Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: At_chr6
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: 56482370
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.32
Warning! 1659275 characters in sequence are not A, C, G, or T
File 119 of 172
Found at i:39630623 original size:28 final size:29
Alignment explanation
Indices: 39630575--39630631 Score: 73
Period size: 28 Copynumber: 2.0 Consensus size: 29
39630565 AATATTTTAA
39630575 TAATATTTTATATAGTTTATTT-AATATT
1 TAATATTTTATATAGTTTATTTAAATATT
* *
39630603 TAATATTTTATCT-TTTATATTTAAATATT
1 TAATATTTTATATAGTT-TATTTAAATATT
39630632 ATTCTTTTGA
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
27 2 0.08
28 17 0.68
29 6 0.24
ACGTcount: A:0.35, C:0.02, G:0.02, T:0.61
Consensus pattern (29 bp):
TAATATTTTATATAGTTTATTTAAATATT
Found at i:39630669 original size:20 final size:21
Alignment explanation
Indices: 39630624--39630669 Score: 67
Period size: 20 Copynumber: 2.2 Consensus size: 21
39630614 CTTTTATATT
*
39630624 TAAATATTATTCTTTTGATAG
1 TAAATATTATTCTTTTAATAG
*
39630645 AAAATATTATTC-TTTAATAG
1 TAAATATTATTCTTTTAATAG
39630665 TAAAT
1 TAAAT
39630670 TGATGGAAAA
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
20 11 0.50
21 11 0.50
ACGTcount: A:0.41, C:0.04, G:0.07, T:0.48
Consensus pattern (21 bp):
TAAATATTATTCTTTTAATAG
Found at i:39633488 original size:29 final size:30
Alignment explanation
Indices: 39633421--39633489 Score: 95
Period size: 29 Copynumber: 2.3 Consensus size: 30
39633411 TATCAAAGTT
*
39633421 ATACATGAACTATGATTTAATATTCAATTTG
1 ATACATGAACTATGATTT-ATATGCAATTTG
* *
39633452 ATATATGAACTTTGATTT-TATGCAATTTG
1 ATACATGAACTATGATTTATATGCAATTTG
39633481 ATACATGAA
1 ATACATGAA
39633490 TATTAAACTT
Statistics
Matches: 34, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
29 18 0.53
31 16 0.47
ACGTcount: A:0.38, C:0.09, G:0.12, T:0.42
Consensus pattern (30 bp):
ATACATGAACTATGATTTATATGCAATTTG
Found at i:39641521 original size:20 final size:20
Alignment explanation
Indices: 39641498--39641535 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
39641488 ACTAAAAAAA
*
39641498 TTTAAACTAATTTTTAAATT
1 TTTAAAATAATTTTTAAATT
39641518 TTTAAAATAATTTTTAAA
1 TTTAAAATAATTTTTAAA
39641536 ATTAAAAAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.45, C:0.03, G:0.00, T:0.53
Consensus pattern (20 bp):
TTTAAAATAATTTTTAAATT
Found at i:39641544 original size:20 final size:20
Alignment explanation
Indices: 39641505--39641544 Score: 53
Period size: 20 Copynumber: 2.0 Consensus size: 20
39641495 AAATTTAAAC
* **
39641505 TAATTTTTAAATTTTTAAAA
1 TAATTTTTAAAATTAAAAAA
39641525 TAATTTTTAAAATTAAAAAA
1 TAATTTTTAAAATTAAAAAA
39641545 ATAAAAATTT
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (20 bp):
TAATTTTTAAAATTAAAAAA
Found at i:39643131 original size:17 final size:17
Alignment explanation
Indices: 39643109--39643151 Score: 86
Period size: 17 Copynumber: 2.5 Consensus size: 17
39643099 TATATCGAAC
39643109 TATTCAAACTCAATGAG
1 TATTCAAACTCAATGAG
39643126 TATTCAAACTCAATGAG
1 TATTCAAACTCAATGAG
39643143 TATTCAAAC
1 TATTCAAAC
39643152 ATTCACTTTC
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 26 1.00
ACGTcount: A:0.42, C:0.19, G:0.09, T:0.30
Consensus pattern (17 bp):
TATTCAAACTCAATGAG
Found at i:39643280 original size:18 final size:18
Alignment explanation
Indices: 39643259--39643541 Score: 169
Period size: 18 Copynumber: 15.3 Consensus size: 18
39643249 GAACAATTAT
*
39643259 TTATTCAATAACAGTCAG
1 TTATTCAGTAACAGTCAG
* * *
39643277 TTATTCGGTAACAATCAA
1 TTATTCAGTAACAGTCAG
* * **
39643295 TTATTCAATAATAACCAG
1 TTATTCAGTAACAGTCAG
*
39643313 TTATTCAGTATCGATCAATTGATCGG
1 TTATTCAGTA---A-C-A--G-TCAG
* *
39643339 TTATCCAGTAACAGTCAA
1 TTATTCAGTAACAGTCAG
*
39643357 TTATTCAGTAA-AATCAG
1 TTATTCAGTAACAGTCAG
* * *
39643374 GTATTCAGTAACAATTAAG
1 TTATTCAGTAAC-AGTCAG
39643393 TTATTCAGTAACAGTCA-
1 TTATTCAGTAACAGTCAG
* *
39643410 TTCATTCAGTGACAATCAG
1 TT-ATTCAGTAACAGTCAG
* *
39643429 TTATTCAGTAA-TGATCAA
1 TTATTCAGTAACAG-TCAG
* *
39643447 TTATTCAGTAATATTCAG
1 TTATTCAGTAACAGTCAG
39643465 TTATTCAGTAACAGTCTA-
1 TTATTCAGTAACAGTC-AG
* * *
39643483 ATATCCAGTAACAGTCAA
1 TTATTCAGTAACAGTCAG
* * *
39643501 TTATCCGGTAACAGTCAA
1 TTATTCAGTAACAGTCAG
* *
39643519 TTATTCAGTAATAATCAG
1 TTATTCAGTAACAGTCAG
39643537 TTATT
1 TTATT
39643542 TTATACCTTT
Statistics
Matches: 203, Mismatches: 46, Indels: 32
0.72 0.16 0.11
Matches are distributed among these distances:
17 17 0.08
18 151 0.74
19 19 0.09
21 2 0.01
22 1 0.00
23 2 0.01
26 11 0.05
ACGTcount: A:0.37, C:0.16, G:0.12, T:0.35
Consensus pattern (18 bp):
TTATTCAGTAACAGTCAG
Found at i:39643314 original size:36 final size:36
Alignment explanation
Indices: 39643246--39643332 Score: 95
Period size: 36 Copynumber: 2.4 Consensus size: 36
39643236 TCATTAACAA
* * **
39643246 TCAG-AACAATTATTTATTCAATAACAGTCAGTTAT
1 TCAGTAACAATCAATTATTCAATAACAACCAGTTAT
* *
39643281 TCGGTAACAATCAATTATTCAATAATAACCAGTTAT
1 TCAGTAACAATCAATTATTCAATAACAACCAGTTAT
* *
39643317 TCAGTATCGATCAATT
1 TCAGTAACAATCAATT
39643333 GATCGGTTAT
Statistics
Matches: 42, Mismatches: 9, Indels: 1
0.81 0.17 0.02
Matches are distributed among these distances:
35 3 0.07
36 39 0.93
ACGTcount: A:0.39, C:0.16, G:0.09, T:0.36
Consensus pattern (36 bp):
TCAGTAACAATCAATTATTCAATAACAACCAGTTAT
Found at i:39643402 original size:54 final size:55
Alignment explanation
Indices: 39643338--39643541 Score: 202
Period size: 54 Copynumber: 3.8 Consensus size: 55
39643328 CAATTGATCG
* * *
39643338 GTTATCCAGTAACAGTCAATTATTCAGTAA-AATCAGGTATTCAGTAACAATTAA
1 GTTATTCAGTAACAGTCAATTATTCAGTAATAATCAGTTATTCAGTAACAATCAA
* * **
39643392 GTTATTCAGTAACAGTC-ATTCATTCAGTGACAATCAGTTATTCAGTAATGATCAA
1 GTTATTCAGTAACAGTCAATT-ATTCAGTAATAATCAGTTATTCAGTAACAATCAA
* * * * * * * *
39643447 -TTATTCAGTAATATTCAGTTATTCAGTAACAGTCTA-ATATCCAGTAACAGTCAA
1 GTTATTCAGTAACAGTCAATTATTCAGTAATAATC-AGTTATTCAGTAACAATCAA
* *
39643501 -TTATCCGGTAACAGTCAATTATTCAGTAATAATCAGTTATT
1 GTTATTCAGTAACAGTCAATTATTCAGTAATAATCAGTTATT
39643542 TTATACCTTT
Statistics
Matches: 120, Mismatches: 25, Indels: 10
0.77 0.16 0.06
Matches are distributed among these distances:
53 4 0.03
54 93 0.77
55 23 0.19
ACGTcount: A:0.37, C:0.16, G:0.13, T:0.35
Consensus pattern (55 bp):
GTTATTCAGTAACAGTCAATTATTCAGTAATAATCAGTTATTCAGTAACAATCAA
Found at i:39643474 original size:72 final size:71
Alignment explanation
Indices: 39643340--39643541 Score: 226
Period size: 72 Copynumber: 2.8 Consensus size: 71
39643330 ATTGATCGGT
* ** * *
39643340 TATCCAGTAACAGTCAATTATTCAGTAAAATCAGGTATTCAGTAACAATTAAGTTATTCAGTAAC
1 TATCCAGTAACAATCAATTATTCAGTAAAATCAATTATTCAGTAA-TATTCAGTTATTCAGTAAC
*
39643405 AGTC-AT
65 AGTCTAA
* * * *
39643411 TCATTCAGTGACAATCAGTTATTCAGTAATGATCAATTATTCAGTAATATTCAGTTATTCAGTAA
1 T-ATCCAGTAACAATCAATTATTCAGTAA-AATCAATTATTCAGTAATATTCAGTTATTCAGTAA
39643476 CAGTCTAA
64 CAGTCTAA
* * * * *
39643484 TATCCAGTAACAGTCAATTATCCGGTAACAGTCAATTATTCAGTAATAATCAGTTATT
1 TATCCAGTAACAATCAATTATTCAGTAA-AATCAATTATTCAGTAATATTCAGTTATT
39643542 TTATACCTTT
Statistics
Matches: 108, Mismatches: 20, Indels: 5
0.81 0.15 0.04
Matches are distributed among these distances:
71 1 0.01
72 91 0.84
73 16 0.15
ACGTcount: A:0.37, C:0.16, G:0.12, T:0.35
Consensus pattern (71 bp):
TATCCAGTAACAATCAATTATTCAGTAAAATCAATTATTCAGTAATATTCAGTTATTCAGTAACA
GTCTAA
Found at i:39643881 original size:256 final size:256
Alignment explanation
Indices: 39643576--39644087 Score: 898
Period size: 256 Copynumber: 2.0 Consensus size: 256
39643566 ACATGACTCG
* *
39643576 AACTCAGACGGATACACGGATCCAACCAACACACCAGTACGGCACATAGTGCCTCATCGGCCGAA
1 AACTCAGACGGATACACAGATCCAACCAACACACCAATACGGCACATAGTGCCTCATCGGCCGAA
* *
39643641 GCCGGAGCCGTAACAATAACAGTACGGTACACAGAGTACCTCATCGAAACAAATCCGAAACAGTA
66 GCCGGAACAGTAACAATAACAGTACGGTACACAGAGTACCTCATCGAAACAAATCCGAAACAGTA
*
39643706 ACAGTAACGGTATCAGTAACAATATCTGACACACAAAGTGCCGAATCGGTAACAGTAACGATAAC
131 ACAGTAACGGTAACAGTAACAATATCTGACACACAAAGTGCCGAATCGGTAACAGTAACGATAAC
39643771 AGTAATAGTAGTCGACACATAAGTGCCTGATCAGTAAGCCGGCAAAACCCGTACTCTTCCA
196 AGTAATAGTAGTCGACACATAAGTGCCTGATCAGTAAGCCGGCAAAACCCGTACTCTTCCA
*
39643832 AACTCAGACGGATACACAGATCCAACCAACACACCAATATGGCACATAGTGCCTCATCGGCCGAA
1 AACTCAGACGGATACACAGATCCAACCAACACACCAATACGGCACATAGTGCCTCATCGGCCGAA
* * * * * * *
39643897 TCCGGAACAGTAATAGTAGCAGTTCGGTACACAGAGTACCTCATCGGAACAAATCTGAAACAGTA
66 GCCGGAACAGTAACAATAACAGTACGGTACACAGAGTACCTCATCGAAACAAATCCGAAACAGTA
*
39643962 ATAGTAACGGTAACAGTAACAATATCTGACACACAAAGTGCCGAATCGGTAACAGTAACGATAAC
131 ACAGTAACGGTAACAGTAACAATATCTGACACACAAAGTGCCGAATCGGTAACAGTAACGATAAC
39644027 AGTAATAGTAGTCGACACATAAGTGCCTGATCAGTAAGCCGGCAAAACCCGTACTCTTCCA
196 AGTAATAGTAGTCGACACATAAGTGCCTGATCAGTAAGCCGGCAAAACCCGTACTCTTCCA
39644088 TATCCTATGG
Statistics
Matches: 242, Mismatches: 14, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
256 242 1.00
ACGTcount: A:0.37, C:0.26, G:0.19, T:0.17
Consensus pattern (256 bp):
AACTCAGACGGATACACAGATCCAACCAACACACCAATACGGCACATAGTGCCTCATCGGCCGAA
GCCGGAACAGTAACAATAACAGTACGGTACACAGAGTACCTCATCGAAACAAATCCGAAACAGTA
ACAGTAACGGTAACAGTAACAATATCTGACACACAAAGTGCCGAATCGGTAACAGTAACGATAAC
AGTAATAGTAGTCGACACATAAGTGCCTGATCAGTAAGCCGGCAAAACCCGTACTCTTCCA
Found at i:39645465 original size:31 final size:32
Alignment explanation
Indices: 39645409--39645471 Score: 85
Period size: 31 Copynumber: 2.0 Consensus size: 32
39645399 CACACTTGTC
*
39645409 ATAATTTAATATATTTATTACATAAAAATCTT
1 ATAATATAATATATTTATTACATAAAAATCTT
*
39645441 ATAATATAA-ATATTTAATTA-ATAAATATCTT
1 ATAATATAATATATTT-ATTACATAAAAATCTT
39645472 TTATAAATAA
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
31 16 0.57
32 12 0.43
ACGTcount: A:0.49, C:0.05, G:0.00, T:0.46
Consensus pattern (32 bp):
ATAATATAATATATTTATTACATAAAAATCTT
Found at i:39645758 original size:119 final size:119
Alignment explanation
Indices: 39645527--39645761 Score: 443
Period size: 119 Copynumber: 2.0 Consensus size: 119
39645517 AATGTATGTA
* *
39645527 TTCAATTTATTACACATGTATTTTATAATTACCACACATTTGTCACTATTTTAATTTATTTCATA
1 TTCAATTTATTACACATGCATTTTATAATTACCACACATTTGTCACTATTTTAATTTATTTAATA
39645592 ATATAATATAATATTAATATTAATTAATAATTATAGCAATAATTTAATATTCTG
66 ATATAATATAATATTAATATTAATTAATAATTATAGCAATAATTTAATATTCTG
39645646 TTCAATTTATTACACATGCATTTTATAATTACCACACATTTGTCACTATTTTAATTTATTTAATA
1 TTCAATTTATTACACATGCATTTTATAATTACCACACATTTGTCACTATTTTAATTTATTTAATA
*
39645711 ATATAATATACTATTAATATTAATTAATAATTATAGCAATAATTTAATATT
66 ATATAATATAATATTAATATTAATTAATAATTATAGCAATAATTTAATATT
39645762 TAAATAAATA
Statistics
Matches: 113, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
119 113 1.00
ACGTcount: A:0.40, C:0.10, G:0.03, T:0.47
Consensus pattern (119 bp):
TTCAATTTATTACACATGCATTTTATAATTACCACACATTTGTCACTATTTTAATTTATTTAATA
ATATAATATAATATTAATATTAATTAATAATTATAGCAATAATTTAATATTCTG
Found at i:39655077 original size:40 final size:40
Alignment explanation
Indices: 39654994--39655085 Score: 107
Period size: 40 Copynumber: 2.4 Consensus size: 40
39654984 GTACCTTTTG
* * *
39654994 GTGTGTAGGGTTGGATGGGTTGATTATATCCCTAAACTTT
1 GTGTGTAGGGTTGGATGGGTCGATTATATCCCCAAACTGT
* * *
39655034 GTGTGTAGGGTTGGGTGGGTCGATTCTATCCCCACA-TG-
1 GTGTGTAGGGTTGGATGGGTCGATTATATCCCCAAACTGT
*
39655072 GTGTGTTGGGTTGG
