Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01018602.1 Corchorus olitorius cultivar O-4 contig18635, 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: 25304
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.34
Found at i:470 original size:22 final size:22
Alignment explanation
Indices: 442--483 Score: 66
Period size: 22 Copynumber: 1.9 Consensus size: 22
432 AGTTCTGAGG
* *
442 CTACCCGGCTCCGGGTACCCCC
1 CTACCCGGCCCCGGGAACCCCC
464 CTACCCGGCCCCGGGAACCC
1 CTACCCGGCCCCGGGAACCC
484 TCAAGAACGC
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.12, C:0.55, G:0.24, T:0.10
Consensus pattern (22 bp):
CTACCCGGCCCCGGGAACCCCC
Found at i:8957 original size:2 final size:2
Alignment explanation
Indices: 8950--8988 Score: 78
Period size: 2 Copynumber: 19.5 Consensus size: 2
8940 ATTTGACAGG
8950 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
8989 TGATAGAAAA
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:11214 original size:130 final size:130
Alignment explanation
Indices: 10962--11221 Score: 382
Period size: 130 Copynumber: 2.0 Consensus size: 130
10952 TTGTTTAAAC
* * * *
10962 TTTTATAGTTTTACTCAACTAAAAACTCTGTTTTTATTTAATTAAATCTAATATCCTTATAACTA
1 TTTTATAATTTTACTCAACTAAAAACTCTATTTCTATTTAATAAAATCTAATATCCTTATAACTA
* * *
11027 TTTTATTTTTACCATTTTACTATTTTAATTAAAAAAAACTTATATAGTAGAATTTTTTAATATAT
66 TTTCATTTTTACCATTTTACTAATTTAATTAAAAAAAACTTATATAGTAGAATTTTTTAAAATAT
* *
11092 TTTTATAATTTTACTCAACTAAAAACTCTATTTCTATTGT-ATAAAATCTAATATCTTTATACCT
1 TTTTATAATTTTACTCAACTAAAAACTCTATTTCTATT-TAATAAAATCTAATATCCTTATAACT
*
11156 ATTTCATTTTTACCATTTTACTAATTTAATT-AAAAAAACTTAGATATATTAGAA-TTTTTAAAA
65 ATTTCATTTTTACCATTTTACTAATTTAATTAAAAAAAACTT--ATATAGTAGAATTTTTTAAAA
11219 TAT
128 TAT
11222 ATTTCTTAAA
Statistics
Matches: 117, Mismatches: 10, Indels: 6
0.88 0.08 0.05
Matches are distributed among these distances:
129 10 0.09
130 96 0.82
131 11 0.09
ACGTcount: A:0.38, C:0.11, G:0.03, T:0.48
Consensus pattern (130 bp):
TTTTATAATTTTACTCAACTAAAAACTCTATTTCTATTTAATAAAATCTAATATCCTTATAACTA
TTTCATTTTTACCATTTTACTAATTTAATTAAAAAAAACTTATATAGTAGAATTTTTTAAAATAT
Found at i:12467 original size:22 final size:22
Alignment explanation
Indices: 12437--12478 Score: 66
Period size: 22 Copynumber: 1.9 Consensus size: 22
12427 GTTTATAATA
*
12437 TTCTTGGGTCATTCAGGTTAAC
1 TTCTCGGGTCATTCAGGTTAAC
*
12459 TTCTCGGGTCATTTAGGTTA
1 TTCTCGGGTCATTCAGGTTA
12479 CAGATTTACC
