Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01014164.1 Corchorus capsularis cultivar CVL-1 contig14185, 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: 17393
ACGTcount: A:0.32, C:0.15, G:0.17, T:0.35
Found at i:3456 original size:11 final size:11
Alignment explanation
Indices: 3438--3475 Score: 51
Period size: 11 Copynumber: 3.5 Consensus size: 11
3428 ATTTGAACTG
*
3438 AAAGAAAAAAG
1 AAAGAAAAAAA
3449 AAA-AAAAAAA
1 AAAGAAAAAAA
*
3459 AAAGAAAAGAA
1 AAAGAAAAAAA
3470 AAAGAA
1 AAAGAA
3476 TTTGAAACTG
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
10 9 0.38
11 15 0.62
ACGTcount: A:0.87, C:0.00, G:0.13, T:0.00
Consensus pattern (11 bp):
AAAGAAAAAAA
Found at i:3461 original size:14 final size:15
Alignment explanation
Indices: 3437--3472 Score: 56
Period size: 14 Copynumber: 2.4 Consensus size: 15
3427 TATTTGAACT
3437 GAAAGAAAAAAGAAAA
1 GAAA-AAAAAAGAAAA
3453 -AAAAAAAAAGAAAA
1 GAAAAAAAAAGAAAA
3467 GAAAAA
1 GAAAAA
3473 GAATTTGAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
14 11 0.58
15 8 0.42
ACGTcount: A:0.86, C:0.00, G:0.14, T:0.00
Consensus pattern (15 bp):
GAAAAAAAAAGAAAA
Found at i:5118 original size:2 final size:2
Alignment explanation
Indices: 5113--5142 Score: 53
Period size: 2 Copynumber: 15.5 Consensus size: 2
5103 AAAAAGGATT
5113 TA TA TA TA TA TA TA TA TA TA -A TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
5143 GAAATTGAGA
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
1 1 0.04
2 26 0.96
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:6158 original size:2 final size:2
Alignment explanation
Indices: 6153--6177 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
6143 CACTAACCTA
6153 AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT A
6178 CTATTCTACT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:6887 original size:45 final size:45
Alignment explanation
Indices: 6838--6934 Score: 153
Period size: 45 Copynumber: 2.2 Consensus size: 45
6828 AGCAACAAAT
* *
6838 AATATTAGTTTTATTTTGATGAATTTCTTAGAGATGAAG-GAGTAG
1 AATATTAGTTTTATTTTGATGAATTACCTAGAGATG-AGTGAGTAG
6883 AATATTAGTTTTATTTTGATGAATTACCTAGAGATGAGTGAGTAG
1 AATATTAGTTTTATTTTGATGAATTACCTAGAGATGAGTGAGTAG
6928 AAT-TTAG
1 AATATTAG
6935 GTAATACATT
Statistics
Matches: 49, Mismatches: 2, Indels: 3
0.91 0.04 0.06
Matches are distributed among these distances:
44 6 0.12
45 43 0.88
ACGTcount: A:0.34, C:0.03, G:0.22, T:0.41
Consensus pattern (45 bp):
AATATTAGTTTTATTTTGATGAATTACCTAGAGATGAGTGAGTAG
Found at i:8581 original size:3 final size:3
Alignment explanation
Indices: 8573--8604 Score: 64
Period size: 3 Copynumber: 10.7 Consensus size: 3
8563 TCCTAAAAGT
8573 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TA
8605 TGTCATGAAA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 29 1.00
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
TAA
Found at i:8658 original size:3 final size:3
