Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold75
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: 1998514
ACGTcount: A:0.34, C:0.16, G:0.17, T:0.34
File 2 of 12
Found at i:221294 original size:122 final size:120
Alignment explanation
Indices: 221059--221387 Score: 493
Period size: 122 Copynumber: 2.7 Consensus size: 120
221049 TGGAAAGGTT
* * *
221059 TGCCACCAACTTGTGTGGGCTTT-TAAAGAAAAGGCGTCATGCCCTTTGAGGACTGGAAGGTGCC
1 TGCCACCAACTTGTGTGGGCTTTAAAAAGAGAAGGCGTCATGCTCTTTGAGGACT-GAAGGTGCC
* * *
221123 ACCAACTTGTGTGGACTTTGCAAAAAGAAAGCATCCTACTCTTTGAGGACTGAAAAG
65 ACCAGCTTGTGTGGGCTTT-TAAAAAGAAAGCATCCTACTCTTTGAGGACTGAAAAG
*
221180 TGCTACCAACTTGTGTGGGCTTTAAAAAGAGAAGGCGTCATGCTCTTTGAGGACTGAAGGTGCCA
1 TGCCACCAACTTGTGTGGGCTTTAAAAAGAGAAGGCGTCATGCTCTTTGAGGACTGAAGGTGCCA
* *
221245 CCAGCTTGTGTGGGCTTTTAAAAAGAGAAGGCGTCCTGCTCTTTGAGGACTGAAAAG
66 CCAGCTTGTGTGGGCTTTTAAAAAGA-AA-GCATCCTACTCTTTGAGGACTGAAAAG
* *
221302 TGCCACCAACTTGTGTGGGCTTTAAAAAGAGAAGGCATCCTGCTCTTTGAGGACTGAA-GTGCCA
1 TGCCACCAACTTGTGTGGGCTTTAAAAAGAGAAGGCGTCATGCTCTTTGAGGACTGAAGGTGCCA
*
221366 CCAGCTTGTGTGTGC-TTTAAAA
66 CCAGCTTGTGTGGGCTTTTAAAA
221388 GGCATCCTGC
Statistics
Matches: 192, Mismatches: 13, Indels: 7
0.91 0.06 0.03
Matches are distributed among these distances:
120 14 0.07
121 70 0.36
122 108 0.56
ACGTcount: A:0.27, C:0.20, G:0.27, T:0.26
Consensus pattern (120 bp):
TGCCACCAACTTGTGTGGGCTTTAAAAAGAGAAGGCGTCATGCTCTTTGAGGACTGAAGGTGCCA
CCAGCTTGTGTGGGCTTTTAAAAAGAAAGCATCCTACTCTTTGAGGACTGAAAAG
Found at i:221628 original size:61 final size:61
Alignment explanation
Indices: 221428--222121 Score: 822
Period size: 61 Copynumber: 11.4 Consensus size: 61
221418 AAAGGAGAGA
221428 GCGTCCTGCTCTTTGAGGACTAGG-AAATGCCACCAACTTGTGTGGGCTTT-AAAAGAAGAAG
1 GCGTCCTGCTCTTTGAGGACT-GGAAAATGCCACCAACTTGTGTGGGCTTTGAAAAGAA-AAG
** *
221489 GCGTCCTGCTCTTTGAGGACT-GAAGGTGCCACCAACTTATGTGGGCTTTG-AAAGAAAAG
1 GCGTCCTGCTCTTTGAGGACTGGAAAATGCCACCAACTTGTGTGGGCTTTGAAAAGAAAAG
* * * *
221548 GTGTCCTGCTCTTTAAGGACTGGAAAATGCCACCCACTTGTGTGGGCTTTGAAAAGAAAAA
1 GCGTCCTGCTCTTTGAGGACTGGAAAATGCCACCAACTTGTGTGGGCTTTGAAAAGAAAAG
* * *
221609 GCATCCTGCTCCTTGAGGACTGGAAAATGCCACCAACTTGTGTGGGCTTTAAAAAGAAAAAG
1 GCGTCCTGCTCTTTGAGGACTGGAAAATGCCACCAACTTGTGTGGGCTTTGAAAAG-AAAAG
* * * *
221671 G-ATCCTACTCTTTGAGGACTGGAAAATGCCACTAACTTGTGTGGGCTTTGAAAGGAAAAG
1 GCGTCCTGCTCTTTGAGGACTGGAAAATGCCACCAACTTGTGTGGGCTTTGAAAAGAAAAG
* *
221731 GCATCCTGCTCTTTGAGGACTGGAAAATGCCACCAACTTGTGTGGGCTTTGAAAGGAAAAG
1 GCGTCCTGCTCTTTGAGGACTGGAAAATGCCACCAACTTGTGTGGGCTTTGAAAAGAAAAG
*
221792 GCGTCCTGCTCTTTGAGGACTCGAAAAGTGCCACCAACTTGTGTGGGCTTT-AAAAGAAAAAG
1 GCGTCCTGCTCTTTGAGGACTGGAAAA-TGCCACCAACTTGTGTGGGCTTTGAAAAG-AAAAG
* ** * * * *
221854 GCGTCTTGCT-TGTTGAGGACT-GAAGGTGCCACCAGCTTATGTGGGTTTTAAAAAGAAAAG
1 GCGTCCTGCTCT-TTGAGGACTGGAAAATGCCACCAACTTGTGTGGGCTTTGAAAAGAAAAG
* * * *
221914 GCGTCTTGCTCATTGAGGACT--AAAAGGTGCCACCAGCTTATGTGGGCTTT-AAAAGAAAAAG
1 GCGTCCTGCTCTTTGAGGACTGGAAAA--TGCCACCAACTTGTGTGGGCTTTGAAAAG-AAAAG
* * ** * * *
221975 GCATCCTGCTCGTTGAGGACT-GAAGGGTGCCACCAACTCGTGTGGGCTTTAAAAAGAAATG
1 GCGTCCTGCTCTTTGAGGACTGGAA-AATGCCACCAACTTGTGTGGGCTTTGAAAAGAAAAG
* * * * *
222036 GTGTCCTGCTCTTTGAGGACT--AAAGGTTCCCCCAACTCGTGTGGGCTTTGAAAAGAAAAAG
1 GCGTCCTGCTCTTTGAGGACTGGAAA-ATGCCACCAACTTGTGTGGGCTTTGAAAAG-AAAAG
222097 GCGTCCTGCTCTTTGAGGACTGGAA
1 GCGTCCTGCTCTTTGAGGACTGGAA
222122 GGGCTAAAAG
Statistics
Matches: 557, Mismatches: 55, Indels: 40
0.85 0.08 0.06
Matches are distributed among these distances:
59 25 0.04
60 138 0.25
61 334 0.60
62 58 0.10
63 2 0.00
ACGTcount: A:0.28, C:0.20, G:0.27, T:0.25
Consensus pattern (61 bp):
GCGTCCTGCTCTTTGAGGACTGGAAAATGCCACCAACTTGTGTGGGCTTTGAAAAGAAAAG
Found at i:221652 original size:275 final size:275
Alignment explanation
Indices: 221156--221968 Score: 793
Period size: 275 Copynumber: 2.8 Consensus size: 275
221146 AAAGAAAGCA
*
221156 TCCTACTCTTTGAGGACTGAAAAGTGCTACCAACTTGTGTGGGCTTTAAAAAGAGAAGGCGTCAT
1 TCCTACTCTTTGAGGACTGAAAAGTGCCACCAACTTGTGTGGGCTTTAAAAAGAGAAGGCGTCAT
* * *
221221 GCTCTTTGAGGACTGAAGGTGCCACCAGCTTGTGTGGGCTTTTAAAAAGAGAAGGCGTCCTGCTC
66 GCTCTTTGAGGACTGAAGGTGCCACCAACTTATGTGGGCTTTTAAAAAGAAAAGGCGTCCTGCTC
* * * *
221286 TTTGAGGACTGAAAAGTGCCACCAACTTGTGTGGGCTTTAAAAAGAGAAGGCATCCTGCTCTTTG
131 TTTAAGGACTGAAAAGTGCCACCAACTTGTGTGGGCTTTAAAAAGAAAAAGCATCCTGCTCCTTG
* * *
221351 AGGACTGAAGTGCCACCAGCTTGTGTGTGCTTTAAAAGGCATCCTGCTTTTTGAGGACAAAAAGG
196 AGGACTGAAATGCCACCAACTTGTGTGGGCTTTAAAAGGCATCCTGCTTTTTGAGGACAAAAAGG
221416 CGAAAGGAGAGAGCG
261 CGAAAGGAGAGAGCG
* *
221431 TCCTGCTCTTTGAGGACTAGGAAA-TGCCACCAACTTGTGTGGGCTTT-AAAAGAAGAAGGCGTC
1 TCCTACTCTTTGAGGACT-GAAAAGTGCCACCAACTTGTGTGGGCTTTAAAAAG-AGAAGGCGTC
* * *
221494 CTGCTCTTTGAGGACTGAAGGTGCCACCAACTTATGTGGGC-TTT-GAAAGAAAAGGTGTCCTGC
64 ATGCTCTTTGAGGACTGAAGGTGCCACCAACTTATGTGGGCTTTTAAAAAGAAAAGGCGTCCTGC
* *
221557 TCTTTAAGGACTGGAAAA-TGCCACCCACTTGTGTGGGCTTTGAAAAGAAAAAGCATCCTGCTCC
129 TCTTTAAGGACT-GAAAAGTGCCACCAACTTGTGTGGGCTTTAAAAAGAAAAAGCATCCTGCTCC
* * *
221621 TTGAGGACTGGAAAATGCCACCAACTTGTGTGGGCTTTAAAAAGAAAAAGGATCCTACTCTTTGA
193 TTGAGGACT-G-AAATGCCACCAACTTGTGTGGGCTTT-AAAAG-----GCATCCTGCTTTTTGA
* *
221686 GGACTGGAAAATGCCACTAACTTGTGTGGGCTTTGAAAGGA-AAAGGCA
250 GGAC-----AA----A--AA--------GGC---GAAAGGAGAGA-GCG
* * * * *
221734 TCCTGCTCTTTGAGGACTGGAAAA-TGCCACCAACTTGTGTGGGCTTTGAAAGGAAAAGGCGTCC
1 TCCTACTCTTTGAGGACT-GAAAAGTGCCACCAACTTGTGTGGGCTTTAAAAAGAGAAGGCGTCA
* * *
221798 TGCTCTTTGAGGACTCGAAAAGTGCCACCAACTTGTGTGGGC-TTT-AAAAGAAAAAGGCGTCTT
65 TGCTCTTTGAGGACT-G-AAGGTGCCACCAACTTATGTGGGCTTTTAAAAAG-AAAAGGCGTCCT
* * * * * * * *
221861 GCT-TGTTGAGGACTG-AAGGTGCCACCAGCTTATGTGGGTTTTAAAAAGAAAAGGCGTCTTGCT
127 GCTCT-TTAAGGACTGAAAAGTGCCACCAACTTGTGTGGGCTTTAAAAAGAAAAAGCATCCTGCT
* * * *
221924 CATTGAGGACTAAAAGGTGCCACCAGCTTATGTGGGCTTTAAAAG
191 CCTTGAGGACTGAAA--TGCCACCAACTTGTGTGGGCTTTAAAAG
221969 AAAAAGGCAT
Statistics
Matches: 450, Mismatches: 46, Indels: 55
0.82 0.08 0.10
Matches are distributed among these distances:
273 77 0.17
274 14 0.03
275 110 0.24
276 9 0.02
281 17 0.04
286 2 0.00
290 1 0.00
292 2 0.00
300 3 0.01
302 2 0.00
303 82 0.18
304 12 0.03
305 98 0.22
306 21 0.05
ACGTcount: A:0.28, C:0.19, G:0.27, T:0.26
Consensus pattern (275 bp):
TCCTACTCTTTGAGGACTGAAAAGTGCCACCAACTTGTGTGGGCTTTAAAAAGAGAAGGCGTCAT
GCTCTTTGAGGACTGAAGGTGCCACCAACTTATGTGGGCTTTTAAAAAGAAAAGGCGTCCTGCTC
TTTAAGGACTGAAAAGTGCCACCAACTTGTGTGGGCTTTAAAAAGAAAAAGCATCCTGCTCCTTG
AGGACTGAAATGCCACCAACTTGTGTGGGCTTTAAAAGGCATCCTGCTTTTTGAGGACAAAAAGG
CGAAAGGAGAGAGCG
Found at i:228342 original size:51 final size:51
Alignment explanation
Indices: 228287--228449 Score: 200
Period size: 51 Copynumber: 3.2 Consensus size: 51
228277 ACAACGAGGC
* * * *
228287 TGGAGTATCCCCGATTATAAAAAATCGATGTTTTAAAAATAAAATCGGGGT
1 TGGAGTATCCCCGATTATGAAAAATCAATATTTTAAAAATAAAGTCGGGGT
* * * *
228338 TGGAGTATCCCCAATTATGAGAAATCAATATTTTAGAAATAAGGTCGGGGT
1 TGGAGTATCCCCGATTATGAAAAATCAATATTTTAAAAATAAAGTCGGGGT
** * * * *
228389 TTAAGTATCCCCGATTGTGACAAATCAATATTTTGAAAATAAAGTCGAGGT
1 TGGAGTATCCCCGATTATGAAAAATCAATATTTTAAAAATAAAGTCGGGGT
228440 TGGAGTATCC
1 TGGAGTATCC
228450 TCTCGAAAAT
Statistics
Matches: 93, Mismatches: 19, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
51 93 1.00
ACGTcount: A:0.36, C:0.13, G:0.21, T:0.30
Consensus pattern (51 bp):
TGGAGTATCCCCGATTATGAAAAATCAATATTTTAAAAATAAAGTCGGGGT
Found at i:228504 original size:28 final size:27
Alignment explanation
Indices: 228437--228508 Score: 92
Period size: 29 Copynumber: 2.6 Consensus size: 27
228427 ATAAAGTCGA
228437 GGTTGGAGTATCCTCTCGAAAATAACAGG
1 GGTTGGAGTATCC-C-CGAAAATAACAGG
*
228466 GGTTGAAGTATCCCCGATGAAATAAC-GG
1 GGTTGGAGTATCCCCGA--AAATAACAGG
228494 GGTTGGAGTATCCCC
1 GGTTGGAGTATCCCC
228509 AATTGTGGAG
Statistics
Matches: 39, Mismatches: 2, Indels: 5
0.85 0.04 0.11
Matches are distributed among these distances:
27 3 0.08
28 17 0.44
29 19 0.49
ACGTcount: A:0.28, C:0.19, G:0.29, T:0.24
Consensus pattern (27 bp):
GGTTGGAGTATCCCCGAAAATAACAGG
Found at i:228556 original size:79 final size:78
Alignment explanation
Indices: 228464--228718 Score: 300
Period size: 79 Copynumber: 3.2 Consensus size: 78
228454 GAAAATAACA
* * *
228464 GGGGTTGAAGTATCCCCGATGAAATAACGGGGTTGGAGTATCCCCAATTGTGGAGAATTGGTGTT
1 GGGGTTGGAGTATCCCCG-TGAAATAACGGGGTTGGAGTATCCCCGATTGTGGAAAATTGGTGTT
228529 TTAGAAATAAAATC
65 TTAGAAATAAAATC
* ** * *
228543 GGGGTTGGAGTATCCCC-TCGAAAATAACGGGGTTGGAGTATCCCTGATTAAGAAAAATTGATGT
1 GGGGTTGGAGTATCCCCGT-G-AAATAACGGGGTTGGAGTATCCCCGATTGTGGAAAATTGGTGT
* *
228607 TTTAAAAATAAAATT
64 TTTAGAAATAAAATC
* *
228622 GGGGTTGGAGTATCCTCTCG-GAAATAACGGGGTTGGAGTATCCTCGATTGT-GAAAAGTCGGTG
1 GGGGTTGGAGTATCC-C-CGTGAAATAACGGGGTTGGAGTATCCCCGATTGTGGAAAA-TTGGTG
*
228685 TTTTGGAAATAAAATC
63 TTTTAGAAATAAAATC
**
228701 GAAGTTGGAGTATCCCCG
1 GGGGTTGGAGTATCCCCG
228719 ATTATGAAAA
Statistics
Matches: 148, Mismatches: 22, Indels: 14
0.80 0.12 0.08
Matches are distributed among these distances:
77 3 0.02
78 6 0.04
79 136 0.92
80 2 0.01
81 1 0.01
ACGTcount: A:0.30, C:0.13, G:0.29, T:0.28
Consensus pattern (78 bp):
GGGGTTGGAGTATCCCCGTGAAATAACGGGGTTGGAGTATCCCCGATTGTGGAAAATTGGTGTTT
TAGAAATAAAATC
Found at i:228714 original size:51 final size:50
Alignment explanation
Indices: 228653--228780 Score: 175
Period size: 51 Copynumber: 2.5 Consensus size: 50
228643 AAATAACGGG
* * * *
228653 GTTGGAGTATCCTCGATTGTGAAAAGTCGGTGTTTTGGAAATAAAATCGAA
1 GTTGGAGTATCCCCGATTATGAAAAATCGGTGTTTTAGAAAT-AAATCGAA
* *
228704 GTTGGAGTATCCCCGATTATGAAAAATGGGTGTTTTAGAAATAAATCGGA
1 GTTGGAGTATCCCCGATTATGAAAAATCGGTGTTTTAGAAATAAATCGAA
* *
228754 GTCGGAGTATCCCCGATTAAGAAAAAT
1 GTTGGAGTATCCCCGATTATGAAAAAT
228781 TGAGAAACTT
Statistics
Matches: 69, Mismatches: 8, Indels: 1
0.88 0.10 0.01
Matches are distributed among these distances:
50 32 0.46
51 37 0.54
ACGTcount: A:0.34, C:0.12, G:0.26, T:0.29
Consensus pattern (50 bp):
GTTGGAGTATCCCCGATTATGAAAAATCGGTGTTTTAGAAATAAATCGAA
Found at i:231241 original size:19 final size:19
Alignment explanation
Indices: 231217--231267 Score: 93
Period size: 19 Copynumber: 2.7 Consensus size: 19
231207 AGCGATACGT
231217 TGTATCGATACAACACTTA
1 TGTATCGATACAACACTTA
*
231236 TGTATCGATACAACACTTC
1 TGTATCGATACAACACTTA
231255 TGTATCGATACAA
1 TGTATCGATACAA
231268 ATCGTTGAAA
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
19 31 1.00
ACGTcount: A:0.35, C:0.22, G:0.12, T:0.31
Consensus pattern (19 bp):
TGTATCGATACAACACTTA
Found at i:231781 original size:28 final size:29
Alignment explanation
Indices: 231740--231799 Score: 77
Period size: 28 Copynumber: 2.1 Consensus size: 29
231730 TCCAACCTAA
* **
231740 TTGGCTCAAAAGCATATAGTAACAATACC
1 TTGGCTCAAAAGCAAATACCAACAATACC
*
231769 TTGG-TCAAAAGCAAATACCAACAATAGC
1 TTGGCTCAAAAGCAAATACCAACAATACC
231797 TTG
1 TTG
231800 TTTCTAGCTT
Statistics
Matches: 27, Mismatches: 4, Indels: 1
0.84 0.12 0.03
Matches are distributed among these distances:
28 23 0.85
29 4 0.15
