Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr04 ID=Chr04-JGI_221_v2.0
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: 62178258
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 912357 characters in sequence are not A, C, G, or T
File 154 of 198
Found at i:48768575 original size:32 final size:32
Alignment explanation
Indices: 48768528--48768588 Score: 104
Period size: 32 Copynumber: 1.9 Consensus size: 32
48768518 TAAATACTCT
48768528 TTATAAATTTAAAAATAATTATAATTTAATAG
1 TTATAAATTTAAAAATAATTATAATTTAATAG
* *
48768560 TTATATATTTCAAAATAATTATAATTTAA
1 TTATAAATTTAAAAATAATTATAATTTAA
48768589 ACTACAATTA
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
32 27 1.00
ACGTcount: A:0.51, C:0.02, G:0.02, T:0.46
Consensus pattern (32 bp):
TTATAAATTTAAAAATAATTATAATTTAATAG
Found at i:48771020 original size:40 final size:40
Alignment explanation
Indices: 48770969--48771047 Score: 158
Period size: 40 Copynumber: 2.0 Consensus size: 40
48770959 AATTAGTTTA
48770969 TTATTTTCCTTCAATTTCTTTGTTTTTCATTTCTTATTTC
1 TTATTTTCCTTCAATTTCTTTGTTTTTCATTTCTTATTTC
48771009 TTATTTTCCTTCAATTTCTTTGTTTTTCATTTCTTATTT
1 TTATTTTCCTTCAATTTCTTTGTTTTTCATTTCTTATTT
48771048 GCTATATTAC
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
40 39 1.00
ACGTcount: A:0.13, C:0.16, G:0.03, T:0.68
Consensus pattern (40 bp):
TTATTTTCCTTCAATTTCTTTGTTTTTCATTTCTTATTTC
Found at i:48775271 original size:20 final size:18
Alignment explanation
Indices: 48775248--48775285 Score: 58
Period size: 18 Copynumber: 2.0 Consensus size: 18
48775238 GTTTTTTTAC
48775248 AAAAATATTACAAAAAAATA
1 AAAAATA-T-CAAAAAAATA
48775268 AAAAATATCAAAAAAATA
1 AAAAATATCAAAAAAATA
48775286 TTAATATTTT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
18 10 0.56
19 1 0.06
20 7 0.39
ACGTcount: A:0.76, C:0.05, G:0.00, T:0.18
Consensus pattern (18 bp):
AAAAATATCAAAAAAATA
Found at i:48776383 original size:18 final size:17
Alignment explanation
Indices: 48776360--48776421 Score: 67
Period size: 18 Copynumber: 3.7 Consensus size: 17
48776350 TAAATACTCT
48776360 TTATAAATTTAAAAATAA
1 TTAT-AATTTAAAAATAA
*
48776378 TTATAATTT---AATAG
1 TTATAATTTAAAAATAA
*
48776392 TTATATATTTCAAAATAA
1 TTATA-ATTTAAAAATAA
48776410 TTATAATTTAAA
1 TTATAATTTAAA
48776422 CTACAATTAT
Statistics
Matches: 37, Mismatches: 3, Indels: 9
0.76 0.06 0.18
Matches are distributed among these distances:
14 9 0.24
15 4 0.11
17 11 0.30
18 13 0.35
ACGTcount: A:0.52, C:0.02, G:0.02, T:0.45
Consensus pattern (17 bp):
TTATAATTTAAAAATAA
Found at i:48776395 original size:14 final size:14
Alignment explanation
Indices: 48776373--48776420 Score: 51
Period size: 14 Copynumber: 3.1 Consensus size: 14
48776363 TAAATTTAAA
48776373 AATAATTATAATTT
1 AATAATTATAATTT
*
48776387 AATAGTTATATATTT
1 AATAATTATA-ATTT
48776402 CAAAATAATTATAATTT
1 ---AATAATTATAATTT
48776419 AA
1 AA
48776421 ACTACAATTA
Statistics
Matches: 28, Mismatches: 2, Indels: 8
0.74 0.05 0.21
Matches are distributed among these distances:
14 11 0.39
15 4 0.14
17 4 0.14
18 9 0.32
ACGTcount: A:0.50, C:0.02, G:0.02, T:0.46
Consensus pattern (14 bp):
AATAATTATAATTT
Found at i:48776407 original size:32 final size:32
Alignment explanation
Indices: 48776360--48776420 Score: 104
Period size: 32 Copynumber: 1.9 Consensus size: 32
48776350 TAAATACTCT
48776360 TTATAAATTTAAAAATAATTATAATTTAATAG
1 TTATAAATTTAAAAATAATTATAATTTAATAG
* *
48776392 TTATATATTTCAAAATAATTATAATTTAA
1 TTATAAATTTAAAAATAATTATAATTTAA
48776421 ACTACAATTA
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
32 27 1.00
ACGTcount: A:0.51, C:0.02, G:0.02, T:0.46
Consensus pattern (32 bp):
TTATAAATTTAAAAATAATTATAATTTAATAG
Found at i:48779415 original size:5 final size:5
Alignment explanation
Indices: 48779405--48779477 Score: 64
Period size: 5 Copynumber: 14.6 Consensus size: 5
48779395 AAAAAAATAT
* *
48779405 TATTA TATTA TAGTAA TGATTA TGTT- T-TTA TATTA TATTA TTATTA
1 TATTA TATTA TA-TTA T-ATTA TATTA TATTA TATTA TATTA -TATTA
48779451 -A-TA TATTA TATTA TATTA TATATA TAT
1 TATTA TATTA TATTA TATTA TAT-TA TAT
48779478 ACATAAAACA
Statistics
Matches: 57, Mismatches: 3, Indels: 15
0.76 0.04 0.20
Matches are distributed among these distances:
3 4 0.07
4 4 0.07
5 32 0.56
6 16 0.28
7 1 0.02
ACGTcount: A:0.38, C:0.00, G:0.04, T:0.58
Consensus pattern (5 bp):
TATTA
Found at i:48779457 original size:19 final size:19
Alignment explanation
Indices: 48779433--48779475 Score: 70
Period size: 19 Copynumber: 2.3 Consensus size: 19
48779423 ATTATGTTTT
48779433 TATATTATATTATTATTA-A
1 TATATTATATTA-TATTATA
48779452 TATATTATATTATATTATA
1 TATATTATATTATATTATA
48779471 TATAT
1 TATAT
48779476 ATACATAAAA
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
18 5 0.22
19 18 0.78
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (19 bp):
TATATTATATTATATTATA
Found at i:48779507 original size:15 final size:15
Alignment explanation
Indices: 48779487--48779528 Score: 57
Period size: 15 Copynumber: 2.7 Consensus size: 15
48779477 TACATAAAAC
*
48779487 AAAAGAAAGAATAGA
1 AAAAGAAAGAAAAGA
48779502 AAAAGAAAGAAAAGA
1 AAAAGAAAGAAAAGA
*
48779517 AACAGAATAGAA
1 AAAAGAA-AGAA
48779529 GAGACGAATC
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
15 20 0.83
16 4 0.17
ACGTcount: A:0.74, C:0.02, G:0.19, T:0.05
Consensus pattern (15 bp):
AAAAGAAAGAAAAGA
Found at i:48779942 original size:17 final size:17
Alignment explanation
Indices: 48779920--48779953 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
48779910 ATGTGGCATG
48779920 TACCTAAGTAATGTATA
1 TACCTAAGTAATGTATA
*
48779937 TACCTAAGTGATGTATA
1 TACCTAAGTAATGTATA
48779954 GGGATAAGTC
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.38, C:0.12, G:0.15, T:0.35
Consensus pattern (17 bp):
TACCTAAGTAATGTATA
Found at i:48782908 original size:40 final size:40
Alignment explanation
Indices: 48782857--48782935 Score: 158
Period size: 40 Copynumber: 2.0 Consensus size: 40
48782847 AATTAGTTTA
48782857 TTATTTTCCTTCAATTTCTTTGTTTTTCATTTCTTATTTC
1 TTATTTTCCTTCAATTTCTTTGTTTTTCATTTCTTATTTC
48782897 TTATTTTCCTTCAATTTCTTTGTTTTTCATTTCTTATTT
1 TTATTTTCCTTCAATTTCTTTGTTTTTCATTTCTTATTT
48782936 GCTATATTAC
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
40 39 1.00
ACGTcount: A:0.13, C:0.16, G:0.03, T:0.68
Consensus pattern (40 bp):
TTATTTTCCTTCAATTTCTTTGTTTTTCATTTCTTATTTC
Found at i:48788294 original size:88 final size:90
Alignment explanation
Indices: 48788145--48788348 Score: 256
Period size: 88 Copynumber: 2.3 Consensus size: 90
48788135 AATTTTTTTA
* *
48788145 AAAAAAAGTAATTAA--CCCTTCCATTTTTTTTTTGCACTCAATAGAGCACTTGAACTTTCAAAA
1 AAAAAAAGCAATTAAGCCCCTT-C-TTTTTATTTTGCACTCAATAGAGCACTTGAACTTTCAAAA
* * **
48788208 TGCATCAAAAAGCCCTTAAGCTTCTTC
64 TGCATAAAAAAACCCTTAAAATTCTTC
* *
48788235 AAAAAAAGCAATTAAGCCCCTTCTTTTTATTTT-CACTCAAT-GGGTACTTGAACTTTCAAAATG
1 AAAAAAAGCAATTAAGCCCCTTCTTTTTATTTTGCACTCAATAGAGCACTTGAACTTTCAAAATG
* *
48788298 CATAAAAAAACCTTTAAAATTTTTC
66 CATAAAAAAACCCTTAAAATTCTTC
*
48788323 -AAAAAAGCAATTAAGCCCCTGCTTTT
1 AAAAAAAGCAATTAAGCCCCTTCTTTT
48788349 ATTAGAAAAT
Statistics
Matches: 101, Mismatches: 11, Indels: 7
0.85 0.09 0.06
Matches are distributed among these distances:
87 25 0.25
88 39 0.39
89 8 0.08
90 23 0.23
91 1 0.01
92 5 0.05
ACGTcount: A:0.37, C:0.21, G:0.09, T:0.33
Consensus pattern (90 bp):
AAAAAAAGCAATTAAGCCCCTTCTTTTTATTTTGCACTCAATAGAGCACTTGAACTTTCAAAATG
CATAAAAAAACCCTTAAAATTCTTC
Found at i:48788385 original size:28 final size:28
Alignment explanation
Indices: 48788354--48788414 Score: 72
Period size: 28 Copynumber: 2.2 Consensus size: 28
48788344 CTTTTATTAG
*
48788354 AAAATTATTAAATTTT-TAAAAATA-TATA
1 AAAATTA-GAAATTTTATAAAAATAGTA-A
*
48788382 AAAATTAGAATTTTTATAAAAATAGTAA
1 AAAATTAGAAATTTTATAAAAATAGTAA
48788410 AAAAT
1 AAAAT
48788415 AAAATTGTAA
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
27 6 0.21
28 21 0.72
29 2 0.07
ACGTcount: A:0.59, C:0.00, G:0.03, T:0.38
Consensus pattern (28 bp):
AAAATTAGAAATTTTATAAAAATAGTAA
Found at i:48788397 original size:26 final size:25
Alignment explanation
Indices: 48788360--48788438 Score: 79
Period size: 26 Copynumber: 3.1 Consensus size: 25
48788350 TTAGAAAATT
48788360 ATTAAATTTTTAAAAATATATAAAA
1 ATTAAATTTTTAAAAATATATAAAA
48788385 ATTAGAATTTTTATAAAA-ATAGTAAAA
1 ATTA-AATTTTTA-AAAATATA-TAAAA
* * * * *
48788412 AATAAAATTGTAAAATTTTATAAAA
1 ATTAAATTTTTAAAAATATATAAAA
48788437 AT
1 AT
48788439 CATAAAAAAT
Statistics
Matches: 44, Mismatches: 6, Indels: 8
0.76 0.10 0.14
Matches are distributed among these distances:
25 13 0.30
26 19 0.43
27 12 0.27
ACGTcount: A:0.58, C:0.00, G:0.04, T:0.38
Consensus pattern (25 bp):
ATTAAATTTTTAAAAATATATAAAA
Found at i:48790287 original size:16 final size:17
Alignment explanation
Indices: 48790259--48790299 Score: 59
Period size: 16 Copynumber: 2.5 Consensus size: 17
48790249 TCTCAAGTTT
48790259 TTTTATCTT-CGAAACTA
1 TTTTAT-TTCCGAAACTA
48790276 -TTTATTTCCGAAACTA
1 TTTTATTTCCGAAACTA
48790292 TTTTATTT
1 TTTTATTT
48790300 TTACTTGTTC
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
15 2 0.09
16 13 0.59
17 7 0.32
ACGTcount: A:0.27, C:0.15, G:0.05, T:0.54
Consensus pattern (17 bp):
TTTTATTTCCGAAACTA
Found at i:48796293 original size:18 final size:18
Alignment explanation
Indices: 48796270--48796306 Score: 65
Period size: 18 Copynumber: 2.1 Consensus size: 18
48796260 TGATTTTTCG
*
48796270 AATTCGAATAACTTGAAT
1 AATTCGAATAAATTGAAT
48796288 AATTCGAATAAATTGAAT
1 AATTCGAATAAATTGAAT
48796306 A
1 A
48796307 TCAAACTATA
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:0.08, G:0.11, T:0.32
Consensus pattern (18 bp):
AATTCGAATAAATTGAAT
Found at i:48796535 original size:19 final size:21
Alignment explanation
Indices: 48796502--48796541 Score: 57
Period size: 19 Copynumber: 2.0 Consensus size: 21
48796492 TTACTCCTCA
*
48796502 AAACTTTTTATTTTTC-CCCT
1 AAACTTTTTACTTTTCACCCT
48796522 AAAC-TTTTACTTTTCACCCT
1 AAACTTTTTACTTTTCACCCT
48796542 TTACTCCCAA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
19 10 0.56
20 8 0.44
ACGTcount: A:0.23, C:0.28, G:0.00, T:0.50
Consensus pattern (21 bp):
AAACTTTTTACTTTTCACCCT
Found at i:48808853 original size:25 final size:25
Alignment explanation
Indices: 48808795--48808854 Score: 70
Period size: 24 Copynumber: 2.4 Consensus size: 25
48808785 AGCTCTAGAT
* *
48808795 AGCCATATACCGAGAAGTTCAAGCG
1 AGCCATATATCGAGAAGTCCAAGCG
*
48808820 AGCCA-ATATCTAGAAGCTCCAAG-G
1 AGCCATATATCGAGAAG-TCCAAGCG
48808844 AGCCATATATC
1 AGCCATATATC
48808855 AGGACGCTCA
Statistics
Matches: 30, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
24 15 0.50
25 15 0.50
ACGTcount: A:0.37, C:0.25, G:0.20, T:0.18
Consensus pattern (25 bp):
AGCCATATATCGAGAAGTCCAAGCG
Found at i:48818527 original size:27 final size:26
Alignment explanation
Indices: 48818484--48818536 Score: 88
Period size: 27 Copynumber: 2.0 Consensus size: 26
48818474 CACCAATGAT
*
