Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: At_chr2
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: 61750188
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.32
Warning! 1877335 characters in sequence are not A, C, G, or T
File 102 of 186
Found at i:33406746 original size:29 final size:29
Alignment explanation
Indices: 33406721--33406775 Score: 76
Period size: 29 Copynumber: 1.9 Consensus size: 29
33406711 TCGCTCAATT
* *
33406721 ATAAAATATTTT-ATTTTAAACACTCAAA
1 ATAAAAAATTTTCAATTTAAACACTCAAA
*
33406749 ATAAAAAATTTTCAATTTAGACACTCA
1 ATAAAAAATTTTCAATTTAAACACTCA
33406776 TGTTATATAG
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
28 11 0.48
29 12 0.52
ACGTcount: A:0.49, C:0.13, G:0.02, T:0.36
Consensus pattern (29 bp):
ATAAAAAATTTTCAATTTAAACACTCAAA
Found at i:33411650 original size:14 final size:14
Alignment explanation
Indices: 33411631--33411690 Score: 57
Period size: 14 Copynumber: 3.9 Consensus size: 14
33411621 AAATTAATGA
33411631 ATTTTTATTTTTAT
1 ATTTTTATTTTTAT
33411645 ATTTTTATTATTATAT
1 ATTTTTATT-TT-TAT
33411661 ATTTTGTAAAATTTTTAT
1 ATTTT-T---ATTTTTAT
*
33411679 ATATTTATTTTT
1 ATTTTTATTTTT
33411691 TAAAAATTGA
Statistics
Matches: 39, Mismatches: 1, Indels: 12
0.75 0.02 0.23
Matches are distributed among these distances:
14 15 0.38
15 2 0.05
16 8 0.21
17 2 0.05
18 7 0.18
19 2 0.05
20 3 0.08
ACGTcount: A:0.28, C:0.00, G:0.02, T:0.70
Consensus pattern (14 bp):
ATTTTTATTTTTAT
Found at i:33411694 original size:24 final size:26
Alignment explanation
Indices: 33411645--33411695 Score: 72
Period size: 26 Copynumber: 2.0 Consensus size: 26
33411635 TTATTTTTAT
33411645 ATTTTTATTATTATATATTTTGTAAA
1 ATTTTTATTATTATATATTTTGTAAA
33411671 ATTTTTATATATT-TAT-TTTT-TAAA
1 ATTTTTAT-TATTATATATTTTGTAAA
33411695 A
1 A
33411696 ATTGATATAT
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
24 5 0.21
25 4 0.17
26 11 0.46
27 4 0.17
ACGTcount: A:0.35, C:0.00, G:0.02, T:0.63
Consensus pattern (26 bp):
ATTTTTATTATTATATATTTTGTAAA
Found at i:33415538 original size:18 final size:17
Alignment explanation
Indices: 33415506--33415539 Score: 50
Period size: 18 Copynumber: 1.9 Consensus size: 17
33415496 TCGGTAATAT
*
33415506 AATTTTAATTTTTTATG
1 AATTTTAAATTTTTATG
33415523 AATTTTAAAATTTTTAT
1 AATTTT-AAATTTTTAT
33415540 TTAATTGAAA
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:0.35, C:0.00, G:0.03, T:0.62
Consensus pattern (17 bp):
AATTTTAAATTTTTATG
Found at i:33425813 original size:13 final size:13
Alignment explanation
Indices: 33425795--33425819 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
33425785 TAATTAAGAG
33425795 AATGATTGATTAC
1 AATGATTGATTAC
33425808 AATGATTGATTA
1 AATGATTGATTA
33425820 AAATAATTCA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.40, C:0.04, G:0.16, T:0.40
Consensus pattern (13 bp):
AATGATTGATTAC
Found at i:33440215 original size:46 final size:46
Alignment explanation
Indices: 33440148--33440320 Score: 210
Period size: 46 Copynumber: 3.7 Consensus size: 46
33440138 TGTAACCCGC
* *
33440148 CCATAAGTGAACTCGGACTCAACTCAACGAGCTCAGGCGTTCGCAT
1 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCAGACGTTCGCAT
* *
33440194 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGATGCCTAGTT-ACAT
1 CCATAAGTGAACTCGGACTCAACTCAACGAGTTC--A-GAC--GTTCGCAT
* * *
33440244 -C-TCA-CGAACTCGGACTCAACTCAACGAGTTCAGACATTCGCAT
1 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCAGACGTTCGCAT
33440287 CCATAAGTGAACTCGGACTCAACTCAACGAGTTC
1 CCATAAGTGAACTCGGACTCAACTCAACGAGTTC
33440321 GGATGCTCAA
Statistics
Matches: 108, Mismatches: 10, Indels: 18
0.79 0.07 0.13
Matches are distributed among these distances:
42 2 0.02
43 3 0.03
44 3 0.03
45 3 0.03
46 59 0.55
47 26 0.24
48 3 0.03
49 3 0.03
50 3 0.03
51 3 0.03
ACGTcount: A:0.30, C:0.29, G:0.19, T:0.21
Consensus pattern (46 bp):
CCATAAGTGAACTCGGACTCAACTCAACGAGTTCAGACGTTCGCAT
Found at i:33440268 original size:93 final size:93
Alignment explanation
Indices: 33440156--33440326 Score: 315
Period size: 93 Copynumber: 1.8 Consensus size: 93
33440146 GCCCATAAGT
* *
33440156 GAACTCGGACTCAACTCAACGAGCTCAGGCGTTCGCATCCATAAGTGAACTCGGACTCAACTCAA
1 GAACTCGGACTCAACTCAACGAGCTCAGACATTCGCATCCATAAGTGAACTCGGACTCAACTCAA
33440221 CGAGTTCGGATGCCTAGTTACATCTCAC
66 CGAGTTCGGATGCCTAGTTACATCTCAC
*
33440249 GAACTCGGACTCAACTCAACGAGTTCAGACATTCGCATCCATAAGTGAACTCGGACTCAACTCAA
1 GAACTCGGACTCAACTCAACGAGCTCAGACATTCGCATCCATAAGTGAACTCGGACTCAACTCAA
33440314 CGAGTTCGGATGC
66 CGAGTTCGGATGC
33440327 TCAATCATCC
Statistics
Matches: 75, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
93 75 1.00
ACGTcount: A:0.29, C:0.29, G:0.20, T:0.21
Consensus pattern (93 bp):
GAACTCGGACTCAACTCAACGAGCTCAGACATTCGCATCCATAAGTGAACTCGGACTCAACTCAA
CGAGTTCGGATGCCTAGTTACATCTCAC
Found at i:33444747 original size:14 final size:14
Alignment explanation
Indices: 33444728--33444760 Score: 66
Period size: 14 Copynumber: 2.4 Consensus size: 14
33444718 TAAAAATCAA
33444728 ACATAGAAATTCAT
1 ACATAGAAATTCAT
33444742 ACATAGAAATTCAT
1 ACATAGAAATTCAT
33444756 ACATA
1 ACATA
33444761 AATAAATCAT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 19 1.00
ACGTcount: A:0.52, C:0.15, G:0.06, T:0.27
Consensus pattern (14 bp):
ACATAGAAATTCAT
Found at i:33446290 original size:67 final size:66
Alignment explanation
Indices: 33446176--33446360 Score: 221
Period size: 67 Copynumber: 2.8 Consensus size: 66
33446166 AGAACAATTT
** * *
33446176 CTTT-ACTATTTTCATTAAAAAGTTAATTTTAATCACACACCGACTAGATAATACTCTCATAGTT
1 CTTTCACTATTTTCATT-AAAAGTTAATTTTAATCACACATTGGCTAGAGAATACTCTCATAGTT
33446240 AA
65 AA
*
33446242 CTTTCACTATTTTCATTGAAAAGTTAATTTTAATCTCACATTGGCTAGAGAATACTCTCATAGTT
1 CTTTCACTATTTTCATT-AAAAGTTAATTTTAATCACACATTGGCTAGAGAATACTCTCATAGTT
*
33446307 CA
65 AA
** * * *
33446309 CTTTTTCACTA-TTTCATTAAAAAATATTTTTAATCCCACATTAGCTAGAGAA
1 C--TTTCACTATTTTCATTAAAAGTTAATTTTAATCACACATTGGCTAGAGAA
33446361 CATTCACATG
Statistics
Matches: 104, Mismatches: 12, Indels: 5
0.86 0.10 0.04
Matches are distributed among these distances:
66 4 0.04
67 85 0.82
68 7 0.07
69 8 0.08
ACGTcount: A:0.35, C:0.18, G:0.08, T:0.39
Consensus pattern (66 bp):
CTTTCACTATTTTCATTAAAAGTTAATTTTAATCACACATTGGCTAGAGAATACTCTCATAGTTA
A
Found at i:33454503 original size:48 final size:48
Alignment explanation
Indices: 33454449--33454630 Score: 197
Period size: 48 Copynumber: 3.8 Consensus size: 48
33454439 AGGGTTATGA
33454449 GAGCTAGTGTAAGACCATGTCT-GAGACATGGCATCGGCCTCGATTTAT
1 GAGCTAGTGTAAGACCATGTCTGGA-ACATGGCATCGGCCTCGATTTAT
* * **** * * *
33454497 GAGCTAGTGTAAGACCATATTTGGAACATGGCATCAATATTGA-TAAGA
1 GAGCTAGTGTAAGACCATGTCTGGAACATGGCATCGGCCTCGATTTA-T
* * * *
33454545 GAGCTAATGTAAGACCATGTCCGGGACATGGCATCGGCCTCGATATAT
1 GAGCTAGTGTAAGACCATGTCTGGAACATGGCATCGGCCTCGATTTAT
* *
33454593 GAGCTAGTGTATGACCATGTTTGGAACATGGCATCGGC
1 GAGCTAGTGTAAGACCATGTCTGGAACATGGCATCGGC
33454631 ACCGGCACCG
Statistics
Matches: 104, Mismatches: 27, Indels: 6
0.76 0.20 0.04
Matches are distributed among these distances:
47 2 0.02
48 99 0.95
49 3 0.03
ACGTcount: A:0.29, C:0.19, G:0.27, T:0.26
Consensus pattern (48 bp):
GAGCTAGTGTAAGACCATGTCTGGAACATGGCATCGGCCTCGATTTAT
Found at i:33454616 original size:96 final size:96
Alignment explanation
Indices: 33454447--33454627 Score: 308
Period size: 96 Copynumber: 1.9 Consensus size: 96
33454437 CTAGGGTTAT
* * *
33454447 GAGAGCTAGTGTAAGACCATGTCTGAGACATGGCATCGGCCTCGATTTATGAGCTAGTGTAAGAC
1 GAGAGCTAATGTAAGACCATGTCCGAGACATGGCATCGGCCTCGATATATGAGCTAGTGTAAGAC
33454512 CATATTTGGAACATGGCATCAATATTGATAA
66 CATATTTGGAACATGGCATCAATATTGATAA
* *
33454543 GAGAGCTAATGTAAGACCATGTCCGGGACATGGCATCGGCCTCGATATATGAGCTAGTGTATGAC
1 GAGAGCTAATGTAAGACCATGTCCGAGACATGGCATCGGCCTCGATATATGAGCTAGTGTAAGAC
*
33454608 CATGTTTGGAACATGGCATC
66 CATATTTGGAACATGGCATC
33454628 GGCACCGGCA
Statistics
Matches: 79, Mismatches: 6, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
96 79 1.00
ACGTcount: A:0.29, C:0.18, G:0.27, T:0.26
Consensus pattern (96 bp):
GAGAGCTAATGTAAGACCATGTCCGAGACATGGCATCGGCCTCGATATATGAGCTAGTGTAAGAC
CATATTTGGAACATGGCATCAATATTGATAA
Found at i:33455454 original size:30 final size:30
Alignment explanation
Indices: 33455399--33455469 Score: 97
Period size: 30 Copynumber: 2.3 Consensus size: 30
33455389 TTGTCTACAC
*
33455399 GTGTAGACACACGGGCGTGTGTCTAGACCGT
1 GTGT-GACACACGGGCATGTGTCTAGACCGT
* * *
33455430 GTGTGACACATGGGCATGTTTCTAGACTGT
1 GTGTGACACACGGGCATGTGTCTAGACCGT
33455460 GTGTGACACA
1 GTGTGACACA
33455470 GGGTTTGCCC
Statistics
Matches: 36, Mismatches: 4, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
30 32 0.89
31 4 0.11
ACGTcount: A:0.21, C:0.20, G:0.32, T:0.27
Consensus pattern (30 bp):
GTGTGACACACGGGCATGTGTCTAGACCGT
Found at i:33457128 original size:43 final size:41
Alignment explanation
Indices: 33456981--33457128 Score: 138
Period size: 43 Copynumber: 3.5 Consensus size: 41
33456971 TATGTGTTAT
* *
33456981 CGTGTAAGACCACGTCTGGGACATTAGCATC-TACTTATGATTTA
1 CGTGTAAGACCAAGTCTGGGACA-TGGCATCGTA-TT-TGA-TTA
* * *
33457025 CGTGTAAGACCAAGTCTGGGACATCGACATTGTATTTGATTT
1 CGTGTAAGACCAAGTCTGGGACAT-GGCATCGTATTTGATTA
* *
33457067 TGTGTAAGACCCTA-TCTGGGACAGTGGCATCGATATTTGATTA
1 CGTGTAAGA-CCAAGTCTGGGACA-TGGCATCG-TATTTGATTA
*
33457110 CATGTAAGACCAAGTCTGG
1 CGTGTAAGACCAAGTCTGG
33457129 ATGTTGGCAT
Statistics
Matches: 85, Mismatches: 13, Indels: 13
0.77 0.12 0.12
Matches are distributed among these distances:
42 27 0.32
43 29 0.34
44 27 0.32
45 2 0.02
ACGTcount: A:0.27, C:0.18, G:0.24, T:0.31
Consensus pattern (41 bp):
CGTGTAAGACCAAGTCTGGGACATGGCATCGTATTTGATTA
Found at i:33476144 original size:42 final size:43
Alignment explanation
Indices: 33476044--33476180 Score: 120
Period size: 43 Copynumber: 3.2 Consensus size: 43
33476034 TGTGTTATCG
* * * * *
33476044 TGTAAGACCACGTTTGGGA-AGTTGGCATCGACT-TATGATTTACG
1 TGTAAGACCATGTTTGGGACA-ATGACATCGA-TATTTGATTT-CA
* *
33476088 TGTAAGGCCATGTTTGGGAC-ATCGACATC-ATATTTGATTTCT
1 TGTAAGACCATGTTTGGGACAAT-GACATCGATATTTGATTTCA
* * *
33476130 TGTAAGACCCTGTTTGGGACAATGTCATCGATATTTGATTACA
1 TGTAAGACCATGTTTGGGACAATGACATCGATATTTGATTTCA
33476173 TGTAAGAC
1 TGTAAGAC
33476181 TAAGTCTGGG
Statistics
Matches: 77, Mismatches: 11, Indels: 11
0.78 0.11 0.11
Matches are distributed among these distances:
42 25 0.32
43 30 0.39
44 22 0.29
ACGTcount: A:0.26, C:0.16, G:0.23, T:0.34
Consensus pattern (43 bp):
TGTAAGACCATGTTTGGGACAATGACATCGATATTTGATTTCA
Found at i:33490371 original size:13 final size:13
Alignment explanation
Indices: 33490348--33490381 Score: 50
Period size: 13 Copynumber: 2.5 Consensus size: 13
33490338 AAACATATTA
33490348 TAAACATTTTGTGT
1 TAAA-ATTTTGTGT
33490362 TAAAATTTTGTGT
1 TAAAATTTTGTGT
33490375 TAGAAAT
1 TA-AAAT
33490382 AATAAAATAA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
13 11 0.58
14 8 0.42
