Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008185.1 Hibiscus syriacus cultivar Beakdansim tig00110788_pilon, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 3563405
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 3 of 16
Found at i:363810 original size:59 final size:59
Alignment explanation
Indices: 363718--363829 Score: 188
Period size: 59 Copynumber: 1.9 Consensus size: 59
363708 AAAAATCGCA
**
363718 ACGATAGTTTAATTCGCCTTGCGATAGTCATTTTCGTGTTGCGATTTTCATTTCGCGTT
1 ACGATAGTCAAATTCGCCTTGCGATAGTCATTTTCGTGTTGCGATTTTCATTTCGCGTT
* *
363777 ACGATAGTCAAATTCGCGTTGCGATAGTCATTTTTGTGTTGCGATTTTCATTT
1 ACGATAGTCAAATTCGCCTTGCGATAGTCATTTTCGTGTTGCGATTTTCATTT
363830 TCGTGTTGCG
Statistics
Matches: 49, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
59 49 1.00
ACGTcount: A:0.19, C:0.17, G:0.21, T:0.44
Consensus pattern (59 bp):
ACGATAGTCAAATTCGCCTTGCGATAGTCATTTTCGTGTTGCGATTTTCATTTCGCGTT
Found at i:363851 original size:20 final size:20
Alignment explanation
Indices: 363812--363851 Score: 62
Period size: 20 Copynumber: 2.0 Consensus size: 20
363802 AGTCATTTTT
* *
363812 GTGTTGCGATTTTCATTTTC
1 GTGTTGCGATTTTAAGTTTC
363832 GTGTTGCGATTTTAAGTTTC
1 GTGTTGCGATTTTAAGTTTC
363852 AGAAACTATT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.12, C:0.12, G:0.23, T:0.53
Consensus pattern (20 bp):
GTGTTGCGATTTTAAGTTTC
Found at i:365919 original size:22 final size:20
Alignment explanation
Indices: 365880--365920 Score: 55
Period size: 20 Copynumber: 1.9 Consensus size: 20
365870 TTTCAATATG
*
365880 CATATATATATATTTCATGA
1 CATATATATATATATCATGA
365900 CATATATATAATCATATCATG
1 CATATATAT-AT-ATATCATG
365921 CACACATGAA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 9 0.50
21 2 0.11
22 7 0.39
ACGTcount: A:0.41, C:0.12, G:0.05, T:0.41
Consensus pattern (20 bp):
CATATATATATATATCATGA
Found at i:366151 original size:15 final size:15
Alignment explanation
Indices: 366131--366165 Score: 70
Period size: 15 Copynumber: 2.3 Consensus size: 15
366121 CCGTAGGACC
366131 ACTACGTCCCGAAGG
1 ACTACGTCCCGAAGG
366146 ACTACGTCCCGAAGG
1 ACTACGTCCCGAAGG
366161 ACTAC
1 ACTAC
366166 AATACCCTCG
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 20 1.00
ACGTcount: A:0.29, C:0.34, G:0.23, T:0.14
Consensus pattern (15 bp):
ACTACGTCCCGAAGG
Found at i:366468 original size:14 final size:15
Alignment explanation
Indices: 366441--366469 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
366431 ATATCATATA
366441 TCTTATGTTTTATGC
1 TCTTATGTTTTATGC
366456 TCTTATG-TTTATGC
1 TCTTATGTTTTATGC
366470 ATATCATGTA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 7 0.50
15 7 0.50
ACGTcount: A:0.14, C:0.14, G:0.14, T:0.59
Consensus pattern (15 bp):
TCTTATGTTTTATGC
Found at i:368384 original size:23 final size:24
Alignment explanation
Indices: 368358--368402 Score: 58
Period size: 23 Copynumber: 1.9 Consensus size: 24
368348 CATTTATTCT
368358 TATAC-CATCTTCATTC-AAATTAC
1 TATACACAT-TTCATTCTAAATTAC
*
368381 TATACACATTTCTTTCTAAATT
1 TATACACATTTCATTCTAAATT
368403 TTACTCATAT
Statistics
Matches: 19, Mismatches: 1, Indels: 3
0.83 0.04 0.13
Matches are distributed among these distances:
23 11 0.58
24 8 0.42
ACGTcount: A:0.33, C:0.22, G:0.00, T:0.44
Consensus pattern (24 bp):
TATACACATTTCATTCTAAATTAC
Found at i:372002 original size:22 final size:20
Alignment explanation
Indices: 371963--372003 Score: 55
Period size: 20 Copynumber: 1.9 Consensus size: 20
371953 TTTCAATATG
*
371963 CATATATATATATTTCATGA
1 CATATATATATATGTCATGA
371983 CATATATATAATCATGTCATG
1 CATATATAT-AT-ATGTCATG
372004 CACACATGAA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 9 0.50
21 2 0.11
22 7 0.39
ACGTcount: A:0.39, C:0.12, G:0.07, T:0.41
Consensus pattern (20 bp):
CATATATATATATGTCATGA
Found at i:372539 original size:14 final size:15
Alignment explanation
Indices: 372511--372540 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
372501 TATCATATAT
372511 CTCTTATGTTTTATG
1 CTCTTATGTTTTATG
372526 CTCTTATG-TTTATG
1 CTCTTATGTTTTATG
372540 C
1 C
372541 ATATCATGTA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 7 0.47
15 8 0.53
ACGTcount: A:0.13, C:0.17, G:0.13, T:0.57
Consensus pattern (15 bp):
CTCTTATGTTTTATG
Found at i:374223 original size:22 final size:22
Alignment explanation
Indices: 374198--374275 Score: 147
Period size: 22 Copynumber: 3.5 Consensus size: 22
374188 GTCAACGGTA
374198 AACGGTCGGGTCGGGTTGGGTC
1 AACGGTCGGGTCGGGTTGGGTC
374220 AACGGTCGGGTCGGGTTGGGTC
1 AACGGTCGGGTCGGGTTGGGTC
*
374242 AACGGTCGGGTCGGGTCGGGTC
1 AACGGTCGGGTCGGGTTGGGTC
374264 AACGGTCGGGTC
1 AACGGTCGGGTC
374276 AGACCGGTCA
Statistics
Matches: 55, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
22 55 1.00
ACGTcount: A:0.10, C:0.21, G:0.49, T:0.21
Consensus pattern (22 bp):
AACGGTCGGGTCGGGTTGGGTC
Found at i:374275 original size:5 final size:5
Alignment explanation
Indices: 374201--374263 Score: 54
Period size: 5 Copynumber: 11.8 Consensus size: 5
374191 AACGGTAAAC
* * * *
374201 GGTCG GGTCG GGTTG GGTCAAC GGTCG GGTCG GGTTG GGTCAAC GGTCG
1 GGTCG GGTCG GGTCG GGTC--G GGTCG GGTCG GGTCG GGTC--G GGTCG
374250 GGTCG GGTCG GGTC
1 GGTCG GGTCG GGTC
374264 AACGGTCGGG
Statistics
Matches: 46, Mismatches: 8, Indels: 8
0.74 0.13 0.13
Matches are distributed among these distances:
5 38 0.83
7 8 0.17
ACGTcount: A:0.06, C:0.19, G:0.52, T:0.22
Consensus pattern (5 bp):
GGTCG
Found at i:374290 original size:9 final size:9
Alignment explanation
Indices: 374272--374359 Score: 86
Period size: 9 Copynumber: 9.3 Consensus size: 9
374262 TCAACGGTCG
*
374272 GGTCAGACC
1 GGTCAAACC
374281 GGTCAAACC
1 GGTCAAACC
*
374290 GGTTCAGACC
1 GG-TCAAACC
374300 GGTCAAACC
1 GGTCAAACC
**
374309 GGTTTGAACC
1 GG-TCAAACC
*
374319 GGTTGAAACC
1 GG-TCAAACC
374329 GGTCAAACC
1 GGTCAAACC
374338 GGTCAGAACC
1 GGTCA-AACC
*
374348 GGTTAAACC
1 GGTCAAACC
374357 GGT
1 GGT
374360 TTCCAGCAGC
Statistics
Matches: 67, Mismatches: 9, Indels: 6
0.82 0.11 0.07
Matches are distributed among these distances:
9 36 0.54
10 31 0.46
ACGTcount: A:0.27, C:0.27, G:0.28, T:0.17
Consensus pattern (9 bp):
GGTCAAACC
Found at i:374329 original size:29 final size:28
Alignment explanation
Indices: 374303--374359 Score: 78
Period size: 29 Copynumber: 2.0 Consensus size: 28
374293 TCAGACCGGT
** *
374303 CAAACCGGTTTGAACCGGTTGAAACCGGT
1 CAAACCGGTCAGAACCGG-TTAAACCGGT
374332 CAAACCGGTCAGAACCGGTTAAACCGGT
1 CAAACCGGTCAGAACCGGTTAAACCGGT
374360 TTCCAGCAGC
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
28 9 0.36
29 16 0.64
ACGTcount: A:0.30, C:0.26, G:0.26, T:0.18
Consensus pattern (28 bp):
CAAACCGGTCAGAACCGGTTAAACCGGT
Found at i:374355 original size:19 final size:18
Alignment explanation
Indices: 374278--374359 Score: 92
Period size: 19 Copynumber: 4.3 Consensus size: 18
374268 GTCGGGTCAG
*
374278 ACCGGTCAAACCGGTTCAG
1 ACCGGTCAAACCGGTT-AA
*
374297 ACCGGTCAAACCGGTTTGA
1 ACCGGTCAAACCGG-TTAA
* *
374316 ACCGGTTGAAACCGGTCAA
1 ACCGG-TCAAACCGGTTAA
374335 ACCGGTCAGAACCGGTTAA
1 ACCGGTCA-AACCGGTTAA
374354 ACCGGT
1 ACCGGT
374360 TTCCAGCAGC
Statistics
Matches: 53, Mismatches: 7, Indels: 6
0.80 0.11 0.09
Matches are distributed among these distances:
18 2 0.04
19 41 0.77
20 10 0.19
ACGTcount: A:0.28, C:0.28, G:0.27, T:0.17
Consensus pattern (18 bp):
ACCGGTCAAACCGGTTAA
Found at i:389154 original size:17 final size:17
Alignment explanation
Indices: 389134--389166 Score: 66
Period size: 17 Copynumber: 1.9 Consensus size: 17
389124 GAAAGTCAAT
389134 GGTCAACGGTCGGGTCG
1 GGTCAACGGTCGGGTCG
389151 GGTCAACGGTCGGGTC
1 GGTCAACGGTCGGGTC
389167 AGACCGGTCA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.12, C:0.24, G:0.45, T:0.18
Consensus pattern (17 bp):
GGTCAACGGTCGGGTCG
Found at i:389189 original size:19 final size:19
Alignment explanation
Indices: 389165--389251 Score: 106
Period size: 19 Copynumber: 4.5 Consensus size: 19
389155 AACGGTCGGG
*
389165 TCAGACCGGTCAAACCGGC
1 TCAGACCGGTCAAACCGGT
*
389184 TCAGACCGGTCAAACCGAT
1 TCAGACCGGTCAAACCGGT
389203 TCAGACCGGTCAAACCGGT
1 TCAGACCGGTCAAACCGGT
*
389222 TC-GAACCGGTTGAAACCGG-
1 TCAG-ACCGG-TCAAACCGGT
389241 TCAGAACCGGT
1 TCAG-ACCGGT
389252 TGAAAATCGG
Statistics
Matches: 61, Mismatches: 4, Indels: 6
0.86 0.06 0.08
Matches are distributed among these distances:
18 1 0.02
19 45 0.74
20 15 0.25
ACGTcount: A:0.28, C:0.31, G:0.26, T:0.15
Consensus pattern (19 bp):
TCAGACCGGTCAAACCGGT
Found at i:389210 original size:10 final size:9
Alignment explanation
Indices: 389163--389221 Score: 64
Period size: 9 Copynumber: 6.3 Consensus size: 9
389153 TCAACGGTCG
389163 GGTCAGACC
1 GGTCAGACC
*
389172 GGTCAAACC
1 GGTCAGACC
389181 GGCTCAGACC
1 GG-TCAGACC
*
389191 GGTCAAACC
1 GGTCAGACC
*
389200 GATTCAGACC
1 G-GTCAGACC
*
389210 GGTCAAACC
1 GGTCAGACC
389219 GGT
1 GGT
389222 TCGAACCGGT
Statistics
Matches: 41, Mismatches: 7, Indels: 4
0.79 0.13 0.08
Matches are distributed among these distances:
9 26 0.63
10 15 0.37
ACGTcount: A:0.27, C:0.32, G:0.27, T:0.14
Consensus pattern (9 bp):
GGTCAGACC
Found at i:390258 original size:19 final size:20
Alignment explanation
Indices: 390222--390259 Score: 76
Period size: 20 Copynumber: 1.9 Consensus size: 20
390212 TTTCATTTAG
390222 GGGGGAATCGATACCCCCCA
1 GGGGGAATCGATACCCCCCA
390242 GGGGGAATCGATACCCCC
1 GGGGGAATCGATACCCCC
390260 TGAACATTCT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.24, C:0.34, G:0.32, T:0.11
Consensus pattern (20 bp):
GGGGGAATCGATACCCCCCA
Found at i:391371 original size:20 final size:19
Alignment explanation
Indices: 391346--391412 Score: 80
Period size: 20 Copynumber: 3.4 Consensus size: 19
391336 AAACTTAAAA
391346 ATCGCAAAGCGAAAATGACT
1 ATCGCAAAGC-AAAATGACT
*
391366 ATCGCAACGCAGAAATGACT
1 ATCGCAAAGCA-AAATGACT
* *
391386 ATCGCAATGCAAATTTGACT
1 ATCGCAAAGCAAA-ATGACT
391406 ATCGCAA
1 ATCGCAA
391413 CGGGATAATC
Statistics
Matches: 42, Mismatches: 3, Indels: 4
0.86 0.06 0.08
Matches are distributed among these distances:
19 3 0.07
20 39 0.93
ACGTcount: A:0.40, C:0.22, G:0.18, T:0.19
Consensus pattern (19 bp):
ATCGCAAAGCAAAATGACT
Found at i:391573 original size:20 final size:20
Alignment explanation
Indices: 391548--391616 Score: 95
Period size: 20 Copynumber: 3.5 Consensus size: 20
391538 GCGATTATCC
*
391548 CGTTGCGATAGTCAAATTCG
