Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: A07
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: 93829987
ACGTcount: A:0.31, C:0.16, G:0.16, T:0.31
Warning! 4250000 characters in sequence are not A, C, G, or T
File 171 of 295
Found at i:54230962 original size:47 final size:47
Alignment explanation
Indices: 54230893--54231016 Score: 151
Period size: 47 Copynumber: 2.7 Consensus size: 47
54230883 CAAGTGATTT
* * * *
54230893 CTGTATAAGACAATATCTGGGATATGGCATCGGTGTGATATATGCTA
1 CTGTATAAGACCATATCTGGGATATGGCATCAGTGAGATATATGATA
* *
54230940 CTGTATAAGACCATATCTGGGATATGGCATCAGTGAGATATGTGATT
1 CTGTATAAGACCATATCTGGGATATGGCATCAGTGAGATATATGATA
* * * *
54230987 C-GTGTAAGACCATAACTGAGCTATGGCATC
1 CTGTATAAGACCATATCTGGGATATGGCATC
54231017 TGTAATGCCC
Statistics
Matches: 67, Mismatches: 10, Indels: 1
0.86 0.13 0.01
Matches are distributed among these distances:
46 25 0.37
47 42 0.63
ACGTcount: A:0.30, C:0.15, G:0.25, T:0.30
Consensus pattern (47 bp):
CTGTATAAGACCATATCTGGGATATGGCATCAGTGAGATATATGATA
Found at i:54232444 original size:40 final size:40
Alignment explanation
Indices: 54232370--54232471 Score: 147
Period size: 40 Copynumber: 2.6 Consensus size: 40
54232360 AACCCAAGTA
*
54232370 CCTTCGGGAT-TTAG-CCGGATATAGCAACTCGCACAAATG
1 CCTTCGGG-TCTTAGCCCGGATATAGCAACTAGCACAAATG
54232409 CCTTCGGGTCTTAGCCCGGATATAGTC-ACTAGCACAAATG
1 CCTTCGGGTCTTAGCCCGGATATAG-CAACTAGCACAAATG
*
54232449 CCTTCGGGACTTAGCCCGGATAT
1 CCTTCGGGTCTTAGCCCGGATAT
54232472 CATTCGAATA
Statistics
Matches: 58, Mismatches: 2, Indels: 5
0.89 0.03 0.08
Matches are distributed among these distances:
38 1 0.02
39 12 0.21
40 44 0.76
41 1 0.02
ACGTcount: A:0.25, C:0.27, G:0.24, T:0.25
Consensus pattern (40 bp):
CCTTCGGGTCTTAGCCCGGATATAGCAACTAGCACAAATG
Found at i:54244990 original size:29 final size:29
Alignment explanation
Indices: 54244957--54245021 Score: 87
Period size: 29 Copynumber: 2.3 Consensus size: 29
54244947 GGCCGTTACA
** *
54244957 CATGGCCTGAAGCCAAATCAGTTGATATT
1 CATGGCCCAAAGCCAAATCAGTTAATATT
54244986 CATGGCCCAAAGCCAAATCAGTTAATA-T
1 CATGGCCCAAAGCCAAATCAGTTAATATT
*
54245014 CACGGCCC
1 CATGGCCC
54245022 GAATTCAAAT
Statistics
Matches: 32, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
28 8 0.25
29 24 0.75
ACGTcount: A:0.32, C:0.28, G:0.18, T:0.22
Consensus pattern (29 bp):
CATGGCCCAAAGCCAAATCAGTTAATATT
Found at i:54245974 original size:27 final size:27
Alignment explanation
Indices: 54245944--54246328 Score: 463
Period size: 27 Copynumber: 14.3 Consensus size: 27
54245934 CCAAAGTACT
54245944 CTCGATTTATAGAATTACCGTTTTACC
1 CTCGATTTATAGAATTACCGTTTTACC
* *
54245971 CTCGATTTACAGAATTACTGTTTTACC
1 CTCGATTTATAGAATTACCGTTTTACC
**
54245998 CTC-AGTTTATAGAATTATTGTTTTACC
1 CTCGA-TTTATAGAATTACCGTTTTACC
54246025 CTCGATTTATAGAATTACCGTTTTACC
1 CTCGATTTATAGAATTACCGTTTTACC
* *
54246052 CTCGATTTGTAAAATTACCGTTTTACC
1 CTCGATTTATAGAATTACCGTTTTACC
* *
54246079 CTTGATTTATAGAATTACTGTTTTACC
1 CTCGATTTATAGAATTACCGTTTTACC
* **
54246106 CTC-AGTTTACAGAATTACTATTTTACC
1 CTCGA-TTTATAGAATTACCGTTTTACC
*
54246133 CTCGATTTATAGAATTACCATTTTACC
1 CTCGATTTATAGAATTACCGTTTTACC
* * *
54246160 CT-TAGTTTACAGAATTACTGTTTTACC
1 CTCGA-TTTATAGAATTACCGTTTTACC
*
54246187 CTCGATTTATAGAATTACTGTTTTACC
1 CTCGATTTATAGAATTACCGTTTTACC
* *
54246214 CTCGATTTGTAAAATTACCGTTTTACC
1 CTCGATTTATAGAATTACCGTTTTACC
* * * *
54246241 CTTGATTTACAGAATTACTGGTTTACC
1 CTCGATTTATAGAATTACCGTTTTACC
* * *
54246268 CTC-AGTTTACAAAATTATCGTTTTACC
1 CTCGA-TTTATAGAATTACCGTTTTACC
*
54246295 CTCGATTTACAGAATTACCGTTTTACC
1 CTCGATTTATAGAATTACCGTTTTACC
*
54246322 CTTGATT
1 CTCGATT
54246329 GTGAAATTAC
Statistics
Matches: 310, Mismatches: 40, Indels: 16
0.85 0.11 0.04
Matches are distributed among these distances:
26 4 0.01
27 302 0.97
28 4 0.01
ACGTcount: A:0.26, C:0.21, G:0.11, T:0.42
Consensus pattern (27 bp):
CTCGATTTATAGAATTACCGTTTTACC
Found at i:54246393 original size:27 final size:27
Alignment explanation
Indices: 54246333--54246524 Score: 214
Period size: 27 Copynumber: 7.3 Consensus size: 27
54246323 TTGATTGTGA
* *
54246333 AATTACTGAAATAACCCTGTAGGGT--
1 AATTACCGAAATACCCCTGTAGGGTAG
*
54246358 -ATT-CCGAAATACCCCTATAGGGTAG
1 AATTACCGAAATACCCCTGTAGGGTAG
* * * *
54246383 AATTACTGAAATACCCTTATAGGATAG
1 AATTACCGAAATACCCCTGTAGGGTAG
*
54246410 AATTACCAAAATACCCCTGTAGGGTAG
1 AATTACCGAAATACCCCTGTAGGGTAG
* *
54246437 AATTATCGAAATACCCTTGTAGGGTAG
1 AATTACCGAAATACCCCTGTAGGGTAG
*
54246464 AAATACCGAAATACCCCTGTAGGGTAG
1 AATTACCGAAATACCCCTGTAGGGTAG
* * *
54246491 AATTACCGAGATACCCTTGT-GGGATAA
1 AATTACCGAAATACCCCTGTAGGG-TAG
54246518 AATTACC
1 AATTACC
54246525 ATTTTGCCCT
Statistics
Matches: 141, Mismatches: 21, Indels: 8
0.83 0.12 0.05
Matches are distributed among these distances:
23 17 0.12
24 3 0.02
26 6 0.04
27 115 0.82
ACGTcount: A:0.36, C:0.19, G:0.19, T:0.26
Consensus pattern (27 bp):
AATTACCGAAATACCCCTGTAGGGTAG
Found at i:54246534 original size:27 final size:26
Alignment explanation
Indices: 54246504--54246567 Score: 67
Period size: 27 Copynumber: 2.4 Consensus size: 26
54246494 TACCGAGATA
*
54246504 CCCTTGTGGGATAAAATTACCATTTTG
1 CCCTTGTGGG-TAAAATGACCATTTTG
* *
54246531 CCCTTAG-GGTGTTAAATGACTATTTTG
1 CCCTT-GTGG-GTAAAATGACCATTTTG
54246558 CCCTTGTGGG
1 CCCTTGTGGG
54246568 CAAGTGACTG
Statistics
Matches: 31, Mismatches: 3, Indels: 7
0.76 0.07 0.17
Matches are distributed among these distances:
26 2 0.06
27 27 0.87
28 2 0.06
ACGTcount: A:0.20, C:0.19, G:0.23, T:0.38
Consensus pattern (26 bp):
CCCTTGTGGGTAAAATGACCATTTTG
Found at i:54246761 original size:27 final size:26
Alignment explanation
Indices: 54246723--54246805 Score: 112
Period size: 27 Copynumber: 3.1 Consensus size: 26
54246713 CGGAGAAAGC
*
54246723 GTTCTGGTGGCTATGCCACAAATATCT
1 GTTCTGGTGGCTCTGCCAC-AATATCT
54246750 GTTCTGGTGGCTCTGCCACAATATCT
1 GTTCTGGTGGCTCTGCCACAATATCT
* * *
54246776 GTATTTGGTGACTCTGTCACAATATCT
1 GT-TCTGGTGGCTCTGCCACAATATCT
54246803 GTT
1 GTT
54246806 GACCGATCGA
Statistics
Matches: 51, Mismatches: 4, Indels: 3
0.88 0.07 0.05
Matches are distributed among these distances:
26 10 0.20
27 41 0.80
ACGTcount: A:0.19, C:0.22, G:0.22, T:0.37
Consensus pattern (26 bp):
GTTCTGGTGGCTCTGCCACAATATCT
Found at i:54246903 original size:27 final size:27
Alignment explanation
Indices: 54246872--54246927 Score: 85
Period size: 27 Copynumber: 2.1 Consensus size: 27
54246862 GGGCCCTCAG
*
54246872 TTTACAAAATTATCGTTTTACCCTCGA
1 TTTACAAAATTACCGTTTTACCCTCGA
* *
54246899 TTTACAGAATTACCGTTTTACCCTTGA
1 TTTACAAAATTACCGTTTTACCCTCGA
54246926 TT
1 TT
54246928 GTGAAATTAC
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
27 26 1.00
ACGTcount: A:0.27, C:0.21, G:0.09, T:0.43
Consensus pattern (27 bp):
TTTACAAAATTACCGTTTTACCCTCGA
Found at i:54246962 original size:27 final size:27
Alignment explanation
Indices: 54246932--54246985 Score: 81
Period size: 27 Copynumber: 2.0 Consensus size: 27
54246922 TTGATTGTGA
* *
54246932 AATTACTGAAATACCCCTGTAGGGTAG
1 AATTACCGAAATACCCCTATAGGGTAG
*
54246959 AATTTCCGAAATACCCCTATAGGGTAG
1 AATTACCGAAATACCCCTATAGGGTAG
54246986 TGTAACACCC
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
27 24 1.00
ACGTcount: A:0.33, C:0.20, G:0.20, T:0.26
Consensus pattern (27 bp):
AATTACCGAAATACCCCTATAGGGTAG
Found at i:54248366 original size:27 final size:27
Alignment explanation
Indices: 54248336--54248513 Score: 169
Period size: 27 Copynumber: 6.6 Consensus size: 27
54248326 ATATTGAGTC
* *
54248336 CGCACACTCAGTGCTATATAATCAACT
1 CGCACACTTAGTGCTACATAATCAACT
* *
54248363 CGCACACTTAGTGCTACGTAATCAAAT
1 CGCACACTTAGTGCTACATAATCAACT
*
54248390 CGCACACTTAGTGCTACATAGTCAAACT
1 CGCACACTTAGTGCTACATAATC-AACT
* ** ** *
54248418 TGCACACTTAGTGCCGCATGGTCAATT
1 CGCACACTTAGTGCTACATAATCAACT
* ***
54248445 CGCACACTTAGTGC-ATCATATTCGTTT
1 CGCACACTTAGTGCTA-CATAATCAACT
* * *
54248472 CGCACACTTAGTGCAACATAGTCAAAT
1 CGCACACTTAGTGCTACATAATCAACT
54248499 CGCACACTTAGTGCT
1 CGCACACTTAGTGCT
54248514 GTACAATTTA
Statistics
Matches: 125, Mismatches: 23, Indels: 6
0.81 0.15 0.04
Matches are distributed among these distances:
27 102 0.82
28 23 0.18
ACGTcount: A:0.29, C:0.28, G:0.16, T:0.28
Consensus pattern (27 bp):
CGCACACTTAGTGCTACATAATCAACT
Found at i:54250341 original size:27 final size:27
Alignment explanation
Indices: 54250298--54250444 Score: 188
Period size: 27 Copynumber: 5.4 Consensus size: 27
54250288 GGCTGTCACA
* *
54250298 GGTAGAATTACTGAAATACCCTTATAG
1 GGTAGAATTACCGAAATACCCTTGTAG
* * *
54250325 GATAGAATTACCAAAATACCCCTGTAG
1 GGTAGAATTACCGAAATACCCTTGTAG
*
54250352 GGTAGAATTATCGAAATACCCTTGTAG
1 GGTAGAATTACCGAAATACCCTTGTAG
* *
54250379 GGTAGAAATACCGAAATACCCCTGTAG
1 GGTAGAATTACCGAAATACCCTTGTAG
*
54250406 GGTAGAATTACCGAGATACCCTTGT-G
1 GGTAGAATTACCGAAATACCCTTGTAG
*
54250432 GGATAAAATTACC
1 GG-TAGAATTACC
54250445 ATTTTGCCCT
Statistics
Matches: 103, Mismatches: 16, Indels: 2
0.85 0.13 0.02
Matches are distributed among these distances:
26 3 0.03
27 100 0.97
ACGTcount: A:0.36, C:0.18, G:0.20, T:0.25
Consensus pattern (27 bp):
GGTAGAATTACCGAAATACCCTTGTAG
Found at i:54250681 original size:27 final size:26
Alignment explanation
Indices: 54250643--54250725 Score: 112
Period size: 27 Copynumber: 3.1 Consensus size: 26
54250633 CGGAGAAAGC
*
54250643 GTTCTGGTGGCTATGCCACAAATATCT
1 GTTCTGGTGGCTCTGCCAC-AATATCT
54250670 GTTCTGGTGGCTCTGCCACAATATCT
1 GTTCTGGTGGCTCTGCCACAATATCT
* * *
54250696 GTATTTGGTGACTCTGTCACAATATCT
1 GT-TCTGGTGGCTCTGCCACAATATCT
54250723 GTT
1 GTT
54250726 GACCGATCGA
Statistics
Matches: 51, Mismatches: 4, Indels: 3
0.88 0.07 0.05
Matches are distributed among these distances:
26 10 0.20
27 41 0.80
ACGTcount: A:0.19, C:0.22, G:0.22, T:0.37
Consensus pattern (26 bp):
GTTCTGGTGGCTCTGCCACAATATCT
Found at i:54250845 original size:22 final size:22
Alignment explanation
Indices: 54250813--54250871 Score: 64
Period size: 22 Copynumber: 2.7 Consensus size: 22
54250803 CCCGTTATTA
*
54250813 ATGGCTCTGTGCCAACCTAAAT
1 ATGGCTTTGTGCCAACCTAAAT
* * * *
54250835 ATGGCTTTGTGCCATCTTGACT
1 ATGGCTTTGTGCCAACCTAAAT
*
54250857 ATGGCTTCGTGCCAA
1 ATGGCTTTGTGCCAA
54250872 ACGTATTTAC
Statistics
Matches: 30, Mismatches: 7, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
22 30 1.00
ACGTcount: A:0.20, C:0.25, G:0.22, T:0.32
Consensus pattern (22 bp):
ATGGCTTTGTGCCAACCTAAAT
Found at i:54251058 original size:27 final size:27
Alignment explanation
Indices: 54251036--54251109 Score: 89
Period size: 27 Copynumber: 2.8 Consensus size: 27
54251026 TAGGTGGGTT
*
54251036 TGCCACATTATCTG-ATTCTGGTGGCTC
1 TGCCACAATATCTGTA-TCTGGTGGCTC
*
54251063 TGCCACAATATCTGTATCTGGTGACTC
1 TGCCACAATATCTGTATCTGGTGGCTC
* *
54251090 TGTCACGATATCTGT-TCTGG
1 TGCCACAATATCTGTATCTGG
54251110 CAGCCATGCT
Statistics
Matches: 42, Mismatches: 4, Indels: 3
0.86 0.08 0.06
Matches are distributed among these distances:
26 5 0.12
27 36 0.86
28 1 0.02
ACGTcount: A:0.18, C:0.24, G:0.22, T:0.36
Consensus pattern (27 bp):
TGCCACAATATCTGTATCTGGTGGCTC
Found at i:54251236 original size:6 final size:6
Alignment explanation
Indices: 54251227--54251413 Score: 136
Period size: 6 Copynumber: 30.8 Consensus size: 6
54251217 TTGCATTCAC
* * *
54251227 ATTCTG ATTCTG ATTCTG -TCACGTA ATTTTG ATTCTG ATTCTG ATTCTG
1 ATTCTG ATTCTG ATTCTG AT-TC-TG ATTCTG ATTCTG ATTCTG ATTCTG
* * *
54251276 -TTACTA ATACTG ATTCTG ATTTTG ATTCTG -TTACTG ATTCTG ATTCTG
1 ATT-CTG ATTCTG ATTCTG ATTCTG ATTCTG ATT-CTG ATTCTG ATTCTG
* * *
54251324 ATTCTG -TCACCTA ATTCTG ATTCTG ATTCTG ATTCTG -TTACTA ATAT-TG
1 ATTCTG AT--TCTG ATTCTG ATTCTG ATTCTG ATTCTG ATT-CTG AT-TCTG
* * *
54251373 ATTCTA ATTCTA ATTCTG -TTACTG TTTCTG ATTCTG ATTCT
1 ATTCTG ATTCTG ATTCTG ATT-CTG ATTCTG ATTCTG ATTCT
54251414 CATTTTGTTT
Statistics
Matches: 144, Mismatches: 21, Indels: 32
0.73 0.11 0.16
Matches are distributed among these distances:
5 11 0.08
6 121 0.84
7 9 0.06
8 3 0.02
ACGTcount: A:0.20, C:0.17, G:0.13, T:0.50
Consensus pattern (6 bp):
ATTCTG
Found at i:54251292 original size:30 final size:30
Alignment explanation
Indices: 54251227--54251422 Score: 206
Period size: 30 Copynumber: 6.7 Consensus size: 30
54251217 TTGCATTCAC
* **
54251227 ATTCTGATTCTGATTCTGTCACGTAATTTTG
1 ATTCTGATTCTGATTCTGTTAC-TAATACTG
54251258 ATTCTGATTCTGATTCTGTTACTAATACTG
1 ATTCTGATTCTGATTCTGTTACTAATACTG
*
54251288 ATTCTGATTTTGATTCTG----T--TACTG
1 ATTCTGATTCTGATTCTGTTACTAATACTG
* *
54251312 ATTCTGATTCTGATTCTGTCACCTAATTCTG
1 ATTCTGATTCTGATTCTGTTA-CTAATACTG
*
54251343 ATTCTGATTCTGATTCTGTTACTAATATTG
1 ATTCTGATTCTGATTCTGTTACTAATACTG
* * ** *
54251373 ATTCTAATTCTAATTCTGTTACTGTTTCTG
1 ATTCTGATTCTGATTCTGTTACTAATACTG
* *
54251403 ATTCTGATTCTCATTTTGTT
1 ATTCTGATTCTGATTCTGTT
54251423 TCCAATTCTG
Statistics
Matches: 140, Mismatches: 18, Indels: 15
0.81 0.10 0.09
Matches are distributed among these distances:
24 22 0.16
26 1 0.01
29 1 0.01
30 71 0.51
31 45 0.32
ACGTcount: A:0.20, C:0.16, G:0.13, T:0.51
Consensus pattern (30 bp):
ATTCTGATTCTGATTCTGTTACTAATACTG
Found at i:54251345 original size:25 final size:24
Alignment explanation
Indices: 54251288--54251354 Score: 98
Period size: 25 Copynumber: 2.8 Consensus size: 24
