Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007905.1 Hibiscus syriacus cultivar Beakdansim tig00110299_pilon, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 2946335
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 11 of 14
Found at i:2178846 original size:189 final size:189
Alignment explanation
Indices: 2178508--2178901 Score: 544
Period size: 189 Copynumber: 2.1 Consensus size: 189
2178498 CAACTAATGT
* *
2178508 TAAAAACATTTGCGGCGTTTTTTTGTCAAAACGCCATAAATGTATCATTAATTTACGGCGTTTGT
1 TAAAAACATTTGCGGCGTTTTTTTATCAAAACGCCATAAATGTATAATTAATTTACGGCGTTTGT
* * * * * * *
2178573 TACTACAACGCCGCTATATGTGCAACCTATTGCGGCGTTTTTGTCAAAACGCTGCTAAAGTACTA
66 TACCAAAACGCCGCTATATGTGCAACCTATTACGGCATTTTTATCAAAACACCGCTAAAGTACTA
*
2178638 ATTTATTGCGGCATTTATTAAAAAACGCCGCTATATGTCTAAAGTTAATGACGTTTAAA
131 ATTTATTACGGCATTTATTAAAAAACGCCGCTATATGTCTAAAGTTAATGACGTTTAAA
* **
2178697 TAAAATACATTTGCGGCG-TTTTTTATCTAAACGCCACT-AATGTATGAATT-ATTTGTGGCGTT
1 TAAAA-ACATTTGCGGCGTTTTTTTATCAAAACGCCA-TAAATGTAT-AATTAATTTACGGCGTT
*
2178759 TGTTACCAAAATGCCGCTATATGTG-AACCATATTACGGCATTTTTATCAAAACACCGCTAAAGT
63 TGTTACCAAAACGCCGCTATATGTGCAACC-TATTACGGCATTTTTATCAAAACACCGCTAAAGT
* * ** *
2178823 ACTAATTTGTTATGGTGTTTATTAAAAAACGCCGCTATATGTCTAAAGTTAATGATGTTTAAA
127 ACTAATTTATTACGGCATTTATTAAAAAACGCCGCTATATGTCTAAAGTTAATGACGTTTAAA
2178886 TAAAAAACATTTGCGG
1 T-AAAAACATTTGCGG
2178902 TACTAATGTA
Statistics
Matches: 181, Mismatches: 19, Indels: 10
0.86 0.09 0.05
Matches are distributed among these distances:
188 4 0.02
189 157 0.87
190 20 0.11
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.35
Consensus pattern (189 bp):
TAAAAACATTTGCGGCGTTTTTTTATCAAAACGCCATAAATGTATAATTAATTTACGGCGTTTGT
TACCAAAACGCCGCTATATGTGCAACCTATTACGGCATTTTTATCAAAACACCGCTAAAGTACTA
ATTTATTACGGCATTTATTAAAAAACGCCGCTATATGTCTAAAGTTAATGACGTTTAAA
Found at i:2179179 original size:318 final size:318
Alignment explanation
Indices: 2178602--2179187 Score: 897
Period size: 318 Copynumber: 1.8 Consensus size: 318
2178592 GTGCAACCTA
* * *
2178602 TTGCGGCGTTTTTGTCAAAACGCTGCTAAAGTACTAATTTATTGCGGCATTTATTAAAAAACGCC
1 TTGCGGCGTTTTTATCAAAACGCCGCTAAAGTACTAATCTATTGCGGCATTTATTAAAAAACGCC
* * * * *
2178667 GCTATATGTCTAAAGTTAATGACGTTTAAATAAAATACATTTGCGGCGTTTTTTATCTAAACGCC
66 GCTATATGTCTAAAGTTAATGACGTTTAAATAAAAAACATTTGCGGCATTTTCTATCAAAAAGCC
* * * * * * **
2178732 ACTAATGTATGAATTATTTGTGGCGTTTGTTACCAAAATGCCGCTATATGTGAACCATATTACGG
131 ACTAAAGTACGAATCATTTGAGGCGTTTGATACCAAAACGCCGCTATATGTGAACCATATTACAA
* * ***
2178797 CATTTTTATCAAAACACCGCTAAAGTACTAATTTGTTATGGTGTTTATTAAAAAACGCCGCTATA
196 CATTTTTATCAAAACACCGCTAAAGTACTAATATGTTACGACATTTATTAAAAAACGCCGCTATA
2178862 TGTCTAAAGTTAATGATGTTTAAATAAAAAACATTTGCGGTACTAATGTACAAATCAT
261 TGTCTAAAGTTAATGATGTTTAAATAAAAAACATTTGCGGTACTAATGTACAAATCAT
2178920 TTGCGGCGTTTGTTATCAAAACGCCGCTAAAGTACTAATCTATTGCGGCATTTATT-AAAAACGC
1 TTGCGGCGTTT-TTATCAAAACGCCGCTAAAGTACTAATCTATTGCGGCATTTATTAAAAAACGC
2178984 CGCTATATGTCTAAAGTTAATGACGTTTAAATAAAAAACATTTGCGGCATTTTCTATCAAAAAGC
65 CGCTATATGTCTAAAGTTAATGACGTTTAAATAAAAAACATTTGCGGCATTTTCTATCAAAAAGC
* *
2179049 CACTAAAGTCCGAATCATTTGCAGG-GTTTGATACCAAAACGCCGCTATATGTTAACCATATTAC
130 CACTAAAGTACGAATCATTTG-AGGCGTTTGATACCAAAACGCCGCTATATGTGAACCATATTAC
* * * *
2179113 AACATTTTTCTCGAAACGCCGCTAAAGTACTAATATGTTGCGACATTTATTAAAAAACGCCGCTA
194 AACATTTTTATCAAAACACCGCTAAAGTACTAATATGTTACGACATTTATTAAAAAACGCCGCTA
2179178 TATGTCTAAA
259 TATGTCTAAA
2179188 TTTAGTGGCG
Statistics
Matches: 239, Mismatches: 27, Indels: 4
0.89 0.10 0.01
Matches are distributed among these distances:
318 196 0.82
319 43 0.18
ACGTcount: A:0.34, C:0.17, G:0.16, T:0.33
Consensus pattern (318 bp):
TTGCGGCGTTTTTATCAAAACGCCGCTAAAGTACTAATCTATTGCGGCATTTATTAAAAAACGCC
GCTATATGTCTAAAGTTAATGACGTTTAAATAAAAAACATTTGCGGCATTTTCTATCAAAAAGCC
ACTAAAGTACGAATCATTTGAGGCGTTTGATACCAAAACGCCGCTATATGTGAACCATATTACAA
CATTTTTATCAAAACACCGCTAAAGTACTAATATGTTACGACATTTATTAAAAAACGCCGCTATA
TGTCTAAAGTTAATGATGTTTAAATAAAAAACATTTGCGGTACTAATGTACAAATCAT
Found at i:2181398 original size:20 final size:20
Alignment explanation
Indices: 2181356--2181398 Score: 52
Period size: 20 Copynumber: 2.1 Consensus size: 20
2181346 CCATTCGTTC
2181356 TAATAAAATAATATATTTATT
1 TAATAAAAT-ATATATTTATT
*
2181377 TAATAAAAT-TAGTATTTTTT
1 TAATAAAATATA-TATTTATT
2181397 TA
1 TA
2181399 TGAAGAATTG
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
19 2 0.10
20 9 0.45
21 9 0.45
ACGTcount: A:0.47, C:0.00, G:0.02, T:0.51
Consensus pattern (20 bp):
TAATAAAATATATATTTATT
Found at i:2186444 original size:36 final size:36
Alignment explanation
Indices: 2186396--2186465 Score: 113
Period size: 36 Copynumber: 1.9 Consensus size: 36
2186386 TTTAAAATAG
2186396 TTGTCTACTCTTTATTTACACGTAGGAAAGAGGTAA
1 TTGTCTACTCTTTATTTACACGTAGGAAAGAGGTAA
* * *
2186432 TTGTCTATTCTTTATTTATATGTAGGAAAGAGGT
1 TTGTCTACTCTTTATTTACACGTAGGAAAGAGGT
2186466 GGAGATTCAC
Statistics
Matches: 31, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
36 31 1.00
ACGTcount: A:0.29, C:0.10, G:0.20, T:0.41
Consensus pattern (36 bp):
TTGTCTACTCTTTATTTACACGTAGGAAAGAGGTAA
Found at i:2191519 original size:15 final size:16
Alignment explanation
Indices: 2191496--2191542 Score: 55
Period size: 16 Copynumber: 3.1 Consensus size: 16
2191486 TTTCTTTCAA
2191496 ATTTA-TTATTTTCTT
1 ATTTATTTATTTTCTT
2191511 A-TTATTTATTTT-TAT
1 ATTTATTTATTTTCT-T
*
2191526 ATTTATTTTTTTTCTT
1 ATTTATTTATTTTCTT
2191542 A
1 A
2191543 ACCAACAAAA
Statistics
Matches: 27, Mismatches: 1, Indels: 7
0.77 0.03 0.20
Matches are distributed among these distances:
14 4 0.15
15 10 0.37
16 12 0.44
17 1 0.04
ACGTcount: A:0.21, C:0.04, G:0.00, T:0.74
Consensus pattern (16 bp):
ATTTATTTATTTTCTT
Found at i:2193531 original size:13 final size:13
Alignment explanation
Indices: 2193513--2193611 Score: 126
Period size: 13 Copynumber: 7.6 Consensus size: 13
2193503 TGCGTCATAA
2193513 ATTTATGACGCGC
1 ATTTATGACGCGC
**
2193526 ATTTATGAAACGC
1 ATTTATGACGCGC
2193539 ATTTATGACGCGC
1 ATTTATGACGCGC
*
2193552 ATTTATGACGCAC
1 ATTTATGACGCGC
*
2193565 ATTTATGACACGC
1 ATTTATGACGCGC
** *
2193578 ATTTATGACATGT
1 ATTTATGACGCGC
*
2193591 ATTTATGACGCAC
1 ATTTATGACGCGC
2193604 ATTTATGA
1 ATTTATGA
2193612 TTCTCATTGC
Statistics
Matches: 73, Mismatches: 13, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
13 73 1.00
ACGTcount: A:0.30, C:0.18, G:0.17, T:0.34
Consensus pattern (13 bp):
ATTTATGACGCGC
Found at i:2193568 original size:39 final size:39
Alignment explanation
Indices: 2193513--2193611 Score: 153
Period size: 39 Copynumber: 2.5 Consensus size: 39
2193503 TGCGTCATAA
* *
2193513 ATTTATGACGCGCATTTATGAAACGCATTTATGACGCGC
1 ATTTATGACGCACATTTATGAAACGCATTTATGACACGC
* * *
2193552 ATTTATGACGCACATTTATGACACGCATTTATGACATGT
1 ATTTATGACGCACATTTATGAAACGCATTTATGACACGC
2193591 ATTTATGACGCACATTTATGA
1 ATTTATGACGCACATTTATGA
2193612 TTCTCATTGC
Statistics
Matches: 55, Mismatches: 5, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
39 55 1.00
ACGTcount: A:0.30, C:0.18, G:0.17, T:0.34
Consensus pattern (39 bp):
ATTTATGACGCACATTTATGAAACGCATTTATGACACGC
Found at i:2214792 original size:21 final size:22
Alignment explanation
Indices: 2214768--2214816 Score: 66
Period size: 21 Copynumber: 2.3 Consensus size: 22
2214758 CACCTAAGTG
2214768 CCACATAT-TTATCCCAAATGA
1 CCACATATATTATCCCAAATGA
* *
2214789 CCACAT-TATTGTCCCGAATGA
1 CCACATATATTATCCCAAATGA
2214810 CCACATA
1 CCACATA
2214817 AAACCCTCGA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
20 1 0.04
21 23 0.96
ACGTcount: A:0.35, C:0.31, G:0.08, T:0.27
Consensus pattern (22 bp):
CCACATATATTATCCCAAATGA
Found at i:2216070 original size:8 final size:8
Alignment explanation
Indices: 2216049--2216118 Score: 86
Period size: 8 Copynumber: 8.8 Consensus size: 8
2216039 CGGTAAGAAG
*
2216049 AAGAAGGA
1 AAGAAAGA
2216057 AAGAAAGA
1 AAGAAAGA
*
2216065 ATGAAAGA
1 AAGAAAGA
*
2216073 AAGAAGGA
1 AAGAAAGA
2216081 AAGAAAGA
1 AAGAAAGA
*
2216089 AGGAAAGA
1 AAGAAAGA
*
2216097 AAGAAGGA
1 AAGAAAGA
2216105 AAGAAAGA
1 AAGAAAGA
*
2216113 AGGAAA
1 AAGAAA
2216119 AGCTTTCAGA
Statistics
Matches: 52, Mismatches: 10, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
8 52 1.00
ACGTcount: A:0.67, C:0.00, G:0.31, T:0.01
Consensus pattern (8 bp):
AAGAAAGA
Found at i:2216070 original size:12 final size:12
Alignment explanation
Indices: 2216049--2216118 Score: 131
Period size: 12 Copynumber: 5.8 Consensus size: 12
2216039 CGGTAAGAAG
2216049 AAGAAGGAAAGA
1 AAGAAGGAAAGA
*
2216061 AAGAATGAAAGA
1 AAGAAGGAAAGA
2216073 AAGAAGGAAAGA
1 AAGAAGGAAAGA
2216085 AAGAAGGAAAGA
1 AAGAAGGAAAGA
2216097 AAGAAGGAAAGA
1 AAGAAGGAAAGA
2216109 AAGAAGGAAA
1 AAGAAGGAAA
2216119 AGCTTTCAGA
Statistics
Matches: 56, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
12 56 1.00
ACGTcount: A:0.67, C:0.00, G:0.31, T:0.01
Consensus pattern (12 bp):
AAGAAGGAAAGA
Found at i:2221679 original size:23 final size:23
Alignment explanation
Indices: 2221578--2221704 Score: 105
Period size: 23 Copynumber: 5.9 Consensus size: 23
2221568 CAGCTCGTAA
2221578 TTTGCACCGAAGTGCCACATA--
1 TTTGCACCGAAGTGCCACATAGG
*
2221599 ATTGTC-CCGAA-TGACCACATAGG
1 TTTG-CACCGAAGTG-CCACATAGG
* *
2221622 -TTACACCGAAGTGTCACATAGG
1 TTTGCACCGAAGTGCCACATAGG
* *
2221644 -TT--A---TAGTGTCACATAGG
1 TTTGCACCGAAGTGCCACATAGG
2221661 TTTGCACCGAAGTGCCACATAGG
1 TTTGCACCGAAGTGCCACATAGG
*
2221684 TTTGCACTGAAGTGCCACATA
1 TTTGCACCGAAGTGCCACATA
2221705 TTTATCCCAA
Statistics
Matches: 87, Mismatches: 7, Indels: 22
0.75 0.06 0.19
Matches are distributed among these distances:
17 13 0.15
18 2 0.02
20 4 0.05
21 16 0.18
22 18 0.21
23 34 0.39
ACGTcount: A:0.29, C:0.24, G:0.22, T:0.25
Consensus pattern (23 bp):
TTTGCACCGAAGTGCCACATAGG
Found at i:2226085 original size:21 final size:22
Alignment explanation
Indices: 2226060--2226104 Score: 56
Period size: 21 Copynumber: 2.1 Consensus size: 22
2226050 GTCTATAAAG
2226060 AGTCACAGGAGAAT-AAATATA
1 AGTCACAGGAGAATGAAATATA
* * *
2226081 AGTCATATGATAATGAAATATA
1 AGTCACAGGAGAATGAAATATA
2226103 AG
1 AG
2226105 ACTATGTGAA
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
21 11 0.55
22 9 0.45
ACGTcount: A:0.51, C:0.07, G:0.18, T:0.24
Consensus pattern (22 bp):
AGTCACAGGAGAATGAAATATA
Found at i:2233230 original size:30 final size:30
Alignment explanation
Indices: 2233196--2233275 Score: 135
Period size: 30 Copynumber: 2.7 Consensus size: 30
2233186 CAAAATGGTT
2233196 TTTGGACTTGAATTGAATTTACAAAACATA
1 TTTGGACTTGAATTGAATTTACAAAACATA
* *
2233226 TTTGGACTTGAATTAAATTTACAAAATATA
1 TTTGGACTTGAATTGAATTTACAAAACATA
2233256 TTTGGACTT-AATTGAATTTA
1 TTTGGACTTGAATTGAATTTA
2233276 TTCAAAATTT
Statistics
Matches: 47, Mismatches: 3, Indels: 1
0.92 0.06 0.02
Matches are distributed among these distances:
29 10 0.21
30 37 0.79
ACGTcount: A:0.39, C:0.07, G:0.12, T:0.41
Consensus pattern (30 bp):
TTTGGACTTGAATTGAATTTACAAAACATA
Found at i:2233373 original size:19 final size:19
Alignment explanation
Indices: 2233340--2233389 Score: 73
Period size: 19 Copynumber: 2.6 Consensus size: 19
2233330 AATGTTTTTA
* *
2233340 TGAATAGTAATTTACTATT
1 TGAACAGTAAATTACTATT
*
2233359 TGAACATTAAATTACTATT
1 TGAACAGTAAATTACTATT
2233378 TGAACAGTAAAT
1 TGAACAGTAAAT
2233390 CACTGTTTCC
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
19 27 1.00
ACGTcount: A:0.42, C:0.08, G:0.10, T:0.40
Consensus pattern (19 bp):
TGAACAGTAAATTACTATT
Found at i:2233533 original size:21 final size:21
Alignment explanation
Indices: 2233507--2233548 Score: 75
Period size: 21 Copynumber: 2.0 Consensus size: 21
2233497 ATTTGAATAT
*
2233507 TATGAAGGGGTATCGATTCCC
1 TATGAAGGGGTACCGATTCCC
2233528 TATGAAGGGGTACCGATTCCC
1 TATGAAGGGGTACCGATTCCC
2233549 CCCATTCTGG
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.24, C:0.21, G:0.29, T:0.26
Consensus pattern (21 bp):
TATGAAGGGGTACCGATTCCC
Found at i:2233614 original size:21 final size:23
Alignment explanation
Indices: 2233576--2233617 Score: 61
Period size: 21 Copynumber: 1.9 Consensus size: 23
2233566 ATTTTTGCAG
2233576 AAAAATCATTCCCAAACGGCTCC
1 AAAAATCATTCCCAAACGGCTCC
*
2233599 AAAAA-CA-TCCCCAACGGCT
1 AAAAATCATTCCCAAACGGCT
2233618 AGATATGACT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
21 11 0.61
22 2 0.11
23 5 0.28
ACGTcount: A:0.40, C:0.36, G:0.10, T:0.14
Consensus pattern (23 bp):
AAAAATCATTCCCAAACGGCTCC
Found at i:2233872 original size:34 final size:32
Alignment explanation
Indices: 2233833--2233902 Score: 104
Period size: 34 Copynumber: 2.1 Consensus size: 32
