Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01024312.1 Corchorus olitorius cultivar O-4 contig24345, 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: 6465
ACGTcount: A:0.37, C:0.18, G:0.14, T:0.31
Found at i:834 original size:66 final size:66
Alignment explanation
Indices: 737--864 Score: 159
Period size: 66 Copynumber: 1.9 Consensus size: 66
727 TTATAGGAAA
* * * * * *
737 ATTATCAAAATTTCATAGTGTTGTTCTCAAAATTTCAAAGATATGTTATCAAAATTACATAATGT
1 ATTATCAAAATTTCATAGAGTGGGTCACAAAATTTCAAAGAAAGGTTATCAAAATTACATAATGT
802 T
66 T
* * *
803 ATTATCAAAATTTCATAGAG-GGGTCAACAAAATTTTATAGAAAGGTTATCAAAATTTCATAA
1 ATTATCAAAATTTCATAGAGTGGGTC-ACAAAATTTCAAAGAAAGGTTATCAAAATTACATAA
865 AAAGGTTATC
Statistics
Matches: 52, Mismatches: 9, Indels: 2
0.83 0.14 0.03
Matches are distributed among these distances:
65 3 0.06
66 49 0.94
ACGTcount: A:0.42, C:0.10, G:0.11, T:0.37
Consensus pattern (66 bp):
ATTATCAAAATTTCATAGAGTGGGTCACAAAATTTCAAAGAAAGGTTATCAAAATTACATAATGT
T
Found at i:871 original size:22 final size:22
Alignment explanation
Indices: 719--876 Score: 99
Period size: 22 Copynumber: 7.2 Consensus size: 22
709 TGGTATTACA
*
719 ATCAAAATTT-ATAGGAAA-ATT
1 ATCAAAATTTCATA-GAAAGGTT
****
740 ATCAAAATTTCATAGTGTTGTT
1 ATCAAAATTTCATAGAAAGGTT
* * * *
762 CTCAAAATTTCAAAGATATGTT
1 ATCAAAATTTCATAGAAAGGTT
* * *
784 ATCAAAATTACAT--AATGTTATT
1 ATCAAAATTTCATAGAAAG--GTT
** *
806 ATCAAAATTTCATAGAGGGGTC
1 ATCAAAATTTCATAGAAAGGTT
* *
828 AACAAAATTTTATAGAAAGGTT
1 ATCAAAATTTCATAGAAAGGTT
*
850 ATCAAAATTTCATAAAAAGGTT
1 ATCAAAATTTCATAGAAAGGTT
872 ATCAA
1 ATCAA
877 GTTTTCAAAA
Statistics
Matches: 102, Mismatches: 29, Indels: 11
0.72 0.20 0.08
Matches are distributed among these distances:
20 1 0.01
21 11 0.11
22 88 0.86
24 2 0.02
ACGTcount: A:0.44, C:0.09, G:0.11, T:0.35
Consensus pattern (22 bp):
ATCAAAATTTCATAGAAAGGTT
Found at i:882 original size:22 final size:22
Alignment explanation
Indices: 832--883 Score: 70
Period size: 22 Copynumber: 2.4 Consensus size: 22
822 GGGGTCAACA
*
832 AAATTTT-ATAGAAAGGTTATC
1 AAATTTTCATAAAAAGGTTATC
*
853 AAAATTTCATAAAAAGGTTATC
1 AAATTTTCATAAAAAGGTTATC
*
875 AAGTTTTCA
1 AAATTTTCA
884 AAATGTGATT
Statistics
Matches: 26, Mismatches: 4, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
21 6 0.23
22 20 0.77
ACGTcount: A:0.44, C:0.08, G:0.12, T:0.37
Consensus pattern (22 bp):
AAATTTTCATAAAAAGGTTATC
Found at i:1033 original size:22 final size:22
Alignment explanation
Indices: 960--1148 Score: 102
