Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01005320.1 Hibiscus syriacus cultivar Beakdansim tig00012040_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: 539900
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 2 of 3
Found at i:186245 original size:44 final size:44
Alignment explanation
Indices: 186170--186256 Score: 120
Period size: 44 Copynumber: 2.0 Consensus size: 44
186160 GTTATATGAT
186170 ATGATCTACGTGATTATATGAAAATGAGATATAAGCTATGTGAC
1 ATGATCTACGTGATTATATGAAAATGAGATATAAGCTATGTGAC
* * *** *
186214 ATGATCTATGTGATTATTTGTCTATGTGATATAAGCTATGTGA
1 ATGATCTACGTGATTATATGAAAATGAGATATAAGCTATGTGA
186257 AATATGTAAA
Statistics
Matches: 37, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
44 37 1.00
ACGTcount: A:0.33, C:0.08, G:0.21, T:0.38
Consensus pattern (44 bp):
ATGATCTACGTGATTATATGAAAATGAGATATAAGCTATGTGAC
Found at i:186254 original size:14 final size:14
Alignment explanation
Indices: 186197--186256 Score: 57
Period size: 14 Copynumber: 4.1 Consensus size: 14
186187 ATGAAAATGA
186197 GATATAAGCTATGT
1 GATATAAGCTATGT
* * *
186211 GACATGATCTATGT
1 GATATAAGCTATGT
**
186225 GATTATTTGTCTATGT
1 GA-TATAAG-CTATGT
186241 GATATAAGCTATGT
1 GATATAAGCTATGT
186255 GA
1 GA
186257 AATATGTAAA
Statistics
Matches: 35, Mismatches: 9, Indels: 4
0.73 0.19 0.08
Matches are distributed among these distances:
14 21 0.60
15 6 0.17
16 8 0.23
ACGTcount: A:0.30, C:0.08, G:0.22, T:0.40
Consensus pattern (14 bp):
GATATAAGCTATGT
Found at i:186361 original size:23 final size:23
Alignment explanation
Indices: 186335--186399 Score: 58
Period size: 23 Copynumber: 2.8 Consensus size: 23
186325 TCAAGGATTC
186335 TACGCGGTCATTCGGGATAATTA
1 TACGCGGTCATTCGGGATAATTA
** * * * *
186358 TACGTAGTCCTTCGGGACATTTT
1 TACGCGGTCATTCGGGATAATTA
* *
186381 TACGCGATCATTCAGGATA
1 TACGCGGTCATTCGGGATA
186400 TATCTATGTG
Statistics
Matches: 30, Mismatches: 12, Indels: 0
0.71 0.29 0.00
Matches are distributed among these distances:
23 30 1.00
ACGTcount: A:0.25, C:0.20, G:0.23, T:0.32
Consensus pattern (23 bp):
TACGCGGTCATTCGGGATAATTA
Found at i:186392 original size:46 final size:46
Alignment explanation
Indices: 186335--186425 Score: 123
Period size: 46 Copynumber: 2.0 Consensus size: 46
186325 TCAAGGATTC
* *
186335 TACGCGGTCATTCGGGATA-AT-TATACGTAGTCCTTCGGGACATTTT
1 TACGCGATCATTCAGGATATATCTAT--GTAGTCCTTCGGGACATTTT
*
186381 TACGCGATCATTCAGGATATATCTATGTGGTCCTTCGGGACATTT
1 TACGCGATCATTCAGGATATATCTATGTAGTCCTTCGGGACATTT
186426 CTATGTGGCA
Statistics
Matches: 40, Mismatches: 3, Indels: 4
0.85 0.06 0.09
Matches are distributed among these distances:
46 35 0.88
47 2 0.05
48 3 0.08
ACGTcount: A:0.22, C:0.20, G:0.23, T:0.35
Consensus pattern (46 bp):
TACGCGATCATTCAGGATATATCTATGTAGTCCTTCGGGACATTTT
Found at i:186432 original size:23 final size:23
Alignment explanation
Indices: 186364--186433 Score: 68
Period size: 23 Copynumber: 3.0 Consensus size: 23
186354 ATTATACGTA
* * *
186364 GTCCTTCGGGACATTTTTACGCG
1 GTCCTTCGGGACATTTCTATGTG
* * * * *
186387 ATCATTCAGGATATATCTATGTG
1 GTCCTTCGGGACATTTCTATGTG
186410 GTCCTTCGGGACATTTCTATGTG
1 GTCCTTCGGGACATTTCTATGTG
186433 G
1 G
186434 CACTTTGGTG
Statistics
Matches: 34, Mismatches: 13, Indels: 0
0.72 0.28 0.00
Matches are distributed among these distances:
23 34 1.00
ACGTcount: A:0.19, C:0.20, G:0.24, T:0.37
Consensus pattern (23 bp):
GTCCTTCGGGACATTTCTATGTG
Found at i:187073 original size:16 final size:16
Alignment explanation
Indices: 187049--187080 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
187039 GATTTCAAAC
*
187049 AAATCTTTTTAAAAGT
1 AAATATTTTTAAAAGT
187065 AAATATTTTTAAAAGT
1 AAATATTTTTAAAAGT
187081 CAATGTGACA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.47, C:0.03, G:0.06, T:0.44
Consensus pattern (16 bp):
AAATATTTTTAAAAGT
Found at i:189357 original size:17 final size:17
Alignment explanation
Indices: 189331--189372 Score: 68
Period size: 17 Copynumber: 2.5 Consensus size: 17
189321 AATTAAAGGG
*
189331 AGATTTGATATTCTCCA
1 AGATTCGATATTCTCCA
189348 AGATTCGATATTCTCCA
1 AGATTCGATATTCTCCA
189365 AGA-TCGAT
1 AGATTCGAT
189373 TTACGTTCTG
Statistics
Matches: 24, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
16 5 0.21
17 19 0.79
ACGTcount: A:0.31, C:0.19, G:0.14, T:0.36
Consensus pattern (17 bp):
AGATTCGATATTCTCCA
Found at i:193514 original size:69 final size:69
Alignment explanation
Indices: 193369--193549 Score: 204
Period size: 69 Copynumber: 2.6 Consensus size: 69
193359 GAGTCAAGGG
* * * * *
193369 TTCTATGTGGTCCTTCGGGAAAATTCTATGTGGTTCCTTCGGGACATTTCTACGCGGTCATTCGA
1 TTCTATGTGGTCCTTCGGGACATTTCTACGCGG-TCCTTCGGGACATATCTACGCGGTCATTCGA
193434 GACAT
65 GACAT
* * * * *
193439 ATCTATGTGGTCCTTCGGGACATTTCTACGCGGTCCTTCGGGACATATCTATGTGGTCTTTCGGG
1 TTCTATGTGGTCCTTCGGGACATTTCTACGCGGTCCTTCGGGACATATCTACGCGGTCATTCGAG
193504 ACAT
66 ACAT
**
193508 TTCTATGTGGAACTTCGGTG-CATATTCTACGCGG-CACTTCGG
1 TTCTATGTGGTCCTTCGG-GACAT-TTCTACGCGGTC-CTTCGG
193550 TGCATATTCT
Statistics
Matches: 95, Mismatches: 13, Indels: 6
0.83 0.11 0.05
Matches are distributed among these distances:
69 50 0.53
70 45 0.47
ACGTcount: A:0.17, C:0.23, G:0.25, T:0.35
Consensus pattern (69 bp):
TTCTATGTGGTCCTTCGGGACATTTCTACGCGGTCCTTCGGGACATATCTACGCGGTCATTCGAG
ACAT
Found at i:193525 original size:23 final size:23
Alignment explanation
Indices: 193369--193517 Score: 190
Period size: 23 Copynumber: 6.4 Consensus size: 23
193359 GAGTCAAGGG
* *
193369 TTCTATGTGGTCCTTCGGGAAAA
1 TTCTATGTGGTCCTTCGGGACAT
193392 TTCTATGTGGTTCCTTCGGGACAT
1 TTCTATGTGG-TCCTTCGGGACAT
* * * *
193416 TTCTACGCGGTCATTCGAGACAT
1 TTCTATGTGGTCCTTCGGGACAT
*
193439 ATCTATGTGGTCCTTCGGGACAT
1 TTCTATGTGGTCCTTCGGGACAT
* *
193462 TTCTACGCGGTCCTTCGGGACAT
1 TTCTATGTGGTCCTTCGGGACAT
* *
193485 ATCTATGTGGTCTTTCGGGACAT
1 TTCTATGTGGTCCTTCGGGACAT
193508 TTCTATGTGG
1 TTCTATGTGG
193518 AACTTCGGTG
Statistics
Matches: 106, Mismatches: 19, Indels: 2
0.83 0.15 0.02
Matches are distributed among these distances:
23 87 0.82
24 19 0.18
ACGTcount: A:0.17, C:0.21, G:0.26, T:0.36
Consensus pattern (23 bp):
TTCTATGTGGTCCTTCGGGACAT
Found at i:193525 original size:46 final size:46
Alignment explanation
Indices: 193377--193512 Score: 211
Period size: 46 Copynumber: 2.9 Consensus size: 46
193367 GGTTCTATGT
*
193377 GGTCCTTCGGGA-AAATTCTATGTGGTTCCTTCGGGACATTTCTACGC
1 GGTCCTTCGGGACATA-TCTATGTGG-TCCTTCGGGACATTTCTACGC
* *
193424 GGTCATTCGAGACATATCTATGTGGTCCTTCGGGACATTTCTACGC
1 GGTCCTTCGGGACATATCTATGTGGTCCTTCGGGACATTTCTACGC
*
193470 GGTCCTTCGGGACATATCTATGTGGTCTTTCGGGACATTTCTA
1 GGTCCTTCGGGACATATCTATGTGGTCCTTCGGGACATTTCTA
193513 TGTGGAACTT
Statistics
Matches: 82, Mismatches: 6, Indels: 3
0.90 0.07 0.03
Matches are distributed among these distances:
46 61 0.74
47 19 0.23
48 2 0.02
ACGTcount: A:0.18, C:0.23, G:0.25, T:0.35
Consensus pattern (46 bp):
GGTCCTTCGGGACATATCTATGTGGTCCTTCGGGACATTTCTACGC
Found at i:193532 original size:46 final size:44
Alignment explanation
Indices: 193393--193532 Score: 163
Period size: 46 Copynumber: 3.0 Consensus size: 44
193383 TCGGGAAAAT
* *
193393 TCTATGTGGTTCCTTCGGGACATTTCTACGCGGTCATTCGAGACATA
1 TCTATGTGG-TCCTTCGGGACATTTCTACGCGGAC-TTCG-GGCATA
*
193440 TCTATGTGGTCCTTCGGGACATTTCTACGCGGTCCTTCGGGACATA
1 TCTATGTGGTCCTTCGGGACATTTCTACGCGG-ACTTCGGG-CATA
* * *
193486 TCTATGTGGTCTTTCGGGACATTTCTATGTGGAACTTCGGTGCATA
1 TCTATGTGGTCCTTCGGGACATTTCTACGCGG-ACTTCGG-GCATA
193532 T
1 T
193533 TCTACGCGGC
Statistics
Matches: 83, Mismatches: 7, Indels: 7
0.86 0.07 0.07
Matches are distributed among these distances:
45 1 0.01
46 71 0.86
47 11 0.13
ACGTcount: A:0.17, C:0.22, G:0.25, T:0.36
Consensus pattern (44 bp):
TCTATGTGGTCCTTCGGGACATTTCTACGCGGACTTCGGGCATA
Found at i:193546 original size:24 final size:24
Alignment explanation
Indices: 193519--193577 Score: 109
Period size: 24 Copynumber: 2.5 Consensus size: 24
193509 TCTATGTGGA
*
193519 ACTTCGGTGCATATTCTACGCGGC
1 ACTTCGGTGCATATTCTACACGGC
193543 ACTTCGGTGCATATTCTACACGGC
1 ACTTCGGTGCATATTCTACACGGC
193567 ACTTCGGTGCA
1 ACTTCGGTGCA
193578 ATTTATACGA
Statistics
Matches: 34, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
24 34 1.00
ACGTcount: A:0.19, C:0.29, G:0.24, T:0.29
Consensus pattern (24 bp):
ACTTCGGTGCATATTCTACACGGC
Found at i:195247 original size:20 final size:20
Alignment explanation
Indices: 195192--195259 Score: 64
Period size: 20 Copynumber: 3.4 Consensus size: 20
195182 GCCGATTTAG
*
195192 GTTGACTCAATTCGGTTCGA
1 GTTGACTCAATTCGATTCGA
* * *** *
195212 GCTGATTCAGGCCGATTCGT
1 GTTGACTCAATTCGATTCGA
*
195232 GTTGACTCAATTCGATTTGA
1 GTTGACTCAATTCGATTCGA
195252 GTTGACTC
1 GTTGACTC
195260 GAATCGGTTC
Statistics
Matches: 34, Mismatches: 14, Indels: 0
0.71 0.29 0.00
Matches are distributed among these distances:
20 34 1.00
ACGTcount: A:0.19, C:0.21, G:0.25, T:0.35
Consensus pattern (20 bp):
GTTGACTCAATTCGATTCGA
Found at i:207036 original size:28 final size:31
Alignment explanation
Indices: 207000--207063 Score: 82
Period size: 31 Copynumber: 2.2 Consensus size: 31
206990 TTAAATACAA
207000 CAAACTTACAATAA-G-TATTAAATGATAAT
1 CAAACTTACAATAATGATATTAAATGATAAT
*
207029 CAAA-TTACAATAATTGATATTAAATGGTAAT
1 CAAACTTACAATAA-TGATATTAAATGATAAT
207060 -AAAC
1 CAAAC
207064 AAAATTAACT
Statistics
Matches: 30, Mismatches: 1, Indels: 6
0.81 0.03 0.16
Matches are distributed among these distances:
28 9 0.30
29 4 0.13
30 4 0.13
31 13 0.43
ACGTcount: A:0.52, C:0.09, G:0.08, T:0.31
Consensus pattern (31 bp):
CAAACTTACAATAATGATATTAAATGATAAT
Found at i:207127 original size:26 final size:24
Alignment explanation
Indices: 207098--207169 Score: 62
Period size: 26 Copynumber: 3.0 Consensus size: 24
207088 AAACTCCAAC
207098 AAATTTAACAAAATAAAGTAAGTATT
1 AAATTTAACAAAATAAAGTAA--ATT
*
207124 AAA-TGAGA-AATAATAAA--AAATT
1 AAATTTA-ACAA-AATAAAGTAAATT
207146 ACAATTTAACAAAATAAAGTAAAT
1 A-AATTTAACAAAATAAAGTAAAT
207170 ACAAATATAA
Statistics
Matches: 37, Mismatches: 2, Indels: 15
0.69 0.04 0.28
Matches are distributed among these distances:
22 4 0.11
23 9 0.24
24 6 0.16
25 8 0.22
26 10 0.27
ACGTcount: A:0.62, C:0.04, G:0.07, T:0.26
Consensus pattern (24 bp):
AAATTTAACAAAATAAAGTAAATT
Found at i:207304 original size:3 final size:3
Alignment explanation
Indices: 207298--207323 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
207288 ATCATCACCA
207298 TCG TCG TCG TCG TCG TCG TCG TCG TC
1 TCG TCG TCG TCG TCG TCG TCG TCG TC
207324 CTGAGCAGAT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.00, C:0.35, G:0.31, T:0.35
Consensus pattern (3 bp):
TCG
Found at i:207686 original size:18 final size:18
Alignment explanation
Indices: 207663--207697 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
207653 GTGATGGCGG
*
207663 CATCATATATGGCTGCGA
1 CATCATAAATGGCTGCGA
*
207681 CATCATAAATGGTTGCG
1 CATCATAAATGGCTGCG
207698 GTGGCTGCTG
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.29, C:0.20, G:0.23, T:0.29
