Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01011943.1 Corchorus olitorius cultivar O-4 contig11976, 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: 37173
ACGTcount: A:0.29, C:0.19, G:0.19, T:0.33
Found at i:2925 original size:6 final size:6
Alignment explanation
Indices: 2914--2961 Score: 53
Period size: 6 Copynumber: 8.2 Consensus size: 6
2904 ACAACATAAC
* * * *
2914 AAAACA AAAACA AAAACG AAATC- GAAACA AAAACA AAAACG AAAACA
1 AAAACA AAAACA AAAACA AAAACA AAAACA AAAACA AAAACA AAAACA
2961 A
1 A
2962 TGTCAAACGA
Statistics
Matches: 34, Mismatches: 7, Indels: 2
0.79 0.16 0.05
Matches are distributed among these distances:
5 3 0.09
6 31 0.91
ACGTcount: A:0.75, C:0.17, G:0.06, T:0.02
Consensus pattern (6 bp):
AAAACA
Found at i:2943 original size:17 final size:17
Alignment explanation
Indices: 2921--2957 Score: 56
Period size: 17 Copynumber: 2.2 Consensus size: 17
2911 AACAAAACAA
* *
2921 AAACAAAAACGAAATCG
1 AAACAAAAACAAAAACG
2938 AAACAAAAACAAAAACG
1 AAACAAAAACAAAAACG
2955 AAA
1 AAA
2958 ACAATGTCAA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.73, C:0.16, G:0.08, T:0.03
Consensus pattern (17 bp):
AAACAAAAACAAAAACG
Found at i:4779 original size:17 final size:16
Alignment explanation
Indices: 4725--4775 Score: 75
Period size: 17 Copynumber: 3.1 Consensus size: 16
4715 GATCACCCCC
*
4725 AGATCACTAGTGATCTA
1 AGATCACCAGTGATC-A
4742 AGATCACCAGTGATGCA
1 AGATCACCAGTGAT-CA
4759 AGATCACCAGTGATCA
1 AGATCACCAGTGATCA
4775 A
1 A
4776 AGATTACATG
Statistics
Matches: 32, Mismatches: 1, Indels: 3
0.89 0.03 0.08
Matches are distributed among these distances:
16 3 0.09
17 28 0.88
18 1 0.03
ACGTcount: A:0.37, C:0.22, G:0.20, T:0.22
Consensus pattern (16 bp):
AGATCACCAGTGATCA
Found at i:6854 original size:21 final size:23
Alignment explanation
Indices: 6805--6854 Score: 59
Period size: 23 Copynumber: 2.3 Consensus size: 23
6795 TTTTGGTCAA
* *
6805 CTTATTAAGTTTTTTCACCTAAC
1 CTTATTAAGATTTTTCACATAAC
*
6828 CTTATTAAGATTTTT-A-ATAAT
1 CTTATTAAGATTTTTCACATAAC
6849 CTTATT
1 CTTATT
6855 GTGAATTTCA
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
21 9 0.38
22 1 0.04
23 14 0.58
ACGTcount: A:0.30, C:0.14, G:0.04, T:0.52
Consensus pattern (23 bp):
CTTATTAAGATTTTTCACATAAC
Found at i:6979 original size:20 final size:19
Alignment explanation
Indices: 6950--6991 Score: 59
Period size: 20 Copynumber: 2.2 Consensus size: 19
6940 ATAACCTTGA
6950 TAATTTGTAGTAA-TATTAT
1 TAATTTGTAGTAACT-TTAT
6969 TAATATTGTAGTAACTTTAT
