Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01002647.1 Hibiscus syriacus cultivar Beakdansim tig00005406_pilon, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 7027529
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 14 of 26
Found at i:3327454 original size:35 final size:35
Alignment explanation
Indices: 3327415--3327507 Score: 98
Period size: 35 Copynumber: 2.7 Consensus size: 35
3327405 TGAGGCACCC
* * *
3327415 TTTGGTGAAGTAACATGACTCTTGGAGA-GGCATTA
1 TTTGGTGAAGTAACATGACTATTGGA-ATGACATCA
** * *
3327450 TTTGGTGAAACAACATGGCTATTGGAATGACATCC
1 TTTGGTGAAGTAACATGACTATTGGAATGACATCA
*
3327485 TTTGGTGAAGTAACATGAATATT
1 TTTGGTGAAGTAACATGACTATT
3327508 TAAATGTCAT
Statistics
Matches: 46, Mismatches: 11, Indels: 2
0.78 0.19 0.03
Matches are distributed among these distances:
34 1 0.02
35 45 0.98
ACGTcount: A:0.31, C:0.12, G:0.25, T:0.32
Consensus pattern (35 bp):
TTTGGTGAAGTAACATGACTATTGGAATGACATCA
Found at i:3327741 original size:29 final size:29
Alignment explanation
Indices: 3327685--3327741 Score: 71
Period size: 29 Copynumber: 2.0 Consensus size: 29
3327675 GTAACCAAAA
* * *
3327685 TATAAATTTTGAAAGTTTAATGGTCATAG
1 TATAAAATTTGAAAGTTTAAGGGACATAG
3327714 TATAAAATTTGAAAAGTTT-AGGGACATA
1 TATAAAATTTG-AAAGTTTAAGGGACATA
3327742 AGTGATAATT
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
29 17 0.71
30 7 0.29
ACGTcount: A:0.42, C:0.04, G:0.18, T:0.37
Consensus pattern (29 bp):
TATAAAATTTGAAAGTTTAAGGGACATAG
Found at i:3328537 original size:54 final size:54
Alignment explanation
Indices: 3328498--3328850 Score: 492
Period size: 54 Copynumber: 6.6 Consensus size: 54
3328488 TAAACATATT
* ** *
3328498 ATGAATTCCTTGATTTGCACACATAGTGCCGAAACGGTTATTCATCCACATAGG
1 ATGAATTCCGTGAAATGCACACTTAGTGCCGAAACGGTTATTCATCCACATAGG
* * *
3328552 ATGAATTTCGTGAAATGCACACTTAGTGCCAAAACGATTATTCATCCACATAGG
1 ATGAATTCCGTGAAATGCACACTTAGTGCCGAAACGGTTATTCATCCACATAGG
* * * * * *
3328606 ATGAATTTCATGAAATACACACTTAGTGCCAAAACAGTTATTCATTCACATAGG
1 ATGAATTCCGTGAAATGCACACTTAGTGCCGAAACGGTTATTCATCCACATAGG
*
3328660 ACGAATTCCGTGAAATGCACACTTAGTGCCGAAACGGTTATTCATCCACATAGG
1 ATGAATTCCGTGAAATGCACACTTAGTGCCGAAACGGTTATTCATCCACATAGG
*
3328714 ATGAA-TCCGTGAAATGCACACTTAGTGCCGAAATGGTTATTCATCCACATAGG
1 ATGAATTCCGTGAAATGCACACTTAGTGCCGAAACGGTTATTCATCCACATAGG
* ** *
3328767 ATGAATTTCGTGAAATATACACTTAGTGCCGAAACGGTTATTCATCCACATAAG
1 ATGAATTCCGTGAAATGCACACTTAGTGCCGAAACGGTTATTCATCCACATAGG
* * **
3328821 CTGAATTCTGTGAAACACACACTTAGTGCC
1 ATGAATTCCGTGAAATGCACACTTAGTGCC
3328851 TATTTGGTAA
Statistics
Matches: 267, Mismatches: 31, Indels: 2
0.89 0.10 0.01
Matches are distributed among these distances:
53 52 0.19
54 215 0.81
ACGTcount: A:0.33, C:0.21, G:0.18, T:0.28
Consensus pattern (54 bp):
ATGAATTCCGTGAAATGCACACTTAGTGCCGAAACGGTTATTCATCCACATAGG
Found at i:3328791 original size:161 final size:162
Alignment explanation
Indices: 3328499--3328850 Score: 528
Period size: 161 Copynumber: 2.2 Consensus size: 162
3328489 AAACATATTA
* ** * *
3328499 TGAATTCCTTGATTTGCACACATAGTGCCGAAACGGTTATTCATCCACATAGGATGAATTTCGTG
1 TGAATTCCGTGAAATGCACACTTAGTGCCGAAACGGTTATTCATCCACATAGGATGAATTCCGTG
3328564 AAATGCACACTTAGTGCCAAAACGATTATTCATCCACATAGGATGAATTTCATGAAATACACACT
66 AAATGCACACTTAGTGCCAAAACGATTATTCATCCACATAGGATGAATTTCATGAAATACACACT
* *
3328629 TAGTGCCAAAACAGTTATTCATTCACATAGGAC
131 TAGTGCCAAAACAGTTATTCATCCACATAAG-C
3328662 -GAATTCCGTGAAATGCACACTTAGTGCCGAAACGGTTATTCATCCACATAGGATGAA-TCCGTG
1 TGAATTCCGTGAAATGCACACTTAGTGCCGAAACGGTTATTCATCCACATAGGATGAATTCCGTG
* * * * *
3328725 AAATGCACACTTAGTGCCGAAATGGTTATTCATCCACATAGGATGAATTTCGTGAAATATACACT
66 AAATGCACACTTAGTGCCAAAACGATTATTCATCCACATAGGATGAATTTCATGAAATACACACT
* *
3328790 TAGTGCCGAAACGGTTATTCATCCACATAAGC
131 TAGTGCCAAAACAGTTATTCATCCACATAAGC
* **
3328822 TGAATTCTGTGAAACACACACTTAGTGCC
1 TGAATTCCGTGAAATGCACACTTAGTGCC
3328851 TATTTGGTAA
Statistics
Matches: 171, Mismatches: 17, Indels: 4
0.89 0.09 0.02
Matches are distributed among these distances:
160 1 0.01
161 117 0.68
162 53 0.31
ACGTcount: A:0.33, C:0.21, G:0.18, T:0.28
Consensus pattern (162 bp):
TGAATTCCGTGAAATGCACACTTAGTGCCGAAACGGTTATTCATCCACATAGGATGAATTCCGTG
AAATGCACACTTAGTGCCAAAACGATTATTCATCCACATAGGATGAATTTCATGAAATACACACT
TAGTGCCAAAACAGTTATTCATCCACATAAGC
Found at i:3329272 original size:20 final size:21
Alignment explanation
Indices: 3329221--3329272 Score: 72
Period size: 20 Copynumber: 2.6 Consensus size: 21
3329211 TGTTTCGAAT
*
3329221 GGTATCGATAC-CTTCCCTTC
1 GGTATCGATACTCTTCCATTC
*
3329241 GGTATTGATACTC-TCCATTC
1 GGTATCGATACTCTTCCATTC
3329261 GGTATCGATACT
1 GGTATCGATACT
3329273 GATTGAATCA
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
20 27 0.96
21 1 0.04
ACGTcount: A:0.19, C:0.27, G:0.17, T:0.37
Consensus pattern (21 bp):
GGTATCGATACTCTTCCATTC
Found at i:3334243 original size:84 final size:84
Alignment explanation
Indices: 3334089--3334258 Score: 232
Period size: 84 Copynumber: 2.0 Consensus size: 84
3334079 GTTGAAACCT
* * * ***
3334089 TGTCAAAATAGTATCGAGATCTTGCATAAAAGCTCTAAACTCCGGAATAGGCATACCTTTAGGTA
1 TGTCAAAATAGTATCGAGAGCTTGCATAAAAGCTCTAAACTCCAGAACAGGCATACCCCGAGGTA
*
3334154 TTGGTGCGCTGGCATTCTC
66 CTGGTGCGCTGGCATTCTC
* * * *
3334173 TGTCAAAATAGTGTCGAGAGCTTGCATAAAATCTCTAAACTTCAGAACAGGCATACCCCGAGGTG
1 TGTCAAAATAGTATCGAGAGCTTGCATAAAAGCTCTAAACTCCAGAACAGGCATACCCCGAGGTA
*
3334238 CTGGTGTGCTGGCATTCTC
66 CTGGTGCGCTGGCATTCTC
3334257 TG
1 TG
3334259 ACGGAATTGG
Statistics
Matches: 74, Mismatches: 12, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
84 74 1.00
ACGTcount: A:0.28, C:0.21, G:0.23, T:0.28
Consensus pattern (84 bp):
TGTCAAAATAGTATCGAGAGCTTGCATAAAAGCTCTAAACTCCAGAACAGGCATACCCCGAGGTA
CTGGTGCGCTGGCATTCTC
Found at i:3335083 original size:54 final size:54
Alignment explanation
Indices: 3335020--3335155 Score: 173
Period size: 54 Copynumber: 2.5 Consensus size: 54
3335010 CTTTATAATG
* * *
3335020 CACCCGTAGTGCCCATACGGTTATTCATAAATATATTATGAATTTCGTGGTTTA
1 CACCCGTAGTGCCCATACGGTTATTCATAAACATATTATAAATTCCGTGGTTTA
* * *
3335074 CACCCGTAGTGCCTATACGATTATTCATAAACATATTATAAATTCCGTGGTTTT
1 CACCCGTAGTGCCCATACGGTTATTCATAAACATATTATAAATTCCGTGGTTTA
* * * * *
3335128 GACACATAGTGCCGAAACGGTTATTCAT
1 CACCCGTAGTGCCCATACGGTTATTCAT
3335156 CCACATAGAA
Statistics
Matches: 70, Mismatches: 12, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
54 70 1.00
ACGTcount: A:0.29, C:0.20, G:0.16, T:0.35
Consensus pattern (54 bp):
CACCCGTAGTGCCCATACGGTTATTCATAAACATATTATAAATTCCGTGGTTTA
Found at i:3335162 original size:54 final size:54
Alignment explanation
Indices: 3335129--3335572 Score: 660
Period size: 54 Copynumber: 8.2 Consensus size: 54
3335119 CGTGGTTTTG
* *
3335129 ACACATAGTGCCGAAACGGTTATTCATCCACATAGAATGAATTCCGTGAAATGC
1 ACACTTAGTGCCGAAACGGTTATTCATCCACATAGGATGAATTCCGTGAAATGC
* * *
3335183 ATACTTAGTGCCGAAATGGTTATTCATCCACATAGGATGAATTTCGTGAAATGC
1 ACACTTAGTGCCGAAACGGTTATTCATCCACATAGGATGAATTCCGTGAAATGC
* * * *
3335237 ACACTTAGTGCTGAAACTGTTATTCATTCACATAGGATGAATTTCGTGAAATGC
1 ACACTTAGTGCCGAAACGGTTATTCATCCACATAGGATGAATTCCGTGAAATGC
*
3335291 ACACTTAGTGCTGAAACGGTTATTCATCCACATAGGATGAATTCCGTGAAATGC
1 ACACTTAGTGCCGAAACGGTTATTCATCCACATAGGATGAATTCCGTGAAATGC
3335345 ACACTTAGTGCCGAAACGGTTATTCAT-CAGCATAGGATGAATTCCGTGAAATGC
1 ACACTTAGTGCCGAAACGGTTATTCATCCA-CATAGGATGAATTCCGTGAAATGC
3335399 ACACTTAGTGCCGAAACGGTTATTCAT-CAGCATAGGATGAATTCCGTGAAATGC
1 ACACTTAGTGCCGAAACGGTTATTCATCCA-CATAGGATGAATTCCGTGAAATGC
* * * *
3335453 ACACTTAGTGCCGAAACGGTTATTCAT-TAGTATATGATGAATTTCGTGAAATGC
1 ACACTTAGTGCCGAAACGGTTATTCATCCA-CATAGGATGAATTCCGTGAAATGC
** * * * *
3335507 ACAGGTAGTGCCGAAATGGTTATTCATCCACATAAGATGTATTCCGTGAAATGT
1 ACACTTAGTGCCGAAACGGTTATTCATCCACATAGGATGAATTCCGTGAAATGC
3335561 ACACTTAGTGCC
1 ACACTTAGTGCC
3335573 TATTTGGTAA
Statistics
Matches: 359, Mismatches: 29, Indels: 4
0.92 0.07 0.01
Matches are distributed among these distances:
53 2 0.01
54 356 0.99
55 1 0.00
ACGTcount: A:0.32, C:0.19, G:0.20, T:0.29
Consensus pattern (54 bp):
ACACTTAGTGCCGAAACGGTTATTCATCCACATAGGATGAATTCCGTGAAATGC
Found at i:3335293 original size:25 final size:25
Alignment explanation
Indices: 3335211--3335293 Score: 60
Period size: 27 Copynumber: 3.2 Consensus size: 25
3335201 GTTATTCATC
3335211 CACATAGGATGAATTTCGTGAAATG
1 CACATAGGATGAATTTCGTGAAATG
* ** * * *
3335236 CACACTTAGTGCTGAAACT-GTTATTCATT
1 CACA--TAG-GATGAATTTCGTGA--AATG
3335265 CACATAGGATGAATTTCGTGAAATG
1 CACATAGGATGAATTTCGTGAAATG
3335290 CACA
1 CACA
3335294 CTTAGTGCTG
Statistics
Matches: 40, Mismatches: 12, Indels: 12
0.62 0.19 0.19
Matches are distributed among these distances:
25 10 0.25
26 6 0.15
27 12 0.30
28 6 0.15
29 6 0.15
ACGTcount: A:0.34, C:0.17, G:0.19, T:0.30
Consensus pattern (25 bp):
CACATAGGATGAATTTCGTGAAATG
Found at i:3335922 original size:20 final size:21
Alignment explanation
Indices: 3335897--3335941 Score: 65
Period size: 22 Copynumber: 2.1 Consensus size: 21
3335887 TGGCTCCTTA
3335897 GTATCGATAC-CCATACCATG
1 GTATCGATACACCATACCATG
*
3335917 GTATCGATACTACCATACTATG
1 GTATCGATAC-ACCATACCATG
3335939 GTA
1 GTA
3335942 CTGATATTAT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
20 10 0.45
22 12 0.55
ACGTcount: A:0.31, C:0.24, G:0.16, T:0.29
Consensus pattern (21 bp):
GTATCGATACACCATACCATG
Found at i:3338939 original size:22 final size:23
Alignment explanation
Indices: 3338913--3338959 Score: 78
Period size: 22 Copynumber: 2.1 Consensus size: 23
3338903 TGGTTGTTAC
*
3338913 ATATGATGTTTATCATGAAT-AT
1 ATATGATATTTATCATGAATGAT
3338935 ATATGATATTTATCATGAATGAT
1 ATATGATATTTATCATGAATGAT
3338958 AT
1 AT
3338960 TTTGGGTATG
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
22 19 0.83
23 4 0.17
ACGTcount: A:0.38, C:0.04, G:0.13, T:0.45
Consensus pattern (23 bp):
ATATGATATTTATCATGAATGAT
Found at i:3339224 original size:61 final size:61
Alignment explanation
Indices: 3339129--3339247 Score: 175
Period size: 61 Copynumber: 2.0 Consensus size: 61
3339119 CAGGGACACT
* * * *
3339129 TAGTGCAGGTGTTGGGCATAACCTTATGTGTCATATCCAGATCAACATTAGAGTGTAAACG
1 TAGTGCAGGTGGTGGGCACAACCTTATGTGTCATATCCAGATCAACACTAGAGCGTAAACG
* * *
3339190 TAGTGTAGGTGGTGGGCACGACCTTATGTGTCATATCCAGATCATCACTAGAGCGTAA
1 TAGTGCAGGTGGTGGGCACAACCTTATGTGTCATATCCAGATCAACACTAGAGCGTAA
3339248 GCTTAATGCA
Statistics
Matches: 51, Mismatches: 7, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
61 51 1.00
ACGTcount: A:0.28, C:0.18, G:0.26, T:0.29
Consensus pattern (61 bp):
TAGTGCAGGTGGTGGGCACAACCTTATGTGTCATATCCAGATCAACACTAGAGCGTAAACG
Found at i:3343671 original size:2 final size:2
Alignment explanation
Indices: 3343664--3343724 Score: 122
Period size: 2 Copynumber: 30.5 Consensus size: 2
3343654 CTTTTAAAAC
3343664 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
3343706 AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT A
3343725 CCCCATCCCA
Statistics
Matches: 59, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 59 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:3343951 original size:24 final size:24
Alignment explanation
Indices: 3343888--3343951 Score: 65
Period size: 24 Copynumber: 2.7 Consensus size: 24
3343878 AAATGGAGAT
*
3343888 ATCAGAAATCAAAACAGAATTCAG
1 ATCAGAAATCAAAACAGAATCCAG
* * * * *
3343912 AACAGATATTAGAACATAATCCAG
1 ATCAGAAATCAAAACAGAATCCAG
*
3343936 ATCAGAAATCATAACA
1 ATCAGAAATCAAAACA
3343952 AATTTCATGT
Statistics
Matches: 30, Mismatches: 10, Indels: 0
0.75 0.25 0.00
Matches are distributed among these distances:
24 30 1.00
ACGTcount: A:0.53, C:0.17, G:0.11, T:0.19
Consensus pattern (24 bp):
ATCAGAAATCAAAACAGAATCCAG
Found at i:3352423 original size:23 final size:23
Alignment explanation
Indices: 3352397--3352447 Score: 93
Period size: 23 Copynumber: 2.2 Consensus size: 23
3352387 GATCTGAACA
*
3352397 GTTGGATCTTGGCAAATCCAACG
1 GTTGGATATTGGCAAATCCAACG
3352420 GTTGGATATTGGCAAATCCAACG
1 GTTGGATATTGGCAAATCCAACG
3352443 GTTGG
1 GTTGG
3352448 TGATGTGGTG
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
23 27 1.00
ACGTcount: A:0.25, C:0.18, G:0.29, T:0.27
Consensus pattern (23 bp):
GTTGGATATTGGCAAATCCAACG
Found at i:3355413 original size:25 final size:25
Alignment explanation
