Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008016.1 Hibiscus syriacus cultivar Beakdansim tig00110482_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: 5469637
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 14 of 25
Found at i:2997389 original size:20 final size:20
Alignment explanation
Indices: 2997357--2997407 Score: 77
Period size: 20 Copynumber: 2.6 Consensus size: 20
2997347 TATAAACTAT
2997357 ATAGTAT-TATAGTTTATAC
1 ATAGTATATATAGTTTATAC
*
2997376 ATGGTATATATAGTTTATAC
1 ATAGTATATATAGTTTATAC
*
2997396 ATAATATATATA
1 ATAGTATATATA
2997408 TATAAACTAT
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
19 6 0.21
20 22 0.79
ACGTcount: A:0.41, C:0.04, G:0.10, T:0.45
Consensus pattern (20 bp):
ATAGTATATATAGTTTATAC
Found at i:2997427 original size:22 final size:19
Alignment explanation
Indices: 2997402--2997470 Score: 70
Period size: 22 Copynumber: 3.5 Consensus size: 19
2997392 ATACATAATA
2997402 TATATATATAAACTATACAGTT
1 TATATATATAAACTATAC---T
2997424 TATATATATAATACATATACT
1 TATATATATAA-AC-TATACT
2997445 T-TATATATAAACTATA-T
1 TATATATATAAACTATACT
*
2997462 TATTTATAT
1 TATATATAT
2997471 TATATATATA
Statistics
Matches: 43, Mismatches: 1, Indels: 10
0.80 0.02 0.19
Matches are distributed among these distances:
17 2 0.05
18 10 0.23
19 2 0.05
20 9 0.21
21 2 0.05
22 11 0.26
23 2 0.05
24 5 0.12
ACGTcount: A:0.45, C:0.07, G:0.01, T:0.46
Consensus pattern (19 bp):
TATATATATAAACTATACT
Found at i:2997468 original size:42 final size:44
Alignment explanation
Indices: 2997391--2997485 Score: 117
Period size: 42 Copynumber: 2.2 Consensus size: 44
2997381 ATATATAGTT
*
2997391 TATACATAATA-TATATATATAAACTATACAGTTTATA-TATATA
1 TATACAT-ATACTTTATATATAAACTATACAGTTTATATTATATA
*
2997434 -ATACATATACTTTATATATAAACTATATTA-TTTATATTATATA
1 TATACATATACTTTATATATAAACTATA-CAGTTTATATTATATA
*
2997477 TATATATAT
1 TATACATAT
2997486 TAGTTGTTTT
Statistics
Matches: 45, Mismatches: 3, Indels: 7
0.82 0.05 0.13
Matches are distributed among these distances:
41 3 0.07
42 28 0.62
43 7 0.16
44 7 0.16
ACGTcount: A:0.46, C:0.06, G:0.01, T:0.46
Consensus pattern (44 bp):
TATACATATACTTTATATATAAACTATACAGTTTATATTATATA
Found at i:2999881 original size:15 final size:14
Alignment explanation
Indices: 2999861--2999893 Score: 50
Period size: 13 Copynumber: 2.4 Consensus size: 14
2999851 TTTTAAATAT
2999861 ATAATTTTATTTTAA
1 ATAATTTT-TTTTAA
2999876 ATAA-TTTTTTTAA
1 ATAATTTTTTTTAA
2999889 ATAAT
1 ATAAT
2999894 CAAAACGTGA
Statistics
Matches: 17, Mismatches: 0, Indels: 3
0.85 0.00 0.15
Matches are distributed among these distances:
13 10 0.59
14 3 0.18
15 4 0.24
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (14 bp):
ATAATTTTTTTTAA
Found at i:3003519 original size:123 final size:123
Alignment explanation
Indices: 3003300--3003545 Score: 492
Period size: 123 Copynumber: 2.0 Consensus size: 123
3003290 AAATCCAAAG
3003300 GGTCAATCATATCATATGTTGATTATTGATTAAAGCTGTATAAGAACTGTCGATGATTTATGATA
1 GGTCAATCATATCATATGTTGATTATTGATTAAAGCTGTATAAGAACTGTCGATGATTTATGATA
3003365 AGCTCTACCTGAATGGATTTCACTCCTGGCCCCTGGGAAAAACTCGATCATCAAGACT
66 AGCTCTACCTGAATGGATTTCACTCCTGGCCCCTGGGAAAAACTCGATCATCAAGACT
3003423 GGTCAATCATATCATATGTTGATTATTGATTAAAGCTGTATAAGAACTGTCGATGATTTATGATA
1 GGTCAATCATATCATATGTTGATTATTGATTAAAGCTGTATAAGAACTGTCGATGATTTATGATA
3003488 AGCTCTACCTGAATGGATTTCACTCCTGGCCCCTGGGAAAAACTCGATCATCAAGACT
66 AGCTCTACCTGAATGGATTTCACTCCTGGCCCCTGGGAAAAACTCGATCATCAAGACT
3003546 CTGTTAATGT
Statistics
Matches: 123, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
123 123 1.00
ACGTcount: A:0.31, C:0.19, G:0.19, T:0.32
Consensus pattern (123 bp):
GGTCAATCATATCATATGTTGATTATTGATTAAAGCTGTATAAGAACTGTCGATGATTTATGATA
AGCTCTACCTGAATGGATTTCACTCCTGGCCCCTGGGAAAAACTCGATCATCAAGACT
Found at i:3004554 original size:20 final size:18
Alignment explanation
Indices: 3004524--3004585 Score: 63
Period size: 20 Copynumber: 3.3 Consensus size: 18
3004514 CAAAGGAATG
*
3004524 AAAATAAAAAATATAAAT
1 AAAAAAAAAAATATAAAT
*
3004542 CAAAGAAAAAAAAT-GAAAT
1 -AAA-AAAAAAAATATAAAT
3004561 AAAAAATAAAAATATTAAAT
1 AAAAAA-AAAAATA-TAAAT
3004581 AAAAA
1 AAAAA
3004586 TTTCAGGGAA
Statistics
Matches: 36, Mismatches: 3, Indels: 7
0.78 0.07 0.15
Matches are distributed among these distances:
17 3 0.08
18 9 0.25
19 7 0.19
20 17 0.47
ACGTcount: A:0.77, C:0.02, G:0.03, T:0.18
Consensus pattern (18 bp):
AAAAAAAAAAATATAAAT
Found at i:3004630 original size:20 final size:19
Alignment explanation
Indices: 3004601--3004640 Score: 53
Period size: 20 Copynumber: 2.1 Consensus size: 19
3004591 GGGAAATAAG
*
3004601 ATAAAAAAAAGAAAAAATA
1 ATAAAAAAAACAAAAAATA
*
3004620 ATAATAAAAAACAAAACATA
1 ATAA-AAAAAACAAAAAATA
3004640 A
1 A
3004641 GGGGAAAAAT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
19 4 0.22
20 14 0.78
ACGTcount: A:0.80, C:0.05, G:0.03, T:0.12
Consensus pattern (19 bp):
ATAAAAAAAACAAAAAATA
Found at i:3006087 original size:37 final size:37
Alignment explanation
Indices: 3005852--3006092 Score: 253
Period size: 36 Copynumber: 6.5 Consensus size: 37
3005842 TTAAAAAAAA
* *
3005852 TAAAAATTATATATTATATATATGTTTTCAAAATGTTT
1 TAAAAACTATATATTATATATA-GTTTTCAAAATGATT
3005890 TAAAAAACTATATATTATATA-AGTTTTCAAAATGATT
1 T-AAAAACTATATATTATATATAGTTTTCAAAATGATT
* *
3005927 TAAAAACTATATATTATATA-AGTTTTGAAAATAATT
1 TAAAAACTATATATTATATATAGTTTTCAAAATGATT
* *
3005963 TCAAAACTATATATTATATAT-TTTTTCAAAAT-ATT
1 TAAAAACTATATATTATATATAGTTTTCAAAATGATT
*
3005998 TGAAAAA-TATATTATATATATATA-TATATTCAAAATGTTT
1 T-AAAAACTATA-TAT-TATATATAGT-T-TTCAAAATGATT
* *
3006038 TAAAAACCATATATTATATATA-TTTTCAAAAATCATT
1 TAAAAACTATATATTATATATAGTTTTC-AAAATGATT
** *
3006075 TGCAAACTATATAATATA
1 TAAAAACTATATATTATA
3006093 AAATATATAT
Statistics
Matches: 176, Mismatches: 16, Indels: 23
0.82 0.07 0.11
Matches are distributed among these distances:
35 8 0.05
36 71 0.40
37 45 0.26
38 12 0.07
39 34 0.19
40 6 0.03
ACGTcount: A:0.47, C:0.06, G:0.04, T:0.44
Consensus pattern (37 bp):
TAAAAACTATATATTATATATAGTTTTCAAAATGATT
Found at i:3009877 original size:19 final size:20
Alignment explanation
Indices: 3009839--3009879 Score: 57
Period size: 19 Copynumber: 2.1 Consensus size: 20
3009829 TCAACTCAAC
*
3009839 CCAGTTCAGTTCTAACTGGA
1 CCAGTTCAGATCTAACTGGA
*
3009859 CCAGTTCA-ATCTTACTGGA
1 CCAGTTCAGATCTAACTGGA
3009878 CC
1 CC
3009880 GGCTGGAGAG
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
19 11 0.58
20 8 0.42
ACGTcount: A:0.24, C:0.29, G:0.17, T:0.29
Consensus pattern (20 bp):
CCAGTTCAGATCTAACTGGA
Found at i:3010764 original size:51 final size:50
Alignment explanation
Indices: 3010707--3010814 Score: 162
Period size: 51 Copynumber: 2.1 Consensus size: 50
3010697 TGAGAGATGT
*
3010707 ACATACTTACACCGATATAAGTATGTACACCTCTCAACCTTAAAAATAAAC
1 ACATACTTACACCGATATAAGTATGTACACCTCCCAACC-TAAAAATAAAC
* * * *
3010758 ATATACTTACACCGGTGTAAGTATGTACATCTCCCAACCTAAAAATAAAC
1 ACATACTTACACCGATATAAGTATGTACACCTCCCAACCTAAAAATAAAC
3010808 ACATACT
1 ACATACT
3010815 AACTATGTAT
Statistics
Matches: 51, Mismatches: 6, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
50 17 0.33
51 34 0.67
ACGTcount: A:0.42, C:0.25, G:0.07, T:0.26
Consensus pattern (50 bp):
ACATACTTACACCGATATAAGTATGTACACCTCCCAACCTAAAAATAAAC
Found at i:3011087 original size:17 final size:16
Alignment explanation
Indices: 3011065--3011097 Score: 57
Period size: 17 Copynumber: 2.0 Consensus size: 16
3011055 AATATTTTTA
3011065 ATAATATTTTAAATAAT
1 ATAATATTTT-AATAAT
3011082 ATAATATTTTAATAAT
1 ATAATATTTTAATAAT
3011098 TTTATTTTTA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 6 0.38
17 10 0.62
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (16 bp):
ATAATATTTTAATAAT
Found at i:3020906 original size:35 final size:35
Alignment explanation
Indices: 3020855--3020926 Score: 90
Period size: 35 Copynumber: 2.1 Consensus size: 35
3020845 GTTAAAATTT
* ** *
3020855 ATATTAATATACTAAATTAGAAGTAGGGCCTATAA
1 ATATTAATAAACTAAATTAGAAACAGAGCCTATAA
* *
3020890 ATATTAATAAATTAAATTATAAACAGAGCCTATAA
1 ATATTAATAAACTAAATTAGAAACAGAGCCTATAA
3020925 AT
1 AT
3020927 TTATTTTTTA
Statistics
Matches: 31, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
35 31 1.00
ACGTcount: A:0.50, C:0.08, G:0.10, T:0.32
Consensus pattern (35 bp):
ATATTAATAAACTAAATTAGAAACAGAGCCTATAA
Found at i:3022516 original size:22 final size:23
Alignment explanation
Indices: 3022491--3022552 Score: 65
Period size: 22 Copynumber: 2.7 Consensus size: 23
3022481 AATAATTTTT
*
3022491 TTTAATTTTTATTTAA-AAATTA
1 TTTAATTTTTATTTAATAAAATA
3022513 TTTAATGATATTTATTTAATAAAATA
1 TTTAAT--T-TTTATTTAATAAAATA
*
3022539 ATTAA-TTTTATTTA
1 TTTAATTTTTATTTA
3022553 TTATAAACAA
Statistics
Matches: 34, Mismatches: 2, Indels: 8
0.77 0.05 0.18
Matches are distributed among these distances:
22 14 0.41
23 1 0.03
24 1 0.03
25 9 0.26
26 9 0.26
ACGTcount: A:0.42, C:0.00, G:0.02, T:0.56
Consensus pattern (23 bp):
TTTAATTTTTATTTAATAAAATA
Found at i:3022550 original size:26 final size:26
Alignment explanation
Indices: 3022498--3022571 Score: 75
Period size: 26 Copynumber: 3.0 Consensus size: 26
3022488 TTTTTTAATT
* * *
3022498 TTTATTTAA-AAATTATTTAATGATA
1 TTTATTTAATAAAATAATTAATTATA
*
3022523 TTTATTTAATAAAATAATTAATTTTA
1 TTTATTTAATAAAATAATTAATTATA
3022549 TTTA-TT-ATAAACA-AATTAATTAT
1 TTTATTTAATAAA-ATAATTAATTAT
3022572 TAATTTTAAA
Statistics
Matches: 42, Mismatches: 5, Indels: 5
0.81 0.10 0.10
Matches are distributed among these distances:
24 14 0.33
25 12 0.29
26 16 0.38
ACGTcount: A:0.46, C:0.01, G:0.01, T:0.51
Consensus pattern (26 bp):
TTTATTTAATAAAATAATTAATTATA
Found at i:3023786 original size:21 final size:21
Alignment explanation
Indices: 3023757--3023797 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
3023747 AGAATTATTA
*
3023757 TAATATTTTAAAATTAATAAT
1 TAATATTTTAAAATAAATAAT
* *
3023778 TAATTTTTTATAATAAATAA
1 TAATATTTTAAAATAAATAA
3023798 AAATGATTAT
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (21 bp):
TAATATTTTAAAATAAATAAT
Found at i:3023828 original size:22 final size:22
Alignment explanation
Indices: 3023785--3023828 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 22
3023775 AATTAATTTT
*
3023785 TTATAATAAATAAAAATGATTA
1 TTATAATAAATAAAAATCATTA
* *
3023807 TTATATTAAATAAATATCATTA
1 TTATAATAAATAAAAATCATTA
3023829 AAATAATTTT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.55, C:0.02, G:0.02, T:0.41
Consensus pattern (22 bp):
TTATAATAAATAAAAATCATTA
Found at i:3024843 original size:21 final size:21
Alignment explanation
Indices: 3024792--3024844 Score: 72
Period size: 21 Copynumber: 2.5 Consensus size: 21
3024782 ATTATTACTA
3024792 TCGCAATGCGATTTTCCAATT
1 TCGCAATGCGATTTTCCAATT
**
3024813 TCGCGTTGCGATTTTCCCAA-T
1 TCGCAATGCGATTTT-CCAATT
3024834 TCGCAATGCGA
1 TCGCAATGCGA
3024845 ATAAGTAAAT
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
21 23 0.85
22 4 0.15
ACGTcount: A:0.21, C:0.26, G:0.19, T:0.34
Consensus pattern (21 bp):
TCGCAATGCGATTTTCCAATT
Found at i:3024898 original size:41 final size:41
Alignment explanation
Indices: 3024871--3025008 Score: 163
Period size: 41 Copynumber: 3.4 Consensus size: 41
3024861 GCGCATTTGG
*
3024871 AAAATCGCTATGCGATACTGACTATCGCAACGCGATAATAC
1 AAAATCGCAATGCGATACTGACTATCGCAACGCGATAATAC
