Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr01 ID=Chr01-JGI_221_v2.0
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 55868233
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 983842 characters in sequence are not A, C, G, or T
File 19 of 187
Found at i:6455034 original size:28 final size:28
Alignment explanation
Indices: 6454977--6455035 Score: 82
Period size: 28 Copynumber: 2.1 Consensus size: 28
6454967 TTTCAACTAA
* * *
6454977 TTAAATATTATCATTATTTTTCAATTAT
1 TTAAATATTATCATAATTATTCAATGAT
*
6455005 TTAAATATTATCATAATTATTGAATGAT
1 TTAAATATTATCATAATTATTCAATGAT
6455033 TTA
1 TTA
6455036 CTTAATTACC
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
28 27 1.00
ACGTcount: A:0.39, C:0.05, G:0.03, T:0.53
Consensus pattern (28 bp):
TTAAATATTATCATAATTATTCAATGAT
Found at i:6456168 original size:18 final size:18
Alignment explanation
Indices: 6456137--6456171 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
6456127 TTGTTGGCCA
6456137 TATGAACAAATGCAATGG
1 TATGAACAAATGCAATGG
* *
6456155 TATGACCAATTGCAATG
1 TATGAACAAATGCAATG
6456172 TGTAAGGTTT
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.40, C:0.14, G:0.20, T:0.26
Consensus pattern (18 bp):
TATGAACAAATGCAATGG
Found at i:6457911 original size:17 final size:18
Alignment explanation
Indices: 6457891--6457924 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
6457881 ATAAGTATGT
6457891 TTTAAT-TCTTTTAAAAG
1 TTTAATCTCTTTTAAAAG
*
6457908 TTTAATCTTTTTTAAAA
1 TTTAATCTCTTTTAAAA
6457925 TATCATTATT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 6 0.40
18 9 0.60
ACGTcount: A:0.35, C:0.06, G:0.03, T:0.56
Consensus pattern (18 bp):
TTTAATCTCTTTTAAAAG
Found at i:6458159 original size:2 final size:2
Alignment explanation
Indices: 6458154--6458181 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
6458144 ACACACACAG
6458154 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
6458182 CAGACTAGCA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:6493216 original size:23 final size:23
Alignment explanation
Indices: 6493183--6493256 Score: 87
Period size: 23 Copynumber: 3.2 Consensus size: 23
6493173 TTTACCCTAT
6493183 TTGGACAGCATATATGCAACAAA
1 TTGGACAGCATATATGCAACAAA
* * *
6493206 TT-GAGCAGCATTTAAGCATCAAAA
1 TTGGA-CAGCATATATGCAAC-AAA
*
6493230 TTGGACAGCATATATGTAACAAA
1 TTGGACAGCATATATGCAACAAA
6493253 TTGG
1 TTGG
6493257 TTCAACTCAT
Statistics
Matches: 41, Mismatches: 7, Indels: 6
0.76 0.13 0.11
Matches are distributed among these distances:
22 2 0.05
23 21 0.51
24 16 0.39
25 2 0.05
ACGTcount: A:0.41, C:0.15, G:0.19, T:0.26
Consensus pattern (23 bp):
TTGGACAGCATATATGCAACAAA
Found at i:6494146 original size:43 final size:43
Alignment explanation
Indices: 6494033--6494161 Score: 131
Period size: 43 Copynumber: 3.0 Consensus size: 43
6494023 AACTCGTACA
* * * *
6494033 ATGCCAACGTCCCAAATGTGGTCTTACATGTAATCACATATCG
1 ATGCCAACGTCCCAGACGTGGTCTTACACGTAAACACATATCG
*
6494076 ATGGC-ACTGTCCCAGACAG-GGTCTTACACGTAAACACA-AGTCG
1 ATGCCAAC-GTCCCAGAC-GTGGTCTTACACGTAAACACATA-TCG
* *
6494119 ATGCCAACGTCCTAGACGTGGTTTTACACG-ATAACACATATCG
1 ATGCCAACGTCCCAGACGTGGTCTTACACGTA-AACACATATCG
6494162 GAAATCCTAT
Statistics
Matches: 71, Mismatches: 8, Indels: 14
0.76 0.09 0.15
Matches are distributed among these distances:
42 5 0.07
43 62 0.87
44 4 0.06
ACGTcount: A:0.30, C:0.26, G:0.19, T:0.24
Consensus pattern (43 bp):
ATGCCAACGTCCCAGACGTGGTCTTACACGTAAACACATATCG
Found at i:6495574 original size:10 final size:10
Alignment explanation
Indices: 6495517--6495575 Score: 50
Period size: 10 Copynumber: 5.9 Consensus size: 10
6495507 TGATAAAAAA
*
6495517 TAAAAGTTA-
1 TAAAAATTAT
*
6495526 TAAAAATGAT
1 TAAAAATTAT
**
6495536 TAAATTTTAAT
1 TAAAAATT-AT
6495547 TAAAAA-TAT
1 TAAAAATTAT
6495556 TAAAAAATTAT
1 T-AAAAATTAT
6495567 TAAAAATTA
1 TAAAAATTA
6495576 GAATTTTTTT
Statistics
Matches: 39, Mismatches: 7, Indels: 7
0.74 0.13 0.13
Matches are distributed among these distances:
9 10 0.26
10 19 0.49
11 10 0.26
ACGTcount: A:0.59, C:0.00, G:0.03, T:0.37
Consensus pattern (10 bp):
TAAAAATTAT
Found at i:6495655 original size:20 final size:21
Alignment explanation
Indices: 6495631--6495682 Score: 58
Period size: 20 Copynumber: 2.6 Consensus size: 21
6495621 AAGTCGTAAG
6495631 AAAATTATAAAAAAT-G-TAA
1 AAAATTATAAAAAATAGTTAA
*
6495650 AGAAA-TAT-AAAATTAGTTAA
1 A-AAATTATAAAAAATAGTTAA
6495670 AAAATTATAAAAA
1 AAAATTATAAAAA
6495683 TATCGTACTA
Statistics
Matches: 27, Mismatches: 1, Indels: 8
0.75 0.03 0.22
Matches are distributed among these distances:
18 5 0.19
19 8 0.30
20 10 0.37
21 4 0.15
ACGTcount: A:0.67, C:0.00, G:0.06, T:0.27
Consensus pattern (21 bp):
AAAATTATAAAAAATAGTTAA
Found at i:6504507 original size:2 final size:2
Alignment explanation
Indices: 6504500--6504536 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
6504490 AAGAGAAGGC
6504500 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
6504537 AATGAAGCTA
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:6505456 original size:3 final size:3
Alignment explanation
Indices: 6505448--6505484 Score: 74
Period size: 3 Copynumber: 12.3 Consensus size: 3
6505438 GTAATTACAT
6505448 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A
6505485 AGCAAAGCCC
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 34 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
ATA
Found at i:6509871 original size:42 final size:42
Alignment explanation
Indices: 6509799--6509944 Score: 145
Period size: 42 Copynumber: 3.5 Consensus size: 42
6509789 CCGAAAGCTG
* * * *
6509799 AACAGAAGCTCATGAA-AGCTAAACAAAAACCCATAAAGGTTG
1 AACAGAAGCTCGT-AAGAGCTGAACAGAAACCCATAAAGGTTA
* *
6509841 AACGGAAGCTCGTAAGAGCTGAACAGAAACCCATAAGGGTTA
1 AACAGAAGCTCGTAAGAGCTGAACAGAAACCCATAAAGGTTA
* * * *
6509883 AACAGAAGCTC-AATAGAGTTGAACAGAAACTCAT-ATGAGTTA
1 AACAGAAGCTCGTA-AGAGCTGAACAGAAACCCATAAAG-GTTA
*
6509925 AACAGAAGCTCGTGAGAGCT
1 AACAGAAGCTCGTAAGAGCT
6509945 AAATGGAAAG
Statistics
Matches: 86, Mismatches: 14, Indels: 8
0.80 0.13 0.07
Matches are distributed among these distances:
41 5 0.06
42 81 0.94
ACGTcount: A:0.44, C:0.18, G:0.22, T:0.16
Consensus pattern (42 bp):
AACAGAAGCTCGTAAGAGCTGAACAGAAACCCATAAAGGTTA
Found at i:6509922 original size:21 final size:21
Alignment explanation
Indices: 6509797--6509931 Score: 87
Period size: 21 Copynumber: 6.4 Consensus size: 21
6509787 GCCCGAAAGC
* *
6509797 TGAACAGAAGCTCATGAA-AGC
1 TGAACAGAAACTCAT-AAGAGT
* * *
6509818 TAAACAAAAACCCATAA-AGGT
1 TGAACAGAAACTCATAAGA-GT
* * * *
6509839 TGAACGGAAGCTCGTAAGAGC
1 TGAACAGAAACTCATAAGAGT
* *
6509860 TGAACAGAAACCCATAAGGGT
1 TGAACAGAAACTCATAAGAGT
* *
6509881 TAAACAGAAGCTCA-ATAGAGT
1 TGAACAGAAACTCATA-AGAGT
*
6509902 TGAACAGAAACTCATATGAGT
1 TGAACAGAAACTCATAAGAGT
*
6509923 TAAACAGAA
1 TGAACAGAA
6509932 GCTCGTGAGA
Statistics
Matches: 84, Mismatches: 26, Indels: 8
0.71 0.22 0.07
Matches are distributed among these distances:
20 4 0.05
21 78 0.93
22 2 0.02
ACGTcount: A:0.46, C:0.17, G:0.21, T:0.16
Consensus pattern (21 bp):
TGAACAGAAACTCATAAGAGT
Found at i:6513805 original size:59 final size:59
Alignment explanation
Indices: 6513738--6513856 Score: 238
Period size: 59 Copynumber: 2.0 Consensus size: 59
6513728 TCGTCCATCC
6513738 AAACCCACCCTTCATTTACTTTAAAAAATGTAAATTAATTTCTGTACATTAGATCAAAG
1 AAACCCACCCTTCATTTACTTTAAAAAATGTAAATTAATTTCTGTACATTAGATCAAAG
6513797 AAACCCACCCTTCATTTACTTTAAAAAATGTAAATTAATTTCTGTACATTAGATCAAAG
1 AAACCCACCCTTCATTTACTTTAAAAAATGTAAATTAATTTCTGTACATTAGATCAAAG
6513856 A
1 A
6513857 GTAAAGTGGT
Statistics
Matches: 60, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
59 60 1.00
ACGTcount: A:0.41, C:0.18, G:0.07, T:0.34
Consensus pattern (59 bp):
AAACCCACCCTTCATTTACTTTAAAAAATGTAAATTAATTTCTGTACATTAGATCAAAG
Found at i:6518208 original size:21 final size:21
Alignment explanation
Indices: 6518182--6518221 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
6518172 TCGTGATCCA
6518182 TTAAAACACGAGAATTTTGTT
1 TTAAAACACGAGAATTTTGTT
* *
6518203 TTAAAACTCTAGAATTTTG
1 TTAAAACACGAGAATTTTG
6518222 AAGCACAAAT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.38, C:0.10, G:0.12, T:0.40
Consensus pattern (21 bp):
TTAAAACACGAGAATTTTGTT
Found at i:6518268 original size:17 final size:17
Alignment explanation
Indices: 6518243--6518362 Score: 100
Period size: 17 Copynumber: 6.9 Consensus size: 17
6518233 TAAAAAAAAA
*
6518243 ACGAAAATTTTTTAAAC
1 ACGAGAATTTTTTAAAC
6518260 ACGAGAATTTTTTTTAAAAC
1 ACGAGAA--TTTTTT-AAAC
*
6518280 ACGAGAATTTTTAAAAC
1 ACGAGAATTTTTTAAAC
** *
6518297 ACG-GAAATTTTAGAAAA
1 ACGAG-AATTTTTTAAAC
*
6518314 AC-AGAAATTTTTAAAAC
1 ACGAG-AATTTTTTAAAC
* *
6518331 ACGACAATTTTTGAAAC
1 ACGAGAATTTTTTAAAC
*
6518348 ACGAGATTTTTTTAA
1 ACGAGAATTTTTTAA
6518363 GACAAAAAAA
Statistics
Matches: 84, Mismatches: 13, Indels: 12
0.77 0.12 0.11
Matches are distributed among these distances:
16 1 0.01
17 60 0.71
18 6 0.07
19 6 0.07
20 11 0.13
ACGTcount: A:0.45, C:0.11, G:0.11, T:0.33
Consensus pattern (17 bp):
ACGAGAATTTTTTAAAC
Found at i:6518279 original size:20 final size:19
Alignment explanation
Indices: 6518250--6518291 Score: 75
Period size: 20 Copynumber: 2.2 Consensus size: 19
6518240 AAAACGAAAA
6518250 TTTTTTAAACACGAGAATT
1 TTTTTTAAACACGAGAATT
6518269 TTTTTTAAAACACGAGAATT
1 TTTTTT-AAACACGAGAATT
6518289 TTT
1 TTT
6518292 AAAACACGGA
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
19 6 0.27
20 16 0.73
ACGTcount: A:0.36, C:0.10, G:0.10, T:0.45
Consensus pattern (19 bp):
TTTTTTAAACACGAGAATT
Found at i:6518314 original size:71 final size:69
Alignment explanation
Indices: 6518182--6518342 Score: 182
Period size: 71 Copynumber: 2.3 Consensus size: 69
6518172 TCGTGATCCA
* * * *
6518182 TTAAAACACGAGAATTTTGTTTTAAAACTCTAGAATTTTGAAGCACAAATTTAAAAAAAAA-ACG
1 TTAAAACACGAGAATTTT-TTTTAAAACACGAGAATTTTAAAACACAAATTTAAAAAAAAACA-G
6518246 AAAATTT
64 -AAATTT
* * *
6518253 TTTAAACACGAGAATTTTTTTTAAAACACGAGAATTTTTAAAACACGGAAATTT-TAGAAAAACA
