Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: CP032253.1 Gossypioides kirkii chromosome KI_11
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: 55708359
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 2600 characters in sequence are not A, C, G, or T
File 138 of 182
Found at i:43112901 original size:16 final size:15
Alignment explanation
Indices: 43112859--43112927 Score: 54
Period size: 16 Copynumber: 4.6 Consensus size: 15
43112849 GATTTCTTTT
*
43112859 TATTTATTATTAATAA
1 TATTTATTA-TATTAA
43112875 TA-TTATT-TATTAA
1 TATTTATTATATTAA
*
43112888 TATTTATTAATATTAT
1 TATTTATT-ATATTAA
* *
43112904 TATATATT-TATTACT
1 TATTTATTATATTA-A
43112919 TATTTATTA
1 TATTTATTA
43112928 AATACCACAG
Statistics
Matches: 44, Mismatches: 4, Indels: 10
0.76 0.07 0.17
Matches are distributed among these distances:
13 7 0.16
14 10 0.23
15 13 0.30
16 14 0.32
ACGTcount: A:0.38, C:0.01, G:0.00, T:0.61
Consensus pattern (15 bp):
TATTTATTATATTAA
Found at i:43113683 original size:17 final size:17
Alignment explanation
Indices: 43113630--43113739 Score: 121
Period size: 17 Copynumber: 6.4 Consensus size: 17
43113620 GACTTTCATC
*
43113630 ATTTAAACTTAGAATAA
1 ATTTAAACTTAAAATAA
* *
43113647 TTTTAAAATTAAAAATAA
1 ATTTAAACTT-AAAATAA
*
43113665 ATTTAAACTTAAAACAA
1 ATTTAAACTTAAAATAA
* *
43113682 ATTTAAATTTAACATAA
1 ATTTAAACTTAAAATAA
* *
43113699 ATTTAAATTTAAAGTAA
1 ATTTAAACTTAAAATAA
* *
43113716 ACTTAATCTTAAAATAA
1 ATTTAAACTTAAAATAA
43113733 ATTTAAA
1 ATTTAAA
43113740 AAATAGGTTT
Statistics
Matches: 75, Mismatches: 17, Indels: 2
0.80 0.18 0.02
Matches are distributed among these distances:
17 61 0.81
18 14 0.19
ACGTcount: A:0.55, C:0.05, G:0.02, T:0.37
Consensus pattern (17 bp):
ATTTAAACTTAAAATAA
Found at i:43113875 original size:17 final size:18
Alignment explanation
Indices: 43113843--43113887 Score: 56
Period size: 17 Copynumber: 2.6 Consensus size: 18
43113833 GAGTAAGTTT
*
43113843 ATAAATAATATAAA-TTG
1 ATAAATAAAATAAATTTG
*
43113860 ATAAATAAAATCAATTTG
1 ATAAATAAAATAAATTTG
*
43113878 AAAAATAAAA
1 ATAAATAAAA
43113888 GAATTAATGA
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
17 12 0.50
18 12 0.50
ACGTcount: A:0.64, C:0.02, G:0.04, T:0.29
Consensus pattern (18 bp):
ATAAATAAAATAAATTTG
Found at i:43115128 original size:16 final size:17
Alignment explanation
Indices: 43115099--43115132 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 17
43115089 CGAAAAAAAA
*
43115099 TTCGAATTTTTTCGAAT
1 TTCGAATTTATTCGAAT
43115116 TTCGAA-TTATTCGAAT
1 TTCGAATTTATTCGAAT
43115132 T
1 T
43115133 GAGCTATTCG
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 10 0.62
17 6 0.38
ACGTcount: A:0.26, C:0.12, G:0.12, T:0.50
Consensus pattern (17 bp):
TTCGAATTTATTCGAAT
Found at i:43119523 original size:29 final size:28
Alignment explanation
Indices: 43119491--43119546 Score: 78
Period size: 29 Copynumber: 2.0 Consensus size: 28
43119481 TTAAATAAAA
43119491 AAATAAGAAAATTT-AATTTTAAACTTTTC
1 AAAT-AGAAAATTTAAATTTTAAA-TTTTC
*
43119520 AAATATAAAATTTAAATTTTAAATTTT
1 AAATAGAAAATTTAAATTTTAAATTTT
43119547 GTTAAAGTAC
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
28 12 0.48
29 13 0.52
ACGTcount: A:0.50, C:0.04, G:0.02, T:0.45
Consensus pattern (28 bp):
AAATAGAAAATTTAAATTTTAAATTTTC
Found at i:43119828 original size:6 final size:6
Alignment explanation
Indices: 43119813--43119843 Score: 55
Period size: 6 Copynumber: 5.3 Consensus size: 6
43119803 AAGGTGCGAA
43119813 AAAAAT -AAAAT AAAAAT AAAAAT AAAAAT AA
1 AAAAAT AAAAAT AAAAAT AAAAAT AAAAAT AA
43119844 TTAAATGACA
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
5 5 0.21
6 19 0.79
ACGTcount: A:0.84, C:0.00, G:0.00, T:0.16
Consensus pattern (6 bp):
AAAAAT
Found at i:43120576 original size:21 final size:22
Alignment explanation
Indices: 43120546--43120587 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 22
43120536 GTTTAAATTT
43120546 GAGATATAA-GGTTTAGGGTTC
1 GAGATATAAGGGTTTAGGGTTC
* *
43120567 GAGATTTAAGGGTTTTGGGTT
1 GAGATATAAGGGTTTAGGGTT
43120588 TAAGATTCAA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
21 8 0.44
22 10 0.56
ACGTcount: A:0.24, C:0.02, G:0.36, T:0.38
Consensus pattern (22 bp):
GAGATATAAGGGTTTAGGGTTC
Found at i:43122485 original size:18 final size:20
Alignment explanation
Indices: 43122464--43122503 Score: 57
Period size: 19 Copynumber: 2.1 Consensus size: 20
43122454 TGTATGATAA
43122464 TTCAAA-ATTATATTTT-TT
1 TTCAAATATTATATTTTATT
*
43122482 TTCAAATGTTATATTTTATT
1 TTCAAATATTATATTTTATT
43122502 TT
1 TT
43122504 TTAACCCTAC
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
18 6 0.32
19 9 0.47
20 4 0.21
ACGTcount: A:0.30, C:0.05, G:0.03, T:0.62
Consensus pattern (20 bp):
TTCAAATATTATATTTTATT
Found at i:43126412 original size:84 final size:84
Alignment explanation
Indices: 43126271--43126439 Score: 320
Period size: 84 Copynumber: 2.0 Consensus size: 84
43126261 TTTCTTAAAA
43126271 AACGATAACGTAAGTAACTAAAACGTAATATTTTAAACATAAATGATTAAAATGTAATCTGAGAC
1 AACGATAACGTAAGTAACTAAAACGTAATATTTTAAACATAAATGATTAAAATGTAATCTGAGAC
43126336 AAACAAAATAACAATTTTT
66 AAACAAAATAACAATTTTT
43126355 AACGATAACGTAAGTAACTAAAACGTAATATTTTAAACATAAATGATTAAAATGTAATCTGAGAC
1 AACGATAACGTAAGTAACTAAAACGTAATATTTTAAACATAAATGATTAAAATGTAATCTGAGAC
* *
43126420 AAATAAAATAACTATTTTT
66 AAACAAAATAACAATTTTT
43126439 A
1 A
43126440 TAGTTTACCC
Statistics
Matches: 83, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
84 83 1.00
ACGTcount: A:0.51, C:0.10, G:0.09, T:0.30
Consensus pattern (84 bp):
AACGATAACGTAAGTAACTAAAACGTAATATTTTAAACATAAATGATTAAAATGTAATCTGAGAC
AAACAAAATAACAATTTTT
Found at i:43131047 original size:66 final size:65
Alignment explanation
Indices: 43130941--43131096 Score: 231
Period size: 66 Copynumber: 2.4 Consensus size: 65
43130931 CAAATTGCTC
* *
43130941 AACTTAAAGAGGAGGCTGCAGCGAGAGAAGCAGAGGCTCAAAAAAATATGATGAACTCCATCTAA
1 AACTTAAAGAGGAGGCTGCAGCGAGAGAAGCAGAGGCTCAAAAAAATATGAAGAACTCCACCTAA
* * *
43131006 AACTTAAAAGAGGAGGCTGCAGTGAGAGAAGCAGAGTCTCAAAAAAATATGAAGAGCTCCACCTA
1 AACTT-AAAGAGGAGGCTGCAGCGAGAGAAGCAGAGGCTCAAAAAAATATGAAGAACTCCACCTA
*
43131071 C
65 A
* *
43131072 AACTTAAAGTGGAGGCAGCAGCGAG
1 AACTTAAAGAGGAGGCTGCAGCGAG
43131097 GCAAGCGAAG
Statistics
Matches: 81, Mismatches: 9, Indels: 2
0.88 0.10 0.02
Matches are distributed among these distances:
65 22 0.27
66 59 0.73
ACGTcount: A:0.42, C:0.17, G:0.26, T:0.15
Consensus pattern (65 bp):
AACTTAAAGAGGAGGCTGCAGCGAGAGAAGCAGAGGCTCAAAAAAATATGAAGAACTCCACCTAA
Found at i:43131458 original size:43 final size:43
Alignment explanation
Indices: 43131410--43131550 Score: 192
Period size: 43 Copynumber: 3.3 Consensus size: 43
43131400 ATCTGTTATA
* * * *
43131410 TTAGCGGCGCTTTTGGAAAAAGCACCGCTAAAAAACATGGTTT
1 TTAGCGGCGCTTGTGGAAAAAGCGCCGCTAAAGAACATGGCTT
* * * *
43131453 TTAGCGGCGCTTGTGGAGAAAGTGGCGCTAAAGAACATGGCCT
1 TTAGCGGCGCTTGTGGAAAAAGCGCCGCTAAAGAACATGGCTT
*
43131496 TTCGCGGCGCTTGTGGAAAAAGCGCCGCTAAAGAACATGGCTT
1 TTAGCGGCGCTTGTGGAAAAAGCGCCGCTAAAGAACATGGCTT
*
43131539 TTAGCAGCGCTT
1 TTAGCGGCGCTT
43131551 TTTCGCGTAA
Statistics
Matches: 83, Mismatches: 15, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
43 83 1.00
ACGTcount: A:0.27, C:0.21, G:0.29, T:0.23
Consensus pattern (43 bp):
TTAGCGGCGCTTGTGGAAAAAGCGCCGCTAAAGAACATGGCTT
Found at i:43131817 original size:24 final size:23
Alignment explanation
Indices: 43131765--43131820 Score: 76
Period size: 24 Copynumber: 2.3 Consensus size: 23
43131755 AAAATTTATA
* *
43131765 TTTTTTAATTATTATAATATTAT
1 TTTTTTAATTATTATAACATTAC
43131788 TATTTTTAATTATTATAAACATTAC
1 T-TTTTTAATTATTAT-AACATTAC
43131813 TTTTTTAA
1 TTTTTTAA
43131821 GAAGATTTAT
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
23 1 0.03
24 21 0.72
25 7 0.24
ACGTcount: A:0.36, C:0.04, G:0.00, T:0.61
Consensus pattern (23 bp):
TTTTTTAATTATTATAACATTAC
Found at i:43133648 original size:17 final size:19
Alignment explanation
Indices: 43133612--43133654 Score: 56
Period size: 20 Copynumber: 2.4 Consensus size: 19
43133602 TTTTTTTATA
43133612 ATTTTTATAATGCATAAATT
1 ATTTTTATAAT-CATAAATT
43133632 ATTTTTATAAT-AT-AATT
1 ATTTTTATAATCATAAATT
43133649 -TTTTTA
1 ATTTTTA
43133655 GATTTATAAT
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
16 6 0.26
17 4 0.17
18 2 0.09
20 11 0.48
ACGTcount: A:0.37, C:0.02, G:0.02, T:0.58
Consensus pattern (19 bp):
ATTTTTATAATCATAAATT
Found at i:43150169 original size:117 final size:117
Alignment explanation
Indices: 43149950--43150170 Score: 302
Period size: 117 Copynumber: 1.9 Consensus size: 117
43149940 TAGATATAAT
*
43149950 TTTAATTTTTAGTTTTTAATTTTCTAAATATAATTACATTACATATCACAATATTTATAATTTCT
1 TTTAATTTTTAGTTTTTAATTTTCTAAATATAATTACATTACATATCACAATATTTATAACTTCT
* * * * * *
43150015 TAATCTCGTGTGTTGGCTTGATGATTAATGATGTTCATTCTCTCAAACCACA
66 GAACCTCATGTGTTGGCTTGATGATCAAGGATATTCATTCTCTCAAACCACA
* * *
43150067 TTTAATTTTTAGTTTTTAATTTTTTTAAATATAATTACATT-CGTATCACAATATTTATAGCTTC
1 TTTAATTTTTAGTTTTTAA-TTTTCTAAATATAATTACATTACATATCACAATATTTATAACTTC
* *
43150131 TGAACCTCATGTGTTGG-TCTGATGGTCAAGGGTATTCATT
65 TGAACCTCATGTGTTGGCT-TGATGATCAAGGATATTCATT
43150171 GTTTCAAGTG
Statistics
Matches: 90, Mismatches: 12, Indels: 4
0.85 0.11 0.04
Matches are distributed among these distances:
116 1 0.01
117 69 0.77
118 20 0.22
ACGTcount: A:0.29, C:0.13, G:0.11, T:0.48
Consensus pattern (117 bp):
TTTAATTTTTAGTTTTTAATTTTCTAAATATAATTACATTACATATCACAATATTTATAACTTCT
GAACCTCATGTGTTGGCTTGATGATCAAGGATATTCATTCTCTCAAACCACA
Found at i:43159057 original size:3 final size:3
Alignment explanation
Indices: 43159045--43159077 Score: 59
Period size: 3 Copynumber: 11.3 Consensus size: 3
43159035 ATCCTGGCCC
43159045 AAT AAT -AT AAT AAT AAT AAT AAT AAT AAT AAT A
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A
43159078 TGTTGAATTG
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
2 2 0.07
3 27 0.93
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:43167412 original size:31 final size:30
Alignment explanation
Indices: 43167376--43167445 Score: 106
Period size: 31 Copynumber: 2.3 Consensus size: 30
43167366 TTTCACATAT
*
43167376 AATTCTCTCAAATTCTCAAATCACT-TTCTA
1 AATTCTCTCAAATTCTCAAATCAATCTT-TA
43167406 ACATTCTCTCAAATTCTCAAATCAATCTTTA
1 A-ATTCTCTCAAATTCTCAAATCAATCTTTA
43167437 AATTCTCTC
1 AATTCTCTC
43167446 TTAAATATTT
Statistics
Matches: 37, Mismatches: 1, Indels: 4
0.88 0.02 0.10
Matches are distributed among these distances:
30 9 0.24
31 26 0.70
32 2 0.05
ACGTcount: A:0.33, C:0.27, G:0.00, T:0.40
Consensus pattern (30 bp):
AATTCTCTCAAATTCTCAAATCAATCTTTA
Found at i:43167492 original size:22 final size:24
Alignment explanation
Indices: 43167462--43167506 Score: 67
Period size: 25 Copynumber: 1.9 Consensus size: 24
43167452 ATTTTCTGAA
43167462 AATA-TTTTTA-AAAAAAATTATT
1 AATACTTTTTATAAAAAAATTATT
43167484 AATACTTTTTTATAAAAAAATTA
1 AATAC-TTTTTATAAAAAAATTA
43167507 ATTAGTTTTT
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
22 4 0.20
24 6 0.30
25 10 0.50
ACGTcount: A:0.53, C:0.02, G:0.00, T:0.44
Consensus pattern (24 bp):
AATACTTTTTATAAAAAAATTATT
Found at i:43173611 original size:24 final size:24
Alignment explanation
Indices: 43173583--43173645 Score: 76
Period size: 24 Copynumber: 2.7 Consensus size: 24
43173573 TACTTCATAT
43173583 ATAAAAATGTCATAAAATAAAGGG
1 ATAAAAATGTCATAAAATAAAGGG
* *
43173607 ATAAAATTGATCA-AAATTAAAGGG
1 ATAAAAATG-TCATAAAATAAAGGG
*
43173631 -TAAACATGTCATAAA
1 ATAAAAATGTCATAAA
43173646 TGACGATTAT
Statistics
Matches: 33, Mismatches: 4, Indels: 5
0.79 0.10 0.12
Matches are distributed among these distances:
22 3 0.09
23 9 0.27
24 18 0.55
25 3 0.09
ACGTcount: A:0.56, C:0.06, G:0.14, T:0.24
