Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01020985.1 Corchorus olitorius cultivar O-4 contig21018, 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: 10115
ACGTcount: A:0.32, C:0.18, G:0.19, T:0.31
Found at i:2611 original size:44 final size:44
Alignment explanation
Indices: 2501--2626 Score: 132
Period size: 44 Copynumber: 2.9 Consensus size: 44
2491 ATATCCATTG
* *
2501 ATATATG-TCATACAT-CTTTCATGCATTGTCCATGTC-TTTGTAT
1 ATATATGCTCATACATAC-ATCATGCATTATCCAT-TCATTTGTAT
* *
2544 ATATATGCTCATACATTCATCATGCATTATCCATCCATTTGTAT
1 ATATATGCTCATACATACATCATGCATTATCCATTCATTTGTAT
* * ** *
2588 ATATATGTTCATGCATAGGTCATGCATTACCCATTCATT
1 ATATATGCTCATACATACATCATGCATTATCCATTCATT
2627 ACTACATGCA
Statistics
Matches: 70, Mismatches: 10, Indels: 5
0.82 0.12 0.06
Matches are distributed among these distances:
43 8 0.11
44 61 0.87
45 1 0.01
ACGTcount: A:0.27, C:0.21, G:0.10, T:0.42
Consensus pattern (44 bp):
ATATATGCTCATACATACATCATGCATTATCCATTCATTTGTAT
Found at i:3770 original size:15 final size:15
Alignment explanation
Indices: 3750--3800 Score: 68
Period size: 15 Copynumber: 3.5 Consensus size: 15
3740 CAAAACATGT
**
3750 TTTTCAAGAAAATTG
1 TTTTCAAGAAAAAGG
3765 TTTTCAAGAAAAAGG
1 TTTTCAAGAAAAAGG
*
3780 TTTTCAA-AAATAGG
1 TTTTCAAGAAAAAGG
3794 TTTTCAA
1 TTTTCAA
3801 AAAGGTTTTG
Statistics
Matches: 33, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
14 13 0.39
15 20 0.61
ACGTcount: A:0.41, C:0.08, G:0.14, T:0.37
Consensus pattern (15 bp):
TTTTCAAGAAAAAGG
Found at i:3806 original size:12 final size:13
Alignment explanation
Indices: 3750--3809 Score: 59
Period size: 15 Copynumber: 4.3 Consensus size: 13
3740 CAAAACATGT
*
3750 TTTTCAAGAAAATTG
1 TTTTCAA-AAAA-GG
3765 TTTTCAAGAAAAAGG
1 TTTTC-A-AAAAAGG
3780 TTTTCAAAAATAGG
1 TTTTCAAAAA-AGG
3794 TTTTC-AAAAAGG
1 TTTTCAAAAAAGG
3806 TTTT
1 TTTT
3810 GAGTCTCTTA
Statistics
Matches: 41, Mismatches: 1, Indels: 9
0.80 0.02 0.18
Matches are distributed among these distances:
12 7 0.17
13 8 0.20
14 9 0.22
15 11 0.27
16 5 0.12
17 1 0.02
ACGTcount: A:0.40, C:0.07, G:0.15, T:0.38
Consensus pattern (13 bp):
TTTTCAAAAAAGG
Found at i:4099 original size:12 final size:12
Alignment explanation
Indices: 4082--4106 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
4072 GTTAAAGTAA
4082 TTCAAATCAAAG
1 TTCAAATCAAAG
4094 TTCAAATCAAAG
1 TTCAAATCAAAG
4106 T
1 T
4107 GAATCAAAAG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.48, C:0.16, G:0.08, T:0.28
Consensus pattern (12 bp):
TTCAAATCAAAG
