Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01021899.1 Corchorus olitorius cultivar O-4 contig21932, 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: 16877
ACGTcount: A:0.33, C:0.16, G:0.20, T:0.31
Found at i:1202 original size:2 final size:2
Alignment explanation
Indices: 1195--1226 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
1185 ATCTAATACA
1195 AT AT AT 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 AT AT AT
1227 TGCCAACTTG
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1548 original size:17 final size:17
Alignment explanation
Indices: 1515--1560 Score: 56
Period size: 17 Copynumber: 2.7 Consensus size: 17
1505 CCGAAATTAG
*
1515 TAATAATTATTGGATAA
1 TAATAATTATTTGATAA
*
1532 TAATAATTATTTTATAA
1 TAATAATTATTTGATAA
* *
1549 TTATTATTATTT
1 TAATAATTATTT
1561 CAGTAAATAA
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
17 25 1.00
ACGTcount: A:0.41, C:0.00, G:0.04, T:0.54
Consensus pattern (17 bp):
TAATAATTATTTGATAA
Found at i:4435 original size:137 final size:137
Alignment explanation
Indices: 4185--4453 Score: 360
Period size: 137 Copynumber: 2.0 Consensus size: 137
4175 CACTTCTCAA
* * * * * *
4185 AACTCAATGGCCAAATTACACACAAAAATAATGGATTTGAAGAAAACATGTTAGGTTTAAGGGAT
1 AACTCAATGGCCAAATCAAACACAAAAACAATGGATCTAAAGAAAACATGTTAGGCTTAAGGGAT
* *
4250 ATTTCAGTAATCAACCACGTGAGAAAAAACCAAAACAGGGAGATAAGGTCACT-CCACATTAAAA
66 ATTTCAGTAATCAACCACATGAGAAAAAACCAAAACAGGGAGAAAAGGT-ACTCCCACATTAAAA
4314 GTTATTAG
130 GTTATTAG
* * * *
4322 AACTCAATGGTCAAATCAAACACAAAGACAATGGATCTAAAGAAAATATGTTAGGCTTAGGGGAT
1 AACTCAATGGCCAAATCAAACACAAAAACAATGGATCTAAAGAAAACATGTTAGGCTTAAGGGAT
* * * * * *
4387 ATTTCAGTGATCAACCACATGAGAAAAGACTAAAACGGGGTGAAAAGGTTCTCCCACATTAAAAG
66 ATTTCAGTAATCAACCACATGAGAAAAAACCAAAACAGGGAGAAAAGGTACTCCCACATTAAAAG
4452 TT
131 TT
4454 GATGGGAGCC
Statistics
Matches: 113, Mismatches: 18, Indels: 2
0.85 0.14 0.02
Matches are distributed among these distances:
136 2 0.02
137 111 0.98
ACGTcount: A:0.43, C:0.16, G:0.19, T:0.22
Consensus pattern (137 bp):
AACTCAATGGCCAAATCAAACACAAAAACAATGGATCTAAAGAAAACATGTTAGGCTTAAGGGAT
ATTTCAGTAATCAACCACATGAGAAAAAACCAAAACAGGGAGAAAAGGTACTCCCACATTAAAAG
TTATTAG
Found at i:6797 original size:574 final size:561
Alignment explanation
Indices: 5728--6875 Score: 1687
Period size: 574 Copynumber: 2.0 Consensus size: 561
5718 TAGTCACTAA
* * * *
5728 AAATAATATATAGTATATACAAGTGGATCGGCCCGCGCTGGCGCGTCGGGCGTTTAGTAATCTAC
1 AAATAATATTTAGTATATACAAGTGGATCGGCCCACACTGGCGCGTCGGGCGTTCAGTAATCTAC
* * *
5793 TCTTTGAACAATTTTCTATCGAATTAAATTGTTTGATACGTAGGAAATTTCGAAAGTACTATGAT
66 -CTTTAAACAATTTTCTATCGAATTAAATTGTTTGATACATAGGAAAGTTCGAAAGTACTATGAT
* *
5858 TTTAGATGTGTTGCATCTTTAAAACGCTATAATATTAACATTGAGCATATGCCCTAAAGTTAGCA
130 TTTAAATGTGTTGCATCTTTAAAACGCTATAATATTAACATTGAGCATATACCCTAAAGTTAGCA
* * **
5923 ATAAATAGTAAATAATTAGTTTGTACATGGACAGGTGCAATAGCTTCAATTTTATTTCCTGCTCT
195 ATAAATAGTAAATAATTAGTTTGTACATGAACAGATGCAATAGCTTCAATTTTATTTCCCCCTCT
* * * * *
5988 AAAGTGTGTAGCACTTAAACAAAAACTAAGTTTACTCTCTTCTTCATATGGACATGAAAGGTCTG
260 AAAGCGTGTAGAACTTAAACAAAAACTAAATTTACTCTCTTCTTCATATGGACATGAAAGGCCTA
*
6053 AAGAGAGGCTACAATTCTAGATAACTAAGGGGTGATAGGATTTATTATAACACATTTATGTGAAA
325 AAGAGAGGCTACAATTCTAGATAACTAAGGGGTGATAAGATTTATTATAACACATTTATGTGAAA
