Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr07 ID=Chr07-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: 60982465
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 868082 characters in sequence are not A, C, G, or T
File 165 of 204
Found at i:49339688 original size:24 final size:24
Alignment explanation
Indices: 49339661--49339724 Score: 83
Period size: 24 Copynumber: 2.7 Consensus size: 24
49339651 GATGCCAAGT
* *
49339661 GTGGAGATGAAAATTAGTACTAGG
1 GTGGAGATGAAAATGAGTACGAGG
*
49339685 GTGGAGATGAAGATGAGTACGAGG
1 GTGGAGATGAAAATGAGTACGAGG
* *
49339709 GTGGAGGTGAAGATGA
1 GTGGAGATGAAAATGA
49339725 AGAAGATGAT
Statistics
Matches: 36, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
24 36 1.00
ACGTcount: A:0.34, C:0.03, G:0.42, T:0.20
Consensus pattern (24 bp):
GTGGAGATGAAAATGAGTACGAGG
Found at i:49341880 original size:19 final size:18
Alignment explanation
Indices: 49341858--49341903 Score: 56
Period size: 19 Copynumber: 2.4 Consensus size: 18
49341848 TGAGAGGTAG
*
49341858 TTTCTTTATTCTTTTTTTA
1 TTTCTTTATT-TTATTTTA
49341877 TTTCGTTTATTTTATTTTA
1 TTTC-TTTATTTTATTTTA
*
49341896 TTTTTTTA
1 TTTCTTTA
49341904 AAGAAGGAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
18 4 0.17
19 14 0.58
20 6 0.25
ACGTcount: A:0.13, C:0.07, G:0.02, T:0.78
Consensus pattern (18 bp):
TTTCTTTATTTTATTTTA
Found at i:49343271 original size:131 final size:131
Alignment explanation
Indices: 49343125--49343396 Score: 472
Period size: 131 Copynumber: 2.1 Consensus size: 131
49343115 GAAAATCTTG
*
49343125 AAAATAAAGGCAATATTCCATATTTAAAAATTCGAGAAGTTGTGCCCTAACTTACTAGGTTTCGA
1 AAAATAAAGGAAATATTCCATATTTAAAAATTCGAGAAGTTGTGCCCTAACTTACTAGGTTTCGA
*
49343190 TTTTTCTCGCGTTGAACCTAAATAACCGAATATCCTTTTAAAACTAAAATAAATGTGTTTTAAAT
66 TTTTTCTCGCGTTGAACCTAAATAACCGAAAATCCTTTTAAAACTAAAATAAATGTGTTTTAAAT
49343255 A
131 A
* * ** *
49343256 AAAATAAAGGAAATATTTCGTATTTGGAAATTCGAGAAGTTGTGCCCTAACTTACTGGGTTTCGA
1 AAAATAAAGGAAATATTCCATATTTAAAAATTCGAGAAGTTGTGCCCTAACTTACTAGGTTTCGA
49343321 TTTTTCTCGCGTTGAACCTAAATAACCGAAAATCCTTTTAAAACTAAAATAAATGTGTTTTAAAT
66 TTTTTCTCGCGTTGAACCTAAATAACCGAAAATCCTTTTAAAACTAAAATAAATGTGTTTTAAAT
49343386 A
131 A
*
49343387 AAAACAAAGG
1 AAAATAAAGG
49343397 CGAGCTTATT
Statistics
Matches: 133, Mismatches: 8, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
131 133 1.00
ACGTcount: A:0.39, C:0.14, G:0.14, T:0.33
Consensus pattern (131 bp):
AAAATAAAGGAAATATTCCATATTTAAAAATTCGAGAAGTTGTGCCCTAACTTACTAGGTTTCGA
TTTTTCTCGCGTTGAACCTAAATAACCGAAAATCCTTTTAAAACTAAAATAAATGTGTTTTAAAT
A
Found at i:49351122 original size:26 final size:26
Alignment explanation
Indices: 49351092--49351145 Score: 65
Period size: 26 Copynumber: 2.1 Consensus size: 26
49351082 ATTATAAAAA
49351092 TAAGAA-GAATAATATAAAAATATATG
1 TAAGAATGAAT-ATATAAAAATATATG
* * *
49351118 TAAGAATGTATATATACATATATATG
1 TAAGAATGAATATATAAAAATATATG
49351144 TA
1 TA
49351146 TGTAAATTAA
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
26 21 0.88
27 3 0.12
ACGTcount: A:0.54, C:0.02, G:0.11, T:0.33
Consensus pattern (26 bp):
TAAGAATGAATATATAAAAATATATG
Found at i:49353315 original size:13 final size:14
Alignment explanation
Indices: 49353287--49353313 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
49353277 ATTGTATCAT
49353287 TTAATATAAAAAAA
1 TTAATATAAAAAAA
49353301 TTAATATAAAAAA
1 TTAATATAAAAAA
49353314 TTGATTCGCG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (14 bp):
TTAATATAAAAAAA
Found at i:49353485 original size:38 final size:38
Alignment explanation
Indices: 49353443--49353520 Score: 138
Period size: 38 Copynumber: 2.1 Consensus size: 38
49353433 TTACATGTAT
*
49353443 AAAAGAAGCATGTGTGAACTTAGTAAATGTTAGGATAC
1 AAAAGAAGCATGTGTGAACTTAGTAAATGTTAAGATAC
*
49353481 AAAAGATGCATGTGTGAACTTAGTAAATGTTAAGATAC
1 AAAAGAAGCATGTGTGAACTTAGTAAATGTTAAGATAC
49353519 AA
1 AA
49353521 TTGGAATGCC
Statistics
Matches: 38, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
38 38 1.00
ACGTcount: A:0.44, C:0.08, G:0.22, T:0.27
Consensus pattern (38 bp):
AAAAGAAGCATGTGTGAACTTAGTAAATGTTAAGATAC
Found at i:49355755 original size:31 final size:30
Alignment explanation
Indices: 49355717--49355830 Score: 108
Period size: 31 Copynumber: 3.8 Consensus size: 30
49355707 TAGGCATCAA
*
49355717 TATTCATATTTGCATTATCATACCCTATAAT
1 TATTCACATTTGCA-TATCATACCCTATAAT
*
49355748 TATTCATATTTGCATATTCATACCCTAT-AT
1 TATTCACATTTGCATA-TCATACCCTATAAT
* *
49355778 TCATTCACA--TACATATCATACCCTGTAAT
1 T-ATTCACATTTGCATATCATACCCTATAAT
* * *
49355807 TTTTCACGTTTGCATTTTCATACC
1 TATTCACATTTGCA-TATCATACC
49355831 TTGTACATTG
Statistics
Matches: 70, Mismatches: 7, Indels: 12
0.79 0.08 0.13
Matches are distributed among these distances:
28 15 0.21
29 8 0.11
30 8 0.11
31 39 0.56
ACGTcount: A:0.29, C:0.23, G:0.04, T:0.44
Consensus pattern (30 bp):
TATTCACATTTGCATATCATACCCTATAAT
Found at i:49357168 original size:26 final size:26
Alignment explanation
Indices: 49357121--49357170 Score: 66
Period size: 26 Copynumber: 1.9 Consensus size: 26
49357111 AAACTCTTCT
* *
49357121 AAAAGAAAACTTAAGAGAAATTTTTA
1 AAAAGAAAACTCAAGAAAAATTTTTA
49357147 AAAAGAAAACTCAA-AAATAATTTT
1 AAAAGAAAACTCAAGAAA-AATTTT
49357171 ATTAAGTGAA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
25 2 0.10
26 19 0.90
ACGTcount: A:0.60, C:0.06, G:0.08, T:0.26
Consensus pattern (26 bp):
AAAAGAAAACTCAAGAAAAATTTTTA
Found at i:49368578 original size:11 final size:11
Alignment explanation
Indices: 49368564--49368641 Score: 74
Period size: 11 Copynumber: 7.4 Consensus size: 11
49368554 TTTTTTTTAA
49368564 TTTTAAAATAT
1 TTTTAAAATAT
49368575 TTTTAAAATAT
1 TTTTAAAATAT
** *
49368586 TTTTTTATTAT
1 TTTTAAAATAT
*
49368597 TTTT----TAA
1 TTTTAAAATAT
49368604 TTTTAAAATAT
1 TTTTAAAATAT
*
49368615 TTTTAAAATGT
1 TTTTAAAATAT
49368626 TTTTAAAATACT
1 TTTTAAAATA-T
49368638 TTTT
1 TTTT
49368642 TTAATTTTTA
Statistics
Matches: 55, Mismatches: 7, Indels: 9
0.77 0.10 0.13
Matches are distributed among these distances:
7 6 0.11
11 44 0.80
12 5 0.09
ACGTcount: A:0.36, C:0.01, G:0.01, T:0.62
Consensus pattern (11 bp):
TTTTAAAATAT
Found at i:49368601 original size:40 final size:40
Alignment explanation
Indices: 49368544--49368656 Score: 156
Period size: 40 Copynumber: 2.8 Consensus size: 40
49368534 TAAATATATT
49368544 TATTTTTTAATT-TTTTTTAATTTTAAAATATTTTTAAAA
1 TATTTTTTAATTATTTTTTAATTTTAAAATATTTTTAAAA
*
49368583 TATTTTTTTATTATTTTTTAATTTTAAAATATTTTTAAAA
1 TATTTTTTAATTATTTTTTAATTTTAAAATATTTTTAAAA
* * *
49368623 TGTTTTTAAAATACTTTTTTTAATTTTTAAAATA
1 TATTTTTTAATTA--TTTTTTAA-TTTTAAAATA
49368657 AATTTTTGGT
Statistics
Matches: 65, Mismatches: 5, Indels: 4
0.88 0.07 0.05
Matches are distributed among these distances:
39 11 0.17
40 36 0.55
42 8 0.12
43 10 0.15
ACGTcount: A:0.35, C:0.01, G:0.01, T:0.63
Consensus pattern (40 bp):
TATTTTTTAATTATTTTTTAATTTTAAAATATTTTTAAAA
Found at i:49368662 original size:21 final size:20
Alignment explanation
Indices: 49368556--49368663 Score: 62
Period size: 21 Copynumber: 5.2 Consensus size: 20
49368546 TTTTTTAATT
49368556 TTTTTTAA-TTTTAAAAT-A
1 TTTTTTAATTTTTAAAATAA
* *** *
49368574 TTTTTAAAATATTTTTTTATTA
1 TTTTT-TAAT-TTTTAAAATAA
49368596 TTTTTTAA-TTTTAAAAT-A
1 TTTTTTAATTTTTAAAATAA
* *
49368614 TTTTTAAAATGTTTTTAAAATACT
1 TTTTT-TAA--TTTTTAAAATA-A
49368638 TTTTTTAATTTTTAAAATAAA
1 TTTTTTAATTTTTAAAAT-AA
49368659 TTTTT
1 TTTTT
49368664 GGTATTTATT
Statistics
Matches: 67, Mismatches: 12, Indels: 19
0.68 0.12 0.19
Matches are distributed among these distances:
18 11 0.16
19 10 0.15
21 23 0.34
22 16 0.24
23 2 0.03
24 5 0.07
ACGTcount: A:0.36, C:0.01, G:0.01, T:0.62
Consensus pattern (20 bp):
TTTTTTAATTTTTAAAATAA
Found at i:49382121 original size:17 final size:19
Alignment explanation
Indices: 49382101--49382145 Score: 67
Period size: 19 Copynumber: 2.4 Consensus size: 19
49382091 TTAAAATAGT
49382101 AACAAAATTA-ACAATAA-
1 AACAAAATTATACAATAAC
49382118 AACAAAAGTTATACAATAAC
1 AACAAAA-TTATACAATAAC
49382138 AACAAAAT
1 AACAAAAT
49382146 AGTAGCAATA
Statistics
Matches: 25, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
17 7 0.28
18 3 0.12
19 8 0.32
20 7 0.28
ACGTcount: A:0.67, C:0.13, G:0.02, T:0.18
Consensus pattern (19 bp):
AACAAAATTATACAATAAC
Found at i:49383051 original size:2 final size:2
Alignment explanation
Indices: 49383044--49383087 Score: 88
Period size: 2 Copynumber: 22.0 Consensus size: 2
49383034 TCACTACTTC
49383044 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
49383086 AT
1 AT
49383088 TGCTTGTAAA
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 42 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:49394242 original size:9 final size:9
Alignment explanation
Indices: 49394224--49394297 Score: 51
Period size: 9 Copynumber: 8.2 Consensus size: 9
49394214 GAAAATGGGA
*
49394224 CCAGGTGGG
1 CCAGGAGGG
49394233 CCAGGAGGG
1 CCAGGAGGG
*
49394242 CCACCG-GGG
1 CCA-GGAGGG
* *
49394251 CCAGGTGGA
1 CCAGGAGGG
49394260 CCAGGAGGG
1 CCAGGAGGG
* ***
49394269 TCTCCAGGG
1 CCAGGAGGG
*
49394278 CCAGGAGGA
1 CCAGGAGGG
49394287 CCAGGAGGG
1 CCAGGAGGG
49394296 CC
1 CC
49394298 TCCAGGATGG
Statistics
Matches: 47, Mismatches: 16, Indels: 4
0.70 0.24 0.06
Matches are distributed among these distances:
8 1 0.02
9 45 0.96
10 1 0.02
ACGTcount: A:0.19, C:0.28, G:0.47, T:0.05
Consensus pattern (9 bp):
CCAGGAGGG
Found at i:49394254 original size:27 final size:27
Alignment explanation
Indices: 49394224--49394303 Score: 106
Period size: 27 Copynumber: 3.0 Consensus size: 27
49394214 GAAAATGGGA
* *
49394224 CCAGGTGGGCCAGGAGGGCCACCGGGG
1 CCAGGTGGACCAGGAGGGCCACCAGGG
* *
49394251 CCAGGTGGACCAGGAGGGTCTCCAGGG
1 CCAGGTGGACCAGGAGGGCCACCAGGG
* *
49394278 CCAGGAGGACCAGGAGGGCCTCCAGG
1 CCAGGTGGACCAGGAGGGCCACCAGG
49394304 ATGGGGCGGT
Statistics
Matches: 47, Mismatches: 6, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
27 47 1.00
ACGTcount: A:0.19, C:0.29, G:0.46, T:0.06
Consensus pattern (27 bp):
CCAGGTGGACCAGGAGGGCCACCAGGG
Found at i:49394448 original size:39 final size:39
Alignment explanation
Indices: 49394284--49394435 Score: 234
Period size: 39 Copynumber: 3.9 Consensus size: 39
49394274 AGGGCCAGGA
* * * *
49394284 GGACCAGGAGGGCCTCCAGGATGGGGCGGTCCTGCACCC
1 GGACCAGGAGGGCCACCGGGGTGGGGCGGTCCTCCACCC
*
49394323 GGACCAGGAGGGCCACCGGGATGGGGCGGTCCTCCACCC
1 GGACCAGGAGGGCCACCGGGGTGGGGCGGTCCTCCACCC
49394362 GGACCAGGAGGGCCACCGGGGTGGGGCGGTCCTCCACCC
1 GGACCAGGAGGGCCACCGGGGTGGGGCGGTCCTCCACCC
*
49394401 GGACCAGG-GGGACCACCGGGGTGGGGCGGCCCTCC
1 GGACCAGGAGGG-CCACCGGGGTGGGGCGGTCCTCC
49394436 GGTCGGACCA
Statistics
Matches: 107, Mismatches: 5, Indels: 2
0.94 0.04 0.02
Matches are distributed among these distances:
38 3 0.03
39 104 0.97
ACGTcount: A:0.14, C:0.35, G:0.43, T:0.08
Consensus pattern (39 bp):
GGACCAGGAGGGCCACCGGGGTGGGGCGGTCCTCCACCC
Found at i:49395994 original size:2 final size:2
