Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr08 129432109
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 129432109
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32
Warning! 350 characters in sequence are not A, C, G, or T
File 9 of 425
Found at i:2433584 original size:71 final size:71
Alignment explanation
Indices: 2433463--2433596 Score: 214
Period size: 71 Copynumber: 1.9 Consensus size: 71
2433453 GTTTTCCAAG
* * *
2433463 AAAATCAGCTCATATTGCGAGAGGTGAGTTGAGCCTCAAGACACGTTGAGGTAATTTCAATTTAT
1 AAAATCAACTCATATTGCGAGAAGTGAGTTGAGCCTCAAGACACGCTGAGGTAATTTCAATTTAT
2433528 GTTTCA
66 GTTTCA
* * *
2433534 AAAATCAACTCATATTGCGAGAAGTGAGTTGAGCCTCAGGGCACGCTGAGGTATTTTCAATTT
1 AAAATCAACTCATATTGCGAGAAGTGAGTTGAGCCTCAAGACACGCTGAGGTAATTTCAATTT
2433597 CTGCTTTTTA
Statistics
Matches: 57, Mismatches: 6, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
71 57 1.00
ACGTcount: A:0.31, C:0.16, G:0.23, T:0.30
Consensus pattern (71 bp):
AAAATCAACTCATATTGCGAGAAGTGAGTTGAGCCTCAAGACACGCTGAGGTAATTTCAATTTAT
GTTTCA
Found at i:2433743 original size:71 final size:71
Alignment explanation
Indices: 2433622--2433874 Score: 294
Period size: 74 Copynumber: 3.5 Consensus size: 71
2433612 TGTTTCCAAG
* * * *
2433622 AAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAAGACACGTTGAGGTAATTTCAATT-TA
1 AAAATCAACTCATATTGCGAGAAGTGAGTTGAGCCTCGAGGCACGCTGAGGTAATTTCAATTCTA
2433686 TGTTTCA
66 T-TTTCA
* * *
2433693 AAAATCAACTCATATCGCGAGAAGTGAGTTGAACCTCGGGGCACGCTGAGGTAATTTCAATTCCT
1 AAAATCAACTCATATTGCGAGAAGTGAGTTGAGCCTCGAGGCACGCTGAGGTAATTTCAATT-CT
* *
2433758 ATTAAATCT
65 ATT--TTCA
* * * *
2433767 AAAATCAACTCATATTGCGAGAAGTGAGTTGAGCCTTGCGGCACGCTAAGGTATTTTCAAATTCT
1 AAAATCAACTCATATTGCGAGAAGTGAGTTGAGCCTCGAGGCACGCTGAGGTAATTTC-AATTCT
2433832 ATTTTCA
65 ATTTTCA
* * *
2433839 AAAGTTAATTCATATTGCGA-AAGGTGAGTTGAGCCT
1 AAAATCAACTCATATTGCGAGAA-GTGAGTTGAGCCT
2433875 TTAATTTTCG
Statistics
Matches: 156, Mismatches: 20, Indels: 11
0.83 0.11 0.06
Matches are distributed among these distances:
71 57 0.37
72 33 0.21
73 3 0.02
74 59 0.38
75 4 0.03
ACGTcount: A:0.32, C:0.17, G:0.21, T:0.30
Consensus pattern (71 bp):
AAAATCAACTCATATTGCGAGAAGTGAGTTGAGCCTCGAGGCACGCTGAGGTAATTTCAATTCTA
TTTTCA
Found at i:2433744 original size:159 final size:160
Alignment explanation
Indices: 2433212--2433754 Score: 1007
Period size: 160 Copynumber: 3.4 Consensus size: 160
2433202 TTGTTTTTTC
2433212 CAAAAATCAACTCATATCGCGAGAAGTGAGTTGAGCCTCAGGGCACGCTGAGGTATTTTCAATTT
1 CAAAAATCAACTCATATCGCGAGAAGTGAGTTGAGCCTCAGGGCACGCTGAGGTATTTTCAATTT
2433277 CTACTTTTTAATTCATGTTTTCCAAGAAAATCAGCTCATATTGCGAGAGGTGAGTTGAGCCTCAA
66 CTACTTTTTAATTCATGTTTTCCAAGAAAATCAGCTCATATTGCGAGAGGTGAGTTGAGCCTCAA
2433342 GACACGTTGAGGTAATTTCAATTTATGTTT
131 GACACGTTGAGGTAATTTCAATTTATGTTT
*
2433372 CAAAAATCAACTCATATTGCGAGAAGTGAGTTGAGCCTCAGGGCACGCTGAGGTATTTTCAATTT
1 CAAAAATCAACTCATATCGCGAGAAGTGAGTTGAGCCTCAGGGCACGCTGAGGTATTTTCAATTT
2433437 CTACTTTTTAATTCATGTTTTCCAAGAAAATCAGCTCATATTGCGAGAGGTGAGTTGAGCCTCAA
66 CTACTTTTTAATTCATGTTTTCCAAGAAAATCAGCTCATATTGCGAGAGGTGAGTTGAGCCTCAA
2433502 GACACGTTGAGGTAATTTCAATTTATGTTT
131 GACACGTTGAGGTAATTTCAATTTATGTTT
*
2433532 CAAAAATCAACTCATATTGCGAGAAGTGAGTTGAGCCTCAGGGCACGCTGAGGTATTTTCAATTT
1 CAAAAATCAACTCATATCGCGAGAAGTGAGTTGAGCCTCAGGGCACGCTGAGGTATTTTCAATTT
* * *
2433597 CTGCTTTTTAGTTCATG-TTTCCAAGAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAA
66 CTACTTTTTAATTCATGTTTTCCAAGAAAATCAGCTCATATTGCGAGAGGTGAGTTGAGCCTCAA
2433661 GACACGTTGAGGTAATTTCAATTTATGTTT
131 GACACGTTGAGGTAATTTCAATTTATGTTT
* * *
2433691 CAAAAATCAACTCATATCGCGAGAAGTGAGTTGAACCTCGGGGCACGCTGAGGTAATTTCAATT
1 CAAAAATCAACTCATATCGCGAGAAGTGAGTTGAGCCTCAGGGCACGCTGAGGTATTTTCAATT
2433755 CCTATTAAAT
Statistics
Matches: 375, Mismatches: 8, Indels: 1
0.98 0.02 0.00
Matches are distributed among these distances:
159 136 0.36
160 239 0.64
ACGTcount: A:0.30, C:0.17, G:0.21, T:0.32
Consensus pattern (160 bp):
CAAAAATCAACTCATATCGCGAGAAGTGAGTTGAGCCTCAGGGCACGCTGAGGTATTTTCAATTT
CTACTTTTTAATTCATGTTTTCCAAGAAAATCAGCTCATATTGCGAGAGGTGAGTTGAGCCTCAA
GACACGTTGAGGTAATTTCAATTTATGTTT
Found at i:2433931 original size:67 final size:65
Alignment explanation
Indices: 2433820--2434061 Score: 272
Period size: 67 Copynumber: 3.6 Consensus size: 65
2433810 CGCTAAGGTA
* * * *
2433820 TTTTCAAATTCTATTTTCAAAAGTTAATTCATATTGCGAAAGGTGAGTTGAGCCTTTAATTTTCG
1 TTTTCAAAATCTATTTTCAAAA-TCAACTCATATTGCGAGAGGTGAGTTGAGCCTTTAATTTTCG
2433885 T
65 T
*
2433886 TTTTCAAAATCTACTTTTCAAAGATCAACTCATATTGCGAGAGGTGAGTTAAGCCTTTAATTTTC
1 TTTTCAAAATCTA-TTTTCAAA-ATCAACTCATATTGCGAGAGGTGAGTTGAGCCTTTAATTTTC
2433951 GT
64 GT
* * *
2433953 TTCTCAAAATCTACTTTTCAAATTATTAACTCATGTTGCGAGAGGTGAGTTGAGCCTTTTAA-TT
1 TTTTCAAAATCTA-TTTTCAAA--ATCAACTCATATTGCGAGAGGTGAGTTGAGCC-TTTAATTT
*
2434017 TCTGC
62 TC-GT
** *
2434022 TTTT-AATTTCTATGTTTCAAAAATCAACCCATATTGCGAG
1 TTTTCAAAATCTAT-TTTC-AAAATCAACTCATATTGCGAG
2434062 GAATATGTTG
Statistics
Matches: 152, Mismatches: 17, Indels: 13
0.84 0.09 0.07
Matches are distributed among these distances:
66 12 0.08
67 84 0.55
68 44 0.29
69 12 0.08
ACGTcount: A:0.29, C:0.16, G:0.14, T:0.41
Consensus pattern (65 bp):
TTTTCAAAATCTATTTTCAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTTTAATTTTCGT
Found at i:2434026 original size:13 final size:13
Alignment explanation
Indices: 2434008--2434032 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
2433998 TGAGTTGAGC
2434008 CTTTTAATTTCTG
1 CTTTTAATTTCTG
2434021 CTTTTAATTTCT
1 CTTTTAATTTCT
2434033 ATGTTTCAAA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.16, C:0.16, G:0.04, T:0.64
Consensus pattern (13 bp):
CTTTTAATTTCTG
Found at i:2436152 original size:2 final size:2
Alignment explanation
Indices: 2436136--2436173 Score: 60
Period size: 2 Copynumber: 19.5 Consensus size: 2
2436126 ATTTGAGTGT
*
2436136 TA TA T- TA TG TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
2436174 TTCCAATGTG
Statistics
Matches: 33, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
1 1 0.03
2 32 0.97
ACGTcount: A:0.45, C:0.00, G:0.03, T:0.53
Consensus pattern (2 bp):
TA
Found at i:2437802 original size:25 final size:25
Alignment explanation
Indices: 2437774--2437845 Score: 72
Period size: 26 Copynumber: 2.8 Consensus size: 25
2437764 ATCTCATGTA
*
2437774 TATGTTTTTTTAATACTATGTTATG
1 TATGTTTTTTTAATGCTATGTTATG
* * *
2437799 TATGTATTTTTCAATGCCATATTATG
1 TATGT-TTTTTTAATGCTATGTTATG
** *
2437825 TACATATTTTTAATGCTATGT
1 TATGTTTTTTTAATGCTATGT
2437846 ATACACTTTG
Statistics
Matches: 36, Mismatches: 10, Indels: 2
0.75 0.21 0.04
Matches are distributed among these distances:
25 17 0.47
26 19 0.53
ACGTcount: A:0.26, C:0.08, G:0.11, T:0.54
Consensus pattern (25 bp):
TATGTTTTTTTAATGCTATGTTATG
Found at i:2437808 original size:27 final size:28
Alignment explanation
Indices: 2437747--2437809 Score: 67
Period size: 27 Copynumber: 2.3 Consensus size: 28
2437737 AATATTATAT
*
2437747 TATA-TTTTTTACATATTATCTCATGTA
1 TATATTTTTTTACATACTATCTCATGTA
* * *
2437774 TATGTTTTTTTA-ATACTATGTTATGTA
1 TATATTTTTTTACATACTATCTCATGTA
*
2437801 TGTATTTTT
1 TATATTTTT
2437810 CAATGCCATA
Statistics
Matches: 29, Mismatches: 6, Indels: 2
0.78 0.16 0.05
Matches are distributed among these distances:
27 22 0.76
28 7 0.24
ACGTcount: A:0.25, C:0.06, G:0.08, T:0.60
Consensus pattern (28 bp):
TATATTTTTTTACATACTATCTCATGTA
Found at i:2439474 original size:2 final size:2
Alignment explanation
Indices: 2439469--2439498 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
2439459 TGTGTACAAT
2439469 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
2439499 AGATTTTTGT
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):
TA
Found at i:2448259 original size:47 final size:47
Alignment explanation
Indices: 2448150--2448260 Score: 154
Period size: 47 Copynumber: 2.4 Consensus size: 47
2448140 CCGGGATAAG
*
2448150 CACATAGTGCTTCATCGGAACAAATCCGGAACTTTAACATTATAGTA
1 CACATAGTGCTTCATCGGAACAAATCCGGAACTTTAACAGTATAGTA
* * *
2448197 CACAAAGTACTTCATCGGAACAAATCCGGAACTTTAACAGTAGTCG-A
1 CACATAGTGCTTCATCGGAACAAATCCGGAACTTTAACAGTA-TAGTA
2448244 CACATAGTG-TCTCATCG
1 CACATAGTGCT-TCATCG
2448261 ACTCAATGTC
Statistics
Matches: 56, Mismatches: 6, Indels: 4
0.85 0.09 0.06
Matches are distributed among these distances:
46 1 0.02
47 53 0.95
48 2 0.04
ACGTcount: A:0.35, C:0.23, G:0.16, T:0.25
Consensus pattern (47 bp):
CACATAGTGCTTCATCGGAACAAATCCGGAACTTTAACAGTATAGTA
Found at i:2452622 original size:5 final size:5
Alignment explanation
Indices: 2452612--2452647 Score: 63
Period size: 5 Copynumber: 7.0 Consensus size: 5
2452602 AATAATTAAG
2452612 TATAT TATAT TATAT TATAT TATAT TATTAT TATAT
1 TATAT TATAT TATAT TATAT TATAT TA-TAT TATAT
2452648 ATAAAAGAAA
Statistics
Matches: 30, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
5 25 0.83
6 5 0.17
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (5 bp):
TATAT
Found at i:2460953 original size:30 final size:33
Alignment explanation
Indices: 2460909--2460979 Score: 82
Period size: 31 Copynumber: 2.3 Consensus size: 33
2460899 CTGCCCATAT
*
2460909 TATT-TTTTTGAATTTTGA-ATTTAATA-TTT-A
1 TATTATTTTTGAA-TTTAATATTTAATAGTTTCA
2460939 TATTATTTTT-AATTTAATATTTAATAGTTTCA
1 TATTATTTTTGAATTTAATATTTAATAGTTTCA
