Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01023085.1 Corchorus olitorius cultivar O-4 contig23118, 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: 17667
ACGTcount: A:0.31, C:0.15, G:0.18, T:0.35
Found at i:813 original size:36 final size:36
Alignment explanation
Indices: 766--835 Score: 113
Period size: 36 Copynumber: 1.9 Consensus size: 36
756 TTCAATAACC
* *
766 TTACATCTTTTGTGATTTTGGTTATCATATTTCTTA
1 TTACATCTTTTGTAATTTTGATTATCATATTTCTTA
*
802 TTACATTTTTTGTAATTTTGATTATCATATTTCT
1 TTACATCTTTTGTAATTTTGATTATCATATTTCT
836 CCAAAATCTC
Statistics
Matches: 31, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
36 31 1.00
ACGTcount: A:0.21, C:0.10, G:0.09, T:0.60
Consensus pattern (36 bp):
TTACATCTTTTGTAATTTTGATTATCATATTTCTTA
Found at i:1723 original size:204 final size:201
Alignment explanation
Indices: 1337--1746 Score: 712
Period size: 204 Copynumber: 2.0 Consensus size: 201
1327 GCTTAATAAC
*
1337 TTTATCAATGGTGAATATTATTAATTTTTTAATTCTAAGAATACTAACAAAGTTGTAGTGAATAA
1 TTTATCAATGGTGAATATTATTAATTTTTTAAGTCTAAGAATACTAACAAAGTTGTAGTGAATAA
* *
1402 GATACAACACATTATTATTATATATAAAACTATACCAAAAAAATTAGTTGAATATTAGTGGTTGA
66 GATACAACACATCACTATTATATATAAAACTATACCAAAAAAATTAGTTGAATATTAGTGGTTGA
*
1467 TTTATTAAATTAAATTAGATCAATGTCAAACAAAATTTCAAAATTATAAAAGACATTAAAGATCT
131 TTTATTAAATTAAATTAGATCAATGTCAAACAAAATTTCAAAATTATAAAAGACATTAAAGATCC
1532 GATTTA
196 GATTTA
* * *
1538 TTTATCAATGGTGAATGTTGTTAATTTTTTAAGTCTAAGATTACTAACAAAGTTGTAGTGAATAA
1 TTTATCAATGGTGAATATTATTAATTTTTTAAGTCTAAGAATACTAACAAAGTTGTAGTGAATAA
1603 GATACAACACATCACTATTATATATATAGAACTATACCAAAAAAAATTAGTTGAATATTAGTGGT
66 GATACAACACATCACTATTATATATA-A-AACTATACC-AAAAAAATTAGTTGAATATTAGTGGT
* *
1668 TGATTTATTAAATTAAATTAGATCAATGTCAAACAAAATTTCAAAATTATAAAAGATATTAAAGG
128 TGATTTATTAAATTAAATTAGATCAATGTCAAACAAAATTTCAAAATTATAAAAGACATTAAAGA
1733 TCCGATTTA
193 TCCGATTTA
1742 TTTAT
1 TTTAT
1747 TATTAAGGAA
Statistics
Matches: 197, Mismatches: 9, Indels: 3
0.94 0.04 0.01
Matches are distributed among these distances:
201 85 0.43
202 1 0.01
203 9 0.05
204 102 0.52
ACGTcount: A:0.44, C:0.08, G:0.11, T:0.37
Consensus pattern (201 bp):
TTTATCAATGGTGAATATTATTAATTTTTTAAGTCTAAGAATACTAACAAAGTTGTAGTGAATAA
GATACAACACATCACTATTATATATAAAACTATACCAAAAAAATTAGTTGAATATTAGTGGTTGA
TTTATTAAATTAAATTAGATCAATGTCAAACAAAATTTCAAAATTATAAAAGACATTAAAGATCC
GATTTA
Found at i:1855 original size:25 final size:24
Alignment explanation
Indices: 1821--1867 Score: 76
Period size: 25 Copynumber: 1.9 Consensus size: 24
1811 ACGTTTGCAC
1821 AAATACCTAAGAATTTGAATTAAAA
1 AAATACCTAAGAATTT-AATTAAAA
*
1846 AAATATCTAAGAATTTAATTAA
1 AAATACCTAAGAATTTAATTAA
1868 TGTAAGTATT
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
24 6 0.29
25 15 0.71
ACGTcount: A:0.55, C:0.06, G:0.06, T:0.32
Consensus pattern (24 bp):
AAATACCTAAGAATTTAATTAAAA
Found at i:2212 original size:42 final size:43
Alignment explanation
Indices: 2161--2254 Score: 120
Period size: 45 Copynumber: 2.2 Consensus size: 43
2151 AGTGCATTAT
*
2161 CTAA-ATTCTA-CTCCATCTCTAGGTAATTCATCAAAATAAAG