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.17, C:0.17, G:0.24, T:0.43
Consensus pattern (22 bp):
TTCTCGGGTCATTCAGGTTAAC
Found at i:14590 original size:17 final size:17
Alignment explanation
Indices: 14557--14604 Score: 57
Period size: 17 Copynumber: 2.9 Consensus size: 17
14547 TTAAATAATT
14557 AATTGTTCTAC--AAAA
1 AATTGTTCTACAAAAAA
*
14572 AA-TGATTCTCCAAAAAA
1 AATTG-TTCTACAAAAAA
14589 AATTGTTCTACAAAAA
1 AATTGTTCTACAAAAA
14605 TGAGTCATGA
Statistics
Matches: 27, Mismatches: 2, Indels: 6
0.77 0.06 0.17
Matches are distributed among these distances:
14 2 0.07
15 7 0.26
17 16 0.59
18 2 0.07
ACGTcount: A:0.50, C:0.15, G:0.06, T:0.29
Consensus pattern (17 bp):
AATTGTTCTACAAAAAA
Found at i:14603 original size:15 final size:15
Alignment explanation
Indices: 14557--14604 Score: 53
Period size: 15 Copynumber: 3.1 Consensus size: 15
14547 TTAAATAATT
14557 AATTGTTCTACAAAA
1 AATTGTTCTACAAAA
*
14572 AA-TGATTCTCCAAAAAA
1 AATTG-TTCT--ACAAAA
14589 AATTGTTCTACAAAA
1 AATTGTTCTACAAAA
14604 A
1 A
14605 TGAGTCATGA
Statistics
Matches: 27, Mismatches: 2, Indels: 8
0.73 0.05 0.22
Matches are distributed among these distances:
14 2 0.07
15 12 0.44
17 11 0.41
18 2 0.07
ACGTcount: A:0.50, C:0.15, G:0.06, T:0.29
Consensus pattern (15 bp):
AATTGTTCTACAAAA
Found at i:17297 original size:6 final size:6
Alignment explanation
Indices: 17286--17328 Score: 68
Period size: 6 Copynumber: 6.8 Consensus size: 6
17276 CCAACTAATA
17286 TATATC TATATC TATATC TATATC TATATAC TATATAC TATAT
1 TATATC TATATC TATATC TATATC TATAT-C TATAT-C TATAT
17329 AAGTTTAAAC
Statistics
Matches: 36, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
6 23 0.64
7 13 0.36
ACGTcount: A:0.37, C:0.14, G:0.00, T:0.49
Consensus pattern (6 bp):
TATATC
Found at i:17616 original size:39 final size:40
Alignment explanation
Indices: 17552--17632 Score: 128
Period size: 39 Copynumber: 2.0 Consensus size: 40
17542 TTTAATTTCT
*
17552 ATGTAATATTTATAATAACTAAAATACTTACATTAATTAA
1 ATGTAATATCTATAATAACTAAAATACTTACATTAATTAA
* *
17592 ATGTAATA-CTATGATAACTGAAATACTTACATTAATTAA
1 ATGTAATATCTATAATAACTAAAATACTTACATTAATTAA
17631 AT
1 AT
17633 TCTCAGGTAT
Statistics
Matches: 38, Mismatches: 3, Indels: 1
0.90 0.07 0.02
Matches are distributed among these distances:
39 30 0.79
40 8 0.21
ACGTcount: A:0.48, C:0.09, G:0.05, T:0.38
Consensus pattern (40 bp):
ATGTAATATCTATAATAACTAAAATACTTACATTAATTAA
Found at i:17659 original size:25 final size:24
