Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01009011.1 Hibiscus syriacus cultivar Beakdansim tig00112399_pilon, whole genome shotgun sequence
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: 579188
ACGTcount: A:0.33, C:0.18, G:0.17, T:0.33
File 3 of 4
Found at i:382703 original size:51 final size:52
Alignment explanation
Indices: 382438--382786 Score: 364
Period size: 55 Copynumber: 6.5 Consensus size: 52
382428 TCCCTTTTTA
* * * * *
382438 TTCAGGGAGTATAAGACTCGCACAATCTTCAGCAAACAGGTCTGCTCCCTATTCG
1 TTCAGAGAGTATAAGACTCG---AATCTTCAACAAACGGGTCCGCTCCCTATTCC
* * * *
382493 TTTAGGGAGTATAAGACTCGAACAATCTTCAACAAACGAGTCCGCTCCCTATTCG
1 TTCAGAGAGTATAAGACTCG---AATCTTCAACAAACGGGTCCGCTCCCTATTCC
* * * * *
382548 TTCAGAGAGTACATGACTCGATCAATCTTCATA-AAACGGGTTCACTCTCTATTCC
1 TTCAGAGAGTATAAGACTCG---AATCTTCA-ACAAACGGGTCCGCTCCCTATTCC
* *
382603 TTCAGAGAGTATAAAACTCGAACAATCTTCAACAAACGGGTCTGCTCCCTATTCC
1 TTCAGAGAGTATAAGACTCG---AATCTTCAACAAACGGGTCCGCTCCCTATTCC
* *
382658 TTCAGAGAGTATAGGACTCG-ATCTTCAACAAACGTGTCCGCTCCCTATTCC
1 TTCAGAGAGTATAAGACTCGAATCTTCAACAAACGGGTCCGCTCCCTATTCC
* *
382709 TTCAGAGAATATAAGACTCG-ATCTTCAACAAACGTGTCCGCTCCCTATTCC
1 TTCAGAGAGTATAAGACTCGAATCTTCAACAAACGGGTCCGCTCCCTATTCC
*
382760 TTCAGAGAGTATAGGACTCG-ATCTTCA
1 TTCAGAGAGTATAAGACTCGAATCTTCA
382787 TAACATGAGT
Statistics
Matches: 260, Mismatches: 32, Indels: 8
0.87 0.11 0.03
Matches are distributed among these distances:
51 103 0.40
54 1 0.00
55 155 0.60
56 1 0.00
ACGTcount: A:0.29, C:0.27, G:0.17, T:0.27
Consensus pattern (52 bp):
TTCAGAGAGTATAAGACTCGAATCTTCAACAAACGGGTCCGCTCCCTATTCC
Found at i:383779 original size:463 final size:466
Alignment explanation
Indices: 382914--383841 Score: 1817
Period size: 463 Copynumber: 2.0 Consensus size: 466
382904 ATCAATTATT
382914 AACATATGCTTGAAAATATTATACTAAAAAATTTAAAATTTGAGAAAATTTCTGAAAATCCATCT
1 AACATATGCTTGAAAATATTATACTAAAAAATTTAAAATTTGAGAAAATTTCTGAAAATCCATCT
382979 CCACCGTGAAAACTTATCTGGAAGCCATTGGATACGTGAATCTACATTGGCTCAATCGTCATCTA
66 CCACCGTGAAAACTTATCTGGAAGCCATTGGATACGTGAATCTACATTGGCTCAATCGTCATCTA
383044 AACATCACTCTTTTCAAAACTTCAAAACTAATTATCCTCATCTTGATGTTTCAATATCTTCAATC
131 AACATCACTCTTTTCAAAACTTCAAAACTAATTATCCTCATCTTGATGTTTCAATATCTTCAATC
383109 TTCCACTATTTTTAGGAAACCTGTAAATGCTTAAGTCATCATGCAATCATGAATGCTATGATCCT
196 TTCCACTATTTTTAGGAAACCTGTAAATGCTTAAGTCATCATGCAATCATGAATGCTATGATCCT
383174 ATTCATGCCTAAAATGCATGTAATTATGCAATTTAATGCGTTTTCTTCTTCGAAGGAACTCCATT
261 ATTCATGCCTAAAATGCATGTAATTATGCAATTTAATGCGTTTTCTTCTTCGAAGGAACTCCATT
*
383239 TCCCTTTATCTCGATGGAACTTGGTTTCGTCTTGGGCACATAACATTTGACCAGTTCACCCCAAT
326 TCCCTTTATCTCGATGGAACTTAGTTTCGTCTTGGGCACATAACATTTGACCAGTTCACCCCAAT
383304 TAACAATCTCAATATCACATCTTTC-G-TTAACAGGCCCTTGACTTCCTTCTTTCTTGAAA-CTG
391 TAACAATCTCAATATCACATCTTTCGGTTTAACAGGCCCTTGACTTCCTTCTTTCTTGAAACCTG
383366 CTAGTACCCAA
456 CTAGTACCCAA
383377 AACATATGCTTGAAAATATTATACTAAAAAATTTAAAATTTGAGAAAATTTCTGAAAATCCATCT
1 AACATATGCTTGAAAATATTATACTAAAAAATTTAAAATTTGAGAAAATTTCTGAAAATCCATCT
383442 CCACCGTGAAAACTTATCTGGAAGCCATTGGATACGTGAATCTACATTGGCTCAATCGTCATCTA
66 CCACCGTGAAAACTTATCTGGAAGCCATTGGATACGTGAATCTACATTGGCTCAATCGTCATCTA
383507 AACATCACTCTTTTCAAAACTTCAAAACTAATTATCCTCATCTTGATGTTTCAATATCTTCAATC
131 AACATCACTCTTTTCAAAACTTCAAAACTAATTATCCTCATCTTGATGTTTCAATATCTTCAATC
*
383572 TTCCACTATTTTTAGGAAACCTGTAAATGCTTAAGTCATCATGTAATCATGAATGCTATGATCCT
196 TTCCACTATTTTTAGGAAACCTGTAAATGCTTAAGTCATCATGCAATCATGAATGCTATGATCCT
383637 ATTCATGCCTAAAATGCATGTAATTATGCAATTTAATGCGTTTTCTTCTTCGAAGGAACTCCATT
261 ATTCATGCCTAAAATGCATGTAATTATGCAATTTAATGCGTTTTCTTCTTCGAAGGAACTCCATT
383702 TCCCTTTATCTCGATGGAACTTAGTTTCGTCTTGGGCACATAACATTTGACCAGTTCACCCCAAT
326 TCCCTTTATCTCGATGGAACTTAGTTTCGTCTTGGGCACATAACATTTGACCAGTTCACCCCAAT
383767 TAACAATCTCAATATCACATCTTTCGGTTTAACAGGCCCTTGACTTCCTTCTTTCTTGAAACCTG
391 TAACAATCTCAATATCACATCTTTCGGTTTAACAGGCCCTTGACTTCCTTCTTTCTTGAAACCTG
383832 CTAGTACCCA
456 CTAGTACCCA
383842 TGACCAACTT
Statistics
Matches: 460, Mismatches: 2, Indels: 3
0.99 0.00 0.01
Matches are distributed among these distances:
463 413 0.90
464 1 0.00
465 33 0.07
466 13 0.03
ACGTcount: A:0.31, C:0.22, G:0.12, T:0.35
Consensus pattern (466 bp):
AACATATGCTTGAAAATATTATACTAAAAAATTTAAAATTTGAGAAAATTTCTGAAAATCCATCT
CCACCGTGAAAACTTATCTGGAAGCCATTGGATACGTGAATCTACATTGGCTCAATCGTCATCTA
AACATCACTCTTTTCAAAACTTCAAAACTAATTATCCTCATCTTGATGTTTCAATATCTTCAATC
TTCCACTATTTTTAGGAAACCTGTAAATGCTTAAGTCATCATGCAATCATGAATGCTATGATCCT
ATTCATGCCTAAAATGCATGTAATTATGCAATTTAATGCGTTTTCTTCTTCGAAGGAACTCCATT
TCCCTTTATCTCGATGGAACTTAGTTTCGTCTTGGGCACATAACATTTGACCAGTTCACCCCAAT
TAACAATCTCAATATCACATCTTTCGGTTTAACAGGCCCTTGACTTCCTTCTTTCTTGAAACCTG
CTAGTACCCAA
Found at i:384632 original size:7 final size:7
Alignment explanation
Indices: 384622--384751 Score: 68
Period size: 7 Copynumber: 17.6 Consensus size: 7
384612 TATTTTTATT
384622 TTTTTTC
1 TTTTTTC
384629 TTTTTTC
1 TTTTTTC
*
384636 ATTTTTC
1 TTTTTTC
*
384643 TTTTTTA
1 TTTTTTC
*
384650 TTTTTTA
1 TTTTTTC
*
384657 TTTTAT-
1 TTTTTTC
384663 TTTTTTC
1 TTTTTTC
*
384670 ATTTTTC
1 TTTTTTC
**
384677 -CATTTC
1 TTTTTTC
384683 TATTTTTC
1 T-TTTTTC
384691 TCTTTTT-
1 T-TTTTTC
*
384698 TTCTTTC
1 TTTTTTC
384705 ATTTTTTC
1 -TTTTTTC
384713 ATCATTTTTC
1 -T--TTTTTC
384723 ATTTGTTCTC
1 -TTT-TT-TC
*
384733 ATTTTTC
1 TTTTTTC
384740 TTTTCTTC
1 TTTT-TTC
384748 TTTT
1 TTTT
384752 CATTTTTTCA
Statistics
Matches: 98, Mismatches: 15, Indels: 19
0.74 0.11 0.14
Matches are distributed among these distances:
6 13 0.13
7 42 0.43
8 29 0.30
9 4 0.04
10 10 0.10
ACGTcount: A:0.09, C:0.15, G:0.01, T:0.75
Consensus pattern (7 bp):
TTTTTTC
Found at i:384675 original size:48 final size:47
Alignment explanation
Indices: 384604--384803 Score: 128
Period size: 48 Copynumber: 4.2 Consensus size: 47
384594 ATCTTGAACC
*
384604 CTTTTATTTATTTTTATT-TTTTTTCTTTTTTCATTTTTCTTTTTTATT
1 CTTTTATTTATTTTT-TTCATTTTTCTTTTTTCATTTTTCTTTTTT-TT
**
384652 -TTTTATTTTATTTTTTTCATTTTTC-CATTTCTATTTTTCTCTTTTTTT
1 CTTTTA-TTTATTTTTTTCATTTTTCTTTTTTC-ATTTTTCT-TTTTTTT
* ** *
384700 CTTTCA-TT-TTTTCATCATTTTTCATTTGTTCTCATTTTTC-TTTTCTT
1 CTTTTATTTATTTTTTTCATTTTTC-TTT-TT-TCATTTTTCTTTTTTTT
** * *
384747 CTTTTCA-TT-TTTTCATCATTTTCTCATTTTTCAATTTTTTTCTTTTTTT
1 CTTTT-ATTTATTTTTTTCATTTT-TCTTTTTTC-ATTTTTCT-TTTTTTT
*
384796 CATTTATT
1 CTTTTATT
384804 CTTAAAGCGA
Statistics
Matches: 123, Mismatches: 14, Indels: 29
0.74 0.08 0.17
Matches are distributed among these distances:
46 15 0.12
47 31 0.25
48 44 0.36
49 31 0.25
50 2 0.02
ACGTcount: A:0.12, C:0.14, G:0.01, T:0.74
Consensus pattern (47 bp):
CTTTTATTTATTTTTTTCATTTTTCTTTTTTCATTTTTCTTTTTTTT
Found at i:384687 original size:35 final size:34
Alignment explanation
Indices: 384623--384710 Score: 106
Period size: 35 Copynumber: 2.5 Consensus size: 34
384613 ATTTTTATTT
* *
384623 TTTTTCTTTTTTCATTTTTCTTTTTTATTTTT-TA
1 TTTTT-TTTTTTCATTTTTCATTTCTATTTTTCTA
*
384657 TTTTATTTTTTTCATTTTTCCATTTCTATTTTTCTC
1 TTTT-TTTTTTTCATTTTT-CATTTCTATTTTTCTA
*
384693 TTTTTTTCTTTCATTTTT
1 TTTTTTTTTTTCATTTTT
384711 TCATCATTTT
Statistics
Matches: 47, Mismatches: 4, Indels: 5
0.84 0.07 0.09
Matches are distributed among these distances:
34 17 0.36
35 25 0.53
36 5 0.11
ACGTcount: A:0.09, C:0.12, G:0.00, T:0.78
Consensus pattern (34 bp):
TTTTTTTTTTTCATTTTTCATTTCTATTTTTCTA
Found at i:384712 original size:8 final size:8
Alignment explanation
Indices: 384701--384800 Score: 59
Period size: 8 Copynumber: 12.0 Consensus size: 8
384691 TCTTTTTTTC
384701 TTTCATTT
1 TTTCATTT
384709 TTTCATCATT
1 TTTCAT--TT
384719 TTTCATTT
1 TTTCATTT
384727 GTTCTCA-TT
1 -TT-TCATTT
384736 TTTC---T
1 TTTCATTT
384741 TTTC-TTCT
1 TTTCATT-T
384749 TTTCATTT
1 TTTCATTT
384757 TTTCATCATT
1 TTTCAT--TT
384767 TTCTCA-TT
1 TT-TCATTT
384775 TTTCAATTTT
1 TTTC-A-TTT
*
384785 TTTCTTTT
1 TTTCATTT
384793 TTTCATTT
1 TTTCATTT
384801 ATTCTTAAAG
Statistics
Matches: 76, Mismatches: 2, Indels: 28
0.72 0.02 0.26
Matches are distributed among these distances:
5 5 0.07
7 4 0.05
8 37 0.49
9 6 0.08
10 21 0.28
11 3 0.04
ACGTcount: A:0.12, C:0.17, G:0.01, T:0.70
Consensus pattern (8 bp):
TTTCATTT
Found at i:384717 original size:11 final size:10
Alignment explanation
Indices: 384685--384805 Score: 50
Period size: 9 Copynumber: 12.7 Consensus size: 10
384675 TCCATTTCTA
*
384685 TTTTTCTCTT
1 TTTTTCTCAT
384695 TTTTTCTTTCAT
1 TTTTTC--TCAT
384707 TTTTTCATCA-
1 TTTTTC-TCAT
384717 -TTTT-TCAT
1 TTTTTCTCAT
*
384725 TTGTTCTCA-
1 TTTTTCTCAT
*
384734 TTTTTCT-TT
1 TTTTTCTCAT
*
384743 TCTTCTTTTCAT
1 T-TT-TTCTCAT
384755 TTTTTCATCA-
1 TTTTTC-TCAT
384765 -TTTTCTCA-
1 TTTTTCTCAT
*
384773 TTTTTC-AAT
1 TTTTTCTCAT
384782 TTTTT-TC-T
1 TTTTTCTCAT
384790 TTTTT-TCAT
1 TTTTTCTCAT
*
384799 TTATTCT
1 TTTTTCT
384806 TAAAGCGAAA
Statistics
Matches: 85, Mismatches: 11, Indels: 30
0.67 0.09 0.24
Matches are distributed among these distances:
7 3 0.04
8 12 0.14
9 34 0.40
10 14 0.16
11 11 0.13
12 11 0.13
ACGTcount: A:0.11, C:0.17, G:0.01, T:0.71
Consensus pattern (10 bp):
TTTTTCTCAT
Found at i:384736 original size:17 final size:18
Alignment explanation
Indices: 384701--384798 Score: 86
Period size: 18 Copynumber: 5.8 Consensus size: 18
384691 TCTTTTTTTC
384701 TTTCATTTTTTCATCATT
1 TTTCATTTTTTCATCATT
*
384719 TTTCATTTGTTC-TCATT
1 TTTCATTTTTTCATCATT
*
384736 TTTC---TTTTCTTC--T
1 TTTCATTTTTTCATCATT
384749 TTTCATTTTTTCATCATT
1 TTTCATTTTTTCATCATT
*
384767 TTCTCA-TTTTTCAAT-TTT
1 TT-TCATTTTTTC-ATCATT
*
384785 TTTCTTTTTTTCAT
1 TTTCATTTTTTCAT
384799 TTATTCTTAA
Statistics
Matches: 66, Mismatches: 5, Indels: 19
0.73 0.06 0.21
Matches are distributed among these distances:
13 5 0.08
14 4 0.06
15 2 0.03
16 7 0.11
17 13 0.20
18 30 0.45
19 5 0.08
ACGTcount: A:0.12, C:0.17, G:0.01, T:0.69
Consensus pattern (18 bp):
TTTCATTTTTTCATCATT
Found at i:390040 original size:60 final size:60
Alignment explanation
Indices: 389947--390064 Score: 236
Period size: 60 Copynumber: 2.0 Consensus size: 60
389937 AAGGCACTTG
389947 TTATTATCCCGATATGGGAATGGATATGGAGGTGTAATAACCACTTTCGAAGACCTTTGT
1 TTATTATCCCGATATGGGAATGGATATGGAGGTGTAATAACCACTTTCGAAGACCTTTGT
390007 TTATTATCCCGATATGGGAATGGATATGGAGGTGTAATAACCACTTTCGAAGACCTTT
1 TTATTATCCCGATATGGGAATGGATATGGAGGTGTAATAACCACTTTCGAAGACCTTT
390065 TCAGCCAATC
Statistics
Matches: 58, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
60 58 1.00
ACGTcount: A:0.29, C:0.15, G:0.23, T:0.33
Consensus pattern (60 bp):
TTATTATCCCGATATGGGAATGGATATGGAGGTGTAATAACCACTTTCGAAGACCTTTGT
Found at i:393080 original size:18 final size:18
Alignment explanation
Indices: 393049--393118 Score: 52
Period size: 18 Copynumber: 3.8 Consensus size: 18
393039 CACTGAATTT
* *
393049 TGTCCTGAATGACCACTA
1 TGTCCCGAAGGACCACTA
* *
393067 TGTCCCGAAGGACCAATGGT
1 TGTCCCGAAGGACCACT--A
* *
393087 TGT-TCGAAGAACCACTA
1 TGTCCCGAAGGACCACTA
*
393104 TGTCCTGAAGGACCA
1 TGTCCCGAAGGACCA
393119 TTGTTTGCCC
Statistics
Matches: 38, Mismatches: 11, Indels: 6
