Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01012212.1 Corchorus olitorius cultivar O-4 contig12245, 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: 13109
ACGTcount: A:0.30, C:0.22, G:0.18, T:0.30
Warning! 1 characters in sequence are not A, C, G, or T
Found at i:483 original size:125 final size:125
Alignment explanation
Indices: 76--730 Score: 1143
Period size: 125 Copynumber: 5.3 Consensus size: 125
66 AAATTAGCTC
* * *
76 GTAGAAGATTAAATATAGCGGCGTTTACTTTAGAAGAGCCACTATTTAGCGGCGTTTATCATGAA
1 GTAGAAGATTAAATATAGCGGCGTTTACTTTAGAAGCGCCACTATTTAGCGGCGTCTGTCATGAA
* *
141 AAACGCCGCTATTCATAACAAATAAATGGTGTTTTTAGTTTCACCAAATTTCTATTCTTT
66 AAACGCCGCTATTCATAACAAATAAATGGTGTTTTTAGTTTCACCGAATTTCTATTGTTT
*
201 GTAGAAGATTATATATAGCGGCGTTTACTTTAGAAGCGCCACTATTTAGCGGCGTCTGTCATGAA
1 GTAGAAGATTAAATATAGCGGCGTTTACTTTAGAAGCGCCACTATTTAGCGGCGTCTGTCATGAA
266 AAACGCCGCTATTCATAAC-AATAAATGGTGTTTTTAGTTTCACCGAATTTCTATTGTTT
66 AAACGCCGCTATTCATAACAAATAAATGGTGTTTTTAGTTTCACCGAATTTCTATTGTTT
*
325 GTAGAAGATTAAATATAGCGGCGTTTACTTTAGAAACGCCACTATTTAGCGGCGTCTGTCATGAA
1 GTAGAAGATTAAATATAGCGGCGTTTACTTTAGAAGCGCCACTATTTAGCGGCGTCTGTCATGAA
* *
390 AAACGCCACTATTCATAACAAATAAATGGTGTTTTTAGTTTCACCGGATTTCTATTGTTT
66 AAACGCCGCTATTCATAACAAATAAATGGTGTTTTTAGTTTCACCGAATTTCTATTGTTT
* * * *
450 GTAGAAGGTTAAATATAGCGGCATTTACTTTAGAAGCGCCACTATTTAGCGGCGTTTATCATGAA
1 GTAGAAGATTAAATATAGCGGCGTTTACTTTAGAAGCGCCACTATTTAGCGGCGTCTGTCATGAA
* *
515 AAACGCCGCTATTCATAACAAATAAATGGTGTTTTTAGTTTCACCAAATTTCTATTCTTT
66 AAACGCCGCTATTCATAACAAATAAATGGTGTTTTTAGTTTCACCGAATTTCTATTGTTT
*
575 GTAGAAGATTATATATAGCGGCGTTTACTTTAGAAGCGCCACTATTTAGCGGCGTCTGTCATGAA
1 GTAGAAGATTAAATATAGCGGCGTTTACTTTAGAAGCGCCACTATTTAGCGGCGTCTGTCATGAA
*
640 AAACGCCGCTATTCATAAC-AATAAATGGTGTTTTTAGTTTCACCGGATTTCTATTGTTT
66 AAACGCCGCTATTCATAACAAATAAATGGTGTTTTTAGTTTCACCGAATTTCTATTGTTT
699 GTAGAAGATTAAATATAGCGGCGTTTACTTTA
1 GTAGAAGATTAAATATAGCGGCGTTTACTTTA
731 AATGGTGTTT
Statistics
Matches: 501, Mismatches: 28, Indels: 3
0.94 0.05 0.01
Matches are distributed among these distances:
124 187 0.37
125 314 0.63
ACGTcount: A:0.30, C:0.16, G:0.18, T:0.35
Consensus pattern (125 bp):
GTAGAAGATTAAATATAGCGGCGTTTACTTTAGAAGCGCCACTATTTAGCGGCGTCTGTCATGAA
AAACGCCGCTATTCATAACAAATAAATGGTGTTTTTAGTTTCACCGAATTTCTATTGTTT
Found at i:514 original size:249 final size:250
Alignment explanation
Indices: 76--730 Score: 1145
Period size: 249 Copynumber: 2.6 Consensus size: 250
66 AAATTAGCTC
* *
76 GTAGAAGATTAAATATAGCGGCGTTTACTTTAGAAGA-GCCACTATTTAGCGGCGTTTATCATGA
1 GTAGAAGATTAAATATAGCGGCGTTTACTTTAGAA-ACGCCACTATTTAGCGGCGTCTGTCATGA
** *
140 AAAACGCCGCTATTCATAACAAATAAATGGTGTTTTTAGTTTCACCAAATTTCTATTCTTTGTAG
65 AAAACGCCGCTATTCATAACAAATAAATGGTGTTTTTAGTTTCACCGGATTTCTATTGTTTGTAG
* *
205 AAGATTATATATAGCGGCGTTTACTTTAGAAGCGCCACTATTTAGCGGCGTCTGTCATGAAAAAC
130 AAGATTAAATATAGCGGCGTTTACTTTAGAAGCGCCACTATTTAGCGGCGTCTATCATGAAAAAC
* *
270 GCCGCTATTCATAAC-AATAAATGGTGTTTTTAGTTTCACCGAATTTCTATTGTTT
195 GCCGCTATTCATAACAAATAAATGGTGTTTTTAGTTTCACCAAATTTCTATTCTTT
325 GTAGAAGATTAAATATAGCGGCGTTTACTTTAGAAACGCCACTATTTAGCGGCGTCTGTCATGAA
