Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: A03
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: 108673976
ACGTcount: A:0.31, C:0.17, G:0.16, T:0.31
Warning! 5040000 characters in sequence are not A, C, G, or T
File 93 of 333
Found at i:29262501 original size:33 final size:34
Alignment explanation
Indices: 29262411--29262502 Score: 100
Period size: 33 Copynumber: 2.8 Consensus size: 34
29262401 CCCACACTAT
* * *
29262411 TACTGTATAGGGCTAAGGCCCAGA-TTGTATTGT
1 TACTGTATAGGGCTAAAGCCCAGACTTGTACTGA
*
29262444 TACTATATAGGGCT-AAGACCCAGACTT-TACTGA
1 TACTGTATAGGGCTAAAG-CCCAGACTTGTACTGA
* *
29262477 TATTGTATAGGGCTAAAGCACAGACT
1 TACTGTATAGGGCTAAAGCCCAGACT
29262503 GTTTTGCATA
Statistics
Matches: 49, Mismatches: 7, Indels: 6
0.79 0.11 0.10
Matches are distributed among these distances:
32 2 0.04
33 42 0.86
34 5 0.10
ACGTcount: A:0.30, C:0.17, G:0.23, T:0.29
Consensus pattern (34 bp):
TACTGTATAGGGCTAAAGCCCAGACTTGTACTGA
Found at i:29263749 original size:40 final size:40
Alignment explanation
Indices: 29263611--29263741 Score: 181
Period size: 40 Copynumber: 3.3 Consensus size: 40
29263601 TATCTTGCAT
* * * *
29263611 ACTAAGTGCCATACATAGCCGAAGCTATCTAAAATCACAC
1 ACTAAGTGCCATATATAGCCGAAGCTATATCAAATCGCAC
**
29263651 ACTAAGTAACATATATAGCCGAAGCTATATCAAATCGCAC
1 ACTAAGTGCCATATATAGCCGAAGCTATATCAAATCGCAC
* * *
29263691 ACTAAGTGCCATATATAGCCGAAGTTATGTCGAATCGCAC
1 ACTAAGTGCCATATATAGCCGAAGCTATATCAAATCGCAC
29263731 ACTAAGTGCCA
1 ACTAAGTGCCA
29263742 CAAATAGCTG
Statistics
Matches: 80, Mismatches: 11, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
40 80 1.00
ACGTcount: A:0.38, C:0.24, G:0.15, T:0.22
Consensus pattern (40 bp):
ACTAAGTGCCATATATAGCCGAAGCTATATCAAATCGCAC
Found at i:29279850 original size:32 final size:32
Alignment explanation
Indices: 29279808--29279873 Score: 82
Period size: 32 Copynumber: 2.0 Consensus size: 32
29279798 ATTTAATTCG
29279808 AAATGTATAAA-AAAGAACCTAAAAATGAAAACT
1 AAATGTATAAAGAAAGAA-C-AAAAATGAAAACT
*
29279841 AAATG-ATAAAGTAATGAACAAAAATGAAAACT
1 AAATGTATAAAG-AAAGAACAAAAATGAAAACT
29279873 A
1 A
29279874 GTTCAAAAGT
Statistics
Matches: 30, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
32 19 0.63
33 6 0.20
34 5 0.17
ACGTcount: A:0.64, C:0.08, G:0.11, T:0.18
Consensus pattern (32 bp):
AAATGTATAAAGAAAGAACAAAAATGAAAACT
Found at i:29279886 original size:31 final size:32
Alignment explanation
Indices: 29279828--29279887 Score: 86
Period size: 32 Copynumber: 1.9 Consensus size: 32
29279818 AAAAGAACCT
*
29279828 AAAAATGAAAACTAAATGATAAAGTAATGAAC
1 AAAAATGAAAACTAAATCATAAAGTAATGAAC
**
29279860 AAAAATGAAAACTAGTTCA-AAAGTAATG
1 AAAAATGAAAACTAAATCATAAAGTAATG
29279888 GAGATTATTG
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
31 9 0.36
32 16 0.64
ACGTcount: A:0.60, C:0.07, G:0.13, T:0.20
Consensus pattern (32 bp):
AAAAATGAAAACTAAATCATAAAGTAATGAAC
Found at i:29289852 original size:13 final size:13
Alignment explanation
Indices: 29289834--29289860 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
29289824 AAAGAAGTCG
29289834 CACACGGGCGTGT
1 CACACGGGCGTGT
29289847 CACACGGGCGTGT
1 CACACGGGCGTGT
29289860 C
1 C
29289861 CTGCTGAGCC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.15, C:0.33, G:0.37, T:0.15
Consensus pattern (13 bp):
CACACGGGCGTGT
Found at i:29307741 original size:30 final size:30
Alignment explanation
Indices: 29307707--29307767 Score: 77
Period size: 30 Copynumber: 2.0 Consensus size: 30
29307697 TCCTTAACTC
29307707 AAACTTTGGAAAAATTACAATTTTGCCCCT
1 AAACTTTGGAAAAATTACAATTTTGCCCCT
* * * * *
29307737 AAACTTTTGCATATTTACACTTTTGCCCCT
1 AAACTTTGGAAAAATTACAATTTTGCCCCT
29307767 A
1 A
29307768 GGCTCGGGAA
Statistics
Matches: 26, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
30 26 1.00
ACGTcount: A:0.31, C:0.23, G:0.08, T:0.38
Consensus pattern (30 bp):
AAACTTTGGAAAAATTACAATTTTGCCCCT
Found at i:29311809 original size:18 final size:19
Alignment explanation
Indices: 29311786--29311821 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
29311776 TAAACTTGGC
*
29311786 ACCATAA-TCATTTAATTT
1 ACCATAATTCAATTAATTT
29311804 ACCATAATTCAATTAATT
1 ACCATAATTCAATTAATT
29311822 CACTAAATTC
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 7 0.44
19 9 0.56
ACGTcount: A:0.42, C:0.17, G:0.00, T:0.42
Consensus pattern (19 bp):
ACCATAATTCAATTAATTT
Found at i:29312154 original size:30 final size:30
Alignment explanation
Indices: 29312120--29312178 Score: 73
Period size: 30 Copynumber: 2.0 Consensus size: 30
29312110 CTTAACTCAA
29312120 ACTTTGGAAAAATTACAATTTTGCCCCTAT
1 ACTTTGGAAAAATTACAATTTTGCCCCTAT
* * * * *
29312150 ACTTTTGCATATTTACACTTTTGCCCCTA
1 ACTTTGGAAAAATTACAATTTTGCCCCTA
29312179 GGCTCGGGAA
Statistics
Matches: 24, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
30 24 1.00
ACGTcount: A:0.27, C:0.24, G:0.08, T:0.41
Consensus pattern (30 bp):
ACTTTGGAAAAATTACAATTTTGCCCCTAT
Found at i:29316582 original size:30 final size:30
Alignment explanation
Indices: 29316548--29316608 Score: 77
Period size: 30 Copynumber: 2.0 Consensus size: 30
29316538 TCGTTAACTC
29316548 AAACTTTGGAAAAATTACAATTTTGCCCCT
1 AAACTTTGGAAAAATTACAATTTTGCCCCT
* * * * *
29316578 AAACTTTTGCATATTTACACTTTTGCCCCT
1 AAACTTTGGAAAAATTACAATTTTGCCCCT
29316608 A
1 A
29316609 GGCTCGGGAA
Statistics
Matches: 26, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
30 26 1.00
ACGTcount: A:0.31, C:0.23, G:0.08, T:0.38
Consensus pattern (30 bp):
AAACTTTGGAAAAATTACAATTTTGCCCCT
Found at i:29318075 original size:25 final size:25
Alignment explanation
Indices: 29318047--29318095 Score: 62
Period size: 25 Copynumber: 2.0 Consensus size: 25
29318037 TTTGGCTTGA
*
29318047 CATTTACTAAGCAATATCAGATATT
1 CATTTACTAAGCAATATCAAATATT
* * *
29318072 CATTTATTAGGTAATATCAAATAT
1 CATTTACTAAGCAATATCAAATAT
29318096 GCAAATTATT
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
25 20 1.00
ACGTcount: A:0.41, C:0.12, G:0.08, T:0.39
Consensus pattern (25 bp):
CATTTACTAAGCAATATCAAATATT
Found at i:29321458 original size:28 final size:28
Alignment explanation
Indices: 29321418--29321529 Score: 127
Period size: 28 Copynumber: 4.0 Consensus size: 28
29321408 CATGACTGTA
* *
29321418 AATGTGATTTGGGCTTAGT-GGTCATATG
1 AATGTGA-TTGGGCTTAATGGGCCATATG
* *
29321446 AATGTGATTTGGGCTTAATGGGCCACATA
1 AATGTGA-TTGGGCTTAATGGGCCATATG
*
29321475 AATGTGATTGGGCCTAATGGGCCATATG
1 AATGTGATTGGGCTTAATGGGCCATATG
* * *
29321503 AAAGAGATTGGGCTTAGTGGGCCATAT
1 AATGTGATTGGGCTTAATGGGCCATAT
29321530 ATATTGGTAA
Statistics
Matches: 72, Mismatches: 11, Indels: 2
0.85 0.13 0.02
Matches are distributed among these distances:
28 59 0.82
29 13 0.18
ACGTcount: A:0.26, C:0.12, G:0.31, T:0.31
Consensus pattern (28 bp):
AATGTGATTGGGCTTAATGGGCCATATG
Found at i:29321524 original size:56 final size:57
Alignment explanation
Indices: 29321416--29321526 Score: 145
Period size: 56 Copynumber: 2.0 Consensus size: 57
29321406 AGCATGACTG
* * * * *
29321416 TAAATGTGATTTGGGCTTAGTGGTCATATGAATGTGATTTGGGCTTAATGGGCCACA
1 TAAATGTGATTTGGGCCTAATGGCCATATGAAAGAGATTTGGGCTTAATGGGCCACA
*
29321473 TAAATGTGA-TTGGGCCTAATGGGCCATATGAAAGAGA-TTGGGCTTAGTGGGCCA
1 TAAATGTGATTTGGGCCTAAT-GGCCATATGAAAGAGATTTGGGCTTAATGGGCCA
29321527 TATATATTGG
Statistics
Matches: 47, Mismatches: 6, Indels: 3
0.84 0.11 0.05
Matches are distributed among these distances:
56 25 0.53
57 22 0.47
ACGTcount: A:0.26, C:0.12, G:0.32, T:0.31
Consensus pattern (57 bp):
TAAATGTGATTTGGGCCTAATGGCCATATGAAAGAGATTTGGGCTTAATGGGCCACA
Found at i:29337048 original size:16 final size:16
Alignment explanation
Indices: 29337027--29337058 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
29337017 GTTGTAATGC
*
29337027 CCCAAAAATCTCGAAA
1 CCCAAAAATCCCGAAA
29337043 CCCAAAAATCCCGAAA
1 CCCAAAAATCCCGAAA
29337059 TCTCAAATTT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.50, C:0.34, G:0.06, T:0.09
Consensus pattern (16 bp):
CCCAAAAATCCCGAAA
Found at i:29340572 original size:24 final size:24
Alignment explanation
Indices: 29340545--29340596 Score: 86
Period size: 24 Copynumber: 2.2 Consensus size: 24
29340535 ATACATGCTC
29340545 TTTCGAGTCATGCTCGGTAAGCTA
1 TTTCGAGTCATGCTCGGTAAGCTA
* *
29340569 TTTCGAGTCATGCTCTGTAAGCTC
1 TTTCGAGTCATGCTCGGTAAGCTA
29340593 TTTC
1 TTTC
29340597 AAGCTGAACA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
24 26 1.00
ACGTcount: A:0.17, C:0.23, G:0.21, T:0.38
Consensus pattern (24 bp):
TTTCGAGTCATGCTCGGTAAGCTA
Found at i:29340667 original size:22 final size:22
Alignment explanation
Indices: 29340585--29340683 Score: 92
Period size: 22 Copynumber: 4.5 Consensus size: 22
29340575 GTCATGCTCT
* *
29340585 GTAAGCTCT-TTCAAGCTGAACA
1 GTAAGCTCTATT-GAGCTGAACG
29340607 GTAAGCTCTATTGAGCTGAACG
1 GTAAGCTCTATTGAGCTGAACG
* * *
29340629 ATAAGCTCTATTAAGCTGAATG
1 GTAAGCTCTATTGAGCTGAACG
* * * *
29340651 GTAAGCTCCAATGAGCTAAAACA
1 GTAAGCTCTATTGAGCT-GAACG
29340674 GTAAGCTCTA
1 GTAAGCTCTA
29340684 ACAAGCTATG
Statistics
Matches: 62, Mismatches: 13, Indels: 3
0.79 0.17 0.04
Matches are distributed among these distances:
22 49 0.79
23 13 0.21
ACGTcount: A:0.34, C:0.19, G:0.20, T:0.26
Consensus pattern (22 bp):
GTAAGCTCTATTGAGCTGAACG
Found at i:29348165 original size:22 final size:22
Alignment explanation
Indices: 29348151--29348259 Score: 148
Period size: 22 Copynumber: 4.9 Consensus size: 22
29348141 AAGCTCCTTC
29348151 GAGCTGAACAGTAAGCTCTATT
1 GAGCTGAACAGTAAGCTCTATT
* *
29348173 GAGCTAAAACGGTAAGCTCTATT
1 GAGCT-GAACAGTAAGCTCTATT
*
29348196 GAGCTGAACGGTACA-CTCTATT
1 GAGCTGAACAGTA-AGCTCTATT
*
29348218 GAGCTGAACAGTAAGCTCTAAT
1 GAGCTGAACAGTAAGCTCTATT
29348240 GAGCTGAAACAGTAAGCTCT
1 GAGCTG-AACAGTAAGCTCT
29348260 TACGAGCTAT
Statistics
Matches: 78, Mismatches: 5, Indels: 7
0.87 0.06 0.08
Matches are distributed among these distances:
21 1 0.01
22 43 0.55
23 34 0.44
ACGTcount: A:0.33, C:0.19, G:0.23, T:0.25
Consensus pattern (22 bp):
GAGCTGAACAGTAAGCTCTATT
Found at i:29348191 original size:45 final size:43
Alignment explanation
Indices: 29348151--29348259 Score: 139
Period size: 45 Copynumber: 2.4 Consensus size: 43
29348141 AAGCTCCTTC
*
29348151 GAGCTGAACAGTAAGCTCTATTGAGCTAAAACGGTAAGCTCTATT
1 GAGCTGAACAGTAAGCTCTATTGAGCT-AAACAGTAAGCTCTA-T
* *
29348196 GAGCTGAACGGTACA-CTCTATTGAGCTGAACAGTAAGCTCTAAT
1 GAGCTGAACAGTA-AGCTCTATTGAGCTAAACAGTAAGCTCT-AT
29348240 GAGCTGAAACAGTAAGCTCT
1 GAGCTG-AACAGTAAGCTCT
29348260 TACGAGCTAT
Statistics
Matches: 56, Mismatches: 4, Indels: 8
0.82 0.06 0.12
Matches are distributed among these distances:
44 20 0.36
45 35 0.62
46 1 0.02
ACGTcount: A:0.33, C:0.19, G:0.23, T:0.25
Consensus pattern (43 bp):
GAGCTGAACAGTAAGCTCTATTGAGCTAAACAGTAAGCTCTAT
Found at i:29352158 original size:44 final size:44
Alignment explanation
Indices: 29352100--29352190 Score: 164
Period size: 44 Copynumber: 2.1 Consensus size: 44
29352090 TTTGAACGAC
*
29352100 CACAAGGTAGCTTACCAAGTAATACTGAACCTAACCCAATTGAA
1 CACAAGGTAGCTTACCAAGTAATACTAAACCTAACCCAATTGAA
*
29352144 CACAAGGTAGCTTACCAAGTAATACTAAACCTAACCTAATTGAA
1 CACAAGGTAGCTTACCAAGTAATACTAAACCTAACCCAATTGAA
29352188 CAC
1 CAC
29352191 CTTAACACAA
Statistics
Matches: 45, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
44 45 1.00
