Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Dt_chr1
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: 96304692
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.32
Warning! 2448173 characters in sequence are not A, C, G, or T
File 175 of 313
Found at i:54361192 original size:23 final size:23
Alignment explanation
Indices: 54361148--54361200 Score: 63
Period size: 23 Copynumber: 2.3 Consensus size: 23
54361138 GTGTCTGAAA
* *
54361148 CGACACACGAGGTGCCTTAAATAT
1 CGACACACAAGGTGCCTGAAAT-T
*
54361172 -GACACACAAGGTGTCTGAAATT
1 CGACACACAAGGTGCCTGAAATT
54361194 CGACACA
1 CGACACA
54361201 TAAACTGCCT
Statistics
Matches: 25, Mismatches: 3, Indels: 3
0.81 0.10 0.10
Matches are distributed among these distances:
22 1 0.04
23 24 0.96
ACGTcount: A:0.36, C:0.25, G:0.21, T:0.19
Consensus pattern (23 bp):
CGACACACAAGGTGCCTGAAATT
Found at i:54361242 original size:23 final size:23
Alignment explanation
Indices: 54361214--54361290 Score: 91
Period size: 23 Copynumber: 3.3 Consensus size: 23
54361204 ACTGCCTGAT
*
54361214 TAAAGTGCATAAAATACAACACA
1 TAAAGTGCATGAAATACAACACA
* * *
54361237 TAAAGTGCCTGATATCCAACACA
1 TAAAGTGCATGAAATACAACACA
* * *
54361260 TAAAGTGCTTGAAATACGACAGA
1 TAAAGTGCATGAAATACAACACA
54361283 TAAAGTGC
1 TAAAGTGC
54361291 CTGAGCGGCA
Statistics
Matches: 45, Mismatches: 9, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
23 45 1.00
ACGTcount: A:0.45, C:0.18, G:0.16, T:0.21
Consensus pattern (23 bp):
TAAAGTGCATGAAATACAACACA
Found at i:54365034 original size:21 final size:21
Alignment explanation
Indices: 54365008--54365049 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
54364998 ATTTTTCCAA
* *
54365008 AGATGTGTATTGGATTGAATT
1 AGATGTGAATTGGATTAAATT
*
54365029 AGATGTGAATTGTATTAAATT
1 AGATGTGAATTGGATTAAATT
54365050 GAGCTAAATT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.33, C:0.00, G:0.24, T:0.43
Consensus pattern (21 bp):
AGATGTGAATTGGATTAAATT
Found at i:54365416 original size:25 final size:26
Alignment explanation
Indices: 54365388--54365473 Score: 97
Period size: 25 Copynumber: 3.4 Consensus size: 26
54365378 CTTATGAGCA
*
54365388 TCCCAATAATTGGCTCTCACGAG-TT
1 TCCCATTAATTGGCTCTCACGAGCTT
* *
54365413 TCCCGTTATTTGGCTCTCACGAGCTT
1 TCCCATTAATTGGCTCTCACGAGCTT
**
54365439 T-CCATTAATTGGCTCTCATAAGC-T
1 TCCCATTAATTGGCTCTCACGAGCTT
54365463 TCCCAATTAAT
1 TCCC-ATTAAT
54365474 GACTCTCCGG
Statistics
Matches: 51, Mismatches: 7, Indels: 5
0.81 0.11 0.08
Matches are distributed among these distances:
24 2 0.04
25 40 0.78
26 9 0.18
ACGTcount: A:0.22, C:0.28, G:0.14, T:0.36
Consensus pattern (26 bp):
TCCCATTAATTGGCTCTCACGAGCTT
Found at i:54365535 original size:24 final size:24
Alignment explanation
Indices: 54365484--54365536 Score: 63
Period size: 24 Copynumber: 2.2 Consensus size: 24
54365474 GACTCTCCGG
*
54365484 AGCTTCTCGATATTGGCTCGCATG
1 AGCTTCTCGATATTGGCTCGCATA
* *
54365508 AGCTTCTCGA-ATTTGGCTCTCTTA
1 AGCTTCTCGATA-TTGGCTCGCATA
54365532 AGCTT
1 AGCTT
54365537 TCTGTTTATA
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
23 1 0.04
24 24 0.96
ACGTcount: A:0.17, C:0.25, G:0.21, T:0.38
Consensus pattern (24 bp):
AGCTTCTCGATATTGGCTCGCATA
Found at i:54365600 original size:25 final size:24
Alignment explanation
Indices: 54365572--54365653 Score: 74
Period size: 25 Copynumber: 3.3 Consensus size: 24
54365562 CCGATAATTG
54365572 GCTCGCAAGAGCTTCCCATTACAT
1 GCTCGCAAGAGCTTCCCATTACAT
** * * *
54365596 CGCTCATATGAGCTTCCCGTTATAT
1 -GCTCGCAAGAGCTTCCCATTACAT
* *
54365621 GGTTCGAAAGAGCTTCCCGATTACAT
1 -GCTCGCAAGAGCTTCCC-ATTACAT
54365647 GCTCGCA
1 GCTCGCA
54365654 TGGGCATACC
Statistics
Matches: 42, Mismatches: 14, Indels: 2
0.72 0.24 0.03
Matches are distributed among these distances:
25 37 0.88
26 5 0.12
ACGTcount: A:0.23, C:0.29, G:0.20, T:0.28
Consensus pattern (24 bp):
GCTCGCAAGAGCTTCCCATTACAT
Found at i:54365632 original size:50 final size:50
Alignment explanation
Indices: 54365552--54365650 Score: 130
Period size: 50 Copynumber: 2.0 Consensus size: 50
54365542 TTATAACTCG
* *
54365552 TATGAGCTTTCCGATAATTGGCTCGCAAGAGCTTCCC-ATTACATCGCTCA
1 TATGAGCTTCCCGATAATTGGCTCGAAAGAGCTTCCCGATTACAT-GCTCA
* *
54365602 TATGAGCTTCCCG-TTATATGGTTCGAAAGAGCTTCCCGATTACATGCTC
1 TATGAGCTTCCCGATAAT-TGGCTCGAAAGAGCTTCCCGATTACATGCTC
54365651 GCATGGGCAT
Statistics
Matches: 43, Mismatches: 4, Indels: 4
0.84 0.08 0.08
Matches are distributed among these distances:
49 3 0.07
50 33 0.77
51 7 0.16
ACGTcount: A:0.23, C:0.26, G:0.19, T:0.31
Consensus pattern (50 bp):
TATGAGCTTCCCGATAATTGGCTCGAAAGAGCTTCCCGATTACATGCTCA
Found at i:54369275 original size:5 final size:5
Alignment explanation
Indices: 54369265--54369297 Score: 57
Period size: 5 Copynumber: 6.6 Consensus size: 5
54369255 TTTTTATGTT
*
54369265 TATAA TATAA TATAA TATAA TGTAA TATAA TAT
1 TATAA TATAA TATAA TATAA TATAA TATAA TAT
54369298 TTTATTTTAT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
5 26 1.00
ACGTcount: A:0.55, C:0.00, G:0.03, T:0.42
Consensus pattern (5 bp):
TATAA
Found at i:54373023 original size:5 final size:5
Alignment explanation
Indices: 54373008--54373051 Score: 56
Period size: 5 Copynumber: 8.8 Consensus size: 5
54372998 AGCTATTAGG
54373008 TTTTGC TTTTC TTTTC TTTT- TTTTC TTTTC -TTTC TTTCTC TTTT
1 TTTT-C TTTTC TTTTC TTTTC TTTTC TTTTC TTTTC TTT-TC TTTT
54373052 TTTACTTGAT
Statistics
Matches: 35, Mismatches: 0, Indels: 7
0.83 0.00 0.17
Matches are distributed among these distances:
4 8 0.23
5 18 0.51
6 9 0.26
ACGTcount: A:0.00, C:0.18, G:0.02, T:0.80
Consensus pattern (5 bp):
TTTTC
Found at i:54373033 original size:14 final size:15
Alignment explanation
Indices: 54373014--54373051 Score: 60
Period size: 14 Copynumber: 2.6 Consensus size: 15
54373004 TAGGTTTTGC
54373014 TTTTCTTTTCTTT-T
1 TTTTCTTTTCTTTCT
54373028 TTTTCTTTTCTTTCT
1 TTTTCTTTTCTTTCT
*
54373043 TTCTCTTTT
1 TTTTCTTTT
54373052 TTTACTTGAT
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
14 13 0.59
15 9 0.41
ACGTcount: A:0.00, C:0.18, G:0.00, T:0.82
Consensus pattern (15 bp):
TTTTCTTTTCTTTCT
Found at i:54374989 original size:17 final size:17
Alignment explanation
Indices: 54374967--54375001 Score: 70
Period size: 17 Copynumber: 2.1 Consensus size: 17
54374957 CTCATTTTCT
54374967 GTTGCTTAGTCTAGTGA
1 GTTGCTTAGTCTAGTGA
54374984 GTTGCTTAGTCTAGTGA
1 GTTGCTTAGTCTAGTGA
54375001 G
1 G
54375002 GTTAAAAATA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.17, C:0.11, G:0.31, T:0.40
Consensus pattern (17 bp):
GTTGCTTAGTCTAGTGA
Found at i:54375320 original size:23 final size:23
Alignment explanation
Indices: 54375294--54375339 Score: 65
Period size: 23 Copynumber: 2.0 Consensus size: 23
54375284 ATGAGAATTT
**
54375294 TTAAAATTTTTAAATCAAAATAA
1 TTAAAATTTAAAAATCAAAATAA
*
54375317 TTAAAATTTAAAAATTAAAATAA
1 TTAAAATTTAAAAATCAAAATAA
54375340 ATAATCTAAA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
23 20 1.00
ACGTcount: A:0.61, C:0.02, G:0.00, T:0.37
Consensus pattern (23 bp):
TTAAAATTTAAAAATCAAAATAA
Found at i:54378341 original size:44 final size:45
Alignment explanation
Indices: 54378286--54378576 Score: 164
Period size: 44 Copynumber: 6.6 Consensus size: 45
54378276 TCATTCTAAC
* * * *
54378286 CCACTGTAACTTTAGAGGTAGA-GGATTTGTCA-CTTTAATCTATT
1 CCACTGCAACTTTAGAGGAAGATAGATTTGT-AGCTTTAATCTACT
* *
54378330 CCACTGCAAC-TT-CAGGAAGATTAGATTTGTAGCTTTAATCTGCT
1 CCACTGCAACTTTAGAGGAAGA-TAGATTTGTAGCTTTAATCTACT
* * * * *
54378374 CCACTGCAACTTTAG-GG-AGATGAGACTCGAATCTTCAATCTACT
1 CCACTGCAACTTTAGAGGAAGAT-AGATTTGTAGCTTTAATCTACT
* * * *
54378418 CCACTGCAACTTCA-A-GAAGATGAGAATTGTAACTTTAATCTGCT
1 CCACTGCAACTTTAGAGGAAGAT-AGATTTGTAGCTTTAATCTACT
* * * * * *
54378462 CCACTACAAC-TT-CAGGAAGATAAGACTTGTAACTTCT-ATTTGCT
1 CCACTGCAACTTTAGAGGAAGAT-AGATTTGTAGCTT-TAATCTACT
* * *
54378506 CCACTGCAACTTCT---GGAAGATAAGACTCGTAGCTTTAATCTGCT
1 CCACTGCAACTT-TAGAGGAAGAT-AGATTTGTAGCTTTAATCTACT
*
54378550 CCATTGCAACTTTAG-GG-AGATAAGATT
1 CCACTGCAACTTTAGAGGAAGAT-AGATT
54378577 CGCTATCTTC
Statistics
Matches: 200, Mismatches: 31, Indels: 32
0.76 0.12 0.12
Matches are distributed among these distances:
42 6 0.03
43 9 0.05
44 176 0.88
45 8 0.04
46 1 0.00
ACGTcount: A:0.30, C:0.21, G:0.18, T:0.32
Consensus pattern (45 bp):
CCACTGCAACTTTAGAGGAAGATAGATTTGTAGCTTTAATCTACT
Found at i:54378437 original size:88 final size:89
Alignment explanation
Indices: 54378322--54378619 Score: 339
Period size: 88 Copynumber: 3.4 Consensus size: 89
54378312 TTGTCACTTT
* * *
54378322 AATCTATTCCACTGCAACTTCAGGAAGATTAGATTTGTAGCTTTAATCTGCTCCACTGCAACTTT
1 AATCTACTCCACTGCAACTTCAGGAAGATAAGAATTGTAGCTTTAATCTGCTCCACTGCAACTTT
*
54378387 AGGGAGATGAGACTCG-AATCTTC
66 AGGGAGATAAGACTCGCAATCTTC
* * * * *
54378410 AATCTACTCCACTGCAACTTCAAGAAGATGAGAATTGTAACTTTAATCTGCTCCACTACAACTTC
1 AATCTACTCCACTGCAACTTCAGGAAGATAAGAATTGTAGCTTTAATCTGCTCCACTGCAACTTT
* * *
54378475 AGGAAGATAAGACTTGTAA-CTTC
66 AGGGAGATAAGACTCGCAATCTTC
* * * * * * *
54378498 TATTTGCTCCACTGCAACTTCTGGAAGATAAGACTCGTAGCTTTAATCTGCTCCATTGCAACTTT
1 AATCTACTCCACTGCAACTTCAGGAAGATAAGAATTGTAGCTTTAATCTGCTCCACTGCAACTTT
* *
54378563 AGGGAGATAAGATTCGCTATCTTC
66 AGGGAGATAAGACTCGCAATCTTC
* * * * * *
54378587 AATTTGCTCTACTACAAATTCAGGGAGATAAGA
1 AATCTACTCCACTGCAACTTCAGGAAGATAAGA
54378620 TTTGCCACGA
Statistics
Matches: 175, Mismatches: 33, Indels: 3
0.83 0.16 0.01
Matches are distributed among these distances:
88 142 0.81
89 33 0.19
ACGTcount: A:0.31, C:0.21, G:0.17, T:0.31
Consensus pattern (89 bp):
AATCTACTCCACTGCAACTTCAGGAAGATAAGAATTGTAGCTTTAATCTGCTCCACTGCAACTTT
AGGGAGATAAGACTCGCAATCTTC
Found at i:54378511 original size:132 final size:131
Alignment explanation
Indices: 54378312--54378619 Score: 332
Period size: 132 Copynumber: 2.3 Consensus size: 131
54378302 GGTAGAGGAT
* ** * * * *
54378312 TTGTCACTTTAATCTATTCCACTGCAACTTCAGGAAGATTAGATTTGTAGCTTTAATCTGCTCCA
1 TTGTAACTTTAATCTGCTCCACTACAACTTCAGGAAGATAAGACTTGTAACTTTAATCTGCTCCA
* * * *
54378377 CTGCAACTT-TAGGGAGATGAGACTCGAATCTTCAATCTACTCCACTGCAACTTCAAGAAGATGA
66 CTGCAACTTCT-GGAAGATAAGACTCGAAGCTTCAATCTACTCCACTGCAACTTCAAGAAGATAA
54378441 GAA
130 G-A
*
54378444 TTGTAACTTTAATCTGCTCCACTACAACTTCAGGAAGATAAGACTTGTAACTTCT-ATTTGCTCC
1 TTGTAACTTTAATCTGCTCCACTACAACTTCAGGAAGATAAGACTTGTAACTT-TAATCTGCTCC
* * * * * * *
54378508 ACTGCAACTTCTGGAAGATAAGACTCGTAGCTTTAATCTGCTCCATTGCAACTTTAGGGAGATAA
65 ACTGCAACTTCTGGAAGATAAGACTCGAAGCTTCAATCTACTCCACTGCAACTTCAAGAAGATAA
54378573 GA
130 GA
* * * * * *
54378575 TTCGCTATCTTCAATTTGCTCTACTACAAATTCAGGGAGATAAGA
1 TT-G-TAACTTTAATCTGCTCCACTACAACTTCAGGAAGATAAGA
54378620 TTTGCCACGA
Statistics
Matches: 147, Mismatches: 25, Indels: 7
0.82 0.14 0.04
Matches are distributed among these distances:
131 3 0.02
132 108 0.73
133 36 0.24
ACGTcount: A:0.30, C:0.21, G:0.17, T:0.32
Consensus pattern (131 bp):
TTGTAACTTTAATCTGCTCCACTACAACTTCAGGAAGATAAGACTTGTAACTTTAATCTGCTCCA
CTGCAACTTCTGGAAGATAAGACTCGAAGCTTCAATCTACTCCACTGCAACTTCAAGAAGATAAG
