Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01019036.1 Corchorus olitorius cultivar O-4 contig19069, 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: 37041
ACGTcount: A:0.33, C:0.17, G:0.19, T:0.31
Warning! 1 characters in sequence are not A, C, G, or T
Found at i:496 original size:22 final size:22
Alignment explanation
Indices: 425--502 Score: 70
Period size: 22 Copynumber: 3.5 Consensus size: 22
415 AATTTCGATA
* * *
425 ACCTATGAAAATTTGGTAA-CC
1 ACCTATGAAATTTTGATAATCT
*
446 ACTCTGTGAAATTTTGATAATCT
1 AC-CTATGAAATTTTGATAATCT
* *
469 TCCTATGAAATTTTGATACTC-
1 ACCTATGAAATTTTGATAATCT
490 ACACTATGAAATT
1 AC-CTATGAAATT
503 GGTAAGCGCA
Statistics
Matches: 46, Mismatches: 8, Indels: 5
0.78 0.14 0.08
Matches are distributed among these distances:
21 3 0.07
22 41 0.89
23 2 0.04
ACGTcount: A:0.35, C:0.17, G:0.12, T:0.37
Consensus pattern (22 bp):
ACCTATGAAATTTTGATAATCT
Found at i:772 original size:43 final size:43
Alignment explanation
Indices: 679--773 Score: 111
Period size: 43 Copynumber: 2.2 Consensus size: 43
669 CCTCCCCCCC
* *
679 ATGAAATTTTGATAACCACACTATAAATTTTGATAACCTTCGT
1 ATGAAATTTTGATAACCACACTAGAAAATTTGATAACCTTCGT
* * * **
722 ATAAAATTTTGTTAACGAC-CTAAGAAAATTTGATAACCTTTTT
1 ATGAAATTTTGATAACCACACT-AGAAAATTTGATAACCTTCGT
765 ATGAAATTT
1 ATGAAATTT
774 GGTAACGCCT
Statistics
Matches: 43, Mismatches: 8, Indels: 2
0.81 0.15 0.04
Matches are distributed among these distances:
42 2 0.05
43 41 0.95
ACGTcount: A:0.39, C:0.13, G:0.09, T:0.39
Consensus pattern (43 bp):
ATGAAATTTTGATAACCACACTAGAAAATTTGATAACCTTCGT
Found at i:797 original size:43 final size:44
Alignment explanation
Indices: 703--801 Score: 114
Period size: 43 Copynumber: 2.3 Consensus size: 44
693 ACCACACTAT
*
703 AAATTTTGATAACCTTCGTATAAAATTTTGTTAACGACCTAAGA
1 AAATTTTGATAACCTTCGTATAAAATTTTGGTAACGACCTAAGA
** * * *
747 AAA-TTTGATAACCTTTTTATGAAA-TTTGGTAACG-CCTGTATA
1 AAATTTTGATAACCTTCGTATAAAATTTTGGTAACGACCT-AAGA
789 AAATTTTGATAAC
1 AAATTTTGATAAC
802 TACACTATGA
Statistics
Matches: 47, Mismatches: 6, Indels: 5
0.81 0.10 0.09
Matches are distributed among these distances:
41 3 0.06
42 14 0.30
43 27 0.57
44 3 0.06
ACGTcount: A:0.37, C:0.12, G:0.12, T:0.38
Consensus pattern (44 bp):
AAATTTTGATAACCTTCGTATAAAATTTTGGTAACGACCTAAGA
Found at i:839 original size:22 final size:22
Alignment explanation
Indices: 592--884 Score: 101
Period size: 22 Copynumber: 13.3 Consensus size: 22
582 CTCTTTATTT
*
592 AATTTTGATAACATCTCCACA--A
1 AATTTTGATAAC--CTCCATATGA
614 AATTTTTG-TAACCTTCCA-ATGA
1 AA-TTTTGATAACC-TCCATATGA
* *
