Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_019168159.1 Durio zibethinus cultivar Musang King isolate D1 unplaced genomic scaffold, Duzib1.0 scaffold_4, 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: 33012953
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.34
Warning! 65000 characters in sequence are not A, C, G, or T
File 12 of 160
Found at i:3675154 original size:23 final size:24
Alignment explanation
Indices: 3675104--3675155 Score: 70
Period size: 23 Copynumber: 2.2 Consensus size: 24
3675094 TATTTTTATA
*
3675104 TTTATATAAATTATAATATATAATT
1 TTTATATAAA-TATAATATATAAAT
*
3675129 TTTATATAAA-ATATTATATAAAT
1 TTTATATAAATATAATATATAAAT
3675152 TTTA
1 TTTA
3675156 ATATTTTATA
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
23 15 0.60
25 10 0.40
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (24 bp):
TTTATATAAATATAATATATAAAT
Found at i:3677966 original size:2 final size:2
Alignment explanation
Indices: 3677961--3678000 Score: 80
Period size: 2 Copynumber: 20.0 Consensus size: 2
3677951 CTTTCCAAAA
3677961 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
3678001 GTTTGGAAAG
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 38 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
CT
Found at i:3685850 original size:12 final size:11
Alignment explanation
Indices: 3685827--3685859 Score: 50
Period size: 12 Copynumber: 3.0 Consensus size: 11
3685817 CCTTCACTCA
3685827 TCTTTCTTCTT
1 TCTTTCTTCTT
3685838 TCTTTCTTTCTT
1 TCTTTC-TTCTT
3685850 TCTTT-TTCTT
1 TCTTTCTTCTT
3685860 ACCCTTGATT
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
10 5 0.24
11 6 0.29
12 10 0.48
ACGTcount: A:0.00, C:0.24, G:0.00, T:0.76
Consensus pattern (11 bp):
TCTTTCTTCTT
Found at i:3689576 original size:17 final size:17
Alignment explanation
Indices: 3689554--3689586 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
3689544 TTTTGGTTAC
3689554 ATTTTAT-TGATTTTTTA
1 ATTTTATAT-ATTTTTTA
3689571 ATTTTATATATTTTTT
1 ATTTTATATATTTTTT
3689587 TTGTTTTCTA
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
17 14 0.93
18 1 0.07
ACGTcount: A:0.24, C:0.00, G:0.03, T:0.73
Consensus pattern (17 bp):
ATTTTATATATTTTTTA
Found at i:3689985 original size:41 final size:41
Alignment explanation
Indices: 3689916--3689993 Score: 106
Period size: 41 Copynumber: 1.9 Consensus size: 41
3689906 TTTAAAATAA
*
3689916 TATAAATAAAATTATATATTATATAAATATATTTTTAATTG
1 TATAAATAAAATTATATATTATAAAAATATATTTTTAATTG
*
3689957 TATAAATAAAAAATTAT-TA-TATAAAAATATTTTTTTA
1 TATAAAT--AAAATTATATATTATAAAAATATATTTTTA
3689994 TTATTAACAA
Statistics
Matches: 33, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
41 23 0.70
42 2 0.06
43 8 0.24
ACGTcount: A:0.51, C:0.00, G:0.01, T:0.47
Consensus pattern (41 bp):
TATAAATAAAATTATATATTATAAAAATATATTTTTAATTG
Found at i:3690586 original size:15 final size:15
Alignment explanation
Indices: 3690561--3690598 Score: 51
Period size: 15 Copynumber: 2.5 Consensus size: 15
3690551 TTTCAATTAT
3690561 TATATTTAATAAA-AA
1 TATA-TTAATAAATAA
3690576 TATTATTAATAAATAA
1 TA-TATTAATAAATAA
3690592 TATATTA
1 TATATTA
3690599 CTAATTGTAA
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
15 15 0.71
16 6 0.29
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (15 bp):
TATATTAATAAATAA
Found at i:3691344 original size:8 final size:8
Alignment explanation
Indices: 3691331--3691358 Score: 56
Period size: 8 Copynumber: 3.5 Consensus size: 8
3691321 AACCAAGAAG
3691331 AATAATTT
1 AATAATTT
3691339 AATAATTT
1 AATAATTT
3691347 AATAATTT
1 AATAATTT
3691355 AATA
1 AATA
3691359 TTGTTTTAGA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 20 1.00
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (8 bp):
AATAATTT
Found at i:3696516 original size:168 final size:168
Alignment explanation
Indices: 3696238--3696574 Score: 629
Period size: 168 Copynumber: 2.0 Consensus size: 168
3696228 AAATGGTGTA
*
3696238 TTTAGTCCCTTTCTTGTTGTAGAACTAGTTGAAACTAGTTTGCGTATTTGGTCCTGTCTTGTTTG
1 TTTAGTCCCTTTCTTGTTGTAGAACTAATTGAAACTAGTTTGCGTATTTGGTCCTGTCTTGTTTG
3696303 CATTGCCAATATGTGGAGAAGTTTGCCATTATGAATGGCATTGTTGTTCTTAAAGTCTTTCTAGC
66 CATTGCCAATATGTGGAGAAGTTTGCCATTATGAATGGCATTGTTGTTCTTAAAGTCTTTCTAGC
3696368 ATATCTGTTGTTTCTTCTTTCCTGAAAGTCTCTATTGT
131 ATATCTGTTGTTTCTTCTTTCCTGAAAGTCTCTATTGT
** * *
3696406 TTTAGTCCCTTTCTTGTTGTAGATTTAATTGAAAGTAGTTTGTGTATTTGGTCCTGTCTTGTTTG
1 TTTAGTCCCTTTCTTGTTGTAGAACTAATTGAAACTAGTTTGCGTATTTGGTCCTGTCTTGTTTG
3696471 CATTGCCAATATGTGGAGAAGTTTGCCATTATGAATGGCATTGTTGTTCTTAAAGTCTTTCTAGC
66 CATTGCCAATATGTGGAGAAGTTTGCCATTATGAATGGCATTGTTGTTCTTAAAGTCTTTCTAGC
3696536 ATATCTGTTGTTTCTTCTTTCCTGAAAGTCTCTATTGT
131 ATATCTGTTGTTTCTTCTTTCCTGAAAGTCTCTATTGT
3696574 T
1 T
3696575 ATATGTTTAC
Statistics
Matches: 164, Mismatches: 5, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
168 164 1.00
ACGTcount: A:0.19, C:0.15, G:0.20, T:0.46
Consensus pattern (168 bp):
TTTAGTCCCTTTCTTGTTGTAGAACTAATTGAAACTAGTTTGCGTATTTGGTCCTGTCTTGTTTG
CATTGCCAATATGTGGAGAAGTTTGCCATTATGAATGGCATTGTTGTTCTTAAAGTCTTTCTAGC
ATATCTGTTGTTTCTTCTTTCCTGAAAGTCTCTATTGT
Found at i:3700185 original size:29 final size:27
Alignment explanation
Indices: 3700119--3700187 Score: 84
Period size: 29 Copynumber: 2.4 Consensus size: 27
3700109 TATTTAGATA
3700119 AATTTTTATATTTTTATTGTATTTAAGT
1 AATTTTTAT-TTTTTATTGTATTTAAGT
* *
3700147 AAGTTATTATTTTTTATTTGTATTTATGT
1 AA-TTTTTATTTTTTA-TTGTATTTAAGT
3700176 ATATTTTTATTT
1 A-ATTTTTATTT
3700188 CAAATAAAAG
Statistics
Matches: 35, Mismatches: 3, Indels: 5
0.81 0.07 0.12
Matches are distributed among these distances:
28 8 0.23
29 26 0.74
30 1 0.03
ACGTcount: A:0.26, C:0.00, G:0.07, T:0.67
Consensus pattern (27 bp):
AATTTTTATTTTTTATTGTATTTAAGT
Found at i:3701344 original size:27 final size:29
Alignment explanation
Indices: 3701286--3701351 Score: 75
Period size: 27 Copynumber: 2.3 Consensus size: 29
3701276 ATAACTTTGT
* * *
3701286 TAATTCAATATAATAAATAAATTTTATTA
1 TAATTAAATATAATAAATAAATTCTATCA
3701315 TAA-TAAATA-AATAAATAAATATCT-TCA
1 TAATTAAATATAATAAATAAAT-TCTATCA
3701342 TAATTAAATA
1 TAATTAAATA
3701352 CTTAATTAAA
Statistics
Matches: 32, Mismatches: 3, Indels: 5
0.80 0.08 0.12
Matches are distributed among these distances:
27 16 0.50
28 13 0.41
29 3 0.09
ACGTcount: A:0.56, C:0.05, G:0.00, T:0.39
Consensus pattern (29 bp):
TAATTAAATATAATAAATAAATTCTATCA
Found at i:3701479 original size:26 final size:26
Alignment explanation
Indices: 3701427--3701487 Score: 70
Period size: 26 Copynumber: 2.3 Consensus size: 26
3701417 ATGAATAAAT
* *
3701427 AACTTTAATCTAAATTATTATATTTA
1 AACTTTAATATAAATTATTATACTTA
*
3701453 AACTTTAA-ATAAATTTATTATGCTTA
1 AACTTTAATATAAA-TTATTATACTTA
*
3701479 AATTTTAAT
1 AACTTTAAT
3701488 TTAATATCTT
Statistics
Matches: 29, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
25 4 0.14
26 25 0.86
ACGTcount: A:0.43, C:0.07, G:0.02, T:0.49
Consensus pattern (26 bp):
AACTTTAATATAAATTATTATACTTA
Found at i:3701628 original size:20 final size:21
Alignment explanation
Indices: 3701589--3701638 Score: 84
Period size: 20 Copynumber: 2.4 Consensus size: 21
3701579 TTTTAATTTT
3701589 AATTTTATCATTACAATAATC
1 AATTTTATCATTACAATAATC
*
3701610 AATTTTATTATTA-AATAATC
1 AATTTTATCATTACAATAATC
3701630 AATTTTATC
1 AATTTTATC
3701639 GAAATCACTT
Statistics
Matches: 27, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
20 15 0.56
21 12 0.44
ACGTcount: A:0.42, C:0.10, G:0.00, T:0.48
Consensus pattern (21 bp):
AATTTTATCATTACAATAATC
Found at i:3715454 original size:11 final size:11
Alignment explanation
Indices: 3715438--3715511 Score: 64
Period size: 11 Copynumber: 6.7 Consensus size: 11
3715428 TTAATATTCT
*
3715438 TTTTATCTTTA
1 TTTTATTTTTA
3715449 TTTTATTTTT-
1 TTTTATTTTTA
*
3715459 TTTTTTTTTTA
1 TTTTATTTTTA
*
3715470 TTTTTTTTTTA
1 TTTTATTTTTA
*
3715481 TTTTTTTATTTCA
1 TTTTATT-TTT-A
3715494 CTTTTA--TTTA
1 -TTTTATTTTTA
3715504 TTTTATTT
1 TTTTATTT
3715512 ATTCTATTTT
Statistics
Matches: 54, Mismatches: 3, Indels: 12
0.78 0.04 0.17
Matches are distributed among these distances:
9 5 0.09
10 10 0.19
11 31 0.57
12 3 0.06
13 1 0.02
14 4 0.07
ACGTcount: A:0.14, C:0.04, G:0.00, T:0.82
Consensus pattern (11 bp):
TTTTATTTTTA
Found at i:3715455 original size:5 final size:5
Alignment explanation
Indices: 3715438--3715521 Score: 59
Period size: 5 Copynumber: 16.8 Consensus size: 5
3715428 TTAATATTCT
* * *
3715438 TTTTA TCTTTA TTTTA TTTTTT TTTTT TTTTA TTTT- TTTT- TTATTT
1 TTTTA T-TTTA TTTTA -TTTTA TTTTA TTTTA TTTTA TTTTA TT-TTA
* *
3715484 TTTTA TTTCA CTTTTA -TTTA TTTTA -TTTA TTCTA TTTT
1 TTTTA TTTTA -TTTTA TTTTA TTTTA TTTTA TTTTA TTTT
3715522 CTTTAAATAA
Statistics
Matches: 65, Mismatches: 7, Indels: 14
0.76 0.08 0.16
Matches are distributed among these distances:
4 14 0.22
5 36 0.55
6 15 0.23
ACGTcount: A:0.14, C:0.05, G:0.00, T:0.81
Consensus pattern (5 bp):
TTTTA
Found at i:3715458 original size:1 final size:1
Alignment explanation
Indices: 3715449--3715487 Score: 51
Period size: 1 Copynumber: 39.0 Consensus size: 1
3715439 TTTATCTTTA
* * *
3715449 TTTTATTTTTTTTTTTTTTTATTTTTTTTTTATTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
3715488 ATTTCACTTT
Statistics
Matches: 32, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
1 32 1.00
ACGTcount: A:0.08, C:0.00, G:0.00, T:0.92
Consensus pattern (1 bp):
T
Found at i:3715509 original size:9 final size:9
Alignment explanation
Indices: 3715445--3715520 Score: 68
Period size: 9 Copynumber: 8.3 Consensus size: 9
3715435 TCTTTTTATC
3715445 TTTATTTTA
1 TTTATTTTA
3715454 TTT-TTTT-
1 TTTATTTTA
*
3715461 TTTTTTTTA
1 TTTATTTTA
*
3715470 TTTTTTTTTTA
1 --TTTATTTTA
3715481 TTT-TTTTA
1 TTTATTTTA
3715489 TTTCACTTTTA
1 TTT-A-TTTTA
3715500 TTTATTTTA
1 TTTATTTTA
*
3715509 TTTATTCTA
1 TTTATTTTA
3715518 TTT
1 TTT
3715521 TCTTTAAATA
Statistics
Matches: 59, Mismatches: 1, Indels: 14
0.80 0.01 0.19
Matches are distributed among these distances:
7 3 0.05
8 16 0.27
9 22 0.37
10 1 0.02
11 17 0.29
ACGTcount: A:0.14, C:0.04, G:0.00, T:0.82
Consensus pattern (9 bp):
TTTATTTTA
Found at i:3715526 original size:23 final size:20
Alignment explanation
Indices: 3715432--3715526 Score: 86
Period size: 19 Copynumber: 4.5 Consensus size: 20
3715422 GTTTATTTAA
* *
3715432 TATTCTTTTTATCTTTAT-TT
1 TATT-TTTTTATTTTTTTATT
*
3715452 TATTTTTTTTTTTTTTTATT
1 TATTTTTTTATTTTTTTATT
3715472 T-TTTTTTTATTTTTTTATT
1 TATTTTTTTATTTTTTTATT
3715491 TCACTTTTATTTATTTTATTTATT
1 T-A-TTTT-TTTATTTT-TTTATT
3715515 CTATTTTCTTTA
1 -TATTTT-TTTA
3715527 AATAAAAATA
Statistics
Matches: 63, Mismatches: 5, Indels: 11
0.80 0.06 0.14
Matches are distributed among these distances:
19 28 0.44
20 7 0.11
22 4 0.06
23 16 0.25
24 7 0.11
25 1 0.02
ACGTcount: A:0.15, C:0.06, G:0.00, T:0.79
Consensus pattern (20 bp):
TATTTTTTTATTTTTTTATT
Found at i:3715609 original size:59 final size:58
Alignment explanation
Indices: 3715546--3715762 Score: 296
Period size: 59 Copynumber: 3.7 Consensus size: 58
3715536 AAAAAATTCC
* *
3715546 AAAAAATATTTTTGGGGAAAAGTTGAAAGTATCAATTTTTCTTAAAAGTAAATTTTCAA
1 AAAAAATATTTTTGAGGAAAAGTTGAAAGTATCAATTTTCCTTAAAA-TAAATTTTCAA
* **
3715605 AAAAAAAATTTTTGAGGAAAAGTTGAAAGTATCAATTTTCCTTAAAAATAAATTTAAAAA
1 AAAAAATATTTTTGAGGAAAAGTTGAAAGTATCAATTTTCCTT-AAAATAAATTT-TCAA
*
3715665 AAAAAAGATTTTTGAGGAAAAGTTGAAAGTATCAATTTTCCTTGAAAATCGAAATTTTC--
1 AAAAAATATTTTTGAGGAAAAGTTGAAAGTATCAATTTTCCTT-AAAAT--AAATTTTCAA
3715724 AAAAAATATTTTTG-GAGAAAAGTTGAAAGTATCAATTTT
1 AAAAAATATTTTTGAG-GAAAAGTTGAAAGTATCAATTTT
3715763 TCCTACACAA
Statistics
Matches: 143, Mismatches: 10, Indels: 10
0.88 0.06 0.06
Matches are distributed among these distances:
58 1 0.01
59 83 0.58
60 53 0.37
62 6 0.04
ACGTcount: A:0.47, C:0.06, G:0.13, T:0.35
Consensus pattern (58 bp):
AAAAAATATTTTTGAGGAAAAGTTGAAAGTATCAATTTTCCTTAAAATAAATTTTCAA
Found at i:3715684 original size:119 final size:118
Alignment explanation
Indices: 3715546--3715762 Score: 332
Period size: 119 Copynumber: 1.8 Consensus size: 118
3715536 AAAAAATTCC
* * *
3715546 AAAAAATATTTTTGGGGAAAAGTTGAAAGTATCAATTTTTCTT-AAAAGT-AAATTTTCAAAAAA
1 AAAAAAGATTTTTGAGGAAAAGTTGAAAGTATCAATTTTCCTTGAAAA-TCAAATTTTC--AAAA
3715609 AAAATTTTT-GAGGAAAAGTTGAAAGTATCAATTTTCCTTAAAAATAAATTTAAAAA
63 AAAATTTTTGGA-GAAAAGTTGAAAGTATCAATTTTCCTTAAAAATAAATTTAAAAA
3715665 AAAAAAGATTTTTGAGGAAAAGTTGAAAGTATCAATTTTCCTTGAAAATCGAAATTTTCAAAAAA
1 AAAAAAGATTTTTGAGGAAAAGTTGAAAGTATCAATTTTCCTTGAAAATC-AAATTTTCAAAAAA
*
3715730 TATTTTTGGAGAAAAGTTGAAAGTATCAATTTT
65 AATTTTTGGAGAAAAGTTGAAAGTATCAATTTT
3715763 TCCTACACAA
Statistics
Matches: 90, Mismatches: 4, Indels: 8
0.88 0.04 0.08
Matches are distributed among these distances:
119 76 0.84
120 6 0.07
121 8 0.09
ACGTcount: A:0.47, C:0.06, G:0.13, T:0.35
Consensus pattern (118 bp):
AAAAAAGATTTTTGAGGAAAAGTTGAAAGTATCAATTTTCCTTGAAAATCAAATTTTCAAAAAAA
ATTTTTGGAGAAAAGTTGAAAGTATCAATTTTCCTTAAAAATAAATTTAAAAA
Found at i:3715815 original size:13 final size:13
Alignment explanation
Indices: 3715799--3715824 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
3715789 CATTCCTTTC
3715799 TATTTTGATTTTT
1 TATTTTGATTTTT
3715812 TATTTTGATTTTT
1 TATTTTGATTTTT
3715825 CTTTAACTAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.15, C:0.00, G:0.08, T:0.77
Consensus pattern (13 bp):
TATTTTGATTTTT
Found at i:3718448 original size:15 final size:15
Alignment explanation
Indices: 3718428--3718458 Score: 62
Period size: 15 Copynumber: 2.1 Consensus size: 15
3718418 TAACGAAAAT
3718428 GATTCAATTTGAGTG
1 GATTCAATTTGAGTG
3718443 GATTCAATTTGAGTG
1 GATTCAATTTGAGTG
3718458 G
1 G
3718459 GAGTATTTTA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.26, C:0.06, G:0.29, T:0.39
Consensus pattern (15 bp):
GATTCAATTTGAGTG
Found at i:3729188 original size:21 final size:19
Alignment explanation
Indices: 3729162--3729205 Score: 61
Period size: 21 Copynumber: 2.2 Consensus size: 19
3729152 GTAAAAATTA
3729162 AAATAAAATAATTTATTTATT
1 AAATAAAATAATTT-TTT-TT
*
3729183 AAATAAAATTATTTTTTTT
1 AAATAAAATAATTTTTTTT
3729202 AAAT
1 AAAT
3729206 TTTATCAACT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
19 6 0.27
20 3 0.14
21 13 0.59
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (19 bp):
AAATAAAATAATTTTTTTT
Found at i:3734450 original size:20 final size:20
Alignment explanation
Indices: 3734427--3734464 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
3734417 TTTAAACACA
* *
3734427 TGTTGACATGATGTAAAATG
1 TGTTAACATGATATAAAATG
3734447 TGTTAACATGATATAAAA
1 TGTTAACATGATATAAAA
3734465 ATTTCATATT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.42, C:0.05, G:0.18, T:0.34
Consensus pattern (20 bp):
TGTTAACATGATATAAAATG
Found at i:3734809 original size:26 final size:27
Alignment explanation
Indices: 3734758--3734813 Score: 69
Period size: 28 Copynumber: 2.0 Consensus size: 27
3734748 CTTTTAAAAA
*
3734758 TTATAAATTAATAAATATGTTATATAT
1 TTATAAATTAATAAATATATTATATAT
*
3734785 TTAT-AATTGATAAATATATATTATATAT
1 TTATAAATTAAT-AA-ATATATTATATAT
3734813 T
1 T
3734814 AAAAAGTTGA
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
26 6 0.24
27 6 0.24
28 13 0.52
ACGTcount: A:0.46, C:0.00, G:0.04, T:0.50
Consensus pattern (27 bp):
TTATAAATTAATAAATATATTATATAT
Found at i:3740161 original size:18 final size:18
Alignment explanation
Indices: 3740138--3740177 Score: 62
Period size: 18 Copynumber: 2.2 Consensus size: 18
3740128 CATGATTGAT
*
3740138 TATTGGTAAGGAGAAATA
1 TATTGGTAAGAAGAAATA
*
3740156 TATTGGTAAGAATAAATA
1 TATTGGTAAGAAGAAATA
3740174 TATT
1 TATT
3740178 TATTGGTAAG
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.45, C:0.00, G:0.20, T:0.35
Consensus pattern (18 bp):
TATTGGTAAGAAGAAATA
Found at i:3740277 original size:15 final size:15
Alignment explanation
Indices: 3740257--3740288 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
3740247 GTGTGCTTTT
3740257 ATGGATGCGAGTGTA
1 ATGGATGCGAGTGTA
*
3740272 ATGGATGTGAGTGTA
1 ATGGATGCGAGTGTA
3740287 AT
1 AT
3740289 AATTACTGTA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.28, C:0.03, G:0.38, T:0.31
Consensus pattern (15 bp):
ATGGATGCGAGTGTA
Found at i:3743285 original size:26 final size:25
Alignment explanation
Indices: 3743237--3743286 Score: 64
Period size: 26 Copynumber: 2.0 Consensus size: 25
3743227 TTATTTGTGA
*
3743237 ATATTAAATGAACATGTTCATAAAC
1 ATATTAAATGAACATATTCATAAAC
* *
3743262 ATATATAAATGAATATATTTATAAA
1 ATAT-TAAATGAACATATTCATAAA
3743287 TAATAAATAA
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
25 4 0.19
26 17 0.81
ACGTcount: A:0.52, C:0.06, G:0.06, T:0.36
Consensus pattern (25 bp):
ATATTAAATGAACATATTCATAAAC
Found at i:3744105 original size:19 final size:19
Alignment explanation
Indices: 3744040--3744116 Score: 63
Period size: 19 Copynumber: 4.2 Consensus size: 19
3744030 ATTTTCTAAT
*
3744040 TTTTAAT-ATTTAAAATTAA
1 TTTTAATAATATAAAA-TAA
*
3744059 TTTTATTAATA-AAAAT-A
1 TTTTAATAATATAAAATAA
*
3744076 TTATTTA-AATATAAAATAA
1 TT-TTAATAATATAAAATAA
**
3744095 TTTTAATAATATTTAATAA
1 TTTTAATAATATAAAATAA
3744114 TTT
1 TTT
3744117 ATTAACTTAA
Statistics
Matches: 46, Mismatches: 7, Indels: 10
0.73 0.11 0.16
Matches are distributed among these distances:
17 7 0.15
18 11 0.24
19 26 0.57
20 2 0.04
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (19 bp):
TTTTAATAATATAAAATAA
Found at i:3749795 original size:16 final size:19
Alignment explanation
Indices: 3749762--3749807 Score: 62
Period size: 16 Copynumber: 2.6 Consensus size: 19
3749752 ATTATTATCG
*
3749762 TATATTTTATTAATATCAT
1 TATATTATATTAATATCAT
