Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01022400.1 Corchorus olitorius cultivar O-4 contig22433, 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: 45000
ACGTcount: A:0.33, C:0.18, G:0.17, T:0.32
Found at i:1169 original size:334 final size:331
Alignment explanation
Indices: 407--1647 Score: 1428
Period size: 321 Copynumber: 3.8 Consensus size: 331
397 TTTGGCTTAA
* * * * *
407 ATCACGGTTTTAAGCTAAAAAAATGCGTTTCGCGGCCCCGACTAAGTGTTGCATGATTTTTGACG
1 ATCACGGTTTTAAGCT--AAAAACGCGTTTCGGGGCCCCGACTCAGTTTTGCATGATTTTTGACA
* * * *
472 CAAAGACTCCTTGATATATCTATATTCATCTAACCAAATCTCAGCAACATTGGATTTAAGGATTT
64 CGAAGACTCCTTGAAATATCTATATTCATCTAACCAAATCTCAGCCACATTGGAATTAAGGATTT
* * * * * *
537 GCTTTTACGAGTATATGAATCATGTTTCGATTTAATTTAAAATTACTTTAG-AAATAATTGGAAA
129 GCTTTTACGAGCATCTGAATCATGTTTCAATTTAATTTAAAATTAATTCAGAAAAAAATTGGAAA
** * *
601 ATTGATATTAGAAGCGTGAAAAACCCTTCAATCTTTTCGACTTTGAATTATATA--CTTTTTGTG
194 AACGATATTAGAAGCGTGAAAAACCCTTCAATCTTTTCGACTTTGAATTATATATTTTTTTTATG
* *
664 AGAATTGTGGCTAAAAATTGAGGTAAAAATTTTCGGTTCAATTTTTG---------CCGAAATCG
259 AGAATTGTGGCT-AAAATTGAGGAAAAAATTTTCGGATCAATTTTTGAAAATTTTTCCGAAATCG
*
720 GGTTATATCC
323 TG-TATATCC
* * * *
730 ATCACGGTTTTAAGTTAAAAACGCGTTTCGGGGCCCCGTCTTAGTTTTGCATGATTTTTGGCACG
1 ATCACGGTTTTAAGCTAAAAACGCGTTTCGGGGCCCCGACTCAGTTTTGCATGATTTTTGACACG
* *
795 AAGACTCCTTGAAATATCTATATTCATCTAACCTAATCTCAACCACATTGGAATTAAGGATTTGC
66 AAGACTCCTTGAAATATCTATATTCATCTAACCAAATCTCAGCCACATTGGAATTAAGGATTTGC
* * *
860 TTTTACGAGCATCTGAATCATGTTTCAATCTAATTTGAAATTAATTTAGAAAAAAATTGGAAAAA
131 TTTTACGAGCATCTGAATCATGTTTCAATTTAATTTAAAATTAATTCAGAAAAAAATTGGAAAAA
* * * * ** *
925 CGATTTTAGAAGCCTGAAATACCCTTCAATCTTTT-TAGGGTTGAATTAT-TACTTTTTTTTTTG
196 CGATATTAGAAGCGTGAAAAACCCTTCAATCTTTTCGA-CTTTGAATTATATA-TTTTTTTTATG
* * *
988 AGAATTGTGGCCACAAATTAAGGAAAAAATTTTCGAATCAATTTTTGCAAAATTTTATCCGAAAT
259 AGAATTGTGGCTA-AAATTGAGGAAAAAATTTTCGGATCAATTTTTG-AAAATTTT-TCCGAAAT
1053 CGTGTACTATCC
321 CGTGTA-TATCC
* * *
1065 ATCACTGTTTTAAACTAAAAACGCGTTTCGGGG-CCCGACTCAGTTTTGCATGATTTTTGCCACG
1 ATCACGGTTTTAAGCTAAAAACGCGTTTCGGGGCCCCGACTCAGTTTTGCATGATTTTTGACACG
* * * * *
1129 AATACTCCTTGAAATATCCACATTCATCTAACCAAATCTCAGCCAAATTGGATTTAAGGATTTG-
66 AAGACTCCTTGAAATATCTATATTCATCTAACCAAATCTCAGCCACATTGGAATTAAGGATTTGC
* * * * * *
1193 TTTTAACGAGCAACGGAATCATTTTTCGATTTAATTTGAAATTAATTCAGAACAAAATT-GAAAA
131 TTTT-ACGAGCATCTGAATCATGTTTCAATTTAATTTAAAATTAATTCAGAAAAAAATTGGAAAA
*
