Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr06 ID=Chr06-JGI_221_v2.0
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: 51074515
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 971674 characters in sequence are not A, C, G, or T
File 119 of 168
Found at i:34565973 original size:27 final size:27
Alignment explanation
Indices: 34565937--34565989 Score: 106
Period size: 27 Copynumber: 2.0 Consensus size: 27
34565927 TCAATGAATT
34565937 GGGGAATCAGCACTTAGCAACCCCTTG
1 GGGGAATCAGCACTTAGCAACCCCTTG
34565964 GGGGAATCAGCACTTAGCAACCCCTT
1 GGGGAATCAGCACTTAGCAACCCCTT
34565990 TTATATTTAA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 26 1.00
ACGTcount: A:0.26, C:0.30, G:0.25, T:0.19
Consensus pattern (27 bp):
GGGGAATCAGCACTTAGCAACCCCTTG
Found at i:34573467 original size:103 final size:103
Alignment explanation
Indices: 34573309--34573613 Score: 488
Period size: 103 Copynumber: 3.0 Consensus size: 103
34573299 CCAGTGATTC
* * *
34573309 GGGGAATCAGCACTTAGCAACCCCTTTCACATTCAAAGATA-TGGTGGAATCAGCACTTAGCAAA
1 GGGGAATCAGCACTTAGCAACCCCCTTCACATTTAAAGATACT-GTGGAATCAGCACTTAGCAAC
*
34573373 CACCAATCATTCGGGGAATCAGCACTTAGCAACCCCTTG
65 CACCAATAATTCGGGGAATCAGCACTTAGCAACCCCTTG
34573412 GGGGAATCAGCACTTAGCAACCCCCTTCACATTTAAAGATACTGTGGAATCAGCACTTAGCAACC
1 GGGGAATCAGCACTTAGCAACCCCCTTCACATTTAAAGATACTGTGGAATCAGCACTTAGCAACC
34573477 ACCAATGAATT-GGGGAATCAGCACTTAGCAACCCCTTG
66 ACCAAT-AATTCGGGGAATCAGCACTTAGCAACCCCTTG
* * *
34573515 GGGGAATCAGCACTTAGCAACCCCCTTTATATTTAAAGATACGGTGGAATCAGCACTTAGCAACC
1 GGGGAATCAGCACTTAGCAACCCCCTTCACATTTAAAGATACTGTGGAATCAGCACTTAGCAACC
* * *
34573580 ACCGATGAGTCGGGGAATCAGCACTTAGCAACCC
66 ACCAATAATTCGGGGAATCAGCACTTAGCAACCC
34573614 ATTCATATTC
Statistics
Matches: 189, Mismatches: 10, Indels: 6
0.92 0.05 0.03
Matches are distributed among these distances:
102 2 0.01
103 183 0.97
104 4 0.02
ACGTcount: A:0.32, C:0.27, G:0.20, T:0.21
Consensus pattern (103 bp):
GGGGAATCAGCACTTAGCAACCCCCTTCACATTTAAAGATACTGTGGAATCAGCACTTAGCAACC
ACCAATAATTCGGGGAATCAGCACTTAGCAACCCCTTG
Found at i:34574707 original size:11 final size:12
Alignment explanation
Indices: 34574679--34574712 Score: 52
Period size: 11 Copynumber: 2.8 Consensus size: 12
34574669 GCCCAAACAT
34574679 CGAAATTTTTGAA
1 CGAAATTTTT-AA
34574692 CGAAATTTTT-A
1 CGAAATTTTTAA
34574703 CGAAATTTTT
1 CGAAATTTTT
34574713 CCGTAAAATC
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
11 11 0.52
13 10 0.48
ACGTcount: A:0.35, C:0.09, G:0.12, T:0.44
Consensus pattern (12 bp):
CGAAATTTTTAA
Found at i:34588069 original size:13 final size:12
Alignment explanation
Indices: 34588051--34588091 Score: 55
Period size: 13 Copynumber: 3.2 Consensus size: 12
34588041 ATCATAAACA
34588051 TTATAAACAAATT
1 TTATAAA-AAATT
*
34588064 TTATAAAAAAATG
1 TTAT-AAAAAATT
34588077 TTATAAAAAATT
1 TTATAAAAAATT
34588089 TTA
1 TTA
34588092 AATTATAATT
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
12 10 0.40
13 12 0.48
14 3 0.12
ACGTcount: A:0.56, C:0.02, G:0.02, T:0.39
Consensus pattern (12 bp):
TTATAAAAAATT
Found at i:34592051 original size:14 final size:14
Alignment explanation
Indices: 34592032--34592060 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
34592022 AGTGATTAAA
34592032 ATGTAATCTGAGAT
1 ATGTAATCTGAGAT
34592046 ATGTAATCTGAGAT
1 ATGTAATCTGAGAT
34592060 A
1 A
34592061 AACAAAAGTG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.38, C:0.07, G:0.21, T:0.34
Consensus pattern (14 bp):
ATGTAATCTGAGAT
Found at i:34600655 original size:40 final size:40
Alignment explanation
Indices: 34600611--34600700 Score: 105
Period size: 39 Copynumber: 2.3 Consensus size: 40
34600601 TCCACGTCAG
*
34600611 CGCGATTTGCTT-CCACGTCAGCAAATCGCGCCT-ACGAGGA
1 CGCGATTTGCTTGCCACGTAAG-AAATCGCG-CTGACGAGGA
* * *
34600651 CGCGATTTG-TTGCCACGTAAGTAATCGCGCTGATGTGGA
1 CGCGATTTGCTTGCCACGTAAGAAATCGCGCTGACGAGGA
34600690 CGCGATTTGCT
1 CGCGATTTGCT
34600701 GACACGTCCC
Statistics
Matches: 43, Mismatches: 4, Indels: 6
0.81 0.08 0.11
Matches are distributed among these distances:
38 2 0.05
39 23 0.53
40 18 0.42
ACGTcount: A:0.20, C:0.27, G:0.28, T:0.26
Consensus pattern (40 bp):
CGCGATTTGCTTGCCACGTAAGAAATCGCGCTGACGAGGA
Found at i:34607138 original size:2 final size:2
Alignment explanation
Indices: 34607131--34607184 Score: 108
Period size: 2 Copynumber: 27.0 Consensus size: 2
34607121 TCCAATTACA
34607131 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
34607173 AT AT AT AT AT AT
1 AT AT AT AT AT AT
34607185 CAATTTACTT
Statistics
Matches: 52, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 52 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:34610637 original size:29 final size:29
Alignment explanation
Indices: 34610595--34610652 Score: 116
Period size: 29 Copynumber: 2.0 Consensus size: 29
34610585 GTCTTCAAAA
34610595 GCAACTTTAAACCCATTCTCAACAAGTTG
1 GCAACTTTAAACCCATTCTCAACAAGTTG
34610624 GCAACTTTAAACCCATTCTCAACAAGTTG
1 GCAACTTTAAACCCATTCTCAACAAGTTG
34610653 TCCAACTCTT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 29 1.00
ACGTcount: A:0.34, C:0.28, G:0.10, T:0.28
Consensus pattern (29 bp):
GCAACTTTAAACCCATTCTCAACAAGTTG
Found at i:34617250 original size:17 final size:17
Alignment explanation
Indices: 34617228--34617272 Score: 58
Period size: 15 Copynumber: 2.8 Consensus size: 17
34617218 AGAAGAACCG
34617228 AGGAAAGAAGAAAAGAA
1 AGGAAAGAAGAAAAGAA
*
34617245 AGGAAAG-AG-AAAGAG
1 AGGAAAGAAGAAAAGAA
*
34617260 AGGGAAGAAGAAA
1 AGGAAAGAAGAAA
34617273 GAATTGGTGG
Statistics
Matches: 24, Mismatches: 2, Indels: 4
0.80 0.07 0.13
Matches are distributed among these distances:
15 11 0.46
16 4 0.17
17 9 0.38
ACGTcount: A:0.64, C:0.00, G:0.36, T:0.00
Consensus pattern (17 bp):
AGGAAAGAAGAAAAGAA
Found at i:34621920 original size:111 final size:111
Alignment explanation
Indices: 34621716--34621936 Score: 268
Period size: 111 Copynumber: 2.0 Consensus size: 111
34621706 TGGTTGCATA
* * *
34621716 TATGTCATCCTGGGTGAAGGAAGAGCAAGTGGAGGAACCTCGACATCCCCTTGACCCTCATTCCG
1 TATGGCATCCTAGGTGAAGGAAGAGCAAGTGGAGGAACCTCGACATCCCCTTGACCCTCACTCCG
* * ** *
34621781 GTCCCTGGTATGCCATTCTATGTATTGTTCTACAGAAGCAGGAGTG
66 GTCCCTGCTATGCCATTCGACATATTGTTCAACAGAAGCAGGAGTG
34621827 TATGGCATCCTAGGTGAAGGAAGAGCAAGTGGAGGAACCTC-AGCATCTCCC-TGACCCTCACTC
1 TATGGCATCCTAGGTGAAGGAAGAGCAAGTGGAGGAACCTCGA-CATC-CCCTTGACCCTCACTC
* * ** * *
34621890 TGAG-CCCTGCTTTGCTGTTCGACATCTTGTTCAACTGAAGCAGGAGT
64 CG-GTCCCTGCTATGCCATTCGACATATTGTTCAACAGAAGCAGGAGT
34621937 AGCAGATGTT
Statistics
Matches: 93, Mismatches: 14, Indels: 6
0.82 0.12 0.05
Matches are distributed among these distances:
110 1 0.01
111 88 0.95
112 4 0.04
ACGTcount: A:0.24, C:0.25, G:0.26, T:0.25
Consensus pattern (111 bp):
TATGGCATCCTAGGTGAAGGAAGAGCAAGTGGAGGAACCTCGACATCCCCTTGACCCTCACTCCG
GTCCCTGCTATGCCATTCGACATATTGTTCAACAGAAGCAGGAGTG
Found at i:34630130 original size:103 final size:103
Alignment explanation
Indices: 34629938--34630133 Score: 250
Period size: 103 Copynumber: 1.9 Consensus size: 103
34629928 AAATGTTTAA
* ** * *
34629938 ATGTAAGACCATAGCTGGGCTATGTCATTTTAATGAAAAGACCATAACTGGGTTATGGCACCTTG
1 ATGTAAGACCATAGCTGGGCTAAGGAATTCTAATGAAAAGACCATAACTGGGTTATGGCACCTTA
* **
34630003 AACGTAAGACCATAGTTGGACCATGGCAGTATAAATAT
66 AACGTAAAACCATAGCAGGACCATGGCAGTATAAATAT
* * *
34630041 ATGTAAGACCATAGTTGGGCTAAGGAATTCTGATGATAAGACCATAACTGGGTTATGGCA-CTAT
1 ATGTAAGACCATAGCTGGGCTAAGGAATTCTAATGAAAAGACCATAACTGGGTTATGGCACCT-T
* * *
34630105 AAATGTAAAACCATGGCAGGGCCATGGCA
65 AAACGTAAAACCATAGCAGGACCATGGCA
34630134 ATGCATGTGT
Statistics
Matches: 78, Mismatches: 14, Indels: 2
0.83 0.15 0.02
Matches are distributed among these distances:
102 2 0.03
103 76 0.97
ACGTcount: A:0.34, C:0.16, G:0.24, T:0.26
Consensus pattern (103 bp):
ATGTAAGACCATAGCTGGGCTAAGGAATTCTAATGAAAAGACCATAACTGGGTTATGGCACCTTA
AACGTAAAACCATAGCAGGACCATGGCAGTATAAATAT
Found at i:34633495 original size:22 final size:22
Alignment explanation
Indices: 34633470--34633535 Score: 66
Period size: 20 Copynumber: 3.1 Consensus size: 22
34633460 AACTAAAAAA
*
34633470 ATTATAAAATA-TAATATTAAAT
1 ATTA-AAAATATTAAAATTAAAT
34633492 ATTAAAAATATTAAAATT-AAT
1 ATTAAAAATATTAAAATTAAAT
** *
34633513 A-TAAACTTATTAAAATTATAT
1 ATTAAAAATATTAAAATTAAAT
34633534 AT
1 AT
34633536 ATATATATAT
Statistics
Matches: 37, Mismatches: 4, Indels: 6
0.79 0.09 0.13
Matches are distributed among these distances:
20 14 0.38
21 13 0.35
22 10 0.27
ACGTcount: A:0.58, C:0.02, G:0.00, T:0.41
Consensus pattern (22 bp):
ATTAAAAATATTAAAATTAAAT
Found at i:34633503 original size:16 final size:15
Alignment explanation
Indices: 34633482--34633511 Score: 51
Period size: 16 Copynumber: 1.9 Consensus size: 15
34633472 TATAAAATAT
34633482 AATATTAAATATTAAA
1 AATATTAAA-ATTAAA
34633498 AATATTAAAATTAA
1 AATATTAAAATTAA
34633512 TATAAACTTA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 5 0.36
16 9 0.64
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (15 bp):
AATATTAAAATTAAA
Found at i:34633513 original size:28 final size:29
Alignment explanation
Indices: 34633466--34633568 Score: 90
Period size: 29 Copynumber: 3.4 Consensus size: 29
34633456 GAAAAACTAA
34633466 AAAAATTATAAAATATAATATTAAA-TATT
1 AAAAATTATAAAATATAATA-TAAACTATT
34633495 AAAAA-TATTAAAAT-TAATATAAACTTATT
1 AAAAATTA-TAAAATATAATATAAAC-TATT
*
34633524 -AAAATTATATATATATATATATAAA-TACTT
1 AAAAATTATA-AAATATA-ATATAAACTA-TT
34633554 ATAAATATTATAAAA
1 A-AAA-ATTATAAAA
34633569 ACCTAAAAAT
Statistics
Matches: 61, Mismatches: 2, Indels: 19
0.74 0.02 0.23
Matches are distributed among these distances:
27 4 0.07
28 13 0.21
29 22 0.36
30 4 0.07
31 7 0.11
32 5 0.08
33 6 0.10
ACGTcount: A:0.59, C:0.02, G:0.00, T:0.39
Consensus pattern (29 bp):
AAAAATTATAAAATATAATATAAACTATT
Found at i:34633566 original size:9 final size:9
Alignment explanation
Indices: 34633487--34633567 Score: 58
Period size: 10 Copynumber: 8.4 Consensus size: 9
34633477 AATATAATAT
34633487 TAAATATTA
1 TAAATATTA
*
34633496 AAAATATTA
1 TAAATATTA
*
34633505 -AAATTAATA
1 TAAA-TATTA
34633514 TAAACTTATTA
1 TAAA--TATTA
34633525 -AAATTATATA
1 TAAA-TAT-TA
*
34633535 TATATATATA
1 TAAATAT-TA
34633545 TAAATACTTA
1 TAAATA-TTA
34633555 TAAATATTA
1 TAAATATTA
34633564 TAAA
1 TAAA
34633568 AACCTAAAAA
Statistics
Matches: 61, Mismatches: 5, Indels: 12
0.78 0.06 0.15
Matches are distributed among these distances:
8 3 0.05
9 23 0.38
10 27 0.44
11 8 0.13
ACGTcount: A:0.57, C:0.02, G:0.00, T:0.41
Consensus pattern (9 bp):
TAAATATTA
Found at i:34634016 original size:16 final size:18
Alignment explanation
Indices: 34633986--34634018 Score: 52
Period size: 16 Copynumber: 1.9 Consensus size: 18
