Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr09 ID=Chr09-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: 70713020
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 1142373 characters in sequence are not A, C, G, or T
File 77 of 226
Found at i:28284286 original size:78 final size:78
Alignment explanation
Indices: 28284193--28284355 Score: 317
Period size: 78 Copynumber: 2.1 Consensus size: 78
28284183 TTCTTTATTT
28284193 TATTATTTATCATCTTTTTATCTTTTACTTTCCAATTTAGTCATTTTCTTTATTTAGTTTTCTAT
1 TATTATTTATCATCTTTTTATCTTTTACTTTCCAATTTAGTCATTTTCTTTATTTAGTTTTCTAT
28284258 GGATGAATCATCA
66 GGATGAATCATCA
28284271 TATTATTTATCATCTTTTTATCTTTTACTTTCCAATTTAGTCATTTTCTTTATTTAGTTTTCTAT
1 TATTATTTATCATCTTTTTATCTTTTACTTTCCAATTTAGTCATTTTCTTTATTTAGTTTTCTAT
28284336 GGATGAATCATCA
66 GGATGAATCATCA
28284349 TACTTAT
1 TA-TTAT
28284356 CTACTAACTC
Statistics
Matches: 84, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
78 80 0.95
79 4 0.05
ACGTcount: A:0.23, C:0.14, G:0.06, T:0.56
Consensus pattern (78 bp):
TATTATTTATCATCTTTTTATCTTTTACTTTCCAATTTAGTCATTTTCTTTATTTAGTTTTCTAT
GGATGAATCATCA
Found at i:28291386 original size:23 final size:25
Alignment explanation
Indices: 28291272--28291388 Score: 91
Period size: 25 Copynumber: 4.7 Consensus size: 25
28291262 TTTTTATTCT
*
28291272 GGAATGCTCATATGAGCACAT-AAACG
1 GGAA-GCTCATATGAGC-CATGTAACG
* * *
28291298 GGAAACTC-TTTCGAGCCACGTAACG
1 GGAAGCTCATAT-GAGCCATGTAACG
* * *
28291323 GGAAACTCATGTGATCCATGTAACG
1 GGAAGCTCATATGAGCCATGTAACG
*
28291348 GGAAGCTCCAGA-GAGCCAT-T-ACG
1 GGAAGCT-CATATGAGCCATGTAACG
28291371 GGAAGCTCATATGAGCCA
1 GGAAGCTCATATGAGCCA
28291389 ATGTCAGGAA
Statistics
Matches: 74, Mismatches: 12, Indels: 13
0.75 0.12 0.13
Matches are distributed among these distances:
22 3 0.04
23 16 0.22
24 5 0.07
25 42 0.57
26 8 0.11
ACGTcount: A:0.32, C:0.23, G:0.26, T:0.19
Consensus pattern (25 bp):
GGAAGCTCATATGAGCCATGTAACG
Found at i:28293212 original size:22 final size:22
Alignment explanation
Indices: 28293187--28293228 Score: 59
Period size: 22 Copynumber: 1.9 Consensus size: 22
28293177 AAAAAGAAAG
28293187 AAATATCATAAAAC-ATAAAACA
1 AAAT-TCATAAAACAATAAAACA
*
28293209 AAATTGATAAAACAATAAAA
1 AAATTCATAAAACAATAAAA
28293229 TGTTATAGAT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
21 8 0.44
22 10 0.56
ACGTcount: A:0.69, C:0.10, G:0.02, T:0.19
Consensus pattern (22 bp):
AAATTCATAAAACAATAAAACA
Found at i:28294305 original size:21 final size:23
Alignment explanation
Indices: 28294263--28294305 Score: 54
Period size: 21 Copynumber: 2.0 Consensus size: 23
28294253 TAATTAATCA
*
28294263 TAAACAGAAGCAAATCTCTTTTC
1 TAAACAGAAGCAAATATCTTTTC
*
28294286 TAAA-AGAAG-AAATATGTTTT
1 TAAACAGAAGCAAATATCTTTT
28294306 AAAAAATTAA
Statistics
Matches: 18, Mismatches: 2, Indels: 2
0.82 0.09 0.09
Matches are distributed among these distances:
21 9 0.50
22 5 0.28
23 4 0.22
ACGTcount: A:0.44, C:0.12, G:0.12, T:0.33
Consensus pattern (23 bp):
TAAACAGAAGCAAATATCTTTTC
Found at i:28294350 original size:21 final size:21
Alignment explanation
Indices: 28294326--28294381 Score: 53
Period size: 20 Copynumber: 2.7 Consensus size: 21
28294316 CTGAACAATT
*
28294326 AAGAAAAAGA-GAAATACAAAA
1 AAGAAAAAGATCAAAT-CAAAA
*
28294347 AAG-AATAGATCAAATCAAAA
1 AAGAAAAAGATCAAATCAAAA
*
28294367 AAGAAATAGAATCAA
1 AAGAAAAAG-ATCAA
28294382 CAATTTGTTC
Statistics
Matches: 30, Mismatches: 2, Indels: 5
0.81 0.05 0.14
Matches are distributed among these distances:
20 13 0.43
21 12 0.40
22 5 0.17
ACGTcount: A:0.70, C:0.07, G:0.12, T:0.11
Consensus pattern (21 bp):
AAGAAAAAGATCAAATCAAAA
Found at i:28294367 original size:20 final size:23
Alignment explanation
Indices: 28294337--28294381 Score: 69
Period size: 21 Copynumber: 2.1 Consensus size: 23
28294327 AGAAAAAGAG
28294337 AAATACAAAAAAG-AATAG-ATC
1 AAATACAAAAAAGAAATAGAATC
28294358 AAAT-CAAAAAAGAAATAGAATC
1 AAATACAAAAAAGAAATAGAATC
28294380 AA
1 AA
28294382 CAATTTGTTC
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
20 8 0.36
21 9 0.41
22 5 0.23
ACGTcount: A:0.69, C:0.09, G:0.09, T:0.13
Consensus pattern (23 bp):
AAATACAAAAAAGAAATAGAATC
Found at i:28295067 original size:21 final size:22
Alignment explanation
Indices: 28295034--28295079 Score: 58
Period size: 21 Copynumber: 2.1 Consensus size: 22
28295024 GGTTTAGTGG
* *
28295034 TTTCTAAATCCAAAATAAGTTT
1 TTTCCAAATCCAAAATAAGGTT
*
28295056 TTTCCAAA-CCAAAGTAAGGTT
1 TTTCCAAATCCAAAATAAGGTT
28295077 TTT
1 TTT
28295080 AGGTCATTAT
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
21 14 0.67
22 7 0.33
ACGTcount: A:0.37, C:0.15, G:0.09, T:0.39
Consensus pattern (22 bp):
TTTCCAAATCCAAAATAAGGTT
Found at i:28297220 original size:34 final size:34
Alignment explanation
Indices: 28297171--28297350 Score: 227
Period size: 34 Copynumber: 5.3 Consensus size: 34
28297161 GAAGAAATGA
* *
28297171 TGCAAGAAAAT-ATGTGTGACCAGGAAAGATTCCC
1 TGCAAG-AAATGATGCGTGAACAGGAAAGATTCCC
* *
28297205 TGCAAGGAATGATGTGTGAACAGGAAAGATTCCC
1 TGCAAGAAATGATGCGTGAACAGGAAAGATTCCC
* * *
28297239 TGCAAGGAATGATGCATGAACAGGAAAGATTCTC
1 TGCAAGAAATGATGCGTGAACAGGAAAGATTCCC
* * * *
28297273 TGCAAGAAAAGACGAGGTGAACATGAAAGATTCCC
1 TGCAAGAAATGATG-CGTGAACAGGAAAGATTCCC
*
28297308 TGCAAGAAATGATGCGTGAACAGGAAATATTCCC
1 TGCAAGAAATGATGCGTGAACAGGAAAGATTCCC
28297342 TGCAAGAAA
1 TGCAAGAAA
28297351 AGACAAGAAA
Statistics
Matches: 127, Mismatches: 17, Indels: 4
0.86 0.11 0.03
Matches are distributed among these distances:
33 3 0.02
34 96 0.76
35 28 0.22
ACGTcount: A:0.39, C:0.16, G:0.26, T:0.19
Consensus pattern (34 bp):
TGCAAGAAATGATGCGTGAACAGGAAAGATTCCC
Found at i:28297246 original size:17 final size:17
Alignment explanation
Indices: 28297192--28297284 Score: 57
Period size: 17 Copynumber: 5.5 Consensus size: 17
28297182 ATGTGTGACC
28297192 AGGAAAGATTCCCTGCA
1 AGGAAAGATTCCCTGCA
* * *
28297209 AGGAATGATGT--GTGAA
1 AGGAAAGAT-TCCCTGCA
28297225 CAGGAAAGATTCCCTGCA
1 -AGGAAAGATTCCCTGCA
* * * *
28297243 AGGAATGA-TGCATGAA
1 AGGAAAGATTCCCTGCA
*
28297259 CAGGAAAGATTCTCTGCA
1 -AGGAAAGATTCCCTGCA
*
28297277 AGAAAAGA
1 AGGAAAGA
28297285 CGAGGTGAAC
Statistics
Matches: 54, Mismatches: 16, Indels: 12
0.66 0.20 0.15
Matches are distributed among these distances:
16 9 0.17
17 37 0.69
18 8 0.15
ACGTcount: A:0.40, C:0.15, G:0.27, T:0.18
Consensus pattern (17 bp):
AGGAAAGATTCCCTGCA
Found at i:28297312 original size:69 final size:68
Alignment explanation
Indices: 28297191--28297354 Score: 238
Period size: 69 Copynumber: 2.4 Consensus size: 68
28297181 TATGTGTGAC
* * * * *
28297191 CAGGAAAGATTCCCTGCAAGGAATGATGTGTGAACAGGAAAGATTCCCTGCAAGGAATGATGCAT
1 CAGGAAAGATTCCCTGCAAGAAAAGACGGGTGAACAGGAAAGATTCCCTGCAAGAAATGATGCAT
28297256 GAA
66 GAA
* * *
28297259 CAGGAAAGATTCTCTGCAAGAAAAGACGAGGTGAACATGAAAGATTCCCTGCAAGAAATGATGCG
1 CAGGAAAGATTCCCTGCAAGAAAAGACG-GGTGAACAGGAAAGATTCCCTGCAAGAAATGATGCA
28297324 TGAA
65 TGAA
*
28297328 CAGGAAATATTCCCTGCAAGAAAAGAC
1 CAGGAAAGATTCCCTGCAAGAAAAGAC
28297355 AAGAAAAAGA
Statistics
Matches: 85, Mismatches: 10, Indels: 1
0.89 0.10 0.01
Matches are distributed among these distances:
68 24 0.28
69 61 0.72
ACGTcount: A:0.40, C:0.17, G:0.26, T:0.18
Consensus pattern (68 bp):
CAGGAAAGATTCCCTGCAAGAAAAGACGGGTGAACAGGAAAGATTCCCTGCAAGAAATGATGCAT
GAA
Found at i:28298328 original size:8 final size:8
Alignment explanation
Indices: 28298315--28298346 Score: 64
Period size: 8 Copynumber: 4.0 Consensus size: 8
28298305 TCATCAGCTC
28298315 TTATTATT
1 TTATTATT
28298323 TTATTATT
1 TTATTATT
28298331 TTATTATT
1 TTATTATT
28298339 TTATTATT
1 TTATTATT
28298347 CTGAATTTTC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 24 1.00
ACGTcount: A:0.25, C:0.00, G:0.00, T:0.75
Consensus pattern (8 bp):
TTATTATT
Found at i:28300264 original size:17 final size:18
Alignment explanation
Indices: 28300226--28300265 Score: 55
Period size: 17 Copynumber: 2.3 Consensus size: 18
28300216 TAAATTCAAA
*
28300226 TAAAACTCTTAAGTATAC
1 TAAAACTCTTAAGTAAAC
*
28300244 TAAAACTC-TAATTAAAC
1 TAAAACTCTTAAGTAAAC
28300261 TAAAA
1 TAAAA
28300266 TTTCTTGTTG
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
17 12 0.60
18 8 0.40
ACGTcount: A:0.53, C:0.15, G:0.03, T:0.30
Consensus pattern (18 bp):
TAAAACTCTTAAGTAAAC
Found at i:28303419 original size:26 final size:26
Alignment explanation
Indices: 28303383--28303434 Score: 95
Period size: 26 Copynumber: 2.0 Consensus size: 26
28303373 ACTCAGAGTG
28303383 ATAGTTTCTTTTATTCATAATCAAAT
1 ATAGTTTCTTTTATTCATAATCAAAT
*
28303409 ATAGTTTCTTTTATTGATAATCAAAT
1 ATAGTTTCTTTTATTCATAATCAAAT
28303435 TTATCCTTCA
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
26 25 1.00
ACGTcount: A:0.35, C:0.10, G:0.06, T:0.50
Consensus pattern (26 bp):
ATAGTTTCTTTTATTCATAATCAAAT
Found at i:28303473 original size:22 final size:22
Alignment explanation
Indices: 28303445--28303488 Score: 88
Period size: 22 Copynumber: 2.0 Consensus size: 22
28303435 TTATCCTTCA
28303445 AGATTTCCAAGATCTTAGACGG
1 AGATTTCCAAGATCTTAGACGG
28303467 AGATTTCCAAGATCTTAGACGG
1 AGATTTCCAAGATCTTAGACGG
28303489 CATGATGCAA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.32, C:0.18, G:0.23, T:0.27
Consensus pattern (22 bp):
AGATTTCCAAGATCTTAGACGG
Found at i:28304483 original size:106 final size:106
Alignment explanation
Indices: 28304296--28304709 Score: 612
Period size: 106 Copynumber: 3.9 Consensus size: 106
28304286 GAGATTTATG
* * * * * *
28304296 AGGATATTCGGCTATTTGGTCGAACGAAAAATCGAAACCTAACACGTTAGGGTACGTTTTCTCGA
1 AGGATATTTGGCTATTTGGTCGAACGAGAAATCGAAACCCAGCACGTTAGGGCACGTTTCCTCGA
* *
28304361 ATTTCCAAACACAAAATATTGCTTTACTTTGAAATTTTAAA
66 ATTTCCAAACGCAAAATATTGCCTTACTTTGAAATTTTAAA
* * * *
28304402 AGGATATTTGGCTATTTGGTCTAACGAGAACTCGAAACCCAGCATGTTAGGACACGTTTCCTCGA
1 AGGATATTTGGCTATTTGGTCGAACGAGAAATCGAAACCCAGCACGTTAGGGCACGTTTCCTCGA
* * *
28304467 ATTTCGAAACGTAAAATATCGCCTTACTTTGAAATTTTAAA
66 ATTTCCAAACGCAAAATATTGCCTTACTTTGAAATTTTAAA
* * *
28304508 AGGATATTTAGCTATTTGGTCGAACAAGAACTCGAAACCCAGCACGTTAGGGCACGTTTCCTCGA
1 AGGATATTTGGCTATTTGGTCGAACGAGAAATCGAAACCCAGCACGTTAGGGCACGTTTCCTCGA
28304573 ATTTCCAAACGCAAAATATTGCCTTACTTTGAAATTTTAAA
66 ATTTCCAAACGCAAAATATTGCCTTACTTTGAAATTTTAAA
*
28304614 AGGATATTTGGCTATAATTTGGTCGAACGAGAGAAATCGAAACCCAGCACGTTAGGGCACGTTTT
1 AGGATATTTGGC--T-ATTTGGTCGAAC--GAGAAATCGAAACCCAGCACGTTAGGGCACGTTTC
28304679 CTCGAATTTCCAAACGCAAAATATTGCCTTA
61 CTCGAATTTCCAAACGCAAAATATTGCCTTA
28304710 TTTTAAAACT
Statistics
Matches: 276, Mismatches: 27, Indels: 5
0.90 0.09 0.02
Matches are distributed among these distances:
106 200 0.72
108 1 0.00
109 12 0.04
111 63 0.23
ACGTcount: A:0.33, C:0.19, G:0.18, T:0.30
Consensus pattern (106 bp):
