Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01016112.1 Corchorus olitorius cultivar O-4 contig16145, 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: 66822
ACGTcount: A:0.32, C:0.17, G:0.18, T:0.33
Found at i:1098 original size:48 final size:48
Alignment explanation
Indices: 1034--1131 Score: 178
Period size: 48 Copynumber: 2.0 Consensus size: 48
1024 AAAAACTATT
* *
1034 TTGATTCATGAGTGTTATGATTTGCTCTAATCTCATAATATTTTTGTA
1 TTGATTCATAAGTGTTATGATTTGCTCTAATCTCATAATATTTTGGTA
1082 TTGATTCATAAGTGTTATGATTTGCTCTAATCTCATAATATTTTGGTA
1 TTGATTCATAAGTGTTATGATTTGCTCTAATCTCATAATATTTTGGTA
1130 TT
1 TT
1132 AAATTAACGT
Statistics
Matches: 48, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
48 48 1.00
ACGTcount: A:0.26, C:0.10, G:0.14, T:0.50
Consensus pattern (48 bp):
TTGATTCATAAGTGTTATGATTTGCTCTAATCTCATAATATTTTGGTA
Found at i:1117 original size:27 final size:27
Alignment explanation
Indices: 1039--1119 Score: 68
Period size: 27 Copynumber: 3.2 Consensus size: 27
1029 CTATTTTGAT
*
1039 TCATGAGTGTTATGATTTGCTCTAATC
1 TCATAAGTGTTATGATTTGCTCTAATC
* * *
1066 TCATAA----TAT-TTTTG-TATTGAT-
1 TCATAAGTGTTATGATTTGCT-CTAATC
1087 TCATAAGTGTTATGATTTGCTCTAATC
1 TCATAAGTGTTATGATTTGCTCTAATC
1114 TCATAA
1 TCATAA
1120 TATTTTGGTA
Statistics
Matches: 39, Mismatches: 7, Indels: 16
0.63 0.11 0.26
Matches are distributed among these distances:
21 7 0.18
22 7 0.18
23 3 0.08
25 3 0.08
26 7 0.18
27 12 0.31
ACGTcount: A:0.27, C:0.12, G:0.14, T:0.47
Consensus pattern (27 bp):
TCATAAGTGTTATGATTTGCTCTAATC
Found at i:2720 original size:14 final size:14
Alignment explanation
Indices: 2701--2731 Score: 62
Period size: 14 Copynumber: 2.2 Consensus size: 14
2691 ACTAACCTTA
2701 AATAAGAAAATTAG
1 AATAAGAAAATTAG
2715 AATAAGAAAATTAG
1 AATAAGAAAATTAG
2729 AAT
1 AAT
2732 TCTTGATTAT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 17 1.00
ACGTcount: A:0.65, C:0.00, G:0.13, T:0.23
Consensus pattern (14 bp):
AATAAGAAAATTAG
Found at i:5151 original size:2 final size:2
Alignment explanation
Indices: 5139--5173 Score: 61
Period size: 2 Copynumber: 17.5 Consensus size: 2
5129 AGCTAGTTAG
*
5139 TA TA AA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
5174 GTGCAACTGT
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
TA
Found at i:5707 original size:74 final size:74
Alignment explanation
Indices: 5623--5765 Score: 218
Period size: 74 Copynumber: 1.9 Consensus size: 74
5613 TGTATATTAC
*
5623 TGTTAAAATATTTTACGCAACAA-T-ATTGAGTTGTTGCATAAAATATAATTCTTTTAGCAACAA
1 TGTTAAAATATTTTACGCAACAACTGAAT-A-TTGTTGCATAAAATATAATTCTTTTAGCAACAA
5686 TAAAATAGTGT
64 TAAAATAGTGT
* * *
5697 TGTTAAAATATTTTACGCAACAACTGAATATTGTTGCGTGAAATATAATTCTTTTAGTAACAATA
