Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: A04
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: 82679320
ACGTcount: A:0.31, C:0.17, G:0.17, T:0.31
Warning! 4050000 characters in sequence are not A, C, G, or T
File 9 of 255
Found at i:2576031 original size:98 final size:98
Alignment explanation
Indices: 2575865--2576231 Score: 527
Period size: 98 Copynumber: 3.7 Consensus size: 98
2575855 TAAGTGTAGC
* * *
2575865 CACTTATCACTTTGTCTCTTGATCAGATAAGTGTAGCTAAAGCTATCACTTATCACTTTTCACTT
1 CACTTATCACTTTGTCACTTGATCAGATAAGTATAGCCAAAGCTATCACTTATCACTTTTCACTT
2575930 GTCACTTGATCAGATAAGTGTAGCCGAAGCTAT
66 GTCACTTGATCAGATAAGTGTAGCCGAAGCTAT
* *
2575963 CACTTATCACTTTGTCACTTGATCAGATAAGTATAGCCGAAGCTATTACTTATCACTTTTCACTT
1 CACTTATCACTTTGTCACTTGATCAGATAAGTATAGCCAAAGCTATCACTTATCACTTTTCACTT
** *
2576028 GTCACTTGATCAGATAAGTGTAGCTAAAGCTAC
66 GTCACTTGATCAGATAAGTGTAGCCGAAGCTAT
* * *
2576061 CACTTATCACTTTGTCACTTGATCAGATAAGTATAGCCGAAGCTATTACTTATCACTTTCCACTT
1 CACTTATCACTTTGTCACTTGATCAGATAAGTATAGCCAAAGCTATCACTTATCACTTTTCACTT
*
2576126 GTCACTTGATCAGATAAGTATAGCCGAAGCTAT
66 GTCACTTGATCAGATAAGTGTAGCCGAAGCTAT
* * * *
2576159 TACTTATCACTTTCCACTTGTCACTTGATCAGATAAGTGTAGCTAAAGCTACCACTTATCACTTT
1 CACTTATCAC--T----TTGTCACTTGATCAGATAAGTATAGCCAAAGCTATCACTTATCACTTT
2576224 GTCACTTG
60 -TCACTTG
2576232 ATCAGAAGTA
Statistics
Matches: 242, Mismatches: 20, Indels: 7
0.90 0.07 0.03
Matches are distributed among these distances:
98 192 0.79
100 1 0.00
104 43 0.18
105 6 0.02
ACGTcount: A:0.28, C:0.22, G:0.14, T:0.35
Consensus pattern (98 bp):
CACTTATCACTTTGTCACTTGATCAGATAAGTATAGCCAAAGCTATCACTTATCACTTTTCACTT
GTCACTTGATCAGATAAGTGTAGCCGAAGCTAT
Found at i:2576232 original size:150 final size:144
Alignment explanation
Indices: 2575876--2576237 Score: 571
Period size: 150 Copynumber: 2.4 Consensus size: 144
2575866 ACTTATCACT
* *
2575876 TTGTCTCTTGATCAGATAAGTGTAGCTAAAGCTATCACTTATCACTTTTCACTTGTCACTTGATC
1 TTGTCACTTGATCAGATAAGTGTAGCTAAAGCTACCACTTATCAC---T---TTGTCACTTGATC
*
2575941 AGATAAGTGTAGCCGAAGCTATCACTTATCACTTTGTCACTTGATCAGATAAGTATAGCCGAAGC
60 AGATAAGTATAGCCGAAGCTATCACTTATCACTTTGTCACTTGATCAGATAAGTATAGCCGAAGC
*
2576006 TATTACTTATCACTTTTCAC
125 TATTACTTATCACTTTCCAC
2576026 TTGTCACTTGATCAGATAAGTGTAGCTAAAGCTACCACTTATCACTTTGTCACTTGATCAGATAA
1 TTGTCACTTGATCAGATAAGTGTAGCTAAAGCTACCACTTATCACTTTGTCACTTGATCAGATAA
*
2576091 GTATAGCCGAAGCTATTACTTATCACTTTCCACTTGTCACTTGATCAGATAAGTATAGCCGAAGC
66 GTATAGCCGAAGCTATCACTTATCAC--T----TTGTCACTTGATCAGATAAGTATAGCCGAAGC
2576156 TATTACTTATCACTTTCCAC
125 TATTACTTATCACTTTCCAC
2576176 TTGTCACTTGATCAGATAAGTGTAGCTAAAGCTACCACTTATCACTTTGTCACTTGATCAGA
1 TTGTCACTTGATCAGATAAGTGTAGCTAAAGCTACCACTTATCACTTTGTCACTTGATCAGA
2576238 AGTACTCAAA
Statistics
Matches: 201, Mismatches: 5, Indels: 12
0.92 0.02 0.06
Matches are distributed among these distances:
144 43 0.21
146 1 0.00
147 1 0.00
150 156 0.78
ACGTcount: A:0.29, C:0.22, G:0.15, T:0.35
Consensus pattern (144 bp):
TTGTCACTTGATCAGATAAGTGTAGCTAAAGCTACCACTTATCACTTTGTCACTTGATCAGATAA
GTATAGCCGAAGCTATCACTTATCACTTTGTCACTTGATCAGATAAGTATAGCCGAAGCTATTAC
TTATCACTTTCCAC
Found at i:2583729 original size:40 final size:40
Alignment explanation
Indices: 2583648--2583729 Score: 101
Period size: 40 Copynumber: 2.0 Consensus size: 40
2583638 TGGAGATGAA
** * * **
2583648 ATTAGCAATATGACAGACAACGTTGGTACTGAATGTTTTT
1 ATTAGCAATATGACAGACAACAATGGGACCGAATGACTTT
*
2583688 ATTAGCAATATGACAGACAACAATGGGACCGACTGACTTT
1 ATTAGCAATATGACAGACAACAATGGGACCGAATGACTTT
2583728 AT
1 AT
2583730 CAACAATGAC
Statistics
Matches: 35, Mismatches: 7, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
40 35 1.00
ACGTcount: A:0.35, C:0.16, G:0.20, T:0.29
Consensus pattern (40 bp):
ATTAGCAATATGACAGACAACAATGGGACCGAATGACTTT
Found at i:2586902 original size:38 final size:38
Alignment explanation
Indices: 2586843--2586948 Score: 105
Period size: 37 Copynumber: 2.8 Consensus size: 38
2586833 CATTTTTAAG
*
2586843 AATAT-AAAGAATATATATAAGTATGTATATG-ATGTA-A
1 AATATGAAA-AATATATATAAGTATGTATAAGAAT-TAGA
* *
2586880 AATATGCATAAATATATGTAAGTA--TATAAGAATTATGA
1 AATATG-AAAAATATATATAAGTATGTATAAGAATTA-GA
*
2586918 AATATGAAAAATATATTTAAGTATGTATAAG
1 AATATGAAAAATATATATAAGTATGTATAAG
2586949 TACGTATATA
Statistics
Matches: 57, Mismatches: 5, Indels: 12
0.77 0.07 0.16
Matches are distributed among these distances:
36 7 0.12
37 22 0.39
38 20 0.35
39 8 0.14
ACGTcount: A:0.51, C:0.01, G:0.13, T:0.35
Consensus pattern (38 bp):
AATATGAAAAATATATATAAGTATGTATAAGAATTAGA
Found at i:2587341 original size:19 final size:17
Alignment explanation
Indices: 2587317--2587433 Score: 59
Period size: 16 Copynumber: 6.9 Consensus size: 17
2587307 TAATATTAGA
2587317 AAAATATATATAATAGTGT
1 AAAATATATATAATA-T-T
2587336 AAAATATAACTAATAATATT
1 AAAATAT-A-T-ATAATATT
*
2587356 AAAATATATACAATGA-T
1 AAAATATATATAAT-ATT
* * *
2587373 AATATATATAAAAGA-T
1 AAAATATATATAATATT
* *
2587389 -ATATGTATAT-ATAATT
1 AAAATATATATAAT-ATT
*
2587405 -ATATA-ATATAATATT
1 AAAATATATATAATATT
2587420 AAAATATA-ATAATA
1 AAAATATATATAATA
2587434 CGACATAAAA
Statistics
Matches: 80, Mismatches: 9, Indels: 21
0.73 0.08 0.19
Matches are distributed among these distances:
14 1 0.01
15 16 0.20
16 19 0.24
17 17 0.21
18 2 0.03
19 8 0.10
20 9 0.11
21 2 0.03
22 6 0.08
ACGTcount: A:0.57, C:0.02, G:0.04, T:0.37
Consensus pattern (17 bp):
AAAATATATATAATATT
Found at i:2587508 original size:20 final size:20
Alignment explanation
Indices: 2587483--2587529 Score: 94
Period size: 20 Copynumber: 2.4 Consensus size: 20
2587473 GAACACATAT
2587483 ATAATACATGAAGAATATAC
1 ATAATACATGAAGAATATAC
2587503 ATAATACATGAAGAATATAC
1 ATAATACATGAAGAATATAC
2587523 ATAATAC
1 ATAATAC
2587530 TAAAATATTT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 27 1.00
ACGTcount: A:0.55, C:0.11, G:0.09, T:0.26
Consensus pattern (20 bp):
ATAATACATGAAGAATATAC
Found at i:2587843 original size:6 final size:6
Alignment explanation
Indices: 2587801--2587834 Score: 50
Period size: 6 Copynumber: 5.5 Consensus size: 6
2587791 ATAAAAATAT
*
2587801 ATACTA ATACATA ATAGTA ATACTA ATACTA ATA
1 ATACTA ATAC-TA ATACTA ATACTA ATACTA ATA
2587835 ATACTAATAA
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
6 20 0.80
7 5 0.20
ACGTcount: A:0.53, C:0.12, G:0.03, T:0.32
Consensus pattern (6 bp):
ATACTA
Found at i:2588335 original size:11 final size:11
Alignment explanation
Indices: 2588319--2588354 Score: 54
Period size: 11 Copynumber: 3.2 Consensus size: 11
2588309 GAAAAAAAAA
2588319 GAAGAGAGAGG
1 GAAGAGAGAGG
*
2588330 GAAGAGAGAAG
1 GAAGAGAGAGG
2588341 GAAGAGAGAAGG
1 GAAGAGAG-AGG
2588353 GA
1 GA
2588355 GGGGGGAAGG
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
11 18 0.82
12 4 0.18
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (11 bp):
GAAGAGAGAGG
Found at i:2600714 original size:16 final size:16
Alignment explanation
Indices: 2600693--2600723 Score: 62
Period size: 16 Copynumber: 1.9 Consensus size: 16
2600683 CATATTTGAG
2600693 TTCAGCAACAATTTGC
1 TTCAGCAACAATTTGC
2600709 TTCAGCAACAATTTG
1 TTCAGCAACAATTTG
2600724 ATTAAATTGT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.32, C:0.23, G:0.13, T:0.32
Consensus pattern (16 bp):
TTCAGCAACAATTTGC
Found at i:2601333 original size:14 final size:14
Alignment explanation
Indices: 2601314--2601341 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
2601304 TCAGGATTTG
2601314 GATTTGAGGTTCAA
1 GATTTGAGGTTCAA
2601328 GATTTGAGGTTCAA
1 GATTTGAGGTTCAA
2601342 CTTCAGATTT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.29, C:0.07, G:0.29, T:0.36
Consensus pattern (14 bp):
GATTTGAGGTTCAA
Found at i:2602123 original size:18 final size:18
Alignment explanation
Indices: 2602100--2602135 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
2602090 CACCGTTTAT
*
2602100 GACACTATTCACGTATAC
1 GACACTATTCACATATAC
2602118 GACACTATTCACATATAC
1 GACACTATTCACATATAC
2602136 AATAGTTGGG
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.36, C:0.28, G:0.08, T:0.28
Consensus pattern (18 bp):
GACACTATTCACATATAC
Found at i:2604249 original size:28 final size:28
Alignment explanation
Indices: 2604217--2604271 Score: 69
Period size: 28 Copynumber: 2.0 Consensus size: 28
2604207 CAAGGCTGAC
2604217 TTTT-ATCT-CTTGATTTCAATTTCAATCT
1 TTTTAATCTACTTG-TTT-AATTTCAATCT
*
2604245 TTTTAATTTACTTGTTTAATTTCAATC
1 TTTTAATCTACTTGTTTAATTTCAATC
2604272 ATTTACTTCA
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
28 14 0.58
29 6 0.25
30 4 0.17
ACGTcount: A:0.24, C:0.15, G:0.04, T:0.58
Consensus pattern (28 bp):
TTTTAATCTACTTGTTTAATTTCAATCT
Found at i:2606979 original size:33 final size:33
Alignment explanation
Indices: 2606937--2607003 Score: 134
Period size: 33 Copynumber: 2.0 Consensus size: 33
2606927 ATTCAGGGAG
2606937 TTGAAACAAACTTTCTCTATTGATTCCATTAAT
1 TTGAAACAAACTTTCTCTATTGATTCCATTAAT
2606970 TTGAAACAAACTTTCTCTATTGATTCCATTAAT
1 TTGAAACAAACTTTCTCTATTGATTCCATTAAT
2607003 T
1 T
2607004 CTAACAAAAT
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
33 34 1.00
ACGTcount: A:0.33, C:0.18, G:0.06, T:0.43
Consensus pattern (33 bp):
TTGAAACAAACTTTCTCTATTGATTCCATTAAT
Found at i:2623864 original size:22 final size:22
Alignment explanation
Indices: 2623820--2623865 Score: 56
Period size: 22 Copynumber: 2.1 Consensus size: 22
2623810 CATTTGGCGA
* *
2623820 TCCTCCAGTGAATTAAATTTGT
1 TCCTCCAGCGAATTAAATGTGT
* *
2623842 TCCTCTAGCGAATTAAGTGTGT
1 TCCTCCAGCGAATTAAATGTGT
2623864 TC
1 TC
2623866 GGTTGCTATT
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.24, C:0.20, G:0.17, T:0.39
Consensus pattern (22 bp):
TCCTCCAGCGAATTAAATGTGT
Found at i:2625726 original size:29 final size:28
Alignment explanation
Indices: 2625694--2625753 Score: 66
Period size: 28 Copynumber: 2.1 Consensus size: 28
2625684 AATTTTATTT
** *
2625694 AATTTAAAAAAGTTATTTGATTAAATTAA
1 AATTTAAAAAA-TTAAGTGATTAAAATAA
* *
2625723 AATTTTAATAATTAAGTGATTAAAATAA
1 AATTTAAAAAATTAAGTGATTAAAATAA
2625751 AAT
1 AAT
2625754 AAACTAAATA
Statistics
Matches: 26, Mismatches: 5, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
28 17 0.65
29 9 0.35
ACGTcount: A:0.53, C:0.00, G:0.07, T:0.40
Consensus pattern (28 bp):
AATTTAAAAAATTAAGTGATTAAAATAA
Found at i:2626308 original size:22 final size:22
Alignment explanation
Indices: 2626283--2626328 Score: 74
Period size: 22 Copynumber: 2.1 Consensus size: 22
2626273 ACGTTGGCGA
*
2626283 TCCTCCAGTGAATTAAGTGTGT