AGGATATTTGGCTATTTGGTCGAACGAGAAATCGAAACCCAGCACGTTAGGGCACGTTTCCTCGA
ATTTCCAAACGCAAAATATTGCCTTACTTTGAAATTTTAAA
Found at i:28313105 original size:31 final size:31
Alignment explanation
Indices: 28313070--28313132 Score: 126
Period size: 31 Copynumber: 2.0 Consensus size: 31
28313060 CCCATAAGAT
28313070 CATTGTTTCACAAACATTAACCATTTTAGAA
1 CATTGTTTCACAAACATTAACCATTTTAGAA
28313101 CATTGTTTCACAAACATTAACCATTTTAGAA
1 CATTGTTTCACAAACATTAACCATTTTAGAA
28313132 C
1 C
28313133 TATCACCCAA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
31 32 1.00
ACGTcount: A:0.38, C:0.21, G:0.06, T:0.35
Consensus pattern (31 bp):
CATTGTTTCACAAACATTAACCATTTTAGAA
Found at i:28313410 original size:2 final size:2
Alignment explanation
Indices: 28313403--28313438 Score: 63
Period size: 2 Copynumber: 18.0 Consensus size: 2
28313393 GAGCAAAACC
*
28313403 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AA AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
28313439 TAACATCAAT
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:28317770 original size:12 final size:12
Alignment explanation
Indices: 28317753--28317778 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
28317743 CAAAACAGGC
28317753 TTTTAGCGGCGT
1 TTTTAGCGGCGT
28317765 TTTTAGCGGCGT
1 TTTTAGCGGCGT
28317777 TT
1 TT
28317779 GGACAAAAAA
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:0.08, C:0.15, G:0.31, T:0.46
Consensus pattern (12 bp):
TTTTAGCGGCGT
Found at i:28317837 original size:39 final size:40
Alignment explanation
Indices: 28317784--28317917 Score: 141
Period size: 39 Copynumber: 3.4 Consensus size: 40
28317774 CGTTTGGACA
*
28317784 AAAAACGCCACTAAAAATTAAGCA-TAGCGGCGCTTTTAT-
1 AAAAACGCCGCTAAAAATTAAGCATTAGCGGCGCTTTT-TG
** ** *
28317823 AAAAACGCCGCTAAAGGTCGAGCATTAGCGGCACTTTTTG
1 AAAAACGCCGCTAAAAATTAAGCATTAGCGGCGCTTTTTG
* * *
28317863 GAAAACGCCGCTAAAAA-TAAACATTAGCGGCGTTTTTTG
1 AAAAACGCCGCTAAAAATTAAGCATTAGCGGCGCTTTTTG
*
28317902 AAAAGCGCCGC-AAAAA
1 AAAAACGCCGCTAAAAA
28317918 GCCTAAACCC
Statistics
Matches: 77, Mismatches: 16, Indels: 5
0.79 0.16 0.05
Matches are distributed among these distances:
38 5 0.06
39 46 0.60
40 26 0.34
ACGTcount: A:0.38, C:0.21, G:0.20, T:0.21
Consensus pattern (40 bp):
AAAAACGCCGCTAAAAATTAAGCATTAGCGGCGCTTTTTG
Found at i:28317998 original size:41 final size:41
Alignment explanation
Indices: 28317941--28318225 Score: 441
Period size: 41 Copynumber: 7.0 Consensus size: 41
28317931 CCGATTTTTG
* *
28317941 GGGCCTTTAGCGGCGTTTTTGAAGAAGCGACGCTAATGCTC
1 GGGCCTTTAGCGGCGTTTTTGAGGAAGCGCCGCTAATGCTC
**
28317982 GGGCCTTTAGCGGCGTTTTTGAGGAAGCATCGCTAATGCTC
1 GGGCCTTTAGCGGCGTTTTTGAGGAAGCGCCGCTAATGCTC
* **
28318023 GGACCTTTAGCGGCGTTTTTGAATAAGCGCCGCTAATGCTC
1 GGGCCTTTAGCGGCGTTTTTGAGGAAGCGCCGCTAATGCTC
*
28318064 GGGCTTTTAGCGGCG-TTTTGAGGGAAGCGCCGCTAATGCTC
1 GGGCCTTTAGCGGCGTTTTTGA-GGAAGCGCCGCTAATGCTC
28318105 GGGCCTTTAGCGGCG-TTTTGAGGGAAGCGCCGCTAATGCTC
1 GGGCCTTTAGCGGCGTTTTTGA-GGAAGCGCCGCTAATGCTC
28318146 GGGCCTTTAGCGGCG-TTTTGAGGGAAGCGCCGCTAATGCTC
1 GGGCCTTTAGCGGCGTTTTTGA-GGAAGCGCCGCTAATGCTC
*
28318187 GGGCCTTTAGCGGCGTTTTTGAAGAAGCGCCGCTAATGC
1 GGGCCTTTAGCGGCGTTTTTGAGGAAGCGCCGCTAATGC
28318226 CCGTTTTTGA
Statistics
Matches: 228, Mismatches: 14, Indels: 4
0.93 0.06 0.02
Matches are distributed among these distances:
40 6 0.03
41 216 0.95
42 6 0.03
ACGTcount: A:0.17, C:0.23, G:0.33, T:0.27
Consensus pattern (41 bp):
GGGCCTTTAGCGGCGTTTTTGAGGAAGCGCCGCTAATGCTC
Found at i:28318598 original size:14 final size:14
Alignment explanation
Indices: 28318581--28318617 Score: 65
Period size: 14 Copynumber: 2.6 Consensus size: 14
28318571 GGGTTTAATA
28318581 TATATGGTTTAGGG
1 TATATGGTTTAGGG
*
28318595 TATATGATTTAGGG
1 TATATGGTTTAGGG
28318609 TATATGGTT
1 TATATGGTT
28318618 AATTTAGGAT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.24, C:0.00, G:0.30, T:0.46
Consensus pattern (14 bp):
TATATGGTTTAGGG
Found at i:28318929 original size:14 final size:13
Alignment explanation
Indices: 28318910--28318969 Score: 66
Period size: 14 Copynumber: 4.3 Consensus size: 13
28318900 TAAATAATAT
28318910 TTAGGGGTTAGTAG
1 TTAGGGGTTAG-AG
*
28318924 TTAGGGATTAGGAG
1 TTAGGGGTTA-GAG
28318938 TTAGGGGTTAGATG
1 TTAGGGGTTAGA-G
*
28318952 TTAGAGGTTAAGAG
1 TTAGGGGTT-AGAG
28318966 TTAG
1 TTAG
28318970 TGATTTAGGG
Statistics
Matches: 40, Mismatches: 3, Indels: 6
0.82 0.06 0.12
Matches are distributed among these distances:
13 2 0.05
14 34 0.85
15 4 0.10
ACGTcount: A:0.27, C:0.00, G:0.40, T:0.33
Consensus pattern (13 bp):
TTAGGGGTTAGAG
Found at i:28318954 original size:28 final size:28
Alignment explanation
Indices: 28318910--28318969 Score: 79
Period size: 28 Copynumber: 2.1 Consensus size: 28
28318900 TAAATAATAT
*
28318910 TTAGGGGTTAGTAGTTAG-GGATTAGGAG
1 TTAGGGGTTAGTAGTTAGAGG-TTAAGAG
28318938 TTAGGGGTTAG-ATGTTAGAGGTTAAGAG
1 TTAGGGGTTAGTA-GTTAGAGGTTAAGAG
28318966 TTAG
1 TTAG
28318970 TGATTTAGGG
Statistics
Matches: 29, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
27 1 0.03
28 26 0.90
29 2 0.07
ACGTcount: A:0.27, C:0.00, G:0.40, T:0.33
Consensus pattern (28 bp):
TTAGGGGTTAGTAGTTAGAGGTTAAGAG
Found at i:28323630 original size:43 final size:43
Alignment explanation
Indices: 28323583--28323784 Score: 314
Period size: 43 Copynumber: 4.7 Consensus size: 43
28323573 AAGATATATT
** * *
28323583 TTTAGCGGCGTTTGTGTAAAAAGTGCCGCTAAAGGTCTTGGTC
1 TTTAGCGGCGTTTGTGGGAAAAGCGCCGCTAAAGGTCATGGTC
*
28323626 TTTAGCGGCGTTTGTGGGAAAAGCGTCGCTAAAGGTCATGGTC
1 TTTAGCGGCGTTTGTGGGAAAAGCGCCGCTAAAGGTCATGGTC
* *
28323669 TTTAGCGACGTTTGTGGGAAAAGCGTCGCTAAAGGTCATGGTC
1 TTTAGCGGCGTTTGTGGGAAAAGCGCCGCTAAAGGTCATGGTC
*
28323712 TTTAGCGGCGTTTGTTGGAAAAGCGCCGCTAAAGGTCATGGTC
1 TTTAGCGGCGTTTGTGGGAAAAGCGCCGCTAAAGGTCATGGTC
* *
28323755 TTTAGCAGCGTTTGTGGGAAAAGCGACGCT
1 TTTAGCGGCGTTTGTGGGAAAAGCGCCGCT
28323785 GTCATTAGCG
Statistics
Matches: 147, Mismatches: 12, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
43 147 1.00
ACGTcount: A:0.22, C:0.17, G:0.33, T:0.29
Consensus pattern (43 bp):
TTTAGCGGCGTTTGTGGGAAAAGCGCCGCTAAAGGTCATGGTC
Found at i:28323876 original size:22 final size:21
Alignment explanation
Indices: 28323843--28323887 Score: 72
Period size: 22 Copynumber: 2.1 Consensus size: 21
28323833 TTTAGCGGCG
*
28323843 CTAAAAAACGCCGCTAAAGGC
1 CTAAAAAACGCCGCTAAAAGC
28323864 CTAAAAAAGCGCCGCTAAAAGC
1 CTAAAAAA-CGCCGCTAAAAGC
28323886 CT
1 CT
28323888 GTTTTGGTGT
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
21 8 0.36
22 14 0.64
ACGTcount: A:0.42, C:0.29, G:0.18, T:0.11
Consensus pattern (21 bp):
CTAAAAAACGCCGCTAAAAGC
Found at i:28326404 original size:35 final size:35
Alignment explanation
Indices: 28326358--28326433 Score: 107
Period size: 35 Copynumber: 2.2 Consensus size: 35
28326348 CCCCTTTCGA
* *
28326358 GGTGTCGCCCCGAAGGACTTGCATACCATTTACAC
1 GGTGTCGCCCCGAAGGACCTACATACCATTTACAC
* * *
28326393 GGTGTCGCCCCGAAGGACCTATATATCATTTACAT
1 GGTGTCGCCCCGAAGGACCTACATACCATTTACAC
28326428 GGTGTC
1 GGTGTC
28326434 TCTCTGAAAG
Statistics
Matches: 36, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
35 36 1.00
ACGTcount: A:0.22, C:0.28, G:0.24, T:0.26
Consensus pattern (35 bp):
GGTGTCGCCCCGAAGGACCTACATACCATTTACAC
Found at i:28339681 original size:28 final size:28
Alignment explanation
Indices: 28339641--28339700 Score: 120
Period size: 28 Copynumber: 2.1 Consensus size: 28
28339631 TTTCAAACGG
28339641 AAGTGAACCATTAAAATGGTTTGATGAC
1 AAGTGAACCATTAAAATGGTTTGATGAC
28339669 AAGTGAACCATTAAAATGGTTTGATGAC
1 AAGTGAACCATTAAAATGGTTTGATGAC
28339697 AAGT
1 AAGT
28339701 TTACTTCTAA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 32 1.00
ACGTcount: A:0.40, C:0.10, G:0.22, T:0.28
Consensus pattern (28 bp):
AAGTGAACCATTAAAATGGTTTGATGAC
Found at i:28344218 original size:18 final size:18
Alignment explanation
Indices: 28344178--28344220 Score: 52
Period size: 18 Copynumber: 2.4 Consensus size: 18
28344168 GTTCAAGGTG
28344178 TAATTAATTTAAAATTTT
1 TAATTAATTTAAAATTTT
* *
28344196 CAATTAA-TTAAATTTATT
1 TAATTAATTTAAAATT-TT
28344214 TAATTAA
1 TAATTAA
28344221 AAATCTATTC
Statistics
Matches: 21, Mismatches: 3, Indels: 2
0.81 0.12 0.08
Matches are distributed among these distances:
17 7 0.33
18 14 0.67
ACGTcount: A:0.47, C:0.02, G:0.00, T:0.51
Consensus pattern (18 bp):
TAATTAATTTAAAATTTT
Found at i:28348305 original size:38 final size:38
Alignment explanation
Indices: 28348263--28348339 Score: 154
Period size: 38 Copynumber: 2.0 Consensus size: 38
28348253 ACAAGTCTAA
28348263 CAATTTTTAGGAATTGTGAACTATCTCAGAGATTTTGT
1 CAATTTTTAGGAATTGTGAACTATCTCAGAGATTTTGT
28348301 CAATTTTTAGGAATTGTGAACTATCTCAGAGATTTTGT
1 CAATTTTTAGGAATTGTGAACTATCTCAGAGATTTTGT
28348339 C
1 C
28348340 CCAAAAATCT
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
38 39 1.00
ACGTcount: A:0.29, C:0.12, G:0.18, T:0.42
Consensus pattern (38 bp):
CAATTTTTAGGAATTGTGAACTATCTCAGAGATTTTGT
Found at i:28366959 original size:20 final size:20
Alignment explanation
Indices: 28366920--28366960 Score: 64
Period size: 20 Copynumber: 2.0 Consensus size: 20
28366910 TAATTTTAAA
**
28366920 TTATTTTTAAAATATTTTTT
1 TTATTTTTAAAATAAATTTT
28366940 TTATTTTTAAAATAAATTTT
1 TTATTTTTAAAATAAATTTT
28366960 T
1 T
28366961 GGTGTTTATT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (20 bp):
TTATTTTTAAAATAAATTTT
Found at i:28372549 original size:23 final size:24
Alignment explanation
Indices: 28372522--28372566 Score: 83
Period size: 24 Copynumber: 1.9 Consensus size: 24
28372512 GTATTTCCTT
28372522 TGAC-AAAAAAATATACCCAAAAA
1 TGACAAAAAAAATATACCCAAAAA
28372545 TGACAAAAAAAATATACCCAAA
1 TGACAAAAAAAATATACCCAAA
28372567 GAACAACAAG
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
23 4 0.19
24 17 0.81
ACGTcount: A:0.64, C:0.18, G:0.04, T:0.13
Consensus pattern (24 bp):
TGACAAAAAAAATATACCCAAAAA
Found at i:28374522 original size:17 final size:19
Alignment explanation
Indices: 28374495--28374529 Score: 56
Period size: 18 Copynumber: 1.9 Consensus size: 19
28374485 CAGAGATTTC
28374495 ATAATAA-TTTTAAAAAAT
1 ATAATAATTTTTAAAAAAT
28374513 ATAA-AATTTTTAAAAAA
1 ATAATAATTTTTAAAAAA
28374530 AGGAGCTCAC
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 2 0.12
18 14 0.88
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (19 bp):
ATAATAATTTTTAAAAAAT
Found at i:28377332 original size:15 final size:14
Alignment explanation
Indices: 28377312--28377371 Score: 50
Period size: 15 Copynumber: 4.0 Consensus size: 14
28377302 ACTTATATAT
28377312 TTAATTTAAACTTAA
1 TTAA-TTAAACTTAA
28377327 TTAATTAAGA-TTAA
1 TTAATTAA-ACTTAA
*
28377341 TTTAATTAACCATTAA
1 -TTAATTAAAC-TTAA
*
28377357 CTAATTAAAACTTAA
