Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01008489.1 Corchorus capsularis cultivar CVL-1 contig08510, 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: 45607
ACGTcount: A:0.34, C:0.18, G:0.17, T:0.32
Found at i:798 original size:332 final size:331
Alignment explanation
Indices: 1--963 Score: 1449
Period size: 332 Copynumber: 2.9 Consensus size: 331
* *
1 CAAAAACCGTGATA-ACGTACACGATTTCAGTTAAAATTTTGCAAAATTTGACCTGAAAGATTTT
1 CAAAAACCGTGATATA-GTACACGATTTCAGTTAAAATTTTGCAAAAATTGACCCGAAAGATTTT
*
65 TCCTCAATTTTTGGACAAAATATTCATAAAAAAATGTATAATTCAACTCTAAAAATATGGAAGGG
65 TCCTCAATTTTTGGACAAAATATTC-TAAAAAAATGTATAATTCAACTCTAAAAATATCGAAGGG
130 TGTTTCATGCTTCTAATATCATTTTTTCTAATTTTTTTTCCGAATTAATTTCGAATTAAATCGAA
129 TGTTTCATGCTTCTAATATCATTTTTTCTAA-TTTTTTTCCGAATTAATTTCGAATTAAATCGAA
* *
195 ACAAGATTCAGATGCTCATAAAAACAAATCCTTAATTGCAATGTGCCTTAGACTCTTTTAGATCA
193 ACAAGATTCAGATGCTCATAAAAACAAATCCTTAATTGCAATGTG-CTGAGACTTTTTTAGATCA
* * * * *
260 ATATAGATATTTCAAGGAGTTTTGGTGCTAAAAATCAGGCAAAACCGAGTCGGTTCCCCGAAACG
257 ATATAGATATTTCAAGGAGTCTTGGCGCCAAAAATCAAGCAAAACCGAGTCGGGTCCCCGAAACG
*
325 CGTTTTTTGA
322 CGTTTTTCGA
* * *
335 CAAAAACTGTG--AT-G--CACGATTTCAGTTAAAATTTTGCAAAAATTGATCCGAAATATTTTT
1 CAAAAACCGTGATATAGTACACGATTTCAGTTAAAATTTTGCAAAAATTGACCCGAAAGATTTTT
* *
395 CCTCAATTTTTGGACAAGATATTC-AGAAAAAATGTATAATTCAACTATAAAAATATCGAAGGGT
66 CCTCAATTTTTGGACAAAATATTCTA-AAAAAATGTATAATTCAACTCTAAAAATATCGAAGGGT
* *
459 GTTTCATGTTTCTAATATCATTTTTTCTAA-TTTTTTCCGAATTAATTTCGAATTAAATCGTAAC
130 GTTTCATGCTTCTAATATCATTTTTTCTAATTTTTTTCCGAATTAATTTCGAATTAAATCGAAAC
*
523 AAGATTTAGATGCTCATAAAAACAAATCCTTAATTGCAATGTGCTGAGACTTTTTTAGATCAATA
195 AAGATTCAGATGCTCATAAAAACAAATCCTTAATTGCAATGTGCTGAGACTTTTTTAGATCAATA
* * *
588 TAGATATTTCATGGAGTCTTGGCGCCAAAAATCAAGCAAAACCGCGTCGGGTCCCCGGAACGCGT
260 TAGATATTTCAAGGAGTCTTGGCGCCAAAAATCAAGCAAAACCGAGTCGGGTCCCCGAAACGCGT
*
653 TTTTCGC
325 TTTTCGA
660 CAAAAACCGTGATATTTAGTACACGATTTCAGTTAAAATTTTGCAAAAATTGACCCGAAAGATTT
1 CAAAAACCGTGATA--TAGTACACGATTTCAGTTAAAATTTTGCAAAAATTGACCCGAAAGATTT
* * *
725 TTCCTCAATTTTTGGACAAAATATTCTTAAAAAATGTATAATTCAACTCTAAAAAGATCGAAAGG
64 TTCCTCAATTTTTGGACAAAATATTCTAAAAAAATGTATAATTCAACTCTAAAAATATCGAAGGG
** * *
790 CATTTCATGCTTCTAATATCATTTTTTTCTAATTTTTTTTGCGAATTAATTTCGAATTAAATTGA
129 TGTTTCATGCTTCTAATATCA-TTTTTTCTAA-TTTTTTTCCGAATTAATTTCGAATTAAATCGA
* * *
855 AACAAGATTCAGATGGTCGTAAAAACAAATCCTGAATTGCAATGTGGCTGAGA-TTTGTTTAGAT
192 AACAAGATTCAGATGCTCATAAAAACAAATCCTTAATTGCAATGT-GCTGAGACTTT-TTTAGAT
* *
919 GAATATAGATATTTCAAGGAGTCTTGGCGCGAAAAATCAAGCAAA
255 CAATATAGATATTTCAAGGAGTCTTGGCGCCAAAAATCAAGCAAA
964 TCCCTTCAAT
Statistics
Matches: 570, Mismatches: 44, Indels: 28
0.89 0.07 0.04
Matches are distributed among these distances:
325 92 0.16
326 75 0.13
327 2 0.00
328 65 0.11
329 66 0.12
330 1 0.00
331 1 0.00
332 120 0.21
333 10 0.02
334 10 0.02
335 72 0.13
336 56 0.10
ACGTcount: A:0.36, C:0.15, G:0.15, T:0.34
Consensus pattern (331 bp):