1 GTGTGTAGGGTTGG
39655086 TTGGAGATGG
Statistics
Matches: 45, Mismatches: 7, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
38 13 0.29
39 1 0.02
40 31 0.69
ACGTcount: A:0.14, C:0.12, G:0.37, T:0.37
Consensus pattern (40 bp):
GTGTGTAGGGTTGGATGGGTCGATTATATCCCCAAACTGT
Found at i:39658137 original size:46 final size:46
Alignment explanation
Indices: 39658001--39658174 Score: 181
Period size: 46 Copynumber: 3.7 Consensus size: 46
39657991 GTTATTGTGG
* ** * *
39658001 GCTAGTGTAAGACATGTCTGGGACATGCATCGGCCACATTATGAGA
1 GCTAGTGTAAGACATGTCTGGGACATGCATCGGCCTCAAGACGAGT
* * * * * *
39658047 GCTTGTATAAGACCATGTCTGGGATATGGAATCGGCATCGAGACGAGT
1 GCTAGTGTAAGA-CATGTCTGGGACAT-GCATCGGCCTCAAGACGAGT
* *
39658095 GCTACTGTAAGACATGTTTGGGACATGCATCGGCCTCAAGACGTAAGT
1 GCTAGTGTAAGACATGTCTGGGACATGCATCGGCCTCAAGACG--AGT
39658143 -C-AGTGTAAGACATGTCTGGGACATGCATCGGC
1 GCTAGTGTAAGACATGTCTGGGACATGCATCGGC
39658175 TACGAGATGA
Statistics
Matches: 103, Mismatches: 21, Indels: 8
0.78 0.16 0.06
Matches are distributed among these distances:
46 53 0.51
47 26 0.25
48 24 0.23
ACGTcount: A:0.27, C:0.20, G:0.29, T:0.24
Consensus pattern (46 bp):
GCTAGTGTAAGACATGTCTGGGACATGCATCGGCCTCAAGACGAGT
Found at i:39658190 original size:46 final size:46
Alignment explanation
Indices: 39658002--39658210 Score: 173
Period size: 46 Copynumber: 4.5 Consensus size: 46
39657992 TTATTGTGGG
* *
39658002 CTAGTGTAAGACATGTCTGGGACATGCATCGGCCACATTATGA-G-AG-
1 CTAGTGTAAGACATGTCTGGGACATGCATCGGCTAC--GA-GACGTAGT
* * * *
39658048 CTTGTATAAGACCATGTCTGGGATATGGAATCGGC-ATCGAGACG-AGT
1 CTAGTGTAAGA-CATGTCTGGGACAT-GCATCGGCTA-CGAGACGTAGT
* * *
39658095 GCTACTGTAAGACATGTTTGGGACATGCATCGGCCT-CAAGACGTAAGT
1 -CTAGTGTAAGACATGTCTGGGACATGCATCGG-CTACGAGACGT-AGT
*
39658143 C-AGTGTAAGACATGTCTGGGACATGCATCGGCTACGAGATGATAGT
1 CTAGTGTAAGACATGTCTGGGACATGCATCGGCTACGAGACG-TAGT
39658189 C-AGTGTAAGACCATGTCTGGGA
1 CTAGTGTAAGA-CATGTCTGGGA
39658211 TATGGCATTG
Statistics
Matches: 134, Mismatches: 16, Indels: 25
0.77 0.09 0.14
Matches are distributed among these distances:
45 4 0.03
46 71 0.53
47 40 0.30
48 19 0.14
ACGTcount: A:0.28, C:0.19, G:0.29, T:0.24
Consensus pattern (46 bp):
CTAGTGTAAGACATGTCTGGGACATGCATCGGCTACGAGACGTAGT
Found at i:39662404 original size:46 final size:46
Alignment explanation
Indices: 39662271--39662406 Score: 184
Period size: 46 Copynumber: 3.0 Consensus size: 46
39662261 TTATCTTCGA
* * * * * *
39662271 CATGATGCCATAGTGTCTTTCAACTATGGTCTTACTCATTTTC-TGT
1 CATGTTGCCATGGTATCTTTCAACCATGGTCTTACACA-TTTCATAT
*
39662317 CATGTTGCCATGGTATCTTTCAACCATGGTCTTAAACATTTCATAT
1 CATGTTGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATAT
*
39662363 CATGTTGTCATGGTATCTTTCAACCATGGTCTTACACATTTCAT
1 CATGTTGCCATGGTATCTTTCAACCATGGTCTTACACATTTCAT
39662407 TTCAGAAAAC
Statistics
Matches: 80, Mismatches: 9, Indels: 2
0.88 0.10 0.02
Matches are distributed among these distances:
45 4 0.05
46 76 0.95
ACGTcount: A:0.23, C:0.22, G:0.14, T:0.41
Consensus pattern (46 bp):
CATGTTGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATAT
Found at i:39668732 original size:46 final size:46
Alignment explanation
Indices: 39668678--39668896 Score: 232
Period size: 46 Copynumber: 4.7 Consensus size: 46
39668668 ATTGTGGGCT
* *
39668678 AGTGTAAGACATGTCTGGGACATGCATCGGCCAC-ATTATGAGAGCC
1 AGTGTAAGACATGTCTGGGACATGCATCGGCCACGA-GATGAGAGTC
* *
39668724 TGTGTAAGACCATGTCTAGGG-CATGGCATCGG-CACCGAGATGAGTG-C
1 AGTGTAAGA-CATGTCT-GGGACAT-GCATCGGCCA-CGAGATGAGAGTC
* * *
39668771 TAATGTAAGACATGTCTGGGACATGCATCGGCCTCGAGACGTA-AGTC
1 -AGTGTAAGACATGTCTGGGACATGCATCGGCCACGAGATG-AGAGTC
* *
39668818 AGTGTAAGACATGTCTGGGACATGCATCGGCTACGAGATGATAGTC
1 AGTGTAAGACATGTCTGGGACATGCATCGGCCACGAGATGAGAGTC
*
39668864 AGTGTAAGACAATGTCTGGGATATGGCATCGGC
1 AGTGTAAGAC-ATGTCTGGGACAT-GCATCGGC
39668897 ACTCTACCCC
Statistics
Matches: 147, Mismatches: 13, Indels: 24
0.80 0.07 0.13
Matches are distributed among these distances:
45 1 0.01
46 75 0.51
47 38 0.26
48 32 0.22
49 1 0.01
ACGTcount: A:0.27, C:0.20, G:0.31, T:0.23
Consensus pattern (46 bp):
AGTGTAAGACATGTCTGGGACATGCATCGGCCACGAGATGAGAGTC
Found at i:39675120 original size:3 final size:3
Alignment explanation
Indices: 39675112--39675144 Score: 66
Period size: 3 Copynumber: 11.0 Consensus size: 3
39675102 AAACCGACCT
39675112 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
39675145 TTATTATTAT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 30 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:39675368 original size:26 final size:25
Alignment explanation
Indices: 39675325--39675373 Score: 62
Period size: 26 Copynumber: 1.9 Consensus size: 25
39675315 ATGAAATAAG
*
39675325 AATTATATATGCTGTTTAATAAATTA
1 AATTATATATACTGTTT-ATAAATTA
* *
39675351 AATTATATATATTTTTTATAAAT
1 AATTATATATACTGTTTATAAAT
39675374 ATTAAAAAAC
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
25 6 0.30
26 14 0.70
ACGTcount: A:0.43, C:0.02, G:0.04, T:0.51
Consensus pattern (25 bp):
AATTATATATACTGTTTATAAATTA
Found at i:39681394 original size:25 final size:25
Alignment explanation
Indices: 39681356--39681422 Score: 71
Period size: 25 Copynumber: 2.7 Consensus size: 25
39681346 TCTCGAGCCA
* *
39681356 TATAACAGGAAGCTCATGTGAGTTG
1 TATAACAAGAAGCTCATCTGAGTTG
* * * *
39681381 TATGACGAGAAGCTTATCTGGGTTG
1 TATAACAAGAAGCTCATCTGAGTTG
*
39681406 TATAACAAGAGGCTCAT
1 TATAACAAGAAGCTCAT
39681423 AAGAGCCATA
Statistics
Matches: 32, Mismatches: 10, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
25 32 1.00
ACGTcount: A:0.31, C:0.13, G:0.27, T:0.28
Consensus pattern (25 bp):
TATAACAAGAAGCTCATCTGAGTTG
Found at i:39681444 original size:24 final size:24
Alignment explanation
Indices: 39681417--39681493 Score: 68
Period size: 24 Copynumber: 3.2 Consensus size: 24
39681407 ATAACAAGAG
39681417 GCTCATAAGAGCCATAATCGGGAA
1 GCTCATAAGAGCCATAATCGGGAA
* *
39681441 GCTCATATGAGCCAATAAT-GGGTA
1 GCTCATAAGAGCC-ATAATCGGGAA
* * *
39681465 GTTC-TGAAGAGCCATTAAACAGGAA
1 GCTCAT-AAGAGCCA-TAATCGGGAA
39681490 GCTC
1 GCTC
39681494 CGGATCGAGA
Statistics
Matches: 41, Mismatches: 8, Indels: 7
0.73 0.14 0.12
Matches are distributed among these distances:
23 2 0.05
24 28 0.68
25 11 0.27
ACGTcount: A:0.35, C:0.19, G:0.25, T:0.21
Consensus pattern (24 bp):
GCTCATAAGAGCCATAATCGGGAA
Found at i:39681556 original size:25 final size:26
Alignment explanation
Indices: 39681525--39681593 Score: 88
Period size: 25 Copynumber: 2.7 Consensus size: 26
39681515 GCCATATCGG
*
39681525 GAAGCTC-CGGAGAGCCATTAATCAA
1 GAAGCTCACGAAGAGCCATTAATCAA
* * *
39681550 GAAGCTCACAAAGAGCC-TTTATCGA
1 GAAGCTCACGAAGAGCCATTAATCAA
39681575 GAAGCTCACGAAGAGCCAT
1 GAAGCTCACGAAGAGCCAT
39681594 ATATCAGGAC
Statistics
Matches: 37, Mismatches: 5, Indels: 3
0.82 0.11 0.07
Matches are distributed among these distances:
25 29 0.78
26 8 0.22
ACGTcount: A:0.36, C:0.25, G:0.23, T:0.16
Consensus pattern (26 bp):
GAAGCTCACGAAGAGCCATTAATCAA
Found at i:39685054 original size:122 final size:122
Alignment explanation
Indices: 39684837--39685080 Score: 461
Period size: 122 Copynumber: 2.0 Consensus size: 122
39684827 AGCCAACTAG
39684837 TACGTATCCAAATTAACATACATTGTTTCACCATCAAACAAGATAACTAAATTTATTTAATCCAC
1 TACGTATCCAAATTAACATACATTGTTTCACCATCAAACAAGATAACTAAATTTATTTAATCCAC
*
39684902 CCATATACTCATATATGTATAGATAGTCATTAAGAGGTGTTATTTGGGATGTCTTAA
66 CCATATACTCATATATGTATAGATAGTCATTAAGAGGTGGTATTTGGGATGTCTTAA
39684959 TACGTATCCAAATTAACATACATTGTTTCACCATCAAACAAGATAACTAAATTTATTTAATCCAC
1 TACGTATCCAAATTAACATACATTGTTTCACCATCAAACAAGATAACTAAATTTATTTAATCCAC
* *
39685024 CCATATACTTATATATGTGTAGATAGTCATTAAGAGGTGGTATTTGGGATGTCTTAA
66 CCATATACTCATATATGTATAGATAGTCATTAAGAGGTGGTATTTGGGATGTCTTAA
39685081 AGTGAGTCTC
Statistics
Matches: 119, Mismatches: 3, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
122 119 1.00
ACGTcount: A:0.36, C:0.16, G:0.12, T:0.35
Consensus pattern (122 bp):
TACGTATCCAAATTAACATACATTGTTTCACCATCAAACAAGATAACTAAATTTATTTAATCCAC
CCATATACTCATATATGTATAGATAGTCATTAAGAGGTGGTATTTGGGATGTCTTAA
Found at i:39685907 original size:57 final size:57
Alignment explanation
Indices: 39685789--39685984 Score: 234
Period size: 56 Copynumber: 3.5 Consensus size: 57
39685779 ATTATTTTGG
* * * * * ** **
39685789 TAATAAACAATAATGGACAACAACAATTAAATA-TCAGTTTGACAGTTTAATTACAA
1 TAATAAATAACAATGAACAACAACAATTAAACACCCTTTTTGACAACTTAATTACAA
* * * *
39685845 TAATAAATAACAATGAAGAACAATAATTAAACACCCTTTTTGACAACTTAATTTCAG
1 TAATAAATAACAATGAACAACAACAATTAAACACCCTTTTTGACAACTTAATTACAA
* *
39685902 TAATAAATAACAATGAACAACAACAATTGAACACCCTTTTT-ACAACTTAATTGCAA
1 TAATAAATAACAATGAACAACAACAATTAAACACCCTTTTTGACAACTTAATTACAA
*
39685958 TAATAAATAACAATAAACAACAACAAT
1 TAATAAATAACAATGAACAACAACAAT
39685985 ATGAACAAAA
Statistics
Matches: 120, Mismatches: 19, Indels: 2
0.85 0.13 0.01
Matches are distributed among these distances:
56 66 0.55
57 54 0.45
ACGTcount: A:0.51, C:0.16, G:0.06, T:0.27
Consensus pattern (57 bp):
TAATAAATAACAATGAACAACAACAATTAAACACCCTTTTTGACAACTTAATTACAA
Found at i:39685991 original size:57 final size:57
Alignment explanation
Indices: 39685826--39685991 Score: 235
Period size: 57 Copynumber: 2.9 Consensus size: 57
39685816 TAAATATCAG
** * * *
39685826 TTTGACAGTTTAATTACAATAATAAATAACAATGAAGAACAATAATTAAACACCCTT
1 TTTGACAACTTAATTACAATAATAAATAACAATGAACAACAACAATTGAACACCCTT
* *
39685883 TTTGACAACTTAATTTCAGTAATAAATAACAATGAACAACAACAATTGAACACCCTT
1 TTTGACAACTTAATTACAATAATAAATAACAATGAACAACAACAATTGAACACCCTT
* *
39685940 TTT-ACAACTTAATTGCAATAATAAATAACAATAAACAACAACAATATGAACA
1 TTTGACAACTTAATTACAATAATAAATAACAATGAACAACAACAAT-TGAACA
39685992 AAAATACACC
Statistics
Matches: 98, Mismatches: 10, Indels: 2
0.89 0.09 0.02
Matches are distributed among these distances:
56 39 0.40
57 59 0.60
ACGTcount: A:0.50, C:0.16, G:0.06, T:0.28
Consensus pattern (57 bp):
TTTGACAACTTAATTACAATAATAAATAACAATGAACAACAACAATTGAACACCCTT
Found at i:39688383 original size:63 final size:63
Alignment explanation
Indices: 39688297--39688496 Score: 192
Period size: 63 Copynumber: 3.2 Consensus size: 63
39688287 TGACCAAACT
* * ** * * *
39688297 GTGTAACTCGCTGTTTTGAGTGTAAAAACCACATGGCCAGGAACACG-GACGTGTGCCTAGGTC
1 GTGTAACTCACTATTTTGAGTGTAAAAACCACACAGCCAGGAACACGAG-CGTATGCCCAGGCC
* *
39688360 GTGTAACTCACTATTTTGGGTGTAAAAACCACACAGCCAGGGACACGAGCGTATGCCCAGGCC
1 GTGTAACTCACTATTTTGAGTGTAAAAACCACACAGCCAGGAACACGAGCGTATGCCCAGGCC
* * * * * * *
39688423 CTGTAACTCACTGTTTAT-AATAT-AAAACCACACAGCCAGGGACA-TAGGCGTGTGCCCAGGCC
1 GTGTAACTCACTATTT-TGAGTGTAAAAACCACACAGCCAGGAACACGA-GCGTATGCCCAGGCC
*
39688485 ATGTAACTCACT
1 GTGTAACTCACT
39688497 GTTTGTGCTT
Statistics
Matches: 117, Mismatches: 17, Indels: 7
0.83 0.12 0.05
Matches are distributed among these distances:
61 1 0.01
62 46 0.39
63 68 0.58
64 2 0.02
ACGTcount: A:0.28, C:0.26, G:0.24, T:0.22
Consensus pattern (63 bp):
GTGTAACTCACTATTTTGAGTGTAAAAACCACACAGCCAGGAACACGAGCGTATGCCCAGGCC
Found at i:39688516 original size:62 final size:62
Alignment explanation
Indices: 39688384--39688500 Score: 191
Period size: 62 Copynumber: 1.9 Consensus size: 62
39688374 TTTGGGTGTA
* *
39688384 AAAACCACACAGCCAGGGACACGAGCGTATGCCCAGGCCCTGTAACTCACTGTTTATAATAT
1 AAAACCACACAGCCAGGGACAAGAGCGTATGCCCAGGCCATGTAACTCACTGTTTATAATAT
*
