Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: D12
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: 63843421
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.32
Warning! 1690000 characters in sequence are not A, C, G, or T
File 132 of 214
Found at i:40129224 original size:15 final size:12
Alignment explanation
Indices: 40129133--40129227 Score: 54
Period size: 12 Copynumber: 7.9 Consensus size: 12
40129123 AGAAACATTT
40129133 TAATAA-AAAGAA
1 TAATAATAAA-AA
40129145 TAATAATAAAAA
1 TAATAATAAAAA
* *
40129157 TAATAACAATAA
1 TAATAATAAAAA
*
40129169 TAA-AAT-AGAA
1 TAATAATAAAAA
** *
40129179 -AATAACGAGAA
1 TAATAATAAAAA
**
40129190 TGCTAATAAAAA
1 TAATAATAAAAA
40129202 TAATAATAATAAA
1 TAATAATAA-AAA
40129215 TAAATAAATAAAA
1 T-AAT-AATAAAA
40129228 TAAACAATGA
Statistics
Matches: 64, Mismatches: 12, Indels: 12
0.73 0.14 0.14
Matches are distributed among these distances:
9 2 0.03
10 5 0.08
11 6 0.09
12 34 0.53
13 7 0.11
14 5 0.08
15 5 0.08
ACGTcount: A:0.69, C:0.03, G:0.05, T:0.22
Consensus pattern (12 bp):
TAATAATAAAAA
Found at i:40134788 original size:15 final size:16
Alignment explanation
Indices: 40134764--40134797 Score: 52
Period size: 15 Copynumber: 2.2 Consensus size: 16
40134754 CACCGTTTTA
40134764 TATTTAATATT-AAAT
1 TATTTAATATTAAAAT
*
40134779 TATTTTATATTAAAAT
1 TATTTAATATTAAAAT
40134795 TAT
1 TAT
40134798 ATAAGTAAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
15 10 0.59
16 7 0.41
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (16 bp):
TATTTAATATTAAAAT
Found at i:40135942 original size:28 final size:28
Alignment explanation
Indices: 40135906--40135963 Score: 66
Period size: 28 Copynumber: 2.1 Consensus size: 28
40135896 TAAGGATTAA
*
40135906 TTTTAATTT-T-TAAATATTATTTAATATT
1 TTTTAATTTATGTAAAT-TTAATT-ATATT
*
40135934 TTTTCATTTATGTAAATTTAATTATATT
1 TTTTAATTTATGTAAATTTAATTATATT
40135962 TT
1 TT
40135964 ATTTTATAAT
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
28 15 0.58
29 6 0.23
30 5 0.19
ACGTcount: A:0.33, C:0.02, G:0.02, T:0.64
Consensus pattern (28 bp):
TTTTAATTTATGTAAATTTAATTATATT
Found at i:40137512 original size:18 final size:18
Alignment explanation
Indices: 40137489--40137532 Score: 70
Period size: 18 Copynumber: 2.4 Consensus size: 18
40137479 TGCCAGGTGC
*
40137489 GTATCCTTGCCCTTATAT
1 GTATCCTTACCCTTATAT
*
40137507 GTATCCTAACCCTTATAT
1 GTATCCTTACCCTTATAT
40137525 GTATCCTT
1 GTATCCTT
40137533 TTCCCAGTCC
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 23 1.00
ACGTcount: A:0.20, C:0.27, G:0.09, T:0.43
Consensus pattern (18 bp):
GTATCCTTACCCTTATAT
Found at i:40138031 original size:93 final size:93
Alignment explanation
Indices: 40137895--40138089 Score: 327
Period size: 93 Copynumber: 2.1 Consensus size: 93
40137885 ACATTGATAT
* * * *
40137895 TTTTTAATATGTTTGTACAAAATGTTTTTATATTGTTTAATTTAATAAAATAAAAGTTGTTTTTA
1 TTTTTAATATATTTGTACAAAATATTTTTATATTATTTAATTTAATAAAATAAAAGTTCTTTTTA
*
40137960 ATATTTTAATAGTAATTTATTTTTTATA
66 ATATTTTAATAGTAATTTATATTTTATA
* *
40137988 TTTTTAATATATTTGTACAAACTATTTTTATATTATTTCATTTAATAAAATAAAAGTTCTTTTTA
1 TTTTTAATATATTTGTACAAAATATTTTTATATTATTTAATTTAATAAAATAAAAGTTCTTTTTA
40138053 ATATTTTAATAGTAATTTATATTTTATA
66 ATATTTTAATAGTAATTTATATTTTATA
40138081 TTTTTAATA
1 TTTTTAATA
40138090 AAATAGGAGT
Statistics
Matches: 95, Mismatches: 7, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
93 95 1.00
ACGTcount: A:0.36, C:0.03, G:0.05, T:0.56
Consensus pattern (93 bp):
TTTTTAATATATTTGTACAAAATATTTTTATATTATTTAATTTAATAAAATAAAAGTTCTTTTTA
ATATTTTAATAGTAATTTATATTTTATA
Found at i:40138092 original size:55 final size:55
Alignment explanation
Indices: 40138028--40138149 Score: 149
Period size: 55 Copynumber: 2.2 Consensus size: 55
40138018 TATTATTTCA
****
40138028 TTTAATAAAATAAAAGTTCTTTTTAATATTTTAATAGTAATTT-ATA-TTTTATATT
1 TTTAATAAAATAAAAGTTCTTTTTAATAAGACAATA-T-ATTTAATATTTTTATATT
** *
40138083 TTTAATAAAATAGGAGTTCTTTTTAATAAGACAATATTTTTAATATTTTTATATT
1 TTTAATAAAATAAAAGTTCTTTTTAATAAGACAATATATTTAATATTTTTATATT
40138138 TTTAATAAAATA
1 TTTAATAAAATA
40138150 GAAATAATGC
Statistics
Matches: 58, Mismatches: 7, Indels: 4
0.84 0.10 0.06
Matches are distributed among these distances:
53 3 0.05
54 4 0.07
55 51 0.88
ACGTcount: A:0.41, C:0.02, G:0.05, T:0.52
Consensus pattern (55 bp):
TTTAATAAAATAAAAGTTCTTTTTAATAAGACAATATATTTAATATTTTTATATT
Found at i:40138131 original size:8 final size:9
Alignment explanation
Indices: 40138115--40138144 Score: 53
Period size: 9 Copynumber: 3.4 Consensus size: 9
40138105 TTAATAAGAC
40138115 AATATTTTT
1 AATATTTTT
40138124 AATATTTTT
1 AATATTTTT
40138133 -ATATTTTT
1 AATATTTTT
40138141 AATA
1 AATA
40138145 AAATAGAAAT
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
8 8 0.40
9 12 0.60
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (9 bp):
AATATTTTT
Found at i:40144313 original size:15 final size:15
Alignment explanation
Indices: 40144293--40144337 Score: 54
Period size: 15 Copynumber: 3.0 Consensus size: 15
40144283 TGAAAGAAGG
40144293 GAAGAAAATAAAATA
1 GAAGAAAATAAAATA
* *
40144308 GAAGAAAATGAAAGA
1 GAAGAAAATAAAATA
* *
40144323 AAATAAAATAAAATA
1 GAAGAAAATAAAATA
40144338 TAAACATGTC
Statistics
Matches: 24, Mismatches: 6, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
15 24 1.00
ACGTcount: A:0.73, C:0.00, G:0.13, T:0.13
Consensus pattern (15 bp):
GAAGAAAATAAAATA
Found at i:40152317 original size:14 final size:15
Alignment explanation
Indices: 40152298--40152329 Score: 57
Period size: 14 Copynumber: 2.2 Consensus size: 15
40152288 TACTAAACTT
40152298 AATAAATGTTTTA-A
1 AATAAATGTTTTACA
40152312 AATAAATGTTTTACA
1 AATAAATGTTTTACA
40152327 AAT
1 AAT
40152330 TTTCGATAAT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 13 0.76
15 4 0.24
ACGTcount: A:0.50, C:0.03, G:0.06, T:0.41
Consensus pattern (15 bp):
AATAAATGTTTTACA
Found at i:40152631 original size:18 final size:17
Alignment explanation
Indices: 40152604--40152637 Score: 59
Period size: 18 Copynumber: 1.9 Consensus size: 17
40152594 ACCAAAAGAT
40152604 ATTTTAATTTTATATTA
1 ATTTTAATTTTATATTA
40152621 ATTTATAATTTTATATT
1 ATTT-TAATTTTATATT
40152638 TTATTTTATT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 4 0.25
18 12 0.75
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (17 bp):
ATTTTAATTTTATATTA
Found at i:40152657 original size:25 final size:24
Alignment explanation
Indices: 40152602--40152660 Score: 68
Period size: 25 Copynumber: 2.4 Consensus size: 24
40152592 TCACCAAAAG
40152602 ATATTTTA-ATTTTATATTAATTT
1 ATATTTTATATTTTATATTAATTT
*
40152625 ATAATTTTATATTTTATTTTATTATTT
1 AT-ATTTTATATTTTATATTA--ATTT
40152652 AT-TTTTATA
1 ATATTTTATA
40152661 ATGATTTTTT
Statistics
Matches: 31, Mismatches: 1, Indels: 6
0.82 0.03 0.16
Matches are distributed among these distances:
23 2 0.06
24 6 0.19
25 17 0.55
27 6 0.19
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (24 bp):
ATATTTTATATTTTATATTAATTT
Found at i:40152919 original size:24 final size:23
Alignment explanation
Indices: 40152868--40152920 Score: 61
Period size: 24 Copynumber: 2.3 Consensus size: 23
40152858 TTAATTTGAT
*
40152868 ATATATTTAAATTACAAACGCAA
1 ATATAATTAAATTACAAACGCAA
* * *
40152891 TTATAATTACAATTACAAAGGTAA
1 ATATAATTA-AATTACAAACGCAA
40152915 ATATAA
1 ATATAA
40152921 AAAATGCATA
Statistics
Matches: 24, Mismatches: 5, Indels: 1
0.80 0.17 0.03
Matches are distributed among these distances:
23 7 0.29
24 17 0.71
ACGTcount: A:0.53, C:0.09, G:0.06, T:0.32
Consensus pattern (23 bp):
ATATAATTAAATTACAAACGCAA
Found at i:40153021 original size:16 final size:18
Alignment explanation
Indices: 40153000--40153038 Score: 55
Period size: 16 Copynumber: 2.3 Consensus size: 18
40152990 AATTATCTTG
*
40153000 ATTTAAAC-TAAAA-TAA
1 ATTTAAACGAAAAATTAA
40153016 ATTTAAACGAAAAATTAA
1 ATTTAAACGAAAAATTAA
40153034 ATTTA
1 ATTTA
40153039 TTATTATACG
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
16 8 0.40
17 4 0.20
18 8 0.40
ACGTcount: A:0.59, C:0.05, G:0.03, T:0.33
Consensus pattern (18 bp):
ATTTAAACGAAAAATTAA
Found at i:40159262 original size:31 final size:29
Alignment explanation
Indices: 40159227--40159296 Score: 86
Period size: 29 Copynumber: 2.3 Consensus size: 29
40159217 ATATCAAAAT
40159227 TATACATGAACTATGAATTAATGTGCAATTG
1 TATACATGAACT-TGAATT-ATGTGCAATTG
* * * *
40159258 TATACATAAACTTTAATTTTGTGCAATTT
1 TATACATGAACTTGAATTATGTGCAATTG
40159287 TATACATGAA
1 TATACATGAA
40159297 ATTTTGATTT
Statistics
Matches: 34, Mismatches: 5, Indels: 2
0.83 0.12 0.05
Matches are distributed among these distances:
29 18 0.53
30 5 0.15
31 11 0.32
ACGTcount: A:0.39, C:0.10, G:0.11, T:0.40
Consensus pattern (29 bp):
TATACATGAACTTGAATTATGTGCAATTG
Found at i:40159512 original size:31 final size:31
Alignment explanation
Indices: 40159449--40159560 Score: 106
Period size: 31 Copynumber: 3.7 Consensus size: 31
40159439 TGACTAAATT
* * * *
40159449 AAAATTAAAGTTTCAAGTATACATTTGAACC
1 AAAATTAAAGTTTCATGTATATAATTGCACC
* *
40159480 AAAATTAGAGTTTCATGTGTATAATTGCACC
1 AAAATTAAAGTTTCATGTATATAATTGCACC
*
40159511 -AAATTACAG-TTCATGTATATAATTGCA-C
1 AAAATTAAAGTTTCATGTATATAATTGCACC
*
40159539 ATTAAATCAAAGTTT-ATGTATA
1 A--AAATTAAAGTTTCATGTATA
40159561 ATTTTGAGAT
Statistics
Matches: 67, Mismatches: 10, Indels: 8
0.79 0.12 0.09
Matches are distributed among these distances:
28 1 0.01
29 17 0.25
30 8 0.12
31 39 0.58
32 2 0.03
ACGTcount: A:0.41, C:0.12, G:0.12, T:0.36
Consensus pattern (31 bp):
AAAATTAAAGTTTCATGTATATAATTGCACC
Found at i:40163431 original size:51 final size:50
Alignment explanation
Indices: 40163369--40163469 Score: 139
Period size: 51 Copynumber: 2.0 Consensus size: 50
40163359 GAGATAAGAC
* ** **
40163369 TTGTAGCTTTAATCTGTTCTACTGTAACTTCAGGGAGATAAGATTTGTAGT
1 TTGTAGCTTTAATCTGCTCTACTACAACTTCAAAGAGATAAGA-TTGTAGT
*
40163420 TTGTAGTTTTAATCTGCTCTACTACAACTTCAAAGAGATAAGATTGTAGT
1 TTGTAGCTTTAATCTGCTCTACTACAACTTCAAAGAGATAAGATTGTAGT
40163470 CTTAATTTGC
Statistics
Matches: 44, Mismatches: 6, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
50 7 0.16
51 37 0.84
ACGTcount: A:0.29, C:0.13, G:0.19, T:0.40
Consensus pattern (50 bp):
TTGTAGCTTTAATCTGCTCTACTACAACTTCAAAGAGATAAGATTGTAGT
Found at i:40163724 original size:45 final size:44
Alignment explanation
Indices: 40163324--40163951 Score: 367
Period size: 44 Copynumber: 14.1 Consensus size: 44
40163314 AGGTATAGGA
* * *
40163324 ATTT-TAGTTTCAATCTACTCCACTACAAC-TCTAGAGAGATAAG
1 ATTTGTAGCTTCAATCTACTCCACTGCAACTTC-AGGGAGATAAG
* * ** * *
40163367 ACTTGTAGCTTTAATCTGTTCTACTGTAACTTCAGGGAGATAAGATTTG
1 ATTTGTAGCTTCAATCTACTCCACTGCAACTTCAGGGAGAT-A-A---G
* * * * * **
40163416 TAGTTTGTAGTTTTAATCTGCTCTACTACAACTTCAAAGAGATAAG
1 -A-TTTGTAGCTTCAATCTACTCCACTGCAACTTCAGGGAGATAAG
* * * * * * * * *
40163462 A-TTGTAGTCTT-AATTTGCCCCTCTGTAATTTTAAGGAAATAAG
1 ATTTGTAG-CTTCAATCTACTCCACTGCAACTTCAGGGAGATAAG
* * * * * * * **
40163505 ACTAGTAGCTTTAATTTGCTCTACTGCAACTTTAAAGAGATAAG
1 ATTTGTAGCTTCAATCTACTCCACTGCAACTTCAGGGAGATAAG
* * * * *** *
40163549 ATTTGTGGCATT-AATTTGCTCCACTGCAATTTCAATAAAATAAG
1 ATTTGTAGC-TTCAATCTACTCCACTGCAACTTCAGGGAGATAAG
* * * ** * *
40163593 ACTTGTAGCTTTAATTTTTTCCACTGTAACTTTAGGGAGATAAG
1 ATTTGTAGCTTCAATCTACTCCACTGCAACTTCAGGGAGATAAG
*
40163637 ATTTGTAGCTTCAATCTACT-CATCTACAAC-TCTAGGGAGATAAG
1 ATTTGTAGCTTCAATCTACTCCA-CTGCAACTTC-AGGGAGATAAG
* * *
40163681 ATTTGCTATCTTTAATCTACTCCACTGCAACTTCAGGGGGATAAG
1 ATTTG-TAGCTTCAATCTACTCCACTGCAACTTCAGGGAGATAAG
* * * * *
40163726 GTTTACTATCTTCAATCTGCTCCACT-CTAACTTCAGGGAAATAAG
1 ATTT-GTAGCTTCAATCTACTCCACTGC-AACTTCAGGGAGATAAG
* * * * *
40163771 ATTTGTAGCTTCAATCTAATCCATTACAACTTCAGGGAAATACG
1 ATTTGTAGCTTCAATCTACTCCACTGCAACTTCAGGGAGATAAG
* * * *
40163815 ATTTGTAGCTCCAATATTCTCCACTGCAACTTCAGGGAGATAAC
1 ATTTGTAGCTTCAATCTACTCCACTGCAACTTCAGGGAGATAAG
* * * * *
40163859 ATTTGTAGCTTTAATTCGA-TCCACTGTAACTTCAGGGATATGAG
1 ATTTGTAGCTTCAA-TCTACTCCACTGCAACTTCAGGGAGATAAG
* *
40163903 ATTTGTAGCTTC-ATCTTGCTCCACTGCATCTTCAGGGAGATAAG
1 ATTTGTAGCTTCAATC-TACTCCACTGCAACTTCAGGGAGATAAG
40163947 ATTTG
1 ATTTG
40163952 CTATATTCAA
Statistics
Matches: 455, Mismatches: 105, Indels: 49
0.75 0.17 0.08
Matches are distributed among these distances:
42 2 0.00
43 41 0.09
44 293 0.64
45 76 0.17
46 6 0.01
49 2 0.00
50 2 0.00
51 33 0.07
ACGTcount: A:0.30, C:0.18, G:0.16, T:0.35
Consensus pattern (44 bp):
ATTTGTAGCTTCAATCTACTCCACTGCAACTTCAGGGAGATAAG
Found at i:40167160 original size:10 final size:10
Alignment explanation
Indices: 40167147--40167181 Score: 52
Period size: 10 Copynumber: 3.5 Consensus size: 10
40167137 AGCTCAAATA
40167147 AGCTCGTTTG
1 AGCTCGTTTG
*
40167157 AGCTCGTTTC
1 AGCTCGTTTG
*
40167167 AGCTAGTTTG
1 AGCTCGTTTG
40167177 AGCTC
1 AGCTC
40167182 ATTTTAATTT
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
10 21 1.00
ACGTcount: A:0.14, C:0.23, G:0.26, T:0.37
Consensus pattern (10 bp):
AGCTCGTTTG
Found at i:40173447 original size:19 final size:20
Alignment explanation
Indices: 40173425--40173476 Score: 65
Period size: 19 Copynumber: 2.7 Consensus size: 20
40173415 GGGTCTTTTT
*
40173425 ATGAAATTTAATGCAT-ATG-
1 ATGAAATGTAATGC-TGATGA
40173444 ATGAAATGTAATGCTGATGA
1 ATGAAATGTAATGCTGATGA
40173464 ATGAAATG-AATGC
1 ATGAAATGTAATGC
40173477 AAAAAGAGGC
Statistics
Matches: 30, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
18 1 0.03
19 21 0.70
20 8 0.27
ACGTcount: A:0.42, C:0.06, G:0.21, T:0.31
Consensus pattern (20 bp):
ATGAAATGTAATGCTGATGA
Found at i:40180915 original size:21 final size:21
Alignment explanation
Indices: 40180882--40180922 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
40180872 AGAAAATTAA
** *
40180882 AATGTAATTTTTTATTATTTT
1 AATGTAAAATTTTATAATTTT