* *
3024912 AAAATCGCAATGCGATACTGACTTTCGCAACGCGATACTTAC
1 AAAATCGCAATGCGATACTGACTATCGCAACGCGATA-ATAC
** ** * *
3024954 --TTTCGCAACACGATACTGACTTTCGCAACGAGATAATAC
1 AAAATCGCAATGCGATACTGACTATCGCAACGCGATAATAC
*
3024993 ATAATCGCAATGCGAT
1 AAAATCGCAATGCGAT
3025009 TTTCAAAGCG
Statistics
Matches: 81, Mismatches: 13, Indels: 6
0.81 0.13 0.06
Matches are distributed among these distances:
39 3 0.04
40 30 0.37
41 45 0.56
42 3 0.04
ACGTcount: A:0.35, C:0.25, G:0.17, T:0.24
Consensus pattern (41 bp):
AAAATCGCAATGCGATACTGACTATCGCAACGCGATAATAC
Found at i:3024905 original size:20 final size:20
Alignment explanation
Indices: 3024882--3024988 Score: 117
Period size: 20 Copynumber: 5.3 Consensus size: 20
3024872 AAATCGCTAT
*
3024882 GCGATACTGACTATCGCAAC
1 GCGATACTGACTTTCGCAAC
* ** *
3024902 GCGATAAT-ACAAAATCGCAAT
1 GCGATACTGAC--TTTCGCAAC
3024923 GCGATACTGACTTTCGCAAC
1 GCGATACTGACTTTCGCAAC
*
3024943 GCGATACTTACTTTCGCAAC
1 GCGATACTGACTTTCGCAAC
*
3024963 ACGATACTGACTTTCGCAAC
1 GCGATACTGACTTTCGCAAC
*
3024983 GAGATA
1 GCGATA
3024989 ATACATAATC
Statistics
Matches: 72, Mismatches: 12, Indels: 6
0.80 0.13 0.07
Matches are distributed among these distances:
19 2 0.03
20 54 0.75
21 14 0.19
22 2 0.03
ACGTcount: A:0.33, C:0.26, G:0.18, T:0.23
Consensus pattern (20 bp):
GCGATACTGACTTTCGCAAC
Found at i:3024971 original size:40 final size:40
Alignment explanation
Indices: 3024883--3025002 Score: 143
Period size: 40 Copynumber: 3.0 Consensus size: 40
3024873 AATCGCTATG
* **
3024883 CGATACTGACTATCGCAACGCGATAATACAAAATCGCAATG
1 CGATACTGACTTTCGCAACGCGATAATAC-AAATCGCAACA
* **
3024924 CGATACTGACTTTCGCAACGCGATACTTAC-TTTCGCAACA
1 CGATACTGACTTTCGCAACGCGATA-ATACAAATCGCAACA
*
3024964 CGATACTGACTTTCGCAACGAGATAATACATAATCGCAA
1 CGATACTGACTTTCGCAACGCGATAATACA-AATCGCAA
3025003 TGCGATTTTC
Statistics
Matches: 66, Mismatches: 10, Indels: 6
0.80 0.12 0.07
Matches are distributed among these distances:
39 3 0.05
40 30 0.45
41 30 0.45
42 3 0.05
ACGTcount: A:0.35, C:0.26, G:0.16, T:0.23
Consensus pattern (40 bp):
CGATACTGACTTTCGCAACGCGATAATACAAATCGCAACA
Found at i:3025203 original size:22 final size:22
Alignment explanation
Indices: 3025175--3025218 Score: 70
Period size: 22 Copynumber: 2.0 Consensus size: 22
3025165 CACTCTCTCA
3025175 CCCATCTCCGACGAAATCCGTC
1 CCCATCTCCGACGAAATCCGTC
**
3025197 CCCATCTCCGGTGAAATCCGTC
1 CCCATCTCCGACGAAATCCGTC
3025219 TATCTCCATC
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.20, C:0.43, G:0.16, T:0.20
Consensus pattern (22 bp):
CCCATCTCCGACGAAATCCGTC
Found at i:3025516 original size:20 final size:20
Alignment explanation
Indices: 3025467--3025525 Score: 73
Period size: 20 Copynumber: 3.0 Consensus size: 20
3025457 TTTATTCTCT
* **
3025467 CGTTGCGATAGTCAAATTCG
1 CGTTGCGATTGTCATTTTCG
3025487 CGTTGCGATTGTCATTTTCG
1 CGTTGCGATTGTCATTTTCG
* *
3025507 TGTTGCGATTTTCATTTTC
1 CGTTGCGATTGTCATTTTC
3025526 AGAAACTATT
Statistics
Matches: 34, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
20 34 1.00
ACGTcount: A:0.15, C:0.19, G:0.22, T:0.44
Consensus pattern (20 bp):
CGTTGCGATTGTCATTTTCG
Found at i:3025716 original size:25 final size:24
Alignment explanation
Indices: 3025662--3025716 Score: 58
Period size: 25 Copynumber: 2.2 Consensus size: 24
3025652 TGTTTATTAT
* *
3025662 TGTTTTTGGTATATCTTCACAGTG
1 TGTTTTTGGTATATCTTAACAGTA
3025686 TAGTTTTTGGTATATC-TAACTTAGTA
1 T-GTTTTTGGTATATCTTAAC--AGTA
3025712 TGTTT
1 TGTTT
3025717 ATTGTTTTTG
Statistics
Matches: 26, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
24 4 0.15
25 18 0.69
26 4 0.15
ACGTcount: A:0.20, C:0.09, G:0.18, T:0.53
Consensus pattern (24 bp):
TGTTTTTGGTATATCTTAACAGTA
Found at i:3026866 original size:18 final size:18
Alignment explanation
Indices: 3026845--3026892 Score: 87
Period size: 18 Copynumber: 2.7 Consensus size: 18
3026835 TCCACTTCGG
3026845 GAGCCATCACCTCACCCA
1 GAGCCATCACCTCACCCA
*
3026863 GAGCTATCACCTCACCCA
1 GAGCCATCACCTCACCCA
3026881 GAGCCATCACCT
1 GAGCCATCACCT
3026893 GATCGACCCG
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
18 28 1.00
ACGTcount: A:0.27, C:0.46, G:0.12, T:0.15
Consensus pattern (18 bp):
GAGCCATCACCTCACCCA
Found at i:3027486 original size:19 final size:20
Alignment explanation
Indices: 3027443--3027498 Score: 69
Period size: 20 Copynumber: 2.9 Consensus size: 20
3027433 TGCAACACAA
3027443 AAATGACTATCGCAACGCGG
1 AAATGACTATCGCAACGCGG
* *
3027463 AAATGGCTATCGCAATGC-G
1 AAATGACTATCGCAACGCGG
**
3027482 AAATGAAAATCGCAACG
1 AAATGACTATCGCAACG
3027499 ACAAAATCGA
Statistics
Matches: 30, Mismatches: 6, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
19 14 0.47
20 16 0.53
ACGTcount: A:0.39, C:0.21, G:0.23, T:0.16
Consensus pattern (20 bp):
AAATGACTATCGCAACGCGG
Found at i:3027506 original size:14 final size:14
Alignment explanation
Indices: 3027487--3027543 Score: 51
Period size: 14 Copynumber: 3.7 Consensus size: 14
3027477 ATGCGAAATG
3027487 AAAATCGCAACGAC
1 AAAATCGCAACGAC
* *
3027501 AAAATCGAAATGCGAAATG
1 AAAATCGCAA--CG--A-C
3027520 AAAATCGCAACGAC
1 AAAATCGCAACGAC
3027534 AAAATCGCAA
1 AAAATCGCAA
3027544 TACGAAATGA
Statistics
Matches: 34, Mismatches: 4, Indels: 10
0.71 0.08 0.21
Matches are distributed among these distances:
14 19 0.56
15 1 0.03
16 2 0.06
17 2 0.06
18 1 0.03
19 9 0.26
ACGTcount: A:0.53, C:0.21, G:0.16, T:0.11
Consensus pattern (14 bp):
AAAATCGCAACGAC
Found at i:3027518 original size:33 final size:33
Alignment explanation
Indices: 3027471--3027564 Score: 170
Period size: 33 Copynumber: 2.8 Consensus size: 33
3027461 GGAAATGGCT
3027471 ATCGCAATGCGAAATGAAAATCGCAACGACAAA
1 ATCGCAATGCGAAATGAAAATCGCAACGACAAA
*
3027504 ATCGAAATGCGAAATGAAAATCGCAACGACAAA
1 ATCGCAATGCGAAATGAAAATCGCAACGACAAA
*
3027537 ATCGCAATACGAAATGAAAATCGCAACG
1 ATCGCAATGCGAAATGAAAATCGCAACG
3027565 CGAAATGAAA
Statistics
Matches: 58, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
33 58 1.00
ACGTcount: A:0.49, C:0.20, G:0.18, T:0.13
Consensus pattern (33 bp):
ATCGCAATGCGAAATGAAAATCGCAACGACAAA
Found at i:3027525 original size:19 final size:19
Alignment explanation
Indices: 3027471--3027586 Score: 108
Period size: 19 Copynumber: 6.6 Consensus size: 19
3027461 GGAAATGGCT
3027471 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
*
3027490 ATCGCAA--CG--A-CAAA
1 ATCGCAATGCGAAATGAAA
*
3027504 ATCGAAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
*
3027523 ATCGCAA--CG--A-CAAA
1 ATCGCAATGCGAAATGAAA
*
3027537 ATCGCAATACGAAATGAAA
1 ATCGCAATGCGAAATGAAA
*
3027556 ATCGCAACGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
*
3027575 ATCGCATTGCGA
1 ATCGCAATGCGA
3027587 TTTTGTCGCT
Statistics
Matches: 77, Mismatches: 10, Indels: 20
0.72 0.09 0.19
Matches are distributed among these distances:
14 19 0.25
15 2 0.03
16 4 0.05
17 4 0.05
18 2 0.03
19 46 0.60
ACGTcount: A:0.47, C:0.20, G:0.19, T:0.14
Consensus pattern (19 bp):
ATCGCAATGCGAAATGAAA
Found at i:3027647 original size:20 final size:20
Alignment explanation
Indices: 3027626--3027699 Score: 94
Period size: 20 Copynumber: 3.6 Consensus size: 20
3027616 GTGATAGCCA
3027626 TTTCTGCGTTGCGATAGTCAT
1 TTTC-GCGTTGCGATAGTCAT
3027647 TTTCGCGTTGCGATAGTCAT
1 TTTCGCGTTGCGATAGTCAT
* * * *
3027667 TTTCGCTTTGCGAAAGTAAG
1 TTTCGCGTTGCGATAGTCAT
*
3027687 TTTCGTGTTGCGA
1 TTTCGCGTTGCGA
3027700 AAGTAAACTA
Statistics
Matches: 47, Mismatches: 6, Indels: 1
0.87 0.11 0.02
Matches are distributed among these distances:
20 43 0.91
21 4 0.09
ACGTcount: A:0.16, C:0.18, G:0.26, T:0.41
Consensus pattern (20 bp):
TTTCGCGTTGCGATAGTCAT
Found at i:3028099 original size:21 final size:20
Alignment explanation
Indices: 3028047--3028107 Score: 68
Period size: 21 Copynumber: 3.0 Consensus size: 20
3028037 GACTCACCTG
3028047 TCATCCCTCAAGAGTCCCCT
1 TCATCCCTCAAGAGTCCCCT
* ** *
3028067 CCAATCATTCAAGAGGCCCCT
1 TC-ATCCCTCAAGAGTCCCCT
3028088 ATCATCCCTCAAGAGTCCCC
1 -TCATCCCTCAAGAGTCCCC
3028108 CCCCCCACCG
Statistics
Matches: 31, Mismatches: 8, Indels: 3
0.74 0.19 0.07
Matches are distributed among these distances:
20 1 0.03
21 29 0.94
22 1 0.03
ACGTcount: A:0.25, C:0.43, G:0.11, T:0.21
Consensus pattern (20 bp):
TCATCCCTCAAGAGTCCCCT
Found at i:3028137 original size:44 final size:42
Alignment explanation
Indices: 3028044--3028137 Score: 116
Period size: 44 Copynumber: 2.2 Consensus size: 42
3028034 CCCGACTCAC
* * *
3028044 CTGTCATCCCTCAAGAGTCCCCTCCAATCATTCAAGAGGCCC
1 CTGTCATCCCTCAAGAGTCCCCCCCAACCATTCAAGAGGCCA
* * *
3028086 CTATCATCCCTCAAGAGTCCCCCCCCCCACCGTTCAAGAGGCCA
1 CTGTCATCCCTCAAGAGT--CCCCCCCAACCATTCAAGAGGCCA
3028130 CTGTCATC
1 CTGTCATC
3028138 GTTGAAGAGG
Statistics
Matches: 43, Mismatches: 7, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
42 17 0.40
44 26 0.60
ACGTcount: A:0.22, C:0.44, G:0.14, T:0.20
Consensus pattern (42 bp):
CTGTCATCCCTCAAGAGTCCCCCCCAACCATTCAAGAGGCCA
Found at i:3029799 original size:20 final size:20
Alignment explanation
Indices: 3029774--3029847 Score: 130
Period size: 20 Copynumber: 3.7 Consensus size: 20
3029764 GCGATTTTCA
3029774 TTTCGCGTTGCGATAGCCAT
1 TTTCGCGTTGCGATAGCCAT
3029794 TTTCGCGTTGCGATAGCCAT
1 TTTCGCGTTGCGATAGCCAT
* *
3029814 TTTCGCATTGCGATAGTCAT
1 TTTCGCGTTGCGATAGCCAT
3029834 TTTCGCGTTGCGAT
1 TTTCGCGTTGCGAT
3029848 TTCCCCGTTG
Statistics
Matches: 51, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 51 1.00
ACGTcount: A:0.15, C:0.23, G:0.24, T:0.38
Consensus pattern (20 bp):
TTTCGCGTTGCGATAGCCAT
Found at i:3030088 original size:21 final size:21
Alignment explanation
Indices: 3030037--3030089 Score: 72
Period size: 21 Copynumber: 2.5 Consensus size: 21
3030027 ATTATTACTA
3030037 TCGCAATGCGATTTTCCAATT
1 TCGCAATGCGATTTTCCAATT
**
3030058 TCGCGTTGCGATTTTCCCAA-T
1 TCGCAATGCGATTTT-CCAATT
3030079 TCGCAATGCGA
1 TCGCAATGCGA
3030090 ATAAGTAAAT
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
21 23 0.85
22 4 0.15
ACGTcount: A:0.21, C:0.26, G:0.19, T:0.34
Consensus pattern (21 bp):
TCGCAATGCGATTTTCCAATT
Found at i:3030122 original size:21 final size:21
Alignment explanation
Indices: 3030079--3030192 Score: 92
Period size: 21 Copynumber: 5.5 Consensus size: 21
3030069 TTTTCCCAAT
* *
3030079 TCGCAATGCGAA-TAAGTAAA
1 TCGCAATGCGAATTTAGAAAA
*
3030099 TCGCAATGCGAATTTGGAAAA
1 TCGCAATGCGAATTTAGAAAA
* **
3030120 TCGCAATGCGATACTT--ACTA
1 TCGCAATGCGA-ATTTAGAAAA
* * *
3030140 TCGCAACGCG-ATAATACAAAA
1 TCGCAATGCGAAT-TTAGAAAA
*
3030161 TCGCAATGCGAATTTGGAAAA
1 TCGCAATGCGAATTTAGAAAA
3030182 TCGCAATGCGA
1 TCGCAATGCGA
3030193 TACTGACTAT
Statistics
Matches: 73, Mismatches: 15, Indels: 11
0.74 0.15 0.11
Matches are distributed among these distances:
18 1 0.01
19 1 0.01
20 23 0.32
21 43 0.59
22 5 0.07
ACGTcount: A:0.39, C:0.19, G:0.20, T:0.22
Consensus pattern (21 bp):
TCGCAATGCGAATTTAGAAAA
Found at i:3030162 original size:62 final size:62
Alignment explanation
Indices: 3030096--3030214 Score: 229
Period size: 62 Copynumber: 1.9 Consensus size: 62
3030086 GCGAATAAGT
*
3030096 AAATCGCAATGCGAATTTGGAAAATCGCAATGCGATACTTACTATCGCAACGCGATAATACA
1 AAATCGCAATGCGAATTTGGAAAATCGCAATGCGATACTGACTATCGCAACGCGATAATACA
3030158 AAATCGCAATGCGAATTTGGAAAATCGCAATGCGATACTGACTATCGCAACGCGATA
1 AAATCGCAATGCGAATTTGGAAAATCGCAATGCGATACTGACTATCGCAACGCGATA
3030215 CTGACTTTCG