39688446 AAAACCACACAGCCAGGGACATAG-GCGTGTGCCCAGGCCATGTAACTCACTGTTT
1 AAAACCACACAGCCAGGGACA-AGAGCGTATGCCCAGGCCATGTAACTCACTGTTT
39688501 GTGCTTGAAA
Statistics
Matches: 51, Mismatches: 3, Indels: 2
0.91 0.05 0.04
Matches are distributed among these distances:
62 50 0.98
63 1 0.02
ACGTcount: A:0.31, C:0.29, G:0.21, T:0.19
Consensus pattern (62 bp):
AAAACCACACAGCCAGGGACAAGAGCGTATGCCCAGGCCATGTAACTCACTGTTTATAATAT
Found at i:39692581 original size:21 final size:21
Alignment explanation
Indices: 39692557--39692600 Score: 70
Period size: 21 Copynumber: 2.1 Consensus size: 21
39692547 GAAAAAGGCA
*
39692557 AGAAAAAAAGAAAAGATAAAT
1 AGAAAAAAAGAAAAGAGAAAT
*
39692578 AGAAAAAAGGAAAAGAGAAAT
1 AGAAAAAAAGAAAAGAGAAAT
39692599 AG
1 AG
39692601 TTGAAGTCTT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.73, C:0.00, G:0.20, T:0.07
Consensus pattern (21 bp):
AGAAAAAAAGAAAAGAGAAAT
Found at i:39705742 original size:14 final size:14
Alignment explanation
Indices: 39705715--39705750 Score: 54
Period size: 14 Copynumber: 2.6 Consensus size: 14
39705705 TTGTTTGACT
*
39705715 GAAAATGGTTTCTG
1 GAAAATGATTTCTG
*
39705729 GAATATGATTTCTG
1 GAAAATGATTTCTG
39705743 GAAAATGA
1 GAAAATGA
39705751 CTTGTTTTTC
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
14 19 1.00
ACGTcount: A:0.36, C:0.06, G:0.25, T:0.33
Consensus pattern (14 bp):
GAAAATGATTTCTG
Found at i:39706947 original size:17 final size:17
Alignment explanation
Indices: 39706925--39706959 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
39706915 TATCATTAAT
*
39706925 ATTAATTGTATAACACA
1 ATTAATTATATAACACA
*
39706942 ATTAATTATATAATACA
1 ATTAATTATATAACACA
39706959 A
1 A
39706960 AATTGTAATA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.51, C:0.09, G:0.03, T:0.37
Consensus pattern (17 bp):
ATTAATTATATAACACA
Found at i:39709296 original size:16 final size:16
Alignment explanation
Indices: 39709272--39709310 Score: 53
Period size: 16 Copynumber: 2.4 Consensus size: 16
39709262 AAATTTAGAA
39709272 TATAATTAAAA-ATAAT
1 TATAATTAAAATA-AAT
*
39709288 TATATTTAAAATAAAT
1 TATAATTAAAATAAAT
39709304 TATAATT
1 TATAATT
39709311 GAATAAACAT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
16 19 0.95
17 1 0.05
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (16 bp):
TATAATTAAAATAAAT
Found at i:39709814 original size:37 final size:37
Alignment explanation
Indices: 39709764--39709834 Score: 133
Period size: 37 Copynumber: 1.9 Consensus size: 37
39709754 CTTGCTTTCG
*
39709764 ATTGAGGTGGAAACTTGAGAAGAGAAACAATCGGTCA
1 ATTGAGGTGGAAACTTGAGAAGAAAAACAATCGGTCA
39709801 ATTGAGGTGGAAACTTGAGAAGAAAAACAATCGG
1 ATTGAGGTGGAAACTTGAGAAGAAAAACAATCGG
39709835 ATAGTGGTTC
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
37 33 1.00
ACGTcount: A:0.42, C:0.10, G:0.30, T:0.18
Consensus pattern (37 bp):
ATTGAGGTGGAAACTTGAGAAGAAAAACAATCGGTCA
Found at i:39720290 original size:43 final size:44
Alignment explanation
Indices: 39720189--39720302 Score: 124
Period size: 43 Copynumber: 2.6 Consensus size: 44
39720179 GGTTACCGAG
* * *
39720189 ATGTGATTACATGTAAGACCATGTCTGGGAAATTGTCATCGTTA
1 ATGTGATTACATGTAAGACCATGTCTGGGAAAGTGGCATCGATA
* * * *
39720233 AT-TGATTTCGTGTAAGACCCTGTCTGGGACAGTGGCATCGAT-
1 ATGTGATTACATGTAAGACCATGTCTGGGAAAGTGGCATCGATA
* * *
39720275 ATGTGATAACATGTAAGGCCATATCTGG
1 ATGTGATTACATGTAAGACCATGTCTGG
39720303 ATATGGCATT
Statistics
Matches: 56, Mismatches: 13, Indels: 3
0.78 0.18 0.04
Matches are distributed among these distances:
42 2 0.04
43 52 0.93
44 2 0.04
ACGTcount: A:0.27, C:0.16, G:0.25, T:0.32
Consensus pattern (44 bp):
ATGTGATTACATGTAAGACCATGTCTGGGAAAGTGGCATCGATA
Found at i:39726667 original size:11 final size:10
Alignment explanation
Indices: 39726653--39726700 Score: 51
Period size: 11 Copynumber: 4.4 Consensus size: 10
39726643 AATAAAAGAC
*
39726653 AAAATAAAGT
1 AAAATAAAAT
39726663 GAAAATGAAAAT
1 -AAAAT-AAAAT
39726675 AAAATAAAAT
1 AAAATAAAAT
39726685 AAAAATAAAAAT
1 -AAAAT-AAAAT
39726697 AAAA
1 AAAA
39726701 ATGATAATAA
Statistics
Matches: 33, Mismatches: 1, Indels: 6
0.82 0.03 0.15
Matches are distributed among these distances:
10 5 0.15
11 19 0.58
12 9 0.27
ACGTcount: A:0.77, C:0.00, G:0.06, T:0.17
Consensus pattern (10 bp):
AAAATAAAAT
Found at i:39726673 original size:6 final size:5
Alignment explanation
Indices: 39726653--39726700 Score: 51
Period size: 6 Copynumber: 8.8 Consensus size: 5
39726643 AATAAAAGAC
*
39726653 AAAAT AAAGT GAAAAT GAAAAT AAAAT AAAAT AAAAAT AAAAAT AAAA
1 AAAAT AAAAT -AAAAT -AAAAT AAAAT AAAAT -AAAAT -AAAAT AAAA
39726701 ATGATAATAA
Statistics
Matches: 39, Mismatches: 2, Indels: 4
0.87 0.04 0.09
Matches are distributed among these distances:
5 18 0.46
6 21 0.54
ACGTcount: A:0.77, C:0.00, G:0.06, T:0.17
Consensus pattern (5 bp):
AAAAT
Found at i:39726701 original size:6 final size:6
Alignment explanation
Indices: 39726664--39726702 Score: 55
Period size: 6 Copynumber: 6.8 Consensus size: 6
39726654 AAATAAAGTG
*
39726664 AAAATG AAAAT- AAAAT- AAAATA AAAATA AAAATA AAAAT
1 AAAATA AAAATA AAAATA AAAATA AAAATA AAAATA AAAAT
39726703 GATAATAAAT
Statistics
Matches: 32, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
5 10 0.31
6 22 0.69
ACGTcount: A:0.79, C:0.00, G:0.03, T:0.18
Consensus pattern (6 bp):
AAAATA
Found at i:39726709 original size:12 final size:12
Alignment explanation
Indices: 39726664--39726711 Score: 64
Period size: 12 Copynumber: 4.2 Consensus size: 12
39726654 AAATAAAGTG
39726664 AAAATGAAAAT-
1 AAAATGAAAATA
39726675 AAAAT-AAAATA
1 AAAATGAAAATA
*
39726686 AAAATAAAAATA
1 AAAATGAAAATA
*
39726698 AAAATGATAATA
1 AAAATGAAAATA
39726710 AA
1 AA
39726712 TAAATAGACT
Statistics
Matches: 33, Mismatches: 2, Indels: 3
0.87 0.05 0.08
Matches are distributed among these distances:
10 5 0.15
11 10 0.30
12 18 0.55
ACGTcount: A:0.77, C:0.00, G:0.04, T:0.19
Consensus pattern (12 bp):
AAAATGAAAATA
Found at i:39726715 original size:22 final size:22
Alignment explanation
Indices: 39726642--39726700 Score: 73
Period size: 22 Copynumber: 2.6 Consensus size: 22
39726632 CTTCAAAAGT
* * *
39726642 AAATAAAAGACAAAATAAAGTGA
1 AAATAAAA-ATAAAATAAAATAA
*
39726665 AAATGAAAATAAAATAAAATAA
1 AAATAAAAATAAAATAAAATAA
39726687 AAATAAAAATAAAA
1 AAATAAAAATAAAA
39726701 ATGATAATAA
Statistics
Matches: 31, Mismatches: 5, Indels: 1
0.84 0.14 0.03
Matches are distributed among these distances:
22 24 0.77
23 7 0.23
ACGTcount: A:0.76, C:0.02, G:0.07, T:0.15
Consensus pattern (22 bp):
AAATAAAAATAAAATAAAATAA
Found at i:39728031 original size:17 final size:20
Alignment explanation
Indices: 39727997--39728035 Score: 57
Period size: 17 Copynumber: 2.1 Consensus size: 20
39727987 ATCAAAGTAG
39727997 TAAAAATAATAGTAATATCC
1 TAAAAATAATAGTAATATCC
39728017 TAAAAAT-ATA-T-ATATCC
1 TAAAAATAATAGTAATATCC
39728034 TA
1 TA
39728036 TCATTGAAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
17 8 0.42
18 1 0.05
19 3 0.16
20 7 0.37
ACGTcount: A:0.54, C:0.10, G:0.03, T:0.33
Consensus pattern (20 bp):
TAAAAATAATAGTAATATCC
Found at i:39734118 original size:28 final size:28
Alignment explanation
Indices: 39734066--39734120 Score: 76
Period size: 28 Copynumber: 1.9 Consensus size: 28
39734056 GTTTCATTCA
39734066 AAACTATTTTAATCTTTTAATATATTTTT
1 AAACTATTTTAA-CTTTTAATATATTTTT
*
39734095 AAACTATTTTTAA-TTTTGATATATTT
1 AAACTA-TTTTAACTTTTAATATATTT
39734121 AATTTATGTT
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
28 12 0.50
29 6 0.25
30 6 0.25
ACGTcount: A:0.35, C:0.05, G:0.02, T:0.58
Consensus pattern (28 bp):
AAACTATTTTAACTTTTAATATATTTTT
Found at i:39734135 original size:16 final size:15
Alignment explanation
Indices: 39734103--39734143 Score: 64
Period size: 16 Copynumber: 2.7 Consensus size: 15
39734093 TTAAACTATT
39734103 TTTAATTTTGATATA
1 TTTAATTTTGATATA
*
39734118 TTTAATTTATGTTATA
1 TTTAATTT-TGATATA
39734134 TTTAATTTTG
1 TTTAATTTTG
39734144 TCTTTAAATA
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
15 10 0.42
16 14 0.58
ACGTcount: A:0.29, C:0.00, G:0.07, T:0.63
Consensus pattern (15 bp):
TTTAATTTTGATATA
Found at i:39745356 original size:86 final size:86
Alignment explanation
Indices: 39745249--39745413 Score: 269
Period size: 86 Copynumber: 1.9 Consensus size: 86
39745239 GCGCCTATCT
*
39745249 GGCCCACACGACCAAAATTGGCCTTGGCTATGTGGATCACACGGCCTGGCCCAGAATT-TCACAC
1 GGCCCACACGACCAAAATTGGCCTTGGCCATGTGGATCACACGGCCTGGCCCAGAATTCT-ACAC
39745313 GCCCATGTGGTTCACTCGTGTG
65 GCCCATGTGGTTCACTCGTGTG
* * *
39745335 GGCCCACACGACCCAAATTGGCCTTGGCCGTGTGGATCACACGGGCTGGCCCAGAATTCTACACG
1 GGCCCACACGACCAAAATTGGCCTTGGCCATGTGGATCACACGGCCTGGCCCAGAATTCTACACG
*
39745400 CCCGTGTGGTTCAC
66 CCCATGTGGTTCAC
39745414 CCATACGGGC
Statistics
Matches: 73, Mismatches: 5, Indels: 2
0.91 0.06 0.03
Matches are distributed among these distances:
86 72 0.99
87 1 0.01
ACGTcount: A:0.20, C:0.33, G:0.27, T:0.21
Consensus pattern (86 bp):
GGCCCACACGACCAAAATTGGCCTTGGCCATGTGGATCACACGGCCTGGCCCAGAATTCTACACG
CCCATGTGGTTCACTCGTGTG
Found at i:39747877 original size:60 final size:57
Alignment explanation
Indices: 39747745--39747879 Score: 153
Period size: 60 Copynumber: 2.3 Consensus size: 57
39747735 TTCATATAAT
* ** * *
39747745 AATAATTATATTAAGAATTTTATTAAATTATATATTATTTTATGAAATTATATTTAAT
1 AATAATTATATTAA-AATATGGTTAAATTATATATTATTTTATGAAAATATATTTAAC
* * *
39747803 AATAATTATGTTAAAATATGGTTAAATTATTTATTATTTTTATAATAAAATATATTTAAC
1 AATAATTATATTAAAATATGGTTAAATTATATATTA-TTTTAT--GAAAATATATTTAAC
*
39747863 AATAATTTTATTAAAAT
1 AATAATTATATTAAAAT
39747880 TTAATAACAA
Statistics
Matches: 64, Mismatches: 10, Indels: 4
0.82 0.13 0.05
Matches are distributed among these distances:
57 18 0.28
58 19 0.30
60 27 0.42
ACGTcount: A:0.46, C:0.01, G:0.04, T:0.50
Consensus pattern (57 bp):
AATAATTATATTAAAATATGGTTAAATTATATATTATTTTATGAAAATATATTTAAC
Found at i:39748071 original size:16 final size:16
Alignment explanation
Indices: 39748050--39748104 Score: 67
Period size: 16 Copynumber: 3.4 Consensus size: 16
39748040 TGAATTATTG
39748050 ATTACAGCTTTATTCC
1 ATTACAGCTTTATTCC
*
39748066 ATTACAG-TTCTATTCA
1 ATTACAGCTT-TATTCC
* *
39748082 ATGACAGCCTTATTCC
1 ATTACAGCTTTATTCC
39748098 ATTACAG
1 ATTACAG
39748105 TGAACCAAAC
Statistics
Matches: 32, Mismatches: 5, Indels: 4
0.78 0.12 0.10
Matches are distributed among these distances:
15 2 0.06
16 29 0.91
17 1 0.03
ACGTcount: A:0.29, C:0.24, G:0.09, T:0.38
Consensus pattern (16 bp):
ATTACAGCTTTATTCC
Found at i:39748455 original size:13 final size:13
Alignment explanation
Indices: 39748437--39748462 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
39748427 CTCAAAAATT
39748437 AAGTATTGAAAAA
1 AAGTATTGAAAAA
39748450 AAGTATTGAAAAA
1 AAGTATTGAAAAA
39748463 TTAAATATTG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.62, C:0.00, G:0.15, T:0.23
Consensus pattern (13 bp):
AAGTATTGAAAAA
Found at i:39748473 original size:15 final size:15
Alignment explanation
Indices: 39748430--39748474 Score: 67
Period size: 15 Copynumber: 3.1 Consensus size: 15
39748420 TGATAAACTC
39748430 AAAAATTAAGTATTG
1 AAAAATTAAGTATTG
39748445 AAAAA--AAGTATTG
1 AAAAATTAAGTATTG
*
39748458 AAAAATTAAATATTG
1 AAAAATTAAGTATTG
39748473 AA
1 AA
39748475 TTTAAGTTAT
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
13 13 0.48
