Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01017654.1 Corchorus olitorius cultivar O-4 contig17687, 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: 23424
ACGTcount: A:0.32, C:0.18, G:0.20, T:0.31
Found at i:1891 original size:5 final size:5
Alignment explanation
Indices: 1883--1962 Score: 69
Period size: 5 Copynumber: 15.6 Consensus size: 5
1873 CAAAAAAAAA
*
1883 AAATC AAATC AAAAATC AAATC AAAGT- ACAATC AAA-A AAATC AAATC
1 AAATC AAATC --AAATC AAATC AAA-TC A-AATC AAATC AAATC AAATC
1930 AAAATC AAA-- AAATC AAATC AAATC AAAATC AAA
1 -AAATC AAATC AAATC AAATC AAATC -AAATC AAA
1963 GGAAAATGGA
Statistics
Matches: 63, Mismatches: 2, Indels: 20
0.74 0.02 0.24
Matches are distributed among these distances:
3 3 0.05
4 3 0.05
5 38 0.60
6 14 0.22
7 5 0.08
ACGTcount: A:0.66, C:0.16, G:0.01, T:0.16
Consensus pattern (5 bp):
AAATC
Found at i:1896 original size:19 final size:19
Alignment explanation
Indices: 1872--1951 Score: 67
Period size: 19 Copynumber: 4.3 Consensus size: 19
1862 ATCAAGAAAT
1872 TCAAAAAAAAAAAATCAAA
1 TCAAAAAAAAAAAATCAAA
**
1891 TC--AAAAATCAAATCAAA
1 TCAAAAAAAAAAAATCAAA
**
1908 GT-ACAATCAAAAAAATCAAA
1 -TCA-AAAAAAAAAAATCAAA
**
1928 TCAAAATCAAAAAATCAAA
1 TCAAAAAAAAAAAATCAAA
1947 TCAAA
1 TCAAA
1952 TCAAAATCAA
Statistics
Matches: 47, Mismatches: 9, Indels: 10
0.71 0.14 0.15
Matches are distributed among these distances:
17 13 0.28
18 1 0.02
19 21 0.45
20 12 0.26
ACGTcount: A:0.69, C:0.15, G:0.01, T:0.15
Consensus pattern (19 bp):
TCAAAAAAAAAAAATCAAA
Found at i:1952 original size:24 final size:23
Alignment explanation
Indices: 1883--1962 Score: 98
Period size: 24 Copynumber: 3.6 Consensus size: 23
1873 CAAAAAAAAA
1883 AAATC-AAATCAAAAATCAAATC
1 AAATCAAAATCAAAAATCAAATC
*
1905 AAAGT-ACAATC-AAAA--AAATC
1 AAA-TCAAAATCAAAAATCAAATC
1925 AAATCAAAATCAAAAAATCAAATC
1 AAATCAAAATC-AAAAATCAAATC
1949 AAATCAAAATCAAA
1 AAATCAAAATCAAA
1963 GGAAAATGGA
Statistics
Matches: 49, Mismatches: 2, Indels: 13
0.77 0.03 0.20
Matches are distributed among these distances:
19 1 0.02
20 13 0.27
22 11 0.22
23 8 0.16
24 16 0.33
ACGTcount: A:0.66, C:0.16, G:0.01, T:0.16
Consensus pattern (23 bp):
AAATCAAAATCAAAAATCAAATC
Found at i:1960 original size:44 final size:42
Alignment explanation
Indices: 1872--1962 Score: 121
Period size: 44 Copynumber: 2.1 Consensus size: 42
1862 ATCAAGAAAT
*
1872 TCAAAAAAAAAAAATCAAATCAAAAATCAAATCAAAGTACAA
1 TCAAAAAAAAAAAATCAAATCAAAAATCAAATCAAAGTAAAA
**
1914 TCAAAAAAATCAAATCAAAATCAAAAAATCAAATCAAA-TCAAAA
