Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold350
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: 1036165
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32
File 3 of 8
Found at i:244521 original size:20 final size:20
Alignment explanation
Indices: 244481--244521 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 20
244471 TACAAAATGA
* *
244481 AATTGTATCGATATAATTAC
1 AATTGTATCGATAAAACTAC
*
244501 AATTGTATCTATAAAACTAC
1 AATTGTATCGATAAAACTAC
244521 A
1 A
244522 TTTCTAGAAC
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.44, C:0.12, G:0.07, T:0.37
Consensus pattern (20 bp):
AATTGTATCGATAAAACTAC
Found at i:245335 original size:33 final size:33
Alignment explanation
Indices: 245298--245364 Score: 98
Period size: 33 Copynumber: 2.0 Consensus size: 33
245288 TTCAACGATT
245298 TGTATCGATACATAAAATGTTGTATCGATACAA
1 TGTATCGATACATAAAATGTTGTATCGATACAA
*** *
245331 TGTATCGATACATATTTTTTTGTATCGATACAA
1 TGTATCGATACATAAAATGTTGTATCGATACAA
245364 T
1 T
245365 TTAAGCTACT
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
33 30 1.00
ACGTcount: A:0.34, C:0.12, G:0.13, T:0.40
Consensus pattern (33 bp):
TGTATCGATACATAAAATGTTGTATCGATACAA
Found at i:245336 original size:13 final size:13
Alignment explanation
Indices: 245318--245342 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
245308 CATAAAATGT
245318 TGTATCGATACAA
1 TGTATCGATACAA
245331 TGTATCGATACA
1 TGTATCGATACA
245343 TATTTTTTTG
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:245424 original size:13 final size:13
Alignment explanation
Indices: 245406--245430 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
245396 ATTACTCAAA
245406 TGTATCGATACAT
1 TGTATCGATACAT
245419 TGTATCGATACA
1 TGTATCGATACA
245431 CTGATCTTTG
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:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:245532 original size:52 final size:52
Alignment explanation
Indices: 245439--245568 Score: 201
Period size: 52 Copynumber: 2.5 Consensus size: 52
245429 CACTGATCTT
* *
245439 TGTATCGATACATGCAGGC-AATTTGCCCAGATGTATCGATACA-TTTTAAAA
1 TGTATCGATACATGCAGGCAAATTTTCCCAGATGTATCGATACACTATT-AAA
245490 TGTATCGATACATGCAGGCAAATTTTCCCAGATGTATCGATACACTATTAAA
1 TGTATCGATACATGCAGGCAAATTTTCCCAGATGTATCGATACACTATTAAA
* *
245542 TGTATCGATACATGCAAGCAACTTTTC
1 TGTATCGATACATGCAGGCAAATTTTC
245569 ATATTTCGGG
Statistics
Matches: 73, Mismatches: 4, Indels: 3
0.91 0.05 0.04
Matches are distributed among these distances:
51 19 0.26
52 51 0.70
53 3 0.04
ACGTcount: A:0.33, C:0.19, G:0.16, T:0.32
Consensus pattern (52 bp):
TGTATCGATACATGCAGGCAAATTTTCCCAGATGTATCGATACACTATTAAA
Found at i:249795 original size:11 final size:11
Alignment explanation
Indices: 249779--249803 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
249769 TAAAGTGAAT
249779 GAAAAAAAGAG
1 GAAAAAAAGAG
249790 GAAAAAAAGAG
1 GAAAAAAAGAG
249801 GAA
1 GAA
249804 CTTCTCATTT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.72, C:0.00, G:0.28, T:0.00
Consensus pattern (11 bp):
GAAAAAAAGAG
Found at i:262368 original size:7 final size:7
Alignment explanation
Indices: 262349--262398 Score: 66
Period size: 7 Copynumber: 7.3 Consensus size: 7
262339 TTATTAATAG
*
262349 GATTTAT
1 GATTTGT
262356 GA-TTGT
1 GATTTGT
262362 GATTTGT
1 GATTTGT
*
262369 GATTTGA
1 GATTTGT
262376 GATTTGT
1 GATTTGT
*
262383 GAATTGT
1 GATTTGT
262390 GATTTGT
1 GATTTGT
262397 GA
1 GA
262399 ATCGTGGTGG
Statistics
Matches: 37, Mismatches: 5, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
6 5 0.14
7 32 0.86
ACGTcount: A:0.22, C:0.00, G:0.28, T:0.50
Consensus pattern (7 bp):
GATTTGT
Found at i:263298 original size:14 final size:14
Alignment explanation
Indices: 263266--263302 Score: 51
Period size: 14 Copynumber: 2.7 Consensus size: 14
263256 AATTCTATTT
263266 TATTACTC-TTGCA
1 TATTACTCTTTGCA
263279 TATTACTCTTTGCA
1 TATTACTCTTTGCA
263293 -AGTTACTCTT
1 TA-TTACTCTT
263303 ATTTGTTACT
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
13 9 0.41
14 13 0.59
ACGTcount: A:0.22, C:0.22, G:0.08, T:0.49
Consensus pattern (14 bp):
TATTACTCTTTGCA
Found at i:264340 original size:15 final size:15
Alignment explanation
Indices: 264320--264348 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
264310 ACATCCCCCA
264320 ATGAAACGTTTAATG
1 ATGAAACGTTTAATG
264335 ATGAAACGTTTAAT
1 ATGAAACGTTTAAT
264349 ATTTTGGAGA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.41, C:0.07, G:0.17, T:0.34
Consensus pattern (15 bp):
ATGAAACGTTTAATG
Found at i:264616 original size:131 final size:131
Alignment explanation
Indices: 264382--264635 Score: 366
Period size: 131 Copynumber: 1.9 Consensus size: 131
264372 TGGAGTATCC
* * * * *
264382 CCTCGGAAATAACGGTGTTGGAGTATCCCCGATTATGAAAAATTAGTGGTTTGGAAATAAAAACG
1 CCTCGGAAATAACGGGGTTGGAATATCCCCGATTATGAAAAATTAATAGTTTAGAAATAAAAACG
*
264447 GGGTTGGAGTATCCCCTCGAAAATAACGGGATTGGAGTATCCCCGATTGTGAAAAATCAGTGTTC
66 GGGTTGGAGTATCCCCTCGAAAATAACGGGATTGGAGTATCCCCGATTATGAAAAATCAGTGTTC
264512 T
131 T
* * * * **
264513 CCTCGGAAATAACGGGGTTTGAATATCCTCGATTGTGAAAAATTAATATTTTAGAAATAAAGCCG
1 CCTCGGAAATAACGGGGTTGGAATATCCCCGATTATGAAAAATTAATAGTTTAGAAATAAAAACG
* *
264578 GGGTTGGAGTATCCCCTTGAAAATAACAGGG-TTGGAGTATCCTCGATTATGAAAAATC
66 GGGTTGGAGTATCCCCTCGAAAATAAC-GGGATTGGAGTATCCCCGATTATGAAAAATC
264636 GGTGATTTGG
Statistics
Matches: 108, Mismatches: 14, Indels: 2
0.87 0.11 0.02
Matches are distributed among these distances:
131 105 0.97
132 3 0.03
ACGTcount: A:0.33, C:0.15, G:0.24, T:0.28
Consensus pattern (131 bp):
CCTCGGAAATAACGGGGTTGGAATATCCCCGATTATGAAAAATTAATAGTTTAGAAATAAAAACG
GGGTTGGAGTATCCCCTCGAAAATAACGGGATTGGAGTATCCCCGATTATGAAAAATCAGTGTTC
T
Found at i:267054 original size:30 final size:30
Alignment explanation
Indices: 267018--267087 Score: 140
Period size: 30 Copynumber: 2.3 Consensus size: 30
267008 CATTGAGAAA
267018 TGTATCGATACATCTAGGTGCAACCTAGAT
1 TGTATCGATACATCTAGGTGCAACCTAGAT
267048 TGTATCGATACATCTAGGTGCAACCTAGAT
1 TGTATCGATACATCTAGGTGCAACCTAGAT
267078 TGTATCGATA
1 TGTATCGATA
267088 TAATGAACAA
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 40 1.00
ACGTcount: A:0.30, C:0.19, G:0.20, T:0.31
Consensus pattern (30 bp):
TGTATCGATACATCTAGGTGCAACCTAGAT
Found at i:267102 original size:50 final size:50
Alignment explanation
Indices: 267048--267159 Score: 170
Period size: 50 Copynumber: 2.2 Consensus size: 50
267038 CAACCTAGAT
* * * * *
267048 TGTATCGATACATCTAGGTGCAACCTAGATTGTATCGATATAATGAACAA
1 TGTATCGATACATCTAGGTGAAACCCAAAATGTATCGATACAATGAACAA
*
267098 TGTATCGATACATCTGGGTGAAACCCAAAATGTATCGATACAATGAACAA
1 TGTATCGATACATCTAGGTGAAACCCAAAATGTATCGATACAATGAACAA
267148 TGTATCGATACA
1 TGTATCGATACA
267160 AATTGTGAAA
Statistics
Matches: 56, Mismatches: 6, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
50 56 1.00
ACGTcount: A:0.38, C:0.17, G:0.18, T:0.28
Consensus pattern (50 bp):
TGTATCGATACATCTAGGTGAAACCCAAAATGTATCGATACAATGAACAA
Found at i:267670 original size:34 final size:34
Alignment explanation
Indices: 267631--267710 Score: 97
Period size: 34 Copynumber: 2.4 Consensus size: 34
267621 CTTTTTAAGG
* *
267631 ACAAAGGAAAAGGAGTACGTCCTGCTCTTTGAGA
1 ACAAAGGAAAAGGAGTACGTCCTGATCTTCGAGA
* * * *
267665 ACAAAGGAAAATGAGTATGTCCTTATCTTCGAGG
1 ACAAAGGAAAAGGAGTACGTCCTGATCTTCGAGA
*
267699 ACAAAGAAAAAG
1 ACAAAGGAAAAG
267711 AGAATGAAAT
Statistics
Matches: 38, Mismatches: 8, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
34 38 1.00
ACGTcount: A:0.41, C:0.15, G:0.24, T:0.20
Consensus pattern (34 bp):
ACAAAGGAAAAGGAGTACGTCCTGATCTTCGAGA
Found at i:267752 original size:42 final size:41
Alignment explanation
Indices: 267698--267800 Score: 104
Period size: 42 Copynumber: 2.5 Consensus size: 41
267688 TATCTTCGAG
* * *
267698 GACAAAG-AAAAA-GAGAATGAAATG-GGTCTTGCTCCTTGAA
1 GACAAAGAAAAAAGGA-AATAAAATGCGTTC-TGCTCCTTCAA
*
267738 GACAAATGAAAAAAGGAAATAAAATGCGTTCTGCTCTTTCAA
1 GACAAA-GAAAAAAGGAAATAAAATGCGTTCTGCTCCTTCAA
267780 GACAAAGGAAAAGAAGGAAAT
1 GACAAA-GAAAA-AAGGAAAT
267801 TAAAGCGCGT
Statistics
Matches: 53, Mismatches: 5, Indels: 7
0.82 0.08 0.11
Matches are distributed among these distances:
40 6 0.11
41 1 0.02
42 33 0.62
43 13 0.25
ACGTcount: A:0.48, C:0.12, G:0.22, T:0.18
Consensus pattern (41 bp):
GACAAAGAAAAAAGGAAATAAAATGCGTTCTGCTCCTTCAA
Found at i:267916 original size:61 final size:60
Alignment explanation
Indices: 267824--268405 Score: 463
Period size: 61 Copynumber: 9.6 Consensus size: 60
267814 GTTTTTTGGG
* * ** *
267824 GACTAGAAGGTGCCACCAACTTGTGTGGGCTTTGCAAGAAGAAAGTGTCCTACTCTTTGAG
1 GACTAAAAGGTGCCACCAACTTGTGTAGGCTTTAAAAGAA-AAAGTGTCCTACTCTTTGAA
* * ** * * * * *
267885 GACTAAAAGGTGCCACTAGCACGTATAGGCTTTAAAAAGGATAGGCGTCCTACTCTTTGAA
1 GACTAAAAGGTGCCACCAACTTGTGTAGGCTTT-AAAAGAAAAAGTGTCCTACTCTTTGAA
* * * *
267946 GATTGAAAGGTGCCACCAACTTGTGTAGGCTTTAAAAGGAAAAGATGTCCTGCTCTTTGAA
1 GACTAAAAGGTGCCACCAACTTGTGTAGGCTTTAAAAGAAAAAG-TGTCCTACTCTTTGAA
* * *
268007 GACTGAAAA-GTGCCACCAACTTGTGTAGGCTTTAAAAGGAAAATGTGTCCTACTTTTTGAG
1 GACT-AAAAGGTGCCACCAACTTGTGTAGGCTTTAAAA-GAAAAAGTGTCCTACTCTTTGAA
* * * * * ** * *
268068 GACTAGAAGGTGCCACCAATTTGTGTGGGCTTTGAAAG-GAAAGCATCCTACACTTTGAG
1 GACTAAAAGGTGCCACCAACTTGTGTAGGCTTTAAAAGAAAAAGTGTCCTACTCTTTGAA
** * * * * *
268127 GACTGGAAGGTGCCACCAACTTGTGTCGGCTTTAAAAGGAAAAG-GCATCATGCTCTTTGAG
1 GACTAAAAGGTGCCACCAACTTGTGTAGGCTTTAAAAGAAAAAGTG--TCCTACTCTTTGAA
* * * * * * * *
268188 GACTAAAAGATACCACGAACTTGTGTGGGTTTTAAAA-AAAAATGCGTCCTGCTCTTTGAG
1 GACTAAAAGGTGCCACCAACTTGTGTAGGCTTTAAAAGAAAAA-GTGTCCTACTCTTTGAA
* * * * * * *
268248 GACTGAAAGGTGCCACCAAATTGTGTGGGCTTTAAAAGGAAAAGGTGTCCTGCCCTTTGAG
1 GACTAAAAGGTGCCACCAACTTGTGTAGGCTTTAAAA-GAAAAAGTGTCCTACTCTTTGAA
* * * * * ** * *
268309 GATTAGAAGGTGCCACCAACTTGTGTGGGCTTTGAAAG-GAAAGCATCCTACTTTTTGAG
1 GACTAAAAGGTGCCACCAACTTGTGTAGGCTTTAAAAGAAAAAGTGTCCTACTCTTTGAA
** * *
268368 GACTGGAAGGTGCTACCAACTTGTGTGGGCTTTAAAAG
1 GACTAAAAGGTGCCACCAACTTGTGTAGGCTTTAAAAG
268406 GGGAAAGAAA
Statistics
Matches: 424, Mismatches: 85, Indels: 26
0.79 0.16 0.05
Matches are distributed among these distances:
59 97 0.23
60 66 0.16
61 244 0.58
62 17 0.04
ACGTcount: A:0.29, C:0.18, G:0.26, T:0.27
Consensus pattern (60 bp):
GACTAAAAGGTGCCACCAACTTGTGTAGGCTTTAAAAGAAAAAGTGTCCTACTCTTTGAA
Found at i:268186 original size:120 final size:120
Alignment explanation
Indices: 267818--268406 Score: 653
Period size: 120 Copynumber: 4.9 Consensus size: 120
267808 CGTCCTGTTT
* * **
267818 TTTGGGGACTAGAAGGTGCCACCAACTTGTGTGGGCTTTGCAAGAAGAAAGTGTCCTACTCTTTG
1 TTTGAGGACTAGAAGGTGCCACCAACTTGTGTGGGCTTTG-AA-AGGAAAGCATCCTACTCTTTG
* * * ** * *
267883 AGGACTAAAAGGTGCCACTAGCACGTATAGGCTTTAAAAAGG-ATAGGCGTCCTACTC
64 AGGACTGAAAGGTGCCACCAACTTGTGTAGGCTTT-AAAAGGAAAAGGCGTCCTACTC
* * * * *
267940 TTTGAAGA-TTGAAAGGTGCCACCAACTTGTGTAGGCTTTAAAAGGAAAAG-ATGTCCTGCTCTT
1 TTTGAGGACTAG-AAGGTGCCACCAACTTGTGTGGGCTTTGAAAGG-AAAGCA--TCCTACTCTT
* * * * *
268003 TGAAGACTGAAAAGTGCCACCAACTTGTGTAGGCTTTAAAAGGAAAATGTGTCCTACTT
62 TGAGGACTGAAAGGTGCCACCAACTTGTGTAGGCTTTAAAAGGAAAAGGCGTCCTACTC
* *
268062 TTTGAGGACTAGAAGGTGCCACCAATTTGTGTGGGCTTTGAAAGGAAAGCATCCTACACTTTGAG
1 TTTGAGGACTAGAAGGTGCCACCAACTTGTGTGGGCTTTGAAAGGAAAGCATCCTACTCTTTGAG
* * * * *
268127 GACTGGAAGGTGCCACCAACTTGTGTCGGCTTTAAAAGGAAAAGGCATCATGCTC
66 GACTGAAAGGTGCCACCAACTTGTGTAGGCTTTAAAAGGAAAAGGCGTCCTACTC
* * * * * * ** * *
268182 TTTGAGGACTAAAAGATACCACGAACTTGTGTGGGTTTTAAAAAAAAATGCGTCCTGCTCTTTGA
1 TTTGAGGACTAGAAGGTGCCACCAACTTGTGTGGGCTTTGAAAGGAAA-GCATCCTACTCTTTGA
* * * * *
268247 GGACTGAAAGGTGCCACCAAATTGTGTGGGCTTTAAAAGGAAAAGGTGTCCTGCCC
65 GGACTGAAAGGTGCCACCAACTTGTGTAGGCTTTAAAAGGAAAAGGCGTCCTACTC
* *
268303 TTTGAGGATTAGAAGGTGCCACCAACTTGTGTGGGCTTTGAAAGGAAAGCATCCTACTTTTTGAG
1 TTTGAGGACTAGAAGGTGCCACCAACTTGTGTGGGCTTTGAAAGGAAAGCATCCTACTCTTTGAG
* * *
268368 GACTGGAAGGTGCTACCAACTTGTGTGGGCTTTAAAAGG
66 GACTGAAAGGTGCCACCAACTTGTGTAGGCTTTAAAAGG
268407 GGAAAGAAAA
Statistics
Matches: 388, Mismatches: 71, Indels: 18
0.81 0.15 0.04
Matches are distributed among these distances:
120 148 0.38
121 119 0.31
122 119 0.31
123 2 0.01
ACGTcount: A:0.29, C:0.18, G:0.26, T:0.27
Consensus pattern (120 bp):
TTTGAGGACTAGAAGGTGCCACCAACTTGTGTGGGCTTTGAAAGGAAAGCATCCTACTCTTTGAG
GACTGAAAGGTGCCACCAACTTGTGTAGGCTTTAAAAGGAAAAGGCGTCCTACTC