2233823 TTTTGTAAAG
*
2233833 GGGAAAGGTTCTAGCTTAGCCCGTGTAAAAGCTA
1 GGGAAAGGTTCTAGCTTAGCCCG-G-AAAAACTA
*
2233867 GGGAAAGGTTCTAGTTTAGCCCGGAAAAACTA
1 GGGAAAGGTTCTAGCTTAGCCCGGAAAAACTA
2233899 GGGA
1 GGGA
2233903 GTTGTAAGGT
Statistics
Matches: 34, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
32 11 0.32
33 1 0.03
34 22 0.65
ACGTcount: A:0.31, C:0.16, G:0.31, T:0.21
Consensus pattern (32 bp):
GGGAAAGGTTCTAGCTTAGCCCGGAAAAACTA
Found at i:2238350 original size:18 final size:20
Alignment explanation
Indices: 2238314--2238350 Score: 51
Period size: 18 Copynumber: 1.9 Consensus size: 20
2238304 TTTCTTTAAA
*
2238314 TTAATATAAGTATTTTCATT
1 TTAATATAAGTATTGTCATT
2238334 TTAATAT-A-TATTGTCAT
1 TTAATATAAGTATTGTCAT
2238351 ATTATGGTGA
Statistics
Matches: 16, Mismatches: 1, Indels: 2
0.84 0.05 0.11
Matches are distributed among these distances:
18 8 0.50
19 1 0.06
20 7 0.44
ACGTcount: A:0.35, C:0.05, G:0.05, T:0.54
Consensus pattern (20 bp):
TTAATATAAGTATTGTCATT
Found at i:2241357 original size:17 final size:20
Alignment explanation
Indices: 2241323--2241360 Score: 62
Period size: 20 Copynumber: 2.0 Consensus size: 20
2241313 ATTAACGGAG
2241323 AATAATAATGTAATTTTTTA
1 AATAATAATGTAATTTTTTA
2241343 AATAATAAT-T-ATTTTTTA
1 AATAATAATGTAATTTTTTA
2241361 TTTTATATTA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
18 8 0.44
19 1 0.06
20 9 0.50
ACGTcount: A:0.45, C:0.00, G:0.03, T:0.53
Consensus pattern (20 bp):
AATAATAATGTAATTTTTTA
Found at i:2241453 original size:26 final size:25
Alignment explanation
Indices: 2241411--2241459 Score: 62
Period size: 25 Copynumber: 1.9 Consensus size: 25
2241401 ATTCTTTTAA
*
2241411 TCGAATCAAAAATAATATATAATTT
1 TCGAATCAAAAATAATAAATAATTT
**
2241436 TCGAATCAAATTTAAATAAATAAT
1 TCGAATCAAAAAT-AATAAATAAT
2241460 ATATTCAAAT
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
25 11 0.55
26 9 0.45
ACGTcount: A:0.53, C:0.08, G:0.04, T:0.35
Consensus pattern (25 bp):
TCGAATCAAAAATAATAAATAATTT
Found at i:2242079 original size:5 final size:5
Alignment explanation
Indices: 2242065--2242128 Score: 101
Period size: 5 Copynumber: 12.8 Consensus size: 5
2242055 TTTAAAAATA
* * *
2242065 ATTAT ATTCT ATTCT ATTCT ATTAT ATTAT ATTAT ATTAT ATTAT ATTAT
1 ATTAT ATTAT ATTAT ATTAT ATTAT ATTAT ATTAT ATTAT ATTAT ATTAT
2242115 ATTAT ATTAT ATTA
1 ATTAT ATTAT ATTA
2242129 AGAGGCATGC
Statistics
Matches: 57, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
5 57 1.00
ACGTcount: A:0.36, C:0.05, G:0.00, T:0.59
Consensus pattern (5 bp):
ATTAT
Found at i:2243380 original size:2 final size:2
Alignment explanation
Indices: 2243375--2243401 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
2243365 TAAATAAATA
2243375 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 A
2243402 AATGTTAGAT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:2243488 original size:2 final size:2
Alignment explanation
Indices: 2243481--2243519 Score: 78
Period size: 2 Copynumber: 19.5 Consensus size: 2
2243471 ATAATAAAGA
2243481 AT 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 AT A
2243520 ATTGTTAGAT
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:2244228 original size:16 final size:16
Alignment explanation
Indices: 2244209--2244243 Score: 61
Period size: 16 Copynumber: 2.2 Consensus size: 16
2244199 CCCTAGCTGA
2244209 TTCAAGTCTAGACCGG
1 TTCAAGTCTAGACCGG
*
2244225 TTCAGGTCTAGACCGG
1 TTCAAGTCTAGACCGG
2244241 TTC
1 TTC
2244244 GGGCTACTGT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.20, C:0.26, G:0.26, T:0.29
Consensus pattern (16 bp):
TTCAAGTCTAGACCGG
Found at i:2244397 original size:2 final size:2
Alignment explanation
Indices: 2244390--2244449 Score: 65
Period size: 2 Copynumber: 31.5 Consensus size: 2
2244380 GAAATGAATA
*
2244390 AT AT AT AT AT AT AT AT AT AT AT AT AT GT -T GA- AT AT A- AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT -AT AT AT AT AT AT
*
2244430 AT AT AA AT AT -T AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT A
2244450 GTGATATAAA
Statistics
Matches: 50, Mismatches: 3, Indels: 10
0.79 0.05 0.16
Matches are distributed among these distances:
1 4 0.08
2 46 0.92
ACGTcount: A:0.50, C:0.00, G:0.03, T:0.47
Consensus pattern (2 bp):
AT
Found at i:2245357 original size:57 final size:57
Alignment explanation
Indices: 2245223--2245427 Score: 199
Period size: 57 Copynumber: 3.6 Consensus size: 57
2245213 GTAAAGTTGA
2245223 GCTTTGAGTTGGATATCCTTCGTTGTGAAGTTGAAATAC-A-A--G--TATTGTTTTG
1 GCTTTGAGTTGGATATCCTTCGTTGTGAAGTTGAAATACAATATTGAATATTG-TTTG
* * * *
2245275 ACTTTGCGTTGGACATCCTTCGTTGTGAAGTTGAAATCCAATATTGAATATTGTTTG
1 GCTTTGAGTTGGATATCCTTCGTTGTGAAGTTGAAATACAATATTGAATATTGTTTG
* * * * * *
2245332 GCTTTGAGTTGGATATCCTTCGTTGTGAAGTTAAAATTCAATCTTGTATAAATTGTGTC
1 GCTTTGAGTTGGATATCCTTCGTTGTGAAGTTGAAATACAATATTG-A-ATATTGTTTG
* * * *
2245391 GCTTCGAGTCT-AATATGCTTCGCTGTGAAGTTGAAAT
1 GCTTTGAGT-TGGATATCCTTCGTTGTGAAGTTGAAAT
2245428 TGACTCTAGT
Statistics
Matches: 126, Mismatches: 18, Indels: 11
0.81 0.12 0.07
Matches are distributed among these distances:
52 35 0.28
53 1 0.01
54 1 0.01
56 1 0.01
57 44 0.35
58 6 0.05
59 37 0.29
60 1 0.01
ACGTcount: A:0.24, C:0.13, G:0.22, T:0.40
Consensus pattern (57 bp):
GCTTTGAGTTGGATATCCTTCGTTGTGAAGTTGAAATACAATATTGAATATTGTTTG
Found at i:2246246 original size:19 final size:19
Alignment explanation
Indices: 2246208--2246262 Score: 64
Period size: 19 Copynumber: 3.0 Consensus size: 19
2246198 CTTGAACCTA
2246208 CCTTATTTC-TTTTCTATTT
1 CCTTATTTCTTTTTCT-TTT
2246227 CCTTATTTCTTTTTCTTTT
1 CCTTATTTCTTTTTCTTTT
2246246 -CTT-TTTCTCTTTT-TTTT
1 CCTTATTTCT-TTTTCTTTT
2246263 ATTTAGGGTC
Statistics
Matches: 34, Mismatches: 0, Indels: 6
0.85 0.00 0.15
Matches are distributed among these distances:
17 9 0.26
18 7 0.21
19 12 0.35
20 6 0.18
ACGTcount: A:0.05, C:0.20, G:0.00, T:0.75
Consensus pattern (19 bp):
CCTTATTTCTTTTTCTTTT
Found at i:2256671 original size:17 final size:18
Alignment explanation
Indices: 2256651--2256688 Score: 60
Period size: 17 Copynumber: 2.2 Consensus size: 18
2256641 TAAAAAAACT
2256651 AAAAAACAAATT-AAAGA
1 AAAAAACAAATTAAAAGA
*
2256668 AAAAAGCAAATTAAAAGA
1 AAAAAACAAATTAAAAGA
2256686 AAA
1 AAA
2256689 TAAAAGAAAT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
17 11 0.58
18 8 0.42
ACGTcount: A:0.76, C:0.05, G:0.08, T:0.11
Consensus pattern (18 bp):
AAAAAACAAATTAAAAGA
Found at i:2257922 original size:16 final size:16
Alignment explanation
Indices: 2257899--2257938 Score: 62
Period size: 16 Copynumber: 2.5 Consensus size: 16
2257889 AACCCTAGCT
2257899 GATTCGGGTCTAAACC
1 GATTCGGGTCTAAACC
* *
2257915 GGTTCGGGTCTAGACC
1 GATTCGGGTCTAAACC
2257931 GATTCGGG
1 GATTCGGG
2257939 CTGCTATTGG
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:0.17, C:0.23, G:0.35, T:0.25
Consensus pattern (16 bp):
GATTCGGGTCTAAACC
Found at i:2258090 original size:2 final size:2
Alignment explanation
Indices: 2258083--2258133 Score: 56
Period size: 2 Copynumber: 27.0 Consensus size: 2
2258073 GAAATGAATA
*
2258083 AT AT AT AT AT AT AT AT AT AT -T GA- AT AT A- AT AT AT AT AA AT
1 AT AT AT AT AT AT AT AT AT AT AT -AT AT AT AT AT AT AT AT AT AT
2258123 AT -T AT AT AT AT
1 AT AT AT AT AT AT
2258134 GGTGATATAA
Statistics
Matches: 42, Mismatches: 2, Indels: 10
0.78 0.04 0.19
Matches are distributed among these distances:
1 4 0.10
2 38 0.90
ACGTcount: A:0.51, C:0.00, G:0.02, T:0.47
Consensus pattern (2 bp):
AT
Found at i:2258114 original size:26 final size:27
Alignment explanation
Indices: 2258077--2258129 Score: 74
Period size: 26 Copynumber: 2.0 Consensus size: 27
2258067 GTAAATGAAA
*
2258077 TGAATAATATATATATATATA-TATAT
1 TGAATAATATATATATAAATATTATAT
2258103 TGAAT-ATAATATATATAAATATTATAT
1 TGAATAAT-ATATATATAAATATTATAT
2258130 ATATGGTGAT
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
25 2 0.08
26 17 0.71
27 5 0.21
ACGTcount: A:0.51, C:0.00, G:0.04, T:0.45
Consensus pattern (27 bp):
TGAATAATATATATATAAATATTATAT
Found at i:2258131 original size:22 final size:23
Alignment explanation
Indices: 2258083--2258132 Score: 70
Period size: 22 Copynumber: 2.3 Consensus size: 23
2258073 GAAATGAATA
*
2258083 ATATAT-ATATATATATATATTG
1 ATATATAATATATATAAATATTG
2258105 A-ATATAATATATATAAATATT-
1 ATATATAATATATATAAATATTG
2258126 ATATATA
1 ATATATA
2258133 TGGTGATATA
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
21 5 0.20
22 20 0.80
ACGTcount: A:0.52, C:0.00, G:0.02, T:0.46
Consensus pattern (23 bp):
ATATATAATATATATAAATATTG
Found at i:2258608 original size:25 final size:25
Alignment explanation
Indices: 2258578--2258632 Score: 110
Period size: 25 Copynumber: 2.2 Consensus size: 25
2258568 ATACAATTTA
2258578 AATCTTTAGATTACATGCCAACTAT
1 AATCTTTAGATTACATGCCAACTAT
2258603 AATCTTTAGATTACATGCCAACTAT
1 AATCTTTAGATTACATGCCAACTAT
2258628 AATCT
1 AATCT
2258633 ATATAACAAA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 30 1.00
ACGTcount: A:0.36, C:0.20, G:0.07, T:0.36
Consensus pattern (25 bp):
AATCTTTAGATTACATGCCAACTAT
Found at i:2265674 original size:22 final size:22
Alignment explanation
Indices: 2265644--2265732 Score: 142
Period size: 22 Copynumber: 4.0 Consensus size: 22
2265634 AGTAGAGGGT
2265644 TACATAGGTCCTTCGGGACATA
1 TACATAGGTCCTTCGGGACATA
*
2265666 TACACAGGTCCTTCGGGACATA
1 TACATAGGTCCTTCGGGACATA
**
2265688 TGTATAGGTCCTTCGGGACATA
1 TACATAGGTCCTTCGGGACATA
*
2265710 TGCATAGGTCCTTCGGGACATA
1 TACATAGGTCCTTCGGGACATA
2265732 T
1 T
2265733 TTCACATGCC
Statistics
Matches: 62, Mismatches: 5, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
22 62 1.00
ACGTcount: A:0.25, C:0.22, G:0.25, T:0.28
Consensus pattern (22 bp):
TACATAGGTCCTTCGGGACATA
Found at i:2266062 original size:16 final size:17
Alignment explanation
Indices: 2266031--2266063 Score: 50
Period size: 18 Copynumber: 1.9 Consensus size: 17
2266021 AAGATATAGA
2266031 ATATGAACATAAGAGATC
1 ATATGAACA-AAGAGATC
2266049 ATATGAAC-AAGAGAT
1 ATATGAACAAAGAGAT
2266064 AAGAGATAAG
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:0.52, C:0.09, G:0.18, T:0.21
Consensus pattern (17 bp):
ATATGAACAAAGAGATC
Found at i:2274370 original size:12 final size:12
Alignment explanation
Indices: 2274350--2274385 Score: 63
Period size: 12 Copynumber: 3.0 Consensus size: 12
2274340 CAAACATATA
*
2274350 TATGCATGCATG
1 TATGTATGCATG
2274362 TATGTATGCATG
1 TATGTATGCATG
2274374 TATGTATGCATG
1 TATGTATGCATG
2274386 ATTCCTTTAT
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
12 23 1.00
ACGTcount: A:0.25, C:0.11, G:0.25, T:0.39
Consensus pattern (12 bp):
TATGTATGCATG
Found at i:2274371 original size:16 final size:16
Alignment explanation
Indices: 2274350--2274381 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
2274340 CAAACATATA
2274350 TATGCATGCATGTATG
1 TATGCATGCATGTATG
*
2274366 TATGCATGTATGTATG
1 TATGCATGCATGTATG
2274382 CATGATTCCT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.25, C:0.09, G:0.25, T:0.41
Consensus pattern (16 bp):
TATGCATGCATGTATG
Found at i:2276047 original size:16 final size:17
Alignment explanation
Indices: 2276014--2276047 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
2276004 ATTTCACGGA
*
2276014 AAAAAAATTCTCACAAC
1 AAAAAAACTCTCACAAC
2276031 AAAAAAACTCTCA-AAC
1 AAAAAAACTCTCACAAC
2276047 A
1 A
2276048 CTCTCCTCCA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 4 0.25
17 12 0.75
ACGTcount: A:0.62, C:0.24, G:0.00, T:0.15
Consensus pattern (17 bp):
AAAAAAACTCTCACAAC
Found at i:2277015 original size:33 final size:35
Alignment explanation
Indices: 2276959--2277393 Score: 142
Period size: 37 Copynumber: 11.4 Consensus size: 35
2276949 TTCAAAGCCG
*
2276959 TTTTTAAAACTATATATTATACATTTTTAAAATTA
1 TTTTAAAAACTATATATTATACATTTTTAAAATTA
2276994 TTTTAAAAACT-T-TATTATACATTTTTAAAATTA
1 TTTTAAAAACTATATATTATACATTTTTAAAATTA
2277027 TTTTAAAATACTATATACTATATACTATATGTTTTCAAAACCGCTTCAAATTA
1 TTTTAAAA-ACTATATA-T-TATAC---AT-TTTT----A-------AAATTA
* ** *
2277080 TTTTAAAAACTATATACTATATGTTTTCAAAACCGTT-
1 TTTTAAAAACTATATATTATACATTTTTAAAA---TTA
* * ** * *
2277117 TTTAAAAAACTATATAATATATGTTTTCAAAAATTG
1 TTTTAAAAACTATATATTATACATTTT-TAAAATTA
* * *** * *
2277153 TTTTCAAAACTATATAATATGTGTTTTCAAAAATTGT
1 TTTTAAAAACTATATATTATACATTTT-TAAAATT-A
* * * * *
2277190 TTTTCAAAACTATATAATATACGTTTTCAAAAATGTG
1 TTTTAAAAACTATATATTATACATTTT-TAAAAT-TA
* * * **
2277227 TTTTCAAAATTATATAATATATGTTTTT-AAATCGTA
1 TTTTAAAAACTATATATTATACATTTTTAAAAT--TA
* * * *
2277263 TTTTCAAAACCATAT-TATATACATTTTCAAAAATCAATTT