48818484 TCAGGGAATCAGTACTTAGCAACCCC
1 TCAGGGAATCAGCACTTAGCAACCCC
48818510 TCAGGGAAATCAGCACTTAGCAACCCC
1 TCAGGG-AATCAGCACTTAGCAACCCC
48818537 CTTCACATTT
Statistics
Matches: 25, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
26 6 0.24
27 19 0.76
ACGTcount: A:0.32, C:0.32, G:0.19, T:0.17
Consensus pattern (26 bp):
TCAGGGAATCAGCACTTAGCAACCCC
Found at i:48818531 original size:102 final size:102
Alignment explanation
Indices: 48818415--48818610 Score: 338
Period size: 102 Copynumber: 1.9 Consensus size: 102
48818405 TGAGTCGGGG
* *
48818415 AATCAGCACTTAGCAACCCCTTTCACATTTAAGATACGGTGGGATCAGCACTTAGCAACCACCAA
1 AATCAGCACTTAGCAACCCCCTTCACATTTAAGATACGGTGGAATCAGCACTTAGCAACCACCAA
* *
48818480 TGATTCAGGGAATCAGTACTTAGCAACCCCTCAGGGA
66 TGAGTCAGGGAATCAGCACTTAGCAACCCCTCAGGGA
48818517 AATCAGCACTTAGCAACCCCCTTCACATTTAAGATACGGTGGAATCAGCACTTAGCAACCACCAA
1 AATCAGCACTTAGCAACCCCCTTCACATTTAAGATACGGTGGAATCAGCACTTAGCAACCACCAA
* *
48818582 TGAGTCGGGGAGTCAGCACTTAGCAACCC
66 TGAGTCAGGGAATCAGCACTTAGCAACCC
48818611 TTTTCACATT
Statistics
Matches: 88, Mismatches: 6, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
102 88 1.00
ACGTcount: A:0.32, C:0.29, G:0.19, T:0.20
Consensus pattern (102 bp):
AATCAGCACTTAGCAACCCCCTTCACATTTAAGATACGGTGGAATCAGCACTTAGCAACCACCAA
TGAGTCAGGGAATCAGCACTTAGCAACCCCTCAGGGA
Found at i:48818576 original size:42 final size:42
Alignment explanation
Indices: 48818517--48818651 Score: 162
Period size: 42 Copynumber: 3.4 Consensus size: 42
48818507 CCCTCAGGGA
*
48818517 AATCAGCACTTAGCAACCCCCTTCACATTTAAGATACGGTGG
1 AATCAGCACTTAGCAACCCACTTCACATTTAAGATACGGTGG
*
48818559 AATCAGCACTTAGCAA-CCAC--CA-A--TGAG-T-CGG-GG
1 AATCAGCACTTAGCAACCCACTTCACATTTAAGATACGGTGG
* **
48818592 AGTCAGCACTTAGCAACCCTTTTCACATTTAAGATACGGTGG
1 AATCAGCACTTAGCAACCCACTTCACATTTAAGATACGGTGG
48818634 AATCAGCACTTAGCAACC
1 AATCAGCACTTAGCAACC
48818652 ACCAATGAAT
Statistics
Matches: 77, Mismatches: 7, Indels: 18
0.75 0.07 0.18
Matches are distributed among these distances:
33 17 0.22
34 5 0.06
35 1 0.01
36 5 0.06
37 1 0.01
38 1 0.01
39 5 0.06
40 1 0.01
41 6 0.08
42 35 0.45
ACGTcount: A:0.32, C:0.27, G:0.19, T:0.22
Consensus pattern (42 bp):
AATCAGCACTTAGCAACCCACTTCACATTTAAGATACGGTGG
Found at i:48818603 original size:33 final size:33
Alignment explanation
Indices: 48818557--48818711 Score: 126
Period size: 33 Copynumber: 4.6 Consensus size: 33
48818547 AAGATACGGT
48818557 GGAATCAGCACTTAGCAACCACCAATGAGTCGG
1 GGAATCAGCACTTAGCAACCACCAATGAGTCGG
* *
48818590 GGAGTCAGCACTTAGCAACC-CTTTTCACATTTAAGATACGG
1 GGAATCAGCACTTAGCAACCAC----CA-A--TGAG-T-CGG
*
48818631 TGGAATCAGCACTTAGCAACCACCAATGAATCGG
1 -GGAATCAGCACTTAGCAACCACCAATGAGTCGG
* *
48818665 GGAATCAGCACTTAGAAACC-CC--T---TGGG
1 GGAATCAGCACTTAGCAACCACCAATGAGTCGG
48818692 GGAATCAGCACTTAGCAACC
1 GGAATCAGCACTTAGCAACC
48818712 CCCTTTATAT
Statistics
Matches: 103, Mismatches: 8, Indels: 28
0.74 0.06 0.20
Matches are distributed among these distances:
27 22 0.21
30 1 0.01
32 3 0.03
33 38 0.37
34 3 0.03
35 1 0.01
36 4 0.04
37 1 0.01
38 1 0.01
39 5 0.05
40 1 0.01
41 3 0.03
42 19 0.18
43 1 0.01
ACGTcount: A:0.32, C:0.26, G:0.22, T:0.19
Consensus pattern (33 bp):
GGAATCAGCACTTAGCAACCACCAATGAGTCGG
Found at i:48818617 original size:75 final size:75
Alignment explanation
Indices: 48818517--48818686 Score: 295
Period size: 75 Copynumber: 2.3 Consensus size: 75
48818507 CCCTCAGGGA
48818517 AATCAGCACTTAGCAACCCCCTTCACATTTAAGATACGGTGGAATCAGCACTTAGCAACCACCAA
1 AATCAGCACTTAGCAACCCCCTTCACATTTAAGATACGGTGGAATCAGCACTTAGCAACCACCAA
*
48818582 TGAGTCGGGG
66 TGAATCGGGG
* **
48818592 AGTCAGCACTTAGCAACCCTTTTCACATTTAAGATACGGTGGAATCAGCACTTAGCAACCACCAA
1 AATCAGCACTTAGCAACCCCCTTCACATTTAAGATACGGTGGAATCAGCACTTAGCAACCACCAA
48818657 TGAATCGGGG
66 TGAATCGGGG
*
48818667 AATCAGCACTTAGAAACCCC
1 AATCAGCACTTAGCAACCCC
48818687 TTGGGGGAAT
Statistics
Matches: 88, Mismatches: 7, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
75 88 1.00
ACGTcount: A:0.33, C:0.28, G:0.19, T:0.21
Consensus pattern (75 bp):
AATCAGCACTTAGCAACCCCCTTCACATTTAAGATACGGTGGAATCAGCACTTAGCAACCACCAA
TGAATCGGGG
Found at i:48818672 original size:177 final size:177
Alignment explanation
Indices: 48818376--48818716 Score: 565
Period size: 177 Copynumber: 1.9 Consensus size: 177
48818366 TATCCGTTAT
* *
48818376 CGGTGGATTCAACATTTAGCAACCACCAATGAGTCGGGGAATCAGCACTTAGCAACCCCTTTCAC
1 CGGTGGAATCAACACTTAGCAACCACCAATGAGTCGGGGAATCAGCACTTAGCAACCCCTTTCAC
* * * *
48818441 ATTTAAGATACGGTGGGATCAGCACTTAGCAACCACCAATGATTCAGGGAATCAGTACTTAGCAA
66 ATTTAAGATACGGTGGAATCAGCACTTAGCAACCACCAATGAATCAGGGAATCAGCACTTAGAAA
48818506 CCCCTCAGGGAAATCAGCACTTAGCAACCCCCTTCACATTTAAGATA
131 CCCCTCAGGGAAATCAGCACTTAGCAACCCCCTTCACATTTAAGATA
* * *
48818553 CGGTGGAATCAGCACTTAGCAACCACCAATGAGTCGGGGAGTCAGCACTTAGCAACCCTTTTCAC
1 CGGTGGAATCAACACTTAGCAACCACCAATGAGTCGGGGAATCAGCACTTAGCAACCCCTTTCAC
*
48818618 ATTTAAGATACGGTGGAATCAGCACTTAGCAACCACCAATGAATCGGGGAATCAGCACTTAGAAA
66 ATTTAAGATACGGTGGAATCAGCACTTAGCAACCACCAATGAATCAGGGAATCAGCACTTAGAAA
** *
48818683 CCCCTTGGGGGAATCAGCACTTAGCAACCCCCTT
131 CCCCTCAGGGAAATCAGCACTTAGCAACCCCCTT
48818717 TATATTCAAT
Statistics
Matches: 151, Mismatches: 13, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
177 151 1.00
ACGTcount: A:0.31, C:0.27, G:0.20, T:0.21
Consensus pattern (177 bp):
CGGTGGAATCAACACTTAGCAACCACCAATGAGTCGGGGAATCAGCACTTAGCAACCCCTTTCAC
ATTTAAGATACGGTGGAATCAGCACTTAGCAACCACCAATGAATCAGGGAATCAGCACTTAGAAA
CCCCTCAGGGAAATCAGCACTTAGCAACCCCCTTCACATTTAAGATA
Found at i:48823003 original size:21 final size:21
Alignment explanation
Indices: 48822979--48823050 Score: 54
Period size: 21 Copynumber: 3.4 Consensus size: 21
48822969 ACATAAATGC
48822979 TAAACAGAAACCCATAAGGGT
1 TAAACAGAAACCCATAAGGGT
** * * * * *
48823000 TAAATGGTAGCTCATAAGAGC
1 TAAACAGAAACCCATAAGGGT
* * *
48823021 TGAACGGAAACCTATAAGGGT
1 TAAACAGAAACCCATAAGGGT
48823042 TAAACAGAA
1 TAAACAGAA
48823051 GCTCAATAGA
Statistics
Matches: 34, Mismatches: 17, Indels: 0
0.67 0.33 0.00
Matches are distributed among these distances:
21 34 1.00
ACGTcount: A:0.44, C:0.15, G:0.22, T:0.18
Consensus pattern (21 bp):
TAAACAGAAACCCATAAGGGT
Found at i:48823032 original size:42 final size:42
Alignment explanation
Indices: 48822985--48823097 Score: 138
Period size: 42 Copynumber: 2.7 Consensus size: 42
48822975 ATGCTAAACA
** *
48822985 GAAACCCATAAGGGTTAAATGGTAGCTC-ATAAGAGCTGAACG
1 GAAACCCATAAGGGTTAAACAGAAGCTCAAT-AGAGCTGAACG
*
48823027 GAAACCTATAAGGGTTAAACAGAAGCTCAATAGAGCTGAACG
1 GAAACCCATAAGGGTTAAACAGAAGCTCAATAGAGCTGAACG
* * * *
48823069 GAAACTCATATGAGTTAAACAAAAGCTCA
1 GAAACCCATAAGGGTTAAACAGAAGCTCA
48823098 TGGGAGCTAA
Statistics
Matches: 61, Mismatches: 9, Indels: 2
0.85 0.12 0.03
Matches are distributed among these distances:
42 59 0.97
43 2 0.03
ACGTcount: A:0.42, C:0.17, G:0.22, T:0.19
Consensus pattern (42 bp):
GAAACCCATAAGGGTTAAACAGAAGCTCAATAGAGCTGAACG
Found at i:48830040 original size:20 final size:21
Alignment explanation
Indices: 48829998--48830040 Score: 52
Period size: 20 Copynumber: 2.1 Consensus size: 21
48829988 TCGAAGACTG
*
48829998 AATAGAAGCACATAAGTGCTA
1 AATAGAAGCACATAAGGGCTA
* *
48830019 AATAGAA-CCCATAAGGGTTA
1 AATAGAAGCACATAAGGGCTA
48830039 AA
1 AA
48830041 CGGAAGCTCA
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
20 12 0.63
21 7 0.37
ACGTcount: A:0.49, C:0.14, G:0.19, T:0.19
Consensus pattern (21 bp):
AATAGAAGCACATAAGGGCTA
Found at i:48832444 original size:27 final size:27
Alignment explanation
Indices: 48832406--48832459 Score: 108
Period size: 27 Copynumber: 2.0 Consensus size: 27
48832396 AGAACCACCG
48832406 CTTGAGTTAGTAAAAATTTGATTTCAT
1 CTTGAGTTAGTAAAAATTTGATTTCAT
48832433 CTTGAGTTAGTAAAAATTTGATTTCAT
1 CTTGAGTTAGTAAAAATTTGATTTCAT
48832460 GATATTCTGC
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 27 1.00
ACGTcount: A:0.33, C:0.07, G:0.15, T:0.44
Consensus pattern (27 bp):
CTTGAGTTAGTAAAAATTTGATTTCAT
Found at i:48837384 original size:47 final size:49
Alignment explanation
Indices: 48837291--48837385 Score: 122
Period size: 47 Copynumber: 2.0 Consensus size: 49
48837281 TCTATTGATA
* *
48837291 AATGAATGTCCATAACCCCCTCAAATTTATCCTATTGTAACCCCTAAAG
1 AATGAATGTCCATAACCCCCTCAAATTCATCATATTGTAACCCCTAAAG
* * * *
48837340 AATGAATGTCTATAA-CCCCT-AAATTCATTATCTTGTAACGCCTAAA
1 AATGAATGTCCATAACCCCCTCAAATTCATCATATTGTAACCCCTAAA
48837386 TCATTTATAG
Statistics
Matches: 40, Mismatches: 6, Indels: 2
0.83 0.12 0.04
Matches are distributed among these distances:
47 21 0.52
48 5 0.12
49 14 0.35
ACGTcount: A:0.36, C:0.25, G:0.08, T:0.31
Consensus pattern (49 bp):
AATGAATGTCCATAACCCCCTCAAATTCATCATATTGTAACCCCTAAAG
Found at i:48841561 original size:19 final size:19
Alignment explanation
Indices: 48841509--48841969 Score: 151
Period size: 19 Copynumber: 23.3 Consensus size: 19
48841499 GCGCCAATGG
*
48841509 GTAATTTTGTATGTATATT
1 GTAATTTTGTATGAATATT
*
48841528 GTAACTTTTTATATGAATATT
1 GTAA--TTTTGTATGAATATT
*
48841549 ATAATTTTGTATGAATATT
1 GTAATTTTGTATGAATATT
*
48841568 GTAATTATTTTAT-AATTAATT
1 GTAATT-TTGTATGAA-T-ATT
* * *
48841589 TTATATTTATAGTTTTTG-AT-TA
1 GTA-ATTT-T-G--TATGAATATT
48841611 GT-ATTTTGTATGAATATT
1 GTAATTTTGTATGAATATT
*
48841629 GTAATTATTTTAT-AATTAATTTT
1 GTAATT-TTGTATGAA-T-A--TT
* * *
48841652 GT-ATTTATAGTTTTGGAT-TA
1 GTAATTT-T-G-TATGAATATT
*
48841672 GT-ATTTTGTATGAATAGT
1 GTAATTTTGTATGAATATT
48841690 GTAATTTTTTGTATGAATATT
1 GTAA--TTTTGTATGAATATT
* *
48841711 GTACTTTTTTATGAATATT
1 GTAATTTTGTATGAATATT
*
48841730 GTAATTATT-T-T--ATAAT
1 GTAATT-TTGTATGAATATT
* *
48841746 -TAATTTTGTATTTATAGTTTTT
1 GTAATTTTGTA-TGA-A--TATT
48841768 GATTAGTATTTTGTATGAATATT
1 G--TA--ATTTTGTATGAATATT
48841791 GTAATTTTGTATGAATATT
1 GTAATTTTGTATGAATATT
*
48841810 GTAATTTT-T-T-AATTTT
1 GTAATTTTGTATGAATATT
* *
48841826 GTATGAATATTG--T-AATTTT
1 G--T-AATTTTGTATGAATATT
48841845 GTAATTTTGTATGAATATT
1 GTAATTTTGTATGAATATT
*
48841864 GTAATTATTTTAT-AATTAATTTT
1 GTAATT-TTGTATGAA-T-A--TT
* * *
48841887 GT-ATTTATAGTTTTGGAT-TA
1 GTAATTT-T-G-TATGAATATT
*
48841907 GT-ATTTTGTATGAATAGT
1 GTAATTTTGTATGAATATT
48841925 GTAATTTTTTGTATGAATATT
1 GTAA--TTTTGTATGAATATT
48841946 GTAATTTT-TATGAATATT
1 GTAATTTTGTATGAATATT
48841964 GTAATT
1 GTAATT
48841970 ATTTTATAAT
Statistics
Matches: 336, Mismatches: 45, Indels: 123
0.67 0.09 0.24
Matches are distributed among these distances:
14 2 0.01
15 6 0.02
16 19 0.06
17 15 0.04
18 30 0.09
19 109 0.32
20 39 0.12
21 63 0.19
22 16 0.05
23 12 0.04
24 7 0.02
25 8 0.02
26 2 0.01
27 8 0.02
ACGTcount: A:0.30, C:0.00, G:0.13, T:0.57
Consensus pattern (19 bp):
GTAATTTTGTATGAATATT
Found at i:48841624 original size:61 final size:60
Alignment explanation
Indices: 48841552--48841934 Score: 257
Period size: 61 Copynumber: 6.5 Consensus size: 60
48841542 GAATATTATA
48841552 ATTTTGTATGAATATTGTAATTATTTTATAATTAATTTTATATTTATAGTTTTTGATTAGT
1 ATTTTGTATGAATATTGTAATTATTTTATAATTAATTTTATATTTATAGTTTTTG-TTAGT
