Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01015061.1 Corchorus olitorius cultivar O-4 contig15094, 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: 33213
ACGTcount: A:0.35, C:0.15, G:0.16, T:0.34
Found at i:796 original size:24 final size:24
Alignment explanation
Indices: 767--814 Score: 87
Period size: 24 Copynumber: 2.0 Consensus size: 24
757 TTTTTTTAAA
767 TATTTATTTTTATAAAAGGATTAG
1 TATTTATTTTTATAAAAGGATTAG
*
791 TATTTATTTTTGTAAAAGGATTAG
1 TATTTATTTTTATAAAAGGATTAG
815 GGTATATCAA
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 23 1.00
ACGTcount: A:0.35, C:0.00, G:0.15, T:0.50
Consensus pattern (24 bp):
TATTTATTTTTATAAAAGGATTAG
Found at i:950 original size:2 final size:2
Alignment explanation
Indices: 938--980 Score: 68
Period size: 2 Copynumber: 21.0 Consensus size: 2
928 AGTTTAGACT
*
938 TA TA TA GTA TA TA GA TA TA TA 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 TA TA TA TA TA TA
981 CTAGTAATTT
Statistics
Matches: 38, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
2 36 0.95
3 2 0.05
ACGTcount: A:0.49, C:0.00, G:0.05, T:0.47
Consensus pattern (2 bp):
TA
Found at i:6435 original size:22 final size:23
Alignment explanation
Indices: 6407--6528 Score: 71
Period size: 22 Copynumber: 5.5 Consensus size: 23
6397 CTCCCTAAGG
6407 AATTTTGATAAACTT-T-TGATGA
1 AATTTTGATAAACTTCTAT-ATGA
*
6429 AATTTTGGT-AACTTCTATATGA
1 AATTTTGATAAACTTCTATATGA
*
6451 AATTTTGAT-AA-TTATATTATGA
1 AATTTTGATAAACTTCTA-TATGA
* * * * **
6473 AGTTTTAAT-AACCTCCATACAA
1 AATTTTGATAAACTTCTATATGA
* *
6495 AATTTTGGT-AACTAC-ACTATGA
1 AATTTTGATAAACTTCTA-TATGA
6517 AATTTTGATAAA
1 AATTTTGATAAA
6529 TTTTCTATGT
Statistics
Matches: 76, Mismatches: 18, Indels: 11
0.72 0.17 0.10
Matches are distributed among these distances:
21 10 0.13
22 61 0.80
23 5 0.07
ACGTcount: A:0.39, C:0.09, G:0.11, T:0.42
Consensus pattern (23 bp):
AATTTTGATAAACTTCTATATGA
Found at i:6473 original size:44 final size:44
Alignment explanation
Indices: 6425--6527 Score: 107
Period size: 44 Copynumber: 2.3 Consensus size: 44
6415 TAAACTTTTG
* * * ** * * *
6425 ATGAAATTTTGGTAACTTCTATATGAAATTTTGATAATTATATT
1 ATGAAATTTTGATAACCTCCATACAAAATTTTGATAACTACACT
* * *
6469 ATGAAGTTTTAATAACCTCCATACAAAATTTTGGTAACTACACT
1 ATGAAATTTTGATAACCTCCATACAAAATTTTGATAACTACACT
6513 ATGAAATTTTGATAA
1 ATGAAATTTTGATAA
6528 ATTTTCTATG
Statistics
Matches: 46, Mismatches: 13, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
44 46 1.00
ACGTcount: A:0.39, C:0.10, G:0.11, T:0.41
Consensus pattern (44 bp):
ATGAAATTTTGATAACCTCCATACAAAATTTTGATAACTACACT
Found at i:8349 original size:16 final size:16
Alignment explanation
Indices: 8324--8355 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
8314 TTTTGTGGCG
*
8324 GTACATATATTAATTT
1 GTACACATATTAATTT
8340 GTACACATATTAATTT
1 GTACACATATTAATTT
