Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01015270.1 Kokia drynarioides strain JFW-HI SEQ_130315, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 1190338
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.34
Warning! 752 characters in sequence are not A, C, G, or T
File 2 of 3
Found at i:390204 original size:26 final size:27
Alignment explanation
Indices: 390174--390230 Score: 75
Period size: 26 Copynumber: 2.2 Consensus size: 27
390164 GTATTATGTG
*
390174 ATAATAATA-ATATAATAT-TAATTAAT
1 ATAATAATATAT-TAATATGAAATTAAT
390200 ATAATAATATATTAATATGAAATTAAT
1 ATAATAATATATTAATATGAAATTAAT
390227 -TAAT
1 ATAAT
390231 TTGATCATAT
Statistics
Matches: 28, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
26 19 0.68
27 9 0.32
ACGTcount: A:0.56, C:0.00, G:0.02, T:0.42
Consensus pattern (27 bp):
ATAATAATATATTAATATGAAATTAAT
Found at i:390205 original size:20 final size:21
Alignment explanation
Indices: 390175--390215 Score: 59
Period size: 20 Copynumber: 2.0 Consensus size: 21
390165 TATTATGTGA
390175 TAATAATAAT-ATAATATTAAT
1 TAATAATAATAAT-ATATTAAT
390196 TAAT-ATAATAATATATTAAT
1 TAATAATAATAATATATTAAT
390216 ATGAAATTAA
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
20 13 0.68
21 6 0.32
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (21 bp):
TAATAATAATAATATATTAAT
Found at i:391269 original size:19 final size:18
Alignment explanation
Indices: 391247--391282 Score: 54
Period size: 19 Copynumber: 1.9 Consensus size: 18
391237 TATGATTTTT
*
391247 ATTTTAAATTAATTTTAAA
1 ATTTTAAAAT-ATTTTAAA
391266 ATTTTAAAATATTTTAA
1 ATTTTAAAATATTTTAA
391283 TTATATTTTT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 7 0.44
19 9 0.56
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (18 bp):
ATTTTAAAATATTTTAAA
Found at i:391279 original size:29 final size:30
Alignment explanation
Indices: 391246--391302 Score: 82
Period size: 29 Copynumber: 1.9 Consensus size: 30
391236 TTATGATTTT
391246 TATTTTAAATTA-ATTTTAAAATT-TTAAAA
1 TATTTT-AATTATATTTTAAAATTATTAAAA
*
391275 TATTTTAATTATATTTTTAAATTATTAA
1 TATTTTAATTATATTTTAAAATTATTAA
391303 TGTTATATCA
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
28 5 0.20
29 16 0.64
30 4 0.16
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (30 bp):
TATTTTAATTATATTTTAAAATTATTAAAA
Found at i:391300 original size:11 final size:10
Alignment explanation
Indices: 391245--391300 Score: 53
Period size: 11 Copynumber: 5.5 Consensus size: 10
391235 ATTATGATTT
391245 TTATTTTAAA
1 TTATTTTAAA
391255 TTAATTTTAAA
1 TT-ATTTTAAA
391266 --ATTTTAAA
1 TTATTTTAAA
* *
391274 ATATTTTAAT
1 TTATTTTAAA
391284 TATATTTTTAAA
1 T-TA-TTTTAAA
391296 TTATT
1 TTATT
391301 AATGTTATAT
Statistics
Matches: 38, Mismatches: 3, Indels: 10
0.75 0.06 0.20
Matches are distributed among these distances:
8 8 0.21
10 11 0.29
11 12 0.32
12 7 0.18
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (10 bp):
TTATTTTAAA
Found at i:398393 original size:17 final size:17
Alignment explanation
Indices: 398371--398405 Score: 70
Period size: 17 Copynumber: 2.1 Consensus size: 17
398361 TCTTTAACAG
398371 AAGAATTTGAAGGAGCA
1 AAGAATTTGAAGGAGCA
398388 AAGAATTTGAAGGAGCA
1 AAGAATTTGAAGGAGCA
398405 A
1 A
398406 CAATAATCTA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.49, C:0.06, G:0.29, T:0.17
Consensus pattern (17 bp):
AAGAATTTGAAGGAGCA
Found at i:406410 original size:6 final size:6
Alignment explanation
Indices: 406345--406408 Score: 101
Period size: 6 Copynumber: 10.7 Consensus size: 6
406335 TCTTCTGTTT
* *
406345 CTTCTG CTTCGG CTTCCG CTTCCG CTTCCG CTTCCG CTTCCG CTTCCG
1 CTTCCG CTTCCG CTTCCG CTTCCG CTTCCG CTTCCG CTTCCG CTTCCG
*
406393 CTTCCG CTTCTG CTTC
1 CTTCCG CTTCCG CTTC
406409 TGGTTTCGAG
Statistics
Matches: 55, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
6 55 1.00
ACGTcount: A:0.00, C:0.45, G:0.17, T:0.38
Consensus pattern (6 bp):
CTTCCG
Found at i:410366 original size:6 final size:6
Alignment explanation
Indices: 410355--410389 Score: 61
Period size: 6 Copynumber: 5.8 Consensus size: 6
410345 TTCCTTAACA
*
410355 GGCTGT GGCTGT GGCTGT GGCTGT GGCTGT TGCTG
1 GGCTGT GGCTGT GGCTGT GGCTGT GGCTGT GGCTG
410390 CTGCTGCATG
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
6 28 1.00
ACGTcount: A:0.00, C:0.17, G:0.49, T:0.34
Consensus pattern (6 bp):
GGCTGT
Found at i:414462 original size:121 final size:121
Alignment explanation
Indices: 414289--414584 Score: 475
Period size: 121 Copynumber: 2.4 Consensus size: 121
414279 AATTATCCCT
* * * * * *
414289 TATTAGAAAGAGATAGAGATGACGTGAAATCGTAATTTCATACAATCCTTTCTCCAAAAATTAAT
1 TATTAAAAAGGGATAGATATGATGTGAAATCATAGTTTCATACAATCCTTTCTCCAAAAATTAAT
414354 TTAAATCCAACTAAAAATGCTAAAAATCAGGAGAAAAATCTAATTTATCATTCCAC
66 TTAAATCCAACTAAAAATGCTAAAAATCAGGAGAAAAATCTAATTTATCATTCCAC
* **
414410 TATTAAAAAGGGATAGATATGATGTGGAATCATAGTTTCATACAATTTTTTCTCCAAAAATTAAT
1 TATTAAAAAGGGATAGATATGATGTGAAATCATAGTTTCATACAATCCTTTCTCCAAAAATTAAT
* *
414475 TTAAATCCAACTAAAAATGCTAAAAATCATGAGAAAAATCTAATTTATCATTTCAC
66 TTAAATCCAACTAAAAATGCTAAAAATCAGGAGAAAAATCTAATTTATCATTCCAC
* *
414531 TATTGAAAAGGGATAGATATGATGTGAAATCACAGTTTCATACAATCCTTTCTC
1 TATTAAAAAGGGATAGATATGATGTGAAATCATAGTTTCATACAATCCTTTCTC
414585 ATGGGATACA
Statistics
Matches: 159, Mismatches: 16, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
121 159 1.00
ACGTcount: A:0.43, C:0.14, G:0.11, T:0.32
Consensus pattern (121 bp):
TATTAAAAAGGGATAGATATGATGTGAAATCATAGTTTCATACAATCCTTTCTCCAAAAATTAAT
TTAAATCCAACTAAAAATGCTAAAAATCAGGAGAAAAATCTAATTTATCATTCCAC
Found at i:426102 original size:18 final size:19
Alignment explanation
Indices: 426068--426105 Score: 53
Period size: 18 Copynumber: 2.1 Consensus size: 19
426058 CATTGAAGAA
426068 ATGAGACAAGAGCTGAATT
1 ATGAGACAAGAGCTGAATT
426087 ATGAGA-AAGA-CATGAATT
1 ATGAGACAAGAGC-TGAATT
426105 A
1 A
426106 CAATCTTCGG
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
17 1 0.06
18 11 0.61
19 6 0.33
ACGTcount: A:0.47, C:0.08, G:0.24, T:0.21
Consensus pattern (19 bp):
ATGAGACAAGAGCTGAATT
Found at i:431990 original size:17 final size:18
Alignment explanation
Indices: 431963--431996 Score: 61
Period size: 17 Copynumber: 1.9 Consensus size: 18
431953 GCTTTAGAGA
431963 ATATGCCAAAATCTTCAC
1 ATATGCCAAAATCTTCAC
431981 ATAT-CCAAAATCTTCA
1 ATATGCCAAAATCTTCA
431997 TAATTGTTAT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 12 0.75
18 4 0.25
ACGTcount: A:0.41, C:0.26, G:0.03, T:0.29
Consensus pattern (18 bp):
ATATGCCAAAATCTTCAC
Found at i:435192 original size:17 final size:17
Alignment explanation
Indices: 435172--435205 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
435162 TCTTTTATAA
435172 TTAAAAAAATAAAAACT
1 TTAAAAAAATAAAAACT
* *
435189 TTAAAAATATGAAAACT
1 TTAAAAAAATAAAAACT
435206 AAAATTAATC
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.65, C:0.06, G:0.03, T:0.26
Consensus pattern (17 bp):
TTAAAAAAATAAAAACT
Found at i:439909 original size:23 final size:21
Alignment explanation
Indices: 439859--439919 Score: 54
Period size: 23 Copynumber: 2.8 Consensus size: 21
439849 AATGGTCAAA
*
439859 ATTAAAT-TTTAATTTTTATG
1 ATTAAATATATAATTTTTATG
439879 ATAGTAAATATATAATTTTTAAATG
1 AT--TAAATATATAATTTTT--ATG
*
439904 ATTAAATA-AAAATTTT
1 ATTAAATATATAATTTT
439920 ATCATTTTTA
Statistics
Matches: 34, Mismatches: 2, Indels: 8
0.77 0.05 0.18
Matches are distributed among these distances:
20 2 0.06
22 12 0.35
23 15 0.44
25 5 0.15
ACGTcount: A:0.46, C:0.00, G:0.05, T:0.49
Consensus pattern (21 bp):
ATTAAATATATAATTTTTATG
Found at i:442895 original size:39 final size:43
Alignment explanation
Indices: 442810--442903 Score: 124
Period size: 39 Copynumber: 2.2 Consensus size: 43
442800 AAATCTATTT
*
442810 TTCTTCTTCAAAGAACCCTAAATTAAACCCCAAATTCATTCATTC
1 TTCTTCTTCAAAGAACCCTAAATTAAACCCC--ATCCATTCATTC
*
442855 TTCTTCTTCAAA-ACCCCTAAATTAAA-CCC-TCCATTC-TTC
1 TTCTTCTTCAAAGAACCCTAAATTAAACCCCATCCATTCATTC
442894 TTCTTCTTCA
1 TTCTTCTTCA
442904 TCAGTTCATC
Statistics
Matches: 47, Mismatches: 2, Indels: 6
0.85 0.04 0.11
Matches are distributed among these distances:
39 13 0.28
40 6 0.13
43 3 0.06
44 13 0.28
45 12 0.26
ACGTcount: A:0.30, C:0.32, G:0.01, T:0.37
Consensus pattern (43 bp):
TTCTTCTTCAAAGAACCCTAAATTAAACCCCATCCATTCATTC
Found at i:444246 original size:23 final size:23
Alignment explanation
Indices: 444220--444269 Score: 59
Period size: 23 Copynumber: 2.2 Consensus size: 23
444210 GCCTTTTTAA
* *
444220 ATTATTATTAATG-TTATTTTATG
1 ATTATGATT-ATGATTATTATATG
444243 ATTATGATTATGATTATTATATG
1 ATTATGATTATGATTATTATATG
444266 -TTAT
1 ATTAT
444270 ATGTTGTATA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
22 7 0.29
23 17 0.71
ACGTcount: A:0.32, C:0.00, G:0.10, T:0.58
Consensus pattern (23 bp):
ATTATGATTATGATTATTATATG
Found at i:468087 original size:18 final size:18
Alignment explanation
Indices: 468064--468104 Score: 57
