Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01007539.1 Corchorus capsularis cultivar CVL-1 contig07560, 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: 46002
ACGTcount: A:0.31, C:0.19, G:0.19, T:0.31
Found at i:971 original size:17 final size:17
Alignment explanation
Indices: 925--974 Score: 64
Period size: 17 Copynumber: 2.9 Consensus size: 17
915 GGGTTGATTC
*
925 TGGCAGCAGGAATCGCG
1 TGGCAGCAGGAATCACG
* * *
942 AGGCTGCAAGAATCACG
1 TGGCAGCAGGAATCACG
959 TGGCAGCAGGAATCAC
1 TGGCAGCAGGAATCAC
975 AGAAGGACCA
Statistics
Matches: 26, Mismatches: 7, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
17 26 1.00
ACGTcount: A:0.30, C:0.24, G:0.34, T:0.12
Consensus pattern (17 bp):
TGGCAGCAGGAATCACG
Found at i:3358 original size:35 final size:35
Alignment explanation
Indices: 3270--3359 Score: 94
Period size: 35 Copynumber: 2.6 Consensus size: 35
3260 ATATTTTTCA
* *
3270 TCAG-ATTCAACACTAGGGGGGCTGCAGCAACCCCT
1 TCAGCATTCAACACT-TGGGGACTGCAGCAACCCCT
**
3305 TCAGCATTCAACGTTTGGGGACTGCAGC-ACCTCCT
1 TCAGCATTCAACACTTGGGGACTGCAGCAACC-CCT
* *
3340 TCATCATTCAATACTTGGGG
1 TCAGCATTCAACACTTGGGG
3360 CTTCAACAAT
Statistics
Matches: 45, Mismatches: 8, Indels: 4
0.79 0.14 0.07
Matches are distributed among these distances:
34 3 0.07
35 34 0.76
36 8 0.18
ACGTcount: A:0.23, C:0.29, G:0.23, T:0.24
Consensus pattern (35 bp):
TCAGCATTCAACACTTGGGGACTGCAGCAACCCCT
Found at i:4543 original size:16 final size:16
Alignment explanation
Indices: 4512--4554 Score: 50
Period size: 16 Copynumber: 2.7 Consensus size: 16
4502 AAAGCTACCA
* *
4512 CAGCAGATTGTTACCG
1 CAGCAGAATGTCACCG
4528 CAGCAGAATGTCACCG
1 CAGCAGAATGTCACCG
* *
4544 TAGCGGAATGT
1 CAGCAGAATGT
4555 ACAAAGCTGA
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
16 23 1.00
ACGTcount: A:0.28, C:0.23, G:0.28, T:0.21
Consensus pattern (16 bp):
CAGCAGAATGTCACCG
Found at i:6883 original size:20 final size:20
Alignment explanation
Indices: 6854--6893 Score: 53
Period size: 20 Copynumber: 2.0 Consensus size: 20
6844 GATGAAGTGT
**
6854 CATAGCTGCGGTAGAGACAA
1 CATAGCTGCGACAGAGACAA
*
6874 CATAGTTGCGACAGAGACAA
1 CATAGCTGCGACAGAGACAA
6894 AAGCATGGCA
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.38, C:0.20, G:0.28, T:0.15
Consensus pattern (20 bp):
CATAGCTGCGACAGAGACAA
Found at i:9071 original size:41 final size:43
Alignment explanation
Indices: 9025--9225 Score: 164
Period size: 41 Copynumber: 4.8 Consensus size: 43
9015 ATTTCTTTCT
**
9025 AAAGTCCTCAAGCACATTTATAACCTAGAGGCACC-C-ATATC
1 AAAGTCCTCAAGCACATTTATAACAAAGAGGCACCTCTATATC
* * * * *
9066 GAAGTCCCCAAGCACAATTATAACAAAGGGGCACCTCTATTTC
1 AAAGTCCTCAAGCACATTTATAACAAAGAGGCACCTCTATATC
* * * *
9109 AAAGTCTTCAAGCACATTTATAACACAGA-GC-CATCTATGTC
1 AAAGTCCTCAAGCACATTTATAACAAAGAGGCACCTCTATATC