1 TCAAAAAAAAAAAATC-AAATC-AAAAATCAAATCAAAGT-AAAA
1958 TCAAA
1 TCAAA
1963 GGAAAATGGA
Statistics
Matches: 43, Mismatches: 3, Indels: 4
0.86 0.06 0.08
Matches are distributed among these distances:
42 14 0.33
43 6 0.14
44 23 0.53
ACGTcount: A:0.68, C:0.15, G:0.01, T:0.15
Consensus pattern (42 bp):
TCAAAAAAAAAAAATCAAATCAAAAATCAAATCAAAGTAAAA
Found at i:2582 original size:31 final size:30
Alignment explanation
Indices: 2519--2578 Score: 120
Period size: 30 Copynumber: 2.0 Consensus size: 30
2509 TTCATAGAGT
2519 GTTGACTCAAATCATGTCTCAGAAAAAAAA
1 GTTGACTCAAATCATGTCTCAGAAAAAAAA
2549 GTTGACTCAAATCATGTCTCAGAAAAAAAA
1 GTTGACTCAAATCATGTCTCAGAAAAAAAA
2579 AGTTTTCAGA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 30 1.00
ACGTcount: A:0.47, C:0.17, G:0.13, T:0.23
Consensus pattern (30 bp):
GTTGACTCAAATCATGTCTCAGAAAAAAAA
Found at i:2677 original size:48 final size:48
Alignment explanation
Indices: 2597--2750 Score: 209
Period size: 48 Copynumber: 3.1 Consensus size: 48
2587 GAACAAGAAG
* *
2597 TTTTACAACAAAATTGCTTTCCATTTATGAGTTCAAGATCAAAATTCGC
1 TTTT-CAATAAAATTGCTTTCCATTTGTGAGTTCAAGATCAAAATTCGC
* * *
2646 TTTTCAATAAAATTGCTTTCCATTCGTGAGTTCAATATCAAAATTTGC
1 TTTTCAATAAAATTGCTTTCCATTTGTGAGTTCAAGATCAAAATTCGC
* * *
2694 TTTTCAAAGTAAGATTGCATTCCATTTGTGAGTCCAAGATCAAAATTCGC
1 TTTTC-AA-TAAAATTGCTTTCCATTTGTGAGTTCAAGATCAAAATTCGC
2744 TTTTCAA
1 TTTTCAA
2751 AGGACATTGA
Statistics
Matches: 92, Mismatches: 11, Indels: 4
0.86 0.10 0.04
Matches are distributed among these distances:
48 44 0.48
49 8 0.09
50 40 0.43
ACGTcount: A:0.32, C:0.18, G:0.12, T:0.38
Consensus pattern (48 bp):
TTTTCAATAAAATTGCTTTCCATTTGTGAGTTCAAGATCAAAATTCGC
Found at i:2736 original size:50 final size:50
Alignment explanation
Indices: 2606--2752 Score: 217
Period size: 50 Copynumber: 3.0 Consensus size: 50
2596 GTTTTACAAC
*
2606 AAAATTGCTTTCCATTTATGAGTTCAAGATCAAAATTCGCTTTTC-AA-T
1 AAAATTGCTTTCCATTTGTGAGTTCAAGATCAAAATTCGCTTTTCAAAGT
* * *
2654 AAAATTGCTTTCCATTCGTGAGTTCAATATCAAAATTTGCTTTTCAAAGT
1 AAAATTGCTTTCCATTTGTGAGTTCAAGATCAAAATTCGCTTTTCAAAGT
* * *
2704 AAGATTGCATTCCATTTGTGAGTCCAAGATCAAAATTCGCTTTTCAAAG
1 AAAATTGCTTTCCATTTGTGAGTTCAAGATCAAAATTCGCTTTTCAAAG
2753 GACATTGAAG
Statistics
Matches: 87, Mismatches: 10, Indels: 2
0.88 0.10 0.02
Matches are distributed among these distances:
48 41 0.47
49 2 0.02
50 44 0.51
ACGTcount: A:0.33, C:0.17, G:0.13, T:0.37
Consensus pattern (50 bp):
AAAATTGCTTTCCATTTGTGAGTTCAAGATCAAAATTCGCTTTTCAAAGT