Indices: 3355377--3355427 Score: 93
Period size: 25 Copynumber: 2.0 Consensus size: 25
3355367 ACAAACTTCG
3355377 TCTGAATATTTGCCTCTAGTATAAT
1 TCTGAATATTTGCCTCTAGTATAAT
*
3355402 TCTGAATTTTTGCCTCTAGTATAAT
1 TCTGAATATTTGCCTCTAGTATAAT
3355427 T
1 T
3355428 TAAAAGCTAC
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
25 25 1.00
ACGTcount: A:0.25, C:0.16, G:0.12, T:0.47
Consensus pattern (25 bp):
TCTGAATATTTGCCTCTAGTATAAT
Found at i:3371197 original size:55 final size:55
Alignment explanation
Indices: 3371113--3371587 Score: 674
Period size: 55 Copynumber: 8.7 Consensus size: 55
3371103 GTGCAAAAAG
*
3371113 TTAAGAAATTCATACTAAGTGGATGAATTTTCGTATGGGTACTTTATGTGTAAAC
1 TTAAGAAATTCATACTAAGTGGATGAATTTTCGTATGGGAACTTTATGTGTAAAC
*
3371168 TTAAGAAATTCATACTAAGTGGATGAATTTCCGTATGGGAAC-TTATGTGTAAA-
1 TTAAGAAATTCATACTAAGTGGATGAATTTTCGTATGGGAACTTTATGTGTAAAC
* * *
3371221 TTAAAGAAATTCATACTAAGTGGATGAATTTCCGTATGGGAAATTTATGTATAAAC
1 TT-AAGAAATTCATACTAAGTGGATGAATTTTCGTATGGGAACTTTATGTGTAAAC
* * *
3371277 TTAAGAAATTCATACTAAGTGGATGAATTTTTGGATGGGCACTTTATGTGTAAAC
1 TTAAGAAATTCATACTAAGTGGATGAATTTTCGTATGGGAACTTTATGTGTAAAC
* *
3371332 TTAAGAAATTCATACTAAGTGGAT-AAATTTCTGTATGGGCACTTTATGTGTAAAC
1 TTAAGAAATTCATACTAAGTGGATGAATTTTC-GTATGGGAACTTTATGTGTAAAC
* *
3371387 TTAAGAAATTCATACTAAGCT-GATGAATTTCCGTATGGGTACTTTATGTGTAAAC
1 TTAAGAAATTCATACTAAG-TGGATGAATTTTCGTATGGGAACTTTATGTGTAAAC
* *
3371442 TTAAGAAATTCATATTAAGCGGATGAATTTTCGTATGGGAACTTTATGTGTAAAC
1 TTAAGAAATTCATACTAAGTGGATGAATTTTCGTATGGGAACTTTATGTGTAAAC
* * *
3371497 TTAAGAAATTCATACTAAGTGGATGAA-TATCTGTATGGGCACTTTATGTGCAAAAC
1 TTAAGAAATTCATACTAAGTGGATGAATTTTC-GTATGGGAACTTTATGTG-TAAAC
* * * *
3371553 -TAGGAAATTCATACTAAGTGTATAAATTTCCGTAT
1 TTAAGAAATTCATACTAAGTGGATGAATTTTCGTAT
3371588 TGGTAGTGGT
Statistics
Matches: 380, Mismatches: 30, Indels: 20
0.88 0.07 0.05
Matches are distributed among these distances:
53 2 0.01
54 58 0.15
55 306 0.81
56 14 0.04
ACGTcount: A:0.35, C:0.10, G:0.19, T:0.36
Consensus pattern (55 bp):
TTAAGAAATTCATACTAAGTGGATGAATTTTCGTATGGGAACTTTATGTGTAAAC
Found at i:3372886 original size:27 final size:27
Alignment explanation
Indices: 3372848--3372900 Score: 106
Period size: 27 Copynumber: 2.0 Consensus size: 27
3372838 TGAAGCAAGC
3372848 TGATCGAGCAGTGCACGAGTATGAGGT
1 TGATCGAGCAGTGCACGAGTATGAGGT
3372875 TGATCGAGCAGTGCACGAGTATGAGG
1 TGATCGAGCAGTGCACGAGTATGAGG
3372901 CTGAATACAA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 26 1.00
ACGTcount: A:0.26, C:0.15, G:0.38, T:0.21
Consensus pattern (27 bp):
TGATCGAGCAGTGCACGAGTATGAGGT
Found at i:3377737 original size:55 final size:55
Alignment explanation
Indices: 3377372--3377731 Score: 526
Period size: 55 Copynumber: 6.5 Consensus size: 55
3377362 GTGCAAAAAG
* * * *
3377372 TTAAGAAATTCATATTAAGTGGTTGAATTTCCATATGGGCATTTTATGTGTAAAC
1 TTAAGAAATTCATACTAAGTGGATGAATTTCCGTATGGGCACTTTATGTGTAAAC
3377427 TTAAGAAATTCATACTAAGTGGATGAATTTCCGTATGGGCACTTTATGTGTAAAC
1 TTAAGAAATTCATACTAAGTGGATGAATTTCCGTATGGGCACTTTATGTGTAAAC
* **
3377482 TTAAGAAATTCATACTAAGTGGATGAATTTTCGTATGGGCACTTTACATGTAAAC
1 TTAAGAAATTCATACTAAGTGGATGAATTTCCGTATGGGCACTTTATGTGTAAAC
* * * *
3377537 TTAAGAAATTTATACTAAGTGGATGAATTTCCGCATGGGCACTTTATGCGTAAAA
1 TTAAGAAATTCATACTAAGTGGATGAATTTCCGTATGGGCACTTTATGTGTAAAC
* *
3377592 TTAAGAAATTCATACGAAGTGGATGAATTTCCGTATGGACACTTTATGTGTAAAC
1 TTAAGAAATTCATACTAAGTGGATGAATTTCCGTATGGGCACTTTATGTGTAAAC
* * *
3377647 TTAAGAAATTCATACTAAGTGGATAAATTTCTGTATGGGCACTTTATGTGCAAAGC
1 TTAAGAAATTCATACTAAGTGGATGAATTTCCGTATGGGCACTTTATGTGTAAA-C
* *
3377703 -T-AGAAAATTCATACTAAGTGTATAAATTT
1 TTAAG-AAATTCATACTAAGTGGATGAATTT
3377732 TTGTATTGGT
Statistics
Matches: 277, Mismatches: 26, Indels: 4
0.90 0.08 0.01
Matches are distributed among these distances:
54 2 0.01
55 274 0.99
56 1 0.00
ACGTcount: A:0.35, C:0.12, G:0.19, T:0.35
Consensus pattern (55 bp):
TTAAGAAATTCATACTAAGTGGATGAATTTCCGTATGGGCACTTTATGTGTAAAC
Found at i:3381499 original size:14 final size:14
Alignment explanation
Indices: 3381477--3381518 Score: 57
Period size: 14 Copynumber: 3.0 Consensus size: 14
3381467 TATATATATA
*
3381477 TGTGTGTGTGTGTG
1 TGTGCGTGTGTGTG
3381491 TGTGCGTGTGTGTG
1 TGTGCGTGTGTGTG
**
3381505 TGCACGTGTGTGTG
1 TGTGCGTGTGTGTG
3381519 AGTAATTTTA
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
14 25 1.00
ACGTcount: A:0.02, C:0.07, G:0.48, T:0.43
Consensus pattern (14 bp):
TGTGCGTGTGTGTG
Found at i:3381507 original size:12 final size:12
Alignment explanation
Indices: 3381477--3381518 Score: 57
Period size: 12 Copynumber: 3.3 Consensus size: 12
3381467 TATATATATA
*
3381477 TGTGTGTGTGTG
1 TGTGTGCGTGTG
3381489 TGTGTGCGTGTG
1 TGTGTGCGTGTG
3381501 TGTGTGCACGTGTG
1 TGTGTG--CGTGTG
3381515 TGTG
1 TGTG
3381519 AGTAATTTTA
Statistics
Matches: 27, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
12 17 0.63
14 10 0.37
ACGTcount: A:0.02, C:0.07, G:0.48, T:0.43
Consensus pattern (12 bp):
TGTGTGCGTGTG
Found at i:3381518 original size:2 final size:2
Alignment explanation
Indices: 3381477--3381506 Score: 51
Period size: 2 Copynumber: 15.0 Consensus size: 2
3381467 TATATATATA
*
3381477 TG TG TG TG TG TG TG TG TG CG TG TG TG TG TG
1 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG
3381507 CACGTGTGTG
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:0.00, C:0.03, G:0.50, T:0.47
Consensus pattern (2 bp):
TG
Found at i:3384094 original size:58 final size:58
Alignment explanation
Indices: 3384023--3384157 Score: 193
Period size: 58 Copynumber: 2.3 Consensus size: 58
3384013 TAAATGTTCA
*
3384023 AAAATGTTCAGAAATTCATACTAAGTGTATGAATTTCCGTATTGGGCT-CTTT-GTGTGC
1 AAAATGTTAAGAAATTCATACTAAGTGTATGAATTTCCGTATTGGG-TACTTTAG-GTGC
*
3384081 AAAATGTTAAGAAATTCATACTAAGTGTATGAATTTTCGTATTGGGTACTTTAGGTGC
1 AAAATGTTAAGAAATTCATACTAAGTGTATGAATTTCCGTATTGGGTACTTTAGGTGC
* * *
3384139 AAAAAGATAAGAAACTCAT
1 AAAATGTTAAGAAATTCAT
3384158 GCCAAAGGTA
Statistics
Matches: 70, Mismatches: 5, Indels: 4
0.89 0.06 0.05
Matches are distributed among these distances:
57 1 0.01
58 68 0.97
59 1 0.01
ACGTcount: A:0.35, C:0.11, G:0.19, T:0.35
Consensus pattern (58 bp):
AAAATGTTAAGAAATTCATACTAAGTGTATGAATTTCCGTATTGGGTACTTTAGGTGC
Found at i:3384173 original size:58 final size:58
Alignment explanation
Indices: 3384032--3384179 Score: 158
Period size: 58 Copynumber: 2.6 Consensus size: 58
3384022 AAAAATGTTC
* * * * * *
3384032 AGAAATTCATACTAAGTGTATGAATTTCCGTATTGGGCTCTTTGTGTGCAAAATGTTA
1 AGAAACTCATACAAAGTGTAAGAATTTTCGTATTGGGCTCTTTGTGTGCAAAAAGATA
* * *
3384090 AGAAATTCATACTAAGTGTATGAATTTTCGTATTGGG-TACTTTAG-GTGCAAAAAGATA
1 AGAAACTCATACAAAGTGTAAGAATTTTCGTATTGGGCT-CTTT-GTGTGCAAAAAGATA
*
3384148 AGAAACTCATGCCAAAG-GTAAGAATTTTCGTA
1 AGAAACTCAT-ACAAAGTGTAAGAATTTTCGTA
3384180 AGTGAAATTG
Statistics
Matches: 80, Mismatches: 7, Indels: 6
0.86 0.08 0.06
Matches are distributed among these distances:
57 1 0.01
58 74 0.93
59 5 0.06
ACGTcount: A:0.34, C:0.11, G:0.20, T:0.34
Consensus pattern (58 bp):
AGAAACTCATACAAAGTGTAAGAATTTTCGTATTGGGCTCTTTGTGTGCAAAAAGATA
Found at i:3384498 original size:68 final size:67
Alignment explanation
Indices: 3384380--3384665 Score: 396
Period size: 68 Copynumber: 4.2 Consensus size: 67
3384370 AAAGATTAAG
* *
3384380 AGGCCTAATTGTGCATTTGATAGAAAGATGTCATTTATGCCAGTTAGATGAAAGGATAAGTGCCT
1 AGGCCTAACTGTGCATTTGACAGAAAG-TGTCATTTATGCCAGTTAGATGAAAGGATAAGTGCCT
3384445 TTA
65 TTA
* *
3384448 AGGCTTAACTGTGCATTTGACAGAAATGTGTCATTTATGCGAGTTAGATGAAAGGATAAGTGCCT
1 AGGCCTAACTGTGCATTTGACAGAAA-GTGTCATTTATGCCAGTTAGATGAAAGGATAAGTGCCT
*
3384513 TTG
65 TTA
* * * * *
3384516 AGGCCTAAATGTGTAATTGACAGAAAGATGTCATTTATGCGAGTT-GATGAAAGGCTAAGTGCC-
1 AGGCCTAACTGTGCATTTGACAGAAAG-TGTCATTTATGCCAGTTAGATGAAAGGATAAGTGCCT
3384579 TTA
65 TTA
* *
3384582 GAGGCCTAACTGTGCATTTGACATAAAGGTGTCATTTATGCCAGTTAGATGAAAGGCTAAGTGCC
1 -AGGCCTAACTGTGCATTTGACAGAAA-GTGTCATTTATGCCAGTTAGATGAAAGGATAAGTGCC
*
3384647 TTTG
64 TTTA
3384651 AGGCCTAACTGTGCA
1 AGGCCTAACTGTGCA
3384666 ATTGGCAAAA
Statistics
Matches: 195, Mismatches: 17, Indels: 12
0.87 0.08 0.05
Matches are distributed among these distances:
66 2 0.01
67 56 0.29
68 134 0.69
69 3 0.02
ACGTcount: A:0.30, C:0.14, G:0.26, T:0.30
Consensus pattern (67 bp):
AGGCCTAACTGTGCATTTGACAGAAAGTGTCATTTATGCCAGTTAGATGAAAGGATAAGTGCCTT
TA
Found at i:3384622 original size:135 final size:136
Alignment explanation
Indices: 3384379--3384669 Score: 451
Period size: 135 Copynumber: 2.1 Consensus size: 136
3384369 AAAAGATTAA
* * *
3384379 GAGGCCTAATTGTGCATTTGATAGAAAGATGTCATTTATGCCAGTTAGATGAAAGGATAAGTGCC
1 GAGGCCTAAATGTGCAATTGACAGAAAGATGTCATTTATGCCAGTTAGATGAAAGGATAAGTGCC
* * *
3384444 TTTAAGGCTTAACTGTGCATTTGACAGAAATGTGTCATTTATGCGAGTTAGATGAAAGGATAAGT
66 TTTAAGGCCTAACTGTGCATTTGACAGAAAGGTGTCATTTATGCCAGTTAGATGAAAGGATAAGT
3384509 GCCTTT
131 GCCTTT
* * *
3384515 GAGGCCTAAATGTGTAATTGACAGAAAGATGTCATTTATGCGAGTT-GATGAAAGGCTAAGTGCC
1 GAGGCCTAAATGTGCAATTGACAGAAAGATGTCATTTATGCCAGTTAGATGAAAGGATAAGTGCC
* *
3384579 -TTAGAGGCCTAACTGTGCATTTGACATAAAGGTGTCATTTATGCCAGTTAGATGAAAGGCTAAG
66 TTTA-AGGCCTAACTGTGCATTTGACAGAAAGGTGTCATTTATGCCAGTTAGATGAAAGGATAAG
3384643 TGCCTTT
130 TGCCTTT
*
3384650 GAGGCCTAACTGTGCAATTG
1 GAGGCCTAAATGTGCAATTG
3384670 GCAAAAATGT
Statistics
Matches: 141, Mismatches: 13, Indels: 3
0.90 0.08 0.02
Matches are distributed among these distances:
134 3 0.02
135 97 0.69
136 41 0.29
ACGTcount: A:0.30, C:0.13, G:0.26, T:0.31
Consensus pattern (136 bp):
GAGGCCTAAATGTGCAATTGACAGAAAGATGTCATTTATGCCAGTTAGATGAAAGGATAAGTGCC
TTTAAGGCCTAACTGTGCATTTGACAGAAAGGTGTCATTTATGCCAGTTAGATGAAAGGATAAGT
GCCTTT
Found at i:3386503 original size:68 final size:68
Alignment explanation
Indices: 3386419--3386703 Score: 405
Period size: 68 Copynumber: 4.2 Consensus size: 68
3386409 AAAAGATTAA
*
3386419 GAGGCCTAACTGTGCATTTGATAGAAAGATGTCATTTATGCCAGTTAGATGAAAGGCTAAGTGCC
1 GAGGCCTAACTGTGCATTTGACAGAAAGATGTCATTTATGCCAGTTAGATGAAAGGCTAAGTGCC
*
3386484 ATT
66 TTT
* * *
3386487 GAGGCCTAACTGTGCATTTGACAGAAAGGTGTCATTTATGCCAGTTAAATGAAAGGATAAGTGCC
1 GAGGCCTAACTGTGCATTTGACAGAAAGATGTCATTTATGCCAGTTAGATGAAAGGCTAAGTGCC
3386552 TTT
66 TTT
* * * * * * * *
3386555 GAGGTCTAACTGTGCATTTGTCAGAAAGATGCCATTTTTTCGAGTTAGGTGAAAGGCTATGTGCC
1 GAGGCCTAACTGTGCATTTGACAGAAAGATGTCATTTATGCCAGTTAGATGAAAGGCTAAGTGCC
3386620 TTT
66 TTT
3386623 GAGGCCTAACTGTGCATTTGACAGAAAGGA-GTCATTTATGCCAGTTAGATG--AGGCTAAGTGC
1 GAGGCCTAACTGTGCATTTGACAGAAA-GATGTCATTTATGCCAGTTAGATGAAAGGCTAAGTGC
*
3386685 TTTT
65 CTTT
*
3386689 AAGGCCTAACTGTGC
1 GAGGCCTAACTGTGC
3386704 CTTTAAGGCA
Statistics
Matches: 190, Mismatches: 26, Indels: 4
0.86 0.12 0.02
Matches are distributed among these distances:
66 27 0.14
68 161 0.85
69 2 0.01
ACGTcount: A:0.28, C:0.15, G:0.26, T:0.31
Consensus pattern (68 bp):
GAGGCCTAACTGTGCATTTGACAGAAAGATGTCATTTATGCCAGTTAGATGAAAGGCTAAGTGCC
TTT
Found at i:3386708 original size:19 final size:19
Alignment explanation
Indices: 3386681--3386722 Score: 57
Period size: 19 Copynumber: 2.2 Consensus size: 19
3386671 ATGAGGCTAA
* * *
3386681 GTGCTTTTAAGGCCTAACT
1 GTGCCTTTAAGGCATAAAT
3386700 GTGCCTTTAAGGCATAAAT
1 GTGCCTTTAAGGCATAAAT
3386719 GTGC
1 GTGC
3386723 AATTGGCAGA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.24, C:0.19, G:0.24, T:0.33
Consensus pattern (19 bp):
GTGCCTTTAAGGCATAAAT
Found at i:3386735 original size:17 final size:18
Alignment explanation
Indices: 3386710--3386744 Score: 54
Period size: 17 Copynumber: 2.0 Consensus size: 18
3386700 GTGCCTTTAA
*
3386710 GGCATAAATGTG-CAATT
1 GGCAGAAATGTGTCAATT
3386727 GGCAGAAATGTGTCAATT
1 GGCAGAAATGTGTCAATT
3386745 ATGCCAGTTA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 11 0.69
18 5 0.31
ACGTcount: A:0.34, C:0.11, G:0.26, T:0.29
Consensus pattern (18 bp):
GGCAGAAATGTGTCAATT
Found at i:3386823 original size:81 final size:81
Alignment explanation
Indices: 3386718--3387029 Score: 330
Period size: 81 Copynumber: 3.9 Consensus size: 81
3386708 AAGGCATAAA
3386718 TGTGCAATTGGCAGAAATG-TGTCAATTATGCCAGTTAGATGAATGGTTAAATATAGTAGAGTAA
1 TGTGCAATTGGCAGAAA-GATGTCAATTATGCCAGTTAGATGAATGGTTAAATATAGTAGAGTAA
3386782 AAGAATAATGGCCTAAC
65 AAGAATAATGGCCTAAC
* * ** *
