Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01011827.1 Corchorus capsularis cultivar CVL-1 contig11848, 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: 37871
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.34
Found at i:675 original size:302 final size:305
Alignment explanation
Indices: 104--709 Score: 952
Period size: 302 Copynumber: 2.0 Consensus size: 305
94 TTTGACATGA
* *
104 TTTTTGGCGCCGAAACTCCTTGAAATATCTATATTCATCTAATTAAGTCTCAGTCAGATTGGATT
1 TTTTTGGCGCCGAAACTCCTTGAAATATCTATATTCATCTAATGAAGTCTCAGCCAGATTGGATT
* * * * * *
169 GAACGATATGTTTTTATGAGTTTTTGAGTCTTGTTTCGATTTCATTAGAAATTAAATTGGAAAGA
66 GAACAATATGTTTTTATGAGCTTCTGAATCTTGTTTCGATTTAATCAGAAATTAAATTGG-AAGA
*
234 AAAATAGGAAAGACCATTTGTGAAGCATGAAAAACCCATAAATCATTTTGGCATTGAATTATAAA
130 AAAATAGGAAAAACCATTTGTGAAGCATGAAAAACCCATAAATCATTTTGGCATTGAATTATAAA
*
299 TTTTTTATAAGTAATGTGGCCAAAAATCAAGGAAAATTTTTTCCTTTCAATTGTTGAAAAATTTT
195 TTTTTTATAAGTAATGTGGCCAAAAATCAAGGAAAATTTTTTCATTTCAATTGTTGAAAAATTTT
364 AGCCGAAATCGTGTAC-TATCCATCACGGTTTCTGGCTGAAAATGG
260 AGCCGAAATCGTGTACATATCCATCACGGTTTCTGGCTGAAAATGG
* * *
409 TTTTTGGCGCCTAGACTCCTTGCAATATCTATATTCATCTAATGAAGTCTCAGCCAGATTGGATT
1 TTTTTGGCGCCGAAACTCCTTGAAATATCTATATTCATCTAATGAAGTCTCAGCCAGATTGGATT
*
474 TAACAATATGTTTTTATGAGCTTCTGAATCTTGTTTCGATTTAATCAGAAATTAAATTGG-A-AA
66 GAACAATATGTTTTTATGAGCTTCTGAATCTTGTTTCGATTTAATCAGAAATTAAATTGGAAGAA
* * *
537 AAATAGGAAAAACCATTTGTGAAGCATGACAAGCCCTTAAAT-ATTTTTGG-AGTTGAATTATAA
131 AAATAGGAAAAACCATTTGTGAAGCATGAAAAACCCATAAATCA-TTTTGGCA-TTGAATTATAA
* * * *
600 ATTTTTTATGAGTACTGTGGCCAAAAATCAAGGAAAATTTTTTCATTTCAATTTTTGCAAAATTT
194 ATTTTTTATAAGTAATGTGGCCAAAAATCAAGGAAAATTTTTTCATTTCAATTGTTGAAAAATTT
665 TAGCCGAAATCGTGTACGATATCCATCACGGTTTCTGGCTGAAAA
259 TAGCCGAAATCGTGTAC-ATATCCATCACGGTTTCTGGCTGAAAA
710 CGCGTTCCGG
Statistics
Matches: 276, Mismatches: 21, Indels: 9
0.90 0.07 0.03
Matches are distributed among these distances:
301 2 0.01
302 134 0.49
303 1 0.00
304 26 0.09
305 113 0.41
ACGTcount: A:0.33, C:0.14, G:0.17, T:0.36
Consensus pattern (305 bp):
TTTTTGGCGCCGAAACTCCTTGAAATATCTATATTCATCTAATGAAGTCTCAGCCAGATTGGATT
GAACAATATGTTTTTATGAGCTTCTGAATCTTGTTTCGATTTAATCAGAAATTAAATTGGAAGAA
AAATAGGAAAAACCATTTGTGAAGCATGAAAAACCCATAAATCATTTTGGCATTGAATTATAAAT
TTTTTATAAGTAATGTGGCCAAAAATCAAGGAAAATTTTTTCATTTCAATTGTTGAAAAATTTTA
GCCGAAATCGTGTACATATCCATCACGGTTTCTGGCTGAAAATGG
Found at i:1321 original size:333 final size:333
Alignment explanation
Indices: 409--2296 Score: 2873
Period size: 333 Copynumber: 5.7 Consensus size: 333
399 CTGAAAATGG
* * * *
409 TTTTTGGCGCCTAGACTCCTTGCAATATCTATATTCATCTAATGAAGTCTCAGCCAGATTGGATT
1 TTTTTGGCGCCGAGACTCCTTGTAATATCTATATTCATCTAATCAAGTCTCAGCCACATTGGATT
* *
474 TAACAATATGTTTTTATGAGCTTCTGAATCTTGTTTCGATTTAATCAGAAATTAAATTGG-AAAA
66 TAACGATATGTTTTTACGAGCTTCTGAATCTTGTTTCGATTTAATCAGAAATTAAATTGGAAAAA
* *
538 AATAGGAAAAACCATTTGTGAAGCATGACAAGCCCTTAAATATTTTTGGAGTTGAATTATAAATT
131 AATAGGAAAAACCATTTGTGAAGCATGAAAAGCCCTTAAATCTTTTTGGAGTTGAATTATAAATT
* * *
603 TTTTATGAGTACTGTGGCCAAAAA-TCAAGGAAAATTTTTTCATTTCAATTTTTGCAAAATTTTA
196 CTTTATGAGCACTGTGGCCAAAAATTCAAGGAAAA-TTTTTCCTTTCAATTTTTGCAAAATTTTA
* *
667 GCCGAAATCGTGTACGATATCCATCACGGTTTCTGGCTGAAAACGCGTTCCGGGGCTCCAGCTCA
260 GCCGAAATCGTGTAC--TATCCATCACGGTTTCTGGCTGAAAACGCGTTCCGGAGCTCCGGCTCA
732 GTTTTGCATGA
323 GTTTTGCATGA
* * *
743 TTTTTGGCCGCAGAGACTCCTTGTAGTATCTGTATTCATCTAATCAAGTCTCAGCCACATTGGAT
1 TTTTTGG-CGCCGAGACTCCTTGTAATATCTATATTCATCTAATCAAGTCTCAGCCACATTGGAT
* *
808 TTAAGGATATGTTTTTACGAGC-TCATGAATCTTGTTTCGATTTAATGAGAAATTAAATTGGAAA
65 TTAACGATATGTTTTTACGAGCTTC-TGAATCTTGTTTCGATTTAATCAGAAATTAAATTGGAAA
872 AAAATAGGAAAAACCATTTGTGAAGCATGAAAAGCCCTTAAATCTTTTTGGAGTTGAATTATAAA
129 AAAATAGGAAAAACCATTTGTGAAGCATGAAAAGCCCTTAAATCTTTTTGGAGTTGAATTATAAA
* * * * **
937 TTCTTTATGAGCATTGTGGCCAAAAATTGATGAAAAATTTTTCGGTTCAATTTTTGCAAAATTTT
194 TTCTTTATGAGCACTGTGGCCAAAAATTCAAGGAAAATTTTTCCTTTCAATTTTTGCAAAATTTT
* * * * *
1002 AGCCGAAAACGTGTACTAACCATCACGGTTTCTGGCTGTAAACGCGTTCCGGGGCCCCGGCTCAG
259 AGCCGAAATCGTGTACTATCCATCACGGTTTCTGGCTGAAAACGCGTTCCGGAGCTCCGGCTCAG
*
1067 TTTGGCATGA
324 TTTTGCATGA
* * * * *
1077 ATTTTGGCGCCGAGACTCCTTGAAATATCTATATTCATCTAATTATGTCTCAGCCAGATTGGATT
1 TTTTTGGCGCCGAGACTCCTTGTAATATCTATATTCATCTAATCAAGTCTCAGCCACATTGGATT
* * *
1142 TAACGATATGTTTTTATGAGCTTCTGAATCTTGTTTTGATTTAATCAGAAATTAAAATGG-AAAA
66 TAACGATATGTTTTTACGAGCTTCTGAATCTTGTTTCGATTTAATCAGAAATTAAATTGGAAAAA
*
1206 AATAGGAAAAACCATTTGTGAAGCATGACAAGCCCTTAAATCTTTTTGGAGTTGAATTATAAATT
131 AATAGGAAAAACCATTTGTGAAGCATGAAAAGCCCTTAAATCTTTTTGGAGTTGAATTATAAATT
* * *
1271 CTTTATGAGTATTGTGGCCAAAAATTCAAGGAAAATTTTCTCCTTTCAATTTTTGCAAAATATTA
196 CTTTATGAGCACTGTGGCCAAAAATTCAAGGAAAATTTT-TCCTTTCAATTTTTGCAAAATTTTA
*
1336 GCCGAAATCGTGTACTATCCATCACGGTTTCTGGCTGAAAACGCGTTCCGTAGCTCCGGCTCAGT
260 GCCGAAATCGTGTACTATCCATCACGGTTTCTGGCTGAAAACGCGTTCCGGAGCTCCGGCTCAGT
1401 TTTGCATGA
325 TTTGCATGA
* * *
1410 TTCTTTGCCGCCGAGACTCCTTGTAATGTCTATATTCATTTAATCAAGTCTCAGCCACATTGGAT
1 TT-TTTGGCGCCGAGACTCCTTGTAATATCTATATTCATCTAATCAAGTCTCAGCCACATTGGAT
* *
1475 TTAAGGATATGTTTTTACGAGCTTCTGAATCTTGTTTCGATTTAATGAGAAATTAAATTGGAAAA
65 TTAACGATATGTTTTTACGAGCTTCTGAATCTTGTTTCGATTTAATCAGAAATTAAATTGGAAAA
* * *
1540 AAATAGGAAAAACCATTTGTGAATCATGAAAAGCCCTTAAATCTTTTTGGTGTTGAATTACAAAC
130 AAATAGGAAAAACCATTTGTGAAGCATGAAAAGCCCTTAAATCTTTTTGGAGTTGAATTATAAA-
* * * *
