Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01021377.1 Corchorus olitorius cultivar O-4 contig21410, 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: 8686
ACGTcount: A:0.33, C:0.16, G:0.15, T:0.36
Found at i:252 original size:13 final size:12
Alignment explanation
Indices: 229--258 Score: 51
Period size: 13 Copynumber: 2.4 Consensus size: 12
219 AAGTTTATTG
229 ATAATATATAAT
1 ATAATATATAAT
241 ATAATAATATAAT
1 ATAAT-ATATAAT
254 ATAAT
1 ATAAT
259 TAACATGATT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 5 0.29
13 12 0.71
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (12 bp):
ATAATATATAAT
Found at i:2989 original size:24 final size:24
Alignment explanation
Indices: 2957--3006 Score: 82
Period size: 24 Copynumber: 2.1 Consensus size: 24
2947 TTCTGCTTTT
**
2957 AATACTAATCTATATTAACTATAA
1 AATACTAATCTATACGAACTATAA
2981 AATACTAATCTATACGAACTATAA
1 AATACTAATCTATACGAACTATAA
3005 AA
1 AA
3007 GCATGAATAA
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.52, C:0.14, G:0.02, T:0.32
Consensus pattern (24 bp):
AATACTAATCTATACGAACTATAA
Found at i:3488 original size:22 final size:22
Alignment explanation
Indices: 3460--3513 Score: 65
Period size: 22 Copynumber: 2.5 Consensus size: 22
3450 TTATGGAGCA
3460 ATCAAAATTTCATA-GGAAAGAT
1 ATCAAAATTTCATATGG-AAGAT
* * *
3482 ATCAAAATTTTATATGGAGGTT
1 ATCAAAATTTCATATGGAAGAT
3504 ATCAAAATTT
1 ATCAAAATTT
3514 TAATAAGAAA
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
22 26 0.93
23 2 0.07
ACGTcount: A:0.44, C:0.07, G:0.13, T:0.35
Consensus pattern (22 bp):
ATCAAAATTTCATATGGAAGAT
Found at i:3673 original size:22 final size:21
Alignment explanation
Indices: 3640--3701 Score: 72
Period size: 22 Copynumber: 2.9 Consensus size: 21
3630 TAATGAGATT
*
3640 AGTTTTCAAAATTTCATAG-G
1 AGTTATCAAAATTTCATAGAG
3660 AGGATTATCAAAATTTCATTAGAG
1 A-G-TTATCAAAATTTCA-TAGAG
*
3684 AGTTATTAAAATTTCATA
1 AGTTATCAAAATTTCATA
3702 AGCGGGAAGC
Statistics
Matches: 36, Mismatches: 2, Indels: 7
0.80 0.04 0.16
Matches are distributed among these distances:
20 1 0.03
21 3 0.08
22 26 0.72
23 4 0.11
24 2 0.06
ACGTcount: A:0.40, C:0.08, G:0.13, T:0.39
Consensus pattern (21 bp):
AGTTATCAAAATTTCATAGAG
Found at i:3814 original size:22 final size:21
Alignment explanation
Indices: 3775--4288 Score: 163
Period size: 22 Copynumber: 23.5 Consensus size: 21
3765 TAGTGTGTAA
3775 ATCAAAATTTC--ATGAGGTT
1 ATCAAAATTTCATATGAGGTT
*
3794 AACAAAATTTCATTATGAGGTT
1 ATCAAAATTTCA-TATGAGGTT
*
3816 AGTTTTCAAAATTTCATAGGAGGGTT
1 A----TCAAAATTTCATATGA-GGTT
*