0.69 0.20 0.11
Matches are distributed among these distances:
17 3 0.08
18 22 0.58
19 10 0.26
20 3 0.08
ACGTcount: A:0.29, C:0.26, G:0.23, T:0.23
Consensus pattern (18 bp):
TGTCCCGAAGGACCACTA
Found at i:394352 original size:20 final size:20
Alignment explanation
Indices: 394327--394364 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
394317 TTCCCCTTGA
394327 AGTGCATCGATGCATTCTAT
1 AGTGCATCGATGCATTCTAT
*
394347 AGTGCATCGATGTATTCT
1 AGTGCATCGATGCATTCT
394365 TTAACATGTG
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.24, C:0.18, G:0.21, T:0.37
Consensus pattern (20 bp):
AGTGCATCGATGCATTCTAT
Found at i:394462 original size:45 final size:45
Alignment explanation
Indices: 394391--394494 Score: 122
Period size: 45 Copynumber: 2.3 Consensus size: 45
394381 TGCACTACCC
* * * *
394391 ATGCATCGATACACAAATTACCTTCGATGTTTTCAT-TTTAAGGGG
1 ATGCATCGATGCACAAATTACATTCGATG-TTTCATCTTTAAAGAG
* * *
394436 ATGCATCGATGCACCAATTGCATTCGATGTTTCTTCTTTAAAGAG
1 ATGCATCGATGCACAAATTACATTCGATGTTTCATCTTTAAAGAG
394481 -TGCATCGATGCACA
1 ATGCATCGATGCACA
394495 TTGAATGTGT
Statistics
Matches: 50, Mismatches: 8, Indels: 3
0.82 0.13 0.05
Matches are distributed among these distances:
44 18 0.36
45 32 0.64
ACGTcount: A:0.28, C:0.20, G:0.18, T:0.34
Consensus pattern (45 bp):
ATGCATCGATGCACAAATTACATTCGATGTTTCATCTTTAAAGAG
Found at i:396374 original size:18 final size:17
Alignment explanation
Indices: 396348--396417 Score: 77
Period size: 17 Copynumber: 3.9 Consensus size: 17
396338 ACTGAATATT
396348 TGTCCGAAGGACCACTA
1 TGTCCGAAGGACCACTA
*
396365 TGTCCCGAAGGACCACTGGT
1 TGT-CCGAAGGACCACT--A
* *
396385 TGTTCGAAGAACCACTA
1 TGTCCGAAGGACCACTA
*
396402 TCTCCGAAGGACCACT
1 TGTCCGAAGGACCACT
396418 GTTTATCCCG
Statistics
Matches: 43, Mismatches: 7, Indels: 6
0.77 0.12 0.11
Matches are distributed among these distances:
17 16 0.37
18 13 0.30
19 11 0.26
20 3 0.07
ACGTcount: A:0.27, C:0.30, G:0.23, T:0.20
Consensus pattern (17 bp):
TGTCCGAAGGACCACTA
Found at i:396430 original size:37 final size:37
Alignment explanation
Indices: 396350--396435 Score: 111
Period size: 37 Copynumber: 2.3 Consensus size: 37
396340 TGAATATTTG
* *
396350 TCCGAAGGACCACTATGTCCCGAAGGACCACTGGTTG
1 TCCGAAGGACCACTATCTCCCGAAGGACCACTGGTTA
* * *
396387 TTCGAAGAACCACTATCT-CCGAAGGACCACTGTTTA
1 TCCGAAGGACCACTATCTCCCGAAGGACCACTGGTTA
396423 TCCCGAAGGACCA
1 T-CCGAAGGACCA
396436 TGATAATCCC
Statistics
Matches: 41, Mismatches: 7, Indels: 2
0.82 0.14 0.04
Matches are distributed among these distances:
36 17 0.41
37 24 0.59
ACGTcount: A:0.28, C:0.30, G:0.22, T:0.20
Consensus pattern (37 bp):
TCCGAAGGACCACTATCTCCCGAAGGACCACTGGTTA
Found at i:397649 original size:20 final size:21
Alignment explanation
Indices: 397624--397683 Score: 77
Period size: 20 Copynumber: 2.8 Consensus size: 21
397614 TTTCCCTTGA
397624 AGTGCATCGATGCATTCT-AC
1 AGTGCATCGATGCATTCTAAC
*
397644 AGTGCATCGATGCATTTTTTAAC
1 AGTGCATCGATGCA--TTCTAAC
397667 ATGTGCATCGATGCATT
1 A-GTGCATCGATGCATT
397684 ACCCATGCAC
Statistics
Matches: 35, Mismatches: 1, Indels: 6
0.83 0.02 0.14
Matches are distributed among these distances:
20 14 0.40
22 5 0.14
23 3 0.09
24 13 0.37
ACGTcount: A:0.25, C:0.20, G:0.20, T:0.35
Consensus pattern (21 bp):
AGTGCATCGATGCATTCTAAC
Found at i:397677 original size:24 final size:22
Alignment explanation
Indices: 397624--397683 Score: 79
Period size: 24 Copynumber: 2.7 Consensus size: 22
397614 TTTCCCTTGA
397624 AGTGCATCGATGCA--TTCTAC
1 AGTGCATCGATGCATTTTCTAC
*
397644 AGTGCATCGATGCATTTTTTAAC
1 AGTGCATCGATGCATTTTCT-AC
397667 ATGTGCATCGATGCATT
1 A-GTGCATCGATGCATT
397684 ACCCATGCAC
Statistics
Matches: 35, Mismatches: 1, Indels: 4
0.88 0.03 0.10
Matches are distributed among these distances:
20 14 0.40
22 3 0.09
23 3 0.09
24 15 0.43
ACGTcount: A:0.25, C:0.20, G:0.20, T:0.35
Consensus pattern (22 bp):
AGTGCATCGATGCATTTTCTAC
Found at i:397775 original size:62 final size:62
Alignment explanation
Indices: 397669--397806 Score: 163
Period size: 62 Copynumber: 2.2 Consensus size: 62
397659 TTTTTAACAT
* * * *
397669 GTGCATCGATGCATTACCCATGCACGATACACAAATTACCTTCGATGTTTCAT-TTTAAGGG
1 GTGCATCGATGCACTACCCATGCACGATACACAAATTACATTCGATGTTTCATCTTTAAAGA
* * * * *
397730 GATGCATCGATGCACT-CCTATGCATCGATGCACCAATTGCATTCGATGTTTCTTCTTTAAAGA
1 G-TGCATCGATGCACTACCCATGCA-CGATACACAAATTACATTCGATGTTTCATCTTTAAAGA
397793 GTGCATCGATGCAC
1 GTGCATCGATGCAC
397807 ATTGCACATT
Statistics
Matches: 65, Mismatches: 9, Indels: 5
0.82 0.11 0.06
Matches are distributed among these distances:
61 8 0.12
62 50 0.77
63 7 0.11
ACGTcount: A:0.26, C:0.24, G:0.19, T:0.31
Consensus pattern (62 bp):
GTGCATCGATGCACTACCCATGCACGATACACAAATTACATTCGATGTTTCATCTTTAAAGA
Found at i:401869 original size:21 final size:21
Alignment explanation
Indices: 401818--401870 Score: 63
Period size: 21 Copynumber: 2.5 Consensus size: 21
401808 GATTAGACTA
*
401818 TCGCAATGCGATTTTCTAATT
1 TCGCAATGCGATTTTCCAATT
**
401839 TCGCGTTGCGATTTTCCCAA-T
1 TCGCAATGCGATTTT-CCAATT
401860 TCGCAATGCGA
1 TCGCAATGCGA
401871 ATAAGTAAAT
Statistics
Matches: 26, Mismatches: 5, Indels: 2
0.79 0.15 0.06
Matches are distributed among these distances:
21 23 0.88
22 3 0.12
ACGTcount: A:0.21, C:0.25, G:0.19, T:0.36
Consensus pattern (21 bp):
TCGCAATGCGATTTTCCAATT
Found at i:402492 original size:18 final size:18
Alignment explanation
Indices: 402458--402493 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
402448 CGAGAGAATC
*
402458 GCAACGCGAAATAAAAAT
1 GCAACGCGAAACAAAAAT
*
402476 GCAACGCGAAACCAAAAT
1 GCAACGCGAAACAAAAAT
402494 CGCATTGCGA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.53, C:0.22, G:0.17, T:0.08
Consensus pattern (18 bp):
GCAACGCGAAACAAAAAT
Found at i:402515 original size:19 final size:19
Alignment explanation
Indices: 402493--402637 Score: 121
Period size: 19 Copynumber: 8.1 Consensus size: 19
402483 GAAACCAAAA
*
402493 TCGCATTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
402512 TCGCGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
*
402531 TCGCGTTGC-A-ATTC---
1 TCGCGTTGCGATTTTCATT
* **
402545 TCTCGTTGCGATAGTCATT
1 TCGCGTTGCGATTTTCATT
402564 TCGCGTTGCGA--TTC---
1 TCGCGTTGCGATTTTCATT
* **
402578 TCTCGTTGCGATAGTCATT
1 TCGCGTTGCGATTTTCATT
*
402597 TCGCGTTGCGATTCTCATT
1 TCGCGTTGCGATTTTCATT
*
402616 ATCTCGTTGCGATTTTCATT
1 -TCGCGTTGCGATTTTCATT
402636 TC
1 TC
402638 AACCAAAATA
Statistics
Matches: 102, Mismatches: 13, Indels: 22
0.74 0.09 0.16
Matches are distributed among these distances:
14 18 0.18
15 1 0.01
16 5 0.05
17 5 0.05
18 1 0.01
19 55 0.54
20 17 0.17
ACGTcount: A:0.13, C:0.23, G:0.20, T:0.43
Consensus pattern (19 bp):
TCGCGTTGCGATTTTCATT
Found at i:402563 original size:33 final size:33
Alignment explanation
Indices: 402515--402612 Score: 169
Period size: 33 Copynumber: 3.0 Consensus size: 33
402505 TTTCATTTCG
** *
402515 CGTTGCGATTTTCATTTCGCGTTGCAATTCTCT
1 CGTTGCGATAGTCATTTCGCGTTGCGATTCTCT
402548 CGTTGCGATAGTCATTTCGCGTTGCGATTCTCT
1 CGTTGCGATAGTCATTTCGCGTTGCGATTCTCT
402581 CGTTGCGATAGTCATTTCGCGTTGCGATTCTC
1 CGTTGCGATAGTCATTTCGCGTTGCGATTCTC
402613 ATTATCTCGT
Statistics
Matches: 62, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
33 62 1.00
ACGTcount: A:0.12, C:0.24, G:0.22, T:0.41
Consensus pattern (33 bp):
CGTTGCGATAGTCATTTCGCGTTGCGATTCTCT
Found at i:404184 original size:203 final size:206
Alignment explanation
Indices: 403835--404243 Score: 781
Period size: 203 Copynumber: 2.0 Consensus size: 206
403825 CACGAATGAG
403835 CAGCCTCCACTTCCTCCACTTCGAGAGCCATCACCTCACCCAGAGCCATCACCTGATCGACCATA
1 CAGCCTCCACTTCCTCCACTTCGAGAGCCATCACCTCACCCAGAGCCATCACCTGATCGACCATA
403900 CTATACACCTCTACAACGAGAGCGCATCACCTATCCCGTCAATCATCGAGCCTCTTCTCCACCAT
66 CTATACACCTCTACAACGAGAGCGCATCACCTATCCCGTCAATCATCGAGCCTCTTCTCCACCAT
403965 CACCTCATGCATATTAATATATATTGTACAAATGTGACTTAAATAT-AAAAC-AAAACA-GACAT
131 CACCTCATGCATATTAATATATATTGTACAAATGTGACTTAAATATAAAAACAAAAACATGACAT
404027 GCTAAACTATA
196 GCTAAACTATA
404038 CAGCCTCCACTTCCTCCACTTCGAGAGCCATCACCTCACCCAGAGCCATCACCTGATCGACCATA
1 CAGCCTCCACTTCCTCCACTTCGAGAGCCATCACCTCACCCAGAGCCATCACCTGATCGACCATA
404103 CTATACACCTCTACAACGAGAGC-CATCACCTATCCCGTCACATCATCGAGCCTCTTCTCCACCA
66 CTATACACCTCTACAACGAGAGCGCATCACCTATCCCGTCA-ATCATCGAGCCTCTTCTCCACCA
404167 TCACCTCATGCATATTAATATATATTGTACAAATGTGACTTAAATATAAAAACAAAAACATGACA
130 TCACCTCATGCATATTAATATATATTGTACAAATGTGACTTAAATATAAAAACAAAAACATGACA
404232 TGCTAAACTATA
195 TGCTAAACTATA
404244 AATTTTAAAA
Statistics
Matches: 202, Mismatches: 0, Indels: 5
0.98 0.00 0.02
Matches are distributed among these distances:
202 17 0.08
203 158 0.78
204 5 0.02
205 6 0.03
206 16 0.08
ACGTcount: A:0.33, C:0.33, G:0.10, T:0.24
Consensus pattern (206 bp):
CAGCCTCCACTTCCTCCACTTCGAGAGCCATCACCTCACCCAGAGCCATCACCTGATCGACCATA
CTATACACCTCTACAACGAGAGCGCATCACCTATCCCGTCAATCATCGAGCCTCTTCTCCACCAT
CACCTCATGCATATTAATATATATTGTACAAATGTGACTTAAATATAAAAACAAAAACATGACAT
GCTAAACTATA
Found at i:407825 original size:3 final size:3
Alignment explanation
Indices: 407817--407854 Score: 67
Period size: 3 Copynumber: 12.7 Consensus size: 3
407807 TTTTTTATAT
*
407817 ATA ATA ATA ATA ATA ATA ATA ATA GTA ATA ATA ATA AT
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA AT
407855 CAAAACGCCC
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
3 33 1.00
ACGTcount: A:0.63, C:0.00, G:0.03, T:0.34
Consensus pattern (3 bp):
ATA
Found at i:408069 original size:2 final size:2
Alignment explanation
Indices: 408062--408122 Score: 53
Period size: 2 Copynumber: 33.5 Consensus size: 2
408052 CCGCCCTATT
* * *
408062 TA TA TA TA TA TA TA TA TA TA TA TA -A TA T- TT TA TA TT TT TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
408102 TA T- TA -A T- TA TA TA TA TA -A TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA T
408123 TTTCGGGTTC
Statistics
Matches: 50, Mismatches: 3, Indels: 12
0.77 0.05 0.18
Matches are distributed among these distances:
1 6 0.12
2 44 0.88
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (2 bp):
TA
Found at i:416624 original size:13 final size:13
Alignment explanation
Indices: 416606--416630 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
416596 TACATATTGA
416606 CATTGGGCTTCTT
1 CATTGGGCTTCTT
416619 CATTGGGCTTCT
1 CATTGGGCTTCT
416631 CTGCTGCTGG
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:0.08, C:0.24, G:0.24, T:0.44
Consensus pattern (13 bp):
CATTGGGCTTCTT
Found at i:438274 original size:23 final size:23
Alignment explanation
Indices: 438247--438307 Score: 106
Period size: 23 Copynumber: 2.7 Consensus size: 23
438237 AATAAATAAT
438247 TAAAATCGAAAACAAAGCGAAAC
1 TAAAATCGAAAACAAAGCGAAAC
*
438270 TAAAATCGAAAACAAAGTGAAAC
1 TAAAATCGAAAACAAAGCGAAAC
438293 TAAAATCG-AAACAAA
1 TAAAATCGAAAACAAA
438308 TTAAATTAAA
Statistics
Matches: 37, Mismatches: 1, Indels: 1
0.95 0.03 0.03
Matches are distributed among these distances:
22 7 0.19
23 30 0.81
