Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Gbar_D02
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: 67659327
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 461372 characters in sequence are not A, C, G, or T
File 169 of 216
Found at i:53195419 original size:63 final size:63
Alignment explanation
Indices: 53195352--53195494 Score: 162
Period size: 63 Copynumber: 2.3 Consensus size: 63
53195342 GCACCAAAAT
* * * ** * *
53195352 AGTGAATTACATGGTTTGGACACATGCCCGTGTCCCAAGCCCGTGTGACTCTAA-TCTATAAAC
1 AGTGAATTACACGGTCTAGACACACCCCCGTATCCCAAGCCCATGTGACTCTAATTC-ATAAAC
* * * *
53195415 AGTGAATCACACGGTCTAGACACGCCCCCGTATCCCTAGCCCATGTGACTCTAATTCATAAAT
1 AGTGAATTACACGGTCTAGACACACCCCCGTATCCCAAGCCCATGTGACTCTAATTCATAAAC
*
53195478 AGTGAGTTACACGGTCT
1 AGTGAATTACACGGTCT
53195495 GCCACACGAC
Statistics
Matches: 66, Mismatches: 13, Indels: 2
0.81 0.16 0.02
Matches are distributed among these distances:
63 64 0.97
64 2 0.03
ACGTcount: A:0.27, C:0.27, G:0.20, T:0.26
Consensus pattern (63 bp):
AGTGAATTACACGGTCTAGACACACCCCCGTATCCCAAGCCCATGTGACTCTAATTCATAAAC
Found at i:53196990 original size:39 final size:39
Alignment explanation
Indices: 53196836--53197011 Score: 176
Period size: 39 Copynumber: 4.5 Consensus size: 39
53196826 ATTCACTTTT
* * * * *
53196836 AAGCATATATCACATTACACATATAATCACATAGCATTTT
1 AAGCATATATCGCAATACTCATATAATCACATAACA-TTC
* * * *
53196876 AA-CATATATCACAATACTCATATACTTACATAACGTTC
1 AAGCATATATCGCAATACTCATATAATCACATAACATTC
* * * *
53196914 AAGCACATAT-GTAATACTCATATATTCACGTAACATTC
1 AAGCATATATCGCAATACTCATATAATCACATAACATTC
* *
53196952 AAGCATATATCGCAATATTCATATAATCACATATCATTC
1 AAGCATATATCGCAATACTCATATAATCACATAACATTC
* *
53196991 AAGTATATGTCGCAATACTCA
1 AAGCATATATCGCAATACTCA
53197012 AAAACATGTT
Statistics
Matches: 111, Mismatches: 23, Indels: 5
0.80 0.17 0.04
Matches are distributed among these distances:
38 35 0.32
39 74 0.67
40 2 0.02
ACGTcount: A:0.41, C:0.21, G:0.06, T:0.32
Consensus pattern (39 bp):
AAGCATATATCGCAATACTCATATAATCACATAACATTC
Found at i:53199040 original size:27 final size:27
Alignment explanation
Indices: 53198979--53199045 Score: 75
Period size: 27 Copynumber: 2.4 Consensus size: 27
53198969 AAGTAAATCA
53198979 AATAAATAATAATTAATCATGAATTAAAT
1 AATAAATAA-AATTAATCA-GAATTAAAT
53199008 AATAAA-AAAATTAATCA-AATATAAAGT
1 AATAAATAAAATTAATCAGAAT-TAAA-T
*
53199035 ATTAAATAAAA
1 AATAAATAAAA
53199046 GAAACTTCTT
Statistics
Matches: 34, Mismatches: 1, Indels: 7
0.81 0.02 0.17
Matches are distributed among these distances:
25 3 0.09
26 4 0.12
27 15 0.44
28 6 0.18
29 6 0.18
ACGTcount: A:0.64, C:0.03, G:0.03, T:0.30
Consensus pattern (27 bp):
AATAAATAAAATTAATCAGAATTAAAT
Found at i:53200855 original size:278 final size:276
Alignment explanation
Indices: 53200358--53200912 Score: 1074
Period size: 278 Copynumber: 2.0 Consensus size: 276
53200348 GAATCCTAAA
53200358 TTATTTTCCCAAAATATTTTAAAGTGAATTTATGATTTAAAAAAATGTATTAGTACTTCATTCAT
1 TTATTTTCCCAAAATATTTTAAAGTGAATTTATGATTTAAAAAAATGTATTAGTACTTCATTCAT
*
53200423 AGTATCAGAACAGGGTTACTTGTAACGCCCCAAAGTTTATATACGGGATTTGTCGAATATTATCA
66 AGTATCAGAACAGGGTTACTTGTAACGCCCCAAAGTTTATATACGGGATTTGTCAAATATTATCA
53200488 TATAATTTAGCACCTGCTTTAGTGGTTAAAGGTTGGACTGTGTATGGTGGGTCGGGGGTTCAAGT
131 TATAATTTAGCACCTGCTTTAGTGGTTAAAGGTTGGACTGTGTATGGTGGGTCGGGGGTTCAAGT
53200553 TCCTTCATGAGTCTTATGATAATAAATTTTTAGGTGTGTGTTGTTTAAGTGGTTGAGTTTGGAGT
196 TCCTTCATGAGTCTTATGATAATAAATTTTTAGGTGTGTGTTGTTTAAGTGGTTGAGTTTGGAGT
53200618 AAATTCAAATGTTTTTTT
261 AAATTC-AAT-TTTTTTT
53200636 TTATTTTCCCAAAATATTTTAAAGTGAATTTATGATTTAAAAAAATGTATTAGTACTTCATTCAT
1 TTATTTTCCCAAAATATTTTAAAGTGAATTTATGATTTAAAAAAATGTATTAGTACTTCATTCAT
53200701 AGTATCAGAACAGGGTTACTTGTAACGCCCCAAAGTTTATATACGGGATTTGTCAAATATTATCA
66 AGTATCAGAACAGGGTTACTTGTAACGCCCCAAAGTTTATATACGGGATTTGTCAAATATTATCA
53200766 TATAATTTAGCACCTGCTTTAGTGGTTAAAGGTTGGACTGTGTATGGTGGGTCGGGGGTTCAAGT
131 TATAATTTAGCACCTGCTTTAGTGGTTAAAGGTTGGACTGTGTATGGTGGGTCGGGGGTTCAAGT
*
53200831 TCCTTCATTAGTCTTATGATAATAAATTTTTAGGTGTGTGTTGTTTAAGTGGTTGAGTTTGGAGT
196 TCCTTCATGAGTCTTATGATAATAAATTTTTAGGTGTGTGTTGTTTAAGTGGTTGAGTTTGGAGT
53200896 AAATTCAATTTTTTTT
261 AAATTCAATTTTTTTT
53200912 T
1 T
53200913 AAAAAAACTG
Statistics
Matches: 275, Mismatches: 2, Indels: 2
0.99 0.01 0.01
Matches are distributed among these distances:
276 8 0.03
277 3 0.01
278 264 0.96
ACGTcount: A:0.28, C:0.10, G:0.20, T:0.41
Consensus pattern (276 bp):
TTATTTTCCCAAAATATTTTAAAGTGAATTTATGATTTAAAAAAATGTATTAGTACTTCATTCAT
AGTATCAGAACAGGGTTACTTGTAACGCCCCAAAGTTTATATACGGGATTTGTCAAATATTATCA
TATAATTTAGCACCTGCTTTAGTGGTTAAAGGTTGGACTGTGTATGGTGGGTCGGGGGTTCAAGT
TCCTTCATGAGTCTTATGATAATAAATTTTTAGGTGTGTGTTGTTTAAGTGGTTGAGTTTGGAGT
AAATTCAATTTTTTTT
Found at i:53201705 original size:33 final size:33
Alignment explanation
Indices: 53201666--53201731 Score: 123
Period size: 33 Copynumber: 2.0 Consensus size: 33
53201656 ATTTGGATCA
*
53201666 TGTGGGCCCCAAACTTAGGATTTTTCCCTAGGG
1 TGTGGGCCCCAAACTCAGGATTTTTCCCTAGGG
53201699 TGTGGGCCCCAAACTCAGGATTTTTCCCTAGGG
