Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01011942.1 Corchorus olitorius cultivar O-4 contig11975, 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: 24778
ACGTcount: A:0.32, C:0.17, G:0.16, T:0.34
Found at i:4136 original size:90 final size:89
Alignment explanation
Indices: 3983--4258 Score: 347
Period size: 90 Copynumber: 3.1 Consensus size: 89
3973 AGGTGATTTT
* * * * * *
3983 CTTAAACAAGAAACTGAGCTTCGAAAGGCAGAGGATGATAAAATGGAACAAGCTGCATCTGAAGA
1 CTTAAACAAGAAACTGAGGTTGGAAACGCAGAGGGTGATAAAA-GGAACAAACTGCGTCTGAAGA
* *
4048 GTTATTAGATTCTGGCAGTTCAGAG
65 GTTACTAGATTCTGGCAGTCCAGAG
* * *
4073 CTTAAACAAGAAAGTGAGGTTGGAAACACAGAGGGTGGTACAAAGGAACAAACTGCGTCTGAAGA
1 CTTAAACAAGAAACTGAGGTTGGAAACGCAGAGGGTGATA-AAAGGAACAAACTGCGTCTGAAGA
*
4138 GTTACTAGATTCTGACA-TCCCAGAG
65 GTTACTAGATTCTGGCAGT-CCAGAG
* * * *
4163 ATTAAACAAGAAACCGAGGTTGGAAATGCAGAGGGTGATAAAAAGGAACAAACTGTGTCTGAAGA
1 CTTAAACAAGAAACTGAGGTTGGAAACGCAGAGGGTGAT-AAAAGGAACAAACTGCGTCTGAAGA
* *
4228 GTTACTAGATTCTGGAAGGCCAGAG
65 GTTACTAGATTCTGGCAGTCCAGAG
4253 CTTAAA
1 CTTAAA
4259 GCTGAGCACT
Statistics
Matches: 159, Mismatches: 23, Indels: 8
0.84 0.12 0.04
Matches are distributed among these distances:
89 1 0.01
90 154 0.97
91 4 0.03
ACGTcount: A:0.39, C:0.14, G:0.26, T:0.20
Consensus pattern (89 bp):
CTTAAACAAGAAACTGAGGTTGGAAACGCAGAGGGTGATAAAAGGAACAAACTGCGTCTGAAGAG
TTACTAGATTCTGGCAGTCCAGAG
Found at i:9353 original size:41 final size:41
Alignment explanation
Indices: 9301--9379 Score: 149
Period size: 41 Copynumber: 1.9 Consensus size: 41
9291 ACTTGTTAAA
*
9301 TACTTTAATTACTAAATTTCATTTTACCATTTTACTCTTTT
1 TACTTTAATTACCAAATTTCATTTTACCATTTTACTCTTTT
9342 TACTTTAATTACCAAATTTCATTTTACCATTTTACTCT
1 TACTTTAATTACCAAATTTCATTTTACCATTTTACTCT
9380 AATTACCAAA
Statistics
Matches: 37, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
41 37 1.00
ACGTcount: A:0.28, C:0.19, G:0.00, T:0.53
Consensus pattern (41 bp):
TACTTTAATTACCAAATTTCATTTTACCATTTTACTCTTTT
Found at i:9440 original size:101 final size:98
Alignment explanation
Indices: 9328--10029 Score: 825
Period size: 101 Copynumber: 6.8 Consensus size: 98
9318 TTCATTTTAC
* * * ** *
9328 CATTTTACTCTTTTTACTTTAATTACCAAATTTCATTTTACCATTT-TACTCTAATTACCAAATT
1 CATTTTAC-CATTTTACTCTAATTACCAAATTCCATTTTACTTTTTATACTTTAATTACCAAATT
*
9392 CCATTTTTACT-TTTTAAATACTTTAATTACCAAATTC
