Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01020423.1 Corchorus olitorius cultivar O-4 contig20456, 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: 9596
ACGTcount: A:0.33, C:0.20, G:0.18, T:0.30
Found at i:471 original size:29 final size:29
Alignment explanation
Indices: 435--506 Score: 103
Period size: 27 Copynumber: 2.6 Consensus size: 29
425 AAATGGATCA
* *
435 AATGACCAAAATGCCCCCCTAAATGTGCG
1 AATGACCAAAATGCCCCCCTAAACGTGCC
*
464 AATGACCAAAATG--CCCCTGAACGTGCC
1 AATGACCAAAATGCCCCCCTAAACGTGCC
491 AATGACCAAAATGCCC
1 AATGACCAAAATGCCC
507 TTGGATGCCC
Statistics
Matches: 38, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
27 24 0.63
29 14 0.37
ACGTcount: A:0.36, C:0.32, G:0.17, T:0.15
Consensus pattern (29 bp):
AATGACCAAAATGCCCCCCTAAACGTGCC
Found at i:1060 original size:30 final size:30
Alignment explanation
Indices: 1024--1179 Score: 251
Period size: 30 Copynumber: 5.2 Consensus size: 30
1014 TTAACTGATG
1024 AAGCAATGATCCTAAACCAGGATTAAAATA
1 AAGCAATGATCCTAAACCAGGATTAAAATA
1054 AAGCAATGA-CCTAAACCAGGATTAAAATA
1 AAGCAATGATCCTAAACCAGGATTAAAATA
* *
1083 AAGCAATGATCCTCAAGCAGGATTAAAATA
1 AAGCAATGATCCTAAACCAGGATTAAAATA
* *
1113 AAGCAGTGATCCCAAACCAGGATTAAAATA
1 AAGCAATGATCCTAAACCAGGATTAAAATA
* *
1143 AAGCTATAATCCTAAACCAGGATTAAAATA
1 AAGCAATGATCCTAAACCAGGATTAAAATA
1173 AAGCAAT
1 AAGCAAT
1180 AAAGCAGCGA
Statistics
Matches: 114, Mismatches: 11, Indels: 2
0.90 0.09 0.02
Matches are distributed among these distances:
29 29 0.25
30 85 0.75
ACGTcount: A:0.49, C:0.17, G:0.14, T:0.19
Consensus pattern (30 bp):
AAGCAATGATCCTAAACCAGGATTAAAATA
Found at i:1193 original size:38 final size:38
Alignment explanation
Indices: 1151--1247 Score: 122
Period size: 38 Copynumber: 2.6 Consensus size: 38
1141 TAAAGCTATA
* * *
1151 ATCCTAAACCAGGATTAAAATAAAGCAATAAAGCAGCG
1 ATCCTAAACCAGGATCAAAATAAAACAATAAAGCAACG
* ** *
1189 ATCCTAAACCAGGATCGAAATAAAATGATAAAGCAATG
1 ATCCTAAACCAGGATCAAAATAAAACAATAAAGCAACG
*
1227 ATCCTAAACCAGGATCGAAAT
1 ATCCTAAACCAGGATCAAAAT
1248 TGACAAAGTA
Statistics
Matches: 52, Mismatches: 7, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
38 52 1.00
ACGTcount: A:0.48, C:0.19, G:0.15, T:0.18
Consensus pattern (38 bp):
ATCCTAAACCAGGATCAAAATAAAACAATAAAGCAACG
Found at i:1604 original size:35 final size:35
Alignment explanation
Indices: 1537--2465 Score: 942
Period size: 35 Copynumber: 26.5 Consensus size: 35
1527 GACATTTAAA
* * * *
1537 CTGGGTCAACTGAAACAAACTGTAGAAAGATTGCC
1 CTGGATCAACTGAAATAAACTGAAGAAAGATCGCC
* * * *
1572 CTGGATCAACTGAAATAAAGTGAACAAGGATTGCC
1 CTGGATCAACTGAAATAAACTGAAGAAAGATCGCC
*
1607 CTGGATCAAATTGAAATAAACT---G-AAGATCGCC
1 CTGGATC-AACTGAAATAAACTGAAGAAAGATCGCC
1639 CTGGATCAACTGAAATAAACTGGATA-AAAGATCGCC
1 CTGGATCAACTGAAATAAACT-GA-AGAAAGATCGCC
*
1675 CTGGATCAACTGAAATAAATTGAAGGAAAGATCGCC
