Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr03 135709677
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: 135709677
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 44 of 438
Found at i:11041002 original size:15 final size:14
Alignment explanation
Indices: 11040982--11041012 Score: 53
Period size: 14 Copynumber: 2.1 Consensus size: 14
11040972 AAAAAAAATC
11040982 TTATTTTATTTTTAT
1 TTATTTTA-TTTTAT
11040997 TTATTTTATTTTAT
1 TTATTTTATTTTAT
11041011 TT
1 TT
11041013 TGATTTTATG
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 8 0.50
15 8 0.50
ACGTcount: A:0.19, C:0.00, G:0.00, T:0.81
Consensus pattern (14 bp):
TTATTTTATTTTAT
Found at i:11042954 original size:16 final size:15
Alignment explanation
Indices: 11042935--11042964 Score: 51
Period size: 16 Copynumber: 1.9 Consensus size: 15
11042925 ACACACACAC
11042935 ACACACACATATATAT
1 ACACACACAT-TATAT
11042951 ACACACACATTATA
1 ACACACACATTATA
11042965 CTATTAAGCA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 4 0.29
16 10 0.71
ACGTcount: A:0.50, C:0.27, G:0.00, T:0.23
Consensus pattern (15 bp):
ACACACACATTATAT
Found at i:11042959 original size:2 final size:2
Alignment explanation
Indices: 11042909--11042943 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
11042899 CCATATTCTA
11042909 AC AC AC AC 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 AC AC AC AC A
11042944 TATATATACA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.51, C:0.49, G:0.00, T:0.00
Consensus pattern (2 bp):
AC
Found at i:11043559 original size:3 final size:3
Alignment explanation
Indices: 11043551--11043632 Score: 155
Period size: 3 Copynumber: 27.0 Consensus size: 3
11043541 TGCTTCAATT
11043551 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
11043599 TTA TTA TTA TTA TTA TTA TTA TTA TTA TGTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA T-TA TTA
11043633 GTGTATACTT
Statistics
Matches: 78, Mismatches: 0, Indels: 2
0.98 0.00 0.03
Matches are distributed among these distances:
3 75 0.96
4 3 0.04
ACGTcount: A:0.33, C:0.00, G:0.01, T:0.66
Consensus pattern (3 bp):
TTA
Found at i:11043739 original size:40 final size:41
Alignment explanation
Indices: 11043651--11043740 Score: 98
Period size: 40 Copynumber: 2.2 Consensus size: 41
11043641 TTCATGTACG
*
11043651 TATATATATATGTAGTAATGTTTTATTACTTCATTTTTATAT
1 TATAT-TATATGTAGTAATGTTTTATTACTTAATTTTTATAT
*
11043693 TTTATTATA-GTAGTAAT-TTTTA-TATCTTAATATTATTAT-T
1 TATATTATATGTAGTAATGTTTTATTA-CTTAAT-TT-TTATAT
11043733 TATATTAT
1 TATATTAT
11043741 TATTATTATT
Statistics
Matches: 42, Mismatches: 3, Indels: 8
0.79 0.06 0.15
Matches are distributed among these distances:
38 2 0.05
39 10 0.24
40 18 0.43
41 8 0.19
42 4 0.10
ACGTcount: A:0.32, C:0.03, G:0.06, T:0.59
Consensus pattern (41 bp):
TATATTATATGTAGTAATGTTTTATTACTTAATTTTTATAT
Found at i:11044824 original size:23 final size:22
Alignment explanation
Indices: 11044789--11044845 Score: 69
Period size: 22 Copynumber: 2.5 Consensus size: 22
11044779 TTTACCCTAC
11044789 TATATTTACTATTAATATTAGTACA
1 TATATTT--TATTAATATT-GTACA
* *
11044814 TATATTTTATTATTCTTGTACA
1 TATATTTTATTAATATTGTACA
11044836 TATATTTTAT
1 TATATTTTAT
11044846 ATATAGTATT
Statistics
Matches: 30, Mismatches: 2, Indels: 3
0.86 0.06 0.09
Matches are distributed among these distances:
22 15 0.50
23 8 0.27
25 7 0.23
ACGTcount: A:0.33, C:0.07, G:0.04, T:0.56
Consensus pattern (22 bp):
TATATTTTATTAATATTGTACA
Found at i:11045091 original size:2 final size:2
Alignment explanation
Indices: 11045084--11045115 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
11045074 ATACTATTAC
11045084 TA 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 TA
11045116 ATGTACATAC
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:11045465 original size:16 final size:16
Alignment explanation
Indices: 11045444--11045481 Score: 76
Period size: 16 Copynumber: 2.4 Consensus size: 16
11045434 GTCCTTCTCA
11045444 AAAATCAAAAGAATTG
1 AAAATCAAAAGAATTG
11045460 AAAATCAAAAGAATTG
1 AAAATCAAAAGAATTG
11045476 AAAATC
1 AAAATC
11045482 CTCGTGTTTC
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 22 1.00
ACGTcount: A:0.63, C:0.08, G:0.11, T:0.18
Consensus pattern (16 bp):
AAAATCAAAAGAATTG
Found at i:11048390 original size:3 final size:3
Alignment explanation
Indices: 11048384--11048485 Score: 156
Period size: 3 Copynumber: 34.7 Consensus size: 3
11048374 TTATTTAAGA
* *
11048384 AAT AAT AAT TAT AATT AA- AAA AAT -AT AAT -AT AAT AAT AAT AAT
1 AAT AAT AAT AAT AA-T AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
11048427 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
11048475 AAT AAT AAT AA
1 AAT AAT AAT AA
11048486 AGAATGAAGA
Statistics
Matches: 92, Mismatches: 3, Indels: 8
0.89 0.03 0.08
Matches are distributed among these distances:
2 6 0.07
3 83 0.90
4 3 0.03
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:11049417 original size:6 final size:6
Alignment explanation
Indices: 11049406--11049443 Score: 67
Period size: 6 Copynumber: 6.3 Consensus size: 6
11049396 TCCGTACCTG
*
11049406 ACTGTT ACTGTT ACTGTT ACTGTT ACTATT ACTGTT AC
1 ACTGTT ACTGTT ACTGTT ACTGTT ACTGTT ACTGTT AC
11049444 CCTTACGGTG
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
6 30 1.00
ACGTcount: A:0.21, C:0.18, G:0.13, T:0.47
Consensus pattern (6 bp):
ACTGTT
Found at i:11049449 original size:18 final size:18
Alignment explanation
Indices: 11049410--11049449 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 18
11049400 TACCTGACTG
* **
11049410 TTACTGTTACTGTTACTG
1 TTACTATTACTGTTACCC
11049428 TTACTATTACTGTTACCC
1 TTACTATTACTGTTACCC
11049446 TTAC
1 TTAC
11049450 GGTGTATTTC
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.20, C:0.23, G:0.10, T:0.47
Consensus pattern (18 bp):
TTACTATTACTGTTACCC
Found at i:11052579 original size:22 final size:22
Alignment explanation
Indices: 11052551--11052606 Score: 85
Period size: 22 Copynumber: 2.5 Consensus size: 22
11052541 CGGGTTGATG
*
11052551 ACACGGGCGTGTCACATCAGCC
1 ACACGGGCGTGTCACACCAGCC
*
11052573 ACACGGGCGTGTTACACCAGCC
1 ACACGGGCGTGTCACACCAGCC
*
11052595 ACACAGGCGTGT
1 ACACGGGCGTGT
11052607 GGTACTATTC
Statistics
Matches: 31, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 31 1.00
ACGTcount: A:0.23, C:0.34, G:0.29, T:0.14
Consensus pattern (22 bp):
ACACGGGCGTGTCACACCAGCC
Found at i:11053784 original size:22 final size:21
Alignment explanation
Indices: 11053740--11053784 Score: 56
Period size: 22 Copynumber: 2.1 Consensus size: 21
11053730 GTCATTGGTG
*
11053740 TAAAAAAAATATAGAATGATT
1 TAAAAAAAATATAGAATAATT
11053761 TAAAAATAAATATA-AATAACTT
1 TAAAAA-AAATATAGAATAA-TT
11053783 TA
1 TA
11053785 TTTTTTTAAA
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
21 10 0.48
22 11 0.52
ACGTcount: A:0.62, C:0.02, G:0.04, T:0.31
Consensus pattern (21 bp):
TAAAAAAAATATAGAATAATT
Found at i:11054581 original size:27 final size:27
Alignment explanation
Indices: 11054551--11054637 Score: 90
Period size: 27 Copynumber: 3.2 Consensus size: 27
11054541 ATTATTTAAT
*
11054551 ATTTTTTCATTTATGTAATTTTAATTA
1 ATTTTTTCATTTATGTATTTTTAATTA
* *
11054578 A--TTTTAATTTTTGAATATTATTTAA-TA
1 ATTTTTTCATTTATG--TATT-TTTAATTA
*
11054605 TTTTTTTCATTTATGTATTTTTAATTA
1 ATTTTTTCATTTATGTATTTTTAATTA
11054632 ATTTTT
1 ATTTTT
11054638 ATTTTATAAT
Statistics
Matches: 47, Mismatches: 7, Indels: 12
0.71 0.11 0.18
Matches are distributed among these distances:
25 10 0.21
26 5 0.11
27 17 0.36
28 5 0.11
29 10 0.21
ACGTcount: A:0.29, C:0.02, G:0.03, T:0.66
Consensus pattern (27 bp):
ATTTTTTCATTTATGTATTTTTAATTA
Found at i:11054605 original size:53 final size:54
Alignment explanation
Indices: 11054525--11054642 Score: 193
Period size: 54 Copynumber: 2.2 Consensus size: 54
11054515 GTAACGATTT
* *
11054525 ATTTTAAATATTGAATATTATTTAATA-TTTTTTCATTTATGTAATTTTAATTA
1 ATTTTAATTTTTGAATATTATTTAATATTTTTTTCATTTATGTAATTTTAATTA
*
11054578 ATTTTAATTTTTGAATATTATTTAATATTTTTTTCATTTATGTATTTTTAATTA
1 ATTTTAATTTTTGAATATTATTTAATATTTTTTTCATTTATGTAATTTTAATTA
*
11054632 ATTTTTATTTT
1 ATTTTAATTTT
11054643 ATAATTTTTT
Statistics
Matches: 60, Mismatches: 4, Indels: 1
0.92 0.06 0.02
Matches are distributed among these distances:
53 25 0.42
54 35 0.58
ACGTcount: A:0.31, C:0.02, G:0.03, T:0.64
Consensus pattern (54 bp):
ATTTTAATTTTTGAATATTATTTAATATTTTTTTCATTTATGTAATTTTAATTA
Found at i:11054616 original size:29 final size:29
Alignment explanation
Indices: 11054535--11054616 Score: 84
Period size: 25 Copynumber: 3.0 Consensus size: 29
11054525 ATTTTAAATA
11054535 TTGAATATTATTTAATA-TTTTTTCATTT
1 TTGAATATTATTTAATATTTTTTTCATTT
* * ** *
11054563 ATG--TAAT-TTTAAT-TAATTTTAATTT
1 TTGAATATTATTTAATATTTTTTTCATTT
11054588 TTGAATATTATTTAATATTTTTTTCATTT
1 TTGAATATTATTTAATATTTTTTTCATTT
11054617 ATGTATTTTT
Statistics
Matches: 39, Mismatches: 10, Indels: 9
0.67 0.17 0.16
Matches are distributed among these distances:
25 16 0.41
26 3 0.08
27 3 0.08
28 8 0.21
29 9 0.23
ACGTcount: A:0.30, C:0.02, G:0.04, T:0.63