Consensus pattern (18 bp):
CATCATAAATGGCTGCGA
Found at i:209407 original size:17 final size:18
Alignment explanation
Indices: 209364--209404 Score: 66
Period size: 18 Copynumber: 2.3 Consensus size: 18
209354 AAATTATATT
209364 AGTAAAATA-TTAAATAA
1 AGTAAAATACTTAAATAA
209381 AGTAAAATACTTAAATAA
1 AGTAAAATACTTAAATAA
*
209399 ATTAAA
1 AGTAAA
209405 TACATAATAT
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
17 9 0.41
18 13 0.59
ACGTcount: A:0.63, C:0.02, G:0.05, T:0.29
Consensus pattern (18 bp):
AGTAAAATACTTAAATAA
Found at i:223539 original size:33 final size:33
Alignment explanation
Indices: 223502--223573 Score: 135
Period size: 33 Copynumber: 2.2 Consensus size: 33
223492 TTAGTATGCA
*
223502 TATTTTCCATTACTTGTACTAGTTGGTCTATAC
1 TATTTGCCATTACTTGTACTAGTTGGTCTATAC
223535 TATTTGCCATTACTTGTACTAGTTGGTCTATAC
1 TATTTGCCATTACTTGTACTAGTTGGTCTATAC
223568 TATTTG
1 TATTTG
223574 TAAAATATAT
Statistics
Matches: 38, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
33 38 1.00
ACGTcount: A:0.21, C:0.17, G:0.14, T:0.49
Consensus pattern (33 bp):
TATTTGCCATTACTTGTACTAGTTGGTCTATAC
Found at i:229099 original size:23 final size:21
Alignment explanation
Indices: 229065--229108 Score: 61
Period size: 23 Copynumber: 2.0 Consensus size: 21
229055 ATATAAAAAA
229065 TTATTTTTTATTAAATATTTTT
1 TTATTTTTTATTAAAT-TTTTT
*
229087 TTATATTTTTATTTAATTTTTT
1 TTAT-TTTTTATTAAATTTTTT
229109 AAATAATTAT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
22 9 0.45
23 11 0.55
ACGTcount: A:0.25, C:0.00, G:0.00, T:0.75
Consensus pattern (21 bp):
TTATTTTTTATTAAATTTTTT
Found at i:231614 original size:26 final size:24
Alignment explanation
Indices: 231542--231595 Score: 67
Period size: 23 Copynumber: 2.3 Consensus size: 24
231532 GTTCTTCCTC
* *
231542 CATCTTCACCTTAAAATCATCT-TT
1 CATCTTCACCAT-ATATCATCTCTT
231566 CATCTTCACCATATATCAT-TCTT
1 CATCTTCACCATATATCATCTCTT
231589 CATCTTC
1 CATCTTC
231596 CCCACCATCT
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
22 1 0.04
23 15 0.56
24 11 0.41
ACGTcount: A:0.26, C:0.31, G:0.00, T:0.43
Consensus pattern (24 bp):
CATCTTCACCATATATCATCTCTT
Found at i:233265 original size:60 final size:59
Alignment explanation
Indices: 233144--233266 Score: 167
Period size: 58 Copynumber: 2.1 Consensus size: 59
233134 AAATGATACG
* *
233144 CTCTCAACCCGTAAACATTCACACAACAATCCTGTCAACTCGAAAATCACCCAACAATC
1 CTCTCAACCCGTAAACATTCACACAACAATCCTCTCAACCCGAAAATCACCCAACAATC
* * * *
233203 CTCTCAACCCTTAAACA-TCACCCAACAATCCTCTTAACCCTTAAACATCACCCAACAATC
1 CTCTCAACCCGTAAACATTCACACAACAATCCTCTCAACCC-GAAA-ATCACCCAACAATC
233263 CTCT
1 CTCT
233267 TATCTTTGAT
Statistics
Matches: 56, Mismatches: 6, Indels: 3
0.86 0.09 0.05
Matches are distributed among these distances:
58 19 0.34
59 19 0.34
60 18 0.32
ACGTcount: A:0.37, C:0.40, G:0.02, T:0.21
Consensus pattern (59 bp):
CTCTCAACCCGTAAACATTCACACAACAATCCTCTCAACCCGAAAATCACCCAACAATC
Found at i:233268 original size:30 final size:30
Alignment explanation
Indices: 233144--233266 Score: 169
Period size: 30 Copynumber: 4.1 Consensus size: 30
233134 AAATGATACG
* *
233144 CTCTCAACCCGTAAACATTCACACAACAATC
1 CTCTCAACCCTTAAACA-TCACCCAACAATC
* * *
233175 CTGTCAACTC-GAAA-ATCACCCAACAATC
1 CTCTCAACCCTTAAACATCACCCAACAATC
233203 CTCTCAACCCTTAAACATCACCCAACAATC
1 CTCTCAACCCTTAAACATCACCCAACAATC
*
233233 CTCTTAACCCTTAAACATCACCCAACAATC
1 CTCTCAACCCTTAAACATCACCCAACAATC
233263 CTCT
1 CTCT
233267 TATCTTTGAT
Statistics
Matches: 82, Mismatches: 8, Indels: 5
0.86 0.08 0.05
Matches are distributed among these distances:
28 20 0.24
29 4 0.05
30 50 0.61
31 8 0.10
ACGTcount: A:0.37, C:0.40, G:0.02, T:0.21
Consensus pattern (30 bp):
CTCTCAACCCTTAAACATCACCCAACAATC
Found at i:244846 original size:13 final size:13
Alignment explanation
Indices: 244824--244857 Score: 52
Period size: 12 Copynumber: 2.7 Consensus size: 13
244814 AAGGGGGGTA
*
244824 ATTTTCAAAATTG
1 ATTTTCAAAAATG
244837 A-TTTCAAAAATG
1 ATTTTCAAAAATG
244849 ATTTTCAAA
1 ATTTTCAAA
244858 GAAAATCTTA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
12 11 0.58
13 8 0.42
ACGTcount: A:0.44, C:0.09, G:0.06, T:0.41
Consensus pattern (13 bp):
ATTTTCAAAAATG
Found at i:253802 original size:20 final size:21
Alignment explanation
Indices: 253764--253807 Score: 81
Period size: 21 Copynumber: 2.1 Consensus size: 21
253754 TAACTTTTTC
253764 TTTTCTCTTTCATTCTTAACT
1 TTTTCTCTTTCATTCTTAACT
253785 TTTTCTCTTTCATT-TTAACT
1 TTTTCTCTTTCATTCTTAACT
253805 TTT
1 TTT
253808 AATTTTTCTC
Statistics
Matches: 23, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
20 9 0.39
21 14 0.61
ACGTcount: A:0.14, C:0.20, G:0.00, T:0.66
Consensus pattern (21 bp):
TTTTCTCTTTCATTCTTAACT
Found at i:253815 original size:20 final size:21
Alignment explanation
Indices: 253769--253815 Score: 60
Period size: 20 Copynumber: 2.3 Consensus size: 21
253759 TTTTCTTTTC
**
253769 TCTTTCATTCTTAACTTTTTC
1 TCTTTCATTCTTAACTTTTAA
253790 TCTTTCATT-TTAACTTTTAA
1 TCTTTCATTCTTAACTTTTAA
*
253810 TTTTTC
1 TCTTTC
253816 TCTCTCATTT
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
20 14 0.61
21 9 0.39
ACGTcount: A:0.17, C:0.19, G:0.00, T:0.64
Consensus pattern (21 bp):
TCTTTCATTCTTAACTTTTAA
Found at i:258359 original size:20 final size:20
Alignment explanation
Indices: 258330--258367 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
258320 TTTCAAAGGG
258330 ATGCACCGATGCACCAATCC
1 ATGCACCGATGCACCAATCC
*
258350 ATGCATCGATGCACCAAT
1 ATGCACCGATGCACCAAT
258368 GAATAAATTG
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.32, C:0.34, G:0.16, T:0.18
Consensus pattern (20 bp):
ATGCACCGATGCACCAATCC
Found at i:258538 original size:64 final size:65
Alignment explanation
Indices: 258378--258539 Score: 236
Period size: 65 Copynumber: 2.5 Consensus size: 65
258368 GAATAAATTG
* * * * * *
258378 AACATCGAATGCAGTTTATGCATCGATGCACTCTCCATGCATCGTTGCACTCAGGTTTTAATGAA
1 AACATCGAATGCATTTTATGCATCGATGCACACACCATGCATCGATGCACTCAGGTCTTAATCAA
* * *
258443 AACATCAAATGCATTTTATGCATCGATGCACACACCATGCATCGATGCACTTAGG-CTTATTCAA
1 AACATCGAATGCATTTTATGCATCGATGCACACACCATGCATCGATGCACTCAGGTCTTAATCAA
258507 AACATCGAATGCATTTTATGCATCGATGCACAC
1 AACATCGAATGCATTTTATGCATCGATGCACAC
258540 TTAGTGCACC
Statistics
Matches: 87, Mismatches: 10, Indels: 1
0.89 0.10 0.01
Matches are distributed among these distances:
64 38 0.44
65 49 0.56
ACGTcount: A:0.31, C:0.24, G:0.16, T:0.29
Consensus pattern (65 bp):
AACATCGAATGCATTTTATGCATCGATGCACACACCATGCATCGATGCACTCAGGTCTTAATCAA
Found at i:258553 original size:64 final size:64
Alignment explanation
Indices: 258378--258557 Score: 227
Period size: 64 Copynumber: 2.8 Consensus size: 64
258368 GAATAAATTG
* * * * *
258378 AACATCGAATGCAGTTTATGCATCGATGCACTCTCCATGCATCGTTGCACTCAGGTTTTAATGAA
1 AACATCGAATGCATTTTATGCATCGATGCACACT-CATGCATCGATGCACTCAGGTCTTAATCAA
* * * *
258443 AACATCAAATGCATTTTATGCATCGATGCACACACCATGCATCGATGCACTTAGG-CTTATTCAA
1 AACATCGAATGCATTTTATGCATCGATGCACAC-TCATGCATCGATGCACTCAGGTCTTAATCAA
* *
258507 AACATCGAATGCATTTTATGCATCGATGCACACTTAGTGCACCGATGCACT
1 AACATCGAATGCATTTTATGCATCGATGCACACTCA-TGCATCGATGCACT
258558 AAGTGTTCTA
Statistics
Matches: 100, Mismatches: 13, Indels: 5
0.85 0.11 0.04
Matches are distributed among these distances:
63 1 0.01
64 51 0.51
65 48 0.48
ACGTcount: A:0.30, C:0.24, G:0.17, T:0.29
Consensus pattern (64 bp):
AACATCGAATGCATTTTATGCATCGATGCACACTCATGCATCGATGCACTCAGGTCTTAATCAA
Found at i:258765 original size:13 final size:13
Alignment explanation
Indices: 258747--258773 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
258737 AGCCATTGAT
258747 CAACAACAAGAAA
1 CAACAACAAGAAA
258760 CAACAACAAGAAA
1 CAACAACAAGAAA
258773 C
1 C
258774 TAGAATCAAG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.67, C:0.26, G:0.07, T:0.00
Consensus pattern (13 bp):
CAACAACAAGAAA
Found at i:266814 original size:19 final size:19
Alignment explanation
Indices: 266790--266843 Score: 108
Period size: 19 Copynumber: 2.8 Consensus size: 19
266780 AATGCAATTT
266790 ATGCATCGATGCACTCTCC
1 ATGCATCGATGCACTCTCC
266809 ATGCATCGATGCACTCTCC
1 ATGCATCGATGCACTCTCC
266828 ATGCATCGATGCACTC
1 ATGCATCGATGCACTC
266844 AGGTTTTAAT
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 35 1.00
ACGTcount: A:0.22, C:0.35, G:0.17, T:0.26
Consensus pattern (19 bp):
ATGCATCGATGCACTCTCC
Found at i:266950 original size:64 final size:65
Alignment explanation
Indices: 266809--266951 Score: 198
Period size: 64 Copynumber: 2.2 Consensus size: 65
266799 TGCACTCTCC
* * * * *
266809 ATGCATCGATGCACTCTCCATGCATCGATGCACTCAGGTTTTAATGAAAACATTGAATGCATTTT
1 ATGCATCGATGCACGCACCATGCATCGATGCACTCAGGTCTTAATCAAAACATCGAATGCATTTT
* * * *
266874 ATGCATCAATGCACGCACCATGCATCGATGCACTTAGG-CTTATTCAAAACATCGAATGCCTTTT
1 ATGCATCGATGCACGCACCATGCATCGATGCACTCAGGTCTTAATCAAAACATCGAATGCATTTT
266938 ATGCATCGATGCAC
1 ATGCATCGATGCAC
266952 ACTTAGTGCA
Statistics
Matches: 68, Mismatches: 10, Indels: 1
0.86 0.13 0.01
Matches are distributed among these distances:
64 34 0.50
65 34 0.50
ACGTcount: A:0.29, C:0.24, G:0.17, T:0.29
Consensus pattern (65 bp):
ATGCATCGATGCACGCACCATGCATCGATGCACTCAGGTCTTAATCAAAACATCGAATGCATTTT
Found at i:266967 original size:64 final size:64
Alignment explanation
Indices: 266809--266971 Score: 186
Period size: 64 Copynumber: 2.5 Consensus size: 64
266799 TGCACTCTCC
* * * *
266809 ATGCATCGATGCACTCTCCATGCATCGATGCACTCAGGTTTTAATGAAAACATTGAATGCATTTT
1 ATGCATCGATGCACACT-CATGCATCGATGCACTCAGGTCTTAATCAAAACATCGAATGCATTTT
* * * *
266874 ATGCATCAATGCACGCAC-CATGCATCGATGCACTTAGG-CTTATTCAAAACATCGAATGCCTTT
1 ATGCATCGATGCA--CACTCATGCATCGATGCACTCAGGTCTTAATCAAAACATCGAATGCATTT
266937 T
64 T
* *
266938 ATGCATCGATGCACACTTAGTGCACCGATGCACT
1 ATGCATCGATGCACACTCA-TGCATCGATGCACT
266972 AAGTGTTCCA
Statistics
Matches: 83, Mismatches: 11, Indels: 9
0.81 0.11 0.09
Matches are distributed among these distances:
62 3 0.04
63 1 0.01
64 46 0.55
65 31 0.37
67 2 0.02
ACGTcount: A:0.29, C:0.25, G:0.17, T:0.29
Consensus pattern (64 bp):
ATGCATCGATGCACACTCATGCATCGATGCACTCAGGTCTTAATCAAAACATCGAATGCATTTT
Found at i:267186 original size:13 final size:13
Alignment explanation
Indices: 267168--267195 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
267158 AGCCATTGAC
267168 CAACAACAAGAAA
1 CAACAACAAGAAA
267181 CAACAACAAGAAA
1 CAACAACAAGAAA
267194 CA
1 CA
267196 TCAAGAAACT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.68, C:0.25, G:0.07, T:0.00
Consensus pattern (13 bp):
CAACAACAAGAAA
Found at i:270119 original size:8 final size:8
Alignment explanation
Indices: 270094--270133 Score: 53
Period size: 8 Copynumber: 4.8 Consensus size: 8
270084 AACTGCAAAA
*
270094 AAATGATT
1 AAATAATT
270102 AAATAAAATT
1 AAAT--AATT
270112 AAATAATT
1 AAATAATT
270120 AAATAATT
1 AAATAATT
270128 AAATAA
1 AAATAA
270134 AATACTAAAA
Statistics