ACGTcount: A:0.35, C:0.03, G:0.15, T:0.47
Consensus pattern (13 bp):
TAAAATTTTGTGT
Found at i:33491734 original size:40 final size:40
Alignment explanation
Indices: 33491689--33491851 Score: 240
Period size: 40 Copynumber: 4.1 Consensus size: 40
33491679 CTAAGATCCA
*
33491689 AAGGCATTTGTGCTAGTGACTATATCCGGGCTAAGTCCCG
1 AAGGCATTTGTGCGAGTGACTATATCCGGGCTAAGTCCCG
* * *
33491729 AAGGCATTTGTGCGAGTTACTATATTCGGGCCAAGTCCCG
1 AAGGCATTTGTGCGAGTGACTATATCCGGGCTAAGTCCCG
* *
33491769 AAGGCATTTGTGTGAGTTACTATATCCGGGCTAAGTCCCG
1 AAGGCATTTGTGCGAGTGACTATATCCGGGCTAAGTCCCG
*
33491809 AAGGCATTTGTGCGAGTTG-CTATATCC-GGCTAAATCCCG
1 AAGGCATTTGTGCGAG-TGACTATATCCGGGCTAAGTCCCG
33491848 AAGG
1 AAGG
33491852 TACTTGGGTT
Statistics
Matches: 112, Mismatches: 10, Indels: 3
0.90 0.08 0.02
Matches are distributed among these distances:
39 15 0.13
40 96 0.86
41 1 0.01
ACGTcount: A:0.23, C:0.21, G:0.28, T:0.28
Consensus pattern (40 bp):
AAGGCATTTGTGCGAGTGACTATATCCGGGCTAAGTCCCG
Found at i:33497515 original size:48 final size:48
Alignment explanation
Indices: 33497437--33497574 Score: 204
Period size: 48 Copynumber: 2.9 Consensus size: 48
33497427 TAGGGTTATT
*
33497437 AGAGCTAGTGTAAGACCATGTCTGGGACATGGCATCGGCCTCAATATG
1 AGAGCTAGTGTAAGACCATGTCTGGGACATGGCATCGGCATCAATATG
* * * ** **
33497485 TGAGGTAGTGTAAGACCATGTTTGAAACATGGCATCGGCATTGATATG
1 AGAGCTAGTGTAAGACCATGTCTGGGACATGGCATCGGCATCAATATG
33497533 AGAGCTAGTGTAAGACCATGTCTGGGACATGGCATCGGCATC
1 AGAGCTAGTGTAAGACCATGTCTGGGACATGGCATCGGCATC
33497575 TTACCCTTTT
Statistics
Matches: 76, Mismatches: 14, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
48 76 1.00
ACGTcount: A:0.28, C:0.18, G:0.30, T:0.25
Consensus pattern (48 bp):
AGAGCTAGTGTAAGACCATGTCTGGGACATGGCATCGGCATCAATATG
Found at i:33499198 original size:27 final size:27
Alignment explanation
Indices: 33499157--33499248 Score: 103
Period size: 27 Copynumber: 3.4 Consensus size: 27
33499147 GGGCAAACTA
* *
33499157 GTCATTTTACCCTACAGGGGTATGTCG
1 GTCATTTTACACTACAAGGGTATGTCG
*
33499184 GTCATTTTACACTACAAGGGTATTTCG
1 GTCATTTTACACTACAAGGGTATGTCG
* * * *
33499211 ATAATTTTACACTACAAAGGTATTTCG
1 GTCATTTTACACTACAAGGGTATGTCG
* *
33499238 ATAATTTTACA
1 GTCATTTTACA
33499249 AATCGGGGGT
Statistics
Matches: 59, Mismatches: 6, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
27 59 1.00
ACGTcount: A:0.29, C:0.17, G:0.16, T:0.37
Consensus pattern (27 bp):
GTCATTTTACACTACAAGGGTATGTCG
Found at i:33499263 original size:27 final size:27
Alignment explanation
Indices: 33499200--33499511 Score: 305
Period size: 27 Copynumber: 11.7 Consensus size: 27
33499190 TTACACTACA
* *
33499200 AGGGTATTTCGATAATTTTAC-ACTACA
1 AGGGTATTTCGATAATTTTACAAAT-CG
*
33499227 AAGGTATTTCGATAATTTTACAAATCG
1 AGGGTATTTCGATAATTTTACAAATCG
* * *
33499254 GGGGTGTTTCGATAAATTTACAAATCG
1 AGGGTATTTCGATAATTTTACAAATCG
* * * *
33499281 AGGGTATTTTGGTAATTTCAC-AATAG
1 AGGGTATTTCGATAATTTTACAAATCG
* *
33499307 AGGGTATTTC-AGTAATTTCACAAATAG
1 AGGGTATTTCGA-TAATTTTACAAATCG
* *
33499334 AGGGTATTTTGGTAATTTTACAAATCG
1 AGGGTATTTCGATAATTTTACAAATCG
* *
33499361 AGGGTATTTTGGTAATTTTACAAATCG
1 AGGGTATTTCGATAATTTTACAAATCG
* * * * * *
33499388 AGGTTATTTTGGTAATTTTA-TAGTCA
1 AGGGTATTTCGATAATTTTACAAATCG
33499414 AGGGTATTTCGATAATTTTACAAATCG
1 AGGGTATTTCGATAATTTTACAAATCG
* *
33499441 AGGGTAATTC-AGTAATTTCAC-AATCG
1 AGGGTATTTCGA-TAATTTTACAAATCG
* *
33499467 AAGGTATTTCGGTAATTTTACAAATCG
1 AGGGTATTTCGATAATTTTACAAATCG
33499494 AGGGTATTTC-AGTAATTT
1 AGGGTATTTCGA-TAATTT
33499512 CTCTTTATTA
Statistics
Matches: 238, Mismatches: 38, Indels: 18
0.81 0.13 0.06
Matches are distributed among these distances:
26 64 0.27
27 172 0.72
28 2 0.01
ACGTcount: A:0.32, C:0.10, G:0.20, T:0.38
Consensus pattern (27 bp):
AGGGTATTTCGATAATTTTACAAATCG
Found at i:33499339 original size:53 final size:53
Alignment explanation
Indices: 33499200--33499512 Score: 306
Period size: 53 Copynumber: 5.9 Consensus size: 53
33499190 TTACACTACA
* * * * * * * *
33499200 AGGGTATTTCGATAATTTTAC-ACTACAAAGGTATTTCGATAATTTTACAAATCG
1 AGGGTATTTCGGTAATTTTACAAAT-CGAGGGTATTTTGGTAATTTCAC-AATAG
* * * *
33499254 GGGGTGTTTCGATAAATTTACAAATCGAGGGTATTTTGGTAATTTCACAATAG
1 AGGGTATTTCGGTAATTTTACAAATCGAGGGTATTTTGGTAATTTCACAATAG
* * * * *
33499307 AGGGTATTTCAGTAATTTCACAAATAGAGGGTATTTTGGTAATTTTACAAATCG
1 AGGGTATTTCGGTAATTTTACAAATCGAGGGTATTTTGGTAATTTCAC-AATAG
* * * * *
33499361 AGGGTATTTTGGTAATTTTACAAATCGAGGTTATTTTGGTAATTTTATAGTCA-
1 AGGGTATTTCGGTAATTTTACAAATCGAGGGTATTTTGGTAATTTCACAAT-AG
* * ** *
33499414 AGGGTATTTCGATAATTTTACAAATCGAGGGTAATTCAGTAATTTCACAATCG
1 AGGGTATTTCGGTAATTTTACAAATCGAGGGTATTTTGGTAATTTCACAATAG
* **
33499467 AAGGTATTTCGGTAATTTTACAAATCGAGGGTATTTCAGTAATTTC
1 AGGGTATTTCGGTAATTTTACAAATCGAGGGTATTTTGGTAATTTC
33499513 TCTTTATTAT
Statistics
Matches: 215, Mismatches: 40, Indels: 9
0.81 0.15 0.03
Matches are distributed among these distances:
53 131 0.61
54 82 0.38
55 2 0.01
ACGTcount: A:0.32, C:0.10, G:0.20, T:0.38
Consensus pattern (53 bp):
AGGGTATTTCGGTAATTTTACAAATCGAGGGTATTTTGGTAATTTCACAATAG
Found at i:33499354 original size:80 final size:80
Alignment explanation
Indices: 33499229--33499511 Score: 338
Period size: 80 Copynumber: 3.5 Consensus size: 80
33499219 ACACTACAAA
* * * * *
33499229 GGTATTTCGATAATTTTACAAATCGGGGGTGTTTCGATAAATTTACAAATCGAGGGTATTTTGGT
1 GGTATTTCGGTAATTTTACAAATAGAGGGTATTTCGATAATTTTACAAATCGAGGGTATTTTGGT
*
33499294 AATTTCACAATAGAG
66 AATTTCACAATCGAG
* * * *
33499309 GGTATTTCAGTAATTTCACAAATAGAGGGTATTTTGGTAATTTTACAAATCGAGGGTATTTTGGT
1 GGTATTTCGGTAATTTTACAAATAGAGGGTATTTCGATAATTTTACAAATCGAGGGTATTTTGGT
*
33499374 AATTTTACAAATCGAG
66 AATTTCAC-AATCGAG
* * * * * **
33499390 GTTATTTTGGTAATTTTA-TAGTCA-AGGGTATTTCGATAATTTTACAAATCGAGGGTAATTCAG
1 GGTATTTCGGTAATTTTACAAAT-AGAGGGTATTTCGATAATTTTACAAATCGAGGGTATTTTGG
*
33499453 TAATTTCACAATCGAA
65 TAATTTCACAATCGAG
*
33499469 GGTATTTCGGTAATTTTACAAATCGAGGGTATTTC-AGTAATTT
1 GGTATTTCGGTAATTTTACAAATAGAGGGTATTTCGA-TAATTT
33499512 CTCTTTATTA
Statistics
Matches: 169, Mismatches: 29, Indels: 10
0.81 0.14 0.05
Matches are distributed among these distances:
79 23 0.14
80 125 0.74
81 21 0.12
ACGTcount: A:0.31, C:0.10, G:0.20, T:0.39
Consensus pattern (80 bp):
GGTATTTCGGTAATTTTACAAATAGAGGGTATTTCGATAATTTTACAAATCGAGGGTATTTTGGT
AATTTCACAATCGAG
Found at i:33509553 original size:28 final size:27
Alignment explanation
Indices: 33509501--33509592 Score: 103
Period size: 28 Copynumber: 3.3 Consensus size: 27
33509491 TGGCCCCTTT
* * *
33509501 AGGCCCAATCTCGTTCACATGGCCCATC
1 AGGCCCAATCACATTCATAT-GCCCATC
* * *
33509529 AGGCCTAATCATATTTATATTGCCCATC
1 AGGCCCAATCACATTCATA-TGCCCATC
33509557 AGGCCCAATCACATTCATATGACCCATC
1 AGGCCCAATCACATTCATATG-CCCATC
33509585 AGGCCCAA
1 AGGCCCAA
33509593 CTGCTTCCCA
Statistics
Matches: 53, Mismatches: 9, Indels: 4
0.80 0.14 0.06
Matches are distributed among these distances:
27 2 0.04
28 50 0.94
29 1 0.02
ACGTcount: A:0.28, C:0.34, G:0.14, T:0.24
Consensus pattern (27 bp):
AGGCCCAATCACATTCATATGCCCATC
Found at i:33513477 original size:19 final size:20
Alignment explanation
Indices: 33513427--33513489 Score: 85
Period size: 19 Copynumber: 3.1 Consensus size: 20
33513417 ACTATTTTTA
33513427 TTAAAAA-TTAATTTTAATCC
1 TTAAAAAGTTAATTTTAAT-C
33513447 TTCAAAAAGTTAATTTTAA-C
1 TT-AAAAAGTTAATTTTAATC
*
33513467 TTAAAAGGTTAATTTTAATC
1 TTAAAAAGTTAATTTTAATC
33513487 TTA
1 TTA
33513490 CAGCTAGAGA
Statistics
Matches: 39, Mismatches: 1, Indels: 6
0.85 0.02 0.13
Matches are distributed among these distances:
19 15 0.38
20 9 0.23
21 5 0.13
22 10 0.26
ACGTcount: A:0.43, C:0.08, G:0.05, T:0.44
Consensus pattern (20 bp):
TTAAAAAGTTAATTTTAATC
Found at i:33515756 original size:10 final size:11
Alignment explanation
Indices: 33515735--33515785 Score: 56
Period size: 10 Copynumber: 4.9 Consensus size: 11
33515725 AAAATGATAG
33515735 GAAATTATTTAA
1 GAAATTA-TTAA
33515747 -AAATTATTAA
1 GAAATTATTAA
*
33515757 -ACATTA-TAA
1 GAAATTATTAA
33515766 GAAATTA-TAA
1 GAAATTATTAA
33515776 GAAATTATTA
1 GAAATTATTA
33515786 TTTTTTTAAA
Statistics
Matches: 35, Mismatches: 2, Indels: 5
0.83 0.05 0.12
Matches are distributed among these distances:
9 3 0.09
10 24 0.69
11 8 0.23
ACGTcount: A:0.55, C:0.02, G:0.06, T:0.37
Consensus pattern (11 bp):
GAAATTATTAA
Found at i:33515770 original size:31 final size:30
Alignment explanation
Indices: 33515712--33515785 Score: 80
Period size: 31 Copynumber: 2.4 Consensus size: 30
33515702 GAGTAGTTTC
*
33515712 TTAAATAATTA-TAAAAATGATAGGAAATTA
1 TTAAA-AATTATTAAAAATGATAAGAAATTA
* *
33515742 TTTAAAAATTATTAAACATTATAAGAAATTA
1 -TTAAAAATTATTAAAAATGATAAGAAATTA
33515773 -TAAGAAATTATTA
1 TTAA-AAATTATTA
33515786 TTTTTTTAAA
Statistics
Matches: 38, Mismatches: 3, Indels: 5
0.83 0.07 0.11
Matches are distributed among these distances:
29 3 0.08
30 14 0.37
31 21 0.55
ACGTcount: A:0.55, C:0.01, G:0.07, T:0.36
Consensus pattern (30 bp):
TTAAAAATTATTAAAAATGATAAGAAATTA
Found at i:33516548 original size:40 final size:40
Alignment explanation
Indices: 33516450--33516940 Score: 585
Period size: 40 Copynumber: 12.2 Consensus size: 40
33516440 TGTTTAATAA
* * *
33516450 AAACGCCGC-AAAAACTGAACAATAGCGGCATTTTTGGCC
1 AAACGCCACTAAAAACTGATCAATAGCGGCGTTTTTGGCC
33516489 AAAACGCCACTAAAAACTGATCAATAGCGGCGTTTTTGGCC
1 -AAACGCCACTAAAAACTGATCAATAGCGGCGTTTTTGGCC
* * *
33516530 AAGCGCCACTAAAAACTGATCAATTGCGGCGTTTTTAGCCC
1 AAACGCCACTAAAAACTGATCAATAGCGGCGTTTTT-GGCC
* * * * *
33516571 AAACGCCACTAAAAACTTATGAATAGCAGCATTTTTGTCC
1 AAACGCCACTAAAAACTGATCAATAGCGGCGTTTTTGGCC
33516611 AAACGCCACTAAAAACTGATCAATAGCGGCGTTTTTGGCC
1 AAACGCCACTAAAAACTGATCAATAGCGGCGTTTTTGGCC
** *
33516651 AAACGCCACTAAAAACTGATCAATAATGGCGTTTTTGTCC
1 AAACGCCACTAAAAACTGATCAATAGCGGCGTTTTTGGCC
* * * * *
33516691 AAACGCCACTAAAAATTGATTAATAACGGCATTTTTTGCCC
1 AAACGCCACTAAAAACTGATCAATAGCGGC-GTTTTTGGCC
* * * * * **
33516732 AAGCACCACTAAAAACTAATTAATAGCGGCATTTTTCTTCC
1 AAACGCCACTAAAAACTGATCAATAGCGGCGTTTTT-GGCC
* *
33516773 AAACGCCACTAAAAACTTG-TGAATAGCGGCGTTTTTGGTC
1 AAACGCCACTAAAAAC-TGATCAATAGCGGCGTTTTTGGCC
* **
33516813 AAACGCCACTAAAAACTTATCAATAGCGGCGTTTTTATCCC
1 AAACGCCACTAAAAACTGATCAATAGCGGCGTTTTT-GGCC
33516854 AAACGCCACTAAAAA-TGATCAATAGCGGCGTTTTTGGTCC
1 AAACGCCACTAAAAACTGATCAATAGCGGCGTTTTTGG-CC
* *
33516894 AAACGCCACT-AAAACTCATCAATAGCGGTGTTTTTGGTCC
1 AAACGCCACTAAAAACTGATCAATAGCGGCGTTTTTGG-CC
33516934 AAACGCC
1 AAACGCC
33516941 GCAAAATGTT
Statistics
Matches: 390, Mismatches: 52, Indels: 18
0.85 0.11 0.04
Matches are distributed among these distances:
39 5 0.01
40 243 0.62
41 141 0.36
42 1 0.00
ACGTcount: A:0.34, C:0.24, G:0.17, T:0.25
Consensus pattern (40 bp):
AAACGCCACTAAAAACTGATCAATAGCGGCGTTTTTGGCC
Found at i:33516559 original size:81 final size:80
Alignment explanation
Indices: 33516450--33516940 Score: 612
Period size: 81 Copynumber: 6.1 Consensus size: 80
33516440 TGTTTAATAA
