Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01013547.1 Corchorus olitorius cultivar O-4 contig13580, 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: 46603
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Found at i:67 original size:16 final size:15
Alignment explanation
Indices: 29--70 Score: 66
Period size: 15 Copynumber: 2.7 Consensus size: 15
19 ACATAGGTTG
*
29 ACAGAAAGCAATTAA
1 ACAGAAAACAATTAA
44 ACAGAAAACAATTAA
1 ACAGAAAACAATTAA
59 ACTAGAAAACAA
1 AC-AGAAAACAA
71 AGCAAAGTAA
Statistics
Matches: 25, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
15 16 0.64
16 9 0.36
ACGTcount: A:0.64, C:0.14, G:0.10, T:0.12
Consensus pattern (15 bp):
ACAGAAAACAATTAA
Found at i:1461 original size:29 final size:31
Alignment explanation
Indices: 1424--1483 Score: 88
Period size: 29 Copynumber: 2.0 Consensus size: 31
1414 CAATCCTTGC
*
1424 TCTTGAAATAAATCTTC-A-AAGTCTTCAAA
1 TCTTCAAATAAATCTTCAATAAGTCTTCAAA
*
1453 TCTTCAAATAAGTCTTCAATAAGTCTTCAAA
1 TCTTCAAATAAATCTTCAATAAGTCTTCAAA
1484 CATGAACTTC
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
29 15 0.56
30 1 0.04
31 11 0.41
ACGTcount: A:0.40, C:0.18, G:0.07, T:0.35
Consensus pattern (31 bp):
TCTTCAAATAAATCTTCAATAAGTCTTCAAA
Found at i:1470 original size:12 final size:12
Alignment explanation
Indices: 1453--1483 Score: 55
Period size: 11 Copynumber: 2.7 Consensus size: 12
1443 AGTCTTCAAA
1453 TCTTCAAATAAG
1 TCTTCAAATAAG
1465 TCTTC-AATAAG
1 TCTTCAAATAAG
1476 TCTTCAAA
1 TCTTCAAA
1484 CATGAACTTC
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
11 11 0.61
12 7 0.39
ACGTcount: A:0.39, C:0.19, G:0.06, T:0.35
Consensus pattern (12 bp):
TCTTCAAATAAG
Found at i:1475 original size:11 final size:11
Alignment explanation
Indices: 1430--1482 Score: 53
Period size: 11 Copynumber: 5.2 Consensus size: 11
1420 TTGCTCTTGA
*
1430 AATAAATCTTC
1 AATAAGTCTTC
1441 -A-AAGTCTTC
1 AATAAGTCTTC
1450 -A-AA-TCTTC
1 AATAAGTCTTC
1458 AAATAAGTCTTC
1 -AATAAGTCTTC
1470 AATAAGTCTTC
1 AATAAGTCTTC
1481 AA
1 AA
1483 ACATGAACTT
Statistics
Matches: 37, Mismatches: 1, Indels: 8
0.80 0.02 0.17
Matches are distributed among these distances:
8 5 0.14
9 10 0.27
10 2 0.05
11 15 0.41
12 5 0.14
ACGTcount: A:0.42, C:0.19, G:0.06, T:0.34
Consensus pattern (11 bp):
AATAAGTCTTC
Found at i:11840 original size:19 final size:19
Alignment explanation
Indices: 11813--11858 Score: 74