1 GTAGAAGATTAAATATAGCGGCGTTTACTTTAGAAACGCCACTATTTAGCGGCGTCTGTCATGAA
*
390 AAACGCCACTATTCATAACAAATAAATGGTGTTTTTAGTTTCACCGGATTTCTATTGTTTGTAGA
66 AAACGCCGCTATTCATAACAAATAAATGGTGTTTTTAGTTTCACCGGATTTCTATTGTTTGTAGA
* * *
455 AGGTTAAATATAGCGGCATTTACTTTAGAAGCGCCACTATTTAGCGGCGTTTATCATGAAAAACG
131 AGATTAAATATAGCGGCGTTTACTTTAGAAGCGCCACTATTTAGCGGCGTCTATCATGAAAAACG
520 CCGCTATTCATAACAAATAAATGGTGTTTTTAGTTTCACCAAATTTCTATTCTTT
196 CCGCTATTCATAACAAATAAATGGTGTTTTTAGTTTCACCAAATTTCTATTCTTT
* *
575 GTAGAAGATTATATATAGCGGCGTTTACTTTAGAAGCGCCACTATTTAGCGGCGTCTGTCATGAA
1 GTAGAAGATTAAATATAGCGGCGTTTACTTTAGAAACGCCACTATTTAGCGGCGTCTGTCATGAA
640 AAACGCCGCTATTCATAAC-AATAAATGGTGTTTTTAGTTTCACCGGATTTCTATTGTTTGTAGA
66 AAACGCCGCTATTCATAACAAATAAATGGTGTTTTTAGTTTCACCGGATTTCTATTGTTTGTAGA
704 AGATTAAATATAGCGGCGTTTACTTTA
131 AGATTAAATATAGCGGCGTTTACTTTA
731 AATGGTGTTT
Statistics
Matches: 386, Mismatches: 18, Indels: 4
0.95 0.04 0.01
Matches are distributed among these distances:
248 1 0.00
249 266 0.69
250 119 0.31
ACGTcount: A:0.30, C:0.16, G:0.18, T:0.35
Consensus pattern (250 bp):
GTAGAAGATTAAATATAGCGGCGTTTACTTTAGAAACGCCACTATTTAGCGGCGTCTGTCATGAA
AAACGCCGCTATTCATAACAAATAAATGGTGTTTTTAGTTTCACCGGATTTCTATTGTTTGTAGA
AGATTAAATATAGCGGCGTTTACTTTAGAAGCGCCACTATTTAGCGGCGTCTATCATGAAAAACG
CCGCTATTCATAACAAATAAATGGTGTTTTTAGTTTCACCAAATTTCTATTCTTT
Found at i:770 original size:68 final size:68
Alignment explanation
Indices: 661--798 Score: 267
Period size: 68 Copynumber: 2.0 Consensus size: 68
651 TTCATAACAA
661 TAAATGGTGTTTTTAGTTTCACCGGATTTCTATTGTTTGTAGAAGATTAAATATAGCGGCGTTTA
1 TAAATGGTGTTTTTAGTTTCACCGGATTTCTATTGTTTGTAGAAGATTAAATATAGCGGCGTTTA
726 CTT
66 CTT
*
729 TAAATGGTGTTTTTAGTTTCACCGGATTTCTATTGTTTGTAGAAGGTTAAATATAGCGGCGTTTA
1 TAAATGGTGTTTTTAGTTTCACCGGATTTCTATTGTTTGTAGAAGATTAAATATAGCGGCGTTTA
794 CTT
66 CTT
797 TA
1 TA
799 GAAGCGCCAC
Statistics
Matches: 69, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
68 69 1.00
ACGTcount: A:0.25, C:0.10, G:0.21, T:0.44
Consensus pattern (68 bp):
TAAATGGTGTTTTTAGTTTCACCGGATTTCTATTGTTTGTAGAAGATTAAATATAGCGGCGTTTA
CTT
Found at i:951 original size:125 final size:124
Alignment explanation
Indices: 729--1047 Score: 557
Period size: 125 Copynumber: 2.6 Consensus size: 124
719 GCGTTTACTT
*
729 TAAATGGTGTTTTTAGTTTCACCGGATTTCTATTGTTTGTAGAAGGTTAAATATAGCGGCGTTTA
1 TAAATGGTGTTTTTAGTTTCACCGGATTTCTATTGTTTGTAGAAGATTAAATATAGCGGCGTTTA
* * *
794 CTTTAGAAGCGCCACTATTTAGCGGCGTCTGTCATGAAAGACGCCGCTATTCATAACAAA
66 CTTTAGAAACGCCACTATTCAGCGGCGTCTGTCATGAAAAACGCCGCTATTCATAAC-AA
** * *
854 TAAATGGTGTTTTTAGTTTCACCAAATTTCTATTCTTTGTAGAAGATTATATATAGCGGCGTTTA
1 TAAATGGTGTTTTTAGTTTCACCGGATTTCTATTGTTTGTAGAAGATTAAATATAGCGGCGTTTA
919 CTTTAGAAACGCCACTATTCAGCGGCGTCTGTCATGAAAAACGCCGCTATTCATAACAA
66 CTTTAGAAACGCCACTATTCAGCGGCGTCTGTCATGAAAAACGCCGCTATTCATAACAA
978 TAAATGGTGTTTTTAGTTTCACCGGATTTCTATTGTTTGTAGAAGATTAAATATAGCGGCGTTTA
1 TAAATGGTGTTTTTAGTTTCACCGGATTTCTATTGTTTGTAGAAGATTAAATATAGCGGCGTTTA
1043 CTTTA
66 CTTTA
1048 AATGGTGTTT
Statistics
