Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01020371.1 Corchorus olitorius cultivar O-4 contig20404, 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: 63420
ACGTcount: A:0.33, C:0.18, G:0.18, T:0.31
Found at i:1210 original size:277 final size:277
Alignment explanation
Indices: 710--1263 Score: 1036
Period size: 277 Copynumber: 2.0 Consensus size: 277
700 ATCCCTTAAG
710 AAAAAAAAATTATGAAGATTCGAATCCTAAATCTTCTTGTTTTTTATATAATTACCTCCGAGAAC
1 AAAAAAAAATTATGAAGATTCGAATCCTAAATCTTCTTGTTTTTTATATAATTACCTCCGAGAAC
*
775 CACCCTTGTCTGTACAGTTGAGTAATTACAATTAGAATAAATCTTTATATGTCTAAACATCTAAA
66 CACCCTTGTCTGTACAGTTGAGTAATTACAATTAGAATAAATCTTTATATGTCCAAACATCTAAA
* * *
840 TGAAAAATCAATAAACAAAGTGAGACTTGAACTCAAGACCTCACAGTCCAGACACGGTACAACCA
131 TAAAAAATCAATAAACAAAGTGAGACTTGAACTCAAGACCTCACAATCCAAACACGGTACAACCA
* *
905 CTAGTTGAGCTAACAACTCGGATGTAACCTTGTCTGTACATAATTAGATATAATAATGTGCATCA
196 CCAGTTGAACTAACAACTCGGATGTAACCTTGTCTGTACATAATTAGATATAATAATGTGCATCA
970 TGTGAATTACGAGTTTT
261 TGTGAATTACGAGTTTT
987 AAAAAAAAATTATGAAGATTCGAATCCTAAATCTTCTTGTTTTTTATATAATTACCTCCGAGAAC
1 AAAAAAAAATTATGAAGATTCGAATCCTAAATCTTCTTGTTTTTTATATAATTACCTCCGAGAAC
*
1052 CACCCTTGTCTGTACATTTGAGTAATTACAATTAGAATAAATCTTTATATGTCCAAACATCTAAA
66 CACCCTTGTCTGTACAGTTGAGTAATTACAATTAGAATAAATCTTTATATGTCCAAACATCTAAA
1117 TAAAAAATCAATAAACAAAGTGAGACTTGAACTCAAGACCTCACAATCCAAACACGGTACAACCA
131 TAAAAAATCAATAAACAAAGTGAGACTTGAACTCAAGACCTCACAATCCAAACACGGTACAACCA
*
1182 CCAGTTGAACTAACAACTCGGGTGTAACCTTGTCTGTACATAATTAGATATAATAATGTGCATCA
196 CCAGTTGAACTAACAACTCGGATGTAACCTTGTCTGTACATAATTAGATATAATAATGTGCATCA
1247 TGTGAATTACGAGTTTT
261 TGTGAATTACGAGTTTT
1264 TATCCGGGAG
Statistics
Matches: 269, Mismatches: 8, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
277 269 1.00
ACGTcount: A:0.38, C:0.18, G:0.13, T:0.31
Consensus pattern (277 bp):
AAAAAAAAATTATGAAGATTCGAATCCTAAATCTTCTTGTTTTTTATATAATTACCTCCGAGAAC
CACCCTTGTCTGTACAGTTGAGTAATTACAATTAGAATAAATCTTTATATGTCCAAACATCTAAA
TAAAAAATCAATAAACAAAGTGAGACTTGAACTCAAGACCTCACAATCCAAACACGGTACAACCA
CCAGTTGAACTAACAACTCGGATGTAACCTTGTCTGTACATAATTAGATATAATAATGTGCATCA
TGTGAATTACGAGTTTT
Found at i:1347 original size:6 final size:6
Alignment explanation
Indices: 1336--1362 Score: 54
Period size: 6 Copynumber: 4.5 Consensus size: 6
1326 TCTTATGTAT
1336 AAAGAA AAAGAA AAAGAA AAAGAA AAA
1 AAAGAA AAAGAA AAAGAA AAAGAA AAA
1363 TTAATTGTGT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 21 1.00
ACGTcount: A:0.85, C:0.00, G:0.15, T:0.00
Consensus pattern (6 bp):
AAAGAA
Found at i:10075 original size:22 final size:21
Alignment explanation
Indices: 10023--10070 Score: 71
Period size: 22 Copynumber: 2.3 Consensus size: 21
10013 TTCATTTATG
10023 GATCTTTTTGGTTATAAAATT
1 GATCTTTTTGGTTATAAAATT
*
10044 GGGTCTTTTTGGTTATAAAATT
