Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01023950.1 Corchorus olitorius cultivar O-4 contig23983, 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: 22919
ACGTcount: A:0.33, C:0.15, G:0.18, T:0.33
Found at i:7793 original size:40 final size:43
Alignment explanation
Indices: 7735--7843 Score: 125
Period size: 40 Copynumber: 2.6 Consensus size: 43
7725 AGATTATCAC
* ** *
7735 AATTTCATAAGGTTGTTATCAAATTTTCA-GTGTGGTT-CC-A
1 AATTTCATAGGGAGGTTATCAAAATTTCAGGTGTGGTTACCAA
7775 AATTTCATAGGGAGGTTATCAAAATTTCATGGTGTGGTTACCAA
1 AATTTCATAGGGAGGTTATCAAAATTTCA-GGTGTGGTTACCAA
* * *
7819 AACTTCATAGGAAGGTTATAAAAAT
1 AATTTCATAGGGAGGTTATCAAAAT
7844 CTCAATTTCA
Statistics
Matches: 58, Mismatches: 7, Indels: 4
0.84 0.10 0.06
Matches are distributed among these distances:
40 25 0.43
42 8 0.14
43 2 0.03
44 23 0.40
ACGTcount: A:0.34, C:0.11, G:0.19, T:0.36
Consensus pattern (43 bp):
AATTTCATAGGGAGGTTATCAAAATTTCAGGTGTGGTTACCAA
Found at i:7799 original size:22 final size:22
Alignment explanation
Indices: 7712--8611 Score: 219
Period size: 22 Copynumber: 39.3 Consensus size: 22
7702 TCTGGTTATT
* *
7712 AAATTTTATAGGGAGATTATCA
1 AAATTTCATAGGGAGGTTATCA
* * **
7734 CAATTTCATAAGGTTGTTATCA
1 AAATTTCATAGGGAGGTTATCA
* * * *
7756 AATTTTC--AGTGTGG-T-TCC
1 AAATTTCATAGGGAGGTTATCA
7774 AAATTTCATAGGGAGGTTATCA
1 AAATTTCATAGGGAGGTTATCA
* *
7796 AAATTTCAT-GGTGTGGTTACCA
1 AAATTTCATAGG-GAGGTTATCA
* * *
7818 AAACTTCATAGGAAGGTTATAAAA
1 AAATTTCATAGGGAGGTTAT--CA
* *
7842 ATCTCAATTTCATAAGGAGATTATCA
1 A----AATTTCATAGGGAGGTTATCA
* **
7868 AAATTTTATAAAGAGGTTATC-
1 AAATTTCATAGGGAGGTTATCA
* *
7889 AAATTCTCATAGAGTGGTTATCA
1 AAATT-TCATAGGGAGGTTATCA
*** * *
7912 AAATTTCATAGATTTCTGATTGTCA
1 AAATTTCATAG---GGAGGTTATCA
* * **
7937 AAATTTCATACGAAAATTATCA
1 AAATTTCATAGGGAGGTTATCA
* * * *
7959 AAATTTCTTAGTGTGGGTATCA
1 AAATTTCATAGGGAGGTTATCA
7981 AAATTTCATAGTGAGAATGTGGTTATCA
1 AAATTTCATAG-G-G-A---GGTTATCA
* *** *
8009 AAATTCCATAGTGGTA-AAAATCT
1 AAATTTCATAG-GG-AGGTTATCA
* *
8032 CAATTTCATAAGGAGGTTATC-
1 AAATTTCATAGGGAGGTTATCA
* *
8053 AAATTTTATA-GTATGGTTATCA
1 AAATTTCATAGGGA-GGTTATCA
* ** *
8075 AAATTTTATAAAGAGGTTAT-T
1 AAATTTCATAGGGAGGTTATCA
*
8096 AAATTCTCAT-GGAGTGGTTATCA
1 AAATT-TCATAGG-GAGGTTATCA
*** * *
8119 AAATTTCATAGATTTCTGATTGTCA
1 AAATTTCATAG---GGAGGTTATCA
* * **
8144 AAATTTCATACGAAAATTATCA
1 AAATTTCATAGGGAGGTTATCA
8166 AAATTTCATAGTGAGAATATGGTT-TCA
1 AAATTTCATAG-G-G---A-GGTTATCA
* * * * *
8193 AACTTCCATAGTGTGGTTACCA
1 AAATTTCATAGGGAGGTTATCA
* ** *
8215 AAATTTCATAGGAATATTATAAAA
1 AAATTTCATAGGGAGGTTAT--CA
*
8239 ATCTCAATTTCATAAGGAGGTTATCA
1 A----AATTTCATAGGGAGGTTATCA
*
8265 AAATTTAATAGGGAGGTCAATTATCA
1 AAATTTCATAGGGAGG----TTATCA
