Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01000143.1 Corchorus olitorius cultivar O-4 contig00143, 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, 651
Length: 1086
ACGTcount: A:0.36, C:0.19, G:0.09, T:0.35
Found at i:31 original size:22 final size:21
Alignment explanation
Indices: 2--675 Score: 177
Period size: 22 Copynumber: 30.6 Consensus size: 21
1 A
2 CTATAAAATTTTGATAACCTC
1 CTATAAAATTTTGATAACCTC
*
23 CATATAAAATTTTGATAA-TTAC
1 C-TATAAAATTTTGATAACCT-C
* * * *
45 ACTATAAAGTTTTTATGACGATGC
1 -CTATAAAATTTTGATAAC-CT-C
* * *
69 C-ATAGAATTTCGAGAACCTC
1 CTATAAAATTTTGATAACCTC
* * *
89 CATATGAAATTTTGTTAACTTCC
1 C-TATAAAATTTTGATAACCT-C
* *
112 CTAATAAAATTTT-CTCACACTCC
1 CT-ATAAAATTTTGATAAC-CT-C
* *
135 CTATAAAATTTTAATAA-TTAC
1 CTATAAAATTTTGATAACCT-C
*
156 CTAATGAAATTTTGATAACCATC
1 CT-ATAAAATTTTGATAACC-TC
*
179 CTATGAAATTTTGATAACCTCC
1 CTATAAAATTTTGATAACCT-C
* * * * * *
201 CAATGAAATGTTGGTAAGCGC
1 CTATAAAATTTTGATAACCTC
*
222 AC-ATTACGAAATTTTGATTACCTTC
1 -CTA-TA--AAATTTTGATAACC-TC
* * * * * *
247 CGATAAAATATAGGTAATCAC
1 CTATAAAATTTTGATAACCTC
* *
268 AT-TACGAAATTTTGATAAACATAC
1 CTATA--AAATTTTGAT-AACCT-C
* *
292 C-ATGAAATTGTGAT-ACCTC
1 CTATAAAATTTTGATAACCTC
*
311 ACTATGAAAATTGT-ATAAACCTCC
1 -CTAT-AAAATTTTGAT-AACCT-C
335 CTATAAAATTTTGATAACCTC
1 CTATAAAATTTTGATAACCTC
* *
356 CATTTGAAATTTTGATAACCT-
1 C-TATAAAATTTTGATAACCTC
* * *
377 C-ATGAAATTTTGAAAACCAC
1 CTATAAAATTTTGATAACCTC
* * *
397 CTCATGAAATTTTGAAAACCAC
1 CT-ATAAAATTTTGATAACCTC
*
419 CTCATGAAATTTTGATAACCATC
1 CT-ATAAAATTTTGATAACC-TC
* * * *
442 TTATGAAATTTTCATAACATCC
1 CTATAAAATTTTGATAACCT-C
*
464 CTATAAACATTTT-ATTACCTC
1 CTATAAA-ATTTTGATAACCTC
*
485 CTCATAAAATTTTGTTAACCTC
1 CT-ATAAAATTTTGATAACCTC
*** * ***
507 CTACGGATTTTTGATAAGAAC
1 CTATAAAATTTTGATAACCTC
* * *
528 GCTATTAAAGTTTGATAACCCC
1 -CTATAAAATTTTGATAACCTC
* * *
550 CAATGAAATTTTGATAATTAACTAC
1 CTATAAAATTTTGAT-A--ACCT-C
* *** *
575 ACCATAAAATTACAATAACTTGC
1 -CTATAAAATTTTGATAACCT-C
* * *
598 CTATGAAATTTTGTTAATCTCC
1 CTATAAAATTTTGATAACCT-C
* *
620 CTATAAAATTTTGAGAACCAC
1 CTATAAAATTTTGATAACCTC
* * *
641 TCTATCAAATTTTGTTAATCTC
1 -CTATAAAATTTTGATAACCTC
663 ACTAT-AAATTTTG
1 -CTATAAAATTTTG
676 GTAAAATCAT
Statistics
Matches: 478, Mismatches: 126, Indels: 98
0.68 0.18 0.14
Matches are distributed among these distances:
19 16 0.03
20 9 0.02
21 59 0.12
22 314 0.66
23 45 0.09
24 21 0.04
25 4 0.01
26 10 0.02
ACGTcount: A:0.37, C:0.18, G:0.09, T:0.36
Consensus pattern (21 bp):
CTATAAAATTTTGATAACCTC
Found at i:206 original size:44 final size:43
Alignment explanation
Indices: 159--566 Score: 223
Period size: 44 Copynumber: 9.3 Consensus size: 43
149 TAATTACCTA
159 ATGAAATTTTGATAACCATCCTATGAAATTTTGATAACCTCCC
1 ATGAAATTTTGATAACCATCCTATGAAATTTTGATAACCTCCC
* * * * * *
202 AATGAAATGTTGGTAAGCGCA-CATTACGAAATTTTGATTACCTTCCG
1 -ATGAAATTTTGATAA-C-CATC-CTATGAAATTTTGATAACC-TCCC
* * * * * * *
249 ATAAAATATAGGTAATCACAT--TACGAAATTTTGATAAACATACC
1 ATGAAATTTTGATAA-C-CATCCTATGAAATTTTGAT-AACCTCCC
* *
293 ATGAAATTGTGAT-ACC-TCACTATGAAA-ATTGTATAAACCTCCC
1 ATGAAATTTTGATAACCATC-CTATGAAATTTTG-AT-AACCTCCC
* *
336 TATAAAATTTTGATAACC-TCCATTTGAAATTTTGATAACCT--C