15 14 0.52
ACGTcount: A:0.60, C:0.00, G:0.11, T:0.29
Consensus pattern (15 bp):
AAAAATTAAGTATTG
Found at i:39753849 original size:256 final size:256
Alignment explanation
Indices: 39753392--39753904 Score: 884
Period size: 256 Copynumber: 2.0 Consensus size: 256
39753382 TTTTGGTGTA
* * *
39753392 AAACGACCAAGGCGTTAGGCCTCAGGGAGTCTGCGCTGCAGAGGCACAAGGAGGGGGTGTGGTGC
1 AAACGACCAAGGCGTTAGGCCTCAGGGAGGCTGCGCTACAGAGGCACAAGGAGGGGGTGCGGTGC
39753457 ATTACAGTTTACGTCTTTTTTTTCTGAAAATGTTTTAAGTGTTTTGGGCTATGGGCTAGGGTGAA
66 ATTACAGTTTACGTCTTTTTTTTCTGAAAATGTTTTAAGTGTTTTGGGCTATGGGCTAGGGTGAA
* * *
39753522 TTTGGGTTATATTGGGCCGTTGTAATTTCGACTGATAACTATTGTAAATGGACTTTGATACTTGG
131 TTTGGGTTATATTGGGCCATTGTAATTTCGACTAATAACTATTGTAAATGGACTTTGATACTTGA
*
39753587 ACTTATTTGCTTATTTTTTGGTTTATTATTATTTTGATGGGCTCGAGAAAATTGGGCTATT
196 ACTTATTTGCTTATTTTTTGGTTTATTATTATTTTGATGGGCTCGAGAAAATTAGGCTATT
*
39753648 AAACGACCAAGGCGTTAGGCCTTAGGG-GGCGTGCGCTACAGAGGCACAAGGAGGGGGTGCGGTG
1 AAACGACCAAGGCGTTAGGCCTCAGGGAGGC-TGCGCTACAGAGGCACAAGGAGGGGGTGCGGTG
*
39753712 CATTACGGTTTACGTCTTTTTTTTCTGAAAATGTTTTAAGTGTTTTGGGCTATGGGCTAGGGTGA
65 CATTACAGTTTACGTCTTTTTTTTCTGAAAATGTTTTAAGTGTTTTGGGCTATGGGCTAGGGTGA
* *
39753777 ATTTGGGTTATATTGGGCCATTGTAATTTGGGCTAATAACTATTGTAAATGGACTTTGATACTTG
130 ATTTGGGTTATATTGGGCCATTGTAATTTCGACTAATAACTATTGTAAATGGACTTTGATACTTG
* * *
39753842 AACTTATTTGTTTATTTTTTGGTTTATTATTATTTTGATGGGCTCGGGCAAATTAGGCTATT
195 AACTTATTTGCTTATTTTTTGGTTTATTATTATTTTGATGGGCTCGAGAAAATTAGGCTATT
39753904 A
1 A
39753905 CAGCTACCCA
Statistics
Matches: 242, Mismatches: 14, Indels: 2
0.94 0.05 0.01
Matches are distributed among these distances:
255 2 0.01
256 240 0.99
ACGTcount: A:0.22, C:0.12, G:0.28, T:0.37
Consensus pattern (256 bp):
AAACGACCAAGGCGTTAGGCCTCAGGGAGGCTGCGCTACAGAGGCACAAGGAGGGGGTGCGGTGC
ATTACAGTTTACGTCTTTTTTTTCTGAAAATGTTTTAAGTGTTTTGGGCTATGGGCTAGGGTGAA
TTTGGGTTATATTGGGCCATTGTAATTTCGACTAATAACTATTGTAAATGGACTTTGATACTTGA
ACTTATTTGCTTATTTTTTGGTTTATTATTATTTTGATGGGCTCGAGAAAATTAGGCTATT
Found at i:39754237 original size:89 final size:88
Alignment explanation
Indices: 39754121--39754423 Score: 247
Period size: 89 Copynumber: 3.4 Consensus size: 88
39754111 TATAGCTTTG
* *
39754121 ATCTGTTCCACTGCTACTTCAAGGAGATAATG-TTTATAGCTTTAATATGCTCTACTACAACTTC
1 ATCTGCTCCACTGCTACTTCAAGGAGATAA-GATTTATAGCTTCAATATGCTC-ACTACAACTTC
39754185 AGAGAGATAAGATTTGCTATCTTCA
64 AGAGAGATAAGATTTGCTATCTTCA
* * * *
39754210 ATCTGCTCCACTGCTACTTCAGGGAGATAAGATTTGTGGCTTCAATATGCTCACTGCAACTTCAG
1 ATCTGCTCCACTGCTACTTCAAGGAGATAAGATTTATAGCTTCAATATGCTCACTACAACTTCAG
* * *
39754275 GGAGATAAGATTCGCCATGGTAACTTCA
66 AGAGATAAGATT-----TGCTATCTTCA
* ** * * * * * * *
39754303 ATCCG-TCTTGCTGCAACTTC-AGGAGAATGAGATTTACTATCTTCGATTTATTC-CACTCCAAA
1 ATCTGCTC-CACTGCTACTTCAAGGAG-ATAAGATTTA-TAGCTTC-A-ATATGCTCACTACAAC
* * *
39754365 TTCAGGGAGATAAGATCTG-TAACTTCA
61 TTCAGAGAGATAAGATTTGCTATCTTCA
* *
39754392 ATCTGCTCCACTGCAACTTCAGGGAGATAAGA
1 ATCTGCTCCACTGCTACTTCAAGGAGATAAGA
39754424 CTTGTGGCTT
Statistics
Matches: 173, Mismatches: 28, Indels: 26
0.76 0.12 0.11
Matches are distributed among these distances:
88 24 0.14
89 72 0.42
90 8 0.05
92 6 0.03
93 30 0.17
94 5 0.03
95 24 0.14
96 4 0.02
ACGTcount: A:0.29, C:0.21, G:0.18, T:0.31
Consensus pattern (88 bp):
ATCTGCTCCACTGCTACTTCAAGGAGATAAGATTTATAGCTTCAATATGCTCACTACAACTTCAG
AGAGATAAGATTTGCTATCTTCA
Found at i:39754574 original size:95 final size:95
Alignment explanation
Indices: 39754354--39754608 Score: 235
Period size: 95 Copynumber: 2.8 Consensus size: 95
39754344 TTCGATTTAT
* * * * * * * *
39754354 TCCACTCCAAATTCAGGGAGATAAGA-TCTGTAACTTCAATCTGCTCCACTGCAACTTCAGGGAG
1 TCCACTGCAACTTCAGGGAGATAAGACT-TGTAGCTTTAATATGCTCTACTACAACTTTAGGGAG
*
39754418 AT-A-A---G-A-CTTGTGGCTTTAGTCTGC
65 ATAAGATTTGTAGCTTGTGGCTTTAGTCTAC
* * * * *
39754442 TCCACTGCAACTTCAGGGAGATTAGGCTTTTAGCTTTAATATGCT-TCATTGCAACTTTAGGGAG
1 TCCACTGCAACTTCAGGGAGATAAGACTTGTAGCTTTAATATGCTCT-ACTACAACTTTAGGGAG
*
39754506 ATAAGATTTGTAGCTTGTAGG-TTTAGTCTAT
65 ATAAGATTTGTAGCTTGT-GGCTTTAGTCTAC
* *
39754537 TCCACTGTAACTTCAGGGAGATAAGACTTGT-GTCTTTAATCTGCTCTACTACAACTTTAGGGAG
1 TCCACTGCAACTTCAGGGAGATAAGACTTGTAG-CTTTAATATGCTCTACTACAACTTTAGGGAG
*
39754601 TTAAGATT
65 ATAAGATT
39754609 CGTCATGATG
Statistics
Matches: 134, Mismatches: 21, Indels: 17
0.78 0.12 0.10
Matches are distributed among these distances:
88 52 0.39
89 2 0.01
90 1 0.01
93 1 0.01
94 2 0.01
95 73 0.54
96 3 0.02
ACGTcount: A:0.27, C:0.19, G:0.21, T:0.34
Consensus pattern (95 bp):
TCCACTGCAACTTCAGGGAGATAAGACTTGTAGCTTTAATATGCTCTACTACAACTTTAGGGAGA
TAAGATTTGTAGCTTGTGGCTTTAGTCTAC
Found at i:39754599 original size:44 final size:43
Alignment explanation
Indices: 39754115--39754606 Score: 188
Period size: 44 Copynumber: 10.9 Consensus size: 43
39754105 GTAACTTATA
* * * * * * *
39754115 GCTTTGATCTGTTCCACTGCTACTTCAAGGAGATAATG-TTTAT
1 GCTTTAATCTGCTCTACTGCAACTTCAGGGAGATAA-GACTTGT
* * * *
39754158 AGCTTTAATATGCTCTACTACAACTTCAGAGAGATAAGATTTGCT
1 -GCTTTAATCTGCTCTACTGCAACTTCAGGGAGATAAGACTTG-T
* * * * *
39754203 ATCTTCAATCTGCTCCACTGCTACTTCAGGGAGATAAGATTTGT
1 -GCTTTAATCTGCTCTACTGCAACTTCAGGGAGATAAGACTTGT
* *
39754247 GGCTTCAATATGCTC-ACTGCAACTTCAGGGAGATAAGA-TTCGCCAT
1 -GCTTTAATCTGCTCTACTGCAACTTCAGGGAGATAAGACTT-G---T
* * * * * *
39754293 GGTAACTTCAATCCG-TCTTGCTGCAACTTCA-GGAGAATGAGATTTACT
1 -G---CTTTAATCTGCTC-TACTGCAACTTCAGGGAG-ATAAGACTT-GT
* ** * ** * * *
39754341 ATCTTCGATTTATTCCACTCCAAATTCAGGGAGATAAGA-TCTGT
1 -GCTTTAATCTGCTCTACTGCAACTTCAGGGAGATAAGACT-TGT
* * *
39754385 AACTTCAATCTGCTCCACTGCAACTTCAGGGAGATAAGACTTGT
1 -GCTTTAATCTGCTCTACTGCAACTTCAGGGAGATAAGACTTGT
* * * * *
39754429 GGCTTTAGTCTGCTCCACTGCAACTTCAGGGAGATTAGGCTTTT
1 -GCTTTAATCTGCTCTACTGCAACTTCAGGGAGATAAGACTTGT
* * * *
39754473 AGCTTTAATATGCT-TCATTGCAACTTTAGGGAGATAAGATTTGT
1 -GCTTTAATCTGCTCT-ACTGCAACTTCAGGGAGATAAGACTTGT
** * *
39754517 AGCTTGTAGGTTTAGTCTATTCCACTGTAACTTCAGGGAGATAAGACTTGT
1 -GCTT-TA-----A-TCTGCTCTACTGCAACTTCAGGGAGATAAGACTTGT
* * *
39754568 GTCTTTAATCTGCTCTACTACAACTTTAGGGAGTTAAGA
1 G-CTTTAATCTGCTCTACTGCAACTTCAGGGAGATAAGA
39754607 TTCGTCATGA
Statistics
Matches: 344, Mismatches: 77, Indels: 54
0.72 0.16 0.11
Matches are distributed among these distances:
42 2 0.01
43 24 0.07
44 180 0.52
45 62 0.18
46 9 0.03
48 3 0.01
49 12 0.03
50 20 0.06
51 32 0.09
ACGTcount: A:0.27, C:0.20, G:0.20, T:0.34
Consensus pattern (43 bp):
GCTTTAATCTGCTCTACTGCAACTTCAGGGAGATAAGACTTGT
Found at i:39760791 original size:15 final size:16
Alignment explanation
Indices: 39760771--39760802 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 16
39760761 GCGATCCTCT
39760771 CTTGAA-AAATTAAAA
1 CTTGAATAAATTAAAA
39760786 CTTGAATAAATTAAAA
1 CTTGAATAAATTAAAA
39760802 C
1 C
39760803 AAGTATTTAA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 6 0.38
16 10 0.62
ACGTcount: A:0.56, C:0.09, G:0.06, T:0.28
Consensus pattern (16 bp):
CTTGAATAAATTAAAA
Found at i:39761498 original size:26 final size:25
Alignment explanation
Indices: 39761469--39761524 Score: 58
Period size: 26 Copynumber: 2.2 Consensus size: 25
39761459 TATATAAGAA
39761469 ATAAGTGGAAAATAAAATAAATATAT
1 ATAAGTGGAAAAT-AAATAAATATAT
** **
39761495 ATAAAGTTTAAGGTAAATAAATATAT
1 AT-AAGTGGAAAATAAATAAATATAT
39761521 ATAA
1 ATAA
39761525 AAAACAAAAA
Statistics
Matches: 25, Mismatches: 4, Indels: 3
0.78 0.12 0.09
Matches are distributed among these distances:
25 2 0.08
26 16 0.64
27 7 0.28
ACGTcount: A:0.59, C:0.00, G:0.11, T:0.30
Consensus pattern (25 bp):
ATAAGTGGAAAATAAATAAATATAT
Found at i:39761578 original size:3 final size:3
Alignment explanation
Indices: 39761564--39761642 Score: 83
Period size: 3 Copynumber: 26.7 Consensus size: 3
39761554 AGAAATAGAG
* * *
39761564 AAT AAT AA- AAT AAT AA- AAT AAT AA- AAT AAAG AAT GAAC AAG AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT -AAT AAT -AAT AAT AAT
*
39761608 AAT AAT AAC AAT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
39761643 GGAATAAAAT
Statistics
Matches: 64, Mismatches: 7, Indels: 10
0.79 0.09 0.12
Matches are distributed among these distances:
2 6 0.09
3 54 0.84
4 4 0.06
ACGTcount: A:0.70, C:0.03, G:0.04, T:0.24
Consensus pattern (3 bp):
AAT
Found at i:39767101 original size:23 final size:23
Alignment explanation
Indices: 39767071--39767117 Score: 94
Period size: 23 Copynumber: 2.0 Consensus size: 23
39767061 GCAAAGTTGT
39767071 ATACTCCTCCACAGTAGGTACTA
1 ATACTCCTCCACAGTAGGTACTA
39767094 ATACTCCTCCACAGTAGGTACTA
1 ATACTCCTCCACAGTAGGTACTA
39767117 A
1 A
39767118 ATCTACCCTC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 24 1.00
ACGTcount: A:0.32, C:0.30, G:0.13, T:0.26
Consensus pattern (23 bp):
ATACTCCTCCACAGTAGGTACTA
Found at i:39768988 original size:3 final size:3
Alignment explanation
Indices: 39768980--39769023 Score: 61
Period size: 3 Copynumber: 14.7 Consensus size: 3
39768970 AGGAAGGGTA
* * *
39768980 AAT AAT AAT AAT GAT AAT AAT AAT ACT AAT AAC AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
39769024 AAACAAAAAA
Statistics
Matches: 35, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
3 35 1.00
ACGTcount: A:0.64, C:0.05, G:0.02, T:0.30
Consensus pattern (3 bp):
AAT
Found at i:39775395 original size:10 final size:10
Alignment explanation
Indices: 39775376--39775419 Score: 61
Period size: 10 Copynumber: 4.4 Consensus size: 10
39775366 AATTTTAGCT
39775376 TTTATCTTTA
1 TTTATCTTTA
*
39775386 TTTATATTTA
1 TTTATCTTTA
*
39775396 TTTACCTTTA
1 TTTATCTTTA
*
39775406 ATTATCTTTA
1 TTTATCTTTA
39775416 TTTA
1 TTTA
39775420 ATTGTATTTA
Statistics
Matches: 28, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
10 28 1.00
ACGTcount: A:0.25, C:0.09, G:0.00, T:0.66
Consensus pattern (10 bp):
TTTATCTTTA
Found at i:39775430 original size:20 final size:20
Alignment explanation
Indices: 39775382--39775430 Score: 55
Period size: 20 Copynumber: 2.5 Consensus size: 20
39775372 AGCTTTTATC
*
39775382 TTTATTTATATTTATTTACC
1 TTTATTTATATTTATTTACA
* *
39775402 TTTAATTATCTTTATTTA-A
1 TTTATTTATATTTATTTACA
39775421 TTGTATTTAT
1 TT-TATTTAT
39775431 TTTTTAGAAT
Statistics
Matches: 24, Mismatches: 4, Indels: 2
0.80 0.13 0.07
Matches are distributed among these distances:
19 2 0.08
20 22 0.92
ACGTcount: A:0.27, C:0.06, G:0.02, T:0.65
Consensus pattern (20 bp):
TTTATTTATATTTATTTACA
Found at i:39776573 original size:23 final size:25
Alignment explanation
Indices: 39776528--39776578 Score: 93
Period size: 25 Copynumber: 2.0 Consensus size: 25
39776518 GGGAAAAAGG
*
39776528 TATGACCGTTTTTTTGAAGAGAGGT
1 TATGACCGTTTTGTTGAAGAGAGGT
39776553 TATGACCGTTTTGTTGAAGAGAGGT
1 TATGACCGTTTTGTTGAAGAGAGGT
39776578 T
1 T
39776579 CTCTTTTGGA
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
25 25 1.00
ACGTcount: A:0.24, C:0.08, G:0.29, T:0.39
Consensus pattern (25 bp):
TATGACCGTTTTGTTGAAGAGAGGT
Found at i:39776912 original size:24 final size:24
Alignment explanation
Indices: 39776884--39776936 Score: 70
Period size: 24 Copynumber: 2.2 Consensus size: 24
39776874 GTTCTAGAAA
* * *
39776884 ATTTAGTATTTATTAGTATAATAT
1 ATTTAGCATTTATAAGCATAATAT
*
39776908 ATTTAGCATTTATAAGCATAATTT
1 ATTTAGCATTTATAAGCATAATAT
39776932 ATTTA
1 ATTTA
39776937 TGGTTTAATT
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.38, C:0.04, G:0.08, T:0.51