ACGTcount: A:0.62, C:0.15, G:0.11, T:0.11
Consensus pattern (23 bp):
TAAAATCGAAAACAAAGCGAAAC
Found at i:444452 original size:23 final size:21
Alignment explanation
Indices: 444414--444463 Score: 55
Period size: 23 Copynumber: 2.3 Consensus size: 21
444404 TAACTATTGA
*
444414 AAAATAAAAAATTTAAATATT
1 AAAATAAAAAAATTAAATATT
*
444435 AAAATAAATCAAAATTAATTATT
1 AAAATAAA--AAAATTAAATATT
*
444458 TAAATA
1 AAAATA
444464 TTAAGCACGT
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
21 8 0.33
23 16 0.67
ACGTcount: A:0.64, C:0.02, G:0.00, T:0.34
Consensus pattern (21 bp):
AAAATAAAAAAATTAAATATT
Found at i:458691 original size:3 final size:3
Alignment explanation
Indices: 458683--458838 Score: 215
Period size: 3 Copynumber: 52.3 Consensus size: 3
458673 TTTATTTATT
* * *
458683 TAA TAA TAA TAA TAA TAT TAA TAA AAA TAA TAA TAA TAA -AA CAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
* * *
458730 TAA TAA TAA TAA TAA TAA TAC TAA TAT TAA TAA AAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
* * * *
458778 TAA TAA TTA TAA TAA TAA TAA TAC TAA TAA TAA TAA TAA TAC TAA TAC
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
458826 TAA TAA TAA TAA T
1 TAA TAA TAA TAA T
458839 TTTAAATGAA
Statistics
Matches: 133, Mismatches: 19, Indels: 2
0.86 0.12 0.01
Matches are distributed among these distances:
2 2 0.02
3 131 0.98
ACGTcount: A:0.63, C:0.03, G:0.00, T:0.33
Consensus pattern (3 bp):
TAA
Found at i:459096 original size:76 final size:76
Alignment explanation
Indices: 458970--459759 Score: 1492
Period size: 76 Copynumber: 10.4 Consensus size: 76
458960 GAAATGTTGA
* *
458970 AAACATCATGCACTGAAGGACTTACAGATGACCCGAAGACTTTGAAAACATCAAAAAGCTCCCGA
1 AAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGCTTTAAAAACATCAAAAAGCTCCCGA
459035 AGGCTTTTTGG
66 AGGCTTTTTGG
459046 AAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGCTTTAAAAACATCAAAAAGCT-CCGA
1 AAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGCTTTAAAAACATCAAAAAGCTCCCGA
459110 AGGCTTTTTGG
66 AGGCTTTTTGG
*
459121 AAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGCTTTAAAAACATCAAAAAGCTCCTGA
1 AAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGCTTTAAAAACATCAAAAAGCTCCCGA
459186 AGGCTTTTTGG
66 AGGCTTTTTGG
459197 AAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGCTTTAAAAACATCAAAAAGCTCCCGA
1 AAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGCTTTAAAAACATCAAAAAGCTCCCGA
459262 AGGCTTTTTGG
66 AGGCTTTTTGG
459273 AAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGCTTTAAAAACATCAAAAAGCTCCCGA
1 AAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGCTTTAAAAACATCAAAAAGCTCCCGA
459338 AGGCTTTTTGG
66 AGGCTTTTTGG
459349 AAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGCTTTAAAAACATCAAAAAGCTCCCGA
1 AAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGCTTTAAAAACATCAAAAAGCTCCCGA
459414 AGGCTTTTTGG
66 AGGCTTTTTGG
*
459425 AAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGCTTTGAAAACATCAAAAAGCTCCCGA
1 AAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGCTTTAAAAACATCAAAAAGCTCCCGA
459490 AGGCTTTTTGG
66 AGGCTTTTTGG
* *
459501 AAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGATTTGAAAACATCAAAAAGCTCCCGA
1 AAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGCTTTAAAAACATCAAAAAGCTCCCGA
459566 AGGCTTTTTGG
66 AGGCTTTTTGG
* *
459577 AAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGATTTGAAAACATCAAAAAGCTCCCGA
1 AAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGCTTTAAAAACATCAAAAAGCTCCCGA
459642 AGGCTTTTTGG
66 AGGCTTTTTGG
*
459653 AAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGCTTTAAAAACATCAAAAAGCTCCTGA
1 AAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGCTTTAAAAACATCAAAAAGCTCCCGA
459718 AGGCTTTTTGG
66 AGGCTTTTTGG
459729 AAACATCATGCACTGAAGGACTTACAGATGA
1 AAACATCATGCACTGAAGGACTTACAGATGA
459760 GGGAAATAGT
Statistics
Matches: 704, Mismatches: 9, Indels: 2
0.98 0.01 0.00
Matches are distributed among these distances:
75 75 0.11
76 629 0.89
ACGTcount: A:0.37, C:0.22, G:0.20, T:0.21
Consensus pattern (76 bp):
AAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGCTTTAAAAACATCAAAAAGCTCCCGA
AGGCTTTTTGG
Found at i:460460 original size:22 final size:22
Alignment explanation
Indices: 460435--460489 Score: 101
Period size: 22 Copynumber: 2.5 Consensus size: 22
460425 CATAAAGCTT
460435 TCATCTTTGAAAAGAGAATCTA
1 TCATCTTTGAAAAGAGAATCTA
*
460457 TCATCTTTAAAAAGAGAATCTA
1 TCATCTTTGAAAAGAGAATCTA
460479 TCATCTTTGAA
1 TCATCTTTGAA
460490 GAGTGTAGAT
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
22 31 1.00
ACGTcount: A:0.40, C:0.15, G:0.11, T:0.35
Consensus pattern (22 bp):
TCATCTTTGAAAAGAGAATCTA
Found at i:463283 original size:82 final size:83
Alignment explanation
Indices: 463146--463353 Score: 328
Period size: 82 Copynumber: 2.5 Consensus size: 83
463136 GTTCCTACCA
* * * *
463146 AACCAGATCATATAACTCGAAGAACACTTCCAGAAGATTCTATTGGCAAATTCATCTTCTAAACT
1 AACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTGGCAAATTCATCTTCCAAACT
463211 CAATGATTG-TTCTGTCC
66 CAATGATTGATTCTGTCC
* *
463228 AACCAAATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTGGCAAATTCATCTTCCAAATT
1 AACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTGGCAAATTCATCTTCCAAACT
*
463293 CAATGCTTGATTCTGTCC
66 CAATGATTGATTCTGTCC
* *
463311 AATCAGATCAGATAACTCAAAGAACACTTCTAGAAGATGCTAT
1 AACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTAT
463354 GAGCATATGG
Statistics
Matches: 115, Mismatches: 10, Indels: 1
0.91 0.08 0.01
Matches are distributed among these distances:
82 67 0.58
83 48 0.42
ACGTcount: A:0.37, C:0.23, G:0.12, T:0.28
Consensus pattern (83 bp):
AACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTGGCAAATTCATCTTCCAAACT
CAATGATTGATTCTGTCC
Found at i:465928 original size:2 final size:2
Alignment explanation
Indices: 465921--465948 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
465911 ACAACAAAGG
465921 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
465949 TAAAGGATAA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:470316 original size:20 final size:21
Alignment explanation
Indices: 470277--470317 Score: 57
Period size: 20 Copynumber: 2.0 Consensus size: 21
470267 AAAATAATAA
470277 AAAAATTGAAAGAAAAGAATT
1 AAAAATTGAAAGAAAAGAATT
* *
470298 AAAAATT-AAATAAATGAATT
1 AAAAATTGAAAGAAAAGAATT
470318 TTTAATTTCT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
20 11 0.61
21 7 0.39
ACGTcount: A:0.66, C:0.00, G:0.10, T:0.24
Consensus pattern (21 bp):
AAAAATTGAAAGAAAAGAATT
Found at i:472431 original size:3 final size:3
Alignment explanation
Indices: 472425--472562 Score: 197
Period size: 3 Copynumber: 46.3 Consensus size: 3
472415 TTTATTTATT
* * * * *
472425 TAA TAA TAA TAA TAT TAT TAA TAA AAA TAA TAA TAA TAA -AA CAA AAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
* *
472472 TAA TAA TAA TAA TAA TAA TAC TAA TAT TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
*
472520 TAA TAA TAA TAA TAA TAA TAA TAC TAA TAA TAA TAA TAA TAA T
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA T
472563 TTTAAATGAA
Statistics
Matches: 122, Mismatches: 12, Indels: 2
0.90 0.09 0.01
Matches are distributed among these distances:
2 2 0.02
3 120 0.98
ACGTcount: A:0.64, C:0.02, G:0.00, T:0.33
Consensus pattern (3 bp):
TAA
Found at i:473370 original size:29 final size:29
Alignment explanation
Indices: 473337--473435 Score: 85
Period size: 29 Copynumber: 3.3 Consensus size: 29
473327 TGAATGCCAT
473337 AGTTTGAGGATGAAATTGTAATGTTTAAA
1 AGTTTGAGGATGAAATTGTAATGTTTAAA
* * *
473366 AGTTTGAGGAT-AAATT-TAGAATGATAGTCAT
1 AGTTTGAGGATGAAATTGT--AATG-T-TTAAA
* * * *
473397 AGTATAAGGATGAAATTGGAATATTTAAA
1 AGTTTGAGGATGAAATTGTAATGTTTAAA
473426 AGTTTGAGGA
1 AGTTTGAGGA
473436 CCAATTTAAA
Statistics
Matches: 52, Mismatches: 12, Indels: 12
0.68 0.16 0.16
Matches are distributed among these distances:
27 1 0.02
28 5 0.10
29 25 0.48
30 2 0.04
31 14 0.27
32 5 0.10
ACGTcount: A:0.40, C:0.01, G:0.24, T:0.34
Consensus pattern (29 bp):
AGTTTGAGGATGAAATTGTAATGTTTAAA
Found at i:473376 original size:60 final size:60
Alignment explanation
Indices: 473275--473447 Score: 224
Period size: 60 Copynumber: 2.9 Consensus size: 60
473265 GTATATAGAT
**
473275 ATAGTTTG-GGATGAAATTGGAATGTTTAAAAAGTTCAAGGATCAATTTAAAATGA-ATGCC
1 ATAGTTTGAGGATGAAATTGGAATGTTT-AAAAGTTTGAGGATCAATTTAAAATGATA-GCC
* * * *
473335 ATAGTTTGAGGATGAAATTGTAATGTTTAAAAGTTTGAGGATAAATTTAGAATGATAGTC
1 ATAGTTTGAGGATGAAATTGGAATGTTTAAAAGTTTGAGGATCAATTTAAAATGATAGCC
* * * *
473395 ATAGTATAAGGATGAAATTGGAATATTTAAAAGTTTGAGGACCAATTTAAAAT
1 ATAGTTTGAGGATGAAATTGGAATGTTTAAAAGTTTGAGGATCAATTTAAAAT
473448 AAGGGTAATA
Statistics
Matches: 98, Mismatches: 13, Indels: 4
0.85 0.11 0.03
Matches are distributed among these distances:
60 79 0.81
61 19 0.19
ACGTcount: A:0.41, C:0.04, G:0.21, T:0.34
Consensus pattern (60 bp):
ATAGTTTGAGGATGAAATTGGAATGTTTAAAAGTTTGAGGATCAATTTAAAATGATAGCC
Found at i:481632 original size:2 final size:2
Alignment explanation
Indices: 481625--481660 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
481615 AAATTGGATT
481625 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
481661 AACTAGGTCA
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:483757 original size:11 final size:11
Alignment explanation
Indices: 483741--483799 Score: 52
Period size: 11 Copynumber: 5.5 Consensus size: 11
483731 TTACATTATA
483741 AAAAATATATT
1 AAAAATATATT
*
483752 AAAAATACATT
1 AAAAATATATT
***
483763 ATTTATA-ATT
1 AAAAATATATT
483773 ATAAAAT-T-TT
1 A-AAAATATATT
483783 AAAAATATATT
1 AAAAATATATT
483794 AAAAAT
1 AAAAAT
483800 TCTATAATAC
Statistics
Matches: 37, Mismatches: 7, Indels: 8
0.71 0.13 0.15
Matches are distributed among these distances:
9 5 0.14
10 8 0.22
11 24 0.65
ACGTcount: A:0.59, C:0.02, G:0.00, T:0.39
Consensus pattern (11 bp):
AAAAATATATT
Found at i:483938 original size:7 final size:7
Alignment explanation
Indices: 483926--484050 Score: 56
Period size: 7 Copynumber: 18.1 Consensus size: 7
483916 GATTACACCA
483926 TAAACCC
1 TAAACCC
483933 TAAACCC
1 TAAACCC
**
483940 TAAACTA
1 TAAACCC
*
483947 TAAATCC
1 TAAACCC
***
483954 TAAGTTC
1 TAAACCC
* *
483961 -AAAACT
1 TAAACCC
*
483967 TAAACCA
1 TAAACCC
*
483974 TATACCC
1 TAAACCC
**
483981 TAAACTA
1 TAAACCC
483988 TAAACCC
1 TAAACCC
**
483995 TAAGTCC
1 TAAACCC
*
484002 -AAAACC
1 TAAACCC
*
484008 TAAACCA
1 TAAACCC
484015 TAAACCC
1 TAAACCC
** *
484022 TAGGCTC
1 TAAACCC
*
484029 TAAGCCC
1 TAAACCC
484036 TAAACCC
1 TAAACCC
484043 TAAACCC
1 TAAACCC
484050 T
1 T
484051 TAATCTAATT
Statistics
Matches: 83, Mismatches: 33, Indels: 4
0.69 0.28 0.03
Matches are distributed among these distances:
6 6 0.07
7 77 0.93
ACGTcount: A:0.43, C:0.32, G:0.04, T:0.21
Consensus pattern (7 bp):
TAAACCC
Found at i:484038 original size:41 final size:41
Alignment explanation
Indices: 483926--484023 Score: 151