Found at i:268290 original size:241 final size:240
Alignment explanation
Indices: 267816--268406 Score: 763
Period size: 241 Copynumber: 2.4 Consensus size: 240
267806 CGCGTCCTGT
* * **
267816 TTTTTGGGGACTAGAAGGTGCCACCAACTTGTGTGGGCTTTGCAAGAAGAAAGTGTCCTACTCTT
1 TTTTTGAGGACTAGAAGGTGCCACCAACTTGTGTGGGCTTTG-AA-AGGAAAGCATCCTACTCTT
** * * ** * * * *
267881 TGAGGACTAAAAGGTGCCACTAGCACGTATAGGCTTTAAAAAGGATAGGCGTCCTACTCTTTGAA
64 TGAGGACTGGAAGGTGCCACCAACTTGTGTAGGCTTT-AAAAGGAAAGGCATCATACTCTTTGAA
* * * *
267946 GATTGAAAGGTGCCACCAACTTGTGTAGGCTTTAAAAGGAAAAGATGTCCTGCTCTTTGAAGACT
128 GACTAAAAGATACCACCAACTTGTGTAGGCTTTAAAA-GAAAAGATGTCCTGCTCTTTGAAGACT
* *
268011 GAAAAGTGCCACCAACTTGTGTAGGCTTTAAAAGGAAAATGTGTCCTAC
192 GAAAAGTGCCACCAAATTGTGTAGGCTTTAAAAGGAAAAGGTGTCCTAC
* *
268060 TTTTTGAGGACTAGAAGGTGCCACCAATTTGTGTGGGCTTTGAAAGGAAAGCATCCTACACTTTG
1 TTTTTGAGGACTAGAAGGTGCCACCAACTTGTGTGGGCTTTGAAAGGAAAGCATCCTACTCTTTG
* * *
268125 AGGACTGGAAGGTGCCACCAACTTGTGTCGGCTTTAAAAGGAAAAGGCATCATGCTCTTTGAGGA
66 AGGACTGGAAGGTGCCACCAACTTGTGTAGGCTTTAAAAGG-AAAGGCATCATACTCTTTGAAGA
* * * *
268190 CTAAAAGATACCACGAACTTGTGTGGGTTTTAAAA-AAAA-ATGCGTCCTGCTCTTTGAGGACTG
130 CTAAAAGATACCACCAACTTGTGTAGGCTTTAAAAGAAAAGAT--GTCCTGCTCTTTGAAGACTG
* * *
268253 AAAGGTGCCACCAAATTGTGTGGGCTTTAAAAGGAAAAGGTGTCCTGC
193 AAAAGTGCCACCAAATTGTGTAGGCTTTAAAAGGAAAAGGTGTCCTAC
** * *
268301 CCTTTGAGGATTAGAAGGTGCCACCAACTTGTGTGGGCTTTGAAAGGAAAGCATCCTACTTTTTG
1 TTTTTGAGGACTAGAAGGTGCCACCAACTTGTGTGGGCTTTGAAAGGAAAGCATCCTACTCTTTG
* *
268366 AGGACTGGAAGGTGCTACCAACTTGTGTGGGCTTTAAAAGG
66 AGGACTGGAAGGTGCCACCAACTTGTGTAGGCTTTAAAAGG
268407 GGAAAGAAAA
Statistics
Matches: 304, Mismatches: 40, Indels: 9
0.86 0.11 0.03
Matches are distributed among these distances:
239 2 0.01
240 4 0.01
241 166 0.55
242 90 0.30
243 2 0.01
244 40 0.13
ACGTcount: A:0.29, C:0.18, G:0.26, T:0.27
Consensus pattern (240 bp):
TTTTTGAGGACTAGAAGGTGCCACCAACTTGTGTGGGCTTTGAAAGGAAAGCATCCTACTCTTTG
AGGACTGGAAGGTGCCACCAACTTGTGTAGGCTTTAAAAGGAAAGGCATCATACTCTTTGAAGAC
TAAAAGATACCACCAACTTGTGTAGGCTTTAAAAGAAAAGATGTCCTGCTCTTTGAAGACTGAAA
AGTGCCACCAAATTGTGTAGGCTTTAAAAGGAAAAGGTGTCCTAC
Found at i:268479 original size:42 final size:42
Alignment explanation
Indices: 268428--268655 Score: 235
Period size: 43 Copynumber: 5.4 Consensus size: 42
268418 GAAGGAGGCA
* *
268428 TCCTTCTCTTTGAGGACTAAAGG-AAAAATGAAATAAAATGCG
1 TCCTGCTCTTTGAGGAC-AAAGGAAAAAAGGAAATAAAATGCG
* * * * *
268470 TCATACTCTTTGAGGACAAAGGAAAAAAAGGAAATTAAGTGTG
1 TCCTGCTCTTTGAGGACAAAGG-AAAAAAGGAAATAAAATGCG
* * * * *
268513 TCCTGCTCTTTAAGAATAAAAG-AAAAAGGAAATAAAATGCA
1 TCCTGCTCTTTGAGGACAAAGGAAAAAAGGAAATAAAATGCG
* * * *
268554 TCCTACTCTTTGAGGACAAAGGAAAAGAAGGAAATTAAGTGTG
1 TCCTGCTCTTTGAGGACAAAGGAAAA-AAGGAAATAAAATGCG
* * *
268597 TCCTGCTCTTTGAGGACAATGGAAAAAAAGAAATAAAATGAG
1 TCCTGCTCTTTGAGGACAAAGGAAAAAAGGAAATAAAATGCG
*
268639 TCCTGCTCTTGGAGGAC
1 TCCTGCTCTTTGAGGAC
268656 TAGAAGGTGC
Statistics
Matches: 150, Mismatches: 32, Indels: 8
0.79 0.17 0.04
Matches are distributed among these distances:
41 37 0.25
42 46 0.31
43 67 0.45
ACGTcount: A:0.42, C:0.13, G:0.21, T:0.24
Consensus pattern (42 bp):
TCCTGCTCTTTGAGGACAAAGGAAAAAAGGAAATAAAATGCG
Found at i:268563 original size:41 final size:41
Alignment explanation
Indices: 268425--268564 Score: 109
Period size: 41 Copynumber: 3.3 Consensus size: 41
268415 AAAGAAGGAG
* * * * *
268425 GCATCCTTCTCTTTGAGGACTAAAGGAAAAATGAAATAAAAT
1 GCATCCTACTCTTT-AAGAATAAAAGAAAAAGGAAATAAAAT
* * * * * * * *
268467 GCGTCATACTCTTTGAGGACAAAGGAAAAAAAGGAAATTAAGT
1 GCATCCTACTCTTTAAGAATAAA--AGAAAAAGGAAATAAAAT
** *
268510 GTGTCCTGCTCTTTAAGAATAAAAGAAAAAGGAAATAAAAT
1 GCATCCTACTCTTTAAGAATAAAAGAAAAAGGAAATAAAAT
268551 GCATCCTACTCTTT
1 GCATCCTACTCTTT
268565 GAGGACAAAG
Statistics
Matches: 71, Mismatches: 25, Indels: 5
0.70 0.25 0.05
Matches are distributed among these distances:
41 30 0.42
42 11 0.15
43 30 0.42
ACGTcount: A:0.42, C:0.14, G:0.18, T:0.26
Consensus pattern (41 bp):
GCATCCTACTCTTTAAGAATAAAAGAAAAAGGAAATAAAAT
Found at i:268622 original size:84 final size:84
Alignment explanation
Indices: 268428--268655 Score: 305
Period size: 84 Copynumber: 2.7 Consensus size: 84
268418 GAAGGAGGCA
* * * *
268428 TCCTTCTCTTTGAGGACTAAAGGAAAAATGAAATAAAATGCGTCATACTCTTTGAGGACAAAGGA
1 TCCTGCTCTTTGAGGAC-AAAGGAAAAAAGAAATAAAATGCATCCTACTCTTTGAGGACAAAGGA
268493 AAAAAAGGAAATTAAGTGTG
65 AAAAAAGGAAATTAAGTGTG
* * * * *
268513 TCCTGCTCTTTAAGAATAAAAGAAAAAGGAAATAAAATGCATCCTACTCTTTGAGGACAAAGGAA
1 TCCTGCTCTTTGAGGACAAAGGAAAAAAGAAATAAAATGCATCCTACTCTTTGAGGACAAAGGAA
*
268578 AAGAAGGAAATTAAGTGTG
66 AAAAAGGAAATTAAGTGTG
* * *
268597 TCCTGCTCTTTGAGGACAATGGAAAAAAAGAAATAAAATG-AGTCCTGCTCTTGGAGGAC
1 TCCTGCTCTTTGAGGACAAAGG-AAAAAAGAAATAAAATGCA-TCCTACTCTTTGAGGAC
268656 TAGAAGGTGC
Statistics
Matches: 124, Mismatches: 17, Indels: 4
0.86 0.12 0.03
Matches are distributed among these distances:
84 80 0.65
85 44 0.35
ACGTcount: A:0.42, C:0.13, G:0.21, T:0.24
Consensus pattern (84 bp):
TCCTGCTCTTTGAGGACAAAGGAAAAAAGAAATAAAATGCATCCTACTCTTTGAGGACAAAGGAA
AAAAAGGAAATTAAGTGTG
Found at i:268785 original size:61 final size:60
Alignment explanation
Indices: 268638--269486 Score: 697
Period size: 61 Copynumber: 13.9 Consensus size: 60
268628 AATAAAATGA
* * * *
268638 GTCCTGCTCTTGGAGGACT-AGAAGGTGCTACCAACTTATGTGGGCTTTGAAAA-GAAA-GC
1 GTCCTGCTCTTTGAGGACTGA-AAGGTGCCACCAACTTGTGTGGGCTTT-AAAAGGAAAGGT
* * * * *
268697 GTCCTACTCTTTAAGGATTTG-AAGGTGCCACCAACTTGTGTGAGCTTTAAAAGGAGGAGGT
1 GTCCTGCTCTTTGAGGA-CTGAAAGGTGCCACCAACTTGTGTGGGCTTTAAAAGGA-AAGGT
* * *
268758 ATCCTGCTCTTTGAGAACTGAAAGGTGCTACCAACTTGTGTGGGCTTTAAAAGGAAAAGGT
1 GTCCTGCTCTTTGAGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTTAAAAGG-AAAGGT
*
268819 GTCCTGCTCTTTGAGGACTGAAAGGTGCCACCAACTCGTGTGGGCTTTAAAAAGGAAAGGT
1 GTCCTGCTCTTTGAGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTT-AAAAGGAAAGGT
** *
268880 GTCCTGCTCTTTGAAAACTGAAAGGTGCTACCAACTTGTGTGGGCTTTAAAAGGAAAAGGT
1 GTCCTGCTCTTTGAGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTTAAAAGG-AAAGGT
* * *
268941 GTCCTGCTCTTTGAGGACT-AGAAGGTGCCACCAACTTTTATGGGCTTT--AAGG-CA---
1 GTCCTGCTCTTTGAGGACTGA-AAGGTGCCACCAACTTGTGTGGGCTTTAAAAGGAAAGGT
* *
268995 -TCCTGCACTTTGAAGACTGAAAGGTGCCACCAACTTGTGTGGGCTTTAAAAGGAAAAAGGAAAG
1 GTCCTGCTCTTTGAGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTTAAAAGG--AAA-G---G
*
269059 C
60 T
* * * * *
269060 GTCCTG-TTTTTGAGGACT-AAAAGTGCCACCAACTCGTGTGGGCTTTAAAAGGAAATGC
1 GTCCTGCTCTTTGAGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTTAAAAGGAAAGGT
* * * **
269118 GTCCTGCTCTTTGAGGACTAAAAAGGCGCCACCAGCTTGTGTGGGCTTTCAAAAGGAAAAGAC
1 GTCCTGCTCTTTGAGGACT-GAAAGGTGCCACCAACTTGTGTGGGCTTT-AAAAGG-AAAGGT
* * ** *
269181 GTCTTGCTCTCTGAGGACT-AAAGAGTGCCACCAACTCATGTGGGCTTTGAAAATGGAAACGAT
1 GTCCTGCTCTTTGAGGACTGAAAG-GTGCCACCAACTTGTGTGGGCTTT-AAAA-GGAAA-GGT
* * * ** * *
269244 GTCTTGCTCTTTGAGGACTAAAGAGGTGCCACTAGTTTGTGTGGGCTTTCCAAAGGAAAAGGC
1 GTCCTGCTCTTTGAGGACTGAA-AGGTGCCACCAACTTGTGTGGGCTTT-AAAAGG-AAAGGT
* * * * ** *
269307 GTCCTGTTCTTTGAAGACT-AAAGAGTGCCACTAACTCGTGTGGGCTTTGAAAAAAAAAAAGAT
1 GTCCTGCTCTTTGAGGACTGAAAG-GTGCCACCAACTTGTGTGGGCTTT---AAAAGGAAAGGT
* * * * * ** * *
269370 GTCATACACTTTGAGGACTAAAGAGGTGCCACCAGCTCATGTGGGCTTTGAAAAGAAAAAGGC
1 GTCCTGCTCTTTGAGGACTGAA-AGGTGCCACCAACTTGTGTGGGCTTT-AAAAG-GAAAGGT
* * * * *
269433 ATCATGCTCTTTGAGGACT-ATAGGGTGCCACCAACTCGTGTAGGCTTTGAAAAG
1 GTCCTGCTCTTTGAGGACTGA-AAGGTGCCACCAACTTGTGTGGGCTTT-AAAAG
269487 AAAAAAGACT
Statistics
Matches: 650, Mismatches: 98, Indels: 81
0.78 0.12 0.10
Matches are distributed among these distances:
53 41 0.06
54 1 0.00
55 4 0.01
57 1 0.00
58 13 0.02
59 55 0.08
60 11 0.02
61 220 0.34
62 99 0.15
63 102 0.16
64 85 0.13
65 13 0.02
66 5 0.01
ACGTcount: A:0.29, C:0.19, G:0.27, T:0.26
Consensus pattern (60 bp):
GTCCTGCTCTTTGAGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTTAAAAGGAAAGGT
Found at i:268866 original size:122 final size:122
Alignment explanation
Indices: 268638--269486 Score: 832
Period size: 126 Copynumber: 6.9 Consensus size: 122
268628 AATAAAATGA
* * * * *
268638 GTCCTGCTCTTGGAGGACTAGAAGGTGCTACCAACTTATGTGGGCTTTGAAAA-G-AAA-GCGTC
1 GTCCTGCTCTTTGAGGACTAAAAGGTGCCACCAACTTGTGTGGGCTTTCAAAAGGAAAAGGCGTC
* * * * * * *
268700 CTACTCTTTAAGGATTTGAAGGTGCCACCAACTTGTGTGAGCTTT-AAAAGGAGGAGGT
66 CTGCTCTTTGAGGA-CTAAAGGTGCCACCAACTCGTGTGGGCTTTGAAAAGGA-AAGGT
* * * * *
268758 ATCCTGCTCTTTGAGAACTGAAAGGTGCTACCAACTTGTGTGGGCTTT-AAAAGGAAAAGGTGTC
1 GTCCTGCTCTTTGAGGACTAAAAGGTGCCACCAACTTGTGTGGGCTTTCAAAAGGAAAAGGCGTC
*
268822 CTGCTCTTTGAGGACTGAAAGGTGCCACCAACTCGTGTGGGCTTTAAAAAGGAAAGGT
66 CTGCTCTTTGAGGACT-AAAGGTGCCACCAACTCGTGTGGGCTTTGAAAAGGAAAGGT
** * * *
268880 GTCCTGCTCTTTGAAAACTGAAAGGTGCTACCAACTTGTGTGGGCTTT-AAAAGGAAAAGGTGTC
1 GTCCTGCTCTTTGAGGACTAAAAGGTGCCACCAACTTGTGTGGGCTTTCAAAAGGAAAAGGCGTC
** * *
268944 CTGCTCTTTGAGGACTAGAAGGTGCCACCAACTTTTATGGGCTTT---AAGG-CA---
66 CTGCTCTTTGAGGACTA-AAGGTGCCACCAACTCGTGTGGGCTTTGAAAAGGAAAGGT
* * *
268995 -TCCTGCACTTTGAAGACTGAAAGGTGCCACCAACTTGTGTGGGCTTT-AAAAGGAAAAAGGAAA
1 GTCCTGCTCTTTGAGGACTAAAAGGTGCCACCAACTTGTGTGGGCTTTCAAAAGG-AAAA-G---
* * * *
269058 GCGTCCTG-TTTTTGAGGACTAAAAGTGCCACCAACTCGTGTGGGCTTT-AAAAGGAAATGC
61 GCGTCCTGCTCTTTGAGGACTAAAGGTGCCACCAACTCGTGTGGGCTTTGAAAAGGAAAGGT
* * *
269118 GTCCTGCTCTTTGAGGACTAAAAAGGCGCCACCAGCTTGTGTGGGCTTTCAAAAGGAAAAGACGT
1 GTCCTGCTCTTTGAGGACT-AAAAGGTGCCACCAACTTGTGTGGGCTTTCAAAAGGAAAAGGCGT
* * * *
269183 CTTGCTCTCTGAGGACTAAAGAGTGCCACCAACTCATGTGGGCTTTGAAAATGGAAACGAT
65 CCTGCTCTTTGAGGACTAAAG-GTGCCACCAACTCGTGTGGGCTTTGAAAA-GGAAA-GGT
* * ** *
269244 GTCTTGCTCTTTGAGGACTAAAGAGGTGCCACTAGTTTGTGTGGGCTTTCCAAAGGAAAAGGCGT
1 GTCCTGCTCTTTGAGGACTAAA-AGGTGCCACCAACTTGTGTGGGCTTTCAAAAGGAAAAGGCGT
* * * ** *
269309 CCTGTTCTTTGAAGACTAAAGAGTGCCACTAACTCGTGTGGGCTTTGAAAAAAAAAAAGAT
65 CCTGCTCTTTGAGGACTAAAG-GTGCCACCAACTCGTGTGGGCTTTG--AAAAGGAAAGGT
* * * * ** * * *
269370 GTCATACACTTTGAGGACTAAAGAGGTGCCACCAGCTCATGTGGGCTTTGAAAAGAAAAAGGCAT
1 GTCCTGCTCTTTGAGGACTAAA-AGGTGCCACCAACTTGTGTGGGCTTTCAAAAGGAAAAGGCGT
* * *
269435 CATGCTCTTTGAGGACTATAGGGTGCCACCAACTCGTGTAGGCTTTGAAAAG
65 CCTGCTCTTTGAGGACTA-AAGGTGCCACCAACTCGTGTGGGCTTTGAAAAG
269487 AAAAAAGACT
Statistics
Matches: 624, Mismatches: 76, Indels: 54
0.83 0.10 0.07
Matches are distributed among these distances:
114 50 0.08
115 4 0.01
116 1 0.00
117 23 0.04
118 13 0.02
119 19 0.03
120 44 0.07
121 11 0.02
122 160 0.26
123 30 0.05
124 25 0.04
125 38 0.06
126 197 0.32
127 5 0.01
128 4 0.01
ACGTcount: A:0.29, C:0.19, G:0.27, T:0.26
Consensus pattern (122 bp):
GTCCTGCTCTTTGAGGACTAAAAGGTGCCACCAACTTGTGTGGGCTTTCAAAAGGAAAAGGCGTC
CTGCTCTTTGAGGACTAAAGGTGCCACCAACTCGTGTGGGCTTTGAAAAGGAAAGGT
Found at i:269022 original size:53 final size:53
Alignment explanation
Indices: 268942--269043 Score: 152
Period size: 53 Copynumber: 1.9 Consensus size: 53
268932 GGAAAAGGTG
* * *
268942 TCCTGCTCTTTGAGGACTAGAAGGTGCCACCAACTTTTATGGGCTTTAAGGCA
1 TCCTGCACTTTGAAGACTAGAAGGTGCCACCAACTTGTATGGGCTTTAAGGCA
*
268995 TCCTGCACTTTGAAGACT-GAAAGGTGCCACCAACTTGTGTGGGCTTTAA
1 TCCTGCACTTTGAAGACTAG-AAGGTGCCACCAACTTGTATGGGCTTTAA
269044 AAGGAAAAAG
Statistics
Matches: 44, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
52 1 0.02
53 43 0.98
ACGTcount: A:0.24, C:0.23, G:0.25, T:0.29
Consensus pattern (53 bp):
TCCTGCACTTTGAAGACTAGAAGGTGCCACCAACTTGTATGGGCTTTAAGGCA
Found at i:269223 original size:62 final size:62
Alignment explanation
Indices: 269002--269491 Score: 461
Period size: 63 Copynumber: 7.8 Consensus size: 62
268992 GCATCCTGCA
* * *
269002 CTTTGAAGACTGAAAG-GTGCCACCAACTTGTGTGGGCTTT-AAAAGGAAAAAGGAAAGCGTCCT
1 CTTTGAGGACT-AAAGAGTGCCACCAACTCGTGTGGGCTTTGAAAAGG-AAAA-G--A-CGTCAT
269065 G-T
60 GCT
* * *
269067 TTTTGAGGACTAAA-AGTGCCACCAACTCGTGTGGGCTTT-AAAAGGAAATG-CGTCCTGCT
1 CTTTGAGGACTAAAGAGTGCCACCAACTCGTGTGGGCTTTGAAAAGGAAAAGACGTCATGCT
* * * * * *
269126 CTTTGAGGACTAAAAAGGCGCCACCAGCTTGTGTGGGCTTTCAAAAGGAAAAGACGTCTTGCT
1 CTTTGAGGACTAAAGA-GTGCCACCAACTCGTGTGGGCTTTGAAAAGGAAAAGACGTCATGCT
* * * * *
269189 CTCTGAGGACTAAAGAGTGCCACCAACTCATGTGGGCTTTGAAAATGGAAACGATGTCTTGCT
1 CTTTGAGGACTAAAGAGTGCCACCAACTCGTGTGGGCTTTGAAAA-GGAAAAGACGTCATGCT
* ** * ** * * *
269252 CTTTGAGGACTAAAGAGGTGCCACTAGTTTGTGTGGGCTTTCCAAAGGAAAAGGCGTCCTGTT
1 CTTTGAGGACTAAAGA-GTGCCACCAACTCGTGTGGGCTTTGAAAAGGAAAAGACGTCATGCT
