Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008856.1 Hibiscus syriacus cultivar Beakdansim tig00112075_pilon, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 559779
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 2 of 3
Found at i:265624 original size:19 final size:18
Alignment explanation
Indices: 265563--265654 Score: 74
Period size: 19 Copynumber: 5.4 Consensus size: 18
265553 GCAACGAGAG
*
265563 AATCGCAACGCGAAATGAA
1 AATCGCAACGCGAAA-CAA
*
265582 AATCGCAA--CG--ACAG
1 AATCGCAACGCGAAACAA
*
265596 AATCGTAACGCGAAACCAA
1 AATCGCAACGCGAAA-CAA
265615 AATCGCAA--CG--ACAA
1 AATCGCAACGCGAAACAA
265629 AATCGCAACGCGAAACCAA
1 AATCGCAACGCGAAA-CAA
265648 AATCGCA
1 AATCGCA
265655 TTGCGATTTT
Statistics
Matches: 58, Mismatches: 5, Indels: 20
0.70 0.06 0.24
Matches are distributed among these distances:
14 19 0.33
15 2 0.03
16 4 0.07
17 4 0.07
18 2 0.03
19 27 0.47
ACGTcount: A:0.47, C:0.27, G:0.17, T:0.09
Consensus pattern (18 bp):
AATCGCAACGCGAAACAA
Found at i:265631 original size:14 final size:14
Alignment explanation
Indices: 265580--265638 Score: 55
Period size: 14 Copynumber: 3.9 Consensus size: 14
265570 ACGCGAAATG
265580 AAAATCGCAACGAC
1 AAAATCGCAACGAC
* *
265594 AGAATCGTAACGCGAAACC
1 AAAATCGCAA--CG--A-C
265613 AAAATCGCAACGAC
1 AAAATCGCAACGAC
265627 AAAATCGCAACG
1 AAAATCGCAACG
265639 CGAAACCAAA
Statistics
Matches: 36, Mismatches: 4, Indels: 10
0.72 0.08 0.20
Matches are distributed among these distances:
14 21 0.58
15 1 0.03
16 2 0.06
17 2 0.06
18 1 0.03
19 9 0.25
ACGTcount: A:0.47, C:0.27, G:0.17, T:0.08
Consensus pattern (14 bp):
AAAATCGCAACGAC
Found at i:265672 original size:19 final size:19
Alignment explanation
Indices: 265650--265788 Score: 137
Period size: 19 Copynumber: 7.6 Consensus size: 19
265640 GAAACCAAAA
*
265650 TCGCATTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
*
265669 TCGCGTTGCGA--TTC-TG
1 TCGCGTTGCGATTTTCATT
265685 T--CGTTGCGATTTTCA-T
1 TCGCGTTGCGATTTTCATT
**
265701 TCGCGTTGCGATTTTGGTT
1 TCGCGTTGCGATTTTCATT
**
265720 TCGCGTTGCGATTTTGGTT
1 TCGCGTTGCGATTTTCATT
* *
265739 TCTCGTTGCGATTCTCATT
1 TCGCGTTGCGATTTTCATT
*
265758 TCGCGTTGCGATTTTAAGTT
1 TCGCGTTGCGATTTTCA-TT
*
265778 TCGTGTTGCGA
1 TCGCGTTGCGA
265789 AAGTAAACTA
Statistics
Matches: 100, Mismatches: 13, Indels: 13
0.79 0.10 0.10
Matches are distributed among these distances:
14 8 0.08
16 6 0.06
17 3 0.03
18 12 0.12
19 59 0.59
20 12 0.12
ACGTcount: A:0.10, C:0.19, G:0.25, T:0.45
Consensus pattern (19 bp):
TCGCGTTGCGATTTTCATT
Found at i:265731 original size:51 final size:54
Alignment explanation
Indices: 265650--265788 Score: 160
Period size: 51 Copynumber: 2.6 Consensus size: 54
265640 GAAACCAAAA
* *
265650 TCGCATTGCGATTTTCA-TTTCGCGTTGCGATTCT-G-TCGTTGCGATTTTCA-T
1 TCGCGTTGCGATTTT-AGTTTCGCGTTGCGATTCTGGTTCGTTGCGATTCTCATT
* *
265701 TCGCGTTGCGATTTTGGTTTCGCGTTGCGATTTTGGTTTCTCGTTGCGATTCTCATT
1 TCGCGTTGCGATTTTAGTTTCGCGTTGCGATTCTGG--T-TCGTTGCGATTCTCATT
*
265758 TCGCGTTGCGATTTTAAGTTTCGTGTTGCGA
1 TCGCGTTGCGATTTT-AGTTTCGCGTTGCGA
265789 AAGTAAACTA
Statistics
Matches: 74, Mismatches: 6, Indels: 9
0.83 0.07 0.10
Matches are distributed among these distances:
51 30 0.41
52 1 0.01
56 14 0.19
57 16 0.22
58 13 0.18
ACGTcount: A:0.10, C:0.19, G:0.25, T:0.45
Consensus pattern (54 bp):
TCGCGTTGCGATTTTAGTTTCGCGTTGCGATTCTGGTTCGTTGCGATTCTCATT
Found at i:267739 original size:14 final size:14
Alignment explanation
Indices: 267706--267742 Score: 56
Period size: 14 Copynumber: 2.6 Consensus size: 14
267696 GATTGTTTAA
267706 TTGATTTGTAAAAG
1 TTGATTTGTAAAAG
**
267720 AAGATTTGTAAAAG
1 TTGATTTGTAAAAG
267734 TTGATTTGT
1 TTGATTTGT
267743 GTAATTGATG
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
14 19 1.00
ACGTcount: A:0.35, C:0.00, G:0.22, T:0.43
Consensus pattern (14 bp):
TTGATTTGTAAAAG
Found at i:267904 original size:19 final size:19
Alignment explanation
Indices: 267876--268136 Score: 285
Period size: 19 Copynumber: 14.7 Consensus size: 19
267866 AACGAGAGAA
*
267876 TCGCAATGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
267895 TCGCATTGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
*
267914 TCCGCATTGCGA--TTC-TC
1 T-CGCATTGCGATTTTCATT
267931 TCG--TTGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
267948 TCGCATTGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
*
267967 TCGCATTGCGA--TTC-TA
1 TCGCATTGCGATTTTCATT
267983 TCG--TTGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
*
268000 TCGCATTACGATTTTCATT
1 TCGCATTGCGATTTTCATT
*
268019 TCCGCATTGCGA--TTC-TC
1 T-CGCATTGCGATTTTCATT
268036 TCG--TTGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
268053 TCGCATTGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
268072 TCGCATTGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
*
268091 TCCGTATTGCGA-TTTC--T
1 T-CGCATTGCGATTTTCATT
*
268108 T-G--TTGGGATTTTCATT
1 TCGCATTGCGATTTTCATT
268124 TCGCATTGCGATT
1 TCGCATTGCGATT
268137 CTCTCGTTGC
Statistics
Matches: 206, Mismatches: 12, Indels: 48
0.77 0.05 0.18
Matches are distributed among these distances:
13 5 0.02
14 22 0.11
15 1 0.00
16 19 0.09
17 22 0.11
18 6 0.03
19 103 0.50
20 28 0.14
ACGTcount: A:0.15, C:0.22, G:0.17, T:0.46
Consensus pattern (19 bp):
TCGCATTGCGATTTTCATT
Found at i:268025 original size:105 final size:104
Alignment explanation
Indices: 267882--268150 Score: 409
Period size: 105 Copynumber: 2.6 Consensus size: 104
267872 AGAATCGCAA
267882 TGCGATTTTCATTTCGCATTGCGATTTTCATTTCCGCATTGCGATTCTCTCGTTGCGATTTTCAT
1 TGCGATTTTCATTTCGCATTGCGATTTTCATTTCCGCATTGCGATTCTCTCGTTGCGATTTTCAT
267947 TTCGCATTGCGATTTTCATTTCGCATTGCGATTCTATC-GT
66 TTCGCATTGCGATTTTCATTTCGCATTGCGATT-T-TCAGT
*
267987 TGCGATTTTCATTTCGCATTACGATTTTCATTTCCGCATTGCGATTCTCTCGTTGCGATTTTCAT
1 TGCGATTTTCATTTCGCATTGCGATTTTCATTTCCGCATTGCGATTCTCTCGTTGCGATTTTCAT
*
268052 TTCGCATTGCGATTTTCATTTCGCATTGCGATTTTCATT
66 TTCGCATTGCGATTTTCATTTCGCATTGCGATTTTCAGT
* * *** *
268091 TCCG-TATTGCGATTTCTTGTTGGGATTTTCATTT-CGCATTGCGATTCTCTCGTTGCGATT
1 TGCGAT-TTTC-ATTTCGCATTGCGATTTTCATTTCCGCATTGCGATTCTCTCGTTGCGATT
268151 GTAATTTCCG
Statistics
Matches: 152, Mismatches: 9, Indels: 7
0.90 0.05 0.04
Matches are distributed among these distances:
103 3 0.02
104 34 0.22
105 115 0.76
ACGTcount: A:0.14, C:0.22, G:0.17, T:0.46
Consensus pattern (104 bp):
TGCGATTTTCATTTCGCATTGCGATTTTCATTTCCGCATTGCGATTCTCTCGTTGCGATTTTCAT
TTCGCATTGCGATTTTCATTTCGCATTGCGATTTTCAGT
Found at i:268158 original size:52 final size:52
Alignment explanation
Indices: 267882--268150 Score: 391
Period size: 52 Copynumber: 5.1 Consensus size: 52
267872 AGAATCGCAA
267882 TGCGATTTTCATTTCGCATTGCGATTTTCATTTCCGCATTGCGATTCTCTCGT
1 TGCGATTTTCATTTCGCATTGCGATTTTCATTT-CGCATTGCGATTCTCTCGT
*
267935 TGCGATTTTCATTTCGCATTGCGATTTTCATTTCGCATTGCGATTCTATCGT
1 TGCGATTTTCATTTCGCATTGCGATTTTCATTTCGCATTGCGATTCTCTCGT
*
267987 TGCGATTTTCATTTCGCATTACGATTTTCATTTCCGCATTGCGATTCTCTCGT
1 TGCGATTTTCATTTCGCATTGCGATTTTCATTT-CGCATTGCGATTCTCTCGT
*
268040 TGCGATTTTCATTTCGCATTGCGATTTTCATTTCGCATTGCGATT-T-TCATT
1 TGCGATTTTCATTTCGCATTGCGATTTTCATTTCGCATTGCGATTCTCTC-GT
* * *** *
268091 TCCG-TATTGCGATTTCTTGTTGGGATTTTCATTTCGCATTGCGATTCTCTCGT
1 TGCGAT-TTTC-ATTTCGCATTGCGATTTTCATTTCGCATTGCGATTCTCTCGT
268144 TGCGATT
1 TGCGATT
268151 GTAATTTCCG
Statistics
Matches: 196, Mismatches: 13, Indels: 14
0.88 0.06 0.06
Matches are distributed among these distances:
50 3 0.02
51 8 0.04
52 93 0.47
53 89 0.45
54 3 0.02
ACGTcount: A:0.14, C:0.22, G:0.17, T:0.46
Consensus pattern (52 bp):
TGCGATTTTCATTTCGCATTGCGATTTTCATTTCGCATTGCGATTCTCTCGT
Found at i:270661 original size:24 final size:24
Alignment explanation
Indices: 270627--270673 Score: 69
Period size: 24 Copynumber: 2.0 Consensus size: 24
270617 CTGAAACATC
270627 ATCAAAATCCGTG-TATTGACCAAT
1 ATCAAAATCCG-GATATTGACCAAT
*
270651 ATCAAAGTCCGGATATTGACCAA
1 ATCAAAATCCGGATATTGACCAA
270674 GACCAAATTT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
23 1 0.05
24 20 0.95
ACGTcount: A:0.38, C:0.21, G:0.15, T:0.26
Consensus pattern (24 bp):
ATCAAAATCCGGATATTGACCAAT
Found at i:271393 original size:20 final size:20
Alignment explanation
Indices: 271365--271613 Score: 259
Period size: 20 Copynumber: 12.4 Consensus size: 20
271355 AAATTTCAGT
* * *
271365 GTTGTGATTTACAGATTCTC
1 GTTGCGATTTACGGATTCGC
**
271385 GTTGCGATTTACGGATTATC
1 GTTGCGATTTACGGATTCGC
*
271405 GTTGCGATTTACGGATTCTC
1 GTTGCGATTTACGGATTCGC
**
271425 GTTGCGATTTACGGATTATC
1 GTTGCGATTTACGGATTCGC
*
271445 GTTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATTCGC
* *
271465 GTTGCGATATACGGATACGC
1 GTTGCGATTTACGGATTCGC
* *
271485 ATTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATTCGC
* * *
271505 GTTGCTATTTACGGATACAC
1 GTTGCGATTTACGGATTCGC
* *
271525 GTTGCGGTTTACGGATACGC
1 GTTGCGATTTACGGATTCGC
*
271545 GTTGCGATTTATGTG-TTCGC
1 GTTGCGATTTACG-GATTCGC
*
271565 GTTGCGATTTATGTG-TTCGC
1 GTTGCGATTTACG-GATTCGC
* **
271585 GTTGCGATTTTCATATTCGC
1 GTTGCGATTTACGGATTCGC
271605 GTTGCGATT
1 GTTGCGATT
271614 CTTGAAAATC
Statistics
Matches: 203, Mismatches: 24, Indels: 4
0.88 0.10 0.02
Matches are distributed among these distances:
20 202 1.00
21 1 0.00
ACGTcount: A:0.18, C:0.18, G:0.27, T:0.38
Consensus pattern (20 bp):
GTTGCGATTTACGGATTCGC
Found at i:271674 original size:42 final size:43
Alignment explanation
Indices: 271581--271679 Score: 100
Period size: 42 Copynumber: 2.4 Consensus size: 43
271571 ATTTATGTGT
* *
271581 TCGCGTTGCG-ATTT-TCATATTCGCGTTGCGATTCTTGAAAA
1 TCGCGTTGCGAATTTGTCATATTCGCATTGCGATTCTTAAAAA
**
271622 TCGCAATGCGAATTTGT-ACTA-TCGCATTGCGATT-TTAAAGAA
1 TCGCGTTGCGAATTTGTCA-TATTCGCATTGCGATTCTTAAA-AA
*
271664 TCGCGTTGCGATTTTG
1 TCGCGTTGCGAATTTG
271680 GAAACTGATT
Statistics
Matches: 47, Mismatches: 7, Indels: 7
0.77 0.11 0.11
Matches are distributed among these distances:
41 12 0.26
42 32 0.68
43 3 0.06
ACGTcount: A:0.22, C:0.18, G:0.22, T:0.37
Consensus pattern (43 bp):
TCGCGTTGCGAATTTGTCATATTCGCATTGCGATTCTTAAAAA
Found at i:274037 original size:48 final size:46
Alignment explanation
Indices: 273930--274039 Score: 116
Period size: 46 Copynumber: 2.3 Consensus size: 46
273920 TAAATGTATA
* * *
273930 CGAACTAGAAATCATGCGGTTAGGTTTATTTTCTCAAACAAGCATG
1 CGAAGTAGATATCATGCGGTTAGGTTTATTTTCTAAAACAAGCATG
* *
273976 CGAATTAGATATCATGCGGTTAGGATTT-TTTTGTGAATAACAAAGCATG
1 CGAAGTAGATATCATGCGGTTAGG-TTTATTTTCT-AA-AAC-AAGCATG
*
274025 -GAGGTAGATATCATG
1 CGAAGTAGATATCATG
274040 TTGGGTAGGA
Statistics
Matches: 54, Mismatches: 6, Indels: 6
0.82 0.09 0.09
Matches are distributed among these distances:
46 27 0.50
47 4 0.07
48 16 0.30
49 7 0.13
ACGTcount: A:0.33, C:0.13, G:0.23, T:0.32
Consensus pattern (46 bp):
CGAAGTAGATATCATGCGGTTAGGTTTATTTTCTAAAACAAGCATG
Found at i:274449 original size:21 final size:21
Alignment explanation
Indices: 274427--274521 Score: 147
Period size: 21 Copynumber: 4.5 Consensus size: 21
274417 TCATACCAAG
*
274427 GACGAGAAGACCATTCACAAG
1 GACGAGAAGACCATTCACAAA
*
274448 GACGAGAAGACCATTCATAAA
1 GACGAGAAGACCATTCACAAA
*
274469 GACGAGAAGACCATTCATAAA
1 GACGAGAAGACCATTCACAAA
274490 GACGAGAAGACCATTCACAAA
1 GACGAGAAGACCATTCACAAA
274511 GAC-ATGAAGAC
1 GACGA-GAAGAC
274522 TATTTTGCAT
Statistics
Matches: 70, Mismatches: 3, Indels: 2
0.93 0.04 0.03
Matches are distributed among these distances:
20 1 0.01
21 69 0.99
ACGTcount: A:0.46, C:0.21, G:0.21, T:0.12
Consensus pattern (21 bp):
GACGAGAAGACCATTCACAAA
Found at i:278331 original size:16 final size:18
Alignment explanation
Indices: 278303--278337 Score: 56
Period size: 17 Copynumber: 2.1 Consensus size: 18
278293 CAATGGGATA
278303 AAAATGTATGAAG-AGTG
1 AAAATGTATGAAGTAGTG
278320 AAAATG-ATGAAGTAGTG
1 AAAATGTATGAAGTAGTG
278337 A
1 A
278338 CAGTGGAGGT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 6 0.35
17 11 0.65
ACGTcount: A:0.49, C:0.00, G:0.29, T:0.23
Consensus pattern (18 bp):
AAAATGTATGAAGTAGTG
Found at i:279207 original size:37 final size:37
Alignment explanation
Indices: 279157--279667 Score: 463
Period size: 37 Copynumber: 13.8 Consensus size: 37
279147 ATGAGACTGG
* *
279157 AGCAAATCAATCTTAAGCATTCACTGAAGAGTAGTGA
1 AGCAAATCCATCTTAAGCCTTCACTGAAGAGTAGTGA
*
279194 AGCAAATCAATCTTAAGCCTTCACTGAAGAGTAGTGA
1 AGCAAATCCATCTTAAGCCTTCACTGAAGAGTAGTGA
* * * * *
279231 AGCAAATTCATCAGTAAGCCTTCCGACAATGATGATTAAGT-C
1 AGCAAATCCATC-TTAAGCCTT-C-AC--TGAAGAGT-AGTGA
** ****
279273 CTCCGGGCCATCTTAAGCCTTCACTGAAGAGTAGTGA
1 AGCAAATCCATCTTAAGCCTTCACTGAAGAGTAGTGA
*
279310 AGCAAATCAATCTTAAGCCTTCACTGAAGAGTAGTGA
1 AGCAAATCCATCTTAAGCCTTCACTGAAGAGTAGTGA
*
279347 AGCAAATCAATCTTAAGCCTTCACTGAAGAGTAGTGA
1 AGCAAATCCATCTTAAGCCTTCACTGAAGAGTAGTGA
* * * * * **
279384 AGCAAATTCATCAGTAAACCTTCCGACAATGATGATTAAGTCC
1 AGCAAATCCATC-TTAAGCCTT-C-AC--TGAAGAGT-AGTGA
** * *
279427 TCCAGA-CCATCTTAAGCCTTCACTGAAAAGTAGTGA
1 AGCAAATCCATCTTAAGCCTTCACTGAAGAGTAGTGA
* *
279463 AGAAAATCCGTCTTAAGCCTT--C---A-AGTAGTGA
1 AGCAAATCCATCTTAAGCCTTCACTGAAGAGTAGTGA
*
279494 AGAAAATCCATCTTAAGCCTTCACTGAAGAGTAGTGA
1 AGCAAATCCATCTTAAGCCTTCACTGAAGAGTAGTGA
* * *
279531 AGC-GATCTATCCTAAGCCTTCACCTG-AGAGTAGTGA
1 AGCAAATCCATCTTAAGCCTTCA-CTGAAGAGTAGTGA
* *
279567 AGC-AATCCATCTTAAGCCTTCACCGGAGAGTAGTGA
1 AGCAAATCCATCTTAAGCCTTCACTGAAGAGTAGTGA
* *
