Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01024571.1 Corchorus olitorius cultivar O-4 contig24604, 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: 16842
ACGTcount: A:0.32, C:0.15, G:0.20, T:0.34
Found at i:769 original size:332 final size:331
Alignment explanation
Indices: 74--1328 Score: 1238
Period size: 325 Copynumber: 3.8 Consensus size: 331
64 ATTATTTCGA
* * * * * ** *
74 TTTTTGGCTAAAAACGCGTTTCGGGACCCCG-GCTTAGTTTTGCATGATTTTTGGCAACGAGACT
1 TTTTTGGCTAAAAACGCGTTCCGGGGCCCTGAG-TCAGTTTTGCAAGATTTTTGGTGACAAGACT
** * * * * * *
138 CCATAAAATATCTATATTCATCTAATCAAATTTCTA-CCACATTGAATTCAAGTATTTGTATTTA
65 CTTTGAAATATCTATATTCATCTAACCAAATCTC-AGCCACATTGAATTTAAGGATTTGTTTTTA
* * * * * *
202 CGAGCATCTGAATCTTGTTTCGAATAAATTAGAAATTAATTCT---AGAAGAATATGAAAAACGA
129 CGAGCATCTGAATCTTGTTTCGATTTAATTAGAAATTAATTCTGAAAAAAAAAAAGGAAAAACGA
* * * **
264 TATTAAAAGCGTGAAAAGTCC-TCCAA--TATTTGGTGTTGAATTATATA--TTTTATGAGTATT
194 TATTAGAAGCGTGAAAAG-CCTTTCAATTTTTTTGACGTTGAATTATATATTTTTTATGAGTATT
* * *
324 GTGGCTAAAAATTGAAGAAAAATATTTCAGATCAATTTTTGCAAAATTTTCGCCGAAATCGTCTA
258 GTGGCTAAAAATTG-AGAAAAATATTTCAGGTCAATTTTTGCAAAATTTTAGCCGAAATCGTGTA
*
389 CCATCACGGC
322 CCATCACGGT
* * * * *
399 TTTTTGGCTAAAAACACGTTCCGGGGCCCCGAGTCAGTTTTGCAAGATTTTTGGTGGCAAAACTA
1 TTTTTGGCTAAAAACGCGTTCCGGGGCCCTGAGTCAGTTTTGCAAGATTTTTGGTGACAAGACTC
* * *
464 TTTGAAATATCTATATTCATCTAAACAAATCTTAGCCACATTGGATTTAAGGATTTGTTTTTACG
66 TTTGAAATATCTATATTCATCTAACCAAATCTCAGCCACATTGAATTTAAGGATTTGTTTTTACG
* * *
529 AGCATTTGAATCATGTTTCGATTTAATTACAAATTAATT-TGAAAACAAAAAAAAGGAAAAACGA
131 AGCATCTGAATCTTGTTTCGATTTAATTAGAAATTAATTCTG-AAA-AAAAAAAAGGAAAAACGA
* * * *
593 TCTTAGAAGCGTGAGAAGCCTTTCAATCTTTTTGACGTTGAATTATAAATTTTTTATGAGTATTG
194 TATTAGAAGCGTGAAAAGCCTTTCAATTTTTTTGACGTTGAATTATATATTTTTTATGAGTATTG
* * * **
658 TGGCTAAAAACTGAGAAAAATA-TTCTTGGTAAATTTTTGCAAAATTTTAGATGAAATCGTGTAC
259 TGGCTAAAAATTGAGAAAAATATTTC-AGGTCAATTTTTGCAAAATTTTAGCCGAAATCGTGTAC
*
722 CATCATGGT
323 CATCACGGT
* * * *
731 TTTTTGGCTAAAAACGCGTTCTGGGGCCCTGGGTCAGTTTTG-AATCATTTTTGG-CACAAGACT
1 TTTTTGGCTAAAAACGCGTTCCGGGGCCCTGAGTCAGTTTTGCAA-GATTTTTGGTGACAAGACT
** * * *
794 CCTTAAAATATATCTATATTCATCTAACCAAATCTCAGCCAAATTGTATTTAGGGATTTGTTTTT
65 -CTTTGAA-ATATCTATATTCATCTAACCAAATCTCAGCCACATTGAATTTAAGGATTTGTTTTT
** * * * * * *
859 ACGAGTTTCTAAATCTTGTTTCGATTTAATCATAAATTAATT-TGGAAATAAAATAGG-AAAACG