Alignment explanation
Indices: 49395987--49396022 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
49395977 GTGATTCGAT
49395987 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
49396023 ACATTGATAA
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:49397377 original size:21 final size:20
Alignment explanation
Indices: 49397340--49397382 Score: 52
Period size: 21 Copynumber: 2.1 Consensus size: 20
49397330 TGAAAATATA
*
49397340 TTAAATATATACTTTTATGT
1 TTAAATATATACTTTTAAGT
49397360 TTAAA-ATATACTAGTTTAAGT
1 TTAAATATATACT--TTTAAGT
49397381 TT
1 TT
49397383 TTTATGTTTT
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
19 7 0.35
20 5 0.25
21 8 0.40
ACGTcount: A:0.37, C:0.05, G:0.07, T:0.51
Consensus pattern (20 bp):
TTAAATATATACTTTTAAGT
Found at i:49397395 original size:16 final size:16
Alignment explanation
Indices: 49397374--49397407 Score: 68
Period size: 16 Copynumber: 2.1 Consensus size: 16
49397364 AATATACTAG
49397374 TTTAAGTTTTTTATGT
1 TTTAAGTTTTTTATGT
49397390 TTTAAGTTTTTTATGT
1 TTTAAGTTTTTTATGT
49397406 TT
1 TT
49397408 AAAAAATATA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.18, C:0.00, G:0.12, T:0.71
Consensus pattern (16 bp):
TTTAAGTTTTTTATGT
Found at i:49397575 original size:19 final size:18
Alignment explanation
Indices: 49397532--49397576 Score: 90
Period size: 18 Copynumber: 2.5 Consensus size: 18
49397522 CTTATTTGTT
49397532 TACAAAAATATTTGATAA
1 TACAAAAATATTTGATAA
49397550 TACAAAAATATTTGATAA
1 TACAAAAATATTTGATAA
49397568 TACAAAAAT
1 TACAAAAAT
49397577 GTAAACTAAT
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:0.58, C:0.07, G:0.04, T:0.31
Consensus pattern (18 bp):
TACAAAAATATTTGATAA
Found at i:49397661 original size:16 final size:16
Alignment explanation
Indices: 49397640--49397681 Score: 66
Period size: 16 Copynumber: 2.6 Consensus size: 16
49397630 AATAATTTAA
*
49397640 TAATTTTACTAACAAT
1 TAATTTTAATAACAAT
49397656 TAATTTTAATAACAAT
1 TAATTTTAATAACAAT
*
49397672 TAGTTTTAAT
1 TAATTTTAAT
49397682 TTTATCAAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
16 24 1.00
ACGTcount: A:0.43, C:0.07, G:0.02, T:0.48
Consensus pattern (16 bp):
TAATTTTAATAACAAT
Found at i:49402714 original size:28 final size:28
Alignment explanation
Indices: 49402646--49402703 Score: 116
Period size: 28 Copynumber: 2.1 Consensus size: 28
49402636 AGGAGGAGAG
49402646 AGACACACATTAGCTTAGTTTTAGCCTT
1 AGACACACATTAGCTTAGTTTTAGCCTT
49402674 AGACACACATTAGCTTAGTTTTAGCCTT
1 AGACACACATTAGCTTAGTTTTAGCCTT
49402702 AG
1 AG
49402704 TTTTCTCTTA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 30 1.00
ACGTcount: A:0.29, C:0.21, G:0.16, T:0.34
Consensus pattern (28 bp):
AGACACACATTAGCTTAGTTTTAGCCTT
Found at i:49403920 original size:2 final size:2
Alignment explanation
Indices: 49403908--49403940 Score: 52
Period size: 2 Copynumber: 17.5 Consensus size: 2
49403898 CATAATTTAA
49403908 AT AT A- AT AT AT AT AT AT AT AT AT AT AT AT -T AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
49403941 ATCACATATA
Statistics
Matches: 29, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
1 2 0.07
2 27 0.93
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:49404112 original size:26 final size:27
Alignment explanation
Indices: 49404083--49404144 Score: 81
Period size: 26 Copynumber: 2.3 Consensus size: 27
49404073 GGTAATGGAA
*
49404083 AGGCGGCACCAAAGGTGCCTTTC-GAT
1 AGGCGGCACCAAAGGTGCCTTTCTCAT
* * *
49404109 AGGCAGCACCGATGGTGCCTTTCTCAT
1 AGGCGGCACCAAAGGTGCCTTTCTCAT
49404136 AGGCGGCAC
1 AGGCGGCAC
49404145 AGGACTAAAA
Statistics
Matches: 30, Mismatches: 5, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
26 20 0.67
27 10 0.33
ACGTcount: A:0.21, C:0.29, G:0.31, T:0.19
Consensus pattern (27 bp):
AGGCGGCACCAAAGGTGCCTTTCTCAT
Found at i:49406484 original size:14 final size:15
Alignment explanation
Indices: 49406462--49406538 Score: 52
Period size: 14 Copynumber: 5.0 Consensus size: 15
49406452 CAATCAAACA
49406462 CCAGAAAAT-ATTTT
1 CCAGAAAATCATTTT
*
49406476 CCAGTAAATCATTTT
1 CCAGAAAATCATTTT
*
49406491 ACAGAAAAGTATAACATTTT
1 CCAG-AAA--AT--CATTTT
*
49406511 CCCG-AAATCATTTT
1 CCAGAAAATCATTTT
*
49406525 ACAGAAAAT-ATTTT
1 CCAGAAAATCATTTT
49406539 ACTGGCAATC
Statistics
Matches: 49, Mismatches: 7, Indels: 14
0.70 0.10 0.20
Matches are distributed among these distances:
14 21 0.43
15 12 0.24
16 4 0.08
18 4 0.08
20 8 0.16
ACGTcount: A:0.42, C:0.16, G:0.08, T:0.35
Consensus pattern (15 bp):
CCAGAAAATCATTTT
Found at i:49411365 original size:4 final size:4
Alignment explanation
Indices: 49411351--49411405 Score: 83
Period size: 4 Copynumber: 13.8 Consensus size: 4
49411341 GTAGGGACGA
* * *
49411351 ATAC GTAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATTC ATAC ATAT
1 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC
49411399 ATAC ATA
1 ATAC ATA
49411406 TACATATATT
Statistics
Matches: 45, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
4 45 1.00
ACGTcount: A:0.47, C:0.22, G:0.02, T:0.29
Consensus pattern (4 bp):
ATAC
Found at i:49424402 original size:21 final size:21
Alignment explanation
Indices: 49424378--49424432 Score: 51
Period size: 20 Copynumber: 2.6 Consensus size: 21
49424368 TCAAAAAAAA
*
49424378 TTTTATGTTGCCTTTTTTTTTT
1 TTTTATGTT-CCTTTTCTTTTT
*
49424400 TTTTTTGTTCC-TTTCTTTTT
1 TTTTATGTTCCTTTTCTTTTT
*
49424420 ACTTT-TGTTCCTT
1 -TTTTATGTTCCTT
49424433 AATATCATAT
Statistics
Matches: 28, Mismatches: 3, Indels: 5
0.78 0.08 0.14
Matches are distributed among these distances:
20 14 0.50
21 6 0.21
22 8 0.29
ACGTcount: A:0.04, C:0.15, G:0.07, T:0.75
Consensus pattern (21 bp):
TTTTATGTTCCTTTTCTTTTT
Found at i:49424403 original size:22 final size:21
Alignment explanation
Indices: 49424378--49424432 Score: 58
Period size: 21 Copynumber: 2.6 Consensus size: 21
49424368 TCAAAAAAAA
*
49424378 TTTTATGTTGCCTTTTTTTTTT
1 TTTTATGTT-CCTTTCTTTTTT
* *
49424400 TTTTTTGTTCCTTTCTTTTTA
1 TTTTATGTTCCTTTCTTTTTT
*
49424421 CTTT-TGTTCCTT
1 TTTTATGTTCCTT
49424433 AATATCATAT
Statistics
Matches: 29, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
20 8 0.28
21 13 0.45
22 8 0.28
ACGTcount: A:0.04, C:0.15, G:0.07, T:0.75
Consensus pattern (21 bp):
TTTTATGTTCCTTTCTTTTTT
Found at i:49427443 original size:26 final size:25
Alignment explanation
Indices: 49427414--49427476 Score: 65
Period size: 26 Copynumber: 2.5 Consensus size: 25
49427404 AGTTTTGGAT
* *
49427414 ATTAAAAATATTTTAAATTTTAATTA
1 ATTAAAAATATTTAAAATGTTAA-TA
*
49427440 ATTATAAAACA-TTAAAATGTTAATA
1 ATTA-AAAATATTTAAAATGTTAATA
*
49427465 TTTAAAAATATT
1 ATTAAAAATATT
49427477 AAATATTTTT
Statistics
Matches: 30, Mismatches: 5, Indels: 5
0.75 0.12 0.12
Matches are distributed among these distances:
24 5 0.17
25 6 0.20
26 14 0.47
27 5 0.17
ACGTcount: A:0.52, C:0.02, G:0.02, T:0.44
Consensus pattern (25 bp):
ATTAAAAATATTTAAAATGTTAATA
Found at i:49441327 original size:6 final size:6
Alignment explanation
Indices: 49441318--49441347 Score: 60
Period size: 6 Copynumber: 5.0 Consensus size: 6
49441308 ATAAATTTAA
49441318 ATATTT ATATTT ATATTT ATATTT ATATTT
1 ATATTT ATATTT ATATTT ATATTT ATATTT
49441348 TTTATTAATT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 24 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (6 bp):
ATATTT
Found at i:49441856 original size:2 final size:2
Alignment explanation
Indices: 49441849--49441879 Score: 55
Period size: 2 Copynumber: 16.0 Consensus size: 2
49441839 AGAAGTGGGG
49441849 TA TA TA TA T- TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
49441880 AAGAAAATCC
Statistics
Matches: 28, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
1 1 0.04
2 27 0.96
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:49443387 original size:7 final size:7
Alignment explanation
Indices: 49443375--49443408 Score: 68
Period size: 7 Copynumber: 4.9 Consensus size: 7
49443365 GAACTTGAAG
49443375 TGAAAAC
1 TGAAAAC
49443382 TGAAAAC
1 TGAAAAC
49443389 TGAAAAC
1 TGAAAAC
49443396 TGAAAAC
1 TGAAAAC
49443403 TGAAAA
1 TGAAAA
49443409 TACCCTTCTA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 27 1.00
ACGTcount: A:0.59, C:0.12, G:0.15, T:0.15
Consensus pattern (7 bp):
TGAAAAC
Found at i:49443850 original size:12 final size:12
Alignment explanation
Indices: 49443833--49443857 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
49443823 GTTAGATGAG
49443833 GCAATGGAGGGA
1 GCAATGGAGGGA
49443845 GCAATGGAGGGA
1 GCAATGGAGGGA
49443857 G
1 G
49443858 GAGTTTGAGT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.32, C:0.08, G:0.52, T:0.08
Consensus pattern (12 bp):
GCAATGGAGGGA
Found at i:49459287 original size:27 final size:26
Alignment explanation
Indices: 49459235--49459287 Score: 61
Period size: 27 Copynumber: 2.0 Consensus size: 26
49459225 AAAAACCCCA
* * *
49459235 TTTTTCCTGTTTCTTTTCTTTCTTTC
1 TTTTTCCTCTTTCCTTTCTCTCTTTC
*
49459261 TTTTTCCTTCTTTCCTTTCTCTGTTTC
1 TTTTTCC-TCTTTCCTTTCTCTCTTTC
49459288 GTTTGCCTAT
Statistics
Matches: 22, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
26 7 0.32
27 15 0.68
ACGTcount: A:0.00, C:0.26, G:0.04, T:0.70
Consensus pattern (26 bp):
TTTTTCCTCTTTCCTTTCTCTCTTTC
Found at i:49459356 original size:14 final size:14
Alignment explanation
Indices: 49459337--49459367 Score: 53
Period size: 14 Copynumber: 2.2 Consensus size: 14
49459327 TTTATATTTA
49459337 AATAATAATAACAT
1 AATAATAATAACAT
*
49459351 AATAATAATAATAT
1 AATAATAATAACAT
49459365 AAT
1 AAT
49459368 TCTTTTACTT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.65, C:0.03, G:0.00, T:0.32
Consensus pattern (14 bp):
AATAATAATAACAT
Found at i:49459508 original size:17 final size:16
Alignment explanation
Indices: 49459486--49459541 Score: 59
Period size: 16 Copynumber: 3.8 Consensus size: 16
49459476 ACATAATATA
49459486 ATAATATATTTTATAAT
1 ATAATATA-TTTATAAT
49459503 ATAATATATTTATAAT
1 ATAATATATTTATAAT
*
49459519 -TAA-ATA-ATAT-AT
1 ATAATATATTTATAAT
49459531 -TAATATATTTA
1 ATAATATATTTA
49459542 AAACATAAAA
Statistics
Matches: 35, Mismatches: 2, Indels: 7
0.80 0.05 0.16
Matches are distributed among these distances:
12 5 0.14
13 6 0.17
14 5 0.14
15 3 0.09
16 8 0.23
17 8 0.23
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (16 bp):
ATAATATATTTATAAT
Found at i:49459525 original size:19 final size:16
Alignment explanation
Indices: 49459485--49459531 Score: 58
Period size: 17 Copynumber: 2.7 Consensus size: 16
49459475 TACATAATAT
49459485 AATAATATATTTTATA
1 AATAATATATTTTATA
49459501 ATATAATATATTTATAATTA
1 A-ATAATATATTT-T-A-TA
49459521 AATAATATATT
1 AATAATATATT
49459532 AATATATTTA
Statistics
Matches: 27, Mismatches: 0, Indels: 5
0.84 0.00 0.16
Matches are distributed among these distances:
16 1 0.04
17 11 0.41
18 1 0.04
19 11 0.41
20 3 0.11
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (16 bp):