Period size: 41 Copynumber: 2.4 Consensus size: 41
483916 GATTACACCA
* * * *
483926 TAAACCCTAAACCCTAAACTATAAATCCTAAGTTCAAAACT
1 TAAACCATAAACCCTAAACTATAAACCCTAAGTCCAAAACC
*
483967 TAAACCATATACCCTAAACTATAAACCCTAAGTCCAAAACC
1 TAAACCATAAACCCTAAACTATAAACCCTAAGTCCAAAACC
484008 TAAACCATAAACCCTA
1 TAAACCATAAACCCTA
484024 GGCTCTAAGC
Statistics
Matches: 51, Mismatches: 6, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
41 51 1.00
ACGTcount: A:0.47, C:0.30, G:0.02, T:0.21
Consensus pattern (41 bp):
TAAACCATAAACCCTAAACTATAAACCCTAAGTCCAAAACC
Found at i:484048 original size:41 final size:41
Alignment explanation
Indices: 483926--484048 Score: 120
Period size: 41 Copynumber: 3.0 Consensus size: 41
483916 GATTACACCA
* * *** *
483926 TAAACCCTAAACCCTAAACTATAAATCCTAAGTTCAAAACT
1 TAAACCATAAACCCTAAACTATAAACCCTAAACCCAAAACC
* **
483967 TAAACCATATACCCTAAACTATAAACCCTAAGTCCAAAACC
1 TAAACCATAAACCCTAAACTATAAACCCTAAACCCAAAACC
** * * *
484008 TAAACCATAAACCCTAGGCTCTAAGCCCTAAACCCTAAACC
1 TAAACCATAAACCCTAAACTATAAACCCTAAACCCAAAACC
484049 CTTAATCTAA
Statistics
Matches: 69, Mismatches: 13, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
41 69 1.00
ACGTcount: A:0.44, C:0.32, G:0.04, T:0.20
Consensus pattern (41 bp):
TAAACCATAAACCCTAAACTATAAACCCTAAACCCAAAACC
Found at i:484170 original size:7 final size:7
Alignment explanation
Indices: 484125--484150 Score: 52
Period size: 7 Copynumber: 3.7 Consensus size: 7
484115 GATTACACCC
484125 TAAACCT
1 TAAACCT
484132 TAAACCT
1 TAAACCT
484139 TAAACCT
1 TAAACCT
484146 TAAAC
1 TAAAC
484151 TATAAATTAT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 19 1.00
ACGTcount: A:0.46, C:0.27, G:0.00, T:0.27
Consensus pattern (7 bp):
TAAACCT
Found at i:484235 original size:14 final size:14
Alignment explanation
Indices: 484201--484243 Score: 59
Period size: 14 Copynumber: 3.1 Consensus size: 14
484191 TCATAAACTA
* *
484201 TAAACCCTAAGCCC
1 TAAACCTTAAACCC
*
484215 TAAACCTTACACCC
1 TAAACCTTAAACCC
484229 TAAACCTTAAACCC
1 TAAACCTTAAACCC
484243 T
1 T
484244 TAATCCGTTT
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
14 25 1.00
ACGTcount: A:0.37, C:0.40, G:0.02, T:0.21
Consensus pattern (14 bp):
TAAACCTTAAACCC
Found at i:484241 original size:7 final size:7
Alignment explanation
Indices: 484201--484243 Score: 50
Period size: 7 Copynumber: 6.1 Consensus size: 7
484191 TCATAAACTA
484201 TAAACCC
1 TAAACCC
*
484208 TAAGCCC
1 TAAACCC
*
484215 TAAACCT
1 TAAACCC
*
484222 TACACCC
1 TAAACCC
*
484229 TAAACCT
1 TAAACCC
484236 TAAACCC
1 TAAACCC
484243 T
1 T
484244 TAATCCGTTT
Statistics
Matches: 28, Mismatches: 8, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
7 28 1.00
ACGTcount: A:0.37, C:0.40, G:0.02, T:0.21
Consensus pattern (7 bp):
TAAACCC
Found at i:485922 original size:22 final size:22
Alignment explanation
Indices: 485905--485961 Score: 105
Period size: 22 Copynumber: 2.6 Consensus size: 22
485895 CTTGATTTGT
485905 GTTTAAATCGAGCCTGATTCGA
1 GTTTAAATCGAGCCTGATTCGA
*
485927 GTTTAAATCGAGTCTGATTCGA
1 GTTTAAATCGAGCCTGATTCGA
485949 GTTTAAATCGAGC
1 GTTTAAATCGAGC
485962 TCTTGAAATT
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
22 33 1.00
ACGTcount: A:0.28, C:0.16, G:0.23, T:0.33
Consensus pattern (22 bp):
GTTTAAATCGAGCCTGATTCGA
Found at i:487477 original size:20 final size:20
Alignment explanation
Indices: 487449--487487 Score: 69
Period size: 20 Copynumber: 1.9 Consensus size: 20
487439 CTCCAACCCT
*
487449 GTGGTAATGTAAGATTACCG
1 GTGGGAATGTAAGATTACCG
487469 GTGGGAATGTAAGATTACC
1 GTGGGAATGTAAGATTACC
487488 AATGAATATG
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.31, C:0.10, G:0.31, T:0.28
Consensus pattern (20 bp):
GTGGGAATGTAAGATTACCG
Found at i:487686 original size:2 final size:2
Alignment explanation
Indices: 487681--487714 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
487671 AAATTCATAA
487681 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
487715 TACAAAATTG
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:488294 original size:21 final size:23
Alignment explanation
Indices: 488244--488299 Score: 64
Period size: 23 Copynumber: 2.6 Consensus size: 23
488234 GTCGAGGGTT
* *
488244 CTATGTAGTCATTCGGGACAAAA
1 CTATGTGGTCATTCGAGACAAAA
*
488267 CTATGTGGTCCTTCGAGAC-AAA
1 CTATGTGGTCATTCGAGACAAAA
488289 -TATGTGG-CATT
1 CTATGTGGTCATT
488300 TCGGTGCAAA
Statistics
Matches: 29, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
20 3 0.10
21 7 0.24
22 3 0.10
23 16 0.55
ACGTcount: A:0.29, C:0.18, G:0.23, T:0.30
Consensus pattern (23 bp):
CTATGTGGTCATTCGAGACAAAA
Found at i:490263 original size:24 final size:24
Alignment explanation
Indices: 490236--490301 Score: 66
Period size: 24 Copynumber: 2.8 Consensus size: 24
490226 AGCTCGTATA
490236 AATTTGCACCGAAGTGCCACGTAG
1 AATTTGCACCGAAGTGCCACGTAG
*
490260 AATTTGTC-CCGAAG-GACCGCGTAG
1 AATTTG-CACCGAAGTG-CCACGTAG
* *
490284 AA-ATGCACCGTAGTGCCA
1 AATTTGCACCGAAGTGCCA
490302 TATAAGATTG
Statistics
Matches: 34, Mismatches: 4, Indels: 9
0.72 0.09 0.19
Matches are distributed among these distances:
22 1 0.03
23 10 0.29
24 22 0.65
25 1 0.03
ACGTcount: A:0.29, C:0.26, G:0.26, T:0.20
Consensus pattern (24 bp):
AATTTGCACCGAAGTGCCACGTAG
Found at i:492675 original size:54 final size:54
Alignment explanation
Indices: 492573--492675 Score: 134
Period size: 54 Copynumber: 1.9 Consensus size: 54
492563 CGAAATGAAA
* * *
492573 ATTCACAAACTCATTATGAATTCCATGGATTACACACATAGTGTCGAAATGGTC
1 ATTCACAAACGCATTATGAATACCATGGATTACACACATAGTGCCGAAATGGTC
* * * **
492627 ATTCATAAACGCATTATGAATACCATGGGTTGCACATTTAGTGCCGAAA
1 ATTCACAAACGCATTATGAATACCATGGATTACACACATAGTGCCGAAA
492676 ATGCACCGTT
Statistics
Matches: 41, Mismatches: 8, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
54 41 1.00
ACGTcount: A:0.35, C:0.19, G:0.17, T:0.29
Consensus pattern (54 bp):
ATTCACAAACGCATTATGAATACCATGGATTACACACATAGTGCCGAAATGGTC
Found at i:497286 original size:21 final size:21
Alignment explanation
Indices: 497260--497304 Score: 90
Period size: 21 Copynumber: 2.1 Consensus size: 21
497250 TCTTAAGCTG
497260 ATAGACCGCTTACCTAGTTCC
1 ATAGACCGCTTACCTAGTTCC
497281 ATAGACCGCTTACCTAGTTCC
1 ATAGACCGCTTACCTAGTTCC
497302 ATA
1 ATA
497305 TGATGATAAT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 24 1.00
ACGTcount: A:0.27, C:0.31, G:0.13, T:0.29
Consensus pattern (21 bp):
ATAGACCGCTTACCTAGTTCC
Found at i:499177 original size:15 final size:15
Alignment explanation
Indices: 499157--499234 Score: 56
Period size: 15 Copynumber: 5.4 Consensus size: 15
499147 AATGTAGTAA
499157 ATTATTATAAAATAT
1 ATTATTATAAAATAT
* * *
499172 ATTATT-TTAACTGT
1 ATTATTATAAAATAT
** * *
499186 -TTAAAATATAATAA
1 ATTATTATAAAATAT
499200 ATGT-TTAT-AAATAT
1 AT-TATTATAAAATAT
499214 ATTATTATAAAATAT
1 ATTATTATAAAATAT
499229 ATTATT
1 ATTATT
499235 TTAACTATTT
Statistics
Matches: 44, Mismatches: 14, Indels: 10
0.65 0.21 0.15
Matches are distributed among these distances:
13 4 0.09
14 18 0.41
15 21 0.48
16 1 0.02
ACGTcount: A:0.47, C:0.01, G:0.03, T:0.49
Consensus pattern (15 bp):
ATTATTATAAAATAT
Found at i:499201 original size:43 final size:43
Alignment explanation
Indices: 499122--499219 Score: 121
Period size: 43 Copynumber: 2.3 Consensus size: 43
499112 TTTATAGTGT
* * * *
499122 TAAAATATATT-CTTTAATTGTTAAAAATGTAGTAAAT-TATTA
1 TAAAATATATTATTTTAACTGTTAAAAATATAATAAATGT-TTA
*
499164 TAAAATATATTATTTTAACTGTTTAAAATATAATAAATGTTTA
1 TAAAATATATTATTTTAACTGTTAAAAATATAATAAATGTTTA
499207 T-AAATATATTATT
1 TAAAATATATTATT
499220 ATAAAATATA
Statistics
Matches: 49, Mismatches: 5, Indels: 4
0.84 0.09 0.07
Matches are distributed among these distances:
42 23 0.47
43 25 0.51
44 1 0.02
ACGTcount: A:0.46, C:0.02, G:0.05, T:0.47
Consensus pattern (43 bp):
TAAAATATATTATTTTAACTGTTAAAAATATAATAAATGTTTA
Found at i:500512 original size:20 final size:20
Alignment explanation
Indices: 500474--500512 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
500464 TAAATTAAAT
* *
500474 ATTAGATAGGATCAGTTTTA
1 ATTAGATAGAATCAATTTTA
*
500494 ATTAGATAGAATTAATTTT
1 ATTAGATAGAATCAATTTT
500513 TATTCTATTA
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:0.38, C:0.03, G:0.15, T:0.44
Consensus pattern (20 bp):
ATTAGATAGAATCAATTTTA
Found at i:500551 original size:20 final size:21
Alignment explanation
Indices: 500526--500565 Score: 64
Period size: 20 Copynumber: 2.0 Consensus size: 21
500516 TCTATTAGTT
*
500526 ATTAGATAGGATCA-TTTTTA
1 ATTAGATAGAATCAGTTTTTA
500546 ATTAGATAGAATCAGTTTTT
1 ATTAGATAGAATCAGTTTTT
500566 TATTCTATTA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 13 0.72
21 5 0.28
ACGTcount: A:0.35, C:0.05, G:0.15, T:0.45
Consensus pattern (21 bp):
ATTAGATAGAATCAGTTTTTA
Found at i:500589 original size:53 final size:51
Alignment explanation
Indices: 500473--500622 Score: 246
Period size: 53 Copynumber: 2.9 Consensus size: 51
500463 CTAAATTAAA
* *
500473 TATTAGATAGGATCAGTTTTAATTAGATAGAATTAATTTTTATTCTATTAGT
1 TATTAGATAGGATCATTTTTAATTAGATAGAA-TCATTTTTATTCTATTAGT
500525 TATTAGATAGGATCATTTTTAATTAGATAGAATCAGTTTTTTATTCTATTAGT
1 TATTAGATAGGATCATTTTTAATTAGATAGAATCA--TTTTTATTCTATTAGT
*
500578 TATTAGATAGGATCATTTTTAATTAAATAGAATCATTTTTATTCT
1 TATTAGATAGGATCATTTTTAATTAGATAGAATCATTTTTATTCT
500623 GTTGCTAATT
Statistics
Matches: 93, Mismatches: 3, Indels: 5
0.92 0.03 0.05
Matches are distributed among these distances:
51 12 0.13
52 31 0.33
53 50 0.54
ACGTcount: A:0.34, C:0.05, G:0.12, T:0.49
Consensus pattern (51 bp):
TATTAGATAGGATCATTTTTAATTAGATAGAATCATTTTTATTCTATTAGT
Found at i:500607 original size:20 final size:20
Alignment explanation
Indices: 500579--500618 Score: 62
Period size: 20 Copynumber: 2.0 Consensus size: 20
500569 TCTATTAGTT
* *
500579 ATTAGATAGGATCATTTTTA
1 ATTAAATAGAATCATTTTTA
500599 ATTAAATAGAATCATTTTTA
1 ATTAAATAGAATCATTTTTA
500619 TTCTGTTGCT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.40, C:0.05, G:0.10, T:0.45
Consensus pattern (20 bp):
ATTAAATAGAATCATTTTTA
Found at i:505207 original size:20 final size:20
Alignment explanation
Indices: 505182--505272 Score: 72
Period size: 20 Copynumber: 5.0 Consensus size: 20
505172 TAAATTAAAT
*
505182 ATTAGATAGGATCAGTTTTA
1 ATTAGATAGAATCAGTTTTA
*
505202 ATTAGATAGAATCAGTTTTT
1 ATTAGATAGAATCAGTTTTA
* *
505222 ATT--CT---ATTAG--TT-
1 ATTAGATAGAATCAGTTTTA
* *
505234 ATTAGATAGGATCATTTTTA
1 ATTAGATAGAATCAGTTTTA
505254 ATTAGATAGAATCAGTTTT
1 ATTAGATAGAATCAGTTTT
505273 TTATTCTATT
Statistics
Matches: 54, Mismatches: 9, Indels: 16
0.68 0.11 0.20
Matches are distributed among these distances:
12 3 0.06
13 2 0.04
14 1 0.02
15 4 0.07
17 3 0.06
18 1 0.02
19 2 0.04
20 38 0.70
ACGTcount: A:0.34, C:0.05, G:0.15, T:0.45
Consensus pattern (20 bp):
ATTAGATAGAATCAGTTTTA
Found at i:505297 original size:53 final size:52
Alignment explanation
Indices: 505181--505330 Score: 275
Period size: 53 Copynumber: 2.9 Consensus size: 52
505171 CTAAATTAAA
*
