Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01020882.1 Corchorus olitorius cultivar O-4 contig20915, 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: 116903
ACGTcount: A:0.32, C:0.18, G:0.19, T:0.32
Found at i:9540 original size:21 final size:19
Alignment explanation
Indices: 9514--9563 Score: 55
Period size: 21 Copynumber: 2.5 Consensus size: 19
9504 CGTTGCTCTA
9514 ATAATCTCATATGTACAAT
1 ATAATCTCATATGTACAAT
* * *
9533 ACCTAATCTAATCTGTACATT
1 A--TAATCTCATATGTACAAT
9554 ATAATCTCAT
1 ATAATCTCAT
9564 CGCACCACTC
Statistics
Matches: 25, Mismatches: 4, Indels: 4
0.76 0.12 0.12
Matches are distributed among these distances:
19 9 0.36
21 16 0.64
ACGTcount: A:0.38, C:0.20, G:0.04, T:0.38
Consensus pattern (19 bp):
ATAATCTCATATGTACAAT
Found at i:10421 original size:2 final size:2
Alignment explanation
Indices: 10414--10515 Score: 93
Period size: 2 Copynumber: 51.5 Consensus size: 2
10404 ATGAATATAA
* * *
10414 AG AG AG AG A- AG TAG AG AG AG AA AG AA AG AG A- AG CG A- AG AG
1 AG AG AG AG AG AG -AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
* * * *
10454 AG AG AA AG AG AC AC AG AG CAG AG AG AG AG AC AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG -AG AG AG AG AG AG AG AG AG AG AG AG
*
10497 AG AG AG AG AG AA AG AG AG A
1 AG AG AG AG AG AG AG AG AG A
10516 AACGTTTCTT
Statistics
Matches: 81, Mismatches: 14, Indels: 10
0.77 0.13 0.10
Matches are distributed among these distances:
1 3 0.04
2 74 0.91
3 4 0.05
ACGTcount: A:0.54, C:0.05, G:0.40, T:0.01
Consensus pattern (2 bp):
AG
Found at i:12356 original size:13 final size:13
Alignment explanation
Indices: 12338--12367 Score: 60
Period size: 13 Copynumber: 2.3 Consensus size: 13
12328 GAACTAACGC
12338 TTTCCCTTATCTT
1 TTTCCCTTATCTT
12351 TTTCCCTTATCTT
1 TTTCCCTTATCTT
12364 TTTC
1 TTTC
12368 TTCATTTGGT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 17 1.00
ACGTcount: A:0.07, C:0.30, G:0.00, T:0.63
Consensus pattern (13 bp):
TTTCCCTTATCTT
Found at i:20635 original size:2 final size:2
Alignment explanation
Indices: 20628--20667 Score: 64
Period size: 2 Copynumber: 20.0 Consensus size: 2
20618 CGGTGCCTCA
20628 AT AT AT AT AT AT AT AT AT AT -T AGT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT A-T AT AT AT AT AT AT AT AT
20668 CCATTTCTCA
Statistics
Matches: 36, Mismatches: 0, Indels: 4
0.90 0.00 0.10
Matches are distributed among these distances:
1 1 0.03
2 33 0.92
3 2 0.06
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.50
Consensus pattern (2 bp):
AT
Found at i:48326 original size:60 final size:60
Alignment explanation
Indices: 48254--48414 Score: 198
Period size: 59 Copynumber: 2.7 Consensus size: 60
48244 GCTAATTGCT
* * * * * *
48254 CAAATAAAGGCCTAATGTTTGTCAAAATGCTTAAATAAGGGCATGATCTTTTAATTTGGC