Period size: 18 Copynumber: 2.3 Consensus size: 18
468054 TTTTTTTAGT
468064 ATTAATTTAAAATT-TTTA
1 ATTAA-TTAAAATTATTTA
*
468082 ATTAATTAAATTTATTTA
1 ATTAATTAAAATTATTTA
468100 ATTAA
1 ATTAA
468105 AAATTTATTT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
17 7 0.33
18 14 0.67
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (18 bp):
ATTAATTAAAATTATTTA
Found at i:468275 original size:14 final size:15
Alignment explanation
Indices: 468232--468282 Score: 59
Period size: 15 Copynumber: 3.5 Consensus size: 15
468222 ACAAAATGAT
*
468232 AATATAAGTAATTAA
1 AATATAAATAATTAA
* * *
468247 AATATAACT-TTTTA
1 AATATAAATAATTAA
468261 AATATAAATAATTAA
1 AATATAAATAATTAA
468276 AATATAA
1 AATATAA
468283 TTTGAAACAA
Statistics
Matches: 29, Mismatches: 6, Indels: 2
0.78 0.16 0.05
Matches are distributed among these distances:
14 11 0.38
15 18 0.62
ACGTcount: A:0.59, C:0.02, G:0.02, T:0.37
Consensus pattern (15 bp):
AATATAAATAATTAA
Found at i:474567 original size:139 final size:139
Alignment explanation
Indices: 474317--474594 Score: 520
Period size: 139 Copynumber: 2.0 Consensus size: 139
474307 CAAAGATGGG
* *
474317 GTTCCTTTCAAAATAAATAAAATTTAAGTACCGCAAGGAACTTCAACAGAAACCCAGGAAAATAA
1 GTTCCTTTCAAAATAAATAAAATTTAAGTACCCCAAAGAACTTCAACAGAAACCCAGGAAAATAA
* *
474382 GATGAACTATGAAAATCTCAAAAACCCAATCAAAGTAGAAGCTTTTAGGAAATTGTAGCAGACAG
66 GATGAACTATGAAAATCTCAAAAACCCAAACAAAGTAGAAGCTTTTAGGAAATTGTAGCACACAG
474447 GGCCATGAA
131 GGCCATGAA
474456 GTTCCTTTCAAAATAAATAAAATTTAAGTACCCCAAAGAACTTCAACAGAAACCCAGGAAAATAA
1 GTTCCTTTCAAAATAAATAAAATTTAAGTACCCCAAAGAACTTCAACAGAAACCCAGGAAAATAA
474521 GATGAACTATGAAAATCTCAAAAACCCAAACAAAGTAGAAGCTTTTAGGAAATTGTAGCACACAG
66 GATGAACTATGAAAATCTCAAAAACCCAAACAAAGTAGAAGCTTTTAGGAAATTGTAGCACACAG
474586 GGCCATGAA
131 GGCCATGAA
474595 TTCATCAAGG
Statistics
Matches: 135, Mismatches: 4, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
139 135 1.00
ACGTcount: A:0.46, C:0.18, G:0.15, T:0.21
Consensus pattern (139 bp):
GTTCCTTTCAAAATAAATAAAATTTAAGTACCCCAAAGAACTTCAACAGAAACCCAGGAAAATAA
GATGAACTATGAAAATCTCAAAAACCCAAACAAAGTAGAAGCTTTTAGGAAATTGTAGCACACAG
GGCCATGAA
Found at i:479289 original size:15 final size:16
Alignment explanation
Indices: 479269--479298 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
479259 AAGTATAGTC
479269 AAATA-TTAAAAAAGT
1 AAATATTTAAAAAAGT
479284 AAATATTTAAAAAAG
1 AAATATTTAAAAAAG
479299 AAGAAGATAC
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 5 0.36
16 9 0.64
ACGTcount: A:0.67, C:0.00, G:0.07, T:0.27
Consensus pattern (16 bp):
AAATATTTAAAAAAGT
Found at i:481247 original size:14 final size:14
Alignment explanation
Indices: 481228--481259 Score: 64
Period size: 14 Copynumber: 2.3 Consensus size: 14
481218 TTAATATTTC
481228 AATTTTTTATTTTA
1 AATTTTTTATTTTA
481242 AATTTTTTATTTTA
1 AATTTTTTATTTTA
481256 AATT
1 AATT
481260 AAAAATTAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (14 bp):
AATTTTTTATTTTA
Found at i:481333 original size:18 final size:20
Alignment explanation
Indices: 481307--481348 Score: 52
Period size: 18 Copynumber: 2.1 Consensus size: 20
481297 CATTAATATG
*
481307 AAATTTTAAA-ATAA-AAAT
1 AAATATTAAATATAATAAAT
481325 AAATATTAAATTATAATAAAT
1 AAATATTAAA-TATAATAAAT
481346 AAA
1 AAA
481349 GAAAATGATA
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
18 9 0.45
20 4 0.20
21 7 0.35
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (20 bp):
AAATATTAAATATAATAAAT
Found at i:491527 original size:18 final size:16
Alignment explanation
Indices: 491496--491539 Score: 56
Period size: 14 Copynumber: 2.8 Consensus size: 16
491486 GGTTTAAGGT
*
491496 TTAAAAATTTTAATTAA
1 TTAAAAA-TTTATTTAA
491513 TT--AAATTTATTTAA
1 TTAAAAATTTATTTAA
491527 TTAAAAATTTATT
1 TTAAAAATTTATT
491540 CTCATTCCAT
Statistics
Matches: 24, Mismatches: 1, Indels: 5
0.80 0.03 0.17
Matches are distributed among these distances:
14 10 0.42
15 3 0.12
16 9 0.38
17 2 0.08
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (16 bp):
TTAAAAATTTATTTAA
Found at i:498620 original size:34 final size:34
Alignment explanation
Indices: 498576--498729 Score: 202
Period size: 34 Copynumber: 4.5 Consensus size: 34
498566 TACTACTGAT
498576 TTGATTTGTTATAAGCATATTAATTGCTATCGTA
1 TTGATTTGTTATAAGCATATTAATTGCTATCGTA
* * * *
498610 TCGATATGTTATAAGCATTTTAATTGCTACCGTA
1 TTGATTTGTTATAAGCATATTAATTGCTATCGTA
*
498644 TTGATTTGTTATAAGCATATTAATTACTATCGTA
1 TTGATTTGTTATAAGCATATTAATTGCTATCGTA
* * * * *
498678 TTGATCTATTATAACCACATTAATTGCTA-CAATA
1 TTGATTTGTTATAAGCATATTAATTGCTATC-GTA
498712 TTGATTTGTTATAAGCAT
1 TTGATTTGTTATAAGCAT
498730 GCGACATTGC
Statistics
Matches: 100, Mismatches: 19, Indels: 2
0.83 0.16 0.02
Matches are distributed among these distances:
33 1 0.01
34 99 0.99
ACGTcount: A:0.32, C:0.12, G:0.12, T:0.44
Consensus pattern (34 bp):
TTGATTTGTTATAAGCATATTAATTGCTATCGTA
Found at i:498661 original size:68 final size:68
Alignment explanation
Indices: 498576--498729 Score: 227
Period size: 68 Copynumber: 2.3 Consensus size: 68
498566 TACTACTGAT
* * * ** *
498576 TTGATTTGTTATAAGCATATTAATTGCTATCGTATCGATATGTTATAAGCATTTTAATTGCTACC
1 TTGATTTGTTATAAGCATATTAATTACTATCGTATCGATATATTATAACCACATTAATTGCTACA
*
498641 GTA
66 ATA
* *
498644 TTGATTTGTTATAAGCATATTAATTACTATCGTATTGATCTATTATAACCACATTAATTGCTACA
1 TTGATTTGTTATAAGCATATTAATTACTATCGTATCGATATATTATAACCACATTAATTGCTACA
498709 ATA
66 ATA
498712 TTGATTTGTTATAAGCAT
1 TTGATTTGTTATAAGCAT
498730 GCGACATTGC
Statistics
Matches: 77, Mismatches: 9, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
68 77 1.00
ACGTcount: A:0.32, C:0.12, G:0.12, T:0.44
Consensus pattern (68 bp):
TTGATTTGTTATAAGCATATTAATTACTATCGTATCGATATATTATAACCACATTAATTGCTACA
ATA
Found at i:499875 original size:18 final size:18
Alignment explanation
Indices: 499852--499886 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
499842 TTACATTTGA
499852 AAAGTAAAAACTAAAAAT
1 AAAGTAAAAACTAAAAAT
*
499870 AAAGTAAAACCTAAAAA
1 AAAGTAAAAACTAAAAA
499887 AGAGAGAGTA
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:0.71, C:0.09, G:0.06, T:0.14
Consensus pattern (18 bp):
AAAGTAAAAACTAAAAAT
Found at i:500845 original size:27 final size:27
Alignment explanation
Indices: 500814--500865 Score: 95
Period size: 27 Copynumber: 1.9 Consensus size: 27
500804 ATTTTTTATT
*
500814 TTGAAATTCATTCCAAAATAAAAATGA
1 TTGAAATTCATTACAAAATAAAAATGA
500841 TTGAAATTCATTACAAAATAAAAAT
1 TTGAAATTCATTACAAAATAAAAAT
500866 TCTTTCATTA
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
27 24 1.00
ACGTcount: A:0.54, C:0.10, G:0.06, T:0.31
Consensus pattern (27 bp):
TTGAAATTCATTACAAAATAAAAATGA
Found at i:501847 original size:15 final size:15
Alignment explanation
Indices: 501827--501860 Score: 59
Period size: 15 Copynumber: 2.3 Consensus size: 15
501817 TTTTTAAAAA
501827 TATTTGTTTATTTAT
1 TATTTGTTTATTTAT
*
501842 TATTTGTTTGTTTAT
1 TATTTGTTTATTTAT
501857 TATT
1 TATT
501861 CATTATCATT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.18, C:0.00, G:0.09, T:0.74
Consensus pattern (15 bp):
TATTTGTTTATTTAT
Found at i:502905 original size:22 final size:22
Alignment explanation
Indices: 502880--502922 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 22
502870 ATTACCATGT
502880 TTATCTAATA-TGTTATAGATAA
1 TTATCTAATATTGTTAT-GATAA
*
502902 TTATTTAATATTGTTATGATA
1 TTATCTAATATTGTTATGATA
502923 CTTACTATTA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
22 13 0.68
23 6 0.32
ACGTcount: A:0.37, C:0.02, G:0.09, T:0.51
Consensus pattern (22 bp):
TTATCTAATATTGTTATGATAA
Found at i:508411 original size:6 final size:7
Alignment explanation
Indices: 508394--508419 Score: 52
Period size: 7 Copynumber: 3.7 Consensus size: 7
508384 TTATGGTTCT
508394 TTTTTTC
1 TTTTTTC
508401 TTTTTTC
1 TTTTTTC
508408 TTTTTTC
1 TTTTTTC
508415 TTTTT
1 TTTTT
508420 AATCACCCAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 19 1.00
ACGTcount: A:0.00, C:0.12, G:0.00, T:0.88
Consensus pattern (7 bp):
TTTTTTC
Found at i:511306 original size:29 final size:27
Alignment explanation
Indices: 511258--511317 Score: 77
Period size: 26 Copynumber: 2.1 Consensus size: 27
511248 GTTCTAATTT
*
511258 TTTTTATTAAACCTTCATTTTT-AAAA
1 TTTTTATTAAACCTTAATTTTTGAAAA
511284 TTTTTATTAAACTCTTAAAATTTTTGAAAA
1 TTTTTATTAAAC-CTT--AATTTTTGAAAA
511314 TTTT
1 TTTT
511318 AAGCCATTGG
Statistics
Matches: 29, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
26 12 0.41
27 3 0.10
29 6 0.21
30 8 0.28
ACGTcount: A:0.35, C:0.08, G:0.02, T:0.55
Consensus pattern (27 bp):
TTTTTATTAAACCTTAATTTTTGAAAA
Found at i:513232 original size:65 final size:65
Alignment explanation
Indices: 513128--513257 Score: 260
Period size: 65 Copynumber: 2.0 Consensus size: 65
513118 CTTTTGAAAA
513128 AGTATTGATATATGTTCTTGTATATTATTTCAGTAATAGTTTTACTTCATGTAGCATAGTTTAAG
1 AGTATTGATATATGTTCTTGTATATTATTTCAGTAATAGTTTTACTTCATGTAGCATAGTTTAAG
513193 AGTATTGATATATGTTCTTGTATATTATTTCAGTAATAGTTTTACTTCATGTAGCATAGTTTAAG