Matches: 29, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
8 22 0.76
10 7 0.24
ACGTcount: A:0.65, C:0.00, G:0.03, T:0.33
Consensus pattern (8 bp):
AAATAATT
Found at i:270120 original size:18 final size:16
Alignment explanation
Indices: 270094--270133 Score: 53
Period size: 18 Copynumber: 2.4 Consensus size: 16
270084 AACTGCAAAA
*
270094 AAATGATTAAATAAAATT
1 AAATAATTAAAT--AATT
270112 AAATAATTAAATAATT
1 AAATAATTAAATAATT
270128 AAATAA
1 AAATAA
270134 AATACTAAAA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
16 10 0.48
18 11 0.52
ACGTcount: A:0.65, C:0.00, G:0.03, T:0.33
Consensus pattern (16 bp):
AAATAATTAAATAATT
Found at i:278352 original size:43 final size:43
Alignment explanation
Indices: 278283--278464 Score: 174
Period size: 43 Copynumber: 4.2 Consensus size: 43
278273 ATTTTATGAA
* *
278283 ATTGTAAAAAATTA-GAGGCCTTAATTATAAAGGTAGAAATTGAG
1 ATTG-AAAAAAATAGGA-GCCTCAATTATAAAGGTAGAAATTGAG
*
278327 ATTGAAAAAAATAGGAGCCTCAATTATAAAGGTA-TAATTGAG
1 ATTGAAAAAAATAGGAGCCTCAATTATAAAGGTAGAAATTGAG
* *** * * * *
278369 ATCGAAAATTCTTAGGGGCCTCAATTAGAAAGTTAGAAAGTGAG
1 ATTGAAAA-AAATAGGAGCCTCAATTATAAAGGTAGAAATTGAG
*
278413 ATT-AAAAAAACTTAAGG-GCCTCAATTATAAAGGTAGAAATTAAG
1 ATTGAAAAAAA--T-AGGAGCCTCAATTATAAAGGTAGAAATTGAG
278457 ATTGAAAA
1 ATTGAAAA
278465 CACATAGAGA
Statistics
Matches: 111, Mismatches: 20, Indels: 13
0.77 0.14 0.09
Matches are distributed among these distances:
42 14 0.13
43 49 0.44
44 41 0.37
45 7 0.06
ACGTcount: A:0.46, C:0.08, G:0.20, T:0.26
Consensus pattern (43 bp):
ATTGAAAAAAATAGGAGCCTCAATTATAAAGGTAGAAATTGAG
Found at i:278432 original size:44 final size:44
Alignment explanation
Indices: 278299--278464 Score: 178
Period size: 44 Copynumber: 3.8 Consensus size: 44
278289 AAAAATTAGA
*
278299 GGCCTTAATTATAAAGGTAGAAATTGAGATTGAAAAAAA--T-AG
1 GGCCTCAATTATAAAGGTAGAAATTGAGATT-AAAAAAACTTAAG
* ** ** *
278341 GAGCCTCAATTATAAAGGTA-TAATTGAGATCGAAAATTCTTAGG
1 G-GCCTCAATTATAAAGGTAGAAATTGAGATTAAAAAAACTTAAG
* * *
278385 GGCCTCAATTAGAAAGTTAGAAAGTGAGATTAAAAAAACTTAAG
1 GGCCTCAATTATAAAGGTAGAAATTGAGATTAAAAAAACTTAAG
* *
278429 GGCCTCAATTATAAAGGTAGAAATTAAGATTGAAAA
1 GGCCTCAATTATAAAGGTAGAAATTGAGATTAAAAA
278465 CACATAGAGA
Statistics
Matches: 98, Mismatches: 21, Indels: 8
0.77 0.17 0.06
Matches are distributed among these distances:
41 4 0.04
42 10 0.10
43 34 0.35
44 50 0.51
ACGTcount: A:0.45, C:0.08, G:0.20, T:0.26
Consensus pattern (44 bp):
GGCCTCAATTATAAAGGTAGAAATTGAGATTAAAAAAACTTAAG
Found at i:279271 original size:3 final size:3
Alignment explanation
Indices: 279263--279335 Score: 146
Period size: 3 Copynumber: 24.3 Consensus size: 3
279253 TGTGATTCTT
279263 GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA
1 GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA
279311 GAA GAA GAA GAA GAA GAA GAA GAA G
1 GAA GAA GAA GAA GAA GAA GAA GAA G
279336 GGTTAACGGG
Statistics
Matches: 70, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 70 1.00
ACGTcount: A:0.66, C:0.00, G:0.34, T:0.00
Consensus pattern (3 bp):
GAA
Found at i:286330 original size:25 final size:22
Alignment explanation
Indices: 286286--286331 Score: 56
Period size: 22 Copynumber: 2.0 Consensus size: 22
286276 AGGATGATGC
286286 ATTATATTTTAGGATTAGATTT
1 ATTATATTTTAGGATTAGATTT
*
286308 ATTATTTTATTAGGAATTAAGATT
1 ATTATATT-TTAGG-ATT-AGATT
286332 AAGTTAAAAC
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
22 7 0.35
23 5 0.25
24 3 0.15
25 5 0.25
ACGTcount: A:0.35, C:0.00, G:0.13, T:0.52
Consensus pattern (22 bp):
ATTATATTTTAGGATTAGATTT
Found at i:286744 original size:59 final size:58
Alignment explanation
Indices: 286637--286756 Score: 179
Period size: 59 Copynumber: 2.1 Consensus size: 58
286627 GGAGGGTTAG
* *
286637 TTAGAGCCATATTATCAATTTTCCTTTTCATTGCGACTAGGATGGTTCGATAGGACAC
1 TTAGAGCCATATTATCAATTTTCCTTTTCATTGCAACTAGGAGGGTTCGATAGGACAC
* *
286695 TTAGAGCTATATTATCAAGTTTTTCTTTTCATTGCAACT-GTGAGGGTTCGATAGGACAC
1 TTAGAGCCATATTATCAA-TTTTCCTTTTCATTGCAACTAG-GAGGGTTCGATAGGACAC
286754 TTA
1 TTA
286757 TCCATCTATT
Statistics
Matches: 56, Mismatches: 4, Indels: 3
0.89 0.06 0.05
Matches are distributed among these distances:
58 18 0.32
59 38 0.68
ACGTcount: A:0.26, C:0.17, G:0.19, T:0.38
Consensus pattern (58 bp):
TTAGAGCCATATTATCAATTTTCCTTTTCATTGCAACTAGGAGGGTTCGATAGGACAC
Found at i:293049 original size:18 final size:18
Alignment explanation
Indices: 293026--293088 Score: 99
Period size: 18 Copynumber: 3.5 Consensus size: 18
293016 CACAACATAA
293026 TCTGTTTCTACAACGCAT
1 TCTGTTTCTACAACGCAT
* *
293044 TTTGTTTCTACAACGTAT
1 TCTGTTTCTACAACGCAT
*
293062 TGTGTTTCTACAACGCAT
1 TCTGTTTCTACAACGCAT
293080 TCTGTTTCT
1 TCTGTTTCT
293089 TTGCACGGTG
Statistics
Matches: 40, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 40 1.00
ACGTcount: A:0.19, C:0.22, G:0.13, T:0.46
Consensus pattern (18 bp):
TCTGTTTCTACAACGCAT
Found at i:293057 original size:36 final size:36
Alignment explanation
Indices: 293009--293088 Score: 115
Period size: 36 Copynumber: 2.2 Consensus size: 36
292999 GTAATTCCCA
*
293009 TTGTTTCCACAACATAATCTGTTTCTACAACGCATT
1 TTGTTTCTACAACATAATCTGTTTCTACAACGCATT
* * *
293045 TTGTTTCTACAACGTATTGTGTTTCTACAACGCATT
1 TTGTTTCTACAACATAATCTGTTTCTACAACGCATT
*
293081 CTGTTTCT
1 TTGTTTCT
293089 TTGCACGGTG
Statistics
Matches: 39, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
36 39 1.00
ACGTcount: A:0.23, C:0.23, G:0.11, T:0.44
Consensus pattern (36 bp):
TTGTTTCTACAACATAATCTGTTTCTACAACGCATT
Found at i:300756 original size:20 final size:20
Alignment explanation
Indices: 300731--300779 Score: 89
Period size: 20 Copynumber: 2.5 Consensus size: 20
300721 TGTTCTTAGT
300731 CACTGTTTGATGGATTTGGC
1 CACTGTTTGATGGATTTGGC
*
300751 CACTGTTTGATGGATTTGGT
1 CACTGTTTGATGGATTTGGC
300771 CACTGTTTG
1 CACTGTTTG
300780 GGACAGGTTT
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 28 1.00
ACGTcount: A:0.14, C:0.14, G:0.29, T:0.43
Consensus pattern (20 bp):
CACTGTTTGATGGATTTGGC
Found at i:301078 original size:24 final size:24
Alignment explanation
Indices: 301046--301111 Score: 82
Period size: 24 Copynumber: 2.8 Consensus size: 24
301036 TTGGCCTACA
*
301046 AAAAGTAATTAGTATTAATAA-AAT
1 AAAAGTAA-TAGTAATAATAATAAT
301070 AAAAGTAATAGTAATAATAATAAT
1 AAAAGTAATAGTAATAATAATAAT
*
301094 AATAA-TAATAATAATAAT
1 AA-AAGTAATAGTAATAAT
301112 TAGTAATATT
Statistics
Matches: 38, Mismatches: 2, Indels: 4
0.86 0.05 0.09
Matches are distributed among these distances:
23 11 0.29
24 25 0.66
25 2 0.05
ACGTcount: A:0.62, C:0.00, G:0.06, T:0.32
Consensus pattern (24 bp):
AAAAGTAATAGTAATAATAATAAT
Found at i:301089 original size:3 final size:3
Alignment explanation
Indices: 301061--301111 Score: 70
Period size: 3 Copynumber: 17.3 Consensus size: 3
301051 TAATTAGTAT
*
301061 TAA TAA -AA TAA -AA GTAA TAG TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA -TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
301105 TAA TAA T
1 TAA TAA T
301112 TAGTAATATT
Statistics
Matches: 43, Mismatches: 2, Indels: 6
0.84 0.04 0.12
Matches are distributed among these distances:
2 4 0.09
3 37 0.86
4 2 0.05
ACGTcount: A:0.65, C:0.00, G:0.04, T:0.31
Consensus pattern (3 bp):
TAA
Found at i:310234 original size:30 final size:30
Alignment explanation
Indices: 310154--310226 Score: 110
Period size: 30 Copynumber: 2.4 Consensus size: 30
310144 ACAAAATTCA
*
310154 TTTCAAGGGAAACAATCTCAAAGATTTATG
1 TTTCAAGGGAAACAATCTCAAAGATTTACG
* *
310184 TTTCAAGGGAAACAATCTCAAAGGTTTGCG
1 TTTCAAGGGAAACAATCTCAAAGATTTACG
*
310214 TTTTAAGGGAAAC
1 TTTCAAGGGAAAC
310227 CGTCTCAAGG
Statistics
Matches: 39, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
30 39 1.00
ACGTcount: A:0.37, C:0.14, G:0.21, T:0.29
Consensus pattern (30 bp):
TTTCAAGGGAAACAATCTCAAAGATTTACG
Found at i:310466 original size:37 final size:37
Alignment explanation
Indices: 310418--310493 Score: 118
Period size: 37 Copynumber: 2.1 Consensus size: 37
310408 GTTCCGAGAG
310418 AAACTGCCTCAAGAGAGACAAAATTTGTGTT-TAAGAA
1 AAACTGCCTCAAGAGAGACAAAATTTGT-TTGTAAGAA
* *
310455 AAACTGTCTCAAGCGAGACAAAATTTGTTTGTAAGAA
1 AAACTGCCTCAAGAGAGACAAAATTTGTTTGTAAGAA
310492 AA
1 AA
310494 TAATCTCAAA
Statistics
Matches: 36, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
36 2 0.06
37 34 0.94
ACGTcount: A:0.43, C:0.13, G:0.18, T:0.25
Consensus pattern (37 bp):
AAACTGCCTCAAGAGAGACAAAATTTGTTTGTAAGAA
Found at i:313863 original size:17 final size:18
Alignment explanation
Indices: 313836--313869 Score: 61
Period size: 17 Copynumber: 1.9 Consensus size: 18
313826 TAACCATTTT
313836 TTTTAAAAAAACAATTAA
1 TTTTAAAAAAACAATTAA
313854 TTTT-AAAAAACAATTA
1 TTTTAAAAAAACAATTA
313870 TGATTATATT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 12 0.75
18 4 0.25
ACGTcount: A:0.59, C:0.06, G:0.00, T:0.35
Consensus pattern (18 bp):
TTTTAAAAAAACAATTAA
Found at i:324291 original size:24 final size:21
Alignment explanation
Indices: 324235--324293 Score: 57
Period size: 24 Copynumber: 2.6 Consensus size: 21
324225 AGATCCAATC
*
324235 AAAATAAAGAG-ACAAAAAGA
1 AAAAGAAAGAGAACAAAAAGA
324255 AAAAGAGAGAGAGAACAACAAAGGA
1 AAAAGA-A-AGAGAACAA-AAA-GA
324280 AAAAGCAAAGAGAA
1 AAAAG-AAAGAGAA
324294 AATAAAAAAG
Statistics
Matches: 32, Mismatches: 1, Indels: 8
0.78 0.02 0.20
Matches are distributed among these distances:
20 5 0.16
21 1 0.03
22 4 0.12
23 4 0.12
24 9 0.28
25 8 0.25
26 1 0.03
ACGTcount: A:0.69, C:0.07, G:0.22, T:0.02
Consensus pattern (21 bp):
AAAAGAAAGAGAACAAAAAGA
Found at i:324291 original size:26 final size:22
Alignment explanation
Indices: 324242--324292 Score: 57
Period size: 25 Copynumber: 2.1 Consensus size: 22
324232 ATCAAAATAA
*
324242 AGAGACAAAAAGAAAAAGAGAG
1 AGAGACAAAAAGAAAAAGAAAG
324264 AGAGAACAACAAAGGAAAAAGCAAAG
1 AGAG-ACAA-AAA-GAAAAAG-AAAG
324290 AGA
1 AGA
324293 AAATAAAAAA
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
22 4 0.17
23 4 0.17
24 3 0.12
25 7 0.29
26 6 0.25
ACGTcount: A:0.67, C:0.08, G:0.25, T:0.00
Consensus pattern (22 bp):
AGAGACAAAAAGAAAAAGAAAG
Found at i:324303 original size:26 final size:25
Alignment explanation
Indices: 324248--324308 Score: 61
Period size: 26 Copynumber: 2.4 Consensus size: 25
324238 ATAAAGAGAC
* *
324248 AAAAA-GAAAAAGAGAGAGAGAACA
1 AAAAAGGAAAAAGAAAGAGAAAACA
* *
324272 ACAAAGGAAAAAGCAAAGAGAAAATA
1 AAAAAGGAAAAAG-AAAGAGAAAACA
324298 AAAAAGAGAAA
1 AAAAAG-GAAA
324309 CAAAAACAAA
Statistics
Matches: 29, Mismatches: 5, Indels: 3
0.78 0.14 0.08
Matches are distributed among these distances:
24 4 0.14
25 7 0.24
26 14 0.48
27 4 0.14
ACGTcount: A:0.72, C:0.05, G:0.21, T:0.02
Consensus pattern (25 bp):
AAAAAGGAAAAAGAAAGAGAAAACA
Found at i:326315 original size:156 final size:156
Alignment explanation
Indices: 326030--326317 Score: 391
Period size: 156 Copynumber: 1.8 Consensus size: 156
326020 CTACAAAAGT
* * * * *
326030 TGTCAACAAATAACTTTCCAGTTTCATTCGGAGCCAATTTCAACTTCACAGCGAATGATATTGGA