1 CTGGATCAACTGAAATAAACTGAA-GAAAGATCGCC
* * *
1711 CTGGATCAACTGAAATAAACTAAATAAGGATCGCC
1 CTGGATCAACTGAAATAAACTGAAGAAAGATCGCC
* *
1746 TTGGGTCAACTGAAATAAACTGAAGAAAGATCGCC
1 CTGGATCAACTGAAATAAACTGAAGAAAGATCGCC
1781 CTGGATCAACTGAAATAAACTGAAGAAAAGATCGCC
1 CTGGATCAACTGAAATAAACTGAAG-AAAGATCGCC
* * *
1817 CTGGATCAACTGAAATAAACTGGATAAGGATCGCC
1 CTGGATCAACTGAAATAAACTGAAGAAAGATCGCC
* * *
1852 CTGG-TCAACTGAAATGAATTGAAGAAAGACCGCC
1 CTGGATCAACTGAAATAAACTGAAGAAAGATCGCC
* * * *
1886 CTAGG-TCAACTAAAATGAATTGAAGAAGAGATCTCC
1 CT-GGATCAACTGAAATAAACTGAAGAA-AGATCGCC
* *
1922 TTGGATCAACTGAAATAAACTAAAGAAAGATCGCC
1 CTGGATCAACTGAAATAAACTGAAGAAAGATCGCC
1957 CTGGATCAACTGAAATAAACTGAAGAAAAGATCGCC
1 CTGGATCAACTGAAATAAACTGAAG-AAAGATCGCC
* *
1993 CTGGATCAACTGAAATAAACCGTAGAAAAGATCGCC
1 CTGGATCAACTGAAATAAACTGAAG-AAAGATCGCC
* * * *
2029 CTGGATCAACTGAAATAAACTGGATAAGGACCGCC
1 CTGGATCAACTGAAATAAACTGAAGAAAGATCGCC
* * * *
2064 CTGGGTCAACTGAAATGAATTGAAGAAAGACCGCC
1 CTGGATCAACTGAAATAAACTGAAGAAAGATCGCC
* * * * * *
2099 CTGGGTCAACTAAAATGAATTGAGGAAGAGATCTCC
1 CTGGATCAACTGAAATAAACTGAAGAA-AGATCGCC
*
2135 CTGGATCAACTGAAATAAACTAAAGAAAGATCGCC
1 CTGGATCAACTGAAATAAACTGAAGAAAGATCGCC
* * * * *
2170 CTAGATCAACTGAAATAAACTGAATAAGGACCACC
1 CTGGATCAACTGAAATAAACTGAAGAAAGATCGCC
* * * *
2205 CTGGGTCAACTGAAATAAACTGAA-TAAGAACCACC
1 CTGGATCAACTGAAATAAACTGAAGAAAG-ATCGCC
* ** *
2240 CTGGGTCAACTGAAATAATTTGAAGAAAGATCACC
1 CTGGATCAACTGAAATAAACTGAAGAAAGATCGCC
* * * *
2275 CTAGATCAACTGAAATAAACTGAATAAGGACCAG-C
1 CTGGATCAACTGAAATAAACTGAAGAAAGATC-GCC
* ** * * *
2310 CTGGGTCAACTGAAATAATTTAAAGAAAGACCACC
1 CTGGATCAACTGAAATAAACTGAAGAAAGATCGCC
* * * *
2345 CTGGGTCGACTGAAATAAACTGAAGAAAGACCACC
1 CTGGATCAACTGAAATAAACTGAAGAAAGATCGCC
* * * * *
2380 TTGGATCAGCTGAAATGAATTGAAGGGAAGATCGCC
1 CTGGATCAACTGAAATAAACTGAA-GAAAGATCGCC
* * * *
2416 CTGGATCAACTGAAAT-GATTGAATAAAGACCGCC
1 CTGGATCAACTGAAATAAACTGAAGAAAGATCGCC
*
2450 CTGGGTCAACTGAAAT
1 CTGGATCAACTGAAAT
2466 TAAATTTGTG
Statistics
Matches: 756, Mismatches: 118, Indels: 41
0.83 0.13 0.04
Matches are distributed among these distances:
31 13 0.02
32 14 0.02
34 52 0.07
35 428 0.57
36 249 0.33
ACGTcount: A:0.41, C:0.19, G:0.21, T:0.19
Consensus pattern (35 bp):
CTGGATCAACTGAAATAAACTGAAGAAAGATCGCC
Found at i:2251 original size:318 final size:313
Alignment explanation
Indices: 1542--2465 Score: 1041
Period size: 318 Copynumber: 2.9 Consensus size: 313
1532 TTAAACTGGG
* * *** * * * **
1542 TCAACTGAAACAAACTGTAGAAAGATTGCCCTGGATCAACTGAAATAAAGTGAACAAGGATTGCC
1 TCAACTGAAATAAACTGAAGAAAGACCACCCTGGGTCAACTGAAATAAACTGAACAAGAATCACC
* *
1607 CTGGATCAAATTGAAATAAACT--G-AAGATCGCCCTGGATCAACTGAAATAAACTGGATAAAAG
66 CTGGATC-AACTGAAATAAACTAAGAAAGATCGCCCTGGATCAACTGAAATAAACT-GAAAAAAG
* * *
1669 ATCGCCCTGGATCAACTGAAATAAATTGAAGGAAAGATCGCCCTGGATCAACTGAAATAAACTAA
129 ATCGCCCTGGATCAACTGAAATAAA-TGTAGAAAAGATCGCCCTGGATCAACTGAAATAAACTGA
