Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr08 129432109
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: 129432109
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32
Warning! 350 characters in sequence are not A, C, G, or T
File 180 of 425
Found at i:54456083 original size:30 final size:30
Alignment explanation
Indices: 54456047--54456103 Score: 89
Period size: 30 Copynumber: 1.9 Consensus size: 30
54456037 AAAATCATAT
54456047 TTTTACAAATTTGCA-TTTTGGCCCCTAAAC
1 TTTTACAAATTTGCACTTTT-GCCCCTAAAC
*
54456077 TTTTACATATTTGCACTTTTGCCCCTA
1 TTTTACAAATTTGCACTTTTGCCCCTA
54456104 TGCTTGGAAG
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
30 21 0.84
31 4 0.16
ACGTcount: A:0.23, C:0.25, G:0.09, T:0.44
Consensus pattern (30 bp):
TTTTACAAATTTGCACTTTTGCCCCTAAAC
Found at i:54457459 original size:7 final size:7
Alignment explanation
Indices: 54457447--54457471 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
54457437 GTTGCCATCT
54457447 TGTTTGA
1 TGTTTGA
54457454 TGTTTGA
1 TGTTTGA
54457461 TGTTTGA
1 TGTTTGA
54457468 TGTT
1 TGTT
54457472 GTGGTGATGA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.12, C:0.00, G:0.28, T:0.60
Consensus pattern (7 bp):
TGTTTGA
Found at i:54458407 original size:27 final size:28
Alignment explanation
Indices: 54458353--54458420 Score: 111
Period size: 27 Copynumber: 2.5 Consensus size: 28
54458343 ATTTGTACAT
54458353 CACTAAGTGTGCGAGTTTGATTATATAG
1 CACTAAGTGTGCGAGTTTGATTATATAG
* *
54458381 CACTAGGTGTGCGAG-TTGATTTTATAG
1 CACTAAGTGTGCGAGTTTGATTATATAG
54458408 CACTAAGTGTGCG
1 CACTAAGTGTGCG
54458421 GACTCACTAT
Statistics
Matches: 37, Mismatches: 3, Indels: 1
0.90 0.07 0.02
Matches are distributed among these distances:
27 23 0.62
28 14 0.38
ACGTcount: A:0.25, C:0.13, G:0.28, T:0.34
Consensus pattern (28 bp):
CACTAAGTGTGCGAGTTTGATTATATAG
Found at i:54462843 original size:12 final size:13
Alignment explanation
Indices: 54462811--54462845 Score: 54
Period size: 12 Copynumber: 2.7 Consensus size: 13
54462801 TAAATTAACA
54462811 AAAGAGATATAAAT
1 AAAGAGA-ATAAAT
54462825 AAAGAGAATAAAT
1 AAAGAGAATAAAT
54462838 -AAGAGAAT
1 AAAGAGAAT
54462846 GCTTATTAAT
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
12 8 0.38
13 6 0.29
14 7 0.33
ACGTcount: A:0.66, C:0.00, G:0.17, T:0.17
Consensus pattern (13 bp):
AAAGAGAATAAAT
Found at i:54463218 original size:21 final size:21
Alignment explanation
Indices: 54463202--54463260 Score: 73
Period size: 21 Copynumber: 2.8 Consensus size: 21
54463192 CGATGTCATT
* *
54463202 ACATTCAATTCTAATGTCACA
1 ACATCCAATTCAAATGTCACA
*
54463223 ACATCCAATTCAAATGTCACG
1 ACATCCAATTCAAATGTCACA
* *
54463244 ACATCCAACTCCAATGT
1 ACATCCAATTCAAATGT
54463261 TGCAACATTC
Statistics
Matches: 33, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
21 33 1.00
ACGTcount: A:0.37, C:0.29, G:0.07, T:0.27
Consensus pattern (21 bp):
ACATCCAATTCAAATGTCACA
Found at i:54465557 original size:40 final size:40
Alignment explanation
Indices: 54465482--54465746 Score: 281
Period size: 40 Copynumber: 6.7 Consensus size: 40
54465472 CGGATATAAC
* * * * *
54465482 CACTCGCAC-AAGGCCGTCAGGTCTTAGCCCGG-ATATGGT
1 CACTCGCACAAATGCCTTCGGGACTTAGCCCGGAAT-TAGT
* * * *
54465521 CACTAGCACAAATGTCTTCGGGTCTTAGCCCAG-ATATAG-
1 CACTCGCACAAATGCCTTCGGGACTTAGCCCGGAAT-TAGT
54465560 CAACTCGCACAAATGCCTTCGGGACTTAGCCCGGAATTAGT
1 C-ACTCGCACAAATGCCTTCGGGACTTAGCCCGGAATTAGT
* * * *
54465601 AACTCGCACCAATGCCTTCGGGACTTGGCCCAGAATTAGT
1 CACTCGCACAAATGCCTTCGGGACTTAGCCCGGAATTAGT
*
54465641 -ATCTCGCACAATTGCCTTCGGGACTTAGCCCGG-ATGTAGT
1 CA-CTCGCACAAATGCCTTCGGGACTTAGCCCGGAAT-TAGT
* *
54465681 AACTCGCACAAATGCCTTCGGGACTTAGCCCGGAATTAAT
1 CACTCGCACAAATGCCTTCGGGACTTAGCCCGGAATTAGT
* *
54465721 CACTAGCACAAATGTCTTCGGGACTT
1 CACTCGCACAAATGCCTTCGGGACTT
54465747 GACCCCATTA
Statistics
Matches: 194, Mismatches: 24, Indels: 15
0.83 0.10 0.06
Matches are distributed among these distances:
39 12 0.06
40 177 0.91
41 5 0.03
ACGTcount: A:0.25, C:0.28, G:0.23, T:0.24
Consensus pattern (40 bp):
CACTCGCACAAATGCCTTCGGGACTTAGCCCGGAATTAGT
Found at i:54465685 original size:120 final size:120
Alignment explanation
Indices: 54465526--54465747 Score: 345
Period size: 120 Copynumber: 1.9 Consensus size: 120
54465516 ATGGTCACTA
* *
54465526 GCACAAATGTCTTCGGGTCTTAGCCCAGATATAGCAACTCGCACAAATGCCTTCGGGACTTAGCC
1 GCACAAATGCCTTCGGGACTTAGCCCAGATATAGCAACTCGCACAAATGCCTTCGGGACTTAGCC
* * *
54465591 CGGAATTAGTAACTCGCACCAATGCCTTCGGGACTTGGCCCAGAATTAGTATCTC
66 CGGAATTAATAACTAGCACAAATGCCTTCGGGACTTGGCCCAGAATTAGTATCTC
* * * *
54465646 GCACAATTGCCTTCGGGACTTAGCCCGGATGTAGTAACTCGCACAAATGCCTTCGGGACTTAGCC
1 GCACAAATGCCTTCGGGACTTAGCCCAGATATAGCAACTCGCACAAATGCCTTCGGGACTTAGCC
* *
54465711 CGGAATTAATCACTAGCACAAATGTCTTCGGGACTTG
66 CGGAATTAATAACTAGCACAAATGCCTTCGGGACTTG
54465748 ACCCCATTAG
Statistics
Matches: 91, Mismatches: 11, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
120 91 1.00
ACGTcount: A:0.26, C:0.27, G:0.23, T:0.24
Consensus pattern (120 bp):
GCACAAATGCCTTCGGGACTTAGCCCAGATATAGCAACTCGCACAAATGCCTTCGGGACTTAGCC
CGGAATTAATAACTAGCACAAATGCCTTCGGGACTTGGCCCAGAATTAGTATCTC
Found at i:54473440 original size:40 final size:40
Alignment explanation
Indices: 54473377--54473523 Score: 224
Period size: 40 Copynumber: 3.7 Consensus size: 40
54473367 TGAATGATAC
*
54473377 CCGGGTTAAGA-CCGAAGGCATTTGTGTGAGTTGCTATAT
1 CCGGGTTAAGACCCGAAGGCATTTGTGCGAGTTGCTATAT
*
54473416 CCGGGTTAAGACCCGAAGGCATTTGTGCGAGTTGTTATAT
1 CCGGGTTAAGACCCGAAGGCATTTGTGCGAGTTGCTATAT
* * *
54473456 CTGGGCTAAGACCCGAAGGCATTTGTGCGAGTTGCTATAC
1 CCGGGTTAAGACCCGAAGGCATTTGTGCGAGTTGCTATAT
* *
54473496 CCGGGTTAAGACCCGAAGGTAATTGTGC
1 CCGGGTTAAGACCCGAAGGCATTTGTGC
54473524 TTGTGGTTAT
Statistics
Matches: 97, Mismatches: 10, Indels: 1
0.90 0.09 0.01
Matches are distributed among these distances:
39 11 0.11
40 86 0.89
ACGTcount: A:0.23, C:0.19, G:0.31, T:0.27
Consensus pattern (40 bp):
CCGGGTTAAGACCCGAAGGCATTTGTGCGAGTTGCTATAT
Found at i:54478112 original size:68 final size:66
Alignment explanation
Indices: 54478040--54478189 Score: 169
Period size: 67 Copynumber: 2.2 Consensus size: 66
54478030 CATCATGTGT
* * * *
54478040 ACAAGAGAGCTACAAGACATTATGATGTAGCTAGGTCGCATGGGTGATACTA-TG-TGTACACCA
1 ACAAGAGAGCTAC--GACA-TAT-ATGTAGCTAGGTCGCATGCGTGATACCAGTGAAGGACACCA
54478103 TGTAG
62 TGTAG
** * *
54478108 ACAAGAGAGCTACGGGATATATGTAGCTAGGTCGCATGCGTGGTTCCAGGTGAAGGACACCATGT
1 ACAAGAGAGCTACGACATATATGTAGCTAGGTCGCATGCGTGATACCA-GTGAAGGACACCATGT
54478173 AG
65 AG
54478175 ACAAGAGAGCTACGA
1 ACAAGAGAGCTACGA
54478190 GATAAACTGG
Statistics
Matches: 70, Mismatches: 9, Indels: 7
0.81 0.10 0.08
Matches are distributed among these distances:
64 24 0.34
65 3 0.04
66 4 0.06
67 26 0.37
68 13 0.19
ACGTcount: A:0.32, C:0.17, G:0.29, T:0.21
Consensus pattern (66 bp):
ACAAGAGAGCTACGACATATATGTAGCTAGGTCGCATGCGTGATACCAGTGAAGGACACCATGTA
G
Found at i:54478145 original size:64 final size:64
Alignment explanation
Indices: 54478064--54478247 Score: 203
Period size: 67 Copynumber: 2.8 Consensus size: 64
54478054 AGACATTATG
* * *
54478064 ATGTAGCTAGGTCGCATGGGTGATACTATGTGTACACCATGTAGACAAGAGAGCTACGGGATAT
1 ATGTAGCTAGGTCGCATGGGTGGTACTATGTGTACACCATGTAGACAAGAGAGCTACGAGATAA
* * * * *
54478128 ATGTAGCTAGGTCGCATGCGTGGTTCCAGGTGAAGGACACCATGTAGACAAGAGAGCTACGAGAT
1 ATGTAGCTAGGTCGCATGGGTGGTACTA--TG-TGTACACCATGTAGACAAGAGAGCTACGAGAT
54478193 AA
63 AA
* * *
54478195 ACTG--GCTAGGTCACATGGGTGGTACTAAGTGTTCACCATGT-GTACAAGAGAGC
1 A-TGTAGCTAGGTCGCATGGGTGGTACTATGTGTACACCATGTAG-ACAAGAGAGC
54478248 CAAACTATAT
Statistics
Matches: 99, Mismatches: 16, Indels: 11
0.79 0.13 0.09
Matches are distributed among these distances:
62 1 0.01
63 19 0.19
64 25 0.25
66 21 0.21
67 31 0.31
68 2 0.02
ACGTcount: A:0.29, C:0.17, G:0.30, T:0.23
Consensus pattern (64 bp):
ATGTAGCTAGGTCGCATGGGTGGTACTATGTGTACACCATGTAGACAAGAGAGCTACGAGATAA
Found at i:54496514 original size:50 final size:49
Alignment explanation
Indices: 54496396--54496571 Score: 199
Period size: 50 Copynumber: 3.5 Consensus size: 49
54496386 TTGGTACGTA
* * * *
54496396 TAGTAGCCTGCACTTAGTACTACACATGCGACCAATTATCCGGTACACG
1 TAGTAGCCTGCACTTAGTACTACACACGTGACCAACTATCCGATACACG
*
54496445 TAGTAGCCTGCACTTAGTACTACACACGTGACCTAACTATCTGATACACG
1 TAGTAGCCTGCACTTAGTACTACACACGTGACC-AACTATCCGATACACG
* * * ** * * *
54496495 TAGTAGCTTGCACTTAGTACTACACACGTGATCGAAGTTATTGGGTACGCA
1 TAGTAGCCTGCACTTAGTACTACACACGTGA-CCAA-CTATCCGATACACG
*
54496546 TAGTAGCCTGTACTTAGTACTACACA
1 TAGTAGCCTGCACTTAGTACTACACA
54496572 TGCGACCTAG
Statistics
Matches: 109, Mismatches: 15, Indels: 4
0.85 0.12 0.03
Matches are distributed among these distances:
49 31 0.28
50 45 0.41
51 33 0.30
ACGTcount: A:0.29, C:0.25, G:0.19, T:0.27
Consensus pattern (49 bp):
TAGTAGCCTGCACTTAGTACTACACACGTGACCAACTATCCGATACACG
Found at i:54496567 original size:101 final size:99
Alignment explanation
Indices: 54496396--54496580 Score: 253
Period size: 101 Copynumber: 1.8 Consensus size: 99
54496386 TTGGTACGTA
* *
54496396 TAGTAGCCTGCACTTAGTACTACACATGCGACCAATTATCCGGTACACGTAGTAGCCTGCACTTA
1 TAGTAGCCTGCACTTAGTACTACACACGCGACCAATTATCCGGTACACATAGTAGCCTGCACTTA
*
54496461 GTACTACACACGTGACCTAACTATCTGATACACG
66 GTACTACACACGCGACCTAACTATCTGATACACG
* * * ** * *
54496495 TAGTAGCTTGCACTTAGTACTACACACGTGATCGAAGTTATTGGGTACGCATAGTAGCCTGTACT
1 TAGTAGCCTGCACTTAGTACTACACACGCGA-CCAA-TTATCCGGTACACATAGTAGCCTGCACT
*
54496560 TAGTACTACACATGCGACCTA
64 TAGTACTACACACGCGACCTA
54496581 GCTACATATA
Statistics
Matches: 73, Mismatches: 11, Indels: 2
0.85 0.13 0.02
Matches are distributed among these distances:
99 28 0.38
100 3 0.04
101 42 0.58
ACGTcount: A:0.29, C:0.25, G:0.19, T:0.27
Consensus pattern (99 bp):
TAGTAGCCTGCACTTAGTACTACACACGCGACCAATTATCCGGTACACATAGTAGCCTGCACTTA
GTACTACACACGCGACCTAACTATCTGATACACG
Found at i:54500514 original size:40 final size:39
Alignment explanation
Indices: 54500459--54500715 Score: 295
Period size: 40 Copynumber: 6.5 Consensus size: 39
54500449 CGGATGATAA
* * *
54500459 CCGGGCTAAGTCCCGAAGGCATTTGCGCTAGTGACTAGTT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTA-TT
* *
54500499 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTATTACAT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTA-TT
* *
54500539 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTATTACAT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTA-TT
* *
54500579 CCGGGATAAGTCCCGAAGGCATTTGTGCGAGCTACTATAT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAT-T
* *
54500619 CCGGGCTAAGTCCCGAAGGCAATGGTGCGAGTTACTATAT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAT-T
* *
54500659 CCGGGCTATGTCCCGAAGGCA-TTGAGCGAG-TAGCTATAT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTA-CTAT-T
* *
54500698 CC-GGTTAAATCCCGAAGG
1 CCGGGCTAAGTCCCGAAGG
54500716 TACTTGGCTT
Statistics
Matches: 195, Mismatches: 20, Indels: 6
0.88 0.09 0.03
Matches are distributed among these distances:
38 15 0.08
39 15 0.08
40 165 0.85
ACGTcount: A:0.23, C:0.23, G:0.29, T:0.25
Consensus pattern (39 bp):
CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATT
Found at i:54500672 original size:120 final size:119
Alignment explanation
Indices: 54500459--54500689 Score: 340
Period size: 120 Copynumber: 1.9 Consensus size: 119
54500449 CGGATGATAA
* * * *
54500459 CCGGGCTAAGTCCCGAAGGCATTTGCGCTAGTGACTAGTTCCGGGCTAAGTCCCGAAGGCATTTG
1 CCGGGATAAGTCCCGAAGGCATTTGCGCGAGTGACTAGTTCCGGGCTAAGTCCCGAAGGCAATGG
* *
54500524 TGCGAGTTATTACATCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTATTACAT
66 TGCGAGTTACTACATCCGGGCTAAGTCCCGAAGGCA-TTGAGCGAGTTATTACAT
*
54500579 CCGGGATAAGTCCCGAAGGCATTTGTGCGAGCT-ACTA-TATCCGGGCTAAGTCCCGAAGGCAAT
1 CCGGGATAAGTCCCGAAGGCATTTGCGCGAG-TGACTAGT-TCCGGGCTAAGTCCCGAAGGCAAT
* *
54500642 GGTGCGAGTTACTATATCCGGGCTATGTCCCGAAGGCATTGAGCGAGT
64 GGTGCGAGTTACTACATCCGGGCTAAGTCCCGAAGGCATTGAGCGAGT
54500690 AGCTATATCC
Statistics
Matches: 100, Mismatches: 9, Indels: 5
0.88 0.08 0.04
Matches are distributed among these distances:
119 10 0.10
120 89 0.89