AATAATATATTTTATA
Found at i:49464274 original size:17 final size:17
Alignment explanation
Indices: 49464241--49464274 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
49464231 TATTTTAGAT
*
49464241 TTTTTATATTTTATTTA
1 TTTTTATATATTATTTA
*
49464258 TTTTTATATATTCTTTA
1 TTTTTATATATTATTTA
49464275 GAATTTTTTA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.24, C:0.03, G:0.00, T:0.74
Consensus pattern (17 bp):
TTTTTATATATTATTTA
Found at i:49495946 original size:31 final size:30
Alignment explanation
Indices: 49495893--49495980 Score: 81
Period size: 30 Copynumber: 2.9 Consensus size: 30
49495883 TTTGGTACCT
* * *
49495893 ACAATTTTTTTTCAATTCGGTACTTAAACTTG
1 ACAATTTTTCTTAAATT-GGTACTTAAA-TTC
49495925 ACAATTTTTCTTAAATTGGTAC-TAAATTC
1 ACAATTTTTCTTAAATTGGTACTTAAATTC
* *
49495954 AGCACTTGTTTC-TAATTTGGTACTTAA
1 A-CAATT-TTTCTTAAATTGGTACTTAA
49495981 GCTTTTTTAG
Statistics
Matches: 48, Mismatches: 5, Indels: 7
0.80 0.08 0.12
Matches are distributed among these distances:
29 3 0.06
30 18 0.38
31 12 0.25
32 15 0.31
ACGTcount: A:0.30, C:0.15, G:0.10, T:0.45
Consensus pattern (30 bp):
ACAATTTTTCTTAAATTGGTACTTAAATTC
Found at i:49496278 original size:34 final size:35
Alignment explanation
Indices: 49496234--49496300 Score: 109
Period size: 34 Copynumber: 1.9 Consensus size: 35
49496224 CAGTAAAATG
49496234 TTTTCCGTAAAATGATTT-CTGGAAAATATTTTAC
1 TTTTCCGTAAAATGATTTACTGGAAAATATTTTAC
* *
49496268 TTTTCTGTAAAATGATTTATTGGAAAATATTTT
1 TTTTCCGTAAAATGATTTACTGGAAAATATTTT
49496301 CTGGTGTTTG
Statistics
Matches: 30, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
34 17 0.57
35 13 0.43
ACGTcount: A:0.33, C:0.07, G:0.12, T:0.48
Consensus pattern (35 bp):
TTTTCCGTAAAATGATTTACTGGAAAATATTTTAC
Found at i:49498814 original size:12 final size:12
Alignment explanation
Indices: 49498797--49498824 Score: 56
Period size: 12 Copynumber: 2.3 Consensus size: 12
49498787 TTTTCCAGAA
49498797 AACATTATATCG
1 AACATTATATCG
49498809 AACATTATATCG
1 AACATTATATCG
49498821 AACA
1 AACA
49498825 CACAAACGGC
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:0.46, C:0.18, G:0.07, T:0.29
Consensus pattern (12 bp):
AACATTATATCG
Found at i:49506040 original size:16 final size:16
Alignment explanation
Indices: 49506019--49506058 Score: 53
Period size: 16 Copynumber: 2.5 Consensus size: 16
49506009 TTTGGTTTGC
*
49506019 TGTAATGGAATAAAGG
1 TGTAATAGAATAAAGG
*
49506035 TGTAATAGAATAGAGG
1 TGTAATAGAATAAAGG
*
49506051 CGTAATAG
1 TGTAATAG
49506059 GTAATTCTTT
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
16 21 1.00
ACGTcount: A:0.42, C:0.03, G:0.30, T:0.25
Consensus pattern (16 bp):
TGTAATAGAATAAAGG
Found at i:49506121 original size:44 final size:46
Alignment explanation
Indices: 49506042--49506130 Score: 155
Period size: 44 Copynumber: 2.0 Consensus size: 46
49506032 AGGTGTAATA
*
49506042 GAATAGAGGCGTAATAGGTAATTCTTTTGTTTGGTTGAATGGAATT
1 GAATAGAGGCGTAATAGGTAATTCTTGTGTTTGGTTGAATGGAATT
49506088 GAATAGAGGCGTAAT-GGT-ATTCTTGTGTTTGGTTGAATGGAAT
1 GAATAGAGGCGTAATAGGTAATTCTTGTGTTTGGTTGAATGGAAT
49506131 AGAAGTGTAA
Statistics
Matches: 42, Mismatches: 1, Indels: 2
0.93 0.02 0.04
Matches are distributed among these distances:
44 24 0.57
45 3 0.07
46 15 0.36
ACGTcount: A:0.27, C:0.04, G:0.30, T:0.38
Consensus pattern (46 bp):
GAATAGAGGCGTAATAGGTAATTCTTGTGTTTGGTTGAATGGAATT
Found at i:49506312 original size:18 final size:18
Alignment explanation
Indices: 49506289--49506422 Score: 81
Period size: 18 Copynumber: 7.9 Consensus size: 18
49506279 TTATTATTAA
49506289 ATATAATTTAATAAAAAT
1 ATATAATTTAATAAAAAT
49506307 ATATAATTTAAT-AAAAT
1 ATATAATTTAATAAAAAT
*
49506324 ATATGAATTTACT-AAAAT
1 ATAT-AATTTAATAAAAAT
* * * *
49506342 -CATAATAT-ATAATACT
1 ATATAATTTAATAAAAAT
* * *
49506358 ATAAAATATAATTTAAAAT
1 ATATAATTTAA-TAAAAAT
* *
49506377 A-ATTA-TT-AT--TAA-
1 ATATAATTTAATAAAAAT
49506389 ATATAATTTAATAAAAAT
1 ATATAATTTAATAAAAAT
*
49506407 ATATAATTTGATAAAA
1 ATATAATTTAATAAAA
49506423 TCCTTAGTAT
Statistics
Matches: 87, Mismatches: 18, Indels: 22
0.69 0.14 0.17
Matches are distributed among these distances:
12 1 0.01
13 5 0.06
14 2 0.02
15 4 0.05
16 8 0.09
17 20 0.23
18 42 0.48
19 5 0.06
ACGTcount: A:0.57, C:0.02, G:0.01, T:0.40
Consensus pattern (18 bp):
ATATAATTTAATAAAAAT
Found at i:49506472 original size:61 final size:60
Alignment explanation
Indices: 49506323--49506505 Score: 203
Period size: 59 Copynumber: 3.0 Consensus size: 60
49506313 TTTAATAAAA
49506323 TATATGAATTTACTAAAATCATAATATATAATACTATAAAATATAATTTAAAATAATTAT
1 TATATGAATTTACTAAAATCATAATATATAATACTATAAAATATAATTTAAAATAATTAT
* * * ** * * * * * *
49506383 TAT-TAAATATAATTTAATAAAAATATATAAT-TTGATAAAATCCTTAGTATT-AAAT-ATTCT
1 TATATGAATTTACTAAAATCATAATATATAATACT-ATAAAAT--ATAAT-TTAAAATAATTAT
49506443 TATATGAATTTACTAAAATCATAATATATAATACTATAAAATATAATTTAAAATAATTAT
1 TATATGAATTTACTAAAATCATAATATATAATACTATAAAATATAATTTAAAATAATTAT
49506503 TAT
1 TAT
49506506 TAAATATAAT
Statistics
Matches: 93, Mismatches: 22, Indels: 16
0.71 0.17 0.12
Matches are distributed among these distances:
58 3 0.03
59 35 0.38
60 17 0.18
61 35 0.38
62 3 0.03
ACGTcount: A:0.51, C:0.05, G:0.02, T:0.42
Consensus pattern (60 bp):
TATATGAATTTACTAAAATCATAATATATAATACTATAAAATATAATTTAAAATAATTAT
Found at i:49506496 original size:12 final size:12
Alignment explanation
Indices: 49506479--49506530 Score: 50
Period size: 12 Copynumber: 4.2 Consensus size: 12
49506469 TATAATACTA
49506479 TAAAATATAATT
1 TAAAATATAATT
*
49506491 TAAAATAATTATT
1 TAAAAT-ATAATT
*
49506504 ATTAAATATAATT
1 -TAAAATATAATT
* *
49506517 TATAATATACTT
1 TAAAATATAATT
49506529 TA
1 TA
49506531 TTATTTTTAA
Statistics
Matches: 32, Mismatches: 6, Indels: 4
0.76 0.14 0.10
Matches are distributed among these distances:
12 17 0.53
13 10 0.31
14 5 0.16
ACGTcount: A:0.52, C:0.02, G:0.00, T:0.46
Consensus pattern (12 bp):
TAAAATATAATT
Found at i:49506531 original size:26 final size:26
Alignment explanation
Indices: 49506481--49506533 Score: 72
Period size: 26 Copynumber: 2.0 Consensus size: 26
49506471 TAATACTATA
*
49506481 AAATATAATTTAAAATAATTATTATT
1 AAATATAATTTAAAATAACTATTATT
*
49506507 AAATATAATTTATAATATACT-TTATT
1 AAATATAATTTAAAATA-ACTATTATT
49506533 A
1 A
49506534 TTTTTAAACT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
26 22 0.92
27 2 0.08
ACGTcount: A:0.51, C:0.02, G:0.00, T:0.47
Consensus pattern (26 bp):
AAATATAATTTAAAATAACTATTATT
Found at i:49512005 original size:11 final size:11
Alignment explanation
Indices: 49511988--49512021 Score: 50
Period size: 11 Copynumber: 3.1 Consensus size: 11
49511978 AGACACCGAT
49511988 CTTCCCTTTCC
1 CTTCCCTTTCC
*
49511999 TTTCCCTTTCC
1 CTTCCCTTTCC
*
49512010 CTTCCCCTTCC
1 CTTCCCTTTCC
49512021 C
1 C
49512022 CTATCCTTGA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
11 20 1.00
ACGTcount: A:0.00, C:0.56, G:0.00, T:0.44
Consensus pattern (11 bp):
CTTCCCTTTCC
Found at i:49514789 original size:22 final size:20
Alignment explanation
Indices: 49514749--49514797 Score: 71
Period size: 20 Copynumber: 2.5 Consensus size: 20
49514739 CAATTTAAAA
49514749 TATAAAAATTTATTAATATG
1 TATAAAAATTTATTAATATG
* *
49514769 TATATAAATTTATTAATATA
1 TATAAAAATTTATTAATATG
*
49514789 TGTAAAAAT
1 TATAAAAAT
49514798 AACGTTTCCG
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 25 1.00
ACGTcount: A:0.51, C:0.00, G:0.04, T:0.45
Consensus pattern (20 bp):
TATAAAAATTTATTAATATG
Found at i:49514844 original size:32 final size:32
Alignment explanation
Indices: 49514808--49514894 Score: 97
Period size: 33 Copynumber: 2.7 Consensus size: 32
49514798 AACGTTTCCG
*
49514808 GAAAATATTTTCAGGAAATC-TGCCAAACAACA
1 GAAAATATTTTCAGCAAATCAT-CCAAACAACA
* *
49514840 GAAAATATTTTACA-CAGATTCATCCAAACACCA
1 GAAAATATTTT-CAGCA-AATCATCCAAACAACA
*
49514873 GAAAATATTTTCAGTAAATCAT
1 GAAAATATTTTCAGCAAATCAT
49514895 TTTCCAAAAA
Statistics
Matches: 46, Mismatches: 5, Indels: 8
0.78 0.08 0.14
Matches are distributed among these distances:
32 19 0.41
33 26 0.57
34 1 0.02
ACGTcount: A:0.46, C:0.18, G:0.09, T:0.26
Consensus pattern (32 bp):
GAAAATATTTTCAGCAAATCATCCAAACAACA
Found at i:49514910 original size:20 final size:21
Alignment explanation
Indices: 49514885--49514925 Score: 66
Period size: 20 Copynumber: 2.0 Consensus size: 21
49514875 AAATATTTTC
49514885 AGTAAATCATTTTCC-AAAAA
1 AGTAAATCATTTTCCGAAAAA
*
49514905 AGTAAATTATTTTCCGAAAAA
1 AGTAAATCATTTTCCGAAAAA
49514926 CATTTTACTG
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 14 0.74
21 5 0.26
ACGTcount: A:0.49, C:0.12, G:0.07, T:0.32
Consensus pattern (21 bp):
AGTAAATCATTTTCCGAAAAA
Found at i:49517760 original size:27 final size:27
Alignment explanation
Indices: 49517723--49517774 Score: 79
Period size: 27 Copynumber: 1.9 Consensus size: 27
49517713 ATTTAGCGGA
*
49517723 GTTGGTTGTTTA-CCTGGACCATTTGTT
1 GTTGGTCGTTTATCC-GGACCATTTGTT
49517750 GTTGGTCGTTTATCCGGACCATTTG
1 GTTGGTCGTTTATCCGGACCATTTG
49517775 CTAAACATCT
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
27 21 0.91
28 2 0.09
ACGTcount: A:0.12, C:0.17, G:0.27, T:0.44
Consensus pattern (27 bp):
GTTGGTCGTTTATCCGGACCATTTGTT
Found at i:49527486 original size:207 final size:207
Alignment explanation
Indices: 49527131--49527894 Score: 782
Period size: 207 Copynumber: 3.7 Consensus size: 207
49527121 AAATTCCTAT
* * * * *
49527131 CTCCCAACTATCATACTAAGGCTCGCAGGTGAAGAGTCGCAGCCTCCAACACAGTTAACAAGAGT
1 CTCCCAACTATCACATTAAGGCTCGCAGGTGAAGAGTCACAACCTCCAACACAGTTAACAAGAGC
* * * * * * * * *
49527196 AAAGCTTCTAGTTGTCACATTATGGCTCGAAGGTGAAGAGCCACAACATTCAACACAATGAGCGA
66 AAAGCTCCCAGCTGTCACATTAAGACTCGAAGGTGAAGAGCCGCAACCTTCAACGCAATTAGCGA
* * * *
49527261 GAGCAAAGCTCCCAACTGTCACATTAAGGGTCGAAGGTGAAGAGCCGTAACCT-TCAACATAATT
131 GAGCAAAGCTCCCAACTGTCATATTAAGGCTCGAAGGTGAAGAGCCGCAACCTCT-AACACAATT
*
49527325 AGCGACAGCAAAG
195 AGCGACAGTAAAG
* * * * *
49527338 CTCCCAACTGTCACATTAAGGTTCGCAGGTGAAGAGTCACAATCTCTAACACAGTTAACAAAAGC
1 CTCCCAACTATCACATTAAGGCTCGCAGGTGAAGAGTCACAACCTCCAACACAGTTAACAAGAGC
* * * * *
49527403 AAAGCTCCCAGCTGCCACATAAAAAATCGAAGGTGAAGAGCCGCAACCTTCAACGCAATTAGTGA
66 AAAGCTCCCAGCTGTCACATTAAGACTCGAAGGTGAAGAGCCGCAACCTTCAACGCAATTAGCGA
* * * * * * *
49527468 AAGCAGAGCTCCCAACTGTCATATTAAGGTTTGTAGGTGAAGAGCCACATCCTCTAACACAATTA
131 GAGCAAAGCTCCCAACTGTCATATTAAGGCTCGAAGGTGAAGAGCCGCAACCTCTAACACAATTA
*
49527533 GCGAGAGTAAAG
196 GCGACAGTAAAG
* * * * ** * *
49527545 CTCCCAACTGTCACATTAAGGCTCGCAGATAAAAAAACATCAACCTTCAACACAGTTAATAAGAG
1 CTCCCAACTATCACATTAAGGCTCGCAGGTGAAGAGTCA-CAACCTCCAACACAGTTAACAAGAG
* ** * *
49527610 TAAAGCTCCCAGCTGTCACATTAAGACTC-ACAGGTGAAGAGTTGCAGCC-TCTAA-GAAAGTTA
65 CAAAGCTCCCAGCTGTCACATTAAGACTCGA-AGGTGAAGAGCCGCAACCTTC-AACGCAA-TTA
* * * * * * *
49527672 GCGAGAGCAAAGCTCTCAGCTGTCATACTAAGACTCGCAGGTGAAGAGCTGCAGCCTCTAACACA
127 GCGAGAGCAAAGCTCCCAACTGTCATATTAAGGCTCGAAGGTGAAGAGCCGCAACCTCTAACACA