1 CTAATATTCTACCTCCATCTCTAGATAATTCATCAAAATAAAG
* * *
2202 CTGATATTCTACTCCTCCATCTCTAGATTATTCATCAAAATAAAT
1 CTAATATTCTA--CCTCCATCTCTAGATAATTCATCAAAATAAAG
2247 CTAATATT
1 CTAATATT
2255 AATTGTTGCT
Statistics
Matches: 44, Mismatches: 5, Indels: 4
0.83 0.09 0.08
Matches are distributed among these distances:
41 3 0.07
42 6 0.14
45 35 0.80
ACGTcount: A:0.36, C:0.22, G:0.05, T:0.36
Consensus pattern (43 bp):
CTAATATTCTACCTCCATCTCTAGATAATTCATCAAAATAAAG
Found at i:2894 original size:22 final size:23
Alignment explanation
Indices: 2863--2908 Score: 60
Period size: 22 Copynumber: 2.0 Consensus size: 23
2853 TAATATTCAC
2863 ACACAATTAAT-ATGAAAT-TAAA
1 ACACAATTAATCAT-AAATATAAA
*
2885 ACACACTTAATCATAAATATAAA
1 ACACAATTAATCATAAATATAAA
2908 A
1 A
2909 ATAGTAAATT
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
22 14 0.67
23 7 0.33
ACGTcount: A:0.59, C:0.13, G:0.02, T:0.26
Consensus pattern (23 bp):
ACACAATTAATCATAAATATAAA
Found at i:8745 original size:32 final size:32
Alignment explanation
Indices: 8708--8865 Score: 201
Period size: 32 Copynumber: 4.9 Consensus size: 32
8698 TATTAAAGAA
*
8708 AACGCCACAGATTAGTGGCGTTTTCTTCAAAG
1 AACGCCACAAATTAGTGGCGTTTTCTTCAAAG
* *
8740 TACGCCACAAATTAGTGGCGTTTCCTTTC-AAG
1 AACGCCACAAATTAGTGGCGTTTTC-TTCAAAG
* *
8772 AACGCCACAAATTAATGGTGTTTTCTTCAAAG
1 AACGCCACAAATTAGTGGCGTTTTCTTCAAAG
* *
8804 AATGCCACAAATTAGTGGCGTTTACTTCAAAG
1 AACGCCACAAATTAGTGGCGTTTTCTTCAAAG
** * *
8836 AACGCCACTGATTTGTGGCGTTTTATTCAA
1 AACGCCACAAATTAGTGGCGTTTTCTTCAA
8866 TAAACACCAT
Statistics
Matches: 107, Mismatches: 17, Indels: 4
0.84 0.13 0.03
Matches are distributed among these distances:
31 3 0.03
32 101 0.94
33 3 0.03
ACGTcount: A:0.29, C:0.21, G:0.19, T:0.31
Consensus pattern (32 bp):
AACGCCACAAATTAGTGGCGTTTTCTTCAAAG
Found at i:8776 original size:64 final size:64
Alignment explanation
Indices: 8676--8865 Score: 224
Period size: 64 Copynumber: 3.0 Consensus size: 64
8666 TACGTGAACA
* * *
8676 AACGCCACTAATTCGTGGCGCTTA-TT-AAAGAAAACGCCACAGATTAGTGGCGTTTTCTTCAAA
1 AACGCCACAAATTAGTGGCGTTTACTTCAAAG--AACGCCACAGATTAGTGGCGTTTTCTTCAAA
8739 G
64 G
* * * * *
8740 TACGCCACAAATTAGTGGCGTTTCCTTTC-AAGAACGCCACAAATTAATGGTGTTTTCTTCAAAG
1 AACGCCACAAATTAGTGGCGTTTAC-TTCAAAGAACGCCACAGATTAGTGGCGTTTTCTTCAAAG
* * * *
8804 AATGCCACAAATTAGTGGCGTTTACTTCAAAGAACGCCACTGATTTGTGGCGTTTTATTCAA
1 AACGCCACAAATTAGTGGCGTTTACTTCAAAGAACGCCACAGATTAGTGGCGTTTTCTTCAA
8866 TAAACACCAT
Statistics
Matches: 105, Mismatches: 17, Indels: 8
0.81 0.13 0.06
Matches are distributed among these distances:
63 3 0.03
64 97 0.92
66 5 0.05
ACGTcount: A:0.30, C:0.21, G:0.19, T:0.30
Consensus pattern (64 bp):
AACGCCACAAATTAGTGGCGTTTACTTCAAAGAACGCCACAGATTAGTGGCGTTTTCTTCAAAG
Found at i:11494 original size:21 final size:22
Alignment explanation
Indices: 11469--11515 Score: 55
Period size: 21 Copynumber: 2.2 Consensus size: 22
11459 TTGAAAGTCA
11469 GTTGAAAAC-TGATG-AGAATAT
1 GTTGAAAACATGA-GAAGAATAT
*
11490 GTTG-AGACATGAGAAGAATAT
1 GTTGAAAACATGAGAAGAATAT
11511 GTTGA
1 GTTGA
11516 GACATGAAGG