1257 ACGATATTATAAGCGTGAAAAACCCTTCAATCTTTTCGACTTTGAATTATATA--TTTTTTATGA
195 ACGATATTAGAAGCGTGAAAAACCCTTCAATCTTTTCGACTTTGAATTATATATTTTTTTTATGA
* * * *
1320 GAATTGTTGCTAAAACTGAGGAAAAAATTTTCGGATCTATTTCTGTAAAATTTTTGCCGAAATCG
260 GAATTGTGGCTAAAATTGAGGAAAAAATTTTCGGATCAATTTTTG-AAAATTTTT-CCGAAATCG
1385 TGTATTATCC
323 TGTA-TATCC
* * * *
1395 ATCACGGTTTTAAGTTAAAAACGCGTTTCGGGGCCCCGACTCAGTATTGTATGATTTTTGACATG
1 ATCACGGTTTTAAGCTAAAAACGCGTTTCGGGGCCCCGACTCAGTTTTGCATGATTTTTGACACG
* * * * *
1460 AAGAATTCTTGAAATATCTATATTCATCTAACCAAATTTTAGCTACATTGG-ATATAAGGATTTG
66 AAGACTCCTTGAAATATCTATATTCATCTAACCAAATCTCAGCCACATTGGAAT-TAAGGATTTG
* * ** * * * * *
1524 TTTTTACAAATATCTAAATCATGTTTCGAGTTAATTTAAAATTAATTCAGAAAAAATTTTGACAA
130 CTTTTACGAGCATCTGAATCATGTTTCAATTTAATTTAAAATTAATTCAGAAAAAAATTGGA-AA
* * * * *
1589 ATAAGAT-TT-GAAACGTGAAAAACCATTCAATCTTTTTGAGTTTGAATTATATATTTTTT
194 A-ACGATATTAGAAGCGTGAAAAACCCTTCAATCTTTTCGACTTTGAATTATATATTTTTT
1648 ATGAGAGTAC
Statistics
Matches: 780, Mismatches: 108, Indels: 49
0.83 0.12 0.05
Matches are distributed among these distances:
321 147 0.19
322 53 0.07
323 16 0.02
324 47 0.06
329 1 0.00
330 85 0.11
331 141 0.18
332 45 0.06
333 55 0.07
334 145 0.19
335 45 0.06
ACGTcount: A:0.33, C:0.15, G:0.15, T:0.37
Consensus pattern (331 bp):
ATCACGGTTTTAAGCTAAAAACGCGTTTCGGGGCCCCGACTCAGTTTTGCATGATTTTTGACACG
AAGACTCCTTGAAATATCTATATTCATCTAACCAAATCTCAGCCACATTGGAATTAAGGATTTGC
TTTTACGAGCATCTGAATCATGTTTCAATTTAATTTAAAATTAATTCAGAAAAAAATTGGAAAAA
CGATATTAGAAGCGTGAAAAACCCTTCAATCTTTTCGACTTTGAATTATATATTTTTTTTATGAG
AATTGTGGCTAAAATTGAGGAAAAAATTTTCGGATCAATTTTTGAAAATTTTTCCGAAATCGTGT
ATATCC
Found at i:9033 original size:2 final size:2
Alignment explanation
Indices: 9026--9064 Score: 78
Period size: 2 Copynumber: 19.5 Consensus size: 2
9016 ATGTTTTATT
9026 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
9065 CTTTCTTTTG
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:17649 original size:3 final size:3
Alignment explanation
Indices: 17625--17683 Score: 52
Period size: 3 Copynumber: 20.0 Consensus size: 3
17615 TTAATTCGTG
* * *
17625 TAA TAA -AA TAC TAA GTAG TAA TAA TTA TAA TAA T-A TATA TAA TAA
1 TAA TAA TAA TAA TAA -TAA TAA TAA TAA TAA TAA TAA TA-A TAA TAA
17670 TAA TAA T-A TAA TAA
1 TAA TAA TAA TAA TAA
17684 GAACCGGAAA
Statistics
Matches: 45, Mismatches: 6, Indels: 10
0.74 0.10 0.16
Matches are distributed among these distances:
2 6 0.13
3 34 0.76
4 5 0.11