ACGTcount: A:0.42, C:0.20, G:0.15, T:0.23
Consensus pattern (29 bp):
TTGGCTCAAAAGCAAATACCAACAATACC
Found at i:234150 original size:18 final size:19
Alignment explanation
Indices: 234127--234165 Score: 53
Period size: 21 Copynumber: 2.0 Consensus size: 19
234117 TTAAATTTTT
234127 ATAATTT-GTATCGATACA
1 ATAATTTAGTATCGATACA
234145 ATAATTTAAGGTATCGATACA
1 ATAATTT-A-GTATCGATACA
234166 TAAGTGAATG
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
18 7 0.39
21 11 0.61
ACGTcount: A:0.41, C:0.10, G:0.13, T:0.36
Consensus pattern (19 bp):
ATAATTTAGTATCGATACA
Found at i:234160 original size:21 final size:21
Alignment explanation
Indices: 234133--234204 Score: 101
Period size: 21 Copynumber: 3.5 Consensus size: 21
234123 TTTTATAATT
* *
234133 TGTATCGATACAATAATTTAA
1 TGTATCGATACAATAAGTGAA
*
234154 GGTATCGATAC-ATAAGTGAA
1 TGTATCGATACAATAAGTGAA
*
234174 TGTATCGATACATTAAGTGAA
1 TGTATCGATACAATAAGTGAA
234195 TGTATCGATA
1 TGTATCGATA
234205 TTGGACCATG
Statistics
Matches: 45, Mismatches: 5, Indels: 2
0.87 0.10 0.04
Matches are distributed among these distances:
20 17 0.38
21 28 0.62
ACGTcount: A:0.39, C:0.10, G:0.18, T:0.33
Consensus pattern (21 bp):
TGTATCGATACAATAAGTGAA
Found at i:234393 original size:42 final size:42
Alignment explanation
Indices: 234328--234699 Score: 367
Period size: 42 Copynumber: 8.9 Consensus size: 42
234318 CAGGACAAAG
* * *
234328 GGAAA-AAGAGTGCGTCCAGCTCTTCGGGGACAAAAGAAAAAA
1 GGAAATAA-AGTGCGTCCTGCTCTTTGAGGACAAAAGAAAAAA
* * *
234370 GAAAATAAAGTGTGTCCTGCTCTTTGAGGACAAAGGAAAAGAA
1 GGAAATAAAGTGCGTCCTGCTCTTTGAGGACAAAAGAAAA-AA
* *
234413 GGAAATAAAGTGCATCCTACTCTTTGAGGACAAAA-AAGAAAA
1 GGAAATAAAGTGCGTCCTGCTCTTTGAGGACAAAAGAA-AAAA
* * * *
234455 GGAAATAAAGTACGTCTTGCCCTTCGAGGACAAAAG-AAAAA
1 GGAAATAAAGTGCGTCCTGCTCTTTGAGGACAAAAGAAAAAA
* * * *
234496 GGAAATAAAGTGTGTCTTGCTATTTGAGGACAAAAGAGAAAA
1 GGAAATAAAGTGCGTCCTGCTCTTTGAGGACAAAAGAAAAAA
* * * * *
234538 GGAAATAAAGTACGTCATGCTCTTTGAGGATAAATGAGAAAA
1 GGAAATAAAGTGCGTCCTGCTCTTTGAGGACAAAAGAAAAAA
* ** * * * *
234580 GGAAATAAAATATGTCTTGCTTTTTGAGGACAAAGGAGAAAA
1 GGAAATAAAGTGCGTCCTGCTCTTTGAGGACAAAAGAAAAAA
* * *
234622 GGAAATAAAGT-CATCCTGCTCTTGGAGGACAAAGGAGAAAAA
1 GGAAATAAAGTGCGTCCTGCTCTTTGAGGACAAAAGA-AAAAA
* *
234664 -GAAATAAAGTGTGTCCCGCTCTTTGAGGACTAAAAG
1 GGAAATAAAGTGCGTCCTGCTCTTTGAGGAC-AAAAG
234700 GTGCCACCAA
Statistics
Matches: 275, Mismatches: 47, Indels: 15
0.82 0.14 0.04
Matches are distributed among these distances:
41 65 0.24
42 170 0.62
43 40 0.15
ACGTcount: A:0.42, C:0.13, G:0.24, T:0.20
Consensus pattern (42 bp):
GGAAATAAAGTGCGTCCTGCTCTTTGAGGACAAAAGAAAAAA
Found at i:234536 original size:83 final size:83
Alignment explanation
Indices: 234328--234699 Score: 399
Period size: 83 Copynumber: 4.4 Consensus size: 83
234318 CAGGACAAAG
* * * * * * **
234328 GGAAA-AAGAGTGCGTCCAGCTCTTCGGGGACAAAAGAAAAAAGAAAATAAAGTGTGTCCTGCTC
1 GGAAATAA-AGTGTGTCCTGCTCTTTGAGGACAAAAGAGAAAAGGAAATAAAGTACGTCCTGCTC
*
234392 TTTGAGGACAAAGGAAAAGAA
65 TTTGAGGACAAAAG-AAA-AA
** * * * *
234413 GGAAATAAAGTGCATCCTACTCTTTGAGGACAAAAAAGAAAAGGAAATAAAGTACGTCTTGCCCT
1 GGAAATAAAGTGTGTCCTGCTCTTTGAGGACAAAAGAGAAAAGGAAATAAAGTACGTCCTGCTCT
*
234478 TCGAGGACAAAAGAAAAA
66 TTGAGGACAAAAGAAAAA
* * *
234496 GGAAATAAAGTGTGTCTTGCTATTTGAGGACAAAAGAGAAAAGGAAATAAAGTACGTCATGCTCT
1 GGAAATAAAGTGTGTCCTGCTCTTTGAGGACAAAAGAGAAAAGGAAATAAAGTACGTCCTGCTCT
* *
234561 TTGAGGATAAATGAGAAAA
66 TTGAGGACAAAAGA-AAAA
* * * * * *
234580 GGAAATAAAATATGTCTTGCTTTTTGAGGACAAAGGAGAAAAGGAAATAAAGT-CATCCTGCTCT
1 GGAAATAAAGTGTGTCCTGCTCTTTGAGGACAAAAGAGAAAAGGAAATAAAGTACGTCCTGCTCT
*
234644 TGGAGGACAAAGGAGAAAAA
66 TTGAGGACAAA--AGAAAAA
*
234664 -GAAATAAAGTGTGTCCCGCTCTTTGAGGACTAAAAG
1 GGAAATAAAGTGTGTCCTGCTCTTTGAGGAC-AAAAG
234700 GTGCCACCAA
Statistics
Matches: 242, Mismatches: 40, Indels: 11
0.83 0.14 0.04
Matches are distributed among these distances:
83 113 0.47
84 64 0.26
85 63 0.26
86 2 0.01
ACGTcount: A:0.42, C:0.13, G:0.24, T:0.20
Consensus pattern (83 bp):
GGAAATAAAGTGTGTCCTGCTCTTTGAGGACAAAAGAGAAAAGGAAATAAAGTACGTCCTGCTCT
TTGAGGACAAAAGAAAAA
Found at i:234581 original size:125 final size:125
Alignment explanation
Indices: 234349--234698 Score: 432
Period size: 125 Copynumber: 2.8 Consensus size: 125
234339 GCGTCCAGCT
* * *
234349 CTTCGGGGACAAAAGAAAAAAGAAAATAAAGTGTGTCCTGCTCTTTGAGGACAAAGGAAAAGAAG
1 CTTCGAGGACAAAAG-AAAAAGGAAATAAAGTGTGTCCTGCTCTTTGAGGACAAAGGAGAA-AAG
* * * *
234414 GAAATAAAGTGCATCCTACTCTTTGAGGACAAAAAAGAAAAGGAAATAAAGTACGTCTTGCC
64 GAAATAAAGTGCGTCCTGCTCTTTGAGGATAAAAAAGAAAAGGAAATAAAATACGTCTTGCC
* * *
234476 CTTCGAGGACAAAAGAAAAAGGAAATAAAGTGTGTCTTGCTATTTGAGGACAAAAGAGAAAAGGA
1 CTTCGAGGACAAAAGAAAAAGGAAATAAAGTGTGTCCTGCTCTTTGAGGACAAAGGAGAAAAGGA
* * ** * *
234541 AATAAAGTACGTCATGCTCTTTGAGGATAAATGAGAAAAGGAAATAAAATATGTCTTGCT
66 AATAAAGTGCGTCCTGCTCTTTGAGGATAAAAAAGAAAAGGAAATAAAATACGTCTTGCC
* * * ** * *
234601 TTTTGAGGACAAAGGAGAAAAGGAAATAAAGT-CATCCTGCTCTTGGAGGACAAAGGAGAAAAAG
1 CTTCGAGGACAAAAGA-AAAAGGAAATAAAGTGTGTCCTGCTCTTTGAGGACAAAGGAGAAAAGG
* *
234665 AAATAAAGTGTGTCCCGCTCTTTGAGGACTAAAA
65 AAATAAAGTGCGTCCTGCTCTTTGAGGA-TAAAA
234699 GGTGCCACCA
Statistics
Matches: 190, Mismatches: 31, Indels: 5
0.84 0.14 0.02
Matches are distributed among these distances:
125 117 0.62
126 59 0.31
127 14 0.07
ACGTcount: A:0.43, C:0.12, G:0.24, T:0.21
Consensus pattern (125 bp):
CTTCGAGGACAAAAGAAAAAGGAAATAAAGTGTGTCCTGCTCTTTGAGGACAAAGGAGAAAAGGA
AATAAAGTGCGTCCTGCTCTTTGAGGATAAAAAAGAAAAGGAAATAAAATACGTCTTGCC
Found at i:234823 original size:62 final size:62
Alignment explanation
Indices: 234681--235012 Score: 403
Period size: 62 Copynumber: 5.3 Consensus size: 62
234671 AGTGTGTCCC
* * * ** *
234681 GCTCTTTGAGGACTAAAAGGTGCCACCAACTTGTGTGGACTTTAAAAAAAGAAAAAAATGTCTT
1 GCTCTTTGAGGACTAAAAGGTGCCACCAACTCGTGTGGGCTTT--AAAAAGAAAAAGACATCCT
* * * *
234745 GCACTTTGAGGACTAAAAGGTGCCCCCAACTCGTGTGGGCTTTAAAAAGAAAAAGGCCTCCT
1 GCTCTTTGAGGACTAAAAGGTGCCACCAACTCGTGTGGGCTTTAAAAAGAAAAAGACATCCT
* *
234807 GCTCTTTGAGGACTAAAAGGTGCCACCAATTTGTGTGGGCTTTAAAAAAAGAAAAAGACATCCT
1 GCTCTTTGAGGACTAAAAGGTGCCACCAACTCGTGTGGGCTTT--AAAAAGAAAAAGACATCCT
* * * * * *
234871 GCTCTTTGAGGACTAAAAGGTGCCACCAACTCGTCTAGACTTTAAAATGAAAAAGACAACTT
1 GCTCTTTGAGGACTAAAAGGTGCCACCAACTCGTGTGGGCTTTAAAAAGAAAAAGACATCCT
* * * * * * *
234933 ACTCTTTGAGAACTAAAGGGTGCCACCAACTCGCGTCGGCTTTAAAAAGAAAAAGACGTTCT
1 GCTCTTTGAGGACTAAAAGGTGCCACCAACTCGTGTGGGCTTTAAAAAGAAAAAGACATCCT
234995 GCTCTTTGAGGACTAAAA
1 GCTCTTTGAGGACTAAAA
235013 AGATAAAAGG
Statistics
Matches: 228, Mismatches: 38, Indels: 6
0.84 0.14 0.02
Matches are distributed among these distances:
62 134 0.59
64 94 0.41
ACGTcount: A:0.35, C:0.20, G:0.21, T:0.24
Consensus pattern (62 bp):
GCTCTTTGAGGACTAAAAGGTGCCACCAACTCGTGTGGGCTTTAAAAAGAAAAAGACATCCT
Found at i:234914 original size:126 final size:126
Alignment explanation
Indices: 234681--235012 Score: 443
Period size: 126 Copynumber: 2.7 Consensus size: 126
234671 AGTGTGTCCC
* * * *
234681 GCTCTTTGAGGACTAAAAGGTGCCACCAACTTGTGTGGACTTTAAAAAAAGAAAAAAATGTCTTG
1 GCTCTTTGAGGACTAAAAGGTGCCACCAACTTGTGTGGGCTTTAAAAAAAGAAAAAGACGTCCTG
* * * * * * **
234746 CACTTTGAGGACTAAAAGGTGCCCCCAACTCGTGTGGGCTTTAAAAAGAAAAAGGCCTCCT
66 CTCTTTGAGGACTAAAAGGTGCCACCAACTCGTCTAGACTTTAAAAAGAAAAAGACAACCT
* *
234807 GCTCTTTGAGGACTAAAAGGTGCCACCAATTTGTGTGGGCTTTAAAAAAAGAAAAAGACATCCTG
1 GCTCTTTGAGGACTAAAAGGTGCCACCAACTTGTGTGGGCTTTAAAAAAAGAAAAAGACGTCCTG
* *
234872 CTCTTTGAGGACTAAAAGGTGCCACCAACTCGTCTAGACTTTAAAATGAAAAAGACAACTT
66 CTCTTTGAGGACTAAAAGGTGCCACCAACTCGTCTAGACTTTAAAAAGAAAAAGACAACCT
* * * * * * *
234933 ACTCTTTGAGAACTAAAGGGTGCCACCAACTCGCGTCGGCTTT--AAAAAGAAAAAGACGTTCTG
1 GCTCTTTGAGGACTAAAAGGTGCCACCAACTTGTGTGGGCTTTAAAAAAAGAAAAAGACGTCCTG
234996 CTCTTTGAGGACTAAAA
66 CTCTTTGAGGACTAAAA
235013 AGATAAAAGG
Statistics
Matches: 181, Mismatches: 25, Indels: 2
0.87 0.12 0.01
Matches are distributed among these distances:
124 35 0.19
126 146 0.81
ACGTcount: A:0.35, C:0.20, G:0.21, T:0.24
Consensus pattern (126 bp):
GCTCTTTGAGGACTAAAAGGTGCCACCAACTTGTGTGGGCTTTAAAAAAAGAAAAAGACGTCCTG
CTCTTTGAGGACTAAAAGGTGCCACCAACTCGTCTAGACTTTAAAAAGAAAAAGACAACCT
Found at i:241059 original size:51 final size:50
Alignment explanation
Indices: 240982--241098 Score: 180
Period size: 51 Copynumber: 2.3 Consensus size: 50
240972 CGAAAACAAC
* * *
240982 AGGGTTGAAGTATCCTCGATGGTGAAAATTTGATATTTTGGAAATAAAAAT
1 AGGGTTGGAGTATCCCCGATGGTGAAAAGTTGATATTTTGGAAAT-AAAAT
*
241033 GGGGTTGGAGTATCCCCGATGGTGAAAAGTTGATATTTTGGAAATAAAAT
1 AGGGTTGGAGTATCCCCGATGGTGAAAAGTTGATATTTTGGAAATAAAAT
*
241083 AGGGTTAGAGTATCCC
1 AGGGTTGGAGTATCCC
241099 TTCAAAAATA
Statistics
Matches: 60, Mismatches: 6, Indels: 1
0.90 0.09 0.01
Matches are distributed among these distances:
50 19 0.32
51 41 0.68
ACGTcount: A:0.33, C:0.09, G:0.27, T:0.31
Consensus pattern (50 bp):
AGGGTTGGAGTATCCCCGATGGTGAAAAGTTGATATTTTGGAAATAAAAT
Found at i:241178 original size:56 final size:57
Alignment explanation
Indices: 241084--241190 Score: 153
Period size: 56 Copynumber: 1.9 Consensus size: 57
241074 AAATAAAATA
* * * *
241084 GGGTTAGAGTATCCCTTCAAAAATAATAGGGTTAGAGTATCCTCGATGGTGAAATTG
1 GGGTTAGAGTATCCCTTAAAAAATAACAGGGTTAGAGTATCCCCGAAGGTGAAATTG
* *
241141 GGGTTGGAGTATCCC-TAAAAAATAACAGGGTTGGAGTATCCCCGAAGGTG
1 GGGTTAGAGTATCCCTTAAAAAATAACAGGGTTAGAGTATCCCCGAAGGTG
241191 GAAAATCGGT
Statistics
Matches: 44, Mismatches: 6, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
56 30 0.68
57 14 0.32
ACGTcount: A:0.31, C:0.14, G:0.29, T:0.26
Consensus pattern (57 bp):
GGGTTAGAGTATCCCTTAAAAAATAACAGGGTTAGAGTATCCCCGAAGGTGAAATTG
Found at i:241262 original size:79 final size:79
Alignment explanation
Indices: 241135--241547 Score: 419
Period size: 79 Copynumber: 5.3 Consensus size: 79
241125 CTCGATGGTG
* *
241135 AAATTGGGGTTGGAGTAT-CCCTAAAAAATAAC-AGGGTTGGAGTATCCCCGAAGGTGGAAAATC
1 AAATCGGGGTTGGAGTATCCCCTAAAAAATAACGA-GGTTAGAGTATCCCCGAAGGTGGAAAATC
* * *
241198 GGTATTTTAGAAAAA
65 AGTGTTTTAGAAATA
* * * *
241213 AAATCGGGGTTGGAGTATCCCCTCAAAAATTACGAGGTTAGAGTATCCCCGATGGTGAAAAATCA
1 AAATCGGGGTTGGAGTATCCCCTAAAAAATAACGAGGTTAGAGTATCCCCGAAGGTGGAAAATCA
241278 GTGTTTTAGAAATA
66 GTGTTTTAGAAATA
* * *
241292 AAATCGGGGTTGGAGTAT-CTCTAAAAAATAAC-AGGGTTGGAGTAT-CCCTAATGGTGGAAAAT
1 AAATCGGGGTTGGAGTATCCCCTAAAAAATAACGA-GGTTAGAGTATCCCCGAA-GGTGGAAAAT
241354 C-GATGTTTTAGAAATA
64 CAG-TGTTTTAGAAATA
* * * * * * *
241370 AAA-CTGAGGTTGGAGTATCCCTTCAGAAATAACGGGGTTAGAGTATCCTCGATA-GTAGAAAAT
1 AAATC-GGGGTTGGAGTATCCCCTAAAAAATAACGAGGTTAGAGTATCCCCGA-AGGTGGAAAAT
241433 CAGTGTTTTAGAAATA
64 CAGTGTTTTAGAAATA
* * * * * **** * * * *
241449 AAACCGGAGTTAGAGTATACCTTTGGCAATAACGGGGTTAGAGTATCCTCGATGGTAGAAAATCA
1 AAATCGGGGTTGGAGTATCCCCTAAAAAATAACGAGGTTAGAGTATCCCCGAAGGTGGAAAATCA
241514 GTGTTTTAGAAATA
66 GTGTTTTAGAAATA
*
241528 AAATCGGGGTTGAAGTATCC
1 AAATCGGGGTTGGAGTATCC
241548 TAATGGTAGA
Statistics
Matches: 283, Mismatches: 39, Indels: 25
0.82 0.11 0.07
Matches are distributed among these distances:
77 7 0.02
78 76 0.27
79 193 0.68
80 6 0.02
81 1 0.00
ACGTcount: A:0.35, C:0.13, G:0.25, T:0.27
Consensus pattern (79 bp):
AAATCGGGGTTGGAGTATCCCCTAAAAAATAACGAGGTTAGAGTATCCCCGAAGGTGGAAAATCA
GTGTTTTAGAAATA
Found at i:241432 original size:157 final size:157
Alignment explanation
Indices: 241135--241547 Score: 483
Period size: 157 Copynumber: 2.6 Consensus size: 157
241125 CTCGATGGTG
* *
241135 AAATTGGGGTTGGAGTATCCCTAAAAAATAACAGGGTTGGAGTATCCCCGAAGGTGGAAAATCGG
1 AAATCGGGGTTGGAGTATCCCTAAAAAATAACAGGGTTGGAGTATCCCCGAAGGTGGAAAATCGA
* *
241200 TATTTTAGAAAAAAAATCGGGGTTGGAGTATCCCCTCAAAAATTACGAGGTTAGAGTATCCCCGA
66 TATTTTAGAAAAAAAATCGAGGTTGGAGTATCCCCTCAAAAATAACGAGGTTAGAGTATCCCCGA
*
241265 TGGTGAAAAATCAGTGTTTTAGAAATA
131 TAGTGAAAAATCAGTGTTTTAGAAATA
* *
241292 AAATCGGGGTTGGAGTATCTCTAAAAAATAACAGGGTTGGAGTAT-CCCTAATGGTGGAAAATCG
1 AAATCGGGGTTGGAGTATCCCTAAAAAATAACAGGGTTGGAGTATCCCCGAA-GGTGGAAAATCG
* * * * * *
241356 ATGTTTTAGAAATAAAA-CTGAGGTTGGAGTATCCCTTCAGAAATAACGGGGTTAGAGTATCCTC
65 ATATTTTAGAAAAAAAATC-GAGGTTGGAGTATCCCCTCAAAAATAACGAGGTTAGAGTATCCCC
241420 GATAGT-AGAAAATCAGTGTTTTAGAAATA
129 GATAGTGA-AAAATCAGTGTTTTAGAAATA
* * * * **** * * * * *
241449 AAACCGGAGTTAGAGTATACCTTTGGCAATAACGGGGTTAGAGTATCCTCGATGGTAGAAAATC-
1 AAATCGGGGTTGGAGTAT-CCCTAAAAAATAACAGGGTTGGAGTATCCCCGAAGGTGGAAAATCG
* * * *
241513 AGTGTTTTAGAAATAAAATCGGGGTTGAAGTATCC
65 A-TATTTTAGAAAAAAAATCGAGGTTGGAGTATCC
241548 TAATGGTAGA
Statistics
Matches: 219, Mismatches: 30, Indels: 13
0.84 0.11 0.05
Matches are distributed among these distances:
156 7 0.03
157 150 0.68
158 58 0.26
159 4 0.02
ACGTcount: A:0.35, C:0.13, G:0.25, T:0.27
Consensus pattern (157 bp):
AAATCGGGGTTGGAGTATCCCTAAAAAATAACAGGGTTGGAGTATCCCCGAAGGTGGAAAATCGA
TATTTTAGAAAAAAAATCGAGGTTGGAGTATCCCCTCAAAAATAACGAGGTTAGAGTATCCCCGA
TAGTGAAAAATCAGTGTTTTAGAAATA
Found at i:241568 original size:50 final size:51
Alignment explanation
Indices: 241481--241589 Score: 168
Period size: 50 Copynumber: 2.2 Consensus size: 51
241471 TTGGCAATAA
* *
241481 CGGGGTTAGAGTATCCTCGATGGTAGAAAATCAGTGTTTTAGAAATAAAAT
1 CGGGGTTAGAGTATCCTCAATGGTAGAAAATCAGTGTTTTAGAAATAAAAC
*
241532 CGGGGTT-GAAGTATCCT-AATGGTAGAAAATCTGTGTTTTAGAAATAAAAC
1 CGGGGTTAG-AGTATCCTCAATGGTAGAAAATCAGTGTTTTAGAAATAAAAC
241582 CGGGGTTA
1 CGGGGTTA
241590 CATGGAGACA
Statistics
Matches: 53, Mismatches: 3, Indels: 4
0.88 0.05 0.07
Matches are distributed among these distances:
50 38 0.72
51 15 0.28
ACGTcount: A:0.34, C:0.10, G:0.27, T:0.29
Consensus pattern (51 bp):
CGGGGTTAGAGTATCCTCAATGGTAGAAAATCAGTGTTTTAGAAATAAAAC
Found at i:243902 original size:20 final size:20
Alignment explanation
Indices: 243879--243919 Score: 64
Period size: 20 Copynumber: 2.0 Consensus size: 20
243869 ACAATGAGAA
*
243879 ATGTATCAATACATTTTCTT
1 ATGTATCAATACATTTCCTT
*
243899 ATGTATCGATACATTTCCTT
1 ATGTATCAATACATTTCCTT
243919 A
1 A
243920 GCAGTATGCA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.29, C:0.17, G:0.07, T:0.46
Consensus pattern (20 bp):
ATGTATCAATACATTTCCTT
Found at i:243970 original size:21 final size:21
Alignment explanation
Indices: 243941--243994 Score: 74
Period size: 20 Copynumber: 2.6 Consensus size: 21
243931 GGTAGTTTTT
* *
243941 TATCGATACATTTTAGGCATG
1 TATCAATACATTTTACGCATG
*
243962 TATCAATACA-TTTACTCATG
1 TATCAATACATTTTACGCATG
243982 TATCAATACATTT
1 TATCAATACATTT
243995 ACTGTTTGTA
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
20 18 0.62
21 11 0.38
ACGTcount: A:0.33, C:0.17, G:0.09, T:0.41
Consensus pattern (21 bp):
TATCAATACATTTTACGCATG
Found at i:244012 original size:21 final size:20
Alignment explanation
Indices: 243958--243997 Score: 80
Period size: 20 Copynumber: 2.0 Consensus size: 20
243948 ACATTTTAGG
243958 CATGTATCAATACATTTACT
1 CATGTATCAATACATTTACT
243978 CATGTATCAATACATTTACT
1 CATGTATCAATACATTTACT
243998 GTTTGTATCG
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.35, C:0.20, G:0.05, T:0.40
Consensus pattern (20 bp):
CATGTATCAATACATTTACT
Found at i:247739 original size:33 final size:33
Alignment explanation
Indices: 247677--247739 Score: 81
Period size: 33 Copynumber: 1.9 Consensus size: 33
247667 TATCATTGTT
* * * *
247677 TGTATCGATACATGGGACATTGTATCGATATAA
1 TGTATCGATACATAGGAAAATGTACCGATATAA
*
247710 TGTATCGATACATAGTAAAATGTACCGATA
1 TGTATCGATACATAGGAAAATGTACCGATA
247740 CATTGTGCCC
Statistics
Matches: 25, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
33 25 1.00
ACGTcount: A:0.37, C:0.13, G:0.19, T:0.32
Consensus pattern (33 bp):
TGTATCGATACATAGGAAAATGTACCGATATAA
Found at i:252731 original size:16 final size:16
Alignment explanation
Indices: 252710--252742 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 16
252700 AGATATCTTT
*
252710 TTAAGGGGGAGTTTTA
1 TTAAGGAGGAGTTTTA
252726 TTAAGGAGGAGTTTTA
1 TTAAGGAGGAGTTTTA
252742 T
1 T
252743 ATATTGAAAA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.27, C:0.00, G:0.33, T:0.39
Consensus pattern (16 bp):
TTAAGGAGGAGTTTTA
Found at i:253428 original size:20 final size:20
Alignment explanation
Indices: 253403--253440 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
253393 GATATTGTTC
*
253403 ATTGTATCGATACATGAAGA
1 ATTGTATCAATACATGAAGA
253423 ATTGTATCAATACATGAA
1 ATTGTATCAATACATGAA
253441 ACTAGCAGTA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.42, C:0.11, G:0.16, T:0.32
Consensus pattern (20 bp):
ATTGTATCAATACATGAAGA
Found at i:254979 original size:208 final size:209
Alignment explanation
Indices: 254621--255038 Score: 820
Period size: 208 Copynumber: 2.0 Consensus size: 209
254611 TTTCAACCAT
254621 GCAAAAAGACTCACTATTGTTGGTGGGACTTAGAGTTCCTAATAATTGCCAAAACTAGTAATTTC
1 GCAAAAAGACTCACTATTGTTGGTGGGACTTAGAGTTCCTAATAATTGCCAAAACTAGTAATTTC
254686 ACTGTCTTAAAACATTTCTATCTTTTATATACTATATATAGTGAGAGTAATTGAGTTTATTATCA
66 ACTGTCTTAAAACATTTCTATCTTTTATATACTATATATAGTGAGAGTAATTGAGTTTATTATCA
*
254751 CTCCCAACTTACTAAATACAAGTGAGTTTGTA-TTTTTTTATAAAAAGTATGTTAAGATCTTGGT
131 CTCCCAACTTACTAAATACAAGTGAGTTTGTATTTTTTTTATAAAAAGTATGTTAAGATCTTAGT
254815 TTTGATATAACAAA
196 TTTGATATAACAAA
254829 GCAAAAAGACTCACTATTGTTGGTGGGACTTAGAGTTCCTAATAATTGCCAAAACTAGTAATTTC
1 GCAAAAAGACTCACTATTGTTGGTGGGACTTAGAGTTCCTAATAATTGCCAAAACTAGTAATTTC
254894 ACTGTCTTAAAACATTTCTATCTTTTATATACTATATATAGTGAGAGTAATTGAGTTTATTATCA
66 ACTGTCTTAAAACATTTCTATCTTTTATATACTATATATAGTGAGAGTAATTGAGTTTATTATCA
254959 CTCCCAACTTACTAAATACAAGTGAGTTTGTATTTTTTTTATAAAAAGTATGTTAAGATCTTAGT
131 CTCCCAACTTACTAAATACAAGTGAGTTTGTATTTTTTTTATAAAAAGTATGTTAAGATCTTAGT
255024 TTTGATATAACAAA
196 TTTGATATAACAAA
255038 G
1 G
255039 TATAAATAAA
Statistics
Matches: 208, Mismatches: 1, Indels: 1
0.99 0.00 0.00
Matches are distributed among these distances:
208 162 0.78
209 46 0.22
ACGTcount: A:0.35, C:0.13, G:0.14, T:0.39
Consensus pattern (209 bp):
GCAAAAAGACTCACTATTGTTGGTGGGACTTAGAGTTCCTAATAATTGCCAAAACTAGTAATTTC
ACTGTCTTAAAACATTTCTATCTTTTATATACTATATATAGTGAGAGTAATTGAGTTTATTATCA
CTCCCAACTTACTAAATACAAGTGAGTTTGTATTTTTTTTATAAAAAGTATGTTAAGATCTTAGT
TTTGATATAACAAA
Found at i:255600 original size:316 final size:318
Alignment explanation
Indices: 255009--255643 Score: 815
Period size: 316 Copynumber: 2.0 Consensus size: 318
254999 ATAAAAAGTA
* *
255009 TGTTAAGATCTTAGTTTTGATATAACAAAGTATAAATAAATCTGAAAAATACTTTGAAAAACTTT
1 TGTTAAGATCTTAGTTTTGATATAACAAAGTATAAATAAATCTGAAAAATACTTTGAAAAACGTA
* * * * *
255074 AATAAGTTTTATTCACTTAAAAACACTCTAAAACCTTGCTCAAAATGATTTCAATATCAAAAATG
66 AACAAATTTTATTCACTCAAAAACACTCTAAAAACATGCTCAAAATGATTTCAATATCAAAAATG
* * *
255139 TTTTAGAGTTAAAGTATAGATGTTTTTCAAGCAATAAATCAAATGTTTTCAAGTAAAAATAATTC
131 TTTTAGAGTTAAAG-ACAAATGTTTTTCAAGCAATAAATCAAATATTTTCAAGTAAAAATAATTC
*
255204 AAAGTATCGATATATAGGTATTTGTATCGATACATAAAGGTTGACTTAAGCTACAAAGGTCAAAA
195 AAAGTATCGATACATAGGTATTTGTATCGATACATAAAGGTTGACTTAAGCTACAAAGGTCAAAA
*
255269 CCCTAGAAAGTATCGATGCACACCCAGATGTATCGATACA-TATTGCTTAGTATCGATAC
260 CCCTAGAAAGTATCGATACACACCCAGATGTATCGATACATTA-TGCTTAGTATCGATAC
* *
255328 TGTTAGGATCTTAGTTTTGATATAACAAAG-ATTGAATAAAATC-GAAAAATA-TTTGAAAAACC
1 TGTTAAGATCTTAGTTTTGATATAACAAAGTA-TAAAT-AAATCTGAAAAATACTTTGAAAAA-C
* * * ** * *
255390 GTAAACAAATTTTGTTCGCTCAAAAACACTCTAAAAACATGTTTTAAGT-A-TTCTATATCAATG
63 GTAAACAAATTTTATTCACTCAAAAACACTCTAAAAACATGCTCAAAATGATTTCAATATCAA--
* ** *
255453 AAA-GTTTTAGAGTTATAA-ACAAATGTTTTTGAA-CCTTAATTCAAATATTTAT-AAGTAAAAA
126 AAATGTTTTAGAGTTA-AAGACAAATGTTTTTCAAGCAATAAATCAAATATTT-TCAAGTAAAAA
* * *
255514 T-ATATCAAAGTATCGATACATAGGTATTTGTATCGATACATTATGGTTGACTTAAGCTATAAAG
189 TAAT-TCAAAGTATCGATACATAGGTATTTGTATCGATACATAAAGGTTGACTTAAGCTACAAAG
* * * *
255578 GTCAAAACCCTTGAATGTATCGATACACACCCAGATGTATCGATTCATTATGCTTTGTATCGATA
253 GTCAAAACCCTAGAAAGTATCGATACACACCCAGATGTATCGATACATTATGCTTAGTATCGATA
255643 C
318 C
255644 ATTATATCGA
Statistics
Matches: 275, Mismatches: 32, Indels: 21
0.84 0.10 0.06
Matches are distributed among these distances:
315 2 0.01
316 137 0.50
317 25 0.09
318 23 0.08
319 83 0.30
320 5 0.02
ACGTcount: A:0.40, C:0.13, G:0.13, T:0.34
Consensus pattern (318 bp):
TGTTAAGATCTTAGTTTTGATATAACAAAGTATAAATAAATCTGAAAAATACTTTGAAAAACGTA
AACAAATTTTATTCACTCAAAAACACTCTAAAAACATGCTCAAAATGATTTCAATATCAAAAATG
TTTTAGAGTTAAAGACAAATGTTTTTCAAGCAATAAATCAAATATTTTCAAGTAAAAATAATTCA
AAGTATCGATACATAGGTATTTGTATCGATACATAAAGGTTGACTTAAGCTACAAAGGTCAAAAC
CCTAGAAAGTATCGATACACACCCAGATGTATCGATACATTATGCTTAGTATCGATAC
Found at i:255743 original size:13 final size:13
Alignment explanation
Indices: 255725--255754 Score: 60
Period size: 13 Copynumber: 2.3 Consensus size: 13
255715 GATACATGGC
255725 ACATTGTATCGAT
1 ACATTGTATCGAT
255738 ACATTGTATCGAT
1 ACATTGTATCGAT
255751 ACAT
1 ACAT
255755 GATGAATTAA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 17 1.00
ACGTcount: A:0.33, C:0.17, G:0.13, T:0.37
Consensus pattern (13 bp):
ACATTGTATCGAT
Found at i:263829 original size:20 final size:19
Alignment explanation
Indices: 263783--263839 Score: 78
Period size: 19 Copynumber: 2.9 Consensus size: 19
263773 TTGTATCGAT
*
263783 ACATTATATCGATACATGC
1 ACATTGTATCGATACATGC
* *
263802 TCATTGTATCGATACATGG
1 ACATTGTATCGATACATGC
263821 ACAATTGTATCGATACATG
1 AC-ATTGTATCGATACATG
263840 AAACTAGCAG
Statistics
Matches: 33, Mismatches: 4, Indels: 1
0.87 0.11 0.03
Matches are distributed among these distances:
19 17 0.52
20 16 0.48
ACGTcount: A:0.33, C:0.18, G:0.16, T:0.33
Consensus pattern (19 bp):
ACATTGTATCGATACATGC
Found at i:263903 original size:13 final size:13
Alignment explanation
Indices: 263885--263911 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
263875 GATATATGGC
263885 ACATTGTATCGAT
1 ACATTGTATCGAT
263898 ACATTGTATCGAT
1 ACATTGTATCGAT
263911 A
1 A
263912 TATGATGAAT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.33, C:0.15, G:0.15, T:0.37
Consensus pattern (13 bp):
ACATTGTATCGAT
Found at i:263910 original size:33 final size:32
Alignment explanation
Indices: 263868--263936 Score: 95
Period size: 33 Copynumber: 2.1 Consensus size: 32
