Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01005946.1 Hibiscus syriacus cultivar Beakdansim tig00013960_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: 2465359
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 3 of 11
Found at i:352227 original size:17 final size:17
Alignment explanation
Indices: 352201--352234 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
352191 ATTACTGTAG
352201 ATTGCATGTTGATCTTC
1 ATTGCATGTTGATCTTC
*
352218 ATTGCCTGTTGATCTTC
1 ATTGCATGTTGATCTTC
352235 CCTACTTTAG
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.15, C:0.21, G:0.18, T:0.47
Consensus pattern (17 bp):
ATTGCATGTTGATCTTC
Found at i:357590 original size:24 final size:24
Alignment explanation
Indices: 357563--357669 Score: 97
Period size: 24 Copynumber: 4.5 Consensus size: 24
357553 AAACGGAGAT
*
357563 ATCAGAAATCAAAACATAATTCAG
1 ATCAGAAATCAAAACAGAATTCAG
* * * *
357587 ATCAGATATCAGAACATAATCCAG
1 ATCAGAAATCAAAACAGAATTCAG
* * * * *
357611 GTTAGGAATCAGAACAGATTTCAG
1 ATCAGAAATCAAAACAGAATTCAG
** *
357635 ATCAGATGTCAAAACAGAATTCAA
1 ATCAGAAATCAAAACAGAATTCAG
357659 ATCAGAAATCA
1 ATCAGAAATCA
357670 GATAAAATAT
Statistics
Matches: 63, Mismatches: 20, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
24 63 1.00
ACGTcount: A:0.48, C:0.17, G:0.14, T:0.21
Consensus pattern (24 bp):
ATCAGAAATCAAAACAGAATTCAG
Found at i:357669 original size:48 final size:48
Alignment explanation
Indices: 357563--357671 Score: 119
Period size: 48 Copynumber: 2.3 Consensus size: 48
357553 AAACGGAGAT
* * * * *
357563 ATCAGAAATCAAAACATAATTCAGATCAGATATCAGAACATAATCCAG
1 ATCAGAAATCAGAACAGAATTCAGATCAGATATCAAAACAGAATCCAA
* * * * * *
357611 GTTAGGAATCAGAACAGATTTCAGATCAGATGTCAAAACAGAATTCAA
1 ATCAGAAATCAGAACAGAATTCAGATCAGATATCAAAACAGAATCCAA
357659 ATCAGAAATCAGA
1 ATCAGAAATCAGA
357672 TAAAATATTC
Statistics
Matches: 47, Mismatches: 14, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
48 47 1.00
ACGTcount: A:0.48, C:0.17, G:0.15, T:0.21
Consensus pattern (48 bp):
ATCAGAAATCAGAACAGAATTCAGATCAGATATCAAAACAGAATCCAA
Found at i:360139 original size:15 final size:15
Alignment explanation
Indices: 360119--360147 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
360109 GGTCAACTCC
360119 GGTCAACGGTCAACG
1 GGTCAACGGTCAACG
360134 GGTCAACGGTCAAC
1 GGTCAACGGTCAAC
360148 ATGTCGGGTC
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:0.28, C:0.28, G:0.31, T:0.14
Consensus pattern (15 bp):
GGTCAACGGTCAACG
Found at i:360165 original size:8 final size:7
Alignment explanation
Indices: 360118--360147 Score: 51
Period size: 7 Copynumber: 4.1 Consensus size: 7
360108 TGGTCAACTC
360118 CGGTCAA
1 CGGTCAA
360125 CGGTCAA
1 CGGTCAA
360132 CGGGTCAA
1 C-GGTCAA
360140 CGGTCAA
1 CGGTCAA
360147 C
1 C
360148 ATGTCGGGTC
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
7 15 0.68
8 7 0.32
ACGTcount: A:0.27, C:0.30, G:0.30, T:0.13
Consensus pattern (7 bp):
CGGTCAA
Found at i:376471 original size:2 final size:2
Alignment explanation
Indices: 376464--376499 Score: 65
Period size: 2 Copynumber: 18.5 Consensus size: 2
376454 GTTATTGATA
376464 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT -T AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
376500 GATTCAACTA
Statistics
Matches: 33, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 32 0.97
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:378257 original size:57 final size:57
Alignment explanation
Indices: 378164--378350 Score: 266
Period size: 57 Copynumber: 3.3 Consensus size: 57
378154 TTTGATTTGC
* ** *
378164 GAAATTCGCGTTGCGATAGTTGTGTTTACCTATATCGGTAATTATCATTGCGAATTT
1 GAAAATCGCGTTGCGATAGTACTGTTTACCTATATCGGTAATTAGCATTGCGAATTT
* *
378221 GAAAATCGCGTTGCCATAGTACTATTTACCTATATCGGTAATTAGCATTGCGAATTT
1 GAAAATCGCGTTGCGATAGTACTGTTTACCTATATCGGTAATTAGCATTGCGAATTT
* * * * *
378278 GAAAATTGCGTTGCGATAATACTGTTTAGCTATATCGGTAATTAGCGTTGCGAATAT
1 GAAAATCGCGTTGCGATAGTACTGTTTACCTATATCGGTAATTAGCATTGCGAATTT
*
378335 GAAAATCTCGTTGCGA
1 GAAAATCGCGTTGCGA
378351 ATTTGAAAAT
Statistics
Matches: 115, Mismatches: 15, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
57 115 1.00
ACGTcount: A:0.28, C:0.15, G:0.21, T:0.36
Consensus pattern (57 bp):
GAAAATCGCGTTGCGATAGTACTGTTTACCTATATCGGTAATTAGCATTGCGAATTT
Found at i:378348 original size:20 final size:20
Alignment explanation
Indices: 378322--378370 Score: 80
Period size: 20 Copynumber: 2.5 Consensus size: 20
378312 TCGGTAATTA
378322 GCGTTGCGAATATGAAAATC
1 GCGTTGCGAATATGAAAATC
* *
378342 TCGTTGCGAATTTGAAAATC
1 GCGTTGCGAATATGAAAATC
378362 GCGTTGCGA
1 GCGTTGCGA
378371 TAGTACTATT
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 26 1.00
ACGTcount: A:0.29, C:0.16, G:0.27, T:0.29
Consensus pattern (20 bp):
GCGTTGCGAATATGAAAATC
Found at i:378366 original size:77 final size:77
Alignment explanation
Indices: 378265--378427 Score: 247
Period size: 77 Copynumber: 2.1 Consensus size: 77
378255 TCGGTAATTA
* *
378265 GCATTGCGAATTTGAAAATTGCGTTGCGATAATACTGTTTAGC-TATATCGGTAATTAGCGTTGC
1 GCATTGCGAATTTGAAAATCGCGTTGCGATAATACTATTTA-CATATATCGGTAATTAGCGTTGC
378329 GAATATGAAAATC
65 GAATATGAAAATC
* * * *
378342 TCGTTGCGAATTTGAAAATCGCGTTGCGATAGTACTATTTACATATATCTGTAATTAGCGTTGCG
1 GCATTGCGAATTTGAAAATCGCGTTGCGATAATACTATTTACATATATCGGTAATTAGCGTTGCG
*
378407 AATTTGAAAATC
66 AATATGAAAATC
378419 GCATTGCGA
1 GCATTGCGA
378428 TAGTATTGTT
Statistics
Matches: 76, Mismatches: 9, Indels: 2
0.87 0.10 0.02
Matches are distributed among these distances:
76 1 0.01
77 75 0.99
ACGTcount: A:0.30, C:0.14, G:0.21, T:0.34
Consensus pattern (77 bp):
GCATTGCGAATTTGAAAATCGCGTTGCGATAATACTATTTACATATATCGGTAATTAGCGTTGCG
AATATGAAAATC
Found at i:378374 original size:134 final size:134
Alignment explanation
Indices: 378211--378562 Score: 551
Period size: 134 Copynumber: 2.6 Consensus size: 134
378201 GTAATTATCA
* * *
378211 TTGCGAATTTGAAAATCGCGTTGCCATAGTACTATTTACCTATATCGGTAATTAGCATTGCGAAT
1 TTGCGAATTTGAAAATCGCGTTGCGATAGTACTATTTACATATATCGGTAATTAGCGTTGCGAAT
* * * *
378276 TTGAAAATTGCGTTGCGATAATACTGTTTAGCTATATCGGTAATTAGCGTTGCGAATATGAAAAT
66 TTGAAAATCGCGTTGCGATAATACTGTTTACCTATATCGGTAATTAACGTTACGAATATGAAAAT
*
378341 CTCG
131 CGCG
*
378345 TTGCGAATTTGAAAATCGCGTTGCGATAGTACTATTTACATATATCTGTAATTAGCGTTGCGAAT
1 TTGCGAATTTGAAAATCGCGTTGCGATAGTACTATTTACATATATCGGTAATTAGCGTTGCGAAT
* * * *
378410 TTGAAAATCGCATTGCGATAGTATTGTTTACCTATATCGGTAATTAACGTTACGAATTTGAAAAT
66 TTGAAAATCGCGTTGCGATAATACTGTTTACCTATATCGGTAATTAACGTTACGAATATGAAAAT
378475 CGCG
131 CGCG
* * *
378479 TTACGAATTTGAAAATCGCGTTGCGATAGTACTGTTTACTTATATCGGTAATTAGCGTTGCGAAT
1 TTGCGAATTTGAAAATCGCGTTGCGATAGTACTATTTACATATATCGGTAATTAGCGTTGCGAAT
*
378544 TTGAAAATCACGTTGCGAT
66 TTGAAAATCGCGTTGCGAT
378563 TTTGGAACCT
Statistics
Matches: 199, Mismatches: 19, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
134 199 1.00
ACGTcount: A:0.30, C:0.14, G:0.20, T:0.36
Consensus pattern (134 bp):
TTGCGAATTTGAAAATCGCGTTGCGATAGTACTATTTACATATATCGGTAATTAGCGTTGCGAAT
TTGAAAATCGCGTTGCGATAATACTGTTTACCTATATCGGTAATTAACGTTACGAATATGAAAAT
CGCG
Found at i:378404 original size:57 final size:57
Alignment explanation
Indices: 378343--378480 Score: 213
Period size: 57 Copynumber: 2.4 Consensus size: 57
378333 ATGAAAATCT
* *
378343 CGTTGCGAATTTGAAAATCGCGTTGCGATAGTACTATTTACATATATCTGTAATTAG
1 CGTTGCGAATTTGAAAATCGCGTTGCGATAGTACTATTTACATATATCGGTAATTAA
* * * *
378400 CGTTGCGAATTTGAAAATCGCATTGCGATAGTATTGTTTACCTATATCGGTAATTAA
1 CGTTGCGAATTTGAAAATCGCGTTGCGATAGTACTATTTACATATATCGGTAATTAA
*
378457 CGTTACGAATTTGAAAATCGCGTT
1 CGTTGCGAATTTGAAAATCGCGTT
378481 ACGAATTTGA
Statistics
Matches: 73, Mismatches: 8, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
57 73 1.00
ACGTcount: A:0.30, C:0.14, G:0.20, T:0.36
Consensus pattern (57 bp):
CGTTGCGAATTTGAAAATCGCGTTGCGATAGTACTATTTACATATATCGGTAATTAA
Found at i:378480 original size:77 final size:77
Alignment explanation
Indices: 378399--378566 Score: 264
Period size: 77 Copynumber: 2.2 Consensus size: 77
378389 TCTGTAATTA
*
378399 GCGTTGCGAATTTGAAAATCGCATTGCGATAGTATTGTTTACCTATATCGGTAATTAACGTTACG
1 GCGTTGCGAATTTGAAAATCGCATTGCGATAGTACTGTTTACCTATATCGGTAATTAACGTTACG
378464 AATTTGAAAATC
66 AATTTGAAAATC
* * * * *
378476 GCGTTACGAATTTGAAAATCGCGTTGCGATAGTACTGTTTACTTATATCGGTAATTAGCGTTGCG
1 GCGTTGCGAATTTGAAAATCGCATTGCGATAGTACTGTTTACCTATATCGGTAATTAACGTTACG
378541 AATTTGAAAATC
66 AATTTGAAAATC
* *
378553 ACGTTGCGATTTTG
1 GCGTTGCGAATTTG
378567 GAACCTGTGT
Statistics
Matches: 82, Mismatches: 9, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
77 82 1.00
ACGTcount: A:0.29, C:0.14, G:0.21, T:0.36
Consensus pattern (77 bp):
GCGTTGCGAATTTGAAAATCGCATTGCGATAGTACTGTTTACCTATATCGGTAATTAACGTTACG
AATTTGAAAATC
Found at i:378482 original size:20 final size:20
Alignment explanation
Indices: 378457--378500 Score: 88
Period size: 20 Copynumber: 2.2 Consensus size: 20
378447 CGGTAATTAA
378457 CGTTACGAATTTGAAAATCG
1 CGTTACGAATTTGAAAATCG
378477 CGTTACGAATTTGAAAATCG
1 CGTTACGAATTTGAAAATCG
378497 CGTT
1 CGTT
378501 GCGATAGTAC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 24 1.00
ACGTcount: A:0.32, C:0.16, G:0.20, T:0.32
Consensus pattern (20 bp):
CGTTACGAATTTGAAAATCG
Found at i:379943 original size:35 final size:35
Alignment explanation
Indices: 379897--379964 Score: 111
Period size: 35 Copynumber: 1.9 Consensus size: 35
379887 CACAATTTGA
379897 TAATATATTTGAATTAATCA-TTGCTATCCGATCGC
1 TAATATATTTGAATTAATCATTTG-TATCCGATCGC
*
379932 TAATATCTTTGAATTAATCATTTGTATCCGATC
1 TAATATATTTGAATTAATCATTTGTATCCGATC
379965 TATTGATCGA
Statistics
Matches: 31, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
35 28 0.90
36 3 0.10
ACGTcount: A:0.31, C:0.16, G:0.10, T:0.43
Consensus pattern (35 bp):
TAATATATTTGAATTAATCATTTGTATCCGATCGC
Found at i:385325 original size:19 final size:19
Alignment explanation
Indices: 385301--385342 Score: 84
Period size: 19 Copynumber: 2.2 Consensus size: 19
385291 TTGCAATTAT
385301 AGGTGACGCTACTGTTTTG
1 AGGTGACGCTACTGTTTTG
385320 AGGTGACGCTACTGTTTTG
1 AGGTGACGCTACTGTTTTG
385339 AGGT
1 AGGT
385343 TCATCTCTTA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 23 1.00
ACGTcount: A:0.17, C:0.14, G:0.33, T:0.36
Consensus pattern (19 bp):
AGGTGACGCTACTGTTTTG
Found at i:391290 original size:2 final size:2
Alignment explanation
Indices: 391283--391322 Score: 80
Period size: 2 Copynumber: 20.0 Consensus size: 2
391273 ACTATTCACA
391283 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
391323 TAATCTATAC
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 38 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:392209 original size:29 final size:29
Alignment explanation
Indices: 392141--392210 Score: 104
Period size: 29 Copynumber: 2.4 Consensus size: 29
392131 ATTTGAATAG
* *
392141 TTTAAATACTTATTTTGATTAAAAATAAT
1 TTTAAATATTTATTTTGATAAAAAATAAT
* *
392170 TTTAAACATTTATTTTGATAAAAAATTAT
1 TTTAAATATTTATTTTGATAAAAAATAAT
392199 TTTAAATATTTA
1 TTTAAATATTTA
392211 AATAAAAATA
Statistics
Matches: 36, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