1 TTAAAACACGAGAATTTTTTTTAAAACACGAGAA-TTTTAAAACAC--AAATTTAAAAAAAAACA
6518317 GAAATTT
63 GAAATTT
*
6518324 TTAAAACACGACAATTTTT
1 TTAAAACACGAGAATTTTT
6518343 GAAACACGAG
Statistics
Matches: 77, Mismatches: 9, Indels: 8
0.82 0.10 0.09
Matches are distributed among these distances:
70 14 0.18
71 49 0.64
72 7 0.09
73 7 0.09
ACGTcount: A:0.47, C:0.11, G:0.10, T:0.32
Consensus pattern (69 bp):
TTAAAACACGAGAATTTTTTTTAAAACACGAGAATTTTAAAACACAAATTTAAAAAAAAACAGAA
ATTT
Found at i:6518359 original size:34 final size:34
Alignment explanation
Indices: 6518243--6518359 Score: 112
Period size: 34 Copynumber: 3.4 Consensus size: 34
6518233 TAAAAAAAAA
* * * *
6518243 ACGAAAATTTTTTAAACACGAGAATTTTTTTTAAAAC
1 ACGAGAATTTTTAAAACACG-GAA--ATTTTTGAAAC
* *
6518280 ACGAGAATTTTTAAAACACGGAAATTTTAGAAAA
1 ACGAGAATTTTTAAAACACGGAAATTTTTGAAAC
6518314 AC-AGAAATTTTTAAAACAC-GACAATTTTTGAAAC
1 ACGAG-AATTTTTAAAACACGGA-AATTTTTGAAAC
*
6518348 ACGAGATTTTTT
1 ACGAGAATTTTT
6518360 TAAGACAAAA
Statistics
Matches: 68, Mismatches: 9, Indels: 9
0.79 0.10 0.10
Matches are distributed among these distances:
33 4 0.06
34 41 0.60
35 2 0.03
36 3 0.04
37 18 0.26
ACGTcount: A:0.44, C:0.11, G:0.11, T:0.33
Consensus pattern (34 bp):
ACGAGAATTTTTAAAACACGGAAATTTTTGAAAC
Found at i:6518423 original size:18 final size:18
Alignment explanation
Indices: 6518397--6518464 Score: 73
Period size: 18 Copynumber: 3.7 Consensus size: 18
6518387 GAAATGCGGG
*
6518397 AATTGTTGAAAACAAGAA
1 AATTTTTGAAAACAAGAA
* *
6518415 AATTTTTGAAAACACGAC
1 AATTTTTGAAAACAAGAA
* *
6518433 AAGTTTTGAAAAACATGAA
1 AATTTTTG-AAAACAAGAA
6518452 AATTTTTGGAAAA
1 AATTTTT-GAAAA
6518465 GCGAAAAGTC
Statistics
Matches: 41, Mismatches: 7, Indels: 3
0.80 0.14 0.06
Matches are distributed among these distances:
18 22 0.54
19 18 0.44
20 1 0.02
ACGTcount: A:0.50, C:0.07, G:0.15, T:0.28
Consensus pattern (18 bp):
AATTTTTGAAAACAAGAA
Found at i:6518584 original size:30 final size:31
Alignment explanation
Indices: 6518550--6518609 Score: 86
Period size: 31 Copynumber: 2.0 Consensus size: 31
6518540 AAAAAACACG
*
6518550 ATTA-TATTTTTTTGAAACACGGGAAATTTC
1 ATTATTATTTTTTTGAAACACGAGAAATTTC
* *
6518580 ATTATTATTTTTTTGAGACATGAGAAATTT
1 ATTATTATTTTTTTGAAACACGAGAAATTT
6518610 TGGAAACATG
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
30 4 0.15
31 22 0.85
ACGTcount: A:0.33, C:0.07, G:0.13, T:0.47
Consensus pattern (31 bp):
ATTATTATTTTTTTGAAACACGAGAAATTTC
Found at i:6518618 original size:18 final size:18
Alignment explanation
Indices: 6518597--6518635 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 18
6518587 TTTTTTTGAG
*
6518597 ACATGAGAAA-TTTTGGAA
1 ACATGA-AAACTTTTGAAA
6518615 ACATGAAAACTTTTGAAA
1 ACATGAAAACTTTTGAAA
6518633 ACA
1 ACA
6518636 CGATTTTTTT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
17 3 0.16
18 16 0.84
ACGTcount: A:0.49, C:0.10, G:0.15, T:0.26
Consensus pattern (18 bp):
ACATGAAAACTTTTGAAA
Found at i:6519303 original size:19 final size:19
Alignment explanation
Indices: 6519278--6519330 Score: 90
Period size: 19 Copynumber: 2.8 Consensus size: 19
6519268 GGGCTGCTGC
6519278 AACGGGTCGGGTCAATTC-
1 AACGGGTCGGGTCAATTCG
6519296 ACACGGGTCGGGTCAATTCG
1 A-ACGGGTCGGGTCAATTCG
6519316 AACGGGTCGGGTCAA
1 AACGGGTCGGGTCAA
6519331 ATAGACCCGA
Statistics
Matches: 33, Mismatches: 0, Indels: 3
0.92 0.00 0.08
Matches are distributed among these distances:
18 1 0.03
19 31 0.94
20 1 0.03
ACGTcount: A:0.23, C:0.23, G:0.36, T:0.19
Consensus pattern (19 bp):
AACGGGTCGGGTCAATTCG
Found at i:6519403 original size:20 final size:18
Alignment explanation
Indices: 6519366--6519444 Score: 79
Period size: 20 Copynumber: 4.1 Consensus size: 18
6519356 TTTTTATATT
*
6519366 TTTCTTTTTTC-CTTTTC
1 TTTCTTTTTTCTTTTTTC
6519383 TTTCATTTTTCTCTTTTTTC
1 TTTC-TTTTT-TCTTTTTTC
6519403 TTTCTTTTTTTTCTCTTTTTC
1 TTTC--TTTTTTCT-TTTTTC
*
6519424 TTTCTTTCTTTCTTCTTTC
1 TTTCTTT-TTTCTTTTTTC
6519443 TT
1 TT
6519445 CCCTTCGACT
Statistics
Matches: 53, Mismatches: 3, Indels: 10
0.80 0.05 0.15
Matches are distributed among these distances:
17 4 0.08
18 5 0.09
19 12 0.23
20 17 0.32
21 15 0.28
ACGTcount: A:0.01, C:0.22, G:0.00, T:0.77
Consensus pattern (18 bp):
TTTCTTTTTTCTTTTTTC
Found at i:6519408 original size:4 final size:4
Alignment explanation
Indices: 6519366--6519444 Score: 60
Period size: 4 Copynumber: 19.5 Consensus size: 4
6519356 TTTTTATATT
*
6519366 TTTC TTT- TTTCC TTTTC TTTC ATTT- TTCTC TTT- TTTC TTTC TTTTT
1 TTTC TTTC TTT-C -TTTC TTTC -TTTC TT-TC TTTC TTTC TTTC -TTTC
6519412 TTTC TCTT- TTTC TTTC TTTC TTTC -TTC TTTC TT
1 TTTC T-TTC TTTC TTTC TTTC TTTC TTTC TTTC TT
6519445 CCCTTCGACT
Statistics
Matches: 62, Mismatches: 2, Indels: 22
0.72 0.02 0.26
Matches are distributed among these distances:
3 13 0.21
4 35 0.56
5 11 0.18
6 3 0.05
ACGTcount: A:0.01, C:0.22, G:0.00, T:0.77
Consensus pattern (4 bp):
TTTC
Found at i:6519439 original size:11 final size:11
Alignment explanation
Indices: 6519366--6519444 Score: 51
Period size: 11 Copynumber: 7.2 Consensus size: 11
6519356 TTTTTATATT
*
6519366 TTTCTTTTTTC
1 TTTCTTCTTTC
*
6519377 CTT-TTCTTTC
1 TTTCTTCTTTC
*
6519387 ATTT-TTCTCTTT
1 -TTTCTTCT-TTC
6519399 TTTCTTTCTTT-
1 TTTC-TTCTTTC
6519410 TTT-TTCTCTT-
1 TTTCTTCT-TTC
6519420 TTTCTTTCTTTC
1 TTTC-TTCTTTC
6519432 TTTCTTCTTTC
1 TTTCTTCTTTC
6519443 TT
1 TT
6519445 CCCTTCGACT
Statistics
Matches: 56, Mismatches: 4, Indels: 16
0.74 0.05 0.21
Matches are distributed among these distances:
9 4 0.07
10 11 0.20
11 25 0.45
12 12 0.21
13 4 0.07
ACGTcount: A:0.01, C:0.22, G:0.00, T:0.77
Consensus pattern (11 bp):
TTTCTTCTTTC
Found at i:6519539 original size:12 final size:13
Alignment explanation
Indices: 6519518--6519546 Score: 51
Period size: 12 Copynumber: 2.3 Consensus size: 13
6519508 TCTCCTCTTC
6519518 TCTTCTTCTTTCT
1 TCTTCTTCTTTCT
6519531 TCTTC-TCTTTCT
1 TCTTCTTCTTTCT
6519543 TCTT
1 TCTT
6519547 GGCTGCTTCT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 11 0.69
13 5 0.31
ACGTcount: A:0.00, C:0.31, G:0.00, T:0.69
Consensus pattern (13 bp):
TCTTCTTCTTTCT
Found at i:6520032 original size:29 final size:29
Alignment explanation
Indices: 6519990--6520076 Score: 93
Period size: 29 Copynumber: 3.0 Consensus size: 29
6519980 TCTAAAAAGT
* * *
6519990 TTAGGGGCCCAAATATAATTTACAAAATA
1 TTAGGGGCCAAAATATAATTTTCAAAAAA
** * *
6520019 TTAGGGGTTAAAATGTAATTTTTGAAAAAA
1 TTAGGGGCCAAAATATAA-TTTTCAAAAAA
*
6520049 TTGGGGGCCAAAATATAATTTTCAAAAA
1 TTAGGGGCCAAAATATAATTTTCAAAAA
6520077 GTACAGAGGT
Statistics
Matches: 45, Mismatches: 12, Indels: 2
0.76 0.20 0.03
Matches are distributed among these distances:
29 23 0.51
30 22 0.49
ACGTcount: A:0.44, C:0.08, G:0.17, T:0.31
Consensus pattern (29 bp):
TTAGGGGCCAAAATATAATTTTCAAAAAA
Found at i:6520036 original size:59 final size:60
Alignment explanation
Indices: 6519973--6520099 Score: 152
Period size: 59 Copynumber: 2.1 Consensus size: 60
6519963 AGGGCTGAAG
* * * *
6519973 TGTAATTTCT-AAAAAGTTTAGGGGCCCAAATATAATTTAC-AAAA-TATTAGGGGTTAAAA
1 TGTAATTTCTGAAAAA-ATTAGGGGCCAAAATATAATTTACAAAAAGTA-CAGAGGTTAAAA
* * *
6520032 TGTAATTTTTGAAAAAATTGGGGGCCAAAATATAATTTTCAAAAAGTACAGAGGTTAAAA
1 TGTAATTTCTGAAAAAATTAGGGGCCAAAATATAATTTACAAAAAGTACAGAGGTTAAAA
6520092 TGTAATTT
1 TGTAATTT
6520100 TTATTTTTTG
Statistics
Matches: 58, Mismatches: 7, Indels: 5
0.83 0.10 0.07
Matches are distributed among these distances:
59 29 0.50
60 27 0.47
61 2 0.03
ACGTcount: A:0.43, C:0.07, G:0.17, T:0.33
Consensus pattern (60 bp):
TGTAATTTCTGAAAAAATTAGGGGCCAAAATATAATTTACAAAAAGTACAGAGGTTAAAA
Found at i:6520068 original size:30 final size:30
Alignment explanation
Indices: 6519990--6520076 Score: 88
Period size: 30 Copynumber: 3.0 Consensus size: 30
6519980 TCTAAAAAGT
* *
6519990 TTAGGGGCCCAAATATAA-TTTACAAAATA
1 TTAGGGGCCAAAATATAATTTTACAAAAAA
** * **
6520019 TTAGGGGTTAAAATGTAATTTTTGAAAAAA
1 TTAGGGGCCAAAATATAATTTTACAAAAAA
*
6520049 TTGGGGGCCAAAATATAATTTT-CAAAAA
1 TTAGGGGCCAAAATATAATTTTACAAAAA
6520077 GTACAGAGGT
Statistics
Matches: 45, Mismatches: 12, Indels: 2
0.76 0.20 0.03
Matches are distributed among these distances:
29 19 0.42
30 26 0.58
ACGTcount: A:0.44, C:0.08, G:0.17, T:0.31
Consensus pattern (30 bp):
TTAGGGGCCAAAATATAATTTTACAAAAAA
Found at i:6521855 original size:26 final size:27
Alignment explanation
Indices: 6521826--6521883 Score: 75
Period size: 26 Copynumber: 2.2 Consensus size: 27
6521816 AAATCCCAAA
*
6521826 TTTTCTTT-CTTTCCTTCCCT-TTTTAG
1 TTTTCTTTCCTTT-CTCCCCTGTTTTAG
*
6521852 TTTTCTTTCCTTTCTCCCCTGTTTTCG
1 TTTTCTTTCCTTTCTCCCCTGTTTTAG
6521879 TTTTC
1 TTTTC
6521884 CTATTCTGTT
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
26 14 0.50
27 14 0.50
ACGTcount: A:0.02, C:0.29, G:0.05, T:0.64
Consensus pattern (27 bp):
TTTTCTTTCCTTTCTCCCCTGTTTTAG
Found at i:6523857 original size:36 final size:36
Alignment explanation
Indices: 6523810--6523881 Score: 144
Period size: 36 Copynumber: 2.0 Consensus size: 36
6523800 AGCTTAGCCT
6523810 TAGCCTTGGTGTACTCCAATCTTGAATTGATCATTG
1 TAGCCTTGGTGTACTCCAATCTTGAATTGATCATTG
6523846 TAGCCTTGGTGTACTCCAATCTTGAATTGATCATTG
1 TAGCCTTGGTGTACTCCAATCTTGAATTGATCATTG
6523882 AAATAGATTT
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
36 36 1.00
ACGTcount: A:0.22, C:0.19, G:0.19, T:0.39
Consensus pattern (36 bp):
TAGCCTTGGTGTACTCCAATCTTGAATTGATCATTG
Found at i:6533543 original size:22 final size:22
Alignment explanation
Indices: 6533518--6533560 Score: 68
Period size: 22 Copynumber: 2.0 Consensus size: 22
6533508 TATCCAAATA
*
6533518 ATAATAATAAAATAGTAGCAAT
1 ATAATAATAAAATAATAGCAAT
*
6533540 ATAATAGTAAAATAATAGCAA
1 ATAATAATAAAATAATAGCAA
6533561 AACAGCAACA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.60, C:0.05, G:0.09, T:0.26
Consensus pattern (22 bp):
ATAATAATAAAATAATAGCAAT
Found at i:6538781 original size:13 final size:13
Alignment explanation
Indices: 6538763--6538793 Score: 55
Period size: 13 Copynumber: 2.5 Consensus size: 13
6538753 TTTTTATTTC
6538763 ATAATTAAAAATA
1 ATAATTAAAAATA
6538776 ATAATTAAAAATA
