Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01011805.1 Corchorus capsularis cultivar CVL-1 contig11826, 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: 69813
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.32
Found at i:2849 original size:22 final size:22
Alignment explanation
Indices: 2821--2864 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 22
2811 GAGATGAGAA
* *
2821 AGTCTTGATCGAAGCCAAGCCT
1 AGTCTTGACCGAAACCAAGCCT
*
2843 AGTCTTGGCCGAAACCAAGCCT
1 AGTCTTGACCGAAACCAAGCCT
2865 GAAGAAGGGG
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.27, C:0.30, G:0.23, T:0.20
Consensus pattern (22 bp):
AGTCTTGACCGAAACCAAGCCT
Found at i:12930 original size:2 final size:2
Alignment explanation
Indices: 12918--12954 Score: 56
Period size: 2 Copynumber: 18.0 Consensus size: 2
12908 ATTCTTAGCC
*
12918 AT AT CAT AT AT AT AT AT AT AT AT AT GT AT AT AT AT AT
1 AT AT -AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
12955 GTAAATATTG
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:0.03, T:0.49
Consensus pattern (2 bp):
AT
Found at i:12955 original size:12 final size:12
Alignment explanation
Indices: 12923--12962 Score: 62
Period size: 12 Copynumber: 3.3 Consensus size: 12
12913 TAGCCATATC
*
12923 ATATATATATAT
1 ATATATATGTAT
12935 ATATATATGTAT
1 ATATATATGTAT
*
12947 ATATATATGTAA
1 ATATATATGTAT
12959 ATAT
1 ATAT
12963 TGTAAGATTG
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
12 26 1.00
ACGTcount: A:0.47, C:0.00, G:0.05, T:0.47
Consensus pattern (12 bp):
ATATATATGTAT
Found at i:23788 original size:16 final size:16
Alignment explanation
Indices: 23763--23793 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
23753 CATCAGTTTT
23763 TTTATCCCAAATTCTA
1 TTTATCCCAAATTCTA
*
23779 TTTATTCCAAATTCT
1 TTTATCCCAAATTCT
23794 GCAAAGTCTC
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.29, C:0.23, G:0.00, T:0.48
Consensus pattern (16 bp):
TTTATCCCAAATTCTA
Found at i:24728 original size:31 final size:31
Alignment explanation
Indices: 24666--24729 Score: 74
Period size: 31 Copynumber: 2.1 Consensus size: 31
24656 TGTCGTACCA
* * **
24666 AAAATGCCACATGGCAATGATACGTTGGACC
1 AAAATGCCACATGGCAAGGACACGTCAGACC
* *
24697 AAAATGCCACGTGGCAAGGCCACGTCAGACC
1 AAAATGCCACATGGCAAGGACACGTCAGACC
24728 AA
1 AA
24730 TACGTTGACG
Statistics
Matches: 27, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
31 27 1.00
ACGTcount: A:0.36, C:0.27, G:0.23, T:0.14
Consensus pattern (31 bp):
AAAATGCCACATGGCAAGGACACGTCAGACC
Found at i:24840 original size:19 final size:19
Alignment explanation
Indices: 24818--24854 Score: 65
Period size: 19 Copynumber: 1.9 Consensus size: 19
24808 CAAATTAAAG
*
24818 TTCACGAGGCAAAATGTCA
1 TTCAAGAGGCAAAATGTCA
24837 TTCAAGAGGCAAAATGTC
1 TTCAAGAGGCAAAATGTC
24855 CCAAATTAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.38, C:0.19, G:0.22, T:0.22
Consensus pattern (19 bp):
TTCAAGAGGCAAAATGTCA
Found at i:24861 original size:48 final size:48
Alignment explanation
Indices: 24806--24928 Score: 246
Period size: 48 Copynumber: 2.6 Consensus size: 48
24796 AAGTTTTTGC
24806 CCCAAATTAAAGTTCACGAGGCAAAATGTCATTCAAGAGGCAAAATGT
1 CCCAAATTAAAGTTCACGAGGCAAAATGTCATTCAAGAGGCAAAATGT
24854 CCCAAATTAAAGTTCACGAGGCAAAATGTCATTCAAGAGGCAAAATGT
1 CCCAAATTAAAGTTCACGAGGCAAAATGTCATTCAAGAGGCAAAATGT
24902 CCCAAATTAAAGTTCACGAGGCAAAAT
1 CCCAAATTAAAGTTCACGAGGCAAAAT
24929 ATCAAAATCA
Statistics
Matches: 75, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