Matches: 182, Mismatches: 12, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
124 68 0.37
125 114 0.63
ACGTcount: A:0.28, C:0.16, G:0.19, T:0.37
Consensus pattern (124 bp):
TAAATGGTGTTTTTAGTTTCACCGGATTTCTATTGTTTGTAGAAGATTAAATATAGCGGCGTTTA
CTTTAGAAACGCCACTATTCAGCGGCGTCTGTCATGAAAAACGCCGCTATTCATAACAA
Found at i:987 original size:317 final size:317
Alignment explanation
Indices: 412--1360 Score: 1772
Period size: 317 Copynumber: 3.0 Consensus size: 317
402 TCATAACAAA
*
412 TAAATGGTGTTTTTAGTTTCACCGGATTTCTATTGTTTGTAGAAGGTTAAATATAGCGGCATTTA
1 TAAATGGTGTTTTTAGTTTCACCGGATTTCTATTGTTTGTAGAAGGTTAAATATAGCGGCGTTTA
* * *
477 CTTTAGAAGCGCCACTATTTAGCGGCGTTTATCATGAAAAACGCCGCTATTCATAACAAATAAAT
66 CTTTAGAAGCGCCACTATTTAGCGGCGTCTGTCATGAAAGACGCCGCTATTCATAACAAATAAAT
542 GGTGTTTTTAGTTTCACCAAATTTCTATTCTTTGTAGAAGATTATATATAGCGGCGTTTACTTTA
131 GGTGTTTTTAGTTTCACCAAATTTCTATTCTTTGTAGAAGATTATATATAGCGGCGTTTACTTTA
607 GAAGCGCCACTATTTAGCGGCGTCTGTCATGAAAAACGCCGCTATTCATAACAATAAATGGTGTT
196 GAAGCGCCACTATTTAGCGGCGTCTGTCATGAAAAACGCCGCTATTCATAACAATAAATGGTGTT
672 TTTAGTTTCACCGGATTTCTATTGTTTGTAGAAGATTAAATATAGCGGCGTTTACTT
261 TTTAGTTTCACCGGATTTCTATTGTTTGTAGAAGATTAAATATAGCGGCGTTTACTT
729 TAAATGGTGTTTTTAGTTTCACCGGATTTCTATTGTTTGTAGAAGGTTAAATATAGCGGCGTTTA
1 TAAATGGTGTTTTTAGTTTCACCGGATTTCTATTGTTTGTAGAAGGTTAAATATAGCGGCGTTTA
794 CTTTAGAAGCGCCACTATTTAGCGGCGTCTGTCATGAAAGACGCCGCTATTCATAACAAATAAAT
66 CTTTAGAAGCGCCACTATTTAGCGGCGTCTGTCATGAAAGACGCCGCTATTCATAACAAATAAAT
859 GGTGTTTTTAGTTTCACCAAATTTCTATTCTTTGTAGAAGATTATATATAGCGGCGTTTACTTTA
131 GGTGTTTTTAGTTTCACCAAATTTCTATTCTTTGTAGAAGATTATATATAGCGGCGTTTACTTTA
* *
924 GAAACGCCACTATTCAGCGGCGTCTGTCATGAAAAACGCCGCTATTCATAACAATAAATGGTGTT
196 GAAGCGCCACTATTTAGCGGCGTCTGTCATGAAAAACGCCGCTATTCATAACAATAAATGGTGTT
989 TTTAGTTTCACCGGATTTCTATTGTTTGTAGAAGATTAAATATAGCGGCGTTTACTT
261 TTTAGTTTCACCGGATTTCTATTGTTTGTAGAAGATTAAATATAGCGGCGTTTACTT
*
1046 TAAATGGTGTTTTTAGTTTCACCGGATTTCTATTGTTTGTAGAAGGTTAAATATAACGGCGTTTA
1 TAAATGGTGTTTTTAGTTTCACCGGATTTCTATTGTTTGTAGAAGGTTAAATATAGCGGCGTTTA
*
1111 CTTTAGAAGCGCCACTATTTAGCGGCGTCTGTCATGAAAGATGCCGCTATTCATAACAAATAAAT
66 CTTTAGAAGCGCCACTATTTAGCGGCGTCTGTCATGAAAGACGCCGCTATTCATAACAAATAAAT
* * *
1176 GGTGTTTTTAGTTTCACCAAATTTCTATTGTTTGTAGAAGATTAAATATAGCGGCGCTTACTTTA
131 GGTGTTTTTAGTTTCACCAAATTTCTATTCTTTGTAGAAGATTATATATAGCGGCGTTTACTTTA
*
1241 GAAGCACCACTATTTAGCGGCGTCTGTCATGAAAAACGCCGCTATTCATAACAAATAAATGGTGT
196 GAAGCGCCACTATTTAGCGGCGTCTGTCATGAAAAACGCCGCTATTCATAAC-AATAAATGGTGT
*
1306 TTTTAGTTTCACCGAATTTCTATTGTTTGTAGAAGATTAAATATAGCGGCGTTTA
260 TTTTAGTTTCACCGGATTTCTATTGTTTGTAGAAGATTAAATATAGCGGCGTTTA
1361 TTCGGCGTTT
Statistics
Matches: 616, Mismatches: 15, Indels: 1
0.97 0.02 0.00
Matches are distributed among these distances:
317 550 0.89
318 66 0.11
ACGTcount: A:0.28, C:0.16, G:0.19, T:0.37
Consensus pattern (317 bp):
TAAATGGTGTTTTTAGTTTCACCGGATTTCTATTGTTTGTAGAAGGTTAAATATAGCGGCGTTTA
CTTTAGAAGCGCCACTATTTAGCGGCGTCTGTCATGAAAGACGCCGCTATTCATAACAAATAAAT
GGTGTTTTTAGTTTCACCAAATTTCTATTCTTTGTAGAAGATTATATATAGCGGCGTTTACTTTA
GAAGCGCCACTATTTAGCGGCGTCTGTCATGAAAAACGCCGCTATTCATAACAATAAATGGTGTT