2460971 T-TTATTTTT
1 TATTATTTTT
2460980 CTTTTATTAA
Statistics
Matches: 36, Mismatches: 1, Indels: 7
0.82 0.02 0.16
Matches are distributed among these distances:
29 4 0.11
30 14 0.39
31 16 0.44
32 2 0.06
ACGTcount: A:0.30, C:0.01, G:0.04, T:0.65
Consensus pattern (33 bp):
TATTATTTTTGAATTTAATATTTAATAGTTTCA
Found at i:2463696 original size:4 final size:4
Alignment explanation
Indices: 2463689--2463718 Score: 51
Period size: 4 Copynumber: 7.5 Consensus size: 4
2463679 ACACGCAAGC
*
2463689 AAAT AAAT AAAT GAAT AAAT AAAT AAAT AA
1 AAAT AAAT AAAT AAAT AAAT AAAT AAAT AA
2463719 TGGTAGAATA
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
4 24 1.00
ACGTcount: A:0.73, C:0.00, G:0.03, T:0.23
Consensus pattern (4 bp):
AAAT
Found at i:2467176 original size:2 final size:2
Alignment explanation
Indices: 2467157--2467198 Score: 50
Period size: 2 Copynumber: 21.0 Consensus size: 2
2467147 CATAACAATA
* *
2467157 AT AT GAT AT AT -T AA AT AT AT AT AT AT AT AT AT AT AT TT AT AT
1 AT AT -AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
2467199 GATGTTAAAA
Statistics
Matches: 34, Mismatches: 4, Indels: 4
0.81 0.10 0.10
Matches are distributed among these distances:
1 1 0.03
2 31 0.91
3 2 0.06
ACGTcount: A:0.48, C:0.00, G:0.02, T:0.50
Consensus pattern (2 bp):
AT
Found at i:2467604 original size:15 final size:15
Alignment explanation
Indices: 2467584--2467618 Score: 54
Period size: 15 Copynumber: 2.3 Consensus size: 15
2467574 ACATGTGTAT
2467584 TAATAAGAA-TATTAA
1 TAATAA-AACTATTAA
2467599 TAATAAAACTATTAA
1 TAATAAAACTATTAA
2467614 TAATA
1 TAATA
2467619 TTTTATAACA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
14 2 0.11
15 17 0.89
ACGTcount: A:0.60, C:0.03, G:0.03, T:0.34
Consensus pattern (15 bp):
TAATAAAACTATTAA
Found at i:2474643 original size:2 final size:2
Alignment explanation
Indices: 2474631--2474660 Score: 51
Period size: 2 Copynumber: 14.5 Consensus size: 2
2474621 TACTTCTCAA
2474631 AT AT CAT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT -AT AT AT AT AT AT AT AT AT AT AT AT A
2474661 ATTACAATGC
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
2 25 0.93
3 2 0.07
ACGTcount: A:0.50, C:0.03, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:2475134 original size:16 final size:16
Alignment explanation
Indices: 2475113--2475152 Score: 53
Period size: 16 Copynumber: 2.5 Consensus size: 16
2475103 TTTGGGAACC
*
2475113 TTAAAATAATTTATTT
1 TTAAAATAATCTATTT
*
2475129 TTAAAAAAATCTATTT
1 TTAAAATAATCTATTT
*
2475145 TTACAATA
1 TTAAAATA
2475153 TTCATATAAA
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
16 20 1.00
ACGTcount: A:0.47, C:0.05, G:0.00, T:0.47
Consensus pattern (16 bp):
TTAAAATAATCTATTT
Found at i:2480430 original size:19 final size:19
Alignment explanation
Indices: 2480395--2480437 Score: 54
Period size: 19 Copynumber: 2.3 Consensus size: 19
2480385 TACGGTTAGG
2480395 TTAAATAAAAATATTAAAT
1 TTAAATAAAAATATTAAAT
*
2480414 TTAAA-AAATAATTTTAAA-
1 TTAAATAAA-AATATTAAAT
2480432 TTAAAT
1 TTAAAT
2480438 TTATTTAAAA
Statistics
Matches: 21, Mismatches: 1, Indels: 4
0.81 0.04 0.15
Matches are distributed among these distances:
18 8 0.38
19 13 0.62
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (19 bp):
TTAAATAAAAATATTAAAT
Found at i:2484322 original size:14 final size:15
Alignment explanation
Indices: 2484291--2484327 Score: 51
Period size: 14 Copynumber: 2.6 Consensus size: 15
2484281 TAGTGATTTA
*
2484291 ATATA-AATATAAAT
1 ATATATAATATAAAC
2484305 ATATATAATA-AAAC
1 ATATATAATATAAAC
2484319 ATATATAAT
1 ATATATAAT
2484328 TAATATAATA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
14 17 0.81
15 4 0.19
ACGTcount: A:0.62, C:0.03, G:0.00, T:0.35
Consensus pattern (15 bp):
ATATATAATATAAAC
Found at i:2484473 original size:19 final size:17
Alignment explanation
Indices: 2484433--2484476 Score: 54
Period size: 19 Copynumber: 2.5 Consensus size: 17
2484423 TTTATCCAAA
2484433 CTTATTTT-TCAAACCT
1 CTTATTTTATCAAACCT
*
2484449 CGTATTTTATCTAAACCCT
1 CTTATTTTATC-AAA-CCT
2484468 CTTATTTTA
1 CTTATTTTA
2484477 CCGATAGGCC
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
16 7 0.30
17 2 0.09
18 3 0.13
19 11 0.48
ACGTcount: A:0.25, C:0.23, G:0.02, T:0.50
Consensus pattern (17 bp):
CTTATTTTATCAAACCT
Found at i:2484921 original size:2 final size:2
Alignment explanation
Indices: 2484914--2484953 Score: 80
Period size: 2 Copynumber: 20.0 Consensus size: 2
2484904 TAAACTATGA
2484914 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
2484954 TTACACACAC
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 38 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:2487020 original size:14 final size:14
Alignment explanation
Indices: 2486992--2487027 Score: 51
Period size: 13 Copynumber: 2.8 Consensus size: 14
2486982 ACTATATTCA
2486992 AATTTTTA-A-TTT
1 AATTTTTATATTTT
2487004 AATTTTTATATTTT
1 AATTTTTATATTTT
2487018 AA-TTTTATAT
1 AATTTTTATAT
2487028 AATTTGATCC
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
12 8 0.36
13 9 0.41
14 5 0.23
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (14 bp):
AATTTTTATATTTT
Found at i:2491131 original size:13 final size:13
Alignment explanation
Indices: 2491115--2491167 Score: 63
Period size: 13 Copynumber: 4.1 Consensus size: 13
2491105 TTTAAACTAA
2491115 ACTTTTCAAAAGC
1 ACTTTTCAAAAGC
* *
2491128 ACTTTTTC-ACATC
1 AC-TTTTCAAAAGC
*
2491141 ACTTTTCAAAAGT
1 ACTTTTCAAAAGC
2491154 ACTTTTCAAAAGC
1 ACTTTTCAAAAGC
2491167 A
1 A
2491168 TTGCCAAACT
Statistics
Matches: 32, Mismatches: 6, Indels: 4
0.76 0.14 0.10
Matches are distributed among these distances:
12 5 0.16
13 22 0.69
14 5 0.16
ACGTcount: A:0.36, C:0.23, G:0.06, T:0.36
Consensus pattern (13 bp):
ACTTTTCAAAAGC
Found at i:2492922 original size:19 final size:20
Alignment explanation
Indices: 2492898--2492936 Score: 62
Period size: 20 Copynumber: 2.0 Consensus size: 20
2492888 AACCCCTTCC
2492898 CCTCTCCC-TCCTCTCTCTT
1 CCTCTCCCTTCCTCTCTCTT
*
2492917 CCTCTCCCTTCTTCTCTCTT
1 CCTCTCCCTTCCTCTCTCTT
2492937 TTTTTTTCTT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
19 8 0.44
20 10 0.56
ACGTcount: A:0.00, C:0.54, G:0.00, T:0.46
Consensus pattern (20 bp):
CCTCTCCCTTCCTCTCTCTT
Found at i:2493618 original size:25 final size:26
Alignment explanation
Indices: 2493589--2493639 Score: 68
Period size: 26 Copynumber: 2.0 Consensus size: 26
2493579 CTTATTTCAT
*
2493589 TAAATAAAAAAT-TTTAAAAATATAA
1 TAAATAAAAAATATTTAAAAACATAA
* *
2493614 TAAATCAAATATATTTAAAAACATAA
1 TAAATAAAAAATATTTAAAAACATAA
2493640 AAACTAATAT
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
25 10 0.45
26 12 0.55
ACGTcount: A:0.65, C:0.04, G:0.00, T:0.31
Consensus pattern (26 bp):
TAAATAAAAAATATTTAAAAACATAA
Found at i:2493653 original size:21 final size:21
Alignment explanation
Indices: 2493620--2493678 Score: 68
Period size: 21 Copynumber: 2.8 Consensus size: 21
2493610 ATAATAAATC
*
2493620 AAAT-ATATTTAAAA-ACATAA
1 AAATAATA-TTAAAACAAATAA
2493640 AAACTAATATTAAAACAAATAA
1 AAA-TAATATTAAAACAAATAA
*
2493662 AAATAATACTAAAACAA
1 AAATAATATTAAAACAA
2493679 TTCTTAAAAC
Statistics
Matches: 34, Mismatches: 2, Indels: 5
0.83 0.05 0.12
Matches are distributed among these distances:
20 3 0.09
21 20 0.59
22 11 0.32
ACGTcount: A:0.68, C:0.08, G:0.00, T:0.24
Consensus pattern (21 bp):
AAATAATATTAAAACAAATAA
Found at i:2494289 original size:15 final size:15
Alignment explanation
Indices: 2494270--2494305 Score: 54
Period size: 15 Copynumber: 2.4 Consensus size: 15
2494260 ATTATCTCTA
2494270 ATATATGTATATATT
1 ATATATGTATATATT
* *
2494285 GTATATGTTTATATT
1 ATATATGTATATATT
2494300 ATATAT
1 ATATAT
2494306 ATTATTTCTT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.36, C:0.00, G:0.08, T:0.56
Consensus pattern (15 bp):
ATATATGTATATATT
Found at i:2494802 original size:17 final size:17
Alignment explanation
Indices: 2494782--2494814 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
2494772 TTCATTTTAA
*
2494782 ATATATATGTTATGTAT
1 ATATATATATTATGTAT
2494799 ATATATATATTATGTA
1 ATATATATATTATGTA
2494815 CCCATATTAG
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.39, C:0.00, G:0.09, T:0.52
Consensus pattern (17 bp):
ATATATATATTATGTAT
Found at i:2494804 original size:19 final size:19
Alignment explanation
Indices: 2494755--2494808 Score: 58
Period size: 19 Copynumber: 2.9 Consensus size: 19
2494745 GTCTGTTATA
*
2494755 TATGTATAT-TGTATATGT
1 TATGTATATATATATATGT
* *
2494773 TCAT-TTTAAATATATATGT
1 T-ATGTATATATATATATGT
2494792 TATGTATATATATATAT
1 TATGTATATATATATAT
2494809 TATGTACCCA
Statistics
Matches: 28, Mismatches: 5, Indels: 5
0.74 0.13 0.13
Matches are distributed among these distances:
18 6 0.21
19 22 0.79
ACGTcount: A:0.35, C:0.02, G:0.09, T:0.54
Consensus pattern (19 bp):
TATGTATATATATATATGT
Found at i:2499442 original size:25 final size:26
Alignment explanation
Indices: 2499383--2499445 Score: 76
Period size: 25 Copynumber: 2.4 Consensus size: 26
2499373 AAATTTATTT
*
2499383 AAATATTATATAAATTACTATTTTTTA
1 AAATATTATATAAATTAC-ATTGTTTA
*
2499410 AAAAATTATA-AAATTAC-TTGTTTA
1 AAATATTATATAAATTACATTGTTTA
2499434 GAAATATTATAT
1 -AAATATTATAT
2499446 TATCAAAAAG
Statistics