121 1 0.01
ACGTcount: A:0.23, C:0.23, G:0.29, T:0.25
Consensus pattern (119 bp):
CCGGGATAAGTCCCGAAGGCATTTGCGCGAGTGACTAGTTCCGGGCTAAGTCCCGAAGGCAATGG
TGCGAGTTACTACATCCGGGCTAAGTCCCGAAGGCATTGAGCGAGTTATTACAT
Found at i:54502870 original size:40 final size:37
Alignment explanation
Indices: 54502764--54502870 Score: 117
Period size: 39 Copynumber: 2.7 Consensus size: 37
54502754 ATCACGATTT
*
54502764 GCACAAATGCCTTCGGGTCTTAGCCCGGATAGAATGCTC
1 GCAC-AATGCCTTCGGGTCTTAGCCCGGATAGAA-GCTA
*
54502803 GCACGAATGCCTTCGGGTCTTAGCCCGGAT-GTAGCCACTA
1 GCAC-AATGCCTTCGGGTCTTAGCCCGGATAGAAG---CTA
*
54502843 GCACAATTGCCTTCGGGTCTTAACCCGG
1 GCACAA-TGCCTTCGGGTCTTAGCCCGG
54502871 TTATAATTTC
Statistics
Matches: 60, Mismatches: 4, Indels: 7
0.85 0.06 0.10
Matches are distributed among these distances:
37 1 0.02
38 2 0.03
39 31 0.52
40 26 0.43
ACGTcount: A:0.21, C:0.30, G:0.26, T:0.23
Consensus pattern (37 bp):
GCACAATGCCTTCGGGTCTTAGCCCGGATAGAAGCTA
Found at i:54513535 original size:27 final size:28
Alignment explanation
Indices: 54513505--54513574 Score: 106
Period size: 27 Copynumber: 2.5 Consensus size: 28
54513495 ATAATAAGTC
*
54513505 CGCACACTTAGTGCTATATAATC-AGCT
1 CGCACACTTAGTGCTATATAATCAAACT
* *
54513532 CGCACACATAGTGCTATATAATCAAATT
1 CGCACACTTAGTGCTATATAATCAAACT
54513560 CGCACACTTAGTGCT
1 CGCACACTTAGTGCT
54513575 GTACAAATTT
Statistics
Matches: 38, Mismatches: 4, Indels: 1
0.88 0.09 0.02
Matches are distributed among these distances:
27 22 0.58
28 16 0.42
ACGTcount: A:0.31, C:0.26, G:0.14, T:0.29
Consensus pattern (28 bp):
CGCACACTTAGTGCTATATAATCAAACT
Found at i:54524278 original size:6 final size:6
Alignment explanation
Indices: 54524267--54524320 Score: 54
Period size: 6 Copynumber: 8.5 Consensus size: 6
54524257 CTTGTTAAAA
** *
54524267 TTCTTT TTCTTT TTCAAT TTCATTT TTCTTT TTCATATT CTCTTT TTCTTT
1 TTCTTT TTCTTT TTCTTT TTC-TTT TTCTTT TTC-T-TT TTCTTT TTCTTT
54524318 TTC
1 TTC
54524321 ACAGACTTTC
Statistics
Matches: 39, Mismatches: 6, Indels: 6
0.76 0.12 0.12
Matches are distributed among these distances:
6 29 0.74
7 6 0.15
8 4 0.10
ACGTcount: A:0.09, C:0.19, G:0.00, T:0.72
Consensus pattern (6 bp):
TTCTTT
Found at i:54524294 original size:19 final size:18
Alignment explanation
Indices: 54524241--54524321 Score: 92
Period size: 18 Copynumber: 4.3 Consensus size: 18
54524231 CTCACTCTCA
54524241 TTTTCAATTT-TCTTTTCT
1 TTTTCAATTTCT-TTTTCT
* * *
54524259 TGTTAAAATTCTTTTTCT
1 TTTTCAATTTCTTTTTCT
54524277 TTTTCAATTTCATTTTTCT
1 TTTTCAATTTC-TTTTTCT
54524296 TTTTCATATTCTCTTTTTCT
1 TTTTCA-ATT-TCTTTTTCT
54524316 TTTTCA
1 TTTTCA
54524322 CAGACTTTCT
Statistics
Matches: 53, Mismatches: 6, Indels: 6
0.82 0.09 0.09
Matches are distributed among these distances:
18 21 0.40
19 14 0.26
20 16 0.30
21 2 0.04
ACGTcount: A:0.15, C:0.16, G:0.01, T:0.68
Consensus pattern (18 bp):
TTTTCAATTTCTTTTTCT
Found at i:54524299 original size:20 final size:20
Alignment explanation
Indices: 54524268--54524321 Score: 85
Period size: 20 Copynumber: 2.8 Consensus size: 20
54524258 TTGTTAAAAT
54524268 TCTTTTTCTTTTTCA-ATT-
1 TCTTTTTCTTTTTCATATTC
54524286 TCATTTTTCTTTTTCATATTC
1 TC-TTTTTCTTTTTCATATTC
54524307 TCTTTTTCTTTTTCA
1 TCTTTTTCTTTTTCA
54524322 CAGACTTTCT
Statistics
Matches: 33, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
18 2 0.06
19 13 0.39
20 16 0.48
21 2 0.06
ACGTcount: A:0.11, C:0.19, G:0.00, T:0.70
Consensus pattern (20 bp):
TCTTTTTCTTTTTCATATTC
Found at i:54524353 original size:17 final size:17
Alignment explanation
Indices: 54524327--54524359 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
54524317 TTTCACAGAC
54524327 TTTCTCTTTTTCTTTCT
1 TTTCTCTTTTTCTTTCT
*
54524344 TTTCTTTTTTTCTTTC
1 TTTCTCTTTTTCTTTC
54524360 ACACTCTTTT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.00, C:0.21, G:0.00, T:0.79
Consensus pattern (17 bp):
TTTCTCTTTTTCTTTCT
Found at i:54526140 original size:20 final size:23
Alignment explanation
Indices: 54526115--54526164 Score: 61
Period size: 20 Copynumber: 2.3 Consensus size: 23
54526105 AGCATCTATG
54526115 TGTTCACAC-AATA-A-TAAAAA
1 TGTTCACACTAATATATTAAAAA
*
54526135 TGTTCACTCTAATATATTAAAAA
1 TGTTCACACTAATATATTAAAAA
54526158 TGGTTCA
1 T-GTTCA
54526165 TGAATTCAGT
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
20 8 0.32
21 4 0.16
22 1 0.04
23 7 0.28
24 5 0.20
ACGTcount: A:0.44, C:0.14, G:0.08, T:0.34
Consensus pattern (23 bp):
TGTTCACACTAATATATTAAAAA
Found at i:54528976 original size:37 final size:37
Alignment explanation
Indices: 54528926--54529001 Score: 125
Period size: 37 Copynumber: 2.1 Consensus size: 37
54528916 GATTTTTCCA
**
54528926 TTTTTATTTAGTTTATTACCAAATGGCCAAAATGCCC
1 TTTTTATTTAGTTTATTACCAAATAACCAAAATGCCC
*
54528963 TTTTTATTTAGTTTATTACCATATAACCAAAATGCCC
1 TTTTTATTTAGTTTATTACCAAATAACCAAAATGCCC
54529000 TT
1 TT
54529002 CCTTACTAAA
Statistics
Matches: 36, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
37 36 1.00
ACGTcount: A:0.30, C:0.18, G:0.08, T:0.43
Consensus pattern (37 bp):
TTTTTATTTAGTTTATTACCAAATAACCAAAATGCCC
Found at i:54536786 original size:19 final size:19
Alignment explanation
Indices: 54536749--54536786 Score: 51
Period size: 19 Copynumber: 2.0 Consensus size: 19
54536739 ACCTGTCAGA
*
54536749 AGAAAATAAATGAAGAATT
1 AGAAAATAAATGAAAAATT
54536768 AGAAAATAAAAT-AAAAATT
1 AGAAAAT-AAATGAAAAATT
54536787 TAAATTGCAA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 13 0.76
20 4 0.24
ACGTcount: A:0.68, C:0.00, G:0.11, T:0.21
Consensus pattern (19 bp):
AGAAAATAAATGAAAAATT
Found at i:54547346 original size:25 final size:25
Alignment explanation
Indices: 54547318--54547397 Score: 60
Period size: 25 Copynumber: 3.2 Consensus size: 25
54547308 TACTACAGTA
54547318 TCAGTATATACTATCTTGAGTGTTT
1 TCAGTATATACTATCTTGAGTGTTT
*
54547343 TCAGTGTA-ATCTATC-TGTAGTAGTTT
1 TCAGTATATA-CTATCTTG-AGT-GTTT
* * *
54547369 T-GGTACATACTATCTAT-AGTATTT
1 TCAGTATATACTATCT-TGAGTGTTT
54547393 TCAGT
1 TCAGT
54547398 TTTTAAACAG
Statistics
Matches: 42, Mismatches: 6, Indels: 14
0.68 0.10 0.23
Matches are distributed among these distances:
24 7 0.17
25 28 0.67
26 6 0.14
27 1 0.02
ACGTcount: A:0.25, C:0.12, G:0.16, T:0.46
Consensus pattern (25 bp):
TCAGTATATACTATCTTGAGTGTTT
Found at i:54551437 original size:23 final size:23
Alignment explanation
Indices: 54551394--54551438 Score: 56
Period size: 23 Copynumber: 2.0 Consensus size: 23
54551384 TAAACCCCTA
*
54551394 AAATGCATAATTTTATGATTTAT
1 AAATGCATAATATTATGATTTAT
*
54551417 AAATGCATGATATT-TGCATTTA
1 AAATGCATAATATTATG-ATTTA
54551439 CTGATGGTAT
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
22 2 0.11
23 17 0.89
ACGTcount: A:0.38, C:0.07, G:0.11, T:0.44
Consensus pattern (23 bp):
AAATGCATAATATTATGATTTAT
Found at i:54561197 original size:20 final size:22
Alignment explanation
Indices: 54561172--54561222 Score: 70
Period size: 20 Copynumber: 2.4 Consensus size: 22
54561162 ATTAAAATAG
54561172 ATAAATTAATTTTTAAT-TA-A
1 ATAAATTAATTTTTAATATACA
*
54561192 ATAAATTATTTTTTAATATACA
1 ATAAATTAATTTTTAATATACA
*
54561214 TTAAATTAA
1 ATAAATTAA
54561223 AAAATAAATT
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
20 16 0.62
21 2 0.08
22 8 0.31
ACGTcount: A:0.49, C:0.02, G:0.00, T:0.49
Consensus pattern (22 bp):
ATAAATTAATTTTTAATATACA
Found at i:54565514 original size:22 final size:22
Alignment explanation
Indices: 54565463--54565516 Score: 63
Period size: 22 Copynumber: 2.5 Consensus size: 22
54565453 TTCAAATAAT
* * * *
54565463 AATAACAAAATAGTAGTAATAT
1 AATAACGAAATAGTAGCAAAAC
*
54565485 AATGACGAAATAGTAGCAAAAC
1 AATAACGAAATAGTAGCAAAAC
54565507 AATAACGAAA
1 AATAACGAAA
54565517 CAACAACAAA
Statistics
Matches: 26, Mismatches: 6, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
22 26 1.00
ACGTcount: A:0.59, C:0.09, G:0.13, T:0.19
Consensus pattern (22 bp):
AATAACGAAATAGTAGCAAAAC
Found at i:54566015 original size:8 final size:8
Alignment explanation
Indices: 54565998--54566031 Score: 50
Period size: 8 Copynumber: 4.2 Consensus size: 8
54565988 AATTTTATGT
*
54565998 TTAATGTA
1 TTAATATA
54566006 TTAATATA
1 TTAATATA
54566014 TTAATATA
1 TTAATATA
*
54566022 TTAATTTA
1 TTAATATA
54566030 TT
1 TT
54566032 TTAATTTTAT
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
8 24 1.00
ACGTcount: A:0.41, C:0.00, G:0.03, T:0.56
Consensus pattern (8 bp):
TTAATATA
Found at i:54568371 original size:24 final size:24
Alignment explanation
Indices: 54568339--54568414 Score: 134
Period size: 24 Copynumber: 3.2 Consensus size: 24
54568329 AGGCTATCAA
*
54568339 GAGAAGATTTAGGAGCTGATAAGG
1 GAGAGGATTTAGGAGCTGATAAGG
54568363 GAGAGGATTTAGGAGCTGATAAGG
1 GAGAGGATTTAGGAGCTGATAAGG
*
54568387 GAGAGGATTTAGGAGCTGATTAGG
1 GAGAGGATTTAGGAGCTGATAAGG
54568411 GAGA
1 GAGA
54568415 ATGGTGTTGG
Statistics
Matches: 50, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 50 1.00
ACGTcount: A:0.34, C:0.04, G:0.41, T:0.21
Consensus pattern (24 bp):
GAGAGGATTTAGGAGCTGATAAGG
Found at i:54569882 original size:27 final size:27
Alignment explanation
Indices: 54569842--54569952 Score: 145
Period size: 27 Copynumber: 4.1 Consensus size: 27
54569832 AGGAAGCGTC
* *
54569842 CTGGTGGCTATGCCACATTTATCTAATT
1 CTGGTGGCTCTGCCACATTTATCT-GTT
*
54569870 -TGGTGGCTCTGCCACATATATCTGTT
1 CTGGTGGCTCTGCCACATTTATCTGTT
*
54569896 CTGGTGGCTCTGCCACAATTATCTGTT
1 CTGGTGGCTCTGCCACATTTATCTGTT
* *
54569923 CTGGTGACTCTGTCACA-TTATCTGTT
1 CTGGTGGCTCTGCCACATTTATCTGTT
54569949 CTGG
1 CTGG
54569953 CAGCCATGCT
Statistics
Matches: 75, Mismatches: 7, Indels: 4
0.87 0.08 0.05
Matches are distributed among these distances:
26 15 0.20
27 60 0.80
ACGTcount: A:0.16, C:0.23, G:0.22, T:0.39
Consensus pattern (27 bp):
CTGGTGGCTCTGCCACATTTATCTGTT
Found at i:54582026 original size:30 final size:30
Alignment explanation
Indices: 54581967--54582065 Score: 126
Period size: 30 Copynumber: 3.3 Consensus size: 30
54581957 TATGGGGCAC
*
54581967 GCCCGTGTGGCAGACCGTGTGTGTCACACAT
1 GCCCGTGTGGCAGGCCGTGTGT-TCACACAT
* *
54581998 GCCCGTGTGGTAGGCTGTGTGTTCACACAT
1 GCCCGTGTGGCAGGCCGTGTGTTCACACAT
* * *
54582028 GCCCATGTGGCAGGCCGTGTGGTCACACAC
1 GCCCGTGTGGCAGGCCGTGTGTTCACACAT
*
54582058 GTCCGTGT
1 GCCCGTGT
54582066 CCCGAACCCA
Statistics
Matches: 58, Mismatches: 10, Indels: 1
0.84 0.14 0.01
Matches are distributed among these distances:
30 39 0.67
31 19 0.33
ACGTcount: A:0.14, C:0.28, G:0.33, T:0.24
Consensus pattern (30 bp):
GCCCGTGTGGCAGGCCGTGTGTTCACACAT
Found at i:54587450 original size:39 final size:40
Alignment explanation
Indices: 54587351--54587541 Score: 129
Period size: 40 Copynumber: 4.8 Consensus size: 40
54587341 TGAATGATGT
* * * * * *
54587351 CCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGACTATAT
1 CCGGGCTAAGTCCCGAAGGCATTCGTGC-GAGTTAATAAAC
* * *
54587391 CCGGACTAGGAT-CCGAAGGCATTCGTGCGAGTTAATAAAT
1 CCGGGCTAAG-TCCCGAAGGCATTCGTGCGAGTTAATAAAC
* * * *
54587431 CCGGGCTAAG-CTCGAAGGCATTTGTGCAAGTTACTAAAC
1 CCGGGCTAAGTCCCGAAGGCATTCGTGCGAGTTAATAAAC
* * * *
54587470 CCGGGTTAAGTCCCGAAGGCATTCGGGCGAGTCACTATAA-
1 CCGGGCTAAGTCCCGAAGGCATTCGTGCGAGTTAATA-AAC
* ** * *
54587510 CTGGGCTTCGTCCCGAAGGCATTTGAGCGAGT
1 CCGGGCTAAGTCCCGAAGGCATTCGTGCGAGT
54587542 CGTTATATCC
Statistics
Matches: 120, Mismatches: 26, Indels: 10
0.77 0.17 0.06
Matches are distributed among these distances:
39 32 0.27
40 79 0.66
41 9 0.08
ACGTcount: A:0.25, C:0.23, G:0.29, T:0.24
Consensus pattern (40 bp):
CCGGGCTAAGTCCCGAAGGCATTCGTGCGAGTTAATAAAC
Found at i:54587492 original size:79 final size:80
Alignment explanation
Indices: 54587350--54587501 Score: 193
Period size: 79 Copynumber: 1.9 Consensus size: 80
54587340 TTGAATGATG
* * *
54587350 TCCGGGCTAAGTCCCGAAGGCTTTGTGCTAAGTGACTATATCCGGACTAGGATCCGAAGGCATTC
1 TCCGGGCTAAGTCCCGAAGGCTTTGTGCTAAGTGACTAAACCCGGACTAAGATCCGAAGGCATTC
*
54587415 GTGCGAGTTAATAAA
66 GGGCGAGTTAATAAA
* * **
54587430 TCCGGGCTAAG-CTCGAAGGCATTTGTGC-AAGTTACTAAACCCGGGTTAAG-TCCCGAAGGCAT
1 TCCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGACTAAACCCGGACTAAGAT-CCGAAGGCAT
54587492 TCGGGCGAGT