* * *
33516450 AAACGCCGC-AAAAACTGAACAATAGCGGCATTTTTGGCCAAAACGCCACTAAAAACTGATCAAT
1 AAACGCCACTAAAAACTGATCAATAGCGGCGTTTTTGGCC-AAACGCCACTAAAAACTGATCAAT
*
33516514 AGCGGCGTTTTTGGCC
65 AGCGGCGTTTTTGTCC
* * * * *
33516530 AAGCGCCACTAAAAACTGATCAATTGCGGCGTTTTTAGCCCAAACGCCACTAAAAACTTATGAAT
1 AAACGCCACTAAAAACTGATCAATAGCGGCGTTTTT-GGCCAAACGCCACTAAAAACTGATCAAT
* *
33516595 AGCAGCATTTTTGTCC
65 AGCGGCGTTTTTGTCC
33516611 AAACGCCACTAAAAACTGATCAATAGCGGCGTTTTTGGCCAAACGCCACTAAAAACTGATCAATA
1 AAACGCCACTAAAAACTGATCAATAGCGGCGTTTTTGGCCAAACGCCACTAAAAACTGATCAATA
**
33516676 ATGGCGTTTTTGTCC
66 GCGGCGTTTTTGTCC
* * * * * * * * *
33516691 AAACGCCACTAAAAATTGATTAATAACGGCATTTTTTGCCCAAGCACCACTAAAAACTAATTAAT
1 AAACGCCACTAAAAACTGATCAATAGCGGC-GTTTTTGGCCAAACGCCACTAAAAACTGATCAAT
* *
33516756 AGCGGCATTTTTCTTCC
65 AGCGGCGTTTTT-GTCC
* * *
33516773 AAACGCCACTAAAAACTTG-TGAATAGCGGCGTTTTTGGTCAAACGCCACTAAAAACTTATCAAT
1 AAACGCCACTAAAAAC-TGATCAATAGCGGCGTTTTTGGCCAAACGCCACTAAAAACTGATCAAT
*
33516837 AGCGGCGTTTTTATCCC
65 AGCGGCGTTTTTGT-CC
*
33516854 AAACGCCACTAAAAA-TGATCAATAGCGGCGTTTTTGGTCCAAACGCCACT-AAAACTCATCAAT
1 AAACGCCACTAAAAACTGATCAATAGCGGCGTTTTTGG-CCAAACGCCACTAAAAACTGATCAAT
*
33516917 AGCGGTGTTTTTGGTCC
65 AGCGGCGTTTTT-GTCC
33516934 AAACGCC
1 AAACGCC
33516941 GCAAAATGTT
Statistics
Matches: 352, Mismatches: 50, Indels: 18
0.84 0.12 0.04
Matches are distributed among these distances:
79 2 0.01
80 122 0.35
81 196 0.56
82 30 0.09
83 2 0.01
ACGTcount: A:0.34, C:0.24, G:0.17, T:0.25
Consensus pattern (80 bp):
AAACGCCACTAAAAACTGATCAATAGCGGCGTTTTTGGCCAAACGCCACTAAAAACTGATCAATA
GCGGCGTTTTTGTCC
Found at i:33516622 original size:121 final size:120
Alignment explanation
Indices: 33516450--33516940 Score: 616
Period size: 121 Copynumber: 4.1 Consensus size: 120
33516440 TGTTTAATAA
* * * *
33516450 AAACGCCGC-AAAAACTGAACAATAGCGGCATTTTTGGCCAAAACGCCACTAAAAACTGATCAAT
1 AAACGCCACTAAAAACTTATCAATAGCGGCATTTTTGTCC-AAACGCCACTAAAAACTGATCAAT
* * *
33516514 AGCGGCGTTTTTGGCCAAGCGCCACTAAAAACTGATCAATTGCGGCGTTTTTAGCCC
65 AGCGGCGTTTTTGGCCAAACGCCACTAAAAACTGATCAATAGCGGCGTTTTT-GTCC
* *
33516571 AAACGCCACTAAAAACTTATGAATAGCAGCATTTTTGTCCAAACGCCACTAAAAACTGATCAATA
1 AAACGCCACTAAAAACTTATCAATAGCGGCATTTTTGTCCAAACGCCACTAAAAACTGATCAATA
**
33516636 GCGGCGTTTTTGGCCAAACGCCACTAAAAACTGATCAATAATGGCGTTTTTGTCC
66 GCGGCGTTTTTGGCCAAACGCCACTAAAAACTGATCAATAGCGGCGTTTTTGTCC
* * * * * * *
33516691 AAACGCCACTAAAAA-TTGATTAATAACGGCATTTTTTGCCCAAGCACCACTAAAAACTAATTAA
1 AAACGCCACTAAAAACTT-ATCAATAGCGGCA-TTTTTGTCCAAACGCCACTAAAAACTGATCAA
* ** *
33516755 TAGCGGCATTTTTCTTCCAAACGCCACTAAAAACTTG-TGAATAGCGGCGTTTTTGGT-C
64 TAGCGGCGTTTTT-GGCCAAACGCCACTAAAAAC-TGATCAATAGCGGCGTTTTT-GTCC
* *
33516813 AAACGCCACTAAAAACTTATCAATAGCGGCGTTTTTATCCCAAACGCCACTAAAAA-TGATCAAT
1 AAACGCCACTAAAAACTTATCAATAGCGGCATTTTTGT-CCAAACGCCACTAAAAACTGATCAAT
* *
33516877 AGCGGCGTTTTTGGTCCAAACGCCACT-AAAACTCATCAATAGCGGTGTTTTTGGTCC
65 AGCGGCGTTTTTGG-CCAAACGCCACTAAAAACTGATCAATAGCGGCGTTTTT-GTCC
33516934 AAACGCC
1 AAACGCC
33516941 GCAAAATGTT
Statistics
Matches: 319, Mismatches: 40, Indels: 22
0.84 0.10 0.06
Matches are distributed among these distances:
119 3 0.01
120 51 0.16
121 161 0.50
122 98 0.31
123 6 0.02
ACGTcount: A:0.34, C:0.24, G:0.17, T:0.25
Consensus pattern (120 bp):
AAACGCCACTAAAAACTTATCAATAGCGGCATTTTTGTCCAAACGCCACTAAAAACTGATCAATA
GCGGCGTTTTTGGCCAAACGCCACTAAAAACTGATCAATAGCGGCGTTTTTGTCC
Found at i:33517268 original size:21 final size:21
Alignment explanation
Indices: 33517244--33517310 Score: 62
Period size: 21 Copynumber: 3.2 Consensus size: 21
33517234 CCTTAAATCT
*
33517244 TAAACATTAAACCCTAAACCC
1 TAAACATTAAACCATAAACCC
** * *
33517265 TAAATTTTAAAACATAAACCA
1 TAAACATTAAACCATAAACCC
* * *
33517286 TAAACACTAATCCATAAACTC
1 TAAACATTAAACCATAAACCC
33517307 TAAA
1 TAAA
33517311 ACCCTAAACC
Statistics
Matches: 34, Mismatches: 12, Indels: 0
0.74 0.26 0.00
Matches are distributed among these distances:
21 34 1.00
ACGTcount: A:0.52, C:0.24, G:0.00, T:0.24
Consensus pattern (21 bp):
TAAACATTAAACCATAAACCC
Found at i:33517274 original size:28 final size:28
Alignment explanation
Indices: 33517229--33517295 Score: 82
Period size: 28 Copynumber: 2.4 Consensus size: 28
33517219 TGGATTTCTG
*
33517229 TAAACCCTTAAATCTT-AAACATTAAACCC
1 TAAACCC-TAAATCTTAAAACA-TAAACCA
*
33517258 TAAACCCTAAATTTTAAAACATAAACCA
1 TAAACCCTAAATCTTAAAACATAAACCA
*
33517286 TAAACACTAA
1 TAAACCCTAA
33517296 TCCATAAACT
Statistics
Matches: 34, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
28 22 0.65
29 12 0.35
ACGTcount: A:0.51, C:0.24, G:0.00, T:0.25
Consensus pattern (28 bp):
TAAACCCTAAATCTTAAAACATAAACCA
Found at i:33517515 original size:38 final size:41
Alignment explanation
Indices: 33517467--33517553 Score: 117
Period size: 43 Copynumber: 2.1 Consensus size: 41
33517457 GTTTAAGGCC
*
33517467 TATGGTTTA-G-GGTTCAATGG-TAGAATATATTTTAAGTT
1 TATGGTTTAGGCGGTTCAATGGATAGAATATATGTTAAGTT
*
33517505 TATGGTTTAGGCCGGTTCAATGGTATAGTATATATGTTAAGTT
1 TATGGTTTAGG-CGGTTCAATGG-ATAGAATATATGTTAAGTT
33517548 TATGGT
1 TATGGT
33517554 ATGGGCCGGG
Statistics
Matches: 42, Mismatches: 2, Indels: 5
0.86 0.04 0.10
Matches are distributed among these distances:
38 9 0.21
39 1 0.02
41 10 0.24
43 22 0.52
ACGTcount: A:0.26, C:0.05, G:0.25, T:0.44
Consensus pattern (41 bp):
TATGGTTTAGGCGGTTCAATGGATAGAATATATGTTAAGTT
Found at i:33517528 original size:41 final size:42
Alignment explanation
Indices: 33517477--33517562 Score: 120
Period size: 43 Copynumber: 2.0 Consensus size: 42
33517467 TATGGTTTAG
* *
33517477 GGTTCAATGG-TAGAATATATTTTAAGTTTATGGTTTAGGCC
1 GGTTCAATGGATAGAATATATGTTAAGTTTATGGTATAGGCC
* *
33517518 GGTTCAATGGTATAGTATATATGTTAAGTTTATGGTATGGGCC
1 GGTTCAATGG-ATAGAATATATGTTAAGTTTATGGTATAGGCC
33517561 GG
1 GG
33517563 GTTTGTTATC
Statistics
Matches: 39, Mismatches: 4, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
41 10 0.26
43 29 0.74
ACGTcount: A:0.26, C:0.07, G:0.28, T:0.40
Consensus pattern (42 bp):
GGTTCAATGGATAGAATATATGTTAAGTTTATGGTATAGGCC
Found at i:33518734 original size:40 final size:40
Alignment explanation
Indices: 33518633--33518734 Score: 123
Period size: 40 Copynumber: 2.5 Consensus size: 40
33518623 CTGCAGAGGC
* *** *
33518633 ATTAGCGGCGTTTTTGTAAAAATGCTGCTAAAAATAGAGA
1 ATTAGCGGCGCTTTTGTAAAACCACTGCAAAAAATAGAGA
* *
33518673 ATTAGTGGCGCTTTTGTAAAACCACTGCAAAAAATTGAGA
1 ATTAGCGGCGCTTTTGTAAAACCACTGCAAAAAATAGAGA
* *
33518713 TTTAGCGACGCTTTTGTAAAAC
1 ATTAGCGGCGCTTTTGTAAAAC
33518735 GCCACTAAAT
Statistics
Matches: 52, Mismatches: 10, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
40 52 1.00
ACGTcount: A:0.35, C:0.14, G:0.21, T:0.30
Consensus pattern (40 bp):
ATTAGCGGCGCTTTTGTAAAACCACTGCAAAAAATAGAGA
Found at i:33522540 original size:16 final size:15
Alignment explanation
Indices: 33522510--33522562 Score: 70
Period size: 16 Copynumber: 3.4 Consensus size: 15
33522500 TTTATCCTTA
*
33522510 GATTATTTTTCATGT
1 GATTTTTTTTCATGT
33522525 GATTTTTTTTCTATGT
1 GATTTTTTTTC-ATGT
*
33522541 GATTTTTTTCCCATGT
1 GATTTTTTT-TCATGT
33522557 GATTTT
1 GATTTT
33522563 CCATAATCTC
Statistics
Matches: 34, Mismatches: 2, Indels: 3
0.87 0.05 0.08
Matches are distributed among these distances:
15 10 0.29
16 23 0.68
17 1 0.03
ACGTcount: A:0.15, C:0.09, G:0.13, T:0.62
Consensus pattern (15 bp):
GATTTTTTTTCATGT
Found at i:33522802 original size:18 final size:18
Alignment explanation
Indices: 33522776--33522882 Score: 92
Period size: 18 Copynumber: 5.8 Consensus size: 18
33522766 AGATATATAT
*
33522776 CATATCTTACATAATTTA
1 CATAACTTACATAATTTA
*
33522794 CATAACTTACAT--TATA
1 CATAACTTACATAATTTA
* *
33522810 CATAAATATATATCATATCTTA
1 CATAACT-TACAT-A-AT-TTA
* **
33522832 CATAATTTACATAATTCG
1 CATAACTTACATAATTTA
*
33522850 GATAACTTACATAATTTA
1 CATAACTTACATAATTTA
33522868 CATAACTTACATAAT
1 CATAACTTACATAAT
33522883 ACATAAATAT
Statistics
Matches: 69, Mismatches: 14, Indels: 12
0.73 0.15 0.13
Matches are distributed among these distances:
16 9 0.13
17 4 0.06
18 40 0.58
19 2 0.03
20 1 0.01
21 5 0.07
22 8 0.12
ACGTcount: A:0.43, C:0.16, G:0.02, T:0.39
Consensus pattern (18 bp):
CATAACTTACATAATTTA
Found at i:33522845 original size:9 final size:9
Alignment explanation
Indices: 33522782--33522882 Score: 73
Period size: 9 Copynumber: 11.0 Consensus size: 9
33522772 ATATCATATC
33522782 TTACATAAT
1 TTACATAAT
*
33522791 TTACATAAC
1 TTACATAAT
33522800 TTACAT--T
1 TTACATAAT
*
33522807 ATACATAAAT
1 TTACAT-AAT
33522817 ATATATCAT-AT
1 -T-TA-CATAAT
33522828 CTTACATAAT
1 -TTACATAAT
33522838 TTACATAAT
1 TTACATAAT
*** *
33522847 TCGGATAAC
1 TTACATAAT
33522856 TTACATAAT
1 TTACATAAT
*
33522865 TTACATAAC
1 TTACATAAT
33522874 TTACATAAT
1 TTACATAAT
33522883 ACATAAATAT
Statistics
Matches: 70, Mismatches: 15, Indels: 14
0.71 0.15 0.14
Matches are distributed among these distances:
7 5 0.07
9 52 0.74
10 5 0.07
11 3 0.04
12 2 0.03
13 3 0.04
ACGTcount: A:0.44, C:0.15, G:0.02, T:0.40
Consensus pattern (9 bp):
TTACATAAT
Found at i:33527980 original size:13 final size:14
Alignment explanation
Indices: 33527964--33527992 Score: 51
Period size: 13 Copynumber: 2.1 Consensus size: 14
33527954 TTATAAATAT
33527964 TTATAATG-TTTAA
1 TTATAATGATTTAA
33527977 TTATAATGATTTAA
1 TTATAATGATTTAA
33527991 TT
1 TT
33527993 TGTCATTAGT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 8 0.53
14 7 0.47
ACGTcount: A:0.38, C:0.00, G:0.07, T:0.55
Consensus pattern (14 bp):
TTATAATGATTTAA
Found at i:33528465 original size:21 final size:21
Alignment explanation
Indices: 33528414--33528475 Score: 70
Period size: 21 Copynumber: 2.9 Consensus size: 21
33528404 GGTAGCAGAT
* * * *
33528414 AGGGAGGCAACGACAGTAGTG
1 AGGGAGGCAGCGGCAGCAGCG
33528435 AGGGAGGCAGCGGCAGCAGCG
1 AGGGAGGCAGCGGCAGCAGCG
*
33528456 AGGGAGGCAGAGGCGAGCAG
1 AGGGAGGCAGCGGC-AGCAG
33528476 AAAGTATGAT
Statistics
Matches: 35, Mismatches: 5, Indels: 1
0.85 0.12 0.02
Matches are distributed among these distances:
21 30 0.86
22 5 0.14
ACGTcount: A:0.29, C:0.18, G:0.50, T:0.03
Consensus pattern (21 bp):
AGGGAGGCAGCGGCAGCAGCG
Found at i:33534634 original size:27 final size:27
Alignment explanation
Indices: 33534596--33534665 Score: 95
Period size: 27 Copynumber: 2.6 Consensus size: 27
33534586 GAAGCGTCCA
*
33534596 GGTGGCTATGCCACATTTATCTGATCT
1 GGTGGCTCTGCCACATTTATCTGATCT
* *
33534623 GGTGGCTCTGCCACAATTATCTGTTCT
1 GGTGGCTCTGCCACATTTATCTGATCT
* *
33534650 GGTGACTCTGTCACAT
1 GGTGGCTCTGCCACAT
33534666 CATCTGTTCT
Statistics
Matches: 37, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
27 37 1.00
ACGTcount: A:0.17, C:0.24, G:0.23, T:0.36
Consensus pattern (27 bp):
GGTGGCTCTGCCACATTTATCTGATCT
Found at i:33534677 original size:26 final size:27
Alignment explanation
Indices: 33534604--33534677 Score: 87
Period size: 27 Copynumber: 2.8 Consensus size: 27
33534594 CAGGTGGCTA