1605 TT-TTTATGAGCACTGTGGCCAAACATT-GAGGAAAAATTTTTCGTTTCAATTTTTGTAAAATTT
194 TTCTTTATGAGCACTGTGGCCAAAAATTCAAGG-AAAATTTTTCCTTTCAATTTTTGCAAAATTT
* *
1668 TAGCCGAAAAT-GTGTACTAACCATCACGGTTTCTGGCTGAAAACGCGTTTCGGAGC-CCTGGCT
258 TAGCCG-AAATCGTGTACTATCCATCACGGTTTCTGGCTGAAAACGCGTTCCGGAGCTCC-GGCT
*
1731 CAGTTTGGCATGA
321 CAGTTTTGCATGA
* * *
1744 TTTTTGGCGCCGAGACTCCTTGAAATATCTATATTCAACTAATCAAGTCTCAGCCAGATTGGATT
1 TTTTTGGCGCCGAGACTCCTTGTAATATCTATATTCATCTAATCAAGTCTCAGCCACATTGGATT
* * * *
1809 TAACGATATGCTTTTATGAGCTTCTGAATCTTGTTTTGATTTAATCAGAAATTAAAATGG-AAAA
66 TAACGATATGTTTTTACGAGCTTCTGAATCTTGTTTCGATTTAATCAGAAATTAAATTGGAAAAA
* *
1873 AATAGGAAAAACCATTTGTGAAGCATGACAAGCCCTTAAATCTTTTTCGCA-TTGAATTATAAAT
131 AATAGGAAAAACCATTTGTGAAGCATGAAAAGCCCTTAAATCTTTTT-GGAGTTGAATTATAAAT
* *
1937 TTTTTATGAGTACTGTGGCCAAAAA-TCAAGGAAAATTTTTCCTTTCAATTTTTGCAAAATTTTA
195 TCTTTATGAGCACTGTGGCCAAAAATTCAAGGAAAATTTTTCCTTTCAATTTTTGCAAAATTTTA
2001 GCCGAAATCGTGTACTATCCATCACGGTTTCTGGCTGAAAACGCGTTCCGGAGCTCCGGCTCAGT
260 GCCGAAATCGTGTACTATCCATCACGGTTTCTGGCTGAAAACGCGTTCCGGAGCTCCGGCTCAGT
2066 TTTGCATGA
325 TTTGCATGA
* *
2075 TTTTTTGCCGCCGAGACTCCTTGTAATATCTATATTCATTTAATCAAGTCTCAGCCACATTGGAT
1 -TTTTTGGCGCCGAGACTCCTTGTAATATCTATATTCATCTAATCAAGTCTCAGCCACATTGGAT
* *
2140 TTAAGGATATGTTTTTACGAGC-TCATGAATCTTGTTTCGATTTAATGAGAAATTAAATTGGAAA
65 TTAACGATATGTTTTTACGAGCTTC-TGAATCTTGTTTCGATTTAATCAGAAATTAAATTGGAAA
2204 AAAATAGGAAAAACCATTTGTGAAGCATGAAAAGCCCTTAAATCTTTTTGGAGTTGAATTATAAA
129 AAAATAGGAAAAACCATTTGTGAAGCATGAAAAGCCCTTAAATCTTTTTGGAGTTGAATTATAAA
* * * *
2269 TTCATTATGAACATTGTGGCGAAAAATT
194 TTCTTTATGAGCACTGTGGCCAAAAATT
2297 GATTAGCCGA
Statistics
Matches: 1405, Mismatches: 127, Indels: 44
0.89 0.08 0.03
Matches are distributed among these distances:
330 4 0.00
331 99 0.07
332 302 0.21
333 389 0.28
334 272 0.19
335 201 0.14
336 131 0.09
337 7 0.00
ACGTcount: A:0.31, C:0.16, G:0.18, T:0.35
Consensus pattern (333 bp):
TTTTTGGCGCCGAGACTCCTTGTAATATCTATATTCATCTAATCAAGTCTCAGCCACATTGGATT
TAACGATATGTTTTTACGAGCTTCTGAATCTTGTTTCGATTTAATCAGAAATTAAATTGGAAAAA
AATAGGAAAAACCATTTGTGAAGCATGAAAAGCCCTTAAATCTTTTTGGAGTTGAATTATAAATT
CTTTATGAGCACTGTGGCCAAAAATTCAAGGAAAATTTTTCCTTTCAATTTTTGCAAAATTTTAG
CCGAAATCGTGTACTATCCATCACGGTTTCTGGCTGAAAACGCGTTCCGGAGCTCCGGCTCAGTT
TTGCATGA
Found at i:1685 original size:667 final size:664
Alignment explanation
Indices: 410--4120 Score: 4767
Period size: 667 Copynumber: 5.6 Consensus size: 664
400 TGAAAATGGT
* * *
410 TTTTGGCGCCTAGACTCCTTGCAATATCTATATTCATCTAATGAAGTCTCAGCCAGATTGGATTT
1 TTTTGGCGCCGAGACTCCTTGAAATATCTATATTCATCTAATCAAGTCTCAGCCAGATTGGATTT
* * *
475 AACAATATGTTTTTATGAGCTTCTGAATCTTGTTTCGATTTAATCAGAAATTAAATTGGAAAAAA
66 AACGATATGTTTTTATGAGCTTCTGAATCTTGTTTTGATTTAATCAGAAATTAAAATGGAAAAAA
*
540 TAGGAAAAACCATTTGTGAAGCATGACAAGCCCTTAAATATTTTTGGAGTTGAATTATAAATTTT
131 TAGGAAAAACCATTTGTGAAGCATGACAAGCCCTTAAATCTTTTTGGAGTTGAATTATAAATTTT
*
605 TTATGAGTACTGTGGCCAAAAATCAAGGAAAATTTTTTCATTTCAATTTTTGCAAAATTTTAGCC
196 TTATGAGTACTGTGGCCAAAAATCAAGGAAAA-TTTTTCCTTTCAATTTTTGCAAAATTTTAGCC
* *
670 GAAATCGTGTACGATATCCATCACGGTTTCTGGCTGAAAACGCGTTCCGGGGCTCCAGCTCAGTT
260 GAAATCGTGTAC--TATCCATCACGGTTTCTGGCTGAAAACGCGTTCCGGAGCTCCGGCTCAGTT
* * * *
735 TTGCATGATTTTTGGCCGCAGAGACTCCTTGTAGTATCTGTATTCATCTAATCAAGTCTCAGCCA
323 TTGCATGATTTTT-GCCGCCGAGACTCCTTGTAATATCTATATTCATTTAATCAAGTCTCAGCCA
800 CATTGGATTTAAGGATATGTTTTTACGAGCTCATGAATCTTGTTTCGATTTAATGAGAAATTAAA
387 CATTGGATTTAAGGATATGTTTTTACGAGCTCATGAATCTTGTTTCGATTTAATGAGAAATTAAA
865 TTGGAAAAAAATAGGAAAAACCATTTGTGAAGCATGAAAAGCCCTTAAATCTTTTTGGAGTTGAA
452 TTGGAAAAAAATAGGAAAAACCATTTGTGAAGCATGAAAAGCCCTTAAATCTTTTTGGAGTTGAA
* * *
930 TTATAAATTCTTTATGAGCATTGTGGCCAAAAATTGATGAAAAATTTTTCGGTTCAATTTTTGCA
517 TTACAAATTCTTTATGAGCACTGTGGCCAAAAATTGAGGAAAAATTTTTCGGTTCAATTTTTGCA
* *
995 AAATTTTAGCCGAAAACGTGTACTAACCATCACGGTTTCTGGCTGTAAACGCGTTCCGGGGCCCC
582 AAATTTTAGCCGAAAACGTGTACTAACCATCACGGTTTCTGGCTGAAAACGCGTTCCGGAGCCCC
1060 GGCTCAGTTTGGCATGAA
647 GGCTCAGTTTGGCATGAA
* *
1078 TTTTGGCGCCGAGACTCCTTGAAATATCTATATTCATCTAATTATGTCTCAGCCAGATTGGATTT
1 TTTTGGCGCCGAGACTCCTTGAAATATCTATATTCATCTAATCAAGTCTCAGCCAGATTGGATTT
1143 AACGATATGTTTTTATGAGCTTCTGAATCTTGTTTTGATTTAATCAGAAATTAAAATGGAAAAAA
66 AACGATATGTTTTTATGAGCTTCTGAATCTTGTTTTGATTTAATCAGAAATTAAAATGGAAAAAA
*
1208 TAGGAAAAACCATTTGTGAAGCATGACAAGCCCTTAAATCTTTTTGGAGTTGAATTATAAATTCT
131 TAGGAAAAACCATTTGTGAAGCATGACAAGCCCTTAAATCTTTTTGGAGTTGAATTATAAATTTT
* *
1273 TTATGAGTATTGTGGCCAAAAATTCAAGGAAAATTTTCTCCTTTCAATTTTTGCAAAATATTAGC
196 TTATGAGTACTGTGGCCAAAAA-TCAAGGAAAATTTT-TCCTTTCAATTTTTGCAAAATTTTAGC
*
1338 CGAAATCGTGTACTATCCATCACGGTTTCTGGCTGAAAACGCGTTCCGTAGCTCCGGCTCAGTTT
259 CGAAATCGTGTACTATCCATCACGGTTTCTGGCTGAAAACGCGTTCCGGAGCTCCGGCTCAGTTT
*
1403 TGCATGATTCTTTGCCGCCGAGACTCCTTGTAATGTCTATATTCATTTAATCAAGTCTCAGCCAC
324 TGCATGATT-TTTGCCGCCGAGACTCCTTGTAATATCTATATTCATTTAATCAAGTCTCAGCCAC
1468 ATTGGATTTAAGGATATGTTTTTACGAGCTTC-TGAATCTTGTTTCGATTTAATGAGAAATTAAA
388 ATTGGATTTAAGGATATGTTTTTACGAGC-TCATGAATCTTGTTTCGATTTAATGAGAAATTAAA
* *
1532 TTGGAAAAAAATAGGAAAAACCATTTGTGAATCATGAAAAGCCCTTAAATCTTTTTGGTGTTGAA
452 TTGGAAAAAAATAGGAAAAACCATTTGTGAAGCATGAAAAGCCCTTAAATCTTTTTGGAGTTGAA
* * *
1597 TTACAAACTT-TTTATGAGCACTGTGGCCAAACATTGAGGAAAAATTTTTCGTTTCAATTTTTGT
517 TTACAAA-TTCTTTATGAGCACTGTGGCCAAAAATTGAGGAAAAATTTTTCGGTTCAATTTTTGC
* *
1661 AAAATTTTAGCCGAAAATGTGTACTAACCATCACGGTTTCTGGCTGAAAACGCGTTTCGGAGCCC