Consensus pattern (29 bp):
TTGAATATTATTTAATATTTTTTTCATTT
Found at i:11056337 original size:35 final size:35
Alignment explanation
Indices: 11056273--11056470 Score: 209
Period size: 35 Copynumber: 5.6 Consensus size: 35
11056263 CATGGCAAAG
*
11056273 TGTGAAACGTAAGGTAT-AGTATTAACCATATTGAGT
1 TGTGAAACGT-AGGTATGA-TATTAACCATACTGAGT
* *
11056309 TGTGAAACGTAGGTATGATATCATCCATACTGAGT
1 TGTGAAACGTAGGTATGATATTAACCATACTGAGT
* * * *
11056344 TGTGAAATGTAGGTATGGTATTAACCATATTCAGT
1 TGTGAAACGTAGGTATGATATTAACCATACTGAGT
*
11056379 TGTGAAACGTAGGTATGATATTATCCATACTGAGT
1 TGTGAAACGTAGGTATGATATTAACCATACTGAGT
** ** ** * *
11056414 TAAGAAACGTAGGTATGGCATTTCCCATACCGAAT
1 TGTGAAACGTAGGTATGATATTAACCATACTGAGT
* *
11056449 TGTGAAATGTAGGTATGGTATT
1 TGTGAAACGTAGGTATGATATT
11056471 TCAATGAGGA
Statistics
Matches: 135, Mismatches: 26, Indels: 3
0.82 0.16 0.02
Matches are distributed among these distances:
35 124 0.92
36 11 0.08
ACGTcount: A:0.32, C:0.11, G:0.23, T:0.33
Consensus pattern (35 bp):
TGTGAAACGTAGGTATGATATTAACCATACTGAGT
Found at i:11056367 original size:70 final size:70
Alignment explanation
Indices: 11056273--11056465 Score: 260
Period size: 70 Copynumber: 2.7 Consensus size: 70
11056263 CATGGCAAAG
*
11056273 TGTGAAACGTAAGGTATAGTATTAACCATATTGAGTTGTGAAACGTAGGTATGATATCATCCATA
1 TGTGAAACGT-AGGTATGGTATTAACCATATTGAGTTGTGAAACGTAGGTATGATATCATCCATA
11056338 CTGAGT
65 CTGAGT
* * *
11056344 TGTGAAATGTAGGTATGGTATTAACCATATTCAGTTGTGAAACGTAGGTATGATATTATCCATAC
1 TGTGAAACGTAGGTATGGTATTAACCATATTGAGTTGTGAAACGTAGGTATGATATCATCCATAC
11056409 TGAGT
66 TGAGT
** * ** ** * *
11056414 TAAGAAACGTAGGTATGGCATTTCCCATACCGAATTGTGAAATGTAGGTATG
1 TGTGAAACGTAGGTATGGTATTAACCATATTGAGTTGTGAAACGTAGGTATG
11056466 GTATTTCAAT
Statistics
Matches: 107, Mismatches: 15, Indels: 1
0.87 0.12 0.01
Matches are distributed among these distances:
70 98 0.92
71 9 0.08
ACGTcount: A:0.33, C:0.11, G:0.23, T:0.33
Consensus pattern (70 bp):
TGTGAAACGTAGGTATGGTATTAACCATATTGAGTTGTGAAACGTAGGTATGATATCATCCATAC
TGAGT
Found at i:11056442 original size:105 final size:105
Alignment explanation
Indices: 11056273--11056470 Score: 276
Period size: 105 Copynumber: 1.9 Consensus size: 105
11056263 CATGGCAAAG
* **
11056273 TGTGAAACGTAAGGTATAGTATTAACCATATTGAGTTGTGAAACGTAGGTATGATATCATCCATA
1 TGTGAAACGTAAGGTATAGTATTAACCATACTGAGTTAAGAAACGTAGGTATGATATCA-CCATA
* *
11056338 CTGAGTTGTGAAATGTAGGTATGGTATTAACCATATTCAGT
65 CCGAATTGTGAAATGTAGGTATGGTATTAACCATATTCAGT
* *
11056379 TGTGAAACGT-AGGTAT-GATATTATCCATACTGAGTTAAGAAACGTAGGTATGGCATTTC-CCA
1 TGTGAAACGTAAGGTATAG-TATTAACCATACTGAGTTAAGAAACGTAGGTAT-G-ATATCACCA
11056441 TACCGAATTGTGAAATGTAGGTATGGTATT
63 TACCGAATTGTGAAATGTAGGTATGGTATT
11056471 TCAATGAGGA
Statistics
Matches: 82, Mismatches: 7, Indels: 7
0.85 0.07 0.07
Matches are distributed among these distances:
104 1 0.01
105 66 0.80
106 11 0.13
107 4 0.05
ACGTcount: A:0.32, C:0.11, G:0.23, T:0.33
Consensus pattern (105 bp):
TGTGAAACGTAAGGTATAGTATTAACCATACTGAGTTAAGAAACGTAGGTATGATATCACCATAC
CGAATTGTGAAATGTAGGTATGGTATTAACCATATTCAGT
Found at i:11057747 original size:7 final size:7
Alignment explanation
Indices: 11057732--11057791 Score: 111
Period size: 7 Copynumber: 8.6 Consensus size: 7
11057722 AGTCGTTTCA
11057732 TATTTAG
1 TATTTAG
*
11057739 TACTTAG
1 TATTTAG
11057746 TATTTAG
1 TATTTAG
11057753 TATTTAG
1 TATTTAG
11057760 TATTTAG
1 TATTTAG
11057767 TATTTAG
1 TATTTAG
11057774 TATTTAG
1 TATTTAG
11057781 TATTTAG
1 TATTTAG
11057788 TATT
1 TATT
11057792 ATGTATATAA
Statistics
Matches: 51, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
7 51 1.00
ACGTcount: A:0.28, C:0.02, G:0.13, T:0.57
Consensus pattern (7 bp):
TATTTAG
Found at i:11058331 original size:30 final size:30
Alignment explanation
Indices: 11058290--11058347 Score: 98
Period size: 30 Copynumber: 1.9 Consensus size: 30
11058280 TGATGGGACG
11058290 AGCCCATCAACAGCGCCCACACAATCACCA
1 AGCCCATCAACAGCGCCCACACAATCACCA
* *
11058320 AGCCTATCAACAGTGCCCACACAATCAC
1 AGCCCATCAACAGCGCCCACACAATCAC
11058348 TGGGCCCGGT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
30 26 1.00
ACGTcount: A:0.36, C:0.43, G:0.10, T:0.10
Consensus pattern (30 bp):
AGCCCATCAACAGCGCCCACACAATCACCA
Found at i:11067055 original size:126 final size:125
Alignment explanation
Indices: 11066830--11067077 Score: 345
Period size: 126 Copynumber: 2.0 Consensus size: 125
11066820 GGTCAAGCAT
*
11066830 GAACTACTGCAGAAAAAGAGCGTCTACATGAGAGATTTTTTCAGAAATTTTGCTGACAGTGCATC
1 GAACTACTGCAGAAAAAGAGCGTCCACATGAGAGATTTTTTCAGAAATTTTGCTGACAGTGCATC
*
11066895 CTACTTGAAGCAGTTTTTACACTATTTGTTCAGAAACATCTTCTCAAAATTATTTTTTTAG
66 CTACTTGAAGCAGTTTTTACACTATTAGTTCAGAAACATCTTCTC-AAATTATTTTTTTAG
* * * * ** * *
11066956 GAACTACTGTAGAAAATGAGCGTCCACGTGGGAGATTTTTTTTGTAATTTTGTTGACAGTGCATC
1 GAACTACTGCAGAAAAAGAGCGTCCACATGAGAGATTTTTTCAGAAATTTTGCTGACAGTGCATC
* * **
11067021 CTTCTTGAAG-TGTTTTTGACACTATTAGTTCAGAAATGTCTTCTCAAATTATTTTTT
66 CTACTTGAAGCAGTTTTT-ACACTATTAGTTCAGAAACATCTTCTCAAATTATTTTTT
11067078 CAGGGTCAAA
Statistics
Matches: 107, Mismatches: 14, Indels: 3
0.86 0.11 0.02
Matches are distributed among these distances:
125 18 0.17
126 89 0.83
ACGTcount: A:0.29, C:0.15, G:0.17, T:0.39
Consensus pattern (125 bp):
GAACTACTGCAGAAAAAGAGCGTCCACATGAGAGATTTTTTCAGAAATTTTGCTGACAGTGCATC
CTACTTGAAGCAGTTTTTACACTATTAGTTCAGAAACATCTTCTCAAATTATTTTTTTAG
Found at i:11068067 original size:18 final size:18
Alignment explanation
Indices: 11068046--11068089 Score: 54
Period size: 18 Copynumber: 2.4 Consensus size: 18
11068036 TCATTCAGAC
*
11068046 ATTCAGTAGCAATCTA-TT
1 ATTCAGTAACAAT-TAGTT
11068064 ATTCAGTAACAATTAGTT
1 ATTCAGTAACAATTAGTT
*
11068082 TTTCAGTA
1 ATTCAGTA
11068090 CTTTTTTTTA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
17 2 0.09
18 21 0.91
ACGTcount: A:0.34, C:0.14, G:0.11, T:0.41
Consensus pattern (18 bp):
ATTCAGTAACAATTAGTT
Found at i:11068522 original size:5 final size:5
Alignment explanation
Indices: 11068501--11068553 Score: 61
Period size: 5 Copynumber: 10.0 Consensus size: 5
11068491 TGTTAAAATA
* *
11068501 TATAT TAAAT TATTAT TATAT TATAG TATAT TATATT ATATAT TATAT
1 TATAT TATAT TA-TAT TATAT TATAT TATAT TATA-T -TATAT TATAT
11068549 TATAT
1 TATAT
11068554 AAATAAGTAA
Statistics
Matches: 41, Mismatches: 4, Indels: 6
0.80 0.08 0.12
Matches are distributed among these distances:
5 31 0.76
6 6 0.15
7 4 0.10
ACGTcount: A:0.42, C:0.00, G:0.02, T:0.57
Consensus pattern (5 bp):
TATAT
Found at i:11068532 original size:10 final size:9
Alignment explanation
Indices: 11068498--11068554 Score: 59
Period size: 8 Copynumber: 6.6 Consensus size: 9
11068488 ATGTGTTAAA
11068498 ATATATATT
1 ATATATATT
*
11068507 AAAT-TATT
1 ATATATATT
11068515 AT-TATATT
1 ATATATATT
11068523 ATAGTATATT
1 ATA-TATATT
11068533 ATAT-TA-T
1 ATATATATT
11068540 ATATTATATT
1 ATA-TATATT
11068550 ATATA
1 ATATA
11068555 AATAAGTAAA
Statistics
Matches: 40, Mismatches: 2, Indels: 12
0.74 0.04 0.22
Matches are distributed among these distances:
7 5 0.12
8 14 0.35
9 8 0.20
10 13 0.32
ACGTcount: A:0.44, C:0.00, G:0.02, T:0.54
Consensus pattern (9 bp):
ATATATATT
Found at i:11068544 original size:12 final size:12
Alignment explanation
Indices: 11068499--11068554 Score: 69
Period size: 12 Copynumber: 4.5 Consensus size: 12
11068489 TGTGTTAAAA
*
11068499 TATATATTAAAT
1 TATATATTATAT
11068511 TAT-TATTATATT
1 TATATATTATA-T
11068523 ATAGTATATTATAT
1 -TA-TATATTATAT
11068537 TATATATTATAT
1 TATATATTATAT
11068549 TATATA
1 TATATA
11068555 AATAAGTAAA
Statistics
Matches: 39, Mismatches: 1, Indels: 8
0.81 0.02 0.17
Matches are distributed among these distances:
11 6 0.15
12 20 0.51
13 4 0.10
14 2 0.05
15 7 0.18
ACGTcount: A:0.43, C:0.00, G:0.02, T:0.55
Consensus pattern (12 bp):
TATATATTATAT
Found at i:11068928 original size:18 final size:19
Alignment explanation
Indices: 11068907--11068945 Score: 62
Period size: 18 Copynumber: 2.1 Consensus size: 19
11068897 ATATATAGAT
11068907 ATATATATTGAATA-TTGA
1 ATATATATTGAATATTTGA
*
11068925 ATATATATTGATTATTTGA
1 ATATATATTGAATATTTGA
11068944 AT
1 AT
11068946 TGAATTGAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
18 13 0.68
19 6 0.32
ACGTcount: A:0.41, C:0.00, G:0.10, T:0.49
Consensus pattern (19 bp):
ATATATATTGAATATTTGA
Found at i:11069461 original size:18 final size:19
Alignment explanation
Indices: 11069440--11069480 Score: 59
Period size: 19 Copynumber: 2.2 Consensus size: 19
11069430 AATGAAATGA
11069440 GAAATTGA-AT-TGAGAATT
1 GAAATTGAGATATGAG-ATT
11069458 GAAATTGAGATATGAGATT
1 GAAATTGAGATATGAGATT
11069477 GAAA
1 GAAA
11069481 ACATGAACCA
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
18 8 0.38
19 9 0.43
20 4 0.19
ACGTcount: A:0.46, C:0.00, G:0.24, T:0.29
Consensus pattern (19 bp):
GAAATTGAGATATGAGATT
Found at i:11073295 original size:18 final size:18
Alignment explanation
Indices: 11073261--11073320 Score: 59
Period size: 18 Copynumber: 3.3 Consensus size: 18
11073251 AATCGGTTAA
* *
11073261 TCAGTAATATTCATTTAT
1 TCAGTAACAGTCATTTAT
* *
11073279 TCAGTATCAGTCGTTTAT