1 TAAT-TTGTAGTAACTTTAT
6989 TAA
1 TAA
6992 ACCTTTTAGT
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
19 4 0.19
20 16 0.76
21 1 0.05
ACGTcount: A:0.38, C:0.02, G:0.10, T:0.50
Consensus pattern (19 bp):
TAATTTGTAGTAACTTTAT
Found at i:8616 original size:21 final size:21
Alignment explanation
Indices: 8571--8610 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
8561 CTTTTACCCG
8571 TTAAGTTTTATAGTAACTTCT
1 TTAAGTTTTATAGTAACTTCT
* *
8592 TTAAGTTTTTTAGTGACTT
1 TTAAGTTTTATAGTAACTT
8611 TATTAATATT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.25, C:0.07, G:0.12, T:0.55
Consensus pattern (21 bp):
TTAAGTTTTATAGTAACTTCT
Found at i:8821 original size:20 final size:20
Alignment explanation
Indices: 8787--8826 Score: 53
Period size: 20 Copynumber: 2.0 Consensus size: 20
8777 TCTTATAAAC
* * *
8787 TTTTTAATAACCCTATTTAA
1 TTTTTAAGAAACCTAATTAA
8807 TTTTTAAGAAACCTAATTAA
1 TTTTTAAGAAACCTAATTAA
8827 GGGTTTTTTA
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.40, C:0.12, G:0.03, T:0.45
Consensus pattern (20 bp):
TTTTTAAGAAACCTAATTAA
Found at i:10404 original size:201 final size:201
Alignment explanation
Indices: 10076--10840 Score: 1093
Period size: 201 Copynumber: 3.8 Consensus size: 201
10066 CAAAAAAATT
* * * * * * *
10076 CCCTAAGGGGA-AACATGTCAACCCTTAAACCTCGCGCATGCAGTCTACTAAACTCCACTGACGG
1 CCCT-AGGGGACAA-ATGTCGACTCTTAAACCCCGCACGTGCAGTATGCTAAACTCCACTGACGG
* * * *
10140 TGTATTGTATAATTTTTTTTTTTGGATTATTATACAATACATTGTCAGTGTAAATTTTGGACTCC
64 TGTATTGTATAATTTTTCTTATAGGATTATTATACAATACACTGTCAGTGTAAATTTTGGACTCC
10205 ATAAGCGGGTTAAGAAGTTGACACATACCCCATTTCATAATTAATTAAATATATTTAATATTAAT
129 ATAAGCGGGTTAAGAAGTTGACACATACCCCATTTCATAATTAATTAAATATATTTAATATTAAT
10270 ACATATTC
194 ACATATTC
* * * *
10278 CCCTAGGGGACAAATGTCGATTCTTAAACCCCGCACGTGCAGTCTGCTAAACTCTACTGACAGTG
1 CCCTAGGGGACAAATGTCGACTCTTAAACCCCGCACGTGCAGTATGCTAAACTCCACTGACGGTG
*
10343 TATTGTATAATTTTTCTTATAGGATTATTATACAACACACTGTCAGTGTAAATTTTGGACTCCAT
66 TATTGTATAATTTTTCTTATAGGATTATTATACAATACACTGTCAGTGTAAATTTTGGACTCCAT
** *
10408 AAGTAGGCTAAGAAGTTGACACATACCCCATTTCATAATTAATTAAATATATTTAATATTAATAC
131 AAGCGGGTTAAGAAGTTGACACATACCCCATTTCATAATTAATTAAATATATTTAATATTAATAC
10473 ATATTC
196 ATATTC
* * * * * * *
10479 CCCTAAGGGACATATGTCGGCCCTTAAACCCTGCATGTGTAGTATGCTAAACTCCACTGACGGTG
1 CCCTAGGGGACAAATGTCGACTCTTAAACCCCGCACGTGCAGTATGCTAAACTCCACTGACGGTG
* *
10544 TATTGTATAACTTTTCTTATAGGATTATTATACAATACACTATCAGTGTAAATTTTGGACTCCAT
66 TATTGTATAATTTTTCTTATAGGATTATTATACAATACACTGTCAGTGTAAATTTTGGACTCCAT