1 TTAATT-AAACTTAA
28377372 GCATAATTAG
Statistics
Matches: 37, Mismatches: 3, Indels: 10
0.74 0.06 0.20
Matches are distributed among these distances:
14 8 0.22
15 22 0.59
16 7 0.19
ACGTcount: A:0.48, C:0.08, G:0.02, T:0.42
Consensus pattern (14 bp):
TTAATTAAACTTAA
Found at i:28378539 original size:28 final size:28
Alignment explanation
Indices: 28378507--28378572 Score: 89
Period size: 28 Copynumber: 2.4 Consensus size: 28
28378497 TTTTAATTTC
*
28378507 GATTCAATTAACTGCTAAAAGATTAAAA
1 GATTCAATTAACGGCTAAAAGATTAAAA
* *
28378535 GATTCAAATAACGGTTAAAAGATTAAAA
1 GATTCAATTAACGGCTAAAAGATTAAAA
*
28378563 -ATTTAATTAA
1 GATTCAATTAA
28378573 TTAAGTTAAT
Statistics
Matches: 33, Mismatches: 5, Indels: 1
0.85 0.13 0.03
Matches are distributed among these distances:
27 8 0.24
28 25 0.76
ACGTcount: A:0.52, C:0.08, G:0.11, T:0.30
Consensus pattern (28 bp):
GATTCAATTAACGGCTAAAAGATTAAAA
Found at i:28390349 original size:21 final size:21
Alignment explanation
Indices: 28390325--28390365 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
28390315 ACCGCCACCA
* *
28390325 CCACCACCTCCTCCTCCTCCT
1 CCACCACCACCTCCACCTCCT
28390346 CCACCACCACCTCCACCTCC
1 CCACCACCACCTCCACCTCC
28390366 ACCTCTACCT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.15, C:0.68, G:0.00, T:0.17
Consensus pattern (21 bp):
CCACCACCACCTCCACCTCCT
Found at i:28390354 original size:24 final size:24
Alignment explanation
Indices: 28390322--28390370 Score: 80
Period size: 24 Copynumber: 2.0 Consensus size: 24
28390312 GTCACCGCCA
* *
28390322 CCACCACCACCTCCTCCTCCTCCT
1 CCACCACCACCTCCACCTCCACCT
28390346 CCACCACCACCTCCACCTCCACCT
1 CCACCACCACCTCCACCTCCACCT
28390370 C
1 C
28390371 TACCTCTACC
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
24 23 1.00
ACGTcount: A:0.16, C:0.67, G:0.00, T:0.16
Consensus pattern (24 bp):
CCACCACCACCTCCACCTCCACCT
Found at i:28390369 original size:6 final size:6
Alignment explanation
Indices: 28390322--28390386 Score: 67
Period size: 6 Copynumber: 10.8 Consensus size: 6
28390312 GTCACCGCCA
* * * *
28390322 CCACCA CCACCT CCTCCT CCTCCT CCACCA CCACCT CCACCT CCACCT
1 CCACCT CCACCT CCACCT CCACCT CCACCT CCACCT CCACCT CCACCT
* * *
28390370 CTACCT CTACCG CCACC
1 CCACCT CCACCT CCACC
28390387 ACTTCCGTAT
Statistics
Matches: 51, Mismatches: 8, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
6 51 1.00
ACGTcount: A:0.17, C:0.65, G:0.02, T:0.17
Consensus pattern (6 bp):
CCACCT
Found at i:28390450 original size:15 final size:15
Alignment explanation
Indices: 28390432--28390494 Score: 63
Period size: 15 Copynumber: 4.2 Consensus size: 15
28390422 CTGAGCCATG
*
28390432 TCCACCTCCACTACC
1 TCCACCTCCACCACC
*
28390447 TCCACCTCCGCCACC
1 TCCACCTCCACCACC
* * *
28390462 TCCTCCTCCTCTACC
1 TCCACCTCCACCACC
* *
28390477 ACCGCCTCCACCACC
1 TCCACCTCCACCACC
28390492 TCC
1 TCC
28390495 TACACCATTC
Statistics
Matches: 38, Mismatches: 10, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
15 38 1.00
ACGTcount: A:0.14, C:0.63, G:0.03, T:0.19
Consensus pattern (15 bp):
TCCACCTCCACCACC
Found at i:28390470 original size:30 final size:30
Alignment explanation
Indices: 28390436--28390495 Score: 84
Period size: 30 Copynumber: 2.0 Consensus size: 30
28390426 GCCATGTCCA
* *
28390436 CCTCCACTACCTCCACCTCCGCCACCTCCT
1 CCTCCACTACCACCACCTCCACCACCTCCT
* *
28390466 CCTCCTCTACCACCGCCTCCACCACCTCCT
1 CCTCCACTACCACCACCTCCACCACCTCCT
28390496 ACACCATTCC
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
30 26 1.00
ACGTcount: A:0.13, C:0.63, G:0.03, T:0.20
Consensus pattern (30 bp):
CCTCCACTACCACCACCTCCACCACCTCCT
Found at i:28390472 original size:9 final size:9
Alignment explanation
Indices: 28390436--28390494 Score: 50
Period size: 9 Copynumber: 6.6 Consensus size: 9
28390426 GCCATGTCCA
28390436 CCTCCA-CT
1 CCTCCACCT
28390444 ACCTCCACCT
1 -CCTCCACCT
*
28390454 CCGCCACCT
1 CCTCCACCT
*
28390463 CCTCCTCCT
1 CCTCCACCT
*
28390472 -CTACCACCG
1 CCT-CCACCT
*
28390481 CCTCCACCA
1 CCTCCACCT
28390490 CCTCC
1 CCTCC
28390495 TACACCATTC
Statistics
Matches: 41, Mismatches: 6, Indels: 6
0.77 0.11 0.11
Matches are distributed among these distances:
8 2 0.05
9 35 0.85
10 4 0.10
ACGTcount: A:0.14, C:0.64, G:0.03, T:0.19
Consensus pattern (9 bp):
CCTCCACCT
Found at i:28390535 original size:12 final size:12
Alignment explanation
Indices: 28390504--28390545 Score: 57
Period size: 12 Copynumber: 3.5 Consensus size: 12
28390494 CTACACCATT
*
28390504 CCCATACCCAGA
1 CCCATATCCAGA
* *
28390516 CCCGTATCCGGA
1 CCCATATCCAGA
28390528 CCCATATCCAGA
1 CCCATATCCAGA
28390540 CCCATA
1 CCCATA
28390546 CCCTTGGCCT
Statistics
Matches: 25, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
12 25 1.00
ACGTcount: A:0.29, C:0.45, G:0.12, T:0.14
Consensus pattern (12 bp):
CCCATATCCAGA
Found at i:28390616 original size:6 final size:6
Alignment explanation
Indices: 28390565--28390614 Score: 55
Period size: 6 Copynumber: 8.3 Consensus size: 6
28390555 TGAACTAGAG
* ** * *
28390565 CCACCT CCACCT CCACCT CCTCCT CCTTCA CCACCT CCACCT CCTCCT
1 CCACCT CCACCT CCACCT CCACCT CCACCT CCACCT CCACCT CCACCT
28390613 CC
1 CC
28390615 TCTACCATAA
Statistics
Matches: 37, Mismatches: 7, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
6 37 1.00
ACGTcount: A:0.12, C:0.66, G:0.00, T:0.22
Consensus pattern (6 bp):
CCACCT
Found at i:28390696 original size:24 final size:24
Alignment explanation
Indices: 28390651--28390697 Score: 78
Period size: 24 Copynumber: 2.0 Consensus size: 24
28390641 CGGAACCCCT
28390651 TCCAGAACCATACCCTAAACCATA
1 TCCAGAACCATACCCTAAACCATA
28390675 TCCAGAACC-TGACCCTAAACCAT
1 TCCAGAACCAT-ACCCTAAACCAT
28390698 TAGCACCACT
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
23 1 0.05
24 21 0.95
ACGTcount: A:0.38, C:0.38, G:0.06, T:0.17
Consensus pattern (24 bp):
TCCAGAACCATACCCTAAACCATA
Found at i:28390754 original size:15 final size:15
Alignment explanation
Indices: 28390701--28390756 Score: 58
Period size: 15 Copynumber: 3.7 Consensus size: 15
28390691 AAACCATTAG
* *
28390701 CACCACTTCCACCTC
1 CACCACCTCCTCCTC
*
28390716 CACCACTTCCTCCTC
1 CACCACCTCCTCCTC
* * *
28390731 CTCCTCCTCCTCCAC
1 CACCACCTCCTCCTC
28390746 CACCACCTCCT
1 CACCACCTCCT
28390757 TTTCCTATAC
Statistics
Matches: 34, Mismatches: 7, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
15 34 1.00
ACGTcount: A:0.14, C:0.62, G:0.00, T:0.23
Consensus pattern (15 bp):
CACCACCTCCTCCTC
Found at i:28392397 original size:28 final size:30
Alignment explanation
Indices: 28392340--28392397 Score: 75
Period size: 30 Copynumber: 2.0 Consensus size: 30
28392330 ATGGTATTTT
**
28392340 TATAAAAAATTTATTTTTCACTATTTTAAA
1 TATAAAAAATTTATTTTTCACTATCGTAAA
*
28392370 TATAAAATATTTATTTTT-A-TATCGTAAA
1 TATAAAAAATTTATTTTTCACTATCGTAAA
28392398 AATTTAAATT
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
28 7 0.28
29 1 0.04
30 17 0.68
ACGTcount: A:0.43, C:0.05, G:0.02, T:0.50
Consensus pattern (30 bp):
TATAAAAAATTTATTTTTCACTATCGTAAA
Found at i:28396312 original size:19 final size:19
Alignment explanation
Indices: 28396284--28396364 Score: 71
Period size: 19 Copynumber: 4.3 Consensus size: 19
28396274 TTTTTTAACA
*
28396284 ATTTTATATTAATTTTAAT
1 ATTTTTTATTAATTTTAAT
28396303 ATTTTTTATT--TTTT-AT
1 ATTTTTTATTAATTTTAAT
*
28396319 GA-TTTTTATAGAATTTTAAT
1 -ATTTTTTAT-TAATTTTAAT
*
28396339 ATGTTTTTATAAATTTTAAAT
1 AT-TTTTTATTAATTTT-AAT
28396360 ATTTT
1 ATTTT
28396365 AAGTACGTTT
Statistics
Matches: 51, Mismatches: 3, Indels: 15
0.74 0.04 0.22
Matches are distributed among these distances:
16 9 0.18
17 5 0.10
19 14 0.27
20 11 0.22
21 12 0.24
ACGTcount: A:0.32, C:0.00, G:0.04, T:0.64
Consensus pattern (19 bp):
ATTTTTTATTAATTTTAAT
Found at i:28396317 original size:37 final size:37
Alignment explanation
Indices: 28396274--28396348 Score: 98
Period size: 37 Copynumber: 2.0 Consensus size: 37
28396264 TTTTTATGAT
*
28396274 TTTTTTAACAATTTTATATTAATTTTAATAT-TTTTTA
1 TTTTTTAACAATTTTATA-GAATTTTAATATGTTTTTA
** *
28396311 TTTTTTATGATTTTTATAGAATTTTAATATGTTTTTA
1 TTTTTTAACAATTTTATAGAATTTTAATATGTTTTTA
28396348 T
1 T
28396349 AAATTTTAAA
Statistics
Matches: 33, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
36 11 0.33
37 22 0.67
ACGTcount: A:0.29, C:0.01, G:0.04, T:0.65
Consensus pattern (37 bp):
TTTTTTAACAATTTTATAGAATTTTAATATGTTTTTA
Found at i:28396355 original size:48 final size:47
Alignment explanation
Indices: 28396264--28396355 Score: 107
Period size: 48 Copynumber: 1.9 Consensus size: 47
28396254 CCTGTTCAAA
* *
28396264 TTTTTATGATTTTTTTAACAATTTTATATTAATTTTAATATTTTTTAT
1 TTTTTATGATTTTTATAACAATTTTATATT-ATTTTAAAATTTTTTAT
*
28396312 TTTTTATGATTTTTAT-AGAATTTTAATATGT-TTTTATAAATTTT
1 TTTTTATGATTTTTATAACAATTTT-ATAT-TATTTTA-AAATTTT
28396356 AAATATTTTA
Statistics
Matches: 38, Mismatches: 3, Indels: 6
0.81 0.06 0.13
Matches are distributed among these distances:
47 12 0.32
48 25 0.66
49 1 0.03
ACGTcount: A:0.29, C:0.01, G:0.04, T:0.65
Consensus pattern (47 bp):
TTTTTATGATTTTTATAACAATTTTATATTATTTTAAAATTTTTTAT
Found at i:28396364 original size:29 final size:30
Alignment explanation
Indices: 28396285--28396394 Score: 90
Period size: 29 Copynumber: 3.8 Consensus size: 30
28396275 TTTTTAACAA
*
28396285 TTTTATATTAA-TTT-TAATATTTT-TTAT-
1 TTTT-TATTAATTTTATAATATTTTAATATG
* *
28396312 TTTTTATGATTTTTATAGA-ATTTTAATATG
1 TTTTTATTAATTTTATA-ATATTTTAATATG
* *
28396342 TTTTTATAAATTTTA-AATATTTTAAGTACG
1 TTTTTATTAATTTTATAATATTTTAA-TATG
*
28396372 -TTTTATTAATTTTATAATTTTTT
1 TTTTTATTAATTTTATAATATTTT
28396395 TATAATTTAT
Statistics
Matches: 67, Mismatches: 8, Indels: 13
0.76 0.09 0.15
Matches are distributed among these distances:
26 4 0.06
27 7 0.10
28 8 0.12
29 25 0.37
30 23 0.34
ACGTcount: A:0.31, C:0.01, G:0.05, T:0.64
Consensus pattern (30 bp):
TTTTTATTAATTTTATAATATTTTAATATG
Found at i:28396412 original size:27 final size:27
Alignment explanation
Indices: 28396373--28396426 Score: 74
Period size: 27 Copynumber: 2.0 Consensus size: 27
28396363 TTAAGTACGT
*
28396373 TTTATTAATTTTATAATTTTTTTATAA
1 TTTATTAATTTTATAATATTTTTATAA
*
28396400 TTTATTAGA-TTTATTATATTTTTATAA
1 TTTATTA-ATTTTATAATATTTTTATAA
28396427 GGTCGTATCA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
27 23 0.96
28 1 0.04
ACGTcount: A:0.33, C:0.00, G:0.02, T:0.65
Consensus pattern (27 bp):
TTTATTAATTTTATAATATTTTTATAA
Found at i:28396509 original size:9 final size:9
Alignment explanation
Indices: 28396283--28396496 Score: 50
Period size: 9 Copynumber: 22.8 Consensus size: 9
28396273 TTTTTTTAAC
28396283 AATTTTATATT
1 AATTTT-TA-T
*
28396294 AATTTTAAT
1 AATTTTTAT
28396303 -ATTTTT-T
1 AATTTTTAT
*
28396310 ATTTTTTAT
1 AATTTTTAT
*
