Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr06 ID=Chr06-JGI_221_v2.0
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: 51074515
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 971674 characters in sequence are not A, C, G, or T
File 154 of 168
Found at i:45853758 original size:6 final size:6
Alignment explanation
Indices: 45853737--45853776 Score: 55
Period size: 6 Copynumber: 6.7 Consensus size: 6
45853727 AATTGGAGAG
*
45853737 AAAACA AAATAGA AAAAGA AAAA-A AAAAGA AAAAGA AAAA
1 AAAAGA AAA-AGA AAAAGA AAAAGA AAAAGA AAAAGA AAAA
45853777 TAATAAAAGG
Statistics
Matches: 31, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
5 5 0.16
6 21 0.68
7 5 0.16
ACGTcount: A:0.85, C:0.03, G:0.10, T:0.03
Consensus pattern (6 bp):
AAAAGA
Found at i:45853765 original size:11 final size:12
Alignment explanation
Indices: 45853737--45853776 Score: 55
Period size: 11 Copynumber: 3.3 Consensus size: 12
45853727 AATTGGAGAG
*
45853737 AAAACAAAATAGA
1 AAAAGAAAA-AGA
45853750 AAAAGAAAAA-A
1 AAAAGAAAAAGA
45853761 AAAAGAAAAAGA
1 AAAAGAAAAAGA
45853773 AAAA
1 AAAA
45853777 TAATAAAAGG
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
11 11 0.44
12 6 0.24
13 8 0.32
ACGTcount: A:0.85, C:0.03, G:0.10, T:0.03
Consensus pattern (12 bp):
AAAAGAAAAAGA
Found at i:45853767 original size:17 final size:17
Alignment explanation
Indices: 45853735--45853776 Score: 66
Period size: 17 Copynumber: 2.4 Consensus size: 17
45853725 ATAATTGGAG
*
45853735 AGAAAACAAAATAGAAAA
1 AGAAAA-AAAAAAGAAAA
45853753 AGAAAAAAAAAAGAAAA
1 AGAAAAAAAAAAGAAAA
45853770 AGAAAAA
1 AGAAAAA
45853777 TAATAAAAGG
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
17 17 0.74
18 6 0.26
ACGTcount: A:0.83, C:0.02, G:0.12, T:0.02
Consensus pattern (17 bp):
AGAAAAAAAAAAGAAAA
Found at i:45855498 original size:3 final size:3
Alignment explanation
Indices: 45855490--45855519 Score: 60
Period size: 3 Copynumber: 10.0 Consensus size: 3
45855480 ATCCGACCCC
45855490 ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG
1 ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG
45855520 CAAGAGTTAA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 27 1.00
ACGTcount: A:0.33, C:0.00, G:0.33, T:0.33
Consensus pattern (3 bp):
ATG
Found at i:45864197 original size:19 final size:19
Alignment explanation
Indices: 45864173--45864210 Score: 76
Period size: 19 Copynumber: 2.0 Consensus size: 19
45864163 ACATGCTCAG
45864173 TTAGTAAGCAATAAAGAAT
1 TTAGTAAGCAATAAAGAAT
45864192 TTAGTAAGCAATAAAGAAT
1 TTAGTAAGCAATAAAGAAT
45864211 ATTTTGCTTA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.53, C:0.05, G:0.16, T:0.26
Consensus pattern (19 bp):
TTAGTAAGCAATAAAGAAT
Found at i:45866902 original size:29 final size:31
Alignment explanation
Indices: 45866845--45866928 Score: 109
Period size: 31 Copynumber: 2.7 Consensus size: 31
45866835 ATTTTAAAAT
* *
45866845 TATACATAAATTTTAATTTAATCCATAATTA
1 TATACATGAATTTTAATTTAGTCCATAATTA
45866876 TATACATGAATTTTAATTTAGT-C-TAATTA
1 TATACATGAATTTTAATTTAGTCCATAATTA
*
45866905 TATACGTGAAATTTTAATTATAGT
1 TATACATG-AATTTTAATT-TAGT
45866929 TCAAATATAT
Statistics
Matches: 48, Mismatches: 3, Indels: 4
0.87 0.05 0.07
Matches are distributed among these distances:
29 13 0.27
30 11 0.23
31 24 0.50
ACGTcount: A:0.40, C:0.07, G:0.06, T:0.46
Consensus pattern (31 bp):
TATACATGAATTTTAATTTAGTCCATAATTA
Found at i:45866936 original size:29 final size:28
Alignment explanation
Indices: 45866845--45866938 Score: 89
Period size: 31 Copynumber: 3.1 Consensus size: 28
45866835 ATTTTAAAAT
* *
45866845 TATACATAAATTTTAATTTAATCCATAATTA
1 TATACATGAATTTTAATTTAGT-C-TAA-TA
45866876 TATACATGAATTTTAATTTAGTCTAATTA
1 TATACATGAATTTTAATTTAGTCTAA-TA
* *
45866905 TATACGTGAAATTTTAATTATAGTTCAAATA
1 TATACATG-AATTTTAATT-TAG-TCTAATA
45866936 TAT
1 TAT
45866939 GCTTGAAACT
Statistics
Matches: 56, Mismatches: 4, Indels: 6
0.85 0.06 0.09
Matches are distributed among these distances:
29 13 0.23
30 11 0.20
31 28 0.50
32 4 0.07
ACGTcount: A:0.41, C:0.07, G:0.05, T:0.46
Consensus pattern (28 bp):
TATACATGAATTTTAATTTAGTCTAATA
Found at i:45867332 original size:31 final size:29
Alignment explanation
Indices: 45867297--45867365 Score: 75
Period size: 31 Copynumber: 2.3 Consensus size: 29
45867287 TAATATTAAA
* *
45867297 TTTATATATAAACGTTATTTTAATGTGTAAT
1 TTTATATATAAACGTTAATTT-A-GTATAAT
* * *
45867328 TTTATGTATTAACTTTAATTTAGTATAAT
1 TTTATATATAAACGTTAATTTAGTATAAT
45867357 TTTATATAT
1 TTTATATAT
45867366 GAAATTTGAG
Statistics
Matches: 32, Mismatches: 6, Indels: 2
0.80 0.15 0.05
Matches are distributed among these distances:
29 14 0.44
30 1 0.03
31 17 0.53
ACGTcount: A:0.35, C:0.03, G:0.07, T:0.55
Consensus pattern (29 bp):
TTTATATATAAACGTTAATTTAGTATAAT
Found at i:45870512 original size:11 final size:11
Alignment explanation
Indices: 45870496--45870521 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
45870486 TATATATAAT
45870496 TAAATATTAAA
1 TAAATATTAAA
45870507 TAAATATTAAA
1 TAAATATTAAA
45870518 TAAA
1 TAAA
45870522 AGAATTATTT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (11 bp):
TAAATATTAAA
Found at i:45873044 original size:23 final size:23
Alignment explanation
Indices: 45873017--45873062 Score: 58
Period size: 24 Copynumber: 2.0 Consensus size: 23
45873007 AAGTATTTTT
45873017 TAAAAT-AGTAAAATAAAAATATA
1 TAAAATGA-TAAAATAAAAATATA
*
45873040 TAAAATGCATAAATTAAAAATAT
1 TAAAATG-ATAAAATAAAAATAT
45873063 CAAAATATAG
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
23 6 0.30
24 13 0.65
25 1 0.05
ACGTcount: A:0.65, C:0.02, G:0.04, T:0.28
Consensus pattern (23 bp):
TAAAATGATAAAATAAAAATATA
Found at i:45874371 original size:43 final size:43
Alignment explanation
Indices: 45874323--45874571 Score: 333
Period size: 43 Copynumber: 5.8 Consensus size: 43
45874313 GCGTCGCTAA
* **
45874323 CTTTAGCGGCGCTTTTCCCACAAACGCCGCTAAAGATTAGGAC
1 CTTTAGCGGCACTTTTCCCACAAACGCCGCTAAAGACCAGGAC
*
45874366 CTTTAGCGGCACTTTTCCCGCAAACGCCGCTAAAGACCAGGAC
1 CTTTAGCGGCACTTTTCCCACAAACGCCGCTAAAGACCAGGAC
* *
45874409 CTTTAGCGGCGCTTCTT-CCGCAAACGCCGCTAAAGACCAGGAC
1 CTTTAGCGGCACTT-TTCCCACAAACGCCGCTAAAGACCAGGAC
* * *
45874452 CTTTAGCGGCACTTCTCCCGA-AAATGCCGCTAAAGACCAAGAC
1 CTTTAGCGGCACTTTTCCC-ACAAACGCCGCTAAAGACCAGGAC
* * *
45874495 CTTTAGCGGCGC-TCTCCCGCAAACGCCGCTAAAGACCAGGAC
1 CTTTAGCGGCACTTTTCCCACAAACGCCGCTAAAGACCAGGAC
* *
45874537 CTTTAGCGGCACTTTTCCCAAAAACGCCACTAAAG
1 CTTTAGCGGCACTTTTCCCACAAACGCCGCTAAAG
45874572 GTCACGAAAA
Statistics
Matches: 182, Mismatches: 19, Indels: 10
0.86 0.09 0.05
Matches are distributed among these distances:
42 38 0.21
43 142 0.78
44 2 0.01
ACGTcount: A:0.27, C:0.34, G:0.20, T:0.19
Consensus pattern (43 bp):
CTTTAGCGGCACTTTTCCCACAAACGCCGCTAAAGACCAGGAC
Found at i:45874570 original size:85 final size:86
Alignment explanation
Indices: 45874323--45874571 Score: 392
Period size: 86 Copynumber: 2.9 Consensus size: 86
45874313 GCGTCGCTAA
* * ** *
45874323 CTTTAGCGGCGCTTTTCCCACAAACGCCGCTAAAGATTAGGACCTTTAGCGGCACTTTTCCCGCA
1 CTTTAGCGGCGCTTCTCCCGCAAACGCCGCTAAAGACCAGGACCTTTAGCGGCACTTTTCCCGAA
*
45874388 AACGCCGCTAAAGACCAGGAC
66 AACGCCGCTAAAGACCAAGAC
* *
45874409 CTTTAGCGGCGCTTCTTCCGCAAACGCCGCTAAAGACCAGGACCTTTAGCGGCACTTCTCCCGAA
1 CTTTAGCGGCGCTTCTCCCGCAAACGCCGCTAAAGACCAGGACCTTTAGCGGCACTTTTCCCGAA
*
45874474 AATGCCGCTAAAGACCAAGAC
66 AACGCCGCTAAAGACCAAGAC
*
45874495 CTTTAGCGGCGC-TCTCCCGCAAACGCCGCTAAAGACCAGGACCTTTAGCGGCACTTTTCCCAAA
1 CTTTAGCGGCGCTTCTCCCGCAAACGCCGCTAAAGACCAGGACCTTTAGCGGCACTTTTCCCGAA
*
45874559 AACGCCACTAAAG
66 AACGCCGCTAAAG
45874572 GTCACGAAAA
Statistics
Matches: 149, Mismatches: 14, Indels: 1
0.91 0.09 0.01
Matches are distributed among these distances:
85 60 0.40
86 89 0.60
ACGTcount: A:0.27, C:0.34, G:0.20, T:0.19
Consensus pattern (86 bp):
CTTTAGCGGCGCTTCTCCCGCAAACGCCGCTAAAGACCAGGACCTTTAGCGGCACTTTTCCCGAA
AACGCCGCTAAAGACCAAGAC
Found at i:45875324 original size:46 final size:46
Alignment explanation
Indices: 45875274--45875900 Score: 206
Period size: 46 Copynumber: 13.7 Consensus size: 46
45875264 AACAAGTTAA
*
45875274 ATTTAAACACTTCAATTTGCACCACTTTAACATATCAATTAACAAC
1 ATTTAAACACTTCAATTTGCACCACTTAAACATATCAATTAACAAC
* * * * * * ** *
45875320 ATTTATACACATCAA-TTACAGCGA-TAAAACATCTCAATTTTCAGC
1 ATTTAAACACTTCAATTTGCA-CCACTTAAACATATCAATTAACAAC
** * * *
45875365 AACTAAACACTTCAATTTGCAGCACTTAAACACT-TCAATTTACAGC
1 ATTTAAACACTTCAATTTGCACCACTTAAACA-TATCAATTAACAAC
* * * *
45875411 ATTTAAACACTTAAATTTTCAGCACTTAAACATATTAATTAACAAC
1 ATTTAAACACTTCAATTTGCACCACTTAAACATATCAATTAACAAC
* * * * * * ** *
45875457 ATTTACACACCTCAA-TTACAGCGA-TAAAACATCTCAATTTCCAGC
1 ATTTAAACACTTCAATTTGCA-CCACTTAAACATATCAATTAACAAC
** * * * * ** *
45875502 AACTAAATACTTCAATTTGTAGCACTTAAACACT-TAAATTTGCAGC
1 ATTTAAACACTTCAATTTGCACCACTTAAACA-TATCAATTAACAAC
* * * * * **
45875548 ACTTAAACACTTCAATTTACAGCATTTAAACACT-TAAATTTGCAAC
1 ATTTAAACACTTCAATTTGCACCACTTAAACA-TATCAATTAACAAC
* * ** * * * ** **
45875594 ACTTAAACA-TATCAGTTAACAACATTTATACACCTCAATT-ACGGC
1 ATTTAAACACT-TCAATTTGCACCACTTAAACATATCAATTAACAAC
* * * ** *
45875639 GA-TAAAACA-TCTCAATTTCCAGCAAC-TAAACACT-TCAATTTGCAGC
1 -ATTTAAACACT-TCAATTTGCA-CCACTTAAACA-TATCAATTAACAAC
* * *** * *
45875685 ACTTAAAACACTTCAATTTGCAGCACTTAAACACGCCAATTTACAGC
1 A-TTTAAACACTTCAATTTGCACCACTTAAACATATCAATTAACAAC
* *
45875732 ATTTAAACACTTAAATTTGCAGCACTTAAACATATCAATTAACAAC
1 ATTTAAACACTTCAATTTGCACCACTTAAACATATCAATTAACAAC
* * * * * * ** *
45875778 ATTTATACACCTCAA-TTACAGCGA-TAAAACATCTCAATTTCCAGC
1 ATTTAAACACTTCAATTTGCA-CCACTTAAACATATCAATTAACAAC
** * * * ** *
45875823 AACTAAGCACTTCAATTTGCAGCACTTAAACACT-GCAATTTGCAGC
1 ATTTAAACACTTCAATTTGCACCACTTAAACA-TATCAATTAACAAC
* * * *
45875869 ACTTAAACACTTCAATTTACAACATTTAAACA
1 ATTTAAACACTTCAATTTGCACCACTTAAACA
45875901 CTTAAATTTG
Statistics
Matches: 438, Mismatches: 119, Indels: 48
0.72 0.20 0.08
Matches are distributed among these distances:
45 122 0.28
46 279 0.64
47 36 0.08
48 1 0.00
ACGTcount: A:0.40, C:0.24, G:0.06, T:0.30
Consensus pattern (46 bp):
ATTTAAACACTTCAATTTGCACCACTTAAACATATCAATTAACAAC
Found at i:45875372 original size:23 final size:23
Alignment explanation
Indices: 45875353--45875931 Score: 357
Period size: 23 Copynumber: 25.3 Consensus size: 23
45875343 ATAAAACATC
45875353 TCAATTTTCAGCAAC-TAAACACT
1 TCAATTTTCAGC-ACTTAAACACT
*
45875376 TCAATTTGCAGCACTTAAACACT
1 TCAATTTTCAGCACTTAAACACT
* *
45875399 TCAATTTACAGCATTTAAACACT
1 TCAATTTTCAGCACTTAAACACT
*
45875422 TAAATTTTCAGCACTTAAACA-T
1 TCAATTTTCAGCACTTAAACACT
* ** * * * *
45875444 ATTAATTAACAACATTTACACACC
1 -TCAATTTTCAGCACTTAAACACT
* *
45875468 TCAA-TTACAGCGA-TAAAACA-T
1 TCAATTTTCAGC-ACTTAAACACT
* *
45875489 CTCAATTTCCAGCAAC-TAAATACT