1 TGTGGGCCCCAAACTCAGGATTTTTCCCTAGGG
53201732 CCATACACGT
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
33 32 1.00
ACGTcount: A:0.18, C:0.26, G:0.27, T:0.29
Consensus pattern (33 bp):
TGTGGGCCCCAAACTCAGGATTTTTCCCTAGGG
Found at i:53204889 original size:16 final size:17
Alignment explanation
Indices: 53204868--53204901 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 17
53204858 AATGTTAGGG
*
53204868 GCAAAAGTGT-AATTTT
1 GCAAAAGTATGAATTTT
53204884 GCAAAAGTATGAATTTT
1 GCAAAAGTATGAATTTT
53204901 G
1 G
53204902 GACTAAATTT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 9 0.56
17 7 0.44
ACGTcount: A:0.38, C:0.06, G:0.21, T:0.35
Consensus pattern (17 bp):
GCAAAAGTATGAATTTT
Found at i:53212225 original size:6 final size:6
Alignment explanation
Indices: 53212211--53212244 Score: 59
Period size: 6 Copynumber: 5.7 Consensus size: 6
53212201 AGGTTTGCAA
*
53212211 AAATGG AAATCG AAATGG AAATGG AAATGG AAAT
1 AAATGG AAATGG AAATGG AAATGG AAATGG AAAT
53212245 TATTGCAATT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
6 26 1.00
ACGTcount: A:0.53, C:0.03, G:0.26, T:0.18
Consensus pattern (6 bp):
AAATGG
Found at i:53212419 original size:27 final size:26
Alignment explanation
Indices: 53212388--53212449 Score: 81
Period size: 27 Copynumber: 2.3 Consensus size: 26
53212378 TATTTTCTCG
53212388 AAATTTTACCAAGGGTAAAATTC-TCAA
1 AAATTTTACCAAGGGTAAAA-TCATC-A
* *
53212415 AAATTTTATCGAGGGTAAAATCATCA
1 AAATTTTACCAAGGGTAAAATCATCA
53212441 AAATTTTAC
1 AAATTTTAC
53212450 TGGGAGTAAA
Statistics
Matches: 31, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
26 11 0.35
27 20 0.65
ACGTcount: A:0.44, C:0.13, G:0.11, T:0.32
Consensus pattern (26 bp):
AAATTTTACCAAGGGTAAAATCATCA
Found at i:53215739 original size:16 final size:17
Alignment explanation
Indices: 53215707--53215740 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 17
53215697 GGGGATTGCG
53215707 TTTGTTTGATGTTTATT
1 TTTGTTTGATGTTTATT
*
53215724 TTTGTTT-ATTTTTATT
1 TTTGTTTGATGTTTATT
53215740 T
1 T
53215741 CGTAATATTT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 9 0.56
17 7 0.44
ACGTcount: A:0.12, C:0.00, G:0.12, T:0.76
Consensus pattern (17 bp):
TTTGTTTGATGTTTATT
Found at i:53231349 original size:49 final size:49
Alignment explanation
Indices: 53231295--53231423 Score: 140
Period size: 48 Copynumber: 2.7 Consensus size: 49
53231285 CCATATAACA
* * ** *
53231295 GGAAGCTCATGTA-AGCCATTAATGGGAAGCTTATTTGGGCTATACAACG
1 GGAAGCTCATGAAGAGCCATTAATGGGAAGCTCATGCGAGCTA-ACAACG
* *