48 75 1.00
ACGTcount: A:0.42, C:0.20, G:0.18, T:0.20
Consensus pattern (48 bp):
CCCAAATTAAAGTTCACGAGGCAAAATGTCATTCAAGAGGCAAAATGT
Found at i:24888 original size:19 final size:19
Alignment explanation
Indices: 24866--24902 Score: 65
Period size: 19 Copynumber: 1.9 Consensus size: 19
24856 CAAATTAAAG
*
24866 TTCACGAGGCAAAATGTCA
1 TTCAAGAGGCAAAATGTCA
24885 TTCAAGAGGCAAAATGTC
1 TTCAAGAGGCAAAATGTC
24903 CCAAATTAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.38, C:0.19, G:0.22, T:0.22
Consensus pattern (19 bp):
TTCAAGAGGCAAAATGTCA
Found at i:27692 original size:13 final size:13
Alignment explanation
Indices: 27674--27702 Score: 58
Period size: 13 Copynumber: 2.2 Consensus size: 13
27664 GGATAGGAAA
27674 TTCAAAAGTACTT
1 TTCAAAAGTACTT
27687 TTCAAAAGTACTT
1 TTCAAAAGTACTT
27700 TTC
1 TTC
27703 GTTTATTTCA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.34, C:0.17, G:0.07, T:0.41
Consensus pattern (13 bp):
TTCAAAAGTACTT
Found at i:33586 original size:6 final size:6
Alignment explanation
Indices: 33575--33614 Score: 62
Period size: 6 Copynumber: 6.7 Consensus size: 6
33565 CTGTCACCAT
* *
33575 CTCTTC CTCTTC CCCTTC CCCTTC CTCTTC CTCTTC CTCT
1 CTCTTC CTCTTC CTCTTC CTCTTC CTCTTC CTCTTC CTCT
33615 ATCACCACCG
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
6 32 1.00
ACGTcount: A:0.00, C:0.55, G:0.00, T:0.45
Consensus pattern (6 bp):
CTCTTC
Found at i:34665 original size:48 final size:48
Alignment explanation
Indices: 34609--34721 Score: 226
Period size: 48 Copynumber: 2.4 Consensus size: 48
34599 CGTCGAATCT
34609 ATAGTGCATGAACAATTTTTTTATATTTTTTCTTTTTGGGGGTTAAAA
1 ATAGTGCATGAACAATTTTTTTATATTTTTTCTTTTTGGGGGTTAAAA
34657 ATAGTGCATGAACAATTTTTTTATATTTTTTCTTTTTGGGGGTTAAAA
1 ATAGTGCATGAACAATTTTTTTATATTTTTTCTTTTTGGGGGTTAAAA
34705 ATAGTGCATGAACAATT
1 ATAGTGCATGAACAATT
34722 GCACATTATG
Statistics
Matches: 65, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
48 65 1.00
ACGTcount: A:0.29, C:0.07, G:0.17, T:0.47
Consensus pattern (48 bp):
ATAGTGCATGAACAATTTTTTTATATTTTTTCTTTTTGGGGGTTAAAA
Found at i:43162 original size:35 final size:35
Alignment explanation
Indices: 43122--43197 Score: 109
Period size: 35 Copynumber: 2.2 Consensus size: 35
43112 TGAGCAAACC
* *
43122 AAAGTCACTAAATTTGCATGAGCAT-TTCTTTCATT
1 AAAGTCACTAAATTTGCATAAACATATT-TTTCATT
43157 AAAGTCACTAAATTTGCATAAACATATTTTTCATT
1 AAAGTCACTAAATTTGCATAAACATATTTTTCATT
*
43192 TAAGTC
1 AAAGTC
43198 TATGCTTGAG
Statistics
Matches: 37, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
35 35 0.95
36 2 0.05
ACGTcount: A:0.36, C:0.16, G:0.09, T:0.39
Consensus pattern (35 bp):
AAAGTCACTAAATTTGCATAAACATATTTTTCATT
Found at i:45836 original size:1 final size:1
Alignment explanation
Indices: 45830--45854 Score: 50
Period size: 1 Copynumber: 25.0 Consensus size: 1
45820 CGTCTTTGGG
45830 TTTTTTTTTTTTTTTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTT
45855 AAACGTTTTG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 24 1.00
ACGTcount: A:0.00, C:0.00, G:0.00, T:1.00
Consensus pattern (1 bp):
T
Found at i:51194 original size:66 final size:66
Alignment explanation
Indices: 51085--51216 Score: 237
Period size: 66 Copynumber: 2.0 Consensus size: 66
51075 GAAATCTATA
* *
51085 ACACCCGAATTGTTAGTTCAACTGGTAGATACACCGTGTCTGGAACGTGAGGTCCTGGGTTTAAT
1 ACACCCGAATTGTTAGCTCAACTGGTAGATACACCGTGCCTGGAACGTGAGGTCCTGGGTTTAAT
51150 C
66 C
*
51151 ACACCCGAATTGTTAGCTCAACTGGTAGATGCACCGTGCCTGGAACGTGAGGTCCTGGGTTTAAT
