Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01020077.1 Corchorus olitorius cultivar O-4 contig20110, 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: 13780
ACGTcount: A:0.32, C:0.17, G:0.18, T:0.33
Found at i:2273 original size:18 final size:18
Alignment explanation
Indices: 2246--2291 Score: 76
Period size: 18 Copynumber: 2.6 Consensus size: 18
2236 GATCACCACC
*
2246 CAAA-ATCACCAGGTGAT
1 CAAAGATCACCAGATGAT
2263 CAAAGATCACCAGATGAT
1 CAAAGATCACCAGATGAT
2281 CAAAGATCACC
1 CAAAGATCACC
2292 CCCAACCAAA
Statistics
Matches: 27, Mismatches: 1, Indels: 1
0.93 0.03 0.03
Matches are distributed among these distances:
17 4 0.15
18 23 0.85
ACGTcount: A:0.43, C:0.26, G:0.15, T:0.15
Consensus pattern (18 bp):
CAAAGATCACCAGATGAT
Found at i:2913 original size:22 final size:22
Alignment explanation
Indices: 2888--2930 Score: 68
Period size: 22 Copynumber: 2.0 Consensus size: 22
2878 TAAATGAAAT
2888 ATTCATATGAAATTATGATAAC
1 ATTCATATGAAATTATGATAAC
* *
2910 ATTCCTATTAAATTATGATAA
1 ATTCATATGAAATTATGATAA
2931 TTACACTTTT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.44, C:0.09, G:0.07, T:0.40
Consensus pattern (22 bp):
ATTCATATGAAATTATGATAAC
Found at i:3302 original size:27 final size:24
Alignment explanation
Indices: 3241--3333 Score: 86
Period size: 23 Copynumber: 3.9 Consensus size: 24
3231 GATAATCAGA
* *
3241 CTATGAAATTGTGAT-AACCT-CG
1 CTATAAAATTTTGATAAACCTCCG
* *
3263 CTATTAAACTTTGATAAACCTTCCTAG
1 CTATAAAATTTTGATAAACC-TCC--G
*
3290 CTATAAAATTTTGATAAATCTCC-
1 CTATAAAATTTTGATAAACCTCCG
3313 CTATAAAATTTTGAT-AACCTC
1 CTATAAAATTTTGATAAACCTC
3334 TTTATGAAAT
Statistics
Matches: 59, Mismatches: 7, Indels: 10
0.78 0.09 0.13
Matches are distributed among these distances:
22 17 0.29
23 19 0.32
24 1 0.02
25 1 0.02
26 3 0.05
27 18 0.31
ACGTcount: A:0.35, C:0.19, G:0.09, T:0.37
Consensus pattern (24 bp):
CTATAAAATTTTGATAAACCTCCG
Found at i:3758 original size:88 final size:87
Alignment explanation
Indices: 3600--3764 Score: 208
Period size: 88 Copynumber: 1.9 Consensus size: 87
3590 AAATACTGCA
** * *
3600 CTATGAAATTTTGGTAATCACATTTTGAAAATTTGATAACCTCTTTATGAAATTTTGATAACCTA
1 CTATGAAATTTTAATAATCACATTATGAAAATTTGATAACCTCCTTATGAAATTTTGATAA-CTA
*
3665 TCTATAAAATTTAGTTGACCCCT
65 ACTATAAAATTTAGTTGACCCCT
* * *
3688 CTATGAAATTTTAATAATCACATTATGTAATTTTGATAGCCTCGCTT-TGAAATTTTGATAA-TA
1 CTATGAAATTTTAATAATCACATTATGAAAATTTGATAACCTC-CTTATGAAATTTTGATAACT-
3751 ACACTATAAAATTT
64 A-ACTATAAAATTT
3765 TGATAATCTT
Statistics
Matches: 66, Mismatches: 8, Indels: 6
0.82 0.10 0.08
Matches are distributed among these distances:
86 1 0.02
87 1 0.02
88 62 0.94
89 2 0.03
ACGTcount: A:0.36, C:0.13, G:0.10, T:0.41
Consensus pattern (87 bp):
CTATGAAATTTTAATAATCACATTATGAAAATTTGATAACCTCCTTATGAAATTTTGATAACTAA
CTATAAAATTTAGTTGACCCCT
Found at i:3854 original size:21 final size:21
Alignment explanation
Indices: 2940--3854 Score: 163
Period size: 22 Copynumber: 42.2 Consensus size: 21
2930 ATTACACTTT
* *
2940 TTTTGATGATCTTCTTATGAAA
1 TTTTGATAACCTTC-TATGAAA
*
2962 TTTTGATAATCTTCCTATGAAA
1 TTTTGATAACCTT-CTATGAAA
* * *
2984 TTTTAATAACGATACTATGAAA
1 TTTTGATAAC-CTTCTATGAAA
* * * *
3006 TTTCGAGAATCTTTTTAT-AAA