1 AGTATTGATATATGTTCTTGTATATTATTTCAGTAATAGTTTTACTTCATGTAGCATAGTTTAAG
513258 GACGTGTAAT
Statistics
Matches: 65, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
65 65 1.00
ACGTcount: A:0.29, C:0.08, G:0.15, T:0.48
Consensus pattern (65 bp):
AGTATTGATATATGTTCTTGTATATTATTTCAGTAATAGTTTTACTTCATGTAGCATAGTTTAAG
Found at i:514934 original size:109 final size:109
Alignment explanation
Indices: 514783--515100 Score: 363
Period size: 109 Copynumber: 2.8 Consensus size: 109
514773 AGTCTTAATA
* * * * *
514783 TGTGCATTTGTCATGGATGGATTTTAT-CTA-GTTATTTATTTTGTATTGATTCCTACATTTGAG
1 TGTGCATTTGCCATGGTTGGATTTTATCCTACGTTA--TGTTTTGTATTGGTTCCTAAATTTGAG
* * *
514846 TCACATCATATGTATTTATGATGCGTGGGTAT-CTAATACTAATATG
64 TCTCATCGTATGTATTTATGATGTGTGGGTATAC-AATACTAATATG
*
514892 TGTGCATTTGCCATAGTTGGATTTTATCCTACGTTATGTTTTGTATTGGTTCCTAAATTTGAGTC
1 TGTGCATTTGCCATGGTTGGATTTTATCCTACGTTATGTTTTGTATTGGTTCCTAAATTTGAGTC
* * * *
514957 TTATCGTATGTATCTATGATGTGTGGGTTTACAATCCTAATATG
66 TCATCGTATGTATTTATGATGTGTGGGTATACAATACTAATATG
* * *
515001 TGCGCATTTGCCATGGTTGGACTTTATCCAGTTATTCATTCGTTGTGTTTTGTATTGGTTCCTAA
1 TGTGCATTTGCCATGGTTGGATTTTATCC------T-A--CGTTATGTTTTGTATTGGTTCCTAA
515066 ATTTGAGTCTCATCGTATGTATTTATGATGTGTGG
57 ATTTGAGTCTCATCGTATGTATTTATGATGTGTGG
515101 ATCTCTAGTC
Statistics
Matches: 178, Mismatches: 19, Indels: 15
0.84 0.09 0.07
Matches are distributed among these distances:
109 111 0.62
110 4 0.02
111 4 0.02
115 1 0.01
116 1 0.01
118 57 0.32
ACGTcount: A:0.21, C:0.13, G:0.20, T:0.46
Consensus pattern (109 bp):
TGTGCATTTGCCATGGTTGGATTTTATCCTACGTTATGTTTTGTATTGGTTCCTAAATTTGAGTC
TCATCGTATGTATTTATGATGTGTGGGTATACAATACTAATATG
Found at i:517788 original size:3 final size:3
Alignment explanation
Indices: 517780--517810 Score: 62
Period size: 3 Copynumber: 10.3 Consensus size: 3
517770 ATGATATGAA
517780 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A
517811 GAAATAAAGA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 28 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:521361 original size:12 final size:11
Alignment explanation
Indices: 521329--521372 Score: 54
Period size: 11 Copynumber: 3.9 Consensus size: 11
521319 TTGATTTGAT
521329 GTTTTGTTTTCTA
1 GTTTT-TTTT-TA
521342 GTTTTTTTTTA
1 GTTTTTTTTTA
*
521353 GTTTCTTTTT-
1 GTTTTTTTTTA
521363 GTTTTTTTTT
1 GTTTTTTTTT
521373 TTTACATTTT
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
10 9 0.31
11 11 0.38
12 4 0.14
13 5 0.17
ACGTcount: A:0.05, C:0.05, G:0.11, T:0.80
Consensus pattern (11 bp):
GTTTTTTTTTA
Found at i:529866 original size:22 final size:22
Alignment explanation
Indices: 529822--529866 Score: 65
Period size: 22 Copynumber: 2.0 Consensus size: 22
529812 TTTAATCTTT
*
529822 TAAAAATTACATTTTACTATCG
1 TAAAAATTACATTTAACTATCG
529844 TAAAAATTACAATTTAACT-TCG
1 TAAAAATTAC-ATTTAACTATCG
529866 T
1 T
529867 CCCCCCTAAA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
22 14 0.67
23 7 0.33
ACGTcount: A:0.42, C:0.13, G:0.04, T:0.40
Consensus pattern (22 bp):
TAAAAATTACATTTAACTATCG
Found at i:545141 original size:24 final size:24
Alignment explanation
Indices: 545113--545189 Score: 145
Period size: 24 Copynumber: 3.2 Consensus size: 24
545103 AGAAATAATC
*
545113 TTTCAGTTAAACTCTGTTTATTTG
1 TTTCAATTAAACTCTGTTTATTTG
545137 TTTCAATTAAACTCTGTTTATTTG
1 TTTCAATTAAACTCTGTTTATTTG
545161 TTTCAATTAAACTCTGTTTATTTG
1 TTTCAATTAAACTCTGTTTATTTG
545185 TTTCA
1 TTTCA
545190 GTCAAATTTT
Statistics
Matches: 52, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
24 52 1.00
ACGTcount: A:0.23, C:0.13, G:0.09, T:0.55
Consensus pattern (24 bp):
TTTCAATTAAACTCTGTTTATTTG
Found at i:547138 original size:24 final size:24
Alignment explanation
Indices: 547110--547172 Score: 90
Period size: 24 Copynumber: 2.6 Consensus size: 24
547100 AGAAATAATC
547110 TTTCAGTTAAACTCTATTTATTTG
1 TTTCAGTTAAACTCTATTTATTTG
* *
547134 TTTCAATTAAACTCTGTTTATTTG
1 TTTCAGTTAAACTCTATTTATTTG
* *
547158 TTTGAGTCAAACTCT
1 TTTCAGTTAAACTCT
547173 TATTAGTCTA
Statistics
Matches: 34, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
24 34 1.00
ACGTcount: A:0.25, C:0.14, G:0.10, T:0.51
Consensus pattern (24 bp):
TTTCAGTTAAACTCTATTTATTTG
Found at i:550007 original size:3 final size:3
Alignment explanation
Indices: 549994--550023 Score: 51
Period size: 3 Copynumber: 10.0 Consensus size: 3
549984 ATGAATTGAT
*
549994 GAA GCA GAA GAA GAA GAA GAA GAA GAA GAA
1 GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA
550024 TTGAGGGTTT
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.63, C:0.03, G:0.33, T:0.00
Consensus pattern (3 bp):
GAA
Found at i:550130 original size:7 final size:7
Alignment explanation
Indices: 550118--550147 Score: 60
Period size: 7 Copynumber: 4.3 Consensus size: 7
550108 AATATGGTAT
550118 TTGGGAA
1 TTGGGAA
550125 TTGGGAA
1 TTGGGAA
550132 TTGGGAA
1 TTGGGAA
550139 TTGGGAA
1 TTGGGAA
550146 TT
1 TT
550148 TCAAGTTTGA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 23 1.00
ACGTcount: A:0.27, C:0.00, G:0.40, T:0.33
Consensus pattern (7 bp):
TTGGGAA
Found at i:555421 original size:2 final size:2
Alignment explanation
Indices: 555408--555437 Score: 51
Period size: 2 Copynumber: 15.0 Consensus size: 2
555398 ATGATCCATT
*
555408 TA TA TT TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
555438 CTAAAAATTC
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (2 bp):
TA
Found at i:560015 original size:26 final size:27
Alignment explanation
Indices: 559963--560015 Score: 65
Period size: 27 Copynumber: 2.0 Consensus size: 27
559953 GGAATCAAGG
*
559963 ATTCAAAATGTTTGAAACTAATGTACT
1 ATTCAAAATGATTGAAACTAATGTACT
*
559990 ATTCAAATTGATT-AAATCTAAT-TACT
1 ATTCAAAATGATTGAAA-CTAATGTACT
560016 TGCATTAACA
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
26 7 0.30
27 16 0.70
ACGTcount: A:0.42, C:0.11, G:0.08, T:0.40
Consensus pattern (27 bp):
ATTCAAAATGATTGAAACTAATGTACT
Found at i:560346 original size:36 final size:38
Alignment explanation
Indices: 560301--560374 Score: 107
Period size: 40 Copynumber: 1.9 Consensus size: 38
560291 CGATTTTAGA
*
560301 TTTTGAATGC-A-TAATAGCCTAATAGGTGTAGAATAT
1 TTTTGAATGCAAGTAACAGCCTAATAGGTGTAGAATAT
560337 TTTTGAATGCGTAAGTAACAGCCTAATAGGTGTAGAAT
1 TTTTGAATGC--AAGTAACAGCCTAATAGGTGTAGAAT
560375 CCTACATGAT
Statistics
Matches: 33, Mismatches: 1, Indels: 4
0.87 0.03 0.11
Matches are distributed among these distances:
36 10 0.30
39 1 0.03
40 22 0.67
ACGTcount: A:0.35, C:0.09, G:0.22, T:0.34
Consensus pattern (38 bp):
TTTTGAATGCAAGTAACAGCCTAATAGGTGTAGAATAT
Found at i:564228 original size:7 final size:8
Alignment explanation
Indices: 564210--564239 Score: 60
Period size: 8 Copynumber: 3.8 Consensus size: 8
564200 CATCAAAATC
564210 AAAATTTA
1 AAAATTTA
564218 AAAATTTA
1 AAAATTTA
564226 AAAATTTA
1 AAAATTTA
564234 AAAATT
1 AAAATT
564240 AATAATAAAC
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 22 1.00
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (8 bp):
AAAATTTA
Found at i:567599 original size:89 final size:89
Alignment explanation
Indices: 567448--567618 Score: 288
Period size: 89 Copynumber: 1.9 Consensus size: 89
567438 AAAAAAAAAA
* * *
567448 AAAACAATAGTAAAGATGTTAAATATTTACGAGAAACCTAAAGTGTTAATAAAATGTCCTGATAA
1 AAAACAATAATAAAGATGTTAAATATTTACGAGAAACCTAAAGTGCTAATAAAATCTCCTGATAA
*
567513 TTAGACGACAGTTTGGATTTTTTT
66 TTAGACAACAGTTTGGATTTTTTT
* *
567537 AAAACAATAATAAAGATGTTAAATATTTATGAGAAACCTAAAGTGCTAATAAAATCTGCTGATAA
1 AAAACAATAATAAAGATGTTAAATATTTACGAGAAACCTAAAGTGCTAATAAAATCTCCTGATAA
567602 TTAGACAACAGTTTGGA
66 TTAGACAACAGTTTGGA
567619 AAATAAGGTA
Statistics
Matches: 76, Mismatches: 6, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
89 76 1.00
ACGTcount: A:0.44, C:0.09, G:0.15, T:0.31
Consensus pattern (89 bp):
AAAACAATAATAAAGATGTTAAATATTTACGAGAAACCTAAAGTGCTAATAAAATCTCCTGATAA
TTAGACAACAGTTTGGATTTTTTT
Found at i:571062 original size:12 final size:13
Alignment explanation
Indices: 571032--571062 Score: 55
Period size: 13 Copynumber: 2.5 Consensus size: 13
571022 TCTTTAGTTG
571032 TTAAATATTAGTA
1 TTAAATATTAGTA
571045 TTAAATATTAGT-
1 TTAAATATTAGTA
571057 TTAAAT
1 TTAAAT
571063 TTAATATGGA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
12 6 0.33
13 12 0.67
ACGTcount: A:0.45, C:0.00, G:0.06, T:0.48
Consensus pattern (13 bp):
TTAAATATTAGTA
Found at i:572696 original size:143 final size:143
Alignment explanation
Indices: 572436--572704 Score: 348
Period size: 143 Copynumber: 1.9 Consensus size: 143
572426 TTTATATTTG
*
572436 TGGATTTGTTATATGCTTGGTTAGTAGTGAATTTGAAATTATTAAAGCTTTTATGAATTTGACAA
1 TGGATTTGTTATATGCTTGGTTAGGAGTGAATTTGAAATTATTAAAGCTTTTATGAATTTGACAA
* * * * *
572501 GTTCATGATTTTTATACTTTTAGAATACATTTTATATTGGAACCTAACTAATTTATTCATAATTA
66 ATTCAGGATTTTTATAATTTCAGAATACATTTTATATTGAAACCTAACTAATTTATTCATAATTA
572566 CTTTTTAAATCCA
131 CTTTTTAAATCCA
* * * *