* * * *
33534604 TGCCACATTTATCTGATCTGGTGGCTC
1 TGCCACAATCATCTGTTCTGGTGACTC
*
33534631 TGCCACAATTATCTGTTCTGGTGACTC
1 TGCCACAATCATCTGTTCTGGTGACTC
*
33534658 TGTCAC-ATCATCTGTTCTGG
1 TGCCACAATCATCTGTTCTGG
33534678 CAGCCATACT
Statistics
Matches: 42, Mismatches: 5, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
26 13 0.31
27 29 0.69
ACGTcount: A:0.16, C:0.26, G:0.20, T:0.38
Consensus pattern (27 bp):
TGCCACAATCATCTGTTCTGGTGACTC
Found at i:33540207 original size:55 final size:54
Alignment explanation
Indices: 33540146--33540253 Score: 173
Period size: 54 Copynumber: 2.0 Consensus size: 54
33540136 TCCCTAGCAC
* *
33540146 TATAAATAGGGGGTGAAGTGACTCTATTT-GGGGGCATCTTTTTTTGTATACACTA
1 TATAAATAGGGGGTGAAGTGA--CTATTTGGGGGGCATCTTTTTCTGTAAACACTA
33540201 TATAAATAGGGGGTGAAGTGACTATTTGGGGGGCATCTTTTTCTGTAAACACT
1 TATAAATAGGGGGTGAAGTGACTATTTGGGGGGCATCTTTTTCTGTAAACACT
33540254 TTCCCCCAAA
Statistics
Matches: 50, Mismatches: 2, Indels: 3
0.91 0.04 0.05
Matches are distributed among these distances:
53 6 0.12
54 23 0.46
55 21 0.42
ACGTcount: A:0.26, C:0.11, G:0.27, T:0.36
Consensus pattern (54 bp):
TATAAATAGGGGGTGAAGTGACTATTTGGGGGGCATCTTTTTCTGTAAACACTA
Found at i:33543905 original size:16 final size:16
Alignment explanation
Indices: 33543886--33543937 Score: 56
Period size: 16 Copynumber: 3.2 Consensus size: 16
33543876 TTTATTTTTC
33543886 TTTTTCTTTTTATTTA
1 TTTTTCTTTTTATTTA
33543902 TTTTT-TCTTTTA-TTA
1 TTTTTCT-TTTTATTTA
33543917 TTTTTTCTTTTCT-TTTA
1 -TTTTTCTTTT-TATTTA
33543934 TTTT
1 TTTT
33543938 ATTTTATTTA
Statistics
Matches: 31, Mismatches: 0, Indels: 10
0.76 0.00 0.24
Matches are distributed among these distances:
15 4 0.13
16 22 0.71
17 5 0.16
ACGTcount: A:0.10, C:0.08, G:0.00, T:0.83
Consensus pattern (16 bp):
TTTTTCTTTTTATTTA
Found at i:33543917 original size:15 final size:15
Alignment explanation
Indices: 33543886--33543945 Score: 68
Period size: 15 Copynumber: 3.9 Consensus size: 15
33543876 TTTATTTTTC
33543886 TTTTTCTTTTTATTTAT
1 TTTTTC-TTTTA-TTAT
33543903 TTTTTCTTTTATTAT
1 TTTTTCTTTTATTAT
*
33543918 TTTTTCTTTTCTT-T
1 TTTTTCTTTTATTAT
*
33543932 TATTTTATTTTATT
1 T-TTTTCTTTTATT
33543946 TAAATATTAA
Statistics
Matches: 39, Mismatches: 3, Indels: 4
0.85 0.07 0.09
Matches are distributed among these distances:
14 2 0.05
15 26 0.67
16 5 0.13
17 6 0.15
ACGTcount: A:0.12, C:0.07, G:0.00, T:0.82
Consensus pattern (15 bp):
TTTTTCTTTTATTAT
Found at i:33543942 original size:20 final size:20
Alignment explanation
Indices: 33543893--33543942 Score: 66
Period size: 20 Copynumber: 2.5 Consensus size: 20
33543883 TTCTTTTTCT
*
33543893 TTTTATTTATTTTTTCTTTTA
1 TTTTATTT-TCTTTTCTTTTA
33543914 TTATT-TTTTCTTTTCTTTTA
1 TT-TTATTTTCTTTTCTTTTA
33543934 TTTTATTTT
1 TTTTATTTT
33543943 ATTTAAATAT
Statistics
Matches: 26, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
19 2 0.08
20 17 0.65
21 5 0.19
22 2 0.08
ACGTcount: A:0.12, C:0.06, G:0.00, T:0.82
Consensus pattern (20 bp):
TTTTATTTTCTTTTCTTTTA
Found at i:33544151 original size:42 final size:42
Alignment explanation
Indices: 33544049--33544153 Score: 167
Period size: 42 Copynumber: 2.5 Consensus size: 42
33544039 ATCCATGGTA
*
33544049 CCAAACAGTTCTATTCCAACCCAAAATGCTATATCCCTGCTG
1 CCAAACAGTTCTATTCCAGCCCAAAATGCTATATCCCTGCTG
*
33544091 CCAAACAGTTCTATTCCAGCCCAGAATGCTATATCCCTG-TAG
1 CCAAACAGTTCTATTCCAGCCCAAAATGCTATATCCCTGCT-G
*
33544133 CCAAACAGTCCTATTCCAGCC
1 CCAAACAGTTCTATTCCAGCC
33544154 TTAGAATCCC
Statistics
Matches: 59, Mismatches: 3, Indels: 2
0.92 0.05 0.03
Matches are distributed among these distances:
41 1 0.02
42 58 0.98
ACGTcount: A:0.30, C:0.34, G:0.11, T:0.25
Consensus pattern (42 bp):
CCAAACAGTTCTATTCCAGCCCAAAATGCTATATCCCTGCTG
Found at i:33545127 original size:118 final size:118
Alignment explanation
Indices: 33544919--33545149 Score: 381
Period size: 118 Copynumber: 2.0 Consensus size: 118
33544909 TGTTTTTCAT
* * *
33544919 GGTTATGAGTACAGCTTAGATCGTGACTGACTGAGTAACCGGTGTAGGGTGCTTGGGTTGTCATT
1 GGTTATGAGTACAGCTCAAATCGTGACTGACTGAGTAACCGGGGTAGGGTGCTTGGGTTGTCATT
33544984 CTACTTCGCGTCAAAAGGTTGTGTGACGTGACAAGTAAAACTCCGCTAGCCGA
66 CTACTTCGCGTCAAAAGGTTGTGTGACGTGACAAGTAAAACTCCGCTAGCCGA
**
33545037 GGTTATGAGTATGGCTCAAATCGTGACTGACTGAGTAACCGGGGTAGGGTGCTTGGGTTGTCATT
1 GGTTATGAGTACAGCTCAAATCGTGACTGACTGAGTAACCGGGGTAGGGTGCTTGGGTTGTCATT
****
33545102 CTACTTCGCGTCAAAAGGTTGTGTGACGTGTTGGGTAAAACTCCGCTA
66 CTACTTCGCGTCAAAAGGTTGTGTGACGTGACAAGTAAAACTCCGCTA
33545150 ACTGGAAATA
Statistics
Matches: 104, Mismatches: 9, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
118 104 1.00
ACGTcount: A:0.23, C:0.18, G:0.31, T:0.29
Consensus pattern (118 bp):
GGTTATGAGTACAGCTCAAATCGTGACTGACTGAGTAACCGGGGTAGGGTGCTTGGGTTGTCATT
CTACTTCGCGTCAAAAGGTTGTGTGACGTGACAAGTAAAACTCCGCTAGCCGA
Found at i:33549584 original size:27 final size:27
Alignment explanation
Indices: 33549546--33549654 Score: 139
Period size: 27 Copynumber: 4.1 Consensus size: 27
33549536 GAAGCGTCCA
*
33549546 GGTGGCTATGCCACATTTATCTGATCT
1 GGTGGCTATGCCACATTTATCTGTTCT
*
33549573 GGTGGCTATGCCACATATATCTGTTCT
1 GGTGGCTATGCCACATTTATCTGTTCT
* *
33549600 GGTGGCTCTGCCACAATTATCTGTTCT
1 GGTGGCTATGCCACATTTATCTGTTCT
* * * *
33549627 GGTGACTCTGTCACA-TCATCTGTTCT
1 GGTGGCTATGCCACATTTATCTGTTCT
33549653 GG
1 GG
33549655 CAGCCATGCT
Statistics
Matches: 74, Mismatches: 8, Indels: 1
0.89 0.10 0.01
Matches are distributed among these distances:
26 12 0.16
27 62 0.84
ACGTcount: A:0.17, C:0.24, G:0.23, T:0.37
Consensus pattern (27 bp):
GGTGGCTATGCCACATTTATCTGTTCT
Found at i:33563641 original size:16 final size:18
Alignment explanation
Indices: 33563612--33563645 Score: 54
Period size: 16 Copynumber: 2.0 Consensus size: 18
33563602 ATTATTTGAT
33563612 AATTATCTTAATTTATAA
1 AATTATCTTAATTTATAA
33563630 AATTAT-TT-ATTTATAA
1 AATTATCTTAATTTATAA
33563646 CAAAAACATG
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 8 0.50
17 2 0.12
18 6 0.38
ACGTcount: A:0.44, C:0.03, G:0.00, T:0.53
Consensus pattern (18 bp):
AATTATCTTAATTTATAA
Found at i:33568043 original size:21 final size:21
Alignment explanation
Indices: 33568007--33568063 Score: 69
Period size: 21 Copynumber: 2.7 Consensus size: 21
33567997 AGAGGAGTGC
* * *
33568007 GTTCTACCGATAGAAGTTCGA
1 GTTCTATCGGTAGAAGTCCGA
* *
33568028 GTTGTATCGGTAGAAGTCCTA
1 GTTCTATCGGTAGAAGTCCGA
33568049 GTTCTATCGGTAGAA
1 GTTCTATCGGTAGAA
33568064 TTCTGTAACC
Statistics
Matches: 30, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
21 30 1.00
ACGTcount: A:0.26, C:0.16, G:0.26, T:0.32
Consensus pattern (21 bp):
GTTCTATCGGTAGAAGTCCGA
Found at i:33568747 original size:26 final size:27
Alignment explanation
Indices: 33568727--33568780 Score: 76
Period size: 27 Copynumber: 2.1 Consensus size: 27
33568717 TAGTACATTT
*
33568727 AAAATA-AAAGCAT-CCAAAGTAAATG
1 AAAATAGAAAACATCCCAAAGTAAATG
*
33568752 AAAATAGAAAACATCCCAAAGTAACTG
1 AAAATAGAAAACATCCCAAAGTAAATG
33568779 AA
1 AA
33568781 TATGCAACCA
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
25 6 0.24
26 6 0.24
27 13 0.52
ACGTcount: A:0.59, C:0.15, G:0.11, T:0.15
Consensus pattern (27 bp):
AAAATAGAAAACATCCCAAAGTAAATG
Found at i:33578043 original size:22 final size:22
Alignment explanation
Indices: 33578018--33578085 Score: 77
Period size: 22 Copynumber: 3.1 Consensus size: 22
33578008 AAATAGATAA
33578018 CATATGTAAAATCATATAATAC
1 CATATGTAAAATCATATAATAC
** * *
33578040 CATA-AAAAAAT-AAATAGATAA
1 CATATGTAAAATCATATA-ATAC
33578061 CATATGTAAAATCATATAATAC
1 CATATGTAAAATCATATAATAC
33578083 CAT
1 CAT
33578086 GTTCAAACAA
Statistics
Matches: 35, Mismatches: 8, Indels: 6
0.71 0.16 0.12
Matches are distributed among these distances:
20 4 0.11
21 12 0.34
22 15 0.43
23 4 0.11
ACGTcount: A:0.56, C:0.12, G:0.04, T:0.28
Consensus pattern (22 bp):
CATATGTAAAATCATATAATAC
Found at i:33578057 original size:43 final size:44
Alignment explanation
Indices: 33577999--33578085 Score: 167
Period size: 43 Copynumber: 2.0 Consensus size: 44
33577989 GAAAAAGGTA
33577999 AAAATAAATAAATAGATAACATATGTAAAATCATATAATACCAT
1 AAAATAAATAAATAGATAACATATGTAAAATCATATAATACCAT
33578043 AAAA-AAATAAATAGATAACATATGTAAAATCATATAATACCAT
1 AAAATAAATAAATAGATAACATATGTAAAATCATATAATACCAT
33578086 GTTCAAACAA
Statistics
Matches: 43, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
43 39 0.91
44 4 0.09
ACGTcount: A:0.60, C:0.09, G:0.05, T:0.26
Consensus pattern (44 bp):
AAAATAAATAAATAGATAACATATGTAAAATCATATAATACCAT
Found at i:33580432 original size:62 final size:62
Alignment explanation
Indices: 33580366--33580490 Score: 241
Period size: 62 Copynumber: 2.0 Consensus size: 62
33580356 AAAATAGGCC
*
33580366 TAACCATAGCTCTATTTATAATATAGCAAGAAGTTTTTATGGCTGCCACCCAAAAGTATCTT
1 TAACCATAGCTCTATTTATAATATAGCAAGAAGTTTTTATGGCTGCCACCCAAAAATATCTT
33580428 TAACCATAGCTCTATTTATAATATAGCAAGAAGTTTTTATGGCTGCCACCCAAAAATATCTT
1 TAACCATAGCTCTATTTATAATATAGCAAGAAGTTTTTATGGCTGCCACCCAAAAATATCTT
33580490 T
1 T
33580491 GCAAATTATT
Statistics
Matches: 62, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
62 62 1.00
ACGTcount: A:0.34, C:0.19, G:0.12, T:0.34
Consensus pattern (62 bp):
TAACCATAGCTCTATTTATAATATAGCAAGAAGTTTTTATGGCTGCCACCCAAAAATATCTT
Found at i:33586121 original size:27 final size:27
Alignment explanation
Indices: 33586090--33586240 Score: 171
Period size: 27 Copynumber: 5.6 Consensus size: 27
33586080 TAAATTGTAC
33586090 AGCACTAAGTGTGCGATTTGACTATGT
1 AGCACTAAGTGTGCGATTTGACTATGT
* **
33586117 TGCACTAAGTGTGCGAAATGTA-TATG-
1 AGCACTAAGTGTGCGATTTG-ACTATGT
* * *
33586143 ATGCACTAAGTGTGCGAATTGACCATGG
1 A-GCACTAAGTGTGCGATTTGACTATGT
*
33586171 GGCACTAAGTGTGCGAGTTTGACTATGT
1 AGCACTAAGTGTGCGA-TTTGACTATGT
* *
33586199 AGCACTAAGTGTGCGATTTGATTATAT
1 AGCACTAAGTGTGCGATTTGACTATGT
*
33586226 AGCACTGAGTGTGCG
1 AGCACTAAGTGTGCG
33586241 GACTCAATAT
Statistics
Matches: 105, Mismatches: 14, Indels: 10
0.81 0.11 0.08
Matches are distributed among these distances:
26 1 0.01
27 80 0.76
28 24 0.23
ACGTcount: A:0.26, C:0.15, G:0.28, T:0.30
Consensus pattern (27 bp):
AGCACTAAGTGTGCGATTTGACTATGT
Found at i:33586284 original size:44 final size:44
Alignment explanation
Indices: 33586234--33586376 Score: 105
Period size: 44 Copynumber: 3.2 Consensus size: 44
33586224 ATAGCACTGA
33586234 GTGTGCGGACTCAATATACATTCGTGAATCATTATGGACACTAT
1 GTGTGCGGACTCAATATACATTCGTGAATCATTATGGACACTAT
* * * * * * **
33586278 GTGTGCGACACGTAGCACTA-A-GTGT-GCGAGTTGATTATATAGCACTGA-
1 GTGTGCG-GAC-T--CAATATACAT-TCGTGA-ATCATTATGGA-CACT-AT
*
33586326 GTGTGCGGACTCAATATACATCCGTGAATCATTATGGACACTAT
1 GTGTGCGGACTCAATATACATTCGTGAATCATTATGGACACTAT
33586370 GTGTGCG
1 GTGTGCG
33586377 ACACTATTGA
Statistics
Matches: 70, Mismatches: 17, Indels: 24
0.63 0.15 0.22
Matches are distributed among these distances:
43 1 0.01
44 22 0.31
45 10 0.14
46 10 0.14
47 11 0.16
48 15 0.21
49 1 0.01
