Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01024867.1 Corchorus olitorius cultivar O-4 contig24900, 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: 8036
ACGTcount: A:0.35, C:0.17, G:0.16, T:0.33
Found at i:201 original size:20 final size:20
Alignment explanation
Indices: 163--204 Score: 57
Period size: 20 Copynumber: 2.1 Consensus size: 20
153 CTTGTTCTTT
* *
163 TGGCACCTGAATTCTTGATG
1 TGGCACCTGAACTCGTGATG
*
183 TGGCACCTGAACTGGTGATG
1 TGGCACCTGAACTCGTGATG
203 TG
1 TG
205 TACTGAATGA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.19, C:0.19, G:0.31, T:0.31
Consensus pattern (20 bp):
TGGCACCTGAACTCGTGATG
Found at i:1496 original size:22 final size:23
Alignment explanation
Indices: 1444--1652 Score: 97
Period size: 22 Copynumber: 9.6 Consensus size: 23
1434 TAACGAGTAC
* *
1444 CAAAATTTAATAGA-A-GGTTAT
1 CAAAATTTCATAGAGATGATTAT
*
1465 C-AAATCTCATAGAG-TGATTAT
1 CAAAATTTCATAGAGATGATTAT
*
1486 CGAAATTTCATAGAGATCGGATTAT
1 CAAAATTTCATAGAGAT--GATTAT
* *
1511 CAAAATTTCATAGTGTTG-TTAT
1 CAAAATTTCATAGAGATGATTAT
* *
1533 CAAAATTACATA-ATG-TGATTGT
1 CAAAATTTCATAGA-GATGATTAT
* * * *
1555 CAAAATTTC--AGAG-GGGTCAA
1 CAAAATTTCATAGAGATGATTAT
* *
1575 C-AAATTTTATAGAGA-GGTTAT
1 CAAAATTTCATAGAGATGATTAT
* * *
1596 CAAATTTTCATAAAGA-GGTTAT
1 CAAAATTTCATAGAGATGATTAT
* * *
1618 CAAATTTTCA-AAATG-TGATTAC
1 CAAAATTTCATAGA-GATGATTAT
1640 CAAAATTTCATAG
1 CAAAATTTCATAG
1653 TGGTATTTCT
Statistics
Matches: 146, Mismatches: 26, Indels: 30
0.72 0.13 0.15
Matches are distributed among these distances:
19 6 0.04
20 15 0.10
21 22 0.15
22 80 0.55
23 3 0.02
25 20 0.14
ACGTcount: A:0.40, C:0.11, G:0.15, T:0.34
Consensus pattern (23 bp):
CAAAATTTCATAGAGATGATTAT
Found at i:1605 original size:85 final size:87
Alignment explanation
Indices: 1488--1649 Score: 202
Period size: 85 Copynumber: 1.9 Consensus size: 87
1478 GTGATTATCG
** ** *
1488 AAATTTCATAGAGATCGGATTATCAAAATTTCATAGTGTTGTTATCAAAATTACATAATGTGATT
1 AAATTTCATAGAGA-CGGATTATCAAAATTTCATAAAGAGGTTATCAAAATTACAAAATGTGATT
**
1553 GTCAAAATTTCAGAGGGGTCAAC
65 ACCAAAATTTCAGAGGGGTCAAC
* * * *
1576 AAATTTTATAGAGA-GG-TTATCAAATTTTCATAAAGAGGTTATCAAATTTTCAAAATGTGATTA
1 AAATTTCATAGAGACGGATTATCAAAATTTCATAAAGAGGTTATCAAAATTACAAAATGTGATTA
1639 CCAAAATTTCA
66 CCAAAATTTCA
1650 TAGTGGTATT
Statistics
Matches: 63, Mismatches: 11, Indels: 3
0.82 0.14 0.04
Matches are distributed among these distances:
85 48 0.76
86 2 0.03
88 13 0.21
ACGTcount: A:0.40, C:0.10, G:0.15, T:0.35
Consensus pattern (87 bp):
