Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008484.1 Hibiscus syriacus cultivar Beakdansim tig00111318_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: 688492
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 1 of 4
Found at i:3896 original size:20 final size:20
Alignment explanation
Indices: 3871--3961 Score: 72
Period size: 20 Copynumber: 5.0 Consensus size: 20
3861 TAAATTAAAT
*
3871 ATTAGATAGGATCAGTTTTA
1 ATTAGATAGAATCAGTTTTA
*
3891 ATTAGATAGAATCAGTTTTT
1 ATTAGATAGAATCAGTTTTA
* *
3911 ATT--CT---ATTAG--TT-
1 ATTAGATAGAATCAGTTTTA
* *
3923 ATTAGATAGGATCATTTTTA
1 ATTAGATAGAATCAGTTTTA
3943 ATTAGATAGAATCAGTTTT
1 ATTAGATAGAATCAGTTTT
3962 TATTCTATAG
Statistics
Matches: 54, Mismatches: 9, Indels: 16
0.68 0.11 0.20
Matches are distributed among these distances:
12 3 0.06
13 2 0.04
14 1 0.02
15 4 0.07
17 3 0.06
18 1 0.02
19 2 0.04
20 38 0.70
ACGTcount: A:0.34, C:0.05, G:0.15, T:0.45
Consensus pattern (20 bp):
ATTAGATAGAATCAGTTTTA
Found at i:3963 original size:21 final size:20
Alignment explanation
Indices: 3923--4013 Score: 65
Period size: 20 Copynumber: 4.0 Consensus size: 20
3913 TCTATTAGTT
*
3923 ATTAGATAGGATCATTTTTA
1 ATTAGATAGAATCATTTTTA
3943 ATTAGATAGAATCAGTTTTTATTCTA
1 ATTAGATAGAATCA----TT-TT-TA
*
3969 TAGTTATTAGATAGGATCATTTTTA
1 -A-TTA---GATAGAATCATTTTTA
3994 ATTAGATAGAATCATTTTTA
1 ATTAGATAGAATCATTTTTA
4014 TTCTGTTGCT
Statistics
Matches: 57, Mismatches: 3, Indels: 22
0.70 0.04 0.27
Matches are distributed among these distances:
20 28 0.49
23 3 0.05
24 3 0.05
25 4 0.07
26 4 0.07
27 3 0.05
28 3 0.05
31 9 0.16
ACGTcount: A:0.35, C:0.05, G:0.13, T:0.46
Consensus pattern (20 bp):
ATTAGATAGAATCATTTTTA
Found at i:3994 original size:51 final size:52
Alignment explanation
Indices: 3870--4017 Score: 273
Period size: 52 Copynumber: 2.9 Consensus size: 52
3860 CTAAATTAAA
*
3870 TATTAGATAGGATCAGTTTTAATTAGATAGAATCAGTTTTTATTCTATTAGT
1 TATTAGATAGGATCATTTTTAATTAGATAGAATCAGTTTTTATTCTATTAGT
3922 TATTAGATAGGATCATTTTTAATTAGATAGAATCAGTTTTTATTCTA-TAGT
1 TATTAGATAGGATCATTTTTAATTAGATAGAATCAGTTTTTATTCTATTAGT
3973 TATTAGATAGGATCATTTTTAATTAGATAGAATCA-TTTTTATTCT
1 TATTAGATAGGATCATTTTTAATTAGATAGAATCAGTTTTTATTCT
4018 GTTGCTAATT
Statistics
Matches: 95, Mismatches: 1, Indels: 2
0.97 0.01 0.02
Matches are distributed among these distances:
50 10 0.11
51 39 0.41
52 46 0.48
ACGTcount: A:0.33, C:0.06, G:0.14, T:0.47
Consensus pattern (52 bp):
TATTAGATAGGATCATTTTTAATTAGATAGAATCAGTTTTTATTCTATTAGT
Found at i:3999 original size:20 final size:20
Alignment explanation
Indices: 3974--4013 Score: 71
Period size: 20 Copynumber: 2.0 Consensus size: 20
3964 TTCTATAGTT
*
3974 ATTAGATAGGATCATTTTTA
1 ATTAGATAGAATCATTTTTA
3994 ATTAGATAGAATCATTTTTA
1 ATTAGATAGAATCATTTTTA
4014 TTCTGTTGCT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.38, C:0.05, G:0.12, T:0.45
Consensus pattern (20 bp):
ATTAGATAGAATCATTTTTA
Found at i:4418 original size:15 final size:16
Alignment explanation
Indices: 4392--4434 Score: 65
Period size: 14 Copynumber: 2.9 Consensus size: 16
4382 AATCAATTAT
4392 TGTAGAAAACAGACTG
1 TGTAGAAAACAGACTG
4408 TGTAG-AAACAGAC--
1 TGTAGAAAACAGACTG
4421 TGTAGAAAACAGAC
1 TGTAGAAAACAGAC
4435 AAGTCTGTTA
Statistics
Matches: 26, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
13 5 0.19
14 8 0.31
15 8 0.31
16 5 0.19
ACGTcount: A:0.47, C:0.14, G:0.23, T:0.16
Consensus pattern (16 bp):
TGTAGAAAACAGACTG
Found at i:6746 original size:50 final size:50
Alignment explanation
Indices: 6648--6740 Score: 163
Period size: 48 Copynumber: 1.9 Consensus size: 50
6638 TAAGGAAAGG
*
6648 ATAGGCTGTAAAGAAATATCGGTTTGAAACAGGTTGAAATTCCTTAACTA
1 ATAGGCTGTAAAGAAATATCGGTTTGAAACAGGCTGAAATTCCTTAACTA
6698 ATAGGCTGTAAAG-AATATCGGTTTG-AACAGGCTGAAATTCCTT
1 ATAGGCTGTAAAGAAATATCGGTTTGAAACAGGCTGAAATTCCTT
6741 GTAACTCTCT
Statistics
Matches: 42, Mismatches: 1, Indels: 2
0.93 0.02 0.04
Matches are distributed among these distances:
48 17 0.40
49 12 0.29
50 13 0.31
ACGTcount: A:0.35, C:0.13, G:0.22, T:0.30
Consensus pattern (50 bp):
ATAGGCTGTAAAGAAATATCGGTTTGAAACAGGCTGAAATTCCTTAACTA
Found at i:8502 original size:14 final size:15
Alignment explanation
Indices: 8467--8510 Score: 72
Period size: 14 Copynumber: 2.9 Consensus size: 15
8457 CCTAATACCA
8467 TGTAGAAAACAGACTG
1 TGTAGAAAACAGAC-G
8483 TGTAGAAAACAGAC-
1 TGTAGAAAACAGACG
8497 TGTAGAAAACAGAC
1 TGTAGAAAACAGAC
8511 AAGTCTGTTT
Statistics
Matches: 28, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
14 14 0.50
16 14 0.50
ACGTcount: A:0.48, C:0.14, G:0.23, T:0.16
Consensus pattern (15 bp):
TGTAGAAAACAGACG
Found at i:18321 original size:42 final size:41
Alignment explanation
Indices: 18274--18370 Score: 131
Period size: 42 Copynumber: 2.3 Consensus size: 41
18264 ATAATTTAAG
* *
18274 TCCTTCGGGCCATCAGTAAGTCTTTCGAGCATGATGATGAAA
1 TCCTTCGGGCCATCAGTAAGTCTTTAGAGCAAGATGAT-AAA
* * *
18316 TCCTTCGGGTCATCTGTAAGTCTTTAGAGCAAGATGATAAG
1 TCCTTCGGGCCATCAGTAAGTCTTTAGAGCAAGATGATAAA
*
18357 TCATTCGGGCCATC
1 TCCTTCGGGCCATC
18371 CATAAAGCCT
Statistics
Matches: 48, Mismatches: 7, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
41 14 0.29
42 34 0.71
ACGTcount: A:0.25, C:0.22, G:0.24, T:0.30
Consensus pattern (41 bp):
TCCTTCGGGCCATCAGTAAGTCTTTAGAGCAAGATGATAAA
Found at i:18552 original size:42 final size:42
Alignment explanation
Indices: 18490--18582 Score: 159
Period size: 42 Copynumber: 2.2 Consensus size: 42
18480 ACTTAGTAAG
* *
18490 TCCTTCGGGCCATCAATAAGTCTTTCGAGCATGATGCTTAAA
1 TCCTTCAGGCCATCAATAAGTCTTTCGAGCATGATGATTAAA
*
18532 TCCTTCAGGCCATCAGTAAGTCTTTCGAGCATGATGATTAAA
1 TCCTTCAGGCCATCAATAAGTCTTTCGAGCATGATGATTAAA
18574 TCCTTCAGG
1 TCCTTCAGG
18583 TAATTTGTAA
Statistics
Matches: 48, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
42 48 1.00
ACGTcount: A:0.26, C:0.24, G:0.19, T:0.31
Consensus pattern (42 bp):
TCCTTCAGGCCATCAATAAGTCTTTCGAGCATGATGATTAAA
Found at i:18639 original size:13 final size:13
Alignment explanation
Indices: 18621--18645 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
18611 TGAAGCAAAT
18621 CCATCAGTAAGTG
1 CCATCAGTAAGTG
18634 CCATCAGTAAGT
1 CCATCAGTAAGT
18646 CTTTCGAGCA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.24, G:0.20, T:0.24
Consensus pattern (13 bp):
CCATCAGTAAGTG
Found at i:18768 original size:80 final size:80
Alignment explanation
Indices: 18635--18916 Score: 451
Period size: 80 Copynumber: 3.5 Consensus size: 80
18625 CAGTAAGTGC
18635 CATCAGTAAGTCTTTCGAGCATGATGATTAAATCCTTCGGGTAACTGGTAAGCCTTCACGGAAGA
1 CATCAGTAAGTCTTTCGAGCATGATGATTAAATCCTTCGGGTAACTGGTAAGCCTTCACGGAAGA
18700 GTAGTGAAGCAAATT
66 GTAGTGAAGCAAATT
* * * ** *
18715 CATCAGTAAGTCTTTCGAGCATGGTAATTAAATCCTTCGGGTAATTTTTAAGCCTTCACCGAAGA
1 CATCAGTAAGTCTTTCGAGCATGATGATTAAATCCTTCGGGTAACTGGTAAGCCTTCACGGAAGA
**
18780 GTAGTGAAGCAAACC
66 GTAGTGAAGCAAATT
18795 CATCAGTAAGTCTTTCGAGCATGATGATTAAATCCTTCGGGTAACTGGTAAGCCTTCACGGAAGA
1 CATCAGTAAGTCTTTCGAGCATGATGATTAAATCCTTCGGGTAACTGGTAAGCCTTCACGGAAGA
18860 GTAGTGAAGCAAATT
66 GTAGTGAAGCAAATT
*
18875 CATCAGTAAGTCTTTCGAGCAGGATG-TTGAAA-CCTTTCGGGT
1 CATCAGTAAGTCTTTCGAGCATGATGATT-AAATCC-TTCGGGT
18917 CATCAGTAAG
Statistics
Matches: 183, Mismatches: 17, Indels: 4
0.90 0.08 0.02
Matches are distributed among these distances:
79 4 0.02
80 179 0.98
ACGTcount: A:0.30, C:0.18, G:0.23, T:0.28
Consensus pattern (80 bp):
CATCAGTAAGTCTTTCGAGCATGATGATTAAATCCTTCGGGTAACTGGTAAGCCTTCACGGAAGA
GTAGTGAAGCAAATT
Found at i:18968 original size:41 final size:42
Alignment explanation
Indices: 18874--18985 Score: 140
Period size: 42 Copynumber: 2.7 Consensus size: 42
18864 TGAAGCAAAT
18874 TCATCAGTAAGTCTTTCGAGCAGGATGTTGAAACCTTTCGGG
1 TCATCAGTAAGTCTTTCGAGCAGGATGTTGAAACCTTTCGGG
* *
18916 TCATCAGTAAGTCTTTCGAGCATGATGATT-AATCC-TTCGGG
1 TCATCAGTAAGTCTTTCGAGCAGGATG-TTGAAACCTTTCGGG
* * *
18957 TCATCCA-TAAGTCCTTCGGGTAGGATGTT
1 TCAT-CAGTAAGTCTTTCGAGCAGGATGTT
18986 TTCACACCAA
Statistics
Matches: 62, Mismatches: 6, Indels: 6
0.84 0.08 0.08
Matches are distributed among these distances:
40 2 0.03
41 26 0.42
42 32 0.52
43 2 0.03
ACGTcount: A:0.23, C:0.20, G:0.24, T:0.33
Consensus pattern (42 bp):
TCATCAGTAAGTCTTTCGAGCAGGATGTTGAAACCTTTCGGG
Found at i:19459 original size:53 final size:53
Alignment explanation
Indices: 19396--19591 Score: 279
Period size: 53 Copynumber: 3.7 Consensus size: 53
19386 ATCAAACCAT
19396 AAGATTGTTCGAGTTCTACTCCCTGAAGCAAGAGGGAGCGAACCCATAGGCAG
1 AAGATTGTTCGAGTTCTACTCCCTGAAGCAAGAGGGAGCGAACCCATAGGCAG
* * * *
19449 AAGATTGTTCGAGTTTTACTCCCTGAAGCAAGAGGGAGCAAACCCGTAGACAG
1 AAGATTGTTCGAGTTCTACTCCCTGAAGCAAGAGGGAGCGAACCCATAGGCAG
* * * *
19502 AAGACTGTTTGAGTTCTACTCCTTGAAGCAAGAGGGAGCGAACCCGCT-GGTC-G
1 AAGATTGTTCGAGTTCTACTCCCTGAAGCAAGAGGGAGCGAACCC-ATAGG-CAG
*
19555 AAGATTGTTCGAGTTCTACTCCCTGAAGCAATAGGGA
1 AAGATTGTTCGAGTTCTACTCCCTGAAGCAAGAGGGA
19592 ACAAACCTTT
Statistics
Matches: 126, Mismatches: 15, Indels: 4
0.87 0.10 0.03
Matches are distributed among these distances:
53 124 0.98
54 2 0.02
ACGTcount: A:0.29, C:0.21, G:0.28, T:0.22
Consensus pattern (53 bp):
AAGATTGTTCGAGTTCTACTCCCTGAAGCAAGAGGGAGCGAACCCATAGGCAG
Found at i:19591 original size:106 final size:106
Alignment explanation
Indices: 19396--19598 Score: 311
Period size: 106 Copynumber: 1.9 Consensus size: 106
19386 ATCAAACCAT
*
19396 AAGATTGTTCGAGTTCTACTCCCTGAAGCAAGAGGGAGCGAACCCATAGGCAGAAGATTGTTCGA
1 AAGACTGTTCGAGTTCTACTCCCTGAAGCAAGAGGGAGCGAACCCATAGGCAGAAGATTGTTCGA
* *
19461 GTTTTACTCCCTGAAGCAAGAGGGAGCAAACCCGTAGACAG
66 GTTCTACTCCCTGAAGCAAGAGGGAACAAACCCGTAGACAG
* * *
19502 AAGACTGTTTGAGTTCTACTCCTTGAAGCAAGAGGGAGCGAACCCGCT-GGTC-GAAGATTGTTC
1 AAGACTGTTCGAGTTCTACTCCCTGAAGCAAGAGGGAGCGAACCC-ATAGG-CAGAAGATTGTTC
*
19565 GAGTTCTACTCCCTGAAGCAATAGGGAACAAACC
64 GAGTTCTACTCCCTGAAGCAAGAGGGAACAAACC
19599 TTTTTTTTAT
Statistics
Matches: 88, Mismatches: 7, Indels: 4
0.89 0.07 0.04
Matches are distributed among these distances:
106 86 0.98
107 2 0.02
ACGTcount: A:0.30, C:0.22, G:0.27, T:0.21
Consensus pattern (106 bp):
AAGACTGTTCGAGTTCTACTCCCTGAAGCAAGAGGGAGCGAACCCATAGGCAGAAGATTGTTCGA
GTTCTACTCCCTGAAGCAAGAGGGAACAAACCCGTAGACAG
Found at i:38343 original size:24 final size:24
Alignment explanation
Indices: 38316--38390 Score: 105
Period size: 24 Copynumber: 3.1 Consensus size: 24
38306 GTTCGTGAAC
*
38316 GTTCGGTTATGTTCATTCGGTTAT
1 GTTCGCTTATGTTCATTCGGTTAT
* *
38340 GTTCGTTTATGTTCGTTCGGTTAT
1 GTTCGCTTATGTTCATTCGGTTAT
**
38364 GTTCGCTTATGTTCATTCATTTAT
1 GTTCGCTTATGTTCATTCGGTTAT
38388 GTT
1 GTT
38391 TAACCCAATC
Statistics
Matches: 45, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
24 45 1.00
ACGTcount: A:0.12, C:0.13, G:0.21, T:0.53
Consensus pattern (24 bp):
GTTCGCTTATGTTCATTCGGTTAT
Found at i:38368 original size:14 final size:14
Alignment explanation
Indices: 38315--38368 Score: 71
Period size: 14 Copynumber: 4.1 Consensus size: 14
38305 CGTTCGTGAA
38315 CGTTCGGTTATGTT
1 CGTTCGGTTATGTT
*
38329 CATTCGGTTATGTT
1 CGTTCGGTTATGTT
38343 CG-T---TTATGTT
1 CGTTCGGTTATGTT
38353 CGTTCGGTTATGTT
1 CGTTCGGTTATGTT
38367 CG
1 CG
38369 CTTATGTTCA
Statistics
Matches: 34, Mismatches: 2, Indels: 8
0.77 0.05 0.18
Matches are distributed among these distances:
10 9 0.26
11 1 0.03
13 1 0.03
14 23 0.68
ACGTcount: A:0.09, C:0.15, G:0.26, T:0.50
Consensus pattern (14 bp):
CGTTCGGTTATGTT
Found at i:39481 original size:10 final size:10
Alignment explanation
Indices: 39466--39504 Score: 50
Period size: 10 Copynumber: 4.3 Consensus size: 10
39456 GGGTTTCTAA
39466 CGTTTATGTT
1 CGTTTATGTT
39476 CGTTTATGTT
1 CGTTTATGTT
39486 CG----TGTT
1 CGTTTATGTT
39492 CGTTTATGTT
1 CGTTTATGTT
39502 CGT
1 CGT
39505 GTTCATTTAT
Statistics
Matches: 25, Mismatches: 0, Indels: 8
0.76 0.00 0.24
Matches are distributed among these distances:
6 6 0.24
10 19 0.76
ACGTcount: A:0.08, C:0.13, G:0.23, T:0.56
Consensus pattern (10 bp):