1 CAAATAAGGGCCTAACGTTTGCCAAAATGCTCAAATAAGGGCACGATCTTTTAATTTGAC
* * * *
48314 CAAATAAGGGCCTAACGTTTGCCAAAATGCTCAAATAA-GACCCGATCTTTTGATTTGAT
1 CAAATAAGGGCCTAACGTTTGCCAAAATGCTCAAATAAGGGCACGATCTTTTAATTTGAC
* * *
48373 CAAATAAGTGTCTTACGTTTGCCAAAATGCTCAAATAAGGGC
1 CAAATAAGGGCCTAACGTTTGCCAAAATGCTCAAATAAGGGC
48415 CTACCATCGA
Statistics
Matches: 86, Mismatches: 14, Indels: 2
0.84 0.14 0.02
Matches are distributed among these distances:
59 50 0.58
60 36 0.42
ACGTcount: A:0.35, C:0.17, G:0.18, T:0.30
Consensus pattern (60 bp):
CAAATAAGGGCCTAACGTTTGCCAAAATGCTCAAATAAGGGCACGATCTTTTAATTTGAC
Found at i:48352 original size:31 final size:30
Alignment explanation
Indices: 48250--48417 Score: 85
Period size: 31 Copynumber: 5.6 Consensus size: 30
48240 TAAGGCTAAT
* *
48250 TGCTCAAATAAAGGCCTAATGTTTGTCAAAA
1 TGCTCAAATAAGGGCCTAACGTTTG-CAAAA
* * * * **
48281 TGCTTAAATAAGGGCATGATC-TTT-TAATT
1 TGCTCAAATAAGGGCCT-AACGTTTGCAAAA
48310 TGGC-CAAATAAGGGCCTAACGTTTGCCAAAA
1 T-GCTCAAATAAGGGCCTAACGTTTG-CAAAA
** * * * **
48341 TGCTCAAATAAGACCCGATCTTTTG--ATT
1 TGCTCAAATAAGGGCCTAACGTTTGCAAAA
* * * *
48369 TGATCAAATAAGTGTCTTACGTTTGCCAAAA
1 TGCTCAAATAAGGGCCTAACGTTTG-CAAAA
48400 TGCTCAAATAAGGGCCTA
1 TGCTCAAATAAGGGCCTA
48418 CCATCGAAAA
Statistics
Matches: 93, Mismatches: 35, Indels: 18
0.64 0.24 0.12
Matches are distributed among these distances:
28 20 0.22
29 17 0.18
30 4 0.04
31 51 0.55
32 1 0.01
ACGTcount: A:0.34, C:0.18, G:0.18, T:0.30
Consensus pattern (30 bp):
TGCTCAAATAAGGGCCTAACGTTTGCAAAA
Found at i:48585 original size:60 final size:61
Alignment explanation
Indices: 48458--48628 Score: 154
Period size: 60 Copynumber: 2.9 Consensus size: 61
48448 TGACGCCAAG
* ** * *
48458 CCCTTATTTGAGATATTTTCGATAACGTTAGACCCTTATTTGGCCAAATTAAAAGATCGGG
1 CCCTTATTTGAGATATTTTCGATAACATTAGACCCTTATTTAACCAAATTAAAAGATCAGA
** ** * *
48519 TTCTTATTTGA-ATATTTTTTATAATATTA-AGCCCTTATTTAACCAAATTAAAAGATTAGA
1 CCCTTATTTGAGATATTTTCGATAACATTAGA-CCCTTATTTAACCAAATTAAAAGATCAGA
* * * *
48579 CCCTTATTTGAG-TTTTTTAGCA-AACATTAGACTCTTATTTAAGC-AATTAA
1 CCCTTATTTGAGATATTTTCG-ATAACATTAGACCCTTATTTAACCAAATTAA
48629 CCTAATTTTA
Statistics
Matches: 87, Mismatches: 19, Indels: 10
0.75 0.16 0.09
Matches are distributed among these distances:
59 7 0.08
60 69 0.79
61 11 0.13
ACGTcount: A:0.33, C:0.15, G:0.12, T:0.40
Consensus pattern (61 bp):
CCCTTATTTGAGATATTTTCGATAACATTAGACCCTTATTTAACCAAATTAAAAGATCAGA
Found at i:49169 original size:2 final size:2
Alignment explanation
Indices: 49128--49160 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
49118 TTCAGTTCAC
49128 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
49161 TATAGAGAGT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.52, C:0.00, G:0.48, T:0.00
Consensus pattern (2 bp):
AG
Found at i:66372 original size:3 final size:3
Alignment explanation