54251278 ACTAATACTG
* * *
54251288 ATTCTGATTTTGATTCTGTTACTG
1 ATTCTGATTCTGATTCTGTCACTA
54251312 ATTCTGATTCTGATTCTGTCACCTA
1 ATTCTGATTCTGATTCTGTCA-CTA
54251337 ATTCTGATTCTGATTCTG
1 ATTCTGATTCTGATTCTG
54251355 ATTCTGTTAC
Statistics
Matches: 39, Mismatches: 3, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
24 19 0.49
25 20 0.51
ACGTcount: A:0.18, C:0.18, G:0.15, T:0.49
Consensus pattern (24 bp):
ATTCTGATTCTGATTCTGTCACTA
Found at i:54251367 original size:85 final size:85
Alignment explanation
Indices: 54251227--54251413 Score: 311
Period size: 85 Copynumber: 2.2 Consensus size: 85
54251217 TTGCATTCAC
* *
54251227 ATTCTGATTCTGATTCTGTCACGTAATTTTGATTCTGATTCTGATTCTGTTACTAATACTGATTC
1 ATTCTGATTCTGATTCTGTCACCTAATTCTGATTCTGATTCTGATTCTGTTACTAATACTGATTC
* * *
54251292 TGATTTTGATTCTGTTACTG
66 TAATTCTAATTCTGTTACTG
*
54251312 ATTCTGATTCTGATTCTGTCACCTAATTCTGATTCTGATTCTGATTCTGTTACTAATATTGATTC
1 ATTCTGATTCTGATTCTGTCACCTAATTCTGATTCTGATTCTGATTCTGTTACTAATACTGATTC
54251377 TAATTCTAATTCTGTTACTG
66 TAATTCTAATTCTGTTACTG
*
54251397 TTTCTGATTCTGATTCT
1 ATTCTGATTCTGATTCT
54251414 CATTTTGTTT
Statistics
Matches: 95, Mismatches: 7, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
85 95 1.00
ACGTcount: A:0.20, C:0.17, G:0.13, T:0.50
Consensus pattern (85 bp):
ATTCTGATTCTGATTCTGTCACCTAATTCTGATTCTGATTCTGATTCTGTTACTAATACTGATTC
TAATTCTAATTCTGTTACTG
Found at i:54256431 original size:27 final size:27
Alignment explanation
Indices: 54256400--54256459 Score: 84
Period size: 27 Copynumber: 2.2 Consensus size: 27
54256390 TATAATACTT
* *
54256400 TAGTTTATCAAATTACCAAAATACCCC
1 TAGTTTATAAAACTACCAAAATACCCC
*
54256427 TAGTTTGTAAAACTACCAAAATACCCC
1 TAGTTTATAAAACTACCAAAATACCCC
*
54256454 TGGTTT
1 TAGTTT
54256460 TATAGAATTA
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
27 29 1.00
ACGTcount: A:0.37, C:0.23, G:0.08, T:0.32
Consensus pattern (27 bp):
TAGTTTATAAAACTACCAAAATACCCC
Found at i:54256510 original size:27 final size:27
Alignment explanation
Indices: 54256472--54256540 Score: 129
Period size: 27 Copynumber: 2.6 Consensus size: 27
54256462 TAGAATTACT
54256472 ATTTACAGAATTACTGTTTTACCCTTG
1 ATTTACAGAATTACTGTTTTACCCTTG
54256499 ATTTACAGAATTACTGTTTTACCCTTG
1 ATTTACAGAATTACTGTTTTACCCTTG
*
54256526 ATTTACAAAATTACT
1 ATTTACAGAATTACT
54256541 AAAATACCCT
Statistics
Matches: 41, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
27 41 1.00
ACGTcount: A:0.30, C:0.17, G:0.09, T:0.43
Consensus pattern (27 bp):
ATTTACAGAATTACTGTTTTACCCTTG
Found at i:54256576 original size:54 final size:54
Alignment explanation
Indices: 54256518--54256850 Score: 278
Period size: 54 Copynumber: 6.1 Consensus size: 54
54256508 ATTACTGTTT
* **
54256518 TACCCTTGATTTACAAAATTACTAAAATACCCTTGGTTTACAAAATTACCAAAA
1 TACCCTTGATTTACAAAATTACCAAAATACCCTTGGTTTGTAAAATTACCAAAA
* * * * *
54256572 TACCCTCGA-TCAGTAAAATTACCAAATTACCC-TGGTTTGTAAAATTACTAAAA
1 TACCCTTGATTTA-CAAAATTACCAAAATACCCTTGGTTTGTAAAATTACCAAAA
* * ** * * * *
54256625 TACCCCTGGTTTGTAAAATTACCATAATACCCCTAGTTTGTAAAATTATCAAAA
1 TACCCTTGATTTACAAAATTACCAAAATACCCTTGGTTTGTAAAATTACCAAAA
* *** * **
54256679 TACCAC-TGGTTTGTGAAATTACCAAAACACCCTTAATTTGTAAAATTACCAAAA
1 TACC-CTTGATTTACAAAATTACCAAAATACCCTTGGTTTGTAAAATTACCAAAA
* * * * *
54256733 TACCCCTGATTTACAAAATTACAAAAATACCCTTGACTTTCTAAAAATTA-TAGAAA
1 TACCCTTGATTTACAAAATTACCAAAATACCCTTG-GTTTGT-AAAATTACCA-AAA
* * ** * *
54256789 TACCATTGGTTTACAAAATTACTGAAATACCCTTGGTTTGTAGATTTACCAAAA
1 TACCCTTGATTTACAAAATTACCAAAATACCCTTGGTTTGTAAAATTACCAAAA
*
54256843 CACCCTTG
1 TACCCTTG
54256851 TAGGGTGAAA
Statistics
Matches: 224, Mismatches: 46, Indels: 18
0.78 0.16 0.06
Matches are distributed among these distances:
53 44 0.20
54 129 0.58
55 11 0.05
56 40 0.18
ACGTcount: A:0.39, C:0.20, G:0.09, T:0.32
Consensus pattern (54 bp):
TACCCTTGATTTACAAAATTACCAAAATACCCTTGGTTTGTAAAATTACCAAAA
Found at i:54256643 original size:80 final size:81
Alignment explanation
Indices: 54256532--54256738 Score: 265
Period size: 80 Copynumber: 2.6 Consensus size: 81
54256522 CTTGATTTAC
**
54256532 AAAATTACTAAAATACCCTTGGTTTACAAAATTACCAAAATACCCTCGA-TCAGTAAAATTACCA
1 AAAATTACTAAAATACCCTTGGTTTGTAAAATTACCAAAATACCC-CGAGTCAGTAAAATTACCA
*
54256596 AATTACC-CTGGTTTGT
65 AAATACCACTGGTTTGT
* * * ** *
54256612 AAAATTACTAAAATACCCCTGGTTTGTAAAATTACCATAATACCCCTAGTTTGTAAAATTATCAA
1 AAAATTACTAAAATACCCTTGGTTTGTAAAATTACCAAAATACCCCGAGTCAGTAAAATTACCAA
54256677 AATACCACTGGTTTGT
66 AATACCACTGGTTTGT
* * * **
54256693 GAAATTACCAAAACACCCTTAATTTGTAAAATTACCAAAATACCCC
1 AAAATTACTAAAATACCCTTGGTTTGTAAAATTACCAAAATACCCC
54256739 TGATTTACAA
Statistics
Matches: 109, Mismatches: 16, Indels: 3
0.85 0.12 0.02
Matches are distributed among these distances:
79 2 0.02
80 59 0.54
81 48 0.44
ACGTcount: A:0.41, C:0.21, G:0.08, T:0.30
Consensus pattern (81 bp):
AAAATTACTAAAATACCCTTGGTTTGTAAAATTACCAAAATACCCCGAGTCAGTAAAATTACCAA
AATACCACTGGTTTGT
Found at i:54256724 original size:81 final size:80
Alignment explanation
Indices: 54256559--54256765 Score: 238
Period size: 81 Copynumber: 2.6 Consensus size: 80
54256549 CTTGGTTTAC
* ** * *
54256559 AAAATTACCAAAATA-CCCTCGATCAGTAAAATTACCAAATTACCCTGGTTTGTAAAATTACTAA
1 AAAATTACCAAAATACCCCTAG-TTTGTAAAATTACCAAAATACCCTGGTTTGTAAAATTACCAA
* **
54256623 AATACCCCTGGTTTGT
65 AACACCCCTAATTTGT
* * *
54256639 AAAATTACCATAATACCCCTAGTTTGTAAAATTATCAAAATACCACTGGTTTGTGAAATTACCAA
1 AAAATTACCAAAATACCCCTAGTTTGTAAAATTACCAAAATACC-CTGGTTTGTAAAATTACCAA
*
54256704 AACACCCTTAATTTGT
65 AACACCCCTAATTTGT
** *
54256720 AAAATTACCAAAATACCCCT-GATTTACAAAATTACAAAAATACCCT
1 AAAATTACCAAAATACCCCTAG-TTTGTAAAATTACCAAAATACCCT
54256766 TGACTTTCTA
Statistics
Matches: 107, Mismatches: 17, Indels: 6
0.82 0.13 0.05
Matches are distributed among these distances:
80 35 0.33
81 72 0.67
ACGTcount: A:0.42, C:0.21, G:0.08, T:0.29
Consensus pattern (80 bp):
AAAATTACCAAAATACCCCTAGTTTGTAAAATTACCAAAATACCCTGGTTTGTAAAATTACCAAA
ACACCCCTAATTTGT
Found at i:54256824 original size:27 final size:27
Alignment explanation
Indices: 54256491--54256827 Score: 200
Period size: 27 Copynumber: 12.4 Consensus size: 27
54256481 ATTACTGTTT
* * ****
54256491 TACCCTTGATTTACAGAATTACTGTTT
1 TACCCTTGGTTTACAAAATTACTAAAA
*
54256518 TACCCTTGATTTACAAAATTACTAAAA
1 TACCCTTGGTTTACAAAATTACTAAAA
*
54256545 TACCCTTGGTTTACAAAATTACCAAAA
1 TACCCTTGGTTTACAAAATTACTAAAA
* * * * * *
54256572 TACCC-TCGATCAGTAAAATTACCAAAT
1 TACCCTTGGTTTA-CAAAATTACTAAAA
**
54256599 TACCC-TGGTTTGTAAAATTACTAAAA
1 TACCCTTGGTTTACAAAATTACTAAAA
* ** * *
54256625 TACCCCTGGTTTGTAAAATTACCATAA
1 TACCCTTGGTTTACAAAATTACTAAAA
* * **
54256652 TACCCCTAGTTTGTAAAATTA-TCAAAA
1 TACCCTTGGTTTACAAAATTACT-AAAA
*** *
54256679 TACCAC-TGGTTTGTGAAATTACCAAAA
1 TACC-CTTGGTTTACAAAATTACTAAAA
* ** ** *
54256706 CACCCTTAATTTGTAAAATTACCAAAA
1 TACCCTTGGTTTACAAAATTACTAAAA
* * *
54256733 TACCCCTGATTTACAAAATTACAAAAA
1 TACCCTTGGTTTACAAAATTACTAAAA
*
54256760 TACCCTTGACTTT-CTAAAAATTA-TAGAAA
1 TACCCTTG-GTTTAC--AAAATTACTA-AAA
* *
54256789 TACCATTGGTTTACAAAATTACTGAAA
1 TACCCTTGGTTTACAAAATTACTAAAA
54256816 TACCCTTGGTTT
1 TACCCTTGGTTT
54256828 GTAGATTTAC
Statistics
Matches: 255, Mismatches: 43, Indels: 24
0.79 0.13 0.07
Matches are distributed among these distances:
26 22 0.09
27 206 0.81
28 9 0.04
29 18 0.07
ACGTcount: A:0.39, C:0.20, G:0.09, T:0.33
Consensus pattern (27 bp):
TACCCTTGGTTTACAAAATTACTAAAA
Found at i:54256920 original size:27 final size:27
Alignment explanation
Indices: 54256868--54256945 Score: 79
Period size: 27 Copynumber: 2.9 Consensus size: 27
54256858 AAATGACTAA
**
54256868 AATACCCCTATTA-GGTAAAAAAACCGT
1 AATACCCCTA-TAGGGTAAAATGACCGT
* *
54256895 AA-AGCCCCTGTAGGGTAAAGTGACCGT
1 AATA-CCCCTATAGGGTAAAATGACCGT
*
54256922 AATACCCCTATATGGTAAAATGAC
1 AATACCCCTATAGGGTAAAATGAC
54256946 GAATATGCCC
Statistics
Matches: 41, Mismatches: 7, Indels: 6
0.76 0.13 0.11
Matches are distributed among these distances:
26 3 0.07
27 37 0.90
28 1 0.02
ACGTcount: A:0.38, C:0.22, G:0.18, T:0.22
Consensus pattern (27 bp):
AATACCCCTATAGGGTAAAATGACCGT
Found at i:54257810 original size:24 final size:25
Alignment explanation
Indices: 54257753--54257818 Score: 107
Period size: 25 Copynumber: 2.7 Consensus size: 25
54257743 AGGAAGTGCT
*
54257753 AAAAGGGCTATGCCCCAGTTTACCG
1 AAAAGGGCTTTGCCCCAGTTTACCG
*
54257778 AAAAGGGCTTTGCCCCAGTTTATC-
1 AAAAGGGCTTTGCCCCAGTTTACCG
54257802 AAAAGGGCTTTGCCCCA
1 AAAAGGGCTTTGCCCCA
54257819 ATTATTAAAA
Statistics
Matches: 39, Mismatches: 2, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
24 17 0.44
25 22 0.56
ACGTcount: A:0.27, C:0.27, G:0.23, T:0.23
Consensus pattern (25 bp):
AAAAGGGCTTTGCCCCAGTTTACCG
Found at i:54257834 original size:24 final size:24
Alignment explanation
Indices: 54257753--54257834 Score: 94
Period size: 25 Copynumber: 3.4 Consensus size: 24
54257743 AGGAAGTGCT
* * *
54257753 AAAAGGGCTATGCCCCAGTTTACC
1 AAAAGGGCTTTGCCCCAGATTATC
*
54257777 GAAAAGGGCTTTGCCCCAGTTTATC
1 -AAAAGGGCTTTGCCCCAGATTATC
*
54257802 AAAAGGGCTTTGCCCCA-ATTATT
1 AAAAGGGCTTTGCCCCAGATTATC
54257825 AAAAGAGGCT
1 AAAAG-GGCT
54257835 AGGCCTCCAT
Statistics
Matches: 52, Mismatches: 4, Indels: 3
0.88 0.07 0.05
Matches are distributed among these distances:
23 9 0.17
24 21 0.40
25 22 0.42
ACGTcount: A:0.30, C:0.23, G:0.22, T:0.24
Consensus pattern (24 bp):
AAAAGGGCTTTGCCCCAGATTATC
Found at i:54258075 original size:31 final size:31
Alignment explanation
Indices: 54258040--54258245 Score: 276
Period size: 31 Copynumber: 6.7 Consensus size: 31
54258030 CATTTACAAT
*
54258040 AAAGGCTTCGGCCCAATGATATGATTTATGA
1 AAAGGCTTCGGCCCAGTGATATGATTTATGA
* *
54258071 AAAGGCTTCGGCGCAGAGATATGATTTATGA
1 AAAGGCTTCGGCCCAGTGATATGATTTATGA
* *
54258102 TAAGGCTTCGGCCTAGTGATATGATTTATGA
1 AAAGGCTTCGGCCCAGTGATATGATTTATGA
*
54258133 TAAGGCTTCGGCCCAGTGATATGATTTATGA
1 AAAGGCTTCGGCCCAGTGATATGATTTATGA
* *
54258164 TAAGGCTTCGGCCTAGTGATATGATTTATGA
1 AAAGGCTTCGGCCCAGTGATATGATTTATGA
* **
54258195 AAAGGCTTCGGCCCAGT-A-ACTG-TTAAACA
1 AAAGGCTTCGGCCCAGTGATA-TGATTTATGA
54258224 AAAGGCTTCGGCCCAGT-ATATG
1 AAAGGCTTCGGCCCAGTGATATG
54258246 CCAAGACTAA
Statistics
Matches: 159, Mismatches: 14, Indels: 6
0.89 0.08 0.03
Matches are distributed among these distances:
29 25 0.16
30 4 0.03
31 130 0.82
ACGTcount: A:0.29, C:0.17, G:0.25, T:0.29
Consensus pattern (31 bp):
AAAGGCTTCGGCCCAGTGATATGATTTATGA
Found at i:54260487 original size:27 final size:27
Alignment explanation
Indices: 54260465--54260993 Score: 202
Period size: 27 Copynumber: 19.6 Consensus size: 27
54260455 TTAGTTTACC
54260465 AAATTA-CATAAATACCCCTAGTTTGTA
1 AAATTACCA-AAATACCCCTAGTTTGTA
*
54260492 AAACTACCAAAATACCCCTAGTTTGTA
1 AAATTACCAAAATACCCCTAGTTTGTA
* *
54260519 AAATTATCAAAATACCCTTAGTTTGTA
1 AAATTACCAAAATACCCCTAGTTTGTA
* *
54260546 AAATTACTAAAATACCCCTAATTTGTA
1 AAATTACCAAAATACCCCTAGTTTGTA
** * **
54260573 AAATTACTGAAATA-CCCTCGACCTGTA
1 AAATTACCAAAATACCCCTAG-TTTGTA
* ** * *
54260600 AACTTATTAAAATA-CCCTCGACTTGTA
1 AAATTACCAAAATACCCCTAG-TTTGTA
* * *
54260627 AAATTACCAAAGTA-CCCTCGATT-TA
1 AAATTACCAAAATACCCCTAGTTTGTA
* **** * *
54260652 CATAATTATCGTTTTA-CCCTCGATT-TA
1 -A-AATTACCAAAATACCCCTAGTTTGTA
*** * *
54260679 CAGAATTACCATTTTA-CCCTCGATTTATA
1 -A-AATTACCAAAATACCCCTAG-TTTGTA
* * *** * *
54260708 GAATTACTATTTTA-CCCTTGATT-TA
1 AAATTACCAAAATACCCCTAGTTTGTA
***** * *
54260733 CAGAATTACTGTTTTA-CCCTCGATTTATA
1 -A-AATTACCAAAATACCCCTAG-TTTGTA
* * * **
54260762 AAATTACTAAAATACCCTTGGTTTACA
1 AAATTACCAAAATACCCCTAGTTTGTA
* **
54260789 AAATTACCAAAATA-CCCTCGATCAGTA
1 AAATTACCAAAATACCCCTAG-TTTGTA
* * *
54260816 AAATTACCAAATTA-CCCTAGTCTATA
1 AAATTACCAAAATACCCCTAGTTTGTA
* ** *
54260842 AAATTACTAAAATACCATTGGTTTGTA
1 AAATTACCAAAATACCCCTAGTTTGTA
*
54260869 AAATTACCATAATACCCCTAGTTTGTA
1 AAATTACCAAAATACCCCTAGTTTGTA
* * * * *
54260896 AAATTATCAAAATACCACTGGTTTATG
1 AAATTACCAAAATACCCCTAGTTTGTA
* *
54260923 AAATTACCAAAATACCCTTAATTTGTA
1 AAATTACCAAAATACCCCTAGTTTGTA
** * **
54260950 AAATTACCAAAATGTCCCTAATTTACA
1 AAATTACCAAAATACCCCTAGTTTGTA
*
54260977 AAATTACAAAAATACCC
1 AAATTACCAAAATACCC
54260994 TTGACTTTCT
Statistics
Matches: 399, Mismatches: 90, Indels: 26
0.77 0.17 0.05
Matches are distributed among these distances:
25 4 0.01
26 29 0.07
27 351 0.88
28 11 0.03
29 4 0.01
ACGTcount: A:0.39, C:0.21, G:0.07, T:0.33
Consensus pattern (27 bp):
AAATTACCAAAATACCCCTAGTTTGTA
Found at i:54260805 original size:54 final size:54
Alignment explanation
Indices: 54260465--54260995 Score: 261
Period size: 54 Copynumber: 9.9 Consensus size: 54
54260455 TTAGTTTACC
* * * * * * *
54260465 AAATTA-CATAAATACCC-CTAGTTTGTAAAACTACCAAAATACCCCTAGTTTGTA
1 AAATTACCA-AAATACCCTCGA-TTTATAAAATTACTAAAATACCCTTAATTTATA
* * * * *
54260519 AAATTATCAAAATACCCT-TAGTTTGTAAAATTACTAAAATACCCCTAATTTGTA
1 AAATTACCAAAATACCCTCGA-TTTATAAAATTACTAAAATACCCTTAATTTATA
** ** * * * ** * *
54260573 AAATTACTGAAATACCCTCGACCTGTAAACTTATTAAAATACCCTCGACTTGTA
1 AAATTACCAAAATACCCTCGATTTATAAAATTACTAAAATACCCTTAATTTATA
* * * ** ** *
54260627 AAATTACCAAAGTACCCTCGATTTACATAATTATCGT--TTTACCCTCGATTTACA
1 AAATTACCAAAATACCCTCGATTTATAAAATTA-C-TAAAATACCCTTAATTTATA