581 AAAATTTTAGCCGAAAACGTGTACTAACCATCACGGTTTCTGGCTGAAAACGCGTTCCGGAGCCC
* *
1726 TGGCTCAGTTTGGCATGAT
646 CGGCTCAGTTTGGCATGAA
*
1745 TTTTGGCGCCGAGACTCCTTGAAATATCTATATTCAACTAATCAAGTCTCAGCCAGATTGGATTT
1 TTTTGGCGCCGAGACTCCTTGAAATATCTATATTCATCTAATCAAGTCTCAGCCAGATTGGATTT
*
1810 AACGATATGCTTTTATGAGCTTCTGAATCTTGTTTTGATTTAATCAGAAATTAAAATGGAAAAAA
66 AACGATATGTTTTTATGAGCTTCTGAATCTTGTTTTGATTTAATCAGAAATTAAAATGGAAAAAA
*
1875 TAGGAAAAACCATTTGTGAAGCATGACAAGCCCTTAAATCTTTTTCGCA-TTGAATTATAAATTT
131 TAGGAAAAACCATTTGTGAAGCATGACAAGCCCTTAAATCTTTTT-GGAGTTGAATTATAAATTT
1939 TTTATGAGTACTGTGGCCAAAAATCAAGGAAAATTTTTCCTTTCAATTTTTGCAAAATTTTAGCC
195 TTTATGAGTACTGTGGCCAAAAATCAAGGAAAATTTTTCCTTTCAATTTTTGCAAAATTTTAGCC
2004 GAAATCGTGTACTATCCATCACGGTTTCTGGCTGAAAACGCGTTCCGGAGCTCCGGCTCAGTTTT
260 GAAATCGTGTACTATCCATCACGGTTTCTGGCTGAAAACGCGTTCCGGAGCTCCGGCTCAGTTTT
2069 GCATGATTTTTTGCCGCCGAGACTCCTTGTAATATCTATATTCATTTAATCAAGTCTCAGCCACA
325 GCATGA-TTTTTGCCGCCGAGACTCCTTGTAATATCTATATTCATTTAATCAAGTCTCAGCCACA
2134 TTGGATTTAAGGATATGTTTTTACGAGCTCATGAATCTTGTTTCGATTTAATGAGAAATTAAATT
389 TTGGATTTAAGGATATGTTTTTACGAGCTCATGAATCTTGTTTCGATTTAATGAGAAATTAAATT
2199 GGAAAAAAATAGGAAAAACCATTTGTGAAGCATGAAAAGCCCTTAAATCTTTTTGGAGTTGAATT
454 GGAAAAAAATAGGAAAAACCATTTGTGAAGCATGAAAAGCCCTTAAATCTTTTTGGAGTTGAATT
* * * * * ** * * ***
2264 ATAAATTCATTATGAACATTGTGGCGAAAAATTGATTAGCCGAAAACGTGTAC---T-AA-CCAT
519 ACAAATTCTTTATGAGCACTGTGGCCAAAAATTG---AG--GAAAAATTTTTCGGTTCAATTTTT
*** * * * * *
2324 -C-ACGGTTT--CTG-----GT-T-GTAA--A-CGC-G-TTCCGG--G-----GC---CCCG-G-
579 GCAAAATTTTAGCCGAAAACGTGTACTAACCATCACGGTTTCTGGCTGAAAACGCGTTCCGGAGC
* * * ** ** *
2361 CTCAGTTTGGCAT-GAAT---
644 CCCGGCTCAGTTTGGCATGAA
* *
2378 -TTTGGCGCCGAGACTCCTTGAAATATCTATATTCATCTAATTATGTCTCAGCCAGATTGGATTT
1 TTTTGGCGCCGAGACTCCTTGAAATATCTATATTCATCTAATCAAGTCTCAGCCAGATTGGATTT
* * *
2442 AACGATATGTTTTTATGAGCTTCTGAATCTTATTTTGATTTAATTAAAAATTAAAATGGAAAAAA
66 AACGATATGTTTTTATGAGCTTCTGAATCTTGTTTTGATTTAATCAGAAATTAAAATGGAAAAAA
* * *
2507 TAGGAAAAACCATTTGTGAAGCATGACAATCCCTTAAATATTTTTGGCGTTGAATTATAAATTTT
131 TAGGAAAAACCATTTGTGAAGCATGACAAGCCCTTAAATCTTTTTGGAGTTGAATTATAAATTTT
* ** *
2572 TTATGAGTACTGTGGCCAAGAATCAAGGAAAAATTTTTTATTTCAATTTTTGCAAAATTTTTGCC
196 TTATGAGTACTGTGGCCAAAAATCAAGG-AAAATTTTTCCTTTCAATTTTTGCAAAATTTTAGCC
* * * *
2637 GAAATCGCGTACGAAATCCATCACGGTTTCTGGCGGAAAACGCGTTCC-GAGTCTCCAGCTCAGT
260 GAAATCGTGTAC--TATCCATCACGGTTTCTGGCTGAAAACGCGTTCCGGAG-CTCCGGCTCAGT
* * * * * * *
2701 TTGGCATGAATTTTGGCGCCGAGACTCCTTGAAATATCTATATTCATCTAATTATGTCTCAGCCA
322 TTTGCATGATTTTTGCCGCCGAGACTCCTTGTAATATCTATATTCATTTAATCAAGTCTCAGCCA
* * * * *
2766 GATTGGATTTAACGATATGTTTTTATGAGCTTC-TGAATCTTGTTTTGATTTAATCAGAAATTAA
387 CATTGGATTTAAGGATATGTTTTTACGAGC-TCATGAATCTTGTTTCGATTTAATGAGAAATTAA
* * * *
2830 AATGG-AAAAAATAGGAAAAACCATATGTGAAGCATGACAAGCCCTTAAATCTTTTTGGCGTTGA
451 ATTGGAAAAAAATAGGAAAAACCATTTGTGAAGCATGAAAAGCCCTTAAATCTTTTTGGAGTTGA
* * * ** * **
2894 ATTATAAATTTTTTATGAGTACTGTGGCCAAAAATCAAGGAAAATTTTTTCCTTTCAATTTTTGC
516 ATTACAAATTCTTTATGAGCACTGTGGCCAAAAATTGAGGAAAAATTTTTCGGTTCAATTTTTGC
* * * *
2959 AAAATTTTAGCCGAAATCGTGTACGATATCCATCACGATTTCTGGCTGAAAACGCGTTCCGGGGC
581 AAAATTTTAGCCGAAAACGTGTAC--TAACCATCACGGTTTCTGGCTGAAAACGCGTTCCGGAGC
* * * *
3024 TCCAGCTCAGTTTTGCATGAT
644 CCCGGCTCAGTTTGGCATGAA
* * * * * * * *
3045 TTTTGACGCAGAGACTCCTTGTAGTATCTGTATTTATCTAATCAAGTCTCAGCTACATTGGATTT
1 TTTTGGCGCCGAGACTCCTTGAAATATCTATATTCATCTAATCAAGTCTCAGCCAGATTGGATTT
* * * * *
3110 AAGGATATGTTTTTACGAGCTTCTGAATCTTGTTTCGATTTAATGAGAAATTAAATTGGAAAACA
66 AACGATATGTTTTTATGAGCTTCTGAATCTTGTTTTGATTTAATCAGAAATTAAAATGGAAAA-A
* *
3175 ATAGGAAAAACCATTTGTGAAGCATGAAAAGCCCTTAAATCTTTTTGGAGTTGAATTATAAATTC
130 ATAGGAAAAACCATTTGTGAAGCATGACAAGCCCTTAAATCTTTTTGGAGTTGAATTATAAATTT
* * * ** * ** *
3240 TTTATGAGCATTGTGGCCAAGAATTGATGAAAATTTTTCGGTTCAATTCTTGCAAAATTTTAGCC
195 TTTATGAGTACTGTGGCCAAAAATCAAGGAAAATTTTTCCTTTCAATTTTTGCAAAATTTTAGCC
* * * * * * * *
3305 GAAAACGTGTACTAACCAACACGGTTTCTGGCTGTAAACGCGTTTCGGGGCCCCGGCTCAGTTTG
260 GAAATCGTGTACTATCCATCACGGTTTCTGGCTGAAAACGCGTTCCGGAGCTCCGGCTCAGTTTT
* * * * * * * * *
3370 GCATGAATTTTGGCGCCAAGACTCCTTGAAATATCTATATTAATCTAATTATGTCTCAGCCAGAT
325 GCATGATTTTTGCCGCCGAGACTCCTTGTAATATCTATATTCATTTAATCAAGTCTCAGCCACAT
* * * * *
3435 TGGATTTAACGATAATTTTTTTATGAGCTTC-TGAATCTTGTTTTGATTTTAATCAGAAATTAAA
390 TGGATTTAAGGAT-ATGTTTTTACGAGC-TCATGAATCTTGTTTCGA-TTTAATGAGAAATTAAA
* * * * *
3499 ATGG-AAAAAATAGGAAAAACCATTTGTGAAGCATTACAAGCCCTTAAATATTTTTGGCGTTGAA
452 TTGGAAAAAAATAGGAAAAACCATTTGTGAAGCATGAAAAGCCCTTAAATCTTTTTGGAGTTGAA
** * * * * *
3563 TTTTAAATTTTTTATGAGTACTGTGGCCAAAAATTAAGGAAAATTTTTTC-CTCTCAATTTTTGC
517 TTACAAATTCTTTATGAGCACTGTGGCCAAAAATTGAGGAAAAATTTTTCGGT-TCAATTTTTGC
* * * * * *
3627 AAAATTTTAGCCGAAATCGAGTACTATCCATCACTGTTTCTGGCTGAAAACGCGTTCCGTAGCTC
581 AAAATTTTAGCCGAAAACGTGTACTAACCATCACGGTTTCTGGCTGAAAACGCGTTCCGGAGCCC
*
3692 CGGCTCAGTTTTGCATG-A
646 CGGCTCAGTTTGGCATGAA
* * *
3710 TTTTCGGCTGCCGAGACTCCTTGTAATATCTATATTCATTTAATCAAGTCTCAGCCACATTGGAT
1 TTTT-GGC-GCCGAGACTCCTTGAAATATCTATATTCATCTAATCAAGTCTCAGCCAGATTGGAT
* * * * * *
3775 TAAAGGATATGTTTTTACGAGC-TCATGAATCTTGTTTCGATTTAATGAGAAATTAAATTGGAAA
64 TTAACGATATGTTTTTATGAGCTTC-TGAATCTTGTTTTGATTTAATCAGAAATTAAAATGG-AA
* * * * * *
3839 AAAATACGAAAAACAATTTGTGAAGCATAAAAAGCCCTTAAATCTTTTCGGCGTTGAATTATAAA
127 AAAATAGGAAAAACCATTTGTGAAGCATGACAAGCCCTTAAATCTTTTTGGAGTTGAATTATAAA
* * * * ** ***