1 ATAATTAAAAATA
6538789 A-AATT
1 ATAATT
6538794 GTTTGCACCC
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
12 4 0.22
13 14 0.78
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (13 bp):
ATAATTAAAAATA
Found at i:6541139 original size:3 final size:3
Alignment explanation
Indices: 6541115--6541162 Score: 69
Period size: 3 Copynumber: 16.0 Consensus size: 3
6541105 ATATATATAG
* * *
6541115 TAA TGA TAA TAG TAA CAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
6541163 CAAAAACTAA
Statistics
Matches: 39, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
3 39 1.00
ACGTcount: A:0.62, C:0.02, G:0.04, T:0.31
Consensus pattern (3 bp):
TAA
Found at i:6541774 original size:10 final size:11
Alignment explanation
Indices: 6541762--6541791 Score: 53
Period size: 10 Copynumber: 2.8 Consensus size: 11
6541752 ATTTTATACG
6541762 AAATAAAACGA
1 AAATAAAACGA
6541773 AAATAAAA-GA
1 AAATAAAACGA
6541783 AAATAAAAC
1 AAATAAAAC
6541792 ACATGTAAAT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
10 10 0.56
11 8 0.44
ACGTcount: A:0.77, C:0.07, G:0.07, T:0.10
Consensus pattern (11 bp):
AAATAAAACGA
Found at i:6551544 original size:15 final size:16
Alignment explanation
Indices: 6551524--6551590 Score: 66
Period size: 15 Copynumber: 4.1 Consensus size: 16
6551514 AACCCAATTT
6551524 TTATTTTA-TTTATTA
1 TTATTTTACTTTATTA
6551539 TTATTTTA-TTTATTA
1 TTATTTTACTTTATTA
*
6551554 TTTTTCTTTACTTTATTTA
1 -TTAT-TTTACTTTA-TTA
* *
6551573 TTACTTTATTTTATTA
1 TTATTTTACTTTATTA
6551589 TT
1 TT
6551591 TATTACTTAT
Statistics
Matches: 44, Mismatches: 4, Indels: 7
0.80 0.07 0.13
Matches are distributed among these distances:
15 15 0.34
16 8 0.18
17 12 0.27
18 6 0.14
19 3 0.07
ACGTcount: A:0.22, C:0.04, G:0.00, T:0.73
Consensus pattern (16 bp):
TTATTTTACTTTATTA
Found at i:6551551 original size:12 final size:12
Alignment explanation
Indices: 6551532--6551591 Score: 63
Period size: 12 Copynumber: 5.2 Consensus size: 12
6551522 TTTTATTTTA
6551532 TTTA-TTATTAT
1 TTTATTTATTAT
6551543 TTTATTTATTAT
1 TTTATTTATTAT
* *
6551555 TTT-TCT-TTAC
1 TTTATTTATTAT
*
6551565 TTTATTTATTAC
1 TTTATTTATTAT
6551577 TTTATTTTATTAT
1 TTTA-TTTATTAT
6551590 TT
1 TT
6551592 ATTACTTATT
Statistics
Matches: 41, Mismatches: 4, Indels: 6
0.80 0.08 0.12
Matches are distributed among these distances:
10 6 0.15
11 8 0.20
12 18 0.44
13 9 0.22
ACGTcount: A:0.22, C:0.05, G:0.00, T:0.73
Consensus pattern (12 bp):
TTTATTTATTAT
Found at i:6551568 original size:22 final size:21
Alignment explanation
Indices: 6551532--6551602 Score: 76
Period size: 22 Copynumber: 3.3 Consensus size: 21
6551522 TTTTATTTTA
6551532 TTTATTATTATTTTATTTATTA-
1 TTTATT-TTA-TTTATTTATTAC
*
6551554 TTTTTCTTTACTTTATTTATTAC
1 TTTAT-TTTA-TTTATTTATTAC
6551577 TTTATTTTA-TTATTTATTAC
1 TTTATTTTATTTATTTATTAC
6551597 -TTATTT
1 TTTATTT
6551603 GGATATTAAT
Statistics
Matches: 44, Mismatches: 3, Indels: 7
0.81 0.06 0.13
Matches are distributed among these distances:
19 6 0.14
20 11 0.25
22 22 0.50
23 5 0.11
ACGTcount: A:0.23, C:0.06, G:0.00, T:0.72
Consensus pattern (21 bp):
TTTATTTTATTTATTTATTAC
Found at i:6551582 original size:8 final size:7
Alignment explanation
Indices: 6551529--6551601 Score: 62
Period size: 7 Copynumber: 10.3 Consensus size: 7
6551519 AATTTTTATT
6551529 TTATTTA
1 TTATTTA
*
6551536 TTATTATT
1 TTATT-TA
6551544 TTATTTA
1 TTATTTA
6551551 TTATTT-
1 TTATTTA
*
6551557 TTCTTTA
1 TTATTTA
6551564 CTTTATTTA
1 --TTATTTA
6551573 TTACTTTA
1 TTA-TTTA
6551581 -T-TTTA
1 TTATTTA
6551586 TTATTTA
1 TTATTTA
*
6551593 TTACTTA
1 TTATTTA
6551600 TT
1 TT
6551602 TGGATATTAA
Statistics
Matches: 54, Mismatches: 5, Indels: 14
0.74 0.07 0.19
Matches are distributed among these distances:
5 4 0.07
6 6 0.11
7 28 0.52
8 10 0.19
9 6 0.11
ACGTcount: A:0.23, C:0.05, G:0.00, T:0.71
Consensus pattern (7 bp):
TTATTTA
Found at i:6552628 original size:3 final size:3
Alignment explanation
Indices: 6552620--6552646 Score: 54
Period size: 3 Copynumber: 9.0 Consensus size: 3
6552610 TAAAGTAAAA
6552620 AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT
6552647 TTGGGGACTA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 24 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:6554334 original size:34 final size:34
Alignment explanation
Indices: 6554282--6554346 Score: 85
Period size: 34 Copynumber: 1.9 Consensus size: 34
6554272 ATTGTATACG
* * * *
6554282 TGAACAGTACCGTCTACGTGAATAGTGTCGTGGA
1 TGAACAATACCGTATACGTAAATAGTATCGTGGA
*
6554316 TGAACAATATCGTATACGTAAATAGTATCGT
1 TGAACAATACCGTATACGTAAATAGTATCGT
6554347 AAACGGTCGT
Statistics
Matches: 26, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
34 26 1.00
ACGTcount: A:0.32, C:0.15, G:0.23, T:0.29
Consensus pattern (34 bp):
TGAACAATACCGTATACGTAAATAGTATCGTGGA
Found at i:6564217 original size:17 final size:16
Alignment explanation
Indices: 6564186--6564232 Score: 51
Period size: 16 Copynumber: 2.9 Consensus size: 16
6564176 AGATATCAAA
*
6564186 ATATAA-TTTTATCAT
1 ATATAATTTTTTTCAT
6564201 ATATTAATTTTTTTCAT
1 ATA-TAATTTTTTTCAT
* *
6564218 TTATCATTTTTTTCA
1 ATATAATTTTTTTCA
6564233 AAGGATTAAA
Statistics
Matches: 27, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
15 3 0.11
16 14 0.52
17 10 0.37
ACGTcount: A:0.30, C:0.09, G:0.00, T:0.62
Consensus pattern (16 bp):
ATATAATTTTTTTCAT
Found at i:6566429 original size:20 final size:21
Alignment explanation
Indices: 6566391--6566431 Score: 57
Period size: 22 Copynumber: 2.0 Consensus size: 21
6566381 ATGGCCTAAT
6566391 TATATAGAATTTTAATAAATAA
1 TATATAGAATTTT-ATAAATAA
*
6566413 TATATATAATTTT-TAAATA
1 TATATAGAATTTTATAAATA
6566432 CTAAATTAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 6 0.33
22 12 0.67
ACGTcount: A:0.51, C:0.00, G:0.02, T:0.46
Consensus pattern (21 bp):
TATATAGAATTTTATAAATAA
Found at i:6568352 original size:3 final size:3
Alignment explanation
Indices: 6568344--6568383 Score: 80
Period size: 3 Copynumber: 13.3 Consensus size: 3
6568334 TTCGAATTAT
6568344 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A
6568384 ATTTTTTAAT
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 37 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:6568732 original size:16 final size:16
Alignment explanation
Indices: 6568713--6568743 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
6568703 TATATGACCA
6568713 ATCATTTATCAAATAT
1 ATCATTTATCAAATAT
*
6568729 ATCATTTATCCAATA
1 ATCATTTATCAAATA
6568744 AAATTCTTTT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.42, C:0.16, G:0.00, T:0.42
Consensus pattern (16 bp):
ATCATTTATCAAATAT
Found at i:6575766 original size:34 final size:33
Alignment explanation
Indices: 6575720--6575843 Score: 126
Period size: 34 Copynumber: 3.7 Consensus size: 33
6575710 TAAATCAGAG
*
6575720 TTTAGAGTTTTTAAAAAAATTAATTAAACTAGGT
1 TTTAG-GTTTTTAAAAAAATTAATTAAATTAGGT
* *
6575754 TTTAGGTGTTTTAAATAAATAAATTAAATTAAGGT
1 TTTAGGT-TTTTAAAAAAATTAATTAAATT-AGGT
* * *
6575789 TTAAAGTTTTTAAGAAAATTAATTAAATTAGG-
1 TTTAGGTTTTTAAAAAAATTAATTAAATTAGGT
* * *
6575821 GTTAGTTTTTTTAAAAAA-TAATT
1 TTTAGGTTTTTAAAAAAATTAATT
6575844 TTGTGTTTAG
Statistics
Matches: 74, Mismatches: 14, Indels: 7
0.78 0.15 0.07
Matches are distributed among these distances:
31 5 0.07
32 12 0.16
33 5 0.07
34 43 0.58
35 9 0.12
ACGTcount: A:0.44, C:0.01, G:0.12, T:0.44
Consensus pattern (33 bp):
TTTAGGTTTTTAAAAAAATTAATTAAATTAGGT
Found at i:6576105 original size:124 final size:126
Alignment explanation
Indices: 6575901--6576419 Score: 724
Period size: 125 Copynumber: 4.2 Consensus size: 126
6575891 TTTTGTTTTT
* * * * * ** * *
6575901 TTTTTTTACAGTAGTTTCAGAATAATTAATTTTGAGAAGACGACTCTGAAAAGATAATGTTAAAA
1 TTTTTCTACAGTAGTTCCTGAAAAAATAATTTTGAGAAGACGGTTCTGAAAAAATAATGTCAAAA
* * * *
6575966 ACGCTTCAAGCAGGATGCACTATTATCAAAATTACTGAAAAAAACT-CCACGTGGACGCTA
66 ACGCTTCAAGCAGGATGCACTGTCAGCAAAATTACTGAAAAAAACTCCCACGTGGACGCTC
*
6576026 TTTTTCTACAGTAGTTCCTGAAAAAATAATTTTGAGAAGACGGTTCT-AAAAAATAATTTCAAAA
1 TTTTTCTACAGTAGTTCCTGAAAAAATAATTTTGAGAAGACGGTTCTGAAAAAATAATGTCAAAA
* * * * *
6576090 ATGCTTCAAGTAGGATGCACTGTCAGTAAATTTACTGAAAAAAGCTCCCACGTGGACGCTC
66 ACGCTTCAAGCAGGATGCACTGTCAGCAAAATTACTGAAAAAAACTCCCACGTGGACGCTC
* *
6576151 TTTTTCTACAGTAGTTCCTG-AAAAATAATTTTGAGAAGACTGTTCTGAAAAAATAGTGTCAAAA
1 TTTTTCTACAGTAGTTCCTGAAAAAATAATTTTGAGAAGACGGTTCTGAAAAAATAATGTCAAAA
* * * **
6576215 ACGCTTAAAGTAAGATGCACTGTCAGCAAAATTACT-AAAAAGGCTCCCACGTGGACGCTC
66 ACGCTTCAAGCAGGATGCACTGTCAGCAAAATTACTGAAAAAAACTCCCACGTGGACGCTC
* *
6576275 TTTTTCTACAGTAGTTCCTGAAAAAATAATTTTAAGAAGACGGTTCTGAAAAAATAGTGTCAAAA
1 TTTTTCTACAGTAGTTCCTGAAAAAATAATTTTGAGAAGACGGTTCTGAAAAAATAATGTCAAAA
* **
6576340 ACACTTCAAGCAGGATGCACTGTCAGCAAAATTACTG-AAAAAACTCCCACGTGGACTATC
66 ACGCTTCAAGCAGGATGCACTGTCAGCAAAATTACTGAAAAAAACTCCCACGTGGACGCTC
6576400 TTTTTCTACAGTAGTTCCTG
1 TTTTTCTACAGTAGTTCCTG
6576420 TTTGGCCTTA
Statistics
Matches: 352, Mismatches: 38, Indels: 8
0.88 0.10 0.02
Matches are distributed among these distances:
124 120 0.34
125 232 0.66
ACGTcount: A:0.37, C:0.17, G:0.17, T:0.29
Consensus pattern (126 bp):
TTTTTCTACAGTAGTTCCTGAAAAAATAATTTTGAGAAGACGGTTCTGAAAAAATAATGTCAAAA
ACGCTTCAAGCAGGATGCACTGTCAGCAAAATTACTGAAAAAAACTCCCACGTGGACGCTC
Found at i:6576389 original size:249 final size:250
Alignment explanation
Indices: 6575901--6576419 Score: 740
Period size: 249 Copynumber: 2.1 Consensus size: 250
6575891 TTTTGTTTTT
* * * * * *
6575901 TTTTTTTACAGTAGTTTCAGAATAATTAATTTTGAGAAGACGACTCTGAAAAGATAATGTTAAAA
1 TTTTTCTACAGTAGTTCCTGAATAAATAATTTTGAGAAGACGACTCTGAAAAAATAATGTCAAAA
* * * *
6575966 ACGCTTCAAGCAGGATGCACTATTATCAAAATTACTGAAAAAAACTCCACGTGGACGCTATTTTT
66 ACGCTTAAAGCAAGATGCACTATCAGCAAAATTACTGAAAAAAACTCCACGTGGACGCTATTTTT
* * **
6576031 CTACAGTAGTTCCTGAAAAAATAATTTTGAGAAGACGGTTCTAAAAAATAATTTCAAAAATGCTT
131 CTACAGTAGTTCCTGAAAAAATAATTTTAAGAAGACGGTTCTAAAAAATAATGTCAAAAACACTT
* * * *
6576096 CAAGTAGGATGCACTGTCAGTAAATTTACTGAAAAAAGCTCCCACGTGGACGCTC
196 CAAGCAGGATGCACTGTCAGCAAAATTACTGAAAAAAGCTCCCACGTGGACGATC