34633976 AATATTTTAA
34633986 ATATGTTTTATTAATTTT
1 ATATGTTTTATTAATTTT
34634004 ATAT-TTTTA-TAATTT
1 ATATGTTTTATTAATTT
34634019 ATTAGATTAT
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 6 0.40
17 5 0.33
18 4 0.27
ACGTcount: A:0.30, C:0.00, G:0.03, T:0.67
Consensus pattern (18 bp):
ATATGTTTTATTAATTTT
Found at i:34634110 original size:25 final size:26
Alignment explanation
Indices: 34634082--34634130 Score: 64
Period size: 25 Copynumber: 1.9 Consensus size: 26
34634072 ATCTTTTTAA
34634082 ATAATTAATCATTTTTAT-ATTTTTG
1 ATAATTAATCATTTTTATGATTTTTG
** *
34634107 ATAATTTTTTATTTTTATGATTTT
1 ATAATTAATCATTTTTATGATTTT
34634131 ATCTATATTT
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
25 15 0.75
26 5 0.25
ACGTcount: A:0.29, C:0.02, G:0.04, T:0.65
Consensus pattern (26 bp):
ATAATTAATCATTTTTATGATTTTTG
Found at i:34634114 original size:17 final size:16
Alignment explanation
Indices: 34634094--34634132 Score: 51
Period size: 17 Copynumber: 2.4 Consensus size: 16
34634084 AATTAATCAT
34634094 TTTTATATTTTTGATAA
1 TTTTATATTTTT-ATAA
* *
34634111 TTTTTTATTTTTATGA
1 TTTTATATTTTTATAA
34634127 TTTTAT
1 TTTTAT
34634133 CTATATTTTT
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
16 8 0.42
17 11 0.58
ACGTcount: A:0.23, C:0.00, G:0.05, T:0.72
Consensus pattern (16 bp):
TTTTATATTTTTATAA
Found at i:34634384 original size:2 final size:2
Alignment explanation
Indices: 34634377--34634406 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
34634367 ATTAGGTGTG
34634377 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
34634407 TAAGGATAAC
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:34638892 original size:15 final size:16
Alignment explanation
Indices: 34638874--34638905 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 16
34638864 TCTTATTTCG
34638874 TATTTTT-ATATTATT
1 TATTTTTAATATTATT
34638889 TATTTTTAATATTATT
1 TATTTTTAATATTATT
34638905 T
1 T
34638906 TTTAAATTAT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 7 0.44
16 9 0.56
ACGTcount: A:0.28, C:0.00, G:0.00, T:0.72
Consensus pattern (16 bp):
TATTTTTAATATTATT
Found at i:34640447 original size:15 final size:16
Alignment explanation
Indices: 34640420--34640449 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
34640410 GGTGATGGTA
34640420 TTAGGTATAAATTATT
1 TTAGGTATAAATTATT
34640436 TTAGGT-TAAATTAT
1 TTAGGTATAAATTAT
34640450 GACTGTGATC
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 8 0.57
16 6 0.43
ACGTcount: A:0.37, C:0.00, G:0.13, T:0.50
Consensus pattern (16 bp):
TTAGGTATAAATTATT
Found at i:34641298 original size:10 final size:10
Alignment explanation
Indices: 34641283--34641335 Score: 61
Period size: 10 Copynumber: 5.3 Consensus size: 10
34641273 TTTAAAATAA
34641283 TTTTATATTT
1 TTTTATATTT
34641293 TTTTATATTT
1 TTTTATATTT
* * **
34641303 TTTAAAATAA
1 TTTTATATTT
*
34641313 TTTTAAATTT
1 TTTTATATTT
34641323 TTTTATATTT
1 TTTTATATTT
34641333 TTT
1 TTT
34641336 AAAAATAATT
Statistics
Matches: 35, Mismatches: 8, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
10 35 1.00
ACGTcount: A:0.28, C:0.00, G:0.00, T:0.72
Consensus pattern (10 bp):
TTTTATATTT
Found at i:34641325 original size:31 final size:30
Alignment explanation
Indices: 34641269--34641363 Score: 165
Period size: 30 Copynumber: 3.2 Consensus size: 30
34641259 CCTCAATTTC
*
34641269 ATTTTTTAAAATAATTTTATATTTTTTTAT
1 ATTTTTTAAAATAATTTTAAATTTTTTTAT
34641299 ATTTTTTAAAATAATTTTAAATTTTTTTAT
1 ATTTTTTAAAATAATTTTAAATTTTTTTAT
34641329 ATTTTTTAAAAATAATTTTAAA-TTTTTTAT
1 ATTTTTT-AAAATAATTTTAAATTTTTTTAT
34641359 ATTTT
1 ATTTT
34641364 CATCAATGGC
Statistics
Matches: 63, Mismatches: 1, Indels: 2
0.95 0.02 0.03
Matches are distributed among these distances:
30 49 0.78
31 14 0.22
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (30 bp):
ATTTTTTAAAATAATTTTAAATTTTTTTAT
Found at i:34643067 original size:26 final size:25
Alignment explanation
Indices: 34643003--34643071 Score: 102
Period size: 25 Copynumber: 2.7 Consensus size: 25
34642993 TTTGAATTTA
*
34643003 TTATCTAATGTAATAAAATAGAAGT
1 TTATTTAATGTAATAAAATAGAAGT
*
34643028 TTATTTAATATAATAAAATAGAAGT
1 TTATTTAATGTAATAAAATAGAAGT
*
34643053 TCTATTTGATGTAATAAAA
1 T-TATTTAATGTAATAAAA
34643072 ACCCTAATTT
Statistics
Matches: 39, Mismatches: 4, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
25 24 0.62
26 15 0.38
ACGTcount: A:0.48, C:0.03, G:0.10, T:0.39
Consensus pattern (25 bp):
TTATTTAATGTAATAAAATAGAAGT
Found at i:34643090 original size:18 final size:18
Alignment explanation
Indices: 34643067--34643203 Score: 76
Period size: 18 Copynumber: 7.7 Consensus size: 18
34643057 TTTGATGTAA
*
34643067 TAAAAACCCTAATTTGA-T
1 TAAAAACCCTAACTT-ACT
34643085 TAAAAACCCTAACTTACT
1 TAAAAACCCTAACTTACT
*
34643103 TAAAAACCCTAAC---CC
1 TAAAAACCCTAACTTACT
*
34643118 T---AA-CCTAACTTAAT
1 TAAAAACCCTAACTTACT
* *
34643132 TAAAAACCCTAACCCTAACCC
1 TAAAAACCCTAA--CTTA-CT
* *
34643153 TAACCCTAA-CCTAACTTAAT
1 TAA---AAACCCTAACTTACT
*
34643173 TAAAAACCCTAACTTAAT
1 TAAAAACCCTAACTTACT
34643191 TAAAAACCCTAAC
1 TAAAAACCCTAAC
34643204 CCTAACCTAA
Statistics
Matches: 92, Mismatches: 12, Indels: 30
0.69 0.09 0.22
Matches are distributed among these distances:
11 6 0.07
12 2 0.02
14 1 0.01
15 2 0.02
17 5 0.05
18 57 0.62
20 6 0.07
21 6 0.07
23 5 0.05
24 2 0.02
ACGTcount: A:0.45, C:0.29, G:0.01, T:0.25
Consensus pattern (18 bp):
TAAAAACCCTAACTTACT
Found at i:34643134 original size:29 final size:29
Alignment explanation
Indices: 34643092--34643422 Score: 311
Period size: 29 Copynumber: 11.8 Consensus size: 29
34643082 GATTAAAAAC
*
34643092 CCTAACTTACTTAAAAACCCTAACCCTAA
1 CCTAACTTAATTAAAAACCCTAACCCTAA
34643121 CCTAACTTAATTAAAAACCCTAACCCTAA
1 CCTAACTTAATTAAAAACCCTAACCCTAA
* * * * *
34643150 CCCTAACCCTAACCTAACTTAA--TTAA---AAA
1 -CCTAA-CTTAA-TTAA--AAACCCTAACCCTAA
34643179 CCCTAACTTAATTAAAAACCCTAACCCTAA
1 -CCTAACTTAATTAAAAACCCTAACCCTAA
34643209 CCTAACTTAATTAAAAACCCTAACCCTAA
1 CCTAACTTAATTAAAAACCCTAACCCTAA
*
34643238 CCTAACTTAATTAAAAACCCTAACTCTAA
1 CCTAACTTAATTAAAAACCCTAACCCTAA
* * *
34643267 CCTAATTTAATTAAAAATCCTAATCCTAA
1 CCTAACTTAATTAAAAACCCTAACCCTAA
* *
34643296 CCTAATTTAATTAAAAACCCTAA-CTTAA
1 CCTAACTTAATTAAAAACCCTAACCCTAA
* * * **
34643324 -TTAA--AAACT-CTAACCCTAA-CCTAA
1 CCTAACTTAATTAAAAACCCTAACCCTAA
34643348 --T---TTAATT-AAAACCCTAACCCTAA
1 CCTAACTTAATTAAAAACCCTAACCCTAA
*
34643371 CCTAACTTAATTAAAAACTCTAACCCTAA
1 CCTAACTTAATTAAAAACCCTAACCCTAA
*
34643400 CCTAATTTAATT-AAAACCCTAAC
1 CCTAACTTAATTAAAAACCCTAAC
34643423 TTAATTAAAA
Statistics
Matches: 253, Mismatches: 31, Indels: 37
0.79 0.10 0.12
Matches are distributed among these distances:
22 11 0.04
23 6 0.02
24 12 0.05
25 6 0.02
27 9 0.04
28 24 0.09
29 166 0.66
30 7 0.03
31 4 0.02
32 6 0.02
34 2 0.01
ACGTcount: A:0.44, C:0.28, G:0.00, T:0.27
Consensus pattern (29 bp):
CCTAACTTAATTAAAAACCCTAACCCTAA
Found at i:34643143 original size:47 final size:47
Alignment explanation
Indices: 34643074--34643232 Score: 240
Period size: 47 Copynumber: 3.5 Consensus size: 47
34643064 TAATAAAAAC
* *
34643074 CCTAATTTGATTAAAAACCCTAACTTACTTAAAAACCCTAACCCTAA
1 CCTAACTTAATTAAAAACCCTAACTTACTTAAAAACCCTAACCCTAA
*
34643121 CCTAACTTAATTAAAAACCCTAAC---CCT---AACCCTAACCCTAA
1 CCTAACTTAATTAAAAACCCTAACTTACTTAAAAACCCTAACCCTAA
*
34643162 CCTAACTTAATTAAAAACCCTAACTTAATTAAAAACCCTAACCCTAA
1 CCTAACTTAATTAAAAACCCTAACTTACTTAAAAACCCTAACCCTAA
34643209 CCTAACTTAATTAAAAACCCTAAC
1 CCTAACTTAATTAAAAACCCTAAC
34643233 CCTAACCTAA
Statistics
Matches: 101, Mismatches: 5, Indels: 12
0.86 0.04 0.10
Matches are distributed among these distances:
41 38 0.38
44 3 0.03
47 60 0.59
ACGTcount: A:0.44, C:0.30, G:0.01, T:0.25
Consensus pattern (47 bp):
CCTAACTTAATTAAAAACCCTAACTTACTTAAAAACCCTAACCCTAA
Found at i:34643155 original size:41 final size:41
Alignment explanation
Indices: 34643107--34643243 Score: 195
Period size: 41 Copynumber: 3.2 Consensus size: 41
34643097 CTTACTTAAA
34643107 AACCCTAACCCTAACCTAACTTAATTAAAAACCCTAACCCT
1 AACCCTAACCCTAACCTAACTTAATTAAAAACCCTAACCCT
**
34643148 AACCCTAACCCTAACCTAACTTAATTAAAAACCCTAACTTAATT
1 AACCCTAACCCTAACCTAACTTAATTAAAAACCCTAAC---CCT
34643192 AAAAACCCTAACCCTAACCTAACTTAATTAAAAACCCTAACCCT
1 ---AACCCTAACCCTAACCTAACTTAATTAAAAACCCTAACCCT
34643236 AA-CCTAAC
1 AACCCTAAC
34643244 TTAATTAAAA
Statistics
Matches: 86, Mismatches: 4, Indels: 13
0.83 0.04 0.13
Matches are distributed among these distances:
40 6 0.07
41 40 0.47
44 2 0.02
47 38 0.44
ACGTcount: A:0.44, C:0.34, G:0.00, T:0.23
Consensus pattern (41 bp):
AACCCTAACCCTAACCTAACTTAATTAAAAACCCTAACCCT
Found at i:34643167 original size:5 final size:6
Alignment explanation
Indices: 34643136--34643167 Score: 57
Period size: 6 Copynumber: 5.5 Consensus size: 6
34643126 CTTAATTAAA
34643136 AACCCT AACCCT AACCCT AACCCT AA-CCT AAC
1 AACCCT AACCCT AACCCT AACCCT AACCCT AAC
34643168 TTAATTAAAA
Statistics
Matches: 25, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
5 5 0.20
6 20 0.80
ACGTcount: A:0.38, C:0.47, G:0.00, T:0.16
Consensus pattern (6 bp):
AACCCT
Found at i:34643180 original size:17 final size:18
Alignment explanation
Indices: 34643162--34643203 Score: 84
Period size: 18 Copynumber: 2.3 Consensus size: 18
34643152 CTAACCCTAA
34643162 CCTAACTTAATTAAAAAC
1 CCTAACTTAATTAAAAAC
34643180 CCTAACTTAATTAAAAAC
1 CCTAACTTAATTAAAAAC
34643198 CCTAAC
1 CCTAAC
34643204 CCTAACCTAA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 24 1.00
ACGTcount: A:0.48, C:0.26, G:0.00, T:0.26
Consensus pattern (18 bp):
CCTAACTTAATTAAAAAC
Found at i:34643323 original size:18 final size:18
Alignment explanation
Indices: 34643296--34643337 Score: 66
Period size: 18 Copynumber: 2.3 Consensus size: 18
34643286 CTAATCCTAA
*
34643296 CCTAATTTAATTAAAAAC
1 CCTAACTTAATTAAAAAC
34643314 CCTAACTTAATTAAAAAC
1 CCTAACTTAATTAAAAAC
*
34643332 TCTAAC
1 CCTAAC
34643338 CCTAACCTAA
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
18 22 1.00
ACGTcount: A:0.48, C:0.21, G:0.00, T:0.31
Consensus pattern (18 bp):
CCTAACTTAATTAAAAAC
Found at i:34643434 original size:75 final size:73
Alignment explanation
Indices: 34643180--34643603 Score: 383
Period size: 75 Copynumber: 5.5 Consensus size: 73
34643170 AATTAAAAAC
*
34643180 CCTAACTTAATTAAAAACCCTAACCCTAACCTAACTTAATTAAAAACCCTAACCCTAACCTAACT
1 CCTAACTTAATTAAAAACCCTAACCCTAACCTAATTTAATT--AAA----AACCCTAACCTAAC-
*
34643245 TAATTAAAAACCCTAACTCTAA
59 ----TAAAAACTCTAA--C-AA
* * * * *
34643267 CCTAATTTAATTAAAAATCCTAATCCTAACCTAATTTAATTAAAAACCCTAACTTAATTAAAAAC
1 CCTAACTTAATTAAAAACCCTAACCCTAACCTAATTTAATTAAAAACCCTAACCTAACTAAAAAC
34643332 TCTAACCCTAA