3904 -ATTATATGAGTAATGTGTCCAAAAATTGAGGAAAAATTTTTCAGCT-AAGTTTTTGCAAAATTT
192 TTTTTTATGAGTACTGTGGCCAAAAATCAAGG-AAAATTTTTCCTTTCAA-TTTTTGCAAAATTT
* * * * * * * * * *
3967 TAGCTGAACTCATCTACTAACCATCACGGTTTCTAGCTGAAAACGCGTT-CGGGGCCCCTGCTTA
255 TAGCCGAAATCGTGTACTATCCATCACGGTTTCTGGCTGAAAACGCGTTCCGGAGCTCCGGCTCA
* * * * **
4031 GTTTAGCAT-ATTTTTGGCGCCGAGACTCCTTGCAATATCTATATTCATCTAATCAAGTCTCAAT
320 GTTTTGCATGATTTTTGCCGCCGAGACTCCTTGTAATATCTATATTCATTTAATCAAGTCTCAGC
4095 CACATTGGATTTAAGGATAT-TTTTTA
385 CACATTGGATTTAAGGATATGTTTTTA
4121 TTTTTGTAAA
Statistics
Matches: 2722, Mismatches: 250, Indels: 147
0.87 0.08 0.05
Matches are distributed among these distances:
628 8 0.00
630 2 0.00
631 2 0.00
632 210 0.08
633 130 0.05
634 114 0.04
635 57 0.02
636 3 0.00
637 7 0.00
638 1 0.00
639 2 0.00
642 4 0.00
643 1 0.00
646 2 0.00
647 1 0.00
648 1 0.00
649 7 0.00
650 1 0.00
651 7 0.00
652 1 0.00
653 1 0.00
654 3 0.00
655 1 0.00
656 2 0.00
658 2 0.00
661 5 0.00
662 1 0.00
663 16 0.01
664 9 0.00
665 370 0.14
666 238 0.09
667 835 0.31
668 537 0.20
669 133 0.05
670 8 0.00
ACGTcount: A:0.31, C:0.16, G:0.18, T:0.35
Consensus pattern (664 bp):
TTTTGGCGCCGAGACTCCTTGAAATATCTATATTCATCTAATCAAGTCTCAGCCAGATTGGATTT
AACGATATGTTTTTATGAGCTTCTGAATCTTGTTTTGATTTAATCAGAAATTAAAATGGAAAAAA
TAGGAAAAACCATTTGTGAAGCATGACAAGCCCTTAAATCTTTTTGGAGTTGAATTATAAATTTT
TTATGAGTACTGTGGCCAAAAATCAAGGAAAATTTTTCCTTTCAATTTTTGCAAAATTTTAGCCG
AAATCGTGTACTATCCATCACGGTTTCTGGCTGAAAACGCGTTCCGGAGCTCCGGCTCAGTTTTG
CATGATTTTTGCCGCCGAGACTCCTTGTAATATCTATATTCATTTAATCAAGTCTCAGCCACATT
GGATTTAAGGATATGTTTTTACGAGCTCATGAATCTTGTTTCGATTTAATGAGAAATTAAATTGG
AAAAAAATAGGAAAAACCATTTGTGAAGCATGAAAAGCCCTTAAATCTTTTTGGAGTTGAATTAC
AAATTCTTTATGAGCACTGTGGCCAAAAATTGAGGAAAAATTTTTCGGTTCAATTTTTGCAAAAT
TTTAGCCGAAAACGTGTACTAACCATCACGGTTTCTGGCTGAAAACGCGTTCCGGAGCCCCGGCT
CAGTTTGGCATGAA
Found at i:2932 original size:334 final size:332
Alignment explanation
Indices: 2299--4121 Score: 2383
Period size: 334 Copynumber: 5.5 Consensus size: 332
2289 GAAAAATTGA
* * * * *
2299 TTAGCCGAAAACGTGTACTAA-CCATCACGGTTTCTGGTTGTAAACGCGTTCCGGGGCCCCGGCT
1 TTAGCCGAAATCGCGTACAAATCCATCACGGTTTCTGGCTGAAAACGCGTTCCGGGGCCCCGGCT
* *
2363 CAGTTTGGCATGAATTTTGGCGCCGAGACTCCTTGAAATATCTATATTCATCTAATTATGTCTCA
66 CAGTTTGGCATGAATTTTGGCGCCGAGACTCCTTGAAATATCTATATTCATCTAATCAAGTCTCA
* * * *
2428 GCCAGATTGGATTTAACGATATGTTTTTATGAGCTTCTGAATCTTATTTTGATTTAATTAAAAAT
131 GCCACATTGGATTTAACGATATGTTTTTATGAGCTTCTGAATCTTGTTTTGATTTAATCAGAAAT
* *
2493 TAAAATGGAAAAAATAGGAAAAACCATTTGTGAAGCATGACAATCCCTTAAATATTTTTGGCGTT
196 TAAAATGGAAAAAATAGGAAAAACCATTTGTGAAGCATGACAAGCCCTTAAATCTTTTTGGCGTT
* *
2558 GAATTATAAATTTTTTATGAGTACTGTGGCCAAGAATCAAGGAAAAATTTTTTATTTCAATTTTT
261 GAATTATAAATTTTTTATGAGTACTGTGGCCAAAAATTAAGG-AAAATTTTTTATTTCAATTTTT
2623 GCAAAATT
325 GCAAAATT
* * * * * *
2631 TTTGCCGAAATCGCGTACGAAATCCATCACGGTTTCTGGCGGAAAACGCGTTCCGAGTCTCCAGC
1 TTAGCCGAAATCGCGTAC-AAATCCATCACGGTTTCTGGCTGAAAACGCGTTCCGGGGCCCCGGC
* *
2696 TCAGTTTGGCATGAATTTTGGCGCCGAGACTCCTTGAAATATCTATATTCATCTAATTATGTCTC
65 TCAGTTTGGCATGAATTTTGGCGCCGAGACTCCTTGAAATATCTATATTCATCTAATCAAGTCTC
*
2761 AGCCAGATTGGATTTAACGATATGTTTTTATGAGCTTCTGAATCTTGTTTTGATTTAATCAGAAA
130 AGCCACATTGGATTTAACGATATGTTTTTATGAGCTTCTGAATCTTGTTTTGATTTAATCAGAAA
*
2826 TTAAAATGGAAAAAATAGGAAAAACCATATGTGAAGCATGACAAGCCCTTAAATCTTTTTGGCGT
195 TTAAAATGGAAAAAATAGGAAAAACCATTTGTGAAGCATGACAAGCCCTTAAATCTTTTTGGCGT
* *
2891 TGAATTATAAATTTTTTATGAGTACTGTGGCCAAAAATCAAGGAAAATTTTTTCCTTTCAATTTT
260 TGAATTATAAATTTTTTATGAGTACTGTGGCCAAAAATTAAGGAAAATTTTTT-ATTTCAATTTT
2956 TGCAAAATT
324 TGCAAAATT
* * * * *
2965 TTAGCCGAAATCGTGTACGATATCCATCACGATTTCTGGCTGAAAACGCGTTCCGGGGCTCCAGC
1 TTAGCCGAAATCGCGTAC-AAATCCATCACGGTTTCTGGCTGAAAACGCGTTCCGGGGCCCCGGC
* * * * * * * *
3030 TCAGTTTTGCATGATTTTTGACGCAGAGACTCCTTGTAGTATCTGTATTTATCTAATCAAGTCTC
65 TCAGTTTGGCATGAATTTTGGCGCCGAGACTCCTTGAAATATCTATATTCATCTAATCAAGTCTC
* * * * *
3095 AGCTACATTGGATTTAAGGATATGTTTTTACGAGCTTCTGAATCTTGTTTCGATTTAATGAGAAA
130 AGCCACATTGGATTTAACGATATGTTTTTATGAGCTTCTGAATCTTGTTTTGATTTAATCAGAAA
* * *
3160 TTAAATTGGAAAACAATAGGAAAAACCATTTGTGAAGCATGAAAAGCCCTTAAATCTTTTTGGAG
195 TTAAAATGGAAAA-AATAGGAAAAACCATTTGTGAAGCATGACAAGCCCTTAAATCTTTTTGGCG
* * * * * * *** *
3225 TTGAATTATAAATTCTTTATGAGCATTGTGGCCAAGAATTGATGAAAATTTTTCGGTTCAATTCT
259 TTGAATTATAAATTTTTTATGAGTACTGTGGCCAAAAATTAAGGAAAATTTTTTATTTCAATTTT
3290 TGCAAAATT
324 TGCAAAATT
* * * * * *
3299 TTAGCCGAAAACGTGTACTAA-CCAACACGGTTTCTGGCTGTAAACGCGTTTCGGGGCCCCGGCT
1 TTAGCCGAAATCGCGTACAAATCCATCACGGTTTCTGGCTGAAAACGCGTTCCGGGGCCCCGGCT
* * * *
3363 CAGTTTGGCATGAATTTTGGCGCCAAGACTCCTTGAAATATCTATATTAATCTAATTATGTCTCA
66 CAGTTTGGCATGAATTTTGGCGCCGAGACTCCTTGAAATATCTATATTCATCTAATCAAGTCTCA
* *
3428 GCCAGATTGGATTTAACGATAATTTTTTTATGAGCTTCTGAATCTTGTTTTGATTTTAATCAGAA
131 GCCACATTGGATTTAACGAT-ATGTTTTTATGAGCTTCTGAATCTTGTTTTGA-TTTAATCAGAA
* *
3493 ATTAAAATGGAAAAAATAGGAAAAACCATTTGTGAAGCATTACAAGCCCTTAAATATTTTTGGCG
194 ATTAAAATGGAAAAAATAGGAAAAACCATTTGTGAAGCATGACAAGCCCTTAAATCTTTTTGGCG
* * *
3558 TTGAATTTTAAATTTTTTATGAGTACTGTGGCCAAAAATTAAGGAAAATTTTTTCCTCTCAATTT
259 TTGAATTATAAATTTTTTATGAGTACTGTGGCCAAAAATTAAGGAAAATTTTTT-ATTTCAATTT
3623 TTGCAAAATT
323 TTGCAAAATT
* * * ** *
3633 TTAGCCGAAATCGAGTAC-TATCCATCACTGTTTCTGGCTGAAAACGCGTTCCGTAGCTCCGGCT
1 TTAGCCGAAATCGCGTACAAATCCATCACGGTTTCTGGCTGAAAACGCGTTCCGGGGCCCCGGCT
* * *