1 TGTCAACAAACAACTTTCCAATTTCATTCAGAACCAATTTCAACTTCACAGCGAAGGATATTGGA
* * * *
326095 CTCGAAACAACGCGACTTACACAAGATTAGATTTCAACTTCACAACGAAGGATATCCAATTCAAA
66 CTCGAAACAACACAACTTACACAAGATTAGATTTCAACTTCACAACGAAGGATAGCCAACTCAAA
326160 GCTCAACTTCACAGCGAAGGAGTGTC
131 GCTCAACTTCACAGCGAAGGAGTGTC
* *
326186 TGTCAACAAACAACTTTCCAATTTCATTCAGAATCAATTTCAACTTCACAGCGAAGGGTATTGGA
1 TGTCAACAAACAACTTTCCAATTTCATTCAGAACCAATTTCAACTTCACAGCGAAGGATATTGGA
* * * * * *
326251 CT-TAAAGCAACACAATTTACTCGAGATT-GAATTTCAACTTCACAACGAATGATAGCTAACTCA
66 CTCGAAA-CAACACAACTTACACAAGATTAG-ATTTCAACTTCACAACGAAGGATAGCCAACTCA
326314 AAGC
129 AAGC
326318 CAATTTGGTG
Statistics
Matches: 113, Mismatches: 17, Indels: 4
0.84 0.13 0.03
Matches are distributed among these distances:
155 4 0.04
156 109 0.96
ACGTcount: A:0.36, C:0.23, G:0.15, T:0.26
Consensus pattern (156 bp):
TGTCAACAAACAACTTTCCAATTTCATTCAGAACCAATTTCAACTTCACAGCGAAGGATATTGGA
CTCGAAACAACACAACTTACACAAGATTAGATTTCAACTTCACAACGAAGGATAGCCAACTCAAA
GCTCAACTTCACAGCGAAGGAGTGTC
Found at i:326432 original size:60 final size:64
Alignment explanation
Indices: 326269--326440 Score: 192
Period size: 65 Copynumber: 2.7 Consensus size: 64
326259 AACACAATTT
* * * * * *
326269 ACTCGAGATTGAATTTCAACTTCACAACGAATGATAGCTAACTCAAAGCCAATTTGGTGAAACTT
1 ACTC-AGATTGGATTTCAACTTCACAACGAAGGATATCCAACTCAAAACCAATTTGGTGAAACTA
* *
326334 ACTCAAGATTGGATTTCAACTTTACGAA-AAAGGATATCCAACTCAAAACCAATTTGGTGAAAC-
1 ACTC-AGATTGGATTTCAACTTCAC-AACGAAGGATATCCAACTCAAAACCAATTTGGTGAAACT
326397 A
64 A
* *
326398 AC-C-G-TTGGATTTTAACTTCACAACGAAGGATATCCAATTCAAA
1 ACTCAGATTGGATTTCAACTTCACAACGAAGGATATCCAACTCAAA
326441 GCTCAAATTT
Statistics
Matches: 92, Mismatches: 13, Indels: 9
0.81 0.11 0.08
Matches are distributed among these distances:
59 2 0.02
60 32 0.35
61 1 0.01
63 1 0.01
64 2 0.02
65 52 0.57
66 2 0.02
ACGTcount: A:0.39, C:0.20, G:0.15, T:0.27
Consensus pattern (64 bp):
ACTCAGATTGGATTTCAACTTCACAACGAAGGATATCCAACTCAAAACCAATTTGGTGAAACTA
Found at i:326547 original size:124 final size:124
Alignment explanation
Indices: 326402--326662 Score: 353
Period size: 124 Copynumber: 2.1 Consensus size: 124
326392 GAAACAACCG
* * * *
326402 TTGGATTTTAACTTCACAACGAAGGATATCCAATTCAAAGCTCAAATTTACAACGAATGAGTCAT
1 TTGGATTTCAACTTCACAACGAAGGATATCCAATTCAAAGCTCAAATTGACAACGAAGGAGCCAT
* * *
326467 CCATGATTTCAACTTCACGACGA-AGGATATTATGCCCACAAGAAGCATCCATCTCTAGA
66 CCACGATTTCAACTTCACGA-GAGAGGATATCATGCCCACAAGAAGCATCCATCTCTAAA
* * *
326526 TTGGATTTCAACTTCACAACGAAGGATATCCAATTTAAAGCTCAACTTGACCACGAAGGAGCCAT
1 TTGGATTTCAACTTCACAACGAAGGATATCCAATTCAAAGCTCAAATTGACAACGAAGGAGCCAT
* * * * * *
326591 CCACGATTTCAACTTCACGATAGAGGATATCCTGTCCACAAGCATCATCCATTTCTAAA
66 CCACGATTTCAACTTCACGAGAGAGGATATCATGCCCACAAGAAGCATCCATCTCTAAA
*
326650 ATGGATTTCAACT
1 TTGGATTTCAACT
326663 CAAAGTCAAT
Statistics
Matches: 119, Mismatches: 17, Indels: 2
0.86 0.12 0.01
Matches are distributed among these distances:
123 1 0.01
124 118 0.99
ACGTcount: A:0.35, C:0.24, G:0.15, T:0.27
Consensus pattern (124 bp):
TTGGATTTCAACTTCACAACGAAGGATATCCAATTCAAAGCTCAAATTGACAACGAAGGAGCCAT
CCACGATTTCAACTTCACGAGAGAGGATATCATGCCCACAAGAAGCATCCATCTCTAAA
Found at i:326798 original size:34 final size:34
Alignment explanation
Indices: 326760--326837 Score: 147
Period size: 34 Copynumber: 2.3 Consensus size: 34
326750 TCCTTGGATT
*
326760 TCAACTTCACGATGAAGGATATTCAACTCCAAGC
1 TCAACTTCACGATGAAGGATATCCAACTCCAAGC
326794 TCAACTTCACGATGAAGGATATCCAACTCCAAGC
1 TCAACTTCACGATGAAGGATATCCAACTCCAAGC
326828 TCAACTTCAC
1 TCAACTTCAC
326838 AACGAATGAG
Statistics
Matches: 43, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
34 43 1.00
ACGTcount: A:0.35, C:0.29, G:0.13, T:0.23
Consensus pattern (34 bp):
TCAACTTCACGATGAAGGATATCCAACTCCAAGC
Found at i:327106 original size:83 final size:83
Alignment explanation
Indices: 326958--327287 Score: 362
Period size: 83 Copynumber: 3.9 Consensus size: 83
326948 CAACCAAGTG
* * **
326958 CAGCATAGCTCAAGGCGAGAAGGGTTATCTGTCAATG-AAACCTTCGAGTTCGATTACATTCAGC
1 CAGCATAGCTCAAGGCGAGAAGGGCTATCTGTC-A-GCAAATCTTTAAGTTCGATTACATTCAGC
327022 TCAAGGACATATCAAATTTA
64 TCAAGGACATATCAAATTTA
* * * *
327042 CAACATAGCTCAAGGCAAGAAGGGCTATTTGTTAGCAAATCTTTAAGTTCGATTACATTCAGCTC
1 CAGCATAGCTCAAGGCGAGAAGGGCTATCTGTCAGCAAATCTTTAAGTTCGATTACATTCAGCTC
*
327107 ATGGACATATCAAATTTA
66 AAGGACATATCAAATTTA
* * * * * ** * *
327125 -ATGCATAACTTAAGGCGAGAAGAGCTATCTGTCAGTAAACCTTCGAGCTCGATTACATTTAGCT
1 CA-GCATAGCTCAAGGCGAGAAGGGCTATCTGTCAGCAAATCTTTAAGTTCGATTACATTCAGCT
*
327189 CATGGACATATCAAATTTA
65 CAAGGACATATCAAATTTA
* * *
327208 CAGCATAGCTCAAGGCGAGAAGGGTTATCTGTCAACAAGAAT-TTTCAAGTTCGATTTCATTCAG
1 CAGCATAGCTCAAGGCGAGAAGGGCTATCTGTCAGC-A-AATCTTT-AAGTTCGATTACATTCAG
*
327272 TTCGAAGG-CATATCAA
63 CTC-AAGGACATATCAA
327288 CCGCATGGTA
Statistics
Matches: 203, Mismatches: 36, Indels: 13
0.81 0.14 0.05
Matches are distributed among these distances:
82 2 0.01
83 140 0.69
84 32 0.16
85 26 0.13
86 3 0.01
ACGTcount: A:0.34, C:0.19, G:0.19, T:0.28
Consensus pattern (83 bp):
CAGCATAGCTCAAGGCGAGAAGGGCTATCTGTCAGCAAATCTTTAAGTTCGATTACATTCAGCTC
AAGGACATATCAAATTTA
Found at i:327182 original size:166 final size:169
Alignment explanation
Indices: 326960--327271 Score: 452
Period size: 166 Copynumber: 1.9 Consensus size: 169
326950 ACCAAGTGCA
* * * *
326960 GCATAGCTCAAGGCGAGAAGGGTTATCTGTCAATGAAACCTTCGAGTTCGATTACATTCAGCTCA
1 GCATAACTCAAGGCGAGAAGAGCTATCTGTCAATGAAACCTTCGAGCTCGATTACATTCAGCTCA
* * *
327025 AGGACATATCAAATTTACAACATAGCTCAAGGCAAGAAGGGCTATTTGTTAGC-A-AATCTTT-A
66 AGGACATATCAAATTTACAACATAGCTCAAGGCAAGAAGGGCTATCTGTCAACAAGAAT-TTTCA
327087 AGTTCGATTACATTCAGCTCATGGACATATCAAATTTAAT
130 AGTTCGATTACATTCAGCTCATGGACATATCAAATTTAAT
* * *
327127 GCATAACTTAAGGCGAGAAGAGCTATCTGTCAGT-AAACCTTCGAGCTCGATTACATTTAGCTCA
1 GCATAACTCAAGGCGAGAAGAGCTATCTGTCAATGAAACCTTCGAGCTCGATTACATTCAGCTCA
* * * *
327191 TGGACATATCAAATTTACAGCATAGCTCAAGGCGAGAAGGGTTATCTGTCAACAAGAATTTTCAA
66 AGGACATATCAAATTTACAACATAGCTCAAGGCAAGAAGGGCTATCTGTCAACAAGAATTTTCAA
*
327256 GTTCGATTTCATTCAG
131 GTTCGATTACATTCAG
327272 TTCGAAGGCA
Statistics
Matches: 127, Mismatches: 15, Indels: 5
0.86 0.10 0.03
Matches are distributed among these distances:
166 74 0.58
167 33 0.26
168 20 0.16
ACGTcount: A:0.33, C:0.19, G:0.19, T:0.29
Consensus pattern (169 bp):
GCATAACTCAAGGCGAGAAGAGCTATCTGTCAATGAAACCTTCGAGCTCGATTACATTCAGCTCA
AGGACATATCAAATTTACAACATAGCTCAAGGCAAGAAGGGCTATCTGTCAACAAGAATTTTCAA
GTTCGATTACATTCAGCTCATGGACATATCAAATTTAAT
Found at i:328563 original size:30 final size:29
Alignment explanation
Indices: 328497--328565 Score: 79
Period size: 29 Copynumber: 2.3 Consensus size: 29
328487 ATGATTTTGA
*
328497 CACTTAAGTTTCTGTTATTTTATTTTAGT
1 CACTTAAGTTTCTGTTATTTTATTTTAAT
*
328526 CACTTAAGTTTTTGTT-TTTGCTATTTTAAT
1 CACTTAAGTTTCTGTTATTT--TATTTTAAT
328556 C-CTTTAAGTT
1 CAC-TTAAGTT
328566 AATGTTTTCA
Statistics
Matches: 35, Mismatches: 2, Indels: 5
0.83 0.05 0.12
Matches are distributed among these distances:
28 3 0.09
29 16 0.46
30 16 0.46
ACGTcount: A:0.20, C:0.12, G:0.10, T:0.58
Consensus pattern (29 bp):
CACTTAAGTTTCTGTTATTTTATTTTAAT
Found at i:334063 original size:39 final size:39
Alignment explanation
Indices: 334018--334135 Score: 227
Period size: 39 Copynumber: 3.0 Consensus size: 39
334008 ATGTCACTTT
334018 CTGATTAATTTGTTAATGGAACTATGAAAATGTGAAATG
1 CTGATTAATTTGTTAATGGAACTATGAAAATGTGAAATG
*
334057 CTGATTAATTTGTTAATAGAACTATGAAAATGTGAAATG
1 CTGATTAATTTGTTAATGGAACTATGAAAATGTGAAATG
334096 CTGATTAATTTGTTAATGGAACTATGAAAATGTGAAATG
1 CTGATTAATTTGTTAATGGAACTATGAAAATGTGAAATG
334135 C
1 C
334136 ATAGGAAATG
Statistics
Matches: 77, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
39 77 1.00
ACGTcount: A:0.39, C:0.06, G:0.19, T:0.36
Consensus pattern (39 bp):
CTGATTAATTTGTTAATGGAACTATGAAAATGTGAAATG
Found at i:335989 original size:21 final size:22
Alignment explanation
Indices: 335963--336012 Score: 75
Period size: 23 Copynumber: 2.3 Consensus size: 22
335953 CACCGAAGTG
335963 CCACATA-TTTGTCCCAAAGGA
1 CCACATAGTTTGTCCCAAAGGA
335984 CCACATAGTTTTGTCCCAAAGGA
1 CCACATAG-TTTGTCCCAAAGGA
*
336007 CTACAT
1 CCACAT
336013 TGAACCATCG
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
21 7 0.27
23 19 0.73
ACGTcount: A:0.32, C:0.28, G:0.14, T:0.26
Consensus pattern (22 bp):
CCACATAGTTTGTCCCAAAGGA
Found at i:336710 original size:18 final size:20
Alignment explanation
Indices: 336671--336717 Score: 71
Period size: 18 Copynumber: 2.5 Consensus size: 20
336661 CTTCCTCTTG
336671 GTATCGATACCTCCACATCA
1 GTATCGATACCTCCACATCA
*
336691 GTATCGATA-CTTCA-ATCA
1 GTATCGATACCTCCACATCA
336709 GTATCGATA
1 GTATCGATA
336718 TTGTTCATCG
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
18 13 0.50
19 4 0.15
20 9 0.35
ACGTcount: A:0.32, C:0.26, G:0.13, T:0.30
Consensus pattern (20 bp):
GTATCGATACCTCCACATCA
Found at i:342816 original size:14 final size:14
Alignment explanation
Indices: 342797--342826 Score: 60
Period size: 14 Copynumber: 2.1 Consensus size: 14
342787 TATATCAAAA
342797 CATCAAAATGTTTT
1 CATCAAAATGTTTT
342811 CATCAAAATGTTTT
1 CATCAAAATGTTTT
342825 CA
1 CA
342827 ACAATCTCCC
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.37, C:0.17, G:0.07, T:0.40
Consensus pattern (14 bp):
CATCAAAATGTTTT
Found at i:342898 original size:13 final size:13
Alignment explanation
Indices: 342880--342912 Score: 59
Period size: 12 Copynumber: 2.6 Consensus size: 13
342870 TAAGATTTTC
342880 TTTGAAAATCATT
1 TTTGAAAATCATT
342893 TTTG-AAATCATT
1 TTTGAAAATCATT
342905 TTTGAAAA
1 TTTGAAAA
342913 ATTACTCTCC
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
12 12 0.63
13 7 0.37
ACGTcount: A:0.39, C:0.06, G:0.09, T:0.45
Consensus pattern (13 bp):
TTTGAAAATCATT
Found at i:343190 original size:16 final size:16
Alignment explanation
Indices: 343149--343184 Score: 56
Period size: 15 Copynumber: 2.3 Consensus size: 16
343139 TAAAATAATG
*
343149 CAAAAAATAAT-AAAC
1 CAAAAAAAAATCAAAC
343164 CAAAAAAAAATCAAAC
1 CAAAAAAAAATCAAAC
343180 CAAAA
1 CAAAA
343185 CCAAATATAT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
15 10 0.53
16 9 0.47
ACGTcount: A:0.75, C:0.17, G:0.00, T:0.08
Consensus pattern (16 bp):
CAAAAAAAAATCAAAC
Found at i:344668 original size:12 final size:13
Alignment explanation
Indices: 344651--344688 Score: 51
Period size: 12 Copynumber: 2.9 Consensus size: 13
344641 ATAGGCAAAA
*
344651 TTTGAAAACTAT-
1 TTTGAAAACAATG
344663 TTTGAAAACAATG
1 TTTGAAAACAATG
344676 TTTGAAAATCAAT
1 TTTGAAAA-CAAT
344689 ATGTAGTTTT
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
12 11 0.48
13 8 0.35
14 4 0.17
ACGTcount: A:0.45, C:0.08, G:0.11, T:0.37
Consensus pattern (13 bp):
TTTGAAAACAATG
Found at i:349356 original size:19 final size:19
Alignment explanation
Indices: 349332--349380 Score: 89
Period size: 19 Copynumber: 2.6 Consensus size: 19
349322 GAATGCATTT
349332 CATGCATCGATGCATATAC