A
Found at i:54378612 original size:45 final size:44
Alignment explanation
Indices: 54378329--54378621 Score: 232
Period size: 44 Copynumber: 6.6 Consensus size: 44
54378319 TTTAATCTAT
* * * * * *
54378329 TCCACTGCAACTTCAGGAAGATTAGATTTGTAGCTTTAATCTGC
1 TCCACTACAACTTCAGGAAGATAAGATTCGTAACTTCAATTTGC
* * * * * * *
54378373 TCCACTGCAACTTTAGGGAGATGAGACTCG-AATCTTCAATCTAC
1 TCCACTACAACTTCAGGAAGATAAGATTCGTAA-CTTCAATTTGC
* * * * *
54378417 TCCACTGCAACTTCAAGAAGATGAGAATT-GTAACTTTAATCTGC
1 TCCACTACAACTTCAGGAAGATAAG-ATTCGTAACTTCAATTTGC
*
54378461 TCCACTACAACTTCAGGAAGATAAGACTT-GTAACTTCTATTTGC
1 TCCACTACAACTTCAGGAAGATAAGA-TTCGTAACTTCAATTTGC
* * * * * *
54378505 TCCACTGCAACTTCTGGAAGATAAGACTCGTAGCTTTAATCTGC
1 TCCACTACAACTTCAGGAAGATAAGATTCGTAACTTCAATTTGC
* * * * *
54378549 TCCATTGCAACTTTAGGGAGATAAGATTCGCTATCTTCAATTTGC
1 TCCACTACAACTTCAGGAAGATAAGATTCG-TAACTTCAATTTGC
* * *
54378594 TCTACTACAAATTCAGGGAGATAAGATT
1 TCCACTACAACTTCAGGAAGATAAGATT
54378622 TGCCACGATG
Statistics
Matches: 203, Mismatches: 40, Indels: 11
0.80 0.16 0.04
Matches are distributed among these distances:
43 3 0.01
44 162 0.80
45 38 0.19
ACGTcount: A:0.30, C:0.22, G:0.17, T:0.31
Consensus pattern (44 bp):
TCCACTACAACTTCAGGAAGATAAGATTCGTAACTTCAATTTGC
Found at i:54386686 original size:19 final size:21
Alignment explanation
Indices: 54386664--54386710 Score: 55
Period size: 19 Copynumber: 2.3 Consensus size: 21
54386654 TTGTGAAACT
*
54386664 TAATGCAT-ATG-ATGAAATA
1 TAATGCATGATGAATGAAAAA
54386683 TAATGC-TGATGAATGAAAAA
1 TAATGCATGATGAATGAAAAA
54386703 TGAATGCA
1 T-AATGCA
54386711 AAGAAAGGCG
Statistics
Matches: 23, Mismatches: 1, Indels: 5
0.79 0.03 0.17
Matches are distributed among these distances:
18 1 0.04
19 9 0.39
20 8 0.35
21 5 0.22
ACGTcount: A:0.47, C:0.06, G:0.19, T:0.28
Consensus pattern (21 bp):
TAATGCATGATGAATGAAAAA
Found at i:54391687 original size:428 final size:428
Alignment explanation
Indices: 54390890--54391701 Score: 1606
Period size: 428 Copynumber: 1.9 Consensus size: 428
54390880 GAACCGACTA
*
54390890 AACCGTAGCTCTGATACCACTAAAATGTAACACCCCTTACCCGTATTCCTTAACAGAACAGAGTA
1 AACCGTAACTCTGATACCACTAAAATGTAACACCCCTTACCCGTATTCCTTAACAGAACAGAGTA
54390955 TGAGGTATTACTATTTTTTTTTAAATTTCGACAGCATTTCTGCTTATTTTTACGTACAACCCCCT
66 TGAGGTATTACTATTTTTTTTTAAATTTCGACAGCATTTCTGCTTATTTTTACGTACAACCCCCT
54391020 GCAAGTTTTCAATCACACTTTCAAACAATTCCAATAATCCAACCAAAAACAGTTGTATGATCATA
131 GCAAGTTTTCAATCACACTTTCAAACAATTCCAATAATCCAACCAAAAACAGTTGTATGATCATA
54391085 CTCAATTTGTCTAATAATAAACATCAACATTTTAAACCGAAACATACTATATATTTGTTTACGCC
196 CTCAATTTGTCTAATAATAAACATCAACATTTTAAACCGAAACATACTATATATTTGTTTACGCC
54391150 ATAATACATAAAGTCGTCTATACATGCCATGTTTCCAAAATATGAGTTGCAAAATACCCAAGCGT
261 ATAATACATAAAGTCGTCTATACATGCCATGTTTCCAAAATATGAGTTGCAAAATACCCAAGCGT
54391215 TGATGATAGTGTAGATGATTATCTCACTCCGCCCAAGTTCCGAGTTGATTGATGTCACTCGGTGC
326 TGATGATAGTGTAGATGATTATCTCACTCCGCCCAAGTTCCGAGTTGATTGATGTCACTCGGTGC
54391280 AAAATATCGTAATTTTTCAATTTACTCCACTACTTTCC
391 AAAATATCGTAATTTTTCAATTTACTCCACTACTTTCC
54391318 AACCGTAACTCTGATACCACTAAAATGTAACACCCCTTACCCGTATTCCTTAACAGAACAGAGTA
1 AACCGTAACTCTGATACCACTAAAATGTAACACCCCTTACCCGTATTCCTTAACAGAACAGAGTA
54391383 TGAGGTATTACTATTTTTTTTTAAATTTCGACAGCATTTCTGCTTATTTTTACGTACAACCCCCT
66 TGAGGTATTACTATTTTTTTTTAAATTTCGACAGCATTTCTGCTTATTTTTACGTACAACCCCCT
54391448 GCAAGTTTTCAATCACACTTTCAAACAATTCCAATAATCCAACCAAAAACAGTTGTATGATCATA
131 GCAAGTTTTCAATCACACTTTCAAACAATTCCAATAATCCAACCAAAAACAGTTGTATGATCATA
*
54391513 CTCAATTTGTCTAATAATAAACATCAACATTTTAAACCGAAACATACTATATATTTGTTTATGCC
196 CTCAATTTGTCTAATAATAAACATCAACATTTTAAACCGAAACATACTATATATTTGTTTACGCC
54391578 ATAATACATAAAGTCGTCTATACATGCCATGTTTCCAAAATATGAGTTGCAAAATACCCAAGCGT
261 ATAATACATAAAGTCGTCTATACATGCCATGTTTCCAAAATATGAGTTGCAAAATACCCAAGCGT
54391643 TGATGATAGTGTAGATGATTATCTCACTCCGCCCAAGTTCCGAGTTGATTGATGTCACT
326 TGATGATAGTGTAGATGATTATCTCACTCCGCCCAAGTTCCGAGTTGATTGATGTCACT
54391702 NNNNNNNNNN
Statistics
Matches: 382, Mismatches: 2, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
428 382 1.00
ACGTcount: A:0.33, C:0.22, G:0.12, T:0.33
Consensus pattern (428 bp):
AACCGTAACTCTGATACCACTAAAATGTAACACCCCTTACCCGTATTCCTTAACAGAACAGAGTA
TGAGGTATTACTATTTTTTTTTAAATTTCGACAGCATTTCTGCTTATTTTTACGTACAACCCCCT
GCAAGTTTTCAATCACACTTTCAAACAATTCCAATAATCCAACCAAAAACAGTTGTATGATCATA
CTCAATTTGTCTAATAATAAACATCAACATTTTAAACCGAAACATACTATATATTTGTTTACGCC
ATAATACATAAAGTCGTCTATACATGCCATGTTTCCAAAATATGAGTTGCAAAATACCCAAGCGT
TGATGATAGTGTAGATGATTATCTCACTCCGCCCAAGTTCCGAGTTGATTGATGTCACTCGGTGC
AAAATATCGTAATTTTTCAATTTACTCCACTACTTTCC
Found at i:54398862 original size:104 final size:104
Alignment explanation
Indices: 54398740--54398963 Score: 378
Period size: 104 Copynumber: 2.2 Consensus size: 104
54398730 AATGGATATC
54398740 GCACTTAGCAACCCCTCGGGGGAATCAGCACATAGCAACCCCCTTTCACATTTCAAAGATATGGT
1 GCACTTAGCAACCCCTCGGGGGAATCAGCACATAGCAACCCCCTTTCACATTTCAAAGATATGGT
* *
54398805 GGAT-ATCGCACTTAGCACCACCAATGAACCGGGGAATCA
66 GGATCA-CGCACATAGCACCACCAATAAACCGGGGAATCA
54398844 GCACTTAGCAACCCCTCGGGGGAATCAGCACATAGCAACCCCCTTTCACATTTCAAAGATATGGT
1 GCACTTAGCAACCCCTCGGGGGAATCAGCACATAGCAACCCCCTTTCACATTTCAAAGATATGGT
* *
54398909 GGATCACGCACATAGCACCACCCATAAATCGGGGAATCA
66 GGATCACGCACATAGCACCACCAATAAACCGGGGAATCA
**
54398948 GCACACAGCAACCCCT
1 GCACTTAGCAACCCCT
54398964 TTTATATACA
Statistics
Matches: 113, Mismatches: 6, Indels: 2
0.93 0.05 0.02
Matches are distributed among these distances:
104 112 0.99
105 1 0.01
ACGTcount: A:0.31, C:0.32, G:0.19, T:0.18
Consensus pattern (104 bp):
GCACTTAGCAACCCCTCGGGGGAATCAGCACATAGCAACCCCCTTTCACATTTCAAAGATATGGT
GGATCACGCACATAGCACCACCAATAAACCGGGGAATCA
Found at i:54399325 original size:29 final size:29
Alignment explanation
Indices: 54399292--54399355 Score: 76
Period size: 30 Copynumber: 2.2 Consensus size: 29
54399282 TAATCCACCA
54399292 CCCAACTTTTTG-AAAATTACAATTTTGCC
1 CCCAAC-TTTTGCAAAATTACAATTTTGCC
* * *
54399321 CCCAAACTTTTGCATAATTACACTTTTGTC
1 CCC-AACTTTTGCAAAATTACAATTTTGCC
54399351 CCCAA
1 CCCAA
54399356 GCTCGGAAAT
Statistics
Matches: 30, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
29 10 0.33
30 20 0.67
ACGTcount: A:0.30, C:0.28, G:0.06, T:0.36
Consensus pattern (29 bp):
CCCAACTTTTGCAAAATTACAATTTTGCC
Found at i:54399329 original size:30 final size:30
Alignment explanation
Indices: 54399299--54399355 Score: 80
Period size: 30 Copynumber: 1.9 Consensus size: 30
54399289 CCACCCAACT
54399299 TTTTG-AAAATTACAATTTTGCCCCCAAAC
1 TTTTGCAAAATTACAATTTTGCCCCCAAAC
* * *
54399328 TTTTGCATAATTACACTTTTGTCCCCAA
1 TTTTGCAAAATTACAATTTTGCCCCCAA
54399356 GCTCGGAAAT
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
29 5 0.21
30 19 0.79
ACGTcount: A:0.30, C:0.25, G:0.07, T:0.39
Consensus pattern (30 bp):
TTTTGCAAAATTACAATTTTGCCCCCAAAC
Found at i:54406730 original size:21 final size:21
Alignment explanation
Indices: 54406684--54406731 Score: 60
Period size: 21 Copynumber: 2.2 Consensus size: 21
54406674 TGTTATGGAC
*
54406684 TTTTGATTTTTGGTTTTATTT
1 TTTTTATTTTTGGTTTTATTT
* *
54406705 ATTTTATTTTTGGTTTGTTTTT
1 TTTTTATTTTTGGTTT-TATTT
54406727 TTTTT
1 TTTTT
54406732 CGGGCCCAAG
Statistics
Matches: 22, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
21 14 0.64
22 8 0.36
ACGTcount: A:0.08, C:0.00, G:0.12, T:0.79
Consensus pattern (21 bp):
TTTTTATTTTTGGTTTTATTT
Found at i:54406960 original size:6 final size:6
Alignment explanation
Indices: 54406951--54406993 Score: 50
Period size: 6 Copynumber: 6.7 Consensus size: 6
54406941 AAAAAATTTG
*
54406951 AATTCC AATTCC TTAAATTCC AATCCC AATTCC AATTCC AATT
1 AATTCC AATTCC ---AATTCC AATTCC AATTCC AATTCC AATT
54406994 TTTATTTTTT
Statistics
Matches: 32, Mismatches: 2, Indels: 6
0.80 0.05 0.15
Matches are distributed among these distances:
6 26 0.81
9 6 0.19
ACGTcount: A:0.35, C:0.30, G:0.00, T:0.35
Consensus pattern (6 bp):
AATTCC
Found at i:54412988 original size:21 final size:22
Alignment explanation
Indices: 54412964--54413015 Score: 70
Period size: 22 Copynumber: 2.4 Consensus size: 22
54412954 CTCGTATATA
* *
54412964 GGTCAAAATGGGTT-AAATACT
1 GGTCAAAATGGATTAAAATACG
*
54412985 GGTCAAAATGGATTAAAATAGG
1 GGTCAAAATGGATTAAAATACG
54413007 GGTCAAAAT
1 GGTCAAAAT
54413016 ATGAAAATGG
Statistics
Matches: 27, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
21 13 0.48
22 14 0.52
ACGTcount: A:0.42, C:0.08, G:0.25, T:0.25
Consensus pattern (22 bp):
GGTCAAAATGGATTAAAATACG
Found at i:54413388 original size:65 final size:65
Alignment explanation
Indices: 54413310--54413435 Score: 166
Period size: 65 Copynumber: 1.9 Consensus size: 65
54413300 AGAAAATGAA
* * *
54413310 GAAGGTGAAAAAGAAAAGAAAA-AGTTAGCAGAAAAGATAAAAGAGAAAGAAA-GTAGAAGGAGA
1 GAAGGTAAAAAAGAAAA-AAAACAATTAACAGAAAAGATAAAAGAGAAAGAAATG-AGAAGGAGA
54413373 AG
64 AG
* * *
54413375 GAAGGTAAAAAAGAAAAAAAACAATTAATAGAGAAGGTAAAAGAGAAAGAAATGAGAAGGA
1 GAAGGTAAAAAAGAAAAAAAACAATTAACAGAAAAGATAAAAGAGAAAGAAATGAGAAGGA
54413436 AAAAAAGAAG
Statistics
Matches: 53, Mismatches: 6, Indels: 4
0.84 0.10 0.06
Matches are distributed among these distances:
64 4 0.08
65 48 0.91
66 1 0.02
ACGTcount: A:0.63, C:0.02, G:0.27, T:0.09
Consensus pattern (65 bp):
GAAGGTAAAAAAGAAAAAAAACAATTAACAGAAAAGATAAAAGAGAAAGAAATGAGAAGGAGAAG
Found at i:54414505 original size:44 final size:44
Alignment explanation
Indices: 54414434--54414545 Score: 170
Period size: 44 Copynumber: 2.5 Consensus size: 44
54414424 ATACATGCAA
* *
54414434 AAATTAGATGCATTGGAAGAAATTTGGAACAAACTTCGTAATTT
1 AAATTAGATGCATTGGAACAAACTTGGAACAAACTTCGTAATTT
* * * *
54414478 AAATGAGATGCATTGCACCAAACTTGGAACAAACTTTGTAATTT
1 AAATTAGATGCATTGGAACAAACTTGGAACAAACTTCGTAATTT
54414522 AAATTAGATGCATTGGAACAAACT
1 AAATTAGATGCATTGGAACAAACT
54414546 CTGTAAAATA
Statistics
Matches: 59, Mismatches: 9, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
44 59 1.00
ACGTcount: A:0.41, C:0.12, G:0.17, T:0.29
Consensus pattern (44 bp):
AAATTAGATGCATTGGAACAAACTTGGAACAAACTTCGTAATTT
Found at i:54427267 original size:3 final size:3
Alignment explanation
Indices: 54427259--54427328 Score: 72
Period size: 3 Copynumber: 24.0 Consensus size: 3
54427249 TATATATAGG
* ** *
54427259 AAT AAT AAT AAT AAT AAT -AT AAT AAT AAT AA- AAG GCT AAT AAT AAA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
* *
54427305 AAT AAT AAT GAT AAT AAA AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT
54427329 GGGGCTATTA
Statistics
Matches: 54, Mismatches: 11, Indels: 4
0.78 0.16 0.06
Matches are distributed among these distances:
2 4 0.07
3 50 0.93
ACGTcount: A:0.66, C:0.01, G:0.04, T:0.29
Consensus pattern (3 bp):
AAT
Found at i:54432154 original size:18 final size:18
Alignment explanation
Indices: 54432131--54432175 Score: 63
Period size: 18 Copynumber: 2.5 Consensus size: 18
54432121 GTTTTGAAAA
**
54432131 TGGTCAAAATTATGTTTC
1 TGGTCAAAATTATAATTC
54432149 TGGTCAAAATTATAATTC
1 TGGTCAAAATTATAATTC
*
54432167 TAGTCAAAA
1 TGGTCAAAA