66 TCTAA--C-AA
* * *
34643343 CCTAATTTAATT-AAAACCCTAACCCTAACCTAACTTAATTAAAAACTCTAACCCTAACCTAATT
1 CCTAACTTAATTAAAAACCCTAACCCTAACCTAATTTAATTAAAAACCCTAA-CCTAA-CTAA--
*
34643407 TAA-T-TAA-AA
62 AAACTCTAACAA
* *
34643416 CCCTAACTTAATTAAAAACCCTAACCCTAACCTAATTTAATT-AAAACCCTAACTTAATTAAAAA
1 -CCTAACTTAATTAAAAACCCTAACCCTAACCTAATTTAATTAAAAACCCTAACCTAACTAAAAA
34643480 CTCTAACCCTAA
65 CTCTAA--C-AA
* * *
34643492 CCTAACTTAATTAAAAACTCTAACCCTAACCTAATTTAATT-AAAACCCTAACTTAATTAAAAAC
1 CCTAACTTAATTAAAAACCCTAACCCTAACCTAATTTAATTAAAAACCCTAACCTAACTAAAAAC
*
34643556 CCTAACCCTAA
66 TCTAA--C-AA
**
34643567 CCTAACTTAATTAAAAAATCTAACCCTAACCTAATTT
1 CCTAACTTAATTAAAAACCCTAACCCTAACCTAATTT
34643604 TACATAATTT
Statistics
Matches: 301, Mismatches: 24, Indels: 36
0.83 0.07 0.10
Matches are distributed among these distances:
70 2 0.01
71 1 0.00
72 6 0.02
73 6 0.02
74 20 0.07
75 171 0.57
76 34 0.11
77 6 0.02
78 1 0.00
79 2 0.01
81 12 0.04
85 3 0.01
87 37 0.12
ACGTcount: A:0.45, C:0.26, G:0.00, T:0.29
Consensus pattern (73 bp):
CCTAACTTAATTAAAAACCCTAACCCTAACCTAATTTAATTAAAAACCCTAACCTAACTAAAAAC
TCTAACAA
Found at i:34643459 original size:29 final size:27
Alignment explanation
Indices: 34643417--34643602 Score: 138
Period size: 29 Copynumber: 7.3 Consensus size: 27
34643407 TAATTAAAAC
34643417 CCTAACTTAATTAAAAACCCTAACCCTAA
1 CCTAA-TTAATT-AAAACCCTAACCCTAA
34643446 CCTAATTTAATTAAAACCCTAA--CT--
1 CCTAA-TTAATTAAAACCCTAACCCTAA
*
34643470 --TAATT-A--AAAACTCTAACCCTAA
1 CCTAATTAATTAAAACCCTAACCCTAA
*
34643492 CCTAACTTAATTAAAAACTCTAACCCTAA
1 CCTAA-TTAATT-AAAACCCTAACCCTAA
34643521 CCTAATTTAATTAAAACCCTAA--CT--
1 CCTAA-TTAATTAAAACCCTAACCCTAA
34643545 --TAATT-A--AAAACCCTAACCCTAA
1 CCTAATTAATTAAAACCCTAACCCTAA
**
34643567 CCTAACTTAATTAAAAAATCTAACCCTAA
1 CCTAA-TTAATT-AAAACCCTAACCCTAA
34643596 CCTAATT
1 CCTAATT
34643603 TTACATAATT
Statistics
Matches: 129, Mismatches: 6, Indels: 45
0.72 0.03 0.25
Matches are distributed among these distances:
18 19 0.15
20 6 0.05
21 4 0.03
22 6 0.05
24 6 0.05
25 4 0.03
26 6 0.05
28 21 0.16
29 57 0.44
ACGTcount: A:0.45, C:0.26, G:0.00, T:0.28
Consensus pattern (27 bp):
CCTAATTAATTAAAACCCTAACCCTAA
Found at i:34643486 original size:18 final size:17
Alignment explanation
Indices: 34643400--34643478 Score: 71
Period size: 17 Copynumber: 4.9 Consensus size: 17
34643390 CTAACCCTAA
*
34643400 CCTAATTTAATTAAAAC
1 CCTAACTTAATTAAAAC
34643417 CCTAACTTAATTAAAAAC
1 CCTAACTTAATT-AAAAC
**
34643435 CCTAAC---CCT--AA-
1 CCTAACTTAATTAAAAC
*
34643446 CCTAATTTAATTAAAAC
1 CCTAACTTAATTAAAAC
34643463 CCTAACTTAATTAAAA
1 CCTAACTTAATTAAAA
34643479 ACTCTAACCC
Statistics
Matches: 48, Mismatches: 7, Indels: 14
0.70 0.10 0.20
Matches are distributed among these distances:
11 5 0.10
12 2 0.04
14 1 0.02
15 1 0.02
16 2 0.04
17 26 0.54
18 11 0.23
ACGTcount: A:0.47, C:0.23, G:0.00, T:0.30
Consensus pattern (17 bp):
CCTAACTTAATTAAAAC
Found at i:34643490 original size:46 final size:45
Alignment explanation
Indices: 34643369--34643507 Score: 224
Period size: 46 Copynumber: 3.0 Consensus size: 45
34643359 CCCTAACCCT
* *
34643369 AACCTAACTTAATTAAAAACTCTAACCCTAACCTAATTTAATTAA
1 AACCTAACTTAATTAAAAACCCTAACCCTAACCTAACTTAATTAA
*
34643414 AACCCTAACTTAATTAAAAACCCTAACCCTAACCTAATTTAATTAA
1 AA-CCTAACTTAATTAAAAACCCTAACCCTAACCTAACTTAATTAA
*
34643460 AACCCTAACTTAATTAAAAACTCTAACCCTAACCTAACTTAATTAA
1 AA-CCTAACTTAATTAAAAACCCTAACCCTAACCTAACTTAATTAA
34643506 AA
1 AA
34643508 ACTCTAACCC
Statistics
Matches: 90, Mismatches: 3, Indels: 1
0.96 0.03 0.01
Matches are distributed among these distances:
45 2 0.02
46 88 0.98
ACGTcount: A:0.47, C:0.24, G:0.00, T:0.29
Consensus pattern (45 bp):
AACCTAACTTAATTAAAAACCCTAACCCTAACCTAACTTAATTAA
Found at i:34643542 original size:46 final size:46
Alignment explanation
Indices: 34643492--34643582 Score: 164
Period size: 46 Copynumber: 2.0 Consensus size: 46
34643482 CTAACCCTAA
* *
34643492 CCTAACTTAATTAAAAACTCTAACCCTAACCTAATTTAATTAAAAC
1 CCTAACTTAATTAAAAACCCTAACCCTAACCTAACTTAATTAAAAC
34643538 CCTAACTTAATTAAAAACCCTAACCCTAACCTAACTTAATTAAAA
1 CCTAACTTAATTAAAAACCCTAACCCTAACCTAACTTAATTAAAA
34643583 AATCTAACCC
Statistics
Matches: 43, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
46 43 1.00
ACGTcount: A:0.46, C:0.25, G:0.00, T:0.29
Consensus pattern (46 bp):
CCTAACTTAATTAAAAACCCTAACCCTAACCTAACTTAATTAAAAC
Found at i:34643547 original size:17 final size:18
Alignment explanation
Indices: 34643521--34643561 Score: 66
Period size: 17 Copynumber: 2.3 Consensus size: 18
34643511 CTAACCCTAA
*
34643521 CCTAATTTAATT-AAAAC
1 CCTAACTTAATTAAAAAC
34643538 CCTAACTTAATTAAAAAC
1 CCTAACTTAATTAAAAAC
34643556 CCTAAC
1 CCTAAC
34643562 CCTAACCTAA
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
17 11 0.50
18 11 0.50
ACGTcount: A:0.46, C:0.24, G:0.00, T:0.29
Consensus pattern (18 bp):
CCTAACTTAATTAAAAAC
Found at i:34643659 original size:55 final size:55
Alignment explanation
Indices: 34643598--34643844 Score: 300
Period size: 55 Copynumber: 4.3 Consensus size: 55
34643588 AACCCTAACC
*
34643598 TAATTTTACATAATTTGATAATTTTACTAACCATTAACACAATTGTTGGACTTAA
1 TAATTTTACATAATTTGATAATTTTACTAACCATTAACACAATTTTTGGACTTAA
34643653 TAATTTTACATAATTTGATAATTTTACTAACCATTAACACAATTTTTGGACTTAA
1 TAATTTTACATAATTTGATAATTTTACTAACCATTAACACAATTTTTGGACTTAA
** * *
34643708 TAATTTTACATAATTTGATAATTTTACCTAATTTAATTAA-A-ATTTCTTTGGCTTAATAATTTT
1 TAATTTTACATAATTTGATAATTTTA-CTAA--CCATTAACACAATT-TTTGG-------A-CTT
34643771 ACA
54 A-A
* *
34643774 TAATTTTACATAATTTGATAATTTTACTAACCATTAACAAAATTTTGGGACTTAA
1 TAATTTTACATAATTTGATAATTTTACTAACCATTAACACAATTTTTGGACTTAA
34643829 TAATTTTACATAATTT
1 TAATTTTACATAATTT
34643845 TACATAATTT
Statistics
Matches: 167, Mismatches: 10, Indels: 30
0.81 0.05 0.14
Matches are distributed among these distances:
55 97 0.58
56 10 0.06
57 7 0.04
58 5 0.03
63 5 0.03
64 6 0.04
65 10 0.06
66 27 0.16
ACGTcount: A:0.38, C:0.11, G:0.06, T:0.45
Consensus pattern (55 bp):
TAATTTTACATAATTTGATAATTTTACTAACCATTAACACAATTTTTGGACTTAA
Found at i:34643730 original size:18 final size:18
Alignment explanation
Indices: 34643707--34643741 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
34643697 TTTGGACTTA
34643707 ATAATTTTACATAATTTG
1 ATAATTTTACATAATTTG
*
34643725 ATAATTTTACCTAATTT
1 ATAATTTTACATAATTT
34643742 AATTAAAATT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.37, C:0.09, G:0.03, T:0.51
Consensus pattern (18 bp):
ATAATTTTACATAATTTG
Found at i:34643778 original size:10 final size:10
Alignment explanation
Indices: 34643763--34643862 Score: 71
Period size: 10 Copynumber: 9.5 Consensus size: 10
34643753 CTTTGGCTTA
34643763 ATAATTTTAC
1 ATAATTTTAC
34643773 ATAATTTTAC
1 ATAATTTTAC
*
34643783 ATAA-TTT-G
1 ATAATTTTAC
34643791 ATAATTTTAC
1 ATAATTTTAC
* *
34643801 -TAACCATTAAC
1 ATAA--TTTTAC
*
34643812 AAAATTTTGGGAC
1 ATAATTTT---AC
34643825 TTAATAATTTTAC
1 ---ATAATTTTAC
34643838 ATAATTTTAC
1 ATAATTTTAC
34643848 ATAATTTTAC
1 ATAATTTTAC
34643858 ATAAT
1 ATAAT
34643863 GTTAGATTTG
Statistics
Matches: 71, Mismatches: 8, Indels: 22
0.70 0.08 0.22
Matches are distributed among these distances:
8 4 0.06
9 9 0.13
10 41 0.58
11 4 0.06
12 2 0.03
13 4 0.06
16 7 0.10
ACGTcount: A:0.41, C:0.10, G:0.04, T:0.45
Consensus pattern (10 bp):
ATAATTTTAC
Found at i:34643785 original size:66 final size:64
Alignment explanation
Indices: 34643707--34643854 Score: 210
Period size: 65 Copynumber: 2.3 Consensus size: 64
34643697 TTTGGACTTA
* * *
34643707 ATAATTTTACATAATTTGATAATTTTACCTAA-TTTAATTAAAATTTCTTTGG-CTTAATAATTT
1 ATAATTTTACATAATTTGATAATTTTA-CTAACATTAA-CAAAA-TT-TTGGGACTTAATAATTT
34643770 TAC
62 TAC
34643773 ATAATTTTACATAATTTGATAATTTTACTAACCATTAACAAAATTTTGGGACTTAATAATTTTAC
1 ATAATTTTACATAATTTGATAATTTTACTAA-CATTAACAAAATTTTGGGACTTAATAATTTTAC
34643838 ATAATTTTACATAATTT
1 ATAATTTTACATAATTT
34643855 TACATAATGT
Statistics
Matches: 76, Mismatches: 3, Indels: 7
0.88 0.03 0.08
Matches are distributed among these distances:
64 4 0.05
65 37 0.49
66 31 0.41
67 4 0.05
ACGTcount: A:0.39, C:0.09, G:0.05, T:0.47
Consensus pattern (64 bp):
ATAATTTTACATAATTTGATAATTTTACTAACATTAACAAAATTTTGGGACTTAATAATTTTAC
Found at i:34647188 original size:123 final size:124
Alignment explanation
Indices: 34646969--34647316 Score: 583
Period size: 124 Copynumber: 2.8 Consensus size: 124
34646959 CCAAACTTGT
* *
34646969 TACTGTAGCAAAATCGCGTCTACGAGGGCGCGATTTCATAATTTCTTCTCAAATAGCATCTTGGT
1 TACTGTAGCAAAATCGCGTCCACGAGGGCGCGATTTCACAATTTCTTCTCAAATAGCATCTTGGT
*
34647034 AGAAGCGATTTTATACTATTTGCTCAGAAACGTCAAAAAAA-TTATTTCTTACATGACC
66 AGAAGCGATTTTATACTATTTGCTCAGAAACGTCAAAAAAATTTATTTCTTACATAACC
* *
34647092 TACTGTAGCAAAATCACGTCCACGAGGGCGCGATTTCACAATTTCTTCTCAAATAGCATCCTGGT
1 TACTGTAGCAAAATCGCGTCCACGAGGGCGCGATTTCACAATTTCTTCTCAAATAGCATCTTGGT
* * *
34647157 AGAGGCGATTTTATAATATTTGCTTAGAAACGTCAAAAAAATTTATTTCTTACATAACC
66 AGAAGCGATTTTATACTATTTGCTCAGAAACGTCAAAAAAATTTATTTCTTACATAACC
*
34647216 TACTGTAGCAAAATCGCGTCCACGGGGGCGCGATTTCACAATTTCTTCTCAAATAGCATCTTGGT
1 TACTGTAGCAAAATCGCGTCCACGAGGGCGCGATTTCACAATTTCTTCTCAAATAGCATCTTGGT
*
34647281 AGAAGCGATTTTATACTATTTGAC-CAGAAATGTCAA
66 AGAAGCGATTTTATACTATTTG-CTCAGAAACGTCAA
34647317 CTCGAAATAA
Statistics
Matches: 208, Mismatches: 15, Indels: 3
0.92 0.07 0.01
Matches are distributed among these distances:
123 99 0.48
124 108 0.52
125 1 0.00
ACGTcount: A:0.32, C:0.20, G:0.17, T:0.31
Consensus pattern (124 bp):
TACTGTAGCAAAATCGCGTCCACGAGGGCGCGATTTCACAATTTCTTCTCAAATAGCATCTTGGT
AGAAGCGATTTTATACTATTTGCTCAGAAACGTCAAAAAAATTTATTTCTTACATAACC
Found at i:34661229 original size:41 final size:41
Alignment explanation
Indices: 34661167--34661307 Score: 192
Period size: 41 Copynumber: 3.4 Consensus size: 41
34661157 ATAATCGAGT
34661167 TTTACGCCTAGCAGGCTTTATGCCGGTGAATTATATCAGGC
1 TTTACGCCTAGCAGGCTTTATGCCGGTGAATTATATCAGGC
* * **
34661208 TTTATGCCTAACAGGCTTTATGCCAATGAATTATATCAGGC
1 TTTACGCCTAGCAGGCTTTATGCCGGTGAATTATATCAGGC
* * ** *
34661249 TTTACGCCTAGCAGGCTTAATGCCGGTGTACCATAACAGGC
1 TTTACGCCTAGCAGGCTTTATGCCGGTGAATTATATCAGGC
*
34661290 TTTATGCCTAGCAGGCTT
1 TTTACGCCTAGCAGGCTT
34661308 CGTGCTGGTT
Statistics
Matches: 86, Mismatches: 14, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
41 86 1.00
ACGTcount: A:0.24, C:0.23, G:0.22, T:0.31
Consensus pattern (41 bp):
TTTACGCCTAGCAGGCTTTATGCCGGTGAATTATATCAGGC
Found at i:34661637 original size:2 final size:2
Alignment explanation
Indices: 34661630--34661671 Score: 75
Period size: 2 Copynumber: 21.0 Consensus size: 2
34661620 GTAGTAGTAG
*
34661630 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA CA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
