Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01004593.1 Hibiscus syriacus cultivar Beakdansim tig00010263_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: 1592963
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 3 of 7
Found at i:437556 original size:2 final size:2
Alignment explanation
Indices: 437549--437609 Score: 86
Period size: 2 Copynumber: 30.5 Consensus size: 2
437539 AAAAGGTAAA
* *
437549 AT AT AT AT AT AT AT AT AT AT AT AT AT AA AT AT GT 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
* *
437591 AT AT AT AA AT AT GT AT AT A
1 AT AT AT AT AT AT AT AT AT A
437610 CTAGTAAAAA
Statistics
Matches: 51, Mismatches: 8, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
2 51 1.00
ACGTcount: A:0.51, C:0.00, G:0.03, T:0.46
Consensus pattern (2 bp):
AT
Found at i:443345 original size:15 final size:17
Alignment explanation
Indices: 443325--443358 Score: 54
Period size: 15 Copynumber: 2.1 Consensus size: 17
443315 TCATTTTTTT
443325 TTAAATTA-AAG-TAGA
1 TTAAATTATAAGATAGA
443340 TTAAATTATAAGATAGA
1 TTAAATTATAAGATAGA
443357 TT
1 TT
443359 GCACCGCCTC
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 8 0.47
16 3 0.18
17 6 0.35
ACGTcount: A:0.50, C:0.00, G:0.12, T:0.38
Consensus pattern (17 bp):
TTAAATTATAAGATAGA
Found at i:448239 original size:20 final size:20
Alignment explanation
Indices: 448214--448268 Score: 67
Period size: 20 Copynumber: 2.8 Consensus size: 20
448204 GCGAAATAAA
448214 AATCGCAACGCGA-TCTCCAG
1 AATCGCAACGCGATTC-CCAG
** *
448234 AATCGCAAATCAATTCCCAG
1 AATCGCAACGCGATTCCCAG
448254 AATCGCAACGCGATT
1 AATCGCAACGCGATT
448269 ATGAAGAATC
Statistics
Matches: 28, Mismatches: 6, Indels: 2
0.78 0.17 0.06
Matches are distributed among these distances:
20 26 0.93
21 2 0.07
ACGTcount: A:0.35, C:0.31, G:0.16, T:0.18
Consensus pattern (20 bp):
AATCGCAACGCGATTCCCAG
Found at i:448278 original size:21 final size:20
Alignment explanation
Indices: 448254--448528 Score: 77
Period size: 20 Copynumber: 13.5 Consensus size: 20
448244 CAATTCCCAG
448254 AATCGCAACGCGATTATGAA
1 AATCGCAACGCGATTATGAA
*
448274 GAATCGCAATGCGA-TA-GTACA
1 -AATCGCAACGCGATTATG-A-A
* ** * * *
448295 AATTCGTATTGCGATTTTCCAG
1 AA-TCGCAACGCGATTAT-GAA
*
448317 AATCGCAACGCGAATATGAA
1 AATCGCAACGCGATTATGAA
**
448337 AATCGCAACGCGAACAT-ATA
1 AATCGCAACGCGATTATGA-A
* *
448357 AATCGCAACGCGATTCTGAC
1 AATCGCAACGCGATTATGAA
* *
448377 TATCGCAA--CGAGTATCCGTAA
1 AATCGCAACGCGATTAT--G-AA
*
448398 AATCGCAACGCG--TATCCGTA
1 AATCGCAACGCGATTAT--GAA
* *
448418 AATCGCAACGACAATACAT-AA
1 AATCGCAACG-CGAT-TATGAA
*
448439 AATCGCAACGCG--TATCCGTA
1 AATCGCAACGCGATTAT--GAA
* * * * *
448459 AATCGTAACGAGAATACGTA
1 AATCGCAACGCGATTATGAA
*
448479 AATCGCAACGCGTATT-TGTA
1 AATCGCAACGCG-ATTATGAA
* * * *
448499 AATCGCAACGAGAATACGTA
1 AATCGCAACGCGATTATGAA
448519 AATCGCAACG
1 AATCGCAACG
448529 AGAATACGTA
Statistics
Matches: 190, Mismatches: 40, Indels: 49
0.68 0.14 0.18
Matches are distributed among these distances:
17 2 0.01
18 5 0.03
19 4 0.02
20 108 0.57
21 61 0.32
22 5 0.03
23 3 0.02
24 2 0.01
ACGTcount: A:0.37, C:0.23, G:0.19, T:0.21
Consensus pattern (20 bp):
AATCGCAACGCGATTATGAA
Found at i:448342 original size:20 final size:20
Alignment explanation
Indices: 448317--448608 Score: 241
Period size: 20 Copynumber: 14.4 Consensus size: 20
448307 GATTTTCCAG
* *
448317 AATCGCAACGCGAATATGAA
1 AATCGCAACGCGAATACGTA
* **
448337 AATCGCAACGCGAACATATA
1 AATCGCAACGCGAATACGTA
*
448357 AATCGCAACGCG-ATTC-TGA
1 AATCGCAACGCGAATACGT-A
* * * *
448376 CTATCGCAACGAGTATCCGTAA
1 -AATCGCAACGCGAATACGT-A
* *
448398 AATCGCAACGCGTATCCGTA
1 AATCGCAACGCGAATACGTA
*
448418 AATCGCAACGAC-AATACATAA
1 AATCGCAACG-CGAATACGT-A
* *
448439 AATCGCAACGCGTATCCGTA
1 AATCGCAACGCGAATACGTA
* *
448459 AATCGTAACGAGAATACGTA
1 AATCGCAACGCGAATACGTA
* **
448479 AATCGCAACGCGTATTTGTA
1 AATCGCAACGCGAATACGTA
*
448499 AATCGCAACGAGAATACGTA
1 AATCGCAACGCGAATACGTA
*
448519 AATCGCAACGAGAATACGTA
1 AATCGCAACGCGAATACGTA
* * *
448539 AATCGCAATGCGTATCCGTA
1 AATCGCAACGCGAATACGTA
*
448559 AATCGCAACTAC-AATACGTAA
1 AATCGCAAC-GCGAATACGT-A
* *
448580 AATCGCAACGCGTATCCGTA
1 AATCGCAACGCGAATACGTA
448600 AATCGCAAC
1 AATCGCAAC
448609 ACGATTTTTA
Statistics
Matches: 220, Mismatches: 42, Indels: 20
0.78 0.15 0.07
Matches are distributed among these distances:
18 1 0.00
19 2 0.01
20 163 0.74
21 52 0.24
22 2 0.01
ACGTcount: A:0.39, C:0.24, G:0.18, T:0.19
Consensus pattern (20 bp):
AATCGCAACGCGAATACGTA
Found at i:448421 original size:81 final size:80
Alignment explanation
Indices: 448317--448567 Score: 238
Period size: 81 Copynumber: 3.1 Consensus size: 80
448307 GATTTTCCAG
* * * *
448317 AATCGCAACGCGAATATGAAAATCGCAACGCGAACATATAAATCGCAACGCG-ATTC-TGACTAT
1 AATCGCAACGCGTATATGTAAATCGCAACGCGAACATATAAATCGCAACGCGTATCCGT-A-AAT
* *
448380 CGCAACGAGTATCCGTAA
64 CGCAACGAGAATACGT-A
** *
448398 AATCGCAACGCGTATCCGTAAATCGCAACGACAATACATA-AAATCGCAACGCGTATCCGTAAAT
1 AATCGCAACGCGTATATGTAAATCGCAACG-CGA-ACATATAAATCGCAACGCGTATCCGTAAAT
*
448462 CGTAACGAGAATACGTA
64 CGCAACGAGAATACGTA
* * * ** * * *
448479 AATCGCAACGCGTATTTGTAAATCGCAACGAGAATACGTAAATCGCAACGAGAATACGTAAATCG
1 AATCGCAACGCGTATATGTAAATCGCAACGCGAACATATAAATCGCAACGCGTATCCGTAAATCG
* * * *
448544 CAATGCGTATCCGTA
66 CAACGAGAATACGTA
448559 AATCGCAAC
1 AATCGCAAC
448568 TACAATACGT
Statistics
Matches: 140, Mismatches: 25, Indels: 11
0.80 0.14 0.06
Matches are distributed among these distances:
79 2 0.01
80 43 0.31
81 55 0.39
82 30 0.21
83 9 0.06
84 1 0.01
ACGTcount: A:0.39, C:0.24, G:0.18, T:0.19
Consensus pattern (80 bp):
AATCGCAACGCGTATATGTAAATCGCAACGCGAACATATAAATCGCAACGCGTATCCGTAAATCG
CAACGAGAATACGTA
Found at i:449208 original size:21 final size:21
Alignment explanation
Indices: 449147--449225 Score: 85
Period size: 20 Copynumber: 3.9 Consensus size: 21
449137 TTCTAAACTT
449147 AAAATCGCAAC-ATGA-AAATG
1 AAAATCGCAACGA-GAGAAATG
*
449167 AAAAGCGCAAC-ACGA-AAATG
1 AAAATCGCAACGA-GAGAAATG
**
449187 ACTATCGCAACGAGAGAAATG
1 AAAATCGCAACGAGAGAAATG
449208 AAAATCGCAACGAGAGAA
1 AAAATCGCAACGAGAGAA
449226 TCGCAACGCG
Statistics
Matches: 50, Mismatches: 7, Indels: 3
0.83 0.12 0.05
Matches are distributed among these distances:
20 28 0.56
21 22 0.44
ACGTcount: A:0.52, C:0.18, G:0.20, T:0.10
Consensus pattern (21 bp):
AAAATCGCAACGAGAGAAATG
Found at i:449229 original size:14 final size:14
Alignment explanation
Indices: 449207--449271 Score: 58
Period size: 14 Copynumber: 4.3 Consensus size: 14
449197 CGAGAGAAAT
449207 GAAAATCGCAACGA
1 GAAAATCGCAACGA
*
449221 GAGAATCGCAACGCGAAA
1 GAAAATCGCAA--CG--A
449239 TGAAAATCGCAACGA
1 -GAAAATCGCAACGA
* *
449254 GATAATCGCAACGC
1 GAAAATCGCAACGA
449268 GAAA
1 GAAA
449272 CCAAAATCGC
Statistics
Matches: 41, Mismatches: 5, Indels: 10
0.73 0.09 0.18
Matches are distributed among these distances:
14 25 0.61
15 1 0.02
16 2 0.05
17 2 0.05
18 1 0.02
19 10 0.24
ACGTcount: A:0.46, C:0.22, G:0.23, T:0.09
Consensus pattern (14 bp):
GAAAATCGCAACGA
Found at i:449243 original size:33 final size:33
Alignment explanation
Indices: 449202--449282 Score: 135
Period size: 33 Copynumber: 2.5 Consensus size: 33
449192 CGCAACGAGA
449202 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
1 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
*
449235 GAAATGAAAATCGCAACGAGATAATCGCAACGC
1 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
**
449268 GAAACCAAAATCGCA
1 GAAATGAAAATCGCA
449283 TTGCGATTTT
Statistics
Matches: 45, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
33 45 1.00
ACGTcount: A:0.47, C:0.22, G:0.21, T:0.10
Consensus pattern (33 bp):
GAAATGAAAATCGCAACGAGAGAATCGCAACGC
Found at i:449300 original size:19 final size:19
Alignment explanation
Indices: 449278--449361 Score: 97
Period size: 19 Copynumber: 4.7 Consensus size: 19
449268 GAAACCAAAA
449278 TCGCATTGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
* *
449297 TCGCGTTGCGATTTTAATT
1 TCGCATTGCGATTTTCATT
*
449316 TCGCATTGCGA--TTC-TC
1 TCGCATTGCGATTTTCATT
449332 TCG--TTGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
*
449349 TCGCGTTGCGATT
1 TCGCATTGCGATT
449362 CTCTCGTTGC
Statistics
Matches: 54, Mismatches: 6, Indels: 10
0.77 0.09 0.14
Matches are distributed among these distances:
14 6 0.11
16 7 0.13
17 6 0.11
19 35 0.65
ACGTcount: A:0.13, C:0.21, G:0.20, T:0.45
Consensus pattern (19 bp):
TCGCATTGCGATTTTCATT
Found at i:449340 original size:14 final size:14
Alignment explanation
Indices: 449321--449374 Score: 54
Period size: 14 Copynumber: 3.5 Consensus size: 14
449311 TAATTTCGCA
449321 TTGCGATTCTCTCG
1 TTGCGATTCTCTCG
*
449335 TTGCGATTTTCATTTCGCG
1 TTGCGA--TTC---TCTCG
449354 TTGCGATTCTCTCG
1 TTGCGATTCTCTCG
449368 TTGCGAT
1 TTGCGAT
449375 AGTCATTTCC
Statistics
Matches: 33, Mismatches: 2, Indels: 10
0.73 0.04 0.22
Matches are distributed among these distances:
14 17 0.52
16 3 0.09
17 3 0.09
19 10 0.30
ACGTcount: A:0.09, C:0.24, G:0.22, T:0.44
Consensus pattern (14 bp):
TTGCGATTCTCTCG
Found at i:449342 original size:33 final size:33
Alignment explanation
Indices: 449300--449374 Score: 132
Period size: 33 Copynumber: 2.3 Consensus size: 33
449290 TTTCATTTCG
449300 CGTTGCGATTTTAATTTCGCATTGCGATTCTCT
1 CGTTGCGATTTTAATTTCGCATTGCGATTCTCT
* *
449333 CGTTGCGATTTTCATTTCGCGTTGCGATTCTCT
1 CGTTGCGATTTTAATTTCGCATTGCGATTCTCT
449366 CGTTGCGAT
1 CGTTGCGAT
449375 AGTCATTTCC
Statistics
Matches: 40, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
33 40 1.00
ACGTcount: A:0.12, C:0.23, G:0.21, T:0.44
Consensus pattern (33 bp):
CGTTGCGATTTTAATTTCGCATTGCGATTCTCT
Found at i:449381 original size:33 final size:33
Alignment explanation
Indices: 449313--449394 Score: 128
Period size: 33 Copynumber: 2.5 Consensus size: 33
449303 TGCGATTTTA
* **
449313 ATTTCGCATTGCGATTCTCTCGTTGCGATTTTC
1 ATTTCGCGTTGCGATTCTCTCGTTGCGATAGTC
449346 ATTTCGCGTTGCGATTCTCTCGTTGCGATAGTC
1 ATTTCGCGTTGCGATTCTCTCGTTGCGATAGTC
449379 ATTTCCGCGTTGCGAT
1 ATTT-CGCGTTGCGAT
449395 AGTCATTCTC
Statistics
Matches: 45, Mismatches: 3, Indels: 1
0.92 0.06 0.02
Matches are distributed among these distances:
33 34 0.76
34 11 0.24
ACGTcount: A:0.12, C:0.24, G:0.22, T:0.41
Consensus pattern (33 bp):
ATTTCGCGTTGCGATTCTCTCGTTGCGATAGTC
Found at i:449421 original size:20 final size:20
Alignment explanation
Indices: 449359--449414 Score: 87
Period size: 20 Copynumber: 2.8 Consensus size: 20
449349 TCGCGTTGCG
449359 ATTCTCTCGTTGCGATAGTC
1 ATTCTCTCGTTGCGATAGTC
*
449379 ATT-TCCGCGTTGCGATAGTC
1 ATTCT-CTCGTTGCGATAGTC
449399 ATTCTCTCGTTGCGAT
1 ATTCTCTCGTTGCGAT
449415 TTTCATTTCA
Statistics
Matches: 32, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
19 1 0.03
20 30 0.94
21 1 0.03
ACGTcount: A:0.14, C:0.25, G:0.21, T:0.39
Consensus pattern (20 bp):
ATTCTCTCGTTGCGATAGTC
Found at i:451261 original size:17 final size:17
Alignment explanation
Indices: 451231--451263 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
451221 GTTGCTGCCA
451231 ATTCTGTTAAACTGTGT
1 ATTCTGTTAAACTGTGT
451248 ATTCT-TTAACACTGTG
1 ATTCTGTTAA-ACTGTG
451264 AAGTTAGTAT
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 4 0.27
