Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01018328.1 Corchorus olitorius cultivar O-4 contig18361, 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: 47180
ACGTcount: A:0.30, C:0.18, G:0.19, T:0.33
Found at i:1113 original size:31 final size:31
Alignment explanation
Indices: 1048--1117 Score: 95
Period size: 31 Copynumber: 2.3 Consensus size: 31
1038 AAATTGACTC
* *
1048 TAGGGACTGATTTGAGTCGATTTTACAATAT
1 TAGGGACTGATTTGAGTCGAATTTACAACAT
* * *
1079 TAGGGACTGATTTGAGTTGAATTTATAACGT
1 TAGGGACTGATTTGAGTCGAATTTACAACAT
1110 TAGGGACT
1 TAGGGACT
1118 TAATTAACCA
Statistics
Matches: 34, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
31 34 1.00
ACGTcount: A:0.29, C:0.09, G:0.26, T:0.37
Consensus pattern (31 bp):
TAGGGACTGATTTGAGTCGAATTTACAACAT
Found at i:2536 original size:202 final size:201
Alignment explanation
Indices: 2178--2575 Score: 609
Period size: 202 Copynumber: 2.0 Consensus size: 201
2168 ATAACTTAAA
*
2178 TACCAAACTACAAAACAAATAAACAAAAAACTTAAACTCAAATTTCTCAAGACTTGAACCCAAGA
1 TACCAAACTACAAAACAAATAAACAAAAAAATTAAACTCAAATTTCTCAAGACTTGAACCCAAGA
* *
2243 CCTCACAGTCCAAGCACAGTGCACTCATCAGTTGGGTTAACAACTCAAGTGCATCAATATGTATA
66 CCTCACAGTCCAAGCACAGTGCACTCACCAGTTGAGTTAACAACTCAAGTGCATCAATATGTATA
* * *
2308 TGTAATTAATTGTACATTTTTACAAAAGGGACATTTTCCC-CCTTGAATTTTTATTTTGGAACTT
131 TGTAATTAACTGTACACTTTTACAAAAGGGACA-TTTCCCTCC-TAAATTTTTATTTTGGAACTT
2372 GTATTACT
194 GTATTACT
* * * ** **
2380 TACCGAACTACCAAACAAATAATCAAAAAAATTAAACTCAAATTTCTTGAGACTTGAACTTAAGA
1 TACCAAACTACAAAACAAATAAACAAAAAAATTAAACTCAAATTTCTCAAGACTTGAACCCAAGA
* * ** *
2445 CCTCACGGTCCAAGCATAGTGCACTCACCAGTTGAGTTAACAACTCGGGTGTATCAATATGTATA
66 CCTCACAGTCCAAGCACAGTGCACTCACCAGTTGAGTTAACAACTCAAGTGCATCAATATGTATA
2510 TGTAATTAACTGTACACTTTTACAAAAGGGACATTTCCCTCCTAAATTTTTATTTTGGAACTTGT
131 TGTAATTAACTGTACACTTTTACAAAAGGGACATTTCCCTCCTAAATTTTTATTTTGGAACTTGT
2575 A
196 A
2576 GTCCTAAACT
Statistics
Matches: 177, Mismatches: 18, Indels: 3
0.89 0.09 0.02
Matches are distributed among these distances:
201 29 0.16
202 148 0.84
ACGTcount: A:0.37, C:0.20, G:0.12, T:0.30
Consensus pattern (201 bp):
TACCAAACTACAAAACAAATAAACAAAAAAATTAAACTCAAATTTCTCAAGACTTGAACCCAAGA
CCTCACAGTCCAAGCACAGTGCACTCACCAGTTGAGTTAACAACTCAAGTGCATCAATATGTATA
TGTAATTAACTGTACACTTTTACAAAAGGGACATTTCCCTCCTAAATTTTTATTTTGGAACTTGT
ATTACT
Found at i:4137 original size:13 final size:13
Alignment explanation
Indices: 4119--4143 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
4109 TTGAGTTTAA
4119 AAATAATTATTAG
1 AAATAATTATTAG
4132 AAATAATTATTA
1 AAATAATTATTA
4144 TTTACAATTA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.56, C:0.00, G:0.04, T:0.40
Consensus pattern (13 bp):
AAATAATTATTAG
Found at i:4366 original size:13 final size:13
Alignment explanation
Indices: 4348--4411 Score: 69
Period size: 13 Copynumber: 4.9 Consensus size: 13
4338 ATTTTATATA
4348 ATAGTAAGATAAG
1 ATAGTAAGATAAG
*
4361 ATAGTAAAATAAG
1 ATAGTAAGATAAG
*
4374 ATAGTAAAAT-AG
1 ATAGTAAGATAAG
4386 -TAAGATAAGATAAG
1 AT-AG-TAAGATAAG
*
4400 ATAATAAGATAA
1 ATAGTAAGATAA
4412 AATATGCATC
Statistics
Matches: 44, Mismatches: 3, Indels: 8
0.80 0.05 0.15
Matches are distributed among these distances:
11 1 0.02
12 4 0.09
13 35 0.80
14 3 0.07
15 1 0.02
ACGTcount: A:0.59, C:0.00, G:0.17, T:0.23
Consensus pattern (13 bp):
ATAGTAAGATAAG
Found at i:4405 original size:21 final size:21
Alignment explanation
