Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01021258.1 Corchorus olitorius cultivar O-4 contig21291, 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: 10071
ACGTcount: A:0.32, C:0.15, G:0.16, T:0.37
Found at i:1605 original size:22 final size:22
Alignment explanation
Indices: 1567--1782 Score: 152
Period size: 22 Copynumber: 9.8 Consensus size: 22
1557 AGATTTGAGA
* *
1567 AGGTTA-CCAAATCTCATAGAG
1 AGGTTATCAAAATTTCATAGAG
* *
1588 TGGTTATCGAAATTTCATAGAG
1 AGGTTATCAAAATTTCATAGAG
*
1610 ATCAGATTATCAAAATTT-ATA-AG
1 ---AGGTTATCAAAATTTCATAGAG
* * *
1633 AAGATTATCAAAATTTTATAGTG
1 -AGGTTATCAAAATTTCATAGAG
*** * *
1656 TTATTATCAAAATTTCAAAGCG
1 AGGTTATCAAAATTTCATAGAG
*
1678 AGGTTATCAAAATTACATA-ATG
1 AGGTTATCAAAATTTCATAGA-G
* * *
1700 TGATTATCAAAATTTTATAGAG
1 AGGTTATCAAAATTTCATAGAG
* * * *
1722 GGGTCAACAAAATTTTATAGAG
1 AGGTTATCAAAATTTCATAGAG
*
1744 AGGTTATCAAAATTTCATAAAG
1 AGGTTATCAAAATTTCATAGAG
*
1766 AGGTTATCAAATTTTCA
1 AGGTTATCAAAATTTCA
1783 AAATGTGATT
Statistics
Matches: 154, Mismatches: 33, Indels: 15
0.76 0.16 0.07
Matches are distributed among these distances:
21 20 0.13
22 115 0.75
23 4 0.03
24 3 0.02
25 12 0.08
ACGTcount: A:0.41, C:0.10, G:0.15, T:0.34
Consensus pattern (22 bp):
AGGTTATCAAAATTTCATAGAG
Found at i:1706 original size:44 final size:45
Alignment explanation
Indices: 1575--1806 Score: 192
Period size: 44 Copynumber: 5.2 Consensus size: 45
1565 GAAGGTTACC
* * *
1575 AAATCTCAT-AGAGTGGTTATCGAAATTTCATAGA-GATCAGATTATCA
1 AAATTTCATAAGAGAGGTTATCAAAATTTCATA-ATG-T--GATTATCA
* * * *
1622 AAATTT-ATAAGA-AGATTATCAAAATTTTATAGTGTTATTATCA
1 AAATTTCATAAGAGAGGTTATCAAAATTTCATAATGTGATTATCA
* *
1665 AAATTTCA-AAGCGAGGTTATCAAAATTACATAATGTGATTATCA
1 AAATTTCATAAGAGAGGTTATCAAAATTTCATAATGTGATTATCA
* * * * * * *
1709 AAATTTTAT-AGAGGGGTCAACAAAATTTTATAGA-GAGGTTATCA
1 AAATTTCATAAGAGAGGTTATCAAAATTTCATA-ATGTGATTATCA
* * *
1753 AAATTTCATAA-AGAGGTTATCAAATTTTCAAAATGTGATTACCA
1 AAATTTCATAAGAGAGGTTATCAAAATTTCATAATGTGATTATCA
1797 AAATTTCATA
1 AAATTTCATA
1807 GTGGTATTTC
Statistics
Matches: 145, Mismatches: 32, Indels: 19
0.74 0.16 0.10
Matches are distributed among these distances:
43 17 0.12
44 99 0.68
45 3 0.02
46 18 0.12
47 8 0.06
ACGTcount: A:0.42, C:0.09, G:0.14, T:0.34
Consensus pattern (45 bp):
AAATTTCATAAGAGAGGTTATCAAAATTTCATAATGTGATTATCA
Found at i:1716 original size:66 final size:66
Alignment explanation
Indices: 1616--1804 Score: 186
Period size: 66 Copynumber: 2.9 Consensus size: 66