* * *
8291 AAATTAT-ATAGTGCA-ATTATCG
1 AAATT-TCATAG-GGAGGTTATCA
* ** *
8313 AAATTTTATAATGAGGTTATAA
1 AAATTTCATAGGGAGGTTATCA
* * *
8335 AAATCTCATAGAGTGGTTATCA
1 AAATTTCATAGGGAGGTTATCA
* * * *
8357 AAATTTCGTAGGAATCCGATTGTCA
1 AAATTTCATAGGGA---GGTTATCA
* *
8382 AAATTTCATA-GTACGGCTATCA
1 AAATTTCATAGGGA-GGTTATCA
* * *
8404 AAATTTCACAGTGTGGTTATCA
1 AAATTTCATAGGGAGGTTATCA
** * *
8426 AAATTTCATATAGAGGTGATTA
1 AAATTTCATAGGGAGGTTATCA
* * *
8448 AATTTTCATAGTGTATGGTTGTCA
1 AAATTTCATAG-GGA-GGTTATCA
* * * * *
8472 AATTTTCATATGGTGGTGATTA
1 AAATTTCATAGGGAGGTTATCA
* * *
8494 AATTTTAATAGTGTGTGGTTATCA
1 AAATTTCATAG-G-GAGGTTATCA
* *
8518 AAATTTCATAGGGAGATTAACA
1 AAATTTCATAGGGAGGTTATCA
* *
8540 AAATTTCATAGGGAGGTCATCG
1 AAATTTCATAGGGAGGTTATCA
* *
8562 AAATTTCATAAGGAGGTTATTA
1 AAATTTCATAGGGAGGTTATCA
* * * *
8584 AAATTTAATAGTGTGATTATCA
1 AAATTTCATAGGGAGGTTATCA
8606 AAATTT
1 AAATTT
8612 TATATTGCAG
Statistics
Matches: 627, Mismatches: 188, Indels: 126
0.67 0.20 0.13
Matches are distributed among these distances:
18 8 0.01
19 1 0.00
20 11 0.02
21 35 0.06
22 365 0.58
23 30 0.05
24 39 0.06
25 50 0.08
26 19 0.03
27 18 0.03
28 51 0.08
ACGTcount: A:0.37, C:0.10, G:0.17, T:0.36
Consensus pattern (22 bp):
AAATTTCATAGGGAGGTTATCA
Found at i:8091 original size:43 final size:44
Alignment explanation
Indices: 8033--8128 Score: 124
Period size: 43 Copynumber: 2.2 Consensus size: 44
8023 TAAAAATCTC
* * *
8033 AATTTCATAAGGAGGTTATCAAATT-TTATAGTA-TGGTTATCAA
1 AATTTCATAAAGAGGTTATCAAATTCTCAT-GGAGTGGTTATCAA
* *
8076 AATTTTATAAAGAGGTTATTAAATTCTCATGGAGTGGTTATCAA
1 AATTTCATAAAGAGGTTATCAAATTCTCATGGAGTGGTTATCAA
8120 AATTTCATA
1 AATTTCATA
8129 GATTTCTGAT
Statistics
Matches: 45, Mismatches: 6, Indels: 3
0.83 0.11 0.06
Matches are distributed among these distances:
43 24 0.53
44 21 0.47
ACGTcount: A:0.38, C:0.07, G:0.16, T:0.40
Consensus pattern (44 bp):
AATTTCATAAAGAGGTTATCAAATTCTCATGGAGTGGTTATCAA
Found at i:8455 original size:44 final size:44
Alignment explanation
Indices: 8403--8616 Score: 178
Period size: 46 Copynumber: 4.8 Consensus size: 44
8393 TACGGCTATC
*
8403 AAAATTTCACAGTGTGGTTATCAAAATTTCATATAGAGGTGATT
1 AAAATTTCATAGTGTGGTTATCAAAATTTCATATAGAGGTGATT
* * * * *
8447 AAATTTTCATAGTGTATGGTTGTCAAATTTTCATATGGTGGTGATT
1 AAAATTTCATAGTG--TGGTTATCAAAATTTCATATAGAGGTGATT
* * ** * * **
8493 AAATTTTAATAGTGTGTGGTTATCAAAATTTCATAGGGAGATTAAC
1 AAAATTTCATA--GTGTGGTTATCAAAATTTCATATAGAGGTGATT
* * * * *
8539 AAAATTTCATAGGGAGGTCATCGAAATTTCATA-AGGAGGTTATT
1 AAAATTTCATAGTGTGGTTATCAAAATTTCATATA-GAGGTGATT
* * *
8583 AAAATTTAATAGTGTGATTATCAAAATTTTATAT
1 AAAATTTCATAGTGTGGTTATCAAAATTTCATAT
8617 TGCAGTATTT
Statistics
Matches: 132, Mismatches: 32, Indels: 11