572579 TGGATTTGTTGTATGTTTGTTTAGGAGTGAATTTGAAATTCTTAAAAG-TATTTATGAATTTGAC
1 TGGATTTGTTATATGCTTGGTTAGGAGTGAATTTGAAATTATT-AAAGCT-TTTATGAATTTGAC
* * * *
572643 AAATTCAGGATTTTTATAAATTTCA-AATATATTTTGTATCT-AAATC-AATTAATTTATTCATA
64 AAATTCAGGATTTTTAT-AATTTCAGAATACATTTTATAT-TGAAACCTAACTAATTTATTCATA
572705 TTGTATGCAT
Statistics
Matches: 108, Mismatches: 14, Indels: 8
0.83 0.11 0.06
Matches are distributed among these distances:
143 54 0.50
144 48 0.44
145 6 0.06
ACGTcount: A:0.33, C:0.07, G:0.13, T:0.46
Consensus pattern (143 bp):
TGGATTTGTTATATGCTTGGTTAGGAGTGAATTTGAAATTATTAAAGCTTTTATGAATTTGACAA
ATTCAGGATTTTTATAATTTCAGAATACATTTTATATTGAAACCTAACTAATTTATTCATAATTA
CTTTTTAAATCCA
Found at i:579778 original size:19 final size:19
Alignment explanation
Indices: 579754--579790 Score: 74
Period size: 19 Copynumber: 1.9 Consensus size: 19
579744 ATCAGAGTTT
579754 CTCACACAAGCTGACATTG
1 CTCACACAAGCTGACATTG
579773 CTCACACAAGCTGACATT
1 CTCACACAAGCTGACATT
579791 TATGAATTGA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.32, C:0.32, G:0.14, T:0.22
Consensus pattern (19 bp):
CTCACACAAGCTGACATTG
Found at i:583027 original size:2 final size:2
Alignment explanation
Indices: 583022--583049 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
583012 TCTTGTGTGT
583022 TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA
583050 AGTTTTACTT
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):
TA
Found at i:589065 original size:4 final size:4
Alignment explanation
Indices: 589056--589080 Score: 50
Period size: 4 Copynumber: 6.2 Consensus size: 4
589046 ATCATTTCAA
589056 AAAT AAAT AAAT AAAT AAAT AAAT A
1 AAAT AAAT AAAT AAAT AAAT AAAT A
589081 CATATATATA
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:0.76, C:0.00, G:0.00, T:0.24
Consensus pattern (4 bp):
AAAT
Found at i:592287 original size:14 final size:15
Alignment explanation
Indices: 592260--592293 Score: 52
Period size: 14 Copynumber: 2.3 Consensus size: 15
592250 AATTTTTTCG
*
592260 ATAAAAATTCAAAAA
1 ATAAAAATTAAAAAA
592275 ATAAAAA-TAAAAAA
1 ATAAAAATTAAAAAA
592289 ATAAA
1 ATAAA
592294 TCAAACAAAG
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
14 11 0.61
15 7 0.39
ACGTcount: A:0.79, C:0.03, G:0.00, T:0.18
Consensus pattern (15 bp):
ATAAAAATTAAAAAA
Found at i:592819 original size:19 final size:18
Alignment explanation
Indices: 592795--592835 Score: 57
Period size: 18 Copynumber: 2.2 Consensus size: 18
592785 AATGTTTTGA
592795 TATTGTATAACTTTTGTT-T
1 TATTGT-TAA-TTTTGTTAT
592814 TATTGTTAATTTTGTTAT
1 TATTGTTAATTTTGTTAT
592832 TATT
1 TATT
592836 TTAGAGGCAT
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
17 7 0.33
18 8 0.38
19 6 0.29
ACGTcount: A:0.22, C:0.02, G:0.10, T:0.66
Consensus pattern (18 bp):
TATTGTTAATTTTGTTAT
Found at i:594831 original size:2 final size:2
Alignment explanation
Indices: 594824--594861 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
594814 AGTTTCAGCA
594824 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
594862 GGGATGAACT
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:595800 original size:43 final size:43
Alignment explanation
Indices: 595739--595821 Score: 166
Period size: 43 Copynumber: 1.9 Consensus size: 43
595729 TATAGTATTA
595739 GAACTTAGAATCACATGACATGAGGTAAAAATAATTGTAATTG
1 GAACTTAGAATCACATGACATGAGGTAAAAATAATTGTAATTG
595782 GAACTTAGAATCACATGACATGAGGTAAAAATAATTGTAA
1 GAACTTAGAATCACATGACATGAGGTAAAAATAATTGTAA
595822 CCACAGATCA
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
43 40 1.00
ACGTcount: A:0.46, C:0.10, G:0.18, T:0.27
Consensus pattern (43 bp):
GAACTTAGAATCACATGACATGAGGTAAAAATAATTGTAATTG
Found at i:595837 original size:43 final size:43
Alignment explanation
Indices: 595747--595837 Score: 112
Period size: 43 Copynumber: 2.1 Consensus size: 43
595737 TAGAACTTAG
**** * *
595747 AATCACATGACATGAGGTAAAAATAATTGTAATTGGAACTTAG
1 AATCACATGACATGAGGTAAAAATAATTGTAACCACAACTCAC
595790 AATCACATGACATGAGGTAAAAATAATTGTAACCACAGA-TCAC
1 AATCACATGACATGAGGTAAAAATAATTGTAACCACA-ACTCAC
595833 AATCA
1 AATCA
595838 AATCAAGTAA
Statistics
Matches: 41, Mismatches: 6, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
43 40 0.98
44 1 0.02
ACGTcount: A:0.46, C:0.14, G:0.15, T:0.24
Consensus pattern (43 bp):
AATCACATGACATGAGGTAAAAATAATTGTAACCACAACTCAC
Found at i:596254 original size:23 final size:21
Alignment explanation
Indices: 596218--596266 Score: 55
Period size: 23 Copynumber: 2.2 Consensus size: 21
596208 ACATTTAAAA
596218 ATTTTAAAATAAATTAAAATACT
1 ATTTTAAAATAAA-TAAAATA-T
*
596241 ATTTTAATAA-AAATAATATAT
1 ATTTTAA-AATAAATAAAATAT
596262 ATTTT
1 ATTTT
596267 TATTAAATAT
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
21 6 0.25
22 6 0.25
23 10 0.42
24 2 0.08
ACGTcount: A:0.53, C:0.02, G:0.00, T:0.45
Consensus pattern (21 bp):
ATTTTAAAATAAATAAAATAT
Found at i:598858 original size:29 final size:31
Alignment explanation
Indices: 598797--598862 Score: 82
Period size: 29 Copynumber: 2.2 Consensus size: 31
598787 GATGACTCGA
* * **
598797 ATAAATTTTTTAATATTTTAATGATTATTTT
1 ATAAATTTTTTAATATTTGAATAATTAAATT
598828 ATAAATTTTTTAA-A-TTGAATAATTAAATT
1 ATAAATTTTTTAATATTTGAATAATTAAATT
598857 ATAAAT
1 ATAAAT
598863 ATACTAATAA
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
29 17 0.55
30 1 0.03
31 13 0.42
ACGTcount: A:0.44, C:0.00, G:0.03, T:0.53
Consensus pattern (31 bp):
ATAAATTTTTTAATATTTGAATAATTAAATT
Found at i:600279 original size:6 final size:6
Alignment explanation
Indices: 600268--600299 Score: 64
Period size: 6 Copynumber: 5.3 Consensus size: 6
600258 TTACACTTCA
600268 TGAAGT TGAAGT TGAAGT TGAAGT TGAAGT TG
1 TGAAGT TGAAGT TGAAGT TGAAGT TGAAGT TG
600300 TGGGTTTAAA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 26 1.00
ACGTcount: A:0.31, C:0.00, G:0.34, T:0.34
Consensus pattern (6 bp):
TGAAGT
Found at i:600901 original size:7 final size:7
Alignment explanation
Indices: 600889--600916 Score: 56
Period size: 7 Copynumber: 4.0 Consensus size: 7
600879 CGAAAAAAAC
600889 TTCGAAT
1 TTCGAAT
600896 TTCGAAT
1 TTCGAAT
600903 TTCGAAT
1 TTCGAAT
600910 TTCGAAT
1 TTCGAAT
600917 AATTCGAATC
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 21 1.00
ACGTcount: A:0.29, C:0.14, G:0.14, T:0.43
Consensus pattern (7 bp):
TTCGAAT
Found at i:605069 original size:29 final size:29
Alignment explanation
Indices: 605006--605072 Score: 75
Period size: 29 Copynumber: 2.3 Consensus size: 29
604996 TACTAAATTT
605006 GAAATTTAATCCATATACTTTTATTTTTA
1 GAAATTTAATCCATATACTTTTATTTTTA
* **
605035 GGAATTTAATCTTTA-ACTTTTCATATTTTA
1 GAAATTTAATCCATATACTTTT-AT-TTTTA
605065 -AAATTTAA
1 GAAATTTAA
605073 GTTCAACTGT
Statistics
Matches: 32, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
28 6 0.19
29 21 0.66
30 5 0.16
ACGTcount: A:0.36, C:0.09, G:0.04, T:0.51
Consensus pattern (29 bp):
GAAATTTAATCCATATACTTTTATTTTTA
Found at i:607547 original size:22 final size:22
Alignment explanation
Indices: 607505--607547 Score: 52
Period size: 22 Copynumber: 2.0 Consensus size: 22
607495 TATCTTAACT
*
607505 ATTTTAATTTATCAATAATTAC
1 ATTTTAATTAATCAATAATTAC
*
607527 ATTTTAAATTAAT-AATTATTA
1 ATTTT-AATTAATCAATAATTA
607548 AATTATCAAA
Statistics
Matches: 18, Mismatches: 2, Indels: 2
0.82 0.09 0.09
Matches are distributed among these distances:
22 12 0.67
23 6 0.33
ACGTcount: A:0.44, C:0.05, G:0.00, T:0.51
Consensus pattern (22 bp):
ATTTTAATTAATCAATAATTAC
Found at i:627285 original size:20 final size:19
Alignment explanation
Indices: 627246--627286 Score: 55
Period size: 20 Copynumber: 2.1 Consensus size: 19
627236 TCCAGAACTT
**
627246 TCTTTTTTTTTTTTTTTTG
1 TCTTTTTTTTTTTTCCTTG
627265 TCTTTTTCTTTTTTTCCTTG
1 TCTTTTT-TTTTTTTCCTTG
627285 TC
1 TC
627287 GTGGAATTAT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
19 7 0.37
20 12 0.63
ACGTcount: A:0.00, C:0.15, G:0.05, T:0.80
Consensus pattern (19 bp):
TCTTTTTTTTTTTTCCTTG
Found at i:629734 original size:28 final size:28
Alignment explanation
Indices: 629703--629756 Score: 74
Period size: 29 Copynumber: 1.9 Consensus size: 28
629693 ATTATTATAT
*
629703 TAATT-ATTTATATATTTATAATTTTAAA
1 TAATTAATTTAAATATTTAT-ATTTTAAA
*
629731 TAATTAATTTAAATTTTTATATTTTA
1 TAATTAATTTAAATATTTATATTTTA
629757 GAAGATTAAA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
28 11 0.48
29 12 0.52
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (28 bp):
TAATTAATTTAAATATTTATATTTTAAA
Found at i:644897 original size:3 final size:3
Alignment explanation
Indices: 644889--644916 Score: 56
Period size: 3 Copynumber: 9.3 Consensus size: 3
644879 CTTTCTTTGT
644889 TTC TTC TTC TTC TTC TTC TTC TTC TTC T
1 TTC TTC TTC TTC TTC TTC TTC TTC TTC T
644917 CGAGGTTCTC
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.00, C:0.32, G:0.00, T:0.68
Consensus pattern (3 bp):
TTC
Found at i:657587 original size:2 final size:2
Alignment explanation