505181 TATTAGATAGGATCAGTTTTAATTAGATAGAATCAGTTTTTATTCTATTAGT
1 TATTAGATAGGATCATTTTTAATTAGATAGAATCAGTTTTTATTCTATTAGT
505233 TATTAGATAGGATCATTTTTAATTAGATAGAATCAGTTTTTTATTCTATTAGT
1 TATTAGATAGGATCATTTTTAATTAGATAGAATCAG-TTTTTATTCTATTAGT
505286 TATTAGATAGGATCATTTTTAATTAGATAGAATCA-TTTTTATTCT
1 TATTAGATAGGATCATTTTTAATTAGATAGAATCAGTTTTTATTCT
505331 GTTGCTAATT
Statistics
Matches: 96, Mismatches: 1, Indels: 3
0.96 0.01 0.03
Matches are distributed among these distances:
51 10 0.10
52 35 0.36
53 51 0.53
ACGTcount: A:0.33, C:0.06, G:0.13, T:0.48
Consensus pattern (52 bp):
TATTAGATAGGATCATTTTTAATTAGATAGAATCAGTTTTTATTCTATTAGT
Found at i:505312 original size:20 final size:20
Alignment explanation
Indices: 505287--505326 Score: 71
Period size: 20 Copynumber: 2.0 Consensus size: 20
505277 TCTATTAGTT
*
505287 ATTAGATAGGATCATTTTTA
1 ATTAGATAGAATCATTTTTA
505307 ATTAGATAGAATCATTTTTA
1 ATTAGATAGAATCATTTTTA
505327 TTCTGTTGCT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.38, C:0.05, G:0.12, T:0.45
Consensus pattern (20 bp):
ATTAGATAGAATCATTTTTA
Found at i:508523 original size:442 final size:435
Alignment explanation
Indices: 507677--508549 Score: 1138
Period size: 442 Copynumber: 2.0 Consensus size: 435
507667 TAAGTTCAAA
*
507677 TTATTCTTGCTTATGTATCATTGTTTAACTGGGAACCTATGTCACTTTGTGAAATGGACTTCACG
1 TTATTCTTGCTTATGTATCATTGTTTAACTGGGAACCTATGTCACTTTGTGAAAAGGACTTCACG
* *
507742 ACTTCAATTGGTGCAATAAGCCATTTTAACTTTTTAATTTGGTTTGACCGAGTTGGTTAGGTGGC
66 ACTTCAATTGGTGCAATAAGCCATTTTAACTTTTTAATTTGGTTTGACCAAGCTGGTTAGGTGGC
* * *
507807 CAAGATCTAAAATTGTTAAAAACGAGAAAAGAAAAGAGAACATGTGAAAAGCTATCTAATAATTC
131 CAAGAACTAAAATTATTAAAAACGAGAAAAGAAAAGAGAACATGT--AAAGCTATATAATAATTC
* * * * *
507872 AAGCCTAATCCCTCTAGAAACCTCAAGGCATAATTTATTGTGATATAAAATGCAAGTCAGATGTC
194 AACCCTAAGCCCTCTAGAAACCTCAAGGCAAAATTCATTGTGATATAAAATACAAGTCAGATGTC
* *
507937 AGGCTCAAACCCAATTTAACTTAAGAAATAGATAAAAGGAAAAAGATTAAAAAATTCTACCTTTC
259 AGGCCCAAACCCAATTTAACTTAAGAAATAGAT-AAA-GAAAAAGATTAAAAAATTCCACCTTTC
* * * *
508002 TCTCCTCATCAGTACACTCTATGGCATGAGGTCACTGCCAAGCTCATCTCCCCTTTCCCCACCCC
322 TCTCCTCATCACTACACCCTATGGCATGAGGCCACTGCCAAGCTCATCTCCCCTCTCCCCACCCC
508067 CCAAATAAAAATAAAATATAAATTCCCTTCTAATCTCCTCAGTCATTCC
387 CCAAATAAAAATAAAATATAAATTCCCTTCTAATCTCCTCAGTCATTCC
*
508116 TTATTCTTGCTTATGTATCATTGTTTAACTGGGGGAACCTATGTCACTTTGTGAAAAGTACTTCA
1 TTATTCTTGCTTATGTATCATTGTTTAACT--GGGAACCTATGTCACTTTGTGAAAAGGACTTCA
* * *
508181 TGACTTCGATATGGTGCAATAAGTCATTTTAACTTTTTAATTTGGTTTGACCAAGCTGGTTAGGT
64 CGACTTCAAT-TGGTGCAATAAGCCATTTTAACTTTTTAATTTGGTTTGACCAAGCTGGTTAGGT
* * * *
508246 GGCTTAA-AACTAAAATTATTAAAAATGAGAAAAGAAAAGAGAACATGT-TA-CTATATAATAGT
128 GGC-CAAGAACTAAAATTATTAAAAACGAGAAAAGAAAAGAGAACATGTAAAGCTATATAATAAT
* * *
508308 TGAACCCTAAGCCCTGTAGAAATCTCAAGGCAAAATTCATTTGTGATATAAAATACAAGTCAGAT
192 TCAACCCTAAGCCCTCTAGAAACCTCAAGGCAAAATTCA-TTGTGATATAAAATACAAGTCAGAT
* * **
508373 GTCAGGCCCAAACCCAATTTACCTTCAA-AAGTAGAT-AA-CCAAAGATTAAAAAAATTCCACC-
256 GTCAGGCCCAAACCCAATTTAACTT-AAGAAATAGATAAAGAAAAAGATT-AAAAAATTCCACCT
* * ** * *
508434 TTCTCATCAGTACA-CCCTATGCCCTATGGCATGAGGCCACTGCCAAGCTCATTTTCCCTCT-CC
319 TTCTC-TC-CT-CATCACTACACCCTATGGCATGAGGCCACTGCCAAGCTCATCTCCCCTCTCCC
** * *
508497 CACCCCCTTAATAAATAA-ATAAATAAAAATACCCTTCTAATCTCCAT-AGTCAT
381 CACCCCCCAAATAAA-AATA-AAATATAAATTCCCTTCTAATCTCC-TCAGTCAT
508550 GCCAACAACT
Statistics
Matches: 379, Mismatches: 42, Indels: 28
0.84 0.09 0.06
Matches are distributed among these distances:
435 12 0.03
436 30 0.08
437 72 0.19
438 45 0.12
439 85 0.22
440 2 0.01
441 39 0.10
442 92 0.24
443 2 0.01
ACGTcount: A:0.35, C:0.21, G:0.14, T:0.30
Consensus pattern (435 bp):
TTATTCTTGCTTATGTATCATTGTTTAACTGGGAACCTATGTCACTTTGTGAAAAGGACTTCACG
ACTTCAATTGGTGCAATAAGCCATTTTAACTTTTTAATTTGGTTTGACCAAGCTGGTTAGGTGGC
CAAGAACTAAAATTATTAAAAACGAGAAAAGAAAAGAGAACATGTAAAGCTATATAATAATTCAA
CCCTAAGCCCTCTAGAAACCTCAAGGCAAAATTCATTGTGATATAAAATACAAGTCAGATGTCAG
GCCCAAACCCAATTTAACTTAAGAAATAGATAAAGAAAAAGATTAAAAAATTCCACCTTTCTCTC
CTCATCACTACACCCTATGGCATGAGGCCACTGCCAAGCTCATCTCCCCTCTCCCCACCCCCCAA
ATAAAAATAAAATATAAATTCCCTTCTAATCTCCTCAGTCATTCC
Found at i:520411 original size:26 final size:25
Alignment explanation
Indices: 520360--520416 Score: 71
Period size: 26 Copynumber: 2.2 Consensus size: 25
520350 AAGAGGGCAA
*
520360 GAGAGAGAGAGAGTAGGAGAGTGAGG
1 GAGAGAGAGAGAG-AGGAGAGAGAGG
520386 GAGAGAGAGAGAG-GGAGAGGGAGAGG
1 GAGAGAGAGAGAGAGGAGA--GAGAGG
520412 GAGAG
1 GAGAG
520417 TTGACAAGAG
Statistics
Matches: 28, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
24 5 0.18
26 23 0.82
ACGTcount: A:0.39, C:0.00, G:0.58, T:0.04
Consensus pattern (25 bp):
GAGAGAGAGAGAGAGGAGAGAGAGG
Found at i:520431 original size:2 final size:2
Alignment explanation
Indices: 520359--520416 Score: 55
Period size: 2 Copynumber: 29.0 Consensus size: 2
520349 AAAGAGGGCA
* * *
520359 AG AG AG AG AG AG AG TAG -G AG AG TG AG GG AG AG AG AG AG AG GG
1 AG AG AG AG AG AG AG -AG AG AG AG AG AG AG AG AG AG AG AG AG AG
* *
520401 AG AG GG AG AG GG AG AG
1 AG AG AG AG AG AG AG AG
520417 TTGACAAGAG
Statistics
Matches: 44, Mismatches: 10, Indels: 4
0.76 0.17 0.07
Matches are distributed among these distances:
1 1 0.02
2 41 0.93
3 2 0.05
ACGTcount: A:0.40, C:0.00, G:0.57, T:0.03
Consensus pattern (2 bp):
AG
Found at i:520496 original size:22 final size:22
Alignment explanation
Indices: 520466--520510 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 22
520456 GATTGAGAGA
*
520466 GGGCAAGAGAGTGAGACAGAAT
1 GGGCAAGAGAGGGAGACAGAAT
* *
520488 GGGCGAGAGAGGGAGAGAGAAT
1 GGGCAAGAGAGGGAGACAGAAT
520510 G
1 G
520511 AGAGAGTGTG
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.38, C:0.07, G:0.49, T:0.07
Consensus pattern (22 bp):
GGGCAAGAGAGGGAGACAGAAT
Found at i:520636 original size:18 final size:18
Alignment explanation
Indices: 520615--520662 Score: 51
Period size: 18 Copynumber: 2.7 Consensus size: 18
520605 ATATATAGAG
*
520615 AGAGAGAGTGGGCAAGAC
1 AGAGAGAGTGAGCAAGAC
* * * *
520633 AGAGATAGAGAGCAATAT
1 AGAGAGAGTGAGCAAGAC
520651 AGAGAGAGTGAG
1 AGAGAGAGTGAG
520663 AGAGTGGGTG
Statistics
Matches: 23, Mismatches: 7, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
18 23 1.00
ACGTcount: A:0.44, C:0.06, G:0.40, T:0.10
Consensus pattern (18 bp):
AGAGAGAGTGAGCAAGAC
Found at i:520658 original size:22 final size:22
Alignment explanation
Indices: 520585--520666 Score: 60
Period size: 22 Copynumber: 3.7 Consensus size: 22
520575 AGAGTAGGCA
520585 AGACAGAGATAGAGAGCAATAT
1 AGACAGAGATAGAGAGCAATAT
* * * ****
520607 ATATAGAGAGAGAGAGTGGGCA-
1 AGACAGAGATAGAGAG-CAATAT
520629 AGACAGAGATAGAGAGCAATAT
1 AGACAGAGATAGAGAGCAATAT
*
520651 AGAGAGAG-TGAGAGAG
1 AGACAGAGAT-AGAGAG
520667 TGGGTGAAAG
Statistics
Matches: 42, Mismatches: 15, Indels: 6
0.67 0.24 0.10
Matches are distributed among these distances:
21 2 0.05
22 39 0.93
23 1 0.02
ACGTcount: A:0.46, C:0.06, G:0.35, T:0.12
Consensus pattern (22 bp):
AGACAGAGATAGAGAGCAATAT
Found at i:520666 original size:12 final size:12
Alignment explanation
Indices: 520651--520694 Score: 52
Period size: 12 Copynumber: 3.7 Consensus size: 12
520641 AGAGCAATAT
520651 AGAGAGAGTGAG
1 AGAGAGAGTGAG
* * *
520663 AGAGTGGGTGAA
1 AGAGAGAGTGAG
*
520675 AGAGAGTGTGAG
1 AGAGAGAGTGAG
520687 AGAGAGAG
1 AGAGAGAG
520695 AGAGTAGGAG
Statistics
Matches: 25, Mismatches: 7, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
12 25 1.00
ACGTcount: A:0.39, C:0.00, G:0.50, T:0.11
Consensus pattern (12 bp):
AGAGAGAGTGAG
Found at i:520688 original size:44 final size:44
Alignment explanation
Indices: 520570--520670 Score: 166
Period size: 44 Copynumber: 2.3 Consensus size: 44
520560 GAGAGAAAAT
* * *
520570 GAGAGAGAGTAGGCAAGACAGAGATAGAGAGCAATATATATAGA
1 GAGAGAGAGTGGGCAAGACAGAGATAGAGAGCAATATAGAGAGA
520614 GAGAGAGAGTGGGCAAGACAGAGATAGAGAGCAATATAGAGAGA
1 GAGAGAGAGTGGGCAAGACAGAGATAGAGAGCAATATAGAGAGA
*
520658 GTGAGAGAGTGGG
1 GAGAGAGAGTGGG
520671 TGAAAGAGAG
Statistics
Matches: 53, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
44 53 1.00
ACGTcount: A:0.44, C:0.06, G:0.39, T:0.12
Consensus pattern (44 bp):
GAGAGAGAGTGGGCAAGACAGAGATAGAGAGCAATATAGAGAGA
Found at i:520696 original size:32 final size:32
Alignment explanation
Indices: 520652--520737 Score: 111
Period size: 32 Copynumber: 2.7 Consensus size: 32
520642 GAGCAATATA
* *
520652 GAGAGAGTGAGAGAGTGGGTGAAAGAGAGTGT
1 GAGAGAGAGAGAGAGTGGGTGAAAGAGAGAGT
* *
520684 GAGAGAGAGAGAGAGTAGGAGAAAGAGAGAGT
1 GAGAGAGAGAGAGAGTGGGTGAAAGAGAGAGT
*
520716 -AGAAGAGAGATAGAGTGGGTGA
1 GAG-AGAGAGAGAGAGTGGGTGA
520738 GGGGGCTTCC
Statistics
Matches: 46, Mismatches: 7, Indels: 2
0.84 0.13 0.04
Matches are distributed among these distances:
31 2 0.04
32 44 0.96
ACGTcount: A:0.41, C:0.00, G:0.48, T:0.12
Consensus pattern (32 bp):
GAGAGAGAGAGAGAGTGGGTGAAAGAGAGAGT
Found at i:520698 original size:18 final size:18
Alignment explanation
Indices: 520675--520714 Score: 55
Period size: 18 Copynumber: 2.2 Consensus size: 18
520665 AGTGGGTGAA
*
520675 AGAGAGT-GTGAGAGAGAG
1 AGAGAGTAG-GAGAAAGAG
520693 AGAGAGTAGGAGAAAGAG
1 AGAGAGTAGGAGAAAGAG
520711 AGAG
1 AGAG
520715 TAGAAGAGAG
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
18 19 0.95
19 1 0.05
ACGTcount: A:0.45, C:0.00, G:0.47, T:0.07
Consensus pattern (18 bp):
AGAGAGTAGGAGAAAGAG
Found at i:520730 original size:18 final size:17
Alignment explanation
Indices: 520650--520731 Score: 73
Period size: 16 Copynumber: 5.1 Consensus size: 17
520640 GAGAGCAATA
*
520650 TAGAGAGAGTGAGAGAG
1 TAGAGAGAGAGAGAGAG
* * * *
520667 T-GGGTGAAAGAGAGTG
1 TAGAGAGAGAGAGAGAG
520683 T-GAGAGAGAGAGAGAG
1 TAGAGAGAGAGAGAGAG
*
520699 TAG-GAGAAAGAGAGAG
1 TAGAGAGAGAGAGAGAG
*
520715 TAGA-AGAGAGATAGAG
1 TAGAGAGAGAGAGAGAG
520731 T
1 T
520732 GGGTGAGGGG
Statistics
Matches: 51, Mismatches: 12, Indels: 5
0.75 0.18 0.07
Matches are distributed among these distances:
16 49 0.96
17 2 0.04
ACGTcount: A:0.43, C:0.00, G:0.45, T:0.12
Consensus pattern (17 bp):
TAGAGAGAGAGAGAGAG
Found at i:522516 original size:16 final size:16
Alignment explanation
Indices: 522495--522525 Score: 62
Period size: 16 Copynumber: 1.9 Consensus size: 16
522485 TCTTTTACTC
522495 ACACTCTCTCTCTCCT
1 ACACTCTCTCTCTCCT
522511 ACACTCTCTCTCTCC
1 ACACTCTCTCTCTCC
522526 CCTCCACACA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.13, C:0.52, G:0.00, T:0.35
Consensus pattern (16 bp):
ACACTCTCTCTCTCCT
Found at i:522561 original size:14 final size:14
Alignment explanation
Indices: 522542--522588 Score: 58
Period size: 14 Copynumber: 3.2 Consensus size: 14
522532 CACACACACA
522542 CACTCTCTCTCATCC
1 CACTCTCTCTCA-CC
*
522557 ACTCTCTCTCTCACC
1 -CACTCTCTCTCACC
*
522572 CACTCTCTCTTACC
1 CACTCTCTCTCACC
522586 CAC
1 CAC
522589 ACGCATCTCT
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
14 15 0.54
15 2 0.07
16 11 0.39
ACGTcount: A:0.15, C:0.53, G:0.00, T:0.32
Consensus pattern (14 bp):
