Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01008624.1 Corchorus capsularis cultivar CVL-1 contig08645, 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: 33788
ACGTcount: A:0.34, C:0.17, G:0.16, T:0.33
Found at i:9130 original size:23 final size:23
Alignment explanation
Indices: 9104--9150 Score: 60
Period size: 23 Copynumber: 2.0 Consensus size: 23
9094 ATTACTGAGC
9104 CCGAAACGAT-TCCGAACCCGAAA
1 CCGAAACGATAT-CGAACCCGAAA
* *
9127 CCGAAAGGATATCGAACTCGAAA
1 CCGAAACGATATCGAACCCGAAA
9150 C
1 C
9151 GACTTGAATC
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
23 20 0.95
24 1 0.05
ACGTcount: A:0.40, C:0.30, G:0.19, T:0.11
Consensus pattern (23 bp):
CCGAAACGATATCGAACCCGAAA
Found at i:13396 original size:26 final size:26
Alignment explanation
Indices: 13362--13415 Score: 65
Period size: 26 Copynumber: 2.1 Consensus size: 26
13352 TGGATCTTCT
*
13362 TTCAATAATT-TCCCAATAACTGGGTC
1 TTCAATAATTCT-CCAATAACTGAGTC
* *
13388 TTCAGTAATTCTCCAATAATTGAGTC
1 TTCAATAATTCTCCAATAACTGAGTC
13414 TT
1 TT
13416 TTTTGAAAGA
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
26 23 0.96
27 1 0.04
ACGTcount: A:0.30, C:0.20, G:0.11, T:0.39
Consensus pattern (26 bp):
TTCAATAATTCTCCAATAACTGAGTC
Found at i:22124 original size:60 final size:60
Alignment explanation
Indices: 22044--22157 Score: 174
Period size: 60 Copynumber: 1.9 Consensus size: 60
22034 TAAGGGCATA
* * *
22044 ATCTTTTAATTTGGCTAAATAAGAGTCTAACGTTTGCCAAAATACTCAAATAAGTGTCCG
1 ATCTTCTAATTTGGCCAAATAAGAGCCTAACGTTTGCCAAAATACTCAAATAAGTGTCCG
* * *
22104 ATCTTCTAGTTTGGCCAAATAAGGGCCTAACGTTTGCCAAAATGCTCAAATAAG
1 ATCTTCTAATTTGGCCAAATAAGAGCCTAACGTTTGCCAAAATACTCAAATAAG
22158 GGCTTGGCAT
Statistics
Matches: 48, Mismatches: 6, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
60 48 1.00
ACGTcount: A:0.34, C:0.18, G:0.17, T:0.31
Consensus pattern (60 bp):
ATCTTCTAATTTGGCCAAATAAGAGCCTAACGTTTGCCAAAATACTCAAATAAGTGTCCG
Found at i:22351 original size:60 final size:58
Alignment explanation
Indices: 22204--22352 Score: 169
Period size: 56 Copynumber: 2.6 Consensus size: 58
22194 TGACGCCAGG
* *
22204 CCCTTATTTGAGCATTTTCGATAACGTTA--CCTTAATTGGCCAAATTAAAAAATTGG
1 CCCTTATTTGAGCATTTTCGATAACGTTAGGCCTTAATTGGCCAAATTAAAAAATCGA
** * * * *
22260 GTCTTATTTGAGCATTTTCGATAACGCTAGGCTCTTGATTGGTCAAATTAAAAGATCGAA
1 CCCTTATTTGAGCATTTTCGATAACGTTAGGC-CTTAATTGGCCAAATTAAAAAATCG-A
*
22320 CCCTTATTTGAGCATTTTGGCA-AACGTTAGGCC
1 CCCTTATTTGAGCATTTTCG-ATAACGTTAGGCC
22353 CTTATTTGAG
Statistics
Matches: 76, Mismatches: 12, Indels: 7
0.80 0.13 0.07
Matches are distributed among these distances:
56 26 0.34
58 1 0.01
59 22 0.29
60 26 0.34
61 1 0.01
ACGTcount: A:0.29, C:0.18, G:0.18, T:0.35
Consensus pattern (58 bp):
CCCTTATTTGAGCATTTTCGATAACGTTAGGCCTTAATTGGCCAAATTAAAAAATCGA
Found at i:26512 original size:179 final size:181
Alignment explanation
Indices: 26156--26517 Score: 613
Period size: 182 Copynumber: 2.0 Consensus size: 181
26146 TTCATGAAAG
** * *
26156 TTGTAGACCATGGAATTACCTTTAAATAGACACTTGAATCACCTTGATCGGTCGAATAGAAAAAA
1 TTGTAGACCATGGAATTACCTTTAAATAGACACCCGAATCACCTTGATCAGTCAAATAGAAAAAA
* * * *
26221 AATAAAAGAATTAAAGCCGAAACATTCAATCGTCCAACCCGTAATTGTAAGTGATTAAATAGTAT
66 AATAAAACAATTAAAGCCGAAACATTCAATCGTCCAACACATAATTGTAAGTGATTAAATAGCAT
26286 AAATTATAAAAGTATGAGGATCATTTAATAAATAATCCAACAAAAAAAATGA
131 AAATTATAAAAGTATGAGGATCATTTAATAAATAATCCAAC-AAAAAAATGA
26338 TTGTAGACCATGGAATTACCTTTAAATAGACACCCGAATCACCTTGATCAGTCAAATAG-AAAAA
1 TTGTAGACCATGGAATTACCTTTAAATAGACACCCGAATCACCTTGATCAGTCAAATAGAAAAAA
*
26402 AA-AAAACAATTAAAGCCGAAACATTCAATCGTCCAACATATAATTGTAAG-GATTAAATAGCAT
66 AATAAAACAATTAAAGCCGAAACATTCAATCGTCCAACACATAATTGTAAGTGATTAAATAGCAT
26465 AAATTATAAAAGTATGAGGATCATTTAATAAATAATCCAACAAAAAAATGA