34661672 AATTTGGGTT
Statistics
Matches: 38, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 38 1.00
ACGTcount: A:0.50, C:0.02, G:0.00, T:0.48
Consensus pattern (2 bp):
TA
Found at i:34666733 original size:46 final size:46
Alignment explanation
Indices: 34666630--34666836 Score: 341
Period size: 46 Copynumber: 4.6 Consensus size: 46
34666620 TACGTATGAT
* *
34666630 CACTTATCAC-TTGTC-CCTGATCAGATAAGTGTAGCT-AGGCTAC
1 CACTTATCACTTTGTCACTTGATCAGATAAGTGTAGCTAAAGCTAC
34666673 CACTTATCACTTTGTCACTTGATCAGATAAGTGTAGCTAAAGCTAC
1 CACTTATCACTTTGTCACTTGATCAGATAAGTGTAGCTAAAGCTAC
*
34666719 CACTTATCACTTTGTCACTTGATCAGATAAGTGTAGCTAAAGCTAT
1 CACTTATCACTTTGTCACTTGATCAGATAAGTGTAGCTAAAGCTAC
* *
34666765 CACTTATCACTTTATCACTTGAACAGATAAGTGTAGCTAAAGCTAC
1 CACTTATCACTTTGTCACTTGATCAGATAAGTGTAGCTAAAGCTAC
34666811 CACTTATCACTTTGTCAC-TGATCAGA
1 CACTTATCACTTTGTCACTTGATCAGA
34666837 AGTACTCAAA
Statistics
Matches: 153, Mismatches: 8, Indels: 4
0.93 0.05 0.02
Matches are distributed among these distances:
43 10 0.07
44 5 0.03
45 27 0.18
46 111 0.73
ACGTcount: A:0.30, C:0.23, G:0.15, T:0.32
Consensus pattern (46 bp):
CACTTATCACTTTGTCACTTGATCAGATAAGTGTAGCTAAAGCTAC
Found at i:34670628 original size:35 final size:34
Alignment explanation
Indices: 34670572--34670638 Score: 91
Period size: 35 Copynumber: 1.9 Consensus size: 34
34670562 GTCAAAACAA
*
34670572 TGTGTTTCATGTTTTATACCGTTTAAATGAAACGG
1 TGTGTTTCATGTTTTACACCGTTT-AATGAAACGG
*
34670607 TGTGCTTT-ATGTTTTGCACCGTTTAATGAAAC
1 TGTG-TTTCATGTTTTACACCGTTTAATGAAAC
34670639 AGTGCAAAGG
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
34 8 0.28
35 18 0.62
36 3 0.10
ACGTcount: A:0.24, C:0.13, G:0.19, T:0.43
Consensus pattern (34 bp):
TGTGTTTCATGTTTTACACCGTTTAATGAAACGG
Found at i:34674272 original size:15 final size:15
Alignment explanation
Indices: 34674252--34674284 Score: 57
Period size: 15 Copynumber: 2.2 Consensus size: 15
34674242 TTTCTCCTCA
*
34674252 GCTGGCTTTTTCTCG
1 GCTGGCTTCTTCTCG
34674267 GCTGGCTTCTTCTCG
1 GCTGGCTTCTTCTCG
34674282 GCT
1 GCT
34674285 TTGGGTGCCA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.00, C:0.30, G:0.27, T:0.42
Consensus pattern (15 bp):
GCTGGCTTCTTCTCG
Found at i:34678413 original size:67 final size:67
Alignment explanation
Indices: 34678334--34678608 Score: 311
Period size: 67 Copynumber: 4.1 Consensus size: 67
34678324 GTCACATCTA
* * * * * *
34678334 TAACCCCATGTTTAGTGTCCTAGCGAACTCTATTTGATGCCATAGTCGAGTTATAGTCTTACACA
1 TAACCCCATGTTTAATGTCCTAGAGAACTCTATTGGATGCCATAGTCGAGCTATGGTCTTACACT
34678399 TG
66 TG
* * * * * * *
34678401 TAACCCCATGTTTAATATCCCGAAAGACCT-TATTAGATGTCATAGTCAAGCTATGGTCTTACAC
1 TAACCCCATGTTTAATGT-CCTAGAGAACTCTATTGGATGCCATAGTCGAGCTATGGTCTTACAC
34678465 TTG
65 TTG
* * * * *
34678468 CAACTCCATGTTTAATGTCATAGCGAAC-CTTATTGGATGTCATAGTCGAGCTATGGTCTTACAC
1 TAACCCCATGTTTAATGTCCTAGAGAACTC-TATTGGATGCCATAGTCGAGCTATGGTCTTACAC
*
34678532 CTG
65 TTG
* * * *
34678535 TAACCCCATGTTTAATGTCCTAGAGGACCCTATTGGATGCAATAGTCGAGCTATGGTCTTGCACT
1 TAACCCCATGTTTAATGTCCTAGAGAACTCTATTGGATGCCATAGTCGAGCTATGGTCTTACACT
34678600 TG
66 TG
34678602 TAACCCC
1 TAACCCC
34678609 GTTACAGCCC
Statistics
Matches: 172, Mismatches: 32, Indels: 8
0.81 0.15 0.04
Matches are distributed among these distances:
66 5 0.03
67 159 0.92
68 8 0.05
ACGTcount: A:0.26, C:0.23, G:0.18, T:0.32
Consensus pattern (67 bp):
TAACCCCATGTTTAATGTCCTAGAGAACTCTATTGGATGCCATAGTCGAGCTATGGTCTTACACT
TG
Found at i:34678580 original size:134 final size:134
Alignment explanation
Indices: 34678339--34678601 Score: 352
Period size: 134 Copynumber: 2.0 Consensus size: 134
34678329 ATCTATAACC
* * * *
34678339 CCATGTTTAGTGTCCTAGCGAACTCTATTTGATGCCATAGTCGAGTTATAGTCTTACACATGTAA
1 CCATGTTTAATGTCATAGCGAACTCTATTGGATGCCATAGTCGAGCTATAGTCTTACACATGTAA
* *
34678404 CCCCATGTTTAATATCCCGAAAGACCTTATTAGATGTCATAGTCAAGCTATGGTCTTACACTTGC
66 CCCCATGTTTAATATCCAGAAAGACCCTATTAGATGTCATAGTCAAGCTATGGTCTTACACTTGC
34678469 AACT
131 AACT
* * *
34678473 CCATGTTTAATGTCATAGCGAAC-CTTATTGGATGTCATAGTCGAGCTATGGTCTTACACCTGTA
1 CCATGTTTAATGTCATAGCGAACTC-TATTGGATGCCATAGTCGAGCTATAGTCTTACACATGTA
* * * * *
34678537 ACCCCATGTTTAATGTCCTAG-AGGACCCTATTGGATG-CAATAGTCGAGCTATGGTCTTGCACT
65 ACCCCATGTTTAATATCC-AGAAAGACCCTATTAGATGTC-ATAGTCAAGCTATGGTCTTACACT
34678600 TG
128 TG
34678602 TAACCCCGTT
Statistics
Matches: 112, Mismatches: 14, Indels: 6
0.85 0.11 0.05
Matches are distributed among these distances:
133 2 0.02
134 109 0.97
135 1 0.01
ACGTcount: A:0.26, C:0.22, G:0.19, T:0.33
Consensus pattern (134 bp):
CCATGTTTAATGTCATAGCGAACTCTATTGGATGCCATAGTCGAGCTATAGTCTTACACATGTAA
CCCCATGTTTAATATCCAGAAAGACCCTATTAGATGTCATAGTCAAGCTATGGTCTTACACTTGC
AACT
Found at i:34683087 original size:19 final size:19
Alignment explanation
Indices: 34683063--34683099 Score: 74
Period size: 19 Copynumber: 1.9 Consensus size: 19
34683053 TACGAAATTC
34683063 CTAAGCTTTCTCTAACCTA
1 CTAAGCTTTCTCTAACCTA
34683082 CTAAGCTTTCTCTAACCT
1 CTAAGCTTTCTCTAACCT
34683100 CACTCTAGTG
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.24, C:0.32, G:0.05, T:0.38
Consensus pattern (19 bp):
CTAAGCTTTCTCTAACCTA
Found at i:34685493 original size:15 final size:15
Alignment explanation
Indices: 34685473--34685514 Score: 66
Period size: 15 Copynumber: 2.8 Consensus size: 15
34685463 TGGCACCCAA
34685473 AGCCGAGAAGAAGCC
1 AGCCGAGAAGAAGCC
*
34685488 AGCCGAGAAAAAGCC
1 AGCCGAGAAGAAGCC
*
34685503 AGCCGAGGAGAA
1 AGCCGAGAAGAA
34685515 AAAAGCCGAG
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
15 24 1.00
ACGTcount: A:0.43, C:0.24, G:0.33, T:0.00
Consensus pattern (15 bp):
AGCCGAGAAGAAGCC
Found at i:34686660 original size:38 final size:38
Alignment explanation
Indices: 34686564--34686670 Score: 178
Period size: 39 Copynumber: 2.8 Consensus size: 38
34686554 ATTATCCAAC
*
34686564 CCAACTCAATAAAACTAAAACTAAAGTCTACCCAATTA
1 CCAACCCAATAAAACTAAAACTAAAGTCTACCCAATTA
*
34686602 CCTAACCCAATAAAACTAAAACTAAAATCTACCCAATTA
1 CC-AACCCAATAAAACTAAAACTAAAGTCTACCCAATTA
*
34686641 CCAACCCAATAAAAATAAAACTAAAGTCTA
1 CCAACCCAATAAAACTAAAACTAAAGTCTA
34686671 ATTCTTAAGT
Statistics
Matches: 64, Mismatches: 4, Indels: 2
0.91 0.06 0.03
Matches are distributed among these distances:
38 28 0.44
39 36 0.56
ACGTcount: A:0.52, C:0.26, G:0.02, T:0.20
Consensus pattern (38 bp):
CCAACCCAATAAAACTAAAACTAAAGTCTACCCAATTA
Found at i:34686822 original size:17 final size:17
Alignment explanation
Indices: 34686802--34686864 Score: 54
Period size: 17 Copynumber: 3.5 Consensus size: 17
34686792 TAATTTCAAG
34686802 AATTATGTAATGTTTTT
1 AATTATGTAATGTTTTT
* ***
34686819 AATTATGTAGTGATTCAA
1 AATTATGTAATG-TTTTT
*
34686837 AGACTTATGTAATATTTTT
1 A-A-TTATGTAATGTTTTT
34686856 AATTATGTA
1 AATTATGTA
34686865 GTGATTCAAT
Statistics
Matches: 34, Mismatches: 9, Indels: 6
0.69 0.18 0.12
Matches are distributed among these distances:
17 18 0.53
18 4 0.12
19 4 0.12
20 8 0.24
ACGTcount: A:0.35, C:0.03, G:0.13, T:0.49
Consensus pattern (17 bp):
AATTATGTAATGTTTTT
Found at i:34686845 original size:37 final size:37
Alignment explanation
Indices: 34686799--34686873 Score: 132
Period size: 37 Copynumber: 2.0 Consensus size: 37
34686789 TGTTAATTTC
*
34686799 AAGAATTATGTAATGTTTTTAATTATGTAGTGATTCA
1 AAGAATTATGTAATATTTTTAATTATGTAGTGATTCA
*
34686836 AAGACTTATGTAATATTTTTAATTATGTAGTGATTCA
1 AAGAATTATGTAATATTTTTAATTATGTAGTGATTCA
34686873 A
1 A
34686874 TTCGGGTAAT
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
37 36 1.00
ACGTcount: A:0.36, C:0.04, G:0.15, T:0.45
Consensus pattern (37 bp):
AAGAATTATGTAATATTTTTAATTATGTAGTGATTCA
Found at i:34687550 original size:21 final size:22
Alignment explanation
Indices: 34687526--34687569 Score: 63
Period size: 21 Copynumber: 2.0 Consensus size: 22
34687516 AAACTACATT
*
34687526 AAAAGAAATGAAGAAG-AGAAG
1 AAAACAAATGAAGAAGCAGAAG
*
34687547 AAAACAAATGGAGAAGCAGAAG
1 AAAACAAATGAAGAAGCAGAAG
34687569 A
1 A
34687570 GAATGAAAAA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
21 14 0.70
22 6 0.30
ACGTcount: A:0.64, C:0.05, G:0.27, T:0.05
Consensus pattern (22 bp):
AAAACAAATGAAGAAGCAGAAG
Found at i:34691125 original size:3 final size:3
Alignment explanation
Indices: 34691119--34691160 Score: 59
Period size: 3 Copynumber: 13.7 Consensus size: 3
34691109 AAATTGTTTT
34691119 TTA TTA TTA CTTA TTA TTA TTA -TA TTTA TTA TTA TTA TTA TT
1 TTA TTA TTA -TTA TTA TTA TTA TTA -TTA TTA TTA TTA TTA TT
34691161 TCCATGTACA
Statistics
Matches: 36, Mismatches: 0, Indels: 6
0.86 0.00 0.14
Matches are distributed among these distances:
2 2 0.06
3 29 0.81
4 5 0.14
ACGTcount: A:0.31, C:0.02, G:0.00, T:0.67
Consensus pattern (3 bp):
TTA
Found at i:34691320 original size:17 final size:17
Alignment explanation
Indices: 34691287--34691320 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
34691277 ATATATATAC
*
34691287 ATATACATTTACATTTT
1 ATATACATATACATTTT
*
34691304 ATATACATATACGTTTT
1 ATATACATATACATTTT
34691321 GTAACACATT
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.35, C:0.12, G:0.03, T:0.50
Consensus pattern (17 bp):
ATATACATATACATTTT
Found at i:34692038 original size:99 final size:97
Alignment explanation
Indices: 34691915--34692172 Score: 272
Period size: 98 Copynumber: 2.6 Consensus size: 97
34691905 ATTCAACACG
* * * *
34691915 TTGTGTCCTAACGTATTGGATGTGATGCATT-GATTTCTCGA-AA-TGAATATT-TTTTAAAAAT
1 TTGTGCCCTAACGTATTGGGTGTGATGC-TTAAATCT-TCGATAAGTGAATATTCTTTT---AA-
*
34691976 AATAAAGGAAATATTCCGAGTTTGGGATTTTAAAGGAA
60 AATAAAGGAAATATTCCGAGTTTGGGATTCTAAAGGAA
* * * * *
34692014 TTGTGCCCTAACGTATTGGGTGTGATTTCTTAAATCTTGGATAAGTGGATGTTCTTTTAAAGTAA
1 TTGTGCCCTAACGTATTGGGTGTGA-TGCTTAAATCTTCGATAAGTGAATATTCTTTTAAAATAA
*
34692079 AGGAAATATTCCGAGTTTGGGATTCTAGAGGAA
65 AGGAAATATTCCGAGTTTGGGATTCTAAAGGAA
* * * * *
34692112 TCGTGCCCTAACGTATTGGGTGTGATTTCTTAAATCTTGGATAAGTGGATGTTCTTTTAAA
1 TTGTGCCCTAACGTATTGGGTGTGA-TGCTTAAATCTTCGATAAGTGAATATTCTTTTAAA
34692173 GTTTTATTGT
Statistics
Matches: 142, Mismatches: 12, Indels: 11
0.86 0.07 0.07
Matches are distributed among these distances:
98 95 0.67
99 30 0.21
100 7 0.05
101 6 0.04
102 4 0.03
ACGTcount: A:0.29, C:0.10, G:0.23, T:0.38
Consensus pattern (97 bp):
TTGTGCCCTAACGTATTGGGTGTGATGCTTAAATCTTCGATAAGTGAATATTCTTTTAAAATAAA
GGAAATATTCCGAGTTTGGGATTCTAAAGGAA
Found at i:34692093 original size:98 final size:98
Alignment explanation
Indices: 34691978--34692174 Score: 367
Period size: 98 Copynumber: 2.0 Consensus size: 98
34691968 TTAAAAATAA
* *
34691978 TAAAGGAAATATTCCGAGTTTGGGATTTTAAAGGAATTGTGCCCTAACGTATTGGGTGTGATTTC
1 TAAAGGAAATATTCCGAGTTTGGGATTCTAAAGGAATCGTGCCCTAACGTATTGGGTGTGATTTC