TTTAGTTTCACCGGATTTCTATTGTTTGTAGAAGATTAAATATAGCGGCGTTTACTT
Found at i:1087 original size:68 final size:68
Alignment explanation
Indices: 978--1115 Score: 258
Period size: 68 Copynumber: 2.0 Consensus size: 68
968 TTCATAACAA
*
978 TAAATGGTGTTTTTAGTTTCACCGGATTTCTATTGTTTGTAGAAGATTAAATATAGCGGCGTTTA
1 TAAATGGTGTTTTTAGTTTCACCGGATTTCTATTGTTTGTAGAAGATTAAATATAACGGCGTTTA
1043 CTT
66 CTT
*
1046 TAAATGGTGTTTTTAGTTTCACCGGATTTCTATTGTTTGTAGAAGGTTAAATATAACGGCGTTTA
1 TAAATGGTGTTTTTAGTTTCACCGGATTTCTATTGTTTGTAGAAGATTAAATATAACGGCGTTTA
1111 CTT
66 CTT
1114 TA
1 TA
1116 GAAGCGCCAC
Statistics
Matches: 68, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
68 68 1.00
ACGTcount: A:0.25, C:0.10, G:0.20, T:0.44
Consensus pattern (68 bp):
TAAATGGTGTTTTTAGTTTCACCGGATTTCTATTGTTTGTAGAAGATTAAATATAACGGCGTTTA
CTT
Found at i:1087 original size:192 final size:193
Alignment explanation
Indices: 854--1240 Score: 650
Period size: 192 Copynumber: 2.0 Consensus size: 193
844 TCATAACAAA
* *
854 TAAATGGTGTTTTTAGTTTCACCAAATTTCTATTCTTTGTAGAAGATTATATATAGCGGCGTTTA
1 TAAATGGTGTTTTTAGTTTCACCAAATTTCTATTCTTTGTAGAAGATTAAATATAACGGCGTTTA
919 CTTTAGAAACGCCACTATTCAGCGGCGTCTGTCATGAAAAACGCCGCTATTCATAAC-AATAAAT
66 CTTTAGAAACGCCACTATTCAGCGGCGTCTGTCATGAAAAACGCCGCTATTCATAACAAATAAAT
** *
983 GGTGTTTTTAGTTTCACCGGATTTCTATTGTTTGTAGAAGATTAAATATAGCGGCGTTTACTT
131 GGTGTTTTTAGTTTCACCAAATTTCTATTGTTTGTAGAAGATTAAATATAGCGGCGCTTACTT
** * *
1046 TAAATGGTGTTTTTAGTTTCACCGGATTTCTATTGTTTGTAGAAGGTTAAATATAACGGCGTTTA
1 TAAATGGTGTTTTTAGTTTCACCAAATTTCTATTCTTTGTAGAAGATTAAATATAACGGCGTTTA
* * * *
1111 CTTTAGAAGCGCCACTATTTAGCGGCGTCTGTCATGAAAGATGCCGCTATTCATAACAAATAAAT
66 CTTTAGAAACGCCACTATTCAGCGGCGTCTGTCATGAAAAACGCCGCTATTCATAACAAATAAAT
1176 GGTGTTTTTAGTTTCACCAAATTTCTATTGTTTGTAGAAGATTAAATATAGCGGCGCTTACTT
131 GGTGTTTTTAGTTTCACCAAATTTCTATTGTTTGTAGAAGATTAAATATAGCGGCGCTTACTT
1239 TA
1 TA
1241 GAAGCACCAC
Statistics
Matches: 181, Mismatches: 13, Indels: 1
0.93 0.07 0.01
Matches are distributed among these distances:
192 112 0.62
193 69 0.38
ACGTcount: A:0.28, C:0.15, G:0.19, T:0.38
Consensus pattern (193 bp):
TAAATGGTGTTTTTAGTTTCACCAAATTTCTATTCTTTGTAGAAGATTAAATATAACGGCGTTTA
CTTTAGAAACGCCACTATTCAGCGGCGTCTGTCATGAAAAACGCCGCTATTCATAACAAATAAAT
GGTGTTTTTAGTTTCACCAAATTTCTATTGTTTGTAGAAGATTAAATATAGCGGCGCTTACTT
Found at i:1177 original size:442 final size:442
Alignment explanation
Indices: 163--1360 Score: 1552
Period size: 442 Copynumber: 2.7 Consensus size: 442
153 TCATAACAAA
** * * * *
163 TAAATGGTGTTTTTAGTTTCACCAAATTTCTATTCTTTGTAGAAGATTATATATAGCGGCGTTTA
1 TAAATGGTGTTTTTAGTTTCACCGGATTTCTATTGTTTGTAGAAGGTTAAATATAACGGCGTTTA
*
228 CTTTAGAAGCGCCACTATTTAGCGGCGTCTGTCATGAAAAACGCCGCTATTCATAACAATAAATG
66 CTTTAGAAGCGCCACTATTTAGCGGCGTCTGTCATGAAAAATGCCGCTATTCATAACAATAAATG
293 GTGTTTTTAGTTTCACCGAATTTCTATTGTTTGTAGAAGATTAAATATAGCGGCGTTTACTTTAG
131 GTGTTTTTAGTTTCACCGAATTTCTATTGTTTGTAGAAGATTAAATATAGCGGCGTTTACTTTAG
* *
358 AAACGCCACTATTTAGCGGCGTCTGTCATGAAAAACGCCACTATTCATAACAAATAAATGGTGTT
196 AAGCGCCACTATTTAGCGGCGTCTGTCATGAAAAACGCCGCTATTCATAACAAATAAATGGTGTT