1 ACACCCGAATTGTTAGCTCAACTGGTAGATACACCGTGCCTGGAACGTGAGGTCCTGGGTTTAAT
51216 C
66 C
51217 TCATGGAATG
Statistics
Matches: 63, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
66 63 1.00
ACGTcount: A:0.23, C:0.23, G:0.27, T:0.27
Consensus pattern (66 bp):
ACACCCGAATTGTTAGCTCAACTGGTAGATACACCGTGCCTGGAACGTGAGGTCCTGGGTTTAAT
C
Found at i:55609 original size:13 final size:14
Alignment explanation
Indices: 55577--55611 Score: 61
Period size: 14 Copynumber: 2.4 Consensus size: 14
55567 ACAAGGTTAA
55577 AAAAATAAAATTACT
1 AAAAA-AAAATTACT
55592 AAAAAAAAATTACT
1 AAAAAAAAATTACT
55606 AAAAAA
1 AAAAAA
55612 GGTGATTATA
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
14 15 0.75
15 5 0.25
ACGTcount: A:0.74, C:0.06, G:0.00, T:0.20
Consensus pattern (14 bp):
AAAAAAAAATTACT
Found at i:55610 original size:15 final size:16
Alignment explanation
Indices: 55576--55611 Score: 58
Period size: 15 Copynumber: 2.4 Consensus size: 16
55566 TACAAGGTTA
55576 AAAAAATAAAATTACT
1 AAAAAATAAAATTACT
55592 -AAAAA-AAAATTACT
1 AAAAAATAAAATTACT
55606 AAAAAA
1 AAAAAA
55612 GGTGATTATA
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
14 9 0.47
15 10 0.53
ACGTcount: A:0.75, C:0.06, G:0.00, T:0.19
Consensus pattern (16 bp):
AAAAAATAAAATTACT
Found at i:57295 original size:26 final size:26
Alignment explanation
Indices: 57259--57311 Score: 106
Period size: 26 Copynumber: 2.0 Consensus size: 26
57249 AATTATTTGC
57259 CATAGATTAATGTAACATTGGGTTGG
1 CATAGATTAATGTAACATTGGGTTGG
57285 CATAGATTAATGTAACATTGGGTTGG
1 CATAGATTAATGTAACATTGGGTTGG
57311 C
1 C
57312 TCATTTTTGT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 27 1.00
ACGTcount: A:0.30, C:0.09, G:0.26, T:0.34
Consensus pattern (26 bp):
CATAGATTAATGTAACATTGGGTTGG
Found at i:60496 original size:7 final size:7
Alignment explanation
Indices: 60484--60513 Score: 60
Period size: 7 Copynumber: 4.3 Consensus size: 7
60474 TTTCACTTGG
60484 TTGAAAC
1 TTGAAAC
60491 TTGAAAC
1 TTGAAAC
60498 TTGAAAC
1 TTGAAAC
60505 TTGAAAC
1 TTGAAAC
60512 TT
1 TT
60514 TGTAACTAAT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 23 1.00
ACGTcount: A:0.40, C:0.13, G:0.13, T:0.33
Consensus pattern (7 bp):
TTGAAAC
Found at i:68905 original size:109 final size:109
Alignment explanation
Indices: 68709--69004 Score: 441
Period size: 109 Copynumber: 2.7 Consensus size: 109
68699 ACTATTATAG
* *
68709 TTTTATTCTACTAGAAACTCTATTTTTATTCAATTAAATTAAATCTAATATCTTTATAATTACTT
1 TTTTATTCTACTAAAAACTCTA---TT-TTC-ATTTAATTAAATCTAATATCTTTATAATTACTT
*
68774 TATTTTTACCAAAAAATTTGGATATACTAAAATTTTTTCTAATATACAA
61 TATTTTTACCAAAAAAATTGGATATACTAAAATTTTTTCTAATATACAA
68823 TTTTATTCTACTAAAAACTCTATTTTCATTTAATTAAATCTAATATCTTTATAATTACTTTATTT
1 TTTTATTCTACTAAAAACTCTATTTTCATTTAATTAAATCTAATATCTTTATAATTACTTTATTT
* *
68888 TTACCAAAAAAATTGGATATATTAAAATTTTTTCTAATATATAA
66 TTACCAAAAAAATTGGATATACTAAAATTTTTTCTAATATACAA
* **
68932 TTTTATTCTACTAAAAACTCTATTTTCATTTAATTAAAT-TCAATATTTTATATATATTTTTTTA
1 TTTTATTCTACTAAAAACTCTATTTTCATTTAATTAAATCT-AATATCTT-TATA-ATTACTTTA
68996 TTTTTACCA
63 TTTTTACCA
69005 TTTTAATTTA
Statistics
Matches: 171, Mismatches: 8, Indels: 9
0.91 0.04 0.05
Matches are distributed among these distances:
108 1 0.01
109 124 0.73
110 7 0.04
111 18 0.11
114 21 0.12
ACGTcount: A:0.38, C:0.11, G:0.02, T:0.50
Consensus pattern (109 bp):
TTTTATTCTACTAAAAACTCTATTTTCATTTAATTAAATCTAATATCTTTATAATTACTTTATTT
TTACCAAAAAAATTGGATATACTAAAATTTTTTCTAATATACAA
Done.