Statistics
Matches: 22, Mismatches: 1, Indels: 5
0.79 0.04 0.18
Matches are distributed among these distances:
20 4 0.18
21 18 0.82
ACGTcount: A:0.40, C:0.04, G:0.28, T:0.28
Consensus pattern (22 bp):
GTTGAAAACATGAGAAGAATAT
Found at i:11516 original size:21 final size:21
Alignment explanation
Indices: 11483--11522 Score: 80
Period size: 21 Copynumber: 1.9 Consensus size: 21
11473 AAAACTGATG
11483 AGAATATGTTGAGACATGAGA
1 AGAATATGTTGAGACATGAGA
11504 AGAATATGTTGAGACATGA
1 AGAATATGTTGAGACATGA
11523 AGGAGAGCTC
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.42, C:0.05, G:0.28, T:0.25
Consensus pattern (21 bp):
AGAATATGTTGAGACATGAGA
Found at i:15427 original size:24 final size:25
Alignment explanation
Indices: 15381--15428 Score: 62
Period size: 24 Copynumber: 2.0 Consensus size: 25
15371 ATTGGAGTAT
*
15381 TTATTTATCTTGTTGCTTAATTTTG
1 TTATTTATCTTGTTGATTAATTTTG
* *
15406 TTATTT-TCTTGTTTATTTATTTT
1 TTATTTATCTTGTTGATTAATTTT
15429 TATTGTTACT
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
24 14 0.70
25 6 0.30
ACGTcount: A:0.15, C:0.06, G:0.08, T:0.71
Consensus pattern (25 bp):
TTATTTATCTTGTTGATTAATTTTG
Found at i:15672 original size:33 final size:32
Alignment explanation
Indices: 15582--15675 Score: 100
Period size: 33 Copynumber: 2.9 Consensus size: 32
15572 ACACCCATCA
* *
15582 CTAGCTCATT-TCTTCTCTCTTCTTTAAATCGAG
1 CTAGCTC-TTGTCTTCTATCTTC-TTCAATCGAG
* * *
15615 CCAGCTCCTGTCGTCTATCTTCTTCAATGCGAG
1 CTAGCTCTTGTCTTCTATCTTCTTCAAT-CGAG
*
15648 CTAGCTCTTGTCTTCTTTCTTCTTCAAT
1 CTAGCTCTTGTCTTCTATCTTCTTCAAT
15676 TCTTGCAAGC
Statistics
Matches: 50, Mismatches: 9, Indels: 4
0.79 0.14 0.06
Matches are distributed among these distances:
32 6 0.12
33 44 0.88
ACGTcount: A:0.15, C:0.30, G:0.12, T:0.44
Consensus pattern (32 bp):
CTAGCTCTTGTCTTCTATCTTCTTCAATCGAG
Found at i:15687 original size:33 final size:33
Alignment explanation
Indices: 15611--15691 Score: 90
Period size: 33 Copynumber: 2.5 Consensus size: 33
15601 TTCTTTAAAT
* *
15611 CGAGCCAGCTCCTGTCGTCTATCTTCTTCAATG
1 CGAGCAAGCTCTTGTCGTCTATCTTCTTCAATG
* * * *
15644 CGAGCTAGCTCTTGTCTTCTTTCTTCTTCAATT
1 CGAGCAAGCTCTTGTCGTCTATCTTCTTCAATG
**
15677 CTTGCAAGCTCTTGT
1 CGAGCAAGCTCTTGT
15692 TGCCTTTCTA
Statistics
Matches: 40, Mismatches: 8, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
33 40 1.00
ACGTcount: A:0.14, C:0.30, G:0.16, T:0.41
Consensus pattern (33 bp):
CGAGCAAGCTCTTGTCGTCTATCTTCTTCAATG
Found at i:16210 original size:36 final size:37
Alignment explanation
Indices: 16141--16215 Score: 116
Period size: 36 Copynumber: 2.0 Consensus size: 37
16131 CTTGTTTCGC
16141 ACATAGCCCTCCCATCACCCTACACAAACAAAAACATA
1 ACATAGCCCTCCCATCA-CCTACACAAACAAAAACATA
* *
16179 ACATATCCCTCCCATCA-CTGCACAAACAAAAACATA
1 ACATAGCCCTCCCATCACCTACACAAACAAAAACATA
16215 A
1 A
16216 TTTAAACAAT
Statistics
Matches: 35, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
36 19 0.54
38 16 0.46
ACGTcount: A:0.45, C:0.37, G:0.03, T:0.15
Consensus pattern (37 bp):
ACATAGCCCTCCCATCACCTACACAAACAAAAACATA
Done.