3386799 TGTGTAATTGGTAGAAAGATGTCAATTATGCCAGTTAGATG-ATGGGTTAAATACCGTTA-AGGA
1 TGTGCAATTGGCAGAAAGATGTCAATTATGCCAGTTAGATGAAT-GGTTAAATATAG-TAGAGTA
* *
3386862 AAAGAATAATAGCCTAAA
64 AAAGAATAATGGCCTAAC
* * * * *
3386880 TATACAATTGG-A-AAATAGGTCTAAATTATGCCAGTTAGATGAATGATTAAATA-ACGTAGAGT
1 TGTGCAATTGGCAGAAAGATGTC--AATTATGCCAGTTAGATGAATGGTTAAATATA-GTAGAGT
3386942 AAAAGAATAATGGCCTAAC
63 AAAAGAATAATGGCCTAAC
* * * * * * * * * *
3386961 TTTGCAATTGGCAGAATGGTGTCAATTATTCCAGTAAGATGAACGGCTAAACATTGTTGAGTAAA
1 TGTGCAATTGGCAGAAAGATGTCAATTATGCCAGTTAGATGAATGGTTAAATATAGTAGAGTAAA
3387026 AGAA
66 AGAA
3387030 GAAAGCTAAA
Statistics
Matches: 189, Mismatches: 31, Indels: 22
0.78 0.13 0.09
Matches are distributed among these distances:
79 7 0.04
80 6 0.03
81 166 0.88
82 5 0.03
83 5 0.03
ACGTcount: A:0.40, C:0.10, G:0.22, T:0.28
Consensus pattern (81 bp):
TGTGCAATTGGCAGAAAGATGTCAATTATGCCAGTTAGATGAATGGTTAAATATAGTAGAGTAAA
AGAATAATGGCCTAAC
Found at i:3390818 original size:58 final size:58
Alignment explanation
Indices: 3390725--3390882 Score: 194
Period size: 58 Copynumber: 2.7 Consensus size: 58
3390715 CTAAAGTGAA
** * * *
3390725 AAAATGTTAAGAAGTTAATACTAAGTGAATAAATTTCCGTATTGGGCA-TTTTGTGTGC
1 AAAATGTTAAGAAACTAATACTAAGTGTATGAATTTCCGTATTGGGCACTTTAG-GTGC
*
3390783 AAAATGTTAAGAAACTCATACTAAGTGTATGAATTTCCGTATTGGGCACTTTAGGTGC
1 AAAATGTTAAGAAACTAATACTAAGTGTATGAATTTCCGTATTGGGCACTTTAGGTGC
* * * *
3390841 AAAAAGATAAGAAACTTATACTAAAG-GTATGAATTTTCGTAT
1 AAAATGTTAAGAAACTAATACT-AAGTGTATGAATTTCCGTAT
3390883 GTGAAATTGT
Statistics
Matches: 88, Mismatches: 10, Indels: 4
0.86 0.10 0.04
Matches are distributed among these distances:
58 81 0.92
59 7 0.08
ACGTcount: A:0.37, C:0.10, G:0.19, T:0.34
Consensus pattern (58 bp):
AAAATGTTAAGAAACTAATACTAAGTGTATGAATTTCCGTATTGGGCACTTTAGGTGC
Found at i:3391172 original size:68 final size:68
Alignment explanation
Indices: 3391083--3391407 Score: 416
Period size: 68 Copynumber: 4.8 Consensus size: 68
3391073 AAAAGATTAA
* * * * *
3391083 GAGGCATAATTGTGCATTTGACAGAAAGATATCATTTATGCTAGTTAGATGAAAGGCCAAGTGCC
1 GAGGCCTAACTGTGCATTTGACAGAAAGGTATCATTTATGCCAGTTAGATGAAAGGCTAAGTGCC
3391148 TTT
66 TTT
* * * * *
3391151 GAGGCCTAACTGTGCATTTGACAAAAATGTATCATTTATGCCAGATAGATGAAATGATAAGTGCC
1 GAGGCCTAACTGTGCATTTGACAGAAAGGTATCATTTATGCCAGTTAGATGAAAGGCTAAGTGCC
3391216 TTT
66 TTT
* * * * *
3391219 GATGCCTAAATGTGCATTTGAAAGAAAGGTTTCATTTATGCGAGTTAGATGAAAGGCTAAGTGCC
1 GAGGCCTAACTGTGCATTTGACAGAAAGGTATCATTTATGCCAGTTAGATGAAAGGCTAAGTGCC
3391284 TTT
66 TTT
* * * * *
3391287 AAGGCCTAACTGTGTATTTGACAGAAAGGTGTCATTTATGCCAGTAAGATGAAAGGCTAAGTACC
1 GAGGCCTAACTGTGCATTTGACAGAAAGGTATCATTTATGCCAGTTAGATGAAAGGCTAAGTGCC
3391352 TTT
66 TTT
* * * * **
3391355 GAGGCCTAACTGTGCAATTGGCAGAAAGGTGTCAATTATGTGAGTTAGATGAA
1 GAGGCCTAACTGTGCATTTGACAGAAAGGTATCATTTATGCCAGTTAGATGAA
3391408 CGGTTAAATA
Statistics
Matches: 220, Mismatches: 37, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
68 220 1.00
ACGTcount: A:0.32, C:0.13, G:0.24, T:0.30
Consensus pattern (68 bp):
GAGGCCTAACTGTGCATTTGACAGAAAGGTATCATTTATGCCAGTTAGATGAAAGGCTAAGTGCC
TTT
Found at i:3391492 original size:81 final size:81
Alignment explanation
Indices: 3391357--3391812 Score: 612
Period size: 81 Copynumber: 5.6 Consensus size: 81
3391347 GTACCTTTGA
*
3391357 GGCCTAACTGTGCAATTGGCAGAAAGGTGTCAATTATGTGAGTTAGATGAACGGTTAAATACCAT
1 GGCCTAACTGTGCAATTGGCAGAAAGGTGTCAATTATGTCAGTTAGATGAACGGTTAAATACCAT
* *
3391422 TGAGTAAACGAATCAT
66 TGAGTAAAAGAATAAT
* * * * * *
3391438 GGCCTAATTGTGCAATTGACATAAAGGTGTCAATTATGTCAGTTAGACGAACGGTCAAATACCGT
1 GGCCTAACTGTGCAATTGGCAGAAAGGTGTCAATTATGTCAGTTAGATGAACGGTTAAATACCAT
3391503 TGAGTAAAAGAATAAT
66 TGAGTAAAAGAATAAT
* ** * * *
3391519 GGCCTAACTGTGCAATTGGAAGAAATATGTCAATTAT-ACGAGTTAGATGAACAGTTAAATACCG
1 GGCCTAACTGTGCAATTGGCAGAAAGGTGTCAATTATGTC-AGTTAGATGAACGGTTAAATACCA
* *
3391583 TTTAGTAAACGAATAAT
65 TTGAGTAAAAGAATAAT
* * * * *
3391600 GGCCTAACTGTGCAATTGGTAAAAAGGTGTCAATTATGTCAGTTAGATGAACAGTTAAGTACAAT
1 GGCCTAACTGTGCAATTGGCAGAAAGGTGTCAATTATGTCAGTTAGATGAACGGTTAAATACCAT
3391665 TGAGTAAAAGAATAAT
66 TGAGTAAAAGAATAAT
* * * *
3391681 GGCCTAACTGTACAATTGGCAGAAAGGTGTCAATTATGCCTGTTAGATGAACGGTTAAATA-TAG
1 GGCCTAACTGTGCAATTGGCAGAAAGGTGTCAATTATGTCAGTTAGATGAACGGTTAAATACCA-
3391745 TTGAGTAAAAGAATAAT
65 TTGAGTAAAAGAATAAT
* * *
3391762 GGCCTAACTATGCAATTGGCAGAAATGTGTCAATTATG-CAGTAAGATGAAC
1 GGCCTAACTGTGCAATTGGCAGAAAGGTGTCAATTATGTCAGTTAGATGAAC
3391813 AATTAAACAT
Statistics
Matches: 328, Mismatches: 44, Indels: 7
0.87 0.12 0.02
Matches are distributed among these distances:
80 13 0.04
81 314 0.96
82 1 0.00
ACGTcount: A:0.37, C:0.12, G:0.23, T:0.28
Consensus pattern (81 bp):
GGCCTAACTGTGCAATTGGCAGAAAGGTGTCAATTATGTCAGTTAGATGAACGGTTAAATACCAT
TGAGTAAAAGAATAAT
Found at i:3391795 original size:243 final size:242
Alignment explanation
Indices: 3391357--3391819 Score: 701
Period size: 243 Copynumber: 1.9 Consensus size: 242
3391347 GTACCTTTGA
* * * *
3391357 GGCCTAACTGTGCAATTGGCAGAAAGGTGTCAATTATGTGAGTTAGATGAACGGTTAAATACCAT
1 GGCCTAACTGTGCAATTGGCAAAAAGGTGTCAATTATGTCAGTTAGATGAACAGTTAAATACAAT
* * * * * *
3391422 TGAGTAAACGAATCATGGCCTAATTGTGCAATTGACATAAAGGTGTCAATTATGTCAGTTAGACG
66 TGAGTAAAAGAATAATGGCCTAACTGTACAATTGACAGAAAGGTGTCAATTATGCCAGTTAGACG
* *
3391487 AACGGTCAAATACCGTTGAGTAAAAGAATAATGGCCTAACTGTGCAATTGGAAGAAATATGTCAA
131 AACGGTCAAATACAGTTGAGTAAAAGAATAATGGCCTAACTATGCAATTGGAAGAAATATGTCAA
* *
3391552 TTATACGAGTTAGATGAACAGTTAAATACCGTTTAGTAAACGAATAAT
196 TTATAC-AGTAAGATGAACAATTAAATACCGTTTAGTAAACGAATAAT
* *
3391600 GGCCTAACTGTGCAATTGGTAAAAAGGTGTCAATTATGTCAGTTAGATGAACAGTTAAGTACAAT
1 GGCCTAACTGTGCAATTGGCAAAAAGGTGTCAATTATGTCAGTTAGATGAACAGTTAAATACAAT
* * *
3391665 TGAGTAAAAGAATAATGGCCTAACTGTACAATTGGCAGAAAGGTGTCAATTATGCCTGTTAGATG
66 TGAGTAAAAGAATAATGGCCTAACTGTACAATTGACAGAAAGGTGTCAATTATGCCAGTTAGACG
* * * *
3391730 AACGGTTAAATATAGTTGAGTAAAAGAATAATGGCCTAACTATGCAATTGGCAGAAATGTGTCAA
131 AACGGTCAAATACAGTTGAGTAAAAGAATAATGGCCTAACTATGCAATTGGAAGAAATATGTCAA
*
3391795 TTATGCAGTAAGATGAACAATTAAA
196 TTATACAGTAAGATGAACAATTAAA
3391820 CATTGTTGAG
Statistics
Matches: 196, Mismatches: 24, Indels: 1
0.89 0.11 0.00
Matches are distributed among these distances:
242 17 0.09
243 179 0.91
ACGTcount: A:0.38, C:0.12, G:0.22, T:0.28
Consensus pattern (242 bp):
GGCCTAACTGTGCAATTGGCAAAAAGGTGTCAATTATGTCAGTTAGATGAACAGTTAAATACAAT
TGAGTAAAAGAATAATGGCCTAACTGTACAATTGACAGAAAGGTGTCAATTATGCCAGTTAGACG
AACGGTCAAATACAGTTGAGTAAAAGAATAATGGCCTAACTATGCAATTGGAAGAAATATGTCAA
TTATACAGTAAGATGAACAATTAAATACCGTTTAGTAAACGAATAAT
Found at i:3391850 original size:29 final size:29
Alignment explanation
Indices: 3391817--3391895 Score: 95
Period size: 29 Copynumber: 2.7 Consensus size: 29
3391807 ATGAACAATT
* *
3391817 AAACATTGTTGAGAAAAAGAAGAAAGGTC
1 AAACACTGTTGAGTAAAAGAAGAAAGGTC
* * * *
3391846 AAACACTATTGAGTAAAAGATGAATGGTT
1 AAACACTGTTGAGTAAAAGAAGAAAGGTC
*
3391875 AAACACTGTTGGGTAAAAGAA
1 AAACACTGTTGAGTAAAAGAA
3391896 TAATAGACTA
Statistics
Matches: 41, Mismatches: 9, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
29 41 1.00
ACGTcount: A:0.48, C:0.08, G:0.23, T:0.22
Consensus pattern (29 bp):
AAACACTGTTGAGTAAAAGAAGAAAGGTC
Found at i:3396433 original size:59 final size:61
Alignment explanation
Indices: 3396369--3396531 Score: 207
Period size: 58 Copynumber: 2.8 Consensus size: 61
3396359 TGGCACTAAA
*
3396369 TGTGCAAAAATGTTAAGAAATTCATACTAAGTGTATGAATTTCT-GTATTGGGCACTTT-G
1 TGTGCAAAAATGTTAAGAAATTCATACTAAGTGTATGAATTTCTCGTATTGGACACTTTAG
* *
3396428 TGTGC-AAAATGTTAAGAAATTCATACTAAGTGTATGAGTTT-TCGTATTGGATACTTTAG
1 TGTGCAAAAATGTTAAGAAATTCATACTAAGTGTATGAATTTCTCGTATTGGACACTTTAG
* * *
3396487 -GTGCAAAAA-GATAAGAAACTCATACCAAAG-GTATGAATTTC-CGTA
1 TGTGCAAAAATGTTAAGAAATTCATA-CTAAGTGTATGAATTTCTCGTA
3396532 AGTGAAATTG
Statistics
Matches: 92, Mismatches: 7, Indels: 11
0.84 0.06 0.10
Matches are distributed among these distances:
57 1 0.01
58 77 0.84
59 14 0.15
ACGTcount: A:0.36, C:0.11, G:0.20, T:0.34
Consensus pattern (61 bp):
TGTGCAAAAATGTTAAGAAATTCATACTAAGTGTATGAATTTCTCGTATTGGACACTTTAG
Found at i:3396844 original size:68 final size:68
Alignment explanation
Indices: 3396735--3397020 Score: 362
Period size: 68 Copynumber: 4.2 Consensus size: 68
3396725 AAAGATTATG
* * * * *
3396735 AGGCCTAACTGTGTATTTGAGAGAAAGATGTC-TTTGATGCCATTTAGATAAAAGGCTACGTGCC
1 AGGCCTAACTGTGCATTTGACAGAAAGATGTCATTT-ATGCCAGTTAGATGAAAGGCTAAGTGCC
3396799 TTTA
65 TTTA
* * *
3396803 AGGCCTAATTGTGCATTTGACAGAAAGGTGTCATTTATGCCAGTTAGATGAAAGGATAAGTGCCT
1 AGGCCTAACTGTGCATTTGACAGAAAGATGTCATTTATGCCAGTTAGATGAAAGGCTAAGTGCCT
*
3396868 TTG
66 TTA
* * * * *
3396871 AGGCCTAATTGTGTAATTGACAGAAATATGTCATTTATGCGAGTT-GATGAAAGGCTAAGTGCC-
1 AGGCCTAACTGTGCATTTGACAGAAAGATGTCATTTATGCCAGTTAGATGAAAGGCTAAGTGCCT
3396934 TTA
66 TTA
* * * *
3396937 GAGGCCTAACTGTGCATTTGACATAAAGGTGTCATTTATGCTAGTTAGATGAAAGGCTAAGTACC
1 -AGGCCTAACTGTGCATTTGACAGAAAGATGTCATTTATGCCAGTTAGATGAAAGGCTAAGTGCC
*
3397002 TTTG
65 TTTA
3397006 AGGCCTAACTGTGCA
1 AGGCCTAACTGTGCA
3397021 ATTGGCAAAA
Statistics
Matches: 189, Mismatches: 25, Indels: 8
0.85 0.11 0.04
Matches are distributed among these distances:
66 2 0.01
67 55 0.29
68 127 0.67
69 5 0.03
ACGTcount: A:0.30, C:0.14, G:0.25, T:0.31
Consensus pattern (68 bp):
AGGCCTAACTGTGCATTTGACAGAAAGATGTCATTTATGCCAGTTAGATGAAAGGCTAAGTGCCT
TTA
Found at i:3396976 original size:135 final size:136
Alignment explanation
Indices: 3396733--3397024 Score: 419
Period size: 135 Copynumber: 2.2 Consensus size: 136
3396723 TAAAAGATTA
* * * *
3396733 TGAGGCCTAACTGTGTATTTGAGAGAAAGATGTCTTTGATGCCATTTAGATAAAAGGCTACGTGC
1 TGAGGCCTAACTGTGTAATTGACAGAAAGATGTCTTTGATGCCAGTTAGATAAAAGGCTAAGTGC
*
3396798 CTTTAAGGCCTAATTGTGCATTTGACAGAAAGGTGTCATTTATGCCAGTTAGATGAAAGGATAAG
66 CTTTAAGGCCTAACTGTGCATTTGACAGAAAGGTGTCATTTATGCCAGTTAGATGAAAGGATAAG
*
3396863 TGCCTT
131 TACCTT
* * * *
3396869 TGAGGCCTAATTGTGTAATTGACAGAAATATGTCATTT-ATGCGAGTT-GATGAAAGGCTAAGTG
1 TGAGGCCTAACTGTGTAATTGACAGAAAGATGTC-TTTGATGCCAGTTAGATAAAAGGCTAAGTG
* * *
3396932 CC-TTAGAGGCCTAACTGTGCATTTGACATAAAGGTGTCATTTATGCTAGTTAGATGAAAGGCTA
65 CCTTTA-AGGCCTAACTGTGCATTTGACAGAAAGGTGTCATTTATGCCAGTTAGATGAAAGGATA
3396996 AGTACCTT
129 AGTACCTT
*
3397004 TGAGGCCTAACTGTGCAATTG
1 TGAGGCCTAACTGTGTAATTG
3397025 GCAAAAATGT
Statistics
Matches: 139, Mismatches: 15, Indels: 5
0.87 0.09 0.03
Matches are distributed among these distances:
134 3 0.02
135 96 0.69
136 37 0.27
137 3 0.02
ACGTcount: A:0.29, C:0.14, G:0.25, T:0.32
Consensus pattern (136 bp):
TGAGGCCTAACTGTGTAATTGACAGAAAGATGTCTTTGATGCCAGTTAGATAAAAGGCTAAGTGC
CTTTAAGGCCTAACTGTGCATTTGACAGAAAGGTGTCATTTATGCCAGTTAGATGAAAGGATAAG
TACCTT
Found at i:3397137 original size:20 final size:19
Alignment explanation
Indices: 3397094--3397137 Score: 52
Period size: 20 Copynumber: 2.3 Consensus size: 19
3397084 TTAAGATTTT
*
3397094 ATATTTGATTTATAATATA
1 ATATTTGATTTATAATAGA
* *
3397113 ATATTTGATTTTTTATTAGA
1 ATATTTGA-TTTATAATAGA
3397133 ATATT
1 ATATT
3397138 ATAAATATTA
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
19 8 0.38
20 13 0.62
ACGTcount: A:0.36, C:0.00, G:0.07, T:0.57
Consensus pattern (19 bp):
ATATTTGATTTATAATAGA
Found at i:3409051 original size:30 final size:30
Alignment explanation
Indices: 3408995--3409053 Score: 75
Period size: 30 Copynumber: 2.0 Consensus size: 30
3408985 GATTTATTTA
* *
3408995 GTGACCAAATTATAAATTTGGTAAAGTTTG
1 GTGACCAAAGTATAAATTTGGAAAAGTTTG
*
3409025 GTGATCAAAGTATAAACTTT-GAAAAGTTT
1 GTGACCAAAGTATAAA-TTTGGAAAAGTTT
3409054 AAGGACCAGA
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
30 22 0.88
31 3 0.12
ACGTcount: A:0.39, C:0.07, G:0.19, T:0.36
Consensus pattern (30 bp):
GTGACCAAAGTATAAATTTGGAAAAGTTTG
Found at i:3417263 original size:27 final size:27
Alignment explanation
Indices: 3417233--3417287 Score: 74
Period size: 27 Copynumber: 2.0 Consensus size: 27
3417223 TAACATATAG
*
3417233 TTTATATATTTTGTATTATGCATGTGA
1 TTTAAATATTTTGTATTATGCATGTGA
* * *
3417260 TTTAAATGTTTTGTGTTATGTATGTGA
1 TTTAAATATTTTGTATTATGCATGTGA
3417287 T
1 T
3417288 GTCGTACAAA
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
27 24 1.00
ACGTcount: A:0.24, C:0.02, G:0.18, T:0.56
Consensus pattern (27 bp):
TTTAAATATTTTGTATTATGCATGTGA