* * ** * * *
269315 CTTTGAAGACTAAAGAGTGCCACTAACTCGTGTGGGCTTTGAAAAAAAAAAAGATGTCATACA
1 CTTTGAGGACTAAAGAGTGCCACCAACTCGTGTGGGCTTTG-AAAAGGAAAAGACGTCATGCT
* * * * *
269378 CTTTGAGGACTAAAGAGGTGCCACCAGCTCATGTGGGCTTTGAAAAGAAAAAGGCATCATGCT
1 CTTTGAGGACTAAAGA-GTGCCACCAACTCGTGTGGGCTTTGAAAAGGAAAAGACGTCATGCT
* * * *
269441 CTTTGAGGACTATAGGGTGCCACCAACTCGTGTAGGCTTTGAAAAGAAAAA
1 CTTTGAGGACTAAAGAGTGCCACCAACTCGTGTGGGCTTTGAAAAGGAAAA
269492 AGACTAAAGA
Statistics
Matches: 354, Mismatches: 61, Indels: 23
0.81 0.14 0.05
Matches are distributed among these distances:
58 7 0.02
59 14 0.04
60 1 0.00
61 21 0.06
62 88 0.25
63 138 0.39
64 76 0.21
65 9 0.03
ACGTcount: A:0.31, C:0.19, G:0.26, T:0.25
Consensus pattern (62 bp):
CTTTGAGGACTAAAGAGTGCCACCAACTCGTGTGGGCTTTGAAAAGGAAAAGACGTCATGCT
Found at i:269595 original size:61 final size:60
Alignment explanation
Indices: 269493--269809 Score: 352
Period size: 61 Copynumber: 5.2 Consensus size: 60
269483 AAAGAAAAAA
* * ** *
269493 GACTAAAGATGCCACCAACTTGTGTAAGC-TTGAAAAGAAAAAAGCGTCCTACTCTTTAAG
1 GACTAAAGGTGCCACCAACTCGTGTGGGCTTTGAAAA-AAAAAAGCGTCCTACTCTTTGAG
* * * * *
269553 GAATAAATGATGCCACCAACTTGTGTGGGCTTTGAAAAAAAAAGGCATCCTACTCTTTGAG
1 GACTAAA-GGTGCCACCAACTCGTGTGGGCTTTGAAAAAAAAAAGCGTCCTACTCTTTGAG
* * * * * *
269614 GACTAAAAGGTGCCACCAACTCATGTGGGCTTTGAACAGAAAAAGGCATCATGCTCTTTGAG
1 GACT-AAAGGTGCCACCAACTCGTGTGGGCTTTGAA-AAAAAAAAGCGTCCTACTCTTTGAG
269676 GACTAAAGGTGCCACCAACTCGTGTGGGC-TTGAAAAAAAAAAGAAAGCGTCCTACTCTTTGAG
1 GACTAAAGGTGCCACCAACTCGTGTGGGCTTTG---AAAAAAA-AAAGCGTCCTACTCTTTGAG
* *
269739 GACTAAAGGGTGCCACCAACTCGAGTGGGCTTT-AAAAAGAAAAAGGTGTCCTACTCTTTGAG
1 GACTAAA-GGTGCCACCAACTCGTGTGGGCTTTGAAAAA-AAAAA-GCGTCCTACTCTTTGAG
269801 GACTAAAGG
1 GACTAAAGG
269810 GCTGAAAGGG
Statistics
Matches: 224, Mismatches: 21, Indels: 23
0.84 0.08 0.09
Matches are distributed among these distances:
60 9 0.04
61 102 0.46
62 65 0.29
63 25 0.11
64 21 0.09
65 2 0.01
ACGTcount: A:0.35, C:0.20, G:0.23, T:0.23
Consensus pattern (60 bp):
GACTAAAGGTGCCACCAACTCGTGTGGGCTTTGAAAAAAAAAAGCGTCCTACTCTTTGAG
Found at i:269616 original size:166 final size:170
Alignment explanation
Indices: 269320--269657 Score: 443
Period size: 166 Copynumber: 2.0 Consensus size: 170
269310 CTGTTCTTTG
* ** * *
269320 AAGACTAAAGAGTGCCACTAACTCGTGTGGGCTTTGAAAAAAAAAAAGATGTCATACACTTTGAG
1 AAGACTAAAGAGTGCCACCAACTCGTGTAAGCTTTGAAAAAAAAAAAGACGTCATACACTTTAAG
* * *
269385 GACTAAAGAGGTGCCACCAGCTCATGTGGGCTTTGAAAAGAAAAAGGCATCATGCTCTTTGAGGA
66 GAATAAAGA-GTGCCACCAACTCATGTGGGCTTTGAAAAGAAAAAGGCATCATACTCTTTGAGGA
* * *
269450 CTATAGGGTGCCACCAACTCGTGTAGGCTTTGAAAAGAAAA
130 CTAAAAGGTGCCACCAACTCATGTAGGCTTTGAAAAGAAAA
* * * *
269491 AAGACTAAAGA-TGCCACCAACTTGTGTAAGC-TTGAAAAGAAAAAAG-CGTCCTACTCTTTAAG
1 AAGACTAAAGAGTGCCACCAACTCGTGTAAGCTTTGAAAAAAAAAAAGACGTCATACACTTTAAG
** *
269553 GAATAAATGA-TGCCACCAACTTGTGTGGGCTTTGAAAA-AAAAAGGCATCCTACTCTTTGAGGA
66 GAATAAA-GAGTGCCACCAACTCATGTGGGCTTTGAAAAGAAAAAGGCATCATACTCTTTGAGGA
* *
269616 CTAAAAGGTGCCACCAACTCATGTGGGCTTTGAACAGAAAA
130 CTAAAAGGTGCCACCAACTCATGTAGGCTTTGAAAAGAAAA
269657 A
1 A
269658 GGCATCATGC
Statistics
Matches: 146, Mismatches: 20, Indels: 7
0.84 0.12 0.04
Matches are distributed among these distances:
166 60 0.41
167 25 0.17
168 18 0.12
169 16 0.11
170 16 0.11
171 11 0.08
ACGTcount: A:0.37, C:0.18, G:0.22, T:0.22
Consensus pattern (170 bp):
AAGACTAAAGAGTGCCACCAACTCGTGTAAGCTTTGAAAAAAAAAAAGACGTCATACACTTTAAG
GAATAAAGAGTGCCACCAACTCATGTGGGCTTTGAAAAGAAAAAGGCATCATACTCTTTGAGGAC
TAAAAGGTGCCACCAACTCATGTAGGCTTTGAAAAGAAAA
Found at i:269756 original size:125 final size:122
Alignment explanation
Indices: 269525--269809 Score: 367
Period size: 125 Copynumber: 2.3 Consensus size: 122
269515 TGTAAGCTTG
* * * * * * *
269525 AAAAGAAAAAAGCGTCCTACTCTTTAAGGAATAAATGATGCCACCAACTTGTGTGGGCTTTGAAA
1 AAAAGAAAAAGGCATCATACTCTTTGAGGACTAAA-GGTGCCACCAACTCGTGTGGGCTTTGAAA
*
269590 AAAAAAGGCATCCTACTCTTTGAGGACTAAAAGGTGCCACCAACTC-ATGTGGGCTTTG
65 AAAAAAGGCATCCTACTCTTTGAGGACTAAAAGGTGCCACCAACTCGA-GTGGGCTTTA
* *
269648 AACAGAAAAAGGCATCATGCTCTTTGAGGACTAAAGGTGCCACCAACTCGTGTGGGC-TTGAAAA
1 AAAAGAAAAAGGCATCATACTCTTTGAGGACTAAAGGTGCCACCAACTCGTGTGGGCTTTG-AAA
* *
269712 AAAAAAGAAAGCGTCCTACTCTTTGAGGACTAAAGGGTGCCACCAACTCGAGTGGGCTTTA
65 AAAAAAG---GCATCCTACTCTTTGAGGACTAAAAGGTGCCACCAACTCGAGTGGGCTTTA
** *
269773 AAAAGAAAAAGGTGTCCTACTCTTTGAGGACTAAAGG
1 AAAAGAAAAAGGCATCATACTCTTTGAGGACTAAAGG
269810 GCTGAAAGGG
Statistics
Matches: 140, Mismatches: 17, Indels: 8
0.85 0.10 0.05
Matches are distributed among these distances:
121 3 0.02
122 30 0.21
123 28 0.20
125 78 0.56
126 1 0.01
ACGTcount: A:0.35, C:0.19, G:0.23, T:0.22
Consensus pattern (122 bp):
AAAAGAAAAAGGCATCATACTCTTTGAGGACTAAAGGTGCCACCAACTCGTGTGGGCTTTGAAAA
AAAAAGGCATCCTACTCTTTGAGGACTAAAAGGTGCCACCAACTCGAGTGGGCTTTA
Found at i:277946 original size:16 final size:16
Alignment explanation
Indices: 277925--277956 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
277915 AGGTGGCTTT
277925 TTGGTAGTACGATTGA
1 TTGGTAGTACGATTGA
*
277941 TTGGTATTACGATTGA
1 TTGGTAGTACGATTGA
277957 GGGAGAGGCT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.25, C:0.06, G:0.28, T:0.41
Consensus pattern (16 bp):
TTGGTAGTACGATTGA
Found at i:283714 original size:76 final size:75
Alignment explanation
Indices: 283634--283891 Score: 263
Period size: 76 Copynumber: 3.3 Consensus size: 75
283624 CAAAAAGAGG
* * * *
283634 CAGGGTTTGATTATCCCCTCGGAATACAGGGTTGGAGTATCCCCGGGATGAAAAATTAATATTTT
1 CAGGGTTGGAGTATCCCCTCGAAATACAGGGTTGGAGTATCCCCGAGA-GAAAAATTAATATTTT
*
283699 TCAAATAAAAA
65 TGAAATAAAAA
* *
283710 CAGGGTTGGAGTATCCCTTCAGAAATAACTA-GGTTGGAGTATCTCCGAGAGGAAAAATTAATAT
1 CAGGGTTGGAGTATCCCCTC-GAAAT-AC-AGGGTTGGAGTATCCCCGAGA-GAAAAATTAATAT
283774 TTTTGGAAATAAAAA
62 TTTT-GAAATAAAAA
* * *
283789 TAGAGTTGGAGTATCTCCTCGAAAATA-ATGGGATTGGAGTA-CCCCTGAGA-AAAAATTAATAT
1 CAGGGTTGGAGTATCCCCTCG-AAATACA-GGG-TTGGAGTATCCCC-GAGAGAAAAATTAATAT
*
283851 TTTGGAAATAAAAA
62 TTTTGAAATAAAAA
* * *
283865 TAGGGTTAGAGTATCCCTTCAGAAATA
1 CAGGGTTGGAGTATCCCCTC-GAAATA
283892 ACGTGGTCGA
Statistics
Matches: 154, Mismatches: 18, Indels: 20
0.80 0.09 0.10
Matches are distributed among these distances:
76 49 0.32
77 20 0.13
78 43 0.28
79 42 0.27
ACGTcount: A:0.37, C:0.13, G:0.22, T:0.28
Consensus pattern (75 bp):
CAGGGTTGGAGTATCCCCTCGAAATACAGGGTTGGAGTATCCCCGAGAGAAAAATTAATATTTTT
GAAATAAAAA
Found at i:283826 original size:79 final size:78
Alignment explanation
Indices: 283663--283893 Score: 296
Period size: 79 Copynumber: 3.0 Consensus size: 78
283653 CGGAATACAG
* * *
283663 GGTTGGAGTATCCCCGGGATGAAAAATTAATATTTTT-CAAATAAAAACAGGGTTGGAGTATCCC
1 GGTTGGAGTATCCCCGAGA-GAAAAATTAATATTTTTGGAAATAAAAATAGGGTTGGAGTATCCC
283727 TTCAGAAATAACTA
65 TTCAGAAATAACTA
* *
283741 GGTTGGAGTATCTCCGAGAGGAAAAATTAATATTTTTGGAAATAAAAATAGAGTTGGAGTATCTC
1 GGTTGGAGTATCCCCGAGA-GAAAAATTAATATTTTTGGAAATAAAAATAGGGTTGGAGTATC-C
*
283806 C-TC-GAAAATAA-TG
64 CTTCAG-AAATAACTA
*
283819 GGATTGGAGTA-CCCCTGAGA-AAAAATTAATA-TTTTGGAAATAAAAATAGGGTTAGAGTATCC
1 GG-TTGGAGTATCCCC-GAGAGAAAAATTAATATTTTTGGAAATAAAAATAGGGTTGGAGTATCC
283881 CTTCAGAAATAAC
64 CTTCAGAAATAAC
283894 GTGGTCGAAA
Statistics
Matches: 135, Mismatches: 10, Indels: 17
0.83 0.06 0.10
Matches are distributed among these distances:
75 2 0.01
76 36 0.27
77 12 0.09
78 41 0.30
79 42 0.31
80 2 0.01
ACGTcount: A:0.39, C:0.12, G:0.21, T:0.28
Consensus pattern (78 bp):
GGTTGGAGTATCCCCGAGAGAAAAATTAATATTTTTGGAAATAAAAATAGGGTTGGAGTATCCCT
TCAGAAATAACTA
Found at i:286514 original size:20 final size:21
Alignment explanation
Indices: 286489--286542 Score: 92
Period size: 20 Copynumber: 2.6 Consensus size: 21
286479 CATTTTAAGC
286489 ATGTATCGATACATTCACT-T
1 ATGTATCGATACATTCACTGT
286509 ATGTATCGATACATTCACTGT
1 ATGTATCGATACATTCACTGT
*
286530 TTGTATCGATACA
1 ATGTATCGATACA
286543 AATTGTAGAA
Statistics
Matches: 32, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
20 19 0.59
21 13 0.41
ACGTcount: A:0.30, C:0.19, G:0.13, T:0.39
Consensus pattern (21 bp):
ATGTATCGATACATTCACTGT
Found at i:289920 original size:28 final size:28
Alignment explanation
Indices: 289859--289929 Score: 90
Period size: 28 Copynumber: 2.5 Consensus size: 28
289849 TTCACAATCA
* *
289859 GGGATACTCCAACCCCGTTATTTCATCG
1 GGGATACTCCAACCCCATTATTTCATAG
* *
289887 GAGATACTCCAACCCCATTATTT-TTGAG
1 GGGATACTCCAACCCCATTATTTCAT-AG
289915 GGGATACTCCAACCC
1 GGGATACTCCAACCC
289930 TGGCTTTATT
Statistics
Matches: 37, Mismatches: 5, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
27 1 0.03
28 36 0.97
ACGTcount: A:0.25, C:0.31, G:0.17, T:0.27
Consensus pattern (28 bp):
GGGATACTCCAACCCCATTATTTCATAG
Found at i:290087 original size:30 final size:28
Alignment explanation
Indices: 290035--290092 Score: 82
Period size: 27 Copynumber: 2.0 Consensus size: 28
290025 TCACAATTGG
290035 GGATACTCCAACCCCATTATTTT-GAAA
1 GGATACTCCAACCCCATTATTTTCGAAA
290062 GGATACTCCAACCCCGATTTTATTTTCGAAA
1 GGATACTCCAACCCC-A--TTATTTTCGAAA
290093 CACCAATTTT
Statistics
Matches: 27, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
27 15 0.56
28 1 0.04
30 7 0.26
31 4 0.15
ACGTcount: A:0.31, C:0.26, G:0.12, T:0.31
Consensus pattern (28 bp):
GGATACTCCAACCCCATTATTTTCGAAA
Found at i:290100 original size:68 final size:68
Alignment explanation
Indices: 289965--290100 Score: 161
Period size: 68 Copynumber: 2.0 Consensus size: 68
289955 TCTCATAATC
* * ** * **
289965 GGGGATACTCCAACCTCGTTATTTCTGAGGGGATACTCCAACCCCAGTTTTATTTCTATTTCACA
1 GGGGATACTCCAACCCCATTATTTCTGAAAGGATACTCCAACCCCAGTTTTATTTCGATAACACA
290030 ATT
66 ATT
290033 GGGGATACTCCAACCCCATTATTT-TGAAAGGATACTCCAACCCC-GATTTTATTTTCGA-AACA
1 GGGGATACTCCAACCCCATTATTTCTGAAAGGATACTCCAACCCCAG-TTTTA-TTTCGATAACA
290095 CCAATT
64 -CAATT
290101 TTCTATAATC
Statistics
Matches: 58, Mismatches: 7, Indels: 6
0.82 0.10 0.08
Matches are distributed among these distances:
66 1 0.02
67 25 0.43
68 32 0.55
ACGTcount: A:0.27, C:0.26, G:0.15, T:0.32
Consensus pattern (68 bp):
GGGGATACTCCAACCCCATTATTTCTGAAAGGATACTCCAACCCCAGTTTTATTTCGATAACACA
ATT
Found at i:302211 original size:1 final size:1
Alignment explanation
Indices: 302205--302272 Score: 55
Period size: 1 Copynumber: 68.0 Consensus size: 1
302195 CCTTTATTCT
* * * * * * ** *
302205 AAAAAAAACAAAAATAAAGAAACAAAAATAAAAAAAAACAAAAGCAAAAAAAAAAAACAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
302270 AAA
1 AAA
302273 GAGAAAAGAA
Statistics
Matches: 50, Mismatches: 17, Indels: 0
0.75 0.25 0.00
Matches are distributed among these distances:
1 50 1.00
ACGTcount: A:0.87, C:0.07, G:0.03, T:0.03
Consensus pattern (1 bp):
A
Found at i:302241 original size:30 final size:29
Alignment explanation
Indices: 302209--302271 Score: 81
Period size: 29 Copynumber: 2.1 Consensus size: 29
302199 TATTCTAAAA
* * *
302209 AAAACAAAAATAAAGAAACAAAAATAAAAA
1 AAAACAAAAACAAA-AAAAAAAAACAAAAA
*
302239 AAAACAAAAGCAAAAAAAAAAAACAAAAA
1 AAAACAAAAACAAAAAAAAAAAACAAAAA
302268 AAAA
1 AAAA
302272 AGAGAAAAGA
Statistics
Matches: 29, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
29 17 0.59
30 12 0.41
ACGTcount: A:0.86, C:0.08, G:0.03, T:0.03
Consensus pattern (29 bp):
AAAACAAAAACAAAAAAAAAAAACAAAAA
Found at i:302253 original size:14 final size:13
Alignment explanation
Indices: 302206--302272 Score: 64
Period size: 15 Copynumber: 4.8 Consensus size: 13
302196 CTTTATTCTA
*
302206 AAAAAAACAAAAAT
1 AAAAAAA-AAAAAC
302220 AAAGAAACAAAAATA-
1 AAA-AAA-AAAAA-AC
302235 AAAAAAAACAAAAGC
1 AAAAAAAA-AAAA-C
302250 AAAAAAAAAAAAC
1 AAAAAAAAAAAAC
302263 AAAAAAAAAA
1 AAAAAAAAAA
302273 GAGAAAAGAA
Statistics
Matches: 47, Mismatches: 0, Indels: 13
0.78 0.00 0.22
Matches are distributed among these distances:
13 14 0.30
14 13 0.28
15 18 0.38
16 2 0.04
ACGTcount: A:0.87, C:0.07, G:0.03, T:0.03
Consensus pattern (13 bp):
AAAAAAAAAAAAC
Found at i:302272 original size:30 final size:30
Alignment explanation
Indices: 302205--302272 Score: 84
Period size: 30 Copynumber: 2.3 Consensus size: 30
302195 CCTTTATTCT
* * *
302205 AAAAAAAACAAAAATAAAGAAACAAAAATA
1 AAAAAAAACAAAAACAAAGAAAAAAAAAAA
*
302235 AAAAAAAACAAAAGCAAA-AAAAAAAAACAA
1 AAAAAAAACAAAAACAAAGAAAAAAAAA-AA
302265 AAAAAAAA
1 AAAAAAAA
302273 GAGAAAAGAA
Statistics
Matches: 33, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