28396319 GATTTTTAT
1 AATTTTTAT
*
28396328 AGAATTTTAAT
1 --AATTTTTAT
*
28396339 ATGTTTTTAT
1 A-ATTTTTAT
*
28396349 AAATTTTA-
1 AATTTTTAT
28396357 AATATTTTAAGT
1 AAT-TTTT-A-T
**
28396369 ACGTTTTATT
1 AATTTTTA-T
28396379 AA-TTTTAT
1 AATTTTTAT
28396387 AATTTTTTTAT
1 AA--TTTTTAT
28396398 AATTTATTA-
1 AATTT-TTAT
*
28396407 GATTTATTAT
1 AATTT-TTAT
28396417 -ATTTTTAT
1 AATTTTTAT
* **
28396425 AAGGTCGTAT
1 AA-TTTTTAT
**
28396435 CAATTTCCAT
1 -AATTTTTAT
28396445 -ATTTTT-T
1 AATTTTTAT
*
28396452 AATATTTAAT
1 AAT-TTTTAT
*
28396462 TATTTTTAT
1 AATTTTTAT
28396471 -ATTTTTGAT
1 AATTTTT-AT
28396480 AATTTTTTAT
1 AA-TTTTTAT
*
28396490 GATTTTT
1 AATTTTT
28396497 TTTTATAATT
Statistics
Matches: 150, Mismatches: 30, Indels: 48
0.66 0.13 0.21
Matches are distributed among these distances:
7 2 0.01
8 31 0.21
9 55 0.37
10 29 0.19
11 32 0.21
12 1 0.01
ACGTcount: A:0.31, C:0.02, G:0.05, T:0.62
Consensus pattern (9 bp):
AATTTTTAT
Found at i:28396517 original size:23 final size:23
Alignment explanation
Indices: 28396472--28396519 Score: 62
Period size: 23 Copynumber: 2.1 Consensus size: 23
28396462 TATTTTTATA
*
28396472 TTTTTGATAATTTTTTATGATTT
1 TTTTTGATAATTTTTTATAATTT
*
28396495 TTTTTTATAATTTTTCTA-AATTT
1 TTTTTGATAATTTTT-TATAATTT
28396518 TT
1 TT
28396520 AATCATTTCT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
23 20 0.91
24 2 0.09
ACGTcount: A:0.23, C:0.02, G:0.04, T:0.71
Consensus pattern (23 bp):
TTTTTGATAATTTTTTATAATTT
Found at i:28402095 original size:2 final size:2
Alignment explanation
Indices: 28402088--28402116 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
28402078 GTGTTAAGTT
28402088 TA TA 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 TA TA T
28402117 TCTTCAAAGT
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:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:28421712 original size:20 final size:18
Alignment explanation
Indices: 28421687--28421726 Score: 53
Period size: 18 Copynumber: 2.1 Consensus size: 18
28421677 TCATGATGTA
28421687 AATAAATAAAAATATTTTAT
1 AATAAA-AAAAATA-TTTAT
*
28421707 AATAAAAAATATATTTAT
1 AATAAAAAAAATATTTAT
28421725 AA
1 AA
28421727 AATTATTTCA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
18 7 0.37
19 6 0.32
20 6 0.32
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (18 bp):
AATAAAAAAAATATTTAT
Found at i:28421990 original size:24 final size:25
Alignment explanation
Indices: 28421948--28421995 Score: 71
Period size: 24 Copynumber: 2.0 Consensus size: 25
28421938 CGTACATAAT
* *
28421948 AAAATCAAAATATATAAAATAAATC
1 AAAATAAAAATATAAAAAATAAATC
28421973 AAAATAAAAAT-TAAAAAATAAAT
1 AAAATAAAAATATAAAAAATAAAT
28421996 TTATTGTTTT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
24 11 0.52
25 10 0.48
ACGTcount: A:0.73, C:0.04, G:0.00, T:0.23
Consensus pattern (25 bp):
AAAATAAAAATATAAAAAATAAATC
Found at i:28424157 original size:23 final size:24
Alignment explanation
Indices: 28424131--28424179 Score: 57
Period size: 23 Copynumber: 2.1 Consensus size: 24
28424121 TTATATTTTG
*
28424131 ATTTGATT-TTTTTTCTTAATG-AT
1 ATTTGATTATTTTAT-TTAATGTAT
*
28424154 ATTTTATTATTTTATTTAATGTAT
1 ATTTGATTATTTTATTTAATGTAT
28424178 AT
1 AT
28424180 ATATATGTGG
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
23 13 0.59
24 9 0.41
ACGTcount: A:0.27, C:0.02, G:0.06, T:0.65
Consensus pattern (24 bp):
ATTTGATTATTTTATTTAATGTAT
Found at i:28425246 original size:2 final size:2
Alignment explanation
Indices: 28425239--28425288 Score: 100
Period size: 2 Copynumber: 25.0 Consensus size: 2
28425229 AATAGTGGTA
28425239 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
28425281 AT AT AT AT
1 AT AT AT AT
28425289 CTCAAGGATG
Statistics
Matches: 48, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 48 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:28430995 original size:569 final size:569
Alignment explanation
Indices: 28429917--28431048 Score: 2104
Period size: 569 Copynumber: 2.0 Consensus size: 569
28429907 TGTAGGCCAC
*
28429917 CTGACCGATTTTAGCTTCGATAGGATAAGGACCATAGAACCTAGGAGAAAGCTTCTGATTTCGCA
1 CTGACCGATTTTAGCTTCGATAGGATAAGGACCATAGAACCTAGGAGAAAGCTTCTAATTTCGCA
*
28429982 TCTTCCTTAGTGAATCTGTAAGGTTGGAGTTTCAGGTATACTAGGTCCCCAACTTCAAACGACCT
66 TCTTCCTTAGTGAATCAGTAAGGTTGGAGTTTCAGGTATACTAGGTCCCCAACTTCAAACGACCT
*
28430047 ATCTGATGTTTTCTTGTCTGTTAACTGCTTCATTCGTTCTTGAGCTTGCTTCAAGTGGAACTTAA
131 ATCTGATCTTTTCTTGTCTGTTAACTGCTTCATTCGTTCTTGAGCTTGCTTCAAGTGGAACTTAA
28430112 GGAGCTTCCTTAAAGTTTCCCTATGTTGAAGTGTTCTATCCACCTTGGCTACTGTGGAAGACCCT
196 GGAGCTTCCTTAAAGTTTCCCTATGTTGAAGTGTTCTATCCACCTTGGCTACTGTGGAAGACCCT
*
28430177 GGCAGGTATAGTAAGTGAATGTGAGGCTCCTAACCATAGAGGGTTGTGTAAGGAATGGTGTTGAT
261 GGCAGGTATAGTAAGTGAATGTGAGGCTCCTAACCATAGAAGGTTGTGTAAGGAATGGTGTTGAT
* *
28430242 AGTCGAGTGGTGTGTGGTGTTATACCACCACTCTGCCAAAGGTAGCCAATGAACCCATTCTGAAA
326 AGTCGAGTGGTATGTGGTGTTATACCACCACTATGCCAAAGGTAGCCAATGAACCCATTCTGAAA
*
28430307 GTTTCTCACCGGTCATGCATCGCAAATAACCCTCAAGGCACTGATTGAGAACTTCTATTTGCCCA
391 GTTTCTCACCGGTCATGCATCGCAAATAACCCTCAAGGCACTGATTGAAAACTTCTATTTGCCCA
*
28430372 TCTGTTTAGGGATGGTATGGAATAGAGAGGTACAGTCGAGTGCCAAGTAGTTTGAATAGTTCTTG
456 TCTGTTTAGGGATGGTATGGAATAAAGAGGTACAGTCGAGTGCCAAGTAGTTTGAATAGTTCTTG
28430437 CCAAAATCTGCTAAGGAATATCTTGTCTCTGTCAGATACGATGGACCAT
521 CCAAAATCTGCTAAGGAATATCTTGTCTCTGTCAGATACGATGGACCAT
28430486 CTGACCGATTTTAGCTTCGATAGGATAAGGACCATAGAACCTAGGAGAAAGCTTCTAATTTCGCA
1 CTGACCGATTTTAGCTTCGATAGGATAAGGACCATAGAACCTAGGAGAAAGCTTCTAATTTCGCA
*
28430551 TCTTCCTTAGTGAATCAGTAAGGTTGGAGTTTTAGGTATACTAGGTCCCCAACTTCAAACGACCT
66 TCTTCCTTAGTGAATCAGTAAGGTTGGAGTTTCAGGTATACTAGGTCCCCAACTTCAAACGACCT
*
28430616 A-CATGATCTTTTCTTGTCTGTTAACTGCTTCATTCGTTCTTGAGCTTGTTTCAAGTGGAACTTA
131 ATC-TGATCTTTTCTTGTCTGTTAACTGCTTCATTCGTTCTTGAGCTTGCTTCAAGTGGAACTTA
28430680 AGGAGCTTCCTTAAAGTTTCCCTATGTTGAAGTGTTCTATCCACCTTGGCTACTGTGGAAGACCC
195 AGGAGCTTCCTTAAAGTTTCCCTATGTTGAAGTGTTCTATCCACCTTGGCTACTGTGGAAGACCC
* *
28430745 TGGGAGGTATAGTAAGTGAATGTGAGGCTCCTGACCATAGAAGGTTGTGTAAGGAATGGTGTTGA
260 TGGCAGGTATAGTAAGTGAATGTGAGGCTCCTAACCATAGAAGGTTGTGTAAGGAATGGTGTTGA
*
28430810 TAGTCGAGTGGTATGTGGTGTTATACCATCACTATGCCAAAGGTAGCCAATGAACCCATTCTGAA
325 TAGTCGAGTGGTATGTGGTGTTATACCACCACTATGCCAAAGGTAGCCAATGAACCCATTCTGAA
* *
28430875 AGTTTCTCATCGGTCATGCATCGCAAATAACCCTCAAGGCACTGATTGAAAACTTTTATTTGCCC
390 AGTTTCTCACCGGTCATGCATCGCAAATAACCCTCAAGGCACTGATTGAAAACTTCTATTTGCCC
*
28430940 ATCTGTTTGGGGATGGTATGGAATAAAGAGGTACAGTCGAGTGCCAAGTAGTTTGAATAGTTCTT
455 ATCTGTTTAGGGATGGTATGGAATAAAGAGGTACAGTCGAGTGCCAAGTAGTTTGAATAGTTCTT
28431005 GCCAAAATCTGCTAAGGAATATCTTGTCTCTGTCAGATACGATG
520 GCCAAAATCTGCTAAGGAATATCTTGTCTCTGTCAGATACGATG
28431049 AACTCTGGAA
Statistics
Matches: 546, Mismatches: 16, Indels: 2
0.97 0.03 0.00
Matches are distributed among these distances:
568 1 0.00
569 545 1.00
ACGTcount: A:0.26, C:0.19, G:0.23, T:0.31
Consensus pattern (569 bp):
CTGACCGATTTTAGCTTCGATAGGATAAGGACCATAGAACCTAGGAGAAAGCTTCTAATTTCGCA
TCTTCCTTAGTGAATCAGTAAGGTTGGAGTTTCAGGTATACTAGGTCCCCAACTTCAAACGACCT
ATCTGATCTTTTCTTGTCTGTTAACTGCTTCATTCGTTCTTGAGCTTGCTTCAAGTGGAACTTAA
GGAGCTTCCTTAAAGTTTCCCTATGTTGAAGTGTTCTATCCACCTTGGCTACTGTGGAAGACCCT
GGCAGGTATAGTAAGTGAATGTGAGGCTCCTAACCATAGAAGGTTGTGTAAGGAATGGTGTTGAT
AGTCGAGTGGTATGTGGTGTTATACCACCACTATGCCAAAGGTAGCCAATGAACCCATTCTGAAA
GTTTCTCACCGGTCATGCATCGCAAATAACCCTCAAGGCACTGATTGAAAACTTCTATTTGCCCA
TCTGTTTAGGGATGGTATGGAATAAAGAGGTACAGTCGAGTGCCAAGTAGTTTGAATAGTTCTTG
CCAAAATCTGCTAAGGAATATCTTGTCTCTGTCAGATACGATGGACCAT
Found at i:28434941 original size:18 final size:20
Alignment explanation
Indices: 28434908--28434950 Score: 63
Period size: 19 Copynumber: 2.2 Consensus size: 20
28434898 GGGATTAAAT
28434908 TGGAAAGATGTTGAA-TTTA
1 TGGAAAGATGTTGAATTTTA
*
28434927 TGGAAA-ATTTTGAATTTTA
1 TGGAAAGATGTTGAATTTTA
28434946 TGGAA
1 TGGAA
28434951 TACATGGATT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
18 7 0.32
19 15 0.68
ACGTcount: A:0.37, C:0.00, G:0.23, T:0.40
Consensus pattern (20 bp):
TGGAAAGATGTTGAATTTTA
Found at i:28435671 original size:26 final size:26
Alignment explanation
Indices: 28435603--28435672 Score: 113
Period size: 26 Copynumber: 2.7 Consensus size: 26
28435593 TTTCTGATTA
* *
28435603 TGGCTCTTCGTGAGCTCCCCGTTAAT
1 TGGCTCTTTGTGAGCTTCCCGTTAAT
*
28435629 TGGCTCTTTGCGAGCTTCCCGTTAAT
1 TGGCTCTTTGTGAGCTTCCCGTTAAT
28435655 TGGCTCTTTGTGAGCTTC
1 TGGCTCTTTGTGAGCTTC
28435673 TCGATATGGC
Statistics
Matches: 40, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
26 40 1.00
ACGTcount: A:0.10, C:0.27, G:0.24, T:0.39
Consensus pattern (26 bp):
TGGCTCTTTGTGAGCTTCCCGTTAAT
Found at i:28436041 original size:38 final size:38
Alignment explanation
Indices: 28435999--28436075 Score: 154
Period size: 38 Copynumber: 2.0 Consensus size: 38
28435989 TGCAAAAACT
28435999 ATGATATGTACATGTTCCTTGGAAACTTGAAATGATAA
1 ATGATATGTACATGTTCCTTGGAAACTTGAAATGATAA
28436037 ATGATATGTACATGTTCCTTGGAAACTTGAAATGATAA
1 ATGATATGTACATGTTCCTTGGAAACTTGAAATGATAA
28436075 A
1 A
28436076 CACATGTATG
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
38 39 1.00
ACGTcount: A:0.38, C:0.10, G:0.18, T:0.34
Consensus pattern (38 bp):
ATGATATGTACATGTTCCTTGGAAACTTGAAATGATAA
Found at i:28437153 original size:52 final size:52
Alignment explanation
Indices: 28437080--28437183 Score: 208
Period size: 52 Copynumber: 2.0 Consensus size: 52
28437070 TACCTGGACA
28437080 AAGAAATAGTGTCAGTCCAGGGCCTTGCCTTCAAGATGGAGCATGACTACCT
1 AAGAAATAGTGTCAGTCCAGGGCCTTGCCTTCAAGATGGAGCATGACTACCT
28437132 AAGAAATAGTGTCAGTCCAGGGCCTTGCCTTCAAGATGGAGCATGACTACCT
1 AAGAAATAGTGTCAGTCCAGGGCCTTGCCTTCAAGATGGAGCATGACTACCT
28437184 TCACCTTAGC
Statistics
Matches: 52, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
52 52 1.00
ACGTcount: A:0.29, C:0.23, G:0.25, T:0.23
Consensus pattern (52 bp):
AAGAAATAGTGTCAGTCCAGGGCCTTGCCTTCAAGATGGAGCATGACTACCT
Found at i:28437724 original size:15 final size:15
Alignment explanation
Indices: 28437706--28437738 Score: 57
Period size: 15 Copynumber: 2.2 Consensus size: 15
28437696 AGAAGAATAG
*
28437706 GAAGAATAGGAGGAA
1 GAAGAATAAGAGGAA
28437721 GAAGAATAAGAGGAA
1 GAAGAATAAGAGGAA
28437736 GAA
1 GAA
28437739 AAAGGAGTAA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.58, C:0.00, G:0.36, T:0.06
Consensus pattern (15 bp):
GAAGAATAAGAGGAA
Found at i:28438360 original size:95 final size:95
Alignment explanation
Indices: 28438197--28438385 Score: 378
Period size: 95 Copynumber: 2.0 Consensus size: 95
28438187 AGATTTACAC
28438197 ATTCATTAGTGTTGTAATTTTAACATGACATAAAATACGACAGAGCGAGCATTGTCTTGACGATG
1 ATTCATTAGTGTTGTAATTTTAACATGACATAAAATACGACAGAGCGAGCATTGTCTTGACGATG
28438262 AGCAACAACCAACCAAACACCAACGAATTT