* * *
49527737 GTTAGTGATAGTAAAG
192 ATTAGCGACAGTAAAG
* * * ** *
49527753 CTCCCAACTATCACATTAAGGCTCACAAGTGAAGAGTCGCAGTCTCCAACACAGTTAATAAGAGC
1 CTCCCAACTATCACATTAAGGCTCGCAGGTGAAGAGTCACAACCTCCAACACAGTTAACAAGAGC
* ** * * * *
49527818 AAAGCTCCCAGCTGTCACATTAAGGCTCGCAA-GTGAAGAGTTGTAGCCTCCAACACAATTAGCG
66 AAAGCTCCCAGCTGTCACATTAAGACTCG-AAGGTGAAGAGCCGCAACCTTCAACGCAATTAGCG
49527882 AGAGCAAAGCTCC
130 AGAGCAAAGCTCC
49527895 TAGCTGCCAC
Statistics
Matches: 457, Mismatches: 91, Indels: 18
0.81 0.16 0.03
Matches are distributed among these distances:
207 292 0.64
208 164 0.36
209 1 0.00
ACGTcount: A:0.35, C:0.25, G:0.20, T:0.20
Consensus pattern (207 bp):
CTCCCAACTATCACATTAAGGCTCGCAGGTGAAGAGTCACAACCTCCAACACAGTTAACAAGAGC
AAAGCTCCCAGCTGTCACATTAAGACTCGAAGGTGAAGAGCCGCAACCTTCAACGCAATTAGCGA
GAGCAAAGCTCCCAACTGTCATATTAAGGCTCGAAGGTGAAGAGCCGCAACCTCTAACACAATTA
GCGACAGTAAAG
Found at i:49527719 original size:277 final size:276
Alignment explanation
Indices: 49527210--49527848 Score: 640
Period size: 277 Copynumber: 2.3 Consensus size: 276
49527200 CTTCTAGTTG
* * * *
49527210 TCACATTATGGCTCGA-AGGTGAAGAGCCACAACAT-TCAACACAATGAGCGAGAGCAAAGCTCC
1 TCACATTAAGGCTC-ACAGGTGAAGAGCCACATCCTCT-AACACAATTAGCGAGAGCAAAGCTCC
* * * * * ** * * * *
49527273 CAACTGTCACATTAAGGGTCGAAGGTGAAGAGCCGTAACCTTCAACATAATTAGCGACAGCAAAG
64 CAACTGTCACATTAAGGCTCGCAGATAAAAAAACATAACCTTCAACACAATTAACAACAGCAAAG
** * * *
49527338 CTCCCAACTGTCACATTAAGGTTCGCAGGTGAAGAGTCACAATCTCTAACACAGTTAACAAAAGC
129 CTCCCAACTGTCACATTAAGACTCACAGGTGAAGAGTCACAACCTCTAACAAAGTTAACAAAAGC
*
49527403 AAAGCTCCCAGCTGCCACATAAAAAATCGAAGGTGAAGAGCCGCAACCT-TCAACGCAATTAGTG
194 AAAGCTCCCAGCTGCCACATAAAAAATCGAAGGTGAAGAGCCGCAACCTCT-AACACAATTAGTG
* *
49527467 AAAGCAGAGCTCCCAACTG
258 AAAGCAAAGCTCCCAACTA
* * *** *
49527486 TCATATTAAGGTTTGTAGGTGAAGAGCCACATCCTCTAACACAATTAGCGAGAGTAAAGCTCCCA
1 TCACATTAAGGCTCACAGGTGAAGAGCCACATCCTCTAACACAATTAGCGAGAGCAAAGCTCCCA
* * * *
49527551 ACTGTCACATTAAGGCTCGCAGATAAAAAAACATCAACCTTCAACACAGTTAATAAGAGTAAAGC
66 ACTGTCACATTAAGGCTCGCAGATAAAAAAACAT-AACCTTCAACACAATTAACAACAGCAAAGC
* ** * * * * *
49527616 TCCCAGCTGTCACATTAAGACTCACAGGTGAAGAGTTGCAGCCTCTAAGAAAGTTAGCGAGAGCA
130 TCCCAACTGTCACATTAAGACTCACAGGTGAAGAGTCACAACCTCTAACAAAGTTAACAAAAGCA
* * * * * * * * *
49527681 AAGCTCTCAGCTGTCATACT-AAGACTCGCAGGTGAAGAGCTGCAGCCTCTAACACAGTTAGTGA
195 AAGCTCCCAGCTGCCACA-TAAAAAATCGAAGGTGAAGAGCCGCAACCTCTAACACAATTAGTGA
* *
49527745 TAGTAAAGCTCCCAACTA
259 AAGCAAAGCTCCCAACTA
* * * * * ***
49527763 TCACATTAAGGCTCACAAGTGAAGAGTCGCAGT-CTCCAACACAGTTAATAAGAGCAAAGCTCCC
1 TCACATTAAGGCTCACAGGTGAAGAGCCACA-TCCTCTAACACAATTAGCGAGAGCAAAGCTCCC
*
49527827 AGCTGTCACATTAAGGCTCGCA
65 AACTGTCACATTAAGGCTCGCA
49527849 AGTGAAGAGT
Statistics
Matches: 291, Mismatches: 66, Indels: 11
0.79 0.18 0.03
Matches are distributed among these distances:
276 79 0.27
277 209 0.72
278 3 0.01
ACGTcount: A:0.36, C:0.25, G:0.20, T:0.20
Consensus pattern (276 bp):
TCACATTAAGGCTCACAGGTGAAGAGCCACATCCTCTAACACAATTAGCGAGAGCAAAGCTCCCA
ACTGTCACATTAAGGCTCGCAGATAAAAAAACATAACCTTCAACACAATTAACAACAGCAAAGCT
CCCAACTGTCACATTAAGACTCACAGGTGAAGAGTCACAACCTCTAACAAAGTTAACAAAAGCAA
AGCTCCCAGCTGCCACATAAAAAATCGAAGGTGAAGAGCCGCAACCTCTAACACAATTAGTGAAA
GCAAAGCTCCCAACTA
Found at i:49527916 original size:138 final size:138
Alignment explanation
Indices: 49527260--49527947 Score: 594
Period size: 138 Copynumber: 5.0 Consensus size: 138
49527250 ACAATGAGCG
* * *
49527260 AGAGCAAAGCTCCCAACTGTCACATTAAGGGTCG-AAGGTGAAGAGCCGTAACCTTCAACATAAT
1 AGAGCAAAGCTCCCAGCTGTCACATTAAGGCTCGCAA-GTGAAGAGCCGTAACCTTCAACACAAT
* * * * * *
49527324 TAGCGACAGCAAAGCTCCCAACTGTCACATTAAGGTTCGCAGGTGAAGAGTCACAATCTCTAACA
65 TAGTGAGAGCAAAGCTCCCAACTGTCACATTAAGGCTCACAGGTGAAGAGTCGCAGTCTCTAACA
49527389 CAGTTAACA
130 CAGTTAACA
* * * *** * *
49527398 AAAGCAAAGCTCCCAGCTGCCACATAAAAAATCG-AAGGTGAAGAGCCGCAACCTTCAACGCAAT
1 AGAGCAAAGCTCCCAGCTGTCACATTAAGGCTCGCAA-GTGAAGAGCCGTAACCTTCAACACAAT
* * * * *** * *
49527462 TAGTGAAAGCAGAGCTCCCAACTGTCATATTAAGGTTTGTAGGTGAAGAGCCACA-TCCTCTAAC
65 TAGTGAGAGCAAAGCTCCCAACTGTCACATTAAGGCTCACAGGTGAAGAGTCGCAGT-CTCTAAC
* * *
49527526 ACAATTAGCG
129 ACAGTTAACA
* * * * ** * *
49527536 AGAGTAAAGCTCCCAACTGTCACATTAAGGCTCGC-AGATAAAAAAACATCAACCTTCAACACAG
1 AGAGCAAAGCTCCCAGCTGTCACATTAAGGCTCGCAAG-TGAAGAGCCGT-AACCTTCAACACAA
* * * * * * * *
49527600 TTAATAAGAGTAAAGCTCCCAGCTGTCACATTAAGACTCACAGGTGAAGAGTTGCAGCCTCTAAG
64 TTAGTGAGAGCAAAGCTCCCAACTGTCACATTAAGGCTCACAGGTGAAGAGTCGCAGTCTCTAAC
* * *
49527665 AAAGTTAGCG
129 ACAGTTAACA
* * * * * * * * *
49527675 AGAGCAAAGCTCTCAGCTGTCATACTAAGACTCGCAGGTGAAGAGCTGCAGCC-TCTAACACAGT
1 AGAGCAAAGCTCCCAGCTGTCACATTAAGGCTCGCAAGTGAAGAGCCGTAACCTTC-AACACAAT
* * * * *
49527739 TAGTGATAGTAAAGCTCCCAACTATCACATTAAGGCTCACAAGTGAAGAGTCGCAGTCTCCAACA
65 TAGTGAGAGCAAAGCTCCCAACTGTCACATTAAGGCTCACAGGTGAAGAGTCGCAGTCTCTAACA
*
49527804 CAGTTAATA
130 CAGTTAACA
** * *
49527813 AGAGCAAAGCTCCCAGCTGTCACATTAAGGCTCGCAAGTGAAGAGTTGTAGCCTCCAACACAATT
1 AGAGCAAAGCTCCCAGCTGTCACATTAAGGCTCGCAAGTGAAGAGCCGTAACCTTCAACACAATT
* * * * * * * * * *
49527878 AGCGAGAGCAAAGCTCCTAGCTGCCACATTAAGACTCACTGATGAATAGTCGCAGCCTCCAACAC
66 AGTGAGAGCAAAGCTCCCAACTGTCACATTAAGGCTCACAGGTGAAGAGTCGCAGTCTCTAACAC
49527943 AGTTA
131 AGTTA
49527948 GCTTGAGTTC
Statistics
Matches: 435, Mismatches: 107, Indels: 16
0.78 0.19 0.03
Matches are distributed among these distances:
137 4 0.01
138 329 0.76
139 101 0.23
140 1 0.00
ACGTcount: A:0.35, C:0.25, G:0.20, T:0.20
Consensus pattern (138 bp):
AGAGCAAAGCTCCCAGCTGTCACATTAAGGCTCGCAAGTGAAGAGCCGTAACCTTCAACACAATT
AGTGAGAGCAAAGCTCCCAACTGTCACATTAAGGCTCACAGGTGAAGAGTCGCAGTCTCTAACAC
AGTTAACA
Found at i:49527935 original size:69 final size:68
Alignment explanation
Indices: 49527160--49527949 Score: 432
Period size: 69 Copynumber: 11.4 Consensus size: 68
49527150 GGCTCGCAGG
* * * * * * * *
49527160 TGAAGAGTCGCAGCCTCCAACACAGTTAACAAGAGTAAAGCTTCTAGTTGTCACATTATGGCTCG
1 TGAAGAGTCGCAGCCTCCAACACAGTTAGCGAGAGCAAAGCTCCCAGCTGTCACATTAAGACTC-
* *
49527225 AAGG
65 ACGA
* * * * * * * * **
49527229 TGAAGAGCCACAACATTCAACACAATGAGCGAGAGCAAAGCTCCCAACTGTCACATTAAGGGTCG
1 TGAAGAGTCGCAGCCTCCAACACAGTTAGCGAGAGCAAAGCTCCCAGCTGTCACATTAAGACTC-
* *
49527294 AAGG
65 ACGA
* * * * * * * * ** *
49527298 TGAAGAGCCGTAACCTTCAACATAATTAGCGACAGCAAAGCTCCCAACTGTCACATTAAGGTTCG
1 TGAAGAGTCGCAGCCTCCAACACAGTTAGCGAGAGCAAAGCTCCCAGCTGTCACATTAAGACTCA
*
49527363 CAGG
66 C-GA
* ** * * * * * * * *
49527367 TGAAGAGTCACAATCTCTAACACAGTTAACAAAAGCAAAGCTCCCAGCTGCCACATAAAAAATCG
1 TGAAGAGTCGCAGCCTCCAACACAGTTAGCGAGAGCAAAGCTCCCAGCTGTCACATTAAGACTC-
* *
49527432 AAGG
65 ACGA
* * * * * * * * * * **
49527436 TGAAGAGCCGCAACCTTCAACGCAATTAGTGAAAGCAGAGCTCCCAACTGTCATATTAAGGTTTG
1 TGAAGAGTCGCAGCCTCCAACACAGTTAGCGAGAGCAAAGCTCCCAGCTGTCACATTAA-GACT-
* *
49527501 TA-GG
64 CACGA
* * * * * * * * *
49527505 TGAAGAGCCACATCCTCTAACACAATTAGCGAGAGTAAAGCTCCCAACTGTCACATTAAGGCTCG
1 TGAAGAGTCGCAGCCTCCAACACAGTTAGCGAGAGCAAAGCTCCCAGCTGTCACATTAAGACTCA
49527570 CAGA
66 C-GA
* * ** * * * *** *
49527574 TAAAAAAACATCAACCTTCAACACAGTTAATAAGAGTAAAGCTCCCAGCTGTCACATTAAGACTC
1 TGAAGAGTC-GCAGCCTCCAACACAGTTAGCGAGAGCAAAGCTCCCAGCTGTCACATTAAGACTC
*
49527639 ACAGG
65 AC-GA
* * * * * * * *
49527644 TGAAGAGTTGCAGCCTCTAAGAAAGTTAGCGAGAGCAAAGCTCTCAGCTGTCATACTAAGACTCG
1 TGAAGAGTCGCAGCCTCCAACACAGTTAGCGAGAGCAAAGCTCCCAGCTGTCACATTAAGACTCA
*
49527709 CAGG
66 C-GA
* * * * * * *
49527713 TGAAGAG-CTGCAGCCTCTAACACAGTTAGTGATAGTAAAGCTCCCAACTATCACATTAAGGCTC
1 TGAAGAGTC-GCAGCCTCCAACACAGTTAGCGAGAGCAAAGCTCCCAGCTGTCACATTAAGACTC
*
49527777 ACAA
65 ACGA
* *** *
49527781 GTGAAGAGTCGCAGTCTCCAACACAGTTAATAAGAGCAAAGCTCCCAGCTGTCACATTAAGGCTC
1 -TGAAGAGTCGCAGCCTCCAACACAGTTAGCGAGAGCAAAGCTCCCAGCTGTCACATTAAGACTC
* *
49527846 GCAA
65 ACGA
* * * * *
49527850 GTGAAGAGTTGTAGCCTCCAACACAATTAGCGAGAGCAAAGCTCCTAGCTGCCACATTAAGACTC
1 -TGAAGAGTCGCAGCCTCCAACACAGTTAGCGAGAGCAAAGCTCCCAGCTGTCACATTAAGACTC
49527915 ACTGA
65 AC-GA
*
49527920 TGAATAGTCGCAGCCTCCAACACAGTTAGC
1 TGAAGAGTCGCAGCCTCCAACACAGTTAGC
49527950 TTGAGTTCAA
Statistics
Matches: 557, Mismatches: 153, Indels: 22
0.76 0.21 0.03
Matches are distributed among these distances:
68 2 0.00
69 499 0.90
70 56 0.10
ACGTcount: A:0.35, C:0.25, G:0.20, T:0.20
Consensus pattern (68 bp):
TGAAGAGTCGCAGCCTCCAACACAGTTAGCGAGAGCAAAGCTCCCAGCTGTCACATTAAGACTCA
CGA
Found at i:49542511 original size:19 final size:20
Alignment explanation
Indices: 49542487--49542535 Score: 64
Period size: 20 Copynumber: 2.5 Consensus size: 20
49542477 TTAGAAATTA
*
49542487 TTTTATCATAA-TAAGATTT
1 TTTTATAATAATTAAGATTT
*
49542506 TTTTATAATAATTAATATTT
1 TTTTATAATAATTAAGATTT
*
49542526 TTTTAAAATA
1 TTTTATAATA
49542536 TAAATTATGT
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
19 10 0.38
20 16 0.62
ACGTcount: A:0.41, C:0.02, G:0.02, T:0.55
Consensus pattern (20 bp):
TTTTATAATAATTAAGATTT
Found at i:49558325 original size:18 final size:18
Alignment explanation
Indices: 49558290--49558329 Score: 55
Period size: 18 Copynumber: 2.2 Consensus size: 18
49558280 TCAAAATGTT
*
49558290 TATAAAAATTCATTAAAA
1 TATAAAAATTCATAAAAA
49558308 TATAAAAATTC-TAAAAAA
1 TATAAAAATTCAT-AAAAA
49558326 TATA
1 TATA
49558330 TAAAGAAAGT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
17 1 0.05
18 19 0.95
ACGTcount: A:0.62, C:0.05, G:0.00, T:0.33
Consensus pattern (18 bp):
TATAAAAATTCATAAAAA
Found at i:49559605 original size:11 final size:11
Alignment explanation
Indices: 49559589--49559614 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
49559579 GGAGGGTAAA
49559589 AAGAGAAATTG
1 AAGAGAAATTG
49559600 AAGAGAAATTG
1 AAGAGAAATTG
49559611 AAGA
1 AAGA
49559615 TGTCTTGGCC
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.58, C:0.00, G:0.27, T:0.15
Consensus pattern (11 bp):
AAGAGAAATTG
Found at i:49562186 original size:41 final size:41
Alignment explanation
Indices: 49562132--49562253 Score: 122
Period size: 41 Copynumber: 3.0 Consensus size: 41
49562122 AAGGTGATTG
* * *
49562132 AACATTTCAGACTTCACATCTAGCAGGTTTGATGCCGGTGA
1 AACATTTCGGACTTCACATCTAGCAGGCTTAATGCCGGTGA
* * **
49562173 AATATTTCGGACTTTATGTCTAGCAGGCTTAATGCCGGTGA
1 AACATTTCGGACTTCACATCTAGCAGGCTTAATGCCGGTGA
* * *
49562214 AACAATTCGGACTAT-A-AGTCTAGCAGGCTAAAAGCCGGTG
1 AACATTTCGGACT-TCACA-TCTAGCAGGCTTAATGCCGGTG
49562254 TACTGAATCA
Statistics
Matches: 67, Mismatches: 12, Indels: 4
0.81 0.14 0.05
Matches are distributed among these distances:
41 66 0.99
42 1 0.01
ACGTcount: A:0.29, C:0.20, G:0.24, T:0.28
Consensus pattern (41 bp):
AACATTTCGGACTTCACATCTAGCAGGCTTAATGCCGGTGA
Found at i:49563282 original size:6 final size:6
Alignment explanation
Indices: 49563250--49563293 Score: 61
Period size: 6 Copynumber: 7.2 Consensus size: 6
49563240 ATAGCACCTA
* *
49563250 AACAGT AATCAGT AACGGT AGCAGT AACAGT AACAGT AACAGT A
1 AACAGT AA-CAGT AACAGT AACAGT AACAGT AACAGT AACAGT A
49563294 TTCAACACAC