ACGTcount: A:0.59, C:0.02, G:0.03, T:0.36
Consensus pattern (3 bp):
TAA
Found at i:17666 original size:18 final size:17
Alignment explanation
Indices: 17625--17683 Score: 66
Period size: 18 Copynumber: 3.4 Consensus size: 17
17615 TTAATTCGTG
*
17625 TAATAA-AATACTAAGTA
1 TAATAATAATAATAA-TA
*
17642 GTAATAATTATAATAATA
1 -TAATAATAATAATAATA
17660 TATATAATAATAATAATA
1 TA-ATAATAATAATAATA
17678 TAATAA
1 TAATAA
17684 GAACCGGAAA
Statistics
Matches: 36, Mismatches: 3, Indels: 5
0.82 0.07 0.11
Matches are distributed among these distances:
17 6 0.17
18 24 0.67
19 6 0.17
ACGTcount: A:0.59, C:0.02, G:0.03, T:0.36
Consensus pattern (17 bp):
TAATAATAATAATAATA
Found at i:17963 original size:19 final size:19
Alignment explanation
Indices: 17939--17978 Score: 80
Period size: 19 Copynumber: 2.1 Consensus size: 19
17929 TTTCTCAAGT
17939 TTTTTTAATGGCAACTTAC
1 TTTTTTAATGGCAACTTAC
17958 TTTTTTAATGGCAACTTAC
1 TTTTTTAATGGCAACTTAC
17977 TT
1 TT
17979 AAAATATATA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 21 1.00
ACGTcount: A:0.25, C:0.15, G:0.10, T:0.50
Consensus pattern (19 bp):
TTTTTTAATGGCAACTTAC
Found at i:18444 original size:30 final size:30
Alignment explanation
Indices: 18408--18473 Score: 114
Period size: 30 Copynumber: 2.2 Consensus size: 30
18398 TACATTCACA
*
18408 ATATTAGAACTCGATATCTTATTTAAGAAT
1 ATATTAGAACTCGATATCTTACTTAAGAAT
18438 ATATTAGAACTCGATATCTTACTTAAGAAT
1 ATATTAGAACTCGATATCTTACTTAAGAAT
*
18468 ACATTA
1 ATATTA
18474 ATCTCATTCA
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
30 34 1.00
ACGTcount: A:0.41, C:0.12, G:0.09, T:0.38
Consensus pattern (30 bp):
ATATTAGAACTCGATATCTTACTTAAGAAT
Found at i:19837 original size:2 final size:2
Alignment explanation
Indices: 19830--19902 Score: 50
Period size: 2 Copynumber: 39.5 Consensus size: 2
19820 CAGTTTTTAT
* * * *
19830 TA TA TA TA TA AA TA TA TA T- TT TA T- TA TA AA TA T- TA AA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
* *
19869 TA TT TA -A GA TA TA TA TA T- TA TA TA TA T- TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
19903 TAGTAATCAG
Statistics
Matches: 55, Mismatches: 10, Indels: 12
0.71 0.13 0.16
Matches are distributed among these distances:
1 6 0.11
2 49 0.89
ACGTcount: A:0.48, C:0.00, G:0.01, T:0.51
Consensus pattern (2 bp):
TA
Found at i:19851 original size:24 final size:24
Alignment explanation
Indices: 19824--19896 Score: 78
Period size: 24 Copynumber: 3.1 Consensus size: 24