Found at i:3417806 original size:27 final size:27
Alignment explanation
Indices: 3417776--3417827 Score: 86
Period size: 27 Copynumber: 1.9 Consensus size: 27
3417766 TATTTATTAT
*
3417776 TTTTGAAGTATTTATGATATTTTATTG
1 TTTTGAAGTAATTATGATATTTTATTG
*
3417803 TTTTGAATTAATTATGATATTTTAT
1 TTTTGAAGTAATTATGATATTTTAT
3417828 GCTTTATCTC
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
27 23 1.00
ACGTcount: A:0.29, C:0.00, G:0.12, T:0.60
Consensus pattern (27 bp):
TTTTGAAGTAATTATGATATTTTATTG
Found at i:3422028 original size:45 final size:45
Alignment explanation
Indices: 3421946--3422209 Score: 383
Period size: 45 Copynumber: 5.9 Consensus size: 45
3421936 GAATAAAAGT
* *
3421946 AAATGCATAACGGTGCATT-TCAGCATAAAAGGTGCCACTAATGA
1 AAATGCATAACGGTGCATTATCGGAATAAAAGGTGCCACTAATGA
* *
3421990 AAATACATAACGGTGCATTATCGGAATAAAAGGTGCCACTAATAA
1 AAATGCATAACGGTGCATTATCGGAATAAAAGGTGCCACTAATGA
*
3422035 AAAT-CAATAACGGTGCATTATCGGCATAAAAGGTGCCACTAATGA
1 AAATGC-ATAACGGTGCATTATCGGAATAAAAGGTGCCACTAATGA
* *
3422080 AAATACATAACGGTGCATTATCGGCATAAAAGGTGCCACTAATGA
1 AAATGCATAACGGTGCATTATCGGAATAAAAGGTGCCACTAATGA
* *
3422125 AAATGCATAACGGTTCATAATC-GACATAAAAGGTGCCACTAATGA
1 AAATGCATAACGGTGCATTATCGGA-ATAAAAGGTGCCACTAATGA
*
3422170 AAATGCATAACGGTGCATTATC-GACATAAAAGGTTCCACT
1 AAATGCATAACGGTGCATTATCGGA-ATAAAAGGTGCCACT
3422210 CATGGTATTT
Statistics
Matches: 203, Mismatches: 13, Indels: 7
0.91 0.06 0.03
Matches are distributed among these distances:
44 20 0.10
45 182 0.90
46 1 0.00
ACGTcount: A:0.41, C:0.18, G:0.19, T:0.23
Consensus pattern (45 bp):
AAATGCATAACGGTGCATTATCGGAATAAAAGGTGCCACTAATGA
Found at i:3422132 original size:26 final size:26
Alignment explanation
Indices: 3422103--3422179 Score: 71
Period size: 26 Copynumber: 3.2 Consensus size: 26
3422093 TGCATTATCG
3422103 GCATAAAAGGTGCCACTAATGAAAAT
1 GCATAAAAGGTGCCACTAATGAAAAT
* *
3422129 GCAT-AACGGT-TCA-TAATCG---A-
1 GCATAAAAGGTGCCACTAAT-GAAAAT
3422149 -CATAAAAGGTGCCACTAATGAAAAT
1 GCATAAAAGGTGCCACTAATGAAAAT
3422174 GCATAA
1 GCATAA
3422180 CGGTGCATTA
Statistics
Matches: 38, Mismatches: 4, Indels: 18
0.63 0.07 0.30
Matches are distributed among these distances:
19 3 0.08
20 5 0.13
21 4 0.11
22 4 0.11
23 4 0.11
24 4 0.11
25 5 0.13
26 9 0.24
ACGTcount: A:0.44, C:0.17, G:0.18, T:0.21
Consensus pattern (26 bp):
GCATAAAAGGTGCCACTAATGAAAAT
Found at i:3428413 original size:19 final size:19
Alignment explanation
Indices: 3428389--3428431 Score: 86
Period size: 19 Copynumber: 2.3 Consensus size: 19
3428379 ACAAAAATTA
3428389 TATCGATACTGAAGGGGAG
1 TATCGATACTGAAGGGGAG
3428408 TATCGATACTGAAGGGGAG
1 TATCGATACTGAAGGGGAG
3428427 TATCG
1 TATCG
3428432 GTACCATAGT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 24 1.00
ACGTcount: A:0.30, C:0.12, G:0.35, T:0.23
Consensus pattern (19 bp):
TATCGATACTGAAGGGGAG
Found at i:3429124 original size:45 final size:45
Alignment explanation
Indices: 3428891--3429109 Score: 314
Period size: 45 Copynumber: 4.9 Consensus size: 45
3428881 GAATAAAAAT
* * * *
3428891 AAATGCATAACGGTGCATT-TAGGCATAAAAGGTGTCACTAATGA
1 AAATGAATAATGGTGCATTATCGGCATAAAAGGTGCCACTAATGA
* * * *
3428935 AAATGAATAATGGTGTATTATCAGCATAAAAGGTGTCACTAATAA
1 AAATGAATAATGGTGCATTATCGGCATAAAAGGTGCCACTAATGA
*
3428980 AAATGTATAATGGTGCATTATCGGCATAAAAGGTGCCACTAATGA
1 AAATGAATAATGGTGCATTATCGGCATAAAAGGTGCCACTAATGA
* * *
3429025 AAATGCATAATTGTGTATTATCGGCATAAAAGGTGCCACTAATGA
1 AAATGAATAATGGTGCATTATCGGCATAAAAGGTGCCACTAATGA
*
3429070 AAATGAATAACGGTGCATTATCGGCATAAAAGGTGCCACT
1 AAATGAATAATGGTGCATTATCGGCATAAAAGGTGCCACT
3429110 CATGGTATTC
Statistics
Matches: 156, Mismatches: 18, Indels: 1
0.89 0.10 0.01
Matches are distributed among these distances:
44 16 0.10
45 140 0.90
ACGTcount: A:0.39, C:0.13, G:0.21, T:0.26
Consensus pattern (45 bp):
AAATGAATAATGGTGCATTATCGGCATAAAAGGTGCCACTAATGA
Found at i:3431078 original size:492 final size:491
Alignment explanation
Indices: 3430155--3431144 Score: 1953
Period size: 492 Copynumber: 2.0 Consensus size: 491
3430145 AAGTAAATAG
3430155 TCAAATTAATATTCATTTAAACTAAAATAAAATATGGTTTAATAAAATAATATTCGTATCTAATA
1 TCAAATTAATATTCATTTAAACTAAAATAAAATATGGTTTAATAAAATAATATTCGTATCTAATA
3430220 ATATTCATTTATAAAACTAGCATATAGAGTTAAAATCAAAAAACAATCCAGACATATCGAATCAG
66 ATATTCATTTATAAAACTAGCATATAGAGTTAAAATCAAAAAACAATCCAGACATATCGAATCAG
3430285 AGCATCAAAATATAAATATCTACATGCCAACTAAGAAATATAAAAATAAAAATATGCCATATTGA
131 AGCATCAAAATATAAATATCTACATGCCAACTAAGAAATATAAAAATAAAAATATGCCATATTGA
*
3430350 ATATGGTTGTCTGAATTGGATCTCAAAATATGGATGTTTGGCCTGGCTCTTACTCATCTATCAAC
196 ATATGGTTGTCTGAATTGGATCTCAAAATATGGATGTTTGACCTGGCTCTTACTCATCTATCAAC
3430415 TTCGCTTTACCAACGTGTGAAACAATCACATGCTAAGTTTTCTACTTAGTGAGGCAACAAATAAT
261 TTCGCTTTACCAACGTGTGAAACAATCACATGCTAAGTTTTCTACTTAGTGAGGCAACAAATAAT
3430480 ATAAATAAAACATTTAACAGATAAAATATATTATATCATATAAAAACATTATTAAAATAAAATAA
326 ATAAATAAAACATTTAACAGATAAAATATATTATATCATATAAAAACATTATTAAAATAAAATAA
3430545 ATATAATTATTAAAACAGATGCTCGTAATAAGAACAGTACTATAAAAATTTCATAAGTAAACTAT
391 ATATAATTATTAAAACAGATGCTCGTAATAAGAACAGTACTATAAAAATTTCATAAGTAAACTAT
3430610 ATTGTTCCATTTTAGATTTATATTTTTCTATTCAGA
456 ATTGTTCCATTTTAGATTTATATTTTTCTATTCAGA
3430646 TCAAATTAATATTCATTTAAACTAAAATAAAATATGGTTTAATAAAATAATATTCGTATCTAATA
1 TCAAATTAATATTCATTTAAACTAAAATAAAATATGGTTTAATAAAATAATATTCGTATCTAATA
*
3430711 ATATTCATTTATAAAACTAGCATATATAGTTAAAATCAAAAAACAATCCAGACATATCGAATCAG
66 ATATTCATTTATAAAACTAGCATATAGAGTTAAAATCAAAAAACAATCCAGACATATCGAATCAG
3430776 AGCATCAAAATATAAATATCTACATGCCAACTAAGAAATATAAAAATAAAAAATATGCCATATTG
131 AGCATCAAAATATAAATATCTACATGCCAACTAAGAAATATAAAAAT-AAAAATATGCCATATTG
3430841 AATATGGTTGTCTGAATTGGATCTCAAAATATGGATGTTTGACCTGGCTCTTACTCATCTATCAA
195 AATATGGTTGTCTGAATTGGATCTCAAAATATGGATGTTTGACCTGGCTCTTACTCATCTATCAA
3430906 CTTCGCTTTACCAACGTGTGAAACAATCACATGCTAAGTTTTCTACTTAGTGAGGCAACAAATAA
260 CTTCGCTTTACCAACGTGTGAAACAATCACATGCTAAGTTTTCTACTTAGTGAGGCAACAAATAA
3430971 TATAAATAAAACATTTAACAGATAAAATATATTATATCATATAAAAACATTATTAAAATAAAATA
325 TATAAATAAAACATTTAACAGATAAAATATATTATATCATATAAAAACATTATTAAAATAAAATA
3431036 AATATAATTATTAAAACAGATGCTCGTAATAAGAACAGTACTATAAAAATTTCATAAGTAAACTA
390 AATATAATTATTAAAACAGATGCTCGTAATAAGAACAGTACTATAAAAATTTCATAAGTAAACTA
3431101 TATTGTTCCATTTTAGATTTATATTTTTCTATTCAGA
455 TATTGTTCCATTTTAGATTTATATTTTTCTATTCAGA
3431138 TCAAATT
1 TCAAATT
3431145 GCCGTCCACT
Statistics
Matches: 496, Mismatches: 2, Indels: 1
0.99 0.00 0.00
Matches are distributed among these distances:
491 176 0.35
492 320 0.65
ACGTcount: A:0.45, C:0.13, G:0.09, T:0.33
Consensus pattern (491 bp):
TCAAATTAATATTCATTTAAACTAAAATAAAATATGGTTTAATAAAATAATATTCGTATCTAATA
ATATTCATTTATAAAACTAGCATATAGAGTTAAAATCAAAAAACAATCCAGACATATCGAATCAG
AGCATCAAAATATAAATATCTACATGCCAACTAAGAAATATAAAAATAAAAATATGCCATATTGA
ATATGGTTGTCTGAATTGGATCTCAAAATATGGATGTTTGACCTGGCTCTTACTCATCTATCAAC
TTCGCTTTACCAACGTGTGAAACAATCACATGCTAAGTTTTCTACTTAGTGAGGCAACAAATAAT
ATAAATAAAACATTTAACAGATAAAATATATTATATCATATAAAAACATTATTAAAATAAAATAA
ATATAATTATTAAAACAGATGCTCGTAATAAGAACAGTACTATAAAAATTTCATAAGTAAACTAT
ATTGTTCCATTTTAGATTTATATTTTTCTATTCAGA
Found at i:3437667 original size:12 final size:12
Alignment explanation
Indices: 3437629--3437673 Score: 56
Period size: 12 Copynumber: 3.7 Consensus size: 12
3437619 TTTAATCAAT
3437629 AATA-TTAATTA
1 AATATTTAATTA
3437640 AATATTTAAATATA
1 AATATTT-AAT-TA
*
3437654 AATGTTTAATTA
1 AATATTTAATTA
3437666 AATATTTA
1 AATATTTA
3437674 GTAATTAAAA
Statistics
Matches: 29, Mismatches: 2, Indels: 5
0.81 0.06 0.14
Matches are distributed among these distances:
11 4 0.14
12 11 0.38
13 6 0.21
14 8 0.28
ACGTcount: A:0.51, C:0.00, G:0.02, T:0.47
Consensus pattern (12 bp):
AATATTTAATTA
Found at i:3440252 original size:30 final size:30
Alignment explanation
Indices: 3440183--3440240 Score: 116
Period size: 30 Copynumber: 1.9 Consensus size: 30
3440173 AATTTAAGGA
3440183 AAAATGTTTTTGGACTTGAATTGAATTTGC
1 AAAATGTTTTTGGACTTGAATTGAATTTGC
3440213 AAAATGTTTTTGGACTTGAATTGAATTT
1 AAAATGTTTTTGGACTTGAATTGAATTT
3440241 ATTCAAAGTT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 28 1.00
ACGTcount: A:0.31, C:0.05, G:0.19, T:0.45
Consensus pattern (30 bp):
AAAATGTTTTTGGACTTGAATTGAATTTGC
Found at i:3440449 original size:21 final size:21
Alignment explanation
Indices: 3440423--3440462 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
3440413 TTGAATTTTA
3440423 TGAAGGAGTACCGATACCCTT
1 TGAAGGAGTACCGATACCCTT
*
3440444 TGAAGGGGTACCGATACCC
1 TGAAGGAGTACCGATACCC
3440463 CCTATCGTGG
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.28, C:0.25, G:0.28, T:0.20
Consensus pattern (21 bp):
TGAAGGAGTACCGATACCCTT
Found at i:3442487 original size:140 final size:140
Alignment explanation
Indices: 3442235--3442514 Score: 560
Period size: 140 Copynumber: 2.0 Consensus size: 140
3442225 TTTTCGATTG
3442235 AATATTTCATGCTAGGTTTAAACATCACATTGAAGGATACTTGACCAGAGGCATATCAAGAATCG
1 AATATTTCATGCTAGGTTTAAACATCACATTGAAGGATACTTGACCAGAGGCATATCAAGAATCG
3442300 AATGCATTTTTGCTTAACTTAGCGGCAATAAGACATTTTCCCGTCAAACCTTTTCAAAGTCAATT
66 AATGCATTTTTGCTTAACTTAGCGGCAATAAGACATTTTCCCGTCAAACCTTTTCAAAGTCAATT
3442365 TCAACTTTAC
131 TCAACTTTAC
3442375 AATATTTCATGCTAGGTTTAAACATCACATTGAAGGATACTTGACCAGAGGCATATCAAGAATCG
1 AATATTTCATGCTAGGTTTAAACATCACATTGAAGGATACTTGACCAGAGGCATATCAAGAATCG
3442440 AATGCATTTTTGCTTAACTTAGCGGCAATAAGACATTTTCCCGTCAAACCTTTTCAAAGTCAATT
66 AATGCATTTTTGCTTAACTTAGCGGCAATAAGACATTTTCCCGTCAAACCTTTTCAAAGTCAATT
3442505 TCAACTTTAC
131 TCAACTTTAC
3442515 GATGGAGGAT
Statistics
Matches: 140, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
140 140 1.00
ACGTcount: A:0.34, C:0.20, G:0.14, T:0.32
Consensus pattern (140 bp):
AATATTTCATGCTAGGTTTAAACATCACATTGAAGGATACTTGACCAGAGGCATATCAAGAATCG
AATGCATTTTTGCTTAACTTAGCGGCAATAAGACATTTTCCCGTCAAACCTTTTCAAAGTCAATT
TCAACTTTAC
Found at i:3442805 original size:218 final size:219
Alignment explanation
Indices: 3442444--3442855 Score: 547
Period size: 218 Copynumber: 1.9 Consensus size: 219
3442434 GAATCGAATG
* * * **
3442444 CATTTTTGCTTAACTTAGCGGCAATAAGACATTTTCCCGTCAAACCTTTTCAAAGTCAATTTCAA
1 CATTTTGGCTTAACTCAGCGGCAATAAGACAATTTCCAATCAAACCTTTTCAAAGTCAATTTCAA
** * * * * * *
3442509 CTTTACGATGGAGGATATTGGGATCGAAATCCAAATCAATTGCATTCGATATTAACTCAACGGCT
66 CTCCACGACGAAGGATATTGGGATCGAAAACCAAATCAATTGCATTCGAGATTAACTCAACGACA
* * *
3442574 AGGAGCTAGTTTCCAATTGAAGTTTTCAAGCCAGGTTTCAACTTCACGAAGAATGATACTTGACT
131 AGCAGCTAGTTTCCAACTGAAGTTTTCAAGCCAGGTTTCAACTTCACGAAGAAAGATACTTGACT
3442639 TGGAGGCACATTAAGAATTGACTA
196 TGGAGGCACATTAAGAATTGACTA
* * * *
3442663 CATTTTGGCTTAACTCAGCGGCGATGAGACAATTTCCAATCAAACCTTTTCGAAGTTAATTTCAA
1 CATTTTGGCTTAACTCAGCGGCAATAAGACAATTTCCAATCAAACCTTTTCAAAGTCAATTTCAA
* ** * * * * *
3442728 CTCCACGACGAAGGATATTGTG-TTTAAAAGCAAATCAATTTCATTCTAGCTTAACTCAGCGACA
66 CTCCACGACGAAGGATATTGGGATCGAAAACCAAATCAATTGCATTCGAGATTAACTCAACGACA
* *
3442792 AGCAGCTAGTTTCCAACTGAAGTTTTCAGGCCAGGTTTCAACTTCACGACGAAAGATACTTGAC
131 AGCAGCTAGTTTCCAACTGAAGTTTTCAAGCCAGGTTTCAACTTCACGAAGAAAGATACTTGAC
3442856 CCGGTTTTGA
Statistics
Matches: 163, Mismatches: 30, Indels: 1
0.84 0.15 0.01
Matches are distributed among these distances:
218 90 0.55
219 73 0.45
ACGTcount: A:0.32, C:0.21, G:0.17, T:0.30
Consensus pattern (219 bp):
CATTTTGGCTTAACTCAGCGGCAATAAGACAATTTCCAATCAAACCTTTTCAAAGTCAATTTCAA
CTCCACGACGAAGGATATTGGGATCGAAAACCAAATCAATTGCATTCGAGATTAACTCAACGACA
AGCAGCTAGTTTCCAACTGAAGTTTTCAAGCCAGGTTTCAACTTCACGAAGAAAGATACTTGACT
TGGAGGCACATTAAGAATTGACTA
Found at i:3443319 original size:2 final size:2
Alignment explanation
Indices: 3443312--3443354 Score: 86
Period size: 2 Copynumber: 21.5 Consensus size: 2
3443302 TAATCTTGAA
3443312 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
3443354 A
1 A
3443355 CATACTAAAT
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 41 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:3444769 original size:5 final size:5
Alignment explanation
Indices: 3444759--3444787 Score: 51
Period size: 5 Copynumber: 6.0 Consensus size: 5
3444749 ATCCAATATT
3444759 TTTTA TTTTA TTTTA TTTTA -TTTA TTTTA
1 TTTTA TTTTA TTTTA TTTTA TTTTA TTTTA
3444788 ATCCTTTCTC
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
