Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01011757.1 Corchorus capsularis cultivar CVL-1 contig11778, 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: 15908
ACGTcount: A:0.34, C:0.19, G:0.18, T:0.30
Found at i:732 original size:18 final size:18
Alignment explanation
Indices: 698--732 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
688 GCTTGATTAA
*
698 TTGATTGGGTTAATGAAT
1 TTGATTGGGTGAATGAAT
*
716 TTGATTGGGTGAGTGAA
1 TTGATTGGGTGAATGAA
733 GTGTCGACCG
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.26, C:0.00, G:0.34, T:0.40
Consensus pattern (18 bp):
TTGATTGGGTGAATGAAT
Found at i:939 original size:18 final size:18
Alignment explanation
Indices: 910--953 Score: 61
Period size: 18 Copynumber: 2.4 Consensus size: 18
900 CCAATTGTCC
*
910 TATTAATTTAGTTTAATT
1 TATTAGTTTAGTTTAATT
* *
928 TGTTAGTTTAGTTTAGTT
1 TATTAGTTTAGTTTAATT
946 TATTAGTT
1 TATTAGTT
954 AATTGAAACA
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
18 22 1.00
ACGTcount: A:0.25, C:0.00, G:0.14, T:0.61
Consensus pattern (18 bp):
TATTAGTTTAGTTTAATT
Found at i:1176 original size:40 final size:39
Alignment explanation
Indices: 1124--1251 Score: 113
Period size: 40 Copynumber: 3.3 Consensus size: 39
1114 TCTTCACTAC
*
1124 TTTAAAGTTTGAGTAACTATTATTTGAGGATTTTAAAGG
1 TTTAAAGTTTGAGTAACTATTATTTGAGGATTTTAAAGA
* * * * *
1163 TTTAAATGTTTGAGTATGC-ATCTCTTT---CACTTTAAA-C
1 TTTAAA-GTTTGAGTA-ACTAT-TATTTGAGGATTTTAAAGA
* *
1200 TTTAAAGTTCGAGTAACTATTATTCGAGGATTTTAAAGA
1 TTTAAAGTTTGAGTAACTATTATTTGAGGATTTTAAAGA
1239 TTTAAAAGTTTGA
1 TTT-AAAGTTTGA
1252 TATTCGAGGA
Statistics
Matches: 67, Mismatches: 13, Indels: 17
0.69 0.13 0.18
Matches are distributed among these distances:
35 4 0.06
36 10 0.15
37 6 0.09
38 14 0.21
39 9 0.13
40 19 0.28
41 5 0.07
ACGTcount: A:0.33, C:0.08, G:0.16, T:0.43
Consensus pattern (39 bp):
TTTAAAGTTTGAGTAACTATTATTTGAGGATTTTAAAGA
Found at i:1258 original size:32 final size:32
Alignment explanation
Indices: 1220--1284 Score: 112
Period size: 32 Copynumber: 2.0 Consensus size: 32
1210 GAGTAACTAT
*
1220 TATTCGAGGATTTTAAAGATTTAAAAGTTTGA
1 TATTCGAGGAATTTAAAGATTTAAAAGTTTGA
*
1252 TATTCGAGGAATTTAGAGATTTAAAAGTTTGA
1 TATTCGAGGAATTTAAAGATTTAAAAGTTTGA
1284 T
1 T
1285 TATGGAAAGG
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
32 31 1.00
ACGTcount: A:0.37, C:0.03, G:0.20, T:0.40
Consensus pattern (32 bp):
TATTCGAGGAATTTAAAGATTTAAAAGTTTGA
Found at i:6276 original size:23 final size:23
Alignment explanation
Indices: 6250--6308 Score: 82
Period size: 25 Copynumber: 2.5 Consensus size: 23
6240 GGTATCTAGA
6250 GCTTTGCTCTGTCCATCTGATAT
1 GCTTTGCTCTGTCCATCTGATAT
* *
6273 GCTTTGCTCTCTATCCATCTGGTAT
1 GCTTTG--CTCTGTCCATCTGATAT
6298 GCTTTGCTCTG
1 GCTTTGCTCTG
6309 ACTAGTGATG
Statistics
Matches: 31, Mismatches: 3, Indels: 4
0.82 0.08 0.11
Matches are distributed among these distances:
23 10 0.32
25 21 0.68
ACGTcount: A:0.10, C:0.27, G:0.19, T:0.44
Consensus pattern (23 bp):
GCTTTGCTCTGTCCATCTGATAT
Found at i:6290 original size:25 final size:25
Alignment explanation
Indices: 6256--6307 Score: 86
Period size: 25 Copynumber: 2.1 Consensus size: 25
6246 TAGAGCTTTG
*
6256 CTCTGTCCATCTGATATGCTTTGCT
1 CTCTATCCATCTGATATGCTTTGCT
*
6281 CTCTATCCATCTGGTATGCTTTGCT
1 CTCTATCCATCTGATATGCTTTGCT
6306 CT
1 CT
6308 GACTAGTGAT
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
25 25 1.00
ACGTcount: A:0.12, C:0.29, G:0.15, T:0.44
Consensus pattern (25 bp):
CTCTATCCATCTGATATGCTTTGCT
Found at i:6527 original size:84 final size:75