1 TTTTGATAA-CCTTCTATGAAA
**
3027 TTTTTTTTAACCTTCTTATGAAA
1 -TTTTGATAACCTTC-TATGAAA
* * * *
3050 TTTTGTTAACCTCCCTAAGGAA
1 TTTTGATAACCT-TCTATGAAA
*
3072 TTTTGA-AGACCTCACTATGAAA
1 TTTTGATA-ACCT-TCTATGAAA
*
3094 TTTTGATAA-CTTCCCAATGAAA
1 TTTTGATAACCTT--CTATGAAA
** *
3116 TTTTGATAACCAACACTATGAGA
1 TTTTGATAACC--TTCTATGAAA
* *
3139 TGTTGATAACC-TCAATATGATA
1 TTTTGATAACCTTC--TATGAAA
* * *
3161 TATTCATAAGCACGT-TATGAAA
1 TTTTGATAA-C-CTTCTATGAAA
* * *
3183 ATTTAAAAACCTTCATATG-AA
1 TTTTGATAACCTTC-TATGAAA
* *
3204 TTGTT-AGTAATCAC-ACTCTGAAA
1 TT-TTGA-TAA-C-CTTCTATGAAA
***
3227 TTTTGATAATCAGACTATGAAA
1 TTTTGATAA-CCTTCTATGAAA
* * *
3249 TTGTGATAACCTCGCTATTAAA
1 TTTTGATAACCT-TCTATGAAA
* *
3271 CTTTGATAAACCTTCCTAGCTATAAAA
1 TTTTGAT-AACC-T--T--CTATGAAA
* * *
3298 TTTTGATAAATCTCCCTATAAAA
1 TTTTGAT-AACCT-TCTATGAAA
*
3321 TTTTGATAACCTCTTTATGAAA
1 TTTTGATAACCT-TCTATGAAA
* *
3343 TCTTGATAA----CTA-CAAA
1 TTTTGATAACCTTCTATGAAA
* *
3359 TTTTGATAACCTCCCTAT-AATT
1 TTTTGATAACCT-TCTATGAA-A
3381 TTTTGATAACC-TCATTATGAAA
1 TTTTGATAACCTTC--TATGAAA
* * *
3403 TTTTGTTAATCTCCCTATGAAA
1 TTTTGATAACCT-TCTATGAAA
* * *
3425 TTTTGATCTACATACTATGAAA
1 TTTTGAT-AACCTTCTATGAAA
* *
3447 TTTTGA-AAACTAAACTATGAAA
1 TTTTGATAACCT--TCTATGAAA
3469 TTTTGATAACCTTCATATGAAA
1 TTTTGATAACCTTC-TATGAAA
* *
3491 TTTTGATATCCTGCT-TGAAA
1 TTTTGATAACCTTCTATGAAA
* * * *
3511 CTTTGATTA-CTCCATGATAAAA
1 TTTTGATAACCTTC-T-ATGAAA
* * *
3533 GTTTAATAACCTTC-CT--AA
1 TTTTGATAACCTTCTATGAAA
* *
3551 -TTTGGTAACCATACTATGAAA
1 TTTTGATAACC-TTCTATGAAA
* * *
3572 ATTTGATAACCTCCCCA-GAAA
1 TTTTGATAACCT-TCTATGAAA
** *
3593 TACTG-----C-ACTATGAAA
1 TTTTGATAACCTTCTATGAAA
*
3608 TTTTGGTAATCACATT-T-TGAAA
1 TTTTGATAA-C-C-TTCTATGAAA
* *
3630 ATTTGATAACCTCTTTATGAAA
1 TTTTGATAACCT-TCTATGAAA
*
3652 TTTTGATAACCTATCTATAAAA
1 TTTTGATAACCT-TCTATGAAA
* * * *
3674 TTTAGTTGACCCCTCTATGAAA
1 TTTTGAT-AACCTTCTATGAAA
* * *
3696 TTTTAATAATCACAT-TATGTAA
1 TTTTGATAA-C-CTTCTATGAAA
* * *
3718 TTTTGATAGCCTCGCTTTGAAA
1 TTTTGATAACCT-TCTATGAAA
* * *
3740 TTTTGATAATAAC-ACTATAAAA
1 TTTTGAT-A-ACCTTCTATGAAA
*
3762 TTTTGATAATCTTCTTAT-AAA
1 TTTTGATAACCTTC-TATGAAA
*
3783 TTTTGATAATCTGATCTCTATGAAA
1 TTTTGATAA-C--CT-TCTATGAAA
* * *
3808 TTTCGATAACCACTCTATGAGA
1 TTTTGATAACC-TTCTATGAAA
*
3830 -TTTGATAACCTTCTATCAAA
1 TTTTGATAACCTTCTATGAAA
3850 TTTTG
1 TTTTG
3855 GTACTCCTTA
Statistics
Matches: 652, Mismatches: 151, Indels: 181
0.66 0.15 0.18
Matches are distributed among these distances:
14 2 0.00
15 7 0.01
16 12 0.02
17 10 0.02
18 4 0.01
19 5 0.01
20 31 0.05
21 62 0.10
22 405 0.62
23 70 0.11
24 10 0.02
25 16 0.02
26 1 0.00
27 17 0.03
ACGTcount: A:0.35, C:0.16, G:0.10, T:0.39
Consensus pattern (21 bp):
TTTTGATAACCTTCTATGAAA
Found at i:7366 original size:7 final size:7
Alignment explanation
Indices: 7354--7389 Score: 72
Period size: 7 Copynumber: 5.1 Consensus size: 7
7344 TGGAACTTGC
7354 TGGGCAG
1 TGGGCAG
7361 TGGGCAG
1 TGGGCAG
7368 TGGGCAG
1 TGGGCAG
7375 TGGGCAG
1 TGGGCAG
7382 TGGGCAG
1 TGGGCAG
7389 T
1 T
7390 CTCATGGTAA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 29 1.00
ACGTcount: A:0.14, C:0.14, G:0.56, T:0.17
Consensus pattern (7 bp):
TGGGCAG
Done.