Consensus pattern (24 bp):
ATAAAAATGTCATAAAATAAAGGG
Found at i:43173646 original size:23 final size:23
Alignment explanation
Indices: 43173586--43173646 Score: 72
Period size: 23 Copynumber: 2.6 Consensus size: 23
43173576 TTCATATATA
*
43173586 AAAATGTCATAAAATAAAGGGAT
1 AAAATGTCATAAATTAAAGGGAT
43173609 AAAATTGATCA-AAATTAAAGGG-T
1 AAAA-TG-TCATAAATTAAAGGGAT
43173632 AAACATGTCATAAAT
1 AAA-ATGTCATAAAT
43173647 GACGATTATC
Statistics
Matches: 33, Mismatches: 1, Indels: 8
0.79 0.02 0.19
Matches are distributed among these distances:
22 3 0.09
23 14 0.42
24 13 0.39
25 3 0.09
ACGTcount: A:0.54, C:0.07, G:0.15, T:0.25
Consensus pattern (23 bp):
AAAATGTCATAAATTAAAGGGAT
Found at i:43175923 original size:16 final size:15
Alignment explanation
Indices: 43175873--43175923 Score: 50
Period size: 16 Copynumber: 3.4 Consensus size: 15
43175863 TCCAAGGTTA
*
43175873 TTCCCAAA-AAGTCG
1 TTCCCAAAGAAGTTG
* *
43175887 TTCCCAATGAGGTTG
1 TTCCCAAAGAAGTTG
*
43175902 TCCCCAAAGGAAGTTG
1 TTCCCAAA-GAAGTTG
43175918 TTCCCA
1 TTCCCA
43175924 CAGGTGCTCA
Statistics
Matches: 28, Mismatches: 7, Indels: 2
0.76 0.19 0.05
Matches are distributed among these distances:
14 7 0.25
15 10 0.36
16 11 0.39
ACGTcount: A:0.27, C:0.27, G:0.20, T:0.25
Consensus pattern (15 bp):
TTCCCAAAGAAGTTG
Found at i:43177160 original size:20 final size:20
Alignment explanation
Indices: 43177123--43177160 Score: 51
Period size: 19 Copynumber: 1.9 Consensus size: 20
43177113 TCTATTTTTA
*
43177123 TTTTAAAAAATTTAATATTC
1 TTTTAAAAAATTAAATATTC
43177143 TTTT-AAAAATTAAGATAT
1 TTTTAAAAAATTAA-ATAT
43177161 AAGTATTATT
Statistics
Matches: 16, Mismatches: 1, Indels: 2
0.84 0.05 0.11
Matches are distributed among these distances:
19 8 0.50
20 8 0.50
ACGTcount: A:0.47, C:0.03, G:0.03, T:0.47
Consensus pattern (20 bp):
TTTTAAAAAATTAAATATTC
Found at i:43177684 original size:17 final size:18
Alignment explanation
Indices: 43177659--43177692 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
43177649 TTTTTTTATG
*
43177659 TTAATAATAT-AAAATAA
1 TTAAAAATATCAAAATAA
43177676 TTAAAAATATCAAAATA
1 TTAAAAATATCAAAATA
43177693 GTATGGAACT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 9 0.60
18 6 0.40
ACGTcount: A:0.65, C:0.03, G:0.00, T:0.32
Consensus pattern (18 bp):
TTAAAAATATCAAAATAA
Found at i:43178461 original size:136 final size:141
Alignment explanation
Indices: 43178316--43178574 Score: 314
Period size: 143 Copynumber: 1.9 Consensus size: 141
43178306 GATTAAAGGG
** * * *
43178316 AAAAAGCTAAAAGTGAGGTAAA-ATTT-TTTGTTATTTTAATTT-TA-TT-TTGTTAGTAATTAT
1 AAAAAGCTAAAAGAAAGATAAATATTTATTTGTTAATTTAATTTAAAGTTATTGTTAGTAATTAT
* *
43178376 TATAAAATATTTTTTAGTTTAATGTTGATGTGATTTGTTA-TAATTTTTTGTTTAGAAGGAAGAT
66 TA-AAAATATTTTTTAGTTTAATGTTGATGTAATTTGTTATTAATTTTTTATTTAGAAGGAAGAT
43178440 TAAGGAAAGAAA
130 TAAGGAAAGAAA
* * * *
43178452 AAAAAGCTAAAAGAAAGATAAATGTGTTTGATTTTTTAATTTAATTTAAAGTTATTTTTGGTAAT
1 AAAAAGCTAAAAGAAAGATAAA--TATTT-ATTTGTTAATTTAATTTAAAGTTATTGTTAGTAAT
* * *
43178517 TATTAAAATTATTTTTTAGTTTAATTTTTATGTAATTTGTTATTAATTTTTTATTTAG
63 TATTAAAAATATTTTTTAGTTTAATGTTGATGTAATTTGTTATTAATTTTTTATTTAG
43178575 TAGAGCAGAT
Statistics
Matches: 100, Mismatches: 14, Indels: 10
0.81 0.11 0.08
Matches are distributed among these distances:
136 19 0.19
139 3 0.03
141 14 0.14
142 1 0.01
143 35 0.35
144 28 0.28
ACGTcount: A:0.36, C:0.01, G:0.14, T:0.49
Consensus pattern (141 bp):
AAAAAGCTAAAAGAAAGATAAATATTTATTTGTTAATTTAATTTAAAGTTATTGTTAGTAATTAT
TAAAAATATTTTTTAGTTTAATGTTGATGTAATTTGTTATTAATTTTTTATTTAGAAGGAAGATT
AAGGAAAGAAA
Found at i:43178632 original size:143 final size:142
Alignment explanation
Indices: 43178368--43178641 Score: 342
Period size: 143 Copynumber: 1.9 Consensus size: 142
43178358 TATTTTGTTA
* *
43178368 GTAATTATTATAAAATATTTTTTAGTTTAATGTTGATGTGATTTGTTATAATTTTTTGTTTAGAA
1 GTAATTATTATAAAATATTTTTTAGTTTAATGTTGATGTAATTTGTTATAATTTTTTATTTAGAA
43178433 GGAAGATTAAGGAAAGAAAAAAAAGCTAAAAGAAAGATAAATGTGTTTGATTTTTTAATTTAATT
66 GGAAGATTAAGGAAAGAAAAAAAA-C-AAAAGAAAGATAAATGTGTTTGATTTTTTAATTTAATT
43178498 TAAAGTTATTTTTG
129 TAAAGTTATTTTTG
* * * *
43178512 GTAATTATTA-AAATTATTTTTTAGTTTAATTTTTATGTAATTTGTTATTAATTTTTTATTTAGT
1 GTAATTATTATAAAATATTTTTTAGTTTAATGTTGATGTAATTTGTTA-TAATTTTTTATTTAGA
* * * * *
43178576 AGAGCAGATTAAAGGGAGAGAAAGAAAAA-AAAAGTAAG-TTAA-GT-TTTGTTGTTTTTAATTT
65 AG-GAAGATT-AA-GGAAAGAAA-AAAAACAAAAGAAAGATAAATGTGTTTGAT-TTTTTAATTT
43178637 AATTT
125 AATTT
43178642 TATTTTTTAG
Statistics
Matches: 113, Mismatches: 11, Indels: 13
0.82 0.08 0.09
Matches are distributed among these distances:
142 5 0.04
143 50 0.44
144 29 0.26
145 14 0.12
146 2 0.02
147 8 0.07
148 5 0.04
ACGTcount: A:0.38, C:0.01, G:0.15, T:0.46
Consensus pattern (142 bp):
GTAATTATTATAAAATATTTTTTAGTTTAATGTTGATGTAATTTGTTATAATTTTTTATTTAGAA
GGAAGATTAAGGAAAGAAAAAAAACAAAAGAAAGATAAATGTGTTTGATTTTTTAATTTAATTTA
AAGTTATTTTTG
Found at i:43179629 original size:19 final size:17
Alignment explanation
Indices: 43179599--43179638 Score: 53
Period size: 19 Copynumber: 2.2 Consensus size: 17
43179589 TAACTGTCTT
43179599 TTTTCCCTTTCTTCTCC
1 TTTTCCCTTTCTTCTCC
*
43179616 TTTTCTCCTCTTCTTCTTC
1 TTTTC-CCT-TTCTTCTCC
43179635 TTTT
1 TTTT
43179639 GCTTAAATCT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
17 5 0.25
18 3 0.15
19 12 0.60
ACGTcount: A:0.00, C:0.35, G:0.00, T:0.65
Consensus pattern (17 bp):
TTTTCCCTTTCTTCTCC
Found at i:43181918 original size:195 final size:195
Alignment explanation
Indices: 43181522--43181969 Score: 580
Period size: 195 Copynumber: 2.3 Consensus size: 195
43181512 GAAATCGACG
* *
43181522 CGATGGCTGAGGTACCGCATATGTTGCGAGTCCTCGACAGCTCGTGTGAGCAGCATCGTGAGTCG
1 CGATGGTTGAGGTACCGCATATGTTGCGAGTCCTCGACAGCTCGTGTGAGCAGCATCGTGACTCG
* * *
43181587 GGAAATGAGAAAAGAATCCAAAAATGGATTACATGCCCCACGATGGCTGAGATTTATGCATAAGT
66 GGAAATGAGAAAAGAATCCAAAAATGGATTACAGGCCCCACGATGGCTAAGATCTATGCATAAGT
* * *
43181652 GCATATTCTCGACAACTTGTGTGAGCAGCATCGTTAGGGAACAGTTATATACACAGATACCGTAT
131 GCATACTCTCGACAACTTGTGTGAGCAGCATCGTTAGGGAACAGTTATATACACAGACACCGTAC
* * * *
43181717 CGATGGTTGAGGTACCGCATATGTTGCGAGACCTTGACATCCCGTGTGAGCAGCATCGTGACTCG
1 CGATGGTTGAGGTACCGCATATGTTGCGAGTCCTCGACAGCTCGTGTGAGCAGCATCGTGACTCG
* * ** * * * *
43181782 GGAAA-GAGATATGAAT-CTTAAATGGATTATAGGCCCTACGATGGCTAAGA-CTATGCTTTA-T
66 GGAAATGAGAAAAGAATCCAAAAATGGATTACAGGCCCCACGATGGCTAAGATCTATGCATAAGT
* * * *
43181843 GCATACTCTCGATAGCTTGTGTGAGCAGCATTGTTAGGGAACAGTTTATAGTACAGACAGGCACC
131 GCATACTCTCGACAACTTGTGTGAGCAGCATCGTTAGGGAACAG-TTATA-TAC--ACAGACACC
43181908 GTAC
192 GTAC
* * * *
43181912 CGATGGTTGGGGTACCGCACACGTTGCGAGTCCTCAACAGCTCGTGTGAGCAGCATCG
1 CGATGGTTGAGGTACCGCATATGTTGCGAGTCCTCGACAGCTCGTGTGAGCAGCATCG
43181970 AGTACTGGTA
Statistics
Matches: 217, Mismatches: 32, Indels: 8
0.84 0.12 0.03
Matches are distributed among these distances:
191 41 0.19
192 12 0.06
193 31 0.14
194 9 0.04
195 124 0.57
ACGTcount: A:0.27, C:0.21, G:0.27, T:0.25
Consensus pattern (195 bp):
CGATGGTTGAGGTACCGCATATGTTGCGAGTCCTCGACAGCTCGTGTGAGCAGCATCGTGACTCG
GGAAATGAGAAAAGAATCCAAAAATGGATTACAGGCCCCACGATGGCTAAGATCTATGCATAAGT
GCATACTCTCGACAACTTGTGTGAGCAGCATCGTTAGGGAACAGTTATATACACAGACACCGTAC
Found at i:43186205 original size:41 final size:41
Alignment explanation
Indices: 43186148--43186243 Score: 149
Period size: 41 Copynumber: 2.3 Consensus size: 41
43186138 GAATTTTATT
* *
43186148 TTAACAAGAATTCTAGTCACCTAATTCTAACAATC-TCTACC
1 TTAACAAGAATTCTAGTCACCCAATTCTAACAATCTTC-AAC
43186189 TTAACAAGAATTCTAGTCACCCAATTCTAACAATCTTCAAC
1 TTAACAAGAATTCTAGTCACCCAATTCTAACAATCTTCAAC
*
43186230 TTGACAAGAATTCT
1 TTAACAAGAATTCT
43186244 CTACGAACAA
Statistics
Matches: 51, Mismatches: 3, Indels: 2
0.91 0.05 0.04
Matches are distributed among these distances:
41 49 0.96
42 2 0.04
ACGTcount: A:0.38, C:0.25, G:0.06, T:0.31
Consensus pattern (41 bp):
TTAACAAGAATTCTAGTCACCCAATTCTAACAATCTTCAAC
Found at i:43186255 original size:17 final size:17
Alignment explanation
Indices: 43186233--43186271 Score: 60
Period size: 17 Copynumber: 2.3 Consensus size: 17
43186223 CTTCAACTTG
* *
43186233 ACAAGAATTCTCTACGA
1 ACAAGAACTCTCAACGA
43186250 ACAAGAACTCTCAACGA
1 ACAAGAACTCTCAACGA
43186267 ACAAG
1 ACAAG
43186272 TTCTCCACCT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
17 20 1.00
ACGTcount: A:0.46, C:0.26, G:0.13, T:0.15
Consensus pattern (17 bp):
ACAAGAACTCTCAACGA
Found at i:43192360 original size:21 final size:21
Alignment explanation
Indices: 43192336--43192384 Score: 55
Period size: 21 Copynumber: 2.3 Consensus size: 21
43192326 GACAATATTG
*
43192336 CCGATACAAGT-ATGACTTGTA
1 CCGATACAAGTCAT-ACTTCTA
* *
43192357 CCGAAACATGTCATACTTCTA
1 CCGATACAAGTCATACTTCTA
43192378 CCGATAC
1 CCGATAC
43192385 TAAAAACTCT
Statistics
Matches: 23, Mismatches: 4, Indels: 2
0.79 0.14 0.07
Matches are distributed among these distances:
21 21 0.91
22 2 0.09
ACGTcount: A:0.33, C:0.27, G:0.14, T:0.27
Consensus pattern (21 bp):
CCGATACAAGTCATACTTCTA
Found at i:43192550 original size:36 final size:36
Alignment explanation
Indices: 43192503--43192572 Score: 115
Period size: 36 Copynumber: 1.9 Consensus size: 36
43192493 ATTGATACAA
*
43192503 CTCAAGCCAGTGAACAACCT-CTCTCCTACCCTGTAC
1 CTCAAGCCAGTGAACAACCTCCT-TCCAACCCTGTAC
43192539 CTCAAGCCAGTGAACAACCTCCTTCCAACCCTGT
1 CTCAAGCCAGTGAACAACCTCCTTCCAACCCTGT
43192573 TCTTCTATCA
Statistics
Matches: 32, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
36 30 0.94
37 2 0.06
ACGTcount: A:0.26, C:0.41, G:0.11, T:0.21
Consensus pattern (36 bp):
CTCAAGCCAGTGAACAACCTCCTTCCAACCCTGTAC
Found at i:43192790 original size:21 final size:21
Alignment explanation
Indices: 43192766--43192816 Score: 59
Period size: 21 Copynumber: 2.4 Consensus size: 21
43192756 GAGATAATAT
*
43192766 TACCGATACAAGT-ATGACTTG
1 TACCGATACAAGTCAT-ACTTC
* *
43192787 TACCGAAACATGTCATACTTC
1 TACCGATACAAGTCATACTTC
43192808 TACCGATAC
1 TACCGATAC
43192817 TAAAAACTCT
Statistics
Matches: 25, Mismatches: 4, Indels: 2
0.81 0.13 0.06
Matches are distributed among these distances:
21 23 0.92
22 2 0.08
ACGTcount: A:0.33, C:0.25, G:0.14, T:0.27
Consensus pattern (21 bp):
TACCGATACAAGTCATACTTC
Found at i:43192982 original size:36 final size:36
Alignment explanation
Indices: 43192935--43193006 Score: 144
Period size: 36 Copynumber: 2.0 Consensus size: 36
43192925 ATTGATACAA
43192935 CTCAAGCCAGTGAACAACCTCTCTCCTACCCTGTAC
1 CTCAAGCCAGTGAACAACCTCTCTCCTACCCTGTAC
43192971 CTCAAGCCAGTGAACAACCTCTCTCCTACCCTGTAC
1 CTCAAGCCAGTGAACAACCTCTCTCCTACCCTGTAC
43193007 TTCTATCGAT
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
36 36 1.00
ACGTcount: A:0.25, C:0.42, G:0.11, T:0.22
Consensus pattern (36 bp):
CTCAAGCCAGTGAACAACCTCTCTCCTACCCTGTAC
Found at i:43193072 original size:432 final size:432
Alignment explanation
Indices: 43192269--43193138 Score: 1625
Period size: 432 Copynumber: 2.0 Consensus size: 432
43192259 ACAAGTACTA
*
43192269 GTAGTTGTCAAGTCGGTAAACAATTGAAGAACAGTGCAGACTTTTACCGATACTCGAGACAATAT
1 GTAGTTGTCAAGTCGGTAAACAATTCAAGAACAGTGCAGACTTTTACCGATACTCGAGACAATAT
*
43192334 TGCCGATACAAGTATGACTTGTACCGAAACATGTCATACTTCTACCGATACTAAAAACTCTAGAG
66 TACCGATACAAGTATGACTTGTACCGAAACATGTCATACTTCTACCGATACTAAAAACTCTAGAG
*
43192399 AGTTAAGAAATCTTACCCTGTAACTTCTACCGATACAAGTATACGAGCTATCGATACTTTTGTGA
131 AGTTAAGAAATCTTACCCTGTAACTTCAACCGATACAAGTATACGAGCTATCGATACTTTTGTGA
*
43192464 GTAGAACTACCAATACTTATTATGCAACTATTGATACAACTCAAGCCAGTGAACAACCTCTCTCC
196 ATAGAACTACCAATACTTATTATGCAACTATTGATACAACTCAAGCCAGTGAACAACCTCTCTCC
*
43192529 TACCCTGTACCTCAAGCCAGTGAACAACCTCCTTCCAACCCTGTTCTTCTATCAATACATGCATG
261 TACCCTGTACCTCAAGCCAGTGAACAACCTCCTTCCAACCCTGTACTTCTATCAATACATGCATG