ACGTcount: A:0.42, C:0.25, G:0.12, T:0.21
Consensus pattern (44 bp):
CACAAGGTAGCTTACCAAGTAATACTAAACCTAACCCAATTGAA
Found at i:29355296 original size:39 final size:39
Alignment explanation
Indices: 29355237--29355355 Score: 202
Period size: 39 Copynumber: 3.1 Consensus size: 39
29355227 ACGTCTACTT
*
29355237 CTTATGGTGCATGTCACAAGGGCACGTCATCGACCTTGC
1 CTTATGGTGCATGTCGCAAGGGCACGTCATCGACCTTGC
*
29355276 CTTATGGTGCATGTCGCAAGGGCACATCATCGACCTTGC
1 CTTATGGTGCATGTCGCAAGGGCACGTCATCGACCTTGC
* *
29355315 CTTATAGTGCATGTCGCAAGGGCACGTCATCAACCTTGC
1 CTTATGGTGCATGTCGCAAGGGCACGTCATCGACCTTGC
29355354 CT
1 CT
29355356 ACTTCATCAC
Statistics
Matches: 75, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
39 75 1.00
ACGTcount: A:0.21, C:0.29, G:0.24, T:0.26
Consensus pattern (39 bp):
CTTATGGTGCATGTCGCAAGGGCACGTCATCGACCTTGC
Found at i:29371179 original size:52 final size:51
Alignment explanation
Indices: 29371104--29371227 Score: 221
Period size: 52 Copynumber: 2.4 Consensus size: 51
29371094 AGGAAATTTC
*
29371104 TCACTTAGCACAATGCCATGGACTTATTTCACTTAGATGCCATGGACTTATT
1 TCACTTAGCACATTGCCATGGACTTATTTCACTTAGATGCCATGGAC-TATT
*
29371156 TCTCTTAGCACATTGCCATGGACTTATTTCACTTAGATGCCATGGACTATT
1 TCACTTAGCACATTGCCATGGACTTATTTCACTTAGATGCCATGGACTATT
29371207 TCACTTAGCACATTGCCATGG
1 TCACTTAGCACATTGCCATGG
29371228 TCTAACCACG
Statistics
Matches: 69, Mismatches: 3, Indels: 1
0.95 0.04 0.01
Matches are distributed among these distances:
51 24 0.35
52 45 0.65
ACGTcount: A:0.25, C:0.24, G:0.16, T:0.35
Consensus pattern (51 bp):
TCACTTAGCACATTGCCATGGACTTATTTCACTTAGATGCCATGGACTATT
Found at i:29371181 original size:28 final size:27
Alignment explanation
Indices: 29371104--29371227 Score: 163
Period size: 24 Copynumber: 4.7 Consensus size: 27
29371094 AGGAAATTTC
29371104 TCACTTAGCACAATGCCATGGACTTATT
1 TCACTTAGCAC-ATGCCATGGACTTATT
29371132 TCACTTAG---ATGCCATGGACTTATT
1 TCACTTAGCACATGCCATGGACTTATT
*
29371156 TCTCTTAGCACATTGCCATGGACTTATT
1 TCACTTAGCACA-TGCCATGGACTTATT
29371184 TCACTTAG---ATGCCATGGAC-TATT
1 TCACTTAGCACATGCCATGGACTTATT
29371207 TCACTTAGCACATTGCCATGG
1 TCACTTAGCACA-TGCCATGG
29371228 TCTAACCACG
Statistics
Matches: 86, Mismatches: 2, Indels: 17
0.82 0.02 0.16
Matches are distributed among these distances:
23 12 0.14
24 33 0.38
25 1 0.01
26 1 0.01
27 9 0.10
28 30 0.35
ACGTcount: A:0.25, C:0.24, G:0.16, T:0.35
Consensus pattern (27 bp):
TCACTTAGCACATGCCATGGACTTATT
Found at i:29376067 original size:37 final size:37
Alignment explanation
Indices: 29376017--29376095 Score: 122
Period size: 37 Copynumber: 2.1 Consensus size: 37
29376007 TTATTACGAA
* * *
29376017 GTCTTACCCGGACATAATCTCCACACGAAGTTATCGG
1 GTCTTACCCGGACAAAATCCCCACACGAAGTCATCGG
*
29376054 GTCTTACCCGGACAAAATCCCCACACGTAGTCATCGG
1 GTCTTACCCGGACAAAATCCCCACACGAAGTCATCGG
29376091 GTCTT
1 GTCTT
29376096 TAGAGCCCGG
Statistics
Matches: 38, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
37 38 1.00
ACGTcount: A:0.25, C:0.32, G:0.19, T:0.24
Consensus pattern (37 bp):
GTCTTACCCGGACAAAATCCCCACACGAAGTCATCGG
Found at i:29376435 original size:49 final size:47
Alignment explanation
Indices: 29376214--29376476 Score: 402
Period size: 47 Copynumber: 5.6 Consensus size: 47
29376204 CCCTTCGGGA
* * * * * *
29376214 CTTATCACATTTATACACTTTCACATCCATCACGTTGGCCACTCGG-
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
*
29376260 CTCTGTCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CT-TATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
29376308 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
29376355 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
*
29376402 CTTATCACATATATATACACTTTCACATTCATCACATTGGCCATTAGGC
1 CTTATCAC--ATATATACACTTTCACATTCATCACATCGGCCATTAGGC
* *
29376451 CTTATCACATATATATACATTCACAT
1 CTTATCACATATATACACTTTCACAT
29376477 CACAATTATC
Statistics
Matches: 202, Mismatches: 11, Indels: 7
0.92 0.05 0.03
Matches are distributed among these distances:
46 2 0.01
47 152 0.75
48 2 0.01
49 46 0.23
ACGTcount: A:0.29, C:0.29, G:0.08, T:0.33
Consensus pattern (47 bp):
CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
Found at i:29380918 original size:34 final size:34
Alignment explanation
Indices: 29380877--29380944 Score: 136
Period size: 34 Copynumber: 2.0 Consensus size: 34
29380867 GTCATTTCAC
29380877 CGAAAAAGTGAAATTTTGATTTCCTAATTTCATT
1 CGAAAAAGTGAAATTTTGATTTCCTAATTTCATT
29380911 CGAAAAAGTGAAATTTTGATTTCCTAATTTCATT
1 CGAAAAAGTGAAATTTTGATTTCCTAATTTCATT
29380945 TAGTGTCTAA
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
34 34 1.00
ACGTcount: A:0.35, C:0.12, G:0.12, T:0.41
Consensus pattern (34 bp):
CGAAAAAGTGAAATTTTGATTTCCTAATTTCATT
Found at i:29381398 original size:46 final size:46
Alignment explanation
Indices: 29381256--29381520 Score: 207
Period size: 46 Copynumber: 5.6 Consensus size: 46
29381246 TGTGTGCTAT
* * ** *
29381256 TGTAAGACATGTCTGGGACATGCATCGACCACACTATGAGAGCCAA
1 TGTAAGACATGTCTGGGACATGCATCGGCCTCAAGATGAGAGCCAG
* ** * *
29381302 TGTAAGACCATGTCTGGGACATGGCATCGGCATTGAGACGAGAGCTAG
1 TGTAAGA-CATGTCTGGGACAT-GCATCGGCCTCAAGATGAGAGCCAG
*
29381350 TGTAAGACATGTTTGGGACATGCATCGGCCTCAAGATGTA-AGCCAG
1 TGTAAGACATGTCTGGGACATGCATCGGCCTCAAGATG-AGAGCCAG
* * * * *
29381396 TGTAAGACATGTCTGGGATATGCACCGG-CT-ATGA-GAGGTGTCAG
1 TGTAAGACATGTCTGGGACATGCATCGGCCTCAAGATGA-GAGCCAG
* * * **
29381440 TGTAAGACCATGTCTGGGACATGGCATCGACAC-AAACATGCTAGAGCTTG
1 TGTAAGA-CATGTCTGGGACAT-GCATCGGC-CTCAAGATG--AGAGCCAG
29381490 TGTAAGACCATGTCTGGGACATGGCATCGGC
1 TGTAAGA-CATGTCTGGGACAT-GCATCGGC
29381521 ACTTGACCCC
Statistics
Matches: 174, Mismatches: 32, Indels: 22
0.76 0.14 0.10
Matches are distributed among these distances:
42 1 0.01
43 1 0.01
44 14 0.08
45 15 0.09
46 55 0.32
47 28 0.16
48 25 0.14
49 1 0.01
50 33 0.19
51 1 0.01
ACGTcount: A:0.28, C:0.20, G:0.29, T:0.22
Consensus pattern (46 bp):
TGTAAGACATGTCTGGGACATGCATCGGCCTCAAGATGAGAGCCAG
Found at i:29381494 original size:94 final size:94
Alignment explanation
Indices: 29381251--29381526 Score: 298
Period size: 94 Copynumber: 2.9 Consensus size: 94
29381241 TTATTTGTGT
* * *
29381251 GCTATTGTAAGACATGTCTGGGACATGCATCGACCACACTATG-AGAGCCAATGTAAGACCATGT
1 GCTAGTGTAAGACATGTCTGGGACATGCATCGACCAAAC-ATGTAGAGCCAGTGTAAGACCATGT
*
29381315 CTGGGACATGGCATCGGCATTGAGACGAGA
65 CTGGGACATGGCACCGGCATTGAGACGAGA
* * * *
29381345 GCTAGTGTAAGACATGTTTGGGACATGCATCGGCCTCAAGATGTA-AGCCAGTGTAAGA-CATGT
1 GCTAGTGTAAGACATGTCTGGGACATGCATCGACC-AAACATGTAGAGCCAGTGTAAGACCATGT
* *
29381408 CTGGGATAT-GCACCGGC-TATGAGA-G-GT
65 CTGGGACATGGCACCGGCAT-TGAGACGAGA
**
29381435 G-TCAGTGTAAGACCATGTCTGGGACATGGCATCGACACAAACATGCTAGAGCTTGTGTAAGACC
1 GCT-AGTGTAAGA-CATGTCTGGGACAT-GCATCGAC-CAAACATG-TAGAGCCAGTGTAAGACC
*
29381499 ATGTCTGGGACATGGCATCGGCACTTGA
61 ATGTCTGGGACATGGCACCGGCA-TTGA
29381527 CCCCATGTTT
Statistics
Matches: 151, Mismatches: 18, Indels: 23
0.79 0.09 0.12
Matches are distributed among these distances:
89 1 0.01
90 11 0.07
91 15 0.10
92 24 0.16
93 16 0.11
94 58 0.38
95 15 0.10
96 7 0.05
97 3 0.02
98 1 0.01
ACGTcount: A:0.28, C:0.20, G:0.29, T:0.23
Consensus pattern (94 bp):
GCTAGTGTAAGACATGTCTGGGACATGCATCGACCAAACATGTAGAGCCAGTGTAAGACCATGTC
TGGGACATGGCACCGGCATTGAGACGAGA
Found at i:29393995 original size:23 final size:23
Alignment explanation
Indices: 29393951--29393995 Score: 65
Period size: 23 Copynumber: 2.0 Consensus size: 23
29393941 ATTCCATGTA
*
29393951 CATATATCATTGTCTCATATTTC
1 CATATATCATTGTATCATATTTC
29393974 CATATATCA-TGTATCATCATTT
1 CATATATCATTGTATCAT-ATTT
29393996 TCATGTATTT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
22 7 0.35
23 13 0.65
ACGTcount: A:0.29, C:0.20, G:0.04, T:0.47
Consensus pattern (23 bp):
CATATATCATTGTATCATATTTC
Found at i:29412341 original size:22 final size:21
Alignment explanation
Indices: 29412323--29412362 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
29412313 CCTGTGTGGT
29412323 CCAAGGGACACACCCGTGTGA
1 CCAAGGGACACACCCGTGTGA
*
29412344 CCCAGGGACACACCCGTGT
1 CCAAGGGACACACCCGTGT
29412363 TGGAGGCCAT
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:0.25, C:0.38, G:0.28, T:0.10
Consensus pattern (21 bp):
CCAAGGGACACACCCGTGTGA
Found at i:29423171 original size:49 final size:48
Alignment explanation
Indices: 29423104--29423230 Score: 152
Period size: 47 Copynumber: 2.7 Consensus size: 48
29423094 TTTGTGCGCT
* * *
29423104 AGTGTAAGA-CATGTTTGGGACATGGCGTCGGCCTTGATTTCGAT-AGTC
1 AGTGTAAGACCATGTTTGGGACATGGCATCGGACTTGA--TCGATGAGCC
*
29423152 AGTGTAAGACCATGTTTGGGACATGGCATC-GACTTGATGGATGAGCC
1 AGTGTAAGACCATGTTTGGGACATGGCATCGGACTTGATCGATGAGCC
* * *
29423199 AGAGTAAGTCCATGTCTGGGACATGGCATCGG
1 AGTGTAAGACCATGTTTGGGACATGGCATCGG
29423231 TATCTTAATC
Statistics
Matches: 69, Mismatches: 7, Indels: 6
0.84 0.09 0.07
Matches are distributed among these distances:
46 4 0.06
47 30 0.43
48 16 0.23
49 19 0.28
ACGTcount: A:0.24, C:0.17, G:0.32, T:0.27
Consensus pattern (48 bp):
AGTGTAAGACCATGTTTGGGACATGGCATCGGACTTGATCGATGAGCC
Found at i:29430242 original size:47 final size:44
Alignment explanation
Indices: 29430174--29430293 Score: 134
Period size: 47 Copynumber: 2.6 Consensus size: 44
29430164 TATTTGTGCA
* * *
29430174 CTAGTGTAAGACATGTTTGGGACATGCATCGGCCACATT-ATGAGAG
1 CTAGTGTAAGACATGTCTGGGACATGCATC-G--AAATTGACGAGAG
*
29430220 CTAGTGTAAAACCATGTCTGGGACATGGCATCGAAATTGAGACGAGAG
1 CTAGTGTAAGA-CATGTCTGGGACAT-GCATCGAAATT--GACGAGAG
29430268 CTAGTGTAAGACATGTCTGGGACATG
1 CTAGTGTAAGACATGTCTGGGACATG
29430294 AATTGGCCTC
Statistics
Matches: 64, Mismatches: 5, Indels: 10
0.81 0.06 0.13
Matches are distributed among these distances:
45 4 0.06
46 11 0.17
47 28 0.44
48 21 0.33
ACGTcount: A:0.30, C:0.17, G:0.29, T:0.24
Consensus pattern (44 bp):
CTAGTGTAAGACATGTCTGGGACATGCATCGAAATTGACGAGAG
Found at i:29433819 original size:21 final size:21
Alignment explanation
Indices: 29433793--29433834 Score: 75
Period size: 21 Copynumber: 2.0 Consensus size: 21
29433783 TTTAAGAGTA
29433793 TAATTAGGCCATGTGAAATAC
1 TAATTAGGCCATGTGAAATAC
*
29433814 TAATTAGGCCATGTTAAATAC
1 TAATTAGGCCATGTGAAATAC
29433835 CATTAAAGTC
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.38, C:0.14, G:0.17, T:0.31
Consensus pattern (21 bp):
TAATTAGGCCATGTGAAATAC
Found at i:29442110 original size:40 final size:40
Alignment explanation
Indices: 29442066--29442154 Score: 160
Period size: 40 Copynumber: 2.2 Consensus size: 40
29442056 TAACAACCAG
29442066 CACGAATGCCTTCGGGACTTAACCCGGTTATAATAACCCA
1 CACGAATGCCTTCGGGACTTAACCCGGTTATAATAACCCA
* *
29442106 CACGAATGCCTTTGGGACTTAACCCGGTTATAATAACCCG
1 CACGAATGCCTTCGGGACTTAACCCGGTTATAATAACCCA
29442146 CACGAATGC
1 CACGAATGC
29442155 TATGCACATA
Statistics
Matches: 47, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
40 47 1.00
ACGTcount: A:0.29, C:0.29, G:0.19, T:0.22
Consensus pattern (40 bp):
CACGAATGCCTTCGGGACTTAACCCGGTTATAATAACCCA
Found at i:29449804 original size:25 final size:25
Alignment explanation
Indices: 29449772--29449820 Score: 71
Period size: 25 Copynumber: 2.0 Consensus size: 25
29449762 CTTTATTATT
*
29449772 ATCATTATGATGAATTACGTGATTA
1 ATCATTATCATGAATTACGTGATTA
* *
29449797 ATCATTATCATGAGTTATGTGATT
1 ATCATTATCATGAATTACGTGATT
29449821 GGTCCTCTGG
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