CACTCTCTCTCACC
Found at i:522565 original size:16 final size:16
Alignment explanation
Indices: 522544--522581 Score: 67
Period size: 16 Copynumber: 2.4 Consensus size: 16
522534 CACACACACA
*
522544 CTCTCTCTCATCCACT
1 CTCTCTCTCACCCACT
522560 CTCTCTCTCACCCACT
1 CTCTCTCTCACCCACT
522576 CTCTCT
1 CTCTCT
522582 TACCCACACG
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
16 21 1.00
ACGTcount: A:0.11, C:0.53, G:0.00, T:0.37
Consensus pattern (16 bp):
CTCTCTCTCACCCACT
Found at i:523265 original size:18 final size:18
Alignment explanation
Indices: 523242--523281 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 18
523232 CTTTCTCTCA
* *
523242 CTCTCTTACCCATTCTAT
1 CTCTCTCACCCATTATAT
*
523260 CTCTCTCCCCCATTATAT
1 CTCTCTCACCCATTATAT
523278 CTCT
1 CTCT
523282 TTCATACTAT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.15, C:0.42, G:0.00, T:0.42
Consensus pattern (18 bp):
CTCTCTCACCCATTATAT
Found at i:523325 original size:30 final size:32
Alignment explanation
Indices: 523291--523351 Score: 90
Period size: 30 Copynumber: 2.0 Consensus size: 32
523281 TTTCATACTA
*
523291 TCCCTCTCTCATTATCTCTCT-A-ATTTTCTC
1 TCCCTATCTCATTATCTCTCTCATATTTTCTC
*
523321 TCCCTATCTCATTCTCTCTCTCATATTTTCT
1 TCCCTATCTCATTATCTCTCTCATATTTTCT
523352 TTATCCCTCT
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
30 19 0.70
31 1 0.04
32 7 0.26
ACGTcount: A:0.13, C:0.36, G:0.00, T:0.51
Consensus pattern (32 bp):
TCCCTATCTCATTATCTCTCTCATATTTTCTC
Found at i:523760 original size:16 final size:16
Alignment explanation
Indices: 523728--523776 Score: 55
Period size: 16 Copynumber: 3.1 Consensus size: 16
523718 TCTTCCCTAT
*
523728 TATCTATTTCCTACTA
1 TATCTATCTCCTACTA
523744 TATCTATCTCC-ATCTA
1 TATCTATCTCCTA-CTA
* *
523760 TTTCTCTCTCCTACTA
1 TATCTATCTCCTACTA
523776 T
1 T
523777 CTCTTTTTAT
Statistics
Matches: 28, Mismatches: 3, Indels: 4
0.80 0.09 0.11
Matches are distributed among these distances:
15 1 0.04
16 26 0.93
17 1 0.04
ACGTcount: A:0.20, C:0.31, G:0.00, T:0.49
Consensus pattern (16 bp):
TATCTATCTCCTACTA
Found at i:523894 original size:2 final size:2
Alignment explanation
Indices: 523889--523961 Score: 67
Period size: 2 Copynumber: 36.5 Consensus size: 2
523879 TTCTCTATTA
* * * *
523889 CT CT CT CT CG CC CT CT CT CT AT CT CT TT CT CT CAT -T CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT C-T CT CT CT CT
* * *
523931 CT CT CT TT CA CT CT CT CT CT GT CT CT CT CT C
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT C
523962 CCACATACTT
Statistics
Matches: 56, Mismatches: 13, Indels: 4
0.77 0.18 0.05
Matches are distributed among these distances:
1 1 0.02
2 54 0.96
3 1 0.02
ACGTcount: A:0.04, C:0.45, G:0.03, T:0.48
Consensus pattern (2 bp):
CT
Found at i:524417 original size:20 final size:22
Alignment explanation
Indices: 524369--524418 Score: 59
Period size: 20 Copynumber: 2.4 Consensus size: 22
524359 TGTACTCTCT
* *
524369 CTTTCTCTGTCACGCACACACT
1 CTTTCTCTGTCACCCACACACA
*
524391 CTCTCTCT-T-ACCCACACACA
1 CTTTCTCTGTCACCCACACACA
524411 CTTTCTCT
1 CTTTCTCT
524419 CATATACTCT
Statistics
Matches: 24, Mismatches: 4, Indels: 2
0.80 0.13 0.07
Matches are distributed among these distances:
20 16 0.67
21 1 0.04
22 7 0.29
ACGTcount: A:0.18, C:0.44, G:0.04, T:0.34
Consensus pattern (22 bp):
CTTTCTCTGTCACCCACACACA
Found at i:525110 original size:38 final size:37
Alignment explanation
Indices: 525068--525154 Score: 106
Period size: 38 Copynumber: 2.3 Consensus size: 37
525058 TTAACCACAT
525068 ACTTTCTCTCTCCCTTCCTC-AGTCTC-TCTCTTACTTAC
1 ACTTTCTCTCTCCCTTCCTCTA-TCTCATCTCTTAC-T-C
*
525106 ACTTTCTCTCTCCTTTCCTCTATCTCTATCTCTTACTC
1 ACTTTCTCTCTCCCTTCCTCTATCTC-ATCTCTTACTC
*
525144 ACATTCTCTCT
1 ACTTTCTCTCT
525155 ATATATCTAT
Statistics
Matches: 44, Mismatches: 2, Indels: 6
0.85 0.04 0.12
Matches are distributed among these distances:
38 34 0.77
39 2 0.05
40 8 0.18
ACGTcount: A:0.11, C:0.40, G:0.01, T:0.47
Consensus pattern (37 bp):
ACTTTCTCTCTCCCTTCCTCTATCTCATCTCTTACTC
Found at i:525468 original size:2 final size:2
Alignment explanation
Indices: 525455--525560 Score: 67
Period size: 2 Copynumber: 53.5 Consensus size: 2
525445 TCTTACTCAT
* * * * * *
525455 TC TC TT TC TC TC TC TC TC GC CC TC TC -C CC TC TG TC TC TA TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
* * * *
525496 TC ATC TC TC TC TC GC -C TA TC TG TC TC TT TC TC TC TC TC T- TC
1 TC -TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
525537 TC TC TC T- TGC TC TAC TC TC TC TC T
1 TC TC TC TC T-C TC T-C TC TC TC TC T
525561 GTTAGCCAAT
Statistics
Matches: 80, Mismatches: 17, Indels: 14
0.72 0.15 0.13
Matches are distributed among these distances:
1 4 0.05
2 71 0.89
3 5 0.06
ACGTcount: A:0.04, C:0.44, G:0.05, T:0.47
Consensus pattern (2 bp):
TC
Found at i:525549 original size:15 final size:14
Alignment explanation
Indices: 525518--525558 Score: 50
Period size: 15 Copynumber: 3.0 Consensus size: 14
525508 CGCCTATCTG
525518 TCTCTT-TCTCTC-
1 TCTCTTCTCTCTCT
525530 TCTCTTCTCTCTCT
1 TCTCTTCTCTCTCT
*
525544 TGCTCTACTCTCTCT
1 T-CTCTTCTCTCTCT
525559 CTGTTAGCCA
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
12 6 0.24
13 6 0.24
14 1 0.04
15 12 0.48
ACGTcount: A:0.02, C:0.41, G:0.02, T:0.54
Consensus pattern (14 bp):
TCTCTTCTCTCTCT
Found at i:525558 original size:36 final size:36
Alignment explanation
Indices: 525463--525562 Score: 103
Period size: 36 Copynumber: 2.7 Consensus size: 36
525453 ATTCTCTTTC
* *
525463 TCTCTCTCTCGCC-CTCTCCCCTCTGTCTCTATCTCA
1 TCTCTCTCTCGCCTATCT-CTCTCTGTCTCTATCTCA
* * * *
525499 TCTCTCTCTCGCCTATCTGTCTCTTTCTCTCTCTCT
1 TCTCTCTCTCGCCTATCTCTCTCTGTCTCTATCTCA
*
525535 TCTCTCTCTTGCTCTACTCTCTCTCTGT
1 TCTCTCTCTCGC-CTA-TCTCTCTCTGT
525563 TAGCCAATCT
Statistics
Matches: 52, Mismatches: 9, Indels: 4
0.80 0.14 0.06
Matches are distributed among these distances:
36 37 0.71
37 6 0.12
38 9 0.17
ACGTcount: A:0.04, C:0.44, G:0.06, T:0.46
Consensus pattern (36 bp):
TCTCTCTCTCGCCTATCTCTCTCTGTCTCTATCTCA
Found at i:526862 original size:16 final size:16
Alignment explanation
Indices: 526843--527000 Score: 79
Period size: 16 Copynumber: 9.7 Consensus size: 16
526833 CTACTATCTC
526843 TCTCTCTCTCTCTCAT
1 TCTCTCTCTCTCTCAT
* * **
526859 TCTCACTCTCTCACCC
1 TCTCTCTCTCTCTCAT
* * *
526875 CCTCTCTCTCTCACAC
1 TCTCTCTCTCTCTCAT
*
526891 ACTCTCTCTCTCTC-T
1 TCTCTCTCTCTCTCAT
* * *
526906 CCTCTTCTCTTTATCTAT
1 TCTC-TCTCTCTCTC-AT
*
526924 T-TC-CTTCTCTCTCTT
1 TCTCTC-TCTCTCTCAT
*
526939 TCTCACACTCTCTCTCAT
1 TCT--CTCTCTCTCTCAT
* * *
526957 TTTATCTCTCTTTCAT
1 TCTCTCTCTCTCTCAT
* *
526973 CTCTTTCTCTATCTCAT
1 -TCTCTCTCTCTCTCAT
526990 TCTCTCTCTCT
1 TCTCTCTCTCT
527001 TGCATCTCTT
Statistics
Matches: 105, Mismatches: 28, Indels: 18
0.70 0.19 0.12
Matches are distributed among these distances:
15 6 0.06
16 71 0.68
17 14 0.13
18 13 0.12
19 1 0.01
ACGTcount: A:0.09, C:0.42, G:0.00, T:0.48
Consensus pattern (16 bp):
TCTCTCTCTCTCTCAT
Found at i:526862 original size:18 final size:18
Alignment explanation
Indices: 526841--527000 Score: 85
Period size: 18 Copynumber: 9.6 Consensus size: 18
526831 TCCTACTATC
526841 TCTCTCTCTCTCTCTCAT
1 TCTCTCTCTCTCTCTCAT
* *
526859 TCTCACTCTCTCAC-C--
1 TCTCTCTCTCTCTCTCAT
* * *
526874 -CCCTCTCTCTCTCACAC
1 TCTCTCTCTCTCTCTCAT
* *
526891 ACTCTCTCTCTCTCTC-C
1 TCTCTCTCTCTCTCTCAT
* *
526908 TCT-TCTCTTTATCT-AT
1 TCTCTCTCTCTCTCTCAT
*
526924 T-TC-CT-TCTCTCTCTT
1 TCTCTCTCTCTCTCTCAT
* *
526939 TCTCACACTCTCTCTCAT
1 TCTCTCTCTCTCTCTCAT
* *
526957 T-T-TATCTCTCTTTCA-
1 TCTCTCTCTCTCTCTCAT
* *
526972 TCTCTTTCTCTATCTCAT
1 TCTCTCTCTCTCTCTCAT
526990 TCTCTCTCTCT
1 TCTCTCTCTCT
527001 TGCATCTCTT
Statistics
Matches: 105, Mismatches: 24, Indels: 26
0.68 0.15 0.17
Matches are distributed among these distances:
14 15 0.14
15 7 0.07
16 22 0.21
17 16 0.15
18 45 0.43
ACGTcount: A:0.09, C:0.42, G:0.00, T:0.48
Consensus pattern (18 bp):
TCTCTCTCTCTCTCTCAT
Found at i:526998 original size:33 final size:33
Alignment explanation
Indices: 526946--527015 Score: 104
Period size: 33 Copynumber: 2.1 Consensus size: 33
526936 CTTTCTCACA
* * *
526946 CTCTCTCTCATTTTATCTCTCTTTCATCTCTTT
1 CTCTATCTCATTCTATCTCTCTTGCATCTCTTT
*
526979 CTCTATCTCATTCTCTCTCTCTTGCATCTCTTT
1 CTCTATCTCATTCTATCTCTCTTGCATCTCTTT
527012 CTCT
1 CTCT
527016 CCCCTTTTTT
Statistics
Matches: 33, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
33 33 1.00
ACGTcount: A:0.09, C:0.36, G:0.01, T:0.54
Consensus pattern (33 bp):
CTCTATCTCATTCTATCTCTCTTGCATCTCTTT
Found at i:527016 original size:2 final size:2
Alignment explanation
Indices: 526825--527000 Score: 71
Period size: 2 Copynumber: 89.5 Consensus size: 2
526815 TCTTATTGTA
* *
526825 TC TC TC TC -C TAC TA TC TC TC TC TC TC TC TC TC AT- TC TC AC TC
1 TC TC TC TC TC T-C TC TC TC TC TC TC TC TC TC TC -TC TC TC TC TC
* * * * * *
526867 TC TC AC CC CC TC TC TC TC TC AC AC AC TC TC TC TC TC TC TC -C
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
* * * * * * *
526908 TC T- TC TC TT TA TC TA TT TC -C T- TC TC TC TC TT TC TC AC AC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
* * * * *
526947 TC TC TC TC AT- TT TA TC TC TC TT TC ATC TC TT TC TC TA TC TC AT-
1 TC TC TC TC -TC TC TC TC TC TC TC TC -TC TC TC TC TC TC TC TC -TC
526990 TC TC TC TC TC T
1 TC TC TC TC TC T
527001 TGCATCTCTT
Statistics
Matches: 134, Mismatches: 27, Indels: 26
0.72 0.14 0.14
Matches are distributed among these distances:
1 8 0.06
2 119 0.89
3 7 0.05
ACGTcount: A:0.10, C:0.43, G:0.00, T:0.48
Consensus pattern (2 bp):
TC
Found at i:527369 original size:2 final size:2
Alignment explanation
Indices: 527364--527388 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
527354 TTCTCTCTCT
527364 CA CA CA CA CA CA CA CA CA CA CA CA C
1 CA CA CA CA CA CA CA CA CA CA CA CA C
527389 TCCCCTCAAT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.52, G:0.00, T:0.00
Consensus pattern (2 bp):
CA
Found at i:527513 original size:20 final size:20
Alignment explanation
Indices: 527485--527527 Score: 68
Period size: 20 Copynumber: 2.1 Consensus size: 20
527475 CTCCCTTTTG
527485 TCCACTTTTTCTATCTCTTA
1 TCCACTTTTTCTATCTCTTA
* *
527505 TCCATTTTTTCTCTCTCTTA
1 TCCACTTTTTCTATCTCTTA
527525 TCC
1 TCC
527528 TCTCACTCTC
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.12, C:0.33, G:0.00, T:0.56
Consensus pattern (20 bp):
TCCACTTTTTCTATCTCTTA
Found at i:527641 original size:19 final size:19
Alignment explanation
Indices: 527617--527677 Score: 60
Period size: 19 Copynumber: 3.4 Consensus size: 19
527607 TCTCACTCCA
527617 ATCTCTCTCGCTTCTCTTT
1 ATCTCTCTCGCTTCTCTTT
*
527636 ATCTCTCT--CTTAC-C--C
1 ATCTCTCTCGCTT-CTCTTT
*
527651 CTCTCTCTCGCTTCTCTTT
1 ATCTCTCTCGCTTCTCTTT
527670 ATCTCTCT
1 ATCTCTCT
527678 TACCCACACT
Statistics
Matches: 32, Mismatches: 4, Indels: 12
0.67 0.08 0.25
Matches are distributed among these distances:
15 7 0.22
16 1 0.03
17 8 0.25
18 1 0.03