54432176 GTGGCTTGCT
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 24 1.00
ACGTcount: A:0.38, C:0.11, G:0.13, T:0.38
Consensus pattern (18 bp):
TGGTCAAAATTATAATTC
Found at i:54432424 original size:21 final size:20
Alignment explanation
Indices: 54432398--54432445 Score: 57
Period size: 18 Copynumber: 2.5 Consensus size: 20
54432388 ATGATGGGAT
54432398 TGGTGGTACTGTTGGGCCGAA
1 TGGTGGTA-TGTTGGGCCGAA
54432419 TGGTGG--TGTTGGGCCGAA
1 TGGTGGTATGTTGGGCCGAA
54432437 -GGATGGTAT
1 TGG-TGGTAT
54432446 TGGGCCTAAT
Statistics
Matches: 24, Mismatches: 0, Indels: 7
0.77 0.00 0.23
Matches are distributed among these distances:
17 2 0.08
18 15 0.62
20 1 0.04
21 6 0.25
ACGTcount: A:0.15, C:0.10, G:0.46, T:0.29
Consensus pattern (20 bp):
TGGTGGTATGTTGGGCCGAA
Found at i:54432443 original size:18 final size:18
Alignment explanation
Indices: 54432407--54432451 Score: 65
Period size: 18 Copynumber: 2.5 Consensus size: 18
54432397 TTGGTGGTAC
54432407 TGTTGGGCCGAATGGTGG
1 TGTTGGGCCGAATGGTGG
54432425 TGTTGGGCCGAA-GGATGG
1 TGTTGGGCCGAATGG-TGG
*
54432443 TATTGGGCC
1 TGTTGGGCC
54432452 TAATATTGGT
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
17 2 0.08
18 23 0.92
ACGTcount: A:0.13, C:0.13, G:0.47, T:0.27
Consensus pattern (18 bp):
TGTTGGGCCGAATGGTGG
Found at i:54438273 original size:17 final size:16
Alignment explanation
Indices: 54438233--54438274 Score: 50
Period size: 17 Copynumber: 2.6 Consensus size: 16
54438223 AATTCAATTT
*
54438233 TAATATAAATATTCAA
1 TAATATAAAAATTCAA
54438249 T-ATGATAAACAATTCAA
1 TAAT-ATAAA-AATTCAA
54438266 TAATATAAA
1 TAATATAAA
54438275 TAATATAATA
Statistics
Matches: 22, Mismatches: 1, Indels: 5
0.79 0.04 0.18
Matches are distributed among these distances:
15 2 0.09
16 6 0.27
17 12 0.55
18 2 0.09
ACGTcount: A:0.57, C:0.07, G:0.02, T:0.33
Consensus pattern (16 bp):
TAATATAAAAATTCAA
Found at i:54438739 original size:9 final size:9
Alignment explanation
Indices: 54438725--54438761 Score: 56
Period size: 9 Copynumber: 4.1 Consensus size: 9
54438715 TATAGTTTGA
54438725 TATTCGAAT
1 TATTCGAAT
54438734 TATTCGAAT
1 TATTCGAAT
*
54438743 TATTCGAGT
1 TATTCGAAT
*
54438752 TATTTGAAT
1 TATTCGAAT
54438761 T
1 T
54438762 CGAAAACTCA
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
9 25 1.00
ACGTcount: A:0.30, C:0.08, G:0.14, T:0.49
Consensus pattern (9 bp):
TATTCGAAT
Found at i:54440492 original size:104 final size:104
Alignment explanation
Indices: 54440312--54440510 Score: 326
Period size: 104 Copynumber: 1.9 Consensus size: 104
54440302 TTGCTTTCAT
* * * * * * *
54440312 TTTATCTTTTGATTCATTTTGAGCACGATAAAGTGGATGTTATCATAAATTTATATGGTTTCTAA
1 TTTATCTTTTGACTCATTTTAAGCACAATAAAGTGGATGTTATCATAAATTCATATAGCTTATAA
*
54440377 TCTAGCATTCATCAATATACAATGTCTTCTCTTAAAGAA
66 TCTAGCATTCATCAATATACAAGGTCTTCTCTTAAAGAA
54440416 TTTATCTTTTGACTCATTTTAAGCACAATAAAGTGGATGTTATCATAAATTCATATAGCTTATAA
1 TTTATCTTTTGACTCATTTTAAGCACAATAAAGTGGATGTTATCATAAATTCATATAGCTTATAA
54440481 TCTAGCATTCATCAATATACAAGGTCTTCT
66 TCTAGCATTCATCAATATACAAGGTCTTCT
54440511 TCCAAAAAAT
Statistics
Matches: 87, Mismatches: 8, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
104 87 1.00
ACGTcount: A:0.33, C:0.15, G:0.12, T:0.41
Consensus pattern (104 bp):
TTTATCTTTTGACTCATTTTAAGCACAATAAAGTGGATGTTATCATAAATTCATATAGCTTATAA
TCTAGCATTCATCAATATACAAGGTCTTCTCTTAAAGAA
Found at i:54448677 original size:2 final size:2
Alignment explanation
Indices: 54448672--54448708 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
54448662 TCAACAGGTT
54448672 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
54448709 TTTTTCCCCA
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.00, C:0.49, G:0.00, T:0.51
Consensus pattern (2 bp):
TC
Found at i:54453025 original size:31 final size:29
Alignment explanation
Indices: 54452944--54453025 Score: 76
Period size: 31 Copynumber: 2.7 Consensus size: 29
54452934 ATAACTATTG
*
54452944 CATAAAAATATTTTAT-ATTCATAATTAA
1 CATAAAAATATATTATAATTCATAATTAA
* * *
54452972 CAATTTTAAAATTTATTTTAATTCATTAATTTAA
1 C-A--TAAAAATATATTATAATTCA-TAA-TTAA
54453006 CATAAAAATATATTATAATT
1 CATAAAAATATATTATAATT
54453026 ACTTTTCTTA
Statistics
Matches: 41, Mismatches: 7, Indels: 9
0.72 0.12 0.16
Matches are distributed among these distances:
28 1 0.02
29 1 0.02
31 25 0.61
32 5 0.12
33 4 0.10
34 5 0.12
ACGTcount: A:0.48, C:0.06, G:0.00, T:0.46
Consensus pattern (29 bp):
CATAAAAATATATTATAATTCATAATTAA
Found at i:54454118 original size:14 final size:14
Alignment explanation
Indices: 54454099--54454137 Score: 78
Period size: 14 Copynumber: 2.8 Consensus size: 14
54454089 CTAAAAAAAT
54454099 AAATCATTTTTCAA
1 AAATCATTTTTCAA
54454113 AAATCATTTTTCAA
1 AAATCATTTTTCAA
54454127 AAATCATTTTT
1 AAATCATTTTT
54454138 AGTAAACCTT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 25 1.00
ACGTcount: A:0.41, C:0.13, G:0.00, T:0.46
Consensus pattern (14 bp):
AAATCATTTTTCAA
Found at i:54454472 original size:22 final size:23
Alignment explanation
Indices: 54454410--54454474 Score: 64
Period size: 22 Copynumber: 2.9 Consensus size: 23
54454400 ATTTAAATTA
* *
54454410 TAAAATTATTTGATATAT-TATT
1 TAAAATTATTTGATAAATATAAT
* *
54454432 TAAAATTAATT-ACAGAATATAAT
1 TAAAATTATTTGATA-AATATAAT
54454455 T-AAATTATTTGATAAATATA
1 TAAAATTATTTGATAAATATA
54454475 GATTTTAAAT
Statistics
Matches: 34, Mismatches: 6, Indels: 6
0.74 0.13 0.13
Matches are distributed among these distances:
21 2 0.06
22 26 0.76
23 6 0.18
ACGTcount: A:0.49, C:0.02, G:0.05, T:0.45
Consensus pattern (23 bp):
TAAAATTATTTGATAAATATAAT
Found at i:54456004 original size:36 final size:36
Alignment explanation
Indices: 54455964--54456035 Score: 144
Period size: 36 Copynumber: 2.0 Consensus size: 36
54455954 ACATAATTGT
54455964 TAACAAATCATCAAAGTGGTGTTCATTGATAATGGG
1 TAACAAATCATCAAAGTGGTGTTCATTGATAATGGG
54456000 TAACAAATCATCAAAGTGGTGTTCATTGATAATGGG
1 TAACAAATCATCAAAGTGGTGTTCATTGATAATGGG
54456036 ATGCTCATAA
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
36 36 1.00
ACGTcount: A:0.36, C:0.11, G:0.22, T:0.31
Consensus pattern (36 bp):
TAACAAATCATCAAAGTGGTGTTCATTGATAATGGG
Found at i:54461722 original size:32 final size:33
Alignment explanation
Indices: 54461681--54461746 Score: 125
Period size: 32 Copynumber: 2.0 Consensus size: 33
54461671 TGTAAATCAA
54461681 TACAATCTCATGCTGAAATAGAAAGTTTT-TTT
1 TACAATCTCATGCTGAAATAGAAAGTTTTATTT
54461713 TACAATCTCATGCTGAAATAGAAAGTTTTATTT
1 TACAATCTCATGCTGAAATAGAAAGTTTTATTT
54461746 T
1 T
54461747 CTCATAAGTA
Statistics
Matches: 33, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
32 29 0.88
33 4 0.12
ACGTcount: A:0.35, C:0.12, G:0.12, T:0.41
Consensus pattern (33 bp):
TACAATCTCATGCTGAAATAGAAAGTTTTATTT
Found at i:54464325 original size:26 final size:25
Alignment explanation
Indices: 54464279--54464329 Score: 59
Period size: 26 Copynumber: 2.0 Consensus size: 25
54464269 ACAAACAAAT
* *
54464279 AATCAACCTAGTTATTATAATATAAG
1 AATCAACATAGTTAATATAAT-TAAG
54464305 AATCAACATCAGTTAAT-TAATTAAG
1 AATCAACAT-AGTTAATATAATTAAG
54464330 CCTAGTCAAA
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
25 4 0.18
26 12 0.55
27 6 0.27
ACGTcount: A:0.47, C:0.12, G:0.08, T:0.33
Consensus pattern (25 bp):
AATCAACATAGTTAATATAATTAAG
Found at i:54467378 original size:18 final size:18
Alignment explanation
Indices: 54467355--54467398 Score: 79
Period size: 18 Copynumber: 2.4 Consensus size: 18
54467345 TTAGTCTACA
54467355 AGCTCGTCTCACTCGAAG
1 AGCTCGTCTCACTCGAAG
54467373 AGCTCGTCTCACTCGAAG
1 AGCTCGTCTCACTCGAAG
*
54467391 ACCTCGTC
1 AGCTCGTC
54467399 AGTCGTGACT
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
18 25 1.00
ACGTcount: A:0.20, C:0.36, G:0.20, T:0.23
Consensus pattern (18 bp):
AGCTCGTCTCACTCGAAG
Found at i:54471576 original size:43 final size:46
Alignment explanation
Indices: 54471528--54471616 Score: 148
Period size: 45 Copynumber: 2.0 Consensus size: 46
54471518 TACGTATGAT
54471528 CACTTATCAC-TTGTC-CCTGATCAGATAAGTGTAGCT-AGGCTAC
1 CACTTATCACTTTGTCACCTGATCAGATAAGTGTAGCTAAGGCTAC
*
54471571 CACTTATCACTTTGTCACTTGATCAGATAAGTGTAGCTAAGGCTAC
1 CACTTATCACTTTGTCACCTGATCAGATAAGTGTAGCTAAGGCTAC
54471617 TTTTTCACTT
Statistics
Matches: 42, Mismatches: 1, Indels: 3
0.91 0.02 0.07
Matches are distributed among these distances:
43 10 0.24
44 5 0.12
45 20 0.48
46 7 0.17
ACGTcount: A:0.27, C:0.24, G:0.18, T:0.31
Consensus pattern (46 bp):
CACTTATCACTTTGTCACCTGATCAGATAAGTGTAGCTAAGGCTAC
Found at i:54471787 original size:36 final size:36
Alignment explanation
Indices: 54471571--54471787 Score: 357
Period size: 36 Copynumber: 6.0 Consensus size: 36
54471561 GCTAGGCTAC
*
54471571 CACTTATCACTTTGTCACTTGATCAGATAAGTGTAG
1 CACTTATCACTTTTTCACTTGATCAGATAAGTGTAG
* * *
54471607 --CTAAGGCTACTTTTTCACTTGATCAGATAAGTATAG
1 CACTTA-TC-ACTTTTTCACTTGATCAGATAAGTGTAG
*
54471643 CACTTATCACTTTTTCACTTGATCAGATAAGTATAG
1 CACTTATCACTTTTTCACTTGATCAGATAAGTGTAG
54471679 CACTTATCACTTTTTCACTTGATCAGATAAGTGTAG
1 CACTTATCACTTTTTCACTTGATCAGATAAGTGTAG
54471715 CACTTATCACTTTTTCACTTGATCAGATAAGTGTAG
1 CACTTATCACTTTTTCACTTGATCAGATAAGTGTAG
54471751 CACTTATCACTTTTTCACTTGATCAGATAAGTGTAG
1 CACTTATCACTTTTTCACTTGATCAGATAAGTGTAG
54471787 C
1 C
54471788 TAAAGCTACC
Statistics
Matches: 170, Mismatches: 7, Indels: 8
0.92 0.04 0.04
Matches are distributed among these distances:
34 3 0.02
35 1 0.01
36 162 0.95
37 1 0.01
38 3 0.02
ACGTcount: A:0.29, C:0.19, G:0.14, T:0.38
Consensus pattern (36 bp):
CACTTATCACTTTTTCACTTGATCAGATAAGTGTAG
Found at i:54474489 original size:20 final size:21
Alignment explanation
Indices: 54474461--54474511 Score: 61
Period size: 20 Copynumber: 2.4 Consensus size: 21
54474451 ATAAAATTTA
54474461 ATTAGAATATATAAACTAT-ATT
1 ATTA-AATATATAAA-TATAATT
*
54474483 -TTAAATATTTAAATATAATT
1 ATTAAATATATAAATATAATT
54474503 ATTAAATAT
1 ATTAAATAT
54474512 TTGTAATTAG
Statistics
Matches: 26, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
19 3 0.12
20 12 0.46
21 11 0.42
ACGTcount: A:0.51, C:0.02, G:0.02, T:0.45
Consensus pattern (21 bp):
ATTAAATATATAAATATAATT
Found at i:54474509 original size:21 final size:21
Alignment explanation
Indices: 54474461--54474513 Score: 65
Period size: 21 Copynumber: 2.5 Consensus size: 21
54474451 ATAAAATTTA
*
54474461 ATTAGAATATATAAACTATATT
1 ATTA-AATATTTAAACTATATT
54474483 -TTAAATATTTAAA-TATAATT
1 ATTAAATATTTAAACTAT-ATT
54474503 ATTAAATATTT
1 ATTAAATATTT
54474514 GTAATTAGAT
Statistics
Matches: 28, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
19 3 0.11
20 12 0.43
21 13 0.46
ACGTcount: A:0.49, C:0.02, G:0.02, T:0.47
Consensus pattern (21 bp):
ATTAAATATTTAAACTATATT
Found at i:54487052 original size:51 final size:51
Alignment explanation
Indices: 54486955--54487070 Score: 121
Period size: 51 Copynumber: 2.3 Consensus size: 51
54486945 TTATTTTTCT
** *
54486955 TATATATATATAAAATACATAATGCATTTATGAAAACAAGGAAAATATA-AA
1 TATATA-ATATAAAATACATAATGCATTTACAAAAAAAAGGAAAATATATAA
