Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: At_chr1
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: 106989029
ACGTcount: A:0.31, C:0.17, G:0.17, T:0.31
Warning! 3754247 characters in sequence are not A, C, G, or T
File 97 of 322
Found at i:31474994 original size:20 final size:20
Alignment explanation
Indices: 31474969--31475015 Score: 58
Period size: 20 Copynumber: 2.4 Consensus size: 20
31474959 ATTGGTTTAC
*
31474969 AAAAATGAAGATTTTTTAAA
1 AAAAATCAAGATTTTTTAAA
** *
31474989 AAAAATCAATTTTTTTTTAA
1 AAAAATCAAGATTTTTTAAA
31475009 AAAAATC
1 AAAAATC
31475016 TGGACTCCTG
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.53, C:0.04, G:0.04, T:0.38
Consensus pattern (20 bp):
AAAAATCAAGATTTTTTAAA
Found at i:31481637 original size:28 final size:28
Alignment explanation
Indices: 31481604--31481668 Score: 105
Period size: 28 Copynumber: 2.3 Consensus size: 28
31481594 ATGTACTAGA
*
31481604 ATACCCCTATGTATGCAAAATTA-CTATT
1 ATACCCCTATGTATGCAAAATGACCT-TT
31481632 ATACCCCTATGTATGCAAAATGACCTTT
1 ATACCCCTATGTATGCAAAATGACCTTT
31481660 ATACCCCTA
1 ATACCCCTA
31481669 GGGTTAATTT
Statistics
Matches: 35, Mismatches: 1, Indels: 2
0.92 0.03 0.05
Matches are distributed among these distances:
28 33 0.94
29 2 0.06
ACGTcount: A:0.34, C:0.26, G:0.08, T:0.32
Consensus pattern (28 bp):
ATACCCCTATGTATGCAAAATGACCTTT
Found at i:31481832 original size:27 final size:27
Alignment explanation
Indices: 31481774--31481863 Score: 110
Period size: 28 Copynumber: 3.2 Consensus size: 27
31481764 AGGTAGCGTC
*
31481774 CTGGTGGCTA-TGCCACAAATTATCTATT
1 CTGGTGGC-ACTGCCACAAA-TATCTGTT
* *
31481802 CTGGTGGCCCTGCCACATATATCTGTT
1 CTGGTGGCACTGCCACAAATATCTGTT
31481829 CTGGTGGCACTGCCACAAAATATCTGTAT
1 CTGGTGGCACTGCCAC-AAATATCTGT-T
31481858 CTGGTG
1 CTGGTG
31481864 ACTCTGTCAC
Statistics
Matches: 54, Mismatches: 5, Indels: 5
0.84 0.08 0.08
Matches are distributed among these distances:
27 22 0.41
28 25 0.46
29 7 0.13
ACGTcount: A:0.21, C:0.24, G:0.22, T:0.32
Consensus pattern (27 bp):
CTGGTGGCACTGCCACAAATATCTGTT
Found at i:31481874 original size:29 final size:28
Alignment explanation
Indices: 31481784--31481874 Score: 94
Period size: 27 Copynumber: 3.2 Consensus size: 28
31481774 CTGGTGGCTA
* * * *
31481784 TGCCACAAATTATCTATTCTGGTGGCCC
1 TGCCACAAAATATCTGTTCTGGTGACAC
* *
31481812 TGCCAC-ATATATCTGTTCTGGTGGCAC
1 TGCCACAAAATATCTGTTCTGGTGACAC
*
31481839 TGCCACAAAATATCTGTATCTGGTGACTC
1 TGCCACAAAATATCTGT-TCTGGTGACAC
*
31481868 TGTCACA
1 TGCCACA
31481875 TTTTCTGTAT
Statistics
Matches: 53, Mismatches: 8, Indels: 3
0.83 0.12 0.05
Matches are distributed among these distances:
27 23 0.43
28 15 0.28
29 15 0.28
ACGTcount: A:0.23, C:0.26, G:0.19, T:0.32
Consensus pattern (28 bp):
TGCCACAAAATATCTGTTCTGGTGACAC
Found at i:31481882 original size:55 final size:56
Alignment explanation
Indices: 31481774--31481888 Score: 137
Period size: 55 Copynumber: 2.1 Consensus size: 56
31481764 AGGTAGCGTC
* *
31481774 CTGGTGGCTATGCCACAAATTATCTATTCTGGTGGCCCTGCCACATATATCTGT-T
1 CTGGTGGCTATGCCACAAAATATCTATTCTGGTGACCCTGCCACATATATCTGTAT
* * * *
31481829 CTGGTGGC-ACTGCCACAAAATATCTGTATCTGGTGACTCTGTCACAT-TTTCTGTAT
1 CTGGTGGCTA-TGCCACAAAATATCTAT-TCTGGTGACCCTGCCACATATATCTGTAT
31481885 CTGG
1 CTGG
31481889 CAGCCATGCT
Statistics
Matches: 51, Mismatches: 6, Indels: 5
0.82 0.10 0.08
Matches are distributed among these distances:
54 1 0.02
55 29 0.57
56 21 0.41
ACGTcount: A:0.20, C:0.24, G:0.21, T:0.35
Consensus pattern (56 bp):
CTGGTGGCTATGCCACAAAATATCTATTCTGGTGACCCTGCCACATATATCTGTAT
Found at i:31483229 original size:42 final size:42
Alignment explanation
Indices: 31483180--31483295 Score: 169
Period size: 42 Copynumber: 2.8 Consensus size: 42
31483170 TTTAAAAACG
* *
31483180 CCGCTAAAAGCCATGACTTTTAGCGGCGTTTGAAAAAAAGCA
1 CCGCTAAAAGTCATGGCTTTTAGCGGCGTTTGAAAAAAAGCA
* * * *
31483222 CCGCTAAAAGTCATGGTTTTTAGTGGCGTCTGTAAAAAAGCA
1 CCGCTAAAAGTCATGGCTTTTAGCGGCGTTTGAAAAAAAGCA
*
31483264 CCACTAAAAGTCATGGCTTTTAGCGGCGTTTG
1 CCGCTAAAAGTCATGGCTTTTAGCGGCGTTTG
31483296 TGGAAAAAAT
Statistics
Matches: 64, Mismatches: 10, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
42 64 1.00
ACGTcount: A:0.30, C:0.20, G:0.23, T:0.27
Consensus pattern (42 bp):
CCGCTAAAAGTCATGGCTTTTAGCGGCGTTTGAAAAAAAGCA
Found at i:31483731 original size:21 final size:21
Alignment explanation
Indices: 31483707--31483779 Score: 85
Period size: 21 Copynumber: 3.5 Consensus size: 21
31483697 CTTCCATTGA
*
31483707 TGCTTCCTCTGCCTCCCTCAC
1 TGCTGCCTCTGCCTCCCTCAC
* *
31483728 TGCTGCCGCTGCCTCCCTCGC
1 TGCTGCCTCTGCCTCCCTCAC
* *
31483749 TGCTG-CTGCTGCCTCTCTCTC
1 TGCTGCCT-CTGCCTCCCTCAC
31483770 TGCTGCCTCT
1 TGCTGCCTCT
31483780 CTCTAAGTTG
Statistics
Matches: 44, Mismatches: 6, Indels: 4
0.81 0.11 0.07
Matches are distributed among these distances:
20 1 0.02
21 41 0.93
22 2 0.05
ACGTcount: A:0.01, C:0.48, G:0.18, T:0.33
Consensus pattern (21 bp):
TGCTGCCTCTGCCTCCCTCAC
Found at i:31483772 original size:15 final size:15
Alignment explanation
Indices: 31483754--31483783 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
31483744 CTCGCTGCTG
31483754 CTGCTGCCTCTCTCT
1 CTGCTGCCTCTCTCT
31483769 CTGCTGCCTCTCTCT
1 CTGCTGCCTCTCTCT
31483784 AAGTTGTTGC
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.00, C:0.47, G:0.13, T:0.40
Consensus pattern (15 bp):
CTGCTGCCTCTCTCT
Found at i:31484201 original size:13 final size:14
Alignment explanation
Indices: 31484176--31484204 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
31484166 TGATGAATTG
31484176 AATTAAACAATTAT
1 AATTAAACAATTAT
31484190 AATTAAAC-ATTAT
1 AATTAAACAATTAT
31484203 AA
1 AA
31484205 ATATTTAGAA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 7 0.47
14 8 0.53
ACGTcount: A:0.59, C:0.07, G:0.00, T:0.34
Consensus pattern (14 bp):
AATTAAACAATTAT
Found at i:31487537 original size:12 final size:12
Alignment explanation
Indices: 31487522--31487547 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
31487512 ATCATCCTCT
31487522 TCATCAGATTCA
1 TCATCAGATTCA
31487534 TCATCAGATTCA
1 TCATCAGATTCA
31487546 TC
1 TC
31487548 CCTCGACTTC
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:0.31, C:0.27, G:0.08, T:0.35
Consensus pattern (12 bp):
TCATCAGATTCA
Found at i:31489254 original size:9 final size:9
Alignment explanation
Indices: 31489240--31489570 Score: 137
Period size: 9 Copynumber: 35.4 Consensus size: 9
31489230 AGGGATTATC
31489240 TTATGTAAA
1 TTATGTAAA
31489249 TTATGTAAGA
1 TTATGTAA-A
* *
31489259 TATAATATATAT
1 T-T-ATGTA-AA
31489271 TTATGT--A
1 TTATGTAAA
*
31489278 TTATGTAAG
1 TTATGTAAA
31489287 TTATGTAAA
1 TTATGTAAA
*
31489296 TTATGTAAG
1 TTATGTAAA
* * **
31489305 GTATTTATC
1 TTATGTAAA
31489314 TTATGTAAA
1 TTATGTAAA
31489323 TTATGTAAGA
1 TTATGTAA-A
31489333 -TATGATATATA
1 TTATG-TA-A-A
31489344 TTTATGT--A
1 -TTATGTAAA
*
31489352 TTATGTAAG
1 TTATGTAAA
31489361 TTATGTAAA
1 TTATGTAAA
*
31489370 TTATGTAAG
1 TTATGTAAA
* **
31489379 TTATTTATC
1 TTATGTAAA
31489388 TTATGTAAA
1 TTATGTAAA
31489397 TTATGTAAGA
1 TTATGTAA-A
*
31489407 -TATGATACGTCA
1 TTATG-TA---AA
31489419 TTATGT--A
1 TTATGTAAA
*
31489426 TTATGTAAG
1 TTATGTAAA
31489435 TTATGTAAA
1 TTATGTAAA
* *
31489444 CTATGTAAG
1 TTATGTAAA
* **
31489453 TTATTTATC
1 TTATGTAAA
31489462 TTATGTAAA
1 TTATGTAAA
31489471 TTATGTAAGA
1 TTATGTAA-A
31489481 -TATGATATATA
1 TTATG-TA-A-A
* *
31489492 TT-TATATA
1 TTATGTAAA
*
31489500 TTATGTAAG
1 TTATGTAAA
31489509 TTATGTAAA
1 TTATGTAAA
31489518 TTATGTAAGA
1 TTATGTAA-A
*
31489528 TATGATATATATA
1 T-T-ATGTA-A-A
31489541 TTTATGT--A
1 -TTATGTAAA
*
31489549 TTATGTAAG
1 TTATGTAAA
31489558 TTATGTAAA
1 TTATGTAAA
31489567 TTAT
1 TTAT
31489571 ATAATATATG
Statistics
Matches: 240, Mismatches: 49, Indels: 66
0.68 0.14 0.19
Matches are distributed among these distances:
7 25 0.10
8 5 0.02
9 155 0.65
10 18 0.08
11 8 0.03
12 16 0.07
13 12 0.05
14 1 0.00
ACGTcount: A:0.37, C:0.02, G:0.14, T:0.47
Consensus pattern (9 bp):
TTATGTAAA
Found at i:31489356 original size:74 final size:74
Alignment explanation
Indices: 31489235--31489526 Score: 514
Period size: 74 Copynumber: 3.9 Consensus size: 74
31489225 ATAAAAGGGA
*
31489235 TTATCTTATGTAAATTATGTAAGATATAATATATATTTATGTATTATGTAAGTTATGTAAATTAT
1 TTATCTTATGTAAATTATGTAAGATATGATATATATTTATGTATTATGTAAGTTATGTAAATTAT
*
31489300 GTAAGGTAT
66 GTAAGTTAT
31489309 TTATCTTATGTAAATTATGTAAGATATGATATATATTTATGTATTATGTAAGTTATGTAAATTAT
1 TTATCTTATGTAAATTATGTAAGATATGATATATATTTATGTATTATGTAAGTTATGTAAATTAT
31489374 GTAAGTTAT
66 GTAAGTTAT
** *
31489383 TTATCTTATGTAAATTATGTAAGATATGATACGTCA-TTATGTATTATGTAAGTTATGTAAACTA
1 TTATCTTATGTAAATTATGTAAGATATGATATAT-ATTTATGTATTATGTAAGTTATGTAAATTA
31489447 TGTAAGTTAT
65 TGTAAGTTAT
*
31489457 TTATCTTATGTAAATTATGTAAGATATGATATATATTTATATATTATGTAAGTTATGTAAATTAT
1 TTATCTTATGTAAATTATGTAAGATATGATATATATTTATGTATTATGTAAGTTATGTAAATTAT
31489522 GTAAG
66 GTAAG
31489527 ATATGATATA
Statistics
Matches: 207, Mismatches: 9, Indels: 4
0.94 0.04 0.02
Matches are distributed among these distances:
73 1 0.00
74 205 0.99
75 1 0.00
ACGTcount: A:0.37, C:0.02, G:0.14, T:0.47
Consensus pattern (74 bp):
TTATCTTATGTAAATTATGTAAGATATGATATATATTTATGTATTATGTAAGTTATGTAAATTAT
GTAAGTTAT
Found at i:31489505 original size:56 final size:52
Alignment explanation
Indices: 31489309--31489592 Score: 164
Period size: 47 Copynumber: 5.8 Consensus size: 52
31489299 TGTAAGGTAT
*
31489309 TTATCTTATGTAAATTATGTAAGATATG-ATATATATTTATGTATTATGTAAG
1 TTAT-TTATGTAAATTATGTAAGATATGAATATATATTTATATATTATGTAAG
* ** * *
31489361 ----TTATGTAAATTATGTAAGTTATTTATCT-TATGTA-A-ATTATGTAAG
1 TTATTTATGTAAATTATGTAAGATATGAATATATATTTATATATTATGTAAG
* * * * * * * * * * *
31489406 ATATGATACGT-CATTATGT-A-TTATGTAA-GT-TATGTAAACTATGTAAGTTAT
1 TTAT-TTATGTAAATTATGTAAGATATG-AATATATATTTATA-TAT-TATGTAAG
31489457 TTATCTTATGTAAATTATGTAAGATATG-ATATATATTTATATATTATGTAAG
1 TTAT-TTATGTAAATTATGTAAGATATGAATATATATTTATATATTATGTAAG
*
31489509 ----TTATGTAAATTATGTAAGATATGATATATATATTTATGTATTATGTAAG
1 TTATTTATGTAAATTATGTAAGATATGA-ATATATATTTATATATTATGTAAG
* *
31489558 ----TTATGTAAATTATATAATATATG-ATATATATTTAT
1 TTATTTATGTAAATTATGTAAGATATGAATATATATTTAT
31489593 GTTGATGGGA
Statistics
Matches: 185, Mismatches: 29, Indels: 41
0.73 0.11 0.16
Matches are distributed among these distances:
45 10 0.05
47 72 0.39
48 6 0.03
49 51 0.28
50 6 0.03
51 12 0.06
52 13 0.07
53 5 0.03
54 10 0.05
ACGTcount: A:0.38, C:0.02, G:0.13, T:0.48
Consensus pattern (52 bp):
TTATTTATGTAAATTATGTAAGATATGAATATATATTTATATATTATGTAAG
Found at i:31489518 original size:47 final size:47
Alignment explanation
Indices: 31489462--31489592 Score: 217
Period size: 49 Copynumber: 2.7 Consensus size: 47
31489452 GTTATTTATC
31489462 TTATGTAAATTATGTAAGATATGATATATATTTATATATTATGTAAG
1 TTATGTAAATTATGTAAGATATGATATATATTTATATATTATGTAAG
*
31489509 TTATGTAAATTATGTAAGATATGATATATATATTTATGTATTATGTAAG
1 TTATGTAAATTATGTAAGATATG--ATATATATTTATATATTATGTAAG
* *
31489558 TTATGTAAATTATATAATATATGATATATATTTAT
1 TTATGTAAATTATGTAAGATATGATATATATTTAT
31489593 GTTGATGGGA
Statistics
Matches: 79, Mismatches: 3, Indels: 4
0.92 0.03 0.05
Matches are distributed among these distances:
47 35 0.44
49 44 0.56
ACGTcount: A:0.40, C:0.00, G:0.11, T:0.48
Consensus pattern (47 bp):
TTATGTAAATTATGTAAGATATGATATATATTTATATATTATGTAAG
Found at i:31489593 original size:40 final size:40
Alignment explanation
Indices: 31489509--31489594 Score: 97
Period size: 40 Copynumber: 2.1 Consensus size: 40
31489499 ATTATGTAAG
* *
31489509 TTATGTAAATTATGTAAGATATGATATATATATTTATGTA
1 TTATGTAAATTATGTAAGATATGATATATATATATATATA
*
31489549 TTATGTAAGTTATGTAA-AT-T-ATATAATATATGATATATA
1 TTATGTAAATTATGTAAGATATGATAT-ATATAT-ATATATA
31489588 TTTATGT
1 -TTATGT
31489595 TGATGGGATT
Statistics
Matches: 40, Mismatches: 3, Indels: 6
0.82 0.06 0.12
Matches are distributed among these distances:
37 4 0.10
38 7 0.17
39 7 0.17
40 22 0.55
ACGTcount: A:0.40, C:0.00, G:0.12, T:0.49
Consensus pattern (40 bp):
TTATGTAAATTATGTAAGATATGATATATATATATATATA
Found at i:31489835 original size:91 final size:91
Alignment explanation
Indices: 31489725--31489973 Score: 396
Period size: 89 Copynumber: 2.8 Consensus size: 91
31489715 AATAATGATT
*