1 -TCAATTTTCAGC-ACTTAAACACT
45875513 TCAATTTGT-AGCACTTAAACACT
1 TCAATTT-TCAGCACTTAAACACT
* *
45875536 TAAATTTGCAGCACTTAAACACT
1 TCAATTTTCAGCACTTAAACACT
* *
45875559 TCAATTTACAGCATTTAAACACT
1 TCAATTTTCAGCACTTAAACACT
* * *
45875582 TAAATTTGCAACACTTAAACA-T
1 TCAATTTTCAGCACTTAAACACT
* ** * * * *
45875604 ATCAGTTAACAACATTTATACACC
1 -TCAATTTTCAGCACTTAAACACT
* * *
45875628 TCAA-TTACGGCGA-TAAAACA-T
1 TCAATTTTCAGC-ACTTAAACACT
*
45875649 CTCAATTTCCAGCAAC-TAAACACT
1 -TCAATTTTCAGC-ACTTAAACACT
*
45875673 TCAATTTGCAGCACTTAAAACACT
1 TCAATTTTCAGCACTT-AAACACT
* *
45875697 TCAATTTGCAGCACTTAAACACG
1 TCAATTTTCAGCACTTAAACACT
* * *
45875720 CCAATTTACAGCATTTAAACACT
1 TCAATTTTCAGCACTTAAACACT
* *
45875743 TAAATTTGCAGCACTTAAACA-T
1 TCAATTTTCAGCACTTAAACACT
** * * * *
45875765 ATCAATTAACAACATTTATACACC
1 -TCAATTTTCAGCACTTAAACACT
* *
45875789 TCAA-TTACAGCGA-TAAAACA-T
1 TCAATTTTCAGC-ACTTAAACACT
* *
45875810 CTCAATTTCCAGCAAC-TAAGCACT
1 -TCAATTTTCAGC-ACTTAAACACT
*
45875834 TCAATTTGCAGCACTTAAACACT
1 TCAATTTTCAGCACTTAAACACT
* *
45875857 GCAATTTGCAGCACTTAAACACT
1 TCAATTTTCAGCACTTAAACACT
* * *
45875880 TCAATTTACAACATTTAAACACT
1 TCAATTTTCAGCACTTAAACACT
* *
45875903 TAAATTTGCAGCACTTAAACA-T
1 TCAATTTTCAGCACTTAAACACT
45875925 ATCAATT
1 -TCAATT
45875932 AACAACATTT
Statistics
Matches: 437, Mismatches: 90, Indels: 58
0.75 0.15 0.10
Matches are distributed among these distances:
22 53 0.12
23 358 0.82
24 26 0.06
ACGTcount: A:0.40, C:0.24, G:0.07, T:0.30
Consensus pattern (23 bp):
TCAATTTTCAGCACTTAAACACT
Found at i:45875519 original size:160 final size:160
Alignment explanation
Indices: 45875353--45875976 Score: 1088
Period size: 160 Copynumber: 3.9 Consensus size: 160
45875343 ATAAAACATC
*
45875353 TCAATTTTCAGCAAC-TAAACACTTCAATTTGCAGCACTTAAACACTTCAATTTACAGCATTTAA
1 TCAATTTGCAGC-ACTTAAACACTTCAATTTGCAGCACTTAAACACTTCAATTTACAGCATTTAA
* * *
45875417 ACACTTAAATTTTCAGCACTTAAACATATTAATTAACAACATTTACACACCTCAATTACAGCGAT
65 ACACTTAAATTTGCAGCACTTAAACATATCAATTAACAACATTTATACACCTCAATTACAGCGAT
*
45875482 AAAACATCTCAATTTCCAGCAACTAAATACT
130 AAAACATCTCAATTTCCAGCAACTAAACACT
* *
45875513 TCAATTTGTAGCACTTAAACACTTAAATTTGCAGCACTTAAACACTTCAATTTACAGCATTTAAA
1 TCAATTTGCAGCACTTAAACACTTCAATTTGCAGCACTTAAACACTTCAATTTACAGCATTTAAA
* * *
45875578 CACTTAAATTTGCAACACTTAAACATATCAGTTAACAACATTTATACACCTCAATTACGGCGATA
66 CACTTAAATTTGCAGCACTTAAACATATCAATTAACAACATTTATACACCTCAATTACAGCGATA
45875643 AAACATCTCAATTTCCAGCAACTAAACACT
131 AAACATCTCAATTTCCAGCAACTAAACACT
**
45875673 TCAATTTGCAGCACTTAAAACACTTCAATTTGCAGCACTTAAACACGCCAATTTACAGCATTTAA
1 TCAATTTGCAGCACTT-AAACACTTCAATTTGCAGCACTTAAACACTTCAATTTACAGCATTTAA
45875738 ACACTTAAATTTGCAGCACTTAAACATATCAATTAACAACATTTATACACCTCAATTACAGCGAT
65 ACACTTAAATTTGCAGCACTTAAACATATCAATTAACAACATTTATACACCTCAATTACAGCGAT
*
45875803 AAAACATCTCAATTTCCAGCAACTAAGCACT
130 AAAACATCTCAATTTCCAGCAACTAAACACT
* *
45875834 TCAATTTGCAGCACTTAAACACTGCAATTTGCAGCACTTAAACACTTCAATTTACAACATTTAAA
1 TCAATTTGCAGCACTTAAACACTTCAATTTGCAGCACTTAAACACTTCAATTTACAGCATTTAAA
45875899 CACTTAAATTTGCAGCACTTAAACATATCAATTAACAACATTTATACACCTCAATTACAGCGATA
66 CACTTAAATTTGCAGCACTTAAACATATCAATTAACAACATTTATACACCTCAATTACAGCGATA
45875964 AAACATCTCAATT
131 AAACATCTCAATT
45875977 NNNNNNNNNN
Statistics
Matches: 440, Mismatches: 22, Indels: 4
0.94 0.05 0.01
Matches are distributed among these distances:
159 2 0.00
160 285 0.65
161 153 0.35
ACGTcount: A:0.40, C:0.24, G:0.06, T:0.30
Consensus pattern (160 bp):
TCAATTTGCAGCACTTAAACACTTCAATTTGCAGCACTTAAACACTTCAATTTACAGCATTTAAA
CACTTAAATTTGCAGCACTTAAACATATCAATTAACAACATTTATACACCTCAATTACAGCGATA
AAACATCTCAATTTCCAGCAACTAAACACT
Found at i:45875520 original size:137 final size:137
Alignment explanation
Indices: 45875274--45875717 Score: 477
Period size: 137 Copynumber: 3.2 Consensus size: 137
45875264 AACAAGTTAA
* * * *
45875274 ATTTAAACACTTCAATTTGCACCACTTTAACATATCAATTAACAACATTTATACACATCAATTAC
1 ATTTAAACACTTCAATTTACAGCACTTAAACATATCAATTAACAACATTTACACACATCAATTAC
* *
45875339 AGCGATAAAACATCTCAATTTTCAGCAACTAAACACTTCAATTTGCAGCACTTAAACACTTCAAT
66 AGCGATAAAACATCTCAATTTCCAGCAACTAAACACTTCAATTTGCAGCACTTAAACACTTAAAT
45875404 TTACAGC
131 TTACAGC
* * * *
45875411 ATTTAAACACTTAAATTTTCAGCACTTAAACATATTAATTAACAACATTTACACACCTCAATTAC
1 ATTTAAACACTTCAATTTACAGCACTTAAACATATCAATTAACAACATTTACACACATCAATTAC
* *
45875476 AGCGATAAAACATCTCAATTTCCAGCAACTAAATACTTCAATTTGTAGCACTTAAACACTTAAAT
66 AGCGATAAAACATCTCAATTTCCAGCAACTAAACACTTCAATTTGCAGCACTTAAACACTTAAAT
*
45875541 TTGCAGC
131 TTACAGC
* * * ** * * * *
45875548 ACTTAAACACTTCAATTTACAGCATTTAAACACT-TAAATTTGCAACACTTAAACATATCAGTTA
1 ATTTAAACACTTCAATTTACAGCACTTAAACA-TATCAATTAACAACATTTACACACATCAATT-
* * * * * * * *
45875612 ACAAC-ATTTATACACCTCAA-TTACGGCGA-TAAA-ACATCTCAATTTCCAGCAAC-TAAACAC
64 ACAGCGA-TAAAACATCTCAATTTCCAGCAACTAAACAC-T-TCAATTTGCAGC-ACTTAAACAC
* *
45875672 TTCAATTTGCAGC
125 TTAAATTTACAGC
* *
45875685 ACTTAAAACACTTCAATTTGCAGCACTTAAACA
1 A-TTTAAACACTTCAATTTACAGCACTTAAACA
45875718 CGCCAATTTA
Statistics
Matches: 262, Mismatches: 38, Indels: 13
0.84 0.12 0.04
Matches are distributed among these distances:
135 2 0.01
136 5 0.02
137 211 0.81
138 44 0.17
ACGTcount: A:0.41, C:0.23, G:0.06, T:0.30
Consensus pattern (137 bp):
ATTTAAACACTTCAATTTACAGCACTTAAACATATCAATTAACAACATTTACACACATCAATTAC
AGCGATAAAACATCTCAATTTCCAGCAACTAAACACTTCAATTTGCAGCACTTAAACACTTAAAT
TTACAGC
Found at i:45875951 original size:321 final size:320
Alignment explanation
Indices: 45875353--45875976 Score: 1088
Period size: 321 Copynumber: 1.9 Consensus size: 320
45875343 ATAAAACATC
* **
45875353 TCAATTTTCAGCAACTAAACACTTCAATTTGCAGCACTTAAACACTTCAATTTACAGCATTTAAA
1 TCAATTTGCAGCAACTAAACACTTCAATTTGCAGCACTTAAACACGCCAATTTACAGCATTTAAA
* *
45875418 CACTTAAATTTTCAGCACTTAAACATATTAATTAACAACATTTACACACCTCAATTACAGCGATA
66 CACTTAAATTTGCAGCACTTAAACATATCAATTAACAACATTTACACACCTCAATTACAGCGATA
* * *
45875483 AAACATCTCAATTTCCAGCAACTAAATACTTCAATTTGTAGCACTTAAACACTTAAATTTGCAGC
131 AAACATCTCAATTTCCAGCAACTAAACACTTCAATTTGCAGCACTTAAACACTGAAATTTGCAGC
* *
45875548 ACTTAAACACTTCAATTTACAGCATTTAAACACTTAAATTTGCAACACTTAAACATATCAGTTAA
196 ACTTAAACACTTCAATTTACAACATTTAAACACTTAAATTTGCAACACTTAAACATATCAATTAA
*
45875613 CAACATTTATACACCTCAATTACGGCGATAAAACATCTCAATTTCCAGCAACTAAACACT
261 CAACATTTATACACCTCAATTACAGCGATAAAACATCTCAATTTCCAGCAACTAAACACT
45875673 TCAATTTGCAGC-ACTTAAAACACTTCAATTTGCAGCACTTAAACACGCCAATTTACAGCATTTA
1 TCAATTTGCAGCAAC-T-AAACACTTCAATTTGCAGCACTTAAACACGCCAATTTACAGCATTTA
*
45875737 AACACTTAAATTTGCAGCACTTAAACATATCAATTAACAACATTTATACACCTCAATTACAGCGA
64 AACACTTAAATTTGCAGCACTTAAACATATCAATTAACAACATTTACACACCTCAATTACAGCGA
* *
45875802 TAAAACATCTCAATTTCCAGCAACTAAGCACTTCAATTTGCAGCACTTAAACACTGCAATTTGCA
129 TAAAACATCTCAATTTCCAGCAACTAAACACTTCAATTTGCAGCACTTAAACACTGAAATTTGCA
*
45875867 GCACTTAAACACTTCAATTTACAACATTTAAACACTTAAATTTGCAGCACTTAAACATATCAATT
194 GCACTTAAACACTTCAATTTACAACATTTAAACACTTAAATTTGCAACACTTAAACATATCAATT
45875932 AACAACATTTATACACCTCAATTACAGCGATAAAACATCTCAATT
259 AACAACATTTATACACCTCAATTACAGCGATAAAACATCTCAATT
45875977 NNNNNNNNNN
Statistics
Matches: 287, Mismatches: 15, Indels: 3
0.94 0.05 0.01
Matches are distributed among these distances:
319 2 0.01
320 12 0.04
321 273 0.95
ACGTcount: A:0.40, C:0.24, G:0.06, T:0.30
Consensus pattern (320 bp):
TCAATTTGCAGCAACTAAACACTTCAATTTGCAGCACTTAAACACGCCAATTTACAGCATTTAAA
CACTTAAATTTGCAGCACTTAAACATATCAATTAACAACATTTACACACCTCAATTACAGCGATA
AAACATCTCAATTTCCAGCAACTAAACACTTCAATTTGCAGCACTTAAACACTGAAATTTGCAGC
ACTTAAACACTTCAATTTACAACATTTAAACACTTAAATTTGCAACACTTAAACATATCAATTAA
CAACATTTATACACCTCAATTACAGCGATAAAACATCTCAATTTCCAGCAACTAAACACT
Found at i:45876255 original size:91 final size:91
Alignment explanation
Indices: 45876103--45876268 Score: 235
Period size: 91 Copynumber: 1.8 Consensus size: 91
45876093 CTTAAACACT
* * *
45876103 TCAATTTACAGCATTTAAACACTTAAATTTGCAGCACTTAAACATATCAGTTAACAACATTTATA
1 TCAATTTACAGCACTTAAACACTTAAATTTGCAGCACTTAAACATATCAATTAACAACATTTAAA
45876168 CACCTCAATTACAGCGATAAAACATC
66 CACCTCAATTACAGCGATAAAACATC
* * ** *
45876194 TCAATTTCCAGCACTTAAACACTTCAATTTGCAGCACTTAAACACT-TCAATTTGCAGCATTTAA
1 TCAATTTACAGCACTTAAACACTTAAATTTGCAGCACTTAAACA-TATCAATTAACAACATTTAA
*
45876258 ACACTTCAATT
65 ACACCTCAATT
45876269 TGCAGCACTT
Statistics
Matches: 65, Mismatches: 9, Indels: 2
0.86 0.12 0.03
Matches are distributed among these distances:
91 64 0.98
92 1 0.02
ACGTcount: A:0.39, C:0.23, G:0.07, T:0.31
Consensus pattern (91 bp):
TCAATTTACAGCACTTAAACACTTAAATTTGCAGCACTTAAACATATCAATTAACAACATTTAAA
CACCTCAATTACAGCGATAAAACATC
Found at i:45876451 original size:23 final size:23
Alignment explanation
Indices: 45876077--45876443 Score: 338
Period size: 23 Copynumber: 16.0 Consensus size: 23
45876067 NNNNNNNNNN
45876077 ACTTCAATTTGCAGCACTTAAAC
1 ACTTCAATTTGCAGCACTTAAAC
* *
45876100 ACTTCAATTTACAGCATTTAAAC
1 ACTTCAATTTGCAGCACTTAAAC
*
45876123 ACTTAAATTTGCAGCACTTAAAC
1 ACTTCAATTTGCAGCACTTAAAC
* ** * * *
45876146 A-TATCAGTTAACAACATTTATAC
1 ACT-TCAATTTGCAGCACTTAAAC
* * *
45876169 ACCTCAA-TTACAGCGA-TAAAAC
1 ACTTCAATTTGCAGC-ACTTAAAC
*
45876191 A-TCTCAATTTCCAGCACTTAAAC
1 ACT-TCAATTTGCAGCACTTAAAC
45876214 ACTTCAATTTGCAGCACTTAAAC
1 ACTTCAATTTGCAGCACTTAAAC
*
45876237 ACTTCAATTTGCAGCATTTAAAC
1 ACTTCAATTTGCAGCACTTAAAC
*
45876260 ACTTCAATTTGCAGCACTTAAAG
1 ACTTCAATTTGCAGCACTTAAAC
** * * *
45876283 A-TATCAATTAACAACATTTATAC
1 ACT-TCAATTTGCAGCACTTAAAC
* * *
45876306 ACCTCAA-TTACAGCGA-TAAAAC
1 ACTTCAATTTGCAGC-ACTTAAAC
* * *
45876328 A-TCTCAATTTCCAACAAC-TAAGC
1 ACT-TCAATTTGCAGC-ACTTAAAC
45876351 ACTTCAATTTGCAGCACTTAAAC
1 ACTTCAATTTGCAGCACTTAAAC
*
45876374 GCTTCAATTTGCAGCACTTAAAC
1 ACTTCAATTTGCAGCACTTAAAC
* *
45876397 ACTTCAATTTACAGCATTTAAAC
1 ACTTCAATTTGCAGCACTTAAAC
*
45876420 ACTTAAATTTGCAGCACTTAAAC
1 ACTTCAATTTGCAGCACTTAAAC
45876443 A
1 A
45876444 TACCAATTAA
Statistics
Matches: 277, Mismatches: 52, Indels: 30
0.77 0.14 0.08
Matches are distributed among these distances:
22 33 0.12
23 242 0.87
24 2 0.01
ACGTcount: A:0.39, C:0.24, G:0.07, T:0.30
Consensus pattern (23 bp):
ACTTCAATTTGCAGCACTTAAAC
Found at i:45876452 original size:137 final size:137
Alignment explanation
Indices: 45876077--45876420 Score: 582
Period size: 137 Copynumber: 2.5 Consensus size: 137
45876067 NNNNNNNNNN
* *
45876077 ACTTCAATTTGCAGCACTTAAACACTTCAATTTACAGCATTTAAACACTTAAATTTGCAGCACTT
1 ACTTCAATTTGCAGCACTTAAACACTTCAATTTGCAGCATTTAAACACTTCAATTTGCAGCACTT
* *
45876142 AAACATATCAGTTAACAACATTTATACACCTCAATTACAGCGATAAAACATCTCAATTTCCAGCA
66 AAACATATCAATTAACAACATTTATACACCTCAATTACAGCGATAAAACATCTCAATTTCCAACA
45876207 CTTAAAC
131 CTTAAAC
45876214 ACTTCAATTTGCAGCACTTAAACACTTCAATTTGCAGCATTTAAACACTTCAATTTGCAGCACTT