* *** * *** * *
54260681 GAATTACCATTTTACCCTCGATTTATAGAATTACTATTTTACCCTTGATTTACA
1 AAATTACCAAAATACCCTCGATTTATAAAATTACTAAAATACCCTTAATTTATA
* ***** ** *
54260735 GAATTACTGTTTTACCCTCGATTTATAAAATTACTAAAATACCCTTGGTTTACA
1 AAATTACCAAAATACCCTCGATTTATAAAATTACTAAAATACCCTTAATTTATA
* * * * *
54260789 AAATTACCAAAATACCCTCGA-TCAGTAAAATTACCAAATTACCC-TAGTCTATA
1 AAATTACCAAAATACCCTCGATTTA-TAAAATTACTAAAATACCCTTAATTTATA
* * * * * * * * * *
54260842 AAATTACTAAAATACCATTGGTTTGTAAAATTACCATAATACCCCTAGTTTGTA
1 AAATTACCAAAATACCCTCGATTTATAAAATTACTAAAATACCCTTAATTTATA
* * * * *
54260896 AAATTATCAAAATACCACT-GGTTTATGAAATTACCAAAATACCCTTAATTTGTA
1 AAATTACCAAAATACC-CTCGATTTATAAAATTACTAAAATACCCTTAATTTATA
* * * *
54260950 AAATTACCAAAATGTCCCT-AATTTACAAAATTACAAAAATACCCTT
1 AAATTACCAAAAT-ACCCTCGATTTATAAAATTACTAAAATACCCTT
54260996 GACTTTCTAA
Statistics
Matches: 384, Mismatches: 81, Indels: 24
0.79 0.17 0.05
Matches are distributed among these distances:
52 1 0.00
53 43 0.11
54 333 0.87
55 6 0.02
56 1 0.00
ACGTcount: A:0.39, C:0.21, G:0.07, T:0.34
Consensus pattern (54 bp):
AAATTACCAAAATACCCTCGATTTATAAAATTACTAAAATACCCTTAATTTATA
Found at i:54261044 original size:27 final size:27
Alignment explanation
Indices: 54261005--54261056 Score: 70
Period size: 27 Copynumber: 1.9 Consensus size: 27
54260995 TGACTTTCTA
54261005 AAAATTATAGAAATACCATTGGTTTAC
1 AAAATTATAGAAATACCATTGGTTTAC
* *
54261032 AAAATTACT-GAAATTCCCTTGGTTT
1 AAAATTA-TAGAAATACCATTGGTTT
54261057 GTAGATTTTC
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
27 21 0.95
28 1 0.05
ACGTcount: A:0.38, C:0.13, G:0.12, T:0.37
Consensus pattern (27 bp):
AAAATTATAGAAATACCATTGGTTTAC
Found at i:54262021 original size:25 final size:24
Alignment explanation
Indices: 54261983--54262051 Score: 111
Period size: 25 Copynumber: 2.8 Consensus size: 24
54261973 AGGAAGTGCT
*
54261983 AAAAGGGCTATGCCCCAGTTTACC
1 AAAAGGGCTTTGCCCCAGTTTACC
*
54262007 GAAAAGGGCTTTGCCCCAGTTTATC
1 -AAAAGGGCTTTGCCCCAGTTTACC
54262032 AAAAGGGCTTTGCCCCAGTT
1 AAAAGGGCTTTGCCCCAGTT
54262052 ATTAAAAGAG
Statistics
Matches: 42, Mismatches: 2, Indels: 1
0.93 0.04 0.02
Matches are distributed among these distances:
24 20 0.48
25 22 0.52
ACGTcount: A:0.26, C:0.26, G:0.23, T:0.25
Consensus pattern (24 bp):
AAAAGGGCTTTGCCCCAGTTTACC
Found at i:54262040 original size:24 final size:24
Alignment explanation
Indices: 54261983--54262064 Score: 112
Period size: 24 Copynumber: 3.4 Consensus size: 24
54261973 AGGAAGTGCT
* *
54261983 AAAAGGGCTATGCCCCAGTTTACC
1 AAAAGGGCTTTGCCCCAGTTTATC
54262007 GAAAAGGGCTTTGCCCCAGTTTATC
1 -AAAAGGGCTTTGCCCCAGTTTATC
*
54262032 AAAAGGGCTTTGCCCCAG-TTATT
1 AAAAGGGCTTTGCCCCAGTTTATC
54262055 AAAAGAGGCT
1 AAAAG-GGCT
54262065 AGGCCTCCAA
Statistics
Matches: 53, Mismatches: 3, Indels: 3
0.90 0.05 0.05
Matches are distributed among these distances:
23 9 0.17
24 22 0.42
25 22 0.42
ACGTcount: A:0.29, C:0.23, G:0.23, T:0.24
Consensus pattern (24 bp):
AAAAGGGCTTTGCCCCAGTTTATC
Found at i:54262307 original size:31 final size:31
Alignment explanation
Indices: 54262271--54262596 Score: 508
Period size: 31 Copynumber: 10.5 Consensus size: 31
54262261 ATTTACAGTA
* *
54262271 AAGGCTTCGGCCCAATGATATGATTTATGAG
1 AAGGCTTCGGCCCAGTGATATGATTTATGAT
* * *
54262302 AAGGCTTTGGCCTAGAGATATGATTTATGAT
1 AAGGCTTCGGCCCAGTGATATGATTTATGAT
54262333 AAGGCTTCGGCCCAGTGATATGATTTATGAT
1 AAGGCTTCGGCCCAGTGATATGATTTATGAT
54262364 AAGGCTTCGGCCCAGTGATATGATTTATGAT
1 AAGGCTTCGGCCCAGTGATATGATTTATGAT
** *
54262395 AAGGCTTCGGCCTTGTGATATGATTTATGAA
1 AAGGCTTCGGCCCAGTGATATGATTTATGAT
* * *
54262426 AATGCTTCGGCCTAGAGATATGATTTATGAT
1 AAGGCTTCGGCCCAGTGATATGATTTATGAT
*
54262457 AAGGCTTCGGCCTAGTGATATGATTTATGAT
1 AAGGCTTCGGCCCAGTGATATGATTTATGAT
*
54262488 AAGGCTTCAGCCCAGTGATATGATTTATGAT
1 AAGGCTTCGGCCCAGTGATATGATTTATGAT
54262519 AAGGCTTCGGCCCAGTGATATGATTTATGAT
1 AAGGCTTCGGCCCAGTGATATGATTTATGAT
* *
54262550 AAGGCTTCGGCCTAGTGATATGATTTATGAA
1 AAGGCTTCGGCCCAGTGATATGATTTATGAT
*
54262581 AAAGCTTCGGCCCAGT
1 AAGGCTTCGGCCCAGT
54262597 AACCGTTAAA
Statistics
Matches: 271, Mismatches: 24, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
31 271 1.00
ACGTcount: A:0.27, C:0.15, G:0.25, T:0.33
Consensus pattern (31 bp):
AAGGCTTCGGCCCAGTGATATGATTTATGAT
Found at i:54266454 original size:25 final size:25
Alignment explanation
Indices: 54266420--54266488 Score: 77
Period size: 25 Copynumber: 2.7 Consensus size: 25
54266410 TTTTATCAAA
*
54266420 AATTCAATTAGTATAAAATATT-AAT
1 AATTCAATTAAT-TAAAATATTAAAT
*
54266445 AATTCAATTAATTAAAATTTTAAAT
1 AATTCAATTAATTAAAATATTAAAT
* *
54266470 AATTAAATAAATTTAAAAT
1 AATTCAATTAA-TTAAAAT
54266489 TTAGGAGGAA
Statistics
Matches: 38, Mismatches: 4, Indels: 3
0.84 0.09 0.07
Matches are distributed among these distances:
24 8 0.21
25 23 0.61
26 7 0.18
ACGTcount: A:0.55, C:0.03, G:0.01, T:0.41
Consensus pattern (25 bp):
AATTCAATTAATTAAAATATTAAAT
Found at i:54270197 original size:33 final size:33
Alignment explanation
Indices: 54270155--54270263 Score: 107
Period size: 33 Copynumber: 3.3 Consensus size: 33
54270145 TATGTAAGTT
*
54270155 CATAGTTGGGCTATAGCATTCTTATGATAAGAC
1 CATAATTGGGCTATAGCATTCTTATGATAAGAC
* * *
54270188 CATAATTGGGTTATGGCA--C-TATGGACGTAAAAC
1 CATAATTGGGCTATAGCATTCTTAT-GA--TAAGAC
* * *
54270221 CATAGTTAGGCTATAGCATTCTGATGATAAGAC
1 CATAATTGGGCTATAGCATTCTTATGATAAGAC
54270254 CATAATTGGG
1 CATAATTGGG
54270264 TTATGGCACT
Statistics
Matches: 58, Mismatches: 12, Indels: 12
0.71 0.15 0.15
Matches are distributed among these distances:
30 3 0.05
31 3 0.05
33 47 0.81
35 3 0.05
36 2 0.03
ACGTcount: A:0.32, C:0.15, G:0.23, T:0.30
Consensus pattern (33 bp):
CATAATTGGGCTATAGCATTCTTATGATAAGAC
Found at i:54270285 original size:33 final size:32
Alignment explanation
Indices: 54270182--54270289 Score: 101
Period size: 33 Copynumber: 3.3 Consensus size: 32
54270172 ATTCTTATGA
* *
54270182 TAAGACCATAATTGGGTTATGGCACTATGGACG
1 TAAGACCATAATTGGGTTATGGCACTA-CGATG
* * * * * *
54270215 TAAAACCATAGTTAGGCTATAGCA-TTCTGATG
1 TAAGACCATAATTGGGTTATGGCACTAC-GATG
54270247 ATAAGACCATAATTGGGTTATGGCACTACGAATG
1 -TAAGACCATAATTGGGTTATGGCACTACG-ATG
54270281 TAAGACCAT
1 TAAGACCAT
54270290 GTCAGGGCCA
Statistics
Matches: 57, Mismatches: 14, Indels: 8
0.72 0.18 0.10
Matches are distributed among these distances:
32 4 0.07
33 48 0.84
34 5 0.09
ACGTcount: A:0.34, C:0.16, G:0.22, T:0.28
Consensus pattern (32 bp):
TAAGACCATAATTGGGTTATGGCACTACGATG
Found at i:54270289 original size:66 final size:66
Alignment explanation
Indices: 54270146--54270289 Score: 216
Period size: 66 Copynumber: 2.2 Consensus size: 66
54270136 CAGTGTTTAT
** * * *
54270146 ATGTAAGTTCATAGTTGGGCTATAGCATTCTTATGATAAGACCATAATTGGGTTATGGCACTATG
1 ATGTAAGACCATAGTTAGGCTATAGCATTCTGATGATAAGACCATAATTGGGTTATGGCACTACG
*
54270211 G
66 A
* *
54270212 ACGTAAAACCATAGTTAGGCTATAGCATTCTGATGATAAGACCATAATTGGGTTATGGCACTACG
1 ATGTAAGACCATAGTTAGGCTATAGCATTCTGATGATAAGACCATAATTGGGTTATGGCACTACG
54270277 A
66 A
54270278 ATGTAAGACCAT
1 ATGTAAGACCAT
54270290 GTCAGGGCCA
Statistics
Matches: 68, Mismatches: 10, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
66 68 1.00
ACGTcount: A:0.33, C:0.15, G:0.22, T:0.31
Consensus pattern (66 bp):
ATGTAAGACCATAGTTAGGCTATAGCATTCTGATGATAAGACCATAATTGGGTTATGGCACTACG
A
Found at i:54273444 original size:54 final size:54
Alignment explanation
Indices: 54273248--54273501 Score: 296
Period size: 54 Copynumber: 4.7 Consensus size: 54
54273238 TTTCCTTTTT
* * * * * * * *
54273248 GAACTTACCATTGTCATGTCTTGACATGGTCTTACGTGGTATCCTTGCCTTAT-
1 GAACTTATCAATGCCATGCCTTGGCATGGTCTTACATGATTTCCTTGCCTTATA
* * *** *
54273301 GAACTCACCAATGCCATGCCTTGGCATGGTCTTACATG-GGACCTTTTCCTTATA
1 GAACTTATCAATGCCATGCCTTGGCATGGTCTTACATGATTTCC-TTGCCTTATA
* * ** *
54273355 GTAACTCATCAATGCCATGGCTTAACATGGTCTTACATGATTTCCTTGCCGTATA
1 G-AACTTATCAATGCCATGCCTTGGCATGGTCTTACATGATTTCCTTGCCTTATA
*
54273410 GAACTTATCAATGTCATGCCTTGGCATGGTCTTACATGATTTCCTTGCCTTATA
1 GAACTTATCAATGCCATGCCTTGGCATGGTCTTACATGATTTCCTTGCCTTATA
54273464 GAACTTATCAATGCCATGCCTTGGCATGGTCTTACATG
1 GAACTTATCAATGCCATGCCTTGGCATGGTCTTACATG
54273502 TATCCTTTCT
Statistics
Matches: 171, Mismatches: 26, Indels: 7
0.84 0.13 0.03
Matches are distributed among these distances:
52 2 0.01
53 40 0.23
54 85 0.50
55 42 0.25
56 2 0.01
ACGTcount: A:0.22, C:0.24, G:0.18, T:0.35
Consensus pattern (54 bp):
GAACTTATCAATGCCATGCCTTGGCATGGTCTTACATGATTTCCTTGCCTTATA
Found at i:54273766 original size:45 final size:44
Alignment explanation
Indices: 54273605--54273767 Score: 146
Period size: 45 Copynumber: 3.5 Consensus size: 44
54273595 CATGTTCCAA
* *
54273605 ACATGGTCTTACATGGTATCCTTGTCTTAGTGCCAATGTCATATCTTG
1 ACATGGTCTTACATGG-ATCCTTGCCTTA---CCAATGTCATGTCTTG
** * ** * * *
54273653 ATGTGGTCTTACATGGAGTCCTTAATCAATGCCGATGCCATGTCTTG
1 ACATGGTCTTACATGGA-TCCTT--GCCTTACCAATGTCATGTCTTG
*
54273700 ACATGGTCTTACACGAGATCCTTGCCTTACCAATGTCATGTCTTG
1 ACATGGTCTTACATG-GATCCTTGCCTTACCAATGTCATGTCTTG
54273745 ACATGGTCTTACATGGTATCCTT
1 ACATGGTCTTACATGG-ATCCTT
54273768 AACCATCAAT
Statistics
Matches: 90, Mismatches: 20, Indels: 13
0.73 0.16 0.11
Matches are distributed among these distances:
44 1 0.01
45 36 0.40
47 31 0.34
48 21 0.23
50 1 0.01
ACGTcount: A:0.21, C:0.23, G:0.20, T:0.36
Consensus pattern (44 bp):
ACATGGTCTTACATGGATCCTTGCCTTACCAATGTCATGTCTTG
Found at i:54274434 original size:30 final size:31
Alignment explanation
Indices: 54274395--54274452 Score: 100
Period size: 30 Copynumber: 1.9 Consensus size: 31
54274385 CTAACTCAAA
54274395 CTTTGGCAAAATTATAATTTTGCCCCTAAAC
1 CTTTGGCAAAATTATAATTTTGCCCCTAAAC
*
54274426 CTTT-GCAAAATTATGATTTTGCCCCTA
1 CTTTGGCAAAATTATAATTTTGCCCCTA
54274453 GGCTCGAAAA
Statistics
Matches: 26, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
30 22 0.85
31 4 0.15
ACGTcount: A:0.29, C:0.22, G:0.10, T:0.38
Consensus pattern (31 bp):
CTTTGGCAAAATTATAATTTTGCCCCTAAAC
Found at i:54280737 original size:28 final size:27
Alignment explanation
Indices: 54280694--54280799 Score: 76
Period size: 28 Copynumber: 3.7 Consensus size: 27
54280684 GAAATCAGTG
54280694 TTAA-CTGGGCCTTAGCCCATATCAATA
1 TTAATCTGGGCC-TAGCCCATATCAATA
54280721 TTAATCTGGGCCATAGCCCCTTACAGTATCAGA-A
1 TTAATCTGGGCC-TAG--CC---CA-TATCA-ATA
*
54280755 -TATAT-TGGGCCTAGCCCATATCAGTA
1 TTA-ATCTGGGCCTAGCCCATATCAATA
54280781 TTAATCTGGGCCGTAGCCC
1 TTAATCTGGGCC-TAGCCC
54280800 TATTACAAGT
Statistics
Matches: 64, Mismatches: 2, Indels: 25
0.70 0.02 0.27
Matches are distributed among these distances:
26 8 0.12
27 14 0.22
28 16 0.25
30 4 0.06
32 3 0.05
33 10 0.16
34 8 0.12
35 1 0.02
ACGTcount: A:0.26, C:0.26, G:0.19, T:0.28
Consensus pattern (27 bp):
TTAATCTGGGCCTAGCCCATATCAATA
Found at i:54280792 original size:27 final size:28
Alignment explanation
Indices: 54280687--54280799 Score: 90
Period size: 27 Copynumber: 3.9 Consensus size: 28
54280677 CTATTCAGAA
* *
54280687 ATCAGTGTTAA-CTGGGCCTTAGCCCAT
1 ATCAGTATTAATCTGGGCCATAGCCCAT
*
54280714 ATCAATATTAATCTGGGCCATAGCCCCTTACAGT
1 ATCAGTATTAATCTGGGCCATAG--CC---CA-T
*
54280748 ATCAG-AATATAT-TGGGCC-TAGCCCAT
1 ATCAGTATTA-ATCTGGGCCATAGCCCAT
*
54280774 ATCAGTATTAATCTGGGCCGTAGCCC
1 ATCAGTATTAATCTGGGCCATAGCCC
54280800 TATTACAAGT
Statistics
Matches: 69, Mismatches: 6, Indels: 21
0.72 0.06 0.22
Matches are distributed among these distances:
26 8 0.12
27 20 0.29
28 16 0.23
30 4 0.06
32 3 0.04
33 11 0.16
34 7 0.10
ACGTcount: A:0.27, C:0.26, G:0.19, T:0.28
Consensus pattern (28 bp):
ATCAGTATTAATCTGGGCCATAGCCCAT
Found at i:54280818 original size:60 final size:59
Alignment explanation
Indices: 54280699--54280835 Score: 170
Period size: 60 Copynumber: 2.3 Consensus size: 59
54280689 CAGTGTTAAC
*
54280699 TGGGCCTTAGCCCATATCAATATTAATCTGGGCCATAGCCCCTTACAGTATCAGAATATAT
1 TGGGCC-TAGCCCATATCAATATTAATCTGGGCCATAGCCCATTACAG-ATCAGAATATAT
* *
54280760 TGGGCCTAGCCCATATCAGTATTAATCTGGGCCGTAGCCCTATTACA-AGTC-GAGATATAT
1 TGGGCCTAGCCCATATCAATATTAATCTGGGCCATAGCCC-ATTACAGA-TCAGA-ATATAT
* *
54280820 TGGGCCTTGGCCATAT
1 TGGGCCTAGCCCATAT
54280836 TAACACAGTT
Statistics
Matches: 68, Mismatches: 5, Indels: 7
0.85 0.06 0.09
Matches are distributed among these distances:
59 3 0.04
60 54 0.79
61 11 0.16
ACGTcount: A:0.26, C:0.24, G:0.20, T:0.29
Consensus pattern (59 bp):
TGGGCCTAGCCCATATCAATATTAATCTGGGCCATAGCCCATTACAGATCAGAATATAT
Found at i:54280882 original size:19 final size:20
Alignment explanation
Indices: 54280840--54280882 Score: 52
Period size: 19 Copynumber: 2.2 Consensus size: 20
54280830 CCATATTAAC
** *
54280840 ACAGTTGGGCCCATTTCAAT
1 ACAGTTGGGCCCATAACAAA
54280860 ACAGTT-GGCCCATAACAAA
1 ACAGTTGGGCCCATAACAAA
54280879 ACAG
1 ACAG
54280883 CCTCATATGA
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
19 14 0.70
20 6 0.30
ACGTcount: A:0.35, C:0.26, G:0.19, T:0.21
Consensus pattern (20 bp):
ACAGTTGGGCCCATAACAAA
Found at i:54283241 original size:19 final size:17
Alignment explanation
Indices: 54283204--54283246 Score: 50
Period size: 19 Copynumber: 2.4 Consensus size: 17
54283194 ATACATGCAG
54283204 TAATATTTTTCTAATAA
1 TAATATTTTTCTAATAA
*
54283221 TAATAATTTTATCTCATAA
1 TAAT-ATTTT-TCTAATAA
*
54283240 TACTATT