1 TTTTAAAAACTATATAT-TATACATTTT---TAA--AATTA
* *
2277303 TTTTAAAAACTATATATTATATATTTTTAAAAATCA
1 TTTTAAAAACTATATATTATACATTTTT-AAAATTA
* * *
2277339 TTTTCTAAAAACTATATGTTATACGTTTTTTCAAAAATA
1 -TTT-TAAAAACTATATATTATAC-ATTTTT-AAAATTA
2277378 TTTTCAAAAACTATAT
1 TTTT-AAAAACTATAT
2277394 TATATTATTA
Statistics
Matches: 321, Mismatches: 38, Indels: 79
0.73 0.09 0.18
Matches are distributed among these distances:
33 29 0.09
34 4 0.01
35 20 0.06
36 60 0.19
37 87 0.27
38 45 0.14
39 10 0.03
40 24 0.07
41 3 0.01
42 8 0.02
46 4 0.01
47 1 0.00
50 4 0.01
52 8 0.02
53 14 0.04
ACGTcount: A:0.41, C:0.10, G:0.04, T:0.45
Consensus pattern (35 bp):
TTTTAAAAACTATATATTATACATTTTTAAAATTA
Found at i:2277122 original size:36 final size:36
Alignment explanation
Indices: 2277080--2277355 Score: 236
Period size: 37 Copynumber: 7.4 Consensus size: 36
2277070 CTTCAAATTA
* *
2277080 TTTTAAAAACTATATACTATATGTTTTCAAAACCGT
1 TTTTAAAAACTATATAATATATGTTTTCAAAATCGT
*
2277116 TTTTAAAAAACTATATAATATATGTTTTCAAAAATTG-
1 TTTT-AAAAACTATATAATATATGTTTTC-AAAATCGT
* * *
2277153 TTTTCAAAACTATATAATATGTGTTTTCAAAAATTGT
1 TTTTAAAAACTATATAATATATGTTTTC-AAAATCGT
* *
2277190 TTTTCAAAACTATATAATATACGTTTTCAAAAAT-GT
1 TTTTAAAAACTATATAATATATGTTTTC-AAAATCGT
* * *
2277226 GTTTTCAAAATTATATAATATATGTTTT-TAAATCGT
1 -TTTTAAAAACTATATAATATATGTTTTCAAAATCGT
* * * ** *
2277262 ATTTTCAAAACCATATTATATACATTTTCAAAAATCAATTT
1 -TTTTAAAAACTATATAATATATGTTTTC-AAAATC---GT
* *
2277303 TTTTAAAAACTATATATTATATAT-TTTTAAAAATCAT
1 TTTTAAAAACTATATA--ATATATGTTTTCAAAATCGT
2277340 TTTCTAAAAACTATAT
1 TTT-TAAAAACTATAT
2277356 GTTATACGTT
Statistics
Matches: 203, Mismatches: 24, Indels: 24
0.81 0.10 0.10
Matches are distributed among these distances:
35 4 0.02
36 60 0.30
37 88 0.43
38 22 0.11
40 19 0.09
41 5 0.02
42 5 0.02
ACGTcount: A:0.42, C:0.09, G:0.04, T:0.45
Consensus pattern (36 bp):
TTTTAAAAACTATATAATATATGTTTTCAAAATCGT
Found at i:2277178 original size:73 final size:72
Alignment explanation
Indices: 2277074--2277398 Score: 305
Period size: 73 Copynumber: 4.4 Consensus size: 72
2277064 AAACCGCTTC
* * * * * *
2277074 AAATTATTTTAAAAACTATATACTATATGTTTTCAAAACCGTTTTTAAAAAACTATATAATATAT
1 AAATTGTTTTCAAAACTATATAATATATGTTTTCAAAATCGTTTTT-CAAAACTATATAATATAC
2277139 GTTTTCAA
65 GTTTTCAA
* *
2277147 AAATTGTTTTCAAAACTATATAATATGTGTTTTCAAAAATTGTTTTTCAAAACTATATAATATAC
1 AAATTGTTTTCAAAACTATATAATATATGTTTTC-AAAATCGTTTTTCAAAACTATATAATATAC
2277212 GTTTTCAA
65 GTTTTCAA
* * * *
2277220 AAATGTGTTTTCAAAATTATATAATATATGTTTT-TAAATCGTATTTTCAAAACCATATTATATA
1 AAAT-TGTTTTCAAAACTATATAATATATGTTTTCAAAATCGT-TTTTCAAAACTATATAATATA
*
2277284 CATTTTCAAAA
64 CGTTTTC--AA
* * * * * **
2277295 ATCAATTTTTTTAAAAACTATATATTATATAT-TTTTAAAAATCATTTTCTAAAAACTATATGTT
1 A--AATTGTTTTCAAAACTATATA--ATATATGTTTTCAAAATCGTTTT-TCAAAACTATATAAT
2277359 ATACGTTTTTTCAA
61 ATACG--TTTTCAA
* *
2277373 AAA-TATTTTCAAAAACTATATTATAT
1 AAATTGTTTTC-AAAACTATATAATAT
2277399 TATTATTTAT
Statistics
Matches: 210, Mismatches: 28, Indels: 27
0.79 0.11 0.10
Matches are distributed among these distances:
72 6 0.03
73 83 0.40
74 41 0.20
75 8 0.04
76 27 0.13
77 10 0.05
78 30 0.14
80 5 0.02
ACGTcount: A:0.42, C:0.09, G:0.04, T:0.45
Consensus pattern (72 bp):
AAATTGTTTTCAAAACTATATAATATATGTTTTCAAAATCGTTTTTCAAAACTATATAATATACG
TTTTCAA
Found at i:2277361 original size:38 final size:38
Alignment explanation
Indices: 2277083--2277393 Score: 148
Period size: 37 Copynumber: 8.3 Consensus size: 38
2277073 CAAATTATTT
* * * * *
2277083 TAAAAACTATATACTATAT-GTTTTCAAAACCGTTTT-
1 TAAAAACTATATATTATATATTTTTAAAAATCATTTTC
* * * **
2277119 TAAAAAACTATATAATATATGTTTTCAAAAATTGTTTTC
1 T-AAAAACTATATATTATATATTTTTAAAAATCATTTTC
* * * * **
2277158 --AAAACTATATAATATGTGTTTTCAAAAATTGTTTT-
1 TAAAAACTATATATTATATATTTTTAAAAATCATTTTC
* * ** * *
2277193 TCAAAACTATATAATATACGTTTTCAAAAAT-GTGTTT-
1 TAAAAACTATATATTATATATTTTTAAAAATCAT-TTTC
* * * *
2277230 TCAAAATTATATAATATATGTTTTT--AAATCGTATTTTC
1 TAAAAACTATATATTATATATTTTTAAAAATC--ATTTTC
* * * *
2277268 --AAAACCATAT-TATATACATTTTCAAAAATCAATTTTTT
1 TAAAAACTATATAT-TATATATTTTTAAAAATC-A-TTTTC
2277306 TAAAAACTATATATTATATATTTTTAAAAATCATTTTC
1 TAAAAACTATATATTATATATTTTTAAAAATCATTTTC
*
2277344 TAAAAACTATATGTTATACGT-TTTTTCAAAAAT-ATTTTC
1 TAAAAACTATATATTATA--TATTTTT-AAAAATCATTTTC
2277383 -AAAAACTATAT
1 TAAAAACTATAT
2277394 TATATTATTA
Statistics
Matches: 229, Mismatches: 26, Indels: 38
0.78 0.09 0.13
Matches are distributed among these distances:
35 4 0.02
36 53 0.23
37 73 0.32
38 54 0.24
39 12 0.05
40 32 0.14
41 1 0.00
ACGTcount: A:0.42, C:0.10, G:0.05, T:0.44
Consensus pattern (38 bp):
TAAAAACTATATATTATATATTTTTAAAAATCATTTTC
Found at i:2280489 original size:18 final size:18
Alignment explanation
Indices: 2280457--2280531 Score: 89
Period size: 18 Copynumber: 4.2 Consensus size: 18
2280447 CAATGAACAC
2280457 TTGTCCC-AGAGGACCACT
1 TTGTCCCGA-AGGACCACT
* *
2280475 TTGTCTCGAATGACCACT
1 TTGTCCCGAAGGACCACT
2280493 TTGTCCCGAAGGACCACT
1 TTGTCCCGAAGGACCACT
* * *
2280511 ATATCCCGAAGTACCACT
1 TTGTCCCGAAGGACCACT
2280529 TTG
1 TTG
2280532 AACCCTCGAC
Statistics
Matches: 47, Mismatches: 9, Indels: 2
0.81 0.16 0.03
Matches are distributed among these distances:
18 46 0.98
19 1 0.02
ACGTcount: A:0.24, C:0.31, G:0.19, T:0.27
Consensus pattern (18 bp):
TTGTCCCGAAGGACCACT
Found at i:2280527 original size:36 final size:36
Alignment explanation
Indices: 2280448--2280531 Score: 93
Period size: 36 Copynumber: 2.4 Consensus size: 36
2280438 CACTAGGGGC
* * * *
2280448 AATGAACAC-TTGTCCCAGAGGACCACTTTGTCTCG
1 AATGACCACTTTGTCCCAGAGGACCACTATATCCCG
2280483 AATGACCACTTTGTCCC-GAAGGACCACTATATCCCG
1 AATGACCACTTTGTCCCAG-AGGACCACTATATCCCG
2280519 AA-GTACCACTTTG
1 AATG-ACCACTTTG
2280532 AACCCTCGAC
Statistics
Matches: 42, Mismatches: 4, Indels: 5
0.82 0.08 0.10
Matches are distributed among these distances:
35 10 0.24
36 32 0.76
ACGTcount: A:0.27, C:0.30, G:0.18, T:0.25
Consensus pattern (36 bp):
AATGACCACTTTGTCCCAGAGGACCACTATATCCCG
Found at i:2282149 original size:18 final size:18
Alignment explanation
Indices: 2282125--2282235 Score: 168
Period size: 18 Copynumber: 6.2 Consensus size: 18
2282115 CACTGAACAC
*
2282125 TTGTCCCAAAGGACCACT
1 TTGTCCCGAAGGACCACT
*
2282143 ATGTCCCGAAGGACCACT
1 TTGTCCCGAAGGACCACT
2282161 TTGTCCCGAAGGACCACT
1 TTGTCCCGAAGGACCACT
2282179 TTGTCCCGAAGGACCACT
1 TTGTCCCGAAGGACCACT
*
2282197 TTGTCTCGAAGGACCACT
1 TTGTCCCGAAGGACCACT
* * *
2282215 ATGTCTCGAAGGACCATT
1 TTGTCCCGAAGGACCACT
2282233 TTG
1 TTG
2282236 AACCCTCAAC
Statistics
Matches: 86, Mismatches: 7, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
18 86 1.00
ACGTcount: A:0.24, C:0.30, G:0.22, T:0.24
Consensus pattern (18 bp):
TTGTCCCGAAGGACCACT
Found at i:2284383 original size:31 final size:31
Alignment explanation
Indices: 2284311--2284387 Score: 88
Period size: 31 Copynumber: 2.5 Consensus size: 31
2284301 CTTTTTGAAA
*
2284311 TTATAATTTTGGTC-CCTAAACTTTTCAAAGT
1 TTATAA-TTTGGTCACCTAAACTTTACAAAGT
*
2284342 TTATACTTTGGTCACC-AAACTTTACAACA-T
1 TTATAATTTGGTCACCTAAACTTTACAA-AGT
2284372 CTTATAATTTGGTCAC
1 -TTATAATTTGGTCAC
2284388 TAACTAAATC
Statistics
Matches: 40, Mismatches: 3, Indels: 6
0.82 0.06 0.12
Matches are distributed among these distances:
30 18 0.45
31 22 0.55
ACGTcount: A:0.30, C:0.19, G:0.09, T:0.42
Consensus pattern (31 bp):
TTATAATTTGGTCACCTAAACTTTACAAAGT
Found at i:2291202 original size:4 final size:4
Alignment explanation
Indices: 2291193--2291237 Score: 54
Period size: 4 Copynumber: 10.5 Consensus size: 4
2291183 CCTAGCAAAA
*
2291193 AAAT AAAT AAAT AAGT GAAAT AAAT AAAT AAAAT AATAT AAAT AA
1 AAAT AAAT AAAT AAAT -AAAT AAAT AAAT -AAAT AA-AT AAAT AA
2291238 CTAACTATAT
Statistics
Matches: 36, Mismatches: 2, Indels: 6
0.82 0.05 0.14
Matches are distributed among these distances:
4 25 0.69
5 11 0.31
ACGTcount: A:0.71, C:0.00, G:0.04, T:0.24
Consensus pattern (4 bp):
AAAT
Found at i:2291215 original size:13 final size:13
Alignment explanation
Indices: 2291193--2291237 Score: 56
Period size: 13 Copynumber: 3.5 Consensus size: 13
2291183 CCTAGCAAAA
2291193 AAAT-AAATAAAT
1 AAATAAAATAAAT
* *
2291205 AAGTGAAATAAAT
1 AAATAAAATAAAT
2291218 AAATAAAATAATAT
1 AAATAAAATAA-AT
2291232 AAATAA
1 AAATAA
2291238 CTAACTATAT
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
12 3 0.11
13 17 0.61
14 8 0.29
ACGTcount: A:0.71, C:0.00, G:0.04, T:0.24
Consensus pattern (13 bp):
AAATAAAATAAAT
Found at i:2291291 original size:35 final size:36
Alignment explanation
Indices: 2291247--2291332 Score: 97
Period size: 35 Copynumber: 2.5 Consensus size: 36
2291237 ACTAACTATA
*
2291247 TATATATTATACGTTTT-CAAAGCCATTTTTAAAAC
1 TATATATTATACGTTTTCCAAAGCCATTTTAAAAAC
** ***
2291282 TATATATTATATATTTTCCAAATTTATTTTAAAAAC
1 TATATATTATACGTTTTCCAAAGCCATTTTAAAAAC
2291318 T-T-TATTATACGTTTT
1 TATATATTATACGTTTT
2291333 TAAAATTATT
Statistics
Matches: 42, Mismatches: 8, Indels: 3
0.79 0.15 0.06
Matches are distributed among these distances:
34 11 0.26
35 16 0.38
36 15 0.36
ACGTcount: A:0.36, C:0.10, G:0.03, T:0.50
Consensus pattern (36 bp):
TATATATTATACGTTTTCCAAAGCCATTTTAAAAAC
Found at i:2291318 original size:36 final size:36
Alignment explanation
Indices: 2291271--2291701 Score: 228
Period size: 37 Copynumber: 11.4 Consensus size: 36
2291261 TTTCAAAGCC
* * * * *
2291271 ATTTTTAAAACTATATATTATATATTTTCCAAATTT
1 ATTTTAAAAACTATATAATATATGTTTTCAAAAATT
* * *
2291307 ATTTTAAAAACT-T-TATTATACGTTTT-TAAAATT
1 ATTTTAAAAACTATATAATATATGTTTTCAAAAATT
** *
2291340 ATTTTAAAAAACTATATTCTATATGTTTTTAAAACCGCTTCAAAATT
1 ATTTT-AAAAACTATATAATATATG-TTTT-------C--AAAAATT
* * *
2291387 ATTTTAAAAACTATATACTCTATGTTTTCAAAACCGTT
1 ATTTTAAAAACTATATAATATATGTTTTCAAAA--ATT
***
2291425 -TAAAAAAAACTATATAATATATGTTTTCAAAAATT
1 ATTTTAAAAACTATATAATATATGTTTTCAAAAATT
* *
2291460 ATTTTCAAAACTATATAATATATATTTTCAAAAATT
1 ATTTTAAAAACTATATAATATATGTTTTCAAAAATT
* *
2291496 ATTTTTCAAAACTATATAATATACGTTTTCAAAAATGT
1 A-TTTTAAAAACTATATAATATATGTTTTCAAAAAT-T
* * * * *
2291534 GTTTTCAAAATTATATAATATATGTTTT-TAAATTGT
1 ATTTTAAAAACTATATAATATATGTTTTCAAAAAT-T
* * **
2291570 AATTTTAAAATC-ATATTATATACATTTTCAAAAATCGAT
1 -ATTTTAAAAACTATATAATATATGTTTTCAAAAAT---T
* * * **
2291609 TTTTTAAAAAATTATATATTATATGTTTTCAAAAACC
1 ATTTT-AAAAACTATATAATATATGTTTTCAAAAATT
* * * *
2291646 GTTTCCTAAAAACTATA-AGTTATACGCTTTTCAAAAAAT
1 ATTT--TAAAAACTATATA-ATATATG-TTTTCAAAAATT
2291685 ATTTTAAAAAACTATAT
1 ATTTT-AAAAACTATAT
2291702 TTTATTATTA
Statistics
Matches: 308, Mismatches: 56, Indels: 59
0.73 0.13 0.14
Matches are distributed among these distances:
33 10 0.03
34 18 0.06
35 4 0.01
36 70 0.23
37 104 0.34
38 33 0.11
39 19 0.06
40 18 0.06
45 4 0.01
46 17 0.06
47 11 0.04
ACGTcount: A:0.43, C:0.10, G:0.04, T:0.44
Consensus pattern (36 bp):
ATTTTAAAAACTATATAATATATGTTTTCAAAAATT
Found at i:2291339 original size:34 final size:36
Alignment explanation
Indices: 2291305--2291373 Score: 99
Period size: 36 Copynumber: 2.0 Consensus size: 36
2291295 TTTTCCAAAT
*
2291305 TTATTTT-AAAAACTTTA-T-TATACGTTTTTAAAA
1 TTATTTTAAAAAACTATATTCTATACGTTTTTAAAA
*
2291338 TTATTTTAAAAAACTATATTCTATATGTTTTTAAAA
1 TTATTTTAAAAAACTATATTCTATACGTTTTTAAAA
2291374 CCGCTTCAAA
Statistics
Matches: 31, Mismatches: 2, Indels: 3
0.86 0.06 0.08
Matches are distributed among these distances:
33 7 0.23
34 9 0.29
35 1 0.03
36 14 0.45
ACGTcount: A:0.41, C:0.06, G:0.03, T:0.51
Consensus pattern (36 bp):
TTATTTTAAAAAACTATATTCTATACGTTTTTAAAA
Found at i:2291411 original size:46 final size:47
Alignment explanation
Indices: 2291334--2291422 Score: 144
Period size: 46 Copynumber: 1.9 Consensus size: 47
2291324 ATACGTTTTT
* *
2291334 AAAATTATTTTAAAAAACTATATTCTATATGTTTTTAAAACCGCTTC
1 AAAATTATTTTAAAAAACTATATACTATATGTTTTCAAAACCGCTTC
*
2291381 AAAATTATTTT-AAAAACTATATACTCTATGTTTTCAAAACCG
1 AAAATTATTTTAAAAAACTATATACTATATGTTTTCAAAACCG
2291423 TTTAAAAAAA
Statistics
Matches: 39, Mismatches: 3, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
46 28 0.72
47 11 0.28
ACGTcount: A:0.42, C:0.13, G:0.04, T:0.40
Consensus pattern (47 bp):
AAAATTATTTTAAAAAACTATATACTATATGTTTTCAAAACCGCTTC
Found at i:2291460 original size:73 final size:73
Alignment explanation
Indices: 2291381--2291701 Score: 220
Period size: 73 Copynumber: 4.3 Consensus size: 73
2291371 AAACCGCTTC
* * * *
2291381 AAAATTATTTTAAAAACTATATACTCTATGTTTTCAAAACCGT-TTAAAAAAAACTATATAATAT
1 AAAATTATTTTCAAAACTATATAATATATGTTTTCAAAA-AGTATTAAAAAAAACTATATAATAT
*
2291445 ATGTTTTCA
65 ACGTTTTCA
* * ****