Consensus pattern (24 bp):
ATTTAGCATTTATAAGCATAATAT
Found at i:39779183 original size:42 final size:42
Alignment explanation
Indices: 39779133--39779244 Score: 156
Period size: 42 Copynumber: 2.7 Consensus size: 42
39779123 TACAGCCTAC
39779133 GCACACGCCAATGTCCTTGCCTGTGTGGCTCAAACAGCATGG
1 GCACACGCCAATGTCCTTGCCTGTGTGGCTCAAACAGCATGG
* * * *
39779175 GCACACGCCAATGTCCTTACCTGTGTGGCTCAGACGGCCTGG
1 GCACACGCCAATGTCCTTGCCTGTGTGGCTCAAACAGCATGG
39779217 GCACACGCTC-ATGTCCTTGGCC-GTGTGG
1 GCACACGC-CAATGTCCTT-GCCTGTGTGG
39779245 TTCTAAAGCG
Statistics
Matches: 63, Mismatches: 5, Indels: 4
0.88 0.07 0.06
Matches are distributed among these distances:
42 60 0.95
43 3 0.05
ACGTcount: A:0.17, C:0.32, G:0.29, T:0.22
Consensus pattern (42 bp):
GCACACGCCAATGTCCTTGCCTGTGTGGCTCAAACAGCATGG
Found at i:39786557 original size:25 final size:25
Alignment explanation
Indices: 39786526--39786638 Score: 111
Period size: 25 Copynumber: 4.6 Consensus size: 25
39786516 TTTCGATACT
*
39786526 CAACTCGTATGAGCTTCCCGTTATA
1 CAACTCGCATGAGCTTCCCGTTATA
* *
39786551 CAGCTCGCATGAGCTTCCCGTTATT
1 CAACTCGCATGAGCTTCCCGTTATA
* * * *
39786576 TAGCTCGCATGAGCTTCCCATTATT
1 CAACTCGCATGAGCTTCCCGTTATA
** * *
39786601 CAACTCAAACGAGCTTACCGTT-TA
1 CAACTCGCATGAGCTTCCCGTTATA
*
39786625 CAACTCGTATGAGC
1 CAACTCGCATGAGC
39786639 ATACATGAAT
Statistics
Matches: 72, Mismatches: 16, Indels: 1
0.81 0.18 0.01
Matches are distributed among these distances:
24 12 0.17
25 60 0.83
ACGTcount: A:0.24, C:0.29, G:0.17, T:0.30
Consensus pattern (25 bp):
CAACTCGCATGAGCTTCCCGTTATA
Found at i:39790080 original size:36 final size:36
Alignment explanation
Indices: 39790040--39790109 Score: 140
Period size: 36 Copynumber: 1.9 Consensus size: 36
39790030 ATTTATTAGC
39790040 ATAAAAATCTTTGCTATTTCTTTTCATATTTAGGGT
1 ATAAAAATCTTTGCTATTTCTTTTCATATTTAGGGT
39790076 ATAAAAATCTTTGCTATTTCTTTTCATATTTAGG
1 ATAAAAATCTTTGCTATTTCTTTTCATATTTAGG
39790110 AGTTTTTTCT
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
36 34 1.00
ACGTcount: A:0.29, C:0.11, G:0.10, T:0.50
Consensus pattern (36 bp):
ATAAAAATCTTTGCTATTTCTTTTCATATTTAGGGT
Found at i:39793021 original size:23 final size:22
Alignment explanation
Indices: 39792995--39793095 Score: 91
Period size: 23 Copynumber: 4.5 Consensus size: 22
39792985 CTCATATGAA
* *
39792995 CTTACCGTTTTAGCTCATTCGAG
1 CTTACCGTTTCAGCTC-TACGAG
*
39793018 CTTACCGATTT-AGCTCGTAAGAG
1 CTTACCG-TTTCAGCTC-TACGAG
39793041 CTTACCGTTTCAGCTCTACGAAG
1 CTTACCGTTTCAGCTCTACG-AG
*
39793064 CTTA-C-TATTCAGCTCTTCGGAG
1 CTTACCGT-TTCAGCTCTAC-GAG
39793086 CTTACCGTTT
1 CTTACCGTTT
39793096 ATCAACTCAG
Statistics
Matches: 66, Mismatches: 5, Indels: 14
0.78 0.06 0.16
Matches are distributed among these distances:
21 1 0.02
22 23 0.35
23 38 0.58
24 4 0.06
ACGTcount: A:0.20, C:0.27, G:0.18, T:0.36
Consensus pattern (22 bp):
CTTACCGTTTCAGCTCTACGAG
Found at i:39793047 original size:46 final size:45
Alignment explanation
Indices: 39792995--39793095 Score: 114
Period size: 45 Copynumber: 2.2 Consensus size: 45
39792985 CTCATATGAA
* * *
39792995 CTTACCGTTTTAGCTCATTCG-AGCTTACCGATTTAGCTCGTAAGAG
1 CTTACCGTTTCAGCTC-TACGAAGCTTA-CGATTCAGCTCGTAAGAG
* * **
39793041 CTTACCGTTTCAGCTCTACGAAGCTTACTATTCAGCTCTTCGGAG
1 CTTACCGTTTCAGCTCTACGAAGCTTACGATTCAGCTCGTAAGAG
39793086 CTTACCGTTT
1 CTTACCGTTT
39793096 ATCAACTCAG
Statistics
Matches: 47, Mismatches: 7, Indels: 3
0.82 0.12 0.05
Matches are distributed among these distances:
45 26 0.55
46 21 0.45
ACGTcount: A:0.20, C:0.27, G:0.18, T:0.36
Consensus pattern (45 bp):
CTTACCGTTTCAGCTCTACGAAGCTTACGATTCAGCTCGTAAGAG
Found at i:39793077 original size:22 final size:22
Alignment explanation
Indices: 39793049--39793090 Score: 66
Period size: 22 Copynumber: 1.9 Consensus size: 22
39793039 AGCTTACCGT
39793049 TTCAGCTCTACGAAGCTTACTA
1 TTCAGCTCTACGAAGCTTACTA
* *
39793071 TTCAGCTCTTCGGAGCTTAC
1 TTCAGCTCTACGAAGCTTAC
39793091 CGTTTATCAA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.21, C:0.29, G:0.17, T:0.33
Consensus pattern (22 bp):
TTCAGCTCTACGAAGCTTACTA
Found at i:39793307 original size:9 final size:9
Alignment explanation
Indices: 39793272--39793317 Score: 53
Period size: 9 Copynumber: 5.3 Consensus size: 9
39793262 TAAGAGCTAT
*
39793272 ATGATTTAC
1 ATGAATTAC
39793281 ATGAATT--
1 ATGAATTAC
39793288 AT-AAGTTAC
1 ATGAA-TTAC
39793297 ATGAATTAC
1 ATGAATTAC
39793306 ATGAATTAC
1 ATGAATTAC
39793315 ATG
1 ATG
39793318 GATTTTATGA
Statistics
Matches: 32, Mismatches: 1, Indels: 8
0.78 0.02 0.20
Matches are distributed among these distances:
6 2 0.06
7 4 0.12
9 24 0.75
10 2 0.06
ACGTcount: A:0.41, C:0.09, G:0.13, T:0.37
Consensus pattern (9 bp):
ATGAATTAC
Found at i:39797739 original size:40 final size:39
Alignment explanation
Indices: 39797674--39797759 Score: 118
Period size: 40 Copynumber: 2.2 Consensus size: 39
39797664 TTTGTATATA
**
39797674 TAGCCGAAGCTATCTCAAATTGCACACCAAGTGCCACTTT
1 TAGCCGAAGCTATCTCAAACCGCACACCAAGTGCCA-TTT
* * *
39797714 TAGCCGAAGCTATTTCGAACCGCACACTAAGTGCCATTT
1 TAGCCGAAGCTATCTCAAACCGCACACCAAGTGCCATTT
39797753 TAGCCGA
1 TAGCCGA
39797760 TAAGTCGTTA
Statistics
Matches: 41, Mismatches: 5, Indels: 1
0.87 0.11 0.02
Matches are distributed among these distances:
39 10 0.24
40 31 0.76
ACGTcount: A:0.29, C:0.29, G:0.17, T:0.24
Consensus pattern (39 bp):
TAGCCGAAGCTATCTCAAACCGCACACCAAGTGCCATTT
Found at i:39803960 original size:23 final size:24
Alignment explanation
Indices: 39803934--39804000 Score: 77
Period size: 22 Copynumber: 2.8 Consensus size: 24
39803924 TTACTCATAT
*
39803934 GAGCTTACTGTTTCAGCTCATT-G
1 GAGCTTACCGTTTCAGCTCATTCG
*
39803957 GAGCTTACCATTT-AGCTC-TTCG
1 GAGCTTACCGTTTCAGCTCATTCG
39803979 GAGCTTACCGTTTATCAGCTCA
1 GAGCTTACCG-TT-TCAGCTCA
39804001 GGAGGAGCTT
Statistics
Matches: 36, Mismatches: 3, Indels: 7
0.78 0.07 0.15
Matches are distributed among these distances:
21 2 0.06
22 15 0.42
23 13 0.36
24 1 0.03
25 5 0.14
ACGTcount: A:0.19, C:0.25, G:0.19, T:0.36
Consensus pattern (24 bp):
GAGCTTACCGTTTCAGCTCATTCG
Found at i:39808342 original size:16 final size:16
Alignment explanation
Indices: 39808323--39808354 Score: 64
Period size: 16 Copynumber: 2.0 Consensus size: 16
39808313 TATTTAAGAG
39808323 TTTTTTTCTTATTATA
1 TTTTTTTCTTATTATA
39808339 TTTTTTTCTTATTATA
1 TTTTTTTCTTATTATA
39808355 AATACCCCAG
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.19, C:0.06, G:0.00, T:0.75
Consensus pattern (16 bp):
TTTTTTTCTTATTATA
Found at i:39811204 original size:17 final size:17
Alignment explanation
Indices: 39811157--39811204 Score: 64
Period size: 17 Copynumber: 2.9 Consensus size: 17
39811147 ATAAACATTA
39811157 AAATATTTAA-ATTTATT
1 AAATATTTAATA-TTATT
*
39811174 ATATATTT-ATATTATT
1 AAATATTTAATATTATT
39811190 AAATATTTAATATTA
1 AAATATTTAATATTA
39811205 CAAGTTAATT
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
16 13 0.48
17 14 0.52
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (17 bp):
AAATATTTAATATTATT
Found at i:39811495 original size:11 final size:11
Alignment explanation
Indices: 39811476--39811506 Score: 53
Period size: 11 Copynumber: 2.8 Consensus size: 11
39811466 ATAGTTTTTA
*
39811476 AATTATTTAAT
1 AATTTTTTAAT
39811487 AATTTTTTAAT
1 AATTTTTTAAT
39811498 AATTTTTTA
1 AATTTTTTA
39811507 TGTCATTGAC
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
11 19 1.00
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (11 bp):
AATTTTTTAAT
Found at i:39812631 original size:3 final size:3
Alignment explanation
Indices: 39812623--39812657 Score: 70
Period size: 3 Copynumber: 11.7 Consensus size: 3
39812613 ATTTTTAAGT
39812623 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
39812658 GTAGTGTGCC
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 32 1.00
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (3 bp):
TTA
Found at i:39814085 original size:9 final size:8
Alignment explanation
Indices: 39814069--39814175 Score: 58
Period size: 8 Copynumber: 12.8 Consensus size: 8
39814059 GACTTTTTAC
39814069 ATTATTAT
1 ATTATTAT
39814077 ATATATTAT
1 AT-TATTAT
39814086 -TTATTAT
1 ATTATTAT
* *
39814093 ACTTTTTAG
1 A-TTATTAT
39814102 ATTATTAT
1 ATTATTAT
39814110 ATATATTAT
1 AT-TATTAT
39814119 -TTATTAT
1 ATTATTAT
*
39814126 ACTTTATTTT
1 A--TTATTAT
39814136 ACTTATT-T
1 A-TTATTAT
39814144 ATTTATTTAT
1 A-TTA-TTAT
* *
39814154 TTTATTGT
1 ATTATTAT
* *
39814162 ATTTTTTT
1 ATTATTAT
39814170 ATTATT
1 ATTATT
39814176 GGTTTGTTTT
Statistics
Matches: 77, Mismatches: 13, Indels: 18
0.71 0.12 0.17
Matches are distributed among these distances:
7 12 0.16
8 29 0.38
9 28 0.36
10 8 0.10
ACGTcount: A:0.29, C:0.03, G:0.02, T:0.66
Consensus pattern (8 bp):
ATTATTAT
Found at i:39814097 original size:33 final size:33
Alignment explanation
Indices: 39814060--39814130 Score: 133
Period size: 33 Copynumber: 2.2 Consensus size: 33
39814050 TTTAGTTTGG
39814060 ACTTTTTACATTATTATATATATTATTTATTAT
1 ACTTTTTACATTATTATATATATTATTTATTAT
*
39814093 ACTTTTTAGATTATTATATATATTATTTATTAT
1 ACTTTTTACATTATTATATATATTATTTATTAT
39814126 ACTTT
1 ACTTT
39814131 ATTTTACTTA
Statistics
Matches: 37, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
33 37 1.00
ACGTcount: A:0.32, C:0.06, G:0.01, T:0.61
Consensus pattern (33 bp):
ACTTTTTACATTATTATATATATTATTTATTAT
Found at i:39814126 original size:12 final size:12
Alignment explanation
Indices: 39814069--39814154 Score: 51
Period size: 12 Copynumber: 7.2 Consensus size: 12
39814059 GACTTTTTAC
39814069 ATTA-TTATATAT
1 ATTATTTAT-TAT
39814081 ATTATTTATTAT
1 ATTATTTATTAT
* *
39814093 A--CTTT-TTAG
1 ATTATTTATTAT
39814102 ATTA-TTATATAT
1 ATTATTTAT-TAT
39814114 ATTATTTATTAT
1 ATTATTTATTAT
39814126 ACTTTATTTTACTTAT
1 A--TTA-TTTA-TTAT
39814142 -TTATTTATT-T
1 ATTATTTATTAT
39814152 ATT
1 ATT
39814155 TTATTGTATT
Statistics
Matches: 59, Mismatches: 4, Indels: 23
0.69 0.05 0.27
Matches are distributed among these distances:
9 4 0.07
10 6 0.10
11 5 0.08
12 22 0.37
13 11 0.19
14 3 0.05
15 4 0.07
16 4 0.07
ACGTcount: A:0.31, C:0.03, G:0.01, T:0.64
Consensus pattern (12 bp):
ATTATTTATTAT
Found at i:39814132 original size:26 final size:25
Alignment explanation
Indices: 39814103--39814174 Score: 69
Period size: 26 Copynumber: 2.9 Consensus size: 25
39814093 ACTTTTTAGA
39814103 TTATTATATATATTATTTATTATACT
1 TTATTATAT-TATTATTTATTATACT
* *
39814129 TTATTTTACTTATTTATTTATT-TATT
1 TTATTATA-TTA-TTATTTATTATACT
*
39814155 TTATTGTATT-TT-TTTATTAT
1 TTATTATATTATTATTTATTAT
39814175 TGGTTTGTTT
Statistics
Matches: 40, Mismatches: 3, Indels: 9
0.77 0.06 0.17
Matches are distributed among these distances:
22 6 0.15
23 3 0.08
25 2 0.05
26 19 0.47
27 10 0.25
ACGTcount: A:0.26, C:0.03, G:0.01, T:0.69
Consensus pattern (25 bp):
TTATTATATTATTATTTATTATACT
Found at i:39814157 original size:13 final size:13
Alignment explanation
Indices: 39814115--39814172 Score: 57
Period size: 13 Copynumber: 4.4 Consensus size: 13
39814105 ATTATATATA
*
39814115 TTATTTATTATACT
1 TTATTTATT-TATT
*
39814129 TTATTTTACTTA-T
1 TTA-TTTATTTATT
39814142 TTATTTATTTATT
1 TTATTTATTTATT
39814155 TTATTGTATTT-TT
1 TTATT-TATTTATT
39814168 TTATT
1 TTATT
39814173 ATTGGTTTGT
Statistics
Matches: 39, Mismatches: 2, Indels: 7
0.81 0.04 0.15
