Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01016370.1 Corchorus capsularis cultivar CVL-1 contig16391, 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: 29646
ACGTcount: A:0.31, C:0.19, G:0.17, T:0.32
Found at i:3444 original size:7 final size:6
Alignment explanation
Indices: 3417--3447 Score: 53
Period size: 6 Copynumber: 5.0 Consensus size: 6
3407 GCAAAGCAAT
3417 TCTAAA TCTAAA TCTAAA TCTAAAA TCTAAA
1 TCTAAA TCTAAA TCTAAA TCT-AAA TCTAAA
3448 GCAAATTAAT
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
6 18 0.75
7 6 0.25
ACGTcount: A:0.52, C:0.16, G:0.00, T:0.32
Consensus pattern (6 bp):
TCTAAA
Found at i:3460 original size:13 final size:13
Alignment explanation
Indices: 3444--3478 Score: 70
Period size: 13 Copynumber: 2.7 Consensus size: 13
3434 ATCTAAAATC
3444 TAAAGCAAATTAA
1 TAAAGCAAATTAA
3457 TAAAGCAAATTAA
1 TAAAGCAAATTAA
3470 TAAAGCAAA
1 TAAAGCAAA
3479 CAATAATTAT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 22 1.00
ACGTcount: A:0.63, C:0.09, G:0.09, T:0.20
Consensus pattern (13 bp):
TAAAGCAAATTAA
Found at i:12064 original size:13 final size:12
Alignment explanation
Indices: 11988--12078 Score: 51
Period size: 13 Copynumber: 7.2 Consensus size: 12
11978 AACTGCCCAA
11988 GCCTGGCCTAGGC
1 GCCTGGCC-AGGC
* *
12001 GCCAGGCCAAGC
1 GCCTGGCCAGGC
*
12013 G-CTGGCCCGCGC
1 GCCTGGCCAG-GC
12025 GCCTGGCCTAGGC
1 GCCTGGCC-AGGC
* *
12038 -ACTGGCCCGCGC
1 GCCTGGCCAG-GC
12050 GCCTGGCCTAGGC
1 GCCTGGCC-AGGC
* *
12063 GCTTGGGCCATGC
1 GCCT-GGCCAGGC
12076 GCC
1 GCC
12079 CTGCTGGCCC
Statistics
Matches: 58, Mismatches: 13, Indels: 14
0.68 0.15 0.16
Matches are distributed among these distances:
11 6 0.10
12 15 0.26
13 31 0.53
14 6 0.10
ACGTcount: A:0.09, C:0.42, G:0.37, T:0.12
Consensus pattern (12 bp):
GCCTGGCCAGGC
Found at i:12081 original size:27 final size:25
Alignment explanation
Indices: 12014--12062 Score: 98
Period size: 25 Copynumber: 2.0 Consensus size: 25
12004 AGGCCAAGCG
12014 CTGGCCCGCGCGCCTGGCCTAGGCA
1 CTGGCCCGCGCGCCTGGCCTAGGCA
12039 CTGGCCCGCGCGCCTGGCCTAGGC
1 CTGGCCCGCGCGCCTGGCCTAGGC
12063 GCTTGGGCCA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 24 1.00
ACGTcount: A:0.06, C:0.45, G:0.37, T:0.12
Consensus pattern (25 bp):
CTGGCCCGCGCGCCTGGCCTAGGCA
Found at i:16838 original size:30 final size:30
Alignment explanation
Indices: 16804--16860 Score: 98
Period size: 30 Copynumber: 1.9 Consensus size: 30
16794 TTATTTTGGC
16804 TACGGGTTTGTCGGGCCAT-CATAGGATGGT
1 TACGGGTTTGTCGGGCC-TGCATAGGATGGT
16834 TACGGGTTTGTCGGGCCTGCATAGGAT
1 TACGGGTTTGTCGGGCCTGCATAGGAT
16861 TGTTTAAGGT
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
29 1 0.04
30 25 0.96
ACGTcount: A:0.16, C:0.18, G:0.37, T:0.30
Consensus pattern (30 bp):
TACGGGTTTGTCGGGCCTGCATAGGATGGT
