Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01008735.1 Corchorus capsularis cultivar CVL-1 contig08756, 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: 64192
ACGTcount: A:0.33, C:0.18, G:0.18, T:0.30
Found at i:561 original size:2 final size:2
Alignment explanation
Indices: 549--594 Score: 76
Period size: 2 Copynumber: 23.5 Consensus size: 2
539 GACTATATCA
*
549 AT AT A- AT AT AT AT AT AT AT AT AT AA AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
590 AT AT A
1 AT AT A
595 AATCAAAACT
Statistics
Matches: 41, Mismatches: 2, Indels: 2
0.91 0.04 0.04
Matches are distributed among these distances:
1 1 0.02
2 40 0.98
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (2 bp):
AT
Found at i:923 original size:12 final size:14
Alignment explanation
Indices: 898--938 Score: 59
Period size: 14 Copynumber: 3.1 Consensus size: 14
888 TTTCTATGTG
*
898 TATCTGTCTCTGTC
1 TATCTATCTCTGTC
912 TATCT-T-TCTGTC
1 TATCTATCTCTGTC
924 TATCTATCTCTGTC
1 TATCTATCTCTGTC
938 T
1 T
939 GTAGCCTAGG
Statistics
Matches: 25, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
12 11 0.44
13 2 0.08
14 12 0.48
ACGTcount: A:0.10, C:0.27, G:0.10, T:0.54
Consensus pattern (14 bp):
TATCTATCTCTGTC
Found at i:6849 original size:13 final size:13
Alignment explanation
Indices: 6831--6855 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
6821 TATATTTATA
6831 TGATAATTATATT
1 TGATAATTATATT
6844 TGATAATTATAT
1 TGATAATTATAT
6856 AATTTTTCTA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.40, C:0.00, G:0.08, T:0.52
Consensus pattern (13 bp):
TGATAATTATATT
Found at i:7074 original size:15 final size:15
Alignment explanation
Indices: 7056--7084 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
7046 AGTTTTAAAA
7056 ATTCAGCACTTAATC
1 ATTCAGCACTTAATC
7071 ATTCAGCACTTAAT
1 ATTCAGCACTTAAT
7085 TTTCAGTTTT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.34, C:0.24, G:0.07, T:0.34
Consensus pattern (15 bp):
ATTCAGCACTTAATC
Found at i:7869 original size:2 final size:2
Alignment explanation
Indices: 7862--7889 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
7852 GTATGTAGTA
7862 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
7890 GTAAGAATAA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:10418 original size:17 final size:17
Alignment explanation
Indices: 10396--10431 Score: 72
Period size: 17 Copynumber: 2.1 Consensus size: 17
10386 TATAGTCGAT
10396 ATGAATCGAGGTATGGA
1 ATGAATCGAGGTATGGA
10413 ATGAATCGAGGTATGGA
1 ATGAATCGAGGTATGGA
10430 AT
1 AT
10432 TTGAGGATGT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.36, C:0.06, G:0.33, T:0.25
Consensus pattern (17 bp):
ATGAATCGAGGTATGGA
Found at i:12146 original size:73 final size:73
Alignment explanation
Indices: 12047--12192 Score: 238
Period size: 73 Copynumber: 2.0 Consensus size: 73
12037 GGTAACTTAA
*
12047 CAGTCGAAAAGATCAAAGAAAAGAAAAAAAACTGACATTGTGTTTTGAAGAGGAAAGTTGCGGCT