1 CATGCATCGATGCATATAC
*
349351 CATGCATCGATGTATATAC
1 CATGCATCGATGCATATAC
349370 CATGCATCGAT
1 CATGCATCGAT
349381 ACACTCAGGG
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
19 29 1.00
ACGTcount: A:0.31, C:0.24, G:0.16, T:0.29
Consensus pattern (19 bp):
CATGCATCGATGCATATAC
Found at i:349464 original size:56 final size:57
Alignment explanation
Indices: 349370--349477 Score: 157
Period size: 56 Copynumber: 1.9 Consensus size: 57
349360 ATGTATATAC
*
349370 CATGCATCGATACACTCAGGGTTTTATGAAAACATCGAATGCATTTGATGCACCAGT
1 CATGCATCGATACACTCAGGCTTTTATGAAAACATCGAATGCATTTGATGCACCAGT
* * *
349427 CATGCATCGATGCACTTAGGCTATTT-TG-AAACATCGAATGCATTTTATGCA
1 CATGCATCGATACACTCAGGCT-TTTATGAAAACATCGAATGCATTTGATGCA
349478 TCAATGCACT
Statistics
Matches: 46, Mismatches: 4, Indels: 3
0.87 0.08 0.06
Matches are distributed among these distances:
56 22 0.48
57 21 0.46
58 3 0.07
ACGTcount: A:0.31, C:0.20, G:0.19, T:0.31
Consensus pattern (57 bp):
CATGCATCGATACACTCAGGCTTTTATGAAAACATCGAATGCATTTGATGCACCAGT
Found at i:353344 original size:19 final size:21
Alignment explanation
Indices: 353301--353352 Score: 81
Period size: 19 Copynumber: 2.6 Consensus size: 21
353291 GAATCCCCTT
353301 TGAAAATACATGATTTTTAAA
1 TGAAAATACATGATTTTTAAA
353322 TGAAAATACATGA-TTTT-AA
1 TGAAAATACATGATTTTTAAA
*
353341 TGAAGATACATG
1 TGAAAATACATG
353353 CTCTTGGCCG
Statistics
Matches: 30, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
19 13 0.43
20 4 0.13
21 13 0.43
ACGTcount: A:0.46, C:0.06, G:0.13, T:0.35
Consensus pattern (21 bp):
TGAAAATACATGATTTTTAAA
Found at i:354281 original size:30 final size:31
Alignment explanation
Indices: 354240--354299 Score: 86
Period size: 30 Copynumber: 2.0 Consensus size: 31
354230 ACATGCTGCC
**
354240 ATGATATCTAAATGATATGCAAACATAATAA
1 ATGATATCTAAAACATATGCAAACATAATAA
*
354271 ATGA-ATCTAAAACATATGTAAACATAATA
1 ATGATATCTAAAACATATGCAAACATAATA
354300 TAAAGCTAAG
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
30 22 0.85
31 4 0.15
ACGTcount: A:0.53, C:0.10, G:0.08, T:0.28
Consensus pattern (31 bp):
ATGATATCTAAAACATATGCAAACATAATAA
Found at i:357545 original size:19 final size:21
Alignment explanation
Indices: 357502--357553 Score: 81
Period size: 19 Copynumber: 2.6 Consensus size: 21
357492 GAAACCCCTT
357502 TGAAAATACATGATTTTTAAA
1 TGAAAATACATGATTTTTAAA
357523 TGAAAATACATGA-TTTT-AA
1 TGAAAATACATGATTTTTAAA
*
357542 TGAAGATACATG
1 TGAAAATACATG
357554 CTCTTGGCCG
Statistics
Matches: 30, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
19 13 0.43
20 4 0.13
21 13 0.43
ACGTcount: A:0.46, C:0.06, G:0.13, T:0.35
Consensus pattern (21 bp):
TGAAAATACATGATTTTTAAA
Found at i:358399 original size:30 final size:31
Alignment explanation
Indices: 358358--358417 Score: 86
Period size: 30 Copynumber: 2.0 Consensus size: 31
358348 ACATGCTGCC
**
358358 ATGATATCTAAATGATATGAAAACATAATAA
1 ATGATATCTAAAACATATGAAAACATAATAA
*
358389 ATGA-ATCTAAAACATATGTAAACATAATA
1 ATGATATCTAAAACATATGAAAACATAATA
358418 TAAAGCTAAG
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
30 22 0.85
31 4 0.15
ACGTcount: A:0.55, C:0.08, G:0.08, T:0.28
Consensus pattern (31 bp):
ATGATATCTAAAACATATGAAAACATAATAA
Found at i:361072 original size:21 final size:22
Alignment explanation
Indices: 361043--361101 Score: 57
Period size: 23 Copynumber: 2.7 Consensus size: 22
361033 TGCATCCCTT
361043 TGAAAGTGCATCGAT-ACACCA
1 TGAAAGTGCATCGATCACACCA
* * * *
361064 TGAAGGTGCACCGATGCACGCCT
1 TGAAAGTGCATCGAT-CACACCA
*
361087 TGAATGTGCATCGAT
1 TGAAAGTGCATCGAT
361102 GCATCCGTCG
Statistics
Matches: 30, Mismatches: 6, Indels: 2
0.79 0.16 0.05
Matches are distributed among these distances:
21 13 0.43
23 17 0.57
ACGTcount: A:0.29, C:0.24, G:0.25, T:0.22
Consensus pattern (22 bp):
TGAAAGTGCATCGATCACACCA
Found at i:361090 original size:44 final size:44
Alignment explanation
Indices: 361003--361101 Score: 114
Period size: 44 Copynumber: 2.2 Consensus size: 44
360993 TTTTGTGCTT
* *
361003 AGTGCATCGATACACTTAACAGTGCATCGATGCATCCCTTTGAA
1 AGTGCATCGATACACTGAACAGTGCACCGATGCATCCCTTTGAA
*
361047 AGTGCATCGATACACCATGAA-GGTGCACCGATGCA-CGCC-TTGAA
1 AGTGCATCGATACA-C-TGAACAGTGCACCGATGCATC-CCTTTGAA
*
361091 TGTGCATCGAT
1 AGTGCATCGAT
361102 GCATCCGTCG
Statistics
Matches: 48, Mismatches: 4, Indels: 6
0.83 0.07 0.10
Matches are distributed among these distances:
44 30 0.62
45 15 0.31
46 3 0.06
ACGTcount: A:0.28, C:0.25, G:0.22, T:0.24
Consensus pattern (44 bp):
AGTGCATCGATACACTGAACAGTGCACCGATGCATCCCTTTGAA
Found at i:361550 original size:14 final size:13
Alignment explanation
Indices: 361517--361543 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
361507 ATTGAAAATC
361517 TAAATTTTATTTT
1 TAAATTTTATTTT
361530 TAAATTTTATTTT
1 TAAATTTTATTTT
361543 T
1 T
361544 TTGATTTAAT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (13 bp):
TAAATTTTATTTT
Found at i:363829 original size:45 final size:44
Alignment explanation
Indices: 363779--363887 Score: 130
Period size: 46 Copynumber: 2.4 Consensus size: 44
363769 TGCACCAATC
363779 CATGCATCGATGCACCATGGAATAAATTG-AACATCGAATGCATTT
1 CATGCATCGATGCACCA-GGAATAAA-TGAAACATCGAATGCATTT
** **
363824 CATGCATCGATGCACTCAGGGTTTTATGAAAACATCGAATGCATTT
1 CATGCATCGATGCAC-CAGGAATAAATG-AAACATCGAATGCATTT
*
363870 GATGCATCGATGCACCAG
1 CATGCATCGATGCACCAG
363888 CCATGCATCG
Statistics
Matches: 56, Mismatches: 5, Indels: 6
0.84 0.07 0.09
Matches are distributed among these distances:
44 2 0.04
45 22 0.39
46 32 0.57
ACGTcount: A:0.32, C:0.21, G:0.20, T:0.27
Consensus pattern (44 bp):
CATGCATCGATGCACCAGGAATAAATGAAACATCGAATGCATTT
Found at i:363931 original size:64 final size:65
Alignment explanation
Indices: 363824--363948 Score: 209
Period size: 64 Copynumber: 1.9 Consensus size: 65
363814 GAATGCATTT
*
363824 CATGCATCGATGCACTCAGGGTTTTATGAAAACATCGAATGCATTTGATGCATCGATGCACCAGC
1 CATGCATCGATGCACTCAGGATTTTATGAAAACATCGAATGCATTTGATGCATCGATGCACCAGC
*
363889 CATGCATCGATGCACTCAGGATATTT-TG-AAACATCGAATGCATTTTATGCATCGATGCAC
1 CATGCATCGATGCACTCAGGAT-TTTATGAAAACATCGAATGCATTTGATGCATCGATGCAC
363949 TGACGCTCCC
Statistics
Matches: 57, Mismatches: 2, Indels: 3
0.92 0.03 0.05
Matches are distributed among these distances:
64 31 0.54
65 23 0.40
66 3 0.05
ACGTcount: A:0.30, C:0.22, G:0.20, T:0.28
Consensus pattern (65 bp):
CATGCATCGATGCACTCAGGATTTTATGAAAACATCGAATGCATTTGATGCATCGATGCACCAGC
Found at i:366530 original size:59 final size:59
Alignment explanation
Indices: 366454--366582 Score: 150
Period size: 59 Copynumber: 2.2 Consensus size: 59
366444 AACAGTCGGT
* * ** *
366454 GACTATTTTTTAACTTTTAATAGTTGAGGGACTGAACAAAGCAATGCCCTATAATTAAGG
1 GACTA-TTTGTAACTTTTAATAGTCGAAAGACTGAACAAAGCAATACCCTATAATTAAGG
* * * * **
366514 GACTATTTGTAACTTTTAATAGTCGAAAGACTTAATAAAGCAATATCCTATAGTTGGGG
1 GACTATTTGTAACTTTTAATAGTCGAAAGACTGAACAAAGCAATACCCTATAATTAAGG
366573 GACTATTTGT
1 GACTATTTGT
366583 GTACTTTACC
Statistics
Matches: 58, Mismatches: 11, Indels: 1
0.83 0.16 0.01
Matches are distributed among these distances:
59 53 0.91
60 5 0.09
ACGTcount: A:0.34, C:0.12, G:0.19, T:0.35
Consensus pattern (59 bp):
GACTATTTGTAACTTTTAATAGTCGAAAGACTGAACAAAGCAATACCCTATAATTAAGG
Found at i:367235 original size:2 final size:2
Alignment explanation
Indices: 367228--367252 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
367218 GAAACTTTTG
367228 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 T
367253 CAACTCTATA
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:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:367428 original size:45 final size:44
Alignment explanation
Indices: 367366--367458 Score: 132
Period size: 45 Copynumber: 2.1 Consensus size: 44
367356 AATCCAGTTA
*
367366 ATTTATTAACACTACAAGTGAGGATTTAAAATATTATCATCTGTT
1 ATTTAATAACACTACAAGTGAGGATTTAAAATATTATCATCT-TT
* ** *
367411 ATTTAATAGCACTACAAGTGAGGATTTAATTTTTTATCATCTTT
1 ATTTAATAACACTACAAGTGAGGATTTAAAATATTATCATCTTT
367455 ATTT
1 ATTT
367459 TTATTTTTTT
Statistics
Matches: 43, Mismatches: 5, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
44 6 0.14
45 37 0.86
ACGTcount: A:0.34, C:0.11, G:0.11, T:0.44
Consensus pattern (44 bp):
ATTTAATAACACTACAAGTGAGGATTTAAAATATTATCATCTTT
Found at i:373082 original size:24 final size:24
Alignment explanation
Indices: 373055--373110 Score: 103
Period size: 24 Copynumber: 2.3 Consensus size: 24
373045 ATATTCTTTC
373055 GCTTCAATTGAGCTCAAATTTTAG
1 GCTTCAATTGAGCTCAAATTTTAG
*
373079 GCTTCAATTGATCTCAAATTTTAG
1 GCTTCAATTGAGCTCAAATTTTAG
373103 GCTTCAAT
1 GCTTCAAT
373111 CAAACTTCTA
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
24 31 1.00
ACGTcount: A:0.29, C:0.18, G:0.14, T:0.39
Consensus pattern (24 bp):
GCTTCAATTGAGCTCAAATTTTAG
Found at i:374383 original size:60 final size:58
Alignment explanation
Indices: 374300--374413 Score: 165
Period size: 60 Copynumber: 1.9 Consensus size: 58
374290 AATGGTACCC
* * *
374300 CGACTATAGAGTGATGCTTTGTTGAGTCTCCTGATTATTAAAAATTATAAAATGGTTCTT
1 CGACTATAGAGTAATGCTTTGTTGAGTC-CC-GACTATTAAAAATTACAAAATGGTTCTT
* *
374360 CGACTATAGGGTAATGCTTTGTTGAGTCCCGACTATTAAAAGTTACAAAATGGT
1 CGACTATAGAGTAATGCTTTGTTGAGTCCCGACTATTAAAAATTACAAAATGGT
374414 CACCAGACTA
Statistics
Matches: 49, Mismatches: 5, Indels: 2
0.88 0.09 0.04
Matches are distributed among these distances:
58 21 0.43
59 2 0.04
60 26 0.53
ACGTcount: A:0.31, C:0.13, G:0.20, T:0.36
Consensus pattern (58 bp):
CGACTATAGAGTAATGCTTTGTTGAGTCCCGACTATTAAAAATTACAAAATGGTTCTT
Found at i:378132 original size:26 final size:26
Alignment explanation
Indices: 378094--378156 Score: 76
Period size: 26 Copynumber: 2.5 Consensus size: 26
378084 ATAAAGGACA
*
378094 CTTA-GTGCA-TATGGTGGCCACAAC
1 CTTATGTGCATTATGGTGGACACAAC
* **
378118 CTTATGTGTATTATGGTGGACATGAC
1 CTTATGTGCATTATGGTGGACACAAC
378144 CTTATGTGCATTA
1 CTTATGTGCATTA
378157 GCACTTTGGT
Statistics
Matches: 32, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
24 4 0.12
25 4 0.12
26 24 0.75
ACGTcount: A:0.24, C:0.17, G:0.24, T:0.35
Consensus pattern (26 bp):
CTTATGTGCATTATGGTGGACACAAC
Found at i:385449 original size:15 final size:15
Alignment explanation
Indices: 385377--385453 Score: 50
Period size: 15 Copynumber: 5.1 Consensus size: 15
385367 TATTAATATA
* *
385377 TGAATGTGTTCTCTG
1 TGAAAGTGTTCTATG
385392 TGAAAGTGCTT-TATG
1 TGAAAGTG-TTCTATG
* * *
385407 TGACTA-CGTTCTACG
1 TGA-AAGTGTTCTATG
* * *
385422 TTAAAATGCTCTATG
1 TGAAAGTGTTCTATG
385437 TGAAAGTGTTCTATG
1 TGAAAGTGTTCTATG
385452 TG
1 TG
385454 GATAAAAGAC
Statistics
Matches: 45, Mismatches: 13, Indels: 8
0.68 0.20 0.12
Matches are distributed among these distances:
14 3 0.07
15 39 0.87
16 3 0.07
ACGTcount: A:0.23, C:0.13, G:0.23, T:0.40
Consensus pattern (15 bp):
TGAAAGTGTTCTATG
Found at i:385607 original size:24 final size:24
Alignment explanation
Indices: 385579--385637 Score: 66
Period size: 24 Copynumber: 2.5 Consensus size: 24