Alignment explanation
Indices: 17623--17669 Score: 67
Period size: 25 Copynumber: 1.9 Consensus size: 24
17613 AATACTTACA
*
17623 TTAATTAAATTCTCAGGTATTTTC
1 TTAATTAAATTCTCACGTATTTTC
*
17647 TTAATTCAAATTCTTACGTATTT
1 TTAATT-AAATTCTCACGTATTT
17670 GTGCAAACGT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
24 6 0.30
25 14 0.70
ACGTcount: A:0.30, C:0.13, G:0.06, T:0.51
Consensus pattern (24 bp):
TTAATTAAATTCTCACGTATTTTC
Found at i:18133 original size:204 final size:203
Alignment explanation
Indices: 17743--18358 Score: 1142
Period size: 204 Copynumber: 3.0 Consensus size: 203
17733 TTCCTTAATA
**
17743 ATAAATAAATATGATCTTTAATATCTTTTATAATTTTGAAATTTTGTTTGACATTGATCTAATTT
1 ATAAATAAATCGGATCTTTAATATCTTTTATAATTTTGAAATTTTGTTTGACATTGATCTAATTT
17808 AATTTAATAAATCAACCACTAATGTTCAACTAATTTTTTTTGGTATAGTTCTATCTATATAATAG
66 AATTTAATAAATCAACCACTAATGTTCAACTAATTTTTTTTGGTATAGTTCTATCTATATAATAG
17873 TAATGTGTTGTATCTTATTCACTACAACTTTGATAGTAACCTTAGACTTAAAAAATTAATAACAT
131 TAATGTGTTGTATCTTATTCACTACAACTTTGATAGTAACCTTAGACTT-AAAAATTAATAACAT
17938 TCACCATTG
195 TCACCATTG
17947 ATAAATAAATCGGATCTTTAATATCTTTTATAATTTTGAAATTTTGTTTGACATTGATCTAATTT
1 ATAAATAAATCGGATCTTTAATATCTTTTATAATTTTGAAATTTTGTTTGACATTGATCTAATTT
18012 AATTTAATAAATCAACCACTAAATGTTCAACTAATTTTTTTTGGTATAGTTCTATCTATATAATA
66 AATTTAATAAATCAACCACT-AATGTTCAACTAATTTTTTTTGGTATAGTTCTATCTATATAATA
18077 GTAATGTGTTGTATCTTATTCACTACAACTTTGATAGTAACCTTAGACTTAAAAATTAATAACAT
130 GTAATGTGTTGTATCTTATTCACTACAACTTTGATAGTAACCTTAGACTTAAAAATTAATAACAT
18142 TCACCATTG
195 TCACCATTG
18151 ATAAATAAATCGGATCTTTAATATCTTTTATAATTTTGAAATTTTGTTTGACATTGATCTAATTT
1 ATAAATAAATCGGATCTTTAATATCTTTTATAATTTTGAAATTTTGTTTGACATTGATCTAATTT
* * *
18216 AATTTAATAAATCAACCACTAATGTTCAACTAATTTTTTTTGGTATAGTTTTATATATATAATAA
66 AATTTAATAAATCAACCACTAATGTTCAACTAATTTTTTTTGGTATAGTTCTATCTATATAATAG
* * *
18281 TAATGTGTCGTATCTTATTCACTACAACTTTGTTAGTAATCTTAGACTTAAAAATTAATAACATT
131 TAATGTGTTGTATCTTATTCACTACAACTTTGATAGTAACCTTAGACTTAAAAATTAATAACATT
18346 CACCATTG
196 CACCATTG
18354 ATAAA
1 ATAAA
18359 GTTATTAAGC
Statistics
Matches: 403, Mismatches: 8, Indels: 3
0.97 0.02 0.01
Matches are distributed among these distances:
203 117 0.29
204 192 0.48
205 94 0.23
ACGTcount: A:0.36, C:0.12, G:0.08, T:0.44
Consensus pattern (203 bp):
ATAAATAAATCGGATCTTTAATATCTTTTATAATTTTGAAATTTTGTTTGACATTGATCTAATTT
AATTTAATAAATCAACCACTAATGTTCAACTAATTTTTTTTGGTATAGTTCTATCTATATAATAG