1 CGTTGCGATAGTCAATTTCG
391568 CGTTGCGATAGTC-ATTTCCG
1 CGTTGCGATAGTCAATTT-CG
* *
391588 CGTTGCGATAGTCATTTTCA
1 CGTTGCGATAGTCAATTTCG
391608 CGTTGCGAT
1 CGTTGCGAT
391617 TTAAGTTTTG
Statistics
Matches: 44, Mismatches: 3, Indels: 4
0.86 0.06 0.08
Matches are distributed among these distances:
19 3 0.07
20 38 0.86
21 3 0.07
ACGTcount: A:0.19, C:0.22, G:0.25, T:0.35
Consensus pattern (20 bp):
CGTTGCGATAGTCAATTTCG
Found at i:391574 original size:34 final size:37
Alignment explanation
Indices: 391530--391617 Score: 92
Period size: 40 Copynumber: 2.4 Consensus size: 37
391520 CGATTTTTAT
*
391530 TTCGCATTGCGATT-A-TCC-CGTTGCGATAGTCAAA
1 TTCGCGTTGCGATTCATTCCGCGTTGCGATAGTCAAA
**
391564 TTCGCGTTGCGATAGTCATTTCCGCGTTGCGATAGTCATT
1 TTCGCGTTGCGAT--TCA-TTCCGCGTTGCGATAGTCAAA
*
391604 TTCACGTTGCGATT
1 TTCGCGTTGCGATT
391618 TAAGTTTTGT
Statistics
Matches: 44, Mismatches: 4, Indels: 8
0.79 0.07 0.14
Matches are distributed among these distances:
34 12 0.27
36 1 0.02
37 1 0.02
38 1 0.02
39 3 0.07
40 26 0.59
ACGTcount: A:0.18, C:0.23, G:0.23, T:0.36
Consensus pattern (37 bp):
TTCGCGTTGCGATTCATTCCGCGTTGCGATAGTCAAA
Found at i:392220 original size:42 final size:42
Alignment explanation
Indices: 392150--392241 Score: 114
Period size: 42 Copynumber: 2.2 Consensus size: 42
392140 TCTCCTATCG
*
392150 TTCAAGAGGCCCCTATCATCCCTCAAGA-GTCTCCTCCCACCA
1 TTCAAGAGGCCCCTATCATCCCTCAAGAGGTC-ACTCCCACCA
* ** * *
392192 TTCAAGAGGCCCCTGTCATCGTTGAAGAGGTCACTCTCACCA
1 TTCAAGAGGCCCCTATCATCCCTCAAGAGGTCACTCCCACCA
392234 TTCAAGAG
1 TTCAAGAG
392242 CCTGATTCAT
Statistics
Matches: 43, Mismatches: 6, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
42 40 0.93
43 3 0.07
ACGTcount: A:0.25, C:0.35, G:0.17, T:0.23
Consensus pattern (42 bp):
TTCAAGAGGCCCCTATCATCCCTCAAGAGGTCACTCCCACCA
Found at i:392240 original size:21 final size:21
Alignment explanation
Indices: 392187--392241 Score: 56
Period size: 21 Copynumber: 2.6 Consensus size: 21
392177 AGTCTCCTCC
* *
392187 CACCATTCAAGAGGCCCCTGT
1 CACCATTCAAGAGGCCACTCT
* * * *
392208 CATCGTTGAAGAGGTCACTCT
1 CACCATTCAAGAGGCCACTCT
392229 CACCATTCAAGAG
1 CACCATTCAAGAG
392242 CCTGATTCAT
Statistics
Matches: 25, Mismatches: 9, Indels: 0
0.74 0.26 0.00
Matches are distributed among these distances:
21 25 1.00
ACGTcount: A:0.27, C:0.31, G:0.20, T:0.22
Consensus pattern (21 bp):
CACCATTCAAGAGGCCACTCT
Found at i:393658 original size:14 final size:14
Alignment explanation
Indices: 393622--393683 Score: 61
Period size: 14 Copynumber: 4.3 Consensus size: 14
393612 TTCCTTGTTT
*
393622 AATTGATTCGTAAA
1 AATTGATTTGTAAA
393636 AATTGATTTGTAAA
1 AATTGATTTGTAAA
* *
393650 AGTTGATTTGTTTAA
1 AATTGATTTG-TAAA
* *
393665 TATTGATGTGTAAA
1 AATTGATTTGTAAA
393679 TAATT
1 -AATT
393684 CTTATTTGTG
Statistics
Matches: 38, Mismatches: 8, Indels: 3
0.78 0.16 0.06
Matches are distributed among these distances:
14 25 0.66
15 13 0.34
ACGTcount: A:0.37, C:0.02, G:0.16, T:0.45
Consensus pattern (14 bp):
AATTGATTTGTAAA
Found at i:393753 original size:63 final size:65
Alignment explanation
Indices: 393636--393793 Score: 248
Period size: 63 Copynumber: 2.4 Consensus size: 65
393626 GATTCGTAAA
*
393636 AATTGATTTGTAAAAGTTGATTTGTTTAATATTGATGTGTAAATAATTCTTATTTGTGCTTGTTT
1 AATTGATTTGTAAAAGTTGATTTGTTTAATATTGATGTGTAAATAATTCTTATTTGTGCTTATTT
*
393701 AATTAATTTGTAAAAGTTGATTTGTTT-A-ATTGATGTGTAAATAATTCTTATTTGTGCTTATTT
1 AATTGATTTGTAAAAGTTGATTTGTTTAATATTGATGTGTAAATAATTCTTATTTGTGCTTATTT
393764 AATTGATTGAAATGTAAAAGTTGATTTGTT
1 AATTGATT----TGTAAAAGTTGATTTGTT
393794 GATTTCAAAC
Statistics
Matches: 86, Mismatches: 3, Indels: 6
0.91 0.03 0.06
Matches are distributed among these distances:
63 41 0.48
64 1 0.01
65 26 0.30
67 18 0.21
ACGTcount: A:0.30, C:0.03, G:0.16, T:0.51
Consensus pattern (65 bp):
AATTGATTTGTAAAAGTTGATTTGTTTAATATTGATGTGTAAATAATTCTTATTTGTGCTTATTT
Found at i:393870 original size:20 final size:19
Alignment explanation
Indices: 393845--393913 Score: 75
Period size: 20 Copynumber: 3.5 Consensus size: 19
393835 ATGTACACTT
393845 TCGCAACGCTAAACTCAAAA
1 TCGCAACGCTAAA-TCAAAA
*
393865 TCGCAATGCTAAAGTCAAAA
1 TCGCAACGCTAAA-TCAAAA
* * *
393885 TTGCAATGCGAAATCCAAAA
1 TCGCAACGCTAAAT-CAAAA
393905 TCGCAACGC
1 TCGCAACGC
393914 GAAAGTCAAT
Statistics
Matches: 42, Mismatches: 6, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
19 1 0.02
20 41 0.98
ACGTcount: A:0.42, C:0.26, G:0.14, T:0.17
Consensus pattern (19 bp):
TCGCAACGCTAAATCAAAA
Found at i:393995 original size:20 final size:20
Alignment explanation
Indices: 393963--394103 Score: 150
Period size: 20 Copynumber: 7.3 Consensus size: 20
393953 GATTTTCTTG
* *
393963 TTGCAATAGTCAAATTCCCA
1 TTGCGATAGTCAAATTCGCA
* *
393983 TTGCGATAATCAAATTCGCG
1 TTGCGATAGTCAAATTCGCA
394003 TTGCGATAGTCAAATTCGCA
1 TTGCGATAGTCAAATTCGCA
* *
394023 TTGCGATAGTCAAATTTGCG
1 TTGCGATAGTCAAATTCGCA
* *
394043 TTGCGAT--T----TTTGCG
1 TTGCGATAGTCAAATTCGCA
*
394057 TTGCGATAGTCATATTCGCA
1 TTGCGATAGTCAAATTCGCA
*
394077 TTGCGATAGTCAAATTCGCG
1 TTGCGATAGTCAAATTCGCA
394097 TTGCGAT
1 TTGCGAT
394104 TTTTGAGTTG
Statistics
Matches: 103, Mismatches: 12, Indels: 12
0.81 0.09 0.09
Matches are distributed among these distances:
14 13 0.13
16 1 0.01
18 1 0.01
20 88 0.85
ACGTcount: A:0.26, C:0.19, G:0.21, T:0.34
Consensus pattern (20 bp):
TTGCGATAGTCAAATTCGCA
Found at i:394047 original size:94 final size:93
Alignment explanation
Indices: 393912--394103 Score: 260
Period size: 94 Copynumber: 2.1 Consensus size: 93
393902 AAATCGCAAC
* * * * *
393912 GCGAAAGTCAATTCACGTTGCGATAGTCTAATATGCTTTGCGATTTTCT-TGTTGCAATAGTCAA
1 GCGATAGTCAATTCACATTGCGATAGTCAAATATGCGTTGCGATTTT-TGCGTTGCAATAGTCAA
393976 ATTCCCATTGCGATAATCAAATTCGCGTT
65 ATTCCCATTGCGATAATCAAATTCGCGTT
* * * *
394005 GCGATAGTCAAATTCGCATTGCGATAGTCAAATTTGCGTTGCGATTTTTGCGTTGCGATAGTCAT
1 GCGATAGTC-AATTCACATTGCGATAGTCAAATATGCGTTGCGATTTTTGCGTTGCAATAGTCAA
* *
394070 ATTCGCATTGCGATAGTCAAATTCGCGTT
65 ATTCCCATTGCGATAATCAAATTCGCGTT
394099 GCGAT
1 GCGAT
394104 TTTTGAGTTG
Statistics
Matches: 86, Mismatches: 11, Indels: 3
0.86 0.11 0.03
Matches are distributed among these distances:
93 9 0.10
94 77 0.90
ACGTcount: A:0.25, C:0.19, G:0.21, T:0.35
Consensus pattern (93 bp):
GCGATAGTCAATTCACATTGCGATAGTCAAATATGCGTTGCGATTTTTGCGTTGCAATAGTCAAA
TTCCCATTGCGATAATCAAATTCGCGTT
Found at i:394056 original size:14 final size:14
Alignment explanation
Indices: 394037--394063 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
394027 GATAGTCAAA
394037 TTTGCGTTGCGATT
1 TTTGCGTTGCGATT
394051 TTTGCGTTGCGAT
1 TTTGCGTTGCGAT
394064 AGTCATATTC
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.07, C:0.15, G:0.30, T:0.48
Consensus pattern (14 bp):
TTTGCGTTGCGATT
Found at i:394058 original size:54 final size:54
Alignment explanation
Indices: 394000--394145 Score: 229
Period size: 54 Copynumber: 2.7 Consensus size: 54
393990 AATCAAATTC
*
394000 GCGTTGCGATAGTCAAATTCGCATTGCGATAGTCAAATTTGCGTTGCGATTTTT
1 GCGTTGCGATAGTCAAATTCGCATTGCGATAGTCAAATTCGCGTTGCGATTTTT
*
394054 GCGTTGCGATAGTCATATTCGCATTGCGATAGTCAAATTCGCGTTGCGATTTTT
1 GCGTTGCGATAGTCAAATTCGCATTGCGATAGTCAAATTCGCGTTGCGATTTTT
* * * * *
394108 GAGTTGTGATAATCAAATTCGCGTTGCGATATTCAAAT
1 GCGTTGCGATAGTCAAATTCGCATTGCGATAGTCAAAT
394146 GAATGTGTAA
Statistics
Matches: 84, Mismatches: 8, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
54 84 1.00
ACGTcount: A:0.24, C:0.16, G:0.23, T:0.36
Consensus pattern (54 bp):
GCGTTGCGATAGTCAAATTCGCATTGCGATAGTCAAATTCGCGTTGCGATTTTT
Found at i:394372 original size:140 final size:140
Alignment explanation
Indices: 394120--394398 Score: 522
Period size: 140 Copynumber: 2.0 Consensus size: 140
394110 GTTGTGATAA
394120 TCAAATTCGCGTTGCGATATTCAAATGAATGTGTAATAAGTGATAACAACTGAACAGATCATAGC
1 TCAAATTCGCGTTGCGATATTCAAATGAATGTGTAATAAGTGATAACAACTGAACAGATCATAGC
**
394185 AATGTTCAAACTCAAGTTACTAATACATGTCTAACTGAAAATGTTAAAAGTTTACACATAAAATA
66 AATGTTCAAACTCAAGTTACTAATACATACCTAACTGAAAATGTTAAAAGTTTACACATAAAATA
394250 CACATAATAG
131 CACATAATAG
*
394260 TCAAATTCGCGTTGCGATATTCAAATGAATGTGTAATAAGTGATAACAACTGAACATATCATAGC
1 TCAAATTCGCGTTGCGATATTCAAATGAATGTGTAATAAGTGATAACAACTGAACAGATCATAGC
*
394325 AATGTTCAAACTCAAGTTACTAATACATACCTAACTGAAAATTTTAAAAGTTTACACATAAAATA
66 AATGTTCAAACTCAAGTTACTAATACATACCTAACTGAAAATGTTAAAAGTTTACACATAAAATA
394390 CACATAATA
131 CACATAATA
394399 CAACGTTTGC
Statistics
Matches: 135, Mismatches: 4, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
140 135 1.00
ACGTcount: A:0.43, C:0.15, G:0.12, T:0.29
Consensus pattern (140 bp):
TCAAATTCGCGTTGCGATATTCAAATGAATGTGTAATAAGTGATAACAACTGAACAGATCATAGC
AATGTTCAAACTCAAGTTACTAATACATACCTAACTGAAAATGTTAAAAGTTTACACATAAAATA
CACATAATAG
Found at i:394479 original size:18 final size:18
Alignment explanation
Indices: 394456--394490 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
394446 AAGCCGGTTG
*
394456 TGATTGGGATTTTGATTT
1 TGATTGCGATTTTGATTT
394474 TGATTGCGATTTTGATT
1 TGATTGCGATTTTGATT
394491 GCCTTTTTCT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.17, C:0.03, G:0.26, T:0.54
Consensus pattern (18 bp):
TGATTGCGATTTTGATTT
Found at i:396764 original size:24 final size:24
Alignment explanation
Indices: 396737--396796 Score: 84
Period size: 24 Copynumber: 2.5 Consensus size: 24
396727 TTGAAACATC
*
396737 ATCAAAATTCGAGTATTGACCAAG
1 ATCAAAATCCGAGTATTGACCAAG
* *
396761 ATCAAAGTCCGGGTATTGACCAAG
1 ATCAAAATCCGAGTATTGACCAAG
*
396785 ATCAAATTCCGA
1 ATCAAAATCCGA
396797 ATACCGACTA
Statistics
Matches: 31, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
24 31 1.00
ACGTcount: A:0.38, C:0.20, G:0.18, T:0.23
Consensus pattern (24 bp):
ATCAAAATCCGAGTATTGACCAAG
Found at i:398048 original size:18 final size:18
Alignment explanation
Indices: 398025--398059 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
398015 ATCGGTCACA
*
398025 ACCCGACCCGACCCGTTT
1 ACCCGACCCGAACCGTTT
398043 ACCCGACCCGAACCGTT
1 ACCCGACCCGAACCGTT
398060 GACCGACGTT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.20, C:0.49, G:0.17, T:0.14
Consensus pattern (18 bp):
ACCCGACCCGAACCGTTT
Found at i:400578 original size:12 final size:12
Alignment explanation
Indices: 400563--400623 Score: 52
Period size: 12 Copynumber: 5.1 Consensus size: 12
400553 TGAATTCTAT
400563 TCTGATTTCTGA