1 TAATATT
54283247 AAAATTTCGT
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
17 4 0.18
18 8 0.36
19 10 0.45
ACGTcount: A:0.40, C:0.09, G:0.00, T:0.51
Consensus pattern (17 bp):
TAATATTTTTCTAATAA
Found at i:54285453 original size:43 final size:42
Alignment explanation
Indices: 54285357--54285473 Score: 139
Period size: 43 Copynumber: 2.8 Consensus size: 42
54285347 CACACGGTAC
* * *
54285357 CATACCAATGCCATATCCCAGATATGGTCTTACATGGGATCT
1 CATATCAATGCCATATCCCAGATATGGTCTTACACGAGATCT
* * *
54285399 CGTATCAATGCCAATAGCCCAGCTATGGTCTTACACGA-AGTCT
1 CATATCAATGCC-ATATCCCAGATATGGTCTTACACGAGA-TCT
54285442 CATAT-AGATGCCATATCCCAGATATGGTCTTA
1 CATATCA-ATGCCATATCCCAGATATGGTCTTA
54285474 TACATAGTCT
Statistics
Matches: 63, Mismatches: 9, Indels: 6
0.81 0.12 0.08
Matches are distributed among these distances:
42 30 0.48
43 33 0.52
ACGTcount: A:0.29, C:0.26, G:0.17, T:0.28
Consensus pattern (42 bp):
CATATCAATGCCATATCCCAGATATGGTCTTACACGAGATCT
Found at i:54285483 original size:42 final size:42
Alignment explanation
Indices: 54285357--54285483 Score: 127
Period size: 42 Copynumber: 3.0 Consensus size: 42
54285347 CACACGGTAC
* *
54285357 CATACCAATGCCATATCCCAGATATGGTC-T-TACATGGGATCT
1 CATATCAATGCCATATCCCAGATATGGTCTTATACAT-AG-TCT
* * * *
54285399 CGTATCAATGCCAATAGCCCAGCTATGGTCTTACACGA-AGTCT
1 CATATCAATGCC-ATATCCCAGATATGGTCTTATAC-ATAGTCT
54285442 CATAT-AGATGCCATATCCCAGATATGGTCTTATACATAGTCT
1 CATATCA-ATGCCATATCCCAGATATGGTCTTATACATAGTCT
54285484 TAGTAACACT
Statistics
Matches: 69, Mismatches: 10, Indels: 12
0.76 0.11 0.13
Matches are distributed among these distances:
41 1 0.01
42 36 0.52
43 27 0.39
44 2 0.03
45 2 0.03
46 1 0.01
ACGTcount: A:0.29, C:0.25, G:0.17, T:0.29
Consensus pattern (42 bp):
CATATCAATGCCATATCCCAGATATGGTCTTATACATAGTCT
Found at i:54291124 original size:34 final size:34
Alignment explanation
Indices: 54291056--54291124 Score: 79
Period size: 34 Copynumber: 2.0 Consensus size: 34
54291046 GTTTGGTTTG
* *
54291056 AGATGATGATATGATGAGTCTTGTGATATAAAAT
1 AGATGATGATATGATGAATCTAGTGATATAAAAT
*
54291090 AGATGAT-ATTATGATGAAT-TAGTGAATATGAAAT
1 AGATGATGA-TATGATGAATCTAGTG-ATATAAAAT
54291124 A
1 A
54291125 TATGTAAGTT
Statistics
Matches: 30, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
33 5 0.17
34 25 0.83
ACGTcount: A:0.42, C:0.01, G:0.22, T:0.35
Consensus pattern (34 bp):
AGATGATGATATGATGAATCTAGTGATATAAAAT
Found at i:54299501 original size:31 final size:32
Alignment explanation
Indices: 54299444--54299505 Score: 90
Period size: 31 Copynumber: 2.0 Consensus size: 32
54299434 ATGAAGTCAC
* *
54299444 CAGATATAGATATTGTGGCTAGGCCACCAGAA
1 CAGATATAGATATTGTGGCGAAGCCACCAGAA
*
54299476 CAGATATATATA-TGTGGCGAAGCCACCAGA
1 CAGATATAGATATTGTGGCGAAGCCACCAGA
54299506 TTGCAGCGAG
Statistics
Matches: 27, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
31 16 0.59
32 11 0.41
ACGTcount: A:0.35, C:0.19, G:0.24, T:0.21
Consensus pattern (32 bp):
CAGATATAGATATTGTGGCGAAGCCACCAGAA
Found at i:54299773 original size:8 final size:8
Alignment explanation
Indices: 54299760--54299791 Score: 55
Period size: 8 Copynumber: 4.0 Consensus size: 8
54299750 TACCAAAGTG
54299760 GGCCCGTT
1 GGCCCGTT
54299768 GGCCCGTT
1 GGCCCGTT
*
54299776 GGCCCATT
1 GGCCCGTT
54299784 GGCCCGTT
1 GGCCCGTT
54299792 TTTGGACCAT
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
8 22 1.00
ACGTcount: A:0.03, C:0.38, G:0.34, T:0.25
Consensus pattern (8 bp):
GGCCCGTT
Found at i:54310931 original size:119 final size:120
Alignment explanation
Indices: 54310755--54310977 Score: 335
Period size: 119 Copynumber: 1.9 Consensus size: 120
54310745 TACTTGTTCA
* * *
54310755 AATGCCTTCGGGACATAGCCCGGTTATAGTAACTCGCACAAATGCCTTCGGATCTTAGTCCGGTT
1 AATGCCTTCGGGACATAGCCCGGATATAGTAACTCGCACAAATGCCTTCGAATCTTAGTCCGGAT
*
54310820 ATAGTAAC-TCGCACAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCACC
66 ATAGTAACTTAGCACAAA-GCCTTCGGGACTTAACCCGGATTTAGTAACTCGCACC
*
54310875 AATGCCTTCGGG-CTTAGCCCGGA-ATTAGTAACTCGCACAAATGCCTTCGAATCTTAGTCCGGA
1 AATGCCTTCGGGACATAGCCCGGATA-TAGTAACTCGCACAAATGCCTTCGAATCTTAGTCCGGA
* * *
54310938 TATGGTCACTTAGCACAAAGCCTTCGGGACTTAGCCCGGA
65 TATAGTAACTTAGCACAAAGCCTTCGGGACTTAACCCGGA
54310978 CATCATTCAA
Statistics
Matches: 93, Mismatches: 8, Indels: 5
0.88 0.08 0.05
Matches are distributed among these distances:
118 1 0.01
119 72 0.77
120 20 0.22
ACGTcount: A:0.26, C:0.27, G:0.22, T:0.25
Consensus pattern (120 bp):
AATGCCTTCGGGACATAGCCCGGATATAGTAACTCGCACAAATGCCTTCGAATCTTAGTCCGGAT
ATAGTAACTTAGCACAAAGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCACC
Found at i:54310977 original size:40 final size:40
Alignment explanation
Indices: 54310753--54310977 Score: 271
Period size: 40 Copynumber: 5.7 Consensus size: 40
54310743 GCTACTTGTT
* *
54310753 CAAATGCCTTCGGGACATAGCCCGGTTATAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGATATAGTAACTCGCA
* *
54310793 CAAATGCCTTC-GGATCTTAGTCCGGTTATAGTAACTCGCA
1 CAAATGCCTTCGGGA-CTTAGCCCGGATATAGTAACTCGCA
* *
54310833 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGATATAGTAACTCGCA
*
54310873 CCAATGCCTTCGGG-CTTAGCCCGGA-ATTAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGATA-TAGTAACTCGCA
* * * * *
54310912 CAAATGCCTTC-GAATCTTAGTCCGGATATGGTCACTTAGCA
1 CAAATGCCTTCGGGA-CTTAGCCCGGATATAGTAAC-TCGCA
54310953 CAAA-GCCTTCGGGACTTAGCCCGGA
1 CAAATGCCTTCGGGACTTAGCCCGGA
54310978 CATCATTCAA
Statistics
Matches: 160, Mismatches: 17, Indels: 16
0.83 0.09 0.08
Matches are distributed among these distances:
38 1 0.01
39 35 0.22
40 110 0.69
41 14 0.09
ACGTcount: A:0.26, C:0.28, G:0.22, T:0.25
Consensus pattern (40 bp):
CAAATGCCTTCGGGACTTAGCCCGGATATAGTAACTCGCA
Found at i:54319187 original size:119 final size:120
Alignment explanation
Indices: 54319011--54319226 Score: 330
Period size: 119 Copynumber: 1.8 Consensus size: 120
54319001 TACTCGTTCA
* *
54319011 AATGCCTTCGGGACATAGCCCGGTTATAGTAACTCGCACAAATGCCTTCGGATCTTAGTCCGGTT
1 AATGCCTTCGGGACATAGCCCGGATATAGTAACTCGCACAAATGCCTTCGGATCTTAGTCCGGAT
*
54319076 ATAGTAAC-TCGCACAAATGCCTTCAGGACTTAACCCAGATTTAGTAACTCGCACC
66 ATAGTAACTTAGCACAAA-GCCTTCAGGACTTAACCCAGATTTAGTAACTCGCACC
*
54319131 AATGCCTTCGGG-CTTAGCCCGGA-ATTAGTAACTCGCACAAATGCCTTCGGATCTTAGTCCGGA
1 AATGCCTTCGGGACATAGCCCGGATA-TAGTAACTCGCACAAATGCCTTCGGATCTTAGTCCGGA
* * *
54319194 TATGGTCACTTAGCACAAAGCCTTCGGGACTTA
65 TATAGTAACTTAGCACAAAGCCTTCAGGACTTA
54319227 GCCCGGACAT
Statistics
Matches: 87, Mismatches: 7, Indels: 5
0.88 0.07 0.05
Matches are distributed among these distances:
118 1 0.01
119 66 0.76
120 20 0.23
ACGTcount: A:0.26, C:0.27, G:0.21, T:0.26
Consensus pattern (120 bp):
AATGCCTTCGGGACATAGCCCGGATATAGTAACTCGCACAAATGCCTTCGGATCTTAGTCCGGAT
ATAGTAACTTAGCACAAAGCCTTCAGGACTTAACCCAGATTTAGTAACTCGCACC
Found at i:54319217 original size:79 final size:79
Alignment explanation
Indices: 54319009--54319233 Score: 222
Period size: 79 Copynumber: 2.8 Consensus size: 79
54318999 GCTACTCGTT
* * * * * * * *
54319009 CAAATGCCTTCGGGACATAGCCCGGTTATAGTAACTCGCACAAATGCCTTCGGATCTTAGTCCGG
1 CAAATGCCTTCAGGACTTAACCCAGATATAGTAACTAGCACAAA-GCCTTCGG-GCTTAGCCCGG
*
54319074 -TTATAGTAACTCGCA
64 AATATAGTAACTCGCA
* * *
54319089 CAAATGCCTTCAGGACTTAACCCAGATTTAGTAACTCGCACCAATGCCTTCGGGCTTAGCCCGGA
1 CAAATGCCTTCAGGACTTAACCCAGATATAGTAACTAGCA-CAAAGCCTTCGGGCTTAGCCCGGA
54319154 AT-TAGTAACTCGCA
65 ATATAGTAACTCGCA
** * * *
54319168 CAAATGCCTTC-GGATCTTAGTCCGGATATGGTCACTTAGCACAAAGCCTTCGGGACTTAGCCCG
1 CAAATGCCTTCAGGA-CTTAACCCAGATATAGTAAC-TAGCACAAAGCCTTCGGG-CTTAGCCCG
54319232 GA
63 GA
54319234 CATCATTCAA
Statistics
Matches: 122, Mismatches: 18, Indels: 10
0.81 0.12 0.07
Matches are distributed among these distances:
78 3 0.02
79 58 0.48
80 58 0.48
81 3 0.02
ACGTcount: A:0.26, C:0.28, G:0.21, T:0.25
Consensus pattern (79 bp):
CAAATGCCTTCAGGACTTAACCCAGATATAGTAACTAGCACAAAGCCTTCGGGCTTAGCCCGGAA
TATAGTAACTCGCA
Found at i:54319233 original size:40 final size:40
Alignment explanation
Indices: 54318992--54319233 Score: 262
Period size: 40 Copynumber: 6.1 Consensus size: 40
54318982 GAATTTAACT
** *
54318992 GGATATAGCT-ACTCGTTCAAATGCCTTCGGGACATAGCCC
1 GGATATAG-TAACTCGCACAAATGCCTTCGGGACTTAGCCC
* *
54319032 GGTTATAGTAACTCGCACAAATGCCTTC-GGATCTTAGTCC
1 GGATATAGTAACTCGCACAAATGCCTTCGGGA-CTTAGCCC
* * *
54319072 GGTTATAGTAACTCGCACAAATGCCTTCAGGACTTAACCC
1 GGATATAGTAACTCGCACAAATGCCTTCGGGACTTAGCCC
* * *
54319112 AGATTTAGTAACTCGCACCAATGCCTTCGGG-CTTAGCCC
1 GGATATAGTAACTCGCACAAATGCCTTCGGGACTTAGCCC
*
54319151 GGA-ATTAGTAACTCGCACAAATGCCTTC-GGATCTTAGTCC
1 GGATA-TAGTAACTCGCACAAATGCCTTCGGGA-CTTAGCCC
* * *
54319191 GGATATGGTCACTTAGCACAAA-GCCTTCGGGACTTAGCCC
1 GGATATAGTAAC-TCGCACAAATGCCTTCGGGACTTAGCCC
54319231 GGA
1 GGA
54319234 CATCATTCAA
Statistics
Matches: 172, Mismatches: 21, Indels: 18
0.82 0.10 0.09
Matches are distributed among these distances:
38 2 0.01
39 35 0.20
40 120 0.70
41 15 0.09
ACGTcount: A:0.26, C:0.27, G:0.21, T:0.26
Consensus pattern (40 bp):
GGATATAGTAACTCGCACAAATGCCTTCGGGACTTAGCCC
Found at i:54328947 original size:40 final size:40
Alignment explanation
Indices: 54328917--54329086 Score: 216
Period size: 40 Copynumber: 4.3 Consensus size: 40
54328907 GGACTAAGAT
* *
54328917 CCGAAGGCCTTTGTGCGAGATACTAAATCCGGGTTAAGTC
1 CCGAAGGCATTCGTGCGAGATACTAAATCCGGGTTAAGTC
* **
54328957 CCGAAGGCATTCGTGCGAGTTGTTAAATCCGGGTTAAGTC
1 CCGAAGGCATTCGTGCGAGATACTAAATCCGGGTTAAGTC
* * ** *
54328997 CCGAAGGCATTCATGCGAGTTGTTAAATCCGGGTTATGTC
1 CCGAAGGCATTCGTGCGAGATACTAAATCCGGGTTAAGTC
* * *
54329037 CCGAAGGCATT-GTGCGAGATACTAAAACCGGGCTATGTC
1 CCGAAGGCATTCGTGCGAGATACTAAATCCGGGTTAAGTC
54329076 CCGAAGGCATT
1 CCGAAGGCATT
54329087 TGAACGAGGA
Statistics
Matches: 117, Mismatches: 13, Indels: 1
0.89 0.10 0.01
Matches are distributed among these distances:
39 33 0.28
40 84 0.72
ACGTcount: A:0.25, C:0.22, G:0.28, T:0.25
Consensus pattern (40 bp):
CCGAAGGCATTCGTGCGAGATACTAAATCCGGGTTAAGTC
Found at i:54329001 original size:80 final size:79
Alignment explanation
Indices: 54328864--54329088 Score: 220
Period size: 80 Copynumber: 2.8 Consensus size: 79
54328854 TTGAATGCTG
* * * * * * * *
54328864 TCCGGGCTAAGTCCCGAAGGCTTTGTGCTA-AGTGAATATATCCGGACTAAGAT-CCGAAGGCCT
1 TCCGGGTTAAGTCCCGAAGGCATTGTGCGAGA-T-ACTAAAACCGGGCTAAG-TCCCGAAGGCAT
54328927 TTGTGCGAGATACTAAA
63 TTGTGCGAGATACTAAA
* ** * * *
54328944 TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTGTTAAATCCGGGTTAAGTCCCGAAGGCATTC
1 TCCGGGTTAAGTCCCGAAGGCATT-GTGCGAGATACTAAAACCGGGCTAAGTCCCGAAGGCATTT
* * **
54329009 ATGCGAGTTGTTAAA
65 GTGCGAGATACTAAA
* *
54329024 TCCGGGTTATGTCCCGAAGGCATTGTGCGAGATACTAAAACCGGGCTATGTCCCGAAGGCATTTG
1 TCCGGGTTAAGTCCCGAAGGCATTGTGCGAGATACTAAAACCGGGCTAAGTCCCGAAGGCATTTG
54329089 AACGAGGAGC
Statistics
Matches: 118, Mismatches: 24, Indels: 7
0.79 0.16 0.05
Matches are distributed among these distances:
79 34 0.29
80 78 0.66
81 6 0.05
ACGTcount: A:0.25, C:0.21, G:0.28, T:0.26
Consensus pattern (79 bp):
TCCGGGTTAAGTCCCGAAGGCATTGTGCGAGATACTAAAACCGGGCTAAGTCCCGAAGGCATTTG
TGCGAGATACTAAA
Found at i:54329106 original size:79 final size:79
Alignment explanation
Indices: 54328939--54329121 Score: 210
Period size: 79 Copynumber: 2.3 Consensus size: 79
54328929 GTGCGAGATA
* ** * *
54328939 CTAAATCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTGTTAAATCCGGGTTAAGTCCCGAAGG
1 CTAAATCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGATACTAAAACCGGGCTAAGTCCCGAAGG
**
54329004 CATTCATGCGAGTTG
66 CATT-ATGCGAGGAG
* * *
54329019 TTAAATCCGGGTTATGTCCCGAAGGCATT-GTGCGAGATACTAAAACCGGGCTATGTCCCGAAGG
1 CTAAATCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGATACTAAAACCGGGCTAAGTCCCGAAGG
54329083 CATT-TGAACGAGGAG
66 CATTATG--CGAGGAG
* *
54329098 CTATATCC-GGTTAAATCCCGAAGG
1 CTAAATCCGGGTTAAGTCCCGAAGG
54329122 TACGTGATTT
Statistics
Matches: 87, Mismatches: 14, Indels: 6
0.81 0.13 0.06
Matches are distributed among these distances:
77 2 0.02
78 14 0.16
79 44 0.51
80 27 0.31
ACGTcount: A:0.26, C:0.21, G:0.28, T:0.25
Consensus pattern (79 bp):
CTAAATCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGATACTAAAACCGGGCTAAGTCCCGAAGG
CATTATGCGAGGAG
Found at i:54336192 original size:40 final size:40
Alignment explanation
Indices: 54336162--54336331 Score: 216
Period size: 40 Copynumber: 4.3 Consensus size: 40
54336152 GGACTAAGAT
* *
54336162 CCGAAGGCCTTTGTGCGAGATACTAAATCCGGGTTAAGTC
1 CCGAAGGCATTCGTGCGAGATACTAAATCCGGGTTAAGTC
* **
54336202 CCGAAGGCATTCGTGCGAGTTGTTAAATCCGGGTTAAGTC
1 CCGAAGGCATTCGTGCGAGATACTAAATCCGGGTTAAGTC
* ** *
54336242 CCGAAGGCATTCGTGCGAGTTGTTAAATCCGGGTTATGTC
1 CCGAAGGCATTCGTGCGAGATACTAAATCCGGGTTAAGTC
* * * *
54336282 CCGAAGGCATT-GTGTGAGATACTAAAACCGGGCTATGTC
1 CCGAAGGCATTCGTGCGAGATACTAAATCCGGGTTAAGTC
54336321 CCGAAGGCATT
1 CCGAAGGCATT
54336332 TGAACGAGGA
Statistics
Matches: 118, Mismatches: 12, Indels: 1
0.90 0.09 0.01
Matches are distributed among these distances:
39 33 0.28
40 85 0.72
ACGTcount: A:0.24, C:0.21, G:0.29, T:0.26
Consensus pattern (40 bp):
CCGAAGGCATTCGTGCGAGATACTAAATCCGGGTTAAGTC
Found at i:54336246 original size:80 final size:79
Alignment explanation
Indices: 54336109--54336333 Score: 220