19 15 0.47
ACGTcount: A:0.07, C:0.41, G:0.03, T:0.49
Consensus pattern (19 bp):
ATCTCTCTCGCTTCTCTTT
Found at i:527642 original size:17 final size:17
Alignment explanation
Indices: 527620--527676 Score: 62
Period size: 17 Copynumber: 3.4 Consensus size: 17
527610 CACTCCAATC
527620 TCTCTCGCTTCTCTTTA
1 TCTCTCGCTTCTCTTTA
* ** *
527637 TCTCTCTCTTAC-CCCTC
1 TCTCTCGCTT-CTCTTTA
527654 TCTCTCGCTTCTCTTTA
1 TCTCTCGCTTCTCTTTA
527671 TCTCTC
1 TCTCTC
527677 TTACCCACAC
Statistics
Matches: 30, Mismatches: 8, Indels: 4
0.71 0.19 0.10
Matches are distributed among these distances:
16 1 0.03
17 28 0.93
18 1 0.03
ACGTcount: A:0.05, C:0.42, G:0.04, T:0.49
Consensus pattern (17 bp):
TCTCTCGCTTCTCTTTA
Found at i:527678 original size:32 final size:33
Alignment explanation
Indices: 527618--527682 Score: 114
Period size: 34 Copynumber: 2.0 Consensus size: 33
527608 CTCACTCCAA
527618 TCTCTCTCGCTTCTCTTTATCTCTCTCTTACCCC
1 TCTCTCTCGCTTCTCTTTA-CTCTCTCTTACCCC
527652 TCTCTCTCGCTTCTCTTTA-TCTCTCTTACCC
1 TCTCTCTCGCTTCTCTTTACTCTCTCTTACCC
527683 ACACTATCTC
Statistics
Matches: 31, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
32 12 0.39
34 19 0.61
ACGTcount: A:0.06, C:0.43, G:0.03, T:0.48
Consensus pattern (33 bp):
TCTCTCTCGCTTCTCTTTACTCTCTCTTACCCC
Found at i:527783 original size:10 final size:10
Alignment explanation
Indices: 527768--527923 Score: 51
Period size: 10 Copynumber: 15.6 Consensus size: 10
527758 ACACAGGTTT
527768 TCTCTCTCTA
1 TCTCTCTCTA
**
527778 TCTCTCTCCC
1 TCTCTCTCTA
*
527788 TCTCGTCGTCTC
1 TCTC-TC-TCTA
527800 TCTCTC-CTA
1 TCTCTCTCTA
527809 T-TCTCT-TAA
1 TCTCTCTCT-A
*
527818 TATCTCTC-A
1 TCTCTCTCTA
527827 --T-TCTCTA
1 TCTCTCTCTA
* *
527834 TCTCTTTCTG
1 TCTCTCTCTA
* *
527844 TTTCTCCCTA
1 TCTCTCTCTA
*
527854 TCTCTCATACGCA
1 TCTCTC-T-C-TA
* *
527867 CTCACTCTTTA
1 -TCTCTCTCTA
527878 TCTCTCTC-A
1 TCTCTCTCTA
527887 T-TCTCTCTTA
1 TCTCTCTC-TA
*
527897 CTCTCTCTATA
1 -TCTCTCTCTA
*
527908 TGTCTCTCTA
1 TCTCTCTCTA
527918 TCTCTC
1 TCTCTC
527924 GCCCTCTCTC
Statistics
Matches: 106, Mismatches: 22, Indels: 36
0.65 0.13 0.22
Matches are distributed among these distances:
6 4 0.04
7 2 0.02
8 11 0.10
9 9 0.08
10 52 0.49
11 8 0.08
12 13 0.12
13 2 0.02
14 5 0.05
ACGTcount: A:0.12, C:0.38, G:0.03, T:0.47
Consensus pattern (10 bp):
TCTCTCTCTA
Found at i:527931 original size:18 final size:17
Alignment explanation
Indices: 527910--527950 Score: 50
Period size: 16 Copynumber: 2.4 Consensus size: 17
527900 TCTCTATATG
527910 TCTCTCTATCTCTCGCC-C
1 TCTCTCTATC-CTC-CCGC
527928 TCTCTC-ATCCTCCCGC
1 TCTCTCTATCCTCCCGC
527944 TCTCTCT
1 TCTCTCT
527951 CACTCATTTT
Statistics
Matches: 21, Mismatches: 0, Indels: 5
0.81 0.00 0.19
Matches are distributed among these distances:
15 2 0.10
16 10 0.48
17 3 0.14
18 6 0.29
ACGTcount: A:0.05, C:0.51, G:0.05, T:0.39
Consensus pattern (17 bp):
TCTCTCTATCCTCCCGC
Found at i:527951 original size:18 final size:17
Alignment explanation
Indices: 527910--527952 Score: 52
Period size: 18 Copynumber: 2.5 Consensus size: 17
527900 TCTCTATATG
*
527910 TCTCTCT-ATCTCTCGC
1 TCTCTCTCATCTCCCGC
*
527926 CCTCTCTCATCCTCCCGC
1 TCTCTCTCAT-CTCCCGC
527944 TCTCTCTCA
1 TCTCTCTCA
527953 CTCATTTTTG
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
16 6 0.27
17 2 0.09
18 14 0.64
ACGTcount: A:0.07, C:0.51, G:0.05, T:0.37
Consensus pattern (17 bp):
TCTCTCTCATCTCCCGC
Found at i:528119 original size:13 final size:12
Alignment explanation
Indices: 528046--528120 Score: 51
Period size: 12 Copynumber: 6.1 Consensus size: 12
528036 TATCACCCTA
* *
528046 TTTATCTATATG
1 TTTATCTATCTC
* *
528058 TCTATCTCTCTC
1 TTTATCTATCTC
* * *
528070 TCTCTCTCTCTC
1 TTTATCTATCTC
528082 TTTATCTATCTC
1 TTTATCTATCTC
* *
528094 TTTTTTCTCTCTC
1 -TTTATCTATCTC
528107 TTTCATCTATCTC
1 TTT-ATCTATCTC
528120 T
1 T
528121 CATATTCTTT
Statistics
Matches: 49, Mismatches: 12, Indels: 3
0.77 0.19 0.05
Matches are distributed among these distances:
12 31 0.63
13 18 0.37
ACGTcount: A:0.11, C:0.31, G:0.01, T:0.57
Consensus pattern (12 bp):
TTTATCTATCTC
Found at i:528292 original size:12 final size:12
Alignment explanation
Indices: 528261--528285 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
528251 ATCTTTTGCC
528261 CTCTCTCTTTCT
1 CTCTCTCTTTCT
528273 CTCTCTCTTTCT
1 CTCTCTCTTTCT
528285 C
1 C
528286 ATTCTCTCAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.00, C:0.44, G:0.00, T:0.56
Consensus pattern (12 bp):
CTCTCTCTTTCT
Found at i:528412 original size:21 final size:19
Alignment explanation
Indices: 528361--528412 Score: 59
Period size: 21 Copynumber: 2.5 Consensus size: 19
528351 CTTACACAAT
528361 CTCTCTATCTCTCTTGCCC
1 CTCTCTATCTCTCTTGCCC
*
528380 CTCTATCAATCTCTCTATGCCC
1 CTC--TCTATCTCTCT-TGCCC
528402 ACTCTCTATCT
1 -CTCTCTATCT
528413 TTCTCTTTCT
Statistics
Matches: 27, Mismatches: 2, Indels: 6
0.77 0.06 0.17
Matches are distributed among these distances:
19 3 0.11
21 16 0.59
22 5 0.19
23 3 0.11
ACGTcount: A:0.13, C:0.42, G:0.04, T:0.40
Consensus pattern (19 bp):
CTCTCTATCTCTCTTGCCC
Found at i:528601 original size:55 final size:57
Alignment explanation
Indices: 528507--528617 Score: 156
Period size: 55 Copynumber: 2.0 Consensus size: 57
528497 CTCTCCCACA
* * *
528507 TATATTTTCTTTATCTCTCGCTAACACTCTCTCTTACCCC-TCTTTACCTCTCTCATAT
1 TATATTTTCTCTATCTATCGC-AACACACTCTCTTACCCCTTC-TTACCTCTCTCATAT
528565 TATA-TTTCTCTATCTATCGC-ACACACTCTCTTACCCCTTCTTACCTCTCTCAT
1 TATATTTTCTCTATCTATCGCAACACACTCTCTTACCCCTTCTTACCTCTCTCAT
528618 TATCTTATCT
Statistics
Matches: 49, Mismatches: 3, Indels: 5
0.86 0.05 0.09
Matches are distributed among these distances:
55 29 0.59
56 2 0.04
57 14 0.29
58 4 0.08
ACGTcount: A:0.18, C:0.36, G:0.02, T:0.44
Consensus pattern (57 bp):
TATATTTTCTCTATCTATCGCAACACACTCTCTTACCCCTTCTTACCTCTCTCATAT
Found at i:528623 original size:17 final size:17
Alignment explanation
Indices: 528603--528635 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
528593 TCTTACCCCT
528603 TCTTACCTCTCTCATTA
1 TCTTACCTCTCTCATTA
*
528620 TCTTATCTCTCTCATT
1 TCTTACCTCTCTCATT
528636 CTCTCATTCA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.15, C:0.33, G:0.00, T:0.52
Consensus pattern (17 bp):
TCTTACCTCTCTCATTA
Found at i:528727 original size:14 final size:13
Alignment explanation
Indices: 528708--528768 Score: 52
Period size: 14 Copynumber: 4.5 Consensus size: 13
528698 CTCTCTGATA
528708 TCTCTCGCCTACTC
1 TCTCTCGCCT-CTC
*
528722 TCTCTCGCCCTATC
1 TCTCTCG-CCTCTC
*
528736 TGTCTC-CCTCTC
1 TCTCTCGCCTCTC
*
528748 TCATACTCTCCTCTC
1 TC-T-CTCGCCTCTC
528763 TCTCTC
1 TCTCTC
528769 TCTCTTCCTA
Statistics
Matches: 39, Mismatches: 4, Indels: 9
0.75 0.08 0.17
Matches are distributed among these distances:
12 6 0.15
13 4 0.10
14 18 0.46
15 11 0.28
ACGTcount: A:0.07, C:0.49, G:0.05, T:0.39
Consensus pattern (13 bp):
TCTCTCGCCTCTC
Found at i:528991 original size:21 final size:21
Alignment explanation
Indices: 528945--529037 Score: 73
Period size: 21 Copynumber: 4.3 Consensus size: 21
528935 CTCATTCGTT
* * *
528945 TTCTCTCTCGCTATCT-TCTA
1 TTCTCTCTCTCTCTCTCTCTC
528965 TATCTCTCTCTCTCTCTCTCTC
1 T-TCTCTCTCTCTCTCTCTCTC
*
528987 TTCTCTCT-TCGTCTCTCTCAC
1 TTCTCTCTCTC-TCTCTCTCTC
* *
529008 TCTCACTCTCATCTCACTCTCTC
1 T-TCTCTCTC-TCTCTCTCTCTC
529031 TTGCTCT
1 TT-CTCT
529038 TATCACGCTA
Statistics
Matches: 58, Mismatches: 8, Indels: 11
0.75 0.10 0.14
Matches are distributed among these distances:
20 3 0.05
21 30 0.52
22 11 0.19
23 12 0.21
24 2 0.03
ACGTcount: A:0.08, C:0.42, G:0.03, T:0.47
Consensus pattern (21 bp):
TTCTCTCTCTCTCTCTCTCTC
Found at i:529070 original size:17 final size:17
Alignment explanation
Indices: 528999--529072 Score: 53
Period size: 17 Copynumber: 4.3 Consensus size: 17
528989 CTCTCTTCGT
* *
528999 CTCTCTCACTCTCACT-
1 CTCTCACACTCTCTCTG
*
529015 CTCATCTCACTCTCTCTTG
1 CTC-TCACACTCTCTC-TG
* * *
529034 CTCTTATCACGCTATC-G
1 CTCTCA-CACTCTCTCTG
529051 CTCTCACACTCTCTCTG
1 CTCTCACACTCTCTCTG
529068 CTCTC
1 CTCTC
529073 TCTCTCTCAC
Statistics
Matches: 45, Mismatches: 8, Indels: 9
0.73 0.13 0.15
Matches are distributed among these distances:
16 10 0.22
17 23 0.51
18 2 0.04
19 10 0.22
ACGTcount: A:0.12, C:0.45, G:0.05, T:0.38
Consensus pattern (17 bp):
CTCTCACACTCTCTCTG
Found at i:529093 original size:2 final size:2
Alignment explanation
Indices: 528967--529080 Score: 74
Period size: 2 Copynumber: 57.0 Consensus size: 2
528957 ATCTTCTATA
*
528967 TC TC TC TC TC TC TC TC TC TC T- TC TC TC T- TC GTC TC TC TC AC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC -TC TC TC TC TC
* * * * * *
529008 TC TC AC TC TC ATC TC AC TC TC TC T- TGC TC T- TA TC AC GC TA TC
1 TC TC TC TC TC -TC TC TC TC TC TC TC T-C TC TC TC TC TC TC TC TC
* * *
529050 GC TC TC AC AC TC TC TC TGC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC T-C TC TC TC TC TC TC
529081 ACTATTTCTC
Statistics
Matches: 88, Mismatches: 16, Indels: 16
0.73 0.13 0.13
Matches are distributed among these distances:
1 4 0.05
2 77 0.88
3 7 0.08
ACGTcount: A:0.08, C:0.45, G:0.04, T:0.43
Consensus pattern (2 bp):
TC
Found at i:529133 original size:25 final size:25
Alignment explanation
Indices: 529087--529154 Score: 84
Period size: 25 Copynumber: 2.7 Consensus size: 25
529077 TCTCACTATT
*
529087 TCTCTCTGGATCCGCTCATGCTCTC
1 TCTCTCTCGATCCGCTCATGCTCTC
*
529112 TCTTCTCTCGA-CCGCTCCTGCTCTC
1 TC-TCTCTCGATCCGCTCATGCTCTC
*
529137 TCTCTCTCGCTCCCGCTC
1 TCTCTCTCGAT-CCGCTC
529155 TTTATCTCTC
Statistics
Matches: 37, Mismatches: 3, Indels: 5
0.82 0.07 0.11
Matches are distributed among these distances:
24 7 0.19
25 17 0.46
26 13 0.35
ACGTcount: A:0.04, C:0.47, G:0.13, T:0.35
Consensus pattern (25 bp):
TCTCTCTCGATCCGCTCATGCTCTC
Found at i:529147 original size:20 final size:19
Alignment explanation
Indices: 529124--529179 Score: 60
Period size: 20 Copynumber: 2.9 Consensus size: 19
529114 TTCTCTCGAC
529124 CGCTCCTGCTCTCTCTCTCT
1 CGCTCC-GCTCTCTCTCTCT
* *
529144 CGCTCCCGCTCTTTATCTCT
1 CGCT-CCGCTCTCTCTCTCT
*
529164 CGC-CCGCTCTCGCTCT
1 CGCTCCGCTCTCTCTCT
529180 TTATCTCTCG
Statistics
Matches: 30, Mismatches: 5, Indels: 4
0.77 0.13 0.10
Matches are distributed among these distances:
18 10 0.33
20 18 0.60
21 2 0.07
ACGTcount: A:0.02, C:0.50, G:0.12, T:0.36
Consensus pattern (19 bp):
CGCTCCGCTCTCTCTCTCT
Found at i:529162 original size:24 final size:24
Alignment explanation
Indices: 529135--529198 Score: 92
Period size: 24 Copynumber: 2.7 Consensus size: 24
529125 GCTCCTGCTC
*
529135 TCTCTCTCTCGCTCCCGCTCTTTA
1 TCTCTCGCTCGCTCCCGCTCTTTA
* *
529159 TCTCTCGCCCGCTCTCGCTCTTTA
1 TCTCTCGCTCGCTCCCGCTCTTTA
*
529183 TCTCTCGCTCTCTCCC
1 TCTCTCGCTCGCTCCC
529199 ACACACTCTC
Statistics
Matches: 34, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
24 34 1.00
ACGTcount: A:0.03, C:0.48, G:0.09, T:0.39
Consensus pattern (24 bp):
TCTCTCGCTCGCTCCCGCTCTTTA
Found at i:529225 original size:16 final size:16