25 21 1.00
ACGTcount: A:0.33, C:0.08, G:0.16, T:0.43
Consensus pattern (25 bp):
ATCATTATCATGAATTACGTGATTA
Found at i:29452436 original size:288 final size:286
Alignment explanation
Indices: 29451920--29452495 Score: 1098
Period size: 288 Copynumber: 2.0 Consensus size: 286
29451910 TATGTGAGTG
*
29451920 TGCAAATGAGAGTGGTGAATGGCTTGGGAAATAGCCATTTCCTTGGCCACACGGGCGGAGACACG
1 TGCAAATGAGAGTGGTGAATGGCTTGGGAAATAGCCATTTCCTTGGCCACACGGGCAGAGACACG
29451985 GCTATGTGTCTCAGCCGTGTGAAGGACAAGGCCTCAAGACACAAGCGTGTGACTTGGCCGTGTGA
66 GCTATGTGTCTCAGCCGTGTGAAGGACAAGGCCTCAAGACACAAGCGTGTGACTTGGCCGTGTGA
29452050 CCCTAAATTGTGCATAACGTCATAAACAAAGAGTTACACGGGCTGAGGACACAGGCGTGTCCCAA
131 CCCTAAATTGTGCATAACGTCATAAACAAAGAGTTACACGGGCTGAGGACACAGGCGTGTCCCAA
*
29452115 GCCACACGGGCCTGTGACTCTCCAACGTATGAAAATTTTTTAATTGTAGTAAAAGTTCCAAAAGC
196 GCCACACGGGCCTGTGACTCTCCAACGTATGAAAATTTGTTAATTGTAGT--AAGTTCCAAAAGC
*
29452180 TTTCGGTTTAGTCCCGAACCACTCCCAA
259 TTTCAGTTTAGTCCCGAACCACTCCCAA
29452208 TGCAAATGAGAGTGGTGAATGGCTTGGGAAATAGCCATTTCCTTGGCCACACGGGCAGAGACACG
1 TGCAAATGAGAGTGGTGAATGGCTTGGGAAATAGCCATTTCCTTGGCCACACGGGCAGAGACACG
29452273 GCTATGTGTCTCAGCCGTGTGAAGGACAAGGCCTCAAGACACAAGCGTGTGACTTGGCCGTGTGA
66 GCTATGTGTCTCAGCCGTGTGAAGGACAAGGCCTCAAGACACAAGCGTGTGACTTGGCCGTGTGA
*
29452338 CCCTAAATTGTGCATAATGTCATAAACAAAGAGTTACACGGGCTGAGGACACAGGCGTGTCCCAA
131 CCCTAAATTGTGCATAACGTCATAAACAAAGAGTTACACGGGCTGAGGACACAGGCGTGTCCCAA
29452403 GCCACACGGGCCTGTGACTCTCCAACGTATGAAAATTTGTTAATTGTAGTAAGTTCCAAAAGCTT
196 GCCACACGGGCCTGTGACTCTCCAACGTATGAAAATTTGTTAATTGTAGTAAGTTCCAAAAGCTT
29452468 TCAGTTTAGTCCCGAACCACTCCCAA
261 TCAGTTTAGTCCCGAACCACTCCCAA
29452494 TG
1 TG
29452496 TATGTTTTGG
Statistics
Matches: 284, Mismatches: 4, Indels: 2
0.98 0.01 0.01
Matches are distributed among these distances:
286 42 0.15
288 242 0.85
ACGTcount: A:0.28, C:0.23, G:0.26, T:0.23
Consensus pattern (286 bp):
TGCAAATGAGAGTGGTGAATGGCTTGGGAAATAGCCATTTCCTTGGCCACACGGGCAGAGACACG
GCTATGTGTCTCAGCCGTGTGAAGGACAAGGCCTCAAGACACAAGCGTGTGACTTGGCCGTGTGA
CCCTAAATTGTGCATAACGTCATAAACAAAGAGTTACACGGGCTGAGGACACAGGCGTGTCCCAA
GCCACACGGGCCTGTGACTCTCCAACGTATGAAAATTTGTTAATTGTAGTAAGTTCCAAAAGCTT
TCAGTTTAGTCCCGAACCACTCCCAA
Found at i:29469512 original size:26 final size:27
Alignment explanation
Indices: 29469483--29469542 Score: 77
Period size: 27 Copynumber: 2.3 Consensus size: 27
29469473 CCACATATAT
*
29469483 ATATCTGT-TCTGGTGGCCTAGCCACA
1 ATATCTGTATCTGGTGACCTAGCCACA
* * *
29469509 ATATCTGTATCTGGTGACTTCGTCACA
1 ATATCTGTATCTGGTGACCTAGCCACA
29469536 ATATCTG
1 ATATCTG
29469543 GCAGCCTCGC
Statistics
Matches: 29, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
26 8 0.28
27 21 0.72
ACGTcount: A:0.22, C:0.23, G:0.20, T:0.35
Consensus pattern (27 bp):
ATATCTGTATCTGGTGACCTAGCCACA
Found at i:29473383 original size:23 final size:24
Alignment explanation
Indices: 29473347--29473396 Score: 68
Period size: 25 Copynumber: 2.1 Consensus size: 24
29473337 ATTTTGTTCA
*
29473347 ATTTTAACTTTTA-TTC-AAAAAT
1 ATTTTAACTGTTATTTCAAAAAAT
29473369 ATTTTAAACTGTTATTTCAAAAAAT
1 ATTTT-AACTGTTATTTCAAAAAAT
29473394 ATT
1 ATT
29473397 ATCAAATAAA
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
22 5 0.21
23 7 0.29
24 3 0.12
25 9 0.38
ACGTcount: A:0.42, C:0.08, G:0.02, T:0.48
Consensus pattern (24 bp):
ATTTTAACTGTTATTTCAAAAAAT
Found at i:29478098 original size:47 final size:47
Alignment explanation
Indices: 29478026--29478810 Score: 1116
Period size: 47 Copynumber: 16.6 Consensus size: 47
29478016 CCCTTCGGGA
* * *
29478026 CTTATCACATTTATACACTTCCACATCCATCACATTGGCCATTCGGC
1 CTTATCACATATATACACTTTCACATTCATCACATTGGCCATTCGGC
*
29478073 CTTATCACATATATAAACTTTCACATTCATCACATTGGCCATTCGGC
1 CTTATCACATATATACACTTTCACATTCATCACATTGGCCATTCGGC
* *
29478120 CTTATCTCATATATGCA-TGTTCACATTCATCACATTGGCCATTCGGC
1 CTTATCACATATATACACT-TTCACATTCATCACATTGGCCATTCGGC
* *
29478167 CTTATCACACATACACA-TGTTCACATTCATCACATTGGCCATTCGGC
1 CTTATCACATATATACACT-TTCACATTCATCACATTGGCCATTCGGC
* *
29478214 CTTATCTCATATATGCA-TGTTCACATTCATCACATTGGCCATTCGGC
1 CTTATCACATATATACACT-TTCACATTCATCACATTGGCCATTCGGC
* *
29478261 CTTATCACACATACACA-TGTTCACATTCATCACATTGGCCATTCGGC
1 CTTATCACATATATACACT-TTCACATTCATCACATTGGCCATTCGGC
* *
29478308 CTTATCACACATACACA-TGTTCACATTCATCACATTGGCCATTCGGC
1 CTTATCACATATATACACT-TTCACATTCATCACATTGGCCATTCGGC
* *
29478355 CTTATCTCATATATGCA-TGTTCACATTCATCACATTGGCCATTCGGC
1 CTTATCACATATATACACT-TTCACATTCATCACATTGGCCATTCGGC
* *
29478402 CTTATCACACATACACA-TGTTCACATTCATCACATTGGCCATTCGGC
1 CTTATCACATATATACACT-TTCACATTCATCACATTGGCCATTCGGC
*
29478449 CTTATCACATATATATACACTTTCACATTCATCACATTGGCCATTAGGC
1 CTTATCAC--ATATATACACTTTCACATTCATCACATTGGCCATTCGGC
* * *
29478498 CTTATCACATATATACACTTTCACATTCATCACATCGGCTATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATTGGCCATTCGGC
* *
29478545 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATTGGCCATTCGGC
* *
29478592 CTTATCACATATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCAC--ATATATACACTTTCACATTCATCACATTGGCCATTCGGC
* * *
29478641 CTTATCACATATATACACTTTCACATTCATCACATCGGCTATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATTGGCCATTCGGC
* *
29478688 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATTGGCCATTCGGC
*
29478735 CTTATCACATATATATACACTTTCACATTCATCACATTGGCCATTAGGC
1 CTTATCAC--ATATATACACTTTCACATTCATCACATTGGCCATTCGGC
29478784 CTTATCACATATATACACTTTCACATT
1 CTTATCACATATATACACTTTCACATT
29478811 TATTCAAATA
Statistics
Matches: 694, Mismatches: 36, Indels: 16
0.93 0.05 0.02
Matches are distributed among these distances:
46 1 0.00
47 557 0.80
49 135 0.19
50 1 0.00
ACGTcount: A:0.28, C:0.29, G:0.09, T:0.33
Consensus pattern (47 bp):
CTTATCACATATATACACTTTCACATTCATCACATTGGCCATTCGGC
Found at i:29478585 original size:143 final size:143
Alignment explanation
Indices: 29478026--29478810 Score: 1153
Period size: 143 Copynumber: 5.5 Consensus size: 143
29478016 CCCTTCGGGA
* * * *
29478026 CTTATCACAT-T-TATACACTTCCACATCCATCACATTGGCCATTCGGCCTTATCACATATATAA
1 CTTATCACATATATATACACTTTCACATTCATCACATTGGCCATTAGGCCTTATCACATATATAC
* *
29478089 ACTTTCACATTCATCACATTGGCCATTCGGCCTTATCTCATATATGCATGTTCACATTCATCACA
66 ACTTTCACATTCATCACATTGGCCATTCGGCCTTATCACATATATACATGTTCACATTCATCACA
29478154 TTGGCCATTCGGC
131 TTGGCCATTCGGC
* * * * *
29478167 CTTATCAC--ACATACACA-TGTTCACATTCATCACATTGGCCATTCGGCCTTATCTCATATATG
1 CTTATCACATATATATACACT-TTCACATTCATCACATTGGCCATTAGGCCTTATCACATATATA
* *
29478229 CA-TGTTCACATTCATCACATTGGCCATTCGGCCTTATCACACATACACATGTTCACATTCATCA
65 CACT-TTCACATTCATCACATTGGCCATTCGGCCTTATCACATATATACATGTTCACATTCATCA
29478293 CATTGGCCATTCGGC
129 CATTGGCCATTCGGC
* * * * *
29478308 CTTATCAC--ACATACACA-TGTTCACATTCATCACATTGGCCATTCGGCCTTATCTCATATATG
1 CTTATCACATATATATACACT-TTCACATTCATCACATTGGCCATTAGGCCTTATCACATATATA
* *
29478370 CA-TGTTCACATTCATCACATTGGCCATTCGGCCTTATCACACATACACATGTTCACATTCATCA
65 CACT-TTCACATTCATCACATTGGCCATTCGGCCTTATCACATATATACATGTTCACATTCATCA
29478434 CATTGGCCATTCGGC
129 CATTGGCCATTCGGC
29478449 CTTATCACATATATATACACTTTCACATTCATCACATTGGCCATTAGGCCTTATCACATATATAC
1 CTTATCACATATATATACACTTTCACATTCATCACATTGGCCATTAGGCCTTATCACATATATAC
* * *
29478514 ACTTTCACATTCATCACATCGGCTATTAGGCCTTATCACATATATACACT-TTCACATTCATCAC
66 ACTTTCACATTCATCACATTGGCCATTCGGCCTTATCACATATATACA-TGTTCACATTCATCAC
* *
29478578 ATCGGCCATTAGGC
130 ATTGGCCATTCGGC
*
29478592 CTTATCACATATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATAC
1 CTTATCACATATATATACACTTTCACATTCATCACATTGGCCATTAGGCCTTATCACATATATAC
* * *
29478657 ACTTTCACATTCATCACATCGGCTATTAGGCCTTATCACATATATACACT-TTCACATTCATCAC
66 ACTTTCACATTCATCACATTGGCCATTCGGCCTTATCACATATATACA-TGTTCACATTCATCAC
* *
29478721 ATCGGCCATTAGGC
130 ATTGGCCATTCGGC
29478735 CTTATCACATATATATACACTTTCACATTCATCACATTGGCCATTAGGCCTTATCACATATATAC
1 CTTATCACATATATATACACTTTCACATTCATCACATTGGCCATTAGGCCTTATCACATATATAC
29478800 ACTTTCACATT
66 ACTTTCACATT
29478811 TATTCAAATA
Statistics
Matches: 610, Mismatches: 25, Indels: 16
0.94 0.04 0.02
Matches are distributed among these distances:
140 2 0.00
141 273 0.45
143 332 0.54
144 3 0.00
ACGTcount: A:0.28, C:0.29, G:0.09, T:0.33
Consensus pattern (143 bp):
CTTATCACATATATATACACTTTCACATTCATCACATTGGCCATTAGGCCTTATCACATATATAC
ACTTTCACATTCATCACATTGGCCATTCGGCCTTATCACATATATACATGTTCACATTCATCACA
TTGGCCATTCGGC
Found at i:29480206 original size:85 final size:85
Alignment explanation
Indices: 29480077--29480255 Score: 349
Period size: 85 Copynumber: 2.1 Consensus size: 85
29480067 TATTTTATTG
*
29480077 CCCATGCCCTTTATTTTATTAATCCTTACATAATGCACTACCCCAACATGTTTATGACATGTTTT
1 CCCATGCTCTTTATTTTATTAATCCTTACATAATGCACTACCCCAACATGTTTATGACATGTTTT
29480142 TAGCCATAACATCTTGTCCA
66 TAGCCATAACATCTTGTCCA
29480162 CCCATGCTCTTTATTTTATTAATCCTTACATAATGCACTACCCCAACATGTTTATGACATGTTTT
1 CCCATGCTCTTTATTTTATTAATCCTTACATAATGCACTACCCCAACATGTTTATGACATGTTTT
29480227 TAGCCATAACATCTTGTCCA
66 TAGCCATAACATCTTGTCCA
29480247 CCCATGCTC
1 CCCATGCTC
29480256 ATGGCCGGCC
Statistics
Matches: 93, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
85 93 1.00
ACGTcount: A:0.26, C:0.28, G:0.08, T:0.37
Consensus pattern (85 bp):
CCCATGCTCTTTATTTTATTAATCCTTACATAATGCACTACCCCAACATGTTTATGACATGTTTT
TAGCCATAACATCTTGTCCA
Found at i:29480944 original size:27 final size:27
Alignment explanation
Indices: 29480871--29480984 Score: 113
Period size: 27 Copynumber: 4.2 Consensus size: 27
29480861 ATTACTGAAA
* ** ***
29480871 TACCCTCGACTTGTAAAATTACCAAAG
1 TACCCTCGATTTACAAAATTACCATTT
* * * *
29480898 TACCCTCGATTTATAGAATTATCGTTT
1 TACCCTCGATTTACAAAATTACCATTT
29480925 TACCCTCGATTTACAAAATTACCATTT
1 TACCCTCGATTTACAAAATTACCATTT
*
29480952 TACTCTC-AGTTTACAAAATTACCATTT
1 TACCCTCGA-TTTACAAAATTACCATTT
29480979 TACCCT
1 TACCCT
29480985 AATTGTGAAA
Statistics
Matches: 72, Mismatches: 14, Indels: 2
0.82 0.16 0.02
Matches are distributed among these distances:
26 1 0.01
27 71 0.99
ACGTcount: A:0.32, C:0.25, G:0.07, T:0.37
Consensus pattern (27 bp):
TACCCTCGATTTACAAAATTACCATTT
Found at i:29481096 original size:27 final size:27
Alignment explanation
Indices: 29481020--29481203 Score: 106
Period size: 27 Copynumber: 6.7 Consensus size: 27
29481010 TATAGGATAG
*
29481020 AATTACCAAAATACCACTAG-TTTG-AGA
1 AATTACCAAAATACC-CTTGATTTGTA-A
* * * **
29481047 AATTATCGAAATACTCTCAATTTGTAA
1 AATTACCAAAATACCCTTGATTTGTAA
**
29481074 AATTACCAAAATACCCTTGATTTACAA
1 AATTACCAAAATACCCTTGATTTGTAA
*
29481101 AATTA-CAGAAATACCCTTGACTTTTTTAAA
1 AATTACCA-AAATACCCTTGA--TTTGT-AA
* * * **
29481131 AATTA-TAAGAATACCATTGGTTTACAA
1 AATTACCAA-AATACCCTTGATTTGTAA
** *
29481158 AATTACTGAAATACCCTTGATTTGTAG
1 AATTACCAAAATACCCTTGATTTGTAA
* *
29481185 ATTTACCAAAACACCCTTG
1 AATTACCAAAATACCCTTG
29481204 TAGGATGAAA
Statistics
Matches: 120, Mismatches: 29, Indels: 16
0.73 0.18 0.10
Matches are distributed among these distances:
26 4 0.03
27 89 0.74
28 6 0.05
29 4 0.03
30 17 0.14
ACGTcount: A:0.41, C:0.18, G:0.09, T:0.33
Consensus pattern (27 bp):
AATTACCAAAATACCCTTGATTTGTAA
Found at i:29481649 original size:20 final size:20
Alignment explanation
Indices: 29481624--29481670 Score: 76
Period size: 20 Copynumber: 2.4 Consensus size: 20
29481614 GTTGGGCCTT
29481624 AATGGGCAAGAATCGGGCCC
1 AATGGGCAAGAATCGGGCCC
**
29481644 AATGGGCTGGAATCGGGCCC
