Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01014913.1 Corchorus olitorius cultivar O-4 contig14946, 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: 42259
ACGTcount: A:0.31, C:0.18, G:0.17, T:0.34
Found at i:21553 original size:2 final size:2
Alignment explanation
Indices: 21548--21572 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
21538 AAAAAATCCA
21548 AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT A
21573 CCAAATGTTA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:34468 original size:71 final size:72
Alignment explanation
Indices: 34329--34516 Score: 288
Period size: 71 Copynumber: 2.6 Consensus size: 72
34319 CTCTCTTCCT
* *
34329 TCTAGATCTGATTTCGTGTATTTCTTTTCATCTTCTGTTGTTGATTTCGTTTTCTTCAGTTTTAA
1 TCTAGATCTGATTTCTTGTATTTCTTTTCATCTTCTGTTCTTGATTTCGTTTTCTTCAGTTTTAA
34394 CTTCCCA
66 CTTCCCA
* * * *
34401 TCTGGATCTCATTTCTTGTGTATCTTTTCATCTTCTGTTCTTGATTTCG-TTTCTTCAGTTTTAA
1 TCTAGATCTGATTTCTTGTATTTCTTTTCATCTTCTGTTCTTGATTTCGTTTTCTTCAGTTTTAA
*
34465 CTTCCCT
66 CTTCCCA
* *
34472 TCTAGATCTGATTTCTTGTATTTCTTTTTATCTTCTTTTCTTGAT
1 TCTAGATCTGATTTCTTGTATTTCTTTTCATCTTCTGTTCTTGAT
34517 AGCTTTGTTT
Statistics
Matches: 103, Mismatches: 13, Indels: 1
0.88 0.11 0.01
Matches are distributed among these distances:
71 60 0.58
72 43 0.42
ACGTcount: A:0.13, C:0.20, G:0.11, T:0.56
Consensus pattern (72 bp):
TCTAGATCTGATTTCTTGTATTTCTTTTCATCTTCTGTTCTTGATTTCGTTTTCTTCAGTTTTAA
CTTCCCA
Found at i:39669 original size:60 final size:59
Alignment explanation
Indices: 39572--39688 Score: 207
Period size: 60 Copynumber: 2.0 Consensus size: 59
39562 GTCATGATGT
*
39572 CATGTAGCACTTCGTTTGAGGTAGAAAGTGGAGTCAACTGGGAGGTACAATTTCCTTTC
1 CATGTAGCACTTCGTTGGAGGTAGAAAGTGGAGTCAACTGGGAGGTACAATTTCCTTTC
*
39631 CATGTTAGCACTTCGTTGGAGGTAGAAAGTTGAGTCAACTGGGAGGTACAATTTCCTT
1 CATG-TAGCACTTCGTTGGAGGTAGAAAGTGGAGTCAACTGGGAGGTACAATTTCCTT
39689 ACCAGTAAAG
Statistics
Matches: 55, Mismatches: 2, Indels: 1
0.95 0.03 0.02
Matches are distributed among these distances:
59 4 0.07
60 51 0.93
ACGTcount: A:0.26, C:0.16, G:0.27, T:0.31
Consensus pattern (59 bp):
CATGTAGCACTTCGTTGGAGGTAGAAAGTGGAGTCAACTGGGAGGTACAATTTCCTTTC
Found at i:39914 original size:33 final size:30