263858 CTGCCACTAT
*
263868 TTGTATCGATATATG-GCACATTGTATCGATACA
1 TTGTATCGATATATGAG-A-ATTATATCGATACA
263901 TTGTATCGATATATGATGAATTATATCGATACA
1 TTGTATCGATATATGA-GAATTATATCGATACA
263934 TTG
1 TTG
263937 CTTCAAACGG
Statistics
Matches: 33, Mismatches: 1, Indels: 4
0.87 0.03 0.11
Matches are distributed among these distances:
33 31 0.94
34 1 0.03
35 1 0.03
ACGTcount: A:0.32, C:0.12, G:0.17, T:0.39
Consensus pattern (32 bp):
TTGTATCGATATATGAGAATTATATCGATACA
Found at i:266209 original size:13 final size:13
Alignment explanation
Indices: 266191--266216 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
266181 TACACAAAGT
266191 ATGTATCGATACA
1 ATGTATCGATACA
266204 ATGTATCGATACA
1 ATGTATCGATACA
266217 CAAAAAATTG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:266214 original size:32 final size:33
Alignment explanation
Indices: 266173--266236 Score: 103
Period size: 32 Copynumber: 2.0 Consensus size: 33
266163 TAGCCAAACT
**
266173 TGTATCGATACACAAAGTA-TGTATCGATACAA
1 TGTATCGATACACAAAAAATTGTATCGATACAA
266205 TGTATCGATACACAAAAAATTGTATCGATACA
1 TGTATCGATACACAAAAAATTGTATCGATACA
266237 TTGGCTTGTA
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
32 17 0.59
33 12 0.41
ACGTcount: A:0.42, C:0.16, G:0.14, T:0.28
Consensus pattern (33 bp):
TGTATCGATACACAAAAAATTGTATCGATACAA
Found at i:270315 original size:15 final size:15
Alignment explanation
Indices: 270295--270325 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
270285 TAAAAATGTC
*
270295 CAAAATGAGGAAGCT
1 CAAAATGAAGAAGCT
270310 CAAAATGAAGAAGCT
1 CAAAATGAAGAAGCT
270325 C
1 C
270326 CAAACGAAAT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.48, C:0.16, G:0.23, T:0.13
Consensus pattern (15 bp):
CAAAATGAAGAAGCT
Found at i:272587 original size:20 final size:20
Alignment explanation
Indices: 272544--272589 Score: 58
Period size: 21 Copynumber: 2.2 Consensus size: 20
272534 AAATCTTTTG
272544 CAAAATACTTGTTTTTCACTT
1 CAAAATACTTGTTTTTCAC-T
*
272565 CAAATTACTTCGTTTTTCA-T
1 CAAAATACTT-GTTTTTCACT
272585 CAAAA
1 CAAAA
272590 CCAGCATCAG
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
20 5 0.23
21 9 0.41
22 8 0.36
ACGTcount: A:0.33, C:0.20, G:0.04, T:0.43
Consensus pattern (20 bp):
CAAAATACTTGTTTTTCACT
Found at i:272906 original size:21 final size:20
Alignment explanation
Indices: 272864--272906 Score: 50
Period size: 20 Copynumber: 2.1 Consensus size: 20
272854 GGCAGCACCA
* *
272864 CCAGGTCGCGACCGGCACTC
1 CCAGGTCACAACCGGCACTC
*
272884 CCAGGTCACAACCAGGCAGTC
1 CCAGGTCACAACC-GGCACTC
272905 CC
1 CC
272907 CACCCTAGTC
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
20 11 0.58
21 8 0.42
ACGTcount: A:0.21, C:0.44, G:0.26, T:0.09
Consensus pattern (20 bp):
CCAGGTCACAACCGGCACTC
Found at i:274085 original size:23 final size:21
Alignment explanation
Indices: 274043--274086 Score: 52
Period size: 23 Copynumber: 2.0 Consensus size: 21
274033 GTTTAATGTT
**
274043 TTTGCTTGACTTTGTGTTTTA
1 TTTGCTTGACTTTGAATTTTA
274064 TTTGCATTGTACTTTGAATTTTA
1 TTTGC-TTG-ACTTTGAATTTTA
274087 ATCTAATATG
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
21 5 0.26
22 3 0.16
23 11 0.58
ACGTcount: A:0.16, C:0.09, G:0.16, T:0.59
Consensus pattern (21 bp):
TTTGCTTGACTTTGAATTTTA
Found at i:274992 original size:13 final size:13
Alignment explanation
Indices: 274974--274999 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
274964 TACACAAAGT
274974 ATGTATCGATACA
1 ATGTATCGATACA
274987 ATGTATCGATACA
1 ATGTATCGATACA
275000 CAAAAATTGT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:274997 original size:32 final size:32
Alignment explanation
Indices: 274956--275018 Score: 101
Period size: 32 Copynumber: 2.0 Consensus size: 32
274946 TAGCCAAACT
*
274956 TGTATCGATACAC-AAAGTATGTATCGATACAA
1 TGTATCGATACACAAAAAT-TGTATCGATACAA
274988 TGTATCGATACACAAAAATTGTATCGATACA
1 TGTATCGATACACAAAAATTGTATCGATACA
275019 TTGGCTTGTA
Statistics
Matches: 29, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
32 25 0.86
33 4 0.14
ACGTcount: A:0.41, C:0.16, G:0.14, T:0.29
Consensus pattern (32 bp):
TGTATCGATACACAAAAATTGTATCGATACAA
Found at i:276010 original size:26 final size:26
Alignment explanation
Indices: 275981--276058 Score: 80
Period size: 23 Copynumber: 3.2 Consensus size: 26
275971 CAAATATGGG
275981 ACAAACTCGCCACAACACATGAAGGC
1 ACAAACTCGCCACAACACATGAAGGC
* *
276007 ACAAA--C-CAAGCAA-ATATG--GG-
1 ACAAACTCGCCA-CAACACATGAAGGC
276027 ACAAACTCGCCACAACACATGAAGGC
1 ACAAACTCGCCACAACACATGAAGGC
276053 ACAAAC
1 ACAAAC
276059 CACGTCAAGG
Statistics
Matches: 40, Mismatches: 4, Indels: 16
0.67 0.07 0.27
Matches are distributed among these distances:
20 5 0.12
21 2 0.05
22 4 0.10
23 12 0.30
24 4 0.10
25 2 0.05
26 11 0.28
ACGTcount: A:0.46, C:0.31, G:0.15, T:0.08
Consensus pattern (26 bp):
ACAAACTCGCCACAACACATGAAGGC
Found at i:276033 original size:46 final size:46
Alignment explanation
Indices: 275966--276060 Score: 190
Period size: 46 Copynumber: 2.1 Consensus size: 46
275956 TGCAATAATG
275966 CCAAGCAAATATGGGACAAACTCGCCACAACACATGAAGGCACAAA
1 CCAAGCAAATATGGGACAAACTCGCCACAACACATGAAGGCACAAA
276012 CCAAGCAAATATGGGACAAACTCGCCACAACACATGAAGGCACAAA
1 CCAAGCAAATATGGGACAAACTCGCCACAACACATGAAGGCACAAA
276058 CCA
1 CCA
276061 CGTCAAGGAA
Statistics
Matches: 49, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
46 49 1.00
ACGTcount: A:0.45, C:0.29, G:0.17, T:0.08
Consensus pattern (46 bp):
CCAAGCAAATATGGGACAAACTCGCCACAACACATGAAGGCACAAA
Found at i:282619 original size:13 final size:13
Alignment explanation
Indices: 282601--282684 Score: 60
Period size: 13 Copynumber: 5.5 Consensus size: 13
282591 AGCTTCGTAG
282601 CGATACATTGTAT
1 CGATACATTGTAT
282614 CGATACAAAACTTATGTAT
1 CGATAC---A-TT--GTAT
282633 CGATACATTGTAT
1 CGATACATTGTAT
282646 CGATACAACACTTATGTAT
1 CGAT---ACA--T-TGTAT
282665 CGATACATTGTAT
1 CGATACATTGTAT
282678 CGATACA
1 CGATACA
282685 AATTGTTGAA
Statistics
Matches: 59, Mismatches: 0, Indels: 24
0.71 0.00 0.29
Matches are distributed among these distances:
13 26 0.44
14 1 0.02
15 2 0.03
16 8 0.14
17 2 0.03
18 1 0.02
19 19 0.32
ACGTcount: A:0.36, C:0.18, G:0.13, T:0.33
Consensus pattern (13 bp):
CGATACATTGTAT
Found at i:282633 original size:19 final size:18
Alignment explanation
Indices: 282609--282671 Score: 73
Period size: 19 Copynumber: 3.7 Consensus size: 18
282599 AGCGATACAT
282609 TGTATCGATACAAAACTTA
1 TGTATCGATAC-AAACTTA
282628 TGTATCGATAC--A--T-
1 TGTATCGATACAAACTTA
282641 TGTATCGATACAACACTTA
1 TGTATCGATACAA-ACTTA
282660 TGTATCGATACA
1 TGTATCGATACA
282672 TTGTATCGAT
Statistics
Matches: 38, Mismatches: 0, Indels: 12
0.76 0.00 0.24
Matches are distributed among these distances:
13 11 0.29
14 1 0.03
16 2 0.05
18 1 0.03
19 23 0.61
ACGTcount: A:0.37, C:0.17, G:0.13, T:0.33
Consensus pattern (18 bp):
TGTATCGATACAAACTTA
Found at i:282637 original size:32 final size:32
Alignment explanation
Indices: 282601--282686 Score: 163
Period size: 32 Copynumber: 2.7 Consensus size: 32
282591 AGCTTCGTAG
282601 CGATACATTGTATCGATACAAAACTTATGTAT
1 CGATACATTGTATCGATACAAAACTTATGTAT
*
282633 CGATACATTGTATCGATACAACACTTATGTAT
1 CGATACATTGTATCGATACAAAACTTATGTAT
282665 CGATACATTGTATCGATACAAA
1 CGATACATTGTATCGATACAAA
282687 TTGTTGAAAT
Statistics
Matches: 52, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
32 52 1.00
ACGTcount: A:0.37, C:0.17, G:0.13, T:0.33
Consensus pattern (32 bp):
CGATACATTGTATCGATACAAAACTTATGTAT
Found at i:284410 original size:20 final size:21
Alignment explanation
Indices: 284385--284426 Score: 77
Period size: 20 Copynumber: 2.0 Consensus size: 21
284375 GGAATTTCCC
284385 ATAATGTATCGATACAT-TGA
1 ATAATGTATCGATACATCTGA
284405 ATAATGTATCGATACATCTGA
1 ATAATGTATCGATACATCTGA
284426 A
1 A
284427 AAACCCAGAT
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
20 17 0.81
21 4 0.19
ACGTcount: A:0.40, C:0.12, G:0.14, T:0.33
Consensus pattern (21 bp):
ATAATGTATCGATACATCTGA
Found at i:284462 original size:20 final size:20
Alignment explanation
Indices: 284437--284497 Score: 64
Period size: 20 Copynumber: 3.4 Consensus size: 20
284427 AAACCCAGAT
284437 GTATCGATACAAAGTTCTTA
1 GTATCGATACAAAGTTCTTA
*
284457 GTATCGATGC--A----TT-
1 GTATCGATACAAAGTTCTTA
284470 GTATCGATACAAAGTTCTTA
1 GTATCGATACAAAGTTCTTA
284490 GTATCGAT
1 GTATCGAT
284498 GCATTGTATC
Statistics
Matches: 32, Mismatches: 2, Indels: 14
0.67 0.04 0.29
Matches are distributed among these distances:
13 9 0.28
14 2 0.06
15 1 0.03
18 1 0.03
19 2 0.06
20 17 0.53
ACGTcount: A:0.31, C:0.15, G:0.18, T:0.36
Consensus pattern (20 bp):
GTATCGATACAAAGTTCTTA
Found at i:284478 original size:33 final size:33
Alignment explanation
Indices: 284436--284513 Score: 156
Period size: 33 Copynumber: 2.4 Consensus size: 33
284426 AAAACCCAGA
284436 TGTATCGATACAAAGTTCTTAGTATCGATGCAT
1 TGTATCGATACAAAGTTCTTAGTATCGATGCAT
284469 TGTATCGATACAAAGTTCTTAGTATCGATGCAT
1 TGTATCGATACAAAGTTCTTAGTATCGATGCAT
284502 TGTATCGATACA
1 TGTATCGATACA
284514 GAGTATTGAT
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
33 45 1.00
ACGTcount: A:0.31, C:0.15, G:0.18, T:0.36
Consensus pattern (33 bp):
TGTATCGATACAAAGTTCTTAGTATCGATGCAT
Found at i:284538 original size:26 final size:26
Alignment explanation
Indices: 284489--284549 Score: 86
Period size: 26 Copynumber: 2.3 Consensus size: 26
284479 CAAAGTTCTT
* *
284489 AGTATCGATGCATTGTATCGATACAG
1 AGTATCGATGCATTGTATCAATACAA
* *
284515 AGTATTGATGCATTGTATTAATACAA
1 AGTATCGATGCATTGTATCAATACAA
284541 AGTATCGAT
1 AGTATCGAT
284550 ACATAGGTAC
Statistics
Matches: 30, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
26 30 1.00
ACGTcount: A:0.34, C:0.11, G:0.20, T:0.34
Consensus pattern (26 bp):
AGTATCGATGCATTGTATCAATACAA
Found at i:284551 original size:13 final size:13
Alignment explanation
Indices: 284488--284555 Score: 55
Period size: 13 Copynumber: 5.2 Consensus size: 13
284478 ACAAAGTTCT
*
284488 TAGTATCGATGCA
1 TAGTATCGATACA
*
284501 TTGTATCGATACA
1 TAGTATCGATACA
* * *
284514 GAGTATTGATGCA
1 TAGTATCGATACA
* **
284527 TTGTATTAATACA
1 TAGTATCGATACA
*
284540 AAGTATCGATACA
1 TAGTATCGATACA
284553 TAG
1 TAG
284556 GTACTATTTA
Statistics
Matches: 40, Mismatches: 15, Indels: 0
0.73 0.27 0.00
Matches are distributed among these distances:
13 40 1.00
ACGTcount: A:0.35, C:0.12, G:0.19, T:0.34
Consensus pattern (13 bp):
TAGTATCGATACA
Found at i:286587 original size:25 final size:25
Alignment explanation
Indices: 286555--286602 Score: 71
Period size: 25 Copynumber: 1.9 Consensus size: 25
286545 AGAGAGATAA
*
286555 TTTGTTAAGAGG-GAGTATTAAATAT
1 TTTGTTAAG-GGAGAGTACTAAATAT
286580 TTTGTTAAGGGAGAGTACTAAAT
1 TTTGTTAAGGGAGAGTACTAAAT
286603 TGAAAATTGC
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
24 2 0.10
25 19 0.90
ACGTcount: A:0.35, C:0.02, G:0.25, T:0.38
Consensus pattern (25 bp):
TTTGTTAAGGGAGAGTACTAAATAT
Found at i:287369 original size:20 final size:21
Alignment explanation