1 TCAGTAACAGTCATTTAT
*
11073297 TCTA-TAACAGTCAATTAT
1 TC-AGTAACAGTCATTTAT
11073315 TCAGTA
1 TCAGTA
11073321 GCAGACAGTC
Statistics
Matches: 33, Mismatches: 7, Indels: 4
0.75 0.16 0.09
Matches are distributed among these distances:
17 1 0.03
18 31 0.94
19 1 0.03
ACGTcount: A:0.32, C:0.15, G:0.10, T:0.43
Consensus pattern (18 bp):
TCAGTAACAGTCATTTAT
Found at i:11073461 original size:6 final size:6
Alignment explanation
Indices: 11073452--11073478 Score: 54
Period size: 6 Copynumber: 4.5 Consensus size: 6
11073442 CACCGTAAGG
11073452 GTAACA GTAACA GTAACA GTAACA GTA
1 GTAACA GTAACA GTAACA GTAACA GTA
11073479 GCGGTACACA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 21 1.00
ACGTcount: A:0.48, C:0.15, G:0.19, T:0.19
Consensus pattern (6 bp):
GTAACA
Found at i:11074206 original size:11 final size:11
Alignment explanation
Indices: 11074190--11074221 Score: 55
Period size: 11 Copynumber: 2.8 Consensus size: 11
11074180 TACATAATAA
11074190 TAATAATAACT
1 TAATAATAACT
11074201 TAATAATAACT
1 TAATAATAACT
11074212 TATATAATAA
1 TA-ATAATAA
11074222 GTAAATATAC
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
11 13 0.65
12 7 0.35
ACGTcount: A:0.56, C:0.06, G:0.00, T:0.38
Consensus pattern (11 bp):
TAATAATAACT
Found at i:11074807 original size:22 final size:21
Alignment explanation
Indices: 11074779--11074831 Score: 70
Period size: 22 Copynumber: 2.4 Consensus size: 21
11074769 TAAACACCAT
11074779 AAACCCTAGTTTAATTTATTTA
1 AAACCCTAGTTT-ATTTATTTA
*
11074801 AAACCCTAACTTTATTTATTTA
1 AAACCCT-AGTTTATTTATTTA
*
11074823 AAACTCTAG
1 AAACCCTAG
11074832 AACCCTAATT
Statistics
Matches: 27, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
21 1 0.04
22 22 0.81
23 4 0.15
ACGTcount: A:0.38, C:0.17, G:0.04, T:0.42
Consensus pattern (21 bp):
AAACCCTAGTTTATTTATTTA
Found at i:11074859 original size:34 final size:34
Alignment explanation
Indices: 11074809--11074877 Score: 95
Period size: 34 Copynumber: 2.0 Consensus size: 34
11074799 TAAAACCCTA
* * *
11074809 ACTTTATTTATTTAAAACTC-TAGAACCCTAATTT
1 ACTTAATTCATTTAAAAATCATA-AACCCTAATTT
11074843 ACTTAATTCATTTAAAAATCATAAACCCTAATTT
1 ACTTAATTCATTTAAAAATCATAAACCCTAATTT
11074877 A
1 A
11074878 AATAATTTTT
Statistics
Matches: 31, Mismatches: 3, Indels: 2
0.86 0.08 0.06
Matches are distributed among these distances:
34 29 0.94
35 2 0.06
ACGTcount: A:0.41, C:0.17, G:0.01, T:0.41
Consensus pattern (34 bp):
ACTTAATTCATTTAAAAATCATAAACCCTAATTT
Found at i:11074884 original size:34 final size:34
Alignment explanation
Indices: 11074818--11074884 Score: 91
Period size: 34 Copynumber: 2.0 Consensus size: 34
11074808 AACTTTATTT
* **
11074818 ATTTAAAACTCTAGAACCCTAATTTACTTAATTC
1 ATTTAAAAATCTAGAACCCTAATTTAAATAATTC
11074852 ATTTAAAAATCATA-AACCCTAATTTAAATAATT
1 ATTTAAAAATC-TAGAACCCTAATTTAAATAATT
11074885 TTTATAAAAT
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
34 27 0.93
35 2 0.07
ACGTcount: A:0.45, C:0.16, G:0.01, T:0.37
Consensus pattern (34 bp):
ATTTAAAAATCTAGAACCCTAATTTAAATAATTC
Found at i:11076469 original size:15 final size:15
Alignment explanation
Indices: 11076449--11076504 Score: 58
Period size: 15 Copynumber: 3.5 Consensus size: 15
11076439 GTTCAATATT
11076449 AATATTTTAATAATA
1 AATATTTTAATAATA
*
11076464 AATATTTATTACAATTATA
1 AATA-TT-TT--AATAATA
*
11076483 AATATATTAATAATA
1 AATATTTTAATAATA
11076498 AATATTT
1 AATATTT
11076505 CGTAGTATAA
Statistics
Matches: 33, Mismatches: 4, Indels: 8
0.73 0.09 0.18
Matches are distributed among these distances:
15 16 0.48
16 2 0.06
17 4 0.12
18 1 0.03
19 10 0.30
ACGTcount: A:0.52, C:0.02, G:0.00, T:0.46
Consensus pattern (15 bp):
AATATTTTAATAATA
Found at i:11076799 original size:2 final size:2
Alignment explanation
Indices: 11076792--11076821 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
11076782 AATATAAATT
11076792 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
11076822 ATAAACTCAA
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:11079266 original size:18 final size:18
Alignment explanation
Indices: 11079238--11079272 Score: 54
Period size: 19 Copynumber: 1.9 Consensus size: 18
11079228 CAGTAACAGG
11079238 AGAAGTGAAG-AAGAAAA
1 AGAAGTGAAGAAAGAAAA
11079255 AGAAGATGAAGAAAGAAA
1 AGAAG-TGAAGAAAGAAA
11079273 GGGAAAGAAG
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 5 0.31
18 5 0.31
19 6 0.38
ACGTcount: A:0.66, C:0.00, G:0.29, T:0.06
Consensus pattern (18 bp):
AGAAGTGAAGAAAGAAAA
Found at i:11080475 original size:15 final size:15
Alignment explanation
Indices: 11080438--11080476 Score: 51
Period size: 15 Copynumber: 2.6 Consensus size: 15
11080428 TTATATAGTC
*
11080438 TCTTCTTATTATTAT
1 TCTTCTTCTTATTAT
* *
11080453 TCTTCTTCTTCTTTT
1 TCTTCTTCTTATTAT
11080468 TCTTCTTCT
1 TCTTCTTCT
11080477 CCTCTGTTAT
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
15 21 1.00
ACGTcount: A:0.08, C:0.23, G:0.00, T:0.69
Consensus pattern (15 bp):
TCTTCTTCTTATTAT
Found at i:11080900 original size:25 final size:26
Alignment explanation
Indices: 11080870--11080926 Score: 64
Period size: 29 Copynumber: 2.2 Consensus size: 26
11080860 TATTTTTGTC
*
11080870 TTTTAT-TAA-AAATTTGTAAATTAAT
1 TTTTATATAATAAATGTGTAAATT-AT
11080895 TTTTATATAATTTAAATGTGTAAATTAT
1 TTTTATATAA--TAAATGTGTAAATTAT
11080923 TTTT
1 TTTT
11080927 CTGTGTTTAT
Statistics
Matches: 27, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
25 6 0.22
26 3 0.11
28 6 0.22
29 12 0.44
ACGTcount: A:0.39, C:0.00, G:0.05, T:0.56
Consensus pattern (26 bp):
TTTTATATAATAAATGTGTAAATTAT
Found at i:11093352 original size:24 final size:26
Alignment explanation
Indices: 11093305--11093357 Score: 74
Period size: 24 Copynumber: 2.1 Consensus size: 26
11093295 TTCTAAAACA
**
11093305 ATAAATTTATTTTTTTAAACAAAATT
1 ATAAATTTATTTTTAGAAACAAAATT
11093331 ATAAATTTA-TTTTAGAAA-AAAATT
1 ATAAATTTATTTTTAGAAACAAAATT
11093355 ATA
1 ATA
11093358 TTGATAAATT
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
24 9 0.36
25 7 0.28
26 9 0.36
ACGTcount: A:0.51, C:0.02, G:0.02, T:0.45
Consensus pattern (26 bp):
ATAAATTTATTTTTAGAAACAAAATT
Found at i:11093380 original size:23 final size:23
Alignment explanation
Indices: 11093350--11093395 Score: 67
Period size: 23 Copynumber: 2.0 Consensus size: 23
11093340 TTTTAGAAAA
11093350 AAATTATATTGATAAATT-GAATT
1 AAATTATATT-ATAAATTGGAATT
*
11093373 AAATTATATTATAGATTGGAATT
1 AAATTATATTATAAATTGGAATT
11093396 TGAACCAATC
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
22 6 0.29
23 15 0.71
ACGTcount: A:0.46, C:0.00, G:0.11, T:0.43
Consensus pattern (23 bp):
AAATTATATTATAAATTGGAATT
Found at i:11094216 original size:26 final size:25
Alignment explanation
Indices: 11094185--11094236 Score: 86
Period size: 25 Copynumber: 2.0 Consensus size: 25
11094175 AAATCATCAA
11094185 CCCAATTAAACCAAACTAAACCCAAC
1 CCCAATTAAACC-AACTAAACCCAAC
*
11094211 CCCAATTAAACCAACTAAGCCCAAC
1 CCCAATTAAACCAACTAAACCCAAC
11094236 C
1 C
11094237 TACCCTAAAC
Statistics
Matches: 25, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
25 13 0.52
26 12 0.48
ACGTcount: A:0.46, C:0.40, G:0.02, T:0.12
Consensus pattern (25 bp):
CCCAATTAAACCAACTAAACCCAAC
Found at i:11097894 original size:21 final size:22
Alignment explanation
Indices: 11097868--11097938 Score: 69
Period size: 21 Copynumber: 3.3 Consensus size: 22
11097858 TTTTAAGTAG
11097868 TTTT-AATGTTATTTAATTATT
1 TTTTAAATGTTATTTAATTATT
*
11097889 TTTTAAAT-TCTA-TTAACTATGT
1 TTTTAAATGT-TATTTAATTAT-T
* *
11097911 TTTTAAACG-TCTTTAATTATT
1 TTTTAAATGTTATTTAATTATT
11097932 TTTTAAA
1 TTTTAAA
11097939 AAATTAATAA
Statistics
Matches: 41, Mismatches: 4, Indels: 10
0.75 0.07 0.18
Matches are distributed among these distances:
21 21 0.51
22 20 0.49
ACGTcount: A:0.31, C:0.06, G:0.04, T:0.59
Consensus pattern (22 bp):
TTTTAAATGTTATTTAATTATT
Found at i:11097902 original size:22 final size:21
Alignment explanation
Indices: 11097877--11097938 Score: 65
Period size: 22 Copynumber: 2.9 Consensus size: 21
11097867 GTTTTAATGT
11097877 TATTTAATTATTTTTTAAATTC-
1 TATTTAATTATTTTTTAAA--CG
*
11097899 TA-TTAACTATGTTTTTAAACG
1 TATTTAATTAT-TTTTTAAACG
*
11097920 TCTTTAATTATTTTTTAAA
1 TATTTAATTATTTTTTAAA
11097939 AAATTAATAA
Statistics
Matches: 34, Mismatches: 3, Indels: 7
0.77 0.07 0.16
Matches are distributed among these distances:
20 1 0.03
21 16 0.47
22 17 0.50
ACGTcount: A:0.32, C:0.06, G:0.03, T:0.58
Consensus pattern (21 bp):
TATTTAATTATTTTTTAAACG
Found at i:11100457 original size:2 final size:2
Alignment explanation
Indices: 11100452--11100480 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
11100442 TAAAAAATAC
11100452 AT AT AT 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
11100481 AGATATGTGG
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:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:11110467 original size:44 final size:45
Alignment explanation
Indices: 11110370--11110494 Score: 126
Period size: 44 Copynumber: 2.8 Consensus size: 45
11110360 GAACGAAATG
** * *
11110370 AGCCATGTAAGTCCATATTAGAAATATGGTTTTGGAGACAGGATTG