Matches are distributed among these distances:
12 7 0.18
13 17 0.44
14 10 0.26
15 5 0.13
ACGTcount: A:0.22, C:0.03, G:0.02, T:0.72
Consensus pattern (13 bp):
TTATTTATTTATT
Found at i:39814166 original size:31 final size:32
Alignment explanation
Indices: 39814073--39814154 Score: 107
Period size: 33 Copynumber: 2.6 Consensus size: 32
39814063 TTTTACATTA
39814073 TTATATATATTATTTATTATACTTT-TTAGATTA-
1 TTATATATATTATTTATTATACTTTATT---TTAC
39814106 TTATATATATTATTTATTATACTTTATTTTAC
1 TTATATATATTATTTATTATACTTTATTTTAC
*
39814138 TTATTTAT-TTATTTATT
1 TTATATATATTATTTATT
39814155 TTATTGTATT
Statistics
Matches: 46, Mismatches: 1, Indels: 6
0.87 0.02 0.11
Matches are distributed among these distances:
31 12 0.26
32 7 0.15
33 25 0.54
34 2 0.04
ACGTcount: A:0.30, C:0.04, G:0.01, T:0.65
Consensus pattern (32 bp):
TTATATATATTATTTATTATACTTTATTTTAC
Found at i:39814192 original size:4 final size:4
Alignment explanation
Indices: 39814115--39814172 Score: 53
Period size: 4 Copynumber: 13.2 Consensus size: 4
39814105 ATTATATATA
*
39814115 TTAT TTAT TATACT TTATT TTAC TTAT TTAT TTAT TTATT TTAT TGTAT
1 TTAT TTAT T-TA-T TTA-T TTAT TTAT TTAT TTAT TTA-T TTAT T-TAT
*
39814164 TTTT TTAT T
1 TTAT TTAT T
39814173 ATTGGTTTGT
Statistics
Matches: 45, Mismatches: 5, Indels: 8
0.78 0.09 0.14
Matches are distributed among these distances:
4 27 0.60
5 16 0.36
6 2 0.04
ACGTcount: A:0.22, C:0.03, G:0.02, T:0.72
Consensus pattern (4 bp):
TTAT
Found at i:39816536 original size:35 final size:34
Alignment explanation
Indices: 39816497--39816608 Score: 84
Period size: 35 Copynumber: 3.2 Consensus size: 34
39816487 TGTTTTCGAG
39816497 GGACTAGCACTTTTGAGCATTGATGTGTTTTGGTT
1 GGACTAGC-CTTTTGAGCATTGATGTGTTTTGGTT
* * * **
39816532 GGACTAGCTCTTATGAGAAAT-AGTGTGTTTTGGAA
1 GGACTAGC-CTTTTGAGCATTGA-TGTGTTTTGGTT
* * *
39816567 GGATTAG-CTTGTGTAAGCATCTGGTGTGTTTTGGTT
1 GGACTAGCCTT-T-TGAGCAT-TGATGTGTTTTGGTT
39816603 GGACTA
1 GGACTA
39816609 ACGATGTACT
Statistics
Matches: 57, Mismatches: 15, Indels: 9
0.70 0.19 0.11
Matches are distributed among these distances:
33 3 0.05
34 1 0.02
35 37 0.65
36 16 0.28
ACGTcount: A:0.21, C:0.10, G:0.30, T:0.39
Consensus pattern (34 bp):
GGACTAGCCTTTTGAGCATTGATGTGTTTTGGTT
Found at i:39818129 original size:23 final size:23
Alignment explanation
Indices: 39818098--39818151 Score: 90
Period size: 23 Copynumber: 2.3 Consensus size: 23
39818088 GTAGTTCCTG
*
39818098 ACTCATTTAAATGGTGTGGGATT
1 ACTCATTTAAACGGTGTGGGATT
*
39818121 ACTCGTTTAAACGGTGTGGGATT
1 ACTCATTTAAACGGTGTGGGATT
39818144 ACTCATTT
1 ACTCATTT
39818152 TTGAAACTAC
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
23 28 1.00
ACGTcount: A:0.24, C:0.13, G:0.24, T:0.39
Consensus pattern (23 bp):
ACTCATTTAAACGGTGTGGGATT
Found at i:39819597 original size:23 final size:22
Alignment explanation
Indices: 39819571--39819639 Score: 54
Period size: 22 Copynumber: 3.2 Consensus size: 22
39819561 TATATAATGC
39819571 AATAACAATGAAGACAAAAATAA
1 AATAACAATGAA-ACAAAAATAA
** *
39819594 AATAAGGATGAAACAATAAT--
1 AATAACAATGAAACAAAAATAA
* *
39819614 AATAA-AATAAAATAAAAATAA
1 AATAACAATGAAACAAAAATAA
39819635 CAATA
1 -AATA
39819640 CATTAATAAT
Statistics
Matches: 36, Mismatches: 7, Indels: 7
0.72 0.14 0.14
Matches are distributed among these distances:
19 10 0.28
20 5 0.14
22 11 0.31
23 10 0.28
ACGTcount: A:0.70, C:0.06, G:0.07, T:0.17
Consensus pattern (22 bp):
AATAACAATGAAACAAAAATAA
Found at i:39819616 original size:3 final size:3
Alignment explanation
Indices: 39819608--39819686 Score: 74
Period size: 3 Copynumber: 26.0 Consensus size: 3
39819598 AGGATGAAAC
* *
39819608 AAT AAT AAT AA- AAT AA- AAT AAA AAT AAC AAT ACATT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A-A-T AAT AAT AAT
*
39819653 AAT AAT AAT AAT GAT AAT ACA- AATT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT A-AT AA-T AAT AAT AAT
39819687 GATGATGTAA
Statistics
Matches: 63, Mismatches: 6, Indels: 14
0.76 0.07 0.17
Matches are distributed among these distances:
2 5 0.08
3 51 0.81
4 5 0.08
5 2 0.03
ACGTcount: A:0.66, C:0.04, G:0.01, T:0.29
Consensus pattern (3 bp):
AAT
Found at i:39819704 original size:28 final size:28
Alignment explanation
Indices: 39819649--39819704 Score: 69
Period size: 28 Copynumber: 2.0 Consensus size: 28
39819639 ACATTAATAA
*
39819649 TAATAATAATAATAATGATAATACAAAT
1 TAATAATAATAATAATGATAATAAAAAT
* *
39819677 TAATAATAATGATGATG-TAAGTAAAAAT
1 TAATAATAATAATAATGATAA-TAAAAAT
39819705 ATAAGTAAAT
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
27 3 0.12
28 21 0.88
ACGTcount: A:0.57, C:0.02, G:0.09, T:0.32
Consensus pattern (28 bp):
TAATAATAATAATAATGATAATAAAAAT
Found at i:39819825 original size:3 final size:3
Alignment explanation
Indices: 39819817--39819955 Score: 58
Period size: 3 Copynumber: 45.7 Consensus size: 3
39819807 GATAGAAAAG
* * *
39819817 ATA ATA ATA ACGTA TTA ATA AGA ATA ATA ATA AT- ATA ATA ATT ATGGA
1 ATA ATA ATA A--TA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA AT--A
* * * *
39819865 A-A A-A ATA ATA TTA AT- ATT TTAA ATA A-G ATA ATA ATA ATA GATA
1 ATA ATA ATA ATA ATA ATA ATA AT-A ATA ATA ATA ATA ATA ATA -ATA
* * *
39819908 GA-A AGTA GTA GTA ATA ATA ATA ATA ATA A-A GATA ATA ATA AAA ATA
1 -ATA A-TA ATA ATA ATA ATA ATA ATA ATA ATA -ATA ATA ATA ATA ATA
39819954 AT
1 AT
39819956 TAATTTGAAA
Statistics
Matches: 105, Mismatches: 17, Indels: 28
0.70 0.11 0.19
Matches are distributed among these distances:
2 11 0.10
3 83 0.79
4 8 0.08
5 3 0.03
ACGTcount: A:0.60, C:0.01, G:0.08, T:0.32
Consensus pattern (3 bp):
ATA
Found at i:39819858 original size:23 final size:22
Alignment explanation
Indices: 39819761--39819858 Score: 65
Period size: 23 Copynumber: 4.3 Consensus size: 22
39819751 TTAATTAGCC
* *
39819761 TAATAATATGATAATAATATTA
1 TAATAATAAGATAATAATAATA
* *
39819783 GTAACAATACAG-TAATAGTAATA
1 -TAATAATA-AGATAATAATAATA
* **
39819806 -AGATAGAAAAGATAATAATAACG
1 TA-ATA-ATAAGATAATAATAATA
*
39819829 TATTAATAAGAATAATAATAATA
1 TAATAATAAG-ATAATAATAATA
39819852 TAATAAT
1 TAATAAT
39819859 TATGGAAAAA
Statistics
Matches: 55, Mismatches: 14, Indels: 12
0.68 0.17 0.15
Matches are distributed among these distances:
21 1 0.02
22 8 0.15
23 44 0.80
24 2 0.04
ACGTcount: A:0.57, C:0.03, G:0.09, T:0.31
Consensus pattern (22 bp):
TAATAATAAGATAATAATAATA
Found at i:39820909 original size:23 final size:24
Alignment explanation
Indices: 39820857--39820916 Score: 68
Period size: 23 Copynumber: 2.5 Consensus size: 24
39820847 TTTAAACCTT
*
39820857 GCAGGTGGCAGAGCAAGCGGAGGA
1 GCAGGTGGCAGAGCAAACGGAGGA
* * *
39820881 GTAGGTGGCTGA-CAAACGGTGGA
1 GCAGGTGGCAGAGCAAACGGAGGA
39820904 GCAGGTGGTCAGA
1 GCAGGTGG-CAGA
39820917 AGATTAGCAT
Statistics
Matches: 29, Mismatches: 6, Indels: 2
0.78 0.16 0.05
Matches are distributed among these distances:
23 16 0.55
24 13 0.45
ACGTcount: A:0.27, C:0.15, G:0.47, T:0.12
Consensus pattern (24 bp):
GCAGGTGGCAGAGCAAACGGAGGA
Found at i:39821525 original size:44 final size:43
Alignment explanation
Indices: 39821342--39821997 Score: 193
Period size: 44 Copynumber: 14.7 Consensus size: 43
39821332 TGCTCCATTG
**
39821342 CTCCACTGCAACTTCAAGGAGATAAGATTTGTAACTTCAATCTA
1 CTCCACTGCAACTTC-AGGAGATAAGATTTGTGGCTTCAATCTA
** * *
39821386 CTCCACTTTATCTTCAGGGAGATAAGATTTGTGG--T-AAT-TCG
1 CTCCACTGCAACTTCA-GGAGATAAGATTTGTGGCTTCAATCT-A
* * * * * *
39821427 CTCCTCTACAACTTCA-GAGGTATGAGATTTGCTGTCTTCAGTCTG
1 CTCCACTGCAACTTCAGGA-G-ATAAGATTTG-TGGCTTCAATCTA
* * *
39821472 CTCCGCTGCAACTTCAGGAAGATAGGACTTGTGGCTTCAATCTA
1 CTCCACTGCAACTTCAGG-AGATAAGATTTGTGGCTTCAATCTA
* * * ** *
39821516 CTCCACTGCAACTTCAAGTAGATAAGATTTTCCATGGTAGATTTGATCCGA
1 CTCCACTGCAACTTC-AGGAGATAAGA--TT---T-GTGGCTTCAAT-CTA
* * * * * * **
39821567 C-CTACTGCAACTTCA-GAGGTATAAGACTCGTCGTTTAAATCCG
1 CTCCACTGCAACTTCAGGA-G-ATAAGATTTGTGGCTTCAATCTA
* * * * *
39821610 CTCCACTACAACTTCAGGGAGATAGGATTAGTTGTCTTCAGTCTA
1 CTCCACTGCAACTTCA-GGAGATAAGATTTG-TGGCTTCAATCTA
* * * *** * * *
39821655 CCCCGCTGCAACTTCAGGGAGATAAGACTTGTAATTTTAACCTG
1 CTCCACTGCAACTTCA-GGAGATAAGATTTGTGGCTTCAATCTA
* * * *
39821699 CTCCACTGCAATTTCAAGGAGATAAG-GTT-T-GCTAT-GATCTG
1 CTCCACTGCAACTTC-AGGAGATAAGATTTGTGGCT-TCAATCTA
* * * * * *
39821740 CTCTATTGCAACTTCAGCGAGATAAGATCTATAATTTATAGCTTCAATTTG
1 CTCCACTGCAACTTCAG-GAGATAAG-------ATTTGTGGCTTCAATCTA
* * * ** * *
39821791 TTCCACTGCAACTTCAGGAAAATAAGATTCGCTATCTTCAGTCTG
1 CTCCACTGCAACTTCAGG-AGATAAGATTTG-TGGCTTCAATCTA
* * *** * * *
39821836 CTCCACTGCAACTTCAGGGAGATAAGACTCGCTATTTTTAGTCTG
1 CTCCACTGCAACTTCA-GGAGATAAGATTTG-TGGCTTCAATCTA
* ** *
39821881 CTCCACTGCAACTTCAAGGAGATAAGACTTGTAACTTCAA-CTTG
1 CTCCACTGCAACTTC-AGGAGATAAGATTTGTGGCTTCAATC-TA
* * ** *
39821925 CTCCACTGTAATTTCAGGGAGATAAGATTAATGGCTTCGATCTA
1 CTCCACTGCAACTTCA-GGAGATAAGATTTGTGGCTTCAATCTA
39821969 CTCCACTGCAACTTCAGGGAGATAAGATT
1 CTCCACTGCAACTTCA-GGAGATAAGATT
39821998 CACCATCTTC
Statistics
Matches: 457, Mismatches: 109, Indels: 92
0.69 0.17 0.14
Matches are distributed among these distances:
39 2 0.00
40 4 0.01
41 49 0.11
42 5 0.01
43 7 0.02
44 180 0.39
45 135 0.30
46 9 0.02
47 1 0.00
48 2 0.00
49 5 0.01
50 28 0.06
51 30 0.07
ACGTcount: A:0.28, C:0.22, G:0.19, T:0.31
Consensus pattern (43 bp):
CTCCACTGCAACTTCAGGAGATAAGATTTGTGGCTTCAATCTA
Found at i:39821845 original size:45 final size:45
Alignment explanation
Indices: 39821609--39822007 Score: 237
Period size: 45 Copynumber: 8.9 Consensus size: 45
39821599 GTTTAAATCC
* * * * *
39821609 GCTCCACTACAACTTCAGGGAGATAGGATTAGTTGTCTTCAGTCT
1 GCTCCACTGCAACTTCAGGGAGATAAGATTCGCTATCTTCAGTCT
* * * * **
39821654 ACCCCGCTGCAACTTCAGGGAGATAAGACTT-G-TAAT-TTTAACCT
1 GCTCCACTGCAACTTCAGGGAGATAAGA-TTCGCT-ATCTTCAGTCT
* * * * *
39821698 GCTCCACTGCAATTTCAAGGAGATAAGGTTTGCTA---TGA-TCT
1 GCTCCACTGCAACTTCAGGGAGATAAGATTCGCTATCTTCAGTCT
* * * *** * *
39821739 GCTCTATTGCAACTTCAGCGAGATAAGATCTATAATTTATAGCTTCAATTT
1 GCTCCACTGCAACTTCAGGGAGATAAGA--T-T-CGCTAT--CTTCAGTCT
* * *
39821790 GTTCCACTGCAACTTCAGGAAAATAAGATTCGCTATCTTCAGTCT
1 GCTCCACTGCAACTTCAGGGAGATAAGATTCGCTATCTTCAGTCT
* * *
39821835 GCTCCACTGCAACTTCAGGGAGATAAGACTCGCTATTTTTAGTCT
1 GCTCCACTGCAACTTCAGGGAGATAAGATTCGCTATCTTCAGTCT
* * *
39821880 GCTCCACTGCAACTTCAAGGAGATAAGACTT-G-TAACTTCA-ACTT
1 GCTCCACTGCAACTTCAGGGAGATAAGA-TTCGCTATCTTCAGTC-T
* * ** **
39821924 GCTCCACTGTAATTTCAGGGAGATAAGATT-AATGGCTTC-GATCT
1 GCTCCACTGCAACTTCAGGGAGATAAGATTCGCTATCTTCAG-TCT
* * *
39821968 ACTCCACTGCAACTTCAGGGAGATAAGATTCACCATCTTC
1 GCTCCACTGCAACTTCAGGGAGATAAGATTCGCTATCTTC
39822008 GATCTATTCC
Statistics
Matches: 269, Mismatches: 65, Indels: 40
0.72 0.17 0.11
Matches are distributed among these distances:
41 24 0.09
42 2 0.01
43 6 0.02
44 95 0.35
45 108 0.40
46 3 0.01
47 3 0.01
48 1 0.00
49 1 0.00
50 2 0.01
51 24 0.09
ACGTcount: A:0.28, C:0.23, G:0.18, T:0.31
Consensus pattern (45 bp):
GCTCCACTGCAACTTCAGGGAGATAAGATTCGCTATCTTCAGTCT
Found at i:39822039 original size:45 final size:45
Alignment explanation
Indices: 39821792--39822052 Score: 117
Period size: 45 Copynumber: 5.8 Consensus size: 45
39821782 TTCAATTTGT
* * * * *
39821792 TCCACTGCAACTTCAGGAAAATAAGATTCGCTATCTTC-AGTCTGC
1 TCCACTACAACTTCAGGGAAATAAGATTCACAATCTTCGA-TCTAC
* * * * * ** *
39821837 TCCACTGCAACTTCAGGGAGATAAGACTCGCTAT-TTTTAGTCTGC