3697 CAGTTTTGCATG-ATTTTCGGCTGCCGAGACTCCTTGTAATATCTATATTCATTTAATCAAGTCT
66 CAGTTTGGCATGAATTTT-GGC-GCCGAGACTCCTTGAAATATCTATATTCATCTAATCAAGTCT
* * * * *
3761 CAGCCACATTGGATTAAAGGATATGTTTTTACGAGC-TCATGAATCTTGTTTCGATTTAATGAGA
129 CAGCCACATTGGATTTAACGATATGTTTTTATGAGCTTC-TGAATCTTGTTTTGATTTAATCAGA
* * * * * *
3825 AATTAAATTGGAAAAAAATACGAAAAACAATTTGTGAAGCATAAAAAGCCCTTAAATCTTTTCGG
193 AATTAAAATGG-AAAAAATAGGAAAAACCATTTGTGAAGCATGACAAGCCCTTAAATCTTTTTGG
* * * * * * **
3890 CGTTGAATTATAAA-ATTATATGAGTAATGTGTCCAAAAATTGAGGAAAAATTTTTCAGCT-AAG
257 CGTTGAATTATAAATTTTTTATGAGTACTGTGGCCAAAAATTAAGG-AAAATTTTTTATTTCAA-
3953 TTTTTGCAAAATT
320 TTTTTGCAAAATT
* * * * * *
3966 TTAGCTGAACTCATC-TACTAA-CCATCACGGTTTCTAGCTGAAAACGCGTT-CGGGGCCCCTGC
1 TTAGCCGAAATC-GCGTACAAATCCATCACGGTTTCTGGCTGAAAACGCGTTCCGGGGCCCCGGC
* * * *
4028 TTAGTTTAGCAT-ATTTTTGGCGCCGAGACTCCTTGCAATATCTATATTCATCTAATCAAGTCTC
65 TCAGTTTGGCATGAATTTTGGCGCCGAGACTCCTTGAAATATCTATATTCATCTAATCAAGTCTC
** *
4092 AATCACATTGGATTTAAGGATAT-TTTTTAT
130 AGCCACATTGGATTTAACGATATGTTTTTAT
4122 TTTTGTAAAA
Statistics
Matches: 1313, Mismatches: 161, Indels: 37
0.87 0.11 0.02
Matches are distributed among these distances:
329 6 0.00
330 61 0.05
331 3 0.00
332 147 0.11
333 243 0.19
334 704 0.54
335 149 0.11
ACGTcount: A:0.31, C:0.17, G:0.18, T:0.35
Consensus pattern (332 bp):
TTAGCCGAAATCGCGTACAAATCCATCACGGTTTCTGGCTGAAAACGCGTTCCGGGGCCCCGGCT
CAGTTTGGCATGAATTTTGGCGCCGAGACTCCTTGAAATATCTATATTCATCTAATCAAGTCTCA
GCCACATTGGATTTAACGATATGTTTTTATGAGCTTCTGAATCTTGTTTTGATTTAATCAGAAAT
TAAAATGGAAAAAATAGGAAAAACCATTTGTGAAGCATGACAAGCCCTTAAATCTTTTTGGCGTT
GAATTATAAATTTTTTATGAGTACTGTGGCCAAAAATTAAGGAAAATTTTTTATTTCAATTTTTG
CAAAATT
Found at i:3275 original size:668 final size:661
Alignment explanation
Indices: 2299--4121 Score: 2632
Period size: 668 Copynumber: 2.7 Consensus size: 661
2289 GAAAAATTGA
* * * * *
2299 TTAGCCGAAAACGTGTACTAACCATCACGGTTTCTGGTTGTAAACGCGTTCCGGGGCCCCGGCTC
1 TTAGCCGAAATCGTGTACTATCCATCAC-GTTTCTGGCTGAAAACGCGTTCCGGGGCTCCGGCTC
* * * * *
2364 AGTTTGGCATGAATTTTGGCGCCGAGACTCCTTGAAATATCTATATTCATCTAATTATGTCTCAG
65 AGTTTTGCATGATTTTTGGCGCCGAGACTCCTTGTAATATCTATATTCATCTAATCAAGTCTCAG
* * * * * * *
2429 CCAGATTGGATTTAACGATATGTTTTTATGAGCTTCTGAATCTTATTTTGATTTAATTAAAAATT
130 CCACATTGGATTTAAGGATATGTTTTTACGAGCTTCTGAATCTTGTTTCGATTTAATGAGAAATT
* * * *
2494 AAAATGGAAAAAATAGGAAAAACCATTTGTGAAGCATGACAATCCCTTAAATATTTTTGGCGTTG
195 AAATTGGAAAAAATAGGAAAAACCATTTGTGAAGCATGAAAAGCCCTTAAATCTTTTTGGCGTTG
* ** * *
2559 AATTATAAATTTTTTATGAGTACTGTGGCCAAGAATCAAGGAAAAATTTTTTATTTCAATTTTTG
260 AATTATAAA-TTTTTATGAGTAATGTGGCCAAGAATTGAGGAAAAATTTTTCAGTTCAATTTTTG
* * * * *
2624 CAAAATTTTTGCCGAAATCGCGTACGAAATCCATCACGGTTTCTGGCGGAAAACGCGTTCCGAGT
324 CAAAATTTTAGCCGAAATCGCGTAC-TAA-CCATCACGGTTTCTGGCTGAAAACGCGTT-CGGGG
*
2689 CTCCAGCTCAGTTTGGCATGAATTTTGGCGCCGAGACTCCTTGAAATATCTATATTCATCTAATT
386 CCCCAGCTCAGTTTGGCATGAATTTTGGCGCCGAGACTCCTTGAAATATCTATATTCATCTAATT
2754 ATGTCTCAGCCAGATTGGATTTAACGATATGTTTTTATGAGCTTCTGAATCTTGTTTTGA-TTTA
451 ATGTCTCAGCCAGATTGGATTTAACGATAT-TTTTTATGAGCTTCTGAATCTTGTTTTGATTTTA
*
2818 ATCAGAAATTAAAATGGAAAAAATAGGAAAAACCATATGTGAAGCATGACAAGCCCTTAAATCTT
515 ATCAGAAATTAAAATGGAAAAAATAGGAAAAACCATATGTGAAGCATGACAAGCCCTTAAATATT
*
2883 TTTGGCGTTGAATTATAAATTTTTTATGAGTACTGTGGCCAAAAATCAAGGAAAATTTTTTCCTT
580 TTTGGCGTTGAATTATAAATTTTTTATGAGTACTGTGGCCAAAAATCAAGGAAAATTTTTTCCTC
2948 TCAATTTTTGCAAAATT
645 TCAATTTTTGCAAAATT
*
2965 TTAGCCGAAATCGTGTACGATATCCATCACGATTTCTGGCTGAAAACGCGTTCCGGGGCTCCAGC
1 TTAGCCGAAATCGTGTAC--TATCCATCACG-TTTCTGGCTGAAAACGCGTTCCGGGGCTCCGGC
* * * * *
3030 TCAGTTTTGCATGATTTTTGACGCAGAGACTCCTTGTAGTATCTGTATTTATCTAATCAAGTCTC
63 TCAGTTTTGCATGATTTTTGGCGCCGAGACTCCTTGTAATATCTATATTCATCTAATCAAGTCTC
*
3095 AGCTACATTGGATTTAAGGATATGTTTTTACGAGCTTCTGAATCTTGTTTCGATTTAATGAGAAA
128 AGCCACATTGGATTTAAGGATATGTTTTTACGAGCTTCTGAATCTTGTTTCGATTTAATGAGAAA
*
3160 TTAAATTGGAAAACAATAGGAAAAACCATTTGTGAAGCATGAAAAGCCCTTAAATCTTTTTGGAG
193 TTAAATTGGAAAA-AATAGGAAAAACCATTTGTGAAGCATGAAAAGCCCTTAAATCTTTTTGGCG
* * * * *
3225 TTGAATTATAAATTCTTTATGAGCATTGTGGCCAAGAATTGATG-AAAATTTTTCGGTTCAATTC
257 TTGAATTATAAATT-TTTATGAGTAATGTGGCCAAGAATTGAGGAAAAATTTTTCAGTTCAATTT
* * * *
3289 TTGCAAAATTTTAGCCGAAAACGTGTACTAACCAACACGGTTTCTGGCTGTAAACGCGTTTCGGG
321 TTGCAAAATTTTAGCCGAAATCGCGTACTAACCATCACGGTTTCTGGCTGAAAACGCG-TTCGGG
* * *
3354 GCCCCGGCTCAGTTTGGCATGAATTTTGGCGCCAAGACTCCTTGAAATATCTATATTAATCTAAT
385 GCCCCAGCTCAGTTTGGCATGAATTTTGGCGCCGAGACTCCTTGAAATATCTATATTCATCTAAT
3419 TATGTCTCAGCCAGATTGGATTTAACGATAATTTTTTTATGAGCTTCTGAATCTTGTTTTGATTT
450 TATGTCTCAGCCAGATTGGATTTAACGAT-A-TTTTTTATGAGCTTCTGAATCTTGTTTTGATTT
* *
3484 TAATCAGAAATTAAAATGGAAAAAATAGGAAAAACCATTTGTGAAGCATTACAAGCCCTTAAATA
513 TAATCAGAAATTAAAATGGAAAAAATAGGAAAAACCATATGTGAAGCATGACAAGCCCTTAAATA
* *
3549 TTTTTGGCGTTGAATTTTAAATTTTTTATGAGTACTGTGGCCAAAAATTAAGGAAAATTTTTTCC
578 TTTTTGGCGTTGAATTATAAATTTTTTATGAGTACTGTGGCCAAAAATCAAGGAAAATTTTTTCC
3614 TCTCAATTTTTGCAAAATT
643 TCTCAATTTTTGCAAAATT
* **
3633 TTAGCCGAAATCGAGTACTATCCATCACTGTTTCTGGCTGAAAACGCGTTCCGTAGCTCCGGCTC
1 TTAGCCGAAATCGTGTACTATCCATCAC-GTTTCTGGCTGAAAACGCGTTCCGGGGCTCCGGCTC
* *
3698 AGTTTTGCATGATTTTCGGCTGCCGAGACTCCTTGTAATATCTATATTCATTTAATCAAGTCTCA
65 AGTTTTGCATGATTTTTGGC-GCCGAGACTCCTTGTAATATCTATATTCATCTAATCAAGTCTCA
*
3763 GCCACATTGGATTAAAGGATATGTTTTTACGAGC-TCATGAATCTTGTTTCGATTTAATGAGAAA
129 GCCACATTGGATTTAAGGATATGTTTTTACGAGCTTC-TGAATCTTGTTTCGATTTAATGAGAAA
