Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01008609.1 Corchorus capsularis cultivar CVL-1 contig08630, 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: 31644
ACGTcount: A:0.33, C:0.19, G:0.15, T:0.33
Found at i:849 original size:2 final size:2
Alignment explanation
Indices: 842--876 Score: 61
Period size: 2 Copynumber: 17.5 Consensus size: 2
832 CCTCCTAAAA
*
842 AT AT AT AT AT AT AT AT AT AT AT AT AT AT CT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
877 ATACAAAATA
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:0.49, C:0.03, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:5607 original size:2 final size:2
Alignment explanation
Indices: 5600--5633 Score: 54
Period size: 2 Copynumber: 18.0 Consensus size: 2
5590 ATAAGACAAC
5600 TA TA TA TA TA TA TA TA TA TA TA TA T- TA TA -A TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
5634 ATAGAATGTA
Statistics
Matches: 30, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
1 2 0.07
2 28 0.93
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:5887 original size:17 final size:17
Alignment explanation
Indices: 5848--5889 Score: 50
Period size: 17 Copynumber: 2.5 Consensus size: 17
5838 ATTACTAACG
*
5848 AAATGAAATTCAACAGA
1 AAATGAAAATCAACAGA
*
5865 ATATGAAAATCAACA-A
1 AAATGAAAATCAACAGA
5881 CAAATGAAA
1 -AAATGAAA
5890 TATATAATTA
Statistics
Matches: 21, Mismatches: 3, Indels: 2
0.81 0.12 0.08
Matches are distributed among these distances:
16 1 0.05
17 20 0.95
ACGTcount: A:0.62, C:0.12, G:0.10, T:0.17
Consensus pattern (17 bp):
AAATGAAAATCAACAGA
Found at i:7057 original size:2 final size:2
Alignment explanation
Indices: 7050--7076 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
7040 TCCTCATTAT
7050 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 T
7077 CTAACGGAAT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:9210 original size:34 final size:34
Alignment explanation
Indices: 9167--9242 Score: 100
Period size: 34 Copynumber: 2.2 Consensus size: 34
9157 GGATTTTATC
* * *
9167 AATTGGTCCTGATATACT-GTCGTCAGGACCCAAT
1 AATTGGTCCTGATAT-CTCATCATCAAGACCCAAT
*
9201 AATTGGTCCTGATATTTCATCATCAAGACCCAAT
1 AATTGGTCCTGATATCTCATCATCAAGACCCAAT
9235 AATTGGTC
1 AATTGGTC
9243 TTGACATCAA
Statistics
Matches: 37, Mismatches: 4, Indels: 2
0.86 0.09 0.05
Matches are distributed among these distances:
33 1 0.03
34 36 0.97
ACGTcount: A:0.29, C:0.22, G:0.17, T:0.32
Consensus pattern (34 bp):
AATTGGTCCTGATATCTCATCATCAAGACCCAAT
Found at i:11896 original size:145 final size:145
Alignment explanation
Indices: 11694--11988 Score: 563
Period size: 145 Copynumber: 2.0 Consensus size: 145
11684 TATTTATCCC
11694 TGGCCAAAATCTTTTGTACACCTAATCTTCGCATAATCGAATCACGAATGCAAATAGGTGTGTTG
1 TGGCCAAAATCTTTTGTACACCTAATCTTCGCATAATCGAATCACGAATGCAAATAGGTGTGTTG
*
11759 GCACTAAATAGCACAGCCGATTTGTCCATATTTATTTTCTGCCTCGAAAGCTTTTTCAAACTTAG
66 GCACTAAATAGCACAGCCGATTTGTCCACATTTATTTTCTGCCTCGAAAGCTTTTTCAAACTTAG