4 4 0.17
5 19 0.83
ACGTcount: A:0.21, C:0.00, G:0.00, T:0.79
Consensus pattern (5 bp):
TTTTA
Found at i:3448049 original size:26 final size:26
Alignment explanation
Indices: 3447985--3448049 Score: 103
Period size: 26 Copynumber: 2.5 Consensus size: 26
3447975 CAAGTCATAG
*
3447985 CATAGTCCGAATCAACCAATATTAAT
1 CATAGTTCGAATCAACCAATATTAAT
*
3448011 CATAGTTCAAATCAACCAATATTAAT
1 CATAGTTCGAATCAACCAATATTAAT
*
3448037 CATAGTTTGAATC
1 CATAGTTCGAATC
3448050 TTATGCAAAT
Statistics
Matches: 35, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
26 35 1.00
ACGTcount: A:0.42, C:0.20, G:0.08, T:0.31
Consensus pattern (26 bp):
CATAGTTCGAATCAACCAATATTAAT
Found at i:3448933 original size:83 final size:82
Alignment explanation
Indices: 3448811--3449091 Score: 411
Period size: 83 Copynumber: 3.4 Consensus size: 82
3448801 ATCTAAAAAT
* * * * *
3448811 AGATAATAATATCTTTTAGATTTAAAATATTAAATATGAGAGTTTTACTTTAACCAAAACTCTTT
1 AGATTATAATATCTTTTAAATTTATAATATTAAA-ATGAGAGTTTTACTCTAACCAAAACTATTT
3448876 TAATATCTAAATTTAAAC
65 TAATATCTAAATTTAAAC
* * * *
3448894 ATATTATAATATCTTTTAAATTTATAATATTAAACATGAGAGTTTTACTCCAATCAAAATTATTT
1 AGATTATAATATCTTTTAAATTTATAATATTAAA-ATGAGAGTTTTACTCTAACCAAAACTATTT
3448959 TAATATCTAAATTTAAAC
65 TAATATCTAAATTTAAAC
*
3448977 AGATTATAATATCTTTTAAATTTATAATATTAAAACTGAAAGTTTTACTCTAACCAAAACTATTT
1 AGATTATAATATCTTTTAAATTTATAATATTAAAA-TGAGAGTTTTACTCTAACCAAAACTATTT
*
3449042 TAATATCTAAATTTAAAT
65 TAATATCTAAATTTAAAC
* *
3449060 AGATAATAATATTTTTTAAATTTA-AATATTAA
1 AGATTATAATATCTTTTAAATTTATAATATTAA
3449092 GCATATATTT
Statistics
Matches: 179, Mismatches: 18, Indels: 3
0.89 0.09 0.01
Matches are distributed among these distances:
82 9 0.05
83 170 0.95
ACGTcount: A:0.44, C:0.09, G:0.04, T:0.43
Consensus pattern (82 bp):
AGATTATAATATCTTTTAAATTTATAATATTAAAATGAGAGTTTTACTCTAACCAAAACTATTTT
AATATCTAAATTTAAAC
Found at i:3449045 original size:166 final size:161
Alignment explanation
Indices: 3448769--3449091 Score: 441
Period size: 166 Copynumber: 2.0 Consensus size: 161
3448759 GAAATTTCGA
* * * *
3448769 GAGAGTTTTACTAAAATTAAAAATCTTTTAATATCTAAAAATAGATAATAATATCTTTTAGATTT
1 GAGAGTTTTACTAAAATCAAAAATATTTTAATATCTAAAAACAGATAATAATATCTTTTAAATTT
* * * * *
3448834 AAAATATTAAATATGAGAGTTTTACTTTAACCAAAACTCTTTTAATATCTAAATTTAAACATATT
66 AAAATATTAAATATGAAAGTTTTACTCTAACCAAAACTATTTTAATATCTAAATTTAAACAGATA
3448899 ATAATATCTTTTAAATTTATAATATTAAACAT
131 ATAATATCTTTTAAATTTA-AATATTAAACAT
** * *
3448931 GAGAGTTTTACTCCAATCAAAATTATTTTAATATCTAAATTTAAACAGATTATAATATCTTTTAA
1 GAGAGTTTTACTAAAATCAAAAATATTTTAATATCT-AA---AAACAGATAATAATATCTTTTAA
* *
3448996 ATTTATAATATTAAA-ACTGAAAGTTTTACTCTAACCAAAACTATTTTAATATCTAAATTTAAAT
62 ATTTAAAATATTAAATA-TGAAAGTTTTACTCTAACCAAAACTATTTTAATATCTAAATTTAAAC
*
3449060 AGATAATAATATTTTTTAAATTTAAATATTAA
126 AGATAATAATATCTTTTAAATTTAAATATTAA
3449092 GCATATATTT
Statistics
Matches: 140, Mismatches: 16, Indels: 7
0.86 0.10 0.04
Matches are distributed among these distances:
162 31 0.22
163 2 0.01
165 9 0.06
166 98 0.70
ACGTcount: A:0.45, C:0.08, G:0.05, T:0.42
Consensus pattern (161 bp):
GAGAGTTTTACTAAAATCAAAAATATTTTAATATCTAAAAACAGATAATAATATCTTTTAAATTT
AAAATATTAAATATGAAAGTTTTACTCTAACCAAAACTATTTTAATATCTAAATTTAAACAGATA
ATAATATCTTTTAAATTTAAATATTAAACAT
Found at i:3449326 original size:20 final size:20
Alignment explanation
Indices: 3449301--3449409 Score: 137
Period size: 20 Copynumber: 5.5 Consensus size: 20
3449291 TGTCCTTTTA
3449301 AATTTGACTATCGCGTTGCG
1 AATTTGACTATCGCGTTGCG
* *
3449321 AATTTGATTATCGCGTTGTG
1 AATTTGACTATCGCGTTGCG
* * * *
3449341 AATTTGACTTTTGTGTTGTG
1 AATTTGACTATCGCGTTGCG
* * *
3449361 AATTTGACTTTTGTGTTGCG
1 AATTTGACTATCGCGTTGCG
3449381 AATTTGACTATCGCGTTGCG
1 AATTTGACTATCGCGTTGCG
3449401 AATTTGACT
1 AATTTGACT
3449410 TTTATGTTGC
Statistics
Matches: 79, Mismatches: 10, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 79 1.00
ACGTcount: A:0.19, C:0.13, G:0.24, T:0.44
Consensus pattern (20 bp):
AATTTGACTATCGCGTTGCG
Found at i:3449364 original size:40 final size:40
Alignment explanation
Indices: 3449301--3449462 Score: 145
Period size: 40 Copynumber: 4.0 Consensus size: 40
3449291 TGTCCTTTTA
*
3449301 AATTTGACTATCGCGTTGCGAATTTGA-TTATCGCGTTGTG
1 AATTTGACTATCGCGTTGCGAATTTGACTT-TCGCGTTGCG
* * * * * *
3449341 AATTTGACTTTTGTGTTGTGAATTTGACTTTTGTGTTGCG
1 AATTTGACTATCGCGTTGCGAATTTGACTTTCGCGTTGCG
***
3449381 AATTTGACTATCGCGTTGCGAATTTGACTTTTATGTTGCG
1 AATTTGACTATCGCGTTGCGAATTTGACTTTCGCGTTGCG
*
3449421 -ATTT-ACAGATTCGCGTTGCG-ATTT-ACATATTCGCGTTGCG
1 AATTTGAC-TA-TCGCGTTGCGAATTTGAC-T-TTCGCGTTGCG
3449461 AA
1 AA
3449463 ATTGGAAACT
Statistics
Matches: 100, Mismatches: 16, Indels: 11
0.79 0.13 0.09
Matches are distributed among these distances:
38 4 0.04
39 10 0.10
40 83 0.83
41 3 0.03
ACGTcount: A:0.20, C:0.14, G:0.23, T:0.43
Consensus pattern (40 bp):
AATTTGACTATCGCGTTGCGAATTTGACTTTCGCGTTGCG
Found at i:3449394 original size:60 final size:60
Alignment explanation
Indices: 3449301--3449462 Score: 188
Period size: 60 Copynumber: 2.7 Consensus size: 60
3449291 TGTCCTTTTA
* * *
3449301 AATTTGACTATCGCGTTGCGAATTTGATTATCGCGTTGTGAATTTGACTTTTGTGTTGTG
1 AATTTGACTATCGCGTTGCGAATTTGACTATCGCGTTGCGAATTTGACTTTTATGTTGTG
* * * *
3449361 AATTTGACTTTTGTGTTGCGAATTTGACTATCGCGTTGCGAATTTGACTTTTATGTTGCG
1 AATTTGACTATCGCGTTGCGAATTTGACTATCGCGTTGCGAATTTGACTTTTATGTTGTG
*
3449421 -ATTT-ACAGATTCGCGTTGCG-ATTT-ACATATTCGCGTTGCGAA
1 AATTTGAC-TA-TCGCGTTGCGAATTTGAC-TA-TCGCGTTGCGAA
3449463 ATTGGAAACT
Statistics
Matches: 87, Mismatches: 11, Indels: 8
0.82 0.10 0.08
Matches are distributed among these distances:
58 4 0.05
59 10 0.11
60 73 0.84
ACGTcount: A:0.20, C:0.14, G:0.23, T:0.43
Consensus pattern (60 bp):
AATTTGACTATCGCGTTGCGAATTTGACTATCGCGTTGCGAATTTGACTTTTATGTTGTG
Found at i:3449438 original size:20 final size:20
Alignment explanation
Indices: 3449415--3449461 Score: 85
Period size: 20 Copynumber: 2.4 Consensus size: 20
3449405 TGACTTTTAT
3449415 GTTGCGATTTACAGATTCGC
1 GTTGCGATTTACAGATTCGC
*
3449435 GTTGCGATTTACATATTCGC
1 GTTGCGATTTACAGATTCGC
3449455 GTTGCGA
1 GTTGCGA
3449462 AATTGGAAAC
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 26 1.00
ACGTcount: A:0.19, C:0.19, G:0.26, T:0.36
Consensus pattern (20 bp):
GTTGCGATTTACAGATTCGC
Found at i:3454488 original size:23 final size:23
Alignment explanation
Indices: 3454458--3454527 Score: 122
Period size: 23 Copynumber: 3.0 Consensus size: 23
3454448 TGTACTTCGA
*
3454458 TGTTGAATCATTCAGCACTGTCT
1 TGTTGAATCATTCAGCACAGTCT
3454481 TGTTGAATCATTCAGCACAGTCT
1 TGTTGAATCATTCAGCACAGTCT
*
3454504 TGCTGAATCATTCAGCACAGTCT
1 TGTTGAATCATTCAGCACAGTCT
3454527 T
1 T
3454528 CATTCAGAGG
Statistics
Matches: 45, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
23 45 1.00
ACGTcount: A:0.24, C:0.23, G:0.17, T:0.36
Consensus pattern (23 bp):
TGTTGAATCATTCAGCACAGTCT
Found at i:3454589 original size:22 final size:22
Alignment explanation
Indices: 3454561--3454622 Score: 124
Period size: 22 Copynumber: 2.8 Consensus size: 22
3454551 CGTTGAATGT
3454561 TGAACGGTTCAGCATTCAGCGC
1 TGAACGGTTCAGCATTCAGCGC
3454583 TGAACGGTTCAGCATTCAGCGC
1 TGAACGGTTCAGCATTCAGCGC
3454605 TGAACGGTTCAGCATTCA
1 TGAACGGTTCAGCATTCA
3454623 AAGCCAAACA
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 40 1.00
ACGTcount: A:0.24, C:0.26, G:0.26, T:0.24
Consensus pattern (22 bp):
TGAACGGTTCAGCATTCAGCGC
Found at i:3460664 original size:4 final size:4
Alignment explanation
Indices: 3460655--3460679 Score: 50
Period size: 4 Copynumber: 6.2 Consensus size: 4
3460645 CTGATCTTCC
3460655 TATT TATT TATT TATT TATT TATT T
1 TATT TATT TATT TATT TATT TATT T
3460680 TGAATTTAAC
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:0.24, C:0.00, G:0.00, T:0.76
Consensus pattern (4 bp):
TATT
Found at i:3463914 original size:21 final size:21
Alignment explanation
Indices: 3463888--3463935 Score: 78
Period size: 21 Copynumber: 2.3 Consensus size: 21
3463878 GGACCAAGAT
*
3463888 AATCAAGTACTATGAAGATAC
1 AATCAAGTACTATGAAGAGAC
*
3463909 AATCAAGTACTATGAAGAGAT
1 AATCAAGTACTATGAAGAGAC
3463930 AATCAA
1 AATCAA
3463936 AGGGCTTGGC
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
21 25 1.00
ACGTcount: A:0.50, C:0.12, G:0.15, T:0.23
Consensus pattern (21 bp):
AATCAAGTACTATGAAGAGAC
Found at i:3465834 original size:36 final size:36
Alignment explanation
Indices: 3465779--3465981 Score: 177
Period size: 36 Copynumber: 5.8 Consensus size: 36
3465769 AGATTGTTTG
* ** *
3465779 TCTCCCTTGAGACAATTTCTCTTAAAACAAATTTTA
1 TCTCACTTGAGACTGTTTCTCTTGAAACAAATTTTA
*
3465815 TCTCACTTGAGACTGTTTCTCTTGAAACAAATTTTG
1 TCTCACTTGAGACTGTTTCTCTTGAAACAAATTTTA
** *
3465851 TCTCGTTTGAAACTGTTTCTCTTGAAACATAA----A
1 TCTCACTTGAGACTGTTTCTCTTGAAACA-AATTTTA
* * *
3465884 -C-C-TTTGAGATTGTTTCTCTTGAAACAAATTTTG
1 TCTCACTTGAGACTGTTTCTCTTGAAACAAATTTTA
** * *
3465917 TCTCGTTTGAGATTGTTTCTCTTGAAACAAATTTTT
1 TCTCACTTGAGACTGTTTCTCTTGAAACAAATTTTA
* * **
3465953 TCACACTTGGGAAAGTTTCTCTTGAAACA
1 TCTCACTTGAGACTGTTTCTCTTGAAACA
3465982 TAAACCTTTG
Statistics
Matches: 140, Mismatches: 19, Indels: 16
0.80 0.11 0.09
Matches are distributed among these distances:
29 2 0.01
30 22 0.16
31 1 0.01
32 1 0.01
34 1 0.01
35 1 0.01
36 110 0.79
37 2 0.01
ACGTcount: A:0.28, C:0.18, G:0.13, T:0.41
Consensus pattern (36 bp):
TCTCACTTGAGACTGTTTCTCTTGAAACAAATTTTA
Found at i:3465934 original size:66 final size:66
Alignment explanation
Indices: 3465821--3465945 Score: 223
Period size: 66 Copynumber: 1.9 Consensus size: 66
3465811 TTTATCTCAC
3465821 TTGAGACTGTTTCTCTTGAAACAAATTTTGTCTCGTTTGAAACTGTTTCTCTTGAAACATAAACC
1 TTGAGACTGTTTCTCTTGAAACAAATTTTGTCTCGTTTGAAACTGTTTCTCTTGAAACATAAACC
3465886 T
66 T
* * *
3465887 TTGAGATTGTTTCTCTTGAAACAAATTTTGTCTCGTTTGAGATTGTTTCTCTTGAAACA
1 TTGAGACTGTTTCTCTTGAAACAAATTTTGTCTCGTTTGAAACTGTTTCTCTTGAAACA
3465946 AATTTTTTCA
Statistics
Matches: 56, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
66 56 1.00
ACGTcount: A:0.26, C:0.16, G:0.15, T:0.43
Consensus pattern (66 bp):
TTGAGACTGTTTCTCTTGAAACAAATTTTGTCTCGTTTGAAACTGTTTCTCTTGAAACATAAACC
T
Found at i:3465971 original size:102 final size:100
Alignment explanation
Indices: 3465794--3466048 Score: 314
Period size: 102 Copynumber: 2.5 Consensus size: 100
3465784 CTTGAGACAA
* * * * * *
3465794 TTTCTCTTAAAACAAATTTTATCTCACTTGAGACTGTTTCTCTTGAAACAAATTTTGTCTCGTTT
1 TTTCTCTTGAAACAAATTTTGTCTC-TTTGAGACTGTTTCTCTTGAAACAAATTTTGTCACCTTG
3465859 GAAACTGTTTCTCTTGAAACATAAACCTTTGAGATTG
65 GAAAC-GTTTCTCTTGAAACATAAACCTTTGAGATTG
* *
3465896 TTTCTCTTGAAACAAATTTTGTCTCGTTTGAGATTGTTTCTCTTGAAACAAATTTTTTCACACTT
1 TTTCTCTTGAAACAAATTTTGTCTC-TTTGAGACTGTTTCTCTTGAAACAAATTTTGTCAC-CTT
*
3465961 GGGAAA-GTTTCTCTTGAAACATAAACCTTTGATATTG
64 -GGAAACGTTTCTCTTGAAACATAAACCTTTGAGATTG
* * ** *
3465998 TTTCTCTCGAAACAAAGTTTCGTCTCTCTTGAGACAATTTCTCTTAAAACA
1 TTTCTCTTGAAACAAA-TTTTGTCTCT-TTGAGACTGTTTCTCTTGAAACA
3466049 TAAACCTTTG
Statistics
Matches: 133, Mismatches: 16, Indels: 7
0.85 0.10 0.04
Matches are distributed among these distances:
102 100 0.75
103 29 0.22
104 4 0.03
ACGTcount: A:0.28, C:0.18, G:0.12, T:0.42
Consensus pattern (100 bp):
TTTCTCTTGAAACAAATTTTGTCTCTTTGAGACTGTTTCTCTTGAAACAAATTTTGTCACCTTGG
AAACGTTTCTCTTGAAACATAAACCTTTGAGATTG
Found at i:3466058 original size:67 final size:67
Alignment explanation
Indices: 3465922--3466112 Score: 251
Period size: 67 Copynumber: 2.9 Consensus size: 67
3465912 TTTTGTCTCG
* ** * * *
3465922 TTTGAGATTGTTTCTCTTGAAACAAA-TTTTTTCACACTTGGGA-AAGTTTCTCTTGAAACATAA
1 TTTGAGATTGTTTCTCTCGAAACAAAGTTTCGTCTCACTTGAGACAA-TTTCTCTTAAAACATAA
3465985 ACC
65 ACC
* *
3465988 TTTGATATTGTTTCTCTCGAAACAAAGTTTCGTCTCTCTTGAGACAATTTCTCTTAAAACATAAA
1 TTTGAGATTGTTTCTCTCGAAACAAAGTTTCGTCTCACTTGAGACAATTTCTCTTAAAACATAAA
3466053 CC
66 CC
* * * *
3466055 TTTGAGGTTGTTTCTCTCGAAACAAAGTTTCGTCTCGCTAGAGACAGTTTCTCTTAAA
1 TTTGAGATTGTTTCTCTCGAAACAAAGTTTCGTCTCACTTGAGACAATTTCTCTTAAA
3466113 GCTCAAATTT
Statistics
Matches: 110, Mismatches: 13, Indels: 3
0.87 0.10 0.02
Matches are distributed among these distances:
66 24 0.22
67 84 0.76
68 2 0.02
ACGTcount: A:0.28, C:0.19, G:0.14, T:0.39
Consensus pattern (67 bp):