31489725 TTTAATTAGGTAATTTAAAAATAAAATAAAAGTAGACAAAATATTTTTCGTGTTTAAAATAAAAT
1 TTTAATTAGGTAATTTAAAAATAAAATAAAAGTAGACAAAATATTTTTCGTGATTAAAATAAAAT
*
31489790 AAAACAAAATTTTAAATACAATTTAA
66 AAAACAAAACTTTAAATACAATTTAA
* *
31489816 TTTAATTAGGTAATTTAAAAATAAAATAAAAGTAGAC--AATTTTTTTCCTGATTAAAATAAAAT
1 TTTAATTAGGTAATTTAAAAATAAAATAAAAGTAGACAAAATATTTTTCGTGATTAAAATAAAAT
*
31489879 AAAATAAAACTTTAAATACAATTTAA
66 AAAACAAAACTTTAAATACAATTTAA
* * *
31489905 TTTAATTAGGTAATTTAAAATTAAAATTAAAGTAGACAAAATATTTATCGTGATT-AAATCAAAA
1 TTTAATTAGGTAATTTAAAAATAAAATAAAAGTAGACAAAATATTTTTCGTGATTAAAAT-AAAA
31489969 TAAAA
65 TAAAA
31489974 TAATATCTTC
Statistics
Matches: 145, Mismatches: 10, Indels: 6
0.90 0.06 0.04
Matches are distributed among these distances:
89 82 0.57
90 4 0.03
91 59 0.41
ACGTcount: A:0.53, C:0.05, G:0.07, T:0.35
Consensus pattern (91 bp):
TTTAATTAGGTAATTTAAAAATAAAATAAAAGTAGACAAAATATTTTTCGTGATTAAAATAAAAT
AAAACAAAACTTTAAATACAATTTAA
Found at i:31494504 original size:26 final size:26
Alignment explanation
Indices: 31494446--31494498 Score: 90
Period size: 26 Copynumber: 2.1 Consensus size: 26
31494436 AGAATTAGAT
31494446 AAAATTTGAAATCTTGAAAATTATTA
1 AAAATTTGAAATCTTGAAAATTATTA
*
31494472 AAAATTTGAAATCTTTAAAATT-TTA
1 AAAATTTGAAATCTTGAAAATTATTA
31494497 AA
1 AA
31494499 TTATTTAATA
Statistics
Matches: 26, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
25 5 0.19
26 21 0.81
ACGTcount: A:0.51, C:0.04, G:0.06, T:0.40
Consensus pattern (26 bp):
AAAATTTGAAATCTTGAAAATTATTA
Found at i:31494505 original size:17 final size:17
Alignment explanation
Indices: 31494449--31494506 Score: 55
Period size: 16 Copynumber: 3.4 Consensus size: 17
31494439 ATTAGATAAA
*
31494449 ATTTGAAATCTTGAAAATT
1 ATTTAAAAT-TTG-AAATT
*
31494468 ATTAAAAATTTGAAA-T
1 ATTTAAAATTTGAAATT
* *
31494484 CTTTAAAATTTTAAATT
1 ATTTAAAATTTGAAATT
31494501 ATTTAA
1 ATTTAA
31494507 TATATATAAA
Statistics
Matches: 32, Mismatches: 6, Indels: 4
0.76 0.14 0.10
Matches are distributed among these distances:
16 13 0.41
17 9 0.28
18 3 0.09
19 7 0.22
ACGTcount: A:0.47, C:0.03, G:0.05, T:0.45
Consensus pattern (17 bp):
ATTTAAAATTTGAAATT
Found at i:31494907 original size:15 final size:14
Alignment explanation
Indices: 31494887--31495014 Score: 58
Period size: 14 Copynumber: 8.7 Consensus size: 14
31494877 TTTTAACTCA
31494887 TAAACCATAAACCCC
1 TAAACCATAAA-CCC
*
31494902 TAAACCTTAAACCC
1 TAAACCATAAACCC
** *
31494916 TAAACCCATAATTCA
1 TAAA-CCATAAACCC
* ***
31494931 TAAACCTTAAAATA
1 TAAACCATAAACCC
*
31494945 TTAACTCATCATAAACCC
1 TAAAC-C---ATAAACCC
*
31494963 TAAACCCTAAACCC
1 TAAACCATAAACCC
* * * *
31494977 TGAACTATATACTC
1 TAAACCATAAACCC
*
31494991 TAAACCATAAACCT
1 TAAACCATAAACCC
*
31495005 TAAACTATAA
1 TAAACCATAA
31495015 TGATAAGTAA
Statistics
Matches: 81, Mismatches: 27, Indels: 11
0.68 0.23 0.09
Matches are distributed among these distances:
14 51 0.63
15 21 0.26
17 1 0.01
18 8 0.10
ACGTcount: A:0.46, C:0.29, G:0.01, T:0.24
Consensus pattern (14 bp):
TAAACCATAAACCC
Found at i:31494926 original size:37 final size:37
Alignment explanation
Indices: 31494848--31494936 Score: 99
Period size: 37 Copynumber: 2.4 Consensus size: 37
31494838 ATCACTAAGT
* ** * *
31494848 CATAATCCATAAACCCCTAAACCTTGAGATTTTAACT
1 CATAATCCATAAACCCCTAAACCTTGAAACCTAAACC
*
31494885 CATAAACCATAAACCCCTAAACCTT-AAACCCTAAACC
1 CATAATCCATAAACCCCTAAACCTTGAAA-CCTAAACC
*
31494922 CATAATTCATAAACC
1 CATAATCCATAAACC
31494937 TTAAAATATT
Statistics
Matches: 43, Mismatches: 8, Indels: 2
0.81 0.15 0.04
Matches are distributed among these distances:
36 2 0.05
37 41 0.95
ACGTcount: A:0.43, C:0.31, G:0.02, T:0.24
Consensus pattern (37 bp):
CATAATCCATAAACCCCTAAACCTTGAAACCTAAACC
Found at i:31494934 original size:22 final size:22
Alignment explanation
Indices: 31494884--31494941 Score: 62
Period size: 22 Copynumber: 2.6 Consensus size: 22
31494874 AGATTTTAAC
*
31494884 TCATAAACCATAAACCCCTAAA
1 TCATAAACCATAAACCCATAAA
* * * *
31494906 CCTTAAACCCTAAACCCATAAT
1 TCATAAACCATAAACCCATAAA
*
31494928 TCATAAACCTTAAA
1 TCATAAACCATAAA
31494942 ATATTAACTC
Statistics
Matches: 28, Mismatches: 8, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
22 28 1.00
ACGTcount: A:0.47, C:0.31, G:0.00, T:0.22
Consensus pattern (22 bp):
TCATAAACCATAAACCCATAAA
Found at i:31494975 original size:14 final size:14
Alignment explanation
Indices: 31494954--31495014 Score: 59
Period size: 14 Copynumber: 4.4 Consensus size: 14
31494944 ATTAACTCAT
31494954 CATAAACCCTAAAC
1 CATAAACCCTAAAC
* *
31494968 CCTAAACCCTGAAC
1 CATAAACCCTAAAC
* * *
31494982 TATATACTCTAAAC
1 CATAAACCCTAAAC
*
31494996 CATAAACCTTAAAC
1 CATAAACCCTAAAC
*
31495010 TATAA
1 CATAA
31495015 TGATAAGTAA
Statistics
Matches: 35, Mismatches: 12, Indels: 0
0.74 0.26 0.00
Matches are distributed among these distances:
14 35 1.00
ACGTcount: A:0.46, C:0.30, G:0.02, T:0.23
Consensus pattern (14 bp):
CATAAACCCTAAAC
Found at i:31495352 original size:41 final size:41
Alignment explanation
Indices: 31495332--31495466 Score: 189
Period size: 41 Copynumber: 3.3 Consensus size: 41
31495322 TTACCAGCAT
31495332 TTTTTCAAAAAGCACCGCTATAGGTCTGAGCATTAGCGGCG
1 TTTTTCAAAAAGCACCGCTATAGGTCTGAGCATTAGCGGCG
* * *
31495373 TTTTTCAAAAAGCGCCCCTATAGGTCTGAGAATTAGCGGCG
1 TTTTTCAAAAAGCACCGCTATAGGTCTGAGCATTAGCGGCG
* * * *
31495414 TTTTTAAAAAAGCACCGCTATATGTTTGAGCATTAGCAGCG
1 TTTTTCAAAAAGCACCGCTATAGGTCTGAGCATTAGCGGCG
*
31495455 CTTTTTAAAAAA
1 -TTTTTCAAAAA
31495467 CGCCACTAAT
Statistics
Matches: 83, Mismatches: 10, Indels: 1
0.88 0.11 0.01
Matches are distributed among these distances:
41 72 0.87
42 11 0.13
ACGTcount: A:0.30, C:0.19, G:0.21, T:0.30
Consensus pattern (41 bp):
TTTTTCAAAAAGCACCGCTATAGGTCTGAGCATTAGCGGCG
Found at i:31497346 original size:50 final size:50
Alignment explanation
Indices: 31497253--31497347 Score: 147
Period size: 50 Copynumber: 1.9 Consensus size: 50
31497243 GGATTACAAC
* *
31497253 TCGATGCCAATGCCATATCCCAGACATGTTCTTGCATGAGATCTCTTATG
1 TCGATGCCAATGCCATATCCCAGACATGGTCTTACATGAGATCTCTTATG
*
31497303 TCGATGCCAATGCCATGTCCCAGACATGGTCTTACAT-AGGATCTC
1 TCGATGCCAATGCCATATCCCAGACATGGTCTTACATGA-GATCTC
31497348 ATATCAACGC
Statistics
Matches: 41, Mismatches: 3, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
49 1 0.02
50 40 0.98
ACGTcount: A:0.24, C:0.27, G:0.19, T:0.29
Consensus pattern (50 bp):
TCGATGCCAATGCCATATCCCAGACATGGTCTTACATGAGATCTCTTATG
Found at i:31502476 original size:27 final size:27
Alignment explanation
Indices: 31502446--31502539 Score: 77
Period size: 26 Copynumber: 3.6 Consensus size: 27
31502436 TGTAGGGTAG
**
31502446 AATTACTGAAATACCATTGGTTTACAA
1 AATTACTGAAATACCATCAGTTTACAA
* *
31502473 AATTCCTG-AATACCCTCAGTTTACAA
1 AATTACTGAAATACCATCAGTTTACAA
** * *
31502499 AATTACCAAAATACCCTC-GATTAGCAA
1 AATTACTGAAATACCATCAGTTTA-CAA
*
31502526 AATTAC-CAAATACC
1 AATTACTGAAATACC
31502540 CCTATTTTGT
Statistics
Matches: 56, Mismatches: 9, Indels: 5
0.80 0.13 0.07
Matches are distributed among these distances:
26 31 0.55
27 25 0.45
ACGTcount: A:0.41, C:0.23, G:0.07, T:0.28
Consensus pattern (27 bp):
AATTACTGAAATACCATCAGTTTACAA
Found at i:31502494 original size:26 final size:26
Alignment explanation
Indices: 31502465--31502757 Score: 135
Period size: 27 Copynumber: 11.0 Consensus size: 26
31502455 AATACCATTG
**
31502465 GTTTACAAAATT-CCTGAATACCCTC
1 GTTTACAAAATTACCAAAATACCCTC
31502490 AGTTTACAAAATTACCAAAATACCCTC
1 -GTTTACAAAATTACCAAAATACCCTC
* *
31502517 GATTAGCAAAATTACC-AAATACCCCTA
1 GTTTA-CAAAATTACCAAAATA-CCCTC
* ** *
31502544 TTTTGTAAAATTACCAAAATACCACTA
1 GTTTACAAAATTACCAAAATACC-CTC
* ** *
31502571 ATTTATGAAATTACCAAAATACCCTT
1 GTTTACAAAATTACCAAAATACCCTC
** ** * * *
31502597 GACCTGTAAAATTATCGAAATACCCTT
1 G-TTTACAAAATTACCAAAATACCCTC
* ** *
31502624 GACTTGTAAAATTA-CATAAATACCCTTA
1 G-TTTACAAAATTACCA-AAATACCC-TC
* * *
31502652 ATTTATAAAATTACCAAAATACCCTT
1 GTTTACAAAATTACCAAAATACCCTC
** * *
31502678 GATTTGGAAAATTACCGAAATACCCTT
1 G-TTTACAAAATTACCAAAATACCCTC
** *
31502705 GATTTGGAAAATTA-CAGAAATACCCCTA
1 G-TTTACAAAATTACCA-AAATA-CCCTC
* *
31502733 ATTTACAAAATTACAAAAATACCCT
1 GTTTACAAAATTACCAAAATACCCT
31502758 TAACTTTCAA
Statistics
Matches: 218, Mismatches: 36, Indels: 26
0.78 0.13 0.09
Matches are distributed among these distances:
26 41 0.19
27 169 0.78
28 8 0.04
ACGTcount: A:0.42, C:0.21, G:0.07, T:0.30
Consensus pattern (26 bp):
GTTTACAAAATTACCAAAATACCCTC
Found at i:31502563 original size:27 final size:26
Alignment explanation
Indices: 31502497--31502841 Score: 248
Period size: 27 Copynumber: 12.8 Consensus size: 26
31502487 CTCAGTTTAC
* * *
31502497 AAAATTACCAAAATACCCTCGATTAGC
1 AAAATTACCAAAATACCCT-TATTTGT
*
31502524 AAAATTACC-AAATACCCCTATTTTGT
1 AAAATTACCAAAATACCCTTA-TTTGT
* *
31502550 AAAATTACCAAAATACCACTAATTTAT
1 AAAATTACCAAAATACC-CTTATTTGT
* **
31502577 GAAATTACCAAAATACCCTTGACCTGT
1 AAAATTACCAAAATACCCTT-ATTTGT
* * *
31502604 AAAATTATCGAAATACCCTTGACTTGT
1 AAAATTACCAAAATACCCTT-ATTTGT
*
31502631 AAAATTA-CATAAATACCCTTAATTTAT
1 AAAATTACCA-AAATACCCTT-ATTTGT
*
31502658 AAAATTACCAAAATACCCTTGATTTGG
1 AAAATTACCAAAATACCCTT-ATTTGT
* *
31502685 AAAATTACCGAAATACCCTTGATTTGG
1 AAAATTACCAAAATACCCTT-ATTTGT
* **
31502712 AAAATTA-CAGAAATACCCCTAATTTAC
1 AAAATTACCA-AAATA-CCCTTATTTGT
* **
31502739 AAAATTACAAAAATACCCTTAACTTTCA
1 AAAATTACCAAAATACCCTT-A-TTTGT
* * ** *
31502767 AAAATTA-TACAAATACCATTGGTTGC
1 AAAATTACCA-AAATACCCTTATTTGT
*
31502793 AAAATTACCAAAATACCCTTGGTTTGT
1 AAAATTACCAAAATACCCTT-ATTTGT
* * *
31502820 AGATTTACCAAAACACCCTTAT
1 AAAATTACCAAAATACCCTTAT
31502842 AGGGTGAAAT
Statistics
Matches: 258, Mismatches: 46, Indels: 29
0.77 0.14 0.09
Matches are distributed among these distances:
25 1 0.00
26 47 0.18
27 182 0.71
28 28 0.11
ACGTcount: A:0.43, C:0.21, G:0.07, T:0.30
Consensus pattern (26 bp):
AAAATTACCAAAATACCCTTATTTGT
Found at i:31502646 original size:81 final size:77
Alignment explanation
Indices: 31502481--31502811 Score: 317
Period size: 81 Copynumber: 4.1 Consensus size: 77
31502471 AAAATTCCTG
* * * * *
31502481 AATACCCTCAGTTTACAAAATTACCAAAATACCCTCGATTAGCAAAATTACCAAATACCCCT-AT
1 AATACCCT-AATTTATAAAATTACCAAAATACCCTTGATT-GCAAAATTACGAAATACCCTTGA-
31502545 TTTGTAAAATTACCAA
63 TTTGTAAAATTA-CAA
* * *
31502561 AATACCACTAATTTATGAAATTACCAAAATACCCTTGACCTGTAAAATTATCGAAATACCCTTGA
1 AATACC-CTAATTTATAAAATTACCAAAATACCCTTGA-TTGCAAAATTA-CGAAATACCCTTGA
*
31502626 CTTGTAAAATTACATA
63 TTTGTAAAATTACA-A
*
31502642 AATACCCTTAATTTATAAAATTACCAAAATACCCTTGATTTGGAAAATTACCGAAATACCCTTGA
1 AATACCC-TAATTTATAAAATTACCAAAATACCCTTGA-TTGCAAAATTA-CGAAATACCCTTGA
*
31502707 TTTGGAAAATTACAGA
63 TTTGTAAAATTACA-A
* * * * *
31502723 AATACCCCTAATTTACAAAATTACAAAAATACCCTTAACTTTCAAAAATTATAC-AAATACCATT
1 AATA-CCCTAATTTATAAAATTACCAAAATACCCTTGA-TTGC-AAAA-T-TACGAAATACCCTT
* *
31502787 G-GTTGCAAAATTACCAA
61 GATTTGTAAAATTA-CAA
31502804 AATACCCT
1 AATACCCT
31502812 TGGTTTGTAG
Statistics
Matches: 214, Mismatches: 26, Indels: 22
0.82 0.10 0.08
Matches are distributed among these distances:
80 46 0.21
81 144 0.67
82 20 0.09
83 2 0.01
84 2 0.01
ACGTcount: A:0.43, C:0.21, G:0.06, T:0.29
Consensus pattern (77 bp):
AATACCCTAATTTATAAAATTACCAAAATACCCTTGATTGCAAAATTACGAAATACCCTTGATTT
GTAAAATTACAA
Found at i:31503122 original size:41 final size:41
Alignment explanation
Indices: 31503077--31503199 Score: 165
Period size: 41 Copynumber: 3.0 Consensus size: 41
31503067 GGGGGAAGAA
* *
31503077 ATTGAGAATCGCATGGTTGCTTGATGACTGTGGATCCACCG
1 ATTGAGGATCGCATGGTTGCTTGACGACTGTGGATCCACCG
* * *
31503118 ATTGAGGATCGCATGGTTTCTTGACGACTGTTGATCCACCA
1 ATTGAGGATCGCATGGTTGCTTGACGACTGTGGATCCACCG
* * * *
31503159 ATTAAGGATCGCATGGTTGCTTAACAACCGTGGATCCACCG
1 ATTGAGGATCGCATGGTTGCTTGACGACTGTGGATCCACCG
31503200 GTGGCTTTTA
Statistics
Matches: 70, Mismatches: 12, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
41 70 1.00
ACGTcount: A:0.24, C:0.22, G:0.26, T:0.28
Consensus pattern (41 bp):
ATTGAGGATCGCATGGTTGCTTGACGACTGTGGATCCACCG
Found at i:31503388 original size:22 final size:21
Alignment explanation
Indices: 31503338--31503400 Score: 72
Period size: 22 Copynumber: 2.9 Consensus size: 21
31503328 CAATTATTCT
*
31503338 TATTATGGCTTTGTGCCAACC
1 TATTATGGCTCTGTGCCAACC