* * * *
1734 ATAAGGATCGCCTTGGGTCAACTGAAATAAACTGAAGAAAGATCGCCCTGGATCAACTGAAATAA
193 ATAAGGACCGCCTTGGGTCAACTGAAATGAATTGAAGAAAGATCGCCCTGGATCAACTGAAATGA
* ** * * *
1799 ACTGAAGAAAAGATCGCCCTGGATCAACTGAAATAAACTGGATAAGGATCGCCCTGG
258 ATTGAAG-AAAGATCGCCCTGGATCAACTGAAATAAACTAAAGAAAGATCGCCCTGA
* * * * * * * * *
1856 TCAACTGAAATGAATTGAAGAAAGACCGCCCTAGGTCAACTAAAATGAATTGAAGAAGAGATCTC
1 TCAACTGAAATAAACTGAAGAAAGACCACCCTGGGTCAACTGAAATAAACTGAACAAGA-ATCAC
*
1921 CTTGGATCAACTGAAATAAACTAAAGAAAGATCGCCCTGGATCAACTGAAATAAACTGAAGAAAA
65 CCTGGATCAACTGAAATAAACT-AAGAAAGATCGCCCTGGATCAACTGAAATAAACTGAA-AAAA
*
1986 GATCGCCCTGGATCAACTGAAATAAACCGTAGAAAAGATCGCCCTGGATCAACTGAAATAAACTG
128 GATCGCCCTGGATCAACTGAAATAAA-TGTAGAAAAGATCGCCCTGGATCAACTGAAATAAACTG
* * * * *
2051 GATAAGGACCGCCCTGGGTCAACTGAAATGAATTGAAGAAAGACCGCCCTGGGTCAACTAAAATG
192 AATAAGGACCGCCTTGGGTCAACTGAAATGAATTGAAGAAAGATCGCCCTGGATCAACTGAAATG
* *
2116 AATTGAGGAAGAGATCTCCCTGGATCAACTGAAATAAACTAAAGAAAGATCGCCCTAGA
257 AATTGAAGAA-AGATCGCCCTGGATCAACTGAAATAAACTAAAGAAAGATCGCCCT-GA
* * * *
2175 TCAACTGAAATAAACTGAATAAGGACCACCCTGGGTCAACTGAAATAAACTGAATAAGAACCACC
1 TCAACTGAAATAAACTGAAGAAAGACCACCCTGGGTCAACTGAAATAAACTGAACAAGAATCACC
* ** * * * *
2240 CTGGGTCAACTGAAATAATTTGAAGAAAGATCACCCTAGATCAACTGAAATAAACTGAATAAGGA
66 CTGGATCAACTGAAATAAACT-AAGAAAGATCGCCCTGGATCAACTGAAATAAACTGAAAAAAGA
* * * * * * * *
2305 CCAG-CCTGGGTCAACTGAAAT-AATTTAAAGAAAGACCACCCTGGGTCGACTGAAATAAACTGA
130 TC-GCCCTGGATCAACTGAAATAAATGTAGA-AAAGATCGCCCTGGATCAACTGAAATAAACTGA
* * * * * *
2368 AGAAAGACCACCTTGGATCAGCTGAAATGAATTGAAGGGAAGATCGCCCTGGATCAACTGAAATG
193 ATAAGGACCGCCTTGGGTCAACTGAAATGAATTGAA-GAAAGATCGCCCTGGATCAACTGAAATG
* * *
2433 -ATTGAATAAAGACCGCCCTGGGTCAACTGAAAT
257 AATTGAAGAAAGATCGCCCTGGATCAACTGAAAT
2466 TAAATTTGTG
Statistics
Matches: 513, Mismatches: 86, Indels: 21
0.83 0.14 0.03
Matches are distributed among these distances:
314 59 0.12
315 34 0.07
316 67 0.13
317 50 0.10
318 253 0.49
319 50 0.10
ACGTcount: A:0.41, C:0.19, G:0.21, T:0.19
Consensus pattern (313 bp):
TCAACTGAAATAAACTGAAGAAAGACCACCCTGGGTCAACTGAAATAAACTGAACAAGAATCACC
CTGGATCAACTGAAATAAACTAAGAAAGATCGCCCTGGATCAACTGAAATAAACTGAAAAAAGAT
CGCCCTGGATCAACTGAAATAAATGTAGAAAAGATCGCCCTGGATCAACTGAAATAAACTGAATA
AGGACCGCCTTGGGTCAACTGAAATGAATTGAAGAAAGATCGCCCTGGATCAACTGAAATGAATT
GAAGAAAGATCGCCCTGGATCAACTGAAATAAACTAAAGAAAGATCGCCCTGA
Found at i:4128 original size:15 final size:16
Alignment explanation
Indices: 4096--4128 Score: 59
Period size: 16 Copynumber: 2.1 Consensus size: 16
4086 TTGGAAACCA
4096 TTTTTGAAAAATCATT
1 TTTTTGAAAAATCATT
4112 TTTTTGAAAAATC-TT
1 TTTTTGAAAAATCATT
4127 TT
1 TT
4129 GAAAGTATGT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 4 0.24
16 13 0.76
ACGTcount: A:0.33, C:0.06, G:0.06, T:0.55
Consensus pattern (16 bp):
TTTTTGAAAAATCATT
Done.