Period size: 19 Copynumber: 2.4 Consensus size: 19
11803 AAATTGCATT
11813 TAATCAGGAAATAAATCTG
1 TAATCAGGAAATAAATCTG
*
11832 TAATTAGGAAATAAATCTG
1 TAATCAGGAAATAAATCTG
*
11851 AAATCAGG
1 TAATCAGG
11859 GACTAGGCCG
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 24 1.00
ACGTcount: A:0.48, C:0.09, G:0.17, T:0.26
Consensus pattern (19 bp):
TAATCAGGAAATAAATCTG
Found at i:17456 original size:177 final size:177
Alignment explanation
Indices: 17156--17484 Score: 532
Period size: 177 Copynumber: 1.9 Consensus size: 177
17146 TTTATTTAGC
* *
17156 TAGCATGTTCAATCAATTTAGTTTTTTGCTAACGTAATTACTAATTGATTGATTTATTTATGGCA
1 TAGCATGTTCAATCAATTGAGTTTTTTGCTAACATAATTACTAATTGATTGATTTATTTATGGCA
* * *
17221 AAATTAAATAATTATGAATAAATTATAACTTTGATTGGCAAAGTTAATTAACGACTAACTTGATT
66 AAATTAAATAATCATCAATAAATTATAACTTTGATTGGCAAAGTTAACTAACGACTAACTTGATT
* *
17286 GATTTATTTATTTAGCATGTTCTTTTTTTTTTTGGCATCAATTTATT
131 CATTTATCTATTTAGCATGTTCTTTTTTTTTTTGGCATCAATTTATT
* * * *
17333 TAGCATGTTCAATCAATTGATTTTTTTGTTAATATAATTACTAATTGATTGATTTATTTATGGTA
1 TAGCATGTTCAATCAATTGAGTTTTTTGCTAACATAATTACTAATTGATTGATTTATTTATGGCA
* *
17398 AAATTAAATAATCATCAATCAATTATAACTTTGATTGGCAAAGTTAACTAATGACTAACTTGATT
66 AAATTAAATAATCATCAATAAATTATAACTTTGATTGGCAAAGTTAACTAACGACTAACTTGATT
*
17463 CATTTGTCTATTTAGCATGTTC
131 CATTTATCTATTTAGCATGTTC
17485 AATAATTAAT
Statistics
Matches: 138, Mismatches: 14, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
177 138 1.00
ACGTcount: A:0.33, C:0.10, G:0.12, T:0.46
Consensus pattern (177 bp):
TAGCATGTTCAATCAATTGAGTTTTTTGCTAACATAATTACTAATTGATTGATTTATTTATGGCA
AAATTAAATAATCATCAATAAATTATAACTTTGATTGGCAAAGTTAACTAACGACTAACTTGATT
CATTTATCTATTTAGCATGTTCTTTTTTTTTTTGGCATCAATTTATT
Found at i:17503 original size:16 final size:16
Alignment explanation
Indices: 17482--17515 Score: 68
Period size: 16 Copynumber: 2.1 Consensus size: 16
17472 ATTTAGCATG
17482 TTCAATAATTAATTTT
1 TTCAATAATTAATTTT
17498 TTCAATAATTAATTTT
1 TTCAATAATTAATTTT
17514 TT
1 TT
17516 TGTAACATAA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.35, C:0.06, G:0.00, T:0.59
Consensus pattern (16 bp):
TTCAATAATTAATTTT
Found at i:17813 original size:166 final size:166
Alignment explanation
Indices: 17498--17816 Score: 525
Period size: 167 Copynumber: 1.9 Consensus size: 166
17488 AATTAATTTT
*
17498 TTCAATAATTAATTTTTTTGTAACATAATCACTAATTGATTTATTTATTTATGGTAATTTTTTTT