Statistics
Matches: 33, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
6 27 0.82
7 6 0.18
ACGTcount: A:0.45, C:0.16, G:0.20, T:0.18
Consensus pattern (6 bp):
AACAGT
Found at i:49563337 original size:45 final size:45
Alignment explanation
Indices: 49563273--49563377 Score: 158
Period size: 45 Copynumber: 2.3 Consensus size: 45
49563263 AACGGTAGCA
* *
49563273 GTAACAGTAACAGTAACAGTATTCAACACACAAAGTGTTGAATCT
1 GTAACAGTAACAGTAACAGTATTCAACACACAAAGTGTCGAATCG
**
49563318 GTAACAGTAA-AGGTAACAGTATTTGACACACAAAGTGTCGAATCG
1 GTAACAGTAACA-GTAACAGTATTCAACACACAAAGTGTCGAATCG
49563363 GTAACAGTAACAGTA
1 GTAACAGTAACAGTA
49563378 GTCGGCATAT
Statistics
Matches: 54, Mismatches: 4, Indels: 4
0.87 0.06 0.06
Matches are distributed among these distances:
44 1 0.02
45 52 0.96
46 1 0.02
ACGTcount: A:0.42, C:0.16, G:0.19, T:0.23
Consensus pattern (45 bp):
GTAACAGTAACAGTAACAGTATTCAACACACAAAGTGTCGAATCG
Found at i:49563658 original size:40 final size:40
Alignment explanation
Indices: 49563567--49563674 Score: 128
Period size: 40 Copynumber: 2.7 Consensus size: 40
49563557 AATTCATTAC
* * * * *
49563567 TTCAGTAATATCACAGTTCAATGCAGTACACATAACAATA
1 TTCAGTAATTTCACAATTCAATTCAGTACACAAAACAACA
*
49563607 TTCAGTAATTTCACAATTCAATTCAGTACTCAAATACAACA
1 TTCAGTAATTTCACAATTCAATTCAGTACACAAA-ACAACA
* *
49563648 TTCAGT-ATTTCATAATTCAGTTCAGTA
1 TTCAGTAATTTCACAATTCAATTCAGTA
49563675 TCAGTCTCAC
Statistics
Matches: 59, Mismatches: 8, Indels: 2
0.86 0.12 0.03
Matches are distributed among these distances:
40 48 0.81
41 11 0.19
ACGTcount: A:0.39, C:0.19, G:0.08, T:0.33
Consensus pattern (40 bp):
TTCAGTAATTTCACAATTCAATTCAGTACACAAAACAACA
Found at i:49563808 original size:26 final size:25
Alignment explanation
Indices: 49563777--49563826 Score: 66
Period size: 25 Copynumber: 2.0 Consensus size: 25
49563767 TAGTTCAATA
49563777 ATTCAATTCAAAC-CATTTCAATTTCT
1 ATTCAA-T-AAACACATTTCAATTTCT
*
49563803 ATTCAATAATCACATTTCAATTTC
1 ATTCAATAAACACATTTCAATTTC
49563827 ACTTAATTCA
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
24 3 0.14
25 13 0.59
26 6 0.27
ACGTcount: A:0.36, C:0.22, G:0.00, T:0.42
Consensus pattern (25 bp):
ATTCAATAAACACATTTCAATTTCT
Found at i:49564805 original size:8 final size:8
Alignment explanation
Indices: 49564792--49564823 Score: 55
Period size: 8 Copynumber: 4.0 Consensus size: 8
49564782 TGCTTTATAT
49564792 ATATAATA
1 ATATAATA
49564800 ATATAATA
1 ATATAATA
*
49564808 TTATAATA
1 ATATAATA
49564816 ATATAATA
1 ATATAATA
49564824 TAACAACATA
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
8 22 1.00
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (8 bp):
ATATAATA
Found at i:49564814 original size:16 final size:17
Alignment explanation
Indices: 49564788--49564825 Score: 69
Period size: 16 Copynumber: 2.3 Consensus size: 17
49564778 CATTTGCTTT
49564788 ATATATATAATAATATA
1 ATATATATAATAATATA
49564805 ATAT-TATAATAATATA
1 ATATATATAATAATATA
49564821 ATATA
1 ATATA
49564826 ACAACATACT
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
16 16 0.80
17 4 0.20
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (17 bp):
ATATATATAATAATATA
Found at i:49565276 original size:31 final size:31
Alignment explanation
Indices: 49565184--49565276 Score: 109
Period size: 32 Copynumber: 3.0 Consensus size: 31
49565174 TATGCATTTA
49565184 GCTATTCATGTTTAAAGTGTATATACATTCG
1 GCTATTCATGTTTAAAGTGTATATACATTCG
* * * *
49565215 GTTATT-ATATTTGTTATGTGTATA-AGCATTCG
1 GCTATTCAT-GTT-TAAAGTGTATATA-CATTCG
49565247 GCTATTCATGTTTAAAGTGTATATACATTC
1 GCTATTCATGTTTAAAGTGTATATACATTC
49565277 TATGATAATA
Statistics
Matches: 49, Mismatches: 8, Indels: 10
0.73 0.12 0.15
Matches are distributed among these distances:
30 2 0.04
31 22 0.45
32 23 0.47
33 2 0.04
ACGTcount: A:0.28, C:0.11, G:0.16, T:0.45
Consensus pattern (31 bp):
GCTATTCATGTTTAAAGTGTATATACATTCG
Found at i:49565288 original size:63 final size:63
Alignment explanation
Indices: 49565166--49565293 Score: 184
Period size: 63 Copynumber: 2.0 Consensus size: 63
49565156 TTGCTAGGCA
* * * * *
49565166 TATGTATATATGCATTTAGCTATTCATGTTTAAAGTGTATATACATTCGGTTATTATATTTGT
1 TATGTATATAAGCATTCAGCTATTCATGTTTAAAGTGTATATACATTCGATGATAATATTTGT
* * *
49565229 TATGTGTATAAGCATTCGGCTATTCATGTTTAAAGTGTATATACATTCTATGATAATATTTGT
1 TATGTATATAAGCATTCAGCTATTCATGTTTAAAGTGTATATACATTCGATGATAATATTTGT
49565292 TA
1 TA
49565294 AGCATATATG
Statistics
Matches: 57, Mismatches: 8, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
63 57 1.00
ACGTcount: A:0.30, C:0.09, G:0.15, T:0.47
Consensus pattern (63 bp):
TATGTATATAAGCATTCAGCTATTCATGTTTAAAGTGTATATACATTCGATGATAATATTTGT
Found at i:49569599 original size:24 final size:21
Alignment explanation
Indices: 49569572--49569621 Score: 64
Period size: 23 Copynumber: 2.2 Consensus size: 21
49569562 AATTGGGCCT
49569572 AAAATTAAATTTTTAAAAAGTAGA
1 AAAATTAAA-TTTTAAAAA-TA-A
*
49569596 AAAACTAAATTTTAAAAATAA
1 AAAATTAAATTTTAAAAATAA
49569617 AAAAT
1 AAAAT
49569622 ATGTGAATTG
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
21 5 0.21
22 2 0.08
23 9 0.38
24 8 0.33
ACGTcount: A:0.64, C:0.02, G:0.04, T:0.30
Consensus pattern (21 bp):
AAAATTAAATTTTAAAAATAA
Found at i:49573455 original size:27 final size:28
Alignment explanation
Indices: 49573396--49573462 Score: 70
Period size: 27 Copynumber: 2.5 Consensus size: 28
49573386 TATACACTGT
*
49573396 TCATGTATGTGAAAGGTATACATACTAC
1 TCATGTATATGAAAGGTATACATACTAC
49573424 T-ATGTATATGAAA-GT-TACATA-TAC
1 TCATGTATATGAAAGGTATACATACTAC
*
49573448 AGTCATGTATCTGAA
1 --TCATGTATATGAA
49573463 GGATGCAATC
Statistics
Matches: 34, Mismatches: 2, Indels: 7
0.79 0.05 0.16
Matches are distributed among these distances:
24 3 0.09
25 6 0.18
26 3 0.09
27 21 0.62
28 1 0.03
ACGTcount: A:0.37, C:0.12, G:0.16, T:0.34
Consensus pattern (28 bp):
TCATGTATATGAAAGGTATACATACTAC
Found at i:49574862 original size:91 final size:91
Alignment explanation
Indices: 49574715--49574922 Score: 335
Period size: 91 Copynumber: 2.3 Consensus size: 91
49574705 TTGATTTTAG
* *
49574715 TAAATTCATATAAGAACATTTTATTATTAAGAATTTTATGAAATTATATATCATTATTAAATTAT
1 TAAATTCATATAAGAA-AATTTATTATCAAGAATTTTATGAAATTATATATCATTATTAAATTAT
* * *
49574780 ATTTAATATTAATTATTTTAAATTGTA
65 ATGTAATAATAATTATTTTAAATTATA
*
49574807 TAAATTCATATAAGAAAATTTATTATCAAGAATTTTATGAAATTATATATTATTATTAAATTATA
1 TAAATTCATATAAGAAAATTTATTATCAAGAATTTTATGAAATTATATATCATTATTAAATTATA
49574872 TGTAATAATAATTATTTTAAATTATA
66 TGTAATAATAATTATTTTAAATTATA
* *
49574898 CAAATTTATATAAGAAAATTTATTA
1 TAAATTCATATAAGAAAATTTATTA
49574923 GTTATAATTA
Statistics
Matches: 108, Mismatches: 8, Indels: 1
0.92 0.07 0.01
Matches are distributed among these distances:
91 92 0.85
92 16 0.15
ACGTcount: A:0.46, C:0.03, G:0.04, T:0.47
Consensus pattern (91 bp):
TAAATTCATATAAGAAAATTTATTATCAAGAATTTTATGAAATTATATATCATTATTAAATTATA
TGTAATAATAATTATTTTAAATTATA
Found at i:49574891 original size:26 final size:28
Alignment explanation
Indices: 49574837--49574897 Score: 81
Period size: 28 Copynumber: 2.2 Consensus size: 28
49574827 TATTATCAAG
* *
49574837 AATTTTATGAAATTATATATTATTATTA
1 AATTATATGAAATAATATATTATTATTA
*
49574865 AATTATATGTAATAATA-ATTATT-TTA
1 AATTATATGAAATAATATATTATTATTA
49574891 AATTATA
1 AATTATA
49574898 CAAATTTATA
Statistics
Matches: 30, Mismatches: 3, Indels: 2
0.86 0.09 0.06
Matches are distributed among these distances:
26 10 0.33
27 6 0.20
28 14 0.47
ACGTcount: A:0.46, C:0.00, G:0.03, T:0.51
Consensus pattern (28 bp):
AATTATATGAAATAATATATTATTATTA
Found at i:49574897 original size:44 final size:43
Alignment explanation
Indices: 49574755--49574897 Score: 121
Period size: 44 Copynumber: 3.2 Consensus size: 43
49574745 GAATTTTATG
* *
49574755 AAATTATATATCATTATTAAATTATATTTAATATTAATTATTTT
1 AAATTATATATTATTATTAAATTATA-TTAATAATAATTATTTT
* ** * *
49574799 AAATTGTATAAATTCATATAAGAAAATT-TATT-ATCAAGAATT-TTATG
1 AAA-T-TATATATT-AT-T-ATTAAATTATATTAAT-AATAATTATT-TT
49574846 AAATTATATATTATTATTAAATTATATGTAATAATAATTATTTT
1 AAATTATATATTATTATTAAATTATAT-TAATAATAATTATTTT
49574890 AAATTATA
1 AAATTATA
49574898 CAAATTTATA
Statistics
Matches: 76, Mismatches: 12, Indels: 22
0.69 0.11 0.20
Matches are distributed among these distances:
42 6 0.08
43 4 0.05
44 21 0.28
45 12 0.16
46 11 0.14
47 13 0.17
48 3 0.04
49 6 0.08
ACGTcount: A:0.46, C:0.02, G:0.03, T:0.48
Consensus pattern (43 bp):
AAATTATATATTATTATTAAATTATATTAATAATAATTATTTT
Found at i:49575459 original size:45 final size:44
Alignment explanation
Indices: 49575359--49575468 Score: 122
Period size: 45 Copynumber: 2.6 Consensus size: 44
49575349 TTTTTCATTA
49575359 TGCTATTACACCTCTATT-C----CATTCAACCAAACACAAGAT
1 TGCTATTACACCTCTATTCCATTACATTCAACCAAACACAAGAT
* * ***
49575398 TACTATTACGCCTCTATTCCATTACATTCAACCAAACAGTTGATT
1 TGCTATTACACCTCTATTCCATTACATTCAACCAAACACAAGA-T
*
49575443 TGCTATTACACCTCTATTCTATTACA
1 TGCTATTACACCTCTATTCCATTACA
49575469 CCTCTATTTC
Statistics
Matches: 57, Mismatches: 8, Indels: 6
0.80 0.11 0.08
Matches are distributed among these distances:
39 16 0.28
40 1 0.02
44 16 0.28
45 24 0.42
ACGTcount: A:0.32, C:0.28, G:0.05, T:0.35
Consensus pattern (44 bp):
TGCTATTACACCTCTATTCCATTACATTCAACCAAACACAAGAT
Found at i:49575466 original size:16 final size:16
Alignment explanation
Indices: 49575445--49575490 Score: 67
Period size: 16 Copynumber: 2.9 Consensus size: 16
49575435 AGTTGATTTG
49575445 CTATTACACCTCTATT
1 CTATTACACCTCTATT
49575461 CTATTACACCTCTATT
1 CTATTACACCTCTATT
*
49575477 -TCATTACGCCTCTA
1 CT-ATTACACCTCTA
49575491 ATCCAATACA
Statistics
Matches: 28, Mismatches: 1, Indels: 2
0.90 0.03 0.06
Matches are distributed among these distances:
15 1 0.04
16 27 0.96
ACGTcount: A:0.24, C:0.33, G:0.02, T:0.41
Consensus pattern (16 bp):
CTATTACACCTCTATT
Found at i:49576995 original size:40 final size:40
Alignment explanation
Indices: 49576940--49577034 Score: 165
Period size: 40 Copynumber: 2.4 Consensus size: 40
49576930 ATCGTTAGAT
*
49576940 CAACC-AAACATACCAGACAGAAGCTCATAAGAGCTGATC
1 CAACCGAAACACACCAGACAGAAGCTCATAAGAGCTGATC
49576979 CAACCGAAACACACCAGACAGAAGCTCATAAGAGCTGATC
1 CAACCGAAACACACCAGACAGAAGCTCATAAGAGCTGATC
*
49577019 CAACTGAAACACACCA
1 CAACCGAAACACACCA
49577035 AACATAGAGT
Statistics
Matches: 53, Mismatches: 2, Indels: 1
0.95 0.04 0.02
Matches are distributed among these distances:
39 5 0.09
40 48 0.91
ACGTcount: A:0.44, C:0.31, G:0.15, T:0.11
Consensus pattern (40 bp):
CAACCGAAACACACCAGACAGAAGCTCATAAGAGCTGATC
Found at i:49577669 original size:23 final size:21
Alignment explanation
Indices: 49577635--49577677 Score: 50
Period size: 22 Copynumber: 2.0 Consensus size: 21
49577625 TAAAACTTAA
49577635 ACTTTTACACTAATAGCGATTG
1 ACTTTTACACTAATA-CGATTG
* *
49577657 ACTTTTTCAACTATTACGATT
1 ACTTTTAC-ACTAATACGATT
49577678 TAGTACTTTT
Statistics
Matches: 18, Mismatches: 2, Indels: 2
0.82 0.09 0.09