1 -ATGAAATTTTGATAACCATCC-TATGAAATTTTGATAACCTCCC
* * *
378 ATGAAATTTTGAAAACCA-CCTCATGAAATTTTGAAAACCACCTC
1 ATGAAATTTTGATAACCATCCT-ATGAAATTTTGATAACCTCC-C
* * *
422 ATGAAATTTTGATAACCATCTTATGAAATTTTCATAACATCCC
1 ATGAAATTTTGATAACCATCCTATGAAATTTTGATAACCTCCC
* * * * *
465 TATAAACATTTT-ATTACC-TCCTCATAAAATTTTGTTAACCTCCT
1 -ATGAA-ATTTTGATAACCATCCT-ATGAAATTTTGATAACCTCCC
* * * * * * *
509 ACGGATTTTTGATAA-GAACGCTATTAAAGTTTGATAACC-CCC
1 ATGAAATTTTGATAACCATC-CTATGAAATTTTGATAACCTCCC
551 AATGAAATTTTGATAA
1 -ATGAAATTTTGATAA
567 TTAACTACAC
Statistics
Matches: 276, Mismatches: 61, Indels: 55
0.70 0.16 0.14
Matches are distributed among these distances:
40 2 0.01
41 33 0.12
42 11 0.04
43 52 0.19
44 115 0.42
45 24 0.09
46 36 0.13
47 3 0.01
ACGTcount: A:0.37, C:0.18, G:0.10, T:0.34
Consensus pattern (43 bp):
ATGAAATTTTGATAACCATCCTATGAAATTTTGATAACCTCCC
Found at i:236 original size:46 final size:44
Alignment explanation
Indices: 183--285 Score: 125
Period size: 46 Copynumber: 2.3 Consensus size: 44
173 ACCATCCTAT
* * *
183 GAAATTTTGATAACCTCCCAATGAAATGTTGGTAAGCGCACATTAC
1 GAAATTTTGATAACCTCCCAATAAAATATAGGTAA--GCACATTAC
* * * *
229 GAAATTTTGATTACCTTCCGATAAAATATAGGTAATCACATTAC
1 GAAATTTTGATAACCTCCCAATAAAATATAGGTAAGCACATTAC
273 GAAATTTTGATAA
1 GAAATTTTGATAA
286 ACATACCATG
Statistics
Matches: 49, Mismatches: 8, Indels: 2
0.83 0.14 0.03
Matches are distributed among these distances:
44 20 0.41
46 29 0.59
ACGTcount: A:0.38, C:0.16, G:0.15, T:0.32
Consensus pattern (44 bp):
GAAATTTTGATAACCTCCCAATAAAATATAGGTAAGCACATTAC
Found at i:796 original size:22 final size:22
Alignment explanation
Indices: 771--812 Score: 66
Period size: 22 Copynumber: 1.9 Consensus size: 22
761 AACCACACTG
* *
771 TGAAATTTTGATAATCTCCCTC
1 TGAAATTTCGATAACCTCCCTC
793 TGAAATTTCGATAACCTCCC
1 TGAAATTTCGATAACCTCCC
813 CACGAAATTT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.29, C:0.26, G:0.10, T:0.36
Consensus pattern (22 bp):
TGAAATTTCGATAACCTCCCTC
Found at i:819 original size:22 final size:22
Alignment explanation
Indices: 772--822 Score: 59
Period size: 22 Copynumber: 2.3 Consensus size: 22
762 ACCACACTGT
* * *
772 GAAATTTTGATAATCTCCCTCT
1 GAAATTTCGATAACCTCCCTCC
794 GAAATTTCGATAACCTCCC-CAC
1 GAAATTTCGATAACCTCCCTC-C
816 GAAATTT
1 GAAATTT
823 TCTTAACCTC
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
21 1 0.04
22 24 0.96
ACGTcount: A:0.31, C:0.25, G:0.10, T:0.33
Consensus pattern (22 bp):
GAAATTTCGATAACCTCCCTCC
Found at i:1036 original size:22 final size:22
Alignment explanation
Indices: 931--1036 Score: 122
Period size: 22 Copynumber: 4.8 Consensus size: 22
921 TAAGAACACC
* *
931 ATGAAATTTTGATAATCTTCCT
1 ATGAAATTTTGATAACCTCCCT
*
953 ATGAAATTTTGATAACCTCCAT
1 ATGAAATTTTGATAACCTCCCT
* * * *
975 ATAAAACTTTCGATAATCGCCCT
1 ATGAAA-TTTTGATAACCTCCCT
*
998 ATGAAATTTTGTTAACCTCCCT
1 ATGAAATTTTGATAACCTCCCT
*
1020 ATGAAATTTTGAAAACC
1 ATGAAATTTTGATAACC
1037 CAGAGTATGA
Statistics
Matches: 68, Mismatches: 15, Indels: 2
0.80 0.18 0.02
Matches are distributed among these distances:
22 51 0.75
23 17 0.25
ACGTcount: A:0.35, C:0.19, G:0.09, T:0.37
Consensus pattern (22 bp):
ATGAAATTTTGATAACCTCCCT
Done.