*
31503359 TACATATGGCTCTGTGCCAACC
1 TA-TTATGGCTCTGTGCCAACC
* *
31503381 TGATTATGGTTGTGTGCCAA
1 T-ATTATGGCTCTGTGCCAA
31503401 ACGTATTTGC
Statistics
Matches: 35, Mismatches: 5, Indels: 3
0.81 0.12 0.07
Matches are distributed among these distances:
21 2 0.06
22 32 0.91
23 1 0.03
ACGTcount: A:0.21, C:0.22, G:0.22, T:0.35
Consensus pattern (21 bp):
TATTATGGCTCTGTGCCAACC
Found at i:31507854 original size:28 final size:28
Alignment explanation
Indices: 31507791--31507888 Score: 128
Period size: 27 Copynumber: 3.5 Consensus size: 28
31507781 ATATTAAGTC
*
31507791 CGCACACTCAGTGCTATATAATC-AACT
1 CGCACACTTAGTGCTATATAATCAAACT
31507818 CGCACACTTAGTGCTATATAATCAAACT
1 CGCACACTTAGTGCTATATAATCAAACT
* * *
31507846 CGCACACTTAGTGCTGA-ACAATTTAAACC
1 CGCACACTTAGTGCT-ATATAA-TCAAACT
31507875 CGCACACTTAGTGC
1 CGCACACTTAGTGC
31507889 CAATCTCATG
Statistics
Matches: 64, Mismatches: 4, Indels: 4
0.89 0.06 0.06
Matches are distributed among these distances:
27 22 0.34
28 22 0.34
29 20 0.31
ACGTcount: A:0.33, C:0.29, G:0.13, T:0.26
Consensus pattern (28 bp):
CGCACACTTAGTGCTATATAATCAAACT
Found at i:31512168 original size:27 final size:26
Alignment explanation
Indices: 31512138--31512322 Score: 106
Period size: 27 Copynumber: 6.8 Consensus size: 26
31512128 TATAGGGTAG
* *
31512138 AATTACTGCAATACCCTTGGTTTATAA
1 AATTACT-AAATACCCTTGGTTTACAA
* *
31512165 AATTAATAAATGCCCTTGGTTTACAA
1 AATTACTAAATACCCTTGGTTTACAA
* * *
31512191 AATTACCAAAATACCC-TCGATTAGCAA
1 AATTA-CTAAATACCCTTGGTTTA-CAA
* * *
31512218 AATTATCAAAATACCCCTGATTTACAA
1 AATTA-CTAAATACCCTTGGTTTACAA
* *
31512245 AATTACAAAAATACCCTTGACTTT-CAAA
1 AATTAC-TAAATACCCTTG-GTTTAC-AA
* * *
31512273 AATTA-TAGAAATACCATTAGTTTGCAA
1 AATTACT--AAATACCCTTGGTTTACAA
* *
31512300 AATTACCGAAATACCCTTAGTTT
1 AATTA-CTAAATACCCTTGGTTT
31512323 TTAAATTTAC
Statistics
Matches: 126, Mismatches: 21, Indels: 22
0.75 0.12 0.13
Matches are distributed among these distances:
26 27 0.21
27 75 0.60
28 24 0.19
ACGTcount: A:0.41, C:0.19, G:0.08, T:0.31
Consensus pattern (26 bp):
AATTACTAAATACCCTTGGTTTACAA
Found at i:31512273 original size:54 final size:55
Alignment explanation
Indices: 31512184--31512287 Score: 142
Period size: 54 Copynumber: 1.9 Consensus size: 55
31512174 ATGCCCTTGG
*
31512184 TTTACAAAATTACCAAAATACCCTCGATTAGC-AAAATTATCA-AAATACCCCTGA
1 TTTACAAAATTACAAAAATACCCTCGATTAGCAAAAATTAT-AGAAATACCCCTGA
* *
31512238 TTTACAAAATTACAAAAATACCCTTGACTT-TCAAAAATTATAGAAATACC
1 TTTACAAAATTACAAAAATACCCTCGA-TTAGCAAAAATTATAGAAATACC
31512288 ATTAGTTTGC
Statistics
Matches: 44, Mismatches: 3, Indels: 5
0.85 0.06 0.10
Matches are distributed among these distances:
54 27 0.61
55 17 0.39
ACGTcount: A:0.46, C:0.21, G:0.05, T:0.28
Consensus pattern (55 bp):
TTTACAAAATTACAAAAATACCCTCGATTAGCAAAAATTATAGAAATACCCCTGA
Found at i:31512301 original size:55 final size:53
Alignment explanation
Indices: 31512183--31512317 Score: 148
Period size: 55 Copynumber: 2.5 Consensus size: 53
31512173 AATGCCCTTG
* *
31512183 GTTTACAAAATTACCAAAATACCCTCGATTAGCAAAATTATCAAAATACCCCT
1 GTTTACAAAATTACCAAAATACCCTTGATTAGCAAAATTATCAAAATACCACT
* * *
31512236 GATTTACAAAATTACAAAAATACCCTTGACTT-TCAAAAATTAT-AGAAATACCATT
1 G-TTTACAAAATTACCAAAATACCCTTGA-TTAGC-AAAATTATCA-AAATACCACT
* *
31512291 AGTTTGCAAAATTACCGAAATACCCTT
1 -GTTTACAAAATTACCAAAATACCCTT
31512318 AGTTTTTAAA
Statistics
Matches: 69, Mismatches: 8, Indels: 8
0.81 0.09 0.09
Matches are distributed among these distances:
53 1 0.01
54 27 0.39
55 40 0.58
56 1 0.01
ACGTcount: A:0.44, C:0.21, G:0.07, T:0.29
Consensus pattern (53 bp):
GTTTACAAAATTACCAAAATACCCTTGATTAGCAAAATTATCAAAATACCACT
Found at i:31512475 original size:20 final size:20
Alignment explanation
Indices: 31512452--31512494 Score: 52
Period size: 20 Copynumber: 2.1 Consensus size: 20
31512442 CTATGTTTTA
31512452 ATTGAGAATG-TATGACTGTG
1 ATTG-GAATGTTATGACTGTG
* *
31512472 ATTGGACTGTTGTGACTGTG
1 ATTGGAATGTTATGACTGTG
31512492 ATT
1 ATT
31512495 TGTATGGTTT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
19 4 0.20
20 16 0.80
ACGTcount: A:0.23, C:0.07, G:0.30, T:0.40
Consensus pattern (20 bp):
ATTGGAATGTTATGACTGTG
Found at i:31512628 original size:41 final size:41
Alignment explanation
Indices: 31512583--31512705 Score: 169
Period size: 41 Copynumber: 3.0 Consensus size: 41
31512573 GGGGGAAGAA
*
31512583 ATTGAGGATTGCATGGTTGTTTGACGA-CTGTGGATCCACCG
1 ATTGAGGATCGCATGGTTGTTTGACGATC-GTGGATCCACCG
* *
31512624 ATTGAGGATCGCATGGTT-TCTTGATGATCGTGGATCTACCG
1 ATTGAGGATCGCATGGTTGT-TTGACGATCGTGGATCCACCG
* *
31512665 ATTAAGGATCGCATGGTTGCTTGACGATCGTGGATCCACCG
1 ATTGAGGATCGCATGGTTGTTTGACGATCGTGGATCCACCG
31512706 GTGGCTTTTA
Statistics
Matches: 72, Mismatches: 7, Indels: 6
0.85 0.08 0.07
Matches are distributed among these distances:
40 1 0.01
41 70 0.97
42 1 0.01
ACGTcount: A:0.20, C:0.19, G:0.30, T:0.31
Consensus pattern (41 bp):
ATTGAGGATCGCATGGTTGTTTGACGATCGTGGATCCACCG
Found at i:31512876 original size:22 final size:22
Alignment explanation
Indices: 31512846--31512904 Score: 84
Period size: 22 Copynumber: 2.7 Consensus size: 22
31512836 AATTATTCTG
*
31512846 ATTATGGCTTTGTGCCAACCTA
1 ATTATGGCTATGTGCCAACCTA
*
31512868 CA-TATGGCTCTGTGCCAACCTA
1 -ATTATGGCTATGTGCCAACCTA
31512890 ATTATGGCTATGTGC
1 ATTATGGCTATGTGC
31512905 TAAACATATT
Statistics
Matches: 33, Mismatches: 2, Indels: 3
0.87 0.05 0.08
Matches are distributed among these distances:
21 1 0.03
22 31 0.94
23 1 0.03
ACGTcount: A:0.22, C:0.24, G:0.20, T:0.34
Consensus pattern (22 bp):
ATTATGGCTATGTGCCAACCTA
Found at i:31513352 original size:32 final size:32
Alignment explanation
Indices: 31513305--31513368 Score: 101
Period size: 32 Copynumber: 2.0 Consensus size: 32
31513295 GCATATGGGT
* *
31513305 TTGATTCTGATATGGGCTAGGCCCAACTGATA
1 TTGATTCTAAGATGGGCTAGGCCCAACTGATA
*
31513337 TTGATTCTAAGATGGGCTAGGCCCAATTGATA
1 TTGATTCTAAGATGGGCTAGGCCCAACTGATA
31513369 CTGTGATGGG
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
32 29 1.00
ACGTcount: A:0.27, C:0.17, G:0.25, T:0.31
Consensus pattern (32 bp):
TTGATTCTAAGATGGGCTAGGCCCAACTGATA
Found at i:31517722 original size:35 final size:34
Alignment explanation
Indices: 31517672--31517761 Score: 99
Period size: 35 Copynumber: 2.6 Consensus size: 34
31517662 ACATACAAAG
*
31517672 TCTATCCCAATCTTTTTAAAATTTCCTTAGATTGA
1 TCTATCCCAA-CTTTTTAAAATTTCCATAGATTGA
** * *
31517707 TCTATCCCAACCTTTTTAAGGTTTGCATAGATTGG
1 TCTATCCCAA-CTTTTTAAAATTTCCATAGATTGA
* *
31517742 TCTATCCTAACTCTTTAAAA
1 TCTATCCCAACTTTTTAAAA
31517762 GTCAGTATAT
Statistics
Matches: 45, Mismatches: 10, Indels: 1
0.80 0.18 0.02
Matches are distributed among these distances:
34 7 0.16
35 38 0.84
ACGTcount: A:0.28, C:0.21, G:0.09, T:0.42
Consensus pattern (34 bp):
TCTATCCCAACTTTTTAAAATTTCCATAGATTGA
Found at i:31526243 original size:24 final size:24
Alignment explanation
Indices: 31526216--31526331 Score: 105
Period size: 24 Copynumber: 4.8 Consensus size: 24
31526206 AAAAGCAAGA
* *
31526216 GAAAAAGGACAAGAAAAAAAGAAT
1 GAAAAAGAAAAAGAAAAAAAGAAT
31526240 GAAAAAGAAAAAGAAAAGAAAG--T
1 GAAAAAGAAAAAGAAAA-AAAGAAT
* *
31526263 CGAGAAAAGGAAAGGAAAAAAAGAAT
1 -GA-AAAAGAAAAAGAAAAAAAGAAT
*
31526289 GAAAAAGAAAAAGAAAAGAA-AAT
1 GAAAAAGAAAAAGAAAAAAAGAAT
*
31526312 CAAGAAA-AAGAAAGAAAAAA
1 GAA-AAAGAA-AAAGAAAAAA
31526332 GTGAGAAAAG
Statistics
Matches: 76, Mismatches: 9, Indels: 14
0.77 0.09 0.14
Matches are distributed among these distances:
23 8 0.11
24 48 0.63
25 19 0.25
26 1 0.01
ACGTcount: A:0.73, C:0.03, G:0.21, T:0.03
Consensus pattern (24 bp):
GAAAAAGAAAAAGAAAAAAAGAAT
Found at i:31526251 original size:6 final size:6
Alignment explanation
Indices: 31526203--31526324 Score: 63
Period size: 6 Copynumber: 19.8 Consensus size: 6
31526193 AAGAGTCTCT
* * * * *
31526203 AGAAAA AGCAAG AGAAAA AGGACA AGAAAA A-AAGAA TGAAAA AGAAAA
1 AGAAAA AGAAAA AGAAAA AGAAAA AGAAAA AGAA-AA AGAAAA AGAAAA
* * * * *
31526251 AG-AAA AGAAAGT CGAGAAA AGGAAA GGAAAA A-AAGAA TGAAAA AGAAAA
1 AGAAAA AGAAA-A AGA-AAA AGAAAA AGAAAA AGAA-AA AGAAAA AGAAAA
31526300 AG-AAA AGAAAATCA AGAAAA AGAAA
1 AGAAAA AG-AAA--A AGAAAA AGAAA
31526325 GAAAAAAGTG
Statistics
Matches: 85, Mismatches: 20, Indels: 22
0.67 0.16 0.17
Matches are distributed among these distances:
5 14 0.16
6 54 0.64
7 9 0.11
8 5 0.06
9 3 0.04
ACGTcount: A:0.72, C:0.03, G:0.21, T:0.03
Consensus pattern (6 bp):
AGAAAA
Found at i:31526271 original size:49 final size:48
Alignment explanation
Indices: 31526218--31526331 Score: 183
Period size: 49 Copynumber: 2.3 Consensus size: 48
31526208 AAGCAAGAGA
* *
31526218 AAAAGGACAAGAAAAAAAGAATGAAAAAGAAAAAGAAAAGAAAGTCGAG
1 AAAAGGA-AAGAAAAAAAGAATGAAAAAGAAAAAGAAAAGAAAATCAAG
31526267 AAAAGGAAAGGAAAAAAAGAATGAAAAAGAAAAAGAAAAGAAAATCAAG
1 AAAAGGAAA-GAAAAAAAGAATGAAAAAGAAAAAGAAAAGAAAATCAAG
*
31526316 AAAAAGAAAGAAAAAA
1 AAAAGGAAAGAAAAAA
31526332 GTGAGAAAAG
Statistics
Matches: 61, Mismatches: 3, Indels: 3
0.91 0.04 0.04
Matches are distributed among these distances:
48 9 0.15
49 52 0.85
ACGTcount: A:0.74, C:0.03, G:0.20, T:0.04
Consensus pattern (48 bp):
AAAAGGAAAGAAAAAAAGAATGAAAAAGAAAAAGAAAAGAAAATCAAG
Found at i:31526317 original size:30 final size:29
Alignment explanation
Indices: 31526265--31526330 Score: 71
Period size: 29 Copynumber: 2.2 Consensus size: 29
31526255 AAGAAAGTCG
* * *
31526265 AGAAAAGGAAAGGAAAAAAAGAATGAA-AA
1 AGAAAAAGAAAAGAAAAAAAGAA-AAAGAA
*
31526294 AGAAAAAGAAAAGAAAATCAAGAAAAAGAA
1 AGAAAAAGAAAAGAAAA-AAAGAAAAAGAA
31526324 AGAAAAA
1 AGAAAAA
31526331 AGTGAGAAAA
Statistics
Matches: 31, Mismatches: 4, Indels: 3
0.82 0.11 0.08
Matches are distributed among these distances:
29 17 0.55
30 14 0.45
ACGTcount: A:0.76, C:0.02, G:0.20, T:0.03
Consensus pattern (29 bp):
AGAAAAAGAAAAGAAAAAAAGAAAAAGAA
Found at i:31526320 original size:10 final size:10
Alignment explanation
Indices: 31526203--31526330 Score: 55
Period size: 10 Copynumber: 11.7 Consensus size: 10
31526193 AAGAGTCTCT
31526203 AGAAAAAGCAA
1 AGAAAAAG-AA
31526214 GAGAAAAAGGACA
1 -AGAAAAA-GA-A
31526227 AGAAAAAAAGAA
1 AG--AAAAAGAA
*
31526239 TGAAAAAGAA
1 AGAAAAAGAA
*
31526249 AAAGAAAAGAA
1 AGA-AAAAGAA
31526260 AGTCGAGAAAAGGAA
1 A---GA-AAAA-GAA
*
31526275 AGGAAAA-AA
1 AGAAAAAGAA
*
31526284 AGAATGAA-AA
1 AGAA-AAAGAA
31526294 AGAAAAAGAA
1 AGAAAAAGAA
**
31526304 A-AGAAAATCA
1 AGA-AAAAGAA
31526314 AGAAAAAGAA
1 AGAAAAAGAA
31526324 AGAAAAA
1 AGAAAAA
31526331 AGTGAGAAAA
Statistics
Matches: 91, Mismatches: 12, Indels: 28
0.69 0.09 0.21
Matches are distributed among these distances:
9 8 0.09
10 38 0.42
11 13 0.14
12 13 0.14
13 4 0.04
14 11 0.12
15 4 0.04
ACGTcount: A:0.73, C:0.03, G:0.21, T:0.03
Consensus pattern (10 bp):
AGAAAAAGAA
Found at i:31526330 original size:20 final size:20
Alignment explanation
Indices: 31526293--31526329 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
31526283 AAGAATGAAA
31526293 AAGAAAAAGAAAAGAAAATC
1 AAGAAAAAGAAAAGAAAATC
31526313 AAGAAAAAG-AAAGAAAA
1 AAGAAAAAGAAAAGAAAA
31526330 AAGTGAGAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
19 8 0.47
20 9 0.53
ACGTcount: A:0.78, C:0.03, G:0.16, T:0.03
Consensus pattern (20 bp):
AAGAAAAAGAAAAGAAAATC
Found at i:31531124 original size:40 final size:40
Alignment explanation
Indices: 31531069--31531242 Score: 147
Period size: 40 Copynumber: 4.4 Consensus size: 40
31531059 TGATAACCGG
* * * *
31531069 GCTAAGTCTCGAAGGCATTTGCGCTAGTGACTAGT-TCCTA
1 GCTAAGTCCCGAAGGCATTTGCGCGAGTGACCA-TATCCGA
* * *
31531109 GCTAAGTCCCGAAGGCATTTGTGCGAGTTACCATATCCGG
1 GCTAAGTCCCGAAGGCATTTGCGCGAGTGACCATATCCGA
* * * *
31531149 GCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATATCCGG
1 GCTAAGTCCCGAAGGCATTTGCGCGAGTGACCATATCCGA
* * * * *
31531189 GCTATGTCCCGAAGGTATTCGAGCGAGT-AGCTATATCCG-
1 GCTAAGTCCCGAAGGCATTTGCGCGAGTGA-CCATATCCGA
* *
31531228 GTTAAATCCCGAAGG
1 GCTAAGTCCCGAAGG
31531243 TACTTGGCTT
Statistics
Matches: 117, Mismatches: 15, Indels: 5
0.85 0.11 0.04
Matches are distributed among these distances:
39 14 0.12
40 103 0.88
ACGTcount: A:0.24, C:0.23, G:0.27, T:0.26
Consensus pattern (40 bp):
GCTAAGTCCCGAAGGCATTTGCGCGAGTGACCATATCCGA
Found at i:31531198 original size:80 final size:80
Alignment explanation