1 TCTGATTTCTGA
*
400575 TCTGGA-TTCTGT
1 TCT-GATTTCTGA
*
400587 TCTGATATCTGA
1 TCTGATTTCTGA
* * *
400599 TATGAATTCTGT
1 TCTGATTTCTGA
*
400611 TTTGATTTCTGA
1 TCTGATTTCTGA
400623 T
1 T
400624 ATCTCCATTT
Statistics
Matches: 37, Mismatches: 10, Indels: 4
0.73 0.20 0.08
Matches are distributed among these distances:
11 2 0.05
12 33 0.89
13 2 0.05
ACGTcount: A:0.18, C:0.13, G:0.18, T:0.51
Consensus pattern (12 bp):
TCTGATTTCTGA
Found at i:400583 original size:24 final size:24
Alignment explanation
Indices: 400553--400625 Score: 101
Period size: 24 Copynumber: 3.0 Consensus size: 24
400543 ATACATTACC
* *
400553 TGAATTCTATTCTGATTTCTGATC
1 TGAATTCTGTTCTGATTTCTGATA
* *
400577 TGGATTCTGTTCTGATATCTGATA
1 TGAATTCTGTTCTGATTTCTGATA
*
400601 TGAATTCTGTTTTGATTTCTGATA
1 TGAATTCTGTTCTGATTTCTGATA
400625 T
1 T
400626 CTCCATTTAC
Statistics
Matches: 42, Mismatches: 7, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
24 42 1.00
ACGTcount: A:0.21, C:0.12, G:0.16, T:0.51
Consensus pattern (24 bp):
TGAATTCTGTTCTGATTTCTGATA
Found at i:400792 original size:2 final size:2
Alignment explanation
Indices: 400785--400823 Score: 78
Period size: 2 Copynumber: 19.5 Consensus size: 2
400775 CGGATGAGGG
400785 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
400824 GTTTTAAAAA
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:401763 original size:20 final size:20
Alignment explanation
Indices: 401738--401804 Score: 134
Period size: 20 Copynumber: 3.4 Consensus size: 20
401728 AAATTCAGCA
401738 TTGCGATAGTCAGAATCGCG
1 TTGCGATAGTCAGAATCGCG
401758 TTGCGATAGTCAGAATCGCG
1 TTGCGATAGTCAGAATCGCG
401778 TTGCGATAGTCAGAATCGCG
1 TTGCGATAGTCAGAATCGCG
401798 TTGCGAT
1 TTGCGAT
401805 TTACATATTC
Statistics
Matches: 47, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 47 1.00
ACGTcount: A:0.24, C:0.19, G:0.30, T:0.27
Consensus pattern (20 bp):
TTGCGATAGTCAGAATCGCG
Found at i:401905 original size:19 final size:19
Alignment explanation
Indices: 401881--401917 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
401871 TGCGATACTG
*
401881 GAGATCACGTTGCGATTTA
1 GAGATCACATTGCGATTTA
*
401900 GAGATCGCATTGCGATTT
1 GAGATCACATTGCGATTT
401918 TGTTGGTCAT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 16 1.00
ACGTcount: A:0.24, C:0.16, G:0.27, T:0.32
Consensus pattern (19 bp):
GAGATCACATTGCGATTTA
Found at i:407115 original size:30 final size:30
Alignment explanation
Indices: 407030--407136 Score: 135
Period size: 30 Copynumber: 3.5 Consensus size: 30
407020 ATAATTTTTA
* *
407030 AATACAATATTAATTTGACTGTTAAACTCT
1 AATACAATATTAATTTGACTATTAAACTTT
* *
407060 AATACAATATCAATTTGACTTTTAAACTTT
1 AATACAATATTAATTTGACTATTAAACTTT
*
407090 AATACAATATTAATTTGACCATTAAA-TGTT
1 AATACAATATTAATTTGACTATTAAACT-TT
*
407120 AAATAAAATATTAATTT
1 -AATACAATATTAATTT
407137 AACTTATGAA
Statistics
Matches: 68, Mismatches: 7, Indels: 3
0.87 0.09 0.04
Matches are distributed among these distances:
29 1 0.01
30 52 0.76
31 15 0.22
ACGTcount: A:0.44, C:0.10, G:0.05, T:0.41
Consensus pattern (30 bp):
AATACAATATTAATTTGACTATTAAACTTT
Found at i:407868 original size:21 final size:20
Alignment explanation
Indices: 407782--407938 Score: 93
Period size: 20 Copynumber: 7.8 Consensus size: 20
407772 AAATGACCAA
**
407782 CAAAATCGCAACGCGA-AAT
1 CAAAATCGCAACGCGATTTT
* ***
407801 AAAAATCGCAACGCGATCCC
1 CAAAATCGCAACGCGATTTT
* ** *
407821 CAGAATCGCAAATC-AGTTTC
1 CAAAATCGCAACGCGA-TTTT
407841 CAAAATCGCAACGCGATTCTT
1 CAAAATCGCAACGCGATT-TT
* * **
407862 GAAAATCGCAATGCGATAGT
1 CAAAATCGCAACGCGATTTT
* **
407882 CAAATTCGCATTGCGATTTT
1 CAAAATCGCAACGCGATTTT
* *
407902 CCAAAATCGCAACGCGAATAT
1 -CAAAATCGCAACGCGATTTT
*
407923 GAAAATCGCAACGCGA
1 CAAAATCGCAACGCGA
407939 ACACATAAAT
Statistics
Matches: 104, Mismatches: 29, Indels: 9
0.73 0.20 0.06
Matches are distributed among these distances:
19 16 0.15
20 56 0.54
21 32 0.31
ACGTcount: A:0.38, C:0.25, G:0.17, T:0.19
Consensus pattern (20 bp):
CAAAATCGCAACGCGATTTT
Found at i:407891 original size:41 final size:41
Alignment explanation
Indices: 407782--407938 Score: 126
Period size: 41 Copynumber: 3.9 Consensus size: 41
407772 AAATGACCAA
* **
407782 CAAAATCGCAACGCGAA-ATAAAAATCGCAACGCGA-TCCC
1 CAAAATCGCAACGCGAATATCAAAATCGCAACGCGATTTTC
* ** * *
407821 CAGAATCGCAAATC-AGTTTCCAAAATCGCAACGCGATTCTT-
1 CAAAATCGCAACGCGAATAT-CAAAATCGCAACGCGATT-TTC
* * * **
407862 GAAAATCGCAATGCG-ATAGTCAAATTCGCATTGCGATTTTC
1 CAAAATCGCAACGCGAATA-TCAAAATCGCAACGCGATTTTC
*
407903 CAAAATCGCAACGCGAATATGAAAATCGCAACGCGA
1 CAAAATCGCAACGCGAATATCAAAATCGCAACGCGA
407939 ACACATAAAT
Statistics
Matches: 87, Mismatches: 23, Indels: 14
0.70 0.19 0.11
Matches are distributed among these distances:
38 1 0.01
39 12 0.14
40 17 0.20
41 53 0.61
42 4 0.05
ACGTcount: A:0.38, C:0.25, G:0.17, T:0.19
Consensus pattern (41 bp):
CAAAATCGCAACGCGAATATCAAAATCGCAACGCGATTTTC
Found at i:407948 original size:20 final size:20
Alignment explanation
Indices: 407925--408098 Score: 118
Period size: 20 Copynumber: 8.7 Consensus size: 20
407915 GCGAATATGA
407925 AAATCGCAACGCG-AACACAT
1 AAATCGCAACGCGTAAC-CAT
* * *
407945 AAATCGCAATGCGTATCCGT
1 AAATCGCAACGCGTAACCAT
* * *
407965 AAATCGCAACGTGTATCCGT
1 AAATCGCAACGCGTAACCAT
****
407985 AAATCGCAACGCGTATGGGT
1 AAATCGCAACGCGTAACCAT
* * *
408005 AAATCGCAATGCGTATCCGT
1 AAATCGCAACGCGTAACCAT
* * **
408025 ATATCGCAACGCGTATCGGT
1 AAATCGCAACGCGTAACCAT
* *
408045 AAATCGCAACG-ATAATACAT
1 AAATCGCAACGCGTAA-CCAT
* *
408065 AAAATCGCAACGCGTATCCGT
1 -AAATCGCAACGCGTAACCAT
408086 AAATCGCAACGCG
1 AAATCGCAACGCG
408099 ATATTTAAAG
Statistics
Matches: 126, Mismatches: 24, Indels: 8
0.80 0.15 0.05
Matches are distributed among these distances:
19 2 0.02
20 107 0.85
21 15 0.12
22 2 0.02
ACGTcount: A:0.34, C:0.25, G:0.20, T:0.20
Consensus pattern (20 bp):
AAATCGCAACGCGTAACCAT
Found at i:407969 original size:40 final size:39
Alignment explanation
Indices: 407905--408099 Score: 183
Period size: 40 Copynumber: 4.9 Consensus size: 39
407895 CGATTTTCCA
* ** *
407905 AAATCGCAACGCGAATATGAAAATCGCAACGCGAACACAT
1 AAATCGCAACGCGTATCCGTAAATCGCAACGCGAAC-CAT
* * * *
407945 AAATCGCAATGCGTATCCGTAAATCGCAACGTGTATCCGT
1 AAATCGCAACGCGTATCCGTAAATCGCAACGCG-AACCAT
** * * *
407985 AAATCGCAACGCGTATGGGTAAATCGCAATGCGTATCCGT
1 AAATCGCAACGCGTATCCGTAAATCGCAACGCG-AACCAT
* * ** *
408025 ATATCGCAACGCGTATCGGTAAATCGCAACGATAATACAT
1 AAATCGCAACGCGTATCCGTAAATCGCAACGCGAA-CCAT
408065 AAAATCGCAACGCGTATCCGTAAATCGCAACGCGA
1 -AAATCGCAACGCGTATCCGTAAATCGCAACGCGA
408100 TATTTAAAGC
Statistics
Matches: 127, Mismatches: 25, Indels: 5
0.81 0.16 0.03
Matches are distributed among these distances:
39 1 0.01
40 94 0.74
41 32 0.25
ACGTcount: A:0.36, C:0.25, G:0.20, T:0.19
Consensus pattern (39 bp):
AAATCGCAACGCGTATCCGTAAATCGCAACGCGAACCAT
Found at i:407990 original size:60 final size:60
Alignment explanation
Indices: 407905--408098 Score: 244
Period size: 60 Copynumber: 3.2 Consensus size: 60
407895 CGATTTTCCA
* ** * *
407905 AAATCGCAACGCGAATATGAAAATCGCAACGCGAACACATAAATCGCAATGCGTATCCGT
1 AAATCGCAACGCGTATCCGTAAATCGCAACGCGAATACATAAATCGCAATGCGTATCCGT
* * ***
407965 AAATCGCAACGTGTATCCGTAAATCGCAACGCGTATGGGTAAATCGCAATGCGTATCCGT
1 AAATCGCAACGCGTATCCGTAAATCGCAACGCGAATACATAAATCGCAATGCGTATCCGT
* * ** *
408025 ATATCGCAACGCGTATCGGTAAATCGCAACGATAATACATAAAATCGCAACGCGTATCCGT
1 AAATCGCAACGCGTATCCGTAAATCGCAACGCGAATACAT-AAATCGCAATGCGTATCCGT
408086 AAATCGCAACGCG
1 AAATCGCAACGCG
408099 ATATTTAAAG
Statistics
Matches: 112, Mismatches: 21, Indels: 1
0.84 0.16 0.01
Matches are distributed among these distances:
60 81 0.72
61 31 0.28
ACGTcount: A:0.36, C:0.25, G:0.20, T:0.20
Consensus pattern (60 bp):
AAATCGCAACGCGTATCCGTAAATCGCAACGCGAATACATAAATCGCAATGCGTATCCGT
Found at i:408520 original size:33 final size:33
Alignment explanation
Indices: 408481--408551 Score: 115
Period size: 33 Copynumber: 2.2 Consensus size: 33
408471 TTCACTTAGA
408481 TTTCATTTCGCGTTACGATTCTCTCGTTGCGAT
1 TTTCATTTCGCGTTACGATTCTCTCGTTGCGAT
***
408514 TTTCATTTCGCGTTGTTATTCTCTCGTTGCGAT
1 TTTCATTTCGCGTTACGATTCTCTCGTTGCGAT
408547 TTTCA
1 TTTCA
408552 AGTTAGTATT
Statistics
Matches: 35, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
33 35 1.00
ACGTcount: A:0.11, C:0.23, G:0.17, T:0.49
Consensus pattern (33 bp):
TTTCATTTCGCGTTACGATTCTCTCGTTGCGAT
Found at i:408688 original size:19 final size:20
Alignment explanation
Indices: 408631--408705 Score: 89
Period size: 20 Copynumber: 3.8 Consensus size: 20
408621 TGCAGAAGAG
* *
408631 TCGCAACGAGATAAATGAAAA
1 TCGCAACGAGA-GAATGACAA
**
408652 TCGCAACGAGAGAATGACTG
1 TCGCAACGAGAGAATGACAA
*
408672 TCGCAACGCGA-AATGACAA
1 TCGCAACGAGAGAATGACAA
408691 TCGCAACGAGAGAAT
1 TCGCAACGAGAGAAT
408706 CGCAACGAGA
Statistics
Matches: 45, Mismatches: 8, Indels: 3
0.80 0.14 0.05
Matches are distributed among these distances:
19 16 0.36
20 18 0.40
21 11 0.24
ACGTcount: A:0.43, C:0.20, G:0.24, T:0.13
Consensus pattern (20 bp):
TCGCAACGAGAGAATGACAA
Found at i:408708 original size:14 final size:14
Alignment explanation
Indices: 408689--408759 Score: 88
Period size: 14 Copynumber: 4.7 Consensus size: 14
408679 GCGAAATGAC
408689 AATCGCAACGAGAG
1 AATCGCAACGAGAG
408703 AATCGCAACGAGAG
1 AATCGCAACGAGAG
*
408717 AATCGCAACGCGAAATGAA
1 AATCGCAA--CG--A-GAG
408736 AATCGCAACGAGAG
1 AATCGCAACGAGAG
408750 AATCGCAACG
1 AATCGCAACG
408760 CGAAACCAAA
Statistics
Matches: 50, Mismatches: 2, Indels: 10
0.81 0.03 0.16
Matches are distributed among these distances:
14 34 0.68
15 1 0.02
16 2 0.04
17 2 0.04
18 1 0.02
19 10 0.20
ACGTcount: A:0.44, C:0.23, G:0.25, T:0.08
Consensus pattern (14 bp):
AATCGCAACGAGAG
Found at i:408740 original size:33 final size:33
Alignment explanation
Indices: 408703--408775 Score: 128
Period size: 33 Copynumber: 2.2 Consensus size: 33
408693 GCAACGAGAG
**
408703 AATCGCAACGAGAGAATCGCAACGCGAAATGAA
1 AATCGCAACGAGAGAATCGCAACGCGAAACCAA
408736 AATCGCAACGAGAGAATCGCAACGCGAAACCAA
1 AATCGCAACGAGAGAATCGCAACGCGAAACCAA
408769 AATCGCA
1 AATCGCA
408776 TTGCGATTTT
Statistics
Matches: 38, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
33 38 1.00
ACGTcount: A:0.45, C:0.25, G:0.22, T:0.08
Consensus pattern (33 bp):
AATCGCAACGAGAGAATCGCAACGCGAAACCAA
Found at i:408812 original size:14 final size:14
Alignment explanation