128 ACGAGCATCTGAATCTTGTTTCGATTTAATTAGAAATTAATTCTGAAAAAAAAAAAGGAAAAACG
* * * *
922 AT-TACAGAAGCGTGAAAAGGGCTTTCAGTTTTTTTGGCGTTGAATTATATATTTTTTATGAGTA
193 ATAT-TAGAAGCGTGAAAA-GCCTTTCAATTTTTTTGACGTTGAATTATATATTTTTTATGAGTA
* * * * * *
986 CTT-TTGTTAGAAATTGAGGAAAAATCTTTCGGGTCAATTTTTGCAAAATTTTAGCCGAAATTGT
256 -TTGTGGCTAAAAATTGA-GAAAAATATTTCAGGTCAATTTTTGCAAAATTTTAGCCGAAATCGT
1050 GTATTAACCATCACGGTTT
319 G---T-ACCATCACGG--T
* * * ** *
1069 TCACTTTTCGGCTAAAAACGCGTTCCAGGG-CCTGACTCAGTTTTGCATGATTTTTTTTGCCAAG
1 T---TTTT-GGCTAAAAACGCGTTCCGGGGCCCTGAGTCAGTTTTGCAAGATTTTTGGTGACAAG
* * *
1133 ACGCCTTGAAATATCTATATTCATCTAACCAAATCTCAGCCACATTAAATTTAAGGATTTGTTTT
62 ACTCTTTGAAATATCTATATTCATCTAACCAAATCTCAGCCACATTGAATTTAAGGATTTGTTTT
* * *
1198 TACGAGCATCTGAATCTTCTTTCGATTTAATTAGAAATTAATTCGGAAAAAATTAGAAA--AAAA
127 TACGAGCATCTGAATCTTGTTTCGATTTAATTAGAAATTAATTCTGAAAAAA--AAAAAGGAAAA
* * * * * ** *
1261 ACAATATTAGAAGCGTTAAAATCTTTTCAGTTTTTTTGATATCGAATTATATATTTTTTATGAGT
190 ACGATATTAGAAGCGTGAAAAGCCTTTCAATTTTTTTGACGTTGAATTATATATTTTTTATGAGT
1326 ATT
255 ATT
1329 TTAGCCAAAG
Statistics
Matches: 761, Mismatches: 131, Indels: 61
0.80 0.14 0.06
Matches are distributed among these distances:
324 2 0.00
325 139 0.18
326 1 0.00
328 3 0.00
329 34 0.04
330 20 0.03
331 86 0.11
332 138 0.18
333 117 0.15
335 1 0.00
336 9 0.01
338 2 0.00
340 90 0.12
341 70 0.09
342 45 0.06
343 4 0.01
ACGTcount: A:0.33, C:0.14, G:0.16, T:0.37
Consensus pattern (331 bp):
TTTTTGGCTAAAAACGCGTTCCGGGGCCCTGAGTCAGTTTTGCAAGATTTTTGGTGACAAGACTC
TTTGAAATATCTATATTCATCTAACCAAATCTCAGCCACATTGAATTTAAGGATTTGTTTTTACG
AGCATCTGAATCTTGTTTCGATTTAATTAGAAATTAATTCTGAAAAAAAAAAAGGAAAAACGATA
TTAGAAGCGTGAAAAGCCTTTCAATTTTTTTGACGTTGAATTATATATTTTTTATGAGTATTGTG
GCTAAAAATTGAGAAAAATATTTCAGGTCAATTTTTGCAAAATTTTAGCCGAAATCGTGTACCAT
CACGGT
Found at i:2447 original size:95 final size:92
Alignment explanation
Indices: 2327--2514 Score: 295
Period size: 95 Copynumber: 2.0 Consensus size: 92
2317 CTTTTACTCA
*
2327 AGCCCCAAAACCCAAACCACCCAAAAAAATTGCTCGAAATCCTAGTAATTTAATATTTATAAAGG
1 AGCCCCAAAACCCAAACCACCCAAAAAAATTGCTCAAAATCCTAGTAATTTAATATTTATAAAGG
2392 GAGTTAATAGTATTTAATTTTTAAATAAAT
66 GAGTT-A-A-TATTTAATTTTTAAATAAAT
* * *
2422 AGCCCCAAAACCCAAACCACCCAAAAAATTTGCTTAAAATCCTAGTAATTTAATATTTATGAAGG
1 AGCCCCAAAACCCAAACCACCCAAAAAAATTGCTCAAAATCCTAGTAATTTAATATTTATAAAGG
* *
2487 TAGTTAATATTTAATTTTTGAATAAAT