CGTTTATGTT
Found at i:39493 original size:16 final size:16
Alignment explanation
Indices: 39472--39520 Score: 80
Period size: 16 Copynumber: 3.1 Consensus size: 16
39462 CTAACGTTTA
39472 TGTTCGTTTATGTTCG
1 TGTTCGTTTATGTTCG
39488 TGTTCGTTTATGTTCG
1 TGTTCGTTTATGTTCG
* *
39504 TGTTCATTTATATTCG
1 TGTTCGTTTATGTTCG
39520 T
1 T
39521 TTATTTATTA
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 31 1.00
ACGTcount: A:0.10, C:0.12, G:0.20, T:0.57
Consensus pattern (16 bp):
TGTTCGTTTATGTTCG
Found at i:39528 original size:14 final size:16
Alignment explanation
Indices: 39472--39528 Score: 64
Period size: 16 Copynumber: 3.7 Consensus size: 16
39462 CTAACGTTTA
* *
39472 TGTTCGTTTATGTTCG
1 TGTTCATTTATATTCG
* *
39488 TGTTCGTTTATGTTCG
1 TGTTCATTTATATTCG
39504 TGTTCATTTATATTCG
1 TGTTCATTTATATTCG
39520 T-TT-ATTTAT
1 TGTTCATTTAT
39529 TAAATGAACG
Statistics
Matches: 39, Mismatches: 2, Indels: 2
0.91 0.05 0.05
Matches are distributed among these distances:
14 6 0.15
15 2 0.05
16 31 0.79
ACGTcount: A:0.12, C:0.11, G:0.18, T:0.60
Consensus pattern (16 bp):
TGTTCATTTATATTCG
Found at i:39611 original size:16 final size:16
Alignment explanation
Indices: 39590--39620 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
39580 AAAAAAATTT
*
39590 TGTTCGTTTATGTTCA
1 TGTTCGTATATGTTCA
39606 TGTTCGTATATGTTC
1 TGTTCGTATATGTTC
39621 GTTTATTTAT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.13, C:0.13, G:0.19, T:0.55
Consensus pattern (16 bp):
TGTTCGTATATGTTCA
Found at i:44239 original size:19 final size:20
Alignment explanation
Indices: 44212--44249 Score: 60
Period size: 19 Copynumber: 1.9 Consensus size: 20
44202 AATTTAATAA
*
44212 ATTTTTATATTT-TTTTTAT
1 ATTTATATATTTATTTTTAT
44231 ATTTATATATTTATTTTTA
1 ATTTATATATTTATTTTTA
44250 CATAAACCAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 11 0.65
20 6 0.35
ACGTcount: A:0.26, C:0.00, G:0.00, T:0.74
Consensus pattern (20 bp):
ATTTATATATTTATTTTTAT
Found at i:46872 original size:3 final size:3
Alignment explanation
Indices: 46803--46854 Score: 63
Period size: 3 Copynumber: 18.0 Consensus size: 3
46793 ATTTTTTGAT
* * *
46803 TTA TTA TAA TTA TT- TTA TTA -TA TTA TTA ATA TTA ATA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
46849 TTA TTA
1 TTA TTA
46855 AATAATAAAT
Statistics
Matches: 41, Mismatches: 6, Indels: 4
0.80 0.12 0.08
Matches are distributed among these distances:
2 4 0.10
3 37 0.90
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (3 bp):
TTA
Found at i:53509 original size:4 final size:4
Alignment explanation
Indices: 53493--53566 Score: 80
Period size: 4 Copynumber: 17.5 Consensus size: 4
53483 GGACATGGAC
53493 ATAA ATAA A-AA ATAA ATAA ATAA ATAA ATAAA ATAAA ATAA ATAA AT-A
1 ATAA ATAA ATAA ATAA ATAA ATAA ATAA AT-AA AT-AA ATAA ATAA ATAA
53541 ATATA ATATA ATAA TATATA ATAA AT
1 ATA-A ATA-A ATAA -ATA-A ATAA AT
53567 GTAATAATAA
Statistics
Matches: 64, Mismatches: 0, Indels: 12
0.84 0.00 0.16
Matches are distributed among these distances:
3 6 0.09
4 33 0.52
5 24 0.38
6 1 0.02
ACGTcount: A:0.72, C:0.00, G:0.00, T:0.28
Consensus pattern (4 bp):
ATAA
Found at i:53744 original size:70 final size:74
Alignment explanation
Indices: 53615--53923 Score: 350
Period size: 70 Copynumber: 4.3 Consensus size: 74
53605 ATTTGTTTTT
* * * *
53615 AAAATATATATTATATGGTTTCAAACCCTTT-CTTAAAAAACCATATATTATACGTTTTCAAAAT
1 AAAATATATATTATATGTTTTCAAACCCTTTATTTTAAAAACTATATATTATACGTTTTCAAAAT
53679 TATTTAAAA
66 TATTTAAAA
* *
53688 AAAATAT-TA-TATATGTTTTCAAACCCTTT-TTTTTAAATC-ATATATTATACGTTTTCAAAAT
1 AAAATATATATTATATGTTTTCAAACCCTTTATTTTAAAAACTATATATTATACGTTTTCAAAAT
* *
53749 CATTTCAAA
66 TATTTAAAA
* *
53758 AAAATATAT-TATATATGTTTTCAAACGCTTTATTTTAAAAAACTATATATTATTCGTTTTCAAA
1 AAAATATATAT-TATATGTTTTCAAACCCTTTATTTT-AAAAACTATATATTATACGTTTTCAAA
* *
53822 ACTATTTTAAA
64 ATTATTTAAAA
* * * * *
53833 AAATTATATACTATAT-TTTTTAAAACC---ATTTTAAAAACTATATATTATACATTTTCAAAAT
1 AAAATATATATTATATGTTTTCAAACCCTTTATTTTAAAAACTATATATTATACGTTTTCAAAAT
**
53894 TATTTTTAA
66 TATTTAAAA
*
53903 AAATTATATATTATATGTTTT
1 AAAATATATATTATATGTTTT
53924 TTAAAAATAA
Statistics
Matches: 204, Mismatches: 24, Indels: 18
0.83 0.10 0.07
Matches are distributed among these distances:
70 85 0.42
71 35 0.17
72 21 0.10
73 11 0.05
74 12 0.06
75 40 0.20
ACGTcount: A:0.42, C:0.10, G:0.03, T:0.45
Consensus pattern (74 bp):
AAAATATATATTATATGTTTTCAAACCCTTTATTTTAAAAACTATATATTATACGTTTTCAAAAT
TATTTAAAA
Found at i:53778 original size:36 final size:36
Alignment explanation
Indices: 53615--53968 Score: 162
Period size: 36 Copynumber: 9.7 Consensus size: 36
53605 ATTTGTTTTT
* ** *
53615 AAAATATA-TATTATATGGTTTCAAACCCTTTCTTAAA
1 AAAATATATTA-TATATGTTTTCAAAATCATT-TTAAA
* *
53652 AAACCATATA-T-TATACGTTTTCAAAATTA-TTTAAA
1 AAA--ATATATTATATATGTTTTCAAAATCATTTTAAA
* * ***
53687 AAAA-ATATTATATATGTTTTC-AAACCCTTTTTTT
1 AAAATATATTATATATGTTTTCAAAATCATTTTAAA
* * *
53721 TAAATCATA-TATTATACGTTTTCAAAATCATTTCAAA
1 AAAAT-ATATTA-TATATGTTTTCAAAATCATTTTAAA
* *
53758 AAAATATATTATATATGTTTTCAAACGCTTTATTTTAAA
1 AAAATATATTATATATGTTTTCAAA---ATCATTTTAAA
*
53797 AAACTATATATTAT-T-CGTTTTCAAAA-CTATTTTAAA
1 AAA--ATATATTATATATGTTTTCAAAATC-ATTTTAAA
* * *
53833 AAATTATA-TACTATAT-TTTTTAAAACCATTTTAAA
1 AAAATATATTA-TATATGTTTTCAAAATCATTTTAAA
* * *
53868 AACTATATATTATACA--TTTTCAAAATTATTTTTAAA
1 AA-AATATATTATATATGTTTTCAAAATCA-TTTTAAA
* * * * *
53904 AATTATATATTATATGTTTTTTAAAAATAAGTTTTCAAA
1 AA-AATATATTATATATGTTTTCAAAATCA-TTTT-AAA
* *
53943 AATTATATATTATATAT-TTTTAAAAA
1 AA-AATATATTATATATGTTTTCAAAA
53969 CTATATTTAA
Statistics
Matches: 246, Mismatches: 45, Indels: 51
0.72 0.13 0.15
Matches are distributed among these distances:
32 3 0.01
33 7 0.03
34 21 0.09
35 38 0.15
36 69 0.28
37 30 0.12
38 23 0.09
39 45 0.18
40 1 0.00
41 9 0.04
ACGTcount: A:0.43, C:0.09, G:0.03, T:0.45
Consensus pattern (36 bp):
AAAATATATTATATATGTTTTCAAAATCATTTTAAA
Found at i:53810 original size:145 final size:143
Alignment explanation
Indices: 53615--53923 Score: 374
Period size: 145 Copynumber: 2.1 Consensus size: 143
53605 ATTTGTTTTT
* *
53615 AAAATATATATTATATGGTTTCAAACCCTTTCTTAAAAAACCATATATTATACGTTTTCAAAATT
1 AAAATATATATTATATGTTTTCAAACCCTTTCTTAAAAAACCATATATTATACGTTTTCAAAACT
* * ** *
53680 ATTTAAAAAAAATAT-TA-TATATGTTTTCAAACCCTTTTTTTTAAA-TCATATATTATACGTTT
66 ATTTAAAAAAAATATATACTATAT-TTTTCAAAACC-ATTTTAAAAACT-ATATATTATACATTT
53742 TCAAAATCATTTCAAA
128 TCAAAATCATTTCAAA
* * * *
53758 AAAATATAT-TATATATGTTTTCAAACGCTTTATTTTAAAAAACTATATATTATTCGTTTTCAAA
1 AAAATATATAT-TATATGTTTTCAAAC-CCTT-TCTTAAAAAACCATATATTATACGTTTTCAAA
* * *
53822 ACTATTTTAAAAAATTATATACTATATTTTTTAAAACCATTTTAAAAACTATATATTATACATTT
63 ACTATTTAAAAAAAATATATACTATATTTTTCAAAACCATTTTAAAAACTATATATTATACATTT
* **
53887 TCAAAATTATTTTTAA
128 TCAAAATCATTTCAAA
*
53903 AAATTATATATTATATGTTTT
1 AAAATATATATTATATGTTTT
53924 TTAAAAATAA
Statistics
Matches: 141, Mismatches: 18, Indels: 12
0.82 0.11 0.07
Matches are distributed among these distances:
142 1 0.01
143 23 0.16
144 3 0.02
145 96 0.68
146 13 0.09
147 5 0.04
ACGTcount: A:0.42, C:0.10, G:0.03, T:0.45
Consensus pattern (143 bp):
AAAATATATATTATATGTTTTCAAACCCTTTCTTAAAAAACCATATATTATACGTTTTCAAAACT
ATTTAAAAAAAATATATACTATATTTTTCAAAACCATTTTAAAAACTATATATTATACATTTTCA
AAATCATTTCAAA
Found at i:53944 original size:145 final size:145
Alignment explanation
Indices: 53647--53999 Score: 340
Period size: 145 Copynumber: 2.4 Consensus size: 145
53637 AAACCCTTTC
* * * * *
53647 TTAAAAAACCATATATTATACGTTTTCAAAATTATTTAAAAAAAATAT-TA-TATATGTTTTCAA
1 TTAAAAAACTATATATTATTCGTTTTCAAAACTATTTTAAAAAATTATATACTATAT-TTTTCAA
* * ** *
53710 ACCCTTTTTTTTAAATCATATATTATACGTTTTCAAAATCATTTCAAAAAAATATATTATATATG
65 AACCTATTTTAAAAATCATATATTATACATTTTCAAAATCATTTCAAAAAAATATATTATATATG
** *
53775 TTTTCAAACGCTTTATT
130 TTTTCAAAC-AATAATT
*
53792 TTAAAAAACTATATATTATTCGTTTTCAAAACTATTTTAAAAAATTATATACTATATTTTTTAAA
1 TTAAAAAACTATATATTATTCGTTTTCAAAACTATTTTAAAAAATTATATACTATATTTTTCAAA
* ** *
53857 ACC-ATTTTAAAAA-CTATATATTATACATTTTCAAAATTATTTTTAAAAATTATA-TATTATAT
66 ACCTATTTTAAAAATC-ATATATTATACATTTTCAAAATCATTTCAAAAAAATATATTA-TATAT
*
53919 GTTTTTTAAA-AATAAGTT
129 G-TTTTCAAACAATAA-TT
* * ** * *
53937 TTCAAAAATTATATATTATATATTTTTAAAAACTATATTTAAAATTATTATATATACTATATT
1 TTAAAAAACTATATATTAT-TCGTTTTCAAAACTAT-TTTAAAA--AAT-TATATACTATATT
54000 ATACAATATA
Statistics
Matches: 172, Mismatches: 25, Indels: 17
0.80 0.12 0.08
Matches are distributed among these distances:
144 5 0.03
145 109 0.63
146 31 0.18
147 12 0.07
149 2 0.01
150 13 0.08
ACGTcount: A:0.43, C:0.08, G:0.02, T:0.46
Consensus pattern (145 bp):
TTAAAAAACTATATATTATTCGTTTTCAAAACTATTTTAAAAAATTATATACTATATTTTTCAAA
ACCTATTTTAAAAATCATATATTATACATTTTCAAAATCATTTCAAAAAAATATATTATATATGT
TTTCAAACAATAATT
Found at i:53987 original size:39 final size:37
Alignment explanation
Indices: 53761--53999 Score: 172
Period size: 36 Copynumber: 6.4 Consensus size: 37
53751 TTTCAAAAAA
** * *
53761 ATATATTATATATGTTTTCAAACGCTTTATTTTAAAAAACT
1 ATATATTATATAT-TTTT-AAAAACTATA-TTT-AAAAATT
** *
53802 ATATATTAT-TCGTTTTCAAAACTAT-TTTAAAAAATT
1 ATATATTATATATTTTTAAAAACTATATTT-AAAAATT
* * *
53838 ATATACTATAT-TTTTT-AAAACCAT-TTTAAAAACT
1 ATATATTATATATTTTTAAAAACTATATTTAAAAATT
* * * *
53872 ATATATTATACA-TTTTCAAAATTATTTTTAAAAATT
1 ATATATTATATATTTTTAAAAACTATATTTAAAAATT
*
53908 ATATATTATATGTTTTTTAAAAA-TA-AGTTTTCAAAAATT
1 ATATATTATAT-ATTTTTAAAAACTATA--TTT-AAAAATT
53947 ATATATTATATATTTTTAAAAACTATATTT-AAAATT
1 ATATATTATATATTTTTAAAAACTATATTTAAAAATT
53983 ATTATATATACTATATT
1 A-TATAT-TA-TATATT
54000 ATACAATATA
Statistics
Matches: 163, Mismatches: 21, Indels: 30
0.76 0.10 0.14
Matches are distributed among these distances:
34 19 0.12
35 16 0.10
36 48 0.29
37 8 0.05
38 31 0.19
39 30 0.18
40 2 0.01
41 9 0.06
ACGTcount: A:0.43, C:0.07, G:0.02, T:0.48
Consensus pattern (37 bp):
ATATATTATATATTTTTAAAAACTATATTTAAAAATT
Found at i:54372 original size:29 final size:27
Alignment explanation
Indices: 54323--54376 Score: 63
Period size: 29 Copynumber: 1.9 Consensus size: 27
54313 ATATTTGATA
54323 TATTAATAAAAAATAAATTTATAAATAT
1 TATTAATAAAAAATAAATTTA-AAATAT
* * *
54351 TATTAGATATAAAATTATTTTAAAAT
1 TATTA-ATAAAAAATAAATTTAAAAT
54377 TTGAACACTA
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
28 9 0.41
29 13 0.59
ACGTcount: A:0.56, C:0.00, G:0.02, T:0.43
Consensus pattern (27 bp):
TATTAATAAAAAATAAATTTAAAATAT
Found at i:56488 original size:20 final size:20
Alignment explanation
Indices: 56458--56615 Score: 81
Period size: 20 Copynumber: 7.8 Consensus size: 20
56448 GTTTTCAGAT
*
56458 TCGCAACGCGATTCTGACTA
1 TCGCAATGCGATTCTGACTA
* ** *
56478 TCGCATTGCGATT-TTCCAAA
1 TCGCAATGCGATTCTGAC-TA
**
56498 TTCGCGTTGCGATTTTCTGACTA
1 -TCGCAATGCGA--TTCTGACTA
* * *
56521 TCGCAATGCGAATATGTA-AA
1 TCGCAATGCGATTCTG-ACTA
* *
56541 TCGCAATGTGATTATGACTA
1 TCGCAATGCGATTCTGACTA
* *
56561 TTGCAATGCGATT-TG-CGAAA
1 TCGCAATGCGATTCTGAC--TA
*
56581 TCGCATTGCGATTCTGACTA
1 TCGCAATGCGATTCTGACTA
*
56601 TCGCAACGCGATTCT
1 TCGCAATGCGATTCT
56616 AACTGTCACA
Statistics
Matches: 102, Mismatches: 25, Indels: 22
0.68 0.17 0.15
Matches are distributed among these distances:
18 1 0.01
19 5 0.05
20 68 0.67
21 13 0.13
22 10 0.10
23 3 0.03
24 2 0.02
ACGTcount: A:0.25, C:0.22, G:0.20, T:0.32
Consensus pattern (20 bp):
TCGCAATGCGATTCTGACTA
Found at i:56493 original size:40 final size:40
Alignment explanation
Indices: 56449--56613 Score: 131
Period size: 40 Copynumber: 4.0 Consensus size: 40
56439 CGCAAATCAG
* * *
56449 TTTTCAGATTCGCAACGCGATTCTGACTATCGCATTGCGA
1 TTTTCAGAATCGCAATGCGATTCTGACTATCGCAATGCGA
**
56489 TTTTCCA-AATTCGCGTTGCGATTTTCTGACTATCGCAATGCGAA
1 TTTT-CAGAA-TCGCAATGCGA--TTCTGACTATCGCAATGCG-A
* * * *
56533 TATGT-A-AATCGCAATGTGATTATGACTATTGCAATGCGA
1 T-TTTCAGAATCGCAATGCGATTCTGACTATCGCAATGCGA
* * *
56572 TTTGC-GAAATCGCATTGCGATTCTGACTATCGCAACGCGA