Found at i:5339 original size:22 final size:23
Alignment explanation
Indices: 5294--5340 Score: 69
Period size: 23 Copynumber: 2.1 Consensus size: 23
5284 AACTCAGAGT
* *
5294 CATTCAACAGGAGTCGTTTGGGG
1 CATTCAACAGAAGTCGATTGGGG
5317 CATTCAACAGAAGTC-ATTGGGG
1 CATTCAACAGAAGTCGATTGGGG
5339 CA
1 CA
5341 ATTTAGAACA
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
22 8 0.36
23 14 0.64
ACGTcount: A:0.28, C:0.19, G:0.30, T:0.23
Consensus pattern (23 bp):
CATTCAACAGAAGTCGATTGGGG
Found at i:6047 original size:67 final size:65
Alignment explanation
Indices: 5937--6121 Score: 237
Period size: 67 Copynumber: 2.8 Consensus size: 65
5927 TTTTAGAAGA
* *
5937 ACACCGGAAGATGGTTTGCTAGAAAGAATTTTCAAGAAT-TGATTGGAAGGCAATCTCATTAAGG
1 ACACC-GAAGACGGTTTGCTAGAAAGAATTTTC-A-AATGTGATTGGAAGACAATCTCATTAAGG
*
6001 AGT
63 AAT
* *
6004 ACACCAGAAGACGGTTTGTTAGAAAGAATTTTCAAATGCTGATTGAAAGACAATCTCATTAAGGA
1 ACACC-GAAGACGGTTTGCTAGAAAGAATTTTCAAATG-TGATTGGAAGACAATCTCATTAAGGA
6069 AT
64 AT
* *
6071 ACATCGAAAGACGGTTTGCTAGAAAGAATTTTCAAATGTTGATCGGAAGAC
1 ACACCG-AAGACGGTTTGCTAGAAAGAATTTTCAAATG-TGATTGGAAGAC
6122 GAACTTGTCA
Statistics
Matches: 104, Mismatches: 11, Indels: 6
0.86 0.09 0.05
Matches are distributed among these distances:
65 3 0.03
66 2 0.02
67 99 0.95
ACGTcount: A:0.38, C:0.13, G:0.23, T:0.26
Consensus pattern (65 bp):
ACACCGAAGACGGTTTGCTAGAAAGAATTTTCAAATGTGATTGGAAGACAATCTCATTAAGGAAT
Found at i:6154 original size:67 final size:66
Alignment explanation
Indices: 5932--6282 Score: 233
Period size: 67 Copynumber: 5.3 Consensus size: 66
5922 GAGGATTTTA
* * * * *
5932 GAAGAACACCGGAAGATGGTTTGCTAGAAAGAATTTTCAAGAATTGATTGGAAGGC-AATCTCAT
1 GAAGTACACCAGAAGATGGTTTGCTAGAAAGAATTTTCAA-AGTTGATCGGAAGACGAA-CT--T
*
5996 -TAAG
62 GTCAG
* * * * *
6000 G-AGTACACCAGAAGACGGTTTGTTAGAAAGAATTTTCAAATGCTGATTGAAAGAC-AATCTCAT
1 GAAGTACACCAGAAGATGGTTTGCTAGAAAGAATTTTCAAA-GTTGATCGGAAGACGAA-CT--T
*
6063 -TAAG
62 GTCAG
* *
6067 GAA-TACATC-GAAAGACGGTTTGCTAGAAAGAATTTTCAAATGTTGATCGGAAGACGAACTTGT
1 GAAGTACACCAG-AAGATGGTTTGCTAGAAAGAATTTTCAAA-GTTGATCGGAAGACGAACTTGT
6130 CAG
64 CAG
* * *
6133 GAAGTACACCAGAAGATGGTTT-CT--TAAGATTTTTCAGAAGTTGATCGGAAGACGATCTTGTC
1 GAAGTACACCAGAAGATGGTTTGCTAGAAAGAATTTTCA-AAGTTGATCGGAAGACGAACTTGTC
*
6195 AA
65 AG
* * * ** * * * *
6197 AAATTACACCAGAGGATGGTTT--T-TCAAGAGTTTCCAGAAGTCGATCGGAAGACGATCTTGTC
1 GAAGTACACCAGAAGATGGTTTGCTAGAAAGAATTTTCA-AAGTTGATCGGAAGACGAACTTGTC
*
6259 AA
65 AG
* *
6261 GAAGTACATCGGAAGATGGTTT
1 GAAGTACACCAGAAGATGGTTT
6283 CTCAAGAGTT
Statistics
