Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01015823.1 Corchorus olitorius cultivar O-4 contig15856, 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: 43237
ACGTcount: A:0.34, C:0.17, G:0.17, T:0.32
Found at i:1817 original size:2 final size:2
Alignment explanation
Indices: 1810--1842 Score: 59
Period size: 2 Copynumber: 17.0 Consensus size: 2
1800 ATTACCCTAT
1810 TA TA TA TA TA TA TA TA T- TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1843 GGTAAGGGAA
Statistics
Matches: 30, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 29 0.97
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:1827 original size:17 final size:17
Alignment explanation
Indices: 1807--1842 Score: 72
Period size: 17 Copynumber: 2.1 Consensus size: 17
1797 TATATTACCC
1807 TATTATATATATATATA
1 TATTATATATATATATA
1824 TATTATATATATATATA
1 TATTATATATATATATA
1841 TA
1 TA
1843 GGTAAGGGAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (17 bp):
TATTATATATATATATA
Found at i:1830 original size:15 final size:15
Alignment explanation
Indices: 1812--1841 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
1802 TACCCTATTA
1812 TATATATATATATAT
1 TATATATATATATAT
1827 TATATATATATATAT
1 TATATATATATATAT
1842 AGGTAAGGGA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (15 bp):
TATATATATATATAT
Found at i:2648 original size:60 final size:58
Alignment explanation
Indices: 2500--2717 Score: 280
Period size: 60 Copynumber: 3.7 Consensus size: 58
2490 GAAGTTAAAA
* *
2500 TTTT-AAATTATAGTTATAAAGAGAAGATTTGCCCGCACAATAAGAAAACTGTTATACAA-TT
1 TTTTCAAATTATAGTTATAAAGAGAA-ATATG--CGCGCAATAAGAAAAC-GTTA-ACAATTT
* *
2561 ATTTCAAATTATAGTTATAAAGAGAAATATGTGCGCAATAAGAAAATCGTTACACAATTT
1 TTTTCAAATTATAGTTATAAAGAGAAATATGCGCGCAATAAGAAAA-CGTTA-ACAATTT
* *
2621 TTTTCAAATTATAGTTATAAAAAGAAATAAGCGCGCAATAAGAAAACCGTT-ACAATTT
1 TTTTCAAATTATAGTTATAAAGAGAAATATGCGCGCAATAAGAAAA-CGTTAACAATTT
*
2679 TTTCCAAATTATAGTTATAAAGAGAAATATGCGCGCAAT
1 TTTTCAAATTATAGTTATAAAGAGAAATATGCGCGCAAT
2718 TTATTATCCA
Statistics
Matches: 141, Mismatches: 13, Indels: 9
0.87 0.08 0.06
Matches are distributed among these distances:
58 43 0.30
59 21 0.15
60 49 0.35
61 7 0.05
62 21 0.15
ACGTcount: A:0.44, C:0.11, G:0.13, T:0.31
Consensus pattern (58 bp):
TTTTCAAATTATAGTTATAAAGAGAAATATGCGCGCAATAAGAAAACGTTAACAATTT
Found at i:2692 original size:118 final size:120
Alignment explanation
Indices: 2500--2717 Score: 318
Period size: 118 Copynumber: 1.8 Consensus size: 120
2490 GAAGTTAAAA
* ** *
2500 TTTTAAATTATAGTTATAAAGAGAAGATTTGCCCGCACAATAAGAAAACTGTTATACAATTATTT
1 TTTTAAATTATAGTTATAAAAAGAAGATAAG-CCGCACAATAAGAAAACCGTTATACAATTATTT
*
2565 CAAATTATAGTTATAAAGAGAAATATGTGCGCAATAAGAAAATCGTTACACAATTT
65 CAAATTATAGTTATAAAGAGAAATATGCGCGCAATAAGAAAATCGTTACACAATTT