1606 AGAGATCAGA
* * * *
1616 TTATCAAAATT-TAT-AAGAAGATTATCAAAATTTTATAGTGTTATTATCAAAATTTCAAAGCGA
1 TTATCAAAATTACATAAAG-AGATTATCAAAATTTTATAGTGTGATTAACAAAATTTCAAAGAGA
1679 GG
65 GG
* * * * * * * *
1681 TTATCAAAATTACATAATGTGATTATCAAAATTTTATAGAGGGGTCAACAAAATTTTATAGAGAG
1 TTATCAAAATTACATAAAGAGATTATCAAAATTTTATAGTGTGATTAACAAAATTTCAAAGAGAG
1746 G
66 G
* * * * *
1747 TTATCAAAATTTCATAAAGAGGTTATC-AAATTTTCAAAATGTGATTACCAAAATTTCA
1 TTATCAAAATTACATAAAGAGATTATCAAAATTTT-ATAGTGTGATTAACAAAATTTCA
1805 TAGTGGTATT
Statistics
Matches: 97, Mismatches: 24, Indels: 5
0.77 0.19 0.04
Matches are distributed among these distances:
65 18 0.19
66 77 0.79
67 2 0.02
ACGTcount: A:0.43, C:0.09, G:0.13, T:0.35
Consensus pattern (66 bp):
TTATCAAAATTACATAAAGAGATTATCAAAATTTTATAGTGTGATTAACAAAATTTCAAAGAGAG
G
Found at i:1740 original size:88 final size:88
Alignment explanation
Indices: 1641--1807 Score: 228
Period size: 88 Copynumber: 1.9 Consensus size: 88
1631 AGAAGATTAT
* ** * *
1641 CAAAATTTTATAGTGTTATTATCAAAATTTCA-AAGCGAGGTTATCAAAATTACATAATGTGATT
1 CAAAATTTTATAGAGAGATTATCAAAATTTCATAA-AGAGGTTATCAAAATTACAAAATGTGATT
* *
1705 ATCAAAATTTTATAGAGGGGTCAA
65 ACCAAAATTTCATAGAGGGGTCAA
* * *
1729 CAAAATTTTATAGAGAGGTTATCAAAATTTCATAAAGAGGTTATCAAATTTTCAAAATGTGATTA
1 CAAAATTTTATAGAGAGATTATCAAAATTTCATAAAGAGGTTATCAAAATTACAAAATGTGATTA
1794 CCAAAATTTCATAG
66 CCAAAATTTCATAG
1808 TGGTATTTCT
Statistics
Matches: 68, Mismatches: 10, Indels: 2
0.85 0.12 0.03
Matches are distributed among these distances:
88 66 0.97
89 2 0.03
ACGTcount: A:0.42, C:0.10, G:0.14, T:0.35
Consensus pattern (88 bp):
CAAAATTTTATAGAGAGATTATCAAAATTTCATAAAGAGGTTATCAAAATTACAAAATGTGATTA
CCAAAATTTCATAGAGGGGTCAA
Found at i:1935 original size:22 final size:22
Alignment explanation
Indices: 1907--2465 Score: 146
Period size: 22 Copynumber: 25.7 Consensus size: 22
1897 TCAGGCATGA
1907 TATCAAAATTTCATATGAAGGT
1 TATCAAAATTTCATATGAAGGT
**
1929 TATCAAAATTTCATAGTTTA-GT
1 TATCAAAATTTCATA-TGAAGGT
* * *
1951 TTTCAAATTTTCATAAG-AGGAT
1 TATCAAAATTTCATATGAAGG-T
* *
1973 TATCAAAATTTCATA-GTATGT
1 TATCAAAATTTCATATGAAGGT
* * * *
1994 AGATCAAAATTTCATAGGGAGAT
1 -TATCAAAATTTCATATGAAGGT
*
2017 TA-AAAAATTTTCATAATG-AGGT
1 TATCAAAA-TTTCAT-ATGAAGGT
** *
2039 TATCAAAAAATCATAGGGAA-GT
1 TATCAAAATTTCATA-TGAAGGT
*
2061 TATCAAAA--T--T-TGTA-GT
1 TATCAAAATTTCATATGAAGGT
* * *
2077 TATCAAGATTTCATAAGGAGGT
1 TATCAAAATTTCATATGAAGGT
* **
2099 TATCAAAATTTTATA-GCGTGGTT
1 TATCAAAATTTCATATG-AAGG-T