17 11 0.73
ACGTcount: A:0.24, C:0.15, G:0.15, T:0.45
Consensus pattern (17 bp):
ATTCTGTTAAACTGTGT
Found at i:451275 original size:94 final size:94
Alignment explanation
Indices: 451113--451492 Score: 611
Period size: 94 Copynumber: 4.1 Consensus size: 94
451103 TAGATTGCTT
* * *
451113 AGTAAATTTATTCGGTTGCTGCCAATACTGCTAAACTGTTTATTCTTTAACACTGTGAAGTTAAT
1 AGTAAATTTATTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAGTTAGT
*
451178 ATTTGTCTTTTGTTTTATCTTTTGGTTG-A
66 ATTTGTC-TTTGTTTTGTCTTTTGGTTGAA
* *
451207 AGTAAAATTATTCGGTTGCTGCCAATTCTGTTAAACTGTGTATTCTTTAACACTGTGAAGTTAGT
1 AGTAAATTTATTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAGTTAGT
*
451272 ATTTGTATTTGTTTTGTCTTTTGGTTGAA
66 ATTTGTCTTTGTTTTGTCTTTTGGTTGAA
*
451301 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAGTTAGT
1 AGTAAATTTATTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAGTTAGT
451366 ATTTGTCTTTGTTTTGTCTTTTGGTTGAA
66 ATTTGTCTTTGTTTTGTCTTTTGGTTGAA
* * * * *
451395 AGTAAATTTGTTCGGTTGCTGTCAATTCTGCTAAACTGTGTATTTTTTAATACTCTGAAGTTAGT
1 AGTAAATTTATTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAGTTAGT
*
451460 ATTTGTCTTTATTTTGTCTTTTGGTTG-A
66 ATTTGTCTTTGTTTTGTCTTTTGGTTGAA
451488 AGTAA
1 AGTAA
451493 TGCAATCCAT
Statistics
Matches: 269, Mismatches: 16, Indels: 3
0.93 0.06 0.01
Matches are distributed among these distances:
93 25 0.09
94 244 0.91
ACGTcount: A:0.22, C:0.12, G:0.18, T:0.48
Consensus pattern (94 bp):
AGTAAATTTATTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAGTTAGT
ATTTGTCTTTGTTTTGTCTTTTGGTTGAA
Found at i:451596 original size:19 final size:19
Alignment explanation
Indices: 451556--451610 Score: 65
Period size: 19 Copynumber: 2.8 Consensus size: 19
451546 CACGAAACTT
*
451556 AAAATCGCAACGTGAAAAATG
1 AAAATCGCAAC--GAGAAATG
**
451577 ACTATCGCAACGAGAAATG
1 AAAATCGCAACGAGAAATG
451596 AAAATCGCAACGAGA
1 AAAATCGCAACGAGA
451611 GAATCGCAAC
Statistics
Matches: 29, Mismatches: 5, Indels: 2
0.81 0.14 0.06
Matches are distributed among these distances:
19 20 0.69
21 9 0.31
ACGTcount: A:0.49, C:0.18, G:0.20, T:0.13
Consensus pattern (19 bp):
AAAATCGCAACGAGAAATG
Found at i:451694 original size:20 final size:20
Alignment explanation
Indices: 451669--451717 Score: 71
Period size: 20 Copynumber: 2.5 Consensus size: 20
451659 GCGATTCTCT
451669 CATTGCGATAGTCAAATTCG
1 CATTGCGATAGTCAAATTCG
**
451689 CATTGCGATAGTCATTTTCG
1 CATTGCGATAGTCAAATTCG
*
451709 CGTTGCGAT
1 CATTGCGAT
451718 TTTAAGTTTC
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:0.22, C:0.20, G:0.22, T:0.35
Consensus pattern (20 bp):
CATTGCGATAGTCAAATTCG
Found at i:452292 original size:21 final size:21
Alignment explanation
Indices: 452201--452305 Score: 95
Period size: 21 Copynumber: 5.0 Consensus size: 21
452191 AACTCACCTG
*
452201 TCATCGTTCAAGAGGCCTCCCC
1 TCATCGTTCAAGAGGCC-CCTC
*
452223 T-ATCGTTCAAGAGGCCCCTA
1 TCATCGTTCAAGAGGCCCCTC
** *
452243 TCATCCCTCAAGAGTCCCCTC
1 TCATCGTTCAAGAGGCCCCTC
* * * *
452264 CCACCGTTCAAGAGGCCACTG
1 TCATCGTTCAAGAGGCCCCTC
* *
452285 TCATCGTTGAAGAGGTCCCTC
1 TCATCGTTCAAGAGGCCCCTC
452306 CCAACATTCT
Statistics
Matches: 63, Mismatches: 19, Indels: 3
0.74 0.22 0.04
Matches are distributed among these distances:
20 3 0.05
21 59 0.94
22 1 0.02
ACGTcount: A:0.21, C:0.37, G:0.19, T:0.23
Consensus pattern (21 bp):
TCATCGTTCAAGAGGCCCCTC
Found at i:452298 original size:42 final size:42
Alignment explanation
Indices: 452198--452308 Score: 118
Period size: 42 Copynumber: 2.6 Consensus size: 42
452188 CCCAACTCAC
* * * *
452198 CTGTCATCGTTCAAGAGGCCTCC-CCTATCGTTCAAGAGGCCC
1 CTGTCATCGTTCAAGAGTCC-CCTCCCACCGTTCAAGAGGCCA
* **
452240 CTATCATCCCTCAAGAGTCCCCTCCCACCGTTCAAGAGGCCA
1 CTGTCATCGTTCAAGAGTCCCCTCCCACCGTTCAAGAGGCCA
*
452282 CTGTCATCGTTGAAGAGGT-CCCTCCCA
1 CTGTCATCGTTCAAGA-GTCCCCTCCCA
452309 ACATTCTAGA
Statistics
Matches: 56, Mismatches: 11, Indels: 4
0.79 0.15 0.06
Matches are distributed among these distances:
41 2 0.04
42 52 0.93
43 2 0.04
ACGTcount: A:0.21, C:0.38, G:0.19, T:0.23
Consensus pattern (42 bp):
CTGTCATCGTTCAAGAGTCCCCTCCCACCGTTCAAGAGGCCA
Found at i:453682 original size:14 final size:14
Alignment explanation
Indices: 453663--453698 Score: 54
Period size: 14 Copynumber: 2.6 Consensus size: 14
453653 ATTGTTTAAT
453663 TGATTTGTAAAAGA
1 TGATTTGTAAAAGA
* *
453677 TGATTTGTAAATGT
1 TGATTTGTAAAAGA
453691 TGATTTGT
1 TGATTTGT
453699 TTAATTGATG
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.31, C:0.00, G:0.22, T:0.47
Consensus pattern (14 bp):
TGATTTGTAAAAGA
Found at i:453892 original size:20 final size:20
Alignment explanation
Indices: 453865--453933 Score: 86
Period size: 20 Copynumber: 3.5 Consensus size: 20
453855 GCGATTCTCT
453865 CGTTGCGATAGTCAATTCCG
1 CGTTGCGATAGTCAATTCCG
* *
453885 CATTGCGATAGTCATTTCCG
1 CGTTGCGATAGTCAATTCCG
* *
453905 TGTTGCGATAATCATATT-CG
1 CGTTGCGATAGTCA-ATTCCG
453925 CGTTGCGAT
1 CGTTGCGAT
453934 TTCCGCGTTG
Statistics
Matches: 41, Mismatches: 7, Indels: 2
0.82 0.14 0.04
Matches are distributed among these distances:
20 39 0.95
21 2 0.05
ACGTcount: A:0.20, C:0.22, G:0.23, T:0.35
Consensus pattern (20 bp):
CGTTGCGATAGTCAATTCCG
Found at i:456433 original size:24 final size:24
Alignment explanation
Indices: 456382--456433 Score: 59
Period size: 24 Copynumber: 2.2 Consensus size: 24
456372 ATCTGAGTAT
** *
456382 TGACCAAGATCAAAGTCCGGGTAT
1 TGACCAAGATCAAAGTCCGAATAC
* *
456406 TGACCAAGATCAAATTTCGAATAC
1 TGACCAAGATCAAAGTCCGAATAC
456430 TGAC
1 TGAC
456434 TAGTACTCAC
Statistics
Matches: 23, Mismatches: 5, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
24 23 1.00
ACGTcount: A:0.37, C:0.21, G:0.19, T:0.23
Consensus pattern (24 bp):
TGACCAAGATCAAAGTCCGAATAC
Found at i:457343 original size:60 final size:60
Alignment explanation
Indices: 457274--457690 Score: 234
Period size: 60 Copynumber: 6.9 Consensus size: 60
457264 CGATAGTCAG
* * * *
457274 AATCTCATTGCGATTTACAGATTCGCATTGCGATTTACGTATTCGCATTGCGATTTACGT
1 AATCGCATTGCGATTTACAGATTCGCGTTGCGATTTACGGATTCGCGTTGCGATTTACGT
* * * * * *
457334 AATCGCATTGCGATTTAC-GTAATCGCATTGCGATTTACGTAATCGCGTTGCGA-AT-CTGG
1 AATCGCATTGCGATTTACAG-ATTCGCGTTGCGATTTACGGATTCGCGTTGCGATTTAC-GT
* * * *
457393 AAACTG-ATTTGCGA--TACCGGTGATCGCGTTGCGAATTATC-GA-TCGCGTTGCGATTTACG-
1 AATC-GCA-TTGCGATTTACAGAT--TCGCGTTGCGATTTA-CGGATTCGCGTTGCGATTTACGT
* * * *
457452 GATACGCGTTGCGATTTTAC-GTATT-GTCGTTGCGATTTACGGATACGCATTGCGATTTACGT
1 AAT-CGCATTGCGA-TTTACAG-ATTCG-CGTTGCGATTTACGGATTCGCGTTGCGATTTACGT
* * * * * *
457514 ATTCTCGTTGCGATTTACAGATACGCGTTGCGATTTACGGATACGCGTTGTGATTTTACGT
1 AATCGCATTGCGATTTACAGATTCGCGTTGCGATTTACGGATTCGCGTTGCGA-TTTACGT
* * * * * * *
457575 -ATTGTCGTTGCGATTTACAGATACGCGTTGCGATTTTATGGATACTCGTTGCGATAGT-CAG-
1 AATCG-CATTGCGATTTACAGATTCGCGTTGCGA-TTTACGGATTCGCGTTGCGAT-TTAC-GT
* * * * ** *
457636 AATCGCGTTGCGAATTATATG-TTCGCGTTGCGATTTTCATATTCGTGTTGCGATT
1 AATCGCATTGCGATTTACA-GATTCGCGTTGCGATTTACGGATTCGCGTTGCGATT
457691 CTGGAAAATT
Statistics
Matches: 283, Mismatches: 45, Indels: 59
0.73 0.12 0.15
Matches are distributed among these distances:
58 4 0.01
59 29 0.10
60 133 0.47
61 89 0.31
62 28 0.10
ACGTcount: A:0.21, C:0.18, G:0.24, T:0.36
Consensus pattern (60 bp):
AATCGCATTGCGATTTACAGATTCGCGTTGCGATTTACGGATTCGCGTTGCGATTTACGT
Found at i:457461 original size:20 final size:20
Alignment explanation
Indices: 457281--457629 Score: 227
Period size: 20 Copynumber: 17.4 Consensus size: 20
457271 CAGAATCTCA
* * *
457281 TTGCGATTTACAGATTCGCA
1 TTGCGATTTACGGATACGCG
* * *
457301 TTGCGATTTACGTATTCGCA
1 TTGCGATTTACGGATACGCG
* *
457321 TTGCGATTTACGTA-ATCGCA
1 TTGCGATTTACGGATA-CGCG
* *
457341 TTGCGATTTACGTA-ATCGCA
1 TTGCGATTTACGGATA-CGCG
*
457361 TTGCGATTTACGTA-ATCGCG
1 TTGCGATTTACGGATA-CGCG
* * **
457381 TTGCGA-AT-CTGGAAACTGAT
1 TTGCGATTTAC-GGATAC-GCG
457401 TTGCGA--TACCGG-TGATCGCG
1 TTGCGATTTA-CGGAT-A-CGCG
*
457421 TTGCGAATTATC-GAT-CGCG
1 TTGCGATTTA-CGGATACGCG
457440 TTGCGATTTACGGATACGCG
1 TTGCGATTTACGGATACGCG
* *
457460 TTGCGATTTTACGTAT-TGTCG
1 TTGCGA-TTTACGGATACG-CG
*
457481 TTGCGATTTACGGATACGCA
1 TTGCGATTTACGGATACGCG
* * *
457501 TTGCGATTTACGTATTCTCG
1 TTGCGATTTACGGATACGCG
*
457521 TTGCGATTTACAGATACGCG
1 TTGCGATTTACGGATACGCG
457541 TTGCGATTTACGGATACGCG
1 TTGCGATTTACGGATACGCG
* * *
457561 TTGTGATTTTACGTAT-TGTCG
1 TTGCGA-TTTACGGATACG-CG
*
457582 TTGCGATTTACAGATACGCG
1 TTGCGATTTACGGATACGCG
* *
457602 TTGCGATTTTATGGATACTCG
1 TTGCGA-TTTACGGATACGCG
457623 TTGCGAT
1 TTGCGAT
457630 AGTCAGAATC
Statistics
Matches: 272, Mismatches: 37, Indels: 40
0.78 0.11 0.11
Matches are distributed among these distances:
18 2 0.01
19 21 0.08
20 192 0.71
21 53 0.19
22 4 0.01
ACGTcount: A:0.21, C:0.19, G:0.25, T:0.36
Consensus pattern (20 bp):
TTGCGATTTACGGATACGCG
Found at i:457572 original size:61 final size:60
Alignment explanation
Indices: 457276--457629 Score: 255
Period size: 60 Copynumber: 5.9 Consensus size: 60
457266 ATAGTCAGAA
* * * * * * *
457276 TCTCATTGCGATTTACAGATTCGCATTGCGATTTACGTATTCGCATTGCGATTTACGTAA
1 TCTCGTTGCGATTTACAGATACGCGTTGCGATTTACGGATACGCGTTGCGATTTACGTAT
* * * * * * *
457336 TCGCATTGCGATTTAC-G-TAATCGCATTGCGATTTACGTA-ATCGCGTTGCGA-AT-CTGGAA
1 TCTCGTTGCGATTTACAGAT-A-CGCGTTGCGATTTACGGATA-CGCGTTGCGATTTAC-GTAT
* * * * *
457395 ACT-GATTTGCGA--TACCGGTGATCGCGTTGCGAATTATC-GAT-CGCGTTGCGATTTACGGAT
1 TCTCG--TTGCGATTTACAGAT-A-CGCGTTGCGATTTA-CGGATACGCGTTGCGATTTACGTAT
* * * *
457455 ACGCGTTGCGATTTTAC-G-TATTGTCGTTGCGATTTACGGATACGCATTGCGATTTACGTAT
1 TCTCGTTGCGA-TTTACAGATA-CG-CGTTGCGATTTACGGATACGCGTTGCGATTTACGTAT
*
457516 TCTCGTTGCGATTTACAGATACGCGTTGCGATTTACGGATACGCGTTGTGATTTTACGTAT
1 TCTCGTTGCGATTTACAGATACGCGTTGCGATTTACGGATACGCGTTGCGA-TTTACGTAT
* * *
457577 TGTCGTTGCGATTTACAGATACGCGTTGCGATTTTATGGATACTCGTTGCGAT
1 TCTCGTTGCGATTTACAGATACGCGTTGCGA-TTTACGGATACGCGTTGCGAT
457630 AGTCAGAATC
Statistics
Matches: 242, Mismatches: 29, Indels: 45
0.77 0.09 0.14
Matches are distributed among these distances:
58 5 0.02
59 27 0.11
60 116 0.48
61 72 0.30
62 22 0.09
ACGTcount: A:0.21, C:0.19, G:0.24, T:0.36
Consensus pattern (60 bp):
TCTCGTTGCGATTTACAGATACGCGTTGCGATTTACGGATACGCGTTGCGATTTACGTAT
Found at i:457645 original size:61 final size:62
Alignment explanation
Indices: 457479--457672 Score: 195
Period size: 61 Copynumber: 3.2 Consensus size: 62
457469 TACGTATTGT
* * *
457479 CGTTGCGA-TTTACGGATACGCATTGCGAT-TTACGTATTC-TCGTTGCGATTTACAGATACG
1 CGTTGCGATTTTACGGATACGCGTTGCGATGTCACG-AATCGTCGTTGCGATTTACAGATACG
* * * * *
457539 CGTTGCGA-TTTACGGATACGCGTTGTGATTTTACGTATTGTCGTTGCGATTTACAGATACG
1 CGTTGCGATTTTACGGATACGCGTTGCGATGTCACGAATCGTCGTTGCGATTTACAGATACG
* * * * *
457600 CGTTGCGATTTTATGGATACTCGTTGCGATAGTCA-GAATCG-CGTTGCGAATTATATG-TTCG
1 CGTTGCGATTTTACGGATACGCGTTGCGAT-GTCACGAATCGTCGTTGCGATTTACA-GATACG
457661 CGTTGCGATTTT
1 CGTTGCGATTTT
457673 CATATTCGTG
Statistics
Matches: 114, Mismatches: 15, Indels: 9
0.83 0.11 0.07
Matches are distributed among these distances:
60 28 0.25
61 61 0.54
62 23 0.20
63 2 0.02
ACGTcount: A:0.20, C:0.18, G:0.25, T:0.37
Consensus pattern (62 bp):
CGTTGCGATTTTACGGATACGCGTTGCGATGTCACGAATCGTCGTTGCGATTTACAGATACG