* *
2621 TTTTCAAATTATAGTTATAAAAAGAA-ATAAG-CGCGCAATAAGAAAACCG-T-TACAATTTTTT
1 TTTT-AAATTATAGTTATAAAAAGAAGATAAGCCGCACAATAAGAAAACCGTTATACAATTATTT
2682 CCAAATTATAGTTATAAAGAGAAATATGCGCGCAAT
65 -CAAATTATAGTTATAAAGAGAAATATGCGCGCAAT
2718 TTATTATCCA
Statistics
Matches: 88, Mismatches: 7, Indels: 7
0.86 0.07 0.07
Matches are distributed among these distances:
117 10 0.11
118 35 0.40
119 16 0.18
121 7 0.08
122 20 0.23
ACGTcount: A:0.44, C:0.11, G:0.13, T:0.31
Consensus pattern (120 bp):
TTTTAAATTATAGTTATAAAAAGAAGATAAGCCGCACAATAAGAAAACCGTTATACAATTATTTC
AAATTATAGTTATAAAGAGAAATATGCGCGCAATAAGAAAATCGTTACACAATTT
Found at i:4604 original size:142 final size:140
Alignment explanation
Indices: 4347--4627 Score: 358
Period size: 142 Copynumber: 2.0 Consensus size: 140
4337 AGACTCAGAC
*
4347 GAGCATGAGATCCTTCTAAACAAAAAAGGTAAATCATTTTAGGCTACACAAATATAGAAGAACAG
1 GAGCATGAGATCCTTCTAAACAAAAAAGGTAAATCATTTTAGGCTACACAAATATAGAAGAACAA
* *
4412 CAAGGGAAGAGTACTGAACACATTGATTGAGAACATCATTATTTTTCTTATTCATCATATTCCAA
66 CAAGGGAAGAGTACTGAAAACATTG--TGACAACATCATTATTTTTCTTATTCATCATATTCCAA
4477 AAGAAAAAGCGT
129 AAGAAAAAGCGT
* *
4489 GAGCATGAGATCCTTCTAAAC-ATAAAGGTTAAATCATTTTAAGGCTGCACAAATATAGAAGAAC
1 GAGCATGAGATCCTTCTAAACAAAAAAGG-TAAATCATTTT-AGGCTACACAAATATAGAAGAAC
*
4553 AACAA-GGAA-AG-ACTGAAAACATTCG-G-CAACATCATTCTTTTTTTCCCCTTATTCATCATA
64 AACAAGGGAAGAGTACTGAAAACATT-GTGACAACATCA-T-TATTTTT---CTTATTCATCATA
* *
4613 TTTCAAAAGAGAAAG
123 TTCCAAAAGAAAAAG
4628 TGTACATGTT
Statistics
Matches: 123, Mismatches: 8, Indels: 16
0.84 0.05 0.11
Matches are distributed among these distances:
137 7 0.06
138 2 0.02
139 6 0.05
140 11 0.09
141 9 0.07
142 62 0.50
143 26 0.21
ACGTcount: A:0.41, C:0.17, G:0.15, T:0.27
Consensus pattern (140 bp):
GAGCATGAGATCCTTCTAAACAAAAAAGGTAAATCATTTTAGGCTACACAAATATAGAAGAACAA
CAAGGGAAGAGTACTGAAAACATTGTGACAACATCATTATTTTTCTTATTCATCATATTCCAAAA
GAAAAAGCGT
Found at i:8976 original size:30 final size:30
Alignment explanation
Indices: 8928--8989 Score: 81
Period size: 29 Copynumber: 2.1 Consensus size: 30
8918 ATTAGGTCAT
* *
8928 TTTGCCCTTTAAACTTCAAA-TCATGATAA
1 TTTGCCCCTTAAACTTCAAATTCAAGATAA
*
8957 TTTGCCCCTTAAATTTTCAAATTCAAGATAA
1 TTTGCCCCTTAAA-CTTCAAATTCAAGATAA
8988 TT
1 TT
8990 AACCTCCTAA
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
29 12 0.43
30 6 0.21
31 10 0.36
ACGTcount: A:0.34, C:0.19, G:0.06, T:0.40
Consensus pattern (30 bp):
TTTGCCCCTTAAACTTCAAATTCAAGATAA
Found at i:9001 original size:31 final size:32
Alignment explanation
Indices: 8966--9031 Score: 107
Period size: 32 Copynumber: 2.1 Consensus size: 32
8956 ATTTGCCCCT
8966 TAAATTT-TCAAATTCAAGATAATTAACCTCC
1 TAAATTTCTCAAATTCAAGATAATTAACCTCC
* *
8997 TAAATTTCTCAAATTCAAGATATTTCACCTCC
1 TAAATTTCTCAAATTCAAGATAATTAACCTCC