CAAAAACCGTGATATAGTACACGATTTCAGTTAAAATTTTGCAAAAATTGACCCGAAAGATTTTT
CCTCAATTTTTGGACAAAATATTCTAAAAAAATGTATAATTCAACTCTAAAAATATCGAAGGGTG
TTTCATGCTTCTAATATCATTTTTTCTAATTTTTTTCCGAATTAATTTCGAATTAAATCGAAACA
AGATTCAGATGCTCATAAAAACAAATCCTTAATTGCAATGTGCTGAGACTTTTTTAGATCAATAT
AGATATTTCAAGGAGTCTTGGCGCCAAAAATCAAGCAAAACCGAGTCGGGTCCCCGAAACGCGTT
TTTCGA
Found at i:2411 original size:11 final size:11
Alignment explanation
Indices: 2392--2435 Score: 52
Period size: 11 Copynumber: 4.0 Consensus size: 11
2382 TACTATATAT
2392 CTAATTAATAA
1 CTAATTAATAA
* *
2403 CTAACTAATAT
1 CTAATTAATAA
*
2414 CTAATTAATAG
1 CTAATTAATAA
*
2425 TTAATTAATAA
1 CTAATTAATAA
2436 TGAATAAATT
Statistics
Matches: 27, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
11 27 1.00
ACGTcount: A:0.50, C:0.09, G:0.02, T:0.39
Consensus pattern (11 bp):
CTAATTAATAA
Found at i:14911 original size:40 final size:40
Alignment explanation
Indices: 14856--14935 Score: 151
Period size: 40 Copynumber: 2.0 Consensus size: 40
14846 AGAGTATATC
14856 ATATGTTATATACTCCAATTACTTGGACTGGTTTTAGGGA
1 ATATGTTATATACTCCAATTACTTGGACTGGTTTTAGGGA
*
14896 ATATGTTATATACTCCGATTACTTGGACTGGTTTTAGGGA
1 ATATGTTATATACTCCAATTACTTGGACTGGTTTTAGGGA
14936 CTATATGGCC
Statistics
Matches: 39, Mismatches: 1, Indels: 0
0.98 0.03 0.00
Matches are distributed among these distances:
40 39 1.00
ACGTcount: A:0.26, C:0.12, G:0.21, T:0.40
Consensus pattern (40 bp):
ATATGTTATATACTCCAATTACTTGGACTGGTTTTAGGGA
Found at i:17927 original size:2 final size:2
Alignment explanation
Indices: 17913--17947 Score: 54
Period size: 2 Copynumber: 17.5 Consensus size: 2
17903 AGAAAGTAAT
17913 TA TA TA CTA -A 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 T
17948 TCAAATTCCA
Statistics
Matches: 31, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
1 1 0.03
2 28 0.90
3 2 0.06
ACGTcount: A:0.49, C:0.03, G:0.00, T:0.49
Consensus pattern (2 bp):
TA
Found at i:19129 original size:8 final size:8
Alignment explanation
Indices: 19116--19141 Score: 52
Period size: 8 Copynumber: 3.2 Consensus size: 8
19106 TACATACCAT
19116 ATTTTGCC
1 ATTTTGCC
19124 ATTTTGCC
1 ATTTTGCC
19132 ATTTTGCC
1 ATTTTGCC
19140 AT
1 AT
19142 GCTTCTCTCT
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:0.15, C:0.23, G:0.12, T:0.50
Consensus pattern (8 bp):
ATTTTGCC
Found at i:20900 original size:7 final size:7
Alignment explanation
Indices: 20888--20924 Score: 74
Period size: 7 Copynumber: 5.3 Consensus size: 7
20878 TTTGTGAATG
20888 ATCATGA
1 ATCATGA
20895 ATCATGA
1 ATCATGA
20902 ATCATGA
1 ATCATGA
20909 ATCATGA
1 ATCATGA
20916 ATCATGA
1 ATCATGA
20923 AT
1 AT
20925 AATAACGACT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 30 1.00
ACGTcount: A:0.43, C:0.14, G:0.14, T:0.30
Consensus pattern (7 bp):
ATCATGA
Found at i:22010 original size:6 final size:6
Alignment explanation
Indices: 22001--22029 Score: 58
Period size: 6 Copynumber: 4.8 Consensus size: 6
21991 CTAATAAGAC
