGGATTTATTTGTCCCAAATGAA
1 AAAGCTAAGGGATTTATTTGTCCC-AA--AA
*
25140 AAAGCTAAGGGATTTTTTTG
1 AAAGCTAAGGGATTTATTTG
25160 GTATTTAAGC
Statistics
Matches: 43, Mismatches: 4, Indels: 4
0.84 0.08 0.08
Matches are distributed among these distances:
27 14 0.33
28 7 0.16
29 2 0.05
31 20 0.47
ACGTcount: A:0.40, C:0.10, G:0.21, T:0.29
Consensus pattern (28 bp):
AAAGCTAAGGGATTTATTTGTCCCAAAA
Found at i:38170 original size:2 final size:2
Alignment explanation
Indices: 38159--38236 Score: 95
Period size: 2 Copynumber: 39.5 Consensus size: 2
38149 TGGTTCTTGA
* * * *
38159 AT AT -T AT AT AT AT AT AT AT AT GT CT AT AT AT AG AC AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
* *
38200 AT AT AT AT AG AC AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
38237 GACACACACA
Statistics
Matches: 66, Mismatches: 9, Indels: 2
0.86 0.12 0.03
Matches are distributed among these distances:
1 1 0.02
2 65 0.98
ACGTcount: A:0.47, C:0.04, G:0.04, T:0.45
Consensus pattern (2 bp):
AT
Found at i:39025 original size:19 final size:19
Alignment explanation
Indices: 39001--39058 Score: 71
Period size: 19 Copynumber: 2.9 Consensus size: 19
38991 CTGTTTAACA
39001 ACTGTACAGATGAGATTAC
1 ACTGTACAGATGAGATTAC
* *
39020 ACTGTACAGATTAGATTAGAT
1 ACTGTACAGATGAGATT--AC
*
39041 ACTGTACATATGAGATTA
1 ACTGTACAGATGAGATTA
39059 TTAGAACAGC
Statistics
Matches: 33, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
19 17 0.52
21 16 0.48
ACGTcount: A:0.38, C:0.12, G:0.19, T:0.31
Consensus pattern (19 bp):
ACTGTACAGATGAGATTAC
Found at i:43115 original size:1 final size:1
Alignment explanation
Indices: 43109--43145 Score: 56
Period size: 1 Copynumber: 37.0 Consensus size: 1
43099 AGCTTTTGGA
* *
43109 TTTTTTTTTTTTTTTTTTTTCTGTTTTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
43146 CATTTGCTAG
Statistics
Matches: 32, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
1 32 1.00
ACGTcount: A:0.00, C:0.03, G:0.03, T:0.95
Consensus pattern (1 bp):
T
Found at i:43127 original size:22 final size:21
Alignment explanation
Indices: 43102--43145 Score: 52
Period size: 21 Copynumber: 2.1 Consensus size: 21
43092 ATTAATTAGC
* *
43102 TTTTGGATTTTTTTTTTTTTT
1 TTTTTGATGTTTTTTTTTTTT
**
43123 TTTTTTCTGTTTTTTTTTTTT
1 TTTTTGATGTTTTTTTTTTTT
43144 TT
1 TT
43146 CATTTGCTAG
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.02, C:0.02, G:0.07, T:0.89
Consensus pattern (21 bp):
TTTTTGATGTTTTTTTTTTTT
Found at i:49866 original size:16 final size:16
Alignment explanation
Indices: 49841--49873 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 16
49831 ATCCATTAAA
49841 ATCTCATAGTACCAGT
1 ATCTCATAGTACCAGT
*
49857 ATCTCGTAGTACCAGT
1 ATCTCATAGTACCAGT
49873 A
1 A
49874 AAGCCTTGTT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.30, C:0.24, G:0.15, T:0.30
Consensus pattern (16 bp):
ATCTCATAGTACCAGT
Found at i:54712 original size:22 final size:23
Alignment explanation
Indices: 54672--54714 Score: 70
Period size: 23 Copynumber: 1.9 Consensus size: 23
54662 TTTGTGGTAA
*
54672 TTTTTTTTTAGATGGGTAGTTTT
1 TTTTTTTTTAGATGAGTAGTTTT
54695 TTTTTTTTTA-ATGAGTAGTT
1 TTTTTTTTTAGATGAGTAGTT
54715 AGTGGATAAG
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