65 CCA-TTTTACTCTTTT---TACTTTAATTACCAAATTT
* * *
9429 CATTTTACTCTTTTTACTTTAATTACCAAATCCCATTTTACTCTTTTTAAATACTTTAATTACCA
1 CATTTTAC-CATTTTACTCTAATTACCAAATTCCATTTTA--CTTTTT--ATACTTTAATTACC-
9494 AATTTCATTTTACCATTTTACTCTTTTTACTTTAATTACCAAATTT
60 AA----A--TT-CCATTTTACTCTTTTTACTTTAATTACCAAATTT
* * *
9540 CAGTTTACCATTTTACTCTAATTACCAAATTCCCTTTTTACTTTTTAAATACTTTAATTACCAAG
1 CATTTTACCATTTTACTCTAATTACCAAATT-CCATTTTACTTTTT--ATACTTTAATTACCAAA
9605 TTCCATTTTACTCTTTTTACTTTAATTACCAAATTT
63 TTCCATTTTACTCTTTTTACTTTAATTACCAAATTT
* *
9641 CATTTTACCATTTTACTCTAATTACCAAATTCCCTTTTTACTTTTTAAATACTTTAATTACCAAG
1 CATTTTACCATTTTACTCTAATTACCAAATT-CCATTTTACTTTTT--ATACTTTAATTACCAAA
9706 TTCCATTTTACTCTTTTTACTTTAATTACCAAATTT
63 TTCCATTTTACTCTTTTTACTTTAATTACCAAATTT
*
9742 CATTTTAACATTTTACTCTAATTACCAAATTCCATTTTTACTTTTTAAATACTTTAATTACCAAA
1 CATTTTACCATTTTACTCTAATTACCAAATTCCA-TTTTACTTTTT--ATACTTTAATTACCAAA
9807 TTCCATTTTACTCTTTTTACTTTAATTACCAAATTT
63 TTCCATTTTACTCTTTTTACTTTAATTACCAAATTT
9843 CATTTTACCATTTTACTCTAATTACCAAATTCCATTTTTACTTTTTAAATACTTTAATTACCAAA
1 CATTTTACCATTTTACTCTAATTACCAAATTCCA-TTTTACTTTTT--ATACTTTAATTACCAAA
**
9908 TTCCATTTTACTCTTTTTACTTTAATTACCAAATCC
63 TTCCATTTTACTCTTTTTACTTTAATTACCAAATTT
* * *** *
9944 CATTTTACTCTTTTTAAATACTTTAATTACCAAATTTTGTTTTACTCTTCTT-TACTTTAATTGC
1 CATTTTAC-C-ATTT---TACTCTAATTACCAAATTCCATTTTACT-TT-TTATACTTTAATTAC
10008 CAAATTCCATTTTTACTCTTTT
59 CAAATTCCA-TTTTACTCTTTT
10030 ATGATTCTAT
Statistics
Matches: 552, Mismatches: 25, Indels: 44
0.89 0.04 0.07
Matches are distributed among these distances:
100 2 0.00
101 373 0.68
102 3 0.01
103 7 0.01
104 20 0.04
105 19 0.03
106 31 0.06
107 4 0.01
108 2 0.00
109 22 0.04
110 20 0.04
111 33 0.06
113 9 0.02
114 7 0.01
ACGTcount: A:0.29, C:0.20, G:0.01, T:0.50
Consensus pattern (98 bp):
CATTTTACCATTTTACTCTAATTACCAAATTCCATTTTACTTTTTATACTTTAATTACCAAATTC
CATTTTACTCTTTTTACTTTAATTACCAAATTT
Found at i:9483 original size:179 final size:172
Alignment explanation
Indices: 9200--10020 Score: 831
Period size: 179 Copynumber: 4.7 Consensus size: 172
9190 TTTTTTTCTT
* *
9200 TAATTACCAAATGT-CATTTTTTACACTTTTCAGT-CTTTAATTACCAAATACCATTCTTACTCT
1 TAATTACCAAAT-TCCA-TTTTT--ACTTTTTA-TACTTTAATTACCAAATTCCATT-TTACTCT
* * * *
9263 TTTGACTTCAATTACCAAATACCATTTTA-CTTGTTAAATACTTTAATTACTAAATTTCATTTTA
60 TTTTACTTTAATTACCAAATTCCATTTTACCTT-TT---TACTTTAATTACCAAATTTCATTTTA
