Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01023504.1 Corchorus olitorius cultivar O-4 contig23537, 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: 19099
ACGTcount: A:0.36, C:0.16, G:0.15, T:0.33
Found at i:641 original size:40 final size:40
Alignment explanation
Indices: 585--660 Score: 134
Period size: 40 Copynumber: 1.9 Consensus size: 40
575 GATTCAAAGT
*
585 ACTATGAAAGGCAAAAGGAATTGTAAATAAAAGATGAGGC
1 ACTATGAAAGGAAAAAGGAATTGTAAATAAAAGATGAGGC
*
625 ACTATGCAAGGAAAAAGGAATTGTAAATAAAAGATG
1 ACTATGAAAGGAAAAAGGAATTGTAAATAAAAGATG
661 GACCAATACT
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
40 34 1.00
ACGTcount: A:0.51, C:0.07, G:0.24, T:0.18
Consensus pattern (40 bp):
ACTATGAAAGGAAAAAGGAATTGTAAATAAAAGATGAGGC
Found at i:3151 original size:22 final size:22
Alignment explanation
Indices: 3110--3152 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 22
3100 TTTAGTTGAG
* *
3110 TAAAATTATAAAAGTAAAATAA
1 TAAAATGATAAAAATAAAATAA
*
3132 TAAAATGATAAAAATGAAATA
1 TAAAATGATAAAAATAAAATA
3153 GTTATAAGGA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.67, C:0.00, G:0.07, T:0.26
Consensus pattern (22 bp):
TAAAATGATAAAAATAAAATAA
Found at i:8193 original size:50 final size:50
Alignment explanation
Indices: 8121--8216 Score: 192
Period size: 50 Copynumber: 1.9 Consensus size: 50
8111 TAATAATATA
8121 ATATATATATAACATAAAAGTCTAATTTTAAGTAATGGCAATTTAATTAT
1 ATATATATATAACATAAAAGTCTAATTTTAAGTAATGGCAATTTAATTAT
8171 ATATATATATAACATAAAAGTCTAATTTTAAGTAATGGCAATTTAA
1 ATATATATATAACATAAAAGTCTAATTTTAAGTAATGGCAATTTAA
8217 AAAAAAGTAA
Statistics
Matches: 46, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
50 46 1.00
ACGTcount: A:0.47, C:0.06, G:0.08, T:0.39
Consensus pattern (50 bp):
ATATATATATAACATAAAAGTCTAATTTTAAGTAATGGCAATTTAATTAT
Found at i:10310 original size:2 final size:2
Alignment explanation
Indices: 10298--10328 Score: 55
Period size: 2 Copynumber: 16.0 Consensus size: 2
10288 CAAATAATAC
10298 AT AT AT A- AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
10329 TGGCTGTTCT
Statistics
Matches: 28, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
1 1 0.04
2 27 0.96
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:11491 original size:26 final size:26
Alignment explanation
Indices: 11444--11514 Score: 69
Period size: 26 Copynumber: 2.9 Consensus size: 26
11434 ATCGACTAAC
*
11444 CATATATATA-AT-ATAATTTATAT-
1 CATATATATATATAATACTTTATATA
* * * *
11467 -TTATATTTATTTAATTCTTTATATA
1 CATATATATATATAATACTTTATATA
11492 CATATATATATATAATACTTTAT
1 CATATATATATATAATACTTTAT
11515 CAAATAAAAA
Statistics
Matches: 35, Mismatches: 9, Indels: 5
0.71 0.18 0.10
Matches are distributed among these distances:
22 7 0.20
23 1 0.03
24 9 0.26
26 18 0.51
ACGTcount: A:0.41, C:0.06, G:0.00, T:0.54
Consensus pattern (26 bp):
CATATATATATATAATACTTTATATA
Found at i:12813 original size:59 final size:60
Alignment explanation
Indices: 12747--12907 Score: 193
Period size: 60 Copynumber: 2.7 Consensus size: 60
12737 GCTAATTGCT
* * * * * *
12747 CAAATAAGAGCCTAATGTT-TGTCAAAATGTTTAAATAA-GGTCTGATCTTTTAATTTGAC
1 CAAATAAGGGCCTAACGTTAT-TCAAAATGCTCAAATAAGGGCCCGATCTTTTAATTTGAC
* * *
12806 CAAATAAGGGCTTAACGTTATTGAAAATGCTCAAATAAGGGCCCGATCTTTTAATTTGGC