29 36 1.00
ACGTcount: A:0.44, C:0.03, G:0.03, T:0.50
Consensus pattern (29 bp):
TTTAAATATTTATTTTGATAAAAAATAAT
Found at i:396461 original size:33 final size:34
Alignment explanation
Indices: 396400--396499 Score: 139
Period size: 33 Copynumber: 3.0 Consensus size: 34
396390 AAATTTAATG
*
396400 TTAAATTTCGAATACTATAATTTATATTTTAAAT
1 TTAAATTTCGAATAATATAATTTATATTTTAAAT
* * * *
396434 TTAAATTT-GAATAATATTATTTTTATTTTTATT
1 TTAAATTTCGAATAATATAATTTATATTTTAAAT
*
396467 TTAAATTTCGAATAATATAATTTGTATTTTAAA
1 TTAAATTTCGAATAATATAATTTATATTTTAAA
396500 AACATTTATC
Statistics
Matches: 56, Mismatches: 9, Indels: 2
0.84 0.13 0.03
Matches are distributed among these distances:
33 28 0.50
34 28 0.50
ACGTcount: A:0.39, C:0.03, G:0.04, T:0.54
Consensus pattern (34 bp):
TTAAATTTCGAATAATATAATTTATATTTTAAAT
Found at i:397036 original size:21 final size:20
Alignment explanation
Indices: 397009--397078 Score: 95
Period size: 21 Copynumber: 3.4 Consensus size: 20
396999 GGTATAAAAC
*
397009 CCTGCGGGCTAGGCATGTAA
1 CCTGCGGGCTAGGAATGTAA
397029 CCTGGCGGGCTAGGAATGTAA
1 CCT-GCGGGCTAGGAATGTAA
*
397050 CCCTGCGGGCTCGGAATGTAA
1 -CCTGCGGGCTAGGAATGTAA
397071 CCCTGCGG
1 -CCTGCGG
397079 AGATGGCATA
Statistics
Matches: 46, Mismatches: 2, Indels: 3
0.90 0.04 0.06
Matches are distributed among these distances:
20 3 0.07
21 40 0.87
22 3 0.07
ACGTcount: A:0.19, C:0.27, G:0.36, T:0.19
Consensus pattern (20 bp):
CCTGCGGGCTAGGAATGTAA
Found at i:397108 original size:21 final size:21
Alignment explanation
Indices: 397082--397129 Score: 60
Period size: 21 Copynumber: 2.3 Consensus size: 21
397072 CCTGCGGAGA
*
397082 TGGCATATAAACTGGTGGGCT
1 TGGCATATAAACTGGAGGGCT
* *
397103 TGGCATATGAAGTGGAGGGCT
1 TGGCATATAAACTGGAGGGCT
*
397124 GGGCAT
1 TGGCAT
397130 GTACCCCTGC
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.23, C:0.12, G:0.40, T:0.25
Consensus pattern (21 bp):
TGGCATATAAACTGGAGGGCT
Found at i:399895 original size:28 final size:28
Alignment explanation
Indices: 399858--399911 Score: 72
Period size: 28 Copynumber: 1.9 Consensus size: 28
399848 ACCATCAATG
*
399858 GAAGGGAAGAAAGAAAATACAGAAACAA
1 GAAGGAAAGAAAGAAAATACAGAAACAA
* * *
399886 GAAGGAAAGAAATAAGATAGAGAAAC
1 GAAGGAAAGAAAGAAAATACAGAAAC
399912 GAGATTCTTT
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
28 22 1.00
ACGTcount: A:0.63, C:0.06, G:0.26, T:0.06
Consensus pattern (28 bp):
GAAGGAAAGAAAGAAAATACAGAAACAA
Found at i:416518 original size:6 final size:6
Alignment explanation
Indices: 416509--416735 Score: 454
Period size: 6 Copynumber: 37.8 Consensus size: 6
416499 AATATACATA
416509 TATATT TATATT TATATT TATATT TATATT TATATT TATATT TATATT
1 TATATT TATATT TATATT TATATT TATATT TATATT TATATT TATATT
416557 TATATT TATATT TATATT TATATT TATATT TATATT TATATT TATATT
1 TATATT TATATT TATATT TATATT TATATT TATATT TATATT TATATT
416605 TATATT TATATT TATATT TATATT TATATT TATATT TATATT TATATT
1 TATATT TATATT TATATT TATATT TATATT TATATT TATATT TATATT
416653 TATATT TATATT TATATT TATATT TATATT TATATT TATATT TATATT
1 TATATT TATATT TATATT TATATT TATATT TATATT TATATT TATATT
416701 TATATT TATATT TATATT TATATT TATATT TATAT
1 TATATT TATATT TATATT TATATT TATATT TATAT
416736 GGCGTTGGTT
Statistics
Matches: 221, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 221 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (6 bp):
TATATT
Found at i:427000 original size:2 final size:2
Alignment explanation
Indices: 426993--427023 Score: 55
Period size: 2 Copynumber: 16.0 Consensus size: 2
426983 GTTAAAAATA
426993 AT AT AT AT AT AT AT AT AT AT AT AT AT A- AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
427024 TAATTATTTA
Statistics
Matches: 28, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
1 1 0.04
2 27 0.96
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:427570 original size:20 final size:20
Alignment explanation
Indices: 427533--427573 Score: 57
Period size: 20 Copynumber: 2.0 Consensus size: 20
427523 CAATTTTTCC
*
427533 TTTTTCTTTATTTTTCATAT
1 TTTTTCTTTATTTATCATAT
427553 TTTTTCTTCTA-TTATCATAT
1 TTTTTCTT-TATTTATCATAT
427573 T
1 T
427574 CTCATTTTCT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
20 17 0.89
21 2 0.11
ACGTcount: A:0.17, C:0.12, G:0.00, T:0.71
Consensus pattern (20 bp):
TTTTTCTTTATTTATCATAT
Found at i:435471 original size:102 final size:103
Alignment explanation
Indices: 435294--435509 Score: 389
Period size: 102 Copynumber: 2.1 Consensus size: 103
435284 CAAAAGATAA
435294 TATCTGTTTAAAATATTTTTTTAATCATTATCAACATACACATAACCTGCAGACGTAACTGATCG
1 TATCTGTTTAAAATATTTTTTTAATCATTATCAACATACACATAACCTGCAGACGTAACTGATCG
*
435359 AACTCTAAACCTCAAGGAATAACAACAACTTGCAGACG
66 AACTCTAAACCTCAAGGAATAACAACAACTTACAGACG
*
435397 TATCTGTTTAAAATA-TTTTTTAATCATTATCAACATACACATAACCTGCAGATGTAACTGATCG
1 TATCTGTTTAAAATATTTTTTTAATCATTATCAACATACACATAACCTGCAGACGTAACTGATCG
*
435461 AACTCTAAACCTCAAGGAATAATAACAACTTACAGACG
66 AACTCTAAACCTCAAGGAATAACAACAACTTACAGACG
*
435499 TAACTGTTTAA
1 TATCTGTTTAA
435510 TTTAAACGAT
Statistics
Matches: 109, Mismatches: 4, Indels: 1
0.96 0.04 0.01
Matches are distributed among these distances:
102 94 0.86
103 15 0.14
ACGTcount: A:0.39, C:0.20, G:0.10, T:0.31
Consensus pattern (103 bp):
TATCTGTTTAAAATATTTTTTTAATCATTATCAACATACACATAACCTGCAGACGTAACTGATCG
AACTCTAAACCTCAAGGAATAACAACAACTTACAGACG
Found at i:437769 original size:2 final size:2
Alignment explanation
Indices: 437764--437788 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
437754 TAATTATTTA
437764 AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT A
437789 ATTTTTGATT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:447981 original size:3 final size:3
Alignment explanation
Indices: 447973--448061 Score: 169
Period size: 3 Copynumber: 29.7 Consensus size: 3
447963 ATTATAAACT
*
447973 TAA TAA TAA AAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
448021 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TA
448062 TACAAATATG
Statistics
Matches: 84, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
3 84 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
TAA
Found at i:448704 original size:12 final size:12
Alignment explanation
Indices: 448684--448713 Score: 51
Period size: 12 Copynumber: 2.5 Consensus size: 12
448674 ATTAGGATAA
*
448684 TATTGTTATTAT
1 TATTTTTATTAT
448696 TATTTTTATTAT
1 TATTTTTATTAT
448708 TATTTT
1 TATTTT
448714 CAATCATTAG
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
12 17 1.00
ACGTcount: A:0.23, C:0.00, G:0.03, T:0.73
Consensus pattern (12 bp):
TATTTTTATTAT
Found at i:449121 original size:17 final size:17
Alignment explanation
Indices: 449084--449120 Score: 51
Period size: 17 Copynumber: 2.3 Consensus size: 17
449074 TAAGGTGAAC
*
449084 ATATTATTATTATAAAA
1 ATATAATTATTATAAAA
449101 ATATAATTATT-T-AAA
1 ATATAATTATTATAAAA
449116 ATATA
1 ATATA
449121 TTTAATTTTG
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
15 8 0.42
16 1 0.05
17 10 0.53
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (17 bp):
ATATAATTATTATAAAA
Found at i:449753 original size:22 final size:22
Alignment explanation
Indices: 449728--449773 Score: 58
Period size: 22 Copynumber: 2.1 Consensus size: 22
449718 TTGAAGCGAA
* *
449728 AAATAAA-ATTTAATATTATAAT
1 AAATAAACATTGAAAATT-TAAT
449750 AAATAAACATTGAAAATTTAAT
1 AAATAAACATTGAAAATTTAAT
449772 AA
1 AA
449774 TGCAAACGAG
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
22 13 0.62
23 8 0.38
ACGTcount: A:0.61, C:0.02, G:0.02, T:0.35
Consensus pattern (22 bp):
AAATAAACATTGAAAATTTAAT
Found at i:450124 original size:20 final size:20
Alignment explanation
Indices: 450047--450124 Score: 57
Period size: 20 Copynumber: 3.6 Consensus size: 20
450037 AACCAAAATT
* *
450047 TTTAAATTTTTAATATATTA
1 TTTAAATATTTAATATATCA
* *
450067 TTTATATATTTAATATATGAACC
1 TTTAAATATTTAATATAT---CA
* *
450090 TGTAGATTAATTTAATATATCA
1 TTTA-AAT-ATTTAATATATCA
450112 TTTAAATATTTAA
1 TTTAAATATTTAA
450125 CTAAAATTCG
Statistics
Matches: 43, Mismatches: 10, Indels: 10
0.68 0.16 0.16
Matches are distributed among these distances:
20 22 0.51
21 2 0.05
22 4 0.09
23 3 0.07
24 1 0.02
25 11 0.26
ACGTcount: A:0.41, C:0.04, G:0.04, T:0.51
Consensus pattern (20 bp):
TTTAAATATTTAATATATCA
Found at i:450224 original size:22 final size:22
Alignment explanation
Indices: 450198--450239 Score: 59
Period size: 22 Copynumber: 1.9 Consensus size: 22
450188 AATTTATGGT
450198 TAAA-TGTAAAAATTTCGATTAA
1 TAAATTGTAAAAA-TTCGATTAA
*
450220 TAAATTTTAAAAATTCGATT
1 TAAATTGTAAAAATTCGATT
450240 CAATCGGTTA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
22 11 0.61
23 7 0.39
ACGTcount: A:0.48, C:0.05, G:0.07, T:0.40
Consensus pattern (22 bp):
TAAATTGTAAAAATTCGATTAA
Found at i:450293 original size:20 final size:21
Alignment explanation
Indices: 450265--450306 Score: 59
Period size: 20 Copynumber: 2.0 Consensus size: 21
450255 ATCACCCTAC
* *
450265 ATCATCGGATAA-AATATGAA
1 ATCACCGGATAATAAAATGAA
450285 ATCACCGGATAATAAAATGAA
1 ATCACCGGATAATAAAATGAA
450306 A
1 A
450307 AGACAACTTG
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
20 11 0.58
21 8 0.42
ACGTcount: A:0.52, C:0.12, G:0.14, T:0.21
Consensus pattern (21 bp):
ATCACCGGATAATAAAATGAA
Found at i:456822 original size:3 final size:3
Alignment explanation
Indices: 456807--456836 Score: 51
Period size: 3 Copynumber: 10.0 Consensus size: 3
456797 TATAATAGTA
*
456807 ATT ATT GTT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
456837 TTTTCTAAAA
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.30, C:0.00, G:0.03, T:0.67
Consensus pattern (3 bp):
ATT
Found at i:457532 original size:13 final size:14
Alignment explanation
Indices: 457502--457535 Score: 52
Period size: 15 Copynumber: 2.4 Consensus size: 14
457492 TTTAAAGAAT
457502 TTAAAATAATAATAA
1 TTAAAATAAT-ATAA
457517 TTAAAATAAT-TAA
1 TTAAAATAATATAA
457530 TTAAAA
1 TTAAAA
457536 ACAGAGGATT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
13 9 0.47
15 10 0.53
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (14 bp):
TTAAAATAATATAA
Found at i:480626 original size:17 final size:16
Alignment explanation
Indices: 480590--480625 Score: 63
Period size: 16 Copynumber: 2.2 Consensus size: 16
480580 ATATAATATT
*
480590 AAAACTTGAACTCAAA
1 AAAACTCGAACTCAAA
480606 AAAACTCGAACTCAAA
1 AAAACTCGAACTCAAA
480622 AAAA
1 AAAA
480626 AATTAAAAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
16 19 1.00
ACGTcount: A:0.61, C:0.19, G:0.06, T:0.14
Consensus pattern (16 bp):
AAAACTCGAACTCAAA
Found at i:480955 original size:24 final size:24
Alignment explanation
Indices: 480894--480945 Score: 86
Period size: 24 Copynumber: 2.2 Consensus size: 24
480884 GTTATAGTTA
* *
480894 ATTTAAATCATTTTGTTTCACTTG
1 ATTTGAATAATTTTGTTTCACTTG
480918 ATTTGAATAATTTTGTTTCACTTG
1 ATTTGAATAATTTTGTTTCACTTG
480942 ATTT
1 ATTT
480946 TATGGTTTTT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
24 26 1.00
ACGTcount: A:0.25, C:0.10, G:0.10, T:0.56
Consensus pattern (24 bp):
ATTTGAATAATTTTGTTTCACTTG