Found at i:457680 original size:20 final size:20
Alignment explanation
Indices: 457281--457690 Score: 195
Period size: 20 Copynumber: 20.4 Consensus size: 20
457271 CAGAATCTCA
*
457281 TTGCGATTTACAGATTCGCA
1 TTGCGATTTACAGATTCGCG
*
457301 TTGCGATTTAC-GTATTCGCA
1 TTGCGATTTACAG-ATTCGCG
* *
457321 TTGCGATTTAC-GTAATCGCA
1 TTGCGATTTACAG-ATTCGCG
* *
457341 TTGCGATTTAC-GTAATCGCA
1 TTGCGATTTACAG-ATTCGCG
*
457361 TTGCGATTTAC-GTAATCGCG
1 TTGCGATTTACAG-ATTCGCG
* ** * * **
457381 TTGCGAATCTGGAAACT-GAT
1 TTGCG-ATTTACAGATTCGCG
* *
457401 TTGCGA--TACCGGTGATCGCG
1 TTGCGATTTACAGAT--TCGCG
*
457421 TTGCGAATTATC-GA-TCGCG
1 TTGCGATTTA-CAGATTCGCG
* *
457440 TTGCGATTTACGGATACGCG
1 TTGCGATTTACAGATTCGCG
457460 TTGCGATTTTAC-GTATT-GTCG
1 TTGCGA-TTTACAG-ATTCG-CG
* * *
457481 TTGCGATTTACGGATACGCA
1 TTGCGATTTACAGATTCGCG
*
457501 TTGCGATTTAC-GTATTCTCG
1 TTGCGATTTACAG-ATTCGCG
*
457521 TTGCGATTTACAGATACGCG
1 TTGCGATTTACAGATTCGCG
* *
457541 TTGCGATTTACGGATACGCG
1 TTGCGATTTACAGATTCGCG
*
457561 TTGTGATTTTAC-GTATT-GTCG
1 TTGCGA-TTTACAG-ATTCG-CG
*
457582 TTGCGATTTACAGATACGCG
1 TTGCGATTTACAGATTCGCG
** * *
457602 TTGCGATTTTATGGATACTCG
1 TTGCGA-TTTACAGATTCGCG
* *
457623 TTGCGATAGT-CAGAATCGCG
1 TTGCGAT-TTACAGATTCGCG
* *
457643 TTGCGAATTATATG-TTCGCG
1 TTGCGATTTACA-GATTCGCG
* * *
457663 TTGCGATTTTCATATTCGTG
1 TTGCGATTTACAGATTCGCG
457683 TTGCGATT
1 TTGCGATT
457691 CTGGAAAATT
Statistics
Matches: 311, Mismatches: 51, Indels: 56
0.74 0.12 0.13
Matches are distributed among these distances:
17 1 0.00
18 1 0.00
19 21 0.07
20 226 0.73
21 58 0.19
22 3 0.01
23 1 0.00
ACGTcount: A:0.21, C:0.18, G:0.25, T:0.36
Consensus pattern (20 bp):
TTGCGATTTACAGATTCGCG
Found at i:458151 original size:37 final size:37
Alignment explanation
Indices: 458078--458152 Score: 91
Period size: 37 Copynumber: 2.0 Consensus size: 37
458068 GTTGGAAAAT
* *
458078 ATTTATATATTTTCTTTAAAAAATTTAAATTCATAAA
1 ATTTATATATTTTCTTTAAAAAATTGAAAATCATAAA
*
458115 ATTTATATATATATT-TTTACAAAATTGAAAAT-ATAAA
1 ATTTATATAT-T-TTCTTTAAAAAATTGAAAATCATAAA
458152 A
1 A
458153 AGGTTTAATG
Statistics
Matches: 33, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
37 16 0.48
38 15 0.45
39 2 0.06
ACGTcount: A:0.49, C:0.04, G:0.01, T:0.45
Consensus pattern (37 bp):
ATTTATATATTTTCTTTAAAAAATTGAAAATCATAAA
Found at i:459267 original size:13 final size:14
Alignment explanation
Indices: 459241--459270 Score: 53
Period size: 13 Copynumber: 2.2 Consensus size: 14
459231 AAATATAGTT
459241 TTTTATATGACGAG
1 TTTTATATGACGAG
459255 TTTTATA-GACGAG
1 TTTTATATGACGAG
459268 TTT
1 TTT
459271 CATAATATAA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 9 0.56
14 7 0.44
ACGTcount: A:0.27, C:0.07, G:0.20, T:0.47
Consensus pattern (14 bp):
TTTTATATGACGAG
Found at i:460043 original size:2 final size:2
Alignment explanation
Indices: 460036--460083 Score: 96
Period size: 2 Copynumber: 24.0 Consensus size: 2
460026 GCTATAGAAC
460036 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
460078 AT AT AT
1 AT AT AT
460084 TTTGTCAATA
Statistics
Matches: 46, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 46 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:481391 original size:41 final size:41
Alignment explanation
Indices: 481341--481421 Score: 126
Period size: 41 Copynumber: 2.0 Consensus size: 41
481331 TTTCAAAAGC
*
481341 GCAACGCGATTTTCCAAATTCGTAACGCGAATAGGTAAATA
1 GCAACGCGATTTTCCAAATTCGCAACGCGAATAGGTAAATA
* * *
481382 GCAATGCGATTTTCCAAATTCGCAATGCGAATATGTAAAT
1 GCAACGCGATTTTCCAAATTCGCAACGCGAATAGGTAAAT
481422 CACAACGATA
Statistics
Matches: 36, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
41 36 1.00
ACGTcount: A:0.36, C:0.19, G:0.19, T:0.27
Consensus pattern (41 bp):
GCAACGCGATTTTCCAAATTCGCAACGCGAATAGGTAAATA
Found at i:481456 original size:61 final size:61
Alignment explanation
Indices: 481364--481530 Score: 201
Period size: 61 Copynumber: 2.7 Consensus size: 61
481354 CCAAATTCGT
* * * *
481364 AACGCGAATAGGTAAATAGCAATGCGATTTTCCAAATTCGCAATGCGAATATGTAAATCAC
1 AACGAGAATATGTAAATAGCAATGCGATTTTCCAAATTCGCAACGCAAATATGTAAATCAC
* * * * *
481425 AACGATAATATGTAAATCGCAACGCGATTTTCCAAAATCGCAACGCAAATATGTAAATCGC
1 AACGAGAATATGTAAATAGCAATGCGATTTTCCAAATTCGCAACGCAAATATGTAAATCAC
* * * *
481486 AACGCGAATATGCAAATTTGCAATGCGATTTT-CAAATCCGCAACG
1 AACGAGAATATGTAAA-TAGCAATGCGATTTTCCAAATTCGCAACG
481531 TTAATTACCG
Statistics
Matches: 89, Mismatches: 16, Indels: 2
0.83 0.15 0.02
Matches are distributed among these distances:
61 76 0.85
62 13 0.15
ACGTcount: A:0.39, C:0.20, G:0.17, T:0.24
Consensus pattern (61 bp):
AACGAGAATATGTAAATAGCAATGCGATTTTCCAAATTCGCAACGCAAATATGTAAATCAC
Found at i:481484 original size:20 final size:20
Alignment explanation
Indices: 481364--481502 Score: 107
Period size: 20 Copynumber: 6.8 Consensus size: 20
481354 CCAAATTCGT
* *
481364 AACGCGAATAGGTAAATAGC
1 AACGCGAATATGTAAATCGC
* * * **
481384 AATGCGATTTTCCAAATTCGC
1 AACGCGAATATGTAAA-TCGC
* *
481405 AATGCGAATATGTAAATCAC
1 AACGCGAATATGTAAATCGC
**
481425 AACGATAATATGTAAATCGC
1 AACGCGAATATGTAAATCGC
* * **
481445 AACGCGATTTTCCAAAATCGC
1 AACGCGAATAT-GTAAATCGC
*
481466 AACGCAAATATGTAAATCGC
1 AACGCGAATATGTAAATCGC
*
481486 AACGCGAATATGCAAAT
1 AACGCGAATATGTAAAT
481503 TTGCAATGCG
Statistics
Matches: 88, Mismatches: 29, Indels: 4
0.73 0.24 0.03
Matches are distributed among these distances:
20 58 0.66
21 30 0.34
ACGTcount: A:0.41, C:0.19, G:0.17, T:0.23
Consensus pattern (20 bp):
AACGCGAATATGTAAATCGC
Found at i:485342 original size:3 final size:3
Alignment explanation
Indices: 485334--485397 Score: 128
Period size: 3 Copynumber: 21.3 Consensus size: 3
485324 TACATTTTGG
485334 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
485382 ATT ATT ATT ATT ATT A
1 ATT ATT ATT ATT ATT A
485398 AATGCTGAAC
Statistics
Matches: 61, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 61 1.00
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
ATT
Found at i:490493 original size:2 final size:2
Alignment explanation
Indices: 490488--490515 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
490478 AATTTTTTTA
490488 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
490516 TTAAATGTTT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:496869 original size:20 final size:20
Alignment explanation
Indices: 496844--496889 Score: 74
Period size: 20 Copynumber: 2.3 Consensus size: 20
496834 AACAACACCC
*
496844 TATACTCGAGGGATCATTTG
1 TATACTCGAGAGATCATTTG
496864 TATACTCGAGAGATCATTTG
1 TATACTCGAGAGATCATTTG
*
496884 TGTACT
1 TATACT
496890 TTACCCAAAG
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
20 24 1.00
ACGTcount: A:0.26, C:0.15, G:0.22, T:0.37
Consensus pattern (20 bp):
TATACTCGAGAGATCATTTG
Found at i:515242 original size:21 final size:20
Alignment explanation
Indices: 515208--515247 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 20
515198 GTTTTCTTAG
515208 TTTTAATCTTTTTAACAAAA
1 TTTTAATCTTTTTAACAAAA
* *
515228 TTTTATATTTTTTTATCAAA
1 TTTTA-ATCTTTTTAACAAA
515248 TATATATGGT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 5 0.29
21 12 0.71
ACGTcount: A:0.35, C:0.07, G:0.00, T:0.57
Consensus pattern (20 bp):
TTTTAATCTTTTTAACAAAA
Found at i:517285 original size:24 final size:24
Alignment explanation
Indices: 517249--517296 Score: 60
Period size: 24 Copynumber: 2.0 Consensus size: 24
517239 TATCAATGAC
* *
517249 TGAAAAAGATTATCCAAAACTATT
1 TGAAAAACATTATCCAAAAATATT
* *
517273 TGAAAAACTTTATTCAAAAATATT
1 TGAAAAACATTATCCAAAAATATT
517297 ACTATCAAGC
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
24 20 1.00
ACGTcount: A:0.50, C:0.10, G:0.06, T:0.33
Consensus pattern (24 bp):
TGAAAAACATTATCCAAAAATATT
Found at i:521279 original size:16 final size:17
Alignment explanation
Indices: 521247--521280 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
521237 ATAATTTAAC
*
521247 TAAAATTTTCTTAATTT
1 TAAAATTTACTTAATTT
521264 TAAAATTTAC-TAATTT
1 TAAAATTTACTTAATTT
521280 T
1 T
521281 TTGAACTCCT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 7 0.44
17 9 0.56
ACGTcount: A:0.38, C:0.06, G:0.00, T:0.56
Consensus pattern (17 bp):
TAAAATTTACTTAATTT
Found at i:536794 original size:24 final size:24
Alignment explanation
Indices: 536758--536807 Score: 66
Period size: 24 Copynumber: 2.1 Consensus size: 24
536748 TTTAATAATT
* *
536758 TAATAATATTATTTTTAT-AATAA
1 TAATAATAATATTTTAATAAATAA
536781 TAATAAATAATATTTTAATAAATAA
1 TAAT-AATAATATTTTAATAAATAA
536806 TA
1 TA
536808 TTTTAATTAA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
23 4 0.17
24 12 0.52
25 7 0.30
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (24 bp):
TAATAATAATATTTTAATAAATAA
Found at i:536801 original size:15 final size:15
Alignment explanation
Indices: 536781--536814 Score: 68
Period size: 15 Copynumber: 2.3 Consensus size: 15
536771 TTTATAATAA
536781 TAATAAATAATATTT
1 TAATAAATAATATTT
536796 TAATAAATAATATTT
1 TAATAAATAATATTT
536811 TAAT
1 TAAT
536815 TAAAATATAC
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 19 1.00
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (15 bp):
TAATAAATAATATTT
Found at i:540575 original size:63 final size:64
Alignment explanation
Indices: 540459--540585 Score: 211
Period size: 63 Copynumber: 2.0 Consensus size: 64
540449 AAGGGAATTA
*
540459 AACCGATTTGGGGACCAAATTAAACGTTTTTTTAAAACAGAGGGAGCCAAAATGAAGTTTACCC
1 AACCGATTTGGGGACCAAATTAAACGTTTTTTCAAAACAGAGGGAGCCAAAATGAAGTTTACCC
* * *
540523 AACCGGTTTGGGGACCAAATTGAATG-TTTTTCAAAACAGAGGGAGCCAAAATGAAGTTTACCC
1 AACCGATTTGGGGACCAAATTAAACGTTTTTTCAAAACAGAGGGAGCCAAAATGAAGTTTACCC
540586 CTTTTAACAA
Statistics
Matches: 59, Mismatches: 4, Indels: 1
0.92 0.06 0.02
Matches are distributed among these distances:
63 36 0.61
64 23 0.39
ACGTcount: A:0.36, C:0.17, G:0.22, T:0.24
Consensus pattern (64 bp):
AACCGATTTGGGGACCAAATTAAACGTTTTTTCAAAACAGAGGGAGCCAAAATGAAGTTTACCC
Found at i:541537 original size:2 final size:2
Alignment explanation
Indices: 541530--541585 Score: 73
Period size: 2 Copynumber: 29.5 Consensus size: 2
541520 CATATGTAAA
541530 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT -T AT A- AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
* *
541570 GT AA AT AT AT -T AT AT A
1 AT AT AT AT AT AT AT AT A
541586 ATGTTAAAAA
Statistics
Matches: 47, Mismatches: 4, Indels: 6
0.82 0.07 0.11
Matches are distributed among these distances:
1 3 0.06
2 44 0.94
ACGTcount: A:0.50, C:0.00, G:0.02, T:0.48
Consensus pattern (2 bp):
AT
Found at i:542216 original size:105 final size:105
Alignment explanation
Indices: 541927--542575 Score: 977
Period size: 105 Copynumber: 6.2 Consensus size: 105
541917 GTCAATCTGT
* * **
541927 TTGTGAAGTTGGAAA-TGGCTATGGAATTGAGAAAT-TATTCGTTGACAGTCAGTC-GTCCCTTC
1 TTGTGAAGTT-GAAATTGGCTCTGAAATTGAGAAATGT-TT-GTTGACAACCAG-CGGTCCCTTC
* * * * * * *
541989 GTTGTGAAGTCGAGCTTGTGCTGTCTTGAGTCCAATATCCTTTG
62 GTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCG
* *
542033 CTGTGAAGTTGAAATTGGCTCTGACATTGAG--ATGTTTGTTGACAACCAGCGGTCCCTTCGTCG
