Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01018542.1 Corchorus olitorius cultivar O-4 contig18575, 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: 55546
ACGTcount: A:0.31, C:0.19, G:0.18, T:0.32
Found at i:337 original size:24 final size:24
Alignment explanation
Indices: 305--365 Score: 122
Period size: 24 Copynumber: 2.5 Consensus size: 24
295 GATTAAAGTA
305 TTGAAAATTTTCATTTTCAATGGT
1 TTGAAAATTTTCATTTTCAATGGT
329 TTGAAAATTTTCATTTTCAATGGT
1 TTGAAAATTTTCATTTTCAATGGT
353 TTGAAAATTTTCA
1 TTGAAAATTTTCA
366 ATGCTTTTTC
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 37 1.00
ACGTcount: A:0.31, C:0.08, G:0.11, T:0.49
Consensus pattern (24 bp):
TTGAAAATTTTCATTTTCAATGGT
Found at i:1775 original size:41 final size:41
Alignment explanation
Indices: 1717--2021 Score: 240
Period size: 41 Copynumber: 7.2 Consensus size: 41
1707 CATATGTTAA
1717 GCAACGACTAACAAAAGTCGTTGCGAAAAGTTTAAGATTTC
1 GCAACGACTAACAAAAGTCGTTGCGAAAAGTTTAAGATTTC
* *
1758 GCAACGACTAACGAAAGTCGTTGCGAGAAGTTTAAGATTTC
1 GCAACGACTAACAAAAGTCGTTGCGAAAAGTTTAAGATTTC
* *
1799 GCAACGACTAACAAAAGTCGCTGCGGAAAGTTTAAGATTTC
1 GCAACGACTAACAAAAGTCGTTGCGAAAAGTTTAAGATTTC
* *** * * * *
1840 GCAACGACTTA-ATCTGTCGTTTC-AAAAGTAATTATGTTTTTT
1 GCAACGACTAACAAAAGTCGTTGCGAAAAGT--TTAAG-ATTTC
* * * ** * * * *
1882 GTAGCGATTTTC-AAGGTCGCTGCGAAAATCAATTAGTAACGTATATTAA
1 GCAACGACTAACAAAAGTCGTTGCG-AAA--AGTT--TAA-G-AT-TT-C
1931 GCAAC-ACCTAACAAAAGTCGTTGCGAAAAGTTTAAGATTTC
1 GCAACGA-CTAACAAAAGTCGTTGCGAAAAGTTTAAGATTTC
* * * *
1972 GCAATGACTAACAAAATTCGCTGCGGAAAGTTTAAGATTTC
1 GCAACGACTAACAAAAGTCGTTGCGAAAAGTTTAAGATTTC
2013 GCAACGACT
1 GCAACGACT
2022 TAATCTGTCG
Statistics
Matches: 205, Mismatches: 43, Indels: 32
0.73 0.15 0.11
Matches are distributed among these distances:
39 5 0.02
40 7 0.03
41 133 0.65
42 19 0.09
43 2 0.01
44 5 0.02
45 3 0.01
46 4 0.02
47 6 0.03
48 3 0.01
49 8 0.04
50 10 0.05
ACGTcount: A:0.35, C:0.17, G:0.20, T:0.28
Consensus pattern (41 bp):
GCAACGACTAACAAAAGTCGTTGCGAAAAGTTTAAGATTTC
Found at i:2192 original size:173 final size:173
Alignment explanation
Indices: 1758--2164 Score: 645
Period size: 173 Copynumber: 2.4 Consensus size: 173
1748 TTAAGATTTC
*
1758 GCAACGACTAACGAAAGTCGTTGCGAGAAGTTTAAGATTTCGCAACGACTAACAAAAGTCGCTGC
1 GCAACGACTAACAAAAGTCGTTGCGAGAAGTTTAAGATTTCGCAACGACTAACAAAAGTCGCTGC
* *
1823 GGAAAGTTTAAGATTTCGCAACGACTTAATCTGTCGTTTCAAAAGTAATTATGTTTTTTGTAGCG
66 GGAAAGTTTAAGATTTCGCAACGACTTAATCTGTCGTTTCAAAAATAATCATGTTTTTTGTAGCG
* * *
1888 ATTTTCAAGGTCGCTGCGAAAATCAATTAGTAACGTATATTAA
131 ACTTTCAAGGTCGCTGCGAAAATCAATTAGTAACATATATCAA
* * *
1931 GCAAC-ACCTAACAAAAGTCGTTGCGAAAAGTTTAAGATTTCGCAATGACTAACAAAATTCGCTG
1 GCAACGA-CTAACAAAAGTCGTTGCGAGAAGTTTAAGATTTCGCAACGACTAACAAAAGTCGCTG
1995 CGGAAAGTTTAAGATTTCGCAACGACTTAATCTGTCGTTTCAAAAATAATCATGTTTTTTGTAGC
65 CGGAAAGTTTAAGATTTCGCAACGACTTAATCTGTCGTTTCAAAAATAATCATGTTTTTTGTAGC