1 AATGGGCAAGAATCGGGCCC
29481664 AATGGGC
1 AATGGGC
29481671 TTTTGGGCCC
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
20 25 1.00
ACGTcount: A:0.26, C:0.23, G:0.38, T:0.13
Consensus pattern (20 bp):
AATGGGCAAGAATCGGGCCC
Found at i:29481671 original size:20 final size:20
Alignment explanation
Indices: 29481633--29481671 Score: 78
Period size: 20 Copynumber: 1.9 Consensus size: 20
29481623 TAATGGGCAA
29481633 GAATCGGGCCCAATGGGCTG
1 GAATCGGGCCCAATGGGCTG
29481653 GAATCGGGCCCAATGGGCT
1 GAATCGGGCCCAATGGGCT
29481672 TTTGGGCCCA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.21, C:0.26, G:0.38, T:0.15
Consensus pattern (20 bp):
GAATCGGGCCCAATGGGCTG
Found at i:29482049 original size:20 final size:20
Alignment explanation
Indices: 29482024--29482090 Score: 100
Period size: 20 Copynumber: 3.4 Consensus size: 20
29482014 GATATGATAT
*
29482024 ACATGAT-TGATATGATATGC
1 ACATGATATG-TATGAAATGC
*
29482044 ACATGATATGTATAAAATGC
1 ACATGATATGTATGAAATGC
29482064 ACATGATATGTATGAAATGC
1 ACATGATATGTATGAAATGC
29482084 ACATGAT
1 ACATGAT
29482091 GTATTCATAA
Statistics
Matches: 43, Mismatches: 3, Indels: 2
0.90 0.06 0.04
Matches are distributed among these distances:
20 41 0.95
21 2 0.05
ACGTcount: A:0.40, C:0.10, G:0.18, T:0.31
Consensus pattern (20 bp):
ACATGATATGTATGAAATGC
Found at i:29482218 original size:52 final size:50
Alignment explanation
Indices: 29482140--29482262 Score: 185
Period size: 52 Copynumber: 2.4 Consensus size: 50
29482130 GAGGAAGTGC
*
29482140 AAAAGGGCTTATGGCCCAGTTTATTGAGAAGGGCTTATGCCCCAGTTTACCG
1 AAAAGGGCTTAT-GCCCAGTTTATTGAAAAGGGCTT-TGCCCCAGTTTACCG
*
29482192 AAAAGGGATTATGCCACAGTTTATTGAAAAGGGCTTTGCCCCAGTTTACCG
1 AAAAGGGCTTATGCC-CAGTTTATTGAAAAGGGCTTTGCCCCAGTTTACCG
29482243 AAAAGGGCTT-TGCCCCAGTT
1 AAAAGGGCTTATG-CCCAGTT
29482263 CTTAAAAGAG
Statistics
Matches: 66, Mismatches: 3, Indels: 6
0.88 0.04 0.08
Matches are distributed among these distances:
50 7 0.11
51 29 0.44
52 30 0.45
ACGTcount: A:0.27, C:0.21, G:0.25, T:0.27
Consensus pattern (50 bp):
AAAAGGGCTTATGCCCAGTTTATTGAAAAGGGCTTTGCCCCAGTTTACCG
Found at i:29482237 original size:25 final size:26
Alignment explanation
Indices: 29482140--29482262 Score: 160
Period size: 26 Copynumber: 4.8 Consensus size: 26
29482130 GAGGAAGTGC
* **
29482140 AAAAGGGCTTATGGCCCAGTTTATTG
1 AAAAGGGCTTATGCCCCAGTTTACCG
*
29482166 AGAAGGGCTTATGCCCCAGTTTACCG
1 AAAAGGGCTTATGCCCCAGTTTACCG
* * **
29482192 AAAAGGGATTATGCCACAGTTTATTG
1 AAAAGGGCTTATGCCCCAGTTTACCG
29482218 AAAAGGGCTT-TGCCCCAGTTTACCG
1 AAAAGGGCTTATGCCCCAGTTTACCG
29482243 AAAAGGGCTT-TGCCCCAGTT
1 AAAAGGGCTTATGCCCCAGTT
29482263 CTTAAAAGAG
Statistics
Matches: 84, Mismatches: 13, Indels: 1
0.86 0.13 0.01
Matches are distributed among these distances:
25 32 0.38
26 52 0.62
ACGTcount: A:0.27, C:0.21, G:0.25, T:0.27
Consensus pattern (26 bp):
AAAAGGGCTTATGCCCCAGTTTACCG
Found at i:29482467 original size:42 final size:42
Alignment explanation
Indices: 29482408--29482499 Score: 130
Period size: 42 Copynumber: 2.2 Consensus size: 42
29482398 TAGTCTCCCC
* * ** *
29482408 AAATGGGCTTGTATACATTCATTGGTATTTCATATGATATTG
1 AAATGGGCTTGCATACATCCATTGACATTACATATGATATTG
*
29482450 AAATGGGCTTGCATACATCCATTGACATTACATGTGATATTG
1 AAATGGGCTTGCATACATCCATTGACATTACATATGATATTG
29482492 AAATGGGC
1 AAATGGGC
29482500 CTATAGGCCA
Statistics
Matches: 44, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
42 44 1.00
ACGTcount: A:0.30, C:0.13, G:0.21, T:0.36
Consensus pattern (42 bp):
AAATGGGCTTGCATACATCCATTGACATTACATATGATATTG
Found at i:29482559 original size:31 final size:31
Alignment explanation
Indices: 29482523--29482632 Score: 184
Period size: 31 Copynumber: 3.5 Consensus size: 31
29482513 CGTTTACAGT
* *
29482523 AAAGGCTTCGGCCTAGTGAAATGATTTATGA
1 AAAGGCTTCGGCCCAGTGATATGATTTATGA
*
29482554 AAAGGCTTCGGCCCAATGATATGATTTATGA
1 AAAGGCTTCGGCCCAGTGATATGATTTATGA
29482585 AAAGGCTTCGGCCCAGTGATATGATTTATGA
1 AAAGGCTTCGGCCCAGTGATATGATTTATGA
*
29482616 AAAGGCTTCGGCTCAGT
1 AAAGGCTTCGGCCCAGT
29482633 AATCGTTAAA
Statistics
Matches: 74, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
31 74 1.00
ACGTcount: A:0.30, C:0.16, G:0.25, T:0.28
Consensus pattern (31 bp):
AAAGGCTTCGGCCCAGTGATATGATTTATGA
Found at i:29485006 original size:27 final size:27
Alignment explanation
Indices: 29484976--29485073 Score: 80
Period size: 27 Copynumber: 3.6 Consensus size: 27
29484966 TGTAGGATAG
*
29484976 AATTACCAAAATACCACT-AGTTTG-AGA
1 AATTACCAAAATACC-CTCAATTTGTA-A
*
29485003 AATTA-CAGATATACCCTCAATTTGTAA
1 AATTACCA-AAATACCCTCAATTTGTAA
* *
29485030 AATTACCAAAATACCC-CTGATTTATAA
1 AATTACCAAAATACCCTC-AATTTGTAA
29485057 AATTA-CAGAAATACCCT
1 AATTACCA-AAATACCCT
29485074 TGACTTTTTA
Statistics
Matches: 59, Mismatches: 5, Indels: 13
0.77 0.06 0.17
Matches are distributed among these distances:
26 7 0.12
27 49 0.83
28 3 0.05
ACGTcount: A:0.44, C:0.20, G:0.07, T:0.29
Consensus pattern (27 bp):
AATTACCAAAATACCCTCAATTTGTAA
Found at i:29485100 original size:30 final size:28
Alignment explanation
Indices: 29485028--29485133 Score: 94
Period size: 27 Copynumber: 3.8 Consensus size: 28
29485018 CTCAATTTGT
* * *
29485028 AAAATTACCAAAATACCCCTGA-TTTAT
1 AAAATTACTAAAATACCCTTGAGTTTAA
*
29485055 AAAATTAC-AGAAATACCCTTGACTTTTTAA
1 AAAATTACTA-AAATACCCTTGA--GTTTAA
* *
29485085 AAAATTA-TAAGAATACCATTG-GTTTAC
1 AAAATTACTAA-AATACCCTTGAGTTTAA
29485112 AAAATTACTAAAATACCCTTGA
1 AAAATTACTAAAATACCCTTGA
29485134 TTTGTAGATT
Statistics
Matches: 65, Mismatches: 6, Indels: 15
0.76 0.07 0.17
Matches are distributed among these distances:
26 1 0.02
27 39 0.60
28 3 0.05
29 1 0.02
30 21 0.32
ACGTcount: A:0.45, C:0.17, G:0.07, T:0.31
Consensus pattern (28 bp):
AAAATTACTAAAATACCCTTGAGTTTAA
Found at i:29485986 original size:20 final size:20
Alignment explanation
Indices: 29485961--29486027 Score: 100
Period size: 20 Copynumber: 3.4 Consensus size: 20
29485951 GATATGATAT
*
29485961 ACATGAT-TGATATGATATGC
1 ACATGATATG-TATGAAATGC
*
29485981 ACATGATATGTATAAAATGC
1 ACATGATATGTATGAAATGC
29486001 ACATGATATGTATGAAATGC
1 ACATGATATGTATGAAATGC
29486021 ACATGAT
1 ACATGAT
29486028 GTATTCATAA
Statistics
Matches: 43, Mismatches: 3, Indels: 2
0.90 0.06 0.04
Matches are distributed among these distances:
20 41 0.95
21 2 0.05
ACGTcount: A:0.40, C:0.10, G:0.18, T:0.31
Consensus pattern (20 bp):
ACATGATATGTATGAAATGC
Found at i:29486158 original size:52 final size:52
Alignment explanation
Indices: 29486077--29486238 Score: 242
Period size: 52 Copynumber: 3.2 Consensus size: 52
29486067 GAGGAAGTGC
* **
29486077 AAAAGGGCTTATACCCCAGTTTATAGAAAAGGGCTTATGCCCCAGTTTATTG
1 AAAAGGGCTTATGCCCCAGTTTACCGAAAAGGGCTTATGCCCCAGTTTATTG
29486129 AAAAGGGCTTATGCCCCAGTTTACCGAAAAGGGCTTATGCCCCAGTTTATTG
1 AAAAGGGCTTATGCCCCAGTTTACCGAAAAGGGCTTATGCCCCAGTTTATTG
* *
29486181 AAAAGGGCTT-TGCCCCAATTTACCGAAAATGGCTT-TGCCCCAG-TTATT-
1 AAAAGGGCTTATGCCCCAGTTTACCGAAAAGGGCTTATGCCCCAGTTTATTG
29486229 AAAAGAGGCT
1 AAAAG-GGCT
29486239 AGGCCTCCAA
Statistics
Matches: 104, Mismatches: 5, Indels: 5
0.91 0.04 0.04
Matches are distributed among these distances:
48 5 0.05
49 9 0.09
50 8 0.08
51 23 0.22
52 59 0.57
ACGTcount: A:0.30, C:0.22, G:0.22, T:0.27
Consensus pattern (52 bp):
AAAAGGGCTTATGCCCCAGTTTACCGAAAAGGGCTTATGCCCCAGTTTATTG
Found at i:29486202 original size:25 final size:26
Alignment explanation
Indices: 29486077--29486238 Score: 215
Period size: 26 Copynumber: 6.3 Consensus size: 26
29486067 GAGGAAGTGC
* *
29486077 AAAAGGGCTTATACCCCAGTTTATAG
1 AAAAGGGCTTATGCCCCAGTTTATTG
29486103 AAAAGGGCTTATGCCCCAGTTTATTG
1 AAAAGGGCTTATGCCCCAGTTTATTG
**
29486129 AAAAGGGCTTATGCCCCAGTTTACCG
1 AAAAGGGCTTATGCCCCAGTTTATTG
29486155 AAAAGGGCTTATGCCCCAGTTTATTG
1 AAAAGGGCTTATGCCCCAGTTTATTG
* **
29486181 AAAAGGGCTT-TGCCCCAATTTACCG
1 AAAAGGGCTTATGCCCCAGTTTATTG
*
29486206 AAAATGGCTT-TGCCCCAG-TTATT-
1 AAAAGGGCTTATGCCCCAGTTTATTG
29486229 AAAAGAGGCT
1 AAAAG-GGCT
29486239 AGGCCTCCAA
Statistics
Matches: 121, Mismatches: 14, Indels: 4
0.87 0.10 0.03
Matches are distributed among these distances:
23 4 0.03
24 7 0.06
25 28 0.23
26 82 0.68
ACGTcount: A:0.30, C:0.22, G:0.22, T:0.27
Consensus pattern (26 bp):
AAAAGGGCTTATGCCCCAGTTTATTG
Found at i:29486430 original size:42 final size:42
Alignment explanation
Indices: 29486371--29486462 Score: 130
Period size: 42 Copynumber: 2.2 Consensus size: 42
29486361 TAGTCTCCCC
* * ** *
29486371 AAATGGGCTTGCTTACATTCATTGGTATTTCATATGATATTG
1 AAATGGGCTTGCATACATCCATTGACATTACATATGATATTG
*
29486413 AAATGGGCTTGCATACATCCATTGACATTACATGTGATATTG
1 AAATGGGCTTGCATACATCCATTGACATTACATATGATATTG
29486455 AAATGGGC
1 AAATGGGC
29486463 CTATGGGCCA
Statistics
Matches: 44, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
42 44 1.00
ACGTcount: A:0.29, C:0.14, G:0.21, T:0.36
Consensus pattern (42 bp):
AAATGGGCTTGCATACATCCATTGACATTACATATGATATTG
Found at i:29486521 original size:31 final size:31
Alignment explanation
Indices: 29486486--29486595 Score: 202
Period size: 31 Copynumber: 3.5 Consensus size: 31
29486476 TGTTTACTGT
*
29486486 AAAGGCTTCGGCCCAGTGAAATGATTTATGA
1 AAAGGCTTCGGCCCAGTGATATGATTTATGA
29486517 AAAGGCTTCGGCCCAGTGATATGATTTATGA
1 AAAGGCTTCGGCCCAGTGATATGATTTATGA
*
29486548 AAAGGCTTCGGCCTAGTGATATGATTTATGA
1 AAAGGCTTCGGCCCAGTGATATGATTTATGA
29486579 AAAGGCTTCGGCCCAGT
1 AAAGGCTTCGGCCCAGT
29486596 AACCGTTAAA
Statistics
Matches: 76, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
31 76 1.00
ACGTcount: A:0.29, C:0.17, G:0.26, T:0.27
Consensus pattern (31 bp):
AAAGGCTTCGGCCCAGTGATATGATTTATGA
Found at i:29489073 original size:27 final size:27
Alignment explanation
Indices: 29488841--29489097 Score: 132
Period size: 27 Copynumber: 9.6 Consensus size: 27
29488831 TTAGCTTACC
** *
29488841 AAATTACTGAAATACCCTCGACTTGTA
1 AAATTACCAAAATACCCTCGATTTGTA
* *
29488868 AAATTACCAAAGTACCCTCGATTTATA
1 AAATTACCAAAATACCCTCGATTTGTA
* * **** **
29488895 GAATTATCGTTTTACCCTCGATTTACA
1 AAATTACCAAAATACCCTCGATTTGTA
*** **
29488922 AAATTACCATTTTACCCTC-AGTTTACA
1 AAATTACCAAAATACCCTCGA-TTTGTA
* ***
29488949 AAATTACTATTTTACCCTCGA-TTGTA
1 AAATTACCAAAATACCCTCGATTTGTA
* * **
29488975 AAATTACTAAAATACCC-CTATAGGATA
1 AAATTACCAAAATACCCTCGATTTG-TA
* *
29489002 GAATTACCAAAATACCACT-GGTTTG-A
1 AAATTACCAAAATACC-CTCGATTTGTA
* *
29489028 GAAATTACCGAAATACCCTCAATTTGTA
1 -AAATTACCAAAATACCCTCGATTTGTA
**
29489056 AAATTACCAAAATACCCT-GATTTACA
1 AAATTACCAAAATACCCTCGATTTGTA
29489082 AAATTA-CAGAAATACC
1 AAATTACCA-AAATACC
29489098 TTTGGCTTTG
Statistics
Matches: 182, Mismatches: 38, Indels: 21
0.76 0.16 0.09
Matches are distributed among these distances:
25 4 0.02
26 40 0.22
27 133 0.73
28 5 0.03
ACGTcount: A:0.39, C:0.21, G:0.09, T:0.31
Consensus pattern (27 bp):
AAATTACCAAAATACCCTCGATTTGTA
Found at i:29489152 original size:27 final size:28
Alignment explanation
Indices: 29489076--29489154 Score: 74
Period size: 30 Copynumber: 2.8 Consensus size: 28
29489066 AATACCCTGA
* *
29489076 TTTACAAAATTACAGAAATACCTTTGGCTT
1 TTTACAAAATTACTGAAATACCATTGG--T
*
29489106 TGTTA-AAAATTA-TAAGAATACCATTGG-
1 T-TTACAAAATTACTGA-AATACCATTGGT
29489133 TTTACAAAATTACTGAAATACC
1 TTTACAAAATTACTGAAATACC
29489155 CTTGATTTGT
Statistics
Matches: 41, Mismatches: 4, Indels: 11
0.73 0.07 0.20