1 TCCTCCAGCGAATTAAGTGTGT
*
2626305 TCCTCTAGCGAATTAAGTGTGT
1 TCCTCCAGCGAATTAAGTGTGT
2626327 TC
1 TC
2626329 GGTTGCTATT
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.22, C:0.20, G:0.22, T:0.37
Consensus pattern (22 bp):
TCCTCCAGCGAATTAAGTGTGT
Found at i:2627552 original size:25 final size:25
Alignment explanation
Indices: 2627523--2627573 Score: 102
Period size: 25 Copynumber: 2.0 Consensus size: 25
2627513 CATTGAGTTT
2627523 CAAAATCAAACTACGGTTTTCTAAA
1 CAAAATCAAACTACGGTTTTCTAAA
2627548 CAAAATCAAACTACGGTTTTCTAAA
1 CAAAATCAAACTACGGTTTTCTAAA
2627573 C
1 C
2627574 TTTGTTTAAC
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 26 1.00
ACGTcount: A:0.43, C:0.22, G:0.08, T:0.27
Consensus pattern (25 bp):
CAAAATCAAACTACGGTTTTCTAAA
Found at i:2629765 original size:13 final size:13
Alignment explanation
Indices: 2629743--2629776 Score: 52
Period size: 12 Copynumber: 2.7 Consensus size: 13
2629733 AAAAAAATTA
*
2629743 ATTAAGTTTTTGT
1 ATTAAATTTTTGT
2629756 ATTAAA-TTTTGT
1 ATTAAATTTTTGT
2629768 ATTAAATTT
1 ATTAAATTT
2629777 ATTTTTTATT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
12 12 0.63
13 7 0.37
ACGTcount: A:0.32, C:0.00, G:0.09, T:0.59
Consensus pattern (13 bp):
ATTAAATTTTTGT
Found at i:2629767 original size:12 final size:12
Alignment explanation
Indices: 2629750--2629776 Score: 54
Period size: 12 Copynumber: 2.2 Consensus size: 12
2629740 TTAATTAAGT
2629750 TTTTGTATTAAA
1 TTTTGTATTAAA
2629762 TTTTGTATTAAA
1 TTTTGTATTAAA
2629774 TTT
1 TTT
2629777 ATTTTTTATT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 15 1.00
ACGTcount: A:0.30, C:0.00, G:0.07, T:0.63
Consensus pattern (12 bp):
TTTTGTATTAAA
Found at i:2629968 original size:26 final size:26
Alignment explanation
Indices: 2629939--2630011 Score: 74
Period size: 27 Copynumber: 2.7 Consensus size: 26
2629929 AAATGATTAA
2629939 AAATAATAAAATTATAAAAAAATATT
1 AAATAATAAAATTATAAAAAAATATT
* * **
2629965 AAATACTAAAATTGATATAAAGTTATT
1 AAATAATAAAATT-ATAAAAAAATATT
*
2629992 AAACTTATAAATATTATAAA
1 AAA-TAATAAA-ATTATAAA
2630012 TATTATGAAA
Statistics
Matches: 37, Mismatches: 7, Indels: 4
0.77 0.15 0.08
Matches are distributed among these distances:
26 12 0.32
27 13 0.35
28 9 0.24
29 3 0.08
ACGTcount: A:0.60, C:0.03, G:0.03, T:0.34
Consensus pattern (26 bp):
AAATAATAAAATTATAAAAAAATATT
Found at i:2630631 original size:19 final size:19
Alignment explanation
Indices: 2630607--2630663 Score: 71
Period size: 19 Copynumber: 2.9 Consensus size: 19
2630597 TTGGAATATT
2630607 TTTTTATAATTTTATTTTA
1 TTTTTATAATTTTATTTTA
*
2630626 TTTTTATAATTTTTTTCTTA
1 TTTTTATAATTTTATT-TTA
2630646 -TTTTATATATTATTATTT
1 TTTTTATA-ATT-TTATTT
2630664 CAATATTTTT
Statistics
Matches: 33, Mismatches: 2, Indels: 5
0.82 0.05 0.12
Matches are distributed among these distances:
19 22 0.67
20 7 0.21
21 4 0.12
ACGTcount: A:0.25, C:0.02, G:0.00, T:0.74
Consensus pattern (19 bp):
TTTTTATAATTTTATTTTA
Found at i:2632514 original size:23 final size:23
Alignment explanation
Indices: 2632484--2632529 Score: 83
Period size: 23 Copynumber: 2.0 Consensus size: 23
2632474 ACTATCATTA
2632484 TCCACGTATAGTATAACAAATTG
1 TCCACGTATAGTATAACAAATTG
*
2632507 TCCACGTATAGTATAACAGATTG
1 TCCACGTATAGTATAACAAATTG
2632530 AATATATATG
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
23 22 1.00
ACGTcount: A:0.37, C:0.17, G:0.15, T:0.30
Consensus pattern (23 bp):
TCCACGTATAGTATAACAAATTG
Found at i:2636500 original size:34 final size:31
Alignment explanation
Indices: 2636458--2636520 Score: 81
Period size: 34 Copynumber: 1.9 Consensus size: 31
2636448 AAAAATATGG
2636458 TAAAATAAACAATATATAATATATAGTATAATA
1 TAAAATAAACAATATATAATA-ATA-TATAATA
* *
2636491 TAAATATAAATAATATGTAATAATATATAA
1 TAAA-ATAAACAATATATAATAATATATAA
2636521 AAATATATAA
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
32 5 0.19
33 7 0.26
34 15 0.56
ACGTcount: A:0.60, C:0.02, G:0.03, T:0.35
Consensus pattern (31 bp):
TAAAATAAACAATATATAATAATATATAATA
Found at i:2636503 original size:10 final size:11
Alignment explanation
Indices: 2636462--2636534 Score: 66
Period size: 10 Copynumber: 6.8 Consensus size: 11
2636452 ATATGGTAAA
*
2636462 ATAAACAATAT
1 ATAAATAATAT
2636473 AT-AATATATAGT
1 ATAAATA-ATA-T
2636485 ATAATATAA-AT
1 ATAA-ATAATAT
2636496 ATAAATAATAT
1 ATAAATAATAT
*
2636507 GT-AATAATAT
1 ATAAATAATAT
2636517 ATAAA-AATAT
1 ATAAATAATAT
2636527 AT-AATAAT
1 ATAAATAAT
2636535 GCGATGGATA
Statistics
Matches: 52, Mismatches: 3, Indels: 15
0.74 0.04 0.21
Matches are distributed among these distances:
9 2 0.04
10 26 0.50
11 15 0.29
12 4 0.08
13 2 0.04
14 3 0.06
ACGTcount: A:0.60, C:0.01, G:0.03, T:0.36
Consensus pattern (11 bp):
ATAAATAATAT
Found at i:2636506 original size:25 final size:25
Alignment explanation
Indices: 2636468--2636517 Score: 68
Period size: 25 Copynumber: 2.0 Consensus size: 25
2636458 TAAAATAAAC
2636468 AATATATAATATATAGT-ATAATATA
1 AATATATAATATAT-GTAATAATATA
2636493 AATATA-AATAATATGTAATAATATA
1 AATATATAAT-ATATGTAATAATATA
2636518 TAAAAATATA
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
24 5 0.22
25 18 0.78
ACGTcount: A:0.58, C:0.00, G:0.04, T:0.38
Consensus pattern (25 bp):
AATATATAATATATGTAATAATATA
Found at i:2636525 original size:20 final size:21
Alignment explanation
Indices: 2636468--2636534 Score: 75
Period size: 20 Copynumber: 3.1 Consensus size: 21
2636458 TAAAATAAAC
2636468 AATATAT-AATATATAGTATAAT
1 AATATATAAATA-ATA-TATAAT
* *
2636490 ATAAATATAAATAATATGTAAT
1 A-ATATATAAATAATATATAAT
2636512 AATATATAAA-AATATATAAT
1 AATATATAAATAATATATAAT
2636532 AAT
1 AAT
2636535 GCGATGGATA
Statistics
Matches: 39, Mismatches: 4, Indels: 6
0.80 0.08 0.12
Matches are distributed among these distances:
20 12 0.31
21 8 0.21
22 7 0.18
23 8 0.21
24 4 0.10
ACGTcount: A:0.60, C:0.00, G:0.03, T:0.37
Consensus pattern (21 bp):
AATATATAAATAATATATAAT
Found at i:2638190 original size:73 final size:73
Alignment explanation
Indices: 2638109--2638347 Score: 273
Period size: 73 Copynumber: 3.1 Consensus size: 73
2638099 TAAGGATGTC
* * * *
2638109 AAATCATCTTGAACCTGTTTGAGAATATTTGAGGGTTATATCTGCAATGTCCTCGATTTGTTCCT
1 AAATCATCTTGAATCTGTTTGAGAACATTTGAGAGTCATATCTGCAATGTCCTCGATTTGTTCCT
2638174 TGTAAACT
66 TGTAAACT
** *
2638182 AAATCATCTT-AGATCTACTTGAGAACATTTGAGAGTCATATCTGCAATGTCATCGATTTGTTCC
1 AAATCATCTTGA-ATCTGTTTGAGAACATTTGAGAGTCATATCTGCAATGTCCTCGATTTGTTCC
2638246 TTGTAAGCACAATGAT
65 TTGTAA--AC-----T
* * *
2638262 GCCAAACCATCTTGAGTCTGTTTGAGAACATTTGAGAGTCATATCTGCAATGTCCTTGATTTGTT
1 ---AAATCATCTTGAATCTGTTTGAGAACATTTGAGAGTCATATCTGCAATGTCCTCGATTTGTT
*
2638327 CCTTCTAAACT
63 CCTTGTAAACT
2638338 AAATCATCTT
1 AAATCATCTT
2638348 AGATCTGCTT
Statistics
Matches: 139, Mismatches: 15, Indels: 24
0.78 0.08 0.13
Matches are distributed among these distances:
72 1 0.01
73 70 0.50
75 2 0.01
76 1 0.01
80 1 0.01
81 2 0.01
83 61 0.44
84 1 0.01
ACGTcount: A:0.28, C:0.18, G:0.16, T:0.37
Consensus pattern (73 bp):
AAATCATCTTGAATCTGTTTGAGAACATTTGAGAGTCATATCTGCAATGTCCTCGATTTGTTCCT
TGTAAACT
Found at i:2638485 original size:119 final size:119
Alignment explanation
Indices: 2638338--2638627 Score: 510
Period size: 119 Copynumber: 2.4 Consensus size: 119
2638328 CTTCTAAACT
* * *
2638338 AAATCATCTTAGATCTGCTTCAGTATAAACATCTGAAGGTTAGATCTGCTATATTTGAGAATGTC
1 AAATCATCTTGGATCTGCTTTAGTATAAACATCTGAAGGTTAGATCTGCTATATTTGAGAACGTC
2638403 TGAGAGTCAAATCTGCTATGTCCTCGATTTGTTCCTTGTAAACACAAGAATACC
66 TGAGAGTCAAATCTGCTATGTCCTCGATTTGTTCCTTGTAAACACAAGAATACC
* *
2638457 AAATCATCTTGGATCTGCTTTAGTATAAACATTTGAAGGTCAGATCTGCTATATTTGAGAACGTC
1 AAATCATCTTGGATCTGCTTTAGTATAAACATCTGAAGGTTAGATCTGCTATATTTGAGAACGTC
2638522 TGAGAGTCAAATCTGCTATGTCCTCGATTTGTTCCTTGTAAACACAAGAATACC
66 TGAGAGTCAAATCTGCTATGTCCTCGATTTGTTCCTTGTAAACACAAGAATACC
*
2638576 AAATCATATTGGATCTGCTTTAGTATAAACATCTGAA-GTCTAGATCTGCTAT
1 AAATCATCTTGGATCTGCTTTAGTATAAACATCTGAAGGT-TAGATCTGCTAT
2638628 TTTCAATTTG
Statistics
Matches: 162, Mismatches: 8, Indels: 2
0.94 0.05 0.01
Matches are distributed among these distances:
118 2 0.01
119 160 0.99
ACGTcount: A:0.31, C:0.18, G:0.17, T:0.34
Consensus pattern (119 bp):
AAATCATCTTGGATCTGCTTTAGTATAAACATCTGAAGGTTAGATCTGCTATATTTGAGAACGTC
TGAGAGTCAAATCTGCTATGTCCTCGATTTGTTCCTTGTAAACACAAGAATACC
Found at i:2646478 original size:37 final size:36
Alignment explanation
Indices: 2646425--2646523 Score: 162
Period size: 37 Copynumber: 2.7 Consensus size: 36
2646415 CCCCACACGT
*
2646425 ACGTAGTTATCGGGTCTTACCCGGACATAATCTCCAC
1 ACGTAGTCATC-GGTCTTACCCGGACATAATCTCCAC
2646462 ACGTAGTCATCAGGTCTTACCCGGACATAATCTCCAC
1 ACGTAGTCATC-GGTCTTACCCGGACATAATCTCCAC
2646499 ACGTAGTCATCGAGTCTTACCCGGA
1 ACGTAGTCATCG-GTCTTACCCGGA
2646524 ATATATTTCC
Statistics
Matches: 59, Mismatches: 2, Indels: 2
0.94 0.03 0.03
Matches are distributed among these distances:
36 1 0.02
37 58 0.98
ACGTcount: A:0.25, C:0.30, G:0.19, T:0.25
Consensus pattern (36 bp):
ACGTAGTCATCGGTCTTACCCGGACATAATCTCCAC
Found at i:2646686 original size:48 final size:48
Alignment explanation
Indices: 2646629--2646906 Score: 466
Period size: 48 Copynumber: 5.8 Consensus size: 48
2646619 AATACACACC
2646629 TTTCACATTAGCCATTCGGCTTTACCACATATACATATCTCATACATA
1 TTTCACATTAGCCATTCGGCTTTACCACATATACATATCTCATACATA
* * *
2646677 TTTCACATTAGCCATTCAGCTTTATCACATATATATATCTCATACATA
1 TTTCACATTAGCCATTCGGCTTTACCACATATACATATCTCATACATA
**
2646725 TTTCATGTTAGCCATTCGGCTTTACCACATATACATATCTCATACATA
1 TTTCACATTAGCCATTCGGCTTTACCACATATACATATCTCATACATA
*
2646773 TTTCACATTAGCCATTCGGCTTTACCACATATATATATCTCATACATA
1 TTTCACATTAGCCATTCGGCTTTACCACATATACATATCTCATACATA
2646821 TTTCACATTAGCCATTCGGCTTTACCACATATACATATCTCATACATA
1 TTTCACATTAGCCATTCGGCTTTACCACATATACATATCTCATACATA
* * * *
2646869 TTTCACACTAGCCATTCAGCTTTACCACACATATATAT
1 TTTCACATTAGCCATTCGGCTTTACCACATATACATAT
2646907 TTATCTTGTA
Statistics
Matches: 214, Mismatches: 16, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
48 214 1.00
ACGTcount: A:0.31, C:0.26, G:0.06, T:0.37
Consensus pattern (48 bp):
TTTCACATTAGCCATTCGGCTTTACCACATATACATATCTCATACATA
Found at i:2652723 original size:12 final size:12
Alignment explanation
Indices: 2652706--2652783 Score: 55
Period size: 12 Copynumber: 7.0 Consensus size: 12
2652696 TAAAATAAAC
2652706 AATATATAATAA
1 AATATATAATAA
2652718 AATATATAAT-A
1 AATATATAATAA
* *
2652729 TATCGTATAATATA
1 AAT-ATATAATA-A
2652743 AATATA-AAT--
1 AATATATAATAA
*
2652752 AATATGTAAT--