636 AATTTTGTTAACCTTCC-TAGGA
1 AATTTTGATAACC-TCCATATGA
* **
658 AACTTTGATAACCTCCCCCCCATGA
1 AATTTTGATAACCT---CCATATGA
*
683 AATTTTGATAACC-ACACTAT-A
1 AATTTTGATAACCTCCA-TATGA
* * *
704 AATTTTGATAACCTTCGTATAA
1 AATTTTGATAACCTCCATATGA
* ** *
726 AATTTTGTTAACGACC-TAAGA
1 AATTTTGATAACCTCCATATGA
* ***
747 AAATTTGATAACCTTTTTATGA
1 AATTTTGATAACCTCCATATGA
* ** *
769 AA-TTTGGTAACGC-CTGTATAA
1 AATTTTGATAAC-CTCCATATGA
*
790 AATTTTGATAA-CTACACTATGA
1 AATTTTGATAACCTCCA-TATGA
**
812 CGTTTTGATAACCTCCATATGA
1 AATTTTGATAACCTCCATATGA
*
834 AATTTT-AGTAACC-ACACTATGA
1 AATTTTGA-TAACCTCCA-TATGA
* * *
856 AAATTTCATAACCTTCC-TATGT
1 AATTTTGATAACC-TCCATATGA
878 AATTTTG
1 AATTTTG
885 GTTTGATTGA
Statistics
Matches: 203, Mismatches: 44, Indels: 48
0.69 0.15 0.16
Matches are distributed among these distances:
20 3 0.01
21 59 0.29
22 113 0.56
23 10 0.05
24 3 0.01
25 15 0.07
ACGTcount: A:0.35, C:0.19, G:0.10, T:0.37
Consensus pattern (22 bp):
AATTTTGATAACCTCCATATGA
Found at i:2196 original size:112 final size:114
Alignment explanation
Indices: 2037--2384 Score: 497
Period size: 112 Copynumber: 3.0 Consensus size: 114
2027 ATTGTTAACA
*
2037 CGTTTGGGATCTAAGAATTAAGGAGTAATTTATA-TATTTTTATTGGAAGAGTTGGTTTGAAGTG
1 CGTTTGGAATCTAAGAATTAAGGAGTAATTTATACTATTTTTATTGGAAGAGTTGGTTTGAAGTG
2101 GAAAATTTAAGGACTTG-CCTCAAAACAATATTCATGGTTGTGGTGGAG
66 GAAAATTTAAGGACTTGACCTCAAAACAATATTCATGGTTGTGGTGGAG
*
2149 CGTTTGGAACCTAAGAATTAAGGAGTAATTTATACTATTTTTA-TGGAAGAGTTGGTTTGAAGTG
1 CGTTTGGAATCTAAGAATTAAGGAGTAATTTATACTATTTTTATTGGAAGAGTTGGTTTGAAGTG
*
2213 GAAAATTTGAGGACTTAAGAAATTCCTCAAAACAATATTCATGGTTGTGGTGGAG
66 GAAAATTTAAGGACTT--G--A--CCTCAAAACAATATTCATGGTTGTGGTGGAG
* * *
2268 CCTTT-GAGATCTAAGAATTAAGGAGAAATTTATACTATTTTTATTGGAAGAGTTGGTTTGAAAT
1 CGTTTGGA-ATCTAAGAATTAAGGAGTAATTTATACTATTTTTATTGGAAGAGTTGGTTTGAAGT
* *
2332 GGAAAAATGAAGGACTTGAAATTCCTCAAAACAATATTCATGGTTGTGGTGGA
65 GGAAAATTTAAGGACTTG--A--CCTCAAAACAATATTCATGGTTGTGGTGGA
2385 TATTCTTCCA
Statistics
Matches: 216, Mismatches: 10, Indels: 14
0.90 0.04 0.06
Matches are distributed among these distances:
112 68 0.31
113 8 0.04
114 1 0.00
118 38 0.18
119 68 0.31
120 33 0.15
ACGTcount: A:0.34, C:0.08, G:0.24, T:0.34
Consensus pattern (114 bp):
CGTTTGGAATCTAAGAATTAAGGAGTAATTTATACTATTTTTATTGGAAGAGTTGGTTTGAAGTG
GAAAATTTAAGGACTTGACCTCAAAACAATATTCATGGTTGTGGTGGAG
Found at i:2298 original size:119 final size:118
Alignment explanation
Indices: 2047--2384 Score: 496
Period size: 119 Copynumber: 2.9 Consensus size: 118
2037 CGTTTGGGAT
* * * *
2047 CTAAGAATTAAGGAGTAATTTATA-TATTTTTATTGGAAGAGTTGGTTTGAAGTGGAAAATTTAA