279603 AGCAAA-CCATTTTAAGCCTTTACTGAAGAGTAGTGA
1 AGCAAATCCATCTTAAGCCTTCACTGAAGAGTAGTGA
* *
279639 AGTAAA-CCATCTTAAGCCTTCACCGAAGA
1 AGCAAATCCATCTTAAGCCTTCACTGAAGA
279668 AATGGTGAAG
Statistics
Matches: 385, Mismatches: 66, Indels: 47
0.77 0.13 0.09
Matches are distributed among these distances:
31 28 0.07
32 1 0.00
33 1 0.00
35 3 0.01
36 118 0.31
37 162 0.42
38 15 0.04
39 6 0.02
40 6 0.02
41 15 0.04
42 21 0.05
43 9 0.02
ACGTcount: A:0.35, C:0.22, G:0.19, T:0.25
Consensus pattern (37 bp):
AGCAAATCCATCTTAAGCCTTCACTGAAGAGTAGTGA
Found at i:279437 original size:153 final size:153
Alignment explanation
Indices: 279157--279667 Score: 651
Period size: 153 Copynumber: 3.4 Consensus size: 153
279147 ATGAGACTGG
*
279157 AGCAAATCAATCTTAAGCATTCACTGAAGAGTAGTGAAGCAAATCAATCTTAAGCCTTCACTGAA
1 AGCAAATCAATCTTAAGCCTTCACTGAAGAGTAGTGAAGCAAATCAATCTTAAGCCTTCACTGAA
* *
279222 GAGTAGTGAAGCAAATTCATCAGTAAGCCTTCCGACAATGATGATTAAGTCCTCCGGGCCATCTT
66 GAGTAGTGAAGCAAATTCATCAGTAAGCCTTCCGACAATGATGATTAAGTCCTCCAGACCATCTT
279287 AAGCCTTCACTGAAGAGTAGTGA
131 AAGCCTTCACTGAAGAGTAGTGA
279310 AGCAAATCAATCTTAAGCCTTCACTGAAGAGTAGTGAAGCAAATCAATCTTAAGCCTTCACTGAA
1 AGCAAATCAATCTTAAGCCTTCACTGAAGAGTAGTGAAGCAAATCAATCTTAAGCCTTCACTGAA
*
279375 GAGTAGTGAAGCAAATTCATCAGTAAACCTTCCGACAATGATGATTAAGTCCTCCAGACCATCTT
66 GAGTAGTGAAGCAAATTCATCAGTAAGCCTTCCGACAATGATGATTAAGTCCTCCAGACCATCTT
*
279440 AAGCCTTCACTGAAAAGTAGTGA
131 AAGCCTTCACTGAAGAGTAGTGA
* ** * *
279463 AGAAAATCCGTCTTAAGCCTT--C---A-AGTAGTGAAGAAAATCCATCTTAAGCCTTCACTGAA
1 AGCAAATCAATCTTAAGCCTTCACTGAAGAGTAGTGAAGCAAATCAATCTTAAGCCTTCACTGAA
* * * * ****
279522 GAGTAGTGAAGC-GA-TCTATC-CTAAGCCTT-C-AC-CTGA-GAGT-AGTGAAGCA-ATCCATC
66 GAGTAGTGAAGCAAATTC-ATCAGTAAGCCTTCCGACAATGATGATTAAGTCCTCCAGA-CCATC
* *
279578 TTAAGCCTTCACCGGAGAGTAGTGA
129 TTAAGCCTTCACTGAAGAGTAGTGA
* * * * * *
279603 AGCAAA-CCATTTTAAGCCTTTACTGAAGAGTAGTGAAGTAAA-CCATCTTAAGCCTTCACCGAA
1 AGCAAATCAATCTTAAGCCTTCACTGAAGAGTAGTGAAGCAAATCAATCTTAAGCCTTCACTGAA
279666 GA
66 GA
279668 AATGGTGAAG
Statistics
Matches: 323, Mismatches: 27, Indels: 25
0.86 0.07 0.07
Matches are distributed among these distances:
139 13 0.04
140 37 0.11
141 4 0.01
142 3 0.01
143 2 0.01
144 24 0.07
145 22 0.07
146 4 0.01
147 46 0.14
148 1 0.00
151 1 0.00
153 166 0.51
ACGTcount: A:0.35, C:0.22, G:0.19, T:0.25
Consensus pattern (153 bp):
AGCAAATCAATCTTAAGCCTTCACTGAAGAGTAGTGAAGCAAATCAATCTTAAGCCTTCACTGAA
GAGTAGTGAAGCAAATTCATCAGTAAGCCTTCCGACAATGATGATTAAGTCCTCCAGACCATCTT
AAGCCTTCACTGAAGAGTAGTGA
Found at i:279492 original size:31 final size:31
Alignment explanation
Indices: 279454--279516 Score: 117
Period size: 31 Copynumber: 2.0 Consensus size: 31
279444 CTTCACTGAA
*
279454 AAGTAGTGAAGAAAATCCGTCTTAAGCCTTC
1 AAGTAGTGAAGAAAATCCATCTTAAGCCTTC
279485 AAGTAGTGAAGAAAATCCATCTTAAGCCTTC
1 AAGTAGTGAAGAAAATCCATCTTAAGCCTTC
279516 A
1 A
279517 CTGAAGAGTA
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
31 31 1.00
ACGTcount: A:0.38, C:0.19, G:0.17, T:0.25
Consensus pattern (31 bp):
AAGTAGTGAAGAAAATCCATCTTAAGCCTTC
Found at i:279589 original size:72 final size:71
Alignment explanation
Indices: 279161--279667 Score: 396
Period size: 79 Copynumber: 6.9 Consensus size: 71
279151 GACTGGAGCA
* * *
279161 AATCAATCTTAAGCATTCACTGAAGAGTAGTGAAGCAAATCAATCTTAAGCCTTCACTGAAGAGT
1 AATCCATCTTAAGCCTTCACTG-AGAGTAGTGAAGC-AATCCATCTTAAGCCTTCACTGAAGAGT
279226 AGTGAAGC
64 AGTGAAGC
* * * **** ***
279234 AAATTCATCAGTAAGCCTTCCGACAATGATGATTAAGTCCTCCGGGCCATCTTAAGCCTTCACTG
1 -AATCCATC-TTAAGCCTT-C-AC--TGA-GAGT-AGTGAAGCAATCCATCTTAAGCCTTCACTG
279299 AAGAGTAGTGAAGC
58 AAGAGTAGTGAAGC
* *
279313 AAATCAATCTTAAGCCTTCACTGAAGAGTAGTGAAGCAAATCAATCTTAAGCCTTCACTGAAGAG
1 -AATCCATCTTAAGCCTTCACTG-AGAGTAGTGAAGC-AATCCATCTTAAGCCTTCACTGAAGAG
279378 TAGTGAAGC
63 TAGTGAAGC
* * * * ****
279387 AAATTCATCAGTAAACCTTCCGACAATGATGATTAAGTCCTCCAGA-CCATCTTAAGCCTTCACT
1 -AATCCATC-TTAAGCCTT-C-AC--TGA-GAGT-AGTGAAGCA-ATCCATCTTAAGCCTTCACT
* *
279451 GAAAAGTAGTGAAGAA
57 GAAGAGTAGTGAAG-C
* *
279467 AATCCGTCTTAAGCCTT--C--A-AGTAGTGAAGAAAATCCATCTTAAGCCTTCACTGAAGAGTA
1 AATCCATCTTAAGCCTTCACTGAGAGTAGTGAAG-CAATCCATCTTAAGCCTTCACTGAAGAGTA
279527 GTGAAGC
65 GTGAAGC
* * * * *
279534 GATCTATCCTAAGCCTTCACCTGAGAGTAGTGAAGCAATCCATCTTAAGCCTTCACCGGAGAGTA
1 AATCCATCTTAAGCCTTCA-CTGAGAGTAGTGAAGCAATCCATCTTAAGCCTTCACTGAAGAGTA
279599 GTGAAGC
65 GTGAAGC
* * * * * *
279606 AAACCATTTTAAGCCTTTACTGAAGAGTAGTGAAGTAAACCATCTTAAGCCTTCACCGAAGA
1 AATCCATCTTAAGCCTTCACTG-AGAGTAGTGAAGCAATCCATCTTAAGCCTTCACTGAAGA
279668 AATGGTGAAG
Statistics
Matches: 341, Mismatches: 65, Indels: 56
0.74 0.14 0.12
Matches are distributed among these distances:
67 17 0.05
68 34 0.10
70 2 0.01
71 3 0.01
72 84 0.25
73 14 0.04
74 51 0.15
75 15 0.04
76 4 0.01
77 5 0.01
78 17 0.05
79 86 0.25
80 9 0.03
ACGTcount: A:0.35, C:0.21, G:0.19, T:0.25
Consensus pattern (71 bp):
AATCCATCTTAAGCCTTCACTGAGAGTAGTGAAGCAATCCATCTTAAGCCTTCACTGAAGAGTAG
TGAAGC
Found at i:279893 original size:56 final size:55
Alignment explanation
Indices: 279680--280280 Score: 661
Period size: 54 Copynumber: 11.0 Consensus size: 55
279670 TGGTGAAGCA
* * *
279680 GAAGAAGA-TGTTCGAGTTCCATACTCCCTAGAGAAAGAGGGAGCGAACCCGTCTT
1 GAAGAAGATTATTCGAGTTCTATACTCCCTAAAGAAAGAGGGAGCGAACCCGT-TT
* * * * * **
279735 -CAGAAGATT-TTCGAGTTCCATACTCCCTAGAGAAAGGGGGAGCGAACCCATAA
1 GAAGAAGATTATTCGAGTTCTATACTCCCTAAAGAAAGAGGGAGCGAACCCGTTT
* * *
279788 GAAGAAGATTATTTGAGTTAC-ATACT-CCTGAAAGAAAGAGAGAGAGAACCCGTTT
1 GAAGAAGATTATTCGAGTT-CTATACTCCCT-AAAGAAAGAGGGAGCGAACCCGTTT
* * * * *
279843 GCAGAATATTATTTGAGTTCTATACTTCCTGAAAGAAAGAGGGAGCGAACCTGTTT
1 GAAGAAGATTATTCGAGTTCTATACTCCCT-AAAGAAAGAGGGAGCGAACCCGTTT
* *
279899 -ATAGAAGATTATTCGAGTTCTATACTTCCTAAAAGAAAGAGGGAGTGAACCCGTTT
1 GA-AGAAGATTATTCGAGTTCTATACTCCCT-AAAGAAAGAGGGAGCGAACCCGTTT
*
279955 GCAA-AAGATTATTCGAGTTCTATACTTCCTGAAAGAAAGAGGGAGCGAACCCGTTT
1 G-AAGAAGATTATTCGAGTTCTATACTCCCT-AAAGAAAGAGGGAGCGAACCCGTTT
*
280011 GAAAAAGATTATTCGAGTTCTATACTCCCTAAAGAAAGAGGGAGCGAACCCGTTT
1 GAAGAAGATTATTCGAGTTCTATACTCCCTAAAGAAAGAGGGAGCGAACCCGTTT
* * * **
280066 GCAGAAGATTATTCGAGTTCTATACTCCCTAGAGAAAGAGGGAGCAAACCCGTAA
1 GAAGAAGATTATTCGAGTTCTATACTCCCTAAAGAAAGAGGGAGCGAACCCGTTT
* *
280121 GAAGAAGA-TGTTCGAGTT-TCATACTCCCTATAGAAAGAGGGAGCGAACCCGTTT
1 GAAGAAGATTATTCGAGTTCT-ATACTCCCTAAAGAAAGAGGGAGCGAACCCGTTT
* * * * * * *
280175 GAAGAAGA-TGTCCGAGTTCCATACTCCCTATATAAAGAGGGGGAGAACCCGTTT
1 GAAGAAGATTATTCGAGTTCTATACTCCCTAAAGAAAGAGGGAGCGAACCCGTTT
* * * *
280229 GAAGAAGA-TGTCCGAGTTCTATACTCCCTGAAA-AATG-GGGAGCAAACCCGTT
1 GAAGAAGATTATTCGAGTTCTATACTCCCT-AAAGAAAGAGGGAGCGAACCCGTT
280281 AATCGAAGAT
Statistics
Matches: 481, Mismatches: 51, Indels: 30
0.86 0.09 0.05
Matches are distributed among these distances:
53 13 0.03
54 176 0.37
55 138 0.29
56 152 0.32
57 1 0.00
58 1 0.00
ACGTcount: A:0.34, C:0.18, G:0.24, T:0.23
Consensus pattern (55 bp):
GAAGAAGATTATTCGAGTTCTATACTCCCTAAAGAAAGAGGGAGCGAACCCGTTT
Found at i:279917 original size:111 final size:110
Alignment explanation
Indices: 279679--280280 Score: 656
Period size: 112 Copynumber: 5.5 Consensus size: 110
279669 ATGGTGAAGC
* *
279679 AGAAGAAGA-TGTTCGAGTTCCATACTCCCTAGAGAAAGAGGGAGCGAACCCGTCTT-CAGAAGA
1 AGAAGAAGATTATTCGAGTT-CATACTCCCTAAAGAAAGAGGGAGCGAACCCGT-TTGCAGAAGA
* * * *
279742 TT-TTCGAGTTCCATACTCCCTAGAGAAAGGGGGAGCGAACCC-ATA
64 TTATTCGAGTTCTATACTCCCTAAAGAAAGAGGGAGCGAACCCGTTA
* * * *
279787 AGAAGAAGATTATTTGAGTTACATACT-CCTGAAAGAAAGAGAGAGAGAACCCGTTTGCAGAATA
1 AGAAGAAGATTATTCGAGTT-CATACTCCCT-AAAGAAAGAGGGAGCGAACCCGTTTGCAGAAGA
* * * *
279851 TTATTTGAGTTCTATACTTCCTGAAAGAAAGAGGGAGCGAACCTGTTT
64 TTATTCGAGTTCTATACTCCCT-AAAGAAAGAGGGAGCGAACCCGTTA
* * * *
279899 A-TAGAAGATTATTCGAGTTCTATACTTCCTAAAAGAAAGAGGGAGTGAACCCGTTTGCAAAAGA
1 AGAAGAAGATTATTCGAGTTC-ATACTCCCT-AAAGAAAGAGGGAGCGAACCCGTTTGCAGAAGA
*
279963 TTATTCGAGTTCTATACTTCCTGAAAGAAAGAGGGAGCGAACCCGTT-
64 TTATTCGAGTTCTATACTCCCT-AAAGAAAGAGGGAGCGAACCCGTTA
* *
280010 TGAAAAAGATTATTCGAGTTCTATACTCCCTAAAGAAAGAGGGAGCGAACCCGTTTGCAGAAGAT
1 AGAAGAAGATTATTCGAGTTC-ATACTCCCTAAAGAAAGAGGGAGCGAACCCGTTTGCAGAAGAT
* *
280075 TATTCGAGTTCTATACTCCCTAGAGAAAGAGGGAGCAAACCCG-TA
65 TATTCGAGTTCTATACTCCCTAAAGAAAGAGGGAGCGAACCCGTTA
* * *
280120 AGAAGAAGA-TGTTCGAGTTTCATACTCCCTATAGAAAGAGGGAGCGAACCCGTTTGAAGAAGA-
1 AGAAGAAGATTATTCGAG-TTCATACTCCCTAAAGAAAGAGGGAGCGAACCCGTTTGCAGAAGAT
* * * * * * *
280183 TGTCCGAGTTCCATACTCCCTATATAAAGAGGGGGAGAACCCGTT-
65 TATTCGAGTTCTATACTCCCTAAAGAAAGAGGGAGCGAACCCGTTA
* * * * *
280228 TGAAGAAGA-TGTCCGAGTTCTATACTCCCTGAAA-AATG-GGGAGCAAACCCGTT
1 AGAAGAAGATTATTCGAGTTC-ATACTCCCT-AAAGAAAGAGGGAGCGAACCCGTT
280281 AATCGAAGAT
Statistics
Matches: 429, Mismatches: 51, Indels: 29
0.84 0.10 0.06
Matches are distributed among these distances:
107 17 0.04
108 76 0.18
109 93 0.22
110 47 0.11
111 91 0.21
112 105 0.24
ACGTcount: A:0.34, C:0.18, G:0.24, T:0.23
Consensus pattern (110 bp):
AGAAGAAGATTATTCGAGTTCATACTCCCTAAAGAAAGAGGGAGCGAACCCGTTTGCAGAAGATT
ATTCGAGTTCTATACTCCCTAAAGAAAGAGGGAGCGAACCCGTTA
Found at i:282206 original size:87 final size:87
Alignment explanation
Indices: 282060--282230 Score: 315
Period size: 87 Copynumber: 2.0 Consensus size: 87
282050 TTTTTTCGCG
*
282060 TGCTCGTTATAGTCACCGTAAGCCATTGACTTTTGTTTATTTCAATTTCGGTATGCGATTCTGAA
1 TGCTCGTTATAATCACCGTAAGCCATTGACTTTTGTTTATTTCAATTTCGGTATGCGATTCTGAA
282125 TACTTCCATTTTAGTCCCCGTA
66 TACTTCCATTTTAGTCCCCGTA
*
282147 TGCTCGTTATAATCACCGTAAGTCATTGACTTTTGTTTATTTCAATTTCGGTATGCGATTCTGAA
1 TGCTCGTTATAATCACCGTAAGCCATTGACTTTTGTTTATTTCAATTTCGGTATGCGATTCTGAA
*
282212 TGCTTCCATTTTAGTCCCC
66 TACTTCCATTTTAGTCCCC
282231 TTATTTTTTA
Statistics
Matches: 81, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
87 81 1.00
ACGTcount: A:0.20, C:0.22, G:0.16, T:0.42
Consensus pattern (87 bp):
TGCTCGTTATAATCACCGTAAGCCATTGACTTTTGTTTATTTCAATTTCGGTATGCGATTCTGAA
TACTTCCATTTTAGTCCCCGTA
Found at i:282953 original size:21 final size:21
Alignment explanation
Indices: 282927--283042 Score: 139
Period size: 21 Copynumber: 5.6 Consensus size: 21
282917 GTTTCCAGAT
* *
282927 TCGCAACGCGAACTTCGACTA
1 TCGCAATGCGAACTTGGACTA
282948 TCGCAATGCGAACTTGGACTA
1 TCGCAATGCGAACTTGGACTA
282969 TCGCAATGCGAACTTGGACTA
1 TCGCAATGCGAACTTGGACTA
* *
282990 TCGCAATGCGAA-TATGTA-AA
1 TCGCAATGCGAACT-TGGACTA
* *
283010 TCGCAATGCGATA-GTCGACTA
1 TCGCAATGCGA-ACTTGGACTA
283031 TCGCAATGCGAA
1 TCGCAATGCGAA
283043 TATGTAAATC
Statistics
Matches: 84, Mismatches: 8, Indels: 7
0.85 0.08 0.07
Matches are distributed among these distances:
20 16 0.19
21 68 0.81
ACGTcount: A:0.31, C:0.24, G:0.22, T:0.22
Consensus pattern (21 bp):
TCGCAATGCGAACTTGGACTA
Found at i:282980 original size:42 final size:41
Alignment explanation
Indices: 282927--283061 Score: 175
Period size: 41 Copynumber: 3.3 Consensus size: 41
282917 GTTTCCAGAT
* *
282927 TCGCAACGCGAACTTCGACTATCGCAATGCGAACT-TGGACTA
1 TCGCAATGCGAACTTCGACTATCGCAATGCGAA-TATGGA-AA
* *
282969 TCGCAATGCGAACTTGGACTATCGCAATGCGAATATGTAAA
1 TCGCAATGCGAACTTCGACTATCGCAATGCGAATATGGAAA
* *
283010 TCGCAATGCGATA-GTCGACTATCGCAATGCGAATATGTAAA
1 TCGCAATGCGA-ACTTCGACTATCGCAATGCGAATATGGAAA
283051 TCGCAATGCGA
1 TCGCAATGCGA
283062 TAGTCCAAAA
Statistics
Matches: 85, Mismatches: 6, Indels: 5
0.89 0.06 0.05
Matches are distributed among these distances:
41 50 0.59
42 35 0.41
ACGTcount: A:0.32, C:0.23, G:0.22, T:0.23
Consensus pattern (41 bp):
TCGCAATGCGAACTTCGACTATCGCAATGCGAATATGGAAA
Found at i:283014 original size:20 final size:20
Alignment explanation
Indices: 282989--283061 Score: 96
Period size: 20 Copynumber: 3.6 Consensus size: 20
282979 AACTTGGACT
282989 ATCGCAATGCGAATATGTAA
1 ATCGCAATGCGAATATGTAA
*
283009 ATCGCAATGCG-ATA-GTCGACT
1 ATCGCAATGCGAATATGT--A-A
283030 ATCGCAATGCGAATATGTAA
1 ATCGCAATGCGAATATGTAA
283050 ATCGCAATGCGA
1 ATCGCAATGCGA
283062 TAGTCCAAAA
Statistics
Matches: 46, Mismatches: 2, Indels: 10
0.79 0.03 0.17
Matches are distributed among these distances:
18 2 0.04
19 3 0.07
20 24 0.52
21 12 0.26
22 3 0.07
23 2 0.04
ACGTcount: A:0.36, C:0.19, G:0.22, T:0.23
Consensus pattern (20 bp):
ATCGCAATGCGAATATGTAA
Found at i:283073 original size:62 final size:62
Alignment explanation
Indices: 282947--283107 Score: 161
Period size: 62 Copynumber: 2.5 Consensus size: 62
282937 AACTTCGACT
* * *
282947 ATCGCAATGCGA-ACTTGGACTATCGCAATGCGAACTTGGACTATCGCAATGCGAATATGTAA
1 ATCGCAATGCGATA-GTCGACTATCGCAATGCGAACTTGGACAATCGCAATGCGAATATGTAA
*
283009 ATCGCAATGCGATAGTCGACTATCGCAATGCGAA-TATGTA-AATCGCAATGCG-ATA-GTCCAA
1 ATCGCAATGCGATAGTCGACTATCGCAATGCGAACT-TGGACAATCGCAATGCGAATATGT---A
283070 A
62 A
*
283071 ATCGCAATCATTGCGATAGTCGACTATCGCATTGCGA
1 ATCGC-A--A-TGCGATAGTCGACTATCGCAATGCGA
283108 TAGTCCAAAA
Statistics
Matches: 85, Mismatches: 5, Indels: 14
0.82 0.05 0.13
Matches are distributed among these distances:
59 2 0.02
60 3 0.04
61 12 0.14
62 40 0.47
63 2 0.02
65 1 0.01
66 25 0.29
ACGTcount: A:0.32, C:0.22, G:0.22, T:0.24
Consensus pattern (62 bp):
ATCGCAATGCGATAGTCGACTATCGCAATGCGAACTTGGACAATCGCAATGCGAATATGTAA
Found at i:283074 original size:21 final size:21
Alignment explanation
Indices: 283007--283123 Score: 96
Period size: 21 Copynumber: 5.4 Consensus size: 21
282997 GCGAATATGT
*
283007 AAATCGCAATGCGATAGTCGA
1 AAATCGCAATGCGATAGTCCA