43192594 AGTTTTACTGAAACAAGTATGCAAAATCTTTAGAATCATACCAAAACATAAGTTTATCAACACCT
326 AGTTTTACTGAAACAAGTATGCAAAATCTTTAGAATCATACCAAAACATAAGTTTATCAACACCT
43192659 ATCATTCATAACATCAAAATGCATGAGAACATTATATAATTC
391 ATCATTCATAACATCAAAATGCATGAGAACATTATATAATTC
* *
43192701 GTAGTTGTCAAGTCGGTAAACAATTCAAGAACAGTGCAGACTTTTACCGATACTTGAGATAATAT
1 GTAGTTGTCAAGTCGGTAAACAATTCAAGAACAGTGCAGACTTTTACCGATACTCGAGACAATAT
43192766 TACCGATACAAGTATGACTTGTACCGAAACATGTCATACTTCTACCGATACTAAAAACTCTAGAG
66 TACCGATACAAGTATGACTTGTACCGAAACATGTCATACTTCTACCGATACTAAAAACTCTAGAG
*
43192831 AGTTAAGAAATCTTACCCTGTAACTTCAACCGGTACAAGTATACGAGCTATCGATACTTTTGTGA
131 AGTTAAGAAATCTTACCCTGTAACTTCAACCGATACAAGTATACGAGCTATCGATACTTTTGTGA
43192896 ATAGAACTACCAATACTTATTATGCAACTATTGATACAACTCAAGCCAGTGAACAACCTCTCTCC
196 ATAGAACTACCAATACTTATTATGCAACTATTGATACAACTCAAGCCAGTGAACAACCTCTCTCC
* *
43192961 TACCCTGTACCTCAAGCCAGTGAACAACCT-CTCTCCTACCCTGTACTTCTATCGATACATGCAT
261 TACCCTGTACCTCAAGCCAGTGAACAACCTCCT-TCCAACCCTGTACTTCTATCAATACATGCAT
43193025 GAGTTTTACTGAAACAAGTATGCAAAATCTTTAGAATCATACCAAAACATAAGTTTATCAACACC
325 GAGTTTTACTGAAACAAGTATGCAAAATCTTTAGAATCATACCAAAACATAAGTTTATCAACACC
*
43193090 TATCATTCATAACATCAAAATGCATTAGAACATTATATAATTC
390 TATCATTCATAACATCAAAATGCATGAGAACATTATATAATTC
43193133 GTAGTT
1 GTAGTT
43193139 TCCCAAATCA
Statistics
Matches: 426, Mismatches: 11, Indels: 2
0.97 0.03 0.00
Matches are distributed among these distances:
431 2 0.00
432 424 1.00
ACGTcount: A:0.36, C:0.23, G:0.13, T:0.29
Consensus pattern (432 bp):
GTAGTTGTCAAGTCGGTAAACAATTCAAGAACAGTGCAGACTTTTACCGATACTCGAGACAATAT
TACCGATACAAGTATGACTTGTACCGAAACATGTCATACTTCTACCGATACTAAAAACTCTAGAG
AGTTAAGAAATCTTACCCTGTAACTTCAACCGATACAAGTATACGAGCTATCGATACTTTTGTGA
ATAGAACTACCAATACTTATTATGCAACTATTGATACAACTCAAGCCAGTGAACAACCTCTCTCC
TACCCTGTACCTCAAGCCAGTGAACAACCTCCTTCCAACCCTGTACTTCTATCAATACATGCATG
AGTTTTACTGAAACAAGTATGCAAAATCTTTAGAATCATACCAAAACATAAGTTTATCAACACCT
ATCATTCATAACATCAAAATGCATGAGAACATTATATAATTC
Found at i:43193816 original size:52 final size:51
Alignment explanation
Indices: 43193753--43194035 Score: 270
Period size: 52 Copynumber: 5.5 Consensus size: 51
43193743 CTCATTTAAC
*
43193753 ACTCACGATGACACAAATTCATC-AAATCTTAAATCTGTAAAAGGA-TCTATAT
1 ACTCACGATGACACAAAGTCATCGAAATCTTAAATC-GT-AAAGGATTC-ATAT
* * ** *
43193805 GCTCACGATGACACATAGTCATCGGACCTCTTAATTCGTAAAGGATTCATAT
1 ACTCACGATGACACAAAGTCATC-GAAATCTTAAATCGTAAAGGATTCATAT
* * * * *
43193857 ACTCACGATGACACATAGCCATCG-GACCTCATAATCAGTAAAGGATTCATAT
1 ACTCACGATGACACAAAGTCATCGAAATCTTA-AATC-GTAAAGGATTCATAT
* * * *
43193909 ACTTACGATGACACATAGTCATCG-GACCTTATAATCCGTAAAGGATTCATAT
1 ACTCACGATGACACAAAGTCATCGAAATCTTA-AAT-CGTAAAGGATTCATAT
* *
43193961 ACTCACGATGACACATAGTCATCG-AATCTCATAAACCGTAAAGGATTCATAT
1 ACTCACGATGACACAAAGTCATCGAAATCT--TAAATCGTAAAGGATTCATAT
* *
43194013 ACTCACGAAGACACACAGTCATC
1 ACTCACGATGACACAAAGTCATC
43194036 AGACCTTTTT
Statistics
Matches: 201, Mismatches: 22, Indels: 16
0.84 0.09 0.07
Matches are distributed among these distances:
50 3 0.01
51 4 0.02
52 176 0.88
53 7 0.03
54 11 0.05
ACGTcount: A:0.37, C:0.23, G:0.14, T:0.26
Consensus pattern (51 bp):
ACTCACGATGACACAAAGTCATCGAAATCTTAAATCGTAAAGGATTCATAT
Found at i:43193933 original size:104 final size:104
Alignment explanation
Indices: 43193792--43194042 Score: 371
Period size: 104 Copynumber: 2.4 Consensus size: 104
43193782 TAAATCTGTA
* *
43193792 AAAGGA-TCTATATGCTCACGATGACACATAGTCATCGGACCTCT-TAATTCGTAAAGGATTCAT
1 AAAGGATTC-ATATACTCACGATGACACATAGTCATCGGACCT-TATAATCCGTAAAGGATTCAT
* *
43193855 ATACTCACGATGACACATAGCCATCGGACCTCATAATCAGT
64 ATACTCACGATGACACATAGCCATCGAACCTCATAAACAGT
*
43193896 AAAGGATTCATATACTTACGATGACACATAGTCATCGGACCTTATAATCCGTAAAGGATTCATAT
1 AAAGGATTCATATACTCACGATGACACATAGTCATCGGACCTTATAATCCGTAAAGGATTCATAT
* * *
43193961 ACTCACGATGACACATAGTCATCGAATCTCATAAACCGT
66 ACTCACGATGACACATAGCCATCGAACCTCATAAACAGT
* * *
43194000 AAAGGATTCATATACTCACGAAGACACACAGTCATCAGACCTT
1 AAAGGATTCATATACTCACGATGACACATAGTCATCGGACCTT
43194043 TTTCATTTAC
Statistics
Matches: 133, Mismatches: 12, Indels: 4
0.89 0.08 0.03
Matches are distributed among these distances:
103 1 0.01
104 130 0.98
105 2 0.02
ACGTcount: A:0.36, C:0.24, G:0.15, T:0.25
Consensus pattern (104 bp):
AAAGGATTCATATACTCACGATGACACATAGTCATCGGACCTTATAATCCGTAAAGGATTCATAT
ACTCACGATGACACATAGCCATCGAACCTCATAAACAGT
Found at i:43194041 original size:156 final size:156
Alignment explanation
Indices: 43193757--43194041 Score: 394
Period size: 156 Copynumber: 1.8 Consensus size: 156
43193747 TTTAACACTC
* * * *
43193757 ACGATGACACAAATTCATCAAATCTTAAATCTGTAAAAGGATCTATATGCTCACGATGACACATA
1 ACGATGACACAAAGTCATCAAACCTTAAATCCGTAAAAGGATCTATATACTCACGATGACACATA
* * ** * * *
43193822 GTCATCGGACCTCTTAATTCGTAAAGGATTCATATACTCACGATGACACATAGCCATCGGACCTC
66 GTCATCGAACCTCATAAACCGTAAAGGATTCATATACTCACGAAGACACACAGCCATCAGACCTC
43193887 ATAATCAGTAAAGGATTCATATACTT
131 ATAATCAGTAAAGGATTCATATACTT
* **
43193913 ACGATGACACATAGTCATCGGACCTTATAATCCGT-AAAGGAT-TCATATACTCACGATGACACA
1 ACGATGACACAAAGTCATCAAACCTTA-AATCCGTAAAAGGATCT-ATATACTCACGATGACACA
* *
43193976 TAGTCATCGAATCTCATAAACCGTAAAGGATTCATATACTCACGAAGACACACAGTCATCAGACC
64 TAGTCATCGAACCTCATAAACCGTAAAGGATTCATATACTCACGAAGACACACAGCCATCAGACC
43194041 T
129 T
43194042 TTTTCATTTA
Statistics
Matches: 111, Mismatches: 16, Indels: 4
0.85 0.12 0.03
Matches are distributed among these distances:
155 1 0.01
156 104 0.94
157 6 0.05
ACGTcount: A:0.37, C:0.23, G:0.14, T:0.26
Consensus pattern (156 bp):
ACGATGACACAAAGTCATCAAACCTTAAATCCGTAAAAGGATCTATATACTCACGATGACACATA
GTCATCGAACCTCATAAACCGTAAAGGATTCATATACTCACGAAGACACACAGCCATCAGACCTC
ATAATCAGTAAAGGATTCATATACTT
Found at i:43195700 original size:12 final size:12
Alignment explanation
Indices: 43195657--43195711 Score: 71
Period size: 12 Copynumber: 4.8 Consensus size: 12
43195647 CCCTTTTACC
43195657 ATTATTATTAAT
1 ATTATTATTAAT
43195669 ATTA-TATT--T
1 ATTATTATTAAT
43195678 ATTATTATTAAT
1 ATTATTATTAAT
*
43195690 ATTATTATTAAC
1 ATTATTATTAAT
*
43195702 GTTATTATTA
1 ATTATTATTA
43195712 CTGTTATTTA
Statistics
Matches: 38, Mismatches: 2, Indels: 6
0.83 0.04 0.13
Matches are distributed among these distances:
9 5 0.13
10 4 0.11
11 4 0.11
12 25 0.66
ACGTcount: A:0.38, C:0.02, G:0.02, T:0.58
Consensus pattern (12 bp):
ATTATTATTAAT
Found at i:43195736 original size:3 final size:3
Alignment explanation
Indices: 43195657--43195727 Score: 54
Period size: 3 Copynumber: 23.3 Consensus size: 3
43195647 CCCTTTTACC
* * **
43195657 ATT ATT ATT AAT ATT A-T ATTT ATT ATT ATT AAT ATT ATT ATT AAC
1 ATT ATT ATT ATT ATT ATT A-TT ATT ATT ATT ATT ATT ATT ATT ATT
* * *
43195702 GTT ATT ATT ACT GTT ATTT ATT ATT A
1 ATT ATT ATT ATT ATT A-TT ATT ATT A
43195728 ACATTATTAC
Statistics
Matches: 51, Mismatches: 14, Indels: 6
0.72 0.20 0.08
Matches are distributed among these distances:
2 2 0.04
3 44 0.86
4 5 0.10
ACGTcount: A:0.35, C:0.03, G:0.03, T:0.59
Consensus pattern (3 bp):
ATT
Found at i:43196465 original size:6 final size:6
Alignment explanation
Indices: 43196454--43196495 Score: 52
Period size: 6 Copynumber: 7.3 Consensus size: 6
43196444 GACACTTTTT
* *
43196454 AATTTA AATTTA AA-ATA AATTTA AATTTA AA-GTA AATTTA AA
1 AATTTA AATTTA AATTTA AATTTA AATTTA AATTTA AATTTA AA
43196496 CTCAAAAAAT
Statistics
Matches: 30, Mismatches: 4, Indels: 4
0.79 0.11 0.11
Matches are distributed among these distances:
5 8 0.27
6 22 0.73
ACGTcount: A:0.57, C:0.00, G:0.02, T:0.40
Consensus pattern (6 bp):
AATTTA
Found at i:43196476 original size:17 final size:17
Alignment explanation
Indices: 43196454--43196544 Score: 92
Period size: 17 Copynumber: 5.2 Consensus size: 17
43196444 GACACTTTTT
43196454 AATTTAAATTTAAAATA
1 AATTTAAATTTAAAATA
*
43196471 AATTTAAATTTAAAGTA
1 AATTTAAATTTAAAATA
** *
43196488 AATTTAAACTCAAAAAATG
1 AATTTAAA-T-TTAAAATA
*
43196507 AATTTAAATTTAGAATA
1 AATTTAAATTTAAAATA
* * *
43196524 AATTCAAACTTAAAGTA
1 AATTTAAATTTAAAATA
43196541 AATT
1 AATT
43196545 AAAAAATTAA
Statistics
Matches: 59, Mismatches: 13, Indels: 4
0.78 0.17 0.05
Matches are distributed among these distances:
17 45 0.76
18 2 0.03
19 12 0.20
ACGTcount: A:0.55, C:0.04, G:0.04, T:0.36
Consensus pattern (17 bp):
AATTTAAATTTAAAATA
Found at i:43196511 original size:36 final size:36
Alignment explanation
Indices: 43196465--43196533 Score: 104
Period size: 36 Copynumber: 1.9 Consensus size: 36
43196455 ATTTAAATTT
*
43196465 AAAATAAATTTAAATTTA-AAGTAAATTTAAACTCAA
1 AAAATAAATTTAAATTTAGAA-TAAATTCAAACTCAA
*
43196501 AAAATGAATTTAAATTTAGAATAAATTCAAACT
1 AAAATAAATTTAAATTTAGAATAAATTCAAACT
43196534 TAAAGTAAAT
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
36 28 0.93
37 2 0.07
ACGTcount: A:0.57, C:0.06, G:0.04, T:0.33
Consensus pattern (36 bp):
AAAATAAATTTAAATTTAGAATAAATTCAAACTCAA
Found at i:43197091 original size:78 final size:78
Alignment explanation
Indices: 43196965--43197226 Score: 301
Period size: 78 Copynumber: 3.4 Consensus size: 78
43196955 TCTGCCCCAA
* * * * * ** * *
43196965 GCTCGGGGTAGGAGATTAGTTGATGGTGATCTACCCCAAGCTCGGGGTAAGGGATCGAATGACTG
1 GCTCGGGGTAAGAGATTGGTTGATGATGATCTGCCCCAAGCTCAGGGTAAAAGATCAAATGGCTG
43197030 TAATATGCCCCTG
66 TAATATGCCCCTG
*
43197043 GCTCGGGGTAAGAGATTGGTTGATGATGATCTGCCCCAAGCTCAGGGTAAAAGATCAAATGGCTT
1 GCTCGGGGTAAGAGATTGGTTGATGATGATCTGCCCCAAGCTCAGGGTAAAAGATCAAATGGCTG
* *
43197108 TAATCTGCCCCAG
66 TAATATGCCCCTG
* * * * *
43197121 ACTCGGGGTAAGAGATCGATTGGTGATGATCTGTCCCAAGCTCAGGGTAAAAGATCAAATGGCTG
1 GCTCGGGGTAAGAGATTGGTTGATGATGATCTGCCCCAAGCTCAGGGTAAAAGATCAAATGGCTG
* ** *
43197186 T-ATTTTACCCTAA
66 TAATATGCCCCT-G
**
43197199 GCTTAGGGTAAGAGATTGGTTGATGATG
1 GCTCGGGGTAAGAGATTGGTTGATGATG
43197227 TAACTTCACT
Statistics
Matches: 154, Mismatches: 29, Indels: 2
0.83 0.16 0.01
Matches are distributed among these distances:
77 6 0.04
78 148 0.96
ACGTcount: A:0.26, C:0.18, G:0.30, T:0.26
Consensus pattern (78 bp):
GCTCGGGGTAAGAGATTGGTTGATGATGATCTGCCCCAAGCTCAGGGTAAAAGATCAAATGGCTG
TAATATGCCCCTG
Found at i:43197092 original size:39 final size:39
Alignment explanation
Indices: 43196954--43197176 Score: 175
Period size: 39 Copynumber: 5.7 Consensus size: 39
43196944 GATAACTACA
* * *
43196954 ATCTGCCCCAAGCTCGGGGTAGGAGAT-TAGTTGATGGTG
1 ATCTGCCCCAAGCTCGGGGTAAGAGATCGA-TTGATGATG
* * * *
43196993 ATCTACCCCAAGCTCGGGGTAAGGGATCGAATGACTG-TA
1 ATCTGCCCCAAGCTCGGGGTAAGAGATCGATTGA-TGATG
* ** * *
43197032 ATATGCCCCTGGCTCGGGGTAAGAGATTGGTTGATGATG
1 ATCTGCCCCAAGCTCGGGGTAAGAGATCGATTGATGATG
* * * * * * *
43197071 ATCTGCCCCAAGCTCAGGGTAAAAGATCAAATGGCT-TTA
1 ATCTGCCCCAAGCTCGGGGTAAGAGATC-GATTGATGATG
*
43197110 ATCTGCCCC-AGACTCGGGGTAAGAGATCGATTGGTGATG
1 ATCTGCCCCAAG-CTCGGGGTAAGAGATCGATTGATGATG
* * *
43197149 ATCTGTCCCAAGCTCAGGGTAAAAGATC
1 ATCTGCCCCAAGCTCGGGGTAAGAGATC
43197177 AAATGGCTGT
Statistics
Matches: 140, Mismatches: 37, Indels: 14
0.73 0.19 0.07
Matches are distributed among these distances:
38 8 0.06
39 124 0.89
40 8 0.06
ACGTcount: A:0.26, C:0.21, G:0.30, T:0.24
Consensus pattern (39 bp):
ATCTGCCCCAAGCTCGGGGTAAGAGATCGATTGATGATG
Found at i:43197201 original size:39 final size:37
Alignment explanation
Indices: 43197077--43197214 Score: 107
Period size: 39 Copynumber: 3.6 Consensus size: 37
43197067 GATGATCTGC
* *
43197077 CCCAAGCTCAGGGTAAAAGATCAAATGGCTTTAATCT
1 CCCAAGCTCAGGGTAAAAGATCAAATGGCTGTATTCT
* * * * * *
43197114 GCCCCAGACTCGGGGTAAGAGATCGATTGG-TGATGATCTGT
1 -CCCAAG-CTCAGGGTAAAAGATCAAATGGCTG-T-AT-TCT
*
43197155 CCCAAGCTCAGGGTAAAAGATCAAATGGCTGTATTTT
1 CCCAAGCTCAGGGTAAAAGATCAAATGGCTGTATTCT
* *
43197192 ACCCTAAGCTTAGGGTAAGAGAT
1 -CCC-AAGCTCAGGGTAAAAGAT
43197215 TGGTTGATGA
Statistics
Matches: 77, Mismatches: 16, Indels: 13
0.73 0.15 0.12
Matches are distributed among these distances:
37 2 0.03
38 11 0.14
39 54 0.70
40 8 0.10
41 2 0.03
ACGTcount: A:0.30, C:0.20, G:0.25, T:0.25
Consensus pattern (37 bp):
CCCAAGCTCAGGGTAAAAGATCAAATGGCTGTATTCT
Found at i:43197395 original size:101 final size:101
Alignment explanation
Indices: 43197281--43197482 Score: 289
Period size: 101 Copynumber: 2.0 Consensus size: 101
43197271 ACTGCTGCAG
* * * * * *
43197281 TTTTAATCTAACTTCGCTAG-AACTTCAGGAAGATAGGATTTGATGTTGAAGCTTCATCTTGCTC
1 TTTTAATCCAACTTCACT-GCAACTTCAAGAAGATAGGAATTGACGTTAAAGCTTCATCTTGCTC
*
43197345 TTACTACAACTTCAGAGAGATAAAGACTTGCTATTGT
65 TTACTACAACTTCAGAGAGATAAAGACTTGCCATTGT
* *
43197382 TTTTAATCCAACTTTACTGCAACTTCAAGAGGATAGGAATTGACGTTAAAGCTTCATCTTGCTCT
1 TTTTAATCCAACTTCACTGCAACTTCAAGAAGATAGGAATTGACGTTAAAGCTTCATCTTGCTCT
* *
43197447 TACTGCAACTTCAGAGAGATAAAGCCTTGCCATTGT
66 TACTACAACTTCAGAGAGATAAAGACTTGCCATTGT
43197483 AGTTTTTATC
Statistics
Matches: 89, Mismatches: 11, Indels: 2
0.87 0.11 0.02
Matches are distributed among these distances:
100 1 0.01
101 88 0.99
ACGTcount: A:0.30, C:0.19, G:0.17, T:0.34
Consensus pattern (101 bp):
TTTTAATCCAACTTCACTGCAACTTCAAGAAGATAGGAATTGACGTTAAAGCTTCATCTTGCTCT
TACTACAACTTCAGAGAGATAAAGACTTGCCATTGT
Found at i:43197818 original size:99 final size:97
Alignment explanation
Indices: 43197675--43197936 Score: 348
Period size: 99 Copynumber: 2.7 Consensus size: 97
43197665 AGGTTCGTCA
* * * * * *
43197675 TTGCGACTTAAACTTTTCCCTTTGTGTCTTCGTGGTACTAGATCCACCGTTGCGGTTTAGATCTT
1 TTGCGGCTTAGACCTTTCCCTTTGTCTCTTCGTGGTACTGGATCCACCGTTGCGGCTTAGATCTT
*
43197740 TCCCTTGTGACTTCGTGGTACTAGATCCGCCG
66 TCCCTTGTGACTTCGTGGTACTAGATCCACCG
*
43197772 TTGCGGCTTAGACCTTTCCCTTCATGTCTCTTCGTGGTACTGGATCCACCGTTGCGGCTTAGATT
1 TTGCGGCTTAGACCTTTCCCTT--TGTCTCTTCGTGGTACTGGATCCACCGTTGCGGCTTAGATC
*
43197837 TTTCCCTTGT-ATCTTCATGGTACTAGATCCACCG
64 TTTCCCTTGTGA-CTTCGTGGTACTAGATCCACCG
* * * * * *
43197871 TTGCGGGTTAGATCTTTCCC-TTGTGTCTTCATGATACTGGATCCGCCGTTGCGGCTTAGATCTT
1 TTGCGGCTTAGACCTTTCCCTTTGTCTCTTCGTGGTACTGGATCCACCGTTGCGGCTTAGATCTT
43197935 TC
66 TC
43197937 TCTTCATGTC
Statistics
Matches: 146, Mismatches: 16, Indels: 7
0.86 0.09 0.04
Matches are distributed among these distances:
96 40 0.27
97 19 0.13
98 2 0.01
99 85 0.58
ACGTcount: A:0.14, C:0.26, G:0.22, T:0.38
Consensus pattern (97 bp):
TTGCGGCTTAGACCTTTCCCTTTGTCTCTTCGTGGTACTGGATCCACCGTTGCGGCTTAGATCTT
TCCCTTGTGACTTCGTGGTACTAGATCCACCG
Found at i:43197871 original size:147 final size:145
Alignment explanation
Indices: 43197688--43197989 Score: 433
Period size: 147 Copynumber: 2.1 Consensus size: 145
43197678 CGACTTAAAC
* * *
43197688 TTTTCCCTTTGTGTCTTCGTGGTACTAGATCCACCGTTGCGGTTTAGATCTTTCCCTTGTGACTT
1 TTTTCCC-TTGTATCTTCATGGTACTAGATCCACCGTTGCGGGTTAGATCTTTCCCTTGTGACTT
* * * *
43197753 CGTGGTACTAGATCCGCCGTTGCGGCTTAGACCTTTCCCTTCATGTCTCTTCGTGGTACTGGATC
65 CATGATACTAGATCCGCCGTTGCGGCTTAGACCTTTCCCTTCATG--TCTTCGCGATACTGGATC
43197818 CACCGTTGCGGCTTAGAT
128 CACCGTTGCGGCTTAGAT
*
43197836 TTTTCCCTTGTATCTTCATGGTACTAGATCCACCGTTGCGGGTTAGATCTTTCCCTTGTGTCTTC
1 TTTTCCCTTGTATCTTCATGGTACTAGATCCACCGTTGCGGGTTAGATCTTTCCCTTGTGACTTC
* * * **
43197901 ATGATACTGGATCCGCCGTTGCGGCTTAGATCTTTCTCTTCATGTCTTCGCGATACTGGATTTAC
66 ATGATACTAGATCCGCCGTTGCGGCTTAGACCTTTCCCTTCATGTCTTCGCGATACTGGATCCAC
* *
43197966 CGTTGTGGCTTCGAT
131 CGTTGCGGCTTAGAT
*
43197981 CTTTCCCTT
1 TTTTCCCTT
43197990 CATGTCTCTG
Statistics
Matches: 138, Mismatches: 16, Indels: 3
0.88 0.10 0.02
Matches are distributed among these distances:
145 38 0.28
147 93 0.67
148 7 0.05
ACGTcount: A:0.13, C:0.26, G:0.22, T:0.39
Consensus pattern (145 bp):
TTTTCCCTTGTATCTTCATGGTACTAGATCCACCGTTGCGGGTTAGATCTTTCCCTTGTGACTTC
ATGATACTAGATCCGCCGTTGCGGCTTAGACCTTTCCCTTCATGTCTTCGCGATACTGGATCCAC
CGTTGCGGCTTAGAT
Found at i:43198101 original size:49 final size:49
Alignment explanation
Indices: 43197689--43198104 Score: 360
Period size: 48 Copynumber: 8.5 Consensus size: 49
43197679 GACTTAAACT
** *
43197689 TTTCCCTTTGTGTCTTCGTGGTACTAGATCCACCGTTGCGGTTTAGATC
1 TTTCCCTTCATGTCTTCGTGGTACTAGATCCACCGTTGCGGCTTAGATC
* * * *
43197738 TTTCCCTT-GTGACTTCGTGGTACTAGATCCGCCGTTGCGGCTTAGACC
1 TTTCCCTTCATGTCTTCGTGGTACTAGATCCACCGTTGCGGCTTAGATC
* *
43197786 TTTCCCTTCATGTCTCTTCGTGGTACTGGATCCACCGTTGCGGCTTAGATT
1 TTTCCCTTCATG--TCTTCGTGGTACTAGATCCACCGTTGCGGCTTAGATC
* * * *
43197837 TTTCCCTT-GTATCTTCATGGTACTAGATCCACCGTTGCGGGTTAGATC
1 TTTCCCTTCATGTCTTCGTGGTACTAGATCCACCGTTGCGGCTTAGATC
* * * * *
43197885 TTTCCCTT-GTGTCTTCATGATACTGGATCCGCCGTTGCGGCTTAGATC
1 TTTCCCTTCATGTCTTCGTGGTACTAGATCCACCGTTGCGGCTTAGATC
* * * * ** * *
43197933 TTTCTCTTCATGTCTTCGCGATACTGGATTTACCGTTGTGGCTTCGATC
1 TTTCCCTTCATGTCTTCGTGGTACTAGATCCACCGTTGCGGCTTAGATC
* * * * * * * *
43197982 TTTCCCTTCATGTC-TCTGAGGTACAAGGTTCGCCGTTGCGACTTAAACCC
1 TTTCCCTTCATGTCTTC-GTGGTACTAGATCCACCGTTGCGGCTTAGA-TC
* * * * * *
43198032 TTT-TCTTTATGT-TT-GTGCGGTACTAGATTCACCTTTGCGACTTAAATC
1 TTTCCCTTCATGTCTTCGT--GGTACTAGATCCACCGTTGCGGCTTAGATC
*
43198080 TTTCCCTTCATGTCTTCGCGGTACT
1 TTTCCCTTCATGTCTTCGTGGTACT
43198105 GGTGACTTGT
Statistics
Matches: 301, Mismatches: 54, Indels: 24
0.79 0.14 0.06
Matches are distributed among these distances:
47 1 0.00
48 133 0.44
49 119 0.40
50 7 0.02
51 41 0.14
ACGTcount: A:0.14, C:0.26, G:0.21, T:0.39
Consensus pattern (49 bp):
TTTCCCTTCATGTCTTCGTGGTACTAGATCCACCGTTGCGGCTTAGATC
Found at i:43198710 original size:48 final size:49
Alignment explanation
Indices: 43198643--43198740 Score: 128
Period size: 48 Copynumber: 2.0 Consensus size: 49
43198633 CATGGTCGCA
* *
43198643 AGGTGAATGAAATTTTATTGGAG-GTAAAGCTCACATAAATGGAAAGATT
1 AGGTGAATGAAATTTTATTGGAGACT-AAGCTCACATAAATGAAAAGATT
* * *
43198692 AGGTGGATG-AATTTTATTGGAGACTAAGCTCGCATGAATGAAAAGATT
1 AGGTGAATGAAATTTTATTGGAGACTAAGCTCACATAAATGAAAAGATT
43198740 A
1 A
43198741 AAATCATTAG
Statistics
Matches: 43, Mismatches: 5, Indels: 3
0.84 0.10 0.06
Matches are distributed among these distances:
48 34 0.79
49 9 0.21
ACGTcount: A:0.39, C:0.07, G:0.26, T:0.29
Consensus pattern (49 bp):
AGGTGAATGAAATTTTATTGGAGACTAAGCTCACATAAATGAAAAGATT
Found at i:43204680 original size:96 final size:96
Alignment explanation
Indices: 43204508--43204690 Score: 244
Period size: 96 Copynumber: 1.9 Consensus size: 96
43204498 AAAAGATATT
** * * *
43204508 CGATTATCTCGATTTCAAGAAAGGTTGCACCTAGTAAGTTAAGGCACAAATTTTTAGAATCGAAG
1 CGATTATCTCGATTTCAAGAAAAATTGCACATAGTAAGTTAAGGCACAAATTTTCAAAATCGAAG
* *
43204573 ATAAGGAAATATTGCCTCGATTAAGGGTATA
66 ATAAAGAAATATCGCCTCGATTAAGGGTATA
* *
43204604 CGATTATTTCGATTTGAAGAAAAATTGCACATAGTAAGTTAAGGCACAAATTTTCAAAATTCGAA
1 CGATTATCTCGATTTCAAGAAAAATTGCACATAGTAAGTTAAGGCACAAATTTTCAAAA-TCGAA
*
43204669 -ATAAA-AGAATATCGCCTTGATT
65 GATAAAGA-AATATCGCCTCGATT
43204691 TTAAAGTTTT
Statistics
Matches: 75, Mismatches: 10, Indels: 4
0.84 0.11 0.04
Matches are distributed among these distances:
95 1 0.01
96 69 0.92
97 5 0.07
ACGTcount: A:0.39, C:0.13, G:0.18, T:0.30
Consensus pattern (96 bp):
CGATTATCTCGATTTCAAGAAAAATTGCACATAGTAAGTTAAGGCACAAATTTTCAAAATCGAAG
ATAAAGAAATATCGCCTCGATTAAGGGTATA
Found at i:43204938 original size:28 final size:28
Alignment explanation
Indices: 43204907--43204968 Score: 99
Period size: 28 Copynumber: 2.2 Consensus size: 28
43204897 AAAATGTGAT
*
43204907 TTTTGGAT-ACTCGAGGGCAAAATGGTAA
1 TTTTGG-TCACTCGAGGGAAAAATGGTAA
43204935 TTTTGGTCACTCGAGGGAAAAATGGTAA
1 TTTTGGTCACTCGAGGGAAAAATGGTAA
43204963 TTTTGG
1 TTTTGG
43204969 GAAAGTTGGG
Statistics
Matches: 32, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
27 1 0.03
28 31 0.97
ACGTcount: A:0.29, C:0.10, G:0.29, T:0.32
Consensus pattern (28 bp):
TTTTGGTCACTCGAGGGAAAAATGGTAA
Found at i:43205040 original size:29 final size:29
Alignment explanation
Indices: 43205008--43205088 Score: 89
Period size: 29 Copynumber: 2.8 Consensus size: 29
43204998 AGACATCCGG
43205008 GGGGTAAAATGGTACTTTTTGGAAGATTC-
1 GGGGTAAAATGGTACTTTTTGGAAG-TTCA
* *
43205037 GGGGTCAAAATGG-AATTTTTGAAAGTTCA
1 GGGGT-AAAATGGTACTTTTTGGAAGTTCA
43205066 GGGGT-AAATGGT-CTTTTTTGGAA
1 GGGGTAAAATGGTAC-TTTTTGGAA
43205089 AAATCAGGGT
Statistics
Matches: 44, Mismatches: 4, Indels: 9
0.77 0.07 0.16
Matches are distributed among these distances:
27 6 0.14
28 11 0.25
29 20 0.45
30 7 0.16
ACGTcount: A:0.28, C:0.06, G:0.31, T:0.35
Consensus pattern (29 bp):
GGGGTAAAATGGTACTTTTTGGAAGTTCA
Found at i:43205085 original size:57 final size:59
Alignment explanation
Indices: 43205008--43205134 Score: 163
Period size: 57 Copynumber: 2.2 Consensus size: 59
43204998 AGACATCCGG
* * *
43205008 GGGGTAAAATGGTACTTTTTGGAAGATTCGGGGTC-AAAATGGAATTTTTG-AAAGTTCA
1 GGGGTAAAATGGTACTTTTTGGAAAAATCAGGGTCAAAAATGGAA-TTTTGAAAAGTTCA
*
43205066 GGGGT-AAATGGT-CTTTTTTGGAAAAATCAGGGTCAAAAATGGAATTTTGAAAAGTTTA
1 GGGGTAAAATGGTAC-TTTTTGGAAAAATCAGGGTCAAAAATGGAATTTTGAAAAGTTCA
43205124 GGGGTCAAAAT
1 GGGGT-AAAAT
43205135 ATGATTTTTG
Statistics
Matches: 60, Mismatches: 4, Indels: 8
0.83 0.06 0.11
Matches are distributed among these distances:
56 1 0.02
57 29 0.48
58 26 0.43
60 4 0.07
ACGTcount: A:0.34, C:0.06, G:0.28, T:0.31
Consensus pattern (59 bp):
GGGGTAAAATGGTACTTTTTGGAAAAATCAGGGTCAAAAATGGAATTTTGAAAAGTTCA
Found at i:43205131 original size:30 final size:30
Alignment explanation
Indices: 43205095--43205156 Score: 81
Period size: 30 Copynumber: 2.1 Consensus size: 30
43205085 GGAAAAATCA
43205095 GGGTCAAAA-ATGGAATTTTGAAAAGTTTAG
1 GGGTCAAAATAT-GAATTTTGAAAAGTTTAG
* * *
43205125 GGGTCAAAATATGATTTTTGGATAGTTTAG
1 GGGTCAAAATATGAATTTTGAAAAGTTTAG
43205155 GG
1 GG
43205157 ACCTCTAGGG
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
30 26 0.93
31 2 0.07
ACGTcount: A:0.34, C:0.03, G:0.29, T:0.34
Consensus pattern (30 bp):
GGGTCAAAATATGAATTTTGAAAAGTTTAG
Found at i:43206331 original size:3 final size:3
Alignment explanation
Indices: 43206265--43206319 Score: 76
Period size: 3 Copynumber: 18.3 Consensus size: 3
43206255 CCCTTTTACC
*
43206265 ATT ATT ATT AAT ATT A-T ATTT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT A-TT ATT ATT ATT ATT ATT ATT ATT ATT
*
43206310 ATT ATG ATT A
1 ATT ATT ATT A
43206320 ACGTTATTAT
Statistics
Matches: 46, Mismatches: 4, Indels: 4
0.85 0.07 0.07
Matches are distributed among these distances:
2 2 0.04
3 42 0.91
4 2 0.04
ACGTcount: A:0.36, C:0.00, G:0.02, T:0.62
Consensus pattern (3 bp):
ATT
Found at i:43206337 original size:12 final size:12
Alignment explanation
Indices: 43206260--43206344 Score: 61
Period size: 12 Copynumber: 7.2 Consensus size: 12
43206250 GATTTCCCTT
*
43206260 TTACCATTATTA
1 TTACTATTATTA
*
43206272 TTAATATTA-TA
1 TTACTATTATTA
43206283 TT--TATTATTA
1 TTACTATTATTA
*
43206293 TTATTATTATTA
1 TTACTATTATTA
* *
43206305 TTATTATTATGA
1 TTACTATTATTA
*
43206317 TTAAC-GTTATTA
1 TT-ACTATTATTA
*
43206329 TTACTGTTATTTA
1 TTACTATTA-TTA
43206342 TTA
1 TTA
43206345 TAAACATTAT
Statistics
Matches: 61, Mismatches: 6, Indels: 11
0.78 0.08 0.14
Matches are distributed among these distances:
9 5 0.08
10 4 0.07
11 6 0.10
12 39 0.64
13 7 0.11
ACGTcount: A:0.33, C:0.05, G:0.04, T:0.59
Consensus pattern (12 bp):
TTACTATTATTA
Found at i:43207091 original size:17 final size:17
Alignment explanation
Indices: 43207086--43207160 Score: 69
Period size: 17 Copynumber: 4.4 Consensus size: 17
43207076 AAAATAAATT
*
43207086 TAAATTTAAATTTAAAG
1 TAAATTTAAATTTAAAA
* **
43207103 TATATTTAAACTAAAAAA
1 TAAATTTAAA-TTTAAAA
*
43207121 TGAATTTAAATTTAAAA
1 TAAATTTAAATTTAAAA
* * *
43207138 TAAATTCAAACTTAAAG
1 TAAATTTAAATTTAAAA
43207155 TAAATT
1 TAAATT
43207161 AAAAAATTAA
Statistics
Matches: 45, Mismatches: 12, Indels: 2
0.76 0.20 0.03
Matches are distributed among these distances:
17 33 0.73
18 12 0.27
ACGTcount: A:0.55, C:0.04, G:0.04, T:0.37