Statistics
Matches: 56, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
62 56 1.00
ACGTcount: A:0.38, C:0.21, G:0.19, T:0.22
Consensus pattern (62 bp):
AAATCGCAATGCGAATTTGGAAAATCGCAATGCGATACTGACTATCGCAACGCGATAATACA
Found at i:3030168 original size:82 final size:82
Alignment explanation
Indices: 3030079--3030253 Score: 228
Period size: 82 Copynumber: 2.1 Consensus size: 82
3030069 TTTTCCCAAT
* * * *
3030079 TCGCAATGCGAA-TAAGTAAATCGCAATGCGA-ATTTGGAAAATCGCAATGCGATACTTACTATC
1 TCGCAATGCGAATTAAGAAAATCGCAATGCGATA-CT-GAAAATCGCAACGCGATACTGACTATC
3030142 GCAACGCGATAATACAAAA
64 GCAACGCGATAATACAAAA
** ** *
3030161 TCGCAATGCGAATTTGGAAAATCGCAATGCGATACTGACTATCGCAACGCGATACTGACTTTCGC
1 TCGCAATGCGAATTAAGAAAATCGCAATGCGATACTGAAAATCGCAACGCGATACTGACTATCGC
*
3030226 AACGCGATAATACAGAA
66 AACGCGATAATACAAAA
3030243 TCGCAATGCGA
1 TCGCAATGCGA
3030254 TTTTCAAAGT
Statistics
Matches: 81, Mismatches: 10, Indels: 4
0.85 0.11 0.04
Matches are distributed among these distances:
82 63 0.78
83 17 0.21
84 1 0.01
ACGTcount: A:0.37, C:0.22, G:0.20, T:0.22
Consensus pattern (82 bp):
TCGCAATGCGAATTAAGAAAATCGCAATGCGATACTGAAAATCGCAACGCGATACTGACTATCGC
AACGCGATAATACAAAA
Found at i:3030206 original size:20 final size:20
Alignment explanation
Indices: 3030181--3030234 Score: 90
Period size: 20 Copynumber: 2.7 Consensus size: 20
3030171 AATTTGGAAA
*
3030181 ATCGCAATGCGATACTGACT
1 ATCGCAACGCGATACTGACT
3030201 ATCGCAACGCGATACTGACT
1 ATCGCAACGCGATACTGACT
*
3030221 TTCGCAACGCGATA
1 ATCGCAACGCGATA
3030235 ATACAGAATC
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 32 1.00
ACGTcount: A:0.30, C:0.28, G:0.20, T:0.22
Consensus pattern (20 bp):
ATCGCAACGCGATACTGACT
Found at i:3031001 original size:24 final size:24
Alignment explanation
Indices: 3030974--3031027 Score: 81
Period size: 24 Copynumber: 2.2 Consensus size: 24
3030964 GTATTCGAAA
*
3030974 TTTGATCTTGGTCAATACCCGGAC
1 TTTGATATTGGTCAATACCCGGAC
* *
3030998 TTTGATATTGGTCAATACTCGGAT
1 TTTGATATTGGTCAATACCCGGAC
3031022 TTTGAT
1 TTTGAT
3031028 GATGTTTCAG
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
24 27 1.00
ACGTcount: A:0.22, C:0.17, G:0.20, T:0.41
Consensus pattern (24 bp):
TTTGATATTGGTCAATACCCGGAC
Found at i:3031219 original size:12 final size:12
Alignment explanation
Indices: 3031202--3031226 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
3031192 ATATAATCCT
3031202 GAAGAAGAAAAA
1 GAAGAAGAAAAA
3031214 GAAGAAGAAAAA
1 GAAGAAGAAAAA
3031226 G
1 G
3031227 TCCCCGAAGA
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:0.72, C:0.00, G:0.28, T:0.00
Consensus pattern (12 bp):
GAAGAAGAAAAA
Found at i:3032899 original size:20 final size:20
Alignment explanation
Indices: 3032821--3032913 Score: 66
Period size: 20 Copynumber: 4.7 Consensus size: 20
3032811 GGCAATCATT
*
3032821 TGACTATCGCAACACGGAAA
1 TGACTATCGCAACACGAAAA
**
3032841 TGACGT-TCGCAATCATC-TTAA
1 TGAC-TATCGCAA-CA-CGAAAA
* *
3032862 TGTCTATCGCAACGCGAAAA
1 TGACTATCGCAACACGAAAA
*
3032882 TGACTATCGCAATACG-AAA
1 TGACTATCGCAACACGAAAA
**
3032901 TGAAAATCGCAAC
1 TGACTATCGCAAC
3032914 GAGAGAATCG
Statistics
Matches: 56, Mismatches: 12, Indels: 11
0.71 0.15 0.14
Matches are distributed among these distances:
19 14 0.25
20 27 0.48
21 14 0.25
22 1 0.02
ACGTcount: A:0.38, C:0.24, G:0.17, T:0.22
Consensus pattern (20 bp):
TGACTATCGCAACACGAAAA
Found at i:3032933 original size:33 final size:33
Alignment explanation
Indices: 3032887--3032980 Score: 161
Period size: 33 Copynumber: 2.8 Consensus size: 33
3032877 GAAAATGACT
*
3032887 ATCGCAATACGAAATGAAAATCGCAACGAGAGA
1 ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
*
3032920 ATCGCAATGCGAAATGAAAATCGCAACGAGGGA
1 ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
*
3032953 ATCGCAAAGCGAAATGAAAATCGCAACG
1 ATCGCAATGCGAAATGAAAATCGCAACG
3032981 TGAATTTAGT
Statistics
Matches: 58, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
33 58 1.00
ACGTcount: A:0.46, C:0.19, G:0.23, T:0.12
Consensus pattern (33 bp):
ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
Found at i:3032976 original size:19 final size:18
Alignment explanation
Indices: 3032887--3032978 Score: 65
Period size: 19 Copynumber: 5.4 Consensus size: 18
3032877 GAAAATGACT
3032887 ATCGCAATACGAAATGAAA
1 ATCGCAA-ACGAAATGAAA
*
3032906 ATCGC-AACG--A-GAGA
1 ATCGCAAACGAAATGAAA
*
3032920 ATCGCAATGCGAAATGAAA
1 ATCGCAA-ACGAAATGAAA
**
3032939 ATCGC-AACG--A-GGGA
1 ATCGCAAACGAAATGAAA
3032953 ATCGCAAAGCGAAATGAAA
1 ATCGCAAA-CGAAATGAAA
3032972 ATCGCAA
1 ATCGCAA
3032979 CGTGAATTTA
Statistics
Matches: 55, Mismatches: 8, Indels: 20
0.66 0.10 0.24
Matches are distributed among these distances:
14 15 0.27
15 5 0.09
16 4 0.07
17 5 0.09
18 4 0.07
19 22 0.40
ACGTcount: A:0.47, C:0.18, G:0.23, T:0.12
Consensus pattern (18 bp):
ATCGCAAACGAAATGAAA
Found at i:3033033 original size:19 final size:19
Alignment explanation
Indices: 3033009--3033055 Score: 85
Period size: 19 Copynumber: 2.5 Consensus size: 19
3032999 GCGATTTTGT
3033009 CGTTGCGATTTTCATTTCG
1 CGTTGCGATTTTCATTTCG
3033028 CGTTGCGATTTTCATTTCG
1 CGTTGCGATTTTCATTTCG
*
3033047 CATTGCGAT
1 CGTTGCGAT
3033056 AGTCATTTTT
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
19 27 1.00
ACGTcount: A:0.13, C:0.21, G:0.21, T:0.45
Consensus pattern (19 bp):
CGTTGCGATTTTCATTTCG
Found at i:3033061 original size:19 final size:19
Alignment explanation
Indices: 3033020--3033063 Score: 61
Period size: 19 Copynumber: 2.3 Consensus size: 19
3033010 GTTGCGATTT
* **
3033020 TCATTTCGCGTTGCGATTT
1 TCATTTCGCATTGCGATAG
3033039 TCATTTCGCATTGCGATAG
1 TCATTTCGCATTGCGATAG
3033058 TCATTT
1 TCATTT
3033064 TTGCCTTCAA
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
19 22 1.00
ACGTcount: A:0.16, C:0.20, G:0.18, T:0.45
Consensus pattern (19 bp):
TCATTTCGCATTGCGATAG
Found at i:3033181 original size:14 final size:14
Alignment explanation
Indices: 3033162--3033198 Score: 65
Period size: 14 Copynumber: 2.6 Consensus size: 14
3033152 TATCAATTAA
3033162 ACAAATCAACTTTT
1 ACAAATCAACTTTT
*
3033176 ACAAATCATCTTTT
1 ACAAATCAACTTTT
3033190 ACAAATCAA
1 ACAAATCAA
3033199 TTAAACAATC
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.46, C:0.22, G:0.00, T:0.32
Consensus pattern (14 bp):
ACAAATCAACTTTT
Found at i:3034634 original size:42 final size:42
Alignment explanation
Indices: 3034588--3034667 Score: 106
Period size: 42 Copynumber: 1.9 Consensus size: 42
3034578 CGATGACAAT
* * *
3034588 GGCCTCTTGAACGGTGGGAGGGGACTCTCGAGGAATGATAGG
1 GGCCTCTTCAACGATAGGAGGGGACTCTCGAGGAATGATAGG
* * *
3034630 GGCCTCTTCAACGATAGGAGTGGACTCTTGAGGGATGA
1 GGCCTCTTCAACGATAGGAGGGGACTCTCGAGGAATGA
3034668 CAAGCGAGTC
Statistics
Matches: 32, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
42 32 1.00
ACGTcount: A:0.23, C:0.17, G:0.39, T:0.21
Consensus pattern (42 bp):
GGCCTCTTCAACGATAGGAGGGGACTCTCGAGGAATGATAGG
Found at i:3036900 original size:20 final size:19
Alignment explanation
Indices: 3036855--3036943 Score: 80
Period size: 20 Copynumber: 4.8 Consensus size: 19
3036845 TCTTTTGGTT
* *
3036855 GAAATGAAAATCGCAATGA
1 GAAATGAAAATCGCAACGC
3036874 GAGAATGAAAATCGCAACGC
1 GA-AATGAAAATCGCAACGC
**
3036894 GGAAATGACTATCGCAA--C
1 -GAAATGAAAATCGCAACGC
*
3036912 G--A-GAGAATCGCAACGC
1 GAAATGAAAATCGCAACGC
3036928 GAAATGAAAATCGCAA
1 GAAATGAAAATCGCAA
3036944 TGAGATAATC
Statistics
Matches: 56, Mismatches: 7, Indels: 14
0.73 0.09 0.18
Matches are distributed among these distances:
14 9 0.16
15 1 0.02
16 2 0.04
17 1 0.02
18 2 0.04
19 12 0.21
20 27 0.48
21 2 0.04
ACGTcount: A:0.46, C:0.18, G:0.24, T:0.12
Consensus pattern (19 bp):
GAAATGAAAATCGCAACGC
Found at i:3036977 original size:33 final size:33
Alignment explanation
Indices: 3036855--3036978 Score: 131
Period size: 33 Copynumber: 3.5 Consensus size: 33
3036845 TCTTTTGGTT
3036855 GAAATGAAAATCGCAATGAGAGAATGAAAATCGCAACGC
1 GAAATGAAAATCGCAAT--GAG-A-G--AATCGCAACGC
** *
3036894 GGAAATGACTATCGCAACGAGAGAATCGCAACGC
1 -GAAATGAAAATCGCAATGAGAGAATCGCAACGC
* *
3036928 GAAATGAAAATCGCAATGAGATAATCACAACGC
1 GAAATGAAAATCGCAATGAGAGAATCGCAACGC
*
3036961 GAAATGAAAATTGCAATG
1 GAAATGAAAATCGCAATG
3036979 CGATTTTGGT
Statistics
Matches: 75, Mismatches: 9, Indels: 7
0.82 0.10 0.08
Matches are distributed among these distances:
33 45 0.60
34 11 0.15
36 1 0.01
37 1 0.01
38 3 0.04
40 14 0.19
ACGTcount: A:0.46, C:0.17, G:0.23, T:0.15
Consensus pattern (33 bp):
GAAATGAAAATCGCAATGAGAGAATCGCAACGC
Found at i:3037608 original size:20 final size:20
Alignment explanation
Indices: 3037585--3037657 Score: 119
Period size: 20 Copynumber: 3.6 Consensus size: 20
3037575 CGATAGTCAG
3037585 ATTCGCATTGCGATTTACGT
1 ATTCGCATTGCGATTTACGT
*
3037605 ATTCGCATTGCGATTTACTT
1 ATTCGCATTGCGATTTACGT
* *
3037625 AATCGCGTTGCGATTTACGT
1 ATTCGCATTGCGATTTACGT
3037645 ATTCGCATTGCGA
1 ATTCGCATTGCGA
3037658 ATTATGAAAG
Statistics
Matches: 47, Mismatches: 6, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 47 1.00
ACGTcount: A:0.21, C:0.21, G:0.21, T:0.38
Consensus pattern (20 bp):
ATTCGCATTGCGATTTACGT
Found at i:3037678 original size:21 final size:20
Alignment explanation
Indices: 3037654--3037707 Score: 56
Period size: 20 Copynumber: 2.6 Consensus size: 20
3037644 TATTCGCATT
3037654 GCGAATTATGAAAGTCGCAAC
1 GCGAATTATGAAA-TCGCAAC
* *
3037675 GCGAATACAT-AAATCGCAAT
1 GCGAAT-TATGAAATCGCAAC
*
3037695 GCGAATTAGGAAA
1 GCGAATTATGAAA
3037708 ATTACATTGC
Statistics
Matches: 27, Mismatches: 4, Indels: 5
0.75 0.11 0.14
Matches are distributed among these distances:
19 1 0.04
20 15 0.56
21 9 0.33
22 2 0.07
ACGTcount: A:0.43, C:0.17, G:0.22, T:0.19
Consensus pattern (20 bp):
GCGAATTATGAAATCGCAAC
Found at i:3037801 original size:21 final size:22
Alignment explanation
Indices: 3037749--3037801 Score: 74
Period size: 21 Copynumber: 2.5 Consensus size: 22
3037739 ATTTACTTAT
3037749 TCGCATTGCG-AATTGGGAAAA
1 TCGCATTGCGAAATTGGGAAAA
**
3037770 TCGCAACGCGAAATT-GGAAAA
1 TCGCATTGCGAAATTGGGAAAA
3037791 TCGCATTGCGA
1 TCGCATTGCGA
3037802 TAGTAATAAT
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
21 23 0.85
22 4 0.15
ACGTcount: A:0.34, C:0.19, G:0.26, T:0.21
Consensus pattern (22 bp):
TCGCATTGCGAAATTGGGAAAA
Found at i:3044607 original size:15 final size:15
Alignment explanation
Indices: 3044587--3044622 Score: 63
Period size: 15 Copynumber: 2.4 Consensus size: 15
3044577 CATCGAGAAA
3044587 AACATCCACCGTCAC
1 AACATCCACCGTCAC
*
3044602 AACATCCACCGTCAT
1 AACATCCACCGTCAC
3044617 AACATC
1 AACATC
3044623 ATCATCCCCT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
15 20 1.00
ACGTcount: A:0.36, C:0.42, G:0.06, T:0.17
Consensus pattern (15 bp):
AACATCCACCGTCAC
Found at i:3044794 original size:21 final size:21
Alignment explanation
Indices: 3044758--3044803 Score: 58
Period size: 21 Copynumber: 2.2 Consensus size: 21
3044748 ACACTGCCGG
*
3044758 TTCAGATGGCATCACAGCCAT
1 TTCAGATGGCATCACAACCAT
*
3044779 TTCAGATGGC-TCCACAACCGT
1 TTCAGATGGCAT-CACAACCAT
3044800 TTCA
1 TTCA
3044804 TATGCCACCG
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
20 1 0.05
21 21 0.95
ACGTcount: A:0.26, C:0.30, G:0.17, T:0.26
Consensus pattern (21 bp):
TTCAGATGGCATCACAACCAT
Found at i:3059654 original size:16 final size:15
Alignment explanation