9029 TAA
1 TAA
9032 CAAAGGGTGA
Statistics
Matches: 32, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
31 7 0.22
32 25 0.78
ACGTcount: A:0.39, C:0.21, G:0.03, T:0.36
Consensus pattern (32 bp):
TAAATTTCTCAAATTCAAGATAATTAACCTCC
Found at i:9556 original size:123 final size:128
Alignment explanation
Indices: 9418--9672 Score: 385
Period size: 131 Copynumber: 2.0 Consensus size: 128
9408 CATTGTTTAA
*
9418 ACTTTTATAGTTTTACTCAACTAAAAACTCTAATTTTATTTAATTAAATCTAATAT-C-T-T-TA
1 ACTTTTACAGTTTTACTCAACTAAAAACTCTAATTTTATTTAATTAAATCTAATATCCTTATCTA
*
9479 -TGATTTTTACCATTTTACTATTTTAATTAAAAAAATTTTATATATTAGAATTTTTTAAATAT
66 TTGATTTTTACCATTTTACTATTTTAATTAAAAAAATTATATATATTAGAATTTTTTAAATAT
*
9541 ACTTTTACAGTTTTACTCAACTAAAAACTCTATTTTTATTTAATTAAATCTAATATCCTTATACC
1 ACTTTTACAGTTTTACTCAACTAAAAACTCTAATTTTATTTAATTAAATCTAATATCCTTAT--C
* * * *
9606 TATTTTATTTTTACCATTTTACTATTTTATTTTAAAAACTTATATATATTAGAATTTTTTAAATA
64 TA-TTGATTTTTACCATTTTACTATTTTAATTAAAAAAATTATATATATTAGAATTTTTTAAATA
9671 T
128 T
9672 A
1 A
9673 TTTCTTAAAT
Statistics
Matches: 117, Mismatches: 7, Indels: 8
0.89 0.05 0.06
Matches are distributed among these distances:
123 54 0.46
124 1 0.01
125 1 0.01
126 1 0.01
129 2 0.02
131 58 0.50
ACGTcount: A:0.37, C:0.11, G:0.02, T:0.51
Consensus pattern (128 bp):
ACTTTTACAGTTTTACTCAACTAAAAACTCTAATTTTATTTAATTAAATCTAATATCCTTATCTA
TTGATTTTTACCATTTTACTATTTTAATTAAAAAAATTATATATATTAGAATTTTTTAAATAT
Found at i:9694 original size:14 final size:13
Alignment explanation
Indices: 9658--9696 Score: 51
Period size: 14 Copynumber: 2.9 Consensus size: 13
9648 TATATATTAG
9658 AATTTTTTAAATA
1 AATTTTTTAAATA
* *
9671 TATTTCTTAAATGA
1 AATTTTTTAAAT-A
9685 AATTTTTTAAAT
1 AATTTTTTAAAT
9697 TTTACAATTT
Statistics
Matches: 21, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
13 10 0.48
14 11 0.52
ACGTcount: A:0.41, C:0.03, G:0.03, T:0.54
Consensus pattern (13 bp):
AATTTTTTAAATA
Found at i:11505 original size:2 final size:2
Alignment explanation
Indices: 11498--11523 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
11488 TAATCTTTGA
11498 AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT
11524 GTACAAAAAT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:19271 original size:50 final size:51
Alignment explanation
Indices: 19217--19314 Score: 162
Period size: 50 Copynumber: 1.9 Consensus size: 51
19207 GATCATAAGA
*
19217 TAAAGGAAGAATAACAAAAACACATTCCAAACGCTTGATACTT-AAATTGG
1 TAAAGGAAGAATAACAAAAACACATTCCAAACACTTGATACTTGAAATTGG
* *
19267 TAAAGGAATAATAACAAAAACACATTCCAAGCACTTGATACTTGAAAT
1 TAAAGGAAGAATAACAAAAACACATTCCAAACACTTGATACTTGAAAT
19315 GGCGATATCA
Statistics
Matches: 44, Mismatches: 3, Indels: 1
0.92 0.06 0.02
Matches are distributed among these distances:
50 40 0.91
51 4 0.09