Matches: 31, Mismatches: 3, Indels: 5
0.79 0.08 0.13
Matches are distributed among these distances:
24 6 0.19
25 9 0.29
26 7 0.23
27 9 0.29
ACGTcount: A:0.48, C:0.03, G:0.03, T:0.46
Consensus pattern (26 bp):
AAATATTATATAAATTACATTGTTTA
Found at i:2500065 original size:22 final size:20
Alignment explanation
Indices: 2500040--2500083 Score: 52
Period size: 20 Copynumber: 2.1 Consensus size: 20
2500030 TGTCTAAAGC
*
2500040 TTCCATTCCAATTCTATTTTTT
1 TTCC-TTCCAA-TCTACTTTTT
*
2500062 TTCCTTTCAATCTACTTTTT
1 TTCCTTCCAATCTACTTTTT
2500082 TT
1 TT
2500084 GAGGGTTCTT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
20 11 0.55
21 5 0.25
22 4 0.20
ACGTcount: A:0.16, C:0.23, G:0.00, T:0.61
Consensus pattern (20 bp):
TTCCTTCCAATCTACTTTTT
Found at i:2510206 original size:24 final size:24
Alignment explanation
Indices: 2510174--2510254 Score: 69
Period size: 24 Copynumber: 3.4 Consensus size: 24
2510164 TGCCCTAATG
2510174 AATAAATATGACTTTTAACATCCA
1 AATAAATATGACTTTTAACATCCA
* * * *
2510198 AATACATAT-TCATGTTAACTAAT--G
1 AATAAATATGAC-TTTTAAC--ATCCA
2510222 AATAAATATGACTTTTAACATCCA
1 AATAAATATGACTTTTAACATCCA
*
2510246 AATACATAT
1 AATAAATAT
2510255 TCATGTTAAG
Statistics
Matches: 42, Mismatches: 9, Indels: 12
0.67 0.14 0.19
Matches are distributed among these distances:
22 2 0.05
23 1 0.02
24 36 0.86
25 1 0.02
26 2 0.05
ACGTcount: A:0.46, C:0.15, G:0.05, T:0.35
Consensus pattern (24 bp):
AATAAATATGACTTTTAACATCCA
Found at i:2510239 original size:48 final size:48
Alignment explanation
Indices: 2510168--2510263 Score: 192
Period size: 48 Copynumber: 2.0 Consensus size: 48
2510158 GTAGTTTGCC
2510168 CTAATGAATAAATATGACTTTTAACATCCAAATACATATTCATGTTAA
1 CTAATGAATAAATATGACTTTTAACATCCAAATACATATTCATGTTAA
2510216 CTAATGAATAAATATGACTTTTAACATCCAAATACATATTCATGTTAA
1 CTAATGAATAAATATGACTTTTAACATCCAAATACATATTCATGTTAA
2510264 GACTCATTTA
Statistics
Matches: 48, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
48 48 1.00
ACGTcount: A:0.44, C:0.15, G:0.06, T:0.35
Consensus pattern (48 bp):
CTAATGAATAAATATGACTTTTAACATCCAAATACATATTCATGTTAA
Found at i:2510263 original size:24 final size:24
Alignment explanation
Indices: 2510188--2510263 Score: 68
Period size: 24 Copynumber: 3.2 Consensus size: 24
2510178 AATATGACTT
2510188 TTAACATCCAAATACATATTCATG
1 TTAACATCCAAATACATATTCATG
* * * *
2510212 TTAACTAAT--GAATAAATA-TGACTT
1 TTAAC--ATCCAAATACATATTCA-TG
2510236 TTAACATCCAAATACATATTCATG
1 TTAACATCCAAATACATATTCATG
2510260 TTAA
1 TTAA
2510264 GACTCATTTA
Statistics
Matches: 38, Mismatches: 8, Indels: 12
0.66 0.14 0.21
Matches are distributed among these distances:
22 2 0.05
23 2 0.05
24 30 0.79
25 2 0.05
26 2 0.05
ACGTcount: A:0.43, C:0.16, G:0.05, T:0.36
Consensus pattern (24 bp):
TTAACATCCAAATACATATTCATG
Found at i:2516428 original size:37 final size:37
Alignment explanation
Indices: 2516378--2516453 Score: 152
Period size: 37 Copynumber: 2.1 Consensus size: 37
2516368 TAGAATATGT
2516378 TAGTCAATCACTCTATCTTTGTCCCATATCATGATTA
1 TAGTCAATCACTCTATCTTTGTCCCATATCATGATTA
2516415 TAGTCAATCACTCTATCTTTGTCCCATATCATGATTA
1 TAGTCAATCACTCTATCTTTGTCCCATATCATGATTA
2516452 TA
1 TA
2516454 CCATTGCATA
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
37 39 1.00
ACGTcount: A:0.28, C:0.24, G:0.08, T:0.41
Consensus pattern (37 bp):
TAGTCAATCACTCTATCTTTGTCCCATATCATGATTA
Found at i:2516445 original size:21 final size:21
Alignment explanation
Indices: 2516384--2516445 Score: 55
Period size: 21 Copynumber: 3.2 Consensus size: 21
2516374 ATGTTAGTCA
2516384 ATCACTCTATCTTTGTCCCAT
1 ATCACTCTATCTTTGTCCCAT
* *
2516405 ATCA-T-GAT-TATAGT--CA-
1 ATCACTCTATCT-TTGTCCCAT
2516421 ATCACTCTATCTTTGTCCCAT
1 ATCACTCTATCTTTGTCCCAT
2516442 ATCA
1 ATCA
2516446 TGATTATACC
Statistics
Matches: 30, Mismatches: 4, Indels: 14
0.62 0.08 0.29
Matches are distributed among these distances:
16 4 0.13
17 3 0.10
18 6 0.20
19 6 0.20
20 3 0.10
21 8 0.27
ACGTcount: A:0.26, C:0.27, G:0.06, T:0.40
Consensus pattern (21 bp):
ATCACTCTATCTTTGTCCCAT
Found at i:2518949 original size:25 final size:25
Alignment explanation
Indices: 2518915--2518962 Score: 87
Period size: 25 Copynumber: 1.9 Consensus size: 25
2518905 GATTTCTAAC
*
2518915 CTCTATGATACTTTTACGCTTAAAA
1 CTCTATGATACTTTTACCCTTAAAA
2518940 CTCTATGATACTTTTACCCTTAA
1 CTCTATGATACTTTTACCCTTAA
2518963 GACACGGCTG
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
25 22 1.00
ACGTcount: A:0.29, C:0.23, G:0.06, T:0.42
Consensus pattern (25 bp):
CTCTATGATACTTTTACCCTTAAAA
Found at i:2521879 original size:18 final size:18
Alignment explanation
Indices: 2521856--2521897 Score: 84
Period size: 18 Copynumber: 2.3 Consensus size: 18
2521846 AAATGGATTA
2521856 GGCCTCAAATAAGATTTT
1 GGCCTCAAATAAGATTTT
2521874 GGCCTCAAATAAGATTTT
1 GGCCTCAAATAAGATTTT
2521892 GGCCTC
1 GGCCTC
2521898 GGCTTGACTT
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:0.29, C:0.21, G:0.19, T:0.31
Consensus pattern (18 bp):
GGCCTCAAATAAGATTTT
Found at i:2521971 original size:22 final size:22
Alignment explanation
Indices: 2521929--2521981 Score: 61
Period size: 22 Copynumber: 2.4 Consensus size: 22
2521919 AACTTTCTTT
** *
2521929 TTTTGCTACCATTTTGTTATTG
1 TTTTGCTACCATTTTAATATTA
*
2521951 TTTTGCTATCATTTTAATATTA
1 TTTTGCTACCATTTTAATATTA
*
2521973 TATTGCTAC
1 TTTTGCTAC
2521982 TATATTATTG
Statistics
Matches: 25, Mismatches: 6, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
22 25 1.00
ACGTcount: A:0.21, C:0.13, G:0.09, T:0.57
Consensus pattern (22 bp):
TTTTGCTACCATTTTAATATTA
Found at i:2523464 original size:2 final size:2
Alignment explanation
Indices: 2523457--2523485 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
2523447 ATGCCCTGGT
2523457 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
2523486 CTTATGTTTT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:2525397 original size:30 final size:30
Alignment explanation
Indices: 2525321--2525397 Score: 86
Period size: 29 Copynumber: 2.6 Consensus size: 30
2525311 CTAAATTTTG
* *
2525321 AAATCTAAAAAGTATATAAAATTAAAATTCT
1 AAATATAAAAA-TATATAAAATTAAAATTCC
*
2525352 AAAAATAAAAA-ATATAAGAATT-AAATTCC
1 AAATATAAAAATATATAA-AATTAAAATTCC
*
2525381 AAATTTAAAAATATATA
1 AAATATAAAAATATATA
2525398 CATTGAGAGA
Statistics
Matches: 39, Mismatches: 5, Indels: 5
0.80 0.10 0.10
Matches are distributed among these distances:
29 21 0.54
30 9 0.23
31 9 0.23
ACGTcount: A:0.62, C:0.05, G:0.03, T:0.30
Consensus pattern (30 bp):
AAATATAAAAATATATAAAATTAAAATTCC
Found at i:2528478 original size:19 final size:18
Alignment explanation
Indices: 2528436--2528478 Score: 50
Period size: 19 Copynumber: 2.3 Consensus size: 18
2528426 AACCTTTTAA
*
2528436 TTTAAAAAAAAATTAAAT
1 TTTAAAAAAAAATTAAAC
*
2528454 TATTAAAAATAAAATTATAC
1 T-TTAAAAA-AAAATTAAAC
2528474 TTTAA
1 TTTAA
2528479 CTCCTAAAAA
Statistics
Matches: 21, Mismatches: 2, Indels: 3
0.81 0.08 0.12
Matches are distributed among these distances:
18 1 0.05
19 11 0.52
20 9 0.43
ACGTcount: A:0.60, C:0.02, G:0.00, T:0.37
Consensus pattern (18 bp):
TTTAAAAAAAAATTAAAC
Found at i:2530977 original size:16 final size:17
Alignment explanation
Indices: 2530949--2530990 Score: 52
Period size: 16 Copynumber: 2.5 Consensus size: 17
2530939 TTTAATCTTT
2530949 TAAAATT-TATAAAAATA
1 TAAAATTAT-TAAAAATA
*
2530966 T-AAATTATTAAAACTA
1 TAAAATTATTAAAAATA
2530982 TAAAATTAT
1 TAAAATTAT
2530991 ATTTTAACCC
Statistics
Matches: 22, Mismatches: 1, Indels: 4
0.81 0.04 0.15
Matches are distributed among these distances:
16 13 0.59
17 9 0.41
ACGTcount: A:0.60, C:0.02, G:0.00, T:0.38
Consensus pattern (17 bp):
TAAAATTATTAAAAATA
Found at i:2532460 original size:23 final size:23
Alignment explanation
Indices: 2532434--2532478 Score: 81
Period size: 23 Copynumber: 2.0 Consensus size: 23
2532424 GTGGCATGAC
*
2532434 CAATAGTGGATTGATTTTTTTTT
1 CAATAGTGGATTGATTTATTTTT
2532457 CAATAGTGGATTGATTTATTTT
1 CAATAGTGGATTGATTTATTTT
2532479 CTCACTTTTT
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
23 21 1.00
ACGTcount: A:0.24, C:0.04, G:0.18, T:0.53
Consensus pattern (23 bp):
CAATAGTGGATTGATTTATTTTT
Found at i:2532856 original size:23 final size:21
Alignment explanation
Indices: 2532810--2532849 Score: 64
Period size: 21 Copynumber: 1.9 Consensus size: 21
2532800 TTCAACCATT
2532810 GTTTTTTATTTCGATTTTGGG
1 GTTTTTTATTTCGATTTTGGG
2532831 GTTTTTT-TTATCGATTTTG
1 GTTTTTTATT-TCGATTTTG
2532850 AATGGTTCGA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 2 0.11
21 16 0.89
ACGTcount: A:0.10, C:0.05, G:0.20, T:0.65
Consensus pattern (21 bp):
GTTTTTTATTTCGATTTTGGG
Found at i:2534250 original size:39 final size:39
Alignment explanation
Indices: 2534186--2534264 Score: 131
Period size: 39 Copynumber: 2.0 Consensus size: 39
2534176 TTTTTAAATT
*
2534186 CATATATTTAGAAAGATCTTGAAGAATCATATCTCCGTA
1 CATATATTTAGAAAGATCTTCAAGAATCATATCTCCGTA
* *
2534225 CATATATTTAGGAAGTTCTTCAAGAATCATATCTCCGTA
1 CATATATTTAGAAAGATCTTCAAGAATCATATCTCCGTA
2534264 C
1 C
2534265 TTAAACCCAT
Statistics
Matches: 37, Mismatches: 3, Indels: 0
0.93 0.08 0.00
Matches are distributed among these distances:
39 37 1.00
ACGTcount: A:0.35, C:0.18, G:0.13, T:0.34
Consensus pattern (39 bp):
CATATATTTAGAAAGATCTTCAAGAATCATATCTCCGTA