Consensus pattern (17 bp):
TAAATTTAAATTTAAAA
Found at i:43207092 original size:23 final size:23
Alignment explanation
Indices: 43207065--43207112 Score: 69
Period size: 23 Copynumber: 2.1 Consensus size: 23
43207055 GACACTTTTT
*
43207065 AATTTTAATTTAAAATAAATTTA
1 AATTTAAATTTAAAATAAATTTA
* *
43207088 AATTTAAATTTAAAGTATATTTA
1 AATTTAAATTTAAAATAAATTTA
43207111 AA
1 AA
43207113 CTAAAAAATG
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:0.52, C:0.00, G:0.02, T:0.46
Consensus pattern (23 bp):
AATTTAAATTTAAAATAAATTTA
Found at i:43207153 original size:41 final size:41
Alignment explanation
Indices: 43207076--43207158 Score: 96
Period size: 41 Copynumber: 2.0 Consensus size: 41
43207066 ATTTTAATTT
* * *
43207076 AAAATAAATTTAAATTTAAATTTAAAGTATATTTAAACTAA
1 AAAATAAATTTAAATTTAAATATAAAGTAAACTTAAACTAA
* * *
43207117 AAAATGAATTTAAATTTAAA-ATAAATTCAAACTTAAAGTAA
1 AAAATAAATTTAAATTTAAATATAAAGT-AAACTTAAACTAA
43207158 A
1 A
43207159 TTAAAAAATT
Statistics
Matches: 35, Mismatches: 6, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
40 5 0.14
41 30 0.86
ACGTcount: A:0.58, C:0.04, G:0.04, T:0.35
Consensus pattern (41 bp):
AAAATAAATTTAAATTTAAATATAAAGTAAACTTAAACTAA
Found at i:43209865 original size:69 final size:69
Alignment explanation
Indices: 43209754--43209893 Score: 280
Period size: 69 Copynumber: 2.0 Consensus size: 69
43209744 TTTATGCAGA
43209754 AAACAGTCACAGATCTCCTAGTCATAGGACATGCAGCCCAATCCAAGTCACAATAGGCTACAAGA
1 AAACAGTCACAGATCTCCTAGTCATAGGACATGCAGCCCAATCCAAGTCACAATAGGCTACAAGA
43209819 TGAC
66 TGAC
43209823 AAACAGTCACAGATCTCCTAGTCATAGGACATGCAGCCCAATCCAAGTCACAATAGGCTACAAGA
1 AAACAGTCACAGATCTCCTAGTCATAGGACATGCAGCCCAATCCAAGTCACAATAGGCTACAAGA
43209888 TGAC
66 TGAC
43209892 AA
1 AA
43209894 TCATTCCTAA
Statistics
Matches: 71, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
69 71 1.00
ACGTcount: A:0.39, C:0.27, G:0.17, T:0.17
Consensus pattern (69 bp):
AAACAGTCACAGATCTCCTAGTCATAGGACATGCAGCCCAATCCAAGTCACAATAGGCTACAAGA
TGAC
Found at i:43239601 original size:31 final size:31
Alignment explanation
Indices: 43239558--43239694 Score: 131
Period size: 31 Copynumber: 4.5 Consensus size: 31
43239548 AATATAATAC
*
43239558 TTGGTACTTAAACTTGACACTTTTTCCTAAT
1 TTGGTACCTAAACTTGACACTTTTTCCTAAT
**
43239589 TTGGTACCTAAACTT---TTTTTTGGTCC-AAT
1 TTGGTACCTAAACTTGACACTTTT--TCCTAAT
* *
43239618 TTGATA-CTCAAACTTGATACTTTTTCCTAAT
1 TTGGTACCT-AAACTTGACACTTTTTCCTAAT
** *
43239649 TTGGTACCTAAACTTGACACTTTTTTTTAAG
1 TTGGTACCTAAACTTGACACTTTTTCCTAAT
*
43239680 TTGGTACTTAAACTT
1 TTGGTACCTAAACTT
43239695 TTTGGGGTCT
Statistics
Matches: 86, Mismatches: 12, Indels: 16
0.75 0.11 0.14
Matches are distributed among these distances:
28 6 0.07
29 14 0.16
30 6 0.07
31 54 0.63
32 6 0.07
ACGTcount: A:0.26, C:0.18, G:0.11, T:0.46
Consensus pattern (31 bp):
TTGGTACCTAAACTTGACACTTTTTCCTAAT
Found at i:43239733 original size:91 final size:90
Alignment explanation
Indices: 43239558--43239749 Score: 228
Period size: 91 Copynumber: 2.1 Consensus size: 90
43239548 AATATAATAC
* * **
43239558 TTGGTACTTAAACTTGACACTTTTTCCTAATTTGGTACCTAAACTTTTTTTTGGTCCAATTTGAT
1 TTGGTACCTAAACTTGACACTTTTTCCTAAGTTGGTACCTAAACTTTTTTGGGGTCCAATTTGAT
43239623 ACTCAAACTTGATACTTTTTCCTAAT
66 ACTCAAACTTGATACTTTTT-CTAAT
** * *
43239649 TTGGTACCTAAACTTGACACTTTTTTTTAAGTTGGTACTTAAAC-TTTTTGGGGTCTAATTT-AG
1 TTGGTACCTAAACTTGACACTTTTTCCTAAGTTGGTACCTAAACTTTTTTGGGGTCCAATTTGA-
**
43239712 TACTTGAACTTGACT-CTTTTTTCTAAT
65 TACTCAAACTTGA-TAC-TTTTTCTAAT
*
43239739 TTGGTATCTAA
1 TTGGTACCTAA
43239750 TTTTTTTTAA
Statistics
Matches: 87, Mismatches: 11, Indels: 7
0.83 0.10 0.07
Matches are distributed among these distances:
89 1 0.01
90 41 0.47
91 45 0.52
ACGTcount: A:0.24, C:0.16, G:0.12, T:0.47
Consensus pattern (90 bp):
TTGGTACCTAAACTTGACACTTTTTCCTAAGTTGGTACCTAAACTTTTTTGGGGTCCAATTTGAT
ACTCAAACTTGATACTTTTTCTAAT
Found at i:43239993 original size:29 final size:28
Alignment explanation
Indices: 43239954--43240059 Score: 124
Period size: 29 Copynumber: 3.6 Consensus size: 28
43239944 AAAAAATGTC
43239954 AAGTTTAGGTACCAAATTGGGTCCAAAAA
1 AAGTTTAGGTACCAAATTGGGT-CAAAAA
* *
43239983 AAGTTTAGGTACCAAATTAGG-AAAAAA
1 AAGTTTAGGTACCAAATTGGGTCAAAAA
*
43240010 TGTCAAGTTCAGGTACCAAATTGGGTCAAAAA
1 ----AAGTTTAGGTACCAAATTGGGTCAAAAA
*
43240042 AAGTTTAGGTACTAAATT
1 AAGTTTAGGTACCAAATT
43240060 AGGAAAAAAT
Statistics
Matches: 65, Mismatches: 7, Indels: 11
0.78 0.08 0.13
Matches are distributed among these distances:
27 5 0.08
28 16 0.25
29 20 0.31
31 19 0.29
32 5 0.08
ACGTcount: A:0.42, C:0.11, G:0.20, T:0.26
Consensus pattern (28 bp):
AAGTTTAGGTACCAAATTGGGTCAAAAA
Found at i:43240049 original size:59 final size:60
Alignment explanation
Indices: 43239918--43240089 Score: 292
Period size: 60 Copynumber: 2.9 Consensus size: 60
43239908 TGAATCTTAA
* * *
43239918 AAAAAAAGCTTAGGTACCAATTTAGGAAAAAATGTCAAGTTTAGGTACCAAATTGGGTCC
1 AAAAAAAGTTTAGGTACCAAATTAGGAAAAAATGTCAAGTTCAGGTACCAAATTGGGTCC
43239978 AAAAAAAGTTTAGGTACCAAATTAGGAAAAAATGTCAAGTTCAGGTACCAAATTGGGT-C
1 AAAAAAAGTTTAGGTACCAAATTAGGAAAAAATGTCAAGTTCAGGTACCAAATTGGGTCC
* *
43240037 AAAAAAAGTTTAGGTACTAAATTAGGAAAAAATGTCAAGTTCAAGTACCAAAT
1 AAAAAAAGTTTAGGTACCAAATTAGGAAAAAATGTCAAGTTCAGGTACCAAAT
43240090 GTTATATTAA
Statistics
Matches: 107, Mismatches: 5, Indels: 1
0.95 0.04 0.01
Matches are distributed among these distances:
59 52 0.49
60 55 0.51
ACGTcount: A:0.45, C:0.12, G:0.19, T:0.24
Consensus pattern (60 bp):
AAAAAAAGTTTAGGTACCAAATTAGGAAAAAATGTCAAGTTCAGGTACCAAATTGGGTCC
Found at i:43240491 original size:20 final size:21
Alignment explanation
Indices: 43240466--43240505 Score: 73
Period size: 20 Copynumber: 2.0 Consensus size: 21
43240456 TGAAGAATTT
43240466 ATAGGTGCCTTTATT-TCTTC
1 ATAGGTGCCTTTATTCTCTTC
43240486 ATAGGTGCCTTTATTCTCTT
1 ATAGGTGCCTTTATTCTCTT
43240506 ACTTATGTTC
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
20 15 0.79
21 4 0.21
ACGTcount: A:0.15, C:0.20, G:0.15, T:0.50
Consensus pattern (21 bp):
ATAGGTGCCTTTATTCTCTTC
Found at i:43241436 original size:20 final size:21
Alignment explanation
Indices: 43241413--43241454 Score: 59
Period size: 20 Copynumber: 2.0 Consensus size: 21
43241403 TAAATTTTTA
*
43241413 AAGGTATTGATA-TTTTATTT
1 AAGGTATAGATACTTTTATTT
43241433 AAGGTATAGATACTTTTTATTT
1 AAGGTATAGATAC-TTTTATTT
43241455 TTGCTTAATT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
20 11 0.58
22 8 0.42
ACGTcount: A:0.31, C:0.02, G:0.14, T:0.52
Consensus pattern (21 bp):
AAGGTATAGATACTTTTATTT
Found at i:43245058 original size:63 final size:60
Alignment explanation
Indices: 43244988--43245157 Score: 236
Period size: 63 Copynumber: 2.8 Consensus size: 60
43244978 TGTTATTTAT
*
43244988 TTATTTATTTATCTATATTCATAAAATAATAAATAAAT-AATAAAACAAAATTAATATTA
1 TTATTTATTTATTTATATTCATAAAATAATAAATAAATAAATAAAACAAAATTAATATTA
* *
43245047 TTTTACATTTATTTATTTATATTCATACAATAATAAATAAATAAATAAAAATAAAATTAATATTA
1 --TT--ATTTATTTATTTATATTCATAAAATAATAAATAAATAAAT-AAAACAAAATTAATATTA
*
43245112 TT-TTTATTTATTTATATTCATAAAAATAATAAATAAATGAATAAAA
1 TTATTTATTTATTTATATTCAT-AAAATAATAAATAAATAAATAAAA
43245158 ATAATAAGAA
Statistics
Matches: 99, Mismatches: 5, Indels: 11
0.86 0.04 0.10
Matches are distributed among these distances:
60 23 0.23
61 20 0.20
63 36 0.36
64 3 0.03
65 17 0.17
ACGTcount: A:0.53, C:0.04, G:0.01, T:0.42
Consensus pattern (60 bp):
TTATTTATTTATTTATATTCATAAAATAATAAATAAATAAATAAAACAAAATTAATATTA
Found at i:43246296 original size:22 final size:22
Alignment explanation
Indices: 43246244--43246299 Score: 76
Period size: 22 Copynumber: 2.5 Consensus size: 22
43246234 AAAATTGTAG
* * *
43246244 CAAAACAACATCGAAATGACAG
1 CAAAACAATAGCGAAATGACAA
*
43246266 CAAAACAATAGCGAAATGCCAA
1 CAAAACAATAGCGAAATGACAA
43246288 CAAAACAATAGC
1 CAAAACAATAGC
43246300 AAAACAACAG
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
22 30 1.00
ACGTcount: A:0.55, C:0.23, G:0.12, T:0.09
Consensus pattern (22 bp):
CAAAACAATAGCGAAATGACAA
Found at i:43247582 original size:41 final size:41
Alignment explanation
Indices: 43247510--43247589 Score: 106
Period size: 41 Copynumber: 2.0 Consensus size: 41
43247500 GCTTATTGTA
*
43247510 TTTTCAATTTGTTTGTTATGTTACGAATTGTTTTAATATAG
1 TTTTCAATTTGTTTGTTATGTTAAGAATTGTTTTAATATAG
* * * * *
43247551 TTTTTAATTTGTTTGTTGTTTTAATATTTGTTTTAATAT
1 TTTTCAATTTGTTTGTTATGTTAAGAATTGTTTTAATAT
43247590 TTTTAAGTGT
Statistics
Matches: 33, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
41 33 1.00
ACGTcount: A:0.23, C:0.03, G:0.12, T:0.62
Consensus pattern (41 bp):
TTTTCAATTTGTTTGTTATGTTAAGAATTGTTTTAATATAG
Found at i:43247583 original size:12 final size:12
Alignment explanation
Indices: 43247566--43247591 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
43247556 AATTTGTTTG
43247566 TTGTTTTAATAT
1 TTGTTTTAATAT
43247578 TTGTTTTAATAT
1 TTGTTTTAATAT
43247590 TT
1 TT
43247592 TTAAGTGTAT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.23, C:0.00, G:0.08, T:0.69
Consensus pattern (12 bp):
TTGTTTTAATAT
Found at i:43248835 original size:18 final size:17
Alignment explanation
Indices: 43248786--43248837 Score: 61
Period size: 18 Copynumber: 3.0 Consensus size: 17
43248776 TTTAAAAAAA
43248786 ATATTATATT-AATTAT
1 ATATTATATTAAATTAT
* *
43248802 ATATTAAATAATAATTAT
1 ATATTATATTA-AATTAT
43248820 ATATTTATATTAAATTAT
1 ATA-TTATATTAAATTAT
43248838 GAACTCAATA
Statistics
Matches: 29, Mismatches: 4, Indels: 4
0.78 0.11 0.11
Matches are distributed among these distances:
16 8 0.28
18 15 0.52
19 6 0.21
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (17 bp):
ATATTATATTAAATTAT
Found at i:43248987 original size:38 final size:40
Alignment explanation
Indices: 43248940--43249026 Score: 117
Period size: 40 Copynumber: 2.2 Consensus size: 40
43248930 ATAAGACATT
*
43248940 TATTATATTTAT-TTA-TATTTTTTAATATAATAAAAAAA
1 TATTATATTTATAGTAGTATTTTTTAATATAATAAAAAAA
**
43248978 TATTATATTTATAGTAGTATTTTTTAATATGTTAAAAAAA
1 TATTATATTTATAGTAGTATTTTTTAATATAATAAAAAAA
*
43249018 TTTTA-ATTT
1 TATTATATTT
43249027 TAACATTTTT
Statistics
Matches: 43, Mismatches: 4, Indels: 3
0.86 0.08 0.06
Matches are distributed among these distances:
38 12 0.28
39 6 0.14
40 25 0.58
ACGTcount: A:0.43, C:0.00, G:0.03, T:0.54
Consensus pattern (40 bp):
TATTATATTTATAGTAGTATTTTTTAATATAATAAAAAAA
Found at i:43250200 original size:21 final size:21
Alignment explanation
Indices: 43250153--43250203 Score: 57
Period size: 21 Copynumber: 2.4 Consensus size: 21
43250143 TTATCATATT
* * *
43250153 ATATATTATTATAAATTGAATT
1 ATATA-TAATATAAATTAAATA
*
43250175 TTATATAATATAAATTAAATA
1 ATATATAATATAAATTAAATA
43250196 ATATATAA
1 ATATATAA
43250204 AAATAATTAA
Statistics
Matches: 24, Mismatches: 5, Indels: 1
0.80 0.17 0.03
Matches are distributed among these distances:
21 20 0.83
22 4 0.17
ACGTcount: A:0.53, C:0.00, G:0.02, T:0.45
Consensus pattern (21 bp):
ATATATAATATAAATTAAATA
Found at i:43250237 original size:22 final size:22
Alignment explanation
Indices: 43250187--43250236 Score: 68
Period size: 22 Copynumber: 2.4 Consensus size: 22
43250177 ATATAATATA
*
43250187 AATT-AAATAATATATAAAAAT
1 AATTAAAATAAAATATAAAAAT
*
43250208 AATTAAAATAAAATATTAAAAT
1 AATTAAAATAAAATATAAAAAT
43250230 -ATTAAAA
1 AATTAAAA
43250237 AACGAATCGG
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
21 11 0.42
22 15 0.58
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (22 bp):
AATTAAAATAAAATATAAAAAT
Found at i:43259874 original size:41 final size:42
Alignment explanation
Indices: 43259816--43259895 Score: 119
Period size: 41 Copynumber: 1.9 Consensus size: 42
43259806 TAATTGGACT
*
43259816 TTTTTATCTCTTGCCTGAAAAAA-TGTTAGTGTTTTTACTACA