* * * *
3827 TTAAATTGGAAAAAAATACGAAAAACAATTTGTGAAGCATAAAAAGCCCTTAAATCTTTTCGGCG
193 TTAAATTGG-AAAAAATAGGAAAAACCATTTGTGAAGCATGAAAAGCCCTTAAATCTTTTTGGCG
* * * * *
3892 TTGAATTATAAAATTATATGAGTAATGTGTCCAAAAATTGAGGAAAAATTTTTCAGCT-AAGTTT
257 TTGAATTATAAATTTTTATGAGTAATGTGGCCAAGAATTGAGGAAAAATTTTTCAGTTCAA-TTT
* * * *
3956 TTGCAAAATTTTAGCTGAACTCATC-TACTAACCATCACGGTTTCTAGCTGAAAACGCGTTCGGG
321 TTGCAAAATTTTAGCCGAAATC-GCGTACTAACCATCACGGTTTCTGGCTGAAAACGCGTTCGGG
* * * * *
4020 GCCCCTGCTTAGTTTAGCAT-ATTTTTGGCGCCGAGACTCCTTGCAATATCTATATTCATCTAAT
385 GCCCCAGCTCAGTTTGGCATGAATTTTGGCGCCGAGACTCCTTGAAATATCTATATTCATCTAAT
* * ** * *
4084 CAAGTCTCAATCACATTGGATTTAAGGATATTTTTTAT
450 TATGTCTCAGCCAGATTGGATTTAACGATATTTTTTAT
4122 TTTTGTAAAA
Statistics
Matches: 1035, Mismatches: 106, Indels: 35
0.88 0.09 0.03
Matches are distributed among these distances:
663 8 0.01
664 1 0.00
665 63 0.06
666 243 0.23
667 265 0.26
668 372 0.36
669 83 0.08
ACGTcount: A:0.31, C:0.17, G:0.18, T:0.35
Consensus pattern (661 bp):
TTAGCCGAAATCGTGTACTATCCATCACGTTTCTGGCTGAAAACGCGTTCCGGGGCTCCGGCTCA
GTTTTGCATGATTTTTGGCGCCGAGACTCCTTGTAATATCTATATTCATCTAATCAAGTCTCAGC
CACATTGGATTTAAGGATATGTTTTTACGAGCTTCTGAATCTTGTTTCGATTTAATGAGAAATTA
AATTGGAAAAAATAGGAAAAACCATTTGTGAAGCATGAAAAGCCCTTAAATCTTTTTGGCGTTGA
ATTATAAATTTTTATGAGTAATGTGGCCAAGAATTGAGGAAAAATTTTTCAGTTCAATTTTTGCA
AAATTTTAGCCGAAATCGCGTACTAACCATCACGGTTTCTGGCTGAAAACGCGTTCGGGGCCCCA
GCTCAGTTTGGCATGAATTTTGGCGCCGAGACTCCTTGAAATATCTATATTCATCTAATTATGTC
TCAGCCAGATTGGATTTAACGATATTTTTTATGAGCTTCTGAATCTTGTTTTGATTTTAATCAGA
AATTAAAATGGAAAAAATAGGAAAAACCATATGTGAAGCATGACAAGCCCTTAAATATTTTTGGC
GTTGAATTATAAATTTTTTATGAGTACTGTGGCCAAAAATCAAGGAAAATTTTTTCCTCTCAATT
TTTGCAAAATT
Found at i:4271 original size:170 final size:169
Alignment explanation
Indices: 3953--4292 Score: 502
Period size: 170 Copynumber: 2.0 Consensus size: 169
3943 TTCAGCTAAG
* * * *
3953 TTTTTGCAAAATTTTAGCTGAACTCATCTACTAACCATCACGGTTTCTAGCTGAAAACGCGTTCG
1 TTTTTGCAAAATTTTAGCCGAAATCATCTACTAAACATCACGATTTCTAGCTGAAAACGCGTTCG
* * *
4018 GGGCCCCTGCTTAGTTTAGCATATTTTTGGCGCCGAGACTCCTTGCAATATCTATATTCATCTAA
66 GGGCCCCGGCTCAGTTTAGCATATTTTTGGCGCCGAGACTCCTTGCAATATCTAAATTCATCTAA
*
4083 TCAAGTCTCAATCACATTGGATTTAAGGATAT-TTTTTA
131 TCAAGTCTCAACCACATTGGATTTAAGGATATGTTTTTA
* * *
4121 TTTTTGTAAAATTTTAGCCGAAATCGTCTACTAAACATCACGATTTCTGGCTGAAAACGCGTTCC
1 TTTTTGCAAAATTTTAGCCGAAATCATCTACTAAACATCACGATTTCTAGCTGAAAACGCGTT-C
* * * * *
4186 GGGGCTCCGGCTCAGTTTTGCATGATTTTTGGCGCCGAGACTCTTTGTAATTTCTAAATTCATCT
65 GGGGCCCCGGCTCAGTTTAGCAT-ATTTTTGGCGCCGAGACTCCTTGCAATATCTAAATTCATCT
*
4251 AATCAAGTCTCAGCCACATTGGATTTAAGGATATGTTTTTA
129 AATCAAGTCTCAACCACATTGGATTTAAGGATATGTTTTTA
4292 T
1 T
4293 GAGCTTCTGA
Statistics
Matches: 152, Mismatches: 17, Indels: 3
0.88 0.10 0.02
Matches are distributed among these distances:
168 56 0.37
169 20 0.13
170 69 0.45
171 7 0.05
ACGTcount: A:0.26, C:0.21, G:0.17, T:0.36
Consensus pattern (169 bp):
TTTTTGCAAAATTTTAGCCGAAATCATCTACTAAACATCACGATTTCTAGCTGAAAACGCGTTCG
GGGCCCCGGCTCAGTTTAGCATATTTTTGGCGCCGAGACTCCTTGCAATATCTAAATTCATCTAA
TCAAGTCTCAACCACATTGGATTTAAGGATATGTTTTTA
Found at i:4600 original size:499 final size:499
Alignment explanation
Indices: 3619--4613 Score: 1475
Period size: 499 Copynumber: 2.0 Consensus size: 499
3609 TTTCCTCTCA
* **
3619 ATTTTTGCAAAATTTTAGCCGAAATCGAGTACTATCCATCACTGTTTCTGGCTGAAAACGCGTTC
1 ATTTTTGCAAAATTTTAGCCGAAATCGACTACTAAACATCACTGTTTCTGGCTGAAAACGCGTTC
* *
3684 CGTAGCTCCGGCTCAGTTTTGCATGATTTTCGGCTGCCGAGACTCCTTGTAATATCTATATTCAT
66 CGGAGCTCCGGCTCAGTTTTGCATGATTTTCGGCTGCCGAGACTCCTTGTAATATCTAAATTCAT
*
3749 TTAATCAAGTCTCAGCCACATTGGATTAAAGGATATGTTTTTACGAGCTCATGAATCTTGTTTCG
131 CTAATCAAGTCTCAGCCACATTGGATTAAAGGATATGTTTTTACGAGCTCATGAATCTTGTTTCG
*
3814 ATTTAATGAGAAATTAAATTGGAAAAAAATACGAAAAACAATTTGTGAAGCATAAAAAGCCCTTA
196 ATTTAATCAGAAATTAAATTGGAAAAAAATACGAAAAACAATTTGTGAAGCATAAAAAGCCCTTA
*
3879 AATCTTTTCGGCGTTGAATTATAAAATTATATGAGTAATGTGTCCAAAAATTGAGGAAAAATTTT
261 AATCTTTTCGGCGTTGAATTATAAAATTATATGAGTAATGTGGCCAAAAATTGAGGAAAAATTTT
* * *
3944 TCAGCTAAGTTTTTGCAAAATTTTAGCTGAACTCATCTACTAACCATCACGGTTTCTAGCTGAAA
326 T-AGCTAACTTTTTCCAAAATTTTAGCCGAACTCATCTACT-ACCATCACGGTTTCTAGCTGAAA
* * * *
4009 ACGCGTTCGGGGCCCCTGCTTAGTTTAGCATATTTTTGGCGCCGAGACTCCTTGCAATATCTATA
389 ACGCGTTCGGGGCCCCTGCTCAATTTAGCATAGTTTTGGCGCCGAGACTCCTTGAAATATCTATA
*
4074 TTCATCTAATCAAGTCTCAATCACATTGGATTTAAGGATATTTTTT
454 TTCATCTAATCAAGTCTCAAGCACATTGGATTTAAGGATATTTTTT
* *
4120 ATTTTTGTAAAATTTTAGCCGAAATCGTCTACTAAACATCAC-GATTTCTGGCTGAAAACGCGTT
1 ATTTTTGCAAAATTTTAGCCGAAATCGACTACTAAACATCACTG-TTTCTGGCTGAAAACGCGTT
* * * *
4184 CCGGGGCTCCGGCTCAGTTTTGCATGATTTTTGGC-GCCGAGACTCTTTGTAATTTCTAAATTCA
65 CCGGAGCTCCGGCTCAGTTTTGCATGATTTTCGGCTGCCGAGACTCCTTGTAATATCTAAATTCA
* *
4248 TCTAATCAAGTCTCAGCCACATTGGATTTAAGGATATGTTTTTATGAGCTTC-TGAATCTTGTTT
130 TCTAATCAAGTCTCAGCCACATTGGATTAAAGGATATGTTTTTACGAGC-TCATGAATCTTGTTT
* * *
4312 CGATTTAATCAGAAATTAAATT-G-AAAAAATAGGAAAAACCATTTGTGAAGCATGAAAAGCCCT
194 CGATTTAATCAGAAATTAAATTGGAAAAAAATACGAAAAACAATTTGTGAAGCATAAAAAGCCCT
* * * * *
4375 TAAATCTTTTTGGTGTTGAATTATAAATTTTTTATGAGTACTGTGGCCAAAAATTGAGGAAAAAT
259 TAAATCTTTTCGGCGTTGAATTATAAA-ATTATATGAGTAATGTGGCCAAAAATTGAGGAAAAAT
* * * * *
4440 TCTTT-GTTTCACTTTTTCCAAAATTTTAGCCGTAA-TCGTGTACT-TCATCACGGTTTCTAGCT
323 T-TTTAG-CTAACTTTTTCCAAAATTTTAGCCG-AACTCATCTACTACCATCACGGTTTCTAGCT
* *