* * * * *
9150 AAAGTCCCCAAACACAATTATAACACAG-GGACAATCCTCTCTA--
1 AAAGTCCTCAAGCACATTTATAACAAAGAGG-C-A-CCTCTATATC
* *
9193 AAAGTCCTCAAACACATTTATAACATAGAGGCA
1 AAAGTCCTCAAGCACATTTATAACAAAGAGGCA
9226 TCCATACTAA
Statistics
Matches: 127, Mismatches: 25, Indels: 15
0.76 0.15 0.09
Matches are distributed among these distances:
41 62 0.49
42 5 0.04
43 53 0.42
44 2 0.02
45 5 0.04
ACGTcount: A:0.39, C:0.27, G:0.12, T:0.22
Consensus pattern (43 bp):
AAAGTCCTCAAGCACATTTATAACAAAGAGGCACCTCTATATC
Found at i:9155 original size:84 final size:83
Alignment explanation
Indices: 9018--9258 Score: 272
Period size: 84 Copynumber: 2.9 Consensus size: 83
9008 TAAGGGCATT
* * *
9018 TCTTTCTAAAGTCCTCAAGCACATTTATAAC-CTAGAGGCACCCATATCGAAGTCCCCAAGCACA
1 TCTTTC-AAAGTCCTCAAGCACATTTATAACAC-AGAGGCATCCAT-TCAAAGTCCCCAAACACA
*
9082 ATTATAACAAAGGGGC-A-CC
63 ATTATAACAAAGGGACAATCC
* * *
9101 TCTATTTCAAAGTCTTCAAGCACATTTATAACACAGAGCCATCTATGTCAAAGTCCCCAAACACA
1 TC--TTTCAAAGTCCTCAAGCACATTTATAACACAGAGGCATCCAT-TCAAAGTCCCCAAACACA
*
9166 ATTATAACACAGGGACAATCC
63 ATTATAACAAAGGGACAATCC
* * * * * *
9187 TCTCTAAAAGTCCTCAAACACATTTATAACATAGAGGCATCCATACTAAAGTCCCTAAACACAAT
1 TCTTTCAAAGTCCTCAAGCACATTTATAACACAGAGGCATCCATTC-AAAGTCCCCAAACACAAT
9252 TATAACA
65 TATAACA
9259 GAATGACAAT
Statistics
Matches: 134, Mismatches: 18, Indels: 11
0.82 0.11 0.07
Matches are distributed among these distances:
83 3 0.02
84 121 0.90
85 6 0.04
86 4 0.03
ACGTcount: A:0.39, C:0.27, G:0.11, T:0.24
Consensus pattern (83 bp):
TCTTTCAAAGTCCTCAAGCACATTTATAACACAGAGGCATCCATTCAAAGTCCCCAAACACAATT
ATAACAAAGGGACAATCC
Found at i:9205 original size:43 final size:40
Alignment explanation
Indices: 9023--9258 Score: 124
Period size: 41 Copynumber: 5.7 Consensus size: 40
9013 GCATTTCTTT
* * *
9023 CTAAAGTCCTCAAGCACATTTATAAC-CTAGAGGCACCCATA
1 CTAAAGTCC-CAAACACAATTATAACAC-AGAGGCATCCATA
* * * * *
9064 -TCGAAGTCCCCAAGCACAATTATAACAAAGGGGCA-CCTCTA
1 CT-AAAGT-CCCAAACACAATTATAACACAGAGGCATCC-ATA
* * * * * *
9105 TTTCAAAGTCTTCAAGCACATTTATAACACAGAGCCATCTAT-
1 -CT-AAAGTC-CCAAACACAATTATAACACAGAGGCATCCATA
* *
9147 GTCAAAGTCCCCAAACACAATTATAACACAG-GGACAATCC-TCT
1 CT-AAAGT-CCCAAACACAATTATAACACAGAGG-C-ATCCAT-A
* *
9190 CTAAAAGTCCTCAAACACATTTATAACATAGAGGCATCCATA
1 CT-AAAGTCC-CAAACACAATTATAACACAGAGGCATCCATA
9232 CTAAAGTCCCTAAACACAATTATAACA
1 CTAAAGTCCC-AAACACAATTATAACA
9259 GAATGACAAT
Statistics
Matches: 153, Mismatches: 25, Indels: 34
0.72 0.12 0.16
Matches are distributed among these distances:
40 5 0.03
41 76 0.50
42 15 0.10
43 54 0.35
44 3 0.02
ACGTcount: A:0.39, C:0.27, G:0.11, T:0.22
Consensus pattern (40 bp):
CTAAAGTCCCAAACACAATTATAACACAGAGGCATCCATA
Found at i:9255 original size:41 final size:43
Alignment explanation