3749781 T-T-TTATATT-ATATCAT
1 TATATTATATTAATATCAT
3749797 TATATTATATT
1 TATATTATATT
3749808 TTAAATTATC
Statistics
Matches: 24, Mismatches: 1, Indels: 5
0.80 0.03 0.17
Matches are distributed among these distances:
16 8 0.33
17 7 0.29
18 8 0.33
19 1 0.04
ACGTcount: A:0.35, C:0.04, G:0.00, T:0.61
Consensus pattern (19 bp):
TATATTATATTAATATCAT
Found at i:3750934 original size:6 final size:6
Alignment explanation
Indices: 3750922--3750962 Score: 55
Period size: 6 Copynumber: 6.8 Consensus size: 6
3750912 CGATGAGGAT
* * *
3750922 GAAGCA GAGGCA GAAGCA GAAGCA GAAGCG GAAGCG GAAGC
1 GAAGCA GAAGCA GAAGCA GAAGCA GAAGCA GAAGCA GAAGC
3750963 GGAGGAACAA
Statistics
Matches: 32, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
6 32 1.00
ACGTcount: A:0.41, C:0.17, G:0.41, T:0.00
Consensus pattern (6 bp):
GAAGCA
Found at i:3750945 original size:18 final size:18
Alignment explanation
Indices: 3750922--3750967 Score: 56
Period size: 18 Copynumber: 2.6 Consensus size: 18
3750912 CGATGAGGAT
3750922 GAAGCAGAGGCAGAAGCA
1 GAAGCAGAGGCAGAAGCA
* * *
3750940 GAAGCAGAAGCGGAAGCG
1 GAAGCAGAGGCAGAAGCA
*
3750958 GAAGCGGAGG
1 GAAGCAGAGG
3750968 AACAACAATA
Statistics
Matches: 23, Mismatches: 5, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
18 23 1.00
ACGTcount: A:0.39, C:0.15, G:0.46, T:0.00
Consensus pattern (18 bp):
GAAGCAGAGGCAGAAGCA
Found at i:3755177 original size:30 final size:30
Alignment explanation
Indices: 3755107--3755178 Score: 74
Period size: 30 Copynumber: 2.4 Consensus size: 30
3755097 ATTCGATTCG
* * * *
3755107 AAATTAAT-AAAATATTATTTTTTAAATAT
1 AAATAAATAAAAATATCATTATATAAATAT
**
3755136 AAATATTTAAAAATATCATTATATAAATAT
1 AAATAAATAAAAATATCATTATATAAATAT
*
3755166 ACATAAATAAAAA
1 AAATAAATAAAAA
3755179 ATTAAATAAT
Statistics
Matches: 33, Mismatches: 9, Indels: 1
0.77 0.21 0.02
Matches are distributed among these distances:
29 5 0.15
30 28 0.85
ACGTcount: A:0.58, C:0.03, G:0.00, T:0.39
Consensus pattern (30 bp):
AAATAAATAAAAATATCATTATATAAATAT
Found at i:3756475 original size:43 final size:44
Alignment explanation
Indices: 3756427--3756514 Score: 108
Period size: 43 Copynumber: 2.0 Consensus size: 44
3756417 TAAAATTAAT
* *
3756427 TTTTTTATAATTTAGATATAT-ATAATTTAAATATGTAT-TTTTTA
1 TTTTTTA-AAATTA-ATATATAATAATTTAAATATATATCTTTTTA
* *
3756471 TTTTTTAAAATTAATTTTTAATAATTTAAATATATATCTTTTTA
1 TTTTTTAAAATTAATATATAATAATTTAAATATATATCTTTTTA
3756515 AATTTAAAAA
Statistics
Matches: 38, Mismatches: 4, Indels: 4
0.83 0.09 0.09
Matches are distributed among these distances:
42 4 0.11
43 21 0.55
44 13 0.34
ACGTcount: A:0.38, C:0.01, G:0.02, T:0.59
Consensus pattern (44 bp):
TTTTTTAAAATTAATATATAATAATTTAAATATATATCTTTTTA
Found at i:3756498 original size:21 final size:22
Alignment explanation
Indices: 3756448--3756522 Score: 66
Period size: 22 Copynumber: 3.5 Consensus size: 22
3756438 TTAGATATAT
*
3756448 ATAATTTAAATATGTATTTTTT
1 ATAATTTAAATATGTATTTTTA
**
3756470 ATTTTTTAAA-AT-TAATTTTTA
1 ATAATTTAAATATGT-ATTTTTA
* *
3756491 ATAATTTAAATATATATCTTTTT
1 ATAATTTAAATATGTAT-TTTTA
3756514 A-AATTTAAA
1 ATAATTTAAA
3756523 AATATTAAAT
Statistics
Matches: 43, Mismatches: 6, Indels: 8
0.75 0.11 0.14
Matches are distributed among these distances:
20 1 0.02
21 16 0.37
22 20 0.47
23 6 0.14
ACGTcount: A:0.41, C:0.01, G:0.01, T:0.56
Consensus pattern (22 bp):
ATAATTTAAATATGTATTTTTA
Found at i:3757499 original size:13 final size:15
Alignment explanation
Indices: 3757470--3757501 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
3757460 ATTTTTTTTA
3757470 ATAATTTAGATATAT
1 ATAATTTAGATATAT
*
3757485 ATAATTTAAATATAT
1 ATAATTTAGATATAT
3757500 AT
1 AT
3757502 CTTTTTATCT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.50, C:0.00, G:0.03, T:0.47
Consensus pattern (15 bp):
ATAATTTAGATATAT
Found at i:3763347 original size:20 final size:21
Alignment explanation
Indices: 3763311--3763352 Score: 59
Period size: 20 Copynumber: 2.0 Consensus size: 21
3763301 CATATTTTAG
3763311 GTTTATTTTAATTTAGACAATT
1 GTTTATTTT-ATTTAGACAATT
*
3763333 GTTTATTTT-TTTAGAGAATT
1 GTTTATTTTATTTAGACAATT
3763353 ATAGTTTATG
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
20 10 0.53
22 9 0.47
ACGTcount: A:0.29, C:0.02, G:0.12, T:0.57
Consensus pattern (21 bp):
GTTTATTTTATTTAGACAATT
Found at i:3763758 original size:19 final size:18
Alignment explanation
Indices: 3763720--3763756 Score: 65
Period size: 18 Copynumber: 2.1 Consensus size: 18
3763710 GATAGAGTGT
3763720 AGTTTTTCGAACAAAAAA
1 AGTTTTTCGAACAAAAAA
*
3763738 AGTTTTTCGTACAAAAAA
1 AGTTTTTCGAACAAAAAA
3763756 A
1 A
3763757 AGCCTTAAAT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.49, C:0.11, G:0.11, T:0.30
Consensus pattern (18 bp):
AGTTTTTCGAACAAAAAA
Found at i:3767399 original size:20 final size:20
Alignment explanation
Indices: 3767357--3767399 Score: 52
Period size: 20 Copynumber: 2.1 Consensus size: 20
3767347 AAGTTTGGTC
* *
3767357 TCTTTTTTTTTTTCTTTTAT
1 TCTTTTTTTTTCTCTTCTAT
3767377 TCTTTTTGTTTTCTCTTCT-T
1 TCTTTTT-TTTTCTCTTCTAT
3767397 TCT
1 TCT
3767400 CTACTTGTTT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
20 11 0.55
21 9 0.45
ACGTcount: A:0.02, C:0.16, G:0.02, T:0.79
Consensus pattern (20 bp):
TCTTTTTTTTTCTCTTCTAT
Found at i:3767766 original size:21 final size:20
Alignment explanation
Indices: 3767742--3767790 Score: 53
Period size: 21 Copynumber: 2.4 Consensus size: 20
3767732 AATTTAAAAG
**
3767742 AAAAAAAAAGAAATTGTAATT
1 AAAAAAAAA-AAATCATAATT
*
3767763 AAAATTAAAAAAATCATAATT
1 AAAA-AAAAAAAATCATAATT
3767784 AAAAAAA
1 AAAAAAA
3767791 GAACATTTTG
Statistics
Matches: 23, Mismatches: 4, Indels: 3
0.77 0.13 0.10
Matches are distributed among these distances:
20 2 0.09
21 17 0.74
22 4 0.17
ACGTcount: A:0.71, C:0.02, G:0.04, T:0.22
Consensus pattern (20 bp):
AAAAAAAAAAAATCATAATT
Found at i:3768860 original size:26 final size:27
Alignment explanation
Indices: 3768831--3768882 Score: 70
Period size: 26 Copynumber: 2.0 Consensus size: 27
3768821 TTTTAAGGTA
* * *
3768831 ATTATATGTATATAT-ATTTATTTTTT
1 ATTAAATGTACATATAATATATTTTTT
3768857 ATTAAATGTACATATAATATATTTTT
1 ATTAAATGTACATATAATATATTTTT
3768883 CTATACATAT
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
26 13 0.59
27 9 0.41
ACGTcount: A:0.37, C:0.02, G:0.04, T:0.58
Consensus pattern (27 bp):
ATTAAATGTACATATAATATATTTTTT
Found at i:3769891 original size:2 final size:2
Alignment explanation
Indices: 3769886--3769910 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
3769876 TTTTACTATG
3769886 AC AC AC AC AC AC AC AC AC AC AC AC A
1 AC AC AC AC AC AC AC AC AC AC AC AC A
3769911 TATATATATA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.48, G:0.00, T:0.00
Consensus pattern (2 bp):
AC
Found at i:3770374 original size:30 final size:28
Alignment explanation
Indices: 3770330--3770409 Score: 90
Period size: 30 Copynumber: 2.7 Consensus size: 28
3770320 GTACTATTCA
*
3770330 ATTTTTAAAAATTTAGTCCTTCTAA-TATT
1 ATTTTTAAAAATTTAGTCC-T-AAATTATT
3770359 ATTTTTAAGAAATTTAGTTCCTAAATTATT
1 ATTTTTAA-AAATTTAG-TCCTAAATTATT
3770389 ATATTTTAAAGAATTTAGTCC
1 AT-TTTTAAA-AATTTAGTCC
3770410 CTGTGCATTA
Statistics
Matches: 45, Mismatches: 1, Indels: 9
0.82 0.02 0.16
Matches are distributed among these distances:
29 10 0.22
30 19 0.42
31 16 0.36
ACGTcount: A:0.36, C:0.09, G:0.06, T:0.49
Consensus pattern (28 bp):
ATTTTTAAAAATTTAGTCCTAAATTATT
Found at i:3770507 original size:29 final size:29
Alignment explanation
Indices: 3770444--3770507 Score: 67
Period size: 29 Copynumber: 2.2 Consensus size: 29
3770434 GAAATCCTTA
3770444 AAAAATAATATTATAAGGACTAAATTACT
1 AAAAATAATATTATAAGGACTAAATTACT
** * **
3770473 CTAAATAATATTA-AAGGGATTAAATTTTT
1 AAAAATAATATTATAA-GGACTAAATTACT
3770502 AAAAAT
1 AAAAAT
3770508 CAAAGAATAT
Statistics
Matches: 27, Mismatches: 7, Indels: 2
0.75 0.19 0.06
Matches are distributed among these distances:
28 2 0.07
29 25 0.93
ACGTcount: A:0.53, C:0.05, G:0.08, T:0.34
Consensus pattern (29 bp):
AAAAATAATATTATAAGGACTAAATTACT
Found at i:3772920 original size:161 final size:161
Alignment explanation
Indices: 3772731--3773211 Score: 683
Period size: 161 Copynumber: 3.0 Consensus size: 161
3772721 GATCTAATCT
* * *
3772731 ACAACATAAATTTAAAATAATATTTTAATTGATCATTAAAATAATTATTTAAATTTATAATGATA
1 ACAACATAAATTTATAATAATATTTTAATTGATCGTTAAAACAATTATTTAAATTTATAATGATA
* * * * * *
3772796 TTTTAACTAACCGTTAAAACATTTACTTTTATATATCAATCACTATAATTGCTATTTTGATCGAT
66 TTTTATCTAATCGTTAAAACAGTTAATTTTATATATCAATCACTAAAATTGATATTTTGATCGAT
3772861 CGTTAAAAGTTATTATTTTTATTTATCATCA
131 CGTTAAAAGTTATTATTTTTATTTATCATCA
* * * *
3772892 ACAATATAAATTTATAATAATATTTTAATTGATCGTTAGAACAGTTATTTAAATTTATAATGATG
1 ACAACATAAATTTATAATAATATTTTAATTGATCGTTAAAACAATTATTTAAATTTATAATGATA
* * * * *