34692043 TTAAATCTTGGATAAGTGGATGTTCTTTTAAAG
66 TTAAATCTTGGATAAGTGGATGTTCTTTTAAAG
*
34692076 TAAAGGAAATATTCCGAGTTTGGGATTCTAGAGGAATCGTGCCCTAACGTATTGGGTGTGATTTC
1 TAAAGGAAATATTCCGAGTTTGGGATTCTAAAGGAATCGTGCCCTAACGTATTGGGTGTGATTTC
34692141 TTAAATCTTGGATAAGTGGATGTTCTTTTAAAG
66 TTAAATCTTGGATAAGTGGATGTTCTTTTAAAG
34692174 T
1 T
34692175 TTTATTGTAC
Statistics
Matches: 96, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
98 96 1.00
ACGTcount: A:0.28, C:0.10, G:0.25, T:0.37
Consensus pattern (98 bp):
TAAAGGAAATATTCCGAGTTTGGGATTCTAAAGGAATCGTGCCCTAACGTATTGGGTGTGATTTC
TTAAATCTTGGATAAGTGGATGTTCTTTTAAAG
Found at i:34693868 original size:39 final size:39
Alignment explanation
Indices: 34693759--34693916 Score: 160
Period size: 39 Copynumber: 3.9 Consensus size: 39
34693749 AGTTTCGAGC
* *
34693759 CTAAATTT-TCCTGTTCATATTTTATTTTTAATCTTGTTT
1 CTAAATTTAT-CTGTTCATATTTTATTTTTAATCCTGATT
* *
34693798 CTAAATTATTTGTATATGTTCATAATTTATTTTTAATCCTGATT
1 CT-AA--A-TT-TATCTGTTCATATTTTATTTTTAATCCTGATT
*
34693842 CTACATTTATCTGTTCATATTTTATTTTTAATCCT-ATTT
1 CTAAATTTATCTGTTCATATTTTATTTTTAATCCTGA-TT
* *
34693881 CTAAATTTTTCTGGTT-GTATTTTATTTTTAATCCTG
1 CTAAATTTATCT-GTTCATATTTTATTTTTAATCCTG
34693917 GTTCAAAACT
Statistics
Matches: 100, Mismatches: 10, Indels: 17
0.79 0.08 0.13
Matches are distributed among these distances:
38 1 0.01
39 58 0.58
40 7 0.07
41 1 0.01
42 1 0.01
43 3 0.03
44 28 0.28
45 1 0.01
ACGTcount: A:0.23, C:0.12, G:0.06, T:0.58
Consensus pattern (39 bp):
CTAAATTTATCTGTTCATATTTTATTTTTAATCCTGATT
Found at i:34695025 original size:14 final size:14
Alignment explanation
Indices: 34695008--34695034 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
34694998 TCTCTCTCCC
34695008 CATTTTTTTCTCTA
1 CATTTTTTTCTCTA
34695022 CATTTTTTTCTCT
1 CATTTTTTTCTCT
34695035 TTATCAAAAC
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.11, C:0.22, G:0.00, T:0.67
Consensus pattern (14 bp):
CATTTTTTTCTCTA
Found at i:34705448 original size:14 final size:14
Alignment explanation
Indices: 34705425--34705464 Score: 53
Period size: 14 Copynumber: 2.9 Consensus size: 14
34705415 ACAAAAAAGT
* *
34705425 AAAACATTTTCCAG
1 AAAACATTTTACAA
*
34705439 AAATCATTTTACAA
1 AAAACATTTTACAA
34705453 AAAACATTTTAC
1 AAAACATTTTAC
34705465 TGCCAATCAA
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
14 22 1.00
ACGTcount: A:0.47, C:0.17, G:0.03, T:0.33
Consensus pattern (14 bp):
AAAACATTTTACAA
Found at i:34705456 original size:35 final size:35
Alignment explanation
Indices: 34705390--34705456 Score: 118
Period size: 34 Copynumber: 1.9 Consensus size: 35
34705380 CAAATATCAG
*
34705390 AAAATATTTTCCAGTAAATCATTTTACAAAAAAGT
1 AAAACATTTTCCAGTAAATCATTTTACAAAAAAGT
34705425 AAAACATTTTCCAG-AAATCATTTTACAAAAAA
1 AAAACATTTTCCAGTAAATCATTTTACAAAAAA
34705457 CATTTTACTG
Statistics
Matches: 31, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
34 18 0.58
35 13 0.42
ACGTcount: A:0.51, C:0.13, G:0.04, T:0.31
Consensus pattern (35 bp):
AAAACATTTTCCAGTAAATCATTTTACAAAAAAGT
Found at i:34706279 original size:15 final size:16
Alignment explanation
Indices: 34706242--34706284 Score: 54
Period size: 15 Copynumber: 2.8 Consensus size: 16
34706232 TGTCGGCCTT
* *
34706242 TTTCTCCTCAGCTGGC
1 TTTCTTCTCGGCTGGC
34706258 TTT-TTCTCGGCTGG-
1 TTTCTTCTCGGCTGGC
34706272 TTTCTTCTCGGCT
1 TTTCTTCTCGGCT
34706285 TTGGGTGCCA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
14 3 0.12
15 18 0.75
16 3 0.12
ACGTcount: A:0.02, C:0.30, G:0.21, T:0.47
Consensus pattern (16 bp):
TTTCTTCTCGGCTGGC
Found at i:34719981 original size:15 final size:15
Alignment explanation
Indices: 34719961--34719989 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
34719951 ATTAAACTAT
34719961 TTCTTTTCAGTCAGA
1 TTCTTTTCAGTCAGA
34719976 TTCTTTTCAGTCAG
1 TTCTTTTCAGTCAG
34719990 TTCAACTAAT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.17, C:0.21, G:0.14, T:0.48
Consensus pattern (15 bp):
TTCTTTTCAGTCAGA
Found at i:34720138 original size:31 final size:31
Alignment explanation
Indices: 34720103--34720165 Score: 126
Period size: 31 Copynumber: 2.0 Consensus size: 31
34720093 ACAAGTCAAC
34720103 CACTCCAACCCTTTATTTAGAACCGATACCA
1 CACTCCAACCCTTTATTTAGAACCGATACCA
34720134 CACTCCAACCCTTTATTTAGAACCGATACCA
1 CACTCCAACCCTTTATTTAGAACCGATACCA
34720165 C
1 C
34720166 CAATTCTTCA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
31 32 1.00
ACGTcount: A:0.32, C:0.37, G:0.06, T:0.25
Consensus pattern (31 bp):
CACTCCAACCCTTTATTTAGAACCGATACCA
Found at i:34724332 original size:19 final size:20
Alignment explanation
Indices: 34724310--34724359 Score: 57
Period size: 20 Copynumber: 2.5 Consensus size: 20
34724300 GGGTTTGAGA
34724310 GGAAGTAAAAGTT-TTGGGG
1 GGAAGTAAAAGTTATTGGGG
* * *
34724329 GGAAATAAAATTTATTTGGG
1 GGAAGTAAAAGTTATTGGGG
*
34724349 GAAAGTAAAAG
1 GGAAGTAAAAG
34724360 GGTTTGTTCA
Statistics
Matches: 24, Mismatches: 6, Indels: 1
0.77 0.19 0.03
Matches are distributed among these distances:
19 11 0.46
20 13 0.54
ACGTcount: A:0.42, C:0.00, G:0.32, T:0.26
Consensus pattern (20 bp):
GGAAGTAAAAGTTATTGGGG
Found at i:34724962 original size:14 final size:14
Alignment explanation
Indices: 34724945--34724983 Score: 60
Period size: 14 Copynumber: 2.8 Consensus size: 14
34724935 AATTAATAAA
* *
34724945 TAAAAATAAAATTC
1 TAAAACTAAAAGTC
34724959 TAAAACTAAAAGTC
1 TAAAACTAAAAGTC
34724973 TAAAACTAAAA
1 TAAAACTAAAA
34724984 CTAATACCCT
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:0.64, C:0.10, G:0.03, T:0.23
Consensus pattern (14 bp):
TAAAACTAAAAGTC
Found at i:34728313 original size:24 final size:24
Alignment explanation
Indices: 34728278--34728325 Score: 69
Period size: 24 Copynumber: 2.0 Consensus size: 24
34728268 CTATATCACA
* * *
34728278 TTTGTGCTTAAATTGTAAACTTTT
1 TTTGTGCCTAAAATGAAAACTTTT
34728302 TTTGTGCCTAAAATGAAAACTTTT
1 TTTGTGCCTAAAATGAAAACTTTT
34728326 GAAAGTTTGG
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
24 21 1.00
ACGTcount: A:0.29, C:0.10, G:0.12, T:0.48
Consensus pattern (24 bp):
TTTGTGCCTAAAATGAAAACTTTT
Found at i:34732700 original size:13 final size:13
Alignment explanation
Indices: 34732682--34732709 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
34732672 GATTGGAATC
34732682 CAGTAAGTTAGGA
1 CAGTAAGTTAGGA
34732695 CAGTAAGTTAGGA
1 CAGTAAGTTAGGA
34732708 CA
1 CA
34732710 CAATCTTTTC
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:0.39, C:0.11, G:0.29, T:0.21
Consensus pattern (13 bp):
CAGTAAGTTAGGA
Found at i:34733138 original size:20 final size:20
Alignment explanation
Indices: 34733113--34733150 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
34733103 AAGCAAATAA
34733113 TATATATATATATATGTATG
1 TATATATATATATATGTATG
*
34733133 TATATATGTATATATGTA
1 TATATATATATATATGTA
34733151 AGAGTTTCAA
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:0.39, C:0.00, G:0.11, T:0.50
Consensus pattern (20 bp):
TATATATATATATATGTATG
Found at i:34733148 original size:8 final size:8
Alignment explanation
Indices: 34733112--34733150 Score: 51
Period size: 8 Copynumber: 4.9 Consensus size: 8
34733102 AAAGCAAATA
*
34733112 ATATATAT
1 ATATGTAT
*
34733120 ATATATAT
1 ATATGTAT
*
34733128 GTATGTAT
1 ATATGTAT
34733136 ATATGTAT
1 ATATGTAT
34733144 ATATGTA
1 ATATGTA
34733151 AGAGTTTCAA
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
8 28 1.00
ACGTcount: A:0.41, C:0.00, G:0.10, T:0.49
Consensus pattern (8 bp):
ATATGTAT
Found at i:34734126 original size:11 final size:11
Alignment explanation
Indices: 34734106--34734135 Score: 51
Period size: 11 Copynumber: 2.7 Consensus size: 11
34734096 AAAATAAAAG
34734106 AAAGAAAAACA
1 AAAGAAAAACA
*
34734117 AAATAAAAACA
1 AAAGAAAAACA
34734128 AAAGAAAA
1 AAAGAAAA
34734136 TCAGAAATCA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
11 17 1.00
ACGTcount: A:0.83, C:0.07, G:0.07, T:0.03
Consensus pattern (11 bp):
AAAGAAAAACA
Found at i:34734663 original size:17 final size:17
Alignment explanation
Indices: 34734636--34734672 Score: 58
Period size: 17 Copynumber: 2.2 Consensus size: 17
34734626 GGGCTATTAC
34734636 AATTTATATATT-AAAT
1 AATTTATATATTAAAAT
34734652 AATTTAATATATTAAAAT
1 AATTT-ATATATTAAAAT
34734670 AAT
1 AAT
34734673 GATTATAGTG
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
16 5 0.26
17 7 0.37
18 7 0.37
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (17 bp):
AATTTATATATTAAAAT
Found at i:34739083 original size:168 final size:168
Alignment explanation
Indices: 34738788--34739102 Score: 454
Period size: 168 Copynumber: 1.9 Consensus size: 168
34738778 CAGAATGGGT
* * *
34738788 TTTTGATCTCAGGTAATTTAAAACTCTTATTTACTTAATGGTGTAATTTTGAATTTCATTGGAAA
1 TTTTGATCTCAGATAATTTAAAACTCTTATTTACTTAATGGTGTAAGTCTGAATTTCATTGGAAA
* ** * *
34738853 TTTTAATTTGTTAGAATTTGATCCTCTTAATTTGCAAAAATTGGAAATTTGATCCTGTTTTTGGT
66 CTTTAATTTGTTAGAATTCCATCCTCTTAATTTACAAAAATTGAAAATTTGATCCTGTTTTTGGT
* *
34738918 GCATACATGCACTTGAACAGTTGGTTTTTGCTAATTTG
131 GAATACATGAACTTGAACAGTTGGTTTTTGCTAATTTG
* *
34738956 TTTTGATCTCCGATAGTTTAAAACTCTTATTTACTTAATGGTGTAAGTCTGAATTTCATTGGAAA
1 TTTTGATCTCAGATAATTTAAAACTCTTATTTACTTAATGGTGTAAGTCTGAATTTCATTGGAAA
* * *
34739021 CTTTAATTTGTTAGACTTCCATCCTCTTATTTTATAAAAATTGAAAATTT-AGT-CTGGTTTTTG
66 CTTTAATTTGTTAGAATTCCATCCTCTTAATTTACAAAAATTGAAAATTTGA-TCCT-GTTTTTG
*
34739084 GTGAATATATGAACTTGAA
129 GTGAATACATGAACTTGAA
34739103 TTGTTAATTT
Statistics
Matches: 129, Mismatches: 16, Indels: 4
0.87 0.11 0.03
Matches are distributed among these distances:
167 3 0.02
168 126 0.98
ACGTcount: A:0.29, C:0.11, G:0.15, T:0.45
Consensus pattern (168 bp):
TTTTGATCTCAGATAATTTAAAACTCTTATTTACTTAATGGTGTAAGTCTGAATTTCATTGGAAA
CTTTAATTTGTTAGAATTCCATCCTCTTAATTTACAAAAATTGAAAATTTGATCCTGTTTTTGGT
GAATACATGAACTTGAACAGTTGGTTTTTGCTAATTTG
Found at i:34745971 original size:24 final size:24
Alignment explanation
Indices: 34745938--34745989 Score: 61
Period size: 24 Copynumber: 2.2 Consensus size: 24
34745928 TTTAAATTAA
*
34745938 AAAAATAAAAGAAGTAAAAT-CTT
1 AAAAATAAAAGAAATAAAATACTT
* *
34745961 AAAAATAAAAATAAATCAAATACTT
1 AAAAAT-AAAAGAAATAAAATACTT
34745986 AAAA
1 AAAA
34745990 CTTATTTAAC
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
23 6 0.25
24 11 0.46
25 7 0.29
ACGTcount: A:0.69, C:0.06, G:0.04, T:0.21
Consensus pattern (24 bp):
AAAAATAAAAGAAATAAAATACTT
Found at i:34753619 original size:2 final size:2
Alignment explanation
Indices: 34753594--34753754 Score: 57
Period size: 2 Copynumber: 82.0 Consensus size: 2
34753584 ATTCTTTTTT
* * * * * *
34753594 TA TA TT TA TA TT TA TA TT TA TA TA TA CA TA CA T- TT TCA TA -A
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T-A TA TA
* * * * *