22 9 0.47
23 10 0.53
ACGTcount: A:0.16, C:0.00, G:0.19, T:0.65
Consensus pattern (23 bp):
TTTTTTTTTAGATGAGTAGTTTT
Found at i:55120 original size:36 final size:36
Alignment explanation
Indices: 55080--55148 Score: 138
Period size: 36 Copynumber: 1.9 Consensus size: 36
55070 TACTGTCTTC
55080 ATCTGGTTTTTTTTACGCTTCATCTTCTCCATCGAG
1 ATCTGGTTTTTTTTACGCTTCATCTTCTCCATCGAG
55116 ATCTGGTTTTTTTTACGCTTCATCTTCTCCATC
1 ATCTGGTTTTTTTTACGCTTCATCTTCTCCATC
55149 CCATCCCCAG
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
36 33 1.00
ACGTcount: A:0.13, C:0.26, G:0.12, T:0.49
Consensus pattern (36 bp):
ATCTGGTTTTTTTTACGCTTCATCTTCTCCATCGAG
Found at i:60650 original size:36 final size:36
Alignment explanation
Indices: 60603--60671 Score: 138
Period size: 36 Copynumber: 1.9 Consensus size: 36
60593 GCTGGGATGG
60603 GATGGAGAAGATGAAGCGTAAAAAAAACCAGATCTC
1 GATGGAGAAGATGAAGCGTAAAAAAAACCAGATCTC
60639 GATGGAGAAGATGAAGCGTAAAAAAAACCAGAT
1 GATGGAGAAGATGAAGCGTAAAAAAAACCAGAT
60672 GAAGATAGTA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
36 33 1.00
ACGTcount: A:0.49, C:0.12, G:0.26, T:0.13
Consensus pattern (36 bp):
GATGGAGAAGATGAAGCGTAAAAAAAACCAGATCTC
Found at i:61910 original size:15 final size:16
Alignment explanation
Indices: 61886--61919 Score: 52
Period size: 15 Copynumber: 2.2 Consensus size: 16
61876 GTATTTTAAA
61886 TCTATCTTCTC-TTCT
1 TCTATCTTCTCTTTCT
*
61901 TCTATTTTCTCTTTCT
1 TCTATCTTCTCTTTCT
61917 TCT
1 TCT
61920 TGGGGAGAAT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
15 10 0.59
16 7 0.41
ACGTcount: A:0.06, C:0.29, G:0.00, T:0.65
Consensus pattern (16 bp):
TCTATCTTCTCTTTCT
Found at i:62906 original size:5 final size:5
Alignment explanation
Indices: 62862--62893 Score: 57
Period size: 5 Copynumber: 6.6 Consensus size: 5
62852 TACTTTTCTC
62862 TTAGT TTA-T TTAGT TTAGT TTAGT TTAGT TTA
1 TTAGT TTAGT TTAGT TTAGT TTAGT TTAGT TTA
62894 TTATTTTTAT
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
4 4 0.15
5 22 0.85
ACGTcount: A:0.22, C:0.00, G:0.16, T:0.62
Consensus pattern (5 bp):
TTAGT
Found at i:69247 original size:16 final size:16
Alignment explanation
Indices: 69226--69272 Score: 62
Period size: 15 Copynumber: 3.1 Consensus size: 16
69216 CCCCCTTATC
69226 TCTCTCTCTTTTCTTT
1 TCTCTCTCTTTTCTTT
*
69242 TCTCTCTC-TTTCCTT
1 TCTCTCTCTTTTCTTT
*
69257 TCT-TCTATTTTCTTT
1 TCTCTCTCTTTTCTTT
69272 T
1 T
69273 TTTTCTCTCT
Statistics
Matches: 27, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
14 3 0.11
15 16 0.59
16 8 0.30
ACGTcount: A:0.02, C:0.30, G:0.00, T:0.68
Consensus pattern (16 bp):
TCTCTCTCTTTTCTTT
Found at i:69474 original size:14 final size:14
Alignment explanation
Indices: 69424--69466 Score: 50
Period size: 15 Copynumber: 2.9 Consensus size: 14
69414 CCCACGACTC
69424 TCTCTCTCTCTCTTT
1 TCTCTCT-TCTCTTT
* *
69439 TCTTTTCTTTTCTTT
1 TC-TCTCTTCTCTTT
69454 TCTCTCTTCTCTT
1 TCTCTCTTCTCTT
69467 CTTCCTCTCC
Statistics
Matches: 23, Mismatches: 4, Indels: 3
0.77 0.13 0.10
Matches are distributed among these distances:
14 9 0.39
15 10 0.43
16 4 0.17
ACGTcount: A:0.00, C:0.33, G:0.00, T:0.67
Consensus pattern (14 bp):
TCTCTCTTCTCTTT
Done.