Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01015752.1 Corchorus capsularis cultivar CVL-1 contig15773, 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: 35353
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32
Found at i:4387 original size:33 final size:32
Alignment explanation
Indices: 4336--4435 Score: 119
Period size: 33 Copynumber: 3.1 Consensus size: 32
4326 ACTTGGAGAT
* *
4336 CCGGCCACGCGACTTGGAGATGCCCGCGCAACA
1 CCGGCCACGCAACATGGAGATGCCCG-GCAACA
* *
4369 CCGGCCATGCAACATGGAGATGCCCGGCCATCA
1 CCGGCCACGCAACATGGAGATGCCCGG-CAACA
** *
4402 CCGGCCACGCAACATGGCCATGCCCGGCTACA
1 CCGGCCACGCAACATGGAGATGCCCGGCAACA
4434 CC
1 CC
4436 CGGAAACTTG
Statistics
Matches: 57, Mismatches: 9, Indels: 3
0.83 0.13 0.04
Matches are distributed among these distances:
32 6 0.11
33 51 0.89
ACGTcount: A:0.22, C:0.41, G:0.27, T:0.10
Consensus pattern (32 bp):
CCGGCCACGCAACATGGAGATGCCCGGCAACA
Found at i:5519 original size:113 final size:113
Alignment explanation
Indices: 5328--5595 Score: 437
Period size: 113 Copynumber: 2.4 Consensus size: 113
5318 GTCTTAACCA
* * *
5328 TAAACGCCGCTAAATAGTGGCGTCTTATGTCCCGGACGCCACCATAATTAATTTTTTCGGAGAAA
1 TAAACGCCGCTAAATAGTGGCGTCTTATGTCCCAGACGCCGCCATAATTAATTTTTTCGGACAAA
* *
5393 TGCAATTTGAGTAAAAATGAAGCCTAACAAATAGCGGCGTCTAGGCCC
66 TGCAAATTAAGTAAAAATGAAGCCTAACAAATAGCGGCGTCTAGGCCC
*
5441 TAAACGCCGCTAAATAGTGGCGTCTTATGTCCCAGACGCCGCCATACTTAATTTTTTCGGACAAA
1 TAAACGCCGCTAAATAGTGGCGTCTTATGTCCCAGACGCCGCCATAATTAATTTTTTCGGACAAA
*
5506 TGCAAATTAAGTAAAAATGAAGCCTAACAAATAGCGGCGTCTAGGCCT
66 TGCAAATTAAGTAAAAATGAAGCCTAACAAATAGCGGCGTCTAGGCCC
* * * *
5554 TAAACACTGCTAAATAGTGGCGTCTGATGTCGCAGACGCCGC
1 TAAACGCCGCTAAATAGTGGCGTCTTATGTCCCAGACGCCGC
5596 TAAATAGTGG
Statistics
Matches: 144, Mismatches: 11, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
113 144 1.00
ACGTcount: A:0.31, C:0.23, G:0.21, T:0.24
Consensus pattern (113 bp):
TAAACGCCGCTAAATAGTGGCGTCTTATGTCCCAGACGCCGCCATAATTAATTTTTTCGGACAAA
TGCAAATTAAGTAAAAATGAAGCCTAACAAATAGCGGCGTCTAGGCCC
Found at i:5601 original size:32 final size:32
Alignment explanation
Indices: 5562--5642 Score: 135
Period size: 32 Copynumber: 2.5 Consensus size: 32
5552 CTTAAACACT
* *
5562 GCTAAATAGTGGCGTCTGATGTCGCAGACGCC
1 GCTAAATAGTGGCGTCTAATGTCACAGACGCC
5594 GCTAAATAGTGGCGTCTAATGTCACAGACGCC
1 GCTAAATAGTGGCGTCTAATGTCACAGACGCC
*
5626 GCTAAATGGTGGCGTCT
1 GCTAAATAGTGGCGTCT
5643 CTGATCCAAA
Statistics
Matches: 46, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
32 46 1.00
ACGTcount: A:0.23, C:0.23, G:0.30, T:0.23
Consensus pattern (32 bp):
GCTAAATAGTGGCGTCTAATGTCACAGACGCC
Found at i:10200 original size:29 final size:29
Alignment explanation
Indices: 10152--10223 Score: 101
Period size: 29 Copynumber: 2.5 Consensus size: 29
10142 ACACTTTCAT
* *
10152 ATAGCGGCGTCTAGATGCCGCCAATCTAA
1 ATAGCGGCGTCTATACGCCGCCAATCTAA
*
10181 ATAGCGGCGTCTATACGCCGCCATTCTAA
1 ATAGCGGCGTCTATACGCCGCCAATCTAA
*
10210 ATAGCGCCG-CTATA
1 ATAGCGGCGTCTATA
10224 TATAGTATTA
Statistics
Matches: 39, Mismatches: 4, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
28 5 0.13
29 34 0.87
ACGTcount: A:0.26, C:0.29, G:0.22, T:0.22