1 CAAATAAGGGCCTAACGTTATTCAAAATGCTCAAATAAGGGCCCGATCTTTTAATTTGAC
12866 CAAATAAGGGCCTAACGTTA-TCAAAAAATGCTCAAATAAGGG
1 CAAATAAGGGCCTAACGTTATTC--AAAATGCTCAAATAAGGG
12908 TATGGCGTCA
Statistics
Matches: 87, Mismatches: 11, Indels: 6
0.84 0.11 0.06
Matches are distributed among these distances:
59 31 0.36
60 38 0.44
61 18 0.21
ACGTcount: A:0.37, C:0.15, G:0.18, T:0.30
Consensus pattern (60 bp):
CAAATAAGGGCCTAACGTTATTCAAAATGCTCAAATAAGGGCCCGATCTTTTAATTTGAC
Found at i:14427 original size:15 final size:15
Alignment explanation
Indices: 14407--14435 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
14397 TAGCTACATT
14407 ATTAAGAGAGTAATA
1 ATTAAGAGAGTAATA
14422 ATTAAGAGAGTAAT
1 ATTAAGAGAGTAAT
14436 TGAAAATGAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.52, C:0.00, G:0.21, T:0.28
Consensus pattern (15 bp):
ATTAAGAGAGTAATA
Found at i:16332 original size:14 final size:14
Alignment explanation
Indices: 16313--16351 Score: 53
Period size: 14 Copynumber: 2.8 Consensus size: 14
16303 TTTTTAGTTG
16313 AGTAAAACTA-TAAA
1 AGTAAAA-TAGTAAA
16327 AGTAAAATAGTAAA
1 AGTAAAATAGTAAA
*
16341 AATAAAATAGT
1 AGTAAAATAGT
16352 TATAAGGATA
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
13 2 0.09
14 21 0.91
ACGTcount: A:0.64, C:0.03, G:0.10, T:0.23
Consensus pattern (14 bp):
AGTAAAATAGTAAA
Found at i:16348 original size:85 final size:85
Alignment explanation
Indices: 16242--16412 Score: 288
Period size: 85 Copynumber: 2.0 Consensus size: 85
16232 TAATTAAATT
* * *
16242 AGTAATATGGTAAAAACAAAATAGGTATAAGGATATTAGATTTAATTAAATAAAAATAGAGTTTT
1 AGTAAAATAGTAAAAACAAAATAGGTATAAGGATATTAGATTTAATTAAATAAAAATAAAGTTTT
*
16307 TAGTTGAGTAAAACTATAAA
66 TAGTTGACTAAAACTATAAA
* *
16327 AGTAAAATAGTAAAAATAAAATAGTTATAAGGATATTAGATTTAATTAAATAAAAATAAAGTTTT
1 AGTAAAATAGTAAAAACAAAATAGGTATAAGGATATTAGATTTAATTAAATAAAAATAAAGTTTT
16392 TAGTTGACTAAAACTATAAA
66 TAGTTGACTAAAACTATAAA
16412 A
1 A
16413 ATTTAAACAA
Statistics
Matches: 80, Mismatches: 6, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
85 80 1.00
ACGTcount: A:0.53, C:0.02, G:0.13, T:0.32
Consensus pattern (85 bp):
AGTAAAATAGTAAAAACAAAATAGGTATAAGGATATTAGATTTAATTAAATAAAAATAAAGTTTT
TAGTTGACTAAAACTATAAA
Found at i:17310 original size:12 final size:12
Alignment explanation
Indices: 17293--17348 Score: 64
Period size: 12 Copynumber: 4.9 Consensus size: 12
17283 CCGTTTAATA
17293 ATTATATATATT
1 ATTATATATATT
* *
17305 ATTATATATGTA
1 ATTATATATATT
17317 ATTATATATATT
1 ATTATATATATT
*
17329 -TAATAT-TATT
1 ATTATATATATT
17339 -TTATATATAT
1 ATTATATATAT
17349 AATACATATT
Statistics
Matches: 37, Mismatches: 6, Indels: 3
0.80 0.13 0.07
Matches are distributed among these distances:
10 9 0.24
11 8 0.22
12 20 0.54
ACGTcount: A:0.41, C:0.00, G:0.02, T:0.57
Consensus pattern (12 bp):
ATTATATATATT
Found at i:17324 original size:14 final size:13
Alignment explanation
Indices: 17291--17373 Score: 60
Period size: 12 Copynumber: 7.2 Consensus size: 13
17281 AACCGTTTAA
17291 TAATTATATATAT
1 TAATTATATATAT
*
17304 T-ATTATATAT-G
1 TAATTATATATAT
17315 TAATTATATATAT
1 TAATTATATATAT
*
17328 T--TAATAT-TAT
1 TAATTATATATAT
17338 T--TTATATATA-
1 TAATTATATATAT
*
17348 TAA-TACATAT-T
1 TAATTATATATAT
*
17359 TAATTATAAATAT