TAATGTGTTGTATCTTATTCACTACAACTTTGATAGTAACCTTAGACTTAAAAATTAATAACATT
CACCATTG
Found at i:18914 original size:36 final size:36
Alignment explanation
Indices: 18874--18943 Score: 113
Period size: 36 Copynumber: 1.9 Consensus size: 36
18864 GAGATTTTGG
* *
18874 AGAAATATGATAATCAAAATTACAAAAAATGTAATA
1 AGAAATATGATAACCAAAATCACAAAAAATGTAATA
*
18910 AGAAATATGATAACCAAAATCACAAAAGATGTAA
1 AGAAATATGATAACCAAAATCACAAAAAATGTAA
18944 GGTTATTGAA
Statistics
Matches: 31, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
36 31 1.00
ACGTcount: A:0.60, C:0.09, G:0.10, T:0.21
Consensus pattern (36 bp):
AGAAATATGATAACCAAAATCACAAAAAATGTAATA
Found at i:19934 original size:29 final size:29
Alignment explanation
Indices: 19902--20038 Score: 159
Period size: 29 Copynumber: 4.8 Consensus size: 29
19892 TTAGGATCAC
*
19902 CTAGGAGCATTTTGGTCATTTTAAAAAAT
1 CTAGGGGCATTTTGGTCATTTTAAAAAAT
*
19931 CTAGGGGCATTTTGGTCATTTTTAAAAAT
1 CTAGGGGCATTTTGGTCATTTTAAAAAAT
** * *
19960 CTAGGGGCATTTTGGTCATTTTGCACATT
1 CTAGGGGCATTTTGGTCATTTTAAAAAAT
*** *
19989 C-AGGGGCATTTTGGTCATTTTTGCACAT
1 CTAGGGGCATTTTGGTCATTTTAAAAAAT
* *
20017 CTAGGGGCATCTTAGTCATTTT
1 CTAGGGGCATTTTGGTCATTTT
20039 TGCACATTCA
Statistics
Matches: 93, Mismatches: 14, Indels: 2
0.85 0.13 0.02
Matches are distributed among these distances:
28 22 0.24
29 71 0.76
ACGTcount: A:0.23, C:0.15, G:0.22, T:0.40
Consensus pattern (29 bp):
CTAGGGGCATTTTGGTCATTTTAAAAAAT
Found at i:20008 original size:86 final size:86
Alignment explanation
Indices: 19908--20097 Score: 256
Period size: 86 Copynumber: 2.2 Consensus size: 86
19898 TCACCTAGGA
* *
19908 GCATTTTGGTCATTTTAAAAAATCTAGGGGCATTTTGGTCATTTTTAAAAA-TCTAGGGGCATTT
1 GCATTTTGGTCATTTTAAAAAATCTAGGGGCATCTTAGTCATTTTTAAAAATTC-AGGGGCATTT
*
19972 TGGTCATTTTGCACATTCAGGG
65 TGGTCATTTTGCACATTCAAGG
*** * ** * *
19994 GCATTTTGGTCATTTTTGCACATCTAGGGGCATCTTAGTCATTTTTGCACATTCATGGGCATTTT
1 GCATTTTGGTCATTTTAAAAAATCTAGGGGCATCTTAGTCATTTTTAAAAATTCAGGGGCATTTT
20059 GGTCATTTTGCACATTCAAGG
66 GGTCATTTTGCACATTCAAGG
*
20080 GCATCTTGGTCATTTTAA
1 GCATTTTGGTCATTTTAA
20098 GCTCTTTTAC
Statistics
Matches: 89, Mismatches: 14, Indels: 2
0.85 0.13 0.02
Matches are distributed among these distances:
86 87 0.98
87 2 0.02
ACGTcount: A:0.23, C:0.16, G:0.21, T:0.41
Consensus pattern (86 bp):
GCATTTTGGTCATTTTAAAAAATCTAGGGGCATCTTAGTCATTTTTAAAAATTCAGGGGCATTTT
GGTCATTTTGCACATTCAAGG
Found at i:20039 original size:29 final size:29