2291454 AAAATTATTTTCAAAACTATATAATATATATTTTCAAAAATTATTTTTCAAAACTATATAATATA
1 AAAATTATTTTCAAAACTATATAATATATGTTTTCAAAAAGTATTAAAAAAAACTATATAATATA
2291519 CGTTTTCA
66 CGTTTTCA
* * * ** ** * *
2291527 AAAATGTGTTTTCAAAATTATATAATATATGTTTTTAAATTGTAATT-TTAAAATC-ATATTATA
1 AAAAT-TATTTTCAAAACTATATAATATATGTTTTCAAAAAGT-ATTAAAAAAAACTATATAATA
*
2291590 TACATTTTCA
64 TACGTTTTCA
* * * * ***
2291600 AAAATCGATTTTTTAAAAAATTATATATTATATGTTTTCAAAAACCGT-TTCCTAAAAACTATA-
1 AAAAT---TATTTT-CAAAACTATATAATATATGTTTTCAAAAA--GTATTAAAAAAAACTATAT
*
2291663 AGTTATACGCTTTTCA
60 A-ATATACG-TTTTCA
* *
2291679 AAAAATATTTTAAAAAACTATAT
1 AAAATTATTTT-CAAAACTATAT
2291702 TTTATTATTA
Statistics
Matches: 199, Mismatches: 37, Indels: 21
0.77 0.14 0.08
Matches are distributed among these distances:
72 1 0.01
73 86 0.43
74 36 0.18
75 8 0.04
76 42 0.21
77 6 0.03
78 10 0.05
79 10 0.05
ACGTcount: A:0.44, C:0.09, G:0.04, T:0.42
Consensus pattern (73 bp):
AAAATTATTTTCAAAACTATATAATATATGTTTTCAAAAAGTATTAAAAAAAACTATATAATATA
CGTTTTCA
Found at i:2292936 original size:15 final size:15
Alignment explanation
Indices: 2292898--2292941 Score: 52
Period size: 15 Copynumber: 2.9 Consensus size: 15
2292888 AATTCTTTAA
* *
2292898 TAATTTATTATTTTAT
1 TAATTT-TTATTATAC
*
2292914 TAAATTTTATTATAC
1 TAATTTTTATTATAC
2292929 TAATTTTTATTAT
1 TAATTTTTATTAT
2292942 TTTTTGCAGT
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
15 19 0.79
16 5 0.21
ACGTcount: A:0.34, C:0.02, G:0.00, T:0.64
Consensus pattern (15 bp):
TAATTTTTATTATAC
Found at i:2295461 original size:22 final size:24
Alignment explanation
Indices: 2295436--2295482 Score: 71
Period size: 23 Copynumber: 2.0 Consensus size: 24
2295426 CCACCGAAAC
2295436 TATTAATTC-TTTTATTTT-TTTA
1 TATTAATTCTTTTTATTTTCTTTA
*
2295458 TATTATTTCTTTTTATTTTCTTTA
1 TATTAATTCTTTTTATTTTCTTTA
2295482 T
1 T
2295483 TTCTTGATCT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
22 8 0.36
23 9 0.41
24 5 0.23
ACGTcount: A:0.19, C:0.06, G:0.00, T:0.74
Consensus pattern (24 bp):
TATTAATTCTTTTTATTTTCTTTA
Found at i:2295483 original size:22 final size:22
Alignment explanation
Indices: 2295436--2295483 Score: 62
Period size: 22 Copynumber: 2.2 Consensus size: 22
2295426 CCACCGAAAC
*
2295436 TATTAATTCTTTTATTTTTTTA
1 TATTAATTCTTTTATTTTCTTA
*
2295458 TATTATTTCTTTTTATTTTCTT-
1 TATTAATTC-TTTTATTTTCTTA
2295480 TATT
1 TATT
2295484 TCTTGATCTT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
22 12 0.52
23 11 0.48
ACGTcount: A:0.19, C:0.06, G:0.00, T:0.75
Consensus pattern (22 bp):
TATTAATTCTTTTATTTTCTTA
Found at i:2297132 original size:82 final size:82
Alignment explanation
Indices: 2296988--2297138 Score: 194
Period size: 82 Copynumber: 1.8 Consensus size: 82
2296978 TCATTGAGGG
* * * * ** *
2296988 CAATTCATAATAGAGGTCTTTCACGGAAACAGCTCTCAACTTGACGTTAGGGGCAGCCTACTACT
1 CAATTCATAACAGAAGTCTTTCACAGAAACACCTCTCAACTTGACGTTAGGAACAACCTACTACT
2297053 CTACCTCCCCTTATCCC
66 CTACCTCCCCTTATCCC
* * * * *
2297070 CAATTCATAACGGAAGTCTTTCACATAAACTCCTCTTAACTTGACGTTAGGAACAACTTACTACT
1 CAATTCATAACAGAAGTCTTTCACAGAAACACCTCTCAACTTGACGTTAGGAACAACCTACTACT
2297135 CTAC
66 CTAC
2297139 ATCTCTTTAT
Statistics
Matches: 57, Mismatches: 12, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
82 57 1.00
ACGTcount: A:0.29, C:0.29, G:0.13, T:0.28
Consensus pattern (82 bp):
CAATTCATAACAGAAGTCTTTCACAGAAACACCTCTCAACTTGACGTTAGGAACAACCTACTACT
CTACCTCCCCTTATCCC
Found at i:2302832 original size:20 final size:20
Alignment explanation
Indices: 2302788--2302826 Score: 60
Period size: 21 Copynumber: 1.9 Consensus size: 20
2302778 TAACTCAACT
2302788 TAAACTATCAATTTTTTTACC
1 TAAACTATCAATTTTTTTA-C
*
2302809 TAAACTTTCAATTTTTTT
1 TAAACTATCAATTTTTTT
2302827 TATAAAAAAT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.31, C:0.15, G:0.00, T:0.54
Consensus pattern (20 bp):
TAAACTATCAATTTTTTTAC
Found at i:2307230 original size:13 final size:13
Alignment explanation
Indices: 2307212--2307237 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
2307202 CTGGTTAATA
2307212 ATCTGTTATGCTG
1 ATCTGTTATGCTG
2307225 ATCTGTTATGCTG
1 ATCTGTTATGCTG
2307238 TTATGAAGCT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.15, C:0.15, G:0.23, T:0.46
Consensus pattern (13 bp):
ATCTGTTATGCTG
Found at i:2307250 original size:11 final size:11
Alignment explanation
Indices: 2307234--2307266 Score: 50
Period size: 11 Copynumber: 3.0 Consensus size: 11
2307224 GATCTGTTAT
2307234 GCTGTTATGAA
1 GCTGTTATGAA
2307245 GCTGTTATGATA
1 GCTGTTATGA-A
2307257 -CTGTTATGAA
1 GCTGTTATGAA
2307267 TTTGTTAGGC
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
10 1 0.05
11 19 0.90
12 1 0.05
ACGTcount: A:0.27, C:0.09, G:0.24, T:0.39
Consensus pattern (11 bp):
GCTGTTATGAA
Found at i:2311775 original size:13 final size:13
Alignment explanation
Indices: 2311757--2311782 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
2311747 CTGGTTAATA
2311757 ATCTGTTATGCTG
1 ATCTGTTATGCTG
2311770 ATCTGTTATGCTG
1 ATCTGTTATGCTG
2311783 TTATGAATTT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.15, C:0.15, G:0.23, T:0.46
Consensus pattern (13 bp):
ATCTGTTATGCTG
Found at i:2314607 original size:13 final size:13
Alignment explanation
Indices: 2314589--2314613 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
2314579 TATACCCACG
2314589 TCGATTGCCGTCC
1 TCGATTGCCGTCC
2314602 TCGATTGCCGTC
1 TCGATTGCCGTC
2314614 GATGAAGTTC
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:0.08, C:0.36, G:0.24, T:0.32
Consensus pattern (13 bp):
TCGATTGCCGTCC
Found at i:2315420 original size:40 final size:40
Alignment explanation
Indices: 2315365--2315448 Score: 141
Period size: 40 Copynumber: 2.1 Consensus size: 40
2315355 TTTAAACTTT
* * *
2315365 TCATTTTGCCACATCACCATGTTTCAGTTTTGCCATATCA
1 TCATTTTGCCACATCACCAGGTTTCACTTTTACCATATCA
2315405 TCATTTTGCCACATCACCAGGTTTCACTTTTACCATATCA
1 TCATTTTGCCACATCACCAGGTTTCACTTTTACCATATCA
2315445 TCAT
1 TCAT
2315449 CTCCGTTAAG
Statistics
Matches: 41, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
40 41 1.00
ACGTcount: A:0.24, C:0.29, G:0.08, T:0.39
Consensus pattern (40 bp):
TCATTTTGCCACATCACCAGGTTTCACTTTTACCATATCA
Found at i:2315507 original size:90 final size:90
Alignment explanation
Indices: 2315399--2315581 Score: 312
Period size: 90 Copynumber: 2.0 Consensus size: 90
2315389 CAGTTTTGCC
* *
2315399 ATATCATCATTTTGCCACATCACCAGGTTTCACTTTTACCATATCATCATCTCCGTTAAGTAGTC
1 ATATCATCATTTTACCACATCACCAGGTTTCACTTTTACCATATCATCATCTCCATTAAGTAGTC
2315464 ACCCGTATTTCAATTTCACGAATCA
66 ACCCGTATTTCAATTTCACGAATCA
* * * *
2315489 ATATCATCATTTTACCACATCTCCATGTTTCAGTTTTACCATATCATCATCTCCATTAAGTGGTC
1 ATATCATCATTTTACCACATCACCAGGTTTCACTTTTACCATATCATCATCTCCATTAAGTAGTC
2315554 ACCCGTATTTCAATTTCACGAATCA
66 ACCCGTATTTCAATTTCACGAATCA
2315579 ATA
1 ATA
2315582 AGTTATGGAT
Statistics
Matches: 87, Mismatches: 6, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
90 87 1.00
ACGTcount: A:0.28, C:0.27, G:0.08, T:0.37
Consensus pattern (90 bp):
ATATCATCATTTTACCACATCACCAGGTTTCACTTTTACCATATCATCATCTCCATTAAGTAGTC
ACCCGTATTTCAATTTCACGAATCA
Found at i:2321965 original size:13 final size:14
Alignment explanation
Indices: 2321947--2321975 Score: 51
Period size: 13 Copynumber: 2.1 Consensus size: 14
2321937 AACACTTTTA
2321947 AATAAAAT-CTCAT
1 AATAAAATGCTCAT
2321960 AATAAAATGCTCAT
1 AATAAAATGCTCAT
2321974 AA
1 AA
2321976 AATTAATTTC
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 8 0.53
14 7 0.47
ACGTcount: A:0.55, C:0.14, G:0.03, T:0.28
Consensus pattern (14 bp):
AATAAAATGCTCAT
Found at i:2324387 original size:30 final size:29
Alignment explanation
Indices: 2324353--2324527 Score: 96
Period size: 29 Copynumber: 6.2 Consensus size: 29
2324343 TTTACACAAT
* *
2324353 TATCACCCTTTTAAGAAATATTTACCAAAA
1 TATCACCATTTTAA-AAATAATTACCAAAA
* * *
2324383 TATCACTATTTTCAAAATAATTACTAAAA
1 TATCACCATTTTAAAAATAATTACCAAAA
** * **
2324412 TATCA-TTTTTTAAGAA-AATTA-TGAAA
1 TATCACCATTTTAAAAATAATTACCAAAA
* * **
2324438 T-T-ATCATTTT-TAAA-AATTATGAAAA
1 TATCACCATTTTAAAAATAATTACCAAAA
* *
2324463 TAGT-ACCATTTTCAAAATAATTACCAGAA
1 TA-TCACCATTTTAAAAATAATTACCAAAA
* * *
2324492 TACCAACATTTTCAAAATAATTACCAAAA
1 TATCACCATTTTAAAAATAATTACCAAAA
*
2324521 TACCACC
1 TATCACC
2324528 CGGTCAACGG
Statistics
Matches: 114, Mismatches: 24, Indels: 15
0.75 0.16 0.10
Matches are distributed among these distances:
24 8 0.07
25 9 0.08
26 5 0.04
27 13 0.11
28 11 0.10
29 57 0.50
30 11 0.10
ACGTcount: A:0.46, C:0.15, G:0.03, T:0.35
Consensus pattern (29 bp):
TATCACCATTTTAAAAATAATTACCAAAA
Found at i:2324411 original size:29 final size:29
Alignment explanation
Indices: 2324368--2324522 Score: 114
Period size: 29 Copynumber: 5.6 Consensus size: 29
2324358 CCCTTTTAAG
*
2324368 AAATATTTACCAAAATATCACTATTTTCA
1 AAATAATTACCAAAATATCACTATTTTCA
* *
2324397 AAATAATTACTAAAATATCA-T-TTTTTA
1 AAATAATTACCAAAATATCACTATTTTCA
** *
2324424 AGAA-AATTATGAAATTATCA-T-TTTT--
1 A-AATAATTACCAAAATATCACTATTTTCA
** *
2324449 AAA-AATTATGAAAATAGT-ACCATTTTCA
1 AAATAATTACCAAAATA-TCACTATTTTCA
* *
2324477 AAATAATTACCAGAATACCAAC-ATTTTCA
1 AAATAATTACCAAAATATC-ACTATTTTCA
2324506 AAATAATTACCAAAATA
1 AAATAATTACCAAAATA
2324523 CCACCCGGTC
Statistics
Matches: 104, Mismatches: 13, Indels: 18
0.77 0.10 0.13
Matches are distributed among these distances:
24 15 0.14
25 2 0.02
26 4 0.04
27 24 0.23
28 6 0.06
29 51 0.49
30 2 0.02
ACGTcount: A:0.49, C:0.12, G:0.03, T:0.35
Consensus pattern (29 bp):
AAATAATTACCAAAATATCACTATTTTCA
Found at i:2324431 original size:27 final size:27
Alignment explanation
Indices: 2324361--2324448 Score: 81
Period size: 27 Copynumber: 3.1 Consensus size: 27
2324351 ATTATCACCC
*
2324361 TTTTAAGAAATATTTACCAAAATATCACTAT
1 TTTTAAGAAA-A-TTACTAAAATATCA-T-T
*
2324392 TTTCAA-AATAATTACTAAAATATCATT
1 TTTTAAGAA-AATTACTAAAATATCATT
*
2324419 TTTTAAGAAAATTA-TGAAATTATCATT
1 TTTTAAGAAAATTACT-AAAATATCATT
2324446 TTT
1 TTT
2324449 AAAAATTATG
Statistics
Matches: 50, Mismatches: 4, Indels: 10
0.78 0.06 0.16
Matches are distributed among these distances:
26 1 0.02
27 24 0.48
28 3 0.06
29 13 0.26
30 3 0.06
31 6 0.12
ACGTcount: A:0.44, C:0.09, G:0.03, T:0.43
Consensus pattern (27 bp):
TTTTAAGAAAATTACTAAAATATCATT
Found at i:2324458 original size:24 final size:27
Alignment explanation
Indices: 2324412--2324461 Score: 79
Period size: 24 Copynumber: 2.0 Consensus size: 27
2324402 ATTACTAAAA
2324412 TATCATTTTTTAAGAAAATTATGAAAT
1 TATCATTTTTTAAGAAAATTATGAAAT
2324439 TATCA-TTTTT-A-AAAATTATGAAA
1 TATCATTTTTTAAGAAAATTATGAAA
2324462 ATAGTACCAT
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
24 12 0.52
25 1 0.04
26 5 0.22
27 5 0.22
ACGTcount: A:0.46, C:0.04, G:0.06, T:0.44
Consensus pattern (27 bp):
TATCATTTTTTAAGAAAATTATGAAAT
Found at i:2324472 original size:27 final size:24
Alignment explanation
Indices: 2324426--2324479 Score: 63
Period size: 27 Copynumber: 2.1 Consensus size: 24
2324416 ATTTTTTAAG
* *
2324426 AAAATTATGAAATTATCATTTTTA
1 AAAATTATGAAATTACCATTTTCA
2324450 AAAATTATGAAAATAGTACCATTTTCA
1 AAAATTATG-AAAT--TACCATTTTCA
2324477 AAA
1 AAA
2324480 TAATTACCAG
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
24 9 0.36
25 4 0.16
27 12 0.48
ACGTcount: A:0.50, C:0.07, G:0.06, T:0.37
Consensus pattern (24 bp):
AAAATTATGAAATTACCATTTTCA
Found at i:2332117 original size:28 final size:28
Alignment explanation
Indices: 2332077--2332133 Score: 96
Period size: 28 Copynumber: 2.0 Consensus size: 28
2332067 AAAAATATAT
* *
2332077 ATAATCTATAGTTTTGAAAACATTTTGA
1 ATAATATAAAGTTTTGAAAACATTTTGA
2332105 ATAATATAAAGTTTTGAAAACATTTTGA
1 ATAATATAAAGTTTTGAAAACATTTTGA
2332133 A
1 A
2332134 AAAAATATAT
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
28 27 1.00
ACGTcount: A:0.44, C:0.05, G:0.11, T:0.40
Consensus pattern (28 bp):
ATAATATAAAGTTTTGAAAACATTTTGA
Found at i:2332183 original size:38 final size:38
Alignment explanation
Indices: 2332105--2332248 Score: 236
Period size: 37 Copynumber: 3.8 Consensus size: 38
2332095 AACATTTTGA
*
2332105 ATAATATAAAGTTTTGAAAACATTTTGAAAAAA-ATAT
1 ATAATATATAGTTTTGAAAACATTTTGAAAAAATATAT
2332142 ATAATATATAGTTTTGAAAACATTTTGAAAAAATATAT
1 ATAATATATAGTTTTGAAAACATTTTGAAAAAATATAT
*
2332180 ATAATATATAGTTTTGACAACATTTTGAAAAAAATATAT
1 ATAATATATAGTTTTGAAAACATTTTG-AAAAAATATAT
*
2332219 ATAATATATAGTTTTTGAAAATATTTTGAA
1 ATAATATATAG-TTTTGAAAACATTTTGAA
2332249 TATATATAAT
Statistics
Matches: 100, Mismatches: 4, Indels: 4
0.93 0.04 0.04
Matches are distributed among these distances:
37 32 0.32
38 30 0.30
39 24 0.24