8356 AAATTTAGAT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.38, C:0.09, G:0.06, T:0.47
Consensus pattern (16 bp):
GTACACATATTAATTT
Found at i:8591 original size:2 final size:2
Alignment explanation
Indices: 8584--8617 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
8574 TTAGATAGTT
8584 TA TA TA TA TA TA 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 TA TA
8618 ATTTGGTTGT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:10820 original size:9 final size:9
Alignment explanation
Indices: 10803--10835 Score: 57
Period size: 9 Copynumber: 3.7 Consensus size: 9
10793 TCAGGTCAGG
*
10803 TTTAAGGGT
1 TTTATGGGT
10812 TTTATGGGT
1 TTTATGGGT
10821 TTTATGGGT
1 TTTATGGGT
10830 TTTATG
1 TTTATG
10836 CTTATGATAA
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
9 23 1.00
ACGTcount: A:0.15, C:0.00, G:0.30, T:0.55
Consensus pattern (9 bp):
TTTATGGGT
Found at i:18709 original size:2 final size:2
Alignment explanation
Indices: 18702--18738 Score: 56
Period size: 2 Copynumber: 18.0 Consensus size: 2
18692 AATTAAACTT
*
18702 TA TA TA TA TA TA TA TA TA TA TA TT TA TA CTA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA -TA TA TA TA
18739 AAAGTACGAA
Statistics
Matches: 32, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
2 30 0.94
3 2 0.06
ACGTcount: A:0.46, C:0.03, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:19677 original size:26 final size:25
Alignment explanation
Indices: 19622--19681 Score: 68
Period size: 26 Copynumber: 2.4 Consensus size: 25
19612 TTATATTTCT
*
19622 AAATTTTCATTATTAAAATTTAGTA
1 AAATTTTCATTATTAAAATTAAGTA
* *
19647 TAATTTT-ATTATTTAAAAATTAATTA
1 AAATTTTCATTA-TT-AAAATTAAGTA
19673 AAATTTTCA
1 AAATTTTCA
19682 ATTTAGACCA
Statistics
Matches: 28, Mismatches: 4, Indels: 4
0.78 0.11 0.11
Matches are distributed among these distances:
24 4 0.14
25 8 0.29
26 15 0.54
27 1 0.04
ACGTcount: A:0.45, C:0.03, G:0.02, T:0.50
Consensus pattern (25 bp):
AAATTTTCATTATTAAAATTAAGTA
Found at i:19930 original size:22 final size:22
Alignment explanation
Indices: 19896--19938 Score: 52
Period size: 21 Copynumber: 1.9 Consensus size: 22
19886 TCAAGACAAT
*
19896 TAAAAACTAAGAGCAATTAAATTA
1 TAAAAAC-AAGAG-AATAAAATTA
19920 TAAAAAC-AGAGAATAAAAT
1 TAAAAACAAGAGAATAAAAT
19939 AAGTTGTGAA
Statistics
Matches: 18, Mismatches: 1, Indels: 3
0.82 0.05 0.14
Matches are distributed among these distances:
21 7 0.39
22 4 0.22
24 7 0.39
ACGTcount: A:0.63, C:0.07, G:0.09, T:0.21
Consensus pattern (22 bp):
TAAAAACAAGAGAATAAAATTA
Found at i:26777 original size:24 final size:23
Alignment explanation
Indices: 26750--26801 Score: 59
Period size: 23 Copynumber: 2.2 Consensus size: 23
26740 AGGTTGCGCA
*
26750 AACTTCAGGGTTCAACCTGGCCCC
1 AACTTCAGGGGT-AACCTGGCCCC
* **
26774 AACTTGAGGGGTAAGTTGGCCCC
1 AACTTCAGGGGTAACCTGGCCCC
26797 AACTT
1 AACTT