64 TCGGGCGAGT
54587502 CACTATAACT
Statistics
Matches: 62, Mismatches: 8, Indels: 5
0.83 0.11 0.07
Matches are distributed among these distances:
78 1 0.02
79 43 0.69
80 18 0.29
ACGTcount: A:0.25, C:0.22, G:0.29, T:0.24
Consensus pattern (80 bp):
TCCGGGCTAAGTCCCGAAGGCTTTGTGCTAAGTGACTAAACCCGGACTAAGATCCGAAGGCATTC
GGGCGAGTTAATAAA
Found at i:54590382 original size:17 final size:17
Alignment explanation
Indices: 54590342--54590383 Score: 75
Period size: 17 Copynumber: 2.5 Consensus size: 17
54590332 CAAAATAGTT
*
54590342 TGTAAGAACAACTTATA
1 TGTAAGGACAACTTATA
54590359 TGTAAGGACAACTTATA
1 TGTAAGGACAACTTATA
54590376 TGTAAGGA
1 TGTAAGGA
54590384 GGTAGGACGA
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
17 24 1.00
ACGTcount: A:0.43, C:0.10, G:0.19, T:0.29
Consensus pattern (17 bp):
TGTAAGGACAACTTATA
Found at i:54594762 original size:30 final size:30
Alignment explanation
Indices: 54594719--54594787 Score: 79
Period size: 30 Copynumber: 2.3 Consensus size: 30
54594709 TAAAGATAAC
* *
54594719 AAGAAAACC-GAATAAAGGAATCTAAG-ATA
1 AAGAAACCCAGAATAAAGAAATC-AAGAATA
* *
54594748 GAGAAACCCAGAATAAAGAAATCCAGAATA
1 AAGAAACCCAGAATAAAGAAATCAAGAATA
54594778 AAGAAACCCA
1 AAGAAACCCA
54594788 AGATACAATA
Statistics
Matches: 33, Mismatches: 5, Indels: 3
0.80 0.12 0.07
Matches are distributed among these distances:
29 9 0.27
30 24 0.73
ACGTcount: A:0.58, C:0.16, G:0.16, T:0.10
Consensus pattern (30 bp):
AAGAAACCCAGAATAAAGAAATCAAGAATA
Found at i:54594773 original size:15 final size:15
Alignment explanation
Indices: 54594719--54594783 Score: 62
Period size: 15 Copynumber: 4.4 Consensus size: 15
54594709 TAAAGATAAC
*
54594719 AAGAAAACC-GAATA
1 AAGAAATCCAGAATA
* *
54594733 AAGGAATCTA-AGATA
1 AAGAAATCCAGA-ATA
* *
54594748 GAGAAACCCAGAATA
1 AAGAAATCCAGAATA
54594763 AAGAAATCCAGAATA
1 AAGAAATCCAGAATA
54594778 AAGAAA
1 AAGAAA
54594784 CCCAAGATAC
Statistics
Matches: 39, Mismatches: 9, Indels: 5
0.74 0.17 0.09
Matches are distributed among these distances:
14 7 0.18
15 31 0.79
16 1 0.03
ACGTcount: A:0.60, C:0.12, G:0.17, T:0.11
Consensus pattern (15 bp):
AAGAAATCCAGAATA
Found at i:54599410 original size:27 final size:27
Alignment explanation
Indices: 54599356--54599466 Score: 154
Period size: 27 Copynumber: 4.1 Consensus size: 27
54599346 AGCATGGCTG
** *
54599356 CCAGAACAGATAA-TGTGATAGAGTCA
1 CCAGAACAGATAATTGTGGCAGAGCCA
54599382 CCAGAACAGATAATTGTGGCAGAGCCA
1 CCAGAACAGATAATTGTGGCAGAGCCA
54599409 CCAGAACAGAT-ATATGTGGCAGAGCCA
1 CCAGAACAGATAAT-TGTGGCAGAGCCA
* *
54599436 CCAGATCAGATAATTGTGGCATAGCCA
1 CCAGAACAGATAATTGTGGCAGAGCCA
54599463 CCAG
1 CCAG
54599467 GACGCTTCCT
Statistics
Matches: 77, Mismatches: 5, Indels: 5
0.89 0.06 0.06
Matches are distributed among these distances:
26 15 0.19
27 60 0.78
28 2 0.03
ACGTcount: A:0.37, C:0.22, G:0.24, T:0.17
Consensus pattern (27 bp):
CCAGAACAGATAATTGTGGCAGAGCCA
Found at i:54599614 original size:26 final size:28
Alignment explanation
Indices: 54599570--54599644 Score: 79
Period size: 26 Copynumber: 2.8 Consensus size: 28
54599560 CAAAAGTAAC
*
54599570 CCTAGGGGTATAAT-GGTAATTTTCT-T-
1 CCTAGGGGTAT-ATCAGTAATTTTCTATA
54599596 CCTAGGGGTATATCAGTAA-TTTCTATA
1 CCTAGGGGTATATCAGTAATTTTCTATA
*
54599623 CATAGGGGTAT-TCAAGTAATTT
1 CCTAGGGGTATATC-AGTAATTT
54599645 CACTATTCCT
Statistics
Matches: 42, Mismatches: 2, Indels: 8
0.81 0.04 0.15
Matches are distributed among these distances:
25 7 0.17
26 18 0.43
27 15 0.36
28 2 0.05
ACGTcount: A:0.28, C:0.12, G:0.21, T:0.39
Consensus pattern (28 bp):
CCTAGGGGTATATCAGTAATTTTCTATA
Found at i:54607320 original size:27 final size:27
Alignment explanation
Indices: 54607266--54607376 Score: 154
Period size: 27 Copynumber: 4.1 Consensus size: 27
54607256 AGCATGGCTG
* *
54607266 CCAGAACAGATAA-TGTGACAGAGTCA
1 CCAGAACAGATAATTGTGGCAGAGCCA
54607292 CCAGAACAGATAATTGTGGCAGAGCCA
1 CCAGAACAGATAATTGTGGCAGAGCCA
*
54607319 CCAGAACAGAT-ATATGTGGCAGAACCA
1 CCAGAACAGATAAT-TGTGGCAGAGCCA
* *
54607346 CCAGATCAGATAATTGTGGCATAGCCA
1 CCAGAACAGATAATTGTGGCAGAGCCA
54607373 CCAG
1 CCAG
54607377 GACGCTTCCT
Statistics
Matches: 76, Mismatches: 6, Indels: 5
0.87 0.07 0.06
Matches are distributed among these distances:
26 15 0.20
27 59 0.78
28 2 0.03
ACGTcount: A:0.38, C:0.23, G:0.23, T:0.16
Consensus pattern (27 bp):
CCAGAACAGATAATTGTGGCAGAGCCA
Found at i:54607524 original size:26 final size:26
Alignment explanation
Indices: 54607476--54607554 Score: 74
Period size: 26 Copynumber: 3.0 Consensus size: 26
54607466 CAGTCAAAAG
*
54607476 TTGC-CCTAGGGGTATAAT-GGTAATT
1 TTGCACCTAGGGGTAT-ATCAGTAATT
54607501 TTGCACCTAGGGGTATATCAGTAATT
1 TTGCACCTAGGGGTATATCAGTAATT
** *
54607527 TCTATACATAGGGGTAT-TCAAGTAATT
1 T-TGCACCTAGGGGTATATC-AGTAATT
54607554 T
1 T
54607555 CACTATTCTT
Statistics
Matches: 46, Mismatches: 4, Indels: 6
0.82 0.07 0.11
Matches are distributed among these distances:
25 6 0.13
26 20 0.43
27 20 0.43
ACGTcount: A:0.28, C:0.13, G:0.23, T:0.37
Consensus pattern (26 bp):
TTGCACCTAGGGGTATATCAGTAATT
Found at i:54608586 original size:12 final size:12
Alignment explanation
Indices: 54608569--54608594 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
54608559 TCTTCGGCAG
54608569 AACAAACTAATT
1 AACAAACTAATT
54608581 AACAAACTAATT
1 AACAAACTAATT
54608593 AA
1 AA
54608595 AAGGGGAGAG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.62, C:0.15, G:0.00, T:0.23
Consensus pattern (12 bp):
AACAAACTAATT
Found at i:54620033 original size:39 final size:39
Alignment explanation
Indices: 54619989--54620239 Score: 405
Period size: 39 Copynumber: 6.5 Consensus size: 39
54619979 CGGGACTTTA
* * *
54619989 AGCCCGAATATAATACCAGCACAAATGCCTTCGGGGCTT
1 AGCCCGGATATAACACCAGCACGAATGCCTTCGGGGCTT
54620028 AGCCCGGATATAACACCAGCACGAATGCCTTCGGGGCTT
1 AGCCCGGATATAACACCAGCACGAATGCCTTCGGGGCTT
* *
54620067 AGCTCGGATATAACACCAGCATGAATGCCTTCGGGGCTT
1 AGCCCGGATATAACACCAGCACGAATGCCTTCGGGGCTT
*
54620106 AGCCCAGATATAACACCAGCACGAATGCCTT-GGGGCTT
1 AGCCCGGATATAACACCAGCACGAATGCCTTCGGGGCTT
* *
54620144 AGCCCGGATATAAAACTAGCACGAATGCCTTCGGGGCTT
1 AGCCCGGATATAACACCAGCACGAATGCCTTCGGGGCTT
*
54620183 AGCCCGGATATAACACCAGCACGAATGCCTTCGAGGCTT
1 AGCCCGGATATAACACCAGCACGAATGCCTTCGGGGCTT
*
54620222 AGCCCGAATATAACACCA
1 AGCCCGGATATAACACCA
54620240 AATCATATAA
Statistics
Matches: 196, Mismatches: 15, Indels: 2
0.92 0.07 0.01
Matches are distributed among these distances:
38 35 0.18
39 161 0.82
ACGTcount: A:0.29, C:0.29, G:0.23, T:0.19
Consensus pattern (39 bp):
AGCCCGGATATAACACCAGCACGAATGCCTTCGGGGCTT
Found at i:54620194 original size:116 final size:117
Alignment explanation
Indices: 54619989--54620239 Score: 416
Period size: 116 Copynumber: 2.2 Consensus size: 117
54619979 CGGGACTTTA
* *
54619989 AGCCCGAATATAATACCAGCACAAATGCCTTCGGGGCTTAGCCCGGATATAACACCAGCACGAAT
1 AGCCCGAATATAACACCAGCACAAATGCCTTCGGGGCTTAGCCCGGATATAAAACCAGCACGAAT
* * *
54620054 GCCTTCGGGGCTTAGCTCGGATATAACACCAGCATGAATGCCTTCGGGGCTT
66 GCCTTCGGGGCTTAGCCCGGATATAACACCAGCACGAATGCCTTCGAGGCTT
* *
54620106 AGCCC-AGATATAACACCAGCACGAATGCCTT-GGGGCTTAGCCCGGATATAAAACTAGCACGAA
1 AGCCCGA-ATATAACACCAGCACAAATGCCTTCGGGGCTTAGCCCGGATATAAAACCAGCACGAA
54620169 TGCCTTCGGGGCTTAGCCCGGATATAACACCAGCACGAATGCCTTCGAGGCTT
65 TGCCTTCGGGGCTTAGCCCGGATATAACACCAGCACGAATGCCTTCGAGGCTT
54620222 AGCCCGAATATAACACCA
1 AGCCCGAATATAACACCA
54620240 AATCATATAA
Statistics
Matches: 125, Mismatches: 7, Indels: 5
0.91 0.05 0.04
Matches are distributed among these distances:
116 97 0.78
117 28 0.22
ACGTcount: A:0.29, C:0.29, G:0.23, T:0.19
Consensus pattern (117 bp):
AGCCCGAATATAACACCAGCACAAATGCCTTCGGGGCTTAGCCCGGATATAAAACCAGCACGAAT
GCCTTCGGGGCTTAGCCCGGATATAACACCAGCACGAATGCCTTCGAGGCTT
Found at i:54622245 original size:18 final size:19
Alignment explanation
Indices: 54622222--54622261 Score: 55
Period size: 18 Copynumber: 2.2 Consensus size: 19
54622212 GTTATAATAT
*
54622222 TAATATTCCTTTAAT-TTA
1 TAATATTCATTTAATATTA
*
54622240 TAATATTCATTTCATATTA
1 TAATATTCATTTAATATTA
54622259 TAA
1 TAA
54622262 AACAATTTAA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
18 13 0.68
19 6 0.32
ACGTcount: A:0.38, C:0.10, G:0.00, T:0.53
Consensus pattern (19 bp):
TAATATTCATTTAATATTA
Found at i:54625526 original size:28 final size:28
Alignment explanation
Indices: 54625493--54625560 Score: 91
Period size: 28 Copynumber: 2.4 Consensus size: 28
54625483 AACTATGAGT
54625493 GTGATTGGGCCTGACGGGCCATATGAAA
1 GTGATTGGGCCTGACGGGCCATATGAAA
* * * *
54625521 GTGATTAGGCTTGATGGGCCATATGAAT
1 GTGATTGGGCCTGACGGGCCATATGAAA
*
54625549 GAGATTGGGCCT
1 GTGATTGGGCCT
54625561 AAAGGGGCCA
Statistics
Matches: 33, Mismatches: 7, Indels: 0
0.82 0.17 0.00
Matches are distributed among these distances:
28 33 1.00
ACGTcount: A:0.24, C:0.15, G:0.35, T:0.26
Consensus pattern (28 bp):
GTGATTGGGCCTGACGGGCCATATGAAA
Found at i:54626849 original size:17 final size:18
Alignment explanation
Indices: 54626818--54626851 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
54626808 TTCAAAAAAG
54626818 GGTTTTCAATGAAAACAA
1 GGTTTTCAATGAAAACAA
*
54626836 GGTTTTCGAT-AAAACA
1 GGTTTTCAATGAAAACA
54626852 CTTCAATGTG
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 6 0.40
18 9 0.60
ACGTcount: A:0.41, C:0.12, G:0.18, T:0.29
Consensus pattern (18 bp):
GGTTTTCAATGAAAACAA
Found at i:54643825 original size:40 final size:40
Alignment explanation
Indices: 54643770--54643994 Score: 274
Period size: 40 Copynumber: 5.6 Consensus size: 40
54643760 TATTCGGATG
54643770 ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCAAGTTACT
1 ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCAAGTTACT
*
54643810 ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTAGTTGCT
1 ATATCCGGGCTAAGTCCCGAAGGCATTTGTGC-A--AGTTACT
* *
54643853 ATA-CTCGGGCTAAGTCCCGAAGGCATTTGTGCTAGTGACT
1 ATATC-CGGGCTAAGTCCCGAAGGCATTTGTGCAAGTTACT
* * * * *
54643893 ATTTTCGGGCTAAGACCCGAAGGCATGTGTGCGAGTTACT
1 ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCAAGTTACT
* * * * *
54643933 ATATCCGGGTTAAGTCCCGAAGGCATTTGCGCGAGTTGCG
1 ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCAAGTTACT
*
54643973 ATATCC-GGCTAAATCCCGAAGG
1 ATATCCGGGCTAAGTCCCGAAGG
54643995 TACTTGGTTT
Statistics
Matches: 160, Mismatches: 20, Indels: 11
0.84 0.10 0.06
Matches are distributed among these distances:
39 14 0.09
40 108 0.68
41 1 0.01
42 1 0.01
43 36 0.22
ACGTcount: A:0.23, C:0.22, G:0.28, T:0.26
Consensus pattern (40 bp):
ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCAAGTTACT
Found at i:54643914 original size:83 final size:80
Alignment explanation
Indices: 54643770--54643994 Score: 269
Period size: 83 Copynumber: 2.8 Consensus size: 80
54643760 TATTCGGATG
* *
54643770 ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCAAGTTACTATATCCGGGCTAAGTCCCGAAGGCA
1 ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCAAGTGACTATATCCGGGCTAAGACCCGAAGGCA
* *
54643835 TTTGTGCGAGTAGTTGCT
66 TGTGTGC--G-AGTTACT
* * *
54643853 ATA-CTCGGGCTAAGTCCCGAAGGCATTTGTGCTAGTGACTATTTTCGGGCTAAGACCCGAAGGC
1 ATATC-CGGGCTAAGTCCCGAAGGCATTTGTGCAAGTGACTATATCCGGGCTAAGACCCGAAGGC
54643917 ATGTGTGCGAGTTACT
65 ATGTGTGCGAGTTACT
* * * *
54643933 ATATCCGGGTTAAGTCCCGAAGGCATTTGCGCGAGTTG-CGATATCC-GGCTAA-ATCCCGAAGG
1 ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCAAG-TGACTATATCCGGGCTAAGA-CCCGAAGG
54643995 TACTTGGTTT
Statistics
Matches: 125, Mismatches: 13, Indels: 12
0.83 0.09 0.08
Matches are distributed among these distances:
78 1 0.01
79 14 0.11
80 41 0.33
81 4 0.03
82 1 0.01
83 64 0.51
ACGTcount: A:0.23, C:0.22, G:0.28, T:0.26
Consensus pattern (80 bp):
ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCAAGTGACTATATCCGGGCTAAGACCCGAAGGCA
TGTGTGCGAGTTACT
Found at i:54648071 original size:2 final size:2
Alignment explanation
Indices: 54648064--54648089 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
54648054 TTAGTCATTA
54648064 AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT
54648090 TGCCGAATGT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:54649752 original size:144 final size:146