ACGTcount: A:0.27, C:0.18, G:0.25, T:0.29
Consensus pattern (44 bp):
GTGTGCGGACTCAATATACATTCGTGAATCATTATGGACACTAT
Found at i:33586354 original size:92 final size:92
Alignment explanation
Indices: 33586197--33586380 Score: 350
Period size: 92 Copynumber: 2.0 Consensus size: 92
33586187 GTTTGACTAT
* *
33586197 GTAGCACTAAGTGTGCGATTTGATTATATAGCACTGAGTGTGCGGACTCAATATACATTCGTGAA
1 GTAGCACTAAGTGTGCGAGTTGATTATATAGCACTGAGTGTGCGGACTCAATATACATCCGTGAA
33586262 TCATTATGGACACTATGTGTGCGACAC
66 TCATTATGGACACTATGTGTGCGACAC
33586289 GTAGCACTAAGTGTGCGAGTTGATTATATAGCACTGAGTGTGCGGACTCAATATACATCCGTGAA
1 GTAGCACTAAGTGTGCGAGTTGATTATATAGCACTGAGTGTGCGGACTCAATATACATCCGTGAA
33586354 TCATTATGGACACTATGTGTGCGACAC
66 TCATTATGGACACTATGTGTGCGACAC
33586381 TATTGAGTCG
Statistics
Matches: 90, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
92 90 1.00
ACGTcount: A:0.28, C:0.18, G:0.24, T:0.29
Consensus pattern (92 bp):
GTAGCACTAAGTGTGCGAGTTGATTATATAGCACTGAGTGTGCGGACTCAATATACATCCGTGAA
TCATTATGGACACTATGTGTGCGACAC
Found at i:33587821 original size:40 final size:40
Alignment explanation
Indices: 33587777--33588001 Score: 246
Period size: 40 Copynumber: 5.7 Consensus size: 40
33587767 GCTACTCGTT
* *
33587777 CAAATGCCTTCGGGACATAGCCCGG-TTGTAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGAAT-TAGTAACTCGCA
* * *
33587817 CAAATGCCTTCGGGATTTAACCCGGATTTAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGAATTAGTAACTCGCA
* *
33587857 CAAATGCCTTCGGG-CTTAGCCCGGAATTAGTATCTCGTA
1 CAAATGCCTTCGGGACTTAGCCCGGAATTAGTAACTCGCA
* *
33587896 CAAATGCCTTC-GGATCTTAGTCCGGAATTAGTATCTCGCA
1 CAAATGCCTTCGGGA-CTTAGCCCGGAATTAGTAACTCGCA
* * * *
33587936 CAAATGCCTTC-GGATCTTAGTCCGG-ATATGGTCACTTAGCA
1 CAAATGCCTTCGGGA-CTTAGCCCGGAAT-TAGTAAC-TCGCA
33587977 CAAA-GCCTTCGGGACTTAGCCCGGA
1 CAAATGCCTTCGGGACTTAGCCCGGA
33588002 CATCATTCAA
Statistics
Matches: 163, Mismatches: 15, Indels: 13
0.85 0.08 0.07
Matches are distributed among these distances:
38 2 0.01
39 33 0.20
40 115 0.71
41 13 0.08
ACGTcount: A:0.25, C:0.26, G:0.23, T:0.26
Consensus pattern (40 bp):
CAAATGCCTTCGGGACTTAGCCCGGAATTAGTAACTCGCA
Found at i:33587899 original size:79 final size:80
Alignment explanation
Indices: 33587777--33587948 Score: 233
Period size: 79 Copynumber: 2.2 Consensus size: 80
33587767 GCTACTCGTT
*
33587777 CAAATGCCTTCGGGACATAGCCCGGTTGTAGTAACTCGCACAAATGCCTTCGGGAT-TTAACCCG
1 CAAATGCCTTCGGGACATAGCCCGGATGTAGTAACTCGCACAAATGCCTTC-GGATCTTAACCCG
*
33587841 GATTTAGTAACTCGCA
65 GAATTAGTAACTCGCA
* * * **
33587857 CAAATGCCTTCGGG-CTTAGCCCGGAAT-TAGTATCTCGTACAAATGCCTTCGGATCTTAGTCCG
1 CAAATGCCTTCGGGACATAGCCCGG-ATGTAGTAACTCGCACAAATGCCTTCGGATCTTAACCCG
*
33587920 GAATTAGTATCTCGCA
65 GAATTAGTAACTCGCA
33587936 CAAATGCCTTCGG
1 CAAATGCCTTCGG
33587949 ATCTTAGTCC
Statistics
Matches: 82, Mismatches: 8, Indels: 5
0.86 0.08 0.05
Matches are distributed among these distances:
78 4 0.05
79 63 0.77
80 15 0.18
ACGTcount: A:0.25, C:0.26, G:0.22, T:0.27
Consensus pattern (80 bp):
CAAATGCCTTCGGGACATAGCCCGGATGTAGTAACTCGCACAAATGCCTTCGGATCTTAACCCGG
AATTAGTAACTCGCA
Found at i:33587961 original size:119 final size:120
Alignment explanation
Indices: 33587771--33588001 Score: 292
Period size: 119 Copynumber: 1.9 Consensus size: 120
33587761 GATATAGCTA
* *
33587771 CTCGTTCAAATGCCTTCGGGACATAGCCCGGTTGTAGTAACTCGCACAAATGCCTTCGGGATTTA
1 CTCGTACAAATGCCTTCGGGACATAGCCCGGATGTAGTAACTCGCACAAATGCCTTCGGGATTTA
* *
33587836 ACCCGGATTTAGTAAC-TCGCACAAATGCCTTCGGG-CTTAGCCCGGAATTAGTAT
66 ACCCGGATATAGTAACTTAGCACAAA-GCCTTCGGGACTTAGCCCGGAATTAGTAT
* * *
33587890 CTCGTACAAATGCCTTC-GGATCTTAGTCCGGAAT-TAGTATCTCGCACAAATGCCTTC-GGATC
1 CTCGTACAAATGCCTTCGGGA-CATAGCCCGG-ATGTAGTAACTCGCACAAATGCCTTCGGGAT-
** * *
33587952 TTAGTCCGGATATGGTCACTTAGCACAAAGCCTTCGGGACTTAGCCCGGA
63 TTAACCCGGATATAGTAACTTAGCACAAAGCCTTCGGGACTTAGCCCGGA
33588002 CATCATTCAA
Statistics
Matches: 96, Mismatches: 11, Indels: 9
0.83 0.09 0.08
Matches are distributed among these distances:
118 7 0.07
119 69 0.72
120 20 0.21
ACGTcount: A:0.24, C:0.26, G:0.23, T:0.27
Consensus pattern (120 bp):
CTCGTACAAATGCCTTCGGGACATAGCCCGGATGTAGTAACTCGCACAAATGCCTTCGGGATTTA
ACCCGGATATAGTAACTTAGCACAAAGCCTTCGGGACTTAGCCCGGAATTAGTAT
Found at i:33596812 original size:19 final size:20
Alignment explanation
Indices: 33596780--33596824 Score: 56
Period size: 19 Copynumber: 2.3 Consensus size: 20
33596770 TTAAGTATTT
*
33596780 AAAATTTTATAAAAATATAA
1 AAAATTATATAAAAATATAA
*
33596800 AAAATTATA-AAAAATGTAA
1 AAAATTATATAAAAATATAA
*
33596819 ATAATT
1 AAAATT
33596825 TATTGAAAAA
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
19 14 0.64
20 8 0.36
ACGTcount: A:0.64, C:0.00, G:0.02, T:0.33
Consensus pattern (20 bp):
AAAATTATATAAAAATATAA
Found at i:33606481 original size:45 final size:45
Alignment explanation
Indices: 33606432--33606528 Score: 124
Period size: 45 Copynumber: 2.2 Consensus size: 45
33606422 GCCATAGTCA
* * **
33606432 TACTCATTTTCGTCTTGATGTCATAACATCTTTCATTTA-GGATTT
1 TACTCATTTTCATCATGATGTCATAACATCTTTCAGCTATGG-TTT
* *
33606477 TACTCATTTTTATCATGATGTCATAACATTTTTCAGCTATGGTTT
1 TACTCATTTTCATCATGATGTCATAACATCTTTCAGCTATGGTTT
33606522 TACTCAT
1 TACTCAT
33606529 CTTGGTGTAT
Statistics
Matches: 45, Mismatches: 6, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
45 43 0.96
46 2 0.04
ACGTcount: A:0.24, C:0.18, G:0.10, T:0.48
Consensus pattern (45 bp):
TACTCATTTTCATCATGATGTCATAACATCTTTCAGCTATGGTTT
Found at i:33610062 original size:22 final size:22
Alignment explanation
Indices: 33610037--33610080 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 22
33610027 TAATCCTATA
33610037 ATAAATTATTAATATAATAAAT
1 ATAAATTATTAATATAATAAAT
* * *
33610059 ATAATTTATTATTTTAATAAAT
1 ATAAATTATTAATATAATAAAT
33610081 TATTTAATAT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (22 bp):
ATAAATTATTAATATAATAAAT
Found at i:33611141 original size:21 final size:20
Alignment explanation
Indices: 33611095--33611141 Score: 51
Period size: 21 Copynumber: 2.2 Consensus size: 20
33611085 TGAAGTTCAA
*
33611095 AAAATCTCCTAATAAACTCT
1 AAAATCTCCTAAAAAACTCT
33611115 ACAAATCCTCCTAAAAAAACTC-
1 A-AAAT-CTCCT-AAAAAACTCT
33611137 AAAAT
1 AAAAT
33611142 ATATAACTGG
Statistics
Matches: 23, Mismatches: 1, Indels: 5
0.79 0.03 0.17
Matches are distributed among these distances:
20 1 0.04
21 8 0.35
22 6 0.26
23 8 0.35
ACGTcount: A:0.51, C:0.26, G:0.00, T:0.23
Consensus pattern (20 bp):
AAAATCTCCTAAAAAACTCT
Found at i:33626609 original size:17 final size:18
Alignment explanation
Indices: 33626582--33626616 Score: 63
Period size: 17 Copynumber: 2.0 Consensus size: 18
33626572 AATAAATATT
33626582 TTTATTTGCTGTAATTTA
1 TTTATTTGCTGTAATTTA
33626600 TTTA-TTGCTGTAATTTA
1 TTTATTTGCTGTAATTTA
33626617 CAAACTTCTA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 13 0.76
18 4 0.24
ACGTcount: A:0.23, C:0.06, G:0.11, T:0.60
Consensus pattern (18 bp):
TTTATTTGCTGTAATTTA
Found at i:33629334 original size:9 final size:9
Alignment explanation
Indices: 33629322--33629391 Score: 95
Period size: 9 Copynumber: 7.8 Consensus size: 9
33629312 TGCTTTTTTT
33629322 GTTAATTCG
1 GTTAATTCG
*
33629331 GTTAATTCA
1 GTTAATTCG
*
33629340 GTTAAATCG
1 GTTAATTCG
* *
33629349 TTTAAATCG
1 GTTAATTCG
*
33629358 GTTAAATCG
1 GTTAATTCG
33629367 GTTAATTCG
1 GTTAATTCG
33629376 GTTAATTCG
1 GTTAATTCG
33629385 GTTAATT
1 GTTAATT
33629392 TTTATACTTA
Statistics
Matches: 55, Mismatches: 6, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
9 55 1.00
ACGTcount: A:0.29, C:0.10, G:0.19, T:0.43
Consensus pattern (9 bp):
GTTAATTCG
Found at i:33629579 original size:12 final size:12
Alignment explanation
Indices: 33629562--33629586 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
33629552 TGCTATTTCG
33629562 GGTCGGTTAACC
1 GGTCGGTTAACC
33629574 GGTCGGTTAACC
1 GGTCGGTTAACC
33629586 G
1 G
33629587 AATGAACACC
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.16, C:0.24, G:0.36, T:0.24
Consensus pattern (12 bp):
GGTCGGTTAACC
Found at i:33635728 original size:21 final size:21
Alignment explanation
Indices: 33635704--33635748 Score: 81
Period size: 21 Copynumber: 2.1 Consensus size: 21
33635694 TATACATATC
33635704 CAATTAGTCTCTCCACTAGCT
1 CAATTAGTCTCTCCACTAGCT
*
33635725 CAATTAGTCTCTCTACTAGCT
1 CAATTAGTCTCTCCACTAGCT
33635746 CAA
1 CAA
33635749 CATAACTCTT
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.27, C:0.31, G:0.09, T:0.33
Consensus pattern (21 bp):
CAATTAGTCTCTCCACTAGCT
Found at i:33637341 original size:14 final size:14
Alignment explanation
Indices: 33637324--33637350 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
33637314 CTCAAAAATT
33637324 TGTATGCAAATGTG
1 TGTATGCAAATGTG
33637338 TGTATGCAAATGT
1 TGTATGCAAATGT
33637351 ATGTGTGTAG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.30, C:0.07, G:0.26, T:0.37
Consensus pattern (14 bp):
TGTATGCAAATGTG
Found at i:33638950 original size:13 final size:14
Alignment explanation
Indices: 33638932--33638965 Score: 54
Period size: 13 Copynumber: 2.6 Consensus size: 14
33638922 TAATCTTATG
33638932 CTTTTTTTTTTC-T
1 CTTTTTTTTTTCAT
33638945 CTTTTTTTTTTCAT
1 CTTTTTTTTTTCAT
33638959 -TTTTTTT
1 CTTTTTTT
33638966 CATGTGATTT
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
13 19 0.95
14 1 0.05
ACGTcount: A:0.03, C:0.12, G:0.00, T:0.85
Consensus pattern (14 bp):
CTTTTTTTTTTCAT
Found at i:33638951 original size:12 final size:12
Alignment explanation
Indices: 33638934--33638966 Score: 50
Period size: 11 Copynumber: 2.8 Consensus size: 12
33638924 ATCTTATGCT
33638934 TTTTTTTTTCTC
1 TTTTTTTTTCTC
33638946 TTTTTTTTT-TC
1 TTTTTTTTTCTC
*
33638957 ATTTTTTTTC
1 TTTTTTTTTC
33638967 ATGTGATTTT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
11 10 0.53
12 9 0.47
ACGTcount: A:0.03, C:0.12, G:0.00, T:0.85
Consensus pattern (12 bp):
TTTTTTTTTCTC
Found at i:33640957 original size:22 final size:20
Alignment explanation
Indices: 33640921--33640962 Score: 57
Period size: 20 Copynumber: 2.0 Consensus size: 20
33640911 CCATTGTTGA
*
33640921 GAAATTGATGAATTAGACTT
1 GAAATTGATGAATTAAACTT
33640941 GAAATTGATAGATATTAAACTT
1 GAAATTGAT-GA-ATTAAACTT
33640963 AGACTATGAA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
20 9 0.47
21 2 0.11
22 8 0.42
ACGTcount: A:0.43, C:0.05, G:0.17, T:0.36
Consensus pattern (20 bp):
GAAATTGATGAATTAAACTT
Found at i:33641591 original size:21 final size:21
Alignment explanation
Indices: 33641565--33641604 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
33641555 TTGAATAGAT
*
33641565 ATGAATTTAGAATGATGATTC
1 ATGAATTGAGAATGATGATTC
33641586 ATGAATTGAGAATGATGAT
1 ATGAATTGAGAATGATGAT
33641605 ATTGAATGCT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.40, C:0.03, G:0.23, T:0.35
Consensus pattern (21 bp):
ATGAATTGAGAATGATGATTC
Found at i:33646714 original size:42 final size:42
Alignment explanation
