Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01009180.1 Corchorus capsularis cultivar CVL-1 contig09201, 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: 12259
ACGTcount: A:0.36, C:0.14, G:0.15, T:0.35
Found at i:401 original size:137 final size:138
Alignment explanation
Indices: 246--504 Score: 466
Period size: 137 Copynumber: 1.9 Consensus size: 138
236 GGAGTATTAT
* *
246 ATATATATATGGGCATGTTTCATATCTGGTTAACAAGTCCTATCCAAAATAAATTGCAGGTATAG
1 ATATATATAT-GGCATGTTTCATATCTGGGTAACAAGTCCTATACAAAATAAATTGCAGGTATAG
*
311 CATTATTAATTTAGTTGTATATTTATGGCCATGTTCATATCTGGTTAAAAGGGGAAATTGATATA
65 CATTATTAATTTAGTTGTATATTTATGGCCATGTTCATATCTGGCTAAAAGGGGAAATTGATATA
376 TTAATTAAA
130 TTAATTAAA
*
385 ATATATATAT-GCATGTTTCATATCTGGGTAACAAGTCTTATACAAAATAAATTGCAGGTATAGC
1 ATATATATATGGCATGTTTCATATCTGGGTAACAAGTCCTATACAAAATAAATTGCAGGTATAGC
449 ATTATTAATTTAGTTGTATATTTATGGCCATGTTCATATCTGGCTAAAAGGGGAAA
66 ATTATTAATTTAGTTGTATATTTATGGCCATGTTCATATCTGGCTAAAAGGGGAAA
505 GGAAATTATA
Statistics
Matches: 116, Mismatches: 4, Indels: 2
0.95 0.03 0.02
Matches are distributed among these distances:
137 106 0.91
139 10 0.09
ACGTcount: A:0.35, C:0.10, G:0.17, T:0.37
Consensus pattern (138 bp):
ATATATATATGGCATGTTTCATATCTGGGTAACAAGTCCTATACAAAATAAATTGCAGGTATAGC
ATTATTAATTTAGTTGTATATTTATGGCCATGTTCATATCTGGCTAAAAGGGGAAATTGATATAT
TAATTAAA
Found at i:895 original size:27 final size:27
Alignment explanation
Indices: 820--896 Score: 84
Period size: 27 Copynumber: 2.8 Consensus size: 27
810 ATGTTATATT
* *
820 ATATATATATATATATAGAAATAATAAAG
1 ATATGTATA-ATA-ATAGAAATAACAAAG
*
849 ATATGTTATAA-AAAAGAAATAACAAAG
1 ATATG-TATAATAATAGAAATAACAAAG
*
876 ATATGTATAATAATATAAATA
1 ATATGTATAATAATAGAAATA
897 TATTATATAG
Statistics
Matches: 41, Mismatches: 5, Indels: 6
0.79 0.10 0.12
Matches are distributed among these distances:
26 5 0.12
27 26 0.63
28 1 0.02
29 5 0.12
30 4 0.10
ACGTcount: A:0.60, C:0.01, G:0.08, T:0.31
Consensus pattern (27 bp):
ATATGTATAATAATAGAAATAACAAAG
Found at i:1202 original size:31 final size:31
Alignment explanation
Indices: 1117--1206 Score: 108
Period size: 31 Copynumber: 2.9 Consensus size: 31
1107 ACGAAATCGA
* * *
1117 CTCAAATCAGTCCTTAACGCTGCAAACTCGG
1 CTCAAATCAGTCCTTAACGTTGCAAAATCAG
* *
1148 TTCAGATCAGTCCTTAACGTTGCAAAATCAG
1 CTCAAATCAGTCCTTAACGTTGCAAAATCAG
* **
1179 CTCAAATCAGTCCCTAATATTGCAAAAT
1 CTCAAATCAGTCCTTAACGTTGCAAAAT
1207 GGACTCAAAT
Statistics
Matches: 49, Mismatches: 10, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
31 49 1.00
ACGTcount: A:0.33, C:0.27, G:0.13, T:0.27
Consensus pattern (31 bp):
CTCAAATCAGTCCTTAACGTTGCAAAATCAG
Found at i:3548 original size:75 final size:74
Alignment explanation
Indices: 3455--3607 Score: 243
Period size: 75 Copynumber: 2.1 Consensus size: 74
3445 TGGTCTTTTC
* * *
3455 ACACTTTTTGGGTGACTAAAAAGCCCCTCTATGAGTTTCCTCTATTCCTTTTCCTTCTACCCTTT
1 ACACTTTTTGGATGACTAAAAAGCCCCTCTATGAGTTTCCCCCATTCCTTTTCCTTCTACCC-TT
3520 TTTCGTAATT
65 TTTCGTAATT
* * *
3530 ACACTTTTTGGATGACTAAAAAGTCCCTTTATGAGTTTCCCCCATTCCTTTTCCTTCTATCCTTT
1 ACACTTTTTGGATGACTAAAAAGCCCCTCTATGAGTTTCCCCCATTCCTTTTCCTTCTACCCTTT
3595 TTCGTAATT
66 TTCGTAATT
3604 ACAC
1 ACAC
3608 ATTTCCCTTC
Statistics
Matches: 72, Mismatches: 6, Indels: 1
0.91 0.08 0.01
Matches are distributed among these distances:
74 16 0.22
75 56 0.78
ACGTcount: A:0.20, C:0.27, G:0.10, T:0.43
Consensus pattern (74 bp):
ACACTTTTTGGATGACTAAAAAGCCCCTCTATGAGTTTCCCCCATTCCTTTTCCTTCTACCCTTT
TTCGTAATT
Found at i:3649 original size:20 final size:21