29 8 0.24
30 25 0.76
ACGTcount: A:0.87, C:0.07, G:0.03, T:0.03
Consensus pattern (30 bp):
AAAAAAAACAAAAACAAAGAAAAAAAAAAA
Found at i:302279 original size:12 final size:11
Alignment explanation
Indices: 302205--302287 Score: 51
Period size: 12 Copynumber: 7.0 Consensus size: 11
302195 CCTTTATTCT
*
302205 AAAAAAAA-CA
1 AAAAAAAAGAA
*
302215 AAAATAAAGAA
1 AAAAAAAAGAA
*
302226 ACAAAAATAAAAA
1 A-AAAAA-AAGAA
302239 AAAACAAAAGCAAAA
1 AAAA-AAAAG---AA
*
302254 AAAAAAAACAA
1 AAAAAAAAGAA
302265 AAAAAAAAGAGA
1 AAAAAAAAGA-A
*
302277 AAAGAAAAGAA
1 AAAAAAAAGAA
302288 CCTGCTTAAG
Statistics
Matches: 57, Mismatches: 8, Indels: 15
0.71 0.10 0.19
Matches are distributed among these distances:
10 7 0.12
11 14 0.25
12 19 0.33
13 7 0.12
14 4 0.07
15 6 0.11
ACGTcount: A:0.84, C:0.06, G:0.07, T:0.02
Consensus pattern (11 bp):
AAAAAAAAGAA
Found at i:302279 original size:13 final size:13
Alignment explanation
Indices: 302205--302284 Score: 65
Period size: 13 Copynumber: 6.2 Consensus size: 13
302195 CCTTTATTCT
*
302205 AAAAAA-AACAAA
1 AAAAAAGAAAAAA
* *
302217 AATAAAGAAACAA
1 AAAAAAGAAAAAA
*
302230 AAATAA-AAAAAA
1 AAAAAAGAAAAAA
*
302242 ACAAAAGCAAAAAA
1 AAAAAAG-AAAAAA
*
302256 AAAAAACAAAAAA
1 AAAAAAGAAAAAA
*
302269 AAAAGAGAAAAGAA
1 AAAAAAGAAAA-AA
302283 AA
1 AA
302285 GAACCTGCTT
Statistics
Matches: 52, Mismatches: 12, Indels: 6
0.74 0.17 0.09
Matches are distributed among these distances:
12 14 0.27
13 23 0.44
14 15 0.29
ACGTcount: A:0.85, C:0.06, G:0.06, T:0.03
Consensus pattern (13 bp):
AAAAAAGAAAAAA
Found at i:302279 original size:19 final size:18
Alignment explanation
Indices: 302205--302272 Score: 72
Period size: 19 Copynumber: 3.9 Consensus size: 18
302195 CCTTTATTCT
302205 AAAA-AAAACAAAAATAAA
1 AAAACAAAACAAAAA-AAA
* *
302223 GAAAC-AAA-AATAAAAA
1 AAAACAAAACAAAAAAAA
302239 AAAACAAAAGCAAAAAAAA
1 AAAACAAAA-CAAAAAAAA
302258 AAAACAAAA-AAAAAA
1 AAAACAAAACAAAAAA
302273 GAGAAAAGAA
Statistics
Matches: 42, Mismatches: 4, Indels: 9
0.76 0.07 0.16
Matches are distributed among these distances:
16 7 0.17
17 13 0.31
18 6 0.14
19 16 0.38
ACGTcount: A:0.87, C:0.07, G:0.03, T:0.03
Consensus pattern (18 bp):
AAAACAAAACAAAAAAAA
Found at i:302827 original size:17 final size:17
Alignment explanation
Indices: 302805--302838 Score: 68
Period size: 17 Copynumber: 2.0 Consensus size: 17
302795 GATAAAGCGT
302805 TTGAAAAAAAAAAAAAA
1 TTGAAAAAAAAAAAAAA
302822 TTGAAAAAAAAAAAAAA
1 TTGAAAAAAAAAAAAAA
302839 AAATTAAATG
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.82, C:0.00, G:0.06, T:0.12
Consensus pattern (17 bp):
TTGAAAAAAAAAAAAAA
Found at i:302871 original size:21 final size:21
Alignment explanation
Indices: 302845--302901 Score: 105
Period size: 21 Copynumber: 2.7 Consensus size: 21
302835 AAAAAAATTA
302845 AATGTATCGATACATTTGTAG
1 AATGTATCGATACATTTGTAG
*
302866 AATGTATCGATACATTTGTGG
1 AATGTATCGATACATTTGTAG
302887 AATGTATCGATACAT
1 AATGTATCGATACAT
302902 CCTACAAATG
Statistics
Matches: 35, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
21 35 1.00
ACGTcount: A:0.33, C:0.11, G:0.19, T:0.37
Consensus pattern (21 bp):
AATGTATCGATACATTTGTAG
Found at i:302981 original size:19 final size:19
Alignment explanation
Indices: 302957--303024 Score: 85
Period size: 19 Copynumber: 3.9 Consensus size: 19
302947 AATTCAACAA
302957 TTTGTATCGATACATAAGT
1 TTTGTATCGATACATAAGT
302976 TTTGTATCGATAC--AA--
1 TTTGTATCGATACATAAGT
302991 --TGTATCGATACATAAGT
1 TTTGTATCGATACATAAGT
*
303008 ATTGTATCGATACATAA
1 TTTGTATCGATACATAA
303025 TTAGCTACTG
Statistics
Matches: 43, Mismatches: 0, Indels: 12
0.78 0.00 0.22
Matches are distributed among these distances:
13 11 0.26
15 2 0.05
17 2 0.05
19 28 0.65
ACGTcount: A:0.35, C:0.12, G:0.15, T:0.38
Consensus pattern (19 bp):
TTTGTATCGATACATAAGT
Found at i:302996 original size:13 final size:13
Alignment explanation
Indices: 302978--303002 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
302968 ACATAAGTTT
302978 TGTATCGATACAA
1 TGTATCGATACAA
302991 TGTATCGATACA
1 TGTATCGATACA
303003 TAAGTATTGT
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:303000 original size:32 final size:32
Alignment explanation
Indices: 302959--303021 Score: 117
Period size: 32 Copynumber: 2.0 Consensus size: 32
302949 TTCAACAATT
*
302959 TGTATCGATACATAAGTTTTGTATCGATACAA
1 TGTATCGATACATAAGTATTGTATCGATACAA
302991 TGTATCGATACATAAGTATTGTATCGATACA
1 TGTATCGATACATAAGTATTGTATCGATACA
303022 TAATTAGCTA
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
32 30 1.00
ACGTcount: A:0.35, C:0.13, G:0.16, T:0.37
Consensus pattern (32 bp):
TGTATCGATACATAAGTATTGTATCGATACAA
Found at i:303082 original size:13 final size:13
Alignment explanation
Indices: 303064--303089 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
303054 CATTTTTCTG
303064 TGTATCGATACAT
1 TGTATCGATACAT
303077 TGTATCGATACAT
1 TGTATCGATACAT
303090 GGATCTTTGT
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:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:303086 original size:33 final size:33
Alignment explanation
Indices: 303044--303110 Score: 98
Period size: 33 Copynumber: 2.0 Consensus size: 33
303034 GCCAAGGAAA
***
303044 TGTATCGATACATTTTTCTGTGTATCGATACAT
1 TGTATCGATACATGGATCTGTGTATCGATACAT
*
303077 TGTATCGATACATGGATCTTTGTATCGATACAT
1 TGTATCGATACATGGATCTGTGTATCGATACAT
303110 T
1 T
303111 TGGAAATTTT
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
33 30 1.00
ACGTcount: A:0.25, C:0.15, G:0.16, T:0.43
Consensus pattern (33 bp):
TGTATCGATACATGGATCTGTGTATCGATACAT
Found at i:305633 original size:28 final size:27
Alignment explanation
Indices: 305566--305638 Score: 94
Period size: 27 Copynumber: 2.7 Consensus size: 27
305556 CTTCACAATC
* *
305566 GGGGACACTCCAACCCCGTTAATCATC
1 GGGGATACTCCAACCCCGTTAATCATA
*
305593 GGGGATACTCCAACCCCGTTATTTC-TGA
1 GGGGATACTCCAACCCCGTTA-ATCAT-A
305621 GGGGATACTCCAACCCCG
1 GGGGATACTCCAACCCCG
305639 ACTTTATTTT
Statistics
Matches: 41, Mismatches: 3, Indels: 3
0.87 0.06 0.06
Matches are distributed among these distances:
27 21 0.51
28 20 0.49
ACGTcount: A:0.23, C:0.34, G:0.22, T:0.21
Consensus pattern (27 bp):
GGGGATACTCCAACCCCGTTAATCATA
Found at i:305683 original size:51 final size:51
Alignment explanation
Indices: 305621--305791 Score: 180
Period size: 51 Copynumber: 3.3 Consensus size: 51
305611 TTATTTCTGA
* * * *
305621 GGGGATACTCCAACCCCGACTTTATTTTGAAAATATCGATTTTTCATAATC
1 GGGGATACTCCAACCCCGATTTTATTTTAAAAATACCAATTTTTCATAATC
* * * * * *
305672 GGGGATACTCCAACCCCGGTTTTATTTTCACAACACCAATTTCTCCTTTAATC
1 GGGGATACTCCAACCCCGATTTTATTTTAAAAATACCAATTT-TTC-ATAATC
** * *
305725 GGGGATACTCCAATTCCGATTTTATTTCCAAAAATACCAATTTTTCACAATC
1 GGGGATACTCCAACCCCGATTTTATTT-TAAAAATACCAATTTTTCATAATC
*
305777 GAGGATACTCCAACC
1 GGGGATACTCCAACC
305792 TCGTTATTTC
Statistics
Matches: 95, Mismatches: 22, Indels: 5
0.78 0.18 0.04
Matches are distributed among these distances:
51 35 0.37
52 18 0.19
53 31 0.33
54 11 0.12
ACGTcount: A:0.29, C:0.26, G:0.12, T:0.33
Consensus pattern (51 bp):
GGGGATACTCCAACCCCGATTTTATTTTAAAAATACCAATTTTTCATAATC
Found at i:305810 original size:28 final size:28
Alignment explanation
Indices: 305774--305855 Score: 96
Period size: 28 Copynumber: 2.9 Consensus size: 28
305764 ATTTTTCACA
*
305774 ATCGAGGATACTCCAACCTCGTTATTTC
1 ATCGGGGATACTCCAACCTCGTTATTTC
* *
305802 ATCGGGGATACTCCAACCCCGTTACTTC
1 ATCGGGGATACTCCAACCTCGTTATTTC
*
305830 --CGAGGGAACACTCCAACCTCGTTATT
1 ATCG-GGG-ATACTCCAACCTCGTTATT
305856 ATCTCCAAAA
Statistics
Matches: 46, Mismatches: 6, Indels: 4
0.82 0.11 0.07
Matches are distributed among these distances:
26 2 0.04
27 3 0.07
28 41 0.89
ACGTcount: A:0.24, C:0.32, G:0.17, T:0.27
Consensus pattern (28 bp):
ATCGGGGATACTCCAACCTCGTTATTTC
Found at i:318281 original size:28 final size:29
Alignment explanation
Indices: 318230--318286 Score: 71
Period size: 28 Copynumber: 2.0 Consensus size: 29
318220 ACCTTCTCTT
318230 CAAAAAAAAGAAAAAAAAACAAAA-AAAA
1 CAAAAAAAAGAAAAAAAAACAAAAGAAAA
* * * *
318258 CAAAACAAAGAAAAAGAGAGAAAAGAAAA
1 CAAAAAAAAGAAAAAAAAACAAAAGAAAA
318287 AACCTACTTA
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
28 20 0.83
29 4 0.17
ACGTcount: A:0.82, C:0.07, G:0.11, T:0.00
Consensus pattern (29 bp):
CAAAAAAAAGAAAAAAAAACAAAAGAAAA
Found at i:319339 original size:55 final size:55
Alignment explanation
Indices: 319254--319766 Score: 788
Period size: 55 Copynumber: 9.3 Consensus size: 55
319244 TCCGCTTTTT
*
319254 AGTCCCCAAAGAGCAGGACACCTCTTAAAGCCCACACAAGTTGGTGGCACCTTTC
1 AGTCCTCAAAGAGCAGGACACCTCTTAAAGCCCACACAAGTTGGTGGCACCTTTC
319309 AGTCCTCAAAGAGCAGGACACCT-TTCAAAGCCCACACAAGTTGGTGGCA--TTGTCC
1 AGTCCTCAAAGAGCAGGACACCTCTT-AAAGCCCACACAAGTTGGTGGCACCTT-T-C
319364 AGTCCTCAAAGAGCAGGACACCTCTTAAAGCCCACACAAGTTGGTGGCACCTTTC
1 AGTCCTCAAAGAGCAGGACACCTCTTAAAGCCCACACAAGTTGGTGGCACCTTTC
319419 AGTCCTCAAAGAGCAGGACACCTCTTAAAGCCCACACAAGTTGGTGGCACCTTTC
1 AGTCCTCAAAGAGCAGGACACCTCTTAAAGCCCACACAAGTTGGTGGCACCTTTC
*
319474 AGTCCCCAAAGAGCAGGACACCTCTTAAAGCCCACACAAGTTGGTGGCACCTTTC
1 AGTCCTCAAAGAGCAGGACACCTCTTAAAGCCCACACAAGTTGGTGGCACCTTTC
*
319529 AGTCCTCAAAGAGCAGGACACCT-TTCAAAGCCCACACAAGTTGGTGGCA-TTTTCC
1 AGTCCTCAAAGAGCAGGACACCTCTT-AAAGCCCACACAAGTTGGTGGCACCTTT-C
319584 AGTCCTCAAAGAGCAGGACACCTCTTAAAGCCCACACAAGTTGGTGGCACCTTTC
1 AGTCCTCAAAGAGCAGGACACCTCTTAAAGCCCACACAAGTTGGTGGCACCTTTC
* * * *
319639 ATTCCCCAAAGAGCAGGACA-CTTTTCAAAGCCCACACAAGTGGGTGGCACCTTTC
1 AGTCCTCAAAGAGCAGGACACCTCTT-AAAGCCCACACAAGTTGGTGGCACCTTTC
* ** * *
319694 AGTCCTCAAAGAGCAGGACGCCT-TTCAAAGCCCACATGAGTTGGTGGCACTTTTT
1 AGTCCTCAAAGAGCAGGACACCTCTT-AAAGCCCACACAAGTTGGTGGCACCTTTC
* *
319749 ACTCCTCAATGAGCAGGA
1 AGTCCTCAAAGAGCAGGA
319767 TACAATTTAT
Statistics
Matches: 427, Mismatches: 19, Indels: 24
0.91 0.04 0.05
Matches are distributed among these distances:
53 2 0.00
54 12 0.03
55 401 0.94
56 10 0.02
57 2 0.00
ACGTcount: A:0.29, C:0.30, G:0.21, T:0.20
Consensus pattern (55 bp):
AGTCCTCAAAGAGCAGGACACCTCTTAAAGCCCACACAAGTTGGTGGCACCTTTC
Found at i:320380 original size:16 final size:16
Alignment explanation
Indices: 320359--320390 Score: 64
Period size: 16 Copynumber: 2.0 Consensus size: 16
320349 GATAAAGTGT
320359 TTGAAAAAAAAAAAAA
1 TTGAAAAAAAAAAAAA
320375 TTGAAAAAAAAAAAAA
1 TTGAAAAAAAAAAAAA
320391 AAAAAAAATT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.81, C:0.00, G:0.06, T:0.12
Consensus pattern (16 bp):
TTGAAAAAAAAAAAAA
Found at i:320427 original size:21 final size:21
Alignment explanation
Indices: 320403--320459 Score: 105
Period size: 21 Copynumber: 2.7 Consensus size: 21
320393 AAAAAATTTA
320403 AATGTATCGATACATTTGTAG
1 AATGTATCGATACATTTGTAG
*
320424 AATGTATCGATACATTTGTGG
1 AATGTATCGATACATTTGTAG
320445 AATGTATCGATACAT
1 AATGTATCGATACAT
320460 CCTACAAATG
Statistics
Matches: 35, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
21 35 1.00
ACGTcount: A:0.33, C:0.11, G:0.19, T:0.37
Consensus pattern (21 bp):
AATGTATCGATACATTTGTAG
Found at i:320539 original size:19 final size:19
Alignment explanation
Indices: 320515--320582 Score: 85
Period size: 19 Copynumber: 3.9 Consensus size: 19
320505 AATTCAACAA
320515 TTTGTATCGATACATAAGT
1 TTTGTATCGATACATAAGT
320534 TTTGTATCGATAC--AA--
1 TTTGTATCGATACATAAGT
320549 --TGTATCGATACATAAGT
1 TTTGTATCGATACATAAGT
*
320566 ATTGTATCGATACATAA
1 TTTGTATCGATACATAA
320583 TTAGCTACTG
Statistics
Matches: 43, Mismatches: 0, Indels: 12
0.78 0.00 0.22
Matches are distributed among these distances:
13 11 0.26
15 2 0.05
17 2 0.05
19 28 0.65
ACGTcount: A:0.35, C:0.12, G:0.15, T:0.38
Consensus pattern (19 bp):
TTTGTATCGATACATAAGT
Found at i:320554 original size:13 final size:13
Alignment explanation
Indices: 320536--320560 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
320526 ACATAAGTTT
320536 TGTATCGATACAA
1 TGTATCGATACAA
320549 TGTATCGATACA
1 TGTATCGATACA
320561 TAAGTATTGT
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:320558 original size:32 final size:32
Alignment explanation
Indices: 320517--320579 Score: 117
Period size: 32 Copynumber: 2.0 Consensus size: 32
320507 TTCAACAATT
*
320517 TGTATCGATACATAAGTTTTGTATCGATACAA
1 TGTATCGATACATAAGTATTGTATCGATACAA
320549 TGTATCGATACATAAGTATTGTATCGATACA
1 TGTATCGATACATAAGTATTGTATCGATACA