1 TTCAATAATTAATTTTTTTGTAACATAATCACTAATTGATTTATTTATTTATGATAATTTTTTTT
* * *
17563 GTAGCTATTTATGGTAAAATTAAATAATTATCAATCAATTAAAACTTTGATTGACAAAATTAATT
66 GTAGCGATTTATGGTAAAATTAAATAATCATCAATCAATTAAAACTTTGATTGACAAAATTAACT
17628 AACGACTAACTTGGATTCATTTATTTATTTACCATG
131 AACGACTAACTTGGATTCATTTATTTATTTACCATG
*
17664 TTCAATAATT-ATTTTTTTGGTAACATAATTACTAATTGATTTATTTATTTATGATAATTTTTTT
1 TTCAATAATTAATTTTTTT-GTAACATAATCACTAATTGATTTATTTATTTATGATAATTTTTTT
* *
17728 TGGTAGCGATTTATGGTAAAATTAAATAATCATCAATCAATTACAACTTTGATTGGCAAAATTAA
65 T-GTAGCGATTTATGGTAAAATTAAATAATCATCAATCAATTAAAACTTTGATTGACAAAATTAA
* *
17793 CTAATGGCTAACTT-GATTCATTTA
129 CTAACGACTAACTTGGATTCATTTA
17817 GCATGTTCAA
Statistics
Matches: 142, Mismatches: 9, Indels: 4
0.92 0.06 0.03
Matches are distributed among these distances:
165 8 0.06
166 64 0.45
167 70 0.49
ACGTcount: A:0.36, C:0.09, G:0.09, T:0.46
Consensus pattern (166 bp):
TTCAATAATTAATTTTTTTGTAACATAATCACTAATTGATTTATTTATTTATGATAATTTTTTTT
GTAGCGATTTATGGTAAAATTAAATAATCATCAATCAATTAAAACTTTGATTGACAAAATTAACT
AACGACTAACTTGGATTCATTTATTTATTTACCATG
Found at i:18180 original size:142 final size:141
Alignment explanation
Indices: 17896--18449 Score: 706
Period size: 142 Copynumber: 3.9 Consensus size: 141
17886 ATAATAGGAG
* * * * *
17896 TAACTTTGATTGACAAAGTTGACTT-AGGACTAACTTGGTTCATTTGTTTATTTAGCATGTTGAA
1 TAACTTTGATTGACAAAGTT-AATTAACGACTAACTTGATTCATTTATTTATTTAGCATGTTCAA
* * *
17960 TCAGTTTA--TTTTTGCTAACATAATTACTAATTGATTCATTTATTCATGGCAAAATTTAATAAT
65 TCAATTTATTTTTTTGC-AACATAATTACTAATTGATTCATTTATTTATGGCAAAATTAAATAAT
* *
18023 CATCAATTAGTTA
129 CATCAATCAATTA
* * * *
18036 TAACTTTGATTGGCAAAGTTAATTAACGACTAATTTGATTCATTTATTTATTTAGTATATTCAAT
1 TAACTTTGATTGACAAAGTTAATTAACGACTAACTTGATTCATTTATTTATTTAGCATGTTCAAT
* * * * *
18101 CAATTTATTTTTTTGCTAACATAATTACTAATTGATTCTTTTATTTATAGCAAAATCAAATCACC
66 CAATTTATTTTTTTGC-AACATAATTACTAATTGATTCATTTATTTATGGCAAAATTAAATAATC
18166 ATCAATCAATTA
130 ATCAATCAATTA
* * *
18178 TAACTTTGATAGACAAAGTTGATTAACAACTAACTTGATTCATTTATTTATTTAGCATGTTCAAT
1 TAACTTTGATTGACAAAGTTAATTAACGACTAACTTGATTCATTTATTTATTTAGCATGTTCAAT
** * * *
18243 CAATTTATTTTTTTGACAACATGTTTTCTAATTTATTTATTTATTTATGGCAAAATTAAATAATC
66 CAATTTATTTTTTTG-CAACATAATTACTAATTGATTCATTTATTTATGGCAAAATTAAATAATC
*
18308 ATTC-GTCAATTA
130 A-TCAATCAATTA
* * * *
18320 TAACTTTGATT-AGCAAAGTTAACTAAAGACTAACTTGGTTCATTTATTTATTTTGCATGTTCAA