Indices: 3059622--3059663 Score: 50
Period size: 15 Copynumber: 2.7 Consensus size: 15
3059612 TTACATTAGA
3059622 TTTCTTTGTTTCCTT
1 TTTCTTTGTTTCCTT
*
3059637 TTTCTCTTG-TTCCAT
1 TTTCT-TTGTTTCCTT
3059652 TTTCTGTTGTTT
1 TTTCT-TTGTTT
3059664 AAACTATTTG
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
15 18 0.78
16 5 0.22
ACGTcount: A:0.02, C:0.19, G:0.10, T:0.69
Consensus pattern (15 bp):
TTTCTTTGTTTCCTT
Found at i:3061236 original size:4 final size:4
Alignment explanation
Indices: 3061227--3061759 Score: 1052
Period size: 4 Copynumber: 133.8 Consensus size: 4
3061217 GGTACAAATT
3061227 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
1 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
3061275 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
1 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
3061323 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
1 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
3061371 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
1 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
3061419 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
1 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
3061467 CATA CATA CATA CATA CATA C--A CATA CATA CATA CATA CATA CATA
1 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
3061513 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
1 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
3061561 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
1 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
3061609 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
1 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
3061657 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
1 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
3061705 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
1 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
3061753 CATA CAT
1 CATA CAT
3061760 GAGTGTTGCG
Statistics
Matches: 527, Mismatches: 0, Indels: 4
0.99 0.00 0.01
Matches are distributed among these distances:
2 2 0.00
4 525 1.00
ACGTcount: A:0.50, C:0.25, G:0.00, T:0.25
Consensus pattern (4 bp):
CATA
Found at i:3075170 original size:14 final size:16
Alignment explanation
Indices: 3075133--3075172 Score: 57
Period size: 17 Copynumber: 2.6 Consensus size: 16
3075123 AATTCAACGG
3075133 GTTGACTCAGATGACGA
1 GTTGACTCAGATGAC-A
3075150 GTTGACTCAGATGA-A
1 GTTGACTCAGATGACA
3075165 -TTGACTCA
1 GTTGACTCA
3075173 ATATGGGTTG
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
14 8 0.35
15 1 0.04
17 14 0.61
ACGTcount: A:0.30, C:0.17, G:0.25, T:0.28
Consensus pattern (16 bp):
GTTGACTCAGATGACA
Found at i:3077446 original size:13 final size:13
Alignment explanation
Indices: 3077428--3077453 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
3077418 CTCGTTACAG
3077428 CTTTAATTTAATA
1 CTTTAATTTAATA
3077441 CTTTAATTTAATA
1 CTTTAATTTAATA
3077454 AAATTTTGCC
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:0.38, C:0.08, G:0.00, T:0.54
Consensus pattern (13 bp):
CTTTAATTTAATA
Found at i:3094924 original size:20 final size:20
Alignment explanation
Indices: 3094901--3094939 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 20
3094891 AATAAAGTCA
3094901 AATATCAAGATTTA-AACAAC
1 AATATCAAG-TTTAGAACAAC
*
3094921 AATATTAAGTTTAGAACAA
1 AATATCAAGTTTAGAACAA
3094940 TAAAATCCAT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 4 0.24
20 13 0.76
ACGTcount: A:0.54, C:0.10, G:0.08, T:0.28
Consensus pattern (20 bp):
AATATCAAGTTTAGAACAAC
Found at i:3094987 original size:75 final size:75
Alignment explanation
Indices: 3094897--3095091 Score: 214
Period size: 75 Copynumber: 2.6 Consensus size: 75
3094887 CATAAATAAA
* * * * *
3094897 GTCAAATATCAAGATTTAAACAACAATATTAAGTTTAGAACAATAAAATCCATAA-ACAAATCAA
1 GTCAAATTTCAAGATTCAAACAATAATATTAAGTCTAGAAAAATAAAATCCATAATA-AAATCAA
3094961 AATATTAAAAT
65 AATATTAAAAT
** * * * * *
3094972 GTCAAATTTCAAGATTCAAATTATAATATTAACTCTAGAATAATAAAATTCATAATAAAATTATA
1 GTCAAATTTCAAGATTCAAACAATAATATTAAGTCTAGAAAAATAAAATCCATAATAAAATCAAA
* *
3095037 ATATTTAAGT
66 ATATTAAAAT
* *
3095047 GTCAAATCTT-AAGACTCAAACCATAATATTAAGTCTAGAAAAATA
1 GTCAAAT-TTCAAGATTCAAACAATAATATTAAGTCTAGAAAAATA
3095092 TTAAACACGA
Statistics
Matches: 100, Mismatches: 18, Indels: 4
0.82 0.15 0.03
Matches are distributed among these distances:
75 97 0.97
76 3 0.03
ACGTcount: A:0.52, C:0.11, G:0.06, T:0.31
Consensus pattern (75 bp):
GTCAAATTTCAAGATTCAAACAATAATATTAAGTCTAGAAAAATAAAATCCATAATAAAATCAAA
ATATTAAAAT
Found at i:3095795 original size:43 final size:43
Alignment explanation
Indices: 3095747--3095832 Score: 172
Period size: 43 Copynumber: 2.0 Consensus size: 43
3095737 ATTTGACTGC
3095747 CTTGTCCTCGTCCCAATCACTATCCCAACCCTGGTCCCAACCT
1 CTTGTCCTCGTCCCAATCACTATCCCAACCCTGGTCCCAACCT
3095790 CTTGTCCTCGTCCCAATCACTATCCCAACCCTGGTCCCAACCT
1 CTTGTCCTCGTCCCAATCACTATCCCAACCCTGGTCCCAACCT
3095833 TCAGCTGTTT
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:0.19, C:0.47, G:0.09, T:0.26
Consensus pattern (43 bp):
CTTGTCCTCGTCCCAATCACTATCCCAACCCTGGTCCCAACCT
Found at i:3097254 original size:2 final size:2
Alignment explanation
Indices: 3097247--3097301 Score: 110
Period size: 2 Copynumber: 27.5 Consensus size: 2
3097237 TATTATTCAA
3097247 AT AT AT AT 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 AT AT AT AT
3097289 AT AT AT AT AT AT A
1 AT AT AT AT AT AT A
3097302 CAAAATAATA
Statistics
Matches: 53, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 53 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:3098056 original size:118 final size:118
Alignment explanation
Indices: 3097902--3098141 Score: 462
Period size: 118 Copynumber: 2.0 Consensus size: 118
3097892 GACTCGAATT
* *
3097902 TGATTTTTCTAAAAAGATATCTAACCCTATTGATTTGGTTCGAGTTAAATTACCATCAATAATTA
1 TGATTTTTCTAAAAAGAAATCTAACCCTATTAATTTGGTTCGAGTTAAATTACCATCAATAATTA
3097967 AAATGGAAATATTTTGCATCTAAATAATCAATATTTTATTTATCTTTTAGAAG
66 AAATGGAAATATTTTGCATCTAAATAATCAATATTTTATTTATCTTTTAGAAG
3098020 TGATTTTTCTAAAAAGAAATCTAACCCTATTAATTTGGTTCGAGTTAAATTACCATCAATAATTA
1 TGATTTTTCTAAAAAGAAATCTAACCCTATTAATTTGGTTCGAGTTAAATTACCATCAATAATTA
3098085 AAATGGAAATATTTTGCATCTAAATAATCAATATTTTATTTATCTTTTAGAAG
66 AAATGGAAATATTTTGCATCTAAATAATCAATATTTTATTTATCTTTTAGAAG
3098138 TGAT
1 TGAT
3098142 CTAATGAACT
Statistics
Matches: 120, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
118 120 1.00
ACGTcount: A:0.38, C:0.11, G:0.10, T:0.41
Consensus pattern (118 bp):
TGATTTTTCTAAAAAGAAATCTAACCCTATTAATTTGGTTCGAGTTAAATTACCATCAATAATTA
AAATGGAAATATTTTGCATCTAAATAATCAATATTTTATTTATCTTTTAGAAG
Found at i:3108840 original size:2 final size:2
Alignment explanation
Indices: 3108835--3108898 Score: 96
Period size: 2 Copynumber: 33.0 Consensus size: 2
3108825 AAAATTAAAT
*
3108835 TA TA TA -A TA TA TA TA TA TA TA TA TA TA TC 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 TA TA TA
*
3108876 TA TA TC TA -A TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA
3108899 AACAGGTTGG
Statistics
Matches: 56, Mismatches: 4, Indels: 4
0.88 0.06 0.06
Matches are distributed among these distances:
1 2 0.04
2 54 0.96
ACGTcount: A:0.48, C:0.03, G:0.00, T:0.48
Consensus pattern (2 bp):
TA
Found at i:3111216 original size:40 final size:39
Alignment explanation
Indices: 3111172--3111313 Score: 91
Period size: 37 Copynumber: 3.4 Consensus size: 39
3111162 TTTTATTATC
3111172 ATTTTATTTTTTATTTTATTTCATGTTTTCTCTTTGATTT
1 ATTTTATTTTTTATTTTATTTCAT-TTTTCTCTTTGATTT
*
3111212 ATTTTTATTTATATATATTT-TTT-A-TTTT-T-TTT-ATCTT
1 A-TTTTATTT-TTTAT-TTTATTTCATTTTTCTCTTTGAT-TT
3111249 ATATTTATTATTTTATTTTTATTTTTACATTTTT-TCCTTTGATTT
1 AT-TTTATT-TTTTA-TTTTA--TTT-CATTTTTCT-CTTTGATTT
3111294 ATTTGATATATTTTTATTTT
1 ATTT--TAT-TTTTTATTTT
3111314 CCTTTGATTT
Statistics
Matches: 81, Mismatches: 2, Indels: 33
0.70 0.02 0.28
Matches are distributed among these distances:
36 3 0.04
37 18 0.22
38 3 0.04
39 4 0.05
40 4 0.05
41 9 0.11
42 8 0.10
43 8 0.10
44 2 0.02
45 11 0.14
46 10 0.12
47 1 0.01
ACGTcount: A:0.20, C:0.05, G:0.03, T:0.73
Consensus pattern (39 bp):
ATTTTATTTTTTATTTTATTTCATTTTTCTCTTTGATTT
Found at i:3111220 original size:6 final size:6
Alignment explanation
Indices: 3111209--3111275 Score: 50
Period size: 6 Copynumber: 10.7 Consensus size: 6
3111199 TTCTCTTTGA
*
3111209 TTTATT TTTATT TATATATAT TTT-TT ATTT-TT TTTATCT TATATT TATTA-T
1 TTTATT TTTATT T-T-TAT-T TTTATT -TTTATT TTTAT-T TTTATT T-TTATT
3111260 TTTATT TTTATT TTTA
1 TTTATT TTTATT TTTA
3111276 CATTTTTTCC
Statistics
Matches: 51, Mismatches: 2, Indels: 16
0.74 0.03 0.23
Matches are distributed among these distances:
5 7 0.14
6 29 0.57
7 9 0.18
8 4 0.08
9 2 0.04
ACGTcount: A:0.22, C:0.01, G:0.00, T:0.76
Consensus pattern (6 bp):
TTTATT
Found at i:3111243 original size:27 final size:29
Alignment explanation
Indices: 3111208--3111273 Score: 84
Period size: 27 Copynumber: 2.3 Consensus size: 29
3111198 TTTCTCTTTG
*
3111208 ATTTATTTTTAT-TTATATATATT-TTTT
1 ATTTTTTTTTATCTTATATATATTATTTT
*
3111235 A-TTTTTTTTATCTTATATTTATTATTTT
1 ATTTTTTTTTATCTTATATATATTATTTT
3111263 ATTTTTATTTT
1 ATTTTT-TTTT
3111274 TACATTTTTT
Statistics
Matches: 33, Mismatches: 2, Indels: 5
0.82 0.05 0.12
Matches are distributed among these distances:
26 9 0.27
27 11 0.33
28 5 0.15
29 4 0.12
30 4 0.12
ACGTcount: A:0.23, C:0.02, G:0.00, T:0.76
Consensus pattern (29 bp):
ATTTTTTTTTATCTTATATATATTATTTT
Found at i:3111257 original size:20 final size:22
Alignment explanation
Indices: 3111208--3111262 Score: 60
Period size: 20 Copynumber: 2.5 Consensus size: 22
3111198 TTTCTCTTTG
3111208 ATTTATTTTTATTTATATATATT
1 ATTTATTTTT-TTTATATATATT
* *
3111231 TTTTATTTTTTTTATCT-TA-T
1 ATTTATTTTTTTTATATATATT
*
3111251 ATTTATTATTTT
1 ATTTATTTTTTT
3111263 ATTTTTATTT
Statistics
Matches: 28, Mismatches: 4, Indels: 3
0.80 0.11 0.09
Matches are distributed among these distances:
20 11 0.39
21 2 0.07
22 6 0.21
23 9 0.32
ACGTcount: A:0.24, C:0.02, G:0.00, T:0.75
Consensus pattern (22 bp):
ATTTATTTTTTTTATATATATT
Found at i:3111336 original size:30 final size:29
Alignment explanation
Indices: 3111280--3111342 Score: 92
Period size: 30 Copynumber: 2.1 Consensus size: 29
3111270 TTTTTACATT
3111280 TTTTCCTTTGATTTATTTGATATATTTTTA
1 TTTTCCTTTGATTTATTTGATATA-TTTTA
*
3111310 TTTTCCTTTGATTTATTT-ATCTTATTTTA
1 TTTTCCTTTGATTTATTTGAT-ATATTTTA
3111339 TTTT
1 TTTT
3111343 ATTTTTTCTC
Statistics
Matches: 31, Mismatches: 1, Indels: 3
0.89 0.03 0.09
Matches are distributed among these distances:
29 11 0.35
30 20 0.65
ACGTcount: A:0.17, C:0.08, G:0.05, T:0.70
Consensus pattern (29 bp):
TTTTCCTTTGATTTATTTGATATATTTTA
Found at i:3111340 original size:75 final size:72
Alignment explanation
Indices: 3111134--3111348 Score: 198
Period size: 69 Copynumber: 3.0 Consensus size: 72
3111124 TTTTCAACTA
* * * *
3111134 TTCATTTTTTCCTTTGATTCATTTAT-TA-TTTTATTATCATTTTATTT-TTTATTTTATTTCAT
1 TTCATTTTTTCCTTTGATTTATTTATATATTTTTATTTTC-TTTTATTTATTTATATTATTTTAT
* *
3111196 GTTTTCTCT
65 -TTTTATTT
* * *
3111205 TTGATTTATT--TTT-ATTTATATATAT-TTTTTATTTT-TTTTATCTTATATT-TATTATTTTA
1 TTCATTTTTTCCTTTGATTTATTTATATATTTTTATTTTCTTTTAT-TTAT-TTATATTATTTTA