3842 ATCAAAATTTCATAGGAGGGTT
1 ATCAAAATTTCATATGA-GGTT
* *
3864 ATTAAAATTTCATA-GTGG-T
1 ATCAAAATTTCATATGAGGTT
*
3883 -TCAAAATTTTCAGTGTGTA-G--
1 ATCAAAA-TTTCA-TATG-AGGTT
*
3903 ATCAAAATTTCATAGGGAGGTT
1 ATCAAAATTTCATA-TGAGGTT
*
3925 AACAAAATTTCATAATGAGGTT
1 ATCAAAATTTCAT-ATGAGGTT
**
3947 ATCAAAAAATCATATAGAGGTT
1 ATCAAAATTTCATAT-GAGGTT
* * * *
3969 ATCGAAATTT-TTGAGGGAAGTTT
1 ATCAAAATTTCAT-A-TG-AGGTT
* * *
3992 ATAAAAATTTTATAGGGAGGTTT
1 ATCAAAATTTCATA-TGAGG-TT
*
4015 ATCAAAATTTCATAACGAGGTT
1 ATCAAAATTTCAT-ATGAGGTT
* * ** * *
4037 ATCACAATTTCGTAGTTCGATA
1 ATCAAAATTTCATA-TGAGGTT
* * * *
4059 ATCAAAATTACACAATGTGATT
1 ATCAAAATTTCA-TATGAGGTT
* **
4081 AGT-AACATTTCAGGTGGAGGTT
1 A-TCAAAATTTCATAT-GAGGTT
* * * * *
4103 TTCAATATTTCATAACGTGCTT
1 ATCAAAATTTCAT-ATGAGGTT
* * *
4125 ATCAACATTTCATAGGAAAGTT
1 ATCAAAATTTCATATG-AGGTT
*
4147 ATCAAATTTTCATAGTGAGGTCT
1 ATCAAAATTTCATA-TGAGGT-T
* *
4170 -TCAAAATCTCATATGGAGGTC
1 ATCAAAATTTCATAT-GAGGTT
* *
4191 AACAAAATTTCATAGGAAGGTT
1 ATCAAAATTTCATATG-AGGTT
* *
4213 AACTAAAATTCCATAAT-AGGTT
1 ATC-AAAATTTCAT-ATGAGGTT
* * * ***
4235 CTCGAAATTCCATAGTGTCATT
1 ATCAAAATTTCATA-TGAGGTT
4257 ATCAAAATTTCATA-GAGGGTT
1 ATCAAAATTTCATATGA-GGTT
4278 CATCAAAATTT
1 -ATCAAAATTT
4289 TAATAGTGTA
Statistics
Matches: 366, Mismatches: 86, Indels: 83
0.68 0.16 0.16
Matches are distributed among these distances:
18 5 0.01
19 18 0.05
20 12 0.03
21 31 0.08
22 231 0.63
23 47 0.13
24 3 0.01
25 4 0.01
26 15 0.04
ACGTcount: A:0.37, C:0.11, G:0.17, T:0.35
Consensus pattern (21 bp):
ATCAAAATTTCATATGAGGTT
Found at i:3864 original size:48 final size:44
Alignment explanation
Indices: 3776--3953 Score: 130
Period size: 48 Copynumber: 4.1 Consensus size: 44
3766 AGTGTGTAAA
*
3776 TCAAAATTTCAT--GAGGTTAACAAAATTTCATTATGAGGTTAGTTT
1 TCAAAATTTCATAGGAGGTTAACAAAATTTCATTAGGAGGTTA---T
*
3821 TCAAAATTTCATAGGAGGGTTATCAAAATTTCA-TAGGAGGGTTAT
1 TCAAAATTTCATAGGA-GGTTAACAAAATTTCATTAGGA-GGTTAT
* *
3866 T-AAAATTTCATA-GTGGTT--CAAAATTTTCAGTGT-GTA-G--A-
1 TCAAAATTTCATAGGAGGTTAACAAAA-TTTCA-T-TAGGAGGTTAT
* *
3904 TCAAAATTTCATAGGGAGGTTAACAAAATTTCATAATGAGGTTA-
1 TCAAAATTTCATA-GGAGGTTAACAAAATTTCATTAGGAGGTTAT
3948 TCAAAA
1 TCAAAA
3954 AATCATATAG
Statistics
Matches: 108, Mismatches: 8, Indels: 35
0.72 0.05 0.23
Matches are distributed among these distances:
38 1 0.01
39 12 0.11
40 5 0.05
41 13 0.12
42 10 0.09
43 8 0.07
44 19 0.18
45 14 0.13
47 6 0.06
48 20 0.19
ACGTcount: A:0.38, C:0.09, G:0.18, T:0.35
Consensus pattern (44 bp):
TCAAAATTTCATAGGAGGTTAACAAAATTTCATTAGGAGGTTAT
Found at i:3993 original size:23 final size:23