* * * *
423 TTTAGTTTCACCGGATTTCTATTGTTTGTAGAAGGTTAAATATAGCGGCATTTACTTTAGAAGCG
261 TTTAGTTTCACCGAATTTCTATTGTTTGTAGAAGATTAAATATAGCGGCGTTTACTTTAGAAACG
* *
488 CCACTATTTAGCGGCGTTTATCATGAAAAACGCCGCTATTCATAACAAATAAATGGTGTTTTTAG
326 CCACTATTCAGCGGCGTCTATCATGAAAAACGCCGCTATTCATAACAAATAAATGGTGTTTTTAG
*
553 TTTCACCAAATTTCTATTCTTTGTAGAAGATTATATATAGCGGCGTTTACTT
391 TTTCACCAAATTTCTATTCTTTGTAGAAGATTAAATATAGCGGCGTTTACTT
* **** * ** * * * *
605 TAGAA--GCGCCACTA-TTT-AGCGG-CGTC---TGTCATGAAAAACGCCGCTATTCATAACAAT
1 TA-AATGGTGTTTTTAGTTTCACCGGATTTCTATTGT-TTGTAGAA-G--G---TT-A-AA-TAT
** *** * ** *** * * * *
662 AAATG-GTGTT--TTTAGTTTCACC-GGATTT--CTATTGTTTGTAGAAGATTAAATATAGCGGC
55 AACGGCGT-TTACTTTAGAAGCGCCACTATTTAGC-GGCGTCTGT-CATGA--AAA-AT-GCCGC
* ** * *
721 -GTT--T-ACTTTAAATGGTGTTTTTAGTTTCACCGGATTTCTATTGTTTGTAGAAGGTTAAATA
113 TATTCATAACAATAAATGGTGTTTTTAGTTTCACCGAATTTCTATTGTTTGTAGAAGATTAAATA
*
782 TAGCGGCGTTTACTTTAGAAGCGCCACTATTTAGCGGCGTCTGTCATGAAAGACGCCGCTATTCA
178 TAGCGGCGTTTACTTTAGAAGCGCCACTATTTAGCGGCGTCTGTCATGAAAAACGCCGCTATTCA
* * *
847 TAACAAATAAATGGTGTTTTTAGTTTCACCAAATTTCTATTCTTTGTAGAAGATTATATATAGCG
243 TAACAAATAAATGGTGTTTTTAGTTTCACCGAATTTCTATTGTTTGTAGAAGATTAAATATAGCG
*
912 GCGTTTACTTTAGAAACGCCACTATTCAGCGGCGTCTGTCATGAAAAACGCCGCTATTCATAAC-
308 GCGTTTACTTTAGAAACGCCACTATTCAGCGGCGTCTATCATGAAAAACGCCGCTATTCATAACA
** *
976 AATAAATGGTGTTTTTAGTTTCACCGGATTTCTATTGTTTGTAGAAGATTAAATATAGCGGCGTT
373 AATAAATGGTGTTTTTAGTTTCACCAAATTTCTATTCTTTGTAGAAGATTAAATATAGCGGCGTT
1041 TACTT
438 TACTT
1046 TAAATGGTGTTTTTAGTTTCACCGGATTTCTATTGTTTGTAGAAGGTTAAATATAACGGCGTTTA
1 TAAATGGTGTTTTTAGTTTCACCGGATTTCTATTGTTTGTAGAAGGTTAAATATAACGGCGTTTA
*
1111 CTTTAGAAGCGCCACTATTTAGCGGCGTCTGTCATGAAAGATGCCGCTATTCATAACAAATAAAT
66 CTTTAGAAGCGCCACTATTTAGCGGCGTCTGTCATGAAAAATGCCGCTATTCATAAC-AATAAAT
* *
1176 GGTGTTTTTAGTTTCACCAAATTTCTATTGTTTGTAGAAGATTAAATATAGCGGCGCTTACTTTA
130 GGTGTTTTTAGTTTCACCGAATTTCTATTGTTTGTAGAAGATTAAATATAGCGGCGTTTACTTTA
*
1241 GAAGCACCACTATTTAGCGGCGTCTGTCATGAAAAACGCCGCTATTCATAACAAATAAATGGTGT
195 GAAGCGCCACTATTTAGCGGCGTCTGTCATGAAAAACGCCGCTATTCATAACAAATAAATGGTGT
1306 TTTTAGTTTCACCGAATTTCTATTGTTTGTAGAAGATTAAATATAGCGGCGTTTA
260 TTTTAGTTTCACCGAATTTCTATTGTTTGTAGAAGATTAAATATAGCGGCGTTTA
1361 TTCGGCGTTT
Statistics
Matches: 623, Mismatches: 96, Indels: 74
0.79 0.12 0.09
Matches are distributed among these distances:
435 2 0.00
436 5 0.01
437 5 0.01
438 13 0.02
439 8 0.01
440 16 0.03
441 88 0.14
442 435 0.70
443 16 0.03
444 11 0.02
445 11 0.02
446 5 0.01
447 5 0.01
448 3 0.00
ACGTcount: A:0.29, C:0.16, G:0.19, T:0.36
Consensus pattern (442 bp):
TAAATGGTGTTTTTAGTTTCACCGGATTTCTATTGTTTGTAGAAGGTTAAATATAACGGCGTTTA
CTTTAGAAGCGCCACTATTTAGCGGCGTCTGTCATGAAAAATGCCGCTATTCATAACAATAAATG
GTGTTTTTAGTTTCACCGAATTTCTATTGTTTGTAGAAGATTAAATATAGCGGCGTTTACTTTAG
AAGCGCCACTATTTAGCGGCGTCTGTCATGAAAAACGCCGCTATTCATAACAAATAAATGGTGTT
TTTAGTTTCACCGAATTTCTATTGTTTGTAGAAGATTAAATATAGCGGCGTTTACTTTAGAAACG
CCACTATTCAGCGGCGTCTATCATGAAAAACGCCGCTATTCATAACAAATAAATGGTGTTTTTAG
TTTCACCAAATTTCTATTCTTTGTAGAAGATTAAATATAGCGGCGTTTACTT