3111264 TTTTTATTT
64 TTTTTATTT
* *
3111273 TTACATTTTTTCCTTTGATTTATTTGATATATTTTTATTTTCCTTTGATTTATTTATCTTATTTT
1 TT-CATTTTTTCCTTTGATTTATTT-ATATATTTTTATTTT-CTTTTATTTATTTATATTATTTT
3111338 A-TTTTATTT
63 ATTTTTATTT
3111347 TT
1 TT
3111349 TCTCCTTTTG
Statistics
Matches: 116, Mismatches: 14, Indels: 25
0.75 0.09 0.16
Matches are distributed among these distances:
67 6 0.05
68 18 0.16
69 28 0.24
70 2 0.02
71 11 0.09
72 7 0.06
73 4 0.03
74 22 0.19
75 13 0.11
76 5 0.04
ACGTcount: A:0.19, C:0.07, G:0.03, T:0.71
Consensus pattern (72 bp):
TTCATTTTTTCCTTTGATTTATTTATATATTTTTATTTTCTTTTATTTATTTATATTATTTTATT
TTTATTT
Found at i:3111369 original size:3 final size:3
Alignment explanation
Indices: 3111361--3111385 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
3111351 TCCTTTTGAT
3111361 TTA TTA TTA TTA TTA TTA TTA TTA T
1 TTA TTA TTA TTA TTA TTA TTA TTA T
3111386 ATGTTTTTTC
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:3111371 original size:75 final size:71
Alignment explanation
Indices: 3111174--3111371 Score: 179
Period size: 74 Copynumber: 2.7 Consensus size: 71
3111164 TTATTATCAT
* * *
3111174 TTTATTTTTTATTTTATTTCATGTTTTCTC-TTTGATTTATTTTTATTTATATATATTTTTTATT
1 TTTATTTTTTATTTTATTTTATTTTTTCTCTTTTGATTTA-TTTTATTTAGATATATTTTTTATT
*
3111238 TTTTTTA
65 TTTTTGA
* * **
3111245 TCTTATATTTATTATTTTATTTTTATTTTTACATTTTTTCCTTTGA-TTTATTT-GATATA-TTT
1 T-TTAT-TTT-TTATTTTA-TTTTATTTTTTC-TCTTTTGATTT-ATTTTATTTAGATATATTTT
3111307 TTATTTTCCTTTGA
60 TTATTTT--TTTGA
3111321 TTTATTTATCTTATTTTATTTTATTTTTTCTCCTTTTGATTTATTATTATT
1 TTTATTT-T-TTATTTTATTTTATTTTTTCT-CTTTTGATTTATT-TTATT
3111372 ATTATTATTA
Statistics
Matches: 101, Mismatches: 13, Indels: 22
0.74 0.10 0.16
Matches are distributed among these distances:
71 1 0.01
72 4 0.04
73 5 0.05
74 39 0.39
75 32 0.32
76 13 0.13
77 6 0.06
78 1 0.01
ACGTcount: A:0.19, C:0.07, G:0.03, T:0.72
Consensus pattern (71 bp):
TTTATTTTTTATTTTATTTTATTTTTTCTCTTTTGATTTATTTTATTTAGATATATTTTTTATTT
TTTTGA
Found at i:3111380 original size:69 final size:69
Alignment explanation
Indices: 3111251--3111380 Score: 160
Period size: 69 Copynumber: 1.9 Consensus size: 69
3111241 TTTATCTTAT
* *
3111251 ATTTATTATTTTATTTTTATTTTTACATTTTTTCCTTTGATTTATTTGATATATTTTTATTTTCC
1 ATTTATTATCTTATTTTTATTTTTACATTTTTTCCTTTGATTTATTTGATATATTATTATTTTCC
3111316 TTTG
66 TTTG
* *
3111320 ATTTATTTATCTTA-TTTTA-TTTTA-TTTTTTCTCCTTTTGATTTATTATTAT-TATTATTATT
1 ATTTA-TTATCTTATTTTTATTTTTACATTTTT-TCC-TTTGATTTATT-TGATATATTATTATT
3111381 ATTATATGTT
Statistics
Matches: 53, Mismatches: 4, Indels: 8
0.82 0.06 0.12
Matches are distributed among these distances:
67 5 0.09
68 8 0.15
69 30 0.57
70 10 0.19
ACGTcount: A:0.20, C:0.07, G:0.03, T:0.70
Consensus pattern (69 bp):
ATTTATTATCTTATTTTTATTTTTACATTTTTTCCTTTGATTTATTTGATATATTATTATTTTCC
TTTG
Found at i:3114465 original size:36 final size:35
Alignment explanation
Indices: 3114393--3114477 Score: 86
Period size: 37 Copynumber: 2.4 Consensus size: 35
3114383 ATCAAGAACA
* *
3114393 AAAAAGAAAAAAAGCAAAGAAACAAGAGAAACAAG
1 AAAAAGGAAAAAAGCAAAGAAACAAGAGAAAAAAG
3114428 AACAAAAGGAAAAAAG-AAAG-AACAA-AGATCAAAAAG
1 -A-AAAAGGAAAAAAGCAAAGAAACAAGAGA--AAAAAG
3114464 AAAAAGGAACAAAA
1 AAAAAGGAA-AAAA
3114478 AGCACATGCA
Statistics
Matches: 43, Mismatches: 2, Indels: 9
0.80 0.04 0.17
Matches are distributed among these distances:
34 11 0.26
35 10 0.23
36 10 0.23
37 12 0.28
ACGTcount: A:0.74, C:0.08, G:0.16, T:0.01
Consensus pattern (35 bp):
AAAAAGGAAAAAAGCAAAGAAACAAGAGAAAAAAG
Found at i:3115096 original size:22 final size:22
Alignment explanation
Indices: 3115067--3115121 Score: 101
Period size: 22 Copynumber: 2.5 Consensus size: 22
3115057 GCTACCCCAT
3115067 CAAACCTTTGAGCATCAAATGC
1 CAAACCTTTGAGCATCAAATGC
*
3115089 TAAACCTTTGAGCATCAAATGC
1 CAAACCTTTGAGCATCAAATGC
3115111 CAAACCTTTGA
1 CAAACCTTTGA
3115122 CCAAACATAA
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:0.36, C:0.25, G:0.13, T:0.25
Consensus pattern (22 bp):
CAAACCTTTGAGCATCAAATGC
Found at i:3116938 original size:423 final size:423
Alignment explanation
Indices: 3116147--3117103 Score: 1596
Period size: 423 Copynumber: 2.3 Consensus size: 423
3116137 ATATCGTGCC
* *
3116147 ACTCGAGACAACACAAGTTCAACTTCACGACGAAGGGACGGCTGGTTGTCAACAAACAAATTCCC
1 ACTCGAGACAACACAAGTTCAACTTCACGACGAAGGGACCGCT-GTTGTCAACAAACAATTTCCC
*
3116212 AATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTCCAGATAACGCAAGTTCAACT
65 AATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTCCAGACAACGCAAGTTCAACT
*
3116277 TCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCCCAATTTCAGAGCCAATTTCAACTTC
130 TCACGACGAAGGGACCGCTGGTTGTCAACAAAAAACTTCCCAATTTCAGAGCCAATTTCAACTTC
* * *
3116342 ACAGCGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCATGACGAAGGGACTGCTGGTTG
195 ACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTG
* *
3116407 TTAACAAACAACTTCCCAATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTCCAG
260 TCAACAAACAACTTCCCAATTTCAGAGCCAATTTCAACTTCACAGCAAAGGATATTGGACTCCAG
* *
3116472 ACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTAGTTGTCAATAAACAATTTCCCAATTTCA
325 ACAACGCAAGTTCAACTTCACGACGAAGAGACCGCTAGTTGTCAACAAACAATTTCCCAATTTCA
*
3116537 GAGCCAATTTCAACTTCACAGCGAAGGATATT-G
390 GAGCCAATTTCAACTTCACAACGAAGGATATTGG
* ** *
3116570 ACTCTAGACAACGTAAGTTCAACTTCACGATGAAGGGACCGCTAGTTGTCAACAAACAATTTCCC
1 ACTCGAGACAACACAAGTTCAACTTCACGACGAAGGGACCGCT-GTTGTCAACAAACAATTTCCC
*
3116635 AATTTCGGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTCCAGACAACGCAAGTTCAACT
65 AATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTCCAGACAACGCAAGTTCAACT
* *
3116700 TCACGACGAAGGGACCGCTGGTTGTCAACAAAAAACTTCTCAATTTCAGAGCCAATTTTAACTTC
130 TCACGACGAAGGGACCGCTGGTTGTCAACAAAAAACTTCCCAATTTCAGAGCCAATTTCAACTTC
3116765 ACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTG
195 ACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTG
* *
3116830 TCAACAAACAACTTCCCAATTTTAGAGCCAATTTCAACTTCACAGCAAAGGATATTGGACTCGAG
260 TCAACAAACAACTTCCCAATTTCAGAGCCAATTTCAACTTCACAGCAAAGGATATTGGACTCCAG
* *
3116895 ACAACGCAAGTTCAACTTCACGACGAAGAGACCGCTGGTTGTCAACAAACAATTTCCCAATTTCG
325 ACAACGCAAGTTCAACTTCACGACGAAGAGACCGCTAGTTGTCAACAAACAATTTCCCAATTTCA
3116960 GAGCCAATTTCAACTTCACAACGAAGGATATTGG
390 GAGCCAATTTCAACTTCACAACGAAGGATATTGG
* *
3116994 ACTCGAGACAATACAAGTTCAACTTCACAACGAAGGGA-CGACTGATTGTCAACAAACAATTTCC
1 ACTCGAGACAACACAAGTTCAACTTCACGACGAAGGGACCG-CTG-TTGTCAACAAACAATTTCC
** *
3117058 CGGTTCCAGAGCCAATTTCAACTTCAC-GACGAAGGATATTGGACTC
64 CAATTTCAGAGCCAATTTCAACTTCACAG-CGAAGGATATTGGACTC
3117104 GGAGCAATAC
Statistics
Matches: 496, Mismatches: 34, Indels: 7
0.92 0.06 0.01
Matches are distributed among these distances:
423 402 0.81
424 94 0.19
ACGTcount: A:0.34, C:0.25, G:0.18, T:0.22
Consensus pattern (423 bp):
ACTCGAGACAACACAAGTTCAACTTCACGACGAAGGGACCGCTGTTGTCAACAAACAATTTCCCA
ATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTT
CACGACGAAGGGACCGCTGGTTGTCAACAAAAAACTTCCCAATTTCAGAGCCAATTTCAACTTCA
CAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGT
CAACAAACAACTTCCCAATTTCAGAGCCAATTTCAACTTCACAGCAAAGGATATTGGACTCCAGA
CAACGCAAGTTCAACTTCACGACGAAGAGACCGCTAGTTGTCAACAAACAATTTCCCAATTTCAG
AGCCAATTTCAACTTCACAACGAAGGATATTGG
Found at i:3117115 original size:106 final size:106
Alignment explanation
Indices: 3116147--3117103 Score: 1542
Period size: 106 Copynumber: 9.0 Consensus size: 106
3116137 ATATCGTGCC
* * * *
3116147 ACTCGAGACAACACAAGTTCAACTTCACGACGAAGGGACGGCTGGTTGTCAACAAACAAATTCCC
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCCC
3116212 AATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGG
66 AATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGG
*
3116253 ACTCCAGATAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCCC
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCCC
3116318 AATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGG
66 AATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGG
* * *
3116359 ACTCCAGACAACGCAAGTTCAACTTCATGACGAAGGGACTGCTGGTTGTTAACAAACAACTTCCC
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCCC
3116424 AATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGG
66 AATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGG
* * *
3116465 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTAGTTGTCAATAAACAATTTCCC
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCCC
3116530 AATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATT-G
66 AATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGG
* * * * *
3116570 ACTCTAGACAACGTAAGTTCAACTTCACGATGAAGGGACCGCTAGTTGTCAACAAACAATTTCCC
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCCC
*
3116635 AATTTCGGAGCCAATTTCAACTTCACAGCGAAGGATATTGG
66 AATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGG
* *
3116676 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAAAAACTTCTC
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCCC
* *
3116741 AATTTCAGAGCCAATTTTAACTTCACAACGAAGGATATTGG
66 AATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGG
3116782 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCCC
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCCC
* *
3116847 AATTTTAGAGCCAATTTCAACTTCACAGCAAAGGATATTGG
66 AATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGG
* * *
3116888 ACTCGAGACAACGCAAGTTCAACTTCACGACGAAGAGACCGCTGGTTGTCAACAAACAATTTCCC
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCCC
* *
3116953 AATTTCGGAGCCAATTTCAACTTCACAACGAAGGATATTGG
66 AATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGG
* ** * * *
3116994 ACTCGAGACAATACAAGTTCAACTTCACAACGAAGGGA-CGACTGATTGTCAACAAACAATTTCC
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCG-CTGGTTGTCAACAAACAACTTCC
** *
3117058 CGGTTCCAGAGCCAATTTCAACTTCAC-GACGAAGGATATTGG
65 CAATTTCAGAGCCAATTTCAACTTCACAG-CGAAGGATATTGG
3117100 ACTC
1 ACTC
3117104 GGAGCAATAC
Statistics
Matches: 795, Mismatches: 53, Indels: 6
0.93 0.06 0.01
Matches are distributed among these distances:
105 102 0.13
106 693 0.87
ACGTcount: A:0.34, C:0.25, G:0.18, T:0.22
Consensus pattern (106 bp):
ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCCC
AATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGG
Found at i:3118576 original size:40 final size:39
Alignment explanation
Indices: 3118532--3118773 Score: 159
Period size: 40 Copynumber: 6.1 Consensus size: 39
3118522 TTTTATTATC
*
3118532 ATTTTATTTTTTATTTTATTTCATGTTTTCTCTTTGATTT
1 ATTTTATTTTTTATTTTATTT-ATTTTTTCTCTTTGATTT
* *
3118572 ATTTTTATTTATATATATTT-TTTATTTTTTTATCTTAT-ATTT
1 A-TTTTATTT-TTTAT-TTTATTTA-TTTTTTCTCTT-TGATTT
* **
3118614 ATTATTTTATTTTTATTTT-TACATTTTTTC-CTTTGATTT
1 ATT-TTAT-TTTTTATTTTATTTATTTTTTCTCTTTGATTT
*
3118653 ATTTGATATATTTTTATTTTATTT-TATTTTC-CTTTGATTT
1 ATTT--TAT-TTTTTATTTTATTTATTTTTTCTCTTTGATTT
*
3118693 A-TTTA--TCTTATTTTATTTTATTTTTTCTCCTTTTGATTT
1 ATTTTATTTTTTATTTTA-TTTATTTTTTCT-C-TTTGATTT
*
3118732 ATTATTATTATTATTATTTTA--TGTTTTTTC-C-TTGATTT
1 ATT-TTATT-TT-TTATTTTATTTATTTTTTCTCTTTGATTT
3118770 ATTT
1 ATTT
3118774 AAAATTTATG
Statistics
Matches: 164, Mismatches: 16, Indels: 47
0.72 0.07 0.21
Matches are distributed among these distances:
34 9 0.05
35 3 0.02
36 6 0.04
37 3 0.02
38 13 0.08
39 21 0.13
40 38 0.23
41 20 0.12