Indices: 408793--408882 Score: 72
Period size: 14 Copynumber: 5.7 Consensus size: 14
408783 TTTTATTTCG
408793 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
*
408807 CGTTGCGATTTTCATTTCG
1 CGTTGCGA--TTC---TCT
408826 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
*
408840 CGTTGCGATTGTCATTTCG
1 CGTTGCGA-T-TC---TCT
408859 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
408873 CGTTGCGATT
1 CGTTGCGATT
408883 TTCATTTCAA
Statistics
Matches: 62, Mismatches: 4, Indels: 20
0.72 0.05 0.23
Matches are distributed among these distances:
14 30 0.48
15 1 0.02
16 5 0.08
17 5 0.08
18 1 0.02
19 20 0.32
ACGTcount: A:0.09, C:0.24, G:0.23, T:0.43
Consensus pattern (14 bp):
CGTTGCGATTCTCT
Found at i:408818 original size:33 final size:33
Alignment explanation
Indices: 408776--408890 Score: 212
Period size: 33 Copynumber: 3.5 Consensus size: 33
408766 CAAAATCGCA
*
408776 TTGCGATTTTTATTTCGCGTTGCGATTCTCTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
408809 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
*
408842 TTGCGATTGTCATTTCGCGTTGCGATTCTCTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
408875 TTGCGATTTTCATTTC
1 TTGCGATTTTCATTTC
408891 AACCAAAAGA
Statistics
Matches: 79, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
33 79 1.00
ACGTcount: A:0.10, C:0.23, G:0.21, T:0.47
Consensus pattern (33 bp):
TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
Found at i:408831 original size:19 final size:19
Alignment explanation
Indices: 408771--408868 Score: 81
Period size: 19 Copynumber: 5.7 Consensus size: 19
408761 GAAACCAAAA
* *
408771 TCGCATTGCGATTTTTATT
1 TCGCGTTGCGATTTTCATT
408790 TCGCGTTGCGA--TTC---
1 TCGCGTTGCGATTTTCATT
*
408804 TCTCGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
408823 TCGCGTTGCGA--TTC---
1 TCGCGTTGCGATTTTCATT
* *
408837 TCTCGTTGCGATTGTCATT
1 TCGCGTTGCGATTTTCATT
408856 TCGCGTTGCGATT
1 TCGCGTTGCGATT
408869 CTCTCGTTGC
Statistics
Matches: 62, Mismatches: 7, Indels: 20
0.70 0.08 0.22
Matches are distributed among these distances:
14 20 0.32
16 5 0.08
17 5 0.08
19 32 0.52
ACGTcount: A:0.10, C:0.22, G:0.22, T:0.45
Consensus pattern (19 bp):
TCGCGTTGCGATTTTCATT
Found at i:410258 original size:12 final size:12
Alignment explanation
Indices: 410241--410265 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
410231 TCTTCGGGGA
410241 CTTTTTCTTCTT
1 CTTTTTCTTCTT
410253 CTTTTTCTTCTT
1 CTTTTTCTTCTT
410265 C
1 C
410266 AGGATTATAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.00, C:0.28, G:0.00, T:0.72
Consensus pattern (12 bp):
CTTTTTCTTCTT
Found at i:410474 original size:24 final size:24
Alignment explanation
Indices: 410440--410486 Score: 69
Period size: 24 Copynumber: 2.0 Consensus size: 24
410430 CTGAAACATC
410440 ATCAAAATCCGTG-TATTGACCAAT
1 ATCAAAATCCG-GATATTGACCAAT
*
410464 ATCAAAGTCCGGATATTGACCAA
1 ATCAAAATCCGGATATTGACCAA
410487 GACCAAATTT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
23 1 0.05
24 20 0.95
ACGTcount: A:0.38, C:0.21, G:0.15, T:0.26
Consensus pattern (24 bp):
ATCAAAATCCGGATATTGACCAAT
Found at i:411197 original size:20 final size:20
Alignment explanation
Indices: 411169--411378 Score: 206
Period size: 20 Copynumber: 10.5 Consensus size: 20
411159 AAATTTCAGT
* ** *
411169 GTTGTGATTTACATATTCTC
1 GTTGCGATTTACGGATTCGC
**
411189 GTTGCGATTTACGGATTATC
1 GTTGCGATTTACGGATTCGC
* *
411209 GTTGCGATTTACAGATTCTC
1 GTTGCGATTTACGGATTCGC
**
411229 GTTGCGATTTACGGATTATC
1 GTTGCGATTTACGGATTCGC
*
411249 GTTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATTCGC
* **
411269 GTTGCGATATACGGAAACGC
1 GTTGCGATTTACGGATTCGC
* *
411289 GTTGCGATTTACGGATACAC
1 GTTGCGATTTACGGATTCGC
*
411309 GTTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATTCGC
* *
411329 ATTGCGATTTATGTG-TTCGC
1 GTTGCGATTTACG-GATTCGC
* **
411349 GTTGCGATTTTCATATTCGC
1 GTTGCGATTTACGGATTCGC
411369 GTTGCGATTT
1 GTTGCGATTT
411379 TGGAAAATCG
Statistics
Matches: 163, Mismatches: 25, Indels: 4
0.85 0.13 0.02
Matches are distributed among these distances:
20 162 0.99
21 1 0.01
ACGTcount: A:0.20, C:0.18, G:0.25, T:0.38
Consensus pattern (20 bp):
GTTGCGATTTACGGATTCGC
Found at i:411415 original size:20 final size:19
Alignment explanation
Indices: 411345--411480 Score: 85
Period size: 20 Copynumber: 6.8 Consensus size: 19
411335 ATTTATGTGT
*
411345 TCGCGTTGCGATTTTCATA
1 TCGCGTTGCGATTTTGATA
*
411364 TTCGCGTTGCGATTTTGGAAAA
1 -TCGCGTTGCGATTTT-G-ATA
** *
411386 TCGCAATGCGAATTTGACTA
1 TCGCGTTGCGATTTTGA-TA
*
411406 TCGCGTTGCGATTTTGGACA
1 TCGCGTTGCGATTTT-GATA
** * **
411426 -CTGATTTGCGATTCTGGGGA
1 TC-GCGTTGCGATT-TTGATA
* *
411446 TCGCGTTGCGATTTTTATT
1 TCGCGTTGCGATTTTGATA
411465 TCGCGTTGCGATTTTG
1 TCGCGTTGCGATTTTG
411481 TTGGTCATTT
Statistics
Matches: 86, Mismatches: 23, Indels: 15
0.69 0.19 0.12
Matches are distributed among these distances:
19 18 0.21
20 50 0.58
21 16 0.19
22 2 0.02
ACGTcount: A:0.17, C:0.18, G:0.26, T:0.39
Consensus pattern (19 bp):
TCGCGTTGCGATTTTGATA
Found at i:415260 original size:23 final size:23
Alignment explanation
Indices: 415234--415282 Score: 73
Period size: 23 Copynumber: 2.1 Consensus size: 23
415224 AATGACCAAG
*
415234 AAAG-CAAATGAAAAATATGTCAC
1 AAAGACAAA-GAAAAACATGTCAC
415257 AAAGACAAAGAAAAACATGTCAC
1 AAAGACAAAGAAAAACATGTCAC
415280 AAA
1 AAA
415283 TGTAGAATTA
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
23 20 0.83
24 4 0.17
ACGTcount: A:0.61, C:0.14, G:0.12, T:0.12
Consensus pattern (23 bp):
AAAGACAAAGAAAAACATGTCAC
Found at i:420294 original size:6 final size:6
Alignment explanation
Indices: 420283--420307 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
420273 ATAGTATAAA
420283 ACTTTT ACTTTT ACTTTT ACTTTT A
1 ACTTTT ACTTTT ACTTTT ACTTTT A
420308 GGATCGTTGG
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.20, C:0.16, G:0.00, T:0.64
Consensus pattern (6 bp):
ACTTTT
Found at i:422524 original size:16 final size:16
Alignment explanation
Indices: 422505--422538 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
422495 CAATATACGA
422505 ATAAAAATATATTTAT
1 ATAAAAATATATTTAT
**
422521 ATAAATGTATATTTAT
1 ATAAAAATATATTTAT
422537 AT
1 AT
422539 TTAGATGTAT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.50, C:0.00, G:0.03, T:0.47
Consensus pattern (16 bp):
ATAAAAATATATTTAT
Found at i:422611 original size:16 final size:18
Alignment explanation
Indices: 422579--422612 Score: 54
Period size: 16 Copynumber: 2.0 Consensus size: 18
422569 TATTAATGTA
422579 TGAATCATTTATATTTTT
1 TGAATCATTTATATTTTT
422597 TGAAT-ATTT-TATTTTT
1 TGAATCATTTATATTTTT
422613 AATAAGAAAT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 7 0.44
17 4 0.25
18 5 0.31
ACGTcount: A:0.26, C:0.03, G:0.06, T:0.65
Consensus pattern (18 bp):
TGAATCATTTATATTTTT
Found at i:423285 original size:130 final size:130
Alignment explanation
Indices: 423081--423328 Score: 415
Period size: 130 Copynumber: 1.9 Consensus size: 130
423071 AATTTTCTTC
* **
423081 TAATTAGGTGGTGACATGTGTCACCAATAACATATATCATGATCATGTGTTAACACATGTCAGAT
1 TAATTAGGTGGTGACATGTGTCACCAATAACACATATCATGATCATGTACTAACACATGTCAGAT
** *
423146 CCTGGTTAAATGATTAATTTATTAAATTTTATTTAATTTAGGACCAAATTGATAGCACATATAAA
66 CCTAATTAAATGATTAATTTATTAAATTCTATTTAATTTAGGACCAAATTGATAGCACATATAAA
* * *
423211 TAATTAGGTGGTGACATGTGTCACCAATGACACGTGTCATGATCATGTACTAACACATGTCAGAT
1 TAATTAGGTGGTGACATGTGTCACCAATAACACATATCATGATCATGTACTAACACATGTCAGAT
423276 CCTAATTAAATGATTAATTTATTAAATTCTATTTAATTTAGGACCAAATTGAT
66 CCTAATTAAATGATTAATTTATTAAATTCTATTTAATTTAGGACCAAATTGAT
423329 TATATAAATA
Statistics
Matches: 109, Mismatches: 9, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
130 109 1.00
ACGTcount: A:0.36, C:0.13, G:0.15, T:0.36
Consensus pattern (130 bp):
TAATTAGGTGGTGACATGTGTCACCAATAACACATATCATGATCATGTACTAACACATGTCAGAT
CCTAATTAAATGATTAATTTATTAAATTCTATTTAATTTAGGACCAAATTGATAGCACATATAAA
Found at i:423775 original size:35 final size:35
Alignment explanation
Indices: 423725--423800 Score: 125
Period size: 35 Copynumber: 2.2 Consensus size: 35
423715 AATTGAATTT
* *
423725 AATTGAATTATTTTGGAATTTAGGGTTTAGAATGA
1 AATTGAATTACTTTGGAAATTAGGGTTTAGAATGA
*
423760 AATTGAATTACTTTGGAAATTGGGGTTTAGAATGA
1 AATTGAATTACTTTGGAAATTAGGGTTTAGAATGA
423795 AATTGA
1 AATTGA
423801 GGATTTTTTG
Statistics
Matches: 38, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
35 38 1.00
ACGTcount: A:0.36, C:0.01, G:0.24, T:0.39
Consensus pattern (35 bp):
AATTGAATTACTTTGGAAATTAGGGTTTAGAATGA
Found at i:427714 original size:23 final size:23
Alignment explanation
Indices: 427687--427730 Score: 63
Period size: 23 Copynumber: 1.9 Consensus size: 23
427677 ATATAATATT
*
427687 ATATTTAA-AAATAATTTATAAAA
1 ATATTCAACAAATAA-TTATAAAA
427710 ATATTCAACAAATAATTATAA
1 ATATTCAACAAATAATTATAA
427731 TTTTTAATAT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
23 13 0.68
24 6 0.32
ACGTcount: A:0.59, C:0.05, G:0.00, T:0.36
Consensus pattern (23 bp):
ATATTCAACAAATAATTATAAAA
Found at i:428029 original size:25 final size:25
Alignment explanation
Indices: 428001--428049 Score: 64
Period size: 25 Copynumber: 2.0 Consensus size: 25
427991 GATGTAATGA
*
428001 TTATGTAATGATTT-TTTTTTTATTT
1 TTAT-TAAAGATTTATTTTTTTATTT
*
428026 TTATTAAAGTTTTATTTTTTTATT
1 TTATTAAAGATTTATTTTTTTATT
428050 ATTAAGTTTT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
24 7 0.33
25 14 0.67
ACGTcount: A:0.22, C:0.00, G:0.06, T:0.71
Consensus pattern (25 bp):
TTATTAAAGATTTATTTTTTTATTT
Found at i:428038 original size:19 final size:19
Alignment explanation
Indices: 428016--428062 Score: 60
Period size: 19 Copynumber: 2.4 Consensus size: 19
428006 TAATGATTTT
428016 TTTTTTATTTTTATTA-AAG
1 TTTTTT-TTTTTATTATAAG
428035 TTTTATTTTTTTATTATTAAG
1 TTTT-TTTTTTTATTA-TAAG
428056 TTTTTTT
1 TTTTTTT
428063 ATTAAAGTAT
Statistics
Matches: 25, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
19 13 0.52
20 5 0.20
21 7 0.28
ACGTcount: A:0.21, C:0.00, G:0.04, T:0.74
Consensus pattern (19 bp):
TTTTTTTTTTTATTATAAG
Found at i:428043 original size:22 final size:21
Alignment explanation
Indices: 428012--428059 Score: 60
Period size: 23 Copynumber: 2.2 Consensus size: 21
428002 TATGTAATGA
* *
428012 TTTTTTTTTTATTTTTATTAAAG
1 TTTTATTTTT-TTATTATT-AAG
428035 TTTTATTTTTTTATTATTAAG
1 TTTTATTTTTTTATTATTAAG