*
2060 GACTTTCAAGGTCGTTGCGAAAATCAATTAGTAACATATATCAA
130 GACTTTCAAGGTCGCTGCGAAAATCAATTAGTAACATATATCAA
* ** * * * *
2104 GCAACGACTAACAAAAGTCGTTGTGAGAAGACTATGATTTTGCAACGACTAATAGAAGTCG
1 GCAACGACTAACAAAAGTCGTTGCGAGAAGTTTAAGATTTCGCAACGACTAACAAAAGTCG
2165 TTGTAAAACT
Statistics
Matches: 212, Mismatches: 20, Indels: 4
0.90 0.08 0.02
Matches are distributed among these distances:
172 1 0.00
173 210 0.99
174 1 0.00
ACGTcount: A:0.35, C:0.17, G:0.19, T:0.29
Consensus pattern (173 bp):
GCAACGACTAACAAAAGTCGTTGCGAGAAGTTTAAGATTTCGCAACGACTAACAAAAGTCGCTGC
GGAAAGTTTAAGATTTCGCAACGACTTAATCTGTCGTTTCAAAAATAATCATGTTTTTTGTAGCG
ACTTTCAAGGTCGCTGCGAAAATCAATTAGTAACATATATCAA
Found at i:20502 original size:39 final size:40
Alignment explanation
Indices: 20446--20526 Score: 137
Period size: 39 Copynumber: 2.0 Consensus size: 40
20436 TTTAATTCCT
20446 ATGTAATATATATAATAACTAAAATACTTACATTAATTAA
1 ATGTAATATATATAATAACTAAAATACTTACATTAATTAA
* *
20486 ATGTAATA-CTATAATAACTGAAATACTTACATTAATTAA
1 ATGTAATATATATAATAACTAAAATACTTACATTAATTAA
20525 AT
1 AT
20527 TCTTAGATAT
Statistics
Matches: 39, Mismatches: 2, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
39 31 0.79
40 8 0.21
ACGTcount: A:0.51, C:0.09, G:0.04, T:0.37
Consensus pattern (40 bp):
ATGTAATATATATAATAACTAAAATACTTACATTAATTAA
Found at i:20553 original size:25 final size:24
Alignment explanation
Indices: 20517--20563 Score: 76
Period size: 25 Copynumber: 1.9 Consensus size: 24
20507 AATACTTACA
20517 TTAATTAAATTCTTAGATATTTTT
1 TTAATTAAATTCTTAGATATTTTT
*
20541 TTAATTCAAATTCTTAGGTATTT
1 TTAATT-AAATTCTTAGATATTT
20564 GTGCAAACGT
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
24 6 0.29
25 15 0.71
ACGTcount: A:0.32, C:0.06, G:0.06, T:0.55
Consensus pattern (24 bp):
TTAATTAAATTCTTAGATATTTTT
Found at i:21138 original size:204 final size:204
Alignment explanation
Indices: 20661--21232 Score: 1046
Period size: 205 Copynumber: 2.8 Consensus size: 204
20651 TCTTAATATC
* *
20661 TTTTGAAATTTTGTTTGACATTGATC---CTTAATTTAATAAATCAACCAGTAATGTTCAACTAA
1 TTTTGAAATTTTGTTTGACATTGATCTAATTTAATTTAATAAATCAACCACTAATGTTCAACTAA
20723 TTTTTTTTGGTATAGTTCTATATATATAATAGTAATGTGTTGTATCTTATTCACTACAACTTTGT
66 TTTTTTTTGGTATAGTTCTATATATATAATAGTAATGTGTTGTATCTTATTCACTACAACTTTGT
20788 TAGTAATCTTAGACTTAAAAAATTAATAACATTCACCATTGATAAATAAATCGGATCTTTAATAT
131 TAGTAATCTTAGACTTAAAAAATTAATAACATTCACCATTGATAAATAAATCGGATCTTTAATAT
20853 CTTTTATAA
196 CTTTTATAA
20862 TTTTGAAATTTTGTTTGACATTGATCTAATTTAATTTAATAAATCAACCACTAATGTTCAACTAA
1 TTTTGAAATTTTGTTTGACATTGATCTAATTTAATTTAATAAATCAACCACTAATGTTCAACTAA
20927 TTTTTTTTGGTATAGTTCTATATATATAATAGTAATGTGTTGTATCTTATTCACTACAACTTTGT
66 TTTTTTTTGGTATAGTTCTATATATATAATAGTAATGTGTTGTATCTTATTCACTACAACTTTGT
*
20992 TAGTAATCCTTAGACTTAAAAAATTAATAACATTTACCATTGATAAATAAATCGGATCTTTAATA
131 TAGTAAT-CTTAGACTTAAAAAATTAATAACATTCACCATTGATAAATAAATCGGATCTTTAATA