Indices: 9150--9258 Score: 120
Period size: 43 Copynumber: 2.6 Consensus size: 43
9140 CATCTATGTC
* *
9150 AAAGTCCCCAAACACAATTATAACACAGGGACAATCCTCTCTA
1 AAAGTCCCTAAACACAATTATAACACAGGGACAATCCTCACTA
* *
9193 AAAGT-CCTCAAACACATTTATAACATAGAGG-C-ATCCAT-ACT-
1 AAAGTCCCT-AAACACAATTATAACACAG-GGACAATCC-TCACTA
9234 AAAGTCCCTAAACACAATTATAACA
1 AAAGTCCCTAAACACAATTATAACA
9259 GAATGACAAT
Statistics
Matches: 57, Mismatches: 5, Indels: 10
0.79 0.07 0.14
Matches are distributed among these distances:
41 20 0.35
42 11 0.19
43 24 0.42
44 2 0.04
ACGTcount: A:0.44, C:0.27, G:0.08, T:0.21
Consensus pattern (43 bp):
AAAGTCCCTAAACACAATTATAACACAGGGACAATCCTCACTA
Found at i:12297 original size:22 final size:22
Alignment explanation
Indices: 12272--12314 Score: 68
Period size: 22 Copynumber: 2.0 Consensus size: 22
12262 TATTAATCTC
**
12272 CTTATTCAATTAGTTAATCAAG
1 CTTATTCAACCAGTTAATCAAG
12294 CTTATTCAACCAGTTAATCAA
1 CTTATTCAACCAGTTAATCAA
12315 ACACCACTCT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.37, C:0.19, G:0.07, T:0.37
Consensus pattern (22 bp):
CTTATTCAACCAGTTAATCAAG
Found at i:13944 original size:21 final size:21
Alignment explanation
Indices: 13906--13946 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
13896 CCTTGGCTTA
*
13906 TGATCTTCAATACTCTTCAAT
1 TGATCTTCAATACACTTCAAT
**
13927 TGATCTTCAATGGACTTCAA
1 TGATCTTCAATACACTTCAA
13947 GACTTCAAGA
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.29, C:0.22, G:0.10, T:0.39
Consensus pattern (21 bp):
TGATCTTCAATACACTTCAAT
Found at i:15078 original size:19 final size:18
Alignment explanation
Indices: 15054--15090 Score: 56
Period size: 19 Copynumber: 2.0 Consensus size: 18
15044 GAAGTTCGTG
*
15054 TTTGAAGATAATTTGAAGA
1 TTTGAAGACAA-TTGAAGA
15073 TTTGAAGACAATTGAAGA
1 TTTGAAGACAATTGAAGA
15091 ATTATTTCAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
18 7 0.41
19 10 0.59
ACGTcount: A:0.43, C:0.03, G:0.22, T:0.32
Consensus pattern (18 bp):
TTTGAAGACAATTGAAGA
Found at i:19157 original size:19 final size:18
Alignment explanation
Indices: 19124--19159 Score: 54
Period size: 19 Copynumber: 1.9 Consensus size: 18
19114 TTGAAATAAT
19124 TCTTCAATGATCTTCAAA
1 TCTTCAATGATCTTCAAA
*
19142 TCTTCAAATTATCTTCAA
1 TCTTC-AATGATCTTCAA
19160 GAAATCTTCA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 5 0.31
19 11 0.69
ACGTcount: A:0.33, C:0.22, G:0.03, T:0.42
Consensus pattern (18 bp):
TCTTCAATGATCTTCAAA
Found at i:29252 original size:15 final size:15
Alignment explanation
Indices: 29217--29253 Score: 56
Period size: 15 Copynumber: 2.5 Consensus size: 15
29207 ACTAAGCCAA
* *
29217 AAGATAAGCCACCAG
1 AAGATGAGCCACAAG
29232 AAGATGAGCCACAAG
1 AAGATGAGCCACAAG
29247 AAGATGA
1 AAGATGA
29254 ACAACTTAGA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