0.75 0.18 0.06
Matches are distributed among these distances:
44 62 0.47
46 67 0.51
48 3 0.02
ACGTcount: A:0.36, C:0.07, G:0.19, T:0.39
Consensus pattern (44 bp):
AAAATTTCATAGTGTGGTTATCAAAATTTCATATAGAGGTGATT
Found at i:8479 original size:24 final size:24
Alignment explanation
Indices: 8447--8528 Score: 89
Period size: 24 Copynumber: 3.5 Consensus size: 24
8437 AGAGGTGATT
*
8447 AAATTTTCATAGTGTATGGTTGTC
1 AAATTTTCATAGTGTGTGGTTGTC
*
8471 AAATTTTCATA-TG-GTGG-TGATT
1 AAATTTTCATAGTGTGTGGTTG-TC
* *
8493 AAATTTTAATAGTGTGTGGTTATC
1 AAATTTTCATAGTGTGTGGTTGTC
*
8517 AAAATTTCATAG
1 AAATTTTCATAG
8529 GGAGATTAAC
Statistics
Matches: 47, Mismatches: 7, Indels: 8
0.76 0.11 0.13
Matches are distributed among these distances:
21 2 0.04
22 14 0.30
23 4 0.09
24 26 0.55
25 1 0.02
ACGTcount: A:0.30, C:0.06, G:0.20, T:0.44
Consensus pattern (24 bp):
AAATTTTCATAGTGTGTGGTTGTC
Found at i:9020 original size:22 final size:22
Alignment explanation
Indices: 9006--9067 Score: 81
Period size: 22 Copynumber: 2.8 Consensus size: 22
8996 TTCATATTGC
9006 GTTTACCAAAATTTCATATGAA
1 GTTTACCAAAATTTCATATGAA
*
9028 GTTTATCAAAATTTCATA-GAGA
1 GTTTACCAAAATTTCATATGA-A
* *
9050 GGTTAACAAAATTTCATA
1 GTTTACCAAAATTTCATA
9068 AGGAGGTTAT
Statistics
Matches: 36, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
21 2 0.06
22 34 0.94
ACGTcount: A:0.42, C:0.11, G:0.11, T:0.35
Consensus pattern (22 bp):
GTTTACCAAAATTTCATATGAA
Found at i:9073 original size:22 final size:22
Alignment explanation
Indices: 9012--9076 Score: 78
Period size: 22 Copynumber: 3.0 Consensus size: 22
9002 TTGCGTTTAC
* * * *
9012 CAAAATTTCATATGAAGTTTAT
1 CAAAATTTCATAAGGAGGTTAA
9034 CAAAATTTCAT-AGAGAGGTTAA
1 CAAAATTTCATAAG-GAGGTTAA
9056 CAAAATTTCATAAGGAGGTTA
1 CAAAATTTCATAAGGAGGTTA
9077 TTGGAGGTTA
Statistics
Matches: 37, Mismatches: 4, Indels: 4
0.82 0.09 0.09
Matches are distributed among these distances:
21 1 0.03
22 34 0.92
23 2 0.05
ACGTcount: A:0.43, C:0.09, G:0.15, T:0.32
Consensus pattern (22 bp):
CAAAATTTCATAAGGAGGTTAA
Found at i:16891 original size:31 final size:30
Alignment explanation
Indices: 16819--16903 Score: 93
Period size: 31 Copynumber: 2.8 Consensus size: 30
16809 TGGGCCTTAG
* *
16819 TAATTAATTATTTGTTTATTATTCA-CATAA
1 TAATTAATTATTGGTTTATTA-TCATAATAA
**
16849 -AAAAAATTATTGGTTTATTATCATAAGTAA
1 TAATTAATTATTGGTTTATTATCATAA-TAA
*
16879 TAATTAATTATTGGTGTATTATCAT
1 TAATTAATTATTGGTTTATTATCAT
16904 TTGATTAGTG
Statistics
Matches: 45, Mismatches: 7, Indels: 5
0.79 0.12 0.09
Matches are distributed among these distances:
28 3 0.07
29 18 0.40
30 3 0.07
31 21 0.47
ACGTcount: A:0.39, C:0.05, G:0.08, T:0.48
Consensus pattern (30 bp):
TAATTAATTATTGGTTTATTATCATAATAA
Done.