Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01024733.1 Corchorus olitorius cultivar O-4 contig24766, 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: 6260
ACGTcount: A:0.32, C:0.18, G:0.17, T:0.33
Found at i:1428 original size:26 final size:27
Alignment explanation
Indices: 1374--1440 Score: 91
Period size: 26 Copynumber: 2.5 Consensus size: 27
1364 CAAACTCTGG
* * *
1374 ATTTTGAGTTTCGAACATGACATGTAA
1 ATTTTGAGTTTTGAACATGAAATGCAA
1401 ATTTTGAGTTTTGAA-ATGAAATGCAA
1 ATTTTGAGTTTTGAACATGAAATGCAA
*
1427 ATTTTGAATTTTGA
1 ATTTTGAGTTTTGA
1441 CTTTTGAGGA
Statistics
Matches: 36, Mismatches: 4, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
26 22 0.61
27 14 0.39
ACGTcount: A:0.34, C:0.06, G:0.18, T:0.42
Consensus pattern (27 bp):
ATTTTGAGTTTTGAACATGAAATGCAA
Found at i:1498 original size:43 final size:43
Alignment explanation
Indices: 1417--1498 Score: 110
Period size: 43 Copynumber: 1.9 Consensus size: 43
1407 AGTTTTGAAA
* *
1417 TGAAATGCAAATTTTGAATTTTGACTTTTGAGGAATGAAATGT
1 TGAAATGCAAATTTTGAAATTTGACTTTTGAGCAATGAAATGT
** * *
1460 TGAAATGCAGGTTTTGAAATTTGATTTTTGAGCCATGAA
1 TGAAATGCAAATTTTGAAATTTGACTTTTGAGCAATGAA
1499 TTTTGAATTT
Statistics
Matches: 33, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
43 33 1.00
ACGTcount: A:0.33, C:0.06, G:0.22, T:0.39
Consensus pattern (43 bp):
TGAAATGCAAATTTTGAAATTTGACTTTTGAGCAATGAAATGT
Found at i:1505 original size:7 final size:7
Alignment explanation
Indices: 1495--1604 Score: 159
Period size: 7 Copynumber: 15.9 Consensus size: 7
1485 TTTTGAGCCA
1495 TGAATTT
1 TGAATTT
1502 TGAATTT
1 TGAATTT
1509 TGAATTT
1 TGAATTT
1516 TGAATTT
1 TGAATTT
1523 TGAATTT
1 TGAATTT
1530 TGAATTT
1 TGAATTT
1537 TG-ATTT
1 TGAATTT
*
1543 TGAGTTT
1 TGAATTT
*
1550 TGAGTTT
1 TGAATTT
*
1557 TGAGTTT
1 TGAATTT
*
1564 TGAGTTT
1 TGAATTT
*
1571 TGAGTTT
1 TGAATTT
*
1578 TGAGTTT
1 TGAATTT
1585 TGAATTT
1 TGAATTT
1592 TGAATTT
1 TGAATTT
1599 TGAATT
1 TGAATT
1605 GCCTATTTGG
Statistics
Matches: 100, Mismatches: 2, Indels: 2
0.96 0.02 0.02
Matches are distributed among these distances:
6 6 0.06
7 94 0.94
ACGTcount: A:0.23, C:0.00, G:0.20, T:0.57
Consensus pattern (7 bp):
TGAATTT
Found at i:1822 original size:33 final size:33
Alignment explanation
Indices: 1757--1822 Score: 87
Period size: 33 Copynumber: 2.0 Consensus size: 33
1747 AGAAACTGTG
* * ** *
1757 GATTTTGAACTTTGAGTTTTGATGTGATATGCA
1 GATTTTGAAATTTGAATTTTGAAATGAAATGCA
1790 GATTTTGAAATTTGAATTTTGAAATGAAATGCA
1 GATTTTGAAATTTGAATTTTGAAATGAAATGCA
1823 AATTGAACTT
Statistics
Matches: 28, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
33 28 1.00
ACGTcount: A:0.32, C:0.05, G:0.21, T:0.42
Consensus pattern (33 bp):
GATTTTGAAATTTGAATTTTGAAATGAAATGCA
Found at i:1930 original size:56 final size:55
Alignment explanation
Indices: 1870--2087 Score: 157
Period size: 55 Copynumber: 4.0 Consensus size: 55
1860 AATTCAACCT
* * * * *
1870 TGATCATGGAAATATTTCTTGGCACGACCGCACTGGATCAA-TTTAGAGATCAACTC
1 TGATCATCGAAA-ACTTCTTGGAAAGACCACACTGGATCAACTTTA-AGATCAACTC
*
1926 TGATCATCGTAAACTTCTTGGAAAGACCACACTGGATCAACTTTAAGATCAACT-
1 TGATCATCGAAAACTTCTTGGAAAGACCACACTGGATCAACTTTAAGATCAACTC
** * **
1980 TAGATTTTTGAAAACTTCTATGG-AAGACCACACATGG-TCGTC-TTAAGATCAACT-
1 T-GATCATCGAAAACTTCT-TGGAAAGACCACAC-TGGATCAACTTTAAGATCAACTC
* * * * *
2034 TAGA-CCTCTAAAAGCTTCTAT-GAAAGATCACACTGGGTCATC-TTAAGATCAACT
1 T-GATCATCGAAAA-CTTCT-TGGAAAGACCACACTGGATCAACTTTAAGATCAACT
2088 TTCTAGAGAG
Statistics
Matches: 137, Mismatches: 18, Indels: 16
0.80 0.11 0.09
Matches are distributed among these distances:
53 9 0.07
54 49 0.36
55 59 0.43
56 20 0.15
ACGTcount: A:0.33, C:0.21, G:0.17, T:0.29
Consensus pattern (55 bp):
TGATCATCGAAAACTTCTTGGAAAGACCACACTGGATCAACTTTAAGATCAACTC
Found at i:1995 original size:55 final size:55
Alignment explanation
Indices: 1895--2088 Score: 184
Period size: 54 Copynumber: 3.5 Consensus size: 55
1885 TTCTTGGCAC
* * * * *
1895 GACCGCACTGGATCAATTTAGAGATCAACTCT-GATCATCGTAAACTTCT-TGGAAA
1 GACCACACTGGATCAACTTA-AGATCAACT-TAGATCTTTGAAAACTTCTATGGAAA
*
1950 GACCACACTGGATCAACTTTAAGATCAACTTAGATTTTTGAAAACTTCTATGG-AA
1 GACCACACTGGATCAAC-TTAAGATCAACTTAGATCTTTGAAAACTTCTATGGAAA
** * *
2005 GACCACACATGG-TCGTCTTAAGATCAACTTAGACCTCT-AAAAGCTTCTAT-GAAA
1 GACCACAC-TGGATCAACTTAAGATCAACTTAGATCTTTGAAAA-CTTCTATGGAAA
* * *
2059 GATCACACTGGGTCATCTTAAGATCAACTT
1 GACCACACTGGATCAACTTAAGATCAACTT
2089 TCTAGAGAGA
Statistics
Matches: 119, Mismatches: 13, Indels: 15
0.81 0.09 0.10
Matches are distributed among these distances:
53 8 0.07
54 52 0.44
55 50 0.42
56 9 0.08
ACGTcount: A:0.34, C:0.22, G:0.16, T:0.28
Consensus pattern (55 bp):
GACCACACTGGATCAACTTAAGATCAACTTAGATCTTTGAAAACTTCTATGGAAA
Found at i:2241 original size:37 final size:36
Alignment explanation
Indices: 2199--2505 Score: 254
Period size: 37 Copynumber: 8.3 Consensus size: 36
2189 TTGAAGAGAC
* * *
2199 ACCTAAACAGGTACCTTAAATAAGGATTTAATAAGAA
1 ACCTAAACAGGGACCTTAAACAA-GATTTGATAAGAA
* * ** * * *
2236 ACCTAAACATGAATTTTGAACAAGATTTTGATGAGAC
1 ACCTAAACAGGGACCTTAAACAAGA-TTTGATAAGAA
*
2273 ACCTAAACAGGGACCTTAAATAAGGATTTGATAAGAA
1 ACCTAAACAGGGACCTTAAACAA-GATTTGATAAGAA
* * * * *
2310 ACCTAAACATGAATCTTAAACAAAATTTTTGACAAGAA
1 ACCTAAACAGGGACCTTAAACAAGA--TTTGATAAGAA
* *
2348 ACCTAAACAGGCACCTTAAATAAGGATTTGATAAGAA
1 ACCTAAACAGGGACCTTAAACAA-GATTTGATAAGAA
* * *
2385 ACCTAAACAGGGATCTTAAACAAGATCTTGATGAGAC
1 ACCTAAACAGGGACCTTAAACAAGAT-TTGATAAGAA
* * * * * * *
2422 ACTTAAATAGGGATCTTGAACCAGATTTCGATGAGAC
1 ACCTAAACAGGGACCTTAAACAAGATTT-GATAAGAA
* * *
2459 ACCTAAACAGGGACCTTAAATAAGGATTTAATAAGAC
1 ACCTAAACAGGGACCTTAAACAA-GATTTGATAAGAA
2496 ACCTAAACAG
1 ACCTAAACAG
2506 AAATCTTGAA
Statistics
Matches: 216, Mismatches: 46, Indels: 16
0.78 0.17 0.06
Matches are distributed among these distances:
36 8 0.04
37 171 0.79
38 36 0.17
39 1 0.00
ACGTcount: A:0.44, C:0.16, G:0.16, T:0.24
Consensus pattern (36 bp):
ACCTAAACAGGGACCTTAAACAAGATTTGATAAGAA
Found at i:2272 original size:74 final size:74
Alignment explanation
Indices: 2185--2428 Score: 353
Period size: 74 Copynumber: 3.3 Consensus size: 74
2175 CCTAAACTGG
* * *
2185 GATTTTGAAGAGACACCTAAACAGGTACCTTAAATAAGGATTTAATAAGAAACCTAAACATGAAT
1 GATTTTGATGAGACACCTAAACAGGCACCTTAAATAAGGATTTGATAAGAAACCTAAACATGAAT
* *
2250 TTTGAACAA
66 CTTAAACAA
*
2259 GATTTTGATGAGACACCTAAACAGGGACCTTAAATAAGGATTTGATAAGAAACCTAAACATGAAT
1 GATTTTGATGAGACACCTAAACAGGCACCTTAAATAAGGATTTGATAAGAAACCTAAACATGAAT
2324 CTTAAACAA
66 CTTAAACAA
* ** * * *
2333 AATTTTTGACAAGAAACCTAAACAGGCACCTTAAATAAGGATTTGATAAGAAACCTAAACAGGGA
1 GA-TTTTGATGAGACACCTAAACAGGCACCTTAAATAAGGATTTGATAAGAAACCTAAACATGAA
2398 TCTTAAACAA
65 TCTTAAACAA
* *
2408 GATCTTGATGAGACACTTAAA
1 GATTTTGATGAGACACCTAAA
2429 TAGGGATCTT
Statistics
Matches: 151, Mismatches: 18, Indels: 2
0.88 0.11 0.01
Matches are distributed among these distances:
74 84 0.56
75 67 0.44
ACGTcount: A:0.45, C:0.15, G:0.16, T:0.25
Consensus pattern (74 bp):
GATTTTGATGAGACACCTAAACAGGCACCTTAAATAAGGATTTGATAAGAAACCTAAACATGAAT
CTTAAACAA
Found at i:2463 original size:149 final size:149
Alignment explanation
Indices: 2199--2467 Score: 387
Period size: 149 Copynumber: 1.8 Consensus size: 149
2189 TTGAAGAGAC
* * * * *
2199 ACCTAAACAGGTACCTTAAATAAGGATTTAATAAGAAACCTAAACATGAATTTTGAACAAGATTT
1 ACCTAAACAGGCACCTTAAATAAGGATTTAATAAGAAACCTAAACAGGAATCTTAAACAAGATCT
*
2264 TGATGAGACACCTAAACAGGGACCTTAAATAAGGATTTGATAAGAAACCTAAACATGAATCTTAA
66 TGATGAGACACCTAAACAGGGACCTTAAACAAGGATTTGATAAGAAACCTAAACATGAATCTTAA
2329 ACAAAATTTTTGACAAGAA
131 ACAAAATTTTTGACAAGAA
* *
2348 ACCTAAACAGGCACCTTAAATAAGGATTTGATAAGAAACCTAAACAGGGATCTTAAACAAGATCT
1 ACCTAAACAGGCACCTTAAATAAGGATTTAATAAGAAACCTAAACAGGAATCTTAAACAAGATCT
* * * * * * *
2413 TGATGAGACACTTAAATAGGGATCTTGAACCA-GATTTCGATGAGACACCTAAACA
66 TGATGAGACACCTAAACAGGGACCTTAAACAAGGATTT-GATAAGAAACCTAAACA
2468 GGGACCTTAA
Statistics
Matches: 104, Mismatches: 15, Indels: 2
0.86 0.12 0.02
Matches are distributed among these distances:
148 5 0.05
149 99 0.95
ACGTcount: A:0.44, C:0.16, G:0.16, T:0.24
Consensus pattern (149 bp):
ACCTAAACAGGCACCTTAAATAAGGATTTAATAAGAAACCTAAACAGGAATCTTAAACAAGATCT
TGATGAGACACCTAAACAGGGACCTTAAACAAGGATTTGATAAGAAACCTAAACATGAATCTTAA
ACAAAATTTTTGACAAGAA
Found at i:2939 original size:26 final size:26
Alignment explanation
Indices: 2878--2932 Score: 110
Period size: 26 Copynumber: 2.1 Consensus size: 26
2868 TGCCCCCCTT
2878 ATCAATCCAAATTGACAACATTTGTC
1 ATCAATCCAAATTGACAACATTTGTC
2904 ATCAATCCAAATTGACAACATTTGTC
1 ATCAATCCAAATTGACAACATTTGTC
2930 ATC
1 ATC
2933 TTTCCAACAT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 29 1.00
ACGTcount: A:0.38, C:0.24, G:0.07, T:0.31
Consensus pattern (26 bp):
ATCAATCCAAATTGACAACATTTGTC
Found at i:3501 original size:20 final size:21
Alignment explanation
Indices: 3476--3519 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
3466 AACCTTTTGA
* *
3476 TTTTTCTTT-CTTTTTTCTTT
1 TTTTTCTTTGCTTTCTCCTTT
3496 TTTTTCTTTGCTTTCTCCTTT
1 TTTTTCTTTGCTTTCTCCTTT
3517 TTT
1 TTT
3520 CTGTTTTCTT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
20 9 0.43
21 12 0.57
ACGTcount: A:0.00, C:0.18, G:0.02, T:0.80
Consensus pattern (21 bp):
TTTTTCTTTGCTTTCTCCTTT
Found at i:4221 original size:14 final size:13
Alignment explanation
Indices: 4156--4220 Score: 87
Period size: 14 Copynumber: 4.8 Consensus size: 13
4146 ACTCAAAACC
4156 TTTTTGAAAACTCA
1 TTTTTGAAAA-TCA
4170 TTTTTGAAAATCA
1 TTTTTGAAAATCA
4183 TTTCTTGAAAA-CAA
1 TTT-TTGAAAATC-A
4197 TTTCTTGAAAATCA
1 TTT-TTGAAAATCA
4211 TTTTTGAAAA
1 TTTTTGAAAA
4221 ACGTCCTTTA
Statistics
Matches: 48, Mismatches: 0, Indels: 7
0.87 0.00 0.13
Matches are distributed among these distances:
13 14 0.29
14 33 0.69
15 1 0.02
ACGTcount: A:0.38, C:0.11, G:0.08, T:0.43
Consensus pattern (13 bp):
TTTTTGAAAATCA
Found at i:4222 original size:28 final size:27
Alignment explanation
Indices: 4156--4220 Score: 96
Period size: 28 Copynumber: 2.4 Consensus size: 27
4146 ACTCAAAACC
*
4156 TTTTTGAAAACTCATTTTTGAAAATCA
1 TTTTTGAAAACTAATTTTTGAAAATCA
4183 TTTCTTGAAAAC-AATTTCTTGAAAATCA
1 TTT-TTGAAAACTAATTT-TTGAAAATCA
4211 TTTTTGAAAA
1 TTTTTGAAAA
4221 ACGTCCTTTA
Statistics
Matches: 35, Mismatches: 1, Indels: 4
0.88 0.03 0.10
Matches are distributed among these distances:
27 14 0.40
28 21 0.60
ACGTcount: A:0.38, C:0.11, G:0.08, T:0.43
Consensus pattern (27 bp):
TTTTTGAAAACTAATTTTTGAAAATCA
Done.