* *
48841613 ATTTTGTATGAATATTGTAATTATTTTATAATTAATTTTGTATTTATAGTTTTGGATTAGT
1 ATTTTGTATGAATATTGTAATTATTTTATAATTAATTTTATATTTATAGTTTTTG-TTAGT
* * * * * * * *
48841674 ATTTTGTATGAATAGTGTAATTTTTTGTATGAA-T-ATTGTACT-TTTTTATGAATATTGTAATT
1 ATTTTGTATGAATATTGTAATTATTT-TAT-AATTAATTTTA-TATTTATA-G-TTTTTGTTAGT
* * * * * * * * *
48841736 ATTTTATAATTAATTTTGTATTTATAGTTTTTGATTAGTATTTTGTA-TGA-A--TATTG-TA--
1 ATTTTGT-ATGAATATTGTAATTAT--TTTATAATTA--ATTTTATATTTATAGTTTTTGTTAGT
* * *
48841794 ATTTTGTATGAATATTGTAA-T-TTTT-TAATT--TTGTATGAATATTGTA-ATTTTG-TA--
1 ATTTTGTATGAATATTGTAATTATTTTATAATTAATTTTAT--AT-TTATAGTTTTTGTTAGT
* *
48841848 ATTTTGTATGAATATTGTAATTATTTTATAATTAATTTTGTATTTATAGTTTTGGATTAGT
1 ATTTTGTATGAATATTGTAATTATTTTATAATTAATTTTATATTTATAGTTTTTG-TTAGT
*
48841909 ATTTTGTATGAATAGTGTAATT-TTTT
1 ATTTTGTATGAATATTGTAATTATTTT
48841935 GTATGAATAT
Statistics
Matches: 252, Mismatches: 41, Indels: 59
0.72 0.12 0.17
Matches are distributed among these distances:
48 4 0.02
50 1 0.00
52 5 0.02
53 4 0.02
54 26 0.10
55 2 0.01
56 9 0.04
57 21 0.08
58 6 0.02
59 6 0.02
60 5 0.02
61 118 0.47
62 15 0.06
63 18 0.07
64 3 0.01
65 3 0.01
66 2 0.01
67 4 0.02
ACGTcount: A:0.30, C:0.00, G:0.13, T:0.57
Consensus pattern (60 bp):
ATTTTGTATGAATATTGTAATTATTTTATAATTAATTTTATATTTATAGTTTTTGTTAGT
Found at i:48841725 original size:101 final size:99
Alignment explanation
Indices: 48841613--48841820 Score: 362
Period size: 101 Copynumber: 2.1 Consensus size: 99
48841603 TTTGATTAGT
*
48841613 ATTTTGTATGAATATTGTAATTATTTTATAATTAATTTTGTATTTATAGTTTTGGATTAGTATTT
1 ATTTTTTATGAATATTGTAATTATTTTATAATTAATTTTGTATTTATAGTTTTGGATTAGTATTT
48841678 TGTATGAATAGTGTAATTTTTTGTATGAATATTGTA
66 TGTATGAATAGTGTAA--TTTTGTATGAATATTGTA
* *
48841714 CTTTTTTATGAATATTGTAATTATTTTATAATTAATTTTGTATTTATAGTTTTTGATTAGTATTT
1 ATTTTTTATGAATATTGTAATTATTTTATAATTAATTTTGTATTTATAGTTTTGGATTAGTATTT
*
48841779 TGTATGAATATTGTAATTTTGTATGAATATTGTA
66 TGTATGAATAGTGTAATTTTGTATGAATATTGTA
48841813 ATTTTTTA
1 ATTTTTTA
48841821 ATTTTGTATG
Statistics
Matches: 102, Mismatches: 5, Indels: 2
0.94 0.05 0.02
Matches are distributed among these distances:
99 25 0.25
101 77 0.75
ACGTcount: A:0.29, C:0.00, G:0.13, T:0.57
Consensus pattern (99 bp):
ATTTTTTATGAATATTGTAATTATTTTATAATTAATTTTGTATTTATAGTTTTGGATTAGTATTT
TGTATGAATAGTGTAATTTTGTATGAATATTGTA
Found at i:48841796 original size:46 final size:46
Alignment explanation
Indices: 48841746--48841932 Score: 139
Period size: 46 Copynumber: 4.2 Consensus size: 46
48841736 ATTTTATAAT
48841746 TAATTTTGTATTTATAGTTTTTGATTAGTATTTTGTATGAATATTG
1 TAATTTTGTATTTATAGTTTTTGATTAGTATTTTGTATGAATATTG
* *
48841792 TAATTTTGTATGAATATTGTAATTTT--TTA--ATTTTGTATGAATATTG
1 TAATTTTGTAT--TTATAGT--TTTTGATTAGTATTTTGTATGAATATTG
* * *
48841838 TAATTTTGTAATTT-T-G--TATGAATATTGTAATTATT-T-T--ATAAT-
1 TAATTTTGT-ATTTATAGTTTTTG-AT-TAGT-ATT-TTGTATGAATATTG
* *
48841880 TAATTTTGTATTTATAGTTTTGGATTAGTATTTTGTATGAATAGTG
1 TAATTTTGTATTTATAGTTTTTGATTAGTATTTTGTATGAATATTG
48841926 TAATTTT
1 TAATTTT
48841933 TTGTATGAAT
Statistics
Matches: 109, Mismatches: 10, Indels: 44
0.67 0.06 0.27
Matches are distributed among these distances:
39 2 0.02
41 6 0.06
42 15 0.14
43 11 0.10
44 3 0.03
45 8 0.07
46 48 0.44
47 4 0.04
48 8 0.07
50 4 0.04
ACGTcount: A:0.29, C:0.00, G:0.14, T:0.57
Consensus pattern (46 bp):
TAATTTTGTATTTATAGTTTTTGATTAGTATTTTGTATGAATATTG
Found at i:48841823 original size:27 final size:27
Alignment explanation
Indices: 48841792--48841875 Score: 150
Period size: 27 Copynumber: 3.1 Consensus size: 27
48841782 ATGAATATTG
48841792 TAATTTTGTATGAATATTGTAATTTTT
1 TAATTTTGTATGAATATTGTAATTTTT
*
48841819 TAATTTTGTATGAATATTGTAATTTTG
1 TAATTTTGTATGAATATTGTAATTTTT
48841846 TAATTTTGTATGAATATTGTAATTATTT
1 TAATTTTGTATGAATATTGTAATT-TTT
48841874 TA
1 TA
48841876 TAATTAATTT
Statistics
Matches: 54, Mismatches: 2, Indels: 1
0.95 0.04 0.02
Matches are distributed among these distances:
27 50 0.93
28 4 0.07
ACGTcount: A:0.31, C:0.00, G:0.12, T:0.57
Consensus pattern (27 bp):
TAATTTTGTATGAATATTGTAATTTTT
Found at i:48841848 original size:8 final size:8
Alignment explanation
Indices: 48841789--48841855 Score: 53
Period size: 8 Copynumber: 7.6 Consensus size: 8
48841779 TGTATGAATA
48841789 TTGTAATT
1 TTGTAATT
*
48841797 TTGTATGAATA
1 TTG--T-AATT
48841808 TTGTAATT
1 TTGTAATT
*
48841816 TTTTAATT
1 TTGTAATT
*
48841824 TTGTATGAATA
1 TTG--T-AATT
48841835 TTGTAATT
1 TTGTAATT
48841843 TTGTAATT
1 TTGTAATT
48841851 TTGTA
1 TTGTA
48841856 TGAATATTGT
Statistics
Matches: 47, Mismatches: 6, Indels: 12
0.72 0.09 0.18
Matches are distributed among these distances:
8 31 0.66
9 2 0.04
10 2 0.04
11 12 0.26
ACGTcount: A:0.28, C:0.00, G:0.13, T:0.58
Consensus pattern (8 bp):
TTGTAATT
Found at i:48841861 original size:134 final size:135
Alignment explanation
Indices: 48841709--48841954 Score: 440
Period size: 134 Copynumber: 1.8 Consensus size: 135
48841699 TGTATGAATA
* * *
48841709 TTGTACTTTTTTATGAATATTGTAATTATTTTATAATTAATTTTGTATTTATAGTTTTTGATTAG
1 TTGTAATTTTGTATGAATATTGTAATTATTTTATAATTAATTTTGTATTTATAGTTTTGGATTAG
*
48841774 TATTTTGTATGAATATTGTAA-TTTTGTATGAATATTGTAATTTTTTAATTTTGTATGAATATTG
66 TATTTTGTATGAATAGTGTAATTTTTGTATGAATATTGTAATTTTTTAATTTTGTATGAATATTG
48841838 TAATT
131 TAATT
48841843 TTGTAATTTTGTATGAATATTGTAATTATTTTATAATTAATTTTGTATTTATAGTTTTGGATTAG
1 TTGTAATTTTGTATGAATATTGTAATTATTTTATAATTAATTTTGTATTTATAGTTTTGGATTAG
48841908 TATTTTGTATGAATAGTGTAATTTTTTGTATGAATATTGTAATTTTT
66 TATTTTGTATGAATAGTGTAA-TTTTTGTATGAATATTGTAATTTTT
48841955 ATGAATATTG
Statistics
Matches: 106, Mismatches: 4, Indels: 2
0.95 0.04 0.02
Matches are distributed among these distances:
134 82 0.77
136 24 0.23
ACGTcount: A:0.29, C:0.00, G:0.13, T:0.58
Consensus pattern (135 bp):
TTGTAATTTTGTATGAATATTGTAATTATTTTATAATTAATTTTGTATTTATAGTTTTGGATTAG
TATTTTGTATGAATAGTGTAATTTTTGTATGAATATTGTAATTTTTTAATTTTGTATGAATATTG
TAATT
Found at i:48841969 original size:100 final size:102
Alignment explanation
Indices: 48841843--48842035 Score: 354
Period size: 100 Copynumber: 1.9 Consensus size: 102
48841833 TATTGTAATT
48841843 TTGTAATTTTGTATGAATATTGTAATTATTTTATAATTAATTTTGTATTTATAGTTTTGGATTAG
1 TTGTAATTTTGTATGAATATTGTAATTATTTTATAATTAATTTTGTATTTATAGTTTTGGATTAG
48841908 TATTTTGTATGAATAGTGTAATT-TTTTGTATGAATA
66 TATTTTGTATGAATAGTGTAATTATTTTGTATGAATA
*
48841944 TTGTAATTTT-TATGAATATTGTAATTATTTTATAATTAATTTTGTATTTATAGTTTTTGATTAG
1 TTGTAATTTTGTATGAATATTGTAATTATTTTATAATTAATTTTGTATTTATAGTTTTGGATTAG
*
48842008 TATTTTGTATGAATATTGTAATTATTTT
66 TATTTTGTATGAATAGTGTAATTATTTT
48842036 ATAATTNNNN
Statistics
Matches: 89, Mismatches: 2, Indels: 2
0.96 0.02 0.02
Matches are distributed among these distances:
100 75 0.84
101 14 0.16
ACGTcount: A:0.30, C:0.00, G:0.13, T:0.58
Consensus pattern (102 bp):
TTGTAATTTTGTATGAATATTGTAATTATTTTATAATTAATTTTGTATTTATAGTTTTGGATTAG
TATTTTGTATGAATAGTGTAATTATTTTGTATGAATA
Found at i:48841984 original size:134 final size:133
Alignment explanation
Indices: 48841705--48841990 Score: 416
Period size: 134 Copynumber: 2.1 Consensus size: 133
48841695 TTTTTGTATG
* * * *
48841705 AATATTGTACTTTTTTATGAATATTGTAATTATTTTATAATTAATTTTGTATTTATAGTTTTTGA
1 AATAATGTAATTTTGTATGAATATTGTAATTATTTTATAATTAATTTTGTATTTATAGTTTTGGA
* *
48841770 TTAGTATTTTGTATGAATATTGTAATTTTGTATGAATATTGTAATTTTTTAATTTTGTATGAATA
66 TTAGTATTTTGTATGAATAGTGTAATTTTGTATGAATATTGTAATTTTTTAATATTGTA-GAATA
48841835 TTGT
130 TTGT
**
48841839 AATTTTGTAATTTTGTATGAATATTGTAATTATTTTATAATTAATTTTGTATTTATAGTTTTGGA
1 AATAATGTAATTTTGTATGAATATTGTAATTATTTTATAATTAATTTTGTATTTATAGTTTTGGA
48841904 TTAGTATTTTGTATGAATAGTGTAATTTTTTGTATGAATATTGTAATTTTTATGAATATTGTA-A
66 TTAGTATTTTGTATGAATAGTGTAA--TTTTGTATGAATATTGTAATTTTT-T-AATATTGTAGA
*
48841968 TTATT-T
127 ATATTGT
*
48841974 TATAAT-TAATTTTGTAT
1 AATAATGTAATTTTGTAT
48841991 TTATAGTTTT
Statistics
Matches: 138, Mismatches: 10, Indels: 8
0.88 0.06 0.05
Matches are distributed among these distances:
134 96 0.70
135 4 0.03
136 29 0.21
137 1 0.01
138 8 0.06
ACGTcount: A:0.30, C:0.00, G:0.12, T:0.57
Consensus pattern (133 bp):
AATAATGTAATTTTGTATGAATATTGTAATTATTTTATAATTAATTTTGTATTTATAGTTTTGGA
TTAGTATTTTGTATGAATAGTGTAATTTTGTATGAATATTGTAATTTTTTAATATTGTAGAATAT
TGT
Found at i:48842581 original size:15 final size:16
Alignment explanation
Indices: 48842545--48842581 Score: 58
Period size: 16 Copynumber: 2.4 Consensus size: 16
48842535 CTCATTTAAT
48842545 TTTTATATAATGTAAC
1 TTTTATATAATGTAAC
*
48842561 TTTTATATTATGTAA-
1 TTTTATATAATGTAAC
48842576 TTTTAT
1 TTTTAT
48842582 TTGATTTTGT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
15 6 0.30
16 14 0.70
ACGTcount: A:0.32, C:0.03, G:0.05, T:0.59
Consensus pattern (16 bp):
TTTTATATAATGTAAC
Found at i:48843155 original size:23 final size:22
Alignment explanation
Indices: 48843121--48843179 Score: 82
Period size: 23 Copynumber: 2.6 Consensus size: 22
48843111 CCCGGCCCGT
48843121 TTTTTAATTAAAATTAAAATTATA
1 TTTTTAA-TAAAATTAAAATTA-A
48843145 TTTTTAATAAAATTAAAATTAA
1 TTTTTAATAAAATTAAAATTAA
* *
48843167 TTGTTATTAAAAT
1 TTTTTAATAAAAT
48843180 AAATTGTTAT
Statistics
Matches: 33, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
22 12 0.36
23 14 0.42
24 7 0.21
ACGTcount: A:0.49, C:0.00, G:0.02, T:0.49
Consensus pattern (22 bp):
TTTTTAATAAAATTAAAATTAA
Found at i:48843177 original size:16 final size:16
Alignment explanation
Indices: 48843156--48843211 Score: 94
Period size: 16 Copynumber: 3.5 Consensus size: 16
48843146 TTTTAATAAA
*
48843156 ATTAAAATTAATTGTT
1 ATTAAAATAAATTGTT
48843172 ATTAAAATAAATTGTT
1 ATTAAAATAAATTGTT
*
48843188 ATCAAAATAAATTGTT
1 ATTAAAATAAATTGTT
48843204 ATTAAAAT
1 ATTAAAAT
48843212 TGTATCAAAT
Statistics
Matches: 37, Mismatches: 3, Indels: 0
0.93 0.08 0.00
Matches are distributed among these distances:
16 37 1.00
ACGTcount: A:0.50, C:0.02, G:0.05, T:0.43
Consensus pattern (16 bp):
ATTAAAATAAATTGTT
Found at i:48843283 original size:19 final size:19
Alignment explanation
Indices: 48843259--48843309 Score: 56
Period size: 16 Copynumber: 2.8 Consensus size: 19
48843249 ATCTAACATT
48843259 TTGTTAATAAAATTATTAA
1 TTGTTAATAAAATTATTAA
48843278 TTGTTAAT----TGTATTAA
1 TTGTTAATAAAAT-TATTAA
*
48843294 TTGTTACTAAAATTAT
1 TTGTTAATAAAATTAT
48843310 CAAATTATAT
Statistics
Matches: 26, Mismatches: 1, Indels: 10
0.70 0.03 0.27
Matches are distributed among these distances:
15 1 0.04
16 13 0.50
19 11 0.42
20 1 0.04
ACGTcount: A:0.39, C:0.02, G:0.08, T:0.51
Consensus pattern (19 bp):
TTGTTAATAAAATTATTAA
Found at i:48847694 original size:10 final size:10
Alignment explanation
Indices: 48847679--48847710 Score: 55
Period size: 10 Copynumber: 3.2 Consensus size: 10
48847669 GCCTAAAATT
48847679 ATATATAATG
1 ATATATAATG
*
48847689 ATATATAATA
1 ATATATAATG
48847699 ATATATAATG
1 ATATATAATG
48847709 AT
1 AT
48847711 GGGGACGGCA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
10 20 1.00