Alignment explanation
Indices: 54649484--54650202 Score: 625
Period size: 144 Copynumber: 4.7 Consensus size: 146
54649474 AAGCTATTGC
* *
54649484 TGAAAT-TGATGTATAAGATATGTATATGTGGTAAAGCCGAATGGCTAATGTGAAATATGTATGA
1 TGAAATAT-ATGTATGAGATATGTATATGTGGTAAAGCCGAATGACTAATGTGAAATATGTATGA
54649548 GATATGTATATGTGGTAAAGCCGAATGGCTAATGTGAAATATGTATGAGATATGTATATGTGGTA
65 GATATGTATATGTGGTAAAGCCGAATGGCTAATGTGAAATATGTATGAGATATGTATATGTGGTA
*
54649613 AAGCCGAATGTCTAATG
130 AAGCCGAATGGCTAATG
* *
54649630 TG-AA-ATATGTATGAGATATGTATATGTGGAAAAGCCGAATGTCTAATGTGAAATATGTATGAG
1 TGAAATATATGTATGAGATATGTATATGTGGTAAAGCCGAATGACTAATGTGAAATATGTATGAG
54649693 ATATGTATATGTGGTAAAGCCGAATGGCTAATGTGAAATATGTATGAGATATGTATATGTGGTAA
66 ATATGTATATGTGGTAAAGCCGAATGGCTAATGTGAAATATGTATGAGATATGTATATGTGGTAA
54649758 AGCCGAATGGCTAATG
131 AGCCGAATGGCTAATG
* * *
54649774 TGAAATATATATATGAGATATGTATATGTGGTAAAGCCGAATGACTAATGTGAAATATATAT-AT
1 TGAAATATATGTATGAGATATGTATATGTGGTAAAGCCGAATGACTAATGTGAAATATGTATGAG
* * * * * *
54649838 ATATATATATAT-ATATATATG-AGATAT-G-TATATGTGGTAAAGCCGAATGGCTAATGTGAAA
66 ATATGTATATGTGGTA-A-A-GCCGA-ATGGCTA-ATGT-G-AAA----TAT-G-T-A--TGAGA
* * * ** * * *
54649899 TATATATATGAGATATGTATATGTGGTAAAGCCGAATG
115 TATGTATAT--G-T-GGTA-AAGCCG-AATGGCTAATG
* * ** * * * * * ** * *
54649937 -GTTAATGTGAAATAT-ATATATATGAGATAT-GTATATGTGGTAAAGCCGAATGGTTAATGTGA
1 TG-AAATAT-ATGTATGAGATATGT-ATATGTGGTA-AAGCCG--AA--TG-A---CTAATGTG-
*
54649999 AATATATATATGAGATATGTATATGTGGTAAAGCCGAATGGCTAATGTGAAATATGTATGAGATA
53 AA-ATATGTATGAGATATGTATATGTGGTAAAGCCGAATGGCTAATGTGAAATATGTATGAGATA
*
54650064 TGCATATGTGGTAAAGCCGAATGG-TCAATG
117 TGTATATGTGGTAAAGCCGAATGGCT-AATG
* * * * *
54650094 TGAAATATATATATGAGACATGTATATGTGGTAAAGTCGAATGGCTAGTGTGAAATATGTATGAG
1 TGAAATATATGTATGAGATATGTATATGTGGTAAAGCCGAATGACTAATGTGAAATATGTATGAG
*
54650159 ATATGTATATGTGGTAAAGCCGAATGGCTAGTGTGAAATATGTA
66 ATATGTATATGTGGTAAAGCCGAATGGCTAATGTGAAATATGTA
54650203 GGCGATGTGT
Statistics
Matches: 458, Mismatches: 67, Indels: 96
0.74 0.11 0.15
Matches are distributed among these distances:
144 138 0.30
145 19 0.04
146 115 0.25
147 6 0.01
148 9 0.02
152 3 0.01
153 1 0.00
154 3 0.01
155 1 0.00
156 13 0.03
157 31 0.07
158 4 0.01
159 4 0.01
160 2 0.00
161 4 0.01
162 4 0.01
163 32 0.07
164 12 0.03
165 1 0.00
166 3 0.01
167 1 0.00
168 3 0.01
169 1 0.00
172 10 0.02
173 6 0.01
174 16 0.03
175 14 0.03
176 2 0.00
ACGTcount: A:0.37, C:0.06, G:0.25, T:0.33
Consensus pattern (146 bp):
TGAAATATATGTATGAGATATGTATATGTGGTAAAGCCGAATGACTAATGTGAAATATGTATGAG
ATATGTATATGTGGTAAAGCCGAATGGCTAATGTGAAATATGTATGAGATATGTATATGTGGTAA
AGCCGAATGGCTAATG
Found at i:54649835 original size:2 final size:2
Alignment explanation
Indices: 54649828--54649857 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
54649818 CTAATGTGAA
54649828 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
54649858 GAGATATGTA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:54649837 original size:50 final size:48
Alignment explanation
Indices: 54649492--54649831 Score: 608
Period size: 48 Copynumber: 7.0 Consensus size: 48
54649482 GCTGAAATTG
*
54649492 ATGTATAAGATATGTATATGTGGTAAAGCCGAATGGCTAATGTGAAAT
1 ATGTATGAGATATGTATATGTGGTAAAGCCGAATGGCTAATGTGAAAT
54649540 ATGTATGAGATATGTATATGTGGTAAAGCCGAATGGCTAATGTGAAAT
1 ATGTATGAGATATGTATATGTGGTAAAGCCGAATGGCTAATGTGAAAT
*
54649588 ATGTATGAGATATGTATATGTGGTAAAGCCGAATGTCTAATGTGAAAT
1 ATGTATGAGATATGTATATGTGGTAAAGCCGAATGGCTAATGTGAAAT
* *
54649636 ATGTATGAGATATGTATATGTGGAAAAGCCGAATGTCTAATGTGAAAT
1 ATGTATGAGATATGTATATGTGGTAAAGCCGAATGGCTAATGTGAAAT
54649684 ATGTATGAGATATGTATATGTGGTAAAGCCGAATGGCTAATGTGAAAT
1 ATGTATGAGATATGTATATGTGGTAAAGCCGAATGGCTAATGTGAAAT
54649732 ATGTATGAGATATGTATATGTGGTAAAGCCGAATGGCTAATGTGAAATAT
1 ATGTATGAGATATGTATATGTGGTAAAGCCGAATGGCTAATGTG-AA-AT
* *
54649782 ATATATGAGATATGTATATGTGGTAAAGCCGAATGACTAATGTGAAAT
1 ATGTATGAGATATGTATATGTGGTAAAGCCGAATGGCTAATGTGAAAT
54649830 AT
1 AT
54649832 ATATATATAT
Statistics
Matches: 283, Mismatches: 7, Indels: 4
0.96 0.02 0.01
Matches are distributed among these distances:
48 235 0.83
49 4 0.01
50 44 0.16
ACGTcount: A:0.37, C:0.06, G:0.25, T:0.32
Consensus pattern (48 bp):
ATGTATGAGATATGTATATGTGGTAAAGCCGAATGGCTAATGTGAAAT
Found at i:54649914 original size:120 final size:120
Alignment explanation
Indices: 54649730--54649959 Score: 433
Period size: 120 Copynumber: 1.9 Consensus size: 120
54649720 CTAATGTGAA
*
54649730 ATATGTATGAGATATGTATATGTGGTAAAGCCGAATGGCTAATGTGAAATATATATATGAGATAT
1 ATATATATGAGATATGTATATGTGGTAAAGCCGAATGGCTAATGTGAAATATATATATGAGATAT
54649795 GTATATGTGGTAAAGCCGAATGACTAATGTGAAATATATATATATATATATATAT
66 GTATATGTGGTAAAGCCGAATGACTAATGTGAAATATATATATATATATATATAT
54649850 ATATATATGAGATATGTATATGTGGTAAAGCCGAATGGCTAATGTGAAATATATATATGAGATAT
1 ATATATATGAGATATGTATATGTGGTAAAGCCGAATGGCTAATGTGAAATATATATATGAGATAT
**
54649915 GTATATGTGGTAAAGCCGAATGGTTAATGTGAAATATATATATAT
66 GTATATGTGGTAAAGCCGAATGACTAATGTGAAATATATATATAT
54649960 GAGATATGTA
Statistics
Matches: 107, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
120 107 1.00
ACGTcount: A:0.40, C:0.05, G:0.21, T:0.35
Consensus pattern (120 bp):
ATATATATGAGATATGTATATGTGGTAAAGCCGAATGGCTAATGTGAAATATATATATGAGATAT
GTATATGTGGTAAAGCCGAATGACTAATGTGAAATATATATATATATATATATAT
Found at i:54650019 original size:222 final size:216
Alignment explanation
Indices: 54649634--54650053 Score: 714
Period size: 222 Copynumber: 1.9 Consensus size: 216
54649624 CTAATGTGAA
* * *
54649634 ATATGTATGAGATATGTATATGTGGAAAAGCCGAATGTCTAATGTGAAATATGTATGAGATATGT
1 ATATATATGAGATATGTATATGTGGAAAAGCCGAATGGCTAATGTGAAATATATATGAGATATGT
*
54649699 ATATGTGGTAAAGCCGAATGGCTAATGTGAAATATGTATGAGATATGTATATGTGGTAAAGCCGA
66 ATATGTGGTAAAGCCGAATGGCTAATGTGAAATATATATGAGATATGTATATGTGGTAAAGCCGA
54649764 ATGGCTAATGTGAAATATATATATGAGATATGTATATGTGGTAAAGCCGAATGACTAATGTGAAA
131 ATGGCTAATGTGAAATATATATATGAGATATGTATATGTGGTAAAGCCGAATGACTAATGTGAAA
54649829 TATATATATATATATATATAT
196 TATATATATATATATATATAT
*
54649850 ATATATATGAGATATGTATATGTGGTAAAGCCGAATGGCTAATGTGAAATATATATATGAGATAT
1 ATATATATGAGATATGTATATGTGGAAAAGCCGAATGGCTAATGTG-AA-ATATATATGAGATAT
*
54649915 GTATATGTGGTAAAGCCGAATGGTTAATGTGAAATATATATATATGAGATATGTATATGTGGTAA
64 GTATATGTGGTAAAGCCGAATGGCTAATGTG--A-A-ATATATATGAGATATGTATATGTGGTAA
* *
54649980 AGCCGAATGGTTAATGTGAAATATATATATGAGATATGTATATGTGGTAAAGCCGAATGGCTAAT
125 AGCCGAATGGCTAATGTGAAATATATATATGAGATATGTATATGTGGTAAAGCCGAATGACTAAT
54650045 GTGAAATAT
190 GTGAAATAT
54650054 GTATGAGATA
Statistics
Matches: 190, Mismatches: 8, Indels: 6
0.93 0.04 0.03
Matches are distributed among these distances:
216 43 0.23
217 2 0.01
218 44 0.23
220 1 0.01
221 1 0.01
222 99 0.52
ACGTcount: A:0.38, C:0.05, G:0.23, T:0.33
Consensus pattern (216 bp):
ATATATATGAGATATGTATATGTGGAAAAGCCGAATGGCTAATGTGAAATATATATGAGATATGT
ATATGTGGTAAAGCCGAATGGCTAATGTGAAATATATATGAGATATGTATATGTGGTAAAGCCGA
ATGGCTAATGTGAAATATATATATGAGATATGTATATGTGGTAAAGCCGAATGACTAATGTGAAA
TATATATATATATATATATAT
Found at i:54650202 original size:48 final size:50
Alignment explanation
Indices: 54649848--54650199 Score: 561
Period size: 50 Copynumber: 7.1 Consensus size: 50
54649838 ATATATATAT
54649848 ATATATATATGAGATATGTATATGTGGTAAAGCCGAATGGCTAATGTGAA
1 ATATATATATGAGATATGTATATGTGGTAAAGCCGAATGGCTAATGTGAA
*
54649898 ATATATATATGAGATATGTATATGTGGTAAAGCCGAATGGTTAATGTGAAA
1 ATATATATATGAGATATGTATATGTGGTAAAGCCGAATGGCTAATGTG-AA
*
54649949 TATATATATATGAGATATGTATATGTGGTAAAGCCGAATGGTTAATGTGAA
1 -ATATATATATGAGATATGTATATGTGGTAAAGCCGAATGGCTAATGTGAA
54650000 ATATATATATGAGATATGTATATGTGGTAAAGCCGAATGGCTAATGTG-A
1 ATATATATATGAGATATGTATATGTGGTAAAGCCGAATGGCTAATGTGAA
* *
54650049 A-ATATGTATGAGATATGCATATGTGGTAAAGCCGAATGG-TCAATGTGAA
1 ATATATATATGAGATATGTATATGTGGTAAAGCCGAATGGCT-AATGTGAA
* * *
54650098 ATATATATATGAGACATGTATATGTGGTAAAGTCGAATGGCTAGTGTG-A
1 ATATATATATGAGATATGTATATGTGGTAAAGCCGAATGGCTAATGTGAA
* *
54650147 A-ATATGTATGAGATATGTATATGTGGTAAAGCCGAATGGCTAGTGTGAA
1 ATATATATATGAGATATGTATATGTGGTAAAGCCGAATGGCTAATGTGAA
54650196 ATAT
1 ATAT
54650200 GTAGGCGATG
Statistics
Matches: 282, Mismatches: 12, Indels: 16
0.91 0.04 0.05
Matches are distributed among these distances:
47 1 0.00
48 85 0.30
49 8 0.03
50 135 0.48
51 5 0.02
52 48 0.17
ACGTcount: A:0.37, C:0.06, G:0.25, T:0.32
Consensus pattern (50 bp):
ATATATATATGAGATATGTATATGTGGTAAAGCCGAATGGCTAATGTGAA
Found at i:54650216 original size:98 final size:98
Alignment explanation
Indices: 54649850--54650199 Score: 567
Period size: 98 Copynumber: 3.5 Consensus size: 98
54649840 ATATATATAT
54649850 ATATATATGAGATATGTATATGTGGTAAAGCCGAATGGCTAATGTGAAATATATATATGAGATAT
1 ATATATATGAGATATGTATATGTGGTAAAGCCGAATGGCTAATGTGAAATATATATATGAGATAT
*
54649915 GTATATGTGGTAAAGCCGAATGGTTAATGTGAAATA
66 GTATATGTGGTAAAGCCGAATGGCTAATGTG--A-A
*
54649951 TATATATATGAGATATGTATATGTGGTAAAGCCGAATGGTTAATGTGAAATATATATATGAGATA
1 -ATATATATGAGATATGTATATGTGGTAAAGCCGAATGGCTAATGTGAAATATATATATGAGATA
54650016 TGTATATGTGGTAAAGCCGAATGGCTAATGTGAA
65 TGTATATGTGGTAAAGCCGAATGGCTAATGTGAA
* * *
54650050 ATATGTATGAGATATGCATATGTGGTAAAGCCGAATGG-TCAATGTGAAATATATATATGAGACA
1 ATATATATGAGATATGTATATGTGGTAAAGCCGAATGGCT-AATGTGAAATATATATATGAGATA
* *
54650114 TGTATATGTGGTAAAGTCGAATGGCTAGTGTGAA
65 TGTATATGTGGTAAAGCCGAATGGCTAATGTGAA
* *
54650148 ATATGTATGAGATATGTATATGTGGTAAAGCCGAATGGCTAGTGTGAAATAT
1 ATATATATGAGATATGTATATGTGGTAAAGCCGAATGGCTAATGTGAAATAT
54650200 GTAGGCGATG
Statistics
Matches: 237, Mismatches: 9, Indels: 8
0.93 0.04 0.03
Matches are distributed among these distances:
97 1 0.00
98 139 0.59
99 2 0.01
100 1 0.00
102 94 0.40
ACGTcount: A:0.37, C:0.06, G:0.25, T:0.32
Consensus pattern (98 bp):
ATATATATGAGATATGTATATGTGGTAAAGCCGAATGGCTAATGTGAAATATATATATGAGATAT
GTATATGTGGTAAAGCCGAATGGCTAATGTGAA
Found at i:54650421 original size:37 final size:37
Alignment explanation
Indices: 54650313--54650421 Score: 173
Period size: 37 Copynumber: 2.9 Consensus size: 37
54650303 GGAAATATAT
*
54650313 TCCGGGTAAGACCCGATGACTACGTGTGGAGATTATG
1 TCCGGGTAAGACCCGATGACTACGTGTGGAGATTTTG
54650350 TCCGGGTAAGACCCGATGACTACGTGTGGAGATTTTG
1 TCCGGGTAAGACCCGATGACTACGTGTGGAGATTTTG
* * * *
54650387 TCCGGGTAGGACCCAATAACTTCGTGTGGAGATTT
1 TCCGGGTAAGACCCGATGACTACGTGTGGAGATTT
54650422 CATCTGAGCT
Statistics
Matches: 67, Mismatches: 5, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
37 67 1.00
ACGTcount: A:0.23, C:0.19, G:0.31, T:0.27
Consensus pattern (37 bp):
TCCGGGTAAGACCCGATGACTACGTGTGGAGATTTTG
Found at i:54653054 original size:79 final size:80
Alignment explanation
Indices: 54652953--54653136 Score: 214
Period size: 79 Copynumber: 2.3 Consensus size: 80
54652943 ACGACTCGCT
** * *
54652953 CAAATGCCTTCGGGACGAAGCCCGGTTATAGTGACTCGCACGAATGCCTTCGGGA-CTTAACCCG
1 CAAATGCCTTCGGGACTTAGCCCGGTT-TAGTAACTCGCACGAATGCCTTC-GGATCCTAACCCG
* *
54653017 GGTTTAGTAACTT-GCA
64 GATATAGTAACTTAGCA
* * **
54653033 CAAATGCCTTCGGG-CTTAGCCCAGATTTATTAACTCGCACGAATGCCTTCGGATCCTAGTCCGG
1 CAAATGCCTTCGGGACTTAGCCC-GGTTTAGTAACTCGCACGAATGCCTTCGGATCCTAACCCGG
*
54653097 ATATAGTCACTTAGCA
65 ATATAGTAACTTAGCA
54653113 CAAA-GCCTTCGGGACTTAGCCCGG
1 CAAATGCCTTCGGGACTTAGCCCGG
54653137 ACATCATTCG
Statistics
Matches: 88, Mismatches: 12, Indels: 9
0.81 0.11 0.08
Matches are distributed among these distances:
78 3 0.03
79 53 0.60
80 32 0.36
ACGTcount: A:0.24, C:0.28, G:0.24, T:0.24
Consensus pattern (80 bp):
CAAATGCCTTCGGGACTTAGCCCGGTTTAGTAACTCGCACGAATGCCTTCGGATCCTAACCCGGA
TATAGTAACTTAGCA
Found at i:54653137 original size:40 final size:39
Alignment explanation
Indices: 54652946--54653137 Score: 154
Period size: 40 Copynumber: 4.8 Consensus size: 39
54652936 GGATATAACG
* ** * *
54652946 ACTCGCTCAAATGCCTTCGGGACGAAGCCCGGTTATAGTG
1 ACTCGCACAAA-GCCTTCGGGACTTAGCCCGGATATAGTA
* * * *
54652986 ACTCGCACGAATGCCTTCGGGACTTAACCCGGGTTTAGTA
1 ACTCGCAC-AAAGCCTTCGGGACTTAGCCCGGATATAGTA
* * * *
54653026 ACTTGCACAAATGCCTTCGGG-CTTAGCCCAGATTTATTA
1 ACTCGCACAAA-GCCTTCGGGACTTAGCCCGGATATAGTA
* * * *
54653065 ACTCGCACGAATGCCTTC-GGATCCTAGTCCGGATATAGTC