Matches are distributed among these distances:
26 3 0.07
27 14 0.34
28 2 0.05
29 1 0.02
30 18 0.44
31 3 0.07
ACGTcount: A:0.42, C:0.14, G:0.10, T:0.34
Consensus pattern (28 bp):
TTTACAAAATTACTGAAATACCATTGGT
Found at i:29489985 original size:20 final size:20
Alignment explanation
Indices: 29489971--29490026 Score: 94
Period size: 20 Copynumber: 2.8 Consensus size: 20
29489961 CATGATTGAG
*
29489971 ATGATATGCACATGATATGT
1 ATGAAATGCACATGATATGT
*
29489991 ATAAAATGCACATGATATGT
1 ATGAAATGCACATGATATGT
29490011 ATGAAATGCACATGAT
1 ATGAAATGCACATGAT
29490027 GTATTCATAA
Statistics
Matches: 33, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
20 33 1.00
ACGTcount: A:0.41, C:0.11, G:0.18, T:0.30
Consensus pattern (20 bp):
ATGAAATGCACATGATATGT
Found at i:29490199 original size:25 final size:26
Alignment explanation
Indices: 29490076--29490237 Score: 233
Period size: 26 Copynumber: 6.3 Consensus size: 26
29490066 GAGGAAGTGC
29490076 AAAAGGGCTTATGCCCCAGTTTATTG
1 AAAAGGGCTTATGCCCCAGTTTATTG
29490102 AAAAGGGCTTATGCCCCAGTTTATTG
1 AAAAGGGCTTATGCCCCAGTTTATTG
* * **
29490128 AAATGGGCTTATGCCCCAATTTACCG
1 AAAAGGGCTTATGCCCCAGTTTATTG
29490154 AAAAGGGCTTATGCCCCAGTTTATTG
1 AAAAGGGCTTATGCCCCAGTTTATTG
*
29490180 AAAAGGGCTT-TGCCCCAGTTTATCG
1 AAAAGGGCTTATGCCCCAGTTTATTG
*
29490205 AAAAGGGCTT-TGCCCCTG-TTATT-
1 AAAAGGGCTTATGCCCCAGTTTATTG
29490228 AAAAGAGGCT
1 AAAAG-GGCT
29490238 AGGCCTCCAA
Statistics
Matches: 124, Mismatches: 11, Indels: 4
0.89 0.08 0.03
Matches are distributed among these distances:
23 5 0.04
24 8 0.06
25 31 0.25
26 80 0.65
ACGTcount: A:0.27, C:0.21, G:0.23, T:0.29
Consensus pattern (26 bp):
AAAAGGGCTTATGCCCCAGTTTATTG
Found at i:29490420 original size:42 final size:42
Alignment explanation
Indices: 29490361--29490452 Score: 139
Period size: 42 Copynumber: 2.2 Consensus size: 42
29490351 TAGTCTCCCC
* ** *
29490361 AAATGGGCTTGCATACATTCATTGGTATTTCATATGATATTG
1 AAATGGGCTTGCATACATCCATTGACATTACATATGATATTG
*
29490403 AAATGGGCTTGCATACATCCATTGACATTACATGTGATATTG
1 AAATGGGCTTGCATACATCCATTGACATTACATATGATATTG
29490445 AAATGGGC
1 AAATGGGC
29490453 CTATGGGCCA
Statistics
Matches: 45, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
42 45 1.00
ACGTcount: A:0.30, C:0.14, G:0.21, T:0.35
Consensus pattern (42 bp):
AAATGGGCTTGCATACATCCATTGACATTACATATGATATTG
Found at i:29490511 original size:31 final size:31
Alignment explanation
Indices: 29490476--29490585 Score: 202
Period size: 31 Copynumber: 3.5 Consensus size: 31
29490466 CGTTTATAGT
*
29490476 AAAGGCTTCGGCCCAGTGAAATGATTTATGA
1 AAAGGCTTCGGCCCAGTGATATGATTTATGA
29490507 AAAGGCTTCGGCCCAGTGATATGATTTATGA
1 AAAGGCTTCGGCCCAGTGATATGATTTATGA
*
29490538 AAAGGCTTCGGCCTAGTGATATGATTTATGA
1 AAAGGCTTCGGCCCAGTGATATGATTTATGA
29490569 AAAGGCTTCGGCCCAGT
1 AAAGGCTTCGGCCCAGT
29490586 AACCGTTAAA
Statistics
Matches: 76, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
31 76 1.00
ACGTcount: A:0.29, C:0.17, G:0.26, T:0.27
Consensus pattern (31 bp):
AAAGGCTTCGGCCCAGTGATATGATTTATGA
Found at i:29492335 original size:22 final size:23
Alignment explanation
Indices: 29492310--29492369 Score: 63
Period size: 22 Copynumber: 2.7 Consensus size: 23
29492300 TGGACTGAAT
29492310 ATAAAAATTTAAACTAAAT-AAA
1 ATAAAAATTTAAACTAAATAAAA
*
29492332 ATAAATAA-ATAAA-TAAATAAAA
1 ATAAA-AATTTAAACTAAATAAAA
*
29492354 ATAAAACTTTACAACT
1 ATAAAAATTTA-AACT
29492370 TGGGCCACTT
Statistics
Matches: 30, Mismatches: 3, Indels: 8
0.73 0.07 0.20
Matches are distributed among these distances:
21 6 0.20
22 19 0.63
23 4 0.13
24 1 0.03
ACGTcount: A:0.67, C:0.07, G:0.00, T:0.27
Consensus pattern (23 bp):
ATAAAAATTTAAACTAAATAAAA
Found at i:29492337 original size:4 final size:4
Alignment explanation
Indices: 29492319--29492352 Score: 50
Period size: 4 Copynumber: 8.0 Consensus size: 4
29492309 TATAAAAATT
29492319 TAAA CTAAA TAAAA TAAA TAAA TAAA TAAA TAAA
1 TAAA -TAAA T-AAA TAAA TAAA TAAA TAAA TAAA
29492353 AATAAAACTT
Statistics
Matches: 28, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
4 20 0.71
5 8 0.29
ACGTcount: A:0.74, C:0.03, G:0.00, T:0.24
Consensus pattern (4 bp):
TAAA
Found at i:29493758 original size:23 final size:22
Alignment explanation
Indices: 29493707--29493758 Score: 54
Period size: 23 Copynumber: 2.3 Consensus size: 22
29493697 CCTCGTCTTT
*
29493707 TTCTTTTGTTTCTTTTTCTAAC
1 TTCTTTTCTTTCTTTTTCTAAC
29493729 -TCATTTTCTCTTCTTTCTTC-AAC
1 TTC-TTTTCT-TTCTTT-TTCTAAC
29493752 TTCTTTT
1 TTCTTTT
29493759 TCAAATTTCT
Statistics
Matches: 25, Mismatches: 1, Indels: 7
0.76 0.03 0.21
Matches are distributed among these distances:
21 2 0.08
22 5 0.20
23 13 0.52
24 5 0.20
ACGTcount: A:0.10, C:0.23, G:0.02, T:0.65
Consensus pattern (22 bp):
TTCTTTTCTTTCTTTTTCTAAC
Found at i:29493773 original size:18 final size:18
Alignment explanation
Indices: 29493752--29493790 Score: 51
Period size: 18 Copynumber: 2.2 Consensus size: 18
29493742 TTTCTTCAAC
* *
29493752 TTCTTTTTCAAATTTCTT
1 TTCTGTTTCAAATTCCTT
*
29493770 TTCTGTTTCACATTCCTT
1 TTCTGTTTCAAATTCCTT
29493788 TTC
1 TTC
29493791 ACTCTCAATC
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.13, C:0.23, G:0.03, T:0.62
Consensus pattern (18 bp):
TTCTGTTTCAAATTCCTT
Found at i:29496147 original size:22 final size:23
Alignment explanation
Indices: 29496122--29496181 Score: 63
Period size: 22 Copynumber: 2.7 Consensus size: 23
29496112 TGGACTGAAT
29496122 ATAAAAATTTAAACTAAAT-AAA
1 ATAAAAATTTAAACTAAATAAAA
*
29496144 ATAAATAA-ATAAA-TAAATAAAA
1 ATAAA-AATTTAAACTAAATAAAA
*
29496166 ATAAAACTTTACAACT
1 ATAAAAATTTA-AACT
29496182 TGGGCCACTT
Statistics
Matches: 30, Mismatches: 3, Indels: 8
0.73 0.07 0.20
Matches are distributed among these distances:
21 6 0.20
22 19 0.63
23 4 0.13
24 1 0.03
ACGTcount: A:0.67, C:0.07, G:0.00, T:0.27
Consensus pattern (23 bp):
ATAAAAATTTAAACTAAATAAAA
Found at i:29496149 original size:4 final size:4
Alignment explanation
Indices: 29496131--29496164 Score: 50
Period size: 4 Copynumber: 8.0 Consensus size: 4
29496121 TATAAAAATT
29496131 TAAA CTAAA TAAAA TAAA TAAA TAAA TAAA TAAA
1 TAAA -TAAA T-AAA TAAA TAAA TAAA TAAA TAAA
29496165 AATAAAACTT
Statistics
Matches: 28, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
4 20 0.71
5 8 0.29
ACGTcount: A:0.74, C:0.03, G:0.00, T:0.24
Consensus pattern (4 bp):
TAAA
Found at i:29499950 original size:28 final size:28
Alignment explanation
Indices: 29499918--29500026 Score: 96
Period size: 28 Copynumber: 3.9 Consensus size: 28
29499908 TTACCAATAT
*
29499918 ATATGGCCCACTAAGCCCAATCTCTTTC
1 ATATGGCCCACTAAGCCCAATCACTTTC
* * *
29499946 ATATGGCCCATTAGGCCGAATCACATTT-
1 ATATGGCCCACTAAGCCCAATCAC-TTTC
* * * *
29499974 ATGTGGCCCATTAGGCCCAAATCACATTC
1 ATATGGCCCACTAAGCCC-AATCACTTTC
*
29500003 ATAT-GACCACTAAGCCCAAATCAC
1 ATATGGCCCACTAAGCCC-AATCAC
29500027 ATTTACAATC
Statistics
Matches: 67, Mismatches: 11, Indels: 6
0.80 0.13 0.07
Matches are distributed among these distances:
28 55 0.82
29 12 0.18
ACGTcount: A:0.30, C:0.31, G:0.14, T:0.25
Consensus pattern (28 bp):
ATATGGCCCACTAAGCCCAATCACTTTC
Found at i:29502089 original size:11 final size:11
Alignment explanation
Indices: 29502073--29502097 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
29502063 ATATCTAGAA
29502073 TTCTCTTCATT
1 TTCTCTTCATT
29502084 TTCTCTTCATT
1 TTCTCTTCATT
29502095 TTC
1 TTC
29502098 ATCAGCTGGA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.08, C:0.28, G:0.00, T:0.64
Consensus pattern (11 bp):
TTCTCTTCATT
Found at i:29503385 original size:25 final size:25
Alignment explanation
Indices: 29503352--29503400 Score: 71
Period size: 25 Copynumber: 2.0 Consensus size: 25
29503342 AATAATTTGC
*
29503352 ATATTTGATATTGCCTAATAAATGA
1 ATATCTGATATTGCCTAATAAATGA
* *
29503377 ATATCTGATATTGCTTAGTAAATG
1 ATATCTGATATTGCCTAATAAATG
29503401 TCAAGCCAAA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
25 21 1.00
ACGTcount: A:0.37, C:0.08, G:0.14, T:0.41
Consensus pattern (25 bp):
ATATCTGATATTGCCTAATAAATGA
Found at i:29504063 original size:10 final size:10
Alignment explanation
Indices: 29504048--29504075 Score: 56
Period size: 10 Copynumber: 2.8 Consensus size: 10
29504038 ATATTACATG
29504048 TTTACTTTGT
1 TTTACTTTGT
29504058 TTTACTTTGT
1 TTTACTTTGT
29504068 TTTACTTT
1 TTTACTTT
29504076 TCCCCTTAAT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 18 1.00
ACGTcount: A:0.11, C:0.11, G:0.07, T:0.71
Consensus pattern (10 bp):
TTTACTTTGT
Found at i:29504425 original size:24 final size:24
Alignment explanation
Indices: 29504396--29504444 Score: 98
Period size: 24 Copynumber: 2.0 Consensus size: 24
29504386 CTCTTAAAGG
29504396 TATGAATAAATGTTATATTTAAAT
1 TATGAATAAATGTTATATTTAAAT
29504420 TATGAATAAATGTTATATTTAAAT
1 TATGAATAAATGTTATATTTAAAT
29504444 T
1 T
29504445 TATGTGTATA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.45, C:0.00, G:0.08, T:0.47
Consensus pattern (24 bp):
TATGAATAAATGTTATATTTAAAT
Found at i:29504636 original size:21 final size:23
Alignment explanation
Indices: 29504589--29504638 Score: 59
Period size: 21 Copynumber: 2.2 Consensus size: 23
29504579 GAAATTGATA
*
29504589 TGAATATGTGATTATTACGAAATC
1 TGAATATGTGATTATTA-GAAAAC
*
29504613 TGAATATTTG-TTATT-GAAAAC
1 TGAATATGTGATTATTAGAAAAC
29504634 TGAAT
1 TGAAT
29504639 TGAATTGTAT
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
21 10 0.42
23 5 0.21
24 9 0.38
ACGTcount: A:0.38, C:0.06, G:0.16, T:0.40
Consensus pattern (23 bp):
TGAATATGTGATTATTAGAAAAC
Found at i:29505189 original size:23 final size:23
Alignment explanation
Indices: 29505138--29505192 Score: 76
Period size: 23 Copynumber: 2.4 Consensus size: 23
29505128 AGCTTTGTCA
29505138 ATCAGGCACTTTATGTGACGTAT
1 ATCAGGCACTTTATGTGACGTAT
*
29505161 ACCAGGCACTTTATGT-ATCGTAT
1 ATCAGGCACTTTATGTGA-CGTAT
*
29505184 TTCAGGCAC
1 ATCAGGCAC
29505193 CTCGTGTGTT
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
22 1 0.04
23 27 0.96
ACGTcount: A:0.25, C:0.22, G:0.20, T:0.33
Consensus pattern (23 bp):
ATCAGGCACTTTATGTGACGTAT
Found at i:29506091 original size:22 final size:22
Alignment explanation
Indices: 29506063--29506131 Score: 77
Period size: 22 Copynumber: 3.1 Consensus size: 22
29506053 TCTTTGATTA
*
29506063 TTAGCACATTAGTGCTCTCCGT
1 TTAGCACATTAGTGCTCTCTGT
*
29506085 TTAGCACATCT-GTGCTATCTGT
1 TTAGCACAT-TAGTGCTCTCTGT
* * *
29506107 ATAACACTTTAGTGCTCTCTGT
1 TTAGCACATTAGTGCTCTCTGT
29506129 TTA
1 TTA
29506132 ATAGTGCATA
Statistics
Matches: 38, Mismatches: 7, Indels: 4
0.78 0.14 0.08
Matches are distributed among these distances:
21 1 0.03
22 36 0.95
23 1 0.03
ACGTcount: A:0.20, C:0.23, G:0.16, T:0.41
Consensus pattern (22 bp):
TTAGCACATTAGTGCTCTCTGT
Found at i:29512921 original size:47 final size:46
Alignment explanation
Indices: 29512853--29513221 Score: 224
Period size: 47 Copynumber: 7.7 Consensus size: 46
29512843 TTTGTGTGCT
*
29512853 AGTGTAAGACATGTCTGGGACATGCACCGGCCACATTATGAGAGCC
1 AGTGTAAGACATGTCTGGGACATGCATCGGCCACATTATGAGAGCC
* *
29512899 AGTGTAAGACCATGTCTGGGACATGGCATC-G--ACATTGAGACGAGAGCT
1 AGTGTAAGA-CATGTCTGGGACAT-GCATCGGCCACATT---ATGAGAGCC
* * *
29512947 AGTGTAAGACATGTTTGGGACATGCATCGGCCCCGAGATGTAAAAGATGAGAGCT
1 AGTGTAAGACATGTCTGGGACATGCATCGG--CC-ACAT-T-----ATGAGAGCC
* *