3772957 TTTTATCTTATCGTTAAAAGAGTTAATTTTATATATCATTTACTAAAATTGTTATTTTGATCGAT
66 TTTTATCTAATCGTTAAAACAGTTAATTTTATATATCAATCACTAAAATTGATATTTTGATCGAT
* * *
3773022 CGTTGAAAGTTACTATTTTTATTTATCATCT
131 CGTTAAAAGTTATTATTTTTATTTATCATCA
* * * *
3773053 ACAACATAAATTTATAATAATATTTTAGTTGACCGTTAAAACAATTATTTAAATTTATGATAATA
1 ACAACATAAATTTATAATAATATTTTAATTGATCGTTAAAACAATTATTTAAATTTATAATGATA
* * * *
3773118 TTTTATCTGATCGTTAAAACAGTTATTTTTATATATCAATCATTAAAATTGATATTTTGATAGAT
66 TTTTATCTAATCGTTAAAACAGTTAATTTTATATATCAATCACTAAAATTGATATTTTGATCGAT
* *
3773183 CATTAAAAATTATTATTTTTATTTATCAT
131 CGTTAAAAGTTATTATTTTTATTTATCAT
3773212 TAAAAATGAC
Statistics
Matches: 280, Mismatches: 40, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
161 280 1.00
ACGTcount: A:0.39, C:0.08, G:0.07, T:0.46
Consensus pattern (161 bp):
ACAACATAAATTTATAATAATATTTTAATTGATCGTTAAAACAATTATTTAAATTTATAATGATA
TTTTATCTAATCGTTAAAACAGTTAATTTTATATATCAATCACTAAAATTGATATTTTGATCGAT
CGTTAAAAGTTATTATTTTTATTTATCATCA
Found at i:3772970 original size:43 final size:43
Alignment explanation
Indices: 3772898--3772981 Score: 107
Period size: 43 Copynumber: 2.0 Consensus size: 43
3772888 ATCAACAATA
*
3772898 TAAATTTATAATAATATTTTAATTGATCGTTAGAACAGTTATT
1 TAAATTTATAATAATATTTTAATTGATCGTTAAAACAGTTATT
* * * *
3772941 TAAATTTATAATGATGTTTT-ATCTTATCGTTAAAAGAGTTA
1 TAAATTTATAATAATATTTTAAT-TGATCGTTAAAACAGTTA
3772982 ATTTTATATA
Statistics
Matches: 35, Mismatches: 5, Indels: 2
0.83 0.12 0.05
Matches are distributed among these distances:
42 2 0.06
43 33 0.94
ACGTcount: A:0.38, C:0.05, G:0.11, T:0.46
Consensus pattern (43 bp):
TAAATTTATAATAATATTTTAATTGATCGTTAAAACAGTTATT
Found at i:3773120 original size:43 final size:43
Alignment explanation
Indices: 3773059--3773145 Score: 131
Period size: 43 Copynumber: 2.0 Consensus size: 43
3773049 ATCTACAACA
3773059 TAAATTTATAATAATATTTTAGT-TGACCGTTAAAACAATTATT
1 TAAATTTATAATAATATTTTA-TCTGACCGTTAAAACAATTATT
* * *
3773102 TAAATTTATGATAATATTTTATCTGATCGTTAAAACAGTTATT
1 TAAATTTATAATAATATTTTATCTGACCGTTAAAACAATTATT
3773145 T
1 T
3773146 TTATATATCA
Statistics
Matches: 40, Mismatches: 3, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
42 1 0.03
43 39 0.98
ACGTcount: A:0.39, C:0.07, G:0.08, T:0.46
Consensus pattern (43 bp):
TAAATTTATAATAATATTTTATCTGACCGTTAAAACAATTATT
Found at i:3773184 original size:25 final size:25
Alignment explanation
Indices: 3773156--3773243 Score: 97
Period size: 25 Copynumber: 3.5 Consensus size: 25
3773146 TTATATATCA
*
3773156 ATCATTAAAATTGATATTTTGATAG
1 ATCATTAAAATTGATATTTTGATTG
* *
3773181 ATCATTAAAAATT-ATTATTTTTATTT
1 ATCATT-AAAATTGA-TATTTTGATTG
* * *
3773207 ATCATTAAAAATGACATTTCGATTG
1 ATCATTAAAATTGATATTTTGATTG
3773232 ATCATTAAAATT
1 ATCATTAAAATT
3773244 AAAAATGATA
Statistics
Matches: 51, Mismatches: 9, Indels: 6
0.77 0.14 0.09
Matches are distributed among these distances:
25 30 0.59
26 21 0.41
ACGTcount: A:0.41, C:0.07, G:0.07, T:0.45
Consensus pattern (25 bp):
ATCATTAAAATTGATATTTTGATTG
Found at i:3773199 original size:26 final size:25
Alignment explanation
Indices: 3773156--3773241 Score: 93
Period size: 26 Copynumber: 3.4 Consensus size: 25
3773146 TTATATATCA
*
3773156 ATCATT-AAAATTGATATTTTGATAG
1 ATCATTAAAAATT-ATATTTTGATTG
* *
3773181 ATCATTAAAAATTATTATTTTTATTT
1 ATCATTAAAAATTA-TATTTTGATTG
* * *
3773207 ATCATTAAAAATGACATTTCGATTG
1 ATCATTAAAAATTATATTTTGATTG
3773232 ATCATTAAAA
1 ATCATTAAAA
3773242 TTAAAAATGA
Statistics
Matches: 51, Mismatches: 8, Indels: 4
0.81 0.13 0.06
Matches are distributed among these distances:
25 24 0.47
26 27 0.53
ACGTcount: A:0.42, C:0.07, G:0.07, T:0.44
Consensus pattern (25 bp):
ATCATTAAAAATTATATTTTGATTG
Found at i:3773248 original size:31 final size:31
Alignment explanation
Indices: 3773210--3773272 Score: 90
Period size: 31 Copynumber: 2.0 Consensus size: 31
3773200 TTTATTTATC
* *
3773210 ATTAAAAATGACATTTCGATTGATCATTAAA
1 ATTAAAAATGACATTTCAATTGATCACTAAA
* *
3773241 ATTAAAAATGATATTTTAATTGATCACTAAA
1 ATTAAAAATGACATTTCAATTGATCACTAAA
3773272 A
1 A
3773273 ATTACTATTT
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
31 28 1.00
ACGTcount: A:0.48, C:0.08, G:0.08, T:0.37
Consensus pattern (31 bp):
ATTAAAAATGACATTTCAATTGATCACTAAA
Found at i:3773253 original size:82 final size:82
Alignment explanation
Indices: 3773159--3773338 Score: 245
Period size: 82 Copynumber: 2.2 Consensus size: 82
3773149 TATATCAATC
* * * * *
3773159 ATTAAAATTGATATTTTGATAGATCATTAAAAATTATTATTTTTATTTATCATTAAAAATGACAT
1 ATTAAAAATGATATTTTAATAGATCACTAAAAATTACTATTTTTATTTATAATTAAAAATGACAT
*
3773224 TTCGAT-TGATCATTAAA
66 TTCAATCT-ATCATTAAA
* * *
3773241 ATTAAAAATGATATTTTAATTGATCACTAAAAATTACTATTTTTATTTATAATTAGATATGACAT
1 ATTAAAAATGATATTTTAATAGATCACTAAAAATTACTATTTTTATTTATAATTAAAAATGACAT
*
3773306 TTCAATCTATCGTTAAA
66 TTCAATCTATCATTAAA
*
3773323 ATTAAAAATAATATTT
1 ATTAAAAATGATATTT
3773339 CAATCGATTG
Statistics
Matches: 86, Mismatches: 11, Indels: 2
0.87 0.11 0.02
Matches are distributed among these distances:
82 85 0.99
83 1 0.01
ACGTcount: A:0.43, C:0.07, G:0.06, T:0.44
Consensus pattern (82 bp):
ATTAAAAATGATATTTTAATAGATCACTAAAAATTACTATTTTTATTTATAATTAAAAATGACAT
TTCAATCTATCATTAAA
Found at i:3774826 original size:2 final size:2
Alignment explanation
Indices: 3774819--3774846 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
3774809 AGAGGTAAAC
3774819 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
3774847 CTAGATTTCC
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:3774865 original size:17 final size:15
Alignment explanation
Indices: 3774843--3774880 Score: 51
Period size: 17 Copynumber: 2.5 Consensus size: 15
3774833 ATATATATAT
3774843 ATATCTAGATTTCCTCC
1 ATATCTA-ATTT-CTCC
3774860 ATATCTAATTTCTCC
1 ATATCTAATTTCTCC
3774875 A-ATCTA
1 ATATCTA
3774881 CGAAGAGCTT
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
14 5 0.24
15 5 0.24
16 4 0.19
17 7 0.33
ACGTcount: A:0.29, C:0.26, G:0.03, T:0.42
Consensus pattern (15 bp):
ATATCTAATTTCTCC
Found at i:3776293 original size:13 final size:13
Alignment explanation
Indices: 3776267--3776300 Score: 50
Period size: 13 Copynumber: 2.6 Consensus size: 13
3776257 ATAATTGTAG
*
3776267 TTTTAATTCCAAA
1 TTTTAATTCAAAA
*
3776280 TTTTACTTCAAAA
1 TTTTAATTCAAAA
3776293 TTTTAATT
1 TTTTAATT
3776301 TGTTGACGTT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
13 18 1.00
ACGTcount: A:0.35, C:0.12, G:0.00, T:0.53
Consensus pattern (13 bp):
TTTTAATTCAAAA
Found at i:3816207 original size:16 final size:15
Alignment explanation
Indices: 3816174--3816245 Score: 56
Period size: 16 Copynumber: 4.6 Consensus size: 15
3816164 TCTGTTTGAC
*
3816174 TTTAATTTTAATAAAA
1 TTTAA-TTTAATATAA
*
3816190 TTTAGATTTAATTTAA
1 TTTA-ATTTAATATAA
* **
3816206 TTATTATTTAATCGAA
1 TT-TAATTTAATATAA
3816222 TTTAAATTTAA-ATAA
1 TTT-AATTTAATATAA
3816237 TTTAATTTA
1 TTTAATTTA
3816246 TTGATAAATC
Statistics
Matches: 45, Mismatches: 8, Indels: 8
0.74 0.13 0.13
Matches are distributed among these distances:
14 6 0.13
15 6 0.13
16 31 0.69
17 2 0.04
ACGTcount: A:0.43, C:0.01, G:0.03, T:0.53
Consensus pattern (15 bp):
TTTAATTTAATATAA
Found at i:3816281 original size:21 final size:22
Alignment explanation
Indices: 3816257--3816302 Score: 69
Period size: 22 Copynumber: 2.1 Consensus size: 22
3816247 TGATAAATCG
3816257 AATTTAAAT-ATTT-TTATATTT
1 AATTTAAATAATTTATTA-ATTT
3816278 AATTTAAATAATTTATTAATTT
1 AATTTAAATAATTTATTAATTT
3816300 AAT
1 AAT
3816303 CGAATTTTTA
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
21 9 0.39
22 11 0.48
23 3 0.13
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (22 bp):
AATTTAAATAATTTATTAATTT
Found at i:3816316 original size:48 final size:52
Alignment explanation
Indices: 3816221--3816323 Score: 133
Period size: 48 Copynumber: 2.0 Consensus size: 52
3816211 ATTTAATCGA
* *
3816221 ATTTAAATTTAAATAATTTAATTTATTGATAAATCGAATTTAAATATTTTTAT
1 ATTTAAATTTAAATAATTTAATTAATT-ATAAATCGAATTTAAATATTTTAAT
**
3816274 ATTT-AATTTAAATAATTT-ATTAATT-T-AATCGAATTTTTATATTTTAAT
1 ATTTAAATTTAAATAATTTAATTAATTATAAATCGAATTTAAATATTTTAAT
3816322 AT
1 AT
3816324 ATTTTTATTA
Statistics
Matches: 46, Mismatches: 4, Indels: 5
0.84 0.07 0.09
Matches are distributed among these distances:
48 21 0.46
49 1 0.02
51 6 0.13
52 14 0.30
53 4 0.09
ACGTcount: A:0.42, C:0.02, G:0.03, T:0.53
Consensus pattern (52 bp):
ATTTAAATTTAAATAATTTAATTAATTATAAATCGAATTTAAATATTTTAAT
Found at i:3816514 original size:12 final size:11
Alignment explanation
Indices: 3816460--3816538 Score: 67
Period size: 11 Copynumber: 7.2 Consensus size: 11
3816450 TTTAATCACG
3816460 AATCAAATTTA
1 AATCAAATTTA
*
3816471 AATTAAA---A
1 AATCAAATTTA
*
3816479 AATAAAATTT-
1 AATCAAATTTA
*
3816489 AATAAAATTTA
1 AATCAAATTTA
3816500 AATCAAATATTA
1 AATCAAAT-TTA
3816512 AATCATAATTTGAA