Alignment explanation
Indices: 8650--8684 Score: 70
Period size: 3 Copynumber: 11.7 Consensus size: 3
8640 ACCCATATAG
8650 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TA
8685 TGTCATGAAA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 32 1.00
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
TAA
Found at i:8917 original size:13 final size:11
Alignment explanation
Indices: 8881--8927 Score: 53
Period size: 11 Copynumber: 4.5 Consensus size: 11
8871 TAATATATAT
*
8881 ATATATA-TAT
1 ATATATACTAC
*
8891 ATATATA-TAT
1 ATATATACTAC
*
8901 ATATATGCTAC
1 ATATATACTAC
8912 ATATATACTAC
1 ATATATACTAC
8923 ATATA
1 ATATA
8928 AAAGTACGAA
Statistics
Matches: 33, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
10 16 0.48
11 17 0.52
ACGTcount: A:0.47, C:0.09, G:0.02, T:0.43
Consensus pattern (11 bp):
ATATATACTAC
Found at i:8918 original size:2 final size:2
Alignment explanation
Indices: 8873--8906 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
8863 AGTAAGGATA
8873 AT AT 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 AT AT
8907 GCTACATATA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:10237 original size:121 final size:121
Alignment explanation
Indices: 10018--10273 Score: 395
Period size: 121 Copynumber: 2.1 Consensus size: 121
10008 TCCAACGGAT
* *
10018 TTTCATACGGAAATAAGGTAAAAAAACAATATGCGATTTTCTTAGCTTTTTTTGTTGCAAAATGT
1 TTTCCTACGGAAATAAGGTAAAAAAACAATATGCGATTTGCTTAGCTTTTTTTGTTGCAAAATGT
* * *
10083 GTTGCAATTTGCAACCAATGTCGTTGCATGAAAATCCGTAGGAAGTTGTCACCGAA
66 GTTGCAATTTGCAACCAACGCCATTGCATGAAAATCCGTAGGAAGTTGTCACCGAA
** * *
10139 TTTCCTACGGAAATAAGGTAAAAAAATTATATGTGATTTGCTTGGCTTTTTTTGTTGCAAAATGT
1 TTTCCTACGGAAATAAGGTAAAAAAACAATATGCGATTTGCTTAGCTTTTTTTGTTGCAAAATGT
** *
10204 GTTGCAATTTGCAACCAACGCCATTGTGTGAAAATCTGTAGGAAGTTGTCACCGAA
66 GTTGCAATTTGCAACCAACGCCATTGCATGAAAATCCGTAGGAAGTTGTCACCGAA
*
10260 TTTCCTTCGGAAAT
1 TTTCCTACGGAAAT
10274 TTTGAACGGA
Statistics
Matches: 122, Mismatches: 13, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
121 122 1.00
ACGTcount: A:0.31, C:0.15, G:0.20, T:0.34
Consensus pattern (121 bp):
TTTCCTACGGAAATAAGGTAAAAAAACAATATGCGATTTGCTTAGCTTTTTTTGTTGCAAAATGT
GTTGCAATTTGCAACCAACGCCATTGCATGAAAATCCGTAGGAAGTTGTCACCGAA
Found at i:14535 original size:32 final size:31
Alignment explanation
Indices: 14488--14549 Score: 97
Period size: 32 Copynumber: 2.0 Consensus size: 31
14478 GCACTAGTTA
*
14488 TATGGTATGGTGTAAAAACCCATTTTGATTG
1 TATGCTATGGTGTAAAAACCCATTTTGATTG
*
14519 TATGCTATGGTTGTAAAAACTCATTTTGATT
1 TATGCTATGG-TGTAAAAACCCATTTTGATT
14550 ATCAATATAT
Statistics
Matches: 28, Mismatches: 2, Indels: 1
0.90 0.06 0.03
Matches are distributed among these distances:
31 9 0.32
32 19 0.68
ACGTcount: A:0.29, C:0.10, G:0.19, T:0.42
Consensus pattern (31 bp):
TATGCTATGGTGTAAAAACCCATTTTGATTG
Found at i:15270 original size:22 final size:23
Alignment explanation
Indices: 15193--15365 Score: 101