42 36 0.22
43 6 0.04
44 1 0.01
45 8 0.05
ACGTcount: A:0.19, C:0.06, G:0.03, T:0.71
Consensus pattern (39 bp):
ATTTTATTTTTTATTTTATTTATTTTTTCTCTTTGATTT
Found at i:3118609 original size:26 final size:26
Alignment explanation
Indices: 3118573--3118627 Score: 85
Period size: 26 Copynumber: 2.1 Consensus size: 26
3118563 CTTTGATTTA
3118573 TTTTTATTTATATATATT-TTTTATT
1 TTTTTATTTATATATATTATTTTATT
*
3118598 TTTTTATCTTATATTTATTATTTTATT
1 TTTTTAT-TTATATATATTATTTTATT
3118625 TTT
1 TTT
3118628 ATTTTTACAT
Statistics
Matches: 27, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
25 7 0.26
26 10 0.37
27 10 0.37
ACGTcount: A:0.22, C:0.02, G:0.00, T:0.76
Consensus pattern (26 bp):
TTTTTATTTATATATATTATTTTATT
Found at i:3118627 original size:50 final size:51
Alignment explanation
Indices: 3118569--3118682 Score: 130
Period size: 50 Copynumber: 2.3 Consensus size: 51
3118559 TTCTCTTTGA
* *
3118569 TTTATTTTTATTTATATATATTTTTT-ATTT-TTTTATCTT-ATAT-TTATTAT
1 TTTATTTTTATTT-T-TACATTTTTTCATTTGATTTAT-TTGATATATTATTAT
* *
3118619 TTTATTTTTATTTTTACATTTTTTCCTTTGATTTATTTGATATATTTTTAT
1 TTTATTTTTATTTTTACATTTTTTCATTTGATTTATTTGATATATTATTAT
3118670 TTTA-TTTTATTTT
1 TTTATTTTTATTTT
3118683 CCTTTGATTT
Statistics
Matches: 56, Mismatches: 4, Indels: 8
0.82 0.06 0.12
Matches are distributed among these distances:
48 9 0.16
49 6 0.11
50 31 0.55
51 10 0.18
ACGTcount: A:0.21, C:0.04, G:0.02, T:0.74
Consensus pattern (51 bp):
TTTATTTTTATTTTTACATTTTTTCATTTGATTTATTTGATATATTATTAT
Found at i:3118633 original size:39 final size:37
Alignment explanation
Indices: 3118534--3118772 Score: 179
Period size: 39 Copynumber: 6.2 Consensus size: 37
3118524 TTATTATCAT
* *
3118534 TTTATT-TTTTA-TTTTATTTCA-TGTTTTCTCTTTGA
1 TTTATTATTTTATTTTTATTTTATTTTTTTC-CTTTGA
* *
3118569 TTTATTTTTATTTATATATATT-TTTTATTTTTTTATCTTAT-A
1 TTTA---TTATTT-TAT-TTTTATTTTATTTTTTT-CCTT-TGA
*
3118611 TTTATTATTTTATTTTTATTTTTACATTTTTTCCTTTGA
1 TTTATTATTTTATTTTTA-TTTTA-TTTTTTTCCTTTGA
*
3118650 TTTATT-TGATATATTTTTATTTTATTTTATTTTCCTTTGA
1 TTTATTAT--TTTATTTTTATTTTA-TTT-TTTTCCTTTGA
*
3118690 TTTATTTATCTTA-TTTTATTTTATTTTTTCTCCTTTTGA
1 TTTA-TTATTTTATTTTTATTTTATTTTTT-TCC-TTTGA
*
3118729 TTTATTATTATTATTATTATTTTATGTTTTTTCC-TTGA
1 TTTATTATT-TTATTTTTATTTTAT-TTTTTTCCTTTGA
3118767 TTTATT
1 TTTATT
3118773 TAAAATTTAT
Statistics
Matches: 166, Mismatches: 14, Indels: 45
0.74 0.06 0.20
Matches are distributed among these distances:
35 4 0.02
37 6 0.04
38 27 0.16
39 53 0.32
40 47 0.28
41 11 0.07
42 17 0.10
43 1 0.01
ACGTcount: A:0.19, C:0.06, G:0.03, T:0.72
Consensus pattern (37 bp):
TTTATTATTTTATTTTTATTTTATTTTTTTCCTTTGA
Found at i:3118639 original size:26 final size:25
Alignment explanation
Indices: 3118569--3118639 Score: 76
Period size: 26 Copynumber: 2.8 Consensus size: 25
3118559 TTCTCTTTGA
*
3118569 TTTATTTTTA--TTTATATATATTT
1 TTTATTTTTATTTTTATATTTATTT
3118592 TTTATTTTT-TTATCTTATATTTATTAT
1 TTTATTTTTATT-T-TTATATTTATT-T
*
3118619 TTTATTTTTATTTTTACATTT
1 TTTATTTTTATTTTTATATTT
3118640 TTTCCTTTGA
Statistics
Matches: 40, Mismatches: 2, Indels: 9
0.78 0.04 0.18
Matches are distributed among these distances:
23 9 0.22
25 1 0.03
26 17 0.43
27 11 0.28
28 2 0.05
ACGTcount: A:0.23, C:0.03, G:0.00, T:0.75
Consensus pattern (25 bp):
TTTATTTTTATTTTTATATTTATTT
Found at i:3118674 original size:5 final size:5
Alignment explanation
Indices: 3118664--3118716 Score: 56
Period size: 5 Copynumber: 10.8 Consensus size: 5
3118654 TTTGATATAT
* * *
3118664 TTTTA TTTTA TTTTA TTTTCC TTTGA -TTTA -TTTA TCTTA TTTTA TTTTA
1 TTTTA TTTTA TTTTA TTTT-A TTTTA TTTTA TTTTA TTTTA TTTTA TTTTA
3118713 TTTT
1 TTTT
3118717 TTCTCCTTTT
Statistics
Matches: 40, Mismatches: 6, Indels: 4
0.80 0.12 0.08
Matches are distributed among these distances:
4 7 0.17
5 30 0.75
6 3 0.08
ACGTcount: A:0.17, C:0.06, G:0.02, T:0.75
Consensus pattern (5 bp):
TTTTA
Found at i:3120728 original size:5 final size:5
Alignment explanation
Indices: 3120707--3120905 Score: 58
Period size: 5 Copynumber: 38.4 Consensus size: 5
3120697 GATTCATTTA
* * *
3120707 TTATT TTATT ATCATT TTATTTT TTATT TTATT TCATGT TT-TCT CTATGAT
1 TTATT TTATT -TTATT TTA--TT TTATT TTATT TTAT-T TTAT-T TTAT--T
*
3120758 TTATTT TTATT TATATAT ATT-TT TTATT TT-TT TTATC TTATAT TTA--
1 TTA-TT TTATT T-TAT-T -TTATT TTATT TTATT TTATT TTAT-T TTATT
* ** * *
3120804 TTATT TTATTT TTATTT TTACAT TT-TT TCCTT TGA-T TTATT TGA-T
1 TTATT TTA-TT TTA-TT TTA-TT TTATT TTATT TTATT TTATT TTATT
* * * *
3120849 ATATTT TTATT TTATT TTATT TTCCTT TGA-T TTA-T TTATC TTATT TTATT
1 TTA-TT TTATT TTATT TTATT TT-ATT TTATT TTATT TTATT TTATT TTATT
3120899 TTATT TT
1 TTATT TT
3120906 TTCTCCTTTT
Statistics
Matches: 145, Mismatches: 27, Indels: 44
0.67 0.12 0.20
Matches are distributed among these distances:
3 3 0.02
4 20 0.14
5 72 0.50
6 38 0.26
7 10 0.07
8 2 0.01
ACGTcount: A:0.20, C:0.06, G:0.03, T:0.72
Consensus pattern (5 bp):
TTATT
Found at i:3120768 original size:6 final size:6
Alignment explanation
Indices: 3120757--3120823 Score: 50
Period size: 6 Copynumber: 10.7 Consensus size: 6
3120747 TTCTCTATGA
*
3120757 TTTATT TTTATT TATATATAT TTT-TT ATTT-TT TTTATCT TATATT TATTA-T
1 TTTATT TTTATT T-T-TAT-T TTTATT -TTTATT TTTAT-T TTTATT T-TTATT
3120808 TTTATT TTTATT TTTA
1 TTTATT TTTATT TTTA
3120824 CATTTTTTCC
Statistics
Matches: 51, Mismatches: 2, Indels: 16
0.74 0.03 0.23
Matches are distributed among these distances:
5 7 0.14
6 29 0.57
7 9 0.18
8 4 0.08
9 2 0.04
ACGTcount: A:0.22, C:0.01, G:0.00, T:0.76
Consensus pattern (6 bp):
TTTATT
Found at i:3120791 original size:27 final size:29
Alignment explanation
Indices: 3120756--3120821 Score: 84
Period size: 27 Copynumber: 2.3 Consensus size: 29
3120746 TTTCTCTATG
*
3120756 ATTTATTTTTAT-TTATATATATT-TTTT
1 ATTTTTTTTTATCTTATATATATTATTTT
*
3120783 A-TTTTTTTTATCTTATATTTATTATTTT
1 ATTTTTTTTTATCTTATATATATTATTTT
3120811 ATTTTTATTTT
1 ATTTTT-TTTT
3120822 TACATTTTTT
Statistics
Matches: 33, Mismatches: 2, Indels: 5
0.82 0.05 0.12
Matches are distributed among these distances:
26 9 0.27
27 11 0.33
28 5 0.15
29 4 0.12
30 4 0.12
ACGTcount: A:0.23, C:0.02, G:0.00, T:0.76
Consensus pattern (29 bp):
ATTTTTTTTTATCTTATATATATTATTTT
Found at i:3120812 original size:51 final size:51
Alignment explanation
Indices: 3120757--3120871 Score: 130
Period size: 51 Copynumber: 2.3 Consensus size: 51
3120747 TTCTCTATGA
* **
3120757 TTTATTTTTATTTATATATATTTTTT-ATTTTTTTTATCTT-ATAT-TTATTAT
1 TTTATTTTTATTT-T-TACATTTTTTCATTTGATTTAT-TTGATATATTATTAT
* *
3120808 TTTATTTTTATTTTTACATTTTTTCCTTTGATTTATTTGATATATTTTTAT
1 TTTATTTTTATTTTTACATTTTTTCATTTGATTTATTTGATATATTATTAT
3120859 TTTA-TTTTATTTT
1 TTTATTTTTATTTT
3120872 CCTTTGATTT
Statistics
Matches: 56, Mismatches: 5, Indels: 7
0.82 0.07 0.10
Matches are distributed among these distances:
49 11 0.20
50 22 0.39
51 23 0.41
ACGTcount: A:0.21, C:0.03, G:0.02, T:0.74
Consensus pattern (51 bp):
TTTATTTTTATTTTTACATTTTTTCATTTGATTTATTTGATATATTATTAT
Found at i:3120818 original size:20 final size:22
Alignment explanation
Indices: 3120758--3120823 Score: 66
Period size: 23 Copynumber: 3.0 Consensus size: 22
3120748 TCTCTATGAT
*
3120758 TTATTTTTATTTATATATATTTT
1 TTATTTTTATTTAT-TATATTTA
3120781 TTATTTTT-TTTATCTTATATTTA
1 TTATTTTTATTTA--TTATATTTA
*
3120804 TTA-TTTTATTT-TTATTTTTA
1 TTATTTTTATTTATTATATTTA
3120824 CATTTTTTCC
Statistics
Matches: 38, Mismatches: 2, Indels: 9
0.78 0.04 0.18
Matches are distributed among these distances:
20 8 0.21
22 8 0.21
23 21 0.55
24 1 0.03
ACGTcount: A:0.23, C:0.02, G:0.00, T:0.76
Consensus pattern (22 bp):
TTATTTTTATTTATTATATTTA
Found at i:3120842 original size:39 final size:38
Alignment explanation
Indices: 3120715--3120961 Score: 189
Period size: 40 Copynumber: 6.1 Consensus size: 38
3120705 TATTATTTTA
* *
3120715 TTATCATTTTATTTTTTATTTTATTTCATGTTTTCTCTATGAT
1 TTATTATTTTA-TTTTTATTTTATTT--T-TTTTC-CTTTGAT
* *
3120758 TTATTTTTATTTATATATATT-TTTTATTTTTTTTATCTTAT-AT
1 TTA---TTATTT-TAT-TTTTATTTTATTTTTTTT-CCTT-TGAT
**
3120801 TTATTATTTTATTTTTATTTTTACATTTTTTCCTTTGAT
1 TTATTATTTTATTTTTA-TTTTATTTTTTTTCCTTTGAT
*
3120840 TTATT-TGATATATTTTTATTTTATTTTATTTTCCTTTGAT
1 TTATTAT--TTTATTTTTATTTTATTTT-TTTTCCTTTGAT
* *
3120880 TTATTTATCTTA-TTTTATTTTATTTTTTCTCCTTTTGAT
1 TTA-TTATTTTATTTTTATTTTATTTTTTTTCC-TTTGAT
* *
3120919 TTATTATTATTATTATTATTTTATGTTTTTTCC-TTGAT
1 TTATTATT-TTATTTTTATTTTATTTTTTTTCCTTTGAT
3120957 TTATT
1 TTATT
3120962 TAAAATTTAT
Statistics
Matches: 168, Mismatches: 18, Indels: 41
0.74 0.08 0.18
Matches are distributed among these distances:
38 24 0.14
39 46 0.27
40 60 0.36
41 2 0.01
42 1 0.01
43 14 0.08
44 2 0.01
46 14 0.08
47 5 0.03
ACGTcount: A:0.19, C:0.06, G:0.03, T:0.71
Consensus pattern (38 bp):
TTATTATTTTATTTTTATTTTATTTTTTTTCCTTTGAT
Found at i:3120867 original size:25 final size:24
Alignment explanation
Indices: 3120757--3120870 Score: 87
Period size: 25 Copynumber: 4.7 Consensus size: 24
3120747 TTCTCTATGA
*
3120757 TTTATTTT-TATTTATATATAT-TT
1 TTTATTTTAT-TTTATTTATATATT
3120780 TTTATTTT-TTTTATCTTATAT-TT
1 TTTATTTTATTTTAT-TTATATATT
* * *
3120803 ATTATTTTATTTTTATTTTTACATT
1 TTTATTTTA-TTTTATTTATATATT
3120828 TTT-TCCTTTGA-TTTATTTGATATATT
1 TTTAT--TTT-ATTTTATTT-ATATATT
3120854 TTTATTTTATTTTATTT
1 TTTATTTTATTTTATTT
3120871 TCCTTTGATT
Statistics
Matches: 74, Mismatches: 7, Indels: 18
0.75 0.07 0.18
Matches are distributed among these distances:
22 5 0.07
23 23 0.31
24 6 0.08
25 27 0.36
26 11 0.15
27 2 0.03
ACGTcount: A:0.21, C:0.04, G:0.02, T:0.74
Consensus pattern (24 bp):
TTTATTTTATTTTATTTATATATT
Found at i:3120882 original size:79 final size:76
Alignment explanation
Indices: 3120763--3120961 Score: 214
Period size: 79 Copynumber: 2.6 Consensus size: 76
3120753 ATGATTTATT
* *
3120763 TTTATTTATATA-TATT-TTTTATTTTTTTTATCTTAT-ATTTATTATTTTATTTTTATTTTTAC
1 TTTATTTATATATTATTATTTTATTTTTTTT-CCTT-TGATTTATTATCTTA-TTTTA-TTTTA-
3120825 ATTTTT-TCC-TTTGA
61 ATTTTTCTCCTTTTGA
* *
3120839 TTTATTTGATATATTTTTATTTTATTTTATTTTCCTTTGATTTATTTATCTTATTTTATTTTATT
1 TTTATTT-ATATATTATTATTTTATTTT-TTTTCCTTTGATTTA-TTATCTTATTTTATTTTAAT
3120904 TTTTCTCCTTTTGA
63 TTTTCTCCTTTTGA
*
3120918 TTTA-TTATTATTATTATTATTTTATGTTTTTTCC-TTGATTTATT
1 TTTATTTA-TA-TATTATTATTTTATTTTTTTTCCTTTGATTTATT
3120962 TAAAATTTAT
Statistics
Matches: 107, Mismatches: 6, Indels: 20
0.80 0.05 0.15
Matches are distributed among these distances:
76 9 0.08
77 19 0.18
78 22 0.21
79 46 0.43
80 11 0.10
ACGTcount: A:0.20, C:0.06, G:0.03, T:0.71
Consensus pattern (76 bp):
TTTATTTATATATTATTATTTTATTTTTTTTCCTTTGATTTATTATCTTATTTTATTTTAATTTT
TCTCCTTTTGA
Found at i:3123765 original size:35 final size:34
Alignment explanation
Indices: 3123680--3123766 Score: 90
Period size: 35 Copynumber: 2.5 Consensus size: 34
3123670 AATATAATTT
*
3123680 TAAATACAACAAACTTACAATAAATATTAAATGG
1 TAAATACAACAAAATTACAATAAATATTAAATGG
*
3123714 TAAATGATAA-ACAAATTACAATAACTGATATTAAATGG
1 TAAAT-ACAACA-AAATTACAATAA---ATATTAAATGG
3123752 T-AATA-AACAAAATTA
1 TAAATACAACAAAATTA
3123767 ACCAAAATAC
Statistics
Matches: 45, Mismatches: 2, Indels: 11
0.78 0.03 0.19
Matches are distributed among these distances:
34 6 0.13
35 22 0.49
36 2 0.04
37 3 0.07
38 12 0.27
ACGTcount: A:0.56, C:0.09, G:0.07, T:0.28