* * *
54487006 TATATACATATAAAATATATTCATGCATTTACAAAAAAAATG-AAATATATAA
1 TATATA-ATATAAAATACA-TAATGCATTTACAAAAAAAAGGAAAATATATAA
*
54487058 -GTATAATATAAAA
1 TATATAATATAAAA
54487071 CGTGGAAAAT
Statistics
Matches: 55, Mismatches: 8, Indels: 5
0.81 0.12 0.07
Matches are distributed among these distances:
50 8 0.15
51 28 0.51
52 19 0.35
ACGTcount: A:0.57, C:0.06, G:0.06, T:0.31
Consensus pattern (51 bp):
TATATAATATAAAATACATAATGCATTTACAAAAAAAAGGAAAATATATAA
Found at i:54487840 original size:21 final size:21
Alignment explanation
Indices: 54487814--54487870 Score: 96
Period size: 21 Copynumber: 2.7 Consensus size: 21
54487804 AATCATATCT
* *
54487814 TCTAAGATTGTATATATCGTA
1 TCTAAGATTGCATATATCATA
54487835 TCTAAGATTGCATATATCATA
1 TCTAAGATTGCATATATCATA
54487856 TCTAAGATTGCATAT
1 TCTAAGATTGCATAT
54487871 CCTCGAAAAT
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
21 34 1.00
ACGTcount: A:0.35, C:0.12, G:0.12, T:0.40
Consensus pattern (21 bp):
TCTAAGATTGCATATATCATA
Found at i:54492033 original size:21 final size:22
Alignment explanation
Indices: 54492009--54492049 Score: 57
Period size: 22 Copynumber: 1.9 Consensus size: 22
54491999 GTTTTGTATG
54492009 TAAATATGT-TTTTTTTCTTCA
1 TAAATATGTCTTTTTTTCTTCA
* *
54492030 TAAATTTTTCTTTTTTTCTT
1 TAAATATGTCTTTTTTTCTT
54492050 ATTCCTTTCA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 7 0.41
22 10 0.59
ACGTcount: A:0.20, C:0.10, G:0.02, T:0.68
Consensus pattern (22 bp):
TAAATATGTCTTTTTTTCTTCA
Found at i:54494386 original size:103 final size:103
Alignment explanation
Indices: 54494204--54494409 Score: 376
Period size: 103 Copynumber: 2.0 Consensus size: 103
54494194 GTCTTCCCTA
*
54494204 AAGCCTTGGGGTATGTGGATGAAGCAGTCACTGATTTATTCGACCGGCTCGATAAGAAGGTTACA
1 AAGCCTTGGGGTATGTGGATGAAGCAGTCACTGATTTATTCGACCGGCTCGACAAGAAGGTTACA
*
54494269 CCGATTCCAACAATTTTGGCAGAAACTTTCAGGTCATT
66 CCAATTCCAACAATTTTGGCAGAAACTTTCAGGTCATT
*
54494307 AAGCCTTGGGGTATGTGGATGAAGCAGTCATTGATTTATTCGACCGGCTCGACAAGAAGGTTACA
1 AAGCCTTGGGGTATGTGGATGAAGCAGTCACTGATTTATTCGACCGGCTCGACAAGAAGGTTACA
*
54494372 CCAATTCCAGCAATTTTGGCAGAAACTTTCAGGTCATT
66 CCAATTCCAACAATTTTGGCAGAAACTTTCAGGTCATT
54494410 GAGTGCATGC
Statistics
Matches: 99, Mismatches: 4, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
103 99 1.00
ACGTcount: A:0.28, C:0.19, G:0.24, T:0.28
Consensus pattern (103 bp):
AAGCCTTGGGGTATGTGGATGAAGCAGTCACTGATTTATTCGACCGGCTCGACAAGAAGGTTACA
CCAATTCCAACAATTTTGGCAGAAACTTTCAGGTCATT
Found at i:54504028 original size:44 final size:43
Alignment explanation
Indices: 54503978--54504611 Score: 367
Period size: 44 Copynumber: 14.6 Consensus size: 43
54503968 TAACAGATCG
* *
54503978 AGTCTTATCTCCTTGAAGTTGCAGTGGAGCAGACTAAGTAGGCA
1 AGTCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAG-AGGCA
* * * *
54504022 AGTCTTATC-CTCCTGAAGTTACGGTGAAGCAGACTGAAGATGGCA
1 AGTCTTATCTC-CCTGAAGTTGCAGTGGAGCAGA-TTAAGA-GGCA
* *
54504067 AATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAA-AGCCA
1 AGTCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAGAGGCA
* * * * ** *
54504109 GTAATCCTATCTCGCTGAAGTTGCAGT-GAGCGGATTAA-AACCTT
1 --AGTCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAGAGGC-A
* * * * * *
54504153 AGATATTATCTCTCTGAAGTTGCAG-AGAGCAGA-T-CGCA-TCT
1 AG-TCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAG-AGGCA
* * * * * *
54504194 ACTCTTATCTCCCTAAAGTTACAGTGAAGCAGACTAAGTGGGCA
1 AGTCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAG-AGGCA
*
54504238 AGTCTTATC-CTCCTGAAGTTGCAGT-GAGGCAGACTAAAGATGGCA
1 AGTCTTATCTC-CCTGAAGTTGCAGTGGA-GCAGA-TTAAGA-GGCA
*
54504283 AATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAA-AGTCGACA
1 AGTCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAGAG--G-CA
* ** * **
54504328 A-TCCTATCTCTTTGAAGTTGCAGTGGAGCGGATTAA-AATCA
1 AGTCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAGAGGCA
* * * * *
54504369 CAGATCTTATCTCTCTGAAGTTGCAG-AGAGCAGA-T-CGCA-TCT
1 -AG-TCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAG-AGGCA
* *
54504411 AGTCTTATCTCCCTGAAGTTGTAGTGGAGCAGACTAAGGAGGCA
1 AGTCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAA-GAGGCA
*
54504455 AGTCTTATC-CTCCTAAAGTTGCAGT-GAGGCAGATTGAAGATGGCA
1 AGTCTTATCTC-CCTGAAGTTGCAGTGGA-GCAGATT-AAGA-GGCA
* * *
54504500 AATCTTATTTCCCCGAAGTTGCAGTGGAGCAGATTAA-A-GCTGA
1 AGTCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAGAGGC--A
* * * ** *
54504543 TAATCCTATCTCCCTGAAGTTGCAGTGGAGCGGATTAA-AACCTT
1 -AGTCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAGAGGC-A
*
54504587 AGATCTTATCTCTCTGAAGTTGCAG
1 AG-TCTTATCTCCCTGAAGTTGCAG
54504612 AGAACAGATC
Statistics
Matches: 465, Mismatches: 80, Indels: 90
0.73 0.13 0.14
Matches are distributed among these distances:
40 38 0.08
41 21 0.05
42 13 0.03
43 59 0.13
44 223 0.48
45 104 0.22
46 7 0.02
ACGTcount: A:0.29, C:0.20, G:0.24, T:0.28
Consensus pattern (43 bp):
AGTCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAGAGGCA
Found at i:54504163 original size:43 final size:43
Alignment explanation
Indices: 54504071--54504186 Score: 135
Period size: 43 Copynumber: 2.7 Consensus size: 43
54504061 ATGGCAAATC
* *
54504071 TTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAGCCAGTAATC
1 TTATCTCCCTGAAGTTGCAGT-GAGCAGATTAAAACCAGTAATA
* * * *
54504115 CTATCTCGCTGAAGTTGCAGTGAGCGGATTAAAACC-TTAGATA
1 TTATCTCCCTGAAGTTGCAGTGAGCAGATTAAAACCAGTA-ATA
* *
54504158 TTATCTCTCTGAAGTTGCAGAGAGCAGAT
1 TTATCTCCCTGAAGTTGCAGTGAGCAGAT
54504187 CGCATCTACT
Statistics
Matches: 61, Mismatches: 10, Indels: 3
0.82 0.14 0.04
Matches are distributed among these distances:
42 2 0.03
43 40 0.66
44 19 0.31
ACGTcount: A:0.29, C:0.19, G:0.23, T:0.28
Consensus pattern (43 bp):
TTATCTCCCTGAAGTTGCAGTGAGCAGATTAAAACCAGTAATA
Found at i:54504302 original size:89 final size:88
Alignment explanation
Indices: 54504196--54504569 Score: 288
Period size: 89 Copynumber: 4.3 Consensus size: 88
54504186 TCGCATCTAC
* *
54504196 TCTTATCTCCCTAAAGTTACAGTGAAGCAGACT-AAGTGGGCAAGTCTTATCCTCCTGAAGTTGC
1 TCTTATCTCCCTGAAGTTGCAGTGAAGCAGACTAAAGT-GGCAAGTCTTAT-CTCCTGAAGTTGC
54504260 AGT-GAGGCAGACTAAAGATGGCAAA
64 AGTGGA-GCAGACTAAAGATGGCAAA
* * * * *
54504285 TCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAGTCGACAA-TCCTATCTCTTTGAAGTTGC
1 TCTTATCTCCCTGAAGTTGCAGTGAAGCAGACTAAAGT-GGCAAGTCTTATCTC-CTGAAGTTGC
* * ** *
54504349 AGTGGAGCGGATTAAA-ATCACAGA
64 AGTGGAGCAGACTAAAGATGGCAAA
* * ** * *
54504373 TCTTATCTCTCTGAAGTTGCAGAG-AGCAGA-TCGCA-T--CTAGTCTTATCTCCCTGAAGTTGT
1 TCTTATCTCCCTGAAGTTGCAGTGAAGCAGACT-AAAGTGGCAAGTCTTATCT-CCTGAAGTTGC
* *
54504433 AGTGGAGCAGACTAAGGA-GGCAAG
64 AGTGGAGCAGACTAAAGATGGCAAA
* * * * * * *
54504457 TCTTATC-CTCCTAAAGTTGCAGTGAGGCAGATTGAAGATGGCAAATCTTATTTCCCCGAAGTTG
1 TCTTATCTC-CCTGAAGTTGCAGTGAAGCAGACTAAAG-TGGCAAGTCTTATCT-CCTGAAGTTG
* *
54504521 CAGTGGAGCAGATTAAAGCT-G-ATAA
63 CAGTGGAGCAGACTAAAGATGGCA-AA
*
54504546 TCCTATCTCCCTGAAGTTGCAGTG
1 TCTTATCTCCCTGAAGTTGCAGTG
54504570 GAGCGGATTA
Statistics
Matches: 224, Mismatches: 44, Indels: 34
0.74 0.15 0.11
Matches are distributed among these distances:
83 3 0.01
84 49 0.22
85 9 0.04
86 3 0.01
87 8 0.04
88 31 0.14
89 110 0.49
90 11 0.05
ACGTcount: A:0.29, C:0.20, G:0.24, T:0.28
Consensus pattern (88 bp):
TCTTATCTCCCTGAAGTTGCAGTGAAGCAGACTAAAGTGGCAAGTCTTATCTCCTGAAGTTGCAG
TGGAGCAGACTAAAGATGGCAAA
Found at i:54504476 original size:217 final size:216
Alignment explanation
Indices: 54503978--54504692 Score: 1050
Period size: 217 Copynumber: 3.3 Consensus size: 216
54503968 TAACAGATCG
* * *
54503978 AGTCTTATCTCCTTGAAGTTGCAGTGGAGCAGACTAAGTAGGCAAGTCTTATCCTCCTGAAGTTA
1 AGTCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTAAGGAGGCAAGTCTTATCCTCCTGAAGTTG
* * *
54504043 CGGTGAAGCAGACTGAAGATGGCAAATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAGCC
66 CAGTGAGGCAGACTGAAGATGGCAAATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAGCG
* *
54504108 AGTAATCCTATCTCGCTGAAGTTGCAGT-GAGCGGATTAAAACCTTAGATATTATCTCTCTGAAG
131 A-TAATCCTATCTCCCTGAAGTTGCAGTGGAGCGGATTAAAACCTTAGATCTTATCTCTCTGAAG
54504172 TTGCAGAGAGCAGATCGCATCT
195 TTGCAGAGAGCAGATCGCATCT
* * * *
54504194 ACTCTTATCTCCCTAAAGTTACAGTGAAGCAGACTAAGTG-GGCAAGTCTTATCCTCCTGAAGTT
1 AGTCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTAAG-GAGGCAAGTCTTATCCTCCTGAAGTT
*
54504258 GCAGTGAGGCAGACTAAAGATGGCAAATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAGT
65 GCAGTGAGGCAGACTGAAGATGGCAAATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAG-
* ** * **
54504323 CGACAATCCTATCTCTTTGAAGTTGCAGTGGAGCGGATTAAAATCACAGATCTTATCTCTCTGAA
129 CGATAATCCTATCTCCCTGAAGTTGCAGTGGAGCGGATTAAAACCTTAGATCTTATCTCTCTGAA
54504388 GTTGCAGAGAGCAGATCGCATCT
194 GTTGCAGAGAGCAGATCGCATCT
* *
54504411 AGTCTTATCTCCCTGAAGTTGTAGTGGAGCAGACTAAGGAGGCAAGTCTTATCCTCCTAAAGTTG
1 AGTCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTAAGGAGGCAAGTCTTATCCTCCTGAAGTTG
* * *
54504476 CAGTGAGGCAGATTGAAGATGGCAAATCTTATTTCCCCGAAGTTGCAGTGGAGCAGATTAAAGCT
66 CAGTGAGGCAGACTGAAGATGGCAAATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAGC-
54504541 GATAATCCTATCTCCCTGAAGTTGCAGTGGAGCGGATTAAAACCTTAGATCTTATCTCTCTGAAG
130 GATAATCCTATCTCCCTGAAGTTGCAGTGGAGCGGATTAAAACCTTAGATCTTATCTCTCTGAAG
*
54504606 TTGCAGAGAACAGATCGCATCT
195 TTGCAGAGAGCAGATCGCATCT
* **
54504628 AGTC--ATC-CTCCTGAAGTTGCAGT-GAGACAGATCGAA-GATACAAGTCTTAT-CTCTCTGAA
1 AGTCTTATCTC-CCTGAAGTTGCAGTGGAG-CAGA-CTAAGGAGGCAAGTCTTATCCTC-CTGAA
54504687 GTTGCA
62 GTTGCA
54504693 ATGGAGTAGA
Statistics
Matches: 450, Mismatches: 40, Indels: 19
0.88 0.08 0.04
Matches are distributed among these distances:
214 7 0.02
215 42 0.09
216 145 0.32
217 256 0.57
ACGTcount: A:0.29, C:0.20, G:0.23, T:0.27
Consensus pattern (216 bp):
AGTCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTAAGGAGGCAAGTCTTATCCTCCTGAAGTTG
CAGTGAGGCAGACTGAAGATGGCAAATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAGCG
ATAATCCTATCTCCCTGAAGTTGCAGTGGAGCGGATTAAAACCTTAGATCTTATCTCTCTGAAGT
TGCAGAGAGCAGATCGCATCT
Found at i:54504562 original size:173 final size:173
Alignment explanation
Indices: 54504238--54504567 Score: 395
Period size: 173 Copynumber: 1.9 Consensus size: 173
54504228 TAAGTGGGCA
*
54504238 AGTCTTATCCTCCTGAAGTTGCAGTGAGGCAGACTAAAGATGGCAAATCTTATCTCCCTGAAGTT
1 AGTCTTATCCTCCTGAAGTTGCAGTGAGGCAGACTAAAGATGGCAAATCTTATCTCCCTAAAGTT
*** *
54504303 GCAGTGGAGCAGATTAAAGTCGACAATCCTATCTCTTTGAAGTTGCAGTGGAGCGGATTAAAATC
66 GCAGTGGAGCAGATTAAAGTCGACAATCCTATCTCCCCGAAGTTGCAGTGGAGCAGATTAAAATC
* *
54504368 ACAGATCTTATCTCTCTGAAGTTGCAGAGAGCAGATCGCATCT
131 ACAGATCCTATCTCCCTGAAGTTGCAGAGAGCAGATCGCATCT
* * *
54504411 AGTCTTAT-CTCCCTGAAGTTGTAGTG-GAGCAGACTAAGGA-GGCAAGTCTTATC-CTCCTAAA
1 AGTCTTATCCT-CCTGAAGTTGCAGTGAG-GCAGACTAAAGATGGCAAATCTTATCTC-CCTAAA
* * * *
54504472 GTTGCAGT-GAGGCAGATTGAAGAT-GGCAAATCTTATTTCCCCGAAGTTGCAGTGGAGCAGATT
63 GTTGCAGTGGA-GCAGATTAAAG-TCGAC-AATCCTATCTCCCCGAAGTTGCAGTGGAGCAGATT
* * *
54504535 AAAGCTGATA-ATCCTATCTCCCTGAAGTTGCAG