1 TAACTTTGATTGA-CAAAGTTAATTAACGACTAACTTGATTCATTTATTTATTTAGCATGTTCAA
* *
18384 TCAATTTATTTTTTT-CAACATAATTACTAATTGATTCATTCATTTATGGAAAAATTAAATAATC
65 TCAATTTATTTTTTTGCAACATAATTACTAATTGATTCATTTATTTATGGCAAAATTAAATAATC
18448 AT
130 AT
18450 TAGCTTTTGG
Statistics
Matches: 357, Mismatches: 51, Indels: 13
0.85 0.12 0.03
Matches are distributed among these distances:
139 4 0.01
140 101 0.28
141 1 0.00
142 248 0.69
143 3 0.01
ACGTcount: A:0.35, C:0.12, G:0.09, T:0.44
Consensus pattern (141 bp):
TAACTTTGATTGACAAAGTTAATTAACGACTAACTTGATTCATTTATTTATTTAGCATGTTCAAT
CAATTTATTTTTTTGCAACATAATTACTAATTGATTCATTTATTTATGGCAAAATTAAATAATCA
TCAATCAATTA
Found at i:24544 original size:42 final size:42
Alignment explanation
Indices: 24485--24565 Score: 137
Period size: 42 Copynumber: 1.9 Consensus size: 42
24475 GCTAAGTCTT
*
24485 GAAAATTTTCTGTAAATTAAGAAATACTCAACTCAAATCATA
1 GAAAATTTTCTGTAAATTAAGAAATACTCAACTAAAATCATA
24527 GAAAATTCTT-TGTAAATTAAGAAATACTCAACTAAAATC
1 GAAAATT-TTCTGTAAATTAAGAAATACTCAACTAAAATC
24566 CTGATCCTTT
Statistics
Matches: 37, Mismatches: 1, Indels: 2
0.93 0.03 0.05
Matches are distributed among these distances:
42 35 0.95
43 2 0.05
ACGTcount: A:0.48, C:0.14, G:0.07, T:0.31
Consensus pattern (42 bp):
GAAAATTTTCTGTAAATTAAGAAATACTCAACTAAAATCATA
Found at i:25913 original size:15 final size:16
Alignment explanation
Indices: 25880--25914 Score: 54
Period size: 15 Copynumber: 2.2 Consensus size: 16
25870 TATTTCGATT
*
25880 TCAATTAATTGATTGA
1 TCAATTAATTGATTAA
25896 TCAATTAA-TGATTAA
1 TCAATTAATTGATTAA
25911 TCAA
1 TCAA
25915 ACTAAAATCA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
15 10 0.56
16 8 0.44
ACGTcount: A:0.43, C:0.09, G:0.09, T:0.40
Consensus pattern (16 bp):
TCAATTAATTGATTAA
Found at i:28349 original size:26 final size:28
Alignment explanation
Indices: 28308--28383 Score: 84
Period size: 26 Copynumber: 2.7 Consensus size: 28
28298 TTTTTGTTTG
28308 AAGAATAATTTTTCTTTTGTTACTTC-AAA
1 AAGAA-AA-TTTTCTTTTGTTACTTCAAAA
* * *
28337 AA-AATATTTTCTTTTCTTTCTTCAAAA
1 AAGAAAATTTTCTTTTGTTACTTCAAAA
28364 AAGAAAATTATTCTTTTGTT
1 AAGAAAATT-TTCTTTTGTT
28384 TCTGAAAAAA
Statistics
Matches: 39, Mismatches: 5, Indels: 6
0.78 0.10 0.12
Matches are distributed among these distances:
26 15 0.38
27 6 0.15
28 7 0.18
29 11 0.28
ACGTcount: A:0.34, C:0.11, G:0.05, T:0.50
Consensus pattern (28 bp):