Found at i:2535720 original size:11 final size:10
Alignment explanation
Indices: 2535693--2535737 Score: 60
Period size: 9 Copynumber: 4.8 Consensus size: 10
2535683 TTATATAATT
2535693 TTAAAATATA
1 TTAAAATATA
*
2535703 -TATAATATA
1 TTAAAATATA
2535712 TTAAAA-ATA
1 TTAAAATATA
2535721 TTAAAA-ATA
1 TTAAAATATA
2535730 TTAAAATA
1 TTAAAATA
2535738 AATATTTTTC
Statistics
Matches: 31, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
9 26 0.84
10 5 0.16
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (10 bp):
TTAAAATATA
Found at i:2535720 original size:20 final size:20
Alignment explanation
Indices: 2535684--2535735 Score: 60
Period size: 18 Copynumber: 2.9 Consensus size: 20
2535674 ATATTATTTT
2535684 TATATAAT-T-TT-AAAATA
1 TATATAATATATTAAAAATA
2535701 TATATAATATATTAAAAATA
1 TATATAATATATTAAAAATA
*
2535721 T-TA-AAAATATTAAAA
1 TATATAATATATTAAAA
2535736 TAAATATTTT
Statistics
Matches: 31, Mismatches: 1, Indels: 5
0.84 0.03 0.14
Matches are distributed among these distances:
17 8 0.26
18 12 0.39
19 4 0.13
20 7 0.23
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (20 bp):
TATATAATATATTAAAAATA
Found at i:2535876 original size:25 final size:25
Alignment explanation
Indices: 2535848--2535895 Score: 62
Period size: 25 Copynumber: 1.9 Consensus size: 25
2535838 TACAATATTC
2535848 AAATAATAACAATAA-AATAGTAACA
1 AAATAATAACAA-AATAATAGTAACA
* *
2535873 AAATAGTAATAAAATAATAGTAA
1 AAATAATAACAAAATAATAGTAA
2535896 AATAAGGAGA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
24 2 0.10
25 18 0.90
ACGTcount: A:0.67, C:0.04, G:0.06, T:0.23
Consensus pattern (25 bp):
AAATAATAACAAAATAATAGTAACA
Found at i:2535945 original size:11 final size:11
Alignment explanation
Indices: 2535801--2535935 Score: 76
Period size: 11 Copynumber: 12.0 Consensus size: 11
2535791 TAAATTCTTC
2535801 TAAAATAATAA
1 TAAAATAATAA
*
2535812 TAAAATTAACAA
1 TAAAA-TAATAA
*
2535824 TAAAATAAGTTTTA
1 TAAAATAA---TAA
* *
2535838 TACAATATTCAA
1 TAAAATAAT-AA
* *
2535850 -ATAATAACAA
1 TAAAATAATAA
*
2535860 TAAAATAGTAA
1 TAAAATAATAA
* *
2535871 CAAAATAGTAA
1 TAAAATAATAA
*
2535882 TAAAATAATAG
1 TAAAATAATAA
**
2535893 TAAAATAAGGA
1 TAAAATAATAA
*
2535904 GAAAATAATAA
1 TAAAATAATAA
* *
2535915 GAAAATAATAT
1 TAAAATAATAA
2535926 TAAAA-AATAA
1 TAAAATAATAA
2535936 AAATAAAATA
Statistics
Matches: 93, Mismatches: 25, Indels: 13
0.71 0.19 0.10
Matches are distributed among these distances:
10 6 0.06
11 69 0.74
12 11 0.12
14 7 0.08
ACGTcount: A:0.64, C:0.04, G:0.06, T:0.26
Consensus pattern (11 bp):
TAAAATAATAA
Found at i:2546858 original size:14 final size:14
Alignment explanation
Indices: 2546835--2546869 Score: 52
Period size: 14 Copynumber: 2.5 Consensus size: 14
2546825 CACAATACCC
*
2546835 AAATAATAACAACA
1 AAATAGTAACAACA
2546849 AAATAGTAACAACA
1 AAATAGTAACAACA
*
2546863 TAATAGT
1 AAATAGT
2546870 GAAATGGCAT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
14 19 1.00
ACGTcount: A:0.63, C:0.11, G:0.06, T:0.20
Consensus pattern (14 bp):
AAATAGTAACAACA
Found at i:2550510 original size:3 final size:3
Alignment explanation
Indices: 2550502--2550549 Score: 96
Period size: 3 Copynumber: 16.0 Consensus size: 3
2550492 TGGGATTTTT
2550502 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
2550550 TATTATTATA
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 45 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:2550556 original size:3 final size:3
Alignment explanation
Indices: 2550550--2550604 Score: 103
Period size: 3 Copynumber: 18.7 Consensus size: 3
2550540 AATAATAATA
2550550 TAT TAT TA- TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
2550597 TAT TAT TA
1 TAT TAT TA
2550605 GAACATATAT
Statistics
Matches: 51, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
2 2 0.04
3 49 0.96
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (3 bp):
TAT
Found at i:2550861 original size:30 final size:31
Alignment explanation
Indices: 2550821--2550885 Score: 91
Period size: 29 Copynumber: 2.1 Consensus size: 31
2550811 ATAGTTTATT
2550821 TTTTTATAATTTTTA-AATAATT-AAAT-TAA
1 TTTTTATAA-TTTTAGAATAATTAAAATATAA
2550850 TTTTTATTAATTTTAGAATAATTAAAATATAA
1 TTTTTA-TAATTTTAGAATAATTAAAATATAA
2550882 TTTT
1 TTTT
2550886 ATTTTTATTA
Statistics
Matches: 32, Mismatches: 0, Indels: 5
0.86 0.00 0.14
Matches are distributed among these distances:
29 11 0.34
30 10 0.31
31 4 0.12
32 7 0.22
ACGTcount: A:0.43, C:0.00, G:0.02, T:0.55
Consensus pattern (31 bp):
TTTTTATAATTTTAGAATAATTAAAATATAA
Found at i:2552571 original size:14 final size:16
Alignment explanation
Indices: 2552552--2552583 Score: 50
Period size: 14 Copynumber: 2.1 Consensus size: 16
2552542 AATTAAAACC
2552552 AATAATT-CA-TTAGA
1 AATAATTACACTTAGA
2552566 AATAATTACACTTAGA
1 AATAATTACACTTAGA
2552582 AA
1 AA
2552584 AAAAAAAGTA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
14 7 0.44
15 2 0.12
16 7 0.44
ACGTcount: A:0.53, C:0.09, G:0.06, T:0.31
Consensus pattern (16 bp):
AATAATTACACTTAGA
Found at i:2555244 original size:15 final size:16
Alignment explanation
Indices: 2555214--2555253 Score: 55
Period size: 15 Copynumber: 2.5 Consensus size: 16
2555204 TAATAAAAAT
2555214 ATAATTTTATTATTTTA
1 ATAA-TTTATTATTTTA
*
2555231 ATAATTTA-TATTTTT
1 ATAATTTATTATTTTA
2555246 ATAATTTA
1 ATAATTTA
2555254 AAAAATAAAT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
15 14 0.64
16 4 0.18
17 4 0.18
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (16 bp):
ATAATTTATTATTTTA
Found at i:2557395 original size:46 final size:46
Alignment explanation
Indices: 2557345--2557443 Score: 189
Period size: 46 Copynumber: 2.2 Consensus size: 46
2557335 GATTTAAATT
*
2557345 TATTTTTGAATTAAAATGTGAAACATAAAAATACTAATATAAAAAA
1 TATTTTTGAACTAAAATGTGAAACATAAAAATACTAATATAAAAAA
2557391 TATTTTTGAACTAAAATGTGAAACATAAAAATACTAATATAAAAAA
1 TATTTTTGAACTAAAATGTGAAACATAAAAATACTAATATAAAAAA
2557437 TATTTTT
1 TATTTTT
2557444 TTTTATTAAT
Statistics
Matches: 52, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
46 52 1.00
ACGTcount: A:0.54, C:0.05, G:0.06, T:0.35
Consensus pattern (46 bp):
TATTTTTGAACTAAAATGTGAAACATAAAAATACTAATATAAAAAA
Found at i:2570573 original size:2 final size:2
Alignment explanation
Indices: 2570566--2570606 Score: 55
Period size: 2 Copynumber: 20.5 Consensus size: 2
2570556 CTTGGAGAGG
* * *
2570566 AT AT AT AT AT AT AT AT AT AT AT AG AT AT AT AC AT AC AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
2570607 AGTGTGAATG
Statistics
Matches: 33, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.51, C:0.05, G:0.02, T:0.41
Consensus pattern (2 bp):
AT
Found at i:2573572 original size:20 final size:20
Alignment explanation
Indices: 2573547--2573587 Score: 82
Period size: 20 Copynumber: 2.0 Consensus size: 20
2573537 ATAAATGAAT
2573547 AGACTAAAATACCTTAAATA
1 AGACTAAAATACCTTAAATA
2573567 AGACTAAAATACCTTAAATA
1 AGACTAAAATACCTTAAATA
2573587 A
1 A
2573588 TATAGTCAAT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.56, C:0.15, G:0.05, T:0.24
Consensus pattern (20 bp):
AGACTAAAATACCTTAAATA
Found at i:2574381 original size:21 final size:21
Alignment explanation
Indices: 2574356--2574397 Score: 61
Period size: 21 Copynumber: 2.1 Consensus size: 21
2574346 GCATTAATTC
2574356 AATA-AAAAAT-TTAAATAAT
1 AATATAAAAATATTAAATAAT
*
2574375 AATATAAATATATTAAATAAT
1 AATATAAAAATATTAAATAAT
2574396 AA
1 AA
2574398 AGGAAATAAA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
19 4 0.20
20 5 0.25
21 11 0.55
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (21 bp):
AATATAAAAATATTAAATAAT
Found at i:2574404 original size:21 final size:21
Alignment explanation
Indices: 2574366--2574405 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
2574356 AATAAAAAAT
*
2574366 TTAAATAATAATATAAATATA
1 TTAAATAATAATAGAAATATA
2574387 TTAAATAATAA-AGGAAATA
1 TTAAATAATAATA-GAAATA
2574406 AATAGTGTGG
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 1 0.06
21 16 0.94
ACGTcount: A:0.62, C:0.00, G:0.05, T:0.33
Consensus pattern (21 bp):
TTAAATAATAATAGAAATATA
Found at i:2579705 original size:5 final size:5
Alignment explanation
Indices: 2579697--2579725 Score: 58
Period size: 5 Copynumber: 5.8 Consensus size: 5
2579687 TCATAAGAGA
2579697 TTTAT TTTAT TTTAT TTTAT TTTAT TTTA
1 TTTAT TTTAT TTTAT TTTAT TTTAT TTTA
2579726 CGAGAACTGA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 24 1.00
ACGTcount: A:0.21, C:0.00, G:0.00, T:0.79
Consensus pattern (5 bp):
TTTAT
Found at i:2579844 original size:2 final size:2
Alignment explanation
Indices: 2579834--2579873 Score: 71
Period size: 2 Copynumber: 20.0 Consensus size: 2
2579824 AAGAACATGA
*
2579834 AT AT CT 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
2579874 TAAAATGTTT
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.47, C:0.03, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:2588547 original size:30 final size:30
Alignment explanation
Indices: 2588513--2588571 Score: 118
Period size: 30 Copynumber: 2.0 Consensus size: 30
2588503 TAATTTAACA
2588513 AATAAATGTCTTTAAAATAATAACAAAATG
1 AATAAATGTCTTTAAAATAATAACAAAATG
2588543 AATAAATGTCTTTAAAATAATAACAAAAT
1 AATAAATGTCTTTAAAATAATAACAAAAT
2588572 TATCAATAAA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 29 1.00