428056 TTTT
1 TTTT
428060 TTTATTAAAG
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
21 7 0.30
22 7 0.30
23 9 0.39
ACGTcount: A:0.21, C:0.00, G:0.04, T:0.75
Consensus pattern (21 bp):
TTTTATTTTTTTATTATTAAG
Found at i:428060 original size:22 final size:23
Alignment explanation
Indices: 428012--428062 Score: 70
Period size: 21 Copynumber: 2.3 Consensus size: 23
428002 TATGTAATGA
*
428012 TTTTTTTTTTATTTTTATTAAAG
1 TTTTTTTTTTATTATTATTAAAG
*
428035 TTTTATTTTT-TTATTATT-AAG
1 TTTTTTTTTTATTATTATTAAAG
428056 TTTTTTT
1 TTTTTTT
428063 ATTAAAGTAT
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
21 9 0.36
22 7 0.28
23 9 0.36
ACGTcount: A:0.20, C:0.00, G:0.04, T:0.76
Consensus pattern (23 bp):
TTTTTTTTTTATTATTATTAAAG
Found at i:429308 original size:11 final size:11
Alignment explanation
Indices: 429294--429345 Score: 54
Period size: 11 Copynumber: 4.9 Consensus size: 11
429284 AGTCATTAAA
429294 ATTATCAAATT
1 ATTATCAAATT
* *
429305 ATTATAAAATG
1 ATTATCAAATT
*
429316 ATTATTAAATT
1 ATTATCAAATT
*
429327 -TTATCGAATT
1 ATTATCAAATT
429337 ATTA-CAAAT
1 ATTATCAAAT
429346 GCTCATGATA
Statistics
Matches: 33, Mismatches: 7, Indels: 3
0.77 0.16 0.07
Matches are distributed among these distances:
10 12 0.36
11 21 0.64
ACGTcount: A:0.46, C:0.06, G:0.04, T:0.44
Consensus pattern (11 bp):
ATTATCAAATT
Found at i:441382 original size:18 final size:18
Alignment explanation
Indices: 441330--441382 Score: 58
Period size: 18 Copynumber: 2.9 Consensus size: 18
441320 CTTCTTATTT
441330 TTATTTTAAT-TACTTTTA
1 TTATTTTAATAT-CTTTTA
441348 TT-TATTTAATCAT-TTTTA
1 TTAT-TTTAAT-ATCTTTTA
441366 TTATTTTAATATCTTTT
1 TTATTTTAATATCTTTT
441383 TACCAAAATT
Statistics
Matches: 30, Mismatches: 0, Indels: 10
0.75 0.00 0.25
Matches are distributed among these distances:
17 3 0.10
18 25 0.83
19 1 0.03
20 1 0.03
ACGTcount: A:0.26, C:0.06, G:0.00, T:0.68
Consensus pattern (18 bp):
TTATTTTAATATCTTTTA
Found at i:442363 original size:60 final size:60
Alignment explanation
Indices: 442296--442422 Score: 166
Period size: 60 Copynumber: 2.1 Consensus size: 60
442286 AATGGTCCCT
* * * *
442296 TGACTATATGGTAATATTTTATTAAATCCCTCAACTATTAAAAGTTACA-ACATGATCCTC
1 TGACTATAGGGTAACACTTTATTAAATCCCTCAACTATTAAAAGTTACATA-ATGATCATC
* * * *
442356 TGACTATAGGGTACCACTTTGTTGAGTCCCTCAACTATTAAAAGTTACATAATGATCATC
1 TGACTATAGGGTAACACTTTATTAAATCCCTCAACTATTAAAAGTTACATAATGATCATC
442416 TGACTAT
1 TGACTAT
442423 TCTTATGTTT
Statistics
Matches: 58, Mismatches: 8, Indels: 2
0.85 0.12 0.03
Matches are distributed among these distances:
60 57 0.98
61 1 0.02
ACGTcount: A:0.34, C:0.19, G:0.12, T:0.35
Consensus pattern (60 bp):
TGACTATAGGGTAACACTTTATTAAATCCCTCAACTATTAAAAGTTACATAATGATCATC
Found at i:443677 original size:23 final size:24
Alignment explanation
Indices: 443638--443692 Score: 69
Period size: 23 Copynumber: 2.4 Consensus size: 24
443628 TTTCGTTTAG
443638 TACAATT-AATTATAAGTAGCAAT
1 TACAATTAAATTATAAGTAGCAAT
* * *
443661 TATAATTAAATTA-AAGTTGTAAT
1 TACAATTAAATTATAAGTAGCAAT
443684 TACAATTAA
1 TACAATTAA
443693 TACACTCAAA
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
23 22 0.81
24 5 0.19
ACGTcount: A:0.49, C:0.05, G:0.07, T:0.38
Consensus pattern (24 bp):
TACAATTAAATTATAAGTAGCAAT
Found at i:445006 original size:14 final size:14
Alignment explanation
Indices: 444973--445006 Score: 50
Period size: 14 Copynumber: 2.4 Consensus size: 14
444963 ATATTAAATT
*
444973 TAAAAAATGTTATA
1 TAAAAAATGTTAAA
444987 TAAAAAATGTTAAAA
1 TAAAAAATGTT-AAA
445002 TAAAA
1 TAAAA
445007 TAAATGAAGA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
14 11 0.61
15 7 0.39
ACGTcount: A:0.65, C:0.00, G:0.06, T:0.29
Consensus pattern (14 bp):
TAAAAAATGTTAAA
Found at i:445122 original size:23 final size:23
Alignment explanation
Indices: 445070--445114 Score: 74
Period size: 23 Copynumber: 2.0 Consensus size: 23
445060 AATATTAAAA
445070 GAGAAAATAAAAGTAAAATAAGT
1 GAGAAAATAAAAGTAAAATAAGT
445093 GAGAAAAT-AAAGATAAAATAAG
1 GAGAAAATAAAAG-TAAAATAAG
445115 ATTAAAAAAA
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
22 4 0.19
23 17 0.81
ACGTcount: A:0.67, C:0.00, G:0.18, T:0.16
Consensus pattern (23 bp):
GAGAAAATAAAAGTAAAATAAGT
Found at i:448237 original size:21 final size:22
Alignment explanation
Indices: 448211--448254 Score: 72
Period size: 21 Copynumber: 2.0 Consensus size: 22
448201 ATTCCCACCC
448211 AATCTTCTTGCTGAAGC-ACTA
1 AATCTTCTTGCTGAAGCTACTA
*
448232 AATCTTCTTGCTGAGGCTACTA
1 AATCTTCTTGCTGAAGCTACTA
448254 A
1 A
448255 CACTCCAAAA
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
21 16 0.76
22 5 0.24
ACGTcount: A:0.27, C:0.23, G:0.16, T:0.34
Consensus pattern (22 bp):
AATCTTCTTGCTGAAGCTACTA
Found at i:456205 original size:20 final size:20
Alignment explanation
Indices: 456158--456511 Score: 300
Period size: 20 Copynumber: 17.2 Consensus size: 20
456148 AATGACCAAC
* *
456158 AAAATCGCAACGCGATAT-C
1 AAAATCGCAACGCGATTTAG
*
456177 AAAACCGCAACGCGATTTAG
1 AAAATCGCAACGCGATTTAG
* * **
456197 AAAAGCGCAACGTTGA-AAAG
1 AAAATCGCAACG-CGATTTAG
* * **
456217 AAGATCGCAACACGATCTTCC
1 AAAATCGCAACGCGAT-TTAG
* * *
456238 AAGAATCGCAATGCGATTCAT
1 AA-AATCGCAACGCGATTTAG
**
456259 AAAATCGCAACGCGATCTTCC
1 AAAATCGCAACGCGAT-TTAG
*
456280 AAGAATCGCAACGCGATTCAG
1 AA-AATCGCAACGCGATTTAG
*
456301 AAAATCGCAACGCGATTCAG
1 AAAATCGCAACGCGATTTAG
*
456321 AAAATCGCAACGCGATTCAG
1 AAAATCGCAACGCGATTTAG
**
456341 AAAATCGCAACGCGATCTTCC
1 AAAATCGCAACGCGAT-TTAG
*
456362 AAGAATCGCAACGCGATTAAG
1 AA-AATCGCAACGCGATTTAG
*
456383 AAAATCGCAACGCGATTCCA-
1 AAAATCGCAACGCGATT-TAG
* **
456403 AGAATCGCAACGCGATCTTCC
1 AAAATCGCAACGCGAT-TTAG
*
456424 AAGAATCGCAACGCGATTAAG
1 AA-AATCGCAACGCGATTTAG
*
456445 AAAATCGCAACGCGATTCAG
1 AAAATCGCAACGCGATTTAG
**
456465 AAAATCGCAACGCGATCTTCC
1 AAAATCGCAACGCGAT-TTAG
*
456486 AAGAATCGCAACGCGATTAAG
1 AA-AATCGCAACGCGATTTAG
456507 AAAAT
1 AAAAT
456512 GAGTAAATTC
Statistics
Matches: 271, Mismatches: 49, Indels: 29
0.78 0.14 0.08
Matches are distributed among these distances:
19 18 0.07
20 155 0.57
21 31 0.11
22 67 0.25
ACGTcount: A:0.39, C:0.25, G:0.19, T:0.16
Consensus pattern (20 bp):
AAAATCGCAACGCGATTTAG
Found at i:456268 original size:62 final size:61
Alignment explanation
Indices: 456158--456511 Score: 405
Period size: 62 Copynumber: 5.8 Consensus size: 61
456148 AATGACCAAC
* * * * * *
456158 AAAATCGCAACGCGAT-AT-CAA-AACCGCAACGCGATTTAGAAAAGCGCAACGTTGAAAAG
1 AAAATCGCAACGCGATCTTCCAAGAATCGCAACGCGATTAAGAAAATCGCAACG-CGATAAG
* * * * * ***
456217 AAGATCGCAACACGATCTTCCAAGAATCGCAATGCGATTCATAAAATCGCAACGCGATCTTCC
1 AAAATCGCAACGCGATCTTCCAAGAATCGCAACGCGATTAAGAAAATCGCAACGCGA--TAAG
* * *
456280 AAGAATCGCAACGCGA--TT-CAGAAAATCGCAACGCGATTCAGAAAATCGCAACGCGATTCAG
1 AA-AATCGCAACGCGATCTTCCA-AGAATCGCAACGCGATTAAGAAAATCGCAACGCGA-TAAG
***
456341 AAAATCGCAACGCGATCTTCCAAGAATCGCAACGCGATTAAGAAAATCGCAACGCGATTCC
1 AAAATCGCAACGCGATCTTCCAAGAATCGCAACGCGATTAAGAAAATCGCAACGCGATAAG
*
456402 AAGAATCGCAACGCGATCTTCCAAGAATCGCAACGCGATTAAGAAAATCGCAACGCGATTCAG
1 AA-AATCGCAACGCGATCTTCCAAGAATCGCAACGCGATTAAGAAAATCGCAACGCGA-TAAG
456465 AAAATCGCAACGCGATCTTCCAAGAATCGCAACGCGATTAAGAAAAT
1 AAAATCGCAACGCGATCTTCCAAGAATCGCAACGCGATTAAGAAAAT
456512 GAGTAAATTC
Statistics
Matches: 253, Mismatches: 30, Indels: 21
0.83 0.10 0.07
Matches are distributed among these distances:
59 14 0.06
60 14 0.06
61 13 0.05
62 194 0.77
63 7 0.03
64 11 0.04
ACGTcount: A:0.39, C:0.25, G:0.19, T:0.16
Consensus pattern (61 bp):
AAAATCGCAACGCGATCTTCCAAGAATCGCAACGCGATTAAGAAAATCGCAACGCGATAAG
Found at i:456327 original size:82 final size:81
Alignment explanation
Indices: 456158--456503 Score: 373
Period size: 82 Copynumber: 4.2 Consensus size: 81
456148 AATGACCAAC
* ** * * **
456158 AAAATCGCAACGCGATATC-AAAACCGCAACGCGAT-TTAGAA-AAGCGCAACGTTGA-AAAGAA
1 AAAATCGCAACGCGAT-TCAAAAATCGCAACGCGATCTTCCAAGAATCGCAACG-CGATTCAGAA
* *
456219 GATCGCAACACGATCTTCCA
64 AATCGCAACGCGA--TTCCA
* *
456239 AGAATCGCAATGCGATTCATAAAATCGCAACGCGATCTTCCAAGAATCGCAACGCGATTCAGAAA
1 AAAATCGCAACGCGATTCA-AAAATCGCAACGCGATCTTCCAAGAATCGCAACGCGATTCAGAAA
456304 ATCGCAACGCGATT-CA
65 ATCGCAACGCGATTCCA
*
456320 GAAAATCGCAACGCGATTCAGAAAATCGCAACGCGATCTTCCAAGAATCGCAACGCGATTAAGAA
1 -AAAATCGCAACGCGATTCA-AAAATCGCAACGCGATCTTCCAAGAATCGCAACGCGATTCAGAA
456385 AATCGCAACGCGATTCCA
64 AATCGCAACGCGATTCCA
* * ***
456403 AGAATCGCAACGCGATCTTCCAAGAATCGCAACGCGAT-TAAGAA-AATCGCAACGCGATTCAGA
1 AAAATCGCAACGCGA--TT-CAAAAATCGCAACGCGATCTTCCAAGAATCGCAACGCGATTCAGA
456466 AAATCGCAACGCGATCTTCCA
63 AAATCGCAACGCGA--TTCCA
*
456487 AGAATCGCAACGCGATT
1 AAAATCGCAACGCGATT
456504 AAGAAAATGA
Statistics
Matches: 232, Mismatches: 21, Indels: 23
0.84 0.08 0.08
Matches are distributed among these distances:
80 2 0.01
81 16 0.07
82 140 0.60
83 11 0.05
84 61 0.26
85 2 0.01
ACGTcount: A:0.38, C:0.26, G:0.19, T:0.16
Consensus pattern (81 bp):
AAAATCGCAACGCGATTCAAAAATCGCAACGCGATCTTCCAAGAATCGCAACGCGATTCAGAAAA
TCGCAACGCGATTCCA
Found at i:456431 original size:124 final size:122
Alignment explanation
Indices: 456160--456511 Score: 503
Period size: 124 Copynumber: 2.9 Consensus size: 122
456150 TGACCAACAA
* * * * * ** *
456160 AATCGCAACGCGATATCAAAACCGCAACGCGATTTAGAAAAGCGCAACGTTGA-AAAGAAGATCG
1 AATCGCAACGCGATTTCAAAATCGCAACGCGATTAAGAAAATCGCAACG-CGATTCAGAAAATCG
* * * *
456224 CAACACGATCTTCCAAGAATCGCAATGCGATTCATAAAATCGCAACGCGATCTTCCAAG
65 CAACGCGATCTTCCAAGAATCGCAACGCGATTAAGAAAATCGCAACGCGA-CTTCCAAG
*
456283 AATCGCAACGCGA-TTCAGAAAATCGCAACGCGATTCAGAAAATCGCAACGCGATTCAGAAAATC
1 AATCGCAACGCGATTTC--AAAATCGCAACGCGATTAAGAAAATCGCAACGCGATTCAGAAAATC
456347 GCAACGCGATCTTCCAAGAATCGCAACGCGATTAAGAAAATCGCAACGCGA-TTCCAAG
64 GCAACGCGATCTTCCAAGAATCGCAACGCGATTAAGAAAATCGCAACGCGACTTCCAAG
456405 AATCGCAACGCGATCTTCCAAGAATCGCAACGCGATTAAGAAAATCGCAACGCGATTCAGAAAAT
1 AATCGCAACGCGAT-TT-CAA-AATCGCAACGCGATTAAGAAAATCGCAACGCGATTCAGAAAAT
456470 CGCAACGCGATCTTCCAAGAATCGCAACGCGATTAAGAAAAT
63 CGCAACGCGATCTTCCAAGAATCGCAACGCGATTAAGAAAAT
456512 GAGTAAATTC
Statistics
Matches: 209, Mismatches: 13, Indels: 13
0.89 0.06 0.06
Matches are distributed among these distances:
122 22 0.11
123 17 0.08
124 169 0.81
125 1 0.00
ACGTcount: A:0.39, C:0.26, G:0.19, T:0.16
Consensus pattern (122 bp):
AATCGCAACGCGATTTCAAAATCGCAACGCGATTAAGAAAATCGCAACGCGATTCAGAAAATCGC