ACGTcount: A:0.53, C:0.00, G:0.06, T:0.41
Consensus pattern (10 bp):
ATATATAATG
Found at i:48848668 original size:18 final size:18
Alignment explanation
Indices: 48848645--48848689 Score: 90
Period size: 18 Copynumber: 2.5 Consensus size: 18
48848635 ATATTTCGGG
48848645 CGGGCCGTCGGGTCAGAC
1 CGGGCCGTCGGGTCAGAC
48848663 CGGGCCGTCGGGTCAGAC
1 CGGGCCGTCGGGTCAGAC
48848681 CGGGCCGTC
1 CGGGCCGTC
48848690 CGGCCCATGG
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 27 1.00
ACGTcount: A:0.09, C:0.36, G:0.44, T:0.11
Consensus pattern (18 bp):
CGGGCCGTCGGGTCAGAC
Found at i:48849576 original size:14 final size:13
Alignment explanation
Indices: 48849554--48849620 Score: 55
Period size: 14 Copynumber: 5.1 Consensus size: 13
48849544 TATGAGATTT
48849554 TTATGTTATGTATA
1 TTATGTTAT-TATA
*
48849568 TTATTTTATTATA
1 TTATGTTATTATA
* * *
48849581 TAAT-ATAATATA
1 TTATGTTATTATA
*
48849593 TTATATTAATTATA
1 TTATGTT-ATTATA
*
48849607 TTATATTATTATA
1 TTATGTTATTATA
48849620 T
1 T
48849621 ATATTAAATA
Statistics
Matches: 44, Mismatches: 7, Indels: 5
0.79 0.12 0.09
Matches are distributed among these distances:
12 9 0.20
13 15 0.34
14 20 0.45
ACGTcount: A:0.39, C:0.00, G:0.03, T:0.58
Consensus pattern (13 bp):
TTATGTTATTATA
Found at i:48849598 original size:5 final size:5
Alignment explanation
Indices: 48849564--48849626 Score: 60
Period size: 5 Copynumber: 12.4 Consensus size: 5
48849554 TTATGTTATG
*
48849564 TATAT TAT-T T-TAT TATAT AATATAA TATAT TATAT TA-AT TATAT TATAT
1 TATAT TATAT TATAT TATAT --TATAT TATAT TATAT TATAT TATAT TATAT
48849613 TATTAT ATATAT TA
1 TA-TAT -TATAT TA
48849627 AATAAAGTAA
Statistics
Matches: 49, Mismatches: 2, Indels: 14
0.75 0.03 0.22
Matches are distributed among these distances:
3 1 0.02
4 8 0.16
5 28 0.57
6 6 0.12
7 6 0.12
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (5 bp):
TATAT
Found at i:48850054 original size:16 final size:16
Alignment explanation
Indices: 48850033--48850071 Score: 78
Period size: 16 Copynumber: 2.4 Consensus size: 16
48850023 GTTCATAGGT
48850033 TTTTGAACATGATTCA
1 TTTTGAACATGATTCA
48850049 TTTTGAACATGATTCA
1 TTTTGAACATGATTCA
48850065 TTTTGAA
1 TTTTGAA
48850072 AAAGTTGTTA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 23 1.00
ACGTcount: A:0.31, C:0.10, G:0.13, T:0.46
Consensus pattern (16 bp):
TTTTGAACATGATTCA
Found at i:48850980 original size:13 final size:13
Alignment explanation
Indices: 48850962--48850986 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
48850952 TTAGTATGTA
48850962 AATATATATATAT
1 AATATATATATAT
48850975 AATATATATATA
1 AATATATATATA
48850987 AATTTAAGAT
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:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (13 bp):
AATATATATATAT
Found at i:48852370 original size:19 final size:19
Alignment explanation
Indices: 48852330--48852370 Score: 55
Period size: 19 Copynumber: 2.2 Consensus size: 19
48852320 TTTATTTTTT
***
48852330 AAATGAAGATAATTATTTA
1 AAATGAAGATAATTAAACA
48852349 AAATGAAGATAATTAAACA
1 AAATGAAGATAATTAAACA
48852368 AAA
1 AAA
48852371 CCATTTAGTA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.61, C:0.02, G:0.10, T:0.27
Consensus pattern (19 bp):
AAATGAAGATAATTAAACA
Found at i:48856607 original size:36 final size:36
Alignment explanation
Indices: 48856567--48856638 Score: 119
Period size: 36 Copynumber: 2.0 Consensus size: 36
48856557 AATATTGCCG
48856567 TTACTGTTACCGATTC-AGCACTTTGTGTGTCGAATA
1 TTACTGTTACCGATTCGA-CACTTTGTGTGTCGAATA
*
48856603 TTACTGTTATCGATTCGACACTTTGTGTGTCGAATA
1 TTACTGTTACCGATTCGACACTTTGTGTGTCGAATA
48856639 CTGTTACCAT
Statistics
Matches: 34, Mismatches: 1, Indels: 2
0.92 0.03 0.05
Matches are distributed among these distances:
36 33 0.97
37 1 0.03
ACGTcount: A:0.22, C:0.18, G:0.19, T:0.40
Consensus pattern (36 bp):
TTACTGTTACCGATTCGACACTTTGTGTGTCGAATA
Found at i:48856792 original size:45 final size:45
Alignment explanation
Indices: 48856603--48856797 Score: 248
Period size: 45 Copynumber: 4.3 Consensus size: 45
48856593 GTGTCGAATA
*
48856603 TTACTGTTA-TCGATTCGACACTTTGTGTGTCGAATACTGTTACCA
1 TTACTGTTACT-GATTCGACACTTTGTGTGTCGAATACTGTTACCG
* * *
48856648 TTATTGTTACTGATTTGACACTTTGTGTGTCGAATATTGTTACCG
1 TTACTGTTACTGATTCGACACTTTGTGTGTCGAATACTGTTACCG
* * *
48856693 TTACTGTTACTAATTCGGCACTTTGTGTGTCGAATACTGTTACTG
1 TTACTGTTACTGATTCGACACTTTGTGTGTCGAATACTGTTACCG
* * * * *
48856738 TTATTGTTACCGATTCGACACTTTATGTGTTGAATACTGTTACTG
1 TTACTGTTACTGATTCGACACTTTGTGTGTCGAATACTGTTACCG
* *
48856783 CTACCGTTACTGATT
1 TTACTGTTACTGATT
48856798 ACTGATAGGT
Statistics
Matches: 129, Mismatches: 20, Indels: 2
0.85 0.13 0.01
Matches are distributed among these distances:
45 128 0.99
46 1 0.01
ACGTcount: A:0.21, C:0.17, G:0.18, T:0.43
Consensus pattern (45 bp):
TTACTGTTACTGATTCGACACTTTGTGTGTCGAATACTGTTACCG
Found at i:48862113 original size:24 final size:24
Alignment explanation
Indices: 48862072--48862155 Score: 71
Period size: 24 Copynumber: 3.3 Consensus size: 24
48862062 TGAAGCTTAA
* *
48862072 AAAATATACAT-ATGATTTACATAT
1 AAAATATATATAAT-ATTTATATAT
48862096 AAAATATATATAATATTTATATTAT
1 AAAATATATATAATATTTATA-TAT
* *
48862121 CAAAATAAATAAAATATGTGTATATAT
1 -AAAATATATATAATAT-T-TATATAT
48862148 ATAAATAT
1 A-AAATAT
48862156 GAGAAAATAT
Statistics
Matches: 49, Mismatches: 5, Indels: 9
0.78 0.08 0.14
Matches are distributed among these distances:
24 16 0.33
25 5 0.10
26 15 0.31
27 9 0.18
28 4 0.08
ACGTcount: A:0.54, C:0.04, G:0.04, T:0.39
Consensus pattern (24 bp):
AAAATATATATAATATTTATATAT
Found at i:48863671 original size:45 final size:44
Alignment explanation
Indices: 48863614--48863734 Score: 156
Period size: 44 Copynumber: 2.7 Consensus size: 44
48863604 CGGCTTTAAC
**
48863614 CTGCTCCACTGCAACTTCAGGGAGATAAGGTTTGTCAT-CTTTAGT
1 CTGCTCCACTGCAACTTCAGGGAGATAAGACTTG-CATAC-TTAGT
* * *
48863659 CTGCCCCACTGCAACTTCA-GAAGGATAAGACTTGCTTACTTAGT
1 CTGCTCCACTGCAACTTCAGGGA-GATAAGACTTGCATACTTAGT
48863703 CTGCTCCACTGCAACTTCAGGGAGATAAGACT
1 CTGCTCCACTGCAACTTCAGGGAGATAAGACT
48863735 AGATGCGATC
Statistics
Matches: 66, Mismatches: 7, Indels: 7
0.82 0.09 0.09
Matches are distributed among these distances:
44 36 0.55
45 30 0.45
ACGTcount: A:0.26, C:0.26, G:0.21, T:0.28
Consensus pattern (44 bp):
CTGCTCCACTGCAACTTCAGGGAGATAAGACTTGCATACTTAGT
Found at i:48863717 original size:44 final size:45
Alignment explanation
Indices: 48863614--48863813 Score: 150
Period size: 44 Copynumber: 4.6 Consensus size: 45
48863604 CGGCTTTAAC
* **
48863614 CTGCTCCACTGCAACTTCAGGGAGATAAGGTTTGTCATCTTTAGT
1 CTGCTCCACTGCAACTTCAGAGAGATAAGACTTGTCATCTTTAGT
* *
48863659 CTGCCCCACTGCAACTTCAGA-AGGATAAGACTTG-CTTAC-TTAGT
1 CTGCTCCACTGCAACTTCAGAGA-GATAAGACTTGTCAT-CTTTAGT
* * *
48863703 CTGCTCCACTGCAACTTCAGGGAGATAAGACTAG--ATGC--GA-T
1 CTGCTCCACTGCAACTTCAGAGAGATAAGACTTGTCAT-CTTTAGT
* * * ** *
48863744 CTGCT-CTCTGTAACTTCAGAGAGATAAGATTTGTGGT-TTTAAT
1 CTGCTCCACTGCAACTTCAGAGAGATAAGACTTGTCATCTTTAGT
* * *
48863787 CCGCTCCACTACAACTTCAGGGAGATA
1 CTGCTCCACTGCAACTTCAGAGAGATA
48863814 GGATCATTGG
Statistics
Matches: 123, Mismatches: 23, Indels: 19
0.75 0.14 0.12
Matches are distributed among these distances:
40 23 0.19
41 6 0.05
42 3 0.02
43 7 0.06
44 54 0.44
45 30 0.24
ACGTcount: A:0.27, C:0.23, G:0.21, T:0.29
Consensus pattern (45 bp):
CTGCTCCACTGCAACTTCAGAGAGATAAGACTTGTCATCTTTAGT
Found at i:48875588 original size:15 final size:15
Alignment explanation
Indices: 48875552--48875590 Score: 53
Period size: 15 Copynumber: 2.6 Consensus size: 15
48875542 GCAAATATCG
*
48875552 TGATAACAAATACAA
1 TGATAATAAATACAA
48875567 T-AGTAATAAATACAA
1 TGA-TAATAAATACAA
48875582 TGATAATAA
1 TGATAATAA
48875591 TTTTAACGAT
Statistics
Matches: 21, Mismatches: 1, Indels: 4
0.81 0.04 0.15
Matches are distributed among these distances:
14 1 0.05
15 19 0.90
16 1 0.05
ACGTcount: A:0.59, C:0.08, G:0.08, T:0.26
Consensus pattern (15 bp):
TGATAATAAATACAA
Found at i:48877552 original size:45 final size:44
Alignment explanation
Indices: 48877495--48877615 Score: 156
Period size: 44 Copynumber: 2.7 Consensus size: 44
48877485 CGGCTTTAAC
**
48877495 CTGCTCCACTGCAACTTCAGGGAGATAAGGTTTGTCAT-CTTTAGT
1 CTGCTCCACTGCAACTTCAGGGAGATAAGACTTG-CATAC-TTAGT
* * *
48877540 CTGCCCCACTGCAACTTCA-GAAGGATAAGACTTGCTTACTTAGT
1 CTGCTCCACTGCAACTTCAGGGA-GATAAGACTTGCATACTTAGT
48877584 CTGCTCCACTGCAACTTCAGGGAGATAAGACT
1 CTGCTCCACTGCAACTTCAGGGAGATAAGACT
48877616 AGATGCGATC
Statistics
Matches: 66, Mismatches: 7, Indels: 7
0.82 0.09 0.09
Matches are distributed among these distances:
44 36 0.55
45 30 0.45
ACGTcount: A:0.26, C:0.26, G:0.21, T:0.28
Consensus pattern (44 bp):
CTGCTCCACTGCAACTTCAGGGAGATAAGACTTGCATACTTAGT
Found at i:48877598 original size:44 final size:45
Alignment explanation
Indices: 48877495--48877694 Score: 150
Period size: 44 Copynumber: 4.6 Consensus size: 45
48877485 CGGCTTTAAC
* **
48877495 CTGCTCCACTGCAACTTCAGGGAGATAAGGTTTGTCATCTTTAGT
1 CTGCTCCACTGCAACTTCAGAGAGATAAGACTTGTCATCTTTAGT
* *
48877540 CTGCCCCACTGCAACTTCAGA-AGGATAAGACTTG-CTTAC-TTAGT
1 CTGCTCCACTGCAACTTCAGAGA-GATAAGACTTGTCAT-CTTTAGT
* * *
48877584 CTGCTCCACTGCAACTTCAGGGAGATAAGACTAG--ATGC--GA-T
1 CTGCTCCACTGCAACTTCAGAGAGATAAGACTTGTCAT-CTTTAGT
* * * ** *
48877625 CTGCT-CTCTGTAACTTCAGAGAGATAAGATTTGTGGT-TTTAAT
1 CTGCTCCACTGCAACTTCAGAGAGATAAGACTTGTCATCTTTAGT
* * *
48877668 CCGCTCCACTACAACTTCAGGGAGATA
1 CTGCTCCACTGCAACTTCAGAGAGATA
48877695 GGATCATTGG
Statistics
Matches: 123, Mismatches: 23, Indels: 19
0.75 0.14 0.12
Matches are distributed among these distances:
40 23 0.19
41 6 0.05
42 3 0.02
43 7 0.06
44 54 0.44
45 30 0.24
ACGTcount: A:0.27, C:0.23, G:0.21, T:0.29
Consensus pattern (45 bp):
CTGCTCCACTGCAACTTCAGAGAGATAAGACTTGTCATCTTTAGT
Found at i:48885515 original size:23 final size:23
Alignment explanation
Indices: 48885488--48885609 Score: 181
Period size: 23 Copynumber: 5.3 Consensus size: 23
48885478 AATGTTATTG
*
48885488 ATCAGTGGTAGCTTCGGCTACGT
1 ATCAGTGGTAGCTTCGGCTACAT
*
48885511 TTCAGTGGTAGCTTCGGCTACAT
1 ATCAGTGGTAGCTTCGGCTACAT
* *
48885534 AACAGTGGTAGCTTCTGCTACAT
1 ATCAGTGGTAGCTTCGGCTACAT
*
48885557 TTCAGTGGTAGCTTCGGCTACAT
1 ATCAGTGGTAGCTTCGGCTACAT
* *
48885580 AACAGTGGTAGCTTCGGCTGCAT
1 ATCAGTGGTAGCTTCGGCTACAT
48885603 ATCAGTG
1 ATCAGTG
48885610 TTGCACTTAT
Statistics
Matches: 87, Mismatches: 12, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
23 87 1.00
ACGTcount: A:0.20, C:0.21, G:0.27, T:0.31
Consensus pattern (23 bp):
ATCAGTGGTAGCTTCGGCTACAT
Found at i:48885543 original size:46 final size:46
Alignment explanation
Indices: 48885490--48885609 Score: 204
Period size: 46 Copynumber: 2.6 Consensus size: 46
48885480 TGTTATTGAT
*
48885490 CAGTGGTAGCTTCGGCTACGTTTCAGTGGTAGCTTCGGCTACATAA
1 CAGTGGTAGCTTCGGCTACATTTCAGTGGTAGCTTCGGCTACATAA
*
48885536 CAGTGGTAGCTTCTGCTACATTTCAGTGGTAGCTTCGGCTACATAA
1 CAGTGGTAGCTTCGGCTACATTTCAGTGGTAGCTTCGGCTACATAA
* *