1 CAGTCGAAAAGATCAAAGAAAAGAAAAAAAACTGACATTGTGTTTTGAAGAGGAAAGCTGCGGCT
12112 GAGGTTTG
66 GAGGTTTG
* ** * *
12120 CAGTCGAAAAGATCAAAGGAAAGAAAAATCACTGACGTTGTGTTTTGAAGAGGAAAGCTGCGGTT
1 CAGTCGAAAAGATCAAAGAAAAGAAAAAAAACTGACATTGTGTTTTGAAGAGGAAAGCTGCGGCT
12185 GAGGTTTG
66 GAGGTTTG
12193 AGAGTTGGAG
Statistics
Matches: 67, Mismatches: 6, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
73 67 1.00
ACGTcount: A:0.38, C:0.10, G:0.29, T:0.23
Consensus pattern (73 bp):
CAGTCGAAAAGATCAAAGAAAAGAAAAAAAACTGACATTGTGTTTTGAAGAGGAAAGCTGCGGCT
GAGGTTTG
Found at i:12290 original size:22 final size:21
Alignment explanation
Indices: 12252--12292 Score: 55
Period size: 22 Copynumber: 1.9 Consensus size: 21
12242 ACCAAAATGA
*
12252 GGGATGGGTACCGAATAGAAG
1 GGGATGGGTACCAAATAGAAG
*
12273 GGGAGTGGGTACTAAATAGA
1 GGGA-TGGGTACCAAATAGA
12293 GGAAATCCAC
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 4 0.24
22 13 0.76
ACGTcount: A:0.34, C:0.07, G:0.41, T:0.17
Consensus pattern (21 bp):
GGGATGGGTACCAAATAGAAG
Found at i:12835 original size:87 final size:86
Alignment explanation
Indices: 12716--13033 Score: 512
Period size: 87 Copynumber: 3.7 Consensus size: 86
12706 AAATTGTTAA
12716 AATAATAATGAGAATATTTTCTAAATCTTGCCAAATTGTGGGAGATTTAGGAGATATTTTAAGAA
1 AATAATAATGAGAATATTTTCTAAATCTTGCCAAATTGTGGGAGATTTAGGAGATATTTTAAGAA
12781 ATAAATAAATAATAAAGATTG
66 ATAAATAAATAATAAAGATTG
* *
12802 AATAGTAATGAGAATATTTCTCTAAATCTTGCCAAATTGTGGGAGATTTAGGAAATATTTTAAGA
1 AATAATAATGAGAATATTT-TCTAAATCTTGCCAAATTGTGGGAGATTTAGGAGATATTTTAAGA
12867 AATAAATAAATAATAAAGATTG
65 AATAAATAAATAATAAAGATTG
* * * *
12889 AATAGTAATGAGAATATTTCTCCAAATCTTGCCAAATTGTGGGATATTTATGAGATATTTTAAGA
1 AATAATAATGAGAATATTT-TCTAAATCTTGCCAAATTGTGGGAGATTTAGGAGATATTTTAAG-
*
12954 AAATAAATAAATTATAAAGATAT-
64 AAATAAATAAATAATAAAGAT-TG
* *
12977 AATAATAATGAGAATATTTTCTAAATCTTGCCAAATTCTGGGAGATTTAGAAGATAT
1 AATAATAATGAGAATATTTTCTAAATCTTGCCAAATTGTGGGAGATTTAGGAGATAT
13034 AAAAAAGGAA
Statistics
Matches: 216, Mismatches: 13, Indels: 5
0.92 0.06 0.02
Matches are distributed among these distances:
86 18 0.08
87 159 0.74
88 38 0.18
89 1 0.00
ACGTcount: A:0.44, C:0.06, G:0.15, T:0.34
Consensus pattern (86 bp):
AATAATAATGAGAATATTTTCTAAATCTTGCCAAATTGTGGGAGATTTAGGAGATATTTTAAGAA
ATAAATAAATAATAAAGATTG
Found at i:16724 original size:21 final size:21
Alignment explanation
Indices: 16700--16740 Score: 73
Period size: 21 Copynumber: 2.0 Consensus size: 21
16690 ACTGAGAGAG
16700 TCACAAGAAGAAATGAGGCAT
1 TCACAAGAAGAAATGAGGCAT
*
16721 TCACAAGAAGAGATGAGGCA
1 TCACAAGAAGAAATGAGGCA
16741 AGAACAAGGC
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.46, C:0.15, G:0.27, T:0.12
Consensus pattern (21 bp):
TCACAAGAAGAAATGAGGCAT
Found at i:16747 original size:21 final size:21
Alignment explanation
Indices: 16702--16748 Score: 58
Period size: 21 Copynumber: 2.2 Consensus size: 21
16692 TGAGAGAGTC
***
16702 ACAAGAAGAAATGAGGCATTC