66 GAGTTAATATTTAATTTTTAAATAAAT
2514 A
1 A
2515 AATACTCCCT
Statistics
Matches: 87, Mismatches: 6, Indels: 3
0.91 0.06 0.03
Matches are distributed among these distances:
92 20 0.23
93 1 0.01
94 1 0.01
95 65 0.75
ACGTcount: A:0.44, C:0.16, G:0.09, T:0.31
Consensus pattern (92 bp):
AGCCCCAAAACCCAAACCACCCAAAAAAATTGCTCAAAATCCTAGTAATTTAATATTTATAAAGG
GAGTTAATATTTAATTTTTAAATAAAT
Found at i:6920 original size:44 final size:45
Alignment explanation
Indices: 6871--7011 Score: 153
Period size: 46 Copynumber: 3.1 Consensus size: 45
6861 GGTATGAAGG
* **
6871 AATTGGTACCAATTGTGTAA-AAAGTTTATACCAT-GGGAAGGAGA
1 AATTGGTACCAATGGTGTAAGAAA-ACTATACCATCGGGAAGGAGA
* *
6915 AATTGGTACCGATGGTGTAAGGAAAACTATACCATCGGGATGGAGA
1 AATTGGTACCAATGGTGTAA-GAAAACTATACCATCGGGAAGGAGA
* * *
6961 AATTGATACCGATGGTGTGAAGAAAACTATACCATC-GGAATTGAGA
1 AATTGGTACCAATGGTGT-AAGAAAACTATACCATCGGGAA-GGAGA
7007 AATTG
1 AATTG
7012 CAACTGATGG
Statistics
Matches: 84, Mismatches: 8, Indels: 8
0.84 0.08 0.08
Matches are distributed among these distances:
44 18 0.21
45 11 0.13
46 53 0.63
47 2 0.02
ACGTcount: A:0.38, C:0.11, G:0.26, T:0.25
Consensus pattern (45 bp):
AATTGGTACCAATGGTGTAAGAAAACTATACCATCGGGAAGGAGA
Found at i:6924 original size:22 final size:23
Alignment explanation
Indices: 6898--6975 Score: 74
Period size: 23 Copynumber: 3.4 Consensus size: 23
6888 TAAAAAGTTT
6898 ATACC-ATGGGAAGGAGAAATTG
1 ATACCGATGGGAAGGAGAAATTG
* *
6920 GTACCGATGGTGTAAGGA-AAACT-
1 ATACCGATGG-G-AAGGAGAAATTG
*
6943 ATACC-ATCGGGATGGAGAAATTG
1 ATACCGAT-GGGAAGGAGAAATTG
6966 ATACCGATGG
1 ATACCGATGG
6976 TGTGAAGAAA
Statistics
Matches: 44, Mismatches: 5, Indels: 13
0.71 0.08 0.21
Matches are distributed among these distances:
21 4 0.09
22 11 0.25
23 17 0.39
24 7 0.16
25 5 0.11
ACGTcount: A:0.36, C:0.13, G:0.31, T:0.21
Consensus pattern (23 bp):
ATACCGATGGGAAGGAGAAATTG
Found at i:6971 original size:46 final size:46
Alignment explanation
Indices: 6897--7011 Score: 171
Period size: 46 Copynumber: 2.5 Consensus size: 46
6887 GTAAAAAGTT
* *
6897 TATACCAT-GGGAAGGAGAAATTGGTACCGATGGTGT-AAGGAAAAC
1 TATACCATCGGGATGGAGAAATTGATACCGATGGTGTGAA-GAAAAC
6942 TATACCATCGGGATGGAGAAATTGATACCGATGGTGTGAAGAAAAC
1 TATACCATCGGGATGGAGAAATTGATACCGATGGTGTGAAGAAAAC
* *
6988 TATACCATCGGAATTGAGAAATTG
1 TATACCATCGGGATGGAGAAATTG
7012 CAACTGATGG
Statistics
Matches: 64, Mismatches: 4, Indels: 3
0.90 0.06 0.04