40 14 0.14
ACGTcount: A:0.49, C:0.03, G:0.08, T:0.40
Consensus pattern (38 bp):
ATAATATATAGTTTTGAAAACATTTTGAAAAAATATAT
Found at i:2332337 original size:13 final size:13
Alignment explanation
Indices: 2332319--2332343 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
2332309 TTTGAAAACA
2332319 TTTTTAGTATTTT
1 TTTTTAGTATTTT
2332332 TTTTTAGTATTT
1 TTTTTAGTATTT
2332344 ATTTATTTAT
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:0.16, C:0.00, G:0.08, T:0.76
Consensus pattern (13 bp):
TTTTTAGTATTTT
Found at i:2339159 original size:110 final size:109
Alignment explanation
Indices: 2338966--2339191 Score: 344
Period size: 110 Copynumber: 2.1 Consensus size: 109
2338956 CTAGCCCGTG
* * * * * *
2338966 ATGACAATATATTCGTTCACTATCGGGTTCCTCCTGAAGCATTAGTTTACTGTTGTACTTGAGGA
1 ATGACAAGAAATTCGTTCACTATCGGGTCCCTCCTGAACCATGAGTTTACTATTGTACTTGAGGA
* *
2339031 TGCCATATCAAAGAAAAACAACAAGAATGCAAGCTTTGATGAGTA
66 TGCCATATCAAAGAAAAACAACAAGAATGCAAGATCTGATGA-TA
*
2339076 ATGACAAGAAATTCGTTCACTATCGGGTCCCTCCTGAACCATGAGTTTATTATTGTACTTGAGGA
1 ATGACAAGAAATTCGTTCACTATCGGGTCCCTCCTGAACCATGAGTTTACTATTGTACTTGAGGA
* *
2339141 TGCCATATCAAAGAAAAACAATAGGAATGCAAGATCTGATGATA
66 TGCCATATCAAAGAAAAACAACAAGAATGCAAGATCTGATGATA
2339185 ATGACAA
1 ATGACAA
2339192 CCCAAATAAG
Statistics
Matches: 105, Mismatches: 11, Indels: 1
0.90 0.09 0.01
Matches are distributed among these distances:
109 9 0.09
110 96 0.91
ACGTcount: A:0.35, C:0.17, G:0.19, T:0.28
Consensus pattern (109 bp):
ATGACAAGAAATTCGTTCACTATCGGGTCCCTCCTGAACCATGAGTTTACTATTGTACTTGAGGA
TGCCATATCAAAGAAAAACAACAAGAATGCAAGATCTGATGATA
Found at i:2353635 original size:45 final size:45
Alignment explanation
Indices: 2353579--2353855 Score: 362
Period size: 45 Copynumber: 6.2 Consensus size: 45
2353569 GAAATAATGC
**
2353579 TATAGTTGAAATGTATATGGGTACATTACCAACAGAAAAGTATGA
1 TATAGTTGAAATGTATATGGGTACATTTTCAACAGAAAAGTATGA
* * * *
2353624 TATAATTGAAATGTATATGGGAACATTTTGAACAGAAAAATAT-A
1 TATAGTTGAAATGTATATGGGTACATTTTCAACAGAAAAGTATGA
* * * *
2353668 CTATAGTTGAAATGCATATGGGTGCATTATCAACAGAAAAGTATGC
1 -TATAGTTGAAATGTATATGGGTACATTTTCAACAGAAAAGTATGA
*
2353714 TATAGTTGAAATGTATATGGGTACATTTTCAACAGAAAAGTATGC
1 TATAGTTGAAATGTATATGGGTACATTTTCAACAGAAAAGTATGA
* *
2353759 TATAGTTGAAATGTATATGGGTACATTTTCAACATAAGAGTAT-A
1 TATAGTTGAAATGTATATGGGTACATTTTCAACAGAAAAGTATGA
* * *
2353803 CTATAGTGGAAATGTATATGGGTACATTTTCAACA-AAAGAGCATGC
1 -TATAGTTGAAATGTATATGGGTACATTTTCAACAGAAA-AGTATGA
2353849 TATAGTT
1 TATAGTT
2353856 TAAAATGCAT
Statistics
Matches: 202, Mismatches: 25, Indels: 10
0.85 0.11 0.04
Matches are distributed among these distances:
44 3 0.01
45 199 0.99
ACGTcount: A:0.40, C:0.09, G:0.19, T:0.32
Consensus pattern (45 bp):
TATAGTTGAAATGTATATGGGTACATTTTCAACAGAAAAGTATGA
Found at i:2353803 original size:135 final size:135
Alignment explanation
Indices: 2353575--2353855 Score: 420
Period size: 135 Copynumber: 2.1 Consensus size: 135
2353565 GCATGAAATA
2353575 ATGCTATAGTTGAAATGTATATGGGTACATTACCAACAGAAAAGTATGATATAATTGAAATGTAT
1 ATGCTATAGTTGAAATGTATATGGGTACATTACCAACAGAAAAGTATGATATAATTGAAATGTAT
* * *
2353640 ATGGGAACATTTTGAACAGAAAAATATACTATAGTTGAAATGCATATGGGTGCATTATCAACAGA
66 ATGGGAACATTTTCAACAGAAAAATATACTATAGTGGAAATGCATATGGGTACATTATCAACA-A
*
2353705 AA-AGT
130 AAGAGC
** * *
2353710 ATGCTATAGTTGAAATGTATATGGGTACATTTTCAACAGAAAAGTATGCTATAGTTGAAATGTAT
1 ATGCTATAGTTGAAATGTATATGGGTACATTACCAACAGAAAAGTATGATATAATTGAAATGTAT
* * * * * *
2353775 ATGGGTACATTTTCAACATAAGAGTATACTATAGTGGAAATGTATATGGGTACATTTTCAACAAA
66 ATGGGAACATTTTCAACAGAAAAATATACTATAGTGGAAATGCATATGGGTACATTATCAACAAA
2353840 AGAGC
131 AGAGC
2353845 ATGCTATAGTT
1 ATGCTATAGTT
2353856 TAAAATGCAT
Statistics
Matches: 131, Mismatches: 14, Indels: 2
0.89 0.10 0.01
Matches are distributed among these distances:
134 3 0.02
135 128 0.98
ACGTcount: A:0.40, C:0.09, G:0.20, T:0.32
Consensus pattern (135 bp):
ATGCTATAGTTGAAATGTATATGGGTACATTACCAACAGAAAAGTATGATATAATTGAAATGTAT
ATGGGAACATTTTCAACAGAAAAATATACTATAGTGGAAATGCATATGGGTACATTATCAACAAA
AGAGC
Found at i:2353849 original size:90 final size:90
Alignment explanation
Indices: 2353575--2353855 Score: 404
Period size: 90 Copynumber: 3.1 Consensus size: 90
2353565 GCATGAAATA
* *
2353575 ATGCTATAGTTGAAATGTATATGGGTACATTACCAACAGAAAAGTATGA-TATAATTGAAATGTA
1 ATGCTATAGTTGAAATGTATATGGGTACATTATCAACAGAAAAGTAT-ACTATAGTTGAAATGTA
* * *
2353639 TATGGGAACATTTTGAACAGAAAAAT
65 TATGGGTACATTTTCAACAGAAAAGT
* * * *
2353665 ATACTATAGTTGAAATGCATATGGGTGCATTATCAACAGAAAAGTATGCTATAGTTGAAATGTAT
1 ATGCTATAGTTGAAATGTATATGGGTACATTATCAACAGAAAAGTATACTATAGTTGAAATGTAT
2353730 ATGGGTACATTTTCAACAGAAAAGT
66 ATGGGTACATTTTCAACAGAAAAGT
* * * *
2353755 ATGCTATAGTTGAAATGTATATGGGTACATTTTCAACATAAGAGTATACTATAGTGGAAATGTAT
1 ATGCTATAGTTGAAATGTATATGGGTACATTATCAACAGAAAAGTATACTATAGTTGAAATGTAT
*
2353820 ATGGGTACATTTTCAACA-AAAGAGC
66 ATGGGTACATTTTCAACAGAAA-AGT
2353845 ATGCTATAGTT
1 ATGCTATAGTT
2353856 TAAAATGCAT
Statistics
Matches: 171, Mismatches: 18, Indels: 4
0.89 0.09 0.02
Matches are distributed among these distances:
89 3 0.02
90 168 0.98
ACGTcount: A:0.40, C:0.09, G:0.20, T:0.32
Consensus pattern (90 bp):
ATGCTATAGTTGAAATGTATATGGGTACATTATCAACAGAAAAGTATACTATAGTTGAAATGTAT
ATGGGTACATTTTCAACAGAAAAGT
Found at i:2359658 original size:19 final size:19
Alignment explanation
Indices: 2359634--2359705 Score: 56
Period size: 19 Copynumber: 3.6 Consensus size: 19
2359624 ACCTAATTTT
2359634 GGTATCGATACCATATAAG
1 GGTATCGATACCATATAAG
2359653 GGTATC-AGTACCATAGTATAG
1 GGTATCGA-TACCATA-TA-AG
* * *
2359674 TAGTATCGATACAATGGTAAG
1 -GGTATCGATACCAT-ATAAG
*
2359695 GGTATCAATAC
1 GGTATCGATAC
2359706 TGGGCCACAT
Statistics
Matches: 42, Mismatches: 5, Indels: 11
0.72 0.09 0.19
Matches are distributed among these distances:
18 1 0.02
19 13 0.31
20 11 0.26
21 4 0.10
22 12 0.29
23 1 0.02
ACGTcount: A:0.36, C:0.14, G:0.22, T:0.28
Consensus pattern (19 bp):
GGTATCGATACCATATAAG
Found at i:2359725 original size:95 final size:94
Alignment explanation
Indices: 2359600--2359802 Score: 237
Period size: 95 Copynumber: 2.1 Consensus size: 94
2359590 CGAACGAAGT
* * *
2359600 GGTATCGATACTGGGTAACATCGAACCTAATTTTGGTATCGATACCATATAA-GGGTATCAGTAC
1 GGTATCGATACTGGGCAACATCGAACCTAATTTTGGTATCGATA-C-TAGAAGGGGTATCAATAC
* *
2359664 CATAGTATAGTAGTATCGATACAATGGTAAG
64 CAAAGTAGAGTAGTATCGATACAATGGTAAG
* * * * * *
2359695 GGTATCAATACTGGGCCACATTGAATCTAATTTTGGTATTGATACTGGAAGGGGGTATCAATACC
1 GGTATCGATACTGGGCAACATCGAACCTAATTTTGGTATCGATACTAGAA-GGGGTATCAATACC
* * * *
2359760 AAATTAGGGTAGTATCGATACCATGGTAGG
65 AAAGTAGAGTAGTATCGATACAATGGTAAG
2359790 GGTATCGATACTG
1 GGTATCGATACTG
2359803 AAGGGTCAGA
Statistics
Matches: 90, Mismatches: 16, Indels: 4
0.82 0.15 0.04
Matches are distributed among these distances:
93 3 0.03
94 1 0.01
95 86 0.96
ACGTcount: A:0.32, C:0.14, G:0.25, T:0.30
Consensus pattern (94 bp):
GGTATCGATACTGGGCAACATCGAACCTAATTTTGGTATCGATACTAGAAGGGGTATCAATACCA
AAGTAGAGTAGTATCGATACAATGGTAAG
Found at i:2360301 original size:45 final size:45
Alignment explanation
Indices: 2360252--2360527 Score: 390
Period size: 45 Copynumber: 6.1 Consensus size: 45
2360242 AAAAGATGAC
* * * * *
2360252 ATAGTTTAAATATACATGGGTACATTATCAACAGAAAAGCATGCT
1 ATAGTTGAAATGTATATGGGTACATTTTCAACAGAAAAGTATGCT
*
2360297 ATAGTTGAAATGTATATGGGTACATTTTCAACAGAAAAGTATACT
1 ATAGTTGAAATGTATATGGGTACATTTTCAACAGAAAAGTATGCT
* * ** * *
2360342 ATAGTTGAAATGCATATGGGTGCATTACCAACAGAAGAGTATGTT
1 ATAGTTGAAATGTATATGGGTACATTTTCAACAGAAAAGTATGCT
*
2360387 ATAGTTGAAATGTATATGGGTACATTTTCAACAGAAAAGTATGTT
1 ATAGTTGAAATGTATATGGGTACATTTTCAACAGAAAAGTATGCT
* *
2360432 ATAGTTGAAATGTATATGGGTACATTTTCAACAGAAGAGTATACT
1 ATAGTTGAAATGTATATGGGTACATTTTCAACAGAAAAGTATGCT
* * *
2360477 ATAGTTGAAATGTATATGGGTAAATTTTCAACAGAAGAGTATGTT
1 ATAGTTGAAATGTATATGGGTACATTTTCAACAGAAAAGTATGCT
2360522 ATAGTT
1 ATAGTT
2360528 TAAAGTGCAT
Statistics
Matches: 207, Mismatches: 24, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
45 207 1.00
ACGTcount: A:0.38, C:0.09, G:0.20, T:0.33
Consensus pattern (45 bp):
ATAGTTGAAATGTATATGGGTACATTTTCAACAGAAAAGTATGCT
Found at i:2360457 original size:135 final size:135
Alignment explanation
Indices: 2360252--2360527 Score: 444
Period size: 135 Copynumber: 2.0 Consensus size: 135
2360242 AAAAGATGAC
*
2360252 ATAGTTTAAATATACATGGGTACATTATCAACAGAAAAGCATGCTATAGTTGAAATGTATATGGG
1 ATAGTTGAAATATACATGGGTACATTATCAACAGAAAAGCATGCTATAGTTGAAATGTATATGGG
**
2360317 TACATTTTCAACAGAAAAGTATACTATAGTTGAAATGCATATGGGTGCATTACCAACAGAAGAGT
66 TACATTTTCAACAGAAAAGTATACTATAGTTGAAATGCATATGGGTAAATTACCAACAGAAGAGT
2360382 ATGTT
131 ATGTT
* * * * *
2360387 ATAGTTGAAATGTATATGGGTACATTTTCAACAGAAAAGTATGTTATAGTTGAAATGTATATGGG
1 ATAGTTGAAATATACATGGGTACATTATCAACAGAAAAGCATGCTATAGTTGAAATGTATATGGG
* * **
2360452 TACATTTTCAACAGAAGAGTATACTATAGTTGAAATGTATATGGGTAAATTTTCAACAGAAGAGT
66 TACATTTTCAACAGAAAAGTATACTATAGTTGAAATGCATATGGGTAAATTACCAACAGAAGAGT
2360517 ATGTT
131 ATGTT
2360522 ATAGTT
1 ATAGTT
2360528 TAAAGTGCAT
Statistics
Matches: 129, Mismatches: 12, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
135 129 1.00
ACGTcount: A:0.38, C:0.09, G:0.20, T:0.33
Consensus pattern (135 bp):
ATAGTTGAAATATACATGGGTACATTATCAACAGAAAAGCATGCTATAGTTGAAATGTATATGGG
TACATTTTCAACAGAAAAGTATACTATAGTTGAAATGCATATGGGTAAATTACCAACAGAAGAGT
ATGTT
Found at i:2363978 original size:45 final size:46
Alignment explanation
Indices: 2363929--2364245 Score: 423
Period size: 45 Copynumber: 7.0 Consensus size: 46
2363919 TTATTGGCAT
* *
2363929 AAAAGGATGTC-ATAGTTGAAATGTATATGGGTACATTATCAACAG
1 AAAAGTATGTCTATAGTTGAAATGTATATGGGTACATTTTCAACAG
*
2363974 AAAAGTATG-CTATAGTTGAAATGTATATGGGTATATTTTCAACAG
1 AAAAGTATGTCTATAGTTGAAATGTATATGGGTACATTTTCAACAG
* * * * * *
2364019 AAAAATAT-ACTATAGTTAAAATGCATATGGGTGCATTATCAACAG
1 AAAAGTATGTCTATAGTTGAAATGTATATGGGTACATTTTCAACAG
*
2364064 AAAAGTATG-CTATAGTTGAAATGTATATGGGTACATTTTCAATAG
1 AAAAGTATGTCTATAGTTGAAATGTATATGGGTACATTTTCAACAG
*
2364109 AAAAGTATGT-TATAGTTGAAATGTATATGGGTACATTTTCAACGG
1 AAAAGTATGTCTATAGTTGAAATGTATATGGGTACATTTTCAACAG
* *
2364154 AAAAGCATGT-TATAGTTGAAATGTATATGGGTACATTTTAAACAG
1 AAAAGTATGTCTATAGTTGAAATGTATATGGGTACATTTTCAACAG
* * * * *
2364199 AAGAGTAT-ACTATAATTGAAATGTATATGCGTACATTTTTAACAG
1 AAAAGTATGTCTATAGTTGAAATGTATATGGGTACATTTTCAACAG
2364244 AA
1 AA
2364246 TAACTAAAGG
Statistics
Matches: 241, Mismatches: 26, Indels: 10
0.87 0.09 0.04
Matches are distributed among these distances:
44 1 0.00
45 240 1.00
ACGTcount: A:0.40, C:0.08, G:0.19, T:0.33
Consensus pattern (46 bp):
AAAAGTATGTCTATAGTTGAAATGTATATGGGTACATTTTCAACAG
Found at i:2364963 original size:5 final size:5
Alignment explanation
Indices: 2364953--2365467 Score: 845
Period size: 5 Copynumber: 103.0 Consensus size: 5
2364943 CCAAGGGTCT
2364953 ATATA ATATA ATATA ATATA ATATA ATATA ATATA ATATA ATATA ATATA
1 ATATA ATATA ATATA ATATA ATATA ATATA ATATA ATATA ATATA ATATA
*
2365003 ATATA AAATA ATATA ATA-A ATATA ATATA ATATA ATATA ATATA ATATA
1 ATATA ATATA ATATA ATATA ATATA ATATA ATATA ATATA ATATA ATATA
2365052 ATATA ATATA ATATA ATATA ATATA ATA-A ATATA TATATA ATATA ATAT-
1 ATATA ATATA ATATA ATATA ATATA ATATA ATATA -ATATA ATATA ATATA
2365101 ATAATA TATATA ATAT- ATA-A ATAT- ATATA ATATA ATATA ATATA ATATA
1 AT-ATA -ATATA ATATA ATATA ATATA ATATA ATATA ATATA ATATA ATATA
2365150 ATATA ATATA ATATA TATATA ATATA ATATA ATAT- A-ATA ATATAA TATATA
1 ATATA ATATA ATATA -ATATA ATATA ATATA ATATA ATATA ATAT-A -ATATA
2365201 ATATA ATATA ATATA ATATA ATATAA TATATA ATATA ATATA ATATA ATATA
1 ATATA ATATA ATATA ATATA ATAT-A -ATATA ATATA ATATA ATATA ATATA
2365253 ATATA ATATA ATATA ATATA ATAATAA ATATA ATATA ATATA ATATA ATATA
1 ATATA ATATA ATATA ATATA AT-AT-A ATATA ATATA ATATA ATATA ATATA
2365305 ATATA ATATA ATATA ATATA ATATA ATATA ATATA ATATA ATATA ATATA
1 ATATA ATATA ATATA ATATA ATATA ATATA ATATA ATATA ATATA ATATA
2365355 ATAT- ATATA ATATA ATAT- ATATA ATATA ATATA ATATA ATATA ATATA
1 ATATA ATATA ATATA ATATA ATATA ATATA ATATA ATATA ATATA ATATA
2365403 ATATA ATATA TATATA ATATA ATAT- ATATA ATATA ATATA ATATA ATATA
1 ATATA ATATA -ATATA ATATA ATATA ATATA ATATA ATATA ATATA ATATA
2365453 ATATA ATATA ATATA
1 ATATA ATATA ATATA
2365468 TAAAGTTTTT
Statistics
Matches: 486, Mismatches: 2, Indels: 44
0.91 0.00 0.08
Matches are distributed among these distances:
3 2 0.00
4 34 0.07
5 411 0.85
6 26 0.05
7 13 0.03
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (5 bp):
ATATA
Found at i:2365491 original size:34 final size:32
Alignment explanation