1 TTTTCAG-AATCGCAATGCGATTCTGACTATCGCAATGCGA
56612 TT
1 TT
56614 CTAACTGTCA
Statistics
Matches: 98, Mismatches: 18, Indels: 18
0.73 0.13 0.13
Matches are distributed among these distances:
38 1 0.01
39 2 0.02
40 52 0.53
41 10 0.10
42 8 0.08
43 21 0.21
44 2 0.02
45 2 0.02
ACGTcount: A:0.25, C:0.21, G:0.20, T:0.33
Consensus pattern (40 bp):
TTTTCAGAATCGCAATGCGATTCTGACTATCGCAATGCGA
Found at i:56627 original size:20 final size:20
Alignment explanation
Indices: 56588--56627 Score: 53
Period size: 20 Copynumber: 2.0 Consensus size: 20
56578 AAATCGCATT
* *
56588 GCGATTCTGACTATCGCAAC
1 GCGATTCTAACTATCACAAC
*
56608 GCGATTCTAACTGTCACAAC
1 GCGATTCTAACTATCACAAC
56628 ACTGAATTTC
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.28, C:0.30, G:0.17, T:0.25
Consensus pattern (20 bp):
GCGATTCTAACTATCACAAC
Found at i:59795 original size:18 final size:18
Alignment explanation
Indices: 59762--59796 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
59752 AGAAAAAGGC
**
59762 AATCAAAATCGTAATCAA
1 AATCAAAATCCCAATCAA
59780 AATCAAAATCCCAATCA
1 AATCAAAATCCCAATCA
59797 CAACTGGCTT
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.54, C:0.23, G:0.03, T:0.20
Consensus pattern (18 bp):
AATCAAAATCCCAATCAA
Found at i:60111 original size:140 final size:140
Alignment explanation
Indices: 59856--60125 Score: 486
Period size: 140 Copynumber: 1.9 Consensus size: 140
59846 AAACATTGTA
* *
59856 TTATGTGTAAACTTTTAACATTTTCAGTTAGGCATGTATTAGTAACTTTAGTTTGAACATTGCTA
1 TTATGTGTAAACTTTTAACATTTTCAGTTAGGCATATATTAGTAACTTGAGTTTGAACATTGCTA
* * *
59921 TGATCTGTTCAGTTGTTATCACTTATTACATATTCATTTGAATATCGCAACGCGAATTTGACTAT
66 TGATATGTTCAATTGTTATCACTTATTACACATTCATTTGAATATCGCAACGCGAATTTGACTAT
59986 TATGTGTATT
131 TATGTGTATT
59996 TTATGTGTAAACTTTTAACATTTTCAGTTAGGCATATATTAGTAACTTGAGTTTGAACATTGCTA
1 TTATGTGTAAACTTTTAACATTTTCAGTTAGGCATATATTAGTAACTTGAGTTTGAACATTGCTA
*
60061 TGATATGTTCAATTGTTATCACTTATTACACATTCATTTGAATATTGCAACGCGAATTTGACTAT
66 TGATATGTTCAATTGTTATCACTTATTACACATTCATTTGAATATCGCAACGCGAATTTGACTAT
60126 CACAACGCGA
Statistics
Matches: 124, Mismatches: 6, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
140 124 1.00
ACGTcount: A:0.29, C:0.13, G:0.14, T:0.43
Consensus pattern (140 bp):
TTATGTGTAAACTTTTAACATTTTCAGTTAGGCATATATTAGTAACTTGAGTTTGAACATTGCTA
TGATATGTTCAATTGTTATCACTTATTACACATTCATTTGAATATCGCAACGCGAATTTGACTAT
TATGTGTATT
Found at i:60121 original size:20 final size:20
Alignment explanation
Indices: 60096--60358 Score: 114
Period size: 20 Copynumber: 13.8 Consensus size: 20
60086 TTACACATTC
*
60096 ATTTGAATATTGCAACGCGA
1 ATTTGAATATCGCAACGCGA
* *
60116 ATTTGACTATCACAACGCGA
1 ATTTGAATATCGCAACGCGA
* *
60136 ATTTGATTATCGCAACTC-A
1 ATTTGAATATCGCAACGCGA
60155 A----AA-ATCGCAACGCGA
1 ATTTGAATATCGCAACGCGA
* *
60170 ATTTGACTATCGCAACACGA
1 ATTTGAATATCGCAACGCGA
* * * *
60190 ATATGACTATCACAATGC-A
1 ATTTGAATATCGCAACGCGA
60209 A----AA-ATCGCAACGCGA
1 ATTTGAATATCGCAACGCGA
** *
60224 ATTTGTCTATCGCAACACGA
1 ATTTGAATATCGCAACGCGA
* *
60244 ATTTGACTATCGCAACG-GCT
1 ATTTGAATATCGCAACGCG-A
* * * *
60264 ATTTGACTATCTCATCGAGA
1 ATTTGAATATCGCAACGCGA
60284 A----AAT-T-GCAACGCGA
1 ATTTGAATATCGCAACGCGA
* *
60298 ATTTGACTATCGCACGCAACACGA
1 ATTTGAATAT----CGCAACGCGA
* * *
60322 ATTTGATTATCGCAACGGGT
1 ATTTGAATATCGCAACGCGA
*
60342 ATTTGACTATCGCAACG
1 ATTTGAATATCGCAACG
60359 AGAAAATCGC
Statistics
Matches: 182, Mismatches: 37, Indels: 48
0.68 0.14 0.18
Matches are distributed among these distances:
14 24 0.13
15 7 0.04
16 2 0.01
18 2 0.01
19 7 0.04
20 122 0.67
21 1 0.01
24 17 0.09
ACGTcount: A:0.34, C:0.23, G:0.17, T:0.26
Consensus pattern (20 bp):
ATTTGAATATCGCAACGCGA
Found at i:60191 original size:54 final size:55
Alignment explanation
Indices: 60107--60259 Score: 238
Period size: 54 Copynumber: 2.8 Consensus size: 55
60097 TTTGAATATT
* * *
60107 GCAACGCGAATTTGACTATCACAACGCGAATTTGATTATCGCAACT-CAAAAATC
1 GCAACGCGAATTTGACTATCGCAACACGAATTTGACTATCGCAACTGCAAAAATC
* *
60161 GCAACGCGAATTTGACTATCGCAACACGAATATGACTATCACAA-TGCAAAAATC
1 GCAACGCGAATTTGACTATCGCAACACGAATTTGACTATCGCAACTGCAAAAATC
*
60215 GCAACGCGAATTTGTCTATCGCAACACGAATTTGACTATCGCAAC
1 GCAACGCGAATTTGACTATCGCAACACGAATTTGACTATCGCAAC
60260 GGCTATTTGA
Statistics
Matches: 89, Mismatches: 8, Indels: 3
0.89 0.08 0.03
Matches are distributed among these distances:
53 1 0.01
54 88 0.99
ACGTcount: A:0.37, C:0.25, G:0.16, T:0.23
Consensus pattern (55 bp):
GCAACGCGAATTTGACTATCGCAACACGAATTTGACTATCGCAACTGCAAAAATC
Found at i:60322 original size:24 final size:24
Alignment explanation
Indices: 60289--60335 Score: 76
Period size: 24 Copynumber: 2.0 Consensus size: 24
60279 CGAGAAAATT
*
60289 GCAACGCGAATTTGACTATCGCAC
1 GCAACACGAATTTGACTATCGCAC
*
60313 GCAACACGAATTTGATTATCGCA
1 GCAACACGAATTTGACTATCGCA
60336 ACGGGTATTT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
24 21 1.00
ACGTcount: A:0.32, C:0.26, G:0.19, T:0.23
Consensus pattern (24 bp):
GCAACACGAATTTGACTATCGCAC
Found at i:60348 original size:78 final size:75
Alignment explanation
Indices: 60160--60402 Score: 262
Period size: 74 Copynumber: 3.2 Consensus size: 75
60150 ACTCAAAAAT
* ** * *
60160 CGCAACGCGAATTTGACTATCGCAACACGAATATGACTATCACAAT-GCA-AAAATCGCAACGCG
1 CGCAACACGAATTTGACTATCGCAACGGGTATTTGACTATCAC-ATCG-AGAAAATCGCAACGCG
*
60223 AATTTGTCTAT-
64 AATTTGACTATC
* * *
60234 CGCAACACGAATTTGACTATCGCAACGGCTATTTGACTATCTCATCGAGAAAATTGCAACGCGAA
1 CGCAACACGAATTTGACTATCGCAACGGGTATTTGACTATCACATCGAGAAAATCGCAACGCGAA
60299 TTTGACTATCGC
66 TTTGACTAT--C
* * * * *
60311 ACGCAACACGAATTTGATTATCGCAACGGGTATTTGACTATCGCAACGAGAAAATCGCAAAGCGT
1 -CGCAACACGAATTTGACTATCGCAACGGGTATTTGACTATCACATCGAGAAAATCGCAACGCGA
*
60376 ATTAGACTAT-
65 ATTTGACTATC
*
60386 CACAACACGAA-TTGACT
1 CGCAACACGAATTTGACT
60403 TTTGTGTTGC
Statistics
Matches: 144, Mismatches: 19, Indels: 13
0.82 0.11 0.07
Matches are distributed among these distances:
73 8 0.06
74 70 0.49
78 66 0.46
ACGTcount: A:0.35, C:0.23, G:0.18, T:0.24
Consensus pattern (75 bp):
CGCAACACGAATTTGACTATCGCAACGGGTATTTGACTATCACATCGAGAAAATCGCAACGCGAA
TTTGACTATC
Found at i:60452 original size:20 final size:20
Alignment explanation
Indices: 60397--60452 Score: 58
Period size: 20 Copynumber: 2.8 Consensus size: 20
60387 ACAACACGAA
*
60397 TTGACTTTTGTGTTGCAATT
1 TTGACTTTAGTGTTGCAATT
* * **
60417 TTGTCTTTCGCATTGCAATT
1 TTGACTTTAGTGTTGCAATT
*
60437 TTGAGTTTAGTGTTGC
1 TTGACTTTAGTGTTGC
60453 GAAAGTGTAC
Statistics
Matches: 27, Mismatches: 9, Indels: 0
0.75 0.25 0.00
Matches are distributed among these distances:
20 27 1.00
ACGTcount: A:0.14, C:0.12, G:0.21, T:0.52
Consensus pattern (20 bp):
TTGACTTTAGTGTTGCAATT
Found at i:62044 original size:42 final size:42
Alignment explanation
Indices: 61965--62057 Score: 107
Period size: 42 Copynumber: 2.2 Consensus size: 42
61955 CCTCTTCAAC
* * *
61965 GATGACAGTGGCCTCTTGAACGGTGGGAGGGGACTCTTGAGG
1 GATGACAGGGGCCTCTTGAACGATGAGAGGGGACTCTTGAGG
* * **
62007 GATGATAGGGGCCTCTTGAACGAT-AGAGGAGGCCTCTTGAAT
1 GATGACAGGGGCCTCTTGAACGATGAGAGG-GGACTCTTGAGG
62049 GATGACAGG
1 GATGACAGG
62058 TGAGTCAGGC
Statistics
Matches: 42, Mismatches: 8, Indels: 2
0.81 0.15 0.04
Matches are distributed among these distances:
41 4 0.10
42 38 0.90
ACGTcount: A:0.24, C:0.16, G:0.39, T:0.22
Consensus pattern (42 bp):
GATGACAGGGGCCTCTTGAACGATGAGAGGGGACTCTTGAGG
Found at i:62578 original size:20 final size:20
Alignment explanation
Indices: 62553--62628 Score: 125
Period size: 20 Copynumber: 3.8 Consensus size: 20
62543 TCGCAACACG
*
62553 AATGACTATCGCAACGCAAA
1 AATGACTATCGCAACGCGAA
62573 AATGACTATCGCAACGCGAA
1 AATGACTATCGCAACGCGAA
62593 AATGACTATCGCAACGCGAA
1 AATGACTATCGCAACGCGAA
**
62613 TTTGACTATCGCAACG
1 AATGACTATCGCAACG
62629 AGAGAATCGC
Statistics
Matches: 53, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 53 1.00
ACGTcount: A:0.38, C:0.25, G:0.18, T:0.18
Consensus pattern (20 bp):
AATGACTATCGCAACGCGAA
Found at i:62869 original size:18 final size:18
Alignment explanation
Indices: 62846--62895 Score: 100
Period size: 18 Copynumber: 2.8 Consensus size: 18
62836 TTTACTAAGC
62846 AATCTAAGTGAAATGGTT
1 AATCTAAGTGAAATGGTT
62864 AATCTAAGTGAAATGGTT
1 AATCTAAGTGAAATGGTT
62882 AATCTAAGTGAAAT
1 AATCTAAGTGAAAT
62896 TACGAGTAAA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 32 1.00
ACGTcount: A:0.42, C:0.06, G:0.20, T:0.32
Consensus pattern (18 bp):
AATCTAAGTGAAATGGTT
Found at i:64712 original size:19 final size:20
Alignment explanation
Indices: 64625--64731 Score: 101
Period size: 20 Copynumber: 5.5 Consensus size: 20
64615 TCTAAAAGTT
*
64625 AAAATCGCAACACGAAAATG
1 AAAATCGCAACGCGAAAATG
**
64645 AAAATCGCAACATGAAAATG
1 AAAATCGCAACGCGAAAATG
** * **
64665 ACTATCGCATCGCGAATTTG
1 AAAATCGCAACGCGAAAATG
**
64685 ACTATCGCAACGC-AAAATG
1 AAAATCGCAACGCGAAAATG
*
64704 AAAATCGCAACGCGAAACTG
1 AAAATCGCAACGCGAAAATG
64724 -AAATCGCA
1 AAAATCGCA
64732 TTGCGATTCT
Statistics
Matches: 72, Mismatches: 14, Indels: 3
0.81 0.16 0.03
Matches are distributed among these distances:
19 23 0.32
20 49 0.68
ACGTcount: A:0.45, C:0.22, G:0.17, T:0.16
Consensus pattern (20 bp):
AAAATCGCAACGCGAAAATG
Found at i:65132 original size:22 final size:22
Alignment explanation
Indices: 65105--65147 Score: 68
Period size: 22 Copynumber: 2.0 Consensus size: 22
65095 GAGATAGACG
65105 GATTTCACCGGAGATGGGGACT
1 GATTTCACCGGAGATGGGGACT
**
65127 GATTTCGTCGGAGATGGGGAC
1 GATTTCACCGGAGATGGGGAC
65148 GGATGTTGCG
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.21, C:0.16, G:0.40, T:0.23
Consensus pattern (22 bp):
GATTTCACCGGAGATGGGGACT
Found at i:65348 original size:20 final size:20
Alignment explanation
Indices: 65323--65440 Score: 148
Period size: 20 Copynumber: 5.9 Consensus size: 20
65313 CGCTTTGAAA
65323 AATCGCATTGCGATAGTCAG
1 AATCGCATTGCGATAGTCAG
*
65343 AATCGCGTTGCGATAGTCAG
1 AATCGCATTGCGATAGTCAG
* *
65363 AATCTCGTTGCGATAGTCAG
1 AATCGCATTGCGATAGTCAG
*
65383 AATCGCATTGCGATAGTCAT
1 AATCGCATTGCGATAGTCAG
* * *
65403 ACTCGCATTGCGAT-TTACAT
1 AATCGCATTGCGATAGT-CAG
*
65423 ATTCGCATTGCGATAGTC
1 AATCGCATTGCGATAGTC
65441 GGAAAATCGC
Statistics
Matches: 87, Mismatches: 9, Indels: 4
0.87 0.09 0.04
Matches are distributed among these distances:
19 1 0.01
20 85 0.98
21 1 0.01
ACGTcount: A:0.26, C:0.21, G:0.23, T:0.30
Consensus pattern (20 bp):
AATCGCATTGCGATAGTCAG
Found at i:65793 original size:22 final size:22
Alignment explanation
Indices: 65768--65812 Score: 56
Period size: 22 Copynumber: 2.0 Consensus size: 22
65758 ACTTTAAGTT
*
65768 TAAAGTTAACATAAATT-CTTAA
1 TAAAGTTAA-ACAAATTACTTAA
*
65790 TAAATTTAAACAAATTACTTAA
1 TAAAGTTAAACAAATTACTTAA
65812 T
1 T
65813 GTTTGGTTTG
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
21 6 0.30
22 14 0.70
ACGTcount: A:0.51, C:0.09, G:0.02, T:0.38
Consensus pattern (22 bp):
TAAAGTTAAACAAATTACTTAA
Found at i:66681 original size:2 final size:2
Alignment explanation
Indices: 66674--66703 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
66664 GTAGTTTTCC
66674 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
66704 AGTAGCCGGT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:70546 original size:41 final size:40
Alignment explanation
Indices: 70491--70569 Score: 97
Period size: 41 Copynumber: 1.9 Consensus size: 40
70481 TGTGAACAAC
* *
70491 AAAGCATATGGGTAGATATCATGT-CGGGTAGGATCTACG
1 AAAGCATATGGGTAGATAGCATGTGAGGGTAGGATCTACG
* *
70530 AAAGCATGATTGGGTAGCTAGCATGTGAGGGTAGGTTCTA
1 AAAGCAT-A-TGGGTAGATAGCATGTGAGGGTAGGATCTA
70570 TTTGATGTAT
Statistics
Matches: 33, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
39 7 0.21
40 1 0.03
41 14 0.42
42 11 0.33
ACGTcount: A:0.29, C:0.11, G:0.33, T:0.27
Consensus pattern (40 bp):
AAAGCATATGGGTAGATAGCATGTGAGGGTAGGATCTACG
Found at i:70911 original size:21 final size:21
Alignment explanation
Indices: 70888--70959 Score: 92
Period size: 21 Copynumber: 3.4 Consensus size: 21