Matches are distributed among these distances:
22 12 0.67
23 6 0.33
ACGTcount: A:0.30, C:0.19, G:0.09, T:0.42
Consensus pattern (21 bp):
ACTTTTACACTAATACGATTG
Found at i:49579570 original size:3 final size:3
Alignment explanation
Indices: 49579562--49579621 Score: 120
Period size: 3 Copynumber: 20.0 Consensus size: 3
49579552 GATTTAGTCC
49579562 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
49579610 TAT TAT TAT TAT
1 TAT TAT TAT TAT
49579622 ATATAGGAGT
Statistics
Matches: 57, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 57 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TAT
Found at i:49579644 original size:10 final size:10
Alignment explanation
Indices: 49579631--49579655 Score: 50
Period size: 10 Copynumber: 2.5 Consensus size: 10
49579621 TATATAGGAG
49579631 TATATTTTTT
1 TATATTTTTT
49579641 TATATTTTTT
1 TATATTTTTT
49579651 TATAT
1 TATAT
49579656 ATACTTATAT
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:0.24, C:0.00, G:0.00, T:0.76
Consensus pattern (10 bp):
TATATTTTTT
Found at i:49579800 original size:13 final size:13
Alignment explanation
Indices: 49579778--49579811 Score: 50
Period size: 13 Copynumber: 2.6 Consensus size: 13
49579768 CTTCATTTTT
*
49579778 TTTTAAATATCTA
1 TTTTATATATCTA
*
49579791 TTTTATATATGTA
1 TTTTATATATCTA
49579804 TTTTATAT
1 TTTTATAT
49579812 TTTATGATTC
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
13 19 1.00
ACGTcount: A:0.32, C:0.03, G:0.03, T:0.62
Consensus pattern (13 bp):
TTTTATATATCTA
Found at i:49579916 original size:13 final size:13
Alignment explanation
Indices: 49579898--49579954 Score: 53
Period size: 13 Copynumber: 4.4 Consensus size: 13
49579888 TGCTTACTTA
49579898 TATATATATTTTT
1 TATATATATTTTT
*
49579911 TATATAGTAATTTT
1 TATATA-TATTTTT
* * **
49579925 AAAATATA-TACT
1 TATATATATTTTT
49579937 TATATATATTTTT
1 TATATATATTTTT
49579950 TATAT
1 TATAT
49579955 TTTTATAATT
Statistics
Matches: 33, Mismatches: 9, Indels: 4
0.72 0.20 0.09
Matches are distributed among these distances:
12 8 0.24
13 15 0.45
14 10 0.30
ACGTcount: A:0.39, C:0.02, G:0.02, T:0.58
Consensus pattern (13 bp):
TATATATATTTTT
Found at i:49580430 original size:109 final size:109
Alignment explanation
Indices: 49580238--49580503 Score: 444
Period size: 109 Copynumber: 2.4 Consensus size: 109
49580228 TTTCTAATTG
* *
49580238 AGGCAATATTTAGCGTTTGGAAATTCGAGAAAACGTGCCCTAAGGTGCTGGGTGTCGATTTTTCT
1 AGGCAATGTTTTGCGTTTGGAAATTCGAGAAAACGTGCCCTAAGGTGCTGGGTGTCGATTTTTCT
* * * *
49580303 CGTTCAACCAAATAGCTAAATATCCTTTTAAAAATTTTACAATA
66 CCTTCAACCAAATAGCTAAATATCCTTTCAAAAATTTCAAAATA
*
49580347 AGGCAATGTTTTGCGTTTGGAAATTCGAGAAAACATGCCCTAAGGTGCTGGGTGTCGATTTTTCT
1 AGGCAATGTTTTGCGTTTGGAAATTCGAGAAAACGTGCCCTAAGGTGCTGGGTGTCGATTTTTCT
*
49580412 CCTTCAACCAAATTGCTAAATATCCTTTCAAAAATTTCAAAATA
66 CCTTCAACCAAATAGCTAAATATCCTTTCAAAAATTTCAAAATA
*
49580456 AGGCAATGTTTTGCGTTTGGAAATTCGAG-GAACGTGCCCTAAGGTGCT
1 AGGCAATGTTTTGCGTTTGGAAATTCGAGAAAACGTGCCCTAAGGTGCT
49580504 TGCCAAATAT
Statistics
Matches: 147, Mismatches: 10, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
108 17 0.12
109 130 0.88
ACGTcount: A:0.30, C:0.17, G:0.20, T:0.32
Consensus pattern (109 bp):
AGGCAATGTTTTGCGTTTGGAAATTCGAGAAAACGTGCCCTAAGGTGCTGGGTGTCGATTTTTCT
CCTTCAACCAAATAGCTAAATATCCTTTCAAAAATTTCAAAATA
Found at i:49588383 original size:30 final size:31
Alignment explanation
Indices: 49588342--49588402 Score: 81
Period size: 30 Copynumber: 2.0 Consensus size: 31
49588332 GTAAGGGTTA
*
49588342 ATTTTACTTTTA-ATATT-ATTTAATATTTTT
1 ATTTTACTTTTATA-ATTCAATTAATATTTTT
*
49588372 ATTTTATTTTTATAATTCAATTAATATTTTT
1 ATTTTACTTTTATAATTCAATTAATATTTTT
49588403 TTATAATTTT
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
30 14 0.52
31 13 0.48
ACGTcount: A:0.31, C:0.03, G:0.00, T:0.66
Consensus pattern (31 bp):
ATTTTACTTTTATAATTCAATTAATATTTTT
Found at i:49589974 original size:18 final size:18
Alignment explanation
Indices: 49589943--49589982 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 18
49589933 TGCAAGGTGC
* *
49589943 GTATCTTAACCCTTATGT
1 GTATCCTAACCCTTATAT
*
49589961 GTATCCTAATCCTTATAT
1 GTATCCTAACCCTTATAT
49589979 GTAT
1 GTAT
49589983 ACTTTTTCCA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.25, C:0.20, G:0.10, T:0.45
Consensus pattern (18 bp):
GTATCCTAACCCTTATAT
Found at i:49590454 original size:61 final size:61
Alignment explanation
Indices: 49590359--49590478 Score: 222
Period size: 61 Copynumber: 2.0 Consensus size: 61
49590349 CATTGATTTA
49590359 TTTTTGAATATTTTTGTACAAATTATTTTTATATTGTTTCATTTAATAAAATAGAAGTTTT
1 TTTTTGAATATTTTTGTACAAATTATTTTTATATTGTTTCATTTAATAAAATAGAAGTTTT
* *
49590420 TTTTTGAATATTTTTGTATAAATTATTTTTATATTGTTTCATTTAATAAATTAGAAGTT
1 TTTTTGAATATTTTTGTACAAATTATTTTTATATTGTTTCATTTAATAAAATAGAAGTT
49590479 GTTGAAACCC
Statistics
Matches: 57, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
61 57 1.00
ACGTcount: A:0.33, C:0.03, G:0.08, T:0.57
Consensus pattern (61 bp):
TTTTTGAATATTTTTGTACAAATTATTTTTATATTGTTTCATTTAATAAAATAGAAGTTTT
Found at i:49591235 original size:19 final size:19
Alignment explanation
Indices: 49591211--49591290 Score: 56
Period size: 19 Copynumber: 4.0 Consensus size: 19
49591201 TACAGTGAAT
49591211 ACAATAATAATAAATAATA
1 ACAATAATAATAAATAATA
*
49591230 ACAATAA-AA-AAATATTCA
1 ACAATAATAATAAATAAT-A
* *
49591248 ATTAATAATACTATATAATAATG
1 A-CAATAATA--ATA-AATAATA
*
49591271 ATAATAATAATGAAATAATA
1 ACAATAATAAT-AAATAATA
49591291 CAAAAATGTA
Statistics
Matches: 48, Mismatches: 5, Indels: 15
0.71 0.07 0.22
Matches are distributed among these distances:
17 6 0.12
18 4 0.08
19 12 0.25
20 9 0.19
21 1 0.02
22 9 0.19
23 2 0.04
24 5 0.10
ACGTcount: A:0.62, C:0.05, G:0.03, T:0.30
Consensus pattern (19 bp):
ACAATAATAATAAATAATA
Found at i:49591309 original size:3 final size:3
Alignment explanation
Indices: 49591213--49591290 Score: 52
Period size: 3 Copynumber: 25.3 Consensus size: 3
49591203 CAGTGAATAC
* * * *
49591213 AAT AAT AAT AAAT AAT AAC AAT AA- AAA AAT ATT CAATT AAT AAT ACT
1 AAT AAT AAT -AAT AAT AAT AAT AAT AAT AAT AAT -AA-T AAT AAT AAT
* *
49591260 ATAT AAT AAT GAT AAT AAT AAT GA- AAT AAT A
1 A-AT AAT AAT AAT AAT AAT AAT AAT AAT AAT A
49591291 CAAAAATGTA
Statistics
Matches: 58, Mismatches: 11, Indels: 12
0.72 0.14 0.15
Matches are distributed among these distances:
2 3 0.05
3 46 0.79
4 8 0.14
5 1 0.02
ACGTcount: A:0.63, C:0.04, G:0.03, T:0.31
Consensus pattern (3 bp):
AAT
Found at i:49592648 original size:16 final size:18
Alignment explanation
Indices: 49592627--49592661 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
49592617 AGTGGGCAAA
49592627 TGGGC-TTTA-GGTTTTT
1 TGGGCTTTTAGGGTTTTT
49592643 TGGGCTTTTAGGGTTTTT
1 TGGGCTTTTAGGGTTTTT
49592661 T
1 T
49592662 TTGTATTTGT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 5 0.29
17 4 0.24
18 8 0.47
ACGTcount: A:0.06, C:0.06, G:0.31, T:0.57
Consensus pattern (18 bp):
TGGGCTTTTAGGGTTTTT
Found at i:49595540 original size:2 final size:2
Alignment explanation
Indices: 49595533--49595569 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
49595523 TTAAACGTTA
49595533 AT AT AT 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 AT AT AT A
49595570 CACGATGTTA
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:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:49598581 original size:36 final size:36
Alignment explanation
Indices: 49598541--49598921 Score: 429
Period size: 36 Copynumber: 10.0 Consensus size: 36
49598531 GGTAGCTTTA
*
49598541 GCTACACTTATCTGATCAAGCGAAAAAGTGATAAGT
1 GCTACACTTATCTGATCAAGTGAAAAAGTGATAAGT
* *
49598577 GCTACACTTATCTGATCAAGAGACAAAGTGATAAGTGGTAGCTAT
1 GCTACACTTATCTGATCAAGTGAAAAAGTGAT-A-----AG---T
49598622 AGCTACACTTATCTGATCAAGTGAAAAAGTGATAAGT
1 -GCTACACTTATCTGATCAAGTGAAAAAGTGATAAGT
* * *
49598659 GTTATACTTATTTGATCAAGTGAAAAAGTGATAAGT
1 GCTACACTTATCTGATCAAGTGAAAAAGTGATAAGT
* *
49598695 GTTATACTTATCTGATCAAGTGAAAAAGTGATAAGT
1 GCTACACTTATCTGATCAAGTGAAAAAGTGATAAGT
* *
49598731 GCTACACTTATCTGATCAAGAGACAAAGTGATAAGT
1 GCTACACTTATCTGATCAAGTGAAAAAGTGATAAGT
* *
49598767 GCTACACTTATCTGATCAAGAGACAAAGTGATAAGTGGTAGCTTT
1 GCTACACTTATCTGATCAAGTGAAAAAGTGAT-A-----AG---T
*
49598812 AGCTACACTGATCTGATCAAGTGAAAAAGTGATAAGT
1 -GCTACACTTATCTGATCAAGTGAAAAAGTGATAAGT
* *
49598849 GTTATACTTATCTGATCAAGTGAAAAAGTGATAAGT
1 GCTACACTTATCTGATCAAGTGAAAAAGTGATAAGT
* *
49598885 GCTATACTTATCTGATCAAGTGACAAAGTGATAAGT
1 GCTACACTTATCTGATCAAGTGAAAAAGTGATAAGT
49598921 G
1 G
49598922 GTAGCTTAGC
Statistics
Matches: 305, Mismatches: 20, Indels: 40
0.84 0.05 0.11
Matches are distributed among these distances:
36 230 0.75
37 4 0.01
40 4 0.01
42 4 0.01
45 4 0.01
46 59 0.19
ACGTcount: A:0.38, C:0.13, G:0.20, T:0.29
Consensus pattern (36 bp):
GCTACACTTATCTGATCAAGTGAAAAAGTGATAAGT
Found at i:49598826 original size:118 final size:117
Alignment explanation
Indices: 49598704--49598947 Score: 416
Period size: 118 Copynumber: 2.1 Consensus size: 117
49598694 TGTTATACTT
*
49598704 ATCTGATCAAGTGAAAAAGTGATAAGTGCTACACTTATCTGATCAAGAGACAAAGTGATAAGTGC
1 ATCTGATCAAGTGAAAAAGTGATAAGTGCTACACTTATCTGATCAAGAGAAAAAGTGATAAGTGC
49598769 TACACTTATCTGATCAAGAGACAAAGTGATAAGTGGTAGCTTTAGCTACACTG
66 TACACTTATCTGATCAAGAGACAAAGTGATAAGTGGTAGC-TTAGCTACACTG
* * *
49598822 ATCTGATCAAGTGAAAAAGTGATAAGTGTTATACTTATCTGATCAAGTGAAAAAGTGATAAGTGC
1 ATCTGATCAAGTGAAAAAGTGATAAGTGCTACACTTATCTGATCAAGAGAAAAAGTGATAAGTGC
* * *
49598887 TATACTTATCTGATCAAGTGACAAAGTGATAAGTGGTAGCTTAGCTACACTT
66 TACACTTATCTGATCAAGAGACAAAGTGATAAGTGGTAGCTTAGCTACACTG
49598939 ATCTGATCA
1 ATCTGATCA
49598948 GGGACAAATG
Statistics
Matches: 119, Mismatches: 7, Indels: 1
0.94 0.06 0.01
Matches are distributed among these distances:
117 20 0.17
118 99 0.83
ACGTcount: A:0.37, C:0.14, G:0.20, T:0.29
Consensus pattern (117 bp):
ATCTGATCAAGTGAAAAAGTGATAAGTGCTACACTTATCTGATCAAGAGAAAAAGTGATAAGTGC
TACACTTATCTGATCAAGAGACAAAGTGATAAGTGGTAGCTTAGCTACACTG
Found at i:49598829 original size:154 final size:144
Alignment explanation
Indices: 49598546--49598921 Score: 509
Period size: 154 Copynumber: 2.5 Consensus size: 144
49598536 CTTTAGCTAC
*
49598546 ACTTATCTGATCAAGCGAAAAAGTGATAAGTGCTACACTTATCTGATCAAGAGACAAAGTGATAA
1 ACTTATCTGATCAAGTGAAAAAGTGATAAGTGCTACACTTATCTGATCAAGAGACAAAGTGAT-A
* * *
49598611 GTGGTAGCTATAGCTACACTTATCTGATCAAGTGAAAAAGTGATAAGTGTTATACTTATTTGATC
65 -----AG---T-GCTACACTTATCTGATCAAGAGAAAAAGTGATAAGTGTTATACTGATCTGATC
49598676 AAGTGAAAAAGTGATAAGTGTTAT
121 AAGTGAAAAAGTGATAAGTGTTAT
49598700 ACTTATCTGATCAAGTGAAAAAGTGATAAGTGCTACACTTATCTGATCAAGAGACAAAGTGATAA
1 ACTTATCTGATCAAGTGAAAAAGTGATAAGTGCTACACTTATCTGATCAAGAGACAAAGTGATAA
*
49598765 GTGCTACACTTATCTGATCAAGAGACAAAGTGATAAGTGGTAGCTTTAGCTACACTGATCTGATC
66 GTGCTACACTTATCTGATCAAGAGAAAAAGTGATAA---GT-G--TTA--T--ACTGATCTGATC
49598830 AAGTGAAAAAGTGATAAGTGTTAT
121 AAGTGAAAAAGTGATAAGTGTTAT
* *