53231344 GGAAGCTCAT-AAGAGCCA-TAATCGGAAAGCTCATGCGAGCTAATAACG
1 GGAAGCTCATGAAGAGCCATTAAT-GGGAAGCTCATGCGAGCTAACAACG
*
53231392 GGTAGCTC-TGAAGAGCCATTAATGGGAAGCTC
1 GGAAGCTCATGAAGAGCCATTAATGGGAAGCTC
53231424 CAAATAGCCA
Statistics
Matches: 67, Mismatches: 9, Indels: 9
0.79 0.11 0.11
Matches are distributed among these distances:
47 1 0.01
48 33 0.49
49 33 0.49
ACGTcount: A:0.33, C:0.19, G:0.27, T:0.22
Consensus pattern (49 bp):
GGAAGCTCATGAAGAGCCATTAATGGGAAGCTCATGCGAGCTAACAACG
Found at i:53231422 original size:24 final size:24
Alignment explanation
Indices: 53231343--53231423 Score: 69
Period size: 24 Copynumber: 3.4 Consensus size: 24
53231333 GCTATACAAC
53231343 GGGAAGCTCAT-AAGAGCCATAAT
1 GGGAAGCTCATGAAGAGCCATAAT
* * * *
53231366 CGGAAAGCTCATG-CGAGCTAATAAC
1 -GGGAAGCTCATGAAGAGC-CATAAT
*
53231391 GGGTAGCTC-TGAAGAGCCATTAAT
1 GGGAAGCTCATGAAGAGCCA-TAAT
53231415 GGGAAGCTC
1 GGGAAGCTC
53231424 CAAATAGCCA
Statistics
Matches: 43, Mismatches: 10, Indels: 8
0.70 0.16 0.13
Matches are distributed among these distances:
23 3 0.07
24 36 0.84
25 4 0.09
ACGTcount: A:0.33, C:0.20, G:0.28, T:0.19
Consensus pattern (24 bp):
GGGAAGCTCATGAAGAGCCATAAT
Found at i:53231518 original size:26 final size:26
Alignment explanation
Indices: 53231465--53231534 Score: 79
Period size: 26 Copynumber: 2.7 Consensus size: 26
53231455 GTCATATTGA
* *
53231465 GAAGCTC-CAGAGAGCCATTAATCAG
1 GAAGCTCACAAAGAACCATTAATCAG
* *
53231490 GAAGCTCACAAAGAACCTTTAATCGG
1 GAAGCTCACAAAGAACCATTAATCAG
* *
53231516 GAAGCTCACGAAGAGCCAT
1 GAAGCTCACAAAGAACCAT
53231535 ATATTGGGAC
Statistics
Matches: 37, Mismatches: 7, Indels: 1
0.82 0.16 0.02
Matches are distributed among these distances:
25 7 0.19
26 30 0.81
ACGTcount: A:0.37, C:0.24, G:0.23, T:0.16
Consensus pattern (26 bp):
GAAGCTCACAAAGAACCATTAATCAG
Found at i:53235182 original size:6 final size:6
Alignment explanation
Indices: 53235171--53235216 Score: 74
Period size: 6 Copynumber: 7.5 Consensus size: 6
53235161 TAGATTTTCA
*
53235171 AAAATG AAAATG AAAATG AAAATG AAAATG AAAATG GAAATAG AAA
1 AAAATG AAAATG AAAATG AAAATG AAAATG AAAATG AAAAT-G AAA
53235217 CGAGGTCCCA
Statistics
Matches: 37, Mismatches: 2, Indels: 1
0.93 0.05 0.03
Matches are distributed among these distances:
6 34 0.92
7 3 0.08
ACGTcount: A:0.67, C:0.00, G:0.17, T:0.15
Consensus pattern (6 bp):
AAAATG
Found at i:53235786 original size:20 final size:18
Alignment explanation
Indices: 53235755--53235804 Score: 59
Period size: 18 Copynumber: 2.7 Consensus size: 18
53235745 TTTGAACTTT