**
283028 CTATCGCAATGCGAATATGT---
1 AAATCGCAATGCG-ATA-GTCCA
283048 AAATCGCAATGCGATAGTCCA
1 AAATCGCAATGCGATAGTCCA
*
283069 AAATCGCAATCATTGCGATAGTCGA
1 AAATCGC-A--A-TGCGATAGTCCA
** *
283094 CTATCGCATTGCGATAGTCCA
1 AAATCGCAATGCGATAGTCCA
283115 AAATCGCAA
1 AAATCGCAA
283124 CGACTGGTGA
Statistics
Matches: 75, Mismatches: 12, Indels: 18
0.71 0.11 0.17
Matches are distributed among these distances:
18 2 0.03
19 3 0.04
20 11 0.15
21 35 0.47
22 4 0.05
23 2 0.03
24 2 0.03
25 16 0.21
ACGTcount: A:0.35, C:0.22, G:0.20, T:0.23
Consensus pattern (21 bp):
AAATCGCAATGCGATAGTCCA
Found at i:283075 original size:41 final size:41
Alignment explanation
Indices: 282989--283078 Score: 153
Period size: 41 Copynumber: 2.2 Consensus size: 41
282979 AACTTGGACT
* **
282989 ATCGCAATGCGAATATGTAAATCGCAATGCGATAGTCGACT
1 ATCGCAATGCGAATATGTAAATCGCAATGCGATAGTCCAAA
283030 ATCGCAATGCGAATATGTAAATCGCAATGCGATAGTCCAAA
1 ATCGCAATGCGAATATGTAAATCGCAATGCGATAGTCCAAA
283071 ATCGCAAT
1 ATCGCAAT
283079 CATTGCGATA
Statistics
Matches: 46, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
41 46 1.00
ACGTcount: A:0.37, C:0.20, G:0.20, T:0.23
Consensus pattern (41 bp):
ATCGCAATGCGAATATGTAAATCGCAATGCGATAGTCCAAA
Found at i:283769 original size:6 final size:6
Alignment explanation
Indices: 283733--283832 Score: 165
Period size: 6 Copynumber: 17.5 Consensus size: 6
283723 GTCCGTCTCG
283733 GGTCG- GGTCG- GGTCG- GGTCG- GGTCG- GGTCGT GGTCGT GGTCGT
1 GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT
283776 GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT
1 GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT
283824 GGTCGT GGT
1 GGTCGT GGT
283833 AATACGTGTC
Statistics
Matches: 94, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
5 25 0.27
6 69 0.73
ACGTcount: A:0.00, C:0.17, G:0.53, T:0.30
Consensus pattern (6 bp):
GGTCGT
Found at i:283955 original size:20 final size:20
Alignment explanation
Indices: 283930--284002 Score: 87
Period size: 20 Copynumber: 3.6 Consensus size: 20
283920 TTTTGGACTA
*
283930 TCGCATTGCAATTTACATAT
1 TCGCATTGCGATTTACATAT
*
283950 TCGCATTGCGATAGT-CGACTA-
1 TCGCATTGCGAT-TTAC-A-TAT
283971 TCGCATTGCGATTTACATAT
1 TCGCATTGCGATTTACATAT
283991 TCGCATTGCGAT
1 TCGCATTGCGAT
284003 AGTCCAAGTT
Statistics
Matches: 45, Mismatches: 3, Indels: 10
0.78 0.05 0.17
Matches are distributed among these distances:
19 2 0.04
20 26 0.58
21 15 0.33
22 2 0.04
ACGTcount: A:0.25, C:0.22, G:0.18, T:0.36
Consensus pattern (20 bp):
TCGCATTGCGATTTACATAT
Found at i:283960 original size:41 final size:41
Alignment explanation
Indices: 283925--284006 Score: 155
Period size: 41 Copynumber: 2.0 Consensus size: 41
283915 TGCGATTTTG
283925 GACTATCGCATTGCAATTTACATATTCGCATTGCGATAGTC
1 GACTATCGCATTGCAATTTACATATTCGCATTGCGATAGTC
*
283966 GACTATCGCATTGCGATTTACATATTCGCATTGCGATAGTC
1 GACTATCGCATTGCAATTTACATATTCGCATTGCGATAGTC
284007 CAAGTTTGCA
Statistics
Matches: 40, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
41 40 1.00
ACGTcount: A:0.26, C:0.22, G:0.18, T:0.34
Consensus pattern (41 bp):
GACTATCGCATTGCAATTTACATATTCGCATTGCGATAGTC
Found at i:283976 original size:21 final size:20
Alignment explanation
Indices: 283949--284064 Score: 92
Period size: 21 Copynumber: 5.6 Consensus size: 20
283939 AATTTACATA
*
283949 TTCGCATTGCGATAGTCGAC
1 TTCGCATTGCGATAGTCAAC
*
283969 TATCGCATTGCGAT-TTACATA-
1 T-TCGCATTGCGATAGT-CA-AC
*
283990 TTCGCATTGCGATAGTCCAAG
1 TTCGCATTGCGATAGT-CAAC
* *
284011 TTTGCATTGCGATAGTCCAAG
1 TTCGCATTGCGATAGT-CAAC
* *
284032 TTCGCGTTGCGATAGTCGAAG
1 TTCGCATTGCGATAGTC-AAC
*
284053 TTCGCGTTGCGA
1 TTCGCATTGCGA
284065 ATCTGGAAAC
Statistics
Matches: 83, Mismatches: 7, Indels: 11
0.82 0.07 0.11
Matches are distributed among these distances:
20 16 0.19
21 66 0.80
22 1 0.01
ACGTcount: A:0.22, C:0.22, G:0.25, T:0.32
Consensus pattern (20 bp):
TTCGCATTGCGATAGTCAAC
Found at i:284018 original size:41 final size:41
Alignment explanation
Indices: 283930--284064 Score: 148
Period size: 41 Copynumber: 3.3 Consensus size: 41
283920 TTTTGGACTA
* * *
283930 TCGCATTGCAATTTACATATTCGCATTGCGATAGT-CGACT
1 TCGCATTGCGATTTACATATTCGCATTGCGATAGTCCAAGT
283970 ATCGCATTGCGATTTACATATTCGCATTGCGATAGTCCAAGT
1 -TCGCATTGCGATTTACATATTCGCATTGCGATAGTCCAAGT
* * * * *
284012 TTGCATTGCGATAGTCCA-AGTTCGCGTTGCGATAGTCGAAGT
1 TCGCATTGCGAT-TTACATA-TTCGCATTGCGATAGTCCAAGT
*
284054 TCGCGTTGCGA
1 TCGCATTGCGA
284065 ATCTGGAAAC
Statistics
Matches: 81, Mismatches: 10, Indels: 5
0.84 0.10 0.05
Matches are distributed among these distances:
41 46 0.57
42 35 0.43
ACGTcount: A:0.23, C:0.21, G:0.23, T:0.33
Consensus pattern (41 bp):
TCGCATTGCGATTTACATATTCGCATTGCGATAGTCCAAGT
Found at i:289018 original size:3 final size:3
Alignment explanation
Indices: 289010--289066 Score: 114
Period size: 3 Copynumber: 19.0 Consensus size: 3
289000 CTGTAATGTA
289010 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
289058 AAT AAT AAT
1 AAT AAT AAT
289067 TGATATCAGA
Statistics
Matches: 54, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 54 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:292637 original size:21 final size:21
Alignment explanation
Indices: 292590--292648 Score: 64
Period size: 21 Copynumber: 2.8 Consensus size: 21
292580 GCTAACGTAG
* * *
292590 CAGTTCACGATGCTGACGTGG
1 CAGTCCACGATGTTGACGTGA
**
292611 TGGTCCACGATGTTGACGTGA
1 CAGTCCACGATGTTGACGTGA
292632 CAGTCCACGATAGTTGA
1 CAGTCCACGAT-GTTGA
292649 TAACGTGGAA
Statistics
Matches: 30, Mismatches: 7, Indels: 1
0.79 0.18 0.03
Matches are distributed among these distances:
21 25 0.83
22 5 0.17
ACGTcount: A:0.22, C:0.22, G:0.31, T:0.25
Consensus pattern (21 bp):
CAGTCCACGATGTTGACGTGA
Found at i:296054 original size:31 final size:31
Alignment explanation
Indices: 296019--296083 Score: 121
Period size: 31 Copynumber: 2.1 Consensus size: 31
296009 TGCCCTTATA
296019 GTAGACTCAATTTATCATTTTCACCCCTATT
1 GTAGACTCAATTTATCATTTTCACCCCTATT
*
296050 GTAGACTCAATTTATCATTTTCGCCCCTATT
1 GTAGACTCAATTTATCATTTTCACCCCTATT
296081 GTA
1 GTA
296084 TTTTCATATT
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
31 33 1.00
ACGTcount: A:0.25, C:0.25, G:0.09, T:0.42
Consensus pattern (31 bp):
GTAGACTCAATTTATCATTTTCACCCCTATT
Found at i:296182 original size:14 final size:14
Alignment explanation
Indices: 296163--296209 Score: 51
Period size: 14 Copynumber: 3.3 Consensus size: 14
296153 TAAGTTAGAG
296163 TTTAGAGTTTATGA
1 TTTAGAGTTTATGA
*
296177 TTTAGAGGTTATGA
1 TTTAGAGTTTATGA
*
296191 GATTATG-GTTTATGA
1 -TTTA-GAGTTTATGA
296206 TTTA
1 TTTA
296210 TAATGTAGAG
Statistics
Matches: 27, Mismatches: 4, Indels: 4
0.77 0.11 0.11
Matches are distributed among these distances:
14 16 0.59
15 10 0.37
16 1 0.04
ACGTcount: A:0.28, C:0.00, G:0.23, T:0.49
Consensus pattern (14 bp):
TTTAGAGTTTATGA
Found at i:296457 original size:19 final size:20
Alignment explanation
Indices: 296435--296475 Score: 57
Period size: 19 Copynumber: 2.1 Consensus size: 20
296425 TTAAATAAAA
*
296435 AAATTAAATAACTT-AACTC
1 AAATTAAATAAATTCAACTC
*
296454 AAATTTAATAAATTCAACTC
1 AAATTAAATAAATTCAACTC
296474 AA
1 AA
296476 CTTGAAAAAA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
19 12 0.63
20 7 0.37
ACGTcount: A:0.54, C:0.15, G:0.00, T:0.32
Consensus pattern (20 bp):
AAATTAAATAAATTCAACTC
Found at i:296507 original size:14 final size:14
Alignment explanation
Indices: 296490--296538 Score: 89
Period size: 14 Copynumber: 3.5 Consensus size: 14
296480 AAAAAATCAA
296490 ATAAAATTAGAATT
1 ATAAAATTAGAATT
296504 ATAAAATTAGAATT
1 ATAAAATTAGAATT
*
296518 ATAAAATTGGAATT
1 ATAAAATTAGAATT
296532 ATAAAAT
1 ATAAAAT
296539 AAAATTCATT
Statistics
Matches: 34, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
14 34 1.00
ACGTcount: A:0.57, C:0.00, G:0.08, T:0.35
Consensus pattern (14 bp):
ATAAAATTAGAATT
Found at i:296570 original size:112 final size:109
Alignment explanation
Indices: 296469--296680 Score: 241
Period size: 112 Copynumber: 1.9 Consensus size: 109
296459 TAATAAATTC
* * *
296469 AACTCAACTTGAAAAAATCAAATAAAATTAGAATTATAA-AATT-AGAATT-ATAAAATTGGAAT
1 AACTCAA-TT-AAAAAATAAAATAAAATTA-AATT-TAATAATTAAAAATTAATAAAATTGAAAT
296531 TATAAAATAAAATTCATTTAAATTAAATAATTAAAAAATTCAAATAAA
62 TATAAAATAAAATTCATTTAAATTAAATAATTAAAAAATTCAAATAAA
* * * ** * *
296579 AATTGAATTATAAAATAAAATTCATTTAAATTTAATAATTCAAAAATTCAAATAAAATTTAAATT
1 AACTCAATTAAAAAATAAAATAAAATTAAATTTAATAATT-AAAAATT--AATAAAATTGAAATT
*
296644 ATAAAATAAAATTCATTTAAATTAAATAAATAAAAAA
63 ATAAAATAAAATTCATTTAAATTAAATAATTAAAAAA
296681 ATATTTGGAC
Statistics
Matches: 85, Mismatches: 11, Indels: 10
0.80 0.10 0.09
Matches are distributed among these distances:
106 3 0.04
107 8 0.09
108 14 0.16
109 7 0.08
110 5 0.06
112 48 0.56
ACGTcount: A:0.59, C:0.05, G:0.03, T:0.33
Consensus pattern (109 bp):
AACTCAATTAAAAAATAAAATAAAATTAAATTTAATAATTAAAAATTAATAAAATTGAAATTATA
AAATAAAATTCATTTAAATTAAATAATTAAAAAATTCAAATAAA
Found at i:296599 original size:56 final size:56
Alignment explanation
Indices: 296520--296680 Score: 268
Period size: 56 Copynumber: 2.9 Consensus size: 56
296510 TTAGAATTAT
296520 AAAATTGGAATTATAAAATAAAATTCATTTAAATTAAATAATTAAAAAATTCAAATA
1 AAAATT-GAATTATAAAATAAAATTCATTTAAATTAAATAATTAAAAAATTCAAATA
* *
296577 AAAATTGAATTATAAAATAAAATTCATTTAAATTTAATAATTCAAAAATTCAAATA
1 AAAATTGAATTATAAAATAAAATTCATTTAAATTAAATAATTAAAAAATTCAAATA
* * *
296633 AAATTTAAATTATAAAATAAAATTCATTTAAATTAAATAAATAAAAAA
1 AAAATTGAATTATAAAATAAAATTCATTTAAATTAAATAATTAAAAAA
296681 ATATTTGGAC
Statistics
Matches: 97, Mismatches: 7, Indels: 1
0.92 0.07 0.01
Matches are distributed among these distances:
56 91 0.94
57 6 0.06
ACGTcount: A:0.60, C:0.04, G:0.02, T:0.34
Consensus pattern (56 bp):
AAAATTGAATTATAAAATAAAATTCATTTAAATTAAATAATTAAAAAATTCAAATA
Found at i:300977 original size:209 final size:211
Alignment explanation
Indices: 300387--301199 Score: 1161
Period size: 209 Copynumber: 3.8 Consensus size: 211
300377 ATTTAAGAAT
* * *
300387 TAAATTGAACAAATATTAAATTATAAATAAAAAGTTAAATAAATTAAACAACACACATTGAAGAG
1 TAAATTGAACAAATATGAAATTACAAATAAAAATTTAAATAAATTAAACAACACACA-T-AAG-G
* ** * * *
300452 AGGTCAAATCGAAATAATTTTAAATTACGAGGTTTAAATTAATACAAAAAATACTAAATTATATC
63 -GATCAAATCGAAATAATTTTAAATTTTGAGGTTGAAATTAATACAAAAAGTACTAAATTATACC
* * * *
300517 CATTTAAAAAGTTATTGGCCAATTAAAAAAATA-AAATTAAGTAATAAGTATAGATCAATTTCAT
127 CATTTAAAAAGTTATGGGCCAATT-TAAAAATAGAAA-TAAGTAATAAGTATGGGTCAATTTCAT
* *
300581 ATACAAATAAAATTTGGATGAC
190 ATGCAAATAAAATTTGGAGGAC
* *
300603 TAAATTGAACAAATAAGAAATTACAAATAAAAGTTTAAATAAATTAAACAACACACATTGATGAG
1 TAAATTGAACAAATATGAAATTACAAATAAAAATTTAAATAAATTAAACAACACACA-T-A--AG
** * *
300668 GGATCAAATTAAAATAATTTTAAATTGTGATGTTGAAATTAATACAAAAAAGTACTAAATTATAC
62 GGATCAAATCGAAATAATTTTAAATTTTGAGGTTGAAATTAATAC-AAAAAGTACTAAATTATAC
* * * *
300733 TCATTTAAAAAGTTATGGGTCAATTTAAAAATAGAAATAAGTAATAAGTATGGGTAAATTCCATA
126 CCATTTAAAAAGTTATGGGCCAATTTAAAAATAGAAATAAGTAATAAGTATGGGTCAATTTCATA
300798 TGCAAATAAAATTTGGAGGAC
191 TGCAAATAAAATTTGGAGGAC
*
300819 TAAATTGAACAAATATGAAATTACAAATAAAAATTTAAATATATTAAACAACACA-A-AAGGGAT
1 TAAATTGAACAAATATGAAATTACAAATAAAAATTTAAATAAATTAAACAACACACATAAGGGAT
*
300882 CAAATCGAAATAATTTTAAATTTTGAGGTTAAAATTAATACAAAAAGTACTAAATTATACCCATT
66 CAAATCGAAATAATTTTAAATTTTGAGGTTGAAATTAATACAAAAAGTACTAAATTATACCCATT
* *
300947 TAAAAAGTTATGGGCCAATTTAAAAATAGAAATAAGTAACAAGTATGGGTCAATTTCATGTGCAA
131 TAAAAAGTTATGGGCCAATTTAAAAATAGAAATAAGTAATAAGTATGGGTCAATTTCATATGCAA
301012 ATAAAATTTGGAGGAC
196 ATAAAATTTGGAGGAC
* *
301028 TAAATTGAACAAATATGAAATTACAAATAAAAATTTAAATATATTAAACAACACA-A-AAAGGAT
1 TAAATTGAACAAATATGAAATTACAAATAAAAATTTAAATAAATTAAACAACACACATAAGGGAT
* *
301091 CAAATCGAAATAATTTTAAATTTTGAGGTTGAAATTAATACAAAATGTACTAAATTATACTCATT
66 CAAATCGAAATAATTTTAAATTTTGAGGTTGAAATTAATACAAAAAGTACTAAATTATACCCATT
* *
301156 TAAAAAGTTATGAGCCAA-TTAATAAATATAAATAAGTAATAAGT
131 TAAAAAGTTATGGGCCAATTTAA-AAATAGAAATAAGTAATAAGT
301200 TGAGAAAAAA
Statistics
Matches: 547, Mismatches: 45, Indels: 17
0.90 0.07 0.03
Matches are distributed among these distances:
208 4 0.01
209 259 0.47
210 42 0.08
212 1 0.00
215 1 0.00
216 195 0.36
217 43 0.08
218 2 0.00
ACGTcount: A:0.51, C:0.08, G:0.11, T:0.30
Consensus pattern (211 bp):
TAAATTGAACAAATATGAAATTACAAATAAAAATTTAAATAAATTAAACAACACACATAAGGGAT
CAAATCGAAATAATTTTAAATTTTGAGGTTGAAATTAATACAAAAAGTACTAAATTATACCCATT
TAAAAAGTTATGGGCCAATTTAAAAATAGAAATAAGTAATAAGTATGGGTCAATTTCATATGCAA
ATAAAATTTGGAGGAC
Found at i:301199 original size:425 final size:427
Alignment explanation
Indices: 300387--301199 Score: 1216
Period size: 425 Copynumber: 1.9 Consensus size: 427
300377 ATTTAAGAAT
* *
300387 TAAATTGAACAAATATTAAATTATAAATAAAAAGTTAAATAAATTAAACAACACACATTGAAGAG
1 TAAATTGAACAAATATGAAATTACAAATAAAAAGTTAAATAAATTAAACAACACACA-T-AAGAG
* * *
300452 AGGTCAAATCGAAATAATTTTAAATTACGAGGTTTAAATTAATACAAAAAATACTAAATTATATC
64 AGATCAAATCGAAATAATTTTAAATTACGAGGTTAAAATTAATACAAAAAATACTAAATTATACC
* *
300517 CATTTAAAAAGTTATTGGCCAATTAAAAAAATAAAATTAAGTAATAAGTATAGATCAATTTCATA
129 CATTTAAAAAGTTATGGGCCAATTAAAAAAATAAAATTAAGTAACAAGTATAGATCAATTTCATA
* *
300582 TACAAATAAAATTTGGATGACTAAATTGAACAAATAAGAAATTACAAATAAAAGTTTAAATAAAT
194 TACAAATAAAATTTGGAGGACTAAATTGAACAAATAAGAAATTACAAATAAAAATTTAAATAAAT
* * *