AAATTTCATAGAGACGGATTATCAAAATTTCATAAAGAGGTTATCAAAATTACAAAATGTGATTA
CCAAAATTTCAGAGGGGTCAAC
Found at i:1829 original size:22 final size:23
Alignment explanation
Indices: 1804--1856 Score: 81
Period size: 23 Copynumber: 2.3 Consensus size: 23
1794 GTATGTAGAT
1804 CAAAATTTCATAA-GGAGATTAA
1 CAAAATTTCATAAGGGAGATTAA
* *
1826 CAAAATTTCATAAGGGAGGTTAT
1 CAAAATTTCATAAGGGAGATTAA
1849 CAAAATTT
1 CAAAATTT
1857 GTAGTTATCA
Statistics
Matches: 28, Mismatches: 2, Indels: 1
0.90 0.06 0.03
Matches are distributed among these distances:
22 13 0.46
23 15 0.54
ACGTcount: A:0.45, C:0.09, G:0.15, T:0.30
Consensus pattern (23 bp):
CAAAATTTCATAAGGGAGATTAA
Found at i:1852 original size:23 final size:22
Alignment explanation
Indices: 1733--2165 Score: 222
Period size: 22 Copynumber: 19.6 Consensus size: 22
1723 TTATGGAGTA
*
1733 ATCAAAATTTC-T-GGGAGGAT
1 ATCAAAATTTCATAGGGAGGTT
* * *
1753 ATCAAAATTTTATATGAAGGTT
1 ATCAAAATTTCATAGGGAGGTT
* * *
1775 ATCAAAATTTCATAGTTTAGTATGTAG
1 ATCAAAATTTCATAG----GGAGGT-T
* *
1802 ATCAAAATTTCATAAGGAGATT
1 ATCAAAATTTCATAGGGAGGTT
*
1824 AACAAAATTTCATAAGGGAGGTT
1 ATCAAAATTTCAT-AGGGAGGTT
*
1847 ATCAAAA-TT--T--GTA-GTT
1 ATCAAAATTTCATAGGGAGGTT
* *
1863 ATCAAGATTTCATAAGGAGGTT
1 ATCAAAATTTCATAGGGAGGTT
*
1885 ATCAAAATTTTATAGGGAGGTTT
1 ATCAAAATTTCATAGGGAGG-TT
* *
1908 ATCAAAATTTTATAGGAAGGTTT
1 ATCAAAATTTCATAGGGAGG-TT
* *
1931 ATCAAAATTTCATAGCGAGGCT
1 ATCAAAATTTCATAGGGAGGTT
* ** * *
1953 ATCACAATTTCATACTGTGATT
1 ATCAAAATTTCATAGGGAGGTT
* * * *
1975 ATCAAAATTTCAGAGTGTGATT
1 ATCAAAATTTCATAGGGAGGTT
* *
1997 A-CTAACAA-TTCATATGGAGATT
1 ATC-AA-AATTTCATAGGGAGGTT
* * * ** *
2019 TTTAAATTTTCATAACGTGGTT
1 ATCAAAATTTCATAGGGAGGTT
* * * *
2041 ATCAATATATAATATGGAGGTT
1 ATCAAAATTTCATAGGGAGGTT
* * **
2063 ATCAACATCTCATAGTGTTGGTT
1 ATCAAAATTTCATAG-GGAGGTT
* * * *
2086 ATCAAAATTTCCTTGAGAAGTT
1 ATCAAAATTTCATAGGGAGGTT
*
2108 ATCAAAATTTCATAGCGAGGTCT
1 ATCAAAATTTCATAGGGAGGT-T
* *
2131 -TCAAAATTCCTTAGGGAGGTT
1 ATCAAAATTTCATAGGGAGGTT
*
2152 AGCAAAATTTCATA
1 ATCAAAATTTCATA
2166 AGGTTAAAAA
Statistics
Matches: 309, Mismatches: 82, Indels: 42
0.71 0.19 0.10
Matches are distributed among these distances:
16 9 0.03
17 4 0.01
19 1 0.00
20 11 0.04
21 6 0.02
22 184 0.60
23 76 0.25
26 4 0.01
27 14 0.05
ACGTcount: A:0.37, C:0.11, G:0.17, T:0.36
Consensus pattern (22 bp):
ATCAAAATTTCATAGGGAGGTT
Found at i:1910 original size:61 final size:61
Alignment explanation
Indices: 1802--1917 Score: 180
Period size: 61 Copynumber: 1.9 Consensus size: 61
1792 TAGTATGTAG