Indices: 287325--287372 Score: 62
Period size: 21 Copynumber: 2.3 Consensus size: 21
287315 ATTGATACTT
* *
287325 TGTATCGATACATACTTGAAT
1 TGTATCGATACATACGTGAAA
*
287346 TGTATCGATACAT-GGTGAAA
1 TGTATCGATACATACGTGAAA
287366 TGTATCG
1 TGTATCG
287373 TTATATTGAG
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
20 11 0.46
21 13 0.54
ACGTcount: A:0.31, C:0.12, G:0.21, T:0.35
Consensus pattern (21 bp):
TGTATCGATACATACGTGAAA
Found at i:287691 original size:16 final size:16
Alignment explanation
Indices: 287672--287702 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
287662 AATATAATAG
*
287672 AAAGTAAATTCTTTAC
1 AAAGGAAATTCTTTAC
287688 AAAGGAAATTCTTTA
1 AAAGGAAATTCTTTA
287703 AAAACAAATG
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.45, C:0.10, G:0.10, T:0.35
Consensus pattern (16 bp):
AAAGGAAATTCTTTAC
Found at i:287962 original size:12 final size:12
Alignment explanation
Indices: 287927--287968 Score: 50
Period size: 12 Copynumber: 3.6 Consensus size: 12
287917 AAGCACTAAA
287927 ATTATAAATT-T
1 ATTATAAATTAT
* * *
287938 TTTATATACTAT
1 ATTATAAATTAT
287950 ATTATAAATTAT
1 ATTATAAATTAT
287962 ATTATAA
1 ATTATAA
287969 TATAAGAGTC
Statistics
Matches: 24, Mismatches: 6, Indels: 1
0.77 0.19 0.03
Matches are distributed among these distances:
11 7 0.29
12 17 0.71
ACGTcount: A:0.45, C:0.02, G:0.00, T:0.52
Consensus pattern (12 bp):
ATTATAAATTAT
Found at i:289867 original size:26 final size:26
Alignment explanation
Indices: 289834--289924 Score: 74
Period size: 26 Copynumber: 3.3 Consensus size: 26
289824 CACTATTCTT
289834 GCTTTCTAAAATTCACTATTGGTCCA
1 GCTTTCTAAAATTCACTATTGGTCCA
** * * ** **
289860 GCTTTCTAAGGTTTTAGTCTCACTATTCTT
1 GCTTTCTAA-AATTCA--CT-ATTGGTCCA
289890 GCTTTCTAAAATTCACTATTGGTCCA
1 GCTTTCTAAAATTCACTATTGGTCCA
289916 GCTTTCTAA
1 GCTTTCTAA
289925 GGTTTTAGTC
Statistics
Matches: 45, Mismatches: 16, Indels: 8
0.65 0.23 0.12
Matches are distributed among these distances:
26 22 0.49
27 5 0.11
29 5 0.11
30 13 0.29
ACGTcount: A:0.23, C:0.22, G:0.12, T:0.43
Consensus pattern (26 bp):
GCTTTCTAAAATTCACTATTGGTCCA
Found at i:289883 original size:33 final size:33
Alignment explanation
Indices: 289846--289942 Score: 97
Period size: 33 Copynumber: 3.2 Consensus size: 33
289836 TTTCTAAAAT
289846 TCACTATTGGTCCAGCTTTCTAAGGTTTTAGTC
1 TCACTATTGGTCCAGCTTTCTAAGGTTTTAGTC
** *
289879 TCACTA-T--TCTTGCTTTCTAA------AAT-
1 TCACTATTGGTCCAGCTTTCTAAGGTTTTAGTC
289902 TCACTATTGGTCCAGCTTTCTAAGGTTTTAGTC
1 TCACTATTGGTCCAGCTTTCTAAGGTTTTAGTC
289935 TCACTATT
1 TCACTATT
289943 CTTGCTTTCT
Statistics
Matches: 48, Mismatches: 6, Indels: 20
0.65 0.08 0.27
Matches are distributed among these distances:
23 6 0.12
24 3 0.06
26 11 0.23
30 11 0.23
32 3 0.06
33 14 0.29
ACGTcount: A:0.21, C:0.22, G:0.13, T:0.44
Consensus pattern (33 bp):
TCACTATTGGTCCAGCTTTCTAAGGTTTTAGTC
Found at i:289886 original size:56 final size:56
Alignment explanation
Indices: 289821--289989 Score: 311
Period size: 56 Copynumber: 3.0 Consensus size: 56
289811 AGCTATCTAT
289821 TCTCACTATTCTTGCTTTCTAAAATTCACTATTGGTCCAGCTTTCTAAGGTTTTAG
1 TCTCACTATTCTTGCTTTCTAAAATTCACTATTGGTCCAGCTTTCTAAGGTTTTAG
289877 TCTCACTATTCTTGCTTTCTAAAATTCACTATTGGTCCAGCTTTCTAAGGTTTTAG
1 TCTCACTATTCTTGCTTTCTAAAATTCACTATTGGTCCAGCTTTCTAAGGTTTTAG
* * *
289933 TCTCACTATTCTTGCTTTCTAAAATTCAATGTTGGTCCAGCTTTCTAAGTTTTTAG
1 TCTCACTATTCTTGCTTTCTAAAATTCACTATTGGTCCAGCTTTCTAAGGTTTTAG
289989 T
1 T
289990 TTTAATCATA
Statistics
Matches: 110, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
56 110 1.00
ACGTcount: A:0.21, C:0.21, G:0.12, T:0.46
Consensus pattern (56 bp):
TCTCACTATTCTTGCTTTCTAAAATTCACTATTGGTCCAGCTTTCTAAGGTTTTAG
Found at i:289896 original size:30 final size:30
Alignment explanation
Indices: 289860--289954 Score: 90
Period size: 30 Copynumber: 3.3 Consensus size: 30
289850 TATTGGTCCA
289860 GCTTTCTAAGGTTTTAGTCTCACTATTCTT
1 GCTTTCTAAGGTTTTAGTCTCACTATTCTT
** * * ** **
289890 GCTTTCTAA-AATTCA--CT-ATTGGTCCA
1 GCTTTCTAAGGTTTTAGTCTCACTATTCTT
289916 GCTTTCTAAGGTTTTAGTCTCACTATTCTT
1 GCTTTCTAAGGTTTTAGTCTCACTATTCTT
289946 GCTTTCTAA
1 GCTTTCTAA
289955 AATTCAATGT
Statistics
Matches: 45, Mismatches: 16, Indels: 8
0.65 0.23 0.12
Matches are distributed among these distances:
26 13 0.29
27 5 0.11
29 5 0.11
30 22 0.49
ACGTcount: A:0.20, C:0.21, G:0.13, T:0.46
Consensus pattern (30 bp):
GCTTTCTAAGGTTTTAGTCTCACTATTCTT
Found at i:293529 original size:141 final size:141
Alignment explanation
Indices: 293275--293553 Score: 558
Period size: 141 Copynumber: 2.0 Consensus size: 141
293265 TTTATTATTA
293275 CGAATGCTTCTCCTCCTTTTCTATTTTTGGTGTTTTTCACACTTATCACTTCAATCCAGATAAGA
1 CGAATGCTTCTCCTCCTTTTCTATTTTTGGTGTTTTTCACACTTATCACTTCAATCCAGATAAGA
293340 ACCATTGGCAGGCTATTAAAATTTACAACTCTCTAACATTGATTTTGTTTTCATGTTATACACCA
66 ACCATTGGCAGGCTATTAAAATTTACAACTCTCTAACATTGATTTTGTTTTCATGTTATACACCA
293405 GATTCGGCCTC
131 GATTCGGCCTC
293416 CGAATGCTTCTCCTCCTTTTCTATTTTTGGTGTTTTTCACACTTATCACTTCAATCCAGATAAGA
1 CGAATGCTTCTCCTCCTTTTCTATTTTTGGTGTTTTTCACACTTATCACTTCAATCCAGATAAGA
293481 ACCATTGGCAGGCTATTAAAATTTACAACTCTCTAACATTGATTTTGTTTTCATGTTATACACCA
66 ACCATTGGCAGGCTATTAAAATTTACAACTCTCTAACATTGATTTTGTTTTCATGTTATACACCA
293546 GATTCGGC
131 GATTCGGC
293554 ATCCTCAAAT
Statistics
Matches: 138, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
141 138 1.00
ACGTcount: A:0.25, C:0.23, G:0.12, T:0.40
Consensus pattern (141 bp):
CGAATGCTTCTCCTCCTTTTCTATTTTTGGTGTTTTTCACACTTATCACTTCAATCCAGATAAGA
ACCATTGGCAGGCTATTAAAATTTACAACTCTCTAACATTGATTTTGTTTTCATGTTATACACCA
GATTCGGCCTC
Found at i:296550 original size:20 final size:20
Alignment explanation
Indices: 296505--296551 Score: 60
Period size: 20 Copynumber: 2.4 Consensus size: 20
296495 TAATGAGTAA
*
296505 AAAAAATTATTGATAATGTT
1 AAAAAATTATTGATAATATT
*
296525 AAAAAATTATTTA-AATATT
1 AAAAAATTATTGATAATATT
296544 AATAAAAT
1 AA-AAAAT
296552 ATTAATATTA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
19 7 0.29
20 17 0.71
ACGTcount: A:0.57, C:0.00, G:0.04, T:0.38
Consensus pattern (20 bp):
AAAAAATTATTGATAATATT
Found at i:296688 original size:19 final size:20
Alignment explanation
Indices: 296664--296708 Score: 74
Period size: 20 Copynumber: 2.3 Consensus size: 20
296654 ATAAGATATA
296664 TTAATATTTA-AATAATTTT
1 TTAATATTTATAATAATTTT
*
296683 TTAATATTTATAATTATTTT
1 TTAATATTTATAATAATTTT
296703 TTAATA
1 TTAATA
296709 AATTTTAAAA
Statistics
Matches: 24, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
19 10 0.42
20 14 0.58
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (20 bp):
TTAATATTTATAATAATTTT
Found at i:296697 original size:17 final size:19
Alignment explanation
Indices: 296664--296702 Score: 55
Period size: 19 Copynumber: 2.1 Consensus size: 19
296654 ATAAGATATA
296664 TTAATATTTAAATAATT-TT
1 TTAATATTT-AATAATTATT
296683 TTAATATTT-ATAATTATT
1 TTAATATTTAATAATTATT
296701 TT
1 TT
296703 TTAATAAATT
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
17 6 0.32
18 4 0.21
19 9 0.47
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (19 bp):
TTAATATTTAATAATTATT
Found at i:296723 original size:14 final size:14
Alignment explanation
Indices: 296706--296757 Score: 50
Period size: 14 Copynumber: 3.5 Consensus size: 14
296696 TTATTTTTTA
296706 ATAAATTTTAAAAT
1 ATAAATTTTAAAAT
**
296720 ATAAAAATTAAAAT
1 ATAAATTTTAAAAT
*
296734 ATTAAATTTAATAATAT
1 A-TAAATTT--TAAAAT
296751 ATAAATT
1 ATAAATT
296758 AATTTTTTTA
Statistics
Matches: 30, Mismatches: 5, Indels: 4
0.77 0.13 0.10
Matches are distributed among these distances:
14 13 0.43
15 5 0.17
16 6 0.20
17 6 0.20
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (14 bp):
ATAAATTTTAAAAT
Found at i:296760 original size:15 final size:14
Alignment explanation
Indices: 296713--296759 Score: 60
Period size: 14 Copynumber: 3.3 Consensus size: 14
296703 TTAATAAATT
*
296713 TTAAAATATAAAAA
1 TTAAAATATATAAA
296727 TTAAAATAT-TAAA
1 TTAAAATATATAAA
296740 TTTAATAATATATAAA
1 -TTAA-AATATATAAA
296756 TTAA
1 TTAA
296760 TTTTTTTATA
Statistics
Matches: 29, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
13 3 0.10
14 13 0.45
15 9 0.31
16 4 0.14
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (14 bp):
TTAAAATATATAAA
Found at i:297473 original size:26 final size:26
Alignment explanation
Indices: 297444--297505 Score: 63
Period size: 26 Copynumber: 2.4 Consensus size: 26
297434 AAATAATTTA
297444 AATATATTATTTATATGTA-ATACTAT
1 AATATATTATTTATATGTATATA-TAT
* * *
297470 AATAAAATATTTATGTGTATATATAT
1 AATATATTATTTATATGTATATATAT
* *
297496 TATGTATTAT
1 AATATATTAT
297506 AATCTATATA
Statistics
Matches: 28, Mismatches: 7, Indels: 2
0.76 0.19 0.05
Matches are distributed among these distances:
26 25 0.89
27 3 0.11
ACGTcount: A:0.42, C:0.02, G:0.06, T:0.50
Consensus pattern (26 bp):
AATATATTATTTATATGTATATATAT
Found at i:297830 original size:21 final size:21
Alignment explanation
Indices: 297804--297847 Score: 70
Period size: 21 Copynumber: 2.1 Consensus size: 21
297794 AGTATTTAAC
*
297804 ATAATTAATTAATTTTATTTT
1 ATAATTAATTAATTATATTTT
*
297825 ATAATTAATTTATTATATTTT
1 ATAATTAATTAATTATATTTT
297846 AT
1 AT
297848 TTTGAAAAAC
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (21 bp):
ATAATTAATTAATTATATTTT
Found at i:299725 original size:20 final size:20
Alignment explanation
Indices: 299700--299753 Score: 83
Period size: 20 Copynumber: 2.7 Consensus size: 20
299690 GTTGGAAGCA
*
299700 ATGTATCGATACAAT-TCATC
1 ATGTATCGATACAATGT-ACC
299720 ATGTATCGATACAATGTACC
1 ATGTATCGATACAATGTACC
299740 ATGTATCGATACAA
1 ATGTATCGATACAA
299754 ACAGTGGTAG
Statistics
Matches: 32, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
20 31 0.97
21 1 0.03
ACGTcount: A:0.37, C:0.19, G:0.13, T:0.31
Consensus pattern (20 bp):
ATGTATCGATACAATGTACC
Found at i:299807 original size:20 final size:20
Alignment explanation
Indices: 299781--299836 Score: 89
Period size: 19 Copynumber: 2.9 Consensus size: 20
299771 ACTGCCAGTT
299781 TCATGTATCGATACAATTG-
1 TCATGTATCGATACAATTGA
299800 TCCATGTATCGATAC-ATTGA
1 T-CATGTATCGATACAATTGA
299820 TCATGTATCGATACAAT
1 TCATGTATCGATACAAT
299837 GTATCGATAC
Statistics
Matches: 34, Mismatches: 0, Indels: 5
0.87 0.00 0.13
Matches are distributed among these distances:
19 18 0.53
20 16 0.47
ACGTcount: A:0.32, C:0.18, G:0.14, T:0.36
Consensus pattern (20 bp):
TCATGTATCGATACAATTGA
Found at i:299840 original size:13 final size:13
Alignment explanation
Indices: 299822--299848 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
299812 TACATTGATC
299822 ATGTATCGATACA
1 ATGTATCGATACA
299835 ATGTATCGATACA
1 ATGTATCGATACA
299848 A
1 A
299849 AGCATAATGT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.41, C:0.15, G:0.15, T:0.30
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:300488 original size:31 final size:31
Alignment explanation
Indices: 300431--300524 Score: 161
Period size: 31 Copynumber: 3.0 Consensus size: 31