300647 TAAACAACACACATTGATGAGGGATCAAATTAAAATAATTTTAAATTGTGATGTTGAAATTAATA
259 TAAACAACACACA-T-A-GAAGGATCAAATCAAAATAATTTTAAATTGTGAGGTTGAAATTAATA
* *
300712 CAAAAAAGTACTAAATTATACTCATTTAAAAAGTTATGGGTCAATTTAAAAATAGAAATAAGTAA
321 CAAAAAAGTACTAAATTATACTCATTTAAAAAGTTATGAGCCAATTTAAAAATAGAAATAAGTAA
300777 TAAGTATGGGTAAATTCCATATGCAAATAAAATTTGGAGGAC
386 TAAGTATGGGTAAATTCCATATGCAAATAAAATTTGGAGGAC
* *
300819 TAAATTGAACAAATATGAAATTACAAATAAAAATTTAAATATATTAAACAACACA-A-AAG-G-G
1 TAAATTGAACAAATATGAAATTACAAATAAAAAGTTAAATAAATTAAACAACACACATAAGAGAG
** *
300880 ATCAAATCGAAATAATTTTAAATTTTGAGGTTAAAATTAATACAAAAAGTACTAAATTATACCCA
66 ATCAAATCGAAATAATTTTAAATTACGAGGTTAAAATTAATACAAAAAATACTAAATTATACCCA
* * * *
300945 TTTAAAAAGTTATGGGCCAATT-TAAAAATAGAAA-TAAGTAACAAGTATGGGTCAATTTCATGT
131 TTTAAAAAGTTATGGGCCAATTAAAAAAATA-AAATTAAGTAACAAGTATAGATCAATTTCATAT
* * *
301008 GCAAATAAAATTTGGAGGACTAAATTGAACAAATATGAAATTACAAATAAAAATTTAAATATATT
195 ACAAATAAAATTTGGAGGACTAAATTGAACAAATAAGAAATTACAAATAAAAATTTAAATAAATT
* *
301073 AAACAACACA-A-A-AAGGATCAAATCGAAATAATTTTAAATTTTGAGGTTGAAATTAATAC-AA
260 AAACAACACACATAGAAGGATCAAATCAAAATAATTTTAAATTGTGAGGTTGAAATTAATACAAA
* *
301134 AATGTACTAAATTATACTCATTTAAAAAGTTATGAGCCAA-TTAATAAATATAAATAAGTAATAA
325 AAAGTACTAAATTATACTCATTTAAAAAGTTATGAGCCAATTTAA-AAATAGAAATAAGTAATAA
301198 GT
389 GT
301200 TGAGAAAAAA
Statistics
Matches: 349, Mismatches: 30, Indels: 18
0.88 0.08 0.05
Matches are distributed among these distances:
417 4 0.01
418 59 0.17
419 42 0.12
421 1 0.00
424 1 0.00
425 102 0.29
426 84 0.24
427 1 0.00
428 3 0.01
431 1 0.00
432 51 0.15
ACGTcount: A:0.51, C:0.08, G:0.11, T:0.30
Consensus pattern (427 bp):
TAAATTGAACAAATATGAAATTACAAATAAAAAGTTAAATAAATTAAACAACACACATAAGAGAG
ATCAAATCGAAATAATTTTAAATTACGAGGTTAAAATTAATACAAAAAATACTAAATTATACCCA
TTTAAAAAGTTATGGGCCAATTAAAAAAATAAAATTAAGTAACAAGTATAGATCAATTTCATATA
CAAATAAAATTTGGAGGACTAAATTGAACAAATAAGAAATTACAAATAAAAATTTAAATAAATTA
AACAACACACATAGAAGGATCAAATCAAAATAATTTTAAATTGTGAGGTTGAAATTAATACAAAA
AAGTACTAAATTATACTCATTTAAAAAGTTATGAGCCAATTTAAAAATAGAAATAAGTAATAAGT
ATGGGTAAATTCCATATGCAAATAAAATTTGGAGGAC
Found at i:301232 original size:2 final size:2
Alignment explanation
Indices: 301225--301554 Score: 79
Period size: 2 Copynumber: 165.0 Consensus size: 2
301215 AACAACTTAG
* *
301225 AT AT AT AT AT AT AT AT AT AT AT A- AT AT AA ACT AT AT A- AT TT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A-T AT AT AT AT AT
* * * *
301266 AT AT AT AA AGT AT AT GT AT -T AT AT AT AT AA ACT AT AT AGT TT
1 AT AT AT AT A-T AT AT AT AT AT AT AT AT AT AT A-T AT AT A-T AT
* * * * *
301308 AT AT AT AT AT -T AT GT AT AA AGT AT AA ACT AT AT AT ACC AT GT
1 AT AT AT AT AT AT AT AT AT AT A-T AT AT A-T AT AT AT A-T AT AT
* *
301350 AT AA ACT AT A- AT ACT AT AT AGT TT AT AT AT GA- ACT AT -T GA-
1 AT AT A-T AT AT AT A-T AT AT A-T AT AT AT AT -AT A-T AT AT -AT
* * * * * *
301390 ACT AT AT AG AA ACT AC AT AGT TT AT GT AT AA AT -T AT AT AT GA-
1 A-T AT AT AT AT A-T AT AT A-T AT AT AT AT AT AT AT AT AT AT -AT
* * * * *
301432 AT -T AT AT AT AA ACT AT AC A- AT TT AT AT TT AT AT AT -T AT GT
1 AT AT AT AT AT AT A-T AT AT AT AT AT AT AT AT AT AT AT AT AT AT
* * *
301472 AT A- AT -T AT AA AT A- AT AT AT AT -T GT AT AA AT -T AT AT -T
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
* *
301508 AT AT AT AT AT AT AT AA AT -T AT AT AGT TT AT AT AT AT AT AGT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT A-T AT AT AT AT AT AT A-T AT
301551 AT AT
1 AT AT
301555 GGCTTAGGGT
Statistics
Matches: 233, Mismatches: 55, Indels: 80
0.63 0.15 0.22
Matches are distributed among these distances:
1 20 0.09
2 192 0.82
3 21 0.09
ACGTcount: A:0.46, C:0.04, G:0.05, T:0.45
Consensus pattern (2 bp):
AT
Found at i:301260 original size:22 final size:23
Alignment explanation
Indices: 301225--301317 Score: 99
Period size: 22 Copynumber: 4.3 Consensus size: 23
301215 AACAACTTAG
*
301225 ATATATATA-TATATATATATAT
1 ATATATAAACTATATATATATAT
301247 A-ATATAAACTATATA-AT-T-T
1 ATATATAAACTATATATATATAT
* *
301266 ATATATAAAGTATATGTAT-TAT
1 ATATATAAACTATATATATATAT
*
301288 ATATATAAACTATATAGTTTATAT
1 ATATATAAACTATATA-TATATAT
301312 ATATAT
1 ATATAT
301318 TATGTATAAA
Statistics
Matches: 59, Mismatches: 6, Indels: 10
0.79 0.08 0.13
Matches are distributed among these distances:
19 2 0.03
20 13 0.22
21 11 0.19
22 22 0.37
23 2 0.03
24 9 0.15
ACGTcount: A:0.48, C:0.02, G:0.03, T:0.46
Consensus pattern (23 bp):
ATATATAAACTATATATATATAT
Found at i:301325 original size:22 final size:24
Alignment explanation
Indices: 301226--301325 Score: 71
Period size: 25 Copynumber: 4.2 Consensus size: 24
301216 ACAACTTAGA
* *
301226 TATATATATATATATATATATAATA
1 TATATGTAT-TATATATATATAATG
* * * * *
301251 TAAACTATATAATTTATATATAAAG
1 TATA-TGTATTATATATATATAATG
*
301276 TATATGTATTATATATATA-AA-C
1 TATATGTATTATATATATATAATG
*
301298 TATATAGT-TTATATATATATTATG
1 TATAT-GTATTATATATATATAATG
301322 TATA
1 TATA
301326 AAGTATAAAC
Statistics
Matches: 59, Mismatches: 12, Indels: 9
0.74 0.15 0.11
Matches are distributed among these distances:
22 16 0.27
23 5 0.08
24 16 0.27
25 17 0.29
26 5 0.08
ACGTcount: A:0.47, C:0.02, G:0.04, T:0.47
Consensus pattern (24 bp):
TATATGTATTATATATATATAATG
Found at i:301425 original size:11 final size:11
Alignment explanation
Indices: 301411--301531 Score: 68
Period size: 11 Copynumber: 10.6 Consensus size: 11
301401 ACTACATAGT
*
301411 TTATGTATAAA
1 TTATATATAAA
*
301422 TTATATATGAA
1 TTATATATAAA
301433 TTATATATAAA
1 TTATATATAAA
* * *
301444 --CTATACAAT
1 TTATATATAAA
*
301453 TTATATTTATATA
1 TTATA--TATAAA
*
301466 TTATGTAT-AA
1 TTATATATAAA
*
301476 TTATAAATAATA
1 TTATATATAA-A
*
301488 TATATTGTATAAA
1 T-TA-TATATAAA
*
301501 TTATATTATATA
1 TTATA-TATAAA
301513 TATATATATAAA
1 T-TATATATAAA
301525 TTATATA
1 TTATATA
301532 GTTTATATAT
Statistics
Matches: 81, Mismatches: 19, Indels: 20
0.68 0.16 0.17
Matches are distributed among these distances:
9 6 0.07
10 7 0.09
11 32 0.40
12 16 0.20
13 15 0.19
14 5 0.06
ACGTcount: A:0.47, C:0.02, G:0.03, T:0.48
Consensus pattern (11 bp):
TTATATATAAA
Found at i:301477 original size:24 final size:25
Alignment explanation
Indices: 301450--301551 Score: 95
Period size: 24 Copynumber: 4.0 Consensus size: 25
301440 TAAACTATAC
301450 AATTTATATTTATATAT-TATGTAT
1 AATTTATATTTATATATATATGTAT
**
301474 AA-TTATAAATA-ATATATATTGTAT
1 AATTTATATTTATATATATA-TGTAT
* *
301498 AAATTATA-TTATATATATATATAT
1 AATTTATATTTATATATATATGTAT
301522 AAATTATATAGTTTATATATATATAGTAT
1 -AATT-TATA-TTTATATATATAT-GTAT
301551 A
1 A
301552 TATGGCTTAG
Statistics
Matches: 63, Mismatches: 6, Indels: 14
0.76 0.07 0.17
Matches are distributed among these distances:
22 4 0.06
23 9 0.14
24 15 0.24
25 15 0.24
26 4 0.06
28 13 0.21
29 3 0.05
ACGTcount: A:0.46, C:0.00, G:0.04, T:0.50
Consensus pattern (25 bp):
AATTTATATTTATATATATATGTAT
Found at i:301568 original size:7 final size:7
Alignment explanation
Indices: 301558--301616 Score: 64
Period size: 7 Copynumber: 8.4 Consensus size: 7
301548 TATATATGGC
301558 TTAGGGT
1 TTAGGGT
301565 TTAGGGT
1 TTAGGGT
**
301572 TTAATGT
1 TTAGGGT
301579 TTAGGGT
1 TTAGGGT
*
301586 GTAGGGT
1 TTAGGGT
301593 TTAGGGT
1 TTAGGGT
* *
301600 TTATGAT
1 TTAGGGT
*
301607 GTAGGGT
1 TTAGGGT
301614 TTA
1 TTA
301617 TATTTATATT
Statistics
Matches: 40, Mismatches: 12, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
7 40 1.00
ACGTcount: A:0.19, C:0.00, G:0.37, T:0.44
Consensus pattern (7 bp):
TTAGGGT
Found at i:301601 original size:21 final size:21
Alignment explanation
Indices: 301558--301616 Score: 73
Period size: 21 Copynumber: 2.8 Consensus size: 21
301548 TATATATGGC
* *
301558 TTAGGGTTTAGGGTTTAATGT
1 TTAGGGTGTAGGGTTTAAGGT
*
301579 TTAGGGTGTAGGGTTTAGGGT
1 TTAGGGTGTAGGGTTTAAGGT
* *
301600 TTATGATGTAGGGTTTA
1 TTAGGGTGTAGGGTTTA
301617 TATTTATATT
Statistics
Matches: 33, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
21 33 1.00
ACGTcount: A:0.19, C:0.00, G:0.37, T:0.44
Consensus pattern (21 bp):
TTAGGGTGTAGGGTTTAAGGT
Found at i:301664 original size:20 final size:20
Alignment explanation
Indices: 301639--301801 Score: 146
Period size: 22 Copynumber: 7.4 Consensus size: 20
301629 TATAAACTAC
*
301639 ATACTATAATTTATATTTAT
1 ATACTATAGTTTATATTTAT
*
301659 ATACTATATTTTATACTATTTAT
1 ATACTATA-GTT-TA-TATTTAT
301682 ATAAACTATAGTTTATATTTAT
1 AT--ACTATAGTTTATATTTAT
*
301704 ATACTATATTTTATACTATTTAT
1 ATACTATA-GTT-TA-TATTTAT
301727 ATAAACTATAGTTTATATTTAT
1 AT--ACTATAGTTTATATTTAT
* *
301749 ATATTATATTTTATACTATTTAT
1 ATACTATA-GTT-TA-TATTTAT
301772 ATAAACTATAGTTTATATTTAT
1 AT--ACTATAGTTTATATTTAT
301794 ATACTATA
1 ATACTATA
301802 TATATGAACT
Statistics
Matches: 120, Mismatches: 8, Indels: 30
0.76 0.05 0.19
Matches are distributed among these distances:
20 25 0.21
21 6 0.05
22 33 0.28
23 33 0.28
24 6 0.05
25 17 0.14
ACGTcount: A:0.39, C:0.06, G:0.02, T:0.53
Consensus pattern (20 bp):
ATACTATAGTTTATATTTAT
Found at i:301690 original size:25 final size:23
Alignment explanation
Indices: 301652--301802 Score: 149
Period size: 23 Copynumber: 6.7 Consensus size: 23
301642 CTATAATTTA
301652 TATTTATATACTATATTTTATAC
1 TATTTATATACTATATTTTATAC
*
301675 TATTTATATAAACTATA-GTT-TA-
1 TATTTATAT--ACTATATTTTATAC
301697 TATTTATATACTATATTTTATAC
1 TATTTATATACTATATTTTATAC
*
301720 TATTTATATAAACTATA-GTT-TA-
1 TATTTATAT--ACTATATTTTATAC
*
301742 TATTTATATATTATATTTTATAC
1 TATTTATATACTATATTTTATAC
*
301765 TATTTATATAAACTATA-GTT-TA-
1 TATTTATAT--ACTATATTTTATAC
301787 TATTTATATACTATAT
1 TATTTATATACTATAT
301803 ATATGAACTA
Statistics
Matches: 108, Mismatches: 7, Indels: 28
0.76 0.05 0.20
Matches are distributed among these distances:
20 17 0.16
21 4 0.04
22 31 0.29
23 33 0.31
24 6 0.06
25 17 0.16
ACGTcount: A:0.38, C:0.06, G:0.02, T:0.54
Consensus pattern (23 bp):
TATTTATATACTATATTTTATAC
Found at i:301697 original size:45 final size:45
Alignment explanation
Indices: 301641--301802 Score: 306
Period size: 45 Copynumber: 3.6 Consensus size: 45
301631 TAAACTACAT
*
301641 ACTATAATTTATATTTATATACTATATTTTATACTATTTATATAA
1 ACTATAGTTTATATTTATATACTATATTTTATACTATTTATATAA
301686 ACTATAGTTTATATTTATATACTATATTTTATACTATTTATATAA
1 ACTATAGTTTATATTTATATACTATATTTTATACTATTTATATAA
*
301731 ACTATAGTTTATATTTATATATTATATTTTATACTATTTATATAA
1 ACTATAGTTTATATTTATATACTATATTTTATACTATTTATATAA
301776 ACTATAGTTTATATTTATATACTATAT
1 ACTATAGTTTATATTTATATACTATAT
301803 ATATGAACTA
Statistics
Matches: 114, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
45 114 1.00
ACGTcount: A:0.38, C:0.06, G:0.02, T:0.54
Consensus pattern (45 bp):
ACTATAGTTTATATTTATATACTATATTTTATACTATTTATATAA
Found at i:301831 original size:31 final size:32
Alignment explanation
Indices: 301760--301844 Score: 104
Period size: 33 Copynumber: 2.7 Consensus size: 32
301750 TATTATATTT
* *
301760 TATACTATTTATATAAACTATAGTTTATATTTA
1 TATACTATATATATAAACTATAGTTTACA-TTA
*
301793 TATACTATATATATGAACTATAGTTTACA-TA
1 TATACTATATATATAAACTATAGTTTACATTA
301824 TGA-ACTATATATATAAA-TATA
1 T-ATACTATATATATAAACTATA
301845 TATATACTAA
Statistics
Matches: 47, Mismatches: 4, Indels: 5
0.84 0.07 0.09
Matches are distributed among these distances:
30 4 0.09
31 16 0.34
32 1 0.02
33 26 0.55
ACGTcount: A:0.44, C:0.07, G:0.05, T:0.45
Consensus pattern (32 bp):
TATACTATATATATAAACTATAGTTTACATTA
Found at i:301884 original size:18 final size:18
Alignment explanation
Indices: 301859--301974 Score: 103
Period size: 18 Copynumber: 6.2 Consensus size: 18
301849 TACTAAGGTT
*
301859 TATA-TTTATATATGAAC
1 TATAGTTTACATATGAAC
* *
301876 TATAGTTTACATATAAAT
1 TATAGTTTACATATGAAC
*
301894 TAT-GTTTATATACT-AAC
1 TATAGTTTACATA-TGAAC
*
301911 TATAGTTTACATATAAAC
1 TATAGTTTACATATGAAC
301929 TATAGTTAATATTTACATATGAAC
1 TATAG------TTTACATATGAAC
301953 TATAGTTTACATATGAAC
1 TATAGTTTACATATGAAC
301971 TATA
1 TATA
301975 TATATAAACT
Statistics
Matches: 82, Mismatches: 7, Indels: 19
0.76 0.06 0.18
Matches are distributed among these distances:
17 18 0.22
18 47 0.57
24 17 0.21
ACGTcount: A:0.41, C:0.09, G:0.07, T:0.43
Consensus pattern (18 bp):
TATAGTTTACATATGAAC
Found at i:301904 original size:35 final size:35
Alignment explanation
Indices: 301858--301966 Score: 121
Period size: 35 Copynumber: 2.9 Consensus size: 35
301848 ATACTAAGGT
*
301858 TTATATTTATATATGAACTATAGTTTACATATAAA
1 TTATGTTTATATATGAACTATAGTTTACATATAAA
301893 TTATGTTTATATACT-AACTATAGTTTACATATAAA
1 TTATGTTTATATA-TGAACTATAGTTTACATATAAA
*
301928 CTATAGTTAATATTTACATATGAACTATAGTTTACATAT
1 TTAT-GTT--TA--T--ATATGAACTATAGTTTACATAT
301967 GAACTATATA
Statistics
Matches: 63, Mismatches: 2, Indels: 11
0.83 0.03 0.14
Matches are distributed among these distances:
35 35 0.56
36 4 0.06
38 2 0.03
40 1 0.02
41 1 0.02
42 20 0.32
ACGTcount: A:0.40, C:0.08, G:0.06, T:0.45
Consensus pattern (35 bp):
TTATGTTTATATATGAACTATAGTTTACATATAAA
Found at i:301988 original size:55 final size:53
Alignment explanation
Indices: 301921--302088 Score: 160
Period size: 55 Copynumber: 3.1 Consensus size: 53
301911 TATAGTTTAC
*
301921 ATATAAACTATAGTTAATATTTACATA-TGAACTATAGTTTACATATGAACTATAT
1 ATATAAACTATAGTTAATATTTACATACT--A-TATAGGTTACATATGAACTATAT
* * * *
301976 ATATAAACTATAGTTGATATTTATATACTATATAGGTTACATGTGACCTATATAT