1 TTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAATGTTTGTTGACAACCAGCGGTCCCTTCGTCG
542096 TGAAGTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCG
66 TGAAGTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCG
** ** *
542136 TTGCAAAGTTGAAATTGGCTCTGAAATTGAGAGGTGTTTATTGACAACCAGCGGTCCCTTCGTCG
1 TTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAATGTTTGTTGACAACCAGCGGTCCCTTCGTCG
* *
542201 TGAAGTTGAACTTGCGTTGTCGGGAGACCAATATCCTTCG
66 TGAAGTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCG
* *
542241 CTGTGAAGTTGAAATTGGCTCTGAATTTGAGAAATGTTTGTTGACAACCAGCGGTCCCTTCGTCG
1 TTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAATGTTTGTTGACAACCAGCGGTCCCTTCGTCG
542306 TGAAGTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCG
66 TGAAGTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCG
*
542346 TTGTGAAGTTGAAATTGGCTCTG-AATTGGAGAAATGTTTGGTGACAACCAGCGGTCCCTTCGTC
1 TTGTGAAGTTGAAATTGGCTCTGAAATT-GAGAAATGTTTGTTGACAACCAGCGGTCCCTTCGTC
542410 GTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCG
65 GTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCG
* *
542451 TTGTGAAGTTGAAATTGGCTCTGAATTTGAGAAATGTTTGTTGACAACCAGCGGTCCCTTCGACG
1 TTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAATGTTTGTTGACAACCAGCGGTCCCTTCGTCG
*
542516 CGAAGTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCG
66 TGAAGTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCG
542556 TTGTGAAGTTGAAATTGGCT
1 TTGTGAAGTTGAAATTGGCT
542576 ATGGGTAAAA
Statistics
Matches: 499, Mismatches: 37, Indels: 15
0.91 0.07 0.03
Matches are distributed among these distances:
102 1 0.00
103 82 0.16
104 7 0.01
105 384 0.77
106 25 0.05
ACGTcount: A:0.22, C:0.18, G:0.27, T:0.33
Consensus pattern (105 bp):
TTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAATGTTTGTTGACAACCAGCGGTCCCTTCGTCG
TGAAGTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCG
Found at i:554244 original size:31 final size:32
Alignment explanation
Indices: 554199--554260 Score: 81
Period size: 31 Copynumber: 2.0 Consensus size: 32
554189 GAAACTCAAC
*
554199 AAAAAGTATTAATAGAAAAGAAAAAAATATAT
1 AAAAAGTATAAATAGAAAAGAAAAAAATATAT
* * *
554231 AAAAA-TATAAATAGATAGGTAAAAAATATA
1 AAAAAGTATAAATAGAAAAGAAAAAAATATA
554261 CATCCATAAA
Statistics
Matches: 26, Mismatches: 4, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
31 21 0.81
32 5 0.19
ACGTcount: A:0.68, C:0.00, G:0.10, T:0.23
Consensus pattern (32 bp):
AAAAAGTATAAATAGAAAAGAAAAAAATATAT
Found at i:554647 original size:63 final size:64
Alignment explanation
Indices: 554531--554657 Score: 211
Period size: 63 Copynumber: 2.0 Consensus size: 64
554521 CAAGGGAATT
*
554531 AACCGATTTGGGGACCAAATTAAACGTTTTTTTAAAACAGAGGGAGCCAAAATGAAGTTTACCC
1 AACCGATTTGGGGACCAAATTAAACGTTTTTTCAAAACAGAGGGAGCCAAAATGAAGTTTACCC
* * *
554595 AACCGGTTTGGGGACCAAATTGAATG-TTTTTCAAAACAGAGGGAGCCAAAATGAAGTTTACCC
1 AACCGATTTGGGGACCAAATTAAACGTTTTTTCAAAACAGAGGGAGCCAAAATGAAGTTTACCC
554658 CTTTTAACAA
Statistics
Matches: 59, Mismatches: 4, Indels: 1
0.92 0.06 0.02
Matches are distributed among these distances:
63 36 0.61
64 23 0.39
ACGTcount: A:0.36, C:0.17, G:0.22, T:0.24
Consensus pattern (64 bp):
AACCGATTTGGGGACCAAATTAAACGTTTTTTCAAAACAGAGGGAGCCAAAATGAAGTTTACCC
Found at i:556932 original size:15 final size:15
Alignment explanation
Indices: 556914--556985 Score: 71
Period size: 15 Copynumber: 4.9 Consensus size: 15
556904 CATTTTACTT
*
556914 AAATTATTTTTATTA
1 AAATTATTATTATTA
556929 AAATTATTATTATT-
1 AAATTATTATTATTA
556943 --ATTATTATTA-TA
1 AAATTATTATTATTA
*
556955 AATATTATGATTATTA
1 AA-ATTATTATTATTA
*
556971 AATACTATTATTATT
1 AA-ATTATTATTATT
556986 TACAAGCCCA
Statistics
Matches: 48, Mismatches: 4, Indels: 9
0.79 0.07 0.15
Matches are distributed among these distances:
11 1 0.02
12 10 0.21
15 22 0.46
16 15 0.31
ACGTcount: A:0.42, C:0.01, G:0.01, T:0.56
Consensus pattern (15 bp):
AAATTATTATTATTA
Found at i:556939 original size:3 final size:3
Alignment explanation
Indices: 556916--556985 Score: 59
Period size: 3 Copynumber: 23.0 Consensus size: 3
556906 TTTTACTTAA
* ** * * *
556916 ATT ATT TTT ATT AAA ATT ATT ATT ATT ATT ATT ATT ATA AAT ATT ATG
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
* *
556964 ATT ATT AAAT ACT ATT ATT ATT
1 ATT ATT -ATT ATT ATT ATT ATT
556986 TACAAGCCCA
Statistics
Matches: 51, Mismatches: 15, Indels: 2
0.75 0.22 0.03
Matches are distributed among these distances:
3 49 0.96
4 2 0.04
ACGTcount: A:0.40, C:0.01, G:0.01, T:0.57
Consensus pattern (3 bp):
ATT
Found at i:558465 original size:21 final size:21
Alignment explanation
Indices: 558439--558483 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
558429 GATTTCTGGG
* *
558439 CAAGGGGAATCGGTACCCATT
1 CAAGGGGAACCGATACCCATT
*
558460 CAAGGGGAACCGATACCCCTT
1 CAAGGGGAACCGATACCCATT
558481 CAA
1 CAA
558484 ACGACAGAAT
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:0.31, C:0.29, G:0.24, T:0.16
Consensus pattern (21 bp):
CAAGGGGAACCGATACCCATT
Found at i:559438 original size:30 final size:31
Alignment explanation
Indices: 559351--559474 Score: 198
Period size: 31 Copynumber: 4.0 Consensus size: 31
559341 AGGGTCGAGG
559351 GTTTACCTATGTTCTTCGGAACATATGGACT
1 GTTTACCTATGTTCTTCGGAACATATGGACT
559382 GTTTACCTATGTTCTTCGGAACATATGGACT
1 GTTTACCTATGTTCTTCGGAACATATGGACT
*
559413 GTTTACCTATGTCCTTCGG-ACATATGGACT
1 GTTTACCTATGTTCTTCGGAACATATGGACT
* *
559443 GATTACCTAGGTTCTTCGGAATC-TATGGACT
1 GTTTACCTATGTTCTTCGGAA-CATATGGACT
559474 G
1 G
559475 GTCCTTCGGG
Statistics
Matches: 87, Mismatches: 4, Indels: 4
0.92 0.04 0.04
Matches are distributed among these distances:
30 27 0.31
31 59 0.68
32 1 0.01
ACGTcount: A:0.22, C:0.20, G:0.21, T:0.37
Consensus pattern (31 bp):
GTTTACCTATGTTCTTCGGAACATATGGACT
Found at i:559451 original size:61 final size:62
Alignment explanation
Indices: 559351--559474 Score: 198
Period size: 61 Copynumber: 2.0 Consensus size: 62
559341 AGGGTCGAGG
* * *
559351 GTTTACCTATGTTCTTCGGAACATATGGACTGTTTACCTATGTTCTTCGGAA-CATATGGACT
1 GTTTACCTATGTCCTTCGGAACATATGGACTGATTACCTAGGTTCTTCGGAATC-TATGGACT
559413 GTTTACCTATGTCCTTCGG-ACATATGGACTGATTACCTAGGTTCTTCGGAATCTATGGACT
1 GTTTACCTATGTCCTTCGGAACATATGGACTGATTACCTAGGTTCTTCGGAATCTATGGACT
559474 G
1 G
559475 GTCCTTCGGG
Statistics
Matches: 58, Mismatches: 3, Indels: 3
0.91 0.05 0.05
Matches are distributed among these distances:
61 39 0.67
62 19 0.33
ACGTcount: A:0.22, C:0.20, G:0.21, T:0.37
Consensus pattern (62 bp):
GTTTACCTATGTCCTTCGGAACATATGGACTGATTACCTAGGTTCTTCGGAATCTATGGACT
Found at i:562517 original size:21 final size:21
Alignment explanation
Indices: 562491--562535 Score: 72
Period size: 21 Copynumber: 2.1 Consensus size: 21
562481 GATTTCTGGG
*
562491 CAAGGGGAATCGATACCCATT
1 CAAGGGGAACCGATACCCATT
*
562512 CAAGGGGAACCGATACCCCTT
1 CAAGGGGAACCGATACCCATT
562533 CAA
1 CAA
562536 ACGACAGAAT
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.33, C:0.29, G:0.22, T:0.16
Consensus pattern (21 bp):
CAAGGGGAACCGATACCCATT
Found at i:563434 original size:31 final size:31
Alignment explanation
Indices: 563396--563520 Score: 198
Period size: 31 Copynumber: 4.0 Consensus size: 31
563386 AGGGTCGAGG
563396 GTTTACCTATGTTCTTCGGAACATATGGACT
1 GTTTACCTATGTTCTTCGGAACATATGGACT
563427 GTTTACCTATGTTCTTCGGAACATATGGACT
1 GTTTACCTATGTTCTTCGGAACATATGGACT
* *
563458 GTTTACCTATGTCCTTCGGGACATATGGACT
1 GTTTACCTATGTTCTTCGGAACATATGGACT
* *
563489 GATTACCTAGGTTCTTCGGAATC-TATGGACT
1 GTTTACCTATGTTCTTCGGAA-CATATGGACT
563520 G
1 G
563521 GTCCTTCGGG
Statistics
Matches: 87, Mismatches: 6, Indels: 2
0.92 0.06 0.02
Matches are distributed among these distances:
31 86 0.99
32 1 0.01
ACGTcount: A:0.22, C:0.20, G:0.22, T:0.37
Consensus pattern (31 bp):
GTTTACCTATGTTCTTCGGAACATATGGACT
Found at i:565766 original size:28 final size:26
Alignment explanation
Indices: 565735--565805 Score: 72
Period size: 30 Copynumber: 2.6 Consensus size: 26
565725 TAATTCTTTC
565735 TTTTCAAAATTTTTATATATACTTATT
1 TTTTCAAAATTTTTATATATA-TTATT
* *
565762 ATTTTCATAATATTTATATGTATATTATT
1 -TTTTCA-AA-ATTTTTATATATATTATT
*
565791 TTTT-AATATTTTTAT
1 TTTTCAAAATTTTTAT
565806 TTTATTTTCA
Statistics
Matches: 37, Mismatches: 4, Indels: 7
0.77 0.08 0.15
Matches are distributed among these distances:
25 7 0.19
26 1 0.03
27 1 0.03
28 10 0.27
29 7 0.19
30 11 0.30
ACGTcount: A:0.32, C:0.04, G:0.01, T:0.62
Consensus pattern (26 bp):
TTTTCAAAATTTTTATATATATTATT
Found at i:565787 original size:26 final size:27
Alignment explanation
Indices: 565735--565801 Score: 75
Period size: 28 Copynumber: 2.5 Consensus size: 27
565725 TAATTCTTTC
* *
565735 TTTTCAAAATTTTTATATATACTTATTA
1 TTTTCATAATATTTATATATAC-TATTA
*
565763 TTTTCATAATATTTATATGTA-TATTA
1 TTTTCATAATATTTATATATACTATTA
*
565789 TTTT-TTAATATTT
1 TTTTCATAATATTT
565802 TTATTTTATT
Statistics
Matches: 35, Mismatches: 4, Indels: 3
0.83 0.10 0.07
Matches are distributed among these distances:
25 8 0.23
26 9 0.26
28 18 0.51
ACGTcount: A:0.33, C:0.04, G:0.01, T:0.61
Consensus pattern (27 bp):
TTTTCATAATATTTATATATACTATTA
Found at i:570944 original size:7 final size:7
Alignment explanation
Indices: 570932--570978 Score: 85
Period size: 7 Copynumber: 6.7 Consensus size: 7
570922 TACTTGAAAA
570932 AAAAAGG
1 AAAAAGG
*
570939 AAAAAGA
1 AAAAAGG
570946 AAAAAGG
1 AAAAAGG
570953 AAAAAGG
1 AAAAAGG
570960 AAAAAGG
1 AAAAAGG
570967 AAAAAGG
1 AAAAAGG
570974 AAAAA
1 AAAAA
570979 AAAAGAAGAA
Statistics
Matches: 38, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
7 38 1.00
ACGTcount: A:0.77, C:0.00, G:0.23, T:0.00
Consensus pattern (7 bp):
AAAAAGG
Found at i:574342 original size:75 final size:75
Alignment explanation
Indices: 574210--574384 Score: 262
Period size: 75 Copynumber: 2.3 Consensus size: 75
574200 ACAAGAAACA
* * *
574210 AATGATGGAGCATGCTGAAAGCCCATTTCATTCATGATCAGGAATGTTGACACATTTTGAACGTT
1 AATGATGGGGCATGCTGAAAGCCCATTTCAATCATGATCAAGAATGTTGACACATTTTGAACGTT
*
574275 TGTATTAGCT
66 TGTATTAGCC
* *
574285 AATGCTGGGGCATGCTGAAAGCCCATTTCAATCA-GAATCAAGAGTGTTGACACATTTTGAACGT
1 AATGATGGGGCATGCTGAAAGCCCATTTCAATCATG-ATCAAGAATGTTGACACATTTTGAACGT
574349 TTGTATTAGCC
65 TTGTATTAGCC
* *
574360 AATGTTGGGGCATGCTGAAGGCCCA
1 AATGATGGGGCATGCTGAAAGCCCA
574385 CATCGTCATA
Statistics
Matches: 91, Mismatches: 8, Indels: 2
0.90 0.08 0.02
Matches are distributed among these distances:
74 1 0.01
75 90 0.99
ACGTcount: A:0.29, C:0.18, G:0.24, T:0.30
Consensus pattern (75 bp):
AATGATGGGGCATGCTGAAAGCCCATTTCAATCATGATCAAGAATGTTGACACATTTTGAACGTT
TGTATTAGCC
Found at i:575610 original size:22 final size:22
Alignment explanation
Indices: 575536--575614 Score: 81
Period size: 22 Copynumber: 3.6 Consensus size: 22
575526 ACATCTACAC
* *
575536 TTTTCAAATATGATAGTTTCTT
1 TTTTCAAAGATGATAGATTCTT
* *
575558 TCTTCAAAGATGGTAGCATATC-T
1 TTTTCAAAGATGATAG-AT-TCTT
*
575581 CTTT-AAAGATGATAGATTCTT
1 TTTTCAAAGATGATAGATTCTT
575602 TTTTCAAAGATGA
1 TTTTCAAAGATGA
575615 AAGCTTTATT
Statistics
Matches: 45, Mismatches: 8, Indels: 8
0.74 0.13 0.13
Matches are distributed among these distances:
20 2 0.04
21 6 0.13
22 31 0.69
23 4 0.09
24 2 0.04
ACGTcount: A:0.32, C:0.11, G:0.14, T:0.43