Matches are distributed among these distances:
45 8 0.12
46 54 0.84
47 2 0.03
ACGTcount: A:0.37, C:0.12, G:0.28, T:0.23
Consensus pattern (46 bp):
TATACCATCGGGATGGAGAAATTGATACCGATGGTGTGAAGAAAAC
Found at i:6984 original size:23 final size:23
Alignment explanation
Indices: 6912--6985 Score: 57
Period size: 23 Copynumber: 3.2 Consensus size: 23
6902 CATGGGAAGG
*
6912 AGAAATTGGTACCGATGGTGT-A
1 AGAAATTGATACCGATGGTGTGA
* *
6934 AGGAAAACT-ATACC-ATCGG-GATGG
1 A-G-AAATTGATACCGAT-GGTG-TGA
6958 AGAAATTGATACCGATGGTGTGA
1 AGAAATTGATACCGATGGTGTGA
6981 AGAAA
1 AGAAA
6986 ACTATACCAT
Statistics
Matches: 39, Mismatches: 5, Indels: 15
0.66 0.08 0.25
Matches are distributed among these distances:
22 8 0.21
23 23 0.59
24 8 0.21
ACGTcount: A:0.38, C:0.11, G:0.30, T:0.22
Consensus pattern (23 bp):
AGAAATTGATACCGATGGTGTGA
Found at i:6992 original size:23 final size:23
Alignment explanation
Indices: 6921--6993 Score: 64
Period size: 23 Copynumber: 3.2 Consensus size: 23
6911 GAGAAATTGG
6921 TACCGATGGTGT-AAGGAAAACTA
1 TACCGATGGTGTGAA-GAAAACTA
* *
6944 TACC-ATCGG-GATGGAG-AAATTGA
1 TACCGAT-GGTG-TGAAGAAAACT-A
6967 TACCGATGGTGTGAAGAAAACTA
1 TACCGATGGTGTGAAGAAAACTA
6990 TACC
1 TACC
6994 ATCGGAATTG
Statistics
Matches: 39, Mismatches: 4, Indels: 14
0.68 0.07 0.25
Matches are distributed among these distances:
22 7 0.18
23 24 0.62
24 8 0.21
ACGTcount: A:0.37, C:0.15, G:0.26, T:0.22
Consensus pattern (23 bp):
TACCGATGGTGTGAAGAAAACTA
Found at i:7538 original size:12 final size:12
Alignment explanation
Indices: 7521--7545 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
7511 AATCACCCCC
7521 AGATCACTAGTG
1 AGATCACTAGTG
7533 AGATCACTAGTG
1 AGATCACTAGTG
7545 A
1 A
7546 TGCAAGATCA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.36, C:0.16, G:0.24, T:0.24
Consensus pattern (12 bp):
AGATCACTAGTG
Found at i:8219 original size:74 final size:75
Alignment explanation
Indices: 8126--8271 Score: 213
Period size: 74 Copynumber: 2.0 Consensus size: 75
8116 CCTCGAACCA
* * * *
8126 AAAAGTACGTACCACTTTATGAGGACCTTATAGGAATACAACCGCTTATTGGAACACT-ACCGAA
1 AAAAGTACATACCACTTTATGAGGACCTTATAGGAATACAACCCCCTAGTGGAACACTAACCGAA
8190 TCTTGAAGAT
66 TCTTGAAGAT
* * * *
8200 AAAAGTACATATCACTTTATGAGGACCTTATAGGAATAGAACCCCCTAGTGGAACATTAATCGAA
1 AAAAGTACATACCACTTTATGAGGACCTTATAGGAATACAACCCCCTAGTGGAACACTAACCGAA
8265 TCTTGAA
66 TCTTGAA
8272 TCTTTTACAT
Statistics