1 ATATAAACTATAGTTAATATTTACATACTATATAGGTTACATATGAAC--TATAT
* * * * *
302031 ATATATATACTATAGTTGATATTTATATACTATATA-ATATATATATAAACTATAT
1 ATATA-A-ACTATAGTTAATATTTACATACTATATAGGT-TACATATGAACTATAT
302086 ATA
1 ATA
302089 CTATATAATA
Statistics
Matches: 97, Mismatches: 10, Indels: 12
0.82 0.08 0.10
Matches are distributed among these distances:
53 15 0.15
54 1 0.01
55 43 0.44
56 3 0.03
57 35 0.36
ACGTcount: A:0.43, C:0.08, G:0.07, T:0.42
Consensus pattern (53 bp):
ATATAAACTATAGTTAATATTTACATACTATATAGGTTACATATGAACTATAT
Found at i:301995 original size:20 final size:19
Alignment explanation
Indices: 301972--302085 Score: 63
Period size: 20 Copynumber: 5.9 Consensus size: 19
301962 CATATGAACT
301972 ATATATATAAACTATAGTTG
1 ATATATATAAACTATA-TTG
* * *
301992 ATATTTATATACTATATAGG
1 ATATATATAAACTATAT-TG
* * * * *
302012 TTACATGTGACCTATA-T-
1 ATATATATAAACTATATTG
*
302029 ATATATATATACTATAGTTG
1 ATATATATAAACTATA-TTG
* *
302049 ATATTTATATACTATATAAT-
1 ATATATATAAACTATAT--TG
302069 ATATATATAAACTATAT
1 ATATATATAAACTATAT
302086 ATACTATATA
Statistics
Matches: 68, Mismatches: 20, Indels: 12
0.68 0.20 0.12
Matches are distributed among these distances:
17 10 0.15
19 3 0.04
20 54 0.79
21 1 0.01
ACGTcount: A:0.42, C:0.07, G:0.07, T:0.44
Consensus pattern (19 bp):
ATATATATAAACTATATTG
Found at i:302002 original size:77 final size:75
Alignment explanation
Indices: 301841--301995 Score: 190
Period size: 77 Copynumber: 2.1 Consensus size: 75
301831 TATATATAAA
* * * * *
301841 TATATATATACTAAGGTTTATATTTATATATGAACTATAGTTTACATATAAATTATGTTTATATA
1 TATATATAAACTAAGGTTAATATTTACATATGAACTATAGTTTACATATAAACTA-GTATATATA
301906 CTAACTATAGTT
65 C-AACTATAGTT
* *
301918 TACATATAAACTATA-GTTAATATTTACATATGAACTATAGTTTACATATGAACTA-TATATATA
1 TATATATAAACTA-AGGTTAATATTTACATATGAACTATAGTTTACATATAAACTAGTATATATA
301981 -AACTATAGTT
65 CAACTATAGTT
*
301991 GATAT
1 TATAT
301996 TTATATACTA
Statistics
Matches: 68, Mismatches: 9, Indels: 6
0.82 0.11 0.07
Matches are distributed among these distances:
73 13 0.19
75 7 0.10
77 47 0.69
78 1 0.01
ACGTcount: A:0.41, C:0.08, G:0.08, T:0.43
Consensus pattern (75 bp):
TATATATAAACTAAGGTTAATATTTACATATGAACTATAGTTTACATATAAACTAGTATATATAC
AACTATAGTT
Found at i:302031 original size:2 final size:2
Alignment explanation
Indices: 302024--302100 Score: 61
Period size: 2 Copynumber: 37.0 Consensus size: 2
302014 ACATGTGACC
*
302024 TA TA TA TA TA TA TA TA CTA TA GT- TGA TA TT TA TA TA CTA TA TA
1 TA TA TA TA TA TA TA TA -TA TA -TA T-A TA TA TA TA TA -TA TA TA
*
302067 -A TA TA TA TA TA AA CTA TA TA TA CTA TA TA -A TA TA
1 TA TA TA TA TA TA TA -TA TA TA TA -TA TA TA TA TA TA
302101 ATTTACATAT
Statistics
Matches: 62, Mismatches: 4, Indels: 18
0.74 0.05 0.21
Matches are distributed among these distances:
1 3 0.05
2 50 0.81
3 9 0.15
ACGTcount: A:0.47, C:0.05, G:0.03, T:0.45
Consensus pattern (2 bp):
TA
Found at i:302084 original size:57 final size:57
Alignment explanation
Indices: 301921--302096 Score: 175
Period size: 57 Copynumber: 3.1 Consensus size: 57
301911 TATAGTTTAC
* * * *
301921 ATATAAACTATAGTTAATATTTACATA-TGAACTATAGTTTACATATGAAC----TATAT
1 ATATAAACTATAGTTGATATTTATATACT--A-TATAGATTACATATAAACTATATATAT
* * * *
301976 ATATAAACTATAGTTGATATTTATATACTATATAGGTTACATGTGACCTATATATAT
1 ATATAAACTATAGTTGATATTTATATACTATATAGATTACATATAAACTATATATAT
* *
302033 ATATATACTATAGTTGATATTTATATACTATATA-ATATATATATAAACTATATATACT
1 ATATAAACTATAGTTGATATTTATATACTATATAGAT-TACATATAAACTATATATA-T
302091 ATATAA
1 ATATAA
302097 TATAATTTAC
Statistics
Matches: 102, Mismatches: 12, Indels: 11
0.82 0.10 0.09
Matches are distributed among these distances:
53 15 0.15
54 1 0.01
55 25 0.25
56 2 0.02
57 53 0.52
58 6 0.06
ACGTcount: A:0.43, C:0.08, G:0.07, T:0.42
Consensus pattern (57 bp):
ATATAAACTATAGTTGATATTTATATACTATATAGATTACATATAAACTATATATAT
Found at i:302178 original size:17 final size:17
Alignment explanation
Indices: 302156--302213 Score: 62
Period size: 17 Copynumber: 3.4 Consensus size: 17
302146 AAATATACAT
302156 TATATAGTTTATTAGTA
1 TATATAGTTTATTAGTA
*** *
302173 TATATAAACTATATAATA
1 TATATAGTTTAT-TAGTA
*
302191 TATATAGTTCATTAGTA
1 TATATAGTTTATTAGTA
302208 TATATA
1 TATATA
302214 AACTATATAT
Statistics
Matches: 31, Mismatches: 9, Indels: 2
0.74 0.21 0.05
Matches are distributed among these distances:
17 19 0.61
18 12 0.39
ACGTcount: A:0.43, C:0.03, G:0.07, T:0.47
Consensus pattern (17 bp):
TATATAGTTTATTAGTA
Found at i:302195 original size:35 final size:35
Alignment explanation
Indices: 302148--302373 Score: 175
Period size: 33 Copynumber: 6.4 Consensus size: 35
302138 AAACCCTAAA
*
302148 ATATACAT-TATATAGTTTATTAGTATATATAAACT
1 ATATA-ATATATATAGTTCATTAGTATATATAAACT
302183 ATATAATATATATAGTTCATTAGTATATATAAACT
1 ATATAATATATATAGTTCATTAGTATATATAAACT
* *
302218 ATAT-AT-TATATAGTTCATTACTATATATAAATT
1 ATATAATATATATAGTTCATTAGTATATATAAACT
* * * *
302251 ATATAGCATATATAAACTATACATTA-TATAGT-T-CATT
1 ATATA--ATATATATAGT-T-CATTAGTATA-TATAAACT
* *
302288 AGTATACATAACCTATATAG-T-ATATGGTATATACAAACT
1 A-TATA-AT-A--TATATAGTTCAT-TAGTATATATAAACT
*
302327 GTAT-AT-TATATAGTTCATTAGTATATATAAACT
1 ATATAATATATATAGTTCATTAGTATATATAAACT
*
302360 ATATAGTATATATA
1 ATATAATATATATA
302374 AATTATATAT
Statistics
Matches: 154, Mismatches: 17, Indels: 40
0.73 0.08 0.19
Matches are distributed among these distances:
32 7 0.05
33 46 0.30
34 7 0.05
35 41 0.27
36 6 0.04
37 15 0.10
38 19 0.12
39 8 0.05
40 5 0.03
ACGTcount: A:0.43, C:0.08, G:0.07, T:0.42
Consensus pattern (35 bp):
ATATAATATATATAGTTCATTAGTATATATAAACT
Found at i:302246 original size:17 final size:16
Alignment explanation
Indices: 302188--302246 Score: 50
Period size: 17 Copynumber: 3.6 Consensus size: 16
302178 AAACTATATA
302188 ATATATATAGTTCATT
1 ATATATATAGTTCATT
**
302204 AGTATATATA-AAC-TAT
1 A-TATATATAGTTCAT-T
302220 ATATTATATAGTTCATT
1 ATA-TATATAGTTCATT
302237 ACTATATATA
1 A-TATATATA
302247 AATTATATAG
Statistics
Matches: 33, Mismatches: 4, Indels: 11
0.69 0.08 0.23
Matches are distributed among these distances:
15 3 0.09
16 10 0.30
17 17 0.52
18 3 0.09
ACGTcount: A:0.42, C:0.07, G:0.05, T:0.46
Consensus pattern (16 bp):
ATATATATAGTTCATT
Found at i:302264 original size:51 final size:51
Alignment explanation
Indices: 302203--302385 Score: 231
Period size: 51 Copynumber: 3.5 Consensus size: 51
302193 TATAGTTCAT
*
302203 TAGTATATATAAACTATATATTATATAGTTCATTACTATATATAAATTATA
1 TAGTATATATAAACTATATATTATATAGTTCATTAGTATATATAAATTATA
* * *
302254 TAGCATATATAAACTATACATTATATAGTTCATTAGTATACATAACCTATATAGTA
1 TAGTATATATAAACTATATATTATATAGTTCATTAGTATATATAA---AT-TA-TA
* * *
302310 TATGGTATATACAAACTGTATATTATATAGTTCATTAGTATATATAAACTATA
1 TA--GTATATATAAACTATATATTATATAGTTCATTAGTATATATAAATTATA
*
302363 TAGTATATATAAATTATATATTA
1 TAGTATATATAAACTATATATTA
302386 ATTTATTAAT
Statistics
Matches: 112, Mismatches: 13, Indels: 14
0.81 0.09 0.10
Matches are distributed among these distances:
51 59 0.53
53 4 0.04
54 4 0.04
55 3 0.03
56 4 0.04
58 38 0.34
ACGTcount: A:0.44, C:0.08, G:0.07, T:0.42
Consensus pattern (51 bp):
TAGTATATATAAACTATATATTATATAGTTCATTAGTATATATAAATTATA
Found at i:302312 original size:58 final size:58
Alignment explanation
Indices: 302250--302371 Score: 181
Period size: 58 Copynumber: 2.1 Consensus size: 58
302240 ATATATAAAT
* *
302250 TATATAGCATATATAAACTATACATTATATAGTTCATTAGTATACATAACCTATATAG
1 TATATAGCATATACAAACTATACATTATATAGTTCATTAGTATACATAAACTATATAG
* * * * *
302308 TATATGGTATATACAAACTGTATATTATATAGTTCATTAGTATATATAAACTATATAG
1 TATATAGCATATACAAACTATACATTATATAGTTCATTAGTATACATAAACTATATAG
302366 TATATA
1 TATATA
302372 TAAATTATAT
Statistics
Matches: 56, Mismatches: 8, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
58 56 1.00
ACGTcount: A:0.43, C:0.09, G:0.08, T:0.40
Consensus pattern (58 bp):
TATATAGCATATACAAACTATACATTATATAGTTCATTAGTATACATAAACTATATAG
Found at i:302368 original size:18 final size:18
Alignment explanation
Indices: 302345--302382 Score: 67
Period size: 18 Copynumber: 2.1 Consensus size: 18
302335 TATAGTTCAT
302345 TAGTATATATAAACTATA
1 TAGTATATATAAACTATA
*
302363 TAGTATATATAAATTATA
1 TAGTATATATAAACTATA
302381 TA
1 TA
302383 TTAATTTATT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.50, C:0.03, G:0.05, T:0.42
Consensus pattern (18 bp):
TAGTATATATAAACTATA
Found at i:302494 original size:34 final size:33
Alignment explanation
Indices: 302456--302577 Score: 91
Period size: 34 Copynumber: 3.8 Consensus size: 33
302446 TGAACAAATT
302456 TTAAATATGAAGCTTAAATTAATAAATTATAACA
1 TTAAATATGAAGCTTAAATTAATAAATTA-AACA
* * *
302490 TTAAATTTG--GATTAAATT-A-AAA--AAA-G
1 TTAAATATGAAGCTTAAATTAATAAATTAAACA
*
302516 TTGAAATATGAAGCTTAAATTAATATATTAAATCA
1 TT-AAATATGAAGCTTAAATTAATAAATTAAA-CA
* *
302551 TTAATTTTGAA-C-TAAATTGAATAAATT
1 TTAAATATGAAGCTTAAATT-AATAAATT
302578 TAAAACTAAG
Statistics
Matches: 68, Mismatches: 10, Indels: 21
0.69 0.10 0.21
Matches are distributed among these distances:
26 2 0.03
27 8 0.12
28 1 0.01
29 8 0.12
30 4 0.06
31 3 0.04
32 14 0.21
33 11 0.16
34 15 0.22
35 2 0.03
ACGTcount: A:0.50, C:0.04, G:0.08, T:0.38
Consensus pattern (33 bp):
TTAAATATGAAGCTTAAATTAATAAATTAAACA
Found at i:302507 original size:61 final size:61
Alignment explanation
Indices: 302437--302578 Score: 178
Period size: 61 Copynumber: 2.3 Consensus size: 61
302427 AAATATATAA
* * *
302437 GGATCAAATTGAACAAATTTTAAATATGAAGCTTAAATTAATAAATTATAA-CATTAAATTT
1 GGATTAAATTGAAAAAATTTGAAATATGAAGCTTAAATTAATAAATTA-AATCATTAAATTT
* * * *
302498 GGATTAAATTAAAAAAAGTTGAAATATGAAGCTTAAATTAATATATTAAATCATTAATTTT
1 GGATTAAATTGAAAAAATTTGAAATATGAAGCTTAAATTAATAAATTAAATCATTAAATTT
* * *
302559 GAACTAAATTGAATAAATTT
1 GGATTAAATTGAAAAAATTT
302579 AAAACTAAGA
Statistics
Matches: 68, Mismatches: 12, Indels: 2
0.83 0.15 0.02
Matches are distributed among these distances:
60 2 0.03
61 66 0.97
ACGTcount: A:0.49, C:0.05, G:0.09, T:0.37
Consensus pattern (61 bp):
GGATTAAATTGAAAAAATTTGAAATATGAAGCTTAAATTAATAAATTAAATCATTAAATTT
Found at i:305678 original size:20 final size:20
Alignment explanation
Indices: 305640--305678 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
305630 CTATTTATTA
*
305640 ATTTAATTATCATAATAAAT
1 ATTTAATTATAATAATAAAT
* *
305660 ATTTTATTATAATATTAAA
1 ATTTAATTATAATAATAAA
305679 AAAGTAATCA
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.49, C:0.03, G:0.00, T:0.49
Consensus pattern (20 bp):
ATTTAATTATAATAATAAAT
Found at i:305837 original size:16 final size:16
Alignment explanation
Indices: 305811--305897 Score: 138
Period size: 16 Copynumber: 5.4 Consensus size: 16
305801 CGGATCATTT
*
305811 ACAGATCAGGTTAAAA
1 ACAGGTCAGGTTAAAA
*
305827 ATAGGTCAGGTTAAAA
1 ACAGGTCAGGTTAAAA
305843 ACAGGTCAGGTTAAAA
1 ACAGGTCAGGTTAAAA
305859 ACAGGTCAGGTTAAAA
1 ACAGGTCAGGTTAAAA
* *
305875 ACAAGTCAGGTTGAAA
1 ACAGGTCAGGTTAAAA
305891 ACAGGTC
1 ACAGGTC
305898 GGGTAATACC
Statistics
Matches: 65, Mismatches: 6, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
16 65 1.00
ACGTcount: A:0.44, C:0.13, G:0.24, T:0.20
Consensus pattern (16 bp):
ACAGGTCAGGTTAAAA
Found at i:310517 original size:62 final size:64
Alignment explanation
Indices: 310407--310542 Score: 186
Period size: 62 Copynumber: 2.2 Consensus size: 64
310397 TCTTTAACAT
* * *
310407 GTGCATCGATGCGCTACTCATGCATCGATACACAAATTACCTTCGATGTTTTCA-TTTTAAGGG
1 GTGCATCGATGCACTACTCATGCATCGATACACAAATTACATTCGATGTTTCCATTTTTAAGGG
* * * * *
310470 GTGCATCGATGCACT-CTTATGCATCGATACACTAATTGCATTTGATGTTTCCATTTTTAATGG
1 GTGCATCGATGCACTACTCATGCATCGATACACAAATTACATTCGATGTTTCCATTTTTAAGGG
310533 GTGCATCGAT
1 GTGCATCGAT
310543 ACACACTGAA
Statistics
Matches: 64, Mismatches: 8, Indels: 2
0.86 0.11 0.03
Matches are distributed among these distances:
62 32 0.50
63 32 0.50
ACGTcount: A:0.24, C:0.21, G:0.19, T:0.36
Consensus pattern (64 bp):
GTGCATCGATGCACTACTCATGCATCGATACACAAATTACATTCGATGTTTCCATTTTTAAGGG
Found at i:311084 original size:16 final size:15
Alignment explanation
Indices: 311063--311092 Score: 51
Period size: 16 Copynumber: 1.9 Consensus size: 15
311053 TGGCTTCCAC
311063 GAGAAGAAGAAGAAAG
1 GAGAAGAAG-AGAAAG
311079 GAGAAGAAGAGAAA
1 GAGAAGAAGAGAAA
311093 TCTGGAGAAA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 5 0.36
16 9 0.64
ACGTcount: A:0.63, C:0.00, G:0.37, T:0.00
Consensus pattern (15 bp):
GAGAAGAAGAGAAAG
Found at i:312307 original size:17 final size:17
Alignment explanation
Indices: 312236--312308 Score: 58
Period size: 17 Copynumber: 4.2 Consensus size: 17
312226 ACAAACTTGT
312236 TTTTAGGTTGTAACAATA
1 TTTTAGGTTGTAAC-ATA
*
312254 CTTTAGGTT-TAACATA
1 TTTTAGGTTGTAACATA
** ***
312270 TTTTTAGGTTACAATGGA
1 -TTTTAGGTTGTAACATA
*
312288 TTTTAGGTTGTAACCTA
1 TTTTAGGTTGTAACATA
312305 TTTT
1 TTTT
312309 TTAAGTTATA
Statistics
Matches: 42, Mismatches: 11, Indels: 5
0.72 0.19 0.09
Matches are distributed among these distances:
16 3 0.07
17 28 0.67
18 11 0.26
ACGTcount: A:0.27, C:0.08, G:0.16, T:0.48
Consensus pattern (17 bp):
TTTTAGGTTGTAACATA
Found at i:312333 original size:37 final size:37
Alignment explanation
Indices: 312258--312416 Score: 164
Period size: 37 Copynumber: 4.3 Consensus size: 37
312248 ACAATACTTT
* * * *
312258 AGGTT-TAACATA-TTTTTAGGTTACAATG-GATTTT