Indices: 2365036--2365560 Score: 186
Period size: 30 Copynumber: 16.5 Consensus size: 32
2365026 AATATAATAT
*
2365036 AATATA-ATATAATATAATATAATATAA--TAT-
1 AATATATATATAATATAATAT-ATA-AAGTTTTA
* **
2365066 AATATA-ATATAATA-AATATATATA-TAATA
1 AATATATATATAATATAATATATAAAGTTTTA
*
2365095 TAATATATA-ATATATATAATATATAAA-TATATA
1 -AATATATATATA-ATATAATATATAAAGT-TTTA
*
2365128 TAATATA-ATATAATATAATATAATATAA--TAT-
1 -AATATATATATAATATAATAT-ATA-AAGTTTTA
**
2365159 AATATATATATAATATAATATAATATAA-TAATA
1 AATATATATATAATATAATAT-ATA-AAGTTTTA
*
2365192 TAATATATAATATAATATAATATAATATAA--TAT-
1 -AATATAT-ATATAATATAATAT-ATA-AAGTTTTA
*
2365225 AATATATAATATAATATAATATAATATAA--TAT-
1 AATATAT-ATATAATATAATAT-ATA-AAGTTTTA
*
2365257 AATATA-ATATAATATAATA-ATAAA--TAT-
1 AATATATATATAATATAATATATAAAGTTTTA
*
2365284 AATATA-ATATAATATAATATAATATAA--TAT-
1 AATATATATATAATATAATAT-ATA-AAGTTTTA
*
2365314 AATATA-ATATAATATAATATAATATAA--TAT-
1 AATATATATATAATATAATAT-ATA-AAGTTTTA
*
2365344 AATATA-ATATAATAT-ATATAATATAA-TATATA
1 AATATATATATAATATAATAT-ATA-AAGT-TTTA
*
2365376 TAATATA-ATATAATATAATATAATATAA--TAT-
1 -AATATATATATAATATAATAT-ATA-AAGTTTTA
2365407 AATATATATATAATATAATATATATAA-TATAATATA
1 AATATATATATAATATAATATATA-AAGT-T--T-TA
2365443 ATATAATATAATATAATATAATATATAAAGTTTTTCA
1 A-AT-ATAT-ATATAATATAATATATAAAG-TTTT-A
* * * *
2365480 AATATATATATAATATAGT-TTTGAAAACATTTTG
1 AATATATATATAATATAATATAT--AAA-GTTTTA
2365514 AATATATATAT-ATATAATATAT--AGTTTTGA
1 AATATATATATAATATAATATATAAAGTTTT-A
*
2365544 AAAATATATATAATATA
1 AATATATATATAATATA
2365561 TACTTTTTGA
Statistics
Matches: 437, Mismatches: 16, Indels: 83
0.82 0.03 0.15
Matches are distributed among these distances:
27 25 0.06
28 8 0.02
29 23 0.05
30 115 0.26
31 47 0.11
32 67 0.15
33 39 0.09
34 46 0.11
35 33 0.08
36 4 0.01
37 5 0.01
38 6 0.01
39 18 0.04
40 1 0.00
ACGTcount: A:0.57, C:0.00, G:0.01, T:0.41
Consensus pattern (32 bp):
AATATATATATAATATAATATATAAAGTTTTA
Found at i:2365530 original size:67 final size:67
Alignment explanation
Indices: 2365447--2365592 Score: 192
Period size: 67 Copynumber: 2.2 Consensus size: 67
2365437 AATATAATAT
*
2365447 AATATA-ATATAATATAATATATAAAGTTTTTCAAATATATATAT-A-ATATA-GTTTTGAAAAC
1 AATATATATAT-ATATAATATAT--AG-TTTTCAAAAATATATATAATATATACGTTTTGAAAAC
2365508 ATTTTG
62 ATTTTG
* *
2365514 AATATATATATATATAATATATAGTTTTGAAAAATATATATAATATATACTTTTTGAAAACATTT
1 AATATATATATATATAATATATAGTTTTCAAAAATATATATAATATATACGTTTTGAAAACATTT
2365579 TG
66 TG
*
2365581 AAAATATATATA
1 AATATATATATA
2365593 ATTTTAAAAC
Statistics
Matches: 71, Mismatches: 4, Indels: 8
0.86 0.05 0.10
Matches are distributed among these distances:
64 15 0.21
65 3 0.04
66 5 0.07
67 44 0.62
68 4 0.06
ACGTcount: A:0.49, C:0.03, G:0.05, T:0.43
Consensus pattern (67 bp):
AATATATATATATATAATATATAGTTTTCAAAAATATATATAATATATACGTTTTGAAAACATTT
TG
Found at i:2365554 original size:26 final size:27
Alignment explanation
Indices: 2365521--2365573 Score: 90
Period size: 26 Copynumber: 2.0 Consensus size: 27
2365511 TTGAATATAT
2365521 ATATATATAATATATA-GTTTTGAAAA
1 ATATATATAATATATACGTTTTGAAAA
*
2365547 ATATATATAATATATACTTTTTGAAAA
1 ATATATATAATATATACGTTTTGAAAA
2365574 CATTTTGAAA
Statistics
Matches: 25, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
26 16 0.64
27 9 0.36
ACGTcount: A:0.49, C:0.02, G:0.06, T:0.43
Consensus pattern (27 bp):
ATATATATAATATATACGTTTTGAAAA
Found at i:2365586 original size:28 final size:27
Alignment explanation
Indices: 2365555--2365620 Score: 80
Period size: 28 Copynumber: 2.4 Consensus size: 27
2365545 AAATATATAT
2365555 AATATATACT-TTTTGAAAACATTTTGAA
1 AATATATA-TATTTT-AAAACATTTTGAA
*
2365583 AATATATATAATTTTAAAACGTTTTGAA
1 AATATATAT-ATTTTAAAACATTTTGAA
*
2365611 ATTATATATA
1 AATATATATA
2365621 ATATATAGTT
Statistics
Matches: 34, Mismatches: 2, Indels: 5
0.83 0.05 0.12
Matches are distributed among these distances:
27 2 0.06
28 28 0.82
29 4 0.12
ACGTcount: A:0.45, C:0.05, G:0.06, T:0.44
Consensus pattern (27 bp):
AATATATATATTTTAAAACATTTTGAA
Found at i:2365608 original size:39 final size:38
Alignment explanation
Indices: 2365538--2365611 Score: 96
Period size: 37 Copynumber: 1.9 Consensus size: 38
2365528 TAATATATAG
* *
2365538 TTTTGAAAAATATATATAATATATACTTTTTGAAAACA
1 TTTTGAAAAATATATATAATATAAACGTTTTGAAAACA
*
2365576 TTTTG-AAAATATATATAATTTTAAAACGTTTTGAAA
1 TTTTGAAAAATATATATAA-TAT-AAACGTTTTGAAA
2365612 TTATATATAA
Statistics
Matches: 31, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
37 13 0.42
38 7 0.23
39 11 0.35
ACGTcount: A:0.46, C:0.04, G:0.07, T:0.43
Consensus pattern (38 bp):
TTTTGAAAAATATATATAATATAAACGTTTTGAAAACA
Found at i:2365618 original size:67 final size:66
Alignment explanation
Indices: 2365452--2365631 Score: 203
Period size: 65 Copynumber: 2.8 Consensus size: 66
2365442 AATATAATAT
**
2365452 AATATA-ATATA-ATATATAAAGTTTT-TCAAATATATAT-ATAATATAGTTTTGAAAACATTTT
1 AATATATATATATA-ATATAAAGTTTTGAAAAATATATATAAT-ATATAGTTTTGAAAACATTTT
2365513 GAA
64 GAA
* * *
2365516 TATATATATATATAATATATAGTTTTGAAAAATATATATAATATATACTTTTTGAAAACATTTTG
1 AATATATATATATAATATAAAGTTTTGAAAAATATATATAATATATA-GTTTTGAAAACATTTTG
2365581 AA
65 AA
** *
2365583 AATATATATA-ATTTTA-AAACGTTTTG-AAATTATATATAATATATAGTTT
1 AATATATATATATAATATAAA-GTTTTGAAAAATATATATAATATATAGTTT
2365632 GATGTATAAG
Statistics
Matches: 99, Mismatches: 11, Indels: 12
0.81 0.09 0.10
Matches are distributed among these distances:
64 8 0.08
65 36 0.36
66 26 0.26
67 29 0.29
ACGTcount: A:0.47, C:0.03, G:0.06, T:0.44
Consensus pattern (66 bp):
AATATATATATATAATATAAAGTTTTGAAAAATATATATAATATATAGTTTTGAAAACATTTTGA
A
Found at i:2374575 original size:25 final size:25
Alignment explanation
Indices: 2374545--2374594 Score: 100
Period size: 25 Copynumber: 2.0 Consensus size: 25
2374535 GCTTTGGGGT
2374545 CGAAAGGCCACCGCGTATGGTGGTC
1 CGAAAGGCCACCGCGTATGGTGGTC
2374570 CGAAAGGCCACCGCGTATGGTGGTC
1 CGAAAGGCCACCGCGTATGGTGGTC
2374595 GGTCCTTGGC
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 25 1.00
ACGTcount: A:0.20, C:0.28, G:0.36, T:0.16
Consensus pattern (25 bp):
CGAAAGGCCACCGCGTATGGTGGTC
Found at i:2375384 original size:49 final size:49
Alignment explanation
Indices: 2375225--2375390 Score: 136
Period size: 49 Copynumber: 3.2 Consensus size: 49
2375215 TGTGTTGTAT
* * * * *
2375225 TTTTAATTTATGCACTTCAGTCACTATTTATTTATGATTCGACTACTACTA
1 TTTT-ATTTATGCA-TTTAGTCATTTTTTATTTATGATTCGGCTACTATTA
* * * * *
2375276 TTTTATTTTATGCATTTTAGTTACTATTTTTTTATTTCTTATTTGGCTATTGTTA
1 TTTTA-TTTATGCA-TTTAG-T-C-A-TTTTTTATTTATGATTCGGCTACTATTA
*
2375331 TTTTATTGTATGCA-TTAGTCATTTTTTATTTATGATTCGGCTACTATTT
1 TTTTATT-TATGCATTTAGTCATTTTTTATTTATGATTCGGCTACTATTA
2375380 TTTTATCTTAT
1 TTTTAT-TTAT
2375391 TACATTTTGG
Statistics
Matches: 91, Mismatches: 17, Indels: 16
0.73 0.14 0.13
Matches are distributed among these distances:
49 31 0.34
50 3 0.03
51 17 0.19
52 2 0.02
53 5 0.05
54 3 0.03
55 30 0.33
ACGTcount: A:0.22, C:0.11, G:0.09, T:0.58
Consensus pattern (49 bp):
TTTTATTTATGCATTTAGTCATTTTTTATTTATGATTCGGCTACTATTA
Found at i:2376126 original size:9 final size:9
Alignment explanation
Indices: 2376114--2376148 Score: 61
Period size: 9 Copynumber: 3.9 Consensus size: 9
2376104 GATTCTTTGG
2376114 ATTTCTTTC
1 ATTTCTTTC
2376123 ATTTCTTTC
1 ATTTCTTTC
2376132 ATTTCTTTC
1 ATTTCTTTC
*
2376141 AATTCTTT
1 ATTTCTTT
2376149 TATTCTTTTT
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
9 25 1.00
ACGTcount: A:0.14, C:0.20, G:0.00, T:0.66
Consensus pattern (9 bp):
ATTTCTTTC
Found at i:2377595 original size:11 final size:11
Alignment explanation
Indices: 2377575--2377630 Score: 53
Period size: 11 Copynumber: 5.1 Consensus size: 11
2377565 GTTAGATAAG
2377575 AAATAATAAAT
1 AAATAATAAAT
*
2377586 AAATATTAAAT
1 AAATAATAAAT
*
2377597 AAATTAAGGAAA-
1 AAA-TAA-TAAAT
2377609 AAATAA-AAAT
1 AAATAATAAAT
*
2377619 AAATAAAAAAT
1 AAATAATAAAT
2377630 A
1 A
2377631 GAAAATAGAA
Statistics
Matches: 38, Mismatches: 3, Indels: 8
0.78 0.06 0.16
Matches are distributed among these distances:
9 3 0.08
10 6 0.16
11 21 0.55
12 5 0.13
13 3 0.08
ACGTcount: A:0.73, C:0.00, G:0.04, T:0.23
Consensus pattern (11 bp):
AAATAATAAAT
Found at i:2379377 original size:31 final size:30
Alignment explanation
Indices: 2379326--2379402 Score: 91
Period size: 31 Copynumber: 2.5 Consensus size: 30
2379316 GTCGAACTCG
*
2379326 AAGGTCTTTGTGTTTTAAGAGAAAAAATTTCA
1 AAGGT-TTTGT-TTTTAAGAGAAAAAACTTCA
* **
2379358 AAGGTTTTTTTTTTCAAGAGAAACGACTTCA
1 AAGGTTTTGTTTTT-AAGAGAAAAAACTTCA
2379389 AAGGTTTTGTTTTT
1 AAGGTTTTGTTTTT
2379403 GTGTTTCAAT
Statistics
Matches: 39, Mismatches: 5, Indels: 3
0.83 0.11 0.06
Matches are distributed among these distances:
30 4 0.10
31 30 0.77
32 5 0.13
ACGTcount: A:0.31, C:0.08, G:0.18, T:0.43
Consensus pattern (30 bp):
AAGGTTTTGTTTTTAAGAGAAAAAACTTCA
Found at i:2379411 original size:37 final size:35
Alignment explanation
Indices: 2379332--2379452 Score: 110
Period size: 34 Copynumber: 3.5 Consensus size: 35
2379322 CTCGAAGGTC
* ***
2379332 TTTGTGTTTTAAGAGAAAAAATTTCAAAG---GTT
1 TTTGTGTTTCAAGAGAAACGCTTTCAAAGATTGTT
* *
2379364 TTT-TTTTTCAAGAGAAACGAC-TTCAAAGGTTTTGTT
1 TTTGTGTTTCAAGAGAAACG-CTTTCAAA-G-ATTGTT
*
2379400 TTTGTGTTTCAATAGAAACGCTTTCAAAGATT-TT
1 TTTGTGTTTCAAGAGAAACGCTTTCAAAGATTGTT
2379434 TTTGTGTTTCAAGAGAAAC
1 TTTGTGTTTCAAGAGAAAC
2379453 TTTATCCAGG
Statistics
Matches: 72, Mismatches: 9, Indels: 14
0.76 0.09 0.15
Matches are distributed among these distances:
31 18 0.25
32 4 0.06
34 20 0.28
35 2 0.03
36 8 0.11
37 20 0.28
ACGTcount: A:0.31, C:0.09, G:0.17, T:0.42
Consensus pattern (35 bp):
TTTGTGTTTCAAGAGAAACGCTTTCAAAGATTGTT
Found at i:2379592 original size:36 final size:36
Alignment explanation
Indices: 2379504--2380246 Score: 635
Period size: 36 Copynumber: 21.0 Consensus size: 36
2379494 TCAGAGATCG
*
2379504 TTGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAACT
1 TTGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAA-T
* * *
2379541 TTGTTTCAAGGGAAACTATCTAAAGAGAGATAAAAT
1 TTGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAAT
* *
2379577 TTGTTTCAAGAGAAACTATCTCAAGAGAGACAAAACT
1 TTGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAA-T
*
2379614 TGGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAAT
1 TTGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAAT
*
2379650 TTGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAAGT
1 TTGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAA-T
* * **
2379687 TAGTTCCAAAAGAAACTGTCTCAA-AGGAGACAAAAT
1 TTGTTTCAAGGGAAACTGTCTCAAGA-GAGACAAAAT
*** *
2379723 TTGTTTCAAGGGAAA------CAA-ATTTA-AAGATT
1 TTGTTTCAAGGGAAACTGTCTCAAGAGAGACAA-AAT
*
2379752 TTGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAAA
1 TTGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAAT
2379788 TTGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAACT
1 TTGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAA-T
** * * *
2379825 TTGTTTTGACGGAAACTATATCAAGAGAGACAAAAT
1 TTGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAAT
* *
2379861 TTGTTTCAAGAGAAATTGTCTCAAGAGAGACAAAACT
1 TTGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAA-T
* * ** *
2379898 TAGTTCCAAAAGAAACTGTCTCAAG-GAAGACGAAAT
1 TTGTTTCAAGGGAAACTGTCTCAAGAG-AGACAAAAT
* * * *
2379934 TTGTTTCAA-GGAAAATATATTC-A-A-AG----ATT
1 TTGTTTCAAGGGAAACTGT-CTCAAGAGAGACAAAAT
2379963 TTGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAAT
1 TTGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAAT
*
2379999 TTGTTTAAAGGGAAACTGTCTCAAGAGAGACAAAACT
1 TTGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAA-T
* * ** * * *
2380036 TAGTTCCAAAAGAAATTGTCTCAAGGGAGACGAAAT
1 TTGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAAT
** *
2380072 TTGTTT-AATGTAAAACATAT-TC-A-A-AG-----AT
1 TTGTTTCAA-GGGAAAC-TGTCTCAAGAGAGACAAAAT
*
2380100 TTCTTTTCAA-GGAAACTGTCTCAAGAGAGACAAAAT
1 TT-GTTTCAAGGGAAACTGTCTCAAGAGAGACAAAAT
* * *
2380136 TTGTTTCAAGGGAAACTATCTCAATAAAGACAAAAT
1 TTGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAAT
** **
2380172 TTGTTTCAATTGAAACTGTCTCAAGAGAGACGAAGTCT
1 TTGTTTCAAGGGAAACTGTCTCAAGAGAGAC-AA-AAT
* * * *
2380210 TATGTTTCGAGGGAAACTATCTCAAGCGAGATAAAAT
1 T-TGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAAT
2380247 CTTCTTTAAA
Statistics
Matches: 566, Mismatches: 97, Indels: 86
0.76 0.13 0.11
Matches are distributed among these distances:
27 2 0.00
28 12 0.02
29 35 0.06
30 15 0.03
31 3 0.01
32 2 0.00
33 4 0.01
35 19 0.03
36 257 0.45
37 189 0.33
38 4 0.01
39 24 0.04