* *
6576151 TTTTTCTACAGTAGTTCCTGAA-AAATAATTTTGAGAAGACTG-TTCTGAAAAAATAGTGTCAAA
1 TTTTTCTACAGTAGTTCCTGAATAAATAATTTTGAGAAGAC-GACTCTGAAAAAATAATGTCAAA
* * ** *
6576214 AACGCTTAAAGTAAGATGCACTGTCAGCAAAATTACT-AAAAAGGCTCCCACGTGGACGCTCTTT
65 AACGCTTAAAGCAAGATGCACTATCAGCAAAATTACTGAAAAAAACT-CCACGTGGACGCTATTT
*
6576278 TTCTACAGTAGTTCCTGAAAAAATAATTTTAAGAAGACGGTTCTGAAAAAATAGTGTCAAAAACA
129 TTCTACAGTAGTTCCTGAAAAAATAATTTTAAGAAGACGGTTCT-AAAAAATAATGTCAAAAACA
*
6576343 CTTCAAGCAGGATGCACTGTCAGCAAAATTACTGAAAAAA-CTCCCACGTGGACTATC
193 CTTCAAGCAGGATGCACTGTCAGCAAAATTACTGAAAAAAGCTCCCACGTGGACGATC
6576400 TTTTTCTACAGTAGTTCCTG
1 TTTTTCTACAGTAGTTCCTG
6576420 TTTGGCCTTA
Statistics
Matches: 239, Mismatches: 27, Indels: 7
0.88 0.10 0.03
Matches are distributed among these distances:
248 7 0.03
249 159 0.67
250 73 0.31
ACGTcount: A:0.37, C:0.17, G:0.17, T:0.29
Consensus pattern (250 bp):
TTTTTCTACAGTAGTTCCTGAATAAATAATTTTGAGAAGACGACTCTGAAAAAATAATGTCAAAA
ACGCTTAAAGCAAGATGCACTATCAGCAAAATTACTGAAAAAAACTCCACGTGGACGCTATTTTT
CTACAGTAGTTCCTGAAAAAATAATTTTAAGAAGACGGTTCTAAAAAATAATGTCAAAAACACTT
CAAGCAGGATGCACTGTCAGCAAAATTACTGAAAAAAGCTCCCACGTGGACGATC
Found at i:6577747 original size:15 final size:15
Alignment explanation
Indices: 6577727--6577766 Score: 71
Period size: 15 Copynumber: 2.7 Consensus size: 15
6577717 TAATATTGTT
*
6577727 ATTACTTAATGTTGC
1 ATTACTTAACGTTGC
6577742 ATTACTTAACGTTGC
1 ATTACTTAACGTTGC
6577757 ATTACTTAAC
1 ATTACTTAAC
6577767 ATACTTTATT
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
15 24 1.00
ACGTcount: A:0.30, C:0.17, G:0.10, T:0.42
Consensus pattern (15 bp):
ATTACTTAACGTTGC
Found at i:6579999 original size:18 final size:18
Alignment explanation
Indices: 6579976--6580012 Score: 65
Period size: 18 Copynumber: 2.1 Consensus size: 18
6579966 GGAAAAGCAA
*
6579976 ACATATAAGGGTTAGGAT
1 ACATATAAGGGCTAGGAT
6579994 ACATATAAGGGCTAGGAT
1 ACATATAAGGGCTAGGAT
6580012 A
1 A
6580013 TGCACCTGGT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.41, C:0.08, G:0.27, T:0.24
Consensus pattern (18 bp):
ACATATAAGGGCTAGGAT
Found at i:6581567 original size:25 final size:24
Alignment explanation
Indices: 6581530--6581581 Score: 61
Period size: 25 Copynumber: 2.1 Consensus size: 24
6581520 ACTGTTATAA
* *
6581530 AAAATTATAAAAT-AAAAACTAATT
1 AAAATTACAAAATGAAAAAAT-ATT
6581554 AAAATTACATAAATGAAAAAATATT
1 AAAATTACA-AAATGAAAAAATATT
6581579 AAA
1 AAA
6581582 TAATATTCAA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
24 8 0.33
25 10 0.42
26 6 0.25
ACGTcount: A:0.67, C:0.04, G:0.02, T:0.27
Consensus pattern (24 bp):
AAAATTACAAAATGAAAAAATATT
Found at i:6592030 original size:59 final size:59
Alignment explanation
Indices: 6591958--6592077 Score: 240
Period size: 59 Copynumber: 2.0 Consensus size: 59
6591948 GTTGTTCAAG
6591958 TAAGGATTTTCTTTTTCCATGACTCTGCATGACTGTCCATATACATTCAACATATTGAC
1 TAAGGATTTTCTTTTTCCATGACTCTGCATGACTGTCCATATACATTCAACATATTGAC
6592017 TAAGGATTTTCTTTTTCCATGACTCTGCATGACTGTCCATATACATTCAACATATTGAC
1 TAAGGATTTTCTTTTTCCATGACTCTGCATGACTGTCCATATACATTCAACATATTGAC
6592076 TA
1 TA
6592078 TAGCTTTGCC
Statistics
Matches: 61, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
59 61 1.00
ACGTcount: A:0.28, C:0.22, G:0.12, T:0.39
Consensus pattern (59 bp):
TAAGGATTTTCTTTTTCCATGACTCTGCATGACTGTCCATATACATTCAACATATTGAC
Found at i:6593589 original size:21 final size:21
Alignment explanation
Indices: 6593565--6593627 Score: 64
Period size: 21 Copynumber: 3.2 Consensus size: 21
6593555 TGGAATATAC
6593565 CTTGTCTTGCAAATTGATTGT
1 CTTGTCTTGCAAATTGATTGT
* **
6593586 CTTGT-TTG-GAA-T-A-TAC
1 CTTGTCTTGCAAATTGATTGT
6593602 CTTGTCTTGCAAATTGATTGT
1 CTTGTCTTGCAAATTGATTGT
6593623 CTTGT
1 CTTGT
6593628 TAGACTATTG
Statistics
Matches: 31, Mismatches: 6, Indels: 10
0.66 0.13 0.21
Matches are distributed among these distances:
16 6 0.19
17 4 0.13
18 3 0.10
19 3 0.10
20 4 0.13
21 11 0.35
ACGTcount: A:0.19, C:0.14, G:0.19, T:0.48
Consensus pattern (21 bp):
CTTGTCTTGCAAATTGATTGT
Found at i:6593593 original size:37 final size:37
Alignment explanation
Indices: 6593545--6593628 Score: 159
Period size: 37 Copynumber: 2.3 Consensus size: 37
6593535 GCAAATTTCT
*
6593545 TTGTTTTGTTTGGAATATACCTTGTCTTGCAAATTGA
1 TTGTCTTGTTTGGAATATACCTTGTCTTGCAAATTGA
6593582 TTGTCTTGTTTGGAATATACCTTGTCTTGCAAATTGA
1 TTGTCTTGTTTGGAATATACCTTGTCTTGCAAATTGA
6593619 TTGTCTTGTT
1 TTGTCTTGTT
6593629 AGACTATTGA
Statistics
Matches: 46, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
37 46 1.00
ACGTcount: A:0.19, C:0.12, G:0.19, T:0.50
Consensus pattern (37 bp):
TTGTCTTGTTTGGAATATACCTTGTCTTGCAAATTGA
Found at i:6598834 original size:68 final size:68
Alignment explanation
Indices: 6598725--6598865 Score: 282
Period size: 68 Copynumber: 2.1 Consensus size: 68
6598715 AGCAATAGCA
6598725 GTTCTTTAGTAATGTTACATGGTTTGGACTTAGCTGTCTTAGTTGTGTCGATAACTATATGACGT
1 GTTCTTTAGTAATGTTACATGGTTTGGACTTAGCTGTCTTAGTTGTGTCGATAACTATATGACGT
6598790 CAT
66 CAT
6598793 GTTCTTTAGTAATGTTACATGGTTTGGACTTAGCTGTCTTAGTTGTGTCGATAACTATATGACGT
1 GTTCTTTAGTAATGTTACATGGTTTGGACTTAGCTGTCTTAGTTGTGTCGATAACTATATGACGT
6598858 CAT
66 CAT
6598861 GTTCT
1 GTTCT
6598866 GTAATTTATT
Statistics
Matches: 73, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
68 73 1.00
ACGTcount: A:0.21, C:0.13, G:0.22, T:0.43
Consensus pattern (68 bp):
GTTCTTTAGTAATGTTACATGGTTTGGACTTAGCTGTCTTAGTTGTGTCGATAACTATATGACGT
CAT
Found at i:6599328 original size:45 final size:45
Alignment explanation
Indices: 6599279--6599434 Score: 186
Period size: 45 Copynumber: 3.6 Consensus size: 45
6599269 CTTGCCCAGC
*
6599279 ACATGGAAAGAGGTGGAAAACAAAAACTATGATAACTTACTTAGA
1 ACATGGAAAGAAGTGGAAAACAAAAACTATGATAACTTACTTAGA
* *
6599324 ACATGGAAAGAAGTGGAAAACAAAGAC-----TAA-TGA---AGA
1 ACATGGAAAGAAGTGGAAAACAAAAACTATGATAACTTACTTAGA
* *
6599360 CACATGGAAAGAGGTGGAAAACAAAAACTATGATAACTTACTTATA
1 -ACATGGAAAGAAGTGGAAAACAAAAACTATGATAACTTACTTAGA
*
6599406 ACATGGAAAGAAGTGGAAAACAAAGACTA
1 ACATGGAAAGAAGTGGAAAACAAAAACTA
6599435 ATGAAGACAA
Statistics
Matches: 92, Mismatches: 9, Indels: 20
0.76 0.07 0.17
Matches are distributed among these distances:
36 3 0.03
37 25 0.27
39 2 0.02
40 3 0.03
42 3 0.03
43 2 0.02
45 52 0.57
46 2 0.02
ACGTcount: A:0.51, C:0.11, G:0.21, T:0.17
Consensus pattern (45 bp):
ACATGGAAAGAAGTGGAAAACAAAAACTATGATAACTTACTTAGA
Found at i:6599366 original size:37 final size:37
Alignment explanation
Indices: 6599324--6599447 Score: 126
Period size: 37 Copynumber: 3.2 Consensus size: 37
6599314 CTTACTTAGA
6599324 ACATGGAAAGAAGTGGAAAACAAAGACTAATGAAGAC
1 ACATGGAAAGAAGTGGAAAACAAAGACTAATGAAGAC
* * *
6599361 ACATGGAAAGAGGTGGAAAACAAAAACT-ATGATAACTTAC
1 ACATGGAAAGAAGTGGAAAACAAAGACTAATG--AA--GAC
6599401 TTATAACATGGAAAGAAGTGGAAAACAAAGACTAATGAAGAC
1 -----ACATGGAAAGAAGTGGAAAACAAAGACTAATGAAGAC
6599443 A-ATGG
1 ACATGG
6599448 GGAGTATATA
Statistics
Matches: 71, Mismatches: 6, Indels: 21
0.72 0.06 0.21
Matches are distributed among these distances:
36 7 0.10
37 27 0.38
38 2 0.03
40 2 0.03
42 2 0.03
44 2 0.03
45 26 0.37
46 3 0.04
ACGTcount: A:0.52, C:0.10, G:0.23, T:0.15
Consensus pattern (37 bp):
ACATGGAAAGAAGTGGAAAACAAAGACTAATGAAGAC
Found at i:6599372 original size:82 final size:82
Alignment explanation
Indices: 6599278--6599447 Score: 324
Period size: 82 Copynumber: 2.1 Consensus size: 82
6599268 ACTTGCCCAG
6599278 CACATGGAAAGAGGTGGAAAACAAAAACTATGATAACTTACTTAGAACATGGAAAGAAGTGGAAA
1 CACATGGAAAGAGGTGGAAAACAAAAACTATGATAACTTACTTAGAACATGGAAAGAAGTGGAAA
6599343 ACAAAGACTAATGAAGA
66 ACAAAGACTAATGAAGA
*
6599360 CACATGGAAAGAGGTGGAAAACAAAAACTATGATAACTTACTTATAACATGGAAAGAAGTGGAAA
1 CACATGGAAAGAGGTGGAAAACAAAAACTATGATAACTTACTTAGAACATGGAAAGAAGTGGAAA
6599425 ACAAAGACTAATGAAGA
66 ACAAAGACTAATGAAGA
6599442 CA-ATGG
1 CACATGG
6599448 GGAGTATATA
Statistics
Matches: 87, Mismatches: 1, Indels: 1
0.98 0.01 0.01
Matches are distributed among these distances:
81 4 0.05
82 83 0.95
ACGTcount: A:0.51, C:0.11, G:0.22, T:0.16
Consensus pattern (82 bp):
CACATGGAAAGAGGTGGAAAACAAAAACTATGATAACTTACTTAGAACATGGAAAGAAGTGGAAA
ACAAAGACTAATGAAGA
Found at i:6600974 original size:18 final size:18
Alignment explanation
Indices: 6600951--6600985 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
6600941 ATATAGAAGA
6600951 GGTTATCGTGGCAGAGGT
1 GGTTATCGTGGCAGAGGT
*
6600969 GGTTATCGTGGTAGAGG
1 GGTTATCGTGGCAGAGG
6600986 AGGTCGAGGC
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.17, C:0.09, G:0.46, T:0.29
Consensus pattern (18 bp):
GGTTATCGTGGCAGAGGT
Found at i:6606009 original size:56 final size:56
Alignment explanation
Indices: 6605934--6606046 Score: 226
Period size: 56 Copynumber: 2.0 Consensus size: 56
6605924 AACCATTAAG
6605934 TGTTTTCTGTAGGATGTTATAAACTAAGGCACCAAATACAGAGATAAACCTAAAAA
1 TGTTTTCTGTAGGATGTTATAAACTAAGGCACCAAATACAGAGATAAACCTAAAAA
6605990 TGTTTTCTGTAGGATGTTATAAACTAAGGCACCAAATACAGAGATAAACCTAAAAA
1 TGTTTTCTGTAGGATGTTATAAACTAAGGCACCAAATACAGAGATAAACCTAAAAA
6606046 T
1 T
6606047 ATTTAAAAAG
Statistics
Matches: 57, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
56 57 1.00
ACGTcount: A:0.42, C:0.14, G:0.16, T:0.27
Consensus pattern (56 bp):
TGTTTTCTGTAGGATGTTATAAACTAAGGCACCAAATACAGAGATAAACCTAAAAA
Found at i:6607856 original size:71 final size:71
Alignment explanation
Indices: 6607681--6607894 Score: 288
Period size: 71 Copynumber: 3.0 Consensus size: 71
6607671 ACTTAAATCG
* * *
6607681 ACAATTCCAATCAGAATCAATAATTACAAGCACGAAATTGAATAACTCTACAACTAATTAACT--
1 ACAATTCCAATCAGAATCAATAATTACAAGCACTAAATTAAATAATTCTACAACTAATTAACTAC
6607744 TAACTA
66 TAACTA
* * * *
6607750 GCAATTGCAATCAGAATCAATAATTACAAGCACTAAACTAAATAATTCTACAACTAGTTAACTAC
1 ACAATTCCAATCAGAATCAATAATTACAAGCACTAAATTAAATAATTCTACAACTAATTAACTAC
6607815 TAACTA
66 TAACTA
* * * * * *
6607821 ACAATTCCAATAAGAATCCATAATTACAAGTACTAAATTATATAATTCTACCATTAATTAACTAC
1 ACAATTCCAATCAGAATCAATAATTACAAGCACTAAATTAAATAATTCTACAACTAATTAACTA-
6607886 CTAACTA
65 CTAACTA
6607893 AC
1 AC
6607895 CCGAACCCGA
Statistics