1 ACAAGAAGAAATGAGGCAAGA
*
16723 ACAAGAAGAGATGAGGCAAGA
1 ACAAGAAGAAATGAGGCAAGA
16744 ACAAG
1 ACAAG
16749 GCGTTATAAG
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.51, C:0.13, G:0.28, T:0.09
Consensus pattern (21 bp):
ACAAGAAGAAATGAGGCAAGA
Found at i:29943 original size:25 final size:25
Alignment explanation
Indices: 29886--29956 Score: 65
Period size: 24 Copynumber: 2.8 Consensus size: 25
29876 AACGGAAAAA
*
29886 GAAAAATTAATTTTTTTTTCAAAAATC
1 GAAAAAATAATTTTTTTTT--AAAATC
*
29913 GAAAAACCTAATTTTTTTTT-AAATC
1 GAAAAA-ATAATTTTTTTTTAAAATC
*
29938 -ACAAAAATCATTTTTTTTT
1 GA-AAAAATAATTTTTTTTT
29957 TTAGAAAAAT
Statistics
Matches: 39, Mismatches: 3, Indels: 7
0.80 0.06 0.14
Matches are distributed among these distances:
24 12 0.31
25 9 0.23
27 6 0.15
28 12 0.31
ACGTcount: A:0.41, C:0.10, G:0.03, T:0.46
Consensus pattern (25 bp):
GAAAAAATAATTTTTTTTTAAAATC
Found at i:32573 original size:18 final size:16
Alignment explanation
Indices: 32544--32578 Score: 52
Period size: 18 Copynumber: 2.1 Consensus size: 16
32534 TCTAAATCTA
32544 AAACAAAATATAAAGC
1 AAACAAAATATAAAGC
32560 AAACAATAATTATAAAGC
1 AAACAA-AA-TATAAAGC
32578 A
1 A
32579 TACTTCTTCT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 6 0.35
17 2 0.12
18 9 0.53
ACGTcount: A:0.66, C:0.11, G:0.06, T:0.17
Consensus pattern (16 bp):
AAACAAAATATAAAGC
Found at i:48825 original size:13 final size:13
Alignment explanation
Indices: 48809--48833 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
48799 GAACATCAGA
48809 AAACAAAAAGAAG
1 AAACAAAAAGAAG
48822 AAACAAAAAGAA
1 AAACAAAAAGAA
48834 AGGCATACCA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.80, C:0.08, G:0.12, T:0.00
Consensus pattern (13 bp):
AAACAAAAAGAAG
Found at i:51251 original size:11 final size:10
Alignment explanation
Indices: 51233--51266 Score: 50
Period size: 11 Copynumber: 3.2 Consensus size: 10
51223 AATAGTCTTC
51233 AAATCTTCAA
1 AAATCTTCAA
51243 AATATCTTCAA
1 AA-ATCTTCAA
51254 GAAATCTTCAA
1 -AAATCTTCAA
51265 AA
1 AA
51267 CACGAACTTC
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
10 4 0.18
11 16 0.73
12 2 0.09
ACGTcount: A:0.50, C:0.18, G:0.03, T:0.29
Consensus pattern (10 bp):
AAATCTTCAA
Found at i:54014 original size:9 final size:9
Alignment explanation
Indices: 54000--54024 Score: 50
Period size: 9 Copynumber: 2.8 Consensus size: 9
53990 GTCAATAGAC
54000 AAAAAAAGA
1 AAAAAAAGA
54009 AAAAAAAGA
1 AAAAAAAGA
54018 AAAAAAA
1 AAAAAAA
54025 AGATGATACC
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 16 1.00
ACGTcount: A:0.92, C:0.00, G:0.08, T:0.00
Consensus pattern (9 bp):
AAAAAAAGA
Found at i:61206 original size:2 final size:2
Alignment explanation
Indices: 61199--61226 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
61189 GATTTCTTCA
61199 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
61227 GATAAATAGA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Done.