48885582 CAGTGGTAGCTTCGGCTGCATATCAGTG
1 CAGTGGTAGCTTCGGCTACATTTCAGTG
48885610 TTGCACTTAT
Statistics
Matches: 69, Mismatches: 5, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
46 69 1.00
ACGTcount: A:0.20, C:0.22, G:0.28, T:0.31
Consensus pattern (46 bp):
CAGTGGTAGCTTCGGCTACATTTCAGTGGTAGCTTCGGCTACATAA
Found at i:48892286 original size:15 final size:15
Alignment explanation
Indices: 48892250--48892288 Score: 53
Period size: 15 Copynumber: 2.6 Consensus size: 15
48892240 GCAAATATCG
*
48892250 TGATAACAAATACAA
1 TGATAATAAATACAA
48892265 T-AGTAATAAATACAA
1 TGA-TAATAAATACAA
48892280 TGATAATAA
1 TGATAATAA
48892289 TTTTAACGAT
Statistics
Matches: 21, Mismatches: 1, Indels: 4
0.81 0.04 0.15
Matches are distributed among these distances:
14 1 0.05
15 19 0.90
16 1 0.05
ACGTcount: A:0.59, C:0.08, G:0.08, T:0.26
Consensus pattern (15 bp):
TGATAATAAATACAA
Found at i:48892621 original size:16 final size:17
Alignment explanation
Indices: 48892590--48892622 Score: 50
Period size: 18 Copynumber: 1.9 Consensus size: 17
48892580 TTAGCTGGAA
48892590 AAAAATATAAATATGTAC
1 AAAAATAT-AATATGTAC
48892608 AAAAATAT-ATATGTA
1 AAAAATATAATATGTA
48892623 TATAGATTTT
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 7 0.47
18 8 0.53
ACGTcount: A:0.61, C:0.03, G:0.06, T:0.30
Consensus pattern (17 bp):
AAAAATATAATATGTAC
Found at i:48893437 original size:32 final size:32
Alignment explanation
Indices: 48893401--48893462 Score: 124
Period size: 32 Copynumber: 1.9 Consensus size: 32
48893391 CCCTAACGGC
48893401 ATTTCAGAAGCATCCAAAGTATCAACCTTTGT
1 ATTTCAGAAGCATCCAAAGTATCAACCTTTGT
48893433 ATTTCAGAAGCATCCAAAGTATCAACCTTT
1 ATTTCAGAAGCATCCAAAGTATCAACCTTT
48893463 AAATGACTCC
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
32 30 1.00
ACGTcount: A:0.35, C:0.23, G:0.11, T:0.31
Consensus pattern (32 bp):
ATTTCAGAAGCATCCAAAGTATCAACCTTTGT
Found at i:48896045 original size:130 final size:130
Alignment explanation
Indices: 48895837--48896086 Score: 333
Period size: 130 Copynumber: 1.9 Consensus size: 130
48895827 AATAGTAATC
* * * * *
48895837 AAGTCATTCATCACAAAGACGAACGACCCGTTACCACATTTACTTTTCCTCAACCATGTAATGGC
1 AAGTCATTCATCACAAAGAAGAACGACCCATGACCACATTTACTTTTCATCAACCATGCAATGGC
* * * *
48895902 AATAAAGGGATATCATTTACCTGTATTTTAGGCTATGAATTCTACTATTCTGAATGTCAATCCAA
66 AATAAAGGAATATCATTTACCAGTATTTTAGGCTATGAATACCACTATTCTGAATGTCAATCCAA
*
48895967 AAGTCATTCATCATAAAGAAGAACGACCCATGACCACATTTACTTTTCATCAACCATGCAAT-GC
1 AAGTCATTCATCACAAAGAAGAACGACCCATGACCACATTTACTTTTCATCAACCATGCAATGGC
* * * * *
48896031 TAAT-GAGAGAATATCATTTAGCAGTGTTTTAGGTTATGAATACCACTATTGTGAAT
66 -AATAAAG-GAATATCATTTACCAGTATTTTAGGCTATGAATACCACTATTCTGAAT
48896087 TACGCTACAT
Statistics
Matches: 103, Mismatches: 15, Indels: 4
0.84 0.12 0.03
Matches are distributed among these distances:
129 4 0.04
130 99 0.96
ACGTcount: A:0.34, C:0.20, G:0.14, T:0.31
Consensus pattern (130 bp):
AAGTCATTCATCACAAAGAAGAACGACCCATGACCACATTTACTTTTCATCAACCATGCAATGGC
AATAAAGGAATATCATTTACCAGTATTTTAGGCTATGAATACCACTATTCTGAATGTCAATCCAA
Found at i:48897450 original size:25 final size:25
Alignment explanation
Indices: 48897395--48897465 Score: 81
Period size: 25 Copynumber: 2.9 Consensus size: 25
48897385 AGCCCTCTCT
* *
48897395 CAAGCCATATGATGAGAAGCTCATG
1 CAAGCCATATAATGGGAAGCTCATG
*
48897420 TAAGCCATATAATGGGAAGCTCATG
1 CAAGCCATATAATGGGAAGCTCATG
* * *
48897445 CGAGCCA-ATAACGGGTAGCTC
1 CAAGCCATATAATGGGAAGCTC
48897466 CGAAGAGCCA
Statistics
Matches: 39, Mismatches: 7, Indels: 1
0.83 0.15 0.02
Matches are distributed among these distances:
24 12 0.31
25 27 0.69
ACGTcount: A:0.34, C:0.21, G:0.25, T:0.20
Consensus pattern (25 bp):
CAAGCCATATAATGGGAAGCTCATG
Found at i:48897491 original size:25 final size:26
Alignment explanation
Indices: 48897461--48897589 Score: 87
Period size: 25 Copynumber: 5.2 Consensus size: 26
48897451 AATAACGGGT
48897461 AGCTCCGAAGAGCCATTA-ATCGAGA
1 AGCTCCGAAGAGCCATTATATCGAGA
* *
48897486 AGCTCCGGATAGCCA-TATATC-AGAA
1 AGCTCCGAAGAGCCATTATATCGAG-A
* *
48897511 AG-TTC-AAGTG--AGTTATATCGAGA
1 AGCTCCGAAGAGCCA-TTATATCGAGA
* *
48897534 AGCTCCGGAGAGCCATTA-ATCAAGA
1 AGCTCCGAAGAGCCATTATATCGAGA
* *
48897559 AGCTCACGAAGGGTCA-TATATCGAGA
1 AGCTC-CGAAGAGCCATTATATCGAGA
*
48897585 CGCTC
1 AGCTC
48897590 ATAAGAGTTG
Statistics
Matches: 78, Mismatches: 15, Indels: 21
0.68 0.13 0.18
Matches are distributed among these distances:
21 1 0.01
23 11 0.14
24 10 0.13
25 35 0.45
26 20 0.26
27 1 0.01
ACGTcount: A:0.34, C:0.22, G:0.24, T:0.20
Consensus pattern (26 bp):
AGCTCCGAAGAGCCATTATATCGAGA
Found at i:48905247 original size:25 final size:25
Alignment explanation
Indices: 48905218--48905279 Score: 97
Period size: 25 Copynumber: 2.5 Consensus size: 25
48905208 GCCCCCTCTC
*
48905218 GAGCCATATAACGGGAAGATCATGT
1 GAGCCATGTAACGGGAAGATCATGT
* *
48905243 GAGCCATGTAATGGGAAGCTCATGT
1 GAGCCATGTAACGGGAAGATCATGT
48905268 GAGCCATGTAAC
1 GAGCCATGTAAC
48905280 TAAAAGCTTA
Statistics
Matches: 33, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
25 33 1.00
ACGTcount: A:0.32, C:0.18, G:0.29, T:0.21
Consensus pattern (25 bp):
GAGCCATGTAACGGGAAGATCATGT
Found at i:48905286 original size:25 final size:25
Alignment explanation
Indices: 48905237--48905287 Score: 68
Period size: 25 Copynumber: 2.0 Consensus size: 25
48905227 AACGGGAAGA
**
48905237 TCATGTGAGCCATGTAATGGGAAGC
1 TCATGTGAGCCATGTAATGAAAAGC
48905262 TCATGTGAGCCATGTAACT-AAAAGC
1 TCATGTGAGCCATGTAA-TGAAAAGC
48905287 T
1 T
48905288 TATCCATGCT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
25 22 0.96
26 1 0.04
ACGTcount: A:0.31, C:0.18, G:0.25, T:0.25
Consensus pattern (25 bp):
TCATGTGAGCCATGTAATGAAAAGC
Found at i:48905398 original size:26 final size:26
Alignment explanation
Indices: 48905342--48905420 Score: 76
Period size: 26 Copynumber: 3.2 Consensus size: 26
48905332 AAGCTCATGC
* *
48905342 GAGCCA-ATAACGAGTAGCTC-CGAA
1 GAGCCATATAACGAGAAGCTCTTGAA
48905366 GAGCCAT-TAATCGAGAAGCTCTTGAA
1 GAGCCATATAA-CGAGAAGCTCTTGAA
* * *
48905392 GGGCCATATAACGAGATGCTCAT-AA
1 GAGCCATATAACGAGAAGCTCTTGAA
48905417 GAGC
1 GAGC
48905421 TGCAGTGTGT
Statistics
Matches: 45, Mismatches: 6, Indels: 7
0.78 0.10 0.12
Matches are distributed among these distances:
24 9 0.20
25 14 0.31
26 19 0.42
27 3 0.07
ACGTcount: A:0.35, C:0.22, G:0.25, T:0.18
Consensus pattern (26 bp):
GAGCCATATAACGAGAAGCTCTTGAA
Found at i:48905419 original size:51 final size:48
Alignment explanation
Indices: 48905300--48905420 Score: 129
Period size: 48 Copynumber: 2.5 Consensus size: 48
48905290 TCCATGCTGT
* *
48905300 ATAACGGGTAGCTCATAAGAGCCATAATCAGGAAGCTCATGCGAGCCA
1 ATAACGAGTAGCTCATAAGAGCCATAATCAGGAAGCTCATGAGAGCCA
** * *
48905348 ATAACGAGTAGCTCCGAAGAGCCATTAATC-GAGAAGCTCTTGAAGGGCCA
1 ATAACGAGTAGCTCATAAGAGCCA-TAATCAG-GAAGCTCATG-AGAGCCA
48905398 TATAACGAG-ATGCTCATAAGAGC
1 -ATAACGAGTA-GCTCATAAGAGC
48905421 TGCAGTGTGT
Statistics
Matches: 60, Mismatches: 8, Indels: 7
0.80 0.11 0.09
Matches are distributed among these distances:
48 22 0.37
49 14 0.23
50 6 0.10
51 18 0.30
ACGTcount: A:0.36, C:0.21, G:0.25, T:0.18
Consensus pattern (48 bp):
ATAACGAGTAGCTCATAAGAGCCATAATCAGGAAGCTCATGAGAGCCA
Found at i:48906165 original size:17 final size:18
Alignment explanation
Indices: 48906137--48906170 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
48906127 ATCTTACCAA
*
48906137 ACATTCATACACTATTAT
1 ACATTCATACACCATTAT
48906155 ACATT-ATACACCATTA
1 ACATTCATACACCATTA
48906171 CTAAGTTTAC
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 10 0.67
18 5 0.33
ACGTcount: A:0.41, C:0.24, G:0.00, T:0.35
Consensus pattern (18 bp):
ACATTCATACACCATTAT
Found at i:48906475 original size:44 final size:44
Alignment explanation
Indices: 48906410--48906571 Score: 234
Period size: 44 Copynumber: 3.5 Consensus size: 44
48906400 ACACGGATCA
* *
48906410 CACTTATCACTTGTCATTGATCAGATAAGCGTAGCTAAAGCTAC
1 CACTTATCACTTGTCACTGATCAGATAAGTGTAGCTAAAGCTAC
*
48906454 CACTTATCACTTGTCACTGATCAGATAAGTATAGCTAAAGCTAC
1 CACTTATCACTTGTCACTGATCAGATAAGTGTAGCTAAAGCTAC
48906498 CACTTATCACTTGTCACTTGTCACTGATCAGATAAGTGTAGCTAAAGCTAC
1 CAC-T-T-A----TCACTTGTCACTGATCAGATAAGTGTAGCTAAAGCTAC
48906549 CACTTATCACTTGTCACTGATCA
1 CACTTATCACTTGTCACTGATCA
48906572 AAAGTACTCA
Statistics
Matches: 107, Mismatches: 4, Indels: 14
0.86 0.03 0.11
Matches are distributed among these distances:
44 61 0.57
45 1 0.01
46 1 0.01
47 1 0.01
48 1 0.01
49 1 0.01
50 1 0.01
51 40 0.37
ACGTcount: A:0.31, C:0.24, G:0.14, T:0.31
Consensus pattern (44 bp):
CACTTATCACTTGTCACTGATCAGATAAGTGTAGCTAAAGCTAC
Found at i:48906509 original size:51 final size:51
Alignment explanation
Indices: 48906454--48906566 Score: 208
Period size: 51 Copynumber: 2.2 Consensus size: 51
48906444 CTAAAGCTAC
*
48906454 CACTTATCACTTGTCACTGATCAGATAAGTATAGCTAAAGCTACCACTTAT
1 CACTTGTCACTTGTCACTGATCAGATAAGTATAGCTAAAGCTACCACTTAT
*
48906505 CACTTGTCACTTGTCACTGATCAGATAAGTGTAGCTAAAGCTACCACTTAT
1 CACTTGTCACTTGTCACTGATCAGATAAGTATAGCTAAAGCTACCACTTAT
48906556 CACTTGTCACT
1 CACTTGTCACT
48906567 GATCAAAAGT
Statistics
Matches: 60, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
51 60 1.00
ACGTcount: A:0.30, C:0.25, G:0.13, T:0.32
Consensus pattern (51 bp):
CACTTGTCACTTGTCACTGATCAGATAAGTATAGCTAAAGCTACCACTTAT
Found at i:48908865 original size:5 final size:5
Alignment explanation
Indices: 48908841--48908874 Score: 50
Period size: 5 Copynumber: 6.4 Consensus size: 5
48908831 TAATTTAATA
48908841 CAATT CATATT CATATT CAATT CAATT CAATT CA
1 CAATT CA-ATT CA-ATT CAATT CAATT CAATT CA
48908875 CATCTTAGGC
Statistics
Matches: 28, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
5 17 0.61
6 11 0.39
ACGTcount: A:0.38, C:0.21, G:0.00, T:0.41
Consensus pattern (5 bp):
CAATT
Found at i:48911419 original size:26 final size:26
Alignment explanation
Indices: 48911362--48911419 Score: 64
Period size: 26 Copynumber: 2.2 Consensus size: 26
48911352 GTTGAGAAAA
* *
48911362 TTATTTAATTGATAAATTGATTTAGT
1 TTATTTAATTAATAAATTAATTTAGT
* *
48911388 TAATTTAATTAATTAATTAATTATA-T
1 TTATTTAATTAATAAATTAATT-TAGT
48911414 TTATTT
1 TTATTT
48911420 TGGTAAATAG
Statistics
Matches: 26, Mismatches: 5, Indels: 2
0.79 0.15 0.06
Matches are distributed among these distances:
26 24 0.92
27 2 0.08
ACGTcount: A:0.38, C:0.00, G:0.05, T:0.57
Consensus pattern (26 bp):
TTATTTAATTAATAAATTAATTTAGT
Found at i:48913532 original size:40 final size:40
Alignment explanation
Indices: 48913477--48913558 Score: 146
Period size: 40 Copynumber: 2.0 Consensus size: 40
48913467 AAGCCCCTAC
* *
48913477 CAGTCCCCTAGATTCACCTATATCTGTATGTAATTACAAG
1 CAGTCCCCTAAATTCACCTAGATCTGTATGTAATTACAAG
48913517 CAGTCCCCTAAATTCACCTAGATCTGTATGTAATTACAAG
1 CAGTCCCCTAAATTCACCTAGATCTGTATGTAATTACAAG
48913557 CA
1 CA
48913559 ATTACAACTG
Statistics
Matches: 40, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
40 40 1.00
ACGTcount: A:0.32, C:0.26, G:0.12, T:0.30
Consensus pattern (40 bp):