1 ACTTCAATTTGCAGCACTTAAACACTTCAATTTGCAGCATTTAAACACTTCAATTTGCAGCACTT
*
45876279 AAAGATATCAATTAACAACATTTATACACCTCAATTACAGCGATAAAACATCTCAATTTCCAACA
66 AAACATATCAATTAACAACATTTATACACCTCAATTACAGCGATAAAACATCTCAATTTCCAAC-
*
45876344 AC-TAAGC
130 ACTTAAAC
* * * *
45876351 ACTTCAATTTGCAGCACTTAAACGCTTCAATTTGCAGCACTTAAACACTTCAATTTACAGCATTT
1 ACTTCAATTTGCAGCACTTAAACACTTCAATTTGCAGCATTTAAACACTTCAATTTGCAGCACTT
45876416 AAACA
66 AAACA
45876421 CTTAAATTTG
Statistics
Matches: 195, Mismatches: 11, Indels: 2
0.94 0.05 0.01
Matches are distributed among these distances:
137 193 0.99
138 2 0.01
ACGTcount: A:0.39, C:0.24, G:0.07, T:0.30
Consensus pattern (137 bp):
ACTTCAATTTGCAGCACTTAAACACTTCAATTTGCAGCATTTAAACACTTCAATTTGCAGCACTT
AAACATATCAATTAACAACATTTATACACCTCAATTACAGCGATAAAACATCTCAATTTCCAACA
CTTAAAC
Found at i:45878095 original size:49 final size:49
Alignment explanation
Indices: 45878023--45878122 Score: 200
Period size: 49 Copynumber: 2.0 Consensus size: 49
45878013 TTTCAGTCCA
45878023 GTGAAATGAAAAGGAAAAAGAAGTGTGATTGGTGTAGGTGTATTGACTG
1 GTGAAATGAAAAGGAAAAAGAAGTGTGATTGGTGTAGGTGTATTGACTG
45878072 GTGAAATGAAAAGGAAAAAGAAGTGTGATTGGTGTAGGTGTATTGACTG
1 GTGAAATGAAAAGGAAAAAGAAGTGTGATTGGTGTAGGTGTATTGACTG
45878121 GT
1 GT
45878123 ATTGTTGGAA
Statistics
Matches: 51, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
49 51 1.00
ACGTcount: A:0.36, C:0.02, G:0.35, T:0.27
Consensus pattern (49 bp):
GTGAAATGAAAAGGAAAAAGAAGTGTGATTGGTGTAGGTGTATTGACTG
Found at i:45879117 original size:7 final size:7
Alignment explanation
Indices: 45879107--45879146 Score: 55
Period size: 7 Copynumber: 5.7 Consensus size: 7
45879097 ATAAACCGTA
45879107 AACCCCT
1 AACCCCT
45879114 AACCCCT
1 AACCCCT
45879121 AACCCCT
1 AACCCCT
*
45879128 AACCCTT
1 AACCCCT
45879135 AAACCCC-
1 -AACCCCT
45879142 AACCC
1 AACCC
45879147 TTATAACTGT
Statistics
Matches: 30, Mismatches: 2, Indels: 3
0.86 0.06 0.09
Matches are distributed among these distances:
6 5 0.17
7 20 0.67
8 5 0.17
ACGTcount: A:0.33, C:0.55, G:0.00, T:0.12
Consensus pattern (7 bp):
AACCCCT
Found at i:45879147 original size:14 final size:15
Alignment explanation
Indices: 45879105--45879149 Score: 67
Period size: 14 Copynumber: 3.1 Consensus size: 15
45879095 ACATAAACCG
*
45879105 TAAACCCCTAACCCC
1 TAAACCCCTAACCCT
45879120 T-AACCCCTAACCCT
1 TAAACCCCTAACCCT
45879134 TAAACCCC-AACCCT
1 TAAACCCCTAACCCT
45879148 TA
1 TA
45879150 TAACTGTCCT
Statistics
Matches: 28, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
14 21 0.75
15 7 0.25
ACGTcount: A:0.33, C:0.49, G:0.00, T:0.18
Consensus pattern (15 bp):
TAAACCCCTAACCCT
Found at i:45880508 original size:41 final size:41
Alignment explanation
Indices: 45880100--45880503 Score: 589
Period size: 41 Copynumber: 9.9 Consensus size: 41
45880090 ATGATAAATT
* * *
45880100 TGAGCATTAGCGGCGCTTCCTCATAAACGCCGCTAAA-A-A
1 TGAGCATTAGCGGCGCTTCTTCAAAAACGCCGCTAAAGACC
**
45880139 TAGAGCATTAGCGGCGCTTCTTCAAAAACGCTACTAAAGACC
1 T-GAGCATTAGCGGCGCTTCTTCAAAAACGCCGCTAAAGACC
*
45880181 TGAGCATTAGCGGCGCTTTTTCAAAAACGCCGCTAAAGACC
1 TGAGCATTAGCGGCGCTTCTTCAAAAACGCCGCTAAAGACC
* *
45880222 TGAGCATTAGCGGCGCTTTTTCAAAAACGCCGCTAAAGCCC
1 TGAGCATTAGCGGCGCTTCTTCAAAAACGCCGCTAAAGACC
* * *
45880263 TAAGCATTAGCGGCCCTT-TTACAAAAACGCCACTAAAGACC
1 TGAGCATTAGCGGCGCTTCTT-CAAAAACGCCGCTAAAGACC
*
45880304 TGAGCTTTAGCGGCGCTTCTTCAAAAACGCCGCTAAAGACC
1 TGAGCATTAGCGGCGCTTCTTCAAAAACGCCGCTAAAGACC
* * *
45880345 TGAGCTTTAGCGGCGCTTCTTCAAAAACGCCGCTAATGCCC
1 TGAGCATTAGCGGCGCTTCTTCAAAAACGCCGCTAAAGACC
*
45880386 TGAGCTTTAGCGGCGCTTCTTCAAAAACGCCGCTAAAGACC
1 TGAGCATTAGCGGCGCTTCTTCAAAAACGCCGCTAAAGACC
* * *
45880427 TGAGCTTTAGCGGCGCTTCTTCAAAAACGCCGCTAATGCCC
1 TGAGCATTAGCGGCGCTTCTTCAAAAACGCCGCTAAAGACC
*
45880468 TTAGCATTAGCGGCGCTTCTTCAAAAACGCCGCTAA
1 TGAGCATTAGCGGCGCTTCTTCAAAAACGCCGCTAA
45880504 TGCCCCCAAA
Statistics
Matches: 335, Mismatches: 25, Indels: 8
0.91 0.07 0.02
Matches are distributed among these distances:
39 1 0.00
40 34 0.10
41 297 0.89
42 3 0.01
ACGTcount: A:0.28, C:0.29, G:0.21, T:0.22
Consensus pattern (41 bp):
TGAGCATTAGCGGCGCTTCTTCAAAAACGCCGCTAAAGACC
Found at i:45880629 original size:40 final size:40
Alignment explanation
Indices: 45880563--45880680 Score: 154
Period size: 40 Copynumber: 3.0 Consensus size: 40
45880553 CGCTTTATGG
45880563 AAAA-CGCCGCTAATGCTC-ATTTTTAGTGGCGTTTTTTA
1 AAAAGCGCCGCTAATGCTCTATTTTTAGTGGCGTTTTTTA
* * *
45880601 AAAAGCGCCGCCAATACTCTATATTTAGTGGCGTTTTATT-
1 AAAAGCGCCGCTAATGCTCTATTTTTAGTGGCGTTTT-TTA
*
45880641 AAAAGCGCCGCTAATGCT-TGATTTTTAGCGGCGTTTTTTA
1 AAAAGCGCCGCTAATGCTCT-ATTTTTAGTGGCGTTTTTTA
45880681 TCTAAACGCC
Statistics
Matches: 68, Mismatches: 7, Indels: 8
0.82 0.08 0.10
Matches are distributed among these distances:
38 4 0.06
39 15 0.22
40 47 0.69
41 2 0.03
ACGTcount: A:0.25, C:0.19, G:0.19, T:0.37
Consensus pattern (40 bp):
AAAAGCGCCGCTAATGCTCTATTTTTAGTGGCGTTTTTTA
Found at i:45882696 original size:89 final size:91
Alignment explanation
Indices: 45882542--45882707 Score: 221
Period size: 89 Copynumber: 1.8 Consensus size: 91
45882532 TCAGTAAATG
* * * *
45882542 TATTTTCATAAAATATCTAATATAATATTTATATTTTAAAAATGTTTAAGGTAGTATTTAAACTA
1 TATTTTCATAAAATATCTAATATAATACTTATACTTTAAAAATGTTCAAGGTAGTACTTAAACTA
45882607 TCAATATATATTTTATTTTTAATTTA
66 TCAATATATATTTTATTTTTAATTTA
* * * *
45882633 TATTTTCATAAAATATC-AAT-TAGTACTTGTACTTTGAAAATGTTCAATGT-GATACTTAAACT
1 TATTTTCATAAAATATCTAATATAATACTTATACTTTAAAAATGTTCAAGGTAG-TACTTAAACT
*
45882695 ATCAATATGTATT
65 ATCAATATATATT
45882708 AGTATTAATA
Statistics
Matches: 65, Mismatches: 9, Indels: 4
0.83 0.12 0.05
Matches are distributed among these distances:
88 1 0.02
89 44 0.68
90 3 0.05
91 17 0.26
ACGTcount: A:0.39, C:0.07, G:0.07, T:0.47
Consensus pattern (91 bp):
TATTTTCATAAAATATCTAATATAATACTTATACTTTAAAAATGTTCAAGGTAGTACTTAAACTA
TCAATATATATTTTATTTTTAATTTA
Found at i:45884738 original size:21 final size:21
Alignment explanation
Indices: 45884713--45884753 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
45884703 CAAAATATAT
45884713 CAAAAACAAAA-ACAAAAAAAC
1 CAAAAA-AAAACACAAAAAAAC
*
45884734 CAAAAAAAAACAGAAAAAAA
1 CAAAAAAAAACACAAAAAAA
45884754 ACCTGGACTG
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 4 0.22
21 14 0.78
ACGTcount: A:0.83, C:0.15, G:0.02, T:0.00
Consensus pattern (21 bp):
CAAAAAAAAACACAAAAAAAC
Found at i:45884823 original size:27 final size:27
Alignment explanation
Indices: 45884782--45884888 Score: 169
Period size: 27 Copynumber: 4.0 Consensus size: 27
45884772 ACTCCCTGGG
*
45884782 ACAAGGGAACACTGTTGGCGGCACCAA
1 ACAAGGGAACCCTGTTGGCGGCACCAA
45884809 ACAAGGGAACCCTGTTGGCGGCACCAA
1 ACAAGGGAACCCTGTTGGCGGCACCAA
**
45884836 ACAAGGGTTCCCTGTTGGCGGCACCAA
1 ACAAGGGAACCCTGTTGGCGGCACCAA
**
45884863 ACAAGGGTTCCCTGTTGGCGGCACCA
1 ACAAGGGAACCCTGTTGGCGGCACCA
45884889 CTCGTGTTAT
Statistics
Matches: 77, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
27 77 1.00
ACGTcount: A:0.26, C:0.29, G:0.30, T:0.15
Consensus pattern (27 bp):
ACAAGGGAACCCTGTTGGCGGCACCAA
Found at i:45885175 original size:3 final size:3
Alignment explanation
Indices: 45885167--45885213 Score: 94
Period size: 3 Copynumber: 15.7 Consensus size: 3
45885157 AATTTTATAG
45885167 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA
45885214 AGATGTTACT
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 44 1.00
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
TAT
Found at i:45885240 original size:12 final size:12
Alignment explanation
Indices: 45885164--45885342 Score: 86
Period size: 12 Copynumber: 14.7 Consensus size: 12
45885154 AAAAATTTTA
45885164 TAGTATTATTAT
1 TAGTATTATTAT
*
45885176 TATTATTATTAT
1 TAGTATTATTAT
*
45885188 TATTATTATTAT
1 TAGTATTATTAT
*
45885200 TATTATTATTAT
1 TAGTATTATTAT
*
45885212 TAAG-A-TGTTACT
1 T-AGTATTATTA-T
*
45885224 TAGTATTATTGT
1 TAGTATTATTAT
* **
45885236 TAGTA-AAAAAT
1 TAGTATTATTAT
*
45885247 TAGTATTATTTT
1 TAGTATTATTAT
45885259 TA-TAGTTAGTTAT
1 TAGTA-TTA-TTAT
*
45885272 TAATAATT-TTAGT
1 TAGT-ATTATTA-T
45885285 TAGTATTATT-T
1 TAGTATTATTAT
45885296 T-GTATATAAAATTAT
1 TAGTAT-T---ATTAT
*
45885311 TAATATTATTAT
1 TAGTATTATTAT
*
45885323 T-GTGTTAGTTAT
1 TAGTATTA-TTAT
*
45885335 TAGGATTA
1 TAGTATTA
45885343 GTGGTTAAAT
Statistics
Matches: 128, Mismatches: 20, Indels: 37
0.69 0.11 0.20
Matches are distributed among these distances:
10 4 0.03
11 22 0.17
12 70 0.55
13 19 0.15
14 6 0.05
15 4 0.03
16 3 0.02
ACGTcount: A:0.35, C:0.01, G:0.09, T:0.55
Consensus pattern (12 bp):
TAGTATTATTAT
Found at i:45885970 original size:18 final size:18
Alignment explanation
Indices: 45885942--45885986 Score: 63
Period size: 18 Copynumber: 2.5 Consensus size: 18
45885932 TTGATATGGT
* *
45885942 TGGTGGTGAAGAAGAATG
1 TGGTGGCGAAGAAGAAGG
*
45885960 TGGTTGCGAAGAAGAAGG
1 TGGTGGCGAAGAAGAAGG
45885978 TGGTGGCGA
1 TGGTGGCGA
45885987 TCATTGGGAT
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
18 23 1.00
ACGTcount: A:0.29, C:0.04, G:0.47, T:0.20
Consensus pattern (18 bp):
TGGTGGCGAAGAAGAAGG
Found at i:45888439 original size:14 final size:14
Alignment explanation
Indices: 45888420--45888460 Score: 64
Period size: 14 Copynumber: 2.9 Consensus size: 14
45888410 TTTTTGTATC
45888420 AATTTAATTATTCT
1 AATTTAATTATTCT
45888434 AATTTAATTATTCT
1 AATTTAATTATTCT
*
45888448 AGTTTAAGTTATT
1 AATTTAA-TTATT
45888461 GTGGTTNNNN
Statistics
Matches: 25, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
14 20 0.80
15 5 0.20
ACGTcount: A:0.34, C:0.05, G:0.05, T:0.56
Consensus pattern (14 bp):
AATTTAATTATTCT
Found at i:45888974 original size:3 final size:3
Alignment explanation
Indices: 45888966--45889021 Score: 112
Period size: 3 Copynumber: 18.7 Consensus size: 3
45888956 AGTAACATCT
45888966 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
45889014 TAA TAA TA
1 TAA TAA TA
45889022 CTATAAAATT
Statistics
Matches: 53, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 53 1.00
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
TAA
Found at i:45889376 original size:27 final size:27
Alignment explanation
Indices: 45889303--45889382 Score: 133
Period size: 27 Copynumber: 3.0 Consensus size: 27
45889293 ATAACACGAG
**
45889303 TGGTGCCGCCAACAGGGAACCCTTGTT
1 TGGTGCCGCCAACAGGGTTCCCTTGTT
45889330 TGGTGCCGCCAACAGGGTTCCCTTGTT
1 TGGTGCCGCCAACAGGGTTCCCTTGTT
*
45889357 TGGTGCCGCCAACAGTGTTCCCTTGT
1 TGGTGCCGCCAACAGGGTTCCCTTGT
45889383 CCCAGGGAGT
Statistics
Matches: 50, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
27 50 1.00
ACGTcount: A:0.14, C:0.30, G:0.29, T:0.28
Consensus pattern (27 bp):
TGGTGCCGCCAACAGGGTTCCCTTGTT
Found at i:45889469 original size:29 final size:28
Alignment explanation