Indices: 33646655--33646739 Score: 161
Period size: 42 Copynumber: 2.0 Consensus size: 42
33646645 AGATTAAAGG
*
33646655 AAATCATGGTTCAAGATTAAATCCAAGAAAAGTGGACCAACC
1 AAATCATGATTCAAGATTAAATCCAAGAAAAGTGGACCAACC
33646697 AAATCATGATTCAAGATTAAATCCAAGAAAAGTGGACCAACC
1 AAATCATGATTCAAGATTAAATCCAAGAAAAGTGGACCAACC
33646739 A
1 A
33646740 TATCCAAATA
Statistics
Matches: 42, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
42 42 1.00
ACGTcount: A:0.47, C:0.19, G:0.15, T:0.19
Consensus pattern (42 bp):
AAATCATGATTCAAGATTAAATCCAAGAAAAGTGGACCAACC
Found at i:33647649 original size:6 final size:6
Alignment explanation
Indices: 33647638--33647673 Score: 72
Period size: 6 Copynumber: 6.0 Consensus size: 6
33647628 TCACAAGATT
33647638 GAACAA GAACAA GAACAA GAACAA GAACAA GAACAA
1 GAACAA GAACAA GAACAA GAACAA GAACAA GAACAA
33647674 TATAAATATA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 30 1.00
ACGTcount: A:0.67, C:0.17, G:0.17, T:0.00
Consensus pattern (6 bp):
GAACAA
Found at i:33650937 original size:14 final size:14
Alignment explanation
Indices: 33650918--33650945 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
33650908 AAATAAGTTT
33650918 AATAATGTCTCATG
1 AATAATGTCTCATG
33650932 AATAATGTCTCATG
1 AATAATGTCTCATG
33650946 CTCGACTCCG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.36, C:0.14, G:0.14, T:0.36
Consensus pattern (14 bp):
AATAATGTCTCATG
Found at i:33657240 original size:18 final size:17
Alignment explanation
Indices: 33657212--33657245 Score: 50
Period size: 18 Copynumber: 1.9 Consensus size: 17
33657202 GGCCTTAGCC
33657212 CATTACAGAATAAGAAA
1 CATTACAGAATAAGAAA
*
33657229 CATTATCAGAATTAGAA
1 CATTA-CAGAATAAGAA
33657246 TCAAAATGAG
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 5 0.33
18 10 0.67
ACGTcount: A:0.53, C:0.12, G:0.12, T:0.24
Consensus pattern (17 bp):
CATTACAGAATAAGAAA
Found at i:33657257 original size:18 final size:18
Alignment explanation
Indices: 33657233--33657309 Score: 84
Period size: 18 Copynumber: 4.2 Consensus size: 18
33657223 AAGAAACATT
*
33657233 ATCAGAATTAGAATCAAA
1 ATCAGAATCAGAATCAAA
* *
33657251 ATGAGAATCAGAATCAGA
1 ATCAGAATCAGAATCAAA
*
33657269 ATCAGAATCAGAATCAGA
1 ATCAGAATCAGAATCAAA
*
33657287 ATCAG-GTGACAGAATCAAA
1 ATCAGAAT--CAGAATCAAA
33657306 ATCA
1 ATCA
33657310 AAATGTGAAT
Statistics
Matches: 51, Mismatches: 6, Indels: 3
0.85 0.10 0.05
Matches are distributed among these distances:
17 1 0.02
18 37 0.73
19 13 0.25
ACGTcount: A:0.51, C:0.14, G:0.17, T:0.18
Consensus pattern (18 bp):
ATCAGAATCAGAATCAAA
Found at i:33657310 original size:6 final size:6
Alignment explanation
Indices: 33657233--33657291 Score: 91
Period size: 6 Copynumber: 9.8 Consensus size: 6
33657223 AAGAAACATT
* * *
33657233 ATCAGA ATTAGA ATCAAA ATGAGA ATCAGA ATCAGA ATCAGA ATCAGA
1 ATCAGA ATCAGA ATCAGA ATCAGA ATCAGA ATCAGA ATCAGA ATCAGA
33657281 ATCAGA ATCAG
1 ATCAGA ATCAG
33657292 GTGACAGAAT
Statistics
Matches: 47, Mismatches: 6, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
6 47 1.00
ACGTcount: A:0.51, C:0.14, G:0.17, T:0.19
Consensus pattern (6 bp):
ATCAGA
Found at i:33657580 original size:27 final size:26
Alignment explanation
Indices: 33657532--33657583 Score: 68
Period size: 27 Copynumber: 2.0 Consensus size: 26
33657522 GCAAGGCTGC
*
33657532 CAGATATTGTGACGAAGTCACCAGAA
1 CAGATATTGTGACGAAGCCACCAGAA
* *
33657558 CAGATATATGTGGCGAGGCCACCAGA
1 CAGATAT-TGTGACGAAGCCACCAGA
33657584 TTGCAGCGAG
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
26 7 0.32
27 15 0.68
ACGTcount: A:0.35, C:0.21, G:0.27, T:0.17
Consensus pattern (26 bp):
CAGATATTGTGACGAAGCCACCAGAA
Found at i:33657858 original size:27 final size:27
Alignment explanation
Indices: 33657828--33658050 Score: 266
Period size: 27 Copynumber: 8.3 Consensus size: 27
33657818 GGGGCAAAAT
* * * *
33657828 GGTAATTTTACCCCATAAGGGTATCTC
1 GGTAATTCTACCCTACAAGGGTATTTC
*
33657855 GGTAATTCTACCCTACAGGGGTATTTC
1 GGTAATTCTACCCTACAAGGGTATTTC
* *
33657882 AGTAATTCTACCCTACAGGGGTATTTC
1 GGTAATTCTACCCTACAAGGGTATTTC
* * *
33657909 GATATTTCTACCCTATAAGGGTATTTC
1 GGTAATTCTACCCTACAAGGGTATTTC
* * *
33657936 GATAATTCTACCCTACAGGGGTATTTT
1 GGTAATTCTACCCTACAAGGGTATTTC
* * *
33657963 AGTAATTCTACCTTACAGGGGTATTTC
1 GGTAATTCTACCCTACAAGGGTATTTC
* *
33657990 GGTATTTCTACCCTACAGGGGTATTTC
1 GGTAATTCTACCCTACAAGGGTATTTC
*
33658017 GGTATTTCTACCCTACAAGGGTATTTC
1 GGTAATTCTACCCTACAAGGGTATTTC
*
33658044 AGTAATT
1 GGTAATT
33658051 TTGTAAATCG
Statistics
Matches: 171, Mismatches: 25, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
27 171 1.00
ACGTcount: A:0.25, C:0.20, G:0.19, T:0.36
Consensus pattern (27 bp):
GGTAATTCTACCCTACAAGGGTATTTC
Found at i:33657952 original size:81 final size:81
Alignment explanation
Indices: 33657832--33658050 Score: 341
Period size: 81 Copynumber: 2.7 Consensus size: 81
33657822 CAAAATGGTA
* *
33657832 ATTT-TACCCCATAAGGGTATCTCGGTAATTCTACCCTACAGGGGTATTTCAGTAATTCTACCCT
1 ATTTCTACCCTATAAGGGTATTTCGGTAATTCTACCCTACAGGGGTATTTCAGTAATTCTACCCT
33657896 ACAGGGGTATTTCGAT
66 ACAGGGGTATTTCGAT
* * *
33657912 ATTTCTACCCTATAAGGGTATTTCGATAATTCTACCCTACAGGGGTATTTTAGTAATTCTACCTT
1 ATTTCTACCCTATAAGGGTATTTCGGTAATTCTACCCTACAGGGGTATTTCAGTAATTCTACCCT
*
33657977 ACAGGGGTATTTCGGT
66 ACAGGGGTATTTCGAT
* * * *
33657993 ATTTCTACCCTACAGGGGTATTTCGGTATTTCTACCCTACAAGGGTATTTCAGTAATT
1 ATTTCTACCCTATAAGGGTATTTCGGTAATTCTACCCTACAGGGGTATTTCAGTAATT
33658051 TTGTAAATCG
Statistics
Matches: 126, Mismatches: 12, Indels: 1
0.91 0.09 0.01
Matches are distributed among these distances:
80 4 0.03
81 122 0.97
ACGTcount: A:0.25, C:0.21, G:0.18, T:0.37
Consensus pattern (81 bp):
ATTTCTACCCTATAAGGGTATTTCGGTAATTCTACCCTACAGGGGTATTTCAGTAATTCTACCCT
ACAGGGGTATTTCGAT
Found at i:33658064 original size:27 final size:27
Alignment explanation
Indices: 33658034--33658132 Score: 69
Period size: 27 Copynumber: 3.7 Consensus size: 27
33658024 CTACCCTACA
33658034 AGGGTATTTCAGTAATTTTGTAAATCG
1 AGGGTATTTCAGTAATTTTGTAAATCG
*** *
33658061 AGGGTAAAAC-GATAATTCTGTAAATC-
1 AGGGTATTTCAG-TAATTTTGTAAATCG
* ** * *
33658087 AGGGGTACTTT-GGTAATTTTACAAGTTG
1 A-GGGTA-TTTCAGTAATTTTGTAAATCG
33658115 AGGGTATTTCAGTAATTT
1 AGGGTATTTCAGTAATTT
33658133 CACAAATTAG
Statistics
Matches: 53, Mismatches: 13, Indels: 12
0.68 0.17 0.15
Matches are distributed among these distances:
26 5 0.09
27 46 0.87
28 2 0.04
ACGTcount: A:0.31, C:0.08, G:0.23, T:0.37
Consensus pattern (27 bp):
AGGGTATTTCAGTAATTTTGTAAATCG
Found at i:33658193 original size:27 final size:27
Alignment explanation
Indices: 33658087--33658276 Score: 193
Period size: 27 Copynumber: 7.0 Consensus size: 27
33658077 TCTGTAAATC
* *
33658087 AGGGGTACTTTGGTAATTTTAC-AAGT
1 AGGGGTATTTTGGTAATTTTACAAACT
* ** * *
33658113 TGAGGGTATTTCAGTAATTTCACAAATT
1 AG-GGGTATTTTGGTAATTTTACAAACT
*
33658141 AGAGGTATTTTGGTAATTTTACAAACT
1 AGGGGTATTTTGGTAATTTTACAAACT
* *
33658168 AGGGGTATTTTGATAATTTTACAAACC
1 AGGGGTATTTTGGTAATTTTACAAACT
* * *
33658195 AGGGGTATTTTGGTGATTTTATAAACC
1 AGGGGTATTTTGGTAATTTTACAAACT
* * * *
33658222 AAGGGTATTCTAGTAATTTTACAAACC
1 AGGGGTATTTTGGTAATTTTACAAACT
* *
33658249 AGGGGTATTTTGGTAATTTGATAAACT
1 AGGGGTATTTTGGTAATTTTACAAACT
33658276 A
1 A
33658277 AAGTATTCTA
Statistics
Matches: 133, Mismatches: 29, Indels: 3
0.81 0.18 0.02
Matches are distributed among these distances:
26 1 0.01
27 128 0.96
28 4 0.03
ACGTcount: A:0.32, C:0.09, G:0.21, T:0.38
Consensus pattern (27 bp):
AGGGGTATTTTGGTAATTTTACAAACT
Found at i:33659379 original size:39 final size:39
Alignment explanation
Indices: 33659335--33659591 Score: 316
Period size: 39 Copynumber: 6.6 Consensus size: 39
33659325 ACAGAAATCT
33659335 GGTGATTATTCGGGCTATGTGCCTAGCAGGCTGTGTGCC
1 GGTGATTATTCGGGCTATGTGCCTAGCAGGCTGTGTGCC
* * * * *
33659374 AGTGATTATTTGGGCTATGTGCCTAGCAGGTTATGTGTC
1 GGTGATTATTCGGGCTATGTGCCTAGCAGGCTGTGTGCC
* ** *
33659413 GATGATTATTCATGCTATGTGCCTAGCAAGCTGTGTGCC
1 GGTGATTATTCGGGCTATGTGCCTAGCAGGCTGTGTGCC
* * *
33659452 AGTGATTATTCGGGCTATGTGCCTAACAGGGTGTGTGCC
1 GGTGATTATTCGGGCTATGTGCCTAGCAGGCTGTGTGCC
* * * *
33659491 GGTGATTATTCAGGCAATGTGCCTAGTAGGCTGTGTGTC
1 GGTGATTATTCGGGCTATGTGCCTAGCAGGCTGTGTGCC
* * * * *
33659530 GGTGATTATTTGGGGTTTGTGCCTAGTAAGCTGTGTGCC
1 GGTGATTATTCGGGCTATGTGCCTAGCAGGCTGTGTGCC
*
33659569 GGTGATTATTCAGGCTATGTGCC
1 GGTGATTATTCGGGCTATGTGCC
33659592 GGTGTATTGA
Statistics
Matches: 179, Mismatches: 39, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
39 179 1.00
ACGTcount: A:0.17, C:0.17, G:0.32, T:0.34
Consensus pattern (39 bp):
GGTGATTATTCGGGCTATGTGCCTAGCAGGCTGTGTGCC
Found at i:33659467 original size:78 final size:78
Alignment explanation
Indices: 33659335--33659591 Score: 352
Period size: 78 Copynumber: 3.3 Consensus size: 78
33659325 ACAGAAATCT
*
33659335 GGTGATTATTCGGGCTATGTGCCTAGCAGGCTGTGTGCCAGTGATTATTTGGGCTATGTGCCTAG
1 GGTGATTATTCAGGCTATGTGCCTAGCAGGCTGTGTGCCAGTGATTATTTGGGCTATGTGCCTAG
* * *
33659400 CAGGTTATGTGTC
66 CAGGCTGTGTGCC
* * * * *
33659413 GATGATTATTCATGCTATGTGCCTAGCAAGCTGTGTGCCAGTGATTATTCGGGCTATGTGCCTAA
1 GGTGATTATTCAGGCTATGTGCCTAGCAGGCTGTGTGCCAGTGATTATTTGGGCTATGTGCCTAG
*
33659478 CAGGGTGTGTGCC
66 CAGGCTGTGTGCC
* * * * * *
33659491 GGTGATTATTCAGGCAATGTGCCTAGTAGGCTGTGTGTCGGTGATTATTTGGGGTTTGTGCCTAG
1 GGTGATTATTCAGGCTATGTGCCTAGCAGGCTGTGTGCCAGTGATTATTTGGGCTATGTGCCTAG
* *
33659556 TAAGCTGTGTGCC
66 CAGGCTGTGTGCC
33659569 GGTGATTATTCAGGCTATGTGCC
1 GGTGATTATTCAGGCTATGTGCC
33659592 GGTGTATTGA
Statistics
Matches: 155, Mismatches: 24, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
78 155 1.00
ACGTcount: A:0.17, C:0.17, G:0.32, T:0.34
Consensus pattern (78 bp):
GGTGATTATTCAGGCTATGTGCCTAGCAGGCTGTGTGCCAGTGATTATTTGGGCTATGTGCCTAG
CAGGCTGTGTGCC
Found at i:33659551 original size:117 final size:117
Alignment explanation
Indices: 33659336--33659591 Score: 350
Period size: 117 Copynumber: 2.2 Consensus size: 117
33659326 CAGAAATCTG
* ** *
33659336 GTGATTATTCGGGCTATGTGCCTAGCAGGCTGTGTGCCAGTGATTATTTGGGCTATGTGCCTAGC
1 GTGATTATTCGGGCTATGTGCCTAACAGGCTGTGTGCCAGTGATTATTCAGGCAATGTGCCTAGC
* *
33659401 AGGTTATGTGTCGATGATTATTCATGCTATGTGCCTAGCAAGCTGTGTGCCA
66 AGGCTATGTGTCGATGATTATTCAGGCTATGTGCCTAGCAAGCTGTGTGCCA
* * *
33659453 GTGATTATTCGGGCTATGTGCCTAACAGGGTGTGTGCCGGTGATTATTCAGGCAATGTGCCTAGT
1 GTGATTATTCGGGCTATGTGCCTAACAGGCTGTGTGCCAGTGATTATTCAGGCAATGTGCCTAGC
* * ** * * * *
33659518 AGGCTGTGTGTCGGTGATTATTTGGGGTTTGTGCCTAGTAAGCTGTGTGCCG
66 AGGCTATGTGTCGATGATTATTCAGGCTATGTGCCTAGCAAGCTGTGTGCCA
*
33659570 GTGATTATTCAGGCTATGTGCC
1 GTGATTATTCGGGCTATGTGCC
33659592 GGTGTATTGA
Statistics
Matches: 121, Mismatches: 18, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
117 121 1.00
ACGTcount: A:0.17, C:0.17, G:0.32, T:0.34
Consensus pattern (117 bp):
GTGATTATTCGGGCTATGTGCCTAACAGGCTGTGTGCCAGTGATTATTCAGGCAATGTGCCTAGC
AGGCTATGTGTCGATGATTATTCAGGCTATGTGCCTAGCAAGCTGTGTGCCA