Matches: 63, Mismatches: 8, Indels: 1
0.88 0.11 0.01
Matches are distributed among these distances:
74 51 0.81
75 12 0.19
ACGTcount: A:0.38, C:0.19, G:0.17, T:0.26
Consensus pattern (75 bp):
AAAAGTACATACCACTTTATGAGGACCTTATAGGAATACAACCCCCTAGTGGAACACTAACCGAA
TCTTGAAGAT
Found at i:8368 original size:21 final size:21
Alignment explanation
Indices: 8329--8368 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
8319 ACCCCTTTGC
*
8329 TGAATAAAAATATTGACTGTA
1 TGAATAAAAATAATGACTGTA
8350 TGAATAAATAATAAT-ACTG
1 TGAATAAA-AATAATGACTG
8369 AACAAAGGAT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
21 12 0.71
22 5 0.29
ACGTcount: A:0.50, C:0.05, G:0.12, T:0.33
Consensus pattern (21 bp):
TGAATAAAAATAATGACTGTA
Found at i:8681 original size:15 final size:15
Alignment explanation
Indices: 8635--8681 Score: 51
Period size: 15 Copynumber: 3.2 Consensus size: 15
8625 TATATTAGCT
8635 AATAATGCCAATTCA
1 AATAATGCCAATTCA
* ***
8650 AAT-CTGCCAAAAAA
1 AATAATGCCAATTCA
8664 AATAATGCCAATTCA
1 AATAATGCCAATTCA
8679 AAT
1 AAT
8682 TGGGTAAAAG
Statistics
Matches: 23, Mismatches: 8, Indels: 2
0.70 0.24 0.06
Matches are distributed among these distances:
14 10 0.43
15 13 0.57
ACGTcount: A:0.51, C:0.19, G:0.06, T:0.23
Consensus pattern (15 bp):
AATAATGCCAATTCA
Found at i:8939 original size:39 final size:38
Alignment explanation
Indices: 8896--8976 Score: 103
Period size: 38 Copynumber: 2.1 Consensus size: 38
8886 TTTTCAGAAT
* * *
8896 AAAAAATTAAA-TATATATT-ATTATAAATTTTTTGAAAA
1 AAAAAATTAAATTATAAATTAACT-TAAA-TCTTTGAAAA
8934 AAAAAATTAAATTATAAATTAACTTAAATCTTTGAAAA
1 AAAAAATTAAATTATAAATTAACTTAAATCTTTGAAAA
8972 AAAAA
1 AAAAA
8977 GGTCAGAATT
Statistics
Matches: 38, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
38 25 0.66
39 11 0.29
40 2 0.05
ACGTcount: A:0.59, C:0.02, G:0.02, T:0.36
Consensus pattern (38 bp):
AAAAAATTAAATTATAAATTAACTTAAATCTTTGAAAA
Found at i:12359 original size:21 final size:22
Alignment explanation
Indices: 12335--12377 Score: 61
Period size: 21 Copynumber: 2.0 Consensus size: 22
12325 GGACCAAATT
*
12335 TGGTTGGATCC-TTAAAAAAAA
1 TGGTTGAATCCTTTAAAAAAAA
*
12356 TGGTTGAATCCTTTCAAAAAAA
1 TGGTTGAATCCTTTAAAAAAAA
12378 CAATAGTTGG
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
21 10 0.53
22 9 0.47
ACGTcount: A:0.42, C:0.12, G:0.16, T:0.30
Consensus pattern (22 bp):
TGGTTGAATCCTTTAAAAAAAA
Done.