1 AGGTTGTAACCTATTTTTTAAGTTATAATGAGATTTA
312292 AGGTTGTAACCTATTTTTTAAGTTATAATGAGATTTA
1 AGGTTGTAACCTATTTTTTAAGTTATAATGAGATTTA
* * *
312329 AGGTTGTAACCTATTTTTCAGGTTATAATGGGATTTTA
1 AGGTTGTAACCTATTTTTTAAGTTATAATGAGA-TTTA
* * *
312367 A-GTTGTAGCCTATTTTTTTCAAAATTATAATGAGATTTT
1 AGGTTGTAACCTA-TTTTTT--AAGTTATAATGAGATTTA
312406 AGGTTGTAACC
1 AGGTTGTAACC
312417 ATATCATAGA
Statistics
Matches: 103, Mismatches: 14, Indels: 10
0.81 0.11 0.08
Matches are distributed among these distances:
34 5 0.05
35 6 0.06
36 14 0.14
37 45 0.44
38 10 0.10
39 4 0.04
40 19 0.18
ACGTcount: A:0.30, C:0.08, G:0.18, T:0.45
Consensus pattern (37 bp):
AGGTTGTAACCTATTTTTTAAGTTATAATGAGATTTA
Found at i:312415 original size:77 final size:72
Alignment explanation
Indices: 312255--312416 Score: 218
Period size: 77 Copynumber: 2.2 Consensus size: 72
312245 GTAACAATAC
* * *
312255 TTTAGGTT-TAACATATTTTTAGGTTACAATGGATTTTAGGTTGTAACCTATTTTTTAAGTTATA
1 TTTAGGTTGTAACCTATTTTTAGGTTACAATGGATTTTAAGTTGTAACCTATTTTTTAAATTATA
312319 ATGAGAT
66 ATGAGAT
* * *
312326 TTAAGGTTGTAACCTATTTTTCAGGTTATAATGGGATTTTAAGTTGTAGCCTATTTTTTTCAAAA
1 TTTAGGTTGTAACCTATTTTT-AGGTTACAAT-GGATTTTAAGTTGTAACCTA-TTTTTT--AAA
312391 TTATAATGAGAT
61 TTATAATGAGAT
312403 TTTAGGTTGTAACC
1 TTTAGGTTGTAACC
312417 ATATCATAGA
Statistics
Matches: 78, Mismatches: 7, Indels: 6
0.86 0.08 0.07
Matches are distributed among these distances:
71 7 0.09
72 11 0.14
73 9 0.12
74 18 0.23
75 6 0.08
77 27 0.35
ACGTcount: A:0.29, C:0.07, G:0.17, T:0.46
Consensus pattern (72 bp):
TTTAGGTTGTAACCTATTTTTAGGTTACAATGGATTTTAAGTTGTAACCTATTTTTTAAATTATA
ATGAGAT
Found at i:312434 original size:95 final size:91
Alignment explanation
Indices: 312334--312507 Score: 226
Period size: 95 Copynumber: 1.9 Consensus size: 91
312324 ATTTAAGGTT
* * *
312334 GTAACCTATTT-TTCAGGTTATAATGGGATTTTA-AGTTGTAGCCTATTTTTTTCAAAATTATAA
1 GTAACCTATTTCTT-AAGTTATAATGGAATTTTATA-TTGTAACCTA--TTTTT--AAATTATAA
*
312397 TGAGATTTTAGGTTGTAACCATATCATAGATA
60 TGAGATTTTAAGTTGTAACCATATCATAGATA
**
312429 GTAACCTATTTCTTAAGTTATAATGGAATTTTATATTGTAACCTATTTTTAGGTTATAATGAGAT
1 GTAACCTATTTCTTAAGTTATAATGGAATTTTATATTGTAACCTATTTTTAAATTATAATGAGAT
312494 TTTAAGTTGTAACC
66 TTTAAGTTGTAACC
312508 TATTTTTACG
Statistics
Matches: 71, Mismatches: 6, Indels: 8
0.84 0.07 0.09
Matches are distributed among these distances:
91 26 0.37
93 5 0.07
95 37 0.52
96 3 0.04
ACGTcount: A:0.32, C:0.09, G:0.15, T:0.44
Consensus pattern (91 bp):
GTAACCTATTTCTTAAGTTATAATGGAATTTTATATTGTAACCTATTTTTAAATTATAATGAGAT
TTTAAGTTGTAACCATATCATAGATA
Found at i:312496 original size:36 final size:35
Alignment explanation
Indices: 312429--312640 Score: 262
Period size: 36 Copynumber: 5.9 Consensus size: 35
312419 ATCATAGATA
* **
312429 GTAACCTATTTCTTAAGTTATAATGGAATTTTATATT
1 GTAACCTATTT-TTAGGTTATAATGG-ATTTTAGGTT
*
312466 GTAACCTATTTTTAGGTTATAATGAGATTTTAAGTT
1 GTAACCTATTTTTAGGTTATAATG-GATTTTAGGTT
*
312502 GTAACCTATTTTTACGTTATAATGGGATTTTAGGTT
1 GTAACCTATTTTTAGGTTATAAT-GGATTTTAGGTT
312538 GTAACCTATTTTTAGGTTATAATGAGATTTTAGGTT
1 GTAACCTATTTTTAGGTTATAATG-GATTTTAGGTT
* * *
312574 GTAACATACTTTTAGGTTATAACTGGATTTTTGGGTT
1 GTAACCTATTTTTAGGTTATAA-TGGA-TTTTAGGTT
* * *
312611 GTAACATGTTTTTAGGTTATAATTGATTTT
1 GTAACCTATTTTTAGGTTATAATGGATTTT
312641 TTAGGTAGTA
Statistics
Matches: 158, Mismatches: 12, Indels: 12
0.87 0.07 0.07
Matches are distributed among these distances:
35 5 0.03
36 110 0.70
37 43 0.27
ACGTcount: A:0.28, C:0.07, G:0.17, T:0.48
Consensus pattern (35 bp):
GTAACCTATTTTTAGGTTATAATGGATTTTAGGTT
Found at i:312610 original size:19 final size:18
Alignment explanation
Indices: 312473--312646 Score: 103
Period size: 18 Copynumber: 9.6 Consensus size: 18
312463 ATTGTAACCT
312473 ATTTTTAGGTTATAA-TG
1 ATTTTTAGGTTATAACTG
* * *
312490 AGATTTTAAGTTGTAACCT-
1 A-TTTTTAGGTTATAA-CTG
*
312509 ATTTTTACGTTATAA-TGGG
1 ATTTTTAGGTTATAACT--G
*
312528 A-TTTTAGGTTGTAACCT-
1 ATTTTTAGGTTATAA-CTG
312545 ATTTTTAGGTTATAA-TG
1 ATTTTTAGGTTATAACTG
* *
312562 AGATTTTAGGTTGTAACAT-
1 A-TTTTTAGGTTATAAC-TG
*
312581 ACTTTTAGGTTATAACTGG
1 ATTTTTAGGTTATAACT-G
* *
312600 ATTTTTGGGTTGTAACATG
1 ATTTTTAGGTTATAAC-TG
*
312619 -TTTTTAGGTTATAATTG
1 ATTTTTAGGTTATAACTG
312636 ATTTTTTAGGT
1 A-TTTTTAGGT
312647 AGTAAACCTG
Statistics
Matches: 120, Mismatches: 19, Indels: 34
0.69 0.11 0.20
Matches are distributed among these distances:
16 2 0.02
17 6 0.05
18 82 0.68
19 26 0.22
20 4 0.03
ACGTcount: A:0.26, C:0.05, G:0.20, T:0.49
Consensus pattern (18 bp):
ATTTTTAGGTTATAACTG
Found at i:312664 original size:19 final size:19
Alignment explanation
Indices: 312642--312681 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 19
312632 ATTGATTTTT
*
312642 TAGGTAGTAAACCTGATTG
1 TAGGTAGGAAACCTGATTG
* *
312661 TAGGTTGGAAACCTGTTTG
1 TAGGTAGGAAACCTGATTG
312680 TA
1 TA
312682 AGTTGGAAAT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.28, C:0.10, G:0.28, T:0.35
Consensus pattern (19 bp):
TAGGTAGGAAACCTGATTG
Found at i:312686 original size:19 final size:19
Alignment explanation
Indices: 312650--312690 Score: 64
Period size: 19 Copynumber: 2.2 Consensus size: 19
312640 TTTAGGTAGT
*
312650 AAACCTGATTGTAGGTTGG
1 AAACCTGATTGTAAGTTGG
*
312669 AAACCTGTTTGTAAGTTGG
1 AAACCTGATTGTAAGTTGG
312688 AAA
1 AAA
312691 TATATGTTAT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.32, C:0.10, G:0.27, T:0.32
Consensus pattern (19 bp):
AAACCTGATTGTAAGTTGG
Found at i:313535 original size:36 final size:36
Alignment explanation
Indices: 313495--313590 Score: 192
Period size: 36 Copynumber: 2.7 Consensus size: 36
313485 ATATATATAT
313495 TGATGTTTATAAGCATGATATACACTCGTTGGTTAC
1 TGATGTTTATAAGCATGATATACACTCGTTGGTTAC
313531 TGATGTTTATAAGCATGATATACACTCGTTGGTTAC
1 TGATGTTTATAAGCATGATATACACTCGTTGGTTAC
313567 TGATGTTTATAAGCATGATATACA
1 TGATGTTTATAAGCATGATATACA
313591 TGTGCTTGCT
Statistics
Matches: 60, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
36 60 1.00
ACGTcount: A:0.30, C:0.12, G:0.19, T:0.39
Consensus pattern (36 bp):
TGATGTTTATAAGCATGATATACACTCGTTGGTTAC
Found at i:313604 original size:36 final size:36
Alignment explanation
Indices: 313495--313626 Score: 180
Period size: 36 Copynumber: 3.7 Consensus size: 36
313485 ATATATATAT
*
313495 TGATGTTTATAAGCATGATATACACTCGTTGGTTAC
1 TGATGTTTATAAGCATGATATACACTCGTTGGCTAC
*
313531 TGATGTTTATAAGCATGATATACACTCGTTGGTTAC
1 TGATGTTTATAAGCATGATATACACTCGTTGGCTAC
*
313567 TGATGTTTATAAGCATGATATACA-T-GTGCTTGCTAC
1 TGATGTTTATAAGCATGATATACACTCGT--TGGCTAC
*
313603 TGAT-TATTATGAGCATGATATACA
1 TGATGT-TTATAAGCATGATATACA
313627 TGTGTTTGCT
Statistics
Matches: 90, Mismatches: 3, Indels: 6
0.91 0.03 0.06
Matches are distributed among these distances:
34 2 0.02
35 2 0.02
36 86 0.96
ACGTcount: A:0.30, C:0.13, G:0.19, T:0.39
Consensus pattern (36 bp):
TGATGTTTATAAGCATGATATACACTCGTTGGCTAC
Found at i:313627 original size:36 final size:36
Alignment explanation
Indices: 313564--313656 Score: 143
Period size: 36 Copynumber: 2.6 Consensus size: 36
313554 ACTCGTTGGT
*
313564 TACTGATGT-TTATAAGCATGATATACATGTGCTTGC
1 TACTGAT-TATTATGAGCATGATATACATGTGCTTGC
*
313600 TACTGATTATTATGAGCATGATATACATGTGTTTGC
1 TACTGATTATTATGAGCATGATATACATGTGCTTGC
*
313636 TATTGATTATTATGAGCATGA
1 TACTGATTATTATGAGCATGA
313657 AACAAATGCA
Statistics
Matches: 53, Mismatches: 3, Indels: 2
0.91 0.05 0.03
Matches are distributed among these distances:
35 1 0.02
36 52 0.98
ACGTcount: A:0.29, C:0.11, G:0.19, T:0.41
Consensus pattern (36 bp):
TACTGATTATTATGAGCATGATATACATGTGCTTGC
Found at i:322270 original size:36 final size:35
Alignment explanation
Indices: 322223--322421 Score: 136
Period size: 36 Copynumber: 5.9 Consensus size: 35
322213 GCAGATTGTA
*
322223 TGTCTCCCTTGAGACAGTTTCTCTTGAAACAAATTT
1 TGTCT-CCTTGAGATAGTTTCTCTTGAAACAAATTT
*
322259 TGTCTCGCTTGAGATAGTTTCTTTTGAAACATAA---
1 TGTCTC-CTTGAGATAGTTTCTCTTGAAACA-AATTT
* * * *
322293 --AC-CTTTGAGATTGTTTCTCTTAAAACAAATTT
1 TGTCTCCTTGAGATAGTTTCTCTTGAAACAAATTT
322325 TGTCTCTCTTGAGATAGTTTCTCTTGAAACATAA---
1 TGTCTC-CTTGAGATAGTTTCTCTTGAAACA-AATTT
* * * * *
322359 --AC-CTTTGAAATTGTTTATCTTGAAACAAATTT
1 TGTCTCCTTGAGATAGTTTCTCTTGAAACAAATTT
*
322391 TGTCTTGCTTGAGACTA-TTTCTCTTGAAACA
1 TGTC-TCCTTGAGA-TAGTTTCTCTTGAAACA
322422 TAAACCTTTG
Statistics
Matches: 123, Mismatches: 22, Indels: 36
0.68 0.12 0.20
Matches are distributed among these distances:
29 4 0.03
30 40 0.33
31 2 0.02
32 2 0.02
34 2 0.02
35 2 0.02
36 66 0.54
37 5 0.04
ACGTcount: A:0.28, C:0.17, G:0.14, T:0.42
Consensus pattern (35 bp):
TGTCTCCTTGAGATAGTTTCTCTTGAAACAAATTT
Found at i:322337 original size:66 final size:66
Alignment explanation
Indices: 322239--322537 Score: 336
Period size: 66 Copynumber: 4.5 Consensus size: 66
322229 CCTTGAGACA
* *
322239 GTTTCTCTTGAAACAAATTTTGTCTCGCTTGAGATAGTTTCTTTTGAAACATAAACCTTTGAGAT
1 GTTTCTCTTGAAACAAATTTTGTCTCTCTTGAGATAGTTTCTCTTGAAACATAAACCTTTGAGAT
322304 T
66 T
* *
322305 GTTTCTCTTAAAACAAATTTTGTCTCTCTTGAGATAGTTTCTCTTGAAACATAAACCTTTGAAAT
1 GTTTCTCTTGAAACAAATTTTGTCTCTCTTGAGATAGTTTCTCTTGAAACATAAACCTTTGAGAT
322370 T
66 T
*
322371 GTTTATCTTGAAACAAATTTTGTCT-TGCTTGAGACTA-TTTCTCTTGAAACATAAACCTTTGAG
1 GTTTCTCTTGAAACAAATTTTGTCTCT-CTTGAGA-TAGTTTCTCTTGAAACATAAACCTTTGAG
322434 ATT
64 ATT
* * ** * * * * * ** * *
322437 GTTTCTCTCGAAATAAAGTTTCATCTCGCTTGAGACACTTTCCCTTGAAGCCCAAA-TTTTGAGG
1 GTTTCTCTTGAAACAAA-TTTTGTCTCTCTTGAGATAGTTTCTCTTGAAACATAAACCTTTGAGA
322501 TT
65 TT
* * * *
322503 GTTTCACTTGAAGCAAA-ATTGATCTCACTTGAGAT
1 GTTTCTCTTGAAACAAATTTTG-TCTCTCTTGAGAT
322538 TATTTTCCTA
Statistics
Matches: 198, Mismatches: 29, Indels: 13
0.82 0.12 0.05
Matches are distributed among these distances:
64 1 0.01
65 12 0.06
66 156 0.79
67 29 0.15
ACGTcount: A:0.28, C:0.17, G:0.14, T:0.40
Consensus pattern (66 bp):
GTTTCTCTTGAAACAAATTTTGTCTCTCTTGAGATAGTTTCTCTTGAAACATAAACCTTTGAGAT
T
Found at i:332791 original size:31 final size:28
Alignment explanation
Indices: 332756--332818 Score: 81
Period size: 29 Copynumber: 2.1 Consensus size: 28
332746 TAGGTCCCTA
332756 AACTTTTACAAAGTTTATATTTTGGCCACTT
1 AACTTTT--AAAGTTTATATTTTGGCCAC-T
* *
332787 AACTTTTAAATTTTATATTTTGGTCACT
1 AACTTTTAAAGTTTATATTTTGGCCACT
332815 AACT
1 AACT
332819 AAAATTTTAG
Statistics
Matches: 30, Mismatches: 2, Indels: 3
0.86 0.06 0.09
Matches are distributed among these distances:
28 5 0.17
29 18 0.60
31 7 0.23
ACGTcount: A:0.30, C:0.14, G:0.08, T:0.48
Consensus pattern (28 bp):
AACTTTTAAAGTTTATATTTTGGCCACT
Found at i:335891 original size:59 final size:59
Alignment explanation
Indices: 335797--335989 Score: 245
Period size: 59 Copynumber: 3.3 Consensus size: 59
335787 ATACGCACCG
* * * * *
335797 TAGTGCTAA-CCCGAGTATGACACATAAGGTTGTGCCCACCATCTACACTAGTTATACAT
1 TAGTGC-AATCCCGAATATGACACATAAGGTCGTGCCCACCATATGCACTAGTTATACTT
335856 TAGTG-AAGTCCCGAATA-GAACACATAAGGTCGTGCCCACCATATGCACTA---ATACTT
1 TAGTGCAA-TCCCGAATATG-ACACATAAGGTCGTGCCCACCATATGCACTAGTTATACTT
* *
335912 TAGTGCAATCCCGAGTATGACACATAAGGTCATGCCCACCATATGCACTAGTTATACTT
1 TAGTGCAATCCCGAATATGACACATAAGGTCGTGCCCACCATATGCACTAGTTATACTT
*
335971 TAGTGCAATCCTGAATATG
1 TAGTGCAATCCCGAATATG
335990 CAGTCTGCTG
Statistics
Matches: 117, Mismatches: 9, Indels: 16
0.82 0.06 0.11
Matches are distributed among these distances:
56 48 0.41
57 5 0.04
58 1 0.01
59 63 0.54
ACGTcount: A:0.32, C:0.24, G:0.18, T:0.26
Consensus pattern (59 bp):
TAGTGCAATCCCGAATATGACACATAAGGTCGTGCCCACCATATGCACTAGTTATACTT
Found at i:338910 original size:18 final size:18
Alignment explanation
Indices: 338867--338943 Score: 59
Period size: 18 Copynumber: 4.3 Consensus size: 18
338857 ACAAACTTAT
338867 TTTTAGGTTGTAA-C-AA
1 TTTTAGGTTGTAACCTAA
338883 TATTTAAGGTTGTAACCTAA
1 T-TTT-AGGTTGTAACCTAA
* *****
338903 TTTTAGGTTATAATGGGG
1 TTTTAGGTTGTAACCTAA
*
338921 TTTTAGGTTGTAACCTAT
1 TTTTAGGTTGTAACCTAA
338939 TTTTA
1 TTTTA
338944 AAGTTATAAT
Statistics
Matches: 45, Mismatches: 12, Indels: 6
0.71 0.19 0.10
Matches are distributed among these distances:
16 1 0.02
17 3 0.07
18 34 0.76
19 4 0.09
20 3 0.07
ACGTcount: A:0.27, C:0.06, G:0.19, T:0.47
Consensus pattern (18 bp):
TTTTAGGTTGTAACCTAA
Found at i:338962 original size:37 final size:36
Alignment explanation
Indices: 338884--339118 Score: 294
Period size: 37 Copynumber: 6.4 Consensus size: 36
338874 TTGTAACAAT
* * *
338884 ATTTAAGGTTGTAACCTAATTTTAGGTTATAATGGG
1 ATTTTAGGTTGTAACCTATTTTTAAGTTATAATGGG
*
338920 GTTTTAGGTTGTAACCTATTTTTAAAGTTATAATGGG
1 ATTTTAGGTTGTAACCTATTTTT-AAGTTATAATGGG
* *
338957 ATTTTATGTTGTAA-CTATTTTTTTAAGTTATGATGGG
1 ATTTTAGGTTGTAACCTA--TTTTTAAGTTATAATGGG
* *
338994 ATTTTA-GTTGTAACCTATTTTTAGGTTATAATGAG
1 ATTTTAGGTTGTAACCTATTTTTAAGTTATAATGGG
* ***
339029 ATTTTAGGTTGTAACCTATTTCATAAGTTATAATATA
1 ATTTTAGGTTGTAACCTATTT-TTAAGTTATAATGGG
*
339066 ATTTTAGGTTGTAACCTATTTTTTAGGTTATAATGGG
1 ATTTTAGGTTGTAACCTA-TTTTTAAGTTATAATGGG
339103 ATTTTAGGTTGTAACC
1 ATTTTAGGTTGTAACC
339119 ATGTTTATAA
Statistics
Matches: 172, Mismatches: 20, Indels: 13
0.84 0.10 0.06
Matches are distributed among these distances:
35 21 0.12
36 44 0.26
37 99 0.58
38 8 0.05
ACGTcount: A:0.28, C:0.06, G:0.19, T:0.47
Consensus pattern (36 bp):
ATTTTAGGTTGTAACCTATTTTTAAGTTATAATGGG
Found at i:339017 original size:109 final size:110
Alignment explanation