Alignment explanation
Indices: 39843--39901 Score: 100
Period size: 30 Copynumber: 2.0 Consensus size: 30
39833 ACAATCTTTC
* *
39843 ATTTCCCATTGTTACATAGGCTACTTTTTG
1 ATTTACCACTGTTACATAGGCTACTTTTTG
39873 ATTTACCACTGTTACATAGGCTACTTTTT
1 ATTTACCACTGTTACATAGGCTACTTTTT
39902 TTTTTTCTAC
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
30 27 1.00
ACGTcount: A:0.22, C:0.20, G:0.12, T:0.46
Consensus pattern (30 bp):
ATTTACCACTGTTACATAGGCTACTTTTTG
Found at i:41899 original size:338 final size:318
Alignment explanation
Indices: 40996--42259 Score: 1020
Period size: 322 Copynumber: 3.9 Consensus size: 318
40986 TGGCAAATTC
* * ** * ** * *
40996 ACTCATAAAATATATATAATTCAACACCAAAAAGATTGGAAGACTTTTCACGCTTTTAATATCGT
1 ACTCAGAAAAAATATATAATTCAATGCCAAAAAAATT-GAAGGTTTTTCACGCTTCTAATATCAT
* * * * * * * *
41061 TTTTCATATTT-TTATTCTGAATTAATTTCTAATTAAATCGAAATAAAATTCAGATGCAT-GTAA
65 TTTT-TTTTTTATTTTTCCG-ATTAATTTCTAATTAAATAGAAACAAGATTGAGATGC-TCGTAA
* * * * * * * *
41124 AAGCAAATCCTTAAATCCAATGTGGCTGGGATTTGATTAGATGAGTAAAGATATTTCAAGGAGTC
127 AAAC-AATTCTTATATCCAATGTGGCTGAGATTTGGTTCGATGAATATAGATATTTCAAGGAGTC
* * * * * * ** *
41189 TCGGT-GACAAAAATCATGC-AAA-TCAGACTGTGG-CCTCGGAATGCGTTTTTA-CTAAAAAAC
191 T--TTCGCCAAAAATCATGCAAAATTGAG-CCG-GGATC-CGAAACACGTTTTTAGC-CAAAAAC
* * * * * *
41249 CGTGATGGTTAGTACACAATTTCGACGAAAAACTAACCCGAAATGTTTATTCTCAATTTTTTGGC
250 CATGATGGTTACTACACGATTTCGGCTAAAAACTAACCCGAAA-GTTT-TTCTCAATTTTTTTGC
41314 CACAAT
313 CACAAT
* * *
41320 ACTCAGAAAAAAAAATATAATTCAATGCCAAAAATATTGACGGCTTTTTCACGCTTCTAATATC-
1 ACTCAG-AAAAAATATATAATTCAATGCCAAAAAAATTGAAGG-TTTTTCACGCTTCTAATATCA
* *** * * *
41384 -GTTTTTCCAT-TTTTTCCGGATTAATTTCTAATTAAATTGAAACAAGATTCAAATGCTCGTAAA
64 TTTTTTTTTTTATTTTTCC-GATTAATTTCTAATTAAATAGAAACAAGATTGAGATGCTCGTAAA
* * * *
41447 AACGAATCCTTATATTCAATGTGGTTGACATTTGGTTCGATGAATAT-GAATATTTCAAGGAGTC
128 AAC-AATTCTTATATCCAATGTGGCTGAGATTTGGTTCGATGAATATAG-ATATTTCAAGGAGTC
* * * * * *
41511 TCTACGTCAAAAATCATGCAAAATTGAGCCGGGTTCCGGAACGCGTTTTTAGCCAATAACCATGA
191 T-TTCGCCAAAAATCATGCAAAATTGAGCCGGGATCCGAAACACGTTTTTAGCCAAAAACCATGA
41576 TGGTTTA-TACATCGATTTCGGCTAAAATTTTGCAAAAACTAACCCGACAAGTTTTTCCTCAATT
255 TGG-TTACTACA-CGATTTCGGC--------T--AAAAACTAACCCGA-AAGTTTTT-CTCAATT