9327 CCATTTTACTCTTTTTACTTTAATTACCAAATTTCATTTTACCATTTTACTC
121 CCATTTTACTCTTTTTACTTTAATTACCAAATTTCATTTTACCATTTTACTC
9379 TAATTACCAAATTCCATTTTTACTTTTTAAATACTTTAATTACCAAATTCCATTTTACTCTTTTT
1 TAATTACCAAATTCCATTTTTACTTTTT--ATACTTTAATTACCAAATTCCATTTTACTCTTTTT
*
9444 ACTTTAATTACCAAATCCCATTTTACTCTTTTTAAATACTTTAATTACCAAATTTCATTTTACCA
64 ACTTTAATTACCAAATTCCATTTTAC-C-TTTT---TACTTTAATTACCAAATTTCATTTTACCA
*
9509 TTTTACTCTTTTTACTTTAATTACCAAATTTCAGTTTACCATTTTACTC
124 TTTTACTCTTTTTACTTTAATTACCAAATTTCATTTTACCATTTTACTC
* *
9558 TAATTACCAAATTCCCTTTTTACTTTTTAAATACTTTAATTACCAAGTTCCATTTTACTCTTTTT
1 TAATTACCAAATTCCATTTTTACTTTTT--ATACTTTAATTACCAAATTCCATTTTACTCTTTTT
* * * *
9623 ACTTTAATTACCAAATTTCATTTTACCATTTTACTCTAATTACCAAA-TTC------CCTTTTTA
64 ACTTTAATTACCAAATTCCATTTTACCTTTTTACTTTAATTACCAAATTTCATTTTACCATTTTA
* * * *
9681 CT-TTTTAAATACTTTAATTACCAAGTTCCATTTTACTCTTTTTACTT
129 CTCTTTT---TACTTTAATTACCAAATTTCATTTTAC-CATTTTACTC
* * * *
9728 TAATTACCAAATTTCATTTTAAC-ATTT-TACTCTAATTACCAAATTCCATTTTTACT-TTTTAA
1 TAATTACCAAATTCCATTTTTACTTTTTATACTTTAATTACCAAATTCCA-TTTTACTCTTTT--
9790 ATACTTTAATTACCAAATTCCATTTTACTCTTTTTACTTTAATTACCAAATTTCATTTTACCATT
63 -TACTTTAATTACCAAATTCCATTTTAC-CTTTTTACTTTAATTACCAAATTTCATTTTACCATT
** ** ** * * *
9855 TTACTCTAATTAC-CAAATT-CCATTTTTACTTTTTA--A--ATACTT
126 TTACTCTTTTTACTTTAATTACCAAATTT-CATTTTACCATTTTACTC
*
9897 TAATTACCAAATTCCA-TTTTACTCTTTT-TACTTTAATTACCAAATCCCATTTTACTCTTTTTA
1 TAATTACCAAATTCCATTTTTACT-TTTTATACTTTAATTACCAAATTCCATTTTACTC-TTTT-
*** * *
9960 AATACTTTAATTACCAAATTTTGTTTTACTCTTCTTTACTTTAATTGCCAAATTCCATTTT
63 --TACTTTAATTACCAAATTCCATTTTAC-CTT-TTTACTTTAATTACCAAATTTCATTTT
10021 TACTCTTTTA
Statistics
Matches: 563, Mismatches: 49, Indels: 67
0.83 0.07 0.10
Matches are distributed among these distances:
166 27 0.05
167 16 0.03
168 5 0.01
169 80 0.14
170 69 0.12
171 38 0.07
172 25 0.04
173 8 0.01
174 25 0.04
175 3 0.01
176 6 0.01
177 46 0.08
178 30 0.05
179 183 0.33
180 2 0.00
ACGTcount: A:0.30, C:0.20, G:0.01, T:0.49
Consensus pattern (172 bp):
TAATTACCAAATTCCATTTTTACTTTTTATACTTTAATTACCAAATTCCATTTTACTCTTTTTAC
TTTAATTACCAAATTCCATTTTACCTTTTTACTTTAATTACCAAATTTCATTTTACCATTTTACT
CTTTTTACTTTAATTACCAAATTTCATTTTACCATTTTACTC
Found at i:9537 original size:41 final size:42
Alignment explanation
Indices: 9461--9558 Score: 153
Period size: 41 Copynumber: 2.3 Consensus size: 42
