Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01012089.1 Corchorus olitorius cultivar O-4 contig12122, 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: 42106
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.33
Found at i:5143 original size:27 final size:27
Alignment explanation
Indices: 5109--5213 Score: 174
Period size: 27 Copynumber: 3.9 Consensus size: 27
5099 ATCCAAATTG
5109 CTCATGACCATCAGGATCCAATTTCAT
1 CTCATGACCATCAGGATCCAATTTCAT
* ***
5136 CTCATGACCATCGGGATCCAATTTTGG
1 CTCATGACCATCAGGATCCAATTTCAT
5163 CTCATGACCATCAGGATCCAATTTCAT
1 CTCATGACCATCAGGATCCAATTTCAT
5190 CTCATGACCATCAGGATCCAATTT
1 CTCATGACCATCAGGATCCAATTT
5214 TGGAAACCAA
Statistics
Matches: 70, Mismatches: 8, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
27 70 1.00
ACGTcount: A:0.28, C:0.29, G:0.14, T:0.30
Consensus pattern (27 bp):
CTCATGACCATCAGGATCCAATTTCAT
Found at i:5172 original size:54 final size:54
Alignment explanation
Indices: 5108--5216 Score: 209
Period size: 54 Copynumber: 2.0 Consensus size: 54
5098 GATCCAAATT
*
5108 GCTCATGACCATCAGGATCCAATTTCATCTCATGACCATCGGGATCCAATTTTG
1 GCTCATGACCATCAGGATCCAATTTCATCTCATGACCATCAGGATCCAATTTTG
5162 GCTCATGACCATCAGGATCCAATTTCATCTCATGACCATCAGGATCCAATTTTG
1 GCTCATGACCATCAGGATCCAATTTCATCTCATGACCATCAGGATCCAATTTTG
5216 G
1 G
5217 AAACCAAAGC
Statistics
Matches: 54, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
54 54 1.00
ACGTcount: A:0.27, C:0.28, G:0.17, T:0.29
Consensus pattern (54 bp):
GCTCATGACCATCAGGATCCAATTTCATCTCATGACCATCAGGATCCAATTTTG
Found at i:8524 original size:12 final size:12
Alignment explanation
Indices: 8507--8532 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
8497 AATCATTGGA
8507 TGGGAGTAGTAT
1 TGGGAGTAGTAT
8519 TGGGAGTAGTAT
1 TGGGAGTAGTAT
8531 TG
1 TG
8533 AAATCATTAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.23, C:0.00, G:0.42, T:0.35
Consensus pattern (12 bp):
TGGGAGTAGTAT
Found at i:10857 original size:28 final size:28
Alignment explanation
Indices: 10801--10857 Score: 64
Period size: 28 Copynumber: 2.0 Consensus size: 28
10791 GTCAATTATT
*
10801 TTTTATGTAAATATTTATTTTTAACTTC
1 TTTTATGTAAATATTTATTTATAACTTC
*
10829 TTTTAT-T-AATATTTAATTTAATAATTTC
1 TTTTATGTAAATATTT-ATTT-ATAACTTC
10857 T
1 T
10858 AAATATCCCA
Statistics
Matches: 25, Mismatches: 2, Indels: 4
0.81 0.06 0.13
Matches are distributed among these distances:
26 7 0.28
27 5 0.20
28 13 0.52
ACGTcount: A:0.32, C:0.05, G:0.02, T:0.61
Consensus pattern (28 bp):
TTTTATGTAAATATTTATTTATAACTTC
Found at i:12285 original size:35 final size:35
Alignment explanation
Indices: 12242--12509 Score: 367
Period size: 35 Copynumber: 7.7 Consensus size: 35
12232 GAAGATCAAC
*
12242 TCAT-AAAAACTTCTTGAAATGCGATCAACTCTGA
1 TCATCAAAAACTTCTTGAAATGAGATCAACTCTGA
* *
12276 TCATCAAAAACTTCTTAAAATGTGATCAACTCTGA
1 TCATCAAAAACTTCTTGAAATGAGATCAACTCTGA
*
12311 TCATCAAAAACTTCTTGAAAGGAGATCAACTCTGA
1 TCATCAAAAACTTCTTGAAATGAGATCAACTCTGA
* * *
12346 TCACCGAAAACTTCTTGAAACGAGATCAACTCTGA
1 TCATCAAAAACTTCTTGAAATGAGATCAACTCTGA
* * * *
12381 TCATCGAAAGCTTCTTGATCAGGAGATCAACTCTGA
1 TCATCAAAAACTTCTTGA-AATGAGATCAACTCTGA
12417 TCATCAAAAACTTCTTGAAATGAGATCAACTCTGA
1 TCATCAAAAACTTCTTGAAATGAGATCAACTCTGA
* * * *
12452 CCATCAAAAACTTCTTGAAACGAGATTAACTCTAA
1 TCATCAAAAACTTCTTGAAATGAGATCAACTCTGA
* *
12487 TCATTAAAAACTTCTTGGAATGA
1 TCATCAAAAACTTCTTGAAATGA
12510 CCGCACTGGA
Statistics
Matches: 208, Mismatches: 24, Indels: 3
0.89 0.10 0.01
Matches are distributed among these distances:
34 4 0.02