40180903 AATGTAAAATTTTATAATTT
1 AATGTAAAATTTTATAATTT
40180923 CTCGAGAGAT
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.37, C:0.00, G:0.05, T:0.59
Consensus pattern (21 bp):
AATGTAAAATTTTATAATTTT
Found at i:40183413 original size:21 final size:20
Alignment explanation
Indices: 40183380--40183422 Score: 50
Period size: 21 Copynumber: 2.1 Consensus size: 20
40183370 TAAAATACCC
*
40183380 TTTTTTAACATTTTAACTAT
1 TTTTTTAACATTTCAACTAT
* *
40183400 TTTTTTATATATTTCAATTAT
1 TTTTTTA-ACATTTCAACTAT
40183421 TT
1 TT
40183423 ATAATTAAAA
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
20 7 0.37
21 12 0.63
ACGTcount: A:0.28, C:0.07, G:0.00, T:0.65
Consensus pattern (20 bp):
TTTTTTAACATTTCAACTAT
Found at i:40186211 original size:31 final size:31
Alignment explanation
Indices: 40186173--40186232 Score: 93
Period size: 31 Copynumber: 1.9 Consensus size: 31
40186163 AAACGGTCAC
* *
40186173 TAAACTATTCGAAAGTTTTCATTTAAGTCGT
1 TAAACTATTCAAAAGTTTTCATCTAAGTCGT
*
40186204 TAAACTATTCAAAAGTTTTTATCTAAGTC
1 TAAACTATTCAAAAGTTTTCATCTAAGTC
40186233 ATTGGAATGT
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
31 26 1.00
ACGTcount: A:0.35, C:0.13, G:0.10, T:0.42
Consensus pattern (31 bp):
TAAACTATTCAAAAGTTTTCATCTAAGTCGT
Found at i:40195478 original size:2 final size:2
Alignment explanation
Indices: 40195473--40195497 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
40195463 ATACACACAT
40195473 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 T
40195498 CATGCAGTTA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:40198401 original size:11 final size:11
Alignment explanation
Indices: 40198385--40198409 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
40198375 GGTGATCCTT
40198385 TTTTATTTTTC
1 TTTTATTTTTC
40198396 TTTTATTTTTC
1 TTTTATTTTTC
40198407 TTT
1 TTT
40198410 GAATCTATTA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.08, C:0.08, G:0.00, T:0.84
Consensus pattern (11 bp):
TTTTATTTTTC
Found at i:40199278 original size:7 final size:7
Alignment explanation
Indices: 40199255--40199288 Score: 52
Period size: 7 Copynumber: 4.9 Consensus size: 7
40199245 TCATCGAGCA
40199255 TTTATTT
1 TTTATTT
40199262 ATTT-TTT
1 -TTTATTT
40199269 TTTATTT
1 TTTATTT
40199276 TTTATTT
1 TTTATTT
40199283 TTTATT
1 TTTATT
40199289 ATTATCTGTA
Statistics
Matches: 25, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
6 3 0.12
7 19 0.76
8 3 0.12
ACGTcount: A:0.15, C:0.00, G:0.00, T:0.85
Consensus pattern (7 bp):
TTTATTT
Found at i:40204685 original size:49 final size:49
Alignment explanation
Indices: 40204631--40204767 Score: 211
Period size: 49 Copynumber: 2.8 Consensus size: 49
40204621 TATTTTCTCG
* *
40204631 ATGCCATAGTCCAACTATGGTCTTACATGTAATCACATAACATATACAA
1 ATGCCATAGCCCAACTATGGTCTTACACGTAATCACATAACATATACAA
* * *
40204680 ATGCCATAGCCCATCTATGGTCTTACACGTAATCACAAAACATATACCA
1 ATGCCATAGCCCAACTATGGTCTTACACGTAATCACATAACATATACAA
* *
40204729 ATGCCATAGCCCAGCTATGGTCTTACACGGAATCACATA
1 ATGCCATAGCCCAACTATGGTCTTACACGTAATCACATA
40204768 TAACTTATTG
Statistics
Matches: 80, Mismatches: 8, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
49 80 1.00
ACGTcount: A:0.36, C:0.26, G:0.12, T:0.26
Consensus pattern (49 bp):
ATGCCATAGCCCAACTATGGTCTTACACGTAATCACATAACATATACAA
Found at i:40211555 original size:44 final size:44
Alignment explanation
Indices: 40211492--40212250 Score: 531
Period size: 44 Copynumber: 16.7 Consensus size: 44
40211482 TCGTCGTGGA
* * *
40211492 AAATCTTATCTCCCTAAAGTTGCAATGGAGCAGATTAAAGCCAC
1 AAATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAGCTAC
* * *
40211536 AAATCTTATCTCCCTAAAGTTGCAATGGAGCAGATTAAAGCCAC
1 AAATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAGCTAC
* * * *
40211580 AAATCTTATCTTCCTGAAGTTACAGTGGAGCAAATTGAAA-ATAGC
1 AAATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATT-AAAGCTA-C
* * * * *
40211625 AAATCCTAT-TACCCTAAAGTTGTAGTGGAACAAATTAAAGCTACAAGTTAC
1 AAATCTTATCT-CCCTGAAGTTGCAGTGGAGCAGATTAAAG---C----TAC
* * * * * *
40211676 AAATCTTATCTCTCTGACGTTGCAGTAGAGTAGATTGAAGTTAC
1 AAATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAGCTAC
* * *
40211720 AAATCTTATCTCCTTGAAGTTGCAGTGAAGCAGATTAAAGCCAC
1 AAATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAGCTAC
* * * *
40211764 AAATCTTATCTCCCTGAAGTTGCAGTTGAGCAGAATGAAGATAGC
1 AAATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAGCTA-C
* ** * **
40211809 AAATCGTATCTTTCTGAAGTTGCAATAAAGCAGATTAAAG-TCAC
1 AAATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAGCT-AC
* * ** *
40211853 AAATCTTATCTCCCTGAAGTTACAGTGGAGCAGATTGAATATAGT
1 AAATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAGCTA-C
* * * * * *
40211898 GAATCGTATCTCACTGAAGTTGTAGTAGAGCAGATTGAAGCTAC
1 AAATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAGCTAC
*
40211942 AAATCTTATCTCCCT-AGAGTTGCAGTGGAGCAGATTAAAGATA-
1 AAATCTTATCTCCCTGA-AGTTGCAGTGGAGCAGATTAAAGCTAC
* * * *
40211985 ATGAATCTTATCTCCTTGAAGTTGCAGTGGATCAGATTGAAGATAGC
1 A--AATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAGCTA-C
* * * * *
40212032 AAACCTTATCTCTCTAAAGTTGCAGTGGAACAAATTAAAGCTAC
1 AAATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAGCTAC
* * * * * *
40212076 AAGATAGAAATCTTAACTCTCTGAAGTTGCAGTGGAACAAATTGAAGATAC
1 -------AAATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAGCTAC
* * * * *
40212127 GAATCTTATTTCCCTAAAGTTGCAGTGGAACAGATTAAGGCTACAAGTTAC
1 AAATCTTATCTCCCTGAAGTTGCAGTGGAGCAGA-T-----TA-AAGCTAC
* * * * *
40212178 AAATCTTATCTCTCTAAAGTTGCAGTGAAGCATATTGAAA-ATAC
1 AAATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATT-AAAGCTAC
* *
40212222 AAATCTTATTTCCCAGAAGTTGCAGTGGA
1 AAATCTTATCTCCCTGAAGTTGCAGTGGA
40212251 ACGGATCTTA
Statistics
Matches: 567, Mismatches: 111, Indels: 74
0.75 0.15 0.10
Matches are distributed among these distances:
43 2 0.00
44 278 0.49
45 177 0.31
46 2 0.00
47 1 0.00
50 2 0.00
51 102 0.18
52 3 0.01
ACGTcount: A:0.35, C:0.17, G:0.19, T:0.29
Consensus pattern (44 bp):
AAATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAGCTAC
Found at i:40211663 original size:89 final size:88
Alignment explanation
Indices: 40211492--40212155 Score: 467
Period size: 89 Copynumber: 7.3 Consensus size: 88
40211482 TCGTCGTGGA
* * * * ** * *
40211492 AAATCTTATCTCCCTAAAGTTGCAATGGAGCAGATTAAAGCCA-CAAATCTTATCTCCCTAAAGT
1 AAATCTTATCTCCCTGAAGTTGCAGTGGAGCAAATTGAAGATAGCAAATCGTATCTCCCTGAAGT
* *
40211556 TGCAATGGAGCAGATTAAAGCCAC
66 TGCAGT-GAACAGATTAAAGCCAC
* * * * *
40211580 AAATCTTATCTTCCTGAAGTTACAGTGGAGCAAATTGAAAATAGCAAATCCTAT-TACCCTAAAG
1 AAATCTTATCTCCCTGAAGTTGCAGTGGAGCAAATTGAAGATAGCAAATCGTATCT-CCCTGAAG
* *
40211644 TTGTAGTGGAACAAATTAAAGCTACAAGTTAC
65 TTGCAGT-GAACAGATTAAAGC--C-----AC
* * * * * * * *
40211676 AAATCTTATCTCTCTGACGTTGCAGTAGAGTAGATTGAAGTTA-CAAATCTTATCTCCTTGAAGT
1 AAATCTTATCTCCCTGAAGTTGCAGTGGAGCAAATTGAAGATAGCAAATCGTATCTCCCTGAAGT
40211740 TGCAGTGAAGCAGATTAAAGCCAC
66 TGCAGTGAA-CAGATTAAAGCCAC
* **
40211764 AAATCTTATCTCCCTGAAGTTGCAGTTGAGCAGAA-TGAAGATAGCAAATCGTATCTTTCTGAAG
1 AAATCTTATCTCCCTGAAGTTGCAGTGGAGCA-AATTGAAGATAGCAAATCGTATCTCCCTGAAG
* * *
40211828 TTGCAATAAAGCAGATTAAAGTCAC
65 TTGCAGTGAA-CAGATTAAAGCCAC
* * * ** *
40211853 AAATCTTATCTCCCTGAAGTTACAGTGGAGCAGATTGAATATAGTGAATCGTATCTCACTGAAGT
1 AAATCTTATCTCCCTGAAGTTGCAGTGGAGCAAATTGAAGATAGCAAATCGTATCTCCCTGAAGT
* * * *
40211918 TGTAGTAGAGCAGATTGAAGCTAC
66 TGCAGT-GAACAGATTAAAGCCAC
* * *** * *
40211942 AAATCTTATCTCCCT-AGAGTTGCAGTGGAGCAGATTAAAGATAATGAATCTTATCTCCTTGAAG
1 AAATCTTATCTCCCTGA-AGTTGCAGTGGAGCAAATTGAAGATAGCAAATCGTATCTCCCTGAAG
* * **
40212006 TTGCAGTGGATCAGATTGAAGATAGC
65 TTGCAGT-GAACAGATTAAAGCCA-C
* * * * * * *
40212032 AAACCTTATCTCTCTAAAGTTGCAGTGGAACAAATTAAAGCTACAAGATAG-AAATCTTAACTCT
1 AAATCTTATCTCCCTGAAGTTGCAGTGGAGCAAATT---G----AAGATAGCAAATCGTATCTCC
* * **
40212096 CTGAAGTTGCAGTGGAACAAATTGAAGATAC
59 CTGAAGTTGCAGT-GAACAGATTAAAGCCAC
* * *
40212127 GAATCTTATTTCCCTAAAGTTGCAGTGGA
1 AAATCTTATCTCCCTGAAGTTGCAGTGGA
40212156 ACAGATTAAG
Statistics
Matches: 468, Mismatches: 83, Indels: 43
0.79 0.14 0.07
Matches are distributed among these distances:
88 74 0.16
89 219 0.47
90 32 0.07
91 2 0.00
93 1 0.00
94 3 0.01
95 57 0.12
96 74 0.16
97 6 0.01
ACGTcount: A:0.35, C:0.17, G:0.19, T:0.28
Consensus pattern (88 bp):
AAATCTTATCTCCCTGAAGTTGCAGTGGAGCAAATTGAAGATAGCAAATCGTATCTCCCTGAAGT
TGCAGTGAACAGATTAAAGCCAC
Found at i:40211848 original size:184 final size:176
Alignment explanation
Indices: 40211492--40211984 Score: 494
Period size: 184 Copynumber: 2.7 Consensus size: 176
40211482 TCGTCGTGGA
* * * ** *
40211492 AAATCTTATCTCCCTAAAGTTGCAATGGAGCAGATTAAAGCCACAAATCTTATCTCCCTAAAGTT
1 AAATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTGAAGTTACAAATCTTATCT-CCTGAAGTT
* * * * *
40211557 GCAATGGAGCAGATTAAAGCCACAAATCTTATCTTCCTGAAGTTACAGTGGAGCA-AATTGAAAA
65 GCAGTGAAGCAGATTAAAGCCACAAATCTTATCTCCCTGAAGTTGCAGTGGAGCAGAA-TGAAGA
* * *
40211621 TAGCAAATCCTATTACCCTAAAGTTGTAGTGGAACAAATTAAAGCTACAAGTTAC
129 TAGCAAATCCTATTACCCTAAAGTTGCAATGAAACAAATTAAAG-T-C-----AC
* * * *
40211676 AAATCTTATCTCTCTGACGTTGCAGTAGAGTAGATTGAAGTTACAAATCTTATCTCCTTGAAGTT
1 AAATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTGAAGTTACAAATCTTATCTCC-TGAAGTT
*
40211741 GCAGTGAAGCAGATTAAAGCCACAAATCTTATCTCCCTGAAGTTGCAGTTGAGCAGAATGAAGAT
65 GCAGTGAAGCAGATTAAAGCCACAAATCTTATCTCCCTGAAGTTGCAGTGGAGCAGAATGAAGAT
* ** * *
40211806 AGCAAATCGTATCT-TTCTGAAGTTGCAAT-AAAGCAGATTAAAGTCAC
130 AGCAAATCCTAT-TACCCTAAAGTTGCAATGAAA-CAAATTAAAGTCAC
* ** *
40211853 AAATCTTATCTCCCTGAAGTTACAGTGGAGCAGATTGAA-TATAGTGAATCGTATCTCACTGAAG
1 AAATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTGAAGT-TA-CAAATCTTATCTC-CTGAAG
* * * * *
40211917 TTGTAGT-AGAGCAGATTGAAGCTACAAATCTTATCTCCCT-AGAGTTGCAGTGGAGCAGATTAA
63 TTGCAGTGA-AGCAGATTAAAGCCACAAATCTTATCTCCCTGA-AGTTGCAGTGGAGCAGAATGA
40211980 AGATA
126 AGATA
40211985 ATGAATCTTA
Statistics
Matches: 262, Mismatches: 38, Indels: 24
0.81 0.12 0.07
Matches are distributed among these distances:
176 1 0.00
177 40 0.15
178 73 0.28
179 1 0.00
182 1 0.00
183 5 0.02
184 138 0.53
185 3 0.01
ACGTcount: A:0.35, C:0.18, G:0.19, T:0.28
Consensus pattern (176 bp):
AAATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTGAAGTTACAAATCTTATCTCCTGAAGTTG
CAGTGAAGCAGATTAAAGCCACAAATCTTATCTCCCTGAAGTTGCAGTGGAGCAGAATGAAGATA
GCAAATCCTATTACCCTAAAGTTGCAATGAAACAAATTAAAGTCAC
Found at i:40212103 original size:51 final size:50
Alignment explanation
Indices: 40212024--40212204 Score: 205
Period size: 51 Copynumber: 3.7 Consensus size: 50
40212014 GATCAGATTG
*
40212024 AAGATAGCAAACCTTATCTCTCTAAAGTTGCAGTGGAACAAATTAAAGCTAC
1 AAGATAG-AAATCTTATCTCTCTAAAGTTGCAGTGGAACAAATT-AAGCTAC
* *
40212076 AAGATAGAAATCTTAACTCTCTGAAGTTGCAGTGGAACAAATT--G----
1 AAGATAGAAATCTTATCTCTCTAAAGTTGCAGTGGAACAAATTAAGCTAC
* * *
40212120 AAGATACG-AATCTTATTTCCCTAAAGTTGCAGTGGAACAGATTAAGGCTAC
1 AAGATA-GAAATCTTATCTCTCTAAAGTTGCAGTGGAACAAATTAA-GCTAC
* *
40212171 AAGTTACAAATCTTATCTCTCTAAAGTTGCAGTG
1 AAGATAGAAATCTTATCTCTCTAAAGTTGCAGTG
40212205 AAGCATATTG
Statistics
Matches: 108, Mismatches: 12, Indels: 19
0.78 0.09 0.14
Matches are distributed among these distances:
44 36 0.33
45 1 0.01
47 1 0.01
48 1 0.01
51 62 0.57
52 7 0.06
ACGTcount: A:0.37, C:0.17, G:0.18, T:0.28
Consensus pattern (50 bp):
AAGATAGAAATCTTATCTCTCTAAAGTTGCAGTGGAACAAATTAAGCTAC
Found at i:40212170 original size:95 final size:95
Alignment explanation
Indices: 40211720--40212252 Score: 434
Period size: 89 Copynumber: 5.8 Consensus size: 95
40211710 TTGAAGTTAC
* ** *
40211720 AAATCTTATCTC-CTTGAAGTTGCAGT-GAAGCAGATTAAAGCCACAAATCTTATCTCCCTGAAG
1 AAATCTTATCTCTC-TGAAGTTGCAGTGGAA-CAGATTGAAGATACAAATCTTATCTCCCTAAAG
* * *
40211783 TTGCAGTTGAGCAG----AA--T-GAAGATAG
64 TTGCAGTGGAACAGATTAAAGCTACAAGATAG
* * * * * *
40211808 CAAATCGTATCTTTCTGAAGTTGCAAT-AAAGCAGATTAAAG-TCACAAATCTTATCTCCCTGAA
1 -AAATCTTATCTCTCTGAAGTTGCAGTGGAA-CAGATTGAAGAT-ACAAATCTTATCTCCCTAAA
* * * *
40211871 GTTACAGTGGAGCAGATTGAA--TA-TAG-T-G
63 GTTGCAGTGGAACAGATTAAAGCTACAAGATAG
* * * * * * *
40211899 -AATCGTATCTCACTGAAGTTGTAGTAGAGCAGATTGAAGCTACAAATCTTATCTCCCTAGAGTT
1 AAATCTTATCTCTCTGAAGTTGCAGTGGAACAGATTGAAGATACAAATCTTATCTCCCTAAAGTT
* *
40211963 GCAGTGGAGCAGATTAAAG--A-TA-AT-G
66 GCAGTGGAACAGATTAAAGCTACAAGATAG
* * *
40211988 -AATCTTATCTC-CTTGAAGTTGCAGTGGATCAGATTGAAGATAGCAAACCTTATCTCTCTAAAG
1 AAATCTTATCTCTC-TGAAGTTGCAGTGGAACAGATTGAAGATA-CAAATCTTATCTCCCTAAAG
*
40212051 TTGCAGTGGAACAAATTAAAGCTACAAGATAG
64 TTGCAGTGGAACAGATTAAAGCTACAAGATAG
* * * *
40212083 AAATCTTAACTCTCTGAAGTTGCAGTGGAACAAATTGAAGATACGAATCTTATTTCCCTAAAGTT
1 AAATCTTATCTCTCTGAAGTTGCAGTGGAACAGATTGAAGATACAAATCTTATCTCCCTAAAGTT
* * *
40212148 GCAGTGGAACAGATTAAGGCTACAAGTTAC
66 GCAGTGGAACAGATTAAAGCTACAAGATAG
* * * *
40212178 AAATCTTATCTCTCTAAAGTTGCAGT-GAAGCATATTGAAAATACAAATCTTATTTCCC-AGAAG
1 AAATCTTATCTCTCTGAAGTTGCAGTGGAA-CAGATTGAAGATACAAATCTTATCTCCCTA-AAG
40212241 TTGCAGTGGAAC
64 TTGCAGTGGAAC
40212253 GGATCTTATC
Statistics
Matches: 376, Mismatches: 46, Indels: 38
0.82 0.10 0.08
Matches are distributed among these distances:
88 1 0.00
89 174 0.46
90 39 0.10
91 1 0.00
92 2 0.01
93 6 0.02
94 6 0.02
95 109 0.29
96 37 0.10
97 1 0.00
ACGTcount: A:0.35, C:0.17, G:0.19, T:0.29
Consensus pattern (95 bp):
AAATCTTATCTCTCTGAAGTTGCAGTGGAACAGATTGAAGATACAAATCTTATCTCCCTAAAGTT
GCAGTGGAACAGATTAAAGCTACAAGATAG
Found at i:40212334 original size:44 final size:44
Alignment explanation
Indices: 40212265--40212368 Score: 136
Period size: 44 Copynumber: 2.4 Consensus size: 44
40212255 ATCTTATCTC
* **
40212265 TCTGAAGTTGTAGTGGAGCAGATTGAAGTGACAAACCCTATACA
1 TCTGAAGTTGTAGTGGAGCAAATTGAAGCAACAAACCCTATACA
* * *
40212309 TCTGAAGTTGTAGTGGAGTAAATTGAAGCAACAAATCCTATACC