9451 TTACCAAATC
*
9461 CCATTTTACTCTTTTTAAATACTTTAATTACCAAATTTCATTTTA
1 CCATTTTACTC-TTTT--ATACTTTAATTACCAAATTTCAGTTTA
9506 CCATTTTACTCTTTT-TACTTTAATTACCAAATTTCAGTTTA
1 CCATTTTACTCTTTTATACTTTAATTACCAAATTTCAGTTTA
9547 CCATTTTACTCT
1 CCATTTTACTCT
9559 AATTACCAAA
Statistics
Matches: 52, Mismatches: 1, Indels: 4
0.91 0.02 0.07
Matches are distributed among these distances:
41 37 0.71
44 4 0.08
45 11 0.21
ACGTcount: A:0.28, C:0.20, G:0.01, T:0.51
Consensus pattern (42 bp):
CCATTTTACTCTTTTATACTTTAATTACCAAATTTCAGTTTA
Found at i:9759 original size:202 final size:202
Alignment explanation
Indices: 9183--9950 Score: 897
Period size: 202 Copynumber: 3.7 Consensus size: 202
9173 TTCAATACTT
* * *
9183 ATTTTACT-TTTTTTCTTTAATTACCAAATGTCATTTTTTA-CACTTTTCAGTCTTTAATTACCA
1 ATTTTACTCTTTTTACTTTAATTACCAAATTTCA--TTTTACCA-TTTT-A--CTCTAATTACCA
* * * * * * *
9246 AATACCATTCTTACTCTTTT---GACTTCAATTACCAAATACCATTTTACT-TGTTAAATACTTT
60 AATTCCCTTTTTACT-TTTTAAATACTTTAATTACCAAATTCCATTTTACTCT-TT--TTACTTT
* * ** ** ** *
9307 AATTACTAAATTTCATTTTACCATTTTACTCTTTTTACTTTAATTACCAAATTT-CATTTTACCA
121 AATTACCAAATTTCATTTTAACATTTTACTCTAATTAC-CAAATT-CCATTTTTACTTTTTA--A
* *
9371 TTTTACTCTAATTACCAAATTCC
182 --ATACTTTAATTACCAAATTCC
* * *
9394 ATTTTTACT-TTTTAAATACTTTAATTACCAAATTCCATTTTACTCTTTTTACTTTAATTACCAA
1 A-TTTTACTCTTTT---TACTTTAATTACCAAATTTCATTTTAC-CATTTTACTCTAATTACCAA
*
9458 A-TCCCATTTTACTCTTTTTAAATACTTTAATTACCAAATTTCATTTTACCATTTTACTCTTTTT
61 ATTCCCTTTTTA--CTTTTTAAATACTTTAATTACC-AA----A--TT-CCATTTTACTCTTTTT
* * *
9522 ACTTTAATTACCAAATTTCAGTTTACCATTTTACTCTAATTACCAAATTCCCTTTTTACTTTTTA
116 ACTTTAATTACCAAATTTCATTTTAACATTTTACTCTAATTACCAAATTCCATTTTTACTTTTTA
*
9587 AATACTTTAATTACCAAGTTCC
181 AATACTTTAATTACCAAATTCC
9609 ATTTTACTCTTTTTACTTTAATTACCAAATTTCATTTTACCATTTTACTCTAATTACCAAATTCC
1 ATTTTACTCTTTTTACTTTAATTACCAAATTTCATTTTACCATTTTACTCTAATTACCAAATTCC
*
9674 CTTTTTACTTTTTAAATACTTTAATTACCAAGTTCCATTTTACTCTTTTTACTTTAATTACCAAA
66 CTTTTTACTTTTTAAATACTTTAATTACCAAATTCCATTTTACTCTTTTTACTTTAATTACCAAA
9739 TTTCATTTTAACATTTTACTCTAATTACCAAATTCCATTTTTACTTTTTAAATACTTTAATTACC
131 TTTCATTTTAACATTTTACTCTAATTACCAAATTCCATTTTTACTTTTTAAATACTTTAATTACC
9804 AAATTCC
196 AAATTCC
9811 ATTTTACTCTTTTTACTTTAATTACCAAATTTCATTTTACCATTTTACTCTAATTACCAAATTCC
1 ATTTTACTCTTTTTACTTTAATTACCAAATTTCATTTTACCATTTTACTCTAATTACCAAATTCC
*