ACGTcount: A:0.58, C:0.07, G:0.05, T:0.31
Consensus pattern (30 bp):
AATAAATGTCTTTAAAATAATAACAAAATG
Found at i:2599649 original size:32 final size:28
Alignment explanation
Indices: 2599595--2599724 Score: 88
Period size: 32 Copynumber: 4.5 Consensus size: 28
2599585 GAGAAAATTC
* *
2599595 AATATTTAATTTTTGATATTTCAAAATTTA
1 AATATTTAATTTTTAAGATTTCAAAA--TA
*
2599625 TATATATTTAATTTTTAAGCTTTCAAAATA
1 -A-ATATTTAATTTTTAAGATTTCAAAATA
* * *
2599655 AATATTTAA-TTTTAAAATTTACCAAACA
1 AATATTTAATTTTTAAGATTT-CAAAATA
*
2599683 AA-A-TTAATTTTTGATA-AGTTCAAAATTA
1 AATATTTAATTTTT-A-AGATTTCAAAA-TA
*
2599711 TATATTTAATTTTT
1 AATATTTAATTTTT
2599725 GCTTATTCAA
Statistics
Matches: 80, Mismatches: 11, Indels: 17
0.74 0.10 0.16
Matches are distributed among these distances:
26 4 0.05
27 18 0.22
28 21 0.26
29 3 0.04
30 11 0.14
31 1 0.01
32 22 0.28
ACGTcount: A:0.42, C:0.05, G:0.03, T:0.49
Consensus pattern (28 bp):
AATATTTAATTTTTAAGATTTCAAAATA
Found at i:2607492 original size:23 final size:23
Alignment explanation
Indices: 2607466--2607509 Score: 63
Period size: 23 Copynumber: 1.9 Consensus size: 23
2607456 ACCAATTATG
2607466 TAATATA-TAAAAACAATATAATA
1 TAATATATTAAAAAC-ATATAATA
*
2607489 TAATATATTATAAACATATAA
1 TAATATATTAAAAACATATAA
2607510 AATAGATTGA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
23 13 0.68
24 6 0.32
ACGTcount: A:0.61, C:0.05, G:0.00, T:0.34
Consensus pattern (23 bp):
TAATATATTAAAAACATATAATA
Found at i:2610817 original size:6 final size:6
Alignment explanation
Indices: 2610806--2610839 Score: 52
Period size: 6 Copynumber: 5.7 Consensus size: 6
2610796 CTTAAAGTTT
2610806 TTTTTG TTTTTG TTTTTG TTTTTTG TTTTT- TTTT
1 TTTTTG TTTTTG TTTTTG -TTTTTG TTTTTG TTTT
2610840 CAAGGATATC
Statistics
Matches: 27, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
5 4 0.15
6 17 0.63
7 6 0.22
ACGTcount: A:0.00, C:0.00, G:0.12, T:0.88
Consensus pattern (6 bp):
TTTTTG
Found at i:2610821 original size:12 final size:12
Alignment explanation
Indices: 2610806--2610839 Score: 52
Period size: 13 Copynumber: 2.8 Consensus size: 12
2610796 CTTAAAGTTT
2610806 TTTTTGTTTTTG
1 TTTTTGTTTTTG
2610818 TTTTTGTTTTTTG
1 TTTTTG-TTTTTG
2610831 TTTTT-TTTT
1 TTTTTGTTTT
2610840 CAAGGATATC
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
11 4 0.19
12 6 0.29
13 11 0.52
ACGTcount: A:0.00, C:0.00, G:0.12, T:0.88
Consensus pattern (12 bp):
TTTTTGTTTTTG
Found at i:2617416 original size:21 final size:21
Alignment explanation
Indices: 2617390--2617430 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
2617380 ATCTGCTCAA
* *
2617390 ACTCCACCTGTTTTGGAGTAC
1 ACTCCACCTGCTGTGGAGTAC
2617411 ACTCCACCTGCTGTGGAGTA
1 ACTCCACCTGCTGTGGAGTA
2617431 TCGCTTGTCT
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:0.20, C:0.29, G:0.22, T:0.29
Consensus pattern (21 bp):
ACTCCACCTGCTGTGGAGTAC
Found at i:2622668 original size:31 final size:33
Alignment explanation
Indices: 2622610--2622670 Score: 83
Period size: 31 Copynumber: 1.9 Consensus size: 33
2622600 CATCATTTCA
*
2622610 ACTCTTTTTTCAAAAGATTAATGATCAAATCCG
1 ACTCTTTTTTCAAAAAATTAATGATCAAATCCG
2622643 ACTC-TTTTT-AAAAAATTAAAT-ATCAAAT
1 ACTCTTTTTTCAAAAAATT-AATGATCAAAT
2622671 TTAACTCAAA
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
31 14 0.54
32 8 0.31
33 4 0.15
ACGTcount: A:0.43, C:0.15, G:0.05, T:0.38
Consensus pattern (33 bp):
ACTCTTTTTTCAAAAAATTAATGATCAAATCCG
Found at i:2629281 original size:18 final size:18
Alignment explanation
Indices: 2629258--2629293 Score: 56
Period size: 18 Copynumber: 2.0 Consensus size: 18
2629248 TTTCCTTTCT
2629258 TTTTTGGC-CTTGTTTATC
1 TTTTTGGCTC-TGTTTATC
2629276 TTTTTGGCTCTGTTTATC
1 TTTTTGGCTCTGTTTATC
2629294 GCAAAACTAT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 16 0.94
19 1 0.06
ACGTcount: A:0.06, C:0.17, G:0.17, T:0.61
Consensus pattern (18 bp):
TTTTTGGCTCTGTTTATC
Found at i:2629424 original size:20 final size:20
Alignment explanation
Indices: 2629399--2629439 Score: 82
Period size: 20 Copynumber: 2.0 Consensus size: 20
2629389 TATGTGTTTA
2629399 AGCATATCTCTAGAGTTGAG
1 AGCATATCTCTAGAGTTGAG
2629419 AGCATATCTCTAGAGTTGAG
1 AGCATATCTCTAGAGTTGAG
2629439 A
1 A
2629440 ATTAAGTTCG
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.32, C:0.15, G:0.24, T:0.29
Consensus pattern (20 bp):
AGCATATCTCTAGAGTTGAG
Found at i:2634780 original size:42 final size:42
Alignment explanation
Indices: 2634713--2634796 Score: 123
Period size: 42 Copynumber: 2.0 Consensus size: 42
2634703 TTTCATAGAG
* * *
2634713 GGTGGTGGTGCAGGAGGACTGGCTCTAATTGGGGCAGCAGGT
1 GGTGGTGGTGCAGGAGAACTAGCTCTAATCGGGGCAGCAGGT
* *
2634755 GGTGGTGGTGGAGGAGAACTAGCTCTAATCGGGGCAGGAGGT
1 GGTGGTGGTGCAGGAGAACTAGCTCTAATCGGGGCAGCAGGT
2634797 TCTGGAGGAA
Statistics
Matches: 37, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
42 37 1.00
ACGTcount: A:0.19, C:0.13, G:0.48, T:0.20
Consensus pattern (42 bp):
GGTGGTGGTGCAGGAGAACTAGCTCTAATCGGGGCAGCAGGT
Found at i:2641359 original size:4 final size:4
Alignment explanation
Indices: 2641340--2641383 Score: 56
Period size: 4 Copynumber: 11.5 Consensus size: 4
2641330 GAAATGATCG
* *
2641340 AATA CATA AGTA AATA AATA AATA AATA AAT- AA-A AATA AATA AA
1 AATA AATA AATA AATA AATA AATA AATA AATA AATA AATA AATA AA
2641384 ACATGGCAAA
Statistics
Matches: 34, Mismatches: 4, Indels: 4
0.81 0.10 0.10
Matches are distributed among these distances:
3 4 0.12
4 30 0.88
ACGTcount: A:0.73, C:0.02, G:0.02, T:0.23
Consensus pattern (4 bp):
AATA
Found at i:2641446 original size:15 final size:15
Alignment explanation
Indices: 2641426--2641457 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
2641416 AAACGATAAT
2641426 AATAATAATAATATA
1 AATAATAATAATATA
*
2641441 AATAATAATATTATA
1 AATAATAATAATATA
2641456 AA
1 AA
2641458 ACGATAATAA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (15 bp):
AATAATAATAATATA
Found at i:2641698 original size:27 final size:27
Alignment explanation
Indices: 2641647--2641699 Score: 79
Period size: 27 Copynumber: 2.0 Consensus size: 27
2641637 TAGATGTATT
*
2641647 AAAATATATATGTAATAATAGAAATAA
1 AAAATATATATGTAATAATAAAAATAA
* *
2641674 AAAATATATATGTAGTATTAAAAATA
1 AAAATATATATGTAATAATAAAAATA
2641700 TATACATAAT
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
27 23 1.00
ACGTcount: A:0.60, C:0.00, G:0.08, T:0.32
Consensus pattern (27 bp):
AAAATATATATGTAATAATAAAAATAA
Found at i:2641965 original size:25 final size:24
Alignment explanation
Indices: 2641905--2641966 Score: 61
Period size: 25 Copynumber: 2.5 Consensus size: 24
2641895 ATGACATATA
* * * *
2641905 TATGAAATATGTACATAATATAGT
1 TATGAAAAATATACATAATAAAAT
*
2641929 TATAAAAGAATATACATAATAAAAT
1 TATGAAA-AATATACATAATAAAAT
2641954 GTATGAAAAATAT
1 -TATGAAAAATAT
2641967 GATATTAACA
Statistics
Matches: 30, Mismatches: 6, Indels: 3
0.77 0.15 0.08
Matches are distributed among these distances:
24 6 0.20
25 18 0.60
26 6 0.20
ACGTcount: A:0.55, C:0.03, G:0.10, T:0.32
Consensus pattern (24 bp):
TATGAAAAATATACATAATAAAAT
Found at i:2641999 original size:35 final size:37
Alignment explanation
Indices: 2641959--2642029 Score: 101
Period size: 35 Copynumber: 2.0 Consensus size: 37
2641949 AAAATGTATG
* *
2641959 AAAAATATGATATT-AACAAT-ATATACATAATATAT
1 AAAAATATAATATTAAAAAATGATATACATAATATAT
*
2641994 AAAAATATAATATTAAAAAATGATATACATGATATA
1 AAAAATATAATATTAAAAAATGATATACATAATATA
2642030 ATATTAATAT
Statistics
Matches: 31, Mismatches: 3, Indels: 2
0.86 0.08 0.06
Matches are distributed among these distances:
35 13 0.42
36 5 0.16
37 13 0.42
ACGTcount: A:0.59, C:0.04, G:0.04, T:0.32
Consensus pattern (37 bp):
AAAAATATAATATTAAAAAATGATATACATAATATAT
Found at i:2642041 original size:20 final size:21
Alignment explanation
Indices: 2642016--2642054 Score: 62
Period size: 20 Copynumber: 1.9 Consensus size: 21
2642006 TTAAAAAATG
2642016 ATATACATG-ATATAATATTA
1 ATATACATGTATATAATATTA
*
2642036 ATATACATGTGTATAATAT
1 ATATACATGTATATAATAT
2642055 GGAGTATAAT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 9 0.53
21 8 0.47
ACGTcount: A:0.46, C:0.05, G:0.08, T:0.41
Consensus pattern (21 bp):
ATATACATGTATATAATATTA
Found at i:2644809 original size:13 final size:13
Alignment explanation
Indices: 2644791--2644815 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
2644781 CGTGGGATCA
2644791 CCGCCGGCCACCG
1 CCGCCGGCCACCG
2644804 CCGCCGGCCACC
1 CCGCCGGCCACC
2644816 ACACGCGGTG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.08, C:0.64, G:0.28, T:0.00
Consensus pattern (13 bp):
CCGCCGGCCACCG
Found at i:2646445 original size:9 final size:9
Alignment explanation
Indices: 2646431--2646455 Score: 50
Period size: 9 Copynumber: 2.8 Consensus size: 9
2646421 AGTTACATAG
2646431 GAACAAAAT
1 GAACAAAAT
2646440 GAACAAAAT
1 GAACAAAAT
2646449 GAACAAA
1 GAACAAA
2646456 TCATGCTGCT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 16 1.00
ACGTcount: A:0.68, C:0.12, G:0.12, T:0.08
Consensus pattern (9 bp):
GAACAAAAT
Found at i:2655349 original size:44 final size:45
Alignment explanation
Indices: 2655296--2655398 Score: 127
Period size: 44 Copynumber: 2.3 Consensus size: 45
2655286 TGTCTTTGAC
* * * *
2655296 ATGGACTTACATGAATTATTCTTGTCTCCAATGCCATA-TATAAT