1 TTTTTATCTCTTACCTGAAAAAATTG-TAGTGTTTTTACTACA
*
43259858 TTTTT-TCTCTTACCTGAAAATATTGTAGTGTTTTTACT
1 TTTTTATCTCTTACCTGAAAAAATTGTAGTGTTTTTACT
43259896 GATATGCCTT
Statistics
Matches: 35, Mismatches: 2, Indels: 3
0.88 0.05 0.08
Matches are distributed among these distances:
41 28 0.80
42 7 0.20
ACGTcount: A:0.24, C:0.14, G:0.11, T:0.51
Consensus pattern (42 bp):
TTTTTATCTCTTACCTGAAAAAATTGTAGTGTTTTTACTACA
Found at i:43263848 original size:16 final size:16
Alignment explanation
Indices: 43263821--43263853 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
43263811 AAAGGTTATG
43263821 AAATCGAATTTGATAAT
1 AAATCGAATTTGA-AAT
43263838 AAATC-AATTTGAAAT
1 AAATCGAATTTGAAAT
43263853 A
1 A
43263854 CAATAAATTA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 4 0.25
16 7 0.44
17 5 0.31
ACGTcount: A:0.52, C:0.06, G:0.09, T:0.33
Consensus pattern (16 bp):
AAATCGAATTTGAAAT
Found at i:43266596 original size:18 final size:16
Alignment explanation
Indices: 43266553--43266599 Score: 58
Period size: 18 Copynumber: 2.8 Consensus size: 16
43266543 CTTGACTCTT
43266553 AAAAATTTAAAATTAA
1 AAAAATTTAAAATTAA
*
43266569 AAAAACTTTAAACTATAA
1 AAAAA-TTTAAAAT-TAA
43266587 AAAATATTTAAAA
1 AAAA-ATTTAAAA
43266600 GTTCATTTTT
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
16 5 0.19
17 7 0.27
18 13 0.50
19 1 0.04
ACGTcount: A:0.66, C:0.04, G:0.00, T:0.30
Consensus pattern (16 bp):
AAAAATTTAAAATTAA
Found at i:43268338 original size:6 final size:6
Alignment explanation
Indices: 43268327--43268360 Score: 68
Period size: 6 Copynumber: 5.7 Consensus size: 6
43268317 ATTTCTCTTT
43268327 AAAATA AAAATA AAAATA AAAATA AAAATA AAAA
1 AAAATA AAAATA AAAATA AAAATA AAAATA AAAA
43268361 ATTCTATTTA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 28 1.00
ACGTcount: A:0.85, C:0.00, G:0.00, T:0.15
Consensus pattern (6 bp):
AAAATA
Found at i:43277590 original size:19 final size:22
Alignment explanation
Indices: 43277561--43277600 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 22
43277551 GGTGGTGAGG
43277561 AAATAAG-AAA-AAAATTGTTA
1 AAATAAGAAAACAAAATTGTTA
43277581 AAAT-AGAAAACAAAATTGTT
1 AAATAAGAAAACAAAATTGTT
43277601 CCCACTTAGA
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
19 2 0.11
20 7 0.39
21 9 0.50
ACGTcount: A:0.62, C:0.03, G:0.10, T:0.25
Consensus pattern (22 bp):
AAATAAGAAAACAAAATTGTTA
Found at i:43279670 original size:23 final size:23
Alignment explanation
Indices: 43279643--43279687 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 23
43279633 TTAGTGGTTT
*
43279643 AAATATACCGTTCAAAAAAATTA
1 AAATAAACCGTTCAAAAAAATTA
* *
43279666 AAATAAACCTTTTAAAAAAATT
1 AAATAAACCGTTCAAAAAAATT
43279688 TGAGATAAGT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.58, C:0.11, G:0.02, T:0.29
Consensus pattern (23 bp):
AAATAAACCGTTCAAAAAAATTA
Found at i:43294528 original size:6 final size:6
Alignment explanation
Indices: 43294517--43294557 Score: 82
Period size: 6 Copynumber: 6.8 Consensus size: 6
43294507 AAATAAAATA
43294517 ATATAC ATATAC ATATAC ATATAC ATATAC ATATAC ATATA
1 ATATAC ATATAC ATATAC ATATAC ATATAC ATATAC ATATA
43294558 AAAGGGATTA
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 35 1.00
ACGTcount: A:0.51, C:0.15, G:0.00, T:0.34
Consensus pattern (6 bp):
ATATAC
Found at i:43294683 original size:30 final size:29
Alignment explanation
Indices: 43294649--43294787 Score: 136
Period size: 30 Copynumber: 4.7 Consensus size: 29
43294639 CATTAAAATC
*
43294649 GGGTTAAATTTGAATTTTTGAAAACTTTAG
1 GGGTTAAATTTAAATTTTTGAAAA-TTTAG
* *
43294679 GGGTTAAATTCAAATTTTTGGAAAATTTAA
1 GGGTTAAATTTAAATTTTT-GAAAATTTAG
* * * *
43294709 GGGTCAAACTCAAATTTTGGGAAAATTTAG
1 GGGTTAAATTTAAATTTT-TGAAAATTTAG
* *
43294739 GGGTTAAATTTGAATTTTTGGAACATTTAG
1 GGGTTAAATTTAAATTTTT-GAAAATTTAG
*
43294769 GGGTCAAA-TTATAATTTTT
1 GGGTTAAATTTA-AATTTTT
43294788 AAATAAAGTA
Statistics
Matches: 90, Mismatches: 15, Indels: 8
0.80 0.13 0.07
Matches are distributed among these distances:
29 2 0.02
30 83 0.92
31 5 0.06
ACGTcount: A:0.35, C:0.05, G:0.20, T:0.40
Consensus pattern (29 bp):
GGGTTAAATTTAAATTTTTGAAAATTTAG
Found at i:43300499 original size:19 final size:19
Alignment explanation
Indices: 43300475--43300519 Score: 72
Period size: 19 Copynumber: 2.4 Consensus size: 19
43300465 AAGCAGCAGG
* *
43300475 GGCATTAGTTAACCTAAAA
1 GGCATTAATTAACCCAAAA
43300494 GGCATTAATTAACCCAAAA
1 GGCATTAATTAACCCAAAA
43300513 GGCATTA
1 GGCATTA
43300520 CCAAGAACTC
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
19 24 1.00
ACGTcount: A:0.42, C:0.18, G:0.16, T:0.24
Consensus pattern (19 bp):
GGCATTAATTAACCCAAAA
Found at i:43305724 original size:77 final size:79
Alignment explanation
Indices: 43305601--43305766 Score: 189
Period size: 77 Copynumber: 2.1 Consensus size: 79
43305591 CTATGGGCAA
* * *
43305601 GGTAAGAGATCTGATGGTCTTTAATCTGCCCTCTATTTAGGGTAAAA-AGTTGAATTGCTTCAAT
1 GGTAAGAGATCGGATGATCTTCAATCTGCCCTCTATTTAGGGTAAAAGA-TTGAATTGCTTCAAT
*
43305665 TTACTT-CATGGTCGG
65 CT-CTTCCATGGTCGG
* * *
43305680 GGTAAGAGATCGGATGATCTTCAAT-TTCCCT-T-TGTTAGGGTAAAAGATTGGATTGCTTTAAT
1 GGTAAGAGATCGGATGATCTTCAATCTGCCCTCTAT-TTAGGGTAAAAGATTGAATTGCTTCAAT
*
43305742 CTGTTCCATGGTCGG
65 CTCTTCCATGGTCGG
*
43305757 GGTAAAAGAT
1 GGTAAGAGAT
43305767 TCGGGGTTGT
Statistics
Matches: 75, Mismatches: 9, Indels: 8
0.82 0.10 0.09
Matches are distributed among these distances:
76 3 0.04
77 44 0.59
78 6 0.08
79 22 0.29
ACGTcount: A:0.26, C:0.14, G:0.25, T:0.36
Consensus pattern (79 bp):
GGTAAGAGATCGGATGATCTTCAATCTGCCCTCTATTTAGGGTAAAAGATTGAATTGCTTCAATC
TCTTCCATGGTCGG
Found at i:43305893 original size:50 final size:50
Alignment explanation
Indices: 43305818--43305950 Score: 185
Period size: 50 Copynumber: 2.7 Consensus size: 50
43305808 ATATTTGTCC
* *
43305818 TTGCGACTTCAATTTGCCCCTCTACAGCTTTAGGTGAATGAGATTCGCCA
1 TTGCGACTTCAATCTGCCCCTCTACAACTTTAGGTGAATGAGATTCGCCA
* *
43305868 TTGCGACTTCAATCTGCCCCTCTACAACTTTAGGTGTATGAGATTTGCCA
1 TTGCGACTTCAATCTGCCCCTCTACAACTTTAGGTGAATGAGATTCGCCA
* * * **
43305918 TTGCGGCTTTAATCCGTTCCTCTACAACTTTAG
1 TTGCGACTTCAATCTGCCCCTCTACAACTTTAG
43305951 AGGTATAGGA
Statistics
Matches: 74, Mismatches: 9, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
50 74 1.00
ACGTcount: A:0.21, C:0.26, G:0.18, T:0.35
Consensus pattern (50 bp):
TTGCGACTTCAATCTGCCCCTCTACAACTTTAGGTGAATGAGATTCGCCA
Found at i:43307953 original size:21 final size:20
Alignment explanation
Indices: 43307894--43307940 Score: 69
Period size: 20 Copynumber: 2.4 Consensus size: 20
43307884 ATTTTGGTTG
*
43307894 CTGTTTTTGTGTTTTTTTAA
1 CTGTTTTAGTGTTTTTTTAA
43307914 CTGTTTTAGTGCTTTTTTT-A
1 CTGTTTTAGTG-TTTTTTTAA
43307934 CTGTTTT
1 CTGTTTT
43307941 GATTGTTATT
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
20 18 0.72
21 7 0.28
ACGTcount: A:0.09, C:0.09, G:0.15, T:0.68
Consensus pattern (20 bp):
CTGTTTTAGTGTTTTTTTAA
Found at i:43307953 original size:24 final size:22
Alignment explanation
Indices: 43307926--43308008 Score: 62
Period size: 23 Copynumber: 3.6 Consensus size: 22
43307916 GTTTTAGTGC
*
43307926 TTTTTTTACTGTTTTGATTGTTA
1 TTTTTTT-TTGTTTTGATTGTTA
* *
43307949 TTTTTGTGTTGCTTTTG-CTGTTA
1 TTTTT-TTTTG-TTTTGATTGTTA
*
43307972 TTTTTGTTGTTGTTTTTATTGTTA
1 TTTTT-TT-TTGTTTTGATTGTTA
*
43307996 -TTTTTATTGTTTT
1 TTTTTTTTTGTTTT
43308009 TAATGTGTTG
Statistics
Matches: 49, Mismatches: 7, Indels: 10
0.74 0.11 0.15
Matches are distributed among these distances:
21 7 0.14
22 1 0.02
23 27 0.55
24 14 0.29
ACGTcount: A:0.08, C:0.04, G:0.16, T:0.72
Consensus pattern (22 bp):
TTTTTTTTTGTTTTGATTGTTA
Found at i:43307970 original size:52 final size:53
Alignment explanation
Indices: 43307862--43307964 Score: 136
Period size: 52 Copynumber: 1.9 Consensus size: 53
43307852 ATTATATTGT
* * * *
43307862 TGTTTTGGTGCTATTTTTTACTATTTTGGTTGCTGTTTTTGTGTTTTTTTAAC
1 TGTTTTAGTGCTATTTTTTACTATTTTGATTGCTATTTTTGTGTTCTTTTAAC
* *
43307915 TGTTTTAGTGCT-TTTTTTACTGTTTTGATTGTTATTTTTGTGTTGCTTTT
1 TGTTTTAGTGCTATTTTTTACTATTTTGATTGCTATTTTTGTGTT-CTTTT
43307965 GCTGTTATTT
Statistics
Matches: 43, Mismatches: 6, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
52 28 0.65
53 15 0.35
ACGTcount: A:0.09, C:0.07, G:0.18, T:0.66
Consensus pattern (53 bp):
TGTTTTAGTGCTATTTTTTACTATTTTGATTGCTATTTTTGTGTTCTTTTAAC
Found at i:43308000 original size:12 final size:12
Alignment explanation
Indices: 43307967--43308006 Score: 62
Period size: 12 Copynumber: 3.3 Consensus size: 12
43307957 TTGCTTTTGC
*
43307967 TGTTATTTTTGT
1 TGTTATTTTTAT
*
43307979 TGTTGTTTTTAT
1 TGTTATTTTTAT
43307991 TGTTATTTTTAT
1 TGTTATTTTTAT
43308003 TGTT
1 TGTT
43308007 TTTAATGTGT
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
12 25 1.00
ACGTcount: A:0.10, C:0.00, G:0.15, T:0.75
Consensus pattern (12 bp):
TGTTATTTTTAT
Found at i:43308026 original size:21 final size:21
Alignment explanation
Indices: 43307978--43308030 Score: 63
Period size: 21 Copynumber: 2.5 Consensus size: 21
43307968 GTTATTTTTG
* *
43307978 TTGTTGTTTTTATTGTTATTT
1 TTGTTGTTTTTAATGTTATGT
*
43307999 TTATTGTTTTTAATGTGT-TGT
1 TTGTTGTTTTTAATGT-TATGT
43308020 TTGTTGTTTTT
1 TTGTTGTTTTT
43308031 TTGCTGCAGT
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
21 26 0.96
22 1 0.04
ACGTcount: A:0.09, C:0.00, G:0.17, T:0.74
Consensus pattern (21 bp):
TTGTTGTTTTTAATGTTATGT
Found at i:43318113 original size:21 final size:22
Alignment explanation
Indices: 43318089--43318140 Score: 67
Period size: 21 Copynumber: 2.5 Consensus size: 22
43318079 AATTTATAAG
43318089 TATAAATAATAAAA-AA-CAATA
1 TATAAATAATAAAATAAGCAA-A
43318110 TATAAATAA-AAAATAAGCAAA
1 TATAAATAATAAAATAAGCAAA
43318131 TA-AAATAATA
1 TATAAATAATA
43318141 TACATATACA
Statistics
Matches: 28, Mismatches: 0, Indels: 6
0.82 0.00 0.18
Matches are distributed among these distances:
20 10 0.36
21 15 0.54
22 3 0.11
ACGTcount: A:0.71, C:0.04, G:0.02, T:0.23
Consensus pattern (22 bp):
TATAAATAATAAAATAAGCAAA
Found at i:43318293 original size:30 final size:30
Alignment explanation
Indices: 43318257--43318482 Score: 171
Period size: 30 Copynumber: 7.6 Consensus size: 30
43318247 AGTTAAATTT
* *
43318257 GAATTTTTAGAAACTTTAGGGGTCAAATCA
1 GAATTTTTGGAAAATTTAGGGGTCAAATCA
*
43318287 GAATTTTTGGAAAATTT-GAGGGTCAAATTA
1 GAATTTTTGGAAAATTTAG-GGGTCAAATCA
* * * *
43318317 GAACTTTTGAAAAATTTAAGGGCCAAATTCA
1 GAATTTTTGGAAAATTTAGGGGTCAAA-TCA
* **
43318348 -AA-TTTTGGAAAATTTAGGGGTTAAATTT
1 GAATTTTTGGAAAATTTAGGGGTCAAATCA
**
43318376 GAATTTCTT-GAAAATTT-GGGGTCAAATTT
1 GAATTT-TTGGAAAATTTAGGGGTCAAATCA
* * * *
43318405 GAATGTTTAGAAAATTTGGGGGCCAAATTCA
1 GAATTTTTGGAAAATTTAGGGGTCAAA-TCA
*
43318436 -AATTTTTGGAAAATTT-GTGGGTTAAACTCA
1 GAATTTTTGGAAAATTTAG-GGGTCAAA-TCA
* *
43318466 -AATTGTTGGAACATTTA
1 GAATTTTTGGAAAATTTA
43318483 AGGGATAAAT
Statistics
Matches: 159, Mismatches: 26, Indels: 21
0.77 0.13 0.10
Matches are distributed among these distances:
28 3 0.02
29 47 0.30
30 104 0.65
31 5 0.03
ACGTcount: A:0.36, C:0.07, G:0.21, T:0.36
Consensus pattern (30 bp):
GAATTTTTGGAAAATTTAGGGGTCAAATCA
Found at i:43318389 original size:60 final size:60
Alignment explanation
Indices: 43318248--43318451 Score: 168
Period size: 59 Copynumber: 3.4 Consensus size: 60
43318238 TTAAAACCGA
* * *
43318248 GTTAAATTTGAATTTTT-AGAAACTTTAGGGGTCAAATCAGAATTTTTGGAAAATTTGAGG
1 GTTAAATTTGAATTTTTGA-AAAATTTAAGGGCCAAATCAGAATTTTTGGAAAATTTGAGG
* * *
43318308 GTCAAATTAGAACTTTTGAAAAATTTAAGGGCCAAATTCA-AA-TTTTGGAAAATTT-AGGG
1 GTTAAATTTGAATTTTTGAAAAATTTAAGGGCCAAA-TCAGAATTTTTGGAAAATTTGA-GG
* * ** * * *
43318367 GTTAAATTTGAATTTCTTG-AAAATTT-GGGGTCAAATTTGAATGTTTAGAAAATTTGGGG
1 GTTAAATTTGAATTT-TTGAAAAATTTAAGGGCCAAATCAGAATTTTTGGAAAATTTGAGG
** ** *
43318426 GCCAAATTCAAATTTTTGGAAAATTT