1 AGCCATGTAAGTCCATATTA-AAATATGGCATTGGAGACAGGAATA
* *
11110416 AGCCATGTAAGTCCATATT-ATATATGGCATTGGAGATAGGAATA
1 AGCCATGTAAGTCCATATTAAAATATGGCATTGGAGACAGGAATA
** * * *
11110460 ATTCATGTAAGTCCATGTCAAAGACATGGCATTGG
1 AGCCATGTAAGTCCATATTAAA-ATATGGCATTGG
11110495 CAGGATATTG
Statistics
Matches: 65, Mismatches: 12, Indels: 4
0.80 0.15 0.05
Matches are distributed among these distances:
44 34 0.52
45 1 0.02
46 30 0.46
ACGTcount: A:0.34, C:0.13, G:0.24, T:0.30
Consensus pattern (45 bp):
AGCCATGTAAGTCCATATTAAAATATGGCATTGGAGACAGGAATA
Found at i:11112380 original size:1 final size:1
Alignment explanation
Indices: 11112374--11112398 Score: 50
Period size: 1 Copynumber: 25.0 Consensus size: 1
11112364 CTCTTTCTTC
11112374 TTTTTTTTTTTTTTTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTT
11112399 AACCTTATTG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 24 1.00
ACGTcount: A:0.00, C:0.00, G:0.00, T:1.00
Consensus pattern (1 bp):
T
Found at i:11113646 original size:50 final size:49
Alignment explanation
Indices: 11113573--11113674 Score: 168
Period size: 50 Copynumber: 2.1 Consensus size: 49
11113563 TCGAAAAAAT
* *
11113573 AAAATGTTATTGATTCAAGTTAATTTTAATAAATATATTTTTTAAATAAA
1 AAAATGTTATTAATTCAAGTTAATTTTAATAAATATA-TTTTTAAACAAA
*
11113623 AAAATGTTATTAATTCAATTTAATTTTAATAAATATATTTTTAAACAAA
1 AAAATGTTATTAATTCAAGTTAATTTTAATAAATATATTTTTAAACAAA
11113672 AAA
1 AAA
11113675 TAATTTAAAT
Statistics
Matches: 49, Mismatches: 3, Indels: 1
0.92 0.06 0.02
Matches are distributed among these distances:
49 14 0.29
50 35 0.71
ACGTcount: A:0.49, C:0.03, G:0.04, T:0.44
Consensus pattern (49 bp):
AAAATGTTATTAATTCAAGTTAATTTTAATAAATATATTTTTAAACAAA
Found at i:11114284 original size:16 final size:17
Alignment explanation
Indices: 11114263--11114317 Score: 62
Period size: 16 Copynumber: 3.4 Consensus size: 17
11114253 GTTTGGTTCA
11114263 CTGTAATGGAATAAG-G
1 CTGTAATGGAATAAGAG
*
11114279 CTGTAATTGAAT-AGAG
1 CTGTAATGGAATAAGAG
*
11114295 TTGTAATGGAAT-AGAG
1 CTGTAATGGAATAAGAG
*
11114311 TTGTAAT
1 CTGTAAT
11114318 CAGTAATTCA
Statistics
Matches: 35, Mismatches: 3, Indels: 2
0.88 0.08 0.05
Matches are distributed among these distances:
15 2 0.06
16 33 0.94
ACGTcount: A:0.36, C:0.04, G:0.27, T:0.33
Consensus pattern (17 bp):
CTGTAATGGAATAAGAG
Found at i:11114369 original size:13 final size:13
Alignment explanation
Indices: 11114351--11114377 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
11114341 ATGAAATGGA
11114351 ATAGAACTGTAAT
1 ATAGAACTGTAAT
11114364 ATAGAACTGTAAT
1 ATAGAACTGTAAT
11114377 A
1 A
11114378 GTATTCTTGT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.48, C:0.07, G:0.15, T:0.30
Consensus pattern (13 bp):
ATAGAACTGTAAT
Found at i:11114620 original size:58 final size:57
Alignment explanation
Indices: 11114490--11114648 Score: 180
Period size: 58 Copynumber: 2.8 Consensus size: 57
11114480 TATTGTTATT
* * * * *
11114490 AAATTTTAATAAAATTACTATTAAAAATAATTTAATAAAAATAATAAATAATTTAACC
1 AAATTTTAATATAATTATTATTAAATATAAATTAAT-AAAATAATAAATAATTTAACA
* * * * *
11114548 ATATTTTAACATAATTATTATTAAATATAACTTAATAAAATAATATATAATTTAATA
1 AAATTTTAATATAATTATTATTAAATATAAATTAATAAAATAATAAATAATTTAACA
*
11114605 AAATTCTTAATATAATTATTATT--ATATAAATTAA-AAAATCATAA
1 AAATT-TTAATATAATTATTATTAAATATAAATTAATAAAATAATAA
11114649 CTATTATTAT
Statistics
Matches: 86, Mismatches: 14, Indels: 5
0.82 0.13 0.05
Matches are distributed among these distances:
55 8 0.09
56 10 0.12
57 22 0.26
58 46 0.53
ACGTcount: A:0.55, C:0.04, G:0.00, T:0.40
Consensus pattern (57 bp):
AAATTTTAATATAATTATTATTAAATATAAATTAATAAAATAATAAATAATTTAACA
Found at i:11118287 original size:21 final size:21
Alignment explanation
Indices: 11118257--11118297 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
11118247 ATAGTGAAAT
*
11118257 AATAGCAAAATAGTGAAAAAC
1 AATAGCAAAACAGTGAAAAAC
*
11118278 AATAGGAAAACAGTGAAAAA
1 AATAGCAAAACAGTGAAAAA
11118298 GTATCAATAT
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:0.63, C:0.07, G:0.17, T:0.12
Consensus pattern (21 bp):
AATAGCAAAACAGTGAAAAAC
Found at i:11130948 original size:33 final size:33
Alignment explanation
Indices: 11130911--11131033 Score: 228
Period size: 33 Copynumber: 3.7 Consensus size: 33
11130901 CTCTGTTTCA
11130911 GTTGCTGGACAGGAGCTGGAATGTGAGTGTTTG
1 GTTGCTGGACAGGAGCTGGAATGTGAGTGTTTG
*
11130944 GTTGCTGGACGGGAGCTGGAATGTGAGTGTTTG
1 GTTGCTGGACAGGAGCTGGAATGTGAGTGTTTG
11130977 GTTGCTGGACAGGAGCTGGAATGTGAGTGTTTG
1 GTTGCTGGACAGGAGCTGGAATGTGAGTGTTTG
*
11131010 GTTGCTGGACAGTAGCTGGAATGT
1 GTTGCTGGACAGGAGCTGGAATGT
11131034 CAAGAAGAAA
Statistics
Matches: 87, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
33 87 1.00
ACGTcount: A:0.18, C:0.10, G:0.42, T:0.30
Consensus pattern (33 bp):
GTTGCTGGACAGGAGCTGGAATGTGAGTGTTTG
Found at i:11136883 original size:24 final size:24
Alignment explanation
Indices: 11136855--11136921 Score: 59
Period size: 24 Copynumber: 2.8 Consensus size: 24
11136845 TCTTCACCAC
11136855 ATAATTAAATTATATATTTTTATG
1 ATAATTAAATTATATATTTTTATG
* * *
11136879 ATAATAAAAATATA-ATTTCATTATT
1 ATAATTAAATTATATATTT--TTATG
*
11136904 TTAA-TAAATTATAT-TTTT
1 ATAATTAAATTATATATTTT
11136922 ATAATTTTAA
Statistics
Matches: 34, Mismatches: 6, Indels: 8
0.71 0.12 0.17
Matches are distributed among these distances:
22 1 0.03
23 4 0.12
24 22 0.65
25 7 0.21
ACGTcount: A:0.45, C:0.01, G:0.01, T:0.52
Consensus pattern (24 bp):
ATAATTAAATTATATATTTTTATG
Found at i:11136892 original size:22 final size:21
Alignment explanation
Indices: 11136866--11136923 Score: 53
Period size: 23 Copynumber: 2.6 Consensus size: 21
11136856 TAATTAAATT
11136866 ATATATTTTTATGATAATAAAA
1 ATATATTTTTATGATAAT-AAA
**
11136888 ATATAATTTCATTATTTTAATAAA
1 ATAT-ATTT--TTATGATAATAAA
*
11136912 TTATATTTTTAT
1 ATATATTTTTAT
11136924 AATTTTAAAA
Statistics
Matches: 30, Mismatches: 3, Indels: 7
0.75 0.08 0.17
Matches are distributed among these distances:
21 4 0.13
22 4 0.13
23 8 0.27
24 6 0.20
25 8 0.27
ACGTcount: A:0.43, C:0.02, G:0.02, T:0.53
Consensus pattern (21 bp):
ATATATTTTTATGATAATAAA
Found at i:11136936 original size:24 final size:24
Alignment explanation
Indices: 11136867--11136938 Score: 67
Period size: 24 Copynumber: 3.1 Consensus size: 24
11136857 AATTAAATTA
* **
11136867 TATATTTTTATGATAAT-AAAAA-
1 TATATTTTTATAATTTTAAAAAAT
* * * *
11136889 TATAATTTCATTATTTTAATAAAT
1 TATATTTTTATAATTTTAAAAAAT
11136913 TATATTTTTATAATTTTAAAAAAT
1 TATATTTTTATAATTTTAAAAAAT
11136937 TA
1 TA
11136939 AATTAAATTA
Statistics
Matches: 38, Mismatches: 10, Indels: 2
0.76 0.20 0.04
Matches are distributed among these distances:
22 12 0.32
23 4 0.11
24 22 0.58
ACGTcount: A:0.46, C:0.01, G:0.01, T:0.51
Consensus pattern (24 bp):
TATATTTTTATAATTTTAAAAAAT
Found at i:11137644 original size:37 final size:37
Alignment explanation
Indices: 11137601--11137671 Score: 108
Period size: 37 Copynumber: 1.9 Consensus size: 37
11137591 TTATTATTAA
*
11137601 ATTTTAATAGGATTATTATTAAAA-ATAATTTAATCAT
1 ATTTTAATAGAATTATTA-TAAAATATAATTTAATCAT
*
11137638 ATTTTAATATAATTATTATAAAATATAATTTAAT
1 ATTTTAATAGAATTATTATAAAATATAATTTAAT
11137672 AAAAATAATT
Statistics
Matches: 31, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
36 5 0.16
37 26 0.84
ACGTcount: A:0.48, C:0.01, G:0.03, T:0.48
Consensus pattern (37 bp):
ATTTTAATAGAATTATTATAAAATATAATTTAATCAT
Found at i:11137670 original size:26 final size:25
Alignment explanation
Indices: 11137628--11137705 Score: 79
Period size: 26 Copynumber: 3.1 Consensus size: 25
11137618 ATTAAAAATA
*
11137628 ATTTAATCATAT-TTTAATATAATT
1 ATTTAATAATATATTTAATATAATT
* *
11137652 ATTATAA-AATATAATTTAATAAAAATA
1 ATT-TAATAATAT-ATTTAAT-ATAATT
*
11137679 ATTTAATAATATTTTTAATATAATT
1 ATTTAATAATATATTTAATATAATT
11137704 AT
1 AT
11137706 CTTTATATTA
Statistics
Matches: 43, Mismatches: 6, Indels: 9
0.74 0.10 0.16
Matches are distributed among these distances:
24 7 0.16
25 9 0.21
26 15 0.35
27 12 0.28
ACGTcount: A:0.50, C:0.01, G:0.00, T:0.49
Consensus pattern (25 bp):
ATTTAATAATATATTTAATATAATT
Found at i:11137681 original size:14 final size:15
Alignment explanation
Indices: 11137643--11137687 Score: 65
Period size: 14 Copynumber: 3.0 Consensus size: 15
11137633 ATCATATTTT
*
11137643 AATATAATTATTATAA
1 AATATAATT-TAATAA
11137659 AATATAATTTAATAA
1 AATATAATTTAATAA
11137674 AA-ATAATTTAATAA
1 AATATAATTTAATAA
11137688 TATTTTTAAT
Statistics
Matches: 28, Mismatches: 1, Indels: 2
0.90 0.03 0.06
Matches are distributed among these distances:
14 12 0.43
15 7 0.25
16 9 0.32
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (15 bp):
AATATAATTTAATAA
Found at i:11137718 original size:51 final size:52
Alignment explanation
Indices: 11137616--11137730 Score: 148
Period size: 51 Copynumber: 2.2 Consensus size: 52
11137606 AATAGGATTA
*
11137616 TTAT-TAAAAATAATTTAATCATATTTTAATATAATTATTATAAAATATAAT
1 TTATATAAAAATAATTTAATAATATTTTAATATAATTATTATAAAATATAAT
* *
11137667 TTA-ATAAAAATAATTTAATAATATTTTTAATATAATTATCT-TTATAT-TAAT
1 TTATATAAAAATAATTTAATAATA-TTTTAATATAATTAT-TATAAAATATAAT