131 AAATTATAAAAGTATGAGGATCATTTAATAAATAATCCAACAAAAAAATGA
26516 TT
1 TT
26518 TGTTTATGGA
Statistics
Matches: 171, Mismatches: 9, Indels: 4
0.93 0.05 0.02
Matches are distributed among these distances:
178 12 0.07
179 53 0.31
180 44 0.26
181 7 0.04
182 55 0.32
ACGTcount: A:0.47, C:0.14, G:0.13, T:0.26
Consensus pattern (181 bp):
TTGTAGACCATGGAATTACCTTTAAATAGACACCCGAATCACCTTGATCAGTCAAATAGAAAAAA
AATAAAACAATTAAAGCCGAAACATTCAATCGTCCAACACATAATTGTAAGTGATTAAATAGCAT
AAATTATAAAAGTATGAGGATCATTTAATAAATAATCCAACAAAAAAATGA
Found at i:28387 original size:13 final size:13
Alignment explanation
Indices: 28369--28396 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
28359 TTGAATATGT
28369 TTTTTCATAATTA
1 TTTTTCATAATTA
28382 TTTTTCATAATTA
1 TTTTTCATAATTA
28395 TT
1 TT
28397 CTTAAGACTT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.29, C:0.07, G:0.00, T:0.64
Consensus pattern (13 bp):
TTTTTCATAATTA
Found at i:28490 original size:23 final size:23
Alignment explanation
Indices: 28463--28528 Score: 118
Period size: 21 Copynumber: 3.0 Consensus size: 23
28453 TATACTTAAC
28463 TTAAAATTACAACTTAAATAAAG
1 TTAAAATTACAACTTAAATAAAG
28486 TTAAAA--ACAACTTAAATAAAG
1 TTAAAATTACAACTTAAATAAAG
28507 TTAAAATTACAACTTAAATAAA
1 TTAAAATTACAACTTAAATAAA
28529 TTTTGATGAA
Statistics
Matches: 41, Mismatches: 0, Indels: 4
0.91 0.00 0.09
Matches are distributed among these distances:
21 21 0.51
23 20 0.49
ACGTcount: A:0.59, C:0.09, G:0.03, T:0.29
Consensus pattern (23 bp):
TTAAAATTACAACTTAAATAAAG
Found at i:29966 original size:16 final size:17
Alignment explanation
Indices: 29932--29975 Score: 56
Period size: 16 Copynumber: 2.7 Consensus size: 17
29922 ATATGAACCT
29932 AAACCC-AAAAAAATCC
1 AAACCCGAAAAAAATCC
*
29948 AAACCCGAAAAAACT-C
1 AAACCCGAAAAAAATCC
*
29964 AAATCCGAAAAA
1 AAACCCGAAAAA
29976 TCTAAAACTC
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
16 18 0.72
17 7 0.28
ACGTcount: A:0.61, C:0.27, G:0.05, T:0.07
Consensus pattern (17 bp):
AAACCCGAAAAAAATCC
Found at i:30087 original size:16 final size:17
Alignment explanation
Indices: 30068--30100 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
30058 AAATAAAATT
*
30068 TTTAT-AATTTAAATAA
1 TTTATAAATATAAATAA
30084 TTTATAAATATAAATAA
1 TTTATAAATATAAATAA
30101 AACAAATTAA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 5 0.33
17 10 0.67
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (17 bp):
TTTATAAATATAAATAA
Found at i:30932 original size:30 final size:31
Alignment explanation
Indices: 30836--30933 Score: 81
Period size: 32 Copynumber: 3.1 Consensus size: 31
30826 ACCCAGTACA
* * * * *
30836 AACCAGAACCCGAATTAACCTGAGCCAAAATT
1 AACCCGAATCCGAATCAACCT-AACCAAATTT
* * *
30868 GACCTGAATCTGAATCAACCTAACCTAAATTT
1 AACCCGAATCCGAATCAACCTAACC-AAATTT
* *
30900 AACCCGAATCCGAATCAACCTGACC-CATTT
1 AACCCGAATCCGAATCAACCTAACCAAATTT
30930 AACC
1 AACC
30934 TGACTTAACT
Statistics
Matches: 53, Mismatches: 12, Indels: 4
0.77 0.17 0.06
Matches are distributed among these distances:
30 8 0.15
31 3 0.06
32 42 0.79
ACGTcount: A:0.39, C:0.31, G:0.10, T:0.20
Consensus pattern (31 bp):
AACCCGAATCCGAATCAACCTAACCAAATTT
Found at i:32895 original size:25 final size:25
Alignment explanation
Indices: 32867--32957 Score: 146
Period size: 25 Copynumber: 3.6 Consensus size: 25
32857 CGCTCATGTT
* *
32867 CTTGCGTTTGGCAAACGAGCCTATG
1 CTTGCGTTTAGCAAACGAGCCTGTG
32892 CTTGCGTTTAGCAAACGAGCCTGTG
1 CTTGCGTTTAGCAAACGAGCCTGTG
*
32917 CTTGCGTTTAGCAAACAAGCCTGTG
1 CTTGCGTTTAGCAAACGAGCCTGTG
*
32942 CTTGCGTTTAGAAAAC
1 CTTGCGTTTAGCAAAC
32958 ACATAGGCTA
Statistics
Matches: 62, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
25 62 1.00
ACGTcount: A:0.23, C:0.23, G:0.25, T:0.29
Consensus pattern (25 bp):
CTTGCGTTTAGCAAACGAGCCTGTG
Done.