Indices: 66364--66415 Score: 54
Period size: 3 Copynumber: 17.3 Consensus size: 3
66354 TTGACCTTTC
* *
66364 ATT ATT ATT ATT ATT ATAT ATT ATT A-T ATT -TT AAT ATT ATA ATT
1 ATT ATT ATT ATT ATT AT-T ATT ATT ATT ATT ATT ATT ATT ATT ATT
66408 ATGT ATT A
1 AT-T ATT A
66416 ACACGTAACA
Statistics
Matches: 41, Mismatches: 4, Indels: 8
0.77 0.08 0.15
Matches are distributed among these distances:
2 4 0.10
3 31 0.76
4 6 0.15
ACGTcount: A:0.38, C:0.00, G:0.02, T:0.60
Consensus pattern (3 bp):
ATT
Found at i:66387 original size:13 final size:12
Alignment explanation
Indices: 66364--66415 Score: 54
Period size: 13 Copynumber: 4.3 Consensus size: 12
66354 TTGACCTTTC
66364 ATTATTATTATT
1 ATTATTATTATT
66376 ATTATATATTATT
1 ATTAT-TATTATT
*
66389 A-TATT-TTAAT
1 ATTATTATTATT
*
66399 ATTATAATTATGT
1 ATTATTATTAT-T
66412 ATTA
1 ATTA
66416 ACACGTAACA
Statistics
Matches: 33, Mismatches: 3, Indels: 7
0.77 0.07 0.16
Matches are distributed among these distances:
10 5 0.15
11 4 0.12
12 11 0.33
13 13 0.39
ACGTcount: A:0.38, C:0.00, G:0.02, T:0.60
Consensus pattern (12 bp):
ATTATTATTATT
Found at i:66387 original size:16 final size:17
Alignment explanation
Indices: 66366--66409 Score: 56
Period size: 16 Copynumber: 2.7 Consensus size: 17
66356 GACCTTTCAT
66366 TATTATTATTATTAT-A
1 TATTATTATTATTATAA
*
66382 TATTATTA-TATTTTAA
1 TATTATTATTATTATAA
*
66398 TATTATAATTAT
1 TATTATTATTAT
66410 GTATTAACAC
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
15 5 0.21
16 16 0.67
17 3 0.12
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (17 bp):
TATTATTATTATTATAA
Found at i:85140 original size:10 final size:11
Alignment explanation
Indices: 85120--85145 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
85110 GGAAAAGGAG
85120 AAAAACAAAAA
1 AAAAACAAAAA
85131 AAAAACAAAAA
1 AAAAACAAAAA
85142 AAAA
1 AAAA
85146 GGTCTGCTCT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.92, C:0.08, G:0.00, T:0.00
Consensus pattern (11 bp):
AAAAACAAAAA
Found at i:89542 original size:17 final size:16
Alignment explanation
Indices: 89499--89538 Score: 53
Period size: 17 Copynumber: 2.4 Consensus size: 16
89489 GTTTGGTTAG
89499 GATCTAAGATCACCAGT
1 GATC-AAGATCACCAGT
*
89516 GATGCAAGATCACCGGT
1 GAT-CAAGATCACCAGT
89533 GATCAA
1 GATCAA
89539 AGATTATATG
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
16 3 0.14
17 17 0.81
18 1 0.05
ACGTcount: A:0.35, C:0.23, G:0.23, T:0.20
Consensus pattern (16 bp):
GATCAAGATCACCAGT
Found at i:96324 original size:32 final size:32
Alignment explanation
Indices: 96288--96357 Score: 131
Period size: 32 Copynumber: 2.2 Consensus size: 32
96278 GAGATTTTTG
*
96288 TCAGACTACTTATAATCATATAAATTATGTCC
1 TCAGAATACTTATAATCATATAAATTATGTCC
96320 TCAGAATACTTATAATCATATAAATTATGTCC
1 TCAGAATACTTATAATCATATAAATTATGTCC