49598854 ACTTATCTGATCAAGTGAAAAAGTGATAAGTGCTATACTTATCTGATCAAGTGACAAAGTGATAA
1 ACTTATCTGATCAAGTGAAAAAGTGATAAGTGCTACACTTATCTGATCAAGAGACAAAGTGATAA
49598919 GTG
66 GTG
49598922 GTAGCTTAGC
Statistics
Matches: 205, Mismatches: 7, Indels: 20
0.88 0.03 0.09
Matches are distributed among these distances:
144 32 0.16
145 1 0.00
147 2 0.01
148 3 0.01
150 3 0.01
152 1 0.00
153 1 0.00
154 162 0.79
ACGTcount: A:0.38, C:0.12, G:0.20, T:0.29
Consensus pattern (144 bp):
ACTTATCTGATCAAGTGAAAAAGTGATAAGTGCTACACTTATCTGATCAAGAGACAAAGTGATAA
GTGCTACACTTATCTGATCAAGAGAAAAAGTGATAAGTGTTATACTGATCTGATCAAGTGAAAAA
GTGATAAGTGTTAT
Found at i:49598838 original size:190 final size:190
Alignment explanation
Indices: 49598541--49598921 Score: 699
Period size: 190 Copynumber: 2.0 Consensus size: 190
49598531 GGTAGCTTTA
*
49598541 GCTACACTTATCTGATCAAGCGAAAAAGTGATAAGTGCTACACTTATCTGATCAAGAGACAAAGT
1 GCTACACTTATCTGATCAAGAGAAAAAGTGATAAGTGCTACACTTATCTGATCAAGAGACAAAGT
* *
49598606 GATAAGTGGTAGCTATAGCTACACTTATCTGATCAAGTGAAAAAGTGATAAGTGTTATACTTATT
66 GATAAGTGGTAGCTATAGCTACACTGATCTGATCAAGTGAAAAAGTGATAAGTGTTATACTTATC
*
49598671 TGATCAAGTGAAAAAGTGATAAGTGTTATACTTATCTGATCAAGTGAAAAAGTGATAAGT
131 TGATCAAGTGAAAAAGTGATAAGTGCTATACTTATCTGATCAAGTGAAAAAGTGATAAGT
*
49598731 GCTACACTTATCTGATCAAGAGACAAAGTGATAAGTGCTACACTTATCTGATCAAGAGACAAAGT
1 GCTACACTTATCTGATCAAGAGAAAAAGTGATAAGTGCTACACTTATCTGATCAAGAGACAAAGT
*
49598796 GATAAGTGGTAGCTTTAGCTACACTGATCTGATCAAGTGAAAAAGTGATAAGTGTTATACTTATC
66 GATAAGTGGTAGCTATAGCTACACTGATCTGATCAAGTGAAAAAGTGATAAGTGTTATACTTATC
*
49598861 TGATCAAGTGAAAAAGTGATAAGTGCTATACTTATCTGATCAAGTGACAAAGTGATAAGT
131 TGATCAAGTGAAAAAGTGATAAGTGCTATACTTATCTGATCAAGTGAAAAAGTGATAAGT
49598921 G
1 G
49598922 GTAGCTTAGC
Statistics
Matches: 184, Mismatches: 7, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
190 184 1.00
ACGTcount: A:0.38, C:0.13, G:0.20, T:0.29
Consensus pattern (190 bp):
GCTACACTTATCTGATCAAGAGAAAAAGTGATAAGTGCTACACTTATCTGATCAAGAGACAAAGT
GATAAGTGGTAGCTATAGCTACACTGATCTGATCAAGTGAAAAAGTGATAAGTGTTATACTTATC
TGATCAAGTGAAAAAGTGATAAGTGCTATACTTATCTGATCAAGTGAAAAAGTGATAAGT
Found at i:49599774 original size:41 final size:41
Alignment explanation
Indices: 49599726--49599815 Score: 180
Period size: 41 Copynumber: 2.2 Consensus size: 41
49599716 GCTGAAAGAG
49599726 TATACTTTCACATGAAAGAAATGGAGTAAGAAAAAGAATTA
1 TATACTTTCACATGAAAGAAATGGAGTAAGAAAAAGAATTA
49599767 TATACTTTCACATGAAAGAAATGGAGTAAGAAAAAGAATTA
1 TATACTTTCACATGAAAGAAATGGAGTAAGAAAAAGAATTA
49599808 TATACTTT
1 TATACTTT
49599816 TAGATATTTG
Statistics
Matches: 49, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
41 49 1.00
ACGTcount: A:0.49, C:0.08, G:0.16, T:0.28
Consensus pattern (41 bp):
TATACTTTCACATGAAAGAAATGGAGTAAGAAAAAGAATTA
Found at i:49600865 original size:20 final size:19
Alignment explanation
Indices: 49600828--49600887 Score: 50
Period size: 19 Copynumber: 3.1 Consensus size: 19
49600818 CTTTCTTGAT
* *
49600828 CTAAATTAATACAAAATTTA
1 CTAAATTTA-ACACAATTTA
* *
49600848 CT-TATTTAATCACTAATTCA
1 CTAAATTTAA-CAC-AATTTA
49600868 CTAAATTTAACACAATTTA
1 CTAAATTTAACACAATTTA
49600887 C
1 C
49600888 ACATTAGGGT
Statistics
Matches: 31, Mismatches: 6, Indels: 7
0.70 0.14 0.16
Matches are distributed among these distances:
18 1 0.03
19 12 0.39
20 12 0.39
21 6 0.19
ACGTcount: A:0.45, C:0.17, G:0.00, T:0.38
Consensus pattern (19 bp):
CTAAATTTAACACAATTTA
Found at i:49602788 original size:7 final size:7
Alignment explanation
Indices: 49602773--49602805 Score: 57
Period size: 7 Copynumber: 4.7 Consensus size: 7
49602763 AACCCTAATC
49602773 AAACCCA
1 AAACCCA
*
49602780 AAACTCA
1 AAACCCA
49602787 AAACCCA
1 AAACCCA
49602794 AAACCCA
1 AAACCCA
49602801 AAACC
1 AAACC
49602806 TAAGCCCTAA
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
7 24 1.00
ACGTcount: A:0.58, C:0.39, G:0.00, T:0.03
Consensus pattern (7 bp):
AAACCCA
Found at i:49607097 original size:15 final size:14
Alignment explanation
Indices: 49607076--49607111 Score: 54
Period size: 15 Copynumber: 2.5 Consensus size: 14
49607066 ATAATCCTTA
*
49607076 ATAATTATCTTAAT
1 ATAATTATCCTAAT
49607090 ATTAATTATCCTAAT
1 A-TAATTATCCTAAT
49607105 ATAATTA
1 ATAATTA
49607112 AAATAGAGTC
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
14 7 0.35
15 13 0.65
ACGTcount: A:0.44, C:0.08, G:0.00, T:0.47
Consensus pattern (14 bp):
ATAATTATCCTAAT
Found at i:49608686 original size:31 final size:31
Alignment explanation
Indices: 49608650--49608711 Score: 115
Period size: 31 Copynumber: 2.0 Consensus size: 31
49608640 GTTATTCAAG
*
49608650 TTAAGGTTTAAACTTGACAATTATTCTCACA
1 TTAAGGTTTAAACTTGACAATTATTCCCACA
49608681 TTAAGGTTTAAACTTGACAATTATTCCCACA
1 TTAAGGTTTAAACTTGACAATTATTCCCACA
49608712 AACAATTGTC
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
31 30 1.00
ACGTcount: A:0.35, C:0.18, G:0.10, T:0.37
Consensus pattern (31 bp):
TTAAGGTTTAAACTTGACAATTATTCCCACA
Found at i:49612863 original size:14 final size:14
Alignment explanation
Indices: 49612844--49612873 Score: 60
Period size: 14 Copynumber: 2.1 Consensus size: 14
49612834 AAAGTAACTC
49612844 ATTCACTTTCTCGA
1 ATTCACTTTCTCGA
49612858 ATTCACTTTCTCGA
1 ATTCACTTTCTCGA
49612872 AT
1 AT
49612874 AGCCTTATTA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.23, C:0.27, G:0.07, T:0.43
Consensus pattern (14 bp):
ATTCACTTTCTCGA
Found at i:49613252 original size:14 final size:14
Alignment explanation
Indices: 49613235--49613261 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
49613225 TCTCACATTT
49613235 ATTTTCTTTTCTCC
1 ATTTTCTTTTCTCC
49613249 ATTTTCTTTTCTC
1 ATTTTCTTTTCTC
49613262 TAGATTTCTG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.07, C:0.26, G:0.00, T:0.67
Consensus pattern (14 bp):
ATTTTCTTTTCTCC
Found at i:49616580 original size:22 final size:20
Alignment explanation
Indices: 49616521--49616581 Score: 59
Period size: 22 Copynumber: 2.9 Consensus size: 20
49616511 ATCGATTCAA
* *
49616521 ATTTTATTAATTTAAATTAT
1 ATTTTATAAATTTATATTAT
*
49616541 ATTTTATAGTATTATATATTAT
1 ATTTTATA-AATT-TATATTAT
49616563 GATTTTAGTAAATTTATAT
1 -ATTTTA-TAAATTTATAT
49616582 AAGAATATTT
Statistics
Matches: 33, Mismatches: 4, Indels: 6
0.77 0.09 0.14
Matches are distributed among these distances:
20 7 0.21
21 3 0.09
22 12 0.36
23 9 0.27
24 2 0.06
ACGTcount: A:0.38, C:0.00, G:0.05, T:0.57
Consensus pattern (20 bp):
ATTTTATAAATTTATATTAT
Found at i:49617130 original size:120 final size:120
Alignment explanation
Indices: 49616526--49617129 Score: 1052
Period size: 120 Copynumber: 5.0 Consensus size: 120
49616516 TTCAAATTTT
*
49616526 ATTAATTTAAATTATATTTTATAGTATTATATATTATGATTTTAGTAAATTTATATAAGAATATT
1 ATTAATTTAAATTATATTTTATAGTATTATATATTATGATTTTAGTAAATTCATATAAGAATATT
*
49616591 TAATATTAAGAATTTTATTAAATTATATATTTTTATTAAATTATATTTAAAAATA
66 TAATATTAAGAATTTTATTAAATTATATATTTTTATTAAATTATATTTAATAATA
49616646 ATTAATTTAAATTATATTTTATAGTATTATATATTATGATTTTAGTAAATTC---TAAGAATATT
1 ATTAATTTAAATTATATTTTATAGTATTATATATTATGATTTTAGTAAATTCATATAAGAATATT
* **
49616708 TAATATTAAGAATCTTATTAAATTATATATTTTTGCTAAATTATATTTTTAATAATA
66 TAATATTAAGAATTTTATTAAATTATATATTTTTATTAAATTATA--TTTAATAATA
* *
49616765 ATTATTTTAAATTATATTTTATAGTATTATATATTATGATTTTAGTAAATTCATTTAAGAATATT
1 ATTAATTTAAATTATATTTTATAGTATTATATATTATGATTTTAGTAAATTCATATAAGAATATT
*
49616830 TAATATTAAGAATTTTATTAAATTATATATTTTTACTAAATTATATTTTAATAATA
66 TAATATTAAGAATTTTATTAAATTATATATTTTTATTAAATTATA-TTTAATAATA
*
49616886 ATTAATTTAAATTATATTTTATAGTATTATATATTATGATTTTAGTAAATTCATTTAAGAATATT
1 ATTAATTTAAATTATATTTTATAGTATTATATATTATGATTTTAGTAAATTCATATAAGAATATT
49616951 TAATATTAAGAATTTTATTAAATTATATATTTTTATTAAATTATATTTAATAATA
66 TAATATTAAGAATTTTATTAAATTATATATTTTTATTAAATTATATTTAATAATA
* * *
49617006 ATTATTTTAAATTATATTTTATAGTATTATATATTATGATTTTATTAAATTCATATAACAATATT
1 ATTAATTTAAATTATATTTTATAGTATTATATATTATGATTTTAGTAAATTCATATAAGAATATT
49617071 TAATATTAAGAATTTTATTAAATTATATATTTTTATTAAATTATATTTAATAATA
66 TAATATTAAGAATTTTATTAAATTATATATTTTTATTAAATTATATTTAATAATA
49617126 ATTA
1 ATTA
49617130 TGTTAAAATA
Statistics
Matches: 465, Mismatches: 14, Indels: 10
0.95 0.03 0.02
Matches are distributed among these distances:
117 52 0.11
119 60 0.13
120 181 0.39
121 119 0.26
122 53 0.11
ACGTcount: A:0.42, C:0.01, G:0.04, T:0.52
Consensus pattern (120 bp):
ATTAATTTAAATTATATTTTATAGTATTATATATTATGATTTTAGTAAATTCATATAAGAATATT
TAATATTAAGAATTTTATTAAATTATATATTTTTATTAAATTATATTTAATAATA
Found at i:49617330 original size:44 final size:46
Alignment explanation
Indices: 49617280--49617367 Score: 153
Period size: 46 Copynumber: 2.0 Consensus size: 46
49617270 CCTCTATTTT
*
49617280 ATTCAACCAAACACAAGAA-TACC-ATTACGCCTCTATTCCATTCC
1 ATTCAACCAAACAAAAGAATTACCTATTACGCCTCTATTCCATTCC
49617324 ATTCAACCAAACAAAAGAATTACCTATTACGCCTCTATTCCATT
1 ATTCAACCAAACAAAAGAATTACCTATTACGCCTCTATTCCATT
49617368 ACGCATCTAT
Statistics
Matches: 41, Mismatches: 1, Indels: 2
0.93 0.02 0.05
Matches are distributed among these distances:
44 18 0.44
45 4 0.10
46 19 0.46
ACGTcount: A:0.38, C:0.31, G:0.05, T:0.27
Consensus pattern (46 bp):
ATTCAACCAAACAAAAGAATTACCTATTACGCCTCTATTCCATTCC
Found at i:49617370 original size:16 final size:16
Alignment explanation
Indices: 49617349--49617397 Score: 80
Period size: 16 Copynumber: 3.1 Consensus size: 16
49617339 AGAATTACCT
49617349 ATTACGCCTCTATTCC
1 ATTACGCCTCTATTCC
*
49617365 ATTACGCATCTATTCC
1 ATTACGCCTCTATTCC
*
49617381 ATAACGCCTCTATTCC
1 ATTACGCCTCTATTCC
49617397 A
1 A
49617398 ATACAGCAAA
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
16 30 1.00
ACGTcount: A:0.24, C:0.35, G:0.06, T:0.35
Consensus pattern (16 bp):
ATTACGCCTCTATTCC
Found at i:49618332 original size:21 final size:21
Alignment explanation
Indices: 49618299--49618339 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
49618289 TCAAAAAAGC
**
49618299 TCTCAAATTTCTCTCTAAATT
1 TCTCAAAGCTCTCTCTAAATT
*
49618320 TCTCAAAGCTCTCTTTAAAT
1 TCTCAAAGCTCTCTCTAAAT
49618340 CACAATTTCC
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.29, C:0.24, G:0.02, T:0.44
Consensus pattern (21 bp):
TCTCAAAGCTCTCTCTAAATT
Found at i:49618521 original size:30 final size:32
Alignment explanation
Indices: 49618487--49618559 Score: 80
Period size: 30 Copynumber: 2.3 Consensus size: 32
49618477 TAATGGTTAA
*
49618487 TTTCAATTTTTG-AATATTATTTAATATTT-T
1 TTTCAATTTTTGTAATATTAATTAATATTTAT
* *
49618517 TTTC-ATTTATGTAATTTTAATTAATATTTAT
1 TTTCAATTTTTGTAATATTAATTAATATTTAT
*
49618548 TTTATAATTTTT
1 TTT-CAATTTTT
49618560 TTATAACAAC
Statistics
Matches: 34, Mismatches: 5, Indels: 5
0.77 0.11 0.11
Matches are distributed among these distances:
29 6 0.18
30 19 0.56
31 4 0.12
33 5 0.15
ACGTcount: A:0.30, C:0.03, G:0.03, T:0.64
Consensus pattern (32 bp):
TTTCAATTTTTGTAATATTAATTAATATTTAT
Found at i:49620090 original size:18 final size:18
Alignment explanation
Indices: 49620067--49620102 Score: 72