125 AAA-ATCACAGATCCTATCTCCCTGAAGTTGCAG
54504568 TGGAGCGGAT
Statistics
Matches: 133, Mismatches: 17, Indels: 14
0.81 0.10 0.09
Matches are distributed among these distances:
171 3 0.02
172 40 0.30
173 87 0.65
174 3 0.02
ACGTcount: A:0.28, C:0.20, G:0.24, T:0.28
Consensus pattern (173 bp):
AGTCTTATCCTCCTGAAGTTGCAGTGAGGCAGACTAAAGATGGCAAATCTTATCTCCCTAAAGTT
GCAGTGGAGCAGATTAAAGTCGACAATCCTATCTCCCCGAAGTTGCAGTGGAGCAGATTAAAATC
ACAGATCCTATCTCCCTGAAGTTGCAGAGAGCAGATCGCATCT
Found at i:54506489 original size:21 final size:22
Alignment explanation
Indices: 54506465--54506505 Score: 57
Period size: 22 Copynumber: 1.9 Consensus size: 22
54506455 GTTTTGTATG
54506465 TAAATATGT-TTTTTTTCTTCA
1 TAAATATGTCTTTTTTTCTTCA
* *
54506486 TAAATTTTTCTTTTTTTCTT
1 TAAATATGTCTTTTTTTCTT
54506506 ATTCCTTTCA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 7 0.41
22 10 0.59
ACGTcount: A:0.20, C:0.10, G:0.02, T:0.68
Consensus pattern (22 bp):
TAAATATGTCTTTTTTTCTTCA
Found at i:54507628 original size:42 final size:43
Alignment explanation
Indices: 54507542--54507634 Score: 109
Period size: 42 Copynumber: 2.2 Consensus size: 43
54507532 TATTTTAGGC
* * * * *
54507542 TTTT-TTTTCTAATTTAGATCTAAGGATTCAAATAGGTTGGAA
1 TTTTATTTTCTAATTTAGATATAAGGATTCAAAAAAGATAGAA
* *
54507584 TTTTATTTTCTAATTTA-ATATTAGGATTCAAAAAAGATATAA
1 TTTTATTTTCTAATTTAGATATAAGGATTCAAAAAAGATAGAA
54507626 TTTTATTTT
1 TTTTATTTT
54507635 ATTTTTTTCT
Statistics
Matches: 43, Mismatches: 7, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
42 31 0.72
43 12 0.28
ACGTcount: A:0.34, C:0.05, G:0.11, T:0.49
Consensus pattern (43 bp):
TTTTATTTTCTAATTTAGATATAAGGATTCAAAAAAGATAGAA
Found at i:54507704 original size:33 final size:33
Alignment explanation
Indices: 54507638--54507705 Score: 93
Period size: 33 Copynumber: 2.1 Consensus size: 33
54507628 TTATTTTATT
* *
54507638 TTTTTCTAATTTAGATCTTAGGATTTAGATAGG
1 TTTTTCTAATTTAGAACTTAGGATTCAGATAGG
*
54507671 TTTTTCTCATTTAGAACTTAGGATTCA-ATTAGG
1 TTTTTCTAATTTAGAACTTAGGATTCAGA-TAGG
54507704 TT
1 TT
54507706 AAAATTTATT
Statistics
Matches: 31, Mismatches: 3, Indels: 2
0.86 0.08 0.06
Matches are distributed among these distances:
32 1 0.03
33 30 0.97
ACGTcount: A:0.26, C:0.09, G:0.16, T:0.49
Consensus pattern (33 bp):
TTTTTCTAATTTAGAACTTAGGATTCAGATAGG
Found at i:54507719 original size:42 final size:43
Alignment explanation
Indices: 54507672--54507760 Score: 117
Period size: 42 Copynumber: 2.1 Consensus size: 43
54507662 TTAGATAGGT
* ** * *
54507672 TTTTCTCATTTAGAACTTAGGATTCAATTAGGTTA-AAATTTA
1 TTTTCTAATTTAGAACTTAACATTCAAATAGGCTAGAAATTTA
*
54507714 TTTTCTAATTTAGATCTTAACATTCAAATAGGCTAGAAATTTA
1 TTTTCTAATTTAGAACTTAACATTCAAATAGGCTAGAAATTTA
54507757 TTTT
1 TTTT
54507761 ATTTTAATAA
Statistics
Matches: 40, Mismatches: 6, Indels: 1
0.85 0.13 0.02
Matches are distributed among these distances:
42 29 0.73
43 11 0.28
ACGTcount: A:0.34, C:0.10, G:0.10, T:0.46
Consensus pattern (43 bp):
TTTTCTAATTTAGAACTTAACATTCAAATAGGCTAGAAATTTA
Found at i:54513378 original size:18 final size:17
Alignment explanation
Indices: 54513355--54513398 Score: 54
Period size: 18 Copynumber: 2.5 Consensus size: 17
54513345 AATTTATAAA
54513355 AAAATATTAA-AAATTATG
1 AAAATATTAATAAA--ATG
54513373 AAAATATATAATAAAATG
1 AAAATAT-TAATAAAATG
54513391 AAAATATT
1 AAAATATT
54513399 TAGATGTTGA
Statistics
Matches: 24, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
17 1 0.04
18 17 0.71
19 3 0.12
20 3 0.12
ACGTcount: A:0.64, C:0.00, G:0.05, T:0.32
Consensus pattern (17 bp):
AAAATATTAATAAAATG
Found at i:54517725 original size:19 final size:18
Alignment explanation
Indices: 54517701--54517738 Score: 67
Period size: 19 Copynumber: 2.1 Consensus size: 18
54517691 TGTACAATAT
54517701 AATTAAATAATATAAATTA
1 AATTAAATAAT-TAAATTA
54517720 AATTAAATAATTAAATTA
1 AATTAAATAATTAAATTA
54517738 A
1 A
54517739 CTGTTTACCC
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
18 8 0.42
19 11 0.58
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (18 bp):
AATTAAATAATTAAATTA
Found at i:54517736 original size:13 final size:14
Alignment explanation
Indices: 54517696--54517738 Score: 63
Period size: 13 Copynumber: 3.1 Consensus size: 14
54517686 CAAAATGTAC
54517696 AATATAATTAAA-T
1 AATATAATTAAATT
54517709 AATATAAATTAAATT
1 AATAT-AATTAAATT
54517724 AA-ATAATTAAATT
1 AATATAATTAAATT
54517737 AA
1 AA
54517739 CTGTTTACCC
Statistics
Matches: 28, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
13 16 0.57
14 9 0.32
15 3 0.11
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (14 bp):
AATATAATTAAATT
Found at i:54520043 original size:21 final size:20
Alignment explanation
Indices: 54520017--54520055 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
54520007 TTATTTTTAT
54520017 TTATATATAAGAAATATAAAA
1 TTATAT-TAAGAAATATAAAA
*
54520038 TTATATTTAGAAATATAA
1 TTATATTAAGAAATATAA
54520056 GCAACTCATT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 11 0.65
21 6 0.35
ACGTcount: A:0.56, C:0.00, G:0.05, T:0.38
Consensus pattern (20 bp):
TTATATTAAGAAATATAAAA
Found at i:54520571 original size:10 final size:10
Alignment explanation
Indices: 54520556--54520596 Score: 57
Period size: 10 Copynumber: 4.0 Consensus size: 10
54520546 ATGAAATTTT
54520556 TAAATAATAA
1 TAAATAATAA
54520566 TAAATAATAA
1 TAAATAATAA
54520576 -ATAATAAATAA
1 TA-AAT-AATAA
54520587 TAAATAATAA
1 TAAATAATAA
54520597 ATAATTATCA
Statistics
Matches: 28, Mismatches: 0, Indels: 6
0.82 0.00 0.18
Matches are distributed among these distances:
9 1 0.04
10 18 0.64
11 8 0.29
12 1 0.04
ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (10 bp):
TAAATAATAA
Found at i:54520619 original size:7 final size:7
Alignment explanation
Indices: 54520561--54520601 Score: 82
Period size: 7 Copynumber: 5.9 Consensus size: 7
54520551 ATTTTTAAAT
54520561 AATAATA
1 AATAATA
54520568 AATAATA
1 AATAATA
54520575 AATAATA
1 AATAATA
54520582 AATAATA
1 AATAATA
54520589 AATAATA
1 AATAATA
54520596 AATAAT
1 AATAAT
54520602 TATCATTATA
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 34 1.00
ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (7 bp):
AATAATA
Found at i:54522009 original size:9 final size:9
Alignment explanation
Indices: 54521997--54522119 Score: 76
Period size: 9 Copynumber: 13.6 Consensus size: 9
54521987 AAAAAAAGGT
54521997 TAAAAATTA
1 TAAAAATTA
54522006 T-AAAATTGA
1 TAAAAATT-A
*
54522015 TAGAAAATCA
1 TA-AAAATTA
54522025 TAAAAATTA
1 TAAAAATTA
* *
54522034 CAAATA-TA
1 TAAAAATTA
* *
54522042 TATAATTTA
1 TAAAAATTA
54522051 TTAAAAA-T-
1 -TAAAAATTA
54522059 TAAAAA-TA
1 TAAAAATTA
** *
54522067 TAGAAACGTG
1 TA-AAAATTA
54522077 TAAAAATTA
1 TAAAAATTA
*
54522086 TAAAAAGTA
1 TAAAAATTA
54522095 TAGAAAATTA
1 TA-AAAATTA
54522105 TAAAAATATA
1 TAAAAAT-TA
54522115 TAAAA
1 TAAAA
54522120 GTTTAAATTC
Statistics
Matches: 87, Mismatches: 17, Indels: 19
0.71 0.14 0.15
Matches are distributed among these distances:
7 7 0.08
8 12 0.14
9 38 0.44
10 25 0.29
11 5 0.06
ACGTcount: A:0.62, C:0.02, G:0.06, T:0.30
Consensus pattern (9 bp):
TAAAAATTA
Found at i:54522097 original size:28 final size:27
Alignment explanation
Indices: 54521997--54522119 Score: 92
Period size: 28 Copynumber: 4.5 Consensus size: 27
54521987 AAAAAAAGGT
*
54521997 TAAAAATTATAAAATTGATAGAAAA-TCA
1 TAAAAATTATAAAAAT-ATAGAAAAGT-A
* * * **
54522025 TAAAAATTACAAATATATA-TAATTTA
1 TAAAAATTATAAAAATATAGAAAAGTA
* *
54522051 TTAAAAA-T-TAAAAATATAGAAACGTG
1 -TAAAAATTATAAAAATATAGAAAAGTA
*
54522077 TAAAAATTATAAAAAGTATAGAAAATTA
1 TAAAAATTATAAAAA-TATAGAAAAGTA
54522105 TAAAAATATATAAAA
1 TAAAAAT-TATAAAA
54522120 GTTTAAATTC
Statistics
Matches: 74, Mismatches: 14, Indels: 13
0.73 0.14 0.13
Matches are distributed among these distances:
25 14 0.19
26 8 0.11
27 16 0.22
28 29 0.39
29 7 0.09
ACGTcount: A:0.62, C:0.02, G:0.06, T:0.30
Consensus pattern (27 bp):
TAAAAATTATAAAAATATAGAAAAGTA
Found at i:54522101 original size:10 final size:9
Alignment explanation
Indices: 54522059--54522126 Score: 50
Period size: 9 Copynumber: 7.4 Consensus size: 9
54522049 TATTAAAAAT
54522059 TAAAAA-TA
1 TAAAAAGTA
* *
54522067 TAGAAACGTG
1 TA-AAAAGTA
*
54522077 TAAAAATTA
1 TAAAAAGTA
54522086 TAAAAAGTA
1 TAAAAAGTA
*
54522095 TAGAAAATTA
1 TA-AAAAGTA
54522105 TAAAAA-TA
1 TAAAAAGTA
*
54522113 TATAAAAGTT
1 TA-AAAAGTA
54522123 TAAA
1 TAAA
54522127 TTCTTTTTAA
Statistics
Matches: 47, Mismatches: 8, Indels: 9
0.73 0.12 0.14
Matches are distributed among these distances:
8 6 0.13
9 27 0.57
10 14 0.30
ACGTcount: A:0.62, C:0.01, G:0.09, T:0.28
Consensus pattern (9 bp):
TAAAAAGTA
Found at i:54522126 original size:18 final size:19
Alignment explanation
Indices: 54522079--54522119 Score: 66
Period size: 19 Copynumber: 2.2 Consensus size: 19
54522069 GAAACGTGTA
54522079 AAAATTATAAAAAGTATAG
1 AAAATTATAAAAAGTATAG
*
54522098 AAAATTATAAAAA-TATAT
1 AAAATTATAAAAAGTATAG
54522116 AAAA
1 AAAA
54522120 GTTTAAATTC
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
18 8 0.38
19 13 0.62
ACGTcount: A:0.68, C:0.00, G:0.05, T:0.27
Consensus pattern (19 bp):
AAAATTATAAAAAGTATAG
Found at i:54522158 original size:22 final size:23
Alignment explanation
Indices: 54522121--54522166 Score: 85
Period size: 22 Copynumber: 2.0 Consensus size: 23
54522111 TATATAAAAG
54522121 TTTAAATTCTTTTTAATTTTATA
1 TTTAAATTCTTTTTAATTTTATA
54522144 TTTAAATT-TTTTTAATTTTATA
1 TTTAAATTCTTTTTAATTTTATA
54522166 T
1 T
54522167 AACCTTAATT
Statistics
Matches: 23, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
22 15 0.65
23 8 0.35
ACGTcount: A:0.30, C:0.02, G:0.00, T:0.67
Consensus pattern (23 bp):
TTTAAATTCTTTTTAATTTTATA
Found at i:54523079 original size:29 final size:29
Alignment explanation
Indices: 54523046--54523113 Score: 118
Period size: 29 Copynumber: 2.3 Consensus size: 29
54523036 TTAAGTGTTC
* *
54523046 TGAAAAAATAATTTTGACGAGATGGGTTT
1 TGAAAAAATAATTTTGACAAGATGAGTTT
54523075 TGAAAAAATAATTTTGACAAGATGAGTTT
1 TGAAAAAATAATTTTGACAAGATGAGTTT
54523104 TGAAAAAATA
1 TGAAAAAATA
54523114 TCCCAGGATT
Statistics
Matches: 37, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
29 37 1.00
ACGTcount: A:0.46, C:0.03, G:0.19, T:0.32
Consensus pattern (29 bp):
TGAAAAAATAATTTTGACAAGATGAGTTT
Found at i:54526652 original size:18 final size:17
Alignment explanation
Indices: 54526614--54526654 Score: 55
Period size: 17 Copynumber: 2.4 Consensus size: 17
54526604 ATAAAAAAAT
*
54526614 AAAAATAGAATGTAGAT
1 AAAAATAGAATGTAGAA
*
54526631 AAAAATAGAATTTAGGAA
1 AAAAATAGAATGTA-GAA
54526649 AAAAAT
1 AAAAAT
54526655 TATTAGAGAA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
17 13 0.62
18 8 0.38
ACGTcount: A:0.63, C:0.00, G:0.15, T:0.22
Consensus pattern (17 bp):
AAAAATAGAATGTAGAA
Found at i:54526679 original size:11 final size:11
Alignment explanation
Indices: 54526665--54526706 Score: 50
Period size: 11 Copynumber: 3.8 Consensus size: 11
54526655 TATTAGAGAA
54526665 TTTGAGAGATT