Matches: 125, Mismatches: 17, Indels: 3
0.86 0.12 0.02
Matches are distributed among these distances:
69 56 0.45
71 60 0.48
72 9 0.07
ACGTcount: A:0.47, C:0.20, G:0.05, T:0.28
Consensus pattern (71 bp):
ACAATTCCAATCAGAATCAATAATTACAAGCACTAAATTAAATAATTCTACAACTAATTAACTAC
TAACTA
Found at i:6610725 original size:20 final size:20
Alignment explanation
Indices: 6610702--6610740 Score: 62
Period size: 20 Copynumber: 1.9 Consensus size: 20
6610692 TTTCAAAACG
6610702 AAAAGAAAAA-AAGAAAAAAT
1 AAAAGAAAAATAA-AAAAAAT
6610722 AAAAGAAAAATAAAAAAAA
1 AAAAGAAAAATAAAAAAAA
6610741 CACAGAGAGC
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 16 0.89
21 2 0.11
ACGTcount: A:0.87, C:0.00, G:0.08, T:0.05
Consensus pattern (20 bp):
AAAAGAAAAATAAAAAAAAT
Found at i:6610731 original size:13 final size:12
Alignment explanation
Indices: 6610696--6610738 Score: 50
Period size: 13 Copynumber: 3.4 Consensus size: 12
6610686 TCCATTTTTC
*
6610696 AAAACGAAAAGAA
1 AAAAAGAAAA-AA
6610709 AAAAAGAAAAAA
1 AAAAAGAAAAAA
*
6610721 TAAAAGAAAAATA
1 AAAAAGAAAAA-A
6610734 AAAAA
1 AAAAA
6610739 AACACAGAGA
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
12 12 0.46
13 14 0.54
ACGTcount: A:0.84, C:0.02, G:0.09, T:0.05
Consensus pattern (12 bp):
AAAAAGAAAAAA
Found at i:6613975 original size:34 final size:34
Alignment explanation
Indices: 6613935--6614025 Score: 128
Period size: 34 Copynumber: 2.6 Consensus size: 34
6613925 AAATTTTTTA
6613935 AAAATTAATTAAATTATGTTTTAGGGGTTTTAAG
1 AAAATTAATTAAATTATGTTTTAGGGGTTTTAAG
* * * * *
6613969 TAAATTAGTTAAATTAGGGTTTAGGGTTTTTAAG
1 AAAATTAATTAAATTATGTTTTAGGGGTTTTAAG
6614003 AAAATTAATTAAATTAGTGTTTT
1 AAAATTAATTAAATTA-TGTTTT
6614026 TTTAAAAAAT
Statistics
Matches: 47, Mismatches: 9, Indels: 1
0.82 0.16 0.02
Matches are distributed among these distances:
34 43 0.91
35 4 0.09
ACGTcount: A:0.37, C:0.00, G:0.18, T:0.45
Consensus pattern (34 bp):
AAAATTAATTAAATTATGTTTTAGGGGTTTTAAG
Found at i:6617349 original size:125 final size:126
Alignment explanation
Indices: 6617196--6617441 Score: 359
Period size: 125 Copynumber: 2.0 Consensus size: 126
6617186 AAAAGTATTG
* * *
6617196 AAAAAAGCTCCCACGTAGACGCTATTTTTCTACAGTAGTTCCTGAAAAAATAATTTTGAGAAGAC
1 AAAAAAGCTCCCACGTAGACACTATTTTTCTACAGTAGTTCCTAAAAAAATAATTTTGAGAAAAC
* *
6617261 GGTTCT-AAAAAATAGTGTGAAAAACGCTTCAAGCAAAATGCACTATCAACAAAATCACTA
66 GGTTCTAAAAAAATAGTGTAAAAAACACTTCAAGCAAAATGCACTATCAACAAAATCACTA
* * * * *
6617321 AAAAAAGCTCTCATGTGGACACTCTTTTTCTACAGTAGTTTCTAAAAAAATAATTTTGAGAAAAC
1 AAAAAAGCTCCCACGTAGACACTATTTTTCTACAGTAGTTCCTAAAAAAATAATTTTGAGAAAAC
** * *
6617386 GGTTCTAAAAAAATAGTGTAAAAAACACTTCAAGCAGGATGCACTGTCAGCAAAAT
66 GGTTCTAAAAAAATAGTGTAAAAAACACTTCAAGCAAAATGCACTATCAACAAAAT
6617442 TACTGAACCC
Statistics
Matches: 106, Mismatches: 14, Indels: 1
0.88 0.12 0.01
Matches are distributed among these distances:
125 63 0.59
126 43 0.41
ACGTcount: A:0.42, C:0.17, G:0.15, T:0.26
Consensus pattern (126 bp):
AAAAAAGCTCCCACGTAGACACTATTTTTCTACAGTAGTTCCTAAAAAAATAATTTTGAGAAAAC
GGTTCTAAAAAAATAGTGTAAAAAACACTTCAAGCAAAATGCACTATCAACAAAATCACTA
Found at i:6620518 original size:24 final size:24
Alignment explanation
Indices: 6620470--6620520 Score: 68
Period size: 24 Copynumber: 2.1 Consensus size: 24
6620460 ACTGTTATAA
* *
6620470 AAAATTATAAAATAAAAATTAATT
1 AAAATTACAAAATAAAAAATAATT
6620494 AAAATTACATAAATAAAAAAT-ATT
1 AAAATTACA-AAATAAAAAATAATT
6620518 AAA
1 AAA
6620521 TAATATTCAA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
24 14 0.58
25 10 0.42
ACGTcount: A:0.69, C:0.02, G:0.00, T:0.29
Consensus pattern (24 bp):
AAAATTACAAAATAAAAAATAATT
Found at i:6624309 original size:24 final size:25
Alignment explanation
Indices: 6624282--6624329 Score: 62
Period size: 25 Copynumber: 2.0 Consensus size: 25
6624272 CCTGTTAAGT
6624282 GCTCTTCG-GAGCTACCCGTTATAG
1 GCTCTTCGTGAGCTACCCGTTATAG
* * *
6624306 GCTCTTTGTGAGCTTCTCGTTATA
1 GCTCTTCGTGAGCTACCCGTTATA
6624330 TTGTTTGGAT
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
24 7 0.35
25 13 0.65
ACGTcount: A:0.15, C:0.25, G:0.23, T:0.38
Consensus pattern (25 bp):
GCTCTTCGTGAGCTACCCGTTATAG
Found at i:6628412 original size:12 final size:12
Alignment explanation
Indices: 6628403--6628428 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
6628393 GCAATTGTAT
6628403 AATAAATTGTGA
1 AATAAATTGTGA
6628415 AATAAATTGTGA
1 AATAAATTGTGA
6628427 AA
1 AA
6628429 AGCTATTTAT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.54, C:0.00, G:0.15, T:0.31
Consensus pattern (12 bp):
AATAAATTGTGA
Found at i:6630852 original size:41 final size:38
Alignment explanation
Indices: 6630756--6630855 Score: 94
Period size: 37 Copynumber: 2.6 Consensus size: 38
6630746 GAAGCAATAG
*
6630756 TTGACACCCAGTGTCTCATCG-GCCAAGCCGAAGAAAT
1 TTGACACCCAGTGTCTCATCGAACCAAGCCGAAGAAAT
** ** * * *
6630793 TTGGTACCCAGTACCTCATCGAATCTATCCGAAGAAATAT
1 TTGACACCCAGTGTCTCATCGAACCAAGCCGAAG-AA-AT
6630833 TATGACACCCAGTGTCTCATCGA
1 T-TGACACCCAGTGTCTCATCGA
6630856 CTCGAGGTCG
Statistics
Matches: 47, Mismatches: 12, Indels: 4
0.75 0.19 0.06
Matches are distributed among these distances:
37 17 0.36
38 8 0.17
39 2 0.04
40 3 0.06
41 17 0.36
ACGTcount: A:0.30, C:0.28, G:0.18, T:0.24
Consensus pattern (38 bp):
TTGACACCCAGTGTCTCATCGAACCAAGCCGAAGAAAT
Found at i:6631187 original size:6 final size:6
Alignment explanation
Indices: 6631172--6631202 Score: 53
Period size: 6 Copynumber: 5.2 Consensus size: 6
6631162 CCACTCATCT
*
6631172 TAATAA TAATAC TAATAC TAATAC TAATAC T
1 TAATAC TAATAC TAATAC TAATAC TAATAC T
6631203 TACCTCACAT
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
6 24 1.00
ACGTcount: A:0.52, C:0.13, G:0.00, T:0.35
Consensus pattern (6 bp):
TAATAC
Found at i:6631917 original size:17 final size:17
Alignment explanation
Indices: 6631897--6631936 Score: 62
Period size: 17 Copynumber: 2.3 Consensus size: 17
6631887 TTTCCTATTC
*
6631897 TGTTTCTTTTCTTCTTT
1 TGTTTCTTTTATTCTTT
6631914 TGTTTCTTTTATTCTTT
1 TGTTTCTTTTATTCTTT
6631931 TAGTTT
1 T-GTTT
6631937 ATGTTTTGTT
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
17 17 0.81
18 4 0.19
ACGTcount: A:0.05, C:0.12, G:0.07, T:0.75
Consensus pattern (17 bp):
TGTTTCTTTTATTCTTT
Found at i:6631980 original size:16 final size:17
Alignment explanation
Indices: 6631952--6631983 Score: 57
Period size: 16 Copynumber: 1.9 Consensus size: 17
6631942 TTGTTTATTA
6631952 TTTAATAAATATAATAC
1 TTTAATAAATATAATAC
6631969 TTTAAT-AATATAATA
1 TTTAATAAATATAATA
6631984 TAATATAATA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 9 0.60
17 6 0.40
ACGTcount: A:0.53, C:0.03, G:0.00, T:0.44
Consensus pattern (17 bp):
TTTAATAAATATAATAC
Found at i:6631981 original size:5 final size:5
Alignment explanation
Indices: 6631973--6632009 Score: 74
Period size: 5 Copynumber: 7.4 Consensus size: 5
6631963 TAATACTTTA
6631973 ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT AT
1 ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT AT
6632010 TTTCTTATAT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 32 1.00
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (5 bp):
ATAAT
Found at i:6639856 original size:13 final size:13
Alignment explanation
Indices: 6639838--6639863 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
6639828 TTAATTAATT
6639838 AATTGAAATTAAA
1 AATTGAAATTAAA
6639851 AATTGAAATTAAA
1 AATTGAAATTAAA
6639864 TTAATTAGTC
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:0.62, C:0.00, G:0.08, T:0.31
Consensus pattern (13 bp):
AATTGAAATTAAA
Found at i:6644462 original size:9 final size:9
Alignment explanation
Indices: 6644443--6644479 Score: 58
Period size: 9 Copynumber: 4.1 Consensus size: 9
6644433 TGAGTTTTCG
6644443 AATTCGAAT
1 AATTCGAAT
6644452 AACTT-GAAT
1 AA-TTCGAAT
6644461 AATTCGAAT
1 AATTCGAAT
6644470 AATTCGAAT
1 AATTCGAAT
6644479 A
1 A
6644480 TAAAACTATA
Statistics
Matches: 26, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
8 2 0.08
9 22 0.85
10 2 0.08
ACGTcount: A:0.46, C:0.11, G:0.11, T:0.32
Consensus pattern (9 bp):
AATTCGAAT
Found at i:6644600 original size:30 final size:30
Alignment explanation
Indices: 6644538--6644600 Score: 76
Period size: 30 Copynumber: 2.1 Consensus size: 30
6644528 ACTTTTCCCT
* *
6644538 CAAAACTTTTACTCCTTCCCACTTTCCCCC
1 CAAAACTTTTACTCCCTCCCACTTCCCCCC
6644568 CAAAACTTTTACTCCCCTCCC-C-TCCCCTCC
1 CAAAACTTTTACT-CCCTCCCACTTCCCC-CC
6644598 CAA
1 CAA
6644601 CCCCCCAATC
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
29 4 0.14
30 19 0.66
31 6 0.21
ACGTcount: A:0.21, C:0.51, G:0.00, T:0.29
Consensus pattern (30 bp):
CAAAACTTTTACTCCCTCCCACTTCCCCCC
Found at i:6648785 original size:7 final size:7
Alignment explanation
Indices: 6648777--6648809 Score: 57
Period size: 7 Copynumber: 4.7 Consensus size: 7
6648767 AATCAATGAC
*
6648777 AAGTGAC
1 AAGTGAT
6648784 AAGTGAT
1 AAGTGAT
6648791 AAGTGAT
1 AAGTGAT
6648798 AAGTGAT
1 AAGTGAT
6648805 AAGTG
1 AAGTG
6648810 GTAGCTTAGC
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
7 25 1.00
ACGTcount: A:0.42, C:0.03, G:0.30, T:0.24
Consensus pattern (7 bp):
AAGTGAT
Found at i:6648841 original size:64 final size:65
Alignment explanation
Indices: 6648729--6648859 Score: 219
Period size: 64 Copynumber: 2.0 Consensus size: 65
6648719 TGAGTACTTC
*
6648729 TGATCAGTGATAAGTGGTAGCTTTAGCTACACTTATCTAATCAATGACAAGTGACAAGTGATAAG
1 TGATAAGTGATAAGTGGTAGCTTTAGCTACACTTATCTAATCAATGACAAGTGACAAGTGATAAG
* * *
6648794 TGATAAGTGATAAGTGGTAGC-TTAGCTACACTTATCTGATCAGTGACAAGTGATAAGTGATAAG
1 TGATAAGTGATAAGTGGTAGCTTTAGCTACACTTATCTAATCAATGACAAGTGACAAGTGATAAG
6648858 TG
1 TG
6648860 GTAGCTTTAG
Statistics
Matches: 62, Mismatches: 4, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
64 42 0.68
65 20 0.32
ACGTcount: A:0.34, C:0.12, G:0.24, T:0.30
Consensus pattern (65 bp):
TGATAAGTGATAAGTGGTAGCTTTAGCTACACTTATCTAATCAATGACAAGTGACAAGTGATAAG
Found at i:6648860 original size:50 final size:51
Alignment explanation
Indices: 6648785--6648910 Score: 218
Period size: 51 Copynumber: 2.5 Consensus size: 51