Indices: 31531065--31531242 Score: 200
Period size: 80 Copynumber: 2.2 Consensus size: 80
31531055 TGGATGATAA
* * * *
31531065 CCGGGCTAAGTCTCGAAGGCATTTGCGCTAGTGACTAGTTCCTAGCTAAGTCCCGAAGGCATTTG
1 CCGGGCTAAGTCCCGAAGGCATTTGCGCGAGTGACTAGTTCCGAGCTAAGTCCCGAAGGCATTCG
*
31531130 TGCGAGTTA-CCATAT
66 AGCGAG-TAGCCATAT
* * * * *
31531145 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTA-TATCCGGGCTATGTCCCGAAGGTATTC
1 CCGGGCTAAGTCCCGAAGGCATTTGCGCGAGTGACTAGT-TCCGAGCTAAGTCCCGAAGGCATTC
*
31531209 GAGCGAGTAGCTATAT
65 GAGCGAGTAGCCATAT
* *
31531225 CC-GGTTAAATCCCGAAGG
1 CCGGGCTAAGTCCCGAAGG
31531243 TACTTGGCTT
Statistics
Matches: 83, Mismatches: 13, Indels: 5
0.82 0.13 0.05
Matches are distributed among these distances:
79 17 0.20
80 66 0.80
ACGTcount: A:0.23, C:0.24, G:0.28, T:0.26
Consensus pattern (80 bp):
CCGGGCTAAGTCCCGAAGGCATTTGCGCGAGTGACTAGTTCCGAGCTAAGTCCCGAAGGCATTCG
AGCGAGTAGCCATAT
Found at i:31532944 original size:75 final size:75
Alignment explanation
Indices: 31532855--31533005 Score: 266
Period size: 75 Copynumber: 2.0 Consensus size: 75
31532845 ACAAGGGACA
*
31532855 GCTCCGGCGGACTCTCAACCTAATGCTAGTAACCCGAATGATGAAGCTAGATAAGCTTTCTATAG
1 GCTCCGGCGGACTCTCAACCTAATGCTAGTAACCCGAATGATGAAGCTAGACAAGCTTTCTATAG
31532920 CGTAATGAAT
66 CGTAATGAAT
* *
31532930 GCTCCGGCGGACTCTCAACCTATTGCTAGTAATCCGAATGATGAAGCTAGACAAGCTTTCTATAG
1 GCTCCGGCGGACTCTCAACCTAATGCTAGTAACCCGAATGATGAAGCTAGACAAGCTTTCTATAG
*
31532995 CGTGATGAAT
66 CGTAATGAAT
31533005 G
1 G
31533006 ATTGGTTCAA
Statistics
Matches: 72, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
75 72 1.00
ACGTcount: A:0.29, C:0.23, G:0.23, T:0.26
Consensus pattern (75 bp):
GCTCCGGCGGACTCTCAACCTAATGCTAGTAACCCGAATGATGAAGCTAGACAAGCTTTCTATAG
CGTAATGAAT
Found at i:31554031 original size:26 final size:27
Alignment explanation
Indices: 31553975--31554030 Score: 67
Period size: 27 Copynumber: 2.1 Consensus size: 27
31553965 ACAAACCATG
* *
31553975 AAAGAAAAACTTTTATGGTGAAATATA
1 AAAGAAAAACCTTTATGGCGAAATATA
* * *
31554002 AAAGAAAAGCCTTTGTGGCGAATTATA
1 AAAGAAAAACCTTTATGGCGAAATATA
31554029 AA
1 AA
31554031 GGGATAGCCT
Statistics
Matches: 24, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
27 24 1.00
ACGTcount: A:0.48, C:0.07, G:0.18, T:0.27
Consensus pattern (27 bp):
AAAGAAAAACCTTTATGGCGAAATATA
Found at i:31557215 original size:27 final size:27
Alignment explanation
Indices: 31557184--31557263 Score: 142
Period size: 27 Copynumber: 3.0 Consensus size: 27
31557174 AATAAATTTT
*
31557184 TCCTACACTAGACACATTAAAATTATG
1 TCCTAAACTAGACACATTAAAATTATG
31557211 TCCTAAACTAGACACATTAAAATTATG
1 TCCTAAACTAGACACATTAAAATTATG
*
31557238 TTCTAAACTAGACACATTAAAATTAT
1 TCCTAAACTAGACACATTAAAATTAT
31557264 ATTAATATAA
Statistics
Matches: 51, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
27 51 1.00
ACGTcount: A:0.44, C:0.19, G:0.06, T:0.31
Consensus pattern (27 bp):
TCCTAAACTAGACACATTAAAATTATG
Found at i:31563598 original size:48 final size:46
Alignment explanation
Indices: 31563431--31563601 Score: 145
Period size: 48 Copynumber: 3.7 Consensus size: 46
31563421 TTATGAGAGC
* * **
31563431 CAGTGTAAGACCATGTCTAGGACATGGCTTCAGCATTAAGACGAAAG-
1 CAGTGTAAGACCATGTCTAGGACATGGCATCAGCACTAAGA-G-GTGT
* * * *
31563478 CTAATGTAAGA-CATGTCTGGGACAT-GCATC-G-ACTACGAGATGTAT
1 C-AGTGTAAGACCATGTCTAGGACATGGCATCAGCACTA--AGAGGTGT
* *
31563523 CAGTGTAAGACCATGTCTAGAATATGGCATCAGCACGTATAGAGGTGT
1 CAGTGTAAGACCATGTCTAGGACATGGCATCAGCAC-TA-AGAGGTGT
*
31563571 CAGTGTAAGACCATGTCTGGGACATGGCATC
1 CAGTGTAAGACCATGTCTAGGACATGGCATC
31563602 GACCCAAATA
Statistics
Matches: 97, Mismatches: 18, Indels: 17
0.73 0.14 0.13
Matches are distributed among these distances:
44 11 0.11
45 13 0.13
46 12 0.12
47 15 0.15
48 44 0.45
49 2 0.02
ACGTcount: A:0.31, C:0.19, G:0.26, T:0.24
Consensus pattern (46 bp):
CAGTGTAAGACCATGTCTAGGACATGGCATCAGCACTAAGAGGTGT
Found at i:31563636 original size:50 final size:50
Alignment explanation
Indices: 31563574--31564398 Score: 1650
Period size: 50 Copynumber: 16.5 Consensus size: 50
31563564 GAGGTGTCAG
31563574 TGTAAGACCATGTCTGGGACATGGCATCGACCCAAATATGTGAGAGATAA
1 TGTAAGACCATGTCTGGGACATGGCATCGACCCAAATATGTGAGAGATAA
31563624 TGTAAGACCATGTCTGGGACATGGCATCGACCCAAATATGTGAGAGATAA
1 TGTAAGACCATGTCTGGGACATGGCATCGACCCAAATATGTGAGAGATAA
31563674 TGTAAGACCATGTCTGGGACATGGCATCGACCCAAATATGTGAGAGATAA
1 TGTAAGACCATGTCTGGGACATGGCATCGACCCAAATATGTGAGAGATAA
31563724 TGTAAGACCATGTCTGGGACATGGCATCGACCCAAATATGTGAGAGATAA
1 TGTAAGACCATGTCTGGGACATGGCATCGACCCAAATATGTGAGAGATAA
31563774 TGTAAGACCATGTCTGGGACATGGCATCGACCCAAATATGTGAGAGATAA
1 TGTAAGACCATGTCTGGGACATGGCATCGACCCAAATATGTGAGAGATAA
31563824 TGTAAGACCATGTCTGGGACATGGCATCGACCCAAATATGTGAGAGATAA
1 TGTAAGACCATGTCTGGGACATGGCATCGACCCAAATATGTGAGAGATAA
31563874 TGTAAGACCATGTCTGGGACATGGCATCGACCCAAATATGTGAGAGATAA
1 TGTAAGACCATGTCTGGGACATGGCATCGACCCAAATATGTGAGAGATAA
31563924 TGTAAGACCATGTCTGGGACATGGCATCGACCCAAATATGTGAGAGATAA
1 TGTAAGACCATGTCTGGGACATGGCATCGACCCAAATATGTGAGAGATAA
31563974 TGTAAGACCATGTCTGGGACATGGCATCGACCCAAATATGTGAGAGATAA
1 TGTAAGACCATGTCTGGGACATGGCATCGACCCAAATATGTGAGAGATAA
31564024 TGTAAGACCATGTCTGGGACATGGCATCGACCCAAATATGTGAGAGATAA
1 TGTAAGACCATGTCTGGGACATGGCATCGACCCAAATATGTGAGAGATAA
31564074 TGTAAGACCATGTCTGGGACATGGCATCGACCCAAATATGTGAGAGATAA
1 TGTAAGACCATGTCTGGGACATGGCATCGACCCAAATATGTGAGAGATAA
31564124 TGTAAGACCATGTCTGGGACATGGCATCGACCCAAATATGTGAGAGATAA
1 TGTAAGACCATGTCTGGGACATGGCATCGACCCAAATATGTGAGAGATAA
31564174 TGTAAGACCATGTCTGGGACATGGCATCGACCCAAATATGTGAGAGATAA
1 TGTAAGACCATGTCTGGGACATGGCATCGACCCAAATATGTGAGAGATAA
31564224 TGTAAGACCATGTCTGGGACATGGCATCGACCCAAATATGTGAGAGATAA
1 TGTAAGACCATGTCTGGGACATGGCATCGACCCAAATATGTGAGAGATAA
31564274 TGTAAGACCATGTCTGGGACATGGCATCGACCCAAATATGTGAGAGATAA
1 TGTAAGACCATGTCTGGGACATGGCATCGACCCAAATATGTGAGAGATAA
31564324 TGTAAGACCATGTCTGGGACATGGCATCGACCCAAATATGTGAGAGATAA
1 TGTAAGACCATGTCTGGGACATGGCATCGACCCAAATATGTGAGAGATAA
31564374 TGTAAGACCATGTCTGGGACATGGC
1 TGTAAGACCATGTCTGGGACATGGC
31564399 GTCAACCTCG
Statistics
Matches: 775, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
50 775 1.00
ACGTcount: A:0.34, C:0.18, G:0.26, T:0.22
Consensus pattern (50 bp):
TGTAAGACCATGTCTGGGACATGGCATCGACCCAAATATGTGAGAGATAA
Found at i:31566205 original size:22 final size:22
Alignment explanation
Indices: 31566156--31566205 Score: 57
Period size: 22 Copynumber: 2.3 Consensus size: 22
31566146 ACTTTTCTTT
* * *
31566156 TCTTTTTTTAATTTTTCGTAAT
1 TCTTTTTTTAATATTTCCTAAA
31566178 TCTTTTTTTAACTATTTCCTAAA
1 TCTTTTTTTAA-TATTTCCTAAA
31566201 T-TTTT
1 TCTTTT
31566206 ACACTTCAAT
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
22 15 0.62
23 9 0.38
ACGTcount: A:0.20, C:0.12, G:0.02, T:0.66
Consensus pattern (22 bp):
TCTTTTTTTAATATTTCCTAAA
Found at i:31567383 original size:20 final size:19
Alignment explanation
Indices: 31567346--31567396 Score: 57
Period size: 20 Copynumber: 2.6 Consensus size: 19
31567336 TAAATGATAG
***
31567346 CAAATTAATTAAATTAAGA
1 CAAATTAATTAGGCTAAGA
*
31567365 CACCATTAATTAGGCTAAGA
1 CA-AATTAATTAGGCTAAGA
31567385 CAAATTAATTAG
1 CAAATTAATTAG
31567397 CACTAGCTAA
Statistics
Matches: 26, Mismatches: 5, Indels: 2
0.79 0.15 0.06
Matches are distributed among these distances:
19 11 0.42
20 15 0.58
ACGTcount: A:0.49, C:0.12, G:0.10, T:0.29
Consensus pattern (19 bp):
CAAATTAATTAGGCTAAGA
Found at i:31567444 original size:27 final size:27
Alignment explanation
Indices: 31567408--31567494 Score: 149
Period size: 27 Copynumber: 3.3 Consensus size: 27
31567398 ACTAGCTAAT
*
31567408 AAATT-TGTCCTACACTAGACACATTA
1 AAATTATGTCCTAAACTAGACACATTA
31567434 AAATTATGTCCTAAACTAGACACATTA
1 AAATTATGTCCTAAACTAGACACATTA
*
31567461 AAATTATGTTCTAAACTAGACACATTA
1 AAATTATGTCCTAAACTAGACACATTA
31567488 AAATTAT
1 AAATTAT
31567495 ATTAATATAA
Statistics
Matches: 58, Mismatches: 2, Indels: 1
0.95 0.03 0.02
Matches are distributed among these distances:
26 5 0.09
27 53 0.91
ACGTcount: A:0.44, C:0.17, G:0.07, T:0.32
Consensus pattern (27 bp):
AAATTATGTCCTAAACTAGACACATTA
Found at i:31568459 original size:38 final size:37
Alignment explanation
Indices: 31568417--31568514 Score: 99
Period size: 38 Copynumber: 2.6 Consensus size: 37
31568407 AAAATCCTTG
*
31568417 TTATAATTATTGTAATTATAATCTAAGATCAAATATTA
1 TTATAATTATTGTAATTATAATCTAAG-TCAAACATTA
* * * **
31568455 TTATAATTACTGTAA-TAGTATTTTTTTGTCAAACATTA
1 TTATAATTATTGTAATTA-TA-ATCTAAGTCAAACATTA
*
31568493 TTATAATTATGGTAATTATAAT
1 TTATAATTATTGTAATTATAAT
31568515 TATTATGATT
Statistics
Matches: 48, Mismatches: 9, Indels: 7
0.75 0.14 0.11
Matches are distributed among these distances:
37 3 0.06
38 40 0.83
39 5 0.10
ACGTcount: A:0.40, C:0.05, G:0.07, T:0.48
Consensus pattern (37 bp):
TTATAATTATTGTAATTATAATCTAAGTCAAACATTA
Found at i:31571806 original size:43 final size:43
Alignment explanation
Indices: 31571752--31571914 Score: 154
Period size: 43 Copynumber: 3.8 Consensus size: 43
31571742 ACTGAGATGT
* *
31571752 GATTACATGTAAGACCATGTCTGGGACATTGGCATTGTATTGC
1 GATTATATGTAAGACCATGTCTGGGACATTGGCATCGTATTGC
* * * * *
31571795 GATTATGTGTAATACCATGTTTGGGACATTGGCGTCGTTAAT-C
1 GATTATATGTAAGACCATGTCTGGGACATTGGCATCG-TATTGC
* *
31571838 GATT-TCATGTAAGACCCTGTCTGGGACAGTGGCATCG-ATATGC
1 GATTAT-ATGTAAGACCATGTCTGGGACATTGGCATCGTAT-TGC
* * * *
31571881 GATAACATGTAAGACCATATCTGGGATA-TGGCAT
1 GATTATATGTAAGACCATGTCTGGGACATTGGCAT
31571915 TGTACGAGCT
Statistics
Matches: 96, Mismatches: 19, Indels: 11
0.76 0.15 0.09
Matches are distributed among these distances:
41 1 0.01
42 8 0.08
43 84 0.88
44 3 0.03
ACGTcount: A:0.26, C:0.17, G:0.26, T:0.31
Consensus pattern (43 bp):
GATTATATGTAAGACCATGTCTGGGACATTGGCATCGTATTGC
Found at i:31576818 original size:40 final size:40
Alignment explanation
Indices: 31576635--31576804 Score: 225
Period size: 40 Copynumber: 4.3 Consensus size: 40
31576625 TCCTCGTTCA
* * * * *
31576635 AATGCCTTCGGGACATAGCCCGGTTTTAGTAACTCACAC-
1 AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
* *
31576674 AATGCCTTCGGGACGTAACCCGGATTTAACAACTCGCACG
1 AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
*
31576714 AATGCCTTCGGGACTTAACCCGGCTTTAATAACTCGCACG
1 AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
* * *
31576754 AATGCCTTCGGGACTTAACCCGGATTTAGTATCTCGCACA
1 AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
*
31576794 AAGGCCTTCGG
1 AATGCCTTCGG
31576805 ATCTTAGTCC
Statistics
Matches: 116, Mismatches: 14, Indels: 1
0.89 0.11 0.01
Matches are distributed among these distances:
39 33 0.28
40 83 0.72
ACGTcount: A:0.25, C:0.29, G:0.22, T:0.24
Consensus pattern (40 bp):
AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
Found at i:31582005 original size:43 final size:43
Alignment explanation
Indices: 31581906--31582007 Score: 100
Period size: 43 Copynumber: 2.4 Consensus size: 43
31581896 ACATAGATTT
* * * *
31581906 GATTACATGTAAGACCATGTCTAGGACATTGGCGTTGTATTGT
1 GATTTCATGTAAGACCATGTCTAGGACATTGGCGTCGTAATGC
* * * *
31581949 GA-TTAAGTATAAGACCATGTCTGGGGCATTGGCGTCGTTAAT-C
1 GATTTCA-TGTAAGACCATGTCTAGGACATTGGCGTCG-TAATGC
31581992 GATTTCATGTAAGACC
1 GATTTCATGTAAGACC
31582008 CTATCTAGAA
Statistics
Matches: 46, Mismatches: 10, Indels: 6
0.74 0.16 0.10
Matches are distributed among these distances:
42 2 0.04
43 38 0.83
44 6 0.13
ACGTcount: A:0.26, C:0.16, G:0.25, T:0.32
Consensus pattern (43 bp):
GATTTCATGTAAGACCATGTCTAGGACATTGGCGTCGTAATGC
Found at i:31583957 original size:50 final size:50
Alignment explanation
Indices: 31583893--31584870 Score: 1561
Period size: 50 Copynumber: 19.5 Consensus size: 50
31583883 CTGGTACGCA
* ** * * * *
31583893 TAGTAGCCTGCACTTAGTACTACACATGTGACCTATCAATCTGGTACACG
1 TAGTAGCCTACACTTAGTACTACACACATGACTTAACCATCTGATACACG
31583943 TAGTAGCCTACACTTAGTACTACACACATGACTTAACCATCTGATACACG
1 TAGTAGCCTACACTTAGTACTACACACATGACTTAACCATCTGATACACG
* ** * * * *
31583993 TAGTAGCCTGCACTTAGTACTACACATGTGACCTATCAATCTGGTACACG
1 TAGTAGCCTACACTTAGTACTACACACATGACTTAACCATCTGATACACG
31584043 TAGTAGCCTACACTTAGTACTACACACATGACTTAACCATCTGATACACG
1 TAGTAGCCTACACTTAGTACTACACACATGACTTAACCATCTGATACACG
*
31584093 TAGTAGCCTGCACTTAGTACTACACACATGACTTAACCATCTGATACACG
1 TAGTAGCCTACACTTAGTACTACACACATGACTTAACCATCTGATACACG
31584143 TAGTAGCCTACACTTAGTACTACACACATGACTTAACCATCTGATACACG