Period size: 22 Copynumber: 8.6 Consensus size: 22
950 ACCAAATTAG
* * *
960 GAAGGTTATTAAACTTTTATTAT
1 GAAGGTTATCAAAATTTCA-TAT
* *
983 GAA-GTAATCAAAATTTC--AG
1 GAAGGTTATCAAAATTTCATAT
*
1002 GAAGGATATCAAAATTTCATAT
1 GAAGGTTATCAAAATTTCATAT
1024 GAAGGTTATCAAAATTTTCATAGT
1 GAAGGTTATCAAAA-TTTCATA-T
** * * *
1048 TTA-GTTTTCGAAATTTCATAA
1 GAAGGTTATCAAAATTTCATAT
*
1069 GAGGGTTATCAAAATTTCATA-
1 GAAGGTTATCAAAATTTCATAT
* * * * *
1090 GTATGTAGATCAAAATTTCAGAG
1 GAAGGT-TATCAAAATTTCATAT
* * *
1113 GGAGATTAACAAAATTTCATAAT
1 GAAGGTTATCAAAATTTCAT-AT
*
1136 -TAGGTTATCAAAA
1 GAAGGTTATCAAAA
1149 AATCATAGGG
Statistics
Matches: 123, Mismatches: 34, Indels: 19
0.70 0.19 0.11
Matches are distributed among these distances:
19 4 0.03
20 12 0.10
21 3 0.02
22 80 0.65
23 22 0.18
24 2 0.02
ACGTcount: A:0.41, C:0.08, G:0.15, T:0.35
Consensus pattern (22 bp):
GAAGGTTATCAAAATTTCATAT
Found at i:1239 original size:23 final size:23
Alignment explanation
Indices: 1185--1240 Score: 71
Period size: 23 Copynumber: 2.5 Consensus size: 23
1175 TAGTTATCAA
*
1185 ATAAGGAGG-TTATCAAAATTTT
1 ATAAGGAGGTTTATCAAAATTTC
1207 AT-AGGAAGGTTTATCAAAATTTC
1 ATAAGG-AGGTTTATCAAAATTTC
*
1230 ATAACGAGGTT
1 ATAAGGAGGTT
1241 ATTACAATTT
Statistics
Matches: 29, Mismatches: 2, Indels: 5
0.81 0.06 0.14
Matches are distributed among these distances:
21 3 0.10
22 5 0.17
23 19 0.66
24 2 0.07
ACGTcount: A:0.39, C:0.07, G:0.20, T:0.34
Consensus pattern (23 bp):
ATAAGGAGGTTTATCAAAATTTC
Found at i:1548 original size:22 final size:22
Alignment explanation
Indices: 1185--1548 Score: 97
Period size: 22 Copynumber: 16.5 Consensus size: 22
1175 TAGTTATCAA
*
1185 ATAAGGAGGTTATCAAAATTTT
1 ATAAGGAGGTTATCAAAATTTC
1207 AT-AGGAAGGTTTATCAAAATTTC
1 ATAAGG-AGG-TTATCAAAATTTC
* * * *
1230 ATAACGAGGTTATTACAATTTT
1 ATAAGGAGGTTATCAAAATTTC
* *
1252 AT-AGTGTGATTATCAAAATTTC
1 ATAAG-GAGGTTATCAAAATTTC
* * *
1274 A-GAGTACGATTA-CTAACAA-TTC
1 ATAAGGA-GGTTATC-AA-AATTTC
* **
1296 ATACGGAGGTT-TTTAAATCTTC
1 ATAAGGAGGTTATCAAAAT-TTC
* * *
1318 ATAACGTA-GTTATCAATATATC
1 ATAA-GGAGGTTATCAAAATTTC
* * * * *
1340 ATATGAAGGTTATCAACATCTA
1 ATAAGGAGGTTATCAAAATTTC
* *
1362 AT-AGTGTTGGTTATTAAAATTTC
1 ATAAG-G-AGGTTATCAAAATTTC
** **
1385 ATTGGGAAATTATCAAAATTTC
1 ATAAGGAGGTTATCAAAATTTC
*
1407 AT-AGTGAGGTCT-TCAAAATTCC
1 ATAAG-GAGGT-TATCAAAATTTC
* * *
1429 TTAGGGAGGTTAACAAAATTTC
1 ATAAGGAGGTTATCAAAATTTC
* * * *
1451 ATAAGAAGGTTA-AAGAAAATTA
1 ATAAGGAGGTTATCA-AAATTTC
** * * * *
1473 ATAAAAAGATTCTCGAAATTCC