320580 TAATTAGCTA
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
32 30 1.00
ACGTcount: A:0.35, C:0.13, G:0.16, T:0.37
Consensus pattern (32 bp):
TGTATCGATACATAAGTATTGTATCGATACAA
Found at i:320640 original size:13 final size:13
Alignment explanation
Indices: 320622--320647 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
320612 CATTTTTCTG
320622 TGTATCGATACAT
1 TGTATCGATACAT
320635 TGTATCGATACAT
1 TGTATCGATACAT
320648 GGATCTTTGT
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:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:320644 original size:33 final size:33
Alignment explanation
Indices: 320602--320668 Score: 98
Period size: 33 Copynumber: 2.0 Consensus size: 33
320592 GCCAAGGAAA
***
320602 TGTATCGATACATTTTTCTGTGTATCGATACAT
1 TGTATCGATACATGGATCTGTGTATCGATACAT
*
320635 TGTATCGATACATGGATCTTTGTATCGATACAT
1 TGTATCGATACATGGATCTGTGTATCGATACAT
320668 T
1 T
320669 TGGAAATTTT
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
33 30 1.00
ACGTcount: A:0.25, C:0.15, G:0.16, T:0.43
Consensus pattern (33 bp):
TGTATCGATACATGGATCTGTGTATCGATACAT
Found at i:323194 original size:28 final size:27
Alignment explanation
Indices: 323127--323199 Score: 94
Period size: 27 Copynumber: 2.7 Consensus size: 27
323117 CTTCACAATC
* *
323127 GGGGACACTCCAACCCCGTTAATCATC
1 GGGGATACTCCAACCCCGTTAATCATA
*
323154 GGGGATACTCCAACCCCGTTATTTC-TGA
1 GGGGATACTCCAACCCCGTTA-ATCAT-A
323182 GGGGATACTCCAACCCCG
1 GGGGATACTCCAACCCCG
323200 ACTTTATTTT
Statistics
Matches: 41, Mismatches: 3, Indels: 3
0.87 0.06 0.06
Matches are distributed among these distances:
27 21 0.51
28 20 0.49
ACGTcount: A:0.23, C:0.34, G:0.22, T:0.21
Consensus pattern (27 bp):
GGGGATACTCCAACCCCGTTAATCATA
Found at i:323244 original size:51 final size:51
Alignment explanation
Indices: 323182--323352 Score: 198
Period size: 51 Copynumber: 3.3 Consensus size: 51
323172 TTATTTCTGA
* * *
323182 GGGGATACTCCAACCCCGACTTTATTTTCAAAATATCGATTTTTCATAATC
1 GGGGATACTCCAACCCCGATTTTATTTTCAAAATACCAATTTTTCATAATC
* * * * *
323233 GGGGATACTCCAACCCCGGTTTTATTTTCACAACACCAATTTCTCCTTTAATC
1 GGGGATACTCCAACCCCGATTTTATTTTCAAAATACCAATTT-TTC-ATAATC
** * *
323286 GGGGATACTCCAATTCCGATTTTATTTCCAAAAATACCAATTTTTCACAATC
1 GGGGATACTCCAACCCCGATTTTATTTTC-AAAATACCAATTTTTCATAATC
*
323338 GAGGATACTCCAACC
1 GGGGATACTCCAACC
323353 TCGTTATTTC
Statistics
Matches: 97, Mismatches: 20, Indels: 5
0.80 0.16 0.04
Matches are distributed among these distances:
51 36 0.37
52 18 0.19
53 32 0.33
54 11 0.11
ACGTcount: A:0.29, C:0.26, G:0.12, T:0.33
Consensus pattern (51 bp):
GGGGATACTCCAACCCCGATTTTATTTTCAAAATACCAATTTTTCATAATC
Found at i:323371 original size:28 final size:28
Alignment explanation
Indices: 323335--323416 Score: 96
Period size: 28 Copynumber: 2.9 Consensus size: 28
323325 ATTTTTCACA
*
323335 ATCGAGGATACTCCAACCTCGTTATTTC
1 ATCGGGGATACTCCAACCTCGTTATTTC
* *
323363 ATCGGGGATACTCCAACCCCGTTACTTC
1 ATCGGGGATACTCCAACCTCGTTATTTC
*
323391 --CGAGGGAACACTCCAACCTCGTTATT
1 ATCG-GGG-ATACTCCAACCTCGTTATT
323417 ATCTCCAAAA
Statistics
Matches: 46, Mismatches: 6, Indels: 4
0.82 0.11 0.07
Matches are distributed among these distances:
26 2 0.04
27 3 0.07
28 41 0.89
ACGTcount: A:0.24, C:0.32, G:0.17, T:0.27
Consensus pattern (28 bp):
ATCGGGGATACTCCAACCTCGTTATTTC
Found at i:325202 original size:93 final size:94
Alignment explanation
Indices: 325001--325203 Score: 277
Period size: 93 Copynumber: 2.1 Consensus size: 94
324991 GGTATCTAAA
**
325001 CTTTCTCCTTTCACTTTTTAGTCCTCAAAGAGCAGGACGCCTTCTCCTTTTAAAGCCCACACAAG
1 CTTTCTCCTTTCACCCTTTAGTCCTCAAAGAGCAGGA---C--CTCCTTTTAAAGCCCACACAAG
325066 TTGGTGGCACTTCCAGTCCTCAAAGAGCAGGACG
61 TTGGTGGCACTTCCAGTCCTCAAAGAGCAGGACG
*
325100 CTCTCTCCTTTCACCCTTTAGTCCTCAAAGAGCAGGA-CTCCTTTTAAAGCCCACACAAGTTGGT
1 CTTTCTCCTTTCACCCTTTAGTCCTCAAAGAGCAGGACCTCCTTTTAAAGCCCACACAAGTTGGT
*
325164 GGCACCTT-CAGTCCTC-AAGAAGCAGGATG
66 GGCA-CTTCCAGTCCTCAAAG-AGCAGGACG
*
325193 CTTTTTCCTTT
1 CTTTCTCCTTT
325204 TAAAGCCCAC
Statistics
Matches: 96, Mismatches: 6, Indels: 10
0.86 0.05 0.09
Matches are distributed among these distances:
92 3 0.03
93 56 0.58
94 3 0.03
99 34 0.35
ACGTcount: A:0.23, C:0.31, G:0.17, T:0.30
Consensus pattern (94 bp):
CTTTCTCCTTTCACCCTTTAGTCCTCAAAGAGCAGGACCTCCTTTTAAAGCCCACACAAGTTGGT
GGCACTTCCAGTCCTCAAAGAGCAGGACG
Found at i:325267 original size:61 final size:60
Alignment explanation
Indices: 325138--326055 Score: 1237
Period size: 61 Copynumber: 15.1 Consensus size: 60
325128 AGAGCAGGAC
* *
325138 TCCTTTTAAAGCCCACACAAGTTGGTGGCACCTTCAGTCCTC-AAGAAGCAGGATGCTTTT
1 TCCTTTTAAAGCCCACACAAGTTGGTGGCACCTTCAGTCCTCAAAG-AGCAGGACGCCTTT
*
325198 TCCTTTTAAAGCCCACACAAGTTGGTGGCACCTTCCAGTCCTCAAAAAGCAGGACGCCTTT
1 TCCTTTTAAAGCCCACACAAGTTGGTGGCACCTT-CAGTCCTCAAAGAGCAGGACGCCTTT
* * *
325259 TCCTTTTAAAGCCTACACAAGCTGGTGGCACCTTCAGTCCTCAAAGAGCAGGACGCTTTT
1 TCCTTTTAAAGCCCACACAAGTTGGTGGCACCTTCAGTCCTCAAAGAGCAGGACGCCTTT
*
325319 TCCTTTTTAAAGCCCACACAAGCTGGTGGCACCTTCAGTCCTCAAAGAGCAGGACGCCTTT
1 TCC-TTTTAAAGCCCACACAAGTTGGTGGCACCTTCAGTCCTCAAAGAGCAGGACGCCTTT
* * * * **
325380 CCCTTTTAAAGCCCACACAAGTTGGTGGCACCTTCAGTCCCCAAAGAGCAAGATGTTTTT
1 TCCTTTTAAAGCCCACACAAGTTGGTGGCACCTTCAGTCCTCAAAGAGCAGGACGCCTTT
* *
325440 TCCTTTTAAAGCCCACACAAGTTGGTGGCACTTTTTAGTCCTCAAAGAGCAGGACGCCTTT
1 TCCTTTTAAAGCCCACACAAGTTGGTGGCAC-CTTCAGTCCTCAAAGAGCAGGACGCCTTT
*
325501 TCCTTTTAAAGTCCACACAAGTTGGTGGCACCTTCAGTCCTCAAAGAGCAGGACGCCTTT
1 TCCTTTTAAAGCCCACACAAGTTGGTGGCACCTTCAGTCCTCAAAGAGCAGGACGCCTTT
* *
325561 TCCTTTTTAAAGCCCACAAAAGCTGGTGGCACCTTCAGTCCTCAAAGAGCAGGACGCCTTT
1 TCC-TTTTAAAGCCCACACAAGTTGGTGGCACCTTCAGTCCTCAAAGAGCAGGACGCCTTT
* * * * *
325622 ACCTTTTAAAGCCCACACAATTTGGTGGCACCTTCAGTCCTCAAGGAGCAGGACACTTTT
1 TCCTTTTAAAGCCCACACAAGTTGGTGGCACCTTCAGTCCTCAAAGAGCAGGACGCCTTT
* * * *
325682 TTCTTTTAAAGCCCACACAAGTTGGTAGCACCTTCTAGTCCTCAAAGAGCAAGACACCTTT
1 TCCTTTTAAAGCCCACACAAGTTGGTGGCACCTTC-AGTCCTCAAAGAGCAGGACGCCTTT
* * *
325743 TCCTTTTAAAGCCCACACAAGCTGGTGGCACCTTCAGTTCTCAAAGAGCAGGATGCCTTT
1 TCCTTTTAAAGCCCACACAAGTTGGTGGCACCTTCAGTCCTCAAAGAGCAGGACGCCTTT
* * *
325803 TCCTTTTTAAAGCCCACACATGTTGGTGGCACTTTTCTAGTCCTCAAAGAGCAGGATGCCTTT
1 TCC-TTTTAAAGCCCACACAAGTTGGTGGCAC-CTTC-AGTCCTCAAAGAGCAGGACGCCTTT
** * ** * *
325866 TCCTTTTAAAGCCCACATGAGTTGTTGGCATTTTTTTAGTCCTCAAAGAGCAGGATGCCTTT
1 TCCTTTTAAAGCCCACACAAGTTGGTGGCA--CCTTCAGTCCTCAAAGAGCAGGACGCCTTT
* ** *
325928 TTCTTGCAAAGCCCACACAAGTTGGTGGCACCTTCTAATCCTCAAAGAGCAGGACGCCTTT
1 TCCTTTTAAAGCCCACACAAGTTGGTGGCACCTTC-AGTCCTCAAAGAGCAGGACGCCTTT
* * * * * *
325989 T-CTTTTCAAAGCCCACACGAGTTGGTGGCACTTTTTTAGTCCTTAAAGAGTAGGACGTCTTT
1 TCCTTTT-AAAGCCCACACAAGTTGGTGGCAC--CTTCAGTCCTCAAAGAGCAGGACGCCTTT
326051 TCCTT
1 TCCTT
326056 CTCTCTTTTG
Statistics
Matches: 761, Mismatches: 81, Indels: 29
0.87 0.09 0.03
Matches are distributed among these distances:
60 283 0.37
61 344 0.45
62 99 0.13
63 35 0.05
ACGTcount: A:0.25, C:0.27, G:0.19, T:0.28
Consensus pattern (60 bp):
TCCTTTTAAAGCCCACACAAGTTGGTGGCACCTTCAGTCCTCAAAGAGCAGGACGCCTTT
Found at i:325358 original size:121 final size:120
Alignment explanation
Indices: 325138--326055 Score: 1241
Period size: 121 Copynumber: 7.5 Consensus size: 120
325128 AGAGCAGGAC
*
325138 TCCTTTTAAAGCCCACACAAGTTGGTGGCACCTTCAGTCCTC-AAGAAGCAGGATGCTTTTTCCT
1 TCCTTTTAAAGCCCACACAAGTTGGTGGCACCTTCAGTCCTCAAAG-AGCAGGACGCTTTTTCCT
*
325202 TTTAAAGCCCACACAAGTTGGTGGCACCTTCCAGTCCTCAAAAAGCAGGACGCCTTT
65 TTTAAAGCCCACACAAGTTGGTGGCACCTT-CAGTCCTCAAAGAGCAGGACGCCTTT
* *
325259 TCCTTTTAAAGCCTACACAAGCTGGTGGCACCTTCAGTCCTCAAAGAGCAGGACGCTTTTTCCTT
1 TCCTTTTAAAGCCCACACAAGTTGGTGGCACCTTCAGTCCTCAAAGAGCAGGACGCTTTTTCC-T
*
325324 TTTAAAGCCCACACAAGCTGGTGGCACCTTCAGTCCTCAAAGAGCAGGACGCCTTT
65 TTTAAAGCCCACACAAGTTGGTGGCACCTTCAGTCCTCAAAGAGCAGGACGCCTTT
* * * * *
325380 CCCTTTTAAAGCCCACACAAGTTGGTGGCACCTTCAGTCCCCAAAGAGCAAGATGTTTTTTCCTT
1 TCCTTTTAAAGCCCACACAAGTTGGTGGCACCTTCAGTCCTCAAAGAGCAGGACGCTTTTTCCTT
* *
325445 TTAAAGCCCACACAAGTTGGTGGCACTTTTTAGTCCTCAAAGAGCAGGACGCCTTT
66 TTAAAGCCCACACAAGTTGGTGGCAC-CTTCAGTCCTCAAAGAGCAGGACGCCTTT
* *
325501 TCCTTTTAAAGTCCACACAAGTTGGTGGCACCTTCAGTCCTCAAAGAGCAGGACGCCTTTTCCTT
1 TCCTTTTAAAGCCCACACAAGTTGGTGGCACCTTCAGTCCTCAAAGAGCAGGACGCTTTTTCC-T
* *
325566 TTTAAAGCCCACAAAAGCTGGTGGCACCTTCAGTCCTCAAAGAGCAGGACGCCTTT
65 TTTAAAGCCCACACAAGTTGGTGGCACCTTCAGTCCTCAAAGAGCAGGACGCCTTT
* * * * *
325622 ACCTTTTAAAGCCCACACAATTTGGTGGCACCTTCAGTCCTCAAGGAGCAGGACACTTTTTTCTT
1 TCCTTTTAAAGCCCACACAAGTTGGTGGCACCTTCAGTCCTCAAAGAGCAGGACGCTTTTTCCTT
* * *
325687 TTAAAGCCCACACAAGTTGGTAGCACCTTCTAGTCCTCAAAGAGCAAGACACCTTT
66 TTAAAGCCCACACAAGTTGGTGGCACCTTC-AGTCCTCAAAGAGCAGGACGCCTTT
* * * *
325743 TCCTTTTAAAGCCCACACAAGCTGGTGGCACCTTCAGTTCTCAAAGAGCAGGATGCCTTTTCCTT
1 TCCTTTTAAAGCCCACACAAGTTGGTGGCACCTTCAGTCCTCAAAGAGCAGGACGCTTTTTCC-T
* * *
325808 TTTAAAGCCCACACATGTTGGTGGCACTTTTCTAGTCCTCAAAGAGCAGGATGCCTTT
65 TTTAAAGCCCACACAAGTTGGTGGCAC-CTTC-AGTCCTCAAAGAGCAGGACGCCTTT
** * ** * *
325866 TCCTTTTAAAGCCCACATGAGTTGTTGGCATTTTTTTAGTCCTCAAAGAGCAGGATGCCTTTTT-
1 TCCTTTTAAAGCCCACACAAGTTGGTGGCA--CCTTCAGTCCTCAAAGAGCAGGACG-CTTTTTC
** *
325930 CTTGCAAAGCCCACACAAGTTGGTGGCACCTTCTAATCCTCAAAGAGCAGGACGCCTTT
63 CTTTTAAAGCCCACACAAGTTGGTGGCACCTTC-AGTCCTCAAAGAGCAGGACGCCTTT
* * * * *
325989 T-CTTTTCAAAGCCCACACGAGTTGGTGGCACTTTTTTAGTCCTTAAAGAGTAGGACG-TCTTTT
1 TCCTTTT-AAAGCCCACACAAGTTGGTGGCAC--CTTCAGTCCTCAAAGAGCAGGACGCT-TTTT
326052 CCTT
62 CCTT
326056 CTCTCTTTTG
Statistics
Matches: 708, Mismatches: 74, Indels: 28
0.87 0.09 0.03
Matches are distributed among these distances:
120 56 0.08
121 381 0.54
122 94 0.13
123 125 0.18
124 25 0.04
125 22 0.03
126 5 0.01
ACGTcount: A:0.25, C:0.27, G:0.19, T:0.28
Consensus pattern (120 bp):
TCCTTTTAAAGCCCACACAAGTTGGTGGCACCTTCAGTCCTCAAAGAGCAGGACGCTTTTTCCTT
TTAAAGCCCACACAAGTTGGTGGCACCTTCAGTCCTCAAAGAGCAGGACGCCTTT
Found at i:326753 original size:20 final size:20
Alignment explanation
Indices: 326727--326839 Score: 131
Period size: 20 Copynumber: 5.5 Consensus size: 20
326717 TTTTACCCAG
326727 ATGTATCGATACATTGTTCA
1 ATGTATCGATACATTGTTCA
* *
326747 TTGTATCGATACATTGTTTA
1 ATGTATCGATACATTGTTCA
*
326767 TTGTATCGATACATTGTTC-
1 ATGTATCGATACATTGTTCA
**
326786 ATGTATCGATACATCTGGGTAAA
1 ATGTATCGATACAT-T--GTTCA
326809 ATGTATCGATACATT-TTGCA
1 ATGTATCGATACATTGTT-CA
326829 ATGTATCGATA
1 ATGTATCGATA
326840 TATTCAGGCA
Statistics
Matches: 80, Mismatches: 8, Indels: 10
0.82 0.08 0.10
Matches are distributed among these distances:
19 14 0.17
20 49 0.61
22 3 0.04
23 14 0.17
ACGTcount: A:0.29, C:0.13, G:0.17, T:0.41
Consensus pattern (20 bp):
ATGTATCGATACATTGTTCA
Found at i:329215 original size:79 final size:78
Alignment explanation
Indices: 329117--329524 Score: 359
Period size: 79 Copynumber: 5.3 Consensus size: 78
329107 CCTAGATTTT
* * *
329117 TTTTCAT-CTCGGGGATACTCCAACCCCATTATTTTTAAGGGGATACTCCAACCCCGGCTTTATT
1 TTTTCATAATCGGGGATACTCCAACCCCATTATTTTTGAGGGGATACTCCAACCTCGGCTTTATT
*
329181 TCTAAAATATTGA
66 TCTAAAACATTGA
** *
329194 TTTCTCATAATCGGGGATACTCCAA-CCCAGTTATTTTTGAGGGG--A-T--AA-CTTTGATTTC
1 TTT-TCATAATCGGGGATACTCCAACCCCA-TTATTTTTGAGGGGATACTCCAACCTCGGCTTT-
* * * ***
329252 ACTCCCAAAACACCAA
63 ATTTCTAAAACATTGA
* * * * **
329268 TTTTCACAATCGAGAATACTCCAACCCCGTTATTTCCGAGGGGATACTCCAACCTCGGCTTTATT
1 TTTTCATAATCGGGGATACTCCAACCCCATTATTTTTGAGGGGATACTCCAACCTCGGCTTTATT
*
329333 TCTAAAATATTGA
66 TCTAAAACATTGA
* ** ** *
329346 TTTCTCATAATCGGGGATACTCCAACCCCGTTATTTCCGATAGGATACTCCAACCTCGGTTTTAT
1 TTT-TCATAATCGGGGATACTCCAACCCCATTATTTTTGAGGGGATACTCCAACCTCGGCTTTAT
* *
329411 TTCTAAAACACTAA
65 TTCTAAAACATTGA
* ** ***
329425 TTTTTCATAATCGGGGATACTCTAACCCCATTATTTTTGAAAGGATACTCCAACC-CCATTTTAT
1 -TTTTCATAATCGGGGATACTCCAACCCCATTATTTTTGAGGGGATACTCCAACCTCGGCTTTAT
*
329489 TT-TCAAAACATCGA
65 TTCT-AAAACATTGA
*
329503 TTTTCTATAATCAGGGATACTC
1 TTTTC-ATAATCGGGGATACTC
329525 TAGCCCCGTT
Statistics
Matches: 267, Mismatches: 49, Indels: 29
0.77 0.14 0.08
Matches are distributed among these distances:
73 35 0.13
74 17 0.06
75 1 0.00
76 2 0.01
77 10 0.04
78 53 0.20
79 146 0.55
80 3 0.01
ACGTcount: A:0.28, C:0.25, G:0.13, T:0.34
Consensus pattern (78 bp):
TTTTCATAATCGGGGATACTCCAACCCCATTATTTTTGAGGGGATACTCCAACCTCGGCTTTATT
TCTAAAACATTGA
Found at i:332684 original size:22 final size:21
Alignment explanation
Indices: 332638--332689 Score: 59