1 TAGTAGCCTACACTTAGTACTACACACATGACTTAACCATCTGATACACG
31584193 TAGTAGCCTACACTTAGTACTACACACATGACTTAACCATCTGATACACG
1 TAGTAGCCTACACTTAGTACTACACACATGACTTAACCATCTGATACACG
31584243 TAGTAGCCTACACTTAGTACTACACACATGACTTAACCATCTGATACACG
1 TAGTAGCCTACACTTAGTACTACACACATGACTTAACCATCTGATACACG
31584293 TAGTAGCCTACACTTAGTACTACACACATGACTTAACCATCTGATACACG
1 TAGTAGCCTACACTTAGTACTACACACATGACTTAACCATCTGATACACG
31584343 TAGTAGCCTACACTTAGTACTACACACATGACTTAACCATCTGATACACG
1 TAGTAGCCTACACTTAGTACTACACACATGACTTAACCATCTGATACACG
31584393 TAGTAGCCTACACTTAGTACTACACACATGACTTAACCATCTGATACACG
1 TAGTAGCCTACACTTAGTACTACACACATGACTTAACCATCTGATACACG
31584443 TAGTAGCCTACACTTAGTACTACACACATGACTTAACCATCTGATACACG
1 TAGTAGCCTACACTTAGTACTACACACATGACTTAACCATCTGATACACG
31584493 TAGTAGCCTACACTTAGTACTACACACATGACTTAACCATCTGATACACG
1 TAGTAGCCTACACTTAGTACTACACACATGACTTAACCATCTGATACACG
31584543 TAGTAGCCTACACTTAGTACTACACACATGACTTAACCATCTGATACACG
1 TAGTAGCCTACACTTAGTACTACACACATGACTTAACCATCTGATACACG
31584593 TAGTAGCCTACACTTAGTACTACACACATGACTTAACCATCTGATACACG
1 TAGTAGCCTACACTTAGTACTACACACATGACTTAACCATCTGATACACG
31584643 TAGTAGCCTACACTTAGTACTACACACATGACTTAACCATCTGATACACG
1 TAGTAGCCTACACTTAGTACTACACACATGACTTAACCATCTGATACACG
* * ** * * *
31584693 TAGTAGCCTACACTTAGTACTACACACGTGA-TCGAAGTTAACGGGTAGCA--
1 TAGTAGCCTACACTTAGTACTACACACATGACT-TAA-CCATCTGATA-CACG
** * ** * * * *
31584743 TAGTAGCCTGGACTTAGTACTACACACATGA-TCGAAGTTAAT-GGGTACGCA
1 TAGTAGCCTACACTTAGTACTACACACATGACT-TAA--CCATCTGATACACG
* **
31584794 TAGTAGCCTGCACTTAGTACTACACATGTGACTTAACCATCTGATACACG
1 TAGTAGCCTACACTTAGTACTACACACATGACTTAACCATCTGATACACG
31584844 TAGTAGCCTACACTTAGTACTACACAC
1 TAGTAGCCTACACTTAGTACTACACAC
31584871 GTGATCGAAG
Statistics
Matches: 871, Mismatches: 49, Indels: 16
0.93 0.05 0.02
Matches are distributed among these distances:
49 4 0.00
50 827 0.95
51 37 0.04
52 3 0.00
ACGTcount: A:0.33, C:0.27, G:0.14, T:0.26
Consensus pattern (50 bp):
TAGTAGCCTACACTTAGTACTACACACATGACTTAACCATCTGATACACG
Found at i:31584898 original size:50 final size:50
Alignment explanation
Indices: 31584693--31584919 Score: 280
Period size: 50 Copynumber: 4.5 Consensus size: 50
31584683 CTGATACACG
*
31584693 TAGTAGCCTACACTTAGTACTACACACGTGATCGAAGTTAACGGGTAGCA
1 TAGTAGCCTGCACTTAGTACTACACACGTGATCGAAGTTAACGGGTAGCA
* * *
31584743 TAGTAGCCTGGACTTAGTACTACACACATGATCGAAGTTAATGGGTACGCA
1 TAGTAGCCTGCACTTAGTACTACACACGTGATCGAAGTTAACGGGTA-GCA
* * ** * * *
31584794 TAGTAGCCTGCACTTAGTACTACACATGTGA-CTTAA-CCATCTGATA-CA
1 TAGTAGCCTGCACTTAGTACTACACACGTGATC-GAAGTTAACGGGTAGCA
*
31584842 CGTAGTAGCCTACACTTAGTACTACACACGTGATCGAAGTTAACGGGTAGCA
1 --TAGTAGCCTGCACTTAGTACTACACACGTGATCGAAGTTAACGGGTAGCA
*
31584894 TAGTAGCCTGGACTTAGTACTACACA
1 TAGTAGCCTGCACTTAGTACTACACA
31584920 TGCGACCTAT
Statistics
Matches: 146, Mismatches: 24, Indels: 14
0.79 0.13 0.08
Matches are distributed among these distances:
48 2 0.01
50 103 0.71
51 39 0.27
52 2 0.01
ACGTcount: A:0.31, C:0.22, G:0.21, T:0.26
Consensus pattern (50 bp):
TAGTAGCCTGCACTTAGTACTACACACGTGATCGAAGTTAACGGGTAGCA
Found at i:31586882 original size:30 final size:32
Alignment explanation
Indices: 31586828--31586889 Score: 92
Period size: 30 Copynumber: 2.0 Consensus size: 32
31586818 AATCCAAAGT
*
31586828 TTAGGTCTTAGGTAAAAATAACCATTTTGCCC
1 TTAGATCTTAGGTAAAAATAACCATTTTGCCC
*
31586860 TTAGATCTT-GGT-AAAATGACCATTTTGCCC
1 TTAGATCTTAGGTAAAAATAACCATTTTGCCC
31586890 CTATGCTTGA
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
30 17 0.61
31 3 0.11
32 8 0.29
ACGTcount: A:0.29, C:0.19, G:0.16, T:0.35
Consensus pattern (32 bp):
TTAGATCTTAGGTAAAAATAACCATTTTGCCC
Found at i:31588492 original size:36 final size:36
Alignment explanation
Indices: 31588445--31588514 Score: 122
Period size: 36 Copynumber: 1.9 Consensus size: 36
31588435 AAGGATGCAA
31588445 CATCTCAACATGTCCTCTAGAATCTGAATCACTCAC
1 CATCTCAACATGTCCTCTAGAATCTGAATCACTCAC
* *
31588481 CATCTCAACATGTCCTCTAGAATTTGAATTACTC
1 CATCTCAACATGTCCTCTAGAATCTGAATCACTC
31588515 TTTTCGACTG
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
36 32 1.00
ACGTcount: A:0.30, C:0.30, G:0.09, T:0.31
Consensus pattern (36 bp):
CATCTCAACATGTCCTCTAGAATCTGAATCACTCAC
Found at i:31597148 original size:46 final size:46
Alignment explanation
Indices: 31597083--31597179 Score: 142
Period size: 46 Copynumber: 2.1 Consensus size: 46
31597073 CTTACATTGA
*
31597083 CACATCTCGTAGCCGATGCATGTCCAAGACACGTCTTACACTAGCT
1 CACATCTCGTAGCCAATGCATGTCCAAGACACGTCTTACACTAGCT
* * *
31597129 TACATCTCG-AGGCCAATGCATGTCCCAGACATGTCTTACACTAGCT
1 CACATCTCGTA-GCCAATGCATGTCCAAGACACGTCTTACACTAGCT
31597175 CACAT
1 CACAT
31597180 TGTAACACCC
Statistics
Matches: 45, Mismatches: 5, Indels: 2
0.87 0.10 0.04
Matches are distributed among these distances:
45 1 0.02
46 44 0.98
ACGTcount: A:0.27, C:0.32, G:0.16, T:0.25
Consensus pattern (46 bp):
CACATCTCGTAGCCAATGCATGTCCAAGACACGTCTTACACTAGCT
Found at i:31599325 original size:79 final size:81
Alignment explanation
Indices: 31599189--31599373 Score: 218
Period size: 79 Copynumber: 2.3 Consensus size: 81
31599179 TTGAATGATG
* *
31599189 TCCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGACCATATCCGGACTAAGATCCGAAGGCATT
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCTAAGTGACCAAATCCGGACTAAGATCCGAAGGCAAT
*
31599253 TGTGCGAGATACTA-A
66 TATGCGAGATACTACA
* * * **
31599268 TTCCGGGCTAAG-CCCGAAGGCATTTGTGC-GAGTTACTAAATCCGGGTTAA-ATCCCGAAGGCA
1 -TCCGGGCTAAGTCCCGAAGGCATTTGTGCTAAGTGACCAAATCCGGACTAAGAT-CCGAAGGCA
*
31599330 ATTATGCGAGTTACTACA
64 ATTATGCGAGATACTACA
* *
31599348 ACCGGGCTATGTCCCGAAGGCATTTG
1 TCCGGGCTAAGTCCCGAAGGCATTTG
31599374 AACGAGTAGC
Statistics
Matches: 90, Mismatches: 11, Indels: 8
0.83 0.10 0.07
Matches are distributed among these distances:
78 2 0.02
79 55 0.61
80 33 0.37
ACGTcount: A:0.26, C:0.23, G:0.26, T:0.24
Consensus pattern (81 bp):
TCCGGGCTAAGTCCCGAAGGCATTTGTGCTAAGTGACCAAATCCGGACTAAGATCCGAAGGCAAT
TATGCGAGATACTACA
Found at i:31599380 original size:40 final size:39
Alignment explanation
Indices: 31599190--31599373 Score: 185
Period size: 40 Copynumber: 4.6 Consensus size: 39
31599180 TGAATGATGT
* * * *
31599190 CCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGACCATAT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGC-GAGTTACTA-AA
* * *
31599230 CCGGACTAAGAT-CCGAAGGCATTTGTGCGAGATACTAATT
1 CCGGGCTAAG-TCCCGAAGGCATTTGTGCGAGTTACTAA-A
31599270 CCGGGCTAAG-CCCGAAGGCATTTGTGCGAGTTACTAAA
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAA
* * * *
31599308 TCCGGGTTAAATCCCGAAGGCAATTATGCGAGTTACTACAA
1 -CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTA-AA
*
31599349 CCGGGCTATGTCCCGAAGGCATTTG
1 CCGGGCTAAGTCCCGAAGGCATTTG
31599374 AACGAGTAGC
Statistics
Matches: 120, Mismatches: 17, Indels: 14
0.79 0.11 0.09
Matches are distributed among these distances:
39 34 0.28
40 76 0.63
41 10 0.08
ACGTcount: A:0.26, C:0.23, G:0.27, T:0.24
Consensus pattern (39 bp):
CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAA
Found at i:31599404 original size:79 final size:79
Alignment explanation
Indices: 31599241--31599406 Score: 194
Period size: 79 Copynumber: 2.1 Consensus size: 79
31599231 CGGACTAAGA
* * * **
31599241 TCCGAAGGCATTTGTGCGAGATACTAATTCCGGGCTAAGCCCGAAGGCATTTGTGCGAGTTACTA
1 TCCGAAGGCAATTATGCGAGATACTAATACCGGGCTAAGCCCGAAGGCATTTGAACGAGTTACTA
*
31599306 AATCCGGGTTAAAT
66 AATCCGGGTAAAAT
* * *
31599320 CCCGAAGGCAATTATGCGAGTTACTACA-ACCGGGCTATGTCCCGAAGGCATTTGAACGAG-TAG
1 TCCGAAGGCAATTATGCGAGATACTA-ATACCGGGCTAAG-CCCGAAGGCATTTGAACGAGTTA-
*
31599383 CTATATCC-GGTAAAAT
63 CTAAATCCGGGTAAAAT
31599399 TCCGAAGG
1 TCCGAAGG
31599407 TACGTGATTT
Statistics
Matches: 73, Mismatches: 11, Indels: 6
0.81 0.12 0.07
Matches are distributed among these distances:
79 47 0.64
80 26 0.36
ACGTcount: A:0.28, C:0.22, G:0.26, T:0.24
Consensus pattern (79 bp):
TCCGAAGGCAATTATGCGAGATACTAATACCGGGCTAAGCCCGAAGGCATTTGAACGAGTTACTA
AATCCGGGTAAAAT
Found at i:31600757 original size:64 final size:66
Alignment explanation
Indices: 31600676--31600800 Score: 209
Period size: 64 Copynumber: 1.9 Consensus size: 66
31600666 GGGGTTTAAA
* *
31600676 GTCTGCTAACACTTCGTGTTCGACTCCGGTGTCGATCTCGGGTTC-GGGTGTTAC-ATTTGATTT
1 GTCTGCTAACACCTCGTGTTCGACTCCGGAGTCGATCTCGGGTTCGGGGTGTTACAATTTGATTT
31600739 G
66 G
*
31600740 GTCTGCTAACACCTCGTGTTCGACTCCGGAGTCGGTCTCGGGTTCGGGGTGTTACAATTTG
1 GTCTGCTAACACCTCGTGTTCGACTCCGGAGTCGATCTCGGGTTCGGGGTGTTACAATTTG
31600801 GCTGTCCACA
Statistics
Matches: 56, Mismatches: 3, Indels: 2
0.92 0.05 0.03
Matches are distributed among these distances:
64 42 0.75
65 9 0.16
66 5 0.09
ACGTcount: A:0.13, C:0.23, G:0.30, T:0.34
Consensus pattern (66 bp):
GTCTGCTAACACCTCGTGTTCGACTCCGGAGTCGATCTCGGGTTCGGGGTGTTACAATTTGATTT
G
Found at i:31602709 original size:22 final size:22
Alignment explanation
Indices: 31602683--31602727 Score: 56
Period size: 22 Copynumber: 2.0 Consensus size: 22
31602673 ATTATGTGTA
31602683 TTAATTCATGATATAA-TTAATT
1 TTAATTCAT-ATATAATTTAATT
* *
31602705 TTAATTTATATCTAATTTAATT
1 TTAATTCATATATAATTTAATT
31602727 T
1 T
31602728 GGATTAAATA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
21 5 0.25
22 15 0.75
ACGTcount: A:0.38, C:0.04, G:0.02, T:0.56
Consensus pattern (22 bp):
TTAATTCATATATAATTTAATT
Found at i:31603414 original size:21 final size:20
Alignment explanation
Indices: 31603369--31603414 Score: 51
Period size: 21 Copynumber: 2.3 Consensus size: 20
31603359 TTGTTGGAAT
31603369 GGTT-AATTTAATCAATTTA
1 GGTTGAATTTAATCAATTTA
*
31603388 GCTTGAATTTAATTC-ATGTTA
1 GGTTGAATTTAA-TCAAT-TTA
31603409 GGTTGA
1 GGTTGA
31603415 TTGCATTTCG
Statistics
Matches: 22, Mismatches: 2, Indels: 4
0.79 0.07 0.14
Matches are distributed among these distances:
19 3 0.14
20 9 0.41
21 10 0.45
ACGTcount: A:0.30, C:0.07, G:0.17, T:0.46
Consensus pattern (20 bp):
GGTTGAATTTAATCAATTTA
Found at i:31607221 original size:42 final size:42
Alignment explanation
Indices: 31607136--31607287 Score: 180
Period size: 42 Copynumber: 3.6 Consensus size: 42
31607126 TGAGATTAGA
* * * *
31607136 GTAAGACCATAT-TGTGATATGGCATCTATATAAGGTTTCGT
1 GTAAGACCATATCTGGGATATGGCATCGATATGAGATTTCGT
* *
31607177 GTAAGACCATATTTGGGATATGGCATCGATATGAGATTTTGT
1 GTAAGACCATATCTGGGATATGGCATCGATATGAGATTTCGT
* * * * * *
31607219 GTAAAACCATAGCTGGGCTATTGGCATCGATACGAGATTACAT
1 GTAAGACCATATCTGGGATA-TGGCATCGATATGAGATTTCGT
31607262 GTAAGACCATATCTGGGATATGGCAT
1 GTAAGACCATATCTGGGATATGGCAT
31607288 TGGTACGGTA
Statistics
Matches: 93, Mismatches: 16, Indels: 3
0.83 0.14 0.03
Matches are distributed among these distances:
41 12 0.13
42 46 0.49
43 35 0.38
ACGTcount: A:0.30, C:0.14, G:0.24, T:0.32
Consensus pattern (42 bp):
GTAAGACCATATCTGGGATATGGCATCGATATGAGATTTCGT
Found at i:31607770 original size:41 final size:40
Alignment explanation
Indices: 31607720--31607806 Score: 147
Period size: 41 Copynumber: 2.1 Consensus size: 40
31607710 AAGAATGGGA
*
31607720 ATATTGAATTTATGAGCTCATCTAAGACTAATGTCATGAT
1 ATATTGAATTGATGAGCTCATCTAAGACTAATGTCATGAT
*
31607760 GTATTAGAATTGATGAGCTCATCTAAGACTAATGTCATGAT
1 ATATT-GAATTGATGAGCTCATCTAAGACTAATGTCATGAT
31607801 ATATTG
1 ATATTG
31607807 TTATGAGACT
Statistics
Matches: 43, Mismatches: 3, Indels: 2
0.90 0.06 0.04
Matches are distributed among these distances:
40 5 0.12
41 38 0.88
ACGTcount: A:0.34, C:0.11, G:0.17, T:0.37
Consensus pattern (40 bp):
ATATTGAATTGATGAGCTCATCTAAGACTAATGTCATGAT
Found at i:31608825 original size:28 final size:29
Alignment explanation
Indices: 31608785--31608839 Score: 76
Period size: 28 Copynumber: 1.9 Consensus size: 29
31608775 CAGGGTTTCT
*
31608785 GACACGGGCGTGT-CTAGGCAGTGTGAGG
1 GACACAGGCGTGTGCTAGGCAGTGTGAGG
* *
31608813 GACACAGGCGTGTGCTTGGCTGTGTGA
1 GACACAGGCGTGTGCTAGGCAGTGTGA
31608840 AAATCCTAGT
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
28 12 0.52
29 11 0.48
ACGTcount: A:0.16, C:0.18, G:0.44, T:0.22
Consensus pattern (29 bp):
GACACAGGCGTGTGCTAGGCAGTGTGAGG
Found at i:31609821 original size:47 final size:46
Alignment explanation
Indices: 31609621--31609936 Score: 232
Period size: 47 Copynumber: 6.7 Consensus size: 46
31609611 ATAAGTTACT
* *
31609621 GATGCCATGTCCCAGACATGGTCTTACACTAGCTATCATTATCGAGGCC