26802 GGAGTTCGTC
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
23 14 0.58
24 10 0.42
ACGTcount: A:0.23, C:0.29, G:0.25, T:0.23
Consensus pattern (23 bp):
AACTTCAGGGGTAACCTGGCCCC
Found at i:27371 original size:22 final size:22
Alignment explanation
Indices: 27324--27380 Score: 64
Period size: 22 Copynumber: 2.6 Consensus size: 22
27314 TGTCTCTCTG
27324 TGGTTA-TAAAATTTCATAAGA
1 TGGTTATTAAAATTTCATAAGA
* *
27345 TGGTTATTATAATTTCATGAGGA
1 TGGTTATTAAAATTTCAT-AAGA
*
27368 -GGTTATCAAAATT
1 TGGTTATTAAAATT
27381 CCATCGTGTG
Statistics
Matches: 30, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
21 6 0.20
22 21 0.70
23 3 0.10
ACGTcount: A:0.37, C:0.05, G:0.18, T:0.40
Consensus pattern (22 bp):
TGGTTATTAAAATTTCATAAGA
Found at i:27393 original size:44 final size:44
Alignment explanation
Indices: 27355--27454 Score: 139
Period size: 44 Copynumber: 2.2 Consensus size: 44
27345 TGGTTATTAT
*
27355 AATTTCATGA-GGAGGTTATCAAAATTCCATCGTGTGGTTACCAA
1 AATTTCAT-ATGGAAGTTATCAAAATTCCATCGTGTGGTTACCAA
*
27399 AATTTCATATGGAAGTTATCAAAATTTCATCGTGTGAAGATTACCAA
1 AATTTCATATGGAAGTTATCAAAATTCCATCGTGTG--G-TTACCAA
27446 AATTTCATA
1 AATTTCATA
27455 GTGTGGTAAC
Statistics
Matches: 50, Mismatches: 2, Indels: 5
0.88 0.04 0.09
Matches are distributed among these distances:
43 1 0.02
44 32 0.64
46 1 0.02
47 16 0.32
ACGTcount: A:0.36, C:0.14, G:0.16, T:0.34
Consensus pattern (44 bp):
AATTTCATATGGAAGTTATCAAAATTCCATCGTGTGGTTACCAA
Found at i:27469 original size:47 final size:43
Alignment explanation
Indices: 27374--27475 Score: 116
Period size: 47 Copynumber: 2.3 Consensus size: 43
27364 AGGAGGTTAT
* * *
27374 CAAAATTCCATCGTGTGGTTACCAAAATTTCATATGGAAGTTAT
1 CAAAATTTCATCGTGTGGTTACCAAAATTTCATATGG-AGTAAC
27418 CAAAATTTCATCGTGTGAAGATTACCAAAATTTCATAGTGTG-GTAAC
1 CAAAATTTCATCGTGTG--G-TTACCAAAATTTCATA-TG-GAGTAAC
27465 CAAAATTTCAT
1 CAAAATTTCAT
27476 AGGATCAGGT
Statistics
Matches: 50, Mismatches: 3, Indels: 7
0.83 0.05 0.12
Matches are distributed among these distances:
44 16 0.32
46 1 0.02
47 30 0.60
48 2 0.04
49 1 0.02
ACGTcount: A:0.36, C:0.16, G:0.15, T:0.33
Consensus pattern (43 bp):
CAAAATTTCATCGTGTGGTTACCAAAATTTCATATGGAGTAAC
Found at i:27476 original size:22 final size:23
Alignment explanation
Indices: 27369--27477 Score: 109
Period size: 22 Copynumber: 4.8 Consensus size: 23
27359 TCATGAGGAG
* * *
27369 GTTATCAAAATTCCATCGTGTG-
1 GTTACCAAAATTTCATAGTGTGA
27391 GTTACCAAAATTTCATA-TG-GAA
1 GTTACCAAAATTTCATAGTGTG-A
* *
27413 GTTATCAAAATTTCATCGTGTGAA
1 GTTACCAAAATTTCATAGTGTG-A
27437 GATTACCAAAATTTCATAGTGTG-
1 G-TTACCAAAATTTCATAGTGTGA
*
27460 GTAACCAAAATTTCATAG
1 GTTACCAAAATTTCATAG
27478 GATCAGGTTA
Statistics
Matches: 74, Mismatches: 8, Indels: 10
0.80 0.09 0.11
Matches are distributed among these distances:
20 1 0.01
21 2 0.03
22 45 0.61
23 3 0.04
24 4 0.05
25 19 0.26