*
11137718 TTATATTAAAATA
1 TTATATAAAAATA
11137731 TTTTTGTTGT
Statistics
Matches: 56, Mismatches: 4, Indels: 7
0.84 0.06 0.10
Matches are distributed among these distances:
51 28 0.50
52 27 0.48
53 1 0.02
ACGTcount: A:0.50, C:0.02, G:0.00, T:0.49
Consensus pattern (52 bp):
TTATATAAAAATAATTTAATAATATTTTAATATAATTATTATAAAATATAAT
Found at i:11137729 original size:52 final size:52
Alignment explanation
Indices: 11137617--11137730 Score: 144
Period size: 52 Copynumber: 2.2 Consensus size: 52
11137607 ATAGGATTAT
*
11137617 TATTAAAAATAATTTAATCATATTTTAATATAATTATTATAAAATATAATTTA
1 TATT-AAAATAATTTAATAATATTTTAATATAATTATTATAAAATATAATTTA
* * *
11137670 -ATAAAAATAATTTAATAATATTTTTAATATAATTATCT-TTATAT-TAATTTA
1 TATTAAAATAATTTAATAATA-TTTTAATATAATTAT-TATAAAATATAATTTA
11137721 TATTAAAATA
1 TATTAAAATA
11137731 TTTTTGTTGT
Statistics
Matches: 53, Mismatches: 5, Indels: 7
0.82 0.08 0.11
Matches are distributed among these distances:
51 23 0.43
52 29 0.55
53 1 0.02
ACGTcount: A:0.50, C:0.02, G:0.00, T:0.48
Consensus pattern (52 bp):
TATTAAAATAATTTAATAATATTTTAATATAATTATTATAAAATATAATTTA
Found at i:11137778 original size:34 final size:34
Alignment explanation
Indices: 11137707--11137801 Score: 109
Period size: 34 Copynumber: 2.8 Consensus size: 34
11137697 TATAATTATC
* **** *
11137707 TTTATATTAATTTATATTAAAATATTTTTGTTGT
1 TTTATATTAAATTATATTAAAATATTTAAAATAT
11137741 TTTATATTAAATTATATTAAAATATTTAAAATAT
1 TTTATATTAAATTATATTAAAATATTTAAAATAT
* *
11137775 TTTATTTTTAAATTATATTCAAATATT
1 TTTA-TATTAAATTATATTAAAATATT
11137802 CAAATACTTT
Statistics
Matches: 52, Mismatches: 8, Indels: 1
0.85 0.13 0.02
Matches are distributed among these distances:
34 32 0.62
35 20 0.38
ACGTcount: A:0.40, C:0.01, G:0.02, T:0.57
Consensus pattern (34 bp):
TTTATATTAAATTATATTAAAATATTTAAAATAT
Found at i:11137807 original size:34 final size:35
Alignment explanation
Indices: 11137747--11137818 Score: 110
Period size: 34 Copynumber: 2.1 Consensus size: 35
11137737 TTGTTTTATA
*
11137747 TTAAATTATATTAAAATATTTAAAATATTTTATTT
1 TTAAATTATATTAAAATATTTAAAATACTTTATTT
* *
11137782 TTAAATTATATTCAAATA-TTCAAATACTTTATTT
1 TTAAATTATATTAAAATATTTAAAATACTTTATTT
11137816 TTA
1 TTA
11137819 TATTTTCTAA
Statistics
Matches: 34, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
34 17 0.50
35 17 0.50
ACGTcount: A:0.43, C:0.04, G:0.00, T:0.53
Consensus pattern (35 bp):
TTAAATTATATTAAAATATTTAAAATACTTTATTT
Found at i:11139520 original size:13 final size:14
Alignment explanation
Indices: 11139493--11139521 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
11139483 TAATGTAACC
11139493 GAAACTAATTAATT
1 GAAACTAATTAATT
11139507 GAAACTAA-TAATT
1 GAAACTAATTAATT
11139520 GA
1 GA
11139522 CAATGAATTA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 7 0.47
14 8 0.53
ACGTcount: A:0.52, C:0.07, G:0.10, T:0.31
Consensus pattern (14 bp):
GAAACTAATTAATT
Found at i:11139690 original size:2 final size:2
Alignment explanation
Indices: 11139683--11139721 Score: 78
Period size: 2 Copynumber: 19.5 Consensus size: 2
11139673 TTGTGAATGT
11139683 TA TA TA TA TA 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
11139722 GTTTTAGTAA
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:11141242 original size:21 final size:20
Alignment explanation
Indices: 11141195--11141244 Score: 55
Period size: 21 Copynumber: 2.5 Consensus size: 20
11141185 ATAGCCCAGG
* * *
11141195 TCGTATGGCTTCACACATGG
1 TCGTGTGGCTTCACACACGC
*
11141215 TCATGTGGCTTCCACACACGC
1 TCGTGTGGCTT-CACACACGC
11141236 TCGTGTGGC
1 TCGTGTGGC
11141245 CAGACCGTGT
Statistics
Matches: 24, Mismatches: 5, Indels: 1
0.80 0.17 0.03
Matches are distributed among these distances:
20 9 0.38
21 15 0.62
ACGTcount: A:0.16, C:0.30, G:0.26, T:0.28
Consensus pattern (20 bp):
TCGTGTGGCTTCACACACGC
Found at i:11147808 original size:63 final size:63
Alignment explanation
Indices: 11147741--11147945 Score: 222
Period size: 63 Copynumber: 3.2 Consensus size: 63
11147731 CAGGAACATG
* *
11147741 GGCGTGTGCCCAGGCCGTGTAACTCACTGTTTGTA-GTATAAAAACCATATGGCC-AGAGACAC
1 GGCGTGTGCCTAGGCCGTGTAACTCACTGTTTGTAGGTATAAAAACCACATGGCCAAG-GACAC
*
11147803 AGGCGTGTGCCTAGGCCGTGTAACTCACTGTTTG-AGGTATAGAAACCACATGGCCAAGGACAC
1 -GGCGTGTGCCTAGGCCGTGTAACTCACTGTTTGTAGGTATAAAAACCACATGGCCAAGGACAC
* * * * * *
11147866 GAGCTTGTGCCTAAGCCATGTAACTCACAGTTTGT-GCT-TAAAAAACCACATTGCCAAGGCACA
1 G-GCGTGTGCCTAGGCCGTGTAACTCACTGTTTGTAGGTAT-AAAAACCACATGGCCAAGG-ACA
*
11147929 TG
63 -C
*
11147931 GGCGTGTGCCAAGGC
1 GGCGTGTGCCTAGGC
11147946 ACATGGGCGT
Statistics
Matches: 121, Mismatches: 14, Indels: 13
0.82 0.09 0.09
Matches are distributed among these distances:
62 3 0.02
63 101 0.83
64 16 0.13
65 1 0.01
ACGTcount: A:0.27, C:0.24, G:0.26, T:0.22
Consensus pattern (63 bp):
GGCGTGTGCCTAGGCCGTGTAACTCACTGTTTGTAGGTATAAAAACCACATGGCCAAGGACAC
Found at i:11147942 original size:20 final size:20
Alignment explanation
Indices: 11147917--11147958 Score: 84
Period size: 20 Copynumber: 2.1 Consensus size: 20
11147907 AAAACCACAT
11147917 TGCCAAGGCACATGGGCGTG
1 TGCCAAGGCACATGGGCGTG
11147937 TGCCAAGGCACATGGGCGTG
1 TGCCAAGGCACATGGGCGTG
11147957 TG
1 TG
11147959 GCAGAATGTT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.19, C:0.24, G:0.40, T:0.17
Consensus pattern (20 bp):
TGCCAAGGCACATGGGCGTG
Found at i:11149304 original size:13 final size:13
Alignment explanation
Indices: 11149286--11149310 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
11149276 CAAACATTTC
11149286 AAAAACACTTTTG
1 AAAAACACTTTTG
11149299 AAAAACACTTTT
1 AAAAACACTTTT
11149311 TCACAGCAAA
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:0.48, C:0.16, G:0.04, T:0.32
Consensus pattern (13 bp):
AAAAACACTTTTG
Found at i:11150992 original size:17 final size:18
Alignment explanation
Indices: 11150972--11151152 Score: 83
Period size: 17 Copynumber: 9.9 Consensus size: 18
11150962 TTCTTTTCAC
11150972 ATATTTAAAAT-TTTAAT
1 ATATTTAAAATATTTAAT
* *
11150989 ATATTTAAAATTTTTAAA
1 ATATTTAAAATATTTAAT
* *
11151007 AT-TTTAAATATATTAAAAA
1 ATATTTAAA-ATATT-TAAT
* *** * *
11151026 ATCTTTTTTATGTTT-AC
1 ATATTTAAAATATTTAAT
* *
11151043 CTATTAAAAATATATTAA-
1 ATATTTAAAATAT-TTAAT
11151061 ATATATTAAAAT-TTTAAT
1 ATAT-TTAAAATATTTAAT
11151079 ATATTTGAAATATATATTGAAT
1 ATATTT-AAA-ATAT-TT-AAT
11151101 ATA-TTAAAATTATATTGAAT
1 ATATTTAAAA-TAT-TT-AAT
*
11151121 ATATTAAAAAT-TTTAAT
1 ATATTTAAAATATTTAAT
11151138 ATA-TTAAAAT-TTTAA
1 ATATTTAAAATATTTAA
11151153 AATTGGTTAT
Statistics
Matches: 129, Mismatches: 20, Indels: 31
0.72 0.11 0.17
Matches are distributed among these distances:
16 11 0.09
17 36 0.28
18 26 0.20
19 20 0.16
20 21 0.16
21 9 0.07
22 6 0.05
ACGTcount: A:0.48, C:0.02, G:0.02, T:0.48
Consensus pattern (18 bp):
ATATTTAAAATATTTAAT
Found at i:11151008 original size:26 final size:27
Alignment explanation
Indices: 11150975--11151025 Score: 86
Period size: 27 Copynumber: 1.9 Consensus size: 27
11150965 TTTTCACATA
*
11150975 TTTAAAATTTT-AATATATTTAAAATT
1 TTTAAAATTTTAAATATATTAAAAATT
11151001 TTTAAAATTTTAAATATATTAAAAA
1 TTTAAAATTTTAAATATATTAAAAA
11151026 ATCTTTTTTA
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
26 11 0.48
27 12 0.52
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (27 bp):
TTTAAAATTTTAAATATATTAAAAATT
Found at i:11151060 original size:11 final size:10
Alignment explanation
Indices: 11151044--11151155 Score: 75
Period size: 9 Copynumber: 11.9 Consensus size: 10
11151034 TATGTTTACC
11151044 TATTAAAAATA
1 TATT-AAAATA
11151055 TATT-AAATA
1 TATTAAAATA
11151064 TATTAAAAT-
1 TATTAAAATA
*
11151073 T-TTAATATA
1 TATTAAAATA
11151082 T-TTGAAATATA
1 TATT-AAA-ATA
*
11151093 TATT-GAATA
1 TATTAAAATA
11151102 TATTAAAATTA
1 TATTAAAA-TA
*
11151113 TATT-GAATA
1 TATTAAAATA
11151122 TATTAAAA-A
1 TATTAAAATA
*
11151131 T-TT-TAATA
1 TATTAAAATA
11151139 TATTAAAAT-
1 TATTAAAATA
11151148 T-TTAAAAT
1 TATTAAAAT
11151156 TGGTTATACT
Statistics
Matches: 82, Mismatches: 8, Indels: 25
0.71 0.07 0.22
Matches are distributed among these distances:
7 2 0.02
8 17 0.21
9 31 0.38
10 16 0.20
11 14 0.17
12 2 0.02
ACGTcount: A:0.52, C:0.00, G:0.03, T:0.46
Consensus pattern (10 bp):
TATTAAAATA
Found at i:11151069 original size:20 final size:19
Alignment explanation
Indices: 11151044--11151146 Score: 108
Period size: 20 Copynumber: 5.4 Consensus size: 19
11151034 TATGTTTACC
11151044 TATTAAAAATATATTAAATA
1 TATTAAAAATATATT-AATA
11151064 TATT-AAAAT-T-TTAATA
1 TATTAAAAATATATTAATA
*
11151080 TATTTGAAATATATATTGAATA
1 TA-TT-AAAAATATATT-AATA
*
11151102 TATTAAAATTATATTGAATA
1 TATTAAAAATATATT-AATA
11151122 TATTAAAAAT-T-TTAATA
1 TATTAAAAATATATTAATA
11151139 TATTAAAA
1 TATTAAAA
11151147 TTTTAAAATT
Statistics
Matches: 73, Mismatches: 4, Indels: 15
0.79 0.04 0.16
Matches are distributed among these distances:
16 6 0.08
17 16 0.22
18 3 0.04
19 10 0.14
20 28 0.38
21 4 0.05
22 6 0.08
ACGTcount: A:0.52, C:0.00, G:0.03, T:0.45
Consensus pattern (19 bp):
TATTAAAAATATATTAATA
Found at i:11151094 original size:38 final size:35
Alignment explanation