Period size: 22 Copynumber: 2.4 Consensus size: 21
332628 TATATTTAAA
* * *
332638 AATTTATTTTAATTTTTGAAT
1 AATTTATTTTAAGTCTTGAAC
332659 AATTTATTTTGAAGTCTTGAAC
1 AATTTATTTT-AAGTCTTGAAC
*
332681 AATTAATTT
1 AATTTATTT
332690 AAGAAGGTTA
Statistics
Matches: 26, Mismatches: 4, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
21 10 0.38
22 16 0.62
ACGTcount: A:0.35, C:0.04, G:0.08, T:0.54
Consensus pattern (21 bp):
AATTTATTTTAAGTCTTGAAC
Found at i:333770 original size:20 final size:21
Alignment explanation
Indices: 333726--333797 Score: 69
Period size: 21 Copynumber: 3.5 Consensus size: 21
333716 TTCAACAATT
* *
333726 TGTATCGATACAATA-GGGTAA
1 TGTATCGATAC-ATACGTGAAA
333747 TGTATCGATACATACGTG-AA
1 TGTATCGATACATACGTGAAA
* *
333767 TGTATTGATACATGTC-TGAAA
1 TGTATCGATACAT-ACGTGAAA
333788 TGTATCGATA
1 TGTATCGATA
333798 GAGGACCATG
Statistics
Matches: 44, Mismatches: 4, Indels: 6
0.81 0.07 0.11
Matches are distributed among these distances:
20 19 0.43
21 25 0.57
ACGTcount: A:0.35, C:0.11, G:0.21, T:0.33
Consensus pattern (21 bp):
TGTATCGATACATACGTGAAA
Found at i:333958 original size:55 final size:53
Alignment explanation
Indices: 333835--333969 Score: 179
Period size: 55 Copynumber: 2.6 Consensus size: 53
333825 TCTAGAAAGA
* * *
333835 AAATGTATCGATACATT-TTC-CATTGTATTGATATATTTTGGGTTTTGACCC
1 AAATGTATCGATACATTCTTCACAATGTATCGATATATTCTGGGTTTTGACCC
* *
333886 AAAGGTATTGATACATTCTTCACAAATGTATCGATATATTCTGGGTTTTTGACCC
1 AAATGTATCGATACATTCTTCAC-AATGTATCGATATATTCTGGG-TTTTGACCC
333941 AAATGTATCGATACATTCTT--CAATGTATC
1 AAATGTATCGATACATTCTTCACAATGTATC
333970 AATACATACA
Statistics
Matches: 73, Mismatches: 7, Indels: 7
0.84 0.08 0.08
Matches are distributed among these distances:
51 15 0.21
52 11 0.15
53 2 0.03
54 18 0.25
55 27 0.37
ACGTcount: A:0.29, C:0.16, G:0.15, T:0.41
Consensus pattern (53 bp):
AAATGTATCGATACATTCTTCACAATGTATCGATATATTCTGGGTTTTGACCC
Found at i:334097 original size:7 final size:7
Alignment explanation
Indices: 334085--334112 Score: 56
Period size: 7 Copynumber: 4.0 Consensus size: 7
334075 CATGTCAATA
334085 TCAAATT
1 TCAAATT
334092 TCAAATT
1 TCAAATT
334099 TCAAATT
1 TCAAATT
334106 TCAAATT
1 TCAAATT
334113 CAAGCTCTGA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 21 1.00
ACGTcount: A:0.43, C:0.14, G:0.00, T:0.43
Consensus pattern (7 bp):
TCAAATT
Found at i:337356 original size:20 final size:20
Alignment explanation
Indices: 337322--337389 Score: 68
Period size: 20 Copynumber: 3.4 Consensus size: 20
337312 AATATATATC
* *
337322 AATACATGGCCAAATGTATG
1 AATACATTGTCAAATGTATG
337342 AATACATTAGT-AAATGTATCG
1 AATACATT-GTCAAATGTAT-G
* *
337363 -ATACATTTTCAAATGTATT
1 AATACATTGTCAAATGTATG
337382 AATACATT
1 AATACATT
337390 CAGGCTTTTT
Statistics
Matches: 40, Mismatches: 4, Indels: 8
0.77 0.08 0.15
Matches are distributed among these distances:
19 1 0.03
20 37 0.93
21 2 0.05
ACGTcount: A:0.41, C:0.12, G:0.12, T:0.35
Consensus pattern (20 bp):
AATACATTGTCAAATGTATG
Found at i:337675 original size:168 final size:165
Alignment explanation
Indices: 337352--337682 Score: 394
Period size: 168 Copynumber: 2.0 Consensus size: 165
337342 AATACATTAG
* * * * *
337352 TAAATGTATCGATACATTTTCAAATGTATTAATACATTCAGGCTTTTTGGTTGAATGTATTGATA
1 TAAATATATCAATACATTTTCAAATGTATTAACACATTCAGGCTTTTTGGTTAAATGTACTGATA
* * * * * *
337417 ATTCCCAATTGTATCGATAAATTTAGGTAATTTTGCCTGATTCATGGTATTTTACTCCCATTGCA
66 ATTCCCAATTATATCAATAAATTCAAGCAATTTTGCCTGATTCATGGCATTTTACTCCCATTGCA
*
337482 CCAGTGATCTCAAACAAGAGTTTAGCCACATTTGC
131 CCAGTGATCTAAAACAAGAGTTTAGCCACATTTGC
* * *
337517 TAAATATATCAATACAATTTTCAAATGTATTGACACATTTAGGCTTTTTTGTTAAATGTACTGAT
1 TAAATATATCAATAC-ATTTTCAAATGTATTAACACATTCAGGCTTTTTGGTTAAATGTACTGAT
* * ** * *
337582 ACAATTCCCAATTATATCAATACATTCAAGCAATTTTGCTTGATTTGTGGCATTTTCCTCCTATT
65 --AATTCCCAATTATATCAATAAATTCAAGCAATTTTGCCTGATTCATGGCATTTTACTCCCATT
* * * *
337647 GTACTAGTGATTTAAAACACA-CGTTTAGCCACATTT
128 GCACCAGTGATCTAAAACA-AGAGTTTAGCCACATTT
337683 TTGTTCTAAA
Statistics
Matches: 137, Mismatches: 25, Indels: 5
0.82 0.15 0.03
Matches are distributed among these distances:
165 13 0.09
166 43 0.31
168 80 0.58
169 1 0.01
ACGTcount: A:0.31, C:0.17, G:0.13, T:0.40
Consensus pattern (165 bp):
TAAATATATCAATACATTTTCAAATGTATTAACACATTCAGGCTTTTTGGTTAAATGTACTGATA
ATTCCCAATTATATCAATAAATTCAAGCAATTTTGCCTGATTCATGGCATTTTACTCCCATTGCA
CCAGTGATCTAAAACAAGAGTTTAGCCACATTTGC
Found at i:338253 original size:20 final size:20
Alignment explanation
Indices: 338223--338279 Score: 69
Period size: 20 Copynumber: 2.8 Consensus size: 20
338213 GTCAAAACCC
338223 TAAATTGTATCGATACACATT
1 TAAA-TGTATCGATACACATT
*
338244 TAAATGTATCGATACAGATT
1 TAAATGTATCGATACACATT
** *
338264 GCATTGTATCGATACA
1 TAAATGTATCGATACA
338280 TTGTATCGAT
Statistics
Matches: 32, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
20 28 0.88
21 4 0.12
ACGTcount: A:0.37, C:0.14, G:0.14, T:0.35
Consensus pattern (20 bp):
TAAATGTATCGATACACATT
Found at i:338283 original size:13 final size:13
Alignment explanation
Indices: 338265--338293 Score: 58
Period size: 13 Copynumber: 2.2 Consensus size: 13
338255 ATACAGATTG
338265 CATTGTATCGATA
1 CATTGTATCGATA
338278 CATTGTATCGATA
1 CATTGTATCGATA
338291 CAT
1 CAT
338294 GACCAAATGT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.31, C:0.17, G:0.14, T:0.38
Consensus pattern (13 bp):
CATTGTATCGATA
Found at i:338306 original size:20 final size:21
Alignment explanation
Indices: 338281--338331 Score: 68
Period size: 20 Copynumber: 2.5 Consensus size: 21
338271 ATCGATACAT
**
338281 TGTATCGATACATGACCAA-A
1 TGTATCGATACATGAAAAAGA
*
338301 TGTATCGATACTTGAAAAAGA
1 TGTATCGATACATGAAAAAGA
338322 TGTATCGATA
1 TGTATCGATA
338332 TAGGTCATTG
Statistics
Matches: 27, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
20 16 0.59
21 11 0.41
ACGTcount: A:0.39, C:0.14, G:0.18, T:0.29
Consensus pattern (21 bp):
TGTATCGATACATGAAAAAGA
Found at i:338402 original size:13 final size:13
Alignment explanation
Indices: 338384--338409 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
338374 ACACACAGTA
338384 TGTATCGATACAT
1 TGTATCGATACAT
338397 TGTATCGATACAT
1 TGTATCGATACAT
338410 CATAAAATGT
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:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:343623 original size:13 final size:13
Alignment explanation
Indices: 343605--343630 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
343595 CAATTTTTTG
343605 TGTATCGATACAT
1 TGTATCGATACAT
343618 TGTATCGATACAT
1 TGTATCGATACAT
343631 ACTTGCTGTA
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:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:343733 original size:20 final size:20
Alignment explanation
Indices: 343689--343744 Score: 69
Period size: 20 Copynumber: 2.8 Consensus size: 20
343679 ACATCTTTTT
*
343689 CATGTATCGATACATTGCAA
1 CATGTATCGATACTTTGCAA
343709 CATGTATCGATACTTTG-AA
1 CATGTATCGATACTTTGCAA
* *
343728 TTATGTATCGAAACTTT
1 -CATGTATCGATACTTT
343745 TAAGGGTTTT
Statistics
Matches: 32, Mismatches: 3, Indels: 2
0.86 0.08 0.05
Matches are distributed among these distances:
19 2 0.06
20 30 0.94
ACGTcount: A:0.32, C:0.16, G:0.14, T:0.38
Consensus pattern (20 bp):
CATGTATCGATACTTTGCAA
Found at i:346190 original size:13 final size:13
Alignment explanation
Indices: 346172--346210 Score: 69
Period size: 13 Copynumber: 3.0 Consensus size: 13
346162 ATAATCACCC
*
346172 TGTATCGATACAG
1 TGTATCGATACAA
346185 TGTATCGATACAA
1 TGTATCGATACAA
346198 TGTATCGATACAA
1 TGTATCGATACAA
346211 AGAAAAATGT
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
13 25 1.00
ACGTcount: A:0.36, C:0.15, G:0.18, T:0.31
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:346221 original size:20 final size:20
Alignment explanation
Indices: 346196--346274 Score: 77
Period size: 20 Copynumber: 3.7 Consensus size: 20
346186 GTATCGATAC
346196 AATGTATCGATACAAAGAAA
1 AATGTATCGATACAAAGAAA
*
346216 AATGTATCGATACATAGAATTTCCA
1 AATGTATCGATACAAAGAA-----A
* *
346241 GATGTATCGATACACAGAAA
1 AATGTATCGATACAAAGAAA
*
346261 CATGTATCGATACA
1 AATGTATCGATACA
346275 TTTTGGACAT
Statistics
Matches: 50, Mismatches: 4, Indels: 10
0.78 0.06 0.16
Matches are distributed among these distances:
20 32 0.64
25 18 0.36
ACGTcount: A:0.44, C:0.15, G:0.15, T:0.25
Consensus pattern (20 bp):
AATGTATCGATACAAAGAAA
Found at i:350153 original size:21 final size:21
Alignment explanation
Indices: 350124--350168 Score: 56
Period size: 21 Copynumber: 2.1 Consensus size: 21
350114 AAGTTTTCAT
*
350124 TTTTCTTAGCTAAC-TCATTA
1 TTTTCTTAGCCAACTTCATTA
*
350144 TTTTCATTAGCCAACTTCTTTA
1 TTTTC-TTAGCCAACTTCATTA
350166 TTT
1 TTT
350169 CAACTTGCAA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
20 5 0.24
21 8 0.38
22 8 0.38
ACGTcount: A:0.22, C:0.20, G:0.04, T:0.53
Consensus pattern (21 bp):
TTTTCTTAGCCAACTTCATTA
Found at i:352400 original size:13 final size:13
Alignment explanation
Indices: 352382--352407 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
352372 CAATTTTTTG
352382 TGTATCGATACAT
1 TGTATCGATACAT
352395 TGTATCGATACAT
1 TGTATCGATACAT
352408 ACTTGCTGTA
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:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:352472 original size:21 final size:21
Alignment explanation
Indices: 352446--352521 Score: 109
Period size: 21 Copynumber: 3.7 Consensus size: 21
352436 CTGCCAAGAA
352446 ATGTATCGATACATCTTTTTC
1 ATGTATCGATACATCTTTTTC
****
352467 ATGTATCGATACAT-TGCAAC
1 ATGTATCGATACATCTTTTTC
352487 ATGTATCGATACATCTTTTTC
1 ATGTATCGATACATCTTTTTC
352508 ATGTATCGATACAT
1 ATGTATCGATACAT
352522 TGCAACATGT
Statistics
Matches: 46, Mismatches: 8, Indels: 2
0.82 0.14 0.04
Matches are distributed among these distances:
20 16 0.35
21 30 0.65
ACGTcount: A:0.29, C:0.18, G:0.12, T:0.41
Consensus pattern (21 bp):
ATGTATCGATACATCTTTTTC
Found at i:352491 original size:20 final size:20
Alignment explanation
Indices: 352466--352539 Score: 103
Period size: 20 Copynumber: 3.6 Consensus size: 20
352456 ACATCTTTTT
352466 CATGTATCGATACATTGCAA
1 CATGTATCGATACATTGCAA
****
352486 CATGTATCGATACATCTTTTT
1 CATGTATCGATACAT-TGCAA
352507 CATGTATCGATACATTGCAA
1 CATGTATCGATACATTGCAA
352527 CATGTATCGATAC
1 CATGTATCGATAC
352540 TTTGAATTGT
Statistics
Matches: 45, Mismatches: 8, Indels: 2
0.82 0.15 0.04
Matches are distributed among these distances:
20 29 0.64
21 16 0.36
ACGTcount: A:0.31, C:0.20, G:0.14, T:0.35
Consensus pattern (20 bp):
CATGTATCGATACATTGCAA
Found at i:352503 original size:41 final size:41
Alignment explanation
Indices: 352446--352539 Score: 188
Period size: 41 Copynumber: 2.3 Consensus size: 41
352436 CTGCCAAGAA
352446 ATGTATCGATACATCTTTTTCATGTATCGATACATTGCAAC
1 ATGTATCGATACATCTTTTTCATGTATCGATACATTGCAAC
352487 ATGTATCGATACATCTTTTTCATGTATCGATACATTGCAAC
1 ATGTATCGATACATCTTTTTCATGTATCGATACATTGCAAC
352528 ATGTATCGATAC
1 ATGTATCGATAC
352540 TTTGAATTGT
Statistics
Matches: 53, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
41 53 1.00
ACGTcount: A:0.30, C:0.19, G:0.13, T:0.38
Consensus pattern (41 bp):
ATGTATCGATACATCTTTTTCATGTATCGATACATTGCAAC
Found at i:354741 original size:21 final size:21
Alignment explanation
Indices: 354710--354761 Score: 68
Period size: 21 Copynumber: 2.4 Consensus size: 21
354700 CCCTAGGCAA
*
354710 CACCCACCAGGTCGCAACCAGG
1 CACCC-CCAGGTCACAACCAGG
*
354732 CACCCCCAGGTCACAACCGGG
1 CACCCCCAGGTCACAACCAGG
354753 CAGCCCCCA
1 CA-CCCCCA
354762 CACTAGCAGC
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
21 16 0.59
22 11 0.41
ACGTcount: A:0.25, C:0.50, G:0.21, T:0.04
Consensus pattern (21 bp):
CACCCCCAGGTCACAACCAGG
Found at i:356709 original size:20 final size:20
Alignment explanation
Indices: 356679--356735 Score: 69
Period size: 20 Copynumber: 2.8 Consensus size: 20
356669 GTCAAAACCC
356679 TAAATTGTATCGATACACATT
1 TAAA-TGTATCGATACACATT
*
356700 TAAATGTATCGATACAGATT
1 TAAATGTATCGATACACATT
** *
356720 GCATTGTATCGATACA
1 TAAATGTATCGATACA
356736 TTGTATTGTT
Statistics
Matches: 32, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
20 28 0.88
21 4 0.12
ACGTcount: A:0.37, C:0.14, G:0.14, T:0.35
Consensus pattern (20 bp):
TAAATGTATCGATACACATT
Found at i:356743 original size:18 final size:18