1 GTTAAATTTGAATTTTTGAAAAATTT
43318452 GTGGGTTAAA
Statistics
Matches: 116, Mismatches: 20, Indels: 17
0.76 0.13 0.11
Matches are distributed among these distances:
57 1 0.01
58 13 0.11
59 65 0.56
60 33 0.28
61 4 0.03
ACGTcount: A:0.36, C:0.06, G:0.20, T:0.37
Consensus pattern (60 bp):
GTTAAATTTGAATTTTTGAAAAATTTAAGGGCCAAATCAGAATTTTTGGAAAATTTGAGG
Found at i:43319557 original size:8 final size:8
Alignment explanation
Indices: 43319546--43319581 Score: 54
Period size: 8 Copynumber: 4.2 Consensus size: 8
43319536 ATAATAAAAT
43319546 TTATTTTA
1 TTATTTTA
43319554 TTATTTTA
1 TTATTTTA
43319562 TTATTTTA
1 TTATTTTA
43319570 TTTATTTATA
1 -TTATTT-TA
43319580 TT
1 TT
43319582 TATTAAATAA
Statistics
Matches: 26, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
8 16 0.62
9 8 0.31
10 2 0.08
ACGTcount: A:0.25, C:0.00, G:0.00, T:0.75
Consensus pattern (8 bp):
TTATTTTA
Found at i:43319612 original size:14 final size:15
Alignment explanation
Indices: 43319586--43319614 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
43319576 TATATTTATT
43319586 AAATAATAAATAAAA
1 AAATAATAAATAAAA
43319601 AAATAA-AAATAAAA
1 AAATAATAAATAAAA
43319615 TGAGTTTTTT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 8 0.57
15 6 0.43
ACGTcount: A:0.83, C:0.00, G:0.00, T:0.17
Consensus pattern (15 bp):
AAATAATAAATAAAA
Found at i:43321445 original size:29 final size:31
Alignment explanation
Indices: 43321413--43321472 Score: 88
Period size: 30 Copynumber: 2.0 Consensus size: 31
43321403 AAAATTACTT
43321413 TTTAA-CTTTTAAAAATAATAAAAA-ATAAA
1 TTTAATCTTTTAAAAATAATAAAAATATAAA
* *
43321442 TTTAATTTTTTAAAAATTATAAAAATATAAA
1 TTTAATCTTTTAAAAATAATAAAAATATAAA
43321473 CCACTCAAAT
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
29 5 0.19
30 17 0.63
31 5 0.19
ACGTcount: A:0.58, C:0.02, G:0.00, T:0.40
Consensus pattern (31 bp):
TTTAATCTTTTAAAAATAATAAAAATATAAA
Found at i:43321826 original size:14 final size:14
Alignment explanation
Indices: 43321807--43321853 Score: 60
Period size: 14 Copynumber: 3.3 Consensus size: 14
43321797 TTTTTATTGT
43321807 TTTTTATTAATTTA
1 TTTTTATTAATTTA
*
43321821 TTTTTATTATTTTTA
1 TTTTTATTA-ATTTA
43321836 TATTTTATT-ATTTA
1 T-TTTTATTAATTTA
43321850 TTTT
1 TTTT
43321854 GATACTATTT
Statistics
Matches: 29, Mismatches: 2, Indels: 5
0.81 0.06 0.14
Matches are distributed among these distances:
13 3 0.10
14 14 0.48
15 5 0.17
16 7 0.24
ACGTcount: A:0.23, C:0.00, G:0.00, T:0.77
Consensus pattern (14 bp):
TTTTTATTAATTTA
Found at i:43321846 original size:25 final size:24
Alignment explanation
Indices: 43321797--43321851 Score: 69
Period size: 23 Copynumber: 2.3 Consensus size: 24
43321787 TTAGTCTTTG
*
43321797 TTTTTATTGTTTTTTATTAATTTA
1 TTTTTATTATTTTTTATTAATTTA
*
43321821 TTTTTATTA-TTTTTA-TATTTTA
1 TTTTTATTATTTTTTATTAATTTA
43321843 TTATTTATT
1 TT-TTTATT
43321852 TTGATACTAT
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
22 8 0.29
23 12 0.43
24 8 0.29
ACGTcount: A:0.22, C:0.00, G:0.02, T:0.76
Consensus pattern (24 bp):
TTTTTATTATTTTTTATTAATTTA
Found at i:43323342 original size:28 final size:25
Alignment explanation
Indices: 43323278--43323346 Score: 75
Period size: 28 Copynumber: 2.6 Consensus size: 25
43323268 TTGGGATAAT
* *
43323278 ATTAAAACTTTTAAAGAAATTTTAA
1 ATTAAAAATTTTAAAGAAATTCTAA
43323303 AGTTAACAAATTTTAAAGAAAATGGTCTAA
1 A-TTAA-AAATTTTAAAG-AAAT--TCTAA
43323333 ATTAAAAATTTTAA
1 ATTAAAAATTTTAA
43323347 TATTTTAAAA
Statistics
Matches: 37, Mismatches: 2, Indels: 7
0.80 0.04 0.15
Matches are distributed among these distances:
25 1 0.03
26 4 0.11
27 10 0.27
28 13 0.35
29 4 0.11
30 5 0.14
ACGTcount: A:0.52, C:0.04, G:0.07, T:0.36
Consensus pattern (25 bp):
ATTAAAAATTTTAAAGAAATTCTAA
Found at i:43325417 original size:21 final size:22
Alignment explanation
Indices: 43325375--43325418 Score: 54
Period size: 22 Copynumber: 2.0 Consensus size: 22
43325365 ATTTCGAATA
* *
43325375 TTTCAGTTTTTATTCTATATGG
1 TTTCAATTTTAATTCTATATGG
*
43325397 TTTCAATTTTAATTTTA-ATGG
1 TTTCAATTTTAATTCTATATGG
43325418 T
1 T
43325419 GAAAAATTGA
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
21 5 0.26
22 14 0.74
ACGTcount: A:0.23, C:0.07, G:0.11, T:0.59
Consensus pattern (22 bp):
TTTCAATTTTAATTCTATATGG
Found at i:43328910 original size:23 final size:23
Alignment explanation
Indices: 43328879--43328932 Score: 83
Period size: 23 Copynumber: 2.3 Consensus size: 23
43328869 CGCAAACATA
*
43328879 TAAATGAACATGTTCGCGAACGT-
1 TAAACGAACATGTTCGCGAAC-TC
43328902 TAAACGAACATGTTCGCGAACTC
1 TAAACGAACATGTTCGCGAACTC
43328925 TAAACGAA
1 TAAACGAA
43328933 TCGAGTTTGA
Statistics
Matches: 29, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
22 1 0.03
23 28 0.97
ACGTcount: A:0.39, C:0.20, G:0.19, T:0.22
Consensus pattern (23 bp):
TAAACGAACATGTTCGCGAACTC
Found at i:43331061 original size:19 final size:18
Alignment explanation
Indices: 43331024--43331076 Score: 54
Period size: 19 Copynumber: 2.9 Consensus size: 18
43331014 TATAAAATAA
*
43331024 TTTAATTAT-TTATTTAAT
1 TTTATTTATATTA-TTAAT
* *
43331042 TTTTTTTCTATATATTAAT
1 TTTATTTATAT-TATTAAT
43331061 TTTATTTATATTATTA
1 TTTATTTATATTATTA
43331077 TTGTAATTTC
Statistics
Matches: 28, Mismatches: 5, Indels: 4
0.76 0.14 0.11
Matches are distributed among these distances:
18 11 0.39
19 15 0.54
20 2 0.07
ACGTcount: A:0.30, C:0.02, G:0.00, T:0.68
Consensus pattern (18 bp):
TTTATTTATATTATTAAT
Found at i:43338932 original size:81 final size:82
Alignment explanation
Indices: 43338790--43338946 Score: 180
Period size: 81 Copynumber: 1.9 Consensus size: 82
43338780 TAATAGTAAA
* * **
43338790 AAAATATAATTTTATTATTTAAATAATTTAATTTTTTTAATTTTTAAAAGATTAATCAAAAT-TT
1 AAAATATAATTTTATTATTTAAATAATTTAAATTCTAAAATTTTTAAAAGATTAATCAAAATATT
43338854 TATCAATTTTAGAGGATC
66 TATC-ATTTTAGAGGATC
* *
43338872 AAAATATAATTTTA-TATTT-ACTAATTTAAAATTCTAAAATTTTT-AAAGGTCTAAAT-AAAAT
1 AAAATATAATTTTATTATTTAAATAATTT-AAATTCTAAAATTTTTAAAAGAT-T-AATCAAAAT
*
43338933 ATTTTTCATTTTAG
63 ATTTATCATTTTAG
43338947 GAGGGGTCAC
Statistics
Matches: 64, Mismatches: 7, Indels: 9
0.80 0.09 0.11
Matches are distributed among these distances:
80 12 0.19
81 30 0.47
82 22 0.34
ACGTcount: A:0.43, C:0.04, G:0.04, T:0.48
Consensus pattern (82 bp):
AAAATATAATTTTATTATTTAAATAATTTAAATTCTAAAATTTTTAAAAGATTAATCAAAATATT
TATCATTTTAGAGGATC
Found at i:43339591 original size:183 final size:187
Alignment explanation
Indices: 43339280--43339664 Score: 606
Period size: 183 Copynumber: 2.1 Consensus size: 187
43339270 AATTTTTAAA
*
43339280 TTTTAAAAATTAATTAATTATTGAAATAATATCCACATGACAATTCACGCCTCAAAATAGATGAA
1 TTTTAAAAATTAATTAATTACT-AAATAATATCCACATGACAATTCACGCCTCAAAATAGATGAA
* **
43339345 AAAGTTAACATATGTTAATTTTATTGATGTGGTATCCATATGCATATCACGTTAACAATTAATTA
65 AAAGTTAACATATGTTAACTTTATTGATGTGACATCCATATGCATATCACGTTAACAATTAATTA
43339410 ATTTTTAAAAAAAAATTA-AAAA-AATA-TTTTTTTATAATTTTATACCTTTTAATAAT
130 ATTTTT-AAAAAAAATTATAAAAGAATATTTTTTTTATAATTTTATACCTTTTAATAAT
*
43339466 TTTTAAAAATTAATTAATTACT-AA-AATGATCCAGATGACAATTCACG-CTCCAAAATAGATGA
1 TTTTAAAAATTAATTAATTACTAAATAAT-ATCCACATGACAATTCACGCCT-CAAAATAGATGA
* *
43339528 AAAA-TTAACATATGTTAACTTTATTGATGTGACATTCATATGTATATCACGTTAACAATTAATT
64 AAAAGTTAACATATGTTAACTTTATTGATGTGACATCCATATGCATATCACGTTAACAATTAATT
43339592 AATTTTTAAAAAAAATTATAAAAGAATATTTTTTTTATAATTTTATACCTTTTAATAAT
129 AATTTTTAAAAAAAATTATAAAAGAATATTTTTTTTATAATTTTATACCTTTTAATAAT
*
43339651 TTTT-ACAATTAATT
1 TTTTAAAAATTAATT
43339665 TTTAAATTTT
Statistics
Matches: 186, Mismatches: 8, Indels: 12
0.90 0.04 0.06
Matches are distributed among these distances:
182 11 0.06
183 71 0.38
184 49 0.26
185 34 0.18
186 21 0.11
ACGTcount: A:0.43, C:0.10, G:0.07, T:0.41
Consensus pattern (187 bp):
TTTTAAAAATTAATTAATTACTAAATAATATCCACATGACAATTCACGCCTCAAAATAGATGAAA
AAGTTAACATATGTTAACTTTATTGATGTGACATCCATATGCATATCACGTTAACAATTAATTAA
TTTTTAAAAAAAATTATAAAAGAATATTTTTTTTATAATTTTATACCTTTTAATAAT
Found at i:43340016 original size:3 final size:3
Alignment explanation
Indices: 43340008--43340039 Score: 64
Period size: 3 Copynumber: 10.7 Consensus size: 3
43339998 AATAATTTAA
43340008 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
43340040 GTTTAAATAT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 29 1.00
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (3 bp):
AAT
Found at i:43341103 original size:14 final size:14
Alignment explanation
Indices: 43341084--43341110 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
43341074 AATAAGATTT
43341084 CCTTGTATTTATAC
1 CCTTGTATTTATAC
43341098 CCTTGTATTTATA
1 CCTTGTATTTATA
43341111 TTATTCAGCC
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.22, C:0.19, G:0.07, T:0.52
Consensus pattern (14 bp):
CCTTGTATTTATAC
Found at i:43347413 original size:15 final size:15
Alignment explanation
Indices: 43347393--43347422 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
43347383 GATGAACCTC
43347393 ATCCTCTTTTTCACT
1 ATCCTCTTTTTCACT
43347408 ATCCTCTTTTTCACT
1 ATCCTCTTTTTCACT
43347423 GGAGTCACTT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.13, C:0.33, G:0.00, T:0.53
Consensus pattern (15 bp):
ATCCTCTTTTTCACT
Found at i:43350267 original size:23 final size:23
Alignment explanation
Indices: 43350095--43350255 Score: 157
Period size: 23 Copynumber: 6.9 Consensus size: 23
43350085 CGAAGTACTT
43350095 AACAGTAAGCACAC-AAGTGCTGGGAA
1 AACAGTAAGCACACAAAGTGC---G-A
*
43350121 AACAGTAAGCACACACAGTGC-A
1 AACAGTAAGCACACAAAGTGCGA
* * * * *
43350143 ATCAGTAGGCGCACATAGCGC-A
1 AACAGTAAGCACACAAAGTGCGA
* *
43350165 AATCAGTAGGCACACGAAGTGCGA
1 AA-CAGTAAGCACACAAAGTGCGA
*
43350189 AACAGTAGGCACACAAAGTGCGA
1 AACAGTAAGCACACAAAGTGCGA
43350212 AACAGTAAGCACACAAAGTGCGA
1 AACAGTAAGCACACAAAGTGCGA
* *
43350235 AACAATAAGCACACACAGTGC
1 AACAGTAAGCACACAAAGTGC
43350256 TGAACGGTAA
Statistics
Matches: 117, Mismatches: 15, Indels: 9
0.83 0.11 0.06
Matches are distributed among these distances:
22 19 0.16
23 76 0.65
24 3 0.03
26 14 0.12
27 5 0.04
ACGTcount: A:0.42, C:0.24, G:0.24, T:0.11
Consensus pattern (23 bp):
AACAGTAAGCACACAAAGTGCGA
Found at i:43356420 original size:23 final size:23
Alignment explanation
Indices: 43356345--43356458 Score: 115
Period size: 23 Copynumber: 5.0 Consensus size: 23
43356335 AAGTGCTGGG
* *
43356345 GAAACAGTAAGCACACACAGTGC
1 GAAACAGTAGGCACACAAAGTGC
* ** * *
43356368 -AATCAGTAGGTGCACATAGCGC
1 GAAACAGTAGGCACACAAAGTGC
*
43356390 -AAATCAGTAGGCACACGAAGTGC
1 GAAA-CAGTAGGCACACAAAGTGC
43356413 GAAACAGTAGGCACACAAAGTGC
1 GAAACAGTAGGCACACAAAGTGC
* *
43356436 GAAACAGTAAGCACACACAGTGC
1 GAAACAGTAGGCACACAAAGTGC
43356459 TGAACGGTAA
Statistics
Matches: 74, Mismatches: 15, Indels: 4
0.80 0.16 0.04
Matches are distributed among these distances:
22 18 0.24
23 53 0.72
24 3 0.04
ACGTcount: A:0.40, C:0.24, G:0.25, T:0.11
Consensus pattern (23 bp):
GAAACAGTAGGCACACAAAGTGC
Found at i:43356444 original size:46 final size:45
Alignment explanation
Indices: 43356345--43356458 Score: 133
Period size: 46 Copynumber: 2.5 Consensus size: 45
43356335 AAGTGCTGGG
* ** *
43356345 GAAACAGTAAGCACACACAGTGCAATCAGTAGGTGCACATAGCGC
1 GAAACAGTAAGCACACACAGTGCAAACAGTAGGCACACAAAGCGC
* *
43356390 -AAATCAGTAGGCACACGA-AGTGCGAAACAGTAGGCACACAAAGTGC
1 GAAA-CAGTAAGCACAC-ACAGTGC-AAACAGTAGGCACACAAAGCGC
43356436 GAAACAGTAAGCACACACAGTGC
1 GAAACAGTAAGCACACACAGTGC
43356459 TGAACGGTAA
Statistics
Matches: 57, Mismatches: 7, Indels: 9
0.78 0.10 0.12
Matches are distributed among these distances:
44 3 0.05
45 17 0.30
46 34 0.60
47 3 0.05
ACGTcount: A:0.40, C:0.24, G:0.25, T:0.11
Consensus pattern (45 bp):
GAAACAGTAAGCACACACAGTGCAAACAGTAGGCACACAAAGCGC
Found at i:43356470 original size:23 final size:23
