Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01019457.1 Corchorus olitorius cultivar O-4 contig19490, 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: 9886
ACGTcount: A:0.35, C:0.15, G:0.15, T:0.36
Found at i:1730 original size:451 final size:454
Alignment explanation
Indices: 884--1794 Score: 1740
Period size: 451 Copynumber: 2.0 Consensus size: 454
874 ATTATTATAA
884 ATAAAGGTGAAATTAATGTCCACTAAACATTGGAATTTGAAGAATTTTTTCAGTTTTAGATTCTG
1 ATAAAGGTGAAATTAATGTCCACTAAACATTGGAATTTGAAGAATTTTTTCAGTTTTAGATTCTG
* *
949 AAAAGTTAAAAAGTTGCCATCCTATATCTTTACATAAATCGTACTTAAATCTCCAATTAACCTGT
66 AAAAGTTAAAAAGTTGACATCCCATATCTTTACATAAATCGTACTTAAATCTCCAATTAACCTGT
1014 TCCATTTGATTGGTATTAAAGTCGTTATTATAAATTCATAACGGTTAATTTTTTTTTTGAAGAAT
131 TCCATTTGATTGGTATTAAAGTCGTTATTATAAATTCATAACGGTTAA-TTTTTTTTTGAAGAAT
1079 TTTTTAAGTTTTAGAATCTAAAAGCCTTTCAATCATAGCTGGGTAAGTTTGTTTAGTCTTAATGT
195 TTTTTAAGTTTTAGAATCTAAAAGCCTTTCAATCATAGCTGGGTAAGTTTGTTTAGTCTTAATGT
1144 TTCTGTTTTTTGTTGGAATAATCAATTTTTCTTCACAGCTTATTATTGCTTAACTTTCTTGACAA
260 TTCTGTTTTTTGTTGGAATAATCAATTTTTCTTCACAGCTTATTATTGCTTAACTTTCTTGACAA
*
1209 CTTCTTAGCTTCTGCGTTTTGATAAATATATTTAAAGGAGTTTAAAGTTAGAATCATGAAGGCGA
325 CTTCTTAGCTTCTGCGTTTTGATAAATATATTTAAAGGAATTTAAAGTTAGAATCATGAAGGCGA
1274 AAAGTTTAAAAACTGACTCTTGAGAGGTATTCTT-AGTTAAAAAACTGCCATCTGATATCTTTAC
390 AAAGTTTAAAAACTGACTCTTGAGAGGTATTCTTAAGTTAAAAAACTGCCATCTGATATCTTTAC
1338 ATAAAGGTGAAATTAATGTCCACTAAACATTGGAATTTGAAGAATTTTTTCAGTTTTAGATTCTG
1 ATAAAGGTGAAATTAATGTCCACTAAACATTGGAATTTGAAGAATTTTTTCAGTTTTAGATTCTG
1403 -AAAGTTAAAAAGTTGACATCCCATATCTTTACATAAATCGTACTTAAATCTCCAATTAACCTGT
66 AAAAGTTAAAAAGTTGACATCCCATATCTTTACATAAATCGTACTTAAATCTCCAATTAACCTGT
1467 TCCATTTGATTGGTATTAAAGTCGTTATTATAAATTCATAACGGTTAA-TTTTTTTTGAAGAATT
131 TCCATTTGATTGGTATTAAAGTCGTTATTATAAATTCATAACGGTTAATTTTTTTTTGAAGAATT
1531 TTTTAAGTTTTAGAATCTAAAAGCCTTTCAATCATAGCTGGGTAAGTTTGTTTAGTCTTAATGTT
196 TTTTAAGTTTTAGAATCTAAAAGCCTTTCAATCATAGCTGGGTAAGTTTGTTTAGTCTTAATGTT
1596 TCTGTTTTTTGTTGGAATAATCAATTTTTCTTCACAGCTTATTATTGCTTAACTTTCTTGACAAC
261 TCTGTTTTTTGTTGGAATAATCAATTTTTCTTCACAGCTTATTATTGCTTAACTTTCTTGACAAC
1661 TTCTTAGCTTCTGCGTTTTGATAAATATATTTAAAGGAATTTAAAGTTAGAATCATG-AGGCGAA
326 TTCTTAGCTTCTGCGTTTTGATAAATATATTTAAAGGAATTTAAAGTTAGAATCATGAAGGCG-A
*
1725 AAAGTTTAAAAACTGACTCTTGAGAGGTATTCTTAAGTTAAAAAGCTGCCATCTGATATCTTTAC
390 AAAGTTTAAAAACTGACTCTTGAGAGGTATTCTTAAGTTAAAAAACTGCCATCTGATATCTTTAC
1790 ATAAA
1 ATAAA
1795 TCGTACTTAA
Statistics
Matches: 451, Mismatches: 4, Indels: 6
0.98 0.01 0.01
Matches are distributed among these distances:
450 5 0.01
451 237 0.53
452 34 0.08
453 110 0.24
454 65 0.14
ACGTcount: A:0.32, C:0.13, G:0.14, T:0.41
Consensus pattern (454 bp):
ATAAAGGTGAAATTAATGTCCACTAAACATTGGAATTTGAAGAATTTTTTCAGTTTTAGATTCTG
AAAAGTTAAAAAGTTGACATCCCATATCTTTACATAAATCGTACTTAAATCTCCAATTAACCTGT
TCCATTTGATTGGTATTAAAGTCGTTATTATAAATTCATAACGGTTAATTTTTTTTTGAAGAATT