CAGTCCCCTAAATTCACCTAGATCTGTATGTAATTACAAG
Found at i:48920254 original size:43 final size:43
Alignment explanation
Indices: 48920156--48920313 Score: 192
Period size: 42 Copynumber: 3.7 Consensus size: 43
48920146 ATGTTCCAAT
* * ** *
48920156 ATCGATTTGAGATCTCGTATAAGACCATATATGGGATATT-GC
1 ATCGATTTGAGATTTCGTGTAAGACCATAGCTGGGCTATTGGC
* *
48920198 ATCAATTTGAGATTTTGTGTAAGACCATAGCTGGGCTATTGGC
1 ATCGATTTGAGATTTCGTGTAAGACCATAGCTGGGCTATTGGC
48920241 ATCGATTTGAGATTTCGTGTAAGACCATAGCTGGGGCTATTGGC
1 ATCGATTTGAGATTTCGTGTAAGACCATAGCT-GGGCTATTGGC
* ** *
48920285 ATCAATACGAGATTTCCATGTAAGACCAT
1 ATCGATTTGAGATTT-CGTGTAAGACCAT
48920314 GTTTGTAACA
Statistics
Matches: 100, Mismatches: 13, Indels: 3
0.86 0.11 0.03
Matches are distributed among these distances:
42 33 0.33
43 32 0.32
44 23 0.23
45 12 0.12
ACGTcount: A:0.28, C:0.16, G:0.23, T:0.32
Consensus pattern (43 bp):
ATCGATTTGAGATTTCGTGTAAGACCATAGCTGGGCTATTGGC
Found at i:48920297 original size:44 final size:43
Alignment explanation
Indices: 48920160--48920313 Score: 193
Period size: 43 Copynumber: 3.6 Consensus size: 43
48920150 TCCAATATCG
* * ** *
48920160 ATTTGAGATCTCGTATAAGACCATATATGGGATATT-GCATCA
1 ATTTGAGATTTCGTGTAAGACCATAGCTGGGCTATTGGCATCA
* *
48920202 ATTTGAGATTTTGTGTAAGACCATAGCTGGGCTATTGGCATCG
1 ATTTGAGATTTCGTGTAAGACCATAGCTGGGCTATTGGCATCA
48920245 ATTTGAGATTTCGTGTAAGACCATAGCTGGGGCTATTGGCATCA
1 ATTTGAGATTTCGTGTAAGACCATAGCT-GGGCTATTGGCATCA
** *
48920289 ATACGAGATTTCCATGTAAGACCAT
1 ATTTGAGATTT-CGTGTAAGACCAT
48920314 GTTTGTAACA
Statistics
Matches: 97, Mismatches: 12, Indels: 3
0.87 0.11 0.03
Matches are distributed among these distances:
42 30 0.31
43 32 0.33
44 23 0.24
45 12 0.12
ACGTcount: A:0.29, C:0.16, G:0.23, T:0.32
Consensus pattern (43 bp):
ATTTGAGATTTCGTGTAAGACCATAGCTGGGCTATTGGCATCA
Found at i:48924828 original size:19 final size:20
Alignment explanation
Indices: 48924791--48924831 Score: 57
Period size: 19 Copynumber: 2.1 Consensus size: 20
48924781 TGATTGTTTG
*
48924791 CTTGATTGATAGAAAATTAT
1 CTTGAATGATAGAAAATTAT
*
48924811 CTTGAATGA-AGAATATTAT
1 CTTGAATGATAGAAAATTAT
48924830 CT
1 CT
48924832 ATGACTGTGA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
19 11 0.58
20 8 0.42
ACGTcount: A:0.39, C:0.07, G:0.15, T:0.39
Consensus pattern (20 bp):
CTTGAATGATAGAAAATTAT
Found at i:48933764 original size:85 final size:84
Alignment explanation
Indices: 48933606--48933776 Score: 245
Period size: 85 Copynumber: 2.0 Consensus size: 84
48933596 TCCAATATCA
* *
48933606 ATTTGAGATCCTGTATAAGACCATATCTAGGATATGACATCGATTTGAGATTCGTGTAAGACCAT
1 ATTTGAGATCCTGTATAAGACCATAGCTAGGATATGACATCGATTTGAGATTCGTATAAGACCAT
*
48933671 AGCTGGGCTATTGGCATCG
66 AGCTGGGCTATTGACATCG
* * * * *
48933690 ATTTGAGA-CTTGTGTAAGACCATAGCTGGGCTATTGGCATCGATTTGAGATTTCGTATAAGACC
1 ATTTGAGATCCTGTATAAGACCATAGCTAGGATA-TGACATCGATTTGAGA-TTCGTATAAGACC
48933754 ATAGCTGGGCTATTGACATCG
64 ATAGCTGGGCTATTGACATCG
48933775 AT
1 AT
48933777 ACAAGATTTC
Statistics
Matches: 77, Mismatches: 8, Indels: 3
0.88 0.09 0.03
Matches are distributed among these distances:
83 20 0.26
84 23 0.30
85 34 0.44
ACGTcount: A:0.27, C:0.16, G:0.25, T:0.32
Consensus pattern (84 bp):
ATTTGAGATCCTGTATAAGACCATAGCTAGGATATGACATCGATTTGAGATTCGTATAAGACCAT
AGCTGGGCTATTGACATCG
Found at i:48933765 original size:43 final size:42
Alignment explanation
Indices: 48933606--48933776 Score: 229
Period size: 42 Copynumber: 4.0 Consensus size: 42
48933596 TCCAATATCA
* * * *
48933606 ATTTGAGATCCTGTATAAGACCATATCTAGGATA-TGACATCG
1 ATTTGAGATTC-GTATAAGACCATAGCTGGGCTATTGACATCG
* *
48933648 ATTTGAGATTCGTGTAAGACCATAGCTGGGCTATTGGCATCG
1 ATTTGAGATTCGTATAAGACCATAGCTGGGCTATTGACATCG
* *
48933690 ATTTGAGACTT-GTGTAAGACCATAGCTGGGCTATTGGCATCG
1 ATTTGAGA-TTCGTATAAGACCATAGCTGGGCTATTGACATCG
48933732 ATTTGAGATTTCGTATAAGACCATAGCTGGGCTATTGACATCG
1 ATTTGAGA-TTCGTATAAGACCATAGCTGGGCTATTGACATCG
48933775 AT
1 AT
48933777 ACAAGATTTC
Statistics
Matches: 117, Mismatches: 9, Indels: 5
0.89 0.07 0.04
Matches are distributed among these distances:
41 18 0.15
42 66 0.56
43 33 0.28
ACGTcount: A:0.27, C:0.16, G:0.25, T:0.32
Consensus pattern (42 bp):
ATTTGAGATTCGTATAAGACCATAGCTGGGCTATTGACATCG
Found at i:48937699 original size:32 final size:32
Alignment explanation
Indices: 48937662--48937729 Score: 111
Period size: 32 Copynumber: 2.2 Consensus size: 32
48937652 GGTTTAAAGT
*
48937662 GCATTCATTACTAGGAGGTTGATTACGAATAA
1 GCATTCATTACTAGGAGGCTGATTACGAATAA
*
48937694 GCATTCATTCCTAGGAGGCTGATTACGAATAA
1 GCATTCATTACTAGGAGGCTGATTACGAATAA
48937726 -CATT
1 GCATT
48937730 ATTTTGGCCT
Statistics
Matches: 34, Mismatches: 2, Indels: 1
0.92 0.05 0.03
Matches are distributed among these distances:
31 4 0.12
32 30 0.88
ACGTcount: A:0.32, C:0.16, G:0.21, T:0.31
Consensus pattern (32 bp):
GCATTCATTACTAGGAGGCTGATTACGAATAA
Found at i:48941058 original size:17 final size:19
Alignment explanation
Indices: 48941022--48941061 Score: 57
Period size: 17 Copynumber: 2.2 Consensus size: 19
48941012 TGTAAATTAT
*
48941022 AAATATATATATAATCTAA
1 AAATATATATATAATATAA
48941041 AAATA-ATATA-AATATAA
1 AAATATATATATAATATAA
48941058 AAAT
1 AAAT
48941062 TTATTGTAAA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
17 10 0.50
18 5 0.25
19 5 0.25
ACGTcount: A:0.65, C:0.03, G:0.00, T:0.33
Consensus pattern (19 bp):
AAATATATATATAATATAA
Found at i:48960862 original size:12 final size:12
Alignment explanation
Indices: 48960845--48960872 Score: 56
Period size: 12 Copynumber: 2.3 Consensus size: 12
48960835 CACACGGCCG
48960845 TGTCCCAGCCCA
1 TGTCCCAGCCCA
48960857 TGTCCCAGCCCA
1 TGTCCCAGCCCA
48960869 TGTC
1 TGTC
48960873 TTACCCATGT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 16 1.00
ACGTcount: A:0.14, C:0.46, G:0.18, T:0.21
Consensus pattern (12 bp):
TGTCCCAGCCCA
Found at i:48961924 original size:101 final size:101
Alignment explanation
Indices: 48961785--48962008 Score: 313
Period size: 101 Copynumber: 2.2 Consensus size: 101
48961775 ACATGCATTA
* * ** *
48961785 CCATGGCCCAGCCATGGTCTTACATTCTTAGTGCCATAACCCAGTTATGGTCTTATCATCAGAAT
1 CCATGGTCCAACCATGGTCTTACATTCAAAGTGCCATAACCCAGTTATGGTCTTATCATCAAAAT
*
48961850 GCCATAACTTAGCTATGGTCTTACTTATAAATACTG
66 GACATAACTTAGCTATGGTCTTACTTATAAATACTG
* * * * * *
48961886 TCATGGTCCAACCATGGTCTTACGTTCAAAGTGTCATAACCTAGTTATGGTCTTTTCATTAAAAT
1 CCATGGTCCAACCATGGTCTTACATTCAAAGTGCCATAACCCAGTTATGGTCTTATCATCAAAAT
** *
48961951 GACATAGTTTAGCTATGGTCTTACTTATAGATACTG
66 GACATAACTTAGCTATGGTCTTACTTATAAATACTG
48961987 CCATGGTCCAACCATGGTCTTA
1 CCATGGTCCAACCATGGTCTTA
48962009 TCCGTCAATT
Statistics
Matches: 107, Mismatches: 16, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
101 107 1.00
ACGTcount: A:0.27, C:0.22, G:0.17, T:0.34
Consensus pattern (101 bp):
CCATGGTCCAACCATGGTCTTACATTCAAAGTGCCATAACCCAGTTATGGTCTTATCATCAAAAT
GACATAACTTAGCTATGGTCTTACTTATAAATACTG
Found at i:48965021 original size:34 final size:34
Alignment explanation
Indices: 48964975--48965046 Score: 126
Period size: 34 Copynumber: 2.1 Consensus size: 34
48964965 ACATTCCTTC
48964975 ATCAGATACCATATAATGAGTGCAGCCATTGTCA
1 ATCAGATACCATATAATGAGTGCAGCCATTGTCA
* *
48965009 ATCAGATGCCATATAATGAGTGCAGTCATTGTCA
1 ATCAGATACCATATAATGAGTGCAGCCATTGTCA
48965043 ATCA
1 ATCA
48965047 ACCAATCCTT
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
34 36 1.00
ACGTcount: A:0.35, C:0.19, G:0.18, T:0.28
Consensus pattern (34 bp):
ATCAGATACCATATAATGAGTGCAGCCATTGTCA
Found at i:48968204 original size:117 final size:117
Alignment explanation
Indices: 48967996--48968206 Score: 341
Period size: 117 Copynumber: 1.8 Consensus size: 117
48967986 TTTGATTTGT
* * *
48967996 TGGTTATTTGTGATTCATTATTACAATTTCAGTGCCACAATGTAGTGTTTGTTTTGTCGATTTTT
1 TGGTTAATTGTGATTCATTATTACAATTTCAGTGCCACAATGTAGGGTTTGTTTTGTCGATTTGT
* * *
48968061 GATGCTATAGTGGTCCCGATGTTGTTGATAAAATTGTTGTCAAAATTGTAGA
66 GATGCGACAGTGGTCCCGATGATGTTGATAAAATTGTTGTCAAAATTGTAGA
* * *
48968113 TGGTTAATTGTGATTTATTATTGCAATTTCAGTGCCACAATGTAGGGTTTGTTTTGTTGATTTGT
1 TGGTTAATTGTGATTCATTATTACAATTTCAGTGCCACAATGTAGGGTTTGTTTTGTCGATTTGT
48968178 GATGCGACAGTGGTCCCGATGATGTTGAT
66 GATGCGACAGTGGTCCCGATGATGTTGAT
48968207 TTCTGTTATC
Statistics
Matches: 85, Mismatches: 9, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
117 85 1.00
ACGTcount: A:0.22, C:0.10, G:0.24, T:0.44
Consensus pattern (117 bp):
TGGTTAATTGTGATTCATTATTACAATTTCAGTGCCACAATGTAGGGTTTGTTTTGTCGATTTGT
GATGCGACAGTGGTCCCGATGATGTTGATAAAATTGTTGTCAAAATTGTAGA
Found at i:48968847 original size:33 final size:32
Alignment explanation
Indices: 48968810--48968885 Score: 89
Period size: 33 Copynumber: 2.3 Consensus size: 32
48968800 TGACTACTGA
* *
48968810 GGAGGGTGATGTTAAAGGGGTGGAAGTTGATGG
1 GGAGGGTGATGATAAAGGGGTAGAAGTTGA-GG
* *
48968843 GGAGGGTGATGATGAAGGGGTAGAATTTGAGG
1 GGAGGGTGATGATAAAGGGGTAGAAGTTGAGG
*
48968875 GTGAAGGTGAT
1 G-GAGGGTGAT
48968886 CTGGAAAAGG
Statistics
Matches: 37, Mismatches: 5, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
32 3 0.08
33 34 0.92
ACGTcount: A:0.26, C:0.00, G:0.50, T:0.24
Consensus pattern (32 bp):
GGAGGGTGATGATAAAGGGGTAGAAGTTGAGG
Found at i:48969151 original size:50 final size:51
Alignment explanation
Indices: 48969053--48969154 Score: 143
Period size: 50 Copynumber: 2.0 Consensus size: 51
48969043 GTGAAGTTGA
* * * * *
48969053 TGCTGATGAATATGCTGGTGATTTTGTAACATCAGATGGAGTGGATAATGT
1 TGCTGATGAATATACTGATGATTTTGCAACATCAGATGGACTAGATAATGT
*
48969104 TGCTGATGAATATATTGATGA-TTTGCAACATCAGATGGACTAGATAATGT
1 TGCTGATGAATATACTGATGATTTTGCAACATCAGATGGACTAGATAATGT
48969154 T
1 T
48969155 ACTGCTGCAC
Statistics
Matches: 45, Mismatches: 6, Indels: 1
0.87 0.12 0.02
Matches are distributed among these distances:
50 27 0.60
51 18 0.40
ACGTcount: A:0.30, C:0.09, G:0.25, T:0.35
Consensus pattern (51 bp):
TGCTGATGAATATACTGATGATTTTGCAACATCAGATGGACTAGATAATGT
Found at i:48970500 original size:32 final size:31
Alignment explanation
Indices: 48970455--48970550 Score: 174
Period size: 31 Copynumber: 3.1 Consensus size: 31
48970445 CTTAGATAAT
48970455 TTTAAAGAGTTTTATTAGGATTCAATTACTC
1 TTTAAAGAGTTTTATTAGGATTCAATTACTC
48970486 TTTAAAGAGTTTTTATTAGGATTCAATTACTC
1 TTTAAAGAG-TTTTATTAGGATTCAATTACTC
*
48970518 TTGAAAGAGTTTTATTAGGATTCAATTACTC
1 TTTAAAGAGTTTTATTAGGATTCAATTACTC
48970549 TT
1 TT
48970551 GTAATTTGCC
Statistics
Matches: 63, Mismatches: 1, Indels: 2
0.95 0.02 0.03
Matches are distributed among these distances:
31 33 0.52
32 30 0.48
ACGTcount: A:0.31, C:0.09, G:0.14, T:0.46
Consensus pattern (31 bp):
TTTAAAGAGTTTTATTAGGATTCAATTACTC
Found at i:48971125 original size:22 final size:22
Alignment explanation
Indices: 48971097--48971143 Score: 60
Period size: 22 Copynumber: 2.2 Consensus size: 22
48971087 CTTATTCTTT
* **
48971097 AAAAAAAA-ACAAAAAAGCGCA
1 AAAAAAAAGAAAAAAAAAAGCA
48971118 AAAAAAAAGAAAAAAAAAAGCA
1 AAAAAAAAGAAAAAAAAAAGCA
48971140 AAAA
1 AAAA
48971144 GCAAAAAAGC