1 ATGGACTTACATGAATCAATCCTGTCTCCAAAGCCATATTATAAT
** *
2655340 ATGGACTTACATGGCTCAATCCTGTCTCCAAAGCCATATTTCTAAT
1 ATGGACTTACATGAATCAATCCTGTCTCCAAAGCCATA-TTATAAT
2655386 ATGGACTTACATG
1 ATGGACTTACATG
2655399 GCTCATTTCT
Statistics
Matches: 50, Mismatches: 7, Indels: 2
0.85 0.12 0.03
Matches are distributed among these distances:
44 32 0.64
46 18 0.36
ACGTcount: A:0.30, C:0.21, G:0.14, T:0.35
Consensus pattern (45 bp):
ATGGACTTACATGAATCAATCCTGTCTCCAAAGCCATATTATAAT
Found at i:2655397 original size:46 final size:44
Alignment explanation
Indices: 2655318--2655403 Score: 136
Period size: 46 Copynumber: 1.9 Consensus size: 44
2655308 GAATTATTCT
*
2655318 TGTCTCCAATGCCATATATAATATGGACTTACATGGCTCAATCC
1 TGTCTCCAAAGCCATATATAATATGGACTTACATGGCTCAATCC
*
2655362 TGTCTCCAAAGCCATATTTCTAATATGGACTTACATGGCTCA
1 TGTCTCCAAAGCCATA--TATAATATGGACTTACATGGCTCA
2655404 TTTCTGTTCT
Statistics
Matches: 38, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
44 15 0.39
46 23 0.61
ACGTcount: A:0.29, C:0.24, G:0.14, T:0.33
Consensus pattern (44 bp):
TGTCTCCAAAGCCATATATAATATGGACTTACATGGCTCAATCC
Found at i:2658128 original size:72 final size:72
Alignment explanation
Indices: 2658011--2658303 Score: 408
Period size: 72 Copynumber: 4.1 Consensus size: 72
2658001 ACTTGATCAC
* * * * *
2658011 ACCACTCAAGTTGTTTGATGACAAATAAAGAT-CAGAAATGTTCACAAGATGAAAAATGGAATCT
1 ACCACTCAAGTTGTTTGATGACAAATAAAG-TGAAGTAAGGTTCACAAGATCAAAAATGAAATCT
2658075 GGTATTGG
65 GGTATTGG
* * *
2658083 ACCACTCAAGTTGTTTGATGACAAATCAAGTGAAGTAAGGTTCACAAGATCACAACTGAAATCTG
1 ACCACTCAAGTTGTTTGATGACAAATAAAGTGAAGTAAGGTTCACAAGATCAAAAATGAAATCTG
2658148 GTATTGG
66 GTATTGG
* * * * *
2658155 ACCACTCAACTTATTTGATGACAAATAAAGTGAATTAAGGTTCACAAGATCAAAAATGAAAGCCG
1 ACCACTCAAGTTGTTTGATGACAAATAAAGTGAAGTAAGGTTCACAAGATCAAAAATGAAATCTG
2658220 GTATTGG
66 GTATTGG
* * * * *
2658227 ACCACTCAAGTTGTTTAATGACAAATCAAGTGAAATAAGGTTCACAAGATCAAAAATGGAATCGG
1 ACCACTCAAGTTGTTTGATGACAAATAAAGTGAAGTAAGGTTCACAAGATCAAAAATGAAATCTG
2658292 GTATTGG
66 GTATTGG
2658299 ACCAC
1 ACCAC
2658304 CAATGTTATT
Statistics
Matches: 196, Mismatches: 24, Indels: 2
0.88 0.11 0.01
Matches are distributed among these distances:
71 1 0.01
72 195 0.99
ACGTcount: A:0.40, C:0.15, G:0.20, T:0.25
Consensus pattern (72 bp):
ACCACTCAAGTTGTTTGATGACAAATAAAGTGAAGTAAGGTTCACAAGATCAAAAATGAAATCTG
GTATTGG
Found at i:2664372 original size:23 final size:23
Alignment explanation
Indices: 2664346--2664389 Score: 63
Period size: 23 Copynumber: 1.9 Consensus size: 23
2664336 GTAAATAGTA
2664346 AAAATA-AATAAAGTATAACAAGC
1 AAAATATAAT-AAGTATAACAAGC
*
2664369 AAAATATAGTAAGTATAACAA
1 AAAATATAATAAGTATAACAA
2664390 TCTATATTTA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
23 17 0.89
24 2 0.11
ACGTcount: A:0.64, C:0.07, G:0.09, T:0.20
Consensus pattern (23 bp):
AAAATATAATAAGTATAACAAGC
Found at i:2666252 original size:133 final size:133
Alignment explanation
Indices: 2666024--2666532 Score: 759
Period size: 133 Copynumber: 3.8 Consensus size: 133
2666014 GATCTGCTGT
* * * * *
2666024 AATTTGATCTGCTTTACTTCTGCTCAGTAAAGATAAGATCTGGTATGTTTAGCCTGCTCCACTCT
1 AATTTGATCTGCTTCACTCCTGCTCAGTGAAGATAAGATCTGGTA--TATAGCCTGCTCCACTCC
* ** * * *
2666089 TGCTTAGCAAATATAAGGCTGGTGGCTGAAATCTGCTCCATTGCTGATACATGGAGATAA-AATT
64 TGCTCAGTGAAGATAAGGCTGGTGGCTGAAATCTGCTCCATTGCCGATACATGGAGATAAGACTT
*
2666153 CACCAA
129 -GCCAA
* * * * *
2666159 AATTTGATCTGCTCCGCTCCTACTCAGCGAAGATAAGATCTAGTATATAGCCTGCTCCACTCCTG
1 AATTTGATCTGCTTCACTCCTGCTCAGTGAAGATAAGATCTGGTATATAGCCTGCTCCACTCCTG
* *
2666224 CTTAGTGAAGATAAGGCTGGTGGCTGAAATCTGCTCCATTTCCGATACATGGAGATAAGACTTGC
66 CTCAGTGAAGATAAGGCTGGTGGCTGAAATCTGCTCCATTGCCGATACATGGAGATAAGACTTGC
2666289 CAA
131 CAA
* *
2666292 AATTTGATCTGCTTCACTCTTGCTCAGTGAAGATAAGATCTGGTATTTAGCCTGCTCCACTCCTG
1 AATTTGATCTGCTTCACTCCTGCTCAGTGAAGATAAGATCTGGTATATAGCCTGCTCCACTCCTG
*
2666357 CTCAGTGAAGATAAGGCTGGTGGCTAAAATCTGCTCCATTGCCGATACATGGAGATAAGACTTGC
66 CTCAGTGAAGATAAGGCTGGTGGCTGAAATCTGCTCCATTGCCGATACATGGAGATAAGACTTGC
2666422 CAA
131 CAA
* * *
2666425 AATTTGATCTGCTTCACTTCTGCTCAGTGAAGATAAGATCTGGTATATAGACTGCTCCACTTCTG
1 AATTTGATCTGCTTCACTCCTGCTCAGTGAAGATAAGATCTGGTATATAGCCTGCTCCACTCCTG
2666490 CTCAGTGAAGATAAGGCTGGTGGCTGAAATCTGCTCCATTGCC
66 CTCAGTGAAGATAAGGCTGGTGGCTGAAATCTGCTCCATTGCC
2666533 CACTAGGGAA
Statistics
Matches: 340, Mismatches: 33, Indels: 4
0.90 0.09 0.01
Matches are distributed among these distances:
133 300 0.88
134 3 0.01
135 37 0.11
ACGTcount: A:0.27, C:0.22, G:0.21, T:0.30
Consensus pattern (133 bp):
AATTTGATCTGCTTCACTCCTGCTCAGTGAAGATAAGATCTGGTATATAGCCTGCTCCACTCCTG
CTCAGTGAAGATAAGGCTGGTGGCTGAAATCTGCTCCATTGCCGATACATGGAGATAAGACTTGC
CAA
Found at i:2666486 original size:43 final size:44
Alignment explanation
Indices: 2666164--2666504 Score: 157
Period size: 43 Copynumber: 7.7 Consensus size: 44
2666154 ACCAAAATTT
* * * * *
2666164 GATCTGCTCCGCTCCTACTCAGCGAAGATAAGATCTAGTATATA
1 GATCTGCTCCACTTCTGCTCAGTGAAGATAAGATCTGGTATATA
* * * * ***
2666208 G-CCTGCTCCACTCCTGCTTAGTGAAGATAAG-GCTGGTGGCTGA
1 GATCTGCTCCACTTCTGCTCAGTGAAGATAAGATCTGGTATAT-A
* * * * * ** * *
2666251 AATCTGCTCCATTTCCGATACA-TGGAGATAAGA-CTTGCCAAAATTT
1 GATCTGCTCCACTTCTGCT-CAGTGAAGATAAGATC-TG-GTATA-TA
* *
2666297 GATCTGCTTCAC-TCTTGCTCAGTGAAGATAAGATCTGGTATTTA
1 GATCTGCTCCACTTC-TGCTCAGTGAAGATAAGATCTGGTATATA
* * * *
2666341 G-CCTGCTCCACTCCTGCTCAGTGAAGATAAG-GCTGGTGGCTA-A
1 GATCTGCTCCACTTCTGCTCAGTGAAGATAAGATCTGGT--ATATA
* * * * ** * *
2666384 AATCTGCTCCA-TTGCCGATACA-TGGAGATAAGA-CTTGCCAAAATTT
1 GATCTGCTCCACTT-CTGCT-CAGTGAAGATAAGATC-TG-GTATA-TA
*
2666430 GATCTGCTTCACTTCTGCTCAGTGAAGATAAGATCTGGTATATA
1 GATCTGCTCCACTTCTGCTCAGTGAAGATAAGATCTGGTATATA
2666474 GA-CTGCTCCACTTCTGCTCAGTGAAGATAAG
1 GATCTGCTCCACTTCTGCTCAGTGAAGATAAG
2666505 GCTGGTGGCT
Statistics
Matches: 211, Mismatches: 62, Indels: 49
0.66 0.19 0.15
Matches are distributed among these distances:
42 10 0.05
43 81 0.38
44 52 0.25
45 16 0.08
46 47 0.22
47 5 0.02
ACGTcount: A:0.27, C:0.23, G:0.21, T:0.29
Consensus pattern (44 bp):
GATCTGCTCCACTTCTGCTCAGTGAAGATAAGATCTGGTATATA
Found at i:2678247 original size:22 final size:20
Alignment explanation
Indices: 2678200--2678247 Score: 51
Period size: 22 Copynumber: 2.3 Consensus size: 20
2678190 ATGCAATATG
2678200 AAAATAGCAATATAATAACC
1 AAAATAGCAATATAATAACC
** *
2678220 CTAATAGCATATATTAATAACT
1 AAAATAGCA-ATA-TAATAACC
2678242 AAAATA
1 AAAATA
2678248 TAGCAAGCAT
Statistics
Matches: 21, Mismatches: 5, Indels: 2
0.75 0.18 0.07
Matches are distributed among these distances:
20 7 0.33
21 3 0.14
22 11 0.52
ACGTcount: A:0.56, C:0.12, G:0.04, T:0.27
Consensus pattern (20 bp):
AAAATAGCAATATAATAACC
Found at i:2678647 original size:23 final size:23
Alignment explanation
Indices: 2678621--2678664 Score: 63
Period size: 23 Copynumber: 1.9 Consensus size: 23
2678611 GTAAATAGTA
2678621 AAAATA-AATAAAGTATAACAAGC
1 AAAATATAAT-AAGTATAACAAGC
*
2678644 AAAATATAGTAAGTATAACAA
1 AAAATATAATAAGTATAACAA
2678665 TCTATATTTA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
23 17 0.89
24 2 0.11
ACGTcount: A:0.64, C:0.07, G:0.09, T:0.20
Consensus pattern (23 bp):
AAAATATAATAAGTATAACAAGC
Found at i:2679055 original size:27 final size:26
Alignment explanation
Indices: 2678998--2679055 Score: 73
Period size: 26 Copynumber: 2.2 Consensus size: 26
2678988 ATAGTATAAT
*
2678998 AAATAGTGGGATAGAAAAAATTAAAA
1 AAATAGTAGGATAGAAAAAATTAAAA
*
2679024 AAATAGTAGGATATAATAAAA-TAAAA
1 AAATAGTAGGATAGAA-AAAATTAAAA
2679050 ATAATA
1 A-AATA
2679056 AATATTACAA
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
26 20 0.71
27 8 0.29
ACGTcount: A:0.64, C:0.00, G:0.14, T:0.22
Consensus pattern (26 bp):
AAATAGTAGGATAGAAAAAATTAAAA
Found at i:2685617 original size:72 final size:72
Alignment explanation
Indices: 2685500--2685767 Score: 405
Period size: 72 Copynumber: 3.7 Consensus size: 72
2685490 ACTTGATCAC
*
2685500 ACCACTCAAGTTGTTTGATGACAAATCAAGTGAAGTAAGGCTCACAAGATCACAATTGAAATCTG
1 ACCACTCAAGTTGTTTGATGACAAATCAAGTGAAGTAAGGTTCACAAGATCACAATTGAAATCTG
2685565 GTATTGG
66 GTATTGG
2685572 ACCACTCAAGTTGTTTGATGACAAATCAAGTGAAGTAAGGTTCACAAGATCACAATTGAAATCTG
1 ACCACTCAAGTTGTTTGATGACAAATCAAGTGAAGTAAGGTTCACAAGATCACAATTGAAATCTG
* *
2685637 GCAATGG
66 GTATTGG
* * * * * *
2685644 ACCACTCAACTTATTTGATGACAAATTAAGTGAA-TGAAGGTTCACAAGATCAAAAAT-AGAACC
1 ACCACTCAAGTTGTTTGATGACAAATCAAGTGAAGT-AAGGTTCACAAGATCACAATTGA-AATC
*
2685707 CGGTATTGG
64 TGGTATTGG
*
2685716 ACCACTCAAGTTGTTTGATGACAAATCAAGTGAAATAAGGTTCACAAGATCA
1 ACCACTCAAGTTGTTTGATGACAAATCAAGTGAAGTAAGGTTCACAAGATCA
2685768 AAAATGGAAT
Statistics
Matches: 178, Mismatches: 15, Indels: 6
0.89 0.08 0.03
Matches are distributed among these distances:
71 2 0.01
72 175 0.98
73 1 0.01
ACGTcount: A:0.38, C:0.17, G:0.19, T:0.25
Consensus pattern (72 bp):
ACCACTCAAGTTGTTTGATGACAAATCAAGTGAAGTAAGGTTCACAAGATCACAATTGAAATCTG
GTATTGG
Found at i:2685813 original size:72 final size:72
Alignment explanation
Indices: 2685500--2685802 Score: 380
Period size: 72 Copynumber: 4.2 Consensus size: 72
2685490 ACTTGATCAC
* * * * *
2685500 ACCACTCAAGTTGTTTGATGACAAATCAAGTGAAGTAAGGCTCACAAGATCACAATTGAAATCTG
1 ACCACTCAAGTTATTTGATGACAAATCAAGTGAAATAAGGTTCACAAGATCAAAAATGAAATCTG
2685565 GTATTGG
66 GTATTGG