66 AGCAACAACCAACCAAACACCAACGAATTT
28438292 ATTCATTAGTGTTGTAATTTTAACATGACATAAAATACGACAGAGCGAGCATTGTCTTGACGATG
1 ATTCATTAGTGTTGTAATTTTAACATGACATAAAATACGACAGAGCGAGCATTGTCTTGACGATG
28438357 AGCAACAACCAACCAAACACCAACGAATT
66 AGCAACAACCAACCAAACACCAACGAATT
28438386 AAACATAGGT
Statistics
Matches: 94, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
95 94 1.00
ACGTcount: A:0.39, C:0.20, G:0.16, T:0.25
Consensus pattern (95 bp):
ATTCATTAGTGTTGTAATTTTAACATGACATAAAATACGACAGAGCGAGCATTGTCTTGACGATG
AGCAACAACCAACCAAACACCAACGAATTT
Found at i:28439472 original size:51 final size:51
Alignment explanation
Indices: 28439412--28439512 Score: 193
Period size: 51 Copynumber: 2.0 Consensus size: 51
28439402 AAAGATTATA
*
28439412 AACTTTTAATTGGTGAAGTAGAACAAATATACAATATGAGTCTACAAAGAC
1 AACTTTTAATTGGTGAAGTAGAACAAATATACAATATGAGCCTACAAAGAC
28439463 AACTTTTAATTGGTGAAGTAGAACAAATATACAATATGAGCCTACAAAGA
1 AACTTTTAATTGGTGAAGTAGAACAAATATACAATATGAGCCTACAAAGA
28439513 AAAAGGAATG
Statistics
Matches: 49, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
51 49 1.00
ACGTcount: A:0.46, C:0.12, G:0.16, T:0.27
Consensus pattern (51 bp):
AACTTTTAATTGGTGAAGTAGAACAAATATACAATATGAGCCTACAAAGAC
Found at i:28441272 original size:263 final size:263
Alignment explanation
Indices: 28440748--28441278 Score: 1001
Period size: 263 Copynumber: 2.0 Consensus size: 263
28440738 AACAGTAGGA
* **
28440748 TATCTGGTTTGTTGACTATATAAAAGTAGGGTAATACTCAAACCAAGAAAGAACCAACCATTAAA
1 TATCTGGTTTGTTGACCATATAAAAGTAGGGTAATACAAAAACCAAGAAAGAACCAACCATTAAA
*
28440813 GAAAACGAGACTGAACCAGTAAAAACCCAGCTTTATAAATATATTTTTCTTCTTGTTTTCAAAAC
66 AAAAACGAGACTGAACCAGTAAAAACCCAGCTTTATAAATATATTTTTCTTCTTGTTTTCAAAAC
28440878 TTTATTCCTAATCAATGAGATTTGAACCATTAACCTCTTGATTTTATAATAAAGATCTTACCAAT
131 TTTATTCCTAATCAATGAGATTTGAACCATTAACCTCTTGATTTTATAATAAAGATCTTACCAAT
28440943 TACCATTAAGCCAAATGTACTTTGTGTTAATTATAAACCATATTTATTATTTATTATACATAAAA
196 TACCATTAAGCCAAATGTACTTTGTGTTAATTATAAACCATATTTATTATTTATTATACATAAAA
28441008 TAG
261 TAG
28441011 TATCTGGTTTGTTGACCATATAAAAGTAGGGTAATACAAAAACCAAGAAAGAACCAACCATTAAA
1 TATCTGGTTTGTTGACCATATAAAAGTAGGGTAATACAAAAACCAAGAAAGAACCAACCATTAAA
*
28441076 AAAAACGAGACTGAACCAGTAAAAACCCAGCTTTGTAAATATATTTTTCTTCTTGTTTTCAAAAC
66 AAAAACGAGACTGAACCAGTAAAAACCCAGCTTTATAAATATATTTTTCTTCTTGTTTTCAAAAC
28441141 -TTATTCCTAATCAATGAGATTTGAACCATTAACCTCTTGATTTTATAATAAAGATCTTACCAAT
131 TTTATTCCTAATCAATGAGATTTGAACCATTAACCTCTTGATTTTATAATAAAGATCTTACCAAT
28441205 TACCATTAAGCCAAATGTACTTTGTGTTAATTATAAACCATATTTATTATTTATTATACATTAAA
196 TACCATTAAGCCAAATGTACTTTGTGTTAATTATAAACCATATTTATTATTTATTATACA-TAAA
28441270 ATAG
260 ATAG
28441274 TATCT
1 TATCT
28441279 AGACATAAAA
Statistics
Matches: 262, Mismatches: 5, Indels: 2
0.97 0.02 0.01
Matches are distributed among these distances:
262 124 0.47
263 138 0.53
ACGTcount: A:0.39, C:0.16, G:0.10, T:0.35
Consensus pattern (263 bp):
TATCTGGTTTGTTGACCATATAAAAGTAGGGTAATACAAAAACCAAGAAAGAACCAACCATTAAA
AAAAACGAGACTGAACCAGTAAAAACCCAGCTTTATAAATATATTTTTCTTCTTGTTTTCAAAAC
TTTATTCCTAATCAATGAGATTTGAACCATTAACCTCTTGATTTTATAATAAAGATCTTACCAAT
TACCATTAAGCCAAATGTACTTTGTGTTAATTATAAACCATATTTATTATTTATTATACATAAAA
TAG
Found at i:28447766 original size:3 final size:3
Alignment explanation
Indices: 28447760--28447789 Score: 53
Period size: 3 Copynumber: 10.3 Consensus size: 3
28447750 TCGCGGATGA
28447760 TGG TGG TGG T-G TGG TGG TGG TGG TGG TGG T
1 TGG TGG TGG TGG TGG TGG TGG TGG TGG TGG T
28447790 TGTCGTCGAC
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
2 2 0.08
3 24 0.92
ACGTcount: A:0.00, C:0.00, G:0.63, T:0.37
Consensus pattern (3 bp):
TGG
Found at i:28450372 original size:25 final size:25
Alignment explanation
Indices: 28450344--28450391 Score: 87
Period size: 25 Copynumber: 1.9 Consensus size: 25
28450334 TTACCAAAAA
*
28450344 TGGAAAATAAAATTGAAGATAACAG
1 TGGAAAATAAAATTAAAGATAACAG
28450369 TGGAAAATAAAATTAAAGATAAC
1 TGGAAAATAAAATTAAAGATAAC
28450392 TTGTAAAATT
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
25 22 1.00
ACGTcount: A:0.58, C:0.04, G:0.17, T:0.21
Consensus pattern (25 bp):
TGGAAAATAAAATTAAAGATAACAG
Found at i:28451895 original size:12 final size:10
Alignment explanation
Indices: 28451868--28451936 Score: 75
Period size: 11 Copynumber: 6.4 Consensus size: 10
28451858 CAACTAAATC
28451868 ATTTCTCTCA
1 ATTTCTCTCA
28451878 ATTTCTCTCTA
1 ATTTCTCTC-A
28451889 ATATTCTCTCA
1 AT-TTCTCTCA
*
28451900 AATTCATCTCA
1 ATTTC-TCTCA
28451911 ATTTCCTCTCA
1 ATTT-CTCTCA
*
28451922 AATTCGTCTCA
1 ATTTC-TCTCA
28451933 ATTT
1 ATTT
28451937 TCTATTTAAA
Statistics
Matches: 50, Mismatches: 4, Indels: 9
0.79 0.06 0.14
Matches are distributed among these distances:
10 13 0.26
11 29 0.58
12 8 0.16
ACGTcount: A:0.25, C:0.28, G:0.01, T:0.46
Consensus pattern (10 bp):
ATTTCTCTCA
Found at i:28451895 original size:22 final size:21
Alignment explanation
Indices: 28451868--28451936 Score: 86
Period size: 22 Copynumber: 3.2 Consensus size: 21
28451858 CAACTAAATC
*
28451868 ATTTCTCTCAATTTC-TCTCTA
1 ATTTCTCTCAAATTCATCTC-A
28451889 ATATTCTCTCAAATTCATCTCA
1 AT-TTCTCTCAAATTCATCTCA
*
28451911 ATTTCCTCTCAAATTCGTCTCA
1 ATTT-CTCTCAAATTCATCTCA
28451933 ATTT
1 ATTT
28451937 TCTATTTAAA
Statistics
Matches: 43, Mismatches: 2, Indels: 5
0.86 0.04 0.10
Matches are distributed among these distances:
21 4 0.09
22 35 0.81
23 4 0.09
ACGTcount: A:0.25, C:0.28, G:0.01, T:0.46
Consensus pattern (21 bp):
ATTTCTCTCAAATTCATCTCA
Found at i:28452004 original size:14 final size:13
Alignment explanation
Indices: 28451981--28452013 Score: 50
Period size: 13 Copynumber: 2.5 Consensus size: 13
28451971 TTAAAAAAAG
28451981 TTTT-AAATTTTAT
1 TTTTAAAATTTT-T
28451994 TTTTAAAATTTTT
1 TTTTAAAATTTTT
28452007 TTTTAAA
1 TTTTAAA
28452014 TCGTAAAAAT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
13 12 0.63
14 7 0.37
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (13 bp):
TTTTAAAATTTTT
Found at i:28453796 original size:18 final size:18
Alignment explanation
Indices: 28453773--28453815 Score: 59
Period size: 18 Copynumber: 2.4 Consensus size: 18
28453763 TGCATGGTGC
* *
28453773 GTATCCTAGCCCTTTTAT
1 GTATCCTAACCCTTATAT
28453791 GTATCCTAACCCTTATAT
1 GTATCCTAACCCTTATAT
*
28453809 GTTTCCT
1 GTATCCT
28453816 TTTTCTAGTC
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 22 1.00
ACGTcount: A:0.19, C:0.28, G:0.09, T:0.44
Consensus pattern (18 bp):
GTATCCTAACCCTTATAT
Found at i:28454081 original size:21 final size:21
Alignment explanation
Indices: 28454057--28454117 Score: 61
Period size: 21 Copynumber: 2.9 Consensus size: 21
28454047 CAACACCGAT
28454057 AACCAG-ATCCCCTACCGGAGG
1 AACCAGAATCCCC-ACCGGAGG
* *
28454078 AACCAGAATCCCCGCCGGAGT
1 AACCAGAATCCCCACCGGAGG
* * *
28454099 AACCACAACCCCCGCCGGA
1 AACCAGAATCCCCACCGGA
28454118 AGCTGGACAA
Statistics
Matches: 35, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
21 29 0.83
22 6 0.17
ACGTcount: A:0.30, C:0.43, G:0.21, T:0.07
Consensus pattern (21 bp):
AACCAGAATCCCCACCGGAGG
Found at i:28457800 original size:126 final size:126
Alignment explanation
Indices: 28457511--28457918 Score: 633
Period size: 125 Copynumber: 3.3 Consensus size: 126
28457501 TGCGCAACTA
* * * *
28457511 TAGCAAAAGCGCGTCCACATGGGAGCTTCTTTCAGTACTTCTACTGA-AAAGGCATCCTGTTTAA
1 TAGCAAAAGCGCATCCACGTGGGAGCTTCTTTCAGTACTTCTGCTGACAAA-GCATCCTGCTTAA
* ** *
28457575 AGCATTTTTGATACTATTTGCTCAGAAACGTCTACTCGAAATTATTTTTT-AGGAGCTATTG
65 AGCATTTTTGACACTATTTGCTTGGAAACGTCTACTCGAAATTATTTTTTCAGGAGCTACTG
* * *
28457636 TAGCAAAAGCGCGTCCACGTGGGAGCTTCTTTCAGTACTTTTGCTGACAAAGCATTCTGCTTAAA
1 TAGCAAAAGCGCATCCACGTGGGAGCTTCTTTCAGTACTTCTGCTGACAAAGCATCCTGCTTAAA
* *
28457701 GCATTTTTGACACTGTTTGCTTGGAAATGTCTACTCGAAATTATTTTTTCAGGAGCTACTG
66 GCATTTTTGACACTATTTGCTTGGAAACGTCTACTCGAAATTATTTTTTCAGGAGCTACTG
28457762 TAGCAAAAGCGCATCCACGTGGGAGCTTCTTTCAGTACTTCTGCTGACAAAGCATCCTGCTTAAA
1 TAGCAAAAGCGCATCCACGTGGGAGCTTCTTTCAGTACTTCTGCTGACAAAGCATCCTGCTTAAA
* * *
28457827 GC-TTTTTTACACTATTTGCTTGGAAACGTCTACTCGAAATTAATTTTTCAGAAGCTACTG
66 GCATTTTTGACACTATTTGCTTGGAAACGTCTACTCGAAATTATTTTTTCAGGAGCTACTG
*
28457887 TAGCAAAAGTGCATCCACGTGGGAGCTTCTTT
1 TAGCAAAAGCGCATCCACGTGGGAGCTTCTTT
28457919 AAATTAGCAA
Statistics
Matches: 261, Mismatches: 20, Indels: 4
0.92 0.07 0.01
Matches are distributed among these distances:
125 184 0.70
126 77 0.30
ACGTcount: A:0.26, C:0.21, G:0.19, T:0.34
Consensus pattern (126 bp):
TAGCAAAAGCGCATCCACGTGGGAGCTTCTTTCAGTACTTCTGCTGACAAAGCATCCTGCTTAAA
GCATTTTTGACACTATTTGCTTGGAAACGTCTACTCGAAATTATTTTTTCAGGAGCTACTG
Found at i:28458210 original size:96 final size:93
Alignment explanation
Indices: 28457951--28458254 Score: 304
Period size: 96 Copynumber: 3.2 Consensus size: 93
28457941 AGTAACCCTA
* **
28457951 AACCCCAAACCCTAATTTATTTGAGTTTTTACTTAAAAACCCTAAATCCTAAACCCTAATCTAAT
1 AACCCTAAACCCTAATTTATTTGA-TTTTTACTTAAAAA-ATTAAA-CCTAAACCCTAATCTAAT
28458016 TTTATAAAAATTTATAATTAATTTACTCAAGT
63 TTT-TAAAAATTTATAATTAATTTACTCAAGT
* * * * * * *
28458048 AACCCTGAACCCTAATTTATTTGATTTTTCCTTAAAAACCTTTAGCTCTAAACCCTTATCTGATT
1 AACCCTAAACCCTAATTTATTTGATTTTTACTTAAAAA-ATTAAAC-CTAAACCCTAATCTAATT
* * *
28458113 TTTAAATGATTTTTAATTAAATTACTCAAGT
64 TTTAAA-AATTTATAATTAATTTACTCAAGT
* * * *
28458144 AACCCTAAACCCTAATTTAATTGATTTTTTCTTAAAAAATAATAAACACGAAA-CCTAATCCAAT
1 AACCCTAAACCCTAATTTATTTGATTTTTACTTAAAAAAT--TAAAC-CTAAACCCTAATCTAAT
* * ** **
28458208 TTTGAAAAATTTATAATTAATTTAATTGACA
63 TTTTAAAAATTTATAATTAATTTACTCAAGT
28458239 AACCCTAAACCCTAAT
1 AACCCTAAACCCTAAT
28458255 CCCTTATTTA
Statistics
Matches: 172, Mismatches: 31, Indels: 10
0.81 0.15 0.05
Matches are distributed among these distances:
95 38 0.22
96 105 0.61
97 29 0.17
ACGTcount: A:0.39, C:0.19, G:0.04, T:0.38
Consensus pattern (93 bp):
AACCCTAAACCCTAATTTATTTGATTTTTACTTAAAAAATTAAACCTAAACCCTAATCTAATTTT
TAAAAATTTATAATTAATTTACTCAAGT
Found at i:28460253 original size:2 final size:2
Alignment explanation
Indices: 28460246--28460276 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
28460236 CAGTTAAGTC
28460246 TA TA TA 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 TA TA TA T
28460277 GATAATAAAC
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:28460601 original size:11 final size:12
Alignment explanation
Indices: 28460576--28460605 Score: 53
Period size: 12 Copynumber: 2.6 Consensus size: 12
28460566 ATTTATATAA
28460576 ATAAAAAATATT
1 ATAAAAAATATT
28460588 ATAAAAAATA-T
1 ATAAAAAATATT
28460599 ATAAAAA
1 ATAAAAA
28460606 CACAATGCAA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
11 8 0.44
12 10 0.56
ACGTcount: A:0.73, C:0.00, G:0.00, T:0.27
Consensus pattern (12 bp):
ATAAAAAATATT