1 CTAAGAATTAAGGAGAAATTTATACTATTTTTATTGGAAGAGTTGGTTTGAAATGGAAAAATGAA
*
2111 GGACTTG-----CCTCAAAACAATATTCATGGTTGTGGTGGAGCGTTTGGAAC
66 GGACTTGAAATTCCTCAAAACAATATTCATGGTTGTGGTGGAGCCTTTGGAAC
* * *
2159 CTAAGAATTAAGGAGTAATTTATACTATTTTTA-TGGAAGAGTTGGTTTGAAGTGGAAAATTTG-
1 CTAAGAATTAAGGAGAAATTTATACTATTTTTATTGGAAGAGTTGGTTTGAAATGGAAAA-ATGA
*
2222 AGGACTTAAGAAATTCCTCAAAACAATATTCATGGTTGTGGTGGAGCCTTT-GAGAT
65 AGGACTT--GAAATTCCTCAAAACAATATTCATGGTTGTGGTGGAGCCTTTGGA-AC
2278 CTAAGAATTAAGGAGAAATTTATACTATTTTTATTGGAAGAGTTGGTTTGAAATGGAAAAATGAA
1 CTAAGAATTAAGGAGAAATTTATACTATTTTTATTGGAAGAGTTGGTTTGAAATGGAAAAATGAA
2343 GGACTTGAAATTCCTCAAAACAATATTCATGGTTGTGGTGGA
66 GGACTTGAAATTCCTCAAAACAATATTCATGGTTGTGGTGGA
2385 TATTCTTCCA
Statistics
Matches: 208, Mismatches: 6, Indels: 18
0.90 0.03 0.08
Matches are distributed among these distances:
112 57 0.27
113 10 0.05
114 1 0.00
118 38 0.18
119 70 0.34
120 32 0.15
ACGTcount: A:0.34, C:0.08, G:0.24, T:0.34
Consensus pattern (118 bp):
CTAAGAATTAAGGAGAAATTTATACTATTTTTATTGGAAGAGTTGGTTTGAAATGGAAAAATGAA
GGACTTGAAATTCCTCAAAACAATATTCATGGTTGTGGTGGAGCCTTTGGAAC
Found at i:2689 original size:105 final size:105
Alignment explanation
Indices: 2569--2778 Score: 357
Period size: 105 Copynumber: 2.0 Consensus size: 105
2559 ATAAAAAATT
* *
2569 TAATGACTAAAAAGAATATTAATTAAAAAATTATTATACTATAATACTGAGAAAATTTTAGAAAT
1 TAATGACTAAAAAGAATATTAATTAAAAAATTATTATACTATAACACTAAGAAAATTTTAGAAAT
*
2634 TTCCCAATTAAGATTTTTGAGTTCGTGATTTTATATAGTA
66 TTCCCAATTAAAATTTTTGAGTTCGTGATTTTATATAGTA
* * *
2674 TAATGACTAATAAGAATATTAATTAAAAAATTATTATACTATAACACTAAGGATATTTTAGAAAT
1 TAATGACTAAAAAGAATATTAATTAAAAAATTATTATACTATAACACTAAGAAAATTTTAGAAAT
*
2739 TTCCCAATTAAAATTTTTTAGTTCGTGATTTTATATAGTA
66 TTCCCAATTAAAATTTTTGAGTTCGTGATTTTATATAGTA
2779 GTAAGATAGT
Statistics
Matches: 98, Mismatches: 7, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
105 98 1.00
ACGTcount: A:0.43, C:0.07, G:0.10, T:0.40
Consensus pattern (105 bp):
TAATGACTAAAAAGAATATTAATTAAAAAATTATTATACTATAACACTAAGAAAATTTTAGAAAT
TTCCCAATTAAAATTTTTGAGTTCGTGATTTTATATAGTA
Found at i:4407 original size:21 final size:21
Alignment explanation
Indices: 4383--4425 Score: 77
Period size: 21 Copynumber: 2.0 Consensus size: 21
4373 AAGTATTAAG
*
4383 AATTTAGCTCCTCATGGATTT
1 AATTTAACTCCTCATGGATTT
4404 AATTTAACTCCTCATGGATTT
1 AATTTAACTCCTCATGGATTT
4425 A
1 A
4426 GTAAAATCCA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.28, C:0.19, G:0.12, T:0.42
Consensus pattern (21 bp):
AATTTAACTCCTCATGGATTT
Found at i:6143 original size:17 final size:18
Alignment explanation