AAGAAAATTTTCTTTTGTTACTTCAAAA
Found at i:28398 original size:26 final size:26
Alignment explanation
Indices: 28317--28396 Score: 88
Period size: 26 Copynumber: 3.0 Consensus size: 26
28307 GAAGAATAAT
* * *
28317 TTTTCTTTTGTTACTTCAAAAAAATA
1 TTTTCTTTTGTTTCTTAAAAAAAAAA
*
28343 TTTTCTTTTCTTTCTTCAAAAAAGAAAA
1 TTTTCTTTTGTTTCTT-AAAAAA-AAAA
*
28371 TTATTCTTTTGTTTCTGAAAAAAAAA
1 TT-TTCTTTTGTTTCTTAAAAAAAAA
28397 TTGTTATTTT
Statistics
Matches: 45, Mismatches: 6, Indels: 5
0.80 0.11 0.09
Matches are distributed among these distances:
26 14 0.31
27 8 0.18
28 11 0.24
29 12 0.27
ACGTcount: A:0.36, C:0.11, G:0.05, T:0.47
Consensus pattern (26 bp):
TTTTCTTTTGTTTCTTAAAAAAAAAA
Found at i:38145 original size:24 final size:24
Alignment explanation
Indices: 38113--38167 Score: 92
Period size: 24 Copynumber: 2.3 Consensus size: 24
38103 CGTATGTCAT
*
38113 CACCCCCGCAACTCAAGAGCTCAC
1 CACCTCCGCAACTCAAGAGCTCAC
38137 CACCTCCGCAACTCAAGAGCTCAC
1 CACCTCCGCAACTCAAGAGCTCAC
*
38161 CGCCTCC
1 CACCTCC
38168 ATGGCTTCTC
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
24 29 1.00
ACGTcount: A:0.25, C:0.51, G:0.13, T:0.11
Consensus pattern (24 bp):
CACCTCCGCAACTCAAGAGCTCAC
Found at i:40752 original size:13 final size:13
Alignment explanation
Indices: 40734--40771 Score: 53
Period size: 13 Copynumber: 3.0 Consensus size: 13
40724 TAGTAATTTC
40734 CTTCTTTTTTCTT
1 CTTCTTTTTTCTT
40747 CTTCTTTTTT-TT
1 CTTCTTTTTTCTT
40759 -TTCATTTTTTCTT
1 CTTC-TTTTTTCTT
40772 ACCTTGTAAT
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
11 3 0.13
12 8 0.35
13 12 0.52
ACGTcount: A:0.03, C:0.18, G:0.00, T:0.79
Consensus pattern (13 bp):
CTTCTTTTTTCTT
Found at i:41180 original size:27 final size:27
Alignment explanation
Indices: 41142--41239 Score: 151
Period size: 27 Copynumber: 3.6 Consensus size: 27
41132 GGAATGTGTA
* * *
41142 AAATGACCAAAATGCCCCTGGATATGC
1 AAATGACTAAAATGCCCCTGAACATGC
*
41169 AAATGACTAAAATACCCCTGAACATGC
1 AAATGACTAAAATGCCCCTGAACATGC
41196 AAATGACTAAAATGCCCCTGAACATGC
1 AAATGACTAAAATGCCCCTGAACATGC
*
41223 AAAAGACTAAAATGCCC
1 AAATGACTAAAATGCCC
41240 ACCTAGGTGA
Statistics
Matches: 65, Mismatches: 6, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
27 65 1.00
ACGTcount: A:0.43, C:0.26, G:0.14, T:0.17
Consensus pattern (27 bp):
AAATGACTAAAATGCCCCTGAACATGC
Found at i:42175 original size:281 final size:282