Alignment explanation
Indices: 356682--356744 Score: 56
Period size: 20 Copynumber: 3.3 Consensus size: 18
356672 AAAACCCTAA
356682 ATTGTATCGATACACATT-T
1 ATTGTATCGAT--ACATTGT
* *
356701 AAATGTATCGATACAGATTGC
1 -ATTGTATCGATAC--ATTGT
356722 ATTGTATCGATACATTGT
1 ATTGTATCGATACATTGT
356740 ATTGT
1 ATTGT
356745 TACATGACCA
Statistics
Matches: 36, Mismatches: 4, Indels: 8
0.75 0.08 0.17
Matches are distributed among these distances:
18 11 0.31
20 25 0.69
ACGTcount: A:0.32, C:0.13, G:0.16, T:0.40
Consensus pattern (18 bp):
ATTGTATCGATACATTGT
Found at i:357561 original size:20 final size:20
Alignment explanation
Indices: 357536--357588 Score: 70
Period size: 20 Copynumber: 2.6 Consensus size: 20
357526 ACCCTGAAAA
* *
357536 GTATCGATATATATTTAATT
1 GTATCGATACATATTGAATT
* *
357556 GTATCGATACATGTTGCATT
1 GTATCGATACATATTGAATT
357576 GTATCGATACATA
1 GTATCGATACATA
357589 AAAAAGATGT
Statistics
Matches: 28, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 28 1.00
ACGTcount: A:0.32, C:0.11, G:0.15, T:0.42
Consensus pattern (20 bp):
GTATCGATACATATTGAATT
Found at i:357677 original size:13 final size:13
Alignment explanation
Indices: 357659--357683 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
357649 ACACATAGTA
357659 TGTATCGATACAT
1 TGTATCGATACAT
357672 TGTATCGATACA
1 TGTATCGATACA
357684 CCATAAAATG
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:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:357680 original size:32 final size:33
Alignment explanation
Indices: 357639--357706 Score: 102
Period size: 33 Copynumber: 2.1 Consensus size: 33
357629 GTAGCCAAAC
**
357639 TTGTATCGATACA-CATAGTATGTATCGATACA
1 TTGTATCGATACACCATAAAATGTATCGATACA
*
357671 TTGTATCGATACACCATAAAATGTATCGATATA
1 TTGTATCGATACACCATAAAATGTATCGATACA
357704 TTG
1 TTG
357707 GCTTGTAACG
Statistics
Matches: 32, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
32 13 0.41
33 19 0.59
ACGTcount: A:0.35, C:0.15, G:0.15, T:0.35
Consensus pattern (33 bp):
TTGTATCGATACACCATAAAATGTATCGATACA
Found at i:363888 original size:20 final size:20
Alignment explanation
Indices: 363863--363924 Score: 75
Period size: 20 Copynumber: 3.5 Consensus size: 20
363853 ATTCAGTTGC
363863 ATCGATACAGCATTCTCTGT
1 ATCGATACAGCATTCTCTGT
363883 ATCGAT--A-CA---T-TGT
1 ATCGATACAGCATTCTCTGT
363896 ATCGATACAGCATTCTCTGT
1 ATCGATACAGCATTCTCTGT
363916 ATCGATACA
1 ATCGATACA
363925 TTATATCGAT
Statistics
Matches: 35, Mismatches: 0, Indels: 14
0.71 0.00 0.29
Matches are distributed among these distances:
13 9 0.26
14 1 0.03
15 1 0.03
16 2 0.06
17 2 0.06
18 1 0.03
19 1 0.03
20 18 0.51
ACGTcount: A:0.29, C:0.23, G:0.15, T:0.34
Consensus pattern (20 bp):
ATCGATACAGCATTCTCTGT
Found at i:363898 original size:13 final size:13
Alignment explanation
Indices: 363880--363950 Score: 61
Period size: 13 Copynumber: 4.9 Consensus size: 13
363870 CAGCATTCTC
363880 TGTATCGATACAT
1 TGTATCGATACAT
363893 TGTATCGATACAGCATTCT
1 TGTATCGAT--A-CA---T
363912 CTGTATCGATACAT
1 -TGTATCGATACAT
* *
363926 TATATCGATACAG
1 TGTATCGATACAT
363939 TGTATCGATACA
1 TGTATCGATACA
363951 AGGGGTTTAT
Statistics
Matches: 48, Mismatches: 3, Indels: 14
0.74 0.05 0.22
Matches are distributed among these distances:
13 31 0.65
14 1 0.02
15 1 0.02
16 2 0.04
17 2 0.04
18 1 0.02
19 1 0.02
20 9 0.19
ACGTcount: A:0.31, C:0.18, G:0.15, T:0.35
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:363905 original size:33 final size:33
Alignment explanation
Indices: 363863--363938 Score: 143
Period size: 33 Copynumber: 2.3 Consensus size: 33
363853 ATTCAGTTGC
*
363863 ATCGATACAGCATTCTCTGTATCGATACATTGT
1 ATCGATACAGCATTCTCTGTATCGATACATTAT
363896 ATCGATACAGCATTCTCTGTATCGATACATTAT
1 ATCGATACAGCATTCTCTGTATCGATACATTAT
363929 ATCGATACAG
1 ATCGATACAG
363939 TGTATCGATA
Statistics
Matches: 42, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
33 42 1.00
ACGTcount: A:0.30, C:0.21, G:0.14, T:0.34
Consensus pattern (33 bp):
ATCGATACAGCATTCTCTGTATCGATACATTAT
Found at i:366486 original size:33 final size:32
Alignment explanation
Indices: 366426--366493 Score: 100
Period size: 33 Copynumber: 2.1 Consensus size: 32
366416 GTAGCCAAAC
* **
366426 TTGTATCGATACACATAGTATGTATCGATACA
1 TTGTATCGAAACACATAAAATGTATCGATACA
366458 TTGTATCGAAACACCATAAAATGTATCGATACA
1 TTGTATCGAAACA-CATAAAATGTATCGATACA
366491 TTG
1 TTG
366494 GCTTGTAACG
Statistics
Matches: 32, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
32 12 0.38
33 20 0.62
ACGTcount: A:0.37, C:0.16, G:0.15, T:0.32
Consensus pattern (32 bp):
TTGTATCGAAACACATAAAATGTATCGATACA
Found at i:369794 original size:20 final size:18
Alignment explanation
Indices: 369757--369795 Score: 51
Period size: 20 Copynumber: 2.1 Consensus size: 18
369747 TTCCTTGCTT
*
369757 TATGTGTTTTTATTTTTC
1 TATGTGTTTTTATATTTC
369775 TATGATGTTTATTATATTTC
1 TATG-TGTTT-TTATATTTC
369795 T
1 T
369796 TTAAGTCTCT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
18 4 0.22
19 5 0.28
20 9 0.50
ACGTcount: A:0.18, C:0.05, G:0.10, T:0.67
Consensus pattern (18 bp):
TATGTGTTTTTATATTTC
Found at i:371081 original size:23 final size:23
Alignment explanation
Indices: 371055--371112 Score: 80
Period size: 23 Copynumber: 2.5 Consensus size: 23
371045 ATTTGTTTAA
371055 ATTAAATAAATATATGTACAAAT
1 ATTAAATAAATATATGTACAAAT
* *
371078 ATTAAATAAATATATTTATAAAT
1 ATTAAATAAATATATGTACAAAT
* *
371101 ACTAAACAAATA
1 ATTAAATAAATA
371113 ATTAACGTTT
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
23 31 1.00
ACGTcount: A:0.59, C:0.05, G:0.02, T:0.34
Consensus pattern (23 bp):
ATTAAATAAATATATGTACAAAT
Found at i:371256 original size:22 final size:22
Alignment explanation
Indices: 371231--371295 Score: 71
Period size: 23 Copynumber: 3.0 Consensus size: 22
371221 TAATATCATT
371231 AATAAAATATAATCAAA-TAATA
1 AATAAAATATAAT-AAATTAATA
*
371253 AATAAAATTTTAATAAATTAATA
1 AATAAAA-TATAATAAATTAATA
* *
371276 AATAAATTATAA-ATATTAAT
1 AATAAAATATAATAAATTAAT
371296 TTATAAATAT
Statistics
Matches: 37, Mismatches: 4, Indels: 5
0.80 0.09 0.11
Matches are distributed among these distances:
21 7 0.19
22 14 0.38
23 16 0.43
ACGTcount: A:0.63, C:0.02, G:0.00, T:0.35
Consensus pattern (22 bp):
AATAAAATATAATAAATTAATA
Found at i:371314 original size:31 final size:32
Alignment explanation
Indices: 371229--371315 Score: 88
Period size: 34 Copynumber: 2.7 Consensus size: 32
371219 AATAATATCA
* *
371229 TTAATAAAATATAATCAAATAATAAATAAAATT
1 TTAAT-AAATATAAACAAATTATAAATAAAATT
* *
371262 TTAATAAATTAATAAATAAATTATAAATATTAA-T
1 TTAATAAA-T-ATAAACAAATTATAAATA-AAATT
371296 TT-ATAAATATAAACAAATTA
1 TTAATAAATATAAACAAATTA
371316 AATATATAGT
Statistics
Matches: 46, Mismatches: 5, Indels: 8
0.78 0.08 0.14
Matches are distributed among these distances:
31 11 0.24
32 4 0.09
33 11 0.24
34 18 0.39
35 2 0.04
ACGTcount: A:0.61, C:0.02, G:0.00, T:0.37
Consensus pattern (32 bp):
TTAATAAATATAAACAAATTATAAATAAAATT
Found at i:371819 original size:19 final size:19
Alignment explanation
Indices: 371743--371883 Score: 65
Period size: 21 Copynumber: 6.8 Consensus size: 19
371733 TTTTTTAATA
*
371743 ATTT-TTTAAAAATTATTT
1 ATTTATTTAAAAATTACTT
*
371761 ATTTATATTTAAAAATTACTA
1 A-TT-TATTTAAAAATTACTT
*
371782 ATTAATATTAAAATTAAAATTACTT
1 ATT--TATT----TAAAAATTACTT
371807 ATTTATTTAAAAAATTA-TT
1 ATTTATTT-AAAAATTACTT
* *
371826 TTTTAATTAAAAAATTACTT
1 ATTT-ATTTAAAAATTACTT
*
371846 ATATT-TTATAAAAA-TATTTT
1 AT-TTATT-TAAAAATTA-CTT
371866 ATTTTTATTTAAAAATTA
1 A--TTTATTTAAAAATTA
371884 TAAATTTTTT
Statistics
Matches: 95, Mismatches: 10, Indels: 32
0.69 0.07 0.23
Matches are distributed among these distances:
18 1 0.01
19 20 0.21
20 24 0.25
21 28 0.29
22 5 0.05
23 4 0.04
25 13 0.14
ACGTcount: A:0.46, C:0.02, G:0.00, T:0.52
Consensus pattern (19 bp):
ATTTATTTAAAAATTACTT
Found at i:371819 original size:25 final size:25
Alignment explanation
Indices: 371755--371818 Score: 76
Period size: 25 Copynumber: 2.6 Consensus size: 25
371745 TTTTTAAAAA
* *
371755 TTATTTATTTATATTTAAAAATTAC
1 TTATTTATTTAAAATTAAAAATTAC
* *
371780 TAATTAATATTAAAATT-AAAATTAC
1 TTATTTAT-TTAAAATTAAAAATTAC
371805 TTATTTATTTAAAA
1 TTATTTATTTAAAA
371819 AATTATTTTT
Statistics
Matches: 32, Mismatches: 6, Indels: 3
0.78 0.15 0.07
Matches are distributed among these distances:
24 6 0.19
25 20 0.62
26 6 0.19
ACGTcount: A:0.47, C:0.03, G:0.00, T:0.50
Consensus pattern (25 bp):
TTATTTATTTAAAATTAAAAATTAC
Found at i:371822 original size:20 final size:20
Alignment explanation
Indices: 371750--371860 Score: 82
Period size: 19 Copynumber: 5.3 Consensus size: 20
371740 ATAATTTTTT
* *
371750 AAAAATTATTTATTTATATTT
1 AAAAATTACTTATTTAT-TTA
* *
371771 AAAAATTACTAATTAATATTAAA
1 AAAAATTACTTATT--TATT-TA
371794 ATTAAAATTACTTATTTATTTA
1 A--AAAATTACTTATTTATTTA
* *
371816 AAAAATTA-TTTTTTAATTA
1 AAAAATTACTTATTTATTTA
*
371835 AAAAATTACTTATAT-TTTA
1 AAAAATTACTTATTTATTTA
371854 TAAAAAT
1 -AAAAAT
371861 ATTTTATTTT
Statistics
Matches: 72, Mismatches: 11, Indels: 15
0.73 0.11 0.15
Matches are distributed among these distances:
19 20 0.28
20 17 0.24
21 12 0.17
22 3 0.04
23 8 0.11
25 12 0.17
ACGTcount: A:0.50, C:0.03, G:0.00, T:0.48
Consensus pattern (20 bp):
AAAAATTACTTATTTATTTA
Found at i:371843 original size:39 final size:42
Alignment explanation
Indices: 371797--371880 Score: 113
Period size: 39 Copynumber: 2.1 Consensus size: 42
371787 TATTAAAATT
371797 AAAATTACTTAT-TTATT-TAAAAA-ATTAT-TTTTTAATTAA
1 AAAATTACTTATATT-TTATAAAAATATTATATTTTTAATTAA
* *
371836 AAAATTACTTATATTTTATAAAAATATTTTATTTTTATTTAA
1 AAAATTACTTATATTTTATAAAAATATTATATTTTTAATTAA
371878 AAA
1 AAA
371881 TTATAAATTT
Statistics
Matches: 39, Mismatches: 2, Indels: 5
0.85 0.04 0.11
Matches are distributed among these distances:
39 14 0.36
40 8 0.21
41 4 0.10
42 13 0.33
ACGTcount: A:0.46, C:0.02, G:0.00, T:0.51
Consensus pattern (42 bp):
AAAATTACTTATATTTTATAAAAATATTATATTTTTAATTAA
Found at i:372306 original size:14 final size:14
Alignment explanation
Indices: 372289--372331 Score: 59
Period size: 14 Copynumber: 3.0 Consensus size: 14
372279 ATATAATTAA
*
372289 TTAATTATATTTTT
1 TTAATTATATTATT
*
372303 TTAATAATATTATT
1 TTAATTATATTATT
372317 TTAATTAGTATTATT
1 TTAATTA-TATTATT
372332 AAATATTTAT
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
14 18 0.72
15 7 0.28
ACGTcount: A:0.35, C:0.00, G:0.02, T:0.63
Consensus pattern (14 bp):
TTAATTATATTATT
Found at i:372600 original size:20 final size:20
Alignment explanation
Indices: 372575--372628 Score: 72
Period size: 20 Copynumber: 2.7 Consensus size: 20
372565 TACCCAAATA
372575 TATCGATACATTCTTCAATG
1 TATCGATACATTCTTCAATG
*** *
372595 TATCGATACATGGATGAATG
1 TATCGATACATTCTTCAATG
372615 TATCGATACATTCT
1 TATCGATACATTCT
372629 GTCTCTTTTA
Statistics
Matches: 27, Mismatches: 7, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
20 27 1.00
ACGTcount: A:0.31, C:0.17, G:0.15, T:0.37
Consensus pattern (20 bp):
TATCGATACATTCTTCAATG
Found at i:372753 original size:17 final size:17
Alignment explanation
Indices: 372731--372768 Score: 76
Period size: 17 Copynumber: 2.2 Consensus size: 17
372721 ATAGGACTTA
372731 ATATATGGTATGAATAC
1 ATATATGGTATGAATAC
372748 ATATATGGTATGAATAC
1 ATATATGGTATGAATAC
372765 ATAT
1 ATAT
372769 TTTCATACTC
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 21 1.00
ACGTcount: A:0.42, C:0.05, G:0.16, T:0.37
Consensus pattern (17 bp):
ATATATGGTATGAATAC
Found at i:386655 original size:18 final size:18
Alignment explanation
Indices: 386632--386679 Score: 71
Period size: 18 Copynumber: 2.7 Consensus size: 18
386622 CCTTTACACC
386632 CAAAAAAAAAACAAAAAA
1 CAAAAAAAAAACAAAAAA
*
386650 CAAAAAAACAACAAAAAA
1 CAAAAAAAAAACAAAAAA
386668 -ATAAAAAAAAAC
1 CA-AAAAAAAAAC
386680 CCAAGAAAAA
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
17 1 0.04
18 26 0.96
ACGTcount: A:0.85, C:0.12, G:0.00, T:0.02
Consensus pattern (18 bp):
CAAAAAAAAAACAAAAAA
Found at i:388032 original size:30 final size:28
Alignment explanation
Indices: 387925--388457 Score: 478
Period size: 28 Copynumber: 18.1 Consensus size: 28
387915 CGTTCATCTC
*
387925 TTCAAAGCCCACAAATCAGTGGCACCCT
1 TTCAAAGCCCACAAGTCAGTGGCACCCT
* *
387953 TTCAAAGCCCACAAGTTAGTGGCACTCT
1 TTCAAAGCCCACAAGTCAGTGGCACCCT
* *
387981 TTCAAAACCCACAAGTTAGTGGCACCCT