* *
6118 GGAAAGGATAATTACAAAAAAGGGTTCAAGGGCAAGAACTGGCTAGAAACTAACCTAGGGTCTTC
390 GGAAAGAATAATTACAAAAAAGGGCTCAAGGGCAAGAACTGGCTAGAAACTAACCTAGGGTCTTC
* *
6183 TTAGTAATTTGGCAAGTGAGAAAACACAGAAAAGGACAAAAAAATTTCAGATGGAGCCTCCTCAT
455 TTAGTAATTTGGCAAGTGAGAAAACACAGAAAAGGACAAAAAAAGTTCAAATGGAGCCTCCTCAT
* * *
6248 CGATCCTCAAAAGGGGCCTTTGGTAAATTCCCTGGGTCTTTC
520 CGATCCTCAAAAGGGGCCTTTGATAAATTCCCTAGGTCATTC
6290 AAATAATATTTAGTATATACAAGTGGATCGGCCCACACTGGCGCGTCGGGCGTTCA-TAAATCTA
1 AAATAATATTTAGTATATACAAGTGGATCGGCCCACACTGGCGCGTCGGGCGTTCAGT-AATCTA
*
6354 -CTTTAAACAATTTTCTGTTCGAATTAAATTGTTTGATACATAGGAAAGTTCGAAAGTACTATGA
65 CCTTTAAACAATTTTCT-ATCGAATTAAATTGTTTGATACATAGGAAAGTTCGAAAGTACTATGA
* * *
6418 TTTTAAATGTGTTGCATCTTTAAAAGGCTATACTATTAACATTGCGCATATACCCTAAAGTTAGC
129 TTTTAAATGTGTTGCATCTTTAAAACGCTATAATATTAACATTGAGCATATACCCTAAAGTTAGC
* * *
6483 AATAAATAGTAAAT-ATTAGTTTGTACATGAACATATGCAATAGCTTTAATTTTGTTTCCCCCTC
194 AATAAATAGTAAATAATTAGTTTGTACATGAACAGATGCAATAGCTTCAATTTTATTTCCCCCTC
*
6547 TAAAGCGTGTAGAACTTAAACAAAAACTAAATTTACTCTCTTCTTCGTATGGACATGAAAGGCCT
259 TAAAGCGTGTAGAACTTAAACAAAAACTAAATTTACTCTCTTCTTCATATGGACATGAAAGGCCT
*
6612 AAAGAGAGGTTACAATTCTAGCATTCATTAGCAAAAGTAGAGATAAGAGG-GATAAGATTTATTA
324 AAAGAGAGGCTACAATTCTAG-A-T-A--A-C-----TA-AG----G-GGTGATAAGATTTATTA
** * *
6676 T-A-GTATTTATGTGAAAGGAAATAATAATTACAAAAAAGGGCTCAAGGGTAAGAACTGGCTAGA
372 TAACACATTTATGTGAAAGGAAAGAATAATTACAAAAAAGGGCTCAAGGGCAAGAACTGGCTAGA
* * *
6739 AACTAATCTAGGGTCTTCTTAGTAATTTGGCAAGTGAGAAAAGACAGAAAATGACAAAAAAAGTT
437 AACTAACCTAGGGTCTTCTTAGTAATTTGGCAAGTGAGAAAACACAGAAAAGGACAAAAAAAGTT
6804 CAAATGGAGCCTCCTCATCGATCCTCAAAAGGGGCCTTTGATAAATTCCCTAGGTCATTC
502 CAAATGGAGCCTCCTCATCGATCCTCAAAAGGGGCCTTTGATAAATTCCCTAGGTCATTC
*
6864 AAATACTATTTA
1 AAATAATATTTA
6876 ACAAGTGATT
Statistics
Matches: 524, Mismatches: 43, Indels: 26
0.88 0.07 0.04
Matches are distributed among these distances:
560 137 0.26
561 120 0.23
562 59 0.11
563 1 0.00
565 1 0.00
566 1 0.00
571 2 0.00
572 2 0.00
574 183 0.35
575 1 0.00
576 15 0.03
577 2 0.00
ACGTcount: A:0.36, C:0.15, G:0.19, T:0.30
Consensus pattern (561 bp):
AAATAATATTTAGTATATACAAGTGGATCGGCCCACACTGGCGCGTCGGGCGTTCAGTAATCTAC
CTTTAAACAATTTTCTATCGAATTAAATTGTTTGATACATAGGAAAGTTCGAAAGTACTATGATT
TTAAATGTGTTGCATCTTTAAAACGCTATAATATTAACATTGAGCATATACCCTAAAGTTAGCAA
TAAATAGTAAATAATTAGTTTGTACATGAACAGATGCAATAGCTTCAATTTTATTTCCCCCTCTA
AAGCGTGTAGAACTTAAACAAAAACTAAATTTACTCTCTTCTTCATATGGACATGAAAGGCCTAA
AGAGAGGCTACAATTCTAGATAACTAAGGGGTGATAAGATTTATTATAACACATTTATGTGAAAG
GAAAGAATAATTACAAAAAAGGGCTCAAGGGCAAGAACTGGCTAGAAACTAACCTAGGGTCTTCT
TAGTAATTTGGCAAGTGAGAAAACACAGAAAAGGACAAAAAAAGTTCAAATGGAGCCTCCTCATC
GATCCTCAAAAGGGGCCTTTGATAAATTCCCTAGGTCATTC
Found at i:7570 original size:2 final size:2
Alignment explanation
Indices: 7563--7606 Score: 52
Period size: 2 Copynumber: 21.5 Consensus size: 2
7553 CTATTTAGTG
* * *
7563 TA TA TA TA TA TA TA TA TT TA TT TA TT TA GTA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA -TA TA TA TA TA TA TA
7606 T
1 T
7607 TAGTGGGTTT
Statistics
Matches: 35, Mismatches: 6, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
2 33 0.94
3 2 0.06
ACGTcount: A:0.41, C:0.00, G:0.02, T:0.57
Consensus pattern (2 bp):
TA
Done.