* * * *
2685572 ACCACTCAAGTTGTTTGATGACAAATCAAGTGAAGTAAGGTTCACAAGATCACAATTGAAATCTG
1 ACCACTCAAGTTATTTGATGACAAATCAAGTGAAATAAGGTTCACAAGATCAAAAATGAAATCTG
* *
2685637 GCAATGG
66 GTATTGG
* * *
2685644 ACCACTCAACTTATTTGATGACAAATTAAGTG-AATGAAGGTTCACAAGATCAAAAAT-AGAACC
1 ACCACTCAAGTTATTTGATGACAAATCAAGTGAAAT-AAGGTTCACAAGATCAAAAATGA-AATC
*
2685707 CGGTATTGG
64 TGGTATTGG
* *
2685716 ACCACTCAAGTTGTTTGATGACAAATCAAGTGAAATAAGGTTCACAAGATCAAAAATGGAATAC-
1 ACCACTCAAGTTATTTGATGACAAATCAAGTGAAATAAGGTTCACAAGATCAAAAATGAAAT-CT
*
2685780 GGTATTGA
65 GGTATTGG
2685788 ACCAC-CAATGTTATT
1 ACCACTCAA-GTTATT
2685803 ATACCTCAAA
Statistics
Matches: 205, Mismatches: 20, Indels: 12
0.86 0.08 0.05
Matches are distributed among these distances:
71 6 0.03
72 195 0.95
73 4 0.02
ACGTcount: A:0.39, C:0.17, G:0.19, T:0.26
Consensus pattern (72 bp):
ACCACTCAAGTTATTTGATGACAAATCAAGTGAAATAAGGTTCACAAGATCAAAAATGAAATCTG
GTATTGG
Found at i:2689398 original size:2 final size:2
Alignment explanation
Indices: 2689391--2689423 Score: 57
Period size: 2 Copynumber: 16.5 Consensus size: 2
2689381 TGTAAGTTGA
*
2689391 AT AT AT AT AT AT AT AT AT AT AT AT AT AA AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
2689424 ATTTAATCTT
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (2 bp):
AT
Found at i:2698439 original size:16 final size:17
Alignment explanation
Indices: 2698409--2698441 Score: 50
Period size: 16 Copynumber: 2.0 Consensus size: 17
2698399 ATGAAAGTTC
*
2698409 TTTTAAAATTTTTAAAA
1 TTTTAAAATTATTAAAA
2698426 TTTT-AAATTATTAAAA
1 TTTTAAAATTATTAAAA
2698442 GTAAAATTTT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 11 0.73
17 4 0.27
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (17 bp):
TTTTAAAATTATTAAAA
Found at i:2699170 original size:16 final size:16
Alignment explanation
Indices: 2699149--2699179 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
2699139 GTGGACCCAT
*
2699149 AAAAAATTGAAAACAA
1 AAAAAAGTGAAAACAA
2699165 AAAAAAGTGAAAACA
1 AAAAAAGTGAAAACA
2699180 TCAATAATTA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.74, C:0.06, G:0.10, T:0.10
Consensus pattern (16 bp):
AAAAAAGTGAAAACAA
Found at i:2699620 original size:2 final size:2
Alignment explanation
Indices: 2699613--2699645 Score: 50
Period size: 2 Copynumber: 17.0 Consensus size: 2
2699603 ATAATTTTGA
*
2699613 AT AT AT AT AT AT AT AT AT AT AT AT GT AT A- AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
2699646 GAACTTGATT
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
1 1 0.04
2 27 0.96
ACGTcount: A:0.48, C:0.00, G:0.03, T:0.48
Consensus pattern (2 bp):
AT
Found at i:2701786 original size:39 final size:39
Alignment explanation
Indices: 2701743--2701866 Score: 230
Period size: 39 Copynumber: 3.2 Consensus size: 39
2701733 CAAAATCTAG
*
2701743 CTGAAGCACATAAGTGTTAAACGGAAGCCCGAAGGCTAA
1 CTGAAGCACATAAGTGCTAAACGGAAGCCCGAAGGCTAA
*
2701782 CTGAAGCACATAAGTGCTAAACGGAAGCCCGGAGGCTAA
1 CTGAAGCACATAAGTGCTAAACGGAAGCCCGAAGGCTAA
2701821 CTGAAGCACATAAGTGCTAAACGGAAGCCCGAAGGCTAA
1 CTGAAGCACATAAGTGCTAAACGGAAGCCCGAAGGCTAA
2701860 CTGAAGC
1 CTGAAGC
2701867 TCATCAGAGC
Statistics
Matches: 82, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
39 82 1.00
ACGTcount: A:0.37, C:0.23, G:0.27, T:0.14
Consensus pattern (39 bp):
CTGAAGCACATAAGTGCTAAACGGAAGCCCGAAGGCTAA
Found at i:2705370 original size:88 final size:88
Alignment explanation
Indices: 2705221--2705395 Score: 350
Period size: 88 Copynumber: 2.0 Consensus size: 88
2705211 AGACATACAT
2705221 TTCACTAGTTGTGTGGTGAGTGCACTATTGGAATATGTTGATATACAGCTTGGTCTTCCAGTTCA
1 TTCACTAGTTGTGTGGTGAGTGCACTATTGGAATATGTTGATATACAGCTTGGTCTTCCAGTTCA
2705286 TGGATTACTTGTAATCGAAGAAC
66 TGGATTACTTGTAATCGAAGAAC
2705309 TTCACTAGTTGTGTGGTGAGTGCACTATTGGAATATGTTGATATACAGCTTGGTCTTCCAGTTCA
1 TTCACTAGTTGTGTGGTGAGTGCACTATTGGAATATGTTGATATACAGCTTGGTCTTCCAGTTCA
2705374 TGGATTACTTGTAATCGAAGAA
66 TGGATTACTTGTAATCGAAGAA
2705396 TCAAGTTCGG
Statistics
Matches: 87, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
88 87 1.00
ACGTcount: A:0.25, C:0.14, G:0.24, T:0.37
Consensus pattern (88 bp):
TTCACTAGTTGTGTGGTGAGTGCACTATTGGAATATGTTGATATACAGCTTGGTCTTCCAGTTCA
TGGATTACTTGTAATCGAAGAAC
Found at i:2711246 original size:70 final size:70
Alignment explanation
Indices: 2711171--2711305 Score: 225
Period size: 70 Copynumber: 1.9 Consensus size: 70
2711161 TAGTTTATTA
* * * *
2711171 CTAATTAATTTGCTGCTGTGATATTGTAAATTAGTGGCTGTCCAAATTAGGACAAATTTATGGTG
1 CTAATTAATATGCTGCTGTAATACTGTAAATTAGTGGCTGTCCAAATTAGGACAAAATTATGGTG
2711236 CTTAG
66 CTTAG
*
2711241 CTAATTAATATGCTGCTGTAATACTGTAAATTATTGGCTGTCCAAATTAGGACAAAATTATGGTG
1 CTAATTAATATGCTGCTGTAATACTGTAAATTAGTGGCTGTCCAAATTAGGACAAAATTATGGTG
2711306 TTATGTGCTA
Statistics
Matches: 60, Mismatches: 5, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
70 60 1.00
ACGTcount: A:0.31, C:0.12, G:0.20, T:0.37
Consensus pattern (70 bp):
CTAATTAATATGCTGCTGTAATACTGTAAATTAGTGGCTGTCCAAATTAGGACAAAATTATGGTG
CTTAG
Found at i:2712187 original size:42 final size:43
Alignment explanation
Indices: 2712120--2712232 Score: 138
Period size: 42 Copynumber: 2.7 Consensus size: 43
2712110 GCTAGTGAAT
* * * *
2712120 AATATTATTGGGCTTCGGGCCTAGCAGGCTATAATGCCGATGC
1 AATAATATCGGGCTTCAGGCCTAGCAGGCTATAATGCCGATGA
* * *
2712163 GATAATATCGGG-TTCAGGCCTAGCAAGCTATAATGCCGGTGA
1 AATAATATCGGGCTTCAGGCCTAGCAGGCTATAATGCCGATGA
* *
2712205 AATGATATCGGGCTTCAAGCCTAGCAGG
1 AATAATATCGGGCTTCAGGCCTAGCAGG
2712233 TGAAATGCCG
Statistics
Matches: 58, Mismatches: 11, Indels: 2
0.82 0.15 0.03
Matches are distributed among these distances:
42 36 0.62
43 22 0.38
ACGTcount: A:0.27, C:0.20, G:0.28, T:0.25
Consensus pattern (43 bp):
AATAATATCGGGCTTCAGGCCTAGCAGGCTATAATGCCGATGA
Found at i:2712270 original size:41 final size:42
Alignment explanation
Indices: 2712194--2712273 Score: 101
Period size: 41 Copynumber: 1.9 Consensus size: 42
2712184 AGCAAGCTAT
* * *
2712194 AATGCCGGTGAAATGATATCGGGCTTCAAGCCTAGCAGGTGA
1 AATGCCGGTGAAATGATATCAGACTTAAAGCCTAGCAGGTGA
*
2712236 AATGCCGGTG-AATGAGT-TCAGACTTAAAGTCTAGCAGG
1 AATGCCGGTGAAATGA-TATCAGACTTAAAGCCTAGCAGG
2712274 CTTCGTGCCG
Statistics
Matches: 33, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
41 22 0.67
42 11 0.33
ACGTcount: A:0.30, C:0.17, G:0.30, T:0.23
Consensus pattern (42 bp):
AATGCCGGTGAAATGATATCAGACTTAAAGCCTAGCAGGTGA
Found at i:2712323 original size:40 final size:41
Alignment explanation
Indices: 2712138--2712323 Score: 139
Period size: 42 Copynumber: 4.5 Consensus size: 41
2712128 TGGGCTTCGG
* * * *
2712138 GCCTAGCAGGCTATAATGCCGATGCGAT-AATATCGGG-TTCAG
1 GCCTAGCAGGCTA-AATGCCGGTG-AATGAAT-TCGGGCTTAAA
* *
2712180 GCCTAGCAAGCTATAATGCCGGTGAAATG-ATATCGGGCTTCAA
1 GCCTAGCAGGCTA-AATGCCGGTG-AATGAAT-TCGGGCTTAAA
* * *
2712223 GCCTAGCAGG-TGAAATGCCGGTGAATGAGTTCAGACTTAAA
1 GCCTAGCAGGCT-AAATGCCGGTGAATGAATTCGGGCTTAAA
* *** *
2712264 GTCTAGCAGGCTTCGTGCCGGTG-ATGAATTCGGGTTTAAA
1 GCCTAGCAGGCTAAATGCCGGTGAATGAATTCGGGCTTAAA
*
2712304 ACCTAGCAGGCTAAATGCCG
1 GCCTAGCAGGCTAAATGCCG
2712324 ATGATTTGAT
Statistics
Matches: 116, Mismatches: 23, Indels: 12
0.77 0.15 0.08
Matches are distributed among these distances:
40 28 0.24
41 29 0.25
42 45 0.39
43 14 0.12
ACGTcount: A:0.27, C:0.20, G:0.28, T:0.24
Consensus pattern (41 bp):
GCCTAGCAGGCTAAATGCCGGTGAATGAATTCGGGCTTAAA
Found at i:2714953 original size:3 final size:3
Alignment explanation
Indices: 2714945--2714982 Score: 76
Period size: 3 Copynumber: 12.7 Consensus size: 3
2714935 ACTTATTACA
2714945 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
2714983 ATAGAACAAA
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 35 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:2715647 original size:26 final size:27
Alignment explanation
Indices: 2715618--2715677 Score: 66
Period size: 31 Copynumber: 2.1 Consensus size: 27
2715608 ATATTTATCG
*
2715618 AAATCACATCCATGACCAGGATGATAA
1 AAATCACATACATGACCAGGATGATAA
*
2715645 AATACTGTCGCATACATGACCAGGATGATAA
1 AA-A---TCACATACATGACCAGGATGATAA
2715676 AA
1 AA
2715678 TCCGTCGCAT
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
27 2 0.07
28 1 0.04
31 24 0.89
ACGTcount: A:0.43, C:0.20, G:0.17, T:0.20
Consensus pattern (27 bp):
AAATCACATACATGACCAGGATGATAA
Found at i:2715687 original size:30 final size:31
Alignment explanation
Indices: 2715628--2715703 Score: 118
Period size: 30 Copynumber: 2.5 Consensus size: 31
2715618 AAATCACATC
*
2715628 CATGACCAGGATGATAAAATACTGTCGCATA
1 CATGACCAGGATGATAAAATACCGTCGCATA
*
2715659 CATGACCAGGATGATAAAAT-CCGTCGCATC
1 CATGACCAGGATGATAAAATACCGTCGCATA
*
2715689 CATGACCGGGATGAT
1 CATGACCAGGATGAT
2715704 TATAGTTGTC
Statistics
Matches: 42, Mismatches: 3, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
30 22 0.52
31 20 0.48
ACGTcount: A:0.34, C:0.22, G:0.22, T:0.21
Consensus pattern (31 bp):
CATGACCAGGATGATAAAATACCGTCGCATA
Found at i:2717337 original size:224 final size:223
Alignment explanation
Indices: 2716958--2717607 Score: 905
Period size: 224 Copynumber: 2.9 Consensus size: 223
2716948 GTAGTGATAC
* * * *
2716958 AACACATGAACAAAGATGCTTTGAATATTGATAACTAAGAAAGGCACATCCATGAGGACTCAAAT
1 AACACATGCACAAAGATGCTTTAAATATTGATAACTAAGAAAGGCACATGCATGAGGACTCACA-
* * * *