Indices: 4352--4415 Score: 58
Period size: 21 Copynumber: 2.9 Consensus size: 21
4342 TATATAATAG
4352 TAAGATAAGATAGTAAAATAAGA
1 TAAGAT-A-ATAGTAAAATAAGA
* *
4375 T-AGTAAAATAGTAAGATAAGA
1 TAAG-ATAATAGTAAAATAAGA
4396 TAAGATAATAAGATAAAATA
1 TAAGATAAT-AG-TAAAATA
4416 TGCATCAAAA
Statistics
Matches: 33, Mismatches: 4, Indels: 8
0.73 0.09 0.18
Matches are distributed among these distances:
21 18 0.55
22 7 0.21
23 8 0.24
ACGTcount: A:0.61, C:0.00, G:0.16, T:0.23
Consensus pattern (21 bp):
TAAGATAATAGTAAAATAAGA
Found at i:12953 original size:23 final size:23
Alignment explanation
Indices: 12919--12966 Score: 87
Period size: 23 Copynumber: 2.1 Consensus size: 23
12909 AATGAGCCTG
12919 CCCAGCCATGAGCCTAGACTTCT
1 CCCAGCCATGAGCCTAGACTTCT
*
12942 CCCAGCCGTGAGCCTAGACTTCT
1 CCCAGCCATGAGCCTAGACTTCT
12965 CC
1 CC
12967 GCTAGACTTC
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
23 24 1.00
ACGTcount: A:0.19, C:0.42, G:0.19, T:0.21
Consensus pattern (23 bp):
CCCAGCCATGAGCCTAGACTTCT
Found at i:14555 original size:14 final size:14
Alignment explanation
Indices: 14521--14548 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
14511 TCTTGCAGAA
14521 ACGCTTGATATGTT
1 ACGCTTGATATGTT
14535 ACGCTTGATATGTT
1 ACGCTTGATATGTT
14549 TGGCTTGCAG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.21, C:0.14, G:0.21, T:0.43
Consensus pattern (14 bp):
ACGCTTGATATGTT
Found at i:32672 original size:16 final size:16
Alignment explanation
Indices: 32651--32681 Score: 62
Period size: 16 Copynumber: 1.9 Consensus size: 16
32641 ATTTGTTTTC
32651 AAGTAGCCAAAAAAAA
1 AAGTAGCCAAAAAAAA
32667 AAGTAGCCAAAAAAA
1 AAGTAGCCAAAAAAA
32682 CTATACTATT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.68, C:0.13, G:0.13, T:0.06
Consensus pattern (16 bp):
AAGTAGCCAAAAAAAA
Found at i:33902 original size:7 final size:7
Alignment explanation
Indices: 33876--33908 Score: 50
Period size: 7 Copynumber: 4.7 Consensus size: 7
33866 GTTGTAGGAC
33876 TATA-TA
1 TATATTA
33882 TATATTA
1 TATATTA
33889 TTATATTA
1 -TATATTA
33897 TATATTA
1 TATATTA
33904 TATAT
1 TATAT
33909 ATAATAATAA
Statistics
Matches: 25, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
6 4 0.16
7 14 0.56
8 7 0.28
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (7 bp):
TATATTA
Found at i:40964 original size:25 final size:24
Alignment explanation
Indices: 40930--41011 Score: 60
Period size: 25 Copynumber: 3.2 Consensus size: 24
40920 TTATATTATC
*
40930 AAAATACATTGAAACAAATTCATGT
1 AAAATGCATTGAAACAAATTCAT-T
* *
40955 AAAATGCATT-ACATTTA-AAATGTAATC
1 AAAATGCATTGA-A---ACAAAT-TCATT
40982 AAAATGCATTGAAACAAATTCATAT
1 AAAATGCATTGAAACAAATTCAT-T
41007 AAAAT
1 AAAAT
41012 AATGTATTAC
Statistics
Matches: 44, Mismatches: 5, Indels: 16
0.68 0.08 0.25
Matches are distributed among these distances:
24 5 0.11
25 19 0.43
27 15 0.34
28 5 0.11
ACGTcount: A:0.52, C:0.11, G:0.07, T:0.29
Consensus pattern (24 bp):
AAAATGCATTGAAACAAATTCATT
Found at i:45680 original size:16 final size:18
Alignment explanation
Indices: 45659--45691 Score: 52
Period size: 16 Copynumber: 1.9 Consensus size: 18
45649 ATAAGAAAAT
45659 TAAAAT-ATTA-ATTGTA
1 TAAAATAATTATATTGTA
45675 TAAAATAATTATATTGT
1 TAAAATAATTATATTGT
45692 TTTAATTGAT
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 6 0.40
17 4 0.27
18 5 0.33
ACGTcount: A:0.48, C:0.00, G:0.06, T:0.45
Consensus pattern (18 bp):
TAAAATAATTATATTGTA
Done.