1 TTTGAGAGATT
54526676 TTTGAGAG-TT
1 TTTGAGAGATT
* *
54526686 GATTGAGAAATT
1 -TTTGAGAGATT
54526698 TTTGAGAGA
1 TTTGAGAGA
54526707 ATTGTGAGAA
Statistics
Matches: 25, Mismatches: 4, Indels: 4
0.76 0.12 0.12
Matches are distributed among these distances:
10 2 0.08
11 21 0.84
12 2 0.08
ACGTcount: A:0.31, C:0.00, G:0.29, T:0.40
Consensus pattern (11 bp):
TTTGAGAGATT
Found at i:54526714 original size:22 final size:22
Alignment explanation
Indices: 54526651--54526718 Score: 72
Period size: 22 Copynumber: 3.2 Consensus size: 22
54526641 TTTAGGAAAA
*
54526651 AAATTATT-AGAGAATT-TGAG
1 AAATTTTTGAGAGAATTGTGAG
*
54526671 AGATTTTTGAGAG--TTGATTGAG
1 AAATTTTTGAGAGAATTG--TGAG
54526693 AAATTTTTGAGAGAATTGTGAG
1 AAATTTTTGAGAGAATTGTGAG
54526715 AAAT
1 AAAT
54526719 GTGAGTGAGA
Statistics
Matches: 39, Mismatches: 3, Indels: 10
0.75 0.06 0.19
Matches are distributed among these distances:
19 2 0.05
20 6 0.15
21 4 0.10
22 24 0.62
24 3 0.08
ACGTcount: A:0.38, C:0.00, G:0.25, T:0.37
Consensus pattern (22 bp):
AAATTTTTGAGAGAATTGTGAG
Found at i:54527236 original size:27 final size:28
Alignment explanation
Indices: 54527195--54527247 Score: 74
Period size: 27 Copynumber: 1.9 Consensus size: 28
54527185 AGTATAATGA
54527195 TAAAATTATACTTT-ACCCCTTAAAGTT
1 TAAAATTATACTTTAACCCCTTAAAGTT
*
54527222 TAAAATT-TACTTTTAACCCTTTAAAG
1 TAAAATTATAC-TTTAACCCCTTAAAG
54527248 CAGTTTTCTG
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
26 3 0.13
27 10 0.43
28 10 0.43
ACGTcount: A:0.38, C:0.17, G:0.04, T:0.42
Consensus pattern (28 bp):
TAAAATTATACTTTAACCCCTTAAAGTT
Found at i:54527569 original size:23 final size:21
Alignment explanation
Indices: 54527537--54527578 Score: 57
Period size: 23 Copynumber: 1.9 Consensus size: 21
54527527 ATATGTTTAA
54527537 TATTAATATAATTATTTAAAATT
1 TATTAATAT-ATT-TTTAAAATT
*
54527560 TATTATTATATTTTTAAAA
1 TATTAATATATTTTTAAAA
54527579 ATATTTATAA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
21 7 0.39
22 3 0.17
23 8 0.44
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (21 bp):
TATTAATATATTTTTAAAATT
Found at i:54527671 original size:24 final size:25
Alignment explanation
Indices: 54527644--54527725 Score: 71
Period size: 30 Copynumber: 3.2 Consensus size: 25
54527634 ACCCTTAAAA
54527644 ATAA-ACATATATATAATTAATTTTAT
1 ATAATACATATATATAATTAA-TTT-T
54527670 AATAAATTACATATATATAATTAATTTT
1 -AT-AA-TACATATATATAATTAATTTT
* *
54527698 ATAATAAAT-TAT-TAACTTATTTTT
1 ATAATACATATATATAA-TTAATTTT
54527722 ATAA
1 ATAA
54527726 ACAAATTCAT
Statistics
Matches: 49, Mismatches: 2, Indels: 11
0.79 0.03 0.18
Matches are distributed among these distances:
23 3 0.06
24 14 0.29
25 4 0.08
26 2 0.04
27 4 0.08
28 3 0.06
29 3 0.06
30 16 0.33
ACGTcount: A:0.49, C:0.04, G:0.00, T:0.48
Consensus pattern (25 bp):
ATAATACATATATATAATTAATTTT
Found at i:54527677 original size:16 final size:16
Alignment explanation
Indices: 54527658--54527708 Score: 63
Period size: 16 Copynumber: 3.3 Consensus size: 16
54527648 ACATATATAT
54527658 AATTAATTTTATAATA
1 AATTAATTTTATAATA
*
54527674 AATTACA-TATAT-AT-
1 AATTA-ATTTTATAATA
54527688 AATTAATTTTATAATA
1 AATTAATTTTATAATA
54527704 AATTA
1 AATTA
54527709 TTAACTTATT
Statistics
Matches: 29, Mismatches: 2, Indels: 8
0.74 0.05 0.21
Matches are distributed among these distances:
13 1 0.03
14 9 0.31
15 4 0.14
16 14 0.48
17 1 0.03
ACGTcount: A:0.51, C:0.02, G:0.00, T:0.47
Consensus pattern (16 bp):
AATTAATTTTATAATA
Found at i:54527683 original size:30 final size:30
Alignment explanation
Indices: 54527648--54527708 Score: 122
Period size: 30 Copynumber: 2.0 Consensus size: 30
54527638 TTAAAAATAA
54527648 ACATATATATAATTAATTTTATAATAAATT
1 ACATATATATAATTAATTTTATAATAAATT
54527678 ACATATATATAATTAATTTTATAATAAATT
1 ACATATATATAATTAATTTTATAATAAATT
54527708 A
1 A
54527709 TTAACTTATT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 31 1.00
ACGTcount: A:0.51, C:0.03, G:0.00, T:0.46
Consensus pattern (30 bp):
ACATATATATAATTAATTTTATAATAAATT
Found at i:54527700 original size:14 final size:14
Alignment explanation
Indices: 54527653--54527700 Score: 53
Period size: 14 Copynumber: 3.3 Consensus size: 14
54527643 AATAAACATA
54527653 TATATAATTAATTT
1 TATATAATTAATTT
*
54527667 TATAATAAATTACA-TA
1 TAT-AT-AATTA-ATTT
54527683 TATATAATTAATTT
1 TATATAATTAATTT
54527697 TATA
1 TATA
54527701 ATAAATTATT
Statistics
Matches: 28, Mismatches: 2, Indels: 8
0.74 0.05 0.21
Matches are distributed among these distances:
13 1 0.04
14 13 0.46
15 4 0.14
16 9 0.32
17 1 0.04
ACGTcount: A:0.48, C:0.02, G:0.00, T:0.50
Consensus pattern (14 bp):
TATATAATTAATTT
Found at i:54530393 original size:5 final size:5
Alignment explanation
Indices: 54530383--54530410 Score: 56
Period size: 5 Copynumber: 5.6 Consensus size: 5
54530373 CTGAATATAC
54530383 AAAGA AAAGA AAAGA AAAGA AAAGA AAA
1 AAAGA AAAGA AAAGA AAAGA AAAGA AAA
54530411 AGCTAGCTAG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 23 1.00
ACGTcount: A:0.82, C:0.00, G:0.18, T:0.00
Consensus pattern (5 bp):
AAAGA
Found at i:54535513 original size:20 final size:18
Alignment explanation
Indices: 54535488--54535530 Score: 52
Period size: 17 Copynumber: 2.3 Consensus size: 18
54535478 TAATACATCA
54535488 AATAATTAATACATATTACC
1 AATAATTAATACA-ATT-CC
*
54535508 AATAA-TAATTCAATTCC
1 AATAATTAATACAATTCC
54535525 AATAAT
1 AATAAT
54535531 AAAACACACA
Statistics
Matches: 21, Mismatches: 1, Indels: 4
0.81 0.04 0.15
Matches are distributed among these distances:
17 7 0.33
18 3 0.14
19 6 0.29
20 5 0.24
ACGTcount: A:0.51, C:0.14, G:0.00, T:0.35
Consensus pattern (18 bp):
AATAATTAATACAATTCC
Found at i:54541888 original size:3 final size:3
Alignment explanation
Indices: 54541880--54541919 Score: 80
Period size: 3 Copynumber: 13.3 Consensus size: 3
54541870 CCTCTGAAAT
54541880 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC T
1 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC T
54541920 CTTTCCGTGA
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 37 1.00
ACGTcount: A:0.00, C:0.33, G:0.00, T:0.68
Consensus pattern (3 bp):
TTC
Found at i:54545370 original size:25 final size:25
Alignment explanation
Indices: 54545324--54545371 Score: 60
Period size: 25 Copynumber: 1.9 Consensus size: 25
54545314 AATTTAGCCA
* * * *
54545324 TTTTTATTTTATTTTTATATTTTTC
1 TTTTAATTTAATTTTCACATTTTTC
54545349 TTTTAATTTAATTTTCACATTTT
1 TTTTAATTTAATTTTCACATTTT
54545372 AATTTTTTGT
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
25 19 1.00
ACGTcount: A:0.21, C:0.06, G:0.00, T:0.73
Consensus pattern (25 bp):
TTTTAATTTAATTTTCACATTTTTC
Found at i:54548451 original size:94 final size:94
Alignment explanation
Indices: 54548229--54548452 Score: 234
Period size: 94 Copynumber: 2.4 Consensus size: 94
54548219 GTTTTTAACC
* * * *
54548229 CACACGGCCTGGACACACGGGTGTGTCCTAGGCCATGTGCACAAAGGAGTGTTCTACAGTGAGTC
1 CACACGGCCTGGACACACGGGCGTGTCCTAGGTCGTATGCACAAAGGAGTGTTCTACAGTGAGTC
* **
54548294 ACATGGCCTGGCGACACGACAGTGTAGCA
66 ACACGGCCTGAAGACACGACAGTGTAGCA
* * * * * * *
54548323 CACATGGCCTGGACGCACGGGCTTGTCATAGGTCGTATGCACAAGGGAGTGTTCTGCAGTGAGTT
1 CACACGGCCTGGACACACGGGCGTGTCCTAGGTCGTATGCACAAAGGAGTGTTCTACAGTGAGTC
** * **
54548388 ACACGGTGTGAAGACATGACCA-TGTAGGT
66 ACACGGCCTGAAGACACGA-CAGTGTAGCA
* * *
54548417 CACACGGCCTAGACACACAGGCGTGTCCTTGGTCGT
1 CACACGGCCTGGACACACGGGCGTGTCCTAGGTCGT
54548453 GTGAGTCTTG
Statistics
Matches: 103, Mismatches: 26, Indels: 2
0.79 0.20 0.02
Matches are distributed among these distances:
94 101 0.98
95 2 0.02
ACGTcount: A:0.23, C:0.25, G:0.31, T:0.21
Consensus pattern (94 bp):
CACACGGCCTGGACACACGGGCGTGTCCTAGGTCGTATGCACAAAGGAGTGTTCTACAGTGAGTC
ACACGGCCTGAAGACACGACAGTGTAGCA
Found at i:54551905 original size:25 final size:27
Alignment explanation
Indices: 54551876--54551939 Score: 82
Period size: 25 Copynumber: 2.4 Consensus size: 27
54551866 TATATTTGTT
54551876 TTTTTATACATATAA-TTAATTT-TATA
1 TTTTTATA-ATATAAGTTAATTTATATA
54551902 TTTTTATAA-A-AAGTTAATTTATATA
1 TTTTTATAATATAAGTTAATTTATATA
54551927 TTTTTATATATAT
1 TTTTTATA-ATAT
54551940 GTATGAATAA
Statistics
Matches: 33, Mismatches: 0, Indels: 8
0.80 0.00 0.20
Matches are distributed among these distances:
23 2 0.06
24 8 0.24
25 13 0.39
26 9 0.27
27 1 0.03
ACGTcount: A:0.39, C:0.02, G:0.02, T:0.58
Consensus pattern (27 bp):
TTTTTATAATATAAGTTAATTTATATA
Found at i:54551977 original size:25 final size:24
Alignment explanation
Indices: 54551922--54551970 Score: 71
Period size: 25 Copynumber: 2.0 Consensus size: 24
54551912 AAGTTAATTT
54551922 ATATATTTTTATATATATGTATGA
1 ATATATTTTTATATATATGTATGA
*
54551946 ATAATATTTTTTTACTATATGTATG
1 AT-ATATTTTTATA-TATATGTATG
54551971 TGTATATAAT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
24 2 0.09
25 10 0.45
26 10 0.45
ACGTcount: A:0.35, C:0.02, G:0.08, T:0.55
Consensus pattern (24 bp):
ATATATTTTTATATATATGTATGA
Found at i:54564524 original size:44 final size:44
Alignment explanation
Indices: 54564411--54564878 Score: 220
Period size: 44 Copynumber: 10.7 Consensus size: 44
54564401 AGTAAGTAGG
* * * **
54564411 TCTTATCCCCCTGAAGTTGTAGTGG-GACAGATCGAAGATGGCA-AA
1 TCTTATCTCCCTGAAGTTGCAGTGGAG-CAGATTGAA-ACCG-ATAA
*
54564456 TCTTATCTCCCTGAGGTTGCAGTGGAGCAGATTGAAACCGATAA
1 TCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTGAAACCGATAA
* * * ***
54564500 TCTGATCTCCTTGAAGTTGTAGTGGAGCAGATT-AAATTAATAGA
1 TCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTGAAACCGATA-A
* * ** * * *
54564544 TCTTATCTCTCTGAAGTTGCAGTAGAGTGGATCGCAA-C-A-AG
1 TCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTGAAACCGATAA
* * *
54564585 TCTTATCTCCCTGAGGTTGCAGTGGAGTAGATTGAAGCCGATAA
1 TCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTGAAACCGATAA
* * * * *** *
54564629 TCCTATCTCCCTGAAGTTGTAGTGAAGCGGATT-AAAGTAATGGA
1 TCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTGAAACCGAT-AA
* * *
54564673 TCTTATCTCTCTGAAGTTGCAGT--AG-AG--TG-AATCGCATCAGG
1 TCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTGAAACCG-AT-A-A
* * * * **
54564714 TCTTATCTCCCTGAGGTTGCAGCGGAGCAGACTGAGTAAGC-A-GG
1 TCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTGA--AACCGATAA
* * *
54564758 TCTTATCCCCCTGAAGTTGCAGT-GAGACAGATCGAAGACC-ACAAA
1 TCTTATCTCCCTGAAGTTGCAGTGGAG-CAGATTGAA-ACCGA-TAA
* * *
54564803 TCTTATCTCCATGAAGTTACAGTGGAGCAGATT-AAGA-CGATGGA
1 TCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTGAA-ACCGAT-AA
* * *
54564847 TCTCATC-CCTCTGAAGTTGTAGTAGAGCAGAT
1 TCTTATCTCC-CTGAAGTTGCAGTGGAGCAGAT
54564879 CACATCAGAC
Statistics
Matches: 319, Mismatches: 77, Indels: 55
0.71 0.17 0.12
Matches are distributed among these distances:
39 3 0.01
40 2 0.01
41 51 0.16
42 5 0.02
43 24 0.08
44 167 0.52
45 57 0.18
46 6 0.02
47 1 0.00
49 3 0.01
ACGTcount: A:0.28, C:0.19, G:0.25, T:0.28
Consensus pattern (44 bp):
TCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTGAAACCGATAA
Found at i:54564645 original size:129 final size:129