Found at i:3437 original size:50 final size:50
Alignment explanation
Indices: 3360--3747 Score: 650
Period size: 50 Copynumber: 7.8 Consensus size: 50
3350 TCCGAATGCT
*
3360 TAGGCTTTTCCACAAGCCGAACTCGTTTCCATACGAGTCAATTATCAACA
1 TAGGCTTTTCCACAAGCCAAACTCGTTTCCATACGAGTCAATTATCAACA
* *
3410 TGGGCTTTTCCACAAGCCGAACTCGTTTCCATACGAGTCAATTATCAACA
1 TAGGCTTTTCCACAAGCCAAACTCGTTTCCATACGAGTCAATTATCAACA
3460 TAGGCTTTTCCACAAGCCAAACTCGTTTCCATACGAGTCAATTATCAACA
1 TAGGCTTTTCCACAAGCCAAACTCGTTTCCATACGAGTCAATTATCAACA
* *
3510 TGGGCTTTTCCACAAGCCGAACTCGTTTCCATACGAGTCAATTATCAACA
1 TAGGCTTTTCCACAAGCCAAACTCGTTTCCATACGAGTCAATTATCAACA
* * *
3560 TGGGCTTTTCCACAAGCCGAACTCATTTCCATACGAGTCAATTATCAACA
1 TAGGCTTTTCCACAAGCCAAACTCGTTTCCATACGAGTCAATTATCAACA
*
3610 CAGGCTTTTCCACAAGCCAAACTCGTTTCCATACGAGTCAATTATCAACA
1 TAGGCTTTTCCACAAGCCAAACTCGTTTCCATACGAGTCAATTATCAACA
*
3660 TAGGCTTTTCCACAAGCCAAACTCGTTTCCATACGTGTCAATTATCAACA
1 TAGGCTTTTCCACAAGCCAAACTCGTTTCCATACGAGTCAATTATCAACA
* * * *
3710 CAAGCTTTTCCACAAGCCAAACTCATTTCCATATGAGT
1 TAGGCTTTTCCACAAGCCAAACTCGTTTCCATACGAGT
3748 TAAGCCTTAC
Statistics
Matches: 321, Mismatches: 17, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
50 321 1.00
ACGTcount: A:0.30, C:0.28, G:0.13, T:0.28
Consensus pattern (50 bp):
TAGGCTTTTCCACAAGCCAAACTCGTTTCCATACGAGTCAATTATCAACA
Found at i:4187 original size:27 final size:28
Alignment explanation
Indices: 4146--4218 Score: 96
Period size: 28 Copynumber: 2.6 Consensus size: 28
4136 TTATATTTGG
* *
4146 GGGGCATTTTAGTCATTTG-A-ACGTCCA
1 GGGGCATTTTGGTCATTTGCACAC-TCAA
4173 GGGGCATTTTGGTCATTTGCACACTCAA
1 GGGGCATTTTGGTCATTTGCACACTCAA
*
4201 GGGGCATTGTGGTCATTT
1 GGGGCATTTTGGTCATTT
4219 TAAGTTAACA
Statistics
Matches: 41, Mismatches: 3, Indels: 3
0.87 0.06 0.06
Matches are distributed among these distances:
27 18 0.44
28 21 0.51
29 2 0.05
ACGTcount: A:0.19, C:0.18, G:0.29, T:0.34
Consensus pattern (28 bp):
GGGGCATTTTGGTCATTTGCACACTCAA
Found at i:8883 original size:2 final size:2
Alignment explanation
Indices: 8870--8899 Score: 51
Period size: 2 Copynumber: 15.0 Consensus size: 2
8860 ACATTTCGAC
*
8870 AT AT AT AA 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
8900 CTTATTGTGT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:12283 original size:13 final size:13
Alignment explanation
Indices: 12265--12289 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
12255 AAAAAAAAAT
12265 CAAAAGTGTTTTC
1 CAAAAGTGTTTTC
12278 CAAAAGTGTTTT
1 CAAAAGTGTTTT