ACGTcount: A:0.49, C:0.16, G:0.12, T:0.22
Consensus pattern (51 bp):
TAAAGGAAGAATAACAAAAACACATTCCAAACACTTGATACTTGAAATTGG
Found at i:22965 original size:147 final size:146
Alignment explanation
Indices: 22698--22988 Score: 354
Period size: 147 Copynumber: 2.0 Consensus size: 146
22688 AGGAAATTGC
** **
22698 AGGAAAAGAAATCAGAGGAAAAAGAAACCGACTTTATACCAAAAGATGAAGTGGTTGAGCAGGAG
1 AGGAAAAGAAATCAGAGGAAAAAGAAACCGACTCCATA-CAAAAGATGAAGTGAATGAGCAGGAG
* * * * * *
22763 GAGCCAAATTCATCATCGAGAAATGAACTGAAAGTAGGGGATGCGAAGAATGAGGTTGAGAAGAG
65 GAGCCAAATTCATCACCGACAAAGGAACAGAAAGTAGGGGATGCAAAGAATGAGGTTAAGAAGAG
22828 TTGTAATGAAAGGGATG
130 TTGTAATGAAAGGGATG
* *
22845 AGGAAAAGAAATCAGAGGAAAAAGAAGCCGAGC-CCATA-AATATGGATGAAGTGAATGAGCAGG
1 AGGAAAAGAAATCAGAGGAAAAAGAAACCGA-CTCCATACAA-A-AGATGAAGTGAATGAGCAGG
* * * * *
22908 AGGAGCTAAATTCATCACCGCCAGAGGAAGAGAAAGT-GGAGGATGCAAATAATGAGGTTAAGAA
63 AGGAGCCAAATTCATCACCGACAAAGGAACAGAAAGTAGG-GGATGCAAAGAATGAGGTTAAGAA
*
22972 GAGTTGTGATGAAAGGG
127 GAGTTGTAATGAAAGGG
22989 TAGAGTTGGA
Statistics
Matches: 122, Mismatches: 18, Indels: 8
0.82 0.12 0.05
Matches are distributed among these distances:
145 2 0.02
146 3 0.02
147 116 0.95
148 1 0.01
ACGTcount: A:0.43, C:0.10, G:0.31, T:0.16
Consensus pattern (146 bp):
AGGAAAAGAAATCAGAGGAAAAAGAAACCGACTCCATACAAAAGATGAAGTGAATGAGCAGGAGG
AGCCAAATTCATCACCGACAAAGGAACAGAAAGTAGGGGATGCAAAGAATGAGGTTAAGAAGAGT
TGTAATGAAAGGGATG
Found at i:25178 original size:6 final size:6
Alignment explanation
Indices: 25167--25191 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
25157 GAAGCCATGG
25167 CAAGCT CAAGCT CAAGCT CAAGCT C
1 CAAGCT CAAGCT CAAGCT CAAGCT C
25192 TCCTCCTCTC
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.32, C:0.36, G:0.16, T:0.16
Consensus pattern (6 bp):
CAAGCT
Found at i:32823 original size:13 final size:13
Alignment explanation
Indices: 32805--32831 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
32795 TGGCCCAAAG
32805 AAAGAAAAAGAAA
1 AAAGAAAAAGAAA
32818 AAAGAAAAAGAAA
1 AAAGAAAAAGAAA
32831 A
1 A
32832 GTAAGCAACC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.85, C:0.00, G:0.15, T:0.00
Consensus pattern (13 bp):
AAAGAAAAAGAAA
Found at i:35960 original size:16 final size:16
Alignment explanation
Indices: 35939--35971 Score: 66
Period size: 16 Copynumber: 2.1 Consensus size: 16
35929 TACTACTTTC
35939 TTTATTTGTCACATTT
1 TTTATTTGTCACATTT
35955 TTTATTTGTCACATTT
1 TTTATTTGTCACATTT
35971 T
1 T
35972 GGTTAACTAT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.18, C:0.12, G:0.06, T:0.64
Consensus pattern (16 bp):
TTTATTTGTCACATTT
Found at i:38012 original size:124 final size:128
Alignment explanation
Indices: 37766--38012 Score: 328
Period size: 124 Copynumber: 1.9 Consensus size: 128