Found at i:33663510 original size:77 final size:77
Alignment explanation
Indices: 33663329--33663604 Score: 301
Period size: 77 Copynumber: 3.5 Consensus size: 77
33663319 ACAGGAAAAG
* * *
33663329 AATCCTAAAAC-AGAATTATTCAATTGATTTCTGTTTGAAACAAAAAAATCAAACAAATCCTGTT
1 AATCCTAAAACAAG-ATTGTTCAATTGATTTTTGTTTGAAAC-AAAAAATCAAACAAATCATGTT
33663393 AAACGACAGAAATAA
64 -AACGACAGAAATAA
* *
33663408 AATCCTGAAACAAAATTGTTCAATTGACTTTTTGTTTGAAAC-AAAAATCAAACAAATCATGTTA
1 AATCCTAAAACAAGATTGTTCAATTGA-TTTTTGTTTGAAACAAAAAATCAAACAAATCATGTTA
* *
33663472 ATGATAGAAATAA
65 ACGACAGAAATAA
* *
33663485 AATCCTAAAACAAGATTGCTT-AATTGATTTTTTGTTTG-AACAAAAAATTAAACAAATCTTGTT
1 AATCCTAAAACAAGATTG-TTCAATTGA-TTTTTGTTTGAAACAAAAAATCAAACAAATCATGTT
* *
33663548 AAACGGCAGTAAT-A
64 -AACGACAGAAATAA
* * * * *
33663562 AATCCTGAAACAGGATTTTTCAATTGAATTTCTATTTGAAACA
1 AATCCTAAAACAAGATTGTTCAATTG-ATTTTTGTTTGAAACA
33663605 TAATTCAATT
Statistics
Matches: 168, Mismatches: 21, Indels: 17
0.82 0.10 0.08
Matches are distributed among these distances:
76 5 0.03
77 92 0.55
78 35 0.21
79 22 0.13
80 14 0.08
ACGTcount: A:0.45, C:0.13, G:0.11, T:0.32
Consensus pattern (77 bp):
AATCCTAAAACAAGATTGTTCAATTGATTTTTGTTTGAAACAAAAAATCAAACAAATCATGTTAA
CGACAGAAATAA
Found at i:33675003 original size:24 final size:24
Alignment explanation
Indices: 33674960--33675005 Score: 65
Period size: 24 Copynumber: 1.9 Consensus size: 24
33674950 TCAAATCAAC
*
33674960 AAGGGATTTTCAACTTAAAGCAGT
1 AAGGGATTTTCAACTCAAAGCAGT
**
33674984 AAGGGATTTTCGGCTCAAAGCA
1 AAGGGATTTTCAACTCAAAGCA
33675006 TCAACAACAA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
24 19 1.00
ACGTcount: A:0.35, C:0.15, G:0.24, T:0.26
Consensus pattern (24 bp):
AAGGGATTTTCAACTCAAAGCAGT
Found at i:33684322 original size:43 final size:44
Alignment explanation
Indices: 33684255--33684343 Score: 137
Period size: 43 Copynumber: 2.0 Consensus size: 44
33684245 TCTGTAAGTT
*
33684255 AAATAATATTAAAATAACCTACACTAATC-AGTGTTTAAGTGGGA
1 AAATAATATTAAAATAACCTACACTAATCAAAT-TTTAAGTGGGA
*
33684299 AAATAATATT-AAATATCCTACACTAATCAAATTTTAAGTGGGA
1 AAATAATATTAAAATAACCTACACTAATCAAATTTTAAGTGGGA
33684342 AA
1 AA
33684344 CTAACAAAAT
Statistics
Matches: 42, Mismatches: 2, Indels: 3
0.89 0.04 0.06
Matches are distributed among these distances:
43 30 0.71
44 12 0.29
ACGTcount: A:0.47, C:0.11, G:0.11, T:0.30
Consensus pattern (44 bp):
AAATAATATTAAAATAACCTACACTAATCAAATTTTAAGTGGGA
Found at i:33685139 original size:21 final size:22
Alignment explanation
Indices: 33685095--33685144 Score: 75
Period size: 22 Copynumber: 2.3 Consensus size: 22
33685085 TGCAAGGCTC
* *
33685095 ACACGTCCGTGTGGTCCAAGGG
1 ACACGCCCATGTGGTCCAAGGG
33685117 ACACGCCCATGTGGTCC-AGGG
1 ACACGCCCATGTGGTCCAAGGG
33685138 ACACGCC
1 ACACGCC
33685145 TGTGTTGGAG
Statistics
Matches: 26, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
21 11 0.42
22 15 0.58
ACGTcount: A:0.20, C:0.34, G:0.32, T:0.14
Consensus pattern (22 bp):
ACACGCCCATGTGGTCCAAGGG
Found at i:33687046 original size:20 final size:20
Alignment explanation
Indices: 33687017--33687061 Score: 63
Period size: 20 Copynumber: 2.2 Consensus size: 20
33687007 AGCACATGTA
* *
33687017 TTCATAAAATTTTAGAATTT
1 TTCATAAAATTTTACAAATT
*
33687037 TTCATCAAATTTTACAAATT
1 TTCATAAAATTTTACAAATT
33687057 TTCAT
1 TTCAT
33687062 TTTAGTCCCT
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.38, C:0.11, G:0.02, T:0.49
Consensus pattern (20 bp):
TTCATAAAATTTTACAAATT
Found at i:33689181 original size:44 final size:44
Alignment explanation
Indices: 33689131--33689217 Score: 129
Period size: 44 Copynumber: 2.0 Consensus size: 44
33689121 GTAGGTCAAA
33689131 TAATATTAAAATAACATATACTAATAAGAGTTTAAGTGAGAAAT
1 TAATATTAAAATAACATATACTAATAAGAGTTTAAGTGAGAAAT
* * * * *
33689175 TAATATTAAAATAGCCTATATTAATCAGAGTTTAAGTGGGAAA
1 TAATATTAAAATAACATATACTAATAAGAGTTTAAGTGAGAAA
33689218 CTAAAAACAA
Statistics
Matches: 38, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
44 38 1.00
ACGTcount: A:0.48, C:0.06, G:0.14, T:0.32
Consensus pattern (44 bp):
TAATATTAAAATAACATATACTAATAAGAGTTTAAGTGAGAAAT
Found at i:33698609 original size:27 final size:27
Alignment explanation
Indices: 33698579--33698640 Score: 74
Period size: 26 Copynumber: 2.3 Consensus size: 27
33698569 ATTTACTAAA
33698579 ATACCCCTAAGTATG-AAAATTACCATC
1 ATACCCCTAAG-ATGCAAAATTACCATC
* * *
33698606 ATACACCT-AGGTGCAAAATTACCATT
1 ATACCCCTAAGATGCAAAATTACCATC
33698632 ATACCCCTA
1 ATACCCCTA
33698641 GGGTTAATTT
Statistics
Matches: 29, Mismatches: 4, Indels: 4
0.78 0.11 0.11
Matches are distributed among these distances:
25 2 0.07
26 20 0.69
27 7 0.24
ACGTcount: A:0.39, C:0.27, G:0.08, T:0.26
Consensus pattern (27 bp):
ATACCCCTAAGATGCAAAATTACCATC
Found at i:33698785 original size:27 final size:27
Alignment explanation
Indices: 33698746--33698859 Score: 133
Period size: 27 Copynumber: 4.2 Consensus size: 27
33698736 GAGGAAGCGT
33698746 TCTGGTGGCTCTGCCACAAATATCTG-A
1 TCTGGTGGCTCTGCCAC-AATATCTGTA
* * * *
33698773 TCTGGTGGTTCTGCCATAAAGATCTGTT
1 TCTGGTGGCTCTGCCA-CAATATCTGTA
*
33698801 TTTGGTGGCTCTGCCACAATATCTGTA
1 TCTGGTGGCTCTGCCACAATATCTGTA
* *
33698828 TCTGGTGACTCTGTCACAATATCTGT-
1 TCTGGTGGCTCTGCCACAATATCTGTA
33698854 TCTGGT
1 TCTGGT
33698860 AGCCATGCTG
Statistics
Matches: 73, Mismatches: 12, Indels: 5
0.81 0.13 0.06
Matches are distributed among these distances:
26 6 0.08
27 53 0.73
28 14 0.19
ACGTcount: A:0.18, C:0.22, G:0.23, T:0.37
Consensus pattern (27 bp):
TCTGGTGGCTCTGCCACAATATCTGTA
Found at i:33705945 original size:23 final size:22
Alignment explanation
Indices: 33705889--33705947 Score: 59
Period size: 23 Copynumber: 2.6 Consensus size: 22
33705879 TGTAACAAAG
* *
33705889 CTTGTGTGAATTATCATTGGCA
1 CTTGTGTGCATTATCATTGGAA
33705911 CTTGTG-GACATTCAT-ATTTGGAA
1 CTTGTGTG-CATT-ATCA-TTGGAA
33705934 CTTGTGTGCATTAT
1 CTTGTGTGCATTAT
33705948 TAGTATGTTA
Statistics
Matches: 31, Mismatches: 2, Indels: 8
0.76 0.05 0.20
Matches are distributed among these distances:
21 1 0.03
22 12 0.39
23 17 0.55
24 1 0.03
ACGTcount: A:0.22, C:0.14, G:0.22, T:0.42
Consensus pattern (22 bp):
CTTGTGTGCATTATCATTGGAA
Found at i:33707289 original size:39 final size:38
Alignment explanation
Indices: 33707246--33707329 Score: 98
Period size: 38 Copynumber: 2.2 Consensus size: 38
33707236 AATTTAGTAT
*
33707246 ATTAAAATA-AAATTAATAAGAATAATTTTTAACATGTAA
1 ATTAAAATATAAAGT-ATAAGAAT-ATTTTTAACATGTAA
* * * *
33707285 ATTAAAATATAAAGTGTAAGACTATTTTTCACATGTCA
1 ATTAAAATATAAAGTATAAGAATATTTTTAACATGTAA
33707323 ATTAAAA
1 ATTAAAA
33707330 ATTTTGCAAC
Statistics
Matches: 39, Mismatches: 5, Indels: 3
0.83 0.11 0.06
Matches are distributed among these distances:
38 20 0.51
39 15 0.38
40 4 0.10
ACGTcount: A:0.51, C:0.06, G:0.07, T:0.36
Consensus pattern (38 bp):
ATTAAAATATAAAGTATAAGAATATTTTTAACATGTAA
Found at i:33708417 original size:30 final size:30
Alignment explanation
Indices: 33708383--33708439 Score: 96
Period size: 30 Copynumber: 1.9 Consensus size: 30
33708373 CACCGCCAAG
*
33708383 CTTGTTACCGCTGAAGATCATGTTTCGGAT
1 CTTGTTACCGCTGAAGATCATGCTTCGGAT
*
33708413 CTTGTTACCGTTGAAGATCATGCTTCG
1 CTTGTTACCGCTGAAGATCATGCTTCG
33708440 TATATTTCAA
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
30 25 1.00
ACGTcount: A:0.19, C:0.21, G:0.23, T:0.37
Consensus pattern (30 bp):
CTTGTTACCGCTGAAGATCATGCTTCGGAT
Found at i:33708467 original size:81 final size:81
Alignment explanation
Indices: 33708332--33708531 Score: 337
Period size: 81 Copynumber: 2.5 Consensus size: 81
33708322 CACCGCCAAG
*
33708332 CTTGTTACCGTTGAAGATCATGCTTCGGATATTTCAAACATCACCGCCAAGCTTGTTACCGCTGA
1 CTTGTTACCGTTGAAGATCATGCTTCGGATATTTCAAACATCACCGCCAAGCTTGTTACCGCTCA
*
33708397 AGATCATGTTTCGGAT
66 AGATCATGTTTCCGAT
* * *
33708413 CTTGTTACCGTTGAAGATCATGCTTCGTATATTTCAAACTTCACCGCCAAGCTTGTTACCGTTCA
1 CTTGTTACCGTTGAAGATCATGCTTCGGATATTTCAAACATCACCGCCAAGCTTGTTACCGCTCA
33708478 AGATCATGTTTCCGAT
66 AGATCATGTTTCCGAT
* *
33708494 CTTGCTACCGTTGAAGATCATGCTTCGGATCTTTCAAA
1 CTTGTTACCGTTGAAGATCATGCTTCGGATATTTCAAA
33708532 AAAAAAATGA
Statistics
Matches: 111, Mismatches: 8, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
81 111 1.00
ACGTcount: A:0.24, C:0.24, G:0.18, T:0.34
Consensus pattern (81 bp):
CTTGTTACCGTTGAAGATCATGCTTCGGATATTTCAAACATCACCGCCAAGCTTGTTACCGCTCA
AGATCATGTTTCCGAT
Found at i:33708503 original size:30 final size:30
Alignment explanation
Indices: 33708464--33708526 Score: 90
Period size: 30 Copynumber: 2.1 Consensus size: 30
33708454 CACCGCCAAG
* *
33708464 CTTGTTACCGTTCAAGATCATGTTTCCGAT
1 CTTGCTACCGTTCAAGATCATGCTTCCGAT
* *
33708494 CTTGCTACCGTTGAAGATCATGCTTCGGAT
1 CTTGCTACCGTTCAAGATCATGCTTCCGAT
33708524 CTT
1 CTT
33708527 TCAAAAAAAA
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
30 29 1.00
ACGTcount: A:0.19, C:0.24, G:0.19, T:0.38
Consensus pattern (30 bp):
CTTGCTACCGTTCAAGATCATGCTTCCGAT
Found at i:33717457 original size:24 final size:21
Alignment explanation
Indices: 33717376--33717444 Score: 95
Period size: 21 Copynumber: 3.3 Consensus size: 21
33717366 CTCGCAAAGA
* * *
33717376 AAAAAG-GAAGTGAGTTAGAC
1 AAAAAGAGAAGTAACTTGGAC
*
33717396 AAAAAGAGAAGCAACTTGGAC
1 AAAAAGAGAAGTAACTTGGAC
33717417 AAAAAGAGAAGTAACTTGGAC
1 AAAAAGAGAAGTAACTTGGAC
33717438 AAAAAGA
1 AAAAAGA
33717445 AACGAAGTGA
Statistics
Matches: 43, Mismatches: 5, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
20 6 0.14
21 37 0.86
ACGTcount: A:0.55, C:0.09, G:0.25, T:0.12
Consensus pattern (21 bp):
AAAAAGAGAAGTAACTTGGAC
Found at i:33719277 original size:27 final size:27
Alignment explanation
Indices: 33719226--33719277 Score: 63
Period size: 27 Copynumber: 1.9 Consensus size: 27
33719216 TAAAAGGGAA
*
33719226 AAATAGGGATTTTAAAGCTTGGAACTT
1 AAATAGGGATTTTAAAGCTTAGAACTT
33719253 AAATA-GG-TTTTAGAAGCTTTAGAAC
1 AAATAGGGATTTTA-AAGC-TTAGAAC
33719278 AAGGTTTTGA
Statistics
Matches: 22, Mismatches: 1, Indels: 4
0.81 0.04 0.15
Matches are distributed among these distances:
25 5 0.23
26 6 0.27
27 11 0.50
ACGTcount: A:0.38, C:0.08, G:0.21, T:0.33
Consensus pattern (27 bp):
AAATAGGGATTTTAAAGCTTAGAACTT
Found at i:33719982 original size:70 final size:75
Alignment explanation
Indices: 33719895--33720070 Score: 193
Period size: 70 Copynumber: 2.3 Consensus size: 75
33719885 ATGTGAAAAA
* * *
33719895 ATTGGAAATTAAAAGTGATTTGAATT-AAGT-AATTGAATT-AT-G-AATTATGTGAATATTTGA
1 ATTGGAAACTAATAGTGATTTGAATTGAA-TAAATTGAATTAATAGAAAATATGTGAATATTTGA
33719955 A-AGTATATTG
65 AGAGTATATTG
*
33719965 ATTGGAAACTAATAGTGATTTGAATTGAATCAAATTGAATTGAATGAAGAAAATATGTGAGTATT
1 ATTGGAAACTAATAGTGATTTGAATTGAAT-AAATTGAATT-AAT--AGAAAATATGTGAATATT
*
33720030 TGAAGTGTATATTG
62 TGAAGAGTATATTG
* *
33720044 ATTGAAAAGTAATTAGTGATTTGAATT
1 ATTGGAAACTAA-TAGTGATTTGAATT
33720071 TGATTGGAAA
Statistics
Matches: 88, Mismatches: 7, Indels: 12