* * *
2122 TATCAAAATTTTATAGGAATGTT
1 TATCAAAATTTCATATGAA-GGT
*
2145 TATCAAAATTTCATA-GCGAGGT
1 TATCAAAATTTCATATG-AAGGT
* * * *
2167 TATCACAATGTCATAGTG-TGAT
1 TATCAAAATTTCATA-TGAAGGT
* * * *
2189 TATCAAAATTTTAGAGTG-TGAT
1 TATCAAAATTTCATA-TGAAGGT
*
2211 TA-CTAATAA-TTCATATGAATGT
1 TATC-AA-AATTTCATATGAAGGT
* * * * *
2233 TTTTAAATTTTCATAACG-TGGT
1 TATCAAAATTTCAT-ATGAAGGT
* *
2255 TATCAATATATCATATGGAA-GT
1 TATCAAAATTTCATAT-GAAGGT
** * * **
2277 TATCAACGTCTCA-GTGTTGGT
1 TATCAAAATTTCATATGAAGGT
*
2298 AATCAAAATTTCAT-TGGGAA-GT
1 TATCAAAATTTCATAT--GAAGGT
2320 TATCAAAATTTCATAGTG-AGGT
1 TATCAAAATTTCATA-TGAAGGT
* * *
2342 CT-TCAAAATTTCTTACGGAGGT
1 -TATCAAAATTTCATATGAAGGT
* *
2364 TAACAAAATTTCATAAGAAGGT
1 TATCAAAATTTCATATGAAGGT
* * **
2386 TA-AAAAATTTTATAAAAAGGT
1 TATCAAAATTTCATATGAAGGT
* * * **
2407 TCTCGAAATTTTATA-GTATCGT
1 TATCAAAATTTCATATG-AAGGT
* * *
2429 TATTAAAATTTCATAAGAAGAT
1 TATCAAAATTTCATATGAAGGT
2451 TATCAAAATTTCATA
1 TATCAAAATTTCATA
2466 AGGAGACCAT
Statistics
Matches: 395, Mismatches: 97, Indels: 90
0.68 0.17 0.15
Matches are distributed among these distances:
16 11 0.03
18 2 0.01
20 4 0.01
21 49 0.12
22 274 0.69
23 51 0.13
24 4 0.01
ACGTcount: A:0.38, C:0.09, G:0.15, T:0.37
Consensus pattern (22 bp):
TATCAAAATTTCATATGAAGGT
Found at i:1986 original size:66 final size:64
Alignment explanation
Indices: 1907--2071 Score: 163
Period size: 66 Copynumber: 2.5 Consensus size: 64
1897 TCAGGCATGA
** ***
1907 TATCAAAATTTCATATGAAGGTTATCAAAATTTCATAGTTTAG-TTTTCAAATTTTCATAA-GAG
1 TATCAAAATTTCATA-GAA-GTTATCAAAATTTCATAG-GGAGATTAAAAAATTTTCATAATGAG
1970 GAT
63 G-T
* *
1973 TATCAAAATTTCATAGTATGTAGATCAAAATTTCATAGGGAGATTAAAAAATTTTCATAATGAGG
1 TATCAAAATTTCATAG-AAGT-TATCAAAATTTCATAGGGAGATTAAAAAATTTTCATAATGAGG
2038 T
64 T
**
2039 TATCAAAAAATCATAGGGAAGTTATCAAAATTT
1 TATCAAAATTTCATA--GAAGTTATCAAAATTT
2072 GTAGTTATCA
Statistics
Matches: 82, Mismatches: 11, Indels: 12
0.78 0.10 0.11
Matches are distributed among these distances:
65 5 0.06
66 69 0.84
67 7 0.09
68 1 0.01
ACGTcount: A:0.42, C:0.08, G:0.13, T:0.36
Consensus pattern (64 bp):
TATCAAAATTTCATAGAAGTTATCAAAATTTCATAGGGAGATTAAAAAATTTTCATAATGAGGT
Found at i:2128 original size:23 final size:22
Alignment explanation
Indices: 2098--2201 Score: 102
Period size: 23 Copynumber: 4.6 Consensus size: 22
2088 CATAAGGAGG
2098 TTATCAAAATTTTATAGCGTGGT
1 TTATCAAAATTTTATAGCGT-GT
2121 TTATCAAAATTTTATAG-GAATGT
1 TTATCAAAATTTTATAGCG--TGT
* * *