96352 TCAGAA
1 TCAGAA
96358 ATTCAATTTA
Statistics
Matches: 37, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
32 37 1.00
ACGTcount: A:0.40, C:0.17, G:0.07, T:0.36
Consensus pattern (32 bp):
TCAGAATACTTATAATCATATAAATTATGTCC
Found at i:97342 original size:7 final size:7
Alignment explanation
Indices: 97330--97355 Score: 52
Period size: 7 Copynumber: 3.7 Consensus size: 7
97320 AACTAGGCTG
97330 TGCGAGT
1 TGCGAGT
97337 TGCGAGT
1 TGCGAGT
97344 TGCGAGT
1 TGCGAGT
97351 TGCGA
1 TGCGA
97356 CTGTAATTAG
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 19 1.00
ACGTcount: A:0.15, C:0.15, G:0.42, T:0.27
Consensus pattern (7 bp):
TGCGAGT
Found at i:98471 original size:15 final size:15
Alignment explanation
Indices: 98451--98481 Score: 62
Period size: 15 Copynumber: 2.1 Consensus size: 15
98441 ACAATAAATT
98451 AACTATCAAATAGAA
1 AACTATCAAATAGAA
98466 AACTATCAAATAGAA
1 AACTATCAAATAGAA
98481 A
1 A
98482 TATGTTAATC
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.61, C:0.13, G:0.06, T:0.19
Consensus pattern (15 bp):
AACTATCAAATAGAA
Found at i:98528 original size:14 final size:14
Alignment explanation
Indices: 98509--98543 Score: 61
Period size: 14 Copynumber: 2.5 Consensus size: 14
98499 CCTTTTAAAT
98509 TAAAATAGTAAAAA
1 TAAAATAGTAAAAA
*
98523 TAAAATGGTAAAAA
1 TAAAATAGTAAAAA
98537 TAAAATA
1 TAAAATA
98544 ATTATAAAAA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
14 19 1.00
ACGTcount: A:0.69, C:0.00, G:0.09, T:0.23
Consensus pattern (14 bp):
TAAAATAGTAAAAA
Found at i:105888 original size:3 final size:3
Alignment explanation
Indices: 105880--105904 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
105870 TCCCACGACC
105880 GCA GCA GCA GCA GCA GCA GCA GCA G
1 GCA GCA GCA GCA GCA GCA GCA GCA G
105905 AACCGGCACC
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.32, C:0.32, G:0.36, T:0.00
Consensus pattern (3 bp):
GCA
Found at i:108616 original size:87 final size:87
Alignment explanation
Indices: 108429--108605 Score: 264
Period size: 87 Copynumber: 2.0 Consensus size: 87
108419 TTCCTCAGAG
* * * *
108429 GAAAAGATCTGAAGCTGATTCAGAAAACTGCCAAGAATTGGATGGGGAAGAATGCAGGGAGGAAA
1 GAAAAGATCTGAAGCTGAGTCAGAAAACTGCCAAGAATTAGAGGGGGAAGAATGCAAGGAGGAAA
* **
108494 ATGAGGAGTTTGAGAGGAAAAA
66 ATGAGGAATCCGAGAGGAAAAA
* *
108516 GAAAAGATCTGAAGCTGAGTCAGAAAACTGCCGAGAATTAGAGGGGGAAGAGTGCAAGGAGGAAA
1 GAAAAGATCTGAAGCTGAGTCAGAAAACTGCCAAGAATTAGAGGGGGAAGAATGCAAGGAGGAAA
*
108581 ATGAGGAATCCGAGAGGACAAA
66 ATGAGGAATCCGAGAGGAAAAA
108603 GAA
1 GAA
108606 GTGCATTGAA
Statistics
Matches: 80, Mismatches: 10, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
87 80 1.00
ACGTcount: A:0.43, C:0.10, G:0.34, T:0.14
Consensus pattern (87 bp):
GAAAAGATCTGAAGCTGAGTCAGAAAACTGCCAAGAATTAGAGGGGGAAGAATGCAAGGAGGAAA
ATGAGGAATCCGAGAGGAAAAA
Done.