Indices: 45889436--45889506 Score: 117
Period size: 29 Copynumber: 2.5 Consensus size: 28
45889426 TTTGTTTTTT
45889436 TATATATTTTGGTAAATAAAAAAAATTTA
1 TATATATTTTGGTAAATAAAAAAAA-TTA
45889465 TATATATTTTGGTAAATAAAAAAAATTA
1 TATATATTTTGGTAAATAAAAAAAATTA
*
45889493 TA-ACATTTTGGTAA
1 TATATATTTTGGTAA
45889507 TTTTATTTTT
Statistics
Matches: 41, Mismatches: 1, Indels: 2
0.93 0.02 0.05
Matches are distributed among these distances:
27 11 0.27
28 5 0.12
29 25 0.61
ACGTcount: A:0.49, C:0.01, G:0.08, T:0.41
Consensus pattern (28 bp):
TATATATTTTGGTAAATAAAAAAAATTA
Found at i:45890919 original size:29 final size:29
Alignment explanation
Indices: 45890863--45890919 Score: 69
Period size: 29 Copynumber: 2.0 Consensus size: 29
45890853 TACCCTAAAA
* * * *
45890863 TTTGAGTGACCAAATTATAAATATTTTAT
1 TTTGAGTGACCAAAATAAAAACACTTTAT
*
45890892 TTTGAGTGACTAAAATAAAAACACTTTA
1 TTTGAGTGACCAAAATAAAAACACTTTA
45890920 AAATTTAAGT
Statistics
Matches: 23, Mismatches: 5, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
29 23 1.00
ACGTcount: A:0.42, C:0.09, G:0.11, T:0.39
Consensus pattern (29 bp):
TTTGAGTGACCAAAATAAAAACACTTTAT
Found at i:45917223 original size:20 final size:20
Alignment explanation
Indices: 45917186--45917224 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
45917176 AATCACTCTA
* *
45917186 TTTCTCGGCTCCCGAGCATG
1 TTTCTCGGCTCACAAGCATG
*
45917206 TTTCTCGGGTCACAAGCAT
1 TTTCTCGGCTCACAAGCAT
45917225 TTGATTCTTT
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.15, C:0.31, G:0.23, T:0.31
Consensus pattern (20 bp):
TTTCTCGGCTCACAAGCATG
Found at i:45917259 original size:3 final size:3
Alignment explanation
Indices: 45917251--45917277 Score: 54
Period size: 3 Copynumber: 9.0 Consensus size: 3
45917241 ATTTTGCAAT
45917251 TAA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA
45917278 GTATAATCTC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 24 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
TAA
Found at i:45927618 original size:37 final size:37
Alignment explanation
Indices: 45927568--45927643 Score: 143
Period size: 37 Copynumber: 2.1 Consensus size: 37
45927558 AATAGGACCA
45927568 AAATATTATAAATAGATAATGTTATTAATTATTTTAT
1 AAATATTATAAATAGATAATGTTATTAATTATTTTAT
*
45927605 AAATATTATAAATAGATAATGTTATTGATTATTTTAT
1 AAATATTATAAATAGATAATGTTATTAATTATTTTAT
45927642 AA
1 AA
45927644 TAAAAAATTT
Statistics
Matches: 38, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
37 38 1.00
ACGTcount: A:0.46, C:0.00, G:0.07, T:0.47
Consensus pattern (37 bp):
AAATATTATAAATAGATAATGTTATTAATTATTTTAT
Found at i:45928302 original size:3 final size:3
Alignment explanation
Indices: 45928296--45928359 Score: 128
Period size: 3 Copynumber: 21.3 Consensus size: 3
45928286 TATTAGTATT
45928296 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
45928344 ATA ATA ATA ATA ATA A
1 ATA ATA ATA ATA ATA A
45928360 GTTTATTTAT
Statistics
Matches: 61, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 61 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:45928920 original size:13 final size:13
Alignment explanation
Indices: 45928902--45928926 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
45928892 AACAATTTTT
45928902 TAATATAAATTTC
1 TAATATAAATTTC
45928915 TAATATAAATTT
1 TAATATAAATTT
45928927 AGTACTTAAT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.48, C:0.04, G:0.00, T:0.48
Consensus pattern (13 bp):
TAATATAAATTTC
Found at i:45929722 original size:16 final size:17
Alignment explanation
Indices: 45929701--45929735 Score: 54
Period size: 17 Copynumber: 2.1 Consensus size: 17
45929691 AAGCTTTAAA
*
45929701 ATGTTGGA-ACTTACCT
1 ATGTTGGACACATACCT
45929717 ATGTTGGACACATACCT
1 ATGTTGGACACATACCT
45929734 AT
1 AT
45929736 ATTAGACATT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
16 8 0.47
17 9 0.53
ACGTcount: A:0.29, C:0.20, G:0.17, T:0.34
Consensus pattern (17 bp):
ATGTTGGACACATACCT
Found at i:45940879 original size:20 final size:21
Alignment explanation
Indices: 45940856--45940894 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
45940846 CATTTATCAT
*
45940856 ATTTT-ATTATTTTACTTTCC
1 ATTTTCATCATTTTACTTTCC
*
45940876 ATTTTCATCATTTTTCTTT
1 ATTTTCATCATTTTACTTT
45940895 ATTTAATTTT
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
20 5 0.31
21 11 0.69
ACGTcount: A:0.18, C:0.15, G:0.00, T:0.67
Consensus pattern (21 bp):
ATTTTCATCATTTTACTTTCC
Found at i:45965591 original size:26 final size:27
Alignment explanation
Indices: 45965524--45965591 Score: 70
Period size: 26 Copynumber: 2.5 Consensus size: 27
45965514 AAATGATAAG
45965524 TACATAAAATCATGAAATTAAATTTGAAA
1 TACATAAAAT-ATGAAATT-AATTTGAAA
* *
45965553 TACATAGAA-ATGATAATT-ATTTGATA
1 TACATAAAATATGA-AATTAATTTGAAA
45965579 TAC-TAAAATATGA
1 TACATAAAATATGA
45965592 CATGGAAAAT
Statistics
Matches: 34, Mismatches: 3, Indels: 7
0.77 0.07 0.16
Matches are distributed among these distances:
25 4 0.12
26 14 0.41
27 4 0.12
28 4 0.12
29 8 0.24
ACGTcount: A:0.51, C:0.06, G:0.09, T:0.34
Consensus pattern (27 bp):
TACATAAAATATGAAATTAATTTGAAA
Found at i:45967460 original size:30 final size:31
Alignment explanation
Indices: 45967397--45967460 Score: 103
Period size: 30 Copynumber: 2.1 Consensus size: 31
45967387 AACTTGTTTA
*
45967397 TTGTTAATTTTTGTTATTATTTTAGAGGCAT
1 TTGTTAATTTTTGTTATTATTTTAGAAGCAT
*
45967428 TTGTTAA-TTTTGTTATTATTTTAGAAGTAT
1 TTGTTAATTTTTGTTATTATTTTAGAAGCAT
45967458 TTG
1 TTG
45967461 CTTGTTAAGT
Statistics
Matches: 31, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
30 24 0.77
31 7 0.23
ACGTcount: A:0.23, C:0.02, G:0.16, T:0.59
Consensus pattern (31 bp):
TTGTTAATTTTTGTTATTATTTTAGAAGCAT
Found at i:45968590 original size:17 final size:17
Alignment explanation
Indices: 45968555--45968590 Score: 54
Period size: 17 Copynumber: 2.1 Consensus size: 17
45968545 TTTAAAGTGT
*
45968555 AATTCTAAAAAAATTAA
1 AATTCTAAAAAAATGAA
*
45968572 AATTCTAAAAATATGAA
1 AATTCTAAAAAAATGAA
45968589 AA
1 AA
45968591 ATCTTTCAAA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.64, C:0.06, G:0.03, T:0.28
Consensus pattern (17 bp):
AATTCTAAAAAAATGAA
Found at i:45969041 original size:12 final size:12
Alignment explanation
Indices: 45969024--45969049 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
45969014 TAATTTTGAT
45969024 ATTATTATTATA
1 ATTATTATTATA
45969036 ATTATTATTATA
1 ATTATTATTATA
45969048 AT
1 AT
45969050 ATGTTAAAGA
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:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (12 bp):
ATTATTATTATA
Found at i:45978041 original size:11 final size:11
Alignment explanation
Indices: 45978023--45978131 Score: 51
Period size: 11 Copynumber: 10.7 Consensus size: 11
45978013 AATTTATACT
45978023 AAAT-ATATTA
1 AAATAATATTA
45978033 AAATAATATTA
1 AAATAATATTA
*
45978044 AGATAAT-TATA
1 AAATAATAT-TA
45978055 TAAA-AAT-TT-
1 -AAATAATATTA
* *
45978064 TAGTAA-A-TA
1 AAATAATATTA
*
45978073 AAAAAATATTA
1 AAATAATATTA
45978084 AAATAA-ATTA
1 AAATAATATTA
45978094 AAATAATA-T-
1 AAATAATATTA
* *
45978103 AAATATTTTTA
1 AAATAATATTA
*
45978114 AAA-AAAATTA
1 AAATAATATTA
*
45978124 AAAAAATA
1 AAATAATA
45978132 ATATGAAAAT
Statistics
Matches: 73, Mismatches: 14, Indels: 23
0.66 0.13 0.21
Matches are distributed among these distances:
8 2 0.03
9 11 0.15
10 26 0.36
11 32 0.44
12 2 0.03
ACGTcount: A:0.64, C:0.00, G:0.02, T:0.34
Consensus pattern (11 bp):
AAATAATATTA
Found at i:45978052 original size:20 final size:20
Alignment explanation
Indices: 45978029--45978124 Score: 63
Period size: 21 Copynumber: 4.8 Consensus size: 20
45978019 TACTAAATAT
*
45978029 ATTAAAATAATATTAAGATA
1 ATTAAAAAAATATTAAGATA
*
45978049 ATTATATAAAAAT-TTTAG-TA
1 ATTA-A-AAAAATATTAAGATA
* *
45978069 AATAAAAAAATATTAAAATAA
1 ATTAAAAAAATATTAAGAT-A
* * * *
45978090 ATTAAAATAATATAAATATT
1 ATTAAAAAAATATTAAGATA
*
45978110 TTTAAAAAAA-ATTAA
1 ATTAAAAAAATATTAA
45978125 AAAAATAATA
Statistics
Matches: 58, Mismatches: 13, Indels: 11
0.71 0.16 0.13
Matches are distributed among these distances:
18 6 0.10
19 8 0.14
20 18 0.31
21 21 0.36
22 5 0.09
ACGTcount: A:0.62, C:0.00, G:0.02, T:0.35
Consensus pattern (20 bp):
ATTAAAAAAATATTAAGATA
Found at i:45980732 original size:22 final size:22
Alignment explanation
Indices: 45980684--45980732 Score: 71
Period size: 22 Copynumber: 2.2 Consensus size: 22
45980674 GAAATGGGAG
*
45980684 GATTTAAATAAAATATAAGATT
1 GATTTAAATAAAATATAAAATT
*
45980706 GATTTAAATAAAATTTAAAATT
1 GATTTAAATAAAATATAAAATT
*
45980728 TATTT
1 GATTT
45980733 TTTATATGAG
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
22 24 1.00
ACGTcount: A:0.51, C:0.00, G:0.06, T:0.43
Consensus pattern (22 bp):
GATTTAAATAAAATATAAAATT
Found at i:45980951 original size:29 final size:28
Alignment explanation
Indices: 45980919--45980981 Score: 74
Period size: 28 Copynumber: 2.2 Consensus size: 28
45980909 AACCCAAAAT
45980919 ATAAAAT-TTTAAAAATTATATTTAATACA
1 ATAAAATATTT-AAAATTAT-TTTAATACA
** *
45980948 ATAAAATATTTATTATTATTTTAATATA
1 ATAAAATATTTAAAATTATTTTAATACA
45980976 ATAAAA
1 ATAAAA
45980982 AAATGTATTA
Statistics
Matches: 30, Mismatches: 3, Indels: 3
0.83 0.08 0.08
Matches are distributed among these distances:
28 14 0.47
29 13 0.43
30 3 0.10
ACGTcount: A:0.54, C:0.02, G:0.00, T:0.44
Consensus pattern (28 bp):
ATAAAATATTTAAAATTATTTTAATACA
Found at i:45980982 original size:29 final size:28
Alignment explanation
Indices: 45980933--45980996 Score: 76
Period size: 29 Copynumber: 2.2 Consensus size: 28
45980923 AATTTTAAAA
* *
45980933 ATTATATTTAATACAATAAAATATTTATT
1 ATTAT-TTTAATACAATAAAAAATGTATT
*
45980962 ATTATTTTAATATAATAAAAAAATGTATT
1 ATTATTTTAATACAAT-AAAAAATGTATT
45980991 A-TATTT
1 ATTATTT
45980997 ATGGTGATGT
Statistics
Matches: 31, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
28 15 0.48
29 16 0.52
ACGTcount: A:0.48, C:0.02, G:0.02, T:0.48
Consensus pattern (28 bp):
ATTATTTTAATACAATAAAAAATGTATT
Found at i:45980995 original size:28 final size:27
Alignment explanation
Indices: 45980933--45980996 Score: 76
Period size: 28 Copynumber: 2.3 Consensus size: 27
45980923 AATTTTAAAA
* *
45980933 ATTATA-TTTAATACAATAAAATATTT
1 ATTATATTTTAATACAATAAAAAATGT
*
45980959 ATTATTATTTTAATATAATAAAAAAATGT
1 ATTA-TATTTTAATACAAT-AAAAAATGT
45980988 ATTATATTT
1 ATTATATTT
45980997 ATGGTGATGT
Statistics
Matches: 32, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
26 4 0.12
27 2 0.06
28 15 0.47
29 11 0.34
ACGTcount: A:0.48, C:0.02, G:0.02, T:0.48
Consensus pattern (27 bp):
ATTATATTTTAATACAATAAAAAATGT
Found at i:45981114 original size:24 final size:24
Alignment explanation
Indices: 45981086--45981133 Score: 69