1 TTCAAAGCCCACAAGTCAGTGGCACCCT
388009 TTCAAAGCCCACGCAAGTCAGTGGCACCCT
1 TTCAAAGCCCA--CAAGTCAGTGGCACCCT
* *
388039 TTCAAAGCCCACAAGTTAGTGGCACTCT
1 TTCAAAGCCCACAAGTCAGTGGCACCCT
* * *
388067 GTCAAAGCCCACAAGTTAGTGGCACTCTT
1 TTCAAAGCCCACAAGTCAGTGGCAC-CCT
*
388096 TTCAAAGCCCACACGAGTCAGTGGCAACTCTT
1 TTCAAAGCCCACA--AGTCAGTGGC-AC-CCT
388128 TTCAAAGCCCACAAGTCAGTGGCACCCT
1 TTCAAAGCCCACAAGTCAGTGGCACCCT
*
388156 TTCAAAGCCCACAAGTGAGTGGCACCCCT
1 TTCAAAGCCCACAAGTCAGTGGCA-CCCT
* *
388185 TTTAAAGCCCACATAAGTTAGTGGCACCCT
1 TTCAAAGCCCAC--AAGTCAGTGGCACCCT
** *
388215 TTCAAAGCCCACACAAGTTGGTGGCAACTCTT
1 TTCAAAG-CC-CACAAGTCAGTGGC-AC-CCT
* * *
388247 TTCCAAGCCCACTAGTCAGTGGCA-TCT
1 TTCAAAGCCCACAAGTCAGTGGCACCCT
* *
388274 CTTCAAAAGACCACAAGTCTA-TGGCGTACCTT
1 -TTC-AAAGCCCACAAGTC-AGTGGC--ACCCT
* *
388306 TTTAAAGCCCACACAAATCAGTGGCACCCT
1 TTCAAAG-CC-CACAAGTCAGTGGCACCCT
* *
388336 TCCAAAGCCCACAAGTCAATGGCACCCT
1 TTCAAAGCCCACAAGTCAGTGGCACCCT
* * *
388364 TTCAAAACCCACAAG-CTAGTGGTAACTCTT
1 TTCAAAGCCCACAAGTC-AGTGG-CAC-CCT
** *
388394 TTCAAAGCCCACACAAGTTGGTGGCAACTCTT
1 TTCAAAG-CC-CACAAGTCAGTGGC-AC-CCT
*
388426 TTCAAAGCCCACATAAGTTAGTGGCACCCT
1 TTCAAAGCCCAC--AAGTCAGTGGCACCCT
388456 TT
1 TT
388458 GTTTTAAAAA
Statistics
Matches: 423, Mismatches: 51, Indels: 60
0.79 0.10 0.11
Matches are distributed among these distances:
27 2 0.00
28 162 0.38
29 50 0.12
30 97 0.23
31 37 0.09
32 75 0.18
ACGTcount: A:0.29, C:0.31, G:0.17, T:0.23
Consensus pattern (28 bp):
TTCAAAGCCCACAAGTCAGTGGCACCCT
Found at i:388152 original size:89 final size:86
Alignment explanation
Indices: 387925--388453 Score: 518
Period size: 89 Copynumber: 6.0 Consensus size: 86
387915 CGTTCATCTC
* *
387925 TTCAAAGCCCACAAATCAGTGGCACCCTTTCAAAG-CC-CACAAGTTAGTGGCACTCTTTCAAAA
1 TTCAAAGCCCACAAGTCAGTGGCACCCTTTCAAAGCCCACACAAGTTAGTGGCACTCTTTCAAAG
*
387988 CCCACAAGTTAGTGGCACCCT
66 CCCACAAGTTAGTGGCACCTT
*
388009 TTCAAAGCCCACGCAAGTCAGTGGCACCCTTTCAAAG-CC-CACAAGTTAGTGGCACTCTGTCAA
1 TTCAAAGCCCA--CAAGTCAGTGGCACCCTTTCAAAGCCCACACAAGTTAGTGGCACTCTTTCAA
388072 AGCCCACAAGTTAGTGGCACTCTT
64 AGCCCACAAGTTAGTGGCAC-CTT
* * *
388096 TTCAAAGCCCACACGAGTCAGTGGCAACTCTTTTCAAAG-CC-CACAAGTCAGTGGCACCCTTTC
1 TTCAAAGCCCACA--AGTCAGTGGC-AC-CCTTTCAAAGCCCACACAAGTTAGTGGCACTCTTTC
*
388159 AAAGCCCACAAGTGAGTGGCACCCCTT
62 AAAGCCCACAAGTTAGTGGCA--CCTT
* *
388186 TT-AAAGCCCACATAAGTTAGTGGCACCCTTTCAAAGCCCACACAAGTTGGTGGCAACTCTTTTC
1 TTCAAAGCCCAC--AAGTCAGTGGCACCCTTTCAAAGCCCACACAAGTTAGTGGC-ACTC-TTTC
* * * * *
388250 CAAGCCCACTAGTCAGTGGCATCTC
62 AAAGCCCACAAGTTAGTGGCACCTT
* * * * * * *
388275 TTCAAAAGACCACAAGTCTA-TGGCGTACCTTTTTAAAGCCCACACAAATCAGTGGCACCCTTCC
1 TTC-AAAGCCCACAAGTC-AGTGGC--ACCCTTTCAAAGCCCACACAAGTTAGTGGCACTCTTTC
* * *
388339 AAAGCCCACAAGTCAATGGCACCCT
62 AAAGCCCACAAGTTAGTGGCACCTT
* * * *
388364 TTCAAAACCCACAAG-CTAGTGGTAACTCTTTTCAAAGCCCACACAAGTTGGTGGCAACTCTTTT
1 TTCAAAGCCCACAAGTC-AGTGG-CAC-CCTTTCAAAGCCCACACAAGTTAGTGGC-ACTC-TTT
388428 CAAAGCCCACATAAGTTAGTGGCACC
61 CAAAGCCCAC--AAGTTAGTGGCACC
388454 CTTTGTTTTA
Statistics
Matches: 373, Mismatches: 45, Indels: 46
0.80 0.10 0.10
Matches are distributed among these distances:
84 11 0.03
85 2 0.01
86 67 0.18
87 37 0.10
88 43 0.12
89 120 0.32
90 24 0.06
91 57 0.15
92 12 0.03
ACGTcount: A:0.29, C:0.31, G:0.17, T:0.22
Consensus pattern (86 bp):
TTCAAAGCCCACAAGTCAGTGGCACCCTTTCAAAGCCCACACAAGTTAGTGGCACTCTTTCAAAG
CCCACAAGTTAGTGGCACCTT
Found at i:388619 original size:49 final size:49
Alignment explanation
Indices: 388552--388686 Score: 216
Period size: 49 Copynumber: 2.8 Consensus size: 49
388542 GGCACCTTTA
* **
388552 TTAGCTCAATGTTGCTGGTCTTGAATCAGCACATTGGTCCACTTTTCCC
1 TTAGCCCAATGTCACTGGTCTTGAATCAGCACATTGGTCCACTTTTCCC
388601 TTAGCCCAATGTCACTGGTCTTGAATCAGCACATTGGTCCACTTTTCCC
1 TTAGCCCAATGTCACTGGTCTTGAATCAGCACATTGGTCCACTTTTCCC
* **
388650 TTAGCCCAATGTCACTGGCCTTGAATTGGCACATTGG
1 TTAGCCCAATGTCACTGGTCTTGAATCAGCACATTGG
388687 CATTCCTCTC
Statistics
Matches: 80, Mismatches: 6, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
49 80 1.00
ACGTcount: A:0.20, C:0.27, G:0.19, T:0.33
Consensus pattern (49 bp):
TTAGCCCAATGTCACTGGTCTTGAATCAGCACATTGGTCCACTTTTCCC
Found at i:389088 original size:20 final size:20
Alignment explanation
Indices: 389063--389120 Score: 82
Period size: 20 Copynumber: 2.9 Consensus size: 20
389053 TTTTTACCCA
389063 AATGTATCGATACATTCTTC
1 AATGTATCGATACATTCTTC
* *
389083 AATGTATCGATACATGT-ATG
1 AATGTATCGATACAT-TCTTC
389103 AATGTATCGATACATTCT
1 AATGTATCGATACATTCT
389121 ATCTTTTTAC
Statistics
Matches: 33, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
19 1 0.03
20 31 0.94
21 1 0.03
ACGTcount: A:0.33, C:0.16, G:0.14, T:0.38
Consensus pattern (20 bp):
AATGTATCGATACATTCTTC
Found at i:390611 original size:13 final size:13
Alignment explanation
Indices: 390593--390618 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
390583 CATTATGCTG
390593 TGTATCGATACAT
1 TGTATCGATACAT
390606 TGTATCGATACAT
1 TGTATCGATACAT
390619 GCTCACTGTA
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:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:390726 original size:13 final size:13
Alignment explanation
Indices: 390708--390733 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
390698 CATGGGACAA
390708 TGTATCGATACAT
1 TGTATCGATACAT
390721 TGTATCGATACAT
1 TGTATCGATACAT
390734 GCTGAAATGT
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:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:390732 original size:33 final size:33
Alignment explanation
Indices: 390690--390753 Score: 103
Period size: 33 Copynumber: 1.9 Consensus size: 33
390680 TCACTATTTA
390690 TATCGATACATG-GGACAATGTATCGATACATTG
1 TATCGATACATGCGGA-AATGTATCGATACATTG
*
390723 TATCGATACATGCTGAAATGTATCGATACAT
1 TATCGATACATGCGGAAATGTATCGATACAT
390754 AACTTGTAAT
Statistics
Matches: 29, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
33 27 0.93
34 2 0.07
ACGTcount: A:0.34, C:0.16, G:0.19, T:0.31
Consensus pattern (33 bp):
TATCGATACATGCGGAAATGTATCGATACATTG
Found at i:393386 original size:78 final size:78
Alignment explanation
Indices: 393257--393412 Score: 312
Period size: 78 Copynumber: 2.0 Consensus size: 78
393247 AAGTACGTAG
393257 ACCACATGATCAATGTCTCGAGTTTTGTAACTCAAGACATAGGTTTCAATAGGCATCCGATCATG
1 ACCACATGATCAATGTCTCGAGTTTTGTAACTCAAGACATAGGTTTCAATAGGCATCCGATCATG
393322 CTTAGCCCGAAAT
66 CTTAGCCCGAAAT
393335 ACCACATGATCAATGTCTCGAGTTTTGTAACTCAAGACATAGGTTTCAATAGGCATCCGATCATG
1 ACCACATGATCAATGTCTCGAGTTTTGTAACTCAAGACATAGGTTTCAATAGGCATCCGATCATG
393400 CTTAGCCCGAAAT
66 CTTAGCCCGAAAT
393413 GATTGGTGGC
Statistics
Matches: 78, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
78 78 1.00
ACGTcount: A:0.31, C:0.23, G:0.18, T:0.28
Consensus pattern (78 bp):
ACCACATGATCAATGTCTCGAGTTTTGTAACTCAAGACATAGGTTTCAATAGGCATCCGATCATG
CTTAGCCCGAAAT
Found at i:398108 original size:50 final size:50
Alignment explanation
Indices: 398046--398265 Score: 361
Period size: 50 Copynumber: 4.4 Consensus size: 50
398036 GTTGATTATC
* *
398046 CTTCACCAACCTTTGACAATAGAGAGAGGTGGTCGTAATTGTTGACGATT
1 CTTCACCAACCTTTGACAATAGAGAGAGGTGGCCATAATTGTTGACGATT
* *
398096 CTTCACCAACCTTTGACAATAGAGAGAGGTGGCCATTATTGTTGATGATT
1 CTTCACCAACCTTTGACAATAGAGAGAGGTGGCCATAATTGTTGACGATT
*
398146 CTTCACCAACCTTTGACAATAAAGAGAGGTGGCCATAATTGTTGACGATT
1 CTTCACCAACCTTTGACAATAGAGAGAGGTGGCCATAATTGTTGACGATT
*
398196 CTTCACCAACCTTTGACAA-ACGGAGAGAGGTGGCCATTATTGTTGACGATT
1 CTTCACCAACCTTTGACAATA--GAGAGAGGTGGCCATAATTGTTGACGATT
398247 CTTCACCAACCTTTGACAA
1 CTTCACCAACCTTTGACAA
398266 ATGTGGCCAT
Statistics
Matches: 159, Mismatches: 9, Indels: 3
0.93 0.05 0.02
Matches are distributed among these distances:
49 1 0.01
50 112 0.70
51 46 0.29
ACGTcount: A:0.29, C:0.21, G:0.21, T:0.29
Consensus pattern (50 bp):
CTTCACCAACCTTTGACAATAGAGAGAGGTGGCCATAATTGTTGACGATT
Found at i:402753 original size:50 final size:50
Alignment explanation
Indices: 402691--402910 Score: 341
Period size: 50 Copynumber: 4.4 Consensus size: 50
402681 GTTGATTATC
*
402691 CTTCACCAACCTTTGACAATAGAGAGAGGTGGTCATAATTGTTGACGATT
1 CTTCACCAACCTTTGACAATAGAGAGAGGTGGCCATAATTGTTGACGATT
* * * *
402741 ATTCACCAACCTTTAACAATAGAGAGAGGTAGCCATTATTGTTGACGATT
1 CTTCACCAACCTTTGACAATAGAGAGAGGTGGCCATAATTGTTGACGATT
*
402791 CTTCACCAACCTTTGACAATAAAGAGAGGTGGCCATAATTGTTGACGATT
1 CTTCACCAACCTTTGACAATAGAGAGAGGTGGCCATAATTGTTGACGATT
* ** *
402841 CTTCACCAACCTTTGACAAATGGAGAGAGGTGATCATTATTGTTGACGATT
1 CTTCACCAACCTTTGAC-AATAGAGAGAGGTGGCCATAATTGTTGACGATT
402892 CTTCACCAACCTTTGACAA
1 CTTCACCAACCTTTGACAA
402911 ATGTGGTCAT
Statistics
Matches: 154, Mismatches: 15, Indels: 2
0.90 0.09 0.01
Matches are distributed among these distances:
50 109 0.71
51 45 0.29
ACGTcount: A:0.31, C:0.20, G:0.19, T:0.30
Consensus pattern (50 bp):
CTTCACCAACCTTTGACAATAGAGAGAGGTGGCCATAATTGTTGACGATT
Found at i:412784 original size:524 final size:524
Alignment explanation
Indices: 411786--412833 Score: 1715
Period size: 524 Copynumber: 2.0 Consensus size: 524
411776 TCATGAAAGC
* *
411786 TGTCGTAAGGTGCGCTCGACCCCGGCGATAGGGCAAATGAGGCACGCTCGACTTAATATCCCTTA
1 TGTCGTAACGTGCGCTCGACCCCGGCGATAGGGCAAATGAGGCACGCTCGACTTAATATCCCTCA
* *
411851 CGATTGGGGATTTCTGTGGCATGATGGGAAATGTGTTGATAAAAGGGGGAAGATCAGTAGATGAA
66 CGATTGGGGATTTATGTGGCATGATGGGAAATGTGTTGATAAAAGGAGGAAGATCAGTAGATGAA
* *
411916 TCGCCCATCTAATTGATCTTCAATGGTCACTACGAAGTGACCGAGATTTTGGAGTCGCCACCGAT
131 TCGCCCATCTAATTGATCTTCAATGGTCACTACGAAGTGACCAAAATTTTGGAGTCGCCACCGAT
*
411981 CATTTCGGGCTAGGCATGATCGGATGCCTATTGAAACCTATGTCTTGAGTTACGAAACTCAAAAC
196 CATTTCGGGCTAGGCATGATCGGATGCCTATTGAAACCCATGTCTTGAGTTACGAAACTCAAAAC
*
412046 ATCGATCCCGTGGTCTACGTACTTTAGAGATTCACCGGTTAGGTTCGGGAGTTGGTTACGCGCAA
261 ATCGATCCCGTGGTCTACCTACTTTAGAGATTCACCGGTTAGGTTCGGGAGTTGGTTACGCGCAA
* *
412111 AGAGGTACAAACCTCCTCGCGACGCCCGAAATCGGTACCTTACTAGCAATGCTTTGACTTAAAGT
326 AGAGGTACAAACCTCCTCGCGACGCCCGAAATCGGTACCTTACTAGCAACGCTTTGACTCAAAGT
* * * *
412176 TGATTTCATTGATTTCGGTTTATCATTATTTCGATATGATCCCTTTCGAATGCATGAATTTTGTG
391 TGATTGCATTGATTTCGATTTATCATTATTTCGATATGATCCCTTTCGAATGCATAAATTTTGTA
* * * ** *
412241 TCAAAATAAATCTAGGTTTTTGGCAATCGTTTTCATCTCATATGCGCCCCGGAGAAATGGGAAAC
456 TCAAAACAAATCCAGG-TTTTGACAAAAGTTTTCATCTCATATGCGCCCCGGAGAAATAGGAAAC
412306 ATAGA
520 ATAGA
* *
412311 TGTCGTAACGTGCGCTCGACCCCGGCGATAGGGCAAATGGGGCACGCTCGACTTAATATCCCTCG
1 TGTCGTAACGTGCGCTCGACCCCGGCGATAGGGCAAATGAGGCACGCTCGACTTAATATCCCTCA
* *
412376 CGATTGGGGATTTATGTGGCATGATGGGAAGTGTGTTGATTAAA-GAGGAAGATCAGTAGATGAA
66 CGATTGGGGATTTATGTGGCATGATGGGAAATGTGTTGATAAAAGGAGGAAGATCAGTAGATGAA
412440 TCGCCCATCTAATTGATCTTCAATGGTCACTACGAAGTGACCAAAATTTTGGAGTCGCCACCGAT
131 TCGCCCATCTAATTGATCTTCAATGGTCACTACGAAGTGACCAAAATTTTGGAGTCGCCACCGAT
412505 CATTTCGGGCTAGGCATGATCGGATGCCTATTGAAACCCATGTCTTGAGTTACGAAACTCAAAAC
196 CATTTCGGGCTAGGCATGATCGGATGCCTATTGAAACCCATGTCTTGAGTTACGAAACTCAAAAC
* * *
412570 ATCGATCCCGTGGTCTGCCTACTTTAGAGATTCGCCGGTTGGGTTCGGGAGTTGGTTACGCGCAA
261 ATCGATCCCGTGGTCTACCTACTTTAGAGATTCACCGGTTAGGTTCGGGAGTTGGTTACGCGCAA
* *
412635 AGAGGTACGAACCTCCTCGCGACGCCCGAAATCGGTACCTTACTAGCAACGTTTTGACTCAATA-
326 AGAGGTACAAACCTCCTCGCGACGCCCGAAATCGGTACCTTACTAGCAACGCTTTGACTCAA-AG
* *
412699 TTGGTTGCATTGATTTCGATTTATCATTATTAT-GATATGATCCCTTTTGAATGCATAAATTTTG
390 TTGATTGCATTGATTTCGATTTATCATTATT-TCGATATGATCCCTTTCGAATGCATAAATTTTG
* * * * * *
412763 TATGAAAGCAAATCCAGGTTTTGATAAAAGTTTTCATCTCATATGCGTCTCGGAGAGATAGGAAA
454 TATCAAAACAAATCCAGGTTTTGACAAAAGTTTTCATCTCATATGCGCCCCGGAGAAATAGGAAA
412828 CATAGA
519 CATAGA
412834 GACATAAAAG
Statistics
Matches: 484, Mismatches: 37, Indels: 6
0.92 0.07 0.01
Matches are distributed among these distances:
523 45 0.09
524 335 0.69
525 104 0.21
ACGTcount: A:0.27, C:0.20, G:0.24, T:0.29
Consensus pattern (524 bp):
TGTCGTAACGTGCGCTCGACCCCGGCGATAGGGCAAATGAGGCACGCTCGACTTAATATCCCTCA
CGATTGGGGATTTATGTGGCATGATGGGAAATGTGTTGATAAAAGGAGGAAGATCAGTAGATGAA
TCGCCCATCTAATTGATCTTCAATGGTCACTACGAAGTGACCAAAATTTTGGAGTCGCCACCGAT
CATTTCGGGCTAGGCATGATCGGATGCCTATTGAAACCCATGTCTTGAGTTACGAAACTCAAAAC
ATCGATCCCGTGGTCTACCTACTTTAGAGATTCACCGGTTAGGTTCGGGAGTTGGTTACGCGCAA
AGAGGTACAAACCTCCTCGCGACGCCCGAAATCGGTACCTTACTAGCAACGCTTTGACTCAAAGT
TGATTGCATTGATTTCGATTTATCATTATTTCGATATGATCCCTTTCGAATGCATAAATTTTGTA
TCAAAACAAATCCAGGTTTTGACAAAAGTTTTCATCTCATATGCGCCCCGGAGAAATAGGAAACA
TAGA
Done.