34753635 TA TA TA TG TA CA TG TA TA TA TA TA TA TT TA TA -A CT- TA TT TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA -TA TA TA TA
* * * * * *
34753676 -A TA TA TA CA TA TA TA CTCA TA TT TT TT TA TA T- TT TA TA -A TT
1 TA TA TA TA TA TA TA TA -T-A TA TA TA TA TA TA TA TA TA TA TA TA
* * *
34753717 TA TA TA CA TA TC TA TA TA TA TA TA TA TA TA TC TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
34753755 CATTATTTTT
Statistics
Matches: 114, Mismatches: 34, Indels: 22
0.67 0.20 0.13
Matches are distributed among these distances:
1 7 0.06
2 103 0.90
3 3 0.03
4 1 0.01
ACGTcount: A:0.40, C:0.07, G:0.01, T:0.52
Consensus pattern (2 bp):
TA
Found at i:34754048 original size:3 final size:3
Alignment explanation
Indices: 34754040--34754066 Score: 54
Period size: 3 Copynumber: 9.0 Consensus size: 3
34754030 TTACATGTCC
34754040 ATT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT
34754067 TAAATGCTTT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 24 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
ATT
Found at i:34754679 original size:22 final size:22
Alignment explanation
Indices: 34754636--34754680 Score: 56
Period size: 22 Copynumber: 2.0 Consensus size: 22
34754626 TCGTGGACCA
* *
34754636 AAATCATTGTTTTAATAAAATC
1 AAATCATTGTATTAAAAAAATC
34754658 AAATCATT-TATTAAAAATAATC
1 AAATCATTGTATTAAAAA-AATC
34754680 A
1 A
34754681 TTTTACGAGG
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
21 7 0.35
22 13 0.65
ACGTcount: A:0.51, C:0.09, G:0.02, T:0.38
Consensus pattern (22 bp):
AAATCATTGTATTAAAAAAATC
Found at i:34760349 original size:51 final size:51
Alignment explanation
Indices: 34760252--34760367 Score: 121
Period size: 51 Copynumber: 2.3 Consensus size: 51
34760242 TTATAAAACT
** *
34760252 TATATATATATAAAATACATAATGCATTTATGAAAACAAGGAAAATATA-AA
1 TATATA-ATATAAAATACATAATGCATTTACAAAAAAAAGGAAAATATATAA
* * *
34760303 TATATACATATAAAATATATTCATGCATTTACAAAAAAAATG-AAATATATAA
1 TATATA-ATATAAAATACA-TAATGCATTTACAAAAAAAAGGAAAATATATAA
*
34760355 -ACATAATATAAAA
1 TATATAATATAAAA
34760368 CGTGGAAAAT
Statistics
Matches: 55, Mismatches: 8, Indels: 5
0.81 0.12 0.07
Matches are distributed among these distances:
50 8 0.15
51 28 0.51
52 19 0.35
ACGTcount: A:0.58, C:0.07, G:0.05, T:0.30
Consensus pattern (51 bp):
TATATAATATAAAATACATAATGCATTTACAAAAAAAAGGAAAATATATAA
Found at i:34760634 original size:3 final size:3
Alignment explanation
Indices: 34760626--34760674 Score: 64
Period size: 3 Copynumber: 16.3 Consensus size: 3
34760616 ATATGTAGGT
* *
34760626 ATA ATA ATA ATA ATA ATA ATA TATA AT- ATA ATA ATA ACA AAA ATA
1 ATA ATA ATA ATA ATA ATA ATA -ATA ATA ATA ATA ATA ATA ATA ATA
34760671 ATA A
1 ATA A
34760675 CAAAATTAAT
Statistics
Matches: 41, Mismatches: 3, Indels: 4
0.85 0.06 0.08
Matches are distributed among these distances:
2 2 0.05
3 36 0.88
4 3 0.07
ACGTcount: A:0.67, C:0.02, G:0.00, T:0.31
Consensus pattern (3 bp):
ATA
Found at i:34760675 original size:12 final size:12
Alignment explanation
Indices: 34760655--34760686 Score: 55
Period size: 12 Copynumber: 2.7 Consensus size: 12
34760645 TATATAATAT
34760655 AATAATAACAAA
1 AATAATAACAAA
34760667 AATAATAACAAA
1 AATAATAACAAA
*
34760679 ATTAATAA
1 AATAATAA
34760687 AATAGACTAA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
12 19 1.00
ACGTcount: A:0.72, C:0.06, G:0.00, T:0.22
Consensus pattern (12 bp):
AATAATAACAAA
Found at i:34760684 original size:27 final size:27
Alignment explanation
Indices: 34760625--34760686 Score: 72
Period size: 27 Copynumber: 2.3 Consensus size: 27
34760615 TATATGTAGG
* * * *
34760625 TATAATAATAATAATAATAATATATAA
1 TATAATAATAACAAAAATAATACAAAA
34760652 TATAATAATAACAAAAATAATAACAAAA
1 TATAATAATAACAAAAATAAT-ACAAAA
34760680 T-TAATAA
1 TATAATAA
34760687 AATAGACTAA
Statistics
Matches: 30, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
27 25 0.83
28 5 0.17
ACGTcount: A:0.66, C:0.03, G:0.00, T:0.31
Consensus pattern (27 bp):
TATAATAATAACAAAAATAATACAAAA
Found at i:34760938 original size:19 final size:21
Alignment explanation
Indices: 34760900--34760938 Score: 55
Period size: 19 Copynumber: 2.0 Consensus size: 21
34760890 CCTTTTTTAA
*
34760900 AATCGTAAATAAGTAAAAAAT
1 AATCGTAAATAAGAAAAAAAT
34760921 AATCG-AAA-AAGAAAAAAA
1 AATCGTAAATAAGAAAAAAA
34760939 CAGTAAGCCA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 9 0.53
20 3 0.18
21 5 0.29
ACGTcount: A:0.69, C:0.05, G:0.10, T:0.15
Consensus pattern (21 bp):
AATCGTAAATAAGAAAAAAAT
Found at i:34761161 original size:21 final size:21
Alignment explanation
Indices: 34761135--34761189 Score: 101
Period size: 21 Copynumber: 2.6 Consensus size: 21
34761125 TCATATCTTT
34761135 TAAGATTGTATATATCATATC
1 TAAGATTGTATATATCATATC
*
34761156 TAAGATTGCATATATCATATC
1 TAAGATTGTATATATCATATC
34761177 TAAGATTGTATAT
1 TAAGATTGTATAT
34761190 CCTCGAAAAT
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
21 32 1.00
ACGTcount: A:0.38, C:0.09, G:0.11, T:0.42
Consensus pattern (21 bp):
TAAGATTGTATATATCATATC
Found at i:34761168 original size:19 final size:20
Alignment explanation
Indices: 34761110--34761184 Score: 78
Period size: 21 Copynumber: 3.5 Consensus size: 20
34761100 AAATTAAATC
* *
34761110 TCTAAGATTACAAAATCATA
1 TCTAAGATTGCAATATCATA
*
34761130 TCTTTTAAGATTGTATATATCATA
1 TC---TAAGATTGCA-ATATCATA
34761154 TCTAAGATTGCATATATCATA
1 TCTAAGATTGCA-ATATCATA
34761175 TCTAAGATTG
1 TCTAAGATTG
34761185 TATATCCTCG
Statistics
Matches: 47, Mismatches: 4, Indels: 7
0.81 0.07 0.12
Matches are distributed among these distances:
20 2 0.04
21 28 0.60
23 8 0.17
24 9 0.19
ACGTcount: A:0.39, C:0.12, G:0.09, T:0.40
Consensus pattern (20 bp):
TCTAAGATTGCAATATCATA
Found at i:34763559 original size:29 final size:29
Alignment explanation
Indices: 34763504--34763573 Score: 70
Period size: 29 Copynumber: 2.4 Consensus size: 29
34763494 ATATTTAAAG
* * * *
34763504 AAATAAATGT-ATTAATTTATTTTTATATT
1 AAATAAATATAATT-ATTTATGTATATAAT
*
34763533 AAATGAATATAATTATTTATGTATATAAT
1 AAATAAATATAATTATTTATGTATATAAT
*
34763562 ATATAAATATAA
1 AAATAAATATAA
34763574 AATGATGTTA
Statistics
Matches: 33, Mismatches: 7, Indels: 2
0.79 0.17 0.05
Matches are distributed among these distances:
29 30 0.91
30 3 0.09
ACGTcount: A:0.49, C:0.00, G:0.04, T:0.47
Consensus pattern (29 bp):
AAATAAATATAATTATTTATGTATATAAT
Found at i:34767953 original size:47 final size:47
Alignment explanation
Indices: 34767884--34767977 Score: 179
Period size: 47 Copynumber: 2.0 Consensus size: 47
34767874 AAGACAACAG
*
34767884 AATGTATGAATTATTTAATAAAATGAGTAGGAGCTGTGGCATGTCCA
1 AATGTATGAAGTATTTAATAAAATGAGTAGGAGCTGTGGCATGTCCA
34767931 AATGTATGAAGTATTTAATAAAATGAGTAGGAGCTGTGGCATGTCCA
1 AATGTATGAAGTATTTAATAAAATGAGTAGGAGCTGTGGCATGTCCA
34767978 TCAAACTTCC
Statistics
Matches: 46, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
47 46 1.00
ACGTcount: A:0.36, C:0.09, G:0.24, T:0.31
Consensus pattern (47 bp):
AATGTATGAAGTATTTAATAAAATGAGTAGGAGCTGTGGCATGTCCA
Found at i:34772080 original size:29 final size:30
Alignment explanation
Indices: 34772038--34772095 Score: 84
Period size: 29 Copynumber: 2.0 Consensus size: 30
34772028 TTTTTGAAAA
*
34772038 TTTAAAAATTTTAAAAATA-TATAAAATTAG
1 TTTAAAAATATTAAAAA-AGTATAAAATTAG
34772068 TTTAAAAA-ATTAAAAAAGTATAAAATTA
1 TTTAAAAATATTAAAAAAGTATAAAATTA
34772096 TAAAAATATT
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
28 1 0.04
29 17 0.65
30 8 0.31
ACGTcount: A:0.60, C:0.00, G:0.03, T:0.36
Consensus pattern (30 bp):
TTTAAAAATATTAAAAAAGTATAAAATTAG
Found at i:34773149 original size:21 final size:21
Alignment explanation
Indices: 34773125--34773165 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
34773115 TAACGAGACC
*
34773125 GCTGATGTGGCAAGTTAACTA
1 GCTGACGTGGCAAGTTAACTA
*
34773146 GCTGACGTGGCCAGTTAACT
1 GCTGACGTGGCAAGTTAACT
34773166 TACCACATTG
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.24, C:0.20, G:0.29, T:0.27
Consensus pattern (21 bp):
GCTGACGTGGCAAGTTAACTA
Found at i:34774083 original size:38 final size:39
Alignment explanation
Indices: 34774017--34774093 Score: 147
Period size: 38 Copynumber: 2.0 Consensus size: 39
34774007 TAAAAGGTTT
34774017 ACATTGGTGCTGATAGGGTTGTTTATCCTCTTCTTCTTC
1 ACATTGGTGCTGATAGGGTTGTTTATCCTCTTCTTCTTC
34774056 ACATTGGTGCTGAT-GGGTTGTTTATCCTCTTCTTCTTC
1 ACATTGGTGCTGATAGGGTTGTTTATCCTCTTCTTCTTC
34774094 TTCTTCTCTT
Statistics
Matches: 38, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
38 24 0.63
39 14 0.37
ACGTcount: A:0.12, C:0.21, G:0.21, T:0.47
Consensus pattern (39 bp):
ACATTGGTGCTGATAGGGTTGTTTATCCTCTTCTTCTTC
Found at i:34777337 original size:28 final size:28
Alignment explanation
Indices: 34777283--34777337 Score: 76
Period size: 28 Copynumber: 2.0 Consensus size: 28
34777273 AGTCCTAAAA
*
34777283 GTTGGATAACCAATTAAGTATAATATTG
1 GTTGGATAACCAATTAAGAATAATATTG
*
34777311 GTTGGATAACCAAATTAA-AATAGTATT
1 GTTGGATAACC-AATTAAGAATAATATT
34777338 AATCGAATTA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
28 18 0.75
29 6 0.25
ACGTcount: A:0.42, C:0.07, G:0.16, T:0.35
Consensus pattern (28 bp):
GTTGGATAACCAATTAAGAATAATATTG
Found at i:34782490 original size:56 final size:57
Alignment explanation
Indices: 34782369--34782492 Score: 171
Period size: 56 Copynumber: 2.2 Consensus size: 57
34782359 GCCATGTCCC
* * * * *
34782369 AGCCCGTGTGAATATATTGACTTAGGACACACAGCCAAGCCACACGCTCGTGTGCTA
1 AGCCCGTGTGAGTATACTAACTTAGGACACACAGCCAAACCACACGCCCGTGTGCTA
* *
34782426 AG-CAGTGTGAGTATACTAACTTAGGTCACACAGCCAAACCACACGCCCGTGTGCT-
1 AGCCCGTGTGAGTATACTAACTTAGGACACACAGCCAAACCACACGCCCGTGTGCTA
34782481 AGCCCGTGTGAG
1 AGCCCGTGTGAG
34782493 CAATTTGAGC
Statistics
Matches: 58, Mismatches: 8, Indels: 3
0.84 0.12 0.04
Matches are distributed among these distances:
55 2 0.03
56 54 0.93
57 2 0.03
ACGTcount: A:0.27, C:0.28, G:0.24, T:0.20
Consensus pattern (57 bp):
AGCCCGTGTGAGTATACTAACTTAGGACACACAGCCAAACCACACGCCCGTGTGCTA
Found at i:34783563 original size:25 final size:25
Alignment explanation
Indices: 34783524--34783640 Score: 119
Period size: 25 Copynumber: 4.7 Consensus size: 25
34783514 CATATAAACG
* * *
34783524 GGAAGCTCTTCCGAGCTATATAACA
1 GGAAGCTCATGCGAGCTAAATAACA
* *
34783549 GGAAGCTTATGCGAGCTAAAAAAC-
1 GGAAGCTCATGCGAGCTAAATAACA
* ** *
34783573 GGAAAGCTCATGCGAGTTGTATATCA
1 GG-AAGCTCATGCGAGCTAAATAACA
*
34783599 GGAAGCTCATGCGAGCTAAATATCA
1 GGAAGCTCATGCGAGCTAAATAACA
*
34783624 GGAAGCTCATGAGAGCT
1 GGAAGCTCATGCGAGCT
34783641 GTGGTGTGTC
Statistics
Matches: 75, Mismatches: 15, Indels: 4
0.80 0.16 0.04
Matches are distributed among these distances:
24 2 0.03
25 71 0.95
26 2 0.03