21057 TCTTTTATAA
195 TCTTTTATAA
*
21067 TTTTGAAATTTTGTTTGACATTGATCTAATTTAATTTAATAAATCAACCACTAATGTTCAACTAC
1 TTTTGAAATTTTGTTTGACATTGATCTAATTTAATTTAATAAATCAACCACTAATGTTCAACTAA
* *
21132 TTTTTTTTTGTATAGTT-T-TATATATAATAATAATGTGTTGTATCTTATTCACTACAACTTTGT
66 TTTTTTTTGGTATAGTTCTATATATATAATAGTAATGTGTTGTATCTTATTCACTACAACTTTGT
21195 TAGTAATCTTAGACTTAAAAAATTAATAACATTCACCA
131 TAGTAATCTTAGACTTAAAAAATTAATAACATTCACCA
21233 AAGTTATTAA
Statistics
Matches: 360, Mismatches: 7, Indels: 7
0.96 0.02 0.02
Matches are distributed among these distances:
201 26 0.07
202 30 0.08
203 51 0.14
204 107 0.30
205 146 0.41
ACGTcount: A:0.35, C:0.12, G:0.09, T:0.44
Consensus pattern (204 bp):
TTTTGAAATTTTGTTTGACATTGATCTAATTTAATTTAATAAATCAACCACTAATGTTCAACTAA
TTTTTTTTGGTATAGTTCTATATATATAATAGTAATGTGTTGTATCTTATTCACTACAACTTTGT
TAGTAATCTTAGACTTAAAAAATTAATAACATTCACCATTGATAAATAAATCGGATCTTTAATAT
CTTTTATAA
Found at i:25546 original size:19 final size:18
Alignment explanation
Indices: 25522--25557 Score: 54
Period size: 19 Copynumber: 1.9 Consensus size: 18
25512 TGAAGACTTA
25522 TTGAAGACAATTTGAAGAT
1 TTGAAGACAA-TTGAAGAT
*
25541 TTGAAGACCATTGAAGA
1 TTGAAGACAATTGAAGA
25558 ATAATTTCAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 7 0.44
19 9 0.56
ACGTcount: A:0.42, C:0.08, G:0.22, T:0.28
Consensus pattern (18 bp):
TTGAAGACAATTGAAGAT
Found at i:25564 original size:30 final size:30
Alignment explanation
Indices: 25510--25569 Score: 77
Period size: 30 Copynumber: 2.0 Consensus size: 30
25500 GAAGTTCGTG
* *
25510 TTTGAAGACTTATTGAAGACAATTTGAAGA
1 TTTGAAGACTCATTGAAGACAATTTCAAGA
*
25540 TTTGAAGAC-CATTGAAGAATAATTTCAAGA
1 TTTGAAGACTCATTGAAG-ACAATTTCAAGA
25570 GCAAGAATTG
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
29 7 0.27
30 19 0.73
ACGTcount: A:0.42, C:0.08, G:0.18, T:0.32
Consensus pattern (30 bp):
TTTGAAGACTCATTGAAGACAATTTCAAGA
Found at i:29272 original size:23 final size:23
Alignment explanation
Indices: 29240--29420 Score: 247
Period size: 23 Copynumber: 7.9 Consensus size: 23
29230 CAAATAAGCC
* * *
29240 AAACATCAACATTTTGAACATCA
1 AAACAACAACATTTTCAACAGCA
* * *
29263 AAACAGCAACATTTTGAACAACA
1 AAACAACAACATTTTCAACAGCA
29286 AAACAACAACATTTTCAACAGCA
1 AAACAACAACATTTTCAACAGCA
*
29309 AAACAACAGCATTTTCAACAGCA
1 AAACAACAACATTTTCAACAGCA
* *
29332 AAACATCAACATTTTCAACAGGA
1 AAACAACAACATTTTCAACAGCA
*
29355 CAAACAACAGCATTTTCAACA-CA
1 -AAACAACAACATTTTCAACAGCA
*
29378 AAATAACAACATTTTCAACAGCA
1 AAACAACAACATTTTCAACAGCA
29401 AAACAACAACATTTTCAACA
1 AAACAACAACATTTTCAACA
29421 AAGAAAACAG
Statistics
Matches: 141, Mismatches: 15, Indels: 4
0.88 0.09 0.03
Matches are distributed among these distances:
22 18 0.13
23 105 0.74
24 18 0.13
ACGTcount: A:0.50, C:0.24, G:0.06, T:0.20
Consensus pattern (23 bp):
AAACAACAACATTTTCAACAGCA
Found at i:33661 original size:21 final size:21