19814 AGTAATCAGT
19824 TTTTATTATATATATAAATATATA
1 TTTTATTATATATATAAATATATA
* *
19848 TTTTATTATAAATATTAA-ATATA
1 TTTTATTATATATATAAATATATA
** *
19871 -TTTAAGATATATATATTATATATA
1 TTTTATTATATATATA-AATATATA
19895 TT
1 TT
19897 ATATATTAGT
Statistics
Matches: 39, Mismatches: 7, Indels: 5
0.76 0.14 0.10
Matches are distributed among these distances:
22 11 0.28
23 6 0.15
24 21 0.54
25 1 0.03
ACGTcount: A:0.45, C:0.00, G:0.01, T:0.53
Consensus pattern (24 bp):
TTTTATTATATATATAAATATATA
Found at i:21594 original size:21 final size:21
Alignment explanation
Indices: 21531--21594 Score: 71
Period size: 21 Copynumber: 3.1 Consensus size: 21
21521 TTGACATTGT
21531 TTAGGTACTGTACAGATGAGA
1 TTAGGTACTGTACAGATGAGA
* *
21552 TTA--CACTGTACAGAAT-AAA
1 TTAGGTACTGTACAG-ATGAGA
*
21571 TTAGGTATTGTACAGATGAGA
1 TTAGGTACTGTACAGATGAGA
21592 TTA
1 TTA
21595 TTAGAGCAAC
Statistics
Matches: 34, Mismatches: 5, Indels: 8
0.72 0.11 0.17
Matches are distributed among these distances:
19 14 0.41
20 4 0.12
21 16 0.47
ACGTcount: A:0.38, C:0.09, G:0.22, T:0.31
Consensus pattern (21 bp):
TTAGGTACTGTACAGATGAGA
Found at i:36276 original size:70 final size:70
Alignment explanation
Indices: 36163--36302 Score: 280
Period size: 70 Copynumber: 2.0 Consensus size: 70
36153 GGTAGCGGTG
36163 CGATTGACACTGTTTAGCAACTGTACAGATGAGATTACACTGTACAGATTAGAATAGATATTGTA
1 CGATTGACACTGTTTAGCAACTGTACAGATGAGATTACACTGTACAGATTAGAATAGATATTGTA
36228 CATAT
66 CATAT
36233 CGATTGACACTGTTTAGCAACTGTACAGATGAGATTACACTGTACAGATTAGAATAGATATTGTA
1 CGATTGACACTGTTTAGCAACTGTACAGATGAGATTACACTGTACAGATTAGAATAGATATTGTA
36298 CATAT
66 CATAT
36303 GAGATTATTA
Statistics
Matches: 70, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
70 70 1.00
ACGTcount: A:0.36, C:0.14, G:0.19, T:0.31
Consensus pattern (70 bp):
CGATTGACACTGTTTAGCAACTGTACAGATGAGATTACACTGTACAGATTAGAATAGATATTGTA
CATAT
Found at i:40452 original size:22 final size:22
Alignment explanation
Indices: 40424--40488 Score: 85
Period size: 22 Copynumber: 3.0 Consensus size: 22
40414 CCTCTATGAA
40424 ATAATCTCCATATGAAATTTTG
1 ATAATCTCCATATGAAATTTTG
* *
40446 ATAATCTCCTTATAAAATTTTG
1 ATAATCTCCATATGAAATTTTG
* * *
40468 TTAATCTCCCTAAGAAATTTT
1 ATAATCTCCATATGAAATTTT
40489 TTCCATCCAA
Statistics
Matches: 37, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 37 1.00
ACGTcount: A:0.35, C:0.15, G:0.06, T:0.43
Consensus pattern (22 bp):
ATAATCTCCATATGAAATTTTG
Done.