70878 CCAAGGATGA
*
70888 GAAGACCGTTCATAAAGACGA-
1 GAAGACCATTCATAAAGAC-AT
* *
70909 GAAGACCATTCACCAAGGACAT
1 GAAGACCATTCA-TAAAGACAT
70931 GAAGACCATTCATAAAGACAT
1 GAAGACCATTCATAAAGACAT
70952 GAAGACCA
1 GAAGACCA
70960 CTTCGCATTG
Statistics
Matches: 44, Mismatches: 5, Indels: 4
0.83 0.09 0.08
Matches are distributed among these distances:
21 27 0.61
22 17 0.39
ACGTcount: A:0.44, C:0.22, G:0.19, T:0.14
Consensus pattern (21 bp):
GAAGACCATTCATAAAGACAT
Found at i:71231 original size:13 final size:13
Alignment explanation
Indices: 71205--71249 Score: 65
Period size: 13 Copynumber: 3.5 Consensus size: 13
71195 TAACACCTTG
71205 TGCA-TTTGCATT
1 TGCATTTTGCATT
*
71217 TGCATTTTTCATT
1 TGCATTTTGCATT
71230 TGCATTTTGCATTT
1 TGCATTTTGCA-TT
71244 TGCATT
1 TGCATT
71250 GCATGTAGTT
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
12 4 0.14
13 17 0.59
14 8 0.28
ACGTcount: A:0.16, C:0.16, G:0.13, T:0.56
Consensus pattern (13 bp):
TGCATTTTGCATT
Found at i:71231 original size:19 final size:19
Alignment explanation
Indices: 71205--71253 Score: 73
Period size: 19 Copynumber: 2.6 Consensus size: 19
71195 TAACACCTTG
71205 TGCATTTGCATTTGCATTT
1 TGCATTTGCATTTGCATTT
*
71224 TTCATTTGCATTTTGCATTT
1 TGCATTTGCA-TTTGCATTT
71244 TGCA-TTGCAT
1 TGCATTTGCAT
71254 GTAGTTATTT
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
18 1 0.04
19 14 0.52
20 12 0.44
ACGTcount: A:0.16, C:0.16, G:0.14, T:0.53
Consensus pattern (19 bp):
TGCATTTGCATTTGCATTT
Found at i:71238 original size:7 final size:7
Alignment explanation
Indices: 71205--71249 Score: 60
Period size: 7 Copynumber: 6.9 Consensus size: 7
71195 TAACACCTTG
71205 TGCA-TT
1 TGCATTT
71211 TGCA-TT
1 TGCATTT
71217 TGCATTT
1 TGCATTT
*
71224 TTCA-TT
1 TGCATTT
71230 TGCATTT
1 TGCATTT
71237 TGCATTT
1 TGCATTT
71244 TGCATT
1 TGCATT
71250 GCATGTAGTT
Statistics
Matches: 35, Mismatches: 2, Indels: 3
0.88 0.05 0.08
Matches are distributed among these distances:
6 15 0.43
7 20 0.57
ACGTcount: A:0.16, C:0.16, G:0.13, T:0.56
Consensus pattern (7 bp):
TGCATTT
Found at i:72842 original size:20 final size:21
Alignment explanation
Indices: 72809--72855 Score: 87
Period size: 20 Copynumber: 2.3 Consensus size: 21
72799 TTTGAAAATG
72809 TTTTTGTTGTTTTTTCTCAAC
1 TTTTTGTTGTTTTTTCTCAAC
72830 TTTTTGTTG-TTTTTCTCAAC
1 TTTTTGTTGTTTTTTCTCAAC
72850 TTTTTG
1 TTTTTG
72856 AAAGGATTTT
Statistics
Matches: 26, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
20 17 0.65
21 9 0.35
ACGTcount: A:0.09, C:0.13, G:0.11, T:0.68
Consensus pattern (21 bp):
TTTTTGTTGTTTTTTCTCAAC
Found at i:75090 original size:124 final size:124
Alignment explanation
Indices: 74881--75104 Score: 297
Period size: 124 Copynumber: 1.8 Consensus size: 124
74871 GGGGCACGAC
* * * *
74881 TGAACCCACATCATGCTGAGATGGCAAGATTCAGACCAAGGAGGCATGAATAATGAGCCTTACAA
1 TGAACCCACATCATACTGAGATGGCAAGATTCAGACCAAGAAGGCATGAAGAATAAGCCTTACAA
* * * *
74946 TTTGAGGTGATGAGGCATTTTGAAGGCCCGTACCAGTTAAGACACTGATGGGGAATGAT
66 TCTAAGATGATGAGGCATTTTGAAGACCCGTACCAGTTAAGACACTGATGGGGAATGAT
* * * * *
75005 TGAACCCATATCATATTGAGA-GGACAAGATTTAGACCAAGAAGGCATTAAGAGTAAGCCTTACA
1 TGAACCCACATCATACTGAGATGG-CAAGATTCAGACCAAGAAGGCATGAAGAATAAGCCTTACA
* *
75069 ATCTAAGATGTTGGGGCATTTTGAAGACCCGTACCA
65 ATCTAAGATGATGAGGCATTTTGAAGACCCGTACCA
75105 TTATAAAATG
Statistics
Matches: 84, Mismatches: 15, Indels: 2
0.83 0.15 0.02
Matches are distributed among these distances:
123 2 0.02
124 82 0.98
ACGTcount: A:0.34, C:0.18, G:0.25, T:0.23
Consensus pattern (124 bp):
TGAACCCACATCATACTGAGATGGCAAGATTCAGACCAAGAAGGCATGAAGAATAAGCCTTACAA
TCTAAGATGATGAGGCATTTTGAAGACCCGTACCAGTTAAGACACTGATGGGGAATGAT
Found at i:77125 original size:54 final size:54
Alignment explanation
Indices: 76887--77494 Score: 692
Period size: 54 Copynumber: 11.2 Consensus size: 54
76877 GAAGCAAAAT
* * **
76887 AAGATTTTCGAGTTCTATACTCCCTGAAGAAAGAAGGAGCGAACCCGT---TTG
1 AAGATTTTCGAGTTCTATACTTCCTGAAGAAAGAGGGAGCGAACCCGTAAGAAG
** * * * ****
76938 AAGATTTTTTAGTTCTATACTCCCTGAAGAAAGAGGGAGCAAACCCATTTTCAG
1 AAGATTTTCGAGTTCTATACTTCCTGAAGAAAGAGGGAGCGAACCCGTAAGAAG
* * **
76992 AAGATTGTTCGAGTTCTATAC-TCTCTGAATAAAGATGGAGCGAACCCGT---TTG
1 AAGATT-TTCGAGTTCTATACTTC-CTGAAGAAAGAGGGAGCGAACCCGTAAGAAG
* **
77044 AAGATTTTCGAGTTCTATACTCCCTGAAGAAAGAGGGAGCGAACCCGTTTGAAG
1 AAGATTTTCGAGTTCTATACTTCCTGAAGAAAGAGGGAGCGAACCCGTAAGAAG
* * ** *
77098 AAGATGTTCGAGTTCTATACTCCCTGAAGAAAGAGGGAGTAAACCCATAAGAAG
1 AAGATTTTCGAGTTCTATACTTCCTGAAGAAAGAGGGAGCGAACCCGTAAGAAG
* *
77152 AAGATTTTCGAGTTCTATATTTCCTGAAGAAAGAGGTAGCGAACCCGTAAGAAG
1 AAGATTTTCGAGTTCTATACTTCCTGAAGAAAGAGGGAGCGAACCCGTAAGAAG
* *
77206 AAGATTCTCGAGTTCTATACTTCCTGAAGAAAGAGGGAGCGAACCCATAAGAAG
1 AAGATTTTCGAGTTCTATACTTCCTGAAGAAAGAGGGAGCGAACCCGTAAGAAG
* * **
77260 AAGATTTTTGAGTTCTATACTTCTTGAAGAAAGAGGGAGCGAACCCGTTTGAAG
1 AAGATTTTCGAGTTCTATACTTCCTGAAGAAAGAGGGAGCGAACCCGTAAGAAG
** *
77314 AAGATGATCGAGCTT-TATATTTCCTGAAGAAAGAGGGAGCGAAGCGAACTCGTAAGAAG
1 AAGATTTTCGAG-TTCTATACTTCCTGAAGAAAGAGGGAGCGAA-C---C-CGTAAGAAG
* * *
77373 AAGATTCTCGAGTTCTATACTTCCTGAAGAGAGAGGGAGCGAACCCGTAAGAAA
1 AAGATTTTCGAGTTCTATACTTCCTGAAGAAAGAGGGAGCGAACCCGTAAGAAG
** *
77427 AAGATTTTTTTAGTTCTATACTTCCTGAAGAAAGAGGGAGCAAACCCGTAAGAAG
1 AAGA-TTTTCGAGTTCTATACTTCCTGAAGAAAGAGGGAGCGAACCCGTAAGAAG
*
77482 AAGACTTTCGAGT
1 AAGATTTTCGAGT
77495 AAGAAGCAGA
Statistics
Matches: 475, Mismatches: 65, Indels: 31
0.83 0.11 0.05
Matches are distributed among these distances:
51 80 0.17
52 8 0.02
54 255 0.54
55 85 0.18
58 4 0.01
59 43 0.09
ACGTcount: A:0.34, C:0.17, G:0.24, T:0.25
Consensus pattern (54 bp):
AAGATTTTCGAGTTCTATACTTCCTGAAGAAAGAGGGAGCGAACCCGTAAGAAG
Found at i:77540 original size:74 final size:74
Alignment explanation
Indices: 77419--77568 Score: 246
Period size: 74 Copynumber: 2.0 Consensus size: 74
77409 GAGCGAACCC
*
77419 GTAAGAAAAAGATTTTTTTAGTTCTATACTTCCTGAAGAAAGAGGGAGCAAACCCGTAAGAAGAA
1 GTAAGAAAAAGATTTTTTGAGTTCTATACTTCCTGAAGAAAGAGGGAGCAAACCCGTAAGAAGAA
*
77484 GACTTTCGA
66 AACTTTCGA
** *
77493 GTAAGAAGCAGATTTTTTGAGTTCTATACTTCCTGAAGAAAGAGGGAGCGAACCCGTAAGAAGAA
1 GTAAGAAAAAGATTTTTTGAGTTCTATACTTCCTGAAGAAAGAGGGAGCAAACCCGTAAGAAGAA
*
77558 AATTTTCGA
66 AACTTTCGA
77567 GT
1 GT
77569 TCTATACTCC
Statistics
Matches: 70, Mismatches: 6, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
74 70 1.00
ACGTcount: A:0.37, C:0.13, G:0.23, T:0.26
Consensus pattern (74 bp):
GTAAGAAAAAGATTTTTTGAGTTCTATACTTCCTGAAGAAAGAGGGAGCAAACCCGTAAGAAGAA
AACTTTCGA
Found at i:77582 original size:54 final size:54
Alignment explanation
Indices: 77506--77750 Score: 391
Period size: 54 Copynumber: 4.5 Consensus size: 54
77496 AGAAGCAGAT
*
77506 TTTTTGAGTTCTATACTTCCTGAAGAAAGAGGGAGCGAACCCGTAAGAAGAAAA
1 TTTTCGAGTTCTATACTTCCTGAAGAAAGAGGGAGCGAACCCGTAAGAAGAAAA
* *
77560 TTTTCGAGTTCTATACTCCCTGAAGAAAGAGGGAGCGAACCCGTAAGAAGAAGA
1 TTTTCGAGTTCTATACTTCCTGAAGAAAGAGGGAGCGAACCCGTAAGAAGAAAA
* *
77614 TTCTCGAGTTCTATACTTCCTGAAGAAAGAGGGAGCGAACCCGTAAGAAGAAGATT
1 TTTTCGAGTTCTATACTTCCTGAAGAAAGAGGGAGCGAACCCGTAAGAAGAA-A-A
* * *
77670 TTTTTGAGTTCTATACTTTCTGAAGAAAGAGGGAGCGAACCCGTAAGAAGAAGA
1 TTTTCGAGTTCTATACTTCCTGAAGAAAGAGGGAGCGAACCCGTAAGAAGAAAA
*
77724 TTTTCGAGTTCTATACTCCCTGAAGAA
1 TTTTCGAGTTCTATACTTCCTGAAGAA
77751 TAGGGAACAT
Statistics
Matches: 174, Mismatches: 15, Indels: 4
0.90 0.08 0.02
Matches are distributed among these distances:
54 125 0.72
56 49 0.28
ACGTcount: A:0.34, C:0.17, G:0.24, T:0.25
Consensus pattern (54 bp):
TTTTCGAGTTCTATACTTCCTGAAGAAAGAGGGAGCGAACCCGTAAGAAGAAAA
Found at i:77602 original size:128 final size:128
Alignment explanation
Indices: 77365--77622 Score: 396
Period size: 128 Copynumber: 2.0 Consensus size: 128
77355 AAGCGAACTC
*
77365 GTAAGAAGAAGATTCTCGAGTTCTATACTTCCTGAAGAGAGAGGGAGCGAACCCGTAAGAAAAAG
1 GTAAGAAGAAGATTCTCGAGTTCTATACTTCCTGAAGAAAGAGGGAGCGAACCCGTAAGAAAAAG
** *
77430 ATTTTTTTAGTTCTATACTTCCTGAAGAAAGAGGGAGCAAACCCGTAAGAAGAAGACTT-TCGA
66 ATTTTTCGAGTTCTATACTCCCTGAAGAAAGAGGGAGCAAACCCGTAAGAAGAAGA-TTCTCGA
* * *
77493 GTAAGAAGCAGATTTTTTGAGTTCTATACTTCCTGAAGAAAGAGGGAGCGAACCCGTAAGAAGAA
1 GTAAGAAGAAGA-TTCTCGAGTTCTATACTTCCTGAAGAAAGAGGGAGCGAACCCGTAAGAA-AA
*
77558 A-A-TTTTCGAGTTCTATACTCCCTGAAGAAAGAGGGAGCGAACCCGTAAGAAGAAGATTCTCGA
64 AGATTTTTCGAGTTCTATACTCCCTGAAGAAAGAGGGAGCAAACCCGTAAGAAGAAGATTCTCGA
77621 GT
1 GT
77623 TCTATACTTC
Statistics
Matches: 119, Mismatches: 8, Indels: 6
0.89 0.06 0.05
Matches are distributed among these distances:
127 2 0.02
128 67 0.56
129 47 0.39
130 3 0.03
ACGTcount: A:0.36, C:0.16, G:0.25, T:0.23
Consensus pattern (128 bp):
GTAAGAAGAAGATTCTCGAGTTCTATACTTCCTGAAGAAAGAGGGAGCGAACCCGTAAGAAAAAG
ATTTTTCGAGTTCTATACTCCCTGAAGAAAGAGGGAGCAAACCCGTAAGAAGAAGATTCTCGA
Found at i:77731 original size:110 final size:108
Alignment explanation
Indices: 77493--77750 Score: 417
Period size: 110 Copynumber: 2.4 Consensus size: 108
77483 AGACTTTCGA
* *
77493 GTAAGAAGCAGATTTTTTGAGTTCTATACTTCCTGAAGAAAGAGGGAGCGAACCCGTAAGAAGAA
1 GTAAGAAGAAGA-TTTTCGAGTTCTATACTTCCTGAAGAAAGAGGGAGCGAACCCGTAAGAAGAA
77558 AATTTTCGAGTTCTATACTCCCTGAAGAAAGAGGGAGCGAACCC
65 AATTTTCGAGTTCTATACTCCCTGAAGAAAGAGGGAGCGAACCC
*
77602 GTAAGAAGAAGATTCTCGAGTTCTATACTTCCTGAAGAAAGAGGGAGCGAACCCGTAAGAAGAAG
1 GTAAGAAGAAGATTTTCGAGTTCTATACTTCCTGAAGAAAGAGGGAGCGAACCCGTAAGAAGAA-
* * **
77667 ATTTTTTTGAGTTCTATACTTTCTGAAGAAAGAGGGAGCGAACCC
65 A-ATTTTCGAGTTCTATACTCCCTGAAGAAAGAGGGAGCGAACCC
*
77712 GTAAGAAGAAGATTTTCGAGTTCTATACTCCCTGAAGAA
1 GTAAGAAGAAGATTTTCGAGTTCTATACTTCCTGAAGAA
77751 TAGGGAACAT
Statistics
Matches: 138, Mismatches: 9, Indels: 3
0.92 0.06 0.02
Matches are distributed among these distances:
108 50 0.36
109 12 0.09
110 76 0.55
ACGTcount: A:0.35, C:0.16, G:0.24, T:0.24
Consensus pattern (108 bp):
GTAAGAAGAAGATTTTCGAGTTCTATACTTCCTGAAGAAAGAGGGAGCGAACCCGTAAGAAGAAA
ATTTTCGAGTTCTATACTCCCTGAAGAAAGAGGGAGCGAACCC
Found at i:77829 original size:55 final size:54
Alignment explanation
Indices: 77719--78220 Score: 686
Period size: 55 Copynumber: 9.2 Consensus size: 54
77709 CCCGTAAGAA
* * *
77719 GAAGATT-TTCGAGT-TCTATACTCCCTGAAGAATAGGGAACATACACGATTGTT
1 GAAGATTGTTCGAGTCTC-ATACTCTCTGAAGAATAGGGAGCAGACACGATTGTT
* * * *
77772 GAAGATTGTTTGAGTCTTATACTCTCTGAAAGAATAGGGAGCAGACACAATTATT
1 GAAGATTGTTCGAGTCTCATACTCTCTG-AAGAATAGGGAGCAGACACGATTGTT
* ** *
77827 GAAGATTGTTTGAGTCTCATACTCTCTGAAAGAATAGGGAGCAGACATAATTATT
1 GAAGATTGTTCGAGTCTCATACTCTCTG-AAGAATAGGGAGCAGACACGATTGTT
* *
77882 AAAGATTGTTCGAGTCTCATACTCTCTGAAGAAATAGGGAGCAGACATGATTGTT
1 GAAGATTGTTCGAGTCTCATACTCTCTGAAG-AATAGGGAGCAGACACGATTGTT
*
77937 GAAGATTGTTCGAGTCTTATACTCTCTGAAGAAATAGGGAGCAGACACGATTGTT
1 GAAGATTGTTCGAGTCTCATACTCTCTGAAG-AATAGGGAGCAGACACGATTGTT
* *
77992 GAAGATTGTTCGAGTCTAATACTCTCTGAAGAAATAGGGAGCATACACGATTGTT
1 GAAGATTGTTCGAGTCTCATACTCTCTGAAG-AATAGGGAGCAGACACGATTGTT
* *
78047 GAAGATTGTTCGAGTCTCATACTCTCTGAAGAAATAAGGAGCATACACGATTGTT
1 GAAGATTGTTCGAGTCTCATACTCTCTGAAG-AATAGGGAGCAGACACGATTGTT
* *
78102 -AAGATTGTTTGAGTCTCATACTCTCTGAAGGAATAAGGAGCAGACACGATTGTT
1 GAAGATTGTTCGAGTCTCATACTCTCTGAA-GAATAGGGAGCAGACACGATTGTT
* * *
78156 GAAGATTGTTCGAGTCTTATACTCTCTGAAGAGATAGGGGGAAGACACGATTGTT
1 GAAGATTGTTCGAGTCTCATACTCTCTGAAGA-ATAGGGAGCAGACACGATTGTT
*
78211 AAAGATTGTT
1 GAAGATTGTT
78221 TGAGCCGACG
Statistics
Matches: 414, Mismatches: 28, Indels: 12
0.91 0.06 0.03
Matches are distributed among these distances:
53 7 0.02
54 70 0.17
55 337 0.81
ACGTcount: A:0.32, C:0.14, G:0.24, T:0.30
Consensus pattern (54 bp):
GAAGATTGTTCGAGTCTCATACTCTCTGAAGAATAGGGAGCAGACACGATTGTT
Found at i:79130 original size:17 final size:17
Alignment explanation
Indices: 79108--79140 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
79098 CTGCTGAAGC
79108 CCCGTGACCAGCTCGCG
1 CCCGTGACCAGCTCGCG
*
79125 CCCGTGACCTGCTCGC
1 CCCGTGACCAGCTCGC
79141 TCCAGAGCCC
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.09, C:0.48, G:0.27, T:0.15
Consensus pattern (17 bp):