1 TCTGAAGTTGTAGTGGAGCAAATTGAAGCAACAAACCCTATACA
* *
40212353 TCTGAAATTGCAGTGG
1 TCTGAAGTTGTAGTGG
40212369 GTTGGAATGA
Statistics
Matches: 52, Mismatches: 8, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
44 52 1.00
ACGTcount: A:0.34, C:0.15, G:0.24, T:0.27
Consensus pattern (44 bp):
TCTGAAGTTGTAGTGGAGCAAATTGAAGCAACAAACCCTATACA
Found at i:40212666 original size:9 final size:9
Alignment explanation
Indices: 40212654--40212682 Score: 58
Period size: 9 Copynumber: 3.2 Consensus size: 9
40212644 AAAAAACCCT
40212654 AATGGCCCA
1 AATGGCCCA
40212663 AATGGCCCA
1 AATGGCCCA
40212672 AATGGCCCA
1 AATGGCCCA
40212681 AA
1 AA
40212683 CACTTAAACT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 20 1.00
ACGTcount: A:0.38, C:0.31, G:0.21, T:0.10
Consensus pattern (9 bp):
AATGGCCCA
Found at i:40216121 original size:47 final size:47
Alignment explanation
Indices: 40215998--40216343 Score: 559
Period size: 47 Copynumber: 7.4 Consensus size: 47
40215988 CCCTTCGGGA
* *
40215998 CTTATCACATTTATACACTTTCACATCCATCACATTGGCCATTCGGC
1 CTTATCACATATATACACTTTCACATTCATCACATTGGCCATTCGGC
* * * *
40216045 CTTATCTCAT-TATACACTTTCACATTCATCACATCGGTCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATTGGCCATTCGGC
*
40216091 CTTATCACATATACACACTTTCACATTCATCACATTGGCCATTCGGC
1 CTTATCACATATATACACTTTCACATTCATCACATTGGCCATTCGGC
* *
40216138 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATTGGCCATTCGGC
* *
40216185 CTTATCACATATACACACTTTCACATTCATCACATTGGCCATTCGAC
1 CTTATCACATATATACACTTTCACATTCATCACATTGGCCATTCGGC
40216232 CTTATCACATATATACACTTTCACATTCATCACATTGGCCATTCGGC
1 CTTATCACATATATACACTTTCACATTCATCACATTGGCCATTCGGC
* *
40216279 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATTGGCCATTCGGC
*
40216326 CTTATCACATATACACAC
1 CTTATCACATATATACAC
40216344 CTTGTACACC
Statistics
Matches: 276, Mismatches: 22, Indels: 2
0.92 0.07 0.01
Matches are distributed among these distances:
46 41 0.15
47 235 0.85
ACGTcount: A:0.29, C:0.31, G:0.08, T:0.33
Consensus pattern (47 bp):
CTTATCACATATATACACTTTCACATTCATCACATTGGCCATTCGGC
Found at i:40216241 original size:22 final size:22
Alignment explanation
Indices: 40216213--40216288 Score: 64
Period size: 22 Copynumber: 3.3 Consensus size: 22
40216203 TTTCACATTC
40216213 ATCACATTGGCCATTCGACCTT
1 ATCACATTGGCCATTCGACCTT
** * *
40216235 ATCACATATATACACTTTC-ACATT
1 ATCACAT-T-GGC-CATTCGACCTT
*
40216259 CATCACATTGGCCATTCGGCCTT
1 -ATCACATTGGCCATTCGACCTT
40216282 ATCACAT
1 ATCACAT
40216289 ATATACACTT
Statistics
Matches: 40, Mismatches: 9, Indels: 10
0.68 0.15 0.17
Matches are distributed among these distances:
22 18 0.45
23 5 0.12
24 6 0.15
25 11 0.28
ACGTcount: A:0.28, C:0.30, G:0.09, T:0.33
Consensus pattern (22 bp):
ATCACATTGGCCATTCGACCTT
Found at i:40220964 original size:26 final size:26
Alignment explanation
Indices: 40220926--40220976 Score: 75
Period size: 26 Copynumber: 2.0 Consensus size: 26
40220916 TGGGGACTTT
40220926 TACCCACACAAGTCCACGTCTACCCC
1 TACCCACACAAGTCCACGTCTACCCC
* * *
40220952 TACCCATATAAGTCCACTTCTACCC
1 TACCCACACAAGTCCACGTCTACCC
40220977 ATACATCTTG
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
26 22 1.00
ACGTcount: A:0.27, C:0.45, G:0.06, T:0.22
Consensus pattern (26 bp):
TACCCACACAAGTCCACGTCTACCCC
Found at i:40222672 original size:8 final size:9
Alignment explanation
Indices: 40222652--40222676 Score: 50
Period size: 9 Copynumber: 2.8 Consensus size: 9
40222642 ATTAAGTTAA
40222652 TTTTAAAGT
1 TTTTAAAGT
40222661 TTTTAAAGT
1 TTTTAAAGT
40222670 TTTTAAA
1 TTTTAAA
40222677 TTTATAATTT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 16 1.00
ACGTcount: A:0.36, C:0.00, G:0.08, T:0.56
Consensus pattern (9 bp):
TTTTAAAGT
Found at i:40225206 original size:26 final size:25
Alignment explanation
Indices: 40225146--40225233 Score: 97
Period size: 26 Copynumber: 3.5 Consensus size: 25
40225136 TATATATAAG
*
40225146 AATGAATAAATTTTCTACAAAAAAA
1 AATGAATAAATTGTCTACAAAAAAA
* * * *
40225171 AACGAGTAAACTTGTATGCAAAAAAA
1 AATGAATAAA-TTGTCTACAAAAAAA
*
40225197 AATGAATAAAATTGTCTAC-AAAACA
1 AATGAAT-AAATTGTCTACAAAAAAA
40225222 AATGAATAAATT
1 AATGAATAAATT
40225234 TGTTAACGAG
Statistics
Matches: 51, Mismatches: 10, Indels: 5
0.77 0.15 0.08
Matches are distributed among these distances:
24 5 0.10
25 20 0.39
26 23 0.45
27 3 0.06
ACGTcount: A:0.57, C:0.09, G:0.09, T:0.25
Consensus pattern (25 bp):
AATGAATAAATTGTCTACAAAAAAA
Found at i:40235074 original size:23 final size:24
Alignment explanation
Indices: 40235048--40235160 Score: 140
Period size: 23 Copynumber: 4.7 Consensus size: 24
40235038 AAAATTTACT
40235048 GTCAATTCATCCTTTACA-TTTCC
1 GTCAATTCATCCTTTACATTTTCC
40235071 GTCAATTCATCCTTTACAATTTTTCC
1 GTCAATTCATCCTTTAC-A-TTTTCC
* * * *
40235097 GTTAGTTCCTCTTTTACATTTTCC
1 GTCAATTCATCCTTTACATTTTCC
* *
40235121 GTTAATTAATCCTTTACATTTT-C
1 GTCAATTCATCCTTTACATTTTCC
40235144 GTCAATTCATCCTTTAC
1 GTCAATTCATCCTTTAC
40235161 CAAGAATGAT
Statistics
Matches: 77, Mismatches: 10, Indels: 6
0.83 0.11 0.06
Matches are distributed among these distances:
23 33 0.43
24 25 0.32
25 1 0.01
26 18 0.23
ACGTcount: A:0.21, C:0.26, G:0.05, T:0.48
Consensus pattern (24 bp):
GTCAATTCATCCTTTACATTTTCC
Found at i:40236021 original size:18 final size:17
Alignment explanation
Indices: 40235979--40236021 Score: 52
Period size: 16 Copynumber: 2.5 Consensus size: 17
40235969 AACCATTAAA
40235979 TCCAATTTTTATCTATT
1 TCCAATTTTTATCTATT
* *
40235996 T-TAATTTTTATTTCATT
1 TCCAATTTTTATCT-ATT
40236013 TCCAATTTT
1 TCCAATTTT
40236022 ACCCTTAATC
Statistics
Matches: 21, Mismatches: 3, Indels: 3
0.78 0.11 0.11
Matches are distributed among these distances:
16 10 0.48
17 5 0.24
18 6 0.29
ACGTcount: A:0.23, C:0.14, G:0.00, T:0.63
Consensus pattern (17 bp):
TCCAATTTTTATCTATT
Found at i:40241675 original size:2 final size:2
Alignment explanation
Indices: 40241668--40241692 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
40241658 GTTCAGAATG
40241668 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 A
40241693 ACCACTCAAG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:40242106 original size:24 final size:24
Alignment explanation
Indices: 40242058--40242103 Score: 67
Period size: 23 Copynumber: 2.0 Consensus size: 24
40242048 TTTTGAGATA
* *
40242058 TTTATAAAATATATTTTCCAAAAT
1 TTTATAAAATATATATTCAAAAAT
40242082 TTTAT-AAATATATATTCAAAAA
1 TTTATAAAATATATATTCAAAAA
40242104 ATTCAAAATT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
23 15 0.75
24 5 0.25
ACGTcount: A:0.50, C:0.07, G:0.00, T:0.43
Consensus pattern (24 bp):
TTTATAAAATATATATTCAAAAAT
Found at i:40244083 original size:15 final size:15
Alignment explanation
Indices: 40244063--40244119 Score: 51
Period size: 15 Copynumber: 3.5 Consensus size: 15
40244053 ATTCAATTTT
40244063 AATATTTTAATAATA
1 AATATTTTAATAATA
*
40244078 AATATTTATTACAATTATA
1 AATA-TT-TT--AATAATA
*
40244097 AATATATTAATAATA
1 AATATTTTAATAATA
*
40244112 AATGTTTT
1 AATATTTT
40244120 GTAGTATAAA
Statistics
Matches: 33, Mismatches: 5, Indels: 8
0.72 0.11 0.17
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:0.49, C:0.02, G:0.02, T:0.47
Consensus pattern (15 bp):
AATATTTTAATAATA
Found at i:40246777 original size:29 final size:31
Alignment explanation
Indices: 40246731--40246794 Score: 96
Period size: 30 Copynumber: 2.1 Consensus size: 31
40246721 AACGATTAAA
**
40246731 TCCCCAGAAACTGGTAAAA-TTGTTATAAGG
1 TCCCCAGAAACTAATAAAATTTGTTATAAGG
40246761 TCCCCA-AAACTAATAAAATTTGTTATAAGG
1 TCCCCAGAAACTAATAAAATTTGTTATAAGG
40246791 TCCC
1 TCCC
40246795 TTTAGAGGTT
Statistics
Matches: 31, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
29 10 0.32
30 21 0.68
ACGTcount: A:0.38, C:0.20, G:0.14, T:0.28
Consensus pattern (31 bp):
TCCCCAGAAACTAATAAAATTTGTTATAAGG
Found at i:40261892 original size:11 final size:11
Alignment explanation
Indices: 40261878--40261907 Score: 60
Period size: 11 Copynumber: 2.7 Consensus size: 11
40261868 AAAATAGTAA
40261878 ATAAATAATAT
1 ATAAATAATAT
40261889 ATAAATAATAT
1 ATAAATAATAT
40261900 ATAAATAA
1 ATAAATAA
40261908 ATGAATAAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 19 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (11 bp):
ATAAATAATAT
Found at i:40263168 original size:22 final size:23
Alignment explanation
Indices: 40263129--40263186 Score: 66
Period size: 22 Copynumber: 2.5 Consensus size: 23
40263119 TAAATGGACT
**
40263129 TTTGATATTTGGACTTATTTATTTA
1 TTTG-TATTTGGTTTTATTTA-TTA
40263154 TTT-T-TTTGGTTTTATTTATTA
1 TTTGTATTTGGTTTTATTTATTA
40263175 TTTGTATTTGGT
1 TTTGTATTTGGT
40263187 CTTGGGCCCG
Statistics
Matches: 29, Mismatches: 2, Indels: 6
0.78 0.05 0.16
Matches are distributed among these distances:
21 6 0.21
22 13 0.45
23 7 0.24
25 3 0.10
ACGTcount: A:0.17, C:0.02, G:0.14, T:0.67
Consensus pattern (23 bp):
TTTGTATTTGGTTTTATTTATTA
Found at i:40263642 original size:93 final size:95
Alignment explanation
Indices: 40263520--40264323 Score: 376
Period size: 93 Copynumber: 8.8 Consensus size: 95
40263510 TAATAACTTC
* * * * *
40263520 AATCTACTCCACTGCAACTTCAGGAAGATAAGGTTTGT-G-G-CTTTAATCTACTCCACTGCAAC
1 AATCTGCTCCACTGCAACTTCAGGGAGATAAGATTTGTAGCGTCTTCAATCTGCTCCACTGCAAC
** *
40263582 TTCAGAGAGATAAGATTTGTAACCCGTCTTC
66 TTCAGAGAGATAAGATTTGT-ACTTGTCTTT
* *
40263613 AATCTGCTCCACTACAACTTTAGGGAGATAAGATTTGTAGCCCGTCTTCAATCTGCTCCACTGCA
1 AATCTGCTCCACTGCAACTTCAGGGAGATAAGATTTGTAG--CGTCTTCAATCTGCTCCACTGCA
* * *
40263678 ACTTCGGGGAGATAA-AGTTTG----TGGCTTT
64 ACTTCAGAGAGATAAGA-TTTGTACTTGTCTTT
* *
40263706 AATCTGCTCCACTGTAACTTCAGGGAGATAAAATTTGTAGCCTGTCTTCAATCTGCTCCACTGCA
1 AATCTGCTCCACTGCAACTTCAGGGAGATAAGATTTGTAG-C-GTCTTCAATCTGCTCCACTGCA
* * * *
40263771 ACTTCAGGGAGATAAGA-TTG-ATTTATTTTT
64 ACTTCAGAGAGATAAGATTTGTACTTGTCTTT
* * * * * * * * *
40263801 AACCTGTTCCACTGTAACTTCAAGGAGAAAAGGTTTGT-G-G-CTTTAATCTGCTCTATTGCAAC
1 AATCTGCTCCACTGCAACTTCAGGGAGATAAGATTTGTAGCGTCTTCAATCTGCTCCACTGCAAC
40263863 TTCA-ATGAGATAAGATTTGTAGCTTGTCTTT
66 TTCAGA-GAGATAAGATTTGTA-CTTGTCTTT
* * * * * * * **
40263894 AATTTGTTCCACTGCAACTTCAAGGAGATAAGA-TTG--GCTTATTTTTAACCTATTCCACTGCA
1 AATCTGCTCCACTGCAACTTCAGGGAGATAAGATTTGTAGC--GTCTTCAATCTGCTCCACTGCA
* * * *
40263956 ACTTTAGGGAGATAA-A---GT--TTG-ATAT
64 ACTTCAGAGAGATAAGATTTGTACTTGTCTTT
* * * * * *
40263981 GATCTGCTCTACTGCAACTTCAGAGAGATAAGATTCGCTA---TCTTCAGTCTGCTCCACTGTAA
1 AATCTGCTCCACTGCAACTTCAGGGAGATAAGATTTG-TAGCGTCTTCAATCTGCTCCACTGCAA
* * *
40264043 CTTTAGGGAGATAAGACTTGTAAC-T-TC---
65 CTTCAGAGAGATAAGATTTGT-ACTTGTCTTT
* * * * * **
40264070 AACCTACTCCACTACAACTTCAGGGAGAT-A-ATGTT-T-GC-T-AT-GATCTGCTCTGCTGCAA
1 AATCTGCTCCACTGCAACTTCAGGGAGATAAGAT-TTGTAGCGTCTTCAATCTGCTCCACTGCAA
* * * * * *
40264128 CTTCAAAGAGATAAGATCTGCAATTTATAACTTC
65 CTTCAGAGAGATAAGATTTG-TACTTGT--CTTT
* * * * * *
40264162 AATCTGTTCTATTGCAACTTCAGGGAAATAAGATTCGCTA---TCTTCAGTCTGCTCCACTGCAA
1 AATCTGCTCCACTGCAACTTCAGGGAGATAAGATTTG-TAGCGTCTTCAATCTGCTCCACTGCAA
* * * *
40264224 CTTCATG-GAGATAATACTAGTA---AT-TTT
65 CTTCA-GAGAGATAAGATTTGTACTTGTCTTT
* * *
40264251 AAACTGCTCCACTGCAACTTCAGGGAGATAAGGTTTGCTAG-GATCTTCAATC--CATCCCACTA
1 AATCTGCTCCACTGCAACTTCAGGGAGATAAGATTTG-TAGCG-TCTTCAATCTGC-T-CCACTG
40264313 CAACTTCAGAG
62 CAACTTCAGAG
40264324 GTATAGGATT
Statistics
Matches: 541, Mismatches: 113, Indels: 115
0.70 0.15 0.15
Matches are distributed among these distances:
85 28 0.05
86 32 0.06
87 34 0.06
88 7 0.01
89 59 0.11
90 35 0.06
91 9 0.02
92 56 0.10
93 145 0.27
94 7 0.01
95 65 0.12
96 27 0.05
97 2 0.00
98 35 0.06
ACGTcount: A:0.28, C:0.21, G:0.18, T:0.32
Consensus pattern (95 bp):
AATCTGCTCCACTGCAACTTCAGGGAGATAAGATTTGTAGCGTCTTCAATCTGCTCCACTGCAAC
TTCAGAGAGATAAGATTTGTACTTGTCTTT
Found at i:40263828 original size:46 final size:46
Alignment explanation
Indices: 40263702--40263970 Score: 175
Period size: 49 Copynumber: 5.8 Consensus size: 46
40263692 AAGTTTGTGG
* * * * * * *
40263702 CTTTAATCTGCTCCACTGTAACTTCAGGGAGATAAAATTTGTAGCCTGT
1 CTTTAACCTGTTCCACTGCAACTTCAAGGAGATAAGA-TTG-A-CTTAT
* * * * *
40263751 CTTCAATCTGCTCCACTGCAACTTCAGGGAGATAAGATTGATTTAT
1 CTTTAACCTGTTCCACTGCAACTTCAAGGAGATAAGATTGACTTAT
* * * * **
40263797 TTTTAACCTGTTCCACTGTAACTTCAAGGAGAAAAGGTT---TGTGG
1 CTTTAACCTGTTCCACTGCAACTTCAAGGAGATAAGATTGACT-TAT
* * * * * *
40263841 CTTTAATCTGCTCTATTGCAACTTCAATGAGATAAGATTTGTAGCTTGT
1 CTTTAACCTGTTCCACTGCAACTTCAAGGAGATAAGA-TTG-A-CTTAT
** *
40263890 CTTTAATTTGTTCCACTGCAACTTCAAGGAGATAAGATTGGCTTAT
1 CTTTAACCTGTTCCACTGCAACTTCAAGGAGATAAGATTGACTTAT
* * * *
40263936 TTTTAACCTATTCCACTGCAACTTTAGGGAGATAA
1 CTTTAACCTGTTCCACTGCAACTTCAAGGAGATAA
40263971 AGTTTGATAT
Statistics
Matches: 174, Mismatches: 39, Indels: 17
0.76 0.17 0.07
Matches are distributed among these distances:
43 1 0.01
44 29 0.17
45 2 0.01
46 66 0.38
47 1 0.01
48 6 0.03
49 68 0.39
50 1 0.01
ACGTcount: A:0.28, C:0.19, G:0.18, T:0.36
Consensus pattern (46 bp):
CTTTAACCTGTTCCACTGCAACTTCAAGGAGATAAGATTGACTTAT
Found at i:40263875 original size:139 final size:139
Alignment explanation
Indices: 40263527--40264287 Score: 597
Period size: 139 Copynumber: 5.5 Consensus size: 139
40263517 TTCAATCTAC
* *
40263527 TCCACTGCAACTTC-AGGAAGATAAGGTTTGTGGCTTTAATCTACTCCACTGCAACTTCAGAGAG
1 TCCACTGCAACTTCAAGG-AGATAAAGTTTGTGGCTTTAATCTGCTCCACTGCAACTTCAGAGAG
* * * * **
40263591 ATAAGATTTGTAACCCGTCTTCAATCTGCTCCACTACAACTTTAGGGAGATAAGATTTGTAGCCC
65 ATAAGATTTGTAGCCTGTCTTCAATCTGCTCCACTGCAACTTCAGGGAGATAAGA-TTG-A-CTT
* * * * *
40263656 GTCTTCAATCTGC
127 ATTTTTAACCTGT
** * *
40263669 TCCACTGCAACTTCGGGGAGATAAAGTTTGTGGCTTTAATCTGCTCCACTGTAACTTCAGGGAGA
1 TCCACTGCAACTTCAAGGAGATAAAGTTTGTGGCTTTAATCTGCTCCACTGCAACTTCAGAGAGA
* *
40263734 TAAAATTTGTAGCCTGTCTTCAATCTGCTCCACTGCAACTTCAGGGAGATAAGATTGATTTATTT