Consensus pattern (34 bp):
TAAATACAACAAAATTACAATAAATATTAAATGG
Found at i:3123799 original size:34 final size:33
Alignment explanation
Indices: 3123761--3123844 Score: 91
Period size: 34 Copynumber: 2.5 Consensus size: 33
3123751 GTAATAAACA
*
3123761 AAATTAACCAAAATACATTAACAA-AAAGTCCAA-C
1 AAATTAA-CAAAATAAATTAA-AATAAA-TCCAACC
3123795 AAATTTAACAAAATAAATTAAAATAAATCCAACC
1 AAA-TTAACAAAATAAATTAAAATAAATCCAACC
**
3123829 AAATTAATGAAATAAA
1 AAATTAACAAAATAAA
3123845 ATAAGTATTA
Statistics
Matches: 44, Mismatches: 3, Indels: 7
0.81 0.06 0.13
Matches are distributed among these distances:
33 18 0.41
34 22 0.50
35 4 0.09
ACGTcount: A:0.62, C:0.14, G:0.02, T:0.21
Consensus pattern (33 bp):
AAATTAACAAAATAAATTAAAATAAATCCAACC
Found at i:3123844 original size:33 final size:34
Alignment explanation
Indices: 3123757--3123833 Score: 95
Period size: 34 Copynumber: 2.2 Consensus size: 34
3123747 AATGGTAATA
* *
3123757 AACAAAATTAACCAAAATACATTAACAAAAAGTCC
1 AACAAATTTAA-CAAAATAAATTAACAAAAAGTCC
3123792 AACAAATTTAACAAAATAAATTAA-AATAAA-TCC
1 AACAAATTTAACAAAATAAATTAACAA-AAAGTCC
3123825 AACCAAATT
1 AA-CAAATT
3123834 AATGAAATAA
Statistics
Matches: 38, Mismatches: 2, Indels: 5
0.84 0.04 0.11
Matches are distributed among these distances:
33 7 0.18
34 21 0.55
35 10 0.26
ACGTcount: A:0.61, C:0.17, G:0.01, T:0.21
Consensus pattern (34 bp):
AACAAATTTAACAAAATAAATTAACAAAAAGTCC
Found at i:3132737 original size:15 final size:15
Alignment explanation
Indices: 3132719--3132757 Score: 60
Period size: 15 Copynumber: 2.6 Consensus size: 15
3132709 TAACCGGTTT
3132719 CGGTTTTAAAAAAAC
1 CGGTTTTAAAAAAAC
*
3132734 CGGTTATAAAAAAAC
1 CGGTTTTAAAAAAAC
*
3132749 CGATTTTAA
1 CGGTTTTAA
3132758 TATTATTAAA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
15 21 1.00
ACGTcount: A:0.46, C:0.13, G:0.13, T:0.28
Consensus pattern (15 bp):
CGGTTTTAAAAAAAC
Found at i:3136379 original size:45 final size:45
Alignment explanation
Indices: 3136267--3136399 Score: 171
Period size: 45 Copynumber: 2.9 Consensus size: 45
3136257 TATTTTTGTT
* * *
3136267 TTTTTTCGAATAAATGCTTGCGAACTAGATATCATACGGTTAGGTTTA
1 TTTTTT-GAAT-AA-GCATGCGAACTAGATATCATGCAGTTAGGTTTA
*
3136315 -TTTTTGAACAAGCATGCGAACTAGATATCATGCAGTTAGGTTTA
1 TTTTTTGAATAAGCATGCGAACTAGATATCATGCAGTTAGGTTTA
*
3136359 TTTTTTGAATAAGCATGCGAATTAGATATCATG-AGGTTAGG
1 TTTTTTGAATAAGCATGCGAACTAGATATCATGCA-GTTAGG
3136400 ATTTCCTTTT
Statistics
Matches: 77, Mismatches: 6, Indels: 7
0.86 0.07 0.08
Matches are distributed among these distances:
44 31 0.40
45 38 0.49
46 3 0.04
47 5 0.06
ACGTcount: A:0.31, C:0.11, G:0.21, T:0.37
Consensus pattern (45 bp):
TTTTTTGAATAAGCATGCGAACTAGATATCATGCAGTTAGGTTTA
Found at i:3146030 original size:6 final size:6
Alignment explanation
Indices: 3146004--3146054 Score: 59
Period size: 6 Copynumber: 8.3 Consensus size: 6
3145994 ATTTCGCTTG
* *
3146004 AAGAAGA AATAAA AA-AAA AAGAGA AAGAAAA AAGAAA AAGAAA AAGAAA
1 AAGAA-A AAGAAA AAGAAA AAGAAA AAG-AAA AAGAAA AAGAAA AAGAAA
3146053 AA
1 AA
3146055 AGGAGGAAAA
Statistics
Matches: 39, Mismatches: 3, Indels: 5
0.83 0.06 0.11
Matches are distributed among these distances:
5 5 0.13
6 25 0.64
7 9 0.23
ACGTcount: A:0.82, C:0.00, G:0.16, T:0.02
Consensus pattern (6 bp):
AAGAAA
Found at i:3146032 original size:24 final size:25
Alignment explanation
Indices: 3146004--3146050 Score: 69
Period size: 24 Copynumber: 1.9 Consensus size: 25
3145994 ATTTCGCTTG
* *
3146004 AAGAAGAAATAAAAA-AAAAAGAGA
1 AAGAAAAAAGAAAAAGAAAAAGAGA
3146028 AAGAAAAAAGAAAAAGAAAAAGA
1 AAGAAAAAAGAAAAAGAAAAAGA
3146051 AAAAAGGAGG
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
24 13 0.65
25 7 0.35
ACGTcount: A:0.81, C:0.00, G:0.17, T:0.02
Consensus pattern (25 bp):
AAGAAAAAAGAAAAAGAAAAAGAGA
Found at i:3146038 original size:28 final size:28
Alignment explanation
Indices: 3146007--3146093 Score: 68
Period size: 30 Copynumber: 3.0 Consensus size: 28
3145997 TCGCTTGAAG
*
3146007 AAGAAATAAAAAAAAAAGAGAAAGAAAA
1 AAGAAAAAAAAAAAAAAGAGAAAGAAAA
* * *
3146035 AAGAAAAAGAAAAAGAAAAAAGGAGGAAAA
1 AAGAAAAA-AAAAA-AAAAGAGAAAGAAAA
* * *
3146065 ATGAAAGAAAATGAAAAATGAGAAA-AAAA
1 AAGAAA-AAAA-AAAAAAAGAGAAAGAAAA
3146094 TTGAAAAATG
Statistics
Matches: 45, Mismatches: 10, Indels: 7
0.73 0.16 0.11
Matches are distributed among these distances:
28 7 0.16
29 9 0.20
30 25 0.56
31 4 0.09
ACGTcount: A:0.77, C:0.00, G:0.18, T:0.05
Consensus pattern (28 bp):
AAGAAAAAAAAAAAAAAGAGAAAGAAAA
Found at i:3146041 original size:19 final size:19
Alignment explanation
Indices: 3146014--3146056 Score: 70
Period size: 19 Copynumber: 2.3 Consensus size: 19
3146004 AAGAAGAAAT
*
3146014 AAAAA-AAAAAGAGAAAGA
1 AAAAAGAAAAAGAAAAAGA
3146032 AAAAAGAAAAAGAAAAAGA
1 AAAAAGAAAAAGAAAAAGA
3146051 AAAAAG
1 AAAAAG
3146057 GAGGAAAAAT
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
18 5 0.22
19 18 0.78
ACGTcount: A:0.84, C:0.00, G:0.16, T:0.00
Consensus pattern (19 bp):
AAAAAGAAAAAGAAAAAGA
Found at i:3146082 original size:18 final size:17
Alignment explanation
Indices: 3146034--3146141 Score: 82
Period size: 17 Copynumber: 6.2 Consensus size: 17
3146024 GAGAAAGAAA
*
3146034 AAAGAAAAAGAAAAA-G
1 AAAGAAAATGAAAAATG
*
3146050 AAA-AAAGGAGGAAAAATG
1 AAAGAAA--ATGAAAAATG
3146068 AAAGAAAATGAAAAATG
1 AAAGAAAATGAAAAATG
*
3146085 AGAAAAAAATTGAAAAATGGTG
1 A-AAGAAAA-TGAAAAA---TG
3146107 AAA-AAAA-GAAAAATG
1 AAAGAAAATGAAAAATG
3146122 -AAGAAAAATGAAAAATG
1 AAAG-AAAATGAAAAATG
3146139 AAA
1 AAA
3146142 AATATAAAAC
Statistics
Matches: 76, Mismatches: 3, Indels: 24
0.74 0.03 0.23
Matches are distributed among these distances:
14 2 0.03
15 5 0.07
16 7 0.09
17 25 0.33
18 18 0.24
19 10 0.13
20 4 0.05
21 2 0.03
22 3 0.04
ACGTcount: A:0.71, C:0.00, G:0.19, T:0.09
Consensus pattern (17 bp):
AAAGAAAATGAAAAATG
Found at i:3148056 original size:55 final size:54
Alignment explanation
Indices: 3147523--3148036 Score: 513
Period size: 55 Copynumber: 9.6 Consensus size: 54
3147513 GTTGAAGATT
* * * * ** *
3147523 GAGTCCTATACTCCCTGAACGAATAGGGAGCGGACAAGTTCGTTGAAGA---TT-
1 GAGTTCTATACTCTCTGAAGGAATAGAGAGCGGACCCGTT-TTTGAAGATTGTTC
* * ** *
3147574 GAGTCCTATACTCTCTGAAGGAATAGGGAGCGGACAAGTTCGTTGAAGA---TT-
1 GAGTTCTATACTCTCTGAAGGAATAGAGAGCGGACCCGTT-TTTGAAGATTGTTC
* ** * *
3147625 GA-TTCCTATACTCTCTGAAGGAATAGGGAGCGGACAAGTTCGTTGAAGATTGTTT
1 GAGTT-CTATACTCTCTGAAGGAATAGAGAGCGGACCCGTT-TTTGAAGATTGTTC
* * *
3147680 GAGTCCTATACTCTCTGAAGGAATAGGGAGCGGACACGTTTATTGAAGA----TC
1 GAGTTCTATACTCTCTGAAGGAATAGAGAGCGGACCCGTTT-TTGAAGATTGTTC
* * *
3147731 GAG-TCTTATACTCCCTGAATGG-ATAGGGAGCGGACCCGTTTGTTGAAGATTTTTC
1 GAGTTC-TATACTCTCTGAA-GGAATAGAGAGCGGACCCGTTT-TTGAAGATTGTTC
*
3147786 GAGTTCTATACTCTCTGAAGGAATAGAGAGCGGACCCGTTTTATGAAGATTGTTT
1 GAGTTCTATACTCTCTGAAGGAATAGAGAGCGGACCCGTTTT-TGAAGATTGTTC
3147841 GAGTTCTATACTCTCTGAAGGAATAGAGAGCGGACCCGTTTTATGAAGATTGTTC
1 GAGTTCTATACTCTCTGAAGGAATAGAGAGCGGACCCGTTTT-TGAAGATTGTTC
3147896 GAGTTCTATACTCTCTGAAGGAATAGAGAGCGGACCCGTTTGTTGAAGATTGTTC
1 GAGTTCTATACTCTCTGAAGGAATAGAGAGCGGACCCGTTT-TTGAAGATTGTTC
* ** * *
3147951 GAGTTCTATACTCTCTGAATGAATAGAGAGCATACACATTTTATGAAGATTGTTC
1 GAGTTCTATACTCTCTGAAGGAATAGAGAGCGGACCCGTTTT-TGAAGATTGTTC
*
3148006 GAG-TCTTATACT-TCCTGAAGGAATAGGGAGC
1 GAGTTC-TATACTCT-CTGAAGGAATAGAGAGC
3148037 AGGCTCGTCA
Statistics
Matches: 420, Mismatches: 23, Indels: 36
0.88 0.05 0.08
Matches are distributed among these distances:
50 2 0.00
51 136 0.32
52 2 0.00
54 9 0.02
55 267 0.64
56 4 0.01
ACGTcount: A:0.28, C:0.16, G:0.26, T:0.30
Consensus pattern (54 bp):
GAGTTCTATACTCTCTGAAGGAATAGAGAGCGGACCCGTTTTTGAAGATTGTTC
Found at i:3150876 original size:32 final size:33
Alignment explanation
Indices: 3150780--3150878 Score: 164
Period size: 33 Copynumber: 3.0 Consensus size: 33
3150770 AACTCAACAT
* * *
3150780 AATTGAAATACTTAAATACTTCCAAGTTTGATA
1 AATTCAAATACTTAAAAACTTCCAAGTTCGATA
3150813 AATTCAAATACTTAAAAACTTCCAAGTTCGATA
1 AATTCAAATACTTAAAAACTTCCAAGTTCGATA
3150846 AATTCAAATACTTAAAAACTT-CAAGTTCGATA
1 AATTCAAATACTTAAAAACTTCCAAGTTCGATA
3150878 A
1 A
3150879 TTGAAACAAA
Statistics
Matches: 63, Mismatches: 3, Indels: 1
0.94 0.04 0.01
Matches are distributed among these distances:
32 12 0.19
33 51 0.81
ACGTcount: A:0.45, C:0.15, G:0.07, T:0.32
Consensus pattern (33 bp):
AATTCAAATACTTAAAAACTTCCAAGTTCGATA
Found at i:3150897 original size:21 final size:21
Alignment explanation
Indices: 3150873--3150914 Score: 75
Period size: 21 Copynumber: 2.0 Consensus size: 21
3150863 ACTTCAAGTT
3150873 CGATAATTGAAACAAAGTTTA
1 CGATAATTGAAACAAAGTTTA
*
3150894 CGATAATTGAAATAAAGTTTA
1 CGATAATTGAAACAAAGTTTA
3150915 AAAATAAACT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.48, C:0.07, G:0.14, T:0.31
Consensus pattern (21 bp):
CGATAATTGAAACAAAGTTTA
Found at i:3152488 original size:3 final size:3
Alignment explanation
Indices: 3152482--3152609 Score: 175
Period size: 3 Copynumber: 42.0 Consensus size: 3
3152472 TTCATTTAAA
** *
3152482 ATT ATT ATT ATT ATT AAA ATT ATT ATT ATT ATT ATT AGT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
* * *
3152530 ATT ATT AGT ATT ATT ATT ATT ATA ATA ATT ATT ATT ATT ATT ATT ATTT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT A-TT
*
3152579 ATT ATT ATT AAT ATT ATAT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT AT-T ATT ATT ATT ATT
3152610 TAATAAATAA
Statistics
Matches: 111, Mismatches: 12, Indels: 4
0.87 0.09 0.03
Matches are distributed among these distances:
3 105 0.95
4 6 0.05
ACGTcount: A:0.38, C:0.00, G:0.02, T:0.61
Consensus pattern (3 bp):
ATT
Found at i:3154041 original size:27 final size:28
Alignment explanation
Indices: 3153981--3154049 Score: 83
Period size: 28 Copynumber: 2.6 Consensus size: 28
3153971 TAATTACAAG
* *
3153981 TTTTATTACTT-TTTATATTTAGTTTTAA
1 TTTTATTA-TTGTTTAAATATAGTTTTAA
3154009 TTTTATTATTGTTTAAATATA-TTTTAA
1 TTTTATTATTGTTTAAATATAGTTTTAA
3154036 TTTTA-TA-TGTTTAA
1 TTTTATTATTGTTTAA
3154050 TATTTTAATT
Statistics
Matches: 38, Mismatches: 2, Indels: 5
0.84 0.04 0.11
Matches are distributed among these distances:
25 7 0.18
26 2 0.05
27 13 0.34
28 16 0.42
ACGTcount: A:0.29, C:0.01, G:0.04, T:0.65
Consensus pattern (28 bp):
TTTTATTATTGTTTAAATATAGTTTTAA
Found at i:3154055 original size:22 final size:26
Alignment explanation
Indices: 3153981--3154068 Score: 78
Period size: 28 Copynumber: 3.4 Consensus size: 26
3153971 TAATTACAAG
*
3153981 TTTTATTACTT-TTTATATTTAGTTTTAA
1 TTTTATTA-TTGTTTA-ATATA-TTTTAA
3154009 TTTTATTATTGTTTAAATATATTTTAA
1 TTTTATTATTGTTT-AATATATTTTAA
3154036 TTTTA-TA-TGTTT-A-ATATTTTAA
1 TTTTATTATTGTTTAATATATTTTAA
*
3154058 TTAGTATTATT
1 TT-TTATTATT
3154069 ATTTTATTTT
Statistics
Matches: 53, Mismatches: 2, Indels: 13
0.78 0.03 0.19
Matches are distributed among these distances:
22 11 0.21
23 3 0.06
24 2 0.04
25 6 0.11
26 2 0.04
27 13 0.25
28 15 0.28
29 1 0.02
ACGTcount: A:0.30, C:0.01, G:0.05, T:0.65
Consensus pattern (26 bp):
TTTTATTATTGTTTAATATATTTTAA
Found at i:3154083 original size:23 final size:24
Alignment explanation
Indices: 3154050--3154096 Score: 69
Period size: 23 Copynumber: 2.0 Consensus size: 24
3154040 ATATGTTTAA
*
3154050 TATTTTAATTAGTAT-TATTATTT
1 TATTTTAATTAATATATATTATTT
*
3154073 TATTTTTATTAATATATATTATTT
1 TATTTTAATTAATATATATTATTT