TTTTAAGTTTTAGAATCTAAAAGCCTTTCAATCATAGCTGGGTAAGTTTGTTTAGTCTTAATGTT
TCTGTTTTTTGTTGGAATAATCAATTTTTCTTCACAGCTTATTATTGCTTAACTTTCTTGACAAC
TTCTTAGCTTCTGCGTTTTGATAAATATATTTAAAGGAATTTAAAGTTAGAATCATGAAGGCGAA
AAGTTTAAAAACTGACTCTTGAGAGGTATTCTTAAGTTAAAAAACTGCCATCTGATATCTTTAC
Found at i:1857 original size:16 final size:16
Alignment explanation
Indices: 1838--1869 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
1828 TGATTGGTAT
1838 TAAAGTCATTATATTA
1 TAAAGTCATTATATTA
*
1854 TAAATTCATTATATTA
1 TAAAGTCATTATATTA
1870 ATCTCCTTTT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.44, C:0.06, G:0.03, T:0.47
Consensus pattern (16 bp):
TAAAGTCATTATATTA
Found at i:3520 original size:36 final size:35
Alignment explanation
Indices: 3480--3554 Score: 111
Period size: 32 Copynumber: 2.2 Consensus size: 35
3470 CTTTCCTAAT
*
3480 AATTTATTATTATATCATTTCCTTCTTAATAATTAA
1 AATTTATTATCAT-TCATTTCCTTCTTAATAATTAA
3516 AA--T-TTATCATTCATTTCCTTCTTAATAATTAA
1 AATTTATTATCATTCATTTCCTTCTTAATAATTAA
3548 AATTTAT
1 AATTTAT
3555 CATGGTAGTA
Statistics
Matches: 35, Mismatches: 1, Indels: 7
0.81 0.02 0.16
Matches are distributed among these distances:
32 24 0.69
33 6 0.17
34 2 0.06
35 1 0.03
36 2 0.06
ACGTcount: A:0.36, C:0.12, G:0.00, T:0.52
Consensus pattern (35 bp):
AATTTATTATCATTCATTTCCTTCTTAATAATTAA
Found at i:3533 original size:32 final size:32
Alignment explanation
Indices: 3494--3557 Score: 128
Period size: 32 Copynumber: 2.0 Consensus size: 32
3484 TATTATTATA
3494 TCATTTCCTTCTTAATAATTAAAATTTATCAT
1 TCATTTCCTTCTTAATAATTAAAATTTATCAT
3526 TCATTTCCTTCTTAATAATTAAAATTTATCAT
1 TCATTTCCTTCTTAATAATTAAAATTTATCAT
3558 GGTAGTAAAC
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
32 32 1.00
ACGTcount: A:0.34, C:0.16, G:0.00, T:0.50
Consensus pattern (32 bp):
TCATTTCCTTCTTAATAATTAAAATTTATCAT
Found at i:6482 original size:51 final size:51
Alignment explanation
Indices: 6381--6492 Score: 126
Period size: 51 Copynumber: 2.2 Consensus size: 51
6371 GTTCTTCATA
6381 TTTT-TCTTGTTTAGATCTTGTCTCAGGACACCTAAACACTCTTTTAGTG-T
1 TTTTCTCTTGTTTAGATCTTGTCTCAGGACA-CTAAACACTCTTTTAGTGTT
*
6431 TTTTCTCTTGTTTCA-ATCTTGTCTCCGGACA-TAAAACACT-TTTTCACGTGTT
1 TTTTCTCTTGTTT-AGATCTTGTCTCAGGACACT-AAACACTCTTTT-A-GTGTT
6483 TCTTTCTCTT
1 T-TTTCTCTT
6493 CAATAACAAT
Statistics
Matches: 54, Mismatches: 1, Indels: 11
0.82 0.02 0.17
Matches are distributed among these distances:
49 5 0.09
50 12 0.22
51 26 0.48
52 3 0.06
53 8 0.15
ACGTcount: A:0.18, C:0.22, G:0.12, T:0.48
Consensus pattern (51 bp):
TTTTCTCTTGTTTAGATCTTGTCTCAGGACACTAAACACTCTTTTAGTGTT
Found at i:7917 original size:2 final size:2
Alignment explanation
Indices: 7910--7949 Score: 53
Period size: 2 Copynumber: 19.5 Consensus size: 2
7900 AGTGTCAATC
* *
7910 AT AT AT AT AT AT AT AT AT AT AT AT AT CT AT CT ACT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A-T AT AT A
7950 AGTCTAAACT
Statistics