Indices: 11151044--11151152 Score: 114
Period size: 38 Copynumber: 2.9 Consensus size: 35
11151034 TATGTTTACC
11151044 TATTAAAAATATATTAAATATATTAAAATTTTAATA
1 TATT-AAAATATATTAAATATATTAAAATTTTAATA
*
11151080 TATTTGAAATATATATTGAATATATTAAAATTATATTGAATA
1 TA-TT-AAA-ATATATTAAATATATTAAAA-T-T-TT-AATA
*
11151122 TATTAAAA-AT-TTTAATATATTAAAATTTTAA
1 TATTAAAATATATTAAATATATTAAAATTTTAA
11151153 AATTGGTTAT
Statistics
Matches: 64, Mismatches: 3, Indels: 15
0.78 0.04 0.18
Matches are distributed among these distances:
33 2 0.03
34 2 0.03
35 1 0.02
36 3 0.05
37 19 0.30
38 21 0.33
39 2 0.03
40 4 0.06
41 4 0.06
42 6 0.09
ACGTcount: A:0.51, C:0.00, G:0.03, T:0.46
Consensus pattern (35 bp):
TATTAAAATATATTAAATATATTAAAATTTTAATA
Found at i:11151095 original size:13 final size:11
Alignment explanation
Indices: 11151076--11151124 Score: 50
Period size: 11 Copynumber: 4.6 Consensus size: 11
11151066 TTAAAATTTT
11151076 AATATAT-TTG
1 AATATATATTG
11151086 AAATATATATTG
1 -AATATATATTG
**
11151098 AATATAT-TAA
1 AATATATATTG
11151108 AAT-TATATTG
1 AATATATATTG
11151118 AATATAT
1 AATATAT
11151125 TAAAAATTTT
Statistics
Matches: 31, Mismatches: 4, Indels: 6
0.76 0.10 0.15
Matches are distributed among these distances:
9 3 0.10
10 8 0.26
11 17 0.55
12 3 0.10
ACGTcount: A:0.49, C:0.00, G:0.06, T:0.45
Consensus pattern (11 bp):
AATATATATTG
Found at i:11155003 original size:3 final size:3
Alignment explanation
Indices: 11154997--11155089 Score: 82
Period size: 3 Copynumber: 30.7 Consensus size: 3
11154987 TTTTTTCCCC
* *
11154997 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAAT GAAT TAT TAT TGT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T-AT -TAT TAT TAT TAT
* * * * *
11155044 TAT TTT CTAC T-T TAT TAG TAT TAT TA- TAT TAT CAC TAT TAT TAT
1 TAT TAT -TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
11155088 TA
1 TA
11155090 CCATATCATT
Statistics
Matches: 71, Mismatches: 14, Indels: 10
0.75 0.15 0.11
Matches are distributed among these distances:
2 3 0.04
3 63 0.89
4 5 0.07
ACGTcount: A:0.32, C:0.04, G:0.03, T:0.60
Consensus pattern (3 bp):
TAT
Found at i:11166164 original size:21 final size:20
Alignment explanation
Indices: 11166140--11166188 Score: 57
Period size: 21 Copynumber: 2.5 Consensus size: 20
11166130 ATAAATTTTA
11166140 AAAATAATAAA-TAATATATAT
1 AAAATAATAAAGTAATAT-T-T
*
11166161 AAAA-AGTAAAGTAATATTT
1 AAAATAATAAAGTAATATTT
11166180 AAAATAATA
1 AAAATAATA
11166189 TATAGGATAT
Statistics
Matches: 24, Mismatches: 2, Indels: 5
0.77 0.06 0.16
Matches are distributed among these distances:
19 5 0.21
20 9 0.38
21 10 0.42
ACGTcount: A:0.65, C:0.00, G:0.04, T:0.31
Consensus pattern (20 bp):
AAAATAATAAAGTAATATTT
Found at i:11166402 original size:16 final size:17
Alignment explanation
Indices: 11166374--11166405 Score: 57
Period size: 16 Copynumber: 1.9 Consensus size: 17
11166364 GAAAGATATT
11166374 TATATTATATTAATAAA
1 TATATTATATTAATAAA
11166391 TATATT-TATTAATAA
1 TATATTATATTAATAA
11166406 CGATTAAAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 9 0.60
17 6 0.40
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (17 bp):
TATATTATATTAATAAA
Found at i:11166712 original size:17 final size:17
Alignment explanation
Indices: 11166690--11166723 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
11166680 AATAGTTCTC
*
11166690 AAATAATTTATTTAATA
1 AAATAATTTATATAATA
11166707 AAATAATTTATATAATA
1 AAATAATTTATATAATA
11166724 TTAAAAATTA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (17 bp):
AAATAATTTATATAATA
Found at i:11166836 original size:16 final size:16
Alignment explanation
Indices: 11166817--11166858 Score: 50
Period size: 16 Copynumber: 2.6 Consensus size: 16
11166807 TTATTTTTCT
11166817 AATTTATTATTAT-TGA
1 AATTTATTATTATAT-A
* *
11166833 AATTTAATATTATATT
1 AATTTATTATTATATA
11166849 AATTTATTAT
1 AATTTATTAT
11166859 CGTTAACTAT
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
16 21 0.95
17 1 0.05
ACGTcount: A:0.40, C:0.00, G:0.02, T:0.57
Consensus pattern (16 bp):
AATTTATTATTATATA
Found at i:11168350 original size:84 final size:84
Alignment explanation
Indices: 11168209--11168377 Score: 329
Period size: 84 Copynumber: 2.0 Consensus size: 84
11168199 TTTCAATTGA
11168209 ACCCATTCATCCTTAAATATTTATGTACTCTTAATTTATTTTTAATTTACTTGTGTAAAATGATT
1 ACCCATTCATCCTTAAATATTTATGTACTCTTAATTTATTTTTAATTTACTTGTGTAAAATGATT
11168274 TCTTATGCAACTTTATATT
66 TCTTATGCAACTTTATATT
*
11168293 ACCCATTCATCCTTAAATATTTATGTACTCTTAATTTATTTTTAATTTATTTGTGTAAAATGATT
1 ACCCATTCATCCTTAAATATTTATGTACTCTTAATTTATTTTTAATTTACTTGTGTAAAATGATT
11168358 TCTTATGCAACTTTATATT
66 TCTTATGCAACTTTATATT
11168377 A
1 A
11168378 ATTGAAATAT
Statistics
Matches: 84, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
84 84 1.00
ACGTcount: A:0.30, C:0.14, G:0.06, T:0.50
Consensus pattern (84 bp):
ACCCATTCATCCTTAAATATTTATGTACTCTTAATTTATTTTTAATTTACTTGTGTAAAATGATT
TCTTATGCAACTTTATATT
Found at i:11169208 original size:37 final size:38
Alignment explanation
Indices: 11169134--11169209 Score: 127
Period size: 39 Copynumber: 2.0 Consensus size: 38
11169124 AAGTGACCAA
*
11169134 ATTCAATGGGCAAAAGATATCTTTTTTTTTTTTAAGAAG
1 ATTCAATGGGCAAAAGATATC-TTTTTTTTTTAAAGAAG
11169173 ATTCAATGGGCAAAAGATATC-TTTTTTTTTAAAGAAG
1 ATTCAATGGGCAAAAGATATCTTTTTTTTTTAAAGAAG
11169210 GATCTATCTT
Statistics
Matches: 36, Mismatches: 1, Indels: 2
0.92 0.03 0.05
Matches are distributed among these distances:
37 15 0.42
39 21 0.58
ACGTcount: A:0.36, C:0.08, G:0.16, T:0.41
Consensus pattern (38 bp):
ATTCAATGGGCAAAAGATATCTTTTTTTTTTAAAGAAG
Found at i:11169709 original size:18 final size:18
Alignment explanation
Indices: 11169686--11169724 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 18
11169676 TAACCAACCA
*
11169686 ATTAACCGAATTCAA-TCG
1 ATTAACCAAATT-AATTCG
11169704 ATTAACCAAATTAATTCG
1 ATTAACCAAATTAATTCG
11169722 ATT
1 ATT
11169725 TTACTTTAGA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
17 2 0.11
18 17 0.89
ACGTcount: A:0.41, C:0.18, G:0.08, T:0.33
Consensus pattern (18 bp):
ATTAACCAAATTAATTCG
Found at i:11170278 original size:3 final size:3
Alignment explanation
Indices: 11170270--11170313 Score: 88
Period size: 3 Copynumber: 14.7 Consensus size: 3
11170260 ATTTTTTAAA
11170270 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT AT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT AT
11170314 AGTTATAATA
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 41 1.00
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
ATT
Found at i:11171155 original size:21 final size:20
Alignment explanation
Indices: 11171125--11171165 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 20
11171115 TAATACAAAA
11171125 ATGAGCCTT-AAATCAAGTTT
1 ATGAGCCTTAAAATC-AGTTT
11171145 ATGAGACCTTAAAATCAGTTT
1 ATGAG-CCTTAAAATCAGTTT
11171166 GTAAATAATT
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
20 5 0.26
21 9 0.47
22 5 0.26
ACGTcount: A:0.37, C:0.15, G:0.15, T:0.34
Consensus pattern (20 bp):
ATGAGCCTTAAAATCAGTTT
Found at i:11171888 original size:2 final size:2
Alignment explanation
Indices: 11171881--11171909 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
11171871 ACAAATGCAA
11171881 AT AT AT 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
11171910 CACATTTATA
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:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:11172330 original size:26 final size:26
Alignment explanation
Indices: 11172294--11172429 Score: 236
Period size: 26 Copynumber: 5.2 Consensus size: 26
11172284 TGATACAAAT
11172294 TGATAATAGGTTAGGTAAATGTTTCA
1 TGATAATAGGTTAGGTAAATGTTTCA
*
11172320 TGATAATAGGTTAGGTAAATGTTCCA
1 TGATAATAGGTTAGGTAAATGTTTCA
*
11172346 TGATAATAGGTTAGGTAAATGTTCCA
1 TGATAATAGGTTAGGTAAATGTTTCA
*
11172372 TGATAATGGGTTAGGTAAATGTTTCA
1 TGATAATAGGTTAGGTAAATGTTTCA
*
11172398 TGATAATGGGTTAGGTAAATGTTTCA
1 TGATAATAGGTTAGGTAAATGTTTCA
11172424 TGATAA
1 TGATAA
11172430 GAATATCATG
Statistics
Matches: 107, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
26 107 1.00
ACGTcount: A:0.34, C:0.05, G:0.24, T:0.37
Consensus pattern (26 bp):
TGATAATAGGTTAGGTAAATGTTTCA
Found at i:11173971 original size:26 final size:26
Alignment explanation
Indices: 11173919--11173971 Score: 63
Period size: 26 Copynumber: 2.0 Consensus size: 26
11173909 TTTACAGTTT
*
11173919 TACCCCTAGGTGATAAATTATCGAAA
1 TACCCCTAGGTGATAAATTACCGAAA
* *
11173945 TACCCCTAGG-GTTAAATTGACCTAAA
1 TACCCCTAGGTGATAAATT-ACCGAAA
11173971 T
1 T
11173972 GCATATTTGA
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
25 7 0.30
26 16 0.70
ACGTcount: A:0.36, C:0.21, G:0.15, T:0.28
Consensus pattern (26 bp):
TACCCCTAGGTGATAAATTACCGAAA
Found at i:11178689 original size:25 final size:24
Alignment explanation
Indices: 11178647--11178699 Score: 61
Period size: 24 Copynumber: 2.2 Consensus size: 24
11178637 AAATTTAGCT
* **
11178647 TTTAATATTTATCTTTTTTGTCAC
1 TTTAAAATTTATCTTTTTAATCAC
*
11178671 TTTAAAATTTATTTATTTTAATCAC
1 TTTAAAATTTATCT-TTTTAATCAC
11178696 TTTA
1 TTTA
11178700 GCTCTTAATT
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
24 12 0.50
25 12 0.50
ACGTcount: A:0.28, C:0.09, G:0.02, T:0.60
Consensus pattern (24 bp):
TTTAAAATTTATCTTTTTAATCAC
Found at i:11178854 original size:29 final size:29
Alignment explanation
Indices: 11178784--11178854 Score: 78
Period size: 26 Copynumber: 2.5 Consensus size: 29
11178774 AAAGAAATTA
*
11178784 TTAAAAGTTATTATAACATTAAATAAAAT
1 TTAAAAATTATTATAACATTAAATAAAAT
*
11178813 TTAAAAA-TA-TATAA-A-TATATAAATAT
1 TTAAAAATTATTATAACATTAAATAAA-AT
11178839 TTAAAAATTATCTATA
1 TTAAAAATTAT-TATA
11178855 TTAACAATAA
Statistics
Matches: 36, Mismatches: 2, Indels: 8
0.78 0.04 0.17
Matches are distributed among these distances:
25 7 0.19
26 10 0.28
27 7 0.19
28 2 0.06
29 10 0.28
ACGTcount: A:0.56, C:0.03, G:0.01, T:0.39
Consensus pattern (29 bp):
TTAAAAATTATTATAACATTAAATAAAAT
Found at i:11181340 original size:14 final size:15
Alignment explanation
Indices: 11181311--11181341 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
11181301 TAAATACGTG
11181311 AAATATAAATTTAAA
1 AAATATAAATTTAAA
11181326 AAATATAAA-TTAAA
1 AAATATAAATTTAAA
11181340 AA
1 AA
11181342 TTTACATATA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 7 0.44
15 9 0.56
ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (15 bp):
AAATATAAATTTAAA
Found at i:11182609 original size:33 final size:34
Alignment explanation
Indices: 11182542--11182609 Score: 120
Period size: 34 Copynumber: 2.0 Consensus size: 34
11182532 CGAATCAAAG
*
11182542 ACTACAAAATTCTAATTCATAATATTTTTTTATT
1 ACTACAAAATTCAAATTCATAATATTTTTTTATT
11182576 ACTACAAAATTCAAATTCATAATA-TTTTTTATT
1 ACTACAAAATTCAAATTCATAATATTTTTTTATT
11182609 A
1 A
11182610 TGTGTTGGAA
Statistics
Matches: 33, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
33 10 0.30
34 23 0.70
ACGTcount: A:0.41, C:0.12, G:0.00, T:0.47
Consensus pattern (34 bp):
ACTACAAAATTCAAATTCATAATATTTTTTTATT
Found at i:11184413 original size:23 final size:23
Alignment explanation
Indices: 11184383--11184426 Score: 79
Period size: 23 Copynumber: 1.9 Consensus size: 23
11184373 TTATTGCGGT
*
11184383 TAGTATAAAAATAATAATAATAA
1 TAGTATAAAAATAACAATAATAA
11184406 TAGTATAAAAATAACAATAAT
1 TAGTATAAAAATAACAATAAT
11184427 TGTAAAATTA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
23 20 1.00
ACGTcount: A:0.64, C:0.02, G:0.05, T:0.30
Consensus pattern (23 bp):
TAGTATAAAAATAACAATAATAA
Found at i:11186143 original size:39 final size:39
Alignment explanation
Indices: 11186100--11186176 Score: 118
Period size: 39 Copynumber: 2.0 Consensus size: 39
11186090 CCCCAGTCAG
* *
11186100 TCAACAAAATGCAAAATTTACTAGAATGCTTAGTGGGAT
1 TCAACAAAATGCAAAATTAACCAGAATGCTTAGTGGGAT
* *
11186139 TCAACAAAATGGAAAATTAACCAGAATTCTTAGTGGGA
1 TCAACAAAATGCAAAATTAACCAGAATGCTTAGTGGGA
11186177 CTGAAAGGAT
Statistics
Matches: 34, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
39 34 1.00
ACGTcount: A:0.43, C:0.13, G:0.18, T:0.26
Consensus pattern (39 bp):
TCAACAAAATGCAAAATTAACCAGAATGCTTAGTGGGAT
Found at i:11194173 original size:22 final size:23
Alignment explanation
Indices: 11194139--11194182 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 23
11194129 CTTTTAGAGT
*
11194139 TTTACTATCAC-AATATAATATA
1 TTTACAATCACAAATATAATATA
*
11194161 TTTACAATTACAAATATAATAT
1 TTTACAATCACAAATATAATAT
11194183 TAGTTTAGAT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
22 9 0.47
23 10 0.53
ACGTcount: A:0.48, C:0.11, G:0.00, T:0.41
Consensus pattern (23 bp):
TTTACAATCACAAATATAATATA
Found at i:11201043 original size:6 final size:6
Alignment explanation
Indices: 11201002--11201031 Score: 60
Period size: 6 Copynumber: 5.0 Consensus size: 6
11200992 GATTTTCTCC
11201002 AAAATG AAAATG AAAATG AAAATG AAAATG
1 AAAATG AAAATG AAAATG AAAATG AAAATG
11201032 GAGAAATGGA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 24 1.00
ACGTcount: A:0.67, C:0.00, G:0.17, T:0.17
Consensus pattern (6 bp):
AAAATG
Found at i:11204301 original size:18 final size:18
Alignment explanation
Indices: 11204268--11204302 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
11204258 TTGAGAAAAG
*
11204268 AATTTAATTGACTAATTT
1 AATTTAATTAACTAATTT
*
11204286 AATTTAATTAATTAATT
1 AATTTAATTAACTAATT
11204303 AATATTTTTT
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:0.43, C:0.03, G:0.03, T:0.51
Consensus pattern (18 bp):
AATTTAATTAACTAATTT
Found at i:11210064 original size:18 final size:18
Alignment explanation
Indices: 11210008--11210064 Score: 53
Period size: 18 Copynumber: 3.2 Consensus size: 18
11209998 CCGGATGATA
11210008 GTCAATAACCAGATTATT
1 GTCAATAACCAGATTATT
** * * *
11210026 GTCTTTTATCA-ATTCAAT
1 GTCAATAACCAGATT-ATT
11210044 GTCAATAACCAGATTATT
1 GTCAATAACCAGATTATT
11210062 GTC
1 GTC
11210065 TTTTATCAAA
Statistics
Matches: 27, Mismatches: 10, Indels: 4
0.66 0.24 0.10
Matches are distributed among these distances:
17 3 0.11
18 21 0.78
19 3 0.11
ACGTcount: A:0.33, C:0.18, G:0.11, T:0.39
Consensus pattern (18 bp):
GTCAATAACCAGATTATT
Found at i:11219400 original size:17 final size:17
Alignment explanation
Indices: 11219378--11219414 Score: 74
Period size: 17 Copynumber: 2.2 Consensus size: 17
11219368 TGTCAAAGGG
11219378 AAACAAATGAATCTTAA
1 AAACAAATGAATCTTAA
11219395 AAACAAATGAATCTTAA
1 AAACAAATGAATCTTAA
11219412 AAA
1 AAA
11219415 ATTAATAAAA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 20 1.00
ACGTcount: A:0.62, C:0.11, G:0.05, T:0.22
Consensus pattern (17 bp):
AAACAAATGAATCTTAA
Found at i:11226218 original size:16 final size:16
Alignment explanation
Indices: 11226197--11226238 Score: 75
Period size: 16 Copynumber: 2.6 Consensus size: 16
11226187 TTGGGTTTTC
11226197 TTATGTTTTTTTATCT
1 TTATGTTTTTTTATCT
11226213 TTATGTTTTTTTATCT
1 TTATGTTTTTTTATCT
11226229 TTATGCTTTT
1 TTATG-TTTT
11226239 GAGATGTTTT
Statistics
Matches: 25, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
16 21 0.84
17 4 0.16
ACGTcount: A:0.12, C:0.07, G:0.07, T:0.74
Consensus pattern (16 bp):
TTATGTTTTTTTATCT
Found at i:11227107 original size:19 final size:19
Alignment explanation
Indices: 11227076--11227113 Score: 60
Period size: 19 Copynumber: 2.0 Consensus size: 19
11227066 TTACAATTTA
11227076 AATTTTCATTTTATTTTCT
1 AATTTTCATTTTATTTTCT
11227095 AATTCTTCA-TTTATTTTCT
1 AATT-TTCATTTTATTTTCT
11227114 TCTGACAGGT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
19 14 0.78
20 4 0.22
ACGTcount: A:0.21, C:0.13, G:0.00, T:0.66
Consensus pattern (19 bp):
AATTTTCATTTTATTTTCT
Found at i:11229043 original size:25 final size:25
Alignment explanation
Indices: 11229015--11229066 Score: 104
Period size: 25 Copynumber: 2.1 Consensus size: 25
11229005 TGCCTTATAA
11229015 AATGTTTAAATAGCTAGGTCTTGAG
1 AATGTTTAAATAGCTAGGTCTTGAG
11229040 AATGTTTAAATAGCTAGGTCTTGAG
1 AATGTTTAAATAGCTAGGTCTTGAG
11229065 AA
1 AA
11229067 ACCCAAGCAA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 27 1.00
ACGTcount: A:0.35, C:0.08, G:0.23, T:0.35
Consensus pattern (25 bp):
AATGTTTAAATAGCTAGGTCTTGAG
Found at i:11235582 original size:55 final size:55
Alignment explanation
Indices: 11235497--11235604 Score: 137
Period size: 55 Copynumber: 2.0 Consensus size: 55
11235487 ATGAAGTCTC
* *
11235497 ACGCCCGTGTTAATCTAATAGGTTCAGCCACGGTTGC-TTGGCACGGGCGTGTCGT
1 ACGCCCGTGTTAATCTAACAGGTTCAGCCACGGTTGCAAT-GCACGGGCGTGTCGT
* * ** *
11235552 ACGCCCGTGTTAATTTGACAGGTTTGGCCACGGTTTCAATGCACGGGCGTGTC
1 ACGCCCGTGTTAATCTAACAGGTTCAGCCACGGTTGCAATGCACGGGCGTGTC
11235605 ACATGCCCGT
Statistics
Matches: 45, Mismatches: 7, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
55 44 0.98
56 1 0.02
ACGTcount: A:0.17, C:0.25, G:0.31, T:0.28
Consensus pattern (55 bp):
ACGCCCGTGTTAATCTAACAGGTTCAGCCACGGTTGCAATGCACGGGCGTGTCGT
Found at i:11239742 original size:13 final size:13
Alignment explanation
Indices: 11239724--11239750 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
11239714 GCTCGGCAGG
11239724 GACACGCCCGTGT
1 GACACGCCCGTGT
11239737 GACACGCCCGTGT
1 GACACGCCCGTGT
11239750 G
1 G
11239751 CGATTACTTC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.15, C:0.37, G:0.33, T:0.15
Consensus pattern (13 bp):
GACACGCCCGTGT
Found at i:11243104 original size:13 final size:13
Alignment explanation
Indices: 11243088--11243114 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
11243078 CTCACACGGG
11243088 CGTGTCACATGGC
1 CGTGTCACATGGC
11243101 CGTGTCACATGGC
1 CGTGTCACATGGC
11243114 C
1 C
11243115 ATTCCCTTTG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.15, C:0.33, G:0.30, T:0.22
Consensus pattern (13 bp):
CGTGTCACATGGC
Found at i:11248490 original size:30 final size:30
Alignment explanation
Indices: 11248455--11248512 Score: 100
Period size: 30 Copynumber: 1.9 Consensus size: 30
11248445 CACGACCATG
11248455 ACACACGGGCGTGTGG-TCTACCCGTGTGTC
1 ACACACGGGCGTGTGGATC-ACCCGTGTGTC
11248485 ACACACGGGCGTGTGGATCACCCGTGTG
1 ACACACGGGCGTGTGGATCACCCGTGTG
11248513 GAAGTGCCTA
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
30 25 0.93
31 2 0.07
ACGTcount: A:0.16, C:0.29, G:0.34, T:0.21
Consensus pattern (30 bp):
ACACACGGGCGTGTGGATCACCCGTGTGTC
Found at i:11250385 original size:5 final size:6
Alignment explanation
Indices: 11250366--11250395 Score: 53
Period size: 6 Copynumber: 5.2 Consensus size: 6
11250356 AAATAAAGGG
11250366 AAATAA AAATAA AAATAA AAAT-A AAATAA A
1 AAATAA AAATAA AAATAA AAATAA AAATAA A
11250396 CAGTGTAACA
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
5 5 0.22
6 18 0.78
ACGTcount: A:0.83, C:0.00, G:0.00, T:0.17
Consensus pattern (6 bp):
AAATAA
Found at i:11263572 original size:14 final size:14
Alignment explanation
Indices: 11263530--11263584 Score: 58
Period size: 14 Copynumber: 3.8 Consensus size: 14
11263520 AATCAAAATT
11263530 TATAATGATATA-AA
1 TATAAT-ATATATAA
*
11263544 TTATGAAAATATATAA
1 -TAT-AATATATATAA
*
11263560 TATAATGTATATAA
1 TATAATATATATAA
11263574 TATAATATATA
1 TATAATATATA
11263585 AAAAAATATC
Statistics
Matches: 34, Mismatches: 4, Indels: 5
0.79 0.09 0.12
Matches are distributed among these distances:
14 19 0.56
15 11 0.32
16 4 0.12
ACGTcount: A:0.55, C:0.00, G:0.05, T:0.40
Consensus pattern (14 bp):
TATAATATATATAA
Found at i:11271929 original size:22 final size:21
Alignment explanation
Indices: 11271903--11271963 Score: 63
Period size: 19 Copynumber: 3.0 Consensus size: 21
11271893 ATTAAATATC
11271903 CAAGATTACAAGATCATATCTT
1 CAAGATTAC-AGATCATATCTT
* *
11271925 CAAGATTGCATATCATATC-T
1 CAAGATTACAGATCATATCTT
* *
11271945 -AAGATTGCATATCATATCT
1 CAAGATTACAGATCATATCT
11271964 AAGATTTTAT
Statistics
Matches: 36, Mismatches: 2, Indels: 4
0.86 0.05 0.10
Matches are distributed among these distances:
19 18 0.50
20 1 0.03
21 9 0.25
22 8 0.22
ACGTcount: A:0.38, C:0.18, G:0.10, T:0.34
Consensus pattern (21 bp):
CAAGATTACAGATCATATCTT
Found at i:11271950 original size:19 final size:19
Alignment explanation
Indices: 11271915--11271993 Score: 117
Period size: 19 Copynumber: 4.2 Consensus size: 19
11271905 AGATTACAAG
11271915 ATCATATCTTCAAGATTGCAT
1 ATCATATC-T-AAGATTGCAT
11271936 ATCATATCTAAGATTGCAT
1 ATCATATCTAAGATTGCAT
*
11271955 ATCATATCTAAGATT--TT
1 ATCATATCTAAGATTGCAT
11271972 ATCATATCTAAGATTGCAT
1 ATCATATCTAAGATTGCAT
11271991 ATC
1 ATC
11271994 CTTAAAGATT
Statistics
Matches: 54, Mismatches: 2, Indels: 6
0.87 0.03 0.10
Matches are distributed among these distances:
17 16 0.30
19 29 0.54
20 1 0.02
21 8 0.15
ACGTcount: A:0.35, C:0.16, G:0.09, T:0.39
Consensus pattern (19 bp):
ATCATATCTAAGATTGCAT
Found at i:11272980 original size:47 final size:47
Alignment explanation
Indices: 11272923--11273052 Score: 188
Period size: 47 Copynumber: 2.8 Consensus size: 47
11272913 ATGTGAATAA
* *
11272923 TACCTTGATTTGGCTATAGGCCATGGTGTAGGTATTCAGAGAGAAGT
1 TACCTTGATTTGGCTATAGGCCATGGTATAGGTACTCAGAGAGAAGT
* * * *
11272970 TACCTTGATTTGGCTATAAGCCATGGTATAGGTACTCCGGGATAAGT
1 TACCTTGATTTGGCTATAGGCCATGGTATAGGTACTCAGAGAGAAGT
* *
11273017 TACCTTGATTTGGCTATGGGTCATGGTATAGGTACT
1 TACCTTGATTTGGCTATAGGCCATGGTATAGGTACT
11273053 TATTGATTAA
Statistics
Matches: 74, Mismatches: 9, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
47 74 1.00
ACGTcount: A:0.24, C:0.15, G:0.28, T:0.34
Consensus pattern (47 bp):
TACCTTGATTTGGCTATAGGCCATGGTATAGGTACTCAGAGAGAAGT
Found at i:11273154 original size:20 final size:20
Alignment explanation
Indices: 11273129--11273177 Score: 80
Period size: 20 Copynumber: 2.5 Consensus size: 20
11273119 TTTGAGAAAG
*
11273129 AGGTACGTACAAGACGGTAC
1 AGGTACGTACAAGACGATAC
*
11273149 AGGTACGTACGAGACGATAC
1 AGGTACGTACAAGACGATAC
11273169 AGGTACGTA
1 AGGTACGTA
11273178 TGGAACCTAT
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
20 27 1.00
ACGTcount: A:0.35, C:0.18, G:0.31, T:0.16
Consensus pattern (20 bp):
AGGTACGTACAAGACGATAC
Found at i:11274487 original size:30 final size:30
Alignment explanation
Indices: 11274451--11274510 Score: 120
Period size: 30 Copynumber: 2.0 Consensus size: 30
11274441 TGTGAAATGT
11274451 TAGTTAACTGTTGTGTTTGGTCGGTAATAC
1 TAGTTAACTGTTGTGTTTGGTCGGTAATAC
11274481 TAGTTAACTGTTGTGTTTGGTCGGTAATAC
1 TAGTTAACTGTTGTGTTTGGTCGGTAATAC
11274511 CTCTCAACCT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 30 1.00
ACGTcount: A:0.20, C:0.10, G:0.27, T:0.43
Consensus pattern (30 bp):
TAGTTAACTGTTGTGTTTGGTCGGTAATAC
Found at i:11279476 original size:30 final size:31
Alignment explanation
Indices: 11279412--11279477 Score: 80
Period size: 30 Copynumber: 2.2 Consensus size: 31
11279402 CTTCCTGCAT
*
11279412 TAAAATCCAACCAAATACAACAAATATAATA
1 TAAAATCCAACCAAATACAACAAATATAACA
* * * *
11279443 TAAAATGCAGCCAAA-ACAGCAAATTTAACA
1 TAAAATCCAACCAAATACAACAAATATAACA
11279473 TAAAA
1 TAAAA
11279478 AATACAACCA
Statistics
Matches: 30, Mismatches: 5, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
30 17 0.57
31 13 0.43
ACGTcount: A:0.59, C:0.18, G:0.05, T:0.18
Consensus pattern (31 bp):
TAAAATCCAACCAAATACAACAAATATAACA
Found at i:11279489 original size:32 final size:30
Alignment explanation
Indices: 11279413--11279490 Score: 75
Period size: 32 Copynumber: 2.5 Consensus size: 30
11279403 TTCCTGCATT
* *
11279413 AAAATCCAACCAAATACAACAAATATAATAT
1 AAAATACAACCAAA-ACAACAAATATAATAA
* * * *
11279444 AAAATGCAGCCAAAACAGCAAATTTAACATAA
1 AAAATACAACCAAAACAACAAATAT-A-ATAA
11279476 AAAATACAACCAAAA
1 AAAATACAACCAAAA
11279491 ACATTAATTC
Statistics
Matches: 38, Mismatches: 7, Indels: 3
0.79 0.15 0.06
Matches are distributed among these distances:
30 9 0.24
31 13 0.34
32 16 0.42
ACGTcount: A:0.62, C:0.19, G:0.04, T:0.15
Consensus pattern (30 bp):
AAAATACAACCAAAACAACAAATATAATAA
Found at i:11285250 original size:9 final size:9
Alignment explanation
Indices: 11285236--11285363 Score: 121
Period size: 9 Copynumber: 13.6 Consensus size: 9
11285226 ATGTATTAGT
11285236 TAAGTTATG
1 TAAGTTATG
11285245 TAAGTTGTTATG
1 TAA---GTTATG
*
11285257 TACGTTATG
1 TAAGTTATG
*
11285266 TGAGTTATG
1 TAAGTTATG
*
11285275 TAAATTATG
1 TAAGTTATG
11285284 TAAGTTATG
1 TAAGTTATG
*
11285293 TGAGTTATG
1 TAAGTTATG
11285302 TAAGTTGTTATG
1 TAA---GTTATG
*
11285314 TAAATTATG
1 TAAGTTATG
*
11285323 TAAGTTATA
1 TAAGTTATG
*
11285332 TGAGTTATG
1 TAAGTTATG
11285341 TAAGTTATG
1 TAAGTTATG
* *
11285350 TAATTTATT
1 TAAGTTATG
11285359 TAAGT
1 TAAGT
11285364 AATGATCAAT
Statistics
Matches: 96, Mismatches: 17, Indels: 12
0.77 0.14 0.10
Matches are distributed among these distances:
9 79 0.82
12 17 0.18
ACGTcount: A:0.31, C:0.01, G:0.21, T:0.47
Consensus pattern (9 bp):
TAAGTTATG
Found at i:11285363 original size:57 final size:57
Alignment explanation
Indices: 11285236--11285363 Score: 175
Period size: 57 Copynumber: 2.2 Consensus size: 57
11285226 ATGTATTAGT
** * *
11285236 TAAGTTATGTAAGTTGTTATGTACGTTATGTGAGTTATGTAAATTATGTAAGTTATG
1 TAAGTTATGTAAGTTGTTATGTAAATTATGTAAGTTATATAAATTATGTAAGTTATG
* * *
11285293 TGAGTTATGTAAGTTGTTATGTAAATTATGTAAGTTATATGAGTTATGTAAGTTATG
1 TAAGTTATGTAAGTTGTTATGTAAATTATGTAAGTTATATAAATTATGTAAGTTATG
* *
11285350 TAATTTATTTAAGT
1 TAAGTTATGTAAGT
11285364 AATGATCAAT
Statistics
Matches: 61, Mismatches: 10, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
57 61 1.00
ACGTcount: A:0.31, C:0.01, G:0.21, T:0.47
Consensus pattern (57 bp):
TAAGTTATGTAAGTTGTTATGTAAATTATGTAAGTTATATAAATTATGTAAGTTATG
Found at i:11289188 original size:11 final size:11
Alignment explanation
Indices: 11289174--11289223 Score: 64
Period size: 11 Copynumber: 4.4 Consensus size: 11
11289164 AATATTTTAA
11289174 AAATTCTTGAC
1 AAATTCTTGAC
* *
11289185 AAATTATTTTGTC
1 AAA-T-TCTTGAC
11289198 AAATTCTTGAC
1 AAATTCTTGAC
11289209 AAATTCTTGAC
1 AAATTCTTGAC
11289220 AAAT
1 AAAT
11289224 ATACAAGTGT
Statistics
Matches: 33, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
11 23 0.70
12 2 0.06
13 8 0.24
ACGTcount: A:0.38, C:0.14, G:0.08, T:0.40
Consensus pattern (11 bp):
AAATTCTTGAC
Found at i:11289621 original size:18 final size:19
Alignment explanation
Indices: 11289600--11289635 Score: 56
Period size: 18 Copynumber: 1.9 Consensus size: 19
11289590 TTTGAAATTC
11289600 TTCATCTCT-CAATTCTAT
1 TTCATCTCTGCAATTCTAT
*
11289618 TTCATCTTTGCAATTCTA
1 TTCATCTCTGCAATTCTA
11289636 CAGAAAGAAG
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 8 0.50
19 8 0.50
ACGTcount: A:0.22, C:0.25, G:0.03, T:0.50
Consensus pattern (19 bp):
TTCATCTCTGCAATTCTAT
Found at i:11290271 original size:40 final size:41
Alignment explanation
Indices: 11290210--11290320 Score: 126
Period size: 40 Copynumber: 2.8 Consensus size: 41
11290200 CAATTAAACA
* *
11290210 TTTAGTGGCG--TTTTACAAAAGCGTCGCTAATTCTC-AGTT
1 TTTAGTGGCGTTTTTTACAAAAGCGCCACTAATTCTCTA-TT
*
11290249 TTT-GTGGCGTTTTTTACGAAAGCGCCACTAATTCTCTATT
1 TTTAGTGGCGTTTTTTACAAAAGCGCCACTAATTCTCTATT
*
11290289 TTTAGTGGCGTTTTTGTA-AAAA-CGCCGCTAAT
1 TTTAGTGGCGTTTTT-TACAAAAGCGCCACTAAT
11290321 GCCTCTGCAC
Statistics
Matches: 62, Mismatches: 5, Indels: 9
0.82 0.07 0.12
Matches are distributed among these distances:
38 6 0.10
39 3 0.05
40 36 0.58
41 15 0.24
42 2 0.03
ACGTcount: A:0.23, C:0.18, G:0.20, T:0.40
Consensus pattern (41 bp):
TTTAGTGGCGTTTTTTACAAAAGCGCCACTAATTCTCTATT
Done.