Found at i:1268 original size:125 final size:125
Alignment explanation
Indices: 1046--1356 Score: 550
Period size: 125 Copynumber: 2.5 Consensus size: 125
1036 GCGTTTACTT
* * * *
1046 TAAATGGTGTTTTTAGTTTCACCGGATTTCTATTGTTTGTAGAAGGTTAAATATAACGGCGTTTA
1 TAAATGGTGTTTTTAGTTTCACCGAATTTCTATTGTTTGTAGAAGATTAAATATAGCGGCGCTTA
* * *
1111 CTTTAGAAGCGCCACTATTTAGCGGCGTCTGTCATGAAAGATGCCGCTATTCATAACAAA
66 CTTTAGAAGCACCACTATTTAGCGGCGTCTGTCATGAAAAACGCCGCTATTCATAACAAA
*
1171 TAAATGGTGTTTTTAGTTTCACCAAATTTCTATTGTTTGTAGAAGATTAAATATAGCGGCGCTTA
1 TAAATGGTGTTTTTAGTTTCACCGAATTTCTATTGTTTGTAGAAGATTAAATATAGCGGCGCTTA
1236 CTTTAGAAGCACCACTATTTAGCGGCGTCTGTCATGAAAAACGCCGCTATTCATAACAAA
66 CTTTAGAAGCACCACTATTTAGCGGCGTCTGTCATGAAAAACGCCGCTATTCATAACAAA
1296 TAAATGGTGTTTTTAGTTTCACCGAATTTCTATTGTTTGTAGAAGATTAAATATAGCGGCG
1 TAAATGGTGTTTTTAGTTTCACCGAATTTCTATTGTTTGTAGAAGATTAAATATAGCGGCG
1357 TTTATTCGGC
Statistics
Matches: 177, Mismatches: 9, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
125 177 1.00
ACGTcount: A:0.29, C:0.15, G:0.20, T:0.36
Consensus pattern (125 bp):
TAAATGGTGTTTTTAGTTTCACCGAATTTCTATTGTTTGTAGAAGATTAAATATAGCGGCGCTTA
CTTTAGAAGCACCACTATTTAGCGGCGTCTGTCATGAAAAACGCCGCTATTCATAACAAA
Found at i:1983 original size:68 final size:68
Alignment explanation
Indices: 1874--2011 Score: 258
Period size: 68 Copynumber: 2.0 Consensus size: 68
1864 TTCATAACAA
*
1874 TAAATGGTGTTTTTAGTTTCACCGGATTTCTATTGTTTGTAGAAGATTAAATATAGCGGCGTTTA
1 TAAATGGTGTTTTTAGTTTCACCGGATTTCAATTGTTTGTAGAAGATTAAATATAGCGGCGTTTA
1939 CTT
66 CTT
*
1942 TAAATGGTGTTTTTAGTTTCACCGGATTTCAATTGTTTGTAGAAGGTTAAATATAGCGGCGTTTA
1 TAAATGGTGTTTTTAGTTTCACCGGATTTCAATTGTTTGTAGAAGATTAAATATAGCGGCGTTTA
2007 CTT
66 CTT
2010 TA
1 TA
2012 GAAGCGCCAC
Statistics
Matches: 68, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
68 68 1.00
ACGTcount: A:0.25, C:0.10, G:0.21, T:0.43
Consensus pattern (68 bp):
TAAATGGTGTTTTTAGTTTCACCGGATTTCAATTGTTTGTAGAAGATTAAATATAGCGGCGTTTA
CTT
Found at i:2249 original size:126 final size:126
Alignment explanation
Indices: 1942--2261 Score: 563
Period size: 126 Copynumber: 2.5 Consensus size: 126
1932 GCGTTTACTT
* *
1942 TAAATGGTGTTTTTAGTTTCACCGGATTTCAATTGTTTGTAGAAGGTTAAATATAGCGGCGTTTA
1 TAAATGGTGTTTTTAGTTTCACCGGATTTCTATTGTTTGTAGAAGATTAAATATAGCGGCGTTTA
*
2007 C-TTTAGAAGCGCCACTATTTAGCGGCGTCTGTCATGAAAGACGCCGCTATTCATAACAAA
66 CTTTTAGAAGCGCCACTATTTAGCGGCGTCTGTCATGAAAAACGCCGCTATTCATAACAAA
** *
2067 TAAATGGTGTTTTTAGTTTCACCAAATTTCTATTGTTTGTAGAAGATTAAATATAGCGGCGCTTA
1 TAAATGGTGTTTTTAGTTTCACCGGATTTCTATTGTTTGTAGAAGATTAAATATAGCGGCGTTTA
2132 CTATTTAGAAGCGCCACTATTTAGCGGCGTCTGTCATGAAAAACGCCGCTATTCATAAC-AA
66 CT-TTTAGAAGCGCCACTATTTAGCGGCGTCTGTCATGAAAAACGCCGCTATTCATAACAAA
2193 TAAATGGTGTTTTTAGTTTCACCGGATTTCTATTGTTTGTAGAAGATTAAATATAGCGGCGTTTA
1 TAAATGGTGTTTTTAGTTTCACCGGATTTCTATTGTTTGTAGAAGATTAAATATAGCGGCGTTTA
2258 CTTT
66 CTTT
2262 AAATGGTGTT
Statistics
Matches: 184, Mismatches: 9, Indels: 4
0.93 0.05 0.02
Matches are distributed among these distances:
125 63 0.34
126 66 0.36
127 55 0.30