Indices: 657582--657609 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
657572 TTTTTTTGAA
657582 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
657610 GGATGTGAAT
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:664040 original size:29 final size:29
Alignment explanation
Indices: 663989--664044 Score: 76
Period size: 29 Copynumber: 1.9 Consensus size: 29
663979 CTCTATACCT
*
663989 GATCAAATTAGTCCCTCTACTATTAAATG
1 GATCAAATTAGTCCCTCGACTATTAAATG
* * *
664018 GATCAATTTAGTCCCTGGGCTATTAAA
1 GATCAAATTAGTCCCTCGACTATTAAA
664045 AAGAATTCAA
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
29 23 1.00
ACGTcount: A:0.32, C:0.20, G:0.14, T:0.34
Consensus pattern (29 bp):
GATCAAATTAGTCCCTCGACTATTAAATG
Found at i:682095 original size:30 final size:30
Alignment explanation
Indices: 682059--682115 Score: 105
Period size: 30 Copynumber: 1.9 Consensus size: 30
682049 TAGTTTTTGC
682059 ATAATGTAATTTATATTATATAAAAATAAT
1 ATAATGTAATTTATATTATATAAAAATAAT
*
682089 ATAATGTGATTTATATTATATAAAAAT
1 ATAATGTAATTTATATTATATAAAAAT
682116 TAAATATGTT
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
30 26 1.00
ACGTcount: A:0.51, C:0.00, G:0.05, T:0.44
Consensus pattern (30 bp):
ATAATGTAATTTATATTATATAAAAATAAT
Found at i:701006 original size:9 final size:9
Alignment explanation
Indices: 700992--701016 Score: 50
Period size: 9 Copynumber: 2.8 Consensus size: 9
700982 ACTGCTAAAC
700992 AAAAAAAGA
1 AAAAAAAGA
701001 AAAAAAAGA
1 AAAAAAAGA
701010 AAAAAAA
1 AAAAAAA
701017 AGAGAGATCA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 16 1.00
ACGTcount: A:0.92, C:0.00, G:0.08, T:0.00
Consensus pattern (9 bp):
AAAAAAAGA
Found at i:717798 original size:30 final size:30
Alignment explanation
Indices: 717758--717821 Score: 85
Period size: 31 Copynumber: 2.1 Consensus size: 30
717748 ATTTTAAGAA
717758 TTGATTAATATCAAATTT-ATATATAAATT
1 TTGATTAATATCAAATTTGATATATAAATT
** *
717787 TTGATTTAATATGTAATTTGATATATGAATT
1 TTGA-TTAATATCAAATTTGATATATAAATT
717818 TTGA
1 TTGA
717822 CTTGGTGTTA
Statistics
Matches: 30, Mismatches: 3, Indels: 2
0.86 0.09 0.06
Matches are distributed among these distances:
29 4 0.13
30 12 0.40
31 14 0.47
ACGTcount: A:0.39, C:0.02, G:0.09, T:0.50
Consensus pattern (30 bp):
TTGATTAATATCAAATTTGATATATAAATT
Found at i:718989 original size:2 final size:2
Alignment explanation
Indices: 718982--719006 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
718972 CTGCACATAA
718982 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 A
719007 AGAAAAAATA
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:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:721566 original size:2 final size:2
Alignment explanation
Indices: 721559--721592 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
721549 ATCAATTGTC
721559 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
721593 TCAAATCTTA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:723902 original size:65 final size:65
Alignment explanation
Indices: 723822--723953 Score: 246
Period size: 65 Copynumber: 2.0 Consensus size: 65
723812 TTTAAATTAG
*
723822 TCCTTATATTTCAAAACATTTTAATTGAATGCTCACAAGTTCAGTTATCGTATCAATTAAGTCTT
1 TCCTTATATTTCAAAACATTTTAATTGAACGCTCACAAGTTCAGTTATCGTATCAATTAAGTCTT
*
723887 TCCTTATATTTCAAAACATTTTAATTGAACGCTCACAAGTTCAGTTATCTTATCAATTAAGTCTT
1 TCCTTATATTTCAAAACATTTTAATTGAACGCTCACAAGTTCAGTTATCGTATCAATTAAGTCTT
723952 TC
1 TC
723954 TGTCTATCTA
Statistics
Matches: 65, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
65 65 1.00
ACGTcount: A:0.32, C:0.18, G:0.08, T:0.42
Consensus pattern (65 bp):
TCCTTATATTTCAAAACATTTTAATTGAACGCTCACAAGTTCAGTTATCGTATCAATTAAGTCTT
Found at i:731037 original size:18 final size:17
Alignment explanation
Indices: 730995--731037 Score: 50
Period size: 18 Copynumber: 2.5 Consensus size: 17
730985 CGGTTAGGTT
730995 ATCGATTCGTCGATTAA
1 ATCGATTCGTCGATTAA
* * *
731012 ATCAATTCGATCGTTTCA
1 ATCGATTCG-TCGATTAA
731030 ATCGATTC
1 ATCGATTC
731038 AATTAAAAAA
Statistics
Matches: 21, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
17 8 0.38
18 13 0.62
ACGTcount: A:0.28, C:0.21, G:0.14, T:0.37
Consensus pattern (17 bp):
ATCGATTCGTCGATTAA
Found at i:741316 original size:39 final size:40
Alignment explanation
Indices: 741248--741418 Score: 115
Period size: 39 Copynumber: 4.4 Consensus size: 40
741238 TCGTGCGATG
** *
741248 TTTACAGTGTCACTGCCAAATCGGA-ATAGCAT-CATAGTA
1 TTTACAGTGTCACTGCCAGTTC-AATATAGCATGCATAGTA
*
741287 TTTACAGTGTCACTGCCAGTTCAATATAGC-TGCACT-GTG
1 TTTACAGTGTCACTGCCAGTTCAATATAGCATGCA-TAGTA
* * * * * * *
741326 TTTACAGTGTCACCGTCAGTTCAGTGTTGTATTGCA-A-TG
1 TTTACAGTGTCACTGCCAGTTCAATATAGCA-TGCATAGTA
* * * *
741365 TTTACAGTGTCACTGTCAGTTCAGTATTGTATTGC--AGTA
1 TTTACAGTGTCACTGCCAGTTCAATATAGCA-TGCATAGTA
741404 TTTACAGTGTCACTG
1 TTTACAGTGTCACTG
741419 TCAATTCAGT
Statistics
Matches: 112, Mismatches: 13, Indels: 14
0.81 0.09 0.10
Matches are distributed among these distances:
38 3 0.03
39 104 0.93
40 1 0.01
41 4 0.04
ACGTcount: A:0.25, C:0.19, G:0.20, T:0.36
Consensus pattern (40 bp):
TTTACAGTGTCACTGCCAGTTCAATATAGCATGCATAGTA
Found at i:741412 original size:117 final size:116
Alignment explanation
Indices: 741283--741493 Score: 282
Period size: 117 Copynumber: 1.8 Consensus size: 116
741273 ATAGCATCAT
* * *
741283 AGTATTTACAGTGTCACTGCCAGTTCAATATAG-CTGCACTGTGTTTACAGTGTCACCG-TCAGT
1 AGTATTTACAGTGTCACTGCCAATTCAATATAGACTGCA--GTGTTGACAATGTCACCGCT-AGT
*
741346 TCAGTGTTGTATTGCAATGTTTACAGTGTCACTGTCAGTTCAGTATTGTATTGC
63 TCAGTATTGTATTGCAATGTTTACAGTGTCACTGTCAGTTCAGTATTGTATTGC
* * * * *
741400 AGTATTTACAGTGTCACTGTCAATTCAGTATTGTATTGCAGTGTTGACAATGTCACTGCTAGTTC
1 AGTATTTACAGTGTCACTGCCAATTCAATATAG-ACTGCAGTGTTGACAATGTCACCGCTAGTTC
*
741465 AGTATTGTATTGCAATGTTTACATTGTCA
65 AGTATTGTATTGCAATGTTTACAGTGTCA
741494 TTATCAATTC
Statistics
Matches: 81, Mismatches: 10, Indels: 6
0.84 0.10 0.06
Matches are distributed among these distances:
117 76 0.94
118 1 0.01
119 4 0.05
ACGTcount: A:0.24, C:0.17, G:0.20, T:0.39
Consensus pattern (116 bp):
AGTATTTACAGTGTCACTGCCAATTCAATATAGACTGCAGTGTTGACAATGTCACCGCTAGTTCA
GTATTGTATTGCAATGTTTACAGTGTCACTGTCAGTTCAGTATTGTATTGC
Found at i:741419 original size:39 final size:39
Alignment explanation
Indices: 741287--741493 Score: 249
Period size: 39 Copynumber: 5.3 Consensus size: 39
741277 CATCATAGTA
* * * *
741287 TTTACAGTGTCACTGCCAGTTCAATATAG--CTGCACTGTG
1 TTTACAGTGTCACTGTCAGTTCAGTATTGTATTGCA--GTG
* * *
741326 TTTACAGTGTCACCGTCAGTTCAGTGTTGTATTGCAATG
1 TTTACAGTGTCACTGTCAGTTCAGTATTGTATTGCAGTG
*
741365 TTTACAGTGTCACTGTCAGTTCAGTATTGTATTGCAGTA
1 TTTACAGTGTCACTGTCAGTTCAGTATTGTATTGCAGTG
*
741404 TTTACAGTGTCACTGTCAATTCAGTATTGTATTGCAGTG
1 TTTACAGTGTCACTGTCAGTTCAGTATTGTATTGCAGTG
* * *
741443 TTGACAATGTCACTG-CTAGTTCAGTATTGTATTGCAATG
1 TTTACAGTGTCACTGTC-AGTTCAGTATTGTATTGCAGTG
*
741482 TTTACATTGTCA
1 TTTACAGTGTCA
741494 TTATCAATTC
Statistics
Matches: 146, Mismatches: 19, Indels: 6
0.85 0.11 0.04
Matches are distributed among these distances:
38 1 0.01
39 141 0.97
41 4 0.03
ACGTcount: A:0.23, C:0.17, G:0.20, T:0.39
Consensus pattern (39 bp):
TTTACAGTGTCACTGTCAGTTCAGTATTGTATTGCAGTG
Found at i:754065 original size:2 final size:2
Alignment explanation
Indices: 754054--754105 Score: 70
Period size: 2 Copynumber: 26.5 Consensus size: 2
754044 TATACATTTT
* *
754054 TA TA TA -A TA TA TA TA TA TA TA GA GA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
*
754095 TA TA GA TA TA T
1 TA TA TA TA TA T
754106 TAATTTTTTT
Statistics
Matches: 45, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
1 1 0.02
2 44 0.98
ACGTcount: A:0.50, C:0.00, G:0.06, T:0.44
Consensus pattern (2 bp):
TA
Found at i:755805 original size:4 final size:4
Alignment explanation
Indices: 755796--755833 Score: 76
Period size: 4 Copynumber: 9.5 Consensus size: 4
755786 GCTAGAGCTT
755796 TTTC TTTC TTTC TTTC TTTC TTTC TTTC TTTC TTTC TT
1 TTTC TTTC TTTC TTTC TTTC TTTC TTTC TTTC TTTC TT
755834 GTTAAAAGGG
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 34 1.00
ACGTcount: A:0.00, C:0.24, G:0.00, T:0.76
Consensus pattern (4 bp):
TTTC
Found at i:757444 original size:43 final size:44
Alignment explanation
Indices: 757383--757473 Score: 175
Period size: 43 Copynumber: 2.1 Consensus size: 44
757373 ATAGGAATAA
757383 TACCGAAATGTAATATTACTTACCACATTATTGGG-TTTTTGGT
1 TACCGAAATGTAATATTACTTACCACATTATTGGGTTTTTTGGT
757426 TACCGAAATGTAATATTACTTACCACATTATTGGGTTTTTTGGT
1 TACCGAAATGTAATATTACTTACCACATTATTGGGTTTTTTGGT
757470 TACC
1 TACC
757474 CTATTTGGTT
Statistics
Matches: 47, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
43 35 0.74
44 12 0.26
ACGTcount: A:0.27, C:0.15, G:0.15, T:0.42
Consensus pattern (44 bp):
TACCGAAATGTAATATTACTTACCACATTATTGGGTTTTTTGGT
Found at i:766202 original size:2 final size:2
Alignment explanation
Indices: 766191--766230 Score: 73
Period size: 2 Copynumber: 20.5 Consensus size: 2