22001 TATGAA TATGAA TATGAA TATGAA TATGA
1 TATGAA TATGAA TATGAA TATGAA TATGA
22030 TGACTCAATC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.17, T:0.34
Consensus pattern (6 bp):
TATGAA
Found at i:22865 original size:2 final size:2
Alignment explanation
Indices: 22860--22889 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
22850 AGTAGTATGC
22860 AT AT AT 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
22890 CATAGCCTGC
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:26995 original size:2 final size:2
Alignment explanation
Indices: 26988--27023 Score: 65
Period size: 2 Copynumber: 18.5 Consensus size: 2
26978 GTTTGGAGAA
26988 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT -T AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
27024 GTTGGGGTAA
Statistics
Matches: 33, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 32 0.97
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:28469 original size:3 final size:3
Alignment explanation
Indices: 28455--28484 Score: 51
Period size: 3 Copynumber: 10.0 Consensus size: 3
28445 ATGCATAATA
*
28455 TAT TAA TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
28485 ATAAGATTAG
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (3 bp):
TAT
Found at i:35230 original size:16 final size:16
Alignment explanation
Indices: 35209--35240 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
35199 GGACACTCCA
35209 CCATGGGCCTCAGCCC
1 CCATGGGCCTCAGCCC
*
35225 CCATGGGCGTCAGCCC
1 CCATGGGCCTCAGCCC
35241 AGCTAGAAGA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.12, C:0.47, G:0.28, T:0.12
Consensus pattern (16 bp):
CCATGGGCCTCAGCCC
Found at i:35471 original size:4 final size:4
Alignment explanation
Indices: 35462--35505 Score: 54
Period size: 4 Copynumber: 11.2 Consensus size: 4
35452 TATAGATATG
* * *
35462 TGTA TGTA TGTA TGTA T-AA TGTA TGTA TGCA TGCA TGTA TGTA T
1 TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA T
35506 ATTTTTGGTC
Statistics
Matches: 35, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
3 2 0.06
4 33 0.94
ACGTcount: A:0.27, C:0.05, G:0.23, T:0.45
Consensus pattern (4 bp):
TGTA
Found at i:40804 original size:6 final size:6
Alignment explanation
Indices: 40793--40817 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
40783 AGAAGACCAA
40793 CCCCAT CCCCAT CCCCAT CCCCAT C
1 CCCCAT CCCCAT CCCCAT CCCCAT C
40818 AAATGGATCA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.16, C:0.68, G:0.00, T:0.16
Consensus pattern (6 bp):
CCCCAT
Found at i:41659 original size:14 final size:15
Alignment explanation
Indices: 41640--41669 Score: 53
Period size: 14 Copynumber: 2.1 Consensus size: 15
41630 TTATAGTGTG
41640 TGTATATATA-TATA
1 TGTATATATATTATA
41654 TGTATATATATTATA
1 TGTATATATATTATA
41669 T
1 T
41670 ATGCAAGACA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 10 0.67
15 5 0.33
ACGTcount: A:0.40, C:0.00, G:0.07, T:0.53
Consensus pattern (15 bp):
TGTATATATATTATA
Done.