Period size: 80 Copynumber: 2.8 Consensus size: 79
54336099 TTGAATGCTG
* * * * * * * *
54336109 TCCGGGCTAAGTCCCGAAGGCTTTGTGCTA-AGTGAATATATCCGGACTAAGAT-CCGAAGGCCT
1 TCCGGGTTAAGTCCCGAAGGCATTGTGCGAGA-T-ACTAAAACCGGGCTAAG-TCCCGAAGGCAT
54336172 TTGTGCGAGATACTAAA
63 TTGTGCGAGATACTAAA
* ** * * *
54336189 TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTGTTAAATCCGGGTTAAGTCCCGAAGGCATTC
1 TCCGGGTTAAGTCCCGAAGGCATT-GTGCGAGATACTAAAACCGGGCTAAGTCCCGAAGGCATTT
* **
54336254 GTGCGAGTTGTTAAA
65 GTGCGAGATACTAAA
* * *
54336269 TCCGGGTTATGTCCCGAAGGCATTGTGTGAGATACTAAAACCGGGCTATGTCCCGAAGGCATTTG
1 TCCGGGTTAAGTCCCGAAGGCATTGTGCGAGATACTAAAACCGGGCTAAGTCCCGAAGGCATTTG
54336334 AACGAGGAGC
Statistics
Matches: 119, Mismatches: 23, Indels: 7
0.80 0.15 0.05
Matches are distributed among these distances:
79 34 0.29
80 79 0.66
81 6 0.05
ACGTcount: A:0.24, C:0.21, G:0.28, T:0.26
Consensus pattern (79 bp):
TCCGGGTTAAGTCCCGAAGGCATTGTGCGAGATACTAAAACCGGGCTAAGTCCCGAAGGCATTTG
TGCGAGATACTAAA
Found at i:54340756 original size:82 final size:82
Alignment explanation
Indices: 54340605--54340999 Score: 595
Period size: 82 Copynumber: 4.9 Consensus size: 82
54340595 ATTACCACAA
* * ** * * *
54340605 GCACAATTGCCTTCGGGTCTTAACCCGG--GCATAGCAACTCGCACGAATGCCTTCGGGTCTTAG
1 GCACAAATGCCTTCGGGTCTTAGCCCGGATATATATCAACTCGCACAAATGCCTGCGGGTCTTAG
*
54340668 CCCGGATATATCAACTT
66 CCCGGATATATCAACTC
*
54340685 GCACAATTGCCTTCGGGTCTTAGCCCGGATATATATCAACTCGCACAAATGCCTGCGGGTCTTAG
1 GCACAAATGCCTTCGGGTCTTAGCCCGGATATATATCAACTCGCACAAATGCCTGCGGGTCTTAG
54340750 CCCGGATATATCAACTC
66 CCCGGATATATCAACTC
*
54340767 GCACAAATGCCTGCGGGTCTTAGCCCGGATATATATCAACTCGCACAAATGCCTGCGGGTCTTAG
1 GCACAAATGCCTTCGGGTCTTAGCCCGGATATATATCAACTCGCACAAATGCCTGCGGGTCTTAG
54340832 CCCGGATATATCAACTC
66 CCCGGATATATCAACTC
* *
54340849 GCACAAATGCCTGCGGGTCTTAGCCCGG--ATATATCAACTCGCACAAATGCCTGCAGGTCTTAG
1 GCACAAATGCCTTCGGGTCTTAGCCCGGATATATATCAACTCGCACAAATGCCTGCGGGTCTTAG
54340912 CCCGGATATATCAACTC
66 CCCGGATATATCAACTC
* * * * *
54340929 GCACAAATGCCTTCGGGTCTTAGCCCGGATA-AAATC-ACTAGCACAATTGCCTTCGGGACTTAG
1 GCACAAATGCCTTCGGGTCTTAGCCCGGATATATATCAACTCGCACAAATGCCTGCGGGTCTTAG
54340992 CCCGGATA
66 CCCGGATA
54341000 AAATTCAAAT
Statistics
Matches: 294, Mismatches: 17, Indels: 8
0.92 0.05 0.03
Matches are distributed among these distances:
80 135 0.46
81 4 0.01
82 155 0.53
ACGTcount: A:0.25, C:0.29, G:0.22, T:0.24
Consensus pattern (82 bp):
GCACAAATGCCTTCGGGTCTTAGCCCGGATATATATCAACTCGCACAAATGCCTGCGGGTCTTAG
CCCGGATATATCAACTC
Found at i:54340841 original size:122 final size:120
Alignment explanation
Indices: 54340605--54340999 Score: 585
Period size: 122 Copynumber: 3.3 Consensus size: 120
54340595 ATTACCACAA
* * * ** * * *
54340605 GCACAATTGCCTTCGGGTCTTAACCCGGGCATAGCAACTCGCACGAATGCCTTCGGGTCTTAGCC
1 GCACAAATGCCTGCGGGTCTTAGCCCGGATATATCAACTCGCACAAATGCCTGCGGGTCTTAGCC
* *
54340670 CGGATATATCAACTTGCACAATTGCCTTCGGGTCTTAGCCCGGATATATATCAACTC
66 CGGATATATCAACTCGCACAAATGCCTTCGGGTCTTAGCCCGG--ATATATCAACTC
54340727 GCACAAATGCCTGCGGGTCTTAGCCCGGATATATCAACTCGCACAAATGCCTGCGGGTCTTAGCC
1 GCACAAATGCCTGCGGGTCTTAGCCCGGATATATCAACTCGCACAAATGCCTGCGGGTCTTAGCC
*
54340792 CGGATATATATCAACTCGCACAAATGCCTGCGGGTCTTAGCCCGGATATATCAACTC
66 CGG--ATATATCAACTCGCACAAATGCCTTCGGGTCTTAGCCCGGATATATCAACTC
*
54340849 GCACAAATGCCTGCGGGTCTTAGCCCGGATATATCAACTCGCACAAATGCCTGCAGGTCTTAGCC
1 GCACAAATGCCTGCGGGTCTTAGCCCGGATATATCAACTCGCACAAATGCCTGCGGGTCTTAGCC
* *
54340914 CGGATATATCAACTCGCACAAATGCCTTCGGGTCTTAGCCCGGATAAAATC-ACTA
66 CGGATATATCAACTCGCACAAATGCCTTCGGGTCTTAGCCCGGAT-ATATCAACTC
* * *
54340969 GCACAATTGCCTTCGGGACTTAGCCCGGATA
1 GCACAAATGCCTGCGGGTCTTAGCCCGGATA
54341000 AAATTCAAAT
Statistics
Matches: 252, Mismatches: 18, Indels: 8
0.91 0.06 0.03
Matches are distributed among these distances:
120 72 0.29
121 4 0.02
122 139 0.55
124 37 0.15
ACGTcount: A:0.25, C:0.29, G:0.22, T:0.24
Consensus pattern (120 bp):
GCACAAATGCCTGCGGGTCTTAGCCCGGATATATCAACTCGCACAAATGCCTGCGGGTCTTAGCC
CGGATATATCAACTCGCACAAATGCCTTCGGGTCTTAGCCCGGATATATCAACTC
Found at i:54341003 original size:40 final size:40
Alignment explanation
Indices: 54340605--54340999 Score: 576
Period size: 40 Copynumber: 9.8 Consensus size: 40
54340595 ATTACCACAA
* * * ** *
54340605 GCACAATTGCCTTCGGGTCTTAACCCGGGCATAGCAACTC
1 GCACAAATGCCTGCGGGTCTTAGCCCGGATATATCAACTC
* * *
54340645 GCACGAATGCCTTCGGGTCTTAGCCCGGATATATCAACTT
1 GCACAAATGCCTGCGGGTCTTAGCCCGGATATATCAACTC
* *
54340685 GCACAATTGCCTTCGGGTCTTAGCCCGGATATATATCAACTC
1 GCACAAATGCCTGCGGGTCTTAGCCCGG--ATATATCAACTC
54340727 GCACAAATGCCTGCGGGTCTTAGCCCGGATATATCAACTC
1 GCACAAATGCCTGCGGGTCTTAGCCCGGATATATCAACTC
54340767 GCACAAATGCCTGCGGGTCTTAGCCCGGATATATATCAACTC
1 GCACAAATGCCTGCGGGTCTTAGCCCGG--ATATATCAACTC
54340809 GCACAAATGCCTGCGGGTCTTAGCCCGGATATATCAACTC
1 GCACAAATGCCTGCGGGTCTTAGCCCGGATATATCAACTC
54340849 GCACAAATGCCTGCGGGTCTTAGCCCGGATATATCAACTC
1 GCACAAATGCCTGCGGGTCTTAGCCCGGATATATCAACTC
*
54340889 GCACAAATGCCTGCAGGTCTTAGCCCGGATATATCAACTC
1 GCACAAATGCCTGCGGGTCTTAGCCCGGATATATCAACTC
* * *
54340929 GCACAAATGCCTTCGGGTCTTAGCCCGGATAAAATC-ACTA
1 GCACAAATGCCTGCGGGTCTTAGCCCGGAT-ATATCAACTC
* * *
54340969 GCACAATTGCCTTCGGGACTTAGCCCGGATA
1 GCACAAATGCCTGCGGGTCTTAGCCCGGATA
54341000 AAATTCAAAT
Statistics
Matches: 331, Mismatches: 19, Indels: 11
0.92 0.05 0.03
Matches are distributed among these distances:
39 1 0.00
40 249 0.75
41 4 0.01
42 77 0.23
ACGTcount: A:0.25, C:0.29, G:0.22, T:0.24
Consensus pattern (40 bp):
GCACAAATGCCTGCGGGTCTTAGCCCGGATATATCAACTC
Found at i:54349950 original size:20 final size:20
Alignment explanation
Indices: 54349925--54349966 Score: 75
Period size: 20 Copynumber: 2.1 Consensus size: 20
54349915 AATCGCACAC
*
54349925 TTAGTGTCAAATACCATTGA
1 TTAGTGCCAAATACCATTGA
54349945 TTAGTGCCAAATACCATTGA
1 TTAGTGCCAAATACCATTGA
54349965 TT
1 TT
54349967 TATCATCGTA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.33, C:0.17, G:0.14, T:0.36
Consensus pattern (20 bp):
TTAGTGCCAAATACCATTGA
Found at i:54351279 original size:28 final size:26
Alignment explanation
Indices: 54351239--54351299 Score: 77
Period size: 26 Copynumber: 2.3 Consensus size: 26
54351229 TTAAAAGAAA
* *
54351239 GCCTTTGTAGCAATATCTGTCAAATGAT
1 GCCTTTATAGC-A-ATCTATCAAATGAT
*
54351267 GCCTTTATGGCAATCTATCAAATGAT
1 GCCTTTATAGCAATCTATCAAATGAT
54351293 GCCTTTA
1 GCCTTTA
54351300 GGGTAAGACT
Statistics
Matches: 30, Mismatches: 3, Indels: 2
0.86 0.09 0.06
Matches are distributed among these distances:
26 20 0.67
27 1 0.03
28 9 0.30
ACGTcount: A:0.28, C:0.20, G:0.16, T:0.36
Consensus pattern (26 bp):
GCCTTTATAGCAATCTATCAAATGAT
Found at i:54352482 original size:18 final size:19
Alignment explanation
Indices: 54352454--54352490 Score: 58
Period size: 18 Copynumber: 2.0 Consensus size: 19
54352444 CAATATTTTC
54352454 CTTTAGAGCTTACTAAGTT
1 CTTTAGAGCTTACTAAGTT
*
54352473 CTTT-GAGCTTACTTAGTT
1 CTTTAGAGCTTACTAAGTT
54352491 ACCTTTCCTT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
18 13 0.76
19 4 0.24
ACGTcount: A:0.22, C:0.16, G:0.16, T:0.46
Consensus pattern (19 bp):
CTTTAGAGCTTACTAAGTT
Found at i:54354909 original size:21 final size:21
Alignment explanation
Indices: 54354885--54354954 Score: 70
Period size: 21 Copynumber: 3.2 Consensus size: 21
54354875 TGATATGAAC
54354885 TCATTGAGTTGTGGTCTGAGT
1 TCATTGAGTTGTGGTCTGAGT
* * *
54354906 TCA-TGATATATGTGACATCTGAGC
1 TCATTGA-GT-TGTG--GTCTGAGT
54354930 TCATTGAGTTGTGGTCTGAGT
1 TCATTGAGTTGTGGTCTGAGT
54354951 TCAT
1 TCAT
54354955 GATGTATACG
Statistics
Matches: 38, Mismatches: 6, Indels: 10
0.70 0.11 0.19
Matches are distributed among these distances:
20 3 0.08
21 14 0.37
22 4 0.11
23 4 0.11
24 10 0.26
25 3 0.08
ACGTcount: A:0.20, C:0.13, G:0.27, T:0.40
Consensus pattern (21 bp):
TCATTGAGTTGTGGTCTGAGT
Found at i:54359091 original size:40 final size:40
Alignment explanation
Indices: 54359043--54359310 Score: 464
Period size: 40 Copynumber: 6.7 Consensus size: 40
54359033 GCAAACACCT
* * *
54359043 TTGCCTTCGGGTCTTAACCCGGACATATCAACTTGCATAA
1 TTGCCTTCGGGTCTTAGCCCGGATATATCAACTCGCATAA
*
54359083 TTGCCTTCGGGTCTTAGCCCGGATATATCATCTCGCATAA
1 TTGCCTTCGGGTCTTAGCCCGGATATATCAACTCGCATAA
* * *
54359123 TTGCCTTCGGGTCATAGCCCGGACATATTAACTCGCATAA
1 TTGCCTTCGGGTCTTAGCCCGGATATATCAACTCGCATAA
54359163 TTGCCTTCGGGTCTTAGCCCGGATATATCAACTCGCATAA
1 TTGCCTTCGGGTCTTAGCCCGGATATATCAACTCGCATAA
*
54359203 TTGCCTTCGGGTCTTAGCCCGGATATATTAACTCGCATAA
1 TTGCCTTCGGGTCTTAGCCCGGATATATCAACTCGCATAA
54359243 TTGCCTTCGGGTCTTAGCCCGGATATATCAACTCGCATAA
1 TTGCCTTCGGGTCTTAGCCCGGATATATCAACTCGCATAA
54359283 TTGCCTTCGGGTCTTAGCCCGGATATAT
1 TTGCCTTCGGGTCTTAGCCCGGATATAT
54359311 TTCAAATGCT
Statistics
Matches: 215, Mismatches: 13, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
40 215 1.00
ACGTcount: A:0.22, C:0.27, G:0.20, T:0.31
Consensus pattern (40 bp):
TTGCCTTCGGGTCTTAGCCCGGATATATCAACTCGCATAA
Found at i:54380718 original size:40 final size:39
Alignment explanation
Indices: 54380681--54380826 Score: 224
Period size: 40 Copynumber: 3.7 Consensus size: 39
54380671 TGAGGAATGT
54380681 TATCCGGGCTTAAAGACCCGCAGGCTTCATGCTGGAATTG
1 TATCCGGGCTTAAAGACCCGCAGGCTT-ATGCTGGAATTG
54380721 TATCCGGGCTTAAAGACCCGCAGGCTATATGCTGGAA-TG
1 TATCCGGGCTTAAAGACCCGCAGGCT-TATGCTGGAATTG
54380760 TTATCCGGGCTTAAAGACCCGCAGGCTT-TGCGCTGGAATTG
1 -TATCCGGGCTTAAAGACCCGCAGGCTTAT--GCTGGAATTG
*
54380801 TATCCGGGCATAAAGACCCGCAGGCT
1 TATCCGGGCTTAAAGACCCGCAGGCT
54380827 ACGAGCTGGT
Statistics
Matches: 100, Mismatches: 1, Indels: 10
0.90 0.01 0.09
Matches are distributed among these distances:
38 1 0.01
39 3 0.03
40 93 0.93
41 3 0.03
ACGTcount: A:0.23, C:0.25, G:0.28, T:0.23
Consensus pattern (39 bp):
TATCCGGGCTTAAAGACCCGCAGGCTTATGCTGGAATTG
Found at i:54380807 original size:80 final size:80
Alignment explanation
Indices: 54380674--54380827 Score: 272
Period size: 80 Copynumber: 1.9 Consensus size: 80
54380664 TGATACTTGA
* *
54380674 GGAATGTTATCCGGGCTTAAAGACCCGCAGGCTTCATGCTGGAATTGTATCCGGGCTTAAAGACC
1 GGAATGTTATCCGGGCTTAAAGACCCGCAGGCTTCACGCTGGAATTGTATCCGGGCATAAAGACC
54380739 CGCAGGCTATATGCT
66 CGCAGGCTATATGCT
**
54380754 GGAATGTTATCCGGGCTTAAAGACCCGCAGGCTTTGCGCTGGAATTGTATCCGGGCATAAAGACC
1 GGAATGTTATCCGGGCTTAAAGACCCGCAGGCTTCACGCTGGAATTGTATCCGGGCATAAAGACC
54380819 CGCAGGCTA
66 CGCAGGCTA
54380828 CGAGCTGGTA
Statistics
Matches: 70, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
80 70 1.00
ACGTcount: A:0.24, C:0.24, G:0.29, T:0.23
Consensus pattern (80 bp):
GGAATGTTATCCGGGCTTAAAGACCCGCAGGCTTCACGCTGGAATTGTATCCGGGCATAAAGACC
CGCAGGCTATATGCT
Found at i:54380835 original size:40 final size:41
Alignment explanation
Indices: 54380681--54380853 Score: 214
Period size: 40 Copynumber: 4.3 Consensus size: 41
54380671 TGAGGAATGT
*
54380681 TATCCGGGCTTAAAGACCCGCAGGCTTC-ATGCTGGAATTG
1 TATCCGGGCTTAAAGACCCGCAGGCTACGATGCTGGAATTG
*
54380721 TATCCGGGCTTAAAGACCCGCAGGCTA-TATGCTGGAA-TG
1 TATCCGGGCTTAAAGACCCGCAGGCTACGATGCTGGAATTG
** *
54380760 TTATCCGGGCTTAAAGACCCGCAGGCTTTG-CGCTGGAATTG
1 -TATCCGGGCTTAAAGACCCGCAGGCTACGATGCTGGAATTG
* * *
54380801 TATCCGGGCATAAAGACCCGCAGGCTACGA-GCTGGTATTA
1 TATCCGGGCTTAAAGACCCGCAGGCTACGATGCTGGAATTG
*
54380841 TA-CCGGGTTTAAA
1 TATCCGGGCTTAAA
54380854 TTCCCGTAGG
Statistics
Matches: 117, Mismatches: 11, Indels: 11
0.84 0.08 0.08
Matches are distributed among these distances:
39 11 0.09
40 104 0.89
41 2 0.02
ACGTcount: A:0.24, C:0.24, G:0.28, T:0.24
Consensus pattern (41 bp):
TATCCGGGCTTAAAGACCCGCAGGCTACGATGCTGGAATTG
Found at i:54388942 original size:40 final size:40
Alignment explanation
Indices: 54388891--54389007 Score: 180
Period size: 40 Copynumber: 2.9 Consensus size: 40
54388881 GGAAAAAAAT
*
54388891 ATAACCCGGTTAAGTCCCGAAGGCATTCGTGCGGGTTATA
1 ATAACCGGGTTAAGTCCCGAAGGCATTCGTGCGGGTTATA
* *
54388931 ATGACCGGGTTAAGTCCCGAAGGCATTCGTGCGGGTTATT
1 ATAACCGGGTTAAGTCCCGAAGGCATTCGTGCGGGTTATA
* * *
54388971 ATAACCGGGTTAAGTTCCGAAGGCATTTGTGCTGGTT
1 ATAACCGGGTTAAGTCCCGAAGGCATTCGTGCGGGTT
54389008 GTTACATCTG
Statistics
Matches: 70, Mismatches: 7, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
40 70 1.00
ACGTcount: A:0.22, C:0.20, G:0.30, T:0.28
Consensus pattern (40 bp):
ATAACCGGGTTAAGTCCCGAAGGCATTCGTGCGGGTTATA
Found at i:54396229 original size:40 final size:40
Alignment explanation
Indices: 54396166--54396283 Score: 182
Period size: 40 Copynumber: 3.0 Consensus size: 40
54396156 TGGAAAAAAA
*
54396166 TATAACCCGGTTAAGTCCCGAAGGCATTCGTGCGGGTTAT
1 TATAACCGGGTTAAGTCCCGAAGGCATTCGTGCGGGTTAT
* *
54396206 TATGACTGGGTTAAGTCCCGAAGGCATTCGTGCGGGTTAT
1 TATAACCGGGTTAAGTCCCGAAGGCATTCGTGCGGGTTAT
* * *
54396246 TATAACCGGGTTAAGTTCCGAAGGCATTTGTGCTGGTT
1 TATAACCGGGTTAAGTCCCGAAGGCATTCGTGCGGGTT
54396284 GTTACATCTG
Statistics
Matches: 70, Mismatches: 8, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
40 70 1.00
ACGTcount: A:0.21, C:0.19, G:0.30, T:0.31
Consensus pattern (40 bp):
TATAACCGGGTTAAGTCCCGAAGGCATTCGTGCGGGTTAT
Found at i:54409188 original size:40 final size:40
Alignment explanation
Indices: 54409157--54409368 Score: 261
Period size: 40 Copynumber: 5.3 Consensus size: 40
54409147 GGACTAAGAT
54409157 CCGAAGGCATTTGTGCGAGATACAAATTCCGGGTTAAGCC