9876 ATTTTTACTTTTTAAATACTTTAATTACCAAATTCCATTTTACTCTTTTTACTTTAATTACCAAA
66 CTTTTTACTTTTTAAATACTTTAATTACCAAATTCCATTTTACTCTTTTTACTTTAATTACCAAA
**
9941 TCCCATTTTA
131 TTTCATTTTA
9951 CTCTTTTTAA
Statistics
Matches: 496, Mismatches: 38, Indels: 55
0.84 0.06 0.09
Matches are distributed among these distances:
202 235 0.47
203 2 0.00
209 2 0.00
210 28 0.06
211 38 0.08
212 48 0.10
213 6 0.01
214 22 0.04
215 44 0.09
217 1 0.00
218 5 0.01
219 11 0.02
220 40 0.08
221 1 0.00
222 12 0.02
223 1 0.00
ACGTcount: A:0.30, C:0.20, G:0.01, T:0.49
Consensus pattern (202 bp):
ATTTTACTCTTTTTACTTTAATTACCAAATTTCATTTTACCATTTTACTCTAATTACCAAATTCC
CTTTTTACTTTTTAAATACTTTAATTACCAAATTCCATTTTACTCTTTTTACTTTAATTACCAAA
TTTCATTTTAACATTTTACTCTAATTACCAAATTCCATTTTTACTTTTTAAATACTTTAATTACC
AAATTCC
Found at i:14010 original size:19 final size:18
Alignment explanation
Indices: 13977--14012 Score: 54
Period size: 19 Copynumber: 1.9 Consensus size: 18
13967 TTGAAATAAT
13977 TCTTCAATGATCTTCAAA
1 TCTTCAATGATCTTCAAA
*
13995 TCTTCAAATTATCTTCAA
1 TCTTC-AATGATCTTCAA
14013 TTAGTCTTCA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 5 0.31
19 11 0.69
ACGTcount: A:0.33, C:0.22, G:0.03, T:0.42
Consensus pattern (18 bp):
TCTTCAATGATCTTCAAA
Found at i:14768 original size:15 final size:15
Alignment explanation
Indices: 14731--14768 Score: 58
Period size: 15 Copynumber: 2.5 Consensus size: 15
14721 AAGAATAAAC
14731 TGCATTTTTTTATTA
1 TGCATTTTTTTATTA
*
14746 TGCCTTTTTTTATTA
1 TGCATTTTTTTATTA
*
14761 TGTATTTT
1 TGCATTTT
14769 CTTGTAACTA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
15 20 1.00
ACGTcount: A:0.16, C:0.08, G:0.08, T:0.68
Consensus pattern (15 bp):
TGCATTTTTTTATTA
Found at i:18768 original size:33 final size:33
Alignment explanation
Indices: 18724--18823 Score: 164
Period size: 33 Copynumber: 3.0 Consensus size: 33
18714 CTCTAGACTT
*
18724 GGAGGCATCCCCAGAGGGCGCCCCACCATGGTG
1 GGAGGCGTCCCCAGAGGGCGCCCCACCATGGTG
18757 GGAGGCGTCCCCAGAGGGCGCCCCACCATGGTG
1 GGAGGCGTCCCCAGAGGGCGCCCCACCATGGTG
* * *
18790 GGAGGCGTCCCCAGGGGGCGCCTCACCACGGTG
1 GGAGGCGTCCCCAGAGGGCGCCCCACCATGGTG
18823 G
1 G
18824 AGGTTTCCCT
Statistics
Matches: 63, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
33 63 1.00
ACGTcount: A:0.15, C:0.36, G:0.40, T:0.09
Consensus pattern (33 bp):
GGAGGCGTCCCCAGAGGGCGCCCCACCATGGTG
Found at i:22646 original size:13 final size:13