53235755 ATTTAATA-TTTTTATAAA
1 ATTTAATATTTTTTAT-AA
53235773 ATTTAATAATTTTTTTATAA
1 ATTTAAT-A-TTTTTTATAA
53235793 ATTT-ATATTTTT
1 ATTTAATATTTTT
53235805 AAAAAATATT
Statistics
Matches: 29, Mismatches: 0, Indels: 7
0.81 0.00 0.19
Matches are distributed among these distances:
17 5 0.17
18 8 0.28
19 3 0.10
20 6 0.21
21 7 0.24
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (18 bp):
ATTTAATATTTTTTATAA
Found at i:53235787 original size:21 final size:19
Alignment explanation
Indices: 53235723--53235804 Score: 62
Period size: 21 Copynumber: 4.2 Consensus size: 19
53235713 TTTTAAATGG
53235723 TTTTTATTAAATTT-TAATT
1 TTTTTA-TAAATTTATAATT
* * *
53235742 TCTTTT-GAACTTTATTTAATA
1 T-TTTTATAAATTTA--TAATT
53235763 TTTTTATAAAATTTAATAATT
1 TTTTTAT-AAATTT-ATAATT
53235784 TTTTTATAAATTTAT-ATT
1 TTTTTATAAATTTATAATT
53235802 TTT
1 TTT
53235805 AAAAAATATT
Statistics
Matches: 50, Mismatches: 6, Indels: 15
0.70 0.08 0.21
Matches are distributed among these distances:
18 11 0.22
19 3 0.06
20 14 0.28
21 16 0.32
22 5 0.10
23 1 0.02
ACGTcount: A:0.33, C:0.02, G:0.01, T:0.63
Consensus pattern (19 bp):
TTTTTATAAATTTATAATT
Found at i:53252174 original size:22 final size:24
Alignment explanation
Indices: 53252147--53252205 Score: 86
Period size: 26 Copynumber: 2.5 Consensus size: 24
53252137 ATCAGGTCAT
53252147 GACACATTAAAATC-G-GCAGCAA
1 GACACATTAAAATCGGAGCAGCAA
53252169 GACACATTAAAATCTGGCAGCAGCAA
1 GACACATTAAAATC-GG-AGCAGCAA
53252195 GACACATTAAA
1 GACACATTAAA
53252206 CTTGTACTTT
Statistics
Matches: 33, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
22 14 0.42
24 1 0.03
26 18 0.55
ACGTcount: A:0.46, C:0.22, G:0.17, T:0.15
Consensus pattern (24 bp):
GACACATTAAAATCGGAGCAGCAA
Found at i:53259437 original size:27 final size:27
Alignment explanation
Indices: 53259398--53259467 Score: 95
Period size: 30 Copynumber: 2.5 Consensus size: 27
53259388 ACATAAAGCC
**
53259398 ATAACAGGCATTTCATCTCCTAGGGGT
1 ATAACAGTTATTTCATCTCCTAGGGGT
53259425 ATAACAGTTATTTTATCATCTCCTAGGGGT
1 ATAACAGTTA--TT-TCATCTCCTAGGGGT
53259455 ATAACAGTTATTT
1 ATAACAGTTATTT
53259468 TATCCTATGA
Statistics
Matches: 38, Mismatches: 2, Indels: 6
0.83 0.04 0.13
Matches are distributed among these distances:
27 9 0.24
28 2 0.05
29 2 0.05
30 25 0.66
ACGTcount: A:0.29, C:0.17, G:0.17, T:0.37
Consensus pattern (27 bp):
ATAACAGTTATTTCATCTCCTAGGGGT
Found at i:53259446 original size:30 final size:30
Alignment explanation
Indices: 53259410--53259471 Score: 124
Period size: 30 Copynumber: 2.1 Consensus size: 30