29513002 AGTGTAAGACATGTCTGGGACATGCATCGGCCTCGA-GATGTA-AGCC
1 AGTGTAAGACATGTCTGGGACATGCATCGGCCAC-ATTATG-AGAGCC
* * * * **
29513048 AATGTAAGACATGTCTGGGACATGCATCGGCTACATGAT--GTGTT
1 AGTGTAAGACATGTCTGGGACATGCATCGGCCACATTATGAGAGCC
* *
29513092 AGTGTAAGACCATGTCTGGGACATGGCATCGG-TACGGA-TACGTGAGAGTC
1 AGTGTAAGA-CATGTCTGGGACAT-GCATCGGCCAC--ATTA--TGAGAGCC
* *
29513142 AGTGTAAGACCATGTTTGGGACATGGCAT-TG--AC-TTAACGTGAGAGCC
1 AGTGTAAGA-CATGTCTGGGACAT-GCATCGGCCACATT-A--TGAGAGCC
29513189 AGTGTAAGACCATGTCTGGGACATGGCATCGGC
1 AGTGTAAGA-CATGTCTGGGACAT-GCATCGGC
29513222 ATTATACCCT
Statistics
Matches: 266, Mismatches: 27, Indels: 57
0.76 0.08 0.16
Matches are distributed among these distances:
44 9 0.03
45 23 0.09
46 63 0.24
47 69 0.26
48 24 0.09
49 1 0.00
50 31 0.12
52 3 0.01
53 4 0.02
55 39 0.15
ACGTcount: A:0.28, C:0.19, G:0.31, T:0.23
Consensus pattern (46 bp):
AGTGTAAGACATGTCTGGGACATGCATCGGCCACATTATGAGAGCC
Found at i:29513023 original size:55 final size:55
Alignment explanation
Indices: 29512940--29513044 Score: 192
Period size: 55 Copynumber: 1.9 Consensus size: 55
29512930 ACATTGAGAC
*
29512940 GAGAGCTAGTGTAAGACATGTTTGGGACATGCATCGGCCCCGAGATGTAAAAGAT
1 GAGAGCTAGTGTAAGACATGTCTGGGACATGCATCGGCCCCGAGATGTAAAAGAT
*
29512995 GAGAGCTAGTGTAAGACATGTCTGGGACATGCATCGGCCTCGAGATGTAA
1 GAGAGCTAGTGTAAGACATGTCTGGGACATGCATCGGCCCCGAGATGTAA
29513045 GCCAATGTAA
Statistics
Matches: 48, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
55 48 1.00
ACGTcount: A:0.30, C:0.17, G:0.31, T:0.22
Consensus pattern (55 bp):
GAGAGCTAGTGTAAGACATGTCTGGGACATGCATCGGCCCCGAGATGTAAAAGAT
Found at i:29513061 original size:101 final size:103
Alignment explanation
Indices: 29512890--29513078 Score: 276
Period size: 101 Copynumber: 1.9 Consensus size: 103
29512880 CGGCCACATT
* * *
29512890 ATGAGAGCCAGTGTAAGACCATGTCTGGGACATGGCATCGACATTGAGACGAGAGCTAGTGTAAG
1 ATGAGAGCCAGTGTAAGACCATGTCTGGGACATGGCATCGACATCGAGACGAGAGCCAATGTAAG
*
29512955 ACATGTTTGGGACATGCATCGGCCCCGAGATGTAAAAG
66 ACATGTCTGGGACATGCATCGGCCCCGAGATGTAAAAG
* * * *
29512993 ATGAGAGCTAGTGTAAGA-CATGTCTGGGACAT-GCATCGGCCTCGAGATGTA-AGCCAATGTAA
1 ATGAGAGCCAGTGTAAGACCATGTCTGGGACATGGCATCGACATCGAGACG-AGAGCCAATGTAA
29513055 GACATGTCTGGGACATGCATCGGC
65 GACATGTCTGGGACATGCATCGGC
29513079 TACATGATGT
Statistics
Matches: 77, Mismatches: 8, Indels: 4
0.87 0.09 0.04
Matches are distributed among these distances:
101 45 0.58
102 15 0.19
103 17 0.22
ACGTcount: A:0.29, C:0.19, G:0.31, T:0.21
Consensus pattern (103 bp):
ATGAGAGCCAGTGTAAGACCATGTCTGGGACATGGCATCGACATCGAGACGAGAGCCAATGTAAG
ACATGTCTGGGACATGCATCGGCCCCGAGATGTAAAAG
Found at i:29513088 original size:46 final size:44
Alignment explanation
Indices: 29513004--29513123 Score: 145
Period size: 46 Copynumber: 2.6 Consensus size: 44
29512994 TGAGAGCTAG
29513004 TGTAAGACATGTCTGGGACATGCATCGGCCTCGAGATGTAAGCCAA
1 TGTAAGACATGTCTGGGACATGCATCGGCCTCGAGATGT--GCCAA
** *
29513050 TGTAAGACATGTCTGGGACATGCATCGG-CTAC-ATGATGTGTTAG
1 TGTAAGACATGTCTGGGACATGCATCGGCCT-CGA-GATGTGCCAA
29513094 TGTAAGACCATGTCTGGGACATGGCATCGG
1 TGTAAGA-CATGTCTGGGACAT-GCATCGG
29513124 TACGGATACG
Statistics
Matches: 67, Mismatches: 3, Indels: 8
0.86 0.04 0.10
Matches are distributed among these distances:
44 9 0.13
45 17 0.25
46 41 0.61
ACGTcount: A:0.26, C:0.19, G:0.30, T:0.25
Consensus pattern (44 bp):
TGTAAGACATGTCTGGGACATGCATCGGCCTCGAGATGTGCCAA
Found at i:29516479 original size:15 final size:15
Alignment explanation
Indices: 29516459--29516488 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
29516449 TTTAAGCAAA
29516459 TATGCCCAAGAATAT
1 TATGCCCAAGAATAT
29516474 TATGCCCAAGAATAT
1 TATGCCCAAGAATAT
29516489 GTGTCTACTA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.40, C:0.20, G:0.13, T:0.27
Consensus pattern (15 bp):
TATGCCCAAGAATAT
Found at i:29525284 original size:26 final size:27
Alignment explanation
Indices: 29525255--29525314 Score: 68
Period size: 27 Copynumber: 2.3 Consensus size: 27
29525245 CCACATATAT
*
29525255 ATATCTGT-TCTGGTGGCCTAGCCACA
1 ATATCTGTATCTGGTGACCTAGCCACA
* * * *
29525281 ATATTTGTATCTGGTGACTTCGTCACA
1 ATATCTGTATCTGGTGACCTAGCCACA
29525308 ATATCTG
1 ATATCTG
29525315 GCAGCCTCGT
Statistics
Matches: 27, Mismatches: 6, Indels: 1
0.79 0.18 0.03
Matches are distributed among these distances:
26 7 0.26
27 20 0.74
ACGTcount: A:0.22, C:0.22, G:0.20, T:0.37
Consensus pattern (27 bp):
ATATCTGTATCTGGTGACCTAGCCACA
Found at i:29534846 original size:19 final size:20
Alignment explanation
Indices: 29534822--29534859 Score: 53
Period size: 19 Copynumber: 1.9 Consensus size: 20
29534812 GGTACCACCA
29534822 AAACAT-ATATCA-CATCTTT
1 AAACATCAT-TCATCATCTTT
29534841 AAACATCATTCATCATCTT
1 AAACATCATTCATCATCTT
29534860 ACCACCTTAT
Statistics
Matches: 17, Mismatches: 0, Indels: 3
0.85 0.00 0.15
Matches are distributed among these distances:
19 9 0.53
20 8 0.47
ACGTcount: A:0.39, C:0.24, G:0.00, T:0.37
Consensus pattern (20 bp):
AAACATCATTCATCATCTTT
Found at i:29535199 original size:93 final size:93
Alignment explanation
Indices: 29535089--29535259 Score: 288
Period size: 93 Copynumber: 1.8 Consensus size: 93
29535079 GCCCCTAAGT
* * *
29535089 GAACTCGGACTCAACTCAACGAGCTCGGGCGTTCGCATCCATAAATGAACTCGGACTCAACTCAA
1 GAACTCGGACTCAACTCAAAGAGCTCGGACATTCGCATCCATAAATGAACTCGGACTCAACTCAA
29535154 CGAGTTCGGATGCCTAGTTACATCTCAC
66 CGAGTTCGGATGCCTAGTTACATCTCAC
* * *
29535182 GAACTCGGACTCAACTCAAAGAGTTCGGACATTTGCATCCATAAGTGAACTCGGACTCAACTCAA
1 GAACTCGGACTCAACTCAAAGAGCTCGGACATTCGCATCCATAAATGAACTCGGACTCAACTCAA
29535247 CGAGTTCGGATGC
66 CGAGTTCGGATGC
29535260 TCAACCATCC
Statistics
Matches: 72, Mismatches: 6, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
93 72 1.00
ACGTcount: A:0.29, C:0.28, G:0.21, T:0.22
Consensus pattern (93 bp):
GAACTCGGACTCAACTCAAAGAGCTCGGACATTCGCATCCATAAATGAACTCGGACTCAACTCAA
CGAGTTCGGATGCCTAGTTACATCTCAC
Found at i:29535256 original size:46 final size:46
Alignment explanation
Indices: 29535084--29535256 Score: 199
Period size: 46 Copynumber: 3.7 Consensus size: 46
29535074 AACCCGCCCC
* * * *
29535084 TAAGTGAACTCGGACTCAACTCAACGAGCTCGGGCGTTCGCATCCA
1 TAAGTGAACTCGGACTCAACTCAACGAGTTCGGACATTTGCATCCA
* * *
29535130 TAAATGAACTCGGACTCAACTCAACGAGTTCGGATGCCTAGTTACAT-C-
1 TAAGTGAACTCGGACTCAACTCAACGAGTTCGGA---C-ATTTGCATCCA
* * *
29535178 TCA-CGAACTCGGACTCAACTCAAAGAGTTCGGACATTTGCATCCA
1 TAAGTGAACTCGGACTCAACTCAACGAGTTCGGACATTTGCATCCA
29535223 TAAGTGAACTCGGACTCAACTCAACGAGTTCGGA
1 TAAGTGAACTCGGACTCAACTCAACGAGTTCGGA
29535257 TGCTCAACCA
Statistics
Matches: 105, Mismatches: 15, Indels: 14
0.78 0.11 0.10
Matches are distributed among these distances:
43 6 0.06
44 2 0.02
45 2 0.02
46 59 0.56
47 28 0.27
48 2 0.02
49 2 0.02
50 4 0.04
ACGTcount: A:0.30, C:0.27, G:0.21, T:0.22
Consensus pattern (46 bp):
TAAGTGAACTCGGACTCAACTCAACGAGTTCGGACATTTGCATCCA
Found at i:29539515 original size:48 final size:48
Alignment explanation
Indices: 29539433--29539721 Score: 290
Period size: 48 Copynumber: 6.0 Consensus size: 48
29539423 GTACTAGGGT
* * * *
29539433 TATGTGAGCGAGTGTAAGACCATGTTTGGAACATGACATCGGCATTTA
1 TATGAGAGCTAGTGTAAGACCATGTTTGGAACATGGCATCGGCATCTA
* * * *
29539481 TATGAGAGCTAGTGTAAGACCATGTATGGGACATGGCATCGGCCTCGA
1 TATGAGAGCTAGTGTAAGACCATGTTTGGAACATGGCATCGGCATCTA
* * * * * * *
29539529 CATGTGAGCTAGTGTAAGACCATGTTTCGAACATGGAATTGACATTTA
1 TATGAGAGCTAGTGTAAGACCATGTTTGGAACATGGCATCGGCATCTA
* * * * * * *
29539577 TATGAGGGCTAGTGTAGGACCATGTCTGGGACATGGCATCGACCTCGA
1 TATGAGAGCTAGTGTAAGACCATGTTTGGAACATGGCATCGGCATCTA
* * *
29539625 CATGTGAGCTAGTGTAAGACCATGTTTGGAACATGGCATCGGCACCAATA
1 TATGAGAGCTAGTGTAAGACCATGTTTGGAACATGGCATCGGCATC--TA
* * * * *
29539675 TATGAGAGCCAGTGTAAGACCATGTCTGGGACATGGCTTCAGCATCT
1 TATGAGAGCTAGTGTAAGACCATGTTTGGAACATGGCATCGGCATCT
29539722 TACCCTTTTG
Statistics
Matches: 190, Mismatches: 49, Indels: 4
0.78 0.20 0.02
Matches are distributed among these distances:
48 151 0.79
50 39 0.21
ACGTcount: A:0.28, C:0.18, G:0.28, T:0.26
Consensus pattern (48 bp):
TATGAGAGCTAGTGTAAGACCATGTTTGGAACATGGCATCGGCATCTA
Found at i:29539598 original size:96 final size:96
Alignment explanation
Indices: 29539434--29539711 Score: 407
Period size: 96 Copynumber: 2.9 Consensus size: 96
29539424 TACTAGGGTT
* *
29539434 ATGTGAGCGAGTGTAAGACCATGTTTGGAACAT-GACATCGGCATTTATATGAGAGCTAGTGTAA
1 ATGTGAGCTAGTGTAAGACCATGTTTGGAACATGGA-ATCGACATTTATATGAGAGCTAGTGTAA
* *
29539498 GACCATGTATGGGACATGGCATCGGCCTCGAC
65 GACCATGTCTGGGACATGGCATCGACCTCGAC
* * * *
29539530 ATGTGAGCTAGTGTAAGACCATGTTTCGAACATGGAATTGACATTTATATGAGGGCTAGTGTAGG
1 ATGTGAGCTAGTGTAAGACCATGTTTGGAACATGGAATCGACATTTATATGAGAGCTAGTGTAAG
29539595 ACCATGTCTGGGACATGGCATCGACCTCGAC
66 ACCATGTCTGGGACATGGCATCGACCTCGAC
* * *
29539626 ATGTGAGCTAGTGTAAGACCATGTTTGGAACATGGCATCGGCACCA-ATATATGAGAGCCAGTGT
1 ATGTGAGCTAGTGTAAGACCATGTTTGGAACATGGAATC-G-A-CATTTATATGAGAGCTAGTGT
29539690 AAGACCATGTCTGGGACATGGC
63 AAGACCATGTCTGGGACATGGC
29539712 TTCAGCATCT
Statistics
Matches: 163, Mismatches: 15, Indels: 6
0.89 0.08 0.03
Matches are distributed among these distances:
96 121 0.74
97 3 0.02
98 37 0.23
99 2 0.01
ACGTcount: A:0.28, C:0.18, G:0.29, T:0.25
Consensus pattern (96 bp):
ATGTGAGCTAGTGTAAGACCATGTTTGGAACATGGAATCGACATTTATATGAGAGCTAGTGTAAG
ACCATGTCTGGGACATGGCATCGACCTCGAC
Found at i:29540795 original size:28 final size:28
Alignment explanation
Indices: 29540758--29540812 Score: 76
Period size: 28 Copynumber: 1.9 Consensus size: 28
29540748 CACGGGCTGA
29540758 GACACAGGCGTGT-CATGGCCGTGTGAGG
1 GACACAGGCGTGTACA-GGCCGTGTGAGG
*
29540786 GACACGGGCGTGTACCAGGCCGTGTGA
1 GACACAGGCGTGTA-CAGGCCGTGTGA
29540813 AAACCCTTGT
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
28 12 0.50
29 10 0.42
30 2 0.08
ACGTcount: A:0.18, C:0.24, G:0.42, T:0.16
Consensus pattern (28 bp):
GACACAGGCGTGTACAGGCCGTGTGAGG
Found at i:29541620 original size:21 final size:22
Alignment explanation
Indices: 29541579--29541629 Score: 77
Period size: 21 Copynumber: 2.4 Consensus size: 22
29541569 GGGCTCACAC
*
29541579 GCCCGTGTGGTCCAAGGGACAT
1 GCCCGTGTGGACCAAGGGACAT
*
29541601 GCCCGTGT-GACCATGGGACAT
1 GCCCGTGTGGACCAAGGGACAT
29541622 GCCCGTGT
1 GCCCGTGT
29541630 CACCCGAGGA
Statistics
Matches: 27, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
21 19 0.70
22 8 0.30
ACGTcount: A:0.16, C:0.29, G:0.35, T:0.20
Consensus pattern (22 bp):
GCCCGTGTGGACCAAGGGACAT
Found at i:29541640 original size:21 final size:21
Alignment explanation
Indices: 29541594--29541649 Score: 69
Period size: 21 Copynumber: 2.7 Consensus size: 21
29541584 TGTGGTCCAA
* *
29541594 GGGACATGCCCGTGTGACCAT
1 GGGACATGCCCGTGTCACCAC
29541615 GGGACATGCCCGTGTCACC-C
1 GGGACATGCCCGTGTCACCAC
*
29541635 GAGGACATGCTCGTG
1 G-GGACATGCCCGTG
29541650 CTACAGGTCA
Statistics
Matches: 31, Mismatches: 3, Indels: 2
0.86 0.08 0.06
Matches are distributed among these distances:
20 1 0.03
21 30 0.97
ACGTcount: A:0.18, C:0.30, G:0.34, T:0.18
Consensus pattern (21 bp):
GGGACATGCCCGTGTCACCAC
Found at i:29545449 original size:46 final size:46
Alignment explanation
Indices: 29545399--29545574 Score: 198
Period size: 46 Copynumber: 3.8 Consensus size: 46
29545389 TGGTTGAGCA
* *
29545399 TCCGAACTCGTTGAGTTGAGTCTGAGTTCACTTATGGATGCGAATG