ACGTcount: A:0.28, C:0.16, G:0.20, T:0.36
Consensus pattern (126 bp):
TAAATGGTGTTTTTAGTTTCACCGGATTTCTATTGTTTGTAGAAGATTAAATATAGCGGCGTTTA
CTTTTAGAAGCGCCACTATTTAGCGGCGTCTGTCATGAAAAACGCCGCTATTCATAACAAA
Found at i:2302 original size:68 final size:68
Alignment explanation
Indices: 2193--2330 Score: 258
Period size: 68 Copynumber: 2.0 Consensus size: 68
2183 TTCATAACAA
2193 TAAATGGTGTTTTTAGTTTCACCGGATTTCTATTGTTTGTAGAAGATTAAATATAGCGGCGTTTA
1 TAAATGGTGTTTTTAGTTTCACCGGATTTCTATTGTTTGTAGAAGATTAAATATAGCGGCGTTTA
2258 CTT
66 CTT
* *
2261 TAAATGGTGTTTTTAGTTTCACCTGATTTCTATTGTTTGTAGAAGGTTAAATATAGCGGCGTTTA
1 TAAATGGTGTTTTTAGTTTCACCGGATTTCTATTGTTTGTAGAAGATTAAATATAGCGGCGTTTA
2326 CTT
66 CTT
2329 TA
1 TA
2331 GAAGCGCCAC
Statistics
Matches: 68, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
68 68 1.00
ACGTcount: A:0.25, C:0.10, G:0.20, T:0.45
Consensus pattern (68 bp):
TAAATGGTGTTTTTAGTTTCACCGGATTTCTATTGTTTGTAGAAGATTAAATATAGCGGCGTTTA
CTT
Found at i:2325 original size:319 final size:317
Alignment explanation
Indices: 1748--2446 Score: 1353
Period size: 319 Copynumber: 2.2 Consensus size: 317
1738 GATTAATCCC
1748 AATAAATGGTGTTTTTAGTTTCACCAAATTTCTATTGTTTGTAGAAGATTAAATATAGCGGCGCT
1 AATAAATGGTGTTTTTAGTTTCACCAAATTTCTATTGTTTGTAGAAGATTAAATATAGCGGCGCT
1813 TACTTTAGAAGCGCCACTATTTAGCGGCGTCTGTCATGAAAAACGCCGCTATTCATAACAATAAA
66 TACTTTAGAAGCGCCACTATTTAGCGGCGTCTGTCATGAAAAACGCCGCTATTCATAACAATAAA
1878 TGGTGTTTTTAGTTTCACCGGATTTCTATTGTTTGTAGAAGATTAAATATAGCGGCGTTTACTTT
131 TGGTGTTTTTAGTTTCACCGGATTTCTATTGTTTGTAGAAGATTAAATATAGCGGCGTTTACTTT
1943 AAATGGTGTTTTTAGTTTCACCGGATTTCAATTGTTTGTAGAAGGTTAAATATAGCGGCGTTTAC
196 AAATGGTGTTTTTAGTTTCACCGGATTTCAATTGTTTGTAGAAGGTTAAATATAGCGGCGTTTAC
*
2008 TTTAGAAGCGCCACTATTTAGCGGCGTCTGTCATGAAAGACGCCGCTATTCATAACA
261 TTTAGAAGCGCCACTATTTAGCGGCGTCTGTCATGAAAAACGCCGCTATTCATAACA
2065 AATAAATGGTGTTTTTAGTTTCACCAAATTTCTATTGTTTGTAGAAGATTAAATATAGCGGCGCT
1 AATAAATGGTGTTTTTAGTTTCACCAAATTTCTATTGTTTGTAGAAGATTAAATATAGCGGCGCT
2130 TACTATTTAGAAGCGCCACTATTTAGCGGCGTCTGTCATGAAAAACGCCGCTATTCATAACAATA
66 TAC--TTTAGAAGCGCCACTATTTAGCGGCGTCTGTCATGAAAAACGCCGCTATTCATAACAATA
2195 AATGGTGTTTTTAGTTTCACCGGATTTCTATTGTTTGTAGAAGATTAAATATAGCGGCGTTTACT
129 AATGGTGTTTTTAGTTTCACCGGATTTCTATTGTTTGTAGAAGATTAAATATAGCGGCGTTTACT
* *
2260 TTAAATGGTGTTTTTAGTTTCACCTGATTTCTATTGTTTGTAGAAGGTTAAATATAGCGGCGTTT
194 TTAAATGGTGTTTTTAGTTTCACCGGATTTCAATTGTTTGTAGAAGGTTAAATATAGCGGCGTTT
2325 ACTTTAGAAGCGCCACTATTTAGCGGCGTCTGTCATGAAAAACGCCGCTATTCATAACA
259 ACTTTAGAAGCGCCACTATTTAGCGGCGTCTGTCATGAAAAACGCCGCTATTCATAACA
2384 AATAAATGGTGTTTTTAGTTTCACCAAATTTCTATTGTTTGTAGAAGATTAAATATAGCGGCG
1 AATAAATGGTGTTTTTAGTTTCACCAAATTTCTATTGTTTGTAGAAGATTAAATATAGCGGCG
2447 TTTATTCGGC
Statistics
Matches: 377, Mismatches: 3, Indels: 2
0.99 0.01 0.01
Matches are distributed among these distances:
317 68 0.18
319 309 0.82
ACGTcount: A:0.28, C:0.15, G:0.20, T:0.37
Consensus pattern (317 bp):
AATAAATGGTGTTTTTAGTTTCACCAAATTTCTATTGTTTGTAGAAGATTAAATATAGCGGCGCT
TACTTTAGAAGCGCCACTATTTAGCGGCGTCTGTCATGAAAAACGCCGCTATTCATAACAATAAA