1 -GATCTTTTTGGTTATAAAATT
10066 -ATCTT
1 GATCTT
10071 GTTTTTAATA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
20 4 0.17
22 20 0.83
ACGTcount: A:0.25, C:0.06, G:0.17, T:0.52
Consensus pattern (21 bp):
GATCTTTTTGGTTATAAAATT
Found at i:22555 original size:30 final size:30
Alignment explanation
Indices: 22521--22590 Score: 88
Period size: 30 Copynumber: 2.4 Consensus size: 30
22511 CTTGGAGGAG
*
22521 GAAGAGGCAGAGTACGAGACAGATTCAGAA
1 GAAGAGGAAGAGTACGAGACAGATTCAGAA
** *
22551 GAAGAGGAAGAGTGTGAGACAGATTTAGAA
1 GAAGAGGAAGAGTACGAGACAGATTCAGAA
*
22581 GAGGA-GAAGA
1 GAAGAGGAAGA
22591 CGGTATACGT
Statistics
Matches: 35, Mismatches: 5, Indels: 1
0.85 0.12 0.02
Matches are distributed among these distances:
29 5 0.14
30 30 0.86
ACGTcount: A:0.44, C:0.07, G:0.37, T:0.11
Consensus pattern (30 bp):
GAAGAGGAAGAGTACGAGACAGATTCAGAA
Found at i:27966 original size:45 final size:45
Alignment explanation
Indices: 27877--28059 Score: 204
Period size: 45 Copynumber: 4.1 Consensus size: 45
27867 CACTAATGGG
* * * *** *
27877 TTCCATTGATGCAGAAGGCATTAGTGATGGCATCATCATAGTTGA
1 TTCCACTGATGCAGAAGGCATCAGCGATGGCATGGCCATTGTTGA
* * * *
27922 TTTCACTGATGCAGAAGGCATTAGCGATGACATGGCCATGGTTGA
1 TTCCACTGATGCAGAAGGCATCAGCGATGGCATGGCCATTGTTGA
* * *
27967 TTCCACTGATGCAGAAGGAATCAGTGATGCCATGGCCATTGTTGA
1 TTCCACTGATGCAGAAGGCATCAGCGATGGCATGGCCATTGTTGA
* * * *
28012 TTCCACTGATGAAGAAGGTATCAGCGATGGCGTGGCTATTGTTGA
1 TTCCACTGATGCAGAAGGCATCAGCGATGGCATGGCCATTGTTGA
28057 TTC
1 TTC
28060 TATTGATACA
Statistics
Matches: 118, Mismatches: 20, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
45 118 1.00
ACGTcount: A:0.26, C:0.17, G:0.27, T:0.29
Consensus pattern (45 bp):
TTCCACTGATGCAGAAGGCATCAGCGATGGCATGGCCATTGTTGA
Found at i:30477 original size:19 final size:20
Alignment explanation
Indices: 30439--30477 Score: 53
Period size: 19 Copynumber: 2.0 Consensus size: 20
30429 GTGCAAATGC
*
30439 TTAAGGAACAGAGAAAGTGA
1 TTAAGGAACAAAGAAAGTGA
*
30459 TTAAGGAA-AAAGTAAGTGA
1 TTAAGGAACAAAGAAAGTGA
30478 ATCAATAATG
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
19 9 0.53
20 8 0.47
ACGTcount: A:0.51, C:0.03, G:0.28, T:0.18
Consensus pattern (20 bp):
TTAAGGAACAAAGAAAGTGA
Found at i:32703 original size:117 final size:117
Alignment explanation
Indices: 32370--32729 Score: 452
Period size: 117 Copynumber: 3.1 Consensus size: 117
32360 CCTCAACCAT
* * * *
32370 CCCCTTATCACTAGACTCATTTACATTACTAGGTACTGCAGAGCTGCTCTCATTAGCAACCAGAA
1 CCCCTTTTCACTAGAGTCAATTACATTACTAGGTACTGCAGAACTGCTCTCATTAGCAACCAGAA
* * * * * *
32435 CATCCTCACTACCATGTAATAATGTCGAAACACCGCCATGTTCTCCAATTGC
66 CATCCTCATTAGCATGCAATAATGTCGAAATACCACCATGTTCTCCAACTGC
** * * * *
32487 CCCCTTTTCACTAGAGTCAATGGCATTACTAGGTACTGCAGAACAGCTCTCATCAGCTACCAGAG