Matches: 33, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
2 31 0.94
3 2 0.06
ACGTcount: A:0.45, C:0.07, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:8221 original size:39 final size:40
Alignment explanation
Indices: 8165--8244 Score: 135
Period size: 39 Copynumber: 2.0 Consensus size: 40
8155 TTTTATTCCT
8165 ATGTAATATATATAATAACTAAAATACTTACATTAATTAA
1 ATGTAATATATATAATAACTAAAATACTTACATTAATTAA
* *
8205 ATGTAATA-GTATAATAACTGAAATACTTACATTAATTAA
1 ATGTAATATATATAATAACTAAAATACTTACATTAATTAA
8244 A
1 A
8245 GTCTTAGGTA
Statistics
Matches: 38, Mismatches: 2, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
39 30 0.79
40 8 0.21
ACGTcount: A:0.51, C:0.07, G:0.05, T:0.36
Consensus pattern (40 bp):
ATGTAATATATATAATAACTAAAATACTTACATTAATTAA
Found at i:8597 original size:204 final size:201
Alignment explanation
Indices: 8355--8764 Score: 721
Period size: 204 Copynumber: 2.0 Consensus size: 201
8345 TTCCTTAATA
* *
8355 ATAAATAAATTGGATCTTAATATCTTTTATAATTTTGAAATTTTGTTTGACATTGATCTAATTTA
1 ATAAATAAATCGGATCTTAATATCTTTTATAATTTTGAAATTTTGTTTGACATTGATATAATTTA
*
8420 ATTTAATAAATCAACCACTAATGTTCAACTAATTTTTTTTGGTATAGTTCTATATATATAATAGT
66 ATTTAATAAATCAACCACTAATGTTCAACTAATTTTTTTTGGTATAGTT-T-TATATATAATAAT
*
8485 AATGTGTAGTATCTTATTCACTACAACTTTGTTAGTAATCTTAGACTTAAAAAATTAATAACATT
129 AATGTGTAGTATCTTATTCACTACAACTTTGTTAATAATCTTAGACTTAAAAAATTAATAACATT
8550 CACCATTG
194 CACCATTG
8558 ATAAATAAATCGGATCTTTAATATCTTTTATAATTTTGAAATTTTGTTTGACATTGATATAATTT
1 ATAAATAAATCGGATC-TTAATATCTTTTATAATTTTGAAATTTTGTTTGACATTGATATAATTT
* *
8623 AATTTAATAAATCAACCACTAATGTTCAACTACTTTTTTTTGGTATAGTTTTATATATGATAATA
65 AATTTAATAAATCAACCACTAATGTTCAACTAATTTTTTTTGGTATAGTTTTATATATAATAATA
* *
8688 ATGTGTTGTATCTTATTTACTACAACTTTGTTAATAATCTTAGACTTAAAAAATTAATAACATTC
130 ATGTGTAGTATCTTATTCACTACAACTTTGTTAATAATCTTAGACTTAAAAAATTAATAACATTC
8753 ACCATTG
195 ACCATTG
8760 ATAAA
1 ATAAA
8765 GTTATTAAGC
Statistics
Matches: 198, Mismatches: 8, Indels: 3
0.95 0.04 0.01
Matches are distributed among these distances:
202 86 0.43
203 16 0.08
204 96 0.48
ACGTcount: A:0.37, C:0.10, G:0.09, T:0.44
Consensus pattern (201 bp):
ATAAATAAATCGGATCTTAATATCTTTTATAATTTTGAAATTTTGTTTGACATTGATATAATTTA
ATTTAATAAATCAACCACTAATGTTCAACTAATTTTTTTTGGTATAGTTTTATATATAATAATAA
TGTGTAGTATCTTATTCACTACAACTTTGTTAATAATCTTAGACTTAAAAAATTAATAACATTCA
CCATTG
Found at i:9331 original size:35 final size:36
Alignment explanation
Indices: 9285--9353 Score: 113
Period size: 35 Copynumber: 1.9 Consensus size: 36
9275 GAGATTTTGG
* *
9285 AGAAATATGATAATCAAAATTACAAAA-ATGTAATA
1 AGAAATATGATAACCAAAATCACAAAAGATGTAATA
9320 AGAAATATGATAACCAAAATCACAAAAGATGTAA
1 AGAAATATGATAACCAAAATCACAAAAGATGTAA
9354 GGTTATTAAA
Statistics
Matches: 31, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
35 25 0.81
36 6 0.19
ACGTcount: A:0.59, C:0.09, G:0.10, T:0.22
Consensus pattern (36 bp):
AGAAATATGATAACCAAAATCACAAAAGATGTAATA
Done.