1 TGTTAAAATATTTTACGCAACAACTGAATATTGTTGCATAAAATATAATTCTTTTAGCAACAATA
5762 AAAT
66 AAAT
5766 GACGTAACGA
Statistics
Matches: 63, Mismatches: 4, Indels: 4
0.89 0.06 0.06
Matches are distributed among these distances:
74 59 0.94
75 2 0.03
76 2 0.03
ACGTcount: A:0.41, C:0.10, G:0.12, T:0.38
Consensus pattern (74 bp):
TGTTAAAATATTTTACGCAACAACTGAATATTGTTGCATAAAATATAATTCTTTTAGCAACAATA
AAATAGTGT
Found at i:5784 original size:74 final size:73
Alignment explanation
Indices: 5626--5784 Score: 180
Period size: 74 Copynumber: 2.2 Consensus size: 73
5616 ATATTACTGT
*
5626 TAAAATATTTTACGCAACAATATTGAGTTGTTGCATAAAATATAATTCTTTTAGCAACAATAAAA
1 TAAAATATTTTACGCAACAATAATGAGTTGTTGCATAAAATATAATTCTTTTAGCAACAATAAAA
***
5691 TAGTGTTG
66 TAGTAACG
* * *
5699 TTAAAATATTTTACGCAACAACTGAAT-A-TTGTTGCGTGAAATATAATTCTTTTAGTAACAATA
1 -TAAAATATTTTACGCAACAA-T-AATGAGTTGTTGCATAAAATATAATTCTTTTAGCAACAATA
5762 AAATGACGTAACG
63 AAAT-A-GTAACG
*
5775 -AAAAGATTTT
1 TAAAATATTTT
5785 TTTAACAACA
Statistics
Matches: 73, Mismatches: 8, Indels: 8
0.82 0.09 0.09
Matches are distributed among these distances:
74 65 0.89
75 3 0.04
76 5 0.07
ACGTcount: A:0.42, C:0.10, G:0.13, T:0.36
Consensus pattern (73 bp):
TAAAATATTTTACGCAACAATAATGAGTTGTTGCATAAAATATAATTCTTTTAGCAACAATAAAA
TAGTAACG
Found at i:8481 original size:75 final size:75
Alignment explanation
Indices: 8336--8503 Score: 180
Period size: 75 Copynumber: 2.2 Consensus size: 75
8326 CTTTTCATCT
* *
8336 CGTTTTGGTCTTTTCGCACTCTGGAATTTAGCAATAGCTCCCATCAACTTTTAACGTGGGAAAGC
1 CGTTTTGGTCTTTTCTCACTCTGGAATTTAGCAATAGCTCCCATAAACTTTTAACGTGGGAAAGC
8401 CTTTTC-GCTC
66 CTTTTCGGC-C
* * * * *
8411 CGTTTTGGTCTTTTCTCACTC-GGCAATTTA-CTGATAGTTCCCATAAACTTTTAATGTTGGAGA
1 CGTTTTGGTCTTTTCTCACTCTGG-AATTTAGC-AATAGCTCCCATAAACTTTTAACGTGGGAAA
***
8474 TTTTTTTCGGCC
64 GCCTTTTCGGCC
* *
8486 CGATTTGATCTTTTCTCA
1 CGTTTTGGTCTTTTCTCA
8504 ATTTATTAGT
Statistics
Matches: 78, Mismatches: 12, Indels: 6
0.81 0.12 0.06
Matches are distributed among these distances:
74 3 0.04
75 73 0.94
76 2 0.03
ACGTcount: A:0.19, C:0.23, G:0.17, T:0.41
Consensus pattern (75 bp):
CGTTTTGGTCTTTTCTCACTCTGGAATTTAGCAATAGCTCCCATAAACTTTTAACGTGGGAAAGC
CTTTTCGGCC
Found at i:9241 original size:2 final size:2
Alignment explanation
Indices: 9234--9263 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
9224 ATATTCATGA
9234 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
9264 GTTATTCTCG
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:26369 original size:51 final size:50
Alignment explanation
Indices: 26268--26369 Score: 111
Period size: 51 Copynumber: 2.0 Consensus size: 50
26258 GTTCTTCATA
* **
26268 TTTTCCTTGTTTAGATCTTGTCTCAGGACAATCAAACACTCTTTTAGTGT
1 TTTTCCTTGTTTAGATCTTGTCTCAGGACAATCAAACACTCGTACAGTGT