ACGTcount: A:0.36, C:0.15, G:0.16, T:0.34
Consensus pattern (23 bp):
GTTACCAAAATTTCATAGTGTGA
Found at i:27765 original size:22 final size:22
Alignment explanation
Indices: 27563--27981 Score: 118
Period size: 22 Copynumber: 19.6 Consensus size: 22
27553 ATCAAAGAGA
*
27563 TTATCAAAATGTCATA-GCAAGG
1 TTATCAAAATTTCATATG-AAGG
*
27585 TTAT-AAGAATTTCATAGTG-TGG
1 TTATCAA-AATTTCATA-TGAAGG
* *
27607 TTAACAAAATTTCATAAGAAGG
1 TTATCAAAATTTCATATGAAGG
* * ** * *
27629 TTA-CTAATATTTTATGGGGATG
1 TTATC-AAAATTTCATATGAAGG
*
27651 TTATCAAAATTTCATACT-ATGG
1 TTATCAAAATTTCATA-TGAAGG
* * *
27673 TTA-CTAAA--T--TAGGAAGC
1 TTATCAAAATTTCATATGAAGG
* * *
27690 TTATTAAACTTTTACTATGAA-G
1 TTATCAAAATTTCA-TATGAAGG
* * *
27712 TAATCAAAATTTC--AGGGAGG
1 TTATCAAAATTTCATATGAAGG
*
27732 ATATC-AAATTTCATATGAAGG
1 TTATCAAAATTTCATATGAAGG
**
27753 TTATCAAAATTTCATAGTTTA-G
1 TTATCAAAATTTCATA-TGAAGG
* * *
27775 TTTTCAAAATTTCATA-GTATG
1 TTATCAAAATTTCATATGAAGG
* * * *
27796 TAGATCAAAATTTCATAGGGAGA
1 T-TATCAAAATTTCATATGAAGG
*
27819 TTAACAAAATTTCATAATG-AGG
1 TTATCAAAATTTCAT-ATGAAGG
**
27841 TTATCAAAAAATCATA-GAGAGG
1 TTATCAAAATTTCATATGA-AGG
*
27863 TTATCAAAA--T--T-TGTA-G
1 TTATCAAAATTTCATATGAAGG
* * *
27879 TTATCAAGATTTCATAAGGAGG
1 TTATCAAAATTTCATATGAAGG
* * * * *
27901 TTATCAAAGTTTTATAGGGAGTT
1 TTATCAAAATTTCATATGAAG-G
* *
27924 TTATCAAAATTTTATA-GCGAGG
1 TTATCAAAATTTCATATG-AAGG
*
27946 TTATCACAATTTCATAGTGTAA--
1 TTATCAAAATTTCATA-TG-AAGG
27968 TTATCAAAATTTCA
1 TTATCAAAATTTCA
27982 GAGTGTGATT
Statistics
Matches: 290, Mismatches: 70, Indels: 74
0.67 0.16 0.17
Matches are distributed among these distances:
16 9 0.03
17 8 0.03
18 5 0.02
19 11 0.04
20 10 0.03
21 22 0.08
22 189 0.65
23 33 0.11
24 3 0.01
ACGTcount: A:0.39, C:0.09, G:0.16, T:0.36
Consensus pattern (22 bp):
TTATCAAAATTTCATATGAAGG
Found at i:27847 original size:44 final size:44
Alignment explanation
Indices: 27714--28138 Score: 220
Period size: 44 Copynumber: 9.8 Consensus size: 44
27704 CTATGAAGTA
27714 ATCAAAATTTC--AGGGAGGA-TATC-AAATTTCATA-TGAAGGTT
1 ATCAAAATTTCATAGGGA-GATTATCAAAATTTCATAGTG-AGGTT
** * * *
27755 ATCAAAATTTCATAGTTTAG-TTTTCAAAATTTCATAGT-ATGTAG
1 ATCAAAATTTCATAG-GGAGATTATCAAAATTTCATAGTGAGGT-T
* *
27799 ATCAAAATTTCATAGGGAGATTAACAAAATTTCATAATGAGGTT
1 ATCAAAATTTCATAGGGAGATTATCAAAATTTCATAGTGAGGTT
** * *
27843 ATCAAAAAATCATAGAGAGGTTATCAAAA-TT--T-GT-A-GTT
1 ATCAAAATTTCATAGGGAGATTATCAAAATTTCATAGTGAGGTT
* * * * * * *
27881 ATCAAGATTTCATAAGGAGGTTATCAAAGTTTTATAGGGAGTTTT
1 ATCAAAATTTCATAGGGAGATTATCAAAATTTCATAGTGAG-GTT
* * * * *
27926 ATCAAAATTTTATAGCGAGGTTATCACAATTTCATAGTGTA-ATT
1 ATCAAAATTTCATAGGGAGATTATCAAAATTTCATAGTG-AGGTT
* * * * * *
27970 ATCAAAATTTCAGAGTGTGATTACTGACAA-TTCATAGGGAGGTT
1 ATCAAAATTTCATAGGGAGATTA-TCAAAATTTCATAGTGAGGTT
* * * * * * * *
28014 TTTAAATTTTCATAGCGTGATTATCAATATATCATA-TAGAAGTT