Matches: 242, Mismatches: 32, Indels: 22
0.82 0.11 0.07
Matches are distributed among these distances:
63 1 0.00
64 105 0.43
65 3 0.01
66 10 0.04
67 118 0.49
68 5 0.02
ACGTcount: A:0.36, C:0.14, G:0.24, T:0.27
Consensus pattern (66 bp):
GAAGTACACCAGAAGATGGTTTGCTAGAAAGAATTTTCAAAGTTGATCGGAAGACGAACTTGTCA
G
Found at i:6176 original size:64 final size:64
Alignment explanation
Indices: 6094--6322 Score: 282
Period size: 64 Copynumber: 3.5 Consensus size: 64
6084 GTTTGCTAGA
* * *
6094 AAGAATTTTCA-AATGTTGATCGGAAGACGAACTTGTCAGGAAGTACACCAGAAGATGGTTTCTT
1 AAGATTTTTCAGAA-GTTGATCGGAAGACGATCTTGTCAAGAAGTACACCAGAAGATGGTTTCTT
* * *
6158 AAGATTTTTCAGAAGTTGATCGGAAGACGATCTTGTCAAAAATTACACCAGAGGATGGTTT-TT
1 AAGATTTTTCAGAAGTTGATCGGAAGACGATCTTGTCAAGAAGTACACCAGAAGATGGTTTCTT
* * * * * *
6221 CAAGAGTTTCCAGAAGTCGATCGGAAGACGATCTTGTCAAGAAGTACATCGGAAGATGGTTTCTC
1 -AAGATTTTTCAGAAGTTGATCGGAAGACGATCTTGTCAAGAAGTACACCAGAAGATGGTTTCTT
* *
6286 AAGAGTTTTTTCAGAAGTTGATTGGAGGACGATCTTG
1 AAGA--TTTTTCAGAAGTTGATCGGAAGACGATCTTG
6323 ATGCACCGGA
Statistics
Matches: 140, Mismatches: 20, Indels: 8
0.83 0.12 0.05
Matches are distributed among these distances:
63 2 0.01
64 109 0.78
65 3 0.02
66 26 0.19
ACGTcount: A:0.32, C:0.14, G:0.25, T:0.29
Consensus pattern (64 bp):
AAGATTTTTCAGAAGTTGATCGGAAGACGATCTTGTCAAGAAGTACACCAGAAGATGGTTTCTT
Found at i:6552 original size:35 final size:35
Alignment explanation
Indices: 6506--6719 Score: 249
Period size: 35 Copynumber: 6.1 Consensus size: 35
6496 ATGAAAATTC
*
6506 TCAAAGTTAGAATCAGATGACTTAGTGTAGCATCT
1 TCAAAGTTAGAATCAGATGACTCAGTGTAGCATCT
* **
6541 TCAAAGCTAGAATCAGATGACTCAACGTAGCATCT
1 TCAAAGTTAGAATCAGATGACTCAGTGTAGCATCT
*
6576 TCAAAGTTAGAATCAGATGACTCGGTGTAGCATCT
1 TCAAAGTTAGAATCAGATGACTCAGTGTAGCATCT
*
6611 TCAAAGTTAGAATCAGATGACTCGGTGTAGCATCT
1 TCAAAGTTAGAATCAGATGACTCAGTGTAGCATCT
* * * *
6646 TCAAAGAT-GAACTCAG-TAGGCTCGGTGCAGCAAATCT
1 TCAAAGTTAGAA-TCAGAT-GACTCAGTGTAGC--ATCT
*
6683 TCAAA--TAG-ATCAGGATGACTCGGTGTAGCATCT
1 TCAAAGTTAGAATCA-GATGACTCAGTGTAGCATCT
6716 TCAA
1 TCAA
6720 TATGGACCCA
Statistics
Matches: 159, Mismatches: 13, Indels: 16
0.85 0.07 0.09
Matches are distributed among these distances:
33 8 0.05
34 7 0.04
35 133 0.84
36 2 0.01
37 9 0.06
ACGTcount: A:0.33, C:0.19, G:0.21, T:0.27
Consensus pattern (35 bp):
TCAAAGTTAGAATCAGATGACTCAGTGTAGCATCT
Found at i:6700 original size:105 final size:104
Alignment explanation
Indices: 6506--6719 Score: 274
Period size: 105 Copynumber: 2.0 Consensus size: 104
6496 ATGAAAATTC
* * *