11824 TAAGAATATCCAACA
131 TAAGAATATCCAACA
11839 TGGCCAAAATCTTTTGTACACCTAATCTTCGCATAATCGAATCACGAATGCAAATAGGTGTGTTG
1 TGGCCAAAATCTTTTGTACACCTAATCTTCGCATAATCGAATCACGAATGCAAATAGGTGTGTTG
*
11904 GCACTAAATAGCACAGCCGATTTGTCCACATTTATTTTCTGCCTCGAAAGCTTTTTCAAACTTCG
66 GCACTAAATAGCACAGCCGATTTGTCCACATTTATTTTCTGCCTCGAAAGCTTTTTCAAACTTAG
*
11969 TCAGAATATCCAACA
131 TAAGAATATCCAACA
11984 TGGCC
1 TGGCC
11989 TCACATTCAT
Statistics
Matches: 147, Mismatches: 3, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
145 147 1.00
ACGTcount: A:0.31, C:0.23, G:0.16, T:0.31
Consensus pattern (145 bp):
TGGCCAAAATCTTTTGTACACCTAATCTTCGCATAATCGAATCACGAATGCAAATAGGTGTGTTG
GCACTAAATAGCACAGCCGATTTGTCCACATTTATTTTCTGCCTCGAAAGCTTTTTCAAACTTAG
TAAGAATATCCAACA
Found at i:18639 original size:1 final size:1
Alignment explanation
Indices: 18633--18661 Score: 58
Period size: 1 Copynumber: 29.0 Consensus size: 1
18623 AGTCTCCTAG
18633 TTTTTTTTTTTTTTTTTTTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTT
18662 CCTTCCTTCC
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 28 1.00
ACGTcount: A:0.00, C:0.00, G:0.00, T:1.00
Consensus pattern (1 bp):
T
Found at i:19081 original size:22 final size:23
Alignment explanation
Indices: 19029--19082 Score: 85
Period size: 23 Copynumber: 2.4 Consensus size: 23
19019 CATAATCAGA
19029 ACTCC-TTGTGAGAGCATTTGAG
1 ACTCCTTTGTGAGAGCATTTGAG
*
19051 ACTCCTTTGTGAGAGCATTTGGG
1 ACTCCTTTGTGAGAGCATTTGAG
19074 A-TCCTTTGT
1 ACTCCTTTGT
19083 TTTGTCTTGC
Statistics
Matches: 30, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
22 13 0.43
23 17 0.57
ACGTcount: A:0.19, C:0.19, G:0.26, T:0.37
Consensus pattern (23 bp):
ACTCCTTTGTGAGAGCATTTGAG
Found at i:23847 original size:2 final size:2
Alignment explanation
Indices: 23840--23876 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
23830 TTATAATCAG
23840 AT AT AT AT AT AT 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 AT AT AT AT AT AT A
23877 GCAAAATTAG
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:25423 original size:18 final size:18
Alignment explanation
Indices: 25400--25439 Score: 55
Period size: 18 Copynumber: 2.2 Consensus size: 18
25390 TAATCTATGG
25400 AAAATGCAA-AAAGTAAGT
1 AAAATGCAATAAAGT-AGT
*
25418 AAAATGGAATAAAGTAGT
1 AAAATGCAATAAAGTAGT
25436 AAAA
1 AAAA
25440 GGCTAAAAGC
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
18 15 0.75
19 5 0.25
ACGTcount: A:0.62, C:0.03, G:0.17, T:0.17
Consensus pattern (18 bp):
AAAATGCAATAAAGTAGT
Found at i:31544 original size:21 final size:21
Alignment explanation
Indices: 31520--31563 Score: 88
Period size: 21 Copynumber: 2.1 Consensus size: 21
31510 ATTTAACACG
31520 TTGGCTTTTATTTTTGTATTT
1 TTGGCTTTTATTTTTGTATTT
31541 TTGGCTTTTATTTTTGTATTT
1 TTGGCTTTTATTTTTGTATTT
31562 TT
1 TT
31564 TTATTTGTCT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.09, C:0.05, G:0.14, T:0.73
Consensus pattern (21 bp):
TTGGCTTTTATTTTTGTATTT
Done.