1 TCCGAGCTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
*** *
29545445 TCCGAGCTCGTTGAGTTGAGTCCGAGTTCGAGAGATGTAACTAG-GAA--
1 TCCGAGCTCGTTGAGTTGAGTCCGAGTTC-ACTTATG-GA-T-GCGAATG
29545492 TCCGAGCTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
1 TCCGAGCTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
* * *
29545538 -CTTGAGCACGTTGAGTTGAGTTCGAGTTCACTTATGG
1 TC-CGAGCTCGTTGAGTTGAGTCCGAGTTCACTTATGG
29545575 GCGGGTTACA
Statistics
Matches: 109, Mismatches: 13, Indels: 16
0.79 0.09 0.12
Matches are distributed among these distances:
43 1 0.01
44 4 0.04
45 2 0.02
46 63 0.58
47 33 0.30
48 1 0.01
49 4 0.04
50 1 0.01
ACGTcount: A:0.22, C:0.18, G:0.30, T:0.31
Consensus pattern (46 bp):
TCCGAGCTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
Found at i:29545557 original size:93 final size:93
Alignment explanation
Indices: 29545398--29545566 Score: 277
Period size: 93 Copynumber: 1.8 Consensus size: 93
29545388 ATGGTTGAGC
* *
29545398 ATCCGAACTCGTTGAGTTGAGTCTGAGTTCACTTATGGATGCGAATGTCCGAGCTCGTTGAGTTG
1 ATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATGTCCGAGCACGTTGAGTTG
29545463 AGTCCGAGTTCGAGAGATGTAACTAGGA
66 AGTCCGAGTTCGAGAGATGTAACTAGGA
* *
29545491 ATCCGAGCTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG-CTTGAGCACGTTGAGTT
1 ATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATGTC-CGAGCACGTTGAGTT
*
29545555 GAGTTCGAGTTC
65 GAGTCCGAGTTC
29545567 ACTTATGGGC
Statistics
Matches: 70, Mismatches: 5, Indels: 2
0.91 0.06 0.03
Matches are distributed among these distances:
92 1 0.01
93 69 0.99
ACGTcount: A:0.22, C:0.18, G:0.30, T:0.30
Consensus pattern (93 bp):
ATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATGTCCGAGCACGTTGAGTTG
AGTCCGAGTTCGAGAGATGTAACTAGGA
Found at i:29560498 original size:13 final size:13
Alignment explanation
Indices: 29560480--29560507 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
29560470 TTAGAAACGT
29560480 ATATTTTCAATGG
1 ATATTTTCAATGG
29560493 ATATTTTCAATGG
1 ATATTTTCAATGG
29560506 AT
1 AT
29560508 TTGATTTTGA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.32, C:0.07, G:0.14, T:0.46
Consensus pattern (13 bp):
ATATTTTCAATGG
Found at i:29561378 original size:24 final size:24
Alignment explanation
Indices: 29561341--29561417 Score: 75
Period size: 24 Copynumber: 3.2 Consensus size: 24
29561331 ATGGTTGTTC
* *
29561341 AACCTTTCATCTTTCATCTCCTTT
1 AACCTTTAACCTTTCATCTCCTTT
* * *
29561365 GACCTTCT-ACCTTTTATCTTCTTT
1 AACCTT-TAACCTTTCATCTCCTTT
*
29561389 AACCTTTAACCTTTCATCTACTTGT
1 AACCTTTAACCTTTCATCTCCTT-T
29561414 AACC
1 AACC
29561418 CCTTTTTTCT
Statistics
Matches: 43, Mismatches: 7, Indels: 5
0.78 0.13 0.09
Matches are distributed among these distances:
23 1 0.02
24 36 0.84
25 6 0.14
ACGTcount: A:0.19, C:0.31, G:0.03, T:0.47
Consensus pattern (24 bp):
AACCTTTAACCTTTCATCTCCTTT
Found at i:29563640 original size:16 final size:16
Alignment explanation
Indices: 29563619--29563656 Score: 51
Period size: 15 Copynumber: 2.4 Consensus size: 16
29563609 TAAAAATAAT
29563619 ACATAAGACTACAAAA
1 ACATAAGACTACAAAA
* *
29563635 ACATAA-ACTTCTAAA
1 ACATAAGACTACAAAA
29563650 ACATAAG
1 ACATAAG
29563657 CTGTTTGAAA
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
15 13 0.68
16 6 0.32
ACGTcount: A:0.58, C:0.18, G:0.05, T:0.18
Consensus pattern (16 bp):
ACATAAGACTACAAAA
Found at i:29566231 original size:16 final size:16
Alignment explanation
Indices: 29566210--29566240 Score: 62
Period size: 16 Copynumber: 1.9 Consensus size: 16
29566200 AAACGAGGAA
29566210 GACCTTGCAACAGAAG
1 GACCTTGCAACAGAAG
29566226 GACCTTGCAACAGAA
1 GACCTTGCAACAGAA
29566241 AAGAAAGCAT
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:0.39, C:0.26, G:0.23, T:0.13
Consensus pattern (16 bp):
GACCTTGCAACAGAAG
Found at i:29567209 original size:7 final size:7
Alignment explanation
Indices: 29567199--29567264 Score: 55
Period size: 7 Copynumber: 9.4 Consensus size: 7
29567189 AATATTTAAG
29567199 TTTTTTA
1 TTTTTTA
29567206 TTTTTTA
1 TTTTTTA
* *
29567213 ATTTTAA
1 TTTTTTA
29567220 TTTTTTAA
1 TTTTTT-A
29567228 TTTTTTAA
1 TTTTTT-A
*
29567236 TTTTTAA
1 TTTTTTA
*
29567243 TTTTTGA
1 TTTTTTA
*
29567250 --GTTTA
1 TTTTTTA
29567255 TTTTTTA
1 TTTTTTA
29567262 TTT
1 TTT
29567265 CGGTTTAATG
Statistics
Matches: 47, Mismatches: 9, Indels: 6
0.76 0.15 0.10
Matches are distributed among these distances:
5 3 0.06
7 30 0.64
8 14 0.30
ACGTcount: A:0.21, C:0.00, G:0.03, T:0.76
Consensus pattern (7 bp):
TTTTTTA
Found at i:29567210 original size:8 final size:8
Alignment explanation
Indices: 29567193--29567247 Score: 73
Period size: 8 Copynumber: 7.2 Consensus size: 8
29567183 ATATTAAATA
29567193 TTTAAGTTT
1 TTTAA-TTT
29567202 TTT-ATTT
1 TTTAATTT
29567209 TTTAA--T
1 TTTAATTT
29567215 TTTAATTT
1 TTTAATTT
29567223 TTTAATTT
1 TTTAATTT
29567231 TTTAA-TT
1 TTTAATTT
29567238 TTTAATTT
1 TTTAATTT
29567246 TT
1 TT
29567248 GAGTTTATTT
Statistics
Matches: 42, Mismatches: 0, Indels: 9
0.82 0.00 0.18
Matches are distributed among these distances:
6 6 0.14
7 13 0.31
8 20 0.48
9 3 0.07
ACGTcount: A:0.24, C:0.00, G:0.02, T:0.75
Consensus pattern (8 bp):
TTTAATTT
Found at i:29567218 original size:22 final size:23
Alignment explanation
Indices: 29567193--29567247 Score: 62
Period size: 22 Copynumber: 2.4 Consensus size: 23
29567183 ATATTAAATA
*
29567193 TTTAAGTTTTTTATTTTTTAA--T
1 TTTAA-TTTTTTAATTTTTAATTT
29567215 TTTAATTTTTTAATTTTTTAA-TT
1 TTTAATTTTTTAA-TTTTTAATTT
29567238 TTTAATTTTT
1 TTTAATTTTT
29567248 GAGTTTATTT
Statistics
Matches: 30, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
21 7 0.23
22 12 0.40
23 11 0.37
ACGTcount: A:0.24, C:0.00, G:0.02, T:0.75
Consensus pattern (23 bp):
TTTAATTTTTTAATTTTTAATTT
Found at i:29569292 original size:40 final size:40
Alignment explanation
Indices: 29569209--29569428 Score: 241
Period size: 40 Copynumber: 5.5 Consensus size: 40
29569199 ACCCAAGTAT
** * *
29569209 CTTCGGGAT-TTAG-CCGGATATAACCACTCGCAC-AAGGC
1 CTTCGGG-TCTTAGCCCGGATATAGTCACTAGCACAAATGC
* *
29569247 CTTCGGGTCTTAGCCCGGATATGGTCACTAGCATAAATGC
1 CTTCGGGTCTTAGCCCGGATATAGTCACTAGCACAAATGC
* * * *
29569287 CTTCGGGACTTAGCCCAGATATAATCGCTAGCACAAATGC
1 CTTCGGGTCTTAGCCCGGATATAGTCACTAGCACAAATGC
* *
29569327 CTTCGGGTCTTAGCCCGGATATAG-CAACTCGGACAAATGC
1 CTTCGGGTCTTAGCCCGGATATAGTC-ACTAGCACAAATGC
* * * *
29569367 CTTCGGATCTTAGTCCGGATATAGTCACTAGCATAAAAGC
1 CTTCGGGTCTTAGCCCGGATATAGTCACTAGCACAAATGC
*
29569407 CTTCGGGACTTAGCCCGGATAT
1 CTTCGGGTCTTAGCCCGGATAT
29569429 CATTCGAATA
Statistics
Matches: 150, Mismatches: 27, Indels: 8
0.81 0.15 0.04
Matches are distributed among these distances:
37 1 0.01
38 11 0.07
39 16 0.11
40 121 0.81
41 1 0.01
ACGTcount: A:0.26, C:0.26, G:0.23, T:0.25
Consensus pattern (40 bp):
CTTCGGGTCTTAGCCCGGATATAGTCACTAGCACAAATGC
Found at i:29576273 original size:27 final size:27
Alignment explanation
Indices: 29576174--29576368 Score: 247
Period size: 27 Copynumber: 7.4 Consensus size: 27
29576164 TGGATAAGTT
* *
29576174 GTAGAATTACCGAAATACCTC-GTAAG
1 GTAGAATTACCGAAATACCCCTGTAGG
29576200 GTAGAATTACCG-AATA-CCCTGTAGG
1 GTAGAATTACCGAAATACCCCTGTAGG
*
29576225 GTAGAATTA-TGAAATACCCCTGTAGG
1 GTAGAATTACCGAAATACCCCTGTAGG
29576251 GTAGAATTACCGAAATACCCCTGTAGG
1 GTAGAATTACCGAAATACCCCTGTAGG
** *
29576278 GTAGAATTATGGAAATACCCTTGTAGG
1 GTAGAATTACCGAAATACCCCTGTAGG
* *
29576305 GTAGAAATACC-AAATACCCCTATAGG
1 GTAGAATTACCGAAATACCCCTGTAGG
* * *
29576331 GTAGAATTACCGAGATACCCTTGTGGG
1 GTAGAATTACCGAAATACCCCTGTAGG
*
29576358 GTAAAATTACC
1 GTAGAATTACC
29576369 ATTTTGCCCC
Statistics
Matches: 146, Mismatches: 18, Indels: 9
0.84 0.10 0.05
Matches are distributed among these distances:
24 3 0.02
25 21 0.14
26 53 0.36
27 69 0.47
ACGTcount: A:0.35, C:0.18, G:0.22, T:0.25
Consensus pattern (27 bp):
GTAGAATTACCGAAATACCCCTGTAGG
Found at i:29576284 original size:53 final size:54
Alignment explanation
Indices: 29576174--29576368 Score: 247
Period size: 53 Copynumber: 3.7 Consensus size: 54
29576164 TGGATAAGTT
* *
29576174 GTAGAATTACCGAAATACCTC-GTAAGGTAGAATTACCG-AATA-CCCTGTAGG
1 GTAGAATTACCGAAATACCCCTGTAGGGTAGAATTACCGAAATACCCCTGTAGG
*
29576225 GTAGAATTA-TGAAATACCCCTGTAGGGTAGAATTACCGAAATACCCCTGTAGG
1 GTAGAATTACCGAAATACCCCTGTAGGGTAGAATTACCGAAATACCCCTGTAGG
** * * *
29576278 GTAGAATTATGGAAATACCCTTGTAGGGTAGAAATACC-AAATACCCCTATAGG
1 GTAGAATTACCGAAATACCCCTGTAGGGTAGAATTACCGAAATACCCCTGTAGG
* * * *
29576331 GTAGAATTACCGAGATACCCTTGTGGGGTAAAATTACC
1 GTAGAATTACCGAAATACCCCTGTAGGGTAGAATTACC
29576369 ATTTTGCCCC
Statistics
Matches: 127, Mismatches: 13, Indels: 6
0.87 0.09 0.04
Matches are distributed among these distances:
50 9 0.07
51 25 0.20
52 4 0.03
53 64 0.50
54 25 0.20
ACGTcount: A:0.35, C:0.18, G:0.22, T:0.25
Consensus pattern (54 bp):
GTAGAATTACCGAAATACCCCTGTAGGGTAGAATTACCGAAATACCCCTGTAGG
Found at i:29577150 original size:27 final size:27
Alignment explanation
Indices: 29577120--29577171 Score: 68
Period size: 27 Copynumber: 1.9 Consensus size: 27
29577110 ATATATATAT
*
29577120 TCTGGTGGCCTAGCCACAATATCTGTA
1 TCTGGTGACCTAGCCACAATATCTGTA
* * *
29577147 TCTGGTGACTTCGTCACAATATCTG
1 TCTGGTGACCTAGCCACAATATCTG
29577172 GCAGCTTCGC
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
27 21 1.00
ACGTcount: A:0.21, C:0.25, G:0.21, T:0.33
Consensus pattern (27 bp):
TCTGGTGACCTAGCCACAATATCTGTA
Found at i:29583800 original size:27 final size:27
Alignment explanation
Indices: 29583770--29583965 Score: 207
Period size: 27 Copynumber: 7.3 Consensus size: 27
29583760 TAAGTTGTAG
* *
29583770 AATTACCGAAACACCCCTGTAAGGTAA
1 AATTACCGAAATACCCCTGTAGGGTAA
*
29583797 AATTACCGAACTACCCCTGTAGGG-AA
1 AATTACCGAAATACCCCTGTAGGGTAA
** * *
29583823 GAATTATTGAAATACCCCTATAGGGTAG
1 -AATTACCGAAATACCCCTGTAGGGTAA
* *
29583851 AATTACCGAAATACCCCTATAGGGTAG
1 AATTACCGAAATACCCCTGTAGGGTAA
*
29583878 AATTACCGAAATACCCTTGTAGGGTAGA
1 AATTACCGAAATACCCCTGTAGGGTA-A
* * * *
29583906 AA-TACTGAAATACCCCTATAAGGTAG
1 AATTACCGAAATACCCCTGTAGGGTAA
* * *
29583932 AATTACCGAGATACCCTTGTGGGGTAA
1 AATTACCGAAATACCCCTGTAGGGTAA
29583959 AATTACC
1 AATTACC
29583966 ATTTTGCCCC
Statistics
Matches: 140, Mismatches: 25, Indels: 8
0.81 0.14 0.05
Matches are distributed among these distances:
26 4 0.03
27 133 0.95
28 3 0.02
ACGTcount: A:0.37, C:0.21, G:0.19, T:0.23
Consensus pattern (27 bp):
AATTACCGAAATACCCCTGTAGGGTAA
Found at i:29583855 original size:54 final size:54
Alignment explanation
Indices: 29583766--29583965 Score: 247
Period size: 54 Copynumber: 3.7 Consensus size: 54
29583756 TAGATAAGTT
* * * * *
29583766 GTAGAATTACCGAAACACCCCTGTAAGGTAAAATTACCGAACTACCCCTGTAGG
1 GTAGAATTACCGAAATACCCCTGTAGGGTAGAATTACCGAAATACCCCTATAGG
* ** *
29583820 GAAGAATTATTGAAATACCCCTATAGGGTAGAATTACCGAAATACCCCTATAGG
1 GTAGAATTACCGAAATACCCCTGTAGGGTAGAATTACCGAAATACCCCTATAGG
* * * *
29583874 GTAGAATTACCGAAATACCCTTGTAGGGTAGAAATACTGAAATACCCCTATAAG
1 GTAGAATTACCGAAATACCCCTGTAGGGTAGAATTACCGAAATACCCCTATAGG
* * * *
29583928 GTAGAATTACCGAGATACCCTTGTGGGGTAAAATTACC
1 GTAGAATTACCGAAATACCCCTGTAGGGTAGAATTACC
29583966 ATTTTGCCCC
Statistics
Matches: 124, Mismatches: 22, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
54 124 1.00
ACGTcount: A:0.36, C:0.20, G:0.20, T:0.23
Consensus pattern (54 bp):