CCCGTGACCAGCTCGCG
Found at i:85984 original size:2 final size:2
Alignment explanation
Indices: 85977--86026 Score: 100
Period size: 2 Copynumber: 25.0 Consensus size: 2
85967 ATATTCACTA
85977 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
86019 AT AT AT AT
1 AT AT AT AT
86027 TCATAAAATT
Statistics
Matches: 48, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 48 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:86167 original size:46 final size:47
Alignment explanation
Indices: 86105--86236 Score: 133
Period size: 53 Copynumber: 2.7 Consensus size: 47
86095 CTTACACCGA
* * * *
86105 TGTAAGTATATATTAATTGCTAAGATATTGAG-CATACTTATATTTG
1 TGTAAGTATGTGTTAATTTCTAAGATATTGAGACATACTTATATTGG
*
86151 TGTAAGTATGTGTTAATTTTTAAGATATTGAGAGATGTACATACTTATATTGG
1 TGTAAGTATGTGTTAATTTCTAAGATATT----GA-G-ACATACTTATATTGG
*
86204 TGTAAGTTTGTGTTAATTTCTAATG-TATTGAGA
1 TGTAAGTATGTGTTAATTTCTAA-GATATTGAGA
86237 GATCTATATA
Statistics
Matches: 71, Mismatches: 7, Indels: 15
0.76 0.08 0.16
Matches are distributed among these distances:
46 25 0.35
47 1 0.01
48 1 0.01
49 2 0.03
50 2 0.03
51 1 0.01
53 38 0.54
54 1 0.01
ACGTcount: A:0.32, C:0.05, G:0.19, T:0.45
Consensus pattern (47 bp):
TGTAAGTATGTGTTAATTTCTAAGATATTGAGACATACTTATATTGG
Found at i:86217 original size:53 final size:53
Alignment explanation
Indices: 86137--86327 Score: 222
Period size: 53 Copynumber: 3.6 Consensus size: 53
86127 AGATATTGAG
* *
86137 CATACTTATATTTGTGTAAGTATGTGTTAATTTTTAAGATATTGAGAGATGTA
1 CATACTTATATTAGTGTAAGTATGTGTTAATTTCTAAGATATTGAGAGATGTA
* * *
86190 CATACTTATATTGGTGTAAGTTTGTGTTAATTTCTAATG-TATTGAGAGATCTA
1 CATACTTATATTAGTGTAAGTATGTGTTAATTTCTAA-GATATTGAGAGATGTA
* * * * * *
86243 TATACTTACATCAATATAAGTGTGTGTTAATTTCTAAGATATTGAGAGATGTA
1 CATACTTATATTAGTGTAAGTATGTGTTAATTTCTAAGATATTGAGAGATGTA
* * * * *
86296 TATATTTATACTAGTGTAAGAATATGTTAATT
1 CATACTTATATTAGTGTAAGTATGTGTTAATT
86328 GCTACACTTT
Statistics
Matches: 115, Mismatches: 21, Indels: 4
0.82 0.15 0.03
Matches are distributed among these distances:
52 1 0.01
53 113 0.98
54 1 0.01
ACGTcount: A:0.33, C:0.06, G:0.17, T:0.44
Consensus pattern (53 bp):
CATACTTATATTAGTGTAAGTATGTGTTAATTTCTAAGATATTGAGAGATGTA
Found at i:87797 original size:2 final size:2
Alignment explanation
Indices: 87790--87818 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
87780 TGCACATCAC
87790 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
87819 TAGTTTTTTT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:92607 original size:22 final size:23
Alignment explanation
Indices: 92581--92632 Score: 77
Period size: 25 Copynumber: 2.2 Consensus size: 23
92571 AATGAAAGTG
92581 TTTTTCTAAGTTAAAGATTATTT
1 TTTTTCTAAGTTAAAGATTATTT
*
92604 TTTTCTCATAAGTTACAGATTATTT
1 TTTT-TC-TAAGTTAAAGATTATTT
92629 TTTT
1 TTTT
92633 CTCATAATAA
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
23 4 0.15
24 2 0.08
25 20 0.77
ACGTcount: A:0.27, C:0.08, G:0.08, T:0.58
Consensus pattern (23 bp):
TTTTTCTAAGTTAAAGATTATTT
Found at i:92618 original size:25 final size:25
Alignment explanation
Indices: 92587--92639 Score: 97
Period size: 25 Copynumber: 2.1 Consensus size: 25
92577 AGTGTTTTTC
92587 TAAGTTAAAGATTATTTTTTTCTCA
1 TAAGTTAAAGATTATTTTTTTCTCA
*
92612 TAAGTTACAGATTATTTTTTTCTCA
1 TAAGTTAAAGATTATTTTTTTCTCA
92637 TAA
1 TAA
92640 TAAATTAAGA
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
25 27 1.00
ACGTcount: A:0.32, C:0.09, G:0.08, T:0.51
Consensus pattern (25 bp):
TAAGTTAAAGATTATTTTTTTCTCA
Found at i:93970 original size:2 final size:2
Alignment explanation
Indices: 93965--93999 Score: 63
Period size: 2 Copynumber: 18.0 Consensus size: 2
93955 TTTTAAAAAA
93965 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT -T AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
94000 GTATCTATTT
Statistics
Matches: 32, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 31 0.97
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
AT
Found at i:94734 original size:20 final size:20
Alignment explanation
Indices: 94640--95088 Score: 582
Period size: 20 Copynumber: 22.4 Consensus size: 20
94630 GATTTTCCAT
* ** *
94640 AATCGCAACGCGAATATGAA
1 AATCGCAACGCGTATCCGTA
* *
94660 AATCGCAACGCG-AACACATA
1 AATCGCAACGCGTATC-CGTA
94680 AATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
*
94700 AATCGCAACGTGTATCCGTA
1 AATCGCAACGCGTATCCGTA
**
94720 AATCGCAACGCGTATGGGTA
1 AATCGCAACGCGTATCCGTA
*
94740 AATCGCAATGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
*
94760 TATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
94780 AATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
* *
94800 AACCGCAACGTGTATCCGTA
1 AATCGCAACGCGTATCCGTA
94820 AATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
*
94840 AATCGCAATGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
94860 AATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
* *
94880 AACCGCAACGTGTATCCGTA
1 AATCGCAACGCGTATCCGTA
94900 AATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
*
94920 AATCGCAATGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
94940 AATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
*
94960 AATCGCAACG-ATAATCCGTA
1 AATCGCAACGCGT-ATCCGTA
94980 AATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
*
95000 AATCGCAACG-ATAATCCGTA
1 AATCGCAACGCGT-ATCCGTA
* * *
95020 AATCGCAACGAGAATCTGTA
1 AATCGCAACGCGTATCCGTA
* *
95040 AATCGCAACG-ATAATCCGAA
1 AATCGCAACGCGT-ATCCGTA
* * *
95060 AATCGCAACGAGAATCTGTA
1 AATCGCAACGCGTATCCGTA
*
95080 AATCACAAC
1 AATCGCAAC
95089 ACTGAAATTT
Statistics
Matches: 377, Mismatches: 44, Indels: 16
0.86 0.10 0.04
Matches are distributed among these distances:
19 3 0.01
20 371 0.98
21 3 0.01
ACGTcount: A:0.34, C:0.27, G:0.19, T:0.20
Consensus pattern (20 bp):
AATCGCAACGCGTATCCGTA
Found at i:95800 original size:24 final size:24
Alignment explanation
Indices: 95761--95807 Score: 69
Period size: 24 Copynumber: 2.0 Consensus size: 24
95751 AAATTTGGTC
95761 TTGGTCAATATCCGGACTTTGATA
1 TTGGTCAATATCCGGACTTTGATA
*
95785 TTGGTCAATA-CACGGATTTTGAT
1 TTGGTCAATATC-CGGACTTTGAT
95808 GATGTTTCAG
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:0.26, C:0.15, G:0.21, T:0.38
Consensus pattern (24 bp):
TTGGTCAATATCCGGACTTTGATA
Found at i:95999 original size:12 final size:12
Alignment explanation
Indices: 95982--96006 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
95972 ATATAATCCT
95982 GAAGAAGAAAAA
1 GAAGAAGAAAAA
95994 GAAGAAGAAAAA
1 GAAGAAGAAAAA
96006 G
1 G
96007 TCCCCGAAGA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.72, C:0.00, G:0.28, T:0.00
Consensus pattern (12 bp):
GAAGAAGAAAAA
Found at i:98332 original size:19 final size:19
Alignment explanation
Indices: 98310--98744 Score: 570
Period size: 19 Copynumber: 24.4 Consensus size: 19
98300 CGGAAAATAC
*
98310 AATCGCAACGCGAAATGAA
1 AATCGCAATGCGAAATGAA
*
98329 AATCCCAA--C---ATGAA
1 AATCGCAATGCGAAATGAA
98343 AATCGCAATGCGGAAATGAA
1 AATCGCAATGC-GAAATGAA
*
98363 AATCGCAA--CG--A-GAG
1 AATCGCAATGCGAAATGAA
98377 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
98396 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
*
98415 AATCGCAACGCG--A-G--
1 AATCGCAATGCGAAATGAA
98429 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
98448 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
*
98467 AATCGCAATACGAAATGAA
1 AATCGCAATGCGAAATGAA
98486 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
98505 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
*
98524 AATCGCAA--CG--A-GAG
1 AATCGCAATGCGAAATGAA
98538 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
98557 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
*
98576 AATCGCAACGCG--A-G--
1 AATCGCAATGCGAAATGAA
98590 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
*
98609 AATCGCAATGCGAAATTAA
1 AATCGCAATGCGAAATGAA
*
98628 AATCGCAATACGAAATGAA
1 AATCGCAATGCGAAATGAA
98647 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
98666 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
98685 AATCGCAA--CGAAA-G--
1 AATCGCAATGCGAAATGAA
98699 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
98718 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
98737 AATCGCAA
1 AATCGCAA
98745 CGAGATAATC
Statistics
Matches: 369, Mismatches: 16, Indels: 62
0.83 0.04 0.14
Matches are distributed among these distances:
14 62 0.17
15 2 0.01
16 15 0.04
17 14 0.04
18 3 0.01
19 260 0.70
20 13 0.04
ACGTcount: A:0.47, C:0.18, G:0.21, T:0.14
Consensus pattern (19 bp):
AATCGCAATGCGAAATGAA
Found at i:98571 original size:161 final size:161
Alignment explanation
Indices: 98338--98766 Score: 813
Period size: 161 Copynumber: 2.7 Consensus size: 161
98328 AAATCCCAAC
98338 ATGAAAATCGCAATGCGGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAAATGAAAATCGCA
1 ATGAAAATCGCAATGC-GAAATGAAAATCGCAACGAGAGAATCGCAATGCGAAATGAAAATCGCA
98403 ATGCGAAATGAAAATCGCAACGCGAGAATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAAA
65 ATGCGAAATGAAAATCGCAACGCGAGAATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAAA
98468 ATCGCAATACGAAATGAAAATCGCAATGCGAA
130 ATCGCAATACGAAATGAAAATCGCAATGCGAA
98500 ATGAAAATCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAAATGAAAATCGCAA
1 ATGAAAATCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAAATGAAAATCGCAA
*
98565 TGCGAAATGAAAATCGCAACGCGAGAATCGCAATGCGAAATGAAAATCGCAATGCGAAATTAAAA
66 TGCGAAATGAAAATCGCAACGCGAGAATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAAAA
98630 TCGCAATACGAAATGAAAATCGCAATGCGAA
131 TCGCAATACGAAATGAAAATCGCAATGCGAA
*
98661 ATGAAAATCGCAATGCGAAATGAAAATCGCAACGAAAGAATCGCAATGCGAAATGAAAATCGCAA
1 ATGAAAATCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAAATGAAAATCGCAA
* *
98726 TGCGAAATGAAAATCGCAACGAGATAATCGCAATGCGAAAT
66 TGCGAAATGAAAATCGCAACGCGAGAATCGCAATGCGAAAT
98767 TATAAACGCA
Statistics
Matches: 263, Mismatches: 4, Indels: 1
0.98 0.01 0.00
Matches are distributed among these distances:
161 247 0.94
162 16 0.06
ACGTcount: A:0.47, C:0.17, G:0.21, T:0.15
Consensus pattern (161 bp):
ATGAAAATCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAAATGAAAATCGCAA
TGCGAAATGAAAATCGCAACGCGAGAATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAAAA
TCGCAATACGAAATGAAAATCGCAATGCGAA
Found at i:98782 original size:52 final size:52
Alignment explanation
Indices: 98338--98766 Score: 696
Period size: 52 Copynumber: 8.0 Consensus size: 52
98328 AAATCCCAAC
98338 ATGAAAATCGCAATGCGGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAA
1 ATGAAAATCGCAATGC-GAAATGAAAATCGCAACGAGAGAATCGCAATGCGAA
*
98391 ATGAAAATCGCAATGCGAAATGAAAATCGCAACGCGAGAATCGCAATGCGAA
1 ATGAAAATCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAA
*
98443 ATGAAAATCGCAATGCGAAATGAAAATCGCAATACGAAATGAAAATCGCAATGCGAA
1 ATGAAAATCGCAATGCGAAATGAAAATCGC-A-ACG--A-GAGAATCGCAATGCGAA
98500 ATGAAAATCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAA
1 ATGAAAATCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAA
*
98552 ATGAAAATCGCAATGCGAAATGAAAATCGCAACGCGAGAATCGCAATGCGAA
1 ATGAAAATCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAA
* *
98604 ATGAAAATCGCAATGCGAAATTAAAATCGCAATACGAAATGAAAATCGCAATGCGAA
1 ATGAAAATCGCAATGCGAAATGAAAATCGC-A-ACG--A-GAGAATCGCAATGCGAA
*
98661 ATGAAAATCGCAATGCGAAATGAAAATCGCAACGAAAGAATCGCAATGCGAA
1 ATGAAAATCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAA
*
98713 ATGAAAATCGCAATGCGAAATGAAAATCGCAACGAGATAATCGCAATGCGAA
1 ATGAAAATCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAA
98765 AT
1 AT
98767 TATAAACGCA
Statistics
Matches: 353, Mismatches: 13, Indels: 21
0.91 0.03 0.05
Matches are distributed among these distances:
52 228 0.65
53 20 0.06
54 6 0.02
55 6 0.02
56 2 0.01
57 91 0.26
ACGTcount: A:0.47, C:0.17, G:0.21, T:0.15
Consensus pattern (52 bp):
ATGAAAATCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAA
Found at i:98882 original size:19 final size:19
Alignment explanation
Indices: 98773--98874 Score: 151
Period size: 19 Copynumber: 5.6 Consensus size: 19
98763 AAATTATAAA
98773 CGCATTGCGATTTTCATTT
1 CGCATTGCGATTTTCATTT
98792 CCGCATTGCGATTTTCATTT
1 -CGCATTGCGATTTTCATTT
*
98812 CGCATTGCGA--TTC-TCT
1 CGCATTGCGATTTTCATTT
98828 CG--TTGCGATTTTCATTT
1 CGCATTGCGATTTTCATTT
98845 CGCATTGCGATTTTCATTT
1 CGCATTGCGATTTTCATTT
98864 CGCATTGCGAT
1 CGCATTGCGAT
98875 AGTCATTTTG
Statistics
Matches: 75, Mismatches: 2, Indels: 11
0.85 0.02 0.12
Matches are distributed among these distances:
14 6 0.08
16 7 0.09
17 7 0.09
19 36 0.48
20 19 0.25
ACGTcount: A:0.15, C:0.24, G:0.18, T:0.44
Consensus pattern (19 bp):
CGCATTGCGATTTTCATTT
Found at i:98999 original size:14 final size:14
Alignment explanation
Indices: 98980--99016 Score: 65
Period size: 14 Copynumber: 2.6 Consensus size: 14
98970 CATCAATTAC
98980 ACAAATCAACTTTT
1 ACAAATCAACTTTT
*
98994 ACAAATCATCTTTT
1 ACAAATCAACTTTT
99008 ACAAATCAA
1 ACAAATCAA
99017 TTAAACAATC
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.46, C:0.22, G:0.00, T:0.32
Consensus pattern (14 bp):
ACAAATCAACTTTT
Found at i:99028 original size:12 final size:12
Alignment explanation
Indices: 99011--99083 Score: 53
Period size: 12 Copynumber: 6.0 Consensus size: 12
99001 ATCTTTTACA
99011 AATCAATTAAAC
1 AATCAATTAAAC
*
99023 AATCAA--AAATTG
1 AATCAATTAAA--C
**
99035 AATCAACTTTTAC
1 AATCAA-TTAAAC
99048 AAATCAATTAAAC
1 A-ATCAATTAAAC
*
99061 AATCAA-AAAAC
1 AATCAATTAAAC
99072 AATCAATTAAAC
1 AATCAATTAAAC
99084 TATTGAATCA
Statistics
Matches: 46, Mismatches: 8, Indels: 14
0.68 0.12 0.21
Matches are distributed among these distances:
10 3 0.07
11 10 0.22
12 21 0.46
13 6 0.13
14 5 0.11
15 1 0.02
ACGTcount: A:0.58, C:0.16, G:0.01, T:0.25
Consensus pattern (12 bp):
AATCAATTAAAC
Found at i:99045 original size:38 final size:38
Alignment explanation
Indices: 98997--99069 Score: 137
Period size: 38 Copynumber: 1.9 Consensus size: 38
98987 AACTTTTACA
*
98997 AATCATCTTTTACAAATCAATTAAACAATCAAAAATTG
1 AATCAACTTTTACAAATCAATTAAACAATCAAAAATTG
99035 AATCAACTTTTACAAATCAATTAAACAATCAAAAA
1 AATCAACTTTTACAAATCAATTAAACAATCAAAAA
99070 ACAATCAATT
Statistics
Matches: 34, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
38 34 1.00
ACGTcount: A:0.53, C:0.16, G:0.01, T:0.29
Consensus pattern (38 bp):
AATCAACTTTTACAAATCAATTAAACAATCAAAAATTG
Found at i:100926 original size:19 final size:19
Alignment explanation
Indices: 100886--101020 Score: 137
Period size: 19 Copynumber: 7.6 Consensus size: 19
100876 TAGTTTACTT
* *
100886 TCGCAACACGAAACTTAAAA
1 TCGCAACGCGAAA-TGAAAA
**
100906 TCGCAACGCGAAACCAAAA
1 TCGCAACGCGAAATGAAAA
100925 TCGCAACGCGAAATGAAAA
1 TCGCAACGCGAAATGAAAA
*
100944 TCGCAA--CGACA-G--AA
1 TCGCAACGCGAAATGAAAA
100958 TCGCAACGCGAAATGAAAA
1 TCGCAACGCGAAATGAAAA
100977 TCGCAA--CGAAA-G--AA
1 TCGCAACGCGAAATGAAAA
100991 TCGCAACGCGAAATGAAAA
1 TCGCAACGCGAAATGAAAA
*
101010 TCGCAATGCGA
1 TCGCAACGCGA
101021 TTTTGGTTTC
Statistics
Matches: 97, Mismatches: 8, Indels: 21
0.77 0.06 0.17
Matches are distributed among these distances:
14 16 0.16
16 11 0.11
17 11 0.11
19 47 0.48
20 12 0.12
ACGTcount: A:0.46, C:0.24, G:0.19, T:0.10
Consensus pattern (19 bp):
TCGCAACGCGAAATGAAAA
Found at i:100961 original size:14 final size:14
Alignment explanation
Indices: 100942--100998 Score: 60
Period size: 14 Copynumber: 3.7 Consensus size: 14
100932 GCGAAATGAA
*
100942 AATCGCAACGACAG
1 AATCGCAACGAAAG
100956 AATCGCAACGCGAAATG
1 AATCGCAA--CGAAA-G
100973 AAAATCGCAACGAAAG
1 --AATCGCAACGAAAG
100989 AATCGCAACG
1 AATCGCAACG
100999 CGAAATGAAA
Statistics
Matches: 37, Mismatches: 1, Indels: 10
0.77 0.02 0.21
Matches are distributed among these distances:
14 18 0.49
16 5 0.14
17 6 0.16
19 8 0.22
ACGTcount: A:0.46, C:0.25, G:0.21, T:0.09
Consensus pattern (14 bp):
AATCGCAACGAAAG
Found at i:100965 original size:33 final size:33
Alignment explanation
Indices: 100923--101015 Score: 177
Period size: 33 Copynumber: 2.8 Consensus size: 33
100913 GCGAAACCAA
*
100923 AATCGCAACGCGAAATGAAAATCGCAACGACAG
1 AATCGCAACGCGAAATGAAAATCGCAACGAAAG
100956 AATCGCAACGCGAAATGAAAATCGCAACGAAAG
1 AATCGCAACGCGAAATGAAAATCGCAACGAAAG
100989 AATCGCAACGCGAAATGAAAATCGCAA
1 AATCGCAACGCGAAATGAAAATCGCAA
101016 TGCGATTTTG
Statistics
Matches: 59, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
33 59 1.00
ACGTcount: A:0.47, C:0.23, G:0.20, T:0.10
Consensus pattern (33 bp):
AATCGCAACGCGAAATGAAAATCGCAACGAAAG
Found at i:101012 original size:52 final size:54
Alignment explanation
Indices: 100886--101020 Score: 131
Period size: 52 Copynumber: 2.5 Consensus size: 54
100876 TAGTTTACTT
*
100886 TCGCAACACGAAACTTAAAATCGCAACGCGAAACCAAAATCGCAACGCGAAATGAAAA
1 TCGCAAC-CGAAA-TGAAAATCGCAACGCGAAACCAAAATCGCAAC-CGAAATG-AAA
* **
100944 TCGCAA-CGACA-G--AATCGCAACGCGAAATGAAAATCGCAA-CGAAA-G-AA
1 TCGCAACCGAAATGAAAATCGCAACGCGAAACCAAAATCGCAACCGAAATGAAA
*
100991 TCGCAACGCGAAATGAAAATCGCAATGCGA
1 TCGCAAC-CGAAATGAAAATCGCAACGCGA
101021 TTTTGGTTTC
Statistics
Matches: 66, Mismatches: 6, Indels: 16
0.75 0.07 0.18
Matches are distributed among these distances:
47 8 0.12
49 5 0.08
50 6 0.09
52 37 0.56
56 4 0.06
58 6 0.09
ACGTcount: A:0.46, C:0.24, G:0.19, T:0.10
Consensus pattern (54 bp):
TCGCAACCGAAATGAAAATCGCAACGCGAAACCAAAATCGCAACCGAAATGAAA
Found at i:101038 original size:19 final size:19
Alignment explanation
Indices: 101016--101144 Score: 125
Period size: 19 Copynumber: 7.3 Consensus size: 19
101006 AAAATCGCAA
101016 TGCGATTTTGGTTTCGCGT
1 TGCGATTTTGGTTTCGCGT
*
101035 TGCGATCTT-G--T--CGT
1 TGCGATTTTGGTTTCGCGT
101049 TGCGATTTTGGTTTCGCGT
1 TGCGATTTTGGTTTCGCGT
*
101068 TGCGATTCT-G--T--CGT
1 TGCGATTTTGGTTTCGCGT
**
101082 TGCGATTTTCATTTCGCGT
1 TGCGATTTTGGTTTCGCGT
101101 TGCGATTTTGGTTTCGCGT
1 TGCGATTTTGGTTTCGCGT
* *
101120 TGCGATTTTAAGTTTCGTGT
1 TGCGATTTT-GGTTTCGCGT
101140 TGCGA
1 TGCGA
101145 AAGTAAACTA
Statistics
Matches: 90, Mismatches: 9, Indels: 21
0.75 0.08 0.17
Matches are distributed among these distances:
14 22 0.24
15 1 0.01
16 2 0.02
17 2 0.02
18 2 0.02
19 48 0.53
20 13 0.14
ACGTcount: A:0.09, C:0.17, G:0.29, T:0.46
Consensus pattern (19 bp):
TGCGATTTTGGTTTCGCGT
Found at i:101058 original size:33 final size:33
Alignment explanation
Indices: 101016--101107 Score: 150
Period size: 33 Copynumber: 2.8 Consensus size: 33
101006 AAAATCGCAA
101016 TGCGATTTTGGTTTCGCGTTGCGA-TCTTGTCGT
1 TGCGATTTTGGTTTCGCGTTGCGATTC-TGTCGT
101049 TGCGATTTTGGTTTCGCGTTGCGATTCTGTCGT
1 TGCGATTTTGGTTTCGCGTTGCGATTCTGTCGT
**
101082 TGCGATTTTCATTTCGCGTTGCGATT
1 TGCGATTTTGGTTTCGCGTTGCGATT
101108 TTGGTTTCGC
Statistics
Matches: 56, Mismatches: 2, Indels: 2
0.93 0.03 0.03
Matches are distributed among these distances:
33 54 0.96
34 2 0.04
ACGTcount: A:0.08, C:0.18, G:0.28, T:0.46
Consensus pattern (33 bp):
TGCGATTTTGGTTTCGCGTTGCGATTCTGTCGT
Found at i:101350 original size:93 final size:93
Alignment explanation
Indices: 101188--101567 Score: 735
Period size: 93 Copynumber: 4.1 Consensus size: 93
101178 TTGAATGGAT
101188 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
1 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
101253 AGTTTAGCAGAATTGGCAGCAACCGAAC
66 AGTTTAGCAGAATTGGCAGCAACCGAAC
*
101281 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAT
1 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
101346 AGTTTAGCAGAATTGGCAGCAACCGAAC
66 AGTTTAGCAGAATTGGCAGCAACCGAAC
101374 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATA-TATTTCACAGTGTTAAAGAATACAC
1 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
101438 AGTTTAGCAGAATTGGCAGCAACCGAAC
66 AGTTTAGCAGAATTGGCAGCAACCGAAC
101466 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
1 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
*
101531 AGTTTAGCAGAATTGGCAGCAACCGAAT
66 AGTTTAGCAGAATTGGCAGCAACCGAAC
101559 AAATTTACT
1 AAATTTACT
101568 AAGCAATCTA
Statistics
Matches: 283, Mismatches: 3, Indels: 2
0.98 0.01 0.01
Matches are distributed among these distances:
92 91 0.32
93 192 0.68
ACGTcount: A:0.46, C:0.18, G:0.13, T:0.23
Consensus pattern (93 bp):
AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
AGTTTAGCAGAATTGGCAGCAACCGAAC
Found at i:101501 original size:185 final size:186
Alignment explanation
Indices: 101188--101567 Score: 735
Period size: 185 Copynumber: 2.0 Consensus size: 186
101178 TTGAATGGAT
101188 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
1 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
101253 AGTTTAGCAGAATTGGCAGCAACCGAACAAATTTACTTTCAACCAAAAGACAAAACAAAGACAAA
66 AGTTTAGCAGAATTGGCAGCAACCGAACAAATTTACTTTCAACCAAAAGACAAAACAAAGACAAA
*
101318 TACTATTTCACAGTGTTAAAGAATACATAGTTTAGCAGAATTGGCAGCAACCGAAC
131 TACTATTTCACAGTGTTAAAGAATACACAGTTTAGCAGAATTGGCAGCAACCGAAC
101374 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATA-TATTTCACAGTGTTAAAGAATACAC
1 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
101438 AGTTTAGCAGAATTGGCAGCAACCGAACAAATTTACTTTCAACCAAAAGACAAAACAAAGACAAA
66 AGTTTAGCAGAATTGGCAGCAACCGAACAAATTTACTTTCAACCAAAAGACAAAACAAAGACAAA
*
101503 TACTATTTCACAGTGTTAAAGAATACACAGTTTAGCAGAATTGGCAGCAACCGAAT
131 TACTATTTCACAGTGTTAAAGAATACACAGTTTAGCAGAATTGGCAGCAACCGAAC
101559 AAATTTACT
1 AAATTTACT
101568 AAGCAATCTA
Statistics
Matches: 192, Mismatches: 2, Indels: 1
0.98 0.01 0.01
Matches are distributed among these distances:
185 153 0.80
186 39 0.20
ACGTcount: A:0.46, C:0.18, G:0.13, T:0.23
Consensus pattern (186 bp):
AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
AGTTTAGCAGAATTGGCAGCAACCGAACAAATTTACTTTCAACCAAAAGACAAAACAAAGACAAA
TACTATTTCACAGTGTTAAAGAATACACAGTTTAGCAGAATTGGCAGCAACCGAAC
Found at i:103293 original size:14 final size:14
Alignment explanation
Indices: 103274--103363 Score: 81
Period size: 14 Copynumber: 5.7 Consensus size: 14
103264 TTGAAATGAA
103274 AATCGCAACGAGAG
1 AATCGCAACGAGAG
103288 AATCGCAACGCGAGATG
1 AATCGCAA--CGAGA-G
103305 ACAATCGCAACGAGAG
1 --AATCGCAACGAGAG
*
103321 AATCGCAACGCGAAATGAA
1 AATCGCAA--CG--A-GAG
103340 AATCGCAACGAGAG
1 AATCGCAACGAGAG
103354 AATCGCAACG
1 AATCGCAACG
103364 CGAAATGAAA
Statistics
Matches: 64, Mismatches: 2, Indels: 20
0.74 0.02 0.23
Matches are distributed among these distances:
14 28 0.44
15 1 0.02
16 8 0.12
17 8 0.12
18 1 0.02
19 18 0.28
ACGTcount: A:0.42, C:0.23, G:0.26, T:0.09
Consensus pattern (14 bp):
AATCGCAACGAGAG
Found at i:103311 original size:33 final size:33
Alignment explanation
Indices: 103266--103380 Score: 212
Period size: 33 Copynumber: 3.5 Consensus size: 33
103256 TCTTTTGGTT
103266 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
1 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
* *
103299 GAGATGACAATCGCAACGAGAGAATCGCAACGC
1 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
103332 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
1 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
103365 GAAATGAAAATCGCAA
1 GAAATGAAAATCGCAA
103381 TGCGATTTTG
Statistics
Matches: 78, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
33 78 1.00
ACGTcount: A:0.45, C:0.21, G:0.24, T:0.10
Consensus pattern (33 bp):
GAAATGAAAATCGCAACGAGAGAATCGCAACGC
Found at i:103312 original size:19 final size:18
Alignment explanation
Indices: 103273--103385 Score: 88
Period size: 19 Copynumber: 6.8 Consensus size: 18
103263 GTTGAAATGA
103273 AAATCGCAA--CGAGA-G
1 AAATCGCAACGCGAGATG
103288 -AATCGCAACGCGAGATG
1 AAATCGCAACGCGAGATG
103305 ACAATCGCAA--CGAGA-G
1 A-AATCGCAACGCGAGATG
*
103321 -AATCGCAACGCGAAATG
1 AAATCGCAACGCGAGATG
103338 AAAATCGCAA--CGAGA-G
1 -AAATCGCAACGCGAGATG
*
103354 -AATCGCAACGCGAAATG
1 AAATCGCAACGCGAGATG
*
103371 AAAATCGCAATGCGA
1 -AAATCGCAACGCGA
103386 TTTTGGTTTC
Statistics
Matches: 79, Mismatches: 4, Indels: 26
0.72 0.04 0.24
Matches are distributed among these distances:
14 24 0.30
16 15 0.19
17 12 0.15