15 20 1.00
ACGTcount: A:0.49, C:0.19, G:0.24, T:0.08
Consensus pattern (15 bp):
AAGATGAGCCACAAG
Found at i:32140 original size:22 final size:22
Alignment explanation
Indices: 32112--32171 Score: 65
Period size: 22 Copynumber: 2.9 Consensus size: 22
32102 GAAGTTCGTG
*
32112 TTTGAAGAATATTTGAAGATAA
1 TTTGAAGAATATTTGAAGACAA
32134 TTTGAAG---ATTTGAAGACAA
1 TTTGAAGAATATTTGAAGACAA
*
32153 -TTGAAGAATTATTTCAAGA
1 TTTGAAGAA-TATTTGAAGA
32172 AGCAAAAATT
Statistics
Matches: 32, Mismatches: 2, Indels: 8
0.76 0.05 0.19
Matches are distributed among these distances:
18 6 0.19
19 11 0.34
22 15 0.47
ACGTcount: A:0.43, C:0.03, G:0.18, T:0.35
Consensus pattern (22 bp):
TTTGAAGAATATTTGAAGACAA
Found at i:32146 original size:19 final size:18
Alignment explanation
Indices: 32122--32159 Score: 58
Period size: 19 Copynumber: 2.1 Consensus size: 18
32112 TTTGAAGAAT
*
32122 ATTTGAAGATAATTTGAAG
1 ATTTGAAGACAA-TTGAAG
32141 ATTTGAAGACAATTGAAG
1 ATTTGAAGACAATTGAAG
32159 A
1 A
32160 ATTATTTCAA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
18 7 0.39
19 11 0.61
ACGTcount: A:0.45, C:0.03, G:0.21, T:0.32
Consensus pattern (18 bp):
ATTTGAAGACAATTGAAG
Found at i:33501 original size:6 final size:6
Alignment explanation
Indices: 33490--33520 Score: 55
Period size: 6 Copynumber: 5.3 Consensus size: 6
33480 ATAATTGCTA
33490 TAGATT TAGATT TAGATT TAGATT TA-ATT TA
1 TAGATT TAGATT TAGATT TAGATT TAGATT TA
33521 TTTTGCTTTG
Statistics
Matches: 25, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
5 5 0.20
6 20 0.80
ACGTcount: A:0.35, C:0.00, G:0.13, T:0.52
Consensus pattern (6 bp):
TAGATT
Found at i:34303 original size:19 final size:18
Alignment explanation
Indices: 34279--34314 Score: 54
Period size: 19 Copynumber: 1.9 Consensus size: 18
34269 TGAAGATTTC
34279 TTGAAGATAATTTGAAGAT
1 TTGAAGATAA-TTGAAGAT
*
34298 TTGAAGATCATTGAAGA
1 TTGAAGATAATTGAAGA
34315 ATTATTTCAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 7 0.44
19 9 0.56
ACGTcount: A:0.42, C:0.03, G:0.22, T:0.33
Consensus pattern (18 bp):
TTGAAGATAATTGAAGAT
Found at i:42419 original size:39 final size:39
Alignment explanation
Indices: 42352--42442 Score: 139
Period size: 39 Copynumber: 2.3 Consensus size: 39
42342 TTCTAGTGAT
* *
42352 GAGAATAAGGAAGGAAAAGAGGATGTGAATCAAGAGAAG
1 GAGAATAAGGAAGGAAAAGAAGAGGTGAATCAAGAGAAG
*
42391 GAGAGTAAGGAAGGAAAAGAAGAGGTGAATCAAGAGAAG
1 GAGAATAAGGAAGGAAAAGAAGAGGTGAATCAAGAGAAG
42430 GA-AATTAAGGAAG
1 GAGAA-TAAGGAAG
42443 AATGATTAAT
Statistics
Matches: 47, Mismatches: 4, Indels: 2
0.89 0.08 0.04
Matches are distributed among these distances:
38 1 0.02
39 46 0.98
ACGTcount: A:0.52, C:0.02, G:0.36, T:0.10
Consensus pattern (39 bp):
GAGAATAAGGAAGGAAAAGAAGAGGTGAATCAAGAGAAG
Done.