1 GATG-CATGTCCCAGACA-GGTCTTACACTGGC-ATCATCATCGAGGCC
* * * * *
31609670 GATGCCATGTCCCAGACATGGTCTTATACTAGCTCTCGTAT-ATACG-TGCT
1 GATG-CATGTCCCAGACA-GGTCTTACACTGGC-ATC--ATCAT-CGAGGCC
* * * *
31609720 GATGCATGTCCCAGACATGTCTTACACTAGCA-CAAC-TCTTA-GCC
1 GATGCATGTCCCAGACAGGTCTTACACTGGCATCATCATC-GAGGCC
* * *
31609764 GATGCATGTCCCAGCCACGTCTTACACTGGCTATCATCGTCGAGGCC
1 GATGCATGTCCCAGACAGGTCTTACACTGGC-ATCATCATCGAGGCC
* * *
31609811 GATGCATGTCCCAGACATGTCTTACACTGGCACTCATC-TCTACGCC
1 GATGCATGTCCCAGACAGGTCTTACACTGGCA-TCATCATCGAGGCC
* * * * *
31609857 AATGACATGTCCCATACATGGTCTTACTCTGGCACTCATAAT-GTGGCC
1 GATG-CATGTCCCAGACA-GGTCTTACACTGGCA-TCATCATCGAGGCC
* *
31609905 TATGCATGTCCCAGACATGTCTTACACTGGCA
1 GATGCATGTCCCAGACAGGTCTTACACTGGCA
31609937 CACAAGAAAT
Statistics
Matches: 222, Mismatches: 31, Indels: 31
0.78 0.11 0.11
Matches are distributed among these distances:
43 1 0.00
44 32 0.14
45 1 0.00
46 28 0.13
47 63 0.28
48 36 0.16
49 49 0.22
50 8 0.04
51 4 0.02
ACGTcount: A:0.23, C:0.30, G:0.19, T:0.27
Consensus pattern (46 bp):
GATGCATGTCCCAGACAGGTCTTACACTGGCATCATCATCGAGGCC
Found at i:31609910 original size:141 final size:140
Alignment explanation
Indices: 31609621--31609935 Score: 341
Period size: 141 Copynumber: 2.2 Consensus size: 140
31609611 ATAAGTTACT
* * *
31609621 GATGCCATGTCCCAGACATGGTCTTACACTAGCTATCATTATCGAGGCCGATGCCATGTCCCAGA
1 GATG-CATGTCCCAGACA-CGTCTTACACTGGCTATCATCATCGAGGCCGATGCCATGTCCCAGA
* * * **
31609686 CATGGTCTTATACTAGCTCTCGTATATACGTGCTGATGCATGTCCCAGACATGTCTTACACTAGC
64 CATGGTCTTACACTAGCACTCATATATACG-GCCAATGCATGTCCCAGACATGTCTTACACTAGC
* *
31609751 ACAACTCTTAGCC
128 ACAAATCGTAGCC
* *
31609764 GATGCATGTCCCAGCCACGTCTTACACTGGCTATCATCGTCGAGGCCGATG-CATGTCCCAGACA
1 GATGCATGTCCCAGACACGTCTTACACTGGCTATCATCATCGAGGCCGATGCCATGTCCCAGACA
* * * * * *
31609828 T-GTCTTACACTGGCACTCATCTCTAC-GCCAATGACATGTCCCATACATGGTCTTACTCTGGCA
66 TGGTCTTACACTAGCACTCATATATACGGCCAATG-CATGTCCCAGACAT-GTCTTACACTAGCA
*
31609891 CTCATAAT-GTGGCC
129 --CA-AATCGTAGCC
* *
31609905 TATGCATGTCCCAGACATGTCTTACACTGGC
1 GATGCATGTCCCAGACACGTCTTACACTGGC
31609936 ACACAAGAAA
Statistics
Matches: 145, Mismatches: 22, Indels: 12
0.81 0.12 0.07
Matches are distributed among these distances:
137 5 0.03
138 13 0.09
139 31 0.21
140 14 0.10
141 64 0.44
142 14 0.10
143 4 0.03
ACGTcount: A:0.23, C:0.30, G:0.19, T:0.27
Consensus pattern (140 bp):
GATGCATGTCCCAGACACGTCTTACACTGGCTATCATCATCGAGGCCGATGCCATGTCCCAGACA
TGGTCTTACACTAGCACTCATATATACGGCCAATGCATGTCCCAGACATGTCTTACACTAGCACA
AATCGTAGCC
Found at i:31609937 original size:94 final size:91
Alignment explanation
Indices: 31609626--31609932 Score: 284
Period size: 94 Copynumber: 3.3 Consensus size: 91
31609616 TTACTGATGC
* *
31609626 CATGTCCCAGACATGGTCTTACACTAGCTATCATTATCGAGGCCGATGCCATGTCCCAGACATGG
1 CATGTCCCAGACAT-GTCTTACACTAGC-ATCA-TCTCTA-GCCGATG-CATGTCCCAGACATGG
* * *
31609691 TCTTA-TACTAGCTCTCGTATATACGT-G-CTGATG
61 TCTTACT-CTGGCACTC--ATA-ATGTGGCCT-ATG
* * *
31609724 CATGTCCCAGACATGTCTTACACTAGCA-CAACTCTTAGCCGATGCATGTCCCAGCCA-CGTCTT
1 CATGTCCCAGACATGTCTTACACTAGCATCATCTC-TAGCCGATGCATGTCCCAGACATGGTCTT
* ** * *
31609787 ACACTGGCTA-TCATCGTCGAGGCCGATG
65 ACTCTGGC-ACTCATAAT-GTGGCCTATG
* * *
31609815 CATGTCCCAGACATGTCTTACACTGGCACTCATCTCTACGCCAATGACATGTCCCATACATGGTC
1 CATGTCCCAGACATGTCTTACACTAGCA-TCATCTCTA-GCCGATG-CATGTCCCAGACATGGTC
31609880 TTACTCTGGCACTCATAATGTGGCCTATG
63 TTACTCTGGCACTCATAATGTGGCCTATG
31609909 CATGTCCCAGACATGTCTTACACT
1 CATGTCCCAGACATGTCTTACACT
31609933 GGCACACAAG
Statistics
Matches: 173, Mismatches: 24, Indels: 28
0.77 0.11 0.12
Matches are distributed among these distances:
90 3 0.02
91 31 0.18
92 15 0.09
93 23 0.13
94 53 0.31
95 20 0.12
96 1 0.01
97 13 0.08
98 14 0.08
ACGTcount: A:0.23, C:0.30, G:0.19, T:0.28
Consensus pattern (91 bp):
CATGTCCCAGACATGTCTTACACTAGCATCATCTCTAGCCGATGCATGTCCCAGACATGGTCTTA
CTCTGGCACTCATAATGTGGCCTATG
Found at i:31615351 original size:76 final size:76
Alignment explanation
Indices: 31615225--31615376 Score: 277
Period size: 76 Copynumber: 2.0 Consensus size: 76
31615215 AAATTAGGGA
*
31615225 CCAAATTGAATAAATTGCAAAACCTGGATTCTAGAAGCAATTTGCATGAAATTGCTTTAGATTAT
1 CCAAATTGAATAAATTGCAAAACCTGGATTCTAGAAGCAATTTACATGAAATTGCTTTAGATTAT
*
31615290 TAATTAGAAGG
66 TAATTAAAAGG
*
31615301 CCAAATTGAATAAATTGCAAAACTTGGATTCTAGAAGCAATTTACATGAAATTGCTTTAGATTAT
1 CCAAATTGAATAAATTGCAAAACCTGGATTCTAGAAGCAATTTACATGAAATTGCTTTAGATTAT
31615366 TAATTAAAAGG
66 TAATTAAAAGG
31615377 TCTTAAAGAG
Statistics
Matches: 73, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
76 73 1.00
ACGTcount: A:0.41, C:0.11, G:0.16, T:0.32
Consensus pattern (76 bp):
CCAAATTGAATAAATTGCAAAACCTGGATTCTAGAAGCAATTTACATGAAATTGCTTTAGATTAT
TAATTAAAAGG
Found at i:31638549 original size:12 final size:12
Alignment explanation
Indices: 31638534--31638559 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
31638524 TTTATTTTCG
31638534 TTTAATTATCAT
1 TTTAATTATCAT
31638546 TTTAATTATCAT
1 TTTAATTATCAT
31638558 TT
1 TT
31638560 ACTATAATAA
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:0.31, C:0.08, G:0.00, T:0.62
Consensus pattern (12 bp):
TTTAATTATCAT
Found at i:31640621 original size:43 final size:43
Alignment explanation
Indices: 31640574--31640697 Score: 203
Period size: 43 Copynumber: 2.9 Consensus size: 43
31640564 TTGAATAACG
* *
31640574 ATGCTAATGTCCCAGGCATGATCTTACATGTAATCACAATACA
1 ATGCTAATGTCCCAGACATGGTCTTACATGTAATCACAATACA
* *
31640617 ATGCTAATGTCCCAGACATGGTCTTACATGTAATCATAATACG
1 ATGCTAATGTCCCAGACATGGTCTTACATGTAATCACAATACA
*
31640660 ATGCCAATGTCCCAGACATGGTCTTACATGTAATCACA
1 ATGCTAATGTCCCAGACATGGTCTTACATGTAATCACA
31640698 TCTCGGTAAT
Statistics
Matches: 75, Mismatches: 6, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
43 75 1.00
ACGTcount: A:0.33, C:0.23, G:0.15, T:0.28
Consensus pattern (43 bp):
ATGCTAATGTCCCAGACATGGTCTTACATGTAATCACAATACA
Found at i:31640644 original size:86 final size:85
Alignment explanation
Indices: 31640538--31640697 Score: 214
Period size: 86 Copynumber: 1.9 Consensus size: 85
31640528 TCGATTCCAT
* * * *
31640538 TGTCCTAGACAGGGTTTTACACGAAAT-TGAATAACGATGCTAATGTCCCAGGCATGATCTTACA
1 TGTCCCAGACAGGGTCTTACACGAAATAT-AAT-ACGATGCCAATGTCCCAGACATGATCTTACA
31640602 TGTAATCACAATACAATGCTAA
64 TGTAATCACAATACAATGCTAA
* * * *
31640624 TGTCCCAGACATGGTCTTACATGTAATCATAATACGATGCCAATGTCCCAGACATGGTCTTACAT
1 TGTCCCAGACAGGGTCTTACACGAAAT-ATAATACGATGCCAATGTCCCAGACATGATCTTACAT
31640689 GTAATCACA
65 GTAATCACA
31640698 TCTCGGTAAT
Statistics
Matches: 64, Mismatches: 8, Indels: 4
0.84 0.11 0.05
Matches are distributed among these distances:
86 60 0.94
87 3 0.05
88 1 0.02
ACGTcount: A:0.33, C:0.22, G:0.17, T:0.28
Consensus pattern (85 bp):
TGTCCCAGACAGGGTCTTACACGAAATATAATACGATGCCAATGTCCCAGACATGATCTTACATG
TAATCACAATACAATGCTAA
Found at i:31645790 original size:27 final size:28
Alignment explanation
Indices: 31645708--31645822 Score: 92
Period size: 27 Copynumber: 4.1 Consensus size: 28
31645698 AGCATGGCTG
* *
31645708 CCAGATACAGA-AA-ATGTGACAGAGTCA
1 CCAGA-ACAGATAATATGTGGCAGAGCCA
* * * * * *
31645735 CCAAATATAGATATTTTGTGGTAGTGCCA
1 CCAGA-ACAGATAATATGTGGCAGAGCCA
*
31645764 CCAGAACAGAT-ATATGTGGCAGGGCCA
1 CCAGAACAGATAATATGTGGCAGAGCCA
* *
31645791 CCAGAACAGATAATTTGTGGCATAGCCA
1 CCAGAACAGATAATATGTGGCAGAGCCA
31645819 CCAG
1 CCAG
31645823 GACGCTTCCT
Statistics
Matches: 68, Mismatches: 17, Indels: 5
0.76 0.19 0.06
Matches are distributed among these distances:
27 32 0.47
28 23 0.34
29 13 0.19
ACGTcount: A:0.36, C:0.20, G:0.23, T:0.21
Consensus pattern (28 bp):
CCAGAACAGATAATATGTGGCAGAGCCA
Found at i:31645975 original size:28 final size:28
Alignment explanation
Indices: 31645928--31645988 Score: 104
Period size: 28 Copynumber: 2.2 Consensus size: 28
31645918 AAATTAACCC
*
31645928 TAGGGGTATAAAGGTCATTTTGCATACA
1 TAGGGGTATAAAGGTAATTTTGCATACA
*
31645956 TAGGGGTATAATGGTAATTTTGCATACA
1 TAGGGGTATAAAGGTAATTTTGCATACA
31645984 TAGGG
1 TAGGG
31645989 AAATTCTTGT
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
28 31 1.00
ACGTcount: A:0.31, C:0.08, G:0.28, T:0.33
Consensus pattern (28 bp):
TAGGGGTATAAAGGTAATTTTGCATACA
Found at i:31649875 original size:38 final size:38
Alignment explanation
Indices: 31649799--31649946 Score: 206
Period size: 39 Copynumber: 3.8 Consensus size: 38
31649789 AATCACCACA
* * *
31649799 ACAAAGCATGCGGGACTTTAAGCCCGGATATAATACCAGC
1 ACAAAGCCTTCGGGAC-TT-AGCCCGGATATAACACCAGC
31649839 ACAAAGCCTTCGGGACTTAGCCCGGATATAACACCAGC
1 ACAAAGCCTTCGGGACTTAGCCCGGATATAACACCAGC
* *
31649877 ACGAATGCCTTCGGGACTTAGCCCGAATATAACACCAGC
1 AC-AAAGCCTTCGGGACTTAGCCCGGATATAACACCAGC
*
31649916 ACAAATGCCTTCGGGAATTAGCCCGGATATA
1 ACAAA-GCCTTCGGGACTTAGCCCGGATATA
31649947 TATCTCACAC
Statistics
Matches: 98, Mismatches: 8, Indels: 5
0.88 0.07 0.05
Matches are distributed among these distances:
38 23 0.23
39 61 0.62
40 14 0.14
ACGTcount: A:0.32, C:0.28, G:0.22, T:0.18
Consensus pattern (38 bp):
ACAAAGCCTTCGGGACTTAGCCCGGATATAACACCAGC
Found at i:31649958 original size:39 final size:40
Alignment explanation
Indices: 31649809--31649979 Score: 203
Period size: 39 Copynumber: 4.4 Consensus size: 40
31649799 ACAAAGCATG
31649809 CGGGACTTTAAGCCCGGATATAAT-ACCAGCACAAA-GCCTT
1 CGGGAC-TT-AGCCCGGATATAATCACCAGCACAAATGCCTT
*
31649849 CGGGACTTAGCCCGGATATAA-CACCAGCACGAATGCCTT
1 CGGGACTTAGCCCGGATATAATCACCAGCACAAATGCCTT
*
31649888 CGGGACTTAGCCCGAATATAA-CACCAGCACAAATGCCTT
1 CGGGACTTAGCCCGGATATAATCACCAGCACAAATGCCTT
* * * *
31649927 CGGGAATTAGCCCGGATATATATC-TCA-CAC-AAGGCCTG
1 CGGGACTTAGCCCGGATATA-ATCACCAGCACAAATGCCTT
*
31649965 CGGGTCTTAGCCCGG
1 CGGGACTTAGCCCGG
31649980 TTAAGATCCT
Statistics
Matches: 117, Mismatches: 10, Indels: 10
0.85 0.07 0.07
Matches are distributed among these distances:
38 42 0.36
39 65 0.56
40 9 0.08
41 1 0.01
ACGTcount: A:0.29, C:0.29, G:0.23, T:0.19
Consensus pattern (40 bp):
CGGGACTTAGCCCGGATATAATCACCAGCACAAATGCCTT
Found at i:31649974 original size:77 final size:77
Alignment explanation
Indices: 31649807--31649978 Score: 215
Period size: 77 Copynumber: 2.2 Consensus size: 77
31649797 CAACAAAGCA
* * *
31649807 TGCGGGACTTTAAGCCCGGATATAATACCAGCACAAAGCCTTCGGGACTTAGCCCGGATATAACA
1 TGCGGGAC-TT-AGCCCGAATATAACACCAGCACAAAGCCTTCGGGAATTAGCCCGGATATAACA
*
31649872 CCAGCACGAATGCC
64 CCAGCACGAAGGCC
*
31649886 TTCGGGACTTAGCCCGAATATAACACCAGCACAAATGCCTTCGGGAATTAGCCCGGATATATATC
1 TGCGGGACTTAGCCCGAATATAACACCAGCACAAA-GCCTTCGGGAATTAGCCCGGATATA-A-C
*
31649951 -TCA-CAC-AAGGCC
63 ACCAGCACGAAGGCC
*
31649963 TGCGGGTCTTAGCCCG
1 TGCGGGACTTAGCCCG
31649979 GTTAAGATCC
Statistics
Matches: 82, Mismatches: 8, Indels: 8
0.84 0.08 0.08
Matches are distributed among these distances:
77 42 0.51
78 29 0.35
79 10 0.12
80 1 0.01
ACGTcount: A:0.28, C:0.29, G:0.23, T:0.20
Consensus pattern (77 bp):
TGCGGGACTTAGCCCGAATATAACACCAGCACAAAGCCTTCGGGAATTAGCCCGGATATAACACC
AGCACGAAGGCC
Found at i:31654133 original size:13 final size:13
Alignment explanation
Indices: 31654115--31654154 Score: 71
Period size: 13 Copynumber: 3.1 Consensus size: 13
31654105 ACACACCTTG
*
31654115 ATTCAAACACTTC
1 ATTCAAACATTTC
31654128 ATTCAAACATTTC
1 ATTCAAACATTTC
31654141 ATTCAAACATTTC
1 ATTCAAACATTTC
31654154 A
1 A
31654155 ACTTTTCATC
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
13 26 1.00
ACGTcount: A:0.40, C:0.25, G:0.00, T:0.35
Consensus pattern (13 bp):
ATTCAAACATTTC
Found at i:31660603 original size:30 final size:30
Alignment explanation
Indices: 31660563--31660622 Score: 84
Period size: 30 Copynumber: 2.0 Consensus size: 30
31660553 TTCCTGAGCC
*
31660563 TAGGGACAAAAGTGTAATTATGCAAAAGTT
1 TAGGGACAAAAATGTAATTATGCAAAAGTT
* * *
31660593 TAGGGGCAAAAATGTAATTTTGCCAAAGTT
1 TAGGGACAAAAATGTAATTATGCAAAAGTT
31660623 CATATAAAAG
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
30 26 1.00
ACGTcount: A:0.40, C:0.08, G:0.23, T:0.28
Consensus pattern (30 bp):
TAGGGACAAAAATGTAATTATGCAAAAGTT
Found at i:31662788 original size:39 final size:40
Alignment explanation
Indices: 31662695--31662863 Score: 243
Period size: 40 Copynumber: 4.2 Consensus size: 40
31662685 ATGCCTTACA
31662695 TAGCCCGG-TTATAGTAACTCGCACAAATGCCTTCGGGACT
1 TAGCCCGGATT-TAGTAACTCGCACAAATGCCTTCGGGACT
* *