Found at i:28461012 original size:19 final size:19
Alignment explanation
Indices: 28460974--28461019 Score: 56
Period size: 19 Copynumber: 2.4 Consensus size: 19
28460964 CATTAAAATC
** *
28460974 TAAGAGATAATTATATTTT
1 TAAGAGATAAAAATAATTT
28460993 TAAGAGATAAAAATAATTT
1 TAAGAGATAAAAATAATTT
*
28461012 TAATAGAT
1 TAAGAGAT
28461020 TTATGTTAAT
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
19 23 1.00
ACGTcount: A:0.50, C:0.00, G:0.11, T:0.39
Consensus pattern (19 bp):
TAAGAGATAAAAATAATTT
Found at i:28461360 original size:29 final size:30
Alignment explanation
Indices: 28461323--28461386 Score: 71
Period size: 31 Copynumber: 2.2 Consensus size: 30
28461313 CGTTTTTCGT
**
28461323 TTTTATCACCT-ATG-T-TTAAAATTTTCTA
1 TTTTATCA-CTAATGTTATTAAAATTTAATA
28461351 TTTTAGTCACTAATGTTATTAAAATTTAATA
1 TTTTA-TCACTAATGTTATTAAAATTTAATA
28461382 TTTTA
1 TTTTA
28461387 ATTACTCATC
Statistics
Matches: 30, Mismatches: 2, Indels: 5
0.81 0.05 0.14
Matches are distributed among these distances:
28 7 0.23
29 6 0.20
30 1 0.03
31 16 0.53
ACGTcount: A:0.33, C:0.09, G:0.05, T:0.53
Consensus pattern (30 bp):
TTTTATCACTAATGTTATTAAAATTTAATA
Found at i:28464918 original size:12 final size:12
Alignment explanation
Indices: 28464898--28464927 Score: 51
Period size: 12 Copynumber: 2.5 Consensus size: 12
28464888 GACGTACGCT
*
28464898 CGTGCCCTAGCC
1 CGTGTCCTAGCC
28464910 CGTGTCCTAGCC
1 CGTGTCCTAGCC
28464922 CGTGTC
1 CGTGTC
28464928 TGAACTAATG
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
12 17 1.00
ACGTcount: A:0.07, C:0.43, G:0.27, T:0.23
Consensus pattern (12 bp):
CGTGTCCTAGCC
Found at i:28465190 original size:65 final size:65
Alignment explanation
Indices: 28464975--28465190 Score: 254
Period size: 65 Copynumber: 3.3 Consensus size: 65
28464965 AGCCACACGT
* * * ** * * *
28464975 CCGTGTGCTAGGCTGTGTGAAAAATGGTGAGCATGTTGACTTATGACACACGGTCAAGCCACATG
1 CCGTGTGCTAGGCTGTGTGAAAAATGTTGGGTATACTGACTTATGTCACACGGCCAA-CCACATA
*
28465040 G
65 C
* * *
28465041 CCGTGTGCTAGGCTGTATGAAAAATGTTGGGTATACTGACTTGTATCACACGGCCAACCACATAC
1 CCGTGTGCTAGGCTGTGTGAAAAATGTTGGGTATACTGACTTATGTCACACGGCCAACCACATAC
* * * *
28465106 CCGTGTGCTAAG-TCCTGTGAAAAATGTTGGGTATACTGACTTATGTCACATGGCCAACCACACA
1 CCGTGTGCTAGGCT-GTGTGAAAAATGTTGGGTATACTGACTTATGTCACACGGCCAACCACATA
28465170 C
65 C
*
28465171 CCGTGTGCTAGGCAGTGTGA
1 CCGTGTGCTAGGCTGTGTGA
28465191 GGCTACTGAC
Statistics
Matches: 126, Mismatches: 22, Indels: 5
0.82 0.14 0.03
Matches are distributed among these distances:
64 1 0.01
65 78 0.62
66 47 0.37
ACGTcount: A:0.26, C:0.22, G:0.26, T:0.25
Consensus pattern (65 bp):
CCGTGTGCTAGGCTGTGTGAAAAATGTTGGGTATACTGACTTATGTCACACGGCCAACCACATAC
Found at i:28465441 original size:133 final size:133
Alignment explanation
Indices: 28465203--28465467 Score: 469
Period size: 133 Copynumber: 2.0 Consensus size: 133
28465193 CTACTGACTT
*
28465203 GTGTTCTTTAAAAGTTACAGGGGACACACAATCGTGTCACTTGGCCGTGTGTCACACACGGCTGA
1 GTGTTCTTTAAAAGTTACAGGGGACACACAATCGTGTCACCTGGCCGTGTGTCACACACGGCTGA
*
28465268 GACACACGCCCATGTGGACAAAAATAGGCCATTTTTCAAGCCATATTTCTCACCCAAATTTGTAC
66 GACACACGCCCATGTGGACAAAAATAGGCCATTTTCCAAGCCATATTTCTCACCCAAATTTGTAC
28465333 CAC
131 CAC
*
28465336 GTGTTCTTTAAAAGTTACAGGGGACACACGA-CTGTGTCACCTGGCCGTGTGTCACACACGGCTG
1 GTGTTCTTTAAAAGTTACAGGGGACACACAATC-GTGTCACCTGGCCGTGTGTCACACACGGCTG
* *
28465400 AGACACACGCCCGTGTGGACAAAAATAGGTCATTTTCCAAGCCATATTTCTCACCCAAATTTGTA
65 AGACACACGCCCATGTGGACAAAAATAGGCCATTTTCCAAGCCATATTTCTCACCCAAATTTGTA
28465465 CCA
130 CCA
28465468 ACCTAAACAC
Statistics
Matches: 126, Mismatches: 5, Indels: 2
0.95 0.04 0.02
Matches are distributed among these distances:
132 1 0.01
133 125 0.99
ACGTcount: A:0.28, C:0.26, G:0.20, T:0.25
Consensus pattern (133 bp):
GTGTTCTTTAAAAGTTACAGGGGACACACAATCGTGTCACCTGGCCGTGTGTCACACACGGCTGA
GACACACGCCCATGTGGACAAAAATAGGCCATTTTCCAAGCCATATTTCTCACCCAAATTTGTAC
CAC
Found at i:28470111 original size:24 final size:24
Alignment explanation
Indices: 28470084--28470154 Score: 81
Period size: 24 Copynumber: 3.0 Consensus size: 24
28470074 TATGGCTATT
* *
28470084 CGGTGCTTCCTGTTAAGTGCTCTC
1 CGGTGCTACCCGTTAAGTGCTCTC
*
28470108 CGGTGCTACCCGTTAAGTGCTCTT
1 CGGTGCTACCCGTTAAGTGCTCTC
* *
28470132 CGGAGCTACCAGTTATAG-GCTCT
1 CGGTGCTACCCGTTA-AGTGCTCT
28470155 TTGTGAGCTT
Statistics
Matches: 41, Mismatches: 5, Indels: 2
0.85 0.10 0.04
Matches are distributed among these distances:
24 39 0.95
25 2 0.05
ACGTcount: A:0.14, C:0.28, G:0.25, T:0.32
Consensus pattern (24 bp):
CGGTGCTACCCGTTAAGTGCTCTC
Found at i:28470171 original size:25 final size:25
Alignment explanation
Indices: 28470095--28470173 Score: 83
Period size: 24 Copynumber: 3.2 Consensus size: 25
28470085 GGTGCTTCCT
* *
28470095 GTTA-AGTGCTCTCCGGTGCTACCC
1 GTTATAGTGCTCTTCGGAGCTACCC
*
28470119 GTTA-AGTGCTCTTCGGAGCTACCA
1 GTTATAGTGCTCTTCGGAGCTACCC
* *
28470143 GTTATAG-GCTCTTTGTGAGCTTCCC
1 GTTATAGTGCTCTTCG-GAGCTACCC
28470168 GTTATA
1 GTTATA
28470174 TTGCCCGGAT
Statistics
Matches: 47, Mismatches: 6, Indels: 3
0.84 0.11 0.05
Matches are distributed among these distances:
24 32 0.68
25 15 0.32
ACGTcount: A:0.16, C:0.25, G:0.24, T:0.34
Consensus pattern (25 bp):
GTTATAGTGCTCTTCGGAGCTACCC
Found at i:28475826 original size:54 final size:54
Alignment explanation
Indices: 28475760--28475894 Score: 202
Period size: 54 Copynumber: 2.5 Consensus size: 54
28475750 CTGAATTAAG
28475760 TCACACGGCCAAGCCACACGCCCGTGTGAAAAATGGTGAGCATACTGACTTGTGA
1 TCACACGGCCAAGCCACACGCCCGTGTGAAAAATGGTGAGCATACTGACTTGT-A
* * * *
28475815 -CACACGCCCAAGCCACACGCCCGTGTGAAAAATGTTGGGTATACTGACTTGTA
1 TCACACGGCCAAGCCACACGCCCGTGTGAAAAATGGTGAGCATACTGACTTGTA
*
28475868 TCACATGGCCAA-CCACACGCCCGTGTG
1 TCACACGGCCAAGCCACACGCCCGTGTG
28475895 CTAGGCCGTG
Statistics
Matches: 73, Mismatches: 6, Indels: 4
0.88 0.07 0.05
Matches are distributed among these distances:
53 16 0.22
54 57 0.78
ACGTcount: A:0.27, C:0.30, G:0.24, T:0.19
Consensus pattern (54 bp):
TCACACGGCCAAGCCACACGCCCGTGTGAAAAATGGTGAGCATACTGACTTGTA
Found at i:28478849 original size:95 final size:95
Alignment explanation
Indices: 28478679--28478867 Score: 324
Period size: 95 Copynumber: 2.0 Consensus size: 95
28478669 AAATTCTACA
*
28478679 AATTTGGAAATAATTTAATTGAGTCGATTTATTCGATGTGGAATTAAATGAGGTGGTCATGAGAA
1 AATTTGGAAATAATTTAATTGAGTCGATTTATTCGATGTGGAATTAAATGAGGTAGTCATGAGAA
*
28478744 TTATTTAACTAGAGAATTTGATTAAAGAAG
66 TTATTCAACTAGAGAATTTGATTAAAGAAG
* * *
28478774 AATTTGGAAATAATTTAATTGAGTTGATTTATTCGATGTGGAATTAAATTAGGTAGTCGTGAGAA
1 AATTTGGAAATAATTTAATTGAGTCGATTTATTCGATGTGGAATTAAATGAGGTAGTCATGAGAA
*
28478839 TTGTTCAACTAGAGAATTTGATTAAAGAA
66 TTATTCAACTAGAGAATTTGATTAAAGAA
28478868 TTTTCTTGAA
Statistics
Matches: 88, Mismatches: 6, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
95 88 1.00
ACGTcount: A:0.38, C:0.04, G:0.22, T:0.37
Consensus pattern (95 bp):
AATTTGGAAATAATTTAATTGAGTCGATTTATTCGATGTGGAATTAAATGAGGTAGTCATGAGAA
TTATTCAACTAGAGAATTTGATTAAAGAAG
Found at i:28479343 original size:12 final size:12
Alignment explanation
Indices: 28479326--28479384 Score: 54
Period size: 12 Copynumber: 5.1 Consensus size: 12
28479316 TTTTAATAAG
28479326 ATTTAATATTAA
1 ATTTAATATTAA
*
28479338 ATTTAAT-CTAA
1 ATTTAATATTAA
28479349 TATTT-ATA-TAA
1 -ATTTAATATTAA
*
28479360 ATATT-AGATTAA
1 AT-TTAATATTAA
28479372 ATTTAATATTAA
1 ATTTAATATTAA
28479384 A
1 A
28479385 GTGATTAATT
Statistics
Matches: 39, Mismatches: 3, Indels: 10
0.75 0.06 0.19
Matches are distributed among these distances:
10 2 0.05
11 14 0.36
12 23 0.59
ACGTcount: A:0.49, C:0.02, G:0.02, T:0.47
Consensus pattern (12 bp):
ATTTAATATTAA
Found at i:28479469 original size:26 final size:24
Alignment explanation
Indices: 28479440--28479489 Score: 64
Period size: 25 Copynumber: 2.0 Consensus size: 24
28479430 AGTTGTAGAG
*
28479440 AGAAAATTCTCTAAAGAGATTATTTC
1 AGAAAATT-TATAAAGAGATT-TTTC
*
28479466 AGAAAATTTATAAAGATATTTTTC
1 AGAAAATTTATAAAGAGATTTTTC
28479490 TAATTTACAA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
24 4 0.18
25 10 0.45
26 8 0.36
ACGTcount: A:0.44, C:0.08, G:0.10, T:0.38
Consensus pattern (24 bp):
AGAAAATTTATAAAGAGATTTTTC
Found at i:28484204 original size:29 final size:30
Alignment explanation
Indices: 28484145--28484202 Score: 89
Period size: 30 Copynumber: 1.9 Consensus size: 30
28484135 TCCGAGCCTT
*
28484145 GGGGCAAAAATGTAATTATGTAAAAGTTTA
1 GGGGCAAAAATGTAATTATGAAAAAGTTTA
* *
28484175 GGGGCAAAATTGTAATTTTGAAAAAGTT
1 GGGGCAAAAATGTAATTATGAAAAAGTT
28484203 AGAGTCGAGG
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
30 25 1.00
ACGTcount: A:0.41, C:0.03, G:0.24, T:0.31
Consensus pattern (30 bp):
GGGGCAAAAATGTAATTATGAAAAAGTTTA
Found at i:28484651 original size:50 final size:50
Alignment explanation
Indices: 28484540--28484788 Score: 291
Period size: 50 Copynumber: 4.8 Consensus size: 50
28484530 ATTTGGGTAA
*
28484540 AGAGATCCCATGTAAGACCATGTCTGGGACATGGCATTGGCATCCTTGAGATCATG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCA-CC--GAG---ATG
**
28484596 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGTGTTGGCACCGAGATG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCGAGATG
* * *
28484646 AGAGGTCTCATGTAAGACCATGTCTGGGACATGACATTGGCACCGAGATA
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCGAGATG
*** * * *
28484696 AGAGGTCCCCCATAAGACCATGTCTGGGACACGGCATGGGCACCGATATG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCGAGATG
** * *
28484746 AGAATATCCCATGTAAGACCATGTTTGGGACATGGCTTTGGCA
1 AG-AGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCA
28484789 TGTTATGATC
Statistics
Matches: 166, Mismatches: 26, Indels: 7
0.83 0.13 0.04
Matches are distributed among these distances:
50 91 0.55
51 31 0.19
53 3 0.02
55 2 0.01
56 39 0.23
ACGTcount: A:0.27, C:0.22, G:0.29, T:0.22
Consensus pattern (50 bp):
AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCGAGATG
Found at i:28492479 original size:21 final size:21
Alignment explanation
Indices: 28492455--28492546 Score: 139
Period size: 21 Copynumber: 4.3 Consensus size: 21
28492445 AGTTTTGGAT
*
28492455 TAGTATTTTGTATGAATATTG
1 TAGTTTTTTGTATGAATATTG
28492476 TAGTTTTTTGTATGAATATTG
1 TAGTTTTTTGTATGAATATTG
*
28492497 TAATTTTTTGTATGAATATTG
1 TAGTTTTTTGTATGAATATTG
*
28492518 TAATTTTTTTGTATGAATATTG
1 T-AGTTTTTTGTATGAATATTG
*
28492540 TAATTTT
1 TAGTTTT
28492547 GTAATTTTGT
Statistics
Matches: 66, Mismatches: 4, Indels: 2
0.92 0.06 0.03
Matches are distributed among these distances:
21 46 0.70
22 20 0.30
ACGTcount: A:0.27, C:0.00, G:0.15, T:0.58
Consensus pattern (21 bp):
TAGTTTTTTGTATGAATATTG
Found at i:28492540 original size:43 final size:42
Alignment explanation
Indices: 28492460--28492546 Score: 156