*
26318 TTTTCTCTTGTTTCA-ATCTTGTCTCCGGAC-ATACAAACACT-GTACACGTGT
1 TTTTC-CTTGTTT-AGATCTTGTCTCAGGACAAT-CAAACACTCGTACA-GTGT
26369 T
1 T
26370 CTTCATTTAG
Statistics
Matches: 44, Mismatches: 4, Indels: 7
0.80 0.07 0.13
Matches are distributed among these distances:
50 9 0.20
51 34 0.77
52 1 0.02
ACGTcount: A:0.22, C:0.23, G:0.14, T:0.42
Consensus pattern (50 bp):
TTTTCCTTGTTTAGATCTTGTCTCAGGACAATCAAACACTCGTACAGTGT
Found at i:30986 original size:52 final size:52
Alignment explanation
Indices: 30908--31012 Score: 192
Period size: 52 Copynumber: 2.0 Consensus size: 52
30898 TTCCTATAAA
30908 TTTTGTAACCTTCCTATGATTTTTGATAATCTCTCTGTGAGATTTGTTAATC
1 TTTTGTAACCTTCCTATGATTTTTGATAATCTCTCTGTGAGATTTGTTAATC
* *
30960 TTTTGTAACCTTTCTATGATTTTTGATAATCTCTTTGTGAGATTTGTTAATC
1 TTTTGTAACCTTCCTATGATTTTTGATAATCTCTCTGTGAGATTTGTTAATC
31012 T
1 T
31013 CCATATAATT
Statistics
Matches: 51, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
52 51 1.00
ACGTcount: A:0.21, C:0.13, G:0.13, T:0.52
Consensus pattern (52 bp):
TTTTGTAACCTTCCTATGATTTTTGATAATCTCTCTGTGAGATTTGTTAATC
Found at i:32318 original size:18 final size:18
Alignment explanation
Indices: 32291--32326 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
32281 AATATCAAAA
32291 GAAACACTAAATTTAAAG
1 GAAACACTAAATTTAAAG
*
32309 GAAACGCTAAATTTAAAG
1 GAAACACTAAATTTAAAG
32327 AATTACGCAA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.53, C:0.11, G:0.14, T:0.22
Consensus pattern (18 bp):
GAAACACTAAATTTAAAG
Found at i:32963 original size:2 final size:2
Alignment explanation
Indices: 32956--32980 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
32946 GTAGTTAGAA
32956 AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT A
32981 ATAGTTTGAG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:33810 original size:26 final size:27
Alignment explanation
Indices: 33751--33811 Score: 72
Period size: 27 Copynumber: 2.3 Consensus size: 27
33741 CTAAATTTCC
33751 ATTATTTTAATAATGGAATAATTAAAAT
1 ATTA-TTTAATAATGGAATAATTAAAAT
* *
33779 ATTATTTAGTAATGGCA-AATTAGAAAT
1 ATTATTTAATAATGGAATAATTA-AAAT
33806 A-TATTT
1 ATTATTT
33812 GAGAAAAAAA
Statistics
Matches: 30, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
26 10 0.33
27 16 0.53
28 4 0.13
ACGTcount: A:0.46, C:0.02, G:0.10, T:0.43
Consensus pattern (27 bp):
ATTATTTAATAATGGAATAATTAAAAT
Found at i:41509 original size:19 final size:20
Alignment explanation
Indices: 41479--41542 Score: 76
Period size: 21 Copynumber: 3.1 Consensus size: 20
41469 TTGACACTGT
41479 TTAGCAACTGTACAGATGAGA
1 TTAGC-ACTGTACAGATGAGA
*
41500 TTA-CACTGTACAGATTAGA
1 TTAGCACTGTACAGATGAGA
* *
41519 TTAGGTATTGTACAGATGAGA
1 TTA-GCACTGTACAGATGAGA
41540 TTA