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
21 8 0.36
22 14 0.64
ACGTcount: A:0.83, C:0.09, G:0.09, T:0.00
Consensus pattern (22 bp):
AAAAAAAAGAAAAAAAAAAGCA
Found at i:48976801 original size:32 final size:31
Alignment explanation
Indices: 48976751--48976846 Score: 174
Period size: 31 Copynumber: 3.1 Consensus size: 31
48976741 NNNNNNTAAT
48976751 TTTAAAGAGTTTTATTAGGATTCAATTACTC
1 TTTAAAGAGTTTTATTAGGATTCAATTACTC
48976782 TTTAAAGAGTTTTTATTAGGATTCAATTACTC
1 TTTAAAGAG-TTTTATTAGGATTCAATTACTC
*
48976814 TTGAAAGAGTTTTATTAGGATTCAATTACTC
1 TTTAAAGAGTTTTATTAGGATTCAATTACTC
48976845 TT
1 TT
48976847 GTAATTTGCC
Statistics
Matches: 63, Mismatches: 1, Indels: 2
0.95 0.02 0.03
Matches are distributed among these distances:
31 33 0.52
32 30 0.48
ACGTcount: A:0.31, C:0.09, G:0.14, T:0.46
Consensus pattern (31 bp):
TTTAAAGAGTTTTATTAGGATTCAATTACTC
Found at i:48979914 original size:17 final size:16
Alignment explanation
Indices: 48979874--48979915 Score: 66
Period size: 16 Copynumber: 2.6 Consensus size: 16
48979864 GAATGCTAAC
*
48979874 GATTTAGGGATTTTAA
1 GATTTAGGGATTTGAA
48979890 GATTTAGGGATTTGAA
1 GATTTAGGGATTTGAA
48979906 GATTTTAGGG
1 GA-TTTAGGG
48979916 GTTCAATAAA
Statistics
Matches: 24, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
16 17 0.71
17 7 0.29
ACGTcount: A:0.29, C:0.00, G:0.31, T:0.40
Consensus pattern (16 bp):
GATTTAGGGATTTGAA
Found at i:48982957 original size:5 final size:5
Alignment explanation
Indices: 48982947--48982973 Score: 54
Period size: 5 Copynumber: 5.4 Consensus size: 5
48982937 AAAATTTTTT
48982947 ATTCG ATTCG ATTCG ATTCG ATTCG AT
1 ATTCG ATTCG ATTCG ATTCG ATTCG AT
48982974 CGAATGCTCA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 22 1.00
ACGTcount: A:0.22, C:0.19, G:0.19, T:0.41
Consensus pattern (5 bp):
ATTCG
Found at i:48983843 original size:6 final size:7
Alignment explanation
Indices: 48983826--48983852 Score: 54
Period size: 7 Copynumber: 3.9 Consensus size: 7
48983816 GCTTGCTGCA
48983826 TTTTTTC
1 TTTTTTC
48983833 TTTTTTC
1 TTTTTTC
48983840 TTTTTTC
1 TTTTTTC
48983847 TTTTTT
1 TTTTTT
48983853 AAGTTACCTT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 20 1.00
ACGTcount: A:0.00, C:0.11, G:0.00, T:0.89
Consensus pattern (7 bp):
TTTTTTC
Found at i:48988150 original size:46 final size:46
Alignment explanation
Indices: 48988083--48988177 Score: 190
Period size: 46 Copynumber: 2.1 Consensus size: 46
48988073 TATGATACAC
48988083 ATATCATTTAAACAACAATATTGTTCATTCTATATCCAATTCATGA
1 ATATCATTTAAACAACAATATTGTTCATTCTATATCCAATTCATGA
48988129 ATATCATTTAAACAACAATATTGTTCATTCTATATCCAATTCATGA
1 ATATCATTTAAACAACAATATTGTTCATTCTATATCCAATTCATGA
48988175 ATA
1 ATA
48988178 CATAATTCAT
Statistics
Matches: 49, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
46 49 1.00
ACGTcount: A:0.40, C:0.17, G:0.04, T:0.39
Consensus pattern (46 bp):
ATATCATTTAAACAACAATATTGTTCATTCTATATCCAATTCATGA
Found at i:48988459 original size:36 final size:40
Alignment explanation
Indices: 48988369--48988473 Score: 119
Period size: 36 Copynumber: 2.7 Consensus size: 40
48988359 AATTCGAAGT
* * *
48988369 AGTAAATTGACACCCAGTATCTCATTGAATAAATCAGAAG
1 AGTAAATTGACACCCAGTGTCTCATCGAATAAATCACAAG
* *
48988409 TAGTAAATTAACACCCAGTGTCTCATCG-TTAAA-C-CAA-
1 -AGTAAATTGACACCCAGTGTCTCATCGAATAAATCACAAG
*
48988446 AGTAAATTGACACCCAGTGCCTCATCGA
1 AGTAAATTGACACCCAGTGTCTCATCGA
48988474 CTCGAAGTCG
Statistics
Matches: 56, Mismatches: 7, Indels: 6
0.81 0.10 0.09
Matches are distributed among these distances:
36 25 0.45
38 2 0.04
39 1 0.02
40 4 0.07
41 24 0.43
ACGTcount: A:0.38, C:0.23, G:0.14, T:0.25
Consensus pattern (40 bp):
AGTAAATTGACACCCAGTGTCTCATCGAATAAATCACAAG
Found at i:48989393 original size:21 final size:20
Alignment explanation
Indices: 48989360--48989398 Score: 51
Period size: 21 Copynumber: 1.9 Consensus size: 20
48989350 CTTCGTCTCA
48989360 TTCTTTCTCCCTTTTCTTTCT
1 TTCTTTCTCCC-TTTCTTTCT
* *
48989381 TTCTTTTTTCCTTTCTTT
1 TTCTTTCTCCCTTTCTTT
48989399 TTCCTTCTGT
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
20 7 0.44
21 9 0.56
ACGTcount: A:0.00, C:0.28, G:0.00, T:0.72
Consensus pattern (20 bp):
TTCTTTCTCCCTTTCTTTCT
Found at i:48989745 original size:13 final size:13
Alignment explanation
Indices: 48989727--48989761 Score: 70
Period size: 13 Copynumber: 2.7 Consensus size: 13
48989717 ACTAACTTCT
48989727 TAAATATTTTTAA
1 TAAATATTTTTAA
48989740 TAAATATTTTTAA
1 TAAATATTTTTAA
48989753 TAAATATTT
1 TAAATATTT
48989762 ATGAGTCTGA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 22 1.00
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (13 bp):
TAAATATTTTTAA
Found at i:48997208 original size:23 final size:23
Alignment explanation
Indices: 48997176--48997219 Score: 70
Period size: 23 Copynumber: 1.9 Consensus size: 23
48997166 ACTACCATTT
48997176 TCTAAATAAAATAATAATAAATA
1 TCTAAATAAAATAATAATAAATA
* *
48997199 TCTAAGTAAAATATTAATAAA
1 TCTAAATAAAATAATAATAAA
48997220 ATAATATTTA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.61, C:0.05, G:0.02, T:0.32
Consensus pattern (23 bp):
TCTAAATAAAATAATAATAAATA
Found at i:48997212 original size:13 final size:11
Alignment explanation
Indices: 48997180--48997222 Score: 52
Period size: 11 Copynumber: 3.8 Consensus size: 11
48997170 CCATTTTCTA
*
48997180 AATAAAATAAT
1 AATAAAATATT
48997191 AAT-AAATATCT
1 AATAAAATAT-T
48997202 AAGTAAAATATT
1 AA-TAAAATATT
48997214 AATAAAATA
1 AATAAAATA
48997223 ATATTTAACT
Statistics
Matches: 28, Mismatches: 1, Indels: 6
0.80 0.03 0.17
Matches are distributed among these distances:
10 5 0.18
11 13 0.46
12 4 0.14
13 6 0.21
ACGTcount: A:0.65, C:0.02, G:0.02, T:0.30
Consensus pattern (11 bp):
AATAAAATATT
Found at i:49003407 original size:123 final size:124
Alignment explanation
Indices: 49003188--49003461 Score: 480
Period size: 123 Copynumber: 2.2 Consensus size: 124
49003178 TTTCGAGTTG
*
49003188 ACGTTTCTG-GTCAAATAGTATAAAATCGCTTCTACCAGGATGCTATTTGAGAAGAAATTGTGAA
1 ACGTTTCTGAGT-AAATAGTATAAAATCACTTCTACCAGGATGCTATTTGAGAAGAAATTGTGAA
*
49003252 ATCGTGCCCTCGTGGATGCGATTTCACTACAGTTGGTCATGTAAGAAATAA-TTTTTTTA
65 ATCGTGCCCTCGTGGACGCGATTTCACTACAGTTGGTCATGTAAGAAATAATTTTTTTTA
49003311 ACGTTTCTGAGTAAATAGTATAAAATCACTTCTACCAGGATGCTATTTGAGAAGAAATTGTGAAA
1 ACGTTTCTGAGTAAATAGTATAAAATCACTTCTACCAGGATGCTATTTGAGAAGAAATTGTGAAA
* *
49003376 TCGTGCCCTCGTGGACGCGATTTCGCTACAGTTGGTCATGTAAGAAATAATTTTTTTTG
66 TCGTGCCCTCGTGGACGCGATTTCACTACAGTTGGTCATGTAAGAAATAATTTTTTTTA
*
49003435 ACGTTTCTGAGCAAATAGTATAAAATC
1 ACGTTTCTGAGTAAATAGTATAAAATC
49003462 GTGCCCTTGT
Statistics
Matches: 144, Mismatches: 5, Indels: 3
0.95 0.03 0.02
Matches are distributed among these distances:
123 109 0.76
124 35 0.24
ACGTcount: A:0.31, C:0.15, G:0.20, T:0.34
Consensus pattern (124 bp):
ACGTTTCTGAGTAAATAGTATAAAATCACTTCTACCAGGATGCTATTTGAGAAGAAATTGTGAAA
TCGTGCCCTCGTGGACGCGATTTCACTACAGTTGGTCATGTAAGAAATAATTTTTTTTA
Found at i:49006722 original size:29 final size:29
Alignment explanation
Indices: 49006658--49006968 Score: 481
Period size: 29 Copynumber: 10.9 Consensus size: 29
49006648 TTTTGTTAAT
*
49006658 GGTTAGGGTTTTTAATTAAATTAAGTTAG
1 GGTTAGGGTTTTTAATTAAATTAGGTTAG
*
49006687 GGTTTAGGTTTTTTAATTAAATTAGGTTAG
1 GG-TTAGGGTTTTTAATTAAATTAGGTTAG
*
49006717 GGTTAGGGTTTTTAATTAAATTATGTTAG
1 GGTTAGGGTTTTTAATTAAATTAGGTTAG
*
49006746 GGTTAGGGTTTTTAATTAAATTAAGTTAG
1 GGTTAGGGTTTTTAATTAAATTAGGTTAG
*
49006775 GGTTAGGGTGTTTAATTAAATTAGGTTAG
1 GGTTAGGGTTTTTAATTAAATTAGGTTAG
49006804 GGTTAGGGTTTTTAATT-AA--A--TTA-
1 GGTTAGGGTTTTTAATTAAATTAGGTTAG
*
49006827 GGTTAGGGTTTTAAATTAAATTAGGTTAG
1 GGTTAGGGTTTTTAATTAAATTAGGTTAG
*
49006856 GGTTAGGGTTTTTAATTAAATTAAGTTAG
1 GGTTAGGGTTTTTAATTAAATTAGGTTAG
*
49006885 AGTTAGGGTTTTTAATTAAATTAGGTTAG
1 GGTTAGGGTTTTTAATTAAATTAGGTTAG
*
49006914 GGTTTAGGGTTTTTAATTAAATTAAGTTAG
1 GG-TTAGGGTTTTTAATTAAATTAGGTTAG
49006944 GGTTAGGGTTTTTAATTAAATTAGG
1 GGTTAGGGTTTTTAATTAAATTAGG
49006969 ATTTTTTTAC
Statistics
Matches: 258, Mismatches: 16, Indels: 16
0.89 0.06 0.06
Matches are distributed among these distances:
23 16 0.06
24 5 0.02
26 2 0.01
28 5 0.02
29 175 0.68
30 55 0.21
ACGTcount: A:0.30, C:0.00, G:0.25, T:0.45
Consensus pattern (29 bp):
GGTTAGGGTTTTTAATTAAATTAGGTTAG
Found at i:49009275 original size:25 final size:25
Alignment explanation
Indices: 49009225--49009280 Score: 64
Period size: 25 Copynumber: 2.3 Consensus size: 25
49009215 CTTTTATAAC
*
49009225 AAATAATAAATTAATAATTATCTAA
1 AAATAATAAATTAATAAATATCTAA
*
49009250 AAATACATAAA-TAA-AAATATCT-T
1 AAATA-ATAAATTAATAAATATCTAA
49009273 AAATAATA
1 AAATAATA
49009281 TTTAAAATTT
Statistics
Matches: 28, Mismatches: 2, Indels: 5
0.80 0.06 0.14
Matches are distributed among these distances:
22 3 0.11
23 5 0.18
24 7 0.25
25 8 0.29
26 5 0.18
ACGTcount: A:0.62, C:0.05, G:0.00, T:0.32
Consensus pattern (25 bp):
AAATAATAAATTAATAAATATCTAA
Found at i:49009390 original size:10 final size:10
Alignment explanation
Indices: 49009371--49009423 Score: 52
Period size: 10 Copynumber: 5.1 Consensus size: 10
49009361 GCCATTGATG
*
49009371 AAAATATAAA
1 AAAATTTAAA
49009381 AAAATTTAAA
1 AAAATTTAAA
* *
49009391 ATTATTTTAAA
1 A-AAATTTAAA
*
49009402 AAAATATAAA
1 AAAATTTAAA
49009412 AAAATTTTAAA
1 AAAA-TTTAAA
49009423 A
1 A
49009424 TTATTTTTAA
Statistics
Matches: 34, Mismatches: 7, Indels: 3
0.77 0.16 0.07
Matches are distributed among these distances:
10 20 0.59
11 14 0.41
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (10 bp):
AAAATTTAAA
Found at i:49009403 original size:21 final size:21
Alignment explanation
Indices: 49009377--49009423 Score: 67
Period size: 21 Copynumber: 2.2 Consensus size: 21
49009367 GATGAAAATA
* **
49009377 TAAAAAAATTTAAAATTATTT
1 TAAAAAAATATAAAAAAATTT
49009398 TAAAAAAATATAAAAAAATTT
1 TAAAAAAATATAAAAAAATTT
49009419 TAAAA
1 TAAAA
49009424 TTATTTTTAA
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (21 bp):
TAAAAAAATATAAAAAAATTT
Found at i:49009406 original size:31 final size:33
Alignment explanation
Indices: 49009371--49009439 Score: 124
Period size: 31 Copynumber: 2.2 Consensus size: 33
49009361 GCCATTGATG
49009371 AAAATATAAAAAAA-TTTAAAATTA-TTTTAAA
1 AAAATATAAAAAAATTTTAAAATTATTTTTAAA
49009402 AAAATATAAAAAAATTTTAAAATTATTTTTAAA
1 AAAATATAAAAAAATTTTAAAATTATTTTTAAA
49009435 AAAAT
1 AAAAT
49009440 GAAATTGAGG
Statistics
Matches: 36, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
31 14 0.39
32 10 0.28
33 12 0.33
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (33 bp):
AAAATATAAAAAAATTTTAAAATTATTTTTAAA
Found at i:49009498 original size:22 final size:22
Alignment explanation
Indices: 49009473--49009544 Score: 128
Period size: 22 Copynumber: 3.3 Consensus size: 22
49009463 TAATATGGAT
49009473 TTGAGA-GATTTTTGGAAGGAAA
1 TTGAGAGGA-TTTTGGAAGGAAA
49009495 TTGAGAGGATTTTGGAAGGAAA
1 TTGAGAGGATTTTGGAAGGAAA
49009517 TTGAGAGGATTTTGGAAGGAAA
1 TTGAGAGGATTTTGGAAGGAAA
49009539 TTGAGA
1 TTGAGA