Consensus pattern (29 bp):
ATAGCGGCGTCTATACGCCGCCAATCTAA
Found at i:11172 original size:42 final size:42
Alignment explanation
Indices: 11126--11212 Score: 122
Period size: 42 Copynumber: 2.1 Consensus size: 42
11116 ACGCATGGTA
* * *
11126 CATCGCACGGGACATCGCAC-GAGCCATCCGGCCACGACCGGC
1 CATCGAACGGGACAACGCACGGA-CCATCCGGCCACAACCGGC
*
11168 CATCGAACGGGCCAACGCACGGACCATCCGGCCACAACCGGC
1 CATCGAACGGGACAACGCACGGACCATCCGGCCACAACCGGC
11210 CAT
1 CAT
11213 TCGATCCATT
Statistics
Matches: 40, Mismatches: 4, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
42 38 0.95
43 2 0.05
ACGTcount: A:0.24, C:0.43, G:0.26, T:0.07
Consensus pattern (42 bp):
CATCGAACGGGACAACGCACGGACCATCCGGCCACAACCGGC
Found at i:13998 original size:8 final size:8
Alignment explanation
Indices: 13985--14010 Score: 52
Period size: 8 Copynumber: 3.2 Consensus size: 8
13975 CTTTAAAAGT
13985 ATGTATAG
1 ATGTATAG
13993 ATGTATAG
1 ATGTATAG
14001 ATGTATAG
1 ATGTATAG
14009 AT
1 AT
14011 AGCTATTGCA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 18 1.00
ACGTcount: A:0.38, C:0.00, G:0.23, T:0.38
Consensus pattern (8 bp):
ATGTATAG
Found at i:19941 original size:13 final size:13
Alignment explanation
Indices: 19923--19949 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
19913 AGTCCAAATA
19923 AACAAAGAACAAG
1 AACAAAGAACAAG
19936 AACAAAGAACAAG
1 AACAAAGAACAAG
19949 A
1 A
19950 CACTTGGTTG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.70, C:0.15, G:0.15, T:0.00
Consensus pattern (13 bp):
AACAAAGAACAAG
Found at i:22313 original size:12 final size:12
Alignment explanation
Indices: 22296--22321 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
22286 GAGAATATAG
22296 AGAGGCAGCGTT
1 AGAGGCAGCGTT
22308 AGAGGCAGCGTT
1 AGAGGCAGCGTT
22320 AG
1 AG
22322 GAGAGTACAG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.27, C:0.15, G:0.42, T:0.15
Consensus pattern (12 bp):
AGAGGCAGCGTT
Found at i:23317 original size:14 final size:14
Alignment explanation
Indices: 23298--23333 Score: 63
Period size: 14 Copynumber: 2.6 Consensus size: 14
23288 GAACATATTT
23298 TATATATATACATA
1 TATATATATACATA
23312 TATATATATACATA
1 TATATATATACATA
*
23326 TACATATA
1 TATATATA
23334 AAACATCATA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.50, C:0.08, G:0.00, T:0.42
Consensus pattern (14 bp):
TATATATATACATA
Found at i:26383 original size:25 final size:26
Alignment explanation
Indices: 26354--26406 Score: 81
Period size: 25 Copynumber: 2.1 Consensus size: 26
26344 AGAGTTAGAT
* *
26354 TTTAGTTTTATGGCAGATTCTAT-GC
1 TTTAGTTTCAAGGCAGATTCTATAGC
26379 TTTAGTTTCAAGGCAGATTCTATAGC
1 TTTAGTTTCAAGGCAGATTCTATAGC
26405 TT
1 TT
26407 CTAAAACTGG
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
25 21 0.84
26 4 0.16
ACGTcount: A:0.23, C:0.13, G:0.19, T:0.45
Consensus pattern (26 bp):
TTTAGTTTCAAGGCAGATTCTATAGC
Found at i:27471 original size:51 final size:51
Alignment explanation
Indices: 27411--27511 Score: 193
Period size: 51 Copynumber: 2.0 Consensus size: 51
27401 AACTTCAATT
27411 ATGGTGTTCTCACCATTTTAAATGCATGATTAATGTTGTTCCCACCTTTTC
1 ATGGTGTTCTCACCATTTTAAATGCATGATTAATGTTGTTCCCACCTTTTC
*