Indices: 6110--6145 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
6100 CTCCTCTTGC
*
6110 ATGAAAACACTTCTTTTT
1 ATGAAAACAATTCTTTTT
6128 ATGAAAACAATT-TTTTT
1 ATGAAAACAATTCTTTTT
6145 A
1 A
6146 ACTACCCTTC
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
17 6 0.35
18 11 0.65
ACGTcount: A:0.39, C:0.11, G:0.06, T:0.44
Consensus pattern (18 bp):
ATGAAAACAATTCTTTTT
Found at i:15922 original size:19 final size:19
Alignment explanation
Indices: 15894--15947 Score: 101
Period size: 19 Copynumber: 2.9 Consensus size: 19
15884 CCATTTGGGT
15894 TTAA-GAGAGAATCAAGCA
1 TTAATGAGAGAATCAAGCA
15912 TTAATGAGAGAATCAAGCA
1 TTAATGAGAGAATCAAGCA
15931 TTAATGAGAGAATCAAG
1 TTAATGAGAGAATCAAG
15948 GAAGATTACA
Statistics
Matches: 35, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
18 4 0.11
19 31 0.89
ACGTcount: A:0.48, C:0.09, G:0.22, T:0.20
Consensus pattern (19 bp):
TTAATGAGAGAATCAAGCA
Found at i:17153 original size:30 final size:30
Alignment explanation
Indices: 17117--17518 Score: 428
Period size: 30 Copynumber: 13.2 Consensus size: 30
17107 ATTTATTCTA
* *
17117 CTTACAAATGACACCAGAAGTTGTCATGGT
1 CTTACAATTGACACCAGAAGTTGTCATGAT
*
17147 CTTACAATTGACACCAGAAGTTGTCATGGT
1 CTTACAATTGACACCAGAAGTTGTCATGAT
* *
17177 CTTACAAATGACACCAGAAGTTGTCATGGT
1 CTTACAATTGACACCAGAAGTTGTCATGAT
* *
17207 CTTGCAATTGACACCAGAAGTTGTCATGCT
1 CTTACAATTGACACCAGAAGTTGTCATGAT
* *
17237 CTTGCAATTGACACCAGAAGTTGCCATGAT
1 CTTACAATTGACACCAGAAGTTGTCATGAT
* *
17267 GTTTCAATTGACACCAGAAGTTGTCATGAT
1 CTTACAATTGACACCAGAAGTTGTCATGAT
* *
17297 GTTTCAATTGACACCAGAAGTTGTCATGAT
1 CTTACAATTGACACCAGAAGTTGTCATGAT
* *
17327 GTTGCAATTGACACCAGAAGTTGTCATGAT
1 CTTACAATTGACACCAGAAGTTGTCATGAT
* *
17357 CTTGCAATTGACACCATAAGTTGTCATGAT
1 CTTACAATTGACACCAGAAGTTGTCATGAT
* ** * *
17387 C-TAGCAATTGATACTTGAAGATGTCATAAT
1 CTTA-CAATTGACACCAGAAGTTGTCATGAT
*
17417 TTTATTCAATTGACACCAGAAGTTGTCATGAT
1 CTTA--CAATTGACACCAGAAGTTGTCATGAT
* * * *** * *
17449 AAATTTCCAATAGACATTTGAAGATGTCATAAT
1 ---CTTACAATTGACACCAGAAGTTGTCATGAT
*
17482 TTTATTCAATTGACACCAGAAGTTGTCATGAT
1 CTTA--CAATTGACACCAGAAGTTGTCATGAT
*
17514 TTTAC
1 CTTAC
17519 CTTTCAAAAT
Statistics
Matches: 323, Mismatches: 41, Indels: 16
0.85 0.11 0.04
Matches are distributed among these distances:
29 1 0.00
30 252 0.78
31 2 0.01
32 45 0.14
33 20 0.06
35 3 0.01
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32
Consensus pattern (30 bp):
CTTACAATTGACACCAGAAGTTGTCATGAT
Found at i:23402 original size:21 final size:21
Alignment explanation
Indices: 23377--23489 Score: 100
Period size: 19 Copynumber: 5.7 Consensus size: 21