31662735 TAGCCCAGATTTAGTAACTCGCACCAATGCCTTCGGG-CT
1 TAGCCCGGATTTAGTAACTCGCACAAATGCCTTCGGGACT
* *
31662774 TAGCCCGGAATTAGTAACTCACACAAATGCCTTCGGGACT
1 TAGCCCGGATTTAGTAACTCGCACAAATGCCTTCGGGACT
* * *
31662814 TAACCCGGATTTAGTAACTCGCACAAATGCCTGCGGGACC
1 TAGCCCGGATTTAGTAACTCGCACAAATGCCTTCGGGACT
*
31662854 TAACCCGGAT
1 TAGCCCGGAT
31662864 ATCATTCGAA
Statistics
Matches: 116, Mismatches: 11, Indels: 4
0.89 0.08 0.03
Matches are distributed among these distances:
39 35 0.30
40 79 0.68
41 2 0.02
ACGTcount: A:0.27, C:0.29, G:0.21, T:0.23
Consensus pattern (40 bp):
TAGCCCGGATTTAGTAACTCGCACAAATGCCTTCGGGACT
Found at i:31674291 original size:34 final size:34
Alignment explanation
Indices: 31674253--31674319 Score: 98
Period size: 34 Copynumber: 2.0 Consensus size: 34
31674243 TATGTTATTG
* * *
31674253 CTTGGTGGATGAATAATGTGGTGTGGAATAGATT
1 CTTGGTGAATGAATAATGAGGTGGGGAATAGATT
*
31674287 CTTGGTGAATGAATGATGAGGTGGGGAATAGAT
1 CTTGGTGAATGAATAATGAGGTGGGGAATAGAT
31674320 GCTAGGAGAT
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
34 29 1.00
ACGTcount: A:0.28, C:0.03, G:0.37, T:0.31
Consensus pattern (34 bp):
CTTGGTGAATGAATAATGAGGTGGGGAATAGATT
Found at i:31684309 original size:43 final size:43
Alignment explanation
Indices: 31684234--31684449 Score: 217
Period size: 43 Copynumber: 5.1 Consensus size: 43
31684224 TGCAATAGCT
* * * *
31684234 CATA-CAATGCC-ATATCCCAGATATGGTATTACATGTTATCA
1 CATATCAATGCCAATGTCCCAGACATGGTCTTACATGTAATCA
* * * * *
31684275 CATATCGATGCCACTGTCCCAGACAAGGTCTTACACGAAATCTA
1 CATATCAATGCCAATGTCCCAGACATGGTCTTACATGTAATC-A
* * * * *
31684319 -ATAACTATGCTAATGTCCCATACATGGTCTTACACGTAATCA
1 CATATCAATGCCAATGTCCCAGACATGGTCTTACATGTAATCA
* *
31684361 CA-ATACAATGCCAATGTCTCAGACATGGTCTTAAATGTAATCA
1 CATAT-CAATGCCAATGTCCCAGACATGGTCTTACATGTAATCA
*
31684404 CAATAT-AATGCCAATGTCTCAGACATGGTCTTACATGTAATCA
1 C-ATATCAATGCCAATGTCCCAGACATGGTCTTACATGTAATCA
31684447 CAT
1 CAT
31684450 CTCGGTAATC
Statistics
Matches: 144, Mismatches: 24, Indels: 13
0.80 0.13 0.07
Matches are distributed among these distances:
41 4 0.03
42 10 0.07
43 126 0.88
44 2 0.01
45 2 0.01
ACGTcount: A:0.34, C:0.24, G:0.13, T:0.29
Consensus pattern (43 bp):
CATATCAATGCCAATGTCCCAGACATGGTCTTACATGTAATCA
Found at i:31691852 original size:13 final size:13
Alignment explanation
Indices: 31691831--31691860 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
31691821 GTATGTTTTA
31691831 ATGTGTTGATATT
1 ATGTGTTGATATT
*
31691844 ATGTTTTGATATT
1 ATGTGTTGATATT
31691857 ATGT
1 ATGT
31691861 AGAAAATATT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.23, C:0.00, G:0.20, T:0.57
Consensus pattern (13 bp):
ATGTGTTGATATT
Found at i:31697396 original size:18 final size:18
Alignment explanation
Indices: 31697373--31697407 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
31697363 TGAGGCCTTC
31697373 GAGCGGCTGGGGTCGTAT
1 GAGCGGCTGGGGTCGTAT
*
31697391 GAGCGGCTGTGGTCGTA
1 GAGCGGCTGGGGTCGTA
31697408 GGTGGAGGAG
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.11, C:0.17, G:0.49, T:0.23
Consensus pattern (18 bp):
GAGCGGCTGGGGTCGTAT
Found at i:31699424 original size:37 final size:37
Alignment explanation
Indices: 31699374--31699452 Score: 113
Period size: 37 Copynumber: 2.1 Consensus size: 37
31699364 TTATTACGAA
* * * *
31699374 GTCTTACCCGGACATAATCTCCACACGAAGTTATCGG
1 GTCTTACCCGGACAAAATCCCCACACGAAGTCATCAG
*
31699411 GTCTTACCCGGACAAAATCCCCACACGTAGTCATCAG
1 GTCTTACCCGGACAAAATCCCCACACGAAGTCATCAG
31699448 GTCTT
1 GTCTT
31699453 TAGAGCTCGG
Statistics
Matches: 37, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
37 37 1.00
ACGTcount: A:0.27, C:0.32, G:0.18, T:0.24
Consensus pattern (37 bp):
GTCTTACCCGGACAAAATCCCCACACGAAGTCATCAG
Found at i:31699738 original size:13 final size:13
Alignment explanation
Indices: 31699720--31699746 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
31699710 CATATATACA
31699720 CTTTCACATTCAT
1 CTTTCACATTCAT
31699733 CTTTCACATTCAT
1 CTTTCACATTCAT
31699746 C
1 C
31699747 ACATCGGCCA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.22, C:0.33, G:0.00, T:0.44
Consensus pattern (13 bp):
CTTTCACATTCAT
Found at i:31699784 original size:47 final size:47
Alignment explanation
Indices: 31699573--31699863 Score: 347
Period size: 47 Copynumber: 6.1 Consensus size: 47
31699563 CTTCGGGACT
* * * * * *
31699573 TATCACATTTATACACTTTCACATCCATCACGTTGGCCACTCGGCCC
1 TATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGCCC
* * *
31699620 TGTCACATATATATACACTTCCACATTCATCACATCGGCCATTAGGCCT
1 TATCAC--ATATATACACTTTCACATTCATCACATCGGCCATTAGGCCC
** *
31699669 TATCACATATATATACACTTTCACATTCATCACATCGGCCTCATATATACAC
1 TATCAC--ATATATACACTTTCACATTCATCACATCGG-C-CAT-TAGGCCC
*
31699721 TTTCAC--AT-T-CATCTTTCACATTCATCACATCGGCCATTAGGCCC
1 TATCACATATATACA-CTTTCACATTCATCACATCGGCCATTAGGCCC
*
31699765 TATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGCCT
1 TATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGCCC
*
31699812 TATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGCCT
1 TATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGCCC
31699859 TATCA
1 TATCA
31699864 TCATTTCATA
Statistics
Matches: 213, Mismatches: 21, Indels: 20
0.84 0.08 0.08
Matches are distributed among these distances:
44 9 0.04
45 3 0.01
46 5 0.02
47 111 0.52
48 4 0.02
49 69 0.32
50 1 0.00
51 3 0.01
52 8 0.04
ACGTcount: A:0.29, C:0.31, G:0.08, T:0.32
Consensus pattern (47 bp):
TATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGCCC
Found at i:31706293 original size:13 final size:13
Alignment explanation
Indices: 31706275--31706303 Score: 58
Period size: 13 Copynumber: 2.2 Consensus size: 13
31706265 GGTTTTTTAT
31706275 TAAACTAATTAAC
1 TAAACTAATTAAC
31706288 TAAACTAATTAAC
1 TAAACTAATTAAC
31706301 TAA
1 TAA
31706304 TTAAACTAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.55, C:0.14, G:0.00, T:0.31
Consensus pattern (13 bp):
TAAACTAATTAAC
Found at i:31717131 original size:43 final size:42
Alignment explanation
Indices: 31717062--31717270 Score: 183
Period size: 43 Copynumber: 4.9 Consensus size: 42
31717052 CAATAGCTCG
* * * * *
31717062 TACAATGCC-ATATCCCAAATATGGTCTTACATGTTATTCAA
1 TACAATGCCAATGTCCCAGACATGGTCTTACACGTAATTCAA
* * *
31717103 TATCAATGCCACTGTCCCAGACAAGGTCTTACACG-AAATCGAA
1 TA-CAATGCCAATGTCCCAGACATGGTCTTACACGTAATTC-AA
* * *
31717146 TAACGATGCCAATGTCCCAGACATGATCTTACACGTAATCGCAA
1 T-ACAATGCCAATGTCCCAGACATGGTCTTACACGTAAT-TCAA
*
31717190 TACAATGCCAATGTCCCAGACATGGTCTTACATGTAA-TCACCA
1 TACAATGCCAATGTCCCAGACATGGTCTTACACGTAATTCA--A
* ** *
31717233 AACAATGCCAATG-CCCTAGACATATTCTTACATGTAAT
1 TACAATGCCAATGTCCC-AGACATGGTCTTACACGTAAT
31717271 CACATCTCAG
Statistics
Matches: 137, Mismatches: 21, Indels: 17
0.78 0.12 0.10
Matches are distributed among these distances:
41 4 0.03
42 13 0.09
43 113 0.82
44 6 0.04
45 1 0.01
ACGTcount: A:0.34, C:0.26, G:0.13, T:0.26
Consensus pattern (42 bp):
TACAATGCCAATGTCCCAGACATGGTCTTACACGTAATTCAA
Found at i:31717205 original size:86 final size:86
Alignment explanation
Indices: 31717100--31717271 Score: 217
Period size: 86 Copynumber: 2.0 Consensus size: 86
31717090 ACATGTTATT
* *
31717100 CAATATCAATGCCACTGTCCCAGACAAGGTCTTACACGAAATCGA-ATAACGATGCCAATGTCCC
1 CAATATCAATGCCAATGTCCCAGACAAGGTCTTACACGAAATC-ACA-AACAATGCCAATG-CCC
31717164 -AGACATGA-TCTTACACGTAATCG
63 TAGACAT-ATTCTTACACGTAATCG
* * *
31717187 CAATA-CAATGCCAATGTCCCAGACATGGTCTTACATGTAATCACCAAACAATGCCAATGCCCTA
1 CAATATCAATGCCAATGTCCCAGACAAGGTCTTACACGAAATCA-CAAACAATGCCAATGCCCTA
*
31717251 GACATATTCTTACATGTAATC
65 GACATATTCTTACACGTAATC
31717272 ACATCTCAGT
Statistics
Matches: 75, Mismatches: 6, Indels: 9
0.83 0.07 0.10
Matches are distributed among these distances:
85 5 0.07
86 64 0.85
87 6 0.08
ACGTcount: A:0.35, C:0.27, G:0.14, T:0.24
Consensus pattern (86 bp):
CAATATCAATGCCAATGTCCCAGACAAGGTCTTACACGAAATCACAAACAATGCCAATGCCCTAG
ACATATTCTTACACGTAATCG
Found at i:31720671 original size:23 final size:22
Alignment explanation
Indices: 31720628--31720672 Score: 54
Period size: 23 Copynumber: 2.0 Consensus size: 22
31720618 GTTAAATTGA
* **
31720628 ATTGTATGTATGTGAGTGTATT
1 ATTGTATGTATATGAAAGTATT
31720650 ATTGTCATGTATATGAAAGTATT
1 ATTGT-ATGTATATGAAAGTATT
31720673 TACATATCTG
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
22 5 0.26
23 14 0.74
ACGTcount: A:0.29, C:0.02, G:0.22, T:0.47
Consensus pattern (22 bp):
ATTGTATGTATATGAAAGTATT
Found at i:31731212 original size:40 final size:40
Alignment explanation
Indices: 31731129--31731471 Score: 485
Period size: 40 Copynumber: 8.6 Consensus size: 40
31731119 TTGAATGCTG
* * * * * *
31731129 TCCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGAATATA
1 TCCGGGTTAAGTCCCGAAGGCATTCGTGC-GAGTTATTAAA
* * * * *
31731169 TCCGGATTAAGAT-CCGAAGGCCTTTGTGCGAGATACTAAA
1 TCCGGGTTAAG-TCCCGAAGGCATTCGTGCGAGTTATTAAA
31731209 TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTATTAAA
1 TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTATTAAA
31731249 TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTATTAAA
1 TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTATTAAA
31731289 TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTATTAAA
1 TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTATTAAA
31731329 TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTATTAAA
1 TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTATTAAA
*
31731369 TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTGTTAAA
1 TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTATTAAA
* * *
31731409 TCCGGGTTATGTCCCGAAGGCATT-GTGTGAGTTACTAAA
1 TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTATTAAA
* * *
31731448 ACCGGGCTATGTCCCGAAGGCATT
1 TCCGGGTTAAGTCCCGAAGGCATT
31731472 TGAACGAGGA
Statistics
Matches: 281, Mismatches: 19, Indels: 7
0.92 0.06 0.02
Matches are distributed among these distances:
39 35 0.12
40 238 0.85
41 8 0.03
ACGTcount: A:0.25, C:0.20, G:0.28, T:0.27
Consensus pattern (40 bp):
TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTATTAAA
Found at i:31735373 original size:29 final size:28
Alignment explanation
Indices: 31735302--31735453 Score: 123
Period size: 29 Copynumber: 5.4 Consensus size: 28
31735292 ACCCCTCCAT
*
31735302 ACATGCATATGGCCCA-CTAGGCCCAATC
1 ACATTCATATGGCCCATC-AGGCCCAATC
* *
31735330 TCA-TCTATATGGCCCATCCGGCCCAATTC
1 ACATTC-ATATGGCCCATCAGGCCCAA-TC
*
31735359 ACATTCATATGGCCCATAAGGCCCAATTC
1 ACATTCATATGGCCCATCAGGCCCAA-TC
* * * **
31735388 ACATTCGTATGGCGCATTAGGATCAATC
1 ACATTCATATGGCCCATCAGGCCCAATC
* *
31735416 TCATTTATATGGCCCATCCA-GCCCAAATC
1 ACATTCATATGGCCCAT-CAGGCCC-AATC
31735445 ACATT-ATAT
1 ACATTCATAT
31735454 CCATGCTTAC
Statistics
Matches: 99, Mismatches: 19, Indels: 12
0.76 0.15 0.09
Matches are distributed among these distances:
27 1 0.01
28 40 0.40
29 56 0.57
30 2 0.02
ACGTcount: A:0.28, C:0.31, G:0.14, T:0.26
Consensus pattern (28 bp):
ACATTCATATGGCCCATCAGGCCCAATC
Found at i:31743112 original size:28 final size:28
Alignment explanation
Indices: 31743055--31743114 Score: 79
Period size: 28 Copynumber: 2.1 Consensus size: 28
31743045 ACATACATGC
*
31743055 ATATGGCCCACTAGGCCCAATCTCATTT
1 ATATGGCCCACTAGGCCCAATATCATTT
31743083 ATATGGCCCATCT-GGCCCAA-ATCATATT
1 ATATGGCCCA-CTAGGCCCAATATCAT-TT
31743111 ATAT
1 ATAT
31743115 CCATGCTCAC
Statistics
Matches: 29, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
27 4 0.14
28 23 0.79
29 2 0.07
ACGTcount: A:0.28, C:0.28, G:0.13, T:0.30
Consensus pattern (28 bp):
ATATGGCCCACTAGGCCCAATATCATTT
Found at i:31743350 original size:16 final size:16
Alignment explanation
Indices: 31743329--31743367 Score: 51
Period size: 16 Copynumber: 2.4 Consensus size: 16
31743319 TTAAACTTTT
*
31743329 GGCTTTTTGACATTTC
1 GGCTTTTCGACATTTC
**
31743345 GGCTTTTCGGTATTTC
1 GGCTTTTCGACATTTC
31743361 GGCTTTT
1 GGCTTTT
31743368 GCCGATCTAC
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:0.08, C:0.18, G:0.23, T:0.51
Consensus pattern (16 bp):
GGCTTTTCGACATTTC
Found at i:31751283 original size:27 final size:27
Alignment explanation
Indices: 31751244--31751296 Score: 79
Period size: 27 Copynumber: 2.0 Consensus size: 27
31751234 ACATTAGGTG
* *
31751244 TTCTTGGAGATCTTCCCCTTCGAAACC
