Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01012347.1 Corchorus olitorius cultivar O-4 contig12380, 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: 37309
ACGTcount: A:0.32, C:0.15, G:0.18, T:0.34
Found at i:75 original size:2 final size:2
Alignment explanation
Indices: 70--108 Score: 51
Period size: 2 Copynumber: 19.5 Consensus size: 2
60 TATATGTATA
* * *
70 TG TG TG TG TA TA TA TG TG TG TG TG TG TG TG TG TG TG TG T
1 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG T
109 ATGCCATGTG
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.08, C:0.00, G:0.41, T:0.51
Consensus pattern (2 bp):
TG
Found at i:81 original size:12 final size:12
Alignment explanation
Indices: 64--102 Score: 51
Period size: 12 Copynumber: 3.2 Consensus size: 12
54 TACATATATA
64 TGTATATGTGTG
1 TGTATATGTGTG
*
76 TGTATATATGTG
1 TGTATATGTGTG
* *
88 TGTGTGTGTGTG
1 TGTATATGTGTG
100 TGT
1 TGT
103 GTGTGTATGC
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
12 23 1.00
ACGTcount: A:0.13, C:0.00, G:0.36, T:0.51
Consensus pattern (12 bp):
TGTATATGTGTG
Found at i:83 original size:20 final size:20
Alignment explanation
Indices: 58--98 Score: 64
Period size: 20 Copynumber: 2.0 Consensus size: 20
48 GTAAATTACA
58 TATATATGTATATGTGTGTG
1 TATATATGTATATGTGTGTG
* *
78 TATATATGTGTGTGTGTGTG
1 TATATATGTATATGTGTGTG
98 T
1 T
99 GTGTGTGTGT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.20, C:0.00, G:0.29, T:0.51
Consensus pattern (20 bp):
TATATATGTATATGTGTGTG
Found at i:107 original size:14 final size:14
Alignment explanation
Indices: 64--110 Score: 67
Period size: 14 Copynumber: 3.4 Consensus size: 14
54 TACATATATA
64 TGTATATGTGTGTG
1 TGTATATGTGTGTG
*
78 TATATATGTGTGTG
1 TGTATATGTGTGTG
* *
92 TGTGTGTGTGTGTG
1 TGTATATGTGTGTG
106 TGTAT
1 TGTAT
111 GCCATGTGAA
Statistics
Matches: 28, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
14 28 1.00
ACGTcount: A:0.13, C:0.00, G:0.36, T:0.51
Consensus pattern (14 bp):
TGTATATGTGTGTG
Found at i:1259 original size:119 final size:118
Alignment explanation
Indices: 1021--1359 Score: 498
Period size: 119 Copynumber: 2.9 Consensus size: 118
1011 CGTTTGGGAT
* *
1021 CTAAGAATTAAGGAGTAATTTATACTATTTTTATTGGAAGAGTTGGTTTGAAGTGGAAAATTTG-
1 CTAAGAATTAAGGAGTAATTTATACTATTTTTATTGGAAGAGTTGGTTTGAAATGGAAAA-ATGA
* * *
1085 AGGA-TT----TGCCTCAAAACAATATTCATGGTTGTGGTGGAGCGTTTGGAAC
65 AGGACTTGAAATTCCTCAAAACAATATTCATGGTTGTGGTGGAGCCTTTAGAAC
* *
1134 CTAAGAATTAAGGAGTAATTTATACTATTTTTA-TGGAAGAGTTGGTTTGAAGTGGAAAATTTG-
1 CTAAGAATTAAGGAGTAATTTATACTATTTTTATTGGAAGAGTTGGTTTGAAATGGAAAA-ATGA
*
1197 AGGACTTGAGAAATTCCTCAAAACAATATTCATGGTTGTGGTGGAGCCTTTA-AGAT
65 AGGACTT--GAAATTCCTCAAAACAATATTCATGGTTGTGGTGGAGCCTTTAGA-AC
1253 CTAAGAATTAAGGAGTAATTTATACTATTTTTATTGGAAGAGTTGGTTTGAAATGGAAAAATGAA
1 CTAAGAATTAAGGAGTAATTTATACTATTTTTATTGGAAGAGTTGGTTTGAAATGGAAAAATGAA
1318 GGACTTGAAATTCCTCAAAACAATATTCATGGTTGTGGTGGA
66 GGACTTGAAATTCCTCAAAACAATATTCATGGTTGTGGTGGA
1360 TATTCTTCCA
Statistics
Matches: 210, Mismatches: 6, Indels: 15
0.91 0.03 0.06
Matches are distributed among these distances:
112 34 0.16
113 35 0.17
118 37 0.18
119 72 0.34
120 32 0.15
ACGTcount: A:0.34, C:0.08, G:0.24, T:0.35
Consensus pattern (118 bp):
CTAAGAATTAAGGAGTAATTTATACTATTTTTATTGGAAGAGTTGGTTTGAAATGGAAAAATGAA
GGACTTGAAATTCCTCAAAACAATATTCATGGTTGTGGTGGAGCCTTTAGAAC
Found at i:1695 original size:105 final size:105
Alignment explanation
Indices: 1573--1782 Score: 330
Period size: 105 Copynumber: 2.0 Consensus size: 105
1563 ATAAAAAATT
* * *
1573 TAATGAGTAAAAAGAATATTAATTAAAAAATTATTATACTATAATACTGAGAAAATTTTAGAAAT
1 TAATGACTAAAAAGAATATTAATTAAAAAATTATTATACTATAACACTAAGAAAATTTTAGAAAT
* *
1638 TTCCCAATTAAGATTTTTGAGTTCGTGATTTTATATAGTA
66 TTCCCAATTAAAATTTCTGAGTTCGTGATTTTATATAGTA
* ***
1678 TAATGACTAATAAGAATATTAATTAAAAAATTATTATACTATAACACTAAGGGTATTTTAGAAAT
1 TAATGACTAAAAAGAATATTAATTAAAAAATTATTATACTATAACACTAAGAAAATTTTAGAAAT
*
1743 TTCCCAATTAAAATTTCTGAGTTTGTGATTTTATATAGTA
66 TTCCCAATTAAAATTTCTGAGTTCGTGATTTTATATAGTA
1783 GTAAGATAGT
Statistics
Matches: 95, Mismatches: 10, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
105 95 1.00
ACGTcount: A:0.43, C:0.07, G:0.11, T:0.40
Consensus pattern (105 bp):
TAATGACTAAAAAGAATATTAATTAAAAAATTATTATACTATAACACTAAGAAAATTTTAGAAAT
TTCCCAATTAAAATTTCTGAGTTCGTGATTTTATATAGTA
Found at i:9570 original size:96 final size:99
Alignment explanation
Indices: 9465--9658 Score: 295
Period size: 96 Copynumber: 2.0 Consensus size: 99
9455 ACTTTTTAAT
* * *
9465 TAAATTAGTAATATCGTAAAAATAAAATAGGTATAAGGATATTAGATTTAAT-AATTAAATA-A-
1 TAAAATAGTAAAATCGTAAAAATAAAATAGGTATAAGGATATTAGATTTAATCAAATAAATATAG
*
9527 AAATAGAGTTTTTAGTTGAGTAAAACTATAAAAG
66 AAATAGAGTTTTTAGTTGACTAAAACTATAAAAG
* * *
9561 TAAAATAGTAAAATGGTAAAAATAAGATAGTTATAAGGATATTAGATTTAATCAAATAAATATAG
1 TAAAATAGTAAAATCGTAAAAATAAAATAGGTATAAGGATATTAGATTTAATCAAATAAATATAG
*
9626 ATATAGAGTTTTTAGTTGACTAAAACTATAAAA
66 AAATAGAGTTTTTAGTTGACTAAAACTATAAAA
9659 ATTTAAACAA
Statistics
Matches: 87, Mismatches: 8, Indels: 3
0.89 0.08 0.03
Matches are distributed among these distances:
96 47 0.54
97 8 0.09
98 1 0.01
99 31 0.36
ACGTcount: A:0.51, C:0.03, G:0.13, T:0.33
Consensus pattern (99 bp):
TAAAATAGTAAAATCGTAAAAATAAAATAGGTATAAGGATATTAGATTTAATCAAATAAATATAG
AAATAGAGTTTTTAGTTGACTAAAACTATAAAAG
Found at i:11215 original size:45 final size:45
Alignment explanation
Indices: 11160--11248 Score: 142
Period size: 45 Copynumber: 2.0 Consensus size: 45
11150 TAGCAAATAA
* *
11160 TTCTACTCCATCTCTAGGTAATTCATCAAAATAAAGCTAATATTC
1 TTCTACTCCATCTCTAGATAATTCATCAAAATAAAACTAATATTC
* *
11205 TTCTCCTCCATCTCTAGATAATTCATCAAAATAAAACTAGTATT
1 TTCTACTCCATCTCTAGATAATTCATCAAAATAAAACTAATATT
11249 AATTGTTGTT
Statistics
Matches: 40, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
45 40 1.00
ACGTcount: A:0.36, C:0.22, G:0.06, T:0.36
Consensus pattern (45 bp):
TTCTACTCCATCTCTAGATAATTCATCAAAATAAAACTAATATTC
Found at i:25876 original size:22 final size:22
Alignment explanation
Indices: 25848--25891 Score: 88
Period size: 22 Copynumber: 2.0 Consensus size: 22
25838 TTGCACGTAT
25848 GTTAATCTATACTATATTAAAA
1 GTTAATCTATACTATATTAAAA
25870 GTTAATCTATACTATATTAAAA
1 GTTAATCTATACTATATTAAAA
25892 AGTATGACAT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.45, C:0.09, G:0.05, T:0.41
Consensus pattern (22 bp):
GTTAATCTATACTATATTAAAA
Found at i:30171 original size:139 final size:134
Alignment explanation
Indices: 29917--30181 Score: 390
Period size: 139 Copynumber: 1.9 Consensus size: 134
29907 TATACATCAC
29917 ATTAGTTTTGAGTTTTGTCAATTTATTTTATTGACCTTAGGAAGGAGTGTATGTTTCTAGGATTT
1 ATTAGTTTTGAGTTTTGTCAATTTATTTTATTGACCTT---AAGGAGTGTATGTTTCTAGGATTT
* *
29982 TGATTGTAATGGTTTAGGGTAATTGTCGTCCAGGGGGTGCGCTCCCTTTGATCACCCACTTCGAA
63 TGATTGTAATGGTTTAGGGTAATTGTCGTCCAAGGGATGCGCTCCCTTTGATCACCCACTTCGAA
30047 ACACCAT
128 ACACCAT
*
30054 ATTAGTTTTGGGTTTTGTCAATTTATTTTATTGACCTT-A-GAGTGTATGTTTCTAGGATTTTGA
1 ATTAGTTTTGAGTTTTGTCAATTTATTTTATTGACCTTAAGGAGTGTATGTTTCTAGGATTTTGA
*
30117 TTGCTTAGAATAATGGTTTAGGGTAATTGTCGTCCAAGGGATGCGCTCTCTTTGATCACCCACTT
66 ----TT-G--TAATGGTTTAGGGTAATTGTCGTCCAAGGGATGCGCTCCCTTTGATCACCCACTT
30182 TCTCTTTTCT
Statistics
Matches: 117, Mismatches: 4, Indels: 12
0.88 0.03 0.09
Matches are distributed among these distances:
132 24 0.21
133 1 0.01
136 2 0.02
137 38 0.32
139 52 0.44
ACGTcount: A:0.22, C:0.14, G:0.23, T:0.42
Consensus pattern (134 bp):
ATTAGTTTTGAGTTTTGTCAATTTATTTTATTGACCTTAAGGAGTGTATGTTTCTAGGATTTTGA
TTGTAATGGTTTAGGGTAATTGTCGTCCAAGGGATGCGCTCCCTTTGATCACCCACTTCGAAACA
CCAT
Found at i:37158 original size:31 final size:31
Alignment explanation
Indices: 37120--37284 Score: 157
Period size: 31 Copynumber: 5.5 Consensus size: 31
37110 TTAGGCTAGT
37120 TGCTCAAATAAGGGCCTAACGTTTGTCAAAA
1 TGCTCAAATAAGGGCCTAACGTTTGTCAAAA
* **
37151 TGCTCAAATAAGGGCCTTATC-TTT-T-AATT
1 TGCTCAAATAAGGGCC-TAACGTTTGTCAAAA
*
37180 TGGC-CAAATAAGGGCCTAACGTTTGCCAAAA
1 T-GCTCAAATAAGGGCCTAACGTTTGTCAAAA
* * **
37211 TGCTCAAATAAAGGCCTGATC-TTT-T-AATT
1 TGCTCAAATAAGGGCCT-AACGTTTGTCAAAA
*
37240 TGGC-CAAATAAGGGCCTAACGTTTGCCAAAA
1 T-GCTCAAATAAGGGCCTAACGTTTGTCAAAA
37271 TGCTCAAATAAGGG
1 TGCTCAAATAAGGG
37285 TCTGGCATCG
Statistics
Matches: 105, Mismatches: 17, Indels: 24
0.72 0.12 0.16
Matches are distributed among these distances:
28 5 0.05
29 36 0.34
30 9 0.09
31 50 0.48
32 5 0.05
ACGTcount: A:0.33, C:0.19, G:0.19, T:0.28
Consensus pattern (31 bp):
TGCTCAAATAAGGGCCTAACGTTTGTCAAAA
Found at i:37217 original size:60 final size:60
Alignment explanation
Indices: 37124--37284 Score: 295
Period size: 60 Copynumber: 2.7 Consensus size: 60
37114 GCTAGTTGCT
* *
37124 CAAATAAGGGCCTAACGTTTGTCAAAATGCTCAAATAAGGGCCTTATCTTTTAATTTGGC
1 CAAATAAGGGCCTAACGTTTGCCAAAATGCTCAAATAAGGGCCTGATCTTTTAATTTGGC
*
37184 CAAATAAGGGCCTAACGTTTGCCAAAATGCTCAAATAAAGGCCTGATCTTTTAATTTGGC
1 CAAATAAGGGCCTAACGTTTGCCAAAATGCTCAAATAAGGGCCTGATCTTTTAATTTGGC
37244 CAAATAAGGGCCTAACGTTTGCCAAAATGCTCAAATAAGGG
1 CAAATAAGGGCCTAACGTTTGCCAAAATGCTCAAATAAGGG
37285 TCTGGCATCG
Statistics
Matches: 97, Mismatches: 4, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
60 97 1.00
ACGTcount: A:0.34, C:0.19, G:0.19, T:0.27
Consensus pattern (60 bp):
CAAATAAGGGCCTAACGTTTGCCAAAATGCTCAAATAAGGGCCTGATCTTTTAATTTGGC
Found at i:37255 original size:29 final size:28
Alignment explanation
Indices: 37155--37257 Score: 100
Period size: 29 Copynumber: 3.5 Consensus size: 28
37145 TCAAAATGCT
37155 CAAATAAGGGCCTTATCTTTTAATTTGGC
1 CAAATAAGGGCC-TATCTTTTAATTTGGC
* * **
37184 CAAATAAGGGCCTAACGTTTGCCAAAAT-GC
1 CAAATAAGGGCCTATC-TTT--TAATTTGGC
*
37214 TCAAATAAAGGCCTGATCTTTTAATTTGGC
1 -CAAATAAGGGCCT-ATCTTTTAATTTGGC
37244 CAAATAAGGGCCTA
1 CAAATAAGGGCCTA
37258 ACGTTTGCCA
Statistics
Matches: 58, Mismatches: 10, Indels: 13
0.72 0.12 0.16
Matches are distributed among these distances:
28 4 0.07
29 30 0.52
30 4 0.07
31 18 0.31
32 2 0.03
ACGTcount: A:0.33, C:0.19, G:0.18, T:0.29
Consensus pattern (28 bp):
CAAATAAGGGCCTATCTTTTAATTTGGC
Done.