ACGTcount: A:0.41, C:0.13, G:0.19, T:0.26
Consensus pattern (36 bp):
TTGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAAT
Found at i:2379593 original size:73 final size:73
Alignment explanation
Indices: 2379504--2380202 Score: 654
Period size: 73 Copynumber: 9.9 Consensus size: 73
2379494 TCAGAGATCG
* *
2379504 TTGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAACTTTGTTTCAAGGGAAACTATCTAAAGAGA
1 TTGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAACTTTGTTTCAAGGGAAACTGTCTCAAGAGA
*
2379569 GATAAAAT
66 GACAAAAT
* *
2379577 TTGTTTCAAGAGAAACTATCTCAAGAGAGACAAAACTTGGTTTCAAGGGAAACTGTCTCAAGAGA
1 TTGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAACTTTGTTTCAAGGGAAACTGTCTCAAGAGA
2379642 GACAAAAT
66 GACAAAAT
* * * **
2379650 TTGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAAGTTAGTTCCAAAAGAAACTGTCTCAA-AGG
1 TTGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAACTTTGTTTCAAGGGAAACTGTCTCAAGA-G
2379714 AGACAAAAT
65 AGACAAAAT
* *** * *
2379723 TTGTTTCAAGGGAAA------CAA-ATTTA-AAGATTTTGTTTCAAGGGAAACTGTCTCAAGAGA
1 TTGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAACTTTGTTTCAAGGGAAACTGTCTCAAGAGA
*
2379780 GACAAAAA
66 GACAAAAT
* ** * * *
2379788 TTGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAACTTTGTTTTGACGGAAACTATATCAAGAGA
1 TTGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAACTTTGTTTCAAGGGAAACTGTCTCAAGAGA
2379853 GACAAAAT
66 GACAAAAT
* * * **
2379861 TTGTTTCAAGAGAAATTGTCTCAAGAGAGACAAAACTTAGTTCCAAAAGAAACTGTCTCAAG-GA
1 TTGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAACTTTGTTTCAAGGGAAACTGTCTCAAGAG-
*
2379925 AGACGAAAT
65 AGACAAAAT
* * * *
2379934 TTGTTTCAAG-GAAAATATATTC-A-A-AG-----ATTTTGTTTCAAGGGAAACTGTCTCAAGAG
1 TTGTTTCAAGAGAAACTGT-CTCAAGAGAGACAAAACTTTGTTTCAAGGGAAACTGTCTCAAGAG
2379990 AGACAAAAT
65 AGACAAAAT
* * * * ** * *
2379999 TTGTTTAAAGGGAAACTGTCTCAAGAGAGACAAAACTTAGTTCCAAAAGAAATTGTCTCAAGGGA
1 TTGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAACTTTGTTTCAAGGGAAACTGTCTCAAGAGA
*
2380064 GACGAAAT
66 GACAAAAT
* *
2380072 TTGTTT-AATGTA-AAACATAT-TC-A-A-AG-----A-TTTCTTTTCAA-GGAAACTGTCTCAA
1 TTGTTTCAA-G-AGAAAC-TGTCTCAAGAGAGACAAAACTTT-GTTTCAAGGGAAACTGTCTCAA
2380124 GAGAGACAAAAT
62 GAGAGACAAAAT
* * * * **
2380136 TTGTTTCAAGGGAAACTATCTCAATAAAGACAAAA-TTTGTTTCAATTGAAACTGTCTCAAGAGA
1 TTGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAACTTTGTTTCAAGGGAAACTGTCTCAAGAGA
2380200 GAC
66 GAC
2380203 GAAGTCTTAT
Statistics
Matches: 511, Mismatches: 77, Indels: 77
0.77 0.12 0.12
Matches are distributed among these distances:
63 3 0.01
64 37 0.07
65 99 0.19
66 12 0.02
67 6 0.01
68 2 0.00
70 4 0.01
71 11 0.02
72 38 0.07
73 297 0.58
74 2 0.00
ACGTcount: A:0.41, C:0.13, G:0.19, T:0.26
Consensus pattern (73 bp):
TTGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAACTTTGTTTCAAGGGAAACTGTCTCAAGAGA
GACAAAAT
Found at i:2379766 original size:211 final size:211
Alignment explanation
Indices: 2379540--2380077 Score: 817
Period size: 211 Copynumber: 2.5 Consensus size: 211
2379530 GAGACAAAAC
* * * * *
2379540 TTTGTTTCAAGGGAAACTATCTAAAGAGAGATAAAATTTGTTTCAAGAGAAACTATCTCAAGAGA
1 TTTGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAATTTGTTTCAAGGGAAACTGTCTCAAGAGA
* *
2379605 GACAAAACTTGGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAATTTGTTTCAAGAGAAACTGTC
66 GACAAAACTTAGTTTCAAAGGAAACTGTCTCAAGAGAGACAAAATTTGTTTCAAGAGAAACTGTC
*
2379670 TCAAGAGAGACAAAAGTTAGTTCCAAAAGAAACTGTCTCAAAGG-AGACAAAATTTGTTTCAAGG
131 TCAAGAGAGACAAAACTTAGTTCCAAAAGAAACTGTCTC-AAGGAAGACAAAATTTGTTTCAAGG
* *
2379734 GAAACAAATTTAAAGAT
195 AAAACAAATTCAAAGAT
*
2379751 TTTGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAAATTGTTTCAAGGGAAACTGTCTCAAGAGA
1 TTTGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAATTTGTTTCAAGGGAAACTGTCTCAAGAGA
* ** * * * *
2379816 GACAAAACTTTGTTTTGACGGAAACTATATCAAGAGAGACAAAATTTGTTTCAAGAGAAATTGTC
66 GACAAAACTTAGTTTCAAAGGAAACTGTCTCAAGAGAGACAAAATTTGTTTCAAGAGAAACTGTC
*
2379881 TCAAGAGAGACAAAACTTAGTTCCAAAAGAAACTGTCTCAAGGAAGACGAAATTTGTTTCAAGGA
131 TCAAGAGAGACAAAACTTAGTTCCAAAAGAAACTGTCTCAAGGAAGACAAAATTTGTTTCAAGGA
* *
2379946 AAATATATTCAAAGAT
196 AAACAAATTCAAAGAT
*
2379962 TTTGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAATTTGTTTAAAGGGAAACTGTCTCAAGAGA
1 TTTGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAATTTGTTTCAAGGGAAACTGTCTCAAGAGA
* * * * *
2380027 GACAAAACTTAGTTCCAAAAGAAATTGTCTCAAGGGAGACGAAATTTGTTT
66 GACAAAACTTAGTTTCAAAGGAAACTGTCTCAAGAGAGACAAAATTTGTTT
2380078 AATGTAAAAC
Statistics
Matches: 294, Mismatches: 32, Indels: 2
0.90 0.10 0.01
Matches are distributed among these distances:
210 4 0.01
211 290 0.99
ACGTcount: A:0.41, C:0.13, G:0.20, T:0.26
Consensus pattern (211 bp):
TTTGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAATTTGTTTCAAGGGAAACTGTCTCAAGAGA
GACAAAACTTAGTTTCAAAGGAAACTGTCTCAAGAGAGACAAAATTTGTTTCAAGAGAAACTGTC
TCAAGAGAGACAAAACTTAGTTCCAAAAGAAACTGTCTCAAGGAAGACAAAATTTGTTTCAAGGA
AAACAAATTCAAAGAT
Found at i:2379990 original size:138 final size:137
Alignment explanation
Indices: 2379835--2380205 Score: 534
Period size: 138 Copynumber: 2.7 Consensus size: 137
2379825 TTGTTTTGAC
* * * *
2379835 GGAAACTATATCAAGAGAGACAAAATTTGTTTCAAGAGAAATTGTCTCAAGAGAGACAAAACTTA
1 GGAAACTGTCTCAAGAGAGACAAAATTTGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAACTTA
*
2379900 GTTCCAAAAGAAACTGTCTCAAGGAAGACGAAATTTGTTTCAA-GGAAAATATATTCAAAGATTT
66 GTTCCAAAAGAAACTGTCTCAAGGAAGACGAAATTTGTTT-AATGGAAAACATATTCAAAGATTT
2379964 -TGTTTCAA
130 CT-TTTCAA
*
2379972 GGGAAACTGTCTCAAGAGAGACAAAATTTGTTTAAAGGGAAACTGTCTCAAGAGAGACAAAACTT
1 -GGAAACTGTCTCAAGAGAGACAAAATTTGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAACTT
* * *
2380037 AGTTCCAAAAGAAATTGTCTCAAGGGAGACGAAATTTGTTTAATGTAAAACATATTCAAAGATTT
65 AGTTCCAAAAGAAACTGTCTCAAGGAAGACGAAATTTGTTTAATGGAAAACATATTCAAAGATTT
2380102 CTTTTCAA
130 CTTTTCAA
* * * *
2380110 GGAAACTGTCTCAAGAGAGACAAAATTTGTTTCAAGGGAAACTATCTCAATAAAGACAAAA-TTT
1 GGAAACTGTCTCAAGAGAGACAAAATTTGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAACTTA
* **
2380174 GTTTCAATTGAAACTGTCTCAA-GAGAGACGAA
66 GTTCCAAAAGAAACTGTCTCAAGGA-AGACGAA
2380206 GTCTTATGTT
Statistics
Matches: 211, Mismatches: 19, Indels: 8
0.89 0.08 0.03
Matches are distributed among these distances:
135 1 0.00
136 27 0.13
137 59 0.28
138 123 0.58
139 1 0.00
ACGTcount: A:0.42, C:0.13, G:0.18, T:0.27
Consensus pattern (137 bp):
GGAAACTGTCTCAAGAGAGACAAAATTTGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAACTTA
GTTCCAAAAGAAACTGTCTCAAGGAAGACGAAATTTGTTTAATGGAAAACATATTCAAAGATTTC
TTTTCAA
Found at i:2380313 original size:73 final size:70
Alignment explanation
Indices: 2380214--2380385 Score: 172
Period size: 73 Copynumber: 2.4 Consensus size: 70
2380204 AAGTCTTATG
* * *
2380214 TTTCGAG-GGAAACTATCTCAAGCGAGATAAAATCTT-CTTT-AAAAATAGTCTTGAGTGAAATG
1 TTTCGAGTGAAAAC-ATCTCAAGCGAGA-AAAATCTTACTTTAAAAAACAATCTTGAGTGAAAT-
2380276 AAATGCATTA
63 AAAT-C-TTA
* *
2380286 TTTCGAGTGAAAACGATCTCAAGCGAGACAAATCTTATTTTAAGAAAAACAATCTTGAGTGAAAT
1 TTTCGAGTGAAAAC-ATCTCAAGCGAGAAAAATCTTACTTT-A-AAAAACAATCTTGAGTGAAAT
*
2380351 AAATCTTC
63 AAATCTTA
*
2380359 TTTCGAGT-AAAACAGTCTCAAGTGAGA
1 TTTCGAGTGAAAACA-TCTCAAGCGAGA
2380386 CAAAGTCTGT
Statistics
Matches: 86, Mismatches: 8, Indels: 12
0.81 0.08 0.11
Matches are distributed among these distances:
71 1 0.01
72 30 0.35
73 31 0.36
74 1 0.01
75 4 0.05
76 19 0.22
ACGTcount: A:0.40, C:0.14, G:0.17, T:0.29
Consensus pattern (70 bp):
TTTCGAGTGAAAACATCTCAAGCGAGAAAAATCTTACTTTAAAAAACAATCTTGAGTGAAATAAA
TCTTA
Found at i:2380320 original size:72 final size:70
Alignment explanation
Indices: 2380214--2380389 Score: 180
Period size: 72 Copynumber: 2.4 Consensus size: 70
2380204 AAGTCTTATG
* * * *
2380214 TTTCGAG-GGAAACTATCTCAAGCGAGATAAAATCTT-CTTT-AAAAATAGTCTTGAGTGAAATG
1 TTTCGAGTGAAAAC-ATCTCAAGCGAGA-CAAATCTTACTTTAAAAAACAATCTTGAGTGAAAT-
2380276 AAATGCATTA
63 AAAT-C-TTA
*
2380286 TTTCGAGTGAAAACGATCTCAAGCGAGACAAATCTTATTTTAAGAAAAACAATCTTGAGTGAAAT
1 TTTCGAGTGAAAAC-ATCTCAAGCGAGACAAATCTTACTTT-A-AAAAACAATCTTGAGTGAAAT
*
2380351 AAATCTTC
63 AAATCTTA
*
2380359 TTTCGAGT-AAAACAGTCTCAAGTGAGACAAA
1 TTTCGAGTGAAAACA-TCTCAAGCGAGACAAA
2380390 GTCTGTTTTA
Statistics
Matches: 90, Mismatches: 8, Indels: 12
0.82 0.07 0.11
Matches are distributed among these distances:
71 1 0.01
72 34 0.38
73 31 0.34
74 1 0.01
75 4 0.04
76 19 0.21
ACGTcount: A:0.40, C:0.14, G:0.17, T:0.28
Consensus pattern (70 bp):
TTTCGAGTGAAAACATCTCAAGCGAGACAAATCTTACTTTAAAAAACAATCTTGAGTGAAATAAA
TCTTA
Found at i:2380371 original size:36 final size:36
Alignment explanation
Indices: 2380262--2380372 Score: 96
Period size: 36 Copynumber: 3.0 Consensus size: 36
2380252 TTAAAAATAG
*
2380262 TCTTGAGTGAAATGAAATGCATTATTTCGAGTGAAAACGA
1 TCTTGAGTGAAAT-AAAT-C-TTATTTCGAGT-AAAACAA
** * * * ** *
2380302 TCTCAAGCGAGACAAATCTTATTTTAAGAAAAACAA
1 TCTTGAGTGAAATAAATCTTATTTCGAGTAAAACAA
*
2380338 TCTTGAGTGAAATAAATCTTCTTTCGAGTAAAACA
1 TCTTGAGTGAAATAAATCTTATTTCGAGTAAAACA
2380373 GTCTCAAGTG
Statistics
Matches: 53, Mismatches: 18, Indels: 4
0.71 0.24 0.05
Matches are distributed among these distances:
36 32 0.60
37 8 0.15
38 1 0.02
39 4 0.08
40 8 0.15
ACGTcount: A:0.41, C:0.14, G:0.16, T:0.30
Consensus pattern (36 bp):
TCTTGAGTGAAATAAATCTTATTTCGAGTAAAACAA
Found at i:2380399 original size:72 final size:76
Alignment explanation
Indices: 2380262--2380412 Score: 206
Period size: 72 Copynumber: 2.0 Consensus size: 76
2380252 TTAAAAATAG
2380262 TCTTGAGTGAAATGAAATGCATTATTTCGAGTGAAAACGATCTCAAGCGAGACAAATCTTATTTT
1 TCTTGAGTGAAATGAAATGCATTATTTCGAGTGAAAACGATCTCAAGCGAGACAAATCTTATTTT
2380327 AAGAAAAACAA
66 AAGAAAAACAA
* * *
2380338 TCTTGAGTGAAAT-AAAT-C-TTCTTTCGAGT-AAAAC-AGTCTCAAGTGAGACAAAGTC-TGTT
1 TCTTGAGTGAAATGAAATGCATTATTTCGAGTGAAAACGA-TCTCAAGCGAGACAAA-TCTTATT
*
2380397 TTAAGAAAAGCAA
64 TTAAGAAAAACAA
2380410 TCT
1 TCT
2380413 CAAGTTAGAT
Statistics
Matches: 69, Mismatches: 4, Indels: 8
0.85 0.05 0.10
Matches are distributed among these distances:
71 1 0.01
72 38 0.55
73 12 0.17
74 1 0.01
75 4 0.06
76 13 0.19
ACGTcount: A:0.40, C:0.14, G:0.17, T:0.29
Consensus pattern (76 bp):
TCTTGAGTGAAATGAAATGCATTATTTCGAGTGAAAACGATCTCAAGCGAGACAAATCTTATTTT
AAGAAAAACAA
Found at i:2380414 original size:36 final size:33
Alignment explanation
Indices: 2380294--2380427 Score: 97
Period size: 36 Copynumber: 3.8 Consensus size: 33
2380284 TATTTCGAGT
* *
2380294 GAAAACGATCTCAAGCGAGACAAATCTTATTTTAA
1 GAAAACAATCTCAAGTGAGACAAATC-T-TTTTAA
** * * *
2380329 GAAAAACAATCTTGAGTGAAATAAATCTTCTTTCGA
1 G-AAAACAATCTCAAGTGAGACAAATCTT-TTT-AA
*
2380365 GTAAAACAGTCTCAAGTGAGACAAAGTCTGTTTTAA
1 G-AAAACAATCTCAAGTGAGACAAA-TCT-TTTTAA
* *
2380401 GAAAAGCAATCTCAAGTTAGATAAATC
1 GAAAA-CAATCTCAAGTGAGACAAATC
2380428 ATCTGAATTA
Statistics
Matches: 76, Mismatches: 17, Indels: 12
0.72 0.16 0.11
Matches are distributed among these distances:
34 1 0.01
35 11 0.14
36 57 0.75
37 6 0.08
38 1 0.01
ACGTcount: A:0.43, C:0.15, G:0.16, T:0.27
Consensus pattern (33 bp):
GAAAACAATCTCAAGTGAGACAAATCTTTTTAA
Found at i:2386763 original size:4 final size:4
Alignment explanation
Indices: 2386747--2386793 Score: 52
Period size: 4 Copynumber: 13.2 Consensus size: 4
2386737 GGGCCCTGCA
2386747 AAAT AAA- AAAT AAAT -AAT -AAT -AAT -AAT -AAT AAAT AAAT AAAT
1 AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAAT
2386789 AAAT A
1 AAAT A
2386794 TTATAATATA
Statistics
Matches: 41, Mismatches: 0, Indels: 4
0.91 0.00 0.09
Matches are distributed among these distances:
3 18 0.44
4 23 0.56
ACGTcount: A:0.74, C:0.00, G:0.00, T:0.26
Consensus pattern (4 bp):
AAAT
Found at i:2386801 original size:12 final size:11
Alignment explanation
Indices: 2386747--2386793 Score: 55
Period size: 9 Copynumber: 4.5 Consensus size: 11
2386737 GGGCCCTGCA
*
2386747 AAATAAAAAAT
1 AAATAAATAAT
2386758 AAAT-AATAAT
1 AAATAAATAAT
2386768 -AAT-AATAAT
1 AAATAAATAAT
2386777 AAATAAATAAAT
1 AAATAAAT-AAT
2386789 AAATA
1 AAATA
2386794 TTATAATATA
Statistics
Matches: 32, Mismatches: 1, Indels: 5
0.84 0.03 0.13
Matches are distributed among these distances:
9 9 0.28
10 8 0.25
11 7 0.22
12 8 0.25
ACGTcount: A:0.74, C:0.00, G:0.00, T:0.26
Consensus pattern (11 bp):
AAATAAATAAT
Found at i:2387271 original size:20 final size:20
Alignment explanation
Indices: 2387246--2387283 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
2387236 TCCCATTTTT
*
2387246 GCATCTTTGCATTTGCATGA
1 GCATCTTTGCATTAGCATGA
2387266 GCATCTTTGCATTAGCAT
1 GCATCTTTGCATTAGCAT
2387284 CCATATATCG