1 AATATATAATAA
2652762 AATATAT-A-AA
1 AATATATAATAA
2652772 AATATATAATAA
1 AATATATAATAA
2652784 TGCGATGGAT
Statistics
Matches: 52, Mismatches: 6, Indels: 16
0.70 0.08 0.22
Matches are distributed among these distances:
9 6 0.12
10 16 0.31
11 4 0.08
12 21 0.40
13 2 0.04
14 3 0.06
ACGTcount: A:0.60, C:0.01, G:0.03, T:0.36
Consensus pattern (12 bp):
AATATATAATAA
Found at i:2652753 original size:10 final size:11
Alignment explanation
Indices: 2652700--2652784 Score: 63
Period size: 10 Copynumber: 7.8 Consensus size: 11
2652690 ATATGGTAAA
*
2652700 ATAAACAATAT
1 ATAAATAATAT
*
2652711 AT-AATAAAAT
1 ATAAATAATAT
*
2652721 ATATAATATATCGT
1 ATA-AATA-AT-AT
2652735 ATAATATAA-AT
1 ATAA-ATAATAT
2652746 ATAAATAATAT
1 ATAAATAATAT
*
2652757 GT-AATAATAT
1 ATAAATAATAT
2652767 ATAAA-AATAT
1 ATAAATAATAT
2652777 AT-AATAAT
1 ATAAATAAT
2652785 GCGATGGATA
Statistics
Matches: 59, Mismatches: 7, Indels: 17
0.71 0.08 0.20
Matches are distributed among these distances:
9 2 0.03
10 31 0.53
11 12 0.20
12 4 0.07
13 3 0.05
14 7 0.12
ACGTcount: A:0.60, C:0.02, G:0.02, T:0.35
Consensus pattern (11 bp):
ATAAATAATAT
Found at i:2652756 original size:25 final size:24
Alignment explanation
Indices: 2652710--2652767 Score: 75
Period size: 25 Copynumber: 2.4 Consensus size: 24
2652700 ATAAACAATA
2652710 TATAATA-AAATATATAATATATCG
1 TATAATATAAATATATAATATAT-G
2652734 TATAATATAAATATA-AATAATATG
1 TATAATATAAATATATAAT-ATATG
2652758 TAATAATATA
1 T-ATAATATA
2652768 TAAAAATATA
Statistics
Matches: 31, Mismatches: 0, Indels: 5
0.86 0.00 0.14
Matches are distributed among these distances:
24 12 0.39
25 19 0.61
ACGTcount: A:0.57, C:0.02, G:0.03, T:0.38
Consensus pattern (24 bp):
TATAATATAAATATATAATATATG
Found at i:2652775 original size:20 final size:21
Alignment explanation
Indices: 2652700--2652784 Score: 82
Period size: 20 Copynumber: 3.9 Consensus size: 21
2652690 ATATGGTAAA
* *
2652700 ATAAACAATATATAATAAAAT
1 ATAAATAATATATAATAATAT
* *
2652721 ATATAATATATCGTATAATATAAAT
1 ATA-AATA-AT-ATATAATA-ATAT
*
2652746 ATAAATAATATGTAATAATAT
1 ATAAATAATATATAATAATAT
2652767 ATAAA-AATATATAATAAT
1 ATAAATAATATATAATAAT
2652785 GCGATGGATA
Statistics
Matches: 54, Mismatches: 6, Indels: 9
0.78 0.09 0.13
Matches are distributed among these distances:
20 12 0.22
21 11 0.20
22 9 0.17
23 4 0.07
24 11 0.20
25 7 0.13
ACGTcount: A:0.60, C:0.02, G:0.02, T:0.35
Consensus pattern (21 bp):
ATAAATAATATATAATAATAT
Found at i:2657173 original size:26 final size:26
Alignment explanation
Indices: 2657144--2657195 Score: 104
Period size: 26 Copynumber: 2.0 Consensus size: 26
2657134 AACGAAAGCA
2657144 AGTAATCTGGATTAAGTATGAAGCTT
1 AGTAATCTGGATTAAGTATGAAGCTT
2657170 AGTAATCTGGATTAAGTATGAAGCTT
1 AGTAATCTGGATTAAGTATGAAGCTT
2657196 TGTCTAGAAA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 26 1.00
ACGTcount: A:0.35, C:0.08, G:0.23, T:0.35
Consensus pattern (26 bp):
AGTAATCTGGATTAAGTATGAAGCTT
Found at i:2659905 original size:42 final size:41
Alignment explanation
Indices: 2659731--2659902 Score: 240
Period size: 41 Copynumber: 4.2 Consensus size: 41
2659721 CAAAAATGCT
* * *
2659731 GCTAAAA-ACTGAGCAATAGCGGCGCTTTTGGTAAAAAGCC
1 GCTAAAAGACAGAGCATTAGCGGCGCTTTTGGTAAAACGCC
*
2659771 GCTAAAAGACAGAGCATTAGTGGCGCTTTTGGTAAAACGCC
1 GCTAAAAGACAGAGCATTAGCGGCGCTTTTGGTAAAACGCC
* *
2659812 GTTAAAAGACAGAGCATTAGCGGCGCTTTTGGTAAAATGCC
1 GCTAAAAGACAGAGCATTAGCGGCGCTTTTGGTAAAACGCC
* *
2659853 GCTAAAAGTCAGAGCATTAGCAGCG-TTTGTGGTCAAAACGCC
1 GCTAAAAGACAGAGCATTAGCGGCGCTTT-TGGT-AAAACGCC
2659895 GCTAAAAG
1 GCTAAAAG
2659903 TCATATAACT
Statistics
Matches: 118, Mismatches: 11, Indels: 4
0.89 0.08 0.03
Matches are distributed among these distances:
40 10 0.08
41 93 0.79
42 15 0.13
ACGTcount: A:0.33, C:0.19, G:0.26, T:0.22
Consensus pattern (41 bp):
GCTAAAAGACAGAGCATTAGCGGCGCTTTTGGTAAAACGCC
Found at i:2659990 original size:14 final size:15
Alignment explanation
Indices: 2659973--2660014 Score: 50
Period size: 14 Copynumber: 2.9 Consensus size: 15
2659963 AAATCCTAAC
2659973 AAACCCTAAACACT-
1 AAACCCTAAACACTA
** *
2659987 AAACTATAAACCCTA
1 AAACCCTAAACACTA
2660002 AAACCCTAAACAC
1 AAACCCTAAACAC
2660015 CGCAATAGGT
Statistics
Matches: 21, Mismatches: 6, Indels: 1
0.75 0.21 0.04
Matches are distributed among these distances:
14 11 0.52
15 10 0.48
ACGTcount: A:0.52, C:0.33, G:0.00, T:0.14
Consensus pattern (15 bp):
AAACCCTAAACACTA
Found at i:2660524 original size:24 final size:24
Alignment explanation
Indices: 2660497--2660545 Score: 89
Period size: 24 Copynumber: 2.0 Consensus size: 24
2660487 CGTATACTTA
*
2660497 TTAAAAGTTTATATAAAAATTAAT
1 TTAAAAGTCTATATAAAAATTAAT
2660521 TTAAAAGTCTATATAAAAATTAAT
1 TTAAAAGTCTATATAAAAATTAAT
2660545 T
1 T
2660546 GTTATTTTGG
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.53, C:0.02, G:0.04, T:0.41
Consensus pattern (24 bp):
TTAAAAGTCTATATAAAAATTAAT
Found at i:2660877 original size:21 final size:21
Alignment explanation
Indices: 2660832--2660899 Score: 109
Period size: 21 Copynumber: 3.2 Consensus size: 21
2660822 TATTTTAAAA
*
2660832 TTTATGGATTATGGATTATGGG
1 TTTATGGATTATGGTTTA-GGG
2660854 TTTATGGATTATGGTTTAGGG
1 TTTATGGATTATGGTTTAGGG
*
2660875 TTTATGGATTATGGTTTATGG
1 TTTATGGATTATGGTTTAGGG
2660896 TTTA
1 TTTA
2660900 AGGGTTGGGG
Statistics
Matches: 44, Mismatches: 2, Indels: 1
0.94 0.04 0.02
Matches are distributed among these distances:
21 27 0.61
22 17 0.39
ACGTcount: A:0.21, C:0.00, G:0.29, T:0.50
Consensus pattern (21 bp):
TTTATGGATTATGGTTTAGGG
Found at i:2660911 original size:21 final size:21
Alignment explanation
Indices: 2660887--2660947 Score: 70
Period size: 21 Copynumber: 2.9 Consensus size: 21
2660877 TATGGATTAT
2660887 GGTTTATGGTTTAAGGGTTGG
1 GGTTTATGGTTTAAGGGTTGG
*
2660908 GGTTTAAGGTTT-AGGTGTTGG
1 GGTTTATGGTTTAAGG-GTTGG
* * *
2660929 GGGTTATGGGTTATGGGTT
1 GGTTTATGGTTTAAGGGTT
2660948 TAGGGGTTAC
Statistics
Matches: 33, Mismatches: 5, Indels: 4
0.79 0.12 0.10
Matches are distributed among these distances:
20 3 0.09
21 28 0.85
22 2 0.06
ACGTcount: A:0.13, C:0.00, G:0.44, T:0.43
Consensus pattern (21 bp):
GGTTTATGGTTTAAGGGTTGG
Found at i:2660918 original size:7 final size:7
Alignment explanation
Indices: 2660832--2660899 Score: 82
Period size: 7 Copynumber: 9.6 Consensus size: 7
2660822 TATTTTAAAA
2660832 TTTATGG
1 TTTATGG
*
2660839 ATTATGG
1 TTTATGG
*
2660846 ATTATGGG
1 TTTAT-GG
2660854 TTTATGG
1 TTTATGG
*
2660861 ATTATGG
1 TTTATGG
*
2660868 TTTAGGG
1 TTTATGG
2660875 TTTATGG
1 TTTATGG
*
2660882 ATTATGG
1 TTTATGG
2660889 TTTATGG
1 TTTATGG
2660896 TTTA
1 TTTA
2660900 AGGGTTGGGG
Statistics
Matches: 52, Mismatches: 8, Indels: 2
0.84 0.13 0.03
Matches are distributed among these distances:
7 46 0.88
8 6 0.12
ACGTcount: A:0.21, C:0.00, G:0.29, T:0.50
Consensus pattern (7 bp):
TTTATGG
Found at i:2663027 original size:26 final size:26
Alignment explanation
Indices: 2662998--2663052 Score: 74
Period size: 26 Copynumber: 2.1 Consensus size: 26
2662988 CATTAAAGTC
* ** *
2662998 AAACTCAGGTATTTAACTGAAAAACA
1 AAACTCAAGTATCAAACTGAAAAAAA
2663024 AAACTCAAGTATCAAACTGAAAAAAA
1 AAACTCAAGTATCAAACTGAAAAAAA
2663050 AAA
1 AAA
2663053 ATTCAAGGCA
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
26 25 1.00
ACGTcount: A:0.58, C:0.15, G:0.09, T:0.18
Consensus pattern (26 bp):
AAACTCAAGTATCAAACTGAAAAAAA
Found at i:2663096 original size:30 final size:30
Alignment explanation
Indices: 2663062--2663191 Score: 147
Period size: 30 Copynumber: 4.2 Consensus size: 30
2663052 AATTCAAGGC
2663062 ACATAATTTAAAGATCAAATTTCATAACTT
1 ACATAATTTAAAGATCAAATTTCATAACTT
*
2663092 ACATAATTTAAAGATCAAAATTCATAACTT
1 ACATAATTTAAAGATCAAATTTCATAACTT
* * *
2663122 ACATAATTTACATA-ACTTACATAA-TACATGAGTT
1 ACATAATTTA-A-AGA--T-CA-AATTTCATAACTT
*
2663156 ACATAATTTAAAGATCAAATTTCAAAACTT
1 ACATAATTTAAAGATCAAATTTCATAACTT
2663186 ACATAA
1 ACATAA
2663192 AACATAACTT
Statistics
Matches: 84, Mismatches: 8, Indels: 16
0.78 0.07 0.15
Matches are distributed among these distances:
29 2 0.02
30 53 0.63
31 3 0.04
32 2 0.02
33 3 0.04
34 19 0.23
35 2 0.02
ACGTcount: A:0.48, C:0.14, G:0.04, T:0.34
Consensus pattern (30 bp):
ACATAATTTAAAGATCAAATTTCATAACTT
Found at i:2663132 original size:9 final size:9
Alignment explanation
Indices: 2663114--2663291 Score: 84
Period size: 9 Copynumber: 20.0 Consensus size: 9
2663104 GATCAAAATT
2663114 CATAACTTA
1 CATAACTTA
*
2663123 CATAATTTA
1 CATAACTTA
2663132 CATAACTTA
1 CATAACTTA
2663141 CATAA--TA
1 CATAACTTA
* *
2663148 CATGAGTTA
1 CATAACTTA
*
2663157 CATAATTTAAA
1 CATAACTT--A
* * *
2663168 GATCAAATTT
1 CAT-AACTTA
*
2663178 CAAAACTTA
1 CATAACTTA
*
2663187 CATAA--AA
1 CATAACTTA
2663194 CATAACTTA
1 CATAACTTA
*
2663203 CATAATTTAAA
1 CATAACTT--A
* * *
2663214 GATCAAATTT
1 CAT-AACTTA
2663224 CATAACTTA
1 CATAACTTA
****
2663233 CAGCTTTTA
1 CATAACTTA
2663242 CATAACTTA
1 CATAACTTA
2663251 CATAA--TA
1 CATAACTTA
*
2663258 AATAACTTA
1 CATAACTTA
2663267 CATAA--TA
1 CATAACTTA
2663274 CATAACTTA
1 CATAACTTA
2663283 CATAACTTA
1 CATAACTTA
2663292 ATTATACTTA
Statistics
Matches: 123, Mismatches: 32, Indels: 28
0.67 0.17 0.15
Matches are distributed among these distances:
7 25 0.20
9 81 0.66
10 3 0.02
11 6 0.05
12 8 0.07
ACGTcount: A:0.47, C:0.16, G:0.03, T:0.34
Consensus pattern (9 bp):
CATAACTTA
Found at i:2663164 original size:64 final size:62
Alignment explanation
Indices: 2663090--2663208 Score: 193
Period size: 64 Copynumber: 1.9 Consensus size: 62
2663080 ATTTCATAAC
* *
2663090 TTACATAATTTAAAGATCAAAATTCATAACTTACATAATTTACATAACTTACATAATACATGAG
1 TTACATAATTTAAAGATCAAAATTCAAAACTTACATAA--AACATAACTTACATAATACATGAG
*
2663154 TTACATAATTTAAAGATCAAATTTCAAAACTTACATAAAACATAACTTACATAAT
1 TTACATAATTTAAAGATCAAAATTCAAAACTTACATAAAACATAACTTACATAAT
2663209 TTAAAGATCA
Statistics
Matches: 52, Mismatches: 3, Indels: 2
0.91 0.05 0.04
Matches are distributed among these distances:
62 16 0.31
64 36 0.69
ACGTcount: A:0.49, C:0.14, G:0.03, T:0.34
Consensus pattern (62 bp):
TTACATAATTTAAAGATCAAAATTCAAAACTTACATAAAACATAACTTACATAATACATGAG
Found at i:2663204 original size:46 final size:46
Alignment explanation
Indices: 2663062--2663234 Score: 179
Period size: 46 Copynumber: 3.7 Consensus size: 46
2663052 AATTCAAGGC
*** **
2663062 ACATAATTTAAAGATCAAATTTCATAACTTACATAATTTA-AAGAT
1 ACATAATTTAAAGATCAAATTTCATAACTTACATAAAACATAACTT
* * ** * * *
2663107 -CAAAATTCATAACTTACATAATTTACATAACTTACATAATACATGAGTT
1 ACATAATTTA-AAGAT-CA-AATTT-CATAACTTACATAAAACATAACTT
*
2663156 ACATAATTTAAAGATCAAATTTCAAAACTTACATAAAACATAACTT
1 ACATAATTTAAAGATCAAATTTCATAACTTACATAAAACATAACTT
2663202 ACATAATTTAAAGATCAAATTTCATAACTTACA
1 ACATAATTTAAAGATCAAATTTCATAACTTACA
2663235 GCTTTTACAT
Statistics
Matches: 105, Mismatches: 17, Indels: 11
0.79 0.13 0.08
Matches are distributed among these distances:
44 7 0.07
45 3 0.03
46 54 0.51
47 10 0.10
48 18 0.17
49 6 0.06
50 7 0.07
ACGTcount: A:0.49, C:0.14, G:0.03, T:0.34
Consensus pattern (46 bp):
ACATAATTTAAAGATCAAATTTCATAACTTACATAAAACATAACTT
Found at i:2663227 original size:21 final size:21
Alignment explanation
Indices: 2663157--2663228 Score: 63
Period size: 21 Copynumber: 3.2 Consensus size: 21
2663147 ACATGAGTTA
2663157 CATAATTTAAAGATCAAATTT
1 CATAATTTAAAGATCAAATTT
* * * * *
2663178 CAAAACTTACATAAAACATAACTTA
1 CATAATTTA-A-AGATCA-AA-TTT
2663203 CATAATTTAAAGATCAAATTT
1 CATAATTTAAAGATCAAATTT
2663224 CATAA
1 CATAA
2663229 CTTACAGCTT
Statistics
Matches: 37, Mismatches: 10, Indels: 8
0.67 0.18 0.15
Matches are distributed among these distances:
21 14 0.38
22 3 0.08
23 8 0.22
24 3 0.08
25 9 0.24
ACGTcount: A:0.51, C:0.14, G:0.03, T:0.32
Consensus pattern (21 bp):
CATAATTTAAAGATCAAATTT
Found at i:2663264 original size:16 final size:16
Alignment explanation
Indices: 2663243--2663287 Score: 81
Period size: 16 Copynumber: 2.8 Consensus size: 16
2663233 CAGCTTTTAC
2663243 ATAACTTACATAATAA
1 ATAACTTACATAATAA
*
2663259 ATAACTTACATAATAC
1 ATAACTTACATAATAA
2663275 ATAACTTACATAA
1 ATAACTTACATAA
2663288 CTTAATTATA
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
16 28 1.00
ACGTcount: A:0.53, C:0.16, G:0.00, T:0.31
Consensus pattern (16 bp):
ATAACTTACATAATAA
Found at i:2668363 original size:13 final size:14
Alignment explanation
Indices: 2668347--2668375 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
2668337 TTCTAAATAT
2668347 TTATAA-TGTTTAA
1 TTATAATTGTTTAA
2668360 TTATAATTGTTTAA
1 TTATAATTGTTTAA
2668374 TT
1 TT
2668376 CAATTCATCA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 6 0.40
14 9 0.60
ACGTcount: A:0.34, C:0.00, G:0.07, T:0.59
Consensus pattern (14 bp):
TTATAATTGTTTAA
Found at i:2670086 original size:29 final size:28
Alignment explanation
Indices: 2670053--2670107 Score: 74
Period size: 29 Copynumber: 1.9 Consensus size: 28
2670043 ATGGTGGATG
* *
2670053 GTAATTCAAAGCTGATTTTTTATTAAGCA
1 GTAATTAAAAGCTGA-ATTTTATTAAGCA
*
2670082 GTAATTAAAAGTTGAATTTTATTAAG
1 GTAATTAAAAGCTGAATTTTATTAAG
2670108 AAAAAATAGA
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
28 10 0.43
29 13 0.57
ACGTcount: A:0.38, C:0.05, G:0.15, T:0.42
Consensus pattern (28 bp):
GTAATTAAAAGCTGAATTTTATTAAGCA
Found at i:2675365 original size:19 final size:17
Alignment explanation
Indices: 2675341--2675375 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 17
2675331 ATTATTTGGA
2675341 TATTGTATAACTTTTATTT
1 TATTGT-TAA-TTTTATTT
2675360 TATTGTTAATTTTATT
1 TATTGTTAATTTTATT
2675376 ACTATTTTAA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 7 0.44
18 3 0.19
19 6 0.38
ACGTcount: A:0.26, C:0.03, G:0.06, T:0.66
Consensus pattern (17 bp):
TATTGTTAATTTTATTT
Found at i:2689220 original size:19 final size:19
Alignment explanation
Indices: 2689196--2689233 Score: 76
Period size: 19 Copynumber: 2.0 Consensus size: 19
2689186 AATTACTAAG
2689196 TTAGAAAATTTGACATGGA
1 TTAGAAAATTTGACATGGA
2689215 TTAGAAAATTTGACATGGA
1 TTAGAAAATTTGACATGGA
2689234 GAATGAATTT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.42, C:0.05, G:0.21, T:0.32
Consensus pattern (19 bp):
TTAGAAAATTTGACATGGA
Found at i:2699535 original size:64 final size:64
Alignment explanation
Indices: 2699434--2699617 Score: 298
Period size: 64 Copynumber: 2.9 Consensus size: 64
2699424 CATAATCATT
*
2699434 CATCTAGTTAGGAGCACTTGATTCATTTCGATCATAGCATTCTAATTGTTTGACATAAACACCA
1 CATCTAGTTAGGAGCACTTGATTCATTTCGATCATAGCATTCTAATTATTTGACATAAACACCA
*
2699498 CATCTAGTTAGGAGCACTTGATTCATTTCGATCATAGCATTTTAATTATTTGACATAAACACCA
1 CATCTAGTTAGGAGCACTTGATTCATTTCGATCATAGCATTCTAATTATTTGACATAAACACCA
* * * *
2699562 CATCTAGTTAGG-GACATTTGATTCATCTCGATCATAGCATCCTAGTTATTTGACAT
1 CATCTAGTTAGGAG-CACTTGATTCATTTCGATCATAGCATTCTAATTATTTGACAT
2699618 GTACAGATAC
Statistics
Matches: 112, Mismatches: 7, Indels: 2
0.93 0.06 0.02
Matches are distributed among these distances:
63 1 0.01
64 111 0.99
ACGTcount: A:0.30, C:0.20, G:0.14, T:0.36
Consensus pattern (64 bp):
CATCTAGTTAGGAGCACTTGATTCATTTCGATCATAGCATTCTAATTATTTGACATAAACACCA
Found at i:2700178 original size:44 final size:44
Alignment explanation
Indices: 2699689--2700164 Score: 596
Period size: 44 Copynumber: 10.8 Consensus size: 44
2699679 GCGAATCCTA
* *
2699689 CAGATTTGGCATCTCTGTATTAGTG-A-AGAGCAGATCAAAGATAA
1 CAGATTTGGCATCTCTGTATT-G-GCAGAGAGCAGATCGAAGATAG
* * *
2699733 CAAATTTGGCGTCTCTGTATTGGCGGAGAGCAGATCGAAGATAG
1 CAGATTTGGCATCTCTGTATTGGCAGAGAGCAGATCGAAGATAG
* * * * * * * *
2699777 CAGATTTAGCGTCTCTATATTGTCAAAGGGCAAATCAAAGATAG
1 CAGATTTGGCATCTCTGTATTGGCAGAGAGCAGATCGAAGATAG
** * *
2699821 CAGATTTGGCATCTCTGTATTGGTGGATAGCAGATCGAAGATAT
1 CAGATTTGGCATCTCTGTATTGGCAGAGAGCAGATCGAAGATAG
* * * * *
2699865 CAGATTTGGCGTCTTTGTATTGTCAGAGGGCAGATTGAAGATAG
1 CAGATTTGGCATCTCTGTATTGGCAGAGAGCAGATCGAAGATAG
*
2699909 CAGATTTGGCATCTCTGTATTGGCGGAGAGCAGATCGAAGATAG
1 CAGATTTGGCATCTCTGTATTGGCAGAGAGCAGATCGAAGATAG
* *
2699953 CAGATTTGGCATCTCTGTATTGGCAGAGAACAAATCGAAGATAG
1 CAGATTTGGCATCTCTGTATTGGCAGAGAGCAGATCGAAGATAG
** *
2699997 CAGATTTGGCATCTCTGTATTGGTGGAGAGCAGATCGAAGATAT
1 CAGATTTGGCATCTCTGTATTGGCAGAGAGCAGATCGAAGATAG
* * * * *
2700041 CAGATTTAGCGTCTCTGTATTGTCAGAGGGCAGATCAAAGATAG
1 CAGATTTGGCATCTCTGTATTGGCAGAGAGCAGATCGAAGATAG
* *
2700085 CAGATTTGGCGTCTCTGTTTTGGCAGAGAGCAGATCGAAGATAG
1 CAGATTTGGCATCTCTGTATTGGCAGAGAGCAGATCGAAGATAG
*
2700129 CAGATTTGACATCTCTGTATTGGCAGAGAGCAGATC
1 CAGATTTGGCATCTCTGTATTGGCAGAGAGCAGATC
2700165 AAAAATAATA
Statistics
Matches: 365, Mismatches: 65, Indels: 4
0.84 0.15 0.01
Matches are distributed among these distances:
42 1 0.00
43 1 0.00
44 363 0.99
ACGTcount: A:0.29, C:0.15, G:0.28, T:0.28
Consensus pattern (44 bp):
CAGATTTGGCATCTCTGTATTGGCAGAGAGCAGATCGAAGATAG
Found at i:2704970 original size:31 final size:30
Alignment explanation
Indices: 2704934--2705005 Score: 81
Period size: 31 Copynumber: 2.4 Consensus size: 30
2704924 GATTAAATCA
*
2704934 AAATTAAAGTTTCAAGTATAGATTTGAACC
1 AAATTAAAGTTTCAAGTATAGAATTGAACC
* * * * *
2704964 ACAATTAGAGTTTCACGTGTATAATTGAATC
1 A-AATTAAAGTTTCAAGTATAGAATTGAACC
2704995 AAATTAAAGTT
1 AAATTAAAGTT
2705006 AATGTATATA
Statistics
Matches: 34, Mismatches: 7, Indels: 2
0.79 0.16 0.05
Matches are distributed among these distances:
30 10 0.29
31 24 0.71
ACGTcount: A:0.42, C:0.10, G:0.14, T:0.35
Consensus pattern (30 bp):
AAATTAAAGTTTCAAGTATAGAATTGAACC
Found at i:2706606 original size:16 final size:16
Alignment explanation
Indices: 2706579--2706618 Score: 53
Period size: 16 Copynumber: 2.5 Consensus size: 16
2706569 TCACAATACT
*
2706579 ATAATGAAATAACTTC
1 ATAATTAAATAACTTC
* *
2706595 ATGATTAAATAAGTTC
1 ATAATTAAATAACTTC
2706611 ATAATTAA
1 ATAATTAA
2706619 TAGGTAAAAA
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:0.50, C:0.07, G:0.07, T:0.35
Consensus pattern (16 bp):
ATAATTAAATAACTTC
Found at i:2707873 original size:14 final size:14
Alignment explanation
Indices: 2707854--2707885 Score: 64
Period size: 14 Copynumber: 2.3 Consensus size: 14
2707844 AGGTCATTAA
2707854 GCCCAACCAAACTG
1 GCCCAACCAAACTG
2707868 GCCCAACCAAACTG
1 GCCCAACCAAACTG
2707882 GCCC
1 GCCC
2707886 GGTGATTGGA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.31, C:0.47, G:0.16, T:0.06
Consensus pattern (14 bp):
GCCCAACCAAACTG
Found at i:2712501 original size:16 final size:16
Alignment explanation
Indices: 2712482--2712532 Score: 59
Period size: 16 Copynumber: 3.1 Consensus size: 16
2712472 TAGAATTCAT
2712482 ATCAATTCTAAAGCAA
1 ATCAATTCTAAAGCAA
* *
2712498 ATCAATT-TATAATTCAT
1 ATCAATTCTA-AA-GCAA
2712515 ATCAATTCTAAAGCAA
1 ATCAATTCTAAAGCAA
2712531 AT
1 AT
2712533 ATTAATAGTA
Statistics
Matches: 28, Mismatches: 4, Indels: 6
0.74 0.11 0.16
Matches are distributed among these distances:
15 2 0.07
16 13 0.46
17 11 0.39
18 2 0.07
ACGTcount: A:0.47, C:0.16, G:0.04, T:0.33
Consensus pattern (16 bp):
ATCAATTCTAAAGCAA
Found at i:2712520 original size:17 final size:17
Alignment explanation
Indices: 2712475--2712526 Score: 63
Period size: 17 Copynumber: 3.1 Consensus size: 17
2712465 AAAAAATTAG
2712475 AATTCATATCAATTCTA
1 AATTCATATCAATTCTA
* *
2712492 AA-GCAAATCAATT-TA
1 AATTCATATCAATTCTA
2712507 TAATTCATATCAATTCTA
1 -AATTCATATCAATTCTA
2712525 AA
1 AA
2712527 GCAAATATTA
Statistics
Matches: 28, Mismatches: 4, Indels: 6
0.74 0.11 0.16
Matches are distributed among these distances:
15 2 0.07
16 11 0.39
17 13 0.46
18 2 0.07
ACGTcount: A:0.46, C:0.15, G:0.02, T:0.37
Consensus pattern (17 bp):
AATTCATATCAATTCTA
Found at i:2714390 original size:15 final size:14
Alignment explanation
Indices: 2714364--2714398 Score: 52
Period size: 15 Copynumber: 2.4 Consensus size: 14
2714354 GTAATAATGA
2714364 AAATATAACAATAT
1 AAATATAACAATAT
*
2714378 ATATATGAACAATAT
1 AAATAT-AACAATAT
2714393 AAATAT
1 AAATAT
2714399 TAAAATAAAA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
14 5 0.28
15 13 0.72
ACGTcount: A:0.60, C:0.06, G:0.03, T:0.31
Consensus pattern (14 bp):
AAATATAACAATAT
Found at i:2714991 original size:25 final size:25
Alignment explanation
Indices: 2714944--2714991 Score: 60
Period size: 25 Copynumber: 1.9 Consensus size: 25
2714934 AATAAAAATA
* *
2714944 AATAAAATAATAGATATTTTATTCG
1 AATAAAATAATAGATAATATATTCG
* *
2714969 AATAAAATTATATATAATATATT
1 AATAAAATAATAGATAATATATT
2714992 ATCAAATTTT
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
25 19 1.00
ACGTcount: A:0.52, C:0.02, G:0.04, T:0.42
Consensus pattern (25 bp):
AATAAAATAATAGATAATATATTCG
Found at i:2720092 original size:20 final size:20
Alignment explanation
Indices: 2720067--2720116 Score: 70
Period size: 17 Copynumber: 2.6 Consensus size: 20
2720057 TGGCTTAAAA
2720067 TTGGTAGTGGATTGTTGTTG
1 TTGGTAGTGGATTGTTGTTG
2720087 TTGGTAGTGG---GTTGTTG
1 TTGGTAGTGGATTGTTGTTG
*
2720104 GTGGTAGTGGATT
1 TTGGTAGTGGATT
2720117 AGTGGATGGT
Statistics
Matches: 26, Mismatches: 1, Indels: 6
0.79 0.03 0.18
Matches are distributed among these distances:
17 16 0.62
20 10 0.38
ACGTcount: A:0.10, C:0.00, G:0.44, T:0.46
Consensus pattern (20 bp):
TTGGTAGTGGATTGTTGTTG
Found at i:2724731 original size:20 final size:20
Alignment explanation
Indices: 2724706--2724755 Score: 70
Period size: 17 Copynumber: 2.6 Consensus size: 20
2724696 TGGCTTAAAA
2724706 TTGGTAGTGGATTGTTGTTG
1 TTGGTAGTGGATTGTTGTTG
2724726 TTGGTAGTGG---GTTGTTG
1 TTGGTAGTGGATTGTTGTTG
*
2724743 GTGGTAGTGGATT
1 TTGGTAGTGGATT
2724756 AGTGGATGGT
Statistics
Matches: 26, Mismatches: 1, Indels: 6
0.79 0.03 0.18
Matches are distributed among these distances:
17 16 0.62
20 10 0.38
ACGTcount: A:0.10, C:0.00, G:0.44, T:0.46
Consensus pattern (20 bp):
TTGGTAGTGGATTGTTGTTG
Found at i:2729596 original size:41 final size:41
Alignment explanation
Indices: 2729535--2729648 Score: 158
Period size: 41 Copynumber: 2.8 Consensus size: 41
2729525 AAAAACACTG
2729535 TTAGTGGTGTTTTA-CTTAAAAACGCCGCTATTCATCAGTTT
1 TTAGTGGTGTTTTAGC-TAAAAACGCCGCTATTCATCAGTTT
* *
2729576 TTAGTGGTGTTTTAGCTAAAAACGCCGCTATTGATTAGTTT
1 TTAGTGGTGTTTTAGCTAAAAACGCCGCTATTCATCAGTTT
* ** *
2729617 TTAGTGGCGTTTGGGCCAAAAACGCCGCTATT
1 TTAGTGGTGTTTTAGCTAAAAACGCCGCTATT
2729649 GTTTAGTTTT
Statistics
Matches: 66, Mismatches: 6, Indels: 2
0.89 0.08 0.03
Matches are distributed among these distances:
41 65 0.98
42 1 0.02
ACGTcount: A:0.24, C:0.17, G:0.22, T:0.38
Consensus pattern (41 bp):
TTAGTGGTGTTTTAGCTAAAAACGCCGCTATTCATCAGTTT
Found at i:2729649 original size:41 final size:41
Alignment explanation
Indices: 2729552--2729659 Score: 153
Period size: 41 Copynumber: 2.6 Consensus size: 41
2729542 TGTTTTACTT
* * * * *
2729552 AAAAACGCCGCTATTCATCAGTTTTTAGTGGTGTTTTAGCT
1 AAAAACGCCGCTATTGATTAGTTTTTAGTGGCGTTTGAGCC
*
2729593 AAAAACGCCGCTATTGATTAGTTTTTAGTGGCGTTTGGGCC
1 AAAAACGCCGCTATTGATTAGTTTTTAGTGGCGTTTGAGCC
*
2729634 AAAAACGCCGCTATTGTTTAGTTTTT
1 AAAAACGCCGCTATTGATTAGTTTTT
2729660 TGCAGCGTTT
Statistics
Matches: 60, Mismatches: 7, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
41 60 1.00
ACGTcount: A:0.24, C:0.17, G:0.21, T:0.38
Consensus pattern (41 bp):
AAAAACGCCGCTATTGATTAGTTTTTAGTGGCGTTTGAGCC
Found at i:2738913 original size:25 final size:25
Alignment explanation
Indices: 2738885--2738933 Score: 64
Period size: 25 Copynumber: 2.0 Consensus size: 25
2738875 TTTTTGGTAA
*
2738885 TAAAAATAAAAAT-ATTTAATTTTAC
1 TAAAAA-AAAAATAATTTAAATTTAC
*
2738910 TAAAAAAACAATAATTTAAATTTA
1 TAAAAAAAAAATAATTTAAATTTA
2738934 TTTGATCAAT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
24 5 0.24
25 16 0.76
ACGTcount: A:0.59, C:0.04, G:0.00, T:0.37
Consensus pattern (25 bp):
TAAAAAAAAAATAATTTAAATTTAC
Found at i:2740729 original size:17 final size:17
Alignment explanation
Indices: 2740707--2740743 Score: 65
Period size: 17 Copynumber: 2.2 Consensus size: 17
2740697 TACTTTACTC
2740707 TTTATTTATTGTTTATT
1 TTTATTTATTGTTTATT
*
2740724 TTTATTTTTTGTTTATT
1 TTTATTTATTGTTTATT
2740741 TTT
1 TTT
2740744 TTCGCATTCG
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.14, C:0.00, G:0.05, T:0.81
Consensus pattern (17 bp):
TTTATTTATTGTTTATT
Found at i:2755852 original size:26 final size:26
Alignment explanation
Indices: 2755821--2755878 Score: 66
Period size: 25 Copynumber: 2.3 Consensus size: 26
2755811 GTAAGAATAT
* * *
2755821 TTTTTTATGAATTTGAT-ATTTATTA
1 TTTTTTATAAATTTAATCATTAATTA
2755846 TTATTTT-TAAATTTAATCATTAATTA
1 TT-TTTTATAAATTTAATCATTAATTA
2755872 TTTTTTA
1 TTTTTTA
2755879 AAAAAAATAT
Statistics
Matches: 27, Mismatches: 3, Indels: 5
0.77 0.09 0.14
Matches are distributed among these distances:
25 14 0.52
26 13 0.48
ACGTcount: A:0.31, C:0.02, G:0.03, T:0.64
Consensus pattern (26 bp):
TTTTTTATAAATTTAATCATTAATTA
Found at i:2772883 original size:9 final size:9
Alignment explanation
Indices: 2772871--2772920 Score: 55
Period size: 9 Copynumber: 5.2 Consensus size: 9
2772861 AAATAAAAAT
2772871 AATTTTAAA
1 AATTTTAAA
2772880 AATTTGTAAA
1 AATTT-TAAA
2772890 ACATTATTAAA
1 A-ATT-TTAAA
*
2772901 ATTTTTAAA
1 AATTTTAAA
*
2772910 AATGTTAAA
1 AATTTTAAA
2772919 AA
1 AA
2772921 AATAAAATTA
Statistics
Matches: 35, Mismatches: 3, Indels: 6
0.80 0.07 0.14
Matches are distributed among these distances:
9 19 0.54
10 7 0.20
11 8 0.23
12 1 0.03
ACGTcount: A:0.54, C:0.02, G:0.04, T:0.40
Consensus pattern (9 bp):
AATTTTAAA
Found at i:2773065 original size:13 final size:13
Alignment explanation
Indices: 2773047--2773072 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
2773037 GACATCATAG
2773047 ACCATGAATGTAA
1 ACCATGAATGTAA
2773060 ACCATGAATGTAA
1 ACCATGAATGTAA
2773073 CATCCCGATT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.46, C:0.15, G:0.15, T:0.23
Consensus pattern (13 bp):
ACCATGAATGTAA
Found at i:2776065 original size:26 final size:26
Alignment explanation
Indices: 2776036--2776088 Score: 72
Period size: 26 Copynumber: 2.0 Consensus size: 26
2776026 TTTACAATTT
2776036 TACCCCTAGGAGATAAATT-ACCGAAA
1 TACCCCTAGG-GATAAATTGACCGAAA
* *
2776062 TACCCCTAGGGTTAAATTGACCTAAA
1 TACCCCTAGGGATAAATTGACCGAAA
2776088 T
1 T
2776089 GCATGTTTGA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
25 7 0.29
26 17 0.71
ACGTcount: A:0.38, C:0.23, G:0.15, T:0.25
Consensus pattern (26 bp):
TACCCCTAGGGATAAATTGACCGAAA
Found at i:2789839 original size:17 final size:18
Alignment explanation
Indices: 2789817--2789850 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
2789807 ATATTCATAA
2789817 TTATATATATA-ATTGTT
1 TTATATATATATATTGTT
*
2789834 TTATATTTATATATTGT
1 TTATATATATATATTGT
2789851 ATGCATAAAT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 10 0.67
18 5 0.33
ACGTcount: A:0.32, C:0.00, G:0.06, T:0.62
Consensus pattern (18 bp):
TTATATATATATATTGTT
Found at i:2799727 original size:15 final size:15
Alignment explanation
Indices: 2799707--2799736 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
2799697 TTTAATCTTT
*
2799707 TATAAATTATAAAAA
1 TATAAACTATAAAAA
2799722 TATAAACTATAAAAA
1 TATAAACTATAAAAA
2799737 ATTAAAATTT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.67, C:0.03, G:0.00, T:0.30
Consensus pattern (15 bp):
TATAAACTATAAAAA
Found at i:2801690 original size:11 final size:12
Alignment explanation
Indices: 2801664--2801689 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
2801654 AAAACAGTAT
2801664 AAAGCTAAAAAA
1 AAAGCTAAAAAA
2801676 AAAGCTAAAAAA
1 AAAGCTAAAAAA
2801688 AA
1 AA
2801690 GGCAGCAGAT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.77, C:0.08, G:0.08, T:0.08
Consensus pattern (12 bp):
AAAGCTAAAAAA
Found at i:2801896 original size:14 final size:14
Alignment explanation
Indices: 2801877--2801937 Score: 72
Period size: 14 Copynumber: 4.4 Consensus size: 14
2801867 CTCATTCGGG
2801877 AAGAAAGGAAAGAA
1 AAGAAAGGAAAGAA
*
2801891 AAGAAAGGAGAGAA
1 AAGAAAGGAAAGAA
2801905 AAGAAA-GAAGAGAA
1 AAGAAAGGAA-AGAA
*
2801919 GAAGAAAAG-AAGAA
1 -AAGAAAGGAAAGAA
2801933 AAGAA
1 AAGAA
2801938 GAGAAGAAGA
Statistics
Matches: 42, Mismatches: 2, Indels: 7
0.82 0.04 0.14
Matches are distributed among these distances:
13 7 0.17
14 27 0.64
15 7 0.17
16 1 0.02
ACGTcount: A:0.70, C:0.00, G:0.30, T:0.00
Consensus pattern (14 bp):
AAGAAAGGAAAGAA
Found at i:2801921 original size:3 final size:3
Alignment explanation
Indices: 2801909--2801952 Score: 60
Period size: 3 Copynumber: 16.0 Consensus size: 3
2801899 AGAGAAAAGA
2801909 AAG AAG -AG AAG AAG AA- AAG AAG AA- AAG AAG -AG AAG AAG AAG AAG
1 AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG
2801953 GAGCAACCAT
Statistics
Matches: 37, Mismatches: 0, Indels: 8
0.82 0.00 0.18
Matches are distributed among these distances:
2 8 0.22
3 29 0.78
ACGTcount: A:0.68, C:0.00, G:0.32, T:0.00
Consensus pattern (3 bp):
AAG
Found at i:2801922 original size:8 final size:8
Alignment explanation
Indices: 2801887--2801952 Score: 68
Period size: 8 Copynumber: 8.6 Consensus size: 8
2801877 AAGAAAGGAA
2801887 AGAA-AAG
1 AGAAGAAG
*
2801894 A-AAGGAG
1 AGAAGAAG
2801901 AGAA-AAG
1 AGAAGAAG
2801908 A-AAGAAG
1 AGAAGAAG
2801915 AGAAGAAG
1 AGAAGAAG
*
2801923 AAAAGAAG
1 AGAAGAAG
*
2801931 AAAAGAAG
1 AGAAGAAG
2801939 AGAAGAAG
1 AGAAGAAG
2801947 AAGAAG
1 -AGAAG
2801953 GAGCAACCAT
Statistics
Matches: 50, Mismatches: 4, Indels: 8
0.81 0.06 0.13
Matches are distributed among these distances:
6 4 0.08
7 11 0.22
8 30 0.60
9 5 0.10
ACGTcount: A:0.68, C:0.00, G:0.32, T:0.00
Consensus pattern (8 bp):
AGAAGAAG
Found at i:2801949 original size:19 final size:18
Alignment explanation
Indices: 2801894--2801951 Score: 71
Period size: 19 Copynumber: 3.1 Consensus size: 18
2801884 GAAAGAAAAG
*
2801894 AAAGGAGAGAAAAGAAAGA
1 AAAGAAGAGAAAAG-AAGA
*
2801913 AGAGAAGAAGAAAAGAAGA
1 AAAGAAG-AGAAAAGAAGA
2801932 AAAGAAGAGAAGAAGAAGA
1 AAAGAAGAGAA-AAGAAGA
2801951 A
1 A
2801952 GGAGCAACCA
Statistics
Matches: 34, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
18 4 0.12
19 23 0.68
20 7 0.21
ACGTcount: A:0.69, C:0.00, G:0.31, T:0.00
Consensus pattern (18 bp):
AAAGAAGAGAAAAGAAGA
Found at i:2802123 original size:11 final size:11
Alignment explanation
Indices: 2802091--2802123 Score: 50
Period size: 11 Copynumber: 3.0 Consensus size: 11
2802081 TATTATTGTT
2802091 GATTTGAATTT-
1 GATTT-AATTTA
2802102 GATTTAATTTA
1 GATTTAATTTA
2802113 GATTTAATTTA
1 GATTTAATTTA
2802124 TAAATTTATT
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
10 5 0.24
11 16 0.76
ACGTcount: A:0.33, C:0.00, G:0.12, T:0.55
Consensus pattern (11 bp):
GATTTAATTTA
Found at i:2802469 original size:36 final size:37
Alignment explanation
Indices: 2802387--2802469 Score: 89
Period size: 36 Copynumber: 2.3 Consensus size: 37
2802377 AGAATATGAG
* *
2802387 AAAAATACAATAAAATATGAAAATAGTATAAAAATAA
1 AAAAATAAAATAAAATACGAAAATAGTATAAAAATAA
* * ***
2802424 TATAA-AAAATAAAATACGAAAATAGTAT-ATTTTAA
1 AAAAATAAAATAAAATACGAAAATAGTATAAAAATAA
2802459 AAAAATAAAAT
1 AAAAATAAAAT
2802470 CCAAAAGTTT
Statistics
Matches: 36, Mismatches: 9, Indels: 3
0.75 0.19 0.06
Matches are distributed among these distances:
35 7 0.19
36 26 0.72
37 3 0.08
ACGTcount: A:0.67, C:0.02, G:0.05, T:0.25
Consensus pattern (37 bp):
AAAAATAAAATAAAATACGAAAATAGTATAAAAATAA
Found at i:2802590 original size:138 final size:137
Alignment explanation
Indices: 2802417--2803431 Score: 1639
Period size: 138 Copynumber: 7.4 Consensus size: 137
2802407 AAATAGTATA
* *
2802417 AAAATAATATAAAAAATAAAATACGAAAATAGTATATTTTAAAAAAATAAAATCCAAAAGTTTTA
1 AAAATAAGATAAAAAATAAAATACGAAAATAGTATATTTT-AAAAAATAAAATCCAATA-TTTTA
* * * *
2802482 AAAATACAAACAAAGGGACAAAATTAGGGTTATTTAAAAAACACTAAAATAATACATTTAAAACA
64 GAAATACAAACAAAGGGACAAAATCAGGGTTATTTTAAAAACACTAAAATAATACATTTGAAACA
2802547 TTATGTACT
129 TTATGTACT
2802556 AAAATAAGAT-AAAAATAAAATACGAAAATAGTATATTTTAAAAAATAAAATCCGAATATTTTAG
1 AAAATAAGATAAAAAATAAAATACGAAAATAGTATATTTTAAAAAATAAAATCC-AATATTTTAG
*
2802620 AAATACAAACAAAGGGTCAAAATCAGGGTTATTTTAAAAACAC-----TAA-ACATTTGAAACAT
65 AAATACAAACAAAGGGACAAAATCAGGGTTATTTTAAAAACACTAAAATAATACATTTGAAACAT
2802679 TATGTACT
130 TATGTACT
*
2802687 AAAATAAGATAAAAAATAAAATACGAAAATAGTATATTTTAAAAAATAAAATTCTAATATTTTAG
1 AAAATAAGATAAAAAATAAAATACGAAAATAGTATATTTTAAAAAATAAAA-TCCAATATTTTAG
* *
2802752 AAATACAAACAAAGGGACAAAATTAAGGTTATTTTAAAAACACTAAAATAATACATTTGAAACAT
65 AAATACAAACAAAGGGACAAAATCAGGGTTATTTTAAAAACACTAAAATAATACATTTGAAACAT
2802817 TATGTACT
130 TATGTACT
*
2802825 TAAATAAGATAAAAAATAAAATACGAAAATAGTATATTTTAAAAAATAAAATCCAAATATTTTAG
1 AAAATAAGATAAAAAATAAAATACGAAAATAGTATATTTTAAAAAATAAAATCC-AATATTTTAG
*
2802890 AAATATAAACAAAGGGACAAAATCAGGGTTATTTTAAAAACACTAAAATAATACATTTGAAACAT
65 AAATACAAACAAAGGGACAAAATCAGGGTTATTTTAAAAACACTAAAATAATACATTTGAAACAT
2802955 TATGTACT
130 TATGTACT
* *
2802963 AAAATAAAATAAAAAATAAAATACGAAAATAGTATATTTTAAAAAAGAAAATCCGAATATTTTAG
1 AAAATAAGATAAAAAATAAAATACGAAAATAGTATATTTTAAAAAATAAAATCC-AATATTTTAG
* * *
2803028 AAATATAAATAAAGTGACAAAATCAGGGTTATTTTAAAAACACTAAAATAATACATTTGAAACAT
65 AAATACAAACAAAGGGACAAAATCAGGGTTATTTTAAAAACACTAAAATAATACATTTGAAACAT
2803093 TATGTACT
130 TATGTACT
* *
2803101 AAAATAAGATAAAAAATAAAATACGAAAAATAGTATATTTTAAAAAATAAAATCTGAATATTCTA
1 AAAATAAGATAAAAAATAAAATACG-AAAATAGTATATTTTAAAAAATAAAATC-CAATATTTTA
* * *
2803166 AAAATACAAACAAAGAGACAAAATCGGGGTTATTTTAAAAACACTAAAATAATACATTTGAAACA
64 GAAATACAAACAAAGGGACAAAATCAGGGTTATTTTAAAAACACTAAAATAATACATTTGAAACA
2803231 TTATGTACT
129 TTATGTACT
2803240 AAAATAAGATAAAAAATAAAATACGAAAAATAGTATATTTTAAAAAATAAAATCCGAATATTTTA
1 AAAATAAGATAAAAAATAAAATACG-AAAATAGTATATTTTAAAAAATAAAATCC-AATATTTTA
* * * *
2803305 GAAATACAAACAAATGGACAAAATCAGAGTTTTTTTAAAAACACTAAATTAATACATTTGAAACA
64 GAAATACAAACAAAGGGACAAAATCAGGGTTATTTTAAAAACACTAAAATAATACATTTGAAACA
2803370 TTATGTACT
129 TTATGTACT
* *
2803379 AAAATAAGATAAAAAATAAAATTCGAAAATAGTATATTTTAAAAAATAGAATC
1 AAAATAAGATAAAAAATAAAATACGAAAATAGTATATTTTAAAAAATAAAATC
2803432 TGAAAATTTT
Statistics
Matches: 821, Mismatches: 42, Indels: 27
0.92 0.05 0.03
Matches are distributed among these distances:
131 30 0.04
132 93 0.11
133 2 0.00
137 64 0.08
138 366 0.45
139 266 0.32
ACGTcount: A:0.56, C:0.08, G:0.08, T:0.28
Consensus pattern (137 bp):
AAAATAAGATAAAAAATAAAATACGAAAATAGTATATTTTAAAAAATAAAATCCAATATTTTAGA
AATACAAACAAAGGGACAAAATCAGGGTTATTTTAAAAACACTAAAATAATACATTTGAAACATT
ATGTACT
Found at i:2805577 original size:72 final size:72
Alignment explanation
Indices: 2805480--2805620 Score: 196
Period size: 72 Copynumber: 2.0 Consensus size: 72
2805470 AGTCTGAGCG
* * *
2805480 ATCGTATTCATATTCGGCTAATACTTCTTATCATCCGAATTT-CCAGAGCAATGACTATTTACC-
1 ATCGCATTCACATTCGGCCAATACTTCTTATCATCCGAATTTACC-GAGCAATGACTATTT-CCT
2805543 GGGCTCGTC
64 GGGCTCGTC
* * *
2805552 ATCGCATTCACATTCGGCCGATACTTCTTATCATCCGGATTTACCGGGCAATGACTATTTCCTGG
1 ATCGCATTCACATTCGGCCAATACTTCTTATCATCCGAATTTACCGAGCAATGACTATTTCCTGG
2805617 GCTC
66 GCTC
2805621 ATCAGGGGGC
Statistics
Matches: 61, Mismatches: 6, Indels: 4
0.86 0.08 0.06
Matches are distributed among these distances:
71 2 0.03
72 57 0.93
73 2 0.03
ACGTcount: A:0.23, C:0.27, G:0.17, T:0.33
Consensus pattern (72 bp):
ATCGCATTCACATTCGGCCAATACTTCTTATCATCCGAATTTACCGAGCAATGACTATTTCCTGG
GCTCGTC
Found at i:2809450 original size:27 final size:28
Alignment explanation
Indices: 2809408--2809476 Score: 81
Period size: 27 Copynumber: 2.5 Consensus size: 28
2809398 CGCCCCTGGC
* *
2809408 AGAGGCAAGACCAGTGCTGCCTT-TGA-T
1 AGAGGCAAGACTAGTGCCG-CTTCTGAGT
2809435 AGAGGCAAGACTAGTGCCGCTTCTGAGT
1 AGAGGCAAGACTAGTGCCGCTTCTGAGT
*
2809463 A-AGACAAGACTAGT
1 AGAGGCAAGACTAGT
2809477 ATTTTATTTT
Statistics
Matches: 37, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
26 3 0.08
27 32 0.86
28 2 0.05
ACGTcount: A:0.30, C:0.20, G:0.29, T:0.20
Consensus pattern (28 bp):
AGAGGCAAGACTAGTGCCGCTTCTGAGT
Found at i:2812231 original size:18 final size:18
Alignment explanation
Indices: 2812205--2812250 Score: 74
Period size: 18 Copynumber: 2.6 Consensus size: 18
2812195 GGTGGTCACG
*
2812205 CCACGCTGACAGGCGGCA
1 CCACCCTGACAGGCGGCA
*
2812223 CCACCCTGATAGGCGGCA
1 CCACCCTGACAGGCGGCA
2812241 CCACCCTGAC
1 CCACCCTGAC
2812251 GTGACTTCTC
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 25 1.00
ACGTcount: A:0.22, C:0.43, G:0.26, T:0.09
Consensus pattern (18 bp):
CCACCCTGACAGGCGGCA
Found at i:2812293 original size:20 final size:20
Alignment explanation
Indices: 2812268--2812316 Score: 62
Period size: 20 Copynumber: 2.4 Consensus size: 20
2812258 CTCCAATAGT
*
2812268 AAAAAAAATTGAAAAAGAAA
1 AAAAAAAACTGAAAAAGAAA
* *
2812288 AAAAAACACTGAAAACGAAA
1 AAAAAAAACTGAAAAAGAAA
2812308 AAATAAAAA
1 AAA-AAAAA
2812317 AATAGGTCAT
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
20 20 0.83
21 4 0.17
ACGTcount: A:0.78, C:0.06, G:0.08, T:0.08
Consensus pattern (20 bp):
AAAAAAAACTGAAAAAGAAA
Found at i:2812487 original size:3 final size:3
Alignment explanation
Indices: 2812479--2812527 Score: 57
Period size: 3 Copynumber: 16.7 Consensus size: 3
2812469 TTTGGAAACA
* *
2812479 AAG AAG AAG AAG AAA AAG AGAG AAG AAG GA- AAG AAG -AG AAG AAG
1 AAG AAG AAG AAG AAG AAG A-AG AAG AAG AAG AAG AAG AAG AAG AAG
2812523 AAG AA
1 AAG AA
2812528 AGAAAAAGGA
Statistics
Matches: 39, Mismatches: 4, Indels: 6
0.80 0.08 0.12
Matches are distributed among these distances:
2 3 0.08
3 33 0.85
4 3 0.08
ACGTcount: A:0.67, C:0.00, G:0.33, T:0.00
Consensus pattern (3 bp):
AAG
Found at i:2812504 original size:16 final size:16
Alignment explanation
Indices: 2812478--2812528 Score: 68
Period size: 18 Copynumber: 3.1 Consensus size: 16
2812468 TTTTGGAAAC
2812478 AAAGA-AGAAGAAGAA
1 AAAGAGAGAAGAAGAA
2812493 AAAGAGAGAAGAAGGAA
1 AAAGAGAGAAGAA-GAA
2812510 AGAAGAGAAGAAGAAGAA
1 A-AAGAG-AGAAGAAGAA
2812528 A
1 A
2812529 GAAAAAGGAG
Statistics
Matches: 32, Mismatches: 0, Indels: 5
0.86 0.00 0.14
Matches are distributed among these distances:
15 5 0.16
16 7 0.22
17 4 0.12
18 9 0.28
19 7 0.22
ACGTcount: A:0.69, C:0.00, G:0.31, T:0.00
Consensus pattern (16 bp):
AAAGAGAGAAGAAGAA
Found at i:2812526 original size:29 final size:30
Alignment explanation
Indices: 2812478--2812537 Score: 86
Period size: 29 Copynumber: 2.0 Consensus size: 30
2812468 TTTTGGAAAC
* *
2812478 AAAGAAGAAGAAGAAAAAGAGAGAAGAAGG
1 AAAGAAGAAGAAGAAAAAGAAAGAAAAAGG
*
2812508 AAAGAAG-AGAAGAAGAAGAAAGAAAAAGG
1 AAAGAAGAAGAAGAAAAAGAAAGAAAAAGG
2812537 A
1 A
2812538 GAGGAGGAGA
Statistics
Matches: 27, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
29 20 0.74
30 7 0.26
ACGTcount: A:0.68, C:0.00, G:0.32, T:0.00
Consensus pattern (30 bp):
AAAGAAGAAGAAGAAAAAGAAAGAAAAAGG
Found at i:2812587 original size:5 final size:6
Alignment explanation
Indices: 2812572--2812596 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
2812562 TGAGAGAAGA
2812572 AAAAAG AAAAAG AAAAAG AAAAAG A
1 AAAAAG AAAAAG AAAAAG AAAAAG A
2812597 GAAGGAGAAG
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.84, C:0.00, G:0.16, T:0.00
Consensus pattern (6 bp):
AAAAAG
Found at i:2812632 original size:20 final size:19
Alignment explanation
Indices: 2812568--2812638 Score: 63
Period size: 20 Copynumber: 3.6 Consensus size: 19
2812558 CGGTTGAGAG
* * *
2812568 AAGAAAAAAGAAAAAGAAA
1 AAGAAGAAAGAGAAGGAAA
2812587 AAGAA-AAAGAGAAGGAGAA
1 AAGAAGAAAGAGAAGGA-AA
*
2812606 GAAGAAGAAGAGGGAAGGAAA
1 -AAGAAGAA-AGAGAAGGAAA
2812627 AAGAAGGAAAGA
1 AAGAA-GAAAGA
2812639 AAAAGGTAAT
Statistics
Matches: 43, Mismatches: 4, Indels: 9
0.77 0.07 0.16
Matches are distributed among these distances:
18 9 0.21
19 7 0.16
20 12 0.28
21 7 0.16
22 8 0.19
ACGTcount: A:0.69, C:0.00, G:0.31, T:0.00
Consensus pattern (19 bp):
AAGAAGAAAGAGAAGGAAA
Found at i:2812635 original size:14 final size:14
Alignment explanation
Indices: 2812574--2812643 Score: 54
Period size: 14 Copynumber: 4.7 Consensus size: 14
2812564 AGAGAAGAAA
2812574 AAAGAAAAAGAA--
1 AAAGAAAAAGAAGG
2812586 AAAGAAAAAGAGAAGG
1 AAAG-AAAA-AGAAGG
*
2812602 AGAAGAAGAAGAAGAGGG
1 A-AAG-A-AA-AAGAAGG
*
2812620 AAGGAAAAAGAAGG
1 AAAGAAAAAGAAGG
2812634 AAAGAAAAAG
1 AAAGAAAAAG
2812644 GTAATTTTTT
Statistics
Matches: 47, Mismatches: 4, Indels: 12
0.75 0.06 0.19
Matches are distributed among these distances:
12 4 0.09
13 4 0.09
14 19 0.40
15 2 0.04
16 2 0.04
17 7 0.15
18 8 0.17
19 1 0.02
ACGTcount: A:0.69, C:0.00, G:0.31, T:0.00
Consensus pattern (14 bp):
AAAGAAAAAGAAGG
Found at i:2813386 original size:131 final size:129
Alignment explanation
Indices: 2813150--2813672 Score: 357
Period size: 144 Copynumber: 3.7 Consensus size: 129
2813140 ATCCGAAAAT
* * * *
2813150 AAAAAAATACGAACAAGGTGCCAAAGTCAGGTTATTTATTAAATTAATATAAAAAAATTAAATAA
1 AAAAAAATAAGAACAAAGTGCCAAAATCAGGTTATTTATTAAATAAATATAAAAAAATTAAATAA
* * * *
2813215 TACATTTGAAAGATTTTATGCTAAAATAAAATACCAAAATAATATATTTTAAAAAATAATATAC
66 TACATTTGAAACATTATATACTAAAATAAAATACAAAAATAATATATTTTAAAAAATAATATAC
* *
2813279 AAAAAAATAAGAATAAAGTGCTAAAATCAGGGTTATTTATTAAA-AAATATAAAAAATATTTAAA
1 AAAAAAATAAGAACAAAGTGCCAAAATCA-GGTTATTTATTAAATAAATATAAAAAA-A-TTAAA
* *
2813343 TAATACATTTGAAACATTATGTACTAAAATAATATAAAGAAATAAAATACGAAAATAATATATTT
63 TAATACATTTGAAAC---AT-TA-T---AT-A-CT--A-AAATAAAATACAAAAATAATATATTT
2813408 TAAAAAATAATATAC
115 TAAAAAATAATATAC
* * * * *
2813423 GAAAATAAAAAAATTACGAAGAAAGTACCAAAATCAGGGTTATTTAGTAAATTAATATAAAGAAA
1 ---AA---AAAAA-TAAGAACAAAGTGCCAAAATCA-GGTTATTTATTAAATAAATATAAA-AAA
* ** * * * * *
2813488 CACTTAAGTAATACATTTGAAATTTTTTTTGCTAAAATATTATAAAAAATAAAATAAGAAAATAA
57 -A-TTAAATAATACATTTGAAACATTATATACT--AA-A--AT--AAAATACAA-AA-ATAAT-A
*
2813553 TATATTTTAAAAAATAATATAC
110 TAT-TTTAAAAAA-TAATATAC
* * *
2813575 GAAAAAAATACGAATAAAGTGCTAAAATCAGGGTTATTTATTGAAA-AAATATAAAAAATACTTA
1 -AAAAAAATAAGAACAAAGTGCCAAAATCA-GGTTATTTATT-AAATAAATATAAAAAA-A-TTA
* *
2813639 AATAATACATTTGAAACATTATGTACTTAAATAA
61 AATAATACATTTGAAACATTATATACTAAAATAA
2813673 TATGAAGAAA
Statistics
Matches: 314, Mismatches: 44, Indels: 63
0.75 0.10 0.15
Matches are distributed among these distances:
129 35 0.11
130 15 0.05
131 19 0.06
134 2 0.01
135 1 0.00
136 1 0.00
138 2 0.01
139 2 0.01
140 2 0.01
141 1 0.00
142 2 0.01
143 7 0.02
144 40 0.13
145 32 0.10
146 38 0.12
147 17 0.05
148 3 0.01
149 5 0.02
150 12 0.04
151 40 0.13
152 16 0.05
153 22 0.07
ACGTcount: A:0.55, C:0.06, G:0.08, T:0.30
Consensus pattern (129 bp):
AAAAAAATAAGAACAAAGTGCCAAAATCAGGTTATTTATTAAATAAATATAAAAAAATTAAATAA
TACATTTGAAACATTATATACTAAAATAAAATACAAAAATAATATATTTTAAAAAATAATATAC
Found at i:2813558 original size:30 final size:30
Alignment explanation
Indices: 2813524--2813584 Score: 86
Period size: 30 Copynumber: 2.0 Consensus size: 30
2813514 TTTTGCTAAA
*
2813524 ATATTATAAAAAATAAAATAAGAAAATAAT
1 ATATTATAAAAAATAAAATAAGAAAAAAAT
* * *
2813554 ATATTTTAAAAAATAATATACGAAAAAAAT
1 ATATTATAAAAAATAAAATAAGAAAAAAAT
2813584 A
1 A
2813585 CGAATAAAGT
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
30 27 1.00
ACGTcount: A:0.67, C:0.02, G:0.03, T:0.28
Consensus pattern (30 bp):
ATATTATAAAAAATAAAATAAGAAAAAAAT
Found at i:2813562 original size:152 final size:144
Alignment explanation
Indices: 2813237--2813675 Score: 619
Period size: 152 Copynumber: 3.0 Consensus size: 144
2813227 ATTTTATGCT
* *
2813237 AAAATAAAATACCAAAATAATATATTTTAAAAAATAATATAC-AAAAAAATAAGAATAAAGTGCT
1 AAAATAAAATACGAAAATAATATATTTTAAAAAATAATATACGAAAAAAATACGAATAAAGTGCT
*
2813301 AAAATCAGGGTTATTTATTAAAAAATATAAAAAATATTTAAATAATACATTTGAAACATTATGTA
66 AAAATCAGGGTTATTTATTAAAAAATATAAAAAATACTTAAATAATACATTTGAAACATTATGTA
2813366 CTAAAATAATATAA
131 CTAAAATAATATAA
*
2813380 AGAAATAAAATACGAAAATAATATATTTTAAAAAATAATATACGAAAATAAAAAAATTACGAAGA
1 A-AAATAAAATACGAAAATAATATATTTTAAAAAATAATATACG-----AAAAAAA-TACGAATA
* * * * * *
2813445 AAGTACCAAAATCAGGGTTATTTAGTAAATTAATATAAAGAAACACTTAAGTAATACATTTGAAA
59 AAGTGCTAAAATCAGGGTTATTTATTAAA-AAATATAAA-AAATACTTAAATAATACATTTGAAA
** * * * *
2813510 TTTTTTTTGCTAAAATATTATAA
122 CATTATGTACTAAAATAATATAA
*
2813533 AAAATAAAATAAGAAAATAATATATTTTAAAAAATAATATACGAAAAAAATACGAATAAAGTGCT
1 AAAATAAAATACGAAAATAATATATTTTAAAAAATAATATACGAAAAAAATACGAATAAAGTGCT
2813598 AAAATCAGGGTTATTTATTGAAAAAATATAAAAAATACTTAAATAATACATTTGAAACATTATGT
66 AAAATCAGGGTTATTTATT-AAAAAATATAAAAAATACTTAAATAATACATTTGAAACATTATGT
*
2813663 ACTTAAATAATAT
130 ACTAAAATAATAT
2813676 GAAGAAAGTG
Statistics
Matches: 254, Mismatches: 31, Indels: 20
0.83 0.10 0.07
Matches are distributed among these distances:
143 1 0.00
144 40 0.16
145 37 0.15
146 38 0.15
147 10 0.04
150 7 0.03
151 32 0.13
152 49 0.19
153 40 0.16
ACGTcount: A:0.56, C:0.06, G:0.08, T:0.30
Consensus pattern (144 bp):
AAAATAAAATACGAAAATAATATATTTTAAAAAATAATATACGAAAAAAATACGAATAAAGTGCT
AAAATCAGGGTTATTTATTAAAAAATATAAAAAATACTTAAATAATACATTTGAAACATTATGTA
CTAAAATAATATAA
Found at i:2813643 original size:91 final size:90
Alignment explanation
Indices: 2813547--2813737 Score: 206
Period size: 90 Copynumber: 2.1 Consensus size: 90
2813537 TAAAATAAGA
* *
2813547 AAATAATATATTTTAAAAAATAATATACGAAAAAAATACGAATAAAGTG-CTAAAATCAGGGTTA
1 AAATAATATA-TTTAAAAAATAATATACGAAAAAAATACGAAGAAAGTGTC-AAAATCAAGGTTA
*
2813611 TTTATTGAAA-AAATATAAAAAATACTT
64 TTTATT-AAATAAATATAAAAAACACTT
* * * * * ** * *
2813638 AAATAATACATTTGAAACATTATGTACTTAAATAATATGAAGAAAGTGTCAAAATCAAGGTTATT
1 AAATAATATATTTAAAAAATAATATACGAAAAAAATACGAAGAAAGTGTCAAAATCAAGGTTATT
* *
2813703 TATTAAATTAGTATAAAAAACACTT
66 TATTAAATAAATATAAAAAACACTT
*
2813728 ACATAATATA
1 AAATAATATA
2813738 CCTAATACAT
Statistics
Matches: 82, Mismatches: 16, Indels: 5
0.80 0.16 0.05
Matches are distributed among these distances:
89 3 0.04
90 69 0.84
91 10 0.12
ACGTcount: A:0.53, C:0.07, G:0.09, T:0.31
Consensus pattern (90 bp):
AAATAATATATTTAAAAAATAATATACGAAAAAAATACGAAGAAAGTGTCAAAATCAAGGTTATT
TATTAAATAAATATAAAAAACACTT
Found at i:2813780 original size:12 final size:13
Alignment explanation
Indices: 2813765--2813800 Score: 56
Period size: 13 Copynumber: 2.8 Consensus size: 13
2813755 ATTTTTTGCT
2813765 AAAATAATATA-A
1 AAAATAATATACA
*
2813777 AAAATAAAATACA
1 AAAATAATATACA
2813790 AAAATAATATA
1 AAAATAATATA
2813801 TTTTAAAAAA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
12 10 0.48
13 11 0.52
ACGTcount: A:0.75, C:0.03, G:0.00, T:0.22
Consensus pattern (13 bp):
AAAATAATATACA
Found at i:2813823 original size:15 final size:14
Alignment explanation
Indices: 2813765--2813827 Score: 51
Period size: 17 Copynumber: 4.4 Consensus size: 14
2813755 ATTTTTTGCT
2813765 AAAATAATAT--AA
1 AAAATAATATACAA
*
2813777 AAAATAAAATAC-A
1 AAAATAATATACAA
*
2813790 AAAATAATATATTTTAA
1 AAAATAATATA---CAA
2813807 AAAATAATATACGAA
1 AAAATAATATAC-AA
2813822 AAAATA
1 AAAATA
2813828 CGAATAAAGT
Statistics
Matches: 40, Mismatches: 4, Indels: 11
0.73 0.07 0.20
Matches are distributed among these distances:
12 9 0.22
13 11 0.28
15 8 0.20
17 12 0.30
ACGTcount: A:0.70, C:0.03, G:0.02, T:0.25
Consensus pattern (14 bp):
AAAATAATATACAA
Found at i:2813913 original size:388 final size:392
Alignment explanation
Indices: 2813343--2814063 Score: 1123
Period size: 388 Copynumber: 1.8 Consensus size: 392
2813333 AATATTTAAA
*
2813343 TAATACATTTGAAACATTATGTACTAAAATAATATAAAGAAATAAAATACGAAAATAATATATTT
1 TAATACATTTGAAACATTATGTACTAAAATAATATAAAGAAATAAAATACAAAAATAATATATTT
2813408 TAAAAAATAATATACGAAAATAAAAAAATTACGAAGAAAGTACCAAAATCAGGGTTATTTAGTAA
66 TAAAAAATAATATACG-----AAAAAAATTACGAAGAAAGTACCAAAATCAGGGTTATTTAGTAA
** * ** * * * *
2813473 ATTAATATAAAGAAACACTTAAGTAATACATTTGAAATTTTTTTTGCTAAAATATTATAAA-AAA
126 AAAAATATAAAGAAACACTTAAATAATACATTTGAAACATTATGTACTAAAATAATATAAAGAAA
* *
2813537 TAAAATA-AGAAAATAATATATTTTAAAAAATAATATACGAAAAAAATACGAATAAAGTGCTAAA
191 TAAAATACA-AAAATAATATATTTTAAAAAA-AAGATACGAAAAAAA-ACAAATAAAGTGCTAAA
* *
2813601 ATCAGGGTTATTTATTGAAAAAATAT-AAAAAATACTTAAATAATACATTTGAAACATTATGTAC
253 ATCAGGGTTATTTATTAAAAAAATATAAAAAAACACTTAAATAATACATTTGAAACATTATGTAC
*
2813665 TTAAATAATATGAAGAAAGTGTCAAAATCAAGGTTATTTATTAAATTAGTATAAAAAACACTTAC
318 TAAAATAATATGAAGAAAGTGTCAAAATCAAGGTTATTTATTAAATTAGTATAAAAAACACTTAC
2813730 ATAATATACC
383 ATAATATACC
* * *
2813740 TAATACATTTGAAACATTTTTTGCTAAAATAATATAAA-AAATAAAATACAAAAATAATATATTT
1 TAATACATTTGAAACATTATGTACTAAAATAATATAAAGAAATAAAATACAAAAATAATATATTT
* * * *
2813804 TAAAAAATAATATACG-AAAAAA-TACGAATAAAGTGCTAAAATCAGGGTTATTTATTAAAAAAA
66 TAAAAAATAATATACGAAAAAAATTACGAAGAAAGTACCAAAATCAGGGTTATTTAGTAAAAAAA
2813867 TATAAA-AAACACTTAAATAATACATTTGAAACATTATGTACTAAAATAATATAAAGAAATAAAA
131 TATAAAGAAACACTTAAATAATACATTTGAAACATTATGTACTAAAATAATATAAAGAAATAAAA
2813931 TACAAAAATAATATATTTTAAAAAAAAGATACGAAAAAAAACAAATAAAGTGCTAAAATCAGGGT
196 TACAAAAATAATATATTTTAAAAAAAAGATACGAAAAAAAACAAATAAAGTGCTAAAATCAGGGT
2813996 TATTTATTAAAAAAATATAAAAAAACACTTAAATAATACATTTGAAACATTATGTACTAAAATAA
261 TATTTATTAAAAAAATATAAAAAAACACTTAAATAATACATTTGAAACATTATGTACTAAAATAA
2814061 TAT
326 TAT
2814064 AAAAAAATAA
Statistics
Matches: 299, Mismatches: 22, Indels: 15
0.89 0.07 0.04
Matches are distributed among these distances:
387 41 0.14
388 103 0.34
389 72 0.24
390 7 0.02
396 41 0.14
397 35 0.12
ACGTcount: A:0.55, C:0.07, G:0.08, T:0.30
Consensus pattern (392 bp):
TAATACATTTGAAACATTATGTACTAAAATAATATAAAGAAATAAAATACAAAAATAATATATTT
TAAAAAATAATATACGAAAAAAATTACGAAGAAAGTACCAAAATCAGGGTTATTTAGTAAAAAAA
TATAAAGAAACACTTAAATAATACATTTGAAACATTATGTACTAAAATAATATAAAGAAATAAAA
TACAAAAATAATATATTTTAAAAAAAAGATACGAAAAAAAACAAATAAAGTGCTAAAATCAGGGT
TATTTATTAAAAAAATATAAAAAAACACTTAAATAATACATTTGAAACATTATGTACTAAAATAA
TATGAAGAAAGTGTCAAAATCAAGGTTATTTATTAAATTAGTATAAAAAACACTTACATAATATA
CC
Found at i:2814041 original size:145 final size:145
Alignment explanation
Indices: 2813740--2814225 Score: 694
Period size: 145 Copynumber: 3.3 Consensus size: 145
2813730 ATAATATACC
* * *
2813740 TAATACATTTGAAACATTTTTTGCTAAAATAATATAAAAAATAAAATACAAAAATAATATATTTT
1 TAATACATTTGAAACATTATGTACTAAAATAATATAAAAAATAAAATACAAAAATAATATATTTT
* * *
2813805 AAAAAATAATATACGAAAAAATACGAATAAAGTGCTAAAATCAGGGTTATTTATTAAAAAAATAT
66 AAAAAATAAGATACGAAAAAAAACAAATAAAGTGCTAAAATCAGGGTTATTTATTAAAAAAATAT
2813870 -AAAAAACACTTAAA
131 AAAAAAACACTTAAA
2813884 TAATACATTTGAAACATTATGTACTAAAATAATATAAAGAAATAAAATACAAAAATAATATATTT
1 TAATACATTTGAAACATTATGTACTAAAATAATATAAA-AAATAAAATACAAAAATAATATATTT
2813949 TAAAAAA-AAGATACGAAAAAAAACAAATAAAGTGCTAAAATCAGGGTTATTTATTAAAAAAATA
65 TAAAAAATAAGATACGAAAAAAAACAAATAAAGTGCTAAAATCAGGGTTATTTATTAAAAAAATA
2814013 TAAAAAAACACTTAAA
130 TAAAAAAACACTTAAA
2814029 TAATACATTTGAAACATTATGTACTAAAATAATATAAAAAAATAAAATA-ATACGAAAGTAATAT
1 TAATACATTTGAAACATTATGTACTAAAATAATAT-AAAAAATAAAATACA-A--AAA-TAATAT
* * **
2814093 ATTTTAAAAAATATGATACGAAAATAAAAAATACGAAA-AAAGTGCCAAAATCAATGTTATTTAT
61 ATTTTAAAAAATAAGATACG---A-AAAAAA-AC-AAATAAAGTGCTAAAATCAGGGTTATTTAT
** *
2814157 TAAATTAATATAAAAAAACACTTACA
120 TAAAAAAATATAAAAAAACACTTAAA
* *
2814183 TAATACATTTGAAACATT-TTTGCTAAAATAATATAAAAAATAA
1 TAATACATTTGAAACATTATGTACTAAAATAATATAAAAAATAA
2814226 TATAGGAAAA
Statistics
Matches: 313, Mismatches: 15, Indels: 20
0.90 0.04 0.06
Matches are distributed among these distances:
144 91 0.29
145 93 0.30
146 3 0.01
147 3 0.01
148 17 0.05
149 7 0.02
152 10 0.03
153 20 0.06
154 66 0.21
155 3 0.01
ACGTcount: A:0.58, C:0.07, G:0.06, T:0.29
Consensus pattern (145 bp):
TAATACATTTGAAACATTATGTACTAAAATAATATAAAAAATAAAATACAAAAATAATATATTTT
AAAAAATAAGATACGAAAAAAAACAAATAAAGTGCTAAAATCAGGGTTATTTATTAAAAAAATAT
AAAAAAACACTTAAA
Found at i:2827723 original size:3 final size:3
Alignment explanation
Indices: 2827699--2827740 Score: 57
Period size: 3 Copynumber: 13.7 Consensus size: 3
2827689 AGAAGAACCA
* *
2827699 AAT AAA AAT AAA AAT AAAT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT -AAT AAT AAT AAT AAT AAT AAT AAT AA
2827741 AGAAATTAAC
Statistics
Matches: 34, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
3 31 0.91
4 3 0.09
ACGTcount: A:0.74, C:0.00, G:0.00, T:0.26
Consensus pattern (3 bp):
AAT
Found at i:2834580 original size:22 final size:22
Alignment explanation
Indices: 2834555--2834599 Score: 56
Period size: 22 Copynumber: 2.0 Consensus size: 22
2834545 TGTAAAATTG
2834555 AAATTC-GGTCATCTGTTAGTAT
1 AAATTCTGGT-ATCTGTTAGTAT
* *
2834577 AAATTCTGGTATTTGTTCGTAT
1 AAATTCTGGTATCTGTTAGTAT
2834599 A
1 A
2834600 TTTGAGACGC
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
22 17 0.85
23 3 0.15
ACGTcount: A:0.27, C:0.11, G:0.18, T:0.44
Consensus pattern (22 bp):
AAATTCTGGTATCTGTTAGTAT
Found at i:2839069 original size:86 final size:85
Alignment explanation
Indices: 2838962--2839133 Score: 326
Period size: 86 Copynumber: 2.0 Consensus size: 85
2838952 TTAAAAAAAA
2838962 AGTTAAAAGTGTATATTTTTAATACATTAAACTTGTGTTGAAATCAATAAAAAATTGTTAATTAA
1 AGTTAAAAGTGTATATTTTTAATACATTAAACTTGTGTTGAAATCAATAAAAAATTGTTAATTAA
*
2839027 TGATTAAGGGTGCAAATAGAC
66 TAATTAA-GGTGCAAATAGAC
2839048 AGTTAAAAGTGTATATTTTTAATACATTAAACTTGTGTTGAAATCAATAAAAAATTGTTAATTAA
1 AGTTAAAAGTGTATATTTTTAATACATTAAACTTGTGTTGAAATCAATAAAAAATTGTTAATTAA
2839113 TAATTAAGGTGCAAATAGAC
66 TAATTAAGGTGCAAATAGAC
2839133 A
1 A
2839134 TACTATCACT
Statistics
Matches: 85, Mismatches: 1, Indels: 1
0.98 0.01 0.01
Matches are distributed among these distances:
85 14 0.16
86 71 0.84
ACGTcount: A:0.44, C:0.06, G:0.14, T:0.36
Consensus pattern (85 bp):
AGTTAAAAGTGTATATTTTTAATACATTAAACTTGTGTTGAAATCAATAAAAAATTGTTAATTAA
TAATTAAGGTGCAAATAGAC
Found at i:2839280 original size:32 final size:33
Alignment explanation
Indices: 2839221--2839294 Score: 123
Period size: 32 Copynumber: 2.3 Consensus size: 33
2839211 ATGAGAATAT
*
2839221 TAGACTTTTGTAATGTATTTTTTTTCTTTAAAG
1 TAGACTTTTGTAACGTATTTTTTTTCTTTAAAG
*
2839254 TAGACTTTTTTAACGTA-TTTTTTTCTTTAAAG
1 TAGACTTTTGTAACGTATTTTTTTTCTTTAAAG
2839286 TAGACTTTT
1 TAGACTTTT
2839295 CCAACATTTT
Statistics
Matches: 39, Mismatches: 2, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
32 24 0.62
33 15 0.38
ACGTcount: A:0.24, C:0.08, G:0.11, T:0.57
Consensus pattern (33 bp):
TAGACTTTTGTAACGTATTTTTTTTCTTTAAAG
Found at i:2839294 original size:17 final size:17
Alignment explanation
Indices: 2839242--2839295 Score: 58
Period size: 17 Copynumber: 3.3 Consensus size: 17
2839232 AATGTATTTT
2839242 TTTTCTTTAAAGTAGAC
1 TTTTCTTTAAAGTAGAC
* ***
2839259 -TTT-TTTAACGTATTT
1 TTTTCTTTAAAGTAGAC
2839274 TTTTCTTTAAAGTAGAC
1 TTTTCTTTAAAGTAGAC
2839291 TTTTC
1 TTTTC
2839296 CAACATTTTG
Statistics
Matches: 27, Mismatches: 8, Indels: 4
0.69 0.21 0.10
Matches are distributed among these distances:
15 8 0.30
16 6 0.22
17 13 0.48
ACGTcount: A:0.24, C:0.11, G:0.09, T:0.56
Consensus pattern (17 bp):
TTTTCTTTAAAGTAGAC
Found at i:2844001 original size:15 final size:16
Alignment explanation
Indices: 2843970--2844002 Score: 50
Period size: 15 Copynumber: 2.1 Consensus size: 16
2843960 TATAAGACCA
2843970 TAAAATTAATAGAAAT
1 TAAAATTAATAGAAAT
*
2843986 TAAAATT-ATCGAAAT
1 TAAAATTAATAGAAAT
2844001 TA
1 TA
2844003 TTAAAGAAGT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
15 9 0.56
16 7 0.44
ACGTcount: A:0.58, C:0.03, G:0.06, T:0.33
Consensus pattern (16 bp):
TAAAATTAATAGAAAT
Found at i:2847209 original size:16 final size:17
Alignment explanation
Indices: 2847171--2847209 Score: 53
Period size: 17 Copynumber: 2.4 Consensus size: 17
2847161 GAATTTGATA
*
2847171 ACTTATATTTATTTGGT
1 ACTTAAATTTATTTGGT
*
2847188 ACTTAAATTTTTTTGG-
1 ACTTAAATTTATTTGGT
2847204 ACTTAA
1 ACTTAA
2847210 CTGGTACTTG
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
16 6 0.30
17 14 0.70
ACGTcount: A:0.28, C:0.08, G:0.10, T:0.54
Consensus pattern (17 bp):
ACTTAAATTTATTTGGT
Found at i:2866193 original size:13 final size:13
Alignment explanation
Indices: 2866175--2866201 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
2866165 TATAAATTTC
2866175 TTTGCATAATGAT
1 TTTGCATAATGAT
2866188 TTTGCATAATGAT
1 TTTGCATAATGAT
2866201 T
1 T
2866202 ACCCATAGTG
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:0.30, C:0.07, G:0.15, T:0.48
Consensus pattern (13 bp):
TTTGCATAATGAT
Found at i:2867337 original size:15 final size:17
Alignment explanation
Indices: 2867317--2867354 Score: 53
Period size: 15 Copynumber: 2.4 Consensus size: 17
2867307 ATTTTAAACC
*
2867317 TAAAATG-ATTTTAA-T
1 TAAAATGAATTTGAACT
2867332 TAAAATGAATTTGAACT
1 TAAAATGAATTTGAACT
2867349 TAAAAT
1 TAAAAT
2867355 AAACAGATGA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
15 7 0.35
16 6 0.30
17 7 0.35
ACGTcount: A:0.50, C:0.03, G:0.08, T:0.39
Consensus pattern (17 bp):
TAAAATGAATTTGAACT
Found at i:2869566 original size:17 final size:17
Alignment explanation
Indices: 2869544--2869577 Score: 52
Period size: 17 Copynumber: 2.0 Consensus size: 17
2869534 AGGGTCACAC
2869544 GGTCGTGTCGC-AGGCCA
1 GGTCGTGT-GCTAGGCCA
2869561 GGTCGTGTGCTAGGCCA
1 GGTCGTGTGCTAGGCCA
2869578 TATAACTCAT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 2 0.12
17 14 0.88
ACGTcount: A:0.12, C:0.26, G:0.41, T:0.21
Consensus pattern (17 bp):
GGTCGTGTGCTAGGCCA
Found at i:2871758 original size:24 final size:24
Alignment explanation
Indices: 2871731--2871780 Score: 100
Period size: 24 Copynumber: 2.1 Consensus size: 24
2871721 CTTTTAAACT
2871731 AATAGAACTCATGTAACTCCCCAA
1 AATAGAACTCATGTAACTCCCCAA
2871755 AATAGAACTCATGTAACTCCCCAA
1 AATAGAACTCATGTAACTCCCCAA
2871779 AA
1 AA
2871781 CTTTTATTTT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 26 1.00
ACGTcount: A:0.44, C:0.28, G:0.08, T:0.20
Consensus pattern (24 bp):
AATAGAACTCATGTAACTCCCCAA
Found at i:2873483 original size:35 final size:35
Alignment explanation
Indices: 2873403--2873484 Score: 87
Period size: 35 Copynumber: 2.3 Consensus size: 35
2873393 GCATATTTGT
* *
2873403 ATCTGTATCTGTATCTGAGATGGGCTAAATCCCAA
1 ATCTGTATCTGAATCTGAGATGGGCTAAAGCCCAA
* * *
2873438 ATCTGCATCTGAATCTGTA-ATGGGCTTAGGCCCAA
1 ATCTGTATCTGAATCTG-AGATGGGCTAAAGCCCAA
2873473 GA-CTGTATCTGA
1 -ATCTGTATCTGA
2873485 CTGATATCTG
Statistics
Matches: 39, Mismatches: 6, Indels: 4
0.80 0.12 0.08
Matches are distributed among these distances:
35 37 0.95
36 2 0.05
ACGTcount: A:0.27, C:0.21, G:0.22, T:0.30
Consensus pattern (35 bp):
ATCTGTATCTGAATCTGAGATGGGCTAAAGCCCAA
Found at i:2874736 original size:18 final size:18
Alignment explanation
Indices: 2874713--2874749 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
2874703 TGAGAATGAG
*
2874713 AGAAAGAACATGAGGGAA
1 AGAAAGAAAATGAGGGAA
*
2874731 AGAAAGAAAATGGGGGAA
1 AGAAAGAAAATGAGGGAA
2874749 A
1 A
2874750 ACGTGGAAAC
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.57, C:0.03, G:0.35, T:0.05
Consensus pattern (18 bp):
AGAAAGAAAATGAGGGAA
Found at i:2875350 original size:21 final size:19
Alignment explanation
Indices: 2875297--2875342 Score: 83
Period size: 19 Copynumber: 2.4 Consensus size: 19
2875287 TGTTATTGAT
2875297 AAATATAATATTTTTTTAG
1 AAATATAATATTTTTTTAG
*
2875316 AAATATAATATTTTTTTGG
1 AAATATAATATTTTTTTAG
2875335 AAATATAA
1 AAATATAA
2875343 AATATTTTAC
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
19 26 1.00
ACGTcount: A:0.46, C:0.00, G:0.07, T:0.48
Consensus pattern (19 bp):
AAATATAATATTTTTTTAG
Found at i:2877566 original size:19 final size:19
Alignment explanation
Indices: 2877542--2877603 Score: 106
Period size: 19 Copynumber: 3.2 Consensus size: 19
2877532 AATCTTTAAG
2877542 GATATGCAATCTTAGATAT
1 GATATGCAATCTTAGATAT
2877561 GATATGCAATCTTAGATAT
1 GATATGCAATCTTAGATAT
2877580 GATATGCAATCTTGAAGATAT
1 GATATGCAATCTT--AGATAT
2877601 GAT
1 GAT
2877604 CTTGTAATCT
Statistics
Matches: 41, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
19 32 0.78
21 9 0.22
ACGTcount: A:0.37, C:0.10, G:0.18, T:0.35
Consensus pattern (19 bp):
GATATGCAATCTTAGATAT
Found at i:2897183 original size:21 final size:20
Alignment explanation
Indices: 2897128--2897187 Score: 61
Period size: 21 Copynumber: 3.0 Consensus size: 20
2897118 GTTATGATTT
* *
2897128 TTTTATGTTTTGTT-ATTGGG
1 TTTT-TGTTTTTTTAATTCGG
*
2897148 TTTTT-TTTATTTAATTCGG
1 TTTTTGTTTTTTTAATTCGG
2897167 TTTTGTGTTTTTTTAATTCGG
1 TTTT-TGTTTTTTTAATTCGG
2897188 ATAGACAGAA
Statistics
Matches: 33, Mismatches: 4, Indels: 5
0.79 0.10 0.12
Matches are distributed among these distances:
18 5 0.15
19 10 0.30
20 5 0.15
21 13 0.39
ACGTcount: A:0.12, C:0.03, G:0.18, T:0.67
Consensus pattern (20 bp):
TTTTTGTTTTTTTAATTCGG
Found at i:2898156 original size:18 final size:18
Alignment explanation
Indices: 2898133--2898169 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
2898123 TGAGAATGAG
*
2898133 AGAAAGAACATGAGGGAA
1 AGAAAGAAAATGAGGGAA
*
2898151 AGAAAGAAAATGGGGGAA
1 AGAAAGAAAATGAGGGAA
2898169 A
1 A
2898170 ACGTGGAAAC
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.57, C:0.03, G:0.35, T:0.05
Consensus pattern (18 bp):
AGAAAGAAAATGAGGGAA
Found at i:2898745 original size:18 final size:19
Alignment explanation
Indices: 2898711--2898755 Score: 74
Period size: 18 Copynumber: 2.4 Consensus size: 19
2898701 TGTTATTGAT
2898711 AAATATAATATTTTTTTAG
1 AAATATAATATTTTTTTAG
*
2898730 AAATATAATA-TTTTTTGG
1 AAATATAATATTTTTTTAG
2898748 AAATATAA
1 AAATATAA
2898756 AATATTTTAC
Statistics
Matches: 25, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
18 15 0.60
19 10 0.40
ACGTcount: A:0.47, C:0.00, G:0.07, T:0.47
Consensus pattern (19 bp):
AAATATAATATTTTTTTAG
Found at i:2898763 original size:18 final size:18
Alignment explanation
Indices: 2898724--2898764 Score: 55
Period size: 18 Copynumber: 2.3 Consensus size: 18
2898714 TATAATATTT
* *
2898724 TTTTAGAAATATAATATT
1 TTTTAGAAATATAAAATA
*
2898742 TTTTGGAAATATAAAATA
1 TTTTAGAAATATAAAATA
2898760 TTTTA
1 TTTTA
2898765 CTATTAAATT
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.44, C:0.00, G:0.07, T:0.49
Consensus pattern (18 bp):
TTTTAGAAATATAAAATA
Found at i:2900026 original size:24 final size:23
Alignment explanation
Indices: 2899947--2900017 Score: 67
Period size: 22 Copynumber: 3.2 Consensus size: 23
2899937 ATTTAAAAAT
* *
2899947 ATTTGTATTAAATATATAAAAT-
1 ATTTATATTAAATATATAATATA
* ** *
2899969 ATCTATA-TAGTTGTATAATATA
1 ATTTATATTAAATATATAATATA
2899991 ATTTATATTAAATATATAA-ATA
1 ATTTATATTAAATATATAATATA
2900013 ATTTA
1 ATTTA
2900018 CTCCTTAAAA
Statistics
Matches: 37, Mismatches: 10, Indels: 4
0.73 0.20 0.08
Matches are distributed among these distances:
21 10 0.27
22 19 0.51
23 8 0.22
ACGTcount: A:0.48, C:0.01, G:0.04, T:0.46
Consensus pattern (23 bp):
ATTTATATTAAATATATAATATA
Found at i:2900953 original size:19 final size:19
Alignment explanation
Indices: 2900929--2900990 Score: 106
Period size: 19 Copynumber: 3.2 Consensus size: 19
2900919 AATCTTTAAG
2900929 GATATGCAATCTTAGATAT
1 GATATGCAATCTTAGATAT
2900948 GATATGCAATCTTAGATAT
1 GATATGCAATCTTAGATAT
2900967 GATATGCAATCTTGAAGATAT
1 GATATGCAATCTT--AGATAT
2900988 GAT
1 GAT
2900991 CTTGTAATCT
Statistics
Matches: 41, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
19 32 0.78
21 9 0.22
ACGTcount: A:0.37, C:0.10, G:0.18, T:0.35
Consensus pattern (19 bp):
GATATGCAATCTTAGATAT
Done.