385569 CCTTTAGAAT
*
385579 AATTCTATGTGGTTCTTCGAGACA
1 AATTCTATGTGGTCCTTCGAGACA
* * *
385603 AATTCTACGCGGTCCTTCGGGACA
1 AATTCTATGTGGTCCTTCGAGACA
*
385627 AA-TATATGTGG
1 AATTCTATGTGG
385638 CACTTCGGTG
Statistics
Matches: 28, Mismatches: 7, Indels: 1
0.78 0.19 0.03
Matches are distributed among these distances:
23 6 0.21
24 22 0.79
ACGTcount: A:0.25, C:0.19, G:0.24, T:0.32
Consensus pattern (24 bp):
AATTCTATGTGGTCCTTCGAGACA
Found at i:388613 original size:47 final size:45
Alignment explanation
Indices: 388545--388669 Score: 153
Period size: 47 Copynumber: 2.8 Consensus size: 45
388535 ATAAAATCTT
*
388545 TTACCATTTATCCCATAAGCTCGTAAGCTTATTTTACCAAAATAC
1 TTACCATTTATTCCATAAGCTCGTAAGCTTATTTTACCAAAATAC
* * * *
388590 TTACCATTTAAATTCCATAAGCTCGTAAGCTTGTTTTTCCTATATAC
1 TTACCATTT--ATTCCATAAGCTCGTAAGCTTATTTTACCAAAATAC
* * *
388637 TTGCCA-TTATTCCGTAAGCTCATAAGCTTATTT
1 TTACCATTTATTCCATAAGCTCGTAAGCTTATTT
388670 GCATGGTTAC
Statistics
Matches: 69, Mismatches: 9, Indels: 5
0.83 0.11 0.06
Matches are distributed among these distances:
44 22 0.32
45 9 0.13
46 2 0.03
47 36 0.52
ACGTcount: A:0.29, C:0.22, G:0.09, T:0.40
Consensus pattern (45 bp):
TTACCATTTATTCCATAAGCTCGTAAGCTTATTTTACCAAAATAC
Found at i:391596 original size:65 final size:62
Alignment explanation
Indices: 391477--391686 Score: 203
Period size: 65 Copynumber: 3.3 Consensus size: 62
391467 TTTATCAAAG
* *
391477 TGATGCACCAATGCACCAATCCATGCATCGATGCACCATGA--ATTAAATTG-AACATCAAATGC
1 TGATGCATCGATGCA-CAA-CCATGCATCGATGCACC-TGACGATT---TTGAAACATCAAATGC
391539 ATT
60 ATT
* * *
391542 TCATGCATCGATGCACATACCATGCATCGATGCA-CTGAGGATTTGATGAAAACATCAAATACAT
1 TGATGCATCGATGCACA-ACCATGCATCGATGCACCTGACGATTT--TG-AAACATCAAATGCAT
391606 T
62 T
* * * *
391607 TGATGCATCGATGCACCAGCCATGCATCGATGCACTCTGACTATTTTGAAACATCGAATGCACT
1 TGATGCATCGATGCA-CAACCATGCATCGATGCAC-CTGACGATTTTGAAACATCAAATGCATT
391671 TGATGCATCGATGCAC
1 TGATGCATCGATGCAC
391687 TCTTAGTGCA
Statistics
Matches: 124, Mismatches: 11, Indels: 22
0.79 0.07 0.14
Matches are distributed among these distances:
61 1 0.01
62 3 0.02
63 4 0.03
64 48 0.39
65 58 0.47
66 2 0.02
67 8 0.06
ACGTcount: A:0.33, C:0.24, G:0.17, T:0.26
Consensus pattern (62 bp):
TGATGCATCGATGCACAACCATGCATCGATGCACCTGACGATTTTGAAACATCAAATGCATT
Found at i:391782 original size:177 final size:178
Alignment explanation
Indices: 391563--391917 Score: 694
Period size: 177 Copynumber: 2.0 Consensus size: 178
391553 TGCACATACC
391563 ATGCATCGATGCACTGAGGATTTGATGAAAACATCAAATACATTTGATGCATCGATGCACCAGCC
1 ATGCATCGATGCACTGAGGATTTGATGAAAACATCAAATACATTTGATGCATCGATGCACCAGCC
391628 ATGCATCGATGCACTCTGACTATTTTGAAACATCGAATGCACTTGATGCATCGATGCACTCTTAG
66 ATGCATCGATGCACTCTGACTATTTTGAAACATCGAATGCACTTGATGCATCGATGCACTCTTAG
391693 TGCACTGATGCACTAAAGGTCTAACGGTC-AAATATTTGAATTTTACA
131 TGCACTGATGCACTAAAGGTCTAACGGTCAAAATATTTGAATTTTACA
*
391740 ATGCATCGATGCACTGAGGATTTGATGAAAACATCGAATACATTTGATGCATCGATGCACCAGCC
1 ATGCATCGATGCACTGAGGATTTGATGAAAACATCAAATACATTTGATGCATCGATGCACCAGCC
391805 ATGCATCGATGCACTCTGACTATTTTGAAACATCGAATGCACTTGATGCATCGATGCACTCTTAG
66 ATGCATCGATGCACTCTGACTATTTTGAAACATCGAATGCACTTGATGCATCGATGCACTCTTAG
391870 TGCACTGATGCACTAAAGGTCTAACGGTCAAAATATTTGAATTTTACA
131 TGCACTGATGCACTAAAGGTCTAACGGTCAAAATATTTGAATTTTACA
391918 CTGATGCACC
Statistics
Matches: 176, Mismatches: 1, Indels: 1
0.99 0.01 0.01
Matches are distributed among these distances:
177 158 0.90
178 18 0.10
ACGTcount: A:0.32, C:0.21, G:0.19, T:0.29
Consensus pattern (178 bp):
ATGCATCGATGCACTGAGGATTTGATGAAAACATCAAATACATTTGATGCATCGATGCACCAGCC
ATGCATCGATGCACTCTGACTATTTTGAAACATCGAATGCACTTGATGCATCGATGCACTCTTAG
TGCACTGATGCACTAAAGGTCTAACGGTCAAAATATTTGAATTTTACA
Found at i:400437 original size:65 final size:63
Alignment explanation
Indices: 400368--400527 Score: 180
Period size: 65 Copynumber: 2.5 Consensus size: 63
400358 AATTAAATTG
* * *
400368 AACATCGAATGCATTTCATACATCTATGCACATACCATGCATCGATGCACTGAGGA-T-TTTATG
1 AACATCGAATGCATTTGATGCATCGATGCACA-ACCATGCATCGATGCACT-AGGACTATTT-TG
400431 AA
63 -A
* * * * *
400433 AACATCAAATGCATTTGATGCATCGATGCACCAGCCATGCGTTGATGCACTATGACTATTTTGA
1 AACATCGAATGCATTTGATGCATCGATGCA-CAACCATGCATCGATGCACTAGGACTATTTTGA
*
400497 AACATCGAATGCACTTGATGCATCGATGCAC
1 AACATCGAATGCATTTGATGCATCGATGCAC
400528 TCTTAGTGCA
Statistics
Matches: 82, Mismatches: 10, Indels: 8
0.82 0.10 0.08
Matches are distributed among these distances:
63 1 0.01
64 32 0.39
65 44 0.54
66 5 0.06
ACGTcount: A:0.32, C:0.23, G:0.17, T:0.28
Consensus pattern (63 bp):
AACATCGAATGCATTTGATGCATCGATGCACAACCATGCATCGATGCACTAGGACTATTTTGA
Found at i:400527 original size:17 final size:19
Alignment explanation
Indices: 400499--400547 Score: 57
Period size: 19 Copynumber: 2.6 Consensus size: 19
400489 TATTTTGAAA
400499 CATCGAATGCACT-TGA-TG
1 CATCG-ATGCACTCTGAGTG
*
400517 CATCGATGCACTCTTAGTG
1 CATCGATGCACTCTGAGTG
*
400536 CACCGATGCACT
1 CATCGATGCACT
400548 AAGGGTCCAA
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
17 7 0.26
18 7 0.26
19 13 0.48
ACGTcount: A:0.24, C:0.29, G:0.20, T:0.27
Consensus pattern (19 bp):
CATCGATGCACTCTGAGTG
Found at i:420559 original size:23 final size:22
Alignment explanation
Indices: 420530--420590 Score: 72
Period size: 20 Copynumber: 2.8 Consensus size: 22
420520 TTCCCCTGTG
420530 GGGGGAATCAGTTCCCCTTCAAA
1 GGGGGAATCAGTTCCCCTTC-AA
*
420553 GGGGGAATCGGTT-CCC-TCAA
1 GGGGGAATCAGTTCCCCTTCAA
* *
420573 GGGGGGATCAATTCCCCT
1 GGGGGAATCAGTTCCCCT
420591 GTAAACCTTC
Statistics
Matches: 32, Mismatches: 4, Indels: 5
0.78 0.10 0.12
Matches are distributed among these distances:
20 12 0.38
21 5 0.16
22 3 0.09
23 12 0.38
ACGTcount: A:0.21, C:0.26, G:0.31, T:0.21
Consensus pattern (22 bp):
GGGGGAATCAGTTCCCCTTCAA
Found at i:420577 original size:21 final size:23
Alignment explanation
Indices: 420529--420590 Score: 76
Period size: 21 Copynumber: 2.8 Consensus size: 23
420519 ATTCCCCTGT
420529 GGGGGGAATCAGTTCCCCTTCAA
1 GGGGGGAATCAGTTCCCCTTCAA
* *
420552 AGGGGGAATCGGTT-CCC-TCAA
1 GGGGGGAATCAGTTCCCCTTCAA
*
420573 GGGGGG-ATCAATTCCCCT
1 GGGGGGAATCAGTTCCCCT
420591 GTAAACCTTC
Statistics
Matches: 32, Mismatches: 5, Indels: 5
0.76 0.12 0.12
Matches are distributed among these distances:
20 5 0.16
21 12 0.38
22 3 0.09
23 12 0.38
ACGTcount: A:0.21, C:0.26, G:0.32, T:0.21
Consensus pattern (23 bp):
GGGGGGAATCAGTTCCCCTTCAA
Found at i:426082 original size:10 final size:10
Alignment explanation
Indices: 426067--426095 Score: 58
Period size: 10 Copynumber: 2.9 Consensus size: 10
426057 CTAAAAAAAC
426067 CAATGGCGGT
1 CAATGGCGGT
426077 CAATGGCGGT
1 CAATGGCGGT
426087 CAATGGCGG
1 CAATGGCGG
426096 CTCGACTCGG
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 19 1.00
ACGTcount: A:0.21, C:0.21, G:0.41, T:0.17
Consensus pattern (10 bp):
CAATGGCGGT
Found at i:428361 original size:114 final size:114
Alignment explanation
Indices: 428138--428363 Score: 296
Period size: 114 Copynumber: 2.0 Consensus size: 114
428128 CGTCAAATCT
* * *
428138 TGTTAAACAAGTTCATCAACCACCCAATCTCGACCTCATTGAGGCGTTCTCAAACTTTAATTGGA
1 TGTTAAACAAGTTCATCAACCACCCAATCCCGACCTCATTGAGGCCTTCTCAAACTTTAATAGGA
** *
428203 ATTGCATATTGGTCCATCGGCTTTTAAGTCTTCATCGGGGGCAAGGTCC
66 ATTGCATATTGGTCCATCACCTTTTAAGTCTTCATCCGGGGCAAGGTCC
* *
428252 TGTTAAACAAGTTCATCAACCTCCCAATCCCGACCTCATTGAGGCACTT-TCAAACTTTGATAGG
1 TGTTAAACAAGTTCATCAACCACCCAATCCCGACCTCATTGAGGC-CTTCTCAAACTTTAATAGG
* * * *
428316 AATTGCATCTTGG-CCAATCACCATTTTTA-TCTTTATCCGGTGCAAGGT
65 AATTGCATATTGGTCC-ATCACC-TTTTAAGTCTTCATCCGGGGCAAGGT
428364 TTTTTCGATC
Statistics
Matches: 97, Mismatches: 12, Indels: 6
0.84 0.10 0.05
Matches are distributed among these distances:
113 2 0.02
114 88 0.91
115 7 0.07
ACGTcount: A:0.26, C:0.25, G:0.17, T:0.31
Consensus pattern (114 bp):
TGTTAAACAAGTTCATCAACCACCCAATCCCGACCTCATTGAGGCCTTCTCAAACTTTAATAGGA
ATTGCATATTGGTCCATCACCTTTTAAGTCTTCATCCGGGGCAAGGTCC
Found at i:433392 original size:20 final size:21
Alignment explanation
Indices: 433364--433408 Score: 56
Period size: 21 Copynumber: 2.2 Consensus size: 21
433354 AAAACCAGAA
*
433364 CCCTAT-GGGGGTATCGATTC
1 CCCTATGGGGGGAATCGATTC
* *
433384 CCCTGTGGGGGGAATCGGTTC
1 CCCTATGGGGGGAATCGATTC
433405 CCCT
1 CCCT
433409 TCAAAGGGGG
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
20 5 0.24
21 16 0.76
ACGTcount: A:0.11, C:0.29, G:0.33, T:0.27
Consensus pattern (21 bp):
CCCTATGGGGGGAATCGATTC
Found at i:433438 original size:21 final size:23
Alignment explanation
Indices: 433390--433440 Score: 79
Period size: 23 Copynumber: 2.3 Consensus size: 23
433380 ATTCCCCTGT
433390 GGGGGGAATCGGTTCCCCTTCAA
1 GGGGGGAATCGGTTCCCCTTCAA
*
433413 AGGGGGAATCGGTT-CCC-TCAA
1 GGGGGGAATCGGTTCCCCTTCAA
433434 GGGGGGA
1 GGGGGGA
433441 TCAATTCCTC
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
21 10 0.38
22 3 0.12
23 13 0.50
ACGTcount: A:0.20, C:0.22, G:0.41, T:0.18
Consensus pattern (23 bp):
GGGGGGAATCGGTTCCCCTTCAA
Found at i:438800 original size:20 final size:19
Alignment explanation
Indices: 438775--438826 Score: 68
Period size: 20 Copynumber: 2.6 Consensus size: 19
438765 CTTGCTAAGT
* *
438775 AGTATCGATACTGAAGGGGG
1 AGTATCGATACCGAA-GGGA
438795 AGTATCGATACCGAAGGGA
1 AGTATCGATACCGAAGGGA
438814 AGGTATCGATACC
1 A-GTATCGATACC
438827 ATTTTGAAAC
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
19 4 0.14
20 25 0.86
ACGTcount: A:0.33, C:0.15, G:0.33, T:0.19
Consensus pattern (19 bp):
AGTATCGATACCGAAGGGA
Found at i:438902 original size:22 final size:20
Alignment explanation
Indices: 438851--438926 Score: 73
Period size: 22 Copynumber: 3.8 Consensus size: 20
438841 TGCAAAAATG
*
438851 GTATCGATACCATA-TCAGA
1 GTATCGATACCATAGTAAGA
* *
438870 GTATTGGTACCATAGTATAGTA
1 GTATCGATACCATAGTA-AG-A
* *
438892 GTATCGATACCATGGTAAGG
1 GTATCGATACCATAGTAAGA
*
438912 GTATCGATACTATAG
1 GTATCGATACCATAG
438927 AGCCAGAAAT
Statistics
Matches: 45, Mismatches: 9, Indels: 5
0.76 0.15 0.08
Matches are distributed among these distances:
19 12 0.27
20 14 0.31
21 4 0.09
22 15 0.33
ACGTcount: A:0.33, C:0.14, G:0.22, T:0.30
Consensus pattern (20 bp):
GTATCGATACCATAGTAAGA
Found at i:439246 original size:54 final size:54
Alignment explanation
Indices: 439164--439455 Score: 397
Period size: 54 Copynumber: 5.3 Consensus size: 54
439154 TTACCAAATA
*
439164 GGCACTAAGTGTGCATTTCACGGAATTCATCCTATGTGGATGAATAACCGTTTC
1 GGCACTAAGTGTGCATTTCACAGAATTCATCCTATGTGGATGAATAACCGTTTC
* *
439218 GGCACTAAGTGTGCATTTCACAGAATTCATCCTATGTGAATAAATAACCGTTTTC
1 GGCACTAAGTGTGCATTTCACAGAATTCATCCTATGTGGATGAATAACCG-TTTC
* **
439273 GGCACTAAGTGTGCATTTCACGGAATTCATCCTATGTGGATGAATAATAGTTTC
1 GGCACTAAGTGTGCATTTCACAGAATTCATCCTATGTGGATGAATAACCGTTTC
* * *
439327 AGTACTAAGTGTGCATTTTTTACAGAATTCATTCATTCTATGTGGATGAATAACCGTTTC
1 GGCACTAAGTGTGCA--TTTCACAGAATTCA-TC---CTATGTGGATGAATAACCGTTTC
*
439387 GACACTAAGTGTGCATTTCAC-GAAATTCATCCTATGTGGATGAATAACCGTTTC