41640 TTTTTGCCACAAT
306 TTTTTGCCACAAT
*
41653 ACTCAGAAAAAATATATAATTTGAA-GCCAAAAAAATTGAATGGTTTTTCACGCTTCTAATATCA
1 ACTCAGAAAAAATATATAA-TTCAATGCCAAAAAAATTGAA-GGTTTTTCACGCTTCTAATATCA
* *
41717 TTTTTATTTTTTATTTTTCCCTTATTTAA-TTCTAATTAAATCGAAACAAAGATTGAGATGCTCG
64 TTTTT-TTTTTTATTTTT-CC-GA-TTAATTTCTAATTAAATAGAAAC-AAGATTGAGATGCTCG
* * * * * *
41781 TAAAAACAAATTCTTAAATCCATTATGGCTGAGATTTTGTTAGATGAATATAGATATTTCAAAGA
124 TAAAAAC-AATTCTTATATCCAATGTGGCTGAGATTTGGTTCGATGAATATAGATATTTCAAGGA
** * * * *
41846 GTCTTTCTGCCAAAAATCATTTAAAACTGAGCCGGGATCCGAAACATGTTTTTAGCCAAAAATCG
188 GTCTTTC-GCCAAAAATCATGCAAAATTGAGCCGGGATCCGAAACACGTTTTTAGCCAAAAACCA
*
41911 TGATGGTTACTACACGATTTTGGCTAAAAACTAACCCGAAAAGTTTTTCTCAA-TTTTTTG-CA-
252 TGATGGTTACTACACGATTTCGGCTAAAAACTAACCCG-AAAGTTTTTCTCAATTTTTTTGCCAC
41973 AAGT
316 AA-T
* * * * *
41977 ATTTAGAAAAAATATATAATTCAATGCCAAAAAGATTGACAGGCTTTCCACGCTTCTAA-ATTCT
1 ACTCAGAAAAAATATATAATTCAATGCCAAAAAAATTGA-AGGTTTTTCACGCTTCTAATA-TC-
* *
42041 AATATCGTTTTTCCTTTT-TTTTTCCGAATTAATTTCTAATTAAATAGAAATAAGGTTCG-GATG
63 -AT-T--TTTTT--TTTTATTTTTCCG-ATTAATTTCTAATTAAATAGAAACAAGATT-GAGATG
* **
42104 CTCATAAAAACAATTCCTTATATGAAATGTGGCTGAGATTTGGTTCGATGAATATAGATATTTCA
120 CTCGTAAAAACAATT-CTTATATCCAATGTGGCTGAGATTTGGTTCGATGAATATAGATATTTCA
* * *
42169 AGGAGTCTTTACGCCAAAAATCATGCAAAATTGAGCCGGGACTCTGAAACGCGTTTTTTTGCCAA
184 AGGAGTCTTT-CGCCAAAAATCATGCAAAATTGAGCCGGGA-TCCGAAACACG-TTTTTAGCCAA
** * *
42234 AAACTGTGATAGTTAGTACACGATTT
246 AAACCATGATGGTTACTACACGATTT
Statistics
Matches: 771, Mismatches: 114, Indels: 105
0.78 0.12 0.11
Matches are distributed among these distances:
321 2 0.00
322 142 0.18
323 29 0.04
324 62 0.08
325 52 0.07
326 11 0.01
327 122 0.16
328 32 0.04
329 41 0.05
330 4 0.01
332 47 0.06
333 49 0.06
334 5 0.01
335 3 0.00
336 5 0.01
337 34 0.04
338 130 0.17
339 1 0.00
ACGTcount: A:0.35, C:0.16, G:0.15, T:0.34
Consensus pattern (318 bp):
ACTCAGAAAAAATATATAATTCAATGCCAAAAAAATTGAAGGTTTTTCACGCTTCTAATATCATT
TTTTTTTTTATTTTTCCGATTAATTTCTAATTAAATAGAAACAAGATTGAGATGCTCGTAAAAAC
AATTCTTATATCCAATGTGGCTGAGATTTGGTTCGATGAATATAGATATTTCAAGGAGTCTTTCG
CCAAAAATCATGCAAAATTGAGCCGGGATCCGAAACACGTTTTTAGCCAAAAACCATGATGGTTA
CTACACGATTTCGGCTAAAAACTAACCCGAAAGTTTTTCTCAATTTTTTTGCCACAAT
Done.