6648775 ACAAGTGACA
*
6648785 AGTGATAAGTGATAAGTGATAAGTGGTAGC-TTAGCTACACTTATCTGATC
1 AGTGACAAGTGATAAGTGATAAGTGGTAGCTTTAGCTACACTTATCTGATC
6648835 AGTGACAAGTGATAAGTGATAAGTGGTAGCTTTAGCTACACTTATCTGATC
1 AGTGACAAGTGATAAGTGATAAGTGGTAGCTTTAGCTACACTTATCTGATC
* *
6648886 AGTGACAAGAGATAAATGATAAGTG
1 AGTGACAAGTGATAAGTGATAAGTG
6648911 ATTCCGTGTA
Statistics
Matches: 72, Mismatches: 3, Indels: 1
0.95 0.04 0.01
Matches are distributed among these distances:
50 29 0.40
51 43 0.60
ACGTcount: A:0.35, C:0.11, G:0.25, T:0.29
Consensus pattern (51 bp):
AGTGACAAGTGATAAGTGATAAGTGGTAGCTTTAGCTACACTTATCTGATC
Found at i:6653318 original size:81 final size:81
Alignment explanation
Indices: 6653179--6653342 Score: 240
Period size: 81 Copynumber: 2.0 Consensus size: 81
6653169 TTCCTCTTTT
* ** *
6653179 GTATCCAAGATAGCTTATTTGAGTAATAGAGATACTTTCACATTCTCTTAACTTTTGCATTATTC
1 GTATCCAAGATAGCTTATTTGAGTAATAGAGACACTTTCACATTCTCCCAACTCTTGCATTATTC
* *
6653244 TTTTGTTCTAATCTAA
66 TCTTGTGCTAATCTAA
* *
6653260 GTATCCAAGCTAGCTTATTTGAGTAATAGAGACA-TTTCCACATTCTCCCAACTCTTGCATTCTT
1 GTATCCAAGATAGCTTATTTGAGTAATAGAGACACTTT-CACATTCTCCCAACTCTTGCATTATT
6653324 CTCTTGTGCTAATCTAA
65 CTCTTGTGCTAATCTAA
6653341 GT
1 GT
6653343 TCCCTTTTCC
Statistics
Matches: 74, Mismatches: 8, Indels: 2
0.88 0.10 0.02
Matches are distributed among these distances:
80 3 0.04
81 71 0.96
ACGTcount: A:0.27, C:0.20, G:0.12, T:0.41
Consensus pattern (81 bp):
GTATCCAAGATAGCTTATTTGAGTAATAGAGACACTTTCACATTCTCCCAACTCTTGCATTATTC
TCTTGTGCTAATCTAA
Found at i:6656101 original size:2 final size:2
Alignment explanation
Indices: 6656094--6656118 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
6656084 TTCTTTCATT
6656094 TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA T
6656119 TTCTCCATTA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:6658655 original size:14 final size:14
Alignment explanation
Indices: 6658636--6658680 Score: 53
Period size: 14 Copynumber: 3.4 Consensus size: 14
6658626 TAAATTTTTT
6658636 TAATATTTATATTA
1 TAATATTTATATTA
6658650 TAATATTATATATT-
1 TAATATT-TATATTA
6658664 T-A-ATTT-TATTA
1 TAATATTTATATTA
6658675 TAATAT
1 TAATAT
6658681 ATAAACATGA
Statistics
Matches: 27, Mismatches: 0, Indels: 9
0.75 0.00 0.25
Matches are distributed among these distances:
10 4 0.15
11 2 0.07
12 4 0.15
13 3 0.11
14 8 0.30
15 6 0.22
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (14 bp):
TAATATTTATATTA
Found at i:6658681 original size:22 final size:21
Alignment explanation
Indices: 6658638--6658683 Score: 56
Period size: 22 Copynumber: 2.1 Consensus size: 21
6658628 AATTTTTTTA
*
6658638 ATATTTATATTATAATATTAT
1 ATATTTATATTATAATAATAT
* *
6658659 ATATTTAATTTTATTATAATAT
1 ATATTT-ATATTATAATAATAT
6658681 ATA
1 ATA
6658684 AACATGAAGC
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
21 6 0.29
22 15 0.71
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (21 bp):
ATATTTATATTATAATAATAT
Found at i:6661694 original size:153 final size:153
Alignment explanation
Indices: 6661416--6661707 Score: 503
Period size: 153 Copynumber: 1.9 Consensus size: 153
6661406 GGATTTTTTA
* * * *
6661416 GATTCCAACTTGGAGGCAGGTGTAAATAAGTTAGATATACTGGAGGGGAGAACGAGGTTGGAGAA
1 GATTCCAACTTGGAGGCAGGTGTAAATAAGTTAGATATACCGGAGGCGAGAACAAGGTTGAAGAA
* *
6661481 GAGTTGTTCCAAAAGCAAGGATAGAAAAGATGATAATATCAAAAGTGAGATTCAGGCCCTTGCTA
66 GAGTTGTTCCAAAAGCAAGGATAGAAAAGATGATAATACCAAAAGTGAGATCCAGGCCCTTGCTA
6661546 AACTCAATCCAGGGCGTTCTTTG
131 AACTCAATCCAGGGCGTTCTTTG
6661569 GATTCCAACTTGGAGGCAGGTGTAAATAAGTTAGATATACCGGAGGCGAGAACAAGGTTGAAGAA
1 GATTCCAACTTGGAGGCAGGTGTAAATAAGTTAGATATACCGGAGGCGAGAACAAGGTTGAAGAA
* * *
6661634 GAGTTGTTCTAAAAGCAAGGATAGAAAAGATGATAATGCCAAAAGTGAGATCCAGGCCCTTGTTA
66 GAGTTGTTCCAAAAGCAAGGATAGAAAAGATGATAATACCAAAAGTGAGATCCAGGCCCTTGCTA
6661699 AACTCAATC
131 AACTCAATC
6661708 TAAAGCTCCT
Statistics
Matches: 130, Mismatches: 9, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
153 130 1.00
ACGTcount: A:0.36, C:0.14, G:0.27, T:0.23
Consensus pattern (153 bp):
GATTCCAACTTGGAGGCAGGTGTAAATAAGTTAGATATACCGGAGGCGAGAACAAGGTTGAAGAA
GAGTTGTTCCAAAAGCAAGGATAGAAAAGATGATAATACCAAAAGTGAGATCCAGGCCCTTGCTA
AACTCAATCCAGGGCGTTCTTTG
Found at i:6667619 original size:27 final size:27
Alignment explanation
Indices: 6667585--6667649 Score: 78
Period size: 27 Copynumber: 2.4 Consensus size: 27
6667575 TGAATGTAGT
*
6667585 AATTTTTATAAAATTTAATA-TAATTAA
1 AATTTTTA-AAAATTTAAAATTAATTAA
* *
6667612 AATTTTTAAAATTTTAAAATTAATTAC
1 AATTTTTAAAAATTTAAAATTAATTAA
*
6667639 AATGTTTAAAA
1 AATTTTTAAAA
6667650 TAATAAAAAT
Statistics
Matches: 33, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
26 9 0.27
27 24 0.73
ACGTcount: A:0.51, C:0.02, G:0.02, T:0.46
Consensus pattern (27 bp):
AATTTTTAAAAATTTAAAATTAATTAA
Found at i:6667656 original size:27 final size:27
Alignment explanation
Indices: 6667605--6667657 Score: 70
Period size: 27 Copynumber: 2.0 Consensus size: 27
6667595 AAATTTAATA
* **
6667605 TAATTAAAATTTTTAAAATTTTAAAAT
1 TAATTAAAATGTTTAAAATAATAAAAT
*
6667632 TAATTACAATGTTTAAAATAATAAAA
1 TAATTAAAATGTTTAAAATAATAAAA
6667658 ATCAATTTTT
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
27 22 1.00
ACGTcount: A:0.55, C:0.02, G:0.02, T:0.42
Consensus pattern (27 bp):
TAATTAAAATGTTTAAAATAATAAAAT
Found at i:6668844 original size:2 final size:2
Alignment explanation
Indices: 6668832--6668876 Score: 72
Period size: 2 Copynumber: 22.5 Consensus size: 2
6668822 ATGATTCAAT
* *
6668832 TA TA AA TA TA TA TA TA TA TA TA TA TA TT TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
6668874 TA T
1 TA T
6668877 TTACTTTTTT
Statistics
Matches: 39, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
2 39 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:6668972 original size:3 final size:3
Alignment explanation
Indices: 6668959--6669004 Score: 85
Period size: 3 Copynumber: 15.7 Consensus size: 3
6668949 AATTTAACTG
6668959 TTA TT- TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
6669005 CAAGATTCAT
Statistics
Matches: 42, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
2 2 0.05
3 40 0.95
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (3 bp):
TTA
Found at i:6675368 original size:41 final size:41
Alignment explanation
Indices: 6675308--6675577 Score: 441
Period size: 41 Copynumber: 6.6 Consensus size: 41
6675298 AGTTTTAAAA
* * *
6675308 CCTAGCAGGCTAAGTGCCGGTGATCTAAATCAGGTTATAAG
1 CCTAGCAGGCTAAGTGCCGGTGAACTGAATCAGGCTATAAG
*
6675349 CCAAGCAGGCTAAGTGCCGGTGAACTGAATCAGGCTATAAG
1 CCTAGCAGGCTAAGTGCCGGTGAACTGAATCAGGCTATAAG
6675390 CCTAGCAGGCTAAGTGCCGGTGAACTGAATCAGGCTATAAG
1 CCTAGCAGGCTAAGTGCCGGTGAACTGAATCAGGCTATAAG
**
6675431 CCTAGCAGGCTAAGTGCCGGTGATTTGAATCAGGCTATAAG
1 CCTAGCAGGCTAAGTGCCGGTGAACTGAATCAGGCTATAAG
*
6675472 CCTAGCAGGCTAAGTGCCGGTGATCTGAATCAGGCTATAAG
1 CCTAGCAGGCTAAGTGCCGGTGAACTGAATCAGGCTATAAG
* * *
6675513 CCTAGCAGGTTAAGTGCCGGTGAACTGGATTAGGCTATAAG
1 CCTAGCAGGCTAAGTGCCGGTGAACTGAATCAGGCTATAAG
*
6675554 CCTAGCAGGCTAAGTGCCAGTGAA
1 CCTAGCAGGCTAAGTGCCGGTGAA
6675578 TCTGTTTAAA
Statistics
Matches: 215, Mismatches: 14, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
41 215 1.00
ACGTcount: A:0.29, C:0.21, G:0.29, T:0.21
Consensus pattern (41 bp):
CCTAGCAGGCTAAGTGCCGGTGAACTGAATCAGGCTATAAG
Found at i:6685550 original size:2 final size:2
Alignment explanation
Indices: 6685543--6685571 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
6685533 CATCAATTTC
6685543 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 A
6685572 GAAAAAGAAA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:6688070 original size:39 final size:43
Alignment explanation
Indices: 6687982--6688076 Score: 117
Period size: 45 Copynumber: 2.3 Consensus size: 43
6687972 TTTGCATGTG
* * *
6687982 TATTTGAAATTATTATTTGAAATATTTCTCATATAAACATAATGA
1 TATTTGAAATAATTAATTGAAATATTTCACATAT-AACATAA-GA
6688027 TATTTGAAATAATTAATTGAAATATTTCACATAT-A-A-AA-A
1 TATTTGAAATAATTAATTGAAATATTTCACATATAACATAAGA
6688066 TATTTGAAATA
1 TATTTGAAATA
6688077 TCATACCTGT
Statistics
Matches: 47, Mismatches: 3, Indels: 6
0.84 0.05 0.11
Matches are distributed among these distances:
39 12 0.26
41 2 0.04
42 1 0.02
43 1 0.02
45 31 0.66
ACGTcount: A:0.46, C:0.05, G:0.06, T:0.42
Consensus pattern (43 bp):
TATTTGAAATAATTAATTGAAATATTTCACATATAACATAAGA
Found at i:6694676 original size:15 final size:15
Alignment explanation
Indices: 6694656--6694692 Score: 65
Period size: 15 Copynumber: 2.5 Consensus size: 15
6694646 ACACACGGTC
*
6694656 GTGTCACCTGGCCGT
1 GTGTCACCTGGCCAT
6694671 GTGTCACCTGGCCAT
1 GTGTCACCTGGCCAT
6694686 GTGTCAC
1 GTGTCAC
6694693 ATACGGCTGA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
15 21 1.00
ACGTcount: A:0.11, C:0.32, G:0.30, T:0.27
Consensus pattern (15 bp):
GTGTCACCTGGCCAT
Found at i:6697078 original size:19 final size:18
Alignment explanation
Indices: 6697056--6697096 Score: 55
Period size: 19 Copynumber: 2.2 Consensus size: 18
6697046 GCTTATTATG
6697056 TTAATTAAGTTAGATTAA
1 TTAATTAAGTTAGATTAA
* *
6697074 CTTAATTAATTTAGGTTAA
1 -TTAATTAAGTTAGATTAA
6697093 TTAA
1 TTAA
6697097 AGATTATTCA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
18 4 0.20
19 16 0.80
ACGTcount: A:0.41, C:0.02, G:0.10, T:0.46
Consensus pattern (18 bp):
TTAATTAAGTTAGATTAA
Found at i:6698697 original size:29 final size:28
Alignment explanation
Indices: 6698656--6698722 Score: 98
Period size: 29 Copynumber: 2.4 Consensus size: 28
6698646 TATAATATAT
* *
6698656 ATAAATTAAAATATTTAAATAAATTTAA
1 ATAAATTAAAATATTGAAATAAATTGAA
*
6698684 ATAAATTAACAATATTGAAATAAGTTGAA
1 ATAAATTAA-AATATTGAAATAAATTGAA
6698713 ATAAATTAAA
1 ATAAATTAAA
6698723 GATGTTAAAA
Statistics
Matches: 35, Mismatches: 3, Indels: 2
0.88 0.08 0.05
Matches are distributed among these distances:
28 10 0.29
29 25 0.71
ACGTcount: A:0.60, C:0.01, G:0.04, T:0.34
Consensus pattern (28 bp):
ATAAATTAAAATATTGAAATAAATTGAA
Found at i:6698733 original size:29 final size:28
Alignment explanation