1 AATCA-AATTT--A
3816526 AATCAAATTTA
1 AATCAAATTTA
3816537 AA
1 AA
3816539 ATTTTTATGT
Statistics
Matches: 57, Mismatches: 3, Indels: 16
0.75 0.04 0.21
Matches are distributed among these distances:
8 7 0.12
10 10 0.18
11 16 0.28
12 10 0.18
13 8 0.14
14 6 0.11
ACGTcount: A:0.59, C:0.05, G:0.01, T:0.34
Consensus pattern (11 bp):
AATCAAATTTA
Found at i:3816530 original size:14 final size:12
Alignment explanation
Indices: 3816493--3816540 Score: 55
Period size: 12 Copynumber: 3.9 Consensus size: 12
3816483 AAATTTAATA
3816493 AAATTT-AAATC
1 AAATTTAAAATC
3816504 AAATATT-AAATC
1 AAAT-TTAAAATC
3816516 ATAATTTGAAAATC
1 A-AATTT-AAAATC
3816530 AAATTTAAAAT
1 AAATTTAAAAT
3816541 TTTTATGTAT
Statistics
Matches: 33, Mismatches: 0, Indels: 7
0.82 0.00 0.17
Matches are distributed among these distances:
11 4 0.12
12 15 0.45
13 8 0.24
14 6 0.18
ACGTcount: A:0.56, C:0.06, G:0.02, T:0.35
Consensus pattern (12 bp):
AAATTTAAAATC
Found at i:3837689 original size:30 final size:28
Alignment explanation
Indices: 3837653--3837734 Score: 110
Period size: 30 Copynumber: 2.8 Consensus size: 28
3837643 TTTTTATTAC
3837653 ATTCAAATAAATTTTTAATCTTTACTTCGT
1 ATTCAAATAAATTTTTAAT-TTTACTT-GT
*
3837683 ATTCAAATAAAATTTTAAATTTTACTTGT
1 ATTCAAAT-AAATTTTTAATTTTACTTGT
* *
3837712 ATTTAAATAAACTTTTAATTTTA
1 ATTCAAATAAATTTTTAATTTTA
3837735 AATTTATACC
Statistics
Matches: 47, Mismatches: 4, Indels: 4
0.85 0.07 0.07
Matches are distributed among these distances:
28 13 0.28
29 9 0.19
30 15 0.32
31 10 0.21
ACGTcount: A:0.39, C:0.09, G:0.02, T:0.50
Consensus pattern (28 bp):
ATTCAAATAAATTTTTAATTTTACTTGT
Found at i:3837828 original size:21 final size:22
Alignment explanation
Indices: 3837785--3837830 Score: 58
Period size: 22 Copynumber: 2.1 Consensus size: 22
3837775 TATTTGAAAT
* * *
3837785 AAAAGTATTTGGATACAAGTAA
1 AAAAATATTTGAATACAAATAA
3837807 AAAAATATTTGAATA-AAATAA
1 AAAAATATTTGAATACAAATAA
3837828 AAA
1 AAA
3837831 TATAAAAACT
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
21 8 0.38
22 13 0.62
ACGTcount: A:0.61, C:0.02, G:0.11, T:0.26
Consensus pattern (22 bp):
AAAAATATTTGAATACAAATAA
Found at i:3852627 original size:37 final size:37
Alignment explanation
Indices: 3852554--3852627 Score: 89
Period size: 37 Copynumber: 2.0 Consensus size: 37
3852544 ATTGTGTGGA
*
3852554 TAATTATTTATTAAAATAATCTAAAATATATAATTTG
1 TAATTATTTATTAAAATAATCTAAAAGATATAATTTG
* *
3852591 TAATTATTTATTTTAAATTATC-AAATAGATAT-ATTTG
1 TAATTATTTA-TTAAAATAATCTAAA-AGATATAATTTG
3852628 ATTTGAAAAA
Statistics
Matches: 32, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
37 18 0.56
38 14 0.44
ACGTcount: A:0.45, C:0.03, G:0.04, T:0.49
Consensus pattern (37 bp):
TAATTATTTATTAAAATAATCTAAAAGATATAATTTG
Found at i:3856030 original size:19 final size:19
Alignment explanation
Indices: 3855998--3856034 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
3855988 TTTGACAAAT
*
3855998 TTAATCAATCAATATATAA
1 TTAATAAATCAATATATAA
*
3856017 TTAATAAATTAATATATA
1 TTAATAAATCAATATATA
3856035 CTACAATTAC
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 16 1.00
ACGTcount: A:0.54, C:0.05, G:0.00, T:0.41
Consensus pattern (19 bp):
TTAATAAATCAATATATAA
Found at i:3857407 original size:32 final size:31
Alignment explanation
Indices: 3857371--3857445 Score: 105
Period size: 32 Copynumber: 2.4 Consensus size: 31
3857361 TAATTAAATA
* *
3857371 TGATTTCATTTGGTAAAATATTAATGCACGTT
1 TGATTTCATTTGATAAAATATTAATGCAC-AT
*
3857403 TGATTTCATTTAATAAAATATTAATGCACAT
1 TGATTTCATTTGATAAAATATTAATGCACAT
*
3857434 GGATTTCATTTG
1 TGATTTCATTTG
3857446 TAATGTTTCA
Statistics
Matches: 38, Mismatches: 5, Indels: 1
0.86 0.11 0.02
Matches are distributed among these distances:
31 11 0.29
32 27 0.71
ACGTcount: A:0.33, C:0.09, G:0.13, T:0.44
Consensus pattern (31 bp):
TGATTTCATTTGATAAAATATTAATGCACAT
Found at i:3858635 original size:2 final size:2
Alignment explanation
Indices: 3858630--3858660 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
3858620 ACATACACAC
3858630 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
3858661 CACAACACAC
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:3861848 original size:22 final size:22
Alignment explanation
Indices: 3861821--3861867 Score: 85
Period size: 22 Copynumber: 2.1 Consensus size: 22
3861811 TCAGAATCTC
3861821 TTTTTCTTCTATTTTTTTCGCT
1 TTTTTCTTCTATTTTTTTCGCT
*
3861843 TTTTTCTTTTATTTTTTTCGCT
1 TTTTTCTTCTATTTTTTTCGCT
3861865 TTT
1 TTT
3861868 ATCTCGGTTA
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
22 24 1.00
ACGTcount: A:0.04, C:0.15, G:0.04, T:0.77
Consensus pattern (22 bp):
TTTTTCTTCTATTTTTTTCGCT
Found at i:3862232 original size:13 final size:14
Alignment explanation
Indices: 3862216--3862249 Score: 54
Period size: 13 Copynumber: 2.6 Consensus size: 14
3862206 AATATTTAAA
3862216 TATTTAAAT-ATTT
1 TATTTAAATAATTT
3862229 TA-TTAAATAATTT
1 TATTTAAATAATTT
3862242 TATTTAAA
1 TATTTAAA
3862250 ATATAATAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
12 6 0.32
13 8 0.42
14 5 0.26
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (14 bp):
TATTTAAATAATTT
Found at i:3862493 original size:42 final size:45
Alignment explanation
Indices: 3862407--3862500 Score: 119
Period size: 42 Copynumber: 2.2 Consensus size: 45
3862397 AAAATAATTT
3862407 AATTA-ATTTATTTTTGAATAATTTAATTTAAAATTAATTGAATA
1 AATTATATTTATTTTTGAATAATTTAATTTAAAATTAATTGAATA
*
3862451 AA-TATATTTA-TTTT-AA-AATTTAAATTTAAAATTTTATT-AATA
1 AATTATATTTATTTTTGAATAATTT-AATTTAAAA-TTAATTGAATA
3862493 AATTATAT
1 AATTATAT
3862501 AATTGTTAAC
Statistics
Matches: 45, Mismatches: 1, Indels: 9
0.82 0.02 0.16
Matches are distributed among these distances:
41 5 0.11
42 17 0.38
43 16 0.36
44 7 0.16
ACGTcount: A:0.47, C:0.00, G:0.02, T:0.51
Consensus pattern (45 bp):
AATTATATTTATTTTTGAATAATTTAATTTAAAATTAATTGAATA
Found at i:3862733 original size:20 final size:20
Alignment explanation
Indices: 3862694--3862731 Score: 62
Period size: 19 Copynumber: 2.0 Consensus size: 20
3862684 TTTTAAATTA
3862694 AATTTATTTAATTATATTTT
1 AATTTATTTAATTATATTTT
3862714 AATTTA-TTAATTAT-TTTT
1 AATTTATTTAATTATATTTT
3862732 TTTTTTTGAA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
18 4 0.22
19 8 0.44
20 6 0.33
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (20 bp):
AATTTATTTAATTATATTTT
Found at i:3863191 original size:2 final size:2
Alignment explanation
Indices: 3863184--3863214 Score: 53
Period size: 2 Copynumber: 15.5 Consensus size: 2
3863174 TTATTGCGCC
*
3863184 CT CT CT CT CT CT CT CT CT CT CA CT CT CT CT C
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT C
3863215 CTTTAGGAGG
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.03, C:0.52, G:0.00, T:0.45
Consensus pattern (2 bp):
CT
Found at i:3863349 original size:18 final size:18
Alignment explanation
Indices: 3863309--3863343 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
3863299 CTTCATATAG
*
3863309 TGGTGGGTATGGCGGTGC
1 TGGTGGCTATGGCGGTGC
*
3863327 TGGTGGCTATGGTGGTG
1 TGGTGGCTATGGCGGTG
3863344 GCGGTGCAGG
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:0.06, C:0.09, G:0.54, T:0.31
Consensus pattern (18 bp):
TGGTGGCTATGGCGGTGC
Found at i:3863716 original size:15 final size:15
Alignment explanation
Indices: 3863696--3863724 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
3863686 AGGAGAGCGT
3863696 GGTGGAAGAGGTGGC
1 GGTGGAAGAGGTGGC
3863711 GGTGGAAGAGGTGG
1 GGTGGAAGAGGTGG
3863725 TGGCCGTGGT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.21, C:0.03, G:0.62, T:0.14
Consensus pattern (15 bp):
GGTGGAAGAGGTGGC
Found at i:3864039 original size:3 final size:3
Alignment explanation
Indices: 3864014--3864055 Score: 57
Period size: 3 Copynumber: 14.0 Consensus size: 3
3864004 CTCTCCTGCG
* * *
3864014 GGT GCT GGT GGT AGT GGT AGT GGT GGT GGT GGT GGT GGT GGT
1 GGT GGT GGT GGT GGT GGT GGT GGT GGT GGT GGT GGT GGT GGT
3864056 TATAACAGAG
Statistics
Matches: 33, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
3 33 1.00
ACGTcount: A:0.05, C:0.02, G:0.60, T:0.33
Consensus pattern (3 bp):
GGT
Found at i:3869318 original size:135 final size:135
Alignment explanation
Indices: 3869111--3869378 Score: 351
Period size: 135 Copynumber: 2.0 Consensus size: 135
3869101 CTTATTTGTT
3869111 TTTGTAAATATGTTAGAAAAAAACATCAAAAAAGACGTTTGCTCAAAGGAAATGCCTTATTTGAA
1 TTTGTAAATATGTTAGAAAAAAACATCAAAAAAGACGTTTGCTCAAA-GAAATGCCTTATTTGAA
* *
3869176 TTTGTAAAGATTATAAAAGATCATCGATCAAATAGGACATTTGTAAAAAAGAAACGTCTTATTTG
65 TTTGTAAAGATTATAAAAGATCATCGATCAAATAAGACATTTGT-AAAAAGAAACGTCTTATTGG
3869241 AATGGGC
129 AATGGGC
** * * * **
3869248 TTTGTAAATATGTT-GAAAAAAGTATCAAATAAGATGTTTGTTCAAA-ACAATGCCTTATTTGTT
1 TTTGTAAATATGTTAGAAAAAAACATCAAAAAAGACGTTTGCTCAAAGA-AATGCCTTATTTGAA