Period size: 43 Copynumber: 2.0 Consensus size: 42
28492450 TGGATTAGTA
28492460 TTTTGTATGAATATTGTAGTTTTTTGTATGAATATTGTAATT
1 TTTTGTATGAATATTGTAGTTTTTTGTATGAATATTGTAATT
*
28492502 TTTTGTATGAATATTGTAATTTTTTTGTATGAATATTGTAATT
1 TTTTGTATGAATATTGT-AGTTTTTTGTATGAATATTGTAATT
28492545 TT
1 TT
28492547 GTAATTTTGT
Statistics
Matches: 43, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
42 17 0.40
43 26 0.60
ACGTcount: A:0.26, C:0.00, G:0.15, T:0.59
Consensus pattern (42 bp):
TTTTGTATGAATATTGTAGTTTTTTGTATGAATATTGTAATT
Found at i:28492678 original size:25 final size:24
Alignment explanation
Indices: 28492611--28492695 Score: 66
Period size: 26 Copynumber: 3.3 Consensus size: 24
28492601 TGTATGAATA
*
28492611 TTGTAATTATTTTATAATTAATTTG
1 TTGTAATTA-TTTAAAATTAATTTG
*
28492636 TTAGTAATT-TATATAAATT-ATTGTG
1 TT-GTAATTATTTA-AAATTAATT-TG
*
28492661 TGTGTAATTATTTAAAATTTAATTTA
1 T-TGTAATTATTTAAAA-TTAATTTG
28492687 TTAGTAATT
1 TT-GTAATT
28492696 TAGGATTAAG
Statistics
Matches: 48, Mismatches: 4, Indels: 15
0.72 0.06 0.22
Matches are distributed among these distances:
24 6 0.12
25 19 0.40
26 20 0.42
27 3 0.06
ACGTcount: A:0.35, C:0.00, G:0.09, T:0.55
Consensus pattern (24 bp):
TTGTAATTATTTAAAATTAATTTG
Found at i:28492802 original size:38 final size:38
Alignment explanation
Indices: 28492757--28492837 Score: 128
Period size: 37 Copynumber: 2.2 Consensus size: 38
28492747 CATATAAAGT
28492757 TTATAAAAAAATAAAAAATCATTTTATTAAAAGTTTAA
1 TTATAAAAAAATAAAAAATCATTTTATTAAAAGTTTAA
* * *
28492795 TTAT-AAAAAATTAAAATTTATTTTATTAAAAGTTTAA
1 TTATAAAAAAATAAAAAATCATTTTATTAAAAGTTTAA
28492832 TTATAA
1 TTATAA
28492838 CCGACTTTTT
Statistics
Matches: 39, Mismatches: 3, Indels: 2
0.89 0.07 0.05
Matches are distributed among these distances:
37 34 0.87
38 5 0.13
ACGTcount: A:0.54, C:0.01, G:0.02, T:0.42
Consensus pattern (38 bp):
TTATAAAAAAATAAAAAATCATTTTATTAAAAGTTTAA
Found at i:28492915 original size:15 final size:15
Alignment explanation
Indices: 28492874--28492915 Score: 57
Period size: 16 Copynumber: 2.7 Consensus size: 15
28492864 GTTAACTCAT
*
28492874 TTAATTTTTATATAA
1 TTAACTTTTATATAA
28492889 TGTAACTTTTATATAA
1 T-TAACTTTTATATAA
*
28492905 TTAAGTTTTAT
1 TTAACTTTTAT
28492916 TTGATTTTGT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
15 10 0.42
16 14 0.58
ACGTcount: A:0.36, C:0.02, G:0.05, T:0.57
Consensus pattern (15 bp):
TTAACTTTTATATAA
Found at i:28496572 original size:22 final size:23
Alignment explanation
Indices: 28496547--28496600 Score: 76
Period size: 22 Copynumber: 2.4 Consensus size: 23
28496537 ATACCTTATT
*
28496547 TTTTTCTTCT-TTTCCTTCCTTC
1 TTTTTCTTCTGCTTCCTTCCTTC
28496569 -TTTTCTTCTGCTTCCTTCCTTC
1 TTTTTCTTCTGCTTCCTTCCTTC
28496591 TTATTTCTTC
1 TT-TTTCTTC
28496601 CGTTTCTCTA
Statistics
Matches: 28, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
21 9 0.32
22 11 0.39
23 1 0.04
24 7 0.25
ACGTcount: A:0.02, C:0.31, G:0.02, T:0.65
Consensus pattern (23 bp):
TTTTTCTTCTGCTTCCTTCCTTC
Found at i:28496572 original size:24 final size:22
Alignment explanation
Indices: 28496540--28496600 Score: 61
Period size: 24 Copynumber: 2.7 Consensus size: 22
28496530 AACCAAAATA
*
28496540 CCTTATTTTTTTCTTCTTTTCCTT
1 CCTTCTTTTTTTCTTC--TTCCTT
* *
28496564 CCTTCTTTTCTTCTGCTTCCTT
1 CCTTCTTTTTTTCTTCTTCCTT
*
28496586 CCTTC-TTATTTCTTC
1 CCTTCTTTTTTTCTTC
28496601 CGTTTCTCTA
Statistics
Matches: 31, Mismatches: 6, Indels: 3
0.77 0.15 0.08
Matches are distributed among these distances:
21 7 0.23
22 11 0.35
24 13 0.42
ACGTcount: A:0.03, C:0.31, G:0.02, T:0.64
Consensus pattern (22 bp):
CCTTCTTTTTTTCTTCTTCCTT
Found at i:28498886 original size:36 final size:36
Alignment explanation
Indices: 28498808--28498888 Score: 94
Period size: 36 Copynumber: 2.2 Consensus size: 36
28498798 ACGAGGTTTA
* *
28498808 GGATTGAATTGTAGAATAAGAAAATATGTGTTTGAG
1 GGATTAAATTGTAGAATAAGAAAATATGTGTTTAAG
* *
28498844 GAATTAAATTGTAGAAT-AGTAAAATTTG-GATTTAAG
1 GGATTAAATTGTAGAATAAG-AAAATATGTG-TTTAAG
28498880 GGATTAAAT
1 GGATTAAAT
28498889 CGTAAAAAAT
Statistics
Matches: 38, Mismatches: 5, Indels: 4
0.81 0.11 0.09
Matches are distributed among these distances:
35 3 0.08
36 35 0.92
ACGTcount: A:0.42, C:0.00, G:0.23, T:0.35
Consensus pattern (36 bp):
GGATTAAATTGTAGAATAAGAAAATATGTGTTTAAG
Found at i:28503393 original size:18 final size:17
Alignment explanation
Indices: 28503363--28503396 Score: 50
Period size: 18 Copynumber: 1.9 Consensus size: 17
28503353 TCTCTTATAG
*
28503363 TTTGATTTTATTTTAAT
1 TTTGATTTAATTTTAAT
28503380 TTTGAATTTAATTTTAA
1 TTTG-ATTTAATTTTAA
28503397 GAATTAGATC
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 4 0.27
18 11 0.73
ACGTcount: A:0.29, C:0.00, G:0.06, T:0.65
Consensus pattern (17 bp):
TTTGATTTAATTTTAAT
Found at i:28513038 original size:41 final size:38
Alignment explanation
Indices: 28512980--28513055 Score: 98
Period size: 38 Copynumber: 1.9 Consensus size: 38
28512970 CCGAATATAA
*
28512980 TAAATATATATTTTTATTTTATTTTTAATTTTAAAATACTT
1 TAAAAATATATTTTTA--TT-TTTTTAATTTTAAAATACTT
* *
28513021 TAAAAATATTTTTTTATTTTTTTATTTTTAAAATA
1 TAAAAATATATTTTTATTTTTTTAATTTTAAAATA
28513056 TTTTTTTGTG
Statistics
Matches: 32, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
38 16 0.50
39 2 0.06
41 14 0.44
ACGTcount: A:0.37, C:0.01, G:0.00, T:0.62
Consensus pattern (38 bp):
TAAAAATATATTTTTATTTTTTTAATTTTAAAATACTT
Found at i:28515040 original size:9 final size:9
Alignment explanation
Indices: 28515026--28515070 Score: 54
Period size: 9 Copynumber: 5.0 Consensus size: 9
28515016 AAACCTCTAA
28515026 GCCTCCGCC
1 GCCTCCGCC
28515035 GCCTCCGCC
1 GCCTCCGCC
*
28515044 GCCACCGCC
1 GCCTCCGCC
* * *
28515053 TCCGCCACC
1 GCCTCCGCC
28515062 GCCTCCGCC
1 GCCTCCGCC
28515071 TCCGCTTCCG
Statistics
Matches: 29, Mismatches: 7, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
9 29 1.00
ACGTcount: A:0.04, C:0.67, G:0.20, T:0.09
Consensus pattern (9 bp):
GCCTCCGCC
Found at i:28515051 original size:6 final size:6
Alignment explanation
Indices: 28515027--28515091 Score: 76
Period size: 6 Copynumber: 10.8 Consensus size: 6
28515017 AACCTCTAAG
* * * * *
28515027 CCTCCG CCGCCT CCGCCG CCACCG CCTCCG CCACCG CCTCCG CCTCCG
1 CCTCCG CCTCCG CCTCCG CCTCCG CCTCCG CCTCCG CCTCCG CCTCCG
*
28515075 CTTCCG CCTCCG CCTCC
1 CCTCCG CCTCCG CCTCC
28515092 ACCACTGCCA
Statistics
Matches: 50, Mismatches: 9, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
6 50 1.00
ACGTcount: A:0.03, C:0.66, G:0.17, T:0.14
Consensus pattern (6 bp):
CCTCCG
Found at i:28515063 original size:18 final size:18
Alignment explanation
Indices: 28515042--28515101 Score: 66
Period size: 18 Copynumber: 3.3 Consensus size: 18
28515032 GCCGCCTCCG
28515042 CCGCCACCGCCTCCGCCA
1 CCGCCACCGCCTCCGCCA
* **
28515060 CCGCCTCCGCCTCCGCTT
1 CCGCCACCGCCTCCGCCA
* *
28515078 CCGCCTCCGCCTCCACCA
1 CCGCCACCGCCTCCGCCA
*
28515096 CTGCCA
1 CCGCCA
28515102 TCATTTGCTC
Statistics
Matches: 34, Mismatches: 8, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
18 34 1.00
ACGTcount: A:0.08, C:0.63, G:0.15, T:0.13
Consensus pattern (18 bp):
CCGCCACCGCCTCCGCCA
Found at i:28518947 original size:12 final size:12
Alignment explanation
Indices: 28518932--28518967 Score: 56
Period size: 12 Copynumber: 3.0 Consensus size: 12
28518922 TGTTGATATG
28518932 GATGATAGTTAT
1 GATGATAGTTAT
28518944 GATGA-AGATTAT
1 GATGATAG-TTAT
28518956 GATGATAGTTAT
1 GATGATAGTTAT
28518968 AACTACTCTG
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
11 2 0.09
12 18 0.82
13 2 0.09
ACGTcount: A:0.36, C:0.00, G:0.25, T:0.39
Consensus pattern (12 bp):
GATGATAGTTAT
Found at i:28521032 original size:17 final size:17
Alignment explanation
Indices: 28521010--28521046 Score: 65
Period size: 17 Copynumber: 2.2 Consensus size: 17
28521000 ATGATTAATA
28521010 TAATTTTTAACATTTTT
1 TAATTTTTAACATTTTT
*
28521027 TAATTTTTAATATTTTT
1 TAATTTTTAACATTTTT
28521044 TAA
1 TAA
28521047 ATTATTAAGT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.32, C:0.03, G:0.00, T:0.65
Consensus pattern (17 bp):
TAATTTTTAACATTTTT
Found at i:28524204 original size:43 final size:43
Alignment explanation
Indices: 28524117--28524326 Score: 217
Period size: 43 Copynumber: 4.9 Consensus size: 43
28524107 AGCTCGTACA
* ** * *** *
28524117 ATGCCAACATCCCAGACATGGTCTTACATGTATTTACAAATCG
1 ATGCCAACGTCCCAGATGTGGTCTTACACGTAAACACAAGTCG
28524160 ATGCC-ACTGTCCCAGATAG-GGTCTTACACGTAAACACAAGTCG
1 ATGCCAAC-GTCCCAGAT-GTGGTCTTACACGTAAACACAAGTCG
* * * *
28524203 ATGCCAACATCCAAGATGTGGTCTTACACGTAAACATAAGTAG
1 ATGCCAACGTCCCAGATGTGGTCTTACACGTAAACACAAGTCG
** * * *
28524246 ATGTTAATGTCCCAGATGTGGTCTTACACGTAAACATAAGTCC
1 ATGCCAACGTCCCAGATGTGGTCTTACACGTAAACACAAGTCG
* *
28524289 ATGCCAACGTTCCAGACGTGGTCTTACACGTAAACACA
1 ATGCCAACGTCCCAGATGTGGTCTTACACGTAAACACA
28524327 TATTGAAAAT
Statistics
Matches: 138, Mismatches: 25, Indels: 8
0.81 0.15 0.05
Matches are distributed among these distances:
42 3 0.02
43 133 0.96
44 2 0.01
ACGTcount: A:0.32, C:0.25, G:0.18, T:0.25
Consensus pattern (43 bp):
ATGCCAACGTCCCAGATGTGGTCTTACACGTAAACACAAGTCG
Found at i:28524262 original size:86 final size:86
Alignment explanation
Indices: 28524167--28524324 Score: 248
Period size: 86 Copynumber: 1.8 Consensus size: 86
28524157 TCGATGCCAC
* *
28524167 TGTCCCAGATAG-GGTCTTACACGTAAACACAAGTCGATGCCAAC-ATCCAAGATGTGGTCTTAC
1 TGTCCCAGAT-GTGGTCTTACACGTAAACACAAGTCCATGCCAACGATCC-AGACGTGGTCTTAC
28524230 ACGTAAACATAAGTAGATGTTAA
64 ACGTAAACATAAGTAGATGTTAA
* *
28524253 TGTCCCAGATGTGGTCTTACACGTAAACATAAGTCCATGCCAACGTTCCAGACGTGGTCTTACAC
1 TGTCCCAGATGTGGTCTTACACGTAAACACAAGTCCATGCCAACGATCCAGACGTGGTCTTACAC
28524318 GTAAACA
66 GTAAACA
28524325 CATATTGAAA
Statistics
Matches: 66, Mismatches: 4, Indels: 4
0.89 0.05 0.05
Matches are distributed among these distances:
85 1 0.02
86 62 0.94
87 3 0.05
ACGTcount: A:0.32, C:0.23, G:0.20, T:0.25
Consensus pattern (86 bp):
TGTCCCAGATGTGGTCTTACACGTAAACACAAGTCCATGCCAACGATCCAGACGTGGTCTTACAC
GTAAACATAAGTAGATGTTAA
Found at i:28529719 original size:18 final size:18
Alignment explanation
Indices: 28529696--28529733 Score: 76
Period size: 18 Copynumber: 2.1 Consensus size: 18
28529686 TTACCAATGC
28529696 TCTTGGTGTGGGTTTAAG
1 TCTTGGTGTGGGTTTAAG
28529714 TCTTGGTGTGGGTTTAAG
1 TCTTGGTGTGGGTTTAAG
28529732 TC
1 TC
28529734 CAATCTCATG
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.11, C:0.08, G:0.37, T:0.45
Consensus pattern (18 bp):
TCTTGGTGTGGGTTTAAG
Found at i:28532334 original size:43 final size:43
Alignment explanation
Indices: 28532272--28532459 Score: 261
Period size: 43 Copynumber: 4.3 Consensus size: 43
28532262 ATGACCTTTA
*