Indices: 6698656--6698734 Score: 95
Period size: 29 Copynumber: 2.8 Consensus size: 28
6698646 TATAATATAT
* *
6698656 ATAAATTAAAATATTTAAATAAATTTAA
1 ATAAATTAAAATATTAAAATAAATTGAA
* *
6698684 ATAAATTAACAATATTGAAATAAGTTGAA
1 ATAAATTAA-AATATTAAAATAAATTGAA
*
6698713 ATAAATTAAAGATGTTAAAATA
1 ATAAATTAAA-ATATTAAAATA
6698735 TTTGAAAGAG
Statistics
Matches: 44, Mismatches: 5, Indels: 3
0.85 0.10 0.06
Matches are distributed among these distances:
28 10 0.23
29 34 0.77
ACGTcount: A:0.58, C:0.01, G:0.06, T:0.34
Consensus pattern (28 bp):
ATAAATTAAAATATTAAAATAAATTGAA
Found at i:6699035 original size:19 final size:18
Alignment explanation
Indices: 6699011--6699062 Score: 54
Period size: 19 Copynumber: 2.8 Consensus size: 18
6699001 AGCTTAAAAC
6699011 AATAATACATATATAATAA
1 AATAATA-ATATATAATAA
*
6699030 AATAAT-GTATAT-ATAA
1 AATAATAATATATAATAA
6699046 AATAAGTAAATATATAA
1 AATAA-T-AATATATAA
6699063 ATGAATAACA
Statistics
Matches: 27, Mismatches: 2, Indels: 7
0.75 0.06 0.19
Matches are distributed among these distances:
16 9 0.33
17 6 0.22
19 11 0.41
20 1 0.04
ACGTcount: A:0.62, C:0.02, G:0.04, T:0.33
Consensus pattern (18 bp):
AATAATAATATATAATAA
Found at i:6699042 original size:17 final size:16
Alignment explanation
Indices: 6699020--6699063 Score: 54
Period size: 17 Copynumber: 2.7 Consensus size: 16
6699010 CAATAATACA
6699020 TATATAATAAAATAATG
1 TATATAATAAAATAA-G
6699037 TATAT-ATAAAATAAG
1 TATATAATAAAATAAG
*
6699052 TAAATATATAAA
1 TATATA-ATAAA
6699064 TGAATAACAT
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
15 5 0.21
16 9 0.38
17 10 0.42
ACGTcount: A:0.61, C:0.00, G:0.05, T:0.34
Consensus pattern (16 bp):
TATATAATAAAATAAG
Found at i:6704412 original size:15 final size:15
Alignment explanation
Indices: 6704377--6704428 Score: 56
Period size: 15 Copynumber: 3.6 Consensus size: 15
6704367 TTAAGAATTT
*
6704377 TATTAAATTAT-ATA
1 TATTTAATTATAATA
6704391 T-TTTAATTATAATA
1 TATTTAATTATAATA
*
6704405 TATTTAATAATAAT-
1 TATTTAATTATAATA
6704419 TATGTTAATT
1 TAT-TTAATT
6704429 TAAATTTTAT
Statistics
Matches: 32, Mismatches: 3, Indels: 5
0.80 0.08 0.12
Matches are distributed among these distances:
13 8 0.25
14 8 0.25
15 16 0.50
ACGTcount: A:0.44, C:0.00, G:0.02, T:0.54
Consensus pattern (15 bp):
TATTTAATTATAATA
Found at i:6704461 original size:120 final size:120
Alignment explanation
Indices: 6704326--6704544 Score: 420
Period size: 120 Copynumber: 1.8 Consensus size: 120
6704316 AACAGGATTT
6704326 TATATTATGAATTGAGTAAATTCATATAAGAATATTAATTATTAAGAATTTTATTAAATTATATA
1 TATATTATGAATTGAGTAAATTCATATAAGAATATTAATTATTAAGAATTTTATTAAATTATATA
6704391 TTTTAATTATAATATATTTAATAATAATTATGTTAATTTAAATTTTATAGTATCA
66 TTTTAATTATAATATATTTAATAATAATTATGTTAATTTAAATTTTATAGTATCA
* *
6704446 TATATTATGATTTGAGTAAATTCATATAAGAATATTGATTATTAAGAATTTTATTAAATTATATA
1 TATATTATGAATTGAGTAAATTCATATAAGAATATTAATTATTAAGAATTTTATTAAATTATATA
6704511 TTTTAATTATAATATATTTAATAATAATTATGTT
66 TTTTAATTATAATATATTTAATAATAATTATGTT
6704545 TAAATATGAT
Statistics
Matches: 97, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
120 97 1.00
ACGTcount: A:0.43, C:0.01, G:0.06, T:0.49
Consensus pattern (120 bp):
TATATTATGAATTGAGTAAATTCATATAAGAATATTAATTATTAAGAATTTTATTAAATTATATA
TTTTAATTATAATATATTTAATAATAATTATGTTAATTTAAATTTTATAGTATCA
Found at i:6704510 original size:61 final size:61
Alignment explanation
Indices: 6704326--6704512 Score: 197
Period size: 61 Copynumber: 3.1 Consensus size: 61
6704316 AACAGGATTT
* *
6704326 TATATTATGAATTGAGTAAATTCATATAAGAATATTAATTATTAAGAATTTTATTAAATTA
1 TATATTATGATTTGAGTAAATTCATATAAGAATATTGATTATTAAGAATTTTATTAAATTA
* * * * * * * * *
6704387 TATATTTTAATTAT-AATATATTTA-ATAATAAT-TATG-TTAATTTA-AATTTTA-TAGTATCA
1 TATATTATGATT-TGAGTAAATTCATATAAGAATAT-TGATT-ATTAAGAATTTTATTA-AATTA
6704446 TATATTATGATTTGAGTAAATTCATATAAGAATATTGATTATTAAGAATTTTATTAAATTA
1 TATATTATGATTTGAGTAAATTCATATAAGAATATTGATTATTAAGAATTTTATTAAATTA
6704507 TATATT
1 TATATT
6704513 TTAATTATAA
Statistics
Matches: 96, Mismatches: 20, Indels: 20
0.71 0.15 0.15
Matches are distributed among these distances:
58 3 0.03
59 30 0.31
60 25 0.26
61 35 0.36
62 3 0.03
ACGTcount: A:0.43, C:0.02, G:0.07, T:0.48
Consensus pattern (61 bp):
TATATTATGATTTGAGTAAATTCATATAAGAATATTGATTATTAAGAATTTTATTAAATTA
Found at i:6704527 original size:16 final size:16
Alignment explanation
Indices: 6704506--6704547 Score: 52
Period size: 15 Copynumber: 2.7 Consensus size: 16
6704496 TTATTAAATT
*
6704506 ATATATTTTAATTATA
1 ATATATTTTAATAATA
6704522 ATATA-TTTAATAATA
1 ATATATTTTAATAATA
6704537 AT-TATGTTTAA
1 ATATAT-TTTAA
6704548 ATATGATTAA
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
14 2 0.09
15 11 0.48
16 10 0.43
ACGTcount: A:0.45, C:0.00, G:0.02, T:0.52
Consensus pattern (16 bp):
ATATATTTTAATAATA
Found at i:6704532 original size:15 final size:15
Alignment explanation
Indices: 6704497--6704538 Score: 52
Period size: 15 Copynumber: 2.9 Consensus size: 15
6704487 TTAAGAATTT
*
6704497 TATTAAATTAT-ATA
1 TATTTAATTATAATA
6704511 T-TTTAATTATAATA
1 TATTTAATTATAATA
*
6704525 TATTTAATAATAAT
1 TATTTAATTATAAT
6704539 TATGTTTAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
13 8 0.33
14 5 0.21
15 11 0.46
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (15 bp):
TATTTAATTATAATA
Found at i:6704777 original size:45 final size:44
Alignment explanation
Indices: 6704688--6704782 Score: 136
Period size: 45 Copynumber: 2.1 Consensus size: 44
6704678 TTACACCTCT
*
6704688 ATTACATTCAACCAAACACAGGATTACTATTACGCCTCTATTCC
1 ATTACATTCAACCAAACACAGGATTACTATTACACCTCTATTCC
*** *
6704732 ATTACATTCAACCAAACAGTTGATTTGCTATTACACCTCTATTCC
1 ATTACATTCAACCAAACACAGGA-TTACTATTACACCTCTATTCC
6704777 ATTACA
1 ATTACA
6704783 CCTCTAATCC
Statistics
Matches: 45, Mismatches: 5, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
44 20 0.44
45 25 0.56
ACGTcount: A:0.34, C:0.27, G:0.06, T:0.33
Consensus pattern (44 bp):
ATTACATTCAACCAAACACAGGATTACTATTACACCTCTATTCC
Found at i:6704782 original size:16 final size:16
Alignment explanation
Indices: 6704761--6704798 Score: 58
Period size: 16 Copynumber: 2.4 Consensus size: 16
6704751 TTGATTTGCT
*
6704761 ATTACACCTCTATTCC
1 ATTACACCTCTAATCC
6704777 ATTACACCTCTAATCC
1 ATTACACCTCTAATCC
*
6704793 AATACA
1 ATTACA
6704799 GCGAATCAAA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
16 20 1.00
ACGTcount: A:0.34, C:0.34, G:0.00, T:0.32
Consensus pattern (16 bp):
ATTACACCTCTAATCC
Found at i:6706970 original size:31 final size:31
Alignment explanation
Indices: 6706915--6706992 Score: 102
Period size: 31 Copynumber: 2.5 Consensus size: 31
6706905 AGGTCATGAT
* * *
6706915 TAAAATTTTAAAAATTTGAAAAGTATAAAGAC
1 TAAAA-TTGAAAAATTTAAAAAGTACAAAGAC
*
6706947 TAAAATTGAAAATTTTAAAAAGTACAAAGAC
1 TAAAATTGAAAAATTTAAAAAGTACAAAGAC
6706978 TAAAATTGAACAAAT
1 TAAAATTGAA-AAAT
6706993 AAAAGAACAG
Statistics
Matches: 40, Mismatches: 5, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
31 32 0.80
32 8 0.20
ACGTcount: A:0.58, C:0.05, G:0.09, T:0.28
Consensus pattern (31 bp):
TAAAATTGAAAAATTTAAAAAGTACAAAGAC
Found at i:6716619 original size:48 final size:47
Alignment explanation
Indices: 6716528--6716619 Score: 105
Period size: 47 Copynumber: 1.9 Consensus size: 47
6716518 TTTTGAGTAA
* * **
6716528 CTTAACTTTTCTCTTTTTTGTTCTTTTATTTTTTCTTTATTTTCCAT
1 CTTAACTTTTCTCTTTATGGTTCTTTTATTTTTTCAATATTTTCCAT
* *
6716575 CTTAACTTTTTTCTCTTATGGTTCTTTT-TTTTTTCCAATCTTTTC
1 CTTAACTTTTCTCT-TTATGGTTCTTTTATTTTTT-CAATATTTTC
6716620 TGCTTCCCTT
Statistics
Matches: 37, Mismatches: 6, Indels: 3
0.80 0.13 0.07
Matches are distributed among these distances:
47 19 0.51
48 18 0.49
ACGTcount: A:0.11, C:0.18, G:0.03, T:0.67
Consensus pattern (47 bp):
CTTAACTTTTCTCTTTATGGTTCTTTTATTTTTTCAATATTTTCCAT
Found at i:6721018 original size:6 final size:6
Alignment explanation
Indices: 6720979--6721016 Score: 58
Period size: 6 Copynumber: 6.3 Consensus size: 6
6720969 ATTCAGCGGC
* *
6720979 GGTGGC GGTGGA GGTGGA GGTGGA GGTGGA GGAGGA GG
1 GGTGGA GGTGGA GGTGGA GGTGGA GGTGGA GGTGGA GG
6721017 AGACAAAAGG
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
6 30 1.00
ACGTcount: A:0.16, C:0.03, G:0.68, T:0.13
Consensus pattern (6 bp):
GGTGGA
Found at i:6735702 original size:15 final size:17
Alignment explanation
Indices: 6735672--6735705 Score: 54
Period size: 15 Copynumber: 2.1 Consensus size: 17
6735662 AGAAATTAAA
6735672 TTATAATTTTTAATAAT
1 TTATAATTTTTAATAAT
6735689 TTAT-ATTTTT-ATAAT
1 TTATAATTTTTAATAAT
6735704 TT
1 TT
6735706 TTAAAAATAA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 7 0.41
16 6 0.35
17 4 0.24
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (17 bp):
TTATAATTTTTAATAAT
Found at i:6739686 original size:4 final size:4
Alignment explanation
Indices: 6739677--6739701 Score: 50
Period size: 4 Copynumber: 6.2 Consensus size: 4
6739667 TTATGAATCC
6739677 TTAA TTAA TTAA TTAA TTAA TTAA T
1 TTAA TTAA TTAA TTAA TTAA TTAA T
6739702 GAGTATATAG
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 21 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (4 bp):
TTAA
Found at i:6747633 original size:17 final size:18
Alignment explanation
Indices: 6747594--6747635 Score: 50
Period size: 17 Copynumber: 2.4 Consensus size: 18
6747584 AATATTTATG
6747594 GATAAAAATTTATAAAAT
1 GATAAAAATTTATAAAAT
* * *
6747612 AATAAAAATTT-TATATT
1 GATAAAAATTTATAAAAT
6747629 GATAAAA
1 GATAAAA
6747636 TAGATATTAA
Statistics
Matches: 20, Mismatches: 4, Indels: 1
0.80 0.16 0.04
Matches are distributed among these distances:
17 10 0.50
18 10 0.50
ACGTcount: A:0.60, C:0.00, G:0.05, T:0.36
Consensus pattern (18 bp):
GATAAAAATTTATAAAAT
Found at i:6748514 original size:45 final size:44
Alignment explanation
Indices: 6748414--6748755 Score: 113
Period size: 44 Copynumber: 7.6 Consensus size: 44
6748404 TTTTTGACCC
* * * * *
6748414 GCTCCACTACAACTTTAGGGGGATAAGATTAGTAGCTTCAGTCT
1 GCTCCACTGCAACTTCAGGGAGATAAGAGTAGTAGCTTCAATCT
* * *
6748458 GCTCTATTGCAACTTCAGGGAGATAAGACGT-GTATTCTTCAATCT