Alignment explanation
Indices: 41671--42224 Score: 993
Period size: 281 Copynumber: 2.0 Consensus size: 282
41661 TAAAAGGTTA
* * *
41671 TTGTGTGATCTACAACTTTCGTCAAGGGTCTGAAGCCTGAATTTAATTAATGAGTTTTGTGGAGG
1 TTGTGTGATCTACAACTTTCGTCAAGGGCCTGAAACCTGAATTTAATTAATGAGTTTCGTGGAGG
*
41736 GTTCAAGAGGGAATTTTTATGTTTGGTCTCCATAAAAAAATATTTTTTTGCTGGATTATTTATCA
66 GTTCAAGAGGGAATTTTTATGTTTGGTCTCCATAAAAAAATATTTTTTTGCTGAATTATTTATCA
41801 AATGATCCTTATACTTTTATGCTTTATGCTATTTAATCTTTTACAATTATGGGTTGGACGATTTA
131 AATGATCCTTATACTTTTATGCTTTATGCTATTTAATCTTTTACAATTATGGGTTGGACGATTTA
41866 ACGCTACGACTTTTAATTTTGTATTTTTTGTTCTATTTCTCCGATTAAGATGATTCAAGTGTCTA
196 ACGCTACGACTTTTAATTTTGTATTTTTTGTTCTATTTCTCCGATTAAGATGATTCAAGTGTCTA
41931 TTAAAATGTGATTCAATTGTCG
261 TTAAAATGTGATTCAATTGTCG
*
41953 TTGTGTGATCTACAACTTTCGTCAAGGGCCTGAAACCTGAATTTGATTAATGAGTTTCGTGGAGG
1 TTGTGTGATCTACAACTTTCGTCAAGGGCCTGAAACCTGAATTTAATTAATGAGTTTCGTGGAGG
* *
42018 GTTCAAGAGGGAATTTTTATGTTTGGTCTCCAT-AAAAAATTTTTTTTTGCTGAATTATTTATGA
66 GTTCAAGAGGGAATTTTTATGTTTGGTCTCCATAAAAAAATATTTTTTTGCTGAATTATTTATCA
* * *
42082 AATGATCCTTATACTTTTATGCTTTATGCTATTTAGTCTTTTGCAATTATGGGTTGGGCGATTTA
131 AATGATCCTTATACTTTTATGCTTTATGCTATTTAATCTTTTACAATTATGGGTTGGACGATTTA
* *
42147 ACGCTACGACTTTTAATTTTGTATTTTTTGTTCTATTTGTCCGATTAAGGTGATTCAAGTGTCTA
196 ACGCTACGACTTTTAATTTTGTATTTTTTGTTCTATTTCTCCGATTAAGATGATTCAAGTGTCTA
42212 TTAAAATGTGATT
261 TTAAAATGTGATT
42225 TCATGATCTA
Statistics
Matches: 260, Mismatches: 12, Indels: 1
0.95 0.04 0.00
Matches are distributed among these distances:
281 166 0.64
282 94 0.36
ACGTcount: A:0.25, C:0.12, G:0.19, T:0.44
Consensus pattern (282 bp):
TTGTGTGATCTACAACTTTCGTCAAGGGCCTGAAACCTGAATTTAATTAATGAGTTTCGTGGAGG
GTTCAAGAGGGAATTTTTATGTTTGGTCTCCATAAAAAAATATTTTTTTGCTGAATTATTTATCA
AATGATCCTTATACTTTTATGCTTTATGCTATTTAATCTTTTACAATTATGGGTTGGACGATTTA
ACGCTACGACTTTTAATTTTGTATTTTTTGTTCTATTTCTCCGATTAAGATGATTCAAGTGTCTA
TTAAAATGTGATTCAATTGTCG
Found at i:44570 original size:12 final size:13
Alignment explanation
Indices: 44552--44581 Score: 53
Period size: 12 Copynumber: 2.4 Consensus size: 13
44542 GTTTTCTTTA
44552 ATTTTCTTGATTG
1 ATTTTCTTGATTG
44565 -TTTTCTTGATTG
1 ATTTTCTTGATTG
44577 ATTTT
1 ATTTT
44582 AATTGCTAGT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
12 12 0.75
13 4 0.25
ACGTcount: A:0.13, C:0.07, G:0.13, T:0.67
Consensus pattern (13 bp):
ATTTTCTTGATTG
Done.