37756 TGGCCAAAAA
37766 AATTAAAATAGTAAAATGGTAAAAATAAAATAGGTATAAGGATATTAGATTTAATTAAATAAAAA
1 AATTAAAATAGTAAAATGGTAAAAAT---ATA-GTATAAGGATATTAGATTTAATTAAATAAAAA
* * ** * *
37831 TAAATTTTTTAGTTGAGTAAAACTGTAAAAGTATATTTAAATAATTCTAATATATATAAATTTTT
62 TAAAGTTTTTAGTTGAGTAAAACTATAAAAGTATATAAAAATAATTCTAAGAAATATAAATTTTT
37896 TT
127 TT
37898 AATTAAAATAGTAAAATGGTAAAAAT-TA-TA-AA-GATATTAGATTTAATTAAATAAAAATAAA
1 AATTAAAATAGTAAAATGGTAAAAATATAGTATAAGGATATTAGATTTAATTAAATAAAAATAAA
37959 GTTTTTAGTTGAGTAAAACTATAAAAGT-T-TAAACAATGACATT-TAAGAAATATA
66 GTTTTTAGTTGAGTAAAACTATAAAAGTATATAAA-AAT-A-ATTCTAAGAAATATA
38013 TTCGAAAAAT
Statistics
Matches: 106, Mismatches: 6, Indels: 14
0.84 0.05 0.11
Matches are distributed among these distances:
122 2 0.02
123 4 0.04
124 65 0.61
125 5 0.05
126 2 0.02
128 2 0.02
132 26 0.25
ACGTcount: A:0.52, C:0.02, G:0.10, T:0.36
Consensus pattern (128 bp):
AATTAAAATAGTAAAATGGTAAAAATATAGTATAAGGATATTAGATTTAATTAAATAAAAATAAA
GTTTTTAGTTGAGTAAAACTATAAAAGTATATAAAAATAATTCTAAGAAATATAAATTTTTTT
Found at i:40309 original size:12 final size:12
Alignment explanation
Indices: 40270--40313 Score: 61
Period size: 12 Copynumber: 3.6 Consensus size: 12
40260 TTTAATCCAG
40270 ATATCGACGGAT
1 ATATCGACGGAT
* *
40282 ATATTGGACAGAT
1 ATA-TCGACGGAT
40295 ATATCGACGGAT
1 ATATCGACGGAT
40307 ATATCGA
1 ATATCGA
40314 GGTATCGATG
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
12 17 0.63
13 10 0.37
ACGTcount: A:0.36, C:0.14, G:0.23, T:0.27
Consensus pattern (12 bp):
ATATCGACGGAT
Found at i:41799 original size:14 final size:14
Alignment explanation
Indices: 41780--41807 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
41770 TTAAAACTTA
41780 ATTTATAATAAAAT
1 ATTTATAATAAAAT
41794 ATTTATAATAAAAT
1 ATTTATAATAAAAT
41808 CAAAATATTA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (14 bp):
ATTTATAATAAAAT
Found at i:41889 original size:29 final size:29
Alignment explanation
Indices: 41847--41903 Score: 114
Period size: 29 Copynumber: 2.0 Consensus size: 29
41837 AGTTACATAT
41847 ATATTATTATTATTTTAATCTTAATTAAC
1 ATATTATTATTATTTTAATCTTAATTAAC
41876 ATATTATTATTATTTTAATCTTAATTAA
1 ATATTATTATTATTTTAATCTTAATTAA
41904 TGAATAATAT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 28 1.00
ACGTcount: A:0.39, C:0.05, G:0.00, T:0.56
Consensus pattern (29 bp):
ATATTATTATTATTTTAATCTTAATTAAC
Found at i:42775 original size:18 final size:18
Alignment explanation
Indices: 42741--42776 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
42731 ATTTCATTTT
*
42741 AATTTTTTTGTTCAATTG
1 AATTTTTTTGTTAAATTG
*
42759 AATTTTTTTTTTAAATTG
1 AATTTTTTTGTTAAATTG
42777 TGTTCAAATT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.25, C:0.03, G:0.08, T:0.64
Consensus pattern (18 bp):
AATTTTTTTGTTAAATTG
Done.