53259400 AACAGGCATT
53259410 TCATCTCCTAGGGGTATAACAGTTATTTTA
1 TCATCTCCTAGGGGTATAACAGTTATTTTA
53259440 TCATCTCCTAGGGGTATAACAGTTATTTTA
1 TCATCTCCTAGGGGTATAACAGTTATTTTA
53259470 TC
1 TC
53259472 CTATGAGGGT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 32 1.00
ACGTcount: A:0.26, C:0.18, G:0.16, T:0.40
Consensus pattern (30 bp):
TCATCTCCTAGGGGTATAACAGTTATTTTA
Found at i:53259494 original size:27 final size:27
Alignment explanation
Indices: 53259464--53259548 Score: 125
Period size: 27 Copynumber: 3.1 Consensus size: 27
53259454 TATAACAGTT
* *
53259464 ATTTTATCCTATGAGGGTATTTCGGTC
1 ATTTTATCCTATGGGGGTAATTCGGTC
*
53259491 ATTTTATCCTATGGGGGTAATTCAGTC
1 ATTTTATCCTATGGGGGTAATTCGGTC
* *
53259518 ATTTTATCCTAAGGGGGTAATTCGATC
1 ATTTTATCCTATGGGGGTAATTCGGTC
53259545 ATTT
1 ATTT
53259549 ATTGACCTCT
Statistics
Matches: 52, Mismatches: 6, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
27 52 1.00
ACGTcount: A:0.22, C:0.14, G:0.21, T:0.42
Consensus pattern (27 bp):
ATTTTATCCTATGGGGGTAATTCGGTC
Found at i:53263161 original size:6 final size:6
Alignment explanation
Indices: 53263136--53263184 Score: 62
Period size: 6 Copynumber: 7.8 Consensus size: 6
53263126 AAAATGAATA
* *
53263136 ATTTCTC ATTTCTA ATTTTC ATTTTC ATTTTC ATTTTC ATTTCC ATTTT
1 ATTT-TC ATTT-TC ATTTTC ATTTTC ATTTTC ATTTTC ATTTTC ATTTT
53263185 GAGAAAACCA
Statistics
Matches: 38, Mismatches: 4, Indels: 1
0.88 0.09 0.02
Matches are distributed among these distances:
6 28 0.74
7 10 0.26
ACGTcount: A:0.18, C:0.18, G:0.00, T:0.63
Consensus pattern (6 bp):
ATTTTC
Found at i:53263957 original size:19 final size:19
Alignment explanation
Indices: 53263933--53263973 Score: 73
Period size: 19 Copynumber: 2.2 Consensus size: 19
53263923 AAGTGAATAA
*
53263933 ATCCATAAATGAATTTAGG
1 ATCCATAAACGAATTTAGG
53263952 ATCCATAAACGAATTTAGG
1 ATCCATAAACGAATTTAGG
53263971 ATC
1 ATC
53263974 TATTCTTCTT
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 21 1.00
ACGTcount: A:0.41, C:0.15, G:0.15, T:0.29
Consensus pattern (19 bp):
ATCCATAAACGAATTTAGG
Found at i:53264186 original size:12 final size:12
Alignment explanation
Indices: 53264169--53264195 Score: 54
Period size: 12 Copynumber: 2.2 Consensus size: 12
53264159 GGAGTGTTTA
53264169 AACGATTAACCG
1 AACGATTAACCG
53264181 AACGATTAACCG
1 AACGATTAACCG
53264193 AAC
1 AAC
53264196 TGAACTAGAA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 15 1.00
ACGTcount: A:0.44, C:0.26, G:0.15, T:0.15
Consensus pattern (12 bp):
AACGATTAACCG