Period size: 24 Copynumber: 2.0 Consensus size: 24
45981076 TTATTTTTAA
*
45981086 AAAAATTATAAATAAAAATTAATCT
1 AAAAATT-TAAATAAAAATGAATCT
*
45981111 AAAAATTTAAATATAAATGAATC
1 AAAAATTTAAATAAAAATGAATC
45981134 AGGTCAGGCT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
24 14 0.67
25 7 0.33
ACGTcount: A:0.62, C:0.04, G:0.02, T:0.31
Consensus pattern (24 bp):
AAAAATTTAAATAAAAATGAATCT
Found at i:45987023 original size:16 final size:17
Alignment explanation
Indices: 45986981--45987023 Score: 56
Period size: 16 Copynumber: 2.7 Consensus size: 17
45986971 AATTATTCTT
45986981 TAAAAAATTA-TAAAGA
1 TAAAAAATTATTAAAGA
*
45986997 TATAAAA-TATTAAA-A
1 TAAAAAATTATTAAAGA
45987012 TAAAAAATTATT
1 TAAAAAATTATT
45987024 TAATGTCCGC
Statistics
Matches: 23, Mismatches: 2, Indels: 4
0.79 0.07 0.14
Matches are distributed among these distances:
15 9 0.39
16 14 0.61
ACGTcount: A:0.65, C:0.00, G:0.02, T:0.33
Consensus pattern (17 bp):
TAAAAAATTATTAAAGA
Found at i:45993472 original size:3 final size:3
Alignment explanation
Indices: 45993464--45993521 Score: 107
Period size: 3 Copynumber: 19.3 Consensus size: 3
45993454 TTTAGCAATT
*
45993464 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTG TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
45993512 TTA TTA TTA T
1 TTA TTA TTA T
45993522 AATTGTTTTT
Statistics
Matches: 53, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
3 53 1.00
ACGTcount: A:0.31, C:0.00, G:0.02, T:0.67
Consensus pattern (3 bp):
TTA
Found at i:45993869 original size:2 final size:2
Alignment explanation
Indices: 45993817--45993850 Score: 50
Period size: 2 Copynumber: 17.0 Consensus size: 2
45993807 TTGTAAATAC
* *
45993817 AT AT AT AT AT AT AT AT TT AT AT AT AT AC AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
45993851 TTTAATTTTT
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.47, C:0.03, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:45994934 original size:19 final size:18
Alignment explanation
Indices: 45994907--45994942 Score: 54
Period size: 19 Copynumber: 1.9 Consensus size: 18
45994897 ATAATTGTCA
*
45994907 TTGTTGTGGTTTATAATTG
1 TTGTGGTGGTTTA-AATTG
45994926 TTGTGGTGGTTTAAATT
1 TTGTGGTGGTTTAAATT
45994943 TTGGTATCTT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 4 0.25
19 12 0.75
ACGTcount: A:0.17, C:0.00, G:0.28, T:0.56
Consensus pattern (18 bp):
TTGTGGTGGTTTAAATTG
Found at i:46004881 original size:21 final size:21
Alignment explanation
Indices: 46004857--46004897 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
46004847 TGAAGGTCCA
*
46004857 AAAAAAAAAACAAAACAAAAC
1 AAAAAAAAAACAAAAAAAAAC
*
46004878 AAAACAAAAACAAAAAAAAA
1 AAAAAAAAAACAAAAAAAAA
46004898 AGGGAAGGAG
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.88, C:0.12, G:0.00, T:0.00
Consensus pattern (21 bp):
AAAAAAAAAACAAAAAAAAAC
Found at i:46004897 original size:10 final size:10
Alignment explanation
Indices: 46004858--46004897 Score: 62
Period size: 10 Copynumber: 3.9 Consensus size: 10
46004848 GAAGGTCCAA
46004858 AAAAAAAAAC
1 AAAAAAAAAC
*
46004868 AAAACAAAAC
1 AAAAAAAAAC
46004878 AAAACAAAAAC
1 AAAA-AAAAAC
46004889 AAAAAAAAA
1 AAAAAAAAA
46004898 AGGGAAGGAG
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
10 18 0.67
11 9 0.33
ACGTcount: A:0.88, C:0.12, G:0.00, T:0.00
Consensus pattern (10 bp):
AAAAAAAAAC
Found at i:46006179 original size:46 final size:46
Alignment explanation
Indices: 46006096--46006528 Score: 246
Period size: 44 Copynumber: 9.8 Consensus size: 46
46006086 ATTATACAGG
* * * * **
46006096 TCTTATTTCCCTGAGACTACAGTGGAACAGACCGAAGAATTTTAGA
1 TCTTATCTCCCTGAGATTACAGCGGAGCAGATTGAAGAATTTTAGA
* **
46006142 TCTTATCTCCCTGAGATTGCAGCGGAGCAGATTGAAG-ATAGTA-A
1 TCTTATCTCCCTGAGATTACAGCGGAGCAGATTGAAGAATTTTAGA
* * * **
46006186 TCCTATCTCCCTGAGATTACAGTGGAGCGGATT-AA-AA-TGAAGGA
1 TCTTATCTCCCTGAGATTACAGCGGAGCAGATTGAAGAATTTTA-GA
* * * * * * *
46006230 TCTTATCTCTCTGA-AGTTACAGCAGAGTAGA-T--CG--TGTCAGG
1 TCTTATCTCCCTGAGA-TTACAGCGGAGCAGATTGAAGAATTTTAGA
* * * ** *
46006271 TCTTATTTCCCTGAGATTACAGTGGAACAGACCGAAGAATTTCAGA
1 TCTTATCTCCCTGAGATTACAGCGGAGCAGATTGAAGAATTTTAGA
* **
46006317 TCTTATCTCCCTGAGATTACAGCGGAGCAGATTGAAG-CTAGTA-A
1 TCTTATCTCCCTGAGATTACAGCGGAGCAGATTGAAGAATTTTAGA
* * * **
46006361 TCCTATCTCCCTGAGATTACAGTGGAGCGGATT-AA-AA-TGAAGGA
1 TCTTATCTCCCTGAGATTACAGCGGAGCAGATTGAAGAATTTTA-GA
* * * * * *
46006405 TCTTATCTCTCTGA-AGTTACAGCAGAGTAGATCG-CG----TTAGG
1 TCTTATCTCCCTGAGA-TTACAGCGGAGCAGATTGAAGAATTTTAGA
* * ** *
46006446 TCTTATTTCCCTGAGATTACAGTGG-GACAGACCGAAGAATTTCAGA
1 TCTTATCTCCCTGAGATTACAGCGGAG-CAGATTGAAGAATTTTAGA
46006492 TCTTATCTCCCTGAGATTACAGCGGAGCAGATTGAAG
1 TCTTATCTCCCTGAGATTACAGCGGAGCAGATTGAAG
46006529 CCAGTAATTC
Statistics
Matches: 286, Mismatches: 75, Indels: 52
0.69 0.18 0.13
Matches are distributed among these distances:
40 1 0.00
41 49 0.17
42 9 0.03
43 8 0.03
44 111 0.39
45 6 0.02
46 101 0.35
47 1 0.00
ACGTcount: A:0.30, C:0.19, G:0.23, T:0.28
Consensus pattern (46 bp):
TCTTATCTCCCTGAGATTACAGCGGAGCAGATTGAAGAATTTTAGA
Found at i:46006383 original size:175 final size:175
Alignment explanation
Indices: 46006092--46006544 Score: 825
Period size: 175 Copynumber: 2.6 Consensus size: 175
46006082 GTTCATTATA
* *
46006092 CAGGTCTTATTTCCCTGAGACTACAGTGGAACAGACCGAAGAATTTTAGATCTTATCTCCCTGAG
1 CAGGTCTTATTTCCCTGAGATTACAGTGGAACAGACCGAAGAATTTCAGATCTTATCTCCCTGAG
* *
46006157 ATTGCAGCGGAGCAGATTGAAGATAGTAATCCTATCTCCCTGAGATTACAGTGGAGCGGATTAAA
66 ATTACAGCGGAGCAGATTGAAGCTAGTAATCCTATCTCCCTGAGATTACAGTGGAGCGGATTAAA
*
46006222 ATGAAGGATCTTATCTCTCTGAAGTTACAGCAGAGTAGATCGTGT
131 ATGAAGGATCTTATCTCTCTGAAGTTACAGCAGAGTAGATCGCGT
46006267 CAGGTCTTATTTCCCTGAGATTACAGTGGAACAGACCGAAGAATTTCAGATCTTATCTCCCTGAG
1 CAGGTCTTATTTCCCTGAGATTACAGTGGAACAGACCGAAGAATTTCAGATCTTATCTCCCTGAG
46006332 ATTACAGCGGAGCAGATTGAAGCTAGTAATCCTATCTCCCTGAGATTACAGTGGAGCGGATTAAA
66 ATTACAGCGGAGCAGATTGAAGCTAGTAATCCTATCTCCCTGAGATTACAGTGGAGCGGATTAAA
46006397 ATGAAGGATCTTATCTCTCTGAAGTTACAGCAGAGTAGATCGCGT
131 ATGAAGGATCTTATCTCTCTGAAGTTACAGCAGAGTAGATCGCGT
* *
46006442 TAGGTCTTATTTCCCTGAGATTACAGTGGGACAGACCGAAGAATTTCAGATCTTATCTCCCTGAG
1 CAGGTCTTATTTCCCTGAGATTACAGTGGAACAGACCGAAGAATTTCAGATCTTATCTCCCTGAG
* *
46006507 ATTACAGCGGAGCAGATTGAAGCCAGTAATTCTATCTC
66 ATTACAGCGGAGCAGATTGAAGCTAGTAATCCTATCTC
46006545 TCCGACGTTA
Statistics
Matches: 269, Mismatches: 9, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
175 269 1.00
ACGTcount: A:0.29, C:0.20, G:0.23, T:0.28
Consensus pattern (175 bp):
CAGGTCTTATTTCCCTGAGATTACAGTGGAACAGACCGAAGAATTTCAGATCTTATCTCCCTGAG
ATTACAGCGGAGCAGATTGAAGCTAGTAATCCTATCTCCCTGAGATTACAGTGGAGCGGATTAAA
ATGAAGGATCTTATCTCTCTGAAGTTACAGCAGAGTAGATCGCGT
Found at i:46009224 original size:19 final size:19
Alignment explanation
Indices: 46009182--46009225 Score: 54
Period size: 19 Copynumber: 2.3 Consensus size: 19
46009172 AAAACCGTTG
46009182 TTTTAATAAAAATCAAATT
1 TTTTAATAAAAATCAAATT
* *
46009201 ATTTATTAAAAA-CAACATT
1 TTTTAATAAAAATCAA-ATT
46009220 TTTTAA
1 TTTTAA
46009226 GGTGACCCAA
Statistics
Matches: 20, Mismatches: 4, Indels: 2
0.77 0.15 0.08
Matches are distributed among these distances:
18 3 0.15
19 17 0.85
ACGTcount: A:0.50, C:0.07, G:0.00, T:0.43
Consensus pattern (19 bp):
TTTTAATAAAAATCAAATT
Found at i:46012058 original size:18 final size:16
Alignment explanation
Indices: 46012035--46012076 Score: 52
Period size: 14 Copynumber: 2.6 Consensus size: 16
46012025 CAAAATGTAA
46012035 TTAATTTAAAATTTTTAT
1 TTAA-TTAAAA-TTTTAT
46012053 TTAATT--AATTTTAT
1 TTAATTAAAATTTTAT
46012067 TTAATTAAAA
1 TTAATTAAAA
46012077 ACTTATTCTC
Statistics
Matches: 22, Mismatches: 0, Indels: 6
0.79 0.00 0.21
Matches are distributed among these distances:
14 12 0.55
15 2 0.09
16 2 0.09
17 2 0.09
18 4 0.18
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (16 bp):
TTAATTAAAATTTTAT
Found at i:46012066 original size:14 final size:14
Alignment explanation
Indices: 46012047--46012074 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
46012037 AATTTAAAAT
46012047 TTTTATTTAATTAA
1 TTTTATTTAATTAA
46012061 TTTTATTTAATTAA
1 TTTTATTTAATTAA
46012075 AAACTTATTC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (14 bp):
TTTTATTTAATTAA
Found at i:46014847 original size:17 final size:18
Alignment explanation
Indices: 46014819--46014852 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
46014809 AATAAGATTC
46014819 TAAATATTTAAAAAAATT
1 TAAATATTTAAAAAAATT
*
46014837 TAAAT-TTTAAATAAAT
1 TAAATATTTAAAAAAAT
46014853 ATTACATACA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 10 0.67
18 5 0.33
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (18 bp):
TAAATATTTAAAAAAATT
Found at i:46020164 original size:50 final size:48
Alignment explanation
Indices: 46020077--46020171 Score: 122
Period size: 50 Copynumber: 1.9 Consensus size: 48
46020067 TGGGTTAATT
*
46020077 AATTTTTTTTAAAAATTGAGATTAATTAAATTTTTTAAAAAATTAACGC
1 AATTTTTTTTAAAAATTGAGATTAATTAAA-TATTTAAAAAATTAACGC
46020126 AATTTTTTTTAAAAAATAT-AGGATTTAATTAAA-ATTTAAAAAATTA
1 AATTTTTTTT-AAAAAT-TGA-GA-TTAATTAAATATTTAAAAAATTA
46020172 GGAACTTTAA
Statistics
Matches: 41, Mismatches: 1, Indels: 7
0.84 0.02 0.14
Matches are distributed among these distances:
49 10 0.24
50 19 0.46
51 3 0.07
52 9 0.22
ACGTcount: A:0.48, C:0.02, G:0.05, T:0.44
Consensus pattern (48 bp):
AATTTTTTTTAAAAATTGAGATTAATTAAATATTTAAAAAATTAACGC
Found at i:46027383 original size:25 final size:26
Alignment explanation
Indices: 46027340--46027391 Score: 88
Period size: 27 Copynumber: 2.0 Consensus size: 26
46027330 GTTATAACTT
46027340 TTTTTTATTTACCAAAAAATATATAAA
1 TTTTTTATTTACC-AAAAATATATAAA
46027367 TTTTTTATTTACC-AAAATATATAAA
1 TTTTTTATTTACCAAAAATATATAAA
46027392 AAAAACTAAA
Statistics
Matches: 25, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
25 12 0.48
27 13 0.52
ACGTcount: A:0.46, C:0.08, G:0.00, T:0.46
Consensus pattern (26 bp):
TTTTTTATTTACCAAAAATATATAAA
Found at i:46027592 original size:18 final size:17
Alignment explanation
Indices: 46027569--46027719 Score: 78
Period size: 18 Copynumber: 8.4 Consensus size: 17
46027559 GAAGGAGAGG
46027569 GGAAG-AAGAAGAAAGAAA
1 GGAAGAAAGAA-AAAG-AA
46027587 GGAAGAAAGAAAAAGAA
1 GGAAGAAAGAAAAAGAA
* *
46027604 GG-A-AAAGGAAAGGAGA
1 GGAAGAAAGAAAAAGA-A
46027620 GGAAAGAAAGAAAAAGAA
1 GG-AAGAAAGAAAAAGAA
** *
46027638 GGAAAGAAAGAGGAAGGGGA
1 GG-AAGAAAGA--AAAAGAA
*
46027658 GGAAAGAAAGAAAAATAA
1 GG-AAGAAAGAAAAAGAA
*
46027676 GGAAAGAAAAGGAAAGGAGAA
1 GG-AAG-AAA-GAAA-AAGAA
46027697 GAGAA-AAA-AAAAAGAA
1 G-GAAGAAAGAAAAAGAA
*
46027713 AGAAGAA
1 GGAAGAA
46027720 GAAGAGGGAA
Statistics
Matches: 106, Mismatches: 15, Indels: 26
0.72 0.10 0.18