Alignment explanation
Indices: 3967--4024 Score: 73
Period size: 23 Copynumber: 2.5 Consensus size: 23
3957 CATATAGAGG
*
3967 TTATCGAAATTTT-TGAGGGAAGT
1 TTATCAAAATTTTAT-AGGGAAGT
* *
3990 TTATAAAAATTTTATAGGGAGGT
1 TTATCAAAATTTTATAGGGAAGT
4013 TTATCAAAATTT
1 TTATCAAAATTT
4025 CATAACGAGG
Statistics
Matches: 30, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
23 29 0.97
24 1 0.03
ACGTcount: A:0.36, C:0.03, G:0.19, T:0.41
Consensus pattern (23 bp):
TTATCAAAATTTTATAGGGAAGT
Found at i:7880 original size:17 final size:18
Alignment explanation
Indices: 7858--7892 Score: 63
Period size: 17 Copynumber: 2.0 Consensus size: 18
7848 GGTTATAAAA
7858 AATCATAGGAA-GTTTAT
1 AATCATAGGAAGGTTTAT
7875 AATCATAGGAAGGTTTAT
1 AATCATAGGAAGGTTTAT
7893 TAAAATTTCA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 11 0.65
18 6 0.35
ACGTcount: A:0.40, C:0.06, G:0.20, T:0.34
Consensus pattern (18 bp):
AATCATAGGAAGGTTTAT
Found at i:7923 original size:22 final size:22
Alignment explanation
Indices: 7877--8014 Score: 111
Period size: 22 Copynumber: 6.2 Consensus size: 22
7867 AAGTTTATAA
* *
7877 TCATAGGAAGGTTTATTAAAATT
1 TCATAGGTAGG-TTATCAAAATT
* *
7900 TCATAGTTAGGTTATCAAAGTT
1 TCATAGGTAGGTTATCAAAATT
* * *
7922 TCATATGG-AGTTTATCACAAGT
1 TCATA-GGTAGGTTATCAAAATT
**
7944 TCATAGGTAAATTATCAAAATT
1 TCATAGGTAGGTTATCAAAATT
*
7966 TCATAGCGT-GGTTATCAAATTT
1 TCATAG-GTAGGTTATCAAAATT
* *
7988 TAATTGGATA-GTTATCAAAATT
1 TCATAGG-TAGGTTATCAAAATT
8010 TCATA
1 TCATA
8015 AAAATATTCA
Statistics
Matches: 89, Mismatches: 21, Indels: 11
0.74 0.17 0.09
Matches are distributed among these distances:
21 3 0.03
22 74 0.83
23 12 0.13
ACGTcount: A:0.36, C:0.09, G:0.15, T:0.39
Consensus pattern (22 bp):
TCATAGGTAGGTTATCAAAATT
Found at i:8003 original size:66 final size:66
Alignment explanation
Indices: 7889--8014 Score: 150
Period size: 66 Copynumber: 1.9 Consensus size: 66
7879 ATAGGAAGGT
* * * *
7889 TTATTAAAATTTCATAGTTAGGTTATCAAAGTTTCATATGGAGTTTATCACAAGTTCATAGGTAA
1 TTATCAAAATTTCATAGGTAGGTTATCAAAGTTTAATATGGAGTTTATCAAAAGTTCATAGGTAA
7954 A
66 A
* *
7955 TTATCAAAATTTCATAGCGT-GGTTATCAAATTTTAAT-TGGA-TAGTTATCAAAATTTCATA
1 TTATCAAAATTTCATAG-GTAGGTTATCAAAGTTTAATATGGAGT--TTATCAAAAGTTCATA
8015 AAAATATTCA
Statistics
Matches: 51, Mismatches: 6, Indels: 6
0.81 0.10 0.10
Matches are distributed among these distances:
64 1 0.02
65 4 0.08
66 45 0.88
67 1 0.02
ACGTcount: A:0.37, C:0.10, G:0.13, T:0.40
Consensus pattern (66 bp):
TTATCAAAATTTCATAGGTAGGTTATCAAAGTTTAATATGGAGTTTATCAAAAGTTCATAGGTAA
A
Done.