1 TTA
41543 TTAGAGCAGC
Statistics
Matches: 37, Mismatches: 4, Indels: 4
0.82 0.09 0.09
Matches are distributed among these distances:
19 17 0.46
20 1 0.03
21 19 0.51
ACGTcount: A:0.36, C:0.11, G:0.22, T:0.31
Consensus pattern (20 bp):
TTAGCACTGTACAGATGAGA
Found at i:51977 original size:2 final size:2
Alignment explanation
Indices: 51970--52022 Score: 58
Period size: 2 Copynumber: 28.0 Consensus size: 2
51960 CCCGTCCCCG
* * *
51970 AT AT AT AT AT AT AT AC AT AT AT AT AT AT AT A- AT -T AT TT AA
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
52010 AT AT A- AT AT AT AT
1 AT AT AT AT AT AT AT
52023 GTGTAAGTTA
Statistics
Matches: 42, Mismatches: 6, Indels: 6
0.78 0.11 0.11
Matches are distributed among these distances:
1 3 0.07
2 39 0.93
ACGTcount: A:0.51, C:0.02, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:58137 original size:14 final size:14
Alignment explanation
Indices: 58118--58148 Score: 62
Period size: 14 Copynumber: 2.2 Consensus size: 14
58108 CTTCAGACTT
58118 TCAGTTTTATTTTC
1 TCAGTTTTATTTTC
58132 TCAGTTTTATTTTC
1 TCAGTTTTATTTTC
58146 TCA
1 TCA
58149 TTCTTTGTAA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 17 1.00
ACGTcount: A:0.16, C:0.16, G:0.06, T:0.61
Consensus pattern (14 bp):
TCAGTTTTATTTTC
Found at i:59638 original size:30 final size:30
Alignment explanation
Indices: 59602--59663 Score: 115
Period size: 30 Copynumber: 2.1 Consensus size: 30
59592 AATTTTATCT
*
59602 TGACTTTTCTCTTATATCCTCAAATTTTAA
1 TGACTTTTCTCTTATACCCTCAAATTTTAA
59632 TGACTTTTCTCTTATACCCTCAAATTTTAA
1 TGACTTTTCTCTTATACCCTCAAATTTTAA
59662 TG
1 TG
59664 GTTTATTAAC
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
30 31 1.00
ACGTcount: A:0.26, C:0.21, G:0.05, T:0.48
Consensus pattern (30 bp):
TGACTTTTCTCTTATACCCTCAAATTTTAA
Found at i:60893 original size:26 final size:26
Alignment explanation
Indices: 60837--60886 Score: 82
Period size: 26 Copynumber: 1.9 Consensus size: 26
60827 AGGGTCACCC
**
60837 AAGGGCATTTTGGTCATTTTTATACT
1 AAGGGCATTTTGGTCATTTGCATACT
60863 AAGGGCATTTTGGTCATTTGCATA
1 AAGGGCATTTTGGTCATTTGCATA
60887 TTCAGGGGCA
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
26 22 1.00
ACGTcount: A:0.24, C:0.12, G:0.22, T:0.42
Consensus pattern (26 bp):
AAGGGCATTTTGGTCATTTGCATACT
Found at i:62223 original size:22 final size:22
Alignment explanation
Indices: 62195--62236 Score: 84
Period size: 22 Copynumber: 1.9 Consensus size: 22
62185 TCTCACCTAC
62195 CCTCATTCTCTGGATACACAGA
1 CCTCATTCTCTGGATACACAGA
62217 CCTCATTCTCTGGATACACA
1 CCTCATTCTCTGGATACACA
62237 CACTCCATAC
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.26, C:0.33, G:0.12, T:0.29
Consensus pattern (22 bp):
CCTCATTCTCTGGATACACAGA
Done.