1 GGCACTAAGTGTGCATTTCACAG-AATTCATCCTATGTGGATGAATAACCGTTTC
* *
439441 TGCACTATGTGTGCA
1 GGCACTAAGTGTGCA
439456 AAACATGAAA
Statistics
Matches: 209, Mismatches: 21, Indels: 16
0.85 0.09 0.07
Matches are distributed among these distances:
54 99 0.47
55 49 0.23
56 12 0.06
57 5 0.02
58 11 0.05
60 33 0.16
ACGTcount: A:0.28, C:0.18, G:0.20, T:0.34
Consensus pattern (54 bp):
GGCACTAAGTGTGCATTTCACAGAATTCATCCTATGTGGATGAATAACCGTTTC
Found at i:443792 original size:65 final size:63
Alignment explanation
Indices: 443673--443882 Score: 189
Period size: 65 Copynumber: 3.3 Consensus size: 63
443663 ATTTTCAGAG
* *
443673 TGATGCACCGATGCACCAATCCATGCATCGATGCAC-CATGA-ATTAAATTG-AACATCGAATGC
1 TGATGCATCGATGCA-CAA-CCATGCATCGATGCACTCAGGATATT---TTGAAACATCGAATGC
443735 ATT
61 ATT
* * * *
443738 TCATGCATCGATGCACATACCATGC-CCTGATGCACTGAGGAT-TTTATGAAAACATCGAATGTA
1 TGATGCATCGATGCACA-ACCATGCATC-GATGCACTCAGGATATTT-TG-AAACATCGAATGCA
443801 TT
62 TT
* * * *
443803 TGATGCAGT-GATGCACCAGCCATGCATCGATGCACTCTGGCTATTTTGAAACATCGAATGCACT
1 TGATGCA-TCGATGCA-CAACCATGCATCGATGCACTCAGGATATTTTGAAACATCGAATGCATT
443867 TGATGCATCGATGCAC
1 TGATGCATCGATGCAC
443883 TGAGAGTCCA
Statistics
Matches: 119, Mismatches: 14, Indels: 26
0.75 0.09 0.16
Matches are distributed among these distances:
62 1 0.01
63 5 0.04
64 42 0.35
65 64 0.54
66 7 0.06
ACGTcount: A:0.30, C:0.24, G:0.20, T:0.27
Consensus pattern (63 bp):
TGATGCATCGATGCACAACCATGCATCGATGCACTCAGGATATTTTGAAACATCGAATGCATT
Found at i:449706 original size:24 final size:23
Alignment explanation
Indices: 449679--449762 Score: 84
Period size: 23 Copynumber: 3.7 Consensus size: 23
449669 TCACTTAACA
449679 GTGCATCGATGCATCCCTTTGAAT
1 GTGCATCGATGCATCCC-TTGAAT
* *
449703 GTGCATCGATTCAT--CTTG-CT
1 GTGCATCGATGCATCCCTTGAAT
* * *
449723 GATACACCGATGCATGCCTTGAAT
1 G-TGCATCGATGCATCCCTTGAAT
449747 GTGCATCGATGCATCC
1 GTGCATCGATGCATCC
449763 GTCGGGTTTT
Statistics
Matches: 47, Mismatches: 9, Indels: 9
0.72 0.14 0.14
Matches are distributed among these distances:
20 2 0.04
21 13 0.28
22 1 0.02
23 16 0.34
24 15 0.32
ACGTcount: A:0.21, C:0.26, G:0.21, T:0.31
Consensus pattern (23 bp):
GTGCATCGATGCATCCCTTGAAT
Found at i:452548 original size:65 final size:63
Alignment explanation
Indices: 452429--452638 Score: 221
Period size: 65 Copynumber: 3.3 Consensus size: 63
452419 TTTTTTAGAG
* * *
452429 TGATGCACCGATGCACCAATCCATGCATCGATGCAC-CATGA-ATTAAATTG-AACATCGAATGC
1 TGATGCATCGATGCA-CAA-CCATGCACCGATGCACTCAGGATATT---TTGAAACATCGAATGC
452491 ATT
61 ATT
* *
452494 TCATGCATCGATGCACATACCATGCACCGATGCACTGAGGAT-TTTATGAAAACATCGAATGCAT
1 TGATGCATCGATGCACA-ACCATGCACCGATGCACTCAGGATATTT-TG-AAACATCGAATGCAT
452558 T
63 T
* * * * *
452559 TGATGCATCGATGCACCAGCCATGCATCGATGCACTCTGGCTATTTTGAAACATCGAATGCACT
1 TGATGCATCGATGCA-CAACCATGCACCGATGCACTCAGGATATTTTGAAACATCGAATGCATT
452623 TGATGCATCGATGCAC
1 TGATGCATCGATGCAC
452639 TCTTAGTGCA
Statistics
Matches: 125, Mismatches: 12, Indels: 18
0.81 0.08 0.12
Matches are distributed among these distances:
62 1 0.01
63 3 0.02
64 47 0.38
65 69 0.55
66 5 0.04
ACGTcount: A:0.30, C:0.25, G:0.19, T:0.26
Consensus pattern (63 bp):
TGATGCATCGATGCACAACCATGCACCGATGCACTCAGGATATTTTGAAACATCGAATGCATT
Found at i:455477 original size:20 final size:20
Alignment explanation
Indices: 455452--455502 Score: 68
Period size: 20 Copynumber: 2.5 Consensus size: 20
455442 ATTGAATCAA
*
455452 TATCGATACCAAATGGGGA-G
1 TATCGATACCAAA-GGGAAGG
*
455472 TATCGATACCGAAGGGAAGG
1 TATCGATACCAAAGGGAAGG
455492 TATCGATACCA
1 TATCGATACCA
455503 TTTCGAAACA
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
19 4 0.15
20 23 0.85
ACGTcount: A:0.35, C:0.18, G:0.27, T:0.20
Consensus pattern (20 bp):
TATCGATACCAAAGGGAAGG
Found at i:455577 original size:22 final size:20
Alignment explanation
Indices: 455527--455596 Score: 63
Period size: 22 Copynumber: 3.5 Consensus size: 20
455517 ACAAAAATGA
*
455527 TATCGATACCATA-TCAGAG
1 TATCGATACCATAGTAAGAG
*
455546 TAT-TAGTACCATAGTATAGTAG
1 TATCGA-TACCATAGTA-AG-AG
* *
455568 TATCGATACCATGGTAAGGG
1 TATCGATACCATAGTAAGAG
455588 TATCGATAC
1 TATCGATAC
455597 TATGGAGCCA
Statistics
Matches: 41, Mismatches: 5, Indels: 9
0.75 0.09 0.16
Matches are distributed among these distances:
18 1 0.02
19 10 0.24
20 11 0.27
21 4 0.10
22 14 0.34
23 1 0.02
ACGTcount: A:0.34, C:0.16, G:0.20, T:0.30
Consensus pattern (20 bp):
TATCGATACCATAGTAAGAG
Found at i:456289 original size:54 final size:54
Alignment explanation
Indices: 455923--456274 Score: 481
Period size: 54 Copynumber: 6.5 Consensus size: 54
455913 ACCAAATAAG
* * * * *
455923 CACTAAGTGTGCATTTTATGGAATTCATCCTATATGGATGAATAAGCATTTC-A
1 CACTAAGTGTGCATTTCACGGAATTCATCCTATGTGGATGAATAACCGTTTCGA
* *
455976 GCACTAAGTGTGCATTTCACAGAATTCATCCTATGTGGATGAATAACCATTTCGA
1 -CACTAAGTGTGCATTTCACGGAATTCATCCTATGTGGATGAATAACCGTTTCGA
* * * *
456031 CAATAAGTATGCATTTCACTGAATTCATCCTATGTGGATGAATAACCATTTCGA
1 CACTAAGTGTGCATTTCACGGAATTCATCCTATGTGGATGAATAACCGTTTCGA
*
456085 CACTAAGTGTGCATTTCACGGAATTCATTCTATGTGGATGAATAACCGTTTCGA
1 CACTAAGTGTGCATTTCACGGAATTCATCCTATGTGGATGAATAACCGTTTCGA
* * * *
456139 CACTAAGTGTGCATTTCACGAAATTCATCCTATATGGATGAATAATCGTTTCAA
1 CACTAAGTGTGCATTTCACGGAATTCATCCTATGTGGATGAATAACCGTTTCGA
* *
456193 CACTAAGTGTGCATTTCACGGAATTCATCCTATGCGGATGAATAACTGTTTCGA
1 CACTAAGTGTGCATTTCACGGAATTCATCCTATGTGGATGAATAACCGTTTCGA
* * ***
456247 CACTATGTGTACAAAACACGGAATTCAT
1 CACTAAGTGTGCATTTCACGGAATTCAT
456275 AATATGTTTA
Statistics
Matches: 268, Mismatches: 29, Indels: 2
0.90 0.10 0.01
Matches are distributed among these distances:
54 267 1.00
55 1 0.00
ACGTcount: A:0.32, C:0.19, G:0.17, T:0.32
Consensus pattern (54 bp):
CACTAAGTGTGCATTTCACGGAATTCATCCTATGTGGATGAATAACCGTTTCGA
Found at i:456303 original size:108 final size:108
Alignment explanation
Indices: 455923--456315 Score: 473
Period size: 108 Copynumber: 3.6 Consensus size: 108
455913 ACCAAATAAG
* * * * * * *
455923 CACTAAGTGTGCATTTTATGGAATTCATCCTATATGGATGAATAAGCATTTCAGCACTAAGTGTG
1 CACTAAGTGTGCATTTCACGGAATTCATCCTATGTGGATGAATAACCGTTTGAACACTAAGTGTG
* *
455988 CATTTCACAGAATTCATCCTATGTGGATGAATAACCATTTCGA
66 CATTTCACGGAATTCATCCTATGTGGATGAATAACCGTTTCGA
* * * *
456031 CAATAAGTATGCATTTCACTGAATTCATCCTATGTGGATGAATAACCATTTCG-ACACTAAGTGT
1 CACTAAGTGTGCATTTCACGGAATTCATCCTATGTGGATGAATAACCGTTT-GAACACTAAGTGT
*
456095 GCATTTCACGGAATTCATTCTATGTGGATGAATAACCGTTTCGA
65 GCATTTCACGGAATTCATCCTATGTGGATGAATAACCGTTTCGA
* * * *
456139 CACTAAGTGTGCATTTCACGAAATTCATCCTATATGGATGAATAATCGTTTCAACACTAAGTGTG
1 CACTAAGTGTGCATTTCACGGAATTCATCCTATGTGGATGAATAACCGTTTGAACACTAAGTGTG
* *
456204 CATTTCACGGAATTCATCCTATGCGGATGAATAACTGTTTCGA
66 CATTTCACGGAATTCATCCTATGTGGATGAATAACCGTTTCGA
* * *** ** ** * * * *
456247 CACTATGTGTACAAAACACGGAATTCATAATATGTTTATGAATGACCGTATGAACACTACGGGTG
1 CACTAAGTGTGCATTTCACGGAATTCATCCTATGTGGATGAATAACCGTTTGAACACTAAGTGTG
456312 CATT
66 CATT
456316 ACAAAGAAAT
Statistics
Matches: 243, Mismatches: 40, Indels: 4
0.85 0.14 0.01
Matches are distributed among these distances:
108 243 1.00
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32
Consensus pattern (108 bp):
CACTAAGTGTGCATTTCACGGAATTCATCCTATGTGGATGAATAACCGTTTGAACACTAAGTGTG
CATTTCACGGAATTCATCCTATGTGGATGAATAACCGTTTCGA
Found at i:456315 original size:162 final size:162
Alignment explanation
Indices: 455942--456315 Score: 430
Period size: 162 Copynumber: 2.3 Consensus size: 162
455932 TGCATTTTAT
** * * * * *
455942 GGAATTCATCCTATATGGATGAATAAGCATTTC-AGCACTAAGTGTGCATTTCACAGAATTCATC
1 GGAATTCATAATATGTGGATGAATAACCGTATCGA-CACTAAGGGTGCATTTCACAGAATTCATC
* * * *
456006 CTATGTGGATGAATAACCATTTCGACAATAAGTATGCATTTCACTGAATTCATCCTATGTGGATG
65 CTATATGGATGAATAACCATTTCAACAATAAGTATGCATTTCACGGAATTCATCCTATGCGGATG
* ***
456071 AATAACCATTTCGACACTAAGTGTGCATTTCAC
130 AATAACCATTTCGACACTAAGTGTACAAAACAC
** * *
456104 GGAATTCATTCTATGTGGATGAATAACCGTTTCGACACTAAGTGTGCATTTCAC-GAAATTCATC
1 GGAATTCATAATATGTGGATGAATAACCGTATCGACACTAAGGGTGCATTTCACAG-AATTCATC
* * * *
456168 CTATATGGATGAATAATCGTTTCAACACTAAGTGTGCATTTCACGGAATTCATCCTATGCGGATG
65 CTATATGGATGAATAACCATTTCAACAATAAGTATGCATTTCACGGAATTCATCCTATGCGGATG
** *
456233 AATAACTGTTTCGACACTATGTGTACAAAACAC
130 AATAACCATTTCGACACTAAGTGTACAAAACAC
** * *
456266 GGAATTCATAATATGTTTATGAATGACCGTAT-GAACACTACGGGTGCATT
1 GGAATTCATAATATGTGGATGAATAACCGTATCG-ACACTAAGGGTGCATT
456316 ACAAAGAAAT
Statistics
Matches: 182, Mismatches: 27, Indels: 6
0.85 0.13 0.03
Matches are distributed among these distances:
161 2 0.01
162 179 0.98
163 1 0.01
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32
Consensus pattern (162 bp):
GGAATTCATAATATGTGGATGAATAACCGTATCGACACTAAGGGTGCATTTCACAGAATTCATCC
TATATGGATGAATAACCATTTCAACAATAAGTATGCATTTCACGGAATTCATCCTATGCGGATGA
ATAACCATTTCGACACTAAGTGTACAAAACAC
Found at i:466297 original size:24 final size:24
Alignment explanation
Indices: 466270--466317 Score: 96
Period size: 24 Copynumber: 2.0 Consensus size: 24
466260 TAAGGAGAAA
466270 ACGTATGGAACTTCCACAAGATTG
1 ACGTATGGAACTTCCACAAGATTG
466294 ACGTATGGAACTTCCACAAGATTG
1 ACGTATGGAACTTCCACAAGATTG
466318 CTAACCGTTG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.33, C:0.21, G:0.21, T:0.25
Consensus pattern (24 bp):
ACGTATGGAACTTCCACAAGATTG
Found at i:467539 original size:30 final size:30
Alignment explanation
Indices: 467503--467568 Score: 114
Period size: 30 Copynumber: 2.2 Consensus size: 30
467493 CCGCCACTGT
467503 CGCTTTTCAAAGCGGAACCAGAAGCAGGAA
1 CGCTTTTCAAAGCGGAACCAGAAGCAGGAA
*
467533 CGCTTTTCAAAGTGGAACCAGAAGCAGGAA
1 CGCTTTTCAAAGCGGAACCAGAAGCAGGAA
*
467563 TGCTTT
1 CGCTTT
467569 CCGCTGCCTC
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
30 34 1.00
ACGTcount: A:0.33, C:0.21, G:0.26, T:0.20
Consensus pattern (30 bp):
CGCTTTTCAAAGCGGAACCAGAAGCAGGAA
Found at i:469835 original size:21 final size:22
Alignment explanation
Indices: 469782--469837 Score: 71
Period size: 22 Copynumber: 2.6 Consensus size: 22
469772 ATATAGGATT
*
469782 TGTCCCGAAGGACCGCATAGAAA
1 TGTCCCGAAGGACCACATAG-AA
*
469805 T-TCCCAAAGGACCACATAG-A
1 TGTCCCGAAGGACCACATAGAA
469825 TGTCCCGAAGGAC
1 TGTCCCGAAGGAC
469838 TACTCCTTAA
Statistics
Matches: 29, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
20 2 0.07
21 10 0.34
22 16 0.55
23 1 0.03
ACGTcount: A:0.34, C:0.29, G:0.23, T:0.14
Consensus pattern (22 bp):
TGTCCCGAAGGACCACATAGAA
Found at i:469920 original size:21 final size:21
Alignment explanation
Indices: 469896--469935 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
469886 CAAAGTACCG
*
469896 CATATATGTTCCAAAGGATTA
1 CATATATGTCCCAAAGGATTA
*
469917 CATATATGTCCCGAAGGAT
1 CATATATGTCCCAAAGGAT
469936 CACGTAGAAC
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.35, C:0.17, G:0.17, T:0.30
Consensus pattern (21 bp):
CATATATGTCCCAAAGGATTA
Found at i:472135 original size:12 final size:13
Alignment explanation
Indices: 472112--472137 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