AACGCGATCTTCCAAGAATCGCAACGCGATTAAGAAAATCGCAACGCGACTTCCAAG
Found at i:456509 original size:42 final size:42
Alignment explanation
Indices: 456215--456511 Score: 403
Period size: 42 Copynumber: 7.2 Consensus size: 42
456205 AACGTTGAAA
* * *
456215 AGAAGATCGCAACACGATCTTCCAAGAATCGCAATGCGATTC
1 AGAAAATCGCAACGCGATCTTCCAAGAATCGCAACGCGATTC
*
456257 ATAAAATCGCAACGCGATCTTCCAAGAATCGCAACGCGATTC
1 AGAAAATCGCAACGCGATCTTCCAAGAATCGCAACGCGATTC
*
456299 AGAAAATCGCAACGCGA--TT-CAGAAAATCGCAACGCGATTC
1 AGAAAATCGCAACGCGATCTTCCA-AGAATCGCAACGCGATTC
*
456339 AGAAAATCGCAACGCGATCTTCCAAGAATCGCAACGCGATTA
1 AGAAAATCGCAACGCGATCTTCCAAGAATCGCAACGCGATTC
456381 AGAAAATCGCAACGCGA--TTCCAAGAATCGCAACGCGATCTTCC
1 AGAAAATCGCAACGCGATCTTCCAAGAATCGCAACGCGA--TT-C
* ***
456424 A-AGAATCGCAACGCGAT-TAAGAA-AATCGCAACGCGATTC
1 AGAAAATCGCAACGCGATCTTCCAAGAATCGCAACGCGATTC
*
456463 AGAAAATCGCAACGCGATCTTCCAAGAATCGCAACGCGATTA
1 AGAAAATCGCAACGCGATCTTCCAAGAATCGCAACGCGATTC
456505 AGAAAAT
1 AGAAAAT
456512 GAGTAAATTC
Statistics
Matches: 226, Mismatches: 18, Indels: 22
0.85 0.07 0.08
Matches are distributed among these distances:
39 4 0.02
40 73 0.32
41 3 0.01
42 140 0.62
43 6 0.03
ACGTcount: A:0.38, C:0.26, G:0.19, T:0.17
Consensus pattern (42 bp):
AGAAAATCGCAACGCGATCTTCCAAGAATCGCAACGCGATTC
Found at i:456617 original size:6 final size:6
Alignment explanation
Indices: 456606--456663 Score: 100
Period size: 6 Copynumber: 9.7 Consensus size: 6
456596 AGACACGTAT
456606 GACCAC GACCAC GACCAC GACCAC GACCAC GACCAC GAACCAC GACCAC
1 GACCAC GACCAC GACCAC GACCAC GACCAC GACCAC G-ACCAC GACCAC
456655 GACC-C GACC
1 GACCAC GACC
456664 CGAGACGAGA
Statistics
Matches: 51, Mismatches: 0, Indels: 3
0.94 0.00 0.06
Matches are distributed among these distances:
5 5 0.10
6 40 0.78
7 6 0.12
ACGTcount: A:0.33, C:0.50, G:0.17, T:0.00
Consensus pattern (6 bp):
GACCAC
Found at i:457181 original size:6 final size:6
Alignment explanation
Indices: 457160--457250 Score: 168
Period size: 6 Copynumber: 15.5 Consensus size: 6
457150 TCTCGTCTCG
457160 GGTCG- GGTCG- GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT
1 GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT
457206 GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGT
1 GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGT
457251 AATACGTGTC
Statistics
Matches: 85, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
5 10 0.12
6 75 0.88
ACGTcount: A:0.00, C:0.16, G:0.52, T:0.32
Consensus pattern (6 bp):
GGTCGT
Found at i:457933 original size:20 final size:20
Alignment explanation
Indices: 457896--457933 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
457886 AATATATTAA
*
457896 AAATTTTAAAATTTTTAATT
1 AAATTTTAAAATTGTTAATT
457916 AAATTATTAAAA-TGTTAA
1 AAATT-TTAAAATTGTTAA
457934 CCTTTATATT
Statistics
Matches: 16, Mismatches: 1, Indels: 2
0.84 0.05 0.11
Matches are distributed among these distances:
20 10 0.62
21 6 0.38
ACGTcount: A:0.50, C:0.00, G:0.03, T:0.47
Consensus pattern (20 bp):
AAATTTTAAAATTGTTAATT
Found at i:461189 original size:16 final size:16
Alignment explanation
Indices: 461168--461198 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
461158 AAAAGCGTTG
461168 TAATTTTAAATAAAAT
1 TAATTTTAAATAAAAT
*
461184 TAATTTTAATTAAAA
1 TAATTTTAAATAAAA
461199 CAACAATTTG
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (16 bp):
TAATTTTAAATAAAAT
Found at i:465866 original size:31 final size:31
Alignment explanation
Indices: 465828--465921 Score: 154
Period size: 31 Copynumber: 3.0 Consensus size: 31
465818 AAGGGTCGAG
*
465828 GTTTACCTATGTTCTTCGGGACATATGGACT
1 GTTTACCTATGTTCTTCGGAACATATGGACT
465859 GTTTACCTATGTTCTTCGGAACATATGGACT
1 GTTTACCTATGTTCTTCGGAACATATGGACT
*
465890 GTTTACCTAGGTTCTTCGGAATC-TATGGACT
1 GTTTACCTATGTTCTTCGGAA-CATATGGACT
465921 G
1 G
465922 GTCCTTCGGG
Statistics
Matches: 60, Mismatches: 2, Indels: 2
0.94 0.03 0.03
Matches are distributed among these distances:
31 59 0.98
32 1 0.02
ACGTcount: A:0.20, C:0.19, G:0.22, T:0.38
Consensus pattern (31 bp):
GTTTACCTATGTTCTTCGGAACATATGGACT
Found at i:470162 original size:31 final size:31
Alignment explanation
Indices: 470124--470217 Score: 154
Period size: 31 Copynumber: 3.0 Consensus size: 31
470114 AAGGGTCGAG
*
470124 GTTTACCTATGTTCTTCGGGACATATGGACT
1 GTTTACCTATGTTCTTCGGAACATATGGACT
470155 GTTTACCTATGTTCTTCGGAACATATGGACT
1 GTTTACCTATGTTCTTCGGAACATATGGACT
*
470186 GTTTACCTAGGTTCTTCGGAATC-TATGGACT
1 GTTTACCTATGTTCTTCGGAA-CATATGGACT
470217 G
1 G
470218 GTCCTTCGGG
Statistics
Matches: 60, Mismatches: 2, Indels: 2
0.94 0.03 0.03
Matches are distributed among these distances:
31 59 0.98
32 1 0.02
ACGTcount: A:0.20, C:0.19, G:0.22, T:0.38
Consensus pattern (31 bp):
GTTTACCTATGTTCTTCGGAACATATGGACT
Found at i:471799 original size:87 final size:87
Alignment explanation
Indices: 471708--471869 Score: 209
Period size: 87 Copynumber: 1.9 Consensus size: 87
471698 TGTGAAAGGA
* * * **
471708 TGAGTTTTACACTATTAATGAA-TTCATAGCCTAGGATTTGGGTTGTCCTAGTGAGACGGACTTG
1 TGAGTTTTACACTATTAAT-AAGTTCATAGCCCAAGATTTGGGTGGTCCTAGTGAGACAAACTTG
471772 ATAAATTCACTTACTTTATATGT
65 ATAAATTCACTTACTTTATATGT
** * * *
471795 TGAGTTTTATGCTCTTAATAAGTTCATAGCCCAATATTTGGGTGGTCCTTGTGAGACAAACTTGA
1 TGAGTTTTACACTATTAATAAGTTCATAGCCCAAGATTTGGGTGGTCCTAGTGAGACAAACTTGA
*
471860 TGAATTCACT
66 TAAATTCACT
471870 GAAACTTAAA
Statistics
Matches: 63, Mismatches: 11, Indels: 2
0.83 0.14 0.03
Matches are distributed among these distances:
86 2 0.03
87 61 0.97
ACGTcount: A:0.27, C:0.15, G:0.20, T:0.38
Consensus pattern (87 bp):
TGAGTTTTACACTATTAATAAGTTCATAGCCCAAGATTTGGGTGGTCCTAGTGAGACAAACTTGA
TAAATTCACTTACTTTATATGT
Found at i:473132 original size:3 final size:3
Alignment explanation
Indices: 473124--473151 Score: 56
Period size: 3 Copynumber: 9.3 Consensus size: 3
473114 TTGAGATTTT
473124 TTA TTA TTA TTA TTA TTA TTA TTA TTA T
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA T
473152 CATCGTGTGT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:492562 original size:48 final size:48
Alignment explanation
Indices: 492509--492645 Score: 170
Period size: 48 Copynumber: 2.9 Consensus size: 48
492499 TAAATATTTT
*
492509 ATCTGATTTTCGACTTGAATTCTGATATGATACTTGACATGGATTCTG
1 ATCTGATTTTCGACATGAATTCTGATATGATACTTGACATGGATTCTG
* * *
492557 ATCTGA-TATCTGACATGAATTCTGATCTGATACTTGACTTGGATTCTG
1 ATCTGATTTTC-GACATGAATTCTGATATGATACTTGACATGGATTCTG
* * * *
492605 ATCTGATACTT-GACCTGGATTTTGATATGATACTTGACATG
1 ATCTGAT-TTTCGACATGAATTCTGATATGATACTTGACATG
492646 AATTATGTTT
Statistics
Matches: 75, Mismatches: 11, Indels: 6
0.82 0.12 0.07
Matches are distributed among these distances:
47 3 0.04
48 71 0.95
50 1 0.01
ACGTcount: A:0.26, C:0.15, G:0.19, T:0.40
Consensus pattern (48 bp):
ATCTGATTTTCGACATGAATTCTGATATGATACTTGACATGGATTCTG
Found at i:492659 original size:24 final size:24
Alignment explanation
Indices: 492527--492645 Score: 168
Period size: 24 Copynumber: 5.0 Consensus size: 24
492517 TTCGACTTGA
*
492527 ATTCTGATATGATACTTGACATGG
1 ATTCTGATCTGATACTTGACATGG
*
492551 ATTCTGATCTGATA-TCTGACATGA
1 ATTCTGATCTGATACT-TGACATGG
*
492575 ATTCTGATCTGATACTTGACTTGG
1 ATTCTGATCTGATACTTGACATGG
*
492599 ATTCTGATCTGATACTTGACCTGG
1 ATTCTGATCTGATACTTGACATGG
* *
492623 ATTTTGATATGATACTTGACATG
1 ATTCTGATCTGATACTTGACATG
492646 AATTATGTTT
Statistics
Matches: 85, Mismatches: 8, Indels: 4
0.88 0.08 0.04
Matches are distributed among these distances:
23 1 0.01
24 83 0.98
25 1 0.01
ACGTcount: A:0.26, C:0.15, G:0.19, T:0.39
Consensus pattern (24 bp):
ATTCTGATCTGATACTTGACATGG
Found at i:495458 original size:21 final size:22
Alignment explanation
Indices: 495414--495466 Score: 58
Period size: 22 Copynumber: 2.5 Consensus size: 22
495404 ATTCCTCTAA
*
495414 TATGT-ATCAAATATTAAATCTT
1 TATGTAAT-AAATATAAAATCTT
495436 TA-GTAGATAAATATAAAAT-TT
1 TATGTA-ATAAATATAAAATCTT
495457 TATGTAATAA
1 TATGTAATAA
495467 TTTCTGTAAT
Statistics
Matches: 27, Mismatches: 1, Indels: 7
0.77 0.03 0.20
Matches are distributed among these distances:
21 10 0.37
22 15 0.56
23 2 0.07
ACGTcount: A:0.47, C:0.04, G:0.08, T:0.42
Consensus pattern (22 bp):
TATGTAATAAATATAAAATCTT
Found at i:505579 original size:46 final size:46
Alignment explanation
Indices: 505486--505579 Score: 152
Period size: 46 Copynumber: 2.0 Consensus size: 46
505476 TACTTTCGTA
* * *
505486 GTTCAGAATTATTTGCTCTGAAGAAAGTGTTAATCTTTCTGTGTGT
1 GTTCAGAATTATTTGCTCAGAAGAAAGTGTTAATCTTTCTCTCTGT
*
505532 GTTCAGAATTATTTGCTCAGAAGAAAGTGTTAATTTTTCTCTCTGT
1 GTTCAGAATTATTTGCTCAGAAGAAAGTGTTAATCTTTCTCTCTGT
505578 GT
1 GT
505580 GTGTGTCTCT
Statistics
Matches: 44, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
46 44 1.00
ACGTcount: A:0.24, C:0.12, G:0.20, T:0.44
Consensus pattern (46 bp):
GTTCAGAATTATTTGCTCAGAAGAAAGTGTTAATCTTTCTCTCTGT
Found at i:532901 original size:27 final size:27
Alignment explanation
Indices: 532870--532922 Score: 106
Period size: 27 Copynumber: 2.0 Consensus size: 27
532860 TGTTAAAGAC
532870 AATCGTTTCTGCATAACCATATGGTCA
1 AATCGTTTCTGCATAACCATATGGTCA
532897 AATCGTTTCTGCATAACCATATGGTC
1 AATCGTTTCTGCATAACCATATGGTC
532923 CACATAAATC
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 26 1.00
ACGTcount: A:0.28, C:0.23, G:0.15, T:0.34
Consensus pattern (27 bp):
AATCGTTTCTGCATAACCATATGGTCA
Found at i:533882 original size:27 final size:26
Alignment explanation
Indices: 533842--533892 Score: 75
Period size: 27 Copynumber: 1.9 Consensus size: 26
533832 CATTTAAATG
*
533842 ATAAACGAATATAAACGAACGAACATA
1 ATAAACGAACATAAACGAAC-AACATA
*
533869 ATAAATGAACATAAACGAACAACA
1 ATAAACGAACATAAACGAACAACA
533893 CAAACGCAAA
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
26 4 0.18
27 18 0.82
ACGTcount: A:0.61, C:0.16, G:0.10, T:0.14
Consensus pattern (26 bp):
ATAAACGAACATAAACGAACAACATA
Found at i:534171 original size:14 final size:14
Alignment explanation
Indices: 534150--534193 Score: 70
Period size: 14 Copynumber: 3.1 Consensus size: 14
534140 GCCTTCTGTT
534150 CAAACATAAATGAA
1 CAAACATAAATGAA
*
534164 CGAACATAAATGAA
1 CAAACATAAATGAA
*
534178 CAAACATAAACGAA
1 CAAACATAAATGAA
534192 CA
1 CA
534194 TATAATCGAA
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
14 27 1.00
ACGTcount: A:0.61, C:0.18, G:0.09, T:0.11
Consensus pattern (14 bp):
CAAACATAAATGAA