300421 AATGCTTTCG
* *
300431 TTAAAAACTTTCTCCCCGATTAAAGAGATTTT
1 TTAAAAAATTTCT-CCCGGTTAAAGAGATTTT
300463 TTAAAAAATTTCTCCCGGTTAAAGAGATTTT
1 TTAAAAAATTTCTCCCGGTTAAAGAGATTTT
300494 TTAAAAAATTTCTCCCGGTTAAAGAGATTTT
1 TTAAAAAATTTCTCCCGGTTAAAGAGATTTT
300525 CTCCCCTTAG
Statistics
Matches: 60, Mismatches: 2, Indels: 1
0.95 0.03 0.02
Matches are distributed among these distances:
31 48 0.80
32 12 0.20
ACGTcount: A:0.35, C:0.15, G:0.12, T:0.38
Consensus pattern (31 bp):
TTAAAAAATTTCTCCCGGTTAAAGAGATTTT
Found at i:300549 original size:30 final size:30
Alignment explanation
Indices: 300513--300573 Score: 104
Period size: 30 Copynumber: 2.0 Consensus size: 30
300503 TTCTCCCGGT
*
300513 TAAAGAGATTTTCTCCCCTTAGATAAAAAA
1 TAAAGAGATTTTCTCCCCCTAGATAAAAAA
*
300543 TAAAGAGATTTTCTCCCCCTGGATAAAAAA
1 TAAAGAGATTTTCTCCCCCTAGATAAAAAA
300573 T
1 T
300574 TTATTTTCAA
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
30 29 1.00
ACGTcount: A:0.41, C:0.18, G:0.11, T:0.30
Consensus pattern (30 bp):
TAAAGAGATTTTCTCCCCCTAGATAAAAAA
Found at i:306981 original size:9 final size:9
Alignment explanation
Indices: 306967--307000 Score: 52
Period size: 9 Copynumber: 3.8 Consensus size: 9
306957 TCCGAGTCAC
306967 CATCATTAT
1 CATCATTAT
306976 CATCATTAT
1 CATCATTAT
306985 CATC-TTCAT
1 CATCATT-AT
306994 CATCATT
1 CATCATT
307001 GATAGTTGAC
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
8 2 0.09
9 19 0.83
10 2 0.09
ACGTcount: A:0.29, C:0.26, G:0.00, T:0.44
Consensus pattern (9 bp):
CATCATTAT
Found at i:308651 original size:33 final size:33
Alignment explanation
Indices: 308584--308653 Score: 97
Period size: 33 Copynumber: 2.1 Consensus size: 33
308574 GCCATTAGAA
* *
308584 ACAATGTATCGATACAATTCATCATATATTGAT
1 ACAATGTATCGATACAATTCACCATATATCGAT
*
308617 ACAATGTATCGATACAATGT-ACCATGTATCGAT
1 ACAATGTATCGATACAAT-TCACCATATATCGAT
308650 ACAA
1 ACAA
308654 ACAGTGGTAG
Statistics
Matches: 33, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
33 32 0.97
34 1 0.03
ACGTcount: A:0.40, C:0.17, G:0.11, T:0.31
Consensus pattern (33 bp):
ACAATGTATCGATACAATTCACCATATATCGAT
Found at i:308724 original size:19 final size:19
Alignment explanation
Indices: 308683--308752 Score: 99
Period size: 19 Copynumber: 3.7 Consensus size: 19
308673 TACCAGTTTC
308683 ATGTATCGATACAATTG-TCT
1 ATGTATCGATAC-ATTGAT-T
308703 ATGTATCGATACATTGATT
1 ATGTATCGATACATTGATT
*
308722 ATGTATCGATACATTGATC
1 ATGTATCGATACATTGATT
308741 ATGTATC-ATACA
1 ATGTATCGATACA
308753 ATGTATCGAT
Statistics
Matches: 48, Mismatches: 1, Indels: 4
0.91 0.02 0.08
Matches are distributed among these distances:
18 5 0.10
19 30 0.62
20 13 0.27
ACGTcount: A:0.33, C:0.14, G:0.14, T:0.39
Consensus pattern (19 bp):
ATGTATCGATACATTGATT
Found at i:309949 original size:47 final size:48
Alignment explanation
Indices: 309880--309992 Score: 192
Period size: 47 Copynumber: 2.4 Consensus size: 48
309870 CCCTTTAAAA
* *
309880 AAAAAATTGTCTCCCTTGATAAAATAATTAAGGC-TCTTTTTTATAAC
1 AAAAAATTTTCCCCCTTGATAAAATAATTAAGGCATCTTTTTTATAAC
309927 AAAAAATTTTCCCCCTTGATAAAATAATTAAGGCATCTTTTTTATAAC
1 AAAAAATTTTCCCCCTTGATAAAATAATTAAGGCATCTTTTTTATAAC
309975 AAAAAATTTCTCCCCCTT
1 AAAAAATTT-TCCCCCTT
309993 TTTGTTATAA
Statistics
Matches: 62, Mismatches: 2, Indels: 2
0.94 0.03 0.03
Matches are distributed among these distances:
47 32 0.52
48 22 0.35
49 8 0.13
ACGTcount: A:0.38, C:0.19, G:0.06, T:0.37
Consensus pattern (48 bp):
AAAAAATTTTCCCCCTTGATAAAATAATTAAGGCATCTTTTTTATAAC
Found at i:310026 original size:15 final size:15
Alignment explanation
Indices: 310005--310044 Score: 71
Period size: 15 Copynumber: 2.7 Consensus size: 15
309995 TGTTATAAAC
310005 CAAAAAATTTATTTT
1 CAAAAAATTTATTTT
*
310020 GAAAAAATTTATTTT
1 CAAAAAATTTATTTT
310035 CAAAAAATTT
1 CAAAAAATTT
310045 CTCCTCCTTT
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
15 23 1.00
ACGTcount: A:0.50, C:0.05, G:0.03, T:0.42
Consensus pattern (15 bp):
CAAAAAATTTATTTT
Found at i:318349 original size:305 final size:305
Alignment explanation
Indices: 317793--318372 Score: 1142
Period size: 305 Copynumber: 1.9 Consensus size: 305
317783 GTTGGAGACT
*
317793 CAAATTTATAGGCTAGAATGTTGACAAACTTGTTGGAGATTGAATGATTGTGTTTGTAGTCGTTG
1 CAAACTTATAGGCTAGAATGTTGACAAACTTGTTGGAGATTGAATGATTGTGTTTGTAGTCGTTG
317858 TTGTCTTGTTTGGTTTTTATTTCCATGCATTCCCGTTACTATGTATCGATACGATTCATAATGTA
66 TTGTCTTGTTTGGTTTTTATTTCCATGCATTCCCGTTACTATGTATCGATACGATTCATAATGTA
*
317923 TCGATATATGCATTTGAAATTAAAACTGTTTATAGCCGTTGGGCATAATGTATCGATACAATTCT
131 TCGATATATGCATTTGAAATTAAAACTGTTTATAGCCATTGGGCATAATGTATCGATACAATTCT
317988 TCATGTATCGATACATTGTCCCATATATCGATACATTTCACTTAAGGTAGCTACTGCCACTTTCA
196 TCATGTATCGATACATTGTCCCATATATCGATACATTTCACTTAAGGTAGCTACTGCCACTTTCA
318053 TGTATCGATACAATTTATAGGCTAGAATGTTGGGCATAATGTTGA
261 TGTATCGATACAATTTATAGGCTAGAATGTTGGGCATAATGTTGA
318098 CAAACTTATAGGCTAGAATGTTGACAAACTTGTTGGAGATTGAATGATTGTGTTTGTAGTCGTTG
1 CAAACTTATAGGCTAGAATGTTGACAAACTTGTTGGAGATTGAATGATTGTGTTTGTAGTCGTTG
318163 TTGTCTTGTTTGGTTTTTATTTCCATGCATTCCCGTTACTATGTATCGATACGATTCATAATGTA
66 TTGTCTTGTTTGGTTTTTATTTCCATGCATTCCCGTTACTATGTATCGATACGATTCATAATGTA
318228 TCGATATATGCATTTGAAATTAAAACTGTTTATAGCCATTGGGCATAATGTATCGATACAATTCT
131 TCGATATATGCATTTGAAATTAAAACTGTTTATAGCCATTGGGCATAATGTATCGATACAATTCT
318293 TCATGTATCGATACATTGTCCCATATATCGATACATTTCACTTAAGGTAGCTACTGCCACTTTCA
196 TCATGTATCGATACATTGTCCCATATATCGATACATTTCACTTAAGGTAGCTACTGCCACTTTCA
318358 TGTATCGATACAATT
261 TGTATCGATACAATT
318373 GAGTATGTAT
Statistics
Matches: 273, Mismatches: 2, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
305 273 1.00
ACGTcount: A:0.28, C:0.15, G:0.18, T:0.39
Consensus pattern (305 bp):
CAAACTTATAGGCTAGAATGTTGACAAACTTGTTGGAGATTGAATGATTGTGTTTGTAGTCGTTG
TTGTCTTGTTTGGTTTTTATTTCCATGCATTCCCGTTACTATGTATCGATACGATTCATAATGTA
TCGATATATGCATTTGAAATTAAAACTGTTTATAGCCATTGGGCATAATGTATCGATACAATTCT
TCATGTATCGATACATTGTCCCATATATCGATACATTTCACTTAAGGTAGCTACTGCCACTTTCA
TGTATCGATACAATTTATAGGCTAGAATGTTGGGCATAATGTTGA
Found at i:318382 original size:20 final size:19
Alignment explanation
Indices: 318357--318447 Score: 83
Period size: 20 Copynumber: 4.6 Consensus size: 19
318347 TGCCACTTTC
*
318357 ATGTATCGATACAATTGAGT
1 ATGTATCGATACAA-TGAAT
* * *
318377 ATGTATTGATATAATGAAC
1 ATGTATCGATACAATGAAT
* *
318396 ATGTATCGATACAAAGCAT
1 ATGTATCGATACAATGAAT
* *
318415 AATATATCGATACATCTGAAT
1 -ATGTATCGATACA-ATGAAT
318436 ATGTATCGATAC
1 ATGTATCGATAC
318448 TTCCTAGGGT
Statistics
Matches: 55, Mismatches: 14, Indels: 4
0.75 0.19 0.05
Matches are distributed among these distances:
19 17 0.31
20 35 0.64
21 3 0.05
ACGTcount: A:0.40, C:0.12, G:0.15, T:0.33
Consensus pattern (19 bp):
ATGTATCGATACAATGAAT
Found at i:319481 original size:21 final size:21
Alignment explanation
Indices: 319455--319495 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
319445 AATAATGAGA
319455 ATTTAATTAATCTTAAATTAT
1 ATTTAATTAATCTTAAATTAT
* *
319476 ATTTAATTACTGTTAAATTA
1 ATTTAATTAATCTTAAATTA
319496 AACTATTATT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.41, C:0.05, G:0.02, T:0.51
Consensus pattern (21 bp):
ATTTAATTAATCTTAAATTAT
Found at i:319611 original size:20 final size:22
Alignment explanation
Indices: 319588--319631 Score: 56
Period size: 23 Copynumber: 2.0 Consensus size: 22
319578 AAATGAATTT
*
319588 ATTAA-AA-TATTTTTATTTAA
1 ATTAATAATTATTATTATTTAA
319608 ATTAATTAATTATTATTATTTAA
1 ATTAA-TAATTATTATTATTTAA
319631 A
1 A
319632 AATTTAATGA
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
20 5 0.25
22 2 0.10
23 13 0.65
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (22 bp):
ATTAATAATTATTATTATTTAA
Found at i:321216 original size:2 final size:2
Alignment explanation
Indices: 321209--321241 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
321199 CCATATTCCA
321209 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 A
321242 CCTCTTGAGT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:322214 original size:7 final size:7
Alignment explanation
Indices: 322202--322236 Score: 63
Period size: 7 Copynumber: 5.1 Consensus size: 7
322192 CCACTCTTTT
322202 GCCAAGG
1 GCCAAGG
322209 GCCAAGG
1 GCCAAGG
322216 GCCAA-G
1 GCCAAGG
322222 GCCAAGG
1 GCCAAGG
322229 GCCAAGG
1 GCCAAGG
322236 G
1 G
322237 GAATCAAGTC
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
6 6 0.22
7 21 0.78
ACGTcount: A:0.29, C:0.29, G:0.43, T:0.00
Consensus pattern (7 bp):
GCCAAGG
Found at i:322226 original size:13 final size:13
Alignment explanation
Indices: 322202--322235 Score: 59
Period size: 13 Copynumber: 2.5 Consensus size: 13
322192 CCACTCTTTT
322202 GCCAAGGGCCAAGG
1 GCCAA-GGCCAAGG
322216 GCCAAGGCCAAGG
1 GCCAAGGCCAAGG
322229 GCCAAGG
1 GCCAAGG
322236 GGAATCAAGT
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
13 15 0.75
14 5 0.25
ACGTcount: A:0.29, C:0.29, G:0.41, T:0.00
Consensus pattern (13 bp):
GCCAAGGCCAAGG
Found at i:326015 original size:2 final size:2
Alignment explanation
Indices: 326003--326041 Score: 69
Period size: 2 Copynumber: 19.5 Consensus size: 2
325993 GAACAAATGT
*
326003 TA TA AA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
326042 GTTCAGCTCA
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
TA
Found at i:329144 original size:2 final size:2
Alignment explanation
Indices: 329139--329170 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
329129 TGAAAAAAAA
329139 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
329171 GTATCTTCCC
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:329565 original size:3 final size:3
Alignment explanation
Indices: 329559--329587 Score: 58
Period size: 3 Copynumber: 9.7 Consensus size: 3
329549 CTAATAATCA
329559 TAT TAT TAT TAT TAT TAT TAT TAT TAT TA
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TA
329588 ATGTGAACAA
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:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
TAT
Found at i:330102 original size:19 final size:19
Alignment explanation
Indices: 330078--330114 Score: 65
Period size: 19 Copynumber: 1.9 Consensus size: 19
330068 AAAATTATAA
330078 TTATTTATTTTGTAAAAAT
1 TTATTTATTTTGTAAAAAT
*
330097 TTATTTATTTTTTAAAAA
1 TTATTTATTTTGTAAAAA
330115 ATTACTCAAT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.38, C:0.00, G:0.03, T:0.59
Consensus pattern (19 bp):
TTATTTATTTTGTAAAAAT
Found at i:330187 original size:25 final size:26
Alignment explanation
Indices: 330153--330213 Score: 63
Period size: 24 Copynumber: 2.4 Consensus size: 26
330143 AAATTTAAAT
330153 TATTTATTTTTAAAAATATTTTT-ACA
1 TATTT-TTTTTAAAAATATTTTTCACA
* ***
330179 TA-TTTTTTTCATTTTATTTTTCACA
1 TATTTTTTTTAAAAATATTTTTCACA
330204 TATTTTTTTT
1 TATTTTTTTT
330214 TTTGCCTATC
Statistics
Matches: 29, Mismatches: 4, Indels: 4
0.78 0.11 0.11
Matches are distributed among these distances:
24 13 0.45
25 7 0.24
26 9 0.31
ACGTcount: A:0.26, C:0.07, G:0.00, T:0.67
Consensus pattern (26 bp):