Alignment explanation
Indices: 43356321--43356458 Score: 111
Period size: 23 Copynumber: 5.9 Consensus size: 23
43356311 CGAAGTACTT
43356321 AACAGTAAGCACAC-AAGTGCTGGGGA
1 AACAGTAAGCACACAAAGTGC----GA
*
43356347 AACAGTAAGCACACACAGTGC-A
1 AACAGTAAGCACACAAAGTGCGA
* * ** * *
43356369 ATCAGTAGGTGCACATAGCGC-A
1 AACAGTAAGCACACAAAGTGCGA
* *
43356391 AATCAGTAGGCACACGAAGTGCGA
1 AA-CAGTAAGCACACAAAGTGCGA
*
43356415 AACAGTAGGCACACAAAGTGCGA
1 AACAGTAAGCACACAAAGTGCGA
*
43356438 AACAGTAAGCACACACAGTGC
1 AACAGTAAGCACACAAAGTGC
43356459 TGAACGGTAA
Statistics
Matches: 93, Mismatches: 16, Indels: 9
0.79 0.14 0.08
Matches are distributed among these distances:
22 18 0.19
23 53 0.57
24 3 0.03
26 14 0.15
27 5 0.05
ACGTcount: A:0.40, C:0.23, G:0.25, T:0.12
Consensus pattern (23 bp):
AACAGTAAGCACACAAAGTGCGA
Found at i:43356767 original size:34 final size:34
Alignment explanation
Indices: 43356724--43356792 Score: 138
Period size: 34 Copynumber: 2.0 Consensus size: 34
43356714 TTTTTACTTT
43356724 AGCCAATTTGTACAGTAAATTCTTTCAATTTACC
1 AGCCAATTTGTACAGTAAATTCTTTCAATTTACC
43356758 AGCCAATTTGTACAGTAAATTCTTTCAATTTACC
1 AGCCAATTTGTACAGTAAATTCTTTCAATTTACC
43356792 A
1 A
43356793 CTTCTTTGCT
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
34 35 1.00
ACGTcount: A:0.33, C:0.20, G:0.09, T:0.38
Consensus pattern (34 bp):
AGCCAATTTGTACAGTAAATTCTTTCAATTTACC
Found at i:43358304 original size:21 final size:19
Alignment explanation
Indices: 43358263--43358302 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 19
43358253 TAAAACTTAG
*
43358263 ATATATATATTTATGTAAA
1 ATATATATATTTATATAAA
*
43358282 ATATATATCTTTAATATAAA
1 ATATATATATTT-ATATAAA
43358302 A
1 A
43358303 ATTAAATGAT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
19 11 0.61
20 7 0.39
ACGTcount: A:0.50, C:0.03, G:0.03, T:0.45
Consensus pattern (19 bp):
ATATATATATTTATATAAA
Found at i:43369308 original size:93 final size:93
Alignment explanation
Indices: 43369194--43370145 Score: 419
Period size: 93 Copynumber: 10.4 Consensus size: 93
43369184 TAATGAATCG
* *
43369194 GATCTCAATGTCCTTGAGGTTACAGTGGAATGGAGTGAAACTTTAGATCCTATCTTCCTAAGGTT
1 GATCTCAATGTCCTTGAGGTTACAGTGGAATGGAGTGAAACTTCAGATCCTATCTTCCTGA-GTT
* *
43369259 ACAGTGAAGT-AGATCAGAACAGGTAGCA
65 ACAGTGAAGTCAGATCAAAACAGGTAACA
* * * * * ** * * * *
43369287 GATCTCAACGTCCTTGAGGTTACGGTGGAGTGAAGTGAAGCACCAAATCCTATATCCCTAAAGTT
1 GATCTCAATGTCCTTGAGGTTACAGTGGAATGGAGTGAAACTTCAGATCCTATCTTCCT-GAGTT
* *
43369352 ACAGT--AGATCGGATCAAAATGAGG-AAC-
65 ACAGTGAAG-TCAGATCAAAA-CAGGTAACA
* * * * *
43369379 GTATCTCAGTGTCCCTGAGGTTACAGTGGAATGGAGAG-AAGTTACA-A---TA-C-CCCTGAGT
1 G-ATCTCAATGTCCTTGAGGTTACAGTGGAATGGAGTGAAACTT-CAGATCCTATCTTCCTGAGT
** * * * **
43369437 TGTAGTGGA-TCAAATCAAAACAAGGAAATG
64 TACAGTGAAGTCAGATCAAAAC-AGGTAACA
* * * *
43369467 GATCTCAACGTCTTTGAGGTTACAGTAGAGTGGAGTGAAACTTCAGATCCTATCTTCCTGATGTT
1 GATCTCAATGTCCTTGAGGTTACAGTGGAATGGAGTGAAACTTCAGATCCTATCTTCCTGA-GTT
* * * *
43369532 ACAGGGAAGT-GGATCAGAACAGGTAGCA
65 ACAGTGAAGTCAGATCAAAACAGGTAACA
* * * * ** * * *
43369560 GATCTCAATGT-CTCTGCGGTTACAGT-AAAGTGGGGTGAAGCACCAGATCTTATATCCCTGAAG
1 GATCTCAATGTCCT-TGAGGTTACAGTGGAA-TGGAGTGAAACTTCAGATCCTATCTTCCTG-AG
* * *
43369623 TTATAGTGGA-TCAGATCAAAA-TGAGTAAC-
63 TTACAGTGAAGTCAGATCAAAACAG-GTAACA
* * *
43369652 GAATCTCAATGCCCTTGAGGTTACAGTGGAATGGAGAG-AAGTTACA-A---TA-C--CCGTGAG
1 G-ATCTCAATGTCCTTGAGGTTACAGTGGAATGGAGTGAAACTT-CAGATCCTATCTTCC-TGAG
* * * * *
43369709 TTATAGTG-GGTCAAATCAAAACA-ATGAAGCG
63 TTACAGTGAAGTCAGATCAAAACAGGT-AA-CA
* * * * * **
43369740 GATCTCAACGTCCCTAAGGTTACAATGG-ACGAGAGTGAAACTTCAGATCCTATCTTTTTGAGGT
1 GATCTCAATGTCCTTGAGGTTACAGTGGAATG-GAGTGAAACTTCAGATCCTATCTTCCTGA-GT
* * * * *
43369804 TACAATGAAGT-GGATTAGAATAGGTAACA
64 TACAGTGAAGTCAGATCAAAACAGGTAACA
* * * * ** *
43369833 GATCTCAACGTCCCTGAGGTTACAGTGGAGTGGAGTGAAGCACCAGATCCTAT-ATCCTTGAAGT
1 GATCTCAATGTCCTTGAGGTTACAGTGGAATGGAGTGAAACTTCAGATCCTATCTTCC-TG-AGT
* * **
43369897 TATAGTGAA-TCGGATCAAAA-ATGAGTAATG
64 TACAGTGAAGTCAGATCAAAACA-G-GTAACA
* * * * * * *
43369927 GATCTTAATATCCTTGAGGTTACGGTGGAATGGAGAG-AAGTTACA-A---AACCTT--TGAGTT
1 GATCTCAATGTCCTTGAGGTTACAGTGGAATGGAGTGAAACTT-CAGATCCTATCTTCCTGAGTT
* * * * *
43369985 ACAGTG-GGTTAAATCAAAATA-ATGAAGCA
65 ACAGTGAAGTCAGATCAAAACAGGT-AA-CA
* * *
43370014 GATCTCAATATGCC-TAAGGTTACAGTGGAGTGGAGTGAAACTTCAGATCCTATCTTCCTGATGT
1 GATCTCAATGT-CCTTGAGGTTACAGTGGAATGGAGTGAAACTTCAGATCCTATCTTCCTGA-GT
* * * *
43370078 TACAGAGAAGT-GGATCAGAACAGGTAGCA
64 TACAGTGAAGTCAGATCAAAACAGGTAACA
* * *
43370107 GAGCTCAATGTCCCTGAGGTTACAGTGGAGTGGAGTGAA
1 GATCTCAATGTCCTTGAGGTTACAGTGGAATGGAGTGAA
43370146 GCACCAAATC
Statistics
Matches: 624, Mismatches: 164, Indels: 142
0.67 0.18 0.15
Matches are distributed among these distances:
85 2 0.00
86 47 0.08
87 116 0.19
88 23 0.04
89 4 0.01
90 1 0.00
91 11 0.02
92 18 0.03
93 302 0.48
94 93 0.15
95 7 0.01
ACGTcount: A:0.32, C:0.16, G:0.25, T:0.26
Consensus pattern (93 bp):
GATCTCAATGTCCTTGAGGTTACAGTGGAATGGAGTGAAACTTCAGATCCTATCTTCCTGAGTTA
CAGTGAAGTCAGATCAAAACAGGTAACA
Found at i:43369486 original size:273 final size:273
Alignment explanation
Indices: 43368980--43370165 Score: 1403
Period size: 273 Copynumber: 4.4 Consensus size: 273
43368970 AAGCATGAAT
* * * * * *
43368980 TCCTATCTTCTTGAGGTTACAATGAAGTGAATCAGAACATGTAGCAAATCTCAATGTCTTTGAGG
1 TCCTATCTTCCTGAGGTTACAGTGAAGTGGATCAGAACAGGTAGCAGATCTCAATGTCCTTGAGG
** * * * * *
43369045 TTACAGTAAAGTAGAGTGAAGCACCAGAT--AATATCCCTAAAGTTATAATGGGTTGGATC-AAA
66 TTACAGTGGAGTGGAGTGAAGCACCAGATCCTATATCCCTAAAGTTATAGTGGATCGGATCAAAA
* * * *
43369107 --A-TAA-G----T-AATGTCCTTGAGGTTACAGTGGAATGAAGAGAAGTTACAATACCTCTAAG
131 TGAGTAACGTATCTCAATGTCCCTGAGGTTACAGTGGAATGGAGAGAAGTTACAATACCCCTGAG
* * * * * *
43369163 TTGCAGTGGGTCAAATCAAAATAATGAATCGGATCTCAATGTCCTTGAGGTTACAGTGGAATGGA
196 TTACAGTGGGTCAAATCAAAACAATGAAACGGATCTCAACGTCCCTAAGGTTACAGTGGAATGGA
*
43369228 GTGAAACTTTAGA
261 GTGAAACTTCAGA
* * *
43369241 TCCTATCTTCCTAAGGTTACAGTGAAGTAGATCAGAACAGGTAGCAGATCTCAACGTCCTTGAGG
1 TCCTATCTTCCTGAGGTTACAGTGAAGTGGATCAGAACAGGTAGCAGATCTCAATGTCCTTGAGG
* * * * *
43369306 TTACGGTGGAGTGAAGTGAAGCACCAAATCCTATATCCCTAAAGTTACAGTAGATCGGATCAAAA
66 TTACAGTGGAGTGGAGTGAAGCACCAGATCCTATATCCCTAAAGTTATAGTGGATCGGATCAAAA
* *
43369371 TGAGGAACGTATCTCAGTGTCCCTGAGGTTACAGTGGAATGGAGAGAAGTTACAATACCCCTGAG
131 TGAGTAACGTATCTCAATGTCCCTGAGGTTACAGTGGAATGGAGAGAAGTTACAATACCCCTGAG
** * * * ** * * *
43369436 TTGTAGTGGATCAAATCAAAACAAGGAAATGGATCTCAACGTCTTTGAGGTTACAGTAGAGTGGA
196 TTACAGTGGGTCAAATCAAAACAATGAAACGGATCTCAACGTCCCTAAGGTTACAGTGGAATGGA
43369501 GTGAAACTTCAGA
261 GTGAAACTTCAGA
* * *
43369514 TCCTATCTTCCTGATGTTACAGGGAAGTGGATCAGAACAGGTAGCAGATCTCAATGT-CTCTGCG
1 TCCTATCTTCCTGAGGTTACAGTGAAGTGGATCAGAACAGGTAGCAGATCTCAATGTCCT-TGAG
** * * * *
43369578 GTTACAGTAAAGTGGGGTGAAGCACCAGATCTTATATCCCTGAAGTTATAGTGGATCAGATCAAA
65 GTTACAGTGGAGTGGAGTGAAGCACCAGATCCTATATCCCTAAAGTTATAGTGGATCGGATCAAA
* *
43369643 ATGAGTAACGAATCTCAATG-CCCTTGAGGTTACAGTGGAATGGAGAGAAGTTACAATACCCGTG
130 ATGAGTAACGTATCTCAATGTCCC-TGAGGTTACAGTGGAATGGAGAGAAGTTACAATACCCCTG
* * * *
43369707 AGTTATAGTGGGTCAAATCAAAACAATGAAGCGGATCTCAACGTCCCTAAGGTTACAATGG-ACG
194 AGTTACAGTGGGTCAAATCAAAACAATGAAACGGATCTCAACGTCCCTAAGGTTACAGTGGAATG
43369771 AGAGTGAAACTTCAGA
259 -GAGTGAAACTTCAGA
** * * * * * *
43369787 TCCTATCTTTTTGAGGTTACAATGAAGTGGATTAGAATAGGTAACAGATCTCAACGTCCCTGAGG
1 TCCTATCTTCCTGAGGTTACAGTGAAGTGGATCAGAACAGGTAGCAGATCTCAATGTCCTTGAGG
* * *
43369852 TTACAGTGGAGTGGAGTGAAGCACCAGATCCTATATCCTTGAAGTTATAGTGAATCGGATCAAAA
66 TTACAGTGGAGTGGAGTGAAGCACCAGATCCTATATCCCTAAAGTTATAGTGGATCGGATC-AAA
* * * * * * * **
43369917 ATGAGTAATGGATCTTAATATCCTTGAGGTTACGGTGGAATGGAGAGAAGTTACAAAACCTTTGA
130 ATGAGTAACGTATCTCAATGTCCCTGAGGTTACAGTGGAATGGAGAGAAGTTACAATACCCCTGA
* * * * ** * *
43369982 GTTACAGTGGGTTAAATCAAAATAATGAAGCAGATCTCAATATGCCTAAGGTTACAGTGGAGTGG
195 GTTACAGTGGGTCAAATCAAAACAATGAAACGGATCTCAACGTCCCTAAGGTTACAGTGGAATGG
43370047 AGTGAAACTTCAGA
260 AGTGAAACTTCAGA
* * * *
43370061 TCCTATCTTCCTGATGTTACAGAGAAGTGGATCAGAACAGGTAGCAGAGCTCAATGTCCCTGAGG
1 TCCTATCTTCCTGAGGTTACAGTGAAGTGGATCAGAACAGGTAGCAGATCTCAATGTCCTTGAGG
*
43370126 TTACAGTGGAGTGGAGTGAAGCACCAAATCCTATATCCCT
66 TTACAGTGGAGTGGAGTGAAGCACCAGATCCTATATCCCT
43370166 GAGTAACGGA
Statistics
Matches: 786, Mismatches: 120, Indels: 25
0.84 0.13 0.03
Matches are distributed among these distances:
261 79 0.10
263 24 0.03
264 3 0.00
266 1 0.00
267 2 0.00
268 1 0.00
272 7 0.01
273 449 0.57
274 217 0.28
275 3 0.00
ACGTcount: A:0.33, C:0.16, G:0.24, T:0.26
Consensus pattern (273 bp):
TCCTATCTTCCTGAGGTTACAGTGAAGTGGATCAGAACAGGTAGCAGATCTCAATGTCCTTGAGG
TTACAGTGGAGTGGAGTGAAGCACCAGATCCTATATCCCTAAAGTTATAGTGGATCGGATCAAAA
TGAGTAACGTATCTCAATGTCCCTGAGGTTACAGTGGAATGGAGAGAAGTTACAATACCCCTGAG
TTACAGTGGGTCAAATCAAAACAATGAAACGGATCTCAACGTCCCTAAGGTTACAGTGGAATGGA
GTGAAACTTCAGA
Found at i:43372315 original size:19 final size:19
Alignment explanation
Indices: 43372274--43372316 Score: 54
Period size: 19 Copynumber: 2.3 Consensus size: 19
43372264 TATATATTTA
43372274 GTTA-TTTATTTATTTTGT
1 GTTATTTTATTTATTTTGT
*
43372292 ATTATTTTATTTA-TTTGAT
1 GTTATTTTATTTATTTTG-T
43372311 GTTATT
1 GTTATT
43372317 AATTTTGCCT
Statistics
Matches: 21, Mismatches: 2, Indels: 3
0.81 0.08 0.12
Matches are distributed among these distances:
18 7 0.33
19 14 0.67
ACGTcount: A:0.21, C:0.00, G:0.09, T:0.70
Consensus pattern (19 bp):
GTTATTTTATTTATTTTGT
Found at i:43377891 original size:39 final size:39
Alignment explanation
Indices: 43377820--43377911 Score: 125
Period size: 39 Copynumber: 2.4 Consensus size: 39
43377810 TCAACTTACT
*
43377820 GAACCAGCAGTGAC-CTACAAACACTGCAATACAATACC
1 GAACCAGCAGTGACACTACAAACACTGAAATACAATACC
*
43377858 GAACCAGCAGTGACACTGA-AAACACTGAAATACAATACT
1 GAACCAGCAGTGACACT-ACAAACACTGAAATACAATACC
**
43377897 GAACTGGCAGTGACA
1 GAACCAGCAGTGACA
43377912 TTGTCAACAT
Statistics
Matches: 48, Mismatches: 4, Indels: 3
0.87 0.07 0.05
Matches are distributed among these distances:
38 14 0.29
39 33 0.69
40 1 0.02
ACGTcount: A:0.42, C:0.26, G:0.17, T:0.14
Consensus pattern (39 bp):
GAACCAGCAGTGACACTACAAACACTGAAATACAATACC
Found at i:43379224 original size:20 final size:20
Alignment explanation
Indices: 43379192--43379241 Score: 68
Period size: 20 Copynumber: 2.5 Consensus size: 20
43379182 TTCTAACCCC
43379192 TAATTTGAAAAACT-TAAACCT
1 TAATTT-AAAAACTCTAAA-CT
43379213 TAATTTAAAAACTCTAAACT
1 TAATTTAAAAACTCTAAACT
43379233 TAA-TTAAAA
1 TAATTTAAAA
43379242 CAAAAACACC
Statistics
Matches: 28, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
19 6 0.21
20 12 0.43
21 10 0.36
ACGTcount: A:0.52, C:0.12, G:0.02, T:0.34
Consensus pattern (20 bp):
TAATTTAAAAACTCTAAACT
Found at i:43379261 original size:27 final size:26
Alignment explanation
Indices: 43379226--43379276 Score: 75
Period size: 27 Copynumber: 1.9 Consensus size: 26
43379216 TTTAAAAACT
*
43379226 CTAAACTTAATTAAAACAAAAACACC
1 CTAAACTTAATAAAAACAAAAACACC
*
43379252 CTAAATCTTAATAAAAATAAAAACA
1 CTAAA-CTTAATAAAAACAAAAACA
43379277 TGTTGAAAAC
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
26 5 0.23
27 17 0.77
ACGTcount: A:0.61, C:0.18, G:0.00, T:0.22
Consensus pattern (26 bp):
CTAAACTTAATAAAAACAAAAACACC
Found at i:43380341 original size:18 final size:17
Alignment explanation
Indices: 43380314--43380347 Score: 50
Period size: 18 Copynumber: 1.9 Consensus size: 17
43380304 TGTCATAAAA
*
43380314 AAAAGTAAATTTAGAAAG
1 AAAAGAAAATTT-GAAAG
43380332 AAAAGAAAATTTGAAA
1 AAAAGAAAATTTGAAA
43380348 TCAATCTTCT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 4 0.27
18 11 0.73
ACGTcount: A:0.65, C:0.00, G:0.15, T:0.21
Consensus pattern (17 bp):
AAAAGAAAATTTGAAAG
Done.