Found at i:18147 original size:28 final size:28
Alignment explanation
Indices: 18115--18184 Score: 104
Period size: 28 Copynumber: 2.5 Consensus size: 28
18105 ATAATTACTT
18115 TATTTTTACTATATTTGGATATATTCAA
1 TATTTTTACTATATTTGGATATATTCAA
*
18143 TATTTTTACTATACTTGGATATATTCAA
1 TATTTTTACTATATTTGGATATATTCAA
* * *
18171 AAATTTTAATATAT
1 TATTTTTACTATAT
18185 AGTTTTATTC
Statistics
Matches: 37, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
28 37 1.00
ACGTcount: A:0.36, C:0.07, G:0.06, T:0.51
Consensus pattern (28 bp):
TATTTTTACTATATTTGGATATATTCAA
Found at i:19916 original size:40 final size:41
Alignment explanation
Indices: 19860--19936 Score: 138
Period size: 40 Copynumber: 1.9 Consensus size: 41
19850 GAGTATATAT
*
19860 ATCCTTTTAAAAATACATTCTTAAATATCCTTAAAAAGTAA
1 ATCCTTTTAAAAATACATTCTTAAATATCCATAAAAAGTAA
19901 ATCC-TTTAAAAATACATTCTTAAATATCCATAAAAA
1 ATCCTTTTAAAAATACATTCTTAAATATCCATAAAAA
19937 ACACATCGCT
Statistics
Matches: 35, Mismatches: 1, Indels: 1
0.95 0.03 0.03
Matches are distributed among these distances:
40 31 0.89
41 4 0.11
ACGTcount: A:0.48, C:0.16, G:0.01, T:0.35
Consensus pattern (41 bp):
ATCCTTTTAAAAATACATTCTTAAATATCCATAAAAAGTAA
Found at i:20404 original size:32 final size:33
Alignment explanation
Indices: 20304--20449 Score: 172
Period size: 33 Copynumber: 4.5 Consensus size: 33
20294 GCTCAAGCCA
20304 CCCCACTGGGGCGGCTTCACCATGGGCAGGCCG
1 CCCCACTGGGGCGGCTTCACCATGGGCAGGCCG
**
20337 CCCCACTGGGGCGGCTTCACCATGAACAGGCCG
1 CCCCACTGGGGCGGCTTCACCATGGGCAGGCCG
* *
20370 CCCCACTGGAGCGGCTTCGCCA-GGGCAGGCCG
1 CCCCACTGGGGCGGCTTCACCATGGGCAGGCCG
** * *
20402 CCCTC-CTGGGGCGGCTTTGCCA-CGGCAGGTCG
1 CCC-CACTGGGGCGGCTTCACCATGGGCAGGCCG
**
20434 CCCCGGTGGGGCGGCT
1 CCCCACTGGGGCGGCT
20450 CGACTACTTT
Statistics
Matches: 100, Mismatches: 11, Indels: 5
0.86 0.09 0.04
Matches are distributed among these distances:
31 1 0.01
32 47 0.47
33 52 0.52
ACGTcount: A:0.11, C:0.39, G:0.37, T:0.13
Consensus pattern (33 bp):
CCCCACTGGGGCGGCTTCACCATGGGCAGGCCG
Found at i:22176 original size:4 final size:4
Alignment explanation
Indices: 22169--22209 Score: 82
Period size: 4 Copynumber: 10.2 Consensus size: 4
22159 ATATATATAT
22169 ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATAG A
1 ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATAG A
22210 GGGAATTACC
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 37 1.00
ACGTcount: A:0.51, C:0.00, G:0.24, T:0.24
Consensus pattern (4 bp):
ATAG
Found at i:22961 original size:30 final size:31
Alignment explanation
Indices: 22926--22998 Score: 89
Period size: 30 Copynumber: 2.4 Consensus size: 31
22916 AGGAGATGGG
22926 ATCGCACCAAAGACAT-CAACAG-ATGGAGGA
1 ATCGCACCAAAGA-ATGCAACAGAATGGAGGA
* **
22956 ATCGCACCAAAG-ATGCCATTGAATGGAGGA
1 ATCGCACCAAAGAATGCAACAGAATGGAGGA
22986 ATCGCACCAAAGA