TTTGAGATTGTTTCTCTCGAAACAAAGTTTCGTCTCACTTGAGACAATTTCTCTTAAAACATAAA
CC
Found at i:3466440 original size:102 final size:102
Alignment explanation
Indices: 3466116--3466442 Score: 435
Period size: 102 Copynumber: 3.2 Consensus size: 102
3466106 TCTTAAAGCT
* * *
3466116 CAAATTTTGAAGTTGTTTCACTTGAAAC-AAATTGATCTCACTTGAGATTGTTTTCCTAAAAACA
1 CAAATTTTGAAATTGTTTCACTTGAAACAAAATTGATCTCACTTGAGATTATTTTCCTAAAAATA
* * * * * * *
3466180 ATTTTTATCTCATTTGAGACA-ATTTCCCTCAAAAAA
66 AATTTTGTCTCACTTGAGATAGTTTTCCCTCGAAACA
* * * *
3466216 CGAATTTTGAAATTGCTTCACTTGAAACAAAATTTATCTCACTTGAGATTATTTTCGTAAAAAAT
1 CAAATTTTGAAATTGTTTCACTTGAAACAAAATTGATCTCACTTGAGATTATTTTCCT-AAAAAT
*
3466281 AAATTTCGTCTCACTTGAGATAGTTTTCCCTCGAAACA
65 AAATTTTGTCTCACTTGAGATAGTTTTCCCTCGAAACA
* *
3466319 CAAATTTTGAAATTGTTTCACTTGAAACAAAATTGATCTCGCTTAAGATTATTTTCCTAAAAATA
1 CAAATTTTGAAATTGTTTCACTTGAAACAAAATTGATCTCACTTGAGATTATTTTCCTAAAAATA
* * *
3466384 AATTTTGTCTCGCCTGAGATAGTTTTCCCTTGAAACA
66 AATTTTGTCTCACTTGAGATAGTTTTCCCTCGAAACA
3466421 CAAATTTTGAAATAT-TTTCACT
1 CAAATTTTGAAAT-TGTTTCACT
3466443 CTAAATTTTT
Statistics
Matches: 198, Mismatches: 25, Indels: 6
0.86 0.11 0.03
Matches are distributed among these distances:
100 25 0.13
101 26 0.13
102 82 0.41
103 65 0.33
ACGTcount: A:0.34, C:0.17, G:0.11, T:0.38
Consensus pattern (102 bp):
CAAATTTTGAAATTGTTTCACTTGAAACAAAATTGATCTCACTTGAGATTATTTTCCTAAAAATA
AATTTTGTCTCACTTGAGATAGTTTTCCCTCGAAACA
Found at i:3466506 original size:14 final size:15
Alignment explanation
Indices: 3466487--3466516 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
3466477 CTTGAAACAT
3466487 ATTTA-TTTTCACTC
1 ATTTATTTTTCACTC
3466501 ATTTATTTTTCACTC
1 ATTTATTTTTCACTC
3466516 A
1 A
3466517 AATGTCGAAT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 5 0.33
15 10 0.67
ACGTcount: A:0.23, C:0.20, G:0.00, T:0.57
Consensus pattern (15 bp):
ATTTATTTTTCACTC
Found at i:3468119 original size:2 final size:2
Alignment explanation
Indices: 3468106--3468142 Score: 65
Period size: 2 Copynumber: 18.5 Consensus size: 2
3468096 TTGACCCTTG
*
3468106 TA TA TT 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 T
3468143 TACTAATTTT
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (2 bp):
TA
Found at i:3468160 original size:5 final size:5
Alignment explanation
Indices: 3468150--3468198 Score: 57
Period size: 5 Copynumber: 10.2 Consensus size: 5
3468140 TATTACTAAT
* * *
3468150 TTTTA TTTTA TTTTG TTTGA TCTTA -TTTA -TTTA TTTTA TTTTA TTTTA
1 TTTTA TTTTA TTTTA TTTTA TTTTA TTTTA TTTTA TTTTA TTTTA TTTTA
3468198 T
1 T
3468199 AAAATGCCCA
Statistics
Matches: 37, Mismatches: 6, Indels: 2
0.82 0.13 0.04
Matches are distributed among these distances:
4 7 0.19
5 30 0.81
ACGTcount: A:0.18, C:0.02, G:0.04, T:0.76
Consensus pattern (5 bp):
TTTTA
Found at i:3472200 original size:21 final size:21
Alignment explanation
Indices: 3472159--3472198 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
3472149 TCTTTTACCC
3472159 CCAAATCTAAAAATCCCAAAT
1 CCAAATCTAAAAATCCCAAAT
*
3472180 CCAAATCTCAAAA-CCCAAA
1 CCAAATCTAAAAATCCCAAA
3472199 ATTCTAAACC
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 6 0.33
21 12 0.67
ACGTcount: A:0.53, C:0.33, G:0.00, T:0.15
Consensus pattern (21 bp):
CCAAATCTAAAAATCCCAAAT
Found at i:3472323 original size:14 final size:14
Alignment explanation
Indices: 3472289--3472327 Score: 51
Period size: 14 Copynumber: 2.8 Consensus size: 14
3472279 AAACCGCAAC
*
3472289 TCCTAAATTCTGAA
1 TCCTAAACTCTGAA
* *
3472303 TCTTAAACTCTGAG
1 TCCTAAACTCTGAA
3472317 TCCTAAACTCT
1 TCCTAAACTCT
3472328 AACCATAATA
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.31, C:0.26, G:0.08, T:0.36
Consensus pattern (14 bp):
TCCTAAACTCTGAA
Found at i:3472491 original size:2 final size:2
Alignment explanation
Indices: 3472484--3472553 Score: 140
Period size: 2 Copynumber: 35.0 Consensus size: 2
3472474 GTGGATCCTA
3472484 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
3472526 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
3472554 TAGACAAAAA
Statistics
Matches: 68, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 68 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:3472959 original size:26 final size:26
Alignment explanation
Indices: 3472930--3472989 Score: 102
Period size: 26 Copynumber: 2.3 Consensus size: 26
3472920 ATTTGGTTTG
3472930 GTTTTGTTGAATATGGTTCAATTTTA
1 GTTTTGTTGAATATGGTTCAATTTTA
* *
3472956 GTTTTTTTGAATTTGGTTCAATTTTA
1 GTTTTGTTGAATATGGTTCAATTTTA
3472982 GTTTTGTT
1 GTTTTGTT
3472990 ATTCCTAAGT
Statistics
Matches: 31, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
26 31 1.00
ACGTcount: A:0.18, C:0.03, G:0.18, T:0.60
Consensus pattern (26 bp):
GTTTTGTTGAATATGGTTCAATTTTA
Found at i:3482084 original size:35 final size:36
Alignment explanation
Indices: 3482031--3482098 Score: 102
Period size: 35 Copynumber: 1.9 Consensus size: 36
3482021 ATTTAGAAGT
3482031 TGGTGATAAAATAAGCGTGAT-ATGGTGATGGAATA
1 TGGTGATAAAATAAGCGTGATAATGGTGATGGAATA
* * *
3482066 TGGTGATGATATAGGCGTGATAATGGTGATGGA
1 TGGTGATAAAATAAGCGTGATAATGGTGATGGA
3482099 CAAATTGTAT
Statistics
Matches: 29, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
35 18 0.62
36 11 0.38
ACGTcount: A:0.32, C:0.03, G:0.35, T:0.29
Consensus pattern (36 bp):
TGGTGATAAAATAAGCGTGATAATGGTGATGGAATA
Found at i:3485352 original size:15 final size:16
Alignment explanation
Indices: 3485301--3485353 Score: 56
Period size: 16 Copynumber: 3.2 Consensus size: 16
3485291 AGATAGTGAA
3485301 ATAAGAAAAGATGAAAG
1 ATAAGAAAA-ATGAAAG
*
3485318 AATAA-AGAAATGAAATG
1 -ATAAGAAAAATGAAA-G
3485335 ATAAGAAAAATG-AAG
1 ATAAGAAAAATGAAAG
3485350 ATAA
1 ATAA
3485354 CTTACAACTC
Statistics
Matches: 31, Mismatches: 2, Indels: 7
0.77 0.05 0.17
Matches are distributed among these distances:
15 5 0.16
16 12 0.39
17 10 0.32
18 4 0.13
ACGTcount: A:0.66, C:0.00, G:0.19, T:0.15
Consensus pattern (16 bp):
ATAAGAAAAATGAAAG
Found at i:3486016 original size:35 final size:36
Alignment explanation
Indices: 3485969--3486036 Score: 120
Period size: 35 Copynumber: 1.9 Consensus size: 36
3485959 ATTTAGAAGT
3485969 TGGTGATAATATAGGCGTGAT-ATGGTGATGGAATA
1 TGGTGATAATATAGGCGTGATAATGGTGATGGAATA
*
3486004 TGGTGATGATATAGGCGTGATAATGGTGATGGA
1 TGGTGATAATATAGGCGTGATAATGGTGATGGA
3486037 CAGATTGTAT
Statistics
Matches: 31, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
35 20 0.65
36 11 0.35
ACGTcount: A:0.29, C:0.03, G:0.37, T:0.31
Consensus pattern (36 bp):
TGGTGATAATATAGGCGTGATAATGGTGATGGAATA
Found at i:3493239 original size:19 final size:18
Alignment explanation
Indices: 3493192--3493262 Score: 65
Period size: 18 Copynumber: 3.9 Consensus size: 18
3493182 TAGTGCTTAA
3493192 AATAAAATAAT-ATAATG
1 AATAAAATAATAATAATG
3493209 AATAAAAATAATAATAATG
1 AAT-AAAATAATAATAATG
* * *
3493228 ACATAAAGTAAT-ATCATT
1 A-ATAAAATAATAATAATG
*
3493246 ATTAAAAGTAATAATAA
1 AATAAAA-TAATAATAA
3493263 AAATTAGAAA
Statistics
Matches: 43, Mismatches: 6, Indels: 8
0.75 0.11 0.14
Matches are distributed among these distances:
17 7 0.16
18 17 0.40
19 17 0.40
20 2 0.05
ACGTcount: A:0.62, C:0.03, G:0.06, T:0.30
Consensus pattern (18 bp):
AATAAAATAATAATAATG
Found at i:3495820 original size:18 final size:18
Alignment explanation
Indices: 3495799--3495836 Score: 51
Period size: 18 Copynumber: 2.1 Consensus size: 18
3495789 TAAGAAGAAG
3495799 GAAA-AAAAGAAGAAAAAA
1 GAAAGAAAA-AAGAAAAAA
*
3495817 GAAAGAAAAAAGGAAAAA
1 GAAAGAAAAAAGAAAAAA
3495835 GA
1 GA
3495837 TGGATTGATT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
18 14 0.78
19 4 0.22
ACGTcount: A:0.79, C:0.00, G:0.21, T:0.00
Consensus pattern (18 bp):
GAAAGAAAAAAGAAAAAA
Found at i:3496299 original size:11 final size:11
Alignment explanation
Indices: 3496283--3496389 Score: 93
Period size: 11 Copynumber: 9.9 Consensus size: 11
3496273 CTCATCCATC
3496283 AGAGAAAAAAA
1 AGAGAAAAAAA
3496294 AGAGAAAAAAA
1 AGAGAAAAAAA
* *
3496305 GGAAAAAAAAA
1 AGAGAAAAAAA
3496316 AGAGAAAAAAA
1 AGAGAAAAAAA
3496327 A-AGAAAAGAAA
1 AGAGAAAA-AAA
*
3496338 A-A-AGAAAAA
1 AGAGAAAAAAA
3496347 AG-GAAAAAAGA
1 AGAGAAAAAA-A
3496358 A-A-AAAAGAAA
1 AGAGAAAA-AAA
3496368 AGA-AAAGAAAA
1 AGAGAAA-AAAA
3496379 AGATGAAAAAA
1 AGA-GAAAAAA
3496390 GATGAAAAAA
Statistics
Matches: 80, Mismatches: 6, Indels: 19
0.76 0.06 0.18
Matches are distributed among these distances:
9 4 0.05
10 20 0.25
11 49 0.61
12 4 0.05
13 3 0.04
ACGTcount: A:0.81, C:0.00, G:0.18, T:0.01
Consensus pattern (11 bp):
AGAGAAAAAAA
Found at i:3496303 original size:10 final size:10
Alignment explanation
Indices: 3496283--3496406 Score: 76
Period size: 10 Copynumber: 11.8 Consensus size: 10
3496273 CTCATCCATC
3496283 AGAGAAAAAAA
1 AGAG-AAAAAA
3496294 AGAGAAAAAA
1 AGAGAAAAAA
*
3496304 AGGAAAAAAAAA
1 A-G-AGAAAAAA
3496316 AGAGAAAAAA
1 AGAGAAAAAA
*
3496326 AAAGAAAAGAA
1 AGAGAAAA-AA
3496337 A-A-AAGAAAA
1 AGAGAA-AAAA
*
3496346 A-AGGAAAAA
1 AGAGAAAAAA
*
3496355 AGAAAAAAAGA
1 AGAGAAAAA-A
*
3496366 AAAGAAAAGAA
1 AGAGAAAA-AA
*
3496377 AAAGATGAAAAA
1 AGAGA--AAAAA
3496389 AGATGAAAAAA
1 AGA-GAAAAAA
3496400 AG-GAAAA
1 AGAGAAAA
3496407 GAAATTGAAT
Statistics
Matches: 93, Mismatches: 9, Indels: 24
0.74 0.07 0.19
Matches are distributed among these distances:
9 16 0.17
10 30 0.32
11 29 0.31
12 13 0.14
13 5 0.05
ACGTcount: A:0.80, C:0.00, G:0.19, T:0.02
Consensus pattern (10 bp):
AGAGAAAAAA
Found at i:3496315 original size:22 final size:22
Alignment explanation
Indices: 3496287--3496400 Score: 112
Period size: 20 Copynumber: 5.2 Consensus size: 22
3496277 TCCATCAGAG
3496287 AAAAAAAAGAGAAAAAAAGGAA
1 AAAAAAAAGAGAAAAAAAGGAA
*
3496309 AAAAAAAAGAGAAAAAAAAAGAA
1 AAAAAAAAGAG-AAAAAAAGGAA
*
3496332 AAGAAAAA-AG-AAAAAAGGAA
1 AAAAAAAAGAGAAAAAAAGGAA
*
3496352 AAAAGAAAA-A-AAGAAAA-GAA
1 AAAA-AAAAGAGAAAAAAAGGAA
* *
3496372 AAGAAAAAGATGAAAAAAGATGAA
1 AAAAAAAAGA-GAAAAAA-AGGAA
3496396 AAAAA
1 AAAAA
3496401 GGAAAAGAAA
Statistics
Matches: 76, Mismatches: 8, Indels: 14
0.78 0.08 0.14
Matches are distributed among these distances:
19 4 0.05
20 19 0.25
21 10 0.13
22 18 0.24
23 18 0.24
24 7 0.09
ACGTcount: A:0.82, C:0.00, G:0.17, T:0.02
Consensus pattern (22 bp):
AAAAAAAAGAGAAAAAAAGGAA
Found at i:3496325 original size:24 final size:25
Alignment explanation
Indices: 3496287--3496389 Score: 101
Period size: 24 Copynumber: 4.2 Consensus size: 25
3496277 TCCATCAGAG
3496287 AAAAAAAAGAG--AA-AAAAAGGAA
1 AAAAAAAAGAGAAAAGAAAAAGGAA
3496309 AAAAAAAAGAGAAAA-AAAAA-GAA
1 AAAAAAAAGAGAAAAGAAAAAGGAA
* *
3496332 AAGAAAAAAGAAAAAAGGAAAAAAGAA
1 AA-AAAAAAGAGAAAA-GAAAAAGGAA
3496359 AAAAAGAAA-AGAAAAGAAAAAGATGAA
1 AAAAA-AAAGAGAAAAGAAAAAG--GAA
3496386 AAAA
1 AAAA
3496390 GATGAAAAAA
Statistics
Matches: 69, Mismatches: 3, Indels: 13
0.81 0.04 0.15
Matches are distributed among these distances:
22 11 0.16
23 5 0.07
24 19 0.28
25 6 0.09
26 13 0.19
27 15 0.22
ACGTcount: A:0.83, C:0.00, G:0.17, T:0.01
Consensus pattern (25 bp):
AAAAAAAAGAGAAAAGAAAAAGGAA
Found at i:3496369 original size:40 final size:42
Alignment explanation
Indices: 3496311--3496399 Score: 130
Period size: 40 Copynumber: 2.1 Consensus size: 42
3496301 AAAAGGAAAA
*
3496311 AAAAAAGAGAAAAAAAAAGAAAAGAAAAA-A-GAAAAAAG-G
1 AAAAAAGAAAAAAAAAAAGAAAAGAAAAAGATGAAAAAAGAG
3496350 AAAAAAGAAAAAAAGAAAAGAAAAGAAAAAGATGAAAAAAGATG
1 AAAAAAGAAAAAAA-AAAAGAAAAGAAAAAGATGAAAAAAGA-G
3496394 AAAAAA
1 AAAAAA
3496400 AGGAAAAGAA
Statistics
Matches: 44, Mismatches: 1, Indels: 5
0.88 0.02 0.10
Matches are distributed among these distances:
39 13 0.30
40 15 0.34
41 1 0.02
42 8 0.18
44 7 0.16
ACGTcount: A:0.81, C:0.00, G:0.17, T:0.02
Consensus pattern (42 bp):
AAAAAAGAAAAAAAAAAAGAAAAGAAAAAGATGAAAAAAGAG
Found at i:3496390 original size:16 final size:15
Alignment explanation
Indices: 3496290--3496391 Score: 84
Period size: 15 Copynumber: 6.5 Consensus size: 15
3496280 ATCAGAGAAA
*
3496290 AAAAAGAGAAAAAAAG
1 AAAAA-AGAAAAAGAG
*
3496306 GAAAAA-AAAAAGAG
1 AAAAAAGAAAAAGAG
*
3496320 AAAAAA-AAAGAAAAG
1 AAAAAAGAAA-AAGAG
3496335 AAAAAAGAAAAA-AGG
1 AAAAAAGAAAAAGA-G
*
3496350 AAAAAAGAAAAAAAGAA
1 AAAAAAG--AAAAAGAG
3496367 AAGAAAAGAAAAAGATG
1 AA-AAAAGAAAAAGA-G
3496384 AAAAAAGA
1 AAAAAAGA