66 TAAGATTTGTAGCCTGTCTTCAATCTGCTCCACTGCAACTTCAGGGAGATAAGATTGACTTATTT
40263799 TTAACCTGT
131 TTAACCTGT
* * *
40263808 TCCACTGTAACTTCAAGGAGA-AAAGGTTTGTGGCTTTAATCTGCTCTATTGCAACTTCA-ATGA
1 TCCACTGCAACTTCAAGGAGATAAA-GTTTGTGGCTTTAATCTGCTCCACTGCAACTTCAGA-GA
* * * * * *
40263871 GATAAGATTTGTAGCTTGTCTTTAATTTGTTCCACTGCAACTTCAAGGAGATAAGATTGGCTTAT
64 GATAAGATTTGTAGCCTGTCTTCAATCTGCTCCACTGCAACTTCAGGGAGATAAGATTGACTTAT
*
40263936 TTTTAACCTAT
129 TTTTAACCTGT
* * * * * *
40263947 TCCACTGCAACTTTAGGGAGATAAAG-TT-T-GATATGATCTGCTCTACTGCAACTTCAGAGAGA
1 TCCACTGCAACTTCAAGGAGATAAAGTTTGTGGCTTTAATCTGCTCCACTGCAACTTCAGAGAGA
* * * * * **
40264009 TAAGA--T-TCG-CTATCTTCAGTCTGCTCCACTGTAACTTTAGGGAGATAAGACTTG---TAAC
66 TAAGATTTGTAGCCTGTCTTCAATCTGCTCCACTGCAACTTCAGGGAGATAAGA-TTGACTTATT
* **
40264067 TTCAACCTAC
130 TTTAACCTGT
* * * * * ** *
40264077 TCCACTACAACTTCAGGGAGATAATG-TT-T-GCTATGATCTGCTCTGCTGCAACTTCAAAGAGA
1 TCCACTGCAACTTCAAGGAGATAAAGTTTGTGGCTTTAATCTGCTCCACTGCAACTTCAGAGAGA
* * *** * * * * *
40264139 TAAGATCTGCAATTTATAACTTCAATCTGTTCTATTGCAACTTCAGGGAAATAAGATTCG-C-TA
66 TAAGATTTGTAGCCTGT--CTTCAATCTGCTCCACTGCAACTTCAGGGAGATAAGATT-GACTTA
* * ** *
40264202 TCTTCAGTCTGC
128 TTTTTAACCTGT
* * * *** * *
40264214 TCCACTGCAACTTCATGGAGATAATA-CTAGTAATTTTAAACTGCTCCACTGCAACTTCAGGGAG
1 TCCACTGCAACTTCAAGGAGATAA-AGTTTGTGGCTTTAATCTGCTCCACTGCAACTTCAGAGAG
*
40264278 ATAAGGTTTG
65 ATAAGATTTG
40264288 CTAGGATCTT
Statistics
Matches: 510, Mismatches: 91, Indels: 38
0.80 0.14 0.06
Matches are distributed among these distances:
130 71 0.14
132 33 0.06
133 5 0.01
134 4 0.01
135 2 0.00
136 63 0.12
137 34 0.07
138 6 0.01
139 146 0.29
140 35 0.07
141 3 0.01
142 106 0.21
143 2 0.00
ACGTcount: A:0.28, C:0.21, G:0.18, T:0.33
Consensus pattern (139 bp):
TCCACTGCAACTTCAAGGAGATAAAGTTTGTGGCTTTAATCTGCTCCACTGCAACTTCAGAGAGA
TAAGATTTGTAGCCTGTCTTCAATCTGCTCCACTGCAACTTCAGGGAGATAAGATTGACTTATTT
TTAACCTGT
Found at i:40264045 original size:45 final size:45
Alignment explanation
Indices: 40263481--40264282 Score: 372
Period size: 44 Copynumber: 17.6 Consensus size: 45
40263471 GTTTTAACTC
* * ** *
40263481 GCTCCACTGCAACTTTAGGGAGATAGGATT-AATAACTTCAATCT
1 GCTCCACTGCAACTTCAGGGAGATAAGATTCGCTATCTTCAATCT
* * * * ** *
40263525 ACTCCACTGCAACTTCAGGAAGATAAGGTTTG-TGGCTTTAATCT
1 GCTCCACTGCAACTTCAGGGAGATAAGATTCGCTATCTTCAATCT
* * *
40263569 ACTCCACTGCAACTTCAGAGAGATAAGATTTG-TAACCCGTCTTCAATCT
1 GCTCCACTGCAACTTCAGGGAGATAAGATTCGCT-A----TCTTCAATCT
* * *
40263618 GCTCCACTACAACTTTAGGGAGATAAGATTTG-TAGCCCGTCTTCAATCT
1 GCTCCACTGCAACTTCAGGGAGATAAGATTCGCTA-----TCTTCAATCT
* * ** *
40263667 GCTCCACTGCAACTTCGGGGAGATAA-AGTTTG-TGGCTTTAATCT
1 GCTCCACTGCAACTTCAGGGAGATAAGA-TTCGCTATCTTCAATCT
* * * *
40263711 GCTCCACTGTAACTTCAGGGAGATAAAATTTGTAGCCTGTCTTCAATCT
1 GCTCCACTGCAACTTCAGGGAGATAAGA--T-TCG-CTATCTTCAATCT
* * * *
40263760 GCTCCACTGCAACTTCAGGGAGATAAGATT-GATTTATTTTTAACCT
1 GCTCCACTGCAACTTCAGGGAGATAAGATTCG--CTATCTTCAATCT
* * * * * * ** *
40263806 GTTCCACTGTAACTTCAAGGAGAAAAGGTTTG-TGGCTTTAATCT
1 GCTCCACTGCAACTTCAGGGAGATAAGATTCGCTATCTTCAATCT
* * ** * * * *
40263850 GCTCTATTGCAACTTCAATGAGATAAGATTTGTAGCTTGTCTTTAATTT
1 GCTCCACTGCAACTTCAGGGAGATAAGA--T-TCGC-TATCTTCAATCT
* * * * * *
40263899 GTTCCACTGCAACTTCAAGGAGATAAGATTGGCTTATTTTTAACCT
1 GCTCCACTGCAACTTCAGGGAGATAAGATTCGC-TATCTTCAATCT
** * * * *
40263945 ATTCCACTGCAACTTTAGGGAGATAA-AGTTTG--AT-AT-GATCT
1 GCTCCACTGCAACTTCAGGGAGATAAGA-TTCGCTATCTTCAATCT
* * *
40263986 GCTCTACTGCAACTTCAGAGAGATAAGATTCGCTATCTTCAGTCT
1 GCTCCACTGCAACTTCAGGGAGATAAGATTCGCTATCTTCAATCT
* * * *
40264031 GCTCCACTGTAACTTTAGGGAGATAAGACTT-G-TAACTTCAACCT
1 GCTCCACTGCAACTTCAGGGAGATAAGA-TTCGCTATCTTCAATCT
* * * *
40264075 ACTCCACTACAACTTCAGGGAGATAATG-TTTGCTA---T-GATCT
1 GCTCCACTGCAACTTCAGGGAGATAA-GATTCGCTATCTTCAATCT
** **
40264116 GCTCTGCTGCAACTTCAAAGAGATAAGA-TCTGCAATTTATAACTTCAATCT
1 GCTCCACTGCAACTTCAGGGAGATAAGATTC-GC----TAT--CTTCAATCT
* * * * *
40264167 GTTCTATTGCAACTTCAGGGAAATAAGATTCGCTATCTTCAGTCT
1 GCTCCACTGCAACTTCAGGGAGATAAGATTCGCTATCTTCAATCT
* * * * * *
40264212 GCTCCACTGCAACTTCATGGAGATAATACTAG-TAAT-TTTAAACT
1 GCTCCACTGCAACTTCAGGGAGATAAGATTCGCT-ATCTTCAATCT
40264256 GCTCCACTGCAACTTCAGGGAGATAAG
1 GCTCCACTGCAACTTCAGGGAGATAAG
40264283 GTTTGCTAGG
Statistics
Matches: 590, Mismatches: 124, Indels: 88
0.74 0.15 0.11
Matches are distributed among these distances:
40 2 0.00
41 52 0.09
42 3 0.01
43 6 0.01
44 189 0.32
45 70 0.12
46 76 0.13
47 10 0.02
48 2 0.00
49 149 0.25
50 1 0.00
51 28 0.05
52 2 0.00
ACGTcount: A:0.29, C:0.21, G:0.18, T:0.32
Consensus pattern (45 bp):
GCTCCACTGCAACTTCAGGGAGATAAGATTCGCTATCTTCAATCT
Found at i:40265258 original size:17 final size:17
Alignment explanation
Indices: 40265210--40265257 Score: 64
Period size: 17 Copynumber: 2.9 Consensus size: 17
40265200 CTCTCCTTTT
*
40265210 TCTTTTTCTTCTTTTCC
1 TCTTTTTTTTCTTTTCC
40265227 T-TTTTCTTTTCTTTTCC
1 TCTTTT-TTTTCTTTTCC
40265244 TCTTTTTTTT-TTTT
1 TCTTTTTTTTCTTTT
40265258 TGAAATTTTT
Statistics
Matches: 28, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
16 8 0.29
17 16 0.57
18 4 0.14
ACGTcount: A:0.00, C:0.21, G:0.00, T:0.79
Consensus pattern (17 bp):
TCTTTTTTTTCTTTTCC
Found at i:40267595 original size:10 final size:10
Alignment explanation
Indices: 40267582--40267606 Score: 50
Period size: 10 Copynumber: 2.5 Consensus size: 10
40267572 AAATATGTAA
40267582 ATATATATGT
1 ATATATATGT
40267592 ATATATATGT
1 ATATATATGT
40267602 ATATA
1 ATATA
40267607 AAAATATGAA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 15 1.00
ACGTcount: A:0.44, C:0.00, G:0.08, T:0.48
Consensus pattern (10 bp):
ATATATATGT
Found at i:40270023 original size:35 final size:35
Alignment explanation
Indices: 40269972--40270047 Score: 143
Period size: 35 Copynumber: 2.2 Consensus size: 35
40269962 ACACTTAAAA
*
40269972 CCTTAACTTTCCCAAGAAACAAAGCTAATTCTTAG
1 CCTTGACTTTCCCAAGAAACAAAGCTAATTCTTAG
40270007 CCTTGACTTTCCCAAGAAACAAAGCTAATTCTTAG
1 CCTTGACTTTCCCAAGAAACAAAGCTAATTCTTAG
40270042 CCTTGA
1 CCTTGA
40270048 TCCGACTCTA
Statistics
Matches: 40, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
35 40 1.00
ACGTcount: A:0.34, C:0.26, G:0.11, T:0.29
Consensus pattern (35 bp):
CCTTGACTTTCCCAAGAAACAAAGCTAATTCTTAG
Found at i:40277505 original size:12 final size:12
Alignment explanation
Indices: 40277488--40277515 Score: 56
Period size: 12 Copynumber: 2.3 Consensus size: 12
40277478 TTGGTTATTG
40277488 CTGTAGCAGCTT
1 CTGTAGCAGCTT
40277500 CTGTAGCAGCTT
1 CTGTAGCAGCTT
40277512 CTGT
1 CTGT
40277516 TTTTTGTATG
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 16 1.00
ACGTcount: A:0.14, C:0.25, G:0.25, T:0.36
Consensus pattern (12 bp):
CTGTAGCAGCTT
Found at i:40280055 original size:93 final size:92
Alignment explanation
Indices: 40279923--40280117 Score: 286
Period size: 93 Copynumber: 2.1 Consensus size: 92
40279913 TTGATTTTAG
* *
40279923 TAAATTCATATAAGAACATTTTATTATTAAGAATTTTATGAAATTATATATCACTA-TATAATTA
1 TAAATTCATATAAGAAAATTTTATTATCAAGAATTTTATGAAATTATATATCACTATTA-AATTA
* *
40279987 TATTTAAT-ATTAATTATTTTAAATTGTA
65 TATGTAATAATT-ATTATTTTAAATTATA
* *
40280015 TAAATTCATATAAGAAAATTTTTATTATCAAGAATTTTATGAAATTATATATTATTATTAAATTA
1 TAAATTCATATAAGAAAA-TTTTATTATCAAGAATTTTATGAAATTATATATCACTATTAAATTA
40280080 TATGTAATAATTATTATTTTAAATTATA
65 TATGTAATAATTATTATTTTAAATTATA
*
40280108 CAAATTCATA
1 TAAATTCATA
40280118 AACTATAATC
Statistics
Matches: 93, Mismatches: 7, Indels: 5
0.89 0.07 0.05
Matches are distributed among these distances:
92 17 0.18
93 71 0.76
94 5 0.05
ACGTcount: A:0.45, C:0.04, G:0.04, T:0.47
Consensus pattern (92 bp):
TAAATTCATATAAGAAAATTTTATTATCAAGAATTTTATGAAATTATATATCACTATTAAATTAT
ATGTAATAATTATTATTTTAAATTATA
Found at i:40280165 original size:48 final size:52
Alignment explanation
Indices: 40280095--40280193 Score: 118
Period size: 52 Copynumber: 2.0 Consensus size: 52
40280085 AATAATTATT
40280095 ATTTTAAATTATACAAATTCATA-AACT-A-T-AATCATATTAGTTATAATA
1 ATTTTAAATTATACAAATTCATATAACTAATTAAATCATATTAGTTATAATA
* * **
40280143 ATTTTAAATTTTATTAAA-TCATATATTTAATTAAATCATATTAGTTATAAT
1 ATTTTAAATTATA-CAAATTCATATAACTAATTAAATCATATTAGTTATAAT
40280194 CATATATTAT
Statistics
Matches: 42, Mismatches: 4, Indels: 6
0.81 0.08 0.12
Matches are distributed among these distances:
48 17 0.40
49 5 0.12
50 1 0.02
51 1 0.02
52 18 0.43
ACGTcount: A:0.45, C:0.06, G:0.02, T:0.46
Consensus pattern (52 bp):
ATTTTAAATTATACAAATTCATATAACTAATTAAATCATATTAGTTATAATA
Found at i:40280175 original size:17 final size:17
Alignment explanation
Indices: 40280150--40280183 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
40280140 ATAATTTTAA
*
40280150 ATTTTATTAAATCATAT
1 ATTTAATTAAATCATAT
40280167 ATTTAATTAAATCATAT
1 ATTTAATTAAATCATAT
40280184 TAGTTATAAT
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:0.44, C:0.06, G:0.00, T:0.50
Consensus pattern (17 bp):
ATTTAATTAAATCATAT
Found at i:40280200 original size:17 final size:16
Alignment explanation
Indices: 40280155--40280202 Score: 55
Period size: 17 Copynumber: 3.0 Consensus size: 16
40280145 TTTAAATTTT
40280155 ATTAAATCATATATTTA
1 ATTAAATCATATA-TTA
40280172 ATTAAATC--ATATTA
1 ATTAAATCATATATTA
*
40280186 GTTATAATCATATATTA
1 ATTA-AATCATATATTA
40280203 TGATTTGAGT
Statistics
Matches: 27, Mismatches: 1, Indels: 6
0.79 0.03 0.18
Matches are distributed among these distances:
14 6 0.22
15 7 0.26
17 14 0.52
ACGTcount: A:0.46, C:0.06, G:0.02, T:0.46
Consensus pattern (16 bp):
ATTAAATCATATATTA
Found at i:40280282 original size:15 final size:15
Alignment explanation
Indices: 40280247--40280298 Score: 56
Period size: 15 Copynumber: 3.6 Consensus size: 15
40280237 TTAAGAATTT
*
40280247 TATTAAATTAT-ATA
1 TATTTAATTATAATA
40280261 T-TTTAATTATAATA
1 TATTTAATTATAATA
*
40280275 TATTTAATAATAAT-
1 TATTTAATTATAATA
40280289 TATGTTAATT
1 TAT-TTAATT
40280299 TATATTTTAC
Statistics
Matches: 32, Mismatches: 3, Indels: 5
0.80 0.08 0.12
Matches are distributed among these distances:
13 8 0.25
14 8 0.25
15 16 0.50
ACGTcount: A:0.44, C:0.00, G:0.02, T:0.54
Consensus pattern (15 bp):
TATTTAATTATAATA
Found at i:40280317 original size:120 final size:120
Alignment explanation
Indices: 40280192--40280414 Score: 403
Period size: 120 Copynumber: 1.9 Consensus size: 120
40280182 ATTAGTTATA
* *
40280192 ATCATATATTATGATTTGAGTAAATTCATAGAATAAT-TTTATTTATTAAGAATTTTATTAAATT
1 ATCATATATTATGATTTGAGTAAATTCATAGAAGAATATTAATTT-TTAAGAATTTTATTAAATT
40280256 ATATATTTTAATTATAATATATTTAATAATAATTATGTTAATTTATATTTTACAGT
65 ATATATTTTAATTATAATATATTTAATAATAATTATGTTAATTTATATTTTACAGT
*
40280312 ATCATATATTATGATTTGAGTAAATTCATATAAGAATATTAATTTTTAAGAATTTTATTAAATTA
1 ATCATATATTATGATTTGAGTAAATTCATAGAAGAATATTAATTTTTAAGAATTTTATTAAATTA
40280377 TATATTTTAATTATAATATATTTAATAATAATTATGTT
66 TATATTTTAATTATAATATATTTAATAATAATTATGTT
40280415 TAAATATGAT
Statistics
Matches: 99, Mismatches: 3, Indels: 2
0.95 0.03 0.02
Matches are distributed among these distances:
120 93 0.94
121 6 0.06
ACGTcount: A:0.42, C:0.02, G:0.06, T:0.50
Consensus pattern (120 bp):
ATCATATATTATGATTTGAGTAAATTCATAGAAGAATATTAATTTTTAAGAATTTTATTAAATTA
TATATTTTAATTATAATATATTTAATAATAATTATGTTAATTTATATTTTACAGT
Found at i:40280397 original size:16 final size:16
Alignment explanation
Indices: 40280376--40280417 Score: 52
Period size: 15 Copynumber: 2.7 Consensus size: 16
40280366 TTATTAAATT
*
40280376 ATATATTTTAATTATA
1 ATATATTTTAATAATA
40280392 ATATA-TTTAATAATA
1 ATATATTTTAATAATA
40280407 AT-TATGTTTAA
1 ATATAT-TTTAA
40280418 ATATGATTAA
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
14 2 0.09
15 11 0.48
16 10 0.43
ACGTcount: A:0.45, C:0.00, G:0.02, T:0.52
Consensus pattern (16 bp):
ATATATTTTAATAATA
Found at i:40280402 original size:15 final size:15
Alignment explanation
Indices: 40280367--40280408 Score: 52
Period size: 15 Copynumber: 2.9 Consensus size: 15
40280357 TTAAGAATTT
*
40280367 TATTAAATTAT-ATA
1 TATTTAATTATAATA
40280381 T-TTTAATTATAATA
1 TATTTAATTATAATA
*
40280395 TATTTAATAATAAT
1 TATTTAATTATAAT
40280409 TATGTTTAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
13 8 0.33
14 5 0.21
15 11 0.46
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (15 bp):
TATTTAATTATAATA
Found at i:40280528 original size:154 final size:156
Alignment explanation
Indices: 40280351--40280664 Score: 560
Period size: 154 Copynumber: 2.0 Consensus size: 156
40280341 ATAAGAATAT
* *
40280351 TAATTTTTAAGAATTTTATTAAATTATATATTTTAATTATAATATATTTAATAATAATTATGTTT
1 TAATTATTAAGAATTTTATTAAATTATATATTTTAATTAAAATATATTTAATAATAATTATGTTT
40280416 AAATATGATTAAATTATTTATTATTGAT-AT-TAATCTTATTAAAATTTAAATAACAATAACAAT
66 AAATATGATTAAATTATTTATTATTGATAATATAATCTTATTAAAATTTAAATAACAATAACAAT
*
40280479 AATAATTTACTAAAACAAATTTATGC
131 AATAATTTACCAAAACAAATTTATGC
40280505 TAATTATTAAGAATTTTATTAAATTATATATTTTAATTAAAATATATTTAATAATAATTATGTTT
1 TAATTATTAAGAATTTTATTAAATTATATATTTTAATTAAAATATATTTAATAATAATTATGTTT
40280570 AAATATGATTAAATTATTTATTATTGATAATAATAATCTTATTAAAATTTAAATAACAATAACAA
66 AAATATGATTAAATTATTTATTATTGATAAT-ATAATCTTATTAAAATTTAAATAACAATAACAA
* *
40280635 TAATCATTTACCAAAACAAATTTCTGC
130 TAATAATTTACCAAAACAAATTTATGC
40280662 TAA
1 TAA
40280665 GGGTATTCTA
Statistics
Matches: 152, Mismatches: 5, Indels: 3
0.95 0.03 0.02
Matches are distributed among these distances:
154 91 0.60
155 2 0.01
157 59 0.39
ACGTcount: A:0.47, C:0.05, G:0.03, T:0.45
Consensus pattern (156 bp):
TAATTATTAAGAATTTTATTAAATTATATATTTTAATTAAAATATATTTAATAATAATTATGTTT
AAATATGATTAAATTATTTATTATTGATAATATAATCTTATTAAAATTTAAATAACAATAACAAT
AATAATTTACCAAAACAAATTTATGC
Found at i:40280545 original size:18 final size:17
Alignment explanation
Indices: 40280517--40280551 Score: 52