Found at i:53265524 original size:14 final size:14
Alignment explanation
Indices: 53265507--53265534 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
53265497 TATAAAGTAC
53265507 TGGGTTAAAAGTCT
1 TGGGTTAAAAGTCT
53265521 TGGGTTAAAAGTCT
1 TGGGTTAAAAGTCT
53265535 AGGAAGTACT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.29, C:0.07, G:0.29, T:0.36
Consensus pattern (14 bp):
TGGGTTAAAAGTCT
Found at i:53269263 original size:18 final size:18
Alignment explanation
Indices: 53269240--53269275 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
53269230 CTATGTTTTT
*
53269240 TCCTTGTAGAGAGTAATG
1 TCCTTGGAGAGAGTAATG
53269258 TCCTTGGAGAGAGTAATG
1 TCCTTGGAGAGAGTAATG
53269276 CAGATATCAC
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:0.28, C:0.11, G:0.31, T:0.31
Consensus pattern (18 bp):
TCCTTGGAGAGAGTAATG
Found at i:53281555 original size:25 final size:25
Alignment explanation
Indices: 53281527--53281609 Score: 80
Period size: 25 Copynumber: 3.3 Consensus size: 25
53281517 TCATATGCAT
*
53281527 GTATGCTCATATGAGTTATGAATCG
1 GTATGCTCATACGAGTTATGAATCG
* *
53281552 GTATGCTC-TCACGAGTTGTGAATCA
1 GTATGCTCAT-ACGAGTTATGAATCG
**
53281577 GTCGGCTCATACGAGTTGA-GAATCG
1 GTATGCTCATACGAGTT-ATGAATCG
*
53281602 GTAAGCTC
1 GTATGCTC
53281610 TCATGAGCTA
Statistics
Matches: 46, Mismatches: 9, Indels: 6
0.75 0.15 0.10
Matches are distributed among these distances:
24 1 0.02
25 44 0.96
26 1 0.02
ACGTcount: A:0.25, C:0.18, G:0.27, T:0.30
Consensus pattern (25 bp):
GTATGCTCATACGAGTTATGAATCG
Found at i:53285859 original size:13 final size:13
Alignment explanation
Indices: 53285841--53285865 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
53285831 AGAGCGATCA
53285841 GCAAAGAAGCAAC
1 GCAAAGAAGCAAC
53285854 GCAAAGAAGCAA
1 GCAAAGAAGCAA
53285866 AGGAGCCTTG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.56, C:0.20, G:0.24, T:0.00
Consensus pattern (13 bp):
GCAAAGAAGCAAC
Found at i:53289584 original size:44 final size:43
Alignment explanation
Indices: 53289508--53290106 Score: 380
Period size: 44 Copynumber: 13.8 Consensus size: 43
53289498 AGATTCATCC
* * * *
53289508 TTTTAATCCGCCCCACTGCAACTTCAGGGAGATAGGATTAGTAG
1 TTTTAATCTGCTCCACTGCAACTTCAGAGAGATAAGATT-GTAG
* * *
53289552 CTTCAATCTACTCCACTGCAACTTCAGAGAGATAAGATTGATA-
1 TTTTAATCTGCTCCACTGCAACTTCAGAGAGATAAGATTG-TAG
* * * *
53289595 TCTTCAACCTGCTCCACTGCAACTTCAGGGAGATAAGGTTTGTTATG
1 T-TTTAATCTGCTCCACTGCAACTTCAGAGAGATAA-GATTG-TA-G
* * * * *
53289642 GTGTGATCTACTCTACTGCAACTTCAGAGAGATAAGATCTGT-G