1 TCCACTACAACTTCAGGGAAATAAGATTCACAATCTTCGA-TCTAC
* * * ** * *
39821882 TCCACTGCAACTTCAAGGAGATAAGACTT-GTAA-CTTC-AACTTGC
1 TCCACTACAACTTCAGGGAAATAAGA-TTCACAATCTTCGATC-TAC
** * *
39821926 TCCACTGTAATTTCAGGGAGATAAGATT---AATGGCTTCGATCTAC
1 TCCACTACAACTTCAGGGAAATAAGATTCACAAT--CTTCGATCTAC
* * * *
39821970 TCCACTGCAACTTCAGGGAGATAAGATTCACCATCTTCGATCTAT
1 TCCACTACAACTTCAGGGAAATAAGATTCACAATCTTCGATCTAC
* * *
39822015 TCCACTACTA-TCTCGGGGAAATAAGATTTACAATCTTC
1 TCCACTACAACT-TCAGGGAAATAAGATTCACAATCTTC
39822053 AGTCTGTTTC
Statistics
Matches: 179, Mismatches: 25, Indels: 24
0.79 0.11 0.11
Matches are distributed among these distances:
41 2 0.01
43 3 0.02
44 62 0.35
45 109 0.61
46 1 0.01
47 2 0.01
ACGTcount: A:0.29, C:0.24, G:0.17, T:0.30
Consensus pattern (45 bp):
TCCACTACAACTTCAGGGAAATAAGATTCACAATCTTCGATCTAC
Found at i:39822268 original size:177 final size:177
Alignment explanation
Indices: 39822005--39822574 Score: 560
Period size: 177 Copynumber: 3.2 Consensus size: 177
39821995 ATTCACCATC
* * ** * * *
39822005 TTCGATCTATTCCACTACTATCTCGGGGAAATAAGATTTACAATCTTCAGTCTGTTTCCTTGCTA
1 TTCGATCTACTCCACTACT-GCTTAGGGAGATAAGATCTACAATCTTCAGTCTGCTTCCTTGCTA
* * * *
39822070 CATCAGGAAGATAAGACTACAATCTTC-GACCTACTCCTTTACTACCTCAGGGAGATAAAGCTGG
65 CATCAAGAAGATAAGACTACAATCTTCAG-CCTGCTCCTTTACTACCTCAGGGAGATAAGGCTAG
* *
39822134 TGGCTAAAATCTACTCCCCTGCTACCTCGGGAAGATAAGCTTTGCCGTT
129 TGGCTAAAATCTGCTCCCCTGCTACCTCGGGAAGATAAGATTTGCCGTT
*
39822183 TTCGATCTACTCCACTACTGCTTAGGGAGAGAAGATCTACAATCTTCAGTCTGCTTCCTTGCTAC
1 TTCGATCTACTCCACTACTGCTTAGGGAGATAAGATCTACAATCTTCAGTCTGCTTCCTTGCTAC
* * * *
39822248 ATCAAGAAGATAATACTACAATTTTCAGCTTGCT-CTCTTACTACCTCAAGGAGATAAGGCTAGT
66 ATCAAGAAGATAAGACTACAATCTTCAGCCTGCTCCT-TTACTACCTCAGGGAGATAAGGCTAGT
** * * * * * *
39822312 GGCTAAAATCTGCTCGTCTGCTACTTCAGGAAGATAGGAGTCGCCATT
130 GGCTAAAATCTGCTCCCCTGCTACCTCGGGAAGATAAGATTTGCCGTT
* * * * * * * * * * *
39822360 TTCGATTTGCCCCACTGCT-ATCTCGAGGATACAAGATCTACAATCTTCAGTCTACTCCCTCGCT
1 TTCGATCTACTCCACTACTGCT-TAG-GGAGATAAGATCTACAATCTTCAGTCTGCTTCCTTGCT
* * * * **
39822424 ACCTC-AGAAAGATAAGACTACAATCTTCAGCCTGCTGCC-TTGCT-GCTTAGGGAGGCAAGGCT
64 ACATCAAG-AAGATAAGACTACAATCTTCAGCCTGCT-CCTTTACTACCTCAGGGAGATAAGGCT
* * ** *
39822486 AGTGGCTGAAATCTGCTCCCTTATTACCTCAGGG-AGATAAGATTTGCCGTC
127 AGTGGCTAAAATCTGCTCCCCTGCTACCTC-GGGAAGATAAGATTTGCCGTT
** *
39822537 TTCGATCTGTTCCACTACTGCCTAGGGAGATAAGATCT
1 TTCGATCTACTCCACTACTGCTTAGGGAGATAAGATCT
39822575 GTAATCTTTA
Statistics
Matches: 314, Mismatches: 69, Indels: 20
0.78 0.17 0.05
Matches are distributed among these distances:
176 14 0.04
177 212 0.68
178 87 0.28
180 1 0.00
ACGTcount: A:0.26, C:0.25, G:0.19, T:0.29
Consensus pattern (177 bp):
TTCGATCTACTCCACTACTGCTTAGGGAGATAAGATCTACAATCTTCAGTCTGCTTCCTTGCTAC
ATCAAGAAGATAAGACTACAATCTTCAGCCTGCTCCTTTACTACCTCAGGGAGATAAGGCTAGTG
GCTAAAATCTGCTCCCCTGCTACCTCGGGAAGATAAGATTTGCCGTT
Found at i:39822297 original size:44 final size:44
Alignment explanation
Indices: 39822219--39822304 Score: 104
Period size: 44 Copynumber: 2.0 Consensus size: 44
39822209 GAGAGAAGAT
*
39822219 CTACAATCTTCAGTCTGCTTCCTTGCTACATCAAGAAGATAATA
1 CTACAATCTTCAGTCTGCTTCCTTACTACATCAAGAAGATAATA
* * *
39822263 CTACAATTTTCAG-CTTGC-TCTCTTACTACCTCAAGGAGATAA
1 CTACAATCTTCAGTC-TGCTTC-CTTACTACATCAAGAAGATAA
39822305 GGCTAGTGGC
Statistics
Matches: 36, Mismatches: 4, Indels: 4
0.82 0.09 0.09
Matches are distributed among these distances:
43 3 0.08
44 33 0.92
ACGTcount: A:0.30, C:0.26, G:0.12, T:0.33
Consensus pattern (44 bp):
CTACAATCTTCAGTCTGCTTCCTTACTACATCAAGAAGATAATA
Found at i:39822564 original size:44 final size:44
Alignment explanation
Indices: 39822516--39822941 Score: 260
Period size: 44 Copynumber: 9.8 Consensus size: 44
39822506 TTATTACCTC
* * *
39822516 AGGGAGATAAGATTTGCCGTCTTCGATCTGTTCCACTACTGCCT
1 AGGGAGATAAGATTTGCAGTCTTCGATCTGCTCCACTACTGCTT
* * * * * *
39822560 AGGGAGATAAGATCTGTAATCTT-TAGCTTACTCCACTACTGCTT
1 AGGGAGATAAGATTTGCAGTCTTCGATC-TGCTCCACTACTGCTT
* * ** * ** *
39822604 AGAGAGAT-AGA-ATGGTGGCTTAAATATGCTCCACTACTGCTT
1 AGGGAGATAAGATTTGCAGTCTTCGATCTGCTCCACTACTGCTT
* * * *
39822646 AGGGAGACAAGATTCGCTGTCTTCGATCTGCTTCACTACTGCTT
1 AGGGAGATAAGATTTGCAGTCTTCGATCTGCTCCACTACTGCTT
* * * * * *
39822690 AGGGAGAAAAGATCTGTAATCTTC-AGCCTACTCCACTACTGCTT
1 AGGGAGATAAGATTTGCAGTCTTCGA-TCTGCTCCACTACTGCTT
* ** *
39822734 AGGGAGATAAGATGGTG--G-CTTAAATCTGCTCCACTAATGCTT
1 AGGGAGATAAGAT-TTGCAGTCTTCGATCTGCTCCACTACTGCTT
* * ** *
39822776 AGGGAGACAAGCTTCACCGTCTTCGATCTGCTCCACTACTGCTT
1 AGGGAGATAAGATTTGCAGTCTTCGATCTGCTCCACTACTGCTT
* * * * *
39822820 AGGGAGATAAGATCTGTAATCTTC-AGCCTGCTCCACTACTGCTC
1 AGGGAGATAAGATTTGCAGTCTTCGA-TCTGCTCCACTACTGCTT
* ** ** * ** *
39822864 AGGGAGACAAG-GCTGGTGGCTTAAATCTGCTCCACTACTACTT
1 AGGGAGATAAGATTTGCAGTCTTCGATCTGCTCCACTACTGCTT
* * *
39822907 AGGGAGACAAGATTAGCCA-TCTTCTATCTGCTCCA
1 AGGGAGATAAGATTTG-CAGTCTTCGATCTGCTCCA
39822942 TTGCTACCTC
Statistics
Matches: 287, Mismatches: 81, Indels: 28
0.72 0.20 0.07
Matches are distributed among these distances:
42 55 0.19
43 45 0.16
44 185 0.64
45 2 0.01
ACGTcount: A:0.26, C:0.24, G:0.22, T:0.29
Consensus pattern (44 bp):
AGGGAGATAAGATTTGCAGTCTTCGATCTGCTCCACTACTGCTT
Found at i:39822670 original size:130 final size:130
Alignment explanation
Indices: 39822516--39822941 Score: 604
Period size: 130 Copynumber: 3.3 Consensus size: 130
39822506 TTATTACCTC
* * *
39822516 AGGGAGATAAGATTTGCCGTCTTCGATCTGTTCCACTACTGCCTAGGGAGATAAGATCTGTAATC
1 AGGGAGACAAGATTCGCCGTCTTCGATCTGTTCCACTACTGCTTAGGGAGATAAGATCTGTAATC
* * * *
39822581 TTTAGCTTACTCCACTACTGCTTAGAGAGATAGAATGGTGGCTTAAATATGCTCCACTACTGCTT
66 TTCAGCCTACTCCACTACTGCTTAGGGAGATAGAATGGTGGCTTAAATCTGCTCCACTACTGCTT
* *
39822646 AGGGAGACAAGATTCGCTGTCTTCGATCTGCTT-CACTACTGCTTAGGGAGAAAAGATCTGTAAT
1 AGGGAGACAAGATTCGCCGTCTTCGATCTG-TTCCACTACTGCTTAGGGAGATAAGATCTGTAAT
*
39822710 CTTCAGCCTACTCCACTACTGCTTAGGGAGATA-AGATGGTGGCTTAAATCTGCTCCACTAATGC
65 CTTCAGCCTACTCCACTACTGCTTAGGGAGATAGA-ATGGTGGCTTAAATCTGCTCCACTACTGC
39822774 TT
129 TT
* * *
39822776 AGGGAGACAAGCTTCACCGTCTTCGATCTGCTCCACTACTGCTTAGGGAGATAAGATCTGTAATC
1 AGGGAGACAAGATTCGCCGTCTTCGATCTGTTCCACTACTGCTTAGGGAGATAAGATCTGTAATC
* * * ** *
39822841 TTCAGCCTGCTCCACTACTGCTCAGGGAGACAAGGCTGGTGGCTTAAATCTGCTCCACTACTACT
66 TTCAGCCTACTCCACTACTGCTTAGGGAGA-TAGAATGGTGGCTTAAATCTGCTCCACTACTGCT
39822906 T
130 T
* * * *
39822907 AGGGAGACAAGATTAGCCATCTTCTATCTGCTCCA
1 AGGGAGACAAGATTCGCCGTCTTCGATCTGTTCCA
39822942 TTGCTACCTC
Statistics
Matches: 264, Mismatches: 27, Indels: 9
0.88 0.09 0.03
Matches are distributed among these distances:
129 2 0.01
130 201 0.76
131 61 0.23
ACGTcount: A:0.26, C:0.24, G:0.22, T:0.29
Consensus pattern (130 bp):
AGGGAGACAAGATTCGCCGTCTTCGATCTGTTCCACTACTGCTTAGGGAGATAAGATCTGTAATC
TTCAGCCTACTCCACTACTGCTTAGGGAGATAGAATGGTGGCTTAAATCTGCTCCACTACTGCTT
Found at i:39822775 original size:86 final size:86
Alignment explanation
Indices: 39822632--39822833 Score: 223
Period size: 86 Copynumber: 2.3 Consensus size: 86
39822622 CTTAAATATG
* * ** * *
39822632 CTCCACTACTGCTTAGGGAGACAAGATTCGCTGTCTTCGATCTGCTTCACTACTGCTTAGGGAGA
1 CTCCACTACTGCTTAGGGAGATAAGA-TCGCTGGCTTAAATCTGCTCCACTAATGCTTAGGGAGA
39822697 AAAGATCTGT-A-ATCTTC-AGCCTA
65 AAAG--CT-TCACATCTTCGA-CCTA
* *
39822720 CTCCACTACTGCTTAGGGAGATAAGAT-GGTGGCTTAAATCTGCTCCACTAATGCTTAGGGAGAC
1 CTCCACTACTGCTTAGGGAGATAAGATCGCTGGCTTAAATCTGCTCCACTAATGCTTAGGGAGAA
* * *
39822784 AAGCTTCACCGTCTTCGATCTG
66 AAGCTTCA-CATCTTCGACCTA
39822806 CTCCACTACTGCTTAGGGAGATAAGATC
1 CTCCACTACTGCTTAGGGAGATAAGATC
39822834 TGTAATCTTC
Statistics
Matches: 98, Mismatches: 11, Indels: 11
0.82 0.09 0.09
Matches are distributed among these distances:
83 1 0.01
84 3 0.03
86 67 0.68
87 2 0.02
88 25 0.26
ACGTcount: A:0.25, C:0.25, G:0.22, T:0.28
Consensus pattern (86 bp):
CTCCACTACTGCTTAGGGAGATAAGATCGCTGGCTTAAATCTGCTCCACTAATGCTTAGGGAGAA
AAGCTTCACATCTTCGACCTA
Found at i:39824653 original size:20 final size:20
Alignment explanation
Indices: 39824628--39824666 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
39824618 CCACGATTCT
39824628 TTTTTTTATTATTTTTGCTC
1 TTTTTTTATTATTTTTGCTC
* *
39824648 TTTTTTTCTTTTTTTTGCT
1 TTTTTTTATTATTTTTGCT
39824667 GCCTTTGCTG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.05, C:0.10, G:0.05, T:0.79
Consensus pattern (20 bp):
TTTTTTTATTATTTTTGCTC
Found at i:39831167 original size:17 final size:18
Alignment explanation
Indices: 39831105--39831171 Score: 59
Period size: 19 Copynumber: 3.7 Consensus size: 18
39831095 AAACTATATG
39831105 ATAAAT-AATAT-ATAAA
1 ATAAATAAATATAATAAA
* *
39831121 A-ATAATAAAAATAATAGA
1 ATA-AATAAATATAATAAA
*
39831139 ATAAGTGAAATATAATAAA
1 ATAAAT-AAATATAATAAA
39831158 ATAAATAATATATA
1 ATAAATAA-ATATA
39831172 TATAGTAAAA
Statistics
Matches: 39, Mismatches: 6, Indels: 9
0.72 0.11 0.17
Matches are distributed among these distances:
15 1 0.03
16 4 0.10
17 4 0.10
18 9 0.23
19 21 0.54
ACGTcount: A:0.67, C:0.00, G:0.04, T:0.28
Consensus pattern (18 bp):
ATAAATAAATATAATAAA
Found at i:39831245 original size:55 final size:58
Alignment explanation
Indices: 39831147--39831257 Score: 156
Period size: 55 Copynumber: 1.9 Consensus size: 58
39831137 GAATAAGTGA
* *
39831147 AATATAATAAAATAAATAATATATATATAGTAAAACTATATAACGTATAATAAAATGTG
1 AATATAATAAAATAAATAATATATATATACTAAAAC-ATATAACATATAATAAAATGTG
* *
39831206 AATATAATAGAATAAAT-A-ATATATATACTAAAA-ATATAACATATAGTAAAAT
1 AATATAATAAAATAAATAATATATATATACTAAAACATATAACATATAATAAAAT
39831258 TTATAAAAAT
Statistics
Matches: 48, Mismatches: 4, Indels: 4
0.86 0.07 0.07
Matches are distributed among these distances:
55 17 0.35
57 14 0.29
58 1 0.02
59 16 0.33
ACGTcount: A:0.59, C:0.04, G:0.05, T:0.32
Consensus pattern (58 bp):
AATATAATAAAATAAATAATATATATATACTAAAACATATAACATATAATAAAATGTG
Found at i:39832749 original size:23 final size:22
Alignment explanation
Indices: 39832723--39832791 Score: 54
Period size: 22 Copynumber: 3.2 Consensus size: 22
39832713 TATATAATGT
39832723 AATAACAATGAAGACAAAAATAA
1 AATAACAATGAA-ACAAAAATAA
** *
39832746 AATAAGGATGAAACAATAAT--
1 AATAACAATGAAACAAAAATAA
* *
39832766 AATAA-AATAAAATAAAAATAA
1 AATAACAATGAAACAAAAATAA
39832787 CAATA
1 -AATA
39832792 CATTAATAAG
Statistics
Matches: 36, Mismatches: 7, Indels: 7
0.72 0.14 0.14
Matches are distributed among these distances:
19 10 0.28
20 5 0.14
22 11 0.31
23 10 0.28
ACGTcount: A:0.70, C:0.06, G:0.07, T:0.17
Consensus pattern (22 bp):
AATAACAATGAAACAAAAATAA
Found at i:39832768 original size:3 final size:3
Alignment explanation
Indices: 39832760--39832864 Score: 67
Period size: 3 Copynumber: 35.0 Consensus size: 3
39832750 AGGATGAAAC
* * * *
39832760 AAT AAT AAT AA- AAT AA- AAT AAA AAT AAC AAT ACATT AAT AAG AGT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A-A-T AAT AAT AAT
** *
39832805 AAT AAT -AT GTT AAT -AT AAAT AAT AAT AAT AAT AAT AAT GAT AAT
1 AAT AAT AAT AAT AAT AAT -AAT AAT AAT AAT AAT AAT AAT AAT AAT
39832849 ACA- AATT AAT AAT AAT
1 A-AT AA-T AAT AAT AAT
39832865 GATGATGTAA
Statistics
Matches: 79, Mismatches: 13, Indels: 20
0.71 0.12 0.18
Matches are distributed among these distances:
2 9 0.11
3 61 0.77
4 7 0.09
5 2 0.03
ACGTcount: A:0.63, C:0.03, G:0.04, T:0.30
Consensus pattern (3 bp):
AAT