* ** * * * *
3869311 TTTGTAAAGATTCTCGAAGATTATCTATCAAATAAGACGTTTGTAAAAGGAAACGTCTTATTGGA
65 TTTGTAAAGATTATAAAAGATCATCGATCAAATAAGACATTTGTAAAAAGAAACGTCTTATTGGA
3869376 ATG
130 ATG
3869379 CTTTAAATAA
Statistics
Matches: 114, Mismatches: 16, Indels: 5
0.84 0.12 0.04
Matches are distributed among these distances:
134 23 0.20
135 50 0.44
136 27 0.24
137 14 0.12
ACGTcount: A:0.40, C:0.10, G:0.17, T:0.33
Consensus pattern (135 bp):
TTTGTAAATATGTTAGAAAAAAACATCAAAAAAGACGTTTGCTCAAAGAAATGCCTTATTTGAAT
TTGTAAAGATTATAAAAGATCATCGATCAAATAAGACATTTGTAAAAAGAAACGTCTTATTGGAA
TGGGC
Found at i:3873093 original size:2 final size:2
Alignment explanation
Indices: 3873088--3873124 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
3873078 ATATATATAT
3873088 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
3873125 ACCGAATCTT
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.51, C:0.00, G:0.49, T:0.00
Consensus pattern (2 bp):
AG
Found at i:3875226 original size:2 final size:2
Alignment explanation
Indices: 3875219--3875259 Score: 59
Period size: 2 Copynumber: 21.5 Consensus size: 2
3875209 AAACCATGTA
*
3875219 AG AG AG AG AG AG AG AG AA AG AG AG AG AG AG AG A- AG A- AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
3875259 A
1 A
3875260 CGTTAATGTA
Statistics
Matches: 35, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
1 2 0.06
2 33 0.94
ACGTcount: A:0.56, C:0.00, G:0.44, T:0.00
Consensus pattern (2 bp):
AG
Found at i:3877856 original size:2 final size:2
Alignment explanation
Indices: 3877843--3877874 Score: 55
Period size: 2 Copynumber: 16.0 Consensus size: 2
3877833 GATCGACGCC
*
3877843 AT AT AT AC 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
3877875 TTTGTGACAT
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.03, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:3879608 original size:3 final size:3
Alignment explanation
Indices: 3879600--3879625 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
3879590 TAACAATGAA
3879600 TCT TCT TCT TCT TCT TCT TCT TCT TC
1 TCT TCT TCT TCT TCT TCT TCT TCT TC
3879626 ATATGAAAGT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.00, C:0.35, G:0.00, T:0.65
Consensus pattern (3 bp):
TCT
Found at i:3885056 original size:16 final size:16
Alignment explanation
Indices: 3885032--3885063 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
3885022 TTTGACTTGT
*
3885032 AAGAGAAGAATTTTAA
1 AAGAAAAGAATTTTAA
3885048 AAGAAAAGAATTTTAA
1 AAGAAAAGAATTTTAA
3885064 TAGGTAAGTT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.59, C:0.00, G:0.16, T:0.25
Consensus pattern (16 bp):
AAGAAAAGAATTTTAA
Found at i:3885091 original size:50 final size:52
Alignment explanation
Indices: 3884985--3885116 Score: 160
Period size: 50 Copynumber: 2.6 Consensus size: 52
3884975 TTTGTAAAAG
* * ** *
3884985 AAGAATTTTAAGATAAAAGAGATTTTTAATAGGTAAGTTTGACTTGTAAGAG
1 AAGAATTTTAAAAGAAAAGAGATTTTTAATAGGTAAGTTTGACTTACAAGAA
3885037 AAGAATTTTAAAAGAAAAGA-A-TTTTAATAGGTAAGTTTGACTTACAAGAA
1 AAGAATTTTAAAAGAAAAGAGATTTTTAATAGGTAAGTTTGACTTACAAGAA
* * * * *
3885087 AAGAATTCTAAGAGGAAAGGGATTCTTAAT
1 AAGAATTTTAAAAGAAAAGAGATTTTTAAT
3885117 GAGCAAGTTT
Statistics
Matches: 68, Mismatches: 10, Indels: 4
0.83 0.12 0.05
Matches are distributed among these distances:
50 42 0.62
51 2 0.03
52 24 0.35
ACGTcount: A:0.45, C:0.04, G:0.20, T:0.31
Consensus pattern (52 bp):
AAGAATTTTAAAAGAAAAGAGATTTTTAATAGGTAAGTTTGACTTACAAGAA
Found at i:3885761 original size:25 final size:25
Alignment explanation
Indices: 3885745--3885834 Score: 103
Period size: 25 Copynumber: 3.6 Consensus size: 25
3885735 GAGTTGAAGA
*
3885745 TTCAAGATGTGAAAAGAGCCGAAAG
1 TTCAAGATGTGAAAAGAGCTGAAAG
*
3885770 TTCGAGATGTGAAAA-AGCTGAAAG
1 TTCAAGATGTGAAAAGAGCTGAAAG
* *
3885794 TTCGAGATGTGAGAAGAGCT-AAAG
1 TTCAAGATGTGAAAAGAGCTGAAAG
* *
3885818 ATTTAAAATGTGAAAAG
1 -TTCAAGATGTGAAAAG
3885835 TGCATGATTT
Statistics
Matches: 56, Mismatches: 7, Indels: 4
0.84 0.10 0.06
Matches are distributed among these distances:
24 26 0.46
25 30 0.54
ACGTcount: A:0.43, C:0.08, G:0.28, T:0.21
Consensus pattern (25 bp):
TTCAAGATGTGAAAAGAGCTGAAAG
Found at i:3885797 original size:24 final size:25
Alignment explanation
Indices: 3885749--3885812 Score: 103
Period size: 24 Copynumber: 2.6 Consensus size: 25
3885739 TGAAGATTCA
3885749 AGATGTGAAAAGAGCCGAAAGTTCG
1 AGATGTGAAAAGAGCCGAAAGTTCG
*
3885774 AGATGTGAAAA-AGCTGAAAGTTCG
1 AGATGTGAAAAGAGCCGAAAGTTCG
*
3885798 AGATGTGAGAAGAGC
1 AGATGTGAAAAGAGC
3885813 TAAAGATTTA
Statistics
Matches: 36, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
24 22 0.61
25 14 0.39
ACGTcount: A:0.41, C:0.09, G:0.33, T:0.17
Consensus pattern (25 bp):
AGATGTGAAAAGAGCCGAAAGTTCG
Found at i:3885817 original size:24 final size:24
Alignment explanation
Indices: 3885729--3885817 Score: 90
Period size: 25 Copynumber: 3.6 Consensus size: 24
3885719 GTTCGAAACA
* * *
3885729 TGAGAAGAGTTGAAGATTCAAGATG
1 TGAGAAGAGCTAAAG-TTCGAGATG
* *
3885754 TGAAAAGAGCCGAAAGTTCGAGATG
1 TGAGAAGAG-CTAAAGTTCGAGATG
*
3885779 TGA-AAAAGCTGAAAGTTCGAGATG
1 TGAGAAGAGCT-AAAGTTCGAGATG
3885803 TGAGAAGAGCTAAAG
1 TGAGAAGAGCTAAAG
3885818 ATTTAAAATG
Statistics
Matches: 53, Mismatches: 8, Indels: 7
0.78 0.12 0.10
Matches are distributed among these distances:
23 1 0.02
24 24 0.45
25 25 0.47
26 3 0.06
ACGTcount: A:0.42, C:0.08, G:0.31, T:0.19
Consensus pattern (24 bp):
TGAGAAGAGCTAAAGTTCGAGATG
Found at i:3886214 original size:52 final size:52
Alignment explanation
Indices: 3886121--3886225 Score: 131
Period size: 52 Copynumber: 2.0 Consensus size: 52
3886111 TGGATAAGAA
* *
3886121 GACTTACAAAAAAAGAATTCTAAGATAAAGAAAATTCTTAATAGATAAGTTT
1 GACTTACAAAAAAAGAATTCTAAGAGAAAGAAAATTCTTAATAGACAAGTTT
* * * * *
3886173 GACTTACAAGAGAAGAATTCTAAGAGGAAAG-AGATTTTTAATTGACAAGTTT
1 GACTTACAAAAAAAGAATTCTAAGA-GAAAGAAAATTCTTAATAGACAAGTTT
3886225 G
1 G
3886226 TATGGTTATA
Statistics
Matches: 45, Mismatches: 7, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
52 41 0.91
53 4 0.09
ACGTcount: A:0.47, C:0.08, G:0.17, T:0.29
Consensus pattern (52 bp):
GACTTACAAAAAAAGAATTCTAAGAGAAAGAAAATTCTTAATAGACAAGTTT
Found at i:3886660 original size:13 final size:13
Alignment explanation
Indices: 3886630--3886666 Score: 51
Period size: 12 Copynumber: 2.9 Consensus size: 13
3886620 AATTATTATT
3886630 TTTTATATATTTAA
1 TTTTAT-TATTTAA
3886644 -TTTATTATTTAA
1 TTTTATTATTTAA
3886656 TTTTATT-TTTA
1 TTTTATTATTTA
3886667 TTGATATAAT
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
12 11 0.50
13 11 0.50
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (13 bp):
TTTTATTATTTAA
Found at i:3886666 original size:12 final size:12
Alignment explanation
Indices: 3886617--3886658 Score: 52
Period size: 12 Copynumber: 3.6 Consensus size: 12
3886607 TTAAATCACG
*
3886617 TTAAATTATTAT
1 TTAATTTATTAT
3886629 TT--TTTATATAT
1 TTAATTTAT-TAT
3886640 TTAATTTATTAT
1 TTAATTTATTAT
3886652 TTAATTT
1 TTAATTT
3886659 TATTTTTATT
Statistics
Matches: 26, Mismatches: 1, Indels: 6
0.79 0.03 0.18
Matches are distributed among these distances:
10 4 0.15
11 5 0.19
12 12 0.46
13 5 0.19
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (12 bp):
TTAATTTATTAT
Found at i:3890224 original size:11 final size:11
Alignment explanation
Indices: 3890208--3890239 Score: 64
Period size: 11 Copynumber: 2.9 Consensus size: 11
3890198 ATTTTAAATC
3890208 ATATTATTTTT
1 ATATTATTTTT
3890219 ATATTATTTTT
1 ATATTATTTTT
3890230 ATATTATTTT
1 ATATTATTTT
3890240 CTTATCATGT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 21 1.00
ACGTcount: A:0.28, C:0.00, G:0.00, T:0.72
Consensus pattern (11 bp):
ATATTATTTTT
Found at i:3890252 original size:22 final size:22
Alignment explanation
Indices: 3890208--3890252 Score: 56
Period size: 22 Copynumber: 2.0 Consensus size: 22
3890198 ATTTTAAATC
* *
3890208 ATATTATTTTTATATTATTTTT
1 ATATTATTTTTATATCATGTTT
3890230 ATATTATTTTCT-TATCATGTTT
1 ATATTATTTT-TATATCATGTTT
3890252 A
1 A
3890253 AAATTATCAG
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
22 19 0.95
23 1 0.05
ACGTcount: A:0.27, C:0.04, G:0.02, T:0.67
Consensus pattern (22 bp):
ATATTATTTTTATATCATGTTT
Found at i:3895835 original size:28 final size:27
Alignment explanation
Indices: 3895798--3895858 Score: 72
Period size: 27 Copynumber: 2.2 Consensus size: 27
3895788 GGAACTCTAT
*
3895798 TTTTCTTTTTTTCTTCTT-T-TATTTTTA
1 TTTT-TTTTTTTCTT-TTATGTATTCTTA
3895825 TTTTTTGTTTTTCTTTTATGTATTCTTA
1 TTTTTT-TTTTTCTTTTATGTATTCTTA
3895853 TTTTTT
1 TTTTTT
3895859 ATGGTTTTTA
Statistics
Matches: 30, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
26 4 0.13
27 13 0.43
28 13 0.43
ACGTcount: A:0.08, C:0.08, G:0.03, T:0.80
Consensus pattern (27 bp):
TTTTTTTTTTTCTTTTATGTATTCTTA