Alignment explanation
Indices: 3619--3657 Score: 71
Period size: 20 Copynumber: 1.9 Consensus size: 21
3609 TTTCCCTTCC
3619 TTAATTGTTTTTAATTAATGT
1 TTAATTGTTTTTAATTAATGT
3640 TTAA-TGTTTTTAATTAAT
1 TTAATTGTTTTTAATTAAT
3658 TGCTTCTAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
20 14 0.78
21 4 0.22
ACGTcount: A:0.31, C:0.00, G:0.08, T:0.62
Consensus pattern (21 bp):
TTAATTGTTTTTAATTAATGT
Found at i:9396 original size:45 final size:45
Alignment explanation
Indices: 9332--9421 Score: 171
Period size: 45 Copynumber: 2.0 Consensus size: 45
9322 TTACTTAAAG
*
9332 GGAACTAGTGTCAGACCATTTGAACTAATCACTTGTTGCATATTA
1 GGAACTAGTGTCAGACCATTTGAACTAATCACTTATTGCATATTA
9377 GGAACTAGTGTCAGACCATTTGAACTAATCACTTATTGCATATTA
1 GGAACTAGTGTCAGACCATTTGAACTAATCACTTATTGCATATTA
9422 TACTCCTATG
Statistics
Matches: 44, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
45 44 1.00
ACGTcount: A:0.32, C:0.18, G:0.17, T:0.33
Consensus pattern (45 bp):
GGAACTAGTGTCAGACCATTTGAACTAATCACTTATTGCATATTA
Found at i:11253 original size:31 final size:31
Alignment explanation
Indices: 11216--11357 Score: 187
Period size: 31 Copynumber: 4.6 Consensus size: 31
11206 TCTAACGTTA
*
11216 CAAAATCGACTTAAATCAGTTCTTAACATTG
1 CAAAATCGACTCAAATCAGTTCTTAACATTG
*
11247 TAAAATCGACTCAAATCAGTTCTTAACATTG
1 CAAAATCGACTCAAATCAGTTCTTAACATTG
* * ***
11278 CAAAATC-AGCTCAAATCAGTCCCTAGTGTTG
1 CAAAATCGA-CTCAAATCAGTTCTTAACATTG
*
11309 CAAAATCGACTCAAATCAGTTCTTAACGTTG
1 CAAAATCGACTCAAATCAGTTCTTAACATTG
*
11340 TAAAATCGACTCAAATCA
1 CAAAATCGACTCAAATCA
11358 ATCCCTAGTG
Statistics
Matches: 96, Mismatches: 13, Indels: 4
0.85 0.12 0.04
Matches are distributed among these distances:
30 1 0.01
31 94 0.98
32 1 0.01
ACGTcount: A:0.38, C:0.22, G:0.11, T:0.29
Consensus pattern (31 bp):
CAAAATCGACTCAAATCAGTTCTTAACATTG
Found at i:11314 original size:62 final size:62
Alignment explanation
Indices: 11248--11385 Score: 224
Period size: 62 Copynumber: 2.2 Consensus size: 62
11238 TTAACATTGT
*
11248 AAAATCGACTCAAATCAGTTCTTAACATTGCAAAATC-AGCTCAAATCAGTCCCTAGTGTTGC
1 AAAATCGACTCAAATCAGTTCTTAACATTGCAAAATCGA-CTCAAATCAATCCCTAGTGTTGC
* *
11310 AAAATCGACTCAAATCAGTTCTTAACGTTGTAAAATCGACTCAAATCAATCCCTAGTGTTGC
1 AAAATCGACTCAAATCAGTTCTTAACATTGCAAAATCGACTCAAATCAATCCCTAGTGTTGC
*
11372 AAAATGGACTCAAA
1 AAAATCGACTCAAA
11386 AGTCAGTTTA
Statistics
Matches: 71, Mismatches: 4, Indels: 2
0.92 0.05 0.03
Matches are distributed among these distances:
62 70 0.99
63 1 0.01
ACGTcount: A:0.38, C:0.22, G:0.13, T:0.27
Consensus pattern (62 bp):
AAAATCGACTCAAATCAGTTCTTAACATTGCAAAATCGACTCAAATCAATCCCTAGTGTTGC
Found at i:11376 original size:31 final size:31
Alignment explanation
Indices: 11207--11385 Score: 180
Period size: 31 Copynumber: 5.8 Consensus size: 31
11197 AATTAAATGT
* * *
11207 CTAACGTTACAAAATCGACTTAAATCAGTTC
1 CTAACGTTGCAAAATCGACTCAAATCAGTCC
* * * *
11238 TTAACATTGTAAAATCGACTCAAATCAGTTC
1 CTAACGTTGCAAAATCGACTCAAATCAGTCC
* *
11269 TTAACATTGCAAAATC-AGCTCAAATCAGTCC
1 CTAACGTTGCAAAATCGA-CTCAAATCAGTCC
** *
11300 CTAGTGTTGCAAAATCGACTCAAATCAGTTC
1 CTAACGTTGCAAAATCGACTCAAATCAGTCC
* * *
11331 TTAACGTTGTAAAATCGACTCAAATCAATCC
1 CTAACGTTGCAAAATCGACTCAAATCAGTCC
** *
11362 CTAGTGTTGCAAAATGGACTCAAA
1 CTAACGTTGCAAAATCGACTCAAA
11386 AGTCAGTTTA
Statistics
Matches: 123, Mismatches: 23, Indels: 4
0.82 0.15 0.03
Matches are distributed among these distances:
30 1 0.01
31 121 0.98
32 1 0.01
ACGTcount: A:0.37, C:0.22, G:0.12, T:0.28
Consensus pattern (31 bp):
CTAACGTTGCAAAATCGACTCAAATCAGTCC
Done.