ACGTcount: A:0.34, C:0.19, G:0.26, T:0.21
Consensus pattern (25 bp):
GGAAGCTCATGCGAGCTAAATAACA
Found at i:34783601 original size:50 final size:50
Alignment explanation
Indices: 34783519--34783618 Score: 137
Period size: 50 Copynumber: 2.0 Consensus size: 50
34783509 ATGAGCATAT
* * *
34783519 AAACGGGAAGCTCTTCCGAGCTATATAACAGGAAGCTTATGCGAGCTAAA
1 AAACGGAAAGCTCATCCGAGCTATATAACAGGAAGCTCATGCGAGCTAAA
* * * *
34783569 AAACGGAAAGCTCATGCGAGTTGTATATCAGGAAGCTCATGCGAGCTAAA
1 AAACGGAAAGCTCATCCGAGCTATATAACAGGAAGCTCATGCGAGCTAAA
34783619 TATCAGGAAG
Statistics
Matches: 43, Mismatches: 7, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
50 43 1.00
ACGTcount: A:0.36, C:0.19, G:0.25, T:0.20
Consensus pattern (50 bp):
AAACGGAAAGCTCATCCGAGCTATATAACAGGAAGCTCATGCGAGCTAAA
Found at i:34783630 original size:50 final size:49
Alignment explanation
Indices: 34783519--34783640 Score: 136
Period size: 50 Copynumber: 2.4 Consensus size: 49
34783509 ATGAGCATAT
* * *
34783519 AAACGGGAAGCTCTTCCGAGCTATATAACAGGAAGCTTATGCGAGCTAAA
1 AAAC-GGAAGCTCATGCGAGCTATATAACAGGAAGCTCATGCGAGCTAAA
* * *
34783569 AAACGGAAAGCTCATGCGAGTTGTATATCAGGAAGCTCATGCGAGCTAAA
1 AAACGG-AAGCTCATGCGAGCTATATAACAGGAAGCTCATGCGAGCTAAA
* * *
34783619 TATCAGGAAGCTCATGAGAGCT
1 AAAC-GGAAGCTCATGCGAGCT
34783641 GTGGTGTGTC
Statistics
Matches: 60, Mismatches: 10, Indels: 4
0.81 0.14 0.05
Matches are distributed among these distances:
49 2 0.03
50 56 0.93
51 2 0.03
ACGTcount: A:0.35, C:0.19, G:0.25, T:0.20
Consensus pattern (49 bp):
AAACGGAAGCTCATGCGAGCTATATAACAGGAAGCTCATGCGAGCTAAA
Found at i:34786729 original size:25 final size:25
Alignment explanation
Indices: 34786654--34786761 Score: 108
Period size: 25 Copynumber: 4.3 Consensus size: 25
34786644 GGTCACCGAT
** * *
34786654 TTCAGCTCTTATGAGCTTCCTGATA
1 TTCAGCTCGCATGAGCTTCCCGTTA
* *
34786679 CTCAGCTCGCATGAGCTTCCTGTTA
1 TTCAGCTCGCATGAGCTTCCCGTTA
* * *
34786704 TTTAGCTCGTATGAGCTTCCCATTA
1 TTCAGCTCGCATGAGCTTCCCGTTA
* * *
34786729 TTCAGCTCACACGAGCTTTCCGTTA
1 TTCAGCTCGCATGAGCTTCCCGTTA
34786754 TTCAGCTC
1 TTCAGCTC
34786762 AGAGGAGCTT
Statistics
Matches: 68, Mismatches: 15, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
25 68 1.00
ACGTcount: A:0.19, C:0.29, G:0.17, T:0.36
Consensus pattern (25 bp):
TTCAGCTCGCATGAGCTTCCCGTTA
Found at i:34786734 original size:50 final size:50
Alignment explanation
Indices: 34786652--34786761 Score: 125
Period size: 50 Copynumber: 2.2 Consensus size: 50
34786642 AGGGTCACCG
* * * *
34786652 ATTTCAGCTCTTATGAGCTTCCTGATACTCAGCTCGCATGAGC-TTCCTGTT
1 ATTT-AGCTCGTATGAGCTTCCTCATACTCAGCTCACACGAGCTTTCC-GTT
*
34786703 ATTTAGCTCGTATGAGCTTCC-CATTATTCAGCTCACACGAGCTTTCCGTT
1 ATTTAGCTCGTATGAGCTTCCTCA-TACTCAGCTCACACGAGCTTTCCGTT
*
34786753 ATTCAGCTC
1 ATTTAGCTC
34786762 AGAGGAGCTT
Statistics
Matches: 51, Mismatches: 6, Indels: 5
0.82 0.10 0.08
Matches are distributed among these distances:
49 1 0.02
50 42 0.82
51 8 0.16
ACGTcount: A:0.19, C:0.28, G:0.16, T:0.36
Consensus pattern (50 bp):
ATTTAGCTCGTATGAGCTTCCTCATACTCAGCTCACACGAGCTTTCCGTT
Found at i:34786762 original size:25 final size:25
Alignment explanation
Indices: 34786654--34786777 Score: 90
Period size: 25 Copynumber: 5.0 Consensus size: 25
34786644 GGTCACCGAT
** *
34786654 TTCAGCTCTTATGAGC-TTCCTGATA
1 TTCAGCTCACATGAGCTTTCC-GTTA
* *
34786679 CTCAGCTCGCATGAGC-TTCCTGTTA
1 TTCAGCTCACATGAGCTTTCC-GTTA
* ** * *
34786704 TTTAGCTCGTATGAGCTTCCCATTA
1 TTCAGCTCACATGAGCTTTCCGTTA
*
34786729 TTCAGCTCACACGAGCTTTCCGTTA
1 TTCAGCTCACATGAGCTTTCCGTTA
* * *
34786754 TTCAGCTCAGAGGAGCTTACCGTT
1 TTCAGCTCACATGAGCTTTCCGTT
34786778 TATAGCTCGT
Statistics
Matches: 80, Mismatches: 18, Indels: 2
0.80 0.18 0.02
Matches are distributed among these distances:
25 77 0.96
26 3 0.04
ACGTcount: A:0.19, C:0.27, G:0.19, T:0.35
Consensus pattern (25 bp):
TTCAGCTCACATGAGCTTTCCGTTA
Found at i:34787497 original size:2 final size:2
Alignment explanation
Indices: 34787490--34787600 Score: 195
Period size: 2 Copynumber: 55.5 Consensus size: 2
34787480 TCAAACATAA
*
34787490 AC AC AC AC AC AC AC AC AC AC AT AC AC AC AC AC AC AC AC AC AC
1 AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC
* *
34787532 AC GC AC AC AC AC AC AC GC AC AC AC AC AC AC AC AC AC AC AC AC
1 AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC
34787574 AC AC AC AC AC AC AC AC AC AC AC AC AC A
1 AC AC AC AC AC AC AC AC AC AC AC AC AC A
34787601 TATATATAAC
Statistics
Matches: 103, Mismatches: 6, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 103 1.00
ACGTcount: A:0.49, C:0.49, G:0.02, T:0.01
Consensus pattern (2 bp):
AC
Found at i:34788214 original size:40 final size:40
Alignment explanation
Indices: 34788164--34788303 Score: 133
Period size: 40 Copynumber: 3.5 Consensus size: 40
34788154 AACACACCAG
* *
34788164 TTTGGCACCCAGTGCCTCATCGGATAATTCAAAGTAATAA
1 TTTGACACCCAGTGCCTCATCGGATAATTCGAAGTAATAA
* * *
34788204 TTTGACACCCAGTGTCTCATCGGCTAAATCGAAGT-A-AA
1 TTTGACACCCAGTGCCTCATCGGATAATTCGAAGTAATAA
* ** ** *
34788242 -TTGGCACATAGTGCCTCATCAAATATATCCGAAGTAATAA
1 TTTGACACCCAGTGCCTCATCGGATA-ATTCGAAGTAATAA
* *
34788282 ATTGACACCCAGTGTCTCATCG
1 TTTGACACCCAGTGCCTCATCG
34788304 ACTCAATGTC
Statistics
Matches: 77, Mismatches: 19, Indels: 7
0.75 0.18 0.07
Matches are distributed among these distances:
37 18 0.23
38 9 0.12
39 2 0.03
40 32 0.42
41 16 0.21
ACGTcount: A:0.32, C:0.24, G:0.17, T:0.27
Consensus pattern (40 bp):
TTTGACACCCAGTGCCTCATCGGATAATTCGAAGTAATAA
Found at i:34789246 original size:5 final size:4
Alignment explanation
Indices: 34789231--34789295 Score: 51
Period size: 4 Copynumber: 15.0 Consensus size: 4
34789221 CTTTCTATTC
*
34789231 TTTA TTTA TTTCA TTTA CTTA TTTA TTTTA TTATA TTTA CTTTA -TTA
1 TTTA TTTA TTT-A TTTA TTTA TTTA -TTTA TT-TA TTTA -TTTA TTTA
*
34789278 TTATA TTATA TATA TTTA
1 TT-TA TT-TA TTTA TTTA
34789296 CTTAAATATT
Statistics
Matches: 51, Mismatches: 4, Indels: 12
0.76 0.06 0.18
Matches are distributed among these distances:
3 3 0.06
4 24 0.47
5 24 0.47
ACGTcount: A:0.29, C:0.05, G:0.00, T:0.66
Consensus pattern (4 bp):
TTTA
Found at i:34789246 original size:9 final size:8
Alignment explanation
Indices: 34789231--34789295 Score: 51
Period size: 9 Copynumber: 7.5 Consensus size: 8
34789221 CTTTCTATTC
34789231 TTTATTTA
1 TTTATTTA
34789239 TTTCATTTA
1 TTT-ATTTA
*
34789248 CTTATTTA
1 TTTATTTA
34789256 TTTTATTATA
1 -TTTATT-TA
34789266 TTTACTTTA
1 TTTA-TTTA
34789275 -TTATTATA
1 TTTATT-TA
*
34789283 TTATATATA
1 TT-TATTTA
34789292 TTTA
1 TTTA
34789296 CTTAAATATT
Statistics
Matches: 47, Mismatches: 3, Indels: 14
0.73 0.05 0.22
Matches are distributed among these distances:
7 2 0.04
8 15 0.32
9 23 0.49
10 7 0.15
ACGTcount: A:0.29, C:0.05, G:0.00, T:0.66
Consensus pattern (8 bp):
TTTATTTA
Found at i:34789268 original size:22 final size:23
Alignment explanation
Indices: 34789231--34789299 Score: 72
Period size: 22 Copynumber: 3.0 Consensus size: 23
34789221 CTTTCTATTC
34789231 TTTA-TTTATT-TCATTTACTTA-
1 TTTATTTTATTAT-ATTTACTTAT
34789252 TTTATTTTATTATATTTACTTTAT
1 TTTATTTTATTATATTTAC-TTAT
*
34789276 TATTATATTATATATATTTACTTA
1 T-TTATTTTAT-TATATTTACTTA
34789300 AATATTAAGT
Statistics
Matches: 41, Mismatches: 1, Indels: 8
0.82 0.02 0.16
Matches are distributed among these distances:
21 4 0.10
22 12 0.29
23 4 0.10
24 1 0.02
25 11 0.27
26 9 0.22
ACGTcount: A:0.29, C:0.06, G:0.00, T:0.65
Consensus pattern (23 bp):
TTTATTTTATTATATTTACTTAT
Found at i:34789269 original size:14 final size:14
Alignment explanation
Indices: 34789250--34789295 Score: 51
Period size: 14 Copynumber: 3.4 Consensus size: 14
34789240 TTCATTTACT
34789250 TATTTATTTTATTA
1 TATTTATTTTATTA
*
34789264 TATTTACTTTATTA
1 TATTTATTTTATTA
* *
34789278 T-TATATTATA-TA
1 TATTTATTTTATTA
34789290 TATTTA
1 TATTTA
34789296 CTTAAATATT
Statistics
Matches: 26, Mismatches: 5, Indels: 3
0.76 0.15 0.09
Matches are distributed among these distances:
12 3 0.12
13 9 0.35
14 14 0.54
ACGTcount: A:0.33, C:0.02, G:0.00, T:0.65
Consensus pattern (14 bp):
TATTTATTTTATTA
Found at i:34789295 original size:26 final size:27
Alignment explanation
Indices: 34789244--34789298 Score: 78
Period size: 26 Copynumber: 2.1 Consensus size: 27
34789234 ATTTATTTCA
*
34789244 TTTACTTATTTATTTTATTATATTTAC
1 TTTACTTATTTATTATATTATATTTAC
34789271 TTTA-TTATTATATTATA-TATATTTAC
1 TTTACTTATT-TATTATATTATATTTAC
34789297 TT
1 TT
34789299 AAATATTAAG
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
26 16 0.62
27 10 0.38
ACGTcount: A:0.29, C:0.05, G:0.00, T:0.65
Consensus pattern (27 bp):
TTTACTTATTTATTATATTATATTTAC
Found at i:34789305 original size:26 final size:25
Alignment explanation
Indices: 34789253--34789306 Score: 72
Period size: 26 Copynumber: 2.1 Consensus size: 25
34789243 ATTTACTTAT
* * *
34789253 TTATTTTATTATATTTACTTTATTA
1 TTATATTATTATATTTACTTAAATA
34789278 TTATATTATATATATTTACTTAAATA
1 TTATATTAT-TATATTTACTTAAATA
34789304 TTA
1 TTA
34789307 AGTAATACAT
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
25 8 0.32
26 17 0.68
ACGTcount: A:0.35, C:0.04, G:0.00, T:0.61
Consensus pattern (25 bp):
TTATATTATTATATTTACTTAAATA
Found at i:34789318 original size:26 final size:26
Alignment explanation
Indices: 34789263--34789320 Score: 64
Period size: 26 Copynumber: 2.2 Consensus size: 26
34789253 TTATTTTATT
* * * *
34789263 ATATTTACTTTATTATTATATTATAT
1 ATATTTACTTAAATATTATATAATAC
34789289 ATATTTACTTAAATATTA-AGTAATAC
1 ATATTTACTTAAATATTATA-TAATAC
34789315 ATATTT
1 ATATTT
34789321 TATTAATATA
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
25 1 0.04
26 26 0.96
ACGTcount: A:0.40, C:0.05, G:0.02, T:0.53
Consensus pattern (26 bp):
ATATTTACTTAAATATTATATAATAC
Found at i:34791261 original size:44 final size:44
Alignment explanation
Indices: 34791212--34792053 Score: 476
Period size: 45 Copynumber: 18.4 Consensus size: 44
34791202 AAAGATGAGA
* *
34791212 TTCAGGGAGATAAGATTAGTAGCTTCAA-CTTGCTCCACTGTAAC
1 TTCAGGGAGATAAGATTTGTAGCTTCAATC-TGCTCCACTGCAAC
* * *
34791256 TTCAGGGGGATAAGATAAGTAACTTGTAGCTTTAATCTGTTCCACTGCAA-
1 TTCA--GGG---AGATAAG--ATTTGTAGCTTCAATCTGCTCCACTGCAAC
* * * * * **
34791306 TTTAGGGAAATAAGATTCGTTGTCTTCAATCTGCTCTACTATAAC
1 TTCAGGGAGATAAGATTTGTAG-CTTCAATCTGCTCCACTGCAAC
* * *
34791351 TTCAGGGAGATAAGATTTGCTATGGCACATTTAATCTGAC-CCATTGTAAC
1 TTCAGGGAGATAAGATTTG-TA--G--C-TTCAATCTG-CTCCACTGCAAC
* * * * ** *
34791401 TTCAGAGG-TATAGGA-TT-TAGTTTCAATCTACTCTGCTGGAAC
1 TTCAG-GGAGATAAGATTTGTAGCTTCAATCTGCTCCACTGCAAC
* *
34791443 TTCAGGGAGATACA-ATTTGTAGCTTTAATCTGCTCCACTGTAAC
1 TTCAGGGAGATA-AGATTTGTAGCTTCAATCTGCTCCACTGCAAC
** ** *
34791487 TTCAGGGTTATAAGATTTGCTATTTTCAATCTGCTCCACCGCAAC
