Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01013859.1 Corchorus olitorius cultivar O-4 contig13892, 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: 1776
ACGTcount: A:0.32, C:0.14, G:0.23, T:0.32
Found at i:114 original size:44 final size:44
Alignment explanation
Indices: 76--803 Score: 186
Period size: 44 Copynumber: 16.4 Consensus size: 44
66 GGTTACTAAT
*
76 ATTTCATGGAGAGGTTATCAAAATTTCATAGTGTGGTTATCAAA
1 ATTTCATAGAGAGGTTATCAAAATTTCATAGTGTGGTTATCAAA
** * * * *
120 ATTTTTTAGTGTGGTTATCAAAATTTCATA-TGAGGGTTATATATAA
1 ATTTCATAGAGAGGTTATCAAAATTTCATAGTG-TGGTTAT-CA-AA
* ** * * * **
166 AGGTCTCAATTTCATGAGGAGTACCAAAATTTGATAG-AAGGTTATC-AA
1 A--TTTC-A-TAGA-GAGG-TTATCAAAATTTCATAGTGTGGTTATCAAA
* * * * * * *
214 ATCTCATAGAGTGATTATCGAAATTTCGTTGCGATCGGATTATCAAA
1 ATTTCATAGAGAGGTTATCAAAATTTCATAGTG-T-GG-TTATCAAA
* *
261 ATTT-ATAG-GAAGATTATCAAAATTTCATAGTAGT-ATTATCAAA
1 ATTTCATAGAG-AGGTTATCAAAATTTCATAGT-GTGGTTATCAAA
* * * *
304 ATTTCAAAGCA-AGGTTATCAAAATTACATAATGTGATTATCAAA
1 ATTTCATAG-AGAGGTTATCAAAATTTCATAGTGTGGTTATCAAA
* * * * * * *
348 ATGTCATAAAGGGGTCAACAAAATTTTATAGAGTGGTTATCAAA
1 ATTTCATAGAGAGGTTATCAAAATTTCATAGTGTGGTTATCAAA
* * * * * * *
392 ATTTCATAAAGAGTTTATCAAATTTTCAAAATGTGATTAACAAA
1 ATTTCATAGAGAGGTTATCAAAATTTCATAGTGTGGTTATCAAA
* *
436 ATTTCATAGTGGTATTTCTGGGAAGGTTATCAAAATTTCATAGTATGGTTA-CCAA
1 ATTTCATA---G-A-------G-AGGTTATCAAAATTTCATAGTGTGGTTATCAAA
* * * * *
491 A--T--TAGAAAGGTTATTAAACTTTTACTA-TGAT-GTAATCAAA
1 ATTTCATAGAGAGGTTATCAAAATTTCA-TAGTG-TGGTTATCAAA
* * ***
531 ATTTC--AGGGAGGATATCAAAATTTCATA-TAAACGTTATCAAA
1 ATTTCATAGAGAGGTTATCAAAATTTCATAGT-GTGGTTATCAAA
** * *
573 ATTTCATAGTTTA-GTTTTCAAAATTTCATAAGAG-GGTTATCAAA
1 ATTTCATAG-AGAGGTTATCAAAATTTCAT-AGTGTGGTTATCAAA
* * * * * * *
617 ATTTCATAG-TATGTAGATCAAAATTTCATAGGGAGATTAACAAA
1 ATTTCATAGAGAGGT-TATCAAAATTTCATAGTGTGGTTATCAAA
*** * *
661 ATTTCATA-ATGAGGTTATCAAAAAAACATAGGGAGGTTATCAAA
1 ATTTCATAGA-GAGGTTATCAAAATTTCATAGTGTGGTTATCAAA
* * *
705 A-TT--T-G-TA-GTTATCAAGATTTCATAATGATGG-TATCAAA
1 ATTTCATAGAGAGGTTATCAAAATTTCATAGTG-TGGTTATCAAA
* * * * * *
743 ATTTCATAGTA-AGGTCT-TCAAAATTCCTTAGGGAGATTAACAAA
1 ATTTCATAG-AGAGGT-TATCAAAATTTCATAGTGTGGTTATCAAA
787 ATTTCATA-AGAAGGTTA
1 ATTTCATAGAG-AGGTTA
804 AAAAAAATTA
Statistics
Matches: 492, Mismatches: 126, Indels: 132
0.66 0.17 0.18
Matches are distributed among these distances:
38 22 0.04
39 23 0.05
40 7 0.01
41 5 0.01
42 44 0.09
43 29 0.06
44 251 0.51
45 11 0.02
46 33 0.07
47 7 0.01
48 7 0.01
50 1 0.00
51 11 0.02
52 13 0.03
53 1 0.00
55 5 0.01
56 22 0.04
ACGTcount: A:0.39, C:0.10, G:0.16, T:0.35
Consensus pattern (44 bp):
ATTTCATAGAGAGGTTATCAAAATTTCATAGTGTGGTTATCAAA
Found at i:159 original size:22 final size:22
Alignment explanation
Indices: 88--149 Score: 106
Period size: 22 Copynumber: 2.8 Consensus size: 22
78 TTCATGGAGA
88 GGTTATCAAAATTTCATAGTGT
1 GGTTATCAAAATTTCATAGTGT
**
110 GGTTATCAAAATTTTTTAGTGT
1 GGTTATCAAAATTTCATAGTGT
132 GGTTATCAAAATTTCATA
1 GGTTATCAAAATTTCATA
150 TGAGGGTTAT
Statistics
Matches: 36, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 36 1.00
ACGTcount: A:0.32, C:0.08, G:0.16, T:0.44
Consensus pattern (22 bp):
GGTTATCAAAATTTCATAGTGT
Found at i:277 original size:21 final size:22
Alignment explanation
Indices: 251--355 Score: 99
Period size: 22 Copynumber: 4.8 Consensus size: 22
241 GTTGCGATCG
251 GATTATCAAAATTT-ATAGGAA
1 GATTATCAAAATTTCATAGGAA
*
272 GATTATCAAAATTTCATA-GTA
1 GATTATCAAAATTTCATAGGAA
* *
293 GTATTATCAAAATTTCAAAGCAA
1 G-ATTATCAAAATTTCATAGGAA
* * * *
316 GGTTATCAAAATTACATAATG-T
1 GATTATCAAAATTTCAT-AGGAA
*
338 GATTATCAAAATGTCATA
1 GATTATCAAAATTTCATA
356 AAGGGGTCAA
Statistics
Matches: 67, Mismatches: 13, Indels: 8
0.76 0.15 0.09
Matches are distributed among these distances:
21 18 0.27
22 46 0.69
23 3 0.04
ACGTcount: A:0.45, C:0.10, G:0.11, T:0.34
Consensus pattern (22 bp):
GATTATCAAAATTTCATAGGAA
Found at i:298 original size:22 final size:22
Alignment explanation
Indices: 252--451 Score: 94
Period size: 22 Copynumber: 9.1 Consensus size: 22
242 TTGCGATCGG
*
252 ATTATCAAAATTT-ATAGGAAG-
1 ATTATCAAAATTTCATA-GTAGT
273 ATTATCAAAATTTCATAGTAGT
1 ATTATCAAAATTTCATAGTAGT
* *
295 ATTATCAAAATTTCAAAGCAAG-
1 ATTATCAAAATTTCATAG-TAGT
* * *
317 GTTATCAAAATTACATAAT-GT
1 ATTATCAAAATTTCATAGTAGT
* * *
338 GATTATCAAAATGTCATA-AAGGG
1 -ATTATCAAAATTTCATAGTA-GT
* * * *
361 GTCAACAAAATTTTATAG-AGT
1 ATTATCAAAATTTCATAGTAGT
*
382 GGTTATCAAAATTTCATAAAG-AGT
1 -ATTATCAAAATTTCAT--AGTAGT
* * *
406 -TTATCAAATTTTCAAAAT-GT
1 ATTATCAAAATTTCATAGTAGT
* *
426 GATTAACAAAATTTCATAGTGGT
1 -ATTATCAAAATTTCATAGTAGT
449 ATT
1 ATT
452 TCTGGGAAGG
Statistics
Matches: 135, Mismatches: 29, Indels: 29
0.70 0.15 0.15
Matches are distributed among these distances:
20 4 0.03
21 17 0.13
22 104 0.77
23 5 0.04
24 5 0.04
ACGTcount: A:0.43, C:0.09, G:0.13, T:0.35
Consensus pattern (22 bp):
ATTATCAAAATTTCATAGTAGT
Found at i:740 original size:126 final size:124
Alignment explanation
Indices: 584--810 Score: 316
Period size: 126 Copynumber: 1.8 Consensus size: 124
574 TTTCATAGTT
* * * *
584 TAGTTTTCAAAATTTCATAAGAGGGTTATCAAAATTTCATAGT-ATGTAGATCAAAATTTCATAG
1 TAGTTATCAAAATTTCATAAGAGGGTTATCAAAATTTCATAGTAAGGT-CATCAAAATTCCATAG
648 GGAGATTAACAAAATTTCATAATG-AGGTTATCAAAAAAACATAGGGAGGTTATCAAAATTTG
65 GGAGATTAACAAAATTTCATAA-GAAGGTTA--AAAAAAACATAGGGAGGTTATCAAAATTTG
* * * *
710 TAGTTATCAAGATTTCATAATGATGG-TATCAAAATTTCATAGTAAGGTCTTCAAAATTCCTTAG
1 TAGTTATCAAAATTTCATAA-GAGGGTTATCAAAATTTCATAGTAAGGTCATCAAAATTCCATAG
774 GGAGATTAACAAAATTTCATAAGAAGGTTAAAAAAAA
65 GGAGATTAACAAAATTTCATAAGAAGGTTAAAAAAAA
811 TTATAAAAGG
Statistics
Matches: 90, Mismatches: 8, Indels: 8
0.85 0.08 0.08
Matches are distributed among these distances:
124 7 0.08
125 1 0.01
126 75 0.83
127 7 0.08
ACGTcount: A:0.43, C:0.09, G:0.16, T:0.32
Consensus pattern (124 bp):
TAGTTATCAAAATTTCATAAGAGGGTTATCAAAATTTCATAGTAAGGTCATCAAAATTCCATAGG
GAGATTAACAAAATTTCATAAGAAGGTTAAAAAAAACATAGGGAGGTTATCAAAATTTG
Found at i:804 original size:22 final size:22
Alignment explanation
Indices: 544--885 Score: 160
Period size: 22 Copynumber: 15.9 Consensus size: 22
534 TCAGGGAGGA
*
544 TATCAAAATTTCATATA-AACGT
1 TATCAAAATTTCATA-AGAAGGT
*
566 TATCAAAATTTCAT-AGTTTA-GT
1 TATCAAAATTTCATAAG--AAGGT
* *
588 TTTCAAAATTTCATAAGAGGGT
1 TATCAAAATTTCATAAGAAGGT
* *
610 TATCAAAATTTCAT-AGTATGT
1 TATCAAAATTTCATAAGAAGGT
* * * *
631 AGATCAAAATTTCATAGGGAGAT
1 -TATCAAAATTTCATAAGAAGGT
*
654 TAACAAAATTTCATAATG-AGGT
1 TATCAAAATTTCATAA-GAAGGT
*** * *
676 TATCAAAAAAACATAGGGAGGT
1 TATCAAAATTTCATAAGAAGGT
*
698 TATCAAAA-TT--T--GTA-GT
1 TATCAAAATTTCATAAGAAGGT
* *
714 TATCAAGATTTCATAATGATGG-
1 TATCAAAATTTCATAA-GAAGGT
736 TATCAAAATTTCAT-AGTAAGGT
1 TATCAAAATTTCATAAG-AAGGT
* * * * *
758 CT-TCAAAATTCCTTAGGGAGAT
1 -TATCAAAATTTCATAAGAAGGT
*
780 TAACAAAATTTCATAAGAAGGT
1 TATCAAAATTTCATAAGAAGGT
** *
802 TAAAAAAAATT-ATAA-AAGGGT
1 TATCAAAATTTCATAAGAA-GGT
* * * **
823 TCTCGAAATTCCAT-AGTATCGT
1 TATCAAAATTTCATAAG-AAGGT
* *
845 TATTAAAATTTCATAGGAAGGT
1 TATCAAAATTTCATAAGAAGGT
867 TATCAAAATTTCATAAGAA
1 TATCAAAATTTCATAAGAA
886 AGTCATCGAA