766181 ATACTTCCAT
766191 TA TA -A TA TA 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 TA TA TA TA TA T
766231 GTCTTTTGTT
Statistics
Matches: 37, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
1 1 0.03
2 36 0.97
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:767552 original size:23 final size:22
Alignment explanation
Indices: 767510--767556 Score: 60
Period size: 23 Copynumber: 2.0 Consensus size: 22
767500 TAAGTTAATC
767510 ATATTATTTTTTTGAAAATATTT
1 ATATTATTTTTTTG-AAATATTT
767533 ATATTATTTTTAATTG-AATATTT
1 ATATTATTTTT--TTGAAATATTT
767556 A
1 A
767557 ATAAGTTTAT
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
23 19 0.86
25 3 0.14
ACGTcount: A:0.36, C:0.00, G:0.04, T:0.60
Consensus pattern (22 bp):
ATATTATTTTTTTGAAATATTT
Found at i:769347 original size:30 final size:30
Alignment explanation
Indices: 769287--769346 Score: 84
Period size: 31 Copynumber: 2.0 Consensus size: 30
769277 ATCTCTTATT
* *
769287 TAAAAATTGAAAAAAAAACTATATTAAAAA
1 TAAAAATTGAAAAAAAAACTACAATAAAAA
*
769317 TAAAAATATGATAAAAAAACTACAATAAAA
1 TAAAAAT-TGAAAAAAAAACTACAATAAAA
769347 TTAATATTAC
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
30 7 0.27
31 19 0.73
ACGTcount: A:0.70, C:0.05, G:0.03, T:0.22
Consensus pattern (30 bp):
TAAAAATTGAAAAAAAAACTACAATAAAAA
Found at i:770267 original size:30 final size:31
Alignment explanation
Indices: 770189--770268 Score: 83
Period size: 30 Copynumber: 2.6 Consensus size: 31
770179 TTGAAGGAAT
* *
770189 CCAAGTTT-GGGGACCAAAATGGACCTAATTG
1 CCAAGTTTAGGGG-CCAAAATGGAACTAATTA
* ** *
770220 CCAAATTTAGGTACCAAAAT-GAACTAGTTA
1 CCAAGTTTAGGGGCCAAAATGGAACTAATTA
770250 CCAAGTTTAGGGGCCAAAA
1 CCAAGTTTAGGGGCCAAAA
770269 ATTATATTAT
Statistics
Matches: 39, Mismatches: 9, Indels: 3
0.76 0.18 0.06
Matches are distributed among these distances:
30 23 0.59
31 14 0.36
32 2 0.05
ACGTcount: A:0.38, C:0.19, G:0.21, T:0.23
Consensus pattern (31 bp):
CCAAGTTTAGGGGCCAAAATGGAACTAATTA
Found at i:778284 original size:101 final size:101
Alignment explanation
Indices: 778109--778311 Score: 388
Period size: 101 Copynumber: 2.0 Consensus size: 101
778099 CTTCACAGAG
*
778109 TAGCCTGCAAGCAAATAGCATGGATTGCATTAAGGGCTACTGCTAGTTTAAGTCGGTTCAAATAT
1 TAGCCTGCAAGCAAATAGCATGGATTGCATTAAGGGCTACTGCTAGTTTAAGTCAGTTCAAATAT
778174 AAAATGGTAGATAAGGTCATGTATTTGTGTTTATAT
66 AAAATGGTAGATAAGGTCATGTATTTGTGTTTATAT
778210 TAGCCTGCAAGCAAATAGCATGGATTGCATTAAGGGCTACTGCTAGTTTAAGTCAGTTCAAATAT
1 TAGCCTGCAAGCAAATAGCATGGATTGCATTAAGGGCTACTGCTAGTTTAAGTCAGTTCAAATAT
*
778275 AAAATGGTAGATAGGGTCATGTATTTGTGTTTATAT
66 AAAATGGTAGATAAGGTCATGTATTTGTGTTTATAT
778311 T
1 T
778312 TGGTTAGTTT
Statistics
Matches: 100, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
101 100 1.00
ACGTcount: A:0.32, C:0.12, G:0.23, T:0.34
Consensus pattern (101 bp):
TAGCCTGCAAGCAAATAGCATGGATTGCATTAAGGGCTACTGCTAGTTTAAGTCAGTTCAAATAT
AAAATGGTAGATAAGGTCATGTATTTGTGTTTATAT
Found at i:778843 original size:14 final size:16
Alignment explanation
Indices: 778826--778860 Score: 56
Period size: 14 Copynumber: 2.3 Consensus size: 16
778816 AAGAATTTAA
778826 TTTAATGAA-A-AAAT
1 TTTAATGAATATAAAT
778840 TTTAATGAATATAAAT
1 TTTAATGAATATAAAT
778856 TTTAA
1 TTTAA
778861 AAAATGAAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
14 9 0.47
15 1 0.05
16 9 0.47
ACGTcount: A:0.51, C:0.00, G:0.06, T:0.43
Consensus pattern (16 bp):
TTTAATGAATATAAAT
Found at i:778895 original size:30 final size:28
Alignment explanation
Indices: 778851--778921 Score: 74
Period size: 29 Copynumber: 2.4 Consensus size: 28
778841 TTAATGAATA
778851 TAAATTTTAAAAAATGAAAA-ATAGAGAGAT
1 TAAATTTTAAAAAAT-AAAATATA-AG-GAT
778881 TAAATTCTT-AAAAATAAAATTATAAGGAT
1 TAAATT-TTAAAAAATAAAA-TATAAGGAT
*
778910 TAAATTTCAAAA
1 TAAATTTTAAAA
778922 TTTGAAGATT
Statistics
Matches: 36, Mismatches: 1, Indels: 9
0.78 0.02 0.20
Matches are distributed among these distances:
28 1 0.03
29 16 0.44
30 14 0.39
31 5 0.14
ACGTcount: A:0.58, C:0.03, G:0.08, T:0.31
Consensus pattern (28 bp):
TAAATTTTAAAAAATAAAATATAAGGAT
Found at i:779830 original size:3 final size:3
Alignment explanation
Indices: 779822--779852 Score: 55
Period size: 3 Copynumber: 10.7 Consensus size: 3
779812 CACCGGCGCC
779822 TCT TCT TCT TCT TCT TCT TCT TCT TC- TCT TC
1 TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TC
779853 AAGCTTGGTC
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
2 2 0.07
3 25 0.93
ACGTcount: A:0.00, C:0.35, G:0.00, T:0.65
Consensus pattern (3 bp):
TCT
Found at i:780770 original size:19 final size:19
Alignment explanation
Indices: 780746--780782 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
780736 GAGTAATGTA
780746 GTTCGAGATTATGTTATTG
1 GTTCGAGATTATGTTATTG
* *
780765 GTTCGAGTTTTTGTTATT
1 GTTCGAGATTATGTTATT
780783 CATGCATCCA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 16 1.00
ACGTcount: A:0.16, C:0.05, G:0.24, T:0.54
Consensus pattern (19 bp):
GTTCGAGATTATGTTATTG
Found at i:785032 original size:33 final size:33
Alignment explanation
Indices: 784990--785065 Score: 107
Period size: 33 Copynumber: 2.3 Consensus size: 33
784980 TTTGATGACT
*
784990 ATGAAGATGATAGCGAATTCGTTGACGACCACG
1 ATGAAGATGATAGCGAATTCGTTGACGACCACA
* * **
785023 ATGAAGATGATAGCGAATTTGTTGATGATGACA
1 ATGAAGATGATAGCGAATTCGTTGACGACCACA
785056 ATGAAGATGA
1 ATGAAGATGA
785066 GGCCGACAAC
Statistics
Matches: 38, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
33 38 1.00
ACGTcount: A:0.37, C:0.11, G:0.28, T:0.25
Consensus pattern (33 bp):
ATGAAGATGATAGCGAATTCGTTGACGACCACA
Found at i:787537 original size:10 final size:9
Alignment explanation
Indices: 787520--787545 Score: 52
Period size: 9 Copynumber: 2.9 Consensus size: 9
787510 ACCTCCAGAC
787520 ATAAAAAAA
1 ATAAAAAAA
787529 ATAAAAAAA
1 ATAAAAAAA
787538 ATAAAAAA
1 ATAAAAAA
787546 TACCAACTAC
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 17 1.00
ACGTcount: A:0.88, C:0.00, G:0.00, T:0.12
Consensus pattern (9 bp):
ATAAAAAAA
Found at i:797878 original size:22 final size:23
Alignment explanation
Indices: 797853--797896 Score: 72
Period size: 23 Copynumber: 2.0 Consensus size: 23
797843 AGATCACTAC
797853 AATAAATT-ATTTTTAAAATTTT
1 AATAAATTCATTTTTAAAATTTT
*
797875 AATATATTCATTTTTAAAATTT
1 AATAAATTCATTTTTAAAATTT
797897 CAAAATTTCA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
22 7 0.35
23 13 0.65
ACGTcount: A:0.43, C:0.02, G:0.00, T:0.55
Consensus pattern (23 bp):
AATAAATTCATTTTTAAAATTTT
Found at i:801594 original size:21 final size:21
Alignment explanation
Indices: 801569--801612 Score: 88
Period size: 21 Copynumber: 2.1 Consensus size: 21
801559 TTGTTGTAAG
801569 TACTACAAGAGTTTTGAATTA
1 TACTACAAGAGTTTTGAATTA
801590 TACTACAAGAGTTTTGAATTA
1 TACTACAAGAGTTTTGAATTA
801611 TA
1 TA
801613 GTTTAATTTC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.39, C:0.09, G:0.14, T:0.39
Consensus pattern (21 bp):
TACTACAAGAGTTTTGAATTA
Found at i:802512 original size:21 final size:22
Alignment explanation
Indices: 802418--802593 Score: 106
Period size: 25 Copynumber: 7.5 Consensus size: 22
802408 ACACTAGCGC
* *
802418 GCTCTCTGTTTAGCACGTCTCGT
1 GCTCTCTGTTTAGCACTTAT-GT
* * *
802441 GCTCTCTATTATTAACACTGTGTGT
1 GCTCTCT-GT-TTAGCACT-TATGT
*
802466 GCTCTCTGTTGCCCAGCACTTATGT
1 GCTCTCTGTT---TAGCACTTATGT
* *
802491 GCTCTCTGATTAGTACTT-TGT
1 GCTCTCTGTTTAGCACTTATGT
*
802512 GTACTCTCTGTTTAGCACTGTGTGT
1 G--CTCTCTGTTTAGCACT-TATGT
802537 GCTCTCTGTTGCCTAGCACTTATGT
1 GCTCTCTGTT---TAGCACTTATGT
*
802562 GCTCTCTG-TTAGTACTT-TGGT
1 GCTCTCTGTTTAGCACTTAT-GT
*
802583 ACTCTCTGTTT
1 GCTCTCTGTTT
802594 GTTCCGTATA
Statistics
Matches: 122, Mismatches: 16, Indels: 31
0.72 0.09 0.18
Matches are distributed among these distances:
20 1 0.01
21 20 0.16
22 8 0.07
23 31 0.25
24 4 0.03
25 44 0.36
26 14 0.11
ACGTcount: A:0.12, C:0.24, G:0.20, T:0.43
Consensus pattern (22 bp):
GCTCTCTGTTTAGCACTTATGT
Found at i:802526 original size:23 final size:23
Alignment explanation
Indices: 802480--802593 Score: 96
Period size: 23 Copynumber: 5.0 Consensus size: 23
802470 TCTGTTGCCC
*
802480 AGCACTTATGTG--CTCTCTGATT
1 AGCACTT-TGTGTACTCTCTGTTT
*
802502 AGTACTTTGTGTACTCTCTGTTT
1 AGCACTTTGTGTACTCTCTGTTT
* *
802525 AGCACTGTGTGTGCTCTCTGTTGCCT
1 AGCACTTTGTGTACTCTCTGTT---T
802551 AGCACTTATGTG--CTCTCTG-TT
1 AGCACTT-TGTGTACTCTCTGTTT
*
802572 AGTACTTTG-GTACTCTCTGTTT
1 AGCACTTTGTGTACTCTCTGTTT
802594 GTTCCGTATA
Statistics
Matches: 76, Mismatches: 7, Indels: 18
0.75 0.07 0.18
Matches are distributed among these distances:
19 1 0.01
20 2 0.03
21 18 0.24
22 8 0.11
23 28 0.37
24 1 0.01
25 7 0.09
26 7 0.09
27 4 0.05
ACGTcount: A:0.13, C:0.22, G:0.20, T:0.45
Consensus pattern (23 bp):
AGCACTTTGTGTACTCTCTGTTT
Found at i:802546 original size:71 final size:69
Alignment explanation
Indices: 802456--802593 Score: 249
Period size: 71 Copynumber: 2.0 Consensus size: 69
802446 CTATTATTAA
