Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01012672.1 Corchorus olitorius cultivar O-4 contig12705, 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: 28112
ACGTcount: A:0.30, C:0.17, G:0.19, T:0.34
Found at i:1158 original size:30 final size:30
Alignment explanation
Indices: 1124--1186 Score: 108
Period size: 30 Copynumber: 2.1 Consensus size: 30
1114 AATTAGACTC
* *
1124 ATTTGATTGTTGTTAGTGTATAATAATTTA
1 ATTTGATTATTGTTAGTGTACAATAATTTA
1154 ATTTGATTATTGTTAGTGTACAATAATTTA
1 ATTTGATTATTGTTAGTGTACAATAATTTA
1184 ATT
1 ATT
1187 GTTAAGCATG
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
30 31 1.00
ACGTcount: A:0.32, C:0.02, G:0.14, T:0.52
Consensus pattern (30 bp):
ATTTGATTATTGTTAGTGTACAATAATTTA
Found at i:1469 original size:22 final size:22
Alignment explanation
Indices: 1444--1495 Score: 86
Period size: 22 Copynumber: 2.4 Consensus size: 22
1434 TCATTTGTTT
1444 ATTTGATTATTTCTATATCGTC
1 ATTTGATTATTTCTATATCGTC
* *
1466 ATTTGATTATTTTTATATGGTC
1 ATTTGATTATTTCTATATCGTC
1488 ATTTGATT
1 ATTTGATT
1496 GTTCTTGGTG
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
22 28 1.00
ACGTcount: A:0.23, C:0.08, G:0.12, T:0.58
Consensus pattern (22 bp):
ATTTGATTATTTCTATATCGTC
Found at i:1572 original size:20 final size:20
Alignment explanation
Indices: 1547--1597 Score: 57
Period size: 23 Copynumber: 2.4 Consensus size: 20
1537 AATTACAAGG
1547 CTTGATTAGGGTAATATGTA
1 CTTGATTAGGGTAATATGTA
*
1567 CTTGATAACTAGGGTCATATGTA
1 CTTGAT---TAGGGTAATATGTA
*
1590 CTTAATTA
1 CTTGATTA
1598 CAAGGCATGT
Statistics
Matches: 26, Mismatches: 2, Indels: 6
0.76 0.06 0.18
Matches are distributed among these distances:
20 8 0.31
23 18 0.69
ACGTcount: A:0.31, C:0.10, G:0.20, T:0.39
Consensus pattern (20 bp):
CTTGATTAGGGTAATATGTA
Found at i:2014 original size:206 final size:206
Alignment explanation
Indices: 1660--2071 Score: 691
Period size: 206 Copynumber: 2.0 Consensus size: 206
1650 ATATATAACA
* * *
1660 TATAACATATATTAAAGTTGGAAAGGAAATTACCCTTTTGTCCAGCTATAAGATGTACCGCATTC
1 TATAACATATATTAAAGTTGGAAAGGAAATTACCCTTTTGTCCAACTATAAGATGCACCACATTC
* * *
1725 ATCCAAGAACAAATTATCAGGGGTATTTCGATACTTTCATACTTAGCTTTTTTGCATCAAGCCCT
66 ACCCAAGAACAAATTATCAGGGATATTTCGATACTTTCATACTCAGCTTTTTTGCATCAAGCCCT
*
1790 GGTAAGGTTCTTCGCTTTGCATATGACGCCGAGTCGGCTCCTATGCCGCTAGCTATGCCCTGCTT
131 AGTAAGGTTCTTCGCTTTGCATATGACGCCGAGTCGGCTCCTATGCCGCTAGCTATGCCCTGCTT
1855 GGTCCCCCGGC
196 GGTCCCCCGGC
*
1866 TATAACATATATTAAAGTTGGAAAGGAAATTACCCTTTTGTCCAACTATAAGATGCACCATATTC
1 TATAACATATATTAAAGTTGGAAAGGAAATTACCCTTTTGTCCAACTATAAGATGCACCACATTC
* * * * *
1931 ACCCAAGAACAAATTGTCAGGGATATTTCGGTACTTTCATGCTCAG-TTTTTTCGCGTTAAGCCC
66 ACCCAAGAACAAATTATCAGGGATATTTCGATACTTTCATACTCAGCTTTTTT-GCATCAAGCCC
1995 TAGTAAGGTTCTTCGCTTTGCATATGACGCCGAGTCGGCTCCTATGCCGCTAGCTATGCCCTGCT
130 TAGTAAGGTTCTTCGCTTTGCATATGACGCCGAGTCGGCTCCTATGCCGCTAGCTATGCCCTGCT
2060 TGGTCCCCCGGC
195 TGGTCCCCCGGC
2072 GCGGTGGAGA
Statistics
Matches: 192, Mismatches: 13, Indels: 2
0.93 0.06 0.01
Matches are distributed among these distances:
205 6 0.03
206 186 0.97
ACGTcount: A:0.25, C:0.25, G:0.19, T:0.31
Consensus pattern (206 bp):
TATAACATATATTAAAGTTGGAAAGGAAATTACCCTTTTGTCCAACTATAAGATGCACCACATTC
ACCCAAGAACAAATTATCAGGGATATTTCGATACTTTCATACTCAGCTTTTTTGCATCAAGCCCT
AGTAAGGTTCTTCGCTTTGCATATGACGCCGAGTCGGCTCCTATGCCGCTAGCTATGCCCTGCTT
GGTCCCCCGGC
Found at i:2297 original size:1 final size:1
Alignment explanation
Indices: 2291--2320 Score: 51
Period size: 1 Copynumber: 30.0 Consensus size: 1
2281 TAATTCTTCG
*
2291 TTTTTTTTTTTTTTTTTTCTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
2321 CTTCTGTATG
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
1 27 1.00
ACGTcount: A:0.00, C:0.03, G:0.00, T:0.97
Consensus pattern (1 bp):
T
Found at i:2315 original size:15 final size:15
Alignment explanation
Indices: 2291--2325 Score: 54
Period size: 15 Copynumber: 2.4 Consensus size: 15
2281 TAATTCTTCG
2291 TTTT-TTTTTTTTTT
1 TTTTCTTTTTTTTTT
2305 TTTTCTTTTTTTTTT
1 TTTTCTTTTTTTTTT
*
2320 TCTTCT
1 TTTTCT
2326 GTATGTCCAA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
14 4 0.21
15 15 0.79
ACGTcount: A:0.00, C:0.09, G:0.00, T:0.91
Consensus pattern (15 bp):
TTTTCTTTTTTTTTT
Found at i:2321 original size:12 final size:12
Alignment explanation
Indices: 2291--2323 Score: 59
Period size: 12 Copynumber: 2.8 Consensus size: 12
2281 TAATTCTTCG
2291 TTTTTTT-TTTT
1 TTTTTTTCTTTT
2302 TTTTTTTCTTTT
1 TTTTTTTCTTTT
2314 TTTTTTTCTT
1 TTTTTTTCTT
2324 CTGTATGTCC
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
11 7 0.33
12 14 0.67
ACGTcount: A:0.00, C:0.06, G:0.00, T:0.94
Consensus pattern (12 bp):
TTTTTTTCTTTT
Found at i:8002 original size:19 final size:18
Alignment explanation
Indices: 7978--8017 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 18
7968 TTGAAGATTT
7978 ATTGAAGACAATTTGAAGA
1 ATTGAAGACAA-TTGAAGA
**
7997 ATTGAAGATGATTGAAGA
1 ATTGAAGACAATTGAAGA
8015 ATT
1 ATT
8018 ATCTCAGGAG
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
18 10 0.53
19 9 0.47
ACGTcount: A:0.45, C:0.03, G:0.23, T:0.30
Consensus pattern (18 bp):
ATTGAAGACAATTGAAGA
Found at i:8996 original size:15 final size:15
Alignment explanation
Indices: 8976--9014 Score: 53
Period size: 15 Copynumber: 2.6 Consensus size: 15
8966 TAACATTTTT
8976 TATATTATAT-ATATA
1 TATATTATATAAT-TA
8991 TATATTATATAATTA
1 TATATTATATAATTA
*
9006 TAAATTATA
1 TATATTATA
9015 ACCTAAAAGT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
15 20 0.91
16 2 0.09
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (15 bp):
TATATTATATAATTA
Found at i:14142 original size:21 final size:21
Alignment explanation
Indices: 14116--14170 Score: 74
Period size: 21 Copynumber: 2.6 Consensus size: 21
14106 CATGGAATCG
**
14116 CCGTGCCACCACCGGTTAAGC
1 CCGTGCCACCACCGGCCAAGC
*
14137 CCGTGCCACCACCGGCCATGC
1 CCGTGCCACCACCGGCCAAGC
*
14158 CCGTGCCATCACC
1 CCGTGCCACCACC
14171 ATTCCGCGCT
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 30 1.00
ACGTcount: A:0.16, C:0.49, G:0.22, T:0.13
Consensus pattern (21 bp):
CCGTGCCACCACCGGCCAAGC
Found at i:15151 original size:28 final size:27
Alignment explanation
Indices: 15076--15192 Score: 153
Period size: 28 Copynumber: 4.3 Consensus size: 27
15066 TCCCATATTG
*
15076 GTCATTTACATGTCCAGGGGCATTTTA
1 GTCATTTGCATGTCCAGGGGCATTTTA
* *
15103 GTCATTTGCATATCCAGGGGCATTTTG
1 GTCATTTGCATGTCCAGGGGCATTTTA
*
15130 GTCATTTTGCATGTCCATGGGCATTTTA
1 GTCA-TTTGCATGTCCAGGGGCATTTTA
**
15158 GTCATTTGCGCGTCCAGAGGGCATTTTA
1 GTCATTTGCATGTCCAG-GGGCATTTTA
*
15186 ATCATTT
1 GTCATTT
15193 AAAGTGCACT
Statistics
Matches: 78, Mismatches: 10, Indels: 3
0.86 0.11 0.03
Matches are distributed among these distances:
27 38 0.49
28 40 0.51
ACGTcount: A:0.20, C:0.19, G:0.23, T:0.38
Consensus pattern (27 bp):
GTCATTTGCATGTCCAGGGGCATTTTA
Found at i:15155 original size:55 final size:55
Alignment explanation
Indices: 15073--15193 Score: 163
Period size: 55 Copynumber: 2.2 Consensus size: 55
15063 ACTTCCCATA
*
15073 TTGGTCATTTACATGTCCAGGGGCATTTTAGTCATTTGCATATCCAG-GGGCATT
1 TTGGTCATTTACATGTCCAGGGGCATTTTAGTCATTTGCACATCCAGAGGGCATT
* * * *
15127 TTGGTCATTTTGCATGTCCATGGGCATTTTAGTCATTTGCGCGTCCAGAGGGCATT
1 TTGGTCA-TTTACATGTCCAGGGGCATTTTAGTCATTTGCACATCCAGAGGGCATT
**
15183 TTAATCATTTA
1 TTGGTCATTTA
15194 AAGTGCACTC
Statistics
Matches: 57, Mismatches: 8, Indels: 3
0.84 0.12 0.04
Matches are distributed among these distances:
54 7 0.12
55 38 0.67
56 12 0.21
ACGTcount: A:0.20, C:0.18, G:0.23, T:0.39
Consensus pattern (55 bp):
TTGGTCATTTACATGTCCAGGGGCATTTTAGTCATTTGCACATCCAGAGGGCATT
Found at i:18480 original size:17 final size:18
Alignment explanation
Indices: 18458--18493 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
18448 AAAGGGTAGT
*
18458 TTAAAA-AATTGTTTTCA
1 TTAAAAGAAGTGTTTTCA
18475 TTAAAAGAAGTGTTTTCA
1 TTAAAAGAAGTGTTTTCA
18493 T
1 T
18494 GCAAGAGGAG
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
17 6 0.35
18 11 0.65
ACGTcount: A:0.39, C:0.06, G:0.11, T:0.44
Consensus pattern (18 bp):
TTAAAAGAAGTGTTTTCA
Found at i:19360 original size:19 final size:18
Alignment explanation
Indices: 19336--19375 Score: 53
Period size: 19 Copynumber: 2.2 Consensus size: 18
19326 TTGAAGATTT
19336 ATTGAAGACAATTAGAAGA
1 ATTGAAGACAATT-GAAGA
**
19355 ATTGAAGATGATTGAAGA
1 ATTGAAGACAATTGAAGA
19373 ATT
1 ATT
19376 ATCTCAAGAG
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
18 8 0.42
19 11 0.58
ACGTcount: A:0.47, C:0.03, G:0.23, T:0.28
Consensus pattern (18 bp):
ATTGAAGACAATTGAAGA
Found at i:20781 original size:20 final size:21
Alignment explanation
Indices: 20747--20785 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
20737 CATAGTTTAG
*
20747 TTTTATTTTACTTTGCTTTGT
1 TTTTAGTTTACTTTGCTTTGT
20768 TTTTAGTTTA-TTTGCTTT
1 TTTTAGTTTACTTTGCTTT
20786 CTTTATAATT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 8 0.47
21 9 0.53
ACGTcount: A:0.10, C:0.08, G:0.10, T:0.72
Consensus pattern (21 bp):
TTTTAGTTTACTTTGCTTTGT
Found at i:21447 original size:15 final size:15
Alignment explanation
Indices: 21429--21463 Score: 52
Period size: 15 Copynumber: 2.3 Consensus size: 15
21419 AACCTTTAGT
*
21429 TTAATTTTCTTTCCA
1 TTAATTTTCATTCCA
*
21444 TTAATTTTGATTCCA
1 TTAATTTTCATTCCA
21459 TTAAT
1 TTAAT
21464 CATTAATTAA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.26, C:0.14, G:0.03, T:0.57
Consensus pattern (15 bp):
TTAATTTTCATTCCA
Done.