1 TTTTAATCTGCTCCACTGCAACTTCAGAGAGATAAGAT-TGTAG
* * * *
53289685 ATTTTAAT-TCGCTCTACTGCAACTTCCGAGAGATAGGATTGGT-T
1 -TTTTAATCT-GCTCCACTGCAACTTCAGAGAGATAAGATT-GTAG
** * *
53289729 TCTTTTGTCTGATCTACTGCAACTTCAGAGAGATAAGATTG--G
1 T-TTTAATCTGCTCCACTGCAACTTCAGAGAGATAAGATTGTAG
* *** * *
53289771 ATGCGATCTGCTCTACTGCAACTTCAGAGAGATAAGATCTGTGG
1 TTTTAATCTGCTCCACTGCAACTTCAGAGAGATAAGAT-TGTAG
** * * * **
53289815 TTTTAATCCACTCCACTGTAACTTCAGGGAGATAGGATTGATTT
1 TTTTAATCTGCTCCACTGCAACTTCAGAGAGATAAGATTG-TAG
** * *
53289859 TTTTTTTCTGCTCCACTGCAACTTCAGGGAGATAAGACTG--G
1 TTTTAATCTGCTCCACTGCAACTTCAGAGAGATAAGATTGTAG
* *** * *
53289900 ATGCGATCTGCTCTACTGCAACTTCAGAGAGATAAGATATGTGG
1 TTTTAATCTGCTCCACTGCAACTTCAGAGAGATAAGAT-TGTAG
* * *
53289944 TTTTAATCTGCTCCACTGCAACTTTC-GGGAGATAGGATTGGT-T
1 TTTTAATCTGCTCCACTGCAAC-TTCAGAGAGATAAGATT-GTAG
** *
53289987 TCTTTTGTCTGCTCCACTGCAACTTCAGGGAGATAAGACTTG-A-
1 T-TTTAATCTGCTCCACTGCAACTTCAGAGAGATAAGA-TTGTAG
*** * * *
53290030 -TACGATCTTCTCTACTGCAACTTCAGAGAGATAAGATCTGTGG
1 TTTTAATCTGCTCCACTGCAACTTCAGAGAGATAAGAT-TGTAG
*
53290073 TTTTAATCCGCTCCACTGCAACTTCA-AGGAGATA
1 TTTTAATCTGCTCCACTGCAACTTCAGA-GAGATA
53290107 GGAGTGGATG
Statistics
Matches: 432, Mismatches: 94, Indels: 58
0.74 0.16 0.10
Matches are distributed among these distances:
40 1 0.00
41 93 0.22
42 4 0.01
43 14 0.03
44 276 0.64
45 15 0.03
46 29 0.07
ACGTcount: A:0.27, C:0.21, G:0.21, T:0.32
Consensus pattern (43 bp):
TTTTAATCTGCTCCACTGCAACTTCAGAGAGATAAGATTGTAG
Found at i:53289839 original size:129 final size:129
Alignment explanation
Indices: 53289522--53290109 Score: 730
Period size: 129 Copynumber: 4.5 Consensus size: 129
53289512 AATCCGCCCC
* * * * * ** * *
53289522 ACTGCAACTTCAGGGAGATAGGAT-TAGTAGCTTCAATCTACTCCACTGCAACTTCAGAGAGATA
1 ACTGCAACTTCAGAGAGATAAGATCT-GTGGTTTTAATCCGCTCCACTGCAACTTCCGGGAGATA
* * * **** * * *
53289586 AGATTGATATCTTCAACCTGCTCCACTGCAACTTCAGGGAGATAAGGTTTGTTATGGTGTGATCT
65 GGATTGGTTTCTTTTGTCTGCTCCACTGCAACTTCAGGGAGATAA-GATTG----GATGCGATCT
*
53289651 ACTCT
125 GCTCT
* * * *
53289656 ACTGCAACTTCAGAGAGATAAGATCTGTGATTTTAATTCGCTCTACTGCAACTTCCGAGAGATAG
1 ACTGCAACTTCAGAGAGATAAGATCTGTGGTTTTAATCCGCTCCACTGCAACTTCCGGGAGATAG
* * *
53289721 GATTGGTTTCTTTTGTCTGATCTACTGCAACTTCAGAGAGATAAGATTGGATGCGATCTGCTCT
66 GATTGGTTTCTTTTGTCTGCTCCACTGCAACTTCAGGGAGATAAGATTGGATGCGATCTGCTCT
* * *
53289785 ACTGCAACTTCAGAGAGATAAGATCTGTGGTTTTAATCCACTCCACTGTAACTTCAGGGAGATAG
1 ACTGCAACTTCAGAGAGATAAGATCTGTGGTTTTAATCCGCTCCACTGCAACTTCCGGGAGATAG
* * * *
53289850 GATTGATTTTTTTTTTