Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01021758.1 Corchorus olitorius cultivar O-4 contig21791, 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: 3039
ACGTcount: A:0.35, C:0.15, G:0.13, T:0.37
Found at i:228 original size:31 final size:31
Alignment explanation
Indices: 162--272 Score: 165
Period size: 31 Copynumber: 3.6 Consensus size: 31
152 CTCATTTTTG
* *
162 AAACGTAAGGGATTAAT-TTGTCCCGAAA--A
1 AAACATAAGGGATT-ATCTTGTCCCAAAAGCA
191 AAACATAAGGGATTATCTTGTCCCAAAAGCA
1 AAACATAAGGGATTATCTTGTCCCAAAAGCA
*
222 AAACATAAGGGATTATCTTTTCCCAAAAGCA
1 AAACATAAGGGATTATCTTGTCCCAAAAGCA
253 AAACATAAGGGATTATCTTG
1 AAACATAAGGGATTATCTTG
273 GGTATTTAGG
Statistics
Matches: 75, Mismatches: 4, Indels: 4
0.90 0.05 0.05
Matches are distributed among these distances:
28 2 0.03
29 23 0.31
31 50 0.67
ACGTcount: A:0.41, C:0.16, G:0.17, T:0.25
Consensus pattern (31 bp):
AAACATAAGGGATTATCTTGTCCCAAAAGCA
Found at i:770 original size:22 final size:22
Alignment explanation
Indices: 722--777 Score: 58
Period size: 22 Copynumber: 2.5 Consensus size: 22
712 TATTTTTATT
*
722 AAATTTTGATAACCACACTATG
1 AAATTTTGATAACCACACTATA
* ** *
744 GAATTTTGATAATTACCCTATA
1 AAATTTTGATAACCACACTATA
*
766 AAATTCTGATAA
1 AAATTTTGATAA
778 ACTCCCAATG
Statistics
Matches: 27, Mismatches: 7, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
22 27 1.00
ACGTcount: A:0.41, C:0.14, G:0.09, T:0.36
Consensus pattern (22 bp):
AAATTTTGATAACCACACTATA
Found at i:1085 original size:22 final size:22
Alignment explanation
Indices: 1060--1166 Score: 96
Period size: 22 Copynumber: 4.9 Consensus size: 22
1050 TTGAACTTTA
* *
1060 ATAACTACACTATGAAATTCTG
1 ATAACCACACTATGAAATTTTG
1082 ATAACCATC-CTATGAAATTTTG
1 ATAACCA-CACTATGAAATTTTG
* *
1104 GTCAA-CACACTCTGAAATTTTG
1 AT-AACCACACTATGAAATTTTG
*
1126 ATAACCACAGTAT-AAATTTGTG
1 ATAACCACACTATGAAATTT-TG
*
1148 ATAACCTCTA-TATGAAATT
1 ATAACCAC-ACTATGAAATT
1167 AATTTTGATG
Statistics
Matches: 70, Mismatches: 8, Indels: 13
0.77 0.09 0.14
Matches are distributed among these distances:
21 9 0.13
22 52 0.74
23 9 0.13
ACGTcount: A:0.38, C:0.18, G:0.10, T:0.34
Consensus pattern (22 bp):
ATAACCACACTATGAAATTTTG
Found at i:1186 original size:26 final size:27
Alignment explanation
Indices: 1140--1192 Score: 65
Period size: 26 Copynumber: 2.0 Consensus size: 27
1130 CCACAGTATA
*
1140 AATTTGTGATAACCTCTATATGAAATT
1 AATTTGTGATAACCTCTATATAAAATT
*
1167 AATTT-TGATGACCT-TAATATAAAATT
1 AATTTGTGATAACCTCT-ATATAAAATT
1193 TTGAATACCA
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
25 1 0.04
26 17 0.74
27 5 0.22
ACGTcount: A:0.40, C:0.09, G:0.09, T:0.42
Consensus pattern (27 bp):
AATTTGTGATAACCTCTATATAAAATT
Found at i:1283 original size:22 final size:22
Alignment explanation
Indices: 1235--1423 Score: 148
Period size: 22 Copynumber: 8.5 Consensus size: 22
1225 GATTTGGTAG
* * **
1235 ACTATGAAATTTGGATAATCAA
1 ACTATGAAATTTTGATAACCTC
1257 ACTATGAAATTTTGATAACCTC
1 ACTATGAAATTTTGATAACCTC
* * * *
1279 CCTATGGAATGTTGATAACTTTC
1 ACTATGAAATTTTGATAAC-CTC
* * *
1302 -CTATAAAATTTAGTGTTAATCTC
1 ACTATGAAATTT--TGATAACCTC
* *
1325 ACTATGAAATTTTGATAAACAC
1 ACTATGAAATTTTGATAACCTC
* * *
1347 AATATGAAACTTTGATTACCT-
1 ACTATGAAATTTTGATAACCTC
* * *
1368 TCTATGAAATTTTTATAACCAC
1 ACTATGAAATTTTGATAACCTC
* *
1390 ATTATGAAATTTTGATAACCAC
1 ACTATGAAATTTTGATAACCTC
1412 ACTATGAAATTT
1 ACTATGAAATTT
1424 CAATAATCCA
Statistics
Matches: 129, Mismatches: 33, Indels: 10
0.75 0.19 0.06
Matches are distributed among these distances:
21 15 0.12
22 95 0.74
23 4 0.03
24 15 0.12
ACGTcount: A:0.38, C:0.14, G:0.10, T:0.38
Consensus pattern (22 bp):
ACTATGAAATTTTGATAACCTC
Found at i:1376 original size:43 final size:44
Alignment explanation
Indices: 1324--1423 Score: 130
Period size: 43 Copynumber: 2.3 Consensus size: 44
1314 GTGTTAATCT
*
1324 CACTATGAAATTTTGATAAACACAATATGAAACTTTGATTACC-
1 CACTATGAAATTTTGATAAACACAATATGAAACTTTGATAACCA
** * * * *
1367 TTCTATGAAATTTTTATAACCACATTATGAAATTTTGATAACCA
1 CACTATGAAATTTTGATAAACACAATATGAAACTTTGATAACCA
1411 CACTATGAAATTT
1 CACTATGAAATTT
1424 CAATAATCCA
Statistics
Matches: 47, Mismatches: 9, Indels: 1
0.82 0.16 0.02
Matches are distributed among these distances:
43 36 0.77
44 11 0.23
ACGTcount: A:0.40, C:0.15, G:0.08, T:0.37
Consensus pattern (44 bp):
CACTATGAAATTTTGATAAACACAATATGAAACTTTGATAACCA
Found at i:1429 original size:22 final size:22
Alignment explanation
Indices: 1324--1435 Score: 100
Period size: 22 Copynumber: 5.1 Consensus size: 22
1314 GTGTTAATCT
* *
1324 CACTATGAAATTTTGATAAACA
1 CACTATGAAATTTTAATAACCA
* * * *
1346 CAATATGAAACTTTGATTACC-
1 CACTATGAAATTTTAATAACCA
** *
1367 TTCTATGAAATTTTTATAACCA
1 CACTATGAAATTTTAATAACCA
* *
1389 CATTATGAAATTTTGATAACCA
1 CACTATGAAATTTTAATAACCA
*
1411 CACTATGAAATTTCAATAATCCA
1 CACTATGAAATTTTAATAA-CCA
1434 CA
1 CA
1436 AAAGTCTTCT
Statistics
Matches: 71, Mismatches: 17, Indels: 3
0.78 0.19 0.03
Matches are distributed among these distances:
21 15 0.21
22 51 0.72
23 5 0.07
ACGTcount: A:0.41, C:0.17, G:0.07, T:0.35
Consensus pattern (22 bp):
CACTATGAAATTTTAATAACCA
Found at i:1706 original size:12 final size:12
Alignment explanation
Indices: 1689--1715 Score: 54
Period size: 12 Copynumber: 2.2 Consensus size: 12
1679 GGTCAAGACT
1689 TTAAATTTATAA
1 TTAAATTTATAA
1701 TTAAATTTATAA
1 TTAAATTTATAA
1713 TTA
1 TTA
1716 TTTTCTATTT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 15 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (12 bp):
TTAAATTTATAA
Found at i:1948 original size:31 final size:29
Alignment explanation
Indices: 1913--1992 Score: 106
Period size: 29 Copynumber: 2.7 Consensus size: 29
1903 GCTAAATACC
* *
1913 CAAAAAAATCCCTTATGTTTTGCTTTTGGGA
1 CAAAATAATCCCTTATGTTTT--TTTGGGGA
1944 CAAAATAATCCCTTATGTTTTTTTGGGGA
1 CAAAATAATCCCTTATGTTTTTTTGGGGA
* *
1973 CAAATTAATCCCTTACGTTT
1 CAAAATAATCCCTTATGTTT
1993 CAAAAATGAG
Statistics
Matches: 45, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
29 25 0.56
31 20 0.44
ACGTcount: A:0.29, C:0.17, G:0.14, T:0.40
Consensus pattern (29 bp):
CAAAATAATCCCTTATGTTTTTTTGGGGA
Found at i:2164 original size:31 final size:31
Alignment explanation
Indices: 2126--2185 Score: 102
Period size: 31 Copynumber: 1.9 Consensus size: 31
2116 CCATCTCAGC
2126 AAGGGACTAATTTGTCCCAAAAGAAAAACAT
1 AAGGGACTAATTTGTCCCAAAAGAAAAACAT
**
2157 AAGGGACTTTTTTGTCCCAAAAGAAAAAC
1 AAGGGACTAATTTGTCCCAAAAGAAAAAC
2186 TTAAAAGACT
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
31 27 1.00
ACGTcount: A:0.45, C:0.17, G:0.17, T:0.22
Consensus pattern (31 bp):
AAGGGACTAATTTGTCCCAAAAGAAAAACAT
Found at i:2196 original size:31 final size:31
Alignment explanation
Indices: 2136--2200 Score: 103
Period size: 31 Copynumber: 2.1 Consensus size: 31
2126 AAGGGACTAA
**
2136 TTTGTCCCAAAAGAAAAACATAAGGGACTTT
1 TTTGTCCCAAAAGAAAAACATAAAAGACTTT
*
2167 TTTGTCCCAAAAGAAAAACTTAAAAGACTTT
1 TTTGTCCCAAAAGAAAAACATAAAAGACTTT
2198 TTT
1 TTT
2201 AGTATTTAGT
Statistics
Matches: 31, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
31 31 1.00
ACGTcount: A:0.42, C:0.15, G:0.12, T:0.31
Consensus pattern (31 bp):
TTTGTCCCAAAAGAAAAACATAAAAGACTTT
Done.