Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01021196.1 Corchorus olitorius cultivar O-4 contig21229, 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: 62191
ACGTcount: A:0.33, C:0.18, G:0.18, T:0.31
Found at i:931 original size:18 final size:18
Alignment explanation
Indices: 908--951 Score: 52
Period size: 18 Copynumber: 2.4 Consensus size: 18
898 AAATTAATTA
908 ATTATTAATTAAATAATG
1 ATTATTAATTAAATAATG
** * *
926 ATTATTTTTTGAATAATT
1 ATTATTAATTAAATAATG
944 ATTATTAA
1 ATTATTAA
952 ATTTCTAGTG
Statistics
Matches: 20, Mismatches: 6, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.43, C:0.00, G:0.05, T:0.52
Consensus pattern (18 bp):
ATTATTAATTAAATAATG
Found at i:2399 original size:51 final size:50
Alignment explanation
Indices: 2298--2399 Score: 127
Period size: 51 Copynumber: 2.0 Consensus size: 50
2288 GTTCTTCATA
* **
2298 TTTTCCTTGTTTAGATCTTGTCTCCGGACAAACAAACACTCTTTTAGTGT
1 TTTTCCTTGTTTAGATCTTGTCTCCGGACAAACAAACACTCGTACAGTGT
*
2348 TTTTCTCTTGTTTCA-ATCTTGTCTCCGGACATACAAACACT-GTACACGTGT
1 TTTTC-CTTGTTT-AGATCTTGTCTCCGGACAAACAAACACTCGTACA-GTGT
2399 T
1 T
2400 CTTCATTCAG
Statistics
Matches: 45, Mismatches: 4, Indels: 5
0.83 0.07 0.09
Matches are distributed among these distances:
50 7 0.16
51 37 0.82
52 1 0.02
ACGTcount: A:0.22, C:0.24, G:0.14, T:0.41
Consensus pattern (50 bp):
TTTTCCTTGTTTAGATCTTGTCTCCGGACAAACAAACACTCGTACAGTGT
Found at i:3309 original size:14 final size:13
Alignment explanation
Indices: 3261--3313 Score: 51
Period size: 13 Copynumber: 4.2 Consensus size: 13
3251 GAGTATCCAA
3261 AAACAAGAAAC-AG
1 AAACAA-AAACAAG
3274 ATAA-AAAAAC-A-
1 A-AACAAAAACAAG
3285 AAACAAAAACAAG
1 AAACAAAAACAAG
3298 AAACAAATAACAAG
1 AAACAAA-AACAAG
3312 AA
1 AA
3314 GGAAGCAGAG
Statistics
Matches: 35, Mismatches: 0, Indels: 9
0.80 0.00 0.20
Matches are distributed among these distances:
10 2 0.06
11 7 0.20
12 6 0.17
13 10 0.29
14 10 0.29
ACGTcount: A:0.75, C:0.13, G:0.08, T:0.04
Consensus pattern (13 bp):
AAACAAAAACAAG
Found at i:4626 original size:57 final size:57
Alignment explanation
Indices: 4551--4664 Score: 228
Period size: 57 Copynumber: 2.0 Consensus size: 57
4541 AACACCCAGG
4551 GATATTACTAAAAGCTCCTTTTGAGAATCGATGAGAAAGCTCGGTTTGAACATTTTT
1 GATATTACTAAAAGCTCCTTTTGAGAATCGATGAGAAAGCTCGGTTTGAACATTTTT
4608 GATATTACTAAAAGCTCCTTTTGAGAATCGATGAGAAAGCTCGGTTTGAACATTTTT
1 GATATTACTAAAAGCTCCTTTTGAGAATCGATGAGAAAGCTCGGTTTGAACATTTTT
4665 TGTCCTTTTA
Statistics
Matches: 57, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
57 57 1.00
ACGTcount: A:0.32, C:0.14, G:0.19, T:0.35
Consensus pattern (57 bp):
GATATTACTAAAAGCTCCTTTTGAGAATCGATGAGAAAGCTCGGTTTGAACATTTTT
Found at i:5895 original size:39 final size:39
Alignment explanation
Indices: 5813--5896 Score: 91
Period size: 39 Copynumber: 2.1 Consensus size: 39
5803 AGTGCCTGGA
* **
5813 GAGGAGAAAACTAAATTGTGAGACAGTGGTGCTTGGAGGG
1 GAGG-GAAAACTAAATTGTGAGAAAGTGGTGCTTGGAAAG
*
5853 GAGGGAAAGCTAAA-TGATGAGAAAGTGGTGGC-TGGAAAG