Consensus pattern (22 bp):
TTTTCAAAGATGATAGATTCTT
Found at i:576424 original size:90 final size:91
Alignment explanation
Indices: 576270--576897 Score: 942
Period size: 90 Copynumber: 6.9 Consensus size: 91
576260 CTACTTCTCA
* *
576270 CATCTGTAAGCCCTTCAGTGCATGATGTCTTC-AAAACCTTCAGGTCATCTGTAAGCCCTTCAGT
1 CATCTGTAAGCCCTTCAGTGCATGATGTTTTCAAAAACCTTCGGGTCATCTGTAAGCCCTTCAGT
*
576334 GCATGATGTCTTCAAAACCTTCGGGT
66 GCATGATGTTTTCAAAACCTTCGGGT
* * * * *
576360 AATCTGTAAGTCCTTCAGTTCTTGAAGTTTTC-AAAACCTTCGGGTCATCTGTAAGCCCTTCAGT
1 CATCTGTAAGCCCTTCAGTGCATGATGTTTTCAAAAACCTTCGGGTCATCTGTAAGCCCTTCAGT
*
576424 GCATGATGTCTGT-AAAACCTTCGGGT
66 GCATGATGT-TTTCAAAACCTTCGGGT
* * * * *
576450 CATCTGTAAGTCCTTCAGTGCTTGATGTCTTC-AAAATCTTCGGGTCATCTGTAAGTCCTTCAGT
1 CATCTGTAAGCCCTTCAGTGCATGATGTTTTCAAAAACCTTCGGGTCATCTGTAAGCCCTTCAGT
*
576514 G-ATTGATGTTTTCAAAACCTTCGGAT
66 GCA-TGATGTTTTCAAAACCTTCGGGT
* * *
576540 CATCTGTAAGTCCTTCAGTGCTTGATGTTTTCAAAAACCTTCAGGTCATCTGTAAGCCCTTCAGT
1 CATCTGTAAGCCCTTCAGTGCATGATGTTTTCAAAAACCTTCGGGTCATCTGTAAGCCCTTCAGT
*
576605 GCATGATGTTTTCAAAAACCTTCGGAT
66 GCATGATGTTTTC-AAAACCTTCGGGT
576632 CATCTGTAAGCCCTTCAGTGCATGATGTTTTCAAAAACCTTCGGGTCATCTGTAAGCCCTTCAGT
1 CATCTGTAAGCCCTTCAGTGCATGATGTTTTCAAAAACCTTCGGGTCATCTGTAAGCCCTTCAGT
576697 GCATGATGTTTTCAAAAACCTTCGGGT
66 GCATGATGTTTTC-AAAACCTTCGGGT
* *
576724 CATCTGTAAGCCCCTTCAGTGCATGATGTTTTCAAAAACCTTCGGGTCATTTGTAAGCCCTTTAG
1 CATCTGTAAG-CCCTTCAGTGCATGATGTTTTCAAAAACCTTCGGGTCATCTGTAAGCCCTTCAG
576789 TGCATGATGTTTTCAAAAACCTTCGGGT
65 TGCATGATGTTTTC-AAAACCTTCGGGT
* * * *
576817 CATCTGTAAGCCCTTCAGTGCATAATGTTTCCAAAAACCTTCGGGTCATCTGTAAGACCTTGAGT
1 CATCTGTAAGCCCTTCAGTGCATGATGTTTTCAAAAACCTTCGGGTCATCTGTAAGCCCTTCAGT
576882 GCATGATGTTTTCAAA
66 GCATGATGTTTTCAAA
576898 CATTTCCATC
Statistics
Matches: 499, Mismatches: 32, Indels: 13
0.92 0.06 0.02
Matches are distributed among these distances:
89 3 0.01
90 187 0.37
91 44 0.09
92 175 0.35
93 90 0.18
ACGTcount: A:0.24, C:0.23, G:0.19, T:0.34
Consensus pattern (91 bp):
CATCTGTAAGCCCTTCAGTGCATGATGTTTTCAAAAACCTTCGGGTCATCTGTAAGCCCTTCAGT
GCATGATGTTTTCAAAACCTTCGGGT
Found at i:576594 original size:46 final size:46
Alignment explanation
Indices: 576270--576897 Score: 948
Period size: 46 Copynumber: 13.8 Consensus size: 46
576260 CTACTTCTCA
* *
576270 CATCTGTAAGCCCTTCAGTGCATGATGTCTTC-AAAACCTTCAGGT
1 CATCTGTAAGCCCTTCAGTGCATGATGTTTTCAAAAACCTTCGGGT
*
576315 CATCTGTAAGCCCTTCAGTGCATGATGTCTTC-AAAACCTTCGGGT
1 CATCTGTAAGCCCTTCAGTGCATGATGTTTTCAAAAACCTTCGGGT
* * * * *
576360 AATCTGTAAGTCCTTCAGTTCTTGAAGTTTTC-AAAACCTTCGGGT
1 CATCTGTAAGCCCTTCAGTGCATGATGTTTTCAAAAACCTTCGGGT
*
576405 CATCTGTAAGCCCTTCAGTGCATGATGTCTGT--AAAACCTTCGGGT
1 CATCTGTAAGCCCTTCAGTGCATGATGT-TTTCAAAAACCTTCGGGT
* * * *
576450 CATCTGTAAGTCCTTCAGTGCTTGATGTCTTC-AAAATCTTCGGGT
1 CATCTGTAAGCCCTTCAGTGCATGATGTTTTCAAAAACCTTCGGGT
* *
576495 CATCTGTAAGTCCTTCAGTG-ATTGATGTTTTC-AAAACCTTCGGAT
1 CATCTGTAAGCCCTTCAGTGCA-TGATGTTTTCAAAAACCTTCGGGT
* * *
576540 CATCTGTAAGTCCTTCAGTGCTTGATGTTTTCAAAAACCTTCAGGT
1 CATCTGTAAGCCCTTCAGTGCATGATGTTTTCAAAAACCTTCGGGT
*
576586 CATCTGTAAGCCCTTCAGTGCATGATGTTTTCAAAAACCTTCGGAT
1 CATCTGTAAGCCCTTCAGTGCATGATGTTTTCAAAAACCTTCGGGT
576632 CATCTGTAAGCCCTTCAGTGCATGATGTTTTCAAAAACCTTCGGGT
1 CATCTGTAAGCCCTTCAGTGCATGATGTTTTCAAAAACCTTCGGGT
576678 CATCTGTAAGCCCTTCAGTGCATGATGTTTTCAAAAACCTTCGGGT
1 CATCTGTAAGCCCTTCAGTGCATGATGTTTTCAAAAACCTTCGGGT
576724 CATCTGTAAGCCCCTTCAGTGCATGATGTTTTCAAAAACCTTCGGGT
1 CATCTGTAAG-CCCTTCAGTGCATGATGTTTTCAAAAACCTTCGGGT
* *
576771 CATTTGTAAGCCCTTTAGTGCATGATGTTTTCAAAAACCTTCGGGT
1 CATCTGTAAGCCCTTCAGTGCATGATGTTTTCAAAAACCTTCGGGT
* *
576817 CATCTGTAAGCCCTTCAGTGCATAATGTTTCCAAAAACCTTCGGGT
1 CATCTGTAAGCCCTTCAGTGCATGATGTTTTCAAAAACCTTCGGGT
* *
576863 CATCTGTAAGACCTTGAGTGCATGATGTTTTCAAA
1 CATCTGTAAGCCCTTCAGTGCATGATGTTTTCAAA
576898 CATTTCCATC
Statistics
Matches: 537, Mismatches: 40, Indels: 11
0.91 0.07 0.02
Matches are distributed among these distances:
44 1 0.00
45 227 0.42
46 264 0.49
47 45 0.08
ACGTcount: A:0.24, C:0.23, G:0.19, T:0.34
Consensus pattern (46 bp):
CATCTGTAAGCCCTTCAGTGCATGATGTTTTCAAAAACCTTCGGGT
Found at i:577041 original size:15 final size:15
Alignment explanation
Indices: 577021--577080 Score: 68
Period size: 15 Copynumber: 3.9 Consensus size: 15
577011 TAAATTACTT
*
577021 AAATTATTTTTATTA
1 AAATTATTATTATTA
577036 AAATTATTATTA-TA
1 AAATTATTATTATTA
*
577050 AATATTATGATTATTA
1 AA-ATTATTATTATTA
*
577066 AATACTATTATTATT
1 AA-ATTATTATTATT
577081 TACAAGCCCA
Statistics
Matches: 39, Mismatches: 4, Indels: 3
0.85 0.09 0.07
Matches are distributed among these distances:
14 4 0.10
15 20 0.51
16 15 0.38
ACGTcount: A:0.43, C:0.02, G:0.02, T:0.53
Consensus pattern (15 bp):
AAATTATTATTATTA
Found at i:582089 original size:45 final size:44
Alignment explanation
Indices: 582008--582161 Score: 168
Period size: 45 Copynumber: 3.3 Consensus size: 44
581998 ATTTAAATAA
** *
582008 TTTAAAATAATTTA-ATAAGGTTATTTATTTTAAAATAATTTAT
1 TTTAAAATAATTTATATAAAATAATTTATTTTAAAATAATTTAT
*
582051 TTTAAAATAATTTATGATAAAATAATTTATTATAAAATAATTTAT
1 TTTAAAATAATTTAT-ATAAAATAATTTATTTTAAAATAATTTAT
*
582096 TTTAAAATAAATTATTATAAAATATGGATTGATTTATTTTAAAATAATTTAT
1 TTTAAAATAATTTA-TAT-AAA-AT--A---ATTTATTTTAAAATAATTTAT
582148 TTT-AAATAATTTAT
1 TTTAAAATAATTTAT
582162 TAGTATGGAT
Statistics
Matches: 94, Mismatches: 7, Indels: 13
0.82 0.06 0.11
Matches are distributed among these distances:
43 14 0.15
45 40 0.43
46 4 0.04
47 2 0.02
49 1 0.01
50 1 0.01
51 9 0.10
52 23 0.24
ACGTcount: A:0.47, C:0.00, G:0.04, T:0.49
Consensus pattern (44 bp):
TTTAAAATAATTTATATAAAATAATTTATTTTAAAATAATTTAT
Found at i:582156 original size:14 final size:15
Alignment explanation
Indices: 582030--582162 Score: 151
Period size: 15 Copynumber: 8.5 Consensus size: 15
582020 TAATAAGGTT
582030 ATTTATTTTAAAATA
1 ATTTATTTTAAAATA
582045 ATTTATTTTAAAATA
1 ATTTATTTTAAAATA
**
582060 ATTTATGATAAAATA
1 ATTTATTTTAAAATA
*
582075 ATTTATTATAAAATA
1 ATTTATTTTAAAATA
582090 ATTTATTTTAAAATA
1 ATTTATTTTAAAATA
* *
582105 AATTATTATAAAATATGGA
1 ATTTATT-TTAAA-AT--A
582124 TTGATTTATTTTAAAATA
1 ---ATTTATTTTAAAATA
582142 ATTTATTTT-AAATA
1 ATTTATTTTAAAATA
582156 ATTTATT
1 ATTTATT
582163 AGTATGGATT
Statistics
Matches: 103, Mismatches: 8, Indels: 15
0.82 0.06 0.12
Matches are distributed among these distances:
14 12 0.12
15 71 0.69
16 4 0.04
17 2 0.02
18 1 0.01
19 1 0.01
20 2 0.02
21 4 0.04
22 6 0.06
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.50
Consensus pattern (15 bp):
ATTTATTTTAAAATA
Found at i:582180 original size:32 final size:31
Alignment explanation
Indices: 582142--582294 Score: 151
Period size: 32 Copynumber: 5.4 Consensus size: 31
582132 TTTTAAAATA
582142 ATTTATTTTAAATAATTTATTAGTATGGATTG
1 ATTTATTTTAAATAATTTATTA-TATGGATTG
*
582174 ATTTA-TTT---TAA---A--ATATGGATTA
1 ATTTATTTTAAATAATTTATTATATGGATTG
582196 ATTTATTTTAAATAATTTATTAGTATGGATTG
1 ATTTATTTTAAATAATTTATTA-TATGGATTG
582228 ATTTATTTT---TAA---A--ATATGGATTG
1 ATTTATTTTAAATAATTTATTATATGGATTG
582251 ATTTATTTTAAATAATTTATTATTATGGATTG
1 ATTTATTTTAAATAATTTATTA-TATGGATTG
582283 ATTTATTTTAAA
1 ATTTATTTTAAA
582295 ATATGGATTG
Statistics
Matches: 100, Mismatches: 2, Indels: 38
0.71 0.01 0.27
Matches are distributed among these distances:
22 13 0.13
23 22 0.22
24 1 0.01
25 1 0.01
26 7 0.07
28 3 0.03
29 5 0.05
31 5 0.05
32 43 0.43
ACGTcount: A:0.36, C:0.00, G:0.10, T:0.54
Consensus pattern (31 bp):
ATTTATTTTAAATAATTTATTATATGGATTG
Found at i:582205 original size:54 final size:54
Alignment explanation
Indices: 582142--582538 Score: 365
Period size: 54 Copynumber: 7.4 Consensus size: 54
582132 TTTTAAAATA
*
582142 ATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAAATATGGATTA
1 ATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAAATATGGATTG
582196 ATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTTAAAATATGGATTG
1 ATTTATTTTAAATAATTTATTAGTATGGATTGATTTA-TTTTAAAATATGGATTG
*
582251 ATTTATTTTAAATAATTTATTATTATGGATTGATTTATTTTAAAATATGGATTG
1 ATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAAATATGGATTG
* *
582305 ATTTA--TT--AT--TGTAGTT-GTATGGATTGATTTATTTT-AAATA---ATTT
1 ATTTATTTTAAATAATTTA-TTAGTATGGATTGATTTATTTTAAAATATGGATTG
* ** * * * **
582349 A-TTAGTATGGATTGATTTATTTAAATATGGATTGATTTATTTT-AAATAATTTATTAG
1 ATTTA-TTTTAAATAATTTA-TT-AGTATGGATTGATTTATTTTAAAAT-ATGGATT-G
** * ** * * * ***
582406 TATGGA-TTGATTTATTTTA-AAATATGGATTGATTTATTATTGTAGTTGTATGGATTG
1 -ATTTATTTTAAATAATTTATTAGTATGGATTGATTTA-T-TT-TA-AAATATGGATTG
*
582463 ATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAAATATGAATTG
1 ATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAAATATGGATTG
582517 ATTTATTTTAAATAATTTATTA
1 ATTTATTTTAAATAATTTATTA
582539 TTGTAGTTGT
Statistics
Matches: 282, Mismatches: 36, Indels: 50
0.77 0.10 0.14
Matches are distributed among these distances:
43 3 0.01
44 4 0.01
46 1 0.00
47 5 0.02
48 22 0.08
49 2 0.01
50 7 0.02
52 24 0.09
53 1 0.00
54 105 0.37
55 55 0.20
56 10 0.04
57 20 0.07
58 21 0.07
59 2 0.01
ACGTcount: A:0.34, C:0.00, G:0.13, T:0.53
Consensus pattern (54 bp):
ATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAAATATGGATTG
Found at i:582217 original size:22 final size:22
Alignment explanation
Indices: 582107--582207 Score: 78
Period size: 22 Copynumber: 4.5 Consensus size: 22
582097 TTAAAATAAA
* *
582107 TTATTATAAAATATGGATTGAT
1 TTATTTTAAAATATGGATTAAT
**
582129 TTATTTTAAAATAATTTATTTTAA-
1 TTATTTTAAAAT-ATGGA--TTAAT
* * * * *
582153 ATAATTTATTAGTATGGATTGAT
1 TTATTTTA-AAATATGGATTAAT
582176 TTATTTTAAAATATGGATTAAT
1 TTATTTTAAAATATGGATTAAT
582198 TTATTTTAAA
1 TTATTTTAAA
582208 TAATTTATTA
Statistics
Matches: 58, Mismatches: 16, Indels: 10
0.69 0.19 0.12
Matches are distributed among these distances:
22 35 0.60
23 9 0.16
24 9 0.16
25 5 0.09
ACGTcount: A:0.40, C:0.00, G:0.09, T:0.51
Consensus pattern (22 bp):
TTATTTTAAAATATGGATTAAT
Found at i:582290 original size:22 final size:23
Alignment explanation
Indices: 582265--582338 Score: 64
Period size: 22 Copynumber: 3.2 Consensus size: 23
582255 ATTTTAAATA
582265 ATTTAT-TATTATGGATTGATTT
1 ATTTATATATTATGGATTGATTT
* *
582287 ATTT-TAAAATATGGATTGATTT
1 ATTTATATATTATGGATTGATTT
*
582309 A-TTATTGTAGTTGTATGGATTGATTT
1 ATTTA-TATA--T-TATGGATTGATTT
582335 ATTT
1 ATTT
582339 TAAATAATTT
Statistics
Matches: 40, Mismatches: 5, Indels: 9
0.74 0.09 0.17
Matches are distributed among these distances:
21 3 0.08
22 19 0.47
23 2 0.05
26 14 0.35
27 2 0.05
ACGTcount: A:0.28, C:0.00, G:0.16, T:0.55
Consensus pattern (23 bp):
ATTTATATATTATGGATTGATTT
Found at i:582349 original size:80 final size:78
Alignment explanation
Indices: 582242--582389 Score: 269
Period size: 80 Copynumber: 1.9 Consensus size: 78
582232 ATTTTTAAAA
*
582242 TATGGATTGATTTATTTTAAATAATTTATTATTATGGATTGATTTATTTTAAAATATGGATTGAT
1 TATGGATTGATTTATTTTAAATAATTTATTAGTATGGATTGATTTA-TTT-AAATATGGATTGAT
582307 TTATTATTGTAGTTG
64 TTATTATTGTAGTTG
582322 TATGGATTGATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTAAATATGGATTGATTT
1 TATGGATTGATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTAAATATGGATTGATTT
582387 ATT
66 ATT
582390 TTAAATAATT
Statistics
Matches: 67, Mismatches: 1, Indels: 2
0.96 0.01 0.03
Matches are distributed among these distances:
78 19 0.28
79 3 0.04
80 45 0.67
ACGTcount: A:0.32, C:0.00, G:0.15, T:0.53
Consensus pattern (78 bp):
TATGGATTGATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTAAATATGGATTGATTT
ATTATTGTAGTTG
Found at i:582400 original size:52 final size:54
Alignment explanation
Indices: 582322--582443 Score: 230
Period size: 52 Copynumber: 2.3 Consensus size: 54
582312 ATTGTAGTTG
582322 TATGGATTGATTTATTTTAAATAATTTATTAGTATGGATTGATTTA-TTT-AAA
1 TATGGATTGATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAAA
582374 TATGGATTGATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAAA
1 TATGGATTGATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAAA
582428 TATGGATTGATTTATT
1 TATGGATTGATTTATT
582444 ATTGTAGTTG
Statistics
Matches: 68, Mismatches: 0, Indels: 2
0.97 0.00 0.03
Matches are distributed among these distances:
52 46 0.68
53 3 0.04
54 19 0.28
ACGTcount: A:0.34, C:0.00, G:0.14, T:0.52
Consensus pattern (54 bp):
TATGGATTGATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAAA
Found at i:582419 original size:132 final size:134
Alignment explanation
Indices: 582187--582538 Score: 654
Period size: 132 Copynumber: 2.6 Consensus size: 134
582177 TATTTTAAAA
*
582187 TATGGATTAATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTTAAAATATGGATTGA
1 TATGGATTGATTTATTTTAAATAATTTATTAGTATGGATTGATTTA-TTTTAAAATATGGATTGA
*
582252 TTTATTTTAAATAATTTATTATTATGGATTGATTTATTTTAAAATATGGATTGATTTATTATTGT
65 TTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAAATATGGATTGATTTATTATTGT
582317 AGTTG
130 AGTTG
582322 TATGGATTGATTTATTTTAAATAATTTATTAGTATGGATTGATTTA-TTT-AAATATGGATTGAT
1 TATGGATTGATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAAATATGGATTGAT
582385 TTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAAATATGGATTGATTTATTATTGTA
66 TTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAAATATGGATTGATTTATTATTGTA
582450 GTTG
131 GTTG
*
582454 TATGGATTGATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAAATATGAATTGAT
1 TATGGATTGATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAAATATGGATTGAT
582519 TTATTTTAAATAATTTATTA
66 TTATTTTAAATAATTTATTA
582539 TTGTAGTTGT
Statistics
Matches: 212, Mismatches: 3, Indels: 5
0.96 0.01 0.02
Matches are distributed among these distances:
132 128 0.60
133 6 0.03
134 33 0.16
135 45 0.21
ACGTcount: A:0.34, C:0.00, G:0.13, T:0.53
Consensus pattern (134 bp):
TATGGATTGATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAAATATGGATTGAT
TTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAAATATGGATTGATTTATTATTGTA
GTTG
Found at i:582461 original size:48 final size:51
Alignment explanation
Indices: 582322--582474 Score: 183
Period size: 52 Copynumber: 3.0 Consensus size: 51
582312 ATTGTAGTTG
*
582322 TATGGATTGATTTATTTTAAATAATTTATTAGTATGGATTGATTTA-TTT-AAA
1 TATGGATTGATTTA-TTT-AAT-ATGTATTAGTATGGATTGATTTATTTTAAAA
*
582374 TATGGATTGATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAAA
1 TATGGATTGATTTA-TTT-AAT-ATGTATTAGTATGGATTGATTTATTTTAAAA
582428 TATGGATTGATTTA-TT-AT-TGTAGTT-GTATGGATTGATTTATTTTAAA
1 TATGGATTGATTTATTTAATATGTA-TTAGTATGGATTGATTTATTTTAAA
582475 TAATTTATTA
Statistics
Matches: 97, Mismatches: 1, Indels: 10
0.90 0.01 0.09
Matches are distributed among these distances:
48 25 0.26
49 2 0.02
50 2 0.02
52 48 0.49
53 3 0.03
54 17 0.18
ACGTcount: A:0.33, C:0.00, G:0.15, T:0.52
Consensus pattern (51 bp):
TATGGATTGATTTATTTAATATGTATTAGTATGGATTGATTTATTTTAAAA
Found at i:582475 original size:80 final size:80
Alignment explanation
Indices: 582374--582523 Score: 291
Period size: 80 Copynumber: 1.9 Consensus size: 80
582364 TTTATTTAAA
*
582374 TATGGATTGATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAAATATGGATTGAT
1 TATGGATTGATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAAATATGAATTGAT
582439 TTATTATTGTAGTTG
66 TTATTATTGTAGTTG
582454 TATGGATTGATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAAATATGAATTGAT
1 TATGGATTGATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAAATATGAATTGAT
582519 TTATT
66 TTATT
582524 TTAAATAATT
Statistics
Matches: 69, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
80 69 1.00
ACGTcount: A:0.33, C:0.00, G:0.15, T:0.53
Consensus pattern (80 bp):
TATGGATTGATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAAATATGAATTGAT
TTATTATTGTAGTTG
Found at i:582511 original size:22 final size:22
Alignment explanation
Indices: 582486--582528 Score: 77
Period size: 22 Copynumber: 2.0 Consensus size: 22
582476 AATTTATTAG
*
582486 TATGGATTGATTTATTTTAAAA
1 TATGAATTGATTTATTTTAAAA
582508 TATGAATTGATTTATTTTAAA
1 TATGAATTGATTTATTTTAAA
582529 TAATTTATTA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.37, C:0.00, G:0.12, T:0.51
Consensus pattern (22 bp):
TATGAATTGATTTATTTTAAAA
Found at i:582588 original size:31 final size:31
Alignment explanation
Indices: 582553--582611 Score: 91
Period size: 31 Copynumber: 1.9 Consensus size: 31
582543 AGTTGTATGG
* *
582553 ATTATTTAAATTTCAGTATTGTAAAACTAAA
1 ATTATTTAAATCTCAGTATTGCAAAACTAAA
*
582584 ATTATTTAAATCTCGGTATTGCAAAACT
1 ATTATTTAAATCTCAGTATTGCAAAACT
582612 CTTTTAAATT
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
31 25 1.00
ACGTcount: A:0.41, C:0.10, G:0.08, T:0.41
Consensus pattern (31 bp):
ATTATTTAAATCTCAGTATTGCAAAACTAAA
Found at i:584440 original size:21 final size:18
Alignment explanation
Indices: 584389--584445 Score: 51
Period size: 19 Copynumber: 2.9 Consensus size: 18
584379 CGTTTTATAC
*
584389 ATTATAATAATTAATTTTA
1 ATTATAA-AATTAATTTAA
584408 ATTATATAAATTAATATTAA
1 ATTATA-AAATTAAT-TTAA
*
584428 TATTATAAGAATTGATTT
1 -ATTATAA-AATTAATTT
584446 TGAATATATT
Statistics
Matches: 32, Mismatches: 2, Indels: 7
0.78 0.05 0.17
Matches are distributed among these distances:
19 13 0.41
20 7 0.22
21 12 0.38
ACGTcount: A:0.47, C:0.00, G:0.04, T:0.49
Consensus pattern (18 bp):
ATTATAAAATTAATTTAA
Found at i:590433 original size:154 final size:155
Alignment explanation
Indices: 590153--590461 Score: 602
Period size: 154 Copynumber: 2.0 Consensus size: 155
590143 CCTAACACTA
590153 ATAAAAACACAATAGCTAGTCACCCTAAAACCCTAGTGCTTGAAAATTAATCAAAATATTAACTA
1 ATAAAAACACAATAGCTAGTCACCCTAAAACCCTAGTGCTTGAAAATTAATCAAAATATTAACTA
*
590218 ATAAAATAACCTAAGTTATCTAATATATCCTAAATTTACATTAAAATTACAATTAAAACTAGAAC
66 ATAAAATAACCTAAGTTATCTAATATATCCTAAATTTACATTAAAATTACAATTAAAACTAGAAA
590283 ATATTAATAGTTTAA-TCTTCAATG
131 ATATTAATAGTTTAATTCTTCAATG
590307 ATAAAAACACAATAGCTAGTCACCCTAAAACCCTAGTGCTTGAAAATTAATCAAAATATTAACTA
1 ATAAAAACACAATAGCTAGTCACCCTAAAACCCTAGTGCTTGAAAATTAATCAAAATATTAACTA
590372 ATAAAATAACCTAAGTTATCTAATATATCCTAAATTTACATTAAAATTACAATTAAAACTAGAAA
66 ATAAAATAACCTAAGTTATCTAATATATCCTAAATTTACATTAAAATTACAATTAAAACTAGAAA
590437 ATATTAATAGTTTAATTCTTCAATG
131 ATATTAATAGTTTAATTCTTCAATG
590462 GCTTGCCTTC
Statistics
Matches: 153, Mismatches: 1, Indels: 1
0.99 0.01 0.01
Matches are distributed among these distances:
154 144 0.94
155 9 0.06
ACGTcount: A:0.48, C:0.15, G:0.06, T:0.31
Consensus pattern (155 bp):
ATAAAAACACAATAGCTAGTCACCCTAAAACCCTAGTGCTTGAAAATTAATCAAAATATTAACTA
ATAAAATAACCTAAGTTATCTAATATATCCTAAATTTACATTAAAATTACAATTAAAACTAGAAA
ATATTAATAGTTTAATTCTTCAATG
Found at i:593716 original size:18 final size:20
Alignment explanation
Indices: 593683--593724 Score: 61
Period size: 19 Copynumber: 2.2 Consensus size: 20
593673 GTAACATCTC
593683 TTAAATAATATATAATAT-T
1 TTAAATAATATATAATATAT
*
593702 TTAAATTAT-TATAATATAT
1 TTAAATAATATATAATATAT
593721 TTAA
1 TTAA
593725 GAATATAATT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
18 8 0.38
19 13 0.62
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (20 bp):
TTAAATAATATATAATATAT
Found at i:597395 original size:19 final size:18
Alignment explanation
Indices: 597371--597459 Score: 79
Period size: 19 Copynumber: 4.7 Consensus size: 18
597361 GGTCGGGTCG
597371 GGTCAGACCGGTCAAACC
1 GGTCAGACCGGTCAAACC
*
597389 GGTTCAGACCGGTCAAACT
1 GG-TCAGACCGGTCAAACC
*
597408 GGTCGAAACCGGTCAAACC
1 GGTC-AGACCGGTCAAACC
* * *
597427 GATCAAAACCGGTTGAAAACC
1 GGTC-AGACCGG-T-CAAACC
*
597448 GGTCAAACCGGT
1 GGTCAGACCGGT
597460 TTCCAGCCCT
Statistics
Matches: 60, Mismatches: 7, Indels: 7
0.81 0.09 0.09
Matches are distributed among these distances:
18 4 0.07
19 40 0.67
20 8 0.13
21 8 0.13
ACGTcount: A:0.31, C:0.28, G:0.26, T:0.15
Consensus pattern (18 bp):
GGTCAGACCGGTCAAACC
Found at i:597416 original size:10 final size:9
Alignment explanation
Indices: 597371--597459 Score: 88
Period size: 9 Copynumber: 9.3 Consensus size: 9
597361 GGTCGGGTCG
*
597371 GGTCAGACC
1 GGTCAAACC
597380 GGTCAAACC
1 GGTCAAACC
*
597389 GGTTCAGACC
1 GG-TCAAACC
*
597399 GGTCAAACT
1 GGTCAAACC
597408 GGTCGAAACC
1 GGTC-AAACC
597418 GGTCAAACC
1 GGTCAAACC
*
597427 GATCAAAACC
1 GGTC-AAACC
*
597437 GGTTGAAAACC
1 GG-T-CAAACC
597448 GGTCAAACC
1 GGTCAAACC
597457 GGT
1 GGT
597460 TTCCAGCCCT
Statistics
Matches: 66, Mismatches: 9, Indels: 10
0.78 0.11 0.12
Matches are distributed among these distances:
9 35 0.53
10 23 0.35
11 8 0.12
ACGTcount: A:0.31, C:0.28, G:0.26, T:0.15
Consensus pattern (9 bp):
GGTCAAACC
Found at i:597457 original size:20 final size:21
Alignment explanation
Indices: 597422--597460 Score: 62
Period size: 20 Copynumber: 1.9 Consensus size: 21
597412 GAAACCGGTC
597422 AAACCGATCAAAACCGGTTGA
1 AAACCGATCAAAACCGGTTGA
*
597443 AAACCGGTC-AAACCGGTT
1 AAACCGATCAAAACCGGTT
597461 TCCAGCCCTC
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 9 0.53
21 8 0.47
ACGTcount: A:0.38, C:0.26, G:0.21, T:0.15
Consensus pattern (21 bp):
AAACCGATCAAAACCGGTTGA
Found at i:601055 original size:16 final size:16
Alignment explanation
Indices: 601034--601066 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 16
601024 AGTTTTATAA
*
601034 TGATTTATATAATATT
1 TGATTTATACAATATT
601050 TGATTTATACAATATT
1 TGATTTATACAATATT
601066 T
1 T
601067 TTAAAAAGAT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.36, C:0.03, G:0.06, T:0.55
Consensus pattern (16 bp):
TGATTTATACAATATT
Found at i:603015 original size:18 final size:18
Alignment explanation
Indices: 602992--603032 Score: 64
Period size: 18 Copynumber: 2.3 Consensus size: 18
602982 TACACAAAGT
602992 CCTCCACCACCTTCCCCA
1 CCTCCACCACCTTCCCCA
* *
603010 CCTCCACCTCCTTCTCCA
1 CCTCCACCACCTTCCCCA
603028 CCTCC
1 CCTCC
603033 TCCTTCACCT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
18 21 1.00
ACGTcount: A:0.12, C:0.66, G:0.00, T:0.22
Consensus pattern (18 bp):
CCTCCACCACCTTCCCCA
Found at i:603026 original size:12 final size:12
Alignment explanation
Indices: 603010--603044 Score: 52
Period size: 12 Copynumber: 2.9 Consensus size: 12
603000 ACCTTCCCCA
603010 CCTCCACCTCCT
1 CCTCCACCTCCT
*
603022 TCTCCACCTCCT
1 CCTCCACCTCCT
*
603034 CCTTCACCTCC
1 CCTCCACCTCC
603045 GGCATGCCCT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
12 20 1.00
ACGTcount: A:0.09, C:0.63, G:0.00, T:0.29
Consensus pattern (12 bp):