Found at i:485513 original size:41 final size:41
Alignment explanation
Indices: 485478--485563 Score: 113
Period size: 41 Copynumber: 2.1 Consensus size: 41
485468 AAACGCTGTT
*
485478 AAAGATTGTACATTAGCGGCA-TTTGTATAAAAAACGCCGCC
1 AAAGAATGTACATTAGCGG-AGTTTGTATAAAAAACGCCGCC
* * *
485519 AAAGAATGTACTTTAGTGGAGTTTGTAT-AAAAACGCCGCT
1 AAAGAATGTACATTAGCGGAGTTTGTATAAAAAACGCCGCC
485559 AAAGA
1 AAAGA
485564 CTATACTTTA
Statistics
Matches: 40, Mismatches: 4, Indels: 3
0.85 0.09 0.06
Matches are distributed among these distances:
40 17 0.43
41 23 0.57
ACGTcount: A:0.38, C:0.15, G:0.21, T:0.26
Consensus pattern (41 bp):
AAAGAATGTACATTAGCGGAGTTTGTATAAAAAACGCCGCC
Found at i:485618 original size:41 final size:41
Alignment explanation
Indices: 485509--485830 Score: 405
Period size: 41 Copynumber: 7.9 Consensus size: 41
485499 TTTGTATAAA
* * * * *
485509 AAACGCCGCCAAAGAAT-GTACTTTAGTGGAGTTTGTATAA
1 AAACGCCGCTAAAGACTCGTACTTTAGTGGCGTTTTTATAC
* *
485549 AAACGCCGCTAAAGACT-ATACTTTAGTGGCGTTTTTAGAC
1 AAACGCCGCTAAAGACTCGTACTTTAGTGGCGTTTTTATAC
** * * *
485589 AAACGCTACTATAGACTCGTACTTTAGTGGTGTTTTTAGAC
1 AAACGCCGCTAAAGACTCGTACTTTAGTGGCGTTTTTATAC
* * *
485630 AAACTCCGCTATAGACTCGTACTTTAGTGGCGTTTTTGTAC
1 AAACGCCGCTAAAGACTCGTACTTTAGTGGCGTTTTTATAC
* *
485671 AAATGCCGCTATAGACTCGTACTTTAGTGGCGTTTTTATAC
1 AAACGCCGCTAAAGACTCGTACTTTAGTGGCGTTTTTATAC
* *
485712 AAACGCCGCTACAGACTCGTACTTTAGTGGCATTTTTATAC
1 AAACGCCGCTAAAGACTCGTACTTTAGTGGCGTTTTTATAC
* *
485753 AAACGCCGCTAAAGACTCGTACTTTAATGGCGTTTGTGTTTAC
1 AAACGCCGCTAAAGACTCGTACTTTAGTGGCGTTT-T-TATAC
* *
485796 AAACGCCGCTAAAGACTTGTATTTTAGTGGCGTTT
1 AAACGCCGCTAAAGACTCGTACTTTAGTGGCGTTT
485831 GTAATAGACT
Statistics
Matches: 248, Mismatches: 31, Indels: 3
0.88 0.11 0.01
Matches are distributed among these distances:
40 47 0.19
41 164 0.66
42 1 0.00
43 36 0.15
ACGTcount: A:0.27, C:0.20, G:0.20, T:0.33
Consensus pattern (41 bp):
AAACGCCGCTAAAGACTCGTACTTTAGTGGCGTTTTTATAC
Found at i:489457 original size:43 final size:42
Alignment explanation
Indices: 489405--489650 Score: 251
Period size: 42 Copynumber: 5.8 Consensus size: 42
489395 TAATGAGCTT
* *
489405 TTTTGCGGCGTTTGTATCAAAAAACGCCGCTATAGATATGAGC
1 TTTTGCGGCGTTTGT-TCCAAAAACGCCGCTATAGATATGACC
489448 TTTTGCGGCGTTTGTATCCAAAAACGCCGCTATAGATATGACC
1 TTTTGCGGCGTTTGT-TCCAAAAACGCCGCTATAGATATGACC
* * * *
489491 ATTTGCGGTGTTTATTCCAAAAACGTCGCTATAGATATGACC
1 TTTTGCGGCGTTTGTTCCAAAAACGCCGCTATAGATATGACC
* * * * *
489533 TTTTGCGACGTTTGTTCCAAAAATGCCACAATAGATCTGACC
1 TTTTGCGGCGTTTGTTCCAAAAACGCCGCTATAGATATGACC
* * ** * * * **
489575 TATTGCGGTGTTTGTTGGACAAACGCCGCTAAATATCAACACC
1 TTTTGCGGCGTTTGTTCCAAAAACGCCGCTATAGAT-ATGACC
* *
489618 TATTGCGGCGTTTG-TCCAACAAACGCCACTATA
1 TTTTGCGGCGTTTGTTCCAA-AAACGCCGCTATA
489651 TATCGTTAAC
Statistics
Matches: 166, Mismatches: 35, Indels: 4
0.81 0.17 0.02
Matches are distributed among these distances:
42 86 0.52
43 80 0.48
ACGTcount: A:0.28, C:0.22, G:0.20, T:0.30
Consensus pattern (42 bp):
TTTTGCGGCGTTTGTTCCAAAAACGCCGCTATAGATATGACC
Found at i:489536 original size:85 final size:84
Alignment explanation
Indices: 489406--489587 Score: 240
Period size: 85 Copynumber: 2.1 Consensus size: 84
489396 AATGAGCTTT
* * * *
489406 TTTGCGGCGTTTGTATCAAAAAACGCCGCTATAGATATGAGCTTTTGCGGCGTTTGTATCCAAAA
1 TTTGCGGTGTTTATATCAAAAAACGCCGCTATAGATATGACCTTTTGCGACGTTTGT-TCCAAAA
* *
489471 ACGCCGCTATAGATATGACC
65 ACGCCACAATAGATATGACC
* *
489491 ATTTGCGGTGTTTAT-TCCAAAAACGTCGCTATAGATATGACCTTTTGCGACGTTTGTTCCAAAA
1 -TTTGCGGTGTTTATATCAAAAAACGCCGCTATAGATATGACCTTTTGCGACGTTTGTTCCAAAA
* *
489555 ATGCCACAATAGATCTGACC
65 ACGCCACAATAGATATGACC
489575 TATTGCGGTGTTT
1 T-TTGCGGTGTTT
489588 GTTGGACAAA
Statistics
Matches: 85, Mismatches: 10, Indels: 4
0.86 0.10 0.04
Matches are distributed among these distances:
83 1 0.01
84 34 0.40
85 38 0.45
86 12 0.14
ACGTcount: A:0.26, C:0.20, G:0.21, T:0.32
Consensus pattern (84 bp):
TTTGCGGTGTTTATATCAAAAAACGCCGCTATAGATATGACCTTTTGCGACGTTTGTTCCAAAAA
CGCCACAATAGATATGACC
Found at i:489636 original size:84 final size:84
Alignment explanation
Indices: 489426--489691 Score: 221
Period size: 85 Copynumber: 3.1 Consensus size: 84
489416 TTGTATCAAA
* ** * * * *
489426 AAACGCCGCTATAGATATGAGCTTTTGCGGCGTTTGTATCCAAAAACGCCGCTATAGATATGACC
1 AAACGCCGCTAAAGATAACACCTATTGCGGCGTTTGT-TCCAAAAACGCCACTATAGATCTGACC
* *
489491 -ATTTGCGGTGTTTATTCCAA
65 TA-TTGCGGTGTTTATTGCAC
* * ** * * * *
489511 AAACGTCGCTATAGATATGACCTTTTGCGACGTTTGTTCCAAAAATGCCACAATAGATCTGACCT
1 AAACGCCGCTAAAGATAACACCTATTGCGGCGTTTGTTCCAAAAACGCCACTATAGATCTGACCT
* *
489576 ATTGCGGTGTTTGTTGGAC
66 ATTGCGGTGTTTATTGCAC
* * *
489595 AAACGCCGCTAAATATCAACACCTATTGCGGCGTTTG-TCCAACAAACGCCACTATATATCGTTA
1 AAACGCCGCTAAAGAT-AACACCTATTGCGGCGTTTGTTCCAA-AAACGCCACTATAGATC-TGA
* * * *
489659 ACTATTGCGGCGTTTTTTGTTACC
63 CCTATTGCGGTGTTTATTG-CA-C
489683 AAACGCCGC
1 AAACGCCGC
489692 GAACTTTAGC
Statistics
Matches: 149, Mismatches: 26, Indels: 9
0.81 0.14 0.05
Matches are distributed among these distances:
84 55 0.37
85 65 0.44
86 18 0.12
87 1 0.01
88 10 0.07
ACGTcount: A:0.27, C:0.23, G:0.20, T:0.30
Consensus pattern (84 bp):
AAACGCCGCTAAAGATAACACCTATTGCGGCGTTTGTTCCAAAAACGCCACTATAGATCTGACCT
ATTGCGGTGTTTATTGCAC
Found at i:489654 original size:43 final size:43
Alignment explanation
Indices: 489572--489673 Score: 114
Period size: 43 Copynumber: 2.4 Consensus size: 43
489562 AATAGATCTG
* *** *
489572 ACCTATTGCGGTGTTTGTTGGACAAACGCCGCTAAATATCAAC
1 ACCTATTGCGGCGTTTGTCCAACAAACGCCACTAAATATCAAC
* ***
489615 ACCTATTGCGGCGTTTGTCCAACAAACGCCACTATATATCGTT
1 ACCTATTGCGGCGTTTGTCCAACAAACGCCACTAAATATCAAC
*
489658 AACTATTGCGGCGTTT
1 ACCTATTGCGGCGTTT
489674 TTTGTTACCA
Statistics
Matches: 49, Mismatches: 10, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
43 49 1.00
ACGTcount: A:0.25, C:0.25, G:0.20, T:0.30
Consensus pattern (43 bp):
ACCTATTGCGGCGTTTGTCCAACAAACGCCACTAAATATCAAC
Found at i:495763 original size:21 final size:21
Alignment explanation
Indices: 495646--495783 Score: 59
Period size: 21 Copynumber: 6.7 Consensus size: 21
495636 ACGCGAAATA
**
495646 AAAATCGCAACGCGA-TCCCC
1 AAAATCGCAACGCGATTTTCC
* ** *
495666 AGAATCGCAAATC-AGTTTCC
1 AAAATCGCAACGCGATTTTCC
*
495686 AAAATCGCAACGCGATTCTT-G
1 AAAATCGCAACGCGATT-TTCC
* * ** *
495707 AAAATCGCGATGCGATAGTAC
1 AAAATCGCAACGCGATTTTCC
* * **
495728 ATATTCGCATTGCGATTTTCC
1 AAAATCGCAACGCGATTTTCC
* * * *
495749 ATAATCGCAACGCGAATAT-G
1 AAAATCGCAACGCGATTTTCC
495769 AAAATCGCAACGCGA
1 AAAATCGCAACGCGA
495784 ACACATAAAT
Statistics
Matches: 85, Mismatches: 29, Indels: 8
0.70 0.24 0.07
Matches are distributed among these distances:
19 1 0.01
20 38 0.45
21 44 0.52
22 2 0.02
ACGTcount: A:0.35, C:0.25, G:0.18, T:0.22
Consensus pattern (21 bp):
AAAATCGCAACGCGATTTTCC
Found at i:495845 original size:20 final size:20
Alignment explanation
Indices: 495751--496119 Score: 458
Period size: 20 Copynumber: 18.4 Consensus size: 20
495741 GATTTTCCAT
* ** *
495751 AATCGCAACGCGAATATGAA
1 AATCGCAACGCGTATCCGTA
* *
495771 AATCGCAACGCG-AACACATA
1 AATCGCAACGCGTATC-CGTA
495791 AATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
*
495811 AATCGCAACGTGTATCCGTA
1 AATCGCAACGCGTATCCGTA
**
495831 AATCGCAACGCGTATGGGTA
1 AATCGCAACGCGTATCCGTA
*
495851 AATCGCAATGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
*
495871 TATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
495891 AATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
* *
495911 AACCGCAACGTGTATCCGTA
1 AATCGCAACGCGTATCCGTA
495931 AATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
*
495951 AATCGCAATGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
495971 AATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
*
495991 AATCGCAACG-ATAATCCGTA
1 AATCGCAACGCGT-ATCCGTA
496011 AATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
*
496031 AATCGCAACG-ATAATCCGTA
1 AATCGCAACGCGT-ATCCGTA
* * *
496051 AATCGCAACGAGAATCTGTA
1 AATCGCAACGCGTATCCGTA
*
496071 AATCGCAACG-ATAATCCGTA
1 AATCGCAACGCGT-ATCCGTA
* * *
496091 AATCGCAACGAGAATCTGTA
1 AATCGCAACGCGTATCCGTA
*
496111 AATCACAAC
1 AATCGCAAC
496120 ACTGAAATTT
Statistics
Matches: 305, Mismatches: 36, Indels: 16
0.85 0.10 0.04
Matches are distributed among these distances:
19 3 0.01
20 299 0.98
21 3 0.01
ACGTcount: A:0.35, C:0.26, G:0.19, T:0.20
Consensus pattern (20 bp):
AATCGCAACGCGTATCCGTA
Found at i:497044 original size:19 final size:19
Alignment explanation
Indices: 497022--497328 Score: 376
Period size: 19 Copynumber: 17.4 Consensus size: 19
497012 CGGAAAATAC
*
497022 AATCGCAACGCGAAATGAA
1 AATCGCAATGCGAAATGAA
*
497041 AATCCCAA--C---ATGAA
1 AATCGCAATGCGAAATGAA
497055 AATCGCAATGCAGAAATGAA
1 AATCGCAATGC-GAAATGAA
*
497075 AATCGCAA--CG--A-GAG
1 AATCGCAATGCGAAATGAA
497089 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
497108 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
*
497127 AATCGCAA--CG--A-GAG
1 AATCGCAATGCGAAATGAA
497141 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
497160 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
*
497179 AATCGCAA--CGACA-G--
1 AATCGCAATGCGAAATGAA
*
497193 AATCGCAATGCGAAATTAA
1 AATCGCAATGCGAAATGAA
497212 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
497231 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
497250 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
497269 AATCGCAA--CGAAA-G--
1 AATCGCAATGCGAAATGAA
497283 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
497302 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
497321 AATCGCAA
1 AATCGCAA
497329 CGAGATAATC
Statistics
Matches: 252, Mismatches: 10, Indels: 52
0.80 0.03 0.17
Matches are distributed among these distances:
14 48 0.19
15 2 0.01
16 16 0.06
17 14 0.06
18 3 0.01
19 156 0.62
20 13 0.05
ACGTcount: A:0.47, C:0.18, G:0.21, T:0.14
Consensus pattern (19 bp):
AATCGCAATGCGAAATGAA
Found at i:497137 original size:52 final size:52
Alignment explanation
Indices: 497050--497328 Score: 388
Period size: 52 Copynumber: 5.2 Consensus size: 52
497040 AAATCCCAAC
497050 ATGAAAATCGCAATGCAGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAA
1 ATGAAAATCGCAATGC-GAAATGAAAATCGCAACGAGAGAATCGCAATGCGAA
497103 ATGAAAATCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAA
1 ATGAAAATCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAA
*
497155 ATGAAAATCGCAATGCGAAATGAAAATCGCAACGACAGAATCGCAATGCGAA
1 ATGAAAATCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAA
* *
497207 ATTAAAATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAAAATCGCAATGCGAA
1 ATGAAAATCGCAATGCGAAATGAAAATCGCAA--CG--A-GAGAATCGCAATGCGAA
*
497264 ATGAAAATCGCAA--CGAAA-G--AATCGCAATGCGAAATGAAAATCGCAATGCGAA
1 ATGAAAATCGCAATGCGAAATGAAAATCGCAA--CG--A-GAGAATCGCAATGCGAA
497316 ATGAAAATCGCAA
1 ATGAAAATCGCAA
497329 CGAGATAATC
Statistics
Matches: 216, Mismatches: 5, Indels: 11
0.93 0.02 0.05
Matches are distributed among these distances:
52 164 0.76
53 16 0.07
54 3 0.01
55 5 0.02
56 1 0.00
57 27 0.12
ACGTcount: A:0.47, C:0.17, G:0.21, T:0.14
Consensus pattern (52 bp):
ATGAAAATCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAA
Found at i:497173 original size:71 final size:71
Alignment explanation
Indices: 497089--497328 Score: 373
Period size: 71 Copynumber: 3.4 Consensus size: 71
497079 GCAACGAGAG
*
497089 AATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGA
1 AATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAAAATCGCAACGAAAGAATCGCAATGCGA
497154 AATGAA
66 AATGAA
* *
497160 AATCGCAATGCGAAATGAAAATCGCAA--CGACA-G--AATCGCAATGCGAAATTAAAATCGCAA
1 AATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAAAATCGCAA--CG-AA--AGAATCGCAA
497220 TGCGAAATGAA
61 TGCGAAATGAA
497231 AATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAAAATCGCAACGAAAGAATCGCAATGCGA
1 AATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAAAATCGCAACGAAAGAATCGCAATGCGA
497296 AATGAA
66 AATGAA
497302 AATCGCAATGCGAAATGAAAATCGCAA
1 AATCGCAATGCGAAATGAAAATCGCAA
497329 CGAGATAATC
Statistics
Matches: 154, Mismatches: 5, Indels: 20
0.86 0.03 0.11
Matches are distributed among these distances:
66 8 0.05
68 3 0.02
69 5 0.03
71 121 0.79
73 6 0.04
74 3 0.02
76 8 0.05
ACGTcount: A:0.47, C:0.17, G:0.21, T:0.15
Consensus pattern (71 bp):
AATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAAAATCGCAACGAAAGAATCGCAATGCGA
AATGAA
Found at i:497329 original size:52 final size:55
Alignment explanation
Indices: 497022--497350 Score: 332
Period size: 52 Copynumber: 6.3 Consensus size: 55
497012 CGGAAAATAC
* *
497022 AATCGCAACGCGAAATGAAAATCCCAA--C---ATGAAAATCGCAATGCAGAAATGAA
1 AATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAAAATCGCAA-GC-GAAATG-A
*
497075 AATCGCAA--CG--A-GAGAATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAAAATCGCAA-GCGAAATG-A
*
497127 AATCGCAA--CG--A-GAGAATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAAAATCGCAA-GCGAAATG-A
* *
497179 AATCGCAA--CGACA-G--AATCGCAATGCGAAATTAAAATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAAAATCGCAA-GCGAAATG-A
497231 AATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAAAATCGCAA-CGAAA-G-
1 AATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAAAATCGCAAGCGAAATGA
*
497283 AATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAAAATCGCAA-CGAGAT--
1 AATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAAAATCGCAAGCGAAATGA
497335 AATCGCAATGCGAAAT
1 AATCGCAATGCGAAAT
497351 TATAAACGCA
Statistics
Matches: 257, Mismatches: 6, Indels: 27
0.89 0.02 0.09
Matches are distributed among these distances:
48 9 0.04
49 1 0.00
50 1 0.00
51 2 0.01
52 181 0.70
53 24 0.09
54 7 0.03
55 6 0.02
57 26 0.10
ACGTcount: A:0.47, C:0.18, G:0.21, T:0.14
Consensus pattern (55 bp):
AATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAAAATCGCAAGCGAAATGA
Found at i:497404 original size:142 final size:142
Alignment explanation
Indices: 497022--497366 Score: 526
Period size: 142 Copynumber: 2.5 Consensus size: 142
497012 CGGAAAATAC
* * *
497022 AATCGCAACGCGAAATGAAAATCCCAACATGA-A-AATCGCAATGCAGAAATGAAAATCGCAA--
1 AATCGCAATGCGAAATGAAAATCGCAAC--GACAGAATCGCAATGC-GAAATTAAAATCGCAATG
* *
497083 CG--A-GAGAATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAAAATCGCAACGAGAGAATC
63 CGAAATGAAAATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAAAATCGCAACGAAAGAATC
497145 GCAATGCGAAATGAA
128 GCAATGCGAAATGAA
497160 AATCGCAATGCGAAATGAAAATCGCAACGACAGAATCGCAATGCGAAATTAAAATCGCAATGCGA
1 AATCGCAATGCGAAATGAAAATCGCAACGACAGAATCGCAATGCGAAATTAAAATCGCAATGCGA
497225 AATGAAAATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAAAATCGCAACGAAAGAATCGCA
66 AATGAAAATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAAAATCGCAACGAAAGAATCGCA
497290 ATGCGAAATGAA
131 ATGCGAAATGAA
* * *
497302 AATCGCAATGCGAAATGAAAATCGCAACGAGATAATCGCAATGCGAAATTATAAA-CGCATTGCG
1 AATCGCAATGCGAAATGAAAATCGCAACGACAGAATCGCAATGCGAAATTA-AAATCGCAATGCG
497366 A
65 A
497367 TTTTCATTTC
Statistics
Matches: 191, Mismatches: 8, Indels: 12
0.91 0.04 0.06
Matches are distributed among these distances:
136 2 0.01
137 16 0.08
138 37 0.19
139 2 0.01
141 1 0.01
142 130 0.68
143 3 0.02
ACGTcount: A:0.46, C:0.18, G:0.21, T:0.15
Consensus pattern (142 bp):
AATCGCAATGCGAAATGAAAATCGCAACGACAGAATCGCAATGCGAAATTAAAATCGCAATGCGA
AATGAAAATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAAAATCGCAACGAAAGAATCGCA
ATGCGAAATGAA
Found at i:497465 original size:19 final size:19
Alignment explanation
Indices: 497357--497457 Score: 142
Period size: 19 Copynumber: 5.6 Consensus size: 19
497347 AAATTATAAA
497357 CGCATTGCGATTTTCATTT
1 CGCATTGCGATTTTCATTT
497376 CCGCATTGCGA-TTTCATTT
1 -CGCATTGCGATTTTCATTT
*
497395 CGCATTGCGA--TTC-TCT
1 CGCATTGCGATTTTCATTT
497411 CG--TTGCGATTTTCATTT
1 CGCATTGCGATTTTCATTT
497428 CGCATTGCGATTTTCATTT
1 CGCATTGCGATTTTCATTT
497447 CGCATTGCGAT
1 CGCATTGCGAT
497458 AGTCATTTTG
Statistics
Matches: 74, Mismatches: 2, Indels: 11
0.85 0.02 0.13
Matches are distributed among these distances:
14 6 0.08
16 7 0.09
17 7 0.09
18 10 0.14
19 34 0.46
20 10 0.14
ACGTcount: A:0.15, C:0.24, G:0.18, T:0.44
Consensus pattern (19 bp):
CGCATTGCGATTTTCATTT
Found at i:497465 original size:38 final size:37
Alignment explanation
Indices: 497357--497457 Score: 140
Period size: 33 Copynumber: 2.8 Consensus size: 37
497347 AAATTATAAA
497357 CGCATTGCGATTTTCATTTCCGCATTGCGATTTCATTT
1 CGCATTGCGATTTTCATTT-CGCATTGCGATTTCATTT
*
497395 CGCATTGCGA--TTC-TCTCG--TTGCGATTTTCATTT
1 CGCATTGCGATTTTCATTTCGCATTGCGA-TTTCATTT
497428 CGCATTGCGATTTTCATTTCGCATTGCGAT
1 CGCATTGCGATTTTCATTTCGCATTGCGAT
497458 AGTCATTTTG
Statistics
Matches: 55, Mismatches: 2, Indels: 13
0.79 0.03 0.19
Matches are distributed among these distances:
32 6 0.11
33 18 0.33
34 2 0.04
35 5 0.09
36 7 0.13
37 1 0.02
38 16 0.29
ACGTcount: A:0.15, C:0.24, G:0.18, T:0.44
Consensus pattern (37 bp):
CGCATTGCGATTTTCATTTCGCATTGCGATTTCATTT
Found at i:497581 original size:14 final size:14
Alignment explanation
Indices: 497562--497598 Score: 65
Period size: 14 Copynumber: 2.6 Consensus size: 14
497552 CATCAATTAC
497562 ACAAATCAACTTTT
1 ACAAATCAACTTTT
*
497576 ACAAATCATCTTTT
1 ACAAATCAACTTTT
497590 ACAAATCAA
1 ACAAATCAA
497599 TTAAACAATC
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.46, C:0.22, G:0.00, T:0.32
Consensus pattern (14 bp):
ACAAATCAACTTTT
Found at i:499592 original size:14 final size:14
Alignment explanation
Indices: 499573--499629 Score: 60
Period size: 14 Copynumber: 3.7 Consensus size: 14
499563 GCGAAATTAA
*
499573 AATCGCAACGACAG
1 AATCGCAACGAAAG
499587 AATCGCAATGCGAAATG
1 AATCGCAA--CGAAA-G
499604 AAAATCGCAACGAAAG
1 --AATCGCAACGAAAG
499620 AATCGCAACG
1 AATCGCAACG
499630 CGAAATGAAA
Statistics
Matches: 37, Mismatches: 1, Indels: 10
0.77 0.02 0.21
Matches are distributed among these distances:
14 18 0.49
16 5 0.14
17 6 0.16
19 8 0.22
ACGTcount: A:0.46, C:0.23, G:0.21, T:0.11
Consensus pattern (14 bp):
AATCGCAACGAAAG
Found at i:499600 original size:33 final size:33
Alignment explanation
Indices: 499554--499646 Score: 159
Period size: 33 Copynumber: 2.8 Consensus size: 33
499544 GCGAAACCAA
* *
499554 AATCGCAACGCGAAATTAAAATCGCAACGACAG
1 AATCGCAACGCGAAATGAAAATCGCAACGAAAG
*
499587 AATCGCAATGCGAAATGAAAATCGCAACGAAAG
1 AATCGCAACGCGAAATGAAAATCGCAACGAAAG
499620 AATCGCAACGCGAAATGAAAATCGCAA
1 AATCGCAACGCGAAATGAAAATCGCAA
499647 TGCGATTTTG
Statistics
Matches: 56, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
33 56 1.00
ACGTcount: A:0.47, C:0.22, G:0.19, T:0.12
Consensus pattern (33 bp):
AATCGCAACGCGAAATGAAAATCGCAACGAAAG
Found at i:499611 original size:19 final size:19
Alignment explanation
Indices: 499517--499651 Score: 119
Period size: 19 Copynumber: 7.6 Consensus size: 19
499507 TAGTTTACTT
* *
499517 TCGCAACACGAAACTTAAAA
1 TCGCAACGCGAAA-TGAAAA
**
499537 TCGCAACGCGAAACCAAAA
1 TCGCAACGCGAAATGAAAA
*
499556 TCGCAACGCGAAATTAAAA
1 TCGCAACGCGAAATGAAAA
*
499575 TCGCAA--CGACA-G--AA
1 TCGCAACGCGAAATGAAAA
*
499589 TCGCAATGCGAAATGAAAA
1 TCGCAACGCGAAATGAAAA
499608 TCGCAA--CGAAA-G--AA
1 TCGCAACGCGAAATGAAAA
499622 TCGCAACGCGAAATGAAAA
1 TCGCAACGCGAAATGAAAA
*
499641 TCGCAATGCGA
1 TCGCAACGCGA
499652 TTTTGGTTTC
Statistics
Matches: 96, Mismatches: 9, Indels: 21
0.76 0.07 0.17
Matches are distributed among these distances:
14 16 0.17
16 10 0.10
17 11 0.11
19 47 0.49
20 12 0.12
ACGTcount: A:0.46, C:0.24, G:0.19, T:0.12
Consensus pattern (19 bp):
TCGCAACGCGAAATGAAAA
Found at i:499669 original size:19 final size:19
Alignment explanation
Indices: 499647--499775 Score: 125
Period size: 19 Copynumber: 7.3 Consensus size: 19
499637 AAAATCGCAA
499647 TGCGATTTTGGTTTCGCGT
1 TGCGATTTTGGTTTCGCGT
*
499666 TGCGATCTT-G--T--CGT
1 TGCGATTTTGGTTTCGCGT
499680 TGCGATTTTGGTTTCGCGT
1 TGCGATTTTGGTTTCGCGT
*
499699 TGCGATTCT-G--T--CGT
1 TGCGATTTTGGTTTCGCGT
**
499713 TGCGATTTTCATTTCGCGT
1 TGCGATTTTGGTTTCGCGT
499732 TGCGATTTTGGTTTCGCGT
1 TGCGATTTTGGTTTCGCGT
* *
499751 TGCGATTTTAAGTTTCGTGT
1 TGCGATTTT-GGTTTCGCGT
499771 TGCGA
1 TGCGA
499776 AAGTAAACTA
Statistics
Matches: 90, Mismatches: 9, Indels: 21
0.75 0.08 0.17
Matches are distributed among these distances:
14 22 0.24
15 1 0.01
16 2 0.02
17 2 0.02
18 2 0.02
19 48 0.53
20 13 0.14
ACGTcount: A:0.09, C:0.17, G:0.29, T:0.46
Consensus pattern (19 bp):
TGCGATTTTGGTTTCGCGT
Found at i:499689 original size:33 final size:33
Alignment explanation
Indices: 499647--499738 Score: 150
Period size: 33 Copynumber: 2.8 Consensus size: 33
499637 AAAATCGCAA
499647 TGCGATTTTGGTTTCGCGTTGCGA-TCTTGTCGT
1 TGCGATTTTGGTTTCGCGTTGCGATTC-TGTCGT
499680 TGCGATTTTGGTTTCGCGTTGCGATTCTGTCGT
1 TGCGATTTTGGTTTCGCGTTGCGATTCTGTCGT
**
499713 TGCGATTTTCATTTCGCGTTGCGATT
1 TGCGATTTTGGTTTCGCGTTGCGATT
499739 TTGGTTTCGC
Statistics
Matches: 56, Mismatches: 2, Indels: 2
0.93 0.03 0.03
Matches are distributed among these distances:
33 54 0.96
34 2 0.04
ACGTcount: A:0.08, C:0.18, G:0.28, T:0.46
Consensus pattern (33 bp):
TGCGATTTTGGTTTCGCGTTGCGATTCTGTCGT
Found at i:500016 original size:93 final size:93
Alignment explanation
Indices: 499819--500381 Score: 1071
Period size: 93 Copynumber: 6.1 Consensus size: 93
499809 TTGAATGGAT
499819 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTG-TAAAGAATACAC
1 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
499883 AGTTTAGCAGAATTGGCAGCAACCGAAC
66 AGTTTAGCAGAATTGGCAGCAACCGAAC
499911 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
1 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
499976 AGTTTAGCAGAATTGGCAGCAACCGAAC
66 AGTTTAGCAGAATTGGCAGCAACCGAAC
500004 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
1 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
500069 AGTTTAGCAGAATTGGCAGCAACCGAAC
66 AGTTTAGCAGAATTGGCAGCAACCGAAC
500097 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAA-A-TATTTCACAGTGTTAAAGAATACAC
1 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
500160 AGTTTAGCAGAATTGGCAGCAACCGAAC
66 AGTTTAGCAGAATTGGCAGCAACCGAAC
500188 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATA-TATTTCACAGTGTTAAAGAATACAC
1 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
500252 AGTTTAGCAGAATTGGCAGCAACCGAAC