23367 ACAGAGAGAA
23377 TTCATACCCAAAGAAAACACA-
1 TTCATACCCAAA-AAAACACAG
* *
23398 TTCATA-CGAAAAAAATACAG
1 TTCATACCCAAAAAAACACAG
*
23418 TTCATACCAAAAAAAAACACAG
1 TTCATACC-CAAAAAAACACAG
*
23440 TTCATACCC--AAAAA-ATAG
1 TTCATACCCAAAAAAACACAG
23458 TTCATA-CC--AAAAACAGCAG
1 TTCATACCCAAAAAAACA-CAG
23477 TTCATA-CCAAAAA
1 TTCATACCCAAAAA
23490 GTTTATACCA
Statistics
Matches: 78, Mismatches: 7, Indels: 14
0.79 0.07 0.14
Matches are distributed among these distances:
17 7 0.09
18 10 0.13
19 22 0.28
20 10 0.13
21 10 0.13
22 19 0.24
ACGTcount: A:0.53, C:0.23, G:0.06, T:0.18
Consensus pattern (21 bp):
TTCATACCCAAAAAAACACAG
Found at i:23424 original size:41 final size:40
Alignment explanation
Indices: 23377--23489 Score: 128
Period size: 41 Copynumber: 2.9 Consensus size: 40
23367 ACAGAGAGAA
* * *
23377 TTCATACCCAAAGAAAACACA-TTCATACGAAAAAAATACAG
1 TTCATACCAAAAAAAAACACAGTTCATACCAAAAAAAT--AG
*
23418 TTCATACCAAAAAAAAACACAGTTCATACCCAAAAAATAG
1 TTCATACCAAAAAAAAACACAGTTCATACCAAAAAAATAG
23458 TTCATACC----AAAAACAGCAGTTCATACCAAAAA
1 TTCATACCAAAAAAAAACA-CAGTTCATACCAAAAA
23490 GTTTATACCA
Statistics
Matches: 65, Mismatches: 5, Indels: 8
0.83 0.06 0.10
Matches are distributed among these distances:
36 7 0.11
37 15 0.23
40 10 0.15
41 19 0.29
42 14 0.22
ACGTcount: A:0.53, C:0.23, G:0.06, T:0.18
Consensus pattern (40 bp):
TTCATACCAAAAAAAAACACAGTTCATACCAAAAAAATAG
Found at i:23429 original size:19 final size:19
Alignment explanation
Indices: 23407--23489 Score: 82
Period size: 22 Copynumber: 4.3 Consensus size: 19
23397 ATTCATACGA
23407 AAAAAATACAGTTCATACC
1 AAAAAATACAGTTCATACC
*
23426 AAAAAAAAACACAGTTCATACCC
1 ---AAAAAATACAGTTCATA-CC
23449 AAAAAAT--AGTTCATACC
1 AAAAAATACAGTTCATACC
*
23466 AAAAACA-GCAGTTCATACC
1 AAAAA-ATACAGTTCATACC
23485 AAAAA
1 AAAAA
23490 GTTTATACCA
Statistics
Matches: 55, Mismatches: 2, Indels: 11
0.81 0.03 0.16
Matches are distributed among these distances:
17 7 0.13
18 9 0.16
19 15 0.27
20 6 0.11
22 16 0.29
23 2 0.04
ACGTcount: A:0.55, C:0.22, G:0.06, T:0.17
Consensus pattern (19 bp):
AAAAAATACAGTTCATACC
Found at i:29251 original size:22 final size:22
Alignment explanation
Indices: 29226--29268 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 22
29216 AAAACCTGTA
29226 AACAGAGTTCCT-TTAACCCATC
1 AACAGAGTTCCTATT-ACCCATC
*
29248 AACAGATTTCCTATTACCCAT
1 AACAGAGTTCCTATTACCCAT
29269 AAAACCATGT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
22 17 0.89
23 2 0.11
ACGTcount: A:0.33, C:0.30, G:0.07, T:0.30
Consensus pattern (22 bp):
AACAGAGTTCCTATTACCCATC
Done.