1 ACTCGCAC-AAAGCCTTCGGGA-CTTAGCCCGGATATAGTA
*
54653105 ACTTAGCACAAAGCCTTCGGGACTTAGCCCGGA
1 AC-TCGCACAAAGCCTTCGGGACTTAGCCCGGA
54653138 CATCATTCGA
Statistics
Matches: 119, Mismatches: 26, Indels: 14
0.75 0.16 0.09
Matches are distributed among these distances:
38 2 0.02
39 29 0.24
40 78 0.66
41 10 0.08
ACGTcount: A:0.24, C:0.28, G:0.23, T:0.24
Consensus pattern (39 bp):
ACTCGCACAAAGCCTTCGGGACTTAGCCCGGATATAGTA
Found at i:54654116 original size:31 final size:31
Alignment explanation
Indices: 54654078--54654141 Score: 119
Period size: 31 Copynumber: 2.1 Consensus size: 31
54654068 AATCCACCAT
54654078 CACATGTATCATCATCAAGCTTCATATTTAA
1 CACATGTATCATCATCAAGCTTCATATTTAA
*
54654109 CACATGTATCATCATCGAGCTTCATATTTAA
1 CACATGTATCATCATCAAGCTTCATATTTAA
54654140 CA
1 CA
54654142 TGCAATGGCA
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
31 32 1.00
ACGTcount: A:0.34, C:0.23, G:0.08, T:0.34
Consensus pattern (31 bp):
CACATGTATCATCATCAAGCTTCATATTTAA
Found at i:54659131 original size:28 final size:28
Alignment explanation
Indices: 54659099--54659197 Score: 112
Period size: 28 Copynumber: 3.5 Consensus size: 28
54659089 ACAATAAGCC
*
54659099 CGCACACTTAGTGCTTAATAGTCGAACT
1 CGCACACTTAGTGCTTAATAATCGAACT
*
54659127 CGCACACTTAGTGC-TATATAATCAAACT
1 CGCACACTTAGTGCTTA-ATAATCGAACT
* * *
54659155 TGCACACTTAGTGCTGT-ATAATTTGAACC
1 CGCACACTTAGTGCT-TAATAA-TCGAACT
54659184 CGCACACTTAGTGC
1 CGCACACTTAGTGC
54659198 CAATTTGTGA
Statistics
Matches: 60, Mismatches: 7, Indels: 7
0.81 0.09 0.09
Matches are distributed among these distances:
27 2 0.03
28 40 0.67
29 17 0.28
30 1 0.02
ACGTcount: A:0.29, C:0.25, G:0.16, T:0.29
Consensus pattern (28 bp):
CGCACACTTAGTGCTTAATAATCGAACT
Found at i:54668109 original size:40 final size:39
Alignment explanation
Indices: 54668065--54668257 Score: 251
Period size: 39 Copynumber: 4.9 Consensus size: 39
54668055 GTTCAAAACA
* * ** * *
54668065 CCTTCGGGACATAGCCCGGTTATGGTAACCCGCACAAATG
1 CCTTCGGG-CTTAGCCCGGATATCATAACTCGCACAATTG
* *
54668105 CCTTCGGGACTTAACCCGGATATCACAACTCGCACAATTG
1 CCTTCGGG-CTTAGCCCGGATATCATAACTCGCACAATTG
*
54668145 CCTTCGGGCTTAGCCCGGATATCATAGCTCGCACAATTG
1 CCTTCGGGCTTAGCCCGGATATCATAACTCGCACAATTG
* *
54668184 CCTTCGGGCTTAGCCCGGATATCACAATTCGCACAATTG
1 CCTTCGGGCTTAGCCCGGATATCATAACTCGCACAATTG
* *
54668223 CCTTCGGGCTTAGCCCGGATATCACAATTCGCACA
1 CCTTCGGGCTTAGCCCGGATATCATAACTCGCACA
54668258 TTCATCACAT
Statistics
Matches: 139, Mismatches: 14, Indels: 1
0.90 0.09 0.01
Matches are distributed among these distances:
39 99 0.71
40 40 0.29
ACGTcount: A:0.24, C:0.32, G:0.21, T:0.23
Consensus pattern (39 bp):
CCTTCGGGCTTAGCCCGGATATCATAACTCGCACAATTG
Found at i:54668176 original size:39 final size:39
Alignment explanation
Indices: 54668095--54668257 Score: 263
Period size: 39 Copynumber: 4.2 Consensus size: 39
54668085 TATGGTAACC
* *
54668095 CGCACAAATGCCTTCGGGACTTAACCCGGATATCACAACT
1 CGCACAATTGCCTTCGGG-CTTAGCCCGGATATCACAACT
* *
54668135 CGCACAATTGCCTTCGGGCTTAGCCCGGATATCATAGCT
1 CGCACAATTGCCTTCGGGCTTAGCCCGGATATCACAACT
*
54668174 CGCACAATTGCCTTCGGGCTTAGCCCGGATATCACAATT
1 CGCACAATTGCCTTCGGGCTTAGCCCGGATATCACAACT
*
54668213 CGCACAATTGCCTTCGGGCTTAGCCCGGATATCACAATT
1 CGCACAATTGCCTTCGGGCTTAGCCCGGATATCACAACT
54668252 CGCACA
1 CGCACA
54668258 TTCATCACAT
Statistics
Matches: 116, Mismatches: 7, Indels: 1
0.94 0.06 0.01
Matches are distributed among these distances:
39 99 0.85
40 17 0.15
ACGTcount: A:0.25, C:0.32, G:0.20, T:0.23
Consensus pattern (39 bp):
CGCACAATTGCCTTCGGGCTTAGCCCGGATATCACAACT
Found at i:54671191 original size:41 final size:40
Alignment explanation
Indices: 54671032--54671210 Score: 188
Period size: 38 Copynumber: 4.5 Consensus size: 40
54671022 AATCAAGCAT
** ** * *
54671032 CTTCGGGGTTTAG-CCGGATATAACCACTCGCAC-AAGGC
1 CTTCGGGACTTAGCCCGGATATAGTCACTAGCACAAATGC
* * *
54671070 CTTCGGGTCTTAGCCCGGATATGGTCACTAGCATAAATGC
1 CTTCGGGACTTAGCCCGGATATAGTCACTAGCACAAATGC
54671110 CTTCGGGACTTAGCCCGGATATAG--ACTAGCACAAATGC
1 CTTCGGGACTTAGCCCGGATATAGTCACTAGCACAAATGC
* * * *
54671148 CTTC-GGATCTTAGTCCGGATGTAGTCGCTTAGCACAAAAGC
1 CTTCGGGA-CTTAGCCCGGATATAGTCAC-TAGCACAAATGC
54671189 CTTCGGGACTTAGCCCGGATAT
1 CTTCGGGACTTAGCCCGGATAT
54671211 CATTCGAGTA
Statistics
Matches: 117, Mismatches: 17, Indels: 11
0.81 0.12 0.08
Matches are distributed among these distances:
37 3 0.03
38 42 0.36
39 15 0.13
40 27 0.23
41 27 0.23
42 3 0.03
ACGTcount: A:0.24, C:0.26, G:0.25, T:0.25
Consensus pattern (40 bp):
CTTCGGGACTTAGCCCGGATATAGTCACTAGCACAAATGC
Found at i:54671926 original size:2 final size:2
Alignment explanation
Indices: 54671919--54671944 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
54671909 ATGTGCAAAC
54671919 AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT
54671945 GTGCAAGAGC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:54677472 original size:40 final size:40
Alignment explanation
Indices: 54677427--54677594 Score: 198
Period size: 40 Copynumber: 4.2 Consensus size: 40
54677417 CGGAATACAA
54677427 CCGGATATAACCACACGCACGAATGCCTTCGGGTCTTAGC
1 CCGGATATAACCACACGCACGAATGCCTTCGGGTCTTAGC
* * * *
54677467 CCGGATATAACGACTCGCACAAATGCCTTCGGGTATTAGC
1 CCGGATATAACCACACGCACGAATGCCTTCGGGTCTTAGC
* * **
54677507 CCGGACATAACAACTTGCACGAATGCCTTCGGGTCTTAGC
1 CCGGATATAACCACACGCACGAATGCCTTCGGGTCTTAGC
* *
54677547 CCGGATA-AAGTCACTA-GCAC-AATTGCCTTCGGGTCTTAAC
1 CCGGATATAA-CCAC-ACGCACGAA-TGCCTTCGGGTCTTAGC
54677587 CCGGATAT
1 CCGGATAT
54677595 CATTCAATTG
Statistics
Matches: 110, Mismatches: 14, Indels: 7
0.84 0.11 0.05
Matches are distributed among these distances:
39 4 0.04
40 106 0.96
ACGTcount: A:0.26, C:0.29, G:0.22, T:0.23
Consensus pattern (40 bp):
CCGGATATAACCACACGCACGAATGCCTTCGGGTCTTAGC
Found at i:54677567 original size:80 final size:80
Alignment explanation
Indices: 54677443--54677591 Score: 230
Period size: 80 Copynumber: 1.9 Consensus size: 80
54677433 ATAACCACAC
* *
54677443 GCACGAATGCCTTCGGGTCTTAGCCCGGATATAACGACTCGCACAAATGCCTTCGGGTATTAGCC
1 GCACGAATGCCTTCGGGTCTTAGCCCGGATATAACGACTAGCACAAATGCCTTCGGGTATTAACC
54677508 CGGACATAACAACTT
66 CGGACATAACAACTT
* *
54677523 GCACGAATGCCTTCGGGTCTTAGCCCGGATA-AA-GTCACTAGCACAATTGCCTTCGGGTCTTAA
1 GCACGAATGCCTTCGGGTCTTAGCCCGGATATAACG--ACTAGCACAAATGCCTTCGGGTATTAA
54677586 CCCGGA
64 CCCGGA
54677592 TATCATTCAA
Statistics
Matches: 63, Mismatches: 4, Indels: 4
0.89 0.06 0.06
Matches are distributed among these distances:
78 1 0.02
79 2 0.03
80 60 0.95
ACGTcount: A:0.25, C:0.29, G:0.23, T:0.23
Consensus pattern (80 bp):
GCACGAATGCCTTCGGGTCTTAGCCCGGATATAACGACTAGCACAAATGCCTTCGGGTATTAACC
CGGACATAACAACTT
Found at i:54682342 original size:40 final size:40
Alignment explanation
Indices: 54682295--54682438 Score: 193
Period size: 40 Copynumber: 3.6 Consensus size: 40
54682285 CTCGCACAAG
* * * *
54682295 GCCTTCGGGTCTTAGCCCGGATATGGTCACTAGCATAAAT
1 GCCTTCGGGACTTAGCCCGGATATAGTCGCTAGCACAAAT
54682335 GCCTTCGGGACTTAGCCCGGATATAGTCGCTAGCACAAAT
1 GCCTTCGGGACTTAGCCCGGATATAGTCGCTAGCACAAAT
* * *
54682375 GCCTTC-GGATCTTAGTCC-GATGTAGTCGCTTAGCACAAAA
1 GCCTTCGGGA-CTTAGCCCGGATATAGTCGC-TAGCACAAAT
54682415 GCCTTCGGGACTTAGCCCGGATAT
1 GCCTTCGGGACTTAGCCCGGATAT
54682439 CATTCGAGTA
Statistics
Matches: 91, Mismatches: 9, Indels: 7
0.85 0.08 0.07
Matches are distributed among these distances:
39 13 0.14
40 71 0.78
41 7 0.08
ACGTcount: A:0.23, C:0.26, G:0.25, T:0.26
Consensus pattern (40 bp):
GCCTTCGGGACTTAGCCCGGATATAGTCGCTAGCACAAAT
Found at i:54686557 original size:28 final size:28
Alignment explanation
Indices: 54686526--54686596 Score: 88
Period size: 28 Copynumber: 2.5 Consensus size: 28
54686516 ACAAGTGGCG
**
54686526 AAAAATATAAAAAATATTTTAATTTATA
1 AAAAATATAAAAAATATTACAATTTATA
* * *
54686554 AAAAATATAAAAATTATTACAATTTTTT
1 AAAAATATAAAAAATATTACAATTTATA
54686582 AAAAATATATAAAAA
1 AAAAATATA-AAAAA
54686597 CATTGAACAT
Statistics
Matches: 36, Mismatches: 6, Indels: 1
0.84 0.14 0.02
Matches are distributed among these distances:
28 32 0.89
29 4 0.11
ACGTcount: A:0.62, C:0.01, G:0.00, T:0.37
Consensus pattern (28 bp):
AAAAATATAAAAAATATTACAATTTATA
Found at i:54686686 original size:37 final size:36
Alignment explanation
Indices: 54686579--54686687 Score: 93
Period size: 34 Copynumber: 3.0 Consensus size: 36
54686569 ATTACAATTT
*
54686579 TTTA-AAAATATATAAAAACATTGAAC--ATTATAAA
1 TTTATAAAATATATAAAAAAATTGAACATATTA-AAA
* * *
54686613 TTT-TAGAAA-ATATAAAAATATAGAAAAACTATTTAAAA
1 TTTATA-AAATATATAAAAAAATTG-AACA-TA-TTAAAA
54686651 TTTATAAAATATATAGAAAAAATTGAACATATTAAAA
1 TTTATAAAATATATA-AAAAAATTGAACATATTAAAA
54686688 AGATATAAAC
Statistics
Matches: 59, Mismatches: 6, Indels: 17
0.72 0.07 0.21
Matches are distributed among these distances:
34 16 0.27
35 5 0.08
37 6 0.10
38 12 0.20
39 13 0.22
40 7 0.12
ACGTcount: A:0.60, C:0.04, G:0.05, T:0.32
Consensus pattern (36 bp):
TTTATAAAATATATAAAAAAATTGAACATATTAAAA
Found at i:54686688 original size:29 final size:29
Alignment explanation
Indices: 54686623--54686694 Score: 76
Period size: 29 Copynumber: 2.4 Consensus size: 29
54686613 TTTTAGAAAA
*
54686623 TATAAAAATATAGAAAAACTATTTAAAATT
1 TATAAAAATATAGAAAAAC-ATTGAAAATT
*
54686653 TATAAAATATATAGAAAAA-ATTGAACATAT
1 TATAAAA-ATATAGAAAAACATTGAAAAT-T
54686683 TA-AAAAGATATA
1 TATAAAA-ATATA
54686695 AACATATTAC
Statistics
Matches: 37, Mismatches: 3, Indels: 5
0.82 0.07 0.11
Matches are distributed among these distances:
29 16 0.43
30 10 0.27
31 11 0.30
ACGTcount: A:0.61, C:0.03, G:0.06, T:0.31
Consensus pattern (29 bp):
TATAAAAATATAGAAAAACATTGAAAATT
Found at i:54686777 original size:2 final size:2
Alignment explanation
Indices: 54686772--54686811 Score: 80
Period size: 2 Copynumber: 20.0 Consensus size: 2
54686762 GAAATTATTC
54686772 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
54686812 GAATACATGA
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 38 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:54689097 original size:16 final size:15
Alignment explanation
Indices: 54689072--54689101 Score: 51
Period size: 16 Copynumber: 1.9 Consensus size: 15
54689062 ATTAAATTAA
54689072 TTAACTAAATGCAAG
1 TTAACTAAATGCAAG
54689087 TTAACCTAAATGCAA
1 TTAA-CTAAATGCAA
54689102 ATGAAATGCA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 4 0.29
16 10 0.71
ACGTcount: A:0.47, C:0.17, G:0.10, T:0.27
Consensus pattern (15 bp):
TTAACTAAATGCAAG
Found at i:54691881 original size:90 final size:90
Alignment explanation
Indices: 54691703--54691872 Score: 218
Period size: 89 Copynumber: 1.9 Consensus size: 90
54691693 ATCGATAAGT
* * *
54691703 GATTTCGTATAAGACCATGACTGGGACATGGCATCGATATGAGGTCTCGTATAAGACCATGTCTG
1 GATTTCGTATAAGACCATGACTGGGACATGGCATCGATAGGAGGTCTCATATAAGACAATGTCTG
*
54691768 GGGCATGGCGTTGGCAATGATTTGA
66 GGACATGGCGTTGGCAATGATTTGA
* * * * * *
54691793 GATTTTGTATAAGACCAT-ATTTGGGATATGGCATCGAT-GGTGGTCTTATGTAAGACAATGTCT
1 GATTTCGTATAAGACCATGA-CTGGGACATGGCATCGATAGGAGGTCTCATATAAGACAATGTCT
*
54691856 GGGACATGGCTTTGGCA
65 GGGACATGGCGTTGGCA
54691873 CCCTATTTGG
Statistics
Matches: 68, Mismatches: 11, Indels: 3
0.83 0.13 0.04
Matches are distributed among these distances:
89 35 0.51
90 33 0.49
ACGTcount: A:0.25, C:0.15, G:0.29, T:0.31
Consensus pattern (90 bp):
GATTTCGTATAAGACCATGACTGGGACATGGCATCGATAGGAGGTCTCATATAAGACAATGTCTG
GGACATGGCGTTGGCAATGATTTGA
Found at i:54694562 original size:22 final size:22
Alignment explanation
Indices: 54694537--54694579 Score: 77
Period size: 22 Copynumber: 2.0 Consensus size: 22
54694527 GGAATGCTTG
54694537 ACCCAATAGACTAGAATGCCCA
1 ACCCAATAGACTAGAATGCCCA
*
54694559 ACCCAATAGACTGGAATGCCC
1 ACCCAATAGACTAGAATGCCC
54694580 CCAGTATGGG
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.37, C:0.33, G:0.16, T:0.14
Consensus pattern (22 bp):
ACCCAATAGACTAGAATGCCCA
Found at i:54699804 original size:47 final size:47
Alignment explanation
Indices: 54699751--54700081 Score: 466
Period size: 47 Copynumber: 7.2 Consensus size: 47
54699741 TTTAGGATTT
* *
54699751 AATGTGATGAATGTGAACTTGCATATGTGTGATAAGGCCAAATGGCC