0.82 0.07 0.11
Matches are distributed among these distances:
70 25 0.28
71 2 0.02
72 9 0.10
74 2 0.02
77 1 0.01
78 17 0.19
79 18 0.20
80 14 0.16
ACGTcount: A:0.41, C:0.01, G:0.20, T:0.38
Consensus pattern (75 bp):
ATTGGAAACTAATAGTGATTTGAATTGAATAAATTGAATTAATAGAAAATATGTGAATATTTGAA
GAGTATATTG
Found at i:33720105 original size:86 final size:78
Alignment explanation
Indices: 33719940--33720090 Score: 194
Period size: 79 Copynumber: 1.9 Consensus size: 78
33719930 AATTATGAAT
* *
33719940 TATGTGAATATTTGAAAGTATATTGATTGGAAACTAATAGTGATTTGAATTGAATCAAATTGAAT
1 TATGTGAATATTTGAAAGTATATTGATTGAAAACTAATAGTGATTTGAATTGAATCAAAATGAAT
*
33720005 TGAATGAAGAAAA
66 TAAATGAAGAAAA
* * * * *
33720018 TATGTGAGTATTTGAAGTGTATATTGATTGAAAAGTAATTAGTGATTTGAATTTGATTGGAAAAT
1 TATGTGAATATTTGAA-AGTATATTGATTGAAAACTAA-TAGTGATTTGAA-TTGAAT-CAAAAT
33720083 GAATTAAA
62 GAATTAAA
33720091 AATATGAATT
Statistics
Matches: 61, Mismatches: 8, Indels: 4
0.84 0.11 0.05
Matches are distributed among these distances:
78 15 0.25
79 18 0.30
80 12 0.20
81 5 0.08
82 11 0.18
ACGTcount: A:0.41, C:0.01, G:0.21, T:0.37
Consensus pattern (78 bp):
TATGTGAATATTTGAAAGTATATTGATTGAAAACTAATAGTGATTTGAATTGAATCAAAATGAAT
TAAATGAAGAAAA
Found at i:33720291 original size:34 final size:36
Alignment explanation
Indices: 33720251--33720317 Score: 104
Period size: 34 Copynumber: 1.9 Consensus size: 36
33720241 AAGTGGAAAA
33720251 GTGAATTTGAATTG-AA-TGAGAATTGA-ATTGAATT
1 GTGAATTTGAATTGAAAGTGA-AATTGACATTGAATT
33720285 GTGAATTTGAATTGAAAGTGAAATTGACATTGA
1 GTGAATTTGAATTGAAAGTGAAATTGACATTGA
33720318 CAGTGATTTG
Statistics
Matches: 30, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
34 14 0.47
35 8 0.27
36 8 0.27
ACGTcount: A:0.39, C:0.01, G:0.24, T:0.36
Consensus pattern (36 bp):
GTGAATTTGAATTGAAAGTGAAATTGACATTGAATT
Found at i:33720309 original size:18 final size:17
Alignment explanation
Indices: 33720248--33720323 Score: 75
Period size: 18 Copynumber: 4.4 Consensus size: 17
33720238 AGGAAGTGGA
*
33720248 AAAGTGAATTTGAATTG
1 AAAGTGAAATTGAATTG
33720265 -AA-TGAGAATTGAATTG
1 AAAGTGA-AATTGAATTG
* *
33720281 AATTGTGAATTTGAATTG
1 AA-AGTGAAATTGAATTG
33720299 AAAGTGAAATTGACATTG
1 AAAGTGAAATTGA-ATTG
*
33720317 ACAGTGA
1 AAAGTGA
33720324 TTTGAAATGT
Statistics
Matches: 48, Mismatches: 6, Indels: 9
0.76 0.10 0.14
Matches are distributed among these distances:
15 3 0.06
16 11 0.23
17 10 0.21
18 21 0.44
19 3 0.06
ACGTcount: A:0.41, C:0.03, G:0.24, T:0.33
Consensus pattern (17 bp):
AAAGTGAAATTGAATTG
Found at i:33720327 original size:34 final size:32
Alignment explanation
Indices: 33720249--33720329 Score: 94
Period size: 34 Copynumber: 2.4 Consensus size: 32
33720239 GGAAGTGGAA
33720249 AAGTGAATTTGAATTGAATGAGAATTGAATTG
1 AAGTGAATTTGAATTGAATGAGAATTGAATTG
33720281 AATTGTGAATTTGAATTGAAAGTGA-AATTGACATTG
1 AA--GTGAATTTGAATTG-AA-TGAGAATTGA-ATTG
33720317 ACAGTG-ATTTGAA
1 A-AGTGAATTTGAA
33720330 ATGTGAATTT
Statistics
Matches: 43, Mismatches: 0, Indels: 10
0.81 0.00 0.19
Matches are distributed among these distances:
32 2 0.05
34 21 0.49
35 11 0.26
36 8 0.19
37 1 0.02
ACGTcount: A:0.40, C:0.02, G:0.23, T:0.35
Consensus pattern (32 bp):
AAGTGAATTTGAATTGAATGAGAATTGAATTG
Found at i:33720893 original size:12 final size:12
Alignment explanation
Indices: 33720876--33720910 Score: 70
Period size: 12 Copynumber: 2.9 Consensus size: 12
33720866 AGTGAAATTA
33720876 TGAATTGAAATG
1 TGAATTGAAATG
33720888 TGAATTGAAATG
1 TGAATTGAAATG
33720900 TGAATTGAAAT
1 TGAATTGAAAT
33720911 TGAGATATTA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 23 1.00
ACGTcount: A:0.43, C:0.00, G:0.23, T:0.34
Consensus pattern (12 bp):
TGAATTGAAATG
Found at i:33721794 original size:21 final size:21
Alignment explanation
Indices: 33721751--33721795 Score: 56
Period size: 21 Copynumber: 2.1 Consensus size: 21
33721741 AGTGGAGGCA
*
33721751 TGTCTCAAGACATGGCTTCAC
1 TGTCTCAAGACATGCCTTCAC
*
33721772 TGTCTTAAGACATAGCCTT-AC
1 TGTCTCAAGACAT-GCCTTCAC
33721793 TGT
1 TGT
33721796 AACAGCCCGT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
21 17 0.81
22 4 0.19
ACGTcount: A:0.24, C:0.24, G:0.18, T:0.33
Consensus pattern (21 bp):
TGTCTCAAGACATGCCTTCAC
Found at i:33725517 original size:26 final size:26
Alignment explanation
Indices: 33725488--33725541 Score: 108
Period size: 26 Copynumber: 2.1 Consensus size: 26
33725478 AAATGCCCAC
33725488 CATGGAACATTTACCTAACCCATTAT
1 CATGGAACATTTACCTAACCCATTAT
33725514 CATGGAACATTTACCTAACCCATTAT
1 CATGGAACATTTACCTAACCCATTAT
33725540 CA
1 CA
33725542 ATTTTTATCA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 28 1.00
ACGTcount: A:0.35, C:0.28, G:0.07, T:0.30
Consensus pattern (26 bp):
CATGGAACATTTACCTAACCCATTAT
Found at i:33728884 original size:17 final size:18
Alignment explanation
Indices: 33728859--33728893 Score: 54
Period size: 17 Copynumber: 2.0 Consensus size: 18
33728849 GACCAATTTG
*
33728859 GGTCGTGTGGG-CCACAC
1 GGTCATGTGGGCCCACAC
33728876 GGTCATGTGGGCCCACAC
1 GGTCATGTGGGCCCACAC
33728894 AGGTGTGTGG
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 10 0.62
18 6 0.38
ACGTcount: A:0.14, C:0.31, G:0.37, T:0.17
Consensus pattern (18 bp):
GGTCATGTGGGCCCACAC
Found at i:33728902 original size:18 final size:17
Alignment explanation
Indices: 33728859--33728904 Score: 58
Period size: 18 Copynumber: 2.6 Consensus size: 17
33728849 GACCAATTTG
33728859 GGTCGTGTGGGCCACAC
1 GGTCGTGTGGGCCACAC
*
33728876 GGTCATGTGGGCCCACAC
1 GGTCGTGTGGG-CCACAC
33728894 AGGT-GTGTGGG
1 -GGTCGTGTGGG
33728905 ACTCTGGGCT
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
17 10 0.40
18 12 0.48
19 3 0.12
ACGTcount: A:0.13, C:0.24, G:0.43, T:0.20
Consensus pattern (17 bp):
GGTCGTGTGGGCCACAC
Found at i:33750860 original size:45 final size:44
Alignment explanation
Indices: 33750808--33750896 Score: 126
Period size: 45 Copynumber: 2.0 Consensus size: 44
33750798 TCCATCCCCG
* * *
33750808 GAATTATATCAAATTC-ATCGAAAGGTAATAGCATCAGATCAGCA
1 GAATTATATCAAATTCGCT-GAAAGGCAATAGCATAAGATCAGCA
33750852 GNAATTATATCAAATTCGCTGAAAGGCAATAGCATAAGATCAGCA
1 G-AATTATATCAAATTCGCTGAAAGGCAATAGCATAAGATCAGCA
33750897 AGAAAACATG
Statistics
Matches: 40, Mismatches: 3, Indels: 3
0.87 0.07 0.07
Matches are distributed among these distances:
44 1 0.03
45 38 0.95
46 1 0.03
ACGTcount: A:0.43, C:0.16, G:0.17, T:0.24
Consensus pattern (44 bp):
GAATTATATCAAATTCGCTGAAAGGCAATAGCATAAGATCAGCA
Found at i:33761408 original size:36 final size:36
Alignment explanation
Indices: 33761363--33761441 Score: 140
Period size: 36 Copynumber: 2.2 Consensus size: 36
33761353 ACACATGCAC
*
33761363 TTTTTATCTCACTCAAGCCTAGTCGAACATTTTTCT
1 TTTTTATCTCACCCAAGCCTAGTCGAACATTTTTCT
33761399 TTTTTATCTCACCCAAGCCTAGTCGAACATTTTTCT
1 TTTTTATCTCACCCAAGCCTAGTCGAACATTTTTCT
*
33761435 TTCTTAT
1 TTTTTAT
33761442 GGTAGCCCAA
Statistics
Matches: 41, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
36 41 1.00
ACGTcount: A:0.22, C:0.25, G:0.08, T:0.46
Consensus pattern (36 bp):
TTTTTATCTCACCCAAGCCTAGTCGAACATTTTTCT
Found at i:33766972 original size:19 final size:17
Alignment explanation
Indices: 33766922--33766973 Score: 52
Period size: 19 Copynumber: 2.9 Consensus size: 17
33766912 TAGATATAAC
33766922 TAAAAATACTATAAAAGG
1 TAAAAATA-TATAAAAGG
*
33766940 TATAAAT-TATTAAAAGTTG
1 TAAAAATATA-TAAAAG--G
33766959 TAAAAATATATAAAA
1 TAAAAATATATAAAA
33766974 ATAGAATTAT
Statistics
Matches: 28, Mismatches: 2, Indels: 7
0.76 0.05 0.19
Matches are distributed among these distances:
16 2 0.07
17 6 0.21
18 6 0.21
19 12 0.43
20 2 0.07
ACGTcount: A:0.60, C:0.02, G:0.08, T:0.31
Consensus pattern (17 bp):
TAAAAATATATAAAAGG
Found at i:33770460 original size:29 final size:29
Alignment explanation
Indices: 33770428--33770484 Score: 114
Period size: 29 Copynumber: 2.0 Consensus size: 29
33770418 AAACTATTGT
33770428 GTTGACATATTATTTCAATAGGTGGAACA
1 GTTGACATATTATTTCAATAGGTGGAACA
33770457 GTTGACATATTATTTCAATAGGTGGAAC
1 GTTGACATATTATTTCAATAGGTGGAAC
33770485 CATGGGCCAA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 28 1.00
ACGTcount: A:0.33, C:0.11, G:0.21, T:0.35
Consensus pattern (29 bp):
GTTGACATATTATTTCAATAGGTGGAACA
Found at i:33771140 original size:21 final size:21
Alignment explanation
Indices: 33771114--33771153 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
33771104 ACGGCCTGCG
*
33771114 CATACGGGCATGTGGAGTAAT
1 CATACGGGCATGTAGAGTAAT
*
33771135 CATACGGGTATGTAGAGTA
1 CATACGGGCATGTAGAGTA
33771154 GGCACAAAAG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.30, C:0.12, G:0.33, T:0.25
Consensus pattern (21 bp):
CATACGGGCATGTAGAGTAAT
Found at i:33773185 original size:19 final size:17
Alignment explanation
Indices: 33773135--33773186 Score: 52
Period size: 19 Copynumber: 2.9 Consensus size: 17
33773125 TAGATATAAC
33773135 TAAAAATACTATAAAAGG
1 TAAAAATA-TATAAAAGG
*
33773153 TATAAAT-TATTAAAAGTTG
1 TAAAAATATA-TAAAAG--G
33773172 TAAAAATATATAAAA
1 TAAAAATATATAAAA
33773187 ATAGAATTAT
Statistics
Matches: 28, Mismatches: 2, Indels: 7
0.76 0.05 0.19
Matches are distributed among these distances:
16 2 0.07
17 6 0.21
18 6 0.21
19 12 0.43
20 2 0.07
ACGTcount: A:0.60, C:0.02, G:0.08, T:0.31
Consensus pattern (17 bp):
TAAAAATATATAAAAGG
Found at i:33782952 original size:13 final size:13
Alignment explanation
Indices: 33782936--33782968 Score: 50
Period size: 13 Copynumber: 2.6 Consensus size: 13
33782926 TTTAATTAAA
*
33782936 TTAGTTAATTAGT
1 TTAGATAATTAGT
33782949 TTAGATAATTAGT
1 TTAGATAATTAGT
33782962 TTA-ATAA
1 TTAGATAA
33782969 ACAAATCCTT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
12 4 0.21
13 15 0.79
ACGTcount: A:0.39, C:0.00, G:0.12, T:0.48
Consensus pattern (13 bp):
TTAGATAATTAGT
Found at i:33793516 original size:17 final size:18
Alignment explanation
Indices: 33793496--33793541 Score: 51
Period size: 17 Copynumber: 2.7 Consensus size: 18
33793486 TTTTTATCAT
*
33793496 TTATCATTTTTCGGGCA-
1 TTATCATTTATCGGGCAC
* *
33793513 TTATAATTGATCGGGCAC
1 TTATCATTTATCGGGCAC
33793531 TT-TCATTTATC
1 TTATCATTTATC
33793542 AAGCTTTAAC
Statistics
Matches: 23, Mismatches: 5, Indels: 2
0.77 0.17 0.07
Matches are distributed among these distances:
17 21 0.91
18 2 0.09
ACGTcount: A:0.22, C:0.17, G:0.15, T:0.46
Consensus pattern (18 bp):
TTATCATTTATCGGGCAC
Found at i:33812302 original size:33 final size:33
Alignment explanation
Indices: 33812265--33812327 Score: 108
Period size: 33 Copynumber: 1.9 Consensus size: 33
33812255 TGTATCTCTC
33812265 AATTACAAACAAGTAAACCCAAATCTAATTTGT
1 AATTACAAACAAGTAAACCCAAATCTAATTTGT
* *
33812298 AATTACAAACAATTAAACCTAAATCTAATT
1 AATTACAAACAAGTAAACCCAAATCTAATT
33812328 GTTAAGTGAC
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
33 28 1.00
ACGTcount: A:0.51, C:0.17, G:0.03, T:0.29
Consensus pattern (33 bp):
AATTACAAACAAGTAAACCCAAATCTAATTTGT
Done.