** *
10609 AAGCGGGTTAAGAAGTTGACACATACCCCATTTCATAATTAAGAAAATATATTTGATATTAATAC
131 AAGCGGGTTAAGAAGTTGACACATACCCCATTTCATAATTAATTAAATATATTTAATATTAATAC
10674 ATATT-
196 ATATTC
* * ** * *
10679 CCCTAAGGGGACACATGTCAACTCTTAAACCTTGCATGTGCAGTATGCTAAACTCTACTGACGGT
1 CCCT-AGGGGACAAATGTCGACTCTTAAACCCCGCACGTGCAGTATGCTAAACTCCACTGACGGT
* * * * *
10744 GTATTGTATACTTTTTCTTATAGGATTATTATACAATTCACTGTCAGTGTAAAGTTTAGACTCTA
65 GTATTGTATAATTTTTCTTATAGGATTATTATACAATACACTGTCAGTGTAAATTTTGGACTCCA
* *
10809 TAAACGGGTTAAGAGGTTGACACATACCCCAT
130 TAAGCGGGTTAAGAAGTTGACACATACCCCAT
10841 ATTATTTATT
Statistics
Matches: 507, Mismatches: 54, Indels: 5
0.90 0.10 0.01
Matches are distributed among these distances:
200 4 0.01
201 497 0.98
202 6 0.01
ACGTcount: A:0.32, C:0.19, G:0.15, T:0.34
Consensus pattern (201 bp):
CCCTAGGGGACAAATGTCGACTCTTAAACCCCGCACGTGCAGTATGCTAAACTCCACTGACGGTG
TATTGTATAATTTTTCTTATAGGATTATTATACAATACACTGTCAGTGTAAATTTTGGACTCCAT
AAGCGGGTTAAGAAGTTGACACATACCCCATTTCATAATTAATTAAATATATTTAATATTAATAC
ATATTC
Found at i:12204 original size:2 final size:2
Alignment explanation
Indices: 12197--12241 Score: 58
Period size: 2 Copynumber: 23.5 Consensus size: 2
12187 TCACCCATTT
* *
12197 TA TA TA TA TA CA -A AA TA TA -A TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
12237 TA TA T
1 TA TA T
12242 TCCCGTGGGA
Statistics
Matches: 39, Mismatches: 2, Indels: 4
0.87 0.04 0.09
Matches are distributed among these distances:
1 2 0.05
2 37 0.95
ACGTcount: A:0.53, C:0.02, G:0.00, T:0.44
Consensus pattern (2 bp):
TA
Found at i:13707 original size:43 final size:43
Alignment explanation
Indices: 13602--14021 Score: 368
Period size: 43 Copynumber: 10.0 Consensus size: 43
13592 CTTTGCCATA
* * *
13602 AAGAGAATTGCCCTTGTGTTATAATTGTGTTTGGGGACTTT-G
1 AAGAGAATTGCCCCTGTGTTATAAATGTGTTTGAGGACTTTAG
* *
13644 --GTATAATTGCCCTTGTGTTATAAATGTGTTTGAGGACTTTTAG
1 AAG-AGAATTGCCCCTGTGTTATAAATGTGTTTGAGGAC-TTTAG
13687 -AGAGAATTGCCCCTGTGTTATAAATGTGTTTGAGGACTTTTAG
1 AAGAGAATTGCCCCTGTGTTATAAATGTGTTTGAGGAC-TTTAG
*
13730 -AGAGAATTGCCCCTGTGTTATAAATGTGTTTGGGGACTTT-G
1 AAGAGAATTGCCCCTGTGTTATAAATGTGTTTGAGGACTTTAG
* * *
13771 ATATAG-A-TGCCTCTGTGTTATAAATGTGTTTGAGGACTTTGG
1 A-AGAGAATTGCCCCTGTGTTATAAATGTGTTTGAGGACTTTAG
* ** * *
13813 AATAGAGGTGCCCCTATGTTATAAATGTGTTTGGGGACTTTAG
1 AAGAGAATTGCCCCTGTGTTATAAATGTGTTTGAGGACTTTAG
* * * *
13856 TATG-G-A-TGCCTCTGTGTTATGAATGTGTTTGAGGACTTTGG
1 -AAGAGAATTGCCCCTGTGTTATAAATGTGTTTGAGGACTTTAG
* * * *