Alignment explanation
Indices: 33635--33674 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
33625 GTCAACACAG
33635 GTCCTGGGCAGGAATTGTCAA
1 GTCCTGGGCAGGAATTGTCAA
*
33656 GTCCTGGGCAGGACTTGTC
1 GTCCTGGGCAGGAATTGTC
33675 CTGTTTTTAG
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.17, C:0.23, G:0.35, T:0.25
Consensus pattern (21 bp):
GTCCTGGGCAGGAATTGTCAA
Found at i:36479 original size:12 final size:12
Alignment explanation
Indices: 36462--36486 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
36452 ATGTCCATTC
36462 TTTGCATCATAG
1 TTTGCATCATAG
36474 TTTGCATCATAG
1 TTTGCATCATAG
36486 T
1 T
36487 AGCCAAATCA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.24, C:0.16, G:0.16, T:0.44
Consensus pattern (12 bp):
TTTGCATCATAG
Found at i:38271 original size:21 final size:21
Alignment explanation
Indices: 38247--38286 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
38237 CTCTTGTCAT
* *
38247 TGGACCTAATGGCATCTTTAA
1 TGGACCAAATGACATCTTTAA
*
38268 TGGATCAAATGACATCTTT
1 TGGACCAAATGACATCTTT
38287 GGCATCTCTT
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 16 1.00
ACGTcount: A:0.30, C:0.17, G:0.17, T:0.35
Consensus pattern (21 bp):
TGGACCAAATGACATCTTTAA
Found at i:47571 original size:58 final size:58
Alignment explanation
Indices: 47501--47628 Score: 152
Period size: 58 Copynumber: 2.2 Consensus size: 58
47491 CAAAAATCCA
* * * *
47501 GGGGCACTTTGGTCATTT-TTCATATTCAGTGGCATTATGGTCAGTTT-TGCACACTCAG
1 GGGGCATTTTGGTCATTTCTGCATATCCAGGGGCATTATGGT-AGTTTGTGCACA-TCAG
* * * *
47559 GGGGCATTTTGGTCATTTCTGCATATCCAGGGGCATTTTGGTTGTTTGTGTACATCCG
1 GGGGCATTTTGGTCATTTCTGCATATCCAGGGGCATTATGGTAGTTTGTGCACATCAG
47617 GGGGCATTTTGG
1 GGGGCATTTTGG
47629 AGCATCTTGG
Statistics
Matches: 60, Mismatches: 8, Indels: 4
0.83 0.11 0.06
Matches are distributed among these distances:
58 36 0.60
59 24 0.40
ACGTcount: A:0.16, C:0.17, G:0.29, T:0.38
Consensus pattern (58 bp):
GGGGCATTTTGGTCATTTCTGCATATCCAGGGGCATTATGGTAGTTTGTGCACATCAG
Found at i:47599 original size:29 final size:28
Alignment explanation
Indices: 47471--47628 Score: 122
Period size: 29 Copynumber: 5.5 Consensus size: 28
47461 AGGATCACCT
* *
47471 AGGGGCATTTTAGTCATTTT-CAAAAATCC
1 AGGGGCATTTTGGTCATTTTGC--ACATCC
* * * *
47500 AGGGGCACTTTGGTCATTTTTCATATTC
1 AGGGGCATTTTGGTCATTTTGCACATCC
* *
47528 AGTGGCATTATGGTCAGTTTTGCACA-CTC
1 AGGGGCATTTTGGTCA-TTTTGCACATC-C
*
47557 AGGGGGCATTTTGGTCATTTCTGCATATCC
1 A-GGGGCATTTTGGTCATTT-TGCACATCC
** *
47587 AGGGGCATTTTGGTTGTTTGTGTACATCC
1 AGGGGCATTTTGGTCATTT-TGCACATCC
*
47616 GGGGGCATTTTGG
1 AGGGGCATTTTGG
47629 AGCATCTTGG
Statistics
Matches: 104, Mismatches: 19, Indels: 12
0.77 0.14 0.09
Matches are distributed among these distances:
28 17 0.16
29 65 0.62
30 21 0.20
31 1 0.01
ACGTcount: A:0.19, C:0.17, G:0.27, T:0.37
Consensus pattern (28 bp):
AGGGGCATTTTGGTCATTTTGCACATCC
Done.