Alignment explanation
Indices: 22628--22662 Score: 61
Period size: 13 Copynumber: 2.7 Consensus size: 13
22618 TGATCAGAAA
22628 ATATATATAATAT
1 ATATATATAATAT
*
22641 ATATATATATTAT
1 ATATATATAATAT
22654 ATATATATA
1 ATATATATA
22663 CACACACATA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
13 21 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (13 bp):
ATATATATAATAT
Found at i:22648 original size:15 final size:15
Alignment explanation
Indices: 22628--22662 Score: 61
Period size: 15 Copynumber: 2.3 Consensus size: 15
22618 TGATCAGAAA
22628 ATATATATAATATAT
1 ATATATATAATATAT
*
22643 ATATATATTATATAT
1 ATATATATAATATAT
22658 ATATA
1 ATATA
22663 CACACACATA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
15 19 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (15 bp):
ATATATATAATATAT
Found at i:22675 original size:2 final size:2
Alignment explanation
Indices: 22628--22662 Score: 56
Period size: 2 Copynumber: 18.5 Consensus size: 2
22618 TGATCAGAAA
22628 AT AT AT AT A- AT AT AT AT AT AT AT -T AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
22663 CACACACATA
Statistics
Matches: 31, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
1 2 0.06
2 29 0.94
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:24467 original size:11 final size:11
Alignment explanation
Indices: 24443--24477 Score: 52
Period size: 11 Copynumber: 3.2 Consensus size: 11
24433 TTAACAGCGC
24443 AACAAAAACAA
1 AACAAAAACAA
* *
24454 AACGAAAACGA
1 AACAAAAACAA
24465 AACAAAAACAA
1 AACAAAAACAA
24476 AA
1 AA
24478 AACAGAAAAA
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
11 20 1.00
ACGTcount: A:0.77, C:0.17, G:0.06, T:0.00
Consensus pattern (11 bp):
AACAAAAACAA
Found at i:24469 original size:16 final size:16
Alignment explanation
Indices: 24448--24506 Score: 50
Period size: 16 Copynumber: 3.7 Consensus size: 16
24438 AGCGCAACAA
24448 AAACAAAACGAAAACG
1 AAACAAAACGAAAACG
*
24464 AAACAAAAACAAAAAAC-
1 AAAC-AAAAC-GAAAACG
*
24481 AGA-AAAACGAAAACG
1 AAACAAAACGAAAACG
* *
24496 ATACCAAACGA
1 AAACAAAACGA
24507 CCCCTTAATT
Statistics
Matches: 34, Mismatches: 5, Indels: 8
0.72 0.11 0.17
Matches are distributed among these distances:
14 5 0.15
15 7 0.21
16 10 0.29
17 7 0.21
18 5 0.15
ACGTcount: A:0.69, C:0.19, G:0.10, T:0.02
Consensus pattern (16 bp):
AAACAAAACGAAAACG
Done.