4502 GAAAACGCGTTCCGGGGTCCCTGCTCAATTTGGCATGAGTTTTGGCGCCGAGACTCCTTGAAATA
385 GAAAACGCGTT-CGGGGCCCCTGCTCAATTTAGCAT-AGTTTTGGCGCCGAGACTCCTTGAAATA
* *
4567 TCTATATTCATCTAATCATGTCTCAGGCACATTGGATTTAAGGATAT
448 TCTATATTCATCTAATCAAGTCTCAAGCACATTGGATTTAAGGATAT
4614 GCTTTAAGAG
Statistics
Matches: 445, Mismatches: 41, Indels: 18
0.88 0.08 0.04
Matches are distributed among these distances:
497 28 0.06
498 83 0.19
499 132 0.30
500 111 0.25
501 91 0.20
ACGTcount: A:0.29, C:0.18, G:0.18, T:0.35
Consensus pattern (499 bp):
ATTTTTGCAAAATTTTAGCCGAAATCGACTACTAAACATCACTGTTTCTGGCTGAAAACGCGTTC
CGGAGCTCCGGCTCAGTTTTGCATGATTTTCGGCTGCCGAGACTCCTTGTAATATCTAAATTCAT
CTAATCAAGTCTCAGCCACATTGGATTAAAGGATATGTTTTTACGAGCTCATGAATCTTGTTTCG
ATTTAATCAGAAATTAAATTGGAAAAAAATACGAAAAACAATTTGTGAAGCATAAAAAGCCCTTA
AATCTTTTCGGCGTTGAATTATAAAATTATATGAGTAATGTGGCCAAAAATTGAGGAAAAATTTT
TAGCTAACTTTTTCCAAAATTTTAGCCGAACTCATCTACTACCATCACGGTTTCTAGCTGAAAAC
GCGTTCGGGGCCCCTGCTCAATTTAGCATAGTTTTGGCGCCGAGACTCCTTGAAATATCTATATT
CATCTAATCAAGTCTCAAGCACATTGGATTTAAGGATATTTTTT
Found at i:4966 original size:330 final size:328
Alignment explanation
Indices: 4120--5415 Score: 1730
Period size: 329 Copynumber: 3.9 Consensus size: 328
4110 GATATTTTTT
* * * *
4120 ATTTTTGTAAAATTTTAGCCGAAATCGTCTACTAAACATCACGATTTCTGGCTGAAAACGCGTTC
1 ATTTTTGCAAAATTTTAGCCGAAATCGTGTACT--CCATCACGGTTTCTGGCTGAAAACGCGTTC
* * * * * *
4185 CGGGGCTCCGGCTCAGTTTTGCATGATTTTTGGCGCCGAGACTCTTTGTAATTTCTAAATTCATC
64 CGGGGCTCCGACTCAGTTTGGCATGATTTTTGGCGCCGAGACTCCTTGAAATATCTATATTCATC
4250 TAATCAAGTCTCAGCCACATTGGATTTAAGGATATGTTTTTATGAGCTTCTGAATCTTGTTTCGA
129 TAATCAAGTCTCAGCCACATTGGATTTAAGGATATGTTTTTATGAGCTTCTGAATCTTGTTTCGA
*
4315 TTTAATCAGAAATTAAATTGAAAAAATAGGAAAAACCATTTGTGAAGCATGAAAAGCCCTTAAAT
194 TTTAATCAGAAATTAATTTGAAAAAATAGGAAAAACCATTTGTGAAGCATGAAAAGCCCTTAAAT
* *
4380 CTTTTTGGTGTTGAATTATAAATTTTTTATGAGTACTGTGGCCAAAAATTGAGGAAAAATTCTTT
259 CTTTTTGGTGTTGAATTATAATTTTTTTATGAGTACTGTGGCCAAAAATTGAGGAAAAATT-TTC
4445 GTTTCA
323 GTTTCA
* * * * *
4451 CTTTTTCCAAAATTTTAGCCGTAATCGTGTACTTCATCACGGTTTCTAGCTGAAAACGCGTTCCG
1 ATTTTTGCAAAATTTTAGCCGAAATCGTGTACTCCATCACGGTTTCTGGCTGAAAACGCGTTCCG
* *
4516 GGG-TCCCTG-CTCAATTTGGCATGAGTTTTGGCGCCGAGACTCCTTGAAATATCTATATTCATC
66 GGGCT-CC-GACTCAGTTTGGCATGATTTTTGGCGCCGAGACTCCTTGAAATATCTATATTCATC
* * * * * *
4579 TAATCATGTCTCAGGCACATTGGATTTAAGGATATG-CTTTAAGAGGTTCTAAATCTTGTTTCGA
129 TAATCAAGTCTCAGCCACATTGGATTTAAGGATATGTTTTTATGAGCTTCTGAATCTTGTTTCGA
* * *
4643 TTTAATCAAAAATCAATTTTGAAAAAAATAGGAAAAACCATTTATGAAGCATGAAAAGCCCTTAA
194 TTTAATCAGAAATTAA-TTTG-AAAAAATAGGAAAAACCATTTGTGAAGCATGAAAAGCCCTTAA
* *
4708 ATCATTTTT-GCGTTGAATTATTAATTTTTTTATGAGTACTGTGGCCAAAAATGGAGGAAAAATT
257 ATC-TTTTTGGTGTTGAATTA-TAATTTTTTTATGAGTACTGTGGCCAAAAATTGAGGAAAAATT
4772 TTCGTTTCA
320 TTCGTTTCA
*
4781 ATTTTTGCAAAATTTTAGCCGAAATCGTGTAC-CCATCACGGTTTCTGGCTGAAAACACGTTCCG
1 ATTTTTGCAAAATTTTAGCCGAAATCGTGTACTCCATCACGGTTTCTGGCTGAAAACGCGTTCCG
* * * * * *
4845 GGGCTTCGACTCAGTTTTGTATGATTTTTGGCGCCGAGACTCCTTGAAATTTCTGTATTCATCAA
66 GGGCTCCGACTCAGTTTGGCATGATTTTTGGCGCCGAGACTCCTTGAAATATCTATATTCATCTA
** * *
4910 ATCAAGTCTCCA-CCACATTAAATTTAAGGATATTTTTTTACGAGCTTCTGAATCTTGTTTCGAT
131 ATCAAGTCT-CAGCCACATTGGATTTAAGGATATGTTTTTATGAGCTTCTGAATCTTGTTTCGAT
* * *
4974 TTAATTAGAAATTAATTTG-GAAAATAGGAAAAACCATATT-TGAATCATGAAAAGCCCTTAAAT
195 TTAATCAGAAATTAATTTGAAAAAATAGGAAAAACCAT-TTGTGAAGCATGAAAAGCCCTTAAAT
* * * **
5037 CTTTTTGGGGTTGAATTATAA-ATTTTTATGAGTATTGTGGCCAAAAATTGAGGAAATTTTTTTC
259 CTTTTTGGTGTTGAATTATAATTTTTTTATGAGTACTGTGGCCAAAAATTGAGGAAA-AATTTTC
5101 GTTTCA
323 GTTTCA
** * *
5107 ATTTTTGCAAAATTTTAGGAGAAAACGTGTACTATCCATCACGGTTTGTGGCTGAAAACGCGTTC
1 ATTTTTGCAAAATTTTAGCCGAAATCGTGTAC--TCCATCACGGTTTCTGGCTGAAAACGCGTTC
* * *
5172 CAGGGCTCCGACTCAGTTTGGCATGATTTTTGACGCCAAGACTCCTTGAAATATCTATATTCATC
64 CGGGGCTCCGACTCAGTTTGGCATGATTTTTGGCGCCGAGACTCCTTGAAATATCTATATTCATC
* * * * * *
5237 TAATCAAGTCTTA-CTACATTGGGTTTAAGGATATGTTTTCATAAGCATCTGAATCTTGTTTCGA
129 TAATCAAGTCTCAGCCACATTGGATTTAAGGATATGTTTTTATGAGCTTCTGAATCTTGTTTCGA
** * * * **
5301 TTTAATTTGAAATTAATTTTGAAAAACATAGTAAAAATCATATGTGAAATATGAAAAGCCCTTAA
194 TTTAATCAGAAATTAA-TTTGAAAAA-ATAGGAAAAACCATTTGTGAAGCATGAAAAGCCCTTAA
*
5366 ATCTTTTTGGTGTTGAATTATATATTTTTTTATGAGTATTGTGGCCAAAA
257 ATCTTTTTGGTGTTGAATTATA-ATTTTTTTATGAGTACTGTGGCCAAAA
5416 TATGAGAAAA
Statistics
Matches: 847, Mismatches: 96, Indels: 42
0.86 0.10 0.04
Matches are distributed among these distances:
325 32 0.04
326 48 0.06
327 50 0.06
328 100 0.12
329 329 0.39
330 137 0.16
331 126 0.15
332 1 0.00
333 24 0.03
ACGTcount: A:0.31, C:0.16, G:0.17, T:0.36
Consensus pattern (328 bp):
ATTTTTGCAAAATTTTAGCCGAAATCGTGTACTCCATCACGGTTTCTGGCTGAAAACGCGTTCCG
GGGCTCCGACTCAGTTTGGCATGATTTTTGGCGCCGAGACTCCTTGAAATATCTATATTCATCTA
ATCAAGTCTCAGCCACATTGGATTTAAGGATATGTTTTTATGAGCTTCTGAATCTTGTTTCGATT
TAATCAGAAATTAATTTGAAAAAATAGGAAAAACCATTTGTGAAGCATGAAAAGCCCTTAAATCT
TTTTGGTGTTGAATTATAATTTTTTTATGAGTACTGTGGCCAAAAATTGAGGAAAAATTTTCGTT
TCA
Found at i:10724 original size:16 final size:16
Alignment explanation
Indices: 10703--10736 Score: 59
Period size: 16 Copynumber: 2.1 Consensus size: 16
10693 CCTAGCTATA
*
10703 GATCAGGCTATTTTTG
1 GATCAGGCCATTTTTG
10719 GATCAGGCCATTTTTG
1 GATCAGGCCATTTTTG
10735 GA
1 GA
10737 GAACTGAGTA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.21, C:0.15, G:0.26, T:0.38
Consensus pattern (16 bp):
GATCAGGCCATTTTTG