Matches are distributed among these distances:
15 12 0.11
16 10 0.09
17 7 0.07
18 31 0.29
19 20 0.19
20 19 0.18
21 6 0.06
22 1 0.01
ACGTcount: A:0.66, C:0.00, G:0.33, T:0.01
Consensus pattern (17 bp):
GGAAGAAAGAAAAAGAA
Found at i:46027602 original size:10 final size:10
Alignment explanation
Indices: 46027571--46027642 Score: 54
Period size: 10 Copynumber: 6.6 Consensus size: 10
46027561 AGGAGAGGGG
*
46027571 AAGAAGAAGA
1 AAGAAAAAGA
46027581 AAGAAAGGAAGA
1 AAGAAA--AAGA
46027593 AAGAAAAAGA
1 AAGAAAAAGA
* *
46027603 AGGAAAAGGA
1 AAGAAAAAGA
46027613 AAGGAGAGGAAAGA
1 AA-GA-A--AAAGA
46027627 AAGAAAAAGA
1 AAGAAAAAGA
*
46027637 AGGAAA
1 AAGAAA
46027643 GAAAGAGGAA
Statistics
Matches: 50, Mismatches: 6, Indels: 12
0.74 0.09 0.18
Matches are distributed among these distances:
10 28 0.56
11 2 0.04
12 12 0.24
13 2 0.04
14 6 0.12
ACGTcount: A:0.68, C:0.00, G:0.32, T:0.00
Consensus pattern (10 bp):
AAGAAAAAGA
Found at i:46027602 original size:22 final size:23
Alignment explanation
Indices: 46027571--46027646 Score: 66
Period size: 24 Copynumber: 3.3 Consensus size: 23
46027561 AGGAGAGGGG
*
46027571 AAGAAGAAGAAAG-AAAGGAAGA
1 AAGAAAAAGAAAGAAAAGGAAGA
*
46027593 AAGAAAAAGAAGGAAAAGGAA-A
1 AAGAAAAAGAAAGAAAAGGAAGA
* * *
46027615 GGAGAGGAAAGAAAGAAAAAGAAGGA
1 -AAGA-AAAAGAAAGAAAAGGAA-GA
46027641 AAGAAA
1 AAGAAA
46027647 GAGGAAGGGG
Statistics
Matches: 41, Mismatches: 8, Indels: 8
0.72 0.14 0.14
Matches are distributed among these distances:
22 12 0.29
23 10 0.24
24 15 0.37
25 3 0.07
26 1 0.02
ACGTcount: A:0.68, C:0.00, G:0.32, T:0.00
Consensus pattern (23 bp):
AAGAAAAAGAAAGAAAAGGAAGA
Found at i:46027602 original size:28 final size:31
Alignment explanation
Indices: 46027570--46027647 Score: 92
Period size: 28 Copynumber: 2.6 Consensus size: 31
46027560 AAGGAGAGGG
46027570 GAAGAAGAAGAAAGAAAGGA-A-GAAAGAAA
1 GAAGAAGAAGAAAGAAAGGAGAGGAAAGAAA
*
46027599 -AAGAAGGAA-AAGGAAAGGAGAGGAAAGAAA
1 GAAGAA-GAAGAAAGAAAGGAGAGGAAAGAAA
*
46027629 GAAAAAGAAGGAAAGAAAG
1 GAAGAAGAA-GAAAGAAAG
46027648 AGGAAGGGGA
Statistics
Matches: 40, Mismatches: 3, Indels: 9
0.77 0.06 0.17
Matches are distributed among these distances:
28 14 0.35
29 4 0.10
30 11 0.28
31 4 0.10
32 7 0.17
ACGTcount: A:0.67, C:0.00, G:0.33, T:0.00
Consensus pattern (31 bp):
GAAGAAGAAGAAAGAAAGGAGAGGAAAGAAA
Found at i:46027625 original size:42 final size:40
Alignment explanation
Indices: 46027556--46027720 Score: 128
Period size: 38 Copynumber: 4.2 Consensus size: 40
46027546 TTGGTGGGGG
* * * * *
46027556 AAAGAAGGAGAGGGGAAGAAGAAGAAAGAAAGGAAGAAAGAA
1 AAAGAAGGAAAAGGAAAGGAGAGGAAAGAAA-GAA-AAAGAA
46027598 AAAGAAGGAAAAGGAAAGGAGAGGAAAGAAAGAAAAAG--
1 AAAGAAGGAAAAGGAAAGGAGAGGAAAGAAAGAAAAAGAA
* * * *
46027636 AAGGAAAGAAAGAGG-AAGGGGAGGAAAGAAAG-AAAA-AT
1 AAAGAAGGAAA-AGGAAAGGAGAGGAAAGAAAGAAAAAGAA
* * *
46027674 AAGGAAAGAAAAGGAAAGGAGAAGAGAA-AAA-AAAAAGAA
1 AAAGAAGGAAAAGGAAAGGAGAGGA-AAGAAAGAAAAAGAA
46027713 AGAAGAAG
1 A-AAGAAG
46027721 AAGAGGGAAT
Statistics
Matches: 102, Mismatches: 13, Indels: 18
0.77 0.10 0.14
Matches are distributed among these distances:
37 7 0.07
38 51 0.50
39 7 0.07
40 8 0.08
41 3 0.03
42 26 0.25
ACGTcount: A:0.65, C:0.00, G:0.35, T:0.01
Consensus pattern (40 bp):
AAAGAAGGAAAAGGAAAGGAGAGGAAAGAAAGAAAAAGAA
Found at i:46027660 original size:38 final size:38
Alignment explanation
Indices: 46027589--46027716 Score: 141
Period size: 38 Copynumber: 3.6 Consensus size: 38
46027579 GAAAGAAAGG
* *
46027589 AAGAAAGAAAAAGAAGG--A-AAAG-GAAAGGAGAGGA
1 AAGAAAGAAAAAGAAGGAAAGAAAGAGGAAGGGGAGGA
46027623 AAGAAAGAAAAAGAAGGAAAGAAAGAGGAAGGGGAGGA
1 AAGAAAGAAAAAGAAGGAAAGAAAGAGGAAGGGGAGGA
* *
46027661 AAGAAAGAAAAATAAGGAAAGAAA-AGGAA-AGGA-GA
1 AAGAAAGAAAAAGAAGGAAAGAAAGAGGAAGGGGAGGA
46027696 AGAGAAA-AAAAA-AA-GAAAGAA
1 A-AGAAAGAAAAAGAAGGAAAGAA
46027717 GAAGAAGAGG
Statistics
Matches: 85, Mismatches: 4, Indels: 11
0.85 0.04 0.11
Matches are distributed among these distances:
33 7 0.08
34 19 0.22
35 8 0.09
36 9 0.11
37 9 0.11
38 33 0.39
ACGTcount: A:0.67, C:0.00, G:0.32, T:0.01
Consensus pattern (38 bp):
AAGAAAGAAAAAGAAGGAAAGAAAGAGGAAGGGGAGGA
Found at i:46027687 original size:10 final size:10
Alignment explanation
Indices: 46027591--46027691 Score: 63
Period size: 10 Copynumber: 10.5 Consensus size: 10
46027581 AAGAAAGGAA
*
46027591 GAAAGAAAAA
1 GAAAGAAAAG
*
46027601 GAAGGAAAAG
1 GAAAGAAAAG
* *
46027611 GAAAGGAGAG
1 GAAAGAAAAG
46027621 GAAAG-AAA-
1 GAAAGAAAAG
46027629 GAAA-AAGAAG
1 GAAAGAA-AAG
46027639 GAAAGAAAGAG
1 GAAAGAAA-AG
***
46027650 G-AAGGGGAG
1 GAAAGAAAAG
46027659 GAAAG-AAA-
1 GAAAGAAAAG
46027667 GAAA-AATAAG
1 GAAAGAA-AAG
46027677 GAAAGAAAAG
1 GAAAGAAAAG
46027687 GAAAG
1 GAAAG
46027692 GAGAAGAGAA
Statistics
Matches: 70, Mismatches: 11, Indels: 20
0.69 0.11 0.20
Matches are distributed among these distances:
8 10 0.14
9 10 0.14
10 43 0.61
11 7 0.10
ACGTcount: A:0.64, C:0.00, G:0.35, T:0.01
Consensus pattern (10 bp):
GAAAGAAAAG
Found at i:46028480 original size:19 final size:19
Alignment explanation
Indices: 46028432--46028483 Score: 68
Period size: 19 Copynumber: 2.7 Consensus size: 19
46028422 AAAATATATA
** *
46028432 TAATATTTTGGTATTTTTT
1 TAATATTTTATTATTTTTG
46028451 TAATATTTTATTATTTTTG
1 TAATATTTTATTATTTTTG
*
46028470 TAATGTTTTATTAT
1 TAATATTTTATTAT
46028484 GGGTTTTATA
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
19 29 1.00
ACGTcount: A:0.25, C:0.00, G:0.08, T:0.67
Consensus pattern (19 bp):
TAATATTTTATTATTTTTG
Found at i:46028508 original size:13 final size:13
Alignment explanation
Indices: 46028490--46028515 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
46028480 TTATGGGTTT
46028490 TATAAAAAAATAA
1 TATAAAAAAATAA
46028503 TATAAAAAAATAA
1 TATAAAAAAATAA
46028516 AAATTACCAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.77, C:0.00, G:0.00, T:0.23
Consensus pattern (13 bp):
TATAAAAAAATAA
Found at i:46028562 original size:28 final size:27
Alignment explanation
Indices: 46028519--46028587 Score: 113
Period size: 27 Copynumber: 2.6 Consensus size: 27
46028509 AAAATAAAAA
*
46028519 TTACCAAAACAT-TATAACTTTTTTTAT
1 TTACCAAAATATATATAA-TTTTTTTAT
46028546 TTACCAAAATATATATAATTTTTTTAT
1 TTACCAAAATATATATAATTTTTTTAT
46028573 TTACCAAAATATATA
1 TTACCAAAATATATA
46028588 AAAAAAGTAA
Statistics
Matches: 40, Mismatches: 1, Indels: 2
0.93 0.02 0.05
Matches are distributed among these distances:
27 35 0.88
28 5 0.12
ACGTcount: A:0.42, C:0.12, G:0.00, T:0.46
Consensus pattern (27 bp):
TTACCAAAATATATATAATTTTTTTAT
Found at i:46028601 original size:8 final size:8
Alignment explanation
Indices: 46028585--46028618 Score: 50
Period size: 8 Copynumber: 4.1 Consensus size: 8
46028575 ACCAAAATAT
46028585 ATAAAAAA
1 ATAAAAAA
46028593 AGTAAAAAA
1 A-TAAAAAA
*
46028602 ACAAAAAA
1 ATAAAAAA
46028610 ATAAAAAA
1 ATAAAAAA
46028618 A
1 A
46028619 AGGAAAAAAA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
8 15 0.65
9 8 0.35
ACGTcount: A:0.85, C:0.03, G:0.03, T:0.09
Consensus pattern (8 bp):
ATAAAAAA
Found at i:46028616 original size:26 final size:27
Alignment explanation
Indices: 46028578--46028628 Score: 77
Period size: 26 Copynumber: 1.9 Consensus size: 27
46028568 TTTATTTACC
* *
46028578 AAAATATATAAAAAAAGTAAAAAAACA
1 AAAAAATATAAAAAAAGGAAAAAAACA
46028605 AAAAAATA-AAAAAAAGGAAAAAAA
1 AAAAAATATAAAAAAAGGAAAAAAA
46028629 ACACACTAAA
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
26 15 0.68
27 7 0.32
ACGTcount: A:0.82, C:0.02, G:0.06, T:0.10
Consensus pattern (27 bp):
AAAAAATATAAAAAAAGGAAAAAAACA
Found at i:46028627 original size:17 final size:17
Alignment explanation
Indices: 46028587--46028618 Score: 57
Period size: 16 Copynumber: 1.9 Consensus size: 17
46028577 CAAAATATAT
46028587 AAAAAAAGTAAAAAAAC
1 AAAAAAAGTAAAAAAAC
46028604 AAAAAAA-TAAAAAAA
1 AAAAAAAGTAAAAAAA
46028619 AGGAAAAAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 8 0.53
17 7 0.47
ACGTcount: A:0.88, C:0.03, G:0.03, T:0.06
Consensus pattern (17 bp):
AAAAAAAGTAAAAAAAC
Found at i:46028629 original size:27 final size:27
Alignment explanation
Indices: 46028578--46028631 Score: 74
Period size: 27 Copynumber: 2.0 Consensus size: 27
46028568 TTTATTTACC
* *
46028578 AAAATATATAAAAAAAGTAAAAAAACA
1 AAAAAATATAAAAAAAGAAAAAAAACA
46028605 AAAAAATA-AAAAAAAGGAAAAAAAACA
1 AAAAAATATAAAAAAA-GAAAAAAAACA
46028632 CACTAAATTA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
26 7 0.29
27 17 0.71
ACGTcount: A:0.81, C:0.04, G:0.06, T:0.09
Consensus pattern (27 bp):
AAAAAATATAAAAAAAGAAAAAAAACA
Found at i:46029322 original size:14 final size:14
Alignment explanation
Indices: 46029288--46029323 Score: 54
Period size: 14 Copynumber: 2.6 Consensus size: 14
46029278 CTCCCAATTT
* *
46029288 ACGGGAGTCCTGTA
1 ACGGGATTCCCGTA
46029302 ACGGGATTCCCGTA
1 ACGGGATTCCCGTA
46029316 ACGGGATT
1 ACGGGATT
46029324 ATCTGCATTT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.22, C:0.22, G:0.33, T:0.22
Consensus pattern (14 bp):
ACGGGATTCCCGTA
Found at i:46029962 original size:17 final size:17
Alignment explanation
Indices: 46029942--46029978 Score: 74
Period size: 17 Copynumber: 2.2 Consensus size: 17
46029932 GGATGGGGAG
46029942 ATGCTATTCTAATATTC
1 ATGCTATTCTAATATTC
46029959 ATGCTATTCTAATATTC
1 ATGCTATTCTAATATTC
46029976 ATG
1 ATG
46029979 ACATCTTACT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 20 1.00
ACGTcount: A:0.30, C:0.16, G:0.08, T:0.46
Consensus pattern (17 bp):
ATGCTATTCTAATATTC
Found at i:46030588 original size:25 final size:25
Alignment explanation
Indices: 46030554--46030605 Score: 104
Period size: 25 Copynumber: 2.1 Consensus size: 25
46030544 CCCAGCCAGA
46030554 TCCGAAACAATCTGGATTTGTCGGT
1 TCCGAAACAATCTGGATTTGTCGGT
46030579 TCCGAAACAATCTGGATTTGTCGGT
1 TCCGAAACAATCTGGATTTGTCGGT
46030604 TC
1 TC
46030606 AGATAGCTAT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 27 1.00
ACGTcount: A:0.23, C:0.21, G:0.23, T:0.33
Consensus pattern (25 bp):
TCCGAAACAATCTGGATTTGTCGGT
Found at i:46033403 original size:18 final size:18
Alignment explanation
Indices: 46033377--46033414 Score: 58
Period size: 18 Copynumber: 2.1 Consensus size: 18
46033367 ATCCCAATGA
* *
46033377 TCGCCACCACCTTCTTCT
1 TCGCAACCACATTCTTCT
46033395 TCGCAACCACATTCTTCT
1 TCGCAACCACATTCTTCT
46033413 TC
1 TC
46033415 ACCACCAACC
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.16, C:0.45, G:0.05, T:0.34
Consensus pattern (18 bp):
TCGCAACCACATTCTTCT
Found at i:46033421 original size:18 final size:18
Alignment explanation
Indices: 46033380--46033421 Score: 57
Period size: 18 Copynumber: 2.3 Consensus size: 18
46033370 CCAATGATCG
* *
46033380 CCACCACCTTCTTCTTCG
1 CCACCACATTCTTCTTCA
*
46033398 CAACCACATTCTTCTTCA