13897 AATAGAGGTT-CCCTTATGTTATAAATGTGTTT-AGGGACTTTAG
1 AAGAGA-ATTGCCCCTGTGTTATAAATGTGTTTGA-GGACTTTAG
* * * *
13940 TATG-G-A-TGCCTCTGTGTTATGAATGTGTTTGAGGACTTTGG
1 -AAGAGAATTGCCCCTGTGTTATAAATGTGTTTGAGGACTTTAG
* ** * * *
13981 AATAGAGGTGCCCCAGTGTTATAATTGTGTTTGGGGACTTT
1 AAGAGAATTGCCCCTGTGTTATAAATGTGTTTGAGGACTTT
14022 TAGTTATTGG
Statistics
Matches: 311, Mismatches: 46, Indels: 41
0.78 0.12 0.10
Matches are distributed among these distances:
40 4 0.01
41 126 0.41
42 11 0.04
43 166 0.53
44 4 0.01
ACGTcount: A:0.23, C:0.10, G:0.28, T:0.39
Consensus pattern (43 bp):
AAGAGAATTGCCCCTGTGTTATAAATGTGTTTGAGGACTTTAG
Found at i:13788 original size:84 final size:84
Alignment explanation
Indices: 13616--14021 Score: 518
Period size: 84 Copynumber: 4.8 Consensus size: 84
13606 GAATTGCCCT
* * * * *
13616 TGTGTTATAATTGTGTTTGGGGACTTTGGTATA-A-TTGCCCTTGTGTTATAAATGTGTTTGAGG
1 TGTGTTATAAATGTGTTTGAGGACTTTGGAATAGAGTTGCCCCTGTGTTATAAATGTGTTTGGGG
* *
13679 ACTTTTAG-AGAGAATTGCCCC
66 AC-TTTAGTATAG-A-TGCCTC
* * *
13700 TGTGTTATAAATGTGTTTGAGGACTTT-TAGAGAGAATTGCCCCTGTGTTATAAATGTGTTTGGG
1 TGTGTTATAAATGTGTTTGAGGACTTTGGA-ATAGAGTTGCCCCTGTGTTATAAATGTGTTTGGG
13764 GACTTT-GATATAGATGCCTC
65 GACTTTAG-TATAGATGCCTC
* *
13784 TGTGTTATAAATGTGTTTGAGGACTTTGGAATAGAGGTGCCCCTATGTTATAAATGTGTTTGGGG
1 TGTGTTATAAATGTGTTTGAGGACTTTGGAATAGAGTTGCCCCTGTGTTATAAATGTGTTTGGGG
*
13849 ACTTTAGTATGGATGCCTC
66 ACTTTAGTATAGATGCCTC
* * * *
13868 TGTGTTATGAATGTGTTTGAGGACTTTGGAATAGAGGTT-CCCTTATGTTATAAATGTGTTTAGG
1 TGTGTTATAAATGTGTTTGAGGACTTTGGAATAGA-GTTGCCCCTGTGTTATAAATGTGTTTGGG
*
13932 GACTTTAGTATGGATGCCTC
65 GACTTTAGTATAGATGCCTC
* * * *
13952 TGTGTTATGAATGTGTTTGAGGACTTTGGAATAGAGGTGCCCCAGTGTTATAATTGTGTTTGGGG
1 TGTGTTATAAATGTGTTTGAGGACTTTGGAATAGAGTTGCCCCTGTGTTATAAATGTGTTTGGGG
14017 ACTTT
66 ACTTT
14022 TAGTTATTGG
Statistics
Matches: 288, Mismatches: 25, Indels: 18
0.87 0.08 0.05
Matches are distributed among these distances:
83 2 0.01
84 245 0.85
85 9 0.03
86 32 0.11
ACGTcount: A:0.22, C:0.10, G:0.28, T:0.40
Consensus pattern (84 bp):
TGTGTTATAAATGTGTTTGAGGACTTTGGAATAGAGTTGCCCCTGTGTTATAAATGTGTTTGGGG
ACTTTAGTATAGATGCCTC
Found at i:17169 original size:15 final size:15
Alignment explanation
Indices: 17151--17191 Score: 73
Period size: 15 Copynumber: 2.7 Consensus size: 15
17141 CTGCGGTTCT
17151 TGCCGAGCCCCTAGC
1 TGCCGAGCCCCTAGC
17166 TGCCGAGCCCCTAGC
1 TGCCGAGCCCCTAGC
*
17181 TGCCAAGCCCC
1 TGCCGAGCCCC
17192 CTGTCGCTCC
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