1 ATCAAAATTTCATAGGGAGATTATCAAAATTTCATAGT-GAGGTT
* * ** *
28058 ATCAACATCTCATAGTGTTGGTTATCAAAATTTCATAGTGAGGTCT
1 ATCAAAATTTCATAG-GGAGATTATCAAAATTTCATAGTGAGGT-T
* * *
28104 -TCAAAATTCCTTAGGGATG-TTAACAAAATTTCATA
1 ATCAAAATTTCATAGGGA-GATTATCAAAATTTCATA
28139 AGAAGGTTAA
Statistics
Matches: 287, Mismatches: 72, Indels: 47
0.71 0.18 0.12
Matches are distributed among these distances:
38 26 0.09
39 3 0.01
40 1 0.00
41 13 0.05
42 1 0.00
43 18 0.06
44 149 0.52
45 73 0.25
46 3 0.01
ACGTcount: A:0.37, C:0.10, G:0.16, T:0.36
Consensus pattern (44 bp):
ATCAAAATTTCATAGGGAGATTATCAAAATTTCATAGTGAGGTT
Found at i:27986 original size:22 final size:22
Alignment explanation
Indices: 27946--27992 Score: 67
Period size: 22 Copynumber: 2.1 Consensus size: 22
27936 TATAGCGAGG
* *
27946 TTATCACAATTTCATAGTGTAA
1 TTATCAAAATTTCAGAGTGTAA
*
27968 TTATCAAAATTTCAGAGTGTGA
1 TTATCAAAATTTCAGAGTGTAA
27990 TTA
1 TTA
27993 CTGACAATTC
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.36, C:0.11, G:0.13, T:0.40
Consensus pattern (22 bp):
TTATCAAAATTTCAGAGTGTAA
Found at i:29255 original size:36 final size:35
Alignment explanation
Indices: 29191--29279 Score: 92
Period size: 36 Copynumber: 2.5 Consensus size: 35
29181 TTTTAATTTT
* * *
29191 AAATATATTATATATATGTTATAAATTAAAAATCTGA
1 AAATATA-TAAATATAT-ATATAAATTAAAAATCAGA
*
29228 AAATATATAAATATATATATAACATTAATAATCAGA
1 AAATATATAAATATATATATAA-ATTAAAAATCAGA
*
29264 AAAT-CA-AAATATATAT
1 AAATATATAAATATATAT
29280 TTTTAATTTA
Statistics
Matches: 46, Mismatches: 5, Indels: 5
0.82 0.09 0.09
Matches are distributed among these distances:
34 10 0.22
35 6 0.13
36 23 0.50
37 7 0.15
ACGTcount: A:0.56, C:0.04, G:0.03, T:0.36
Consensus pattern (35 bp):
AAATATATAAATATATATATAAATTAAAAATCAGA
Found at i:31089 original size:14 final size:14
Alignment explanation
Indices: 31067--31119 Score: 52
Period size: 14 Copynumber: 3.6 Consensus size: 14
31057 GATCTTTCGG
*
31067 GTTTTAGTCAGTTT
1 GTTTGAGTCAGTTT
31081 GTTTGAGTCAGTTT
1 GTTTGAGTCAGTTT
* * *
31095 TTTTCGAATCAGTTA
1 GTTT-GAGTCAGTTT
31110 GTATTGAGTC
1 GT-TTGAGTC
31120 TGAGTCTGCC
Statistics
Matches: 31, Mismatches: 6, Indels: 3
0.77 0.15 0.08
Matches are distributed among these distances:
14 16 0.52
15 13 0.42
16 2 0.06
ACGTcount: A:0.19, C:0.09, G:0.23, T:0.49
Consensus pattern (14 bp):
GTTTGAGTCAGTTT
Found at i:32877 original size:17 final size:17
Alignment explanation
Indices: 32851--32898 Score: 60
Period size: 17 Copynumber: 2.8 Consensus size: 17
32841 GTAATCTTTG
*
32851 ATCACCGGTGATCTTAC
1 ATCACTGGTGATCTTAC
* *
32868 ATTACTGGTGATCTTAG
1 ATCACTGGTGATCTTAC
*
32885 ATCACTAGTGATCT
1 ATCACTGGTGATCT
32899 GGGGGGTGGT
Statistics
Matches: 26, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
17 26 1.00
ACGTcount: A:0.25, C:0.21, G:0.19, T:0.35
Consensus pattern (17 bp):
ATCACTGGTGATCTTAC
Done.