1 CCACCACATTCTTCTTCA
46033416 CCACCA
1 CCACCA
46033422 ACCATATCAA
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.21, C:0.48, G:0.02, T:0.29
Consensus pattern (18 bp):
CCACCACATTCTTCTTCA
Found at i:46034171 original size:3 final size:3
Alignment explanation
Indices: 46034163--46034224 Score: 115
Period size: 3 Copynumber: 20.7 Consensus size: 3
46034153 AGTAACATCT
*
46034163 TAA TAA TAA TAA GAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
46034211 TAA TAA TAA TAA TA
1 TAA TAA TAA TAA TA
46034225 CTATAAAATT
Statistics
Matches: 57, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
3 57 1.00
ACGTcount: A:0.66, C:0.00, G:0.02, T:0.32
Consensus pattern (3 bp):
TAA
Found at i:46034559 original size:27 final size:27
Alignment explanation
Indices: 46034518--46034620 Score: 109
Period size: 27 Copynumber: 3.8 Consensus size: 27
46034508 AACACGAGTA
* * *
46034518 GTGCCGCCAATCTGGTTGGCC-GGACTG
1 GTGCCGCCAACCTGGTT-CCCTCGACTG
46034545 GTGCCGCCAACCTGGTTCCCTCGACTG
1 GTGCCGCCAACCTGGTTCCCTCGACTG
* * **
46034572 GTGCCGCCAACCTGCTTCCCTTGTTTG
1 GTGCCGCCAACCTGGTTCCCTCGACTG
**
46034599 GTGCCGCCAACCTACTTCCCTC
1 GTGCCGCCAACCTGGTTCCCTC
46034621 CACCCAAGGA
Statistics
Matches: 66, Mismatches: 9, Indels: 2
0.86 0.12 0.03
Matches are distributed among these distances:
26 2 0.03
27 64 0.97
ACGTcount: A:0.11, C:0.39, G:0.25, T:0.25
Consensus pattern (27 bp):
GTGCCGCCAACCTGGTTCCCTCGACTG
Found at i:46034673 original size:8 final size:8
Alignment explanation
Indices: 46034652--46034690 Score: 53
Period size: 8 Copynumber: 4.9 Consensus size: 8
46034642 AGTTCAAGTT
*
46034652 TTTTTTTC
1 TTTTTTTA
46034660 TGTTTTTTA
1 T-TTTTTTA
46034669 TTTTTTTA
1 TTTTTTTA
46034677 -TTTTTTA
1 TTTTTTTA
46034684 TTTTTTT
1 TTTTTTT
46034691 GATATATTTT
Statistics
Matches: 28, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
7 7 0.25
8 14 0.50
9 7 0.25
ACGTcount: A:0.08, C:0.03, G:0.03, T:0.87
Consensus pattern (8 bp):
TTTTTTTA
Found at i:46034680 original size:15 final size:15
Alignment explanation
Indices: 46034662--46034690 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
46034652 TTTTTTTCTG
46034662 TTTTTTATTTTTTTA
1 TTTTTTATTTTTTTA
46034677 TTTTTTATTTTTTT
1 TTTTTTATTTTTTT
46034691 GATATATTTT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.10, C:0.00, G:0.00, T:0.90
Consensus pattern (15 bp):
TTTTTTATTTTTTTA
Found at i:46034722 original size:27 final size:29
Alignment explanation
Indices: 46034692--46034760 Score: 99
Period size: 28 Copynumber: 2.5 Consensus size: 29
46034682 TATTTTTTTG
46034692 ATATATTTTGGTAAAT-AAAAAAA-TTAT
1 ATATATTTTGGTAAATAAAAAAAAGTTAT
*
46034719 ATATATTTTAGTAAATAAAAAAAAGTTAT
1 ATATATTTTGGTAAATAAAAAAAAGTTAT
*
46034748 A-ACATTTTGGTAA
1 ATATATTTTGGTAA
46034761 TTTTTTTATA
Statistics
Matches: 37, Mismatches: 3, Indels: 3
0.86 0.07 0.07
Matches are distributed among these distances:
27 15 0.41
28 17 0.46
29 5 0.14
ACGTcount: A:0.51, C:0.01, G:0.09, T:0.39
Consensus pattern (29 bp):
ATATATTTTGGTAAATAAAAAAAAGTTAT
Found at i:46034825 original size:15 final size:15
Alignment explanation
Indices: 46034805--46034836 Score: 64
Period size: 15 Copynumber: 2.1 Consensus size: 15
46034795 TACACCTATT
46034805 TCCTACTACCAACAA
1 TCCTACTACCAACAA
46034820 TCCTACTACCAACAA
1 TCCTACTACCAACAA
46034835 TC
1 TC
46034837 GTCTTTGGTC
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.38, C:0.41, G:0.00, T:0.22
Consensus pattern (15 bp):
TCCTACTACCAACAA
Found at i:46035754 original size:43 final size:42
Alignment explanation
Indices: 46035700--46036004 Score: 360
Period size: 43 Copynumber: 7.3 Consensus size: 42
46035690 TTTTTTCTAA
*
46035700 AAACGCCGCTAAAGACAAGGACCTTTAGCGGCGCTTCTACCAC
1 AAACGCCGCTAAAGACAA-GACCTTTAGCGGCGCTTTTACCAC
* *
46035743 AAACGCTGCTAAAGACCAAGACCTTTAGCGGCGCTTTTCCCAC
1 AAACGCCGCTAAAGA-CAAGACCTTTAGCGGCGCTTTTACCAC
* * * *
46035786 -AACGCCGCTAAAGACCAGGTCCTTTAGCGGCGTTTTTTCCAC
1 AAACGCCGCTAAAGA-CAAGACCTTTAGCGGCGCTTTTACCAC
* *
46035828 AAA---CG----A-CCAAGACCTTTAGCGGCGCTTTT-CCTAA
1 AAACGCCGCTAAAGACAAGACCTTTAGCGGCGCTTTTACC-AC
*
46035862 AAACGCCGCTAAAGACCAAGACCTTTAGCGGCGCTTATACCAC
1 AAACGCCGCTAAAGA-CAAGACCTTTAGCGGCGCTTTTACCAC
46035905 AAACGCCGCTAAAGACTAAGACCTTTAGCGGCGCTTTTACCAC
1 AAACGCCGCTAAAGAC-AAGACCTTTAGCGGCGCTTTTACCAC
* *
46035948 AAACGCCGCTAAAGACTAAAACCTTTAGCGGCGCTTTTTATCAC
1 AAACGCCGCTAAAGAC-AAGACCTTTAGCGGCGC-TTTTACCAC
46035992 AAACGCCGCTAAA
1 AAACGCCGCTAAA
46036005 AACAGAATCT
Statistics
Matches: 228, Mismatches: 19, Indels: 29
0.83 0.07 0.11
Matches are distributed among these distances:
33 2 0.01
34 23 0.10
36 1 0.00
37 2 0.01
40 2 0.01
41 1 0.00
42 38 0.17
43 133 0.58
44 26 0.11
ACGTcount: A:0.30, C:0.31, G:0.19, T:0.21
Consensus pattern (42 bp):
AAACGCCGCTAAAGACAAGACCTTTAGCGGCGCTTTTACCAC
Found at i:46035871 original size:162 final size:165
Alignment explanation
Indices: 46035677--46035996 Score: 488
Period size: 162 Copynumber: 2.0 Consensus size: 165
46035667 GCGTCGCTAA
* * *
46035677 CTTTAGCGGCGTTTTTTTTCTAAAAACGCCGCTAAAGA-CAAGGACCTTTAGCGGCGCTTCTACC
1 CTTTAGCGGCG-TCTTTTCCTAAAAACGCCGCTAAAGACCAA-GACCTTTAGCGGCGCTTATACC
* * **
46035741 ACAAACGCTGCTAAAGACCAAGACCTTTAGCGGCGCTTTTCCCAC-AACGCCGCTAAAGACCAGG
64 ACAAACGCCGCTAAAGACCAAGACCTTTAGCGGCGCTTTTACCACAAACGCCGCTAAAGACCAAA
*
46035805 TCCTTTAGCGGCG-TTTTT-TCCACAAACGACCAAGAC
129 ACCTTTAGCGGCGCTTTTTAT-CACAAACGACCAAGAC
46035841 CTTTAGCGGCG-CTTTTCCTAAAAACGCCGCTAAAGACCAAGACCTTTAGCGGCGCTTATACCAC
1 CTTTAGCGGCGTCTTTTCCTAAAAACGCCGCTAAAGACCAAGACCTTTAGCGGCGCTTATACCAC
* *
46035905 AAACGCCGCTAAAGACTAAGACCTTTAGCGGCGCTTTTACCACAAACGCCGCTAAAGACTAAAAC
66 AAACGCCGCTAAAGACCAAGACCTTTAGCGGCGCTTTTACCACAAACGCCGCTAAAGACCAAAAC
46035970 CTTTAGCGGCGCTTTTTATCACAAACG
131 CTTTAGCGGCGCTTTTTATCACAAACG
46035997 CCGCTAAAAA
Statistics
Matches: 142, Mismatches: 10, Indels: 8
0.89 0.06 0.05
Matches are distributed among these distances:
162 86 0.61
163 31 0.22
164 24 0.17
165 1 0.01
ACGTcount: A:0.28, C:0.30, G:0.19, T:0.23
Consensus pattern (165 bp):
CTTTAGCGGCGTCTTTTCCTAAAAACGCCGCTAAAGACCAAGACCTTTAGCGGCGCTTATACCAC
AAACGCCGCTAAAGACCAAGACCTTTAGCGGCGCTTTTACCACAAACGCCGCTAAAGACCAAAAC
CTTTAGCGGCGCTTTTTATCACAAACGACCAAGAC
Found at i:46036458 original size:37 final size:37
Alignment explanation
Indices: 46036408--46036483 Score: 134
Period size: 37 Copynumber: 2.1 Consensus size: 37
46036398 TTTATCAAAC
46036408 TAGTTAAGAAATACATGGTGCAGCCATGCAATATAAA
1 TAGTTAAGAAATACATGGTGCAGCCATGCAATATAAA
* *
46036445 TAGTTAAGAAATACATTGTGCAGCCATGCAGTATAAA
1 TAGTTAAGAAATACATGGTGCAGCCATGCAATATAAA
46036482 TA
1 TA
46036484 CAATAGAATC
Statistics
Matches: 37, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
37 37 1.00
ACGTcount: A:0.42, C:0.13, G:0.18, T:0.26
Consensus pattern (37 bp):
TAGTTAAGAAATACATGGTGCAGCCATGCAATATAAA
Found at i:46036811 original size:23 final size:23
Alignment explanation
Indices: 46036761--46036812 Score: 59
Period size: 23 Copynumber: 2.3 Consensus size: 23
46036751 GTTAGGTGTC
* *
46036761 AGTATAAAGACATGTCAGATATG
1 AGTATGAAGACATGTCAGAGATG
* * *
46036784 GGTATGAAGGCATGTCTGAGATG
1 AGTATGAAGACATGTCAGAGATG
46036807 AGTATG
1 AGTATG
46036813 TTCAATTTTT
Statistics
Matches: 23, Mismatches: 6, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.35, C:0.08, G:0.31, T:0.27
Consensus pattern (23 bp):
AGTATGAAGACATGTCAGAGATG
Found at i:46037288 original size:12 final size:12
Alignment explanation
Indices: 46037271--46037300 Score: 60
Period size: 12 Copynumber: 2.5 Consensus size: 12
46037261 CAAGACAGAT
46037271 CAAATTTTAAAG
1 CAAATTTTAAAG
46037283 CAAATTTTAAAG
1 CAAATTTTAAAG
46037295 CAAATT
1 CAAATT
46037301 GCTGCTGAAT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 18 1.00
ACGTcount: A:0.50, C:0.10, G:0.07, T:0.33
Consensus pattern (12 bp):
CAAATTTTAAAG
Found at i:46039500 original size:22 final size:22
Alignment explanation
Indices: 46039457--46039501 Score: 56
Period size: 22 Copynumber: 2.1 Consensus size: 22
46039447 TCTTGGATGT
*
46039457 GGGAAATTAGGGATTTTAGGGG
1 GGGAAATTAGGGATTTCAGGGG
* *
46039479 GGGAAGTTGGGGATTTC-GGGG
1 GGGAAATTAGGGATTTCAGGGG
46039500 GG
1 GG
46039502 AGGGGGGTAG
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
21 6 0.30
22 14 0.70
ACGTcount: A:0.20, C:0.02, G:0.53, T:0.24
Consensus pattern (22 bp):
GGGAAATTAGGGATTTCAGGGG
Found at i:46043875 original size:7 final size:7
Alignment explanation
Indices: 46043865--46043889 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
46043855 ACTAACTCTT
46043865 AACCCCA
1 AACCCCA
46043872 AACCCCA
1 AACCCCA
46043879 AACCCCA
1 AACCCCA
46043886 AACC
1 AACC
46043890 ACTAACCTCT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.44, C:0.56, G:0.00, T:0.00
Consensus pattern (7 bp):
AACCCCA
Found at i:46043977 original size:82 final size:82
Alignment explanation
Indices: 46043880--46044040 Score: 243
Period size: 82 Copynumber: 2.0 Consensus size: 82
46043870 CAAACCCCAA
* * *
46043880 ACCCCAAACCACTAACCTCTAAACCTTATTTAATATAGAAATTAAAAAACACTAATTGATCTAAA
1 ACCCCAAACCACTAACCCCTAAACATTATTTAATATAGAAATTAAAAAACACTAATTAATCTAAA
*
46043945 TCATAAACCCTAACATG
66 CCATAAACCCTAACATG
* *
46043962 ACCCCAAATCC-CTAACCCCTAAACATTATTTAATATATAAATTAAAACACACTAATTAATCTAA
1 ACCCCAAA-CCACTAACCCCTAAACATTATTTAATATAGAAATTAAAAAACACTAATTAATCTAA
*
46044026 ACCCTAAACCCTAAC
65 ACCATAAACCCTAAC
46044041 CTAACACTAA
Statistics
Matches: 71, Mismatches: 7, Indels: 2
0.89 0.09 0.03
Matches are distributed among these distances:
82 69 0.97
83 2 0.03
ACGTcount: A:0.46, C:0.27, G:0.02, T:0.25
Consensus pattern (82 bp):
ACCCCAAACCACTAACCCCTAAACATTATTTAATATAGAAATTAAAAAACACTAATTAATCTAAA
CCATAAACCCTAACATG
Found at i:46044064 original size:82 final size:82
Alignment explanation
Indices: 46043893--46044066 Score: 222
Period size: 82 Copynumber: 2.1 Consensus size: 82
46043883 CCAAACCACT
* * *
46043893 AACCTCTAAACCTTATTTAATATAGAAATTAAAAAACACTAATTGATCTAAATCATAAACCCTAA
1 AACC-CTAAACATTATTTAATATAGAAATTAAAAAACACTAATTAATCTAAACCATAAACCCTAA
* * *
46043958 CATGACCCCAAATCCCTA
65 CATAACACCAAATCCATA
* * * *
46043976 ACCCCTAAACATTATTTAATATATAAATTAAAACACACTAATTAATCTAAACCCTAAACCCTAAC
1 AACCCTAAACATTATTTAATATAGAAATTAAAAAACACTAATTAATCTAAACCATAAACCCTAAC
* * *
46044041 CTAACACTAAATCTATA
66 ATAACACCAAATCCATA
46044058 AACCCTAAA
1 AACCCTAAA
46044067 TCCCTAACTC
Statistics
Matches: 77, Mismatches: 14, Indels: 1
0.84 0.15 0.01
Matches are distributed among these distances:
82 74 0.96
83 3 0.04
ACGTcount: A:0.47, C:0.25, G:0.02, T:0.26
Consensus pattern (82 bp):
AACCCTAAACATTATTTAATATAGAAATTAAAAAACACTAATTAATCTAAACCATAAACCCTAAC
ATAACACCAAATCCATA
Found at i:46044082 original size:29 final size:28