3154097 GATTAAACTT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
23 13 0.62
24 8 0.38
ACGTcount: A:0.32, C:0.00, G:0.02, T:0.66
Consensus pattern (24 bp):
TATTTTAATTAATATATATTATTT
Found at i:3154239 original size:16 final size:16
Alignment explanation
Indices: 3154220--3154271 Score: 56
Period size: 15 Copynumber: 3.4 Consensus size: 16
3154210 TTAAGTTTAC
3154220 TTAAATTATTTTACTT
1 TTAAATTATTTTACTT
3154236 TTAAA-T-TTTTACATT
1 TTAAATTATTTTAC-TT
* *
3154251 TTTAATTA-TTTATTT
1 TTAAATTATTTTACTT
3154266 TTAAAT
1 TTAAAT
3154272 ATTAAAGAAA
Statistics
Matches: 30, Mismatches: 3, Indels: 7
0.75 0.08 0.17
Matches are distributed among these distances:
14 6 0.20
15 14 0.47
16 10 0.33
ACGTcount: A:0.33, C:0.04, G:0.00, T:0.63
Consensus pattern (16 bp):
TTAAATTATTTTACTT
Found at i:3154873 original size:20 final size:20
Alignment explanation
Indices: 3154846--3154891 Score: 56
Period size: 22 Copynumber: 2.1 Consensus size: 20
3154836 TCTTTCAATT
*
3154846 TTTATTATTTTTATATATTATTA
1 TTTATTA-TTTTATTTA-T-TTA
3154869 TTTATTATTTTATTTATTTA
1 TTTATTATTTTATTTATTTA
3154889 TTT
1 TTT
3154892 TATTCAAGAA
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
20 6 0.27
21 1 0.05
22 8 0.36
23 7 0.32
ACGTcount: A:0.26, C:0.00, G:0.00, T:0.74
Consensus pattern (20 bp):
TTTATTATTTTATTTATTTA
Found at i:3154885 original size:16 final size:15
Alignment explanation
Indices: 3154845--3154890 Score: 58
Period size: 16 Copynumber: 2.9 Consensus size: 15
3154835 TTCTTTCAAT
3154845 TTTTATTATTT-TTA
1 TTTTATTATTTATTA
3154859 TATATTATTATTTATTA
1 T-T-TTATTATTTATTA
3154876 TTTTATTTATTTATT
1 TTTTA-TTATTTATT
3154891 TTATTCAAGA
Statistics
Matches: 28, Mismatches: 0, Indels: 6
0.82 0.00 0.18
Matches are distributed among these distances:
14 1 0.04
15 4 0.14
16 19 0.68
17 4 0.14
ACGTcount: A:0.26, C:0.00, G:0.00, T:0.74
Consensus pattern (15 bp):
TTTTATTATTTATTA
Found at i:3154889 original size:13 final size:14
Alignment explanation
Indices: 3154846--3154895 Score: 63
Period size: 13 Copynumber: 3.9 Consensus size: 14
3154836 TCTTTCAATT
3154846 TTTATTATT-TTTA
1 TTTATTATTATTTA
*
3154859 TATATTATTATTTA
1 TTTATTATTATTTA
3154873 -TTATT-TTATTTA
1 TTTATTATTATTTA
3154885 TTTATT-TTATT
1 TTTATTATTATT
3154896 CAAGAATTAA
Statistics
Matches: 33, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
12 7 0.21
13 22 0.67
14 4 0.12
ACGTcount: A:0.26, C:0.00, G:0.00, T:0.74
Consensus pattern (14 bp):
TTTATTATTATTTA
Found at i:3157228 original size:7 final size:7
Alignment explanation
Indices: 3157193--3157234 Score: 59
Period size: 7 Copynumber: 6.0 Consensus size: 7
3157183 TTTTCATACA
3157193 TGCATTT
1 TGCATTT
3157200 T-CATTT
1 TGCATTT
3157206 TGCATCTT
1 TGCAT-TT
3157214 TGCATTT
1 TGCATTT
*
3157221 TTCATTT
1 TGCATTT
3157228 TGCATTT
1 TGCATTT
3157235 ATATTTTTAT
Statistics
Matches: 31, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
6 6 0.19
7 18 0.58
8 7 0.23
ACGTcount: A:0.14, C:0.17, G:0.10, T:0.60
Consensus pattern (7 bp):
TGCATTT
Found at i:3157259 original size:20 final size:20
Alignment explanation
Indices: 3157197--3157259 Score: 65
Period size: 20 Copynumber: 3.0 Consensus size: 20
3157187 CATACATGCA
*
3157197 TTTTCATTTTGCATCTTTGCAT
1 TTTTCATTTTGCA--TTTGTAT
*
3157219 TTTTCATTTTGCATTTATAT
1 TTTTCATTTTGCATTTGTAT
*
3157239 TTTT-ATGTTTGCTTTTGTAT
1 TTTTCAT-TTTGCATTTGTAT
3157259 T
1 T
3157260 GCACAATTTA
Statistics
Matches: 36, Mismatches: 4, Indels: 4
0.82 0.09 0.09
Matches are distributed among these distances:
19 2 0.06
20 21 0.58
22 13 0.36
ACGTcount: A:0.14, C:0.11, G:0.10, T:0.65
Consensus pattern (20 bp):
TTTTCATTTTGCATTTGTAT
Found at i:3165505 original size:165 final size:164
Alignment explanation
Indices: 3165233--3165553 Score: 531
Period size: 165 Copynumber: 1.9 Consensus size: 164
3165223 AGAATGAGCA
* *
3165233 TTATCTTGAGATTGGGGCATGTTACCCAATCAATATGTTATTTCAAAAACATAATGAGAAAACGA
1 TTATCTTGAGATTGGGGCATGTTACCCAATCAACAGGTTATTT-AAAAACATAATGAGAAAACGA
* *
3165298 TTTTCATAGTTTCTCATTTCATCTTTTCTAAAATGAAATTGTTGAAAAGTAAGAAAACGATTTTC
65 TTTCCAAAGTTTCTCATTTCATCTTTTCTAAAATGAAATTGTTGAAAAGTAAGAAAACGATTTTC
3165363 TTAG-TTTTTTACTTAGTAAACTATTTCCAACAACC
130 TTAGTTTTTTTACTTAGTAAAC-ATTTCCAACAACC
*
3165398 TTATCTTGAGATTGGGGCATGTTACCCAATCAACAGGTTATCTT-GAAACATAATGAGAAAACGA
1 TTATCTTGAGATTGGGGCATGTTACCCAATCAACAGGTTAT-TTAAAAACATAATGAGAAAACGA
3165462 TTTCCAAAGTTTCTCA-TTCAATCTTTTCTGAAAATGAAATTGTTGAAAAGTAAGAAAACGATTT
65 TTTCCAAAGTTTCTCATTTC-ATCTTTTCT-AAAATGAAATTGTTGAAAAGTAAGAAAACGATTT
3165526 TCTTAGTTTTTTTACTTAGTAAACATTT
128 TCTTAGTTTTTTTACTTAGTAAACATTT
3165554 TCCCTCGAAA
Statistics
Matches: 147, Mismatches: 5, Indels: 8
0.92 0.03 0.05
Matches are distributed among these distances:
163 3 0.02
164 42 0.29
165 83 0.56
166 19 0.13
ACGTcount: A:0.35, C:0.14, G:0.13, T:0.38
Consensus pattern (164 bp):
TTATCTTGAGATTGGGGCATGTTACCCAATCAACAGGTTATTTAAAAACATAATGAGAAAACGAT
TTCCAAAGTTTCTCATTTCATCTTTTCTAAAATGAAATTGTTGAAAAGTAAGAAAACGATTTTCT
TAGTTTTTTTACTTAGTAAACATTTCCAACAACC
Found at i:3165857 original size:36 final size:36
Alignment explanation
Indices: 3165598--3165864 Score: 189
Period size: 36 Copynumber: 7.3 Consensus size: 36
3165588 ATTTTCCTTA
* *
3165598 AAACAAAATTTGCCTCGCTCGAGACAGTTTCACTCG
1 AAACAAAATTTGTCTCGCTCGAGATAGTTTCACTCG
* * * * * * **
3165634 AAATAGCAATTTATCTCACTTGAGATTGTTTTC-CTTA
1 AAACA-AAATTTGTCTCGCTCGAGATAG-TTTCACTCG
* *
3165671 AAACAAAATTTGCCTCGCTCGAGACAGTTTCACTCG
1 AAACAAAATTTGTCTCGCTCGAGATAGTTTCACTCG
* * * * * * ** **
3165707 AAATAGCAATTTATCTCACTTGAGATTGTTTTTCTTA
1 AAACA-AAATTTGTCTCGCTCGAGATAGTTTCACTCG
*
3165744 AAACAAAATTTGTCTCGCTCGAGACAGTTTCACTCG
1 AAACAAAATTTGTCTCGCTCGAGATAGTTTCACTCG
* * * * **
3165780 AAA-AAGCAATTTATCTCACTTGAGATTGTTTTC-CTTA
1 AAACAA--AATTTGTCTCGCTCGAGATAG-TTTCACTCG
3165817 AAACAAAATTTGTCTCGCTCGAGATAGTTTCACTCG
1 AAACAAAATTTGTCTCGCTCGAGATAGTTTCACTCG
3165853 AAACATAAATTT
1 AAACA-AAATTT
3165865 TCATCACTCG
Statistics
Matches: 165, Mismatches: 56, Indels: 19
0.69 0.23 0.08
Matches are distributed among these distances:
35 10 0.06
36 73 0.44
37 72 0.44
38 10 0.06
ACGTcount: A:0.32, C:0.21, G:0.13, T:0.34
Consensus pattern (36 bp):
AAACAAAATTTGTCTCGCTCGAGATAGTTTCACTCG
Found at i:3165872 original size:73 final size:73
Alignment explanation
Indices: 3165552--3165855 Score: 545
Period size: 73 Copynumber: 4.2 Consensus size: 73
3165542 TAGTAAACAT
* *
3165552 TTTCCCTCGAAATAGCAATTTATCTCACTTGAGATTATTTTCCTTAAAACAAAATTTGCCTCGCT
1 TTTCACTCGAAATAGCAATTTATCTCACTTGAGATTGTTTTCCTTAAAACAAAATTTGCCTCGCT
3165617 CGAGACAG
66 CGAGACAG
3165625 TTTCACTCGAAATAGCAATTTATCTCACTTGAGATTGTTTTCCTTAAAACAAAATTTGCCTCGCT
1 TTTCACTCGAAATAGCAATTTATCTCACTTGAGATTGTTTTCCTTAAAACAAAATTTGCCTCGCT
3165690 CGAGACAG
66 CGAGACAG
* *
3165698 TTTCACTCGAAATAGCAATTTATCTCACTTGAGATTGTTTTTCTTAAAACAAAATTTGTCTCGCT
1 TTTCACTCGAAATAGCAATTTATCTCACTTGAGATTGTTTTCCTTAAAACAAAATTTGCCTCGCT
3165763 CGAGACAG
66 CGAGACAG
* *
3165771 TTTCACTCGAAAAAGCAATTTATCTCACTTGAGATTGTTTTCCTTAAAACAAAATTTGTCTCGCT
1 TTTCACTCGAAATAGCAATTTATCTCACTTGAGATTGTTTTCCTTAAAACAAAATTTGCCTCGCT
*
3165836 CGAGATAG
66 CGAGACAG
3165844 TTTCACTCGAAA
1 TTTCACTCGAAA
3165856 CATAAATTTT
Statistics
Matches: 224, Mismatches: 7, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
73 224 1.00
ACGTcount: A:0.31, C:0.21, G:0.13, T:0.35
Consensus pattern (73 bp):
TTTCACTCGAAATAGCAATTTATCTCACTTGAGATTGTTTTCCTTAAAACAAAATTTGCCTCGCT
CGAGACAG
Found at i:3165875 original size:37 final size:36
Alignment explanation
Indices: 3165568--3165875 Score: 185
Period size: 36 Copynumber: 8.4 Consensus size: 36
3165558 TCGAAATAGC
* * **
3165568 AATTTATCTCACTTGAGATTATTTTC-CTTAAAACAA
1 AATTTATCTCACTCGAGA-TAGTTTCACTCGAAACAA
** * * * *
3165604 AATTTGCCTCGCTCGAGACAGTTTCACTCGAAATAGC
1 AATTTATCTCACTCGAGATAGTTTCACTCGAAACA-A
* * **
3165641 AATTTATCTCACTTGAGATTGTTTTC-CTTAAAACAA
1 AATTTATCTCACTCGAGATAG-TTTCACTCGAAACAA
** * * * *
3165677 AATTTGCCTCGCTCGAGACAGTTTCACTCGAAATAGC
1 AATTTATCTCACTCGAGATAGTTTCACTCGAAACA-A
* * ** **
3165714 AATTTATCTCACTTGAGATTGTTTTTCTTAAAACAA
1 AATTTATCTCACTCGAGATAGTTTCACTCGAAACAA
* * *
3165750 AATTTGTCTCGCTCGAGACAGTTTCACTCGAAA-AA
1 AATTTATCTCACTCGAGATAGTTTCACTCGAAACAA
* * **
3165785 GCAATTTATCTCACTTGAGATTGTTTTC-CTTAAAACAA
1 --AATTTATCTCACTCGAGATAG-TTTCACTCGAAACAA
* *
3165823 AATTTGTCTCGCTCGAGATAGTTTCACTCGAAACATA
1 AATTTATCTCACTCGAGATAGTTTCACTCGAAACA-A
3165860 AATTT-TCATCACTCGA
1 AATTTATC-TCACTCGA
3165876 TGGATCAGCT
Statistics
Matches: 195, Mismatches: 65, Indels: 23
0.69 0.23 0.08
Matches are distributed among these distances:
35 15 0.08
36 91 0.47
37 79 0.41
38 10 0.05
ACGTcount: A:0.31, C:0.21, G:0.13, T:0.35
Consensus pattern (36 bp):
AATTTATCTCACTCGAGATAGTTTCACTCGAAACAA
Found at i:3165958 original size:20 final size:20
Alignment explanation
Indices: 3165933--3166048 Score: 56
Period size: 20 Copynumber: 5.3 Consensus size: 20
3165923 TGTTTTCAAA
3165933 ACCTTCGAGTCATCTGTAAG
1 ACCTTCGAGTCATCTGTAAG
* *
3165953 ACCTTC-AGTGCATGATGTTTTCAAA
1 ACCTTCGAGT-CAT-CTG---T-AAG
3165978 ACCTTCGAGTCATCTGTAAG
1 ACCTTCGAGTCATCTGTAAG
* * *
3165998 CCCTTC-AGTGCATGATGTTTTCAAA
1 ACCTTCGAGT-CAT-CTG---T-AAG
3166023 ACCTTCGAGTCATCTGTAAG
1 ACCTTCGAGTCATCTGTAAG
*
3166043 CCCTTC
1 ACCTTC
3166049 AGTGCATGAT
Statistics
Matches: 71, Mismatches: 11, Indels: 28
0.65 0.10 0.25
Matches are distributed among these distances:
19 6 0.08
20 26 0.37
21 6 0.08
24 6 0.08
25 21 0.30
26 6 0.08
ACGTcount: A:0.24, C:0.26, G:0.17, T:0.33
Consensus pattern (20 bp):
ACCTTCGAGTCATCTGTAAG
Found at i:3165973 original size:45 final size:45
Alignment explanation
Indices: 3165920--3166156 Score: 429
Period size: 45 Copynumber: 5.3 Consensus size: 45
3165910 GGGAGCTTTT
*
3165920 TGATGTTTTCAAAACCTTCGAGTCATCTGTAAGACCTTCAGTGCA
1 TGATGTTTTCAAAACCTTCGAGTCATCTGTAAGCCCTTCAGTGCA
3165965 TGATGTTTTCAAAACCTTCGAGTCATCTGTAAGCCCTTCAGTGCA
1 TGATGTTTTCAAAACCTTCGAGTCATCTGTAAGCCCTTCAGTGCA
3166010 TGATGTTTTCAAAACCTTCGAGTCATCTGTAAGCCCTTCAGTGCA
1 TGATGTTTTCAAAACCTTCGAGTCATCTGTAAGCCCTTCAGTGCA
*
3166055 TGATGTTTTCAAAACCTTCGAGTCATCTATAAGCCCTTCAGTGCA
1 TGATGTTTTCAAAACCTTCGAGTCATCTGTAAGCCCTTCAGTGCA
* * *
3166100 TGATGTTTTCAAAACCTTCGGGTCATCTATAAGCTCTTCAGTGCA
1 TGATGTTTTCAAAACCTTCGAGTCATCTGTAAGCCCTTCAGTGCA
3166145 TGATGTTTTCAA
1 TGATGTTTTCAA
3166157 CATTTCCATC
Statistics
Matches: 188, Mismatches: 4, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
45 188 1.00
ACGTcount: A:0.25, C:0.23, G:0.17, T:0.35
Consensus pattern (45 bp):
TGATGTTTTCAAAACCTTCGAGTCATCTGTAAGCCCTTCAGTGCA
Found at i:3166289 original size:3 final size:3
Alignment explanation
Indices: 3166283--3166386 Score: 136
Period size: 3 Copynumber: 34.0 Consensus size: 3
3166273 TTCATTTAAA
** *
3166283 ATT ATT ATT ATT ATT AAA ATT ATT ATT ATT ATT ATT AGT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
* * *
3166331 ATT ATT AGT AAT ATT ATT ATT ATTT ATT ATT ATT AAT ATT ATAT ATT
1 ATT ATT ATT ATT ATT ATT ATT A-TT ATT ATT ATT ATT ATT AT-T ATT
3166378 ATT ATT ATT
1 ATT ATT ATT
3166387 TAATAAATAA
Statistics
Matches: 88, Mismatches: 11, Indels: 4
0.85 0.11 0.04
Matches are distributed among these distances:
3 82 0.93
4 6 0.07
ACGTcount: A:0.38, C:0.00, G:0.02, T:0.61
Consensus pattern (3 bp):
ATT
Done.