3496392 TGAAAAAAAG
Statistics
Matches: 72, Mismatches: 6, Indels: 16
0.77 0.06 0.17
Matches are distributed among these distances:
14 16 0.22
15 21 0.29
16 20 0.28
17 9 0.12
18 6 0.08
ACGTcount: A:0.81, C:0.00, G:0.18, T:0.01
Consensus pattern (15 bp):
AAAAAAGAAAAAGAG
Found at i:3496399 original size:1 final size:1
Alignment explanation
Indices: 3496287--3496379 Score: 51
Period size: 1 Copynumber: 93.0 Consensus size: 1
3496277 TCCATCAGAG
* * ** * * * * * **
3496287 AAAAAAAAGAGAAAAAAAGGAAAAAAAAAAGAGAAAAAAAAAGAAAAGAAAAAAGAAAAAAGGAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
* * * *
3496352 AAAAGAAAAAAAGAAAAGAAAAGAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAA
3496380 GATGAAAAAA
Statistics
Matches: 66, Mismatches: 26, Indels: 0
0.72 0.28 0.00
Matches are distributed among these distances:
1 66 1.00
ACGTcount: A:0.84, C:0.00, G:0.16, T:0.00
Consensus pattern (1 bp):
A
Found at i:3496407 original size:27 final size:26
Alignment explanation
Indices: 3496285--3496409 Score: 91
Period size: 26 Copynumber: 4.7 Consensus size: 26
3496275 CATCCATCAG
*
3496285 AGAAAAAAAAGAGAAAAAAAGGAAAAAA
1 AGAAAAAAAAG-GAAAAGAA-GAAAAAA
*
3496313 A-AAAGAGAAAA-AAAAAGAA-AAGAAAA
1 AGAAA-A-AAAAGGAAAAGAAGAA-AAAA
*
3496339 A-AGAAAAAAGGAAAA-AAGAAAAAA
1 AGAAAAAAAAGGAAAAGAAGAAAAAA
* *
3496363 AGAAAAGAAAAGAAAAAGATG-AAAAA
1 AGAAAA-AAAAGGAAAAGAAGAAAAAA
3496389 AGATGAAAAAAAGGAAAAGAA
1 AGA--AAAAAAAGGAAAAGAA
3496410 ATTGAATCAT
Statistics
Matches: 78, Mismatches: 9, Indels: 21
0.72 0.08 0.19
Matches are distributed among these distances:
24 11 0.14
25 12 0.15
26 24 0.31
27 22 0.28
28 5 0.06
29 4 0.05
ACGTcount: A:0.80, C:0.00, G:0.18, T:0.02
Consensus pattern (26 bp):
AGAAAAAAAAGGAAAAGAAGAAAAAA
Found at i:3496410 original size:24 final size:22
Alignment explanation
Indices: 3496283--3496373 Score: 58
Period size: 23 Copynumber: 4.0 Consensus size: 22
3496273 CTCATCCATC
* *
3496283 AGAGAAAAAAAAGAGAAAAAAA
1 AGAGAAAAAAAGGAAAAAAAAA
* * *
3496305 GGAAAAAAAAAAGAGAAAAAAAA
1 AGAGAAAAAAAGGA-AAAAAAAA
* *
3496328 AGAAAAGAAAAAAGAAAAAAGGAAA
1 AGAGAA-AAAAAGGAAAAAA--AAA
* *
3496353 AAAGAAAAAAA-GAAAAGAAAA
1 AGAGAAAAAAAGGAAAAAAAAA
3496374 GAAAAAGATG
Statistics
Matches: 58, Mismatches: 7, Indels: 9
0.78 0.09 0.12
Matches are distributed among these distances:
21 3 0.05
22 12 0.21
23 23 0.40
24 13 0.22
25 7 0.12
ACGTcount: A:0.82, C:0.00, G:0.18, T:0.00
Consensus pattern (22 bp):
AGAGAAAAAAAGGAAAAAAAAA
Found at i:3498004 original size:51 final size:52
Alignment explanation
Indices: 3497936--3498069 Score: 191
Period size: 51 Copynumber: 2.6 Consensus size: 52
3497926 ATCTATCTGG
* *
3497936 GGCATCTTGAAGGCTCACATCAGCATAAAAAAGACATAAGTTATCCATGTG-
1 GGCATCTTGAAGGCTCACATCAGCATAAAAAAGACAGAAGTAATCCATGTGA
* * * *
3497987 GGTATCTTAAAGTCTCACATCAGCATGAAAAAGACAGAAGTAATCCATGTGA
1 GGCATCTTGAAGGCTCACATCAGCATAAAAAAGACAGAAGTAATCCATGTGA
3498039 GGCATCTTGAAGGCTCACA-CTAGCATAAAAA
1 GGCATCTTGAAGGCTCACATC-AGCATAAAAA
3498070 GGTTGGGATA
Statistics
Matches: 71, Mismatches: 10, Indels: 3
0.85 0.12 0.04
Matches are distributed among these distances:
51 46 0.65
52 25 0.35
ACGTcount: A:0.39, C:0.19, G:0.19, T:0.22
Consensus pattern (52 bp):
GGCATCTTGAAGGCTCACATCAGCATAAAAAAGACAGAAGTAATCCATGTGA
Found at i:3499566 original size:64 final size:63
Alignment explanation
Indices: 3499461--3499633 Score: 229
Period size: 64 Copynumber: 2.7 Consensus size: 63
3499451 AAACAAGGCT
* * * * *
3499461 TTTAGAGTCAATTTAAACTTCACAGTGAATGATATTGGACTCAACAAACAACTTTTTAGTTTCA
1 TTTAGAGTCAATTTCAACTTCACAGCGAAGGATATT-GACTCAAAAAACAACTTTTCAGTTTCA
* * * *
3499525 TTTAGAGACAATTTCAACTTCACAACGAAGGATATTAGACTCAAAAAATAACTTTTCATTTTCA
1 TTTAGAGTCAATTTCAACTTCACAGCGAAGGATATT-GACTCAAAAAACAACTTTTCAGTTTCA
*
3499589 TTCAGAGTCAATTTCAACTTCACAGCGAAGGATATTGAACTCAAA
1 TTTAGAGTCAATTTCAACTTCACAGCGAAGGATATTG-ACTCAAA
3499634 GTAATACAAC
Statistics
Matches: 95, Mismatches: 13, Indels: 2
0.86 0.12 0.02
Matches are distributed among these distances:
63 1 0.01
64 94 0.99
ACGTcount: A:0.38, C:0.17, G:0.12, T:0.32
Consensus pattern (63 bp):
TTTAGAGTCAATTTCAACTTCACAGCGAAGGATATTGACTCAAAAAACAACTTTTCAGTTTCA
Found at i:3499688 original size:55 final size:54
Alignment explanation
Indices: 3499599--3499792 Score: 211
Period size: 55 Copynumber: 3.7 Consensus size: 54
3499589 TTCAGAGTCA
* ** * *
3499599 ATTTCAACTTCACAGCGAAGGATATTGAACTCAAAGTAATACAACCAAAGATTGG
1 ATTTCAACTTCACAACGAAGGATATCCAATTCAAAG-AATACAATCAAAGATTGG
* * *
3499654 ATTTCAACTTCACAACGAAGGATATCCAATTC--A-AAT-CATTCAGAG-TT-A
1 ATTTCAACTTCACAACGAAGGATATCCAATTCAAAGAATACAATCAAAGATTGG
** *
3499702 ATTTCAACTTCACAACGAAGGATATTGAATTCAAAGCAATAAAATCAAAGATTGG
1 ATTTCAACTTCACAACGAAGGATATCCAATTCAAAG-AATACAATCAAAGATTGG
* *
3499757 ATTTCAACTTCACGATGAAGGATATCCAATTCAAAG
1 ATTTCAACTTCACAACGAAGGATATCCAATTCAAAG
3499793 CTCAACTTCA
Statistics
Matches: 114, Mismatches: 18, Indels: 14
0.78 0.12 0.10
Matches are distributed among these distances:
48 30 0.26
49 2 0.02
50 7 0.06
51 3 0.03
52 3 0.03
53 7 0.06
54 2 0.02
55 60 0.53
ACGTcount: A:0.42, C:0.18, G:0.14, T:0.26
Consensus pattern (54 bp):
ATTTCAACTTCACAACGAAGGATATCCAATTCAAAGAATACAATCAAAGATTGG
Found at i:3499765 original size:103 final size:103
Alignment explanation
Indices: 3499586--3499791 Score: 340
Period size: 103 Copynumber: 2.0 Consensus size: 103
3499576 CTTTTCATTT
* * *
3499586 TCATTCAGAGTCAATTTCAACTTCACAGCGAAGGATATTGAACTCAAAGTAATACAACCAAAGAT
1 TCATTCAGAGTCAATTTCAACTTCACAACGAAGGATATTGAACTCAAAGCAATAAAACCAAAGAT
3499651 TGGATTTCAACTTCACAACGAAGGATATCCAATTCAAA
66 TGGATTTCAACTTCACAACGAAGGATATCCAATTCAAA
* * *
3499689 TCATTCAGAGTTAATTTCAACTTCACAACGAAGGATATTGAATTCAAAGCAATAAAATCAAAGAT
1 TCATTCAGAGTCAATTTCAACTTCACAACGAAGGATATTGAACTCAAAGCAATAAAACCAAAGAT
* *
3499754 TGGATTTCAACTTCACGATGAAGGATATCCAATTCAAA
66 TGGATTTCAACTTCACAACGAAGGATATCCAATTCAAA
3499792 GCTCAACTTC
Statistics
Matches: 95, Mismatches: 8, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
103 95 1.00
ACGTcount: A:0.41, C:0.18, G:0.14, T:0.27
Consensus pattern (103 bp):
TCATTCAGAGTCAATTTCAACTTCACAACGAAGGATATTGAACTCAAAGCAATAAAACCAAAGAT
TGGATTTCAACTTCACAACGAAGGATATCCAATTCAAA
Found at i:3500378 original size:137 final size:137
Alignment explanation
Indices: 3500132--3500786 Score: 930
Period size: 137 Copynumber: 4.8 Consensus size: 137
3500122 TCGTTTCCAT
* * * * *
3500132 CAACATCATCCTTAGATAGCCAAATGTCCTCATCACAAATGAACCATGTTATCTCAAATATCTTT
1 CAACATCATTCTTAGATAGCCAGATGTCCTCATCACGAAGGAACCGTGTTATCTCAAATATCTTT
3500197 AAAGATGGTCAGACGTCCTCATCACGAAGGAACAATGTCATCCACCGATCAA-AACTCCTCATCA
66 AAAGATGGTCAGACGTCCTCATCACGAAGGAACAATGTCATCCACCGAT-AAGAACTCCTCATCA
3500261 CGAAGGAG
130 CGAAGGAG
3500269 CAACATCATTCTTAGATAGCCAGATGTCCTCATCACGAAGGAACCGTGTTATCTCAAATATCTTT
1 CAACATCATTCTTAGATAGCCAGATGTCCTCATCACGAAGGAACCGTGTTATCTCAAATATCTTT
*
3500334 AAAGATGGTCAGACGTCCTCATCACGAAGGAACAATGTCATCCACCGATAAGAGCTCCTCATCAC
66 AAAGATGGTCAGACGTCCTCATCACGAAGGAACAATGTCATCCACCGATAAGAACTCCTCATCAC
*
3500399 GAAGGTG
131 GAAGGAG
* *
3500406 CAACATCATTCTTAGATAGCCAGATGTCTTCATCACGAAGGAACAGTGTTATCTCAAATATCTTT
1 CAACATCATTCTTAGATAGCCAGATGTCCTCATCACGAAGGAACCGTGTTATCTCAAATATCTTT
** * * **
3500471 AAAGATGG-CTAGACGTTGTCATCATGAAGGAATAATGTCATCCACTTATAAGAACTCCTCATCA
66 AAAGATGGTC-AGACGTCCTCATCACGAAGGAACAATGTCATCCACCGATAAGAACTCCTCATCA
*
3500535 CCAAGGAG
130 CGAAGGAG
*
3500543 CAACATAATTCTTAGATAGCCAGATG---TCATCACGAAGGAACCGTGTTATCTCAAATATCTTT
1 CAACATCATTCTTAGATAGCCAGATGTCCTCATCACGAAGGAACCGTGTTATCTCAAATATCTTT
* * * * *
3500605 AAAGATGGGCAGACGTCCTCATCACGAAGGAACAATGTCATCCATCGATTAGAACTCCTCAGCAT
66 AAAGATGGTCAGACGTCCTCATCACGAAGGAACAATGTCATCCACCGATAAGAACTCCTCATCAC
3500670 GCAA-GAG
131 G-AAGGAG
* * * * *
3500677 CTGA-GTCATTCTTAGATAGCCAGATGTCATCATCACAAAGGAACCGTGTTATCTCAAATATATT
1 C-AACATCATTCTTAGATAGCCAGATGTCCTCATCACGAAGGAACCGTGTTATCTCAAATATCTT
* * * * *
3500741 CAAAGATGGCCAGACTTCCTCATCATG-AGGAACAATGTCATACACC
65 TAAAGATGGTCAGACGTCCTCATCACGAAGGAACAATGTCATCCACC
3500787 AGTTGGATCT
Statistics
Matches: 468, Mismatches: 42, Indels: 17
0.89 0.08 0.03
Matches are distributed among these distances:
134 112 0.24
135 4 0.01
136 20 0.04
137 332 0.71
ACGTcount: A:0.34, C:0.24, G:0.17, T:0.25
Consensus pattern (137 bp):
CAACATCATTCTTAGATAGCCAGATGTCCTCATCACGAAGGAACCGTGTTATCTCAAATATCTTT
AAAGATGGTCAGACGTCCTCATCACGAAGGAACAATGTCATCCACCGATAAGAACTCCTCATCAC
GAAGGAG
Found at i:3500701 original size:271 final size:271
Alignment explanation
Indices: 3500133--3500786 Score: 928
Period size: 271 Copynumber: 2.4 Consensus size: 271
3500123 CGTTTCCATC
* * * *
3500133 AACATCATCCTTAGATAGCCAAATGTCCTCATCACAAATGAACCA-TGTTATCTCAAATATCTTT
1 AACATCATTCTTAGATAGCCAGATGTCATCATCACAAAGGAA-CAGTGTTATCTCAAATATCTTT
* *
3500197 AAAGATGG-TCAGACGTCCTCATCACGAAGGAACAATGTCATCCACCGATCAAAACTCCTCATCA
65 AAAGATGGCT-AGACGTTCTCATCATGAAGGAACAATGTCATCCACCGATCAAAACTCCTCATCA
* *
3500261 CGAAGGAGCAACATCATTCTTAGATAGCCAGATGTCCTCATCACGAAGGAACCGTGTTATCTCAA
129 CCAAGGAGCAACATAATTCTTAGATAGCCAGATG--CTCATCACGAAGGAACCGTGTTATCTCAA
* *
3500326 ATATCTTTAAAGATGGTCAGACGTCCTCATCACGAAGGAACAATGTCATCCACCGATAAGAGCTC
192 ATATCTTTAAAGATGGGCAGACGTCCTCATCACGAAGGAACAATGTCATCCACCGATAAGAACTC
*
3500391 CTCATCACGAAGGTG
257 CTCAGCACGAAGGTG
* *
3500406 CAACATCATTCTTAGATAGCCAGATGTCTTCATCACGAAGGAACAGTGTTATCTCAAATATCTTT
1 -AACATCATTCTTAGATAGCCAGATGTCATCATCACAAAGGAACAGTGTTATCTCAAATATCTTT
* * **
3500471 AAAGATGGCTAGACGTTGTCATCATGAAGGAATAATGTCATCCACTTAT-AAGAACTCCTCATCA
65 AAAGATGGCTAGACGTTCTCATCATGAAGGAACAATGTCATCCACCGATCAA-AACTCCTCATCA
3500535 CCAAGGAGCAACATAATTCTTAGATAGCCAGATG-TCATCACGAAGGAACCGTGTTATCTCAAAT
129 CCAAGGAGCAACATAATTCTTAGATAGCCAGATGCTCATCACGAAGGAACCGTGTTATCTCAAAT
* *
3500599 ATCTTTAAAGATGGGCAGACGTCCTCATCACGAAGGAACAATGTCATCCATCGATTAGAACTCCT
194 ATCTTTAAAGATGGGCAGACGTCCTCATCACGAAGGAACAATGTCATCCACCGATAAGAACTCCT
*
3500664 CAGCATGCAAGAGCTG
259 CAGCACG-AAG-G-TG
* * * *
3500680 -A-GTCATTCTTAGATAGCCAGATGTCATCATCACAAAGGAACCGTGTTATCTCAAATATATTCA
1 AACATCATTCTTAGATAGCCAGATGTCATCATCACAAAGGAACAGTGTTATCTCAAATATCTTTA
* *
3500743 AAGATGGCCAGAC-TTCCTCATCATG-AGGAACAATGTCATACACC
66 AAGATGGCTAGACGTT-CTCATCATGAAGGAACAATGTCATCCACC
3500787 AGTTGGATCT
Statistics
Matches: 343, Mismatches: 30, Indels: 18
0.88 0.08 0.05
Matches are distributed among these distances:
270 18 0.05
271 172 0.50
272 4 0.01
273 5 0.01
274 143 0.42
275 1 0.00
ACGTcount: A:0.34, C:0.24, G:0.17, T:0.25
Consensus pattern (271 bp):
AACATCATTCTTAGATAGCCAGATGTCATCATCACAAAGGAACAGTGTTATCTCAAATATCTTTA
AAGATGGCTAGACGTTCTCATCATGAAGGAACAATGTCATCCACCGATCAAAACTCCTCATCACC
AAGGAGCAACATAATTCTTAGATAGCCAGATGCTCATCACGAAGGAACCGTGTTATCTCAAATAT
CTTTAAAGATGGGCAGACGTCCTCATCACGAAGGAACAATGTCATCCACCGATAAGAACTCCTCA
GCACGAAGGTG
Found at i:3500955 original size:3 final size:3
Alignment explanation
Indices: 3500947--3500990 Score: 79
Period size: 3 Copynumber: 14.7 Consensus size: 3
3500937 GAGACTATCA
*
3500947 TAT TAT TAT TAT TAT TAT TGT TAT TAT TAT TAT TAT TAT TAT TA
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA
3500991 CAAAAAAAAT
Statistics
Matches: 39, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
3 39 1.00
ACGTcount: A:0.32, C:0.00, G:0.02, T:0.66
Consensus pattern (3 bp):
TAT
Found at i:3501672 original size:14 final size:14
Alignment explanation
Indices: 3501653--3501682 Score: 60
Period size: 14 Copynumber: 2.1 Consensus size: 14
3501643 GGAGAGCTTC
3501653 TATCTCTTTAGAGA
1 TATCTCTTTAGAGA
3501667 TATCTCTTTAGAGA
1 TATCTCTTTAGAGA
3501681 TA
1 TA
3501683 GAAGCAAAAC
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.30, C:0.13, G:0.13, T:0.43
Consensus pattern (14 bp):
TATCTCTTTAGAGA
Found at i:3501731 original size:10 final size:10
Alignment explanation
Indices: 3501694--3501724 Score: 62
Period size: 10 Copynumber: 3.1 Consensus size: 10
3501684 AAGCAAAACA
3501694 GAAAAATGAG
1 GAAAAATGAG
3501704 GAAAAATGAG
1 GAAAAATGAG
3501714 GAAAAATGAG
1 GAAAAATGAG
3501724 G
1 G
3501725 GGAAATGGCT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 21 1.00
ACGTcount: A:0.58, C:0.00, G:0.32, T:0.10
Consensus pattern (10 bp):
GAAAAATGAG
Found at i:3502205 original size:17 final size:18
Alignment explanation