Period size: 18 Copynumber: 2.0 Consensus size: 18
49620057 TGTCAGGTGC
49620067 GTATCCTAACCCTTATAT
1 GTATCCTAACCCTTATAT
49620085 GTATCCTAACCCTTATAT
1 GTATCCTAACCCTTATAT
49620103 ATTTTCTTTT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.28, C:0.28, G:0.06, T:0.39
Consensus pattern (18 bp):
GTATCCTAACCCTTATAT
Found at i:49620381 original size:21 final size:21
Alignment explanation
Indices: 49620357--49620400 Score: 70
Period size: 21 Copynumber: 2.1 Consensus size: 21
49620347 CCACAACCAG
*
49620357 AACAACCACAACCCTCGCCGA
1 AACAACCACAACCCCCGCCGA
*
49620378 AACAACCACAACCCCCGTCGA
1 AACAACCACAACCCCCGCCGA
49620399 AA
1 AA
49620401 GCTCAACCAA
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.41, C:0.45, G:0.09, T:0.05
Consensus pattern (21 bp):
AACAACCACAACCCCCGCCGA
Found at i:49620650 original size:62 final size:61
Alignment explanation
Indices: 49620481--49620671 Score: 223
Period size: 62 Copynumber: 3.1 Consensus size: 61
49620471 TGTATTAATT
* * * * *
49620481 TTTTTAATATATTTGTACGAACTATTTTTATATTGTT-T-C-ATTTAATAAAATAAAAGTTG
1 TTTTGAATATATTTATACAAATTATTTTTATATT-TTGTCCTATTTAATAAAATAGAAGTTG
*
49620540 TTTTGAATATATTTATACAAATTATTTTTATA-TTTGATCCTATTTAATAAAATAGGAGTTG
1 TTTTGAATATATTTATACAAATTATTTTTATATTTTG-TCCTATTTAATAAAATAGAAGTTG
*
49620601 TTTTGAATAT-TTTAATAGTC-AATTATTTTTATATTTTGTCCTATTTAATAAAATAGAAGTTT
1 TTTTGAATATATTT-ATA--CAAATTATTTTTATATTTTGTCCTATTTAATAAAATAGAAGTTG
*
49620663 TTTTTAATA
1 TTTTGAATA
49620672 AGGCAATAGA
Statistics
Matches: 115, Mismatches: 9, Indels: 13
0.84 0.07 0.09
Matches are distributed among these distances:
57 2 0.02
58 1 0.01
59 29 0.25
60 4 0.03
61 31 0.27
62 43 0.37
63 5 0.04
ACGTcount: A:0.35, C:0.05, G:0.08, T:0.52
Consensus pattern (61 bp):
TTTTGAATATATTTATACAAATTATTTTTATATTTTGTCCTATTTAATAAAATAGAAGTTG
Found at i:49623980 original size:126 final size:125
Alignment explanation
Indices: 49623818--49624246 Score: 522
Period size: 126 Copynumber: 3.4 Consensus size: 125
49623808 AAGTAGGATG
* * * * ** *
49623818 TACTGTAGAAAAAGAGCGTCCAGGTGGGAATTTTTTTCAGTACTTTTGTTGACAGTGCATCTTGC
1 TACTATAGAAAAAAAACGTCCAGCTGGGAGCTTTTTT-AGTACTTTTGCTGACAGTGCATCTTGC
*
49623883 TTGAAGTGTTTTTACCCTATTTTTTCAGAACCATCTTCTCAAAATTATTTTTTTCAAAAAC
65 TTGAAGCGTTTTTACCCTATTTTTTCAGAACCATCTTCTCAAAATTATTTTTTTCAAAAAC
* ** * * * *
49623944 TACTATAGAAAAAAAAGGTCCATTTGGGAGCTTTTTTTAGTACTTTTGCTAACGGTGCATCCTGT
1 TACTATAGAAAAAAAACGTCCAGCTGGGAGC-TTTTTTAGTACTTTTGCTGACAGTGCATCTTGC
* * *
49624009 TTGAAGCGTTTTTGACCCTATTTTTTTAGAATCATCTTCTCAAAATTA-TTTTTTCAGAAAC
65 TTGAAGCGTTTTT-ACCCTATTTTTTCAGAACCATCTTCTCAAAATTATTTTTTTCAAAAAC
* * *
49624070 TACTGTAGAAAAATAACGTCCAGCTGGGAGCTTTTTTAGTACTTTTGCTGGCAGTGCATCTTGCT
1 TACTATAGAAAAAAAACGTCCAGCTGGGAGCTTTTTTAGTACTTTTGCTGACAGTGCATCTTGCT
* * *
49624135 TGAAGCGTTTTTTACCCTATTTTTTCAGAACCATATTCTCAAAATTA-TTTTTT-AGAAAT
66 TGAAGCG-TTTTTACCCTATTTTTTCAGAACCATCTTCTCAAAATTATTTTTTTCAAAAAC
* * * * * *
49624194 TACTGTAGAAAAATAGCATCCAGCTGGGAGCTTTTGTCAATACTTTTGCTGAC
1 TACTATAGAAAAAAAACGTCCAGCTGGGAGCTTTT-TTAGTACTTTTGCTGAC
49624247 TGAACAAAAA
Statistics
Matches: 263, Mismatches: 36, Indels: 9
0.85 0.12 0.03
Matches are distributed among these distances:
124 38 0.14
125 87 0.33
126 100 0.38
127 38 0.14
ACGTcount: A:0.27, C:0.17, G:0.16, T:0.40
Consensus pattern (125 bp):
TACTATAGAAAAAAAACGTCCAGCTGGGAGCTTTTTTAGTACTTTTGCTGACAGTGCATCTTGCT
TGAAGCGTTTTTACCCTATTTTTTCAGAACCATCTTCTCAAAATTATTTTTTTCAAAAAC
Found at i:49624152 original size:125 final size:125
Alignment explanation
Indices: 49623818--49624246 Score: 565
Period size: 125 Copynumber: 3.4 Consensus size: 125
49623808 AAGTAGGATG
* * * ** *
49623818 TACTGTAGAAAAAGAGCGTCCAGGTGGGAATTTTTTTCAGTACTTTTGTTGACAGTGCATCTTGC
1 TACTGTAGAAAAATAACGTCCAGCTGGGAGCTTTTTT-AGTACTTTTGCTGACAGTGCATCTTGC
* *
49623883 TTGAAGTG-TTTTTACCCTATTTTTTCAGAACCATCTTCTCAAAATTATTTTTTTCAAAAAC
65 TTGAAGCGTTTTTTACCCTATTTTTTCAGAACCATCTTCTCAAAATTA-TTTTTTCAGAAAC
* * * ** * * * *
49623944 TACTATAGAAAAAAAAGGTCCATTTGGGAGCTTTTTTTAGTACTTTTGCTAACGGTGCATCCTGT
1 TACTGTAGAAAAATAACGTCCAGCTGGGAGC-TTTTTTAGTACTTTTGCTGACAGTGCATCTTGC
* * *
49624009 TTGAAGCGTTTTTGACCCTATTTTTTTAGAATCATCTTCTCAAAATTATTTTTTCAGAAAC
65 TTGAAGCGTTTTTTACCCTATTTTTTCAGAACCATCTTCTCAAAATTATTTTTTCAGAAAC
*
49624070 TACTGTAGAAAAATAACGTCCAGCTGGGAGCTTTTTTAGTACTTTTGCTGGCAGTGCATCTTGCT
1 TACTGTAGAAAAATAACGTCCAGCTGGGAGCTTTTTTAGTACTTTTGCTGACAGTGCATCTTGCT
* *
49624135 TGAAGCGTTTTTTACCCTATTTTTTCAGAACCATATTCTCAAAATTATTTTTT-AGAAAT
66 TGAAGCGTTTTTTACCCTATTTTTTCAGAACCATCTTCTCAAAATTATTTTTTCAGAAAC
* * * *
49624194 TACTGTAGAAAAATAGCATCCAGCTGGGAGCTTTTGTCAATACTTTTGCTGAC
1 TACTGTAGAAAAATAACGTCCAGCTGGGAGCTTTT-TTAGTACTTTTGCTGAC
49624247 TGAACAAAAA
Statistics
Matches: 262, Mismatches: 38, Indels: 7
0.85 0.12 0.02
Matches are distributed among these distances:
124 38 0.15
125 92 0.35
126 90 0.34
127 42 0.16
ACGTcount: A:0.27, C:0.17, G:0.16, T:0.40
Consensus pattern (125 bp):
TACTGTAGAAAAATAACGTCCAGCTGGGAGCTTTTTTAGTACTTTTGCTGACAGTGCATCTTGCT
TGAAGCGTTTTTTACCCTATTTTTTCAGAACCATCTTCTCAAAATTATTTTTTCAGAAAC
Found at i:49624420 original size:33 final size:34
Alignment explanation
Indices: 49624367--49624436 Score: 115
Period size: 33 Copynumber: 2.1 Consensus size: 34
49624357 TTCCTAAACC
*
49624367 TTAATTTATTTTTTTTAAAACAATAAACCCTAAT
1 TTAATTTATTTTTTTAAAAACAATAAACCCTAAT
*
49624401 TTAATTTA-TTTTTTAAAAACCATAAACCCTAAT
1 TTAATTTATTTTTTTAAAAACAATAAACCCTAAT
49624434 TTA
1 TTA
49624437 TTTTCTCCAA
Statistics
Matches: 34, Mismatches: 2, Indels: 1
0.92 0.05 0.03
Matches are distributed among these distances:
33 26 0.76
34 8 0.24
ACGTcount: A:0.41, C:0.13, G:0.00, T:0.46
Consensus pattern (34 bp):
TTAATTTATTTTTTTAAAAACAATAAACCCTAAT
Found at i:49624456 original size:29 final size:28
Alignment explanation
Indices: 49624402--49624457 Score: 76
Period size: 29 Copynumber: 2.0 Consensus size: 28
49624392 AACCCTAATT
*
49624402 TAATTTATTTTTTAAAAACCATAAACCC
1 TAATTTATTTTTCAAAAACCATAAACCC
* *
49624430 TAATTTATTTTCTCCAAAACCCTAAACC
1 TAATTTATTTT-TCAAAAACCATAAACC
49624458 TTAAATAAAT
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
28 11 0.46
29 13 0.54
ACGTcount: A:0.39, C:0.23, G:0.00, T:0.38
Consensus pattern (28 bp):
TAATTTATTTTTCAAAAACCATAAACCC
Found at i:49626141 original size:19 final size:18
Alignment explanation
Indices: 49626092--49626142 Score: 59
Period size: 17 Copynumber: 2.8 Consensus size: 18
49626082 TTAACGTATG
49626092 ATTATATTAAAATATAATA
1 ATTA-ATTAAAATATAATA
* *
49626111 A-AAATTATAATATAATTA
1 ATTAATTAAAATATAA-TA
49626129 ATTAATTAAAATAT
1 ATTAATTAAAATAT
49626143 TTTTATAACT
Statistics
Matches: 26, Mismatches: 4, Indels: 4
0.76 0.12 0.12
Matches are distributed among these distances:
17 11 0.42
18 4 0.15
19 11 0.42
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (18 bp):
ATTAATTAAAATATAATA
Found at i:49628680 original size:22 final size:22
Alignment explanation
Indices: 49628652--49628693 Score: 59
Period size: 22 Copynumber: 1.9 Consensus size: 22
49628642 TAAAATTAAG
49628652 TAAAAATTATATAAT-TATATAA
1 TAAAAA-TATATAATATATATAA
*
49628674 TAAAAATATATTATATATAT
1 TAAAAATATATAATATATAT
49628694 CATTATGTTA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
21 7 0.39
22 11 0.61
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (22 bp):
TAAAAATATATAATATATATAA
Found at i:49629276 original size:184 final size:186
Alignment explanation
Indices: 49629065--49629432 Score: 652
Period size: 184 Copynumber: 2.0 Consensus size: 186
49629055 TTAAAAAATA
49629065 AATATTACACATATAAAAATTAAATTTACTAAAAATAATGATATTTATAATAATTATTTGATGTT
1 AATATTACACATATAAAAATTAAATTTACTAAAAATAATGATATTTATAATAATTATTTGATGTT
49629130 ATAAATAAAAGA-ATTATTAATTAAAAAT-AAAAAAATTGAAAACAATATATTTATTAATT-AAA
66 ATAAATAAAAGAGA-TATTAATTAAAAATAAAAAAAATTGAAAACAATATATTTATTAATTAAAA
*
49629192 AAAGCTTAAAATAACATGAAATAAAAATTACAAATGTGTTTAGAAAAGGAATTGAAC
130 AAAGCTTAAAACAACATGAAATAAAAATTACAAATGTGTTTAGAAAAGGAATTGAAC
*
49629249 AATATTACACATATAAAAATTAAATTTACTAAAAATAATGATATTTATAATAATTATTTGATTTT
1 AATATTACACATATAAAAATTAAATTTACTAAAAATAATGATATTTATAATAATTATTTGATGTT
*
49629314 ATAAATAAAAGAGATATTAATTAAAAGTAAAAAAAATTGAAAACAATATATTTATTAATTAAAAA
66 ATAAATAAAAGAGATATTAATTAAAAATAAAAAAAATTGAAAACAATATATTTATTAATT-AAAA
* *
49629379 AAAGCTTAAAACAATATGAAATAAAAATTACAAATGTGTTTAGAAAATGAATTG
130 AAAGCTTAAAACAACATGAAATAAAAATTACAAATGTGTTTAGAAAAGGAATTG
49629433 GACCTAAGAA
Statistics
Matches: 175, Mismatches: 5, Indels: 5
0.95 0.03 0.03
Matches are distributed among these distances:
184 89 0.51
185 32 0.18
187 54 0.31
ACGTcount: A:0.55, C:0.04, G:0.07, T:0.33
Consensus pattern (186 bp):
AATATTACACATATAAAAATTAAATTTACTAAAAATAATGATATTTATAATAATTATTTGATGTT
ATAAATAAAAGAGATATTAATTAAAAATAAAAAAAATTGAAAACAATATATTTATTAATTAAAAA
AAGCTTAAAACAACATGAAATAAAAATTACAAATGTGTTTAGAAAAGGAATTGAAC
Found at i:49629371 original size:34 final size:32
Alignment explanation
Indices: 49629327--49629395 Score: 77
Period size: 32 Copynumber: 2.1 Consensus size: 32
49629317 AATAAAAGAG
49629327 ATATTAATTAAAAGTAAAAAAAA-TTGAAAACAAT
1 ATATTAATT--AAGTAAAAAAAACTT-AAAACAAT
* *
49629361 ATATTTATTAATTAAAAAAAAGCTTAAAACAAT
1 ATATTAATTAAGTAAAAAAAA-CTTAAAACAAT
49629394 AT
1 AT
49629396 GAAATAAAAA
Statistics
Matches: 31, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
32 11 0.35
33 10 0.32
34 10 0.32
ACGTcount: A:0.61, C:0.04, G:0.04, T:0.30
Consensus pattern (32 bp):
ATATTAATTAAGTAAAAAAAACTTAAAACAAT
Found at i:49634214 original size:2 final size:2
Alignment explanation
Indices: 49634207--49634241 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
49634197 CTCAATCTTT
49634207 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
49634242 TTATATATAT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.00, C:0.49, G:0.00, T:0.51
Consensus pattern (2 bp):
TC
Found at i:49645671 original size:2 final size:2
Alignment explanation
Indices: 49645664--49645696 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
49645654 CACATCCTTA
49645664 AT 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 AT A
49645697 ACATGCTTAT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:49646813 original size:11 final size:11
Alignment explanation
Indices: 49646797--49646872 Score: 50
Period size: 11 Copynumber: 7.0 Consensus size: 11
49646787 ATATATACTA
49646797 AATAAATTAAT
1 AATAAATTAAT
*
49646808 AATAAAATAAT
1 AATAAATTAAT
*
49646819 AA-AATATTATTT
1 AATAA-ATTA-AT
49646831 AA-AAATTAA-
1 AATAAATTAAT
* * *
49646840 ATTAAAATATT
1 AATAAATTAAT
*
49646851 AATAAACTAAT
1 AATAAATTAAT
*
49646862 AATTAATTAAT
1 AATAAATTAAT
49646873 TAATTAATCT
Statistics
Matches: 49, Mismatches: 12, Indels: 8
0.71 0.17 0.12
Matches are distributed among these distances:
9 1 0.02
10 7 0.14
11 36 0.73
12 5 0.10
ACGTcount: A:0.62, C:0.01, G:0.00, T:0.37
Consensus pattern (11 bp):
AATAAATTAAT
Done.