35 173 0.83
36 31 0.15
ACGTcount: A:0.38, C:0.21, G:0.13, T:0.28
Consensus pattern (35 bp):
TCATCAAAAACTTCTTGAAATGAGATCAACTCTGA
Found at i:12442 original size:106 final size:105
Alignment explanation
Indices: 12246--12502 Score: 370
Period size: 106 Copynumber: 2.4 Consensus size: 105
12236 ATCAACTCAT
* * * *
12246 AAAAACTTCTTGAAATGCGATCAACTCTGATCATCAAAAACTTCTTAAAATGTGATCAACTCTGA
1 AAAAACTTCTTGAAACGAGATCAACTCTGATCATCAAAAACTTCTTAAAAGGAGATCAACTCTGA
*
12311 TCATCAAAAACTTCTTGAAAGGAGATCAACTCTGATCACC
66 TCATCAAAAACTTCTTGAAAGGAGATCAACTCTGACCACC
* * * **
12351 GAAAACTTCTTGAAACGAGATCAACTCTGATCATCGAAAGCTTCTTGATCAGGAGATCAACTCTG
1 AAAAACTTCTTGAAACGAGATCAACTCTGATCATCAAAAACTTCTT-AAAAGGAGATCAACTCTG
* *
12416 ATCATCAAAAACTTCTTGAAATGAGATCAACTCTGACCATC
65 ATCATCAAAAACTTCTTGAAAGGAGATCAACTCTGACCACC
* * *
12457 AAAAACTTCTTGAAACGAGATTAACTCTAATCATTAAAAACTTCTT
1 AAAAACTTCTTGAAACGAGATCAACTCTGATCATCAAAAACTTCTT
12503 GGAATGACCG
Statistics
Matches: 133, Mismatches: 18, Indels: 1
0.88 0.12 0.01
Matches are distributed among these distances:
105 41 0.31
106 92 0.69
ACGTcount: A:0.39, C:0.21, G:0.12, T:0.28
Consensus pattern (105 bp):
AAAAACTTCTTGAAACGAGATCAACTCTGATCATCAAAAACTTCTTAAAAGGAGATCAACTCTGA
TCATCAAAAACTTCTTGAAAGGAGATCAACTCTGACCACC
Found at i:31408 original size:14 final size:15
Alignment explanation
Indices: 31382--31411 Score: 53
Period size: 14 Copynumber: 2.1 Consensus size: 15
31372 TAAGACCCAA
31382 TCCTTGTTTATTTAT
1 TCCTTGTTTATTTAT
31397 TCCTTG-TTATTTAT
1 TCCTTGTTTATTTAT
31411 T
1 T
31412 TTTCCTAGTT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 9 0.60
15 6 0.40
ACGTcount: A:0.13, C:0.13, G:0.07, T:0.67
Consensus pattern (15 bp):
TCCTTGTTTATTTAT
Found at i:32279 original size:54 final size:51
Alignment explanation
Indices: 32170--32297 Score: 148
Period size: 54 Copynumber: 2.4 Consensus size: 51
32160 TTATAAACTA
* * *
32170 AAATTATCTTTTATTTAATAAAATCTACATTGTTATAATTTTACATATTTT
1 AAATTATCATTTATTTAATAAAATCTACATTGTTATAATTTCACATATTAT
* * *
32221 AAATTATCATTTATTTAATAAAATTTATGTTATTGTTATAATTTCACCTATTAT
1 AAATTATCATTTATTTAATAAAATCTA---CATTGTTATAATTTCACATATTAT
* *
32275 AAATTATTATTAAATTTAATAAA
1 AAATTATCATT-TATTTAATAAA
32298 CTTCATATAA
Statistics
Matches: 65, Mismatches: 8, Indels: 4
0.84 0.10 0.05
Matches are distributed among these distances:
51 25 0.38
54 30 0.46
55 10 0.15
ACGTcount: A:0.41, C:0.06, G:0.02, T:0.51
Consensus pattern (51 bp):
AAATTATCATTTATTTAATAAAATCTACATTGTTATAATTTCACATATTAT
Found at i:32603 original size:15 final size:15
Alignment explanation
Indices: 32583--32616 Score: 59
Period size: 15 Copynumber: 2.3 Consensus size: 15
32573 AATTTAGATA
*
32583 TTATATAAATACTAT
1 TTATATAAACACTAT
32598 TTATATAAACACTAT
1 TTATATAAACACTAT
32613 TTAT
1 TTAT
32617 TTGAATAATT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.44, C:0.09, G:0.00, T:0.47
Consensus pattern (15 bp):
TTATATAAACACTAT
Found at i:33647 original size:21 final size:21
Alignment explanation
Indices: 33596--33659 Score: 60
Period size: 21 Copynumber: 3.1 Consensus size: 21
33586 TTGACACTGT
* *
33596 TTAGGTACTGTACAAATGAGA
1 TTAGGTACTGTACAGATGAAA
* *
33617 TTA--CACTGTACAGATTAAA
1 TTAGGTACTGTACAGATGAAA
* *
33636 TTAGGTACTGTATAGATGAGA
1 TTAGGTACTGTACAGATGAAA
33657 TTA
1 TTA
33660 TTAGAACAAC
Statistics
Matches: 33, Mismatches: 8, Indels: 4
0.73 0.18 0.09
Matches are distributed among these distances:
19 15 0.45
21 18 0.55
ACGTcount: A:0.38, C:0.09, G:0.20, T:0.33
Consensus pattern (21 bp):
TTAGGTACTGTACAGATGAAA
Done.