6506 TCAAAGTTAGAATCAGATGACTTAGTGTAGCATCTTCAAAGCTAGAATCAGATGACTCAACGTAG
1 TCAAAGTTAGAATCAGATGACTCAGTGTAGCATCTTCAAAGATAGAATCAGATGACTCAACGCAG
6571 CATCTTCAAAGTTAGAATCAGATGACTCGGTGTAGCATCT
66 CATCTTCAAAG-TAGAATCAGATGACTCGGTGTAGCATCT
* * ***
6611 TCAAAGTTAGAATCAGATGACTCGGTGTAGCATCTTCAAAGAT-GAACTCAG-TAGGCTCGGTGC
1 TCAAAGTTAGAATCAGATGACTCAGTGTAGCATCTTCAAAGATAGAA-TCAGAT-GACTCAACGC
6674 AGCAAATCTTCAAA-TAG-ATCAGGATGACTCGGTGTAGCATCT
64 AGC--ATCTTCAAAGTAGAATCA-GATGACTCGGTGTAGCATCT
6716 TCAA
1 TCAA
6720 TATGGACCCA
Statistics
Matches: 96, Mismatches: 8, Indels: 10
0.84 0.07 0.09
Matches are distributed among these distances:
104 8 0.08
105 79 0.82
107 9 0.09
ACGTcount: A:0.33, C:0.19, G:0.21, T:0.27
Consensus pattern (104 bp):
TCAAAGTTAGAATCAGATGACTCAGTGTAGCATCTTCAAAGATAGAATCAGATGACTCAACGCAG
CATCTTCAAAGTAGAATCAGATGACTCGGTGTAGCATCT
Found at i:6752 original size:69 final size:70
Alignment explanation
Indices: 6607--6776 Score: 245
Period size: 69 Copynumber: 2.4 Consensus size: 70
6597 TCGGTGTAGC
*
6607 ATCTTCAAAGTTAGAATCA-GATGACTCGGTGTAGCATCTTCAAAGATGAACTCAGTAGGCTCGG
1 ATCTTCAAA--TAG-ATCAGGATGACTCGGTGTAGCATCTTCAAAGATGAACCCAGTAGGCTCGG
6671 TGCAGCAA
63 TGCAGCAA
* * * *
6679 ATCTTCAAATAGATCAGGATGACTCGGTGTAGCATCTTC-AATATGGACCCAGTGGGCTCGTTGC
1 ATCTTCAAATAGATCAGGATGACTCGGTGTAGCATCTTCAAAGATGAACCCAGTAGGCTCGGTGC
6743 AGCAA
66 AGCAA
*
6748 ATCTTCAAATAGATCAGGATGATTCGGTG
1 ATCTTCAAATAGATCAGGATGACTCGGTG
6777 AATCAAGTCA
Statistics
Matches: 91, Mismatches: 6, Indels: 5
0.89 0.06 0.05
Matches are distributed among these distances:
69 57 0.63
70 25 0.27
72 9 0.10
ACGTcount: A:0.30, C:0.19, G:0.24, T:0.26
Consensus pattern (70 bp):
ATCTTCAAATAGATCAGGATGACTCGGTGTAGCATCTTCAAAGATGAACCCAGTAGGCTCGGTGC
AGCAA
Found at i:9434 original size:28 final size:28
Alignment explanation
Indices: 9391--9544 Score: 245
Period size: 28 Copynumber: 5.5 Consensus size: 28
9381 CTTTACTTCC
* **
9391 CATTTTGGTCACTTTTCATAACCAGGGG
1 CATTTTGGTCATTTTTCATGTCCAGGGG
9419 CATTTTGGTCATTTTTCATGTCCAGGGG
1 CATTTTGGTCATTTTTCATGTCCAGGGG
*
9447 CATTTTGGTCATTTTTCATATCCAGGGG
1 CATTTTGGTCATTTTTCATGTCCAGGGG
*
9475 CATTTTGGTCATTTTTTATGTCCAGGGG
1 CATTTTGGTCATTTTTCATGTCCAGGGG
*
9503 CATTTTGGTCACTTTTCATGTCCAGGGG
1 CATTTTGGTCATTTTTCATGTCCAGGGG
*
9531 CATTTTGGTAATTT
1 CATTTTGGTCATTT
9545 CAAGTGTACT
Statistics
Matches: 116, Mismatches: 10, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
28 116 1.00
ACGTcount: A:0.17, C:0.18, G:0.23, T:0.43
Consensus pattern (28 bp):
CATTTTGGTCATTTTTCATGTCCAGGGG
Done.