Found at i:39832785 original size:22 final size:25
Alignment explanation
Indices: 39832741--39832791 Score: 63
Period size: 25 Copynumber: 2.2 Consensus size: 25
39832731 TGAAGACAAA
* *
39832741 AATAAAATAAGGATGAAACAATAAT
1 AATAAAATAAGAATGAAACAATAAC
39832766 AATAAAATAA-AAT-AAA-AATAAC
1 AATAAAATAAGAATGAAACAATAAC
39832788 AATA
1 AATA
39832792 CATTAATAAG
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
22 9 0.38
23 3 0.12
24 2 0.08
25 10 0.42
ACGTcount: A:0.71, C:0.04, G:0.06, T:0.20
Consensus pattern (25 bp):
AATAAAATAAGAATGAAACAATAAC
Found at i:39832799 original size:30 final size:29
Alignment explanation
Indices: 39832739--39832800 Score: 72
Period size: 30 Copynumber: 2.1 Consensus size: 29
39832729 AATGAAGACA
**
39832739 AAAATAAAATAAGGATGAAACAATAATAAT
1 AAAATAAAATAAAAAT-AAACAATAATAAT
39832769 AAAATAAAATAAAAAT-AACAATACATTAAT
1 AAAATAAAATAAAAATAAACAATA-A-TAAT
39832799 AA
1 AA
39832801 GAGTAATAAT
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
28 7 0.25
29 1 0.04
30 20 0.71
ACGTcount: A:0.69, C:0.05, G:0.05, T:0.21
Consensus pattern (29 bp):
AAAATAAAATAAAAATAAACAATAATAAT
Found at i:39832882 original size:28 final size:28
Alignment explanation
Indices: 39832804--39832882 Score: 72
Period size: 28 Copynumber: 2.8 Consensus size: 28
39832794 TTAATAAGAG
* *
39832804 TAATAAT-ATGTTAATATAAATAATAATAA
1 TAATAATAATGATAATA-AAA-ATTAATAA
*
39832833 TAATAATAATGATAATACAAATTAATAA
1 TAATAATAATGATAATAAAAATTAATAA
* *
39832861 TAATGATGATG-TAAGTAAAAAT
1 TAATAATAATGATAA-TAAAAAT
39832883 ATAAGTAAAT
Statistics
Matches: 42, Mismatches: 6, Indels: 5
0.79 0.11 0.09
Matches are distributed among these distances:
27 3 0.07
28 22 0.52
29 9 0.21
30 8 0.19
ACGTcount: A:0.57, C:0.01, G:0.08, T:0.34
Consensus pattern (28 bp):
TAATAATAATGATAATAAAAATTAATAA
Found at i:39833112 original size:3 final size:3
Alignment explanation
Indices: 39833106--39833166 Score: 72
Period size: 3 Copynumber: 20.3 Consensus size: 3
39833096 AATAATACGT
*
39833106 TAA TAA TAA TAA TAA TAG TAA -ATA TAA TAA TAA TAA TAA TAA -ATA
1 TAA TAA TAA TAA TAA TAA TAA TA-A TAA TAA TAA TAA TAA TAA TA-A
*
39833151 TAA TAA TAA AAA TAA T
1 TAA TAA TAA TAA TAA T
39833167 TAATTTGAAA
Statistics
Matches: 50, Mismatches: 4, Indels: 8
0.81 0.06 0.13
Matches are distributed among these distances:
2 2 0.04
3 46 0.92
4 2 0.04
ACGTcount: A:0.66, C:0.00, G:0.02, T:0.33
Consensus pattern (3 bp):
TAA
Found at i:39833134 original size:21 final size:21
Alignment explanation
Indices: 39833108--39833166 Score: 100
Period size: 21 Copynumber: 2.8 Consensus size: 21
39833098 TAATACGTTA
*
39833108 ATAATAATAATAATAGTAAAT
1 ATAATAATAATAATAATAAAT
39833129 ATAATAATAATAATAATAAAT
1 ATAATAATAATAATAATAAAT
*
39833150 ATAATAATAAAAATAAT
1 ATAATAATAATAATAAT
39833167 TAATTTGAAA
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 36 1.00
ACGTcount: A:0.66, C:0.00, G:0.02, T:0.32
Consensus pattern (21 bp):
ATAATAATAATAATAATAAAT
Found at i:39845793 original size:20 final size:20
Alignment explanation
Indices: 39845760--39845798 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 20
39845750 TTATTATTAA
*
39845760 TTTTATATGTAAAATATATT
1 TTTTATATGTAAAAAATATT
39845780 TTTTATATAG-AAAAAATAT
1 TTTTATAT-GTAAAAAATAT
39845799 CCATTCTCTA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 16 0.94
21 1 0.06
ACGTcount: A:0.46, C:0.00, G:0.05, T:0.49
Consensus pattern (20 bp):
TTTTATATGTAAAAAATATT
Found at i:39848572 original size:56 final size:56
Alignment explanation
Indices: 39848440--39848585 Score: 147
Period size: 56 Copynumber: 2.6 Consensus size: 56
39848430 ATTATGCTTT
* * *
39848440 TTTTTTAAAAAAAATTAATTAAGCTCTCCTAATTTTTTTGAAAATTTTCATGAATACACA
1 TTTTTT-AAAAAAATTAATT-AGATC-CCCAAATTTTTT-AAAATTTTCATGAATACACA
* * * *
39848500 TTTTCT-AAAAATTTAATTAGATCCCCAAATTTTTT-AAATTTTCATTAA-ACTTCTA
1 TTTTTTAAAAAAATTAATTAGATCCCCAAATTTTTTAAAATTTTCATGAATAC-AC-A
39848555 TTTTTTAAAAAAATTAATTAGA-CCCCAAATT
1 TTTTTTAAAAAAATTAATTAGATCCCCAAATT
39848586 CTTAGTCGTA
Statistics
Matches: 74, Mismatches: 9, Indels: 11
0.79 0.10 0.12
Matches are distributed among these distances:
53 2 0.03
54 13 0.18
55 15 0.20
56 24 0.32
57 4 0.05
58 11 0.15
60 5 0.07
ACGTcount: A:0.40, C:0.13, G:0.03, T:0.44
Consensus pattern (56 bp):
TTTTTTAAAAAAATTAATTAGATCCCCAAATTTTTTAAAATTTTCATGAATACACA
Found at i:39849253 original size:14 final size:15
Alignment explanation
Indices: 39849234--39849262 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
39849224 TTTAATAGTT
39849234 TTAAATATT-TTTTA
1 TTAAATATTCTTTTA
39849248 TTAAATATTCTTTTA
1 TTAAATATTCTTTTA
39849263 ACATATTTAC
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 9 0.64
15 5 0.36
ACGTcount: A:0.34, C:0.03, G:0.00, T:0.62
Consensus pattern (15 bp):
TTAAATATTCTTTTA
Found at i:39849288 original size:17 final size:17
Alignment explanation
Indices: 39849266--39849304 Score: 53
Period size: 17 Copynumber: 2.3 Consensus size: 17
39849256 TCTTTTAACA
39849266 TATTTA-CATTATAGTAT
1 TATTTATCATTATAG-AT
*
39849283 TATTTATTATTATAGAT
1 TATTTATCATTATAGAT
39849300 TATTT
1 TATTT
39849305 TTTATACCTT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
17 13 0.65
18 7 0.35
ACGTcount: A:0.33, C:0.03, G:0.05, T:0.59
Consensus pattern (17 bp):
TATTTATCATTATAGAT
Found at i:39853899 original size:19 final size:19
Alignment explanation
Indices: 39853857--39853899 Score: 52
Period size: 19 Copynumber: 2.3 Consensus size: 19
39853847 TTAGATATCC
*
39853857 TTAAATTATGTTTCACATT
1 TTAAATTATGTTTCAAATT
*
39853876 CTAAATTTAT-TTTCAAATT
1 TTAAA-TTATGTTTCAAATT
39853895 TTAAA
1 TTAAA
39853900 ATGTACTAAT
Statistics
Matches: 20, Mismatches: 3, Indels: 2
0.80 0.12 0.08
Matches are distributed among these distances:
19 16 0.80
20 4 0.20
ACGTcount: A:0.37, C:0.09, G:0.02, T:0.51
Consensus pattern (19 bp):
TTAAATTATGTTTCAAATT
Found at i:39858591 original size:37 final size:37
Alignment explanation
Indices: 39858541--39858612 Score: 144
Period size: 37 Copynumber: 1.9 Consensus size: 37
39858531 TAGGGGAATG
39858541 TTTTCGTCCTAGTAGAGGTCTTCGACAAGGTGACCTA
1 TTTTCGTCCTAGTAGAGGTCTTCGACAAGGTGACCTA
39858578 TTTTCGTCCTAGTAGAGGTCTTCGACAAGGTGACC
1 TTTTCGTCCTAGTAGAGGTCTTCGACAAGGTGACC
39858613 CTTTGAGTTT
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
37 35 1.00
ACGTcount: A:0.21, C:0.22, G:0.25, T:0.32
Consensus pattern (37 bp):
TTTTCGTCCTAGTAGAGGTCTTCGACAAGGTGACCTA
Found at i:39861267 original size:20 final size:20
Alignment explanation
Indices: 39861213--39861273 Score: 76
Period size: 20 Copynumber: 3.2 Consensus size: 20
39861203 ATAGGCTTTT
*
39861213 GCTTTCCCAATAAAATATAG
1 GCTTTCCCAGTAAAATATAG
*
39861233 GCTTT---AG-ATAATATAG
1 GCTTTCCCAGTAAAATATAG
39861249 GCTTTCCCAGTAAAATATAG
1 GCTTTCCCAGTAAAATATAG
39861269 GCTTT
1 GCTTT
39861274 ATTGATATTC
Statistics
Matches: 34, Mismatches: 3, Indels: 8
0.76 0.07 0.18
Matches are distributed among these distances:
16 13 0.38
17 1 0.03
19 2 0.06
20 18 0.53
ACGTcount: A:0.34, C:0.16, G:0.15, T:0.34
Consensus pattern (20 bp):
GCTTTCCCAGTAAAATATAG
Found at i:39861671 original size:51 final size:52
Alignment explanation
Indices: 39861615--39861725 Score: 145
Period size: 51 Copynumber: 2.2 Consensus size: 52
39861605 AATTTGTATA
* * * * *
39861615 TAAAAAATTTAACCCTCAACTTTTACATATTA-TATCAATTTAGTCATAATT-
1 TAAAAAAATTAACCCTCAAATATTACA-AATAGTATCAATTTAATCATAATTC
*
39861666 TAAAAAAATTAACCCTCAAATATTACAAATAGTTTCAATTTAATCATAATTC
1 TAAAAAAATTAACCCTCAAATATTACAAATAGTATCAATTTAATCATAATTC
39861718 TAAAAAAA
1 TAAAAAAA
39861726 GTTTTATGGA
Statistics
Matches: 52, Mismatches: 6, Indels: 3
0.85 0.10 0.05
Matches are distributed among these distances:
50 3 0.06
51 41 0.79
52 8 0.15
ACGTcount: A:0.48, C:0.14, G:0.02, T:0.36
Consensus pattern (52 bp):
TAAAAAAATTAACCCTCAAATATTACAAATAGTATCAATTTAATCATAATTC
Found at i:39862026 original size:39 final size:39
Alignment explanation
Indices: 39861942--39862030 Score: 101
Period size: 39 Copynumber: 2.3 Consensus size: 39
39861932 AGCTTAATAC
*
39861942 TATTATATTAATAATAATTTTTAAAAAAAATATTTAAAA
1 TATTATATTTATAATAATTTTTAAAAAAAATATTTAAAA
* * * *
39861981 TATTATATTTTTAAT-ATTTTTAAACATACATATTT-AAT
1 TATTATATTTATAATAATTTTTAAA-AAAAATATTTAAAA
39862019 TATTTATATTTA
1 TA-TTATATTTA
39862031 GTCATATAAT
Statistics
Matches: 42, Mismatches: 6, Indels: 4
0.81 0.12 0.08
Matches are distributed among these distances:
38 13 0.31
39 29 0.69
ACGTcount: A:0.46, C:0.02, G:0.00, T:0.52
Consensus pattern (39 bp):
TATTATATTTATAATAATTTTTAAAAAAAATATTTAAAA
Found at i:39862140 original size:15 final size:15
Alignment explanation
Indices: 39862101--39862142 Score: 54
Period size: 14 Copynumber: 3.0 Consensus size: 15
39862091 TTTCAATTTT
*
39862101 ATTTT-AATAATA-A
1 ATTTTAAATAAAATA
39862114 ATTTTAAA-AAAATA
1 ATTTTAAATAAAATA
39862128 ATTTTAAATAAAATA
1 ATTTTAAATAAAATA
39862143 TTATTCACAT
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
13 8 0.32
14 11 0.44
15 6 0.24
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (15 bp):
ATTTTAAATAAAATA
Found at i:39862194 original size:15 final size:15
Alignment explanation
Indices: 39862169--39862230 Score: 61
Period size: 15 Copynumber: 3.8 Consensus size: 15
39862159 GAAAATATTC
39862169 AATATAATATTTTAAT
1 AATA-AATATTTTAAT
39862185 AATAAATATTTATTATAGT
1 AATAAATA-TT-TTA-A-T
* *
39862204 TATAAATATATTAAT
1 AATAAATATTTTAAT
39862219 AATAAATATTTT
1 AATAAATATTTT
39862231 GTAGTATAAA
Statistics
Matches: 38, Mismatches: 4, Indels: 9
0.75 0.08 0.18
Matches are distributed among these distances:
15 15 0.39
16 7 0.18
17 6 0.16
18 2 0.05
19 8 0.21
ACGTcount: A:0.50, C:0.00, G:0.02, T:0.48
Consensus pattern (15 bp):
AATAAATATTTTAAT
Found at i:39862708 original size:14 final size:14
Alignment explanation
Indices: 39862689--39862727 Score: 60
Period size: 14 Copynumber: 2.8 Consensus size: 14
39862679 CCAGAAAAGT
39862689 AAATCATTTTCCAG
1 AAATCATTTTCCAG
*
39862703 AAATCATTTTCTAG
1 AAATCATTTTCCAG
*
39862717 AAGTCATTTTC
1 AAATCATTTTC
39862728 AGTAAAACAA
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
14 23 1.00
ACGTcount: A:0.33, C:0.18, G:0.08, T:0.41
Consensus pattern (14 bp):
AAATCATTTTCCAG
Found at i:39867463 original size:29 final size:30
Alignment explanation
Indices: 39867399--39867464 Score: 71
Period size: 29 Copynumber: 2.2 Consensus size: 30
39867389 ATTTGGCCTT
* * * *
39867399 ATTTGATTCTTTTTAATAGTACAGGTATTA
1 ATTTGATTCTATTTAATAATACAGGGACTA
* *
39867429 AATTGATT-TATTTAATAATAGAGGGACTA
1 ATTTGATTCTATTTAATAATACAGGGACTA
39867458 ATTTGAT
1 ATTTGAT
39867465 ACAGTAATAC
Statistics
Matches: 29, Mismatches: 7, Indels: 1
0.78 0.19 0.03
Matches are distributed among these distances:
29 22 0.76
30 7 0.24
ACGTcount: A:0.35, C:0.05, G:0.15, T:0.45
Consensus pattern (30 bp):
ATTTGATTCTATTTAATAATACAGGGACTA
Found at i:39869240 original size:16 final size:16
Alignment explanation
Indices: 39869219--39869249 Score: 62
Period size: 16 Copynumber: 1.9 Consensus size: 16
39869209 CAATACTATC
39869219 CTTGTACTTACTTGCT
1 CTTGTACTTACTTGCT
39869235 CTTGTACTTACTTGC
1 CTTGTACTTACTTGC
39869250 AGCTCACCCA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.13, C:0.26, G:0.13, T:0.48
Consensus pattern (16 bp):
CTTGTACTTACTTGCT
Done.