Alignment explanation
Indices: 54564456--54564744 Score: 463
Period size: 129 Copynumber: 2.2 Consensus size: 129
54564446 AGATGGCAAA
*
54564456 TCTTATCTCCCTGAGGTTGCAGTGGAGCAGATTGAAACCGATAATCTGATCTCCTTGAAGTTGTA
1 TCTTATCTCCCTGAGGTTGCAGTGGAGCAGATTGAAACCGATAATCTGATCTCCCTGAAGTTGTA
* * *
54564521 GTGGAGCAGATTAAATTAATAGATCTTATCTCTCTGAAGTTGCAGTAGAGTGGATCGCAACAAG
66 GTGAAGCAGATTAAAGTAATAGATCTTATCTCTCTGAAGTTGCAGTAGAGTGAATCGCAACAAG
* *
54564585 TCTTATCTCCCTGAGGTTGCAGTGGAGTAGATTGAAGCCGATAATCCT-ATCTCCCTGAAGTTGT
1 TCTTATCTCCCTGAGGTTGCAGTGGAGCAGATTGAAACCGATAAT-CTGATCTCCCTGAAGTTGT
* * * *
54564649 AGTGAAGCGGATTAAAGTAATGGATCTTATCTCTCTGAAGTTGCAGTAGAGTGAATCGCATCAGG
65 AGTGAAGCAGATTAAAGTAATAGATCTTATCTCTCTGAAGTTGCAGTAGAGTGAATCGCAACAAG
*
54564714 TCTTATCTCCCTGAGGTTGCAGCGGAGCAGA
1 TCTTATCTCCCTGAGGTTGCAGTGGAGCAGA
54564745 CTGAGTAAGC
Statistics
Matches: 147, Mismatches: 12, Indels: 2
0.91 0.07 0.01
Matches are distributed among these distances:
129 145 0.99
130 2 0.01
ACGTcount: A:0.27, C:0.18, G:0.25, T:0.30
Consensus pattern (129 bp):
TCTTATCTCCCTGAGGTTGCAGTGGAGCAGATTGAAACCGATAATCTGATCTCCCTGAAGTTGTA
GTGAAGCAGATTAAAGTAATAGATCTTATCTCTCTGAAGTTGCAGTAGAGTGAATCGCAACAAG
Found at i:54564770 original size:129 final size:129
Alignment explanation
Indices: 54564456--54564782 Score: 428
Period size: 129 Copynumber: 2.5 Consensus size: 129
54564446 AGATGGCAAA
* * *
54564456 TCTTATCTCCCTGAGGTTGCAGTGGAGCAGATTGA-AACCGATAATCTGATCTCCTTGAAGTTGT
1 TCTTATCTCCCTGAGGTTGCAGTGGAGCAGA-TGAGAAGCGATAATCTTATCTCCCTGAAGTTGT
* * *
54564520 AGTGGAGCAGATTAAATTAATAGATCTTATCTCTCTGAAGTTGCAGTAGAGTGGATCGCAACAAG
65 AGTGAAGCAGATTAAAGTAATAGATCTTATCTCTCTGAAGTTGCAGTAGAGTGAATCGCAACAAG
* * *
54564585 TCTTATCTCCCTGAGGTTGCAGTGGAGTAGAT-TGAAGCCGATAATCCTATCTCCCTGAAGTTGT
1 TCTTATCTCCCTGAGGTTGCAGTGGAGCAGATGAGAAG-CGATAATCTTATCTCCCTGAAGTTGT
* * * *
54564649 AGTGAAGCGGATTAAAGTAATGGATCTTATCTCTCTGAAGTTGCAGTAGAGTGAATCGCATCAGG
65 AGTGAAGCAGATTAAAGTAATAGATCTTATCTCTCTGAAGTTGCAGTAGAGTGAATCGCAACAAG
* ** *
54564714 TCTTATCTCCCTGAGGTTGCAGCGGAGCAGACTGAGTAAGC-A-GGTCTTATCCCCCTGAAGTTG
1 TCTTATCTCCCTGAGGTTGCAGTGGAGCAGA-TGAG-AAGCGATAATCTTATCTCCCTGAAGTTG
*
54564777 CAGTGA
64 TAGTGA
54564783 GACAGATCGA
Statistics
Matches: 172, Mismatches: 21, Indels: 10
0.85 0.10 0.05
Matches are distributed among these distances:
128 3 0.02
129 162 0.94
130 2 0.01
131 2 0.01
132 3 0.02
ACGTcount: A:0.26, C:0.19, G:0.25, T:0.29
Consensus pattern (129 bp):
TCTTATCTCCCTGAGGTTGCAGTGGAGCAGATGAGAAGCGATAATCTTATCTCCCTGAAGTTGTA
GTGAAGCAGATTAAAGTAATAGATCTTATCTCTCTGAAGTTGCAGTAGAGTGAATCGCAACAAG
Found at i:54565036 original size:44 final size:45
Alignment explanation
Indices: 54564931--54565082 Score: 130
Period size: 44 Copynumber: 3.4 Consensus size: 45
54564921 GCTACAATCC
* * *
54564931 CCCTGAAGTTACAGTGG-GACAGATTGAAGATGGCAAATCTTATCT
1 CCCTGAAGTTGCAGTGGAG-CAGATTGAAGACGACAAATCTTATCT
* * * * *
54564976 CCCTGAGGTTGTAGTGGAGCAGATTGAAGCCGATAATTC-TATCT
1 CCCTGAAGTTGCAGTGGAGCAGATTGAAGACGACAAATCTTATCT
** * * *
54565020 CCCTGAAGTTGCAGTGGAGCAGACAGAAGA-AACCAATCCTATCT
1 CCCTGAAGTTGCAGTGGAGCAGATTGAAGACGACAAATCTTATCT
* * *
54565064 CCCTAAAGTTACAATGGAG
1 CCCTGAAGTTGCAGTGGAG
54565083 TGGATTAAAA
Statistics
Matches: 85, Mismatches: 20, Indels: 5
0.77 0.18 0.05
Matches are distributed among these distances:
43 4 0.05
44 51 0.60
45 29 0.34
46 1 0.01
ACGTcount: A:0.31, C:0.20, G:0.24, T:0.24
Consensus pattern (45 bp):
CCCTGAAGTTGCAGTGGAGCAGATTGAAGACGACAAATCTTATCT
Found at i:54566669 original size:25 final size:27
Alignment explanation
Indices: 54566640--54566703 Score: 82
Period size: 25 Copynumber: 2.4 Consensus size: 27
54566630 TATATTTGTT
54566640 TTTTTATACATATAA-TTAATTT-TATA
1 TTTTTATA-ATATAAGTTAATTTATATA
54566666 TTTTTATAA-A-AAGTTAATTTATATA
1 TTTTTATAATATAAGTTAATTTATATA
54566691 TTTTTATATATAT
1 TTTTTATA-ATAT
54566704 GTATGAATAA
Statistics
Matches: 33, Mismatches: 0, Indels: 8
0.80 0.00 0.20
Matches are distributed among these distances:
23 2 0.06
24 8 0.24
25 13 0.39
26 9 0.27
27 1 0.03
ACGTcount: A:0.39, C:0.02, G:0.02, T:0.58
Consensus pattern (27 bp):
TTTTTATAATATAAGTTAATTTATATA
Found at i:54566737 original size:30 final size:27
Alignment explanation
Indices: 54566686--54566745 Score: 68
Period size: 30 Copynumber: 2.1 Consensus size: 27
54566676 AAGTTAATTT
54566686 ATATATTTTTATATATATGTATGA-ATA
1 ATATATTTTTATATATATGTAT-ATATA
*
54566713 ATATTTTTTTACTATACGTATGTATATATA
1 ATATATTTTTA-TATA--TATGTATATATA
54566743 ATA
1 ATA
54566746 ATACATTATT
Statistics
Matches: 28, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
27 10 0.36
28 4 0.14
29 1 0.04
30 13 0.46
ACGTcount: A:0.38, C:0.03, G:0.07, T:0.52
Consensus pattern (27 bp):
ATATATTTTTATATATATGTATATATA
Found at i:54568251 original size:29 final size:29
Alignment explanation
Indices: 54568207--54568385 Score: 211
Period size: 29 Copynumber: 6.2 Consensus size: 29
54568197 GAGGTCTCGA
54568207 GCCACTGGTTTTCCAAATTTTACAATTTT
1 GCCACTGGTTTTCCAAATTTTACAATTTT
* * * *
54568236 GTCACTGATTTTCCAAATTTTATAGTTTT
1 GCCACTGGTTTTCCAAATTTTACAATTTT
* * *
54568265 GCCACT-GTTATTCCAGATTTT-CAGTTCT
1 GCCACTGGTT-TTCCAAATTTTACAATTTT
*
54568293 GCCACTGGTTTTCCAAATTTTACAATTCT
1 GCCACTGGTTTTCCAAATTTTACAATTTT
* *
54568322 ACCACT-GTTATTCCAGATTTTACAATTTT
1 GCCACTGGTT-TTCCAAATTTTACAATTTT
* *
54568351 GCCACTGGTTTTCCAGATTTTACAGTTTT
1 GCCACTGGTTTTCCAAATTTTACAATTTT
54568380 GCCACT
1 GCCACT
54568386 CTTCTTCAAA
Statistics
Matches: 129, Mismatches: 16, Indels: 10
0.83 0.10 0.06
Matches are distributed among these distances:
28 26 0.20
29 100 0.78
30 3 0.02
ACGTcount: A:0.22, C:0.22, G:0.12, T:0.44
Consensus pattern (29 bp):
GCCACTGGTTTTCCAAATTTTACAATTTT
Found at i:54568352 original size:86 final size:87
Alignment explanation
Indices: 54568207--54568385 Score: 256
Period size: 86 Copynumber: 2.1 Consensus size: 87
54568197 GAGGTCTCGA
* ** * *
54568207 GCCACTGGTTTTCCAAATTTTACAATTTTGTCACTGATTTTCCAAATTTTATAGTTTTGCCACT-
1 GCCACTGGTTTTCCAAATTTTACAATTCTACCACTGATTTTCCAAATTTTACAATTTTGCCACTG
54568271 GTTATTCCAGATTTT-CAGTTCT
66 GTT-TTCCAGATTTTACAGTTCT
*
54568293 GCCACTGGTTTTCCAAATTTTACAATTCTACCACTG-TTATTCCAGATTTTACAATTTTGCCACT
1 GCCACTGGTTTTCCAAATTTTACAATTCTACCACTGATT-TTCCAAATTTTACAATTTTGCCACT
*
54568357 GGTTTTCCAGATTTTACAGTTTT
65 GGTTTTCCAGATTTTACAGTTCT
54568380 GCCACT
1 GCCACT
54568386 CTTCTTCAAA
Statistics
Matches: 83, Mismatches: 7, Indels: 5
0.87 0.07 0.05
Matches are distributed among these distances:
85 2 0.02
86 66 0.80
87 15 0.18
ACGTcount: A:0.22, C:0.22, G:0.12, T:0.44
Consensus pattern (87 bp):
GCCACTGGTTTTCCAAATTTTACAATTCTACCACTGATTTTCCAAATTTTACAATTTTGCCACTG
GTTTTCCAGATTTTACAGTTCT
Found at i:54571677 original size:12 final size:12
Alignment explanation
Indices: 54571660--54571685 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
54571650 TTCATGAATC
54571660 AAATTACATATT
1 AAATTACATATT
54571672 AAATTACATATT
1 AAATTACATATT
54571684 AA
1 AA
54571686 CTTTAAAAGG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.54, C:0.08, G:0.00, T:0.38
Consensus pattern (12 bp):
AAATTACATATT
Found at i:54571874 original size:19 final size:19
Alignment explanation
Indices: 54571852--54571898 Score: 53
Period size: 19 Copynumber: 2.5 Consensus size: 19
54571842 TAAAATTCAT
54571852 ATTTATTTATTGGA-TATA
1 ATTTATTTATTGGAGTATA
*
54571870 GATTTATGTA-TGGAGTATA
1 -ATTTATTTATTGGAGTATA
*
54571889 ATTTTTTTAT
1 ATTTATTTAT
54571899 AAAACATTTG
Statistics
Matches: 23, Mismatches: 3, Indels: 4
0.77 0.10 0.13
Matches are distributed among these distances:
18 11 0.48
19 12 0.52
ACGTcount: A:0.30, C:0.00, G:0.15, T:0.55
Consensus pattern (19 bp):
ATTTATTTATTGGAGTATA
Found at i:54572150 original size:18 final size:20
Alignment explanation
Indices: 54572113--54572150 Score: 53
Period size: 20 Copynumber: 2.0 Consensus size: 20
54572103 AAAGAGCTCA
*
54572113 TTTTATAAATAATTTTATTT
1 TTTTATAAATAATTTAATTT
54572133 TTTTATAAA-AA-TTAATTT
1 TTTTATAAATAATTTAATTT
54572151 GAATAAAGTC
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
18 6 0.35
19 2 0.12
20 9 0.53
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (20 bp):
TTTTATAAATAATTTAATTT
Found at i:54572332 original size:14 final size:14
Alignment explanation
Indices: 54572294--54572322 Score: 51
Period size: 13 Copynumber: 2.1 Consensus size: 14
54572284 TAATAACATA
54572294 ATAAATTA-TTAAT
1 ATAAATTATTTAAT
54572307 ATAAATTATTTAAT
1 ATAAATTATTTAAT
54572321 AT
1 AT
54572323 TATATTTTTA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 8 0.53
14 7 0.47
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (14 bp):
ATAAATTATTTAAT
Found at i:54573334 original size:20 final size:20
Alignment explanation
Indices: 54573309--54573358 Score: 70
Period size: 17 Copynumber: 2.6 Consensus size: 20
54573299 TGGCTTAAAA
54573309 TTGGTAGTGGATTGTTGTTG
1 TTGGTAGTGGATTGTTGTTG
54573329 TTGGTAGTGG---GTTGTTG
1 TTGGTAGTGGATTGTTGTTG
*
54573346 GTGGTAGTGGATT
1 TTGGTAGTGGATT
54573359 AGTGGATGGT
Statistics
Matches: 26, Mismatches: 1, Indels: 6
0.79 0.03 0.18
Matches are distributed among these distances:
17 16 0.62
20 10 0.38
ACGTcount: A:0.10, C:0.00, G:0.44, T:0.46
Consensus pattern (20 bp):
TTGGTAGTGGATTGTTGTTG
Found at i:54577973 original size:20 final size:20
Alignment explanation
Indices: 54577948--54577997 Score: 70
Period size: 17 Copynumber: 2.6 Consensus size: 20
54577938 TGGCTTAAAA
54577948 TTGGTAGTGGATTGTTGTTG
1 TTGGTAGTGGATTGTTGTTG
54577968 TTGGTAGTGG---GTTGTTG
1 TTGGTAGTGGATTGTTGTTG
*
54577985 GTGGTAGTGGATT
1 TTGGTAGTGGATT
54577998 AGTGGATGGT
Statistics
Matches: 26, Mismatches: 1, Indels: 6
0.79 0.03 0.18
Matches are distributed among these distances:
17 16 0.62
20 10 0.38
ACGTcount: A:0.10, C:0.00, G:0.44, T:0.46
Consensus pattern (20 bp):
TTGGTAGTGGATTGTTGTTG
Found at i:54580548 original size:23 final size:22
Alignment explanation
Indices: 54580512--54580574 Score: 65
Period size: 23 Copynumber: 2.8 Consensus size: 22
54580502 AAATTATATA
54580512 CAAT-TATATGAAATTAAAAAATT
1 CAATATATAT-AAATTAAAAAA-T
54580535 CAATATATATAAATTTAAAAAAT
1 CAATATATATAAA-TTAAAAAAT
* * *
54580558 AAAAATATTTAAATTAA
1 CAATATATATAAATTAA
54580575 GAATGGATCA
Statistics
Matches: 35, Mismatches: 3, Indels: 5
0.81 0.07 0.12
Matches are distributed among these distances:
22 4 0.11
23 18 0.51
24 13 0.37
ACGTcount: A:0.60, C:0.03, G:0.02, T:0.35
Consensus pattern (22 bp):
CAATATATATAAATTAAAAAAT
Found at i:54580552 original size:24 final size:23
Alignment explanation
Indices: 54580512--54580557 Score: 67
Period size: 24 Copynumber: 2.0 Consensus size: 23
54580502 AAATTATATA
54580512 CAATTATATGAAATTAAAAAATT
1 CAATTATATGAAATTAAAAAATT
54580535 CAATATATAT-AAATTTAAAAAAT
1 CAAT-TATATGAAA-TTAAAAAAT
54580558 AAAAATATTT
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
23 7 0.33
24 14 0.67
ACGTcount: A:0.59, C:0.04, G:0.02, T:0.35
Consensus pattern (23 bp):
CAATTATATGAAATTAAAAAATT