19 28 0.35
ACGTcount: A:0.43, C:0.22, G:0.25, T:0.10
Consensus pattern (18 bp):
AAATCGCAACGCGAGATG
Found at i:103416 original size:14 final size:14
Alignment explanation
Indices: 103397--103451 Score: 56
Period size: 14 Copynumber: 3.6 Consensus size: 14
103387 TTTGGTTTCG
103397 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
*
103411 CGTTGCGATTTTCATTTCG
1 CGTTGCGA--TTC---TCT
103430 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
103444 CGTTGCGA
1 CGTTGCGA
103452 CAGTCATTCT
Statistics
Matches: 34, Mismatches: 2, Indels: 10
0.74 0.04 0.22
Matches are distributed among these distances:
14 18 0.53
16 3 0.09
17 3 0.09
19 10 0.29
ACGTcount: A:0.09, C:0.25, G:0.24, T:0.42
Consensus pattern (14 bp):
CGTTGCGATTCTCT
Found at i:103429 original size:33 final size:33
Alignment explanation
Indices: 103381--103451 Score: 124
Period size: 33 Copynumber: 2.2 Consensus size: 33
103371 AAAATCGCAA
**
103381 TGCGATTTTGGTTTCGCGTTGCGATTCTCTCGT
1 TGCGATTTTCATTTCGCGTTGCGATTCTCTCGT
103414 TGCGATTTTCATTTCGCGTTGCGATTCTCTCGT
1 TGCGATTTTCATTTCGCGTTGCGATTCTCTCGT
103447 TGCGA
1 TGCGA
103452 CAGTCATTCT
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
33 36 1.00
ACGTcount: A:0.08, C:0.23, G:0.25, T:0.44
Consensus pattern (33 bp):
TGCGATTTTCATTTCGCGTTGCGATTCTCTCGT
Found at i:103459 original size:33 final size:33
Alignment explanation
Indices: 103392--103473 Score: 119
Period size: 33 Copynumber: 2.5 Consensus size: 33
103382 GCGATTTTGG
***
103392 TTTCGCGTTGCGATTCTCTCGTTGCGATTTTCA
1 TTTCGCGTTGCGATTCTCTCGTTGCGACAGTCA
103425 TTTCGCGTTGCGATTCTCTCGTTGCGACAGTCA
1 TTTCGCGTTGCGATTCTCTCGTTGCGACAGTCA
*
103458 TTCTCTCGTTGCGATT
1 TT-TCGCGTTGCGATT
103474 TTCATTTATC
Statistics
Matches: 44, Mismatches: 4, Indels: 1
0.90 0.08 0.02
Matches are distributed among these distances:
33 32 0.73
34 12 0.27
ACGTcount: A:0.10, C:0.26, G:0.22, T:0.43
Consensus pattern (33 bp):
TTTCGCGTTGCGATTCTCTCGTTGCGACAGTCA
Found at i:103478 original size:20 final size:20
Alignment explanation
Indices: 103404--103492 Score: 75
Period size: 20 Copynumber: 4.8 Consensus size: 20
103394 TCGCGTTGCG
103404 ATTCTCTCGTTGCGATTTTC
1 ATTCTCTCGTTGCGATTTTC
*
103424 ATT-TCGCGTTGCG------
1 ATTCTCTCGTTGCGATTTTC
***
103437 ATTCTCTCGTTGCGACAGTC
1 ATTCTCTCGTTGCGATTTTC
103457 ATTCTCTCGTTGCGATTTTC
1 ATTCTCTCGTTGCGATTTTC
*
103477 ATTTATCTCGTTGCGA
1 A-TTCTCTCGTTGCGA
103493 CTCTTCTGCA
Statistics
Matches: 55, Mismatches: 6, Indels: 15
0.72 0.08 0.20
Matches are distributed among these distances:
13 3 0.05
14 9 0.16
19 9 0.16
20 21 0.38
21 13 0.24
ACGTcount: A:0.12, C:0.25, G:0.19, T:0.44
Consensus pattern (20 bp):
ATTCTCTCGTTGCGATTTTC
Found at i:103614 original size:33 final size:33
Alignment explanation
Indices: 103572--103642 Score: 124
Period size: 33 Copynumber: 2.2 Consensus size: 33
103562 AATACTAACT
103572 TGAAAATCGCAACGAGAGAATAGCAACGCGAAA
1 TGAAAATCGCAACGAGAGAATAGCAACGCGAAA
* *
103605 TGAAAATCGCAACGAGAGAATCGTAACGCGAAA
1 TGAAAATCGCAACGAGAGAATAGCAACGCGAAA
103638 TGAAA
1 TGAAA
103643 TCTAAGTGAA
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
33 36 1.00
ACGTcount: A:0.48, C:0.17, G:0.24, T:0.11
Consensus pattern (33 bp):
TGAAAATCGCAACGAGAGAATAGCAACGCGAAA
Found at i:103876 original size:22 final size:22
Alignment explanation
Indices: 103824--103878 Score: 74
Period size: 22 Copynumber: 2.5 Consensus size: 22
103814 TGGTTGTGAG
**
103824 GGATTTCGCCGGAGATGGGGAC
1 GGATTTCTTCGGAGATGGGGAC
**
103846 GGAAATCTTCGGAGATGGGGAC
1 GGATTTCTTCGGAGATGGGGAC
103868 GGATTTCTTCG
1 GGATTTCTTCG
103879 CCGTAGAGAG
Statistics
Matches: 27, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
22 27 1.00
ACGTcount: A:0.20, C:0.16, G:0.40, T:0.24
Consensus pattern (22 bp):
GGATTTCTTCGGAGATGGGGAC
Found at i:104049 original size:20 final size:20
Alignment explanation
Indices: 104024--104198 Score: 183
Period size: 20 Copynumber: 8.7 Consensus size: 20
104014 CTTTAAATAT
104024 CGCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
* *
104044 CGCGTTGCGATTTTATGTATTA
1 CGCGTTGCGA-TTTACGGA-TA
*
104066 -TCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
*
104085 CGCGTTGCGATATACGGATA
1 CGCGTTGCGATTTACGGATA
* **
104105 CGCATTGCGATTTACCCCATA
1 CGCGTTGCGATTTA-CGGATA
104126 CGCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
* *
104146 CGCGTTGCGATTTATGTG-TT
1 CGCGTTGCGATTTACG-GATA
* ** *
104166 CGCGTTGCGATTTTCATATT
1 CGCGTTGCGATTTACGGATA
104186 CGCGTTGCGATTT
1 CGCGTTGCGATTT
104199 TGGAAAATCG
Statistics
Matches: 129, Mismatches: 20, Indels: 12
0.80 0.12 0.07
Matches are distributed among these distances:
19 2 0.02
20 93 0.72
21 32 0.25
22 2 0.02
ACGTcount: A:0.18, C:0.20, G:0.26, T:0.36
Consensus pattern (20 bp):
CGCGTTGCGATTTACGGATA
Found at i:104101 original size:61 final size:62
Alignment explanation
Indices: 104024--104179 Score: 194
Period size: 61 Copynumber: 2.5 Consensus size: 62
104014 CTTTAAATAT
*** *
104024 CGCGTTGCGATTTACGGATACGCGTTGCGATTTTA-TGTATTA-TCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATACGCGTTGCGATTTTACCCCA-TACGCGTTGCGATTTACGGATA
* *
104085 CGCGTTGCGATATACGGATACGCATTGCGA-TTTACCCCATACGCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATACGCGTTGCGATTTTACCCCATACGCGTTGCGATTTACGGATA
* *
104146 CGCGTTGCGATTTATGTG-TTCGCGTTGCGATTTT
1 CGCGTTGCGATTTACG-GATACGCGTTGCGATTTT
104180 CATATTCGCG
Statistics
Matches: 81, Mismatches: 10, Indels: 7
0.83 0.10 0.07
Matches are distributed among these distances:
60 6 0.07
61 71 0.88
62 4 0.05
ACGTcount: A:0.19, C:0.20, G:0.26, T:0.35
Consensus pattern (62 bp):
CGCGTTGCGATTTACGGATACGCGTTGCGATTTTACCCCATACGCGTTGCGATTTACGGATA
Found at i:104127 original size:41 final size:40
Alignment explanation
Indices: 104069--104159 Score: 137
Period size: 41 Copynumber: 2.2 Consensus size: 40
104059 TGTATTATCG
**
104069 TTGCGATTTACGGATACGCGTTGCGATATACGGATACGCA
1 TTGCGATTTACCCATACGCGTTGCGATATACGGATACGCA
* *
104109 TTGCGATTTACCCCATACGCGTTGCGATTTACGGATACGCG
1 TTGCGATTTA-CCCATACGCGTTGCGATATACGGATACGCA
104150 TTGCGATTTA
1 TTGCGATTTA
104160 TGTGTTCGCG
Statistics
Matches: 46, Mismatches: 4, Indels: 1
0.90 0.08 0.02
Matches are distributed among these distances:
40 10 0.22
41 36 0.78
ACGTcount: A:0.22, C:0.22, G:0.25, T:0.31
Consensus pattern (40 bp):
TTGCGATTTACCCATACGCGTTGCGATATACGGATACGCA
Found at i:104215 original size:21 final size:20
Alignment explanation
Indices: 104191--104267 Score: 57
Period size: 21 Copynumber: 3.7 Consensus size: 20
104181 ATATTCGCGT
104191 TGCGATTTTGGAAAATCGCAA
1 TGCGATTTTGGAAAATCGC-A
* * **
104212 TGCGAATTTGTACTATCGCA
1 TGCGATTTTGGAAAATCGCA
* *
104232 TCGCGATTTT-CAAGAATCGCGT
1 T-GCGATTTTGGAA-AATCGC-A
104254 TGCGATTTTGGAAA
1 TGCGATTTTGGAAA
104268 CTGATTTGCG
Statistics
Matches: 42, Mismatches: 10, Indels: 8
0.70 0.17 0.13
Matches are distributed among these distances:
20 3 0.07
21 36 0.86
22 3 0.07
ACGTcount: A:0.27, C:0.17, G:0.23, T:0.32
Consensus pattern (20 bp):
TGCGATTTTGGAAAATCGCA
Found at i:104278 original size:20 final size:20
Alignment explanation
Indices: 104253--104304 Score: 95
Period size: 20 Copynumber: 2.6 Consensus size: 20
104243 AAGAATCGCG
*
104253 TTGCGATTTTGGAAACTGAT
1 TTGCGATTCTGGAAACTGAT
104273 TTGCGATTCTGGAAACTGAT
1 TTGCGATTCTGGAAACTGAT
104293 TTGCGATTCTGG
1 TTGCGATTCTGG
104305 GGATCGCGTT
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 31 1.00
ACGTcount: A:0.21, C:0.13, G:0.27, T:0.38
Consensus pattern (20 bp):
TTGCGATTCTGGAAACTGAT
Found at i:105231 original size:110 final size:107
Alignment explanation
Indices: 105030--105281 Score: 355
Period size: 110 Copynumber: 2.3 Consensus size: 107
105020 TTCCGAGTCT
*
105030 AATATCCTCTGTTGTGAAGTTGAAATTGGCTCTG--GAACTGAAAAATTGTTTGTTGACAGCCAG
1 AATATCCTC-GTTGTGAAGTTGAAATTGGCTCTGAAGAACTGAAAAATTGTTTGTTGACAACCAG
*
105093 TCGCCCATTCACTGTGAAGTTGAGCTTGTGTTGTCTCGAGTTC
65 TCGCCCATTCACTATGAAGTTGAGCTTGTGTTGTCTCGAGTTC
* * *
105136 AATATCCTTCGTTGTGAAGTTGAAATTGACTCTGAATGAAACTGAAAAGTTGTTTGTTGACAATC
1 AATATCC-TCGTTGTGAAGTTGAAATTGGCTCTGAA-G-AACTGAAAAATTGTTTGTTGACAACC
* ** * *
105201 AGTCGCCCCTTCGTTATGAATTTGAGCTTGTGTTGTCTTGAGTTC
63 AGTCGCCCATTCACTATGAAGTTGAGCTTGTGTTGTCTCGAGTTC
105246 AATATCCCTCGTTGTGAAGTTGAAATTGGCTCTGAA
1 AATAT-CCTCGTTGTGAAGTTGAAATTGGCTCTGAA
105282 ATTGGGAAGC
Statistics
Matches: 129, Mismatches: 11, Indels: 8
0.87 0.07 0.05
Matches are distributed among these distances:
106 30 0.23
107 2 0.02
109 1 0.01
110 94 0.73
111 2 0.02
ACGTcount: A:0.24, C:0.17, G:0.23, T:0.36
Consensus pattern (107 bp):
AATATCCTCGTTGTGAAGTTGAAATTGGCTCTGAAGAACTGAAAAATTGTTTGTTGACAACCAGT
CGCCCATTCACTATGAAGTTGAGCTTGTGTTGTCTCGAGTTC
Found at i:106046 original size:68 final size:67
Alignment explanation
Indices: 105919--106138 Score: 241
Period size: 65 Copynumber: 3.3 Consensus size: 67
105909 AAAGAGATAG
* * * * * *
105919 AATTCGTTTCAAGGGAAAT-GATCTCAAAGATATTTGTTGTTTCATGAAAAACAGTCTCAAGGGA
1 AATTTGTTTTAAGGGAAATAAAT-TCAAAGAT-TTTG-TGTTTCAAGAGAAACTGTCTCAAGGGA
105983 AACAA
63 AACAA
** *
105988 AATTTTGTTTTAAGGGAAATAAATTTGAAGATTTTGTGTTTCAAGAGAAACTGTCTCAAGGGAGA
1 AA-TTTGTTTTAAGGGAAATAAATTCAAAGATTTTGTGTTTCAAGAGAAACTGTCTCAAGGGAAA
106053 CAA
65 CAA
* *
106056 AATTTGTTTT-AGGAGAAATAAATTCAAAGA-TTT-TGTTTCAAGGGAAACTGTCTCAAGAGAAA
1 AATTTGTTTTAAGG-GAAATAAATTCAAAGATTTTGTGTTTCAAGAGAAACTGTCTCAAGGGAAA
*
106118 CGA
65 CAA
* *
106121 AATTTGTTTCAAGAGAAA
1 AATTTGTTTTAAGGGAAA
106139 CTGTCTCAAG
Statistics
Matches: 130, Mismatches: 17, Indels: 12
0.82 0.11 0.08
Matches are distributed among these distances:
65 41 0.32
66 8 0.06
67 22 0.17
68 30 0.23
69 6 0.05
70 21 0.16
71 2 0.02
ACGTcount: A:0.39, C:0.10, G:0.20, T:0.31
Consensus pattern (67 bp):
AATTTGTTTTAAGGGAAATAAATTCAAAGATTTTGTGTTTCAAGAGAAACTGTCTCAAGGGAAAC
AA
Found at i:106072 original size:36 final size:36
Alignment explanation
Indices: 106024--106312 Score: 200
Period size: 36 Copynumber: 8.4 Consensus size: 36
106014 GAAGATTTTG
*
106024 TGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAATT
1 TGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAATT
* * **
106060 TGTTTTAGGAGAAA-----T--A-A-ATTCAAAGATTT
1 TGTTTCAAGAGAAACTGTCTCAAGAGAGACAAA-AT-T
* * *
106089 TGTTTCAAGGGAAACTGTCTCAAGAGAAACGAAATT
1 TGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAATT
106125 TGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAACTT
1 TGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAA-TT
* * * * *
106162 AGTTCCAAAAGAAACTGTCTCAAGGGAGACGAAATT
1 TGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAATT
* * * *
106198 TGTTTCAA-ATAAAACATAT-TC-----A-A-ATATTT
1 TGTTTCAAGA-GAAAC-TGTCTCAAGAGAGACAAAATT
* *
106227 TGTTTTAAGGGAAACTGTCTCAAGAGAGACAAAATT
1 TGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAATT
* *
106263 TGTTTCAAGGGAAACTGTCTCAAGAGAGACGAAATT
1 TGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAATT
* *
106299 TATTTCAAGGGAAA
1 TGTTTCAAGAGAAA
106313 TGTTTGCAAT
Statistics
Matches: 195, Mismatches: 35, Indels: 46
0.71 0.13 0.17
Matches are distributed among these distances:
27 5 0.03
28 4 0.02
29 29 0.15
30 1 0.01
31 2 0.01
34 2 0.01
35 2 0.01
36 110 0.56
37 36 0.18
38 4 0.02
ACGTcount: A:0.40, C:0.12, G:0.20, T:0.28
Consensus pattern (36 bp):
TGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAATT
Found at i:106198 original size:138 final size:138
Alignment explanation
Indices: 106033--106292 Score: 407
Period size: 138 Copynumber: 1.9 Consensus size: 138
106023 GTGTTTCAAG
* *
106033 AGAAACTGTCTCAAGGGAGACAAAATTTGTTTTAGGAGAAATA-A-ATTCAAAGATTTTGTTTCA
1 AGAAACTGTCTCAAGGGAGACAAAATTTGTTTCA-AAGAAA-ACATATTCAAAGATTTTGTTTCA
*
106096 AGGGAAACTGTCTCAAGAGAAACGAAATTTGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAACT
64 AGGGAAACTGTCTCAAGAGAAACAAAATTTGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAACT
106161 TAGTTCCAAA
129 TAGTTCCAAA
* * * *