Found at i:14440 original size:6 final size:6
Alignment explanation
Indices: 14429--14496 Score: 79
Period size: 6 Copynumber: 11.8 Consensus size: 6
14419 GATCATCACC
* *
14429 ACCATG ACCATG ACCATG ACCATG ACCATG ACC--- ACCATC ACCATC
1 ACCATG ACCATG ACCATG ACCATG ACCATG ACCATG ACCATG ACCATG
* *
14474 ATCATG ATCATG ACCATG ACCAT
1 ACCATG ACCATG ACCATG ACCAT
14497 TCCCACAAGT
Statistics
Matches: 56, Mismatches: 3, Indels: 6
0.86 0.05 0.09
Matches are distributed among these distances:
3 3 0.05
6 53 0.95
ACGTcount: A:0.34, C:0.35, G:0.12, T:0.19
Consensus pattern (6 bp):
ACCATG
Found at i:14456 original size:27 final size:27
Alignment explanation
Indices: 14415--14472 Score: 53
Period size: 27 Copynumber: 2.1 Consensus size: 27
14405 AAATGGCTTC
* * * *
14415 CCATGATCATCACCACCATGACCATGA
1 CCATGACCATGACCACCATCACCATCA
** *
14442 CCATGACCATGACCATGACCACCATCA
1 CCATGACCATGACCACCATCACCATCA
14469 CCAT
1 CCAT
14473 CATCATGATC
Statistics
Matches: 24, Mismatches: 7, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
27 24 1.00
ACGTcount: A:0.33, C:0.40, G:0.10, T:0.17
Consensus pattern (27 bp):
CCATGACCATGACCACCATCACCATCA
Found at i:14463 original size:33 final size:33
Alignment explanation
Indices: 14415--14495 Score: 108
Period size: 33 Copynumber: 2.5 Consensus size: 33
14405 AAATGGCTTC
* * * *
14415 CCATGATCATCACCACCATGACCATGACCATGA
1 CCATGACCATGACCACCATCACCATCACCATGA
*
14448 CCATGACCATGACCACCATCACCATCATCATGA
1 CCATGACCATGACCACCATCACCATCACCATGA
*
14481 TCATGACCATGACCA
1 CCATGACCATGACCA
14496 TTCCCACAAG
Statistics
Matches: 42, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
33 42 1.00
ACGTcount: A:0.33, C:0.37, G:0.11, T:0.19
Consensus pattern (33 bp):
CCATGACCATGACCACCATCACCATCACCATGA
Found at i:14479 original size:27 final size:27
Alignment explanation
Indices: 14435--14489 Score: 74
Period size: 27 Copynumber: 2.0 Consensus size: 27
14425 CACCACCATG
* *
14435 ACCATGACCATGACCATGACCATGACC
1 ACCATCACCATCACCATGACCATGACC
* *
14462 ACCATCACCATCATCATGATCATGACC
1 ACCATCACCATCACCATGACCATGACC
14489 A
1 A
14490 TGACCATTCC
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
27 24 1.00
ACGTcount: A:0.35, C:0.36, G:0.11, T:0.18
Consensus pattern (27 bp):
ACCATCACCATCACCATGACCATGACC
Found at i:18283 original size:23 final size:23
Alignment explanation
Indices: 18239--18283 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 23
18229 TGGACAGATA
**
18239 AGCTTCCAAATTGTTGTGACTAC
1 AGCTTCCAAATTGTTGCCACTAC
*
18262 AGCTTCCACATTGTTGCCACTA
1 AGCTTCCAAATTGTTGCCACTA
18284 TAACACTGCA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.24, C:0.27, G:0.16, T:0.33
Consensus pattern (23 bp):
AGCTTCCAAATTGTTGCCACTAC
Found at i:21031 original size:9 final size:9
Alignment explanation
Indices: 21017--21045 Score: 58
Period size: 9 Copynumber: 3.2 Consensus size: 9
21007 ATAGAAGGAT
21017 GGCAATTGG
1 GGCAATTGG
21026 GGCAATTGG
1 GGCAATTGG
21035 GGCAATTGG
1 GGCAATTGG
21044 GG
1 GG
21046 ATTTTACGTC
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 20 1.00
ACGTcount: A:0.21, C:0.10, G:0.48, T:0.21
Consensus pattern (9 bp):
GGCAATTGG
Found at i:25465 original size:2 final size:2
Alignment explanation
Indices: 25458--25482 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
25448 CAGATTAATA
25458 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
25483 AATAGGGTAA
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:26459 original size:15 final size:15
Alignment explanation
Indices: 26439--26470 Score: 64
Period size: 15 Copynumber: 2.1 Consensus size: 15
26429 CAATATCACA
26439 AAGATATATCTAACT
1 AAGATATATCTAACT
26454 AAGATATATCTAACT
1 AAGATATATCTAACT
26469 AA
1 AA
26471 ATGCAGCCAA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.50, C:0.12, G:0.06, T:0.31
Consensus pattern (15 bp):
AAGATATATCTAACT
Found at i:27519 original size:2 final size:2
Alignment explanation
Indices: 27512--27541 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
27502 GATTGGATAT
27512 AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC
1 AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC
27542 TGATATACAT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.50, G:0.00, T:0.00
Consensus pattern (2 bp):
AC
Found at i:28598 original size:6 final size:6
Alignment explanation
Indices: 28589--28625 Score: 56
Period size: 6 Copynumber: 6.2 Consensus size: 6
28579 TTGCTGCTGC
* *
28589 TGATGT TGATGT TGATGT TGATGA TGATGA TGATGT T
1 TGATGT TGATGT TGATGT TGATGT TGATGT TGATGT T
28626 CGCCGTAATT
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
6 29 1.00
ACGTcount: A:0.22, C:0.00, G:0.32, T:0.46
Consensus pattern (6 bp):
TGATGT
Found at i:34299 original size:3 final size:3
Alignment explanation
Indices: 34291--34319 Score: 58
Period size: 3 Copynumber: 9.7 Consensus size: 3
34281 TAACTATTAT
34291 ATA ATA ATA ATA ATA ATA ATA ATA ATA AT
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA AT
34320 TCATGCGGCG
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
ATA
Found at i:35777 original size:2 final size:2
Alignment explanation
Indices: 35770--35804 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
35760 AATAATATGG
35770 AT AT AT AT AT 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 AT AT AT AT AT A
35805 CTAGTATTTA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Done.