Indices: 338884--339118 Score: 332
Period size: 109 Copynumber: 2.1 Consensus size: 110
338874 TTGTAACAAT
* * * *
338884 ATTTAAGGTTGTAACCTAATTTTAGGTTATAATGGGGTTTTAGGTTGTAACCTATTT-TTAAAGT
1 ATTTTAGGTTGTAACCTAATTTTAGGTTATAATGAGATTTTAGGTTGTAACCTATTTCAT-AAGT
* * * *
338948 TATAATGGGATTTTATGTTGTAA-CTATTTTTTTAAGTTATGATGGG
65 TATAATAGAATTTTAGGTTGTAACCTA-TTTTTTAAGTTATAATGGG
*
338994 ATTTTA-GTTGTAACCTATTTTTAGGTTATAATGAGATTTTAGGTTGTAACCTATTTCATAAGTT
1 ATTTTAGGTTGTAACCTAATTTTAGGTTATAATGAGATTTTAGGTTGTAACCTATTTCATAAGTT
* *
339058 ATAATATAATTTTAGGTTGTAACCTATTTTTTAGGTTATAATGGG
66 ATAATAGAATTTTAGGTTGTAACCTATTTTTTAAGTTATAATGGG
339103 ATTTTAGGTTGTAACC
1 ATTTTAGGTTGTAACC
339119 ATGTTTATAA
Statistics
Matches: 111, Mismatches: 11, Indels: 6
0.87 0.09 0.05
Matches are distributed among these distances:
109 93 0.84
110 18 0.16
ACGTcount: A:0.28, C:0.06, G:0.19, T:0.47
Consensus pattern (110 bp):
ATTTTAGGTTGTAACCTAATTTTAGGTTATAATGAGATTTTAGGTTGTAACCTATTTCATAAGTT
ATAATAGAATTTTAGGTTGTAACCTATTTTTTAAGTTATAATGGG
Found at i:339198 original size:36 final size:35
Alignment explanation
Indices: 339123--339206 Score: 87
Period size: 36 Copynumber: 2.3 Consensus size: 35
339113 GTAACCATGT
** * * *
339123 TTATAAGCATGATATACATGTGCTTGCTATTGATTA
1 TTAT-AGCATGATATACATGTAATTGCTACTAATAA
*
339159 TTATCAGCATGATATACATGTAATTTCTACTAATAA
1 TTAT-AGCATGATATACATGTAATTGCTACTAATAA
339195 TTATATGCATGA
1 TTATA-GCATGA
339207 CACACATGCT
Statistics
Matches: 40, Mismatches: 7, Indels: 2
0.82 0.14 0.04
Matches are distributed among these distances:
35 1 0.03
36 39 0.98
ACGTcount: A:0.35, C:0.12, G:0.13, T:0.40
Consensus pattern (35 bp):
TTATAGCATGATATACATGTAATTGCTACTAATAA
Found at i:347285 original size:134 final size:133
Alignment explanation
Indices: 347040--348513 Score: 1408
Period size: 134 Copynumber: 10.8 Consensus size: 133
347030 TAATGTTTAA
* *
347040 TTTCCAGATTTGATATTCCCTGAGTGACAGCGGAACAAGTCTGCCCCGATTCAATCTTTCCTGAG
1 TTTCAAGATTTGATATTCCCTGAGTGACAGCGGAACAAGTCTGCCCCGATTCAATCTTCCCTGAG
* * * *
347105 TGACAACGGAAAT-GATCAACTCCTCTAGATCTGATATTCCCTTCAGAAGAAGTGTG-ACATATC
66 TGACAGCGG-AATGGATCAACTCC-CCAGATCTGATATTCCCTTCAGAAGAAGCG-GAACAAATC
*
347168 TCTCTC
128 CCTCTC
* * * *
347174 ATTCAAGATTTGATATTCCCTGAGTGATAGCGGAACAAGTCTGTCCCGATTCAATCTTCTCTGAG
1 TTTCAAGATTTGATATTCCCTGAGTGACAGCGGAACAAGTCTGCCCCGATTCAATCTTCCCTGAG
* * * * * *
347239 TGATAGCAGAATGGATCAACTCTCCCATATATGATATTCTCTTCAGAAGAAGCGGAACAGATCCC
66 TGACAGCGGAATGGATCAACTC-CCCAGATCTGATATTCCCTTCAGAAGAAGCGGAACAAATCCC
347304 TCTC
130 TCTC
*** * *
347308 TTTCAAGATTTGATATTCCCTGAGTGACAATAGAATAAGTCTACCCCGATTCAATCTTCCCTATG
1 TTTCAAGATTTGATATTCCCTGAGTGACAGCGGAACAAGTCTGCCCCGATTCAATCTTCCC----
* * * * ** *
347373 TGACAGTGTGACAGCAGAGTGGATCAACTCACCAAAATCTGATATTTTCTTCAGAGGAAGCGGAA
62 TG--A--GTGACAGCGGAATGGATCAACTC-CCCAGATCTGATATTCCCTTCAGAAGAAGCGGAA
347438 CAAATCCCTCTC
122 CAAATCCCTCTC
* * * *
347450 TTTCAAGATTTGATATTCCCTGAGTGATAGTGGAACAAGTCTGCCCTGACTCAATCTTCCCTGAG
1 TTTCAAGATTTGATATTCCCTGAGTGACAGCGGAACAAGTCTGCCCCGATTCAATCTTCCCTGAG
* * * * *
347515 TGACAGCGGAATGGATCAACTTCCCCATATATGATATTCCCTTAAGAAGAAGCGGGACAAATCTC
66 TGACAGCGGAATGGATCAAC-TCCCCAGATCTGATATTCCCTTCAGAAGAAGCGGAACAAATCCC
347580 TCTC
130 TCTC
*
347584 TTTCAAGATTTGATATTCCCTGAGTGACAGCGGAATAAGTCTG-CCCGATTCAATCTTCCCTGAG
1 TTTCAAGATTTGATATTCCCTGAGTGACAGCGGAACAAGTCTGCCCCGATTCAATCTTCCCTGAG
* * * * * *
347648 TGACAGCGGAATAGATCAACTCCCCATATCTTATATTCCATTCAGAAGAAGCGGAACATATCCAT
66 TGACAGCGGAATGGATCAACTCCCCAGATCTGATATTCCCTTCAGAAGAAGCGGAACAAATCCCT
*
347713 TTC
131 CTC
* * * * * *
347716 TTTCAAGAATTGATATTCCTTGAGTGACAGGGGAACAAGTCTTCCCCGATTTAATCTTCTCTGAG
1 TTTCAAGATTTGATATTCCCTGAGTGACAGCGGAACAAGTCTGCCCCGATTCAATCTTCCCTGAG
* * * *
347781 TGATAGCGGAATGGATCAACTCACCCAGATCTAATATTCTCTTCAGAAGAAGTGGAACAAATCCC
66 TGACAGCGGAATGGATCAACTC-CCCAGATCTGATATTCCCTTCAGAAGAAGCGGAACAAATCCC
347846 TCTC
130 TCTC
*** * ** * * * * * *** **
347850 TTTCAAGATCAAATCCCTCTCTTTCAAGATTTGATATTCTCTGAGTGAC-AGTGGAATAAGTCTT
1 TTTCAAGATTTGAT--AT-TC---CCTGA-GTGACA---GC-G-G-AACAAGT---CT-GCCCCG
* * * * *
347914 CCTCGATTGAATCTTCCCTGAGTGACAGTGGAATGGATCGACCCCCCAGATCCGATATTCCCTTC
49 -----ATTCAATCTTCCCTGAGTGACAGCGGAATGGATCAACTCCCCAGATCTGATATTCCCTTC
** * *
347979 AGAAGAAGAAGAACATATCCCTCTA
109 AGAAGAAGCGGAACAAATCCCTCTC
* *
348004 TTTCAAGATTTGATATTCCCTGAGTGACAGCGGAACAAGTCTGCCCCGGTTCAATCTTCCATGAG
1 TTTCAAGATTTGATATTCCCTGAGTGACAGCGGAACAAGTCTGCCCCGATTCAATCTTCCCTGAG
* * * * *
348069 TGATAGTGGAATGGATCAACTCCTCTAGATCTGATATTCCCTTCAGAAAAAGCGGAACATATCCC
66 TGACAGCGGAATGGATCAACTCC-CCAGATCTGATATTCCCTTCAGAAGAAGCGGAACAAATCCC
348134 TCTC
130 TCTC
* * ** *
348138 TTTCAAGATTTGATATTCCTTGAGTAACAGCGGAACAAGTCTGCCTTGATTCAATATTCCCTGAG
1 TTTCAAGATTTGATATTCCCTGAGTGACAGCGGAACAAGTCTGCCCCGATTCAATCTTCCCTGAG
** * * * * * *
348203 TGACAATGAAATGGATCAATATCCCCAGATCTGATATTTCCTTTAGAAGAAGCGAAACAGATCCC
66 TGACAGCGGAATGGATCAA-CTCCCCAGATCTGATATTCCCTTCAGAAGAAGCGGAACAAATCCC
*
348268 TCTA
130 TCTC
* * *** * *
348272 TTCCAAGATTTGATATTCCTTGAGTGACAAAAGAACAAGTATGCCCCAATTCAATCTTCCCTGAG
1 TTTCAAGATTTGATATTCCCTGAGTGACAGCGGAACAAGTCTGCCCCGATTCAATCTTCCCTGAG
* * * * * * * *
348337 TGATAGCAGAATAGATCAACATCCCTAAATCTAATATTCCCTCCAGAATAAGCGGAACAAATCCC
66 TGACAGCGGAATGGATCAAC-TCCCCAGATCTGATATTCCCTTCAGAAGAAGCGGAACAAATCCC
348402 TCTC
130 TCTC
* * * * * *
348406 TTTCAAGATTTGATATTCCCTAAGTAACAGCGGAACCAGTCTGTCTCGATTCAATCTTCCCTAAG
1 TTTCAAGATTTGATATTCCCTGAGTGACAGCGGAACAAGTCTGCCCCGATTCAATCTTCCCTGAG
** *
348471 TGACAGCAAAATGGATCAACATCCCCCAGATATGATATTCCCT
66 TGACAGCGGAATGGATCAAC-T-CCCCAGATCTGATATTCCCT
348514 GAGTGAAAGC
Statistics
Matches: 1091, Mismatches: 208, Indels: 81
0.79 0.15 0.06
Matches are distributed among these distances:
132 77 0.07
133 115 0.11
134 634 0.58
135 22 0.02
136 2 0.00
137 2 0.00
138 5 0.00
139 1 0.00
140 4 0.00
141 6 0.01
142 119 0.11
143 1 0.00
144 1 0.00
145 1 0.00
146 4 0.00
147 6 0.01
148 3 0.00
149 1 0.00
150 1 0.00
151 2 0.00
152 1 0.00
154 50 0.05
155 33 0.03
ACGTcount: A:0.30, C:0.24, G:0.18, T:0.29
Consensus pattern (133 bp):
TTTCAAGATTTGATATTCCCTGAGTGACAGCGGAACAAGTCTGCCCCGATTCAATCTTCCCTGAG
TGACAGCGGAATGGATCAACTCCCCAGATCTGATATTCCCTTCAGAAGAAGCGGAACAAATCCCT
CTC
Found at i:347864 original size:21 final size:21
Alignment explanation
Indices: 347838--347879 Score: 84
Period size: 21 Copynumber: 2.0 Consensus size: 21
347828 AGAAGTGGAA
347838 CAAATCCCTCTCTTTCAAGAT
1 CAAATCCCTCTCTTTCAAGAT
347859 CAAATCCCTCTCTTTCAAGAT
1 CAAATCCCTCTCTTTCAAGAT
347880 TTGATATTCT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.29, C:0.33, G:0.05, T:0.33
Consensus pattern (21 bp):
CAAATCCCTCTCTTTCAAGAT
Found at i:348693 original size:3 final size:3
Alignment explanation
Indices: 348687--348737 Score: 70
Period size: 3 Copynumber: 17.3 Consensus size: 3
348677 ATAATAATAA
*
348687 TAT TAT TAT TAT TAT TAT TAT TAT TA- TAT TAAT TAA TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T-AT TAT TAT TAT TAT
348732 T-T TAT T
1 TAT TAT T
348738 TTTTATATCC
Statistics
Matches: 43, Mismatches: 2, Indels: 6
0.84 0.04 0.12
Matches are distributed among these distances:
2 4 0.09
3 36 0.84
4 3 0.07
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (3 bp):
TAT
Found at i:348856 original size:22 final size:23
Alignment explanation
Indices: 348799--348857 Score: 75
Period size: 23 Copynumber: 2.6 Consensus size: 23
348789 GTAGCCTAGA
* * *
348799 TACAAGCATACCCGGAGCCCAAT
1 TACAAGCAAACTCGGAGACCAAT
348822 TACAAGCAAACTCGGAGACCAAT
1 TACAAGCAAACTCGGAGACCAAT
*
348845 TAC-ATCAAACTCG
1 TACAAGCAAACTCG
348858 AAGCTTATCT
Statistics
Matches: 32, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
22 9 0.28
23 23 0.72
ACGTcount: A:0.39, C:0.31, G:0.15, T:0.15
Consensus pattern (23 bp):
TACAAGCAAACTCGGAGACCAAT
Found at i:353368 original size:31 final size:32
Alignment explanation
Indices: 353333--353394 Score: 99
Period size: 32 Copynumber: 2.0 Consensus size: 32
353323 TAAACTTATC
353333 TTTTTAG-TCAAAATAGATACCTAAAGTATTT
1 TTTTTAGATCAAAATAGATACCTAAAGTATTT
* *
353364 TTTTTTGATCAAAATAGGTACCTAAAGTATT
1 TTTTTAGATCAAAATAGATACCTAAAGTATT
353395 CAATTTTTTT
Statistics
Matches: 28, Mismatches: 2, Indels: 1
0.90 0.06 0.03
Matches are distributed among these distances:
31 6 0.21
32 22 0.79
ACGTcount: A:0.37, C:0.10, G:0.11, T:0.42
Consensus pattern (32 bp):
TTTTTAGATCAAAATAGATACCTAAAGTATTT
Found at i:368789 original size:23 final size:24
Alignment explanation
Indices: 368759--368804 Score: 67
Period size: 25 Copynumber: 1.9 Consensus size: 24
368749 AAATATAACA
*
368759 AAAATATAA-ATAATATAAATAAG
1 AAAATATAATATAATAAAAATAAG
368782 AAAATATAATTATAATAAAAATA
1 AAAATATAA-TATAATAAAAATA
368805 TATTTTATAT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
23 9 0.45
25 11 0.55
ACGTcount: A:0.70, C:0.00, G:0.02, T:0.28
Consensus pattern (24 bp):
AAAATATAATATAATAAAAATAAG
Found at i:371644 original size:10 final size:10
Alignment explanation
Indices: 371629--371673 Score: 56
Period size: 10 Copynumber: 4.6 Consensus size: 10
371619 ACATATTTTT
371629 AATAAATTAA
1 AATAAATTAA
*
371639 AATAAA-TAT
1 AATAAATTAA
*
371648 ATTAAATTAA
1 AATAAATTAA
*
371658 AATAAATTTA
1 AATAAATTAA
371668 AATAAA
1 AATAAA
371674 AATACATGGC
Statistics
Matches: 29, Mismatches: 5, Indels: 2
0.81 0.14 0.06
Matches are distributed among these distances:
9 7 0.24
10 22 0.76
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (10 bp):
AATAAATTAA
Found at i:373177 original size:48 final size:48
Alignment explanation
Indices: 373074--373293 Score: 312
Period size: 48 Copynumber: 4.7 Consensus size: 48
373064 CAAAATGCCA
* *
373074 TAAACCATGTATTCCATAAGCTCGTAAGCTTA-TTTACCAATATACCA
1 TAAACCATTTATTCCATAAGCTCGTAAGCTTATTTTACCAATATACCT
*
373121 TAAACCATTTATTCCATAAGCTCGTAAGATTATTTTACCAATATACCT
1 TAAACCATTTATTCCATAAGCTCGTAAGCTTATTTTACCAATATACCT
*
373169 TAAACCATTTATTCCATAAGCTCATAAGCTTATTTTACCAATATA-CT
1 TAAACCATTTATTCCATAAGCTCGTAAGCTTATTTTACCAATATACCT
* *
373216 T--ATCATTTAATCCCATAAGCTCGTAAGCTTATTTTACCAATATACC-
1 TAAACCATTT-ATTCCATAAGCTCGTAAGCTTATTTTACCAATATACCT
*
373262 T--GCCA-TTATTCCATAAGCTCGTAAGCTTATTT
1 TAAACCATTTATTCCATAAGCTCGTAAGCTTATTT
373294 GCCAGTTTAT
Statistics
Matches: 159, Mismatches: 11, Indels: 9
0.89 0.06 0.05
Matches are distributed among these distances:
44 24 0.15
45 8 0.05
46 36 0.23
47 34 0.21
48 57 0.36
ACGTcount: A:0.34, C:0.22, G:0.07, T:0.37
Consensus pattern (48 bp):
TAAACCATTTATTCCATAAGCTCGTAAGCTTATTTTACCAATATACCT
Found at i:373261 original size:94 final size:95
Alignment explanation
Indices: 373074--373293 Score: 310
Period size: 94 Copynumber: 2.4 Consensus size: 95
373064 CAAAATGCCA
* *
373074 TAAACCATGTATTCCATAAGCTCGTAAGCTTA-TTTACCAATATACCATAAACCATTTATTCCAT
1 TAAACCATTTATTCCATAAGCTCGTAAGCTTATTTTACCAATATACCATAAACCATTTATCCCAT
373138 AAGCTCGTAAGATTATTTTACCAATATACC
66 AAGCTCGTAAGATTATTTTACCAATATACC
* * *
373168 TTAAACCATTTATTCCATAAGCTCATAAGCTTATTTTACCAATATA-C-T-TATCATTTAATCCC
1 -TAAACCATTTATTCCATAAGCTCGTAAGCTTATTTTACCAATATACCATAAACCATTT-ATCCC
*
373230 ATAAGCTCGTAAGCTTATTTTACCAATATACC
64 ATAAGCTCGTAAGATTATTTTACCAATATACC
*
373262 T--GCCA-TTATTCCATAAGCTCGTAAGCTTATTT
1 TAAACCATTTATTCCATAAGCTCGTAAGCTTATTT
373294 GCCAGTTTAT
Statistics
Matches: 115, Mismatches: 8, Indels: 9
0.87 0.06 0.07
Matches are distributed among these distances:
90 26 0.23
91 3 0.03
93 7 0.06
94 36 0.31
95 31 0.27
96 12 0.10
ACGTcount: A:0.34, C:0.22, G:0.07, T:0.37
Consensus pattern (95 bp):
TAAACCATTTATTCCATAAGCTCGTAAGCTTATTTTACCAATATACCATAAACCATTTATCCCAT
AAGCTCGTAAGATTATTTTACCAATATACC
Found at i:377248 original size:9 final size:9
Alignment explanation
Indices: 377197--377280 Score: 55
Period size: 9 Copynumber: 9.3 Consensus size: 9
377187 AAGTGAAATA
377197 TTTTTTTCT
1 TTTTTTTCT
*
377206 ATTTTCTTCT
1 -TTTTTTTCT
* *
377216 TCTTCTTCT
1 TTTTTTTCT
* * *
377225 TCTTCTTCC
1 TTTTTTTCT
*
377234 TATTTTT-T
1 TTTTTTTCT
*
377242 TCTTTTTCT
1 TTTTTTTCT
*
377251 TTTTATTCAT
1 TTTTTTTC-T
377261 TTTTTTTCT
1 TTTTTTTCT
377270 TTTTTTT-T
1 TTTTTTTCT
377278 TTT
1 TTT
377281 ATATTATATT
Statistics
Matches: 62, Mismatches: 10, Indels: 6
0.79 0.13 0.08
Matches are distributed among these distances:
8 10 0.16
9 36 0.58
10 16 0.26
ACGTcount: A:0.05, C:0.17, G:0.00, T:0.79
Consensus pattern (9 bp):
TTTTTTTCT
Found at i:377251 original size:26 final size:25
Alignment explanation
Indices: 377206--377273 Score: 73
Period size: 26 Copynumber: 2.6 Consensus size: 25
377196 ATTTTTTTCT
* *
377206 ATTTTCTTCTTCTTCTTCTTCTTCTTC
1 ATTTT-TT-TTCTTTTTCTTCTTATTC
* *
377233 CTATTTTTTTCTTTTTCTTTTTATTC
1 AT-TTTTTTTCTTTTTCTTCTTATTC
377259 ATTTTTTTTCTTTTT
1 ATTTTTTTTCTTTTT
377274 TTTTTTTATA
Statistics
Matches: 35, Mismatches: 5, Indels: 4
0.80 0.11 0.09
Matches are distributed among these distances:
25 13 0.37
26 16 0.46
27 3 0.09
28 3 0.09
ACGTcount: A:0.06, C:0.19, G:0.00, T:0.75
Consensus pattern (25 bp):
ATTTTTTTTCTTTTTCTTCTTATTC
Found at i:377276 original size:28 final size:26
Alignment explanation
Indices: 377236--377294 Score: 66
Period size: 27 Copynumber: 2.2 Consensus size: 26
377226 CTTCTTCCTA
*
377236 TTTTTTTCTTTTTCTTTT-TATTCATTT
1 TTTTTTTCTTTTT-TTTTATATT-ATAT
*
377263 TTTTTCTTTTTTTTTTTTATATTATAT
1 TTTTT-TTCTTTTTTTTTATATTATAT