Found at i:3895838 original size:24 final size:22
Alignment explanation
Indices: 3895795--3895857 Score: 63
Period size: 24 Copynumber: 2.7 Consensus size: 22
3895785 CAAGGAACTC
3895795 TATTTTTCTTTTTTTCTTCTTT
1 TATTTTTCTTTTTTTCTTCTTT
* *
3895817 TATTTTTATTTTTTGTTTTTCTTT
1 TATTTTT-CTTTTT-TTCTTCTTT
*
3895841 TATGTATTCTTATTTTT
1 TAT-TTTTCTT-TTTTT
3895858 TATGGTTTTT
Statistics
Matches: 33, Mismatches: 4, Indels: 6
0.77 0.09 0.14
Matches are distributed among these distances:
22 7 0.21
23 5 0.15
24 15 0.45
25 6 0.18
ACGTcount: A:0.10, C:0.08, G:0.03, T:0.79
Consensus pattern (22 bp):
TATTTTTCTTTTTTTCTTCTTT
Found at i:3912903 original size:29 final size:29
Alignment explanation
Indices: 3912832--3912904 Score: 96
Period size: 29 Copynumber: 2.5 Consensus size: 29
3912822 TAAAAATATG
*
3912832 TATTTAAAAATTTAATTGATGAAAATAAA
1 TATTTAAATATTTAATTGATGAAAATAAA
*
3912861 TATTTAAATTTTTAATTGAAT-AAGAATAAA
1 TATTTAAATATTTAATTG-ATGAA-AATAAA
3912891 TATTT-AATATTTAA
1 TATTTAAATATTTAA
3912905 ATTTATTATA
Statistics
Matches: 39, Mismatches: 3, Indels: 4
0.85 0.07 0.09
Matches are distributed among these distances:
29 26 0.67
30 13 0.33
ACGTcount: A:0.51, C:0.00, G:0.05, T:0.44
Consensus pattern (29 bp):
TATTTAAATATTTAATTGATGAAAATAAA
Found at i:3918288 original size:27 final size:27
Alignment explanation
Indices: 3918220--3918302 Score: 89
Period size: 27 Copynumber: 3.0 Consensus size: 27
3918210 TAAAACAAGT
* *
3918220 TTTATTATT-T-TAATATAATAAATAAGT
1 TTTATTATTATATAATA-AACAAATAA-A
*
3918247 TTATATTATTATATAATAAAGAAATAAA
1 TT-TATTATTATATAATAAACAAATAAA
*
3918275 TTTATTATTATATAATAAACTAATAAA
1 TTTATTATTATATAATAAACAAATAAA
3918302 T
1 T
3918303 AAATAAATTT
Statistics
Matches: 49, Mismatches: 4, Indels: 6
0.83 0.07 0.10
Matches are distributed among these distances:
27 26 0.53
28 9 0.18
29 9 0.18
30 5 0.10
ACGTcount: A:0.51, C:0.01, G:0.02, T:0.46
Consensus pattern (27 bp):
TTTATTATTATATAATAAACAAATAAA
Found at i:3918562 original size:18 final size:20
Alignment explanation
Indices: 3918539--3918591 Score: 56
Period size: 20 Copynumber: 2.7 Consensus size: 20
3918529 ACAATTATAG
*
3918539 TAATTAATTTTAT-T-TTCA
1 TAATTAATTTTATCTCATCA
*
3918557 TAATTATTTTTTATCTCATCA
1 TAATTA-ATTTTATCTCATCA
*
3918578 AAATTAATTTTATC
1 TAATTAATTTTATC
3918592 GTCTATCAAA
Statistics
Matches: 28, Mismatches: 4, Indels: 4
0.78 0.11 0.11
Matches are distributed among these distances:
18 6 0.21
19 6 0.21
20 8 0.29
21 8 0.29
ACGTcount: A:0.34, C:0.09, G:0.00, T:0.57
Consensus pattern (20 bp):
TAATTAATTTTATCTCATCA
Found at i:3918588 original size:21 final size:23
Alignment explanation
Indices: 3918558--3918609 Score: 65
Period size: 22 Copynumber: 2.4 Consensus size: 23
3918548 TTATTTTCAT
*
3918558 AATTATTTTTTATC-TC-ATCAA
1 AATTAATTTTTATCGTCTATCAA
3918579 AATTAA-TTTTATCGTCTATCAA
1 AATTAATTTTTATCGTCTATCAA
*
3918601 AATAAATTT
1 AATTAATTT
3918610 AATTTTAAAA
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
20 7 0.27
21 7 0.27
22 10 0.38
23 2 0.08
ACGTcount: A:0.38, C:0.12, G:0.02, T:0.48
Consensus pattern (23 bp):
AATTAATTTTTATCGTCTATCAA
Found at i:3918590 original size:20 final size:22
Alignment explanation
Indices: 3918565--3918609 Score: 67
Period size: 22 Copynumber: 2.1 Consensus size: 22
3918555 CATAATTATT
*
3918565 TTTTATC-TC-ATCAAAATTAA
1 TTTTATCGTCTATCAAAATAAA
3918585 TTTTATCGTCTATCAAAATAAA
1 TTTTATCGTCTATCAAAATAAA
3918607 TTT
1 TTT
3918610 AATTTTAAAA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
20 7 0.32
21 2 0.09
22 13 0.59
ACGTcount: A:0.38, C:0.13, G:0.02, T:0.47
Consensus pattern (22 bp):
TTTTATCGTCTATCAAAATAAA
Found at i:3924527 original size:23 final size:23
Alignment explanation
Indices: 3924501--3924545 Score: 65
Period size: 23 Copynumber: 2.0 Consensus size: 23
3924491 GATGTAAATA
*
3924501 AATATATTTGAATG-AATTTAAAG
1 AATATA-TTAAATGAAATTTAAAG
3924524 AATATATTAAATGAAATTTAAA
1 AATATATTAAATGAAATTTAAA
3924546 AATTTTTCAT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
22 6 0.30
23 14 0.70
ACGTcount: A:0.53, C:0.00, G:0.09, T:0.38
Consensus pattern (23 bp):
AATATATTAAATGAAATTTAAAG
Found at i:3925465 original size:22 final size:21
Alignment explanation
Indices: 3925435--3925487 Score: 54
Period size: 21 Copynumber: 2.5 Consensus size: 21
3925425 AAACTTTGCT
*
3925435 ATTTTTATTTAAAATTA-TTAA
1 ATTTATATTT-AAATTACTTAA
*
3925456 ATATTATATTTTAATTACTTAA
1 AT-TTATATTTAAATTACTTAA
*
3925478 ATTTAAATTT
1 ATTTATATTT
3925488 TTTTGTTAGA
Statistics
Matches: 27, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
21 14 0.52
22 13 0.48
ACGTcount: A:0.42, C:0.02, G:0.00, T:0.57
Consensus pattern (21 bp):
ATTTATATTTAAATTACTTAA
Found at i:3925489 original size:22 final size:21
Alignment explanation
Indices: 3925447--3925488 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
3925437 TTTTATTTAA
*
3925447 AATTATTAAATATTATATTTT
1 AATTATTAAATATTAAATTTT
3925468 AATTACTTAAAT-TTAAATTTT
1 AATTA-TTAAATATTAAATTTT
3925489 TTTGTTAGAG
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
21 13 0.68
22 6 0.32
ACGTcount: A:0.43, C:0.02, G:0.00, T:0.55
Consensus pattern (21 bp):
AATTATTAAATATTAAATTTT
Found at i:3926353 original size:20 final size:19
Alignment explanation
Indices: 3926314--3926353 Score: 62
Period size: 19 Copynumber: 2.1 Consensus size: 19
3926304 AAAAAGATGA
*
3926314 TATTAAAATTTTTATTTTT
1 TATTAAAATTTTTATCTTT
3926333 TATTAAAATTTTTGATCTTT
1 TATTAAAATTTTT-ATCTTT
3926353 T
1 T
3926354 CGATCTATTA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
19 13 0.68
20 6 0.32
ACGTcount: A:0.30, C:0.03, G:0.03, T:0.65
Consensus pattern (19 bp):
TATTAAAATTTTTATCTTT
Found at i:3926507 original size:27 final size:26
Alignment explanation
Indices: 3926453--3926507 Score: 67
Period size: 27 Copynumber: 2.1 Consensus size: 26
3926443 TTGATAAAAA
* *
3926453 ATTATAATAAAATAAGATAAGATGAT
1 ATTATAATAAAATAAAATAAGATAAT
3926479 ATTATAAATAAAATAAAATTAA-ATAAT
1 ATTAT-AATAAAATAAAA-TAAGATAAT
3926506 AT
1 AT
3926508 CATCATATTT
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
26 5 0.20
27 17 0.68
28 3 0.12
ACGTcount: A:0.62, C:0.00, G:0.05, T:0.33
Consensus pattern (26 bp):
ATTATAATAAAATAAAATAAGATAAT
Found at i:3942596 original size:63 final size:68
Alignment explanation
Indices: 3942491--3942681 Score: 239
Period size: 63 Copynumber: 2.8 Consensus size: 68
3942481 TATGCATGAA
* * *
3942491 AGACGTCAGAATTAGGCTATGGTATTGACAAAGCCGATCCTCAGGCAGTTTAAGGTTAAAAGAA-
1 AGAC-TCAGAATTAGTCTATGGTCTTGACAAAGTCGATCCTCAGGCAGTTTAAGGTTAAAAGAAT
*
3942555 GA-T
65 AAGT
* * *
3942558 -G-C-CAGAATTAGTCTATAGTCTTGACAAGGTCGATCCTCAGGCAGTTTAAGTTTAAAAGAATA
1 AGACTCAGAATTAGTCTATGGTCTTGACAAAGTCGATCCTCAGGCAGTTTAAGGTTAAAAGAATA
3942620 AGT
66 AGT
* *
3942623 CAGAACTCAGAATTAGTCTGTGGTCTTGACAAAGTCGATCCTCAGGCAATTTAAGGTTA
1 -AG-ACTCAGAATTAGTCTATGGTCTTGACAAAGTCGATCCTCAGGCAGTTTAAGGTTA
3942682 TGGTTTATAG
Statistics
Matches: 105, Mismatches: 12, Indels: 11
0.82 0.09 0.09
Matches are distributed among these distances:
63 52 0.50
64 1 0.01
65 2 0.02
66 1 0.01
67 1 0.01
69 1 0.01
70 47 0.45
ACGTcount: A:0.34, C:0.16, G:0.23, T:0.27
Consensus pattern (68 bp):
AGACTCAGAATTAGTCTATGGTCTTGACAAAGTCGATCCTCAGGCAGTTTAAGGTTAAAAGAATA
AGT
Found at i:3942923 original size:3 final size:3
Alignment explanation
Indices: 3942917--3942962 Score: 92
Period size: 3 Copynumber: 15.3 Consensus size: 3
3942907 CAACATGATG
3942917 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A
3942963 CAAGATCAAC
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 43 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:3953833 original size:22 final size:21
Alignment explanation
Indices: 3953807--3953856 Score: 64
Period size: 22 Copynumber: 2.3 Consensus size: 21
3953797 TAAAATTTTA
*
3953807 AAATTTTATTTGAATTTCAATC
1 AAATTTTATTT-AATTTAAATC
*
3953829 AAATTTTTATTTAATTTAAATT
1 AAA-TTTTATTTAATTTAAATC
3953851 AAATTT
1 AAATTT
3953857 ATCAGTTTGA
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
21 3 0.12
22 14 0.56
23 8 0.32
ACGTcount: A:0.40, C:0.04, G:0.02, T:0.54
Consensus pattern (21 bp):
AAATTTTATTTAATTTAAATC
Found at i:3954079 original size:35 final size:32
Alignment explanation
Indices: 3954015--3954084 Score: 86
Period size: 35 Copynumber: 2.1 Consensus size: 32
3954005 ATTTAATTCG
* *
3954015 ATTTAATTTTTTATATTTTTAATTAAAATTTA
1 ATTTAATTTTATATATTTTAAATTAAAATTTA
*
3954047 ATTTAATTTTAATATATATTTAATATTTAAATTTA
1 ATTTAATTTT-ATATAT-TTTAA-ATTAAAATTTA
3954082 ATT
1 ATT
3954085 CGAATAAAAA
Statistics
Matches: 32, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
32 10 0.31
33 5 0.16
34 4 0.12
35 13 0.41
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (32 bp):
ATTTAATTTTATATATTTTAAATTAAAATTTA
Found at i:3954555 original size:35 final size:35