Alignment explanation
Indices: 6368--6533 Score: 233
Period size: 84 Copynumber: 2.1 Consensus size: 75
6358 CAACAGGACA
6368 ACTTAACATTTGATCCAACCAGTAATTTTCTTAATTTATTTATAATTCTAAATCTACCATATTTT
1 ACTTAACATTTGATCCAACCAGTAATTTTCTTAATTTATTTATAATTCTAAATCTACCATATTTT
6433 TGCATAACGG
66 TGCATAACGG
6443 ACTTAACATTTGATCCAACCAGCGTTTGTAATTTTCTTAATTTATATTATAAAATTCTAAATCTA
1 ACTTAACATTTGATCCAACCA------GTAATTTTCTTAATTTAT-TTAT--AATTCTAAATCTA
*
6508 CCCTATTTTTGCATAACGG
57 CCATATTTTTGCATAACGG
6527 ACGTTAA
1 AC-TTAA
6534 TATATTAAAA
Statistics
Matches: 80, Mismatches: 1, Indels: 10
0.88 0.01 0.11
Matches are distributed among these distances:
75 21 0.26
81 18 0.22
82 4 0.05
84 33 0.41
85 4 0.05
ACGTcount: A:0.33, C:0.17, G:0.08, T:0.42
Consensus pattern (75 bp):
ACTTAACATTTGATCCAACCAGTAATTTTCTTAATTTATTTATAATTCTAAATCTACCATATTTT
TGCATAACGG
Found at i:7740 original size:223 final size:223
Alignment explanation
Indices: 7471--7916 Score: 711
Period size: 223 Copynumber: 2.0 Consensus size: 223
7461 CATTTCTAAA
*
7471 ACTGTAAGCTCAGAAGCCAAGCGTAACAAATACATCTCATAGAAGAATCCAACAAATAGATTCTT
1 ACTGTAAGCTCAGAAGCCAAGCGTAACAAATAAATCTCATAGAAGAATCCAACAAATAGATTCTT
7536 CTTACATGTTATTGCTTCATCACTGCAAGAAAAAACTATAAAAAAAGGAA-TCGAATATCACTCC
66 CTTACATGTTATTGCTTCATCACTGCAAGAAAAAACTATAAAAAAAGGAACT-GAATATCAC-CC
* * * *
7600 TTTAGAAAAACAAATCTTCAGTCAACCT-AA-AT-TTAGAAGTTTTACCAGTTAGTTGAAACATC
129 -TTAGAAAAACAAATCATCAGTCAACCTAAACATCTAACAAGTTTCACCAGTTAGTTGAAACAT-
7662 TTATCTTAGATACAAAGTTAGACCCTTGATTT
192 TTATCTTAGATACAAAGTTAGACCCTTGATTT
*
7694 ACTGTAAGCTCAGAAGCCAAGCGTAACAAGTAAATCTCATAGAAGAATCCAACAAATAGATTCTT
1 ACTGTAAGCTCAGAAGCCAAGCGTAACAAATAAATCTCATAGAAGAATCCAACAAATAGATTCTT
7759 CTTACATGTTATTGCTTCATCACTGCAAGAAAAAACTATAAAAAAAGGAACTGAATATCACCCTT
66 CTTACATGTTATTGCTTCATCACTGCAAGAAAAAACTATAAAAAAAGGAACTGAATATCACCCTT
* * * * *
7824 AGACATACAAATCATCAGTTAACTTAAACATCTAACAAGTTTCACCAGTTAGTTGAAACATTTGT
131 AGAAAAACAAATCATCAGTCAACCTAAACATCTAACAAGTTTCACCAGTTAGTTGAAACATTTAT
* *
7889 CTTAGATACACAGTTAGACCTTTGATTT
196 CTTAGATACAAAGTTAGACCCTTGATTT
7917 TATAAACTTT
Statistics
Matches: 206, Mismatches: 13, Indels: 8
0.91 0.06 0.04
Matches are distributed among these distances:
221 22 0.11
222 4 0.02
223 153 0.74
224 27 0.13
ACGTcount: A:0.40, C:0.19, G:0.12, T:0.28
Consensus pattern (223 bp):
ACTGTAAGCTCAGAAGCCAAGCGTAACAAATAAATCTCATAGAAGAATCCAACAAATAGATTCTT
CTTACATGTTATTGCTTCATCACTGCAAGAAAAAACTATAAAAAAAGGAACTGAATATCACCCTT
AGAAAAACAAATCATCAGTCAACCTAAACATCTAACAAGTTTCACCAGTTAGTTGAAACATTTAT
CTTAGATACAAAGTTAGACCCTTGATTT
Found at i:9190 original size:23 final size:24
Alignment explanation
Indices: 9164--9211 Score: 71
Period size: 24 Copynumber: 2.0 Consensus size: 24
9154 AAAATAACTT
*
9164 AAACTCCAAC-CGAAAAAAAAAAA
1 AAACTCCAACAAGAAAAAAAAAAA
*
9187 AAACTCCAACAAGGAAAAAAAAAA
1 AAACTCCAACAAGAAAAAAAAAAA
9211 A
1 A
9212 GTATTTTCTT
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
23 10 0.45
24 12 0.55
ACGTcount: A:0.71, C:0.19, G:0.06, T:0.04
Consensus pattern (24 bp):
AAACTCCAACAAGAAAAAAAAAAA
Found at i:15649 original size:10 final size:10
Alignment explanation
Indices: 15630--15663 Score: 59
Period size: 10 Copynumber: 3.4 Consensus size: 10
15620 AAAAAACCTA
*
15630 CCCGTTCCAT
1 CCCGTCCCAT
15640 CCCGTCCCAT
1 CCCGTCCCAT
15650 CCCGTCCCAT
1 CCCGTCCCAT
15660 CCCG
1 CCCG
15664 ATCCTTACTG
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
10 23 1.00
ACGTcount: A:0.09, C:0.59, G:0.12, T:0.21
Consensus pattern (10 bp):
CCCGTCCCAT
Done.