1 ATCGCACCAAAGA
22999 TGCCATTTGA
Statistics
Matches: 37, Mismatches: 3, Indels: 5
0.82 0.07 0.11
Matches are distributed among these distances:
28 2 0.05
29 3 0.08
30 32 0.86
ACGTcount: A:0.41, C:0.23, G:0.23, T:0.12
Consensus pattern (31 bp):
ATCGCACCAAAGAATGCAACAGAATGGAGGA
Found at i:22999 original size:30 final size:30
Alignment explanation
Indices: 22948--23005 Score: 116
Period size: 30 Copynumber: 1.9 Consensus size: 30
22938 ACATCAACAG
22948 ATGGAGGAATCGCACCAAAGATGCCATTGA
1 ATGGAGGAATCGCACCAAAGATGCCATTGA
22978 ATGGAGGAATCGCACCAAAGATGCCATT
1 ATGGAGGAATCGCACCAAAGATGCCATT
23006 TGATCCTTTG
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 28 1.00
ACGTcount: A:0.36, C:0.21, G:0.26, T:0.17
Consensus pattern (30 bp):
ATGGAGGAATCGCACCAAAGATGCCATTGA
Found at i:27409 original size:10 final size:10
Alignment explanation
Indices: 27396--27421 Score: 52
Period size: 10 Copynumber: 2.6 Consensus size: 10
27386 AAATCTCAAT
27396 ATATCCGTAA
1 ATATCCGTAA
27406 ATATCCGTAA
1 ATATCCGTAA
27416 ATATCC
1 ATATCC
27422 ATATTAAATT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 16 1.00
ACGTcount: A:0.38, C:0.23, G:0.08, T:0.31
Consensus pattern (10 bp):
ATATCCGTAA
Found at i:28035 original size:20 final size:22
Alignment explanation
Indices: 28010--28063 Score: 67
Period size: 24 Copynumber: 2.5 Consensus size: 22
28000 TTTTGAATTT
28010 CATCGATA-CCA-CGATATATC
1 CATCGATATCCATCGATATATC
28030 CATCGATATATCCATCGATATATC
1 CATCG--ATATCCATCGATATATC
*
28054 CGTCGATATC
1 CATCGATATC
28064 TGTATTAAAC
Statistics
Matches: 29, Mismatches: 1, Indels: 6
0.81 0.03 0.17
Matches are distributed among these distances:
20 5 0.17
22 8 0.28
23 3 0.10
24 13 0.45
ACGTcount: A:0.31, C:0.28, G:0.11, T:0.30
Consensus pattern (22 bp):
CATCGATATCCATCGATATATC
Found at i:28038 original size:12 final size:12
Alignment explanation
Indices: 28021--28062 Score: 75
Period size: 12 Copynumber: 3.5 Consensus size: 12
28011 ATCGATACCA
28021 CGATATATCCAT
1 CGATATATCCAT
28033 CGATATATCCAT
1 CGATATATCCAT
*
28045 CGATATATCCGT
1 CGATATATCCAT
28057 CGATAT
1 CGATAT
28063 CTGTATTAAA
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
12 29 1.00
ACGTcount: A:0.31, C:0.24, G:0.12, T:0.33
Consensus pattern (12 bp):
CGATATATCCAT
Found at i:28604 original size:32 final size:32
Alignment explanation
Indices: 28550--28613 Score: 76
Period size: 32 Copynumber: 2.0 Consensus size: 32
28540 GGGTATCATG
*** *
28550 TTCCCATTAGTTGTATTGGTCATAGT-CATATC
1 TTCCCATTAGTCACATTAGTCAT-GTACATATC
28582 TTCCCATTAGTCACATTAGTCATGTACATATC
1 TTCCCATTAGTCACATTAGTCATGTACATATC
28614 CATTTTCATT
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
31 2 0.07
32 25 0.93
ACGTcount: A:0.25, C:0.22, G:0.12, T:0.41
Consensus pattern (32 bp):
TTCCCATTAGTCACATTAGTCATGTACATATC
Done.