1 CCCCTTTTCACTAGAGTCAATTACATTACTAGGTACTGCAGAACTGCTCTCATTAGCAACCAGAA
* * * * *
32552 CATCCTCATTAGCGTGCACTAATGTCGAAATACCAACATGTTCTACAACAGC
66 CATCCTCATTAGCATGCAATAATGTCGAAATACCACCATGTTCTCCAACTGC
* *
32604 CCCCTTTTCACTAGAGTCACTTACATTACTAGGTACTGCACAACTGCTCTCATTAGCAACCAGAA
1 CCCCTTTTCACTAGAGTCAATTACATTACTAGGTACTGCAGAACTGCTCTCATTAGCAACCAGAA
* * * *
32669 CATCCTCATTAGAATCCAATAATG-CTGAATTACCACCATCTTCTCCAACTGC
66 CATCCTCATTAGCATGCAATAATGTC-GAAATACCACCATGTTCTCCAACTGC
*
32721 CCCCGTTTC
1 CCCCTTTTC
32730 CTTTTCTGCT
Statistics
Matches: 203, Mismatches: 39, Indels: 2
0.83 0.16 0.01
Matches are distributed among these distances:
116 1 0.00
117 202 1.00
ACGTcount: A:0.29, C:0.31, G:0.13, T:0.27
Consensus pattern (117 bp):
CCCCTTTTCACTAGAGTCAATTACATTACTAGGTACTGCAGAACTGCTCTCATTAGCAACCAGAA
CATCCTCATTAGCATGCAATAATGTCGAAATACCACCATGTTCTCCAACTGC
Found at i:53118 original size:4 final size:4
Alignment explanation
Indices: 53111--53223 Score: 199
Period size: 4 Copynumber: 28.2 Consensus size: 4
53101 ATAGAGAGAG
53111 AAGA AAGA AAGA AAGA AAGA AAGA AAGA AAGA AAGA AAGA AAGA AAGA
1 AAGA AAGA AAGA AAGA AAGA AAGA AAGA AAGA AAGA AAGA AAGA AAGA
53159 AAGA AAGA AAGA AAGA AAGA AAGA AAGA AAGA AAGA AAGA AAGA AAGA
1 AAGA AAGA AAGA AAGA AAGA AAGA AAGA AAGA AAGA AAGA AAGA AAGA
* * *
53207 ATGA ATGA ATGA AAGA A
1 AAGA AAGA AAGA AAGA A
53224 CATAACTTGT
Statistics
Matches: 107, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
4 107 1.00
ACGTcount: A:0.73, C:0.00, G:0.25, T:0.03
Consensus pattern (4 bp):
AAGA
Found at i:56761 original size:13 final size:13
Alignment explanation
Indices: 56743--56770 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
56733 CTACATTCCG
56743 ATAGCACCTGTCC
1 ATAGCACCTGTCC
56756 ATAGCACCTGTCC
1 ATAGCACCTGTCC
56769 AT
1 AT
56771 TCGCAATCTT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.25, C:0.36, G:0.14, T:0.25
Consensus pattern (13 bp):
ATAGCACCTGTCC
Found at i:60496 original size:5 final size:5
Alignment explanation
Indices: 60486--60512 Score: 54
Period size: 5 Copynumber: 5.4 Consensus size: 5
60476 AAATATTTAT
60486 ATATG ATATG ATATG ATATG ATATG AT
1 ATATG ATATG ATATG ATATG ATATG AT
60513 TCTTTTATTT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 22 1.00
ACGTcount: A:0.41, C:0.00, G:0.19, T:0.41
Consensus pattern (5 bp):
ATATG
Found at i:63248 original size:18 final size:19
Alignment explanation
Indices: 63209--63249 Score: 57
Period size: 21 Copynumber: 2.1 Consensus size: 19
63199 GTACTTCCAT
63209 TGTGATGCTCCCACTTTTCAA
1 TGTGATGCTCCCA--TTTCAA
63230 TGTGATGCTCCCA-TTCAA
1 TGTGATGCTCCCATTTCAA
63248 TG
1 TG
63250 CTGACCATTG
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
18 7 0.35
21 13 0.65
ACGTcount: A:0.20, C:0.27, G:0.17, T:0.37
Consensus pattern (19 bp):
TGTGATGCTCCCATTTCAA
Done.