Period size: 22 Copynumber: 7.7 Consensus size: 23
15183 CACTGGGAGG
* * *
15193 TTATCAAAA-ATCATAGCAA-GA
1 TTATCAAAATTTCATAGAAAGGT
15214 TTA-CAAAATTTCATAGAAAGGT
1 TTATCAAAATTTCATAGAAAGGT
* **
15236 TTATTAAAATTTCATAGTTAGG-
1 TTATCAAAATTTCATAGAAAGGT
* * *
15258 TTATCAAAGTTTCATATAGA-GT
1 TTATCAAAATTTCATAGAAAGGT
* * *
15280 TTATCATAATTTCATATATAA-AT
1 TTATCAAAATTTCATAGA-AAGGT
***
15303 TT-TCAAAATTTCATAGCGTGGT
1 TTATCAAAATTTCATAGAAAGGT
* *
15325 TT-TCAAAATTTAATAGATAGGAT
1 TTATCAAAATTTCATAGAAAGG-T
15348 AGTTATCAAAATTTCATA
1 --TTATCAAAATTTCATA
15366 AAAATATTCA
Statistics
Matches: 116, Mismatches: 26, Indels: 15
0.74 0.17 0.10
Matches are distributed among these distances:
20 5 0.04
21 12 0.10
22 65 0.56
23 20 0.17
25 2 0.02
26 12 0.10
ACGTcount: A:0.41, C:0.09, G:0.11, T:0.39
Consensus pattern (23 bp):
TTATCAAAATTTCATAGAAAGGT
Found at i:15404 original size:36 final size:36
Alignment explanation
Indices: 15364--15440 Score: 154
Period size: 36 Copynumber: 2.1 Consensus size: 36
15354 CAAAATTTCA
15364 TAAAAATATTCAATCAAAACATTGGGTCACGAAAGC
1 TAAAAATATTCAATCAAAACATTGGGTCACGAAAGC
15400 TAAAAATATTCAATCAAAACATTGGGTCACGAAAGC
1 TAAAAATATTCAATCAAAACATTGGGTCACGAAAGC
15436 TAAAA
1 TAAAA
15441 CTAATATAAT
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
36 41 1.00
ACGTcount: A:0.49, C:0.16, G:0.13, T:0.22
Consensus pattern (36 bp):
TAAAAATATTCAATCAAAACATTGGGTCACGAAAGC
Found at i:15456 original size:2 final size:2
Alignment explanation
Indices: 15444--15473 Score: 53
Period size: 2 Copynumber: 15.5 Consensus size: 2
15434 GCTAAAACTA
15444 AT AT A- AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
15474 CTGTACATAA
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
1 1 0.04
2 26 0.96
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:16199 original size:12 final size:13
Alignment explanation
Indices: 16174--16233 Score: 56
Period size: 13 Copynumber: 4.7 Consensus size: 13
16164 GTCTGTTCAG
16174 TATTTTA-T-AAT
1 TATTTTATTAAAT
16185 TA-TTTATTAAAT
1 TATTTTATTAAAT
16197 TATTTTATTAAAT
1 TATTTTATTAAAT
*
16210 TCAATATT-TTATAAT
1 T--ATTTTATTA-AAT
16225 TATTTTATT
1 TATTTTATT
16234 TTTACCATTT
Statistics
Matches: 40, Mismatches: 2, Indels: 11
0.75 0.04 0.21
Matches are distributed among these distances:
10 4 0.10
11 3 0.08
12 5 0.12
13 15 0.38
14 5 0.12
15 8 0.20
ACGTcount: A:0.37, C:0.02, G:0.00, T:0.62
Consensus pattern (13 bp):
TATTTTATTAAAT
Found at i:17027 original size:5 final size:6
Alignment explanation
Indices: 16987--17025 Score: 62
Period size: 6 Copynumber: 6.7 Consensus size: 6
16977 TATACTTAAG
*
16987 ATTTTG ATTTTA ATTTTA ATTTTA ATTTTA A-TTTA ATTT
1 ATTTTA ATTTTA ATTTTA ATTTTA ATTTTA ATTTTA ATTT
17026 AAATATATTA
Statistics
Matches: 31, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
5 5 0.16
6 26 0.84
ACGTcount: A:0.31, C:0.00, G:0.03, T:0.67
Consensus pattern (6 bp):
ATTTTA
Done.