Period size: 18 Copynumber: 2.0 Consensus size: 17
40280507 ATTATTAAGA
*
40280517 ATTTTATTAAATTATAT
1 ATTTTATTAAAATATAT
40280534 ATTTTAATTAAAATATAT
1 ATTTT-ATTAAAATATAT
40280552 TTAATAATAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 5 0.31
18 11 0.69
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (17 bp):
ATTTTATTAAAATATAT
Found at i:40280805 original size:16 final size:16
Alignment explanation
Indices: 40280784--40280822 Score: 51
Period size: 16 Copynumber: 2.4 Consensus size: 16
40280774 TTGATTTGCT
*
40280784 ATTACACAGCTTTTCC
1 ATTACACAGCTATTCC
**
40280800 ATTACACCTCTATTCC
1 ATTACACAGCTATTCC
40280816 ATTACAC
1 ATTACAC
40280823 CTCTAATCCA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
16 20 1.00
ACGTcount: A:0.28, C:0.33, G:0.03, T:0.36
Consensus pattern (16 bp):
ATTACACAGCTATTCC
Found at i:40280823 original size:16 final size:16
Alignment explanation
Indices: 40280797--40280853 Score: 87
Period size: 16 Copynumber: 3.6 Consensus size: 16
40280787 ACACAGCTTT
* *
40280797 TCCATTACACCTCTAT
1 TCCAATACACCTCTAA
*
40280813 TCCATTACACCTCTAA
1 TCCAATACACCTCTAA
40280829 TCCAATACACCTCTAA
1 TCCAATACACCTCTAA
40280845 TCCAATACA
1 TCCAATACA
40280854 GCGAACCAAA
Statistics
Matches: 39, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
16 39 1.00
ACGTcount: A:0.33, C:0.37, G:0.00, T:0.30
Consensus pattern (16 bp):
TCCAATACACCTCTAA
Found at i:40281074 original size:16 final size:16
Alignment explanation
Indices: 40281005--40281072 Score: 109
Period size: 16 Copynumber: 4.2 Consensus size: 16
40280995 TTTGGTTCGC
40281005 TGTATTGGATTAGAGG
1 TGTATTGGATTAGAGG
40281021 TGTATTGGATTAGAGG
1 TGTATTGGATTAGAGG
40281037 TGTATTGGATTAGAGG
1 TGTATTGGATTAGAGG
* * *
40281053 TGTAATGGAATAGATG
1 TGTATTGGATTAGAGG
40281069 TGTA
1 TGTA
40281073 ATAGCAAATC
Statistics
Matches: 49, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 49 1.00
ACGTcount: A:0.28, C:0.00, G:0.35, T:0.37
Consensus pattern (16 bp):
TGTATTGGATTAGAGG
Found at i:40281104 original size:45 final size:44
Alignment explanation
Indices: 40281053--40281147 Score: 127
Period size: 45 Copynumber: 2.1 Consensus size: 44
40281043 GGATTAGAGG
* * *
40281053 TGTAATGGAATAGATGTGTAATAGCAAATCAACTGTTTGGTTGAA
1 TGTAATGGAATAGAGGCGTAATAGCAAAAC-ACTGTTTGGTTGAA
* **
40281098 TGTAATGGAATAGAGGCGTAATAGTAAAACTGTGTTTGGTTGAA
1 TGTAATGGAATAGAGGCGTAATAGCAAAACACTGTTTGGTTGAA
40281142 TGTAAT
1 TGTAAT
40281148 AGAGGTGTAA
Statistics
Matches: 44, Mismatches: 6, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
44 18 0.41
45 26 0.59
ACGTcount: A:0.35, C:0.05, G:0.26, T:0.34
Consensus pattern (44 bp):
TGTAATGGAATAGAGGCGTAATAGCAAAACACTGTTTGGTTGAA
Found at i:40281330 original size:18 final size:17
Alignment explanation
Indices: 40281309--40281343 Score: 52
Period size: 18 Copynumber: 2.0 Consensus size: 17
40281299 TTATTATTTA
*
40281309 ATATATTTTAATTAAAAT
1 ATATAATTTAA-TAAAAT
40281327 ATATAATTTAATAAAAT
1 ATATAATTTAATAAAAT
40281344 TCTTAATAAT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 6 0.38
18 10 0.62
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (17 bp):
ATATAATTTAATAAAAT
Found at i:40281337 original size:28 final size:27
Alignment explanation
Indices: 40281267--40281339 Score: 76
Period size: 27 Copynumber: 2.7 Consensus size: 27
40281257 TTTATTATCA
*
40281267 AAAATAAATAATTTAATCATATTTAAAC
1 AAAATATATAATTTAAT-ATATTTAAAC
* * **
40281295 ATAAT-TATTATTTAATATATTTTAATT
1 AAAATATATAATTTAATATA-TTTAAAC
40281322 AAAATATATAATTTAATA
1 AAAATATATAATTTAATA
40281340 AAATTCTTAA
Statistics
Matches: 36, Mismatches: 7, Indels: 4
0.77 0.15 0.09
Matches are distributed among these distances:
26 3 0.08
27 18 0.50
28 15 0.42
ACGTcount: A:0.52, C:0.03, G:0.00, T:0.45
Consensus pattern (27 bp):
AAAATATATAATTTAATATATTTAAAC
Found at i:40281477 original size:18 final size:17
Alignment explanation
Indices: 40281456--40281490 Score: 52
Period size: 18 Copynumber: 2.0 Consensus size: 17
40281446 TTATTATTAA
*
40281456 ATATATTTTAATTAAAAT
1 ATATAATTTAA-TAAAAT
40281474 ATATAATTTAATAAAAT
1 ATATAATTTAATAAAAT
40281491 TCTTAATAAT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 6 0.38
18 10 0.62
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (17 bp):
ATATAATTTAATAAAAT
Found at i:40281502 original size:147 final size:149
Alignment explanation
Indices: 40281228--40281502 Score: 500
Period size: 147 Copynumber: 1.9 Consensus size: 149
40281218 ATGATTATTG
*
40281228 TTATTGTTATTTAAATTTTAATAAGATTATTTATTATCAAAAATAAATAATTTAATCATATTTAA
1 TTATTGTTATTTAAATTTTAATAAGATTATTTAATATCAAAAATAAATAATTTAATCATATTTAA
*
40281293 ACATAATTATTATTTAATATATTTTAATTAAAATATATAATTTAATAAAATTCTTAATAATTAGC
66 ACATAATTATTATTAAATATATTTTAATTAAAATATATAATTTAATAAAATTCTTAATAATTAGC
40281358 AGAAATTTGTTTTGGTAAA
131 AGAAATTTGTTTTGGTAAA
* *
40281377 TTATT-TTATTTAAATTTTAATAAGATTA-TTAATATCAATAATAAATAATTTACTCATATTTAA
1 TTATTGTTATTTAAATTTTAATAAGATTATTTAATATCAAAAATAAATAATTTAATCATATTTAA
40281440 ACATAATTATTATTAAATATATTTTAATTAAAATATATAATTTAATAAAATTCTTAATAATTA
66 ACATAATTATTATTAAATATATTTTAATTAAAATATATAATTTAATAAAATTCTTAATAATTA
40281503 ATATTCTTAT
Statistics
Matches: 122, Mismatches: 4, Indels: 2
0.95 0.03 0.02
Matches are distributed among these distances:
147 94 0.77
148 23 0.19
149 5 0.04
ACGTcount: A:0.46, C:0.04, G:0.03, T:0.47
Consensus pattern (149 bp):
TTATTGTTATTTAAATTTTAATAAGATTATTTAATATCAAAAATAAATAATTTAATCATATTTAA
ACATAATTATTATTAAATATATTTTAATTAAAATATATAATTTAATAAAATTCTTAATAATTAGC
AGAAATTTGTTTTGGTAAA
Found at i:40281598 original size:18 final size:17
Alignment explanation
Indices: 40281558--40281610 Score: 53
Period size: 16 Copynumber: 3.4 Consensus size: 17
40281548 AAATATAAAT
40281558 TAAAATA-ATAA-TT-A
1 TAAAATATATAATTTAA
*
40281572 TTAAATATAT--TTTAA
1 TAAAATATATAATTTAA
40281587 TTAAAATATATAATTTAA
1 -TAAAATATATAATTTAA
40281605 TAAAAT
1 TAAAAT
40281611 TCTAATAATC
Statistics
Matches: 31, Mismatches: 2, Indels: 9
0.74 0.05 0.21
Matches are distributed among these distances:
14 8 0.26
15 3 0.10
16 9 0.29
17 6 0.19
18 5 0.16
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (17 bp):
TAAAATATATAATTTAA
Found at i:40281668 original size:60 final size:59
Alignment explanation
Indices: 40281484--40281670 Score: 157
Period size: 60 Copynumber: 3.1 Consensus size: 59
40281474 ATATAATTTA
*
40281484 ATAAAATTCTTAATAATTAATATTCTTATATGAATTTACTCAAATCATAATATATGATACT
1 ATAAAATTC-TAATAA-TAATATTCTTATATGAATTTACTAAAATCATAATATATGATACT
* * ** * * * ** * * * *
40281545 GTAAAATAT-AAATTAA-AATAATAATTAT-TAAATATATTTTAATTAAAATATATAAT-TT
1 ATAAAAT-TCTAA-TAATAAT-ATTCTTATATGAATTTACTAAAATCATAATATATGATACT
40281603 AATAAAATTCTAATAATCAATATTCTTATATGAATTTACTAAAATCATAATATATGATACT
1 -ATAAAATTCTAATAAT-AATATTCTTATATGAATTTACTAAAATCATAATATATGATACT
40281664 ATAAAAT
1 ATAAAAT
40281671 ATAATTTGAA
Statistics
Matches: 91, Mismatches: 26, Indels: 19
0.67 0.19 0.14
Matches are distributed among these distances:
58 5 0.05
59 37 0.41
60 38 0.42
61 10 0.11
62 1 0.01
ACGTcount: A:0.50, C:0.06, G:0.03, T:0.41
Consensus pattern (59 bp):
ATAAAATTCTAATAATAATATTCTTATATGAATTTACTAAAATCATAATATATGATACT
Found at i:40281669 original size:119 final size:120
Alignment explanation
Indices: 40281436--40281730 Score: 495
Period size: 119 Copynumber: 2.5 Consensus size: 120
40281426 TTACTCATAT
*
40281436 TTAAACATAATTATTATTAAATATATTTTAATTAAAATATATAATTTAATAAAATTCTTAATAAT
1 TTAAA-ATAATAATTATTAAATATATTTTAATTAAAATATATAATTTAATAAAATTCTTAATAAT
* * *
40281501 TAATATTCTTATATGAATTTACTCAAATCATAATATATGATACTGTAAAATATAAA
65 CAATATTCTTATATGAATTTACTAAAATCATAATATATGATACTATAAAATATAAA
40281557 TTAAAATAATAATTATTAAATATATTTTAATTAAAATATATAATTTAATAAAATTC-TAATAATC
1 TTAAAATAATAATTATTAAATATATTTTAATTAAAATATATAATTTAATAAAATTCTTAATAATC
*
40281621 AATATTCTTATATGAATTTACTAAAATCATAATATATGATACTATAAAATATAAT
66 AATATTCTTATATGAATTTACTAAAATCATAATATATGATACTATAAAATATAAA
* *
40281676 TTGAAATAATTAA-TATTAAATATATTTTAATTAAAATATATGATTTAATAAAATT
1 TTAAAATAA-TAATTATTAAATATATTTTAATTAAAATATATAATTTAATAAAATT
40281731 TAAAATAATT
Statistics
Matches: 166, Mismatches: 7, Indels: 4
0.94 0.04 0.02
Matches are distributed among these distances:
119 108 0.65
120 53 0.32
121 5 0.03
ACGTcount: A:0.50, C:0.04, G:0.02, T:0.43
Consensus pattern (120 bp):
TTAAAATAATAATTATTAAATATATTTTAATTAAAATATATAATTTAATAAAATTCTTAATAATC
AATATTCTTATATGAATTTACTAAAATCATAATATATGATACTATAAAATATAAA
Found at i:40284764 original size:29 final size:31
Alignment explanation
Indices: 40284708--40284766 Score: 86
Period size: 29 Copynumber: 2.0 Consensus size: 31
40284698 AATTTCATAT
* *
40284708 CTTAATGTGAGAACAATTGTCAAGTTTAAGC
1 CTTAATATGAGAACAATTGTCAAATTTAAGC
40284739 CTTAATATGAG-A-AATTGTCAAATTTAAG
1 CTTAATATGAGAACAATTGTCAAATTTAAG
40284767 GATTAACTTA
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
29 15 0.58
30 1 0.04
31 10 0.38
ACGTcount: A:0.39, C:0.10, G:0.17, T:0.34
Consensus pattern (31 bp):
CTTAATATGAGAACAATTGTCAAATTTAAGC
Found at i:40287966 original size:31 final size:31
Alignment explanation
Indices: 40287903--40287970 Score: 84
Period size: 31 Copynumber: 2.2 Consensus size: 31
40287893 TTAACAGCCT
* *
40287903 AGTGATTTAAATAAAAACTTTTGAGTAATTC
1 AGTGACTTAAATAAAAACTTTTGAATAATTC
* *
40287934 AGTGACTTAAATGAAAACTTTCT-AATAGTTC
1 AGTGACTTAAATAAAAACTTT-TGAATAATTC
40287965 AGTGAC
1 AGTGAC
40287971 CATTTTTTAA
Statistics
Matches: 32, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
31 31 0.97
32 1 0.03
ACGTcount: A:0.40, C:0.10, G:0.15, T:0.35
Consensus pattern (31 bp):
AGTGACTTAAATAAAAACTTTTGAATAATTC
Found at i:40290246 original size:46 final size:47
Alignment explanation
Indices: 40290178--40290277 Score: 193
Period size: 46 Copynumber: 2.1 Consensus size: 47
40290168 ACTTTCATAC
40290178 CAAGCTGAGCTGCCATTGCCATAACTCAAAAGACAACAAAGCTTGAG
1 CAAGCTGAGCTGCCATTGCCATAACTCAAAAGACAACAAAGCTTGAG
40290225 CAAGCT-AGCTGCCATTGCCATAACTCAAAAGACAACAAAGCTTGAG
1 CAAGCTGAGCTGCCATTGCCATAACTCAAAAGACAACAAAGCTTGAG
40290271 CAAGCTG
1 CAAGCTG
40290278 TCTTCATCAG
Statistics
Matches: 52, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
46 46 0.88
47 6 0.12
ACGTcount: A:0.38, C:0.26, G:0.19, T:0.17
Consensus pattern (47 bp):
CAAGCTGAGCTGCCATTGCCATAACTCAAAAGACAACAAAGCTTGAG
Found at i:40292024 original size:41 final size:41
Alignment explanation
Indices: 40291973--40292132 Score: 212
Period size: 42 Copynumber: 3.9 Consensus size: 41
40291963 CAAACAAAAA
**
40291973 CGCCGCTAAAGGTCATGTTCTTTAGCGGCGTTTTTTTTAAG
1 CGCCGCTAAAGAACATGTTCTTTAGCGGCGTTTTTTTTAAG
*
40292014 CGCCTCTAAAGAACATGTTCTTTAGCGGCGTTTTTTTCTAAG
1 CGCCGCTAAAGAACATGTTCTTTAGCGGCGTTTTTTT-TAAG
* * *
40292056 CGACGCTAAAGAACATGTTCTTTAGTGGCGATTTTTATTAAG
1 CGCCGCTAAAGAACATGTTCTTTAGCGGCG-TTTTTTTTAAG
* * * *
40292098 CACCGCTAAAGAACATGATCCTTAGCGGCGCTTTT
1 CGCCGCTAAAGAACATGTTCTTTAGCGGCGTTTTT
40292133 ATACAAAAAC
Statistics
Matches: 104, Mismatches: 13, Indels: 4
0.86 0.11 0.03
Matches are distributed among these distances:
41 38 0.37
42 60 0.58
43 6 0.06
ACGTcount: A:0.23, C:0.21, G:0.21, T:0.35
Consensus pattern (41 bp):
CGCCGCTAAAGAACATGTTCTTTAGCGGCGTTTTTTTTAAG
Found at i:40292538 original size:21 final size:21
Alignment explanation
Indices: 40292514--40292564 Score: 93
Period size: 21 Copynumber: 2.4 Consensus size: 21
40292504 TTCTTTTGAA
40292514 CCTCTGCTTCTCTCGCTGCAG
1 CCTCTGCTTCTCTCGCTGCAG
*
40292535 CCTCTGCTTCTCTCGCTGCCG
1 CCTCTGCTTCTCTCGCTGCAG
40292556 CCTCTGCTT
1 CCTCTGCTT
40292565 TAAGTTGTAG
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
21 29 1.00
ACGTcount: A:0.02, C:0.45, G:0.18, T:0.35
Consensus pattern (21 bp):
CCTCTGCTTCTCTCGCTGCAG
Found at i:40292617 original size:87 final size:87
Alignment explanation
Indices: 40292449--40292608 Score: 275
Period size: 87 Copynumber: 1.8 Consensus size: 87
40292439 TTCTACTCTG
*
40292449 CTCTGCTTCTCTCGCTGCAGCCTCTGCTTTAAGTTGTAGCTGGAGTTCTTCATATTTCTTTTGAA
1 CTCTGCTTCTCTCGCTGCAGCCTCTGCTTTAAGTTGTAGCTGGAGTTCTTCATATTTCCTTTGAA
** *
40292514 CCTCTGCTTCTCTCGCTGCAGC
66 CCTCAACTTCGCTCGCTGCAGC
*
40292536 CTCTGCTTCTCTCGCTGCCGCCTCTGCTTTAAGTTGTAGCTGGAGTTCTTCATATTTCCTTTGAA
1 CTCTGCTTCTCTCGCTGCAGCCTCTGCTTTAAGTTGTAGCTGGAGTTCTTCATATTTCCTTTGAA
40292601 CCTCAACT
66 CCTCAACT
40292609 GTGGTCGCTT
Statistics
Matches: 69, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
87 69 1.00
ACGTcount: A:0.12, C:0.30, G:0.17, T:0.40
Consensus pattern (87 bp):
CTCTGCTTCTCTCGCTGCAGCCTCTGCTTTAAGTTGTAGCTGGAGTTCTTCATATTTCCTTTGAA
CCTCAACTTCGCTCGCTGCAGC
Found at i:40293060 original size:43 final size:43
Alignment explanation
Indices: 40292899--40293103 Score: 256
Period size: 42 Copynumber: 4.8 Consensus size: 43
40292889 GCGTCGCTAA
* * *
40292899 CTTTAGCGGCGCTTTTCCCATAAACGCCGCTAAAGACCATGAT
1 CTTTAGCGGCGCTTTTCCCACAAACGCCGCTAAAGACCAAGAC
* *
40292942 CTTTAGCGGCGC--TTCCCTACAAATGCCACTAAAGACCAAGAC
1 CTTTAGCGGCGCTTTTCCC-ACAAACGCCGCTAAAGACCAAGAC
* *
40292984 CTTTAGCGGCGC-TTCCCCACAAACGTCGCTAAAGACCAAGAC
1 CTTTAGCGGCGCTTTTCCCACAAACGCCGCTAAAGACCAAGAC
* * * *
40293026 CTTTAGCGACGCTTTTCCCACAAACGCCGCTAAAGA-TATTGAG
1 CTTTAGCGGCGCTTTTCCCACAAACGCCGCTAAAGACCA-AGAC
40293069 CTTTAGCGGCGCTTTTTCCCACAAACGCCGCTAAA
1 CTTTAGCGGCGC-TTTTCCCACAAACGCCGCTAAA
40293104 AATATATCTT
Statistics
Matches: 141, Mismatches: 16, Indels: 9
0.85 0.10 0.05
Matches are distributed among these distances:
41 5 0.04
42 64 0.45
43 50 0.35
44 22 0.16
ACGTcount: A:0.27, C:0.32, G:0.18, T:0.22
Consensus pattern (43 bp):
CTTTAGCGGCGCTTTTCCCACAAACGCCGCTAAAGACCAAGAC
Found at i:40293131 original size:16 final size:16
Alignment explanation
Indices: 40293101--40293130 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
40293091 AAACGCCGCT