12290 TAAGTATGTT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.12, G:0.16, T:0.40
Consensus pattern (13 bp):
CAAAAGTGTTTTC
Found at i:15427 original size:21 final size:22
Alignment explanation
Indices: 15403--15444 Score: 68
Period size: 21 Copynumber: 2.0 Consensus size: 22
15393 TTTGCCTCAT
15403 GCATTCATTCAT-CATGCCATG
1 GCATTCATTCATGCATGCCATG
*
15424 GCATTCATTCATGCATTCCAT
1 GCATTCATTCATGCATGCCAT
15445 TAAACCTTAG
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 12 0.63
22 7 0.37
ACGTcount: A:0.24, C:0.29, G:0.12, T:0.36
Consensus pattern (22 bp):
GCATTCATTCATGCATGCCATG
Found at i:17441 original size:71 final size:71
Alignment explanation
Indices: 17348--17533 Score: 293
Period size: 71 Copynumber: 2.6 Consensus size: 71
17338 TAAAAACTAG
*
17348 ACAAGTCCTGCCCAGGACTTGACAACTCCTGCCCAGGAGC-TGGTCTGTTGAAAGACGGAAGAAA
1 ACAAGTCCTGCCCAGGACTTGACAACTCCTGCCCAGGA-CTTGGTCTGTTGAAAAACGGAAGAAA
17412 AATCAGA
65 AATCAGA
* * *
17419 ACAACTCCCGCCCAGGACTTGACAACTCTTGCCCAGGACTTGGTCTGTTGAAAAACGGAAGAAAA
1 ACAAGTCCTGCCCAGGACTTGACAACTCCTGCCCAGGACTTGGTCTGTTGAAAAACGGAAGAAAA
*
17484 TTCAGA
66 ATCAGA
*
17490 ACAAGTCCTGTCCAGGACTTGGACAACTCCTGCCCAGGACTTGG
1 ACAAGTCCTGCCCAGGACTT-GACAACTCCTGCCCAGGACTTGG
17534 ACAACTCCTG
Statistics
Matches: 104, Mismatches: 9, Indels: 3
0.90 0.08 0.03
Matches are distributed among these distances:
70 1 0.01
71 81 0.78
72 22 0.21
ACGTcount: A:0.30, C:0.27, G:0.24, T:0.19
Consensus pattern (71 bp):
ACAAGTCCTGCCCAGGACTTGACAACTCCTGCCCAGGACTTGGTCTGTTGAAAAACGGAAGAAAA
ATCAGA
Found at i:17445 original size:21 final size:21
Alignment explanation
Indices: 17419--17460 Score: 66
Period size: 21 Copynumber: 2.0 Consensus size: 21
17409 AAAAATCAGA
17419 ACAACTCCCGCCCAGGACTTG
1 ACAACTCCCGCCCAGGACTTG
**
17440 ACAACTCTTGCCCAGGACTTG
1 ACAACTCCCGCCCAGGACTTG
17461 GTCTGTTGAA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.24, C:0.38, G:0.19, T:0.19
Consensus pattern (21 bp):
ACAACTCCCGCCCAGGACTTG
Found at i:17520 original size:22 final size:22
Alignment explanation
Indices: 17490--17554 Score: 112
Period size: 22 Copynumber: 3.0 Consensus size: 22
17480 AAAATTCAGA
* *
17490 ACAAGTCCTGTCCAGGACTTGG
1 ACAACTCCTGCCCAGGACTTGG
17512 ACAACTCCTGCCCAGGACTTGG
1 ACAACTCCTGCCCAGGACTTGG
17534 ACAACTCCTGCCCAGGACTTG
1 ACAACTCCTGCCCAGGACTTG
17555 TTGCGGAAAA
Statistics
Matches: 41, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 41 1.00
ACGTcount: A:0.23, C:0.34, G:0.23, T:0.20
Consensus pattern (22 bp):
ACAACTCCTGCCCAGGACTTGG
Done.