TGGTGTTTTTAGTTTCACCGGATTTCTATTGTTTGTAGAAGATTAAATATAGCGGCGTTTACTTT
AAATGGTGTTTTTAGTTTCACCGGATTTCAATTGTTTGTAGAAGGTTAAATATAGCGGCGTTTAC
TTTAGAAGCGCCACTATTTAGCGGCGTCTGTCATGAAAAACGCCGCTATTCATAACA
Found at i:2443 original size:193 final size:193
Alignment explanation
Indices: 2067--2450 Score: 689
Period size: 193 Copynumber: 2.0 Consensus size: 193
2057 TCATAACAAA
2067 TAAATGGTGTTTTTAGTTTCACCAAATTTCTATTGTTTGTAGAAGATTAAATATAGCGGCGCTTA
1 TAAATGGTGTTTTTAGTTTCACCAAATTTCTATTGTTTGTAGAAGATTAAATATAGCGGCGCTTA
2132 CTATTTAGAAGCGCCACTATTTAGCGGCGTCTGTCATGAAAAACGCCGCTATTCATAACAATAAA
66 C-ATTTAGAAGCGCCACTATTTAGCGGCGTCTGTCATGAAAAACGCCGCTATTCATAACAATAAA
**
2197 TGGTGTTTTTAGTTTCACCGGATTTCTATTGTTTGTAGAAGATTAAATATAGCGGCGTTTACTT
130 TGGTGTTTTTAGTTTCACCAAATTTCTATTGTTTGTAGAAGATTAAATATAGCGGCGTTTACTT
** * *
2261 TAAATGGTGTTTTTAGTTTCACCTGATTTCTATTGTTTGTAGAAGGTTAAATATAGCGGCGTTTA
1 TAAATGGTGTTTTTAGTTTCACCAAATTTCTATTGTTTGTAGAAGATTAAATATAGCGGCGCTTA
2326 C-TTTAGAAGCGCCACTATTTAGCGGCGTCTGTCATGAAAAACGCCGCTATTCATAACAAATAAA
66 CATTTAGAAGCGCCACTATTTAGCGGCGTCTGTCATGAAAAACGCCGCTATTCATAAC-AATAAA
2390 TGGTGTTTTTAGTTTCACCAAATTTCTATTGTTTGTAGAAGATTAAATATAGCGGCGTTTA
130 TGGTGTTTTTAGTTTCACCAAATTTCTATTGTTTGTAGAAGATTAAATATAGCGGCGTTTA
2451 TTCGGCGTTT
Statistics
Matches: 183, Mismatches: 6, Indels: 3
0.95 0.03 0.02
Matches are distributed among these distances:
192 56 0.31
193 65 0.36
194 62 0.34
ACGTcount: A:0.28, C:0.15, G:0.19, T:0.38
Consensus pattern (193 bp):
TAAATGGTGTTTTTAGTTTCACCAAATTTCTATTGTTTGTAGAAGATTAAATATAGCGGCGCTTA
CATTTAGAAGCGCCACTATTTAGCGGCGTCTGTCATGAAAAACGCCGCTATTCATAACAATAAAT
GGTGTTTTTAGTTTCACCAAATTTCTATTGTTTGTAGAAGATTAAATATAGCGGCGTTTACTT
Found at i:10267 original size:30 final size:30
Alignment explanation
Indices: 10233--10316 Score: 76
Period size: 30 Copynumber: 3.1 Consensus size: 30
10223 GTTGAACATG
10233 TTTTGGGCCGAAGTTGTCCTGCGCAACAAC
1 TTTTGGGCCGAAGTTGTCCTGCGCAACAAC
** *
10263 TTTTGTCCCGAA---GT--T--G-AACAAG
1 TTTTGGGCCGAAGTTGTCCTGCGCAACAAC
*
10285 TTCTGGGCCGAAGTTGTCCTGCGCAACAAC
1 TTTTGGGCCGAAGTTGTCCTGCGCAACAAC
10315 TT
1 TT
10317 CTCTTTTCGA
Statistics
Matches: 39, Mismatches: 7, Indels: 16
0.63 0.11 0.26
Matches are distributed among these distances:
22 14 0.36
23 1 0.03
25 3 0.08
27 3 0.08
29 1 0.03
30 17 0.44
ACGTcount: A:0.21, C:0.25, G:0.25, T:0.29
Consensus pattern (30 bp):
TTTTGGGCCGAAGTTGTCCTGCGCAACAAC
Found at i:10280 original size:52 final size:52
Alignment explanation
Indices: 10202--10318 Score: 207
Period size: 52 Copynumber: 2.2 Consensus size: 52
10192 TTTTTCTTTC
* *
10202 CGCAACAACTTCTGTCCCGAAGTTGAACATGTTTTGGGCCGAAGTTGTCCTG
1 CGCAACAACTTCTGTCCCGAAGTTGAACAAGTTCTGGGCCGAAGTTGTCCTG
*
10254 CGCAACAACTTTTGTCCCGAAGTTGAACAAGTTCTGGGCCGAAGTTGTCCTG
1 CGCAACAACTTCTGTCCCGAAGTTGAACAAGTTCTGGGCCGAAGTTGTCCTG
10306 CGCAACAACTTCT
1 CGCAACAACTTCT
10319 CTTTTCGACA
Statistics
Matches: 61, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
52 61 1.00
ACGTcount: A:0.23, C:0.26, G:0.23, T:0.27
Consensus pattern (52 bp):
CGCAACAACTTCTGTCCCGAAGTTGAACAAGTTCTGGGCCGAAGTTGTCCTG
Done.