Statistics
Matches: 234, Mismatches: 60, Indels: 52
0.68 0.17 0.15
Matches are distributed among these distances:
16 9 0.04
17 4 0.02
19 2 0.01
20 4 0.02
21 23 0.10
22 180 0.77
23 12 0.05
ACGTcount: A:0.42, C:0.10, G:0.14, T:0.34
Consensus pattern (22 bp):
TATCAAAATTTCATAAGAAGGT
Found at i:1532 original size:26 final size:26
Alignment explanation
Indices: 1485--1552 Score: 84
Period size: 27 Copynumber: 2.6 Consensus size: 26
1475 CACGCGCGAT
* *
1485 GTCACATGTGGAGGTGTCCG-TTGGAG
1 GTCACGTGT-GAGGTGTACGTTTGGAG
1511 GTCACGTGTGAGGTCGTACGTTTGGAG
1 GTCACGTGTGAGGT-GTACGTTTGGAG
*
1538 GTCACGTGTGGGGTG
1 GTCACGTGTGAGGTG
1553 CCAGCTGGTT
Statistics
Matches: 37, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
25 5 0.14
26 13 0.35
27 19 0.51
ACGTcount: A:0.13, C:0.15, G:0.44, T:0.28
Consensus pattern (26 bp):
GTCACGTGTGAGGTGTACGTTTGGAG
Found at i:1685 original size:23 final size:23
Alignment explanation
Indices: 1655--1776 Score: 198
Period size: 23 Copynumber: 5.5 Consensus size: 23
1645 CGCCGCGATA
1655 TGGAAGTGGTCGGTCGCCAGGTT
1 TGGAAGTGGTCGGTCGCCAGGTT
* *
1678 TGGAAGTGGTCGG--G-C-GCTA
1 TGGAAGTGGTCGGTCGCCAGGTT
1697 TGGAAGTGGTCGGTCGCCAGGTT
1 TGGAAGTGGTCGGTCGCCAGGTT
1720 TGGAAGTGGTCGGTCGCCAGGTT
1 TGGAAGTGGTCGGTCGCCAGGTT
1743 TGGAAGTGGTCGGTCGCCAGGTT
1 TGGAAGTGGTCGGTCGCCAGGTT
1766 TGGAAGTGGTC
1 TGGAAGTGGTC
Statistics
Matches: 91, Mismatches: 4, Indels: 8
0.88 0.04 0.08
Matches are distributed among these distances:
19 15 0.16
20 1 0.01
21 2 0.02
22 1 0.01
23 72 0.79
ACGTcount: A:0.14, C:0.16, G:0.44, T:0.25
Consensus pattern (23 bp):
TGGAAGTGGTCGGTCGCCAGGTT
Found at i:1712 original size:42 final size:45
Alignment explanation
Indices: 1653--1776 Score: 200
Period size: 42 Copynumber: 2.8 Consensus size: 45
1643 AGCGCCGCGA
1653 TATGGAAGTGGTCGGTCGCCAGGTTTGGAAGTGGTCGG-G-C-GC
1 TATGGAAGTGGTCGGTCGCCAGGTTTGGAAGTGGTCGGCGCCAGC
*
1695 TATGGAAGTGGTCGGTCGCCAGGTTTGGAAGTGGTCGGTCGCCAGG
1 TATGGAAGTGGTCGGTCGCCAGGTTTGGAAGTGGTCGG-CGCCAGC
*
1741 TTTGGAAGTGGTCGGTCGCCAGGTTTGGAAGTGGTC
1 TATGGAAGTGGTCGGTCGCCAGGTTTGGAAGTGGTC
Statistics
Matches: 76, Mismatches: 2, Indels: 4
0.93 0.02 0.05
Matches are distributed among these distances:
42 38 0.50
44 1 0.01
45 1 0.01
46 36 0.47
ACGTcount: A:0.15, C:0.16, G:0.44, T:0.26
Consensus pattern (45 bp):
TATGGAAGTGGTCGGTCGCCAGGTTTGGAAGTGGTCGGCGCCAGC
Done.