Alignment explanation
Indices: 19933--20095 Score: 208
Period size: 29 Copynumber: 5.7 Consensus size: 29
19923 TAAAAAATCT
* * *
19933 AGGGGCATTTTGGTCATTTTT-AAAAATC
1 AGGGGCATTTTGGTCATTTTTGCACATTC
19961 TAGGGGCATTTTGGTCA-TTTTGCACATTC
1 -AGGGGCATTTTGGTCATTTTTGCACATTC
19990 AGGGGCATTTTGGTCATTTTTGCACA-TC
1 AGGGGCATTTTGGTCATTTTTGCACATTC
* *
20018 TAGGGGCATCTTAGTCATTTTTGCACATTC
1 -AGGGGCATTTTGGTCATTTTTGCACATTC
*
20048 ATGGGCATTTTGGTCA-TTTTGCACATTC
1 AGGGGCATTTTGGTCATTTTTGCACATTC
* *
20076 AAGGGCATCTTGGTCATTTT
1 AGGGGCATTTTGGTCATTTT
20096 AAGCTCTTTT
Statistics
Matches: 119, Mismatches: 10, Indels: 10
0.86 0.07 0.07
Matches are distributed among these distances:
28 48 0.40
29 69 0.58
30 2 0.02
ACGTcount: A:0.20, C:0.17, G:0.23, T:0.40
Consensus pattern (29 bp):
AGGGGCATTTTGGTCATTTTTGCACATTC
Found at i:20068 original size:57 final size:58
Alignment explanation
Indices: 19933--20095 Score: 233
Period size: 57 Copynumber: 2.8 Consensus size: 58
19923 TAAAAAATCT
** * *
19933 AGGGGCATTTTGGTCATTTTTAAAAATCTAGGGGCATTTTGGTCA-TTTTGCACATTC
1 AGGGGCATTTTGGTCATTTTTGCACATCTAGGGGCATCTTGGTCATTTTTGCACATTC
*
19990 AGGGGCATTTTGGTCATTTTTGCACATCTAGGGGCATCTTAGTCATTTTTGCACATTC
1 AGGGGCATTTTGGTCATTTTTGCACATCTAGGGGCATCTTGGTCATTTTTGCACATTC
* *
20048 ATGGGCATTTTGGTCA-TTTTGCACAT-TCAAGGGCATCTTGGTCATTTT
1 AGGGGCATTTTGGTCATTTTTGCACATCT-AGGGGCATCTTGGTCATTTT
20096 AAGCTCTTTT
Statistics
Matches: 96, Mismatches: 8, Indels: 4
0.89 0.07 0.04
Matches are distributed among these distances:
56 1 0.01
57 68 0.71
58 27 0.28
ACGTcount: A:0.20, C:0.17, G:0.23, T:0.40
Consensus pattern (58 bp):
AGGGGCATTTTGGTCATTTTTGCACATCTAGGGGCATCTTGGTCATTTTTGCACATTC
Found at i:24690 original size:58 final size:58
Alignment explanation
Indices: 24587--24701 Score: 169
Period size: 58 Copynumber: 2.0 Consensus size: 58
24577 ATAGCATCAT
* *
24587 GCCTCGGTCCTAAAACGTCTTTTTTAGGCATCTAATAAAAAAACATGTCACTCGATAA
1 GCCTCGGTCCGAAAACGCCTTTTTTAGGCATCTAATAAAAAAACATGTCACTCGATAA
* * *
24645 GCCTCGGTCCGAAAACGCCTTTTTTTATGCATCTAAT-AAAGAACATGTCACTTGATA
1 GCCTCGGTCCGAAAACGCC-TTTTTTAGGCATCTAATAAAAAAACATGTCACTCGATA
24702 TTTGATTAAT
Statistics
Matches: 51, Mismatches: 5, Indels: 2
0.88 0.09 0.03
Matches are distributed among these distances:
58 35 0.69
59 16 0.31
ACGTcount: A:0.32, C:0.23, G:0.15, T:0.30
Consensus pattern (58 bp):
GCCTCGGTCCGAAAACGCCTTTTTTAGGCATCTAATAAAAAAACATGTCACTCGATAA
Done.