1 CCGAAGGCATTTGTGCGAGATACAAATTCCGGGTTAAGCC
54409197 CCGAAGGCATTTGTGCGAGATACAAATTCCGGGTTAAGCC
1 CCGAAGGCATTTGTGCGAGATACAAATTCCGGGTTAAGCC
* *
54409237 CCGAAGGCCTTTGTGCGAGATACTAAA-TCCGGGTTAAGTC
1 CCGAAGGCATTTGTGCGAGATAC-AAATTCCGGGTTAAGCC
* * * *
54409277 CCGAAGGCATTCGTGCGAGTTATTAAA-TCCGGGTTAAGTC
1 CCGAAGGCATTTGTGCGAGATA-CAAATTCCGGGTTAAGCC
* * * * * *
54409317 CCGAAGGCA-TTGTGTGAGTTACTAAA-ACCGGGCTATGTC
1 CCGAAGGCATTTGTGCGAGATAC-AAATTCCGGGTTAAGCC
54409356 CCGAAGGCATTTG
1 CCGAAGGCATTTG
54409369 AACGAGGAGC
Statistics
Matches: 156, Mismatches: 12, Indels: 8
0.89 0.07 0.05
Matches are distributed among these distances:
39 32 0.21
40 121 0.78
41 3 0.02
ACGTcount: A:0.26, C:0.22, G:0.28, T:0.25
Consensus pattern (40 bp):
CCGAAGGCATTTGTGCGAGATACAAATTCCGGGTTAAGCC
Found at i:54409386 original size:79 final size:80
Alignment explanation
Indices: 54409105--54409401 Score: 214
Period size: 80 Copynumber: 3.7 Consensus size: 80
54409095 TGAATGCTGT
* ** * * * ** **
54409105 CCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGAATATATCCGGACTAAGAT-CCGAAGGCATT
1 CCGGGCTAAGTCCCGAAGGCATTCGAAC-GAGTGACTAAATCCGGGTTAAG-TCCCGAAGGCCAT
*
54409168 TGTGCGAGATAC-AAATT
64 TGTGCGAGATACTAAA-A
* * * ** * *
54409185 CCGGGTTAAGCCCCGAAGGCATTTGTGCGAGAT-AC-AAATTCCGGGTTAAGCCCCGAAGGCCTT
1 CCGGGCTAAGTCCCGAAGGCATTCGAACGAG-TGACTAAA-TCCGGGTTAAGTCCCGAAGGCCAT
*
54409248 TGTGCGAGATACTAAAT
64 TGTGCGAGATACTAAAA
* ** * *
54409265 CCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTATTAAATCCGGGTTAAGTCCCGAAGG-CATTG
1 CCGGGCTAAGTCCCGAAGGCATTCGAACGAGTGACTAAATCCGGGTTAAGTCCCGAAGGCCATTG
* *
54409329 TGTGAGTTACTAAAA
66 TGCGAGATACTAAAA
* * * *
54409344 CCGGGCTATGTCCCGAAGGCATTTGAACGAG-GAGCTATATCC-GGTTAAATCCCGAAGG
1 CCGGGCTAAGTCCCGAAGGCATTCGAACGAGTGA-CTAAATCCGGGTTAAGTCCCGAAGG
54409402 TACGTGATTT
Statistics
Matches: 183, Mismatches: 26, Indels: 18
0.81 0.11 0.08
Matches are distributed among these distances:
78 16 0.09
79 51 0.28
80 102 0.56
81 14 0.08
ACGTcount: A:0.27, C:0.22, G:0.28, T:0.24
Consensus pattern (80 bp):
CCGGGCTAAGTCCCGAAGGCATTCGAACGAGTGACTAAATCCGGGTTAAGTCCCGAAGGCCATTG
TGCGAGATACTAAAA
Found at i:54416928 original size:27 final size:27
Alignment explanation
Indices: 54416873--54416932 Score: 77
Period size: 27 Copynumber: 2.2 Consensus size: 27
54416863 GACATTTCAA
* * *
54416873 TCATTTTACCACATAAGGGCTATAAAG
1 TCATTTTACCACAAAAGGGCAAAAAAG
54416900 TCATTTTACCACAAAAGGG-AAAAATAG
1 TCATTTTACCACAAAAGGGCAAAAA-AG
54416927 TCATTT
1 TCATTT
54416933 CATCAAATTG
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
26 3 0.10
27 26 0.90
ACGTcount: A:0.40, C:0.17, G:0.13, T:0.30
Consensus pattern (27 bp):
TCATTTTACCACAAAAGGGCAAAAAAG
Found at i:54418370 original size:27 final size:27
Alignment explanation
Indices: 54418340--54418401 Score: 97
Period size: 27 Copynumber: 2.3 Consensus size: 27
54418330 GGGACATTTC
* *
54418340 AGTCATTTTACCATAGAACGGTAAAAT
1 AGTCATTTTACCACAAAACGGTAAAAT
*
54418367 AGTCATTTTATCACAAAACGGTAAAAT
1 AGTCATTTTACCACAAAACGGTAAAAT
54418394 AGTCATTT
1 AGTCATTT
54418402 CATCAAATTA
Statistics
Matches: 32, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
27 32 1.00
ACGTcount: A:0.40, C:0.15, G:0.13, T:0.32
Consensus pattern (27 bp):
AGTCATTTTACCACAAAACGGTAAAAT
Found at i:54421879 original size:48 final size:48
Alignment explanation
Indices: 54421808--54421951 Score: 216
Period size: 48 Copynumber: 3.0 Consensus size: 48
54421798 CGAAAGTCTT
* * * *
54421808 GCACCCTAGGTGCCAATATCATGGCTTGAAGCCAAATCAATGAAGCTC
1 GCACCCGAAGTGCTAATATCATGGCTCGAAGCCAAATCAATGAAGCTC
54421856 GCACCCGAAGTGCTAATATCATGGCTCGAAGCCAAATCAATGAAGCTC
1 GCACCCGAAGTGCTAATATCATGGCTCGAAGCCAAATCAATGAAGCTC
* * * *
54421904 ACACCCGAAGTGCTAATATCATGGCTCGAAACCAGATCAATAAAGCTC
1 GCACCCGAAGTGCTAATATCATGGCTCGAAGCCAAATCAATGAAGCTC
54421952 CTAAGGACAT
Statistics
Matches: 88, Mismatches: 8, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
48 88 1.00
ACGTcount: A:0.34, C:0.27, G:0.19, T:0.19
Consensus pattern (48 bp):
GCACCCGAAGTGCTAATATCATGGCTCGAAGCCAAATCAATGAAGCTC
Found at i:54421882 original size:27 final size:27
Alignment explanation
Indices: 54421852--54421931 Score: 66
Period size: 27 Copynumber: 3.2 Consensus size: 27
54421842 AATCAATGAA
54421852 GCTCGCACCCGAAGTGCTAATATCATG
1 GCTCGCACCCGAAGTGCTAATATCATG
* * *
54421879 GCTCGAAGCC-AAAT-C-AATGA--A--
1 GCTCGCACCCGAAGTGCTAAT-ATCATG
*
54421900 GCTCACACCCGAAGTGCTAATATCATG
1 GCTCGCACCCGAAGTGCTAATATCATG
54421927 GCTCG
1 GCTCG
54421932 AAACCAGATC
Statistics
Matches: 37, Mismatches: 8, Indels: 16
0.61 0.13 0.26
Matches are distributed among these distances:
21 7 0.19
22 3 0.08
23 3 0.08
24 6 0.16
25 3 0.08
26 3 0.08
27 12 0.32
ACGTcount: A:0.30, C:0.29, G:0.21, T:0.20
Consensus pattern (27 bp):
GCTCGCACCCGAAGTGCTAATATCATG
Found at i:54425432 original size:14 final size:14
Alignment explanation
Indices: 54425413--54425454 Score: 68
Period size: 14 Copynumber: 3.1 Consensus size: 14
54425403 ACGAGGCTCA
54425413 TTTGCTTCCTTTGC
1 TTTGCTTCCTTTGC
*
54425427 TTTGCTTCCTTCGC
1 TTTGCTTCCTTTGC
54425441 TTTGC-TCCTTTGC
1 TTTGCTTCCTTTGC
54425454 T
1 T
54425455 AATGGCTCTC
Statistics
Matches: 26, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
13 8 0.31
14 18 0.69
ACGTcount: A:0.00, C:0.31, G:0.14, T:0.55
Consensus pattern (14 bp):
TTTGCTTCCTTTGC
Found at i:54429578 original size:40 final size:40
Alignment explanation
Indices: 54429526--54429669 Score: 152
Period size: 40 Copynumber: 3.6 Consensus size: 40
54429516 TAACTCATAC
* *
54429526 AATGCCTTCGGGACTTAACCCGGATTTTAA-AACTCGCACG
1 AATGCCTTCGGGACTTAACCCGGA-ATTAATAACTCGCACA
54429566 AATGCCTTCGGGACTTAACCCGGAATTAATAACTCGCACA
1 AATGCCTTCGGGACTTAACCCGGAATTAATAACTCGCACA
** * * *
54429606 AATGCCTTC-GGATCTTAGTCCGG-ATATAGTCACTTAGCACA
1 AATGCCTTCGGGA-CTTAACCCGGAAT-TAATAAC-TCGCACA
*
54429647 AA-GCCTTCGGGACTTAGCCCGGA
1 AATGCCTTCGGGACTTAACCCGGA
54429670 CAGCATTCAA
Statistics
Matches: 90, Mismatches: 8, Indels: 11
0.83 0.07 0.10
Matches are distributed among these distances:
39 9 0.10
40 70 0.78
41 11 0.12
ACGTcount: A:0.28, C:0.27, G:0.21, T:0.24
Consensus pattern (40 bp):
AATGCCTTCGGGACTTAACCCGGAATTAATAACTCGCACA
Found at i:54433686 original size:43 final size:43
Alignment explanation
Indices: 54433533--54433687 Score: 165
Period size: 43 Copynumber: 3.7 Consensus size: 43
54433523 ATCGTACAAA
* *
54433533 GCCAACGTCCCAGACGTGGTCTTACATGCT-ATCACATATCGAT
1 GCCAACGTCCCAGACATGGTCTTACACG-TAATCACATATCGAT
* * *
54433576 GCC-ACTGTCCCAGACAGGGTCTTACAC-AAATCAAATA-CGAT
1 GCCAAC-GTCCCAGACATGGTCTTACACGTAATCACATATCGAT
** * **
54433617 GCTGATGTCCCAGACATGGTCTTACACGTAATCACATATTAAT
1 GCCAACGTCCCAGACATGGTCTTACACGTAATCACATATCGAT
*
54433660 GCCAACATCCCAGACATGGTCTTACACG
1 GCCAACGTCCCAGACATGGTCTTACACG
54433688 AGAACACATA
Statistics
Matches: 91, Mismatches: 16, Indels: 10
0.78 0.14 0.09
Matches are distributed among these distances:
41 26 0.29
42 18 0.20
43 47 0.52
ACGTcount: A:0.30, C:0.29, G:0.17, T:0.24
Consensus pattern (43 bp):
GCCAACGTCCCAGACATGGTCTTACACGTAATCACATATCGAT
Found at i:54435546 original size:40 final size:40
Alignment explanation
Indices: 54435308--54435532 Score: 296
Period size: 40 Copynumber: 5.7 Consensus size: 40
54435298 TTGAATGATG
* * * *
54435308 TCCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGACCATA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGC-GAGTTACTAAA
* * *
54435348 TCCGGACTAAGAT-CCGAAGGCATTTGTGCGAGATACTAAT
1 TCCGGGCTAAG-TCCCGAAGGCATTTGTGCGAGTTACTAAA
54435388 TCCGGGCTAAG-CCCGAAGGCATTTGTGCGAGTTACTAAA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAA
*
54435427 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAA
* *
54435467 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAATTACTATAA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTA-AA
*
54435508 -CCGGGCTATGTCCCGAAGGCATTTG
1 TCCGGGCTAAGTCCCGAAGGCATTTG
54435533 AACGAGGAGC
Statistics
Matches: 166, Mismatches: 14, Indels: 10
0.87 0.07 0.05
Matches are distributed among these distances:
39 35 0.21
40 121 0.73
41 10 0.06
ACGTcount: A:0.25, C:0.22, G:0.27, T:0.26
Consensus pattern (40 bp):
TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAA
Found at i:54435554 original size:119 final size:119
Alignment explanation
Indices: 54435308--54435565 Score: 285
Period size: 119 Copynumber: 2.2 Consensus size: 119
54435298 TTGAATGATG
* *
54435308 TCCGGGCTAAGTCCCGAAGGCTTTGTGCTAAGTGACCATATCCGGACTAAGATCCGAAGGCATTT
1 TCCGGGTTAAGTCCCGAAGGCTTTGTGCTAAGTGACCAAATCCGGACTAAGATCCGAAGGCATTT
* ** *
54435373 GTGCGAGATACTAATTCCGGGCTAAGCCCGAAGGCATTTGTGCGAGTTACTAAA
66 GTGCGAGATACTAATACCGGGCTAAGCCCGAAGGCATTTGAACGAGTGACTAAA
* * * **
54435427 TCCGGGTTAAGTCCCGAAGGCATTTGTGC-GAGTTACTAAATCCGGGTTAAG-TCCCGAAGGCAT
1 TCCGGGTTAAGTCCCGAAGGC-TTTGTGCTAAGTGACCAAATCCGGACTAAGAT-CCGAAGGCAT
* *
54435490 TTGTGCGA-ATTACT-ATAACCGGGCTATGTCCCGAAGGCATTTGAACGAG-GAGCTATA
64 TTGTGCGAGA-TACTAAT-ACCGGGCTAAG-CCCGAAGGCATTTGAACGAGTGA-CTAAA
* *
54435547 TCC-GGTTAAATTCCGAAGG
1 TCCGGGTTAAGTCCCGAAGG
54435566 TACGTGATTT
Statistics
Matches: 118, Mismatches: 15, Indels: 12
0.81 0.10 0.08
Matches are distributed among these distances:
118 4 0.03
119 82 0.69
120 32 0.27
ACGTcount: A:0.26, C:0.22, G:0.27, T:0.25
Consensus pattern (119 bp):
TCCGGGTTAAGTCCCGAAGGCTTTGTGCTAAGTGACCAAATCCGGACTAAGATCCGAAGGCATTT
GTGCGAGATACTAATACCGGGCTAAGCCCGAAGGCATTTGAACGAGTGACTAAA
Found at i:54438304 original size:39 final size:40
Alignment explanation
Indices: 54438261--54438428 Score: 148
Period size: 40 Copynumber: 4.2 Consensus size: 40
54438251 CTCGTTCAAG
* * * *
54438261 TGCCTTCGGGACATAGCCCGG-TTATAGTAACTCATAC-AA
1 TGCCTTCGGGACTTAACCCGGATTATA-AAACTCACACGAA
* *
54438300 TGCCTTCGGGACTTAACCCGGATTTTAAAACTCGCACGAA
1 TGCCTTCGGGACTTAACCCGGATTATAAAACTCACACGAA
* * *
54438340 TGCCTTCGGGACTTAACCCGGAATTAGT--ATCTCGCACAAA
1 TGCCTTCGGGACTTAACCCGG-ATTA-TAAAACTCACACGAA
* * * *
54438380 GGCCTTCGGGACTTAACCCGGAATTA-ATAACTCGCACAAA
1 TGCCTTCGGGACTTAACCCGG-ATTATAAAACTCACACGAA
54438420 TGCCTTCGG
1 TGCCTTCGG
54438429 ATCTTAGTCC
Statistics
Matches: 111, Mismatches: 12, Indels: 11
0.83 0.09 0.08
Matches are distributed among these distances:
39 26 0.23
40 81 0.73
41 3 0.03
42 1 0.01
ACGTcount: A:0.27, C:0.27, G:0.21, T:0.24
Consensus pattern (40 bp):
TGCCTTCGGGACTTAACCCGGATTATAAAACTCACACGAA
Found at i:54438412 original size:80 final size:80
Alignment explanation
Indices: 54438296--54438481 Score: 229
Period size: 80 Copynumber: 2.3 Consensus size: 80
54438286 AGTAACTCAT
* * *
54438296 ACAATGCCTTCGGGACTTAACCCGGATTTTAAAACTCGCACGAATGCCTTCGGGA-CTTAACCCG
1 ACAAAGCCTTCGGGACTTAACCCGGATATTAAAACTCGCACAAATGCCTTC-GGATCTTAACCCG
*
54438360 GA-ATTAGT-A-TCTCGC
65 GATA-TAGTCACT-TAGC
**
54438375 ACAAAGGCCTTCGGGACTTAACCCGGA-ATTAATAACTCGCACAAATGCCTTCGGATCTTAGTCC
1 ACAAA-GCCTTCGGGACTTAACCCGGATATTAA-AACTCGCACAAATGCCTTCGGATCTTAACCC
54438439 GGATATAGTCACTTAGC
64 GGATATAGTCACTTAGC
*
54438456 ACAAAGCCTTCGGGACTTAGCCCGGA
1 ACAAAGCCTTCGGGACTTAACCCGGA
54438482 CAGCATTCAA
Statistics
Matches: 94, Mismatches: 7, Indels: 11
0.84 0.06 0.10
Matches are distributed among these distances:
79 11 0.12
80 72 0.77
81 10 0.11
82 1 0.01
ACGTcount: A:0.28, C:0.27, G:0.21, T:0.24
Consensus pattern (80 bp):
ACAAAGCCTTCGGGACTTAACCCGGATATTAAAACTCGCACAAATGCCTTCGGATCTTAACCCGG
ATATAGTCACTTAGC
Found at i:54438441 original size:40 final size:40
Alignment explanation
Indices: 54438298--54438481 Score: 205
Period size: 40 Copynumber: 4.6 Consensus size: 40
54438288 TAACTCATAC
* *
54438298 AATGCCTTCGGGACTTAACCCGGATTTTAA-AACTCGCACG
1 AATGCCTTCGGGACTTAACCCGGA-ATTAATAACTCGCACA
* *
54438338 AATGCCTTCGGGACTTAACCCGGAATTAGTATCTCGCACA
1 AATGCCTTCGGGACTTAACCCGGAATTAATAACTCGCACA
*
54438378 AAGGCCTTCGGGACTTAACCCGGAATTAATAACTCGCACA
1 AATGCCTTCGGGACTTAACCCGGAATTAATAACTCGCACA
** * * *
54438418 AATGCCTTC-GGATCTTAGTCCGG-ATATAGTCACTTAGCACA
1 AATGCCTTCGGGA-CTTAACCCGGAAT-TAATAAC-TCGCACA
*
54438459 AA-GCCTTCGGGACTTAGCCCGGA
1 AATGCCTTCGGGACTTAACCCGGA
54438482 CAGCATTCAA
Statistics
Matches: 124, Mismatches: 14, Indels: 11
0.83 0.09 0.07
Matches are distributed among these distances:
39 8 0.06
40 105 0.85
41 11 0.09
ACGTcount: A:0.28, C:0.27, G:0.21, T:0.24
Consensus pattern (40 bp):
AATGCCTTCGGGACTTAACCCGGAATTAATAACTCGCACA
Found at i:54452091 original size:40 final size:40
Alignment explanation
Indices: 54451994--54452179 Score: 243
Period size: 40 Copynumber: 4.7 Consensus size: 40
54451984 TCGAATGATG
* * * *
54451994 TCCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGACCATA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGC-GAGTTACTAAA
* *
54452034 TTCGGACTAAGAT-CCGAAGGCATTTGTGCGAGTTACTAAA
1 TCCGGGCTAAG-TCCCGAAGGCATTTGTGCGAGTTACTAAA
*
54452074 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAA
*
54452114 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTA-AA
*
54452155 -CCGGGCTATGTCCCGAAGGCATTTG
1 TCCGGGCTAAGTCCCGAAGGCATTTG
54452180 AACGAGTAGC
Statistics
Matches: 131, Mismatches: 11, Indels: 8
0.87 0.07 0.05
Matches are distributed among these distances:
39 1 0.01
40 120 0.92
41 10 0.08