106171 AGAAACTGTCTCAAGGGAGACGAAATTTGTTTCAAATAAAACATATTCAAATATTTTGTTTTAAG
1 AGAAACTGTCTCAAGGGAGACAAAATTTGTTTCAAAGAAAACATATTCAAAGATTTTGTTTCAAG
* *
106236 GGAAACTGTCTCAAGAGAGACAAAATTTGTTTCAAGGGAAACTGTCTCAAGAGAGAC
66 GGAAACTGTCTCAAGAGAAACAAAATTTGTTTCAAGAGAAACTGTCTCAAGAGAGAC
106293 GAAATTTATT
Statistics
Matches: 111, Mismatches: 9, Indels: 4
0.90 0.07 0.03
Matches are distributed among these distances:
136 1 0.01
137 5 0.05
138 105 0.95
ACGTcount: A:0.40, C:0.13, G:0.20, T:0.27
Consensus pattern (138 bp):
AGAAACTGTCTCAAGGGAGACAAAATTTGTTTCAAAGAAAACATATTCAAAGATTTTGTTTCAAG
GGAAACTGTCTCAAGAGAAACAAAATTTGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAACTTA
GTTCCAAA
Found at i:106305 original size:101 final size:101
Alignment explanation
Indices: 106123--106393 Score: 314
Period size: 101 Copynumber: 2.7 Consensus size: 101
106113 AGAAACGAAA
* * ** *
106123 TTTGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAACTTAGTTCCAAAAGAAACTGTCTCAAGGG
1 TTTGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAACTTTGTTTCAAGGGAAACTGTCTCAAGAG
* *
106188 AGACGAAATTTGTTTCAAATAAAACATATT-CAAATAT
66 AGACGAAATTTATTTCAAAGAAAACAT-TTGC-AATAT
* *
106225 TTTGTTTTAAGGGAAACTGTCTCAAGAGAGACAAAA-TTTGTTTCAAGGGAAACTGTCTCAAGAG
1 TTTGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAACTTTGTTTCAAGGGAAACTGTCTCAAGAG
* * ** *
106289 AGACGAAATTTATTTCAAGGGAAATGTTTGCAATGT
66 AGACGAAATTTATTTCAAAGAAAACATTTGCAATAT
* * * *
106325 TTATGTTTCAAGAGAAACTGTCTCAAGGGAGGA-AAAATTTTGTTTCAAGGGAAATTATCTCAAG
1 TT-TGTTTCAAGAGAAACTGTCTCAAGAGA-GACAAAACTTTGTTTCAAGGGAAACTGTCTCAAG
*
106389 CGAGA
64 AGAGA
106394 TAAAATCTTC
Statistics
Matches: 145, Mismatches: 20, Indels: 8
0.84 0.12 0.05
Matches are distributed among these distances:
100 8 0.06
101 73 0.50
102 64 0.44
ACGTcount: A:0.38, C:0.13, G:0.20, T:0.29
Consensus pattern (101 bp):
TTTGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAACTTTGTTTCAAGGGAAACTGTCTCAAGAG
AGACGAAATTTATTTCAAAGAAAACATTTGCAATAT
Found at i:107004 original size:10 final size:11
Alignment explanation
Indices: 106979--107004 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
106969 ATATCAATTA
106979 AAAAAGTTTTG
1 AAAAAGTTTTG
106990 AAAAAGTTTTG
1 AAAAAGTTTTG
107001 AAAA
1 AAAA
107005 TATCGCCCCT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.54, C:0.00, G:0.15, T:0.31
Consensus pattern (11 bp):
AAAAAGTTTTG
Found at i:107987 original size:15 final size:13
Alignment explanation
Indices: 107925--107979 Score: 83
Period size: 13 Copynumber: 4.2 Consensus size: 13
107915 TTTTCTTCAA
*
107925 TTCTCCTTTGTTTT
1 TTCT-CTTTGCTTT
*
107939 TTATCTTTGCTTT
1 TTCTCTTTGCTTT
107952 TTCTCTTTGCTTT
1 TTCTCTTTGCTTT
107965 TTCTCTTTGCTTT
1 TTCTCTTTGCTTT
107978 TT
1 TT
107980 TTCTCTTTTT
Statistics
Matches: 38, Mismatches: 3, Indels: 1
0.90 0.07 0.02
Matches are distributed among these distances:
13 35 0.92
14 3 0.08
ACGTcount: A:0.02, C:0.20, G:0.07, T:0.71
Consensus pattern (13 bp):
TTCTCTTTGCTTT
Found at i:107991 original size:13 final size:13
Alignment explanation
Indices: 107925--107992 Score: 75
Period size: 13 Copynumber: 5.1 Consensus size: 13
107915 TTTTCTTCAA
107925 TTCTCCTTTGTTTT
1 TTCT-CTTTGTTTT
* *
107939 TTATCTTTGCTTT
1 TTCTCTTTGTTTT
*
107952 TTCTCTTTGCTTT
1 TTCTCTTTGTTTT
107965 TTCTCTTTGCTTTTT
1 TTCTCTTTG--TTTT
107980 TTCTCTTT-TTTT
1 TTCTCTTTGTTTT
107992 T
1 T
107993 CTGATTGAAT
Statistics
Matches: 48, Mismatches: 4, Indels: 6
0.83 0.07 0.10
Matches are distributed among these distances:
12 5 0.10
13 29 0.60
14 3 0.06
15 11 0.23
ACGTcount: A:0.01, C:0.19, G:0.06, T:0.74
Consensus pattern (13 bp):
TTCTCTTTGTTTT
Found at i:111463 original size:18 final size:18
Alignment explanation
Indices: 111397--111465 Score: 57
Period size: 18 Copynumber: 3.5 Consensus size: 18
111387 AAATAAAAAC
*
111397 AAAAATAGAATATTAAGA
1 AAAAATATAATATTAAGA
*
111415 AATATATATATATATGTAAACGTA
1 AA-AAATATA-ATAT-T-AA-G-A
*
111439 TAAAATATAATATTAAGA
1 AAAAATATAATATTAAGA
111457 AAAAATATA
1 AAAAATATA
111466 TATACATAGC
Statistics
Matches: 40, Mismatches: 5, Indels: 12
0.70 0.09 0.21
Matches are distributed among these distances:
18 11 0.28
19 6 0.15
20 6 0.15
21 2 0.05
22 6 0.15
23 7 0.17
24 2 0.05
ACGTcount: A:0.61, C:0.01, G:0.07, T:0.30
Consensus pattern (18 bp):
AAAAATATAATATTAAGA
Found at i:111489 original size:45 final size:42
Alignment explanation
Indices: 111397--111494 Score: 99
Period size: 42 Copynumber: 2.3 Consensus size: 42
111387 AAATAAAAAC
* * * * *
111397 AAAAATAGAATATTAAGAAATATATATATATATGTAAACGTA
1 AAAAATATAATATTAAGAAAAATATATATACATGCAAACGGA
* *
111439 TAAAATATAATATTAAGAAAAAATATATATACATAGCAAATGGA
1 AAAAATATAATATTAAG-AAAAATATATATACAT-GCAAACGGA
111483 GAAAAAT-TAATA
1 -AAAAATATAATA
111495 CATATATATA
Statistics
Matches: 45, Mismatches: 8, Indels: 4
0.79 0.14 0.07
Matches are distributed among these distances:
42 15 0.33
43 14 0.31
44 11 0.24
45 5 0.11
ACGTcount: A:0.59, C:0.03, G:0.09, T:0.29
Consensus pattern (42 bp):
AAAAATATAATATTAAGAAAAATATATATACATGCAAACGGA
Found at i:111529 original size:14 final size:14
Alignment explanation
Indices: 111521--111557 Score: 51
Period size: 14 Copynumber: 2.8 Consensus size: 14
111511 TATAAGATAT
111521 ATATAATAAAAATA
1 ATATAATAAAAATA
*
111535 ATATAATATAAATA
1 ATATAATAAAAATA
111549 A-ATAA-AAAA
1 ATATAATAAAA
111558 GAGGAATATA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
12 3 0.14
13 4 0.19
14 14 0.67
ACGTcount: A:0.73, C:0.00, G:0.00, T:0.27
Consensus pattern (14 bp):
ATATAATAAAAATA
Found at i:111557 original size:25 final size:26
Alignment explanation
Indices: 111509--111585 Score: 72
Period size: 25 Copynumber: 3.0 Consensus size: 26
111499 TATATATAAT
* *
111509 GATATAAGATATATATAAT-AAAAATA
1 GATATAATATAAATA-AATAAAAAATA
*
111535 -ATATAATATAAATAAATAAAAAAGA
1 GATATAATATAAATAAATAAAAAATA
111560 GGA-AT-ATAGTAAATAAATAAAAAATA
1 -GATATAATA-TAAATAAATAAAAAATA
111586 TAATTAAAAA
Statistics
Matches: 43, Mismatches: 4, Indels: 8
0.78 0.07 0.15
Matches are distributed among these distances:
24 3 0.07
25 21 0.49
26 18 0.42
27 1 0.02
ACGTcount: A:0.66, C:0.00, G:0.08, T:0.26
Consensus pattern (26 bp):
GATATAATATAAATAAATAAAAAATA
Found at i:113124 original size:3 final size:3
Alignment explanation
Indices: 113116--113157 Score: 84
Period size: 3 Copynumber: 14.0 Consensus size: 3
113106 ATTCCATTGA
113116 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
113158 ACAATTTGAG
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 39 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TAT
Found at i:119600 original size:3 final size:3
Alignment explanation
Indices: 119594--119676 Score: 82
Period size: 3 Copynumber: 27.7 Consensus size: 3
119584 TTTATTTGAA
* * * *
119594 TAT TAT T-T ATAT TAT TAT TAT TAT TAT TAT AAT AAT AAT AAT TAT
1 TAT TAT TAT -TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
119639 TAT TAT TA- TAT ATAT TAT TA- TAT ATAT TAT TAT TAT TA
1 TAT TAT TAT TAT -TAT TAT TAT TAT -TAT TAT TAT TAT TA
119677 AAAAAATAAT
Statistics
Matches: 72, Mismatches: 2, Indels: 12
0.84 0.02 0.14
Matches are distributed among these distances:
2 5 0.07
3 60 0.83
4 7 0.10
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (3 bp):
TAT
Found at i:123538 original size:14 final size:14
Alignment explanation
Indices: 123518--123553 Score: 54
Period size: 14 Copynumber: 2.6 Consensus size: 14
123508 ATTTCAAATA
123518 ATTTACATTTACAT
1 ATTTACATTTACAT
* *
123532 TTTTACATTTGCAT
1 ATTTACATTTACAT
123546 ATTTACAT
1 ATTTACAT
123554 CTGGCATCTT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
14 19 1.00
ACGTcount: A:0.31, C:0.14, G:0.03, T:0.53
Consensus pattern (14 bp):
ATTTACATTTACAT
Found at i:126887 original size:6 final size:6
Alignment explanation
Indices: 126861--126977 Score: 54
Period size: 6 Copynumber: 20.5 Consensus size: 6
126851 TCCAGCAAAG
* * * *
126861 AAAGAA GAAGGA AAA-AA AAAGAA AAAGGAA AAA-AA CAA-AA ATA-AA
1 AAAGAA AAAGAA AAAGAA AAAGAA AAA-GAA AAAGAA AAAGAA AAAGAA
* * * * *
126906 AAACAA AACA-AA AAAGAA AAGGAA AAGGAA AAGGAA AAA-AA GAA-AA
1 AAAGAA AA-AGAA AAAGAA AAAGAA AAAGAA AAAGAA AAAGAA AAAGAA
*
126952 AAAGAA AAA-AA GAAA-AA AAGGAA AAA
1 AAAGAA AAAGAA -AAAGAA AAAGAA AAA
126978 AGGAAAAAAG
Statistics
Matches: 89, Mismatches: 14, Indels: 16
0.75 0.12 0.13
Matches are distributed among these distances:
5 28 0.31
6 54 0.61
7 7 0.08
ACGTcount: A:0.80, C:0.03, G:0.16, T:0.01
Consensus pattern (6 bp):
AAAGAA
Found at i:126894 original size:16 final size:16
Alignment explanation
Indices: 126861--126994 Score: 87
Period size: 17 Copynumber: 8.1 Consensus size: 16
126851 TCCAGCAAAG
*
126861 AAAGAAGAAGGAAAAAA
1 AAAGAAAAAGG-AAAAA
126878 AAAGAAAAAGGAAAAA
1 AAAGAAAAAGGAAAAA
*
126894 AACA-AAAATA-AAAAACA
1 AA-AGAAAA-AGGAAAA-A
* *
126911 AAACAAAAAAGAAAAGGA
1 AAAGAAAAAGGAAAA--A
*
126929 AAAGGAAAAGG-AAAA
1 AAAGAAAAAGGAAAAA
*
126944 AAAGAAAAAAAGAAAAA
1 AAAG-AAAAAGGAAAAA
*
126961 AAGAAAAAAAGG-AAAA
1 AA-AGAAAAAGGAAAAA
*
126977 AAGGAAAAAAGGAAAAA
1 AAAG-AAAAAGGAAAAA
126994 A
1 A
126995 GGAAAAAAAA
Statistics
Matches: 93, Mismatches: 13, Indels: 22
0.73 0.10 0.17
Matches are distributed among these distances:
15 5 0.05
16 35 0.38
17 43 0.46
18 10 0.11
ACGTcount: A:0.80, C:0.02, G:0.17, T:0.01
Consensus pattern (16 bp):
AAAGAAAAAGGAAAAA
Found at i:126950 original size:8 final size:8
Alignment explanation
Indices: 126874--127003 Score: 106
Period size: 8 Copynumber: 15.9 Consensus size: 8
126864 GAAGAAGGAA
126874 AAAAAAAG
1 AAAAAAAG
*
126882 -AAAAAGG
1 AAAAAAAG
*
126889 AAAAAAAC
1 AAAAAAAG
126897 AAAAATAA-
1 AAAAA-AAG
126905 AAAACAAA-
1 AAAA-AAAG
126913 ACAAAAAAG
1 A-AAAAAAG
126922 AAAAGGAAA-
1 AAAA--AAAG
* *
126931 AGGAAAAGG
1 A-AAAAAAG
126940 AAAAAAAG
1 AAAAAAAG
126948 AAAAAAAG
1 AAAAAAAG
126956 AAAAAAAG
1 AAAAAAAG
126964 AAAAAAAGG
1 AAAAAAA-G
*
126973 AAAAAAGG
1 AAAAAAAG
*
126981 AAAAAAGG
1 AAAAAAAG
*
126989 AAAAAAGG
1 AAAAAAAG
126997 AAAAAAA
1 AAAAAAA
127004 AATTGAATCA
Statistics
Matches: 103, Mismatches: 9, Indels: 20
0.78 0.07 0.15
Matches are distributed among these distances:
7 6 0.06
8 76 0.74
9 16 0.16
10 5 0.05
ACGTcount: A:0.81, C:0.02, G:0.16, T:0.01
Consensus pattern (8 bp):
AAAAAAAG
Found at i:126952 original size:33 final size:32
Alignment explanation
Indices: 126874--127003 Score: 120
Period size: 33 Copynumber: 3.9 Consensus size: 32
126864 GAAGAAGGAA
* * *
126874 AAAAAAAGAAAAAGGAAAAAAACAAAAATAA-A
1 AAAAAAAGAAAAAAGAAAAAAAGAAAAA-AAGG
* **
126906 AAACAAAACAAAAAAGAAAAGGAAA-AGGAAAAGG
1 AAA-AAAAGAAAAAAGAAAA--AAAGAAAAAAAGG
126940 AAAAAAAGAAAAAAAGAAAAAAAGAAAAAAAGG
1 AAAAAAAG-AAAAAAGAAAAAAAGAAAAAAAGG
* *
126973 AAAAAAGGAAAAAAGGAAAAAAGGAAAAAAA
1 AAAAAAAGAAAAAA-GAAAAAAAGAAAAAAA
127004 AATTGAATCA
Statistics
Matches: 81, Mismatches: 10, Indels: 13
0.78 0.10 0.12
Matches are distributed among these distances:
32 12 0.15
33 49 0.60
34 17 0.21
35 3 0.04
ACGTcount: A:0.81, C:0.02, G:0.16, T:0.01
Consensus pattern (32 bp):
AAAAAAAGAAAAAAGAAAAAAAGAAAAAAAGG
Found at i:126961 original size:24 final size:24
Alignment explanation
Indices: 126874--127003 Score: 115
Period size: 25 Copynumber: 5.3 Consensus size: 24
126864 GAAGAAGGAA
*
126874 AAAAAAAG-AAAAAGGAAAAAAAC
1 AAAAAAAGAAAAAAGGAAAAAAAG
*
126897 AAAAATAA-AAAACAA-AACAAAAAAG
1 AAAAA-AAGAAAA-AAGGA-AAAAAAG
*
126922 AAAAGGAAA-AGGAAAAGGAAAAAAAG
1 AAAA--AAAGA-AAAAAGGAAAAAAAG
*
126948 AAAAAAAGAAAAAAAGAAAAAAAGG
1 AAAAAAAGAAAAAAGGAAAAAAA-G
* *
126973 AAAAAAGGAAAAAAGGAAAAAAGG
1 AAAAAAAGAAAAAAGGAAAAAAAG
126997 AAAAAAA
1 AAAAAAA
127004 AATTGAATCA
Statistics
Matches: 87, Mismatches: 10, Indels: 19
0.75 0.09 0.16
Matches are distributed among these distances:
23 5 0.06
24 28 0.32
25 34 0.39
26 16 0.18
27 4 0.05
ACGTcount: A:0.81, C:0.02, G:0.16, T:0.01
Consensus pattern (24 bp):
AAAAAAAGAAAAAAGGAAAAAAAG
Done.