TATTTTTTTTAAAAATATTTTTCACA
Found at i:331309 original size:13 final size:13
Alignment explanation
Indices: 331293--331324 Score: 57
Period size: 12 Copynumber: 2.5 Consensus size: 13
331283 TAAATTTTTA
331293 AAATTAAAAAATT
1 AAATTAAAAAATT
331306 AAATT-AAAAATT
1 AAATTAAAAAATT
331318 AAATTAA
1 AAATTAA
331325 TTAAATTTTT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
12 12 0.67
13 6 0.33
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (13 bp):
AAATTAAAAAATT
Found at i:331328 original size:21 final size:20
Alignment explanation
Indices: 331292--331331 Score: 62
Period size: 20 Copynumber: 1.9 Consensus size: 20
331282 ATAAATTTTT
331292 AAAATTAAAAAATTAAATTA
1 AAAATTAAAAAATTAAATTA
*
331312 AAAATTAAATTAATTAAATT
1 AAAATTAAA-AAATTAAATT
331332 TTTGATTTTT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 9 0.50
21 9 0.50
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (20 bp):
AAAATTAAAAAATTAAATTA
Found at i:337479 original size:10 final size:10
Alignment explanation
Indices: 337461--337514 Score: 54
Period size: 10 Copynumber: 5.1 Consensus size: 10
337451 GTTGCTCATA
*
337461 TCTTATTCTT
1 TCTTCTTCTT
337471 TCTTCTTCTCT
1 TCTTCTTCT-T
*
337482 TGCTTCTTCATA
1 T-CTTCTTC-TT
*
337494 TCTTTTTCTT
1 TCTTCTTCTT
337504 TCTTCTTCTT
1 TCTTCTTCTT
337514 T
1 T
337515 TGCTTCCTCT
Statistics
Matches: 36, Mismatches: 5, Indels: 6
0.77 0.11 0.13
Matches are distributed among these distances:
10 19 0.53
11 8 0.22
12 8 0.22
13 1 0.03
ACGTcount: A:0.06, C:0.26, G:0.02, T:0.67
Consensus pattern (10 bp):
TCTTCTTCTT
Found at i:337490 original size:15 final size:15
Alignment explanation
Indices: 337470--337520 Score: 57
Period size: 15 Copynumber: 3.2 Consensus size: 15
337460 ATCTTATTCT
*
337470 TTCTTCTTCTCTTGC
1 TTCTTCTTCTTTTGC
*
337485 TTCTTCATATCTTTTTC
1 TTCTTC-T-TCTTTTGC
337502 TTTCTTCTTCTTTTGC
1 -TTCTTCTTCTTTTGC
337518 TTC
1 TTC
337521 CTCTAACTTA
Statistics
Matches: 30, Mismatches: 3, Indels: 6
0.77 0.08 0.15
Matches are distributed among these distances:
15 9 0.30
16 8 0.27
17 7 0.23
18 6 0.20
ACGTcount: A:0.04, C:0.27, G:0.04, T:0.65
Consensus pattern (15 bp):
TTCTTCTTCTTTTGC
Found at i:337493 original size:33 final size:33
Alignment explanation
Indices: 337456--337520 Score: 112
Period size: 33 Copynumber: 2.0 Consensus size: 33
337446 TTGAAGTTGC
337456 TCATATCTTATTCTTTCTTCTTCTCTTGCTTCT
1 TCATATCTTATTCTTTCTTCTTCTCTTGCTTCT
* *
337489 TCATATCTTTTTCTTTCTTCTTCTTTTGCTTC
1 TCATATCTTATTCTTTCTTCTTCTCTTGCTTC
337521 CTCTAACTTA
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
33 30 1.00
ACGTcount: A:0.08, C:0.26, G:0.03, T:0.63
Consensus pattern (33 bp):
TCATATCTTATTCTTTCTTCTTCTCTTGCTTCT
Found at i:337508 original size:18 final size:18
Alignment explanation
Indices: 337456--337508 Score: 58
Period size: 18 Copynumber: 3.1 Consensus size: 18
337446 TTGAAGTTGC
*
337456 TCATATCTTATTCTTTCT
1 TCATATCTTTTTCTTTCT
* *
337474 TC-T-TCTCTTGC-TTCT
1 TCATATCTTTTTCTTTCT
337489 TCATATCTTTTTCTTTCT
1 TCATATCTTTTTCTTTCT
337507 TC
1 TC
337509 TTCTTTTGCT
Statistics
Matches: 27, Mismatches: 5, Indels: 6
0.71 0.13 0.16
Matches are distributed among these distances:
15 6 0.22
16 6 0.22
17 7 0.26
18 8 0.30
ACGTcount: A:0.09, C:0.26, G:0.02, T:0.62
Consensus pattern (18 bp):
TCATATCTTTTTCTTTCT
Found at i:339150 original size:2 final size:2
Alignment explanation
Indices: 339145--339177 Score: 52
Period size: 2 Copynumber: 17.5 Consensus size: 2
339135 ATTAAAAAAA
339145 AT AT AT AT AT -T AT AT -T 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
339178 ACAAATCAAA
Statistics
Matches: 29, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
1 2 0.07
2 27 0.93
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
AT
Found at i:339163 original size:14 final size:12
Alignment explanation
Indices: 339145--339177 Score: 52
Period size: 11 Copynumber: 2.9 Consensus size: 12
339135 ATTAAAAAAA
339145 ATATATATAT-T
1 ATATATATATAT
339156 ATAT-TATATAT
1 ATATATATATAT
339167 ATATATATATA
1 ATATATATATA
339178 ACAAATCAAA
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
10 5 0.25
11 9 0.45
12 6 0.30
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (12 bp):
ATATATATATAT
Found at i:343630 original size:22 final size:22
Alignment explanation
Indices: 343584--343635 Score: 59
Period size: 22 Copynumber: 2.3 Consensus size: 22
343574 TATTTGTCTT
* *
343584 TTTTTTTTTTTTTGCTCTTTGG
1 TTTTTTTGTTTTTCCTCTTTGG
* *
343606 TTTTTTTGTTTTTCCTTTTTTG
1 TTTTTTTGTTTTTCCTCTTTGG
343628 TTTCTTTT
1 TTT-TTTT
343636 ATGGAATTAC
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
22 21 0.84
23 4 0.16
ACGTcount: A:0.00, C:0.10, G:0.10, T:0.81
Consensus pattern (22 bp):
TTTTTTTGTTTTTCCTCTTTGG
Found at i:344608 original size:18 final size:18
Alignment explanation
Indices: 344574--344608 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
344564 TAATTTTTTA
*
344574 AATATAAATAATATAATG
1 AATATAAAAAATATAATG
*
344592 AATATAAAAAATTTAAT
1 AATATAAAAAATATAAT
344609 ATATGTATCA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.63, C:0.00, G:0.03, T:0.34
Consensus pattern (18 bp):
AATATAAAAAATATAATG
Found at i:344642 original size:19 final size:19
Alignment explanation
Indices: 344618--344664 Score: 53
Period size: 19 Copynumber: 2.5 Consensus size: 19
344608 TATATGTATC
344618 ATATTTATAATATTT-TGAT
1 ATATTTATAATATTTAT-AT
*
344637 ATATTTA-ATTATTTATAT
1 ATATTTATAATATTTATAT
344655 AGTATTTATA
1 A-TATTTATA
344665 TCTATATAAC
Statistics
Matches: 24, Mismatches: 1, Indels: 5
0.80 0.03 0.17
Matches are distributed among these distances:
18 9 0.38
19 14 0.58
20 1 0.04
ACGTcount: A:0.38, C:0.00, G:0.04, T:0.57
Consensus pattern (19 bp):
ATATTTATAATATTTATAT
Found at i:344833 original size:12 final size:12
Alignment explanation
Indices: 344812--344845 Score: 52
Period size: 11 Copynumber: 2.9 Consensus size: 12
344802 TAATTATAAA
*
344812 AATATAAAAATT
1 AATATTAAAATT
344824 AATATTAAAA-T
1 AATATTAAAATT
344835 AATATTAAAAT
1 AATATTAAAAT
344846 ATTTTTTAAA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
11 11 0.55
12 9 0.45
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (12 bp):
AATATTAAAATT
Found at i:344839 original size:11 final size:11
Alignment explanation
Indices: 344812--344861 Score: 55
Period size: 12 Copynumber: 4.4 Consensus size: 11
344802 TAATTATAAA
*
344812 AATATAAAAATT
1 AATATTAAAA-T
344824 AATATTAAAAT
1 AATATTAAAAT
344835 AATATTAAAAT
1 AATATTAAAAT
* *
344846 ATTTTTTAAAAT
1 A-ATATTAAAAT
344858 AATA
1 AATA
344862 AAATAAATTT
Statistics
Matches: 32, Mismatches: 5, Indels: 3
0.80 0.12 0.08
Matches are distributed among these distances:
11 14 0.44
12 18 0.56
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (11 bp):
AATATTAAAAT
Found at i:352654 original size:19 final size:18
Alignment explanation
Indices: 352630--352692 Score: 73
Period size: 19 Copynumber: 3.7 Consensus size: 18
352620 AACAAGTAAC
352630 TGTATCGATACATAAGTGT
1 TGTATCGATACATAA-TGT
352649 TGTATCGATAC--AA---
1 TGTATCGATACATAATGT
352662 TGTATCGATACATAAATGT
1 TGTATCGATACAT-AATGT
352681 TGTATCGATACA
1 TGTATCGATACA
352693 ATGTATCGCT
Statistics
Matches: 38, Mismatches: 0, Indels: 12
0.76 0.00 0.24
Matches are distributed among these distances:
13 11 0.29
16 2 0.05
17 2 0.05
19 23 0.61
ACGTcount: A:0.35, C:0.13, G:0.17, T:0.35
Consensus pattern (18 bp):
TGTATCGATACATAATGT
Found at i:352667 original size:13 final size:13
Alignment explanation
Indices: 352649--352673 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
352639 ACATAAGTGT
352649 TGTATCGATACAA
1 TGTATCGATACAA
352662 TGTATCGATACA
1 TGTATCGATACA
352674 TAAATGTTGT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:352671 original size:32 final size:32
Alignment explanation
Indices: 352630--352700 Score: 133
Period size: 32 Copynumber: 2.2 Consensus size: 32
352620 AACAAGTAAC
*
352630 TGTATCGATACATAAGTGTTGTATCGATACAA
1 TGTATCGATACATAAATGTTGTATCGATACAA
352662 TGTATCGATACATAAATGTTGTATCGATACAA
1 TGTATCGATACATAAATGTTGTATCGATACAA
352694 TGTATCG
1 TGTATCG
352701 CTACGAAGCT
Statistics
Matches: 38, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
32 38 1.00
ACGTcount: A:0.34, C:0.13, G:0.18, T:0.35
Consensus pattern (32 bp):
TGTATCGATACATAAATGTTGTATCGATACAA
Found at i:359719 original size:6 final size:6
Alignment explanation
Indices: 359708--359783 Score: 86
Period size: 6 Copynumber: 13.0 Consensus size: 6
359698 CTCAAAAGTG
* * *
359708 CAAAAA CAAAAA -AAAAA C-AAAA CAACAA CAACAA C-AACA CAAAAA
1 CAAAAA CAAAAA CAAAAA CAAAAA CAAAAA CAAAAA CAAAAA CAAAAA
*
359753 AAGAAAA CAAAAA CAAAAA CAAAAA CAAAAA
1 CA-AAAA CAAAAA CAAAAA CAAAAA CAAAAA
359784 TACACACAAA
Statistics
Matches: 60, Mismatches: 6, Indels: 8
0.81 0.08 0.11
Matches are distributed among these distances:
5 13 0.22
6 42 0.70
7 5 0.08
ACGTcount: A:0.80, C:0.18, G:0.01, T:0.00
Consensus pattern (6 bp):
CAAAAA
Found at i:359730 original size:46 final size:47
Alignment explanation
Indices: 359642--359735 Score: 163
Period size: 46 Copynumber: 2.0 Consensus size: 47
359632 AAAAGTGTAT
359642 GGAGTTCCCTCAAAAGTGCAAAAAAAAAAAAAAAAAACAAAACAACAA
1 GGAGTTCCCTCAAAAGTGC-AAAAAAAAAAAAAAAAACAAAACAACAA
*
359690 GGAGTTCCCTCAAAAGTGC-AAAAACAAAAAAAAAACAAAACAACAA
1 GGAGTTCCCTCAAAAGTGCAAAAAAAAAAAAAAAAACAAAACAACAA
359736 CAACAACAAC
Statistics
Matches: 45, Mismatches: 1, Indels: 2
0.94 0.02 0.04
Matches are distributed among these distances:
46 26 0.58
48 19 0.42
ACGTcount: A:0.63, C:0.18, G:0.11, T:0.09
Consensus pattern (47 bp):
GGAGTTCCCTCAAAAGTGCAAAAAAAAAAAAAAAAACAAAACAACAA
Found at i:359754 original size:30 final size:31
Alignment explanation
Indices: 359718--359799 Score: 94
Period size: 30 Copynumber: 2.6 Consensus size: 31
359708 CAAAAACAAA
* * *
359718 AAAAAAACAAAACAACAACAACAAC-AACAC
1 AAAAAAACAAAACAAAAACAAAAACAAAAAC
*
359748 AAAAAAAGAAAACAAAAACAAAAACAAAAAC
1 AAAAAAACAAAACAAAAACAAAAACAAAAAC
359779 AAAAATACACACAAACAAAAA
1 AAAAA-A-ACA-AAACAAAAA
359800 AAAGAAAAAA
Statistics
Matches: 43, Mismatches: 5, Indels: 4
0.83 0.10 0.08
Matches are distributed among these distances:
30 22 0.51
31 9 0.21
32 1 0.02
33 2 0.05
34 9 0.21
ACGTcount: A:0.78, C:0.20, G:0.01, T:0.01
Consensus pattern (31 bp):
AAAAAAACAAAACAAAAACAAAAACAAAAAC
Found at i:359771 original size:48 final size:47
Alignment explanation
Indices: 359710--359812 Score: 135
Period size: 48 Copynumber: 2.2 Consensus size: 47
359700 CAAAAGTGCA
359710 AAAACAAAAAAAAAAC-AAAACAACAACA-ACA-AC-AACACAAAAAAAG
1 AAAACAAAAAAAAAACAAAAACAA-AA-ATACACACAAACA-AAAAAAAG
359756 AAAACAAAAACAAAAACAAAAACAAAAATACACACAAACAAAAAAAAG
1 AAAACAAAAA-AAAAACAAAAACAAAAATACACACAAACAAAAAAAAG
359804 AAAA-AAAAA
1 AAAACAAAAA
359813 GGAAGAGAAC
Statistics
Matches: 52, Mismatches: 0, Indels: 9
0.85 0.00 0.15
Matches are distributed among these distances:
46 11 0.21
47 16 0.31
48 21 0.40
49 4 0.08
ACGTcount: A:0.81, C:0.17, G:0.02, T:0.01