Alignment explanation
Indices: 529206--529244 Score: 51
Period size: 16 Copynumber: 2.4 Consensus size: 16
529196 CCCACACACT
* *
529206 CTCTCTCGCTTTATCC
1 CTCTCTCACTATATCC
*
529222 CTCTCTCACTATATCG
1 CTCTCTCACTATATCC
529238 CTCTCTC
1 CTCTCTC
529245 TCTCACCACA
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:0.10, C:0.44, G:0.05, T:0.41
Consensus pattern (16 bp):
CTCTCTCACTATATCC
Found at i:533422 original size:30 final size:29
Alignment explanation
Indices: 533384--533448 Score: 78
Period size: 30 Copynumber: 2.2 Consensus size: 29
533374 ATCACAAATA
*
533384 TTTAATTTA-ATTTAATTTAATTAAATAAT
1 TTTAATTTATA-TTAATATAATTAAATAAT
* *
533413 TTTATATTTATATTACTATCATTAAATAAT
1 TTTA-ATTTATATTAATATAATTAAATAAT
533443 TTTAAT
1 TTTAAT
533449 GAAAGAAAAT
Statistics
Matches: 31, Mismatches: 3, Indels: 4
0.82 0.08 0.11
Matches are distributed among these distances:
29 6 0.19
30 24 0.77
31 1 0.03
ACGTcount: A:0.42, C:0.03, G:0.00, T:0.55
Consensus pattern (29 bp):
TTTAATTTATATTAATATAATTAAATAAT
Found at i:537497 original size:35 final size:35
Alignment explanation
Indices: 537458--537562 Score: 95
Period size: 35 Copynumber: 3.0 Consensus size: 35
537448 ATACGTAATG
537458 AATTACCAATTCGATCAGTCTGAACCTATATAAGA
1 AATTACCAATTCGATCAGTCTGAACCTATATAAGA
** * * * *
537493 AATTACTTATTTGATCGAG-CTGAACCTGTCGTAAGG
1 AATTACCAATTCGATC-AGTCTGAACCTAT-ATAAGA
* * * *
537529 AATTACCAGTTCTATCGGTCTGAACTTATATAAG
1 AATTACCAATTCGATCAGTCTGAACCTATATAAG
537563 GAGTTATCAG
Statistics
Matches: 52, Mismatches: 15, Indels: 6
0.71 0.21 0.08
Matches are distributed among these distances:
35 27 0.52
36 25 0.48
ACGTcount: A:0.33, C:0.18, G:0.16, T:0.32
Consensus pattern (35 bp):
AATTACCAATTCGATCAGTCTGAACCTATATAAGA
Found at i:537581 original size:71 final size:71
Alignment explanation
Indices: 537451--537591 Score: 176
Period size: 71 Copynumber: 2.0 Consensus size: 71
537441 ACCTTAGATA
* * *
537451 CGTAATGAATTACCAATTCGATCAGTCTGAACCTATATAAGAAATTACTTATTTGATCGAGCTGA
1 CGTAAGGAATTACCAATTCGATCAGTCTGAACCTATATAAGAAATTACTCATTTAATCGAGCTGA
537516 ACCTGT
66 ACCTGT
* * * * * * *
537522 CGTAAGGAATTACCAGTTCTATCGGTCTGAACTTATATAAGGAGTTA-TCAGTTTAATCGAGTTG
1 CGTAAGGAATTACCAATTCGATCAGTCTGAACCTATATAAGAAATTACTCA-TTTAATCGAGCTG
537586 AACCTG
65 AACCTG
537592 CAAAGACTTT
Statistics
Matches: 59, Mismatches: 10, Indels: 2
0.83 0.14 0.03
Matches are distributed among these distances:
70 2 0.03
71 57 0.97
ACGTcount: A:0.32, C:0.17, G:0.18, T:0.33
Consensus pattern (71 bp):
CGTAAGGAATTACCAATTCGATCAGTCTGAACCTATATAAGAAATTACTCATTTAATCGAGCTGA
ACCTGT
Found at i:540841 original size:5 final size:5
Alignment explanation
Indices: 540831--540855 Score: 50
Period size: 5 Copynumber: 5.0 Consensus size: 5
540821 TAAGCTCGTC
540831 CCCCT CCCCT CCCCT CCCCT CCCCT
1 CCCCT CCCCT CCCCT CCCCT CCCCT
540856 TAACTTGGGT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 20 1.00
ACGTcount: A:0.00, C:0.80, G:0.00, T:0.20
Consensus pattern (5 bp):
CCCCT
Found at i:550624 original size:136 final size:140
Alignment explanation
Indices: 550375--550637 Score: 354
Period size: 136 Copynumber: 1.9 Consensus size: 140
550365 GTGTTTGGGA
* * *** *
550375 CATGGGTATTTTAAGAAATATGATGAGTTTGAGCAACATTAGCTCAAGATTCATCACCTATGTAT
1 CATGGGTATTTTAAGAAAAATGAAGAGTTTGAGCAACATTAGAAAAAGATACATCACCTA-GTAT
* * * * *
550440 ATGTAAATGTTTAACTTGCTTGGCTTCTCGTGAAGATAATTGAGTAGGGTCTGATGAAAAATAAA
65 ATGTAAATGTTTAACTTGCCTGGCTTCTCATGAAGAGAATGGAGTAGGGCCTGATGAAAAATAAA
550505 CGAGTTTCGGT
130 CGAGTTTCGGT
* * *
550516 CATGGGTATTTTAAGAAAAATGAAGAGTTTGAGCAACA-TAGAAAAATATACAT-GCC-A-TCTA
1 CATGGGTATTTTAAGAAAAATGAAGAGTTTGAGCAACATTAGAAAAAGATACATCACCTAGTATA
*
550577 TGTAAATGTTTAACTTGCCTGGCTTCTCATGAAGAGAATGGAGTAGGGCCTGTTGAAAAAT
66 TGTAAATGTTTAACTTGCCTGGCTTCTCATGAAGAGAATGGAGTAGGGCCTGATGAAAAAT
550638 GAAGTGATAG
Statistics
Matches: 107, Mismatches: 15, Indels: 5
0.84 0.12 0.04
Matches are distributed among these distances:
136 58 0.54
138 1 0.01
139 2 0.02
140 10 0.09
141 36 0.34
ACGTcount: A:0.34, C:0.12, G:0.22, T:0.32
Consensus pattern (140 bp):
CATGGGTATTTTAAGAAAAATGAAGAGTTTGAGCAACATTAGAAAAAGATACATCACCTAGTATA
TGTAAATGTTTAACTTGCCTGGCTTCTCATGAAGAGAATGGAGTAGGGCCTGATGAAAAATAAAC
GAGTTTCGGT
Found at i:555480 original size:23 final size:23
Alignment explanation
Indices: 555454--555501 Score: 69
Period size: 23 Copynumber: 2.1 Consensus size: 23
555444 ATAAAGTACA
*
555454 ATAACATACTAGGTAGCGCTTAT
1 ATAACATAATAGGTAGCGCTTAT
**
555477 ATAATGTAATAGGTAGCGCTTAT
1 ATAACATAATAGGTAGCGCTTAT
555500 AT
1 AT
555502 TTACCTATTT
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
23 22 1.00
ACGTcount: A:0.35, C:0.12, G:0.19, T:0.33
Consensus pattern (23 bp):
ATAACATAATAGGTAGCGCTTAT
Found at i:560144 original size:3 final size:3
Alignment explanation
Indices: 560136--560220 Score: 75
Period size: 3 Copynumber: 29.0 Consensus size: 3
560126 ACTTGTTTGG
* **
560136 ATC ATC ATC -TC ATC ATC ATC ATC ATC ATC GTC ATC ATC -TC ATC GCC
1 ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC
* * * * * *
560182 AGC TTC ATC GTC ATC ATC GTC ATC ATC GTC ATC TTC ATC
1 ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC
560221 GTCAGCTTCA
Statistics
Matches: 63, Mismatches: 17, Indels: 4
0.75 0.20 0.05
Matches are distributed among these distances:
2 4 0.06
3 59 0.94
ACGTcount: A:0.24, C:0.35, G:0.07, T:0.34
Consensus pattern (3 bp):
ATC
Found at i:560221 original size:12 final size:12
Alignment explanation
Indices: 560148--560232 Score: 65
Period size: 12 Copynumber: 7.4 Consensus size: 12
560138 CATCATCTCA
* *
560148 TCATCATCATCA
1 TCATCGTCATCT
560160 TCATCGTCATCAT
1 TCATCGTCATC-T
* *
560173 CTCATCGCCAGCT
1 -TCATCGTCATCT
560186 TCATCGTCA---
1 TCATCGTCATCT
560195 TCATCGTCA---
1 TCATCGTCATCT
560204 TCATCGTCATCT
1 TCATCGTCATCT
*
560216 TCATCGTCAGCT
1 TCATCGTCATCT
560228 TCATC
1 TCATC
560233 TTCTGCGACC
Statistics
Matches: 62, Mismatches: 6, Indels: 10
0.79 0.08 0.13
Matches are distributed among these distances:
9 18 0.29
12 34 0.55
13 1 0.02
14 9 0.15
ACGTcount: A:0.21, C:0.35, G:0.09, T:0.34
Consensus pattern (12 bp):
TCATCGTCATCT
Found at i:560231 original size:18 final size:18
Alignment explanation
Indices: 560169--560235 Score: 55
Period size: 21 Copynumber: 3.4 Consensus size: 18
560159 ATCATCGTCA
*
560169 TCATC-TCATCGCCAGCT
1 TCATCTTCATCGTCAGCT
*
560186 TCATCGTCATCATCGTCATCAT
1 TCATC-T--TCATCGTCAGC-T
560208 CGTCATCTTCATCGTCAGCT
1 --TCATCTTCATCGTCAGCT
560228 TCATCTTC
1 TCATCTTC
560236 TGCGACCGCT
Statistics
Matches: 40, Mismatches: 3, Indels: 13
0.71 0.05 0.23
Matches are distributed among these distances:
17 5 0.12
18 8 0.20
20 1 0.03
21 19 0.47
22 1 0.03
23 1 0.03
24 5 0.12
ACGTcount: A:0.18, C:0.36, G:0.10, T:0.36
Consensus pattern (18 bp):
TCATCTTCATCGTCAGCT
Found at i:562201 original size:190 final size:196
Alignment explanation
Indices: 561682--562629 Score: 1483
Period size: 190 Copynumber: 4.9 Consensus size: 196
561672 TTTAAATTAG
*
561682 TATCGACACAAAATATATTAGTGTCGACACATTATTTAGACATATTCTCTCATAAAACCGGTATA
1 TATCGACACAAAA-CTATTAGTGTCGACACATTATTTAGACATATTCTCTCATAAAACCGGTATA
561747 ATTGTACC-G-TAGATTGAAAATTACATATTACATTATACTTTTGGGTTCGATGA-TTTGGGATC
65 ATTGTACCGGTTAGATTGAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGATC
* ** *
561809 GACAC-TTTATATATGGATCGACAC-TTATGGGTGCACCCTGTTTTCCATTCATTCTGGAAAAAA
130 GACACTTTTATATATGGATCGACACTTTATGGGTGCACCTTGTTTTTAATTCATTCTGAAAAAAA
561872 AA
195 AA
*
561874 -ATCGACAC-AAACTATATTAGTGTCG--ACATTATTTAGACATATCCTCTCATAAAACCGGTAT
1 TATCGACACAAAAC--TATTAGTGTCGACACATTATTTAGACATATTCTCTCATAAAACCGGTAT
561935 AATTGTACCGGTTAGATTGAAAAATTACATATTA-ATTATACTTTTGGGTTCGATGATTTTGGGA
64 AATTGTACCGGTTAGATTG-AAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGA
561999 TCGACACTTTTATATATGGATCGACACTTTATGGGTGCACCTTGTTTTTAATTCATTCTGAAAAA
128 TCGACACTTTTATATATGGATCGACACTTTATGGGTGCACCTTGTTTTTAATTCATTCTGAAAAA
562064 AAAA
193 AAAA
562068 TATCGACACAAAACTATTAGTGTCGACACATTATTTAGACATATTCTCTCA-AAAACC-GTATAA
1 TATCGACACAAAACTATTAGTGTCGACACATTATTTAGACATATTCTCTCATAAAACCGGTATAA
*
562131 -TGTACCGGTT-GATT-AAGATTACATA-TACATTATACTTTTGGGTTCGATGATTTTGGGATCG
66 TTGTACCGGTTAGATTGAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGATCG
562192 ACACTTTTATATATGGATCGACACTTTATGGGTGCACCTTGTTTTTAATTCATTCTGGAAAAAAA
131 ACACTTTTATATATGGATCGACACTTTATGGGTGCACCTTGTTTTTAATTCATTCT-G-AAAAAA
562257 AAA
194 AAA
*
562260 TATCGACACAACTA-TATTAGTGTCGACACATTA-TTAGACATATTCTCTCATAAAACCGGTATA
1 TATCGACACAA-AACTATTAGTGTCGACACATTATTTAGACATATTCTCTCATAAAACCGGTATA
562323 ATTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGGA
65 ATTGTACCGGTTAGATTG-AAAATTACATATTACATTATACTTTTGGGTTCGATGATTTT-GGGA
*
562388 TCGACACTTTTTATATATGGATCGACACTTTATGGGTGCACCTTGTTTTTAATTCATTCTGGAAA
128 TCGACAC-TTTTATATATGGATCGACACTTTATGGGTGCACCTTGTTTTTAATTCATTCTGAAAA
562453 AAAAA
192 AAAAA
562458 TATCGACAC-AAACTATATTAGTGTCGACACATTA-TTAGACATATTCTCTCATAAAAACC-GTA
1 TATCGACACAAAAC--TATTAGTGTCGACACATTATTTAGACATATTCTCTCAT-AAAACCGGTA
* *
562520 TAA-T-TACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGTTTCGATGTTTTTGGG
63 TAATTGTACCGGTTAGATTG-AAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGG
* * *
562583 ATTGACACTTTTTTATATGGATCGACACTTTATGGGTGCACCCTGTT
127 ATCGACACTTTTATATATGGATCGACACTTTATGGGTGCACCTTGTT
562630 GGCCATATTG
Statistics
Matches: 710, Mismatches: 17, Indels: 55
0.91 0.02 0.07
Matches are distributed among these distances:
189 46 0.06
190 103 0.15
191 66 0.09
192 77 0.11
193 36 0.05
194 64 0.09
195 55 0.08
196 38 0.05
197 65 0.09
198 47 0.07
199 55 0.08
200 58 0.08
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (196 bp):
TATCGACACAAAACTATTAGTGTCGACACATTATTTAGACATATTCTCTCATAAAACCGGTATAA
TTGTACCGGTTAGATTGAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGATCG
ACACTTTTATATATGGATCGACACTTTATGGGTGCACCTTGTTTTTAATTCATTCTGAAAAAAAA
A
Found at i:564584 original size:33 final size:33
Alignment explanation
Indices: 564547--564612 Score: 96
Period size: 33 Copynumber: 2.0 Consensus size: 33
564537 CATCTTAATA
*
564547 TCACCCCTTAACACCGAAACTTCTTTCACCACT
1 TCACCCCTCAACACCGAAACTTCTTTCACCACT
***
564580 TCACCCCTCAACACCTCTACTTCTTTCACCACT
1 TCACCCCTCAACACCGAAACTTCTTTCACCACT
564613 CCATCTATTT
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
33 29 1.00
ACGTcount: A:0.24, C:0.45, G:0.02, T:0.29
Consensus pattern (33 bp):
TCACCCCTCAACACCGAAACTTCTTTCACCACT
Found at i:566892 original size:17 final size:18
Alignment explanation
Indices: 566870--566911 Score: 68
Period size: 19 Copynumber: 2.3 Consensus size: 18
566860 ATATATCCGG
566870 TATCATT-TTACCGGTTT
1 TATCATTGTTACCGGTTT
566887 TATCATTTGTTACCGGTTT
1 TATCA-TTGTTACCGGTTT
566906 TATCAT
1 TATCAT
566912 ATTTTTACCT
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
17 5 0.22
18 3 0.13
19 15 0.65
ACGTcount: A:0.19, C:0.17, G:0.12, T:0.52
Consensus pattern (18 bp):
TATCATTGTTACCGGTTT
Done.