66 AGTTTAGCAGAATTGGCAGCAACCGAAC
*
500280 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATATAC
1 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
* *
500345 AGTTTAGCAGAATTGGCAGCAACTGAAT
66 AGTTTAGCAGAATTGGCAGCAACCGAAC
500373 AAATTTACT
1 AAATTTACT
500382 AAGCAATCTA
Statistics
Matches: 465, Mismatches: 3, Indels: 5
0.98 0.01 0.01
Matches are distributed among these distances:
91 90 0.19
92 146 0.31
93 229 0.49
ACGTcount: A:0.47, C:0.18, G:0.13, T:0.22
Consensus pattern (93 bp):
AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
AGTTTAGCAGAATTGGCAGCAACCGAAC
Found at i:500314 original size:276 final size:278
Alignment explanation
Indices: 499819--500381 Score: 1069
Period size: 276 Copynumber: 2.0 Consensus size: 278
499809 TTGAATGGAT
499819 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTAAAGAATACACA
1 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTAAAGAATACACA
499884 GTTTAGCAGAATTGGCAGCAACCGAACAAATTTACTTTCAACCAAAAGACAAAACAAAGACAAAT
66 GTTTAGCAGAATTGGCAGCAACCGAACAAATTTACTTTCAACCAAAAGACAAAACAAAGACAAAT
499949 ACTATTTCACAGTGTTAAAGAATACACAGTTTAGCAGAATTGGCAGCAACCGAACAAATTTACTT
131 ACTATTTCACAGTGTTAAAGAATACACAGTTTAGCAGAATTGGCAGCAACCGAACAAATTTACTT
500014 TCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTTTAGCAG
196 TCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTTTAGCAG
500079 AATTGGCAGCAACCGAAC
261 AATTGGCAGCAACCGAAC
500097 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAA-A-TATTTCACAGTGTTAAAGAATACAC
1 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTG-TAAAGAATACAC
500160 AGTTTAGCAGAATTGGCAGCAACCGAACAAATTTACTTTCAACCAAAAGACAAAACAAAGACAAA
65 AGTTTAGCAGAATTGGCAGCAACCGAACAAATTTACTTTCAACCAAAAGACAAAACAAAGACAAA
500225 TA-TATTTCACAGTGTTAAAGAATACACAGTTTAGCAGAATTGGCAGCAACCGAACAAATTTACT
130 TACTATTTCACAGTGTTAAAGAATACACAGTTTAGCAGAATTGGCAGCAACCGAACAAATTTACT
*
500289 TTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATATACAGTTTAGCA
195 TTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTTTAGCA
* *
500354 GAATTGGCAGCAACTGAAT
260 GAATTGGCAGCAACCGAAC
500373 AAATTTACT
1 AAATTTACT
500382 AAGCAATCTA
Statistics
Matches: 281, Mismatches: 3, Indels: 4
0.98 0.01 0.01
Matches are distributed among these distances:
276 164 0.58
277 80 0.28
278 37 0.13
ACGTcount: A:0.47, C:0.18, G:0.13, T:0.22
Consensus pattern (278 bp):
AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTAAAGAATACACA
GTTTAGCAGAATTGGCAGCAACCGAACAAATTTACTTTCAACCAAAAGACAAAACAAAGACAAAT
ACTATTTCACAGTGTTAAAGAATACACAGTTTAGCAGAATTGGCAGCAACCGAACAAATTTACTT
TCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTTTAGCAG
AATTGGCAGCAACCGAAC
Found at i:502103 original size:14 final size:14
Alignment explanation
Indices: 502084--502173 Score: 81
Period size: 14 Copynumber: 5.7 Consensus size: 14
502074 TTGAAATGAA
502084 AATCGCAACGAGAG
1 AATCGCAACGAGAG
502098 AATCGCAACGCGAGATG
1 AATCGCAA--CGAGA-G
502115 ACAATCGCAACGAGAG
1 --AATCGCAACGAGAG
*
502131 AATCGCAACGCGAAATGAA
1 AATCGCAA--CG--A-GAG
502150 AATCGCAACGAGAG
1 AATCGCAACGAGAG
502164 AATCGCAACG
1 AATCGCAACG
502174 CGAAATGAAA
Statistics
Matches: 64, Mismatches: 2, Indels: 20
0.74 0.02 0.23
Matches are distributed among these distances:
14 28 0.44
15 1 0.02
16 8 0.12
17 8 0.12
18 1 0.02
19 18 0.28
ACGTcount: A:0.42, C:0.23, G:0.26, T:0.09
Consensus pattern (14 bp):
AATCGCAACGAGAG
Found at i:502121 original size:33 final size:33
Alignment explanation
Indices: 502076--502190 Score: 212
Period size: 33 Copynumber: 3.5 Consensus size: 33
502066 TCTTTTGGTT
502076 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
1 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
* *
502109 GAGATGACAATCGCAACGAGAGAATCGCAACGC
1 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
502142 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
1 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
502175 GAAATGAAAATCGCAA
1 GAAATGAAAATCGCAA
502191 TGCGATTTTG
Statistics
Matches: 78, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
33 78 1.00
ACGTcount: A:0.45, C:0.21, G:0.24, T:0.10
Consensus pattern (33 bp):
GAAATGAAAATCGCAACGAGAGAATCGCAACGC
Found at i:502122 original size:19 final size:18
Alignment explanation
Indices: 502083--502195 Score: 88
Period size: 19 Copynumber: 6.8 Consensus size: 18
502073 GTTGAAATGA
502083 AAATCGCAA--CGAGA-G
1 AAATCGCAACGCGAGATG
502098 -AATCGCAACGCGAGATG
1 AAATCGCAACGCGAGATG
502115 ACAATCGCAA--CGAGA-G
1 A-AATCGCAACGCGAGATG
*
502131 -AATCGCAACGCGAAATG
1 AAATCGCAACGCGAGATG
502148 AAAATCGCAA--CGAGA-G
1 -AAATCGCAACGCGAGATG
*
502164 -AATCGCAACGCGAAATG
1 AAATCGCAACGCGAGATG
*
502181 AAAATCGCAATGCGA
1 -AAATCGCAACGCGA
502196 TTTTGGTTTC
Statistics
Matches: 79, Mismatches: 4, Indels: 26
0.72 0.04 0.24
Matches are distributed among these distances:
14 24 0.30
16 15 0.19
17 12 0.15
19 28 0.35
ACGTcount: A:0.43, C:0.22, G:0.25, T:0.10
Consensus pattern (18 bp):
AAATCGCAACGCGAGATG
Found at i:502226 original size:14 final size:14
Alignment explanation
Indices: 502207--502261 Score: 56
Period size: 14 Copynumber: 3.6 Consensus size: 14
502197 TTTGGTTTCG
502207 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
*
502221 CGTTGCGATTTTCATTTCG
1 CGTTGCGA--TTC---TCT
502240 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
502254 CGTTGCGA
1 CGTTGCGA
502262 CAGTCATTCT
Statistics
Matches: 34, Mismatches: 2, Indels: 10
0.74 0.04 0.22
Matches are distributed among these distances:
14 18 0.53
16 3 0.09
17 3 0.09
19 10 0.29
ACGTcount: A:0.09, C:0.25, G:0.24, T:0.42
Consensus pattern (14 bp):
CGTTGCGATTCTCT
Found at i:502239 original size:33 final size:33
Alignment explanation
Indices: 502191--502261 Score: 124
Period size: 33 Copynumber: 2.2 Consensus size: 33
502181 AAAATCGCAA
**
502191 TGCGATTTTGGTTTCGCGTTGCGATTCTCTCGT
1 TGCGATTTTCATTTCGCGTTGCGATTCTCTCGT
502224 TGCGATTTTCATTTCGCGTTGCGATTCTCTCGT
1 TGCGATTTTCATTTCGCGTTGCGATTCTCTCGT
502257 TGCGA
1 TGCGA
502262 CAGTCATTCT
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
33 36 1.00
ACGTcount: A:0.08, C:0.23, G:0.25, T:0.44
Consensus pattern (33 bp):
TGCGATTTTCATTTCGCGTTGCGATTCTCTCGT
Found at i:502269 original size:33 final size:33
Alignment explanation
Indices: 502202--502283 Score: 119
Period size: 33 Copynumber: 2.5 Consensus size: 33
502192 GCGATTTTGG
***
502202 TTTCGCGTTGCGATTCTCTCGTTGCGATTTTCA
1 TTTCGCGTTGCGATTCTCTCGTTGCGACAGTCA
502235 TTTCGCGTTGCGATTCTCTCGTTGCGACAGTCA
1 TTTCGCGTTGCGATTCTCTCGTTGCGACAGTCA
*
502268 TTCTCTCGTTGCGATT
1 TT-TCGCGTTGCGATT
502284 TTCATTTATC
Statistics
Matches: 44, Mismatches: 4, Indels: 1
0.90 0.08 0.02
Matches are distributed among these distances:
33 32 0.73
34 12 0.27
ACGTcount: A:0.10, C:0.26, G:0.22, T:0.43
Consensus pattern (33 bp):
TTTCGCGTTGCGATTCTCTCGTTGCGACAGTCA
Found at i:502288 original size:20 final size:20
Alignment explanation
Indices: 502214--502302 Score: 75
Period size: 20 Copynumber: 4.8 Consensus size: 20
502204 TCGCGTTGCG
502214 ATTCTCTCGTTGCGATTTTC
1 ATTCTCTCGTTGCGATTTTC
*
502234 ATT-TCGCGTTGCG------
1 ATTCTCTCGTTGCGATTTTC
***
502247 ATTCTCTCGTTGCGACAGTC
1 ATTCTCTCGTTGCGATTTTC
502267 ATTCTCTCGTTGCGATTTTC
1 ATTCTCTCGTTGCGATTTTC
*
502287 ATTTATCTCGTTGCGA
1 A-TTCTCTCGTTGCGA
502303 CTCTTCTGCA
Statistics
Matches: 55, Mismatches: 6, Indels: 15
0.72 0.08 0.20
Matches are distributed among these distances:
13 3 0.05
14 9 0.16
19 9 0.16
20 21 0.38
21 13 0.24
ACGTcount: A:0.12, C:0.25, G:0.19, T:0.44
Consensus pattern (20 bp):
ATTCTCTCGTTGCGATTTTC
Found at i:502424 original size:33 final size:33
Alignment explanation
Indices: 502382--502452 Score: 115
Period size: 33 Copynumber: 2.2 Consensus size: 33
502372 AATACTAACT
*
502382 TGAAAATCGCAACGAGAGAATAGCAACGCGAAA
1 TGAAAATCGCAACGACAGAATAGCAACGCGAAA
* *
502415 TGAAAATCGCAACGACAGAATCGTAACGCGAAA
1 TGAAAATCGCAACGACAGAATAGCAACGCGAAA
502448 TGAAA
1 TGAAA
502453 TCTAAGTGAA
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:0.48, C:0.18, G:0.23, T:0.11
Consensus pattern (33 bp):
TGAAAATCGCAACGACAGAATAGCAACGCGAAA
Found at i:502684 original size:22 final size:22
Alignment explanation
Indices: 502632--502686 Score: 74
Period size: 22 Copynumber: 2.5 Consensus size: 22
502622 TGGTTGTGAG
**
502632 GGATTTCGCCGGAGATGGGGAC
1 GGATTTCTTCGGAGATGGGGAC
**
502654 GGAAATCTTCGGAGATGGGGAC
1 GGATTTCTTCGGAGATGGGGAC
502676 GGATTTCTTCG
1 GGATTTCTTCG
502687 CCGTAGAGAG
Statistics
Matches: 27, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
22 27 1.00
ACGTcount: A:0.20, C:0.16, G:0.40, T:0.24
Consensus pattern (22 bp):
GGATTTCTTCGGAGATGGGGAC
Found at i:502857 original size:20 final size:20
Alignment explanation
Indices: 502832--503005 Score: 217
Period size: 20 Copynumber: 8.7 Consensus size: 20
502822 CTTTAAATAT
502832 CGCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
* *
502852 CGCGTTGCGATTTTATGTATTA
1 CGCGTTGCGA-TTTACGGA-TA
*
502874 -TCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
*
502893 CGCGTTGCGATATACGGATA
1 CGCGTTGCGATTTACGGATA
* **
502913 CGCATTGCGATTTACCCATA
1 CGCGTTGCGATTTACGGATA
502933 CGCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
*
502953 CACGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
* *
502973 CGCGTTGCGATTTATGTG-TT
1 CGCGTTGCGATTTACG-GATA
502993 CGCGTTGCGATTT
1 CGCGTTGCGATTT
503006 TCATCATATT
Statistics
Matches: 132, Mismatches: 18, Indels: 8
0.84 0.11 0.05
Matches are distributed among these distances:
19 2 0.02
20 113 0.86
21 15 0.11
22 2 0.02
ACGTcount: A:0.20, C:0.20, G:0.26, T:0.34
Consensus pattern (20 bp):
CGCGTTGCGATTTACGGATA
Found at i:502997 original size:60 final size:60
Alignment explanation
Indices: 502834--503005 Score: 245
Period size: 60 Copynumber: 2.9 Consensus size: 60
502824 TTAAATATCG
** *
502834 CGTTGCGATTTACGGATACGCGTTGCGATTTTATGTATTATCGTTGCGATTTACGGATACG
1 CGTTGCGATTTACGGATACGCGTTGCGA-TTTATGTATTCGCGTTGCGATTTACGGATACA
* * *** *
502895 CGTTGCGATATACGGATACGCATTGCGATTTACCCATACGCGTTGCGATTTACGGATACA
1 CGTTGCGATTTACGGATACGCGTTGCGATTTATGTATTCGCGTTGCGATTTACGGATACA
*
502955 CGTTGCGATTTACGGATACGCGTTGCGATTTATGTGTTCGCGTTGCGATTT
1 CGTTGCGATTTACGGATACGCGTTGCGATTTATGTATTCGCGTTGCGATTT
503006 TCATCATATT
Statistics
Matches: 95, Mismatches: 16, Indels: 1
0.85 0.14 0.01
Matches are distributed among these distances:
60 69 0.73
61 26 0.27
ACGTcount: A:0.20, C:0.19, G:0.26, T:0.35
Consensus pattern (60 bp):
CGTTGCGATTTACGGATACGCGTTGCGATTTATGTATTCGCGTTGCGATTTACGGATACA
Found at i:503108 original size:20 final size:20
Alignment explanation
Indices: 503083--503134 Score: 95
Period size: 20 Copynumber: 2.6 Consensus size: 20
503073 AAGAATCGCG
*
503083 TTGCGATTTTGGAAACTGAT
1 TTGCGATTCTGGAAACTGAT
503103 TTGCGATTCTGGAAACTGAT
1 TTGCGATTCTGGAAACTGAT
503123 TTGCGATTCTGG
1 TTGCGATTCTGG
503135 GGATCGCGTT
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 31 1.00
ACGTcount: A:0.21, C:0.13, G:0.27, T:0.38
Consensus pattern (20 bp):
TTGCGATTCTGGAAACTGAT
Found at i:504323 original size:31 final size:31
Alignment explanation