377290 TTTTT
1 TTTTT
377295 AGCTCTTATG
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
27 17 0.61
28 11 0.39
ACGTcount: A:0.10, C:0.07, G:0.00, T:0.83
Consensus pattern (26 bp):
TTTTTTTCTTTTTTTTTATATTATAT
Found at i:377719 original size:106 final size:106
Alignment explanation
Indices: 377534--377739 Score: 358
Period size: 106 Copynumber: 1.9 Consensus size: 106
377524 ACTCAATCGC
* * *
377534 AACCATTCAATACGAACCCATAGATACTAGATTAATGCCTTGATAACCATTAATATTGAATTTCA
1 AACCATTCAATACGAACCCATAGATACAAGATTAATGCCTTGATAACCATTAATATTGAAATCCA
*
377599 CCTCTCAATCTGGAGGTAACCCAAATAATAAATCTGGAGGT
66 CCTCTCAATATGGAGGTAACCCAAATAATAAATCTGGAGGT
*
377640 AACCATTCAATACGAACCCATAGATACAAGATTAATGCCTTGATAATCATTAATATTGAAATCCA
1 AACCATTCAATACGAACCCATAGATACAAGATTAATGCCTTGATAACCATTAATATTGAAATCCA
*
377705 CCTCTCCATATGGAGGTAACCCAAATAATAAATCT
66 CCTCTCAATATGGAGGTAACCCAAATAATAAATCT
377740 AAAAATACAT
Statistics
Matches: 94, Mismatches: 6, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
106 94 1.00
ACGTcount: A:0.39, C:0.21, G:0.12, T:0.28
Consensus pattern (106 bp):
AACCATTCAATACGAACCCATAGATACAAGATTAATGCCTTGATAACCATTAATATTGAAATCCA
CCTCTCAATATGGAGGTAACCCAAATAATAAATCTGGAGGT
Found at i:379188 original size:17 final size:17
Alignment explanation
Indices: 379166--379247 Score: 146
Period size: 17 Copynumber: 4.8 Consensus size: 17
379156 AAACGTGGGT
379166 ACTGTTCATTACTATTC
1 ACTGTTCATTACTATTC
379183 ACTGTTCATTACTATTC
1 ACTGTTCATTACTATTC
*
379200 ACTGTTTATTACTATTC
1 ACTGTTCATTACTATTC
*
379217 AATGTTCATTACTATTC
1 ACTGTTCATTACTATTC
379234 ACTGTTCATTACTA
1 ACTGTTCATTACTA
379248 CTATTACTAT
Statistics
Matches: 61, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 61 1.00
ACGTcount: A:0.26, C:0.21, G:0.06, T:0.48
Consensus pattern (17 bp):
ACTGTTCATTACTATTC
Found at i:379671 original size:48 final size:48
Alignment explanation
Indices: 379566--379784 Score: 292
Period size: 48 Copynumber: 4.7 Consensus size: 48
379556 CAAAATGCCA
*
379566 TAAACCATTTATTCCATAAGCTCGTAAGCTTA-TTTACCAATATACCG
1 TAAACCATTTATTCCATAAGCTCGTAAGCTTATTTTACCAATATACCT
* * * *
379613 TAAACAATTTATTCTATAAGCTCATAAGTTTATTTTACCAATATACCT
1 TAAACCATTTATTCCATAAGCTCGTAAGCTTATTTTACCAATATACCT
*
379661 TAAACCATTTATTCCATAAGCTCATAAGCTTATTTTACCAATATA-CT
1 TAAACCATTTATTCCATAAGCTCGTAAGCTTATTTTACCAATATACCT
* *
379708 T--ACCATTTAATCCCATAAGCTCGTAAGCTTATTTTACAAATATACCT
1 TAAACCATTT-ATTCCATAAGCTCGTAAGCTTATTTTACCAATATACCT
*
379755 T---CCA-TTATTCCATAAGCTCGTAAGTTTATT
1 TAAACCATTTATTCCATAAGCTCGTAAGCTTATT
379785 CGTCAGTTTA
Statistics
Matches: 156, Mismatches: 13, Indels: 9
0.88 0.07 0.05
Matches are distributed among these distances:
44 22 0.14
45 9 0.06
46 35 0.22
47 34 0.22
48 56 0.36
ACGTcount: A:0.34, C:0.21, G:0.06, T:0.38
Consensus pattern (48 bp):
TAAACCATTTATTCCATAAGCTCGTAAGCTTATTTTACCAATATACCT
Found at i:379682 original size:95 final size:93
Alignment explanation
Indices: 379566--379784 Score: 286
Period size: 94 Copynumber: 2.4 Consensus size: 93
379556 CAAAATGCCA
* *
379566 TAAACCATTTATTCCATAAGCTCGTAAGCTTATTTACCAATATACCGTAAACAATTT-ATTCTAT
1 TAAACCATTTATTCCATAAGCTCGTAAGCTTATTTACCAATATA-C-T-AACAATTTAATCCCAT
* *
379630 AAGCTCATAAGTTTATTTTACCAATATACCT
63 AAGCTCATAAGCTTATTTTACAAATATACCT
* * *
379661 TAAACCATTTATTCCATAAGCTCATAAGCTTATTTTACCAATATACTTACCATTTAATCCCATAA
1 TAAACCATTTATTCCATAAGCTCGTAAGCTTA-TTTACCAATATACTAACAATTTAATCCCATAA
*
379726 GCTCGTAAGCTTATTTTACAAATATACCT
65 GCTCATAAGCTTATTTTACAAATATACCT
*
379755 T---CCA-TTATTCCATAAGCTCGTAAGTTTATT
1 TAAACCATTTATTCCATAAGCTCGTAAGCTTATT
379785 CGTCAGTTTA
Statistics
Matches: 112, Mismatches: 10, Indels: 10
0.85 0.08 0.08
Matches are distributed among these distances:
89 2 0.02
90 22 0.20
91 3 0.03
93 6 0.05
94 35 0.31
95 32 0.29
96 12 0.11
ACGTcount: A:0.34, C:0.21, G:0.06, T:0.38
Consensus pattern (93 bp):
TAAACCATTTATTCCATAAGCTCGTAAGCTTATTTACCAATATACTAACAATTTAATCCCATAAG
CTCATAAGCTTATTTTACAAATATACCT
Found at i:383846 original size:3 final size:3
Alignment explanation
Indices: 383840--383902 Score: 74
Period size: 3 Copynumber: 20.7 Consensus size: 3
383830 TTTTTCTATT
* *
383840 TTC TTC TTC TTC GTC TTC TTC TTC TTC TTTC TATT TTC TTC TTC TT-
1 TTC TTC TTC TTC TTC TTC TTC TTC TTC -TTC T-TC TTC TTC TTC TTC
*
383886 TTC TTC TTC TTT TTC TT
1 TTC TTC TTC TTC TTC TT
383903 TTTATTCTTT
Statistics
Matches: 51, Mismatches: 6, Indels: 6
0.81 0.10 0.10
Matches are distributed among these distances:
2 2 0.04
3 44 0.86
4 5 0.10
ACGTcount: A:0.02, C:0.27, G:0.02, T:0.70
Consensus pattern (3 bp):
TTC
Found at i:383864 original size:28 final size:28
Alignment explanation
Indices: 383833--383902 Score: 79
Period size: 31 Copynumber: 2.4 Consensus size: 28
383823 CTCATTTTTT
383833 TTCTATTTTCTTCTTCTTCGTC-TTCTTC
1 TTCT-TTTTCTTCTTCTTCGTCTTTCTTC
* *
383861 TTCTTCTTTCTATTTTCTTCTTCTTTTCTTC
1 TTCTT-TTTCT-TCTTCTTCGTC-TTTCTTC
383892 TTCTTTTTCTT
1 TTCTTTTTCTT
383903 TTTATTCTTT
Statistics
Matches: 36, Mismatches: 2, Indels: 7
0.80 0.04 0.16
Matches are distributed among these distances:
27 1 0.03
28 9 0.25
29 10 0.28
30 5 0.14
31 11 0.31
ACGTcount: A:0.03, C:0.26, G:0.01, T:0.70
Consensus pattern (28 bp):
TTCTTTTTCTTCTTCTTCGTCTTTCTTC
Found at i:383903 original size:6 final size:6
Alignment explanation
Indices: 383830--383918 Score: 63
Period size: 6 Copynumber: 13.8 Consensus size: 6
383820 TCTCTCATTT
* *
383830 TTTTTC TATTTTC TTCTTC TTCGTCTTC TTCTTC TTCTTTC TATTTTC
1 TTTTTC T-TTTTC TTTTTC TT--T-TTC TTTTTC TT-TTTC T-TTTTC
* * *
383878 TTCTTC -TTTTC TTCTTC TTTTTC TTTTTA TTCTTTC TTTTT
1 TTTTTC TTTTTC TTTTTC TTTTTC TTTTTC TT-TTTC TTTTT
383919 ATTCTGTTTT
Statistics
Matches: 65, Mismatches: 10, Indels: 16
0.71 0.11 0.18
Matches are distributed among these distances:
5 4 0.06
6 35 0.54
7 20 0.31
8 1 0.02
9 5 0.08
ACGTcount: A:0.03, C:0.22, G:0.01, T:0.73
Consensus pattern (6 bp):
TTTTTC
Found at i:383904 original size:28 final size:29
Alignment explanation
Indices: 383833--383904 Score: 92
Period size: 28 Copynumber: 2.4 Consensus size: 29
383823 CTCATTTTTT
383833 TTCTATTTTCTTCTTCTTCGTCTTCTTCTTC
1 TTCT-TTTTCTT-TTCTTCGTCTTCTTCTTC
* * *
383864 TTCTTTCTATTTTCTTCTTCTT-TTCTTC
1 TTCTTTTTCTTTTCTTCGTCTTCTTCTTC
383892 TTCTTTTTCTTTT
1 TTCTTTTTCTTTT
383905 TATTCTTTCT
Statistics
Matches: 36, Mismatches: 5, Indels: 3
0.82 0.11 0.07
Matches are distributed among these distances:
28 17 0.47
29 10 0.28
30 5 0.14
31 4 0.11
ACGTcount: A:0.03, C:0.25, G:0.01, T:0.71
Consensus pattern (29 bp):
TTCTTTTTCTTTTCTTCGTCTTCTTCTTC
Found at i:383911 original size:43 final size:44
Alignment explanation
Indices: 383838--383923 Score: 113
Period size: 43 Copynumber: 2.0 Consensus size: 44
383828 TTTTTTTCTA
* *
383838 TTTTCTTCTTCTTCGTCTTCTTCTTCTTCTTTCTATTTTCTTCTTC
1 TTTTCTTCTTCTTC-TCTTCTTCTTATTCTTTCT-TTTTATTCTTC
*
383884 TTTTCTTCTTCTT-T-TTCTTTTTATTCTTTCTTTTTATTCT
1 TTTTCTTCTTCTTCTCTTCTTCTTATTCTTTCTTTTTATTCT
383924 GTTTTTATAT
Statistics
Matches: 37, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
42 8 0.22
43 15 0.41
44 1 0.03
46 13 0.35
ACGTcount: A:0.03, C:0.23, G:0.01, T:0.72
Consensus pattern (44 bp):
TTTTCTTCTTCTTCTCTTCTTCTTATTCTTTCTTTTTATTCTTC
Found at i:383915 original size:13 final size:13
Alignment explanation
Indices: 383897--383923 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
383887 TCTTCTTCTT
383897 TTTCTTTTTATTC
1 TTTCTTTTTATTC
383910 TTTCTTTTTATTC
1 TTTCTTTTTATTC
383923 T
1 T
383924 GTTTTTATAT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.07, C:0.15, G:0.00, T:0.78
Consensus pattern (13 bp):
TTTCTTTTTATTC
Found at i:389141 original size:22 final size:24
Alignment explanation
Indices: 389096--389144 Score: 66
Period size: 22 Copynumber: 2.1 Consensus size: 24
389086 TTTGGATCTG
*
389096 TTTGGGCCTCAGGTCTAGGTTTTA
1 TTTGGGCCTCAGGTCTAGGGTTTA
*
389120 TTTGGGCCT-A-GTTTAGGGTTTA
1 TTTGGGCCTCAGGTCTAGGGTTTA
389142 TTT
1 TTT
389145 TAGGTCTATT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
22 13 0.57
23 1 0.04
24 9 0.39
ACGTcount: A:0.12, C:0.12, G:0.29, T:0.47
Consensus pattern (24 bp):
TTTGGGCCTCAGGTCTAGGGTTTA
Found at i:389615 original size:91 final size:91
Alignment explanation
Indices: 389515--390018 Score: 697
Period size: 91 Copynumber: 5.5 Consensus size: 91
389505 GAAAATATTA
* *
389515 TTCTCATTATGAACTTCTTCTCCCACATTGGATTAGTTCTTCTCATTATGAACTCTCCACTGGAA
1 TTCTCATTATGAACTTCTTCTCCCTCATTGGATGAGTTCTTCTCATTATGAACTCTCCACTGGAA
*
389580 ATGTTGAGCCAAGGTTGAACAAGTTT
66 ATGTTGAGCCAAGGTTGAACAAGTTC
* ** * * * *
389606 TTCTCATTATGAATTTCTTCTCCCTCATCAGATTAATTATGCTCATTATGAACTCTCCACTGGAA
1 TTCTCATTATGAACTTCTTCTCCCTCATTGGATGAGTTCTTCTCATTATGAACTCTCCACTGGAA
389671 ATGTTGAGCCAAGGTTGAACAAGTTC
66 ATGTTGAGCCAAGGTTGAACAAGTTC
* * *
389697 TTCTCATTATGAATTTCTCCTCCCTCGTTGGATGAGTTCTTCTCATTATGAACTCTCCACTGGAA
1 TTCTCATTATGAACTTCTTCTCCCTCATTGGATGAGTTCTTCTCATTATGAACTCTCCACTGGAA
* * *
389762 ATATTGAACCAAAGTTGAACAAGTTC
66 ATGTTGAGCCAAGGTTGAACAAGTTC
* * *
389788 TTCTCATTATGAACTTTTTCTCCCTTATTGGATGAATTCTTCTCATTATGAACTCTCCACTGGAA
1 TTCTCATTATGAACTTCTTCTCCCTCATTGGATGAGTTCTTCTCATTATGAACTCTCCACTGGAA
* ** *
389853 ATATTGAGCCAAATTTGAAAAAGTTC
66 ATGTTGAGCCAAGGTTGAACAAGTTC
* * *
389879 TTCTCATTATGAATTTATTCTCCCT-ATTGGAT-ATGTTCTTCTCATTATGAAATCTCCACTGGA
1 TTCTCATTATGAACTTCTTCTCCCTCATTGGATGA-GTTCTTCTCATTATGAACTCTCCACTGGA
* *
389942 AATGTTTAGCCAAGGTTAAACAAGTTC
65 AATGTTGAGCCAAGGTTGAACAAGTTC
* * * *
389969 TTATCATTATGAACTTCTCCTCCCTCGTTGGATGAGTTCTTATCATTATG
1 TTCTCATTATGAACTTCTTCTCCCTCATTGGATGAGTTCTTCTCATTATG
390019 TTCTTCTCAT
Statistics
Matches: 366, Mismatches: 44, Indels: 6
0.88 0.11 0.01
Matches are distributed among these distances:
89 1 0.00
90 76 0.21
91 288 0.79
92 1 0.00
ACGTcount: A:0.26, C:0.21, G:0.14, T:0.38
Consensus pattern (91 bp):
TTCTCATTATGAACTTCTTCTCCCTCATTGGATGAGTTCTTCTCATTATGAACTCTCCACTGGAA
ATGTTGAGCCAAGGTTGAACAAGTTC
Found at i:391017 original size:19 final size:19
Alignment explanation
Indices: 390990--391063 Score: 69
Period size: 19 Copynumber: 3.7 Consensus size: 19
390980 TCTCATTCTC
*
390990 TTTTCCTTTTCTTTTGCTTT-
1 TTTT-CTTTTATTTT-CTTTA
*
391010 TTTTCTTTTATTTTTCTTTTC
1 TTTTCTTTTA-TTTTC-TTTA
*
391031 TTTTCTTTTATTTTATTTA
1 TTTTCTTTTATTTTCTTTA
*
391050 TTTTCTTTTCTTTT
1 TTTTCTTTTATTTT
391064 TTTTCCTTTT
Statistics
Matches: 47, Mismatches: 4, Indels: 7
0.81 0.07 0.12
Matches are distributed among these distances:
19 22 0.47
20 15 0.32
21 10 0.21
ACGTcount: A:0.05, C:0.14, G:0.01, T:0.80
Consensus pattern (19 bp):
TTTTCTTTTATTTTCTTTA
Found at i:391018 original size:5 final size:5
Alignment explanation
Indices: 390988--391073 Score: 72
Period size: 5 Copynumber: 17.2 Consensus size: 5
390978 CCTCTCATTC
*
390988 TCTTT TCCTTT TCTTT TGC-TT T-TTT TCTTT TATTTT TCTTT TCTTT
1 TCTTT T-CTTT TCTTT T-CTTT TCTTT TCTTT T-CTTT TCTTT TCTTT
* * *
391034 TCTTT TATTT T-ATT TATTT TCTTT TCTTT T-TTT TCCTTT T
1 TCTTT TCTTT TCTTT TCTTT TCTTT TCTTT TCTTT T-CTTT T
391074 TCTTCTTAGG
Statistics
Matches: 67, Mismatches: 6, Indels: 15
0.76 0.07 0.17
Matches are distributed among these distances:
4 10 0.15
5 43 0.64
6 14 0.21
ACGTcount: A:0.05, C:0.15, G:0.01, T:0.79
Consensus pattern (5 bp):
TCTTT
Found at i:391031 original size:30 final size:30
Alignment explanation
Indices: 390990--391067 Score: 101
Period size: 30 Copynumber: 2.7 Consensus size: 30
390980 TCTCATTCTC
*
390990 TTTTCCTTTTCTTTTGCTTTT-TTTCT-TTTA
1 TTTTTCTTTTCTTTT-CTTTTATTT-TATTTA
391020 TTTTTCTTTTCTTTTCTTTTATTTTATTTA
1 TTTTTCTTTTCTTTTCTTTTATTTTATTTA
391050 -TTTTCTTTTCTTTT-TTTT
1 TTTTTCTTTTCTTTTCTTTT
391068 CCTTTTTCTT
Statistics
Matches: 45, Mismatches: 1, Indels: 6
0.87 0.02 0.12
Matches are distributed among these distances:
28 4 0.09
29 20 0.44
30 21 0.47
ACGTcount: A:0.05, C:0.13, G:0.01, T:0.81
Consensus pattern (30 bp):
TTTTTCTTTTCTTTTCTTTTATTTTATTTA
Found at i:391033 original size:24 final size:26
Alignment explanation
Indices: 390996--391066 Score: 83
Period size: 25 Copynumber: 2.7 Consensus size: 26
390986 TCTCTTTTCC
*
390996 TTTTCTTTTGCTTTTTTTCTTTTA-T-
1 TTTTCTTTT-CTTTTTTTATTTTATTA
391021 TTTTCTTTTCTTTTCTTTTATTTTATTTA
1 TTTTCTTTTC-TTT-TTTTATTTTA-TTA
391050 TTTTCTTTTCTTTTTTT
1 TTTTCTTTTCTTTTTTT
391067 TCCTTTTTCT
Statistics
Matches: 40, Mismatches: 1, Indels: 8
0.82 0.02 0.16
Matches are distributed among these distances:
24 1 0.03
25 12 0.30
26 9 0.22
27 4 0.10
28 4 0.10
29 10 0.25
ACGTcount: A:0.06, C:0.11, G:0.01, T:0.82
Consensus pattern (26 bp):
TTTTCTTTTCTTTTTTTATTTTATTA
Found at i:391079 original size:24 final size:22
Alignment explanation
Indices: 391001--391080 Score: 51
Period size: 21 Copynumber: 3.7 Consensus size: 22
390991 TTTCCTTTTC
* *
391001 TTTTGCTTTTTTTCTTTTATTT
1 TTTTTCTTTTTTTCTTTTCTTT
* * *
391023 TTCTT-TTCTTTTC-TTT-TAT
1 TTTTTCTTTTTTTCTTTTCTTT
* *
391042 TTTAT-TTATTTTCTTTTCTTT
1 TTTTTCTTTTTTTCTTTTCTTT
391063 TTTTTCCTTTTTCTTCTT
1 TTTTT-CTTTTT-TTCTT
391081 AGGTGTGGTA
Statistics
Matches: 43, Mismatches: 10, Indels: 8
0.70 0.16 0.13
Matches are distributed among these distances:
19 12 0.28
20 6 0.14
21 13 0.30
22 3 0.07
23 4 0.09
24 5 0.12
ACGTcount: A:0.05, C:0.14, G:0.01, T:0.80
Consensus pattern (22 bp):
TTTTTCTTTTTTTCTTTTCTTT
Done.