1 AATGTGATGAATGTGAACATGCATATATGTGATAAGGCCAAATGGCC
* * *
54699798 AATGTGATGAATGTGAACATGCATATACGTGATAAGGCCGAATGGAC
1 AATGTGATGAATGTGAACATGCATATATGTGATAAGGCCAAATGGCC
* *
54699845 AATGTGATGAATGTGAACTTGCATATGTGTGATAAGGCCAAATGGCC
1 AATGTGATGAATGTGAACATGCATATATGTGATAAGGCCAAATGGCC
* *
54699892 AATGTGATGAATGTGAACATGCATATACGTGATAAGGCCGAATGGCC
1 AATGTGATGAATGTGAACATGCATATATGTGATAAGGCCAAATGGCC
* *
54699939 AATGTGATGAATGTGAACTTGCATATGTGTGATAAGGCCAAATGGCC
1 AATGTGATGAATGTGAACATGCATATATGTGATAAGGCCAAATGGCC
54699986 AATGTGATGAATGTGAACATGCATATA--TG-T---G---AATGGCC
1 AATGTGATGAATGTGAACATGCATATATGTGATAAGGCCAAATGGCC
* *
54700024 AATGTGATGAATGTGAACATGCATATATGTGATAAGG-TAGAATGGTC
1 AATGTGATGAATGTGAACATGCATATATGTGATAAGGCCA-AATGGCC
54700071 AATGTGATGAA
1 AATGTGATGAA
54700082 CGTGGAAGTG
Statistics
Matches: 254, Mismatches: 21, Indels: 18
0.87 0.07 0.06
Matches are distributed among these distances:
38 34 0.13
40 2 0.01
41 2 0.01
44 2 0.01
45 2 0.01
47 212 0.83
ACGTcount: A:0.34, C:0.11, G:0.27, T:0.27
Consensus pattern (47 bp):
AATGTGATGAATGTGAACATGCATATATGTGATAAGGCCAAATGGCC
Found at i:54699849 original size:94 final size:94
Alignment explanation
Indices: 54699751--54700081 Score: 538
Period size: 94 Copynumber: 3.6 Consensus size: 94
54699741 TTTAGGATTT
54699751 AATGTGATGAATGTGAACTTGCATATGTGTGATAAGGCCAAATGGCCAATGTGATGAATGTGAAC
1 AATGTGATGAATGTGAACTTGCATATGTGTGATAAGGCCAAATGGCCAATGTGATGAATGTGAAC
*
54699816 ATGCATATACGTGATAAGGCCGAATGGAC
66 ATGCATATACGTGATAAGGCCGAATGGCC
54699845 AATGTGATGAATGTGAACTTGCATATGTGTGATAAGGCCAAATGGCCAATGTGATGAATGTGAAC
1 AATGTGATGAATGTGAACTTGCATATGTGTGATAAGGCCAAATGGCCAATGTGATGAATGTGAAC
54699910 ATGCATATACGTGATAAGGCCGAATGGCC
66 ATGCATATACGTGATAAGGCCGAATGGCC
54699939 AATGTGATGAATGTGAACTTGCATATGTGTGATAAGGCCAAATGGCCAATGTGATGAATGTGAAC
1 AATGTGATGAATGTGAACTTGCATATGTGTGATAAGGCCAAATGGCCAATGTGATGAATGTGAAC
54700004 ATGCATATA--TG-T------GAATGGCC
66 ATGCATATACGTGATAAGGCCGAATGGCC
* * * *
54700024 AATGTGATGAATGTGAACATGCATATATGTGATAAGG-TAGAATGGTCAATGTGATGAA
1 AATGTGATGAATGTGAACTTGCATATGTGTGATAAGGCCA-AATGGCCAATGTGATGAA
54700082 CGTGGAAGTG
Statistics
Matches: 231, Mismatches: 5, Indels: 11
0.94 0.02 0.04
Matches are distributed among these distances:
84 1 0.00
85 60 0.26
91 1 0.00
92 2 0.01
94 167 0.72
ACGTcount: A:0.34, C:0.11, G:0.27, T:0.27
Consensus pattern (94 bp):
AATGTGATGAATGTGAACTTGCATATGTGTGATAAGGCCAAATGGCCAATGTGATGAATGTGAAC
ATGCATATACGTGATAAGGCCGAATGGCC
Found at i:54700020 original size:22 final size:22
Alignment explanation
Indices: 54699993--54700055 Score: 59
Period size: 22 Copynumber: 3.1 Consensus size: 22
54699983 GCCAATGTGA
54699993 TGAATGTGAACATGCATATATG
1 TGAATGTGAACATGCATATATG
*
54700015 TGAATG-G--C---CA-ATGTG
1 TGAATGTGAACATGCATATATG
54700030 ATGAATGTGAACATGCATATATG
1 -TGAATGTGAACATGCATATATG
54700053 TGA
1 TGA
54700056 TAAGGTAGAA
Statistics
Matches: 31, Mismatches: 2, Indels: 16
0.63 0.04 0.33
Matches are distributed among these distances:
15 4 0.13
16 8 0.26
17 1 0.03
19 2 0.06
21 1 0.03
22 11 0.35
23 4 0.13
ACGTcount: A:0.35, C:0.10, G:0.25, T:0.30
Consensus pattern (22 bp):
TGAATGTGAACATGCATATATG
Found at i:54700021 original size:38 final size:38
Alignment explanation
Indices: 54699979--54700055 Score: 154
Period size: 38 Copynumber: 2.0 Consensus size: 38
54699969 GATAAGGCCA
54699979 AATGGCCAATGTGATGAATGTGAACATGCATATATGTG
1 AATGGCCAATGTGATGAATGTGAACATGCATATATGTG
54700017 AATGGCCAATGTGATGAATGTGAACATGCATATATGTG
1 AATGGCCAATGTGATGAATGTGAACATGCATATATGTG
54700055 A
1 A
54700056 TAAGGTAGAA
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
38 39 1.00
ACGTcount: A:0.35, C:0.10, G:0.26, T:0.29
Consensus pattern (38 bp):
AATGGCCAATGTGATGAATGTGAACATGCATATATGTG
Found at i:54700075 original size:38 final size:38
Alignment explanation
Indices: 54699985--54700077 Score: 109
Period size: 38 Copynumber: 2.4 Consensus size: 38
54699975 GCCAAATGGC
* * *
54699985 CAATGTGATGAATGTGAACATGCATATATGTGAATGGC
1 CAATGTGATCAATGTGAACATGCATATATGTGAAAGGA
*
54700023 CAATGTGATGAATGTGAACATGCATATATGTGATAAGGTA
1 CAATGTGATCAATGTGAACATGCATATATGTGA-AAGG-A
*
54700063 GAATG-G-TCAATGTGA
1 CAATGTGATCAATGTGA
54700078 TGAACGTGGA
Statistics
Matches: 49, Mismatches: 4, Indels: 4
0.86 0.07 0.07
Matches are distributed among these distances:
38 41 0.84
39 4 0.08
40 4 0.08
ACGTcount: A:0.35, C:0.09, G:0.27, T:0.29
Consensus pattern (38 bp):
CAATGTGATCAATGTGAACATGCATATATGTGAAAGGA
Found at i:54705200 original size:31 final size:31
Alignment explanation
Indices: 54705159--54705222 Score: 92
Period size: 31 Copynumber: 2.1 Consensus size: 31
54705149 CCTTTTCATA
* *
54705159 TTTCATATTTCATAACACTGGGCTGAAGCCT
1 TTTCAAATTTCATAACACTGGGCCGAAGCCT
**
54705190 TTTCAAATTTCATATTACTGGGCCGAAGCCT
1 TTTCAAATTTCATAACACTGGGCCGAAGCCT
54705221 TT
1 TT
54705223 ACGGTAAACG
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
31 29 1.00
ACGTcount: A:0.25, C:0.22, G:0.16, T:0.38
Consensus pattern (31 bp):
TTTCAAATTTCATAACACTGGGCCGAAGCCT
Found at i:54705464 original size:24 final size:23
Alignment explanation
Indices: 54705438--54705556 Score: 195
Period size: 23 Copynumber: 5.1 Consensus size: 23
54705428 CCTAGCCTCT
*
54705438 TTTAATAACAGGGGCA-AAGCCC
1 TTTAATAACTGGGGCATAAGCCC
54705460 TTTTTAATAACTGGGGCATAAGCCC
1 --TTTAATAACTGGGGCATAAGCCC
54705485 TTTAATAACTGGGGCATAAGCCC
1 TTTAATAACTGGGGCATAAGCCC
54705508 TTTAATAACTGGGGCATAAGCCC
1 TTTAATAACTGGGGCATAAGCCC
*
54705531 TTTAATAACTGGGGCGTAAGCCC
1 TTTAATAACTGGGGCATAAGCCC
54705554 TTT
1 TTT
54705557 TGCACTTCCT
Statistics
Matches: 92, Mismatches: 2, Indels: 3
0.95 0.02 0.03
Matches are distributed among these distances:
23 71 0.77
24 15 0.16
25 6 0.07
ACGTcount: A:0.29, C:0.21, G:0.22, T:0.28
Consensus pattern (23 bp):
TTTAATAACTGGGGCATAAGCCC
Found at i:54705632 original size:20 final size:20
Alignment explanation
Indices: 54705607--54705673 Score: 116
Period size: 20 Copynumber: 3.4 Consensus size: 20
54705597 TTATAAATAC
54705607 ATCATGTGCATATCATACAT
1 ATCATGTGCATATCATACAT
54705627 ATCATGTGCATATCATACAT
1 ATCATGTGCATATCATACAT
*
54705647 GTCATGTGCATATCATACAT
1 ATCATGTGCATATCATACAT
*
54705667 ACCATGT
1 ATCATGT
54705674 TTATCAAAAT
Statistics
Matches: 44, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 44 1.00
ACGTcount: A:0.33, C:0.21, G:0.12, T:0.34
Consensus pattern (20 bp):
ATCATGTGCATATCATACAT
Found at i:54705638 original size:11 final size:11
Alignment explanation
Indices: 54705607--54705662 Score: 57
Period size: 11 Copynumber: 5.5 Consensus size: 11
54705597 TTATAAATAC
54705607 ATCATGTGCAT
1 ATCATGTGCAT
*
54705618 ATCA--TACAT
1 ATCATGTGCAT
54705627 ATCATGTGCAT
1 ATCATGTGCAT
*
54705638 ATCA--TACAT
1 ATCATGTGCAT
*
54705647 GTCATGTGCAT
1 ATCATGTGCAT
54705658 ATCAT
1 ATCAT
54705663 ACATACCATG
Statistics
Matches: 35, Mismatches: 6, Indels: 8
0.71 0.12 0.16
Matches are distributed among these distances:
9 15 0.43
11 20 0.57
ACGTcount: A:0.32, C:0.20, G:0.12, T:0.36
Consensus pattern (11 bp):
ATCATGTGCAT
Found at i:54705742 original size:25 final size:25
Alignment explanation
Indices: 54705710--54705757 Score: 69
Period size: 25 Copynumber: 1.9 Consensus size: 25
54705700 ATGTATAAAC
* * *
54705710 CCTAGGGGTATAATGGTCATTTTTA
1 CCTAGGGGCAAAACGGTCATTTTTA
54705735 CCTAGGGGCAAAACGGTCATTTT
1 CCTAGGGGCAAAACGGTCATTTT
54705758 CATATTATAA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
25 20 1.00
ACGTcount: A:0.25, C:0.17, G:0.25, T:0.33
Consensus pattern (25 bp):
CCTAGGGGCAAAACGGTCATTTTTA
Found at i:54706978 original size:27 final size:27
Alignment explanation
Indices: 54706916--54706993 Score: 88
Period size: 27 Copynumber: 2.9 Consensus size: 27
54706906 GGGCATATTC
54706916 GTCATTTTACCATACAGGGGTATTACG
1 GTCATTTTACCATACAGGGGTATTACG
* *
54706943 GTCACTTTACCCTACAGGGGCT-TTACG
1 GTCATTTTACCATACAGGGG-TATTACG
* *
54706970 GTCTTTTTACC-TAATAGGGGTATT
1 GTCATTTTACCAT-ACAGGGGTATT
54706994 TTAGTCATTT
Statistics
Matches: 43, Mismatches: 5, Indels: 6
0.80 0.09 0.11
Matches are distributed among these distances:
26 2 0.05
27 40 0.93
28 1 0.02
ACGTcount: A:0.22, C:0.21, G:0.22, T:0.36
Consensus pattern (27 bp):
GTCATTTTACCATACAGGGGTATTACG
Found at i:54707064 original size:27 final size:27
Alignment explanation
Indices: 54707011--54707263 Score: 175
Period size: 27 Copynumber: 9.3 Consensus size: 27
54707001 TTTCATCCTA
* * * * *
54707011 CAAGGGTGTTTTGGTAAATCTACAAAC
1 CAAGGGTATTTTAGTAATTTTATAAAC
* *
54707038 CAAGGGTATTTCAGTAATTTTGTAAAC
1 CAAGGGTATTTTAGTAATTTTATAAAC
* * *
54707065 CAATGGTATTTCTA-TAATTTTTAGAAAGT
1 CAAGGGTATTT-TAGTAA-TTTTATAAA-C
* * * *
54707094 CAAGGGTATTTTTGTAACTTTGTAAAT
1 CAAGGGTATTTTAGTAATTTTATAAAC
* * * *
54707121 CAGGGGTATTTTGGTAATTTTACAAAT
1 CAAGGGTATTTTAGTAATTTTATAAAC
** ** * *
54707148 TGAGGGTATTTCGGTAATTTCACAAAC
1 CAAGGGTATTTTAGTAATTTTATAAAC
* *
54707175 CAAGGGTATTTTGGTAATTTTACAAAC
1 CAAGGGTATTTTAGTAATTTTATAAAC
* * *
54707202 CAGGGGTATTTTGGTAATTTTACAAAC
1 CAAGGGTATTTTAGTAATTTTATAAAC
* * *
54707229 TAAGGGTATTTTAGTAATTTTGTAAAT
1 CAAGGGTATTTTAGTAATTTTATAAAC
*
54707256 CGAGGGTA
1 CAAGGGTA
54707264 AAACAGTAAT
Statistics
Matches: 181, Mismatches: 41, Indels: 8
0.79 0.18 0.03
Matches are distributed among these distances:
27 153 0.85
28 15 0.08
29 13 0.07
ACGTcount: A:0.32, C:0.09, G:0.21, T:0.38
Consensus pattern (27 bp):
CAAGGGTATTTTAGTAATTTTATAAAC
Found at i:54707182 original size:54 final size:54
Alignment explanation
Indices: 54707011--54707263 Score: 197
Period size: 54 Copynumber: 4.6 Consensus size: 54
54707001 TTTCATCCTA
* * * * * * ***
54707011 CAAGGGTGTTTTGGTAAATCTACAAACCAAGGGTATTTCAGTAATTTTGTAAAC
1 CAAGGGTATTTTGGTAATTTTACAAATCGAGGGTATTTCGGTAATTTCACAAAC
* * * * ** ** *
54707065 CAATGGTATTTCT-ATAATTTTTAGAAAGTCAAGGGTATTTTTGTAACTTT-GTAAAT
1 CAAGGGTATTT-TGGTAA-TTTTACAAA-TCGAGGGTATTTCGGTAA-TTTCACAAAC
* *
54707121 CAGGGGTATTTTGGTAATTTTACAAATTGAGGGTATTTCGGTAATTTCACAAAC
1 CAAGGGTATTTTGGTAATTTTACAAATCGAGGGTATTTCGGTAATTTCACAAAC
* * *
54707175 CAAGGGTATTTTGGTAATTTTACAAA-CCAGGGGTATTTTGGTAATTTTACAAAC
1 CAAGGGTATTTTGGTAATTTTACAAATCGA-GGGTATTTCGGTAATTTCACAAAC
* * **
54707229 TAAGGGTATTTTAGTAATTTTGTAAATCGAGGGTA
1 CAAGGGTATTTTGGTAATTTTACAAATCGAGGGTA
54707264 AAACAGTAAT
Statistics
Matches: 160, Mismatches: 31, Indels: 16
0.77 0.15 0.08
Matches are distributed among these distances:
53 4 0.03
54 103 0.64
55 18 0.11
56 32 0.20
57 3 0.02
ACGTcount: A:0.32, C:0.09, G:0.21, T:0.38
Consensus pattern (54 bp):
CAAGGGTATTTTGGTAATTTTACAAATCGAGGGTATTTCGGTAATTTCACAAAC
Found at i:54707214 original size:81 final size:81
Alignment explanation
Indices: 54707011--54707248 Score: 244
Period size: 81 Copynumber: 2.9 Consensus size: 81
54707001 TTTCATCCTA
* * * * ** ** * *
54707011 CAAGGGTGTTTTGGTAAATCTACAAACCAAGGGTATTTCAGTAATTTTGTAAACCAATGGTATTT
1 CAAGGGTATTTTGGTAACTTTACAAACCAGGGGTATTTTGGTAATTTTACAAACTAAGGGTATTT
* * *
54707076 CTA-TAATTTTTAGAAAGT
66 C-AGTAA-TTTCACAAA-C
* ** * * *
54707094 CAAGGGTATTTTTGTAACTTTGTAAATCAGGGGTATTTTGGTAATTTTACAAATTGAGGGTATTT
1 CAAGGGTATTTTGGTAACTTTACAAACCAGGGGTATTTTGGTAATTTTACAAACTAAGGGTATTT
*
54707159 CGGTAATTTCACAAAC
66 CAGTAATTTCACAAAC
*
54707175 CAAGGGTATTTTGGTAATTTTACAAACCAGGGGTATTTTGGTAATTTTACAAACTAAGGGTATTT
1 CAAGGGTATTTTGGTAACTTTACAAACCAGGGGTATTTTGGTAATTTTACAAACTAAGGGTATTT
*
54707240 TAGTAATTT
66 CAGTAATTT
54707249 TGTAAATCGA
Statistics
Matches: 125, Mismatches: 29, Indels: 4
0.79 0.18 0.03
Matches are distributed among these distances:
81 65 0.52
82 7 0.06
83 53 0.42
ACGTcount: A:0.32, C:0.10, G:0.20, T:0.39
Consensus pattern (81 bp):
CAAGGGTATTTTGGTAACTTTACAAACCAGGGGTATTTTGGTAATTTTACAAACTAAGGGTATTT
CAGTAATTTCACAAAC
Found at i:54707271 original size:27 final size:27
Alignment explanation
Indices: 54707241--54707452 Score: 234
Period size: 27 Copynumber: 7.9 Consensus size: 27
54707231 AGGGTATTTT
*
54707241 AGTAATTTTGTAAATCGAGGGTAAAAC
1 AGTAATTCTGTAAATCGAGGGTAAAAC
** *
54707268 AGTAATTCTGTAAATTAAGGGTAAAAT
1 AGTAATTCTGTAAATCGAGGGTAAAAC
*
54707295 AGTAATTCTATAAATCGAGGGTAAAAC