1802 ATCAAAATTTCATAAGGAGATTAACAAAATTTCATAAGGGAGGTTATCAAAATTTGTAGTT
1 ATCAAAATTTCATAAGGAGATTAACAAAATTTCATAAGGGAGGTTATCAAAATTTGTAGTT
* * * *
1863 ATCAAGATTTCATAAGGAGGTTATCAAAATTTTAT-AGGGAGGTTTATCAAAATTT
1 ATCAAAATTTCATAAGGAGATTAACAAAATTTCATAAGGGAGG-TTATCAAAATTT
1918 TATAGGAAGG
Statistics
Matches: 50, Mismatches: 4, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
60 7 0.14
61 43 0.86
ACGTcount: A:0.41, C:0.08, G:0.17, T:0.34
Consensus pattern (61 bp):
ATCAAAATTTCATAAGGAGATTAACAAAATTTCATAAGGGAGGTTATCAAAATTTGTAGTT
Found at i:2255 original size:23 final size:22
Alignment explanation
Indices: 2212--2266 Score: 67
Period size: 22 Copynumber: 2.5 Consensus size: 22
2202 CCATATTATC
*
2212 GTTATGAAAATTTTCATAGGAAG
1 GTTATCAAAATTTTCATAGG-AG
2235 GTTATCAAAA-TTTCATAAGGAG
1 GTTATCAAAATTTTCAT-AGGAG
*
2257 GTCATCAAAA
1 GTTATCAAAA
2267 ATAGTGTAAT
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
22 17 0.59
23 12 0.41
ACGTcount: A:0.42, C:0.09, G:0.18, T:0.31
Consensus pattern (22 bp):
GTTATCAAAATTTTCATAGGAG
Found at i:4059 original size:22 final size:23
Alignment explanation
Indices: 4031--4073 Score: 79
Period size: 22 Copynumber: 1.9 Consensus size: 23
4021 TAGAAGGAGT
4031 AGGTTTTACT-TTCCTACTAGAA
1 AGGTTTTACTATTCCTACTAGAA
4053 AGGTTTTACTATTCCTACTAG
1 AGGTTTTACTATTCCTACTAG
4074 GATTAGGATT
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
22 10 0.50
23 10 0.50
ACGTcount: A:0.26, C:0.19, G:0.14, T:0.42
Consensus pattern (23 bp):
AGGTTTTACTATTCCTACTAGAA
Found at i:4697 original size:23 final size:23
Alignment explanation
Indices: 4669--4899 Score: 327
Period size: 23 Copynumber: 10.0 Consensus size: 23
4659 AAGACAAATA
*
4669 AGCAAAACAACAACATTTTGAAC
1 AGCAAAACAACAACATTTTCAAC
* *
4692 ATCAAAACAACAACATTTTGAAC
1 AGCAAAACAACAACATTTTCAAC
* *
4715 AACAAAACAACACCATTTTCAAC
1 AGCAAAACAACAACATTTTCAAC
*
4738 AGCAAAACAACAACATTTTGAAC
1 AGCAAAACAACAACATTTTCAAC
* *
4761 AACAAAACAACACCATTTTCAAC
1 AGCAAAACAACAACATTTTCAAC
* * * *
4784 AGCAAAATAGCACCAATTTCAAC
1 AGCAAAACAACAACATTTTCAAC
* *
4807 AGCAAAACAACAGCATTTTCAAT
1 AGCAAAACAACAACATTTTCAAC
*
4830 ACCAAAACAACAACATTTTCAAC
1 AGCAAAACAACAACATTTTCAAC
4853 AGCAAAACAACAACATTTTCAAC
1 AGCAAAACAACAACATTTTCAAC
4876 AGCAAAACAACAACATTTTCAAC
1 AGCAAAACAACAACATTTTCAAC
4899 A
1 A
4900 AAGAAAATAG
Statistics
Matches: 185, Mismatches: 23, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
23 185 1.00
ACGTcount: A:0.52, C:0.26, G:0.05, T:0.18
Consensus pattern (23 bp):
AGCAAAACAACAACATTTTCAAC
Done.