1 GAGGGAAAACTAAATTG-TGAGAAAGTGGT-GCTTGGAAAG
5892 GAGGG
1 GAGGG
5897 GTGGAGTAGG
Statistics
Matches: 38, Mismatches: 4, Indels: 5
0.81 0.09 0.11
Matches are distributed among these distances:
38 2 0.05
39 30 0.79
40 6 0.16
ACGTcount: A:0.35, C:0.06, G:0.43, T:0.17
Consensus pattern (39 bp):
GAGGGAAAACTAAATTGTGAGAAAGTGGTGCTTGGAAAG
Found at i:21800 original size:161 final size:160
Alignment explanation
Indices: 21497--21930 Score: 507
Period size: 161 Copynumber: 2.7 Consensus size: 160
21487 CAGGAATAGG
* * * *
21497 AACAACACCTTCCGATGAGGAAGGGCAGACTGAGAAAAGATAAAGAACACCTTCCTATGAGGAAG
1 AACAACACCTTCCGATGAGGAAGGGCAAACTG-GAAATGATAAACAACACCTTCCAATGAGGAAG
* * * * ** *
21562 GGCAAACTGGTAA-ACTTAATAACTCCTTCCGATGGGGAAGGGCAAACCGGAATGTCAACAACAC
65 GGCAAACTGGAAATACTT-ACAACACCTTCCGATGAGGAAGGGCAAATTGAAATGTCAACAACAC
*
21626 CTTCCGATGAGGAAGGGCAAACTGGGAATGTA
129 CTTCCGATGAGGAAGGGCAAACTGGAAATGTA
* * *
21658 AATAACACCTTTCGATGAGGAAGGGCAAACTGGGAATG-TAAACAACACCTTCCAATGAGGAAGG
1 AACAACACCTTCCGATGAGGAAGGGCAAACTGGAAATGATAAACAACACCTTCCAATGAGGAAGG
* * *
21722 GCAAACTGGGAATACTTACAACACCTTCCGATGAAGAAGGGCAAATTGACAAATG-CTGACAACA
66 GCAAACTGGAAATACTTACAACACCTTCCGATGAGGAAGGGCAAATTG--AAATGTC-AACAACA
* *
21786 CCTTCTGATGAGGAAGGGCAAACTGGAAATGTT
128 CCTTCCGATGAGGAAGGGCAAACTGGAAATGTA
* * * *** *
21819 GACAACACCTTCCTATGAGGAAGGGCAAACTGGAAATGCT-GGTAACACCTTACAATGAGGAAGG
1 AACAACACCTTCCGATGAGGAAGGGCAAACTGGAAATGATAAACAACACCTTCCAATGAGGAAGG
* * * * *
21883 GCAAATTGGAAATGCTGACAATACCTTTCGATGAGGAAGGGCAAATTG
66 GCAAACTGGAAATACTTACAACACCTTCCGATGAGGAAGGGCAAATTG
21931 GTAATTCTGA
Statistics
Matches: 233, Mismatches: 35, Indels: 10
0.84 0.13 0.04
Matches are distributed among these distances:
159 60 0.26
160 9 0.04
161 163 0.70
162 1 0.00
ACGTcount: A:0.37, C:0.19, G:0.26, T:0.18
Consensus pattern (160 bp):
AACAACACCTTCCGATGAGGAAGGGCAAACTGGAAATGATAAACAACACCTTCCAATGAGGAAGG
GCAAACTGGAAATACTTACAACACCTTCCGATGAGGAAGGGCAAATTGAAATGTCAACAACACCT
TCCGATGAGGAAGGGCAAACTGGAAATGTA
Found at i:21928 original size:40 final size:40
Alignment explanation
Indices: 21498--21944 Score: 438
Period size: 40 Copynumber: 11.1 Consensus size: 40
21488 AGGAATAGGA
* * * *
21498 ACAACACCTTCCGATGAGGAAGGGCAGACTGAGAAAAGATAA
1 ACAACACCTTCCGATGAGGAAGGGCAAACTG-GAAATGCT-G
* * *
21540 AGAACACCTTCCTATGAGGAAGGGCAAACTGGTAAA--CTTA
1 ACAACACCTTCCGATGAGGAAGGGCAAACTGG-AAATGC-TG
* * * * *
21580 ATAACTCCTTCCGATGGGGAAGGGCAAACCGG-AATG-TCA
1 ACAACACCTTCCGATGAGGAAGGGCAAACTGGAAATGCT-G
* *
21619 ACAACACCTTCCGATGAGGAAGGGCAAACTGGGAATG-TAA
1 ACAACACCTTCCGATGAGGAAGGGCAAACTGGAAATGCT-G
* * * *
21659 ATAACACCTTTCGATGAGGAAGGGCAAACTGGGAATG-TAA
1 ACAACACCTTCCGATGAGGAAGGGCAAACTGGAAATGCT-G
* * * *
21699 ACAACACCTTCCAATGAGGAAGGGCAAACTGGGAATACTT
1 ACAACACCTTCCGATGAGGAAGGGCAAACTGGAAATGCTG
* * *
21739 ACAACACCTTCCGATGAAGAAGGGCAAATTGACAAATGCTG
1 ACAACACCTTCCGATGAGGAAGGGCAAACTG-GAAATGCTG
* *
21780 ACAACACCTTCTGATGAGGAAGGGCAAACTGGAAATGTTG