15 25 1.00
ACGTcount: A:0.15, C:0.49, G:0.24, T:0.12
Consensus pattern (15 bp):
TGCCGAGCCCCTAGC
Found at i:23964 original size:19 final size:18
Alignment explanation
Indices: 23940--23975 Score: 54
Period size: 19 Copynumber: 1.9 Consensus size: 18
23930 TGAAGACTTA
23940 TTGAAGACAATTTGAAGAT
1 TTGAAGACAA-TTGAAGAT
*
23959 TTGAAGACCATTGAAGA
1 TTGAAGACAATTGAAGA
23976 ATAATTTCAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 7 0.44
19 9 0.56
ACGTcount: A:0.42, C:0.08, G:0.22, T:0.28
Consensus pattern (18 bp):
TTGAAGACAATTGAAGAT
Found at i:23982 original size:30 final size:30
Alignment explanation
Indices: 23927--23987 Score: 79
Period size: 30 Copynumber: 2.0 Consensus size: 30
23917 CGAAGTTCGT
* *
23927 ATTTGAAGACTTATTGAAGACAATTTGAAG
1 ATTTGAAGACTCATTGAAGACAATTTCAAG
*
23957 ATTTGAAGAC-CATTGAAGAATAATTTCAAG
1 ATTTGAAGACTCATTGAAG-ACAATTTCAAG
23987 A
1 A
23988 AGCAAGAATT
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
29 7 0.26
30 20 0.74
ACGTcount: A:0.43, C:0.08, G:0.18, T:0.31
Consensus pattern (30 bp):
ATTTGAAGACTCATTGAAGACAATTTCAAG
Found at i:29421 original size:18 final size:18
Alignment explanation
Indices: 29398--29434 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
29388 AAAGGGTAAT
*
29398 TAAAAAAAATTGTTTTCA
1 TAAAAAAAAGTGTTTTCA
*
29416 TAAAAAGAAGTGTTTTCA
1 TAAAAAAAAGTGTTTTCA
29434 T
1 T
29435 GATAGAGGAG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.46, C:0.05, G:0.11, T:0.38
Consensus pattern (18 bp):
TAAAAAAAAGTGTTTTCA
Found at i:30303 original size:19 final size:18
Alignment explanation
Indices: 30279--30314 Score: 54
Period size: 19 Copynumber: 1.9 Consensus size: 18
30269 TGAAGACTTA
30279 TTGAAGACAATTTGAAGAT
1 TTGAAGACAA-TTGAAGAT
*
30298 TTGAAGACCATTGAAGA
1 TTGAAGACAATTGAAGA
30315 ATAATTTCAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 7 0.44
19 9 0.56
ACGTcount: A:0.42, C:0.08, G:0.22, T:0.28
Consensus pattern (18 bp):
TTGAAGACAATTGAAGAT
Found at i:30321 original size:30 final size:30
Alignment explanation
Indices: 30267--30326 Score: 77
Period size: 30 Copynumber: 2.0 Consensus size: 30
30257 GAAGTTCGTG
* *
30267 TTTGAAGACTTATTGAAGACAATTTGAAGA
1 TTTGAAGACTCATTGAAGACAATTTCAAGA
*
30297 TTTGAAGAC-CATTGAAGAATAATTTCAAGA
1 TTTGAAGACTCATTGAAG-ACAATTTCAAGA
30327 AGCAAGAATT
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
29 7 0.27
30 19 0.73
ACGTcount: A:0.42, C:0.08, G:0.18, T:0.32
Consensus pattern (30 bp):
TTTGAAGACTCATTGAAGACAATTTCAAGA
Done.