Indices: 504285--504344 Score: 120
Period size: 31 Copynumber: 1.9 Consensus size: 31
504275 GCGGATATCT
504285 TCACTAAAGTCTGACATTGATGTCACAAACC
1 TCACTAAAGTCTGACATTGATGTCACAAACC
504316 TCACTAAAGTCTGACATTGATGTCACAAA
1 TCACTAAAGTCTGACATTGATGTCACAAA
504345 ACTTTTAGCC
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
31 29 1.00
ACGTcount: A:0.37, C:0.23, G:0.13, T:0.27
Consensus pattern (31 bp):
TCACTAAAGTCTGACATTGATGTCACAAACC
Found at i:506099 original size:31 final size:31
Alignment explanation
Indices: 506061--506245 Score: 318
Period size: 31 Copynumber: 6.0 Consensus size: 31
506051 CCCGAAGGAC
* *
506061 CAGTCCATA-GATTCCGAAGAACCTAGGTAAT
1 CAGTCCATATG-TTCCGAAGAACATAGGTAAA
* *
506092 CAGTCCATATGTCCCGAAGGACATAGGTAAA
1 CAGTCCATATGTTCCGAAGAACATAGGTAAA
506123 CAGTCCATATGTTCCGAAGAACATAGGTAAA
1 CAGTCCATATGTTCCGAAGAACATAGGTAAA
506154 CAGTCCATATGTTCCGAAGAACATAGGTAAA
1 CAGTCCATATGTTCCGAAGAACATAGGTAAA
506185 CAGTCCATATGTTCCGAAGAACATAGGTAAA
1 CAGTCCATATGTTCCGAAGAACATAGGTAAA
506216 CAGTCCATATGTTCCGAAGAACATAGGTAA
1 CAGTCCATATGTTCCGAAGAACATAGGTAA
506246 CCCTCGACCC
Statistics
Matches: 147, Mismatches: 6, Indels: 2
0.95 0.04 0.01
Matches are distributed among these distances:
31 146 0.99
32 1 0.01
ACGTcount: A:0.37, C:0.21, G:0.20, T:0.22
Consensus pattern (31 bp):
CAGTCCATATGTTCCGAAGAACATAGGTAAA
Found at i:507044 original size:21 final size:21
Alignment explanation
Indices: 507014--507058 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
507004 ATTCTGTCGT
* *
507014 TTGAAGGGGTATCGGTTCCCC
1 TTGAAGGGGTACCGATTCCCC
*
507035 TTGAATGGGTACCGATTCCCC
1 TTGAAGGGGTACCGATTCCCC
507056 TTG
1 TTG
507059 CCCAGAAATC
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.16, C:0.24, G:0.29, T:0.31
Consensus pattern (21 bp):
TTGAAGGGGTACCGATTCCCC
Found at i:510048 original size:31 final size:31
Alignment explanation
Indices: 510010--510194 Score: 318
Period size: 31 Copynumber: 6.0 Consensus size: 31
510000 CCCGAAGGAC
* *
510010 CAGTCCATA-GATTCCGAAGAACCTAGGTAAT
1 CAGTCCATATG-TTCCGAAGAACATAGGTAAA
* *
510041 CAGTCCATATGTCCCGAAGGACATAGGTAAA
1 CAGTCCATATGTTCCGAAGAACATAGGTAAA
510072 CAGTCCATATGTTCCGAAGAACATAGGTAAA
1 CAGTCCATATGTTCCGAAGAACATAGGTAAA
510103 CAGTCCATATGTTCCGAAGAACATAGGTAAA
1 CAGTCCATATGTTCCGAAGAACATAGGTAAA
510134 CAGTCCATATGTTCCGAAGAACATAGGTAAA
1 CAGTCCATATGTTCCGAAGAACATAGGTAAA
510165 CAGTCCATATGTTCCGAAGAACATAGGTAA
1 CAGTCCATATGTTCCGAAGAACATAGGTAA
510195 CCCTCGACCC
Statistics
Matches: 147, Mismatches: 6, Indels: 2
0.95 0.04 0.01
Matches are distributed among these distances:
31 146 0.99
32 1 0.01
ACGTcount: A:0.37, C:0.21, G:0.20, T:0.22
Consensus pattern (31 bp):
CAGTCCATATGTTCCGAAGAACATAGGTAAA
Found at i:510995 original size:21 final size:21
Alignment explanation
Indices: 510965--511009 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
510955 ATTCTGTCGT
* *
510965 TTGAAGGGGTATCGGTTCCCC
1 TTGAAGGGGTACCGATTCCCC
*
510986 TTGAATGGGTACCGATTCCCC
1 TTGAAGGGGTACCGATTCCCC
511007 TTG
1 TTG
511010 CCCAGAAATC
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.16, C:0.24, G:0.29, T:0.31
Consensus pattern (21 bp):
TTGAAGGGGTACCGATTCCCC
Found at i:514004 original size:31 final size:31
Alignment explanation
Indices: 513966--514150 Score: 318
Period size: 31 Copynumber: 6.0 Consensus size: 31
513956 CCCGAAGGAC
* *
513966 CAGTCCATA-GATTCCGAAGAACCTAGGTAAT
1 CAGTCCATATG-TTCCGAAGAACATAGGTAAA
* *
513997 CAGTCCATATGTCCCGAAGGACATAGGTAAA
1 CAGTCCATATGTTCCGAAGAACATAGGTAAA
514028 CAGTCCATATGTTCCGAAGAACATAGGTAAA
1 CAGTCCATATGTTCCGAAGAACATAGGTAAA
514059 CAGTCCATATGTTCCGAAGAACATAGGTAAA
1 CAGTCCATATGTTCCGAAGAACATAGGTAAA
514090 CAGTCCATATGTTCCGAAGAACATAGGTAAA
1 CAGTCCATATGTTCCGAAGAACATAGGTAAA
514121 CAGTCCATATGTTCCGAAGAACATAGGTAA
1 CAGTCCATATGTTCCGAAGAACATAGGTAA
514151 CCCTCGACCC
Statistics
Matches: 147, Mismatches: 6, Indels: 2
0.95 0.04 0.01
Matches are distributed among these distances:
31 146 0.99
32 1 0.01
ACGTcount: A:0.37, C:0.21, G:0.20, T:0.22
Consensus pattern (31 bp):
CAGTCCATATGTTCCGAAGAACATAGGTAAA
Found at i:514951 original size:21 final size:21
Alignment explanation
Indices: 514921--514965 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
514911 ATTCTGTCGT
* *
514921 TTGAAGGGGTATCGGTTCCCC
1 TTGAAGGGGTACCGATTCCCC
*
514942 TTGAATGGGTACCGATTCCCC
1 TTGAAGGGGTACCGATTCCCC
514963 TTG
1 TTG
514966 CCCAGAAATC
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.16, C:0.24, G:0.29, T:0.31
Consensus pattern (21 bp):
TTGAAGGGGTACCGATTCCCC
Found at i:520926 original size:33 final size:33
Alignment explanation
Indices: 520881--520948 Score: 127
Period size: 33 Copynumber: 2.1 Consensus size: 33
520871 AAAGGTATAA
*
520881 AATAGTCTCTTGATTACAAGATACTACTTTGTT
1 AATAGTCCCTTGATTACAAGATACTACTTTGTT
520914 AATAGTCCCTTGATTACAAGATACTACTTTGTT
1 AATAGTCCCTTGATTACAAGATACTACTTTGTT
520947 AA
1 AA
520949 GTCCTTTACT
Statistics
Matches: 34, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
33 34 1.00
ACGTcount: A:0.32, C:0.16, G:0.12, T:0.40
Consensus pattern (33 bp):
AATAGTCCCTTGATTACAAGATACTACTTTGTT
Found at i:521809 original size:21 final size:22
Alignment explanation
Indices: 521764--521811 Score: 62
Period size: 22 Copynumber: 2.2 Consensus size: 22
521754 TCGACATTTC
* *
521764 ATTTTAAGATAAAAATATCCCT
1 ATTTTAAGACAAAAATATCCAT
*
521786 ATTTTAAGACAAAAA-ATCTAT
1 ATTTTAAGACAAAAATATCCAT
521807 ATTTT
1 ATTTT
521812 GGAATGTTTA
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
21 9 0.39
22 14 0.61
ACGTcount: A:0.46, C:0.10, G:0.04, T:0.40
Consensus pattern (22 bp):
ATTTTAAGACAAAAATATCCAT
Found at i:524267 original size:2 final size:2
Alignment explanation
Indices: 524256--524300 Score: 83
Period size: 2 Copynumber: 23.0 Consensus size: 2
524246 ACTTTGTACA
524256 AT AT -T AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
524297 AT AT
1 AT AT
524301 TAAATTATGA
Statistics
Matches: 42, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
1 1 0.02
2 41 0.98
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
AT
Found at i:524801 original size:2 final size:2
Alignment explanation
Indices: 524794--524837 Score: 88
Period size: 2 Copynumber: 22.0 Consensus size: 2
524784 GAACTTGTCC
524794 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
524836 AT
1 AT
524838 CAACTTTGTT
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 42 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:528840 original size:2 final size:2
Alignment explanation
Indices: 528833--528858 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
528823 ACACGACACA
528833 AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT
528859 TCATTTTTAT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:532248 original size:174 final size:174
Alignment explanation
Indices: 531951--532292 Score: 603
Period size: 174 Copynumber: 2.0 Consensus size: 174
531941 CAAAACCCTT
*
531951 ACTAAGATTAGTACGAGCACAGGTCATGCGAAACAAGACTGGCCTATGATCCGAACCAAGACGAT
1 ACTAAGATTAGTACGAGAACAGGTCATGCGAAACAAGACTGGCCTATGATCCGAACCAAGACGAT
*
532016 CCAGGTGAAAAATAGAAGAATCGGGATAAGCACTCAACCAACAAGAATTGACAAGGCATCGATCT
66 CCAGGTGAAAAATAGAAGAATCGAGATAAGCACTCAACCAACAAGAATTGACAAGGCATCGATCT
532081 AGCCTTTGTTGCAAGTTACCTCGACACCAAGTAAAAGGCTTTTG
131 AGCCTTTGTTGCAAGTTACCTCGACACCAAGTAAAAGGCTTTTG
*
532125 ACTAAGATTAGTACGAGAACAGGTCATGCGAAACAAGACTGGCCTATGGTCCGAACCAAGACGAT
1 ACTAAGATTAGTACGAGAACAGGTCATGCGAAACAAGACTGGCCTATGATCCGAACCAAGACGAT
* ** * *
532190 CCAGGTGTATGATAGAAGAATCGAGATAAGTACTCAACCAACAAGAATTGATAAGGCATCGATCT
66 CCAGGTGAAAAATAGAAGAATCGAGATAAGCACTCAACCAACAAGAATTGACAAGGCATCGATCT
*
532255 AGCCTTTGTTGCAATTTACCTCGACACCAAGTAAAAGG
131 AGCCTTTGTTGCAAGTTACCTCGACACCAAGTAAAAGG
532293 AGGGCCATGG
Statistics
Matches: 159, Mismatches: 9, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
174 159 1.00
ACGTcount: A:0.37, C:0.21, G:0.22, T:0.20
Consensus pattern (174 bp):
ACTAAGATTAGTACGAGAACAGGTCATGCGAAACAAGACTGGCCTATGATCCGAACCAAGACGAT
CCAGGTGAAAAATAGAAGAATCGAGATAAGCACTCAACCAACAAGAATTGACAAGGCATCGATCT
AGCCTTTGTTGCAAGTTACCTCGACACCAAGTAAAAGGCTTTTG
Found at i:533974 original size:17 final size:17
Alignment explanation
Indices: 533948--533982 Score: 61
Period size: 17 Copynumber: 2.1 Consensus size: 17
533938 TAGTTTGTAA
533948 TTGTTAATCGTCACTTG
1 TTGTTAATCGTCACTTG
*
533965 TTGTTGATCGTCACTTG
1 TTGTTAATCGTCACTTG
533982 T
1 T
533983 CTTTTCTTTT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.14, C:0.17, G:0.20, T:0.49
Consensus pattern (17 bp):
TTGTTAATCGTCACTTG
Found at i:534100 original size:23 final size:23
Alignment explanation
Indices: 534039--534098 Score: 79
Period size: 23 Copynumber: 2.7 Consensus size: 23
534029 TGTTACATGT
* *
534039 TTTACCTCTTCCTTTATGACACG
1 TTTATCTCTTCCTTTGTGACACG
534062 TTTATCTCTGT-CTTTGTGACAC-
1 TTTATCTCT-TCCTTTGTGACACG
534084 TTTATCTCTTCCTTT
1 TTTATCTCTTCCTTT
534099 TGGTAGTTTT
Statistics
Matches: 33, Mismatches: 2, Indels: 5
0.82 0.05 0.12
Matches are distributed among these distances:
21 1 0.03
22 13 0.39
23 18 0.55
24 1 0.03
ACGTcount: A:0.13, C:0.27, G:0.08, T:0.52
Consensus pattern (23 bp):
TTTATCTCTTCCTTTGTGACACG
Found at i:536592 original size:21 final size:21
Alignment explanation
Indices: 536568--536609 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
536558 AAAACTGTGG
* *
536568 ACTGCTATGTTAGCACCGTAA
1 ACTGCTACGTCAGCACCGTAA
*
536589 ACTGCTACGTCAGCATCGTAA
1 ACTGCTACGTCAGCACCGTAA
536610 CGGTCAACGA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.29, C:0.26, G:0.19, T:0.26
Consensus pattern (21 bp):
ACTGCTACGTCAGCACCGTAA
Found at i:538872 original size:17 final size:16
Alignment explanation
Indices: 538839--538881 Score: 68
Period size: 17 Copynumber: 2.6 Consensus size: 16
538829 TTATGTCAAC
*
538839 TTCATTACATGTTTTG
1 TTCATTATATGTTTTG
538855 TTCATTATATGTTTTTG
1 TTCATTATATG-TTTTG
538872 TTCATTATAT
1 TTCATTATAT
538882 ATTGCTAGGT
Statistics
Matches: 25, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
16 10 0.40
17 15 0.60
ACGTcount: A:0.21, C:0.09, G:0.09, T:0.60
Consensus pattern (16 bp):
TTCATTATATGTTTTG
Found at i:555255 original size:55 final size:55
Alignment explanation
Indices: 554823--555299 Score: 526
Period size: 55 Copynumber: 8.7 Consensus size: 55
554813 TGATAAGTCT
* *
554823 GCTCCCTATTCCTTCAGGGAGTATA-AGACTCGAACAATCTTCAACAAACGTGG-CT
1 GCTCCCTATTCCTTCAGAGAGTATAGA-ACTCGAACAATCTTCAACAAACG-GGTCC
* * * * *
554878 GCTCCCTATTCATTCAGGGAGTATA-AGACTCGAACAATCTTCAGCAAACGTGTCT
1 GCTCCCTATTCCTTCAGAGAGTATAGA-ACTCGAACAATCTTCAACAAACGGGTCC
* * * *
554933 GCTCCCTATTCGTTCAGGGAGTATA-AGACTCGAACAATCTTCAATAAAACGGGCCC
1 GCTCCCTATTCCTTCAGAGAGTATAGA-ACTCGAACAATCTTCAA-CAAACGGGTCC
* * *** **
554989 GCTCTCTATTCCTTCAGAGTGTATAGAACTCGAACAATCTTCAACAAATATGTAT
1 GCTCCCTATTCCTTCAGAGAGTATAGAACTCGAACAATCTTCAACAAACGGGTCC
* * * *
555044 GCTCCCTATTTCTTCAGAGAGTATAGGACTTG----ATCTTCAACAAACGTGTCC
1 GCTCCCTATTCCTTCAGAGAGTATAGAACTCGAACAATCTTCAACAAACGGGTCC
* * *
555095 GCTCCCTATTTCTTCAGAGAGTATAGGACTCGAACAATCTTTATA-AAACGGGTCC
1 GCTCCCTATTCCTTCAGAGAGTATAGAACTCGAACAATCTTCA-ACAAACGGGTCC