1 GCTCCACTGCAACTTCAGGGAGATAAGA-GTAGTA-GCTTCAATCT
* ** * * * *
6748503 GCTCCACTGCAACTTTAGAAAGATACGACTTGTAGCTTCAATCC
1 GCTCCACTGCAACTTCAGGGAGATAAGAGTAGTAGCTTCAATCT
* * * * * * * * * * *
6748547 ACTCTACTGCGACTTTAGGG-GGTGAG-GTTTGTGGTTTTAGTCT
1 GCTCCACTGCAACTTCAGGGAGATAAGAG-TAGTAGCTTCAATCT
** * * *
6748590 GCTCCACTGCAA-TGTCAGGGAGATAAGACTTGTCATGGTAAATTTAACCC
1 GCTCCACTGCAACT-TCAGGGAGATAAGA---GT-A--GTAGCTTCAATCT
* * * * * * *
6748640 GAC-CTACTGTAACTTCAGAGG-TATAGGATTCA-TCGCTTTAATCT
1 G-CTCCACTGCAACTTCAG-GGAGATAAGAGT-AGTAGCTTCAATCT
* * * * * *
6748684 GCTCTATTGCAACTTTAGGGAGATAGGATTAATAGCTTCAATCT
1 GCTCCACTGCAACTTCAGGGAGATAAGAGTAGTAGCTTCAATCT
*
6748728 GCTCCACTACAACTTCAGGGAGATAAGA
1 GCTCCACTGCAACTTCAGGGAGATAAGA
6748756 TTGGTTATTT
Statistics
Matches: 214, Mismatches: 65, Indels: 38
0.68 0.21 0.12
Matches are distributed among these distances:
42 1 0.00
43 31 0.14
44 115 0.54
45 34 0.16
47 4 0.02
48 1 0.00
50 24 0.11
51 4 0.02
ACGTcount: A:0.27, C:0.20, G:0.22, T:0.31
Consensus pattern (44 bp):
GCTCCACTGCAACTTCAGGGAGATAAGAGTAGTAGCTTCAATCT
Found at i:6748710 original size:44 final size:44
Alignment explanation
Indices: 6748662--6748757 Score: 120
Period size: 44 Copynumber: 2.2 Consensus size: 44
6748652 CTTCAGAGGT
* * * * * * *
6748662 ATAGGATTCATCGCTTTAATCTGCTCTATTGCAACTTTAGGGAG
1 ATAGGATTAATAGCTTCAATCTGCTCCACTACAACTTCAGGGAG
6748706 ATAGGATTAATAGCTTCAATCTGCTCCACTACAACTTCAGGGAG
1 ATAGGATTAATAGCTTCAATCTGCTCCACTACAACTTCAGGGAG
*
6748750 ATAAGATT
1 ATAGGATT
6748758 GGTTATTTAT
Statistics
Matches: 44, Mismatches: 8, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
44 44 1.00
ACGTcount: A:0.30, C:0.19, G:0.19, T:0.32
Consensus pattern (44 bp):
ATAGGATTAATAGCTTCAATCTGCTCCACTACAACTTCAGGGAG
Found at i:6748953 original size:50 final size:50
Alignment explanation
Indices: 6748875--6749260 Score: 360
Period size: 50 Copynumber: 7.7 Consensus size: 50
6748865 GATCTGTTCA
** *
6748875 CCAGGGAAGTAAGATTCGTTGTTGTAGCTTCAATCTATTTAACTGCAATA
1 CCAGGGAAGTAAGATTCACTGTTGTAGCTTCAATCTATTTAACTGCAATG
* * * * * * ** * **
6748925 TCGGGGAAGCAAGATTCACTATTGTAGCTTAAATCTGTTCCACTACACCG
1 CCAGGGAAGTAAGATTCACTGTTGTAGCTTCAATCTATTTAACTGCAATG
** *
6748975 CCAAAGAAGTAAGATTCGCTGTTGTAGCTTCAATCTATTTAACTGCAATG
1 CCAGGGAAGTAAGATTCACTGTTGTAGCTTCAATCTATTTAACTGCAATG
* * * * * * * ***
6749025 TC-GATGAAGCAAGATTCGCCGTTGTAGCTTCAATCTGTTTCACTGCACCA
1 CCAG-GGAAGTAAGATTCACTGTTGTAGCTTCAATCTATTTAACTGCAATG
* *
6749075 CCAGGGAAGTAAGATTCACTATTGTAGCTTCAATCTATTTAACTGTAATG
1 CCAGGGAAGTAAGATTCACTGTTGTAGCTTCAATCTATTTAACTGCAATG
* * * ** **
6749125 TCGGGGAAGTAAGATTCACTGTTGTAGCTTCAATCTGTTCCACTGCACCG
1 CCAGGGAAGTAAGATTCACTGTTGTAGCTTCAATCTATTTAACTGCAATG
* ** *
6749175 CTAGGGAAGTAAGATTTGCTGTTGTAGCTTCAATCTATTTAACTGCCATG
1 CCAGGGAAGTAAGATTCACTGTTGTAGCTTCAATCTATTTAACTGCAATG
* * * *
6749225 CCAAGGAAGCAAGATTCACTGTTGTAACTTTAATCT
1 CCAGGGAAGTAAGATTCACTGTTGTAGCTTCAATCT
6749261 GTTCCACTGC
Statistics
Matches: 257, Mismatches: 77, Indels: 4
0.76 0.23 0.01
Matches are distributed among these distances:
50 256 1.00
51 1 0.00
ACGTcount: A:0.28, C:0.20, G:0.20, T:0.32
Consensus pattern (50 bp):
CCAGGGAAGTAAGATTCACTGTTGTAGCTTCAATCTATTTAACTGCAATG
Found at i:6749053 original size:100 final size:100
Alignment explanation
Indices: 6748875--6749281 Score: 580
Period size: 100 Copynumber: 4.1 Consensus size: 100
6748865 GATCTGTTCA
* * *
6748875 CCAGGGAAGTAAGATTCGTTGTTGTAGCTTCAATCTATTTAACTGCAATATCGGGGAAGCAAGAT
1 CCAGGGAAGTAAGATTCGCTGTTGTAGCTTCAATCTATTTAACTGCAATGTCGAGGAAGCAAGAT
* * *
6748940 TCACTATTGTAGCTTAAATCTGTTCCACTACACCG
66 TCACTGTTGTAGCTTCAATCTGTTCCACTGCACCG
** *
6748975 CCAAAGAAGTAAGATTCGCTGTTGTAGCTTCAATCTATTTAACTGCAATGTCGATGAAGCAAGAT
1 CCAGGGAAGTAAGATTCGCTGTTGTAGCTTCAATCTATTTAACTGCAATGTCGAGGAAGCAAGAT
* * * *
6749040 TCGCCGTTGTAGCTTCAATCTGTTTCACTGCACCA
66 TCACTGTTGTAGCTTCAATCTGTTCCACTGCACCG
* * * * *
6749075 CCAGGGAAGTAAGATTCACTATTGTAGCTTCAATCTATTTAACTGTAATGTCGGGGAAGTAAGAT
1 CCAGGGAAGTAAGATTCGCTGTTGTAGCTTCAATCTATTTAACTGCAATGTCGAGGAAGCAAGAT
6749140 TCACTGTTGTAGCTTCAATCTGTTCCACTGCACCG
66 TCACTGTTGTAGCTTCAATCTGTTCCACTGCACCG
* * * * *
6749175 CTAGGGAAGTAAGATTTGCTGTTGTAGCTTCAATCTATTTAACTGCCATGCCAAGGAAGCAAGAT
1 CCAGGGAAGTAAGATTCGCTGTTGTAGCTTCAATCTATTTAACTGCAATGTCGAGGAAGCAAGAT
* *
6749240 TCACTGTTGTAACTTTAATCTGTTCCACTGCACCG
66 TCACTGTTGTAGCTTCAATCTGTTCCACTGCACCG
*
6749275 CTAGGGA
1 CCAGGGA
6749282 GATAAGGTTG
Statistics
Matches: 270, Mismatches: 37, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
100 270 1.00
ACGTcount: A:0.28, C:0.21, G:0.20, T:0.31
Consensus pattern (100 bp):
CCAGGGAAGTAAGATTCGCTGTTGTAGCTTCAATCTATTTAACTGCAATGTCGAGGAAGCAAGAT
TCACTGTTGTAGCTTCAATCTGTTCCACTGCACCG
Found at i:6749325 original size:44 final size:45
Alignment explanation
Indices: 6749252--6749427 Score: 131
Period size: 46 Copynumber: 3.9 Consensus size: 45
6749242 ACTGTTGTAA
* **
6749252 CTTTAATCTGTTCCACTGC-ACCGCTAGGGAGATAAGGTTGG-TGG
1 CTTTAATCTGCTCCACTGCAACTTC-AGGGAGATAAGGTTGGTTGG
** **
6749296 CTTTAATCTGCTCCACTGCAACTTCAGGGAGATAAAATTTGGCCGG
1 CTTTAATCTGCTCCACTGCAACTTCAGGGAGAT-AAGGTTGGTTGG
* * ** * * **
6749342 TCTTCAATCTACTCTGCTGCAACTTCAGAGAGATAAGATTGGTTTAT
1 -CTTTAATCTGCTCCACTGCAACTTCAGGGAGATAAGGTTGG-TTGG
* * * *
6749389 TTTTAACCTGTTCCACTACAACTTCAGGGAGATAAGGTT
1 CTTTAATCTGCTCCACTGCAACTTCAGGGAGATAAGGTT
6749428 TGATGAGATC
Statistics
Matches: 100, Mismatches: 27, Indels: 8
0.74 0.20 0.06
Matches are distributed among these distances:
44 26 0.26
45 9 0.09
46 37 0.37
47 28 0.28
ACGTcount: A:0.26, C:0.21, G:0.22, T:0.32
Consensus pattern (45 bp):
CTTTAATCTGCTCCACTGCAACTTCAGGGAGATAAGGTTGGTTGG
Found at i:6749577 original size:46 final size:45
Alignment explanation
Indices: 6749523--6749704 Score: 170
Period size: 46 Copynumber: 4.0 Consensus size: 45
6749513 TAAAATTCGC
*
6749523 TATCTTCAGTCTACTCTACTACAACTTCAGGGAGATAAGACTTGGT
1 TATCTTCAGTCTACTCTACTGCAACTTCAGGGAGATAAGACTT-GT
* * * *
6749569 TATCTTCAGTGTGCTCCACTGCAACTTTAGGGAGATAAGACTTGT
1 TATCTTCAGTCTACTCTACTGCAACTTCAGGGAGATAAGACTTGT
* * * * * *
6749614 TATAGTGTGA-TCTGCTCTACTGCAACTTTAGAGAGATAAGA-TATAT
1 TAT-CT-TCAGTCTACTCTACTGCAACTTCAGGGAGATAAGACT-TGT
* * * * *
6749660 TATCTTCAGTCTACTGTACTGTAACCTCAGTGAGACAAGACTTGT
1 TATCTTCAGTCTACTCTACTGCAACTTCAGGGAGATAAGACTTGT
6749705 AGCTTCAACT
Statistics
Matches: 110, Mismatches: 21, Indels: 11
0.77 0.15 0.08
Matches are distributed among these distances:
44 2 0.02
45 33 0.30
46 73 0.66
47 2 0.02
ACGTcount: A:0.28, C:0.19, G:0.19, T:0.34
Consensus pattern (45 bp):
TATCTTCAGTCTACTCTACTGCAACTTCAGGGAGATAAGACTTGT
Found at i:6749832 original size:44 final size:44
Alignment explanation
Indices: 6749784--6749901 Score: 191
Period size: 44 Copynumber: 2.7 Consensus size: 44
6749774 CCATCATTTT
* *
6749784 AATCCACTCCACTGTAACTTCAGGGAGATAGGACTAGTAACTTC
1 AATCCGCTCCACTGCAACTTCAGGGAGATAGGACTAGTAACTTC
*
6749828 AATCCGCTCCACTGCAACTTCAGGGAGATAGGGCTAGTAACTTC
1 AATCCGCTCCACTGCAACTTCAGGGAGATAGGACTAGTAACTTC
**
6749872 AATTTGCTCCACTGCAACTTCAGGGAGATA
1 AATCCGCTCCACTGCAACTTCAGGGAGATA
6749902 AGATTTTCCA
Statistics
Matches: 69, Mismatches: 5, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
44 69 1.00
ACGTcount: A:0.30, C:0.25, G:0.20, T:0.25
Consensus pattern (44 bp):
AATCCGCTCCACTGCAACTTCAGGGAGATAGGACTAGTAACTTC
Found at i:6750135 original size:21 final size:21
Alignment explanation
Indices: 6750094--6750137 Score: 61
Period size: 21 Copynumber: 2.1 Consensus size: 21
6750084 GATTCGCTGC
*
6750094 CTTCAGCTTTAATCCCCTCCA
1 CTTCAGCTTTAATCCACTCCA
* *
6750115 CTTCAGCTTTAATCTATTCCA
1 CTTCAGCTTTAATCCACTCCA
6750136 CT
1 CT
6750138 ACAATGCCAA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.20, C:0.36, G:0.05, T:0.39
Consensus pattern (21 bp):
CTTCAGCTTTAATCCACTCCA
Found at i:6750394 original size:45 final size:45
Alignment explanation
Indices: 6750314--6750786 Score: 569
Period size: 45 Copynumber: 10.6 Consensus size: 45
6750304 TTTGGACCTG
* * * *
6750314 CTTCACTGCCAGTACAGGAAGACAAGATCTACTATCTTCGATCTA
1 CTTCGCTGCCAATACAGGAAGACAAGACCTGCTATCTTCGATCTA
** *
6750359 CTTTACTGTCAATACAGGAAGACAAGACCTGCTATCTTCGATCTA
1 CTTCGCTGCCAATACAGGAAGACAAGACCTGCTATCTTCGATCTA
*
6750404 CTTCGCTGCCAATATAGGAAGACAAGACCTGCTATCTTCGATCTA
1 CTTCGCTGCCAATACAGGAAGACAAGACCTGCTATCTTCGATCTA
* * *
6750449 CTTCGTTGCCAATACAGGAAAACAAGACCTGCTATCTTTGATCTA
1 CTTCGCTGCCAATACAGGAAGACAAGACCTGCTATCTTCGATCTA
** * * *
6750494 CTTTACTGCCAATACAGGAAGACAATACCTGATATCTTTGATCTA
1 CTTCGCTGCCAATACAGGAAGACAAGACCTGCTATCTTCGATCTA
*
6750539 CTTCGCTGCCAATACAGGAAGACAAGACTTGCTATCTTCGATCTA
1 CTTCGCTGCCAATACAGGAAGACAAGACCTGCTATCTTCGATCTA
* * * * * *
6750584 CTCCGCTGCCAATATAGGAATACAATATCTGCTATATTCGATCTA
1 CTTCGCTGCCAATACAGGAAGACAAGACCTGCTATCTTCGATCTA
* *
6750629 CTTCGTTACCAATACAGGAAGACAAGACCTGCTATCTTCGATCTA
1 CTTCGCTGCCAATACAGGAAGACAAGACCTGCTATCTTCGATCTA
* * * * *
6750674 CTACGTTGCCAATATAGGAAGACAAGATCTGCTATCTTCGACCTA
1 CTTCGCTGCCAATACAGGAAGACAAGACCTGCTATCTTCGATCTA
* * * * *
6750719 CTCTACTGCTG-C-TTA-GGGAA-ACGAGGCTTG-TATCTTCGATCTA
1 CT-T-C-GCTGCCAATACAGGAAGACAAGACCTGCTATCTTCGATCTA
6750762 CTTCGCTGCCAATACAGGAAGACAA
1 CTTCGCTGCCAATACAGGAAGACAA
6750787 TATCTACAAT
Statistics
Matches: 364, Mismatches: 57, Indels: 15
0.83 0.13 0.03
Matches are distributed among these distances:
40 4 0.01
41 2 0.01
42 3 0.01
43 18 0.05
44 9 0.02
45 321 0.88
46 2 0.01
47 2 0.01
48 3 0.01
ACGTcount: A:0.30, C:0.25, G:0.17, T:0.28
Consensus pattern (45 bp):
CTTCGCTGCCAATACAGGAAGACAAGACCTGCTATCTTCGATCTA
Found at i:6751135 original size:24 final size:24
Alignment explanation
Indices: 6751103--6751154 Score: 77
Period size: 24 Copynumber: 2.2 Consensus size: 24
6751093 ACCGGATTCC
* *
6751103 CCACTATAATCTTCAAGGTTCAAT
1 CCACCATAACCTTCAAGGTTCAAT
*
6751127 CCACCATAACCTTTAAGGTTCAAT
1 CCACCATAACCTTCAAGGTTCAAT
6751151 CCAC
1 CCAC
6751155 TGCACCTTTG
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.33, C:0.31, G:0.08, T:0.29
Consensus pattern (24 bp):
CCACCATAACCTTCAAGGTTCAAT
Done.