1 TAATTATATATAT
17372 TA
1 TA
17374 CTAAACGGTT
Statistics
Matches: 55, Mismatches: 7, Indels: 16
0.71 0.09 0.21
Matches are distributed among these distances:
10 10 0.18
11 17 0.31
12 23 0.42
13 5 0.09
ACGTcount: A:0.45, C:0.01, G:0.01, T:0.53
Consensus pattern (13 bp):
TAATTATATATAT
Found at i:18513 original size:22 final size:22
Alignment explanation
Indices: 18492--18534 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 22
18482 TAGTTGAGTA
*
18492 AAAAT-ATAAAAGTAAAATAGT
1 AAAATGATAAAAATAAAATAGT
*
18513 AAAATGGTAAAAATAAAATAGT
1 AAAATGATAAAAATAAAATAGT
18535 TATAAGGATA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
21 5 0.26
22 14 0.74
ACGTcount: A:0.65, C:0.00, G:0.12, T:0.23
Consensus pattern (22 bp):
AAAATGATAAAAATAAAATAGT
Found at i:18513 original size:93 final size:93
Alignment explanation
Indices: 18411--18595 Score: 298
Period size: 93 Copynumber: 2.0 Consensus size: 93
18401 ACTTTTTAAT
* * *
18411 TAAATTAGTAATATTGTAAAAATAAAATAGGTATAAAGATATTAGATTTAATTAAATAAAAATAG
1 TAAAATAGTAAAATGGTAAAAATAAAATAGGTATAAAGATATTAGATTTAATTAAATAAAAATAG
*
18476 AGTTTTTAGTTGAGTAAAAATATAAAAG
66 AGTTTTTAGTTGACTAAAAATATAAAAG
* * *
18504 TAAAATAGTAAAATGGTAAAAATAAAATAGTTATAAGGATATTAGATTTAATTAAATATAAATAG
1 TAAAATAGTAAAATGGTAAAAATAAAATAGGTATAAAGATATTAGATTTAATTAAATAAAAATAG
*
18569 AGTTTTTAGTTGACTAAAACTATAAAA
66 AGTTTTTAGTTGACTAAAAATATAAAA
18596 ATTTAAACAA
Statistics
Matches: 84, Mismatches: 8, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
93 84 1.00
ACGTcount: A:0.52, C:0.01, G:0.12, T:0.34
Consensus pattern (93 bp):
TAAAATAGTAAAATGGTAAAAATAAAATAGGTATAAAGATATTAGATTTAATTAAATAAAAATAG
AGTTTTTAGTTGACTAAAAATATAAAAG
Found at i:18529 original size:14 final size:14
Alignment explanation
Indices: 18488--18534 Score: 51
Period size: 14 Copynumber: 3.2 Consensus size: 14
18478 TTTTTAGTTG
18488 AGTAAAAATATAAA-
1 AGTAAAAATA-AAAT
18502 AGTAAAATAGTAAAAT
1 AGTAAAA-A-TAAAAT
*
18518 GGTAAAAATAAAAT
1 AGTAAAAATAAAAT
18532 AGT
1 AGT
18535 TATAAGGATA
Statistics
Matches: 28, Mismatches: 2, Indels: 6
0.78 0.06 0.17
Matches are distributed among these distances:
14 15 0.54
15 5 0.18
16 8 0.29
ACGTcount: A:0.64, C:0.00, G:0.13, T:0.23
Consensus pattern (14 bp):
AGTAAAAATAAAAT
Found at i:18647 original size:93 final size:93
Alignment explanation
Indices: 18426--18626 Score: 244
Period size: 93 Copynumber: 2.2 Consensus size: 93
18416 TAGTAATATT
* * *
18426 GTAAAAATAAAATAG-GTATAAAGATATTAGATTTAATTAAATAAAAATAGAGTTTTTAGTTGAG
1 GTAAAAATAAAATAGTG-ATAAGGATATGAGATTTAATTAAATAAAAATAGAGTTTTTAGTTGAC
* *
18490 TAAAAATATAAAAGTAAAATAGTAAAATG
65 TAAAAATATAAAAGTAAAACAATAAAATG
* * *
18519 GTAAAAATAAAATAGTTATAAGGATATTAGATTTAATTAAATATAAATAGAGTTTTTAGTTGACT
1 GTAAAAATAAAATAGTGATAAGGATATGAGATTTAATTAAATAAAAATAGAGTTTTTAGTTGACT
* * * *
18584 AAAACTATAAAAATTTAAACAATAACAT-
66 AAAAATAT-AAAAGTAAAACAATAAAATG
*
18612 TTAAGAAATAAAATA
1 GTAA-AAATAAAATA
18627 AGGATATGAT
Statistics
Matches: 94, Mismatches: 11, Indels: 5
0.85 0.10 0.05
Matches are distributed among these distances:
93 70 0.74
94 24 0.26
ACGTcount: A:0.54, C:0.02, G:0.11, T:0.32
Consensus pattern (93 bp):
GTAAAAATAAAATAGTGATAAGGATATGAGATTTAATTAAATAAAAATAGAGTTTTTAGTTGACT
AAAAATATAAAAGTAAAACAATAAAATG
Done.