Alignment explanation
Indices: 46044040--46044100 Score: 68
Period size: 29 Copynumber: 2.1 Consensus size: 28
46044030 TAAACCCTAA
*
46044040 CCTAACACTAAATCTATAAACCCTAAATC
1 CCTAACACTAAATCTAT-AACCCTAAACC
* * * *
46044069 CCTAACTCTTAATCTCTAACCCTTAACC
1 CCTAACACTAAATCTATAACCCTAAACC
46044097 CCTA
1 CCTA
46044101 TCCCCTAACT
Statistics
Matches: 27, Mismatches: 5, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
28 13 0.48
29 14 0.52
ACGTcount: A:0.36, C:0.36, G:0.00, T:0.28
Consensus pattern (28 bp):
CCTAACACTAAATCTATAACCCTAAACC
Found at i:46044087 original size:14 final size:14
Alignment explanation
Indices: 46044058--46044100 Score: 50
Period size: 14 Copynumber: 3.1 Consensus size: 14
46044048 TAAATCTATA
*
46044058 AACCCTAAATCCCT
1 AACCCTTAATCCCT
* *
46044072 AACTCTTAATCTCT
1 AACCCTTAATCCCT
*
46044086 AACCCTTAACCCCT
1 AACCCTTAATCCCT
46044100 A
1 A
46044101 TCCCCTAACT
Statistics
Matches: 23, Mismatches: 6, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
14 23 1.00
ACGTcount: A:0.33, C:0.40, G:0.00, T:0.28
Consensus pattern (14 bp):
AACCCTTAATCCCT
Found at i:46044594 original size:41 final size:41
Alignment explanation
Indices: 46044537--46044736 Score: 305
Period size: 41 Copynumber: 4.9 Consensus size: 41
46044527 AAATGTTTTT
**
46044537 GCGGCGCTTTTTCAAAAACGCCGCTAAAGCCCTGAGCATTA
1 GCGGCGCTTTTTCAAAAACGCCGCTAAAGATCTGAGCATTA
46044578 GCGGCGCTTTTTCAAAAACGCCGCTAAAGATCTGAGCATTA
1 GCGGCGCTTTTTCAAAAACGCCGCTAAAGATCTGAGCATTA
* * *
46044619 GCGGCCCTTTCTC-AAAACGCTGCTAAAGATCTGAGCATTA
1 GCGGCGCTTTTTCAAAAACGCCGCTAAAGATCTGAGCATTA
*
46044659 GCGGCGCTTTTTTAAAAACGCCGCTAAAGATCTGAGCATTAA
1 GCGGCGCTTTTTCAAAAACGCCGCTAAAGATCTGAGCATT-A
*
46044701 GCGGCGCTTCTTC-AAAACGACCGCTAAAGATCTGAG
1 GCGGCGCTTTTTCAAAAACG-CCGCTAAAGATCTGAG
46044737 NNNNNNNNNN
Statistics
Matches: 145, Mismatches: 11, Indels: 5
0.90 0.07 0.03
Matches are distributed among these distances:
40 36 0.25
41 81 0.56
42 28 0.19
ACGTcount: A:0.28, C:0.26, G:0.22, T:0.23
Consensus pattern (41 bp):
GCGGCGCTTTTTCAAAAACGCCGCTAAAGATCTGAGCATTA
Found at i:46044676 original size:81 final size:82
Alignment explanation
Indices: 46044537--46044736 Score: 305
Period size: 81 Copynumber: 2.4 Consensus size: 82
46044527 AAATGTTTTT
* **
46044537 GCGGCGCTTTTTCAAAAACGCCGCTAAAGCCCTGAGCATTAGCGGCGCTTTTTCAAAAACGCCGC
1 GCGGCGCTTTCTC-AAAACGCCGCTAAAGATCTGAGCATTAGCGGCGCTTTTTCAAAAACGCCGC
46044602 TAAAGATCTGAGCATT-A
65 TAAAGATCTGAGCATTAA
* * *
46044619 GCGGCCCTTTCTCAAAACGCTGCTAAAGATCTGAGCATTAGCGGCGCTTTTTTAAAAACGCCGCT
1 GCGGCGCTTTCTCAAAACGCCGCTAAAGATCTGAGCATTAGCGGCGCTTTTTCAAAAACGCCGCT
46044684 AAAGATCTGAGCATTAA
66 AAAGATCTGAGCATTAA
46044701 GCGGCGC-TTCTTCAAAACGACCGCTAAAGATCTGAG
1 GCGGCGCTTTC-TCAAAACG-CCGCTAAAGATCTGAG
46044737 NNNNNNNNNN
Statistics
Matches: 107, Mismatches: 8, Indels: 5
0.89 0.07 0.04
Matches are distributed among these distances:
81 66 0.62
82 26 0.24
83 15 0.14
ACGTcount: A:0.28, C:0.26, G:0.22, T:0.23
Consensus pattern (82 bp):
GCGGCGCTTTCTCAAAACGCCGCTAAAGATCTGAGCATTAGCGGCGCTTTTTCAAAAACGCCGCT
AAAGATCTGAGCATTAA
Found at i:46045662 original size:30 final size:31
Alignment explanation
Indices: 46045626--46045705 Score: 85
Period size: 31 Copynumber: 2.6 Consensus size: 31
46045616 GATTGAATCA
* *
46045626 AAATTAAAGTTTCATGTGTATAATT-ATATC
1 AAATTAAAGTTTCATGTATAGAATTAATATC
* *
46045656 AAATTAAAATTT-ATGTATCGAATTACATATC
1 AAATTAAAGTTTCATGTATAGAATTA-ATATC
*
46045687 GAATTAAAG-TTCATGTATA
1 AAATTAAAGTTTCATGTATA
46045706 CTTTTGTGAT
Statistics
Matches: 40, Mismatches: 7, Indels: 5
0.77 0.13 0.10
Matches are distributed among these distances:
29 9 0.22
30 13 0.32
31 18 0.45
ACGTcount: A:0.42, C:0.07, G:0.10, T:0.40
Consensus pattern (31 bp):
AAATTAAAGTTTCATGTATAGAATTAATATC
Found at i:46050740 original size:19 final size:17
Alignment explanation
Indices: 46050708--46050742 Score: 52
Period size: 19 Copynumber: 1.9 Consensus size: 17
46050698 CAATCGTCAT
46050708 TTTAAAATTTTTAAATA
1 TTTAAAATTTTTAAATA
46050725 TTTAATAATATTTTAAAT
1 TTTAA-AAT-TTTTAAAT
46050743 GATGGTTTTT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 5 0.31
18 3 0.19
19 8 0.50
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (17 bp):
TTTAAAATTTTTAAATA
Found at i:46051057 original size:14 final size:16
Alignment explanation
Indices: 46051038--46051075 Score: 53
Period size: 16 Copynumber: 2.5 Consensus size: 16
46051028 ATCACCCGTG
46051038 TTAATTTTT-TA-AAA
1 TTAATTTTTATATAAA
46051052 TTAATTTTTATATAAA
1 TTAATTTTTATATAAA
*
46051068 ATAATTTT
1 TTAATTTT
46051076 AAAAATATAG
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
14 9 0.43
15 2 0.10
16 10 0.48
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (16 bp):
TTAATTTTTATATAAA
Found at i:46051368 original size:2 final size:2
Alignment explanation
Indices: 46051357--46051388 Score: 57
Period size: 2 Copynumber: 16.5 Consensus size: 2
46051347 ATTACGTAAA
46051357 AT AT -T AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
46051389 ATCTCAATCT
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 28 0.97
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:46051817 original size:19 final size:18
Alignment explanation
Indices: 46051774--46051817 Score: 52
Period size: 19 Copynumber: 2.4 Consensus size: 18
46051764 TTTCACTTGT
46051774 TTAAATTGAAAATTTAAA
1 TTAAATTGAAAATTTAAA
* **
46051792 TTGAATTGATAAATTTCGA
1 TTAAATTGA-AAATTTAAA
46051811 TTAAATT
1 TTAAATT
46051818 TAAATATGTT
Statistics
Matches: 21, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
18 8 0.38
19 13 0.62
ACGTcount: A:0.45, C:0.02, G:0.09, T:0.43
Consensus pattern (18 bp):
TTAAATTGAAAATTTAAA
Found at i:46056253 original size:31 final size:31
Alignment explanation
Indices: 46056164--46056254 Score: 102
Period size: 31 Copynumber: 3.0 Consensus size: 31
46056154 ATGATTAGTG
*
46056164 AAAATTG-A-ATTAAATGAATA-TTTCATGTAT
1 AAAATTGCACATTAAATCAA-AGTTT-ATGTAT
*
46056194 AAAATTGCACA--AAATCAAAGTTTTTGTAT
1 AAAATTGCACATTAAATCAAAGTTTATGTAT
*
46056223 AAAATTGCACATTAAATTAAAGTTTATGTAT
1 AAAATTGCACATTAAATCAAAGTTTATGTAT
46056254 A
1 A
46056255 GTTTTGAGAT
Statistics
Matches: 52, Mismatches: 4, Indels: 9
0.80 0.06 0.14
Matches are distributed among these distances:
29 17 0.33
30 16 0.31
31 18 0.35
32 1 0.02
ACGTcount: A:0.46, C:0.07, G:0.10, T:0.37
Consensus pattern (31 bp):
AAAATTGCACATTAAATCAAAGTTTATGTAT
Found at i:46056607 original size:19 final size:19
Alignment explanation
Indices: 46056572--46056609 Score: 51
Period size: 19 Copynumber: 2.0 Consensus size: 19
46056562 AAAAATTCAA
*
46056572 ATAAAAATAACTCAAAATT
1 ATAAAAATAACTAAAAATT
46056591 ATAAAAATTAA-TAAAAATT
1 ATAAAAA-TAACTAAAAATT
46056610 CACAAAATTA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 14 0.82
20 3 0.18
ACGTcount: A:0.66, C:0.05, G:0.00, T:0.29
Consensus pattern (19 bp):
ATAAAAATAACTAAAAATT
Found at i:46061498 original size:13 final size:13
Alignment explanation
Indices: 46061480--46061505 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
46061470 AACAATTCCG
46061480 TTTATGTTTTTTA
1 TTTATGTTTTTTA
46061493 TTTATGTTTTTTA
1 TTTATGTTTTTTA
46061506 GATTGGAACG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.15, C:0.00, G:0.08, T:0.77
Consensus pattern (13 bp):
TTTATGTTTTTTA
Found at i:46068892 original size:43 final size:43
Alignment explanation
Indices: 46068844--46068929 Score: 172
Period size: 43 Copynumber: 2.0 Consensus size: 43
46068834 AAAATATATG
46068844 TAAGGCCAACGTAAAGCTTTGGTTGAGTGGTTTAAGGTTTTAC
1 TAAGGCCAACGTAAAGCTTTGGTTGAGTGGTTTAAGGTTTTAC
46068887 TAAGGCCAACGTAAAGCTTTGGTTGAGTGGTTTAAGGTTTTAC
1 TAAGGCCAACGTAAAGCTTTGGTTGAGTGGTTTAAGGTTTTAC
46068930 CAATGATATT
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
43 43 1.00
ACGTcount: A:0.26, C:0.12, G:0.28, T:0.35
Consensus pattern (43 bp):
TAAGGCCAACGTAAAGCTTTGGTTGAGTGGTTTAAGGTTTTAC
Found at i:46069743 original size:31 final size:29
Alignment explanation
Indices: 46069668--46069746 Score: 86
Period size: 29 Copynumber: 2.7 Consensus size: 29
46069658 TGTTTGGTTC
* *
46069668 ATGTTACATTTTAGTCACTTATGTTTGAA
1 ATGTAACATTTTAGTCACTTATGTTTCAA
* * *
46069697 ATGTTACGTTTTAGTCACTTATGTTATCATG
1 ATGTAACATTTTAGTCACTTATGTT-TCA-A
*
46069728 TTGTAACATTTTAGTCACT
1 ATGTAACATTTTAGTCACT
46069747 GAGCCGTTAG
Statistics
Matches: 42, Mismatches: 6, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
29 24 0.57
30 2 0.05
31 16 0.38
ACGTcount: A:0.25, C:0.13, G:0.14, T:0.48
Consensus pattern (29 bp):
ATGTAACATTTTAGTCACTTATGTTTCAA
Found at i:46080813 original size:3 final size:3
Alignment explanation
Indices: 46080805--46080841 Score: 74
Period size: 3 Copynumber: 12.3 Consensus size: 3
46080795 CTTTATACCT
46080805 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A
46080842 ACAGAAACAA
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 34 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
ATA
Found at i:46084840 original size:17 final size:17
Alignment explanation
Indices: 46084820--46084862 Score: 61
Period size: 17 Copynumber: 2.5 Consensus size: 17
46084810 ATTATTCAAA
46084820 TATTTGATTTAT-TTAAT
1 TATTT-ATTTATCTTAAT
*
46084837 TATTTTTTTATCTTAAT
1 TATTTATTTATCTTAAT
46084854 TATTTATTT
1 TATTTATTT
46084863 TAATTTTTCG
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
16 5 0.22
17 18 0.78
ACGTcount: A:0.26, C:0.02, G:0.02, T:0.70
Consensus pattern (17 bp):
TATTTATTTATCTTAAT
Found at i:46094452 original size:26 final size:26
Alignment explanation
Indices: 46094416--46094470 Score: 101
Period size: 26 Copynumber: 2.1 Consensus size: 26
46094406 TTTTTACCTA
46094416 TTAGAAATGGGAGCTTTATAATGTTT
1 TTAGAAATGGGAGCTTTATAATGTTT
*
46094442 TTAGAGATGGGAGCTTTATAATGTTT
1 TTAGAAATGGGAGCTTTATAATGTTT
46094468 TTA
1 TTA
46094471 CTTTCTTCAC
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
26 28 1.00
ACGTcount: A:0.29, C:0.04, G:0.24, T:0.44
Consensus pattern (26 bp):
TTAGAAATGGGAGCTTTATAATGTTT
Found at i:46094831 original size:11 final size:11
Alignment explanation
Indices: 46094815--46094887 Score: 71
Period size: 10 Copynumber: 6.7 Consensus size: 11
46094805 TATTTTACAA
46094815 ATTTAAAAAAT
1 ATTTAAAAAAT
*
46094826 ATTTAAAAAAA
1 ATTTAAAAAAT
*
46094837 ATTT-TAAAAT
1 ATTTAAAAAAT
*
46094847 -TTAAAAAAAT
1 ATTTAAAAAAT
46094857 -TTTAAAAAAGT
1 ATTTAAAAAA-T
*
46094868 ATTTTAAAAAT
1 ATTTAAAAAAT
46094879 ATTTTAAAA
1 A-TTTAAAA
46094888 TTAAAAAATA
Statistics
Matches: 50, Mismatches: 8, Indels: 7
0.77 0.12 0.11
Matches are distributed among these distances:
9 2 0.04
10 17 0.34
11 17 0.34
12 14 0.28
ACGTcount: A:0.60, C:0.00, G:0.01, T:0.38
Consensus pattern (11 bp):
ATTTAAAAAAT
Done.