27462 ATGGTGTTCTCACCATTTTAAATGCATGATTAATGTTGTTTCCACCTTTT
1 ATGGTGTTCTCACCATTTTAAATGCATGATTAATGTTGTTCCCACCTTTT
27512 TAAATTCCAT
Statistics
Matches: 49, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
51 49 1.00
ACGTcount: A:0.22, C:0.20, G:0.14, T:0.45
Consensus pattern (51 bp):
ATGGTGTTCTCACCATTTTAAATGCATGATTAATGTTGTTCCCACCTTTTC
Found at i:30094 original size:31 final size:32
Alignment explanation
Indices: 30059--30118 Score: 104
Period size: 32 Copynumber: 1.9 Consensus size: 32
30049 AATATTTATA
30059 AATTTAATGAAAT-AAAATAGAGTTTTTATTG
1 AATTTAATGAAATAAAAATAGAGTTTTTATTG
*
30090 AATTTAATTAAATAAAAATAGAGTTTTTA
1 AATTTAATGAAATAAAAATAGAGTTTTTA
30119 GTAGAATAAA
Statistics
Matches: 27, Mismatches: 1, Indels: 1
0.93 0.03 0.03
Matches are distributed among these distances:
31 12 0.44
32 15 0.56
ACGTcount: A:0.48, C:0.00, G:0.10, T:0.42
Consensus pattern (32 bp):
AATTTAATGAAATAAAAATAGAGTTTTTATTG
Found at i:30612 original size:5 final size:5
Alignment explanation
Indices: 30597--30633 Score: 65
Period size: 5 Copynumber: 7.4 Consensus size: 5
30587 CGAAGCTAAC
*
30597 TTCTT TCCTT TTCTT TTCTT TTCTT TTCTT TTCTT TT
1 TTCTT TTCTT TTCTT TTCTT TTCTT TTCTT TTCTT TT
30634 TAGAGAACTC
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
5 30 1.00
ACGTcount: A:0.00, C:0.22, G:0.00, T:0.78
Consensus pattern (5 bp):
TTCTT
Found at i:32248 original size:33 final size:33
Alignment explanation
Indices: 32211--32278 Score: 100
Period size: 33 Copynumber: 2.1 Consensus size: 33
32201 AGCACTAGTG
* *
32211 ACCGGCCATGCGACTTGGAGAAGCCCGGCCAAC
1 ACCGGCCACGCGACTCGGAGAAGCCCGGCCAAC
* *
32244 ACCGGCCACGTGACTCGGAGATGCCCGGCCAAC
1 ACCGGCCACGCGACTCGGAGAAGCCCGGCCAAC
32277 AC
1 AC
32279 TAGTGACCGG
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
33 31 1.00
ACGTcount: A:0.24, C:0.38, G:0.29, T:0.09
Consensus pattern (33 bp):
ACCGGCCACGCGACTCGGAGAAGCCCGGCCAAC
Found at i:34838 original size:33 final size:33
Alignment explanation
Indices: 34800--34871 Score: 117
Period size: 33 Copynumber: 2.2 Consensus size: 33
34790 TTGAAGAGAG
34800 TGTTTTAAGTGTTGTTTGCAATGACACTAAATC
1 TGTTTTAAGTGTTGTTTGCAATGACACTAAATC
** *
34833 TGTTTTAAGTGTTGTTTGTGATGATACTAAATC
1 TGTTTTAAGTGTTGTTTGCAATGACACTAAATC
34866 TGTTTT
1 TGTTTT
34872 GGATGCTAAT
Statistics
Matches: 36, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
33 36 1.00
ACGTcount: A:0.24, C:0.08, G:0.19, T:0.49
Consensus pattern (33 bp):
TGTTTTAAGTGTTGTTTGCAATGACACTAAATC
Found at i:34927 original size:33 final size:32
Alignment explanation
Indices: 34890--34971 Score: 84
Period size: 27 Copynumber: 2.7 Consensus size: 32
34880 ATTGTGATGA
*
34890 AAATAATTCTGTTTTGGTTGATCATAGCATTAC
1 AAATAA-TCTGTTTTGGCTGATCATAGCATTAC
*
34923 AAATAA----TTTT-GCTGATCATAGCATTGC
1 AAATAATCTGTTTTGGCTGATCATAGCATTAC
*
34950 AAATAATCCTGTTTTGGGTGAT
1 AAATAAT-CTGTTTTGGCTGAT
34972 GAGAAAGAGA
Statistics
Matches: 40, Mismatches: 3, Indels: 12
0.73 0.05 0.22
Matches are distributed among these distances:
27 21 0.52
28 4 0.10
32 4 0.10
33 11 0.28
ACGTcount: A:0.30, C:0.12, G:0.17, T:0.40
Consensus pattern (32 bp):
AAATAATCTGTTTTGGCTGATCATAGCATTAC
Done.