ACGTcount: A:0.24, C:0.22, G:0.27, T:0.27
Consensus pattern (40 bp):
TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAA
Found at i:54452186 original size:80 final size:79
Alignment explanation
Indices: 54452047--54452202 Score: 226
Period size: 80 Copynumber: 2.0 Consensus size: 79
54452037 GGACTAAGAT
* **
54452047 CCGAAGGCATTTGTGCGAGTTACTAAATCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTA-CT
1 CCGAAGGCATTTGTGCGAGTTACTAAATCCGGGCTAAGTCCCGAAGGCATTTGAACGAG-TAGCT
54452111 AAATCCGGGTTAAGTC
65 AAATCC-GGTTAAGTC
*
54452127 CCGAAGGCATTTGTGCGAGTTACTATAA-CCGGGCTATGTCCCGAAGGCATTTGAACGAGTAGCT
1 CCGAAGGCATTTGTGCGAGTTACTA-AATCCGGGCTAAGTCCCGAAGGCATTTGAACGAGTAGCT
*
54452191 ATATCCGGTTAA
65 AAATCCGGTTAA
54452203 ATTCTGAAGG
Statistics
Matches: 69, Mismatches: 5, Indels: 5
0.87 0.06 0.06
Matches are distributed among these distances:
79 8 0.12
80 59 0.86
81 2 0.03
ACGTcount: A:0.26, C:0.21, G:0.27, T:0.27
Consensus pattern (79 bp):
CCGAAGGCATTTGTGCGAGTTACTAAATCCGGGCTAAGTCCCGAAGGCATTTGAACGAGTAGCTA
AATCCGGTTAAGTC
Found at i:54464411 original size:16 final size:17
Alignment explanation
Indices: 54464379--54464412 Score: 52
Period size: 18 Copynumber: 2.0 Consensus size: 17
54464369 TTATTGTCGA
54464379 AAAATAATTAAATATTAT
1 AAAATAATT-AATATTAT
54464397 AAAATAATT-ATATTAT
1 AAAATAATTAATATTAT
54464413 GTTAAAAATA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 7 0.44
18 9 0.56
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (17 bp):
AAAATAATTAATATTAT
Found at i:54475233 original size:29 final size:29
Alignment explanation
Indices: 54475174--54475234 Score: 70
Period size: 29 Copynumber: 2.1 Consensus size: 29
54475164 ATTTATTTTA
*
54475174 CAATTTAACCCCTGAATTTACACTTTTCT
1 CAATTTAACCCCTGAATGTACACTTTTCT
* * *
54475203 CAATTTAATCCCT-AATGTGCATTTTTACT
1 CAATTTAACCCCTGAATGTACACTTTT-CT
54475232 CAA
1 CAA
54475235 AATCACTTTA
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
28 10 0.37
29 17 0.63
ACGTcount: A:0.30, C:0.25, G:0.05, T:0.41
Consensus pattern (29 bp):
CAATTTAACCCCTGAATGTACACTTTTCT
Found at i:54486281 original size:28 final size:28
Alignment explanation
Indices: 54486249--54486304 Score: 103
Period size: 28 Copynumber: 2.0 Consensus size: 28
54486239 ACTATGGCCA
*
54486249 AATGCTTCAAAGTGCAATAATGGAGCTT
1 AATGCTTCAAAGTACAATAATGGAGCTT
54486277 AATGCTTCAAAGTACAATAATGGAGCTT
1 AATGCTTCAAAGTACAATAATGGAGCTT
54486305 TTCTTCCCTT
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
28 27 1.00
ACGTcount: A:0.38, C:0.14, G:0.20, T:0.29
Consensus pattern (28 bp):
AATGCTTCAAAGTACAATAATGGAGCTT
Found at i:54487957 original size:27 final size:27
Alignment explanation
Indices: 54487920--54487980 Score: 115
Period size: 27 Copynumber: 2.3 Consensus size: 27
54487910 AATTAAATTC
54487920 AATG-TTATACGAACTTACTAAGCTTA
1 AATGCTTATACGAACTTACTAAGCTTA
54487946 AATGCTTATACGAACTTACTAAGCTTA
1 AATGCTTATACGAACTTACTAAGCTTA
54487973 AATGCTTA
1 AATGCTTA
54487981 CTCTATGTTA
Statistics
Matches: 34, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
26 4 0.12
27 30 0.88
ACGTcount: A:0.38, C:0.16, G:0.11, T:0.34
Consensus pattern (27 bp):
AATGCTTATACGAACTTACTAAGCTTA
Found at i:54490874 original size:16 final size:16
Alignment explanation
Indices: 54490853--54490896 Score: 52
Period size: 16 Copynumber: 2.8 Consensus size: 16
54490843 AGGTAAGTAT
54490853 TTTTTTCTTTTTATCA
1 TTTTTTCTTTTTATCA
* * * *
54490869 TTTTTTATTCTAATCC
1 TTTTTTCTTTTTATCA
54490885 TTTTTTCTTTTT
1 TTTTTTCTTTTT
54490897 GTGCAGCTAA
Statistics
Matches: 21, Mismatches: 7, Indels: 0
0.75 0.25 0.00
Matches are distributed among these distances:
16 21 1.00
ACGTcount: A:0.11, C:0.14, G:0.00, T:0.75
Consensus pattern (16 bp):
TTTTTTCTTTTTATCA
Found at i:54493172 original size:40 final size:40
Alignment explanation
Indices: 54493122--54493434 Score: 448
Period size: 40 Copynumber: 7.7 Consensus size: 40
54493112 TACCACAAGG
* * * * *
54493122 ACAATTGCCTTCGGGTCTTAACCCCGG-CATAGCAACTCGC
1 ACAAATGCCTGCGGGTCTT-AGCCCGGATATATCAACTCGC
* * *
54493162 ACGAATGCCTTCGGGTCTTAGCCCGGATATATCAACTTGC
1 ACAAATGCCTGCGGGTCTTAGCCCGGATATATCAACTCGC
* * *
54493202 ACAATTGCCTTCGGGTCTTAGCCCGGATATATATCAACTTGC
1 ACAAATGCCTGCGGGTCTTAGCCCGG--ATATATCAACTCGC
*
54493244 ACAAATGCCTGCGGGTCTTAGCCCGGATATATCAACTTGC
1 ACAAATGCCTGCGGGTCTTAGCCCGGATATATCAACTCGC
* *
54493284 ACAATTGCCTTCGGGTCTTAGCCCGGATATATATCAACTCGC
1 ACAAATGCCTGCGGGTCTTAGCCCGG--ATATATCAACTCGC
54493326 ACAAATGCCTGCGGGTCTTAGCCCGGATATATCAACTCGC
1 ACAAATGCCTGCGGGTCTTAGCCCGGATATATCAACTCGC
54493366 ACAAATGCCTGCGGGTCTTAGCCCGGATATATCAACTCGC
1 ACAAATGCCTGCGGGTCTTAGCCCGGATATATCAACTCGC
54493406 ACAAATGCCTGCGGGTCTTAGCCCGGATA
1 ACAAATGCCTGCGGGTCTTAGCCCGGATA
54493435 AAATCCAAAT
Statistics
Matches: 253, Mismatches: 15, Indels: 10
0.91 0.05 0.04
Matches are distributed among these distances:
39 6 0.02
40 172 0.68
42 75 0.30
ACGTcount: A:0.24, C:0.29, G:0.22, T:0.25
Consensus pattern (40 bp):
ACAAATGCCTGCGGGTCTTAGCCCGGATATATCAACTCGC
Found at i:54493270 original size:82 final size:80
Alignment explanation
Indices: 54493122--54493434 Score: 493
Period size: 82 Copynumber: 3.9 Consensus size: 80
54493112 TACCACAAGG
* * * * *
54493122 ACAATTGCCTTCGGGTCTTAACCCCGG-CATAGCAACTCGCACGAATGCCTTCGGGTCTTAGCCC
1 ACAATTGCCTTCGGGTCTT-AGCCCGGATATATCAACTCGCACAAATGCCTGCGGGTCTTAGCCC
54493186 GGATATATCAACTTGC
65 GGATATATCAACTTGC
*
54493202 ACAATTGCCTTCGGGTCTTAGCCCGGATATATATCAACTTGCACAAATGCCTGCGGGTCTTAGCC
1 ACAATTGCCTTCGGGTCTTAGCCCGG--ATATATCAACTCGCACAAATGCCTGCGGGTCTTAGCC
54493267 CGGATATATCAACTTGC
64 CGGATATATCAACTTGC
54493284 ACAATTGCCTTCGGGTCTTAGCCCGGATATATATCAACTCGCACAAATGCCTGCGGGTCTTAGCC
1 ACAATTGCCTTCGGGTCTTAGCCCGG--ATATATCAACTCGCACAAATGCCTGCGGGTCTTAGCC
*
54493349 CGGATATATCAACTCGC
64 CGGATATATCAACTTGC
* *
54493366 ACAAATGCCTGCGGGTCTTAGCCCGGATATATCAACTCGCACAAATGCCTGCGGGTCTTAGCCCG
1 ACAATTGCCTTCGGGTCTTAGCCCGGATATATCAACTCGCACAAATGCCTGCGGGTCTTAGCCCG
54493431 GATA
66 GATA
54493435 AAATCCAAAT
Statistics
Matches: 220, Mismatches: 10, Indels: 6
0.93 0.04 0.03
Matches are distributed among these distances:
79 6 0.03
80 62 0.28
82 152 0.69
ACGTcount: A:0.24, C:0.29, G:0.22, T:0.25
Consensus pattern (80 bp):
ACAATTGCCTTCGGGTCTTAGCCCGGATATATCAACTCGCACAAATGCCTGCGGGTCTTAGCCCG
GATATATCAACTTGC
Found at i:54493305 original size:122 final size:119
Alignment explanation
Indices: 54493122--54493434 Score: 448
Period size: 122 Copynumber: 2.6 Consensus size: 119
54493112 TACCACAAGG
* * * * *
54493122 ACAATTGCCTTCGGGTCTTAACCCCGG-CATAGCAACTCGCACGAATGCCTTCGGGTCTTAGCCC
1 ACAAATGCCTGCGGGTCTT-AGCCCGGATATATCAACTCGCAC-AATGCCTTCGGGTCTTAGCCC
* * * *
54493186 GGATATATCAACTTGCACAATTGCCTTCGGGTCTTAGCCCGGATATATATCAACTTGC
64 GGATATATCAACTCGCACAAATGCCTGCGGGTCTTAGCCCGG--ATATATCAACTCGC
*
54493244 ACAAATGCCTGCGGGTCTTAGCCCGGATATATCAACTTGCACAATTGCCTTCGGGTCTTAGCCCG
1 ACAAATGCCTGCGGGTCTTAGCCCGGATATATCAACTCGCACAA-TGCCTTCGGGTCTTAGCCCG
54493309 GATATATATCAACTCGCACAAATGCCTGCGGGTCTTAGCCCGGATATATCAACTCGC
65 G--ATATATCAACTCGCACAAATGCCTGCGGGTCTTAGCCCGGATATATCAACTCGC
*
54493366 ACAAATGCCTGCGGGTCTTAGCCCGGATATATCAACTCGCACAAATGCCTGCGGGTCTTAGCCCG
1 ACAAATGCCTGCGGGTCTTAGCCCGGATATATCAACTCGCAC-AATGCCTTCGGGTCTTAGCCCG
54493431 GATA
65 GATA
54493435 AAATCCAAAT
Statistics
Matches: 174, Mismatches: 12, Indels: 12
0.88 0.06 0.06
Matches are distributed among these distances:
120 3 0.02
121 8 0.05
122 124 0.71
123 2 0.01
124 37 0.21
ACGTcount: A:0.24, C:0.29, G:0.22, T:0.25
Consensus pattern (119 bp):
ACAAATGCCTGCGGGTCTTAGCCCGGATATATCAACTCGCACAATGCCTTCGGGTCTTAGCCCGG
ATATATCAACTCGCACAAATGCCTGCGGGTCTTAGCCCGGATATATCAACTCGC
Found at i:54501893 original size:40 final size:40
Alignment explanation
Indices: 54501803--54502140 Score: 397
Period size: 40 Copynumber: 8.8 Consensus size: 40
54501793 ATTACCACAA
* * *
54501803 GCACAATTGCCTTCGGGTCTTAACCCGG-CATAGCAACTC
1 GCACAATTGCCTTCGGGTCTTAGCCCGGATATATCAACTC
*
54501842 GCACGAA-TGCCTTCGGGTCTTAGCCCGGATATATCAACTT
1 GCAC-AATTGCCTTCGGGTCTTAGCCCGGATATATCAACTC
54501882 GCACAATTGCCTTCGGGTCTTAGCCCGGATATATATCAACTC
1 GCACAATTGCCTTCGGGTCTTAGCCCGG--ATATATCAACTC
* *
54501924 GCACAA-TGCCTGCGGGTCTTAGCCCGGATATATCAACTT
1 GCACAATTGCCTTCGGGTCTTAGCCCGGATATATCAACTC
54501963 GCACAATTG-CTTCGGGTCTTAGCCCGGAATATATCAACTC
1 GCACAATTGCCTTCGGGTCTTAGCCCGG-ATATATCAACTC
*
54502003 GCACAAATGCC-T-GGGTCTTAG-CCGGATATAT-AACT-
1 GCACAATTGCCTTCGGGTCTTAGCCCGGATATATCAACTC
*
54502038 GCA-AA-TGCC-GC-GG-C-TAG-CCGG-TATATC-ACTC
1 GCACAATTGCCTTCGGGTCTTAGCCCGGATATATCAACTC
* *
54502069 GCACAAATTGCCTGCGAGTCTTAGCCCGGATATATCAACTC
1 GCAC-AATTGCCTTCGGGTCTTAGCCCGGATATATCAACTC
* *
54502110 GCACAAATGCCTGCGGGTCTTAGCCCGGATA
1 GCACAATTGCCTTCGGGTCTTAGCCCGGATA
54502141 AAATCCAAAT
Statistics
Matches: 264, Mismatches: 14, Indels: 41
0.83 0.04 0.13
Matches are distributed among these distances:
30 8 0.03
31 10 0.04
32 1 0.00
33 8 0.03
34 6 0.02
35 5 0.02
36 5 0.02
37 7 0.03
38 7 0.03
39 73 0.28
40 88 0.33
41 29 0.11
42 17 0.06
ACGTcount: A:0.24, C:0.29, G:0.22, T:0.25
Consensus pattern (40 bp):
GCACAATTGCCTTCGGGTCTTAGCCCGGATATATCAACTC
Found at i:54502150 original size:107 final size:108
Alignment explanation
Indices: 54501836--54502152 Score: 326
Period size: 107 Copynumber: 2.8 Consensus size: 108
54501826 CCCGGCATAG
* * * *
54501836 CAACTCGCACGAA-TGCCTTCGGGTCTTAGCCCGG-ATATATCAACTTGCACAATTGCCTTCGGG
1 CAACTCGCAC-AATTG-CTGCGAGTCTTAGCCCGGAATATATCAACTCGCACAAATGCC-T-GGG
54501899 TCTTAGCCCGGATATATATCAACTCGCACAATGCCTGCGGGTCTTAGCCCGGATATAT
62 TCTTAG-CCGG--ATATAT-AACTC-CA-AATGCC-GC-GG-C-TAG-CCGGATATAT
* * *
54501957 CAACTTGCACAATTGCTTCGGGTCTTAGCCCGGAATATATCAACTCGCACAAATGCCTGGGTCTT
1 CAACTCGCACAATTGCTGCGAGTCTTAGCCCGGAATATATCAACTCGCACAAATGCCTGGGTCTT
*
54502022 AGCCGGATATATAACTGCAAATGCCGCGGCTAGCCGG-TATAT
66 AGCCGGATATATAACTCCAAATGCCGCGGCTAGCCGGATATAT
54502064 C-ACTCGCACAAATTGCCTGCGAGTCTTAGCCCGG-ATATATCAACTCGCACAAATGCCTGCGGG
1 CAACTCGCAC-AATTG-CTGCGAGTCTTAGCCCGGAATATATCAACTCGCACAAATGCCT--GGG
54502127 TCTTAGCCCGGATA-A-AA-TCCAAATGC
62 TCTTAG-CCGGATATATAACTCCAAATGC
54502153 TCATGCACAT
Statistics
Matches: 181, Mismatches: 8, Indels: 28
0.83 0.04 0.13
Matches are distributed among these distances:
106 7 0.04
107 43 0.24
108 22 0.12
109 13 0.07
110 8 0.04
111 2 0.01
112 2 0.01
113 6 0.03
114 2 0.01
115 4 0.02
116 6 0.03
118 4 0.02
119 9 0.05
120 21 0.12
121 32 0.18
ACGTcount: A:0.26, C:0.28, G:0.21, T:0.25
Consensus pattern (108 bp):
CAACTCGCACAATTGCTGCGAGTCTTAGCCCGGAATATATCAACTCGCACAAATGCCTGGGTCTT
AGCCGGATATATAACTCCAAATGCCGCGGCTAGCCGGATATAT
Found at i:54513545 original size:80 final size:80
Alignment explanation
Indices: 54513457--54513604 Score: 269
Period size: 80 Copynumber: 1.9 Consensus size: 80
54513447 CTCGTTGCCT
*
54513457 GTGGGTCTTTATGCCCGGATACAATTCCAGCACGAAGCCTGCGGGTCTTTAAGCCCGGATAACAT
1 GTGGGTCTTTAAGCCCGGATACAATTCCAGCACGAAGCCTGCGGGTCTTTAAGCCCGGATAACAT
54513522 TCCAGCATATAGCTC
66 TCCAGCATATAGCTC
* *
54513537 GTGGGTCTTTAAGCCCGGATACAATTCCAGCACGAAGCCTGCGGGTCTTTAAGGCCTGATAACAT
1 GTGGGTCTTTAAGCCCGGATACAATTCCAGCACGAAGCCTGCGGGTCTTTAAGCCCGGATAACAT
54513602 TCC
66 TCC
54513605 TCAAGTATCA
Statistics
Matches: 65, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
80 65 1.00
ACGTcount: A:0.24, C:0.27, G:0.24, T:0.25
Consensus pattern (80 bp):
GTGGGTCTTTAAGCCCGGATACAATTCCAGCACGAAGCCTGCGGGTCTTTAAGCCCGGATAACAT
TCCAGCATATAGCTC
Found at i:54513604 original size:40 final size:40
Alignment explanation
Indices: 54513453--54513589 Score: 190
Period size: 40 Copynumber: 3.4 Consensus size: 40
54513443 CCAGCTCGTT
* *
54513453 GCCTGTGGGTCTTTATGCCCGGATACAATTCCAGCACGAA
1 GCCTGCGGGTCTTTAAGCCCGGATACAATTCCAGCACGAA
*
54513493 GCCTGCGGGTCTTTAAGCCCGGATA-ACATTCCAGCA-TATA
1 GCCTGCGGGTCTTTAAGCCCGGATACA-ATTCCAGCACGA-A
*
54513533 G-CTCGTGGGTCTTTAAGCCCGGATACAATTCCAGCACGAA
1 GCCT-GCGGGTCTTTAAGCCCGGATACAATTCCAGCACGAA
54513573 GCCTGCGGGTCTTTAAG
1 GCCTGCGGGTCTTTAAG
54513590 GCCTGATAAC
Statistics
Matches: 85, Mismatches: 6, Indels: 12
0.83 0.06 0.12
Matches are distributed among these distances:
39 4 0.05
40 77 0.91
41 4 0.05
ACGTcount: A:0.23, C:0.27, G:0.26, T:0.25
Consensus pattern (40 bp):
GCCTGCGGGTCTTTAAGCCCGGATACAATTCCAGCACGAA
Found at i:54528819 original size:27 final size:26
Alignment explanation
Indices: 54528756--54528881 Score: 164
Period size: 27 Copynumber: 4.8 Consensus size: 26
54528746 GCTACCTGAA
* * *
54528756 CCCTCATGTGATAAAATAATGA-TTT
1 CCCTTATGTGATAAAATGACGATTTT
54528781 CCCTTATGTGATAAAATGACGATTTT
1 CCCTTATGTGATAAAATGACGATTTT
*
54528807 GCCCTTATGTGATAAAATGACAAATTTT
1 -CCCTTATGTGATAAAATGAC-GATTTT
*
54528835 CCCTTATGTGATAAAATAACGATTTT
1 CCCTTATGTGATAAAATGACGATTTT
*
54528861 GCCCTTATGTGATAAGATGAC
1 -CCCTTATGTGATAAAATGAC
54528882 CGAAATACCT
Statistics
Matches: 89, Mismatches: 8, Indels: 6
0.86 0.08 0.06
Matches are distributed among these distances:
25 19 0.21
26 8 0.09
27 57 0.64
28 5 0.06
ACGTcount: A:0.33, C:0.16, G:0.15, T:0.36
Consensus pattern (26 bp):
CCCTTATGTGATAAAATGACGATTTT
Found at i:54528843 original size:54 final size:54
Alignment explanation
Indices: 54528778--54528881 Score: 190