Found at i:534285 original size:40 final size:40
Alignment explanation
Indices: 534236--534338 Score: 170
Period size: 40 Copynumber: 2.6 Consensus size: 40
534226 AACGAGTCAT
* * *
534236 TTGTTCGTGTTCGTTCGTTTAATTATACGAACGTAAAATC
1 TTGTTCGTGTTCGTTCATTTAATTAAACGAACGCAAAATC
534276 TTGTTCGTGTTCGTTCATTTAATTAAACGAACGCAAAATC
1 TTGTTCGTGTTCGTTCATTTAATTAAACGAACGCAAAATC
*
534316 TTGTTCATGTTCGTTCATTTAAT
1 TTGTTCGTGTTCGTTCATTTAAT
534339 AAATAAACGA
Statistics
Matches: 59, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
40 59 1.00
ACGTcount: A:0.25, C:0.16, G:0.16, T:0.44
Consensus pattern (40 bp):
TTGTTCGTGTTCGTTCATTTAATTAAACGAACGCAAAATC
Found at i:539609 original size:40 final size:42
Alignment explanation
Indices: 539542--539642 Score: 109
Period size: 41 Copynumber: 2.5 Consensus size: 42
539532 AAATGATTAA
* *
539542 CAAATTCGCAACGCGAA-TTCTAATTTCGTAACAT-AGTTTC
1 CAAATTCGCAACTCGAATTTCTAATTTCGCAACATGAGTTTC
* * *
539582 CAAATTCGCAACTCGAATTTCT-TTTTCGCAACGTGATTTTC
1 CAAATTCGCAACTCGAATTTCTAATTTCGCAACATGAGTTTC
* * *
539623 TAAATTTGTAACTCGAATTT
1 CAAATTCGCAACTCGAATTT
539643 AAAAATCACA
Statistics
Matches: 51, Mismatches: 8, Indels: 3
0.82 0.13 0.05
Matches are distributed among these distances:
40 25 0.49
41 26 0.51
ACGTcount: A:0.30, C:0.21, G:0.12, T:0.38
Consensus pattern (42 bp):
CAAATTCGCAACTCGAATTTCTAATTTCGCAACATGAGTTTC
Found at i:541249 original size:36 final size:36
Alignment explanation
Indices: 541202--541274 Score: 137
Period size: 36 Copynumber: 2.0 Consensus size: 36
541192 GTAAATATTA
*
541202 TGGGTAAATTTTCAATTCAGATGTTATTTTAACTGT
1 TGGGTAAATTTTCAATCCAGATGTTATTTTAACTGT
541238 TGGGTAAATTTTCAATCCAGATGTTATTTTAACTGT
1 TGGGTAAATTTTCAATCCAGATGTTATTTTAACTGT
541274 T
1 T
541275 TGGATATGTT
Statistics
Matches: 36, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
36 36 1.00
ACGTcount: A:0.27, C:0.10, G:0.16, T:0.47
Consensus pattern (36 bp):
TGGGTAAATTTTCAATCCAGATGTTATTTTAACTGT
Found at i:541791 original size:15 final size:15
Alignment explanation
Indices: 541768--541799 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
541758 CGCCCCGCAT
541768 CCGCACCGCATCCAC
1 CCGCACCGCATCCAC
*
541783 CCGCCCCGCATCCAC
1 CCGCACCGCATCCAC
541798 CC
1 CC
541800 TCCCACATCC
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.16, C:0.66, G:0.12, T:0.06
Consensus pattern (15 bp):
CCGCACCGCATCCAC
Found at i:554841 original size:60 final size:60
Alignment explanation
Indices: 554793--554993 Score: 303
Period size: 60 Copynumber: 3.4 Consensus size: 60
554783 GAATTCATTA
*
554793 ACTATTAAAAGTTACAAAATGATCTCTCGACTATAGGATATTACTTTGTTGAGTCATCTT
1 ACTATTAAAAGTCACAAAATGATCTCTCGACTATAGGATATTACTTTGTTGAGTCATCTT
* * * *
554853 ACTATTAAAAGTCACAAAATGTTCACTAGACTATAGGATATTACTTTGTTGAGTCATGTT
1 ACTATTAAAAGTCACAAAATGATCTCTCGACTATAGGATATTACTTTGTTGAGTCATCTT
* * * * * *
554913 ACTATTAAAAGTTACAAAATGATATCTCAACTGTAAGATATTACTTTGTTGAGTCCTCTT
1 ACTATTAAAAGTCACAAAATGATCTCTCGACTATAGGATATTACTTTGTTGAGTCATCTT
554973 ACTATTAAAAGTCACAAAATG
1 ACTATTAAAAGTCACAAAATG
554994 TTCACTTGAC
Statistics
Matches: 125, Mismatches: 16, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
60 125 1.00
ACGTcount: A:0.36, C:0.14, G:0.13, T:0.36
Consensus pattern (60 bp):
ACTATTAAAAGTCACAAAATGATCTCTCGACTATAGGATATTACTTTGTTGAGTCATCTT
Found at i:555894 original size:19 final size:17
Alignment explanation
Indices: 555870--555916 Score: 58
Period size: 19 Copynumber: 2.6 Consensus size: 17
555860 GGATGAAACA
555870 AATAAAAAAAATGAAATTG
1 AATAAAAAAAAT-AAA-TG
555889 AATAAAATAAAATAAATG
1 AATAAAA-AAAATAAATG
*
555907 AAGAAAAAAA
1 AATAAAAAAA
555917 TATAGATACA
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
17 3 0.12
18 8 0.31
19 10 0.38
20 5 0.19
ACGTcount: A:0.74, C:0.00, G:0.09, T:0.17
Consensus pattern (17 bp):
AATAAAAAAAATAAATG
Found at i:555895 original size:18 final size:17
Alignment explanation
Indices: 555873--555916 Score: 52
Period size: 18 Copynumber: 2.4 Consensus size: 17
555863 TGAAACAAAT
*
555873 AAAAAAAATGAAATTGAAT
1 AAAAAAAAT-AAA-TGAAG
555892 AAAATAAAATAAATGAAG
1 AAAA-AAAATAAATGAAG
555910 AAAAAAA
1 AAAAAAA
555917 TATAGATACA
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
17 3 0.13
18 8 0.35
19 7 0.30
20 5 0.22
ACGTcount: A:0.75, C:0.00, G:0.09, T:0.16
Consensus pattern (17 bp):
AAAAAAAATAAATGAAG
Found at i:556037 original size:8 final size:8
Alignment explanation
Indices: 556018--556061 Score: 52
Period size: 8 Copynumber: 5.2 Consensus size: 8
556008 AATAAATAGT
556018 ATAAATAAA
1 ATAAA-AAA
556027 ATAAAAAA
1 ATAAAAAA
556035 ATAAAAAA
1 ATAAAAAA
*
556043 TATATAAAA
1 -ATAAAAAA
*
556052 ATATAAAA
1 ATAAAAAA
556060 AT
1 AT
556062 GTATGTATAA
Statistics
Matches: 33, Mismatches: 1, Indels: 3
0.89 0.03 0.08
Matches are distributed among these distances:
8 21 0.64
9 12 0.36
ACGTcount: A:0.77, C:0.00, G:0.00, T:0.23
Consensus pattern (8 bp):
ATAAAAAA
Found at i:556038 original size:17 final size:17
Alignment explanation
Indices: 556002--556060 Score: 57
Period size: 18 Copynumber: 3.3 Consensus size: 17
555992 AAACATAATG
* *
556002 AAAATAAATAAATAGTAT
1 AAAA-AAATAAAAAATAT
556020 AAATAAAATAAAAAA-AT
1 AAA-AAAATAAAAAATAT
556037 AAAAAATATATAAAAATAT
1 AAAAAA-ATA-AAAAATAT
556056 AAAAA
1 AAAAA
556061 TGTATGTATA
Statistics
Matches: 35, Mismatches: 2, Indels: 7
0.80 0.05 0.16
Matches are distributed among these distances:
16 3 0.09
17 8 0.23
18 16 0.46
19 8 0.23
ACGTcount: A:0.76, C:0.00, G:0.02, T:0.22
Consensus pattern (17 bp):
AAAAAAATAAAAAATAT
Found at i:556343 original size:12 final size:13
Alignment explanation
Indices: 556322--556356 Score: 54
Period size: 13 Copynumber: 2.7 Consensus size: 13
556312 AATGAAAAAA
556322 AAATATAATAAAT
1 AAATATAATAAAT
556335 AAATA-AATAAAT
1 AAATATAATAAAT
556347 AAAATATAAT
1 -AAATATAAT
556357 TATATATATA
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
12 7 0.35
13 10 0.50
14 3 0.15
ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (13 bp):
AAATATAATAAAT
Found at i:557810 original size:106 final size:106
Alignment explanation
Indices: 557626--558901 Score: 1995
Period size: 106 Copynumber: 12.0 Consensus size: 106
557616 GCATTGTTCC
* * *
557626 GAGTCCAATATCC-TC-CATCGTGAAGTTGAAATTGGCTCTGGAA-TCAGGAAATTGTTTGTTGA
1 GAGTCCAATATCCTTCGC-T-GTGAAGTTGAAATTGGCTCTGAAATTGA-GAAGTTGTTTGTTGA
* * * *
557688 CAACCAGCCGTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCTC
63 CAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* * * *
557732 GAGTCCAATATCCTTTGTTGTGAAGTTGAAATTGGCTCCGAAATTGAGAAATTGTTTGTTGACAA
1 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTTGTTGACAA
*
557797 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTC
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* * *
557838 GAGTCCAATATCATTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTGTTGACAA
1 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTTGTTGACAA
*
557903 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTACGTTGTCTG
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* *
557944 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTATTTGTTGACAA
1 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTTGTTGACAA
*
558009 CCAGCGGTCCCTTCGTTGTGAAGTTGAACTTGCGTTGTCTG
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* *
558050 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCCGAAATTGAGAAATTGTTTGTTGACAA
1 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTTGTTGACAA
*
558115 CCAACGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* * * * *
558156 GAGTACAATATCTTTCGCTGTGAAGTTGAAATTGGCTAC-AAAATTGGGAAATTGTTTGTTGACA
1 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCT-CTGAAATTGAGAAGTTGTTTGTTGACA
* *
558220 ACCAGCAGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTC
65 ACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* *
558262 GAGTCAAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTGTTGACAA
1 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTTGTTGACAA
558327 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* *
558368 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTTTTTGTTGACAA
1 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTTGTTGACAA
558433 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* * *
558474 GAGTCCAATATCATTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTATTGACAA
1 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTTGTTGACAA
* * *
558539 CCAACGGTCCCTTCGTCATGAAGTTGAACTTGCGTTGTCTT
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* * * *
558580 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATTATTTATTGACAA
1 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTTGTTGACAA
* *
558645 TCAGCAGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
558686 GAGTCCAATATCCTTCGGC-GTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTTGTTGACA
1 GAGTCCAATATCCTTC-GCTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTTGTTGACA
558750 ACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
65 ACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* *
558792 GAGTCCAATATCCTTCGCTGTGATGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTGTTGACAA
1 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTTGTTGACAA
** * * * *
558857 CCAGTTGTCCCTTCGTTGTTAAGTTGAACTTGTGTTGTCTC
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
558898 GAGT
1 GAGT
558902 GGCACGATAT
Statistics
Matches: 1089, Mismatches: 74, Indels: 14
0.93 0.06 0.01
Matches are distributed among these distances:
105 3 0.00
106 1079 0.99
107 7 0.01
ACGTcount: A:0.23, C:0.18, G:0.25, T:0.34
Consensus pattern (106 bp):
GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTTGTTGACAA
CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
Found at i:559874 original size:22 final size:22
Alignment explanation
Indices: 559848--559902 Score: 101
Period size: 22 Copynumber: 2.5 Consensus size: 22
559838 TTGTGTTTGG
*
559848 TCAAAGGTTTGGCATTTGATGT
1 TCAAAGGTTTGGCATTTGATGC
559870 TCAAAGGTTTGGCATTTGATGC
1 TCAAAGGTTTGGCATTTGATGC
559892 TCAAAGGTTTG
1 TCAAAGGTTTG
559903 ATGGGGTAGC
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
22 32 1.00
ACGTcount: A:0.24, C:0.11, G:0.27, T:0.38
Consensus pattern (22 bp):
TCAAAGGTTTGGCATTTGATGC