1 ATAAGGAGGTTATCAAAATTTC
* ** *
1495 AT-AGTATCATTATTAAAATTTC
1 ATAAGGA-GGTTATCAAAATTTC
1517 AT-AGGAAGGTTATCAAAATTTC
1 ATAAGG-AGGTTATCAAAATTTC
1539 ATAAGGAGGT
1 ATAAGGAGGT
1549 CATAAAAAAT
Statistics
Matches: 240, Mismatches: 75, Indels: 54
0.65 0.20 0.15
Matches are distributed among these distances:
20 2 0.01
21 14 0.06
22 174 0.73
23 47 0.20
24 3 0.01
ACGTcount: A:0.39, C:0.10, G:0.16, T:0.35
Consensus pattern (22 bp):
ATAAGGAGGTTATCAAAATTTC
Found at i:1558 original size:23 final size:22
Alignment explanation
Indices: 1509--1556 Score: 62
Period size: 22 Copynumber: 2.2 Consensus size: 22
1499 TATCATTATT
* *
1509 AAAATTTCATAGGAAGGTTATC
1 AAAATTTCATAGGAAGGTCATA
1531 AAAATTTCATAAGG-AGGTCATA
1 AAAATTTCAT-AGGAAGGTCATA
1553 AAAA
1 AAAA
1557 ATAGTATAAT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
22 20 0.87
23 3 0.13
ACGTcount: A:0.48, C:0.08, G:0.17, T:0.27
Consensus pattern (22 bp):
AAAATTTCATAGGAAGGTCATA
Found at i:1570 original size:40 final size:40
Alignment explanation
Indices: 1526--1628 Score: 161
Period size: 40 Copynumber: 2.6 Consensus size: 40
1516 CATAGGAAGG
* * *
1526 TTATCAAAATTTCATAAGGAGGTCATAAAAAATAGTATAA
1 TTATCATAATTTAATACGGAGGTCATAAAAAATAGTATAA
* *
1566 TTATCATAATTTAATACGAAGGTCATAAAAAATAGTGTAA
1 TTATCATAATTTAATACGGAGGTCATAAAAAATAGTATAA
1606 TTATCATAATTTAATACGGAGGT
1 TTATCATAATTTAATACGGAGGT
1629 TATCATAATT
Statistics
Matches: 57, Mismatches: 6, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
40 57 1.00
ACGTcount: A:0.46, C:0.08, G:0.14, T:0.33
Consensus pattern (40 bp):
TTATCATAATTTAATACGGAGGTCATAAAAAATAGTATAA
Found at i:1775 original size:13 final size:13
Alignment explanation
Indices: 1757--1786 Score: 60
Period size: 13 Copynumber: 2.3 Consensus size: 13
1747 TCAAAGTAAT
1757 TAATTTACACATC
1 TAATTTACACATC
1770 TAATTTACACATC
1 TAATTTACACATC
1783 TAAT
1 TAAT
1787 GAATATTTTA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 17 1.00
ACGTcount: A:0.40, C:0.20, G:0.00, T:0.40
Consensus pattern (13 bp):
TAATTTACACATC
Found at i:6223 original size:22 final size:23
Alignment explanation
Indices: 6184--6226 Score: 79
Period size: 22 Copynumber: 1.9 Consensus size: 23
6174 AATCCTAATC
6184 CTGGTAGGAATAGTAAAACCTTT
1 CTGGTAGGAATAGTAAAACCTTT
6207 CTGGTAGGAA-AGTAAAACCT
1 CTGGTAGGAATAGTAAAACCT
6227 ACTCCTTCTA
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:0.37, C:0.14, G:0.23, T:0.26
Consensus pattern (23 bp):
CTGGTAGGAATAGTAAAACCTTT
Done.