CCTCCACCTCCT
Found at i:603109 original size:27 final size:27
Alignment explanation
Indices: 603054--603122 Score: 84
Period size: 27 Copynumber: 2.6 Consensus size: 27
603044 CGGCATGCCC
* ***
603054 TCCACCGCCGTCACCACCGGTGTTTTA
1 TCCACCACCGTCACCACCGGTGCAGTA
*
603081 TCCACCACCATCACCACCGGTGCAGTA
1 TCCACCACCGTCACCACCGGTGCAGTA
*
603108 TCCGCCACCGTCACC
1 TCCACCACCGTCACC
603123 GAAAAAGCCT
Statistics
Matches: 35, Mismatches: 7, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
27 35 1.00
ACGTcount: A:0.19, C:0.46, G:0.16, T:0.19
Consensus pattern (27 bp):
TCCACCACCGTCACCACCGGTGCAGTA
Found at i:603367 original size:153 final size:154
Alignment explanation
Indices: 603089--603395 Score: 598
Period size: 153 Copynumber: 2.0 Consensus size: 154
603079 TATCCACCAC
603089 CATCACCACCGGTGCAGTATCCGCCACCGTCACCGAAAAAGCCTCCGTCCCATAGCTGTCCAGCT
1 CATCACCACCGGTGCAGTATCCGCCACCGTCACCGAAAAAGCCTCCGTCCCATAGCTGTCCAGCT
603154 GGACCTACTCCACCATCCGTTATATACACAACTGGTCCACCAGGGAGCCTGTATCCTATCGAGC-
66 GGACCTACTCCACCATCCGTTATATACACAACTGGTCCACCAGGGAGCCTGTATCCTATCGAGCA
603218 AAATTTTGGTGGTGCGAGCCGGAA
131 AAATTTTGGTGGTGCGAGCCGGAA
*
603242 CATCACCACCGGTGCAGTATCCGCCACCGTCACCGAAAAAGCCTCCGTCCCATTGCTGTCCAGCT
1 CATCACCACCGGTGCAGTATCCGCCACCGTCACCGAAAAAGCCTCCGTCCCATAGCTGTCCAGCT
603307 GGACCTACTCCACCATCCGTTATATACACAACTGGTCCACCAGGGAGCCTGTATCCTATCGAGCA
66 GGACCTACTCCACCATCCGTTATATACACAACTGGTCCACCAGGGAGCCTGTATCCTATCGAGCA
603372 AAATTTTGGTGGTGCGAGCCGGAA
131 AAATTTTGGTGGTGCGAGCCGGAA
603396 TTTGGAAGTG
Statistics
Matches: 152, Mismatches: 1, Indels: 1
0.99 0.01 0.01
Matches are distributed among these distances:
153 128 0.84
154 24 0.16
ACGTcount: A:0.24, C:0.34, G:0.21, T:0.21
Consensus pattern (154 bp):
CATCACCACCGGTGCAGTATCCGCCACCGTCACCGAAAAAGCCTCCGTCCCATAGCTGTCCAGCT
GGACCTACTCCACCATCCGTTATATACACAACTGGTCCACCAGGGAGCCTGTATCCTATCGAGCA
AAATTTTGGTGGTGCGAGCCGGAA
Found at i:604303 original size:7 final size:7
Alignment explanation
Indices: 604291--604317 Score: 54
Period size: 7 Copynumber: 3.9 Consensus size: 7
604281 TTTAAGTTAT
604291 AATAATA
1 AATAATA
604298 AATAATA
1 AATAATA
604305 AATAATA
1 AATAATA
604312 AATAAT
1 AATAAT
604318 CTATTAAGTT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 20 1.00
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (7 bp):
AATAATA
Found at i:606745 original size:18 final size:19
Alignment explanation
Indices: 606703--606746 Score: 54
Period size: 20 Copynumber: 2.3 Consensus size: 19
606693 TTTGGTTTAC
*
606703 GGAATGTAAGATTATCAGTG
1 GGAATATAAGATTATCAG-G
*
606723 GGAATATAAGATTATTA-G
1 GGAATATAAGATTATCAGG
606741 GGAATA
1 GGAATA
606747 GGATTACTGA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
18 7 0.32
20 15 0.68
ACGTcount: A:0.41, C:0.02, G:0.27, T:0.30
Consensus pattern (19 bp):
GGAATATAAGATTATCAGG
Found at i:621139 original size:31 final size:31
Alignment explanation
Indices: 621101--621171 Score: 133
Period size: 31 Copynumber: 2.3 Consensus size: 31
621091 GTACCCGTGA
621101 TTCTCCCGACCGTTCATCTGCTCGACCCAAT
1 TTCTCCCGACCGTTCATCTGCTCGACCCAAT
*
621132 TTCTCCCGACCGTTCGTCTGCTCGACCCAAT
1 TTCTCCCGACCGTTCATCTGCTCGACCCAAT
621163 TTCTCCCGA
1 TTCTCCCGA
621172 TTCGCTTGTT
Statistics
Matches: 39, Mismatches: 1, Indels: 0
0.98 0.03 0.00
Matches are distributed among these distances:
31 39 1.00
ACGTcount: A:0.14, C:0.42, G:0.14, T:0.30
Consensus pattern (31 bp):
TTCTCCCGACCGTTCATCTGCTCGACCCAAT
Found at i:624506 original size:17 final size:17
Alignment explanation
Indices: 624486--624523 Score: 58
Period size: 17 Copynumber: 2.2 Consensus size: 17
624476 GGAAGTCAAC
* *
624486 GGTCAATGGTTGGGTCG
1 GGTCAACGGTCGGGTCG
624503 GGTCAACGGTCGGGTCG
1 GGTCAACGGTCGGGTCG
624520 GGTC
1 GGTC
624524 GGTCGGGCCG
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.11, C:0.18, G:0.47, T:0.24
Consensus pattern (17 bp):
GGTCAACGGTCGGGTCG
Found at i:624553 original size:10 final size:10
Alignment explanation
Indices: 624540--624604 Score: 53
Period size: 10 Copynumber: 6.6 Consensus size: 10
624530 GCCGGGTCAG
*
624540 ACCGATCAAA
1 ACCGGTCAAA
*
624550 ACCGGTCGAA
1 ACCGGTCAAA
*
624560 ACAGGTC-AA
1 ACCGGTCAAA
624569 ACCGGTCAAA
1 ACCGGTCAAA
* *
624579 ACCGTTTGAAA
1 ACCG-GTCAAA
*
624590 ATCGGTC-AA
1 ACCGGTCAAA
624599 ACCGGT
1 ACCGGT
624605 TTCCAGCAGC
Statistics
Matches: 43, Mismatches: 10, Indels: 5
0.74 0.17 0.09
Matches are distributed among these distances:
9 15 0.35
10 21 0.49
11 7 0.16
ACGTcount: A:0.37, C:0.26, G:0.22, T:0.15
Consensus pattern (10 bp):
ACCGGTCAAA
Found at i:624589 original size:29 final size:29
Alignment explanation
Indices: 624534--624604 Score: 81
Period size: 29 Copynumber: 2.4 Consensus size: 29
624524 GGTCGGGCCG
* *
624534 GGTCAGACCGATCAAAACCGGTCG-AAAC
1 GGTCAAACCGGTCAAAACCGGTCGAAAAC
* *
624562 AGGTCAAACCGGTCAAAACCGTTTGAAAATC
1 -GGTCAAACCGGTCAAAACCGGTCGAAAA-C
624593 GGTCAAACCGGT
1 GGTCAAACCGGT
624605 TTCCAGCAGC
Statistics
Matches: 36, Mismatches: 4, Indels: 3
0.84 0.09 0.07
Matches are distributed among these distances:
29 20 0.56
30 15 0.42
31 1 0.03
ACGTcount: A:0.35, C:0.25, G:0.24, T:0.15
Consensus pattern (29 bp):
GGTCAAACCGGTCAAAACCGGTCGAAAAC
Found at i:629397 original size:21 final size:21
Alignment explanation
Indices: 629371--629415 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
629361 GATTTCTGGG
* *
629371 CAAGGGGAATCGGTACCCATT
1 CAAGGGGAACCGATACCCATT
*
629392 CAAGGGGAACCGATACCCCTT
1 CAAGGGGAACCGATACCCATT
629413 CAA
1 CAA
629416 ACGAACAAGA
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:0.31, C:0.29, G:0.24, T:0.16
Consensus pattern (21 bp):
CAAGGGGAACCGATACCCATT
Found at i:630023 original size:18 final size:18
Alignment explanation
Indices: 630000--630034 Score: 54
Period size: 18 Copynumber: 1.9 Consensus size: 18
629990 CTAGGAGATT
630000 TGAACATA-AATGATAAGA
1 TGAACATATAA-GATAAGA
630018 TGAACATATAAGATAAG
1 TGAACATATAAGATAAG
630035 CTAGATGGGA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 14 0.88
19 2 0.12
ACGTcount: A:0.54, C:0.06, G:0.17, T:0.23
Consensus pattern (18 bp):
TGAACATATAAGATAAGA
Found at i:630536 original size:2 final size:2
Alignment explanation
Indices: 630529--630558 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
630519 ATGATATGAA
630529 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
630559 GTGAAAACAA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:631130 original size:149 final size:149
Alignment explanation
Indices: 630945--631397 Score: 888
Period size: 149 Copynumber: 3.0 Consensus size: 149
630935 GAGTCGAGGG
630945 TCTACGCGGTTCTTAGGGACATATGTATATTCTTTGGAACCTGTGTGAAGTCTGGAAAGACACAT
1 TCTACGCGGTTCTTAGGGACATATGTATATTCTTTGGAACCTGTGTGAAGTCTGGAAAGACACAT
631010 ACTTGATCCCTAGCATATGTATATGATTCTTACAGAATTCTATGTGGTCCTTATGGACATTATTA
66 ACTTGATCCCTAGCATATGTATATGATTCTTACAGAATTCTATGTGGTCCTTATGGACATTATTA
631075 TATGGCACTACGGTGCAAT
131 TATGGCACTACGGTGCAAT
*
631094 TCTACGCGGTTCTTAGGGACATATGTATATTCTTTGGAACCTGTGTGAAGTCTGGAAAGACATAT
1 TCTACGCGGTTCTTAGGGACATATGTATATTCTTTGGAACCTGTGTGAAGTCTGGAAAGACACAT
631159 ACTTGATCCCTAGCATATGTATATGATTCTTACAGAATTCTATGTGGTCCTTATGGACATTATTA
66 ACTTGATCCCTAGCATATGTATATGATTCTTACAGAATTCTATGTGGTCCTTATGGACATTATTA
631224 TATGGCACTACGGTGCAAT
131 TATGGCACTACGGTGCAAT
631243 TCTACGCGGTTCTTAGGGACATATGTATATTCTTTGGAACCTGTGTGAAGTCTGGAAAGACACAT
1 TCTACGCGGTTCTTAGGGACATATGTATATTCTTTGGAACCTGTGTGAAGTCTGGAAAGACACAT
*
631308 ACTTGATCCCTAGCATATGTATATGATTCTTACAGAATTCTATGTGGTCCTTATGGACATCATTA
66 ACTTGATCCCTAGCATATGTATATGATTCTTACAGAATTCTATGTGGTCCTTATGGACATTATTA
631373 TATGGCACTACGGTGCAAT
131 TATGGCACTACGGTGCAAT
631392 TCTACG
1 TCTACG
631398 GGGCACTTCG
Statistics
Matches: 301, Mismatches: 3, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
149 301 1.00
ACGTcount: A:0.27, C:0.18, G:0.21, T:0.35
Consensus pattern (149 bp):
TCTACGCGGTTCTTAGGGACATATGTATATTCTTTGGAACCTGTGTGAAGTCTGGAAAGACACAT
ACTTGATCCCTAGCATATGTATATGATTCTTACAGAATTCTATGTGGTCCTTATGGACATTATTA
TATGGCACTACGGTGCAAT
Found at i:631420 original size:23 final size:23
Alignment explanation
Indices: 631376--631420 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 23
631366 ATCATTATAT
*
631376 GGCACTACGGTGCAATTCTACGG
1 GGCACTACGGTGCAATTATACGG
* *
631399 GGCACTTCGGTGCATTTATACG
1 GGCACTACGGTGCAATTATACG
631421 AGCTGTGGTG
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.20, C:0.24, G:0.29, T:0.27
Consensus pattern (23 bp):
GGCACTACGGTGCAATTATACGG
Found at i:635292 original size:12 final size:12
Alignment explanation
Indices: 635275--635307 Score: 66
Period size: 12 Copynumber: 2.8 Consensus size: 12
635265 GGTTGGGTTG
635275 GGTCGGGTCAAC
1 GGTCGGGTCAAC
635287 GGTCGGGTCAAC
1 GGTCGGGTCAAC
635299 GGTCGGGTC
1 GGTCGGGTC
635308 GGGTCGGTCG
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 21 1.00
ACGTcount: A:0.12, C:0.24, G:0.45, T:0.18
Consensus pattern (12 bp):
GGTCGGGTCAAC
Found at i:646089 original size:15 final size:16
Alignment explanation
Indices: 646057--646089 Score: 50
Period size: 15 Copynumber: 2.1 Consensus size: 16
646047 AAAATCTTTC
646057 TTTCCCGTTCTAGATT
1 TTTCCCGTTCTAGATT
*
646073 TTTCCCG-TCTGGATT
1 TTTCCCGTTCTAGATT
646088 TT
1 TT
646090 GATCTGCCAC
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
15 9 0.56
16 7 0.44
ACGTcount: A:0.09, C:0.24, G:0.15, T:0.52
Consensus pattern (16 bp):
TTTCCCGTTCTAGATT
Found at i:647342 original size:15 final size:15
Alignment explanation
Indices: 647322--647351 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
647312 AAACTTTGAA
*
647322 AAACATTTTTCAAAG
1 AAACATTTTCCAAAG
647337 AAACATTTTCCAAAG
1 AAACATTTTCCAAAG
647352 TTGGTTGCCA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.47, C:0.17, G:0.07, T:0.30
Consensus pattern (15 bp):
AAACATTTTCCAAAG
Found at i:648505 original size:19 final size:20
Alignment explanation
Indices: 648477--648523 Score: 66
Period size: 18 Copynumber: 2.5 Consensus size: 20
648467 AAAATATAAA
648477 AATT-AAAATAATA-AAGTT
1 AATTAAAAATAATATAAGTT
648495 AATTAAAAATAATATAAGTT
1 AATTAAAAATAATATAAGTT
648515 -A-TAAAAATA
1 AATTAAAAATA
648524 TTATGCGGAT
Statistics
Matches: 27, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
18 12 0.44
19 10 0.37
20 5 0.19
ACGTcount: A:0.64, C:0.00, G:0.04, T:0.32
Consensus pattern (20 bp):
AATTAAAAATAATATAAGTT
Found at i:653629 original size:48 final size:48
Alignment explanation
Indices: 653573--653666 Score: 188
Period size: 48 Copynumber: 2.0 Consensus size: 48
653563 TTAACTTATT
653573 TAATATTACTATGATTTAAGTTATTTTAAGATCGTTAACATAATCCTC
1 TAATATTACTATGATTTAAGTTATTTTAAGATCGTTAACATAATCCTC
653621 TAATATTACTATGATTTAAGTTATTTTAAGATCGTTAACATAATCC
1 TAATATTACTATGATTTAAGTTATTTTAAGATCGTTAACATAATCC
653667 ACTAGATCTA
Statistics
Matches: 46, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
48 46 1.00
ACGTcount: A:0.36, C:0.12, G:0.09, T:0.44
Consensus pattern (48 bp):
TAATATTACTATGATTTAAGTTATTTTAAGATCGTTAACATAATCCTC
Found at i:663615 original size:171 final size:171
Alignment explanation
Indices: 663330--663671 Score: 684
Period size: 171 Copynumber: 2.0 Consensus size: 171