40293101 AAAAATATATCTTTTA
1 AAAAATATATCTTTTA
40293117 AAAAATATAT-TTTT
1 AAAAATATATCTTTT
40293131 TTCAAATAAT
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:0.03, G:0.00, T:0.47
Consensus pattern (16 bp):
AAAAATATATCTTTTA
Found at i:40293442 original size:43 final size:43
Alignment explanation
Indices: 40293376--40293466 Score: 130
Period size: 43 Copynumber: 2.1 Consensus size: 43
40293366 ATATATGCAA
* * * *
40293376 GGTAATAAAATATACAATGCATTTTCTTAATCAAGTAAATCTT
1 GGTAATAAAAGATACAATACATTTACTTAATCAAGGAAATCTT
*
40293419 GGTAATAAAAGATATAATACATTTACTTAATCAAGGAAATCTT
1 GGTAATAAAAGATACAATACATTTACTTAATCAAGGAAATCTT
40293462 -GTAAT
1 GGTAAT
40293467 GAACTCAAAG
Statistics
Matches: 43, Mismatches: 5, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
42 5 0.12
43 38 0.88
ACGTcount: A:0.44, C:0.10, G:0.11, T:0.35
Consensus pattern (43 bp):
GGTAATAAAAGATACAATACATTTACTTAATCAAGGAAATCTT
Found at i:40298390 original size:41 final size:41
Alignment explanation
Indices: 40298333--40298577 Score: 382
Period size: 41 Copynumber: 6.0 Consensus size: 41
40298323 TCAAAAGCGG
* *
40298333 GCATTAGCGGCGCTTTTTCAAAAATGCCGCTAAAGGCCCAA
1 GCATTAGCGGCGCTTTTTCAAAAACGCCGCTAAAGGCCCGA
*
40298374 GCATTAGCGGCGCTTTTTAAAAAACGCCGCTAAAGGCCCGA
1 GCATTAGCGGCGCTTTTTCAAAAACGCCGCTAAAGGCCCGA
*
40298415 GCATTAGCGGCGCTTATTCAAAAACGCCGCTAAAGGCCCGA
1 GCATTAGCGGCGCTTTTTCAAAAACGCCGCTAAAGGCCCGA
* *
40298456 GCATTAGCGGCGCTTCTTCACAAACGCCGCTAAAGGCCCGA
1 GCATTAGCGGCGCTTTTTCAAAAACGCCGCTAAAGGCCCGA
* * *
40298497 GCATTAGTGGCGCTTATTCAAAAACGCCGCTAAAGGCCCGT
1 GCATTAGCGGCGCTTTTTCAAAAACGCCGCTAAAGGCCCGA
* *
40298538 GAATTAGCGGCGCTTTTTTTAAAAACGCCGCTAAAGGCCC
1 GCATTAGCGGCGC-TTTTTCAAAAACGCCGCTAAAGGCCC
40298578 CAAAACTCAG
Statistics
Matches: 188, Mismatches: 15, Indels: 1
0.92 0.07 0.00
Matches are distributed among these distances:
41 164 0.87
42 24 0.13
ACGTcount: A:0.28, C:0.28, G:0.24, T:0.20
Consensus pattern (41 bp):
GCATTAGCGGCGCTTTTTCAAAAACGCCGCTAAAGGCCCGA
Found at i:40298759 original size:41 final size:41
Alignment explanation
Indices: 40298631--40298763 Score: 141
Period size: 40 Copynumber: 3.3 Consensus size: 41
40298621 CACTTTTTGG
* **
40298631 AAAA-CGCCGGTAATGCTT-ATTTTTAGCGGCGTTTTCCA-
1 AAAAGCGCCGCTAATGCTTGATTTTTAGCGGCGTTTTTTAT
* ** *
40298669 AAAAGCGCCGCTAATGCTCGACCTTTAGCAGCG-TTTTTAT
1 AAAAGCGCCGCTAATGCTTGATTTTTAGCGGCGTTTTTTAT
*
40298709 AAAAGCGCCGCTAATGCTTGATTTTTAGTGGCGTTTTTTAT
1 AAAAGCGCCGCTAATGCTTGATTTTTAGCGGCGTTTTTTAT
*
40298750 CCAAA-CGCCGCTAA
1 -AAAAGCGCCGCTAA
40298764 AAACGCCGCT
Statistics
Matches: 77, Mismatches: 13, Indels: 7
0.79 0.13 0.07
Matches are distributed among these distances:
38 4 0.05
39 16 0.21
40 38 0.49
41 16 0.21
42 3 0.04
ACGTcount: A:0.25, C:0.23, G:0.20, T:0.32
Consensus pattern (41 bp):
AAAAGCGCCGCTAATGCTTGATTTTTAGCGGCGTTTTTTAT
Found at i:40298769 original size:12 final size:12
Alignment explanation
Indices: 40298752--40298777 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
40298742 TTTTTTATCC
40298752 AAACGCCGCTAA
1 AAACGCCGCTAA
40298764 AAACGCCGCTAA
1 AAACGCCGCTAA
40298776 AA
1 AA
40298778 GCCTATTTTG
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:0.46, C:0.31, G:0.15, T:0.08
Consensus pattern (12 bp):
AAACGCCGCTAA
Found at i:40303686 original size:26 final size:26
Alignment explanation
Indices: 40303654--40303711 Score: 98
Period size: 26 Copynumber: 2.2 Consensus size: 26
40303644 TTAAAACGCC
40303654 AGTTATAACCATAAATGAGTTATGTA
1 AGTTATAACCATAAATGAGTTATGTA
* *
40303680 ATTTATAACCATAAATGATTTATGTA
1 AGTTATAACCATAAATGAGTTATGTA
40303706 AGTTAT
1 AGTTAT
40303712 GTAAGTTATT
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
26 29 1.00
ACGTcount: A:0.41, C:0.07, G:0.12, T:0.40
Consensus pattern (26 bp):
AGTTATAACCATAAATGAGTTATGTA
Found at i:40303713 original size:9 final size:9
Alignment explanation
Indices: 40303699--40303940 Score: 180
Period size: 9 Copynumber: 27.4 Consensus size: 9
40303689 CATAAATGAT
40303699 TTATGTAAG
1 TTATGTAAG
40303708 TTATGTAAG
1 TTATGTAAG
* *
40303717 TTATTTAGG
1 TTATGTAAG
**
40303726 CAATGT-A-
1 TTATGTAAG
*
40303733 TTATGTAAA
1 TTATGTAAG
*
40303742 TAATGTAAG
1 TTATGTAAG
*
40303751 TTA-GGAATG
1 TTATGTAA-G
40303760 TTATGT-A-
1 TTATGTAAG
40303767 TTATGTAAG
1 TTATGTAAG
*
40303776 TTATTTAAG
1 TTATGTAAG
40303785 TTATGTAAG
1 TTATGTAAG
40303794 TTATGTAAG
1 TTATGTAAG
* *
40303803 TTATTTAAT
1 TTATGTAAG
40303812 TTATGTAAG
1 TTATGTAAG
40303821 TTATGTAAG
1 TTATGTAAG
* *
40303830 TTATTTAGG
1 TTATGTAAG
**
40303839 CAATGT-A-
1 TTATGTAAG
*
40303846 TTATGTAAA
1 TTATGTAAG
*
40303855 TAATGTAAG
1 TTATGTAAG
*
40303864 TTA-GGAAGG
1 TTATGTAA-G
40303873 TTATGT-A-
1 TTATGTAAG
40303880 TTATGTAAG
1 TTATGTAAG
*
40303889 TTATTTAATAAG
1 TTA--T-GTAAG
40303901 TTATGTAAG
1 TTATGTAAG
* *
40303910 TTATTTAAT
1 TTATGTAAG
*
40303919 TTATGTAAC
1 TTATGTAAG
40303928 TTATGTAAG
1 TTATGTAAG
40303937 TTAT
1 TTAT
40303941 TTAGGCAATG
Statistics
Matches: 179, Mismatches: 39, Indels: 30
0.72 0.16 0.12
Matches are distributed among these distances:
7 20 0.11
8 10 0.06
9 138 0.77
10 3 0.02
11 1 0.01
12 7 0.04
ACGTcount: A:0.35, C:0.01, G:0.18, T:0.46
Consensus pattern (9 bp):
TTATGTAAG
Found at i:40303748 original size:34 final size:36
Alignment explanation
Indices: 40303699--40303952 Score: 142
Period size: 34 Copynumber: 6.9 Consensus size: 36
40303689 CATAAATGAT
40303699 TTATGTAAGTTATGTAAGTTATTTAGGCAATGT-A-
1 TTATGTAAGTTATGTAAGTTATTTAGGCAATGTAAG
* * * *
40303733 TTATGTAAATAATGTAAGTTAGGAATGTTATGTATTATGTAAG
1 TTATGTAAGTTATGTAAGTT----AT-TTAGGCA--ATGTAAG
* * * ** * *
40303776 TTATTTAAGTTATGTAAGTTATGTAAGTTATTTAAT
1 TTATGTAAGTTATGTAAGTTATTTAGGCAATGTAAG
40303812 TTATGTAAGTTATGTAAGTTATTTAGGCAATGT-A-
1 TTATGTAAGTTATGTAAGTTATTTAGGCAATGTAAG
* * *** **
40303846 TTATGTAAATAATGTAAGTTAGGAAGGTTATGT-A-
1 TTATGTAAGTTATGTAAGTTATTTAGGCAATGTAAG
* * * ** * *
40303880 TTATGTAAGTTATTTAATAAGTTATGTAAGTTATTTAAT
1 TTATGTAAGTTA--T-GTAAGTTATTTAGGCAATGTAAG
*
40303919 TTATGTAACTTATGTAAGTTATTTAGGCAATGTA
1 TTATGTAAGTTATGTAAGTTATTTAGGCAATGTA
40303953 CTATGTTAGT
Statistics
Matches: 167, Mismatches: 39, Indels: 26
0.72 0.17 0.11
Matches are distributed among these distances:
34 55 0.33
35 1 0.01
36 48 0.29
37 16 0.10
38 7 0.04
39 18 0.11
41 4 0.02
42 1 0.01
43 17 0.10
ACGTcount: A:0.35, C:0.02, G:0.19, T:0.45
Consensus pattern (36 bp):
TTATGTAAGTTATGTAAGTTATTTAGGCAATGTAAG
Found at i:40303749 original size:43 final size:43
Alignment explanation
Indices: 40303701--40303828 Score: 111
Period size: 43 Copynumber: 2.9 Consensus size: 43
40303691 TAAATGATTT
40303701 ATGTAAGTTATGTAAGTTATTTAGGCAATGT-A-TTATGTAAATA
1 ATGTAAGTTATGTAAGTTATTTA--CAATGTAAGTTATGTAAATA
* * ** * * *
40303744 ATGTAAGTTA-GGAATGTTATGTATTATGTAAGTTATTTAAGTT
1 ATGTAAGTTATGTAA-GTTATTTACAATGTAAGTTATGTAAATA
40303787 ATGTAAGTTATGTAAGTTATTTA-ATTTATGTAAGTTATGTAA
1 ATGTAAGTTATGTAAGTTATTTACA---ATGTAAGTTATGTAA
40303829 GTTATTTAGG
Statistics
Matches: 67, Mismatches: 11, Indels: 12
0.74 0.12 0.13
Matches are distributed among these distances:
41 4 0.06
42 4 0.06
43 42 0.63
44 3 0.04
45 14 0.21
ACGTcount: A:0.35, C:0.01, G:0.19, T:0.45
Consensus pattern (43 bp):
ATGTAAGTTATGTAAGTTATTTACAATGTAAGTTATGTAAATA
Found at i:40303831 original size:113 final size:107
Alignment explanation
Indices: 40303697--40303958 Score: 443
Period size: 113 Copynumber: 2.4 Consensus size: 107
40303687 ACCATAAATG
*
40303697 ATTTATGTAAGTTATGTAAGTTATTTAGGCAATGTATTATGTAAATAATGTAAGTTAGGAATGTT
1 ATTTATGTAAGTTATGTAAGTTATTTAGGCAATGTATTATGTAAATAATGTAAGTTAGGAAGGTT
40303762 ATGTATTATGTAAGTTATTTAAGTTATGTAAGTTATGTAAGTTATTTA
66 ATGTATTATGTAAGTTATTT-A---A--TAAGTTATGTAAGTTATTTA
40303810 ATTTATGTAAGTTATGTAAGTTATTTAGGCAATGTATTATGTAAATAATGTAAGTTAGGAAGGTT
1 ATTTATGTAAGTTATGTAAGTTATTTAGGCAATGTATTATGTAAATAATGTAAGTTAGGAAGGTT
40303875 ATGTATTATGTAAGTTATTTAATAAGTTATGTAAGTTATTTA
66 ATGTATTATGTAAGTTATTTAATAAGTTATGTAAGTTATTTA
* *
40303917 ATTTATGTAACTTATGTAAGTTATTTAGGCAATGTACTATGT
1 ATTTATGTAAGTTATGTAAGTTATTTAGGCAATGTATTATGT
40303959 TAGTTATTAT
Statistics
Matches: 146, Mismatches: 3, Indels: 6
0.94 0.02 0.04
Matches are distributed among these distances:
107 60 0.41
109 1 0.01
112 1 0.01
113 84 0.58
ACGTcount: A:0.34, C:0.02, G:0.18, T:0.45
Consensus pattern (107 bp):
ATTTATGTAAGTTATGTAAGTTATTTAGGCAATGTATTATGTAAATAATGTAAGTTAGGAAGGTT
ATGTATTATGTAAGTTATTTAATAAGTTATGTAAGTTATTTA
Found at i:40303992 original size:29 final size:29
Alignment explanation
Indices: 40303960--40304066 Score: 99
Period size: 29 Copynumber: 3.5 Consensus size: 29
40303950 GTACTATGTT
40303960 AGTTATTATGTTATTATATAAGTTATGCA
1 AGTTATTATGTTATTATATAAGTTATGCA
* * * **
40303989 AGTTACATTATATGTGTTCATAT-ATTGTATGTT
1 AGTT--ATTATGT-TATT-ATATAAGT-TATGCA
40304022 AGTTATTATGTTATTATATAAGTTATGCA
1 AGTTATTATGTTATTATATAAGTTATGCA
*
40304051 AGTTATATAAGTTATT
1 AGTTAT-TATGTTATT
40304067 TAAGTTGTGT
Statistics
Matches: 60, Mismatches: 11, Indels: 13
0.71 0.13 0.15
Matches are distributed among these distances:
29 18 0.30
30 13 0.22
31 12 0.20
32 5 0.08
33 12 0.20
ACGTcount: A:0.33, C:0.04, G:0.14, T:0.50
Consensus pattern (29 bp):
AGTTATTATGTTATTATATAAGTTATGCA
Found at i:40304003 original size:33 final size:33
Alignment explanation
Indices: 40303957--40304055 Score: 93
Period size: 33 Copynumber: 3.1 Consensus size: 33
40303947 AATGTACTAT
*
40303957 GTTAGTTATTATGTTATTATATAAGTTATGCAA
1 GTTAATTATTATGTTATTATATAAGTTATGCAA
* * *
40303990 GTTACATTA-TATGTGT-TCATAT-A--T-TGTAT
1 GTTA-ATTATTATGT-TATTATATAAGTTATGCAA
*
40304019 GTTAGTTATTATGTTATTATATAAGTTATGCAA
1 GTTAATTATTATGTTATTATATAAGTTATGCAA
40304052 GTTA
1 GTTA
40304056 TATAAGTTAT
Statistics
Matches: 50, Mismatches: 8, Indels: 16
0.68 0.11 0.22
Matches are distributed among these distances:
28 4 0.08
29 17 0.34
30 2 0.04
32 2 0.04
33 21 0.42
34 4 0.08
ACGTcount: A:0.31, C:0.04, G:0.15, T:0.49
Consensus pattern (33 bp):
GTTAATTATTATGTTATTATATAAGTTATGCAA
Found at i:40304462 original size:25 final size:25
Alignment explanation
Indices: 40304427--40304474 Score: 71
Period size: 25 Copynumber: 1.9 Consensus size: 25
40304417 TTGCTGCATT
*
40304427 ATAATTTAAAAAAT-TAAATTAATAC
1 ATAATTAAAAAAATAT-AATTAATAC
40304452 ATAATTAAAAAAATATAATTAAT
1 ATAATTAAAAAAATATAATTAAT
40304475 CCCTTCAAAA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
25 20 0.95
26 1 0.05
ACGTcount: A:0.62, C:0.02, G:0.00, T:0.35
Consensus pattern (25 bp):
ATAATTAAAAAAATATAATTAATAC
Found at i:40305753 original size:191 final size:191
Alignment explanation
Indices: 40305429--40305809 Score: 618
Period size: 191 Copynumber: 2.0 Consensus size: 191
40305419 GAAGCAACAC
40305429 GGAATTTAAAGAGAAAGGAAAAACAAAGCGAGCATTAGAGAAAGAAAAAATCAAACAGAAAAATG
1 GGAATTTAAAGAGAAAGGAAAAACAAAGCGAGCATTAGAGAAAGAAAAAATCAAACAGAAAAATG
* * *
40305494 AACAGCTATATACGTATTCAACGAAAAAAGTAGGGATTTGGAAAGATTTTTACTAGTCAGCCCAG
66 AACAGCCATATACGGAGTCAACGAAAAAAGTAGGGATTTGGAAAGATTTTTACTAGTCAGCCCAG
* * * *
40305559 ACGAGAAGCAACATTCGATCGAGAAGAGGGGAAATTGTTGTTGAAGGGGTGAAAGGTCTAT
131 ACGAGAAGCAACATTCGACCGAGAAGAGGGGAAATCGTCGTTGAAGAGGTGAAAGGTCTAT
* *
40305620 GGAATTTAAAGAGAAAGGAAAAACAAAGCGGGCATTAGAGAAAGAAAAAATCGAACAGAAAAATG
1 GGAATTTAAAGAGAAAGGAAAAACAAAGCGAGCATTAGAGAAAGAAAAAATCAAACAGAAAAATG
* * * *
40305685 AACAGCCATATACGGAGTCAACGGAGAAATTAGGGATTTGGAAAGTTTTTTACTAGTCAGCCCAG
66 AACAGCCATATACGGAGTCAACGAAAAAAGTAGGGATTTGGAAAGATTTTTACTAGTCAGCCCAG
* * *
40305750 ACGAGAAGCGATATTCGACCGAGAAGAGGGGAAATCGTCGTTGAAGAGGTTAAAGGTCTA
131 ACGAGAAGCAACATTCGACCGAGAAGAGGGGAAATCGTCGTTGAAGAGGTGAAAGGTCTA
40305810 GGGATTTGCA
Statistics
Matches: 174, Mismatches: 16, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
191 174 1.00
ACGTcount: A:0.43, C:0.12, G:0.26, T:0.19
Consensus pattern (191 bp):
GGAATTTAAAGAGAAAGGAAAAACAAAGCGAGCATTAGAGAAAGAAAAAATCAAACAGAAAAATG
AACAGCCATATACGGAGTCAACGAAAAAAGTAGGGATTTGGAAAGATTTTTACTAGTCAGCCCAG
ACGAGAAGCAACATTCGACCGAGAAGAGGGGAAATCGTCGTTGAAGAGGTGAAAGGTCTAT
Found at i:40306501 original size:21 final size:21
Alignment explanation
Indices: 40306477--40306520 Score: 54
Period size: 21 Copynumber: 2.1 Consensus size: 21
40306467 AACCCCTATC
* *
40306477 CCTTAATCTCCAACC-TCTAAA
1 CCTTAAACTCAAACCAT-TAAA
40306498 CCTTAAACTCAAACCATTAAA
1 CCTTAAACTCAAACCATTAAA
40306519 CC
1 CC
40306521 AAGTACCCTT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
21 19 0.95
22 1 0.05
ACGTcount: A:0.39, C:0.36, G:0.00, T:0.25
Consensus pattern (21 bp):
CCTTAAACTCAAACCATTAAA
Found at i:40307461 original size:114 final size:112
Alignment explanation
Indices: 40307260--40307891 Score: 616
Period size: 114 Copynumber: 5.7 Consensus size: 112
40307250 TTTCGGTTTA
* * * * * *
40307260 AAACGATACGTTTTGGTTAAGATTTTTTTGCGGCGCTTTGTATAATGCGCCGCTAATGATGTACT
1 AAACGATGCGTTTTGGTT-A-ATATTTTTACGGCGCTTTTTATAATGTGCCGCTAATGATGTGCT
* *
40307325 TTCGCGGCG--TTTCACTCTAGCGCCACTAATTCTAAAATACCTCAAGACC
64 TTAGCGGCGTTTTTCA-T-AAGCGCCACTAATTCTAAAATACCTCAAGACC
* * * * *
40307374 AAACGATGCGTTTTGGTTAATATTTTTTACGGCGCCTTTCATAATGTGCCGGTAGCT-CTGTGCT
1 AAACGATGCGTTTTGGTTAATA-TTTTTACGGCGCTTTTTATAATGTGCCGCTA-ATGATGTGCT
* *
40307438 TTAGCGGCGTTTGTTCATAAGCGCCACTAATTCTAATATACCTCAATACC
64 TTAGCGGCGTTT-TTCATAAGCGCCACTAATTCTAAAATACCTCAAGACC
* * * * *
40307488 AAACGCTGTGTTTTGGTAAAGATATTTTACGGCGCTTTTTATAATGCGCCGCTAATGATGTGCTT
1 AAACGATGCGTTTTGGTTAATAT-TTTTACGGCGCTTTTTATAATGTGCCGCTAATGATGTGCTT
*
40307553 TAGCGGCGTTTTATTATAAGCGCCACTAATTCTAAAATACCTCAAGACC
65 TAGCGGCGTTTT-TCATAAGCGCCACTAATTCTAAAATACCTCAAGACC
* * * * * * * *
40307602 AAACGATACATTTTTGTTAATATTTTTGCTGCGCTTTTTATATTGTGCCGCTAATGATGTTCGTT
1 AAACGATGCGTTTTGGTTAATATTTTTACGGCGCTTTTTATAATGTGCCGCTAATGATGTGCTTT
*
40307667 AGCGGCGTTTCATT-ATAAGCGCCGCTAATTCTAAAATACCTCAAGACC
66 AGCGGCGTTT--TTCATAAGCGCCACTAATTCTAAAATACCTCAAGACC
* * * *
40307715 AAACAATGCGCTTTT-GTTAATATATTTGCGGCGCTTTTTATAA--T---GC-----A---GCAT
1 AAACGATGCG-TTTTGGTTAATATTTTTACGGCGCTTTTTATAATGTGCCGCTAATGATGTGCTT
*
40307766 TAGCGGCGTTTTTCCATAAGCGCCACTAATTCTAATATACCTCAAGACC
65 TAGCGGCGTTTTT-CATAAGCGCCACTAATTCTAAAATACCTCAAGACC
* * * * ** * * *
40307815 AAACGCTGCGTTTTGGTTAAGATATTCTGCGGCGCTTTTTGCATTGCGCCGCTAATTATGTGCTT
1 AAACGATGCGTTTTGGTTAATAT-TTTTACGGCGCTTTTTATAATGTGCCGCTAATGATGTGCTT
40307880 TAGCGGCGTTTT
65 TAGCGGCGTTTT
40307892 ACGAAGATCG
Statistics
Matches: 428, Mismatches: 62, Indels: 56
0.78 0.11 0.10
Matches are distributed among these distances:
98 2 0.00
99 4 0.01
100 60 0.14
101 15 0.04
103 1 0.00
106 2 0.00
108 2 0.00
111 2 0.00
112 2 0.00
113 153 0.36
114 178 0.42
115 3 0.01
116 4 0.01
ACGTcount: A:0.24, C:0.21, G:0.19, T:0.36
Consensus pattern (112 bp):
AAACGATGCGTTTTGGTTAATATTTTTACGGCGCTTTTTATAATGTGCCGCTAATGATGTGCTTT
AGCGGCGTTTTTCATAAGCGCCACTAATTCTAAAATACCTCAAGACC
Found at i:40307675 original size:227 final size:226
Alignment explanation
Indices: 40307268--40307890 Score: 688
Period size: 227 Copynumber: 2.8 Consensus size: 226
40307258 TAAAACGATA
* * * *
40307268 CGTTTTGGTTAAGATTTTTTTGCGGCGCTTTGTATAATGCGCCGCTAATGATGTACTTTCGCGGC
1 CGTTTTGGTTAAGA-TATTTTGCGGCGCTTTTTATAATGCGCCGCTAATGATGTGCTTTAGCGGC
* * *
40307333 GTTTCACTCT-AGCGCCACTAATTCTAAAATACCTCAAGACCAAACGATGCGTTTTGGTTAATAT
65 GTTTTATTATAAGCGCCACTAATTCTAAAATACCTCAAGACCAAACGATGCGTTTTGGTTAATA-
* * * * * * * *
40307397 TTTTTACGGCGCCTTTCATAATGTGCCGGTAGCTCTGTGCTTTAGCGGCGTTT-GTTCATAAGCG
129 TTTTTGCGGCGCTTTTTATATTGTGCCGCTA-ATATGTGCTTTAGCGGCGTTTCATT-ATAAGCG
* * **
40307461 CCACTAATTCTAATATACCTCAATACCAAACGCTG
192 CCACTAATTCTAAAATACCTCAAGACCAAACAATG
* * *
40307496 TGTTTTGGTAAAGATATTTTACGGCGCTTTTTATAATGCGCCGCTAATGATGTGCTTTAGCGGCG
1 CGTTTTGGTTAAGATATTTTGCGGCGCTTTTTATAATGCGCCGCTAATGATGTGCTTTAGCGGCG
* * *
40307561 TTTTATTATAAGCGCCACTAATTCTAAAATACCTCAAGACCAAACGATACATTTTTGTTAATATT
66 TTTTATTATAAGCGCCACTAATTCTAAAATACCTCAAGACCAAACGATGCGTTTTGGTTAATATT
* * * *
40307626 TTTGCTGCGCTTTTTATATTGTGCCGCTAATGATGTTCGTTAGCGGCGTTTCATTATAAGCGCCG
131 TTTGCGGCGCTTTTTATATTGTGCCGCTAAT-ATGTGCTTTAGCGGCGTTTCATTATAAGCGCCA
40307691 CTAATTCTAAAATACCTCAAGACCAAACAATG
195 CTAATTCTAAAATACCTCAAGACCAAACAATG
* *
40307723 CGCTTTT-GTTAATATA-TTTGCGGCGCTTTTTATAAT-----GC-----A---GCATTAGCGGC
1 CG-TTTTGGTTAAGATATTTTGCGGCGCTTTTTATAATGCGCCGCTAATGATGTGCTTTAGCGGC
* * * *
40307773 GTTTT-TCCATAAGCGCCACTAATTCTAATATACCTCAAGACCAAACGCTGCGTTTTGGTTAAGA
65 GTTTTAT-TATAAGCGCCACTAATTCTAAAATACCTCAAGACCAAACGATGCGTTTTGGTTAATA
* ** *
40307837 TATTCTGCGGCGCTTTTTGCATTGCGCCGCTAATTATGTGCTTTAGCGGCGTTT
129 T-TTTTGCGGCGCTTTTTATATTGTGCCGCTAA-TATGTGCTTTAGCGGCGTTT
40307891 TACGAAGATC
Statistics
Matches: 340, Mismatches: 48, Indels: 28
0.82 0.12 0.07
Matches are distributed among these distances:
212 1 0.00
213 66 0.19
214 43 0.13
215 1 0.00
216 1 0.00
221 2 0.01
226 20 0.06
227 138 0.41
228 68 0.20
ACGTcount: A:0.24, C:0.21, G:0.19, T:0.36
Consensus pattern (226 bp):
CGTTTTGGTTAAGATATTTTGCGGCGCTTTTTATAATGCGCCGCTAATGATGTGCTTTAGCGGCG
TTTTATTATAAGCGCCACTAATTCTAAAATACCTCAAGACCAAACGATGCGTTTTGGTTAATATT
TTTGCGGCGCTTTTTATATTGTGCCGCTAATATGTGCTTTAGCGGCGTTTCATTATAAGCGCCAC
TAATTCTAAAATACCTCAAGACCAAACAATG
Found at i:40307682 original size:113 final size:113
Alignment explanation
Indices: 40307260--40307760 Score: 605
Period size: 113 Copynumber: 4.4 Consensus size: 113
40307250 TTTCGGTTTA
* * * *
40307260 AAACGATACGTTTTGGTTAAGATTTTTTTGCGGCGCTTTGTATAATGCGCCGCTAATGATGTACT
1 AAACGATGCGTTTTGGTT-A-ATATTTTTGCGGCGCTTTTTATAATGCGCCGCTAATGATGTGCT
* * *
40307325 TTCGCGGCGTTTCACTCT-AGCGCCACTAATTCTAAAATACCTCAAGACC
64 TTAGCGGCGTTTCATTATAAGCGCCACTAATTCTAAAATACCTCAAGACC
* * * * * * *
40307374 AAACGATGCGTTTTGGTTAATATTTTTTACGGCGCCTTTCATAATGTGCCGGTAGCT-CTGTGCT
1 AAACGATGCGTTTTGGTTAATA-TTTTTGCGGCGCTTTTTATAATGCGCCGCTA-ATGATGTGCT
* * *
40307438 TTAGCGGCGTTT-GTTCATAAGCGCCACTAATTCTAATATACCTCAATACC
64 TTAGCGGCGTTTCATT-ATAAGCGCCACTAATTCTAAAATACCTCAAGACC
* * * * *
40307488 AAACGCTGTGTTTTGGTAAAGATATTTTACGGCGCTTTTTATAATGCGCCGCTAATGATGTGCTT
1 AAACGATGCGTTTTGGTTAATAT-TTTTGCGGCGCTTTTTATAATGCGCCGCTAATGATGTGCTT
*
40307553 TAGCGGCGTTTTATTATAAGCGCCACTAATTCTAAAATACCTCAAGACC
65 TAGCGGCGTTTCATTATAAGCGCCACTAATTCTAAAATACCTCAAGACC
* * * * * * * *
40307602 AAACGATACATTTTTGTTAATATTTTTGCTGCGCTTTTTATATTGTGCCGCTAATGATGTTCGTT
1 AAACGATGCGTTTTGGTTAATATTTTTGCGGCGCTTTTTATAATGCGCCGCTAATGATGTGCTTT
*
40307667 AGCGGCGTTTCATTATAAGCGCCGCTAATTCTAAAATACCTCAAGACC
66 AGCGGCGTTTCATTATAAGCGCCACTAATTCTAAAATACCTCAAGACC
* *
40307715 AAACAATGCGCTTTT-GTTAATATATTTGCGGCGCTTTTTATAATGC
1 AAACGATGCG-TTTTGGTTAATATTTTTGCGGCGCTTTTTATAATGC
40307761 AGCATTAGCG
Statistics
Matches: 327, Mismatches: 52, Indels: 17
0.83 0.13 0.04
Matches are distributed among these distances:
112 3 0.01
113 161 0.49
114 161 0.49
115 2 0.01
ACGTcount: A:0.25, C:0.20, G:0.19, T:0.36
Consensus pattern (113 bp):
AAACGATGCGTTTTGGTTAATATTTTTGCGGCGCTTTTTATAATGCGCCGCTAATGATGTGCTTT
AGCGGCGTTTCATTATAAGCGCCACTAATTCTAAAATACCTCAAGACC
Found at i:40307840 original size:100 final size:100
Alignment explanation
Indices: 40307665--40307854 Score: 278
Period size: 100 Copynumber: 1.9 Consensus size: 100
40307655 ATGATGTTCG
*
40307665 TTAGCGGCGTTTCATTATAAGCGCCGCTAATTCTAAAATACCTCAAGACCAAACAATGCGCTTTT
1 TTAGCGGCGTTT-ATTATAAGCGCCACTAATTCTAAAATACCTCAAGACCAAACAATGCGCTTTT
*
40307730 GTTAATATATT-TGCGGCGCTTTTTATAATGCAGCA
65 GTTAAGATATTCTGCGGCGCTTTTTATAATGCAGCA
* **
40307765 TTAGCGGCGTTT-TTCCATAAGCGCCACTAATTCTAATATACCTCAAGACCAAACGCTGCG-TTT
1 TTAGCGGCGTTTATT--ATAAGCGCCACTAATTCTAAAATACCTCAAGACCAAACAATGCGCTTT
40307828 TGGTTAAGATATTCTGCGGCGCTTTTT
64 T-GTTAAGATATTCTGCGGCGCTTTTT
40307855 GCATTGCGCC
Statistics
Matches: 81, Mismatches: 5, Indels: 7
0.87 0.05 0.08
Matches are distributed among these distances:
98 2 0.02
99 4 0.05
100 62 0.77
101 13 0.16
ACGTcount: A:0.26, C:0.22, G:0.18, T:0.34
Consensus pattern (100 bp):
TTAGCGGCGTTTATTATAAGCGCCACTAATTCTAAAATACCTCAAGACCAAACAATGCGCTTTTG
TTAAGATATTCTGCGGCGCTTTTTATAATGCAGCA
Found at i:40314891 original size:12 final size:12
Alignment explanation
Indices: 40314874--40314898 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
40314864 CAGAGTCTAT
40314874 TAACAATATTTA
1 TAACAATATTTA
40314886 TAACAATATTTA
1 TAACAATATTTA
40314898 T
1 T
40314899 GTTATAAAAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.48, C:0.08, G:0.00, T:0.44
Consensus pattern (12 bp):
TAACAATATTTA
Found at i:40317607 original size:15 final size:15
Alignment explanation
Indices: 40317587--40317624 Score: 67
Period size: 15 Copynumber: 2.5 Consensus size: 15
40317577 AGGATTTGGT
40317587 TTGTTTATTTTATTA
1 TTGTTTATTTTATTA
40317602 TTGTTTATTTTATTA
1 TTGTTTATTTTATTA
*
40317617 TTATTTAT
1 TTGTTTAT
40317625 CATTTAAATA
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
15 22 1.00
ACGTcount: A:0.21, C:0.00, G:0.05, T:0.74
Consensus pattern (15 bp):
TTGTTTATTTTATTA
Found at i:40317648 original size:13 final size:13
Alignment explanation
Indices: 40317626--40317677 Score: 54
Period size: 13 Copynumber: 4.1 Consensus size: 13
40317616 ATTATTTATC
40317626 ATTTAAATATATA
1 ATTTAAATATATA
*
40317639 ATTTATATATATA
1 ATTTAAATATATA
*
40317652 AATTAAA-ATAT-
1 ATTTAAATATATA
*
40317663 ATTAATAATATATA
1 ATTTA-AATATATA
40317677 A
1 A
40317678 ATAATATTTT
Statistics
Matches: 31, Mismatches: 5, Indels: 5
0.76 0.12 0.12
Matches are distributed among these distances:
11 3 0.10
12 6 0.19
13 21 0.68
14 1 0.03
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (13 bp):
ATTTAAATATATA
Found at i:40317673 original size:25 final size:25
Alignment explanation
Indices: 40317628--40317697 Score: 76
Period size: 22 Copynumber: 2.9 Consensus size: 25
40317618 TATTTATCAT
*
40317628 TTAAATATATAATTTAT-ATATATAAA
1 TTAAA-ATAT-ATTAATAATATATAAA
40317654 TTAAAATATATTAATAATATATAAA
1 TTAAAATATATTAATAATATATAAA
*
40317679 -T--AATATTTTAATAATATAT
1 TTAAAATATATTAATAATATAT
40317698 TAATAATATT
Statistics
Matches: 41, Mismatches: 2, Indels: 6
0.84 0.04 0.12
Matches are distributed among these distances:
22 17 0.41
24 6 0.15
25 13 0.32
26 5 0.12
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (25 bp):
TTAAAATATATTAATAATATATAAA
Found at i:40317674 original size:11 final size:11
Alignment explanation
Indices: 40317653--40317716 Score: 89
Period size: 11 Copynumber: 6.1 Consensus size: 11
40317643 ATATATATAA
40317653 ATTAA-AATAT
1 ATTAATAATAT
40317663 ATTAATAATAT
1 ATTAATAATAT
*
40317674 ATAAATAATAT
1 ATTAATAATAT
*
40317685 TTTAATAATAT
1 ATTAATAATAT
40317696 ATTAAT-A-AT
1 ATTAATAATAT
40317705 ATTAATAATAT
1 ATTAATAATAT
40317716 A
1 A
40317717 GAAAGAAAAT
Statistics
Matches: 47, Mismatches: 4, Indels: 5
0.84 0.07 0.09
Matches are distributed among these distances:
9 8 0.17
10 7 0.15
11 32 0.68
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (11 bp):
ATTAATAATAT
Found at i:40317705 original size:25 final size:25
Alignment explanation
Indices: 40317645--40317705 Score: 67
Period size: 22 Copynumber: 2.6 Consensus size: 25
40317635 TATAATTTAT
*
40317645 ATATATAAATTAA-AATATATTAATA
1 ATATATTAA-TAATAATATATTAATA
*
40317670 ATATA-T-A-AATAATATTTTAATA
1 ATATATTAATAATAATATATTAATA
40317692 ATATATTAATAATA
1 ATATATTAATAATA
40317706 TTAATAATAT
Statistics
Matches: 30, Mismatches: 2, Indels: 8
0.75 0.05 0.20
Matches are distributed among these distances:
21 2 0.07
22 16 0.53
23 2 0.07
24 1 0.03
25 9 0.30
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (25 bp):
ATATATTAATAATAATATATTAATA
Found at i:40317727 original size:22 final size:20
Alignment explanation
Indices: 40317656--40317728 Score: 56
Period size: 22 Copynumber: 3.5 Consensus size: 20
40317646 TATATAAATT
*
40317656 AAAATATATTAATAATATATA
1 AAAAAATATTAATAATATA-A
* * *
40317677 AATAATATTTTAATAATATAT
1 AA-AAAATATTAATAATATAA
* *
40317698 TAATAATATTAATAATATAGA
1 AAAAAATATTAATAATATA-A
40317719 AAGAAAATAT
1 AA-AAAATAT
40317729 GCATTATATA
Statistics
Matches: 40, Mismatches: 9, Indels: 5
0.74 0.17 0.09
Matches are distributed among these distances:
20 14 0.35
21 4 0.10
22 22 0.55
ACGTcount: A:0.59, C:0.00, G:0.03, T:0.38
Consensus pattern (20 bp):
AAAAAATATTAATAATATAA
Found at i:40322836 original size:98 final size:98
Alignment explanation
Indices: 40322719--40322905 Score: 311
Period size: 98 Copynumber: 1.9 Consensus size: 98
40322709 CATGAAGGGA
*
40322719 ATATTCCGAGTTTGAGATTCTAAAGGAATTGTGCCCTAACGTATTGGGTGTGATTTCTTAAATCT
1 ATATTCCGAGTTTGAGATTCTAAAGGAATCGTGCCCTAACGTATTGGGTGTGATTTCTTAAATCT
*
40322784 TGGATAAGTGGATATTCTTTTAAATTAAAGGAC
66 TGGATAAGTGGATACTCTTTTAAATTAAAGGAC
* * *
40322817 ATATTCCGAGTTTGGGATTCTAAAGGAATCGTGCCCTAATGTATTGGGTGTGGTTTCTTAAATCT
1 ATATTCCGAGTTTGAGATTCTAAAGGAATCGTGCCCTAACGTATTGGGTGTGATTTCTTAAATCT
* *
40322882 TGGATGAGTGGATGCTCTTTTAAA
66 TGGATAAGTGGATACTCTTTTAAA
40322906 ATTTTTATAT
Statistics
Matches: 82, Mismatches: 7, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
98 82 1.00
ACGTcount: A:0.27, C:0.12, G:0.24, T:0.38
Consensus pattern (98 bp):
ATATTCCGAGTTTGAGATTCTAAAGGAATCGTGCCCTAACGTATTGGGTGTGATTTCTTAAATCT
TGGATAAGTGGATACTCTTTTAAATTAAAGGAC
Found at i:40334366 original size:44 final size:43
Alignment explanation
Indices: 40334286--40335020 Score: 270
Period size: 44 Copynumber: 16.7 Consensus size: 43
40334276 AAACACCAAG
* * * ** *
40334286 TCTTATCTCCCTGAGCAGCAGTGGAGAAGGGTGAAGATTGTAGA
1 TCTTATCTCCCTAAGCAGTAGTGGAGCAGATTGAAGA-TGAAGA
* *
40334330 TCTTATCTCCCTAAGCAGTAGTGGAGCAGATCGAAGACGGCAA-A
1 TCTTATCTCCCTAAGCAGTAGTGGAGCAGATTGAAGA-TG-AAGA
* * **
40334374 TCTTATCTTTCC-AAG-A-TAGTGGGAAGCAGATTTAAGCCACCAAG-
1 TCTTATC-TCCCTAAGCAGTAGT-GG-AGCAGATTGAAG--ATGAAGA
* * * * * * *
40334418 CCTTGTCTCTCTGAGCAGCAGTGGAGAAGGTTGAAGATTGAAGA
1 TCTTATCTCCCTAAGCAGTAGTGGAGCAGATTGAAGA-TGAAGA
* **
40334462 TCTTATCTCCCTAAGCAGTAGTGGAGCAGATCGAAGATGGCGAA
1 TCTTATCTCCCTAAGCAGTAGTGGAGCAGATTGAAGATGAAG-A
* * **
40334506 TCTTATCTTTCC-AAG-A-TAGTGGGAAGCAGATTTAAGCCACCAAG-
1 TCTTATC-TCCCTAAGCAGTAGT-GG-AGCAGATTGAAG--ATGAAGA
* * * * * *
40334550 CCTTGTCTCCCTGAGCAGCAGTGGAGAAGGTTGAAGATTGAAGA
1 TCTTATCTCCCTAAGCAGTAGTGGAGCAGATTGAAGA-TGAAGA
* **
40334594 TCTTATCTCCCTAAGCAGTAGTGGAGCAGATCGAAGATGGCGAA
1 TCTTATCTCCCTAAGCAGTAGTGGAGCAGATTGAAGATGAAG-A
* * **
40334638 TCTTATCTTTCC-AAG-A-TAGTTGGAAGCAGATTTAAGCCACCAAG-
1 TCTTATC-TCCCTAAGCAGTAG-TGG-AGCAGATTGAAG--ATGAAGA
* * * * * *
40334682 CCTTGTCTCCCTGAGCAGCAGTGGAGAAGGTTGAAGATTGAAGA
1 TCTTATCTCCCTAAGCAGTAGTGGAGCAGATTGAAGA-TGAAGA
* * * * **
40334726 TCTTATCTCCTTAAGTAGTAGTGGAGCAGATCGAAGACGGCGAA
1 TCTTATCTCCCTAAGCAGTAGTGGAGCAGATTGAAGATGAAG-A
* * * **
40334770 TCTTATCTTTCC-AAG-A-TAGTGGAAAGCAGTTTTAAGCCACCAAG-
1 TCTTATC-TCCCTAAGCAGTAGTGG--AGCAGATTGAAG--ATGAAGA
* * * * * * *
40334814 CCTTGTCTCCCTGAGCAGCAGTGGAGAAGGTTGAAGATTGTAGA
1 TCTTATCTCCCTAAGCAGTAGTGGAGCAGATTGAAGA-TGAAGA
* * **
40334858 TCTTATCTCCCTAAGCAGTAGTGGAGCAGATCGAAGACGGCGAA
1 TCTTATCTCCCTAAGCAGTAGTGGAGCAGATTGAAGATGAAG-A
* * **
40334902 TCTTATCTTTCC-AAG-A-TAGTGGAAAGCAGATTTAAGCCACCAAG-
1 TCTTATC-TCCCTAAGCAGTAGTGG--AGCAGATTGAAG--ATGAAGA
* * * * * * * * *
40334946 CCTTGTCTCCCTGAGTAGCAGCGGAGAAAATTGAAGATTGTAGA
1 TCTTATCTCCCTAAGCAGTAGTGGAGCAGATTGAAGA-TGAAGA
40334990 TCTTATCTCCCTAAGCAGTAGTGGAGCAGAT
1 TCTTATCTCCCTAAGCAGTAGTGGAGCAGAT
40335021 CAAAGAAGGC
Statistics
Matches: 490, Mismatches: 145, Indels: 112
0.66 0.19 0.15
Matches are distributed among these distances:
42 28 0.06
43 49 0.10
44 358 0.73
45 27 0.06
46 28 0.06
ACGTcount: A:0.30, C:0.20, G:0.26, T:0.25
Consensus pattern (43 bp):
TCTTATCTCCCTAAGCAGTAGTGGAGCAGATTGAAGATGAAGA
Found at i:40334516 original size:132 final size:132
Alignment explanation
Indices: 40334279--40335041 Score: 1319
Period size: 132 Copynumber: 5.8 Consensus size: 132
40334269 ACTGGTGAAA
* * * *
40334279 CACCAAGTCTTATCTCCCTGAGCAGCAGTGGAGAAGGGTGAAGATTGTAGATCTTATCTCCCTAA
1 CACCAAGCCTTGTCTCCCTGAGCAGCAGTGGAGAAGGTTGAAGATTGAAGATCTTATCTCCCTAA
*
40334344 GCAGTAGTGGAGCAGATCGAAGACGGCAAATCTTATCTTTCCAAGATAGTGGGAAGCAGATTTAA
66 GCAGTAGTGGAGCAGATCGAAGACGGCGAATCTTATCTTTCCAAGATAGTGGGAAGCAGATTTAA
40334409 GC
131 GC
*
40334411 CACCAAGCCTTGTCTCTCTGAGCAGCAGTGGAGAAGGTTGAAGATTGAAGATCTTATCTCCCTAA
1 CACCAAGCCTTGTCTCCCTGAGCAGCAGTGGAGAAGGTTGAAGATTGAAGATCTTATCTCCCTAA
*
40334476 GCAGTAGTGGAGCAGATCGAAGATGGCGAATCTTATCTTTCCAAGATAGTGGGAAGCAGATTTAA
66 GCAGTAGTGGAGCAGATCGAAGACGGCGAATCTTATCTTTCCAAGATAGTGGGAAGCAGATTTAA
40334541 GC
131 GC
40334543 CACCAAGCCTTGTCTCCCTGAGCAGCAGTGGAGAAGGTTGAAGATTGAAGATCTTATCTCCCTAA
1 CACCAAGCCTTGTCTCCCTGAGCAGCAGTGGAGAAGGTTGAAGATTGAAGATCTTATCTCCCTAA
* *
40334608 GCAGTAGTGGAGCAGATCGAAGATGGCGAATCTTATCTTTCCAAGATAGTTGGAAGCAGATTTAA
66 GCAGTAGTGGAGCAGATCGAAGACGGCGAATCTTATCTTTCCAAGATAGTGGGAAGCAGATTTAA
40334673 GC
131 GC
*
40334675 CACCAAGCCTTGTCTCCCTGAGCAGCAGTGGAGAAGGTTGAAGATTGAAGATCTTATCTCCTTAA
1 CACCAAGCCTTGTCTCCCTGAGCAGCAGTGGAGAAGGTTGAAGATTGAAGATCTTATCTCCCTAA
* * *
40334740 GTAGTAGTGGAGCAGATCGAAGACGGCGAATCTTATCTTTCCAAGATAGTGGAAAGCAGTTTTAA
66 GCAGTAGTGGAGCAGATCGAAGACGGCGAATCTTATCTTTCCAAGATAGTGGGAAGCAGATTTAA
40334805 GC
131 GC
*
40334807 CACCAAGCCTTGTCTCCCTGAGCAGCAGTGGAGAAGGTTGAAGATTGTAGATCTTATCTCCCTAA
1 CACCAAGCCTTGTCTCCCTGAGCAGCAGTGGAGAAGGTTGAAGATTGAAGATCTTATCTCCCTAA
*
40334872 GCAGTAGTGGAGCAGATCGAAGACGGCGAATCTTATCTTTCCAAGATAGTGGAAAGCAGATTTAA
66 GCAGTAGTGGAGCAGATCGAAGACGGCGAATCTTATCTTTCCAAGATAGTGGGAAGCAGATTTAA
40334937 GC
131 GC
* * ** *
40334939 CACCAAGCCTTGTCTCCCTGAGTAGCAGCGGAGAAAATTGAAGATTGTAGATCTTATCTCCCTAA
1 CACCAAGCCTTGTCTCCCTGAGCAGCAGTGGAGAAGGTTGAAGATTGAAGATCTTATCTCCCTAA
* * *
40335004 GCAGTAGTGGAGCAGATCAAAGAAGGCAAATCTTATCT
66 GCAGTAGTGGAGCAGATCGAAGACGGCGAATCTTATCT
40335042 CCCTGAATTT
Statistics
Matches: 605, Mismatches: 26, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
132 605 1.00
ACGTcount: A:0.30, C:0.20, G:0.25, T:0.25
Consensus pattern (132 bp):
CACCAAGCCTTGTCTCCCTGAGCAGCAGTGGAGAAGGTTGAAGATTGAAGATCTTATCTCCCTAA
GCAGTAGTGGAGCAGATCGAAGACGGCGAATCTTATCTTTCCAAGATAGTGGGAAGCAGATTTAA
GC
Found at i:40335125 original size:396 final size:396
Alignment explanation
Indices: 40334279--40335130 Score: 1245
Period size: 396 Copynumber: 2.2 Consensus size: 396
40334269 ACTGGTGAAA
* * ** * **
40334279 CACCAAGTCTTATCTCCCTGAGCAGCAGTGGAGAAGGGTGAAGATTGTAGATCTTATCTCCCTAA
1 CACCAAGCCTTATCTCCCTAAGCAGCAGTGGAGAAGATTGAAGAATCAAGATCTTATCTCCCTAA
*
40334344 GCAGTAGTGGAGCAGATCGAAGACGGCAAATCTTATCTTTCCAAGATAGTGGGAAGCAGATTTAA
66 GCAGTAGTGGAGCAGATCGAAGACGGCAAATCTTATCTTTCCAAGATAGTGGAAAGCAGATTTAA
*
40334409 GCCACCAAGCCTTGTCTCTCTGAGCAGCAGTGGAGAAGGTTGAAGATTGAAGATCTTATCTCCCT
131 GCCACCAAGCCTTGTCTCCCTGAGCAGCAGTGGAGAAGGTTGAAGATTGAAGATCTTATCTCCCT
* *
40334474 AAGCAGTAGTGGAGCAGATCGAAGATGGCGAATCTTATCTTTCCAAGATAGTGGGAAGCAGATTT
196 AAGCAGTAGTGGAGCAGATCGAAGACGGCGAATCTTATCTTTCCAAGATAGTGGAAAGCAGATTT
* **
40334539 AAGCCACCAAGCCTTGTCTCCCTGAGCAGCAGTGGAGAAGGTTGAAGATTGAAGATCTTATCTCC
261 AAGCCACCAAGCCTTGTCTCCCTGAGCAGCAGCGGAGAAAATTGAAGATTGAAGATCTTATCTCC
* * * * *
40334604 CTAAGCAGTAGTGGAGCAGATCGAAGATGGCGAATCTTATCTTTCCAAGATAGTTGGAAGCAGAT
326 CTAAGCAGTAGTGGAGCAGATCAAAGAAGGCAAATCTTATCTTCCCAAGATAGTTGGAAGCAAAT
*
40334669 TTAAGC
391 TAAAGC
* * * * * *
40334675 CACCAAGCCTTGTCTCCCTGAGCAGCAGTGGAGAAGGTTGAAGATTGAAGATCTTATCTCCTTAA
1 CACCAAGCCTTATCTCCCTAAGCAGCAGTGGAGAAGATTGAAGAATCAAGATCTTATCTCCCTAA
* * *
40334740 GTAGTAGTGGAGCAGATCGAAGACGGCGAATCTTATCTTTCCAAGATAGTGGAAAGCAGTTTTAA
66 GCAGTAGTGGAGCAGATCGAAGACGGCAAATCTTATCTTTCCAAGATAGTGGAAAGCAGATTTAA
*
40334805 GCCACCAAGCCTTGTCTCCCTGAGCAGCAGTGGAGAAGGTTGAAGATTGTAGATCTTATCTCCCT
131 GCCACCAAGCCTTGTCTCCCTGAGCAGCAGTGGAGAAGGTTGAAGATTGAAGATCTTATCTCCCT
40334870 AAGCAGTAGTGGAGCAGATCGAAGACGGCGAATCTTATCTTTCCAAGATAGTGGAAAGCAGATTT
196 AAGCAGTAGTGGAGCAGATCGAAGACGGCGAATCTTATCTTTCCAAGATAGTGGAAAGCAGATTT
* *
40334935 AAGCCACCAAGCCTTGTCTCCCTGAGTAGCAGCGGAGAAAATTGAAGATTGTAGATCTTATCTCC
261 AAGCCACCAAGCCTTGTCTCCCTGAGCAGCAGCGGAGAAAATTGAAGATTGAAGATCTTATCTCC
**
40335000 CTAAGCAGTAGTGGAGCAGATCAAAGAAGGCAAATCTTATC-TCCCTGAATTTGCAG-TGG-AGC
326 CTAAGCAGTAGTGGAGCAGATCAAAGAAGGCAAATCTTATCTTCCC--AAGAT--AGTTGGAAGC
40335062 AAATTAAAGC
387 AAATTAAAGC
*
40335072 CTA-CAATCC-TATCTCCCTAACGTC-GCAGTGG-GATAGATT-AA-AATCACAGATCTTATCTC
1 C-ACCAAGCCTTATCTCCCTAA-G-CAGCAGTGGAGA-AGATTGAAGAATCA-AGATCTTATCTC
40335131 TCTGAAGTTG
Statistics
Matches: 415, Mismatches: 32, Indels: 18
0.89 0.07 0.04
Matches are distributed among these distances:
395 6 0.01
396 370 0.89
397 32 0.08
398 5 0.01
399 2 0.00
ACGTcount: A:0.30, C:0.20, G:0.25, T:0.25
Consensus pattern (396 bp):
CACCAAGCCTTATCTCCCTAAGCAGCAGTGGAGAAGATTGAAGAATCAAGATCTTATCTCCCTAA
GCAGTAGTGGAGCAGATCGAAGACGGCAAATCTTATCTTTCCAAGATAGTGGAAAGCAGATTTAA
GCCACCAAGCCTTGTCTCCCTGAGCAGCAGTGGAGAAGGTTGAAGATTGAAGATCTTATCTCCCT
AAGCAGTAGTGGAGCAGATCGAAGACGGCGAATCTTATCTTTCCAAGATAGTGGAAAGCAGATTT
AAGCCACCAAGCCTTGTCTCCCTGAGCAGCAGCGGAGAAAATTGAAGATTGAAGATCTTATCTCC
CTAAGCAGTAGTGGAGCAGATCAAAGAAGGCAAATCTTATCTTCCCAAGATAGTTGGAAGCAAAT
TAAAGC
Found at i:40337381 original size:21 final size:22
Alignment explanation
Indices: 40337357--40337407 Score: 59
Period size: 23 Copynumber: 2.3 Consensus size: 22
40337347 CAATTAAACT
* *
40337357 TAAAAAATTTAATT-TCAAAAA
1 TAAAAAACTAAATTCTCAAAAA
*
40337378 TAAAAATACTAAATTCTTAAAAA
1 TAAAAA-ACTAAATTCTCAAAAA
40337401 TAAAAAA
1 TAAAAAA
40337408 AATTGCTATT
Statistics
Matches: 25, Mismatches: 3, Indels: 3
0.81 0.10 0.10
Matches are distributed among these distances:
21 6 0.24
22 7 0.28
23 12 0.48
ACGTcount: A:0.65, C:0.06, G:0.00, T:0.29
Consensus pattern (22 bp):
TAAAAAACTAAATTCTCAAAAA
Found at i:40347824 original size:17 final size:18
Alignment explanation
Indices: 40347791--40347826 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
40347781 TAATGAATAC
*
40347791 ATAAAATAATATTATATA
1 ATAAAAGAATATTATATA
40347809 ATAAAAGAAT-TTATATA
1 ATAAAAGAATATTATATA
40347826 A
1 A
40347827 AAATTAAGTT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
17 8 0.47
18 9 0.53
ACGTcount: A:0.61, C:0.00, G:0.03, T:0.36
Consensus pattern (18 bp):
ATAAAAGAATATTATATA
Found at i:40348999 original size:7 final size:7
Alignment explanation
Indices: 40348987--40349039 Score: 61
Period size: 8 Copynumber: 7.0 Consensus size: 7
40348977 TTAAAATGGA
40348987 TTATTTT
1 TTATTTT
40348994 TTATTTT
1 TTATTTT
40349001 TTATTTTT
1 TTA-TTTT
40349009 ATTATTTT
1 -TTATTTT
40349017 TTATATTT
1 TTAT-TTT
*
40349025 TTGTTTAT
1 TTATTT-T
40349033 TTATTTT
1 TTATTTT
40349040 CGATTTGGGC
Statistics
Matches: 40, Mismatches: 2, Indels: 8
0.80 0.04 0.16
Matches are distributed among these distances:
7 17 0.43
8 20 0.50
9 3 0.08
ACGTcount: A:0.17, C:0.00, G:0.02, T:0.81
Consensus pattern (7 bp):
TTATTTT
Found at i:40349013 original size:23 final size:22
Alignment explanation
Indices: 40348986--40349039 Score: 72
Period size: 23 Copynumber: 2.4 Consensus size: 22
40348976 TTTAAAATGG
* *
40348986 ATTATTTTTTATTTTTTATTTTT
1 ATTATTTTTTATATTTT-TGTTT
40349009 ATTATTTTTTATATTTTTGTTT
1 ATTATTTTTTATATTTTTGTTT
40349031 ATTTATTTT
1 A-TTATTTT
40349040 CGATTTGGGC
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
22 5 0.18
23 23 0.82
ACGTcount: A:0.19, C:0.00, G:0.02, T:0.80
Consensus pattern (22 bp):
ATTATTTTTTATATTTTTGTTT
Found at i:40349033 original size:10 final size:9
Alignment explanation
Indices: 40348997--40349039 Score: 50
Period size: 9 Copynumber: 4.6 Consensus size: 9
40348987 TTATTTTTTA
40348997 TTTTTTATT
1 TTTTTTATT
*
40349006 TTTATTATT
1 TTTTTTATT
*
40349015 TTTTATATT
1 TTTTTTATT
40349024 TTTGTTTATT
1 TTT-TTTATT
40349034 TATTTT
1 T-TTTT
40349040 CGATTTGGGC
Statistics
Matches: 28, Mismatches: 4, Indels: 3
0.80 0.11 0.09
Matches are distributed among these distances:
9 18 0.64
10 8 0.29
11 2 0.07
ACGTcount: A:0.16, C:0.00, G:0.02, T:0.81
Consensus pattern (9 bp):
TTTTTTATT
Found at i:40349479 original size:111 final size:111
Alignment explanation
Indices: 40349283--40349502 Score: 341
Period size: 111 Copynumber: 2.0 Consensus size: 111
40349273 TCCCTACTCT
* * *
40349283 TGAAGATAAGATTCGCCGTCTCCAATATGCTCCACTATTGCTTAGGGAGAAAAGATCTGTGATTT
1 TGAAGATAAGATTCGCCGTCTCCAATATGCTCCACTACTGCTTAGGGAGAAAAGATCTATAATTT
40349348 CCAACCTATTCCACTACTGACCAGGGAGATAGGACTTGTGGCTTCC
66 CCAACCTATTCCACTACTGACCAGGGAGATAGGACTTGTGGCTTCC
* * * * ** *
40349394 TGAAGATAAGATTCGCTGTCTTCGATCTGCTCTGCTACTGCTTAGGGAGACAAGATCTATAATTT
1 TGAAGATAAGATTCGCCGTCTCCAATATGCTCCACTACTGCTTAGGGAGAAAAGATCTATAATTT
*
40349459 CCAACCTATTCCACTGCTGACCAGGGAGATAGGACTTGTGGCTT
66 CCAACCTATTCCACTACTGACCAGGGAGATAGGACTTGTGGCTT
40349503 AAATTTGCTT
Statistics
Matches: 98, Mismatches: 11, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
111 98 1.00
ACGTcount: A:0.26, C:0.23, G:0.22, T:0.29
Consensus pattern (111 bp):
TGAAGATAAGATTCGCCGTCTCCAATATGCTCCACTACTGCTTAGGGAGAAAAGATCTATAATTT
CCAACCTATTCCACTACTGACCAGGGAGATAGGACTTGTGGCTTCC
Found at i:40349624 original size:128 final size:128
Alignment explanation
Indices: 40349394--40350136 Score: 986
Period size: 128 Copynumber: 5.8 Consensus size: 128
40349384 TGTGGCTTCC
* * * *
40349394 TGAAGATAAGATTCGCTGTCTTCGATCTGCTCTGCTACTGCTTAGGGAGACAAGATCTATAATTT
1 TGAAGATAAGATTCGCCGTATTCGATCTGCTCCGCTACTGCTTAGGGAGACAAGATCTGTAATTT
* * *
40349459 CCAACCTATTCCACTGCTGACCAGGGAGATAGGACTTGTGGCTTAAATTTGCTTCCCTACTCT
66 TCAACCTATTCCACTGCTGACCAGGGAGATAGAACTTGTGGCTTAAATCTGCTTCCCTACTCT
* * * *
40349522 TGAAGATAAGATTCGCCATATTTGATTTGCTCTGCTACTGCTTAGGGAGACAAGATCTGTAATTT
1 TGAAGATAAGATTCGCCGTATTCGATCTGCTCCGCTACTGCTTAGGGAGACAAGATCTGTAATTT
*
40349587 TCAACCTATTCCACTGCTGACCAGGGAGATATAACTTGTGGCTTAAATCTGCTTCCCTACTCT
66 TCAACCTATTCCACTGCTGACCAGGGAGATAGAACTTGTGGCTTAAATCTGCTTCCCTACTCT
* *
40349650 TGAAGATAAGATTAGCCGTATTCGATCTGCTCCGCTACTGCTTATGGAGACAAGATCTGTAATTT
1 TGAAGATAAGATTCGCCGTATTCGATCTGCTCCGCTACTGCTTAGGGAGACAAGATCTGTAATTT
40349715 TCAACCTATTCCACTGCTGACCAGGGAGATA-AGACTTGTGGCTTAAATCTGCTTCCCTACTCT
66 TCAACCTATTCCACTGCTGACCAGGGAGATAGA-ACTTGTGGCTTAAATCTGCTTCCCTACTCT
* *
40349778 TGAAGATAAGATTCGCCGTATTCGATCTGCTCCGCTACTACTTAGGGAGACAATATCTGTAATTT
1 TGAAGATAAGATTCGCCGTATTCGATCTGCTCCGCTACTGCTTAGGGAGACAAGATCTGTAATTT
* *
40349843 CCAACCTATTCCACTGCTGACCAGGGAGATAGGACTTGTGGCTTAAATCTGCTTCCCTACTCT
66 TCAACCTATTCCACTGCTGACCAGGGAGATAGAACTTGTGGCTTAAATCTGCTTCCCTACTCT
* * * *
40349906 TGAAGATAAGATTCACCGTATTCGATCTGCTCCGCTACTGCTTAGGGAGATAAGATCTGAAATCT
1 TGAAGATAAGATTCGCCGTATTCGATCTGCTCCGCTACTGCTTAGGGAGACAAGATCTGTAATTT
* * * * * * * **
40349971 TCAATCTATTCCACTGCTGCCCAGAGAGATAGAA-TTACTGGCTTCAATGTACTCTACTGTAACC
66 TCAACCTATTCCACTGCTGACCAGGGAGATAGAACTT-GTGGCTTAAATCTGCT-T-CCCT-A-C
* *
40350035 ACA
126 TCT
* * * * * * * * * * * *
40350038 AGGAGGTAAAATCCACCATCTTCGATCTGCTCCACTACTGCTTAGGGACATAAGATCTGTAATCT
1 TGAAGATAAGATTCGCCGTATTCGATCTGCTCCGCTACTGCTTAGGGAGACAAGATCTGTAATTT
* **
40350103 TCAATCTATTCCACTGCCAACCAGGGAGATAGAA
66 TCAACCTATTCCACTGCTGACCAGGGAGATAGAA
40350137 TTACTGGCTT
Statistics
Matches: 553, Mismatches: 55, Indels: 10
0.89 0.09 0.02
Matches are distributed among these distances:
127 3 0.01
128 459 0.83
129 1 0.00
130 2 0.00
131 1 0.00
132 87 0.16
ACGTcount: A:0.27, C:0.24, G:0.19, T:0.30
Consensus pattern (128 bp):
TGAAGATAAGATTCGCCGTATTCGATCTGCTCCGCTACTGCTTAGGGAGACAAGATCTGTAATTT
TCAACCTATTCCACTGCTGACCAGGGAGATAGAACTTGTGGCTTAAATCTGCTTCCCTACTCT
Found at i:40350570 original size:132 final size:132
Alignment explanation
Indices: 40349926--40350515 Score: 1054
Period size: 132 Copynumber: 4.5 Consensus size: 132
40349916 ATTCACCGTA
* * * ***
40349926 TTCGATCTGCTCCGCTACTGCTTAGGGAGATAAGATCTGAAATCTTCAATCTATTCCACTGCTGC
1 TTCGATCTGCTCCACTACTGCTTAGGGACATAAGATCTGTAATCTTCAATCTATTCCACTGCCAA
* * *
40349991 CCAGAGAGATAGAATTACTGGCTTCAATGTACTCTACTGTAACCACAAGGAGGTAAAATCCACCA
66 CCAGGGAGATAGAATTACTGGCTTCAATGTACTCCACTGTAACCACAGGGAGGTAAAATCCACCA
40350056 TC
131 TC
40350058 TTCGATCTGCTCCACTACTGCTTAGGGACATAAGATCTGTAATCTTCAATCTATTCCACTGCCAA
1 TTCGATCTGCTCCACTACTGCTTAGGGACATAAGATCTGTAATCTTCAATCTATTCCACTGCCAA
*
40350123 CCAGGGAGATAGAATTACTGGCTTCAATGTACACCACTGTAACCACAGGGAGGTAAAATCCACCA
66 CCAGGGAGATAGAATTACTGGCTTCAATGTACTCCACTGTAACCACAGGGAGGTAAAATCCACCA
40350188 TC
131 TC
40350190 TTCGATCTGCTCCACTACTGCTTAGGGACATAAGATCTGTAATCTTCAATCTATTCCACTGCCAA
1 TTCGATCTGCTCCACTACTGCTTAGGGACATAAGATCTGTAATCTTCAATCTATTCCACTGCCAA
40350255 CCAGGGAGATAGAATTACTGGCTTCAATGTACTCCACTGTAACCACAGGGAGGTAAAATCCACCA
66 CCAGGGAGATAGAATTACTGGCTTCAATGTACTCCACTGTAACCACAGGGAGGTAAAATCCACCA
40350320 TC
131 TC
*
40350322 TTCGATCTGCTCAACTACTGCTTAGGGACATAAGATCTGTAATCTTCAATCTATTCCACTGCCAA
1 TTCGATCTGCTCCACTACTGCTTAGGGACATAAGATCTGTAATCTTCAATCTATTCCACTGCCAA
40350387 CCAGGGAGATAGAATTACTGGCTTCAATGTACTCCACTGTAACCACAGGGAGGTAAAATCCACCA
66 CCAGGGAGATAGAATTACTGGCTTCAATGTACTCCACTGTAACCACAGGGAGGTAAAATCCACCA
40350452 TC
131 TC
* * *
40350454 TTCGATCTGCTCCACTACTGCTTAGGGAGATAAGATTTGTAATCTTTAATCTATTCCACTGC
1 TTCGATCTGCTCCACTACTGCTTAGGGACATAAGATCTGTAATCTTCAATCTATTCCACTGC
40350516 TGCCTAGGGA
Statistics
Matches: 442, Mismatches: 16, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
132 442 1.00
ACGTcount: A:0.29, C:0.26, G:0.17, T:0.28
Consensus pattern (132 bp):
TTCGATCTGCTCCACTACTGCTTAGGGACATAAGATCTGTAATCTTCAATCTATTCCACTGCCAA
CCAGGGAGATAGAATTACTGGCTTCAATGTACTCCACTGTAACCACAGGGAGGTAAAATCCACCA
TC
Done.