28532272 ACAAACGCCGCTAAAGACCACGACCTTTAGCGGCGATTTTTTC
1 ACAAACGCCGCTAATGACCACGACCTTTAGCGGCGATTTTTTC
* * **
28532315 ACAAACGCCGCTAATGACCAGGACCTTTAGCGGCGCTTTTGCC
1 ACAAACGCCGCTAATGACCACGACCTTTAGCGGCGATTTTTTC
*
28532358 ACAAACGCCGCTAAAGACC-CTGACCTTTAGCGGCGATTTTTTCC
1 ACAAACGCCGCTAATGACCAC-GACCTTTAGCGGCGATTTTTT-C
* * *
28532402 ACAAACGCCGCTAATGACAACGACCTTTAGCGGCGCTTTTTTA
1 ACAAACGCCGCTAATGACCACGACCTTTAGCGGCGATTTTTTC
*
28532445 AAAAACGCCGCTAAT
1 ACAAACGCCGCTAAT
28532460 TTTGGCAGAT
Statistics
Matches: 127, Mismatches: 15, Indels: 6
0.86 0.10 0.04
Matches are distributed among these distances:
43 88 0.69
44 38 0.30
45 1 0.01
ACGTcount: A:0.28, C:0.30, G:0.19, T:0.23
Consensus pattern (43 bp):
ACAAACGCCGCTAATGACCACGACCTTTAGCGGCGATTTTTTC
Found at i:28532439 original size:87 final size:86
Alignment explanation
Indices: 28532272--28532441 Score: 297
Period size: 86 Copynumber: 2.0 Consensus size: 86
28532262 ATGACCTTTA
* *
28532272 ACAAACGCCGCTAAAGACCACGACCTTTAGCGGCGATTTTTTCACAAACGCCGCTAATGACCAGG
1 ACAAACGCCGCTAAAGACCACGACCTTTAGCGGCGATTTTTTCACAAACGCCGCTAATGACAACG
28532337 ACCTTTAGCGGCGCTTTTGCC
66 ACCTTTAGCGGCGCTTTTGCC
28532358 ACAAACGCCGCTAAAGACC-CTGACCTTTAGCGGCGATTTTTTCCACAAACGCCGCTAATGACAA
1 ACAAACGCCGCTAAAGACCAC-GACCTTTAGCGGCGATTTTTT-CACAAACGCCGCTAATGACAA
28532422 CGACCTTTAGCGGCGCTTTT
64 CGACCTTTAGCGGCGCTTTT
28532442 TTAAAAAACG
Statistics
Matches: 80, Mismatches: 2, Indels: 3
0.94 0.02 0.04
Matches are distributed among these distances:
85 1 0.01
86 40 0.50
87 39 0.49
ACGTcount: A:0.26, C:0.31, G:0.20, T:0.23
Consensus pattern (86 bp):
ACAAACGCCGCTAAAGACCACGACCTTTAGCGGCGATTTTTTCACAAACGCCGCTAATGACAACG
ACCTTTAGCGGCGCTTTTGCC
Found at i:28532451 original size:87 final size:86
Alignment explanation
Indices: 28532268--28532458 Score: 303
Period size: 87 Copynumber: 2.2 Consensus size: 86
28532258 GACCATGACC
28532268 TTTAACAAACGCCGCTAAAGACCACGACCTTTAGCGGCGATTTTTTCACAAACGCCGCTAATGAC
1 TTTAACAAACGCCGCTAAAGACCACGACCTTTAGCGGCGATTTTTTCACAAACGCCGCTAATGAC
* *
28532333 CAGGACCTTTAGCGGCGCTTT
66 AACGACCTTTAGCGGCGCTTT
***
28532354 TGCCACAAACGCCGCTAAAGACC-CTGACCTTTAGCGGCGATTTTTTCCACAAACGCCGCTAATG
1 TTTAACAAACGCCGCTAAAGACCAC-GACCTTTAGCGGCGATTTTTT-CACAAACGCCGCTAATG
28532418 ACAACGACCTTTAGCGGCGCTTT
64 ACAACGACCTTTAGCGGCGCTTT
*
28532441 TTTAAAAAACGCCGCTAA
1 TTTAACAAACGCCGCTAA
28532459 TTTTGGCAGA
Statistics
Matches: 94, Mismatches: 9, Indels: 3
0.89 0.08 0.03
Matches are distributed among these distances:
85 1 0.01
86 41 0.44
87 52 0.55
ACGTcount: A:0.28, C:0.30, G:0.19, T:0.24
Consensus pattern (86 bp):
TTTAACAAACGCCGCTAAAGACCACGACCTTTAGCGGCGATTTTTTCACAAACGCCGCTAATGAC
AACGACCTTTAGCGGCGCTTT
Found at i:28532664 original size:19 final size:19
Alignment explanation
Indices: 28532640--28532676 Score: 65
Period size: 19 Copynumber: 1.9 Consensus size: 19
28532630 ACAAAAATGA
*
28532640 TAAAAGTTAAAATGATAAT
1 TAAAAGTCAAAATGATAAT
28532659 TAAAAGTCAAAATGATAA
1 TAAAAGTCAAAATGATAA
28532677 AAATATTTAC
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.59, C:0.03, G:0.11, T:0.27
Consensus pattern (19 bp):
TAAAAGTCAAAATGATAAT
Found at i:28535878 original size:16 final size:16
Alignment explanation
Indices: 28535859--28535890 Score: 64
Period size: 16 Copynumber: 2.0 Consensus size: 16
28535849 TATTTATTTC
28535859 TTAATTGTATCTTTTA
1 TTAATTGTATCTTTTA
28535875 TTAATTGTATCTTTTA
1 TTAATTGTATCTTTTA
28535891 ATTACTAAGT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.25, C:0.06, G:0.06, T:0.62
Consensus pattern (16 bp):
TTAATTGTATCTTTTA
Found at i:28536295 original size:2 final size:2
Alignment explanation
Indices: 28536290--28536316 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
28536280 TAAAGTTATC
28536290 TA 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 TA T
28536317 CTATTAATTA
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:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:28536617 original size:22 final size:22
Alignment explanation
Indices: 28536591--28536639 Score: 71
Period size: 22 Copynumber: 2.2 Consensus size: 22
28536581 ACCCAAAACA
* *
28536591 CTAAATCCCTAACTCCTAACCC
1 CTAAATCCCAAACCCCTAACCC
*
28536613 TTAAATCCCAAACCCCTAACCC
1 CTAAATCCCAAACCCCTAACCC
28536635 CTAAA
1 CTAAA
28536640 CCAATAAACC
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
22 23 1.00
ACGTcount: A:0.37, C:0.43, G:0.00, T:0.20
Consensus pattern (22 bp):
CTAAATCCCAAACCCCTAACCC
Found at i:28536689 original size:21 final size:21
Alignment explanation
Indices: 28536646--28536691 Score: 56
Period size: 21 Copynumber: 2.2 Consensus size: 21
28536636 TAAACCAATA
* **
28536646 AACCTTAAACTCCTAACTTCT
1 AACCTTAAACCCCTAACCCCT
*
28536667 AACCTTTAACCCCTAACCCCT
1 AACCTTAAACCCCTAACCCCT
28536688 AACC
1 AACC
28536692 AATAAACCTT
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.33, C:0.41, G:0.00, T:0.26
Consensus pattern (21 bp):
AACCTTAAACCCCTAACCCCT
Found at i:28537116 original size:41 final size:41
Alignment explanation
Indices: 28537054--28537366 Score: 405
Period size: 41 Copynumber: 7.6 Consensus size: 41
28537044 TTAACAAATA
* *
28537054 TTCTACAAAAACGCCGCTAAAGGCCCGAGCATTAGTGGCGC
1 TTCTTCAAAAACGCCGCTAAAGGCCCGAGCATTAGCGGCGC
* * *
28537095 TTTTTCAAAAACGCAGCTAAAGGCCCAAGCATTAGCGGCGC
1 TTCTTCAAAAACGCCGCTAAAGGCCCGAGCATTAGCGGCGC
*
28537136 TTCTTCAAAAACGCCGCTAAAGGCCCGAGCATTAGCGTCG-
1 TTCTTCAAAAACGCCGCTAAAGGCCCGAGCATTAGCGGCGC
* * *
28537176 TTGCTTCAAAAACGCCGCTAAAGGCCCCAGCAGTAGCAGCG-
1 TT-CTTCAAAAACGCCGCTAAAGGCCCGAGCATTAGCGGCGC
* * ** *
28537217 TTTTTGAAGAAGTGCCGCTAAAGGCCAGAGCATTAGCGGCGC
1 TTCTTCAA-AAACGCCGCTAAAGGCCCGAGCATTAGCGGCGC
* *
28537259 TGCTTAAAAAACGCCGCTAAAGGCCCGAGCATTAGCGGCGC
1 TTCTTCAAAAACGCCGCTAAAGGCCCGAGCATTAGCGGCGC
* *
28537300 TTTTTCAAAAACGCCGCTAAAGGCCCGAGCATTAGTGGCGC
1 TTCTTCAAAAACGCCGCTAAAGGCCCGAGCATTAGCGGCGC
* * *
28537341 TTCTTAAAAAACGCCACTACAGGCCC
1 TTCTTCAAAAACGCCGCTAAAGGCCC
28537367 CAAAAACTCA
Statistics
Matches: 234, Mismatches: 35, Indels: 6
0.85 0.13 0.02
Matches are distributed among these distances:
40 6 0.03
41 223 0.95
42 5 0.02
ACGTcount: A:0.29, C:0.28, G:0.24, T:0.19
Consensus pattern (41 bp):
TTCTTCAAAAACGCCGCTAAAGGCCCGAGCATTAGCGGCGC
Found at i:28541258 original size:37 final size:37
Alignment explanation
Indices: 28541210--28541593 Score: 362
Period size: 37 Copynumber: 10.2 Consensus size: 37
28541200 GAAAATGGAA
* * * *
28541210 TACTGAATATACTGAATGTGCTCAAAAGAGAAATGTC
1 TACTGATTATACTGAATGTGCTCAAACGAGCAATATC
* *
28541247 TACTAATTATACTGAAAGTTGCTCAAACGAGCAATATCC
1 TACTGATTATACTGAATG-TGCTCAAACGAGCAATAT-C
* * *
28541286 T-CTGATTATACTGAATGGGCTCAAATGAGCAATGTC
1 TACTGATTATACTGAATGTGCTCAAACGAGCAATATC
* * * *
28541322 TAATGCTTATATTGAATGTACTCAAACGAGCAATATC
1 TACTGATTATACTGAATGTGCTCAAACGAGCAATATC
* *
28541359 TACTG-TATCTACTGAATGTGCTCGAAA-GAGCAATGTC
1 TACTGAT-TATACTGAATGTGCTC-AAACGAGCAATATC
* *
28541396 TACTGATTATACTGAAAGTTGTTCAAACGAGCAATATC
1 TACTGATTATACTGAATG-TGCTCAAACGAGCAATATC
* * *
28541434 CACTAATTATACTGAATGGGCTCAAACGAGCAATATC
1 TACTGATTATACTGAATGTGCTCAAACGAGCAATATC
* * * * *
28541471 TACTGAATATACTAAACGTGCTCAAAAGAGCAATGTC
1 TACTGATTATACTGAATGTGCTCAAACGAGCAATATC
* * *
28541508 TACTGATTATACTGAAAGTTGCTCAAACAAGCGATATC
1 TACTGATTATACTGAATG-TGCTCAAACGAGCAATATC
* * *
28541546 CACTGATTATAC-GAAATTCATGCTCAAACGAGCATTATC
1 TACTGATTATACTG-AA-T-GTGCTCAAACGAGCAATATC
* *
28541585 CAATGATTA
1 TACTGATTA
28541594 CGTGAAATAA
Statistics
Matches: 281, Mismatches: 54, Indels: 22
0.79 0.15 0.06
Matches are distributed among these distances:
36 3 0.01
37 163 0.58
38 89 0.32
39 26 0.09
ACGTcount: A:0.37, C:0.18, G:0.16, T:0.29
Consensus pattern (37 bp):
TACTGATTATACTGAATGTGCTCAAACGAGCAATATC
Found at i:28541411 original size:149 final size:147
Alignment explanation
Indices: 28541210--28541586 Score: 450
Period size: 149 Copynumber: 2.5 Consensus size: 147
28541200 GAAAATGGAA
* *
28541210 TACTGAATATACTGAATGTGCTCAAAAGAGAAATGTCTACTAATTATACTGAAAGTTGCTCAAAC
1 TACTG-ATATACTGAATGTGCTC-AAAGAGCAATGTCTACTGATTATACTGAAAGTTGCTCAAAC
* * * * ** * * *
28541275 GAGCAATATCCTCTGATTATACTGAATGGGCTCAAATGAGCAATGTCTAATGCTTATATTGAATG
64 GAGCAATATCCACTAATTATACTGAATGGGCTCAAACGAGCAATATCTAATGAATATACTAAACG
*
28541340 TACTCAAACGAGCAATATC
129 TACTCAAAAGAGCAATATC
* *
28541359 TACTGTATCTACTGAATGTGCTCGAAAGAGCAATGTCTACTGATTATACTGAAAGTTGTTCAAAC
1 TACTG-ATATACTGAATGTGCTC-AAAGAGCAATGTCTACTGATTATACTGAAAGTTGCTCAAAC
*
28541424 GAGCAATATCCACTAATTATACTGAATGGGCTCAAACGAGCAATATCTACTGAATATACTAAACG
64 GAGCAATATCCACTAATTATACTGAATGGGCTCAAACGAGCAATATCTAATGAATATACTAAACG
* *
28541489 TGCTCAAAAGAGCAATGTC
129 TACTCAAAAGAGCAATATC
* * * * * *
28541508 TACTGATTATACTGAAAGTTGCTCAAACAAGCGATATCCACTGATTATAC-GAAATTCATGCTCA
1 TACTGA-TATACTGAATG-TGCTCAAA-GAGCAATGTCTACTGATTATACTGAAAGT--TGCTCA
*
28541572 AACGAGCATTATCCA
61 AACGAGCAATATCCA
28541587 ATGATTACGT
Statistics
Matches: 195, Mismatches: 28, Indels: 8
0.84 0.12 0.03
Matches are distributed among these distances:
148 1 0.01
149 152 0.78
150 23 0.12
151 19 0.10
ACGTcount: A:0.37, C:0.19, G:0.16, T:0.28
Consensus pattern (147 bp):
TACTGATATACTGAATGTGCTCAAAGAGCAATGTCTACTGATTATACTGAAAGTTGCTCAAACGA
GCAATATCCACTAATTATACTGAATGGGCTCAAACGAGCAATATCTAATGAATATACTAAACGTA
CTCAAAAGAGCAATATC
Found at i:28541422 original size:112 final size:111
Alignment explanation
Indices: 28541217--28541557 Score: 368
Period size: 112 Copynumber: 3.0 Consensus size: 111
28541207 GAATACTGAA
* * *
28541217 TATACTGAATGTG-CTCAAAAGAGAAATGTCTACT-AATTATACTGAAAGTTGCTCAAACGAGCA
1 TATACTGAATG-GACTCAAACGAGCAATATCTACTGAA-TATACTGAAAG-TGCTCAAA-GAGCA
* * * * * * **
28541280 ATATCCT-CTGATTATACTGAATG-GGCTCAAATGAGCAATGTCTAATGCT
62 ATGT-CTACTGATTATACTGAAAGTTGCTCAAACGAGCAATATCCAATAAT
* * * * *
28541329 TATATTGAATGTACTCAAACGAGCAATATCTACTGTATCTACTGAATGTGCTCGAAAGAGCAATG
1 TATACTGAATGGACTCAAACGAGCAATATCTACTGAATATACTGAAAGTGCTC-AAAGAGCAATG
* *
28541394 TCTACTGATTATACTGAAAGTTGTTCAAACGAGCAATATCCACTAAT
65 TCTACTGATTATACTGAAAGTTGCTCAAACGAGCAATATCCAATAAT
*
28541441 TATACTGAATGGGCTCAAACGAGCAATATCTACTGAATATACT-AAACGTGCTCAAAAGAGCAAT
1 TATACTGAATGGACTCAAACGAGCAATATCTACTGAATATACTGAAA-GTGCTC-AAAGAGCAAT
* * * *
28541505 GTCTACTGATTATACTGAAAGTTGCTCAAACAAGCGATATCCACTGAT
64 GTCTACTGATTATACTGAAAGTTGCTCAAACGAGCAATATCCAATAAT
28541553 TATAC
1 TATAC
28541558 GAAATTCATG
Statistics
Matches: 194, Mismatches: 29, Indels: 12
0.83 0.12 0.05
Matches are distributed among these distances:
110 2 0.01
111 30 0.15
112 161 0.83
113 1 0.01
ACGTcount: A:0.36, C:0.18, G:0.17, T:0.29
Consensus pattern (111 bp):
TATACTGAATGGACTCAAACGAGCAATATCTACTGAATATACTGAAAGTGCTCAAAGAGCAATGT
CTACTGATTATACTGAAAGTTGCTCAAACGAGCAATATCCAATAAT
Done.