663320 ACCCGTGTCC
663330 GCATATGCATTGGACATGATCGTTTGGCATGTGTACTTTGAGGAAAATGTGTTGGAGTAAAATAA
1 GCATATGCATTGGACATGATCGTTTGGCATGTGTACTTTGAGGAAAATGTGTTGGAGTAAAATAA
663395 AAAATTGCTGTGGCAAATTGTGGTTGCTTCCAGAAGTTGTTTTGTGCCCACTAACTGCCACGATA
66 AAAATTGCTGTGGCAAATTGTGGTTGCTTCCAGAAGTTGTTTTGTGCCCACTAACTGCCACGATA
663460 ACAATATGAACACTCCTGTGGAGAGCTCATAGTCTGAGGTT
131 ACAATATGAACACTCCTGTGGAGAGCTCATAGTCTGAGGTT
663501 GCATATGCATTGGACATGATCGTTTGGCATGTGTACTTTGAGGAAAATGTGTTGGAGTAAAATAA
1 GCATATGCATTGGACATGATCGTTTGGCATGTGTACTTTGAGGAAAATGTGTTGGAGTAAAATAA
663566 AAAATTGCTGTGGCAAATTGTGGTTGCTTCCAGAAGTTGTTTTGTGCCCACTAACTGCCACGATA
66 AAAATTGCTGTGGCAAATTGTGGTTGCTTCCAGAAGTTGTTTTGTGCCCACTAACTGCCACGATA
663631 ACAATATGAACACTCCTGTGGAGAGCTCATAGTCTGAGGTT
131 ACAATATGAACACTCCTGTGGAGAGCTCATAGTCTGAGGTT
663672 ACATTTATGC
Statistics
Matches: 171, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
171 171 1.00
ACGTcount: A:0.28, C:0.16, G:0.25, T:0.31
Consensus pattern (171 bp):
GCATATGCATTGGACATGATCGTTTGGCATGTGTACTTTGAGGAAAATGTGTTGGAGTAAAATAA
AAAATTGCTGTGGCAAATTGTGGTTGCTTCCAGAAGTTGTTTTGTGCCCACTAACTGCCACGATA
ACAATATGAACACTCCTGTGGAGAGCTCATAGTCTGAGGTT
Found at i:679028 original size:70 final size:70
Alignment explanation
Indices: 678922--679056 Score: 270
Period size: 70 Copynumber: 1.9 Consensus size: 70
678912 TCAATTATGA
678922 ATTTTCCTACTCAGATAAAGAGATTAACGGAGGTGATTGTATTATTGAAAATTTTAAATTTTTAT
1 ATTTTCCTACTCAGATAAAGAGATTAACGGAGGTGATTGTATTATTGAAAATTTTAAATTTTTAT
678987 TATTT
66 TATTT
678992 ATTTTCCTACTCAGATAAAGAGATTAACGGAGGTGATTGTATTATTGAAAATTTTAAATTTTTAT
1 ATTTTCCTACTCAGATAAAGAGATTAACGGAGGTGATTGTATTATTGAAAATTTTAAATTTTTAT
679057 ATAATTTAAA
Statistics
Matches: 65, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
70 65 1.00
ACGTcount: A:0.35, C:0.07, G:0.15, T:0.43
Consensus pattern (70 bp):
ATTTTCCTACTCAGATAAAGAGATTAACGGAGGTGATTGTATTATTGAAAATTTTAAATTTTTAT
TATTT
Found at i:679066 original size:17 final size:17
Alignment explanation
Indices: 679044--679096 Score: 65
Period size: 17 Copynumber: 3.2 Consensus size: 17
679034 TATTGAAAAT
679044 TTTAAATTTTTATATAA
1 TTTAAATTTTTATATAA
**
679061 TTTAAATTTTTATATTT
1 TTTAAATTTTTATATAA
*
679078 TTTAAA-ATTTATA-AA
1 TTTAAATTTTTATATAA
679093 TTTA
1 TTTA
679097 TCCGTAACAT
Statistics
Matches: 31, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
15 4 0.13
16 6 0.19
17 21 0.68
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (17 bp):
TTTAAATTTTTATATAA
Found at i:682840 original size:12 final size:12
Alignment explanation
Indices: 682823--682856 Score: 52
Period size: 12 Copynumber: 2.8 Consensus size: 12
682813 AAAAACATAA
682823 TATAAATAATAT
1 TATAAATAATAT
682835 TATAAATAATTAT
1 TATAAATAA-TAT
682848 TA-AAATAAT
1 TATAAATAAT
682857 CTAAAACTAA
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
11 1 0.05
12 15 0.71
13 5 0.24
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (12 bp):
TATAAATAATAT
Found at i:685978 original size:2 final size:2
Alignment explanation
Indices: 685973--686007 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
685963 ATATATAAAA
685973 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
686008 TATGAAATGG
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:0.51, C:0.00, G:0.49, T:0.00
Consensus pattern (2 bp):
AG
Found at i:688598 original size:29 final size:29
Alignment explanation
Indices: 688563--688644 Score: 137
Period size: 29 Copynumber: 2.8 Consensus size: 29
688553 AAACTAAATT
*
688563 GATGTCATTACTTACATCATTTAATTAAA
1 GATGTCATTGCTTACATCATTTAATTAAA
*
688592 GATGTCATTGCTTACATCATTTAATTAAT
1 GATGTCATTGCTTACATCATTTAATTAAA
688621 GATGTCATTGCTTACATCAATTTA
1 GATGTCATTGCTTACATC-ATTTA
688645 GTTAGGTGAG
Statistics
Matches: 50, Mismatches: 2, Indels: 1
0.94 0.04 0.02
Matches are distributed among these distances:
29 45 0.90
30 5 0.10
ACGTcount: A:0.33, C:0.15, G:0.10, T:0.43
Consensus pattern (29 bp):
GATGTCATTGCTTACATCATTTAATTAAA
Found at i:693361 original size:29 final size:29
Alignment explanation
Indices: 693326--693407 Score: 137
Period size: 29 Copynumber: 2.8 Consensus size: 29
693316 AAACTAAATT
*
693326 GATGTCATTACTTACATCATTTAATTAAA
1 GATGTCATTGCTTACATCATTTAATTAAA
*
693355 GATGTCATTGCTTACATCATTTAATTAAT
1 GATGTCATTGCTTACATCATTTAATTAAA
693384 GATGTCATTGCTTACATCAATTTA
1 GATGTCATTGCTTACATC-ATTTA
693408 GTTAGGTGAG
Statistics
Matches: 50, Mismatches: 2, Indels: 1
0.94 0.04 0.02
Matches are distributed among these distances:
29 45 0.90
30 5 0.10
ACGTcount: A:0.33, C:0.15, G:0.10, T:0.43
Consensus pattern (29 bp):
GATGTCATTGCTTACATCATTTAATTAAA
Found at i:697001 original size:2 final size:2
Alignment explanation
Indices: 696994--697031 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
696984 TAAGTAGATC
696994 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
697032 TAGAAAGTTT
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:699686 original size:20 final size:19
Alignment explanation
Indices: 699649--699686 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 19
699639 CTATAAAAAC
*
699649 ATGATTTTAAACATTAAAT
1 ATGATTTTAAAAATTAAAT
699668 ATGATTTTAAAAAATTAAA
1 ATGATTTT-AAAAATTAAA
699687 AATTTAAATA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 8 0.47
20 9 0.53
ACGTcount: A:0.53, C:0.03, G:0.05, T:0.39
Consensus pattern (19 bp):
ATGATTTTAAAAATTAAAT
Found at i:699704 original size:21 final size:21
Alignment explanation
Indices: 699678--699722 Score: 54
Period size: 21 Copynumber: 2.1 Consensus size: 21
699668 ATGATTTTAA
699678 AAAATTAAAAATTTAAATACT
1 AAAATTAAAAATTTAAATACT
* * * *
699699 AAAATTGATAATTTATATATT
1 AAAATTAAAAATTTAAATACT
699720 AAA
1 AAA
699723 CTAGTAATTT
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.58, C:0.02, G:0.02, T:0.38
Consensus pattern (21 bp):
AAAATTAAAAATTTAAATACT
Found at i:703183 original size:2 final size:2
Alignment explanation
Indices: 703176--703200 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
703166 TGTTAGAACC
703176 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
703201 GTTTAAAAAA
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:705347 original size:41 final size:41
Alignment explanation
Indices: 705262--705349 Score: 97
Period size: 41 Copynumber: 2.1 Consensus size: 41
705252 TAATTAGCGA
* **
705262 CGTTTTCATAGAAACGCCACAAAAGAGTTGGACTATAGTGG
1 CGTTTTCATAGAAACGCCACAAAAGAGTTGGAATATAGCAG
* * * *
705303 CGTTTTCATAGAAACGCCGCAAAATA-TTAGTAATTTAGCAG
1 CGTTTTCATAGAAACGCCACAAAAGAGTT-GGAATATAGCAG
705344 CGTTTT
1 CGTTTT
705350 TACAAAAACG
Statistics
Matches: 39, Mismatches: 7, Indels: 2
0.81 0.15 0.04
Matches are distributed among these distances:
40 2 0.05
41 37 0.95
ACGTcount: A:0.33, C:0.17, G:0.20, T:0.30
Consensus pattern (41 bp):
CGTTTTCATAGAAACGCCACAAAAGAGTTGGAATATAGCAG
Found at i:705450 original size:41 final size:40
Alignment explanation
Indices: 705301--705451 Score: 121
Period size: 41 Copynumber: 3.6 Consensus size: 40
705291 GGACTATAGT
* *
705301 GGCGTTTT-CATAGAAACGCCGCAAAAT-ATTAGTAATTTAGC
1 GGCGTTTTACA-A-AAACGCCGC-AAATGATTCGTACTTTAGC
* * * *
705342 AGCGTTTTTACAAAAACGCCTC-AATAGATTC-CACATATAGC
1 GGCG-TTTTACAAAAACGCCGCAAAT-GATTCGTAC-TTTAGC
* *
705383 GGCGTTTTTCTAACAAACGCCGCAAATGATTCGTACTTTAGT
1 GGCGTTTTAC-AA-AAACGCCGCAAATGATTCGTACTTTAGC
705425 GGCGTTTTGACAAAAACGCCGCAAATG
1 GGCGTTTT-ACAAAAACGCCGCAAATG
705452 TTTTAAACAT
Statistics
Matches: 87, Mismatches: 13, Indels: 20
0.73 0.11 0.17
Matches are distributed among these distances:
39 3 0.03
40 6 0.07
41 38 0.44
42 32 0.37
43 8 0.09
ACGTcount: A:0.32, C:0.21, G:0.19, T:0.28
Consensus pattern (40 bp):
GGCGTTTTACAAAAACGCCGCAAATGATTCGTACTTTAGC
Found at i:707303 original size:36 final size:36
Alignment explanation
Indices: 707215--707316 Score: 169
Period size: 31 Copynumber: 3.0 Consensus size: 36
707205 TTCAATCTAT
707215 TTTCTTTTTGTTGAAGTTACATTTCTGGCAGGCCTA
1 TTTCTTTTTGTTGAAGTTACATTTCTGGCAGGCCTA
707251 TTTC----T-TTGAAGTTACATTTCTGGCAGGCCTA
1 TTTCTTTTTGTTGAAGTTACATTTCTGGCAGGCCTA
707282 TTTCTTTTTGTTGAAGTTACATTTCTGGCAGGCCT
1 TTTCTTTTTGTTGAAGTTACATTTCTGGCAGGCCT
707317 CTTTGGGTTA
Statistics
Matches: 61, Mismatches: 0, Indels: 10
0.86 0.00 0.14
Matches are distributed among these distances:
31 30 0.49
32 1 0.02
35 1 0.02
36 29 0.48
ACGTcount: A:0.17, C:0.18, G:0.20, T:0.46
Consensus pattern (36 bp):
TTTCTTTTTGTTGAAGTTACATTTCTGGCAGGCCTA
Found at i:708872 original size:21 final size:21
Alignment explanation
Indices: 708840--708905 Score: 62
Period size: 21 Copynumber: 3.1 Consensus size: 21
708830 AGCGGAAAAT
*
708840 GAAGCAAG-GGAAGCCGAGAGA
1 GAAGC-AGCGGAAGCAGAGAGA
* *
708861 GCAGCAGCGGAAGTAGAGAGA
1 GAAGCAGCGGAAGCAGAGAGA
* * *
708882 GAAGCAGTGGCAGCACAGAGA
1 GAAGCAGCGGAAGCAGAGAGA
708903 GAA
1 GAA
708906 TCAACATATC
Statistics
Matches: 36, Mismatches: 8, Indels: 2
0.78 0.17 0.04
Matches are distributed among these distances:
20 2 0.06
21 34 0.94
ACGTcount: A:0.41, C:0.15, G:0.41, T:0.03
Consensus pattern (21 bp):
GAAGCAGCGGAAGCAGAGAGA
Found at i:709325 original size:43 final size:43
Alignment explanation
Indices: 709225--709342 Score: 127
Period size: 42 Copynumber: 2.8 Consensus size: 43
709215 ATTCTGTGTT
*
709225 ATTTAGCGGCGTTTGTA-ACAAAAACGCCGTAATATACCATAC
1 ATTTAGCGGCGTTTGTATACAAAAACGCCCTAATATACCATAC
* * *
709267 ATTTAGCGGCGTTTGTATCATAAAAATGCCACT-ATATACCA-AT
1 ATTTAGCGGCGTTTGTAT-ACAAAAACGCC-CTAATATACCATAC
* *
709310 TTTTAGCGGCGTTTGTAT-TAAAAACGCCGCTAA
1 ATTTAGCGGCGTTTGTATACAAAAACGCC-CTAA
709343 ACCTCAACGC
Statistics
Matches: 65, Mismatches: 7, Indels: 8
0.81 0.09 0.10
Matches are distributed among these distances:
41 11 0.17
42 18 0.28
43 18 0.28
44 17 0.26
45 1 0.02
ACGTcount: A:0.33, C:0.19, G:0.17, T:0.31
Consensus pattern (43 bp):
ATTTAGCGGCGTTTGTATACAAAAACGCCCTAATATACCATAC
Found at i:709430 original size:43 final size:43
Alignment explanation
Indices: 709315--709437 Score: 149
Period size: 43 Copynumber: 2.9 Consensus size: 43
709305 CCAATTTTTA
* * * * *
709315 GCGGCGTTTGTA-TTAAAAACGCCGCTAAACCTCAACGCCTATT
1 GCGGCGTTT-TAGCTAAAAACGTCGCTAAATCTCAACACATATT
* * *
709358 GTGGCGTTCTAGCTAAAAACATCGCTAAATCTCAACACATATT
1 GCGGCGTTTTAGCTAAAAACGTCGCTAAATCTCAACACATATT
*
709401 GCGGCGTTTTAGCTAAAAACGTCGCTAAATATCAACA
1 GCGGCGTTTTAGCTAAAAACGTCGCTAAATCTCAACA
709438 ACTTTGGCGG
Statistics
Matches: 67, Mismatches: 12, Indels: 2
0.83 0.15 0.02
Matches are distributed among these distances:
42 2 0.03
43 65 0.97
ACGTcount: A:0.33, C:0.24, G:0.17, T:0.26
Consensus pattern (43 bp):
GCGGCGTTTTAGCTAAAAACGTCGCTAAATCTCAACACATATT
Found at i:710942 original size:21 final size:21
Alignment explanation
Indices: 710887--710942 Score: 60
Period size: 21 Copynumber: 2.7 Consensus size: 21
710877 GGTTAAACCC
*
710887 TTTAATCA-AAAGGATAAGTCA
1 TTTAAT-AGAAAGGTTAAGTCA
*
710908 TTTAATAGAAAGGTTAAGTCC
1 TTTAATAGAAAGGTTAAGTCA
* *
710929 TTTTATTGAAAGGT
1 TTTAATAGAAAGGT
710943 CTTAACCCTT
Statistics
Matches: 30, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
20 1 0.03
21 29 0.97
ACGTcount: A:0.39, C:0.07, G:0.18, T:0.36
Consensus pattern (21 bp):
TTTAATAGAAAGGTTAAGTCA
Done.