1 AGTAATTCTGTAAATCGAGGGTAAAAC
*
54707322 -GATAATTCTATAAATCGAGGGTAAAAC
1 AG-TAATTCTGTAAATCGAGGGTAAAAC
* * *
54707349 GGTAATTCTATAAGTCGAGGGTAAAAC
1 AGTAATTCTGTAAATCGAGGGTAAAAC
*
54707376 -GATAATTATGTAAATC-AGGGGTAAAAC
1 AG-TAATTCTGTAAATCGA-GGGTAAAAC
* *
54707403 GGTAATTATGTAAATCTG-GGGTAAAAC
1 AGTAATTCTGTAAATC-GAGGGTAAAAC
* *
54707430 GGTAATTCTGTAAATCGGGGGTA
1 AGTAATTCTGTAAATCGAGGGTA
54707453 CTTTGGTAAT
Statistics
Matches: 164, Mismatches: 13, Indels: 16
0.85 0.07 0.08
Matches are distributed among these distances:
26 4 0.02
27 158 0.96
28 2 0.01
ACGTcount: A:0.40, C:0.08, G:0.23, T:0.28
Consensus pattern (27 bp):
AGTAATTCTGTAAATCGAGGGTAAAAC
Found at i:54707273 original size:54 final size:54
Alignment explanation
Indices: 54707215--54707375 Score: 164
Period size: 54 Copynumber: 3.0 Consensus size: 54
54707205 GGGTATTTTG
* *** * *
54707215 GTAATTTTACAAACTAAGGGTATTTTAGTAATTTTGTAAATCGAGGGTAAAACA
1 GTAATTCTACAAACTAAGGGTAAAATAGTAATTCTATAAATCGAGGGTAAAACA
** *
54707269 GTAATTCTGTAAATTAAGGGTAAAATAGTAATTCTATAAATCGAGGGTAAAAC-
1 GTAATTCTACAAACTAAGGGTAAAATAGTAATTCTATAAATCGAGGGTAAAACA
* * ** *
54707322 GATAATTCTATAAA-TCGAGGGTAAAACGGTAATTCTATAAGTCGAGGGTAAAAC
1 G-TAATTCTACAAACT-AAGGGTAAAATAGTAATTCTATAAATCGAGGGTAAAAC
54707376 GATAATTATG
Statistics
Matches: 91, Mismatches: 14, Indels: 4
0.83 0.13 0.04
Matches are distributed among these distances:
53 2 0.02
54 89 0.98
ACGTcount: A:0.41, C:0.09, G:0.20, T:0.30
Consensus pattern (54 bp):
GTAATTCTACAAACTAAGGGTAAAATAGTAATTCTATAAATCGAGGGTAAAACA
Found at i:54707479 original size:27 final size:27
Alignment explanation
Indices: 54707458--54707547 Score: 119
Period size: 27 Copynumber: 3.3 Consensus size: 27
54707448 GGGTACTTTG
*
54707458 GTAATTTTACAAGTCGAAGGTATTTCA
1 GTAATTTTACAAATCGAAGGTATTTCA
*
54707485 GTAATTTTACAAATCGAGGGTATTTCA
1 GTAATTTTACAAATCGAAGGTATTTCA
* * *
54707512 GTATTTTTACAAA-CTAAGGGTATTTCG
1 GTAATTTTACAAATCGAA-GGTATTTCA
54707539 GTAATTTTA
1 GTAATTTTA
54707548 GTAAACTAAA
Statistics
Matches: 55, Mismatches: 7, Indels: 2
0.86 0.11 0.03
Matches are distributed among these distances:
26 2 0.04
27 53 0.96
ACGTcount: A:0.32, C:0.10, G:0.18, T:0.40
Consensus pattern (27 bp):
GTAATTTTACAAATCGAAGGTATTTCA
Found at i:54707499 original size:54 final size:54
Alignment explanation
Indices: 54707441--54707547 Score: 128
Period size: 54 Copynumber: 2.0 Consensus size: 54
54707431 GTAATTCTGT
* * *
54707441 AAATCGGGGGTACTTT-GGTAATTTTACAAGTCGAA-GGTATTTCAGTAATTTTAC
1 AAATCGAGGGTA-TTTCAGTAATTTTACAA-ACGAAGGGTATTTCAGTAATTTTAC
* * *
54707495 AAATCGAGGGTATTTCAGTATTTTTACAAACTAAGGGTATTTCGGTAATTTTA
1 AAATCGAGGGTATTTCAGTAATTTTACAAACGAAGGGTATTTCAGTAATTTTA
54707548 GTAAACTAAA
Statistics
Matches: 45, Mismatches: 6, Indels: 4
0.82 0.11 0.07
Matches are distributed among these distances:
53 6 0.13
54 39 0.87
ACGTcount: A:0.31, C:0.10, G:0.21, T:0.38
Consensus pattern (54 bp):
AAATCGAGGGTATTTCAGTAATTTTACAAACGAAGGGTATTTCAGTAATTTTAC
Found at i:54707506 original size:81 final size:80
Alignment explanation
Indices: 54707114--54707506 Score: 231
Period size: 81 Copynumber: 4.8 Consensus size: 80
54707104 TTTGTAACTT
* * * * * * *
54707114 TGTAAATCAGGGGTATTTTGGTAATTTTACAAATTGAGGGTATTTCGGTAATTTCACAAACCAAG
1 TGTAAATCAGGGGTAATTTGGTAATTTTAC-AATCGAGGGTATTTCAGTAATTTTATAAATCGAG
**** *
54707179 GGTATTTTGGTAATTT
65 GGTAAAACGGTAATTC
** * * * * * *
54707195 TACAAACCAGGGGTATTTTGGTAATTTTACAAACTAAGGGTATTTTAGTAATTTTGTAAATCGAG
1 TGTAAATCAGGGGTAATTTGGTAATTTTACAATC-GAGGGTATTTCAGTAATTTTATAAATCGAG
*
54707260 GGTAAAACAGTAATTC
65 GGTAAAACGGTAATTC
* * ** * *** *
54707276 TGTAAATTAAGGGTAAAATAGTAATTCTATA-AATCGAGGGTAAAAC-GATAATTCTATAAATCG
1 TGTAAATCAGGGGTAATTTGGTAATT-T-TACAATCGAGGGTATTTCAG-TAATTTTATAAATCG
54707339 AGGGTAAAACGGTAATTC
63 AGGGTAAAACGGTAATTC
* * *** * *** * * *
54707357 TATAAGTC-GAGGGTAAAACGATAATTATGTA-AATC-AGGGGTAAAACGGTAATTATGTAAATC
1 TGTAAATCAG-GGGTAATTTGGTAATT-T-TACAATCGA-GGGTATTTCAGTAATTTTATAAATC
54707419 TG-GGGTAAAACGGTAATTC
62 -GAGGGTAAAACGGTAATTC
* * * *
54707438 TGTAAATCGGGGGTACTTTGGTAATTTTACAAGTCGAAGGTATTTCAGTAATTTTACAAATCGAG
1 TGTAAATCAGGGGTAATTTGGTAATTTTACAA-TCGAGGGTATTTCAGTAATTTTATAAATCGAG
54707503 GGTA
65 GGTA
54707507 TTTCAGTATT
Statistics
Matches: 236, Mismatches: 63, Indels: 26
0.73 0.19 0.08
Matches are distributed among these distances:
79 2 0.01
80 8 0.03
81 216 0.92
82 8 0.03
83 2 0.01
ACGTcount: A:0.36, C:0.09, G:0.22, T:0.33
Consensus pattern (80 bp):
TGTAAATCAGGGGTAATTTGGTAATTTTACAATCGAGGGTATTTCAGTAATTTTATAAATCGAGG
GTAAAACGGTAATTC
Found at i:54707561 original size:27 final size:27
Alignment explanation
Indices: 54707458--54707562 Score: 90
Period size: 27 Copynumber: 3.9 Consensus size: 27
54707448 GGGTACTTTG
* *
54707458 GTAATTTTACAAGTCGAAG-GTATTTCA
1 GTAATTTTACAA-ACTAAGAGTATTTCA
* *
54707485 GTAATTTTACAAA-TCGAGGGTATTTCA
1 GTAATTTTACAAACT-AAGAGTATTTCA
* * *
54707512 GTATTTTTACAAACTAAGGGTATTTCG
1 GTAATTTTACAAACTAAGAGTATTTCA
*
54707539 GTAATTTTAGTAAACTAA-AGTATT
1 GTAATTTTA-CAAACTAAGAGTATT
54707563 CTAAACATGG
Statistics
Matches: 65, Mismatches: 9, Indels: 8
0.79 0.11 0.10
Matches are distributed among these distances:
26 2 0.03
27 55 0.85
28 8 0.12
ACGTcount: A:0.34, C:0.10, G:0.17, T:0.39
Consensus pattern (27 bp):
GTAATTTTACAAACTAAGAGTATTTCA
Found at i:54725818 original size:18 final size:18
Alignment explanation
Indices: 54725795--54725853 Score: 75
Period size: 18 Copynumber: 3.3 Consensus size: 18
54725785 TAGCCCATTT
*
54725795 CAGTAATAGTAATCAGTG
1 CAGTAACAGTAATCAGTG
* *
54725813 CAGTAACCA-TGATCAATG
1 CAGTAA-CAGTAATCAGTG
54725831 CAGTAACAGTAATCAGTG
1 CAGTAACAGTAATCAGTG
54725849 CAGTA
1 CAGTA
54725854 TGTAAACAGA
Statistics
Matches: 34, Mismatches: 5, Indels: 4
0.79 0.12 0.09
Matches are distributed among these distances:
17 2 0.06
18 31 0.91
19 1 0.03
ACGTcount: A:0.39, C:0.17, G:0.20, T:0.24
Consensus pattern (18 bp):
CAGTAACAGTAATCAGTG
Found at i:54726139 original size:23 final size:23
Alignment explanation
Indices: 54726112--54726161 Score: 68
Period size: 23 Copynumber: 2.2 Consensus size: 23
54726102 ACCCCATACA
54726112 ATGCAACATA-ATATTATACATGG-
1 ATGCAACATACATA-TA-ACATGGC
54726135 ATGCAACATACATATAACATGGC
1 ATGCAACATACATATAACATGGC
54726158 ATGC
1 ATGC
54726162 TCAAATACAG
Statistics
Matches: 25, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
22 6 0.24
23 16 0.64
24 3 0.12
ACGTcount: A:0.42, C:0.18, G:0.14, T:0.26
Consensus pattern (23 bp):
ATGCAACATACATATAACATGGC
Found at i:54726286 original size:27 final size:27
Alignment explanation
Indices: 54726251--54726596 Score: 435
Period size: 27 Copynumber: 12.8 Consensus size: 27
54726241 CAGGGTTATT
54726251 TCGTCCATTTTATCACATAAGGGCAAAA
1 TCGT-CATTTTATCACATAAGGGCAAAA
*
54726279 TCATCATTTTATCACATAAGGG-AAAA
1 TCGTCATTTTATCACATAAGGGCAAAA
* * *
54726305 TTCTTCATTTTATCACGTAAAGGCAAAA
1 -TCGTCATTTTATCACATAAGGGCAAAA
* *
54726333 TCGTCATCTTATCACCTAAGGGCAAAA
1 TCGTCATTTTATCACATAAGGGCAAAA
* * * *
54726360 TTGTCATTTTATCACCTAAAGACAAAA
1 TCGTCATTTTATCACATAAGGGCAAAA
* **
54726387 TCGTCATTTTATCACGTAAAAGCAAAA
1 TCGTCATTTTATCACATAAGGGCAAAA
*
54726414 TCGTCATTTTATCATATAAGGGCAAAA
1 TCGTCATTTTATCACATAAGGGCAAAA
* * * *
54726441 TTGTCATTTTGTCACATAAAGGTAAAA
1 TCGTCATTTTATCACATAAGGGCAAAA
* *
54726468 TCATCATTTTATCACATAAGGGCAAGA
1 TCGTCATTTTATCACATAAGGGCAAAA
* *
54726495 TCGTCATTTTATCATATTAGGG-AAAA
1 TCGTCATTTTATCACATAAGGGCAAAA
*
54726521 TCGTCATTTTATCACATAAGGTCAAAA
1 TCGTCATTTTATCACATAAGGGCAAAA
54726548 TCGTCATTTTATCACATAAGGGCAAAA
1 TCGTCATTTTATCACATAAGGGCAAAA
* *
54726575 TTGTCATTTTATCACATGAGGG
1 TCGTCATTTTATCACATAAGGG
54726597 TTCAGGTACG
Statistics
Matches: 274, Mismatches: 41, Indels: 7
0.85 0.13 0.02
Matches are distributed among these distances:
26 26 0.09
27 241 0.88
28 7 0.03
ACGTcount: A:0.36, C:0.17, G:0.14, T:0.33
Consensus pattern (27 bp):
TCGTCATTTTATCACATAAGGGCAAAA
Found at i:54738142 original size:29 final size:28
Alignment explanation
Indices: 54738054--54738148 Score: 100
Period size: 29 Copynumber: 3.3 Consensus size: 28
54738044 TACTCAATCA
** *
54738054 CGCACACTTAGTGCCATGTGATTCAAGCC
1 CGCACACTTAGTGCCAT-ACATTCAAGCT
* * * *
54738083 CGCACACATAGTGCCATATAGTCCAAACT
1 CGCACACTTAGTGCCATACA-TTCAAGCT
54738112 CGCACACTTAGTGCCATACATTACAAGCT
1 CGCACACTTAGTGCCATACATT-CAAGCT
54738141 CGCACACT
1 CGCACACT
54738149 CAGCCAATCT
Statistics
Matches: 54, Mismatches: 10, Indels: 4
0.79 0.15 0.06
Matches are distributed among these distances:
28 2 0.04
29 52 0.96
ACGTcount: A:0.29, C:0.33, G:0.16, T:0.22
Consensus pattern (28 bp):
CGCACACTTAGTGCCATACATTCAAGCT
Found at i:54740207 original size:21 final size:21
Alignment explanation
Indices: 54740181--54740220 Score: 80
Period size: 21 Copynumber: 1.9 Consensus size: 21
54740171 ACACGGGCAT
54740181 ATGGGCATGTTGTCCAGCCCC
1 ATGGGCATGTTGTCCAGCCCC
54740202 ATGGGCATGTTGTCCAGCC
1 ATGGGCATGTTGTCCAGCC
54740221 ATTTGTCCCC
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.15, C:0.30, G:0.30, T:0.25
Consensus pattern (21 bp):
ATGGGCATGTTGTCCAGCCCC
Found at i:54742516 original size:54 final size:54
Alignment explanation
Indices: 54742431--54742615 Score: 289
Period size: 54 Copynumber: 3.4 Consensus size: 54
54742421 TTACAGCGGA
* * *
54742431 ATTACCAGTCCAGGCTAAATCCCCTGAAGTAATAACTCATAGAGCAATGTCAGG
1 ATTACCAGTCCAGGCTAAATCCCCCGTAGTAATAACTCATAGAGCAATGTCGGG
54742485 ATTACCAGTCCAGGCTAAATCCCCCGTAGTAATAACTCATAGAGCAATGTCGGG
1 ATTACCAGTCCAGGCTAAATCCCCCGTAGTAATAACTCATAGAGCAATGTCGGG
** * *
54742539 ATTACCAGTCCAGGCTAAATCTTCCATAGTAATAACTCATAGAGCAATGCCGGG
1 ATTACCAGTCCAGGCTAAATCCCCCGTAGTAATAACTCATAGAGCAATGTCGGG
* *
54742593 ATTACCAATCCAAGCTAAATCCC
1 ATTACCAGTCCAGGCTAAATCCC
54742616 TTTTAATGAC
Statistics
Matches: 120, Mismatches: 11, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
54 120 1.00
ACGTcount: A:0.34, C:0.26, G:0.17, T:0.23
Consensus pattern (54 bp):
ATTACCAGTCCAGGCTAAATCCCCCGTAGTAATAACTCATAGAGCAATGTCGGG
Found at i:54749562 original size:27 final size:28
Alignment explanation
Indices: 54749532--54749601 Score: 106
Period size: 27 Copynumber: 2.5 Consensus size: 28
54749522 ATAATAAGTC
*
54749532 CGCACACTTAGTGCTATATAATC-AGCT
1 CGCACACTTAGTGCTATATAATCAAACT
* *
54749559 CGCACACATAGTGCTATATAATCAAATT
1 CGCACACTTAGTGCTATATAATCAAACT
54749587 CGCACACTTAGTGCT
1 CGCACACTTAGTGCT
54749602 GTACAAATTT
Statistics
Matches: 38, Mismatches: 4, Indels: 1
0.88 0.09 0.02
Matches are distributed among these distances:
27 22 0.58
28 16 0.42
ACGTcount: A:0.31, C:0.26, G:0.14, T:0.29
Consensus pattern (28 bp):
CGCACACTTAGTGCTATATAATCAAACT
Found at i:54760836 original size:29 final size:29
Alignment explanation
Indices: 54760802--54760904 Score: 154
Period size: 29 Copynumber: 3.6 Consensus size: 29
54760792 TAATCAGCGG
** *
54760802 CGCACACTTAGTGCCATATACTTT-AAACT
1 CGCACACTTAGTGCCATGCA-TTTCAAGCT
54760831 CGCACACTTAGTGCCATGCATTTCAAGCT
1 CGCACACTTAGTGCCATGCATTTCAAGCT
54760860 CGCACACTTAGTGCCATGCATTTCAAGCT
1 CGCACACTTAGTGCCATGCATTTCAAGCT
*
54760889 CGCACACTCAGTGCCA
1 CGCACACTTAGTGCCA
54760905 ATCTCTCAAC
Statistics
Matches: 69, Mismatches: 4, Indels: 2
0.92 0.05 0.03
Matches are distributed among these distances:
28 3 0.04
29 66 0.96
ACGTcount: A:0.26, C:0.32, G:0.16, T:0.26
Consensus pattern (29 bp):
CGCACACTTAGTGCCATGCATTTCAAGCT
Found at i:54763943 original size:40 final size:40
Alignment explanation
Indices: 54763864--54764031 Score: 223
Period size: 40 Copynumber: 4.2 Consensus size: 40
54763854 CAGATGATAA
* * **
54763864 CCGGACTAAGATCCGAAGGCATTCGTGCGAGTTGCTATAT
1 CCGGGCTAAGACCCGAAGGCATTTATGCGAGTTGCTATAT
* * * *
54763904 CCGGGCTATGTCCCGAAGGCATTTATGCTAG-TGATTATAT
1 CCGGGCTAAGACCCGAAGGCATTTATGCGAGTTG-CTATAT
*
54763944 CCGGGCTAAGACCCGAAGGCATTTGTGCGAGTTGCTATAT
1 CCGGGCTAAGACCCGAAGGCATTTATGCGAGTTGCTATAT
*
54763984 CCGGGCTAAGACCCGAAGGCATTTGTGCGAGTTGCTATAT
1 CCGGGCTAAGACCCGAAGGCATTTATGCGAGTTGCTATAT
54764024 CC-GGCTAA
1 CCGGGCTAA
54764032 ATCCCAAAGA
Statistics
Matches: 113, Mismatches: 13, Indels: 5
0.86 0.10 0.04