Period size: 54 Copynumber: 1.9 Consensus size: 54
54528768 AAAATAATGA
*
54528778 TTTCCCTTATGTGATAAAATGACGATTTTGCCCTTATGTGATAAAATGACAAAT
1 TTTCCCTTATGTGATAAAATAACGATTTTGCCCTTATGTGATAAAATGACAAAT
*
54528832 TTTCCCTTATGTGATAAAATAACGATTTTGCCCTTATGTGATAAGATGAC
1 TTTCCCTTATGTGATAAAATAACGATTTTGCCCTTATGTGATAAAATGAC
54528882 CGAAATACCT
Statistics
Matches: 48, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
54 48 1.00
ACGTcount: A:0.32, C:0.15, G:0.15, T:0.38
Consensus pattern (54 bp):
TTTCCCTTATGTGATAAAATAACGATTTTGCCCTTATGTGATAAAATGACAAAT
Found at i:54552834 original size:18 final size:18
Alignment explanation
Indices: 54552813--54552848 Score: 72
Period size: 18 Copynumber: 2.0 Consensus size: 18
54552803 GTGTTAGTAG
54552813 TGATAATAGTTTTTATCT
1 TGATAATAGTTTTTATCT
54552831 TGATAATAGTTTTTATCT
1 TGATAATAGTTTTTATCT
54552849 AAGAAATCAG
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.28, C:0.06, G:0.11, T:0.56
Consensus pattern (18 bp):
TGATAATAGTTTTTATCT
Found at i:54554471 original size:46 final size:44
Alignment explanation
Indices: 54554418--54554544 Score: 141
Period size: 47 Copynumber: 2.8 Consensus size: 44
54554408 TCATTTGTGT
54554418 GAGCTAGTGTAAAACATGTCTGGGACATGCATCGGCCACATT-ATGA-
1 GAGCTAGTGTAAAACATGTCTGGGACATGCATC-G--ACATTGA-GAC
*
54554464 GAGCTAGTGTAAGACCATGTCTGGGACATGGCATCGACATTGAGAC
1 GAGCTAGTGTAA-AACATGTCTGGGACAT-GCATCGACATTGAGAC
* *
54554510 GAGTGCCAGTGTAAGACATGTCTGGGACATGCATC
1 GA--GCTAGTGTAAAACATGTCTGGGACATGCATC
54554545 AGCCTCGGGA
Statistics
Matches: 71, Mismatches: 4, Indels: 12
0.82 0.05 0.14
Matches are distributed among these distances:
45 7 0.10
46 20 0.28
47 30 0.42
48 14 0.20
ACGTcount: A:0.28, C:0.20, G:0.29, T:0.23
Consensus pattern (44 bp):
GAGCTAGTGTAAAACATGTCTGGGACATGCATCGACATTGAGAC
Found at i:54556735 original size:20 final size:20
Alignment explanation
Indices: 54556710--54556747 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
54556700 GTAACATATA
54556710 TCATGAACTCAGACCACAAC
1 TCATGAACTCAGACCACAAC
* *
54556730 TCATGAGCTCAGATCACA
1 TCATGAACTCAGACCACA
54556748 TAGTTTTGTA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.37, C:0.32, G:0.13, T:0.18
Consensus pattern (20 bp):
TCATGAACTCAGACCACAAC
Found at i:54559240 original size:36 final size:37
Alignment explanation
Indices: 54559168--54559245 Score: 113
Period size: 36 Copynumber: 2.1 Consensus size: 37
54559158 TTATTACGAA
* * *
54559168 GTCTTACCCGGACATAATCTCCACACGAAGTTATCGG
1 GTCTTACCCAGACATAATCCCCACACGAAGTCATCGG
*
54559205 GTCTTACCCAGACA-AATCCCCACACGTAGTCATCGG
1 GTCTTACCCAGACATAATCCCCACACGAAGTCATCGG
54559241 GTCTT
1 GTCTT
54559246 TAGAGCTCGG
Statistics
Matches: 37, Mismatches: 4, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
36 24 0.65
37 13 0.35
ACGTcount: A:0.26, C:0.32, G:0.18, T:0.24
Consensus pattern (37 bp):
GTCTTACCCAGACATAATCCCCACACGAAGTCATCGG
Found at i:54559523 original size:47 final size:47
Alignment explanation
Indices: 54559363--54559684 Score: 554
Period size: 47 Copynumber: 6.7 Consensus size: 47
54559353 GCCCTTCGGG
*
54559363 ACTTATCACATTCATCACATCGGCCATTAGGCCCTATCACATATATATAC
1 ACTT-TCACATTCATCACATCGGCCATTAGGCCTTATCAC--ATATATAC
*
54559413 ACTTTCACATTCATCACATCGGCCATTAGGCCCTATCACATATATATAC
1 ACTTTCACATTCATCACATCGGCCATTAGGCCTTATCAC--ATATATAC
*
54559462 ACTTTCACATTCATCACATCGGCCATTAGGCATTATCACATATATAC
1 ACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATAC
54559509 ACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATAC
1 ACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATAC
*
54559556 ACTTTCACATTCATCACATCGGCCATTAGGCATTATCACATATATAC
1 ACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATAC
*
54559603 ACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATAT
1 ACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATAC
54559650 ACTTTCACATTCATCACATCGGCCATTAGGCCTTA
1 ACTTTCACATTCATCACATCGGCCATTAGGCCTTA
54559685 CTATCATTTC
Statistics
Matches: 266, Mismatches: 6, Indels: 3
0.97 0.02 0.01
Matches are distributed among these distances:
47 180 0.68
49 82 0.31
50 4 0.02
ACGTcount: A:0.30, C:0.29, G:0.09, T:0.32
Consensus pattern (47 bp):
ACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATAC
Found at i:54563196 original size:40 final size:40
Alignment explanation
Indices: 54563151--54563386 Score: 210
Period size: 40 Copynumber: 5.9 Consensus size: 40
54563141 CGAATACACG
* * * *
54563151 TCACCAGCATGATTGCTCTTCGGGACCTAGCCCGGACATA
1 TCACCAGCACGAATGCTCTTCGGGACTTAGCCCGGATATA
* * ** *
54563191 ACACCAGCACGAATGCTCTTTGGGGTTTAGCACGGATATA
1 TCACCAGCACGAATGCTCTTCGGGACTTAGCCCGGATATA
* * *
54563231 TCACTAGCACGAATGCTCTTCGGAACTTAGCCCGGATACA
1 TCACCAGCACGAATGCTCTTCGGGACTTAGCCCGGATATA
* * *
54563271 TCACTAGCATGAATGCTCTTCGGGACTTAGCCCGGATTTA
1 TCACCAGCACGAATGCTCTTCGGGACTTAGCCCGGATATA
* * * * *
54563311 GTAACTC-GCACCAATGC-CTTCGGGTCTTAGTCCGGATATGG
1 -TCAC-CAGCACGAATGCTCTTCGGGACTTAGCCCGGATAT-A
* *
54563352 TCACTTAGCAC-AAAGC-CTTCGGGACTTAGCCCGGA
1 TCAC-CAGCACGAATGCTCTTCGGGACTTAGCCCGGA
54563387 CATCATTCGA
Statistics
Matches: 158, Mismatches: 34, Indels: 8
0.79 0.17 0.04
Matches are distributed among these distances:
40 143 0.91
41 15 0.09
ACGTcount: A:0.24, C:0.28, G:0.23, T:0.25
Consensus pattern (40 bp):
TCACCAGCACGAATGCTCTTCGGGACTTAGCCCGGATATA
Found at i:54563372 original size:120 final size:120
Alignment explanation
Indices: 54563151--54563386 Score: 270
Period size: 120 Copynumber: 2.0 Consensus size: 120
54563141 CGAATACACG
* * *
54563151 TCACCAGCATGATTGCTCTTCGGGACCTAGCCCGGACATAACACCAGCACGAATGCTCTTTGGGG
1 TCACCAGCATGAATGCTCTTCGGGACCTAGCCCGGACATAACACCAGCACCAATGCTCTTTCGGG
*
54563216 TTTAGCACGGATATATCACTAGCACGAATGCTCTTCGGAACTTAGCCCGGATACA
66 TTTAGCACGGATATATCACTAGCACGAAAGCTCTTCGGAACTTAGCCCGGATACA
* * * *
54563271 TCACTAGCATGAATGCTCTTCGGGACTTAGCCCGGATTTAGTAAC-TC-GCACCAATGC-C-TTC
1 TCACCAGCATGAATGCTCTTCGGGACCTAGCCCGGA--CA-TAACACCAGCACCAATGCTCTTTC
* *
54563332 GGGTCTTAGTC-CGGATATGGTCACTTAGCAC-AAAGC-CTTCGGGACTTAGCCCGGA
63 GGGT-TTAG-CACGGATAT-ATCAC-TAGCACGAAAGCTCTTCGGAACTTAGCCCGGA
54563387 CATCATTCGA
Statistics
Matches: 99, Mismatches: 10, Indels: 14
0.80 0.08 0.11
Matches are distributed among these distances:
119 6 0.06
120 63 0.64
121 18 0.18
122 8 0.08
123 4 0.04
ACGTcount: A:0.24, C:0.28, G:0.23, T:0.25
Consensus pattern (120 bp):
TCACCAGCATGAATGCTCTTCGGGACCTAGCCCGGACATAACACCAGCACCAATGCTCTTTCGGG
TTTAGCACGGATATATCACTAGCACGAAAGCTCTTCGGAACTTAGCCCGGATACA
Found at i:54563731 original size:29 final size:29
Alignment explanation
Indices: 54563692--54563770 Score: 106
Period size: 29 Copynumber: 2.7 Consensus size: 29
54563682 CTTAATAAAC
*
54563692 AACCACGCACACTTAGTGCCATGTACTTT-A
1 AACC-CGCACACTTAGTGCCATGCA-TTTCA
*
54563722 AACTCGCACACTTAGTGCCATGCATTTCA
1 AACCCGCACACTTAGTGCCATGCATTTCA
*
54563751 AGCCCGCACACTTAGTGCCA
1 AACCCGCACACTTAGTGCCA
54563771 ATCTCACAAC
Statistics
Matches: 44, Mismatches: 4, Indels: 3
0.86 0.08 0.06
Matches are distributed among these distances:
28 3 0.07
29 38 0.86
30 3 0.07
ACGTcount: A:0.28, C:0.33, G:0.15, T:0.24
Consensus pattern (29 bp):
AACCCGCACACTTAGTGCCATGCATTTCA
Found at i:54565749 original size:36 final size:37
Alignment explanation
Indices: 54565677--54565754 Score: 122
Period size: 36 Copynumber: 2.1 Consensus size: 37
54565667 TTATTACGAA
* *
54565677 GTCTTACCCGGACATAATCTCCACACGAAGTTATCGG
1 GTCTTACCCGGACATAATCCCCACACGAAGTCATCGG
*
54565714 GTCTTACCCGGACA-AATCCCCACACGTAGTCATCGG
1 GTCTTACCCGGACATAATCCCCACACGAAGTCATCGG
54565750 GTCTT
1 GTCTT
54565755 TAGAGCTCGG
Statistics
Matches: 38, Mismatches: 3, Indels: 1
0.90 0.07 0.02
Matches are distributed among these distances:
36 24 0.63
37 14 0.37
ACGTcount: A:0.24, C:0.32, G:0.19, T:0.24
Consensus pattern (37 bp):
GTCTTACCCGGACATAATCCCCACACGAAGTCATCGG
Found at i:54566032 original size:47 final size:47
Alignment explanation
Indices: 54565872--54566240 Score: 648
Period size: 47 Copynumber: 7.7 Consensus size: 47
54565862 GCCCTTCGGG
*
54565872 ACTTATCACATTCATCACATCGGCCATTAGGCCCTATCACATATATATAC
1 ACTT-TCACATTCATCACATCGGCCATTAGGCCTTATCAC--ATATATAC
*
54565922 ACTTTCACATTCATCACATCGGCCATTAGGCCCTATCACATATATATAC
1 ACTTTCACATTCATCACATCGGCCATTAGGCCTTATCAC--ATATATAC
*
54565971 ACTTTCACATTCATCACATCGGCCATTAGGCATTATCACATATATAC
1 ACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATAC
*
54566018 ACTTTCACATTCATCACATCGGCCATTAGGCCTTATCATATATATAC
1 ACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATAC
*
54566065 ACTTTCACATTCATCACATCGGCCATTAGGCATTATCACATATATAC
1 ACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATAC
54566112 ACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATAC
1 ACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATAC
54566159 ACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATAC
1 ACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATAC
54566206 ACTTTCACATTCATCACATCGGCCATTAGGCCTTA
1 ACTTTCACATTCATCACATCGGCCATTAGGCCTTA
54566241 CTATCATTTC
Statistics
Matches: 312, Mismatches: 7, Indels: 3
0.97 0.02 0.01
Matches are distributed among these distances:
47 226 0.72
49 82 0.26
50 4 0.01
ACGTcount: A:0.30, C:0.29, G:0.09, T:0.32
Consensus pattern (47 bp):
ACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATAC
Found at i:54569148 original size:21 final size:22
Alignment explanation
Indices: 54569115--54569155 Score: 57
Period size: 21 Copynumber: 1.9 Consensus size: 22
54569105 TTCATTTATG
*
54569115 TTTCATTGGCACATA-ATCATA
1 TTTCATTGCCACATACATCATA
*
54569136 TTTCATTTCCACATACATCA
1 TTTCATTGCCACATACATCA
54569156 CAATACATTC
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 13 0.76
22 4 0.24
ACGTcount: A:0.32, C:0.24, G:0.05, T:0.39
Consensus pattern (22 bp):
TTTCATTGCCACATACATCATA
Found at i:54569633 original size:28 final size:28
Alignment explanation
Indices: 54569565--54569643 Score: 88
Period size: 28 Copynumber: 2.8 Consensus size: 28
54569555 GAATCATTCG
54569565 ATATTTCGTACACTAAGT-CTCATTGTCA
1 ATATTTCGTACACTAAGTGC-CATTGTCA
* * * *
54569593 ATATCTCGCACACAAAGTGCCATTTTCA
1 ATATTTCGTACACTAAGTGCCATTGTCA
* *
54569621 ATATTTCATACACTGAGTGCCAT
1 ATATTTCGTACACTAAGTGCCAT
54569644 ATTTGATTGC
Statistics
Matches: 41, Mismatches: 9, Indels: 2
0.79 0.17 0.04
Matches are distributed among these distances:
28 40 0.98
29 1 0.02
ACGTcount: A:0.30, C:0.24, G:0.11, T:0.34
Consensus pattern (28 bp):
ATATTTCGTACACTAAGTGCCATTGTCA
Found at i:54575076 original size:28 final size:28
Alignment explanation
Indices: 54574998--54575078 Score: 103
Period size: 28 Copynumber: 2.9 Consensus size: 28
54574988 ATCATAACTG
*
54574998 TAAATCTGATTGGGCCTAAT-GGCCGTA
1 TAAATATGATTGGGCCTAATGGGCCGTA
* *
54575025 TGAATGTGATTTGGGCCTAATGGGCC-TCA
1 TAAATATGA-TTGGGCCTAATGGGCCGT-A
54575054 TAAATATGATTGGGCCTAATGGGCC
1 TAAATATGATTGGGCCTAATGGGCC
54575079 ATATGGAAGA
Statistics
Matches: 47, Mismatches: 4, Indels: 5
0.84 0.07 0.09
Matches are distributed among these distances:
27 7 0.15
28 28 0.60
29 12 0.26
ACGTcount: A:0.25, C:0.17, G:0.28, T:0.30
Consensus pattern (28 bp):
TAAATATGATTGGGCCTAATGGGCCGTA
Found at i:54575092 original size:28 final size:27
Alignment explanation
Indices: 54575005--54575129 Score: 92
Period size: 28 Copynumber: 4.4 Consensus size: 27
54574995 CTGTAAATCT
* *
54575005 GATTGGGCCTAAT-GGCCGTATGAATGT
1 GATTGGGCCTAATGGGCCATATGAA-GA
* *
54575032 GATTTGGGCCTAATGGGCC-TCATAAATA
1 GA-TTGGGCCTAATGGGCCAT-ATGAAGA
54575060 TGATTGGGCCTAATGGGCCATATGGAAGA
1 -GATTGGGCCTAATGGGCCATAT-GAAGA
* * *
54575089 GATTAGGCCTATTGGGCTATATATGGAAGA
1 GATTGGGCCTAATGGGC--CATAT-GAAGA
*
54575119 GATTAGGCCTA
1 GATTGGGCCTA
54575130 GTATATGATG
Statistics
Matches: 82, Mismatches: 8, Indels: 13
0.80 0.08 0.13
Matches are distributed among these distances:
27 2 0.02
28 45 0.55
29 14 0.17
30 21 0.26
ACGTcount: A:0.27, C:0.14, G:0.30, T:0.28
Consensus pattern (27 bp):
GATTGGGCCTAATGGGCCATATGAAGA
Found at i:54575098 original size:56 final size:56
Alignment explanation
Indices: 54574998--54575105 Score: 139
Period size: 56 Copynumber: 1.9 Consensus size: 56
54574988 ATCATAACTG
* * * *
54574998 TAAATCTGATTGGGCCTAATGGCCGTATGAATGTGATTTGGGCCTAATGGGCCTCA
1 TAAATATGATTGGGCCTAATGGCCATATGAATGAGATTTAGGCCTAATGGGCCTCA
*
54575054 TAAATATGATTGGGCCTAATGGGCCATATGGAA-GAGA-TTAGGCCTATTGGGC
1 TAAATATGATTGGGCCTAAT-GGCCATAT-GAATGAGATTTAGGCCTAATGGGC
54575106 TATATATGGA
Statistics
Matches: 45, Mismatches: 5, Indels: 4
0.83 0.09 0.07
Matches are distributed among these distances:
56 32 0.71
57 10 0.22
58 3 0.07
ACGTcount: A:0.26, C:0.16, G:0.30, T:0.29
Consensus pattern (56 bp):
TAAATATGATTGGGCCTAATGGCCATATGAATGAGATTTAGGCCTAATGGGCCTCA
Found at i:54586197 original size:19 final size:19
Alignment explanation
Indices: 54586173--54586215 Score: 86
Period size: 19 Copynumber: 2.3 Consensus size: 19
54586163 ATCGTGTCAC
54586173 ATTAAAGTGTTTTTCGTAA
1 ATTAAAGTGTTTTTCGTAA
54586192 ATTAAAGTGTTTTTCGTAA
1 ATTAAAGTGTTTTTCGTAA
54586211 ATTAA
1 ATTAA
54586216 CTTCTTAAGT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 24 1.00
ACGTcount: A:0.35, C:0.05, G:0.14, T:0.47
Consensus pattern (19 bp):
ATTAAAGTGTTTTTCGTAA
Done.