*
555150 GCTCTCTATTCCTTCAGAGAGTATAGAACTCGAACAATCTTCAACAAACGGGTCC
1 GCTCCCTATTCCTTCAGAGAGTATAGAACTCGAACAATCTTCAACAAACGGGTCC
* *
555205 GCTCTCTATTCCTTCAGAGAGTATAGAACTCGAACAATCTTCAACAAACGGGTTC
1 GCTCCCTATTCCTTCAGAGAGTATAGAACTCGAACAATCTTCAACAAACGGGTCC
* * * *
555260 GCTCCCTCTTTC-TCTAGGGAGTATGGAACTCGAAC-ATCTT
1 GCTCCCTATTCCTTC-AGAGAGTATAGAACTCGAACAATCTT
555300 TTTCTTACGG
Statistics
Matches: 370, Mismatches: 42, Indels: 21
0.85 0.10 0.05
Matches are distributed among these distances:
51 46 0.12
54 9 0.02
55 268 0.72
56 46 0.12
57 1 0.00
ACGTcount: A:0.29, C:0.26, G:0.17, T:0.28
Consensus pattern (55 bp):
GCTCCCTATTCCTTCAGAGAGTATAGAACTCGAACAATCTTCAACAAACGGGTCC
Found at i:555318 original size:54 final size:54
Alignment explanation
Indices: 555252--555412 Score: 288
Period size: 54 Copynumber: 3.0 Consensus size: 54
555242 TCTTCAACAA
555252 ACGGGTTCGCTCCCTCTTTCTCTAGGGAGTATGGAACTCGAACATCTTT-TTCTT
1 ACGGGTTCGCTCCCTCTTTCTCTAGGGAGTATGGAACTCGAACAT-TTTCTTCTT
555306 ACGGGTTCGCTCCCTCTTTCTCTAGGGAGTATGGAACTCGAACATTTTCTTCTT
1 ACGGGTTCGCTCCCTCTTTCTCTAGGGAGTATGGAACTCGAACATTTTCTTCTT
* *
555360 ACAGGTTCGCTCCCTCTTTCTCTAGGGAGTATGAAACTCGAACATTTTCTTCT
1 ACGGGTTCGCTCCCTCTTTCTCTAGGGAGTATGGAACTCGAACATTTTCTTCT
555413 GCTTTACTAC
Statistics
Matches: 104, Mismatches: 2, Indels: 2
0.96 0.02 0.02
Matches are distributed among these distances:
53 3 0.03
54 101 0.97
ACGTcount: A:0.18, C:0.26, G:0.19, T:0.37
Consensus pattern (54 bp):
ACGGGTTCGCTCCCTCTTTCTCTAGGGAGTATGGAACTCGAACATTTTCTTCTT
Found at i:555911 original size:37 final size:36
Alignment explanation
Indices: 555817--555912 Score: 129
Period size: 36 Copynumber: 2.6 Consensus size: 36
555807 AAAAAAAATA
* * * *
555817 TGCTTCACTACTCTTCGATGAAGGCTTAAGATGGTT
1 TGCTTCACTACTCTTTGGTGAAGGCTCAAAATGGTT
* *
555853 TGCTTCACTACTCGTTAGTGAAGGCTCAAAATGGATT
1 TGCTTCACTACTCTTTGGTGAAGGCTCAAAATGG-TT
555890 TGCTTCACTACTCTTTGGTGAAG
1 TGCTTCACTACTCTTTGGTGAAG
555913 ACTTGGCTTT
Statistics
Matches: 51, Mismatches: 8, Indels: 1
0.85 0.13 0.02
Matches are distributed among these distances:
36 28 0.55
37 23 0.45
ACGTcount: A:0.23, C:0.20, G:0.22, T:0.35
Consensus pattern (36 bp):
TGCTTCACTACTCTTTGGTGAAGGCTCAAAATGGTT
Found at i:560660 original size:72 final size:72
Alignment explanation
Indices: 560543--560693 Score: 266
Period size: 72 Copynumber: 2.1 Consensus size: 72
560533 CCCCTAATAG
560543 GTTCTTGATCAGTTGCTATCATCACATTGGCTGCACCACTAACATTCAGATTCTCACCCGAAGTC
1 GTTCTTGATCAGTTGCTATCATCACATTGGCTGCACCACTAACATTCAGATTCTCACCCGAAGTC
*
560608 TTCATCT
66 TTCATAT
* *
560615 GTTCTTGATCATTTGCTATCATCACATTGGTTGCACCACTAACATTCAGATTCTCACCCGAAGTC
1 GTTCTTGATCAGTTGCTATCATCACATTGGCTGCACCACTAACATTCAGATTCTCACCCGAAGTC
560680 TTCATAT
66 TTCATAT
*
560687 TTTCTTG
1 GTTCTTG
560694 TGTAATAGGG
Statistics
Matches: 75, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
72 75 1.00
ACGTcount: A:0.23, C:0.27, G:0.13, T:0.36
Consensus pattern (72 bp):
GTTCTTGATCAGTTGCTATCATCACATTGGCTGCACCACTAACATTCAGATTCTCACCCGAAGTC
TTCATAT
Found at i:561442 original size:55 final size:55
Alignment explanation
Indices: 561348--561478 Score: 163
Period size: 55 Copynumber: 2.4 Consensus size: 55
561338 AACATCTTCA
* ** * *
561348 GGATGTCTTTCTTTGTGGATCGGTCTTCAATCAGTTTCAAATTTCTTCATTCATC
1 GGATGTCCTTCTTCATGAATCGGTCTTCAATCAGGTTCAAATTTCTTCATTCATC
* * *
561403 GGATGTCCTTCTTCATGAATCGTTCTTCAGTCAGGTTCAAATTTCTTCATTCGTC
1 GGATGTCCTTCTTCATGAATCGGTCTTCAATCAGGTTCAAATTTCTTCATTCATC
** *
561458 AAATGTTCTTCTTCATGAATC
1 GGATGTCCTTCTTCATGAATC
561479 ATCTGAATGC
Statistics
Matches: 65, Mismatches: 11, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
55 65 1.00
ACGTcount: A:0.20, C:0.21, G:0.15, T:0.44
Consensus pattern (55 bp):
GGATGTCCTTCTTCATGAATCGGTCTTCAATCAGGTTCAAATTTCTTCATTCATC
Found at i:567784 original size:31 final size:31
Alignment explanation
Indices: 567741--567812 Score: 99
Period size: 31 Copynumber: 2.3 Consensus size: 31
567731 TTAACCCGTG
*
567741 GTGATCACATCTTAAATAAATAAAAACAAAA
1 GTGATCATATCTTAAATAAATAAAAACAAAA
* * *
567772 GTGATCATATCTTAATTAAATAAAAACGAAT
1 GTGATCATATCTTAAATAAATAAAAACAAAA
*
567803 GTGATAATAT
1 GTGATCATAT
567813 ATTATCTATT
Statistics
Matches: 36, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
31 36 1.00
ACGTcount: A:0.51, C:0.10, G:0.10, T:0.29
Consensus pattern (31 bp):
GTGATCATATCTTAAATAAATAAAAACAAAA
Found at i:572326 original size:111 final size:112
Alignment explanation
Indices: 572169--572390 Score: 428
Period size: 112 Copynumber: 2.0 Consensus size: 112
572159 CACAATCGCA
*
572169 TCTTAAACAAATATTGATAATGACTCCCAAAACCATATATATAGAGAGAGAGTTA-GATTCACTT
1 TCTTAAACAAAGATTGATAATGACTCCCAAAACCATATATATAGAGAGAGAGTTAGGATTCACTT
572233 ACACAACGTAAAACTCTTTAGTTTTACACAGATTTAGAACTGTTTGC
66 ACACAACGTAAAACTCTTTAGTTTTACACAGATTTAGAACTGTTTGC
572280 TCTTAAACAAAGATTGATAATGACTCCCAAAACCATATATATAGAGAGAGAGTTAGGATTCACTT
1 TCTTAAACAAAGATTGATAATGACTCCCAAAACCATATATATAGAGAGAGAGTTAGGATTCACTT
572345 ACACAACGTAAAACTCTTTAGTTTTACACAGATTTAGAACTGTTTG
66 ACACAACGTAAAACTCTTTAGTTTTACACAGATTTAGAACTGTTTG
572391 ATAAGTGAAA
Statistics
Matches: 109, Mismatches: 1, Indels: 1
0.98 0.01 0.01
Matches are distributed among these distances:
111 54 0.50
112 55 0.50
ACGTcount: A:0.39, C:0.17, G:0.14, T:0.31
Consensus pattern (112 bp):
TCTTAAACAAAGATTGATAATGACTCCCAAAACCATATATATAGAGAGAGAGTTAGGATTCACTT
ACACAACGTAAAACTCTTTAGTTTTACACAGATTTAGAACTGTTTGC
Found at i:575440 original size:28 final size:28
Alignment explanation
Indices: 575409--575473 Score: 121
Period size: 28 Copynumber: 2.3 Consensus size: 28
575399 TGGCTTGCTA
575409 ACATAATGTTTCAAGCAGTGACTCGATG
1 ACATAATGTTTCAAGCAGTGACTCGATG
*
575437 ACATAATATTTCAAGCAGTGACTCGATG
1 ACATAATGTTTCAAGCAGTGACTCGATG
575465 ACATAATGT
1 ACATAATGT
575474 AAATAAATAA
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
28 35 1.00
ACGTcount: A:0.35, C:0.17, G:0.18, T:0.29
Consensus pattern (28 bp):
ACATAATGTTTCAAGCAGTGACTCGATG
Found at i:581520 original size:43 final size:43
Alignment explanation
Indices: 581468--581551 Score: 159
Period size: 43 Copynumber: 2.0 Consensus size: 43
581458 GCATGAGTTC
*
581468 CACTCAATTATGTATTTACATTTTATTTTAATAGTTTAATACT
1 CACTCAATTATGTATTTACATTTTATTTTAATAATTTAATACT
581511 CACTCAATTATGTATTTACATTTTATTTTAATAATTTAATA
1 CACTCAATTATGTATTTACATTTTATTTTAATAATTTAATA
581552 ATAACACCCT
Statistics
Matches: 40, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
43 40 1.00
ACGTcount: A:0.35, C:0.11, G:0.04, T:0.51
Consensus pattern (43 bp):
CACTCAATTATGTATTTACATTTTATTTTAATAATTTAATACT
Found at i:582978 original size:21 final size:21
Alignment explanation
Indices: 582949--582988 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
582939 ATAATTATTA
*
582949 TAATATTTTAAAATTAATAAT
1 TAATATTTTAAAATAAATAAT
* *
582970 TAATTTTTTATAATAAATA
1 TAATATTTTAAAATAAATA
582989 TTATAAATGT
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 16 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (21 bp):
TAATATTTTAAAATAAATAAT
Found at i:592775 original size:17 final size:17
Alignment explanation
Indices: 592753--592805 Score: 54
Period size: 17 Copynumber: 3.0 Consensus size: 17
592743 ATTTAATAAC
592753 TTAAAATTAAATATTTT
1 TTAAAATTAAATATTTT
*
592770 TTAAAAATAACAT-TTTT
1 TTAAAATTAA-ATATTTT
*
592787 TTGAAAATAATAATATTTT
1 TT-AAAATTA-AATATTTT
592806 CACCTCATAA
Statistics
Matches: 29, Mismatches: 3, Indels: 6
0.76 0.08 0.16
Matches are distributed among these distances:
17 15 0.52
18 9 0.31
19 5 0.17
ACGTcount: A:0.47, C:0.02, G:0.02, T:0.49
Consensus pattern (17 bp):
TTAAAATTAAATATTTT
Found at i:599099 original size:32 final size:31
Alignment explanation
Indices: 599063--599127 Score: 85
Period size: 31 Copynumber: 2.1 Consensus size: 31
599053 AAAACATAAA
*
599063 ATTTTGATCACTTTCATTTCGTTTTAATTAAG
1 ATTTTG-TCACTTTCATCTCGTTTTAATTAAG
* **
599095 ATTTTGTCATTTTTGTCTCGTTTTAATTAAG
1 ATTTTGTCACTTTCATCTCGTTTTAATTAAG
599126 AT
1 AT
599128 GTAGTAACTG
Statistics
Matches: 29, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
31 23 0.79
32 6 0.21
ACGTcount: A:0.23, C:0.11, G:0.11, T:0.55
Consensus pattern (31 bp):
ATTTTGTCACTTTCATCTCGTTTTAATTAAG
Found at i:608467 original size:28 final size:28
Alignment explanation
Indices: 608427--608482 Score: 112
Period size: 28 Copynumber: 2.0 Consensus size: 28
608417 CCACGTTGGA
608427 TGTAAATGGCTATTTAAAGTTAAACGTC
1 TGTAAATGGCTATTTAAAGTTAAACGTC
608455 TGTAAATGGCTATTTAAAGTTAAACGTC
1 TGTAAATGGCTATTTAAAGTTAAACGTC
608483 ATGCCGATGG
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 28 1.00
ACGTcount: A:0.36, C:0.11, G:0.18, T:0.36
Consensus pattern (28 bp):
TGTAAATGGCTATTTAAAGTTAAACGTC
Found at i:611214 original size:28 final size:28
Alignment explanation
Indices: 611182--611239 Score: 116
Period size: 28 Copynumber: 2.1 Consensus size: 28
611172 AAGGAGGTTA
611182 TATCTGTCACCCGCTGAATCATCTACGT
1 TATCTGTCACCCGCTGAATCATCTACGT
611210 TATCTGTCACCCGCTGAATCATCTACGT
1 TATCTGTCACCCGCTGAATCATCTACGT
611238 TA
1 TA
611240 GTTCCTCTCT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 30 1.00
ACGTcount: A:0.22, C:0.31, G:0.14, T:0.33
Consensus pattern (28 bp):
TATCTGTCACCCGCTGAATCATCTACGT
Found at i:616524 original size:3 final size:3
Alignment explanation
Indices: 616516--616613 Score: 171
Period size: 3 Copynumber: 33.0 Consensus size: 3
616506 ATTTAATATT
* *
616516 TAA TAA TAA TAG TAA TAA TGA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
616564 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA T-A TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
616611 TAA
1 TAA
616614 ATATGGATAA
Statistics
Matches: 90, Mismatches: 4, Indels: 2
0.94 0.04 0.02
Matches are distributed among these distances:
2 2 0.02
3 88 0.98
ACGTcount: A:0.64, C:0.00, G:0.02, T:0.34
Consensus pattern (3 bp):
TAA
Found at i:617184 original size:113 final size:113
Alignment explanation
Indices: 616935--617355 Score: 718
Period size: 113 Copynumber: 3.7 Consensus size: 113
616925 AGAATTATGC
* * * * *
616935 AAAAAGTTGAACAAGTTCTTCTTATTATGAACTTCTTCTTTCTTCTTCAGATGAGTTCTTCTTAT
1 AAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCAT
* * * * * *
617000 TATGAAC-TTCTCTGGAAAAGATAATCCATCAATTGATGAATTCAAGT
66 TATGAACTTTCTCTGGAAAGGCTGATCCATCAAATGATGAACTCAGGT
617047 AAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCAT
1 AAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCAT
* *
617112 TATGAACTTCCTCTGGAAAGGCTGATCCATCAAATGATGGACTCAGGT
66 TATGAACTTTCTCTGGAAAGGCTGATCCATCAAATGATGAACTCAGGT
617160 AAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCAT
1 AAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCAT
617225 TATGAACTTTCTCTGGAAAGGCTGATCCATCAAATGATGAACTCAGGT
66 TATGAACTTTCTCTGGAAAGGCTGATCCATCAAATGATGAACTCAGGT
617273 AAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCAT
1 AAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCAT
617338 TATGAACTTTCTCTGGAA
66 TATGAACTTTCTCTGGAA
617356 GAAATGATCT
Statistics
Matches: 293, Mismatches: 15, Indels: 1
0.95 0.05 0.00
Matches are distributed among these distances:
112 67 0.23
113 226 0.77
ACGTcount: A:0.29, C:0.19, G:0.14, T:0.38
Consensus pattern (113 bp):
AAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCAT
TATGAACTTTCTCTGGAAAGGCTGATCCATCAAATGATGAACTCAGGT
Found at i:618381 original size:84 final size:83
Alignment explanation
Indices: 618111--618489 Score: 631
Period size: 82 Copynumber: 4.6 Consensus size: 83
618101 CCTACTGAAT
* *
618111 CAGATCAGATAACTCAAAGAACACTT-CAGAAGATGCTA-TGAACACATTCATCTTTTAAACTCA
1 CAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTGAGCACATTCATCTTCTAAACTCA
618174 ATGATTGTTCTGTCCAAC
66 ATGATTGTTCTGTCCAAC
* *
618192 CAGATCAGATAACTCAAAGAACACTTCCAAAAGATGCTATTGA-CAAATTCATCTTCTAAACTCA
1 CAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTGAGCACATTCATCTTCTAAACTCA
618256 ATGATTGTTCTGTCCAAC
66 ATGATTGTTCTGTCCAAC
* * * *
618274 CAGATCAGATAACTCAAAGAACACTTTCAAAAGATGCTATTGAGCTCATTCATCTTCTAAATTCA
1 CAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTGAGCACATTCATCTTCTAAACTCA
618339 ATGATTGGTTCTGTCCAAC
66 ATGATT-GTTCTGTCCAAC
*
618358 CAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTGAGCACATTCATCTTCTAAATTCA
1 CAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTGAGCACATTCATCTTCTAAACTCA
*
618423 ATGATGGTTCTGT-CAAC
66 ATGATTGTTCTGTCCAAC
618440 CAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTGAGCACATT
1 CAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTGAGCACATT
618490 ATATTTGTTC
Statistics
Matches: 283, Mismatches: 11, Indels: 7
0.94 0.04 0.02
Matches are distributed among these distances:
81 26 0.09
82 144 0.51
83 34 0.12
84 79 0.28
ACGTcount: A:0.37, C:0.22, G:0.13, T:0.28
Consensus pattern (83 bp):
CAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTGAGCACATTCATCTTCTAAACTCA
ATGATTGTTCTGTCCAAC
Found at i:618382 original size:166 final size:165
Alignment explanation
Indices: 618111--618489 Score: 629
Period size: 166 Copynumber: 2.3 Consensus size: 165
618101 CCTACTGAAT
* *
618111 CAGATCAGATAACTCAAAGAACAC-TTCAGAAGATGCTA-TGAACACATTCATCTTTTAAACTCA
1 CAGATCAGATAACTCAAAGAACACTTTCAGAAGATGCTATTGAGCACATTCATCTTCTAAACTCA
618174 ATGATTGTTCTGTCCAACCAGATCAGATAACTCAAAGAACACTTCCAAAAGATGCTATTGA-CAA
66 ATGATTGTTCTGTCCAACCAGATCAGATAACTCAAAGAACACTTCCAAAAGATGCTATTGAGCAA
*
618238 ATTCATCTTCTAAACTCAATGATTGTTCTGTCCAAC
131 ATTCATCTTCTAAACTCAATGATGGTTCTGT-CAAC
* * *
618274 CAGATCAGATAACTCAAAGAACACTTTCAAAAGATGCTATTGAGCTCATTCATCTTCTAAATTCA
1 CAGATCAGATAACTCAAAGAACACTTTCAGAAGATGCTATTGAGCACATTCATCTTCTAAACTCA
*
618339 ATGATTGGTTCTGTCCAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTGAGCA
66 ATGATT-GTTCTGTCCAACCAGATCAGATAACTCAAAGAACACTTCCAAAAGATGCTATTGAGCA
* *
618404 CATTCATCTTCTAAATTCAATGATGGTTCTGTCAAC
130 AATTCATCTTCTAAACTCAATGATGGTTCTGTCAAC
*
618440 CAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTGAGCACATT
1 CAGATCAGATAACTCAAAGAACACTTTCAGAAGATGCTATTGAGCACATT
618490 ATATTTGTTC
Statistics
Matches: 200, Mismatches: 12, Indels: 5
0.92 0.06 0.02
Matches are distributed among these distances:
163 24 0.12
164 13 0.06
165 27 0.14
166 105 0.52
167 31 0.16
ACGTcount: A:0.37, C:0.22, G:0.13, T:0.28
Consensus pattern (165 bp):
CAGATCAGATAACTCAAAGAACACTTTCAGAAGATGCTATTGAGCACATTCATCTTCTAAACTCA
ATGATTGTTCTGTCCAACCAGATCAGATAACTCAAAGAACACTTCCAAAAGATGCTATTGAGCAA
ATTCATCTTCTAAACTCAATGATGGTTCTGTCAAC
Found at i:630140 original size:24 final size:23
Alignment explanation
Indices: 630089--630156 Score: 75
Period size: 24 Copynumber: 2.9 Consensus size: 23
630079 ACTTGCAAAT
* *
630089 AAAATAAAACATATAAATATTATG
1 AAAATAAAA-ATATAAAAATTATA
*
630113 AAAATAATAAATATAAAAATTTTA
1 AAAATAA-AAATATAAAAATTATA
*
630137 AAAAGAAAAAT-TAAAAATTA
1 AAAATAAAAATATAAAAATTA
630157 AATATGAATT
Statistics
Matches: 38, Mismatches: 5, Indels: 4
0.81 0.11 0.09
Matches are distributed among these distances:
22 8 0.21
23 4 0.11
24 24 0.63
25 2 0.05
ACGTcount: A:0.68, C:0.01, G:0.03, T:0.28
Consensus pattern (23 bp):
AAAATAAAAATATAAAAATTATA
Found at i:630879 original size:18 final size:19
Alignment explanation
Indices: 630866--630901 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
630856 AAAAAATATT
630866 TAAAAACA-ATAAAATAAA
1 TAAAAACATATAAAATAAA
*
630884 TGAAAACATATAAAATAA
1 TAAAAACATATAAAATAA
630902 CTGACTAAAT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 7 0.44
19 9 0.56
ACGTcount: A:0.72, C:0.06, G:0.03, T:0.19
Consensus pattern (19 bp):
TAAAAACATATAAAATAAA
Found at i:632188 original size:3 final size:3
Alignment explanation
Indices: 632180--632283 Score: 172
Period size: 3 Copynumber: 34.7 Consensus size: 3
632170 TTAATATATT
* *
632180 TAA TAA TAA TAG TAA TAA TGA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
* *
632228 TAA TAA TAA TAA TAG TAA TAA TAA TAA TAA TAA TAA TAA TAT TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
632276 TAA TAA TA
1 TAA TAA TA
632284 TGGATAAAAA
Statistics
Matches: 93, Mismatches: 8, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
3 93 1.00
ACGTcount: A:0.62, C:0.00, G:0.03, T:0.35
Consensus pattern (3 bp):
TAA
Found at i:636383 original size:20 final size:20
Alignment explanation
Indices: 636360--636406 Score: 85
Period size: 20 Copynumber: 2.4 Consensus size: 20
636350 AATTTGTAAA
*
636360 TCGCAACACAGAAGTCAAAT
1 TCGCAACACAAAAGTCAAAT
636380 TCGCAACACAAAAGTCAAAT
1 TCGCAACACAAAAGTCAAAT
636400 TCGCAAC
1 TCGCAAC
636407 GCCATAATCA
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 26 1.00
ACGTcount: A:0.45, C:0.28, G:0.13, T:0.15
Consensus pattern (20 bp):
TCGCAACACAAAAGTCAAAT
Found at i:636417 original size:20 final size:21
Alignment explanation
Indices: 636371--636428 Score: 75
Period size: 20 Copynumber: 2.9 Consensus size: 21
636361 CGCAACACAG
*
636371 AAGTCAAATTCGCAAC-ACAA
1 AAGTCAAATTCGCAACGCCAA
*
636391 AAGTCAAATTCGCAACGCCAT
1 AAGTCAAATTCGCAACGCCAA
*
636412 AA-TCAAATTTGCAACGC
1 AAGTCAAATTCGCAACGC
636429 GAAACACAAT
Statistics
Matches: 34, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
20 30 0.88
21 4 0.12
ACGTcount: A:0.43, C:0.26, G:0.12, T:0.19
Consensus pattern (21 bp):
AAGTCAAATTCGCAACGCCAA
Found at i:636567 original size:22 final size:22
Alignment explanation
Indices: 636542--636592 Score: 86
Period size: 22 Copynumber: 2.3 Consensus size: 22
636532 CTACGGCGAC
636542 ATCCGTCCCCATCTT-CGACGAA
1 ATCCGTCCCCAT-TTCCGACGAA
636564 ATCCGTCCCCATTTCCGACGAA
1 ATCCGTCCCCATTTCCGACGAA
636586 ATCCGTC
1 ATCCGTC
636593 TATCTCCATC
Statistics
Matches: 28, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
21 2 0.07
22 26 0.93
ACGTcount: A:0.22, C:0.41, G:0.14, T:0.24
Consensus pattern (22 bp):
ATCCGTCCCCATTTCCGACGAA
Found at i:636651 original size:2 final size:2
Alignment explanation
Indices: 636644--636678 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
636634 CATGACATGT
636644 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 T
636679 TAATAATTAA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:641564 original size:16 final size:16
Alignment explanation
Indices: 641543--641585 Score: 61
Period size: 16 Copynumber: 2.7 Consensus size: 16
641533 AAAGAAAAGA
641543 AAAAATAAATAATAAT
1 AAAAATAAATAATAAT
*
641559 AAAAAT-AATAAATAGT
1 AAAAATAAAT-AATAAT
641575 AAAAATAAATA
1 AAAAATAAATA
641586 TGAAAAATCA
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
15 3 0.12
16 18 0.75
17 3 0.12
ACGTcount: A:0.74, C:0.00, G:0.02, T:0.23
Consensus pattern (16 bp):
AAAAATAAATAATAAT
Found at i:646228 original size:16 final size:16
Alignment explanation
Indices: 646164--646228 Score: 51
Period size: 17 Copynumber: 3.9 Consensus size: 16
646154 TATTAATCTA
*
646164 TAAAAATTA-ATTTCT
1 TAAAAATTATTTTTCT
* *
646179 TAAAAAATATTTTTATAAT
1 TAAAAATTA-TTTT-T-CT
*
646198 TAAAAATTTTCTTTTCT
1 TAAAAATTAT-TTTTCT
646215 TAAAAATTATTTTT
1 TAAAAATTATTTTT
646229 AAAAAAATAC
Statistics
Matches: 38, Mismatches: 7, Indels: 9
0.70 0.13 0.17
Matches are distributed among these distances:
15 8 0.21
16 4 0.11
17 12 0.32
18 3 0.08
19 11 0.29
ACGTcount: A:0.43, C:0.05, G:0.00, T:0.52
Consensus pattern (16 bp):
TAAAAATTATTTTTCT
Found at i:649156 original size:60 final size:60
Alignment explanation
Indices: 649078--649224 Score: 217
Period size: 60 Copynumber: 2.4 Consensus size: 60
649068 GAGTCGAGGG
*
649078 TTACCTATGTCTTTCGGGACATATGGACAGAA-TACCTATGTCTTTCGGGACATATGGACAG
1 TTACCTATGT-TTTCGGGACATATGGACAGAATTA-CTATGTCTTTCGGGACATATGGACAA
649139 TATACCTA-GTTTTCGGGACATATGGACAGAATTACTATGTCTTTCGGGACATATGGACAA
1 T-TACCTATGTTTTCGGGACATATGGACAGAATTACTATGTCTTTCGGGACATATGGACAA
* * *
649199 TTACCTATGTCTTAGGAACATATGGA
1 TTACCTATGTTTTCGGGACATATGGA
649225 TAGGTTCTTC
Statistics
Matches: 79, Mismatches: 4, Indels: 7
0.88 0.04 0.08
Matches are distributed among these distances:
59 6 0.08
60 62 0.78
61 5 0.06
62 6 0.08
ACGTcount: A:0.29, C:0.18, G:0.22, T:0.32
Consensus pattern (60 bp):
TTACCTATGTTTTCGGGACATATGGACAGAATTACTATGTCTTTCGGGACATATGGACAA
Found at i:649162 original size:29 final size:31
Alignment explanation
Indices: 649079--649224 Score: 212
Period size: 31 Copynumber: 4.8 Consensus size: 31
649069 AGTCGAGGGT
649079 TACCTATGTCTTTCGGGACATATGGACAGAA
1 TACCTATGTCTTTCGGGACATATGGACAGAA
*
649110 TACCTATGTCTTTCGGGACATATGGACAGTA
1 TACCTATGTCTTTCGGGACATATGGACAGAA
649141 TACCTA-GT-TTTCGGGACATATGGACAGAA
1 TACCTATGTCTTTCGGGACATATGGACAGAA
*
649170 TTA-CTATGTCTTTCGGGACATATGGACA-AT
1 -TACCTATGTCTTTCGGGACATATGGACAGAA
* *
649200 TACCTATGTC-TTAGGAACATATGGA
1 TACCTATGTCTTTCGGGACATATGGA
649225 TAGGTTCTTC
Statistics
Matches: 106, Mismatches: 5, Indels: 10
0.88 0.04 0.08
Matches are distributed among these distances:
29 38 0.36
30 14 0.13
31 54 0.51
ACGTcount: A:0.29, C:0.18, G:0.22, T:0.32
Consensus pattern (31 bp):
TACCTATGTCTTTCGGGACATATGGACAGAA
Found at i:651455 original size:21 final size:20
Alignment explanation
Indices: 651418--651459 Score: 50
Period size: 21 Copynumber: 2.0 Consensus size: 20
651408 TAGAAACACG
651418 ATAATTTTTTTAATTTAATTA
1 ATAATTTTTTTAATTT-ATTA
*
651439 ATAATTTTATTT-TTTTATTA
1 ATAATTTT-TTTAATTTATTA
651459 A
1 A
651460 AAACAAAATA
Statistics
Matches: 19, Mismatches: 1, Indels: 3
0.83 0.04 0.13
Matches are distributed among these distances:
20 5 0.26
21 11 0.58
22 3 0.16
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (20 bp):
ATAATTTTTTTAATTTATTA
Found at i:662110 original size:60 final size:60
Alignment explanation
Indices: 662043--662180 Score: 258
Period size: 60 Copynumber: 2.3 Consensus size: 60
662033 TCGGATGACC
*
662043 ATTTTGTAACTTTTAATAGTCGAGGGACTCAACAGAGCAACACTGTATAGTTAAAGGACT
1 ATTTTGTAACTTTTAATAGTCGAGGGACTCAACAGAGCAACACTGTATAGTTAAAGCACT
662103 ATTTTGTAACTTTTAATAGTCGAGGGACTCAACAGAGCAACACTGTATAGTTAAAGCACT
1 ATTTTGTAACTTTTAATAGTCGAGGGACTCAACAGAGCAACACTGTATAGTTAAAGCACT
*
662163 ATTTTGTAATTTTTAATA
1 ATTTTGTAACTTTTAATA
662181 ATTAAAGTAC
Statistics
Matches: 76, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
60 76 1.00
ACGTcount: A:0.35, C:0.14, G:0.17, T:0.34
Consensus pattern (60 bp):
ATTTTGTAACTTTTAATAGTCGAGGGACTCAACAGAGCAACACTGTATAGTTAAAGCACT
Done.