GTAGAATTACCGAAATACCCCTGTAGGGTAGAATTACCGAAATACCCCTATAGG
Found at i:29583901 original size:81 final size:81
Alignment explanation
Indices: 29583766--29583965 Score: 283
Period size: 81 Copynumber: 2.5 Consensus size: 81
29583756 TAGATAAGTT
* * * * *
29583766 GTAGAATTACCGAAACACCCCTGTAAGGTAAAATTACCGAACTACCCCTGTAGGGAAGAATTATT
1 GTAGAATTACCGAAATACCCCTGTAGGGTAAAATTACCGAAATACCCCTGTAGGGAAGAAATACT
*
29583831 GAAATACCCCTATAGG
66 GAAATACCCCTATAAG
* * * *
29583847 GTAGAATTACCGAAATACCCCTATAGGGTAGAATTACCGAAATACCCTTGTAGGGTAGAAATACT
1 GTAGAATTACCGAAATACCCCTGTAGGGTAAAATTACCGAAATACCCCTGTAGGGAAGAAATACT
29583912 GAAATACCCCTATAAG
66 GAAATACCCCTATAAG
* * *
29583928 GTAGAATTACCGAGATACCCTTGTGGGGTAAAATTACC
1 GTAGAATTACCGAAATACCCCTGTAGGGTAAAATTACC
29583966 ATTTTGCCCC
Statistics
Matches: 104, Mismatches: 15, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
81 104 1.00
ACGTcount: A:0.36, C:0.20, G:0.20, T:0.23
Consensus pattern (81 bp):
GTAGAATTACCGAAATACCCCTGTAGGGTAAAATTACCGAAATACCCCTGTAGGGAAGAAATACT
GAAATACCCCTATAAG
Found at i:29584744 original size:27 final size:26
Alignment explanation
Indices: 29584706--29584765 Score: 66
Period size: 27 Copynumber: 2.3 Consensus size: 26
29584696 CCACATATAT
* *
29584706 ATATTTGTTCTGGTGGCCTAGCCACA
1 ATATCTGTTCTGGTGACCTAGCCACA
* * *
29584732 ATATCTGTATCTGGTGACTTCGTCACA
1 ATATCTGT-TCTGGTGACCTAGCCACA
29584759 ATATCTG
1 ATATCTG
29584766 GCAGCCTCGT
Statistics
Matches: 28, Mismatches: 5, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
26 7 0.25
27 21 0.75
ACGTcount: A:0.22, C:0.22, G:0.20, T:0.37
Consensus pattern (26 bp):
ATATCTGTTCTGGTGACCTAGCCACA
Found at i:29586784 original size:40 final size:40
Alignment explanation
Indices: 29586714--29586899 Score: 146
Period size: 40 Copynumber: 4.7 Consensus size: 40
29586704 ATAATTATTG
* * *
29586714 ATGAATGCACTTACGTGCCACTGTTTGTACTTCAGTACCC
1 ATGATTGCACTTACGTGCCCCTATTTGTACTTCAGTACCC
29586754 ATGATTGCACTTACGTGCCCCT-TTTCGTACTTC-GATACCC
1 ATGATTGCACTTACGTGCCCCTATTT-GTACTTCAG-TACCC
* * * ** * * *
29586794 CTGATTGCACATGCGTGCCTTTGTTTGTACTTCGGTACCG
1 ATGATTGCACTTACGTGCCCCTATTTGTACTTCAGTACCC
* * *
29586834 TTTATTGCA-TATACGTGCCTCTATTTGTACTT-AGGTACCC
1 ATGATTGCACT-TACGTGCCCCTATTTGTACTTCA-GTACCC
* * * *
29586874 CTAAATGCACTTACATGCCCCTATTT
1 ATGATTGCACTTACGTGCCCCTATTT
29586900 ATATGCTGGT
Statistics
Matches: 118, Mismatches: 21, Indels: 14
0.77 0.14 0.09
Matches are distributed among these distances:
39 4 0.03
40 109 0.92
41 5 0.04
ACGTcount: A:0.19, C:0.27, G:0.17, T:0.37
Consensus pattern (40 bp):
ATGATTGCACTTACGTGCCCCTATTTGTACTTCAGTACCC
Found at i:29586883 original size:80 final size:80
Alignment explanation
Indices: 29586717--29586892 Score: 185
Period size: 80 Copynumber: 2.2 Consensus size: 80
29586707 ATTATTGATG
*
29586717 AATGCACTTACGTGCCACTGTTTGTACTTCAGTACCCATGATTGCACTTACGTGCCCCTTTTCGT
1 AATGCACATACGTGCCACTGTTTGTACTTCAGTACCCATGATTGCACTTACGTGCCCCTTTTCGT
* *
29586782 ACTTCGATACCCCTG
66 ACTTAGATACCCCTA
* * ** * ** * *
29586797 ATTGCACATGCGTGCCTTTGTTTGTACTTCGGTACCGTTTATTGCA-TATACGTGCCTCTATTT-
1 AATGCACATACGTGCCACTGTTTGTACTTCAGTACCCATGATTGCACT-TACGTGCCCCT-TTTC
*
29586860 GTACTTAGGTACCCCTA
64 GTACTTAGATACCCCTA
* *
29586877 AATGCACTTACATGCC
1 AATGCACATACGTGCC
29586893 CCTATTTATA
Statistics
Matches: 77, Mismatches: 17, Indels: 4
0.79 0.17 0.04
Matches are distributed among these distances:
79 1 0.01
80 73 0.95
81 3 0.04
ACGTcount: A:0.19, C:0.28, G:0.17, T:0.36
Consensus pattern (80 bp):
AATGCACATACGTGCCACTGTTTGTACTTCAGTACCCATGATTGCACTTACGTGCCCCTTTTCGT
ACTTAGATACCCCTA
Found at i:29592565 original size:35 final size:35
Alignment explanation
Indices: 29592526--29592592 Score: 93
Period size: 35 Copynumber: 1.9 Consensus size: 35
29592516 TAACATAATT
29592526 GATACA-TAACAACCATACC-ATTTTGGCCATTTAAA
1 GATACATTAAC-A-CATACCAATTTTGGCCATTTAAA
*
29592561 GATACATTAACACATACCAATTTTGGTCATTT
1 GATACATTAACACATACCAATTTTGGCCATTT
29592593 CTAAGCATAC
Statistics
Matches: 29, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
34 6 0.21
35 19 0.66
36 4 0.14
ACGTcount: A:0.37, C:0.21, G:0.09, T:0.33
Consensus pattern (35 bp):
GATACATTAACACATACCAATTTTGGCCATTTAAA
Found at i:29593223 original size:31 final size:31
Alignment explanation
Indices: 29593183--29593248 Score: 114
Period size: 31 Copynumber: 2.1 Consensus size: 31
29593173 AACCCTTCCT
*
29593183 GCATTAAATCCAACCAAAAACAGCAAATATA
1 GCATGAAATCCAACCAAAAACAGCAAATATA
*
29593214 GCATGAAATCCAACCAAAAATAGCAAATATA
1 GCATGAAATCCAACCAAAAACAGCAAATATA
29593245 GCAT
1 GCAT
29593249 AAAAATACAA
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
31 33 1.00
ACGTcount: A:0.53, C:0.21, G:0.09, T:0.17
Consensus pattern (31 bp):
GCATGAAATCCAACCAAAAACAGCAAATATA
Found at i:29593264 original size:31 final size:31
Alignment explanation
Indices: 29593183--29593267 Score: 98
Period size: 31 Copynumber: 2.7 Consensus size: 31
29593173 AACCCTTCCT
* *
29593183 GCATTAAATCCAACCAAAAACAGCAAATATA
1 GCATAAAATACAACCAAAAACAGCAAATATA
* * *
29593214 GCATGAAATCCAACCAAAAATAGCAAATATA
1 GCATAAAATACAACCAAAAACAGCAAATATA
**
29593245 GCATAAAAATACAATAAAAAACA
1 GCAT-AAAATACAACCAAAAACA
29593268 TTAAATCTAA
Statistics
Matches: 46, Mismatches: 7, Indels: 1
0.85 0.13 0.02
Matches are distributed among these distances:
31 33 0.72
32 13 0.28
ACGTcount: A:0.59, C:0.19, G:0.07, T:0.15
Consensus pattern (31 bp):
GCATAAAATACAACCAAAAACAGCAAATATA
Found at i:29593557 original size:21 final size:21
Alignment explanation
Indices: 29593502--29593557 Score: 76
Period size: 21 Copynumber: 2.7 Consensus size: 21
29593492 TACTGCCATT
*
29593502 GCTGCTGCCTCTACCTCCCTC
1 GCTGCTGCCTCTGCCTCCCTC
* *
29593523 GCTACTGCCGCTGCCTCCCTC
1 GCTGCTGCCTCTGCCTCCCTC
*
29593544 TCTGCTGCCTCTGC
1 GCTGCTGCCTCTGC
29593558 TCTAAGTTGT
Statistics
Matches: 29, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
21 29 1.00
ACGTcount: A:0.04, C:0.50, G:0.18, T:0.29
Consensus pattern (21 bp):
GCTGCTGCCTCTGCCTCCCTC
Found at i:29593985 original size:13 final size:14
Alignment explanation
Indices: 29593959--29593987 Score: 51
Period size: 13 Copynumber: 2.1 Consensus size: 14
29593949 ACTAACGATG
29593959 AATTAAACCATTAT
1 AATTAAACCATTAT
29593973 AATTAAA-CATTAT
1 AATTAAACCATTAT
29593986 AA
1 AA
29593988 ATATTTATAA
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:0.55, C:0.10, G:0.00, T:0.34
Consensus pattern (14 bp):
AATTAAACCATTAT
Found at i:29599062 original size:9 final size:9
Alignment explanation
Indices: 29599048--29599159 Score: 152
Period size: 9 Copynumber: 12.4 Consensus size: 9
29599038 AGTATAATTA
29599048 AGTTATGTG
1 AGTTATGTG
29599057 AGTTATGTG
1 AGTTATGTG
29599066 AGTTATGTG
1 AGTTATGTG
29599075 AGTTATGTG
1 AGTTATGTG
*
29599084 AGTTATGTA
1 AGTTATGTG
*
29599093 AGTTATGTA
1 AGTTATGTG
29599102 AGTTATGTG
1 AGTTATGTG
*
29599111 AGTTATGTA
1 AGTTATGTG
* *
29599120 AGTTATATA
1 AGTTATGTG
*
29599129 AGTTATGTT
1 AGTTATGTG
29599138 AGTTATGTG
1 AGTTATGTG
* *
29599147 AGCTATGTA
1 AGTTATGTG
29599156 AGTT
1 AGTT
29599160 CAAGTATATA
Statistics
Matches: 93, Mismatches: 10, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
9 93 1.00
ACGTcount: A:0.28, C:0.01, G:0.27, T:0.45
Consensus pattern (9 bp):
AGTTATGTG
Found at i:29599078 original size:27 final size:27
Alignment explanation
Indices: 29599046--29599159 Score: 174
Period size: 27 Copynumber: 4.2 Consensus size: 27
29599036 TAAGTATAAT
*
29599046 TAAGTTATGTGAGTTATGTGAGTTATG
1 TAAGTTATGTGAGTTATGTAAGTTATG
*
29599073 TGAGTTATGTGAGTTATGTAAGTTATG
1 TAAGTTATGTGAGTTATGTAAGTTATG
*
29599100 TAAGTTATGTGAGTTATGTAAGTTATA
1 TAAGTTATGTGAGTTATGTAAGTTATG
* * *
29599127 TAAGTTATGTTAGTTATGTGAGCTATG
1 TAAGTTATGTGAGTTATGTAAGTTATG
29599154 TAAGTT
1 TAAGTT
29599160 CAAGTATATA
Statistics
Matches: 79, Mismatches: 8, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
27 79 1.00
ACGTcount: A:0.28, C:0.01, G:0.26, T:0.45
Consensus pattern (27 bp):
TAAGTTATGTGAGTTATGTAAGTTATG
Found at i:29599465 original size:15 final size:15
Alignment explanation
Indices: 29599429--29599487 Score: 50
Period size: 14 Copynumber: 3.9 Consensus size: 15
29599419 AATCACATGG
*
29599429 AAAAAAAATATTT-T
1 AAAAATAATATTTAT
29599443 AATTAAATAATATTTAT
1 AA--AAATAATATTTAT
* *
29599460 AAAAATTATATTAAT
1 AAAAATAATATTTAT
*
29599475 -TAAATAATATTTA
1 AAAAATAATATTTA
29599488 AATAAATTAA
Statistics
Matches: 36, Mismatches: 6, Indels: 6
0.75 0.12 0.12
Matches are distributed among these distances:
14 12 0.33
15 11 0.31
16 10 0.28
17 3 0.08
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (15 bp):
AAAAATAATATTTAT
Found at i:29599481 original size:20 final size:20
Alignment explanation
Indices: 29599458--29599517 Score: 59
Period size: 20 Copynumber: 3.0 Consensus size: 20
29599448 AATAATATTT
29599458 ATAAAAATTATATTAATTAA
1 ATAAAAATTATATTAATTAA
* * * *
29599478 ATAATATTTAAATAAATT-A
1 ATAAAAATTATATTAATTAA
**
29599497 ATCTAAATTATATTAATTAA
1 ATAAAAATTATATTAATTAA
29599517 A
1 A
29599518 ATAAGATTGA
Statistics
Matches: 29, Mismatches: 10, Indels: 2
0.71 0.24 0.05
Matches are distributed among these distances:
19 13 0.45
20 16 0.55
ACGTcount: A:0.57, C:0.02, G:0.00, T:0.42
Consensus pattern (20 bp):
ATAAAAATTATATTAATTAA
Found at i:29599490 original size:25 final size:26
Alignment explanation
Indices: 29599441--29599521 Score: 76
Period size: 29 Copynumber: 3.0 Consensus size: 26
29599431 AAAAAATATT
*
29599441 TTAATTAAATAATATTTATAAAAATTATA
1 TTAATTAAATAATA-TTAT-AAAA-TAAA
29599470 TTAATTAAATAATATT-T-AAATAAA
1 TTAATTAAATAATATTATAAAATAAA
*
29599494 TTAATCTAAATTATATTAATTAAAATAA
1 TTAAT-TAAATAATATT-A-TAAAATAA
29599522 GATTGAACCT
Statistics
Matches: 45, Mismatches: 2, Indels: 10
0.79 0.04 0.18
Matches are distributed among these distances:
24 8 0.18
25 13 0.29
27 1 0.02
28 3 0.07
29 20 0.44
ACGTcount: A:0.56, C:0.01, G:0.00, T:0.43
Consensus pattern (26 bp):
TTAATTAAATAATATTATAAAATAAA
Found at i:29599494 original size:29 final size:29
Alignment explanation
Indices: 29599431--29599496 Score: 98
Period size: 29 Copynumber: 2.3 Consensus size: 29
29599421 TCACATGGAA
* *
29599431 AAAAAATATTTTAATTAAATAATATTTAT
1 AAAAATTATATTAATTAAATAATATTTAT
29599460 AAAAATTATATTAATTAAATAATATTTA-
1 AAAAATTATATTAATTAAATAATATTTAT
29599488 AATAAATTA
1 AA-AAATTA
29599497 ATCTAAATTA
Statistics
Matches: 34, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
28 2 0.06
29 32 0.94
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (29 bp):
AAAAATTATATTAATTAAATAATATTTAT
Found at i:29599511 original size:15 final size:13
Alignment explanation
Indices: 29599434--29599517 Score: 64
Period size: 15 Copynumber: 6.2 Consensus size: 13
29599424 CATGGAAAAA
*
29599434 AAATATTTTAATT
1 AAATATATTAATT
* *
29599447 AAATAATATTTATAA
1 AAAT-ATATTAAT-T
29599462 AAATTATATTAATT
1 AAA-TATATTAATT
*
29599476 AAATA-A-TATTT
1 AAATATATTAATT
*
29599487 AAATAAATTAATCT
1 AAATATATTAAT-T
29599501 AAATTATATTAATT
1 AAA-TATATTAATT
29599515 AAA
1 AAA
29599518 ATAAGATTGA
Statistics
Matches: 56, Mismatches: 8, Indels: 13
0.73 0.10 0.17
Matches are distributed among these distances:
11 9 0.16
12 2 0.04
13 9 0.16
14 17 0.30
15 18 0.32
16 1 0.02
ACGTcount: A:0.55, C:0.01, G:0.00, T:0.44
Consensus pattern (13 bp):
AAATATATTAATT
Done.