Matches are distributed among these distances:
39 8 0.07
40 103 0.91
41 2 0.02
ACGTcount: A:0.23, C:0.23, G:0.28, T:0.26
Consensus pattern (40 bp):
CCGGGCTAAGACCCGAAGGCATTTATGCGAGTTGCTATAT
Found at i:54767285 original size:12 final size:13
Alignment explanation
Indices: 54767251--54767290 Score: 55
Period size: 13 Copynumber: 3.0 Consensus size: 13
54767241 TTTTTTTAAG
54767251 TAGTTTATTGATA
1 TAGTTTATTGATA
54767264 TAGTCATTATT-ATA
1 TAGT--TTATTGATA
54767278 TAGTTTATTGATA
1 TAGTTTATTGATA
54767291 AAAATAAAAT
Statistics
Matches: 24, Mismatches: 0, Indels: 6
0.80 0.00 0.20
Matches are distributed among these distances:
12 5 0.21
13 7 0.29
14 7 0.29
15 5 0.21
ACGTcount: A:0.33, C:0.03, G:0.12, T:0.53
Consensus pattern (13 bp):
TAGTTTATTGATA
Found at i:54786874 original size:40 final size:39
Alignment explanation
Indices: 54786830--54787025 Score: 252
Period size: 40 Copynumber: 4.9 Consensus size: 39
54786820 GGATATAGCT
* *
54786830 ACTCGCTCAAATGCCTTCGGGACATAGCCCAGTTATAGTA
1 ACTCGCACAAATGCCTTCGGGACTTAGCCC-GTTATAGTA
*
54786870 ACTCGCACCAAA-GCCTTCGGGACTTAGCCCGGATT-TGGTA
1 ACTCGCA-CAAATGCCTTCGGGACTTAGCCC-G-TTATAGTA
**
54786910 ACTCGCACAAATGCCTTCGGGACTTAGCCCGGAATTAGTA
1 ACTCGCACAAATGCCTTCGGGACTTAGCCCGTTA-TAGTA
**
54786950 ACTCGCACAAATGCCTTCGGGACTTAGCCCGGAATTAGTA
1 ACTCGCACAAATGCCTTCGGGACTTAGCCCGTTA-TAGTA
54786990 ACTCGCACAAATGCCTTCGGGACTTAGCCCGGTTAT
1 ACTCGCACAAATGCCTTCGGGACTTAGCCC-GTTAT
54787026 CATCCGAATA
Statistics
Matches: 141, Mismatches: 9, Indels: 12
0.87 0.06 0.07
Matches are distributed among these distances:
39 5 0.04
40 128 0.91
41 8 0.06
ACGTcount: A:0.26, C:0.29, G:0.22, T:0.23
Consensus pattern (39 bp):
ACTCGCACAAATGCCTTCGGGACTTAGCCCGTTATAGTA
Found at i:54786951 original size:80 final size:80
Alignment explanation
Indices: 54786830--54787021 Score: 298
Period size: 80 Copynumber: 2.4 Consensus size: 80
54786820 GGATATAGCT
* * * *
54786830 ACTCGCTCAAATGCCTTCGGGACATAGCCCAGTTATAGTAACTCGCACCAAA-GCCTTCGGGACT
1 ACTCGCACAAATGCCTTCGGGACTTAGCCCGGATATAGTAACTCGCA-CAAATGCCTTCGGGACT
* *
54786894 TAGCCCGGATTTGGTA
65 TAGCCCGGAATTAGTA
54786910 ACTCGCACAAATGCCTTCGGGACTTAGCCCGGA-ATTAGTAACTCGCACAAATGCCTTCGGGACT
1 ACTCGCACAAATGCCTTCGGGACTTAGCCCGGATA-TAGTAACTCGCACAAATGCCTTCGGGACT
54786974 TAGCCCGGAATTAGTA
65 TAGCCCGGAATTAGTA
54786990 ACTCGCACAAATGCCTTCGGGACTTAGCCCGG
1 ACTCGCACAAATGCCTTCGGGACTTAGCCCGG
54787022 TTATCATCCG
Statistics
Matches: 104, Mismatches: 6, Indels: 4
0.91 0.05 0.04
Matches are distributed among these distances:
79 5 0.05
80 99 0.95
ACGTcount: A:0.26, C:0.29, G:0.23, T:0.22
Consensus pattern (80 bp):
ACTCGCACAAATGCCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATGCCTTCGGGACTT
AGCCCGGAATTAGTA
Found at i:54792855 original size:40 final size:40
Alignment explanation
Indices: 54792811--54792966 Score: 235
Period size: 40 Copynumber: 3.9 Consensus size: 40
54792801 GGATATAGCT
* *
54792811 ACTCGCTCAAATGCCTTCGGGACATAGCCCGGTTATAGTA
1 ACTCGCACAAATGCCTTCGGGACTTAGCCCGGTTATAGTA
* *
54792851 ACTCGCACCAATGCCTTCGGGACTTAGCCCGGATT-TGGTA
1 ACTCGCACAAATGCCTTCGGGACTTAGCCCGG-TTATAGTA
*
54792891 ACTCGCACAAATGCCTTCGGGACTTAGCCCGG-AATTAGTA
1 ACTCGCACAAATGCCTTCGGGACTTAGCCCGGTTA-TAGTA
54792931 ACTCGCACAAATGCCTTCGGGACTTAGCCCGGTTAT
1 ACTCGCACAAATGCCTTCGGGACTTAGCCCGGTTAT
54792967 CATCCGAATA
Statistics
Matches: 104, Mismatches: 8, Indels: 8
0.87 0.07 0.07
Matches are distributed among these distances:
40 101 0.97
41 3 0.03
ACGTcount: A:0.24, C:0.29, G:0.23, T:0.24
Consensus pattern (40 bp):
ACTCGCACAAATGCCTTCGGGACTTAGCCCGGTTATAGTA
Found at i:54798789 original size:40 final size:40
Alignment explanation
Indices: 54798745--54798940 Score: 272
Period size: 40 Copynumber: 4.9 Consensus size: 40
54798735 GGATATAGCT
* *
54798745 ACTCGCTCAAATGCCTTCGGGACATAGCCCGGTTATAGTA
1 ACTCGCACAAATGCCTTCGGGACTTAGCCCGGTTATAGTA
* * *
54798785 ACTCGCACCAATGCCTTTGGGACTTAGCCCGGATT-TGGTA
1 ACTCGCACAAATGCCTTCGGGACTTAGCCCGG-TTATAGTA
*
54798825 ACTCGCACAAATGCCTTCGGGACTTAGCCCGG-AATTAGTA
1 ACTCGCACAAATGCCTTCGGGACTTAGCCCGGTTA-TAGTA
*
54798865 ACTCGCACAAATGCCTTCGGGACTTAGCCCGG-AATTAGTA
1 ACTCGCACAAATGCCTTCGGGACTTAGCCCGGTTA-TAGTA
*
54798905 ACTCTCACAAATGCCTTCGGGACTTAGCCCGGTTAT
1 ACTCGCACAAATGCCTTCGGGACTTAGCCCGGTTAT
54798941 CATCCGAATA
Statistics
Matches: 141, Mismatches: 11, Indels: 8
0.88 0.07 0.05
Matches are distributed among these distances:
40 138 0.98
41 3 0.02
ACGTcount: A:0.24, C:0.28, G:0.22, T:0.25
Consensus pattern (40 bp):
ACTCGCACAAATGCCTTCGGGACTTAGCCCGGTTATAGTA
Found at i:54806208 original size:28 final size:28
Alignment explanation
Indices: 54806168--54806278 Score: 152
Period size: 28 Copynumber: 3.9 Consensus size: 28
54806158 CATGACTGTA
54806168 AATGTGATTTGGGCCTAAT-GGCCATATG
1 AATGTGA-TTGGGCCTAATGGGCCATATG
* *
54806196 AATGTGATTTGGGCCTAATGGGCCACATA
1 AATGTGA-TTGGGCCTAATGGGCCATATG
54806225 AATGTGATTGGGCCTAATGGGCCATATG
1 AATGTGATTGGGCCTAATGGGCCATATG
* * *
54806253 AATGAGATTGGGCCTAGTAGGCCATA
1 AATGTGATTGGGCCTAATGGGCCATA
54806279 ATCATGTATG
Statistics
Matches: 75, Mismatches: 7, Indels: 2
0.89 0.08 0.02
Matches are distributed among these distances:
28 61 0.81
29 14 0.19
ACGTcount: A:0.27, C:0.15, G:0.30, T:0.28
Consensus pattern (28 bp):
AATGTGATTGGGCCTAATGGGCCATATG
Found at i:54806276 original size:56 final size:57
Alignment explanation
Indices: 54806166--54806276 Score: 172
Period size: 56 Copynumber: 2.0 Consensus size: 57
54806156 AGCATGACTG
* *
54806166 TAAATGTGATTTGGGCCTAATGGCCATATGAATGTGATTTGGGCCTAATGGGCCACA
1 TAAATGTGATTTGGGCCTAATGGCCATATGAATGAGATTTGGGCCTAATAGGCCACA
*
54806223 TAAATGTGA-TTGGGCCTAATGGGCCATATGAATGAGA-TTGGGCCTAGTAGGCCA
1 TAAATGTGATTTGGGCCTAAT-GGCCATATGAATGAGATTTGGGCCTAATAGGCCA
54806277 TAATCATGTA
Statistics
Matches: 50, Mismatches: 3, Indels: 3
0.89 0.05 0.05
Matches are distributed among these distances:
56 26 0.52
57 24 0.48
ACGTcount: A:0.27, C:0.15, G:0.30, T:0.28
Consensus pattern (57 bp):
TAAATGTGATTTGGGCCTAATGGCCATATGAATGAGATTTGGGCCTAATAGGCCACA
Found at i:54820747 original size:18 final size:18
Alignment explanation
Indices: 54820724--54820760 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
54820714 TAGGTAAAAT
**
54820724 GACCGTAATGGCCCTATA
1 GACCGTAATACCCCTATA
54820742 GACCGTAATACCCCTATA
1 GACCGTAATACCCCTATA
54820760 G
1 G
54820761 GGTAAAATGA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.30, C:0.30, G:0.19, T:0.22
Consensus pattern (18 bp):
GACCGTAATACCCCTATA
Found at i:54820790 original size:27 final size:27
Alignment explanation
Indices: 54820742--54820904 Score: 186
Period size: 27 Copynumber: 6.1 Consensus size: 27
54820732 TGGCCCTATA
* *
54820742 GACCGTAATACCCCTATAGGGTAAAAT
1 GACCGTAATGCCCCTGTAGGGTAAAAT
* *
54820769 GACTGTGATGCCCCTGTAGGGTAAAAT
1 GACCGTAATGCCCCTGTAGGGTAAAAT
**
54820796 GACCGTAACCCCCCTGTAGGGTAAAAT
1 GACCGTAATGCCCCTGTAGGGTAAAAT
* * *
54820823 GATCGTAATGCCCCGGTAGGATAAAAT
1 GACCGTAATGCCCCTGTAGGGTAAAAT
* *
54820850 AACCGTAATG-CCCTGTAGGGGAAAAT
1 GACCGTAATGCCCCTGTAGGGTAAAAT
* *
54820876 GACCGTAATACCTCTGTATGGG-AAAAT
1 GACCGTAATGCCCCTGTA-GGGTAAAAT
54820903 GA
1 GA
54820905 TGATTATGCC
Statistics
Matches: 113, Mismatches: 21, Indels: 4
0.82 0.15 0.03
Matches are distributed among these distances:
26 21 0.19
27 89 0.79
28 3 0.03
ACGTcount: A:0.33, C:0.21, G:0.25, T:0.22
Consensus pattern (27 bp):
GACCGTAATGCCCCTGTAGGGTAAAAT
Found at i:54828937 original size:33 final size:34
Alignment explanation
Indices: 54828894--54828988 Score: 120
Period size: 34 Copynumber: 2.8 Consensus size: 34
54828884 ACTTTATTGA
* * *
54828894 TACTGTAATGGACTTAGGCCC-CACTGATACTAT
1 TACTGAAATGGGCTTAGGCCCAAACTGATACTAT
*
54828927 TACTGAAATGGGCTTAGGCCCAAACTGCTACTAT
1 TACTGAAATGGGCTTAGGCCCAAACTGATACTAT
* * *
54828961 TATTGAAATGGGCTAAGGCCCTAACTGA
1 TACTGAAATGGGCTTAGGCCCAAACTGA
54828989 GACTGCAATG
Statistics
Matches: 53, Mismatches: 8, Indels: 1
0.85 0.13 0.02
Matches are distributed among these distances:
33 19 0.36
34 34 0.64
ACGTcount: A:0.29, C:0.22, G:0.21, T:0.27
Consensus pattern (34 bp):
TACTGAAATGGGCTTAGGCCCAAACTGATACTAT
Found at i:54831591 original size:28 final size:28
Alignment explanation
Indices: 54831526--54831626 Score: 114
Period size: 28 Copynumber: 3.5 Consensus size: 28
54831516 ATAGTGAATC
*
54831526 CGCACACTTAGTGCTATATGTATTC-AACT
1 CGCACACTTAGTGCTATA--TAATCAAACT
54831555 CGCACACTTAGTGCTATATAATCAAACT
1 CGCACACTTAGTGCTATATAATCAAACT
* * * *
54831583 CGCACACTTAGTGCTGTACAATTTTAAACC
1 CGCACACTTAGTGCTATATAA--TCAAACT
54831613 CGCACACTTAGTGC
1 CGCACACTTAGTGC
54831627 CAATCTTGTC
Statistics
Matches: 64, Mismatches: 5, Indels: 5
0.86 0.07 0.07
Matches are distributed among these distances:
27 4 0.06
28 23 0.36
29 18 0.28
30 19 0.30
ACGTcount: A:0.30, C:0.27, G:0.14, T:0.30
Consensus pattern (28 bp):
CGCACACTTAGTGCTATATAATCAAACT
Found at i:54836698 original size:19 final size:19
Alignment explanation
Indices: 54836674--54836712 Score: 78
Period size: 19 Copynumber: 2.1 Consensus size: 19
54836664 ATGGTTGAAA
54836674 GGGTGGTGTGAGTAATCAG
1 GGGTGGTGTGAGTAATCAG
54836693 GGGTGGTGTGAGTAATCAG
1 GGGTGGTGTGAGTAATCAG
54836712 G
1 G
54836713 TTGATGCCAC
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.21, C:0.05, G:0.49, T:0.26
Consensus pattern (19 bp):
GGGTGGTGTGAGTAATCAG
Found at i:54842580 original size:13 final size:13
Alignment explanation
Indices: 54842562--54842593 Score: 55
Period size: 13 Copynumber: 2.5 Consensus size: 13
54842552 AAGATCATTA
54842562 AATACTGGCACGG
1 AATACTGGCACGG
54842575 AATACTGGCACGG
1 AATACTGGCACGG
*
54842588 TATACT
1 AATACT
54842594 ATCGTGAAGC
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
13 18 1.00
ACGTcount: A:0.31, C:0.22, G:0.25, T:0.22
Consensus pattern (13 bp):
AATACTGGCACGG
Found at i:54854481 original size:30 final size:31
Alignment explanation
Indices: 54854441--54854533 Score: 163
Period size: 30 Copynumber: 3.1 Consensus size: 31
54854431 CCCTTTTATA
*
54854441 TTTCATATTTCATAATACTGGGCCGAAGCCT
1 TTTCATATTTCATATTACTGGGCCGAAGCCT
54854472 TTT-ATATTTCATATTACTGGGCC-AAGCCT
1 TTTCATATTTCATATTACTGGGCCGAAGCCT
54854501 TTTCATATTTCATATTACTGGGCCGAAGCCT
1 TTTCATATTTCATATTACTGGGCCGAAGCCT
54854532 TT
1 TT
54854534 ACTGTAAACG
Statistics
Matches: 59, Mismatches: 1, Indels: 4
0.92 0.02 0.06
Matches are distributed among these distances:
29 9 0.15
30 39 0.66
31 11 0.19
ACGTcount: A:0.24, C:0.22, G:0.15, T:0.40
Consensus pattern (31 bp):
TTTCATATTTCATATTACTGGGCCGAAGCCT
Found at i:54854776 original size:24 final size:24
Alignment explanation
Indices: 54854725--54854843 Score: 170
Period size: 24 Copynumber: 5.0 Consensus size: 24
54854715 GCTTTATCAT
*
54854725 ATAACTGGAGGCCT-AGCCTCTTTTA
1 ATAACTGG-GGCATAAGCC-CTTTTA
* *
54854750 ATAACTGGGGCAAAAGCCCTTTCA
1 ATAACTGGGGCATAAGCCCTTTTA
54854774 ATAACTGGGGCATAAGCCCTTTT-
1 ATAACTGGGGCATAAGCCCTTTTA
*
54854797 ATAACTGGGGCATAAGCCCTTTTG
1 ATAACTGGGGCATAAGCCCTTTTA
54854821 ATAACTGGGGCATAAGCCCTTTT
1 ATAACTGGGGCATAAGCCCTTTT
54854844 TCACTTCCTC
Statistics
Matches: 87, Mismatches: 5, Indels: 5
0.90 0.05 0.05
Matches are distributed among these distances:
23 23 0.26
24 52 0.60
25 12 0.14
ACGTcount: A:0.27, C:0.23, G:0.22, T:0.29
Consensus pattern (24 bp):
ATAACTGGGGCATAAGCCCTTTTA
Found at i:54854804 original size:47 final size:48
Alignment explanation
Indices: 54854725--54854843 Score: 170
Period size: 47 Copynumber: 2.5 Consensus size: 48
54854715 GCTTTATCAT
*
54854725 ATAACTGGAGGCCT-AGCCTCTTTTAATAACTGGGGCAAAAGCCCTTTCA
1 ATAACTGG-GGCATAAGCC-CTTTTAATAACTGGGGCAAAAGCCCTTTCA
* **
54854774 ATAACTGGGGCATAAGCCCTTTT-ATAACTGGGGCATAAGCCCTTTTG
1 ATAACTGGGGCATAAGCCCTTTTAATAACTGGGGCAAAAGCCCTTTCA
54854821 ATAACTGGGGCATAAGCCCTTTT
1 ATAACTGGGGCATAAGCCCTTTT
54854844 TCACTTCCTC
Statistics
Matches: 65, Mismatches: 4, Indels: 4
0.89 0.05 0.05
Matches are distributed among these distances:
47 44 0.68
48 9 0.14
49 12 0.18
ACGTcount: A:0.27, C:0.23, G:0.22, T:0.29
Consensus pattern (48 bp):
ATAACTGGGGCATAAGCCCTTTTAATAACTGGGGCAAAAGCCCTTTCA
Done.