2717023 GAGAC--TGGATGGCCAAAATAAATGATATAAAGCTAGAAGAGACATATAAGTTGCGAGCTTCAC
65 -AGACTGTGGACGACCAAAACAAATGATATAAAGCTAGAAGAG--A-ATAAGTTGTGAGCTTCAC
*
2717086 TACTATGCCAATATGTAAATCAATCTAACTATTTAGGAGCTTAAGTTCTAGATAATGATAAACTC
126 TACTATGCCAAAATGTAAATCAATCTAACTATTTAGGAGCTTAAGTTCTAGATAATGATAAACTC
2717151 AATTGCGAACCATCGAAGATCTCCATATCATTA
191 AATTGCGAACCATCGAAGATCTCCATATCATTA
* * *
2717184 AACACATGCACAAAGATTCTTTCAAATATTGGTAACTAAAAAAGGCACATGCATGAGGACTCGAC
1 AACACATGCACAAAGATGCTTT-AAATATTGATAACTAAGAAAGGCACATGCATGAGGACTC-AC
2717249 AAGACTGTGGACGACCAAAACAAATGATATAAAGCTAGAAGAG-ATAAGTTGTGAGCTTCACTAC
64 AAGACTGTGGACGACCAAAACAAATGATATAAAGCTAGAAGAGAATAAGTTGTGAGCTTCACTAC
* * *
2717313 TATGCCAAAATGTAAACCAATCTAACTATTTAGGAGCTTAAGTTCTAGATAAGGATAAGCTCAAT
129 TATGCCAAAATGTAAATCAATCTAACTATTTAGGAGCTTAAGTTCTAGATAATGATAAACTCAAT
* * *
2717378 TGTGAACCATTGAGGATCTCCATATCATTA
194 TGCGAACCATCGAAGATCTCCATATCATTA
*
2717408 AACACATGCCCAAAGATGCTTTGAAATATTTGATAACTAAGAAAGGCACATGCATGAGGACTCAA
1 AACACATGCACAAAGATGCTTT-AAATA-TTGATAACTAAGAAAGGCACATGCATGAGGACTC--
*
2717473 ACAAGACTGTGGAC-AGCCAAAACAAATGATATAAAACTAGAAGAGACATATAAGTTGTGAGCTT
62 ACAAGACTGTGGACGA-CCAAAACAAATGATATAAAGCTAGAAGAG--A-ATAAGTTGTGAGCTT
* * *
2717537 CACTAAC-ATGCCAAAATGTAAATCAATCTAACTATTTAGGAGCTTAAGTTCTTGACAATAATAA
123 CACT-ACTATGCCAAAATGTAAATCAATCTAACTATTTAGGAGCTTAAGTTCTAGATAATGATAA
*
2717601 ACACAAT
187 ACTCAAT
2717608 CACGAACCTT
Statistics
Matches: 380, Mismatches: 32, Indels: 20
0.88 0.07 0.05
Matches are distributed among these distances:
224 133 0.35
225 33 0.09
226 66 0.17
227 35 0.09
228 35 0.09
230 76 0.20
231 2 0.01
ACGTcount: A:0.41, C:0.17, G:0.17, T:0.25
Consensus pattern (223 bp):
AACACATGCACAAAGATGCTTTAAATATTGATAACTAAGAAAGGCACATGCATGAGGACTCACAA
GACTGTGGACGACCAAAACAAATGATATAAAGCTAGAAGAGAATAAGTTGTGAGCTTCACTACTA
TGCCAAAATGTAAATCAATCTAACTATTTAGGAGCTTAAGTTCTAGATAATGATAAACTCAATTG
CGAACCATCGAAGATCTCCATATCATTA
Found at i:2720681 original size:2 final size:2
Alignment explanation
Indices: 2720676--2720708 Score: 59
Period size: 2 Copynumber: 17.0 Consensus size: 2
2720666 TTAATACAAT
2720676 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T- TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
2720709 AGCATGAACA
Statistics
Matches: 30, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 29 0.97
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:2722153 original size:21 final size:21
Alignment explanation
Indices: 2722122--2722177 Score: 60
Period size: 21 Copynumber: 2.6 Consensus size: 21
2722112 TAGTTAAATG
2722122 ATTTTTAATTTAATATTTAAT-A
1 ATTTTT-ATTT-ATATTTAATAA
* *
2722144 ATTTTTATTTTTATTTATTAA
1 ATTTTTATTTATATTTAATAA
*
2722165 ATTTTTATATATA
1 ATTTTTATTTATA
2722178 GTCATCGTAA
Statistics
Matches: 29, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
20 7 0.24
21 16 0.55
22 6 0.21
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (21 bp):
ATTTTTATTTATATTTAATAA
Found at i:2739777 original size:13 final size:13
Alignment explanation
Indices: 2739759--2739786 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
2739749 AATAGAAGAA
2739759 AGCCATTACAAAT
1 AGCCATTACAAAT
2739772 AGCCATTACAAAT
1 AGCCATTACAAAT
2739785 AG
1 AG
2739787 AAGAAAGCCA
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:0.46, C:0.21, G:0.11, T:0.21
Consensus pattern (13 bp):
AGCCATTACAAAT
Found at i:2741585 original size:29 final size:29
Alignment explanation
Indices: 2741511--2741585 Score: 75
Period size: 31 Copynumber: 2.6 Consensus size: 29
2741501 AATTAATTTC
2741511 AAAATTAT-T-CATGAATTTTAATTTAAT
1 AAAATTATATACATGAATTTTAATTTAAT
* * *
2741538 ATGTAATT-TGATATATGAATTTTAATTTAGT
1 A--AAATTAT-ATACATGAATTTTAATTTAAT
2741569 AAAATTATATACATGAA
1 AAAATTATATACATGAA
2741586 ATTGGACTTG
Statistics
Matches: 37, Mismatches: 5, Indels: 10
0.71 0.10 0.19
Matches are distributed among these distances:
27 1 0.03
28 1 0.03
29 16 0.43
30 2 0.05
31 17 0.46
ACGTcount: A:0.44, C:0.03, G:0.08, T:0.45
Consensus pattern (29 bp):
AAAATTATATACATGAATTTTAATTTAAT
Found at i:2744285 original size:21 final size:21
Alignment explanation
Indices: 2744253--2744299 Score: 58
Period size: 21 Copynumber: 2.2 Consensus size: 21
2744243 TCTTTTCATA
*
2744253 ATTTTTATTTTTAAAAAATAT
1 ATTTTTAATTTTAAAAAATAT
* * *
2744274 TTTTTTAATTTTTAAATATAT
1 ATTTTTAATTTTAAAAAATAT
2744295 ATTTT
1 ATTTT
2744300 ATGTAAAATA
Statistics
Matches: 21, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (21 bp):
ATTTTTAATTTTAAAAAATAT
Found at i:2745762 original size:36 final size:36
Alignment explanation
Indices: 2745690--2745771 Score: 96
Period size: 36 Copynumber: 2.3 Consensus size: 36
2745680 GTTAATGAAT
* * *
2745690 AATAAATAAATAAAAATATTTTTAATTTTAGGTATA
1 AATAAATAAAGAAAAATATTATTAATTATAGGTATA
*
2745726 AA-ATAATAAAGAATAAATATTATTAATTATA-TTATA
1 AATA-AATAAAGAA-AAATATTATTAATTATAGGTATA
2745762 AATAAATAAA
1 AATAAATAAA
2745772 ATGCAAATCA
Statistics
Matches: 39, Mismatches: 4, Indels: 6
0.80 0.08 0.12
Matches are distributed among these distances:
35 1 0.03
36 22 0.56
37 16 0.41
ACGTcount: A:0.59, C:0.00, G:0.04, T:0.38
Consensus pattern (36 bp):
AATAAATAAAGAAAAATATTATTAATTATAGGTATA
Found at i:2746554 original size:9 final size:10
Alignment explanation
Indices: 2746540--2746571 Score: 50
Period size: 9 Copynumber: 3.4 Consensus size: 10
2746530 TTAAAAACAT
2746540 AATACA-TAA
1 AATACATTAA
2746549 AATACATTAA
1 AATACATTAA
2746559 AA-ACATTAA
1 AATACATTAA
2746568 AATA
1 AATA
2746572 AATGTTTCTT
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
9 15 0.71
10 6 0.29
ACGTcount: A:0.66, C:0.09, G:0.00, T:0.25
Consensus pattern (10 bp):
AATACATTAA
Found at i:2748636 original size:18 final size:18
Alignment explanation
Indices: 2748605--2748639 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
2748595 TTTAAGTTAT
*
2748605 TTATTTAAAAATATAAAA
1 TTATTGAAAAATATAAAA
*
2748623 TTATTGAAACATATAAA
1 TTATTGAAAAATATAAA
2748640 TACATACCTT
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.57, C:0.03, G:0.03, T:0.37
Consensus pattern (18 bp):
TTATTGAAAAATATAAAA
Found at i:2754807 original size:23 final size:23
Alignment explanation
Indices: 2754761--2754806 Score: 76
Period size: 22 Copynumber: 2.0 Consensus size: 23
2754751 AAAAGGCAAC
*
2754761 TAAAAGTATTTTTTTTTACTTTT
1 TAAAAGCATTTTTTTTTACTTTT
2754784 TAAAAGCA-TTTTTTTTACTTTT
1 TAAAAGCATTTTTTTTTACTTTT
2754806 T
1 T
2754807 TTTTCTTTCG
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
22 15 0.68
23 7 0.32
ACGTcount: A:0.26, C:0.07, G:0.04, T:0.63
Consensus pattern (23 bp):
TAAAAGCATTTTTTTTTACTTTT
Found at i:2755407 original size:18 final size:19
Alignment explanation
Indices: 2755386--2755423 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 19
2755376 AAATATATAC
2755386 AATAATTAAAT-T-ATAAAA
1 AATAA-TAAATATCATAAAA
2755404 AATAATAAATATCATAAAA
1 AATAATAAATATCATAAAA
2755423 A
1 A
2755424 TTATAAATCT
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
17 5 0.28
18 6 0.33
19 7 0.39
ACGTcount: A:0.68, C:0.03, G:0.00, T:0.29
Consensus pattern (19 bp):
AATAATAAATATCATAAAA
Found at i:2762665 original size:21 final size:21
Alignment explanation
Indices: 2762641--2762681 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
2762631 CATCGTCTAT
* *
2762641 TTATGCTTTATATTTATTTGA
1 TTATACTTTATAATTATTTGA
*
2762662 TTATACTTTTTAATTATTTG
1 TTATACTTTATAATTATTTG
2762682 GACATGTACT
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.24, C:0.05, G:0.07, T:0.63
Consensus pattern (21 bp):
TTATACTTTATAATTATTTGA
Found at i:2773006 original size:22 final size:22
Alignment explanation
Indices: 2772978--2773033 Score: 67
Period size: 24 Copynumber: 2.5 Consensus size: 22
2772968 AAATAATAAA
2772978 AGAAATATATAACAAATAACAT
1 AGAAATATATAACAAATAACAT
**
2773000 AGAAATATATGTATGAAATAACAT
1 AGAAATATA--TAACAAATAACAT
*
2773024 AAAAATATAT
1 AGAAATATAT
2773034 GAATAGCGCA
Statistics
Matches: 29, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
22 10 0.34
24 19 0.66
ACGTcount: A:0.61, C:0.05, G:0.07, T:0.27
Consensus pattern (22 bp):
AGAAATATATAACAAATAACAT
Found at i:2773327 original size:25 final size:25
Alignment explanation
Indices: 2773290--2773373 Score: 73
Period size: 27 Copynumber: 3.2 Consensus size: 25
2773280 TTATAAGAAA
*
2773290 ATATAACTAATAATATTGAAAATATAT
1 ATATAAC--ATAATATTAAAAATATAT
*
2773317 ATATAACATAATATTTAAAACACATAT
1 ATATAACATAATA-TTAAAA-ATATAT
**
2773344 ATATATGAT-ATA-TAAAAATTATAT
1 ATATAACATAATATTAAAAA-TATAT
2773368 ATATAA
1 ATATAA
2773374 TACACTATAT
Statistics
Matches: 48, Mismatches: 6, Indels: 9
0.76 0.10 0.14
Matches are distributed among these distances:
23 1 0.02
24 14 0.29
25 6 0.12
26 8 0.17
27 19 0.40
ACGTcount: A:0.56, C:0.05, G:0.02, T:0.37
Consensus pattern (25 bp):
ATATAACATAATATTAAAAATATAT
Found at i:2775416 original size:13 final size:14
Alignment explanation
Indices: 2775381--2775414 Score: 50
Period size: 14 Copynumber: 2.4 Consensus size: 14
2775371 AGTTGATTTT
2775381 TGAAAAATAAAAAC
1 TGAAAAATAAAAAC
* *
2775395 TGAAAAATAGAAAT
1 TGAAAAATAAAAAC
2775409 TGAAAA
1 TGAAAA
2775415 TACCTCAGCG
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.68, C:0.03, G:0.12, T:0.18
Consensus pattern (14 bp):
TGAAAAATAAAAAC
Done.