1 TTCAGGGAGATAAGATTTG-TAGCTTCAATCTGCTCCACTGCAAC
* * * **
34791532 TTTAGGGAAATAAGATTTTCTATTTTCAATCTGCTCCACTGCAAC
1 TTCAGGGAGATAAGA-TTTGTAGCTTCAATCTGCTCCACTGCAAC
* * ** *
34791577 TTCAGGGAGATAAAGTTTGTAACTTGTAGCTTTAATCTTTTCCACGGCAAC
1 TTCAGGGAGAT-AA----G--ATTTGTAGCTTCAATCTGCTCCACTGCAAC
* * ** *
34791628 TTCAGGGAAATAAGATTCGCTATATTCAATCTGCTCCACTACAAC
1 TTCAGGGAGATAAGATTTG-TAGCTTCAATCTGCTCCACTGCAAC
* *
34791673 TTCAGGGAGATGAGATTTGTAGCTTCAATCTGCTCCATTGCAAC
1 TTCAGGGAGATAAGATTTGTAGCTTCAATCTGCTCCACTGCAAC
* * * *
34791717 TTCAAGGAGATAAGATTTGTAACTTGTAGCTTTAATCTGTTCCACTACAAC
1 TTCAGGGAGATAAGA----T---TTGTAGCTTCAATCTGCTCCACTGCAAC
** * * * *
34791768 TTTTGGGAAATAAGATTTGCTATCTAT-AATCTGTTCCACTGCAAG
1 TTCAGGGAGATAAGATTTG-TAGCT-TCAATCTGCTCCACTGCAAC
* ** * * *
34791813 TTCATGGAGATAAGATTCACTATCTTCAATCTGCTTCACTTCAAC
1 TTCAGGGAGATAAGATT-TGTAGCTTCAATCTGCTCCACTGCAAC
* * ** * *
34791858 TTTAGAGAGATAAGATTTGCTATATTCAATCTGATCCACTGTAAC
1 TTCAGGGAGATAAGATTTG-TAGCTTCAATCTGCTCCACTGCAAC
* * ** * *
34791903 TTCAGGGAAATAAGATTTTCTATTTTCAATCTGCTCTACTGTAAC
1 TTCAGGGAGATAAGA-TTTGTAGCTTCAATCTGCTCCACTGCAAC
* * * * * * * *
34791948 TTTAAGGTGATAAGATTTTTTTGTTTTAATCTGCTCCTCTGCAAC
1 TTCAGGGAGATAAGA-TTTGTAGCTTCAATCTGCTCCACTGCAAC
* * * * *
34791993 TTTAGGGAGATAAGATTTATGGCTTTAATCTGCTCCACTCCAAC
1 TTCAGGGAGATAAGATTTGTAGCTTCAATCTGCTCCACTGCAAC
34792037 TTCAGGGAGATAAGATT
1 TTCAGGGAGATAAGATT
34792054 CACCACGATG
Statistics
Matches: 613, Mismatches: 139, Indels: 92
0.73 0.16 0.11
Matches are distributed among these distances:
41 3 0.00
42 22 0.04
43 8 0.01
44 135 0.22
45 289 0.47
46 14 0.02
47 3 0.00
48 5 0.01
49 10 0.02
50 31 0.05
51 91 0.15
52 2 0.00
ACGTcount: A:0.29, C:0.19, G:0.17, T:0.35
Consensus pattern (44 bp):
TTCAGGGAGATAAGATTTGTAGCTTCAATCTGCTCCACTGCAAC
Found at i:34791760 original size:140 final size:140
Alignment explanation
Indices: 34791459--34792053 Score: 567
Period size: 140 Copynumber: 4.3 Consensus size: 140
34791449 GAGATACAAT
* **
34791459 TTGTAGCTTTAATCTGCTCCACTGTAACTTCAGGGTTATAAGATTTGCTATTTTCAATCTGCTCC
1 TTGTAGCTTTAATCTGCTCCACTGCAACTTCAGGGAAATAAGATTTGCTATTTTCAATCTGCTCC
* * * ** * *
34791524 ACCGCAACTTTAGGGAAATAAGATTTTCTATTTTCAATCTGCTCCACTGCAACTTCAGGGAGATA
66 ACTGCAACTTCAGGGAGATAAGATTTTCTAGCTTCAATCTGCTCCATTGCAACTTCAAGGAGATA
34791589 A-AGTTTGTAAC
131 AGA-TTTGT-AC
** * * *
34791600 TTGTAGCTTTAATCTTTTCCACGGCAACTTCAGGGAAATAAGATTCGCTATATTCAATCTGCTCC
1 TTGTAGCTTTAATCTGCTCCACTGCAACTTCAGGGAAATAAGATTTGCTATTTTCAATCTGCTCC
* * *
34791665 ACTACAACTTCAGGGAGATGAGA-TTTGTAGCTTCAATCTGCTCCATTGCAACTTCAAGGAGATA
66 ACTGCAACTTCAGGGAGATAAGATTTTCTAGCTTCAATCTGCTCCATTGCAACTTCAAGGAGATA
34791729 AGATTTGTAAC
131 AGATTTGT-AC
* * ** * *
34791740 TTGTAGCTTTAATCTGTTCCACTACAACTTTTGGGAAATAAGATTTGCTATCTAT-AATCTGTTC
1 TTGTAGCTTTAATCTGCTCCACTGCAACTTCAGGGAAATAAGATTTGCTAT-TTTCAATCTGCTC
* * ** * * *
34791804 CACTGCAAGTTCATGGAGATAAGATTCACTATCTTCAATCTGCTTCACTT-CAACTT-TAGAGAG
65 CACTGCAACTTCAGGGAGATAAGATTTTCTAGCTTCAATCTGCTCCA-TTGCAACTTCAAG-GAG
34791867 ATAAGATTTG--C
128 ATAAGATTTGTAC
* * * * * *
34791878 -TATA--TTCAATCTGATCCACTGTAACTTCAGGGAAATAAGATTTTCTATTTTCAATCTGCTCT
1 TTGTAGCTTTAATCTGCTCCACTGCAACTTCAGGGAAATAAGATTTGCTATTTTCAATCTGCTCC
* * * * * * * * * *
34791940 ACTGTAACTTTAAGGTGATAAGATTTTTTTGTTTTAATCTGCTCC-TCTGCAACTTTAGGGAGAT
66 ACTGCAACTTCAGGGAGATAAGATTTTCTAGCTTCAATCTGCTCCAT-TGCAACTTCAAGGAGAT
34792004 AAGA-TT-TA-
130 AAGATTTGTAC
* *
34792012 -TG--GCTTTAATCTGCTCCACTCCAACTTCAGGGAGATAAGATT
1 TTGTAGCTTTAATCTGCTCCACTGCAACTTCAGGGAAATAAGATT
34792054 CACCACGATG
Statistics
Matches: 372, Mismatches: 69, Indels: 33
0.78 0.15 0.07
Matches are distributed among these distances:
133 1 0.00
134 39 0.10
135 92 0.25
136 1 0.00
137 3 0.01
138 1 0.00
140 120 0.32
141 113 0.30
142 2 0.01
ACGTcount: A:0.28, C:0.19, G:0.16, T:0.36
Consensus pattern (140 bp):
TTGTAGCTTTAATCTGCTCCACTGCAACTTCAGGGAAATAAGATTTGCTATTTTCAATCTGCTCC
ACTGCAACTTCAGGGAGATAAGATTTTCTAGCTTCAATCTGCTCCATTGCAACTTCAAGGAGATA
AGATTTGTAC
Found at i:34791781 original size:51 final size:51
Alignment explanation
Indices: 34791689--34791786 Score: 124
Period size: 51 Copynumber: 1.9 Consensus size: 51
34791679 GAGATGAGAT
* * *
34791689 TTGTAGCTTCAATCTGCTCCATTGCAACTTCAAGGAGATAAGATTTGTAAC
1 TTGTAGCTTCAATCTGCTCCACTACAACTTCAAGGAAATAAGATTTGTAAC
* * ***
34791740 TTGTAGCTTTAATCTGTTCCACTACAACTTTTGGGAAATAAGATTTG
1 TTGTAGCTTCAATCTGCTCCACTACAACTTCAAGGAAATAAGATTTG
34791787 CTATCTATAA
Statistics
Matches: 39, Mismatches: 8, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
51 39 1.00
ACGTcount: A:0.29, C:0.17, G:0.17, T:0.37
Consensus pattern (51 bp):
TTGTAGCTTCAATCTGCTCCACTACAACTTCAAGGAAATAAGATTTGTAAC
Found at i:34800883 original size:15 final size:16
Alignment explanation
Indices: 34800863--34800896 Score: 52
Period size: 16 Copynumber: 2.2 Consensus size: 16
34800853 TTATTATTTA
34800863 TTTTTGGTT-TTTATT
1 TTTTTGGTTATTTATT
*
34800878 TTTTTGTTTATTTATT
1 TTTTTGGTTATTTATT
34800894 TTT
1 TTT
34800897 GATTTTGGGC
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
15 8 0.47
16 9 0.53
ACGTcount: A:0.09, C:0.00, G:0.09, T:0.82
Consensus pattern (16 bp):
TTTTTGGTTATTTATT
Found at i:34800897 original size:14 final size:14
Alignment explanation
Indices: 34800856--34800897 Score: 50
Period size: 14 Copynumber: 2.9 Consensus size: 14
34800846 TTGGGTTTTA
34800856 TTATTTATTTTTGGT
1 TTATTTATTTTT-GT
*
34800871 TT-TTATTTTTTTGT
1 TTATT-TATTTTTGT
34800885 TTATTTATTTTTG
1 TTATTTATTTTTG
34800898 ATTTTGGGCT
Statistics
Matches: 23, Mismatches: 2, Indels: 5
0.77 0.07 0.17
Matches are distributed among these distances:
14 13 0.57
15 10 0.43
ACGTcount: A:0.12, C:0.00, G:0.10, T:0.79
Consensus pattern (14 bp):
TTATTTATTTTTGT
Found at i:34801513 original size:165 final size:163
Alignment explanation
Indices: 34801222--34801519 Score: 359
Period size: 165 Copynumber: 1.8 Consensus size: 163
34801212 AAAAAAAATC
34801222 TATCATGACGAATTTGAATGAATATTTTAAGAAAAAATTCACAACAATATTTTCAATGTTATTTT
1 TATCATGACGAATTTGAATGAATATTTTAAGAAAAAATTCACAACAATATTTTCAATGTTATTTT
* * * * * * *
34801287 TATTGCAACATGAATATCAAGTGAATATTTTTTTATTTAAAATTTTAAACCAATGAATTTAATAG
66 TATTACAACATAAATATCAAATAAATATTTTTTTATTTAAAATATCAAACCAATAAATTTAATAG
34801352 AAAGATTTTAATAGTGGTTCCAAAAAATTATTT
131 AAAGATTTTAATAGTGGTTCCAAAAAATTATTT
* * * *
34801385 TATCATGATGAATTTGAAT-AATAATTTTTAAGCAAAAAA-TCTACAATAATATTTTTATTGTTA
1 TATCATGACGAATTTGAATGAAT-A-TTTTAAG-AAAAAATTC-ACAACAATATTTTCAATGTTA
*** * * ***
34801448 TTTTTATTATTTCTTAAATATTAAATAAATA-TTTTTTATTTTAAAATATCACGTCAATAAATTT
62 TTTTTATTACAACATAAATATCAAATAAATATTTTTTTA-TTTAAAATATCAAACCAATAAATTT
34801512 AATAGAAA
126 AATAGAAA
34801520 TATTCTAACA
Statistics
Matches: 111, Mismatches: 19, Indels: 8
0.80 0.14 0.06
Matches are distributed among these distances:
162 3 0.03
163 19 0.17
164 16 0.14
165 73 0.66
ACGTcount: A:0.42, C:0.07, G:0.08, T:0.43
Consensus pattern (163 bp):
TATCATGACGAATTTGAATGAATATTTTAAGAAAAAATTCACAACAATATTTTCAATGTTATTTT
TATTACAACATAAATATCAAATAAATATTTTTTTATTTAAAATATCAAACCAATAAATTTAATAG
AAAGATTTTAATAGTGGTTCCAAAAAATTATTT
Found at i:34818420 original size:2 final size:2
Alignment explanation
Indices: 34818413--34818448 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
34818403 TAATGAAACC
34818413 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
34818449 CTGCATTAAG
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:34820938 original size:28 final size:28
Alignment explanation
Indices: 34820904--34820977 Score: 121
Period size: 28 Copynumber: 2.6 Consensus size: 28
34820894 TTTTACTCTG
*
34820904 AACCTTGAATATTGAACCTTAAACTCCA
1 AACCTTGAACATTGAACCTTAAACTCCA
*
34820932 ACCCTTGAACATTGAACCTTAAACTCCA
1 AACCTTGAACATTGAACCTTAAACTCCA
*
34820960 AACCTTAAACATTGAACC
1 AACCTTGAACATTGAACC
34820978 CTGAACCTTG
Statistics
Matches: 42, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
28 42 1.00
ACGTcount: A:0.39, C:0.28, G:0.07, T:0.26
Consensus pattern (28 bp):
AACCTTGAACATTGAACCTTAAACTCCA
Found at i:34820977 original size:14 final size:14
Alignment explanation
Indices: 34820902--34820977 Score: 57
Period size: 14 Copynumber: 5.4 Consensus size: 14
34820892 TTTTTTACTC
* *
34820902 TGAACCTTGAATAT
1 TGAACCTTAAACAT
34820916 TGAACCTTAAAC-T
1 TGAACCTTAAACAT
** *
34820929 CCAACCCTTGAACAT
1 TGAA-CCTTAAACAT
34820944 TGAACCTTAAAC-T
1 TGAACCTTAAACAT
**
34820957 CCAAACCTTAAACAT
1 -TGAACCTTAAACAT
34820972 TGAACC
1 TGAACC
34820978 CTGAACCTTG
Statistics
Matches: 46, Mismatches: 12, Indels: 8
0.70 0.18 0.12
Matches are distributed among these distances:
13 4 0.09
14 38 0.83
15 4 0.09
ACGTcount: A:0.38, C:0.28, G:0.08, T:0.26
Consensus pattern (14 bp):
TGAACCTTAAACAT
Found at i:34823188 original size:29 final size:30
Alignment explanation
Indices: 34823155--34823229 Score: 75
Period size: 29 Copynumber: 2.6 Consensus size: 30
34823145 ATTATTCAAA
34823155 AAATTAAAAAAATAATTTA-AATTAAATTT
1 AAATTAAAAAAATAATTTATAATTAAATTT
* * * **
34823184 AAATT-TATATATTTTTTATAATTAAATTT
1 AAATTAAAAAAATAATTTATAATTAAATTT
34823213 AAA-TAAAAATAATAATT
1 AAATTAAAAA-AATAATT
34823230 AAACAATAAA
Statistics
Matches: 33, Mismatches: 10, Indels: 5
0.69 0.21 0.10
Matches are distributed among these distances:
28 9 0.27
29 20 0.61
30 4 0.12
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (30 bp):
AAATTAAAAAAATAATTTATAATTAAATTT
Found at i:34823467 original size:46 final size:44
Alignment explanation
Indices: 34823415--34823502 Score: 124
Period size: 44 Copynumber: 2.0 Consensus size: 44
34823405 GGTTCGCTGT
34823415 AATGGAATAAAACTGTAATCAATAATTC-AAGTGTTTGGTTGAATGG
1 AATGGAATAAAACTGTAA-CAAT-ATTCTAA-TGTTTGGTTGAATGG
* *
34823461 AATGGAATAGAACTGTAACAATATTCTTATGTTTGGTTGAAT
1 AATGGAATAAAACTGTAACAATATTCTAATGTTTGGTTGAAT
34823503 AGATTGATAT
Statistics
Matches: 39, Mismatches: 2, Indels: 4
0.87 0.04 0.09
Matches are distributed among these distances:
44 17 0.44
45 5 0.13
46 17 0.44
ACGTcount: A:0.38, C:0.07, G:0.20, T:0.35
Consensus pattern (44 bp):
AATGGAATAAAACTGTAACAATATTCTAATGTTTGGTTGAATGG
Found at i:34826998 original size:19 final size:19
Alignment explanation
Indices: 34826974--34827044 Score: 115
Period size: 19 Copynumber: 3.7 Consensus size: 19
34826964 TTATATCTTT
34826974 TAAGATTGCATATCATATC
1 TAAGATTGCATATCATATC
** *
34826993 TAAGATTATATATTATATC
1 TAAGATTGCATATCATATC
34827012 TAAGATTGCATATCATATC
1 TAAGATTGCATATCATATC
34827031 TAAGATTGCATATC
1 TAAGATTGCATATC
34827045 CCTGAAGATT
Statistics
Matches: 46, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
19 46 1.00
ACGTcount: A:0.38, C:0.13, G:0.10, T:0.39
Consensus pattern (19 bp):
TAAGATTGCATATCATATC
Done.