Indices: 3502183--3502216 Score: 61
Period size: 17 Copynumber: 1.9 Consensus size: 18
3502173 TAGTGCTTAA
3502183 AATAAAATAAT-ATAATG
1 AATAAAATAATAATAATG
3502200 AATAAAATAATAATAAT
1 AATAAAATAATAATAAT
3502217 AATGACATAA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 11 0.69
18 5 0.31
ACGTcount: A:0.68, C:0.00, G:0.03, T:0.29
Consensus pattern (18 bp):
AATAAAATAATAATAATG
Found at i:3502386 original size:29 final size:27
Alignment explanation
Indices: 3502322--3502385 Score: 128
Period size: 27 Copynumber: 2.4 Consensus size: 27
3502312 AAGTTGTGTC
3502322 CACATTTTTTATATATTTTCTTAATCT
1 CACATTTTTTATATATTTTCTTAATCT
3502349 CACATTTTTTATATATTTTCTTAATCT
1 CACATTTTTTATATATTTTCTTAATCT
3502376 CACATTTTTT
1 CACATTTTTT
3502386 TATTAATTAA
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 37 1.00
ACGTcount: A:0.25, C:0.16, G:0.00, T:0.59
Consensus pattern (27 bp):
CACATTTTTTATATATTTTCTTAATCT
Found at i:3505870 original size:12 final size:12
Alignment explanation
Indices: 3505853--3505883 Score: 53
Period size: 12 Copynumber: 2.6 Consensus size: 12
3505843 TATATGGGGA
3505853 CCATCTCCAGTT
1 CCATCTCCAGTT
3505865 CCATCTCCAGTT
1 CCATCTCCAGTT
*
3505877 CTATCTC
1 CCATCTC
3505884 TTGAATGCTC
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
12 18 1.00
ACGTcount: A:0.16, C:0.42, G:0.06, T:0.35
Consensus pattern (12 bp):
CCATCTCCAGTT
Found at i:3509899 original size:189 final size:189
Alignment explanation
Indices: 3509564--3509924 Score: 542
Period size: 189 Copynumber: 1.9 Consensus size: 189
3509554 AGAGTTCATG
* * *
3509564 AAGGACAAATGTGTTATACATGTCCCTATATAAAGGAGAGAAGTATACCTTGAAAGGGAGCTTTA
1 AAGGAAAAATGTGCTATACATGTCCCTATATAAAGGAGAGAAGTATACCTTAAAAGGGAGCTTTA
* * * * * *
3509629 TACCACCACCATCTCTCTGATTGAGCTACATGTCCCGATCATCCCTTTCATCAGCACTGAAGCCA
66 TACCACCACCATCTCTCTGATTGAGCTACAAGCCCCAATCATCCCTTTAATAAGCAATGAAGCCA
** *
3509694 TGGCCATGGCGTGCTAAGCCACCCTCCGAAGTACCTCAGGTGATCGAGCACACCCTCCA
131 TAACCATGGCGTGCTAAGACACCCTCCGAAGTACCTCAGGTGATCGAGCACACCCTCCA
* *
3509753 AAGGAAAAATGTGCTATAGATGTCCCTATATAAATGAGAGAAGTATACCTTAAAAGGGAGCTTTA
1 AAGGAAAAATGTGCTATACATGTCCCTATATAAAGGAGAGAAGTATACCTTAAAAGGGAGCTTTA
* *
3509818 TAGCACCACCATCTCTCTGATTGAGCTACAAGCCCCAATCATCCCTTTAATAAGCAATGAATCCA
66 TACCACCACCATCTCTCTGATTGAGCTACAAGCCCCAATCATCCCTTTAATAAGCAATGAAGCCA
* ** *
3509883 TAACCATGGTGTGCTAAGACACTTTCTGAAGTACCTCAGGTG
131 TAACCATGGCGTGCTAAGACACCCTCCGAAGTACCTCAGGTG
3509925 TAGAATACGA
Statistics
Matches: 152, Mismatches: 20, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
189 152 1.00
ACGTcount: A:0.31, C:0.25, G:0.19, T:0.25
Consensus pattern (189 bp):
AAGGAAAAATGTGCTATACATGTCCCTATATAAAGGAGAGAAGTATACCTTAAAAGGGAGCTTTA
TACCACCACCATCTCTCTGATTGAGCTACAAGCCCCAATCATCCCTTTAATAAGCAATGAAGCCA
TAACCATGGCGTGCTAAGACACCCTCCGAAGTACCTCAGGTGATCGAGCACACCCTCCA
Found at i:3515462 original size:13 final size:13
Alignment explanation
Indices: 3515444--3515469 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
3515434 ACTTTACCAT
3515444 AAAATAATTTAAA
1 AAAATAATTTAAA
3515457 AAAATAATTTAAA
1 AAAATAATTTAAA
3515470 TATGAGACTC
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (13 bp):
AAAATAATTTAAA
Found at i:3516239 original size:49 final size:49
Alignment explanation
Indices: 3516178--3516280 Score: 181
Period size: 49 Copynumber: 2.1 Consensus size: 49
3516168 CAAGCACCTT
*
3516178 AAAT-TGTAAAACACTAAATATACTAACGAGTAAAGACTTTTGTGGTTG
1 AAATCTGTAAAACACTAAATATACTAACGAGTAAAGACTTTTGTGGTCG
*
3516226 AAATCTGTAAAACACTAAATATACTAATGAGTAAAGACTTTTGTGGTCG
1 AAATCTGTAAAACACTAAATATACTAACGAGTAAAGACTTTTGTGGTCG
3516275 AAATCT
1 AAATCT
3516281 TGAGCGGAAG
Statistics
Matches: 52, Mismatches: 2, Indels: 1
0.95 0.04 0.02
Matches are distributed among these distances:
48 4 0.08
49 48 0.92
ACGTcount: A:0.42, C:0.12, G:0.16, T:0.31
Consensus pattern (49 bp):
AAATCTGTAAAACACTAAATATACTAACGAGTAAAGACTTTTGTGGTCG
Found at i:3516857 original size:20 final size:21
Alignment explanation
Indices: 3516790--3516864 Score: 143
Period size: 21 Copynumber: 3.6 Consensus size: 21
3516780 CGTAACTCAG
3516790 TTTCCAAATTCGCGTTGCGAT
1 TTTCCAAATTCGCGTTGCGAT
3516811 TTTCCAAATTCGCGTTGCGAT
1 TTTCCAAATTCGCGTTGCGAT
3516832 TTTCCAAATTCGCGTTGCGA-
1 TTTCCAAATTCGCGTTGCGAT
3516852 TTTCCAAATTCGC
1 TTTCCAAATTCGC
3516865 AACTCGATTT
Statistics
Matches: 54, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
20 13 0.24
21 41 0.76
ACGTcount: A:0.20, C:0.25, G:0.17, T:0.37
Consensus pattern (21 bp):
TTTCCAAATTCGCGTTGCGAT
Found at i:3516872 original size:20 final size:22
Alignment explanation
Indices: 3516790--3516887 Score: 82
Period size: 21 Copynumber: 4.7 Consensus size: 22
3516780 CGTAACTCAG
**
3516790 TTTCCAAATTCGC-GTTGCGAT
1 TTTCCAAATTCGCAACTGCGAT
**
3516811 TTTCCAAATTCGC-GTTGCGAT
1 TTTCCAAATTCGCAACTGCGAT
**
3516832 TTTCCAAATTCGC-GTTGCGA-
1 TTTCCAAATTCGCAACTGCGAT
3516852 TTTCCAAATTCGCAACT-CGA-
1 TTTCCAAATTCGCAACTGCGAT
**
3516872 TTTCTGAATTCGCAAC
1 TTTCCAAATTCGCAAC
3516888 GGGAATTTTG
Statistics
Matches: 72, Mismatches: 4, Indels: 3
0.91 0.05 0.04
Matches are distributed among these distances:
20 30 0.42
21 42 0.58
ACGTcount: A:0.22, C:0.26, G:0.16, T:0.36
Consensus pattern (22 bp):
TTTCCAAATTCGCAACTGCGAT
Found at i:3516904 original size:40 final size:40
Alignment explanation
Indices: 3516860--3516947 Score: 124
Period size: 40 Copynumber: 2.2 Consensus size: 40
3516850 GATTTCCAAA
** **
3516860 TTCGCAACTCGA-TTTCTGAATTCGCAACGGGAATTTTGTT
1 TTCGCAACTCGATTTTC-GAATTCGCAACACGAATTTTAAT
3516900 TTCGCAACTCGATTTTCGAATTCGCAACACGAATTTTAAT
1 TTCGCAACTCGATTTTCGAATTCGCAACACGAATTTTAAT
3516940 TTCGCAAC
1 TTCGCAAC
3516948 AGGTTTTAGT
Statistics
Matches: 43, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
40 39 0.91
41 4 0.09
ACGTcount: A:0.26, C:0.23, G:0.16, T:0.35
Consensus pattern (40 bp):
TTCGCAACTCGATTTTCGAATTCGCAACACGAATTTTAAT
Found at i:3516923 original size:20 final size:20
Alignment explanation
Indices: 3516858--3516927 Score: 72
Period size: 20 Copynumber: 3.5 Consensus size: 20
3516848 GCGATTTCCA
3516858 AATTCGCAACTCGA-TTTCTG
1 AATTCGCAACTCGATTTTC-G
**
3516878 AATTCGCAACGGGAATTTT-G
1 AATTCGCAACTCG-ATTTTCG
**
3516898 TTTTCGCAACTCGATTTTCG
1 AATTCGCAACTCGATTTTCG
3516918 AATTCGCAAC
1 AATTCGCAAC
3516928 ACGAATTTTA
Statistics
Matches: 39, Mismatches: 8, Indels: 6
0.74 0.15 0.11
Matches are distributed among these distances:
19 5 0.13
20 30 0.77
21 1 0.03
22 3 0.08
ACGTcount: A:0.26, C:0.23, G:0.17, T:0.34
Consensus pattern (20 bp):
AATTCGCAACTCGATTTTCG
Found at i:3516943 original size:20 final size:19
Alignment explanation
Indices: 3516899--3516967 Score: 70
Period size: 20 Copynumber: 3.6 Consensus size: 19
3516889 GGAATTTTGT
*
3516899 TTTCGCAACTCGATTTTCGAA
1 TTTCGCAACACGATTTT--AA
3516920 -TTCGCAACACGAATTTTAA
1 TTTCGCAACACG-ATTTTAA
* *
3516939 TTTCGCAACA-GGTTTTAG
1 TTTCGCAACACGATTTTAA
3516957 TTTCGCAACAC
1 TTTCGCAACAC
3516968 AAATGTTTTG
Statistics
Matches: 42, Mismatches: 3, Indels: 8
0.79 0.06 0.15
Matches are distributed among these distances:
18 15 0.36
19 3 0.07
20 19 0.45
21 5 0.12
ACGTcount: A:0.28, C:0.23, G:0.14, T:0.35
Consensus pattern (19 bp):
TTTCGCAACACGATTTTAA
Found at i:3517756 original size:12 final size:12
Alignment explanation
Indices: 3517735--3517768 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
3517725 ACCACATTTC
*
3517735 CAATACCAAACA
1 CAATATCAAACA
3517747 CAATATCAAACA
1 CAATATCAAACA
*
3517759 CAATCTCAAA
1 CAATATCAAA
3517769 ATCCGCAACC
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
12 20 1.00
ACGTcount: A:0.56, C:0.29, G:0.00, T:0.15
Consensus pattern (12 bp):
CAATATCAAACA
Found at i:3518152 original size:25 final size:26
Alignment explanation
Indices: 3518118--3518166 Score: 75
Period size: 25 Copynumber: 1.9 Consensus size: 26
3518108 ATTCATATAA
3518118 CCCTGAAGAAGAA-GAAAA-AAGAAGT
1 CCCTGAAGAA-AAGGAAAAGAAGAAGT
3518143 CCCTGAAGAAAAGGAAAAGAAGAA
1 CCCTGAAGAAAAGGAAAAGAAGAA
3518167 AATGCCACGG
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
24 2 0.09
25 15 0.68
26 5 0.23
ACGTcount: A:0.57, C:0.12, G:0.24, T:0.06
Consensus pattern (26 bp):
CCCTGAAGAAAAGGAAAAGAAGAAGT
Found at i:3520216 original size:18 final size:18
Alignment explanation
Indices: 3520193--3520228 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
3520183 ATGCAAAAGG
3520193 AAATCAAAATCACAATCA
1 AAATCAAAATCACAATCA
*
3520211 AAATCAAAATCCCAATCA
1 AAATCAAAATCACAATCA
3520229 CAACCGGCTT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.58, C:0.25, G:0.00, T:0.17
Consensus pattern (18 bp):
AAATCAAAATCACAATCA
Found at i:3520628 original size:13 final size:14
Alignment explanation
Indices: 3520612--3520644 Score: 59
Period size: 13 Copynumber: 2.4 Consensus size: 14
3520602 CATCAATTAA
3520612 ACAAATCAAC-TTT
1 ACAAATCAACTTTT
3520625 ACAAATCAACTTTT
1 ACAAATCAACTTTT
3520639 ACAAAT
1 ACAAAT
3520645 ACATCAATTT
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
13 10 0.53
14 9 0.47
ACGTcount: A:0.48, C:0.21, G:0.00, T:0.30
Consensus pattern (14 bp):
ACAAATCAACTTTT
Found at i:3521678 original size:21 final size:21
Alignment explanation
Indices: 3521652--3521704 Score: 97
Period size: 21 Copynumber: 2.5 Consensus size: 21
3521642 TTCCATGCAT
*
3521652 TTAGGTCCTCTACCAATAATA
1 TTAGGTCCTCAACCAATAATA
3521673 TTAGGTCCTCAACCAATAATA
1 TTAGGTCCTCAACCAATAATA
3521694 TTAGGTCCTCA
1 TTAGGTCCTCA
3521705 TAAATAGGTT
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
21 31 1.00
ACGTcount: A:0.32, C:0.25, G:0.11, T:0.32
Consensus pattern (21 bp):
TTAGGTCCTCAACCAATAATA
Found at i:3522619 original size:20 final size:20
Alignment explanation
Indices: 3522594--3522675 Score: 103
Period size: 20 Copynumber: 4.1 Consensus size: 20
3522584 AATAGTTTCT
*
3522594 GAAAATGAAAATTGCAACGC
1 GAAAATGAAAATCGCAACGC
3522614 GAAAATGAAAATCGCAACGC
1 GAAAATGAAAATCGCAACGC
*
3522634 G-AAATGAAAATCGCAACGT
1 GAAAATGAAAATCGCAACGC
** *
3522653 GAATTTGGAAAATCGCAATGC
1 GAAAAT-GAAAATCGCAACGC
3522674 GA
1 GA
3522676 TTTACATATT
Statistics
Matches: 54, Mismatches: 6, Indels: 3
0.86 0.10 0.05
Matches are distributed among these distances:
19 18 0.33
20 22 0.41
21 14 0.26
ACGTcount: A:0.46, C:0.16, G:0.22, T:0.16
Consensus pattern (20 bp):
GAAAATGAAAATCGCAACGC
Found at i:3522650 original size:39 final size:40
Alignment explanation
Indices: 3522596--3522675 Score: 108
Period size: 39 Copynumber: 2.0 Consensus size: 40
3522586 TAGTTTCTGA
*
3522596 AAATGAAAATTGCAACGCGAAAAT-GAAAATCGCAACGCG
1 AAATGAAAATCGCAACGCGAAAATGGAAAATCGCAACGCG
* ** *
3522635 AAATGAAAATCGCAACGTGAATTTGGAAAATCGCAATGCG
1 AAATGAAAATCGCAACGCGAAAATGGAAAATCGCAACGCG
3522675 A
1 A
3522676 TTTACATATT
Statistics
Matches: 35, Mismatches: 5, Indels: 1
0.85 0.12 0.02
Matches are distributed among these distances:
39 20 0.57
40 15 0.43
ACGTcount: A:0.46, C:0.16, G:0.21, T:0.16
Consensus pattern (40 bp):
AAATGAAAATCGCAACGCGAAAATGGAAAATCGCAACGCG
Found at i:3522665 original size:21 final size:19
Alignment explanation
Indices: 3522596--3522675 Score: 97
Period size: 19 Copynumber: 4.1 Consensus size: 19
3522586 TAGTTTCTGA
*
3522596 AAATGAAAATTGCAACGCG
1 AAATGAAAATCGCAACGCG
3522615 AAAATGAAAATCGCAACGCG
1 -AAATGAAAATCGCAACGCG
*
3522635 AAATGAAAATCGCAACGTG
1 AAATGAAAATCGCAACGCG
* *
3522654 AATTTGGAAAATCGCAATGCG
1 AA-AT-GAAAATCGCAACGCG
3522675 A
1 A
3522676 TTTACATATT
Statistics
Matches: 53, Mismatches: 5, Indels: 3
0.87 0.08 0.05
Matches are distributed among these distances:
19 20 0.38
20 19 0.36
21 14 0.26
ACGTcount: A:0.46, C:0.16, G:0.21, T:0.16
Consensus pattern (19 bp):
AAATGAAAATCGCAACGCG
Found at i:3526069 original size:26 final size:25
Alignment explanation
Indices: 3526018--3526069 Score: 70
Period size: 26 Copynumber: 2.0 Consensus size: 25
3526008 AATATATTTG
*
3526018 AAAATAAAACTTAAAATAAAATAAA
1 AAAATAAAACTTAAAATAAAAGAAA
3526043 AAAATGAAAACTTGAAAA-AAAAGAAA
1 AAAAT-AAAACTT-AAAATAAAAGAAA
3526069 A
1 A
3526070 GAGAGAATTT
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
25 5 0.21
26 15 0.62
27 4 0.17
ACGTcount: A:0.75, C:0.04, G:0.06, T:0.15
Consensus pattern (25 bp):
AAAATAAAACTTAAAATAAAAGAAA
Done.