472102 TAAATCCAAC
472112 CAAATAAAAAAAT
1 CAAATAAAAAAAT
472125 CAAATAAAAAAAT
1 CAAATAAAAAAAT
472138 ATGGGATCTC
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.77, C:0.08, G:0.00, T:0.15
Consensus pattern (13 bp):
CAAATAAAAAAAT
Found at i:473306 original size:17 final size:17
Alignment explanation
Indices: 473284--473324 Score: 57
Period size: 17 Copynumber: 2.4 Consensus size: 17
473274 TTATATGGTG
473284 ATTATATATGGTTA-TGT
1 ATTATATAT-GTTATTGT
*
473301 ATTATATATTTTATTGT
1 ATTATATATGTTATTGT
473318 ATTATAT
1 ATTATAT
473325 GTAGGGGTAT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
16 3 0.14
17 19 0.86
ACGTcount: A:0.32, C:0.00, G:0.10, T:0.59
Consensus pattern (17 bp):
ATTATATATGTTATTGT
Found at i:479968 original size:54 final size:54
Alignment explanation
Indices: 479871--480800 Score: 1147
Period size: 54 Copynumber: 17.4 Consensus size: 54
479861 TTCTTTGAGA
** *
479871 TGCACACGCAGTGCTTATACGGTCGTTCATCAACATATGATGAATTCCGTGGGT
1 TGCACACTTAGTGCCTATACGGTCGTTCATCAACATATGATGAATTCCGTGGGT
* * * * * * *
479925 TACACACTTAGTTCCTACACTGTCGTTCATAAACGTATTATGAATTCCGTGGGT
1 TGCACACTTAGTGCCTATACGGTCGTTCATCAACATATGATGAATTCCGTGGGT
* * * * * * *
479979 TGCACACTCAATGCCTATACGATCGTTCATAAATATATTATGAATTTCGTGGGT
1 TGCACACTTAGTGCCTATACGGTCGTTCATCAACATATGATGAATTCCGTGGGT
* * * * * * **
480033 TGCACACTTAGAGCATATACGGTCATTCATAAACGTATTATGAATTTTGTGGGT
1 TGCACACTTAGTGCCTATACGGTCGTTCATCAACATATGATGAATTCCGTGGGT
* * ** * * *
480087 TGTACACTCAGTGCCTATACAATCGTTCATAAATATATTATGAATTCCGTGGGT
1 TGCACACTTAGTGCCTATACGGTCGTTCATCAACATATGATGAATTCCGTGGGT
* *
480141 TGCACACTTAGAGCCTATACGGTCGTTCATCAACATATGATGAATTCTGTGGG-
1 TGCACACTTAGTGCCTATACGGTCGTTCATCAACATATGATGAATTCCGTGGGT
* *
480194 TGCA-ACTTAGTG-CTATACGGTCGTTCATCTACATATGATGAATTCTGTGGGT
1 TGCACACTTAGTGCCTATACGGTCGTTCATCAACATATGATGAATTCCGTGGGT
**
480246 TGCACACTTAGTGCCTATACGGTCGTTCATCAACATATGATG-ATTTTGTGGGT
1 TGCACACTTAGTGCCTATACGGTCGTTCATCAACATATGATGAATTCCGTGGGT
* * * **
480299 TACACACTTAGTGCCTATACGGTCGTT-ATAAACATATTATGAATTTTGTGGGT
1 TGCACACTTAGTGCCTATACGGTCGTTCATCAACATATGATGAATTCCGTGGGT
**
480352 TGCACACTTAGTGCCTATACGGTCGTTCATCAACATATGATGAATTTAGTGGGT
1 TGCACACTTAGTGCCTATACGGTCGTTCATCAACATATGATGAATTCCGTGGGT
* *
480406 TGCACACTTAGTTCCTATACGGTTGTTCATCAACATATGATGAATTCCGTGGGT
1 TGCACACTTAGTGCCTATACGGTCGTTCATCAACATATGATGAATTCCGTGGGT
* * * *
480460 TACACACTTAGTGCCTATACTGTCGTTCATTAACATATGATGAATT-TGTTGGGT
1 TGCACACTTAGTGCCTATACGGTCGTTCATCAACATATGATGAATTCCG-TGGGT
* * * * *
480514 TACACACTTAGTGCCTATACGTTCATTCA-AAACATATTATGAATTCCGTGGGT
1 TGCACACTTAGTGCCTATACGGTCGTTCATCAACATATGATGAATTCCGTGGGT
* * **
480567 TGCACACTTAATTCCTATATAGTCGTTCATCAACATATGATGAATTCCGTGGGT
1 TGCACACTTAGTGCCTATACGGTCGTTCATCAACATATGATGAATTCCGTGGGT
* ** *
480621 TGCACACTTAGTGGCTATACGGTCGTTCATCAATGTATGATGAATT-CGTGAGT
1 TGCACACTTAGTGCCTATACGGTCGTTCATCAACATATGATGAATTCCGTGGGT
* *
480674 TGCACACTTAGTGCCTATACGGTCGTTCATCAACATATGATGAATTCTGTTGGT
1 TGCACACTTAGTGCCTATACGGTCGTTCATCAACATATGATGAATTCCGTGGGT
* * * *
480728 TACACACTTAGTGCCTATATGATCGTTCATCAACATATGATGAATTCTGTGGGT
1 TGCACACTTAGTGCCTATACGGTCGTTCATCAACATATGATGAATTCCGTGGGT
* *
480782 TGCATACTTAGTGTCTATA
1 TGCACACTTAGTGCCTATA
480801 GCACACATAG
Statistics
Matches: 761, Mismatches: 106, Indels: 18
0.86 0.12 0.02
Matches are distributed among these distances:
51 38 0.05
52 23 0.03
53 176 0.23
54 524 0.69
ACGTcount: A:0.26, C:0.19, G:0.20, T:0.35
Consensus pattern (54 bp):
TGCACACTTAGTGCCTATACGGTCGTTCATCAACATATGATGAATTCCGTGGGT
Found at i:480567 original size:161 final size:161
Alignment explanation
Indices: 479871--480800 Score: 1181
Period size: 161 Copynumber: 5.8 Consensus size: 161
479861 TTCTTTGAGA
** * * *
479871 TGCACACGCAGTGCTTATACGGTCGTTCATCAACATATGATGAATTCCGTGGGTTACACACTTAG
1 TGCACACTTAGTGCCTATACGGTCGTTCATCAACATATGATGAATTCTGTGGGTTGCACACTTAG
* * * * * * * * *
479936 TTCCTACACTGTCGTTCATAAACGTATTATGAATTCCGTGGGTTGCACACTCAATGCCTATACGA
66 TGCCTATACGGTCGTTCATCAACATATGATGAATTCCGTGGGTTGCACACTTAGTGCCTATACGG
* *
480001 TCGTTCATAAATATATTATGAATTTCGTGGGT
131 TCGTTCATAAACATATGATGAATTT-GTGGGT
* * * * * * * * *
480033 TGCACACTTAGAGCATATACGGTCATTCATAAACGTATTATGAATTTTGTGGGTTGTACACTCAG
1 TGCACACTTAGTGCCTATACGGTCGTTCATCAACATATGATGAATTCTGTGGGTTGCACACTTAG
** * * * *
480098 TGCCTATACAATCGTTCATAAATATATTATGAATTCCGTGGGTTGCACACTTAGAGCCTATACGG
66 TGCCTATACGGTCGTTCATCAACATATGATGAATTCCGTGGGTTGCACACTTAGTGCCTATACGG
*
480163 TCGTTCATCAACATATGATGAATTCTGTGGG-
131 TCGTTCATAAACATATGATGAATT-TGTGGGT
*
480194 TGCA-ACTTAGTG-CTATACGGTCGTTCATCTACATATGATGAATTCTGTGGGTTGCACACTTAG
1 TGCACACTTAGTGCCTATACGGTCGTTCATCAACATATGATGAATTCTGTGGGTTGCACACTTAG
** *
480257 TGCCTATACGGTCGTTCATCAACATATGATG-ATTTTGTGGGTTACACACTTAGTGCCTATACGG
66 TGCCTATACGGTCGTTCATCAACATATGATGAATTCCGTGGGTTGCACACTTAGTGCCTATACGG
*
480321 TCGTT-ATAAACATATTATGAATTTTGTGGGT
131 TCGTTCATAAACATATGATGAA-TTTGTGGGT
480352 TGCACACTTAGTGCCTATACGGTCGTTCATCAACATATGATGAATT-TAGTGGGTTGCACACTTA
1 TGCACACTTAGTGCCTATACGGTCGTTCATCAACATATGATGAATTCT-GTGGGTTGCACACTTA
* * * *
480416 GTTCCTATACGGTTGTTCATCAACATATGATGAATTCCGTGGGTTACACACTTAGTGCCTATACT
65 GTGCCTATACGGTCGTTCATCAACATATGATGAATTCCGTGGGTTGCACACTTAGTGCCTATACG
*
480481 GTCGTTCATTAACATATGATGAATTTGTTGGGT
130 GTCGTTCATAAACATATGATGAATTTG-TGGGT
* * * * * * *
480514 TACACACTTAGTGCCTATACGTTCATTCA-AAACATATTATGAATTCCGTGGGTTGCACACTTAA
1 TGCACACTTAGTGCCTATACGGTCGTTCATCAACATATGATGAATTCTGTGGGTTGCACACTTAG
* ** *
480578 TTCCTATATAGTCGTTCATCAACATATGATGAATTCCGTGGGTTGCACACTTAGTGGCTATACGG
66 TGCCTATACGGTCGTTCATCAACATATGATGAATTCCGTGGGTTGCACACTTAGTGCCTATACGG
* ** * *
480643 TCGTTCATCAATGTATGATGAATTCGTGAGT
131 TCGTTCATAAACATATGATGAATTTGTGGGT
* *
480674 TGCACACTTAGTGCCTATACGGTCGTTCATCAACATATGATGAATTCTGTTGGTTACACACTTAG
1 TGCACACTTAGTGCCTATACGGTCGTTCATCAACATATGATGAATTCTGTGGGTTGCACACTTAG
* * * * *
480739 TGCCTATATGATCGTTCATCAACATATGATGAATTCTGTGGGTTGCATACTTAGTGTCTATA
66 TGCCTATACGGTCGTTCATCAACATATGATGAATTCCGTGGGTTGCACACTTAGTGCCTATA
480801 GCACACATAG
Statistics
Matches: 669, Mismatches: 88, Indels: 23
0.86 0.11 0.03
Matches are distributed among these distances:
157 20 0.03
158 40 0.06
159 77 0.12
160 114 0.17
161 239 0.36
162 178 0.27
163 1 0.00
ACGTcount: A:0.26, C:0.19, G:0.20, T:0.35
Consensus pattern (161 bp):
TGCACACTTAGTGCCTATACGGTCGTTCATCAACATATGATGAATTCTGTGGGTTGCACACTTAG
TGCCTATACGGTCGTTCATCAACATATGATGAATTCCGTGGGTTGCACACTTAGTGCCTATACGG
TCGTTCATAAACATATGATGAATTTGTGGGT
Found at i:481094 original size:18 final size:18
Alignment explanation
Indices: 481073--481113 Score: 55
Period size: 18 Copynumber: 2.3 Consensus size: 18
481063 GTACTATTAT
* *
481073 TTTCAATTTCTATTACAA
1 TTTCAATCTATATTACAA
*
481091 TTTCAGTCTATATTACAA
1 TTTCAATCTATATTACAA
481109 TTTCA
1 TTTCA
481114 GGCTCAATAG
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.32, C:0.17, G:0.02, T:0.49
Consensus pattern (18 bp):
TTTCAATCTATATTACAA
Found at i:485562 original size:54 final size:54
Alignment explanation
Indices: 485442--486215 Score: 939
Period size: 54 Copynumber: 14.4 Consensus size: 54
485432 TTCTTTGAGA
* * * * *
485442 TGCACACGTAGTACCTATACAGTCGTTCATCAAAATATGATGAA-TTCGTGGAT
1 TGCACACTTAGTGCCTATACGGTCGTTCATCAACATATGATGAATTTCGTGGGT
* * * * * *
485495 TTCACACTTAGTGCCTAAACAGTCGTTCATAAACACATTATGAATTTCGTGGGT
1 TGCACACTTAGTGCCTATACGGTCGTTCATCAACATATGATGAATTTCGTGGGT
* * * * *
485549 TGCACACTTAGTGCCTATACGGTTGTTCATAAACATATTATGAATTCCATGGGT
1 TGCACACTTAGTGCCTATACGGTCGTTCATCAACATATGATGAATTTCGTGGGT
* * * *
485603 TCCACACTTAGTGCCTATACGGTTGTTCATCAACATATGATGAATTCCGTAGGT
1 TGCACACTTAGTGCCTATACGGTCGTTCATCAACATATGATGAATTTCGTGGGT
* ** *
485657 TGCACACTTACTGCCTATACGGTAATTCATCAACATATGATGAATTCCGTGGGT
1 TGCACACTTAGTGCCTATACGGTCGTTCATCAACATATGATGAATTTCGTGGGT
* *
485711 TGTACACTTAGTGCCTATATGGTCGTTCATCAACATATGATGAATTAT-GTGGGT
1 TGCACACTTAGTGCCTATACGGTCGTTCATCAACATATGATGAATT-TCGTGGGT
* * *
485765 TGCACACTTAGTGCCTATACGGTCGTTCATAAACATATTATGAATTTCGTGAGT
1 TGCACACTTAGTGCCTATACGGTCGTTCATCAACATATGATGAATTTCGTGGGT
* * * * *
485819 TACACATTTAGTGCCTATACGATCGTTAATCAACATATGATGAA-TTCTATGGGT
1 TGCACACTTAGTGCCTATACGGTCGTTCATCAACATATGATGAATTTC-GTGGGT
* * * * *
485873 TGCATACTTAGTTCCTATACGGCCCTTCATCAACATATGATGAA-TTCTGTGTGT
1 TGCACACTTAGTGCCTATACGGTCGTTCATCAACATATGATGAATTTC-GTGGGT
* * * *
485927 TGCACACATAGTTCCTATACGGTCTTTCATCAACATATGATGAATTACGTGGGT
1 TGCACACTTAGTGCCTATACGGTCGTTCATCAACATATGATGAATTTCGTGGGT
* * * * *
485981 TGTACACTTAGTGCCTATAAGGTCGTTCATAAAGATATTATGAA-TTCAGTGGGT
1 TGCACACTTAGTGCCTATACGGTCGTTCATCAACATATGATGAATTTC-GTGGGT
** * *
486035 TATACACTTAGTGCCTATACGGTCGTTCATTAACATATGATG-ATTTCAATGGGT
1 TGCACACTTAGTGCCTATACGGTCGTTCATCAACATATGATGAATTTC-GTGGGT
* * *
486089 TACACACTTATTGCCTATACGGTCATTCATCAACATATGATGAATTTCGTGGGT
1 TGCACACTTAGTGCCTATACGGTCGTTCATCAACATATGATGAATTTCGTGGGT
* *
486143 TGCACACTTAGTGCCTATACGGTCGTTTATCAACATATGATAAATTTCGTGGGT
1 TGCACACTTAGTGCCTATACGGTCGTTCATCAACATATGATGAATTTCGTGGGT
*
486197 TGCACACTTAATGCCTATA
1 TGCACACTTAGTGCCTATA
486216 ATATACATAG
Statistics
Matches: 626, Mismatches: 87, Indels: 15
0.86 0.12 0.02
Matches are distributed among these distances:
53 43 0.07
54 576 0.92
55 7 0.01
ACGTcount: A:0.28, C:0.19, G:0.18, T:0.34
Consensus pattern (54 bp):
TGCACACTTAGTGCCTATACGGTCGTTCATCAACATATGATGAATTTCGTGGGT
Found at i:490715 original size:26 final size:26
Alignment explanation
Indices: 490685--490734 Score: 100
Period size: 26 Copynumber: 1.9 Consensus size: 26
490675 TTTCAGCTGA
490685 CCTTGTATGCACGTACACCTAGCTTC
1 CCTTGTATGCACGTACACCTAGCTTC
490711 CCTTGTATGCACGTACACCTAGCT
1 CCTTGTATGCACGTACACCTAGCT
490735 GCCAGCCTCC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 24 1.00
ACGTcount: A:0.20, C:0.34, G:0.16, T:0.30
Consensus pattern (26 bp):
CCTTGTATGCACGTACACCTAGCTTC
Found at i:492168 original size:4 final size:4
Alignment explanation
Indices: 492159--492213 Score: 65
Period size: 4 Copynumber: 13.8 Consensus size: 4
492149 TTCATCTTGT
* * * * *
492159 CATA CATA CATG CATA CATG CATA CATG CATA CATG CATA CATG CATA
1 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
492207 CATA CAT
1 CATA CAT
492214 GCATGCATAA
Statistics
Matches: 41, Mismatches: 10, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
4 41 1.00
ACGTcount: A:0.40, C:0.25, G:0.09, T:0.25
Consensus pattern (4 bp):
CATA
Found at i:492174 original size:8 final size:8
Alignment explanation
Indices: 492163--492222 Score: 102
Period size: 8 Copynumber: 7.5 Consensus size: 8
492153 TCTTGTCATA
492163 CATACATG
1 CATACATG
492171 CATACATG
1 CATACATG
492179 CATACATG
1 CATACATG
492187 CATACATG
1 CATACATG
492195 CATACATG
1 CATACATG
*
492203 CATACATA
1 CATACATG
*
492211 CATGCATG
1 CATACATG
492219 CATA
1 CATA
492223 ATTCTTACAG
Statistics
Matches: 48, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
8 48 1.00
ACGTcount: A:0.38, C:0.25, G:0.12, T:0.25
Consensus pattern (8 bp):
CATACATG
Done.