802456 CACTGTGTGTGCTCTCTGTTGCCCAGCACTTATGTGCTCTCTGATTAGTACTTTGTGTACTCTCT
1 CACTGTGTGTGCTCTCTGTTGCCCAGCACTTATGTGCTCTCTG-TTAGTACTTTG-GTACTCTCT
802521 GTTTAG
64 GTTTAG
*
802527 CACTGTGTGTGCTCTCTGTTGCCTAGCACTTATGTGCTCTCTGTTAGTACTTTGGTACTCTCTGT
1 CACTGTGTGTGCTCTCTGTTGCCCAGCACTTATGTGCTCTCTGTTAGTACTTTGGTACTCTCTGT
802592 TT
66 TT
802594 GTTCCGTATA
Statistics
Matches: 66, Mismatches: 1, Indels: 2
0.96 0.01 0.03
Matches are distributed among these distances:
69 13 0.20
70 11 0.17
71 42 0.64
ACGTcount: A:0.12, C:0.24, G:0.21, T:0.43
Consensus pattern (69 bp):
CACTGTGTGTGCTCTCTGTTGCCCAGCACTTATGTGCTCTCTGTTAGTACTTTGGTACTCTCTGT
TTAG
Found at i:803276 original size:17 final size:19
Alignment explanation
Indices: 803244--803278 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
803234 TTTTTTGAAT
803244 TTTTTTATCATAAATATTC
1 TTTTTTATCATAAATATTC
803263 TTTTTTAT-AT-AATATT
1 TTTTTTATCATAAATATT
803279 TAAAACTACC
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 6 0.38
18 2 0.12
19 8 0.50
ACGTcount: A:0.31, C:0.06, G:0.00, T:0.63
Consensus pattern (19 bp):
TTTTTTATCATAAATATTC
Found at i:803702 original size:29 final size:28
Alignment explanation
Indices: 803649--803716 Score: 75
Period size: 29 Copynumber: 2.4 Consensus size: 28
803639 TTTTTTCAAA
* *
803649 TTTAAAATTTAATTTCTCTAATTTTATT
1 TTTAAAATTTAATTTATCCAATTTTATT
* *
803677 TTTAAGAATTTAATTTATCCACTTTTAAAT
1 TTTAA-AATTTAATTTATCCAATTTT-ATT
803707 TTT-AAATTTA
1 TTTAAAATTTA
803717 CAATATAACC
Statistics
Matches: 34, Mismatches: 4, Indels: 4
0.81 0.10 0.10
Matches are distributed among these distances:
28 11 0.32
29 18 0.53
30 5 0.15
ACGTcount: A:0.35, C:0.07, G:0.01, T:0.56
Consensus pattern (28 bp):
TTTAAAATTTAATTTATCCAATTTTATT
Found at i:803831 original size:18 final size:18
Alignment explanation
Indices: 803788--803828 Score: 57
Period size: 17 Copynumber: 2.3 Consensus size: 18
803778 AAAATATCAC
803788 ATTAATAAATTTATAAAAA
1 ATTAAT-AATTTATAAAAA
*
803807 ATTAATAATTT-TAATAA
1 ATTAATAATTTATAAAAA
803824 ATTAA
1 ATTAA
803829 ATATAAAATT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
17 10 0.48
18 5 0.24
19 6 0.29
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (18 bp):
ATTAATAATTTATAAAAA
Found at i:804436 original size:67 final size:68
Alignment explanation
Indices: 804358--804489 Score: 185
Period size: 68 Copynumber: 2.0 Consensus size: 68
804348 CAAATTTGTC
* * *
804358 TCAAAACTTGAATATTTGAAACTCATT-AGCAAAAGATTCAATATCTTTAATTCCAATATCTTCT
1 TCAAAACTTGAATATTTAAAACTCATTAACCAAAAGATTCAATATATTTAATTCCAATATCTTCT
804422 GTT
66 GTT
* * * * *
804425 TCAAAGCTTGAATTTTTAAAACTCATTAACCTAAAGATTCAATATATTTGATTTCAATATCTTCT
1 TCAAAACTTGAATATTTAAAACTCATTAACCAAAAGATTCAATATATTTAATTCCAATATCTTCT
804490 TCCCGTTAAG
Statistics
Matches: 56, Mismatches: 8, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
67 24 0.43
68 32 0.57
ACGTcount: A:0.37, C:0.16, G:0.07, T:0.40
Consensus pattern (68 bp):
TCAAAACTTGAATATTTAAAACTCATTAACCAAAAGATTCAATATATTTAATTCCAATATCTTCT
GTT
Found at i:804682 original size:16 final size:17
Alignment explanation
Indices: 804651--804685 Score: 54
Period size: 16 Copynumber: 2.1 Consensus size: 17
804641 TTAAAAAAAC
804651 TTAATTAATTAAATTTAT
1 TTAATTAA-TAAATTTAT
804669 TTAATTAA-AAATTTAT
1 TTAATTAATAAATTTAT
804685 T
1 T
804686 CTCATTCCAT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 9 0.53
18 8 0.47
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (17 bp):
TTAATTAATAAATTTAT
Found at i:806919 original size:12 final size:12
Alignment explanation
Indices: 806866--806910 Score: 56
Period size: 12 Copynumber: 3.8 Consensus size: 12
806856 ATAACATCCA
*
806866 AACAAAAA-AAT
1 AACAAAAATAAC
* *
806877 AACTAAAACAAC
1 AACAAAAATAAC
806889 AACAAAAATAAC
1 AACAAAAATAAC
806901 AACAAAAATA
1 AACAAAAATA
806911 GCATCAAAAG
Statistics
Matches: 29, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
11 7 0.24
12 22 0.76
ACGTcount: A:0.76, C:0.16, G:0.00, T:0.09
Consensus pattern (12 bp):
AACAAAAATAAC
Found at i:807661 original size:36 final size:36
Alignment explanation
Indices: 807579--807661 Score: 82
Period size: 35 Copynumber: 2.3 Consensus size: 36
807569 TAATTATCAA
* *
807579 TTTAAATATTTTTTAACAAAAATGTTTTTTCTACATT
1 TTTAAATA-TTTTCAACAAAAATGATTTTTCTACATT
* *
807616 GTT-ATTATTTTCAACAAATAAT-ATTTTTC-ACATTT
1 TTTAAATATTTTCAACAAA-AATGATTTTTCTACA-TT
807651 TTTAAATATTT
1 TTTAAATATTT
807662 ATATATACTA
Statistics
Matches: 37, Mismatches: 6, Indels: 7
0.74 0.12 0.14
Matches are distributed among these distances:
34 3 0.08
35 20 0.54
36 12 0.32
37 2 0.05
ACGTcount: A:0.35, C:0.08, G:0.02, T:0.54
Consensus pattern (36 bp):
TTTAAATATTTTCAACAAAAATGATTTTTCTACATT
Found at i:809751 original size:20 final size:17
Alignment explanation
Indices: 809708--809742 Score: 70
Period size: 17 Copynumber: 2.1 Consensus size: 17
809698 ATTAAAATGA
809708 AATTAATTATTTTTTTT
1 AATTAATTATTTTTTTT
809725 AATTAATTATTTTTTTT
1 AATTAATTATTTTTTTT
809742 A
1 A
809743 TAGTATAATA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (17 bp):
AATTAATTATTTTTTTT
Found at i:810679 original size:20 final size:21
Alignment explanation
Indices: 810656--810695 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
810646 ATCTAAATTT
810656 TAAATT-TAAAAAATAAAAAC
1 TAAATTCTAAAAAATAAAAAC
**
810676 TAAATTCTTTAAAATAAAAA
1 TAAATTCTAAAAAATAAAAA
810696 TATAAAAACT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 6 0.35
21 11 0.65
ACGTcount: A:0.65, C:0.05, G:0.00, T:0.30
Consensus pattern (21 bp):
TAAATTCTAAAAAATAAAAAC
Found at i:812209 original size:22 final size:22
Alignment explanation
Indices: 812159--812209 Score: 52
Period size: 22 Copynumber: 2.4 Consensus size: 22
812149 ATTAAATATA
812159 TTTT-AATATTTATTATAATTT
1 TTTTAAATATTTATTATAATTT
* * *
812180 TATAAAATATTTATTA-ACTTCT
1 TTTTAAATATTTATTATAATT-T
812202 TTTTAAAT
1 TTTTAAAT
812210 TTAAAAAATT
Statistics
Matches: 23, Mismatches: 5, Indels: 3
0.74 0.16 0.10
Matches are distributed among these distances:
21 5 0.22
22 18 0.78
ACGTcount: A:0.37, C:0.04, G:0.00, T:0.59
Consensus pattern (22 bp):
TTTTAAATATTTATTATAATTT
Found at i:817182 original size:14 final size:12
Alignment explanation
Indices: 817161--817196 Score: 54
Period size: 14 Copynumber: 2.8 Consensus size: 12
817151 TTTTAGTATG
817161 TTTTATTATTAT
1 TTTTATTATTAT
817173 ATTGTTATTATTAT
1 -TT-TTATTATTAT
817187 TTTTATTATT
1 TTTTATTATT
817197 TAGATATTAT
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
12 8 0.36
13 4 0.18
14 10 0.45
ACGTcount: A:0.25, C:0.00, G:0.03, T:0.72
Consensus pattern (12 bp):
TTTTATTATTAT
Found at i:821462 original size:17 final size:17
Alignment explanation
Indices: 821421--821463 Score: 50
Period size: 18 Copynumber: 2.5 Consensus size: 17
821411 AAACATTAAA
* *
821421 AATATTTTTTATATTTT
1 AATATTTTTAATAGTTT
*
821438 TATAATTTTTAATAGTTT
1 AAT-ATTTTTAATAGTTT
821456 AATATTTT
1 AATATTTT
821464 AAATTTTAAA
Statistics
Matches: 21, Mismatches: 4, Indels: 2
0.78 0.15 0.07
Matches are distributed among these distances:
17 7 0.33
18 14 0.67
ACGTcount: A:0.33, C:0.00, G:0.02, T:0.65
Consensus pattern (17 bp):
AATATTTTTAATAGTTT
Found at i:827913 original size:29 final size:28
Alignment explanation
Indices: 827855--827914 Score: 68
Period size: 30 Copynumber: 2.1 Consensus size: 28
827845 TAACATTAAC
*
827855 AATTAAAGCTAAATTTTGAAATATAAAA
1 AATTAAAGCTAAATTCTGAAATATAAAA
*
827883 AATTATAAGGCTAAATTCT-AAATTTACAAA
1 AATTA-AA-GCTAAATTCTGAAATATA-AAA
827913 AA
1 AA
827915 ATTATAGGTA
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
28 5 0.19
29 8 0.30
30 14 0.52
ACGTcount: A:0.55, C:0.07, G:0.07, T:0.32
Consensus pattern (28 bp):
AATTAAAGCTAAATTCTGAAATATAAAA
Found at i:827914 original size:30 final size:30
Alignment explanation
Indices: 827855--827920 Score: 75
Period size: 31 Copynumber: 2.2 Consensus size: 30
827845 TAACATTAAC
*
827855 AATTA-AAGCTAAATTTTGAAATAT-AAAA
1 AATTATAAGCTAAATTCTGAAATATAAAAA
*
827883 AATTATAAGGCTAAATTCT-AAATTTACAAAA
1 AATTATAA-GCTAAATTCTGAAATATA-AAAA
827914 AATTATA
1 AATTATA
827921 GGTATTTAGA
Statistics
Matches: 32, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
28 5 0.16
29 7 0.22
30 9 0.28
31 11 0.34
ACGTcount: A:0.55, C:0.06, G:0.06, T:0.33
Consensus pattern (30 bp):
AATTATAAGCTAAATTCTGAAATATAAAAA
Found at i:829187 original size:205 final size:205
Alignment explanation
Indices: 828829--829445 Score: 889
Period size: 205 Copynumber: 3.0 Consensus size: 205
828819 AGAAATTAGA
* * * * * *
828829 AAGTTGAATGCCTTAATAAGGATGCATGGTATGGTGTTTCTATCTTGTAAAGCTTGAAAACTGT-
1 AAGTTGAATGCCTTAATATGGATGCATGATATAGTGTTTCCATCTTGTAATGCTCGAAAACTGTA
* * *
828893 GTATTAACCAGAATGGATGAAAGTATAATTGCATCTTGTGTTTTGTGTTTTAAAATTAGTAATAT
66 G-A--AACCAGAGTGGATGAAAGTATAATTGCATCTTGTGTTTTGTGTTTCAAAATTAGCAATAT
* * *
828958 TTCTGTCATTAACTGCTGATTTGCATGTTCTGCTGCTCTGCCTTGTTTTCATTTGGATGATTTTA