Consensus pattern (47 bp):
AAAACAAAAAAAAAACAAAAACAAAAATACACACAAACAAAAAAAAG
Found at i:359793 original size:18 final size:18
Alignment explanation
Indices: 359708--359783 Score: 86
Period size: 17 Copynumber: 4.3 Consensus size: 18
359698 CTCAAAAGTG
359708 CAAAAACAAAAA-AAAAA
1 CAAAAACAAAAACAAAAA
* *
359725 C-AAAACAACAACAACAA
1 CAAAAACAAAAACAAAAA
* *
359742 C-AACACAAAAAAAGAAAA
1 CAAAAACAAAAACA-AAAA
359760 CAAAAACAAAAACAAAAA
1 CAAAAACAAAAACAAAAA
359778 CAAAAA
1 CAAAAA
359784 TACACACAAA
Statistics
Matches: 48, Mismatches: 8, Indels: 5
0.79 0.13 0.08
Matches are distributed among these distances:
16 9 0.19
17 15 0.31
18 14 0.29
19 10 0.21
ACGTcount: A:0.80, C:0.18, G:0.01, T:0.00
Consensus pattern (18 bp):
CAAAAACAAAAACAAAAA
Found at i:359810 original size:12 final size:12
Alignment explanation
Indices: 359709--359812 Score: 68
Period size: 12 Copynumber: 8.2 Consensus size: 12
359699 TCAAAAGTGC
359709 AAAAAC-AAAAA
1 AAAAACAAAAAA
359720 AAAAACAAAACAA
1 AAAAACAAAA-AA
*
359733 CAACAACAACAACACA
1 -AAAAACAA-AA-A-A
*
359749 AAAAA-AGAAAAC
1 AAAAACA-AAAAA
*
359761 AAAAACAAAAAC
1 AAAAACAAAAAA
*
359773 AAAAACAAAAAT
1 AAAAACAAAAAA
* *
359785 ACACACAAACAAA
1 AAAAACAAA-AAA
*
359798 AAAAAGAAAAAA
1 AAAAACAAAAAA
359810 AAA
1 AAA
359813 GGAAGAGAAC
Statistics
Matches: 75, Mismatches: 10, Indels: 15
0.75 0.10 0.15
Matches are distributed among these distances:
11 6 0.08
12 37 0.49
13 12 0.16
14 10 0.13
15 9 0.12
16 1 0.01
ACGTcount: A:0.81, C:0.16, G:0.02, T:0.01
Consensus pattern (12 bp):
AAAAACAAAAAA
Found at i:359810 original size:58 final size:52
Alignment explanation
Indices: 359708--359813 Score: 122
Period size: 58 Copynumber: 1.9 Consensus size: 52
359698 CTCAAAAGTG
* * *
359708 CAAAAACAAAAAAAAAACAAAACAACAACAACAACAACACAAAAAAAGAAAA
1 CAAAAACAAAAAAAAAACAAAACAACAACAAAAAAAACAAAAAAAAAGAAAA
*
359760 CAAAAACAAAAACAAAAACAAAAATACACACAAACAAAAAAAAGAAAAAAAAAG
1 CAAAAACAAAAA-AAAAAC--AAA-ACA-AC-AACAAAAAAAACAAAAAAAAAG
359814 GAAGAGAACA
Statistics
Matches: 44, Mismatches: 4, Indels: 6
0.81 0.07 0.11
Matches are distributed among these distances:
52 12 0.27
53 6 0.14
55 3 0.07
56 3 0.07
57 2 0.05
58 18 0.41
ACGTcount: A:0.79, C:0.17, G:0.03, T:0.01
Consensus pattern (52 bp):
CAAAAACAAAAAAAAAACAAAACAACAACAAAAAAAACAAAAAAAAAGAAAA
Found at i:361109 original size:31 final size:30
Alignment explanation
Indices: 361043--361124 Score: 128
Period size: 30 Copynumber: 2.7 Consensus size: 30
361033 ATACCTTCTT
*
361043 AAAGTCCACGACTCAGTGACATTTTGTCCC
1 AAAGTCCACGACTCAGTGGCATTTTGTCCC
*
361073 AAAGTCCACGACTCAGTGGCATTTTTTCTCC
1 AAAGTCCACGACTCAGTGGCATTTTGTC-CC
*
361104 AAAGTCCACAACTCAGTGGCA
1 AAAGTCCACGACTCAGTGGCA
361125 ATCTCTTTTC
Statistics
Matches: 48, Mismatches: 3, Indels: 1
0.92 0.06 0.02
Matches are distributed among these distances:
30 26 0.54
31 22 0.46
ACGTcount: A:0.28, C:0.29, G:0.17, T:0.26
Consensus pattern (30 bp):
AAAGTCCACGACTCAGTGGCATTTTGTCCC
Found at i:361138 original size:31 final size:31
Alignment explanation
Indices: 361072--361219 Score: 105
Period size: 31 Copynumber: 4.7 Consensus size: 31
361062 CATTTTGTCC
* *
361072 CAAAGTCCACGACTCAGTGGC-AT-TTTTTCT
1 CAAAGTCCACAACTCAGTGGCAATCTCTTT-T
361102 CCAAAGTCCACAACTCAGTGGCAATCTCTTTT
1 -CAAAGTCCACAACTCAGTGGCAATCTCTTTT
*
361134 CAAAGTCCACAACTTC-GTGGC-A-CCCTTTT
1 CAAAGTCCACAAC-TCAGTGGCAATCTCTTTT
*
361163 --AAGTCCACAACTCTA-TGGCATCTTTCTCCTTTT
1 CAAAGTCCACAACTC-AGTGGCA---ATCT-CTTTT
* *
361196 CAAAAGCCCACAAGTCAGTGGCAA
1 C-AAAGTCCACAACTCAGTGGCAA
361220 CCTATAAAAG
Statistics
Matches: 94, Mismatches: 8, Indels: 28
0.72 0.06 0.22
Matches are distributed among these distances:
26 2 0.02
27 15 0.16
29 6 0.06
30 1 0.01
31 38 0.40
32 6 0.06
33 9 0.10
35 1 0.01
36 16 0.17
ACGTcount: A:0.27, C:0.30, G:0.14, T:0.28
Consensus pattern (31 bp):
CAAAGTCCACAACTCAGTGGCAATCTCTTTT
Found at i:361181 original size:27 final size:29
Alignment explanation
Indices: 361104--361184 Score: 80
Period size: 27 Copynumber: 2.8 Consensus size: 29
361094 TTTTTTCTCC
*
361104 AAAGTCCACAACTC-AGTGGCAATCTCTTTT
1 AAAGTCCACAACTCTA-TGGC-ATCCCTTTT
*
361134 CAAAGTCCACAACT-TCGTGGCA-CCCTTTT
1 -AAAGTCCACAACTCT-ATGGCATCCCTTTT
361163 -AAGTCCACAACTCTATGGCATC
1 AAAGTCCACAACTCTATGGCATC
361185 TTTCTCCTTT
Statistics
Matches: 43, Mismatches: 3, Indels: 11
0.75 0.05 0.19
Matches are distributed among these distances:
27 17 0.40
28 2 0.05
29 6 0.14
30 1 0.02
31 17 0.40
ACGTcount: A:0.28, C:0.31, G:0.14, T:0.27
Consensus pattern (29 bp):
AAAGTCCACAACTCTATGGCATCCCTTTT
Found at i:361327 original size:49 final size:49
Alignment explanation
Indices: 361255--361725 Score: 477
Period size: 49 Copynumber: 9.8 Consensus size: 49
361245 AGCATATTCT
* * * *
361255 TTTAAGCCCAATATCGCTGGCCTTGAATTAGCATATTGGCACCTTCACC
1 TTTAAGTCCAATATCGCTGGCCTTGAATCAGCACATTGGCACCTTCATC
* * *
361304 TTTAAGTCCAATGTTGCTGGCCTTGAATCAGCACATTGGCATCTTCATC
1 TTTAAGTCCAATATCGCTGGCCTTGAATCAGCACATTGGCACCTTCATC
** * *
361353 TTTAAGTCCGGTATCGCTGGCCTTGAATCAGCATATTGGCACCGTCATC
1 TTTAAGTCCAATATCGCTGGCCTTGAATCAGCACATTGGCACCTTCATC
*
361402 TTTAAGAT-CAATTTCGCTGGCCTTGAATCAGCACATTGGCA----C--C
1 TTTAAG-TCCAATATCGCTGGCCTTGAATCAGCACATTGGCACCTTCATC
* * ** *
361445 TTTAAGTCCAATATCGCTAGCCTTGAATCAGCATATTGGCACCTTTGTA
1 TTTAAGTCCAATATCGCTGGCCTTGAATCAGCACATTGGCACCTTCATC
* * *
361494 TTTAAGACCAATGTCGCTGGCCTTAAATCAGCACATTGGCA-C--CA--
1 TTTAAGTCCAATATCGCTGGCCTTGAATCAGCACATTGGCACCTTCATC
* *
361538 -TTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCGCCTTTGTCATC
1 TTTAAGTCCAATATCGCTGGCCTTGAATCAGCACATTGGCACC--T-TCATC
* *
361589 TTTAAGTCCAATGTCGCTGGCCTTGAATCAGCACATTGGCACC-TCTGTC
1 TTTAAGTCCAATATCGCTGGCCTTGAATCAGCACATTGGCACCTTC-ATC
* *
361638 TTT-AGTACTAATGTCGCTGGCCTTGAATCAGCACATTGGCACCTTCATC
1 TTTAAGT-CCAATATCGCTGGCCTTGAATCAGCACATTGGCACCTTCATC
* * * * * * *
361687 TTCAAGACTAAATGTCGCTGACCGTGAATCAACACATTG
1 TTTAAGTC-CAATATCGCTGGCCTTGAATCAGCACATTG
361726 ACATCCTTTT
Statistics
Matches: 353, Mismatches: 47, Indels: 43
0.80 0.11 0.10
Matches are distributed among these distances:
42 1 0.00
43 72 0.20
44 1 0.00
45 1 0.00
48 6 0.02
49 202 0.57
50 31 0.09
52 39 0.11
ACGTcount: A:0.24, C:0.26, G:0.19, T:0.31
Consensus pattern (49 bp):
TTTAAGTCCAATATCGCTGGCCTTGAATCAGCACATTGGCACCTTCATC
Found at i:361446 original size:21 final size:20
Alignment explanation
Indices: 361422--361489 Score: 50
Period size: 21 Copynumber: 3.2 Consensus size: 20
361412 ATTTCGCTGG
361422 CCTTGAATCAGCACATTGGCA
1 CCTTGAATCAGCA-ATTGGCA
* *
361443 CCTTTAAGTC--CAATATCGCTA
1 CCTTGAA-TCAGCAAT-TGGC-A
361464 GCCTTGAATCAGCATATTGGCA
1 -CCTTGAATCAGCA-ATTGGCA
361486 CCTT
1 CCTT
361490 TGTATTTAAG
Statistics
Matches: 36, Mismatches: 4, Indels: 14
0.67 0.07 0.26
Matches are distributed among these distances:
19 2 0.06
20 5 0.14
21 13 0.36
22 9 0.25
23 5 0.14
24 2 0.06
ACGTcount: A:0.26, C:0.28, G:0.16, T:0.29
Consensus pattern (20 bp):
CCTTGAATCAGCAATTGGCA
Found at i:361498 original size:92 final size:94
Alignment explanation
Indices: 361255--361734 Score: 524
Period size: 92 Copynumber: 5.0 Consensus size: 94
361245 AGCATATTCT
* * ** *
361255 TTTAAGCCCAATATCGCTGGCCTTGAATTAGCATATTGGCACCTTCACCTTTAAGTCCAATGTTG
1 TTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTTCATATTTAAGTCCAATGTCG
361320 CTGGCCTTGAATCAGCACATTGGCATCTTCATC
66 CTGGCCTTGAATCAGCACATTGGCA---TC-TC
** * * *
361353 TTTAAGTCCGGTATCGCTGGCCTTGAATCAGCATATTGGCACCGTCATCTTTAAGAT-CAATTTC
1 TTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTTCATATTTAAG-TCCAATGTC
361417 GCTGGCCTTGAATCAGCACATTGGCA-C-C
65 GCTGGCCTTGAATCAGCACATTGGCATCTC
* ** *
361445 TTTAAGTCCAATATCGCTAGCCTTGAATCAGCATATTGGCACCTTTGTATTTAAGACCAATGTCG
1 TTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTTCATATTTAAGTCCAATGTCG
*
361510 CTGGCCTTAAATCAGCACATTGGCA-C-C
66 CTGGCCTTGAATCAGCACATTGGCATCTC
* * *
361537 ATTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCGCCTTTGTCATCTTTAAGTCCAATG
1 TTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCACC--T-TCATATTTAAGTCCAATG
361602 TCGCTGGCCTTGAATCAGCACATTGGCACCTCTGTC
63 TCGCTGGCCTTGAATCAGCACATTGGCA--TC--TC
* * * * * * *
361638 TTT-AGTACTAATGTCGCTGGCCTTGAATCAGCACATTGGCACCTTCATCTTCAAGACTAAATGT
1 TTTAAGT-CCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTTCATATTTAAGTC-CAATGT
* * * *
361702 CGCTGACCGTGAATCAACACATTGACATC-C
64 CGCTGGCCTTGAATCAGCACATTGGCATCTC
361732 TTT
1 TTT
361735 TTCTCATCTT
Statistics
Matches: 331, Mismatches: 38, Indels: 30
0.83 0.10 0.08
Matches are distributed among these distances:
92 122 0.37
94 6 0.02
95 41 0.12
97 2 0.01
98 92 0.28
99 30 0.09
100 3 0.01
101 35 0.11
ACGTcount: A:0.24, C:0.26, G:0.18, T:0.31
Consensus pattern (94 bp):
TTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTTCATATTTAAGTCCAATGTCG
CTGGCCTTGAATCAGCACATTGGCATCTC
Found at i:361941 original size:176 final size:173
Alignment explanation
Indices: 361647--362028 Score: 568
Period size: 176 Copynumber: 2.2 Consensus size: 173
361637 CTTTAGTACT
361647 AATGTCGCTGGCCTTGAATCAGCACATTGGCACCTTCATCTTCAAGACTAAATGTCGCTGACCGT
1 AATGTCGCTGGCCTTGAATCAGCACATTGGCACCTTCATCTTCAAGACTAAATGTCGCTGACCGT
361712 GAATCAACACATTGACATCCTTTTTCTCATCTTTAAACCCAATATCATTGGCCGTGAATCAACAT
66 GAATCAACACATTGACATCCTTTTTCTCATCTTTAAACCCAATATCATTGGCCGTGAATCAACAT
*
361777 ATTGGTCCTTTTATCACTCCTCCCCCTCATCATCTTTAAAACCC
131 ATTGGTCCTTTTATCACTCCTCACCCTCATCATCTTT-AAACCC
* * *
361821 AATGTCGCTGGCCTTGAATCAGCACATTGGCATTCTGCTCATCTTCAAGTCT-AATGTTGCTGAC
1 AATGTCGCTGGCCTTGAATCAGCACATTGGCA-CCT--TCATCTTCAAGACTAAATGTCGCTGAC
* * * *
361885 CGTGAATCAGCATATTGACATCCTTTTTCTCATCTTTTAACCCAATATCGTTGGCCGTGAATCAA
63 CGTGAATCAACACATTGACATCCTTTTTCTCATCTTTAAACCCAATATCATTGGCCGTGAATCAA
* * **
361950 CGTATTGGTCCTTTTATCACTCCTCATCCTCATCATCTTTAAGTCC
128 CATATTGGTCCTTTTATCACTCCTCACCCTCATCATCTTTAAACCC
* * * * *
361996 AGTGTGGCAGGCCTTGAATCTGCACAGTGGCAC
1 AATGTCGCTGGCCTTGAATCAGCACATTGGCAC
362029 ATTGCAAAAC
Statistics
Matches: 187, Mismatches: 18, Indels: 6
0.89 0.09 0.03
Matches are distributed among these distances:
174 32 0.17
175 33 0.18
176 109 0.58
177 13 0.07
ACGTcount: A:0.24, C:0.28, G:0.15, T:0.33
Consensus pattern (173 bp):
AATGTCGCTGGCCTTGAATCAGCACATTGGCACCTTCATCTTCAAGACTAAATGTCGCTGACCGT
GAATCAACACATTGACATCCTTTTTCTCATCTTTAAACCCAATATCATTGGCCGTGAATCAACAT
ATTGGTCCTTTTATCACTCCTCACCCTCATCATCTTTAAACCC
Found at i:362665 original size:32 final size:32
Alignment explanation
Indices: 362616--362686 Score: 106
Period size: 32 Copynumber: 2.2 Consensus size: 32
362606 AACAAGTAAC
*
362616 TGTATCGACACATAAGTGCTGTATCGACACAA
1 TGTATCGACACACAAGTGCTGTATCGACACAA
* * *
362648 TGTATCGATACACAAGTGTTGTATCGATACAA
1 TGTATCGACACACAAGTGCTGTATCGACACAA
362680 TGTATCG
1 TGTATCG
362687 CTACGAAGCT
Statistics
Matches: 35, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
32 35 1.00
ACGTcount: A:0.32, C:0.18, G:0.20, T:0.30
Consensus pattern (32 bp):
TGTATCGACACACAAGTGCTGTATCGACACAA
Done.