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.21, C:0.21, G:0.18, T:0.39
Consensus pattern (20 bp):
GCATCTTTGCATTAGCATGA
Found at i:2388655 original size:21 final size:18
Alignment explanation
Indices: 2388638--2388715 Score: 84
Period size: 19 Copynumber: 4.1 Consensus size: 18
2388628 CATAAAATAT
2388638 AGAAAAAAGGAAACAAAAAA
1 AGAAAAAAGG-AA-AAAAAA
2388658 AGGAAAAAAGGAAAAAAAA
1 A-GAAAAAAGGAAAAAAAA
**
2388677 AGAAAAAAAAAAAAAAAAA
1 AG-AAAAAAGGAAAAAAAA
*
2388696 AGAAAAAAAAGAAAAAAAA
1 AG-AAAAAAGGAAAAAAAA
2388715 A
1 A
2388716 AAGAGAAGAA
Statistics
Matches: 53, Mismatches: 3, Indels: 5
0.87 0.05 0.08
Matches are distributed among these distances:
18 1 0.02
19 40 0.75
20 3 0.06
21 9 0.17
ACGTcount: A:0.86, C:0.01, G:0.13, T:0.00
Consensus pattern (18 bp):
AGAAAAAAGGAAAAAAAA
Found at i:2388666 original size:9 final size:9
Alignment explanation
Indices: 2388652--2388738 Score: 86
Period size: 9 Copynumber: 9.3 Consensus size: 9
2388642 AAAAGGAAAC
*
2388652 AAAAAAAGG
1 AAAAAAAGA
*
2388661 AAAAAAGGAA
1 AAAAAAAG-A
2388671 AAAAAAAGAA
1 AAAAAAAG-A
*
2388681 AAAAAAAAA
1 AAAAAAAGA
2388690 AAAAAAAGA
1 AAAAAAAGA
2388699 AAAAAAAGA
1 AAAAAAAGA
2388708 AAAAAAA-A
1 AAAAAAAGA
* *
2388716 AAGAGAAGA
1 AAAAAAAGA
2388725 AAGAAGAAAGA
1 AA-AA-AAAGA
2388736 AAA
1 AAA
2388739 CCGATCAAAT
Statistics
Matches: 65, Mismatches: 9, Indels: 7
0.80 0.11 0.09
Matches are distributed among these distances:
8 6 0.09
9 35 0.54
10 18 0.28
11 6 0.09
ACGTcount: A:0.85, C:0.00, G:0.15, T:0.00
Consensus pattern (9 bp):
AAAAAAAGA
Found at i:2388673 original size:1 final size:1
Alignment explanation
Indices: 2388669--2388717 Score: 71
Period size: 1 Copynumber: 49.0 Consensus size: 1
2388659 GGAAAAAAGG
* * *
2388669 AAAAAAAAAGAAAAAAAAAAAAAAAAAAGAAAAAAAAGAAAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
2388718 GAGAAGAAAG
Statistics
Matches: 42, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
1 42 1.00
ACGTcount: A:0.94, C:0.00, G:0.06, T:0.00
Consensus pattern (1 bp):
A
Found at i:2388674 original size:19 final size:19
Alignment explanation
Indices: 2388652--2388715 Score: 101
Period size: 19 Copynumber: 3.4 Consensus size: 19
2388642 AAAAGGAAAC
* *
2388652 AAAAAAAGGAAAAAAGGAA
1 AAAAAAAGAAAAAAAAGAA
*
2388671 AAAAAAAGAAAAAAAAAAA
1 AAAAAAAGAAAAAAAAGAA
2388690 AAAAAAAGAAAAAAAAGAA
1 AAAAAAAGAAAAAAAAGAA
2388709 AAAAAAA
1 AAAAAAA
2388716 AAGAGAAGAA
Statistics
Matches: 41, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
19 41 1.00
ACGTcount: A:0.89, C:0.00, G:0.11, T:0.00
Consensus pattern (19 bp):
AAAAAAAGAAAAAAAAGAA
Found at i:2388675 original size:18 final size:18
Alignment explanation
Indices: 2388652--2388738 Score: 86
Period size: 19 Copynumber: 4.7 Consensus size: 18
2388642 AAAAGGAAAC
* *
2388652 AAAAAAAGGAAAAAAGGAA
1 AAAAAAAGAAAAAAAAG-A
*
2388671 AAAAAAAGAAAAAAAAAAA
1 AAAAAAAG-AAAAAAAAGA
2388690 AAAAAAAGAAAAAAAAGA
1 AAAAAAAGAAAAAAAAGA
* *
2388708 AAAAAAA-AAAGAGAAGA
1 AAAAAAAGAAAAAAAAGA
2388725 AAGAAGAAAGAAAA
1 AA-AA-AAAGAAAA
2388739 CCGATCAAAT
Statistics
Matches: 57, Mismatches: 7, Indels: 7
0.80 0.10 0.10
Matches are distributed among these distances:
17 10 0.18
18 18 0.32
19 20 0.35
20 9 0.16
ACGTcount: A:0.85, C:0.00, G:0.15, T:0.00
Consensus pattern (18 bp):
AAAAAAAGAAAAAAAAGA
Found at i:2388715 original size:28 final size:30
Alignment explanation
Indices: 2388661--2388738 Score: 79
Period size: 30 Copynumber: 2.6 Consensus size: 30
2388651 CAAAAAAAGG
*
2388661 AAAAAAG-GAAAAAAAAAGAAAAAAAAAAAA
1 AAAAAAGAGAAAAAAAAA-AAAAAAAAAGAA
*
2388691 AAAAAAGA-AAAAAAAGAAAAAAAAAAAGAG
1 AAAAAAGAGAAAAAAA-AAAAAAAAAAAGAA
* *
2388721 AAGAAAGAAGAAAGAAAA
1 AAAAAAG-AGAAAAAAAA
2388739 CCGATCAAAT
Statistics
Matches: 40, Mismatches: 4, Indels: 7
0.78 0.08 0.14
Matches are distributed among these distances:
30 30 0.75
31 4 0.10
32 6 0.15
ACGTcount: A:0.86, C:0.00, G:0.14, T:0.00
Consensus pattern (30 bp):
AAAAAAGAGAAAAAAAAAAAAAAAAAAGAA
Found at i:2388716 original size:21 final size:20
Alignment explanation
Indices: 2388619--2388729 Score: 109
Period size: 21 Copynumber: 5.5 Consensus size: 20
2388609 AAGATATGGC
* * *
2388619 AAAAAAAGACATAAAATATAG
1 AAAAAAAGA-AAAAAAAAAAG
* *
2388640 AAAAAAGGAAACAAAAAAAG
1 AAAAAAAGAAAAAAAAAAAG
* *
2388660 GAAAAAAG-GAAAAAAAAAG
1 AAAAAAAGAAAAAAAAAAAG
2388679 AAAAAAA-AAAAAAAAAAAG
1 AAAAAAAGAAAAAAAAAAAG
2388698 AAAAAAAAGAAAAAAAAAAAG
1 -AAAAAAAGAAAAAAAAAAAG
*
2388719 AGAAGAAAGAA
1 A-AAAAAAGAA
2388730 GAAAGAAAAC
Statistics
Matches: 74, Mismatches: 12, Indels: 8
0.79 0.13 0.09
Matches are distributed among these distances:
19 25 0.34
20 21 0.28
21 28 0.38
ACGTcount: A:0.82, C:0.02, G:0.14, T:0.03
Consensus pattern (20 bp):
AAAAAAAGAAAAAAAAAAAG
Found at i:2388728 original size:30 final size:30
Alignment explanation
Indices: 2388640--2388729 Score: 114
Period size: 28 Copynumber: 3.0 Consensus size: 30
2388630 TAAAATATAG
* *
2388640 AAAAAAGGAAACAAAAAAAG-GAAAAAAGGAA
1 AAAAAAAGAAAAAAAAAAAGAGAAAAAA-G-A
2388671 AAAAAAAGAAAAAAAAAAA-A-AAAAAAGA
1 AAAAAAAGAAAAAAAAAAAGAGAAAAAAGA
*
2388699 AAAAAAAGAAAAAAAAAAAGAGAAGAAAGA
1 AAAAAAAGAAAAAAAAAAAGAGAAAAAAGA
2388729 A
1 A
2388730 GAAAGAAAAC
Statistics
Matches: 53, Mismatches: 3, Indels: 7
0.84 0.05 0.11
Matches are distributed among these distances:
28 20 0.38
29 2 0.04
30 14 0.26
31 17 0.32
ACGTcount: A:0.84, C:0.01, G:0.14, T:0.00
Consensus pattern (30 bp):
AAAAAAAGAAAAAAAAAAAGAGAAAAAAGA
Found at i:2390790 original size:55 final size:58
Alignment explanation
Indices: 2390721--2390830 Score: 145
Period size: 59 Copynumber: 1.9 Consensus size: 58
2390711 TCTAAGCCTA
* * *
2390721 ATTTTCAAATGAGTTTTTAGAA-A-TTAAGCCTGATTTTCAGGGGTTTCTTGATGATG
1 ATTTTCAAATGAGTTTTTAAAAGAGTTAAGCCTAATTTTCAGGGGTTCCTTGATGATG
*
2390777 ATTTTC-AATGAGTTTTTAAAAGGTAGTTAAGCCTAATTTTTAGGGGTTCCTTGA
1 ATTTTCAAATGAGTTTTTAAAA-G-AGTTAAGCCTAATTTTCAGGGGTTCCTTGA
2390831 CAACTAAGAA
Statistics
Matches: 46, Mismatches: 4, Indels: 5
0.84 0.07 0.09
Matches are distributed among these distances:
55 14 0.30
56 6 0.13
58 1 0.02
59 25 0.54
ACGTcount: A:0.27, C:0.09, G:0.21, T:0.43
Consensus pattern (58 bp):
ATTTTCAAATGAGTTTTTAAAAGAGTTAAGCCTAATTTTCAGGGGTTCCTTGATGATG
Found at i:2390981 original size:41 final size:42
Alignment explanation
Indices: 2390874--2390992 Score: 134
Period size: 42 Copynumber: 2.9 Consensus size: 42
2390864 TTTTTGATTA
*
2390874 ATAAGTCCTTCGGGTCAT-CAGTAAGTCTTTCAAGCATGATGC
1 ATAAGTCCTTCGGGTCATCCA-TAAGTCTTTCAAGCAAGATGC
* * * *
2390916 TTAAATCCTTCGGGTCATCTATAAGTCTTTCGAGCAAGATG-
1 ATAAGTCCTTCGGGTCATCCATAAGTCTTTCAAGCAAGATGC
* * * *
2390957 ATAAGTCATTCGGGCCATCCATAAGACCTTCAAGCA
1 ATAAGTCCTTCGGGTCATCCATAAGTCTTTCAAGCA
2390993 GTATGTTTTC
Statistics
Matches: 63, Mismatches: 13, Indels: 3
0.80 0.16 0.04
Matches are distributed among these distances:
41 28 0.44
42 34 0.54
43 1 0.02
ACGTcount: A:0.29, C:0.23, G:0.19, T:0.29
Consensus pattern (42 bp):
ATAAGTCCTTCGGGTCATCCATAAGTCTTTCAAGCAAGATGC
Found at i:2391234 original size:273 final size:274
Alignment explanation
Indices: 2390722--2391652 Score: 1422
Period size: 275 Copynumber: 3.4 Consensus size: 274
2390712 CTAAGCCTAA
* * * * *
2390722 TTTTCAAATGAGTTTTTAGAAATTAAGCCTGATTTTCAGGGGTTTCTTGATGATGATTTTCAATG
1 TTTTCAAATGAGTTTTTAGAAACTAAGCCTGATTTTCAGGGGTTTCTTGATGATTATCTCCAAAG
* *
2390787 AGTTTTTAAAAGGTAGTTAAGCCTAATTTTTAGGGGTTCCTTGACAACTAAGAAACTAAGCTTGA
66 AGTTTTTAAAAGGAAGCTAAGCCTAATTTTTAGGGGTTCCTTGACAACTAAGAAACTAAGCTTGA
* * * * *
2390852 TTTTCAAGGGTTTTTTTGATTAATAAGTCCTTCGGGTCATCAGTAAGTCTTTCAAGCATGATGCT
131 TTTTCAAGGG-TTTCTTGATGAGTAAGTCCTTCGGGACATCAGTAAGTCTTTCGAGCATGATGCT
2390917 TAAATCCTTCGGGTCATCTATAAGTCTTTCGAGCAAGATGATAAGTCATTCGGGCCATCCATAAG
195 TAAATCCTTCGGGTCATCTATAAGTCTTTCGAGCAAGATGATAAGTC-TTCGGGCCATCCATAAG
*
2390982 ACCTTCAAGCAGTATG
259 ACCTTCAAGCAGAATG
* *
2390998 TTTTCAAATGAG-TTCTAGAAACTAAGCCTGATTTTTAGGGGTTTCTTGATGATTATCTCCAAAG
1 TTTTCAAATGAGTTTTTAGAAACTAAGCCTGATTTTCAGGGGTTTCTTGATGATTATCTCCAAAG
*
2391062 AGTTTTTAAAAGGAAGCTAAGCCTAATTTTTA-GGGTTCATTGACAACTAAGAAACTAAGCTTGA
66 AGTTTTTAAAAGGAAGCTAAGCCTAATTTTTAGGGGTTCCTTGACAACTAAGAAACTAAGCTTGA
* *
2391126 TTTTCAAAGGTTTCTTGATGAGTAAGTCCTTCGGGAAATCAGTAAGTCTTTCGAGCATGATGCTT
131 TTTTCAAGGGTTTCTTGATGAGTAAGTCCTTCGGGACATCAGTAAGTCTTTCGAGCATGATGCTT
*
2391191 AAATCCTTCGGGCCATCTATAAGTCTTTCGAGCAAGATGATAAGTTCTTCGGGCCATCCATAAGA
196 AAATCCTTCGGGTCATCTATAAGTCTTTCGAGCAAGATGATAAG-TCTTCGGGCCATCCATAAGA
*
2391256 CCTTCAGGCAGAATG
260 CCTTCAAGCAGAATG
* *
2391271 CTTTCAAATGAGTTTTTAGAAACTAAGCCT-AGTTTTTAGGGGTTTCTTGATGATTATCTCCAAA
1 TTTTCAAATGAGTTTTTAGAAACTAAGCCTGA-TTTTCAGGGGTTTCTTGATGATTATCTCCAAA
*
2391335 GAGTTTTTAAAAGGAAGCTAAGCCTAATTTTTAGGGGTTCCTTGACAATTAAGAAACTAAGCTTG
65 GAGTTTTTAAAAGGAAGCTAAGCCTAATTTTTAGGGGTTCCTTGACAACTAAGAAACTAAGCTTG
* * * *
2391400 ATTTTTAAGGGTTTCTTGATGAGTAAGTCCTTTGGGCCATCAATAAGTCTTTCGAGCATGATGCT
130 ATTTTCAAGGGTTTCTTGATGAGTAAGTCCTTCGGGACATCAGTAAGTCTTTCGAGCATGATGCT
* * * *
2391465 TAAATCCTTCGGGTCACCTATAAGTCTTTCGAGTAAGATGATAAGTCCTTCGGACTATCCATAA-
195 TAAATCCTTCGGGTCATCTATAAGTCTTTCGAGCAAGATGATAAGT-CTTCGGGCCATCCATAAG
* *
2391529 ACCTTCGAGCAGGATG
259 ACCTTCAAGCAGAATG
* * * *
2391545 TTTTCAAATGACTTTTTAAAAACTAGGCCTAATTTTCAGGGGTTTCTTGATGATTATCTCCAAAG
1 TTTTCAAATGAGTTTTTAGAAACTAAGCCTGATTTTCAGGGGTTTCTTGATGATTATCTCCAAAG
* * *
2391610 AATTTTT-AAAGGAAGTTAAGCCTAATTTTTAGGGATTCCTTGA
66 AGTTTTTAAAAGGAAGCTAAGCCTAATTTTTAGGGGTTCCTTGA
2391653 TGACAACTAA
Statistics
Matches: 603, Mismatches: 46, Indels: 15
0.91 0.07 0.02
Matches are distributed among these distances:
273 169 0.28
274 201 0.33
275 221 0.37
276 12 0.02
ACGTcount: A:0.29, C:0.16, G:0.20, T:0.35
Consensus pattern (274 bp):
TTTTCAAATGAGTTTTTAGAAACTAAGCCTGATTTTCAGGGGTTTCTTGATGATTATCTCCAAAG
AGTTTTTAAAAGGAAGCTAAGCCTAATTTTTAGGGGTTCCTTGACAACTAAGAAACTAAGCTTGA
TTTTCAAGGGTTTCTTGATGAGTAAGTCCTTCGGGACATCAGTAAGTCTTTCGAGCATGATGCTT
AAATCCTTCGGGTCATCTATAAGTCTTTCGAGCAAGATGATAAGTCTTCGGGCCATCCATAAGAC
CTTCAAGCAGAATG
Found at i:2391254 original size:41 final size:41
Alignment explanation
Indices: 2391142--2391254 Score: 129
Period size: 42 Copynumber: 2.7 Consensus size: 41
2391132 AAGGTTTCTT
** *
2391142 GATGAGTAAGTCCTTCGGGAAAT-CAGTAAGTCTTTCGAGCAT
1 GATGA-TAAGTCCTTCGGGCCATCCA-TAAGTCTTTCGAGCAA
* * *
2391184 GATGCTTAAATCCTTCGGGCCATCTATAAGTCTTTCGAGCAA
1 GATG-ATAAGTCCTTCGGGCCATCCATAAGTCTTTCGAGCAA
*
2391226 GATGATAAGTTCTTCGGGCCATCCATAAG
1 GATGATAAGTCCTTCGGGCCATCCATAAG
2391255 ACCTTCAGGC
Statistics
Matches: 59, Mismatches: 10, Indels: 5
0.80 0.14 0.07
Matches are distributed among these distances:
41 21 0.36
42 37 0.63
43 1 0.02
ACGTcount: A:0.27, C:0.20, G:0.23, T:0.29
Consensus pattern (41 bp):
GATGATAAGTCCTTCGGGCCATCCATAAGTCTTTCGAGCAA
Found at i:2392785 original size:133 final size:134
Alignment explanation
Indices: 2392492--2392962 Score: 653
Period size: 133 Copynumber: 3.5 Consensus size: 134
2392482 TAAACCAATC
* * *
2392492 AACATTTCCAATGGAGAGTTCATATTGAGAATAACTCAT-CTACAGAGGGAGAAGAAGTTCATAA
1 AACATTTCAAATGGAGAGTTCATAATGAGAAGAACTCATCCTACAGAGGGAGAAGAAGTTCATAA
* * * * * *
2392556 CGAGAAGAGTTTGTTCGACCTATTACTCAATTACAACATTTCGAATTAGTGACACTTCACTTGAG
66 TGAGAAGAGCTTGTTCGACCTATCACTCGATT-CAACATTTCGAATCAGTGACACCTCACTTGAG
2392621 GGATT
130 GGATT
*
2392626 GACATTTCAAATGGAGAGTTCATAATGAGAAGAACTCATCCTACAGAGGGAGAAGAAGTTCATAA
1 AACATTTCAAATGGAGAGTTCATAATGAGAAGAACTCATCCTACAGAGGGAGAAGAAGTTCATAA
* ** * *
2392691 TGAGAAGAGCTTGTTCGACCTATCACTCGATTC-ACGTTTCGAATCAGTGATGCCTCGCTTAAGG
66 TGAGAAGAGCTTGTTCGACCTATCACTCGATTCAACATTTCGAATCAGTGACACCTCACTTGAGG
2392755 GATT
131 GATT
* *
2392759 AACATTTCAAATGGAGAGTTCATAATGAGAAGAACTCGTCCGACAGAGGGAGAAGAAGTTCATAA
1 AACATTTCAAATGGAGAGTTCATAATGAGAAGAACTCATCCTACAGAGGGAGAAGAAGTTCATAA
* ** * *
2392824 TGAGAAGAGCTTGTTCGACCTATCGCTCGATTCATGACATTTAAAATCAGTAACACCTCACTCGA
66 TGAGAAGAGCTTGTTCGACCTATCACTCGATTCA--ACATTTCGAATCAGTGACACCTCACTTGA
*
2392889 GGGATC
129 GGGATT
* *
2392895 AACATTTCCAGTGGAGAGTTCATAATGAGAAGAACTCATCC-A-ATGAGGGAGAAGAAGTTCATA
1 AACATTTCAAATGGAGAGTTCATAATGAGAAGAACTCATCCTACA-GAGGGAGAAGAAGTTCATA
2392958 ATGAG
65 ATGAG
2392963 GAGAACTTTT
Statistics
Matches: 300, Mismatches: 32, Indels: 9
0.88 0.09 0.03
Matches are distributed among these distances:
133 122 0.41
134 37 0.12
135 78 0.26
136 63 0.21
ACGTcount: A:0.35, C:0.17, G:0.22, T:0.26
Consensus pattern (134 bp):
AACATTTCAAATGGAGAGTTCATAATGAGAAGAACTCATCCTACAGAGGGAGAAGAAGTTCATAA
TGAGAAGAGCTTGTTCGACCTATCACTCGATTCAACATTTCGAATCAGTGACACCTCACTTGAGG
GATT
Done.