1 ACAACACCTTCCGATGAGGAAGGGCAAACTGGAAATGCTG
*
21820 ACAACACCTTCCTATGAGGAAGGGCAAACTGGAAATGCTG
1 ACAACACCTTCCGATGAGGAAGGGCAAACTGGAAATGCTG
** * * *
21860 GTAACACCTTACAATGAGGAAGGGCAAATTGGAAATGCTG
1 ACAACACCTTCCGATGAGGAAGGGCAAACTGGAAATGCTG
* * * * *
21900 ACAATACCTTTCGATGAGGAAGGGCAAATTGGTAATTCTG
1 ACAACACCTTCCGATGAGGAAGGGCAAACTGGAAATGCTG
21940 ACAAC
1 ACAAC
21945 TGTTCTTTTC
Statistics
Matches: 348, Mismatches: 49, Indels: 18
0.84 0.12 0.04
Matches are distributed among these distances:
38 3 0.01
39 29 0.08
40 249 0.72
41 36 0.10
42 31 0.09
ACGTcount: A:0.37, C:0.19, G:0.25, T:0.18
Consensus pattern (40 bp):
ACAACACCTTCCGATGAGGAAGGGCAAACTGGAAATGCTG
Found at i:24166 original size:17 final size:17
Alignment explanation
Indices: 24146--24196 Score: 59
Period size: 17 Copynumber: 3.0 Consensus size: 17
24136 CCGAGTGTAG
24146 AGAGAGAATCAGTGTGT
1 AGAGAGAATCAGTGTGT
* **
24163 AGAGAGAGTCAAAGTGT
1 AGAGAGAATCAGTGTGT
24180 AG-GAGAATTCAGTGTGT
1 AGAGAGAA-TCAGTGTGT
24197 GTTCATCGAA
Statistics
Matches: 27, Mismatches: 6, Indels: 2
0.77 0.17 0.06
Matches are distributed among these distances:
16 4 0.15
17 23 0.85
ACGTcount: A:0.35, C:0.06, G:0.35, T:0.24
Consensus pattern (17 bp):
AGAGAGAATCAGTGTGT
Found at i:32757 original size:15 final size:15
Alignment explanation
Indices: 32737--32769 Score: 57
Period size: 15 Copynumber: 2.2 Consensus size: 15
32727 GAATTTACAA
32737 ATGACCAAAATGCCC
1 ATGACCAAAATGCCC
*
32752 ATGACCAGAATGCCC
1 ATGACCAAAATGCCC
32767 ATG
1 ATG
32770 GGTGATCCTA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.36, C:0.30, G:0.18, T:0.15
Consensus pattern (15 bp):
ATGACCAAAATGCCC
Found at i:35903 original size:29 final size:29
Alignment explanation
Indices: 35870--35925 Score: 78
Period size: 29 Copynumber: 1.9 Consensus size: 29
35860 TTGCTTATTC
*
35870 TATCTTTCAATTG-TTGATTTGAATTGCCA
1 TATCTTGCAATTGATTGA-TTGAATTGCCA
*
35899 TATCTTGCTATTGATTGATTGAATTGC
1 TATCTTGCAATTGATTGATTGAATTGC
35926 AATTATTTTT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
29 20 0.83
30 4 0.17
ACGTcount: A:0.23, C:0.12, G:0.16, T:0.48
Consensus pattern (29 bp):
TATCTTGCAATTGATTGATTGAATTGCCA
Found at i:51610 original size:44 final size:44
Alignment explanation
Indices: 51473--51622 Score: 205
Period size: 43 Copynumber: 3.5 Consensus size: 44
51463 GCATTGTCAC
* * * *
51473 AAAGAAAGTAAAAGGAAAAATCGTGGTGTGAAAAGGAAA-TTTA
1 AAAGAAAGTTAAAGAAAAAATCGCGGTGTGAAAAGGAAACCTTA
* *
51516 AAAGAAAGTTAAAGAAAAAATCACGGTATGAAAAGGAAACC-TA
1 AAAGAAAGTTAAAGAAAAAATCGCGGTGTGAAAAGGAAACCTTA
* *
51559 AAAGAAAGTTAAAGAAAAAATTGCAGTGTGAAAAGGAAACCTTA
1 AAAGAAAGTTAAAGAAAAAATCGCGGTGTGAAAAGGAAACCTTA
*
51603 GAAGAAAGTTAAAGAAAAAA
1 AAAGAAAGTTAAAGAAAAAA
51623 AGGTAAGCAT
Statistics
Matches: 94, Mismatches: 11, Indels: 3
0.87 0.10 0.03
Matches are distributed among these distances:
43 73 0.78
44 21 0.22
ACGTcount: A:0.57, C:0.05, G:0.21, T:0.16
Consensus pattern (44 bp):
AAAGAAAGTTAAAGAAAAAATCGCGGTGTGAAAAGGAAACCTTA
Done.