Found at i:560537 original size:22 final size:23
Alignment explanation
Indices: 560511--560561 Score: 70
Period size: 23 Copynumber: 2.3 Consensus size: 23
560501 TCCCTTTTGA
560511 TTTTTGTTCTT-TCTTTTTT-TT
1 TTTTTGTTCTTGTCTTTTTTGTT
*
560532 TGTTTTCTTCTTGTCTTTTTTGTT
1 T-TTTTGTTCTTGTCTTTTTTGTT
560556 TTTTTG
1 TTTTTG
560562 CCCTTTTTGT
Statistics
Matches: 25, Mismatches: 2, Indels: 4
0.81 0.06 0.13
Matches are distributed among these distances:
21 1 0.04
22 9 0.36
23 12 0.48
24 3 0.12
ACGTcount: A:0.00, C:0.10, G:0.10, T:0.80
Consensus pattern (23 bp):
TTTTTGTTCTTGTCTTTTTTGTT
Found at i:565140 original size:19 final size:17
Alignment explanation
Indices: 565116--565162 Score: 58
Period size: 19 Copynumber: 2.6 Consensus size: 17
565106 GGATGAAACA
565116 AATAAAAAAAATAAAATTG
1 AATAAAAAAAAT-AAA-TG
565135 AATAAAATAAAATAAATG
1 AATAAAA-AAAATAAATG
*
565153 AAGAAAAAAA
1 AATAAAAAAA
565163 TATAGATACA
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
17 3 0.12
18 8 0.31
19 10 0.38
20 5 0.19
ACGTcount: A:0.77, C:0.00, G:0.06, T:0.17
Consensus pattern (17 bp):
AATAAAAAAAATAAATG
Found at i:565287 original size:27 final size:28
Alignment explanation
Indices: 565252--565313 Score: 72
Period size: 27 Copynumber: 2.2 Consensus size: 28
565242 AAACATAATG
* * *
565252 AAAATAAATAAATAGTATAAAT-AAAAT
1 AAAAAAAATAAAAAATATAAATAAAAAT
*
565279 AAAAAAAATAAAAAATATATATAAAAAT
1 AAAAAAAATAAAAAATATAAATAAAAAT
*
565307 ATAAAAA
1 AAAAAAA
565314 TGTATGTATA
Statistics
Matches: 29, Mismatches: 5, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
27 18 0.62
28 11 0.38
ACGTcount: A:0.76, C:0.00, G:0.02, T:0.23
Consensus pattern (28 bp):
AAAAAAAATAAAAAATATAAATAAAAAT
Found at i:565314 original size:27 final size:31
Alignment explanation
Indices: 565252--565313 Score: 85
Period size: 28 Copynumber: 2.1 Consensus size: 31
565242 AAACATAATG
565252 AAAATAAATAAATAGTATAAATAAAATAAAA
1 AAAATAAATAAATAGTATAAATAAAATAAAA
* *
565283 AAAATAAA-AAATA-TATATA-AAAATATAA
1 AAAATAAATAAATAGTATAAATAAAATAAAA
565311 AAA
1 AAA
565314 TGTATGTATA
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
28 11 0.38
29 5 0.17
30 5 0.17
31 8 0.28
ACGTcount: A:0.76, C:0.00, G:0.02, T:0.23
Consensus pattern (31 bp):
AAAATAAATAAATAGTATAAATAAAATAAAA
Found at i:566063 original size:32 final size:32
Alignment explanation
Indices: 566027--566087 Score: 86
Period size: 32 Copynumber: 1.9 Consensus size: 32
566017 ATGCTTGTGG
*
566027 ATCCTATCTTTAGGAGTTTAAATAATAGCTCT
1 ATCCTATCTTTAGAAGTTTAAATAATAGCTCT
* * *
566059 ATCCTATTTTTAGAAGTTTGAATCATAGC
1 ATCCTATCTTTAGAAGTTTAAATAATAGC
566088 AAAATTTTAT
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
32 25 1.00
ACGTcount: A:0.31, C:0.15, G:0.13, T:0.41
Consensus pattern (32 bp):
ATCCTATCTTTAGAAGTTTAAATAATAGCTCT
Found at i:574809 original size:20 final size:20
Alignment explanation
Indices: 574735--574808 Score: 130
Period size: 20 Copynumber: 3.7 Consensus size: 20
574725 AACATTCCCA
574735 GTAATCTTACATTCCCACTG
1 GTAATCTTACATTCCCACTG
574755 GTAATCTTACATTCCCACTG
1 GTAATCTTACATTCCCACTG
*
574775 GTAATCTTACATTCTCACTG
1 GTAATCTTACATTCCCACTG
*
574795 ATAATCTTACATTC
1 GTAATCTTACATTC
574809 TGTGAACCAA
Statistics
Matches: 52, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 52 1.00
ACGTcount: A:0.27, C:0.27, G:0.08, T:0.38
Consensus pattern (20 bp):
GTAATCTTACATTCCCACTG
Found at i:575269 original size:18 final size:19
Alignment explanation
Indices: 575228--575266 Score: 60
Period size: 20 Copynumber: 2.0 Consensus size: 19
575218 TTGGTTCACA
*
575228 GAATGTAAGATTATCAGTGG
1 GAATGTAAGATTACCAG-GG
575248 GAATGTAAGATTACCAGGG
1 GAATGTAAGATTACCAGGG
575267 AATATAATTA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
19 2 0.11
20 16 0.89
ACGTcount: A:0.36, C:0.08, G:0.31, T:0.26
Consensus pattern (19 bp):
GAATGTAAGATTACCAGGG
Found at i:575494 original size:37 final size:37
Alignment explanation
Indices: 575421--575495 Score: 98
Period size: 38 Copynumber: 2.0 Consensus size: 37
575411 GTTGAGAAAT
* *
575421 ATTTATATATTTTCTTTAAAAAATTTAAATTCATAAA
1 ATTTATATATTTTCTTTAAAAAATTAAAAATCATAAA
* *
575458 ATTTATATAATTTTTTTTACAAAATTAAAAAT-ATAAA
1 ATTTATAT-ATTTTCTTTAAAAAATTAAAAATCATAAA
575495 A
1 A
575496 AGGTTTAATG
Statistics
Matches: 33, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
37 14 0.42
38 19 0.58
ACGTcount: A:0.49, C:0.04, G:0.00, T:0.47
Consensus pattern (37 bp):
ATTTATATATTTTCTTTAAAAAATTAAAAATCATAAA
Found at i:576838 original size:19 final size:19
Alignment explanation
Indices: 576815--576862 Score: 71
Period size: 18 Copynumber: 2.5 Consensus size: 19
576805 TAATGATTAT
576815 TTTTTTATTATTTATTAAAG
1 TTTTTTATTA-TTATTAAAG
*
576835 TTTTTT-TTATTGTTAAAG
1 TTTTTTATTATTATTAAAG
576853 TTTTTTATTA
1 TTTTTTATTA
576863 AATTATTTTT
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
18 14 0.54
19 6 0.23
20 6 0.23
ACGTcount: A:0.25, C:0.00, G:0.06, T:0.69
Consensus pattern (19 bp):
TTTTTTATTATTATTAAAG
Found at i:577739 original size:26 final size:26
Alignment explanation
Indices: 577700--577754 Score: 67
Period size: 26 Copynumber: 2.1 Consensus size: 26
577690 TTTTATAATA
**
577700 ATAAATTTTTTATAATTTT-AAAAATT
1 ATAAATTTCATAT-ATTTTAAAAAATT
577726 ATAAATTTCATATATTTTGAAAAAATT
1 ATAAATTTCATATATTTT-AAAAAATT
577753 AT
1 AT
577755 TGAATAATAA
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
25 5 0.20
26 11 0.44
27 9 0.36
ACGTcount: A:0.47, C:0.02, G:0.02, T:0.49
Consensus pattern (26 bp):
ATAAATTTCATATATTTTAAAAAATT
Found at i:578363 original size:333 final size:333
Alignment explanation
Indices: 577746--578681 Score: 1579
Period size: 333 Copynumber: 2.8 Consensus size: 333
577736 TATATTTTGA
* *
577746 AAAAATTATTGAATAATAATTTATTTGATCCTCCAATTGTAATTAAAAAGTTTATTTTAATA-TT
1 AAAAATTAATGAATAATAATTCATTTGATCCT-CAATTGTAATT-AAAAGTTTATTTTAATATTT
* * *
577810 TTTATATTTTTAAACAATTAATTTTAAAAGGTAATAATTTTTTAAAAAATGTATGAAATTTATTA
64 TTTATATTTTTAAACAATTAATTTTAAAAGGTAATAATTTTTTCAAAAATATATGAAATTTATAA
*
577875 TTTTTTAAATTATAAAATATTTATCATCATCATCATCATTTTGTAAAAGAAATACTAGTTATAAA
129 TTTTTAAAATTATAAAATATTTAT--T-ATCATCATCATTTTGTAAAAGAAATACTAGTTATAAA
*
577940 ACTTTTATAAAATTATTCATATTTTAAAATACTTACCCTCAAAGTTTTTATATACTAGGTTATAT
191 ACTTTTATAAAATTATTCATATTTTAAAATACTTACCCTCAAAGTTTTTATATACTAGATTATAT
578005 GTATTGTGTAATTTTAATACAAAAATTTAAATAATTTTATTAAAAATGAATAAACATTATTAAAT
256 GTATTGTGTAATTTTAATACAAAAATTTAAATAATTTTATTAAAAATGAATAAACATTATTAAAT
* *
578070 GTTGTTAAAAATT
321 ATTGTTAAAAAGT
578083 AAAAATTAATGAATAATAATTCATTTGATCCATCAATTGTAATTAAAAGTTTATTTTAATATTTT
1 AAAAATTAATGAATAATAATTCATTTGATCC-TCAATTGTAATTAAAAGTTTATTTTAATATTTT
578148 TTATATTTTTAAACAATTAATTTTAAAAGGTAAT-ATTTTTTCAAAAATATATGAAATTTATAAT
65 TTATATTTTTAAACAATTAATTTTAAAAGGTAATAATTTTTTCAAAAATATATGAAATTTATAAT
578212 TTTTAAAATTATAAAATATTTATTATCATCATCATTTTGTAAAAGAAATACTAGTTATAAAACTT
130 TTTTAAAATTATAAAATATTTATTATCATCATCATTTTGTAAAAGAAATACTAGTTATAAAACTT
*
578277 TTATAAAATTATTCATATTTTAAAATACTTATCCTCAAAGTTTTTATATACTAGATTATATGTAT
195 TTATAAAATTATTCATATTTTAAAATACTTACCCTCAAAGTTTTTATATACTAGATTATATGTAT
* *
578342 TGTGTAATTTTAATGCAAAAATTTAAATAATTTTATTAAAAATGAATAAACATTATTAACTATTG
260 TGTGTAATTTTAATACAAAAATTTAAATAATTTTATTAAAAATGAATAAACATTATTAAATATTG
578407 TTAAAAAGT
325 TTAAAAAGT
*
578416 AAAAATTAATGAATAATAATTCATTTAATTCCTCAATTGTAATTAAAAGTTTATTTTAATATTTT
1 AAAAATTAATGAATAATAATTCATTTGA-TCCTCAATTGTAATTAAAAGTTTATTTTAATA--TT
578481 TTTTATATTTTTAAACAATTAATTTTAAAAGGTAATAATTTTTTCAAAAATATATGAAATTTATA
63 TTTTATATTTTTAAACAATTAATTTTAAAAGGTAATAATTTTTTCAAAAATATATGAAATTTATA
* * *
578546 ATTTTTAAATTTTTAAAATATTTATTATCATCATCATTATTTTATAAAAGAAATACTAGTTATAA
128 ATTTTTAAAATTATAAAATATTTATTATCATCATC---ATTTTGTAAAAGAAATACTAGTTATAA
** *
578611 AACTTTTATAAAATTATTCATATTTTAAAATACTTACCCTCAAAGTTTTCCTATTCTAGATTATA
190 AACTTTTATAAAATTATTCATATTTTAAAATACTTACCCTCAAAGTTTTTATATACTAGATTATA
578676 TGTATT
255 TGTATT
578682 TGTTGAGTTA
Statistics
Matches: 570, Mismatches: 20, Indels: 16
0.94 0.03 0.03
Matches are distributed among these distances:
333 230 0.40
334 4 0.01
335 38 0.07
336 127 0.22
337 77 0.14
338 1 0.00
339 93 0.16
ACGTcount: A:0.43, C:0.07, G:0.05, T:0.45
Consensus pattern (333 bp):
AAAAATTAATGAATAATAATTCATTTGATCCTCAATTGTAATTAAAAGTTTATTTTAATATTTTT
TATATTTTTAAACAATTAATTTTAAAAGGTAATAATTTTTTCAAAAATATATGAAATTTATAATT
TTTAAAATTATAAAATATTTATTATCATCATCATTTTGTAAAAGAAATACTAGTTATAAAACTTT
TATAAAATTATTCATATTTTAAAATACTTACCCTCAAAGTTTTTATATACTAGATTATATGTATT
GTGTAATTTTAATACAAAAATTTAAATAATTTTATTAAAAATGAATAAACATTATTAAATATTGT
TAAAAAGT
Found at i:584225 original size:20 final size:20
Alignment explanation
Indices: 584200--584237 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
584190 GAATGCTAGA
*
584200 GGGGAATCGATACCCCCAGG
1 GGGGAACCGATACCCCCAGG
*
584220 GGGGAACCGATTCCCCCA
1 GGGGAACCGATACCCCCA
584238 TATAAAAAAA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.24, C:0.34, G:0.32, T:0.11
Consensus pattern (20 bp):
GGGGAACCGATACCCCCAGG
Found at i:584923 original size:23 final size:23
Alignment explanation
Indices: 584879--584923 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 23
584869 ATTATTATAT
*
584879 GGCACTACGGTGCAATTCTACGC
1 GGCACTACGGTGCAATTATACGC
* *
584902 GGCACTTCGGTGCATTTATACG
1 GGCACTACGGTGCAATTATACG
584924 AGCTGTGGTG
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.20, C:0.27, G:0.27, T:0.27
Consensus pattern (23 bp):
GGCACTACGGTGCAATTATACGC
Found at i:590922 original size:21 final size:21
Alignment explanation
Indices: 590880--590922 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
590870 TTTCTGGGCT
* *
590880 AGGGGAATCGGTACCCATTCA
1 AGGGGAATCGATACCCACTCA
*
590901 AGGGGAATCGATACCCCCTCA
1 AGGGGAATCGATACCCACTCA
590922 A
1 A
590923 CGAATATGAA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.30, C:0.28, G:0.26, T:0.16
Consensus pattern (21 bp):
AGGGGAATCGATACCCACTCA
Found at i:590974 original size:20 final size:20
Alignment explanation
Indices: 590949--590986 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
590939 GAATGCTAGA
*
590949 GGGGAATCGATACCCCCAGG
1 GGGGAACCGATACCCCCAGG
*
590969 GGGGAACCGATTCCCCCA
1 GGGGAACCGATACCCCCA
590987 TATAAAAAAA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.24, C:0.34, G:0.32, T:0.11
Consensus pattern (20 bp):
GGGGAACCGATACCCCCAGG
Done.