2144 TTATCAAAATTTCATAGCGAGG
1 TTATCAAAATTTTATAGCGTGT
* * * * *
2166 TTATCACAATGTCATAGTGTGA
1 TTATCAAAATTTTATAGCGTGT
2188 TTATCAAAATTTTA
1 TTATCAAAATTTTA
2202 GAGTGTGATT
Statistics
Matches: 67, Mismatches: 11, Indels: 7
0.79 0.13 0.08
Matches are distributed among these distances:
22 30 0.45
23 35 0.52
24 2 0.03
ACGTcount: A:0.36, C:0.10, G:0.14, T:0.40
Consensus pattern (22 bp):
TTATCAAAATTTTATAGCGTGT
Found at i:2150 original size:46 final size:44
Alignment explanation
Indices: 2098--2201 Score: 120
Period size: 46 Copynumber: 2.3 Consensus size: 44
2088 CATAAGGAGG
* * * *
2098 TTATCAAAATTTTATAGCGTGGTTTATCAAAATTTTATAG-GAATGT
1 TTATCAAAATTTTATAGCGAGG-TTATCAAAATGTCATAGTG--TGA
* *
2144 TTATCAAAATTTCATAGCGAGGTTATCACAATGTCATAGTGTGA
1 TTATCAAAATTTTATAGCGAGGTTATCAAAATGTCATAGTGTGA
2188 TTATCAAAATTTTA
1 TTATCAAAATTTTA
2202 GAGTGTGATT
Statistics
Matches: 50, Mismatches: 7, Indels: 4
0.82 0.11 0.07
Matches are distributed among these distances:
44 15 0.30
45 14 0.28
46 21 0.42
ACGTcount: A:0.36, C:0.10, G:0.14, T:0.40
Consensus pattern (44 bp):
TTATCAAAATTTTATAGCGAGGTTATCAAAATGTCATAGTGTGA
Found at i:2477 original size:22 final size:22
Alignment explanation
Indices: 2433--2480 Score: 69
Period size: 22 Copynumber: 2.2 Consensus size: 22
2423 TATCGTTATT
**
2433 AAAATTTCATAAGAAGATTATC
1 AAAATTTCATAAGAAGACCATC
*
2455 AAAATTTCATAAGGAGACCATC
1 AAAATTTCATAAGAAGACCATC
2477 AAAA
1 AAAA
2481 ATAGTGTAAT
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
22 23 1.00
ACGTcount: A:0.52, C:0.12, G:0.10, T:0.25
Consensus pattern (22 bp):
AAAATTTCATAAGAAGACCATC
Found at i:4752 original size:2 final size:2
Alignment explanation
Indices: 4745--4775 Score: 55
Period size: 2 Copynumber: 16.0 Consensus size: 2
4735 AGATTAAAAC
4745 AT AT AT AT AT AT AT AT AT AT AT AT AT A- AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
4776 TGCGTGGATC
Statistics
Matches: 28, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
1 1 0.04
2 27 0.96
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:8913 original size:3 final size:3
Alignment explanation
Indices: 8905--8935 Score: 62
Period size: 3 Copynumber: 10.3 Consensus size: 3
8895 AGTAATGCTT
8905 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC T
1 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC T
8936 CTTTTTTTTT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 28 1.00
ACGTcount: A:0.00, C:0.32, G:0.00, T:0.68
Consensus pattern (3 bp):
TTC
Done.