49009545 TAGGATTTGT
Statistics
Matches: 49, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
22 47 0.96
23 2 0.04
ACGTcount: A:0.36, C:0.00, G:0.35, T:0.29
Consensus pattern (22 bp):
TTGAGAGGATTTTGGAAGGAAA
Found at i:49012261 original size:2 final size:2
Alignment explanation
Indices: 49012254--49012285 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
49012244 TATGTGTTAA
49012254 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
49012286 TAAGGGTGAA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:49026107 original size:28 final size:28
Alignment explanation
Indices: 49026065--49026134 Score: 97
Period size: 28 Copynumber: 2.5 Consensus size: 28
49026055 AGGGGTTCAG
* *
49026065 CATTGGGTGCCGCCTGTCAGGTACCCTC
1 CATTGGGTGCCGCCTATCAGGAACCCTC
*
49026093 CATTGGGTGCTGCCTATCAGGAACCCTC
1 CATTGGGTGCCGCCTATCAGGAACCCTC
*
49026121 CACT-GGTGCCGCCT
1 CATTGGGTGCCGCCT
49026135 CTCAATCATC
Statistics
Matches: 37, Mismatches: 5, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
27 9 0.24
28 28 0.76
ACGTcount: A:0.13, C:0.36, G:0.27, T:0.24
Consensus pattern (28 bp):
CATTGGGTGCCGCCTATCAGGAACCCTC
Found at i:49034513 original size:28 final size:27
Alignment explanation
Indices: 49034455--49034515 Score: 70
Period size: 28 Copynumber: 2.2 Consensus size: 27
49034445 TTTTTTACAG
**
49034455 AAATAGTATAGAAAAAAAAAAATACTG
1 AAATAGTATAGAAAAAAAAAAATACCA
*
49034482 AAATAGTAT-GATAGAAAAAAAATTACCA
1 AAATAGTATAGA-A-AAAAAAAAATACCA
49034510 AAATAG
1 AAATAG
49034516 GTTACTTTTT
Statistics
Matches: 29, Mismatches: 3, Indels: 3
0.83 0.09 0.09
Matches are distributed among these distances:
26 2 0.07
27 10 0.34
28 17 0.59
ACGTcount: A:0.64, C:0.05, G:0.11, T:0.20
Consensus pattern (27 bp):
AAATAGTATAGAAAAAAAAAAATACCA
Found at i:49034689 original size:13 final size:13
Alignment explanation
Indices: 49034671--49034716 Score: 51
Period size: 13 Copynumber: 3.5 Consensus size: 13
49034661 GTAGGCGCCA
49034671 ATGGAGGAGCCTC
1 ATGGAGGAGCCTC
49034684 ATGGA-GAGGCGC-C
1 ATGGAGGA-GC-CTC
49034697 AATGGAGGAGCCTC
1 -ATGGAGGAGCCTC
49034711 ATGGAG
1 ATGGAG
49034717 AGGCGCCAAT
Statistics
Matches: 28, Mismatches: 0, Indels: 10
0.74 0.00 0.26
Matches are distributed among these distances:
12 2 0.07
13 15 0.54
14 9 0.32
15 2 0.07
ACGTcount: A:0.26, C:0.20, G:0.41, T:0.13
Consensus pattern (13 bp):
ATGGAGGAGCCTC
Found at i:49034693 original size:27 final size:27
Alignment explanation
Indices: 49034663--49034728 Score: 132
Period size: 27 Copynumber: 2.4 Consensus size: 27
49034653 CCTGTCTAGT
49034663 AGGCGCCAATGGAGGAGCCTCATGGAG
1 AGGCGCCAATGGAGGAGCCTCATGGAG
49034690 AGGCGCCAATGGAGGAGCCTCATGGAG
1 AGGCGCCAATGGAGGAGCCTCATGGAG
49034717 AGGCGCCAATGG
1 AGGCGCCAATGG
49034729 TGCCCTCTGC
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 39 1.00
ACGTcount: A:0.26, C:0.23, G:0.41, T:0.11
Consensus pattern (27 bp):
AGGCGCCAATGGAGGAGCCTCATGGAG
Found at i:49035065 original size:22 final size:21
Alignment explanation
Indices: 49035039--49035329 Score: 125
Period size: 22 Copynumber: 13.0 Consensus size: 21
49035029 TAGATTAGAA
*
49035039 TTTTGTATGAATATTTTAACTT
1 TTTTGTATGAATATTATAA-TT
49035061 TTTTGTATGAATATTATAATT
1 TTTTGTATGAATATTATAATT
*
49035082 TTTT-TATGAATATTGTAA--
1 TTTTGTATGAATATTATAATT
* *
49035100 TGTTGTATGAATATTGTAATT
1 TTTTGTATGAATATTATAATT
*
49035121 ATTT-TAT--A-ATTA-AATT
1 TTTTGTATGAATATTATAATT
**
49035137 TGTATT-TATAGTTTTGGATTAGTAATT
1 T-T-TTGTAT-G-AAT--ATTA-TAATT
*
49035164 TTTTGTATGAATATTGTAATTTTGT
1 TTTTGTATGAATATTATAA---T-T
49035189 AATTTTGTATGAATATTGCA-AATT
1 --TTTTGTATGAATATT--ATAATT
*
49035213 TTTTGTATGAATATTGTAATTTTGT
1 TTTTGTATGAATATTATAA---T-T
*
49035238 AATTTTGTATGAATATTATATTT
1 --TTTTGTATGAATATTATAATT
*
49035261 TTTTGTATGAATATTGTAATATTATAA
1 TTTTGTATGAATA-T-T-ATA--AT-T
**
49035288 TTTTGTATGAATATTGCAATTT
1 TTTTGTATGAATATTATAA-TT
*
49035310 TTTTGTATGAATATTGTAAT
1 TTTTGTATGAATATTATAAT
49035330 ATTGTAATTT
Statistics
Matches: 211, Mismatches: 21, Indels: 75
0.69 0.07 0.24
Matches are distributed among these distances:
16 4 0.02
17 4 0.02
18 9 0.04
19 14 0.07
20 16 0.08
21 27 0.13
22 56 0.27
23 3 0.01
24 9 0.04
25 11 0.05
26 6 0.03
27 50 0.24
28 2 0.01
ACGTcount: A:0.31, C:0.01, G:0.13, T:0.55
Consensus pattern (21 bp):
TTTTGTATGAATATTATAATT
Found at i:49035089 original size:20 final size:20
Alignment explanation
Indices: 49035039--49035411 Score: 117
Period size: 27 Copynumber: 16.4 Consensus size: 20
49035029 TAGATTAGAA
* *
49035039 TTTTGTATGAATATTTTAACT
1 TTTTTTATGAATATTGTAA-T
*
49035060 TTTTTGTATGAATATTATAAT
1 TTTTT-TATGAATATTGTAAT
49035081 TTTTTTATGAATATTGTAA-
1 TTTTTTATGAATATTGTAAT
* *
49035100 TGTTGTATGAATATTGTAAT
1 TTTTTTATGAATATTGTAAT
*
49035120 TATTTTAT-AATTAAATTTGT-AT
1 TTTTTTATGAA-T--A-TTGTAAT
* *
49035142 TTATAGTTT-TGGAT-TAGTAAT
1 TT-T--TTTATGAATATTGTAAT
49035163 TTTTTGTATGAATATTGTAATTTT
1 TTTTT-TATGAATATTGTAA---T
*
49035187 GTAATTTTGTATGAATATTGCAAAT
1 -T--TTTT-TATGAATATTG-TAAT
49035212 TTTTTGTATGAATATTGTAATTTT
1 TTTTT-TATGAATATTGTAA---T
* *
49035236 GTAATTTTGTATGAATATTATATT
1 -T--TTTT-TATGAATATTGTAAT
49035260 TTTTTGTATGAATATTGTAATATT
1 TTTTT-TATGAATATTGT-A-A-T
*
49035284 ATAATTTTGTATGAATATTGCAATT
1 -T--TTTT-TATGAATATTGTAA-T
49035309 TTTTTGTATGAATATTGTAATATT
1 TTTTT-TATGAATATTGT-A-A-T
49035333 GTAATTTTGTATGAATATTGTAAT
1 -T--TTTT-TATGAATATTGTAAT
** *
49035357 GTGGGGATATATTGTAATATTGTAAT
1 -T---TTTTTA-TG-AATATTGTAAT
49035383 TTTTTGTATGAATATTGTAAT
1 TTTTT-TATGAATATTGTAAT
*
49035404 TATTTTAT
1 TTTTTTAT
49035412 AATTAATTTG
Statistics
Matches: 281, Mismatches: 29, Indels: 85
0.71 0.07 0.22
Matches are distributed among these distances:
18 2 0.01
19 20 0.07
20 31 0.11
21 52 0.19
22 53 0.19
23 9 0.03
24 16 0.06
25 17 0.06
26 13 0.05
27 66 0.23
28 2 0.01
ACGTcount: A:0.31, C:0.01, G:0.14, T:0.55
Consensus pattern (20 bp):
TTTTTTATGAATATTGTAAT
Found at i:49035110 original size:19 final size:19
Alignment explanation
Indices: 49035063--49035119 Score: 78
Period size: 19 Copynumber: 2.9 Consensus size: 19
49035053 TTTAACTTTT
* *
49035063 TTGTATGAATATTATAATTT
1 TTGTATGAATATTGTAA-TG
*
49035083 TTTTATGAATATTGTAATG
1 TTGTATGAATATTGTAATG
49035102 TTGTATGAATATTGTAAT
1 TTGTATGAATATTGTAAT
49035120 TATTTTATAA
Statistics
Matches: 33, Mismatches: 4, Indels: 1
0.87 0.11 0.03
Matches are distributed among these distances:
19 18 0.55
20 15 0.45
ACGTcount: A:0.33, C:0.00, G:0.14, T:0.53
Consensus pattern (19 bp):
TTGTATGAATATTGTAATG
Found at i:49035198 original size:27 final size:26
Alignment explanation
Indices: 49035164--49035356 Score: 223
Period size: 27 Copynumber: 7.8 Consensus size: 26
49035154 ATTAGTAATT
*
49035164 TTTTGTATGAATATTGTAATTTTGTAA
1 TTTTGTATGAATATTGTAATATT-TAA
*
49035191 TTTTGTATGAATATTGCAA-A-TT--
1 TTTTGTATGAATATTGTAATATTTAA
*
49035213 TTTTGTATGAATATTGTAATTTTGTAA
1 TTTTGTATGAATATTGTAATATT-TAA
49035240 TTTTGTATGAATA-T-T-ATATTT--
1 TTTTGTATGAATATTGTAATATTTAA
49035261 TTTTGTATGAATATTGTAATATTATAA
1 TTTTGTATGAATATTGTAATATT-TAA
*
49035288 TTTTGTATGAATATTG-CA-ATTT--
1 TTTTGTATGAATATTGTAATATTTAA
49035310 TTTTGTATGAATATTGTAATATTGTAA
1 TTTTGTATGAATATTGTAATATT-TAA
49035337 TTTTGTATGAATATTGTAAT
1 TTTTGTATGAATATTGTAAT
49035357 GTGGGGATAT
Statistics
Matches: 143, Mismatches: 7, Indels: 32
0.79 0.04 0.18
Matches are distributed among these distances:
21 13 0.09
22 35 0.24
23 3 0.02
24 15 0.10
25 8 0.06
26 2 0.01
27 67 0.47
ACGTcount: A:0.31, C:0.01, G:0.13, T:0.54
Consensus pattern (26 bp):
TTTTGTATGAATATTGTAATATTTAA
Found at i:49035213 original size:49 final size:49
Alignment explanation
Indices: 49035160--49035399 Score: 321
Period size: 49 Copynumber: 5.0 Consensus size: 49
49035150 TTGGATTAGT
*
49035160 AATTTTTTGTATGAATATTGTAATTTTGTAATTTTGTATGAATATTGCA
1 AATTTTTTGTATGAATATTGTAATATTGTAATTTTGTATGAATATTGCA
*
49035209 AATTTTTTGTATGAATATTGTAATTTTGTAATTTTGTATGAATATT--A
1 AATTTTTTGTATGAATATTGTAATATTGTAATTTTGTATGAATATTGCA
* *
49035256 TATTTTTTTGTATGAATATTGTAATATTATAATTTTGTATGAATATTGCA
1 -AATTTTTTGTATGAATATTGTAATATTGTAATTTTGTATGAATATTGCA
* *
49035306 ATTTTTTTGTATGAATATTGTAATATTGTAATTTTGTATGAATATTG-T
1 AATTTTTTGTATGAATATTGTAATATTGTAATTTTGTATGAATATTGCA
* ** *
49035354 AA-TGTGGGGAT--ATATTGTAATATTGTAATTTTTTGTATGAATATTG
1 AATTTTTTGTATGAATATTGTAATATTGTAA--TTTTGTATGAATATTG
49035400 TAATTATTTT
Statistics
Matches: 176, Mismatches: 10, Indels: 12
0.89 0.05 0.06
Matches are distributed among these distances:
45 17 0.10
47 22 0.12
48 44 0.25
49 92 0.52
50 1 0.01
ACGTcount: A:0.31, C:0.01, G:0.15, T:0.53
Consensus pattern (49 bp):
AATTTTTTGTATGAATATTGTAATATTGTAATTTTGTATGAATATTGCA
Found at i:49035277 original size:97 final size:97
Alignment explanation
Indices: 49035162--49035351 Score: 344
Period size: 97 Copynumber: 2.0 Consensus size: 97
49035152 GGATTAGTAA
* *
49035162 TTTTTTGTATGAATATTGTAATTTTGTAATTTTGTATGAATATTGCAAATTTTTTGTATGAATAT
1 TTTTTTGTATGAATATTGTAATATTATAATTTTGTATGAATATTGCAAATTTTTTGTATGAATAT
*
49035227 TGTAATTTTGTAATTTTGTATGAATATTATAT
66 TGTAATATTGTAATTTTGTATGAATATTATAT
*
49035259 TTTTTTGTATGAATATTGTAATATTATAATTTTGTATGAATATTGCAATTTTTTTGTATGAATAT
1 TTTTTTGTATGAATATTGTAATATTATAATTTTGTATGAATATTGCAAATTTTTTGTATGAATAT
49035324 TGTAATATTGTAATTTTGTATGAATATT
66 TGTAATATTGTAATTTTGTATGAATATT
49035352 GTAATGTGGG
Statistics
Matches: 89, Mismatches: 4, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
97 89 1.00
ACGTcount: A:0.31, C:0.01, G:0.13, T:0.55
Consensus pattern (97 bp):
TTTTTTGTATGAATATTGTAATATTATAATTTTGTATGAATATTGCAAATTTTTTGTATGAATAT
TGTAATATTGTAATTTTGTATGAATATTATAT
Found at i:49035302 original size:19 final size:19
Alignment explanation
Indices: 49035278--49035335 Score: 53
Period size: 22 Copynumber: 2.9 Consensus size: 19
49035268 TGAATATTGT
49035278 AATATTATAATTTTGTATG
1 AATATTATAATTTTGTATG
**
49035297 AATATTGCAATTTTTTTGTATG
1 AATATT---ATAATTTTGTATG
* *
49035319 AATATTGTAATATTGTA
1 AATATTATAATTTTGTA
49035336 ATTTTGTATG
Statistics
Matches: 30, Mismatches: 6, Indels: 6
0.71 0.14 0.14
Matches are distributed among these distances:
19 13 0.43
22 17 0.57
ACGTcount: A:0.34, C:0.02, G:0.12, T:0.52
Consensus pattern (19 bp):
AATATTATAATTTTGTATG
Found at i:49035349 original size:19 final size:19
Alignment explanation
Indices: 49035278--49035356 Score: 66
Period size: 19 Copynumber: 4.6 Consensus size: 19
49035268 TGAATATTGT
*
49035278 AATATTATAATTTTGTATG
1 AATATTGTAATTTTGTATG
* *
49035297 AATATTGCAATTTT-TTTG
1 AATATTGTAATTTTGTATG
*
49035315 --TA-TG-AATATTG--T-
1 AATATTGTAATTTTGTATG
49035327 AATATTGTAATTTTGTATG
1 AATATTGTAATTTTGTATG
49035346 AATATTGTAAT
1 AATATTGTAAT
49035357 GTGGGGATAT
Statistics
Matches: 47, Mismatches: 5, Indels: 16
0.69 0.07 0.24
Matches are distributed among these distances:
13 1 0.02
14 7 0.15
15 4 0.09
16 8 0.17
18 4 0.09
19 23 0.49
ACGTcount: A:0.34, C:0.01, G:0.13, T:0.52
Consensus pattern (19 bp):
AATATTGTAATTTTGTATG
Done.