Alignment explanation
Indices: 3954512--3954581 Score: 140
Period size: 35 Copynumber: 2.0 Consensus size: 35
3954502 TAAATAACTT
3954512 TTATACATATTCTTTAAAACTTAAGAACCTTCAAC
1 TTATACATATTCTTTAAAACTTAAGAACCTTCAAC
3954547 TTATACATATTCTTTAAAACTTAAGAACCTTCAAC
1 TTATACATATTCTTTAAAACTTAAGAACCTTCAAC
3954582 ATTGGTATTC
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
35 35 1.00
ACGTcount: A:0.40, C:0.20, G:0.03, T:0.37
Consensus pattern (35 bp):
TTATACATATTCTTTAAAACTTAAGAACCTTCAAC
Found at i:3954569 original size:20 final size:20
Alignment explanation
Indices: 3954512--3954569 Score: 54
Period size: 20 Copynumber: 3.1 Consensus size: 20
3954502 TAAATAACTT
3954512 TTATACATATTCTTTAAAAC
1 TTATACATATTCTTTAAAAC
* * *
3954532 TTA-AGA-A--CCTT-CAAC
1 TTATACATATTCTTTAAAAC
3954547 TTATACATATTCTTTAAAAC
1 TTATACATATTCTTTAAAAC
3954567 TTA
1 TTA
3954570 AGAACCTTCA
Statistics
Matches: 27, Mismatches: 6, Indels: 10
0.63 0.14 0.23
Matches are distributed among these distances:
15 6 0.22
16 5 0.19
17 1 0.04
18 1 0.04
19 5 0.19
20 9 0.33
ACGTcount: A:0.40, C:0.17, G:0.02, T:0.41
Consensus pattern (20 bp):
TTATACATATTCTTTAAAAC
Found at i:3955867 original size:16 final size:18
Alignment explanation
Indices: 3955831--3955866 Score: 65
Period size: 17 Copynumber: 2.1 Consensus size: 18
3955821 TGATTTATAA
3955831 TTATAATTTAAATAAATT
1 TTATAATTTAAATAAATT
3955849 TTAT-ATTTAAATAAATT
1 TTATAATTTAAATAAATT
3955866 T
1 T
3955867 AAGTTTATTT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
17 14 0.78
18 4 0.22
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (18 bp):
TTATAATTTAAATAAATT
Found at i:3956008 original size:2 final size:2
Alignment explanation
Indices: 3956001--3956026 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
3955991 ATATTCTCAA
3956001 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
3956027 CATGCATACC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:3958814 original size:16 final size:18
Alignment explanation
Indices: 3958778--3958813 Score: 65
Period size: 17 Copynumber: 2.1 Consensus size: 18
3958768 TGATTTATAA
3958778 TTATAATTTAAATAAATT
1 TTATAATTTAAATAAATT
3958796 TTAT-ATTTAAATAAATT
1 TTATAATTTAAATAAATT
3958813 T
1 T
3958814 AAGTTTATTT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
17 14 0.78
18 4 0.22
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (18 bp):
TTATAATTTAAATAAATT
Found at i:3960469 original size:16 final size:17
Alignment explanation
Indices: 3960431--3960476 Score: 53
Period size: 16 Copynumber: 2.8 Consensus size: 17
3960421 AATATTATAT
3960431 TTAAT-ATTATTAAAAA
1 TTAATAATTATTAAAAA
*
3960447 TTAAATAATTA-TACAAA
1 TT-AATAATTATTAAAAA
3960464 TTAATAATT-TTAA
1 TTAATAATTATTAA
3960477 TTAGATCCAT
Statistics
Matches: 25, Mismatches: 2, Indels: 6
0.76 0.06 0.18
Matches are distributed among these distances:
16 11 0.44
17 10 0.40
18 4 0.16
ACGTcount: A:0.54, C:0.02, G:0.00, T:0.43
Consensus pattern (17 bp):
TTAATAATTATTAAAAA
Found at i:3961007 original size:10 final size:10
Alignment explanation
Indices: 3960992--3961016 Score: 50
Period size: 10 Copynumber: 2.5 Consensus size: 10
3960982 AAAAGATCTC
3960992 AAACAAAATA
1 AAACAAAATA
3961002 AAACAAAATA
1 AAACAAAATA
3961012 AAACA
1 AAACA
3961017 CATCAAAATA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 15 1.00
ACGTcount: A:0.80, C:0.12, G:0.00, T:0.08
Consensus pattern (10 bp):
AAACAAAATA
Found at i:3961208 original size:49 final size:49
Alignment explanation
Indices: 3961136--3961238 Score: 143
Period size: 49 Copynumber: 2.1 Consensus size: 49
3961126 CCCTCAAGCA
* * *
3961136 TAACTATTTGCTTAGATAAAATAAGAACTGAATATGCAAGGTTTCATCC
1 TAACTATTTACTTAGATAAAATAAGAACTGAATATGCAAGATTGCATCC
* * *
3961185 TAACTATTTACTTAGGTAAAATAAGTATTGAATATGCAAGATTGCATCC
1 TAACTATTTACTTAGATAAAATAAGAACTGAATATGCAAGATTGCATCC
*
3961234 CAACT
1 TAACT
3961239 TGACAACATG
Statistics
Matches: 47, Mismatches: 7, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
49 47 1.00
ACGTcount: A:0.39, C:0.15, G:0.14, T:0.33
Consensus pattern (49 bp):
TAACTATTTACTTAGATAAAATAAGAACTGAATATGCAAGATTGCATCC
Found at i:3972711 original size:23 final size:23
Alignment explanation
Indices: 3972673--3972717 Score: 72
Period size: 23 Copynumber: 2.0 Consensus size: 23
3972663 AGTTGCTTGG
*
3972673 ACACTGGAATGGCTCGCCTGTTT
1 ACACTGGAATGACTCGCCTGTTT
*
3972696 ACACTGGGATGACTCGCCTGTT
1 ACACTGGAATGACTCGCCTGTT
3972718 GCAACAGTGG
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
23 20 1.00
ACGTcount: A:0.18, C:0.27, G:0.27, T:0.29
Consensus pattern (23 bp):
ACACTGGAATGACTCGCCTGTTT
Found at i:3973452 original size:18 final size:19
Alignment explanation
Indices: 3973414--3973452 Score: 53
Period size: 20 Copynumber: 2.1 Consensus size: 19
3973404 GTCTATGTGA
3973414 TCTCTAATGAAAGATGGTTT
1 TCTCTAATGAAAGA-GGTTT
*
3973434 TCTCTAATGTAAG-GGTTT
1 TCTCTAATGAAAGAGGTTT
3973452 T
1 T
3973453 ACAAAATTGT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
18 6 0.33
20 12 0.67
ACGTcount: A:0.26, C:0.10, G:0.21, T:0.44
Consensus pattern (19 bp):
TCTCTAATGAAAGAGGTTT
Found at i:3989990 original size:6 final size:6
Alignment explanation
Indices: 3989979--3990013 Score: 70
Period size: 6 Copynumber: 5.8 Consensus size: 6
3989969 TTTAATTTAG
3989979 TCCAAC TCCAAC TCCAAC TCCAAC TCCAAC TCCAA
1 TCCAAC TCCAAC TCCAAC TCCAAC TCCAAC TCCAA
3990014 AGCCAATTAT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 29 1.00
ACGTcount: A:0.34, C:0.49, G:0.00, T:0.17
Consensus pattern (6 bp):
TCCAAC
Found at i:3990019 original size:18 final size:18
Alignment explanation
Indices: 3989980--3990019 Score: 62
Period size: 18 Copynumber: 2.2 Consensus size: 18
3989970 TTAATTTAGT
**
3989980 CCAACTCCAACTCCAACT
1 CCAACTCCAACTCCAAAG
3989998 CCAACTCCAACTCCAAAG
1 CCAACTCCAACTCCAAAG
3990016 CCAA
1 CCAA
3990020 TTATTTATTT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.38, C:0.47, G:0.03, T:0.12
Consensus pattern (18 bp):
CCAACTCCAACTCCAAAG
Found at i:3990868 original size:4 final size:4
Alignment explanation
Indices: 3990859--3990884 Score: 52
Period size: 4 Copynumber: 6.5 Consensus size: 4
3990849 CAACATTAAG
3990859 ATTA ATTA ATTA ATTA ATTA ATTA AT
1 ATTA ATTA ATTA ATTA ATTA ATTA AT
3990885 AAAACCTACT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 22 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (4 bp):
ATTA
Found at i:3995303 original size:30 final size:30
Alignment explanation
Indices: 3995267--3995327 Score: 95
Period size: 30 Copynumber: 2.0 Consensus size: 30
3995257 ATTCATGCGA
*
3995267 ATAGATATAAGTTACATTTAATAATTTTAG
1 ATAGATATAAATTACATTTAATAATTTTAG
**
3995297 ATAGATATAAATTGTATTTAATAATTTTAG
1 ATAGATATAAATTACATTTAATAATTTTAG
3995327 A
1 A
3995328 CAAATTAAAT
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
30 28 1.00
ACGTcount: A:0.44, C:0.02, G:0.10, T:0.44
Consensus pattern (30 bp):
ATAGATATAAATTACATTTAATAATTTTAG
Found at i:3996125 original size:11 final size:12
Alignment explanation
Indices: 3996111--3996157 Score: 60
Period size: 12 Copynumber: 3.9 Consensus size: 12
3996101 TAAAAATAAA
3996111 AAAATAAAT-TT
1 AAAATAAATATT
**
3996122 AAAATACTTATT
1 AAAATAAATATT
3996134 AAATATAAATATT
1 AAA-ATAAATATT
3996147 AAAATAAATAT
1 AAAATAAATAT
3996158 AATATAAACA
Statistics
Matches: 30, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
11 7 0.23
12 13 0.43
13 10 0.33
ACGTcount: A:0.62, C:0.02, G:0.00, T:0.36
Consensus pattern (12 bp):
AAAATAAATATT
Found at i:3996144 original size:36 final size:35
Alignment explanation
Indices: 3996088--3996189 Score: 93
Period size: 35 Copynumber: 2.8 Consensus size: 35
3996078 TGTACTCATT
3996088 AAATACTTAAAAATAAAAATAAAAAAATAAATTTA
1 AAATACTTAAAAATAAAAATAAAAAAATAAATTTA
* *
3996123 AAATACTTATTAAATATAAATATTAAAATAAATATAATATA
1 AAATACTTA--AAA-ATAAA-AATAAAA-AAATA-AATTTA
3996164 AACAT--TTAAAAATAATAAA-AAAAAAA
1 AA-ATACTTAAAAATAA-AAATAAAAAAA
3996190 CTCTAAACTT
Statistics
Matches: 56, Mismatches: 3, Indels: 16
0.75 0.04 0.21
Matches are distributed among these distances:
35 12 0.21
36 4 0.07
37 8 0.14
38 9 0.16
39 6 0.11
40 8 0.14
41 7 0.12
42 2 0.04
ACGTcount: A:0.69, C:0.03, G:0.00, T:0.28
Consensus pattern (35 bp):
AAATACTTAAAAATAAAAATAAAAAAATAAATTTA
Found at i:3999707 original size:26 final size:26
Alignment explanation
Indices: 3999678--3999731 Score: 99
Period size: 26 Copynumber: 2.1 Consensus size: 26
3999668 GTTCACTCTC
3999678 AAACATTCAAACACACACCCTAACAG
1 AAACATTCAAACACACACCCTAACAG
*
3999704 AAACATTCAAACACACACCCTAATAG
1 AAACATTCAAACACACACCCTAACAG
3999730 AA
1 AA
3999732 CGTAAATCTC
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
26 27 1.00
ACGTcount: A:0.52, C:0.31, G:0.04, T:0.13
Consensus pattern (26 bp):
AAACATTCAAACACACACCCTAACAG
Done.