128 TTCTGTCATTAACTGCTAATTTGCATGTTCTGCTGCTCTGCCTTGTTTTCATTTGGATAATTGTA
829023 CCATATATAATGT
193 CCATATATAATGT
* * *
829036 AAGTTGATTGCATTAATATGGATGCATGATATAGTGTTTCCATCTTGTAATGCTCAAAAACTGTA
1 AAGTTGAATGCCTTAATATGGATGCATGATATAGTGTTTCCATCTTGTAATGCTCGAAAACTGTA
*
829101 GAAACCAGAGTGAATTG-AAGTATAATTGCATCTTGTGTTTTGTGTTTCAAAATTAGCAATATTT
66 GAAACCAGAGTGGA-TGAAAGTATAATTGCATCTTGTGTTTTGTGTTTCAAAATTAGCAATATTT
* *
829165 CTGTCTTTAACTGCTAATTTGCATGTTCTGCTGCTCTGCCTTGTTTTCTTTTGGATAATTGTACC
130 CTGTCATTAACTGCTAATTTGCATGTTCTGCTGCTCTGCCTTGTTTTCATTTGGATAATTGTACC
* * *
829230 ATGTAAAATGC
195 ATATATAATGT
* *
829241 GAGTTGAATGCCTTAATATGGATGCATGATATAGTGTTTCCATCTTGTAATGCTCGGAAACTGTA
1 AAGTTGAATGCCTTAATATGGATGCATGATATAGTGTTTCCATCTTGTAATGCTCGAAAACTGTA
* * * *
829306 TAAACCAGAGTGGATGAAAGTATAATTGCATCTTGTGTTTTATGTTTCAAAATTAGCATTATTTT
66 GAAACCAGAGTGGATGAAAGTATAATTGCATCTTGTGTTTTGTGTTTCAAAATTAGCAATATTTC
* * *
829371 TGTCATTAACTGCTGATTTTG-TTGTTCTGCTGCCCTGCCTTGTTTTCATTTGGATAATTGTACC
131 TGTCATTAACTGCT-AATTTGCATGTTCTGCTGCTCTGCCTTGTTTTCATTTGGATAATTGTACC
*
829435 ATACATAATGT
195 ATATATAATGT
829446 GATAATTCCT
Statistics
Matches: 366, Mismatches: 40, Indels: 10
0.88 0.10 0.02
Matches are distributed among these distances:
204 2 0.01
205 300 0.82
206 7 0.02
207 56 0.15
208 1 0.00
ACGTcount: A:0.27, C:0.13, G:0.19, T:0.41
Consensus pattern (205 bp):
AAGTTGAATGCCTTAATATGGATGCATGATATAGTGTTTCCATCTTGTAATGCTCGAAAACTGTA
GAAACCAGAGTGGATGAAAGTATAATTGCATCTTGTGTTTTGTGTTTCAAAATTAGCAATATTTC
TGTCATTAACTGCTAATTTGCATGTTCTGCTGCTCTGCCTTGTTTTCATTTGGATAATTGTACCA
TATATAATGT
Found at i:834785 original size:15 final size:16
Alignment explanation
Indices: 834765--834797 Score: 50
Period size: 15 Copynumber: 2.1 Consensus size: 16
834755 ATTGTTTATT
*
834765 ATATATTATA-TTTAA
1 ATATATTAAATTTTAA
834780 ATATATTAAATTTTAA
1 ATATATTAAATTTTAA
834796 AT
1 AT
834798 TTATAGTTTT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
15 9 0.56
16 7 0.44
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (16 bp):
ATATATTAAATTTTAA
Found at i:845159 original size:14 final size:15
Alignment explanation
Indices: 845132--845160 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
845122 TTTAAATTTA
845132 TAAATTATAAAAATT
1 TAAATTATAAAAATT
845147 TAAATTA-AAAAATT
1 TAAATTATAAAAATT
845161 ATCATTTTAG
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 7 0.50
15 7 0.50
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (15 bp):
TAAATTATAAAAATT
Found at i:849948 original size:3 final size:3
Alignment explanation
Indices: 849940--849965 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
849930 CCAAACTTAA
849940 AAT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AA
849966 AACTGGCGTG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (3 bp):
AAT
Found at i:851114 original size:29 final size:26
Alignment explanation
Indices: 851050--851116 Score: 64
Period size: 27 Copynumber: 2.4 Consensus size: 26
851040 ATACCATATC
*
851050 AATTATTATATCAATAATTTATAATA
1 AATTATTAAATCAATAATTTATAATA
*
851076 ATTTAATTAAATCAA-AATTTCATATATAA
1 AATT-ATTAAATCAATAATTT-ATA-AT-A
851105 AATTACTTAAAT
1 AATTA-TTAAAT
851117 TCATTAAACA
Statistics
Matches: 33, Mismatches: 3, Indels: 7
0.77 0.07 0.16
Matches are distributed among these distances:
26 8 0.24
27 12 0.36
28 3 0.09
29 10 0.30
ACGTcount: A:0.51, C:0.06, G:0.00, T:0.43
Consensus pattern (26 bp):
AATTATTAAATCAATAATTTATAATA
Found at i:851757 original size:17 final size:18
Alignment explanation
Indices: 851718--851759 Score: 68
Period size: 18 Copynumber: 2.4 Consensus size: 18
851708 AGTGTTTTTT
*
851718 AAAAATATTTTTGATATA
1 AAAAATACTTTTGATATA
851736 AAAAATACTTTTGA-ATA
1 AAAAATACTTTTGATATA
851753 AAAAATA
1 AAAAATA
851760 ATGCTAAACA
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
17 10 0.43
18 13 0.57
ACGTcount: A:0.57, C:0.02, G:0.05, T:0.36
Consensus pattern (18 bp):
AAAAATACTTTTGATATA
Found at i:853995 original size:78 final size:78
Alignment explanation
Indices: 853866--854330 Score: 822
Period size: 78 Copynumber: 6.0 Consensus size: 78
853856 TTAAAAATCA
* * * **
853866 TTAAAATTCCGGCCATAATTTTAATTCAGAGTAAATAACTCCGTTTAAACAAAGTAGTTGAAACT
1 TTAAAATTCCGGCCATCATTTTAATTGAGAGTAAATTACTCCCCTTAAACAAAGTAGTTGAAACT
853931 TCCATTATTTATC
66 TCCATTATTTATC
*
853944 TTAAAATTCCGGCCATCATTTTAATTGAGAGTAAATAACTCCCCTTAAACAAAGTAGTTGAAACT
1 TTAAAATTCCGGCCATCATTTTAATTGAGAGTAAATTACTCCCCTTAAACAAAGTAGTTGAAACT
854009 TCCATTATTTATC
66 TCCATTATTTATC
* * *
854022 TTAAAATTCCAGCCATCATTTTATTTGAGAGTAAATTACTCCCCTTAAACAAAGTAGTTTAAACT
1 TTAAAATTCCGGCCATCATTTTAATTGAGAGTAAATTACTCCCCTTAAACAAAGTAGTTGAAACT
854087 TCCATTATTTATC
66 TCCATTATTTATC
*
854100 TTAAAATTCCGGCCATCATTTTAATTGAGAGTAAATTACTCCCCTTAAACAAAGTAGTTTAAACT
1 TTAAAATTCCGGCCATCATTTTAATTGAGAGTAAATTACTCCCCTTAAACAAAGTAGTTGAAACT
854165 TCCATTATTTATC
66 TCCATTATTTATC
*
854178 TTAAAATTCCGGCCATCATTTTAATTGAGAGTAAATTACTCCCCTTAAACAAAATAGTTGAAACT
1 TTAAAATTCCGGCCATCATTTTAATTGAGAGTAAATTACTCCCCTTAAACAAAGTAGTTGAAACT
854243 TCCATTATTTATC
66 TCCATTATTTATC
*
854256 TTAAAATTCCAGCCATCATTTTAATTGAGAGTAAATTACTCCCCTTAAACAAAGTAGTTGAAACT
1 TTAAAATTCCGGCCATCATTTTAATTGAGAGTAAATTACTCCCCTTAAACAAAGTAGTTGAAACT
854321 TCCATTATTT
66 TCCATTATTT
854331 TTTAGTAGTA
Statistics
Matches: 373, Mismatches: 14, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
78 373 1.00
ACGTcount: A:0.36, C:0.19, G:0.09, T:0.36
Consensus pattern (78 bp):
TTAAAATTCCGGCCATCATTTTAATTGAGAGTAAATTACTCCCCTTAAACAAAGTAGTTGAAACT
TCCATTATTTATC
Found at i:860655 original size:23 final size:24
Alignment explanation
Indices: 860617--860664 Score: 71
Period size: 23 Copynumber: 2.0 Consensus size: 24
860607 AATATTAATT
*
860617 ACAAACAAATACTAATCACTAAAA
1 ACAAACAAATAATAATCACTAAAA
*
860641 ACAAA-AAATAATAATTACTAAAA
1 ACAAACAAATAATAATCACTAAAA
860664 A
1 A
860665 AACGCCCAAT
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
23 17 0.77
24 5 0.23
ACGTcount: A:0.67, C:0.15, G:0.00, T:0.19
Consensus pattern (24 bp):
ACAAACAAATAATAATCACTAAAA
Found at i:866674 original size:27 final size:28
Alignment explanation
Indices: 866632--866686 Score: 85
Period size: 27 Copynumber: 2.0 Consensus size: 28
866622 GAATAACAAA
*
866632 AAAATATATTTCAAAACTTGTTTAAATT
1 AAAATATATTTCAAAACTTATTTAAATT
*
866660 AAAAT-TATTTTAAAACTTATTTAAATT
1 AAAATATATTTCAAAACTTATTTAAATT
866687 TGAGCTGAAT
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
27 20 0.80
28 5 0.20
ACGTcount: A:0.47, C:0.05, G:0.02, T:0.45
Consensus pattern (28 bp):
AAAATATATTTCAAAACTTATTTAAATT
Found at i:871905 original size:31 final size:30
Alignment explanation
Indices: 871868--871954 Score: 90
Period size: 31 Copynumber: 2.8 Consensus size: 30
871858 CAATTAGACT
871868 CTTCAAAAGCTTTTGTAAAATTTTATT-AAAC
1 CTTCAAAA--TTTTGTAAAATTTTATTAAAAC
*
871899 CTTCAAAATTTT-TGAAAATTCTCATTAAAAC
1 CTTCAAAATTTTGT-AAAATT-TTATTAAAAC
*
871930 CCTCAAAATATTT-TAAAATTTTATT
1 CTTCAAAAT-TTTGTAAAATTTTATT
871955 TTGACTCCCC
Statistics
Matches: 49, Mismatches: 3, Indels: 9
0.80 0.05 0.15
Matches are distributed among these distances:
28 1 0.02
29 10 0.20
30 8 0.16
31 26 0.53
32 4 0.08
ACGTcount: A:0.40, C:0.14, G:0.03, T:0.43
Consensus pattern (30 bp):
CTTCAAAATTTTGTAAAATTTTATTAAAAC
Found at i:871969 original size:94 final size:94
Alignment explanation
Indices: 871779--871969 Score: 210
Period size: 93 Copynumber: 2.0 Consensus size: 94
871769 AATTAAACCT
** * * *
871779 AAAGCTTTTGTAAATTTTAATTAGGCCTCCCAAAAATTTTGAAATTTCTCATTAAACCTTTTAAA
1 AAAGCTTTTGTAAATTTTAATTAAACCTCCCAAAAATTTTGAAAATTCTCATTAAACCTCTCAAA
**
871844 ATTTTTAAAAATTTCAATTAGACTCTTCA
66 ATTTTTAAAAATTTCAATTAGACTCCCCA
* *
871873 AAAGCTTTTGTAAAATTTT-ATTAAACCT-TCAAAATTTTTGAAAATTCTCATTAAAACC-CTCA
1 AAAGCTTTTGT-AAATTTTAATTAAACCTCCCAAAAATTTTGAAAATTCTCATT-AAACCTCTCA
* * *
871935 AAATATTTT-AAAATTTTATTTTGACTCCCCCA
64 AAAT-TTTTAAAAATTTCAATTAGACT-CCCCA
871967 AAA
1 AAA
871970 TTTAATGCCA
Statistics
Matches: 81, Mismatches: 12, Indels: 8
0.80 0.12 0.08
Matches are distributed among these distances:
93 41 0.51
94 33 0.41
95 7 0.09
ACGTcount: A:0.39, C:0.16, G:0.05, T:0.40
Consensus pattern (94 bp):
AAAGCTTTTGTAAATTTTAATTAAACCTCCCAAAAATTTTGAAAATTCTCATTAAACCTCTCAAA
ATTTTTAAAAATTTCAATTAGACTCCCCA
Found at i:880997 original size:31 final size:30
Alignment explanation
Indices: 880962--881058 Score: 97
Period size: 31 Copynumber: 3.2 Consensus size: 30
880952 TTGGTATTTG
*
880962 AACTTGACACATTCTTTTAATTTGGTACTCA
1 AACTTGACAC-TTTTTTTAATTTGGTACTCA
* *
880993 AACTTGACATTTTTTTCTAATTTAGTAC-CTA
1 AACTTGACACTTTTTT-TAATTTGGTACTC-A
* * * *
881024 AACTGGACACTTTTTTTAAGTTGATACTTA
1 AACTTGACACTTTTTTTAATTTGGTACTCA
881054 AACTT
1 AACTT
881059 TTTGAGATCC
Statistics
Matches: 53, Mismatches: 10, Indels: 7
0.76 0.14 0.10
Matches are distributed among these distances:
30 19 0.36
31 34 0.64
ACGTcount: A:0.30, C:0.16, G:0.09, T:0.44
Consensus pattern (30 bp):
AACTTGACACTTTTTTTAATTTGGTACTCA
Done.