Found at i:54580847 original size:21 final size:21
Alignment explanation
Indices: 54580823--54580864 Score: 68
Period size: 21 Copynumber: 2.0 Consensus size: 21
54580813 ATTTTTTCTA
54580823 AAGTTAAAA-GTCAAAACTATT
1 AAGTTAAAAGGT-AAAACTATT
54580844 AAGTTAAAAGGTAAAACTATT
1 AAGTTAAAAGGTAAAACTATT
54580865 TCGTTTTGAT
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
21 18 0.90
22 2 0.10
ACGTcount: A:0.52, C:0.07, G:0.12, T:0.29
Consensus pattern (21 bp):
AAGTTAAAAGGTAAAACTATT
Found at i:54585430 original size:23 final size:22
Alignment explanation
Indices: 54585378--54585430 Score: 56
Period size: 23 Copynumber: 2.4 Consensus size: 22
54585368 TCCACGTCTT
*
54585378 TTTCTTTTGTTTCTTTTTCTAA
1 TTTCTTTTCTTTCTTTTTCTAA
54585400 -TTCATTTTCTCTTCTTTCTTC-AA
1 TTTC-TTTTCT-TTCTTT-TTCTAA
54585423 TTTCTTTT
1 TTTCTTTT
54585431 TCACTCTCAA
Statistics
Matches: 26, Mismatches: 1, Indels: 7
0.76 0.03 0.21
Matches are distributed among these distances:
21 3 0.12
22 5 0.19
23 12 0.46
24 6 0.23
ACGTcount: A:0.09, C:0.19, G:0.02, T:0.70
Consensus pattern (22 bp):
TTTCTTTTCTTTCTTTTTCTAA
Found at i:54596470 original size:20 final size:22
Alignment explanation
Indices: 54596435--54596478 Score: 74
Period size: 20 Copynumber: 2.1 Consensus size: 22
54596425 AATTATATCA
54596435 TTGATATTTATATTTTTTAAAT
1 TTGATATTTATATTTTTTAAAT
54596457 TTGATA-TT-TATTTTTTAAAT
1 TTGATATTTATATTTTTTAAAT
54596477 TT
1 TT
54596479 TAAAAATATA
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
20 14 0.64
21 2 0.09
22 6 0.27
ACGTcount: A:0.30, C:0.00, G:0.05, T:0.66
Consensus pattern (22 bp):
TTGATATTTATATTTTTTAAAT
Found at i:54598016 original size:73 final size:73
Alignment explanation
Indices: 54597934--54598119 Score: 363
Period size: 73 Copynumber: 2.5 Consensus size: 73
54597924 TATTATTATT
*
54597934 TGGATGTAATGATGTAACTTAGTTGTATTCCAACTAAGTTTGTTAGTGGTAGTAGGTGGTGATTT
1 TGGATGTAATGATGAAACTTAGTTGTATTCCAACTAAGTTTGTTAGTGGTAGTAGGTGGTGATTT
54597999 ATTTTAAG
66 ATTTTAAG
54598007 TGGATGTAATGATGAAACTTAGTTGTATTCCAACTAAGTTTGTTAGTGGTAGTAGGTGGTGATTT
1 TGGATGTAATGATGAAACTTAGTTGTATTCCAACTAAGTTTGTTAGTGGTAGTAGGTGGTGATTT
54598072 ATTTTAAG
66 ATTTTAAG
54598080 TGGATGTAATGATGAAACTTAGTTGTATTCCAACTAAGTT
1 TGGATGTAATGATGAAACTTAGTTGTATTCCAACTAAGTT
54598120 GTCAAGTTGT
Statistics
Matches: 112, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
73 112 1.00
ACGTcount: A:0.28, C:0.06, G:0.25, T:0.41
Consensus pattern (73 bp):
TGGATGTAATGATGAAACTTAGTTGTATTCCAACTAAGTTTGTTAGTGGTAGTAGGTGGTGATTT
ATTTTAAG
Found at i:54613207 original size:22 final size:22
Alignment explanation
Indices: 54613162--54613207 Score: 56
Period size: 22 Copynumber: 2.1 Consensus size: 22
54613152 ACTGATCGAC
* **
54613162 ATGTTGCAACACGGGGAGTTGA
1 ATGTTGCAACACAGGGAGCAGA
*
54613184 ATGTTGCAACATAGGGAGCAGA
1 ATGTTGCAACACAGGGAGCAGA
54613206 AT
1 AT
54613208 AGCATAATTT
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.33, C:0.13, G:0.33, T:0.22
Consensus pattern (22 bp):
ATGTTGCAACACAGGGAGCAGA
Found at i:54615371 original size:31 final size:31
Alignment explanation
Indices: 54615336--54615397 Score: 99
Period size: 31 Copynumber: 2.0 Consensus size: 31
54615326 TATATGGAGG
*
54615336 AGACAAACCTCTCTTCTACT-ATATTAACAAT
1 AGACAAACCTCTCTTCCACTGA-ATTAACAAT
54615367 AGACAAACCTCTCTTCCACTGAATTAACAAT
1 AGACAAACCTCTCTTCCACTGAATTAACAAT
54615398 CCCACTGAGG
Statistics
Matches: 29, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
31 28 0.97
32 1 0.03
ACGTcount: A:0.39, C:0.27, G:0.05, T:0.29
Consensus pattern (31 bp):
AGACAAACCTCTCTTCCACTGAATTAACAAT
Found at i:54619584 original size:20 final size:20
Alignment explanation
Indices: 54619559--54619599 Score: 82
Period size: 20 Copynumber: 2.0 Consensus size: 20
54619549 AAGTTTGTTT
54619559 TATTTTTTCTTTCTCTGATA
1 TATTTTTTCTTTCTCTGATA
54619579 TATTTTTTCTTTCTCTGATA
1 TATTTTTTCTTTCTCTGATA
54619599 T
1 T
54619600 CCCAGTAGTG
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.15, C:0.15, G:0.05, T:0.66
Consensus pattern (20 bp):
TATTTTTTCTTTCTCTGATA
Found at i:54620731 original size:12 final size:12
Alignment explanation
Indices: 54620714--54620739 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
54620704 TTTCCGTAAT
54620714 TTCTTTCTTACA
1 TTCTTTCTTACA
54620726 TTCTTTCTTACA
1 TTCTTTCTTACA
54620738 TT
1 TT
54620740 TGTATTTATC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.15, C:0.23, G:0.00, T:0.62
Consensus pattern (12 bp):
TTCTTTCTTACA
Found at i:54622815 original size:9 final size:9
Alignment explanation
Indices: 54622801--54622835 Score: 61
Period size: 9 Copynumber: 3.9 Consensus size: 9
54622791 TTGCAAAAAG
54622801 GACGATGAC
1 GACGATGAC
54622810 GACGATGAC
1 GACGATGAC
*
54622819 GACAATGAC
1 GACGATGAC
54622828 GACGATGA
1 GACGATGA
54622836 TGTTTCTTTG
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
9 24 1.00
ACGTcount: A:0.37, C:0.20, G:0.31, T:0.11
Consensus pattern (9 bp):
GACGATGAC
Found at i:54623090 original size:18 final size:18
Alignment explanation
Indices: 54623067--54623112 Score: 74
Period size: 18 Copynumber: 2.6 Consensus size: 18
54623057 GGTTGCAAAA
54623067 AGGACGATGACGATGATG
1 AGGACGATGACGATGATG
*
54623085 AGGACGATGAGGATGATG
1 AGGACGATGACGATGATG
*
54623103 AGGATGATGA
1 AGGACGATGA
54623113 TGTTTCTTCG
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
18 26 1.00
ACGTcount: A:0.35, C:0.07, G:0.41, T:0.17
Consensus pattern (18 bp):
AGGACGATGACGATGATG
Found at i:54623093 original size:9 final size:9
Alignment explanation
Indices: 54623067--54623112 Score: 65
Period size: 9 Copynumber: 5.1 Consensus size: 9
54623057 GGTTGCAAAA
*
54623067 AGGACGATG
1 AGGATGATG
*
54623076 ACGATGATG
1 AGGATGATG
*
54623085 AGGACGATG
1 AGGATGATG
54623094 AGGATGATG
1 AGGATGATG
54623103 AGGATGATG
1 AGGATGATG
54623112 A
1 A
54623113 TGTTTCTTCG
Statistics
Matches: 32, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
9 32 1.00
ACGTcount: A:0.35, C:0.07, G:0.41, T:0.17
Consensus pattern (9 bp):
AGGATGATG
Found at i:54623248 original size:277 final size:269
Alignment explanation
Indices: 54622752--54623265 Score: 877
Period size: 277 Copynumber: 1.9 Consensus size: 269
54622742 ATCAATTTGA
*
54622752 TTATCTAATTATTTATTCTTATTTAATGTTAGAAATTGGTTGCAAAAAGGACGATGACGACGATG
1 TTATCTAATTATTTATTCTCATTTAATGTTAGAAATTGGTTGCAAAAAGGACGATGACGACGATG
*
54622817 ACGACAATGACGACGATGATGTTTCTTTGGTAGCTTTTTAAGATACTTTCTTTCTAAATGTTTAA
66 ACGACAATGACGACGATGATGTTTCTTCGGTAGCTTTTTAAGATACTTTCTTTCTAAATGTTTAA
54622882 AATTTAATTTAGCTTACAATTTATATTTTGTTATGAAATTAAATATGTTGATGGATTAATGTATG
131 AATTTAATTTAGCTTACAATTTATATTTTGTTATGAAATTAAATATGTTGATGGATTAATGTATG
54622947 AATATTATGGTTTGTTGCTTAATTTTCCAAAGTCATTTTGGACTTTGGAGGTATGTGTACTTGTG
196 AATATTATGGTTTGTTGCTTAATTTTCCAAAGTCATTTTGGACTTTGGAGGTATGTGTACTTGTG
54623012 GGGTTTAAC
261 GGGTTTAAC
* *
54623021 TTAT-TAATTGTTTATTCTCATTTAATGTTAGAAATTGGTTGCAAAAAGGACGATGACGATGATG
1 TTATCTAATTATTTATTCTCATTTAATGTTAGAAATTGGTTGCAAAAAGGACGATGACGACGAT-
* * *
54623085 AGGACGATGAGGATGATGAGGATGATGATGTTTCTTCGGTAGCTTTTTAAGATACTTTCTTTCTA
65 --GAC---GA-CA--ATGACGACGATGATGTTTCTTCGGTAGCTTTTTAAGATACTTTCTTTCTA
54623150 AATGTTTAAAATTTAATTTAGCTTACAATTTATATTTTGTTATGAAATTAAATATGTTGATGGAT
122 AATGTTTAAAATTTAATTTAGCTTACAATTTATATTTTGTTATGAAATTAAATATGTTGATGGAT
54623215 TAATGTATGAATATTATGGTTTGTTGCTTAATTTTCCAAAGTCATTTTGGA
187 TAATGTATGAATATTATGGTTTGTTGCTTAATTTTCCAAAGTCATTTTGGA
54623266 GGTATATGTA
Statistics
Matches: 229, Mismatches: 7, Indels: 10
0.93 0.03 0.04
Matches are distributed among these distances:
268 56 0.24
269 4 0.02
271 3 0.01
274 2 0.01
275 1 0.00
277 163 0.71
ACGTcount: A:0.30, C:0.08, G:0.19, T:0.43
Consensus pattern (269 bp):
TTATCTAATTATTTATTCTCATTTAATGTTAGAAATTGGTTGCAAAAAGGACGATGACGACGATG
ACGACAATGACGACGATGATGTTTCTTCGGTAGCTTTTTAAGATACTTTCTTTCTAAATGTTTAA
AATTTAATTTAGCTTACAATTTATATTTTGTTATGAAATTAAATATGTTGATGGATTAATGTATG
AATATTATGGTTTGTTGCTTAATTTTCCAAAGTCATTTTGGACTTTGGAGGTATGTGTACTTGTG
GGGTTTAAC
Found at i:54623300 original size:11 final size:11
Alignment explanation
Indices: 54623277--54623308 Score: 55
Period size: 11 Copynumber: 2.8 Consensus size: 11
54623267 GTATATGTAT
54623277 ATGTGCTTATGG
1 ATGTGC-TATGG
54623289 ATGTGCTATGG
1 ATGTGCTATGG
54623300 ATGTGCTAT
1 ATGTGCTAT
54623309 CTATATGTAT
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
11 14 0.70
12 6 0.30
ACGTcount: A:0.19, C:0.09, G:0.31, T:0.41
Consensus pattern (11 bp):
ATGTGCTATGG
Found at i:54624164 original size:16 final size:18
Alignment explanation
Indices: 54624138--54624171 Score: 54
Period size: 17 Copynumber: 2.0 Consensus size: 18
54624128 TTGGAATTGG
54624138 ATTGAGAAAATT-ATTTA
1 ATTGAGAAAATTAATTTA
54624155 ATTG-GAAAATTAATTTA
1 ATTGAGAAAATTAATTTA
54624172 GTTAATTTAA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 7 0.44
17 9 0.56
ACGTcount: A:0.47, C:0.00, G:0.12, T:0.41
Consensus pattern (18 bp):
ATTGAGAAAATTAATTTA
Found at i:54632137 original size:22 final size:21
Alignment explanation
Indices: 54632112--54632155 Score: 54
Period size: 22 Copynumber: 2.0 Consensus size: 21
54632102 TGATAAACTT
54632112 TAATATATA-ATTATATTATTTA
1 TAATATATATATTA-ATT-TTTA
*
54632134 TAATTTATATATTAATTTTTA
1 TAATATATATATTAATTTTTA
54632155 T
1 T
54632156 CAACTTAGCT
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
21 5 0.25
22 11 0.55
23 4 0.20
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (21 bp):
TAATATATATATTAATTTTTA
Found at i:54638331 original size:18 final size:17
Alignment explanation
Indices: 54638304--54638337 Score: 59
Period size: 18 Copynumber: 1.9 Consensus size: 17
54638294 TAACAGACTT
54638304 ATTCACCAAGCCTTTAG
1 ATTCACCAAGCCTTTAG
54638321 ATTCAACCAAGCCTTTA
1 ATTC-ACCAAGCCTTTA
54638338 AATTTGGGTC
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 4 0.25
18 12 0.75
ACGTcount: A:0.32, C:0.29, G:0.09, T:0.29
Consensus pattern (17 bp):
ATTCACCAAGCCTTTAG
Found at i:54643554 original size:19 final size:19
Alignment explanation
Indices: 54643512--54643557 Score: 67
Period size: 19 Copynumber: 2.4 Consensus size: 19
54643502 CATAATTAAT
54643512 AATTCAATTTTGATATAAA
1 AATTCAATTTTGATATAAA
*
54643531 TATTCAATTTTGAT-TAAA
1 AATTCAATTTTGATATAAA
54643549 CAATTCAAT
1 -AATTCAAT
54643558 AATATAAATA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
18 4 0.17
19 20 0.83
ACGTcount: A:0.43, C:0.09, G:0.04, T:0.43
Consensus pattern (19 bp):
AATTCAATTTTGATATAAA
Found at i:54643704 original size:20 final size:19
Alignment explanation
Indices: 54643676--54643715 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 19
54643666 TTTATTTGAG
*
54643676 AGTAAAGGGTGAGAAATAAA
1 AGTAAAGGG-GAAAAATAAA
*
54643696 AGTATAGGGGAAAAATAAA
1 AGTAAAGGGGAAAAATAAA
54643715 A
1 A
54643716 AGTTTTGGGG
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
19 10 0.56
20 8 0.44
ACGTcount: A:0.57, C:0.00, G:0.28, T:0.15
Consensus pattern (19 bp):
AGTAAAGGGGAAAAATAAA
Done.