1 TTCTTGGAAATCTTCCCCTTCAAAACC
*
31751271 TTCTTGGAAATCTTTCCCTTCAAAAC
1 TTCTTGGAAATCTTCCCCTTCAAAAC
31751297 ATTTCCCTTT
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
27 23 1.00
ACGTcount: A:0.23, C:0.30, G:0.11, T:0.36
Consensus pattern (27 bp):
TTCTTGGAAATCTTCCCCTTCAAAACC
Found at i:31757235 original size:30 final size:30
Alignment explanation
Indices: 31757201--31757260 Score: 93
Period size: 30 Copynumber: 2.0 Consensus size: 30
31757191 CTTTAATACG
*
31757201 AACTTTGGCAAAATTACATTTTTGCCCCTA
1 AACTTTGGCAAAATTACACTTTTGCCCCTA
* *
31757231 AACTTTTGCATAATTACACTTTTGCCCCTA
1 AACTTTGGCAAAATTACACTTTTGCCCCTA
31757261 GGCTCGGGAA
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
30 27 1.00
ACGTcount: A:0.28, C:0.25, G:0.08, T:0.38
Consensus pattern (30 bp):
AACTTTGGCAAAATTACACTTTTGCCCCTA
Found at i:31766273 original size:15 final size:14
Alignment explanation
Indices: 31766240--31766277 Score: 51
Period size: 14 Copynumber: 2.7 Consensus size: 14
31766230 CATTTTTTAT
*
31766240 AAAAG-AAAAAGAA
1 AAAAGAAAAAAAAA
31766253 AAAAGAAAAAAAAA
1 AAAAGAAAAAAAAA
31766267 AAGAAGAAAAA
1 AA-AAGAAAAA
31766278 GAGCTGGTAG
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
13 5 0.23
14 9 0.41
15 8 0.36
ACGTcount: A:0.87, C:0.00, G:0.13, T:0.00
Consensus pattern (14 bp):
AAAAGAAAAAAAAA
Found at i:31766276 original size:13 final size:12
Alignment explanation
Indices: 31766240--31766277 Score: 58
Period size: 13 Copynumber: 3.0 Consensus size: 12
31766230 CATTTTTTAT
31766240 AAAAGAAAAAGAA
1 AAAAGAAAAA-AA
31766253 AAAAGAAAAAAA
1 AAAAGAAAAAAA
31766265 AAAAGAAGAAAAA
1 AAAAGAA-AAAAA
31766278 GAGCTGGTAG
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
12 9 0.38
13 15 0.62
ACGTcount: A:0.87, C:0.00, G:0.13, T:0.00
Consensus pattern (12 bp):
AAAAGAAAAAAA
Found at i:31773094 original size:6 final size:6
Alignment explanation
Indices: 31773083--31773107 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
31773073 GCAATGATGT
31773083 AAAGGA AAAGGA AAAGGA AAAGGA A
1 AAAGGA AAAGGA AAAGGA AAAGGA A
31773108 TGGTTTTGAC
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.68, C:0.00, G:0.32, T:0.00
Consensus pattern (6 bp):
AAAGGA
Found at i:31777529 original size:28 final size:28
Alignment explanation
Indices: 31777485--31777592 Score: 112
Period size: 28 Copynumber: 3.9 Consensus size: 28
31777475 ACATACCTGT
* * *
31777485 ATATAGCCCATTCGGCCCAATCTCTTTC
1 ATATGGCCCATTAGGCCCAATCACTTTC
*
31777513 ATATGGCCCAGTAGGCCCAATCACATTT-
1 ATATGGCCCATTAGGCCCAATCAC-TTTC
* * *
31777541 ATGTGGCTCATTAGGCCCAAATCACATTC
1 ATATGGCCCATTAGGCCC-AATCACTTTC
*
31777570 ATACGG-CCATTAGGCCCAATCAC
1 ATATGGCCCATTAGGCCCAATCAC
31777593 ATTTACAATT
Statistics
Matches: 66, Mismatches: 11, Indels: 7
0.79 0.13 0.08
Matches are distributed among these distances:
27 6 0.09
28 47 0.71
29 13 0.20
ACGTcount: A:0.27, C:0.31, G:0.16, T:0.26
Consensus pattern (28 bp):
ATATGGCCCATTAGGCCCAATCACTTTC
Found at i:31780638 original size:141 final size:141
Alignment explanation
Indices: 31780449--31780727 Score: 522
Period size: 141 Copynumber: 2.0 Consensus size: 141
31780439 TTCATTTTGT
* *
31780449 TTATGGCCATAAGATATGTCTCATTTTGATGAAGGTTGTCAACTTACTAATTGTGCATGTCATAC
1 TTATGGCCATAAGATATGTCTCATTTTGATGAAGGTTGTAAACCTACTAATTGTGCATGTCATAC
* *
31780514 TTGAATGTTTCATGGCATGGTTAATGTGATATACCATGGATGGATATGTGTATTGTGGTTGAATC
66 TTGAATGTTTCATGACATGGTTAATATGATATACCATGGATGGATATGTGTATTGTGGTTGAATC
31780579 ACTTGGAGTGG
131 ACTTGGAGTGG
31780590 TTATGGCCATAAGATATGTCTCATTTTGATGAAGGTTGTAAACCTACTAATTGTGCATGTCATAC
1 TTATGGCCATAAGATATGTCTCATTTTGATGAAGGTTGTAAACCTACTAATTGTGCATGTCATAC
31780655 TTGAATGTTTCATGACATGGTTAATATGATATACCATGGATGGATATGTGTATTGTGGTTGAATC
66 TTGAATGTTTCATGACATGGTTAATATGATATACCATGGATGGATATGTGTATTGTGGTTGAATC
31780720 ACTTGGAG
131 ACTTGGAG
31780728 ATGGCTAGGA
Statistics
Matches: 134, Mismatches: 4, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
141 134 1.00
ACGTcount: A:0.27, C:0.11, G:0.24, T:0.38
Consensus pattern (141 bp):
TTATGGCCATAAGATATGTCTCATTTTGATGAAGGTTGTAAACCTACTAATTGTGCATGTCATAC
TTGAATGTTTCATGACATGGTTAATATGATATACCATGGATGGATATGTGTATTGTGGTTGAATC
ACTTGGAGTGG
Found at i:31780828 original size:30 final size:30
Alignment explanation
Indices: 31780794--31780860 Score: 125
Period size: 30 Copynumber: 2.2 Consensus size: 30
31780784 TGACATGCAA
*
31780794 CATTGAAGTGTTTTTTGAAAACCATGTTTT
1 CATTGAAGTGTTTTTCGAAAACCATGTTTT
31780824 CATTGAAGTGTTTTTCGAAAACCATGTTTT
1 CATTGAAGTGTTTTTCGAAAACCATGTTTT
31780854 CATTGAA
1 CATTGAA
31780861 AACCCTTCTT
Statistics
Matches: 36, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
30 36 1.00
ACGTcount: A:0.28, C:0.12, G:0.16, T:0.43
Consensus pattern (30 bp):
CATTGAAGTGTTTTTCGAAAACCATGTTTT
Found at i:31780863 original size:18 final size:18
Alignment explanation
Indices: 31780808--31780864 Score: 54
Period size: 18 Copynumber: 3.5 Consensus size: 18
31780798 GAAGTGTTTT
31780808 TTGAAAACCATGTTTTCA
1 TTGAAAACCATGTTTTCA
*
31780826 TTG--AA--GTGTTTT--
1 TTGAAAACCATGTTTTCA
*
31780838 TCGAAAACCATGTTTTCA
1 TTGAAAACCATGTTTTCA
31780856 TTGAAAACC
1 TTGAAAACC
31780865 CTTCTTAAAG
Statistics
Matches: 29, Mismatches: 4, Indels: 12
0.64 0.09 0.27
Matches are distributed among these distances:
12 2 0.07
14 8 0.28
16 8 0.28
18 11 0.38
ACGTcount: A:0.32, C:0.16, G:0.14, T:0.39
Consensus pattern (18 bp):
TTGAAAACCATGTTTTCA
Found at i:31782322 original size:27 final size:27
Alignment explanation
Indices: 31782292--31782391 Score: 123
Period size: 27 Copynumber: 3.7 Consensus size: 27
31782282 TACCCTATAG
*
31782292 GGGTAGTTT-GGTAATTTTCCAAACCGA
1 GGGTA-TTTCGGTAATTTTACAAACCGA
* *
31782319 GGGTATTTCGGTAATTTTACAAATCGG
1 GGGTATTTCGGTAATTTTACAAACCGA
*
31782346 GGGTATTTCGGTAATTTTACAAAATCGA
1 GGGTATTTCGGTAATTTTAC-AAACCGA
*
31782374 -GGTATTTCGATAATTTTA
1 GGGTATTTCGGTAATTTTA
31782392 AACAGTTTGG
Statistics
Matches: 66, Mismatches: 5, Indels: 4
0.88 0.07 0.05
Matches are distributed among these distances:
26 3 0.05
27 57 0.86
28 6 0.09
ACGTcount: A:0.28, C:0.11, G:0.23, T:0.38
Consensus pattern (27 bp):
GGGTATTTCGGTAATTTTACAAACCGA
Found at i:31793843 original size:27 final size:27
Alignment explanation
Indices: 31793808--31794013 Score: 161
Period size: 27 Copynumber: 7.6 Consensus size: 27
31793798 TTATTTTACC
31793808 AAATTACCAAAATACCCTCGATTAGCA
1 AAATTACCAAAATACCCTCGATTAGCA
31793835 AAATTACCAAAATACCCTCGATTAGCA
1 AAATTACCAAAATACCCTCGATTAGCA
* * * * *
31793862 AAATTACTAGAATACCCTTGGTTTA-TA
1 AAATTACCAAAATACCC-TCGATTAGCA
* * *
31793889 AAATCACCAAAATACCCT-TAGTTTGCA
1 AAATTACCAAAATACCCTCGA-TTAGCA
* * **
31793916 AAATTACCAATATACCC-CTGATTTGTG
1 AAATTACCAAAATACCCTC-GATTAGCA
* * *
31793943 AAATTATCGAAATACCCTCGACTT-GTA
1 AAATTACCAAAATACCCTCGA-TTAGCA
* *
31793970 AAATTACCAAAGTACCCCCGATTTA-CA
1 AAATTACCAAAATACCCTCGA-TTAGCA
**
31793997 AAATTATTAAAATACCC
1 AAATTACCAAAATACCC
31794014 CTGTAGGGTA
Statistics
Matches: 141, Mismatches: 30, Indels: 16
0.75 0.16 0.09
Matches are distributed among these distances:
26 3 0.02
27 129 0.91
28 9 0.06
ACGTcount: A:0.41, C:0.23, G:0.08, T:0.28
Consensus pattern (27 bp):
AAATTACCAAAATACCCTCGATTAGCA
Found at i:31793972 original size:81 final size:81
Alignment explanation
Indices: 31793808--31794013 Score: 195
Period size: 81 Copynumber: 2.5 Consensus size: 81
31793798 TTATTTTACC
* *
31793808 AAATTACCAAAATACCCTCGATTAGCAAAATTACCAAAATACCCTCGATTAGCAAAATTACTAGA
1 AAATTACCAAAATACCCTAGATTAGCAAAATTACCAAAATACCCTCGATTAGCAAAATTACGAGA
* **
31793873 ATACCCTTGGTTTATA
66 ATACCCTCGACTTATA
* * * * **
31793889 AAATCACCAAAATACCCTTAG-TTTGCAAAATTACCAATATACCC-CTGATTTGTGAAATTATCG
1 AAATTACCAAAATACCC-TAGATTAGCAAAATTACCAAAATACCCTC-GATTAGCAAAATTA-CG
*
31793952 A-AATACCCTCGACTTGTA
63 AGAATACCCTCGACTTATA
* ** **
31793970 AAATTACCAAAGTACCCCCGATTTA-CAAAATTATTAAAATACCC
1 AAATTACCAAAATACCCTAGA-TTAGCAAAATTACCAAAATACCC
31794014 CTGTAGGGTA
Statistics
Matches: 100, Mismatches: 20, Indels: 10
0.77 0.15 0.08
Matches are distributed among these distances:
80 2 0.02
81 92 0.92
82 6 0.06
ACGTcount: A:0.41, C:0.23, G:0.08, T:0.28
Consensus pattern (81 bp):
AAATTACCAAAATACCCTAGATTAGCAAAATTACCAAAATACCCTCGATTAGCAAAATTACGAGA
ATACCCTCGACTTATA
Found at i:31794036 original size:27 final size:27
Alignment explanation
Indices: 31794006--31794112 Score: 133
Period size: 27 Copynumber: 4.0 Consensus size: 27
31793996 AAAATTATTA
* *
31794006 AAATACCCCTGTAGGGTAGAGTTACTG
1 AAATACCCCTGTAGGGTAGAATTACCG
* * * *
31794033 AAATACGCTTGTAGGCTAGAAATACCG
1 AAATACCCCTGTAGGGTAGAATTACCG
31794060 AAATACCCCTGTAGGGTAGAATTACCG
1 AAATACCCCTGTAGGGTAGAATTACCG
* * *
31794087 AGATACCCTTGTAGGGTAAAATTACC
1 AAATACCCCTGTAGGGTAGAATTACC
31794113 ATTTTGCCCC
Statistics
Matches: 67, Mismatches: 13, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
27 67 1.00
ACGTcount: A:0.34, C:0.20, G:0.22, T:0.24
Consensus pattern (27 bp):
AAATACCCCTGTAGGGTAGAATTACCG
Found at i:31794493 original size:22 final size:22
Alignment explanation
Indices: 31794460--31794518 Score: 66
Period size: 22 Copynumber: 2.7 Consensus size: 22
31794450 CACGTTATCG
31794460 ATGGC-TCTGTGCCAACCTAAAT
1 ATGGCTTC-GTGCCAACCTAAAT
* * * *
31794482 ATGGCTTCGTGCCATCTTGACT
1 ATGGCTTCGTGCCAACCTAAAT
31794504 ATGGCTTCGTGCCAA
1 ATGGCTTCGTGCCAA
31794519 ACGTATTTAC
Statistics
Matches: 31, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
22 29 0.94
23 2 0.06
ACGTcount: A:0.20, C:0.27, G:0.22, T:0.31
Consensus pattern (22 bp):
ATGGCTTCGTGCCAACCTAAAT
Found at i:31794705 original size:27 final size:26
Alignment explanation
Indices: 31794675--31794776 Score: 123
Period size: 27 Copynumber: 3.8 Consensus size: 26
31794665 ATTCTGTTAA
* *
31794675 GTGGCTTTGCCACATTATCTCGTTCTG
1 GTGGCTATGCCACAATATCT-GTTCTG
31794702 GTGGCTATGCCACAAATATCTGTTCTG
1 GTGGCTATGCCAC-AATATCTGTTCTG
*
31794729 GTGGCTCTGCCACAATATCTGTATCTG
1 GTGGCTATGCCACAATATCTGT-TCTG
* * *
31794756 GTGACTCTGTCACAATATCTG
1 GTGGCTATGCCACAATATCTG
31794777 ATAACTGAGC
Statistics
Matches: 68, Mismatches: 5, Indels: 4
0.88 0.06 0.05
Matches are distributed among these distances:
26 9 0.13
27 53 0.78
28 6 0.09
ACGTcount: A:0.19, C:0.25, G:0.22, T:0.35
Consensus pattern (26 bp):
GTGGCTATGCCACAATATCTGTTCTG
Found at i:31794951 original size:6 final size:6
Alignment explanation
Indices: 31794936--31795148 Score: 181
Period size: 6 Copynumber: 34.8 Consensus size: 6
31794926 ATTCTGTTAC
* * *
31794936 CTGATA CTGATT CTGATT TTGATT CTG-TT ACCTGATA CTGATT CTGATT
1 CTGATT CTGATT CTGATT CTGATT CTGATT --CTGATT CTGATT CTGATT
* * *
31794985 TTGATT CTG-TT ACCTG-TT ACTGATT CTGATT CTGATT CTG-TCAC CTAATT
1 CTGATT CTGATT --CTGATT -CTGATT CTGATT CTGATT CTGAT--T CTGATT
* *
31795035 CTGATT CTGATT CTGATT CTG-TT ACTAATA CTGATT CTGATT CTGATT
1 CTGATT CTGATT CTGATT CTGATT -CTGATT CTGATT CTGATT CTGATT
*
31795083 CTG-TT ACTGATT CTGATT CTGATT CTG-TCAT CTAATT CTGATT CTGATT
1 CTGATT -CTGATT CTGATT CTGATT CTGAT--T CTGATT CTGATT CTGATT
31795132 CTGATT CT-AGTT CTGAT
1 CTGATT CTGA-TT CTGAT
31795149 AATGTTTCTT
Statistics
Matches: 171, Mismatches: 18, Indels: 36
0.76 0.08 0.16
Matches are distributed among these distances:
5 11 0.06
6 138 0.81
7 19 0.11
8 3 0.02
ACGTcount: A:0.19, C:0.18, G:0.15, T:0.48
Consensus pattern (6 bp):
CTGATT
Found at i:31794964 original size:31 final size:31
Alignment explanation
Indices: 31794926--31795109 Score: 282
Period size: 31 Copynumber: 6.0 Consensus size: 31
31794916 CTGATTTTTT
*
31794926 ATTCTGTTACCTGATACTGATTCTGATTTTG
1 ATTCTGTTACCTGATACTGATTCTGATTCTG
*
31794957 ATTCTGTTACCTGATACTGATTCTGATTTTG
1 ATTCTGTTACCTGATACTGATTCTGATTCTG
*
31794988 ATTCTGTTACCTGTTACTGATTCTGATTCTG
1 ATTCTGTTACCTGATACTGATTCTGATTCTG
* * *
31795019 ATTCTGTCACCTAATTCTGATTCTGATTCTG
1 ATTCTGTTACCTGATACTGATTCTGATTCTG
*
31795050 ATTCTGTTA-CTAATACTGATTCTGATTCTG
1 ATTCTGTTACCTGATACTGATTCTGATTCTG
*
31795080 ATTCTGTTA-CTGATTCTGATTCTGATTCTG
1 ATTCTGTTACCTGATACTGATTCTGATTCTG
31795110 TCATCTAATT
Statistics
Matches: 143, Mismatches: 10, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
30 48 0.34
31 95 0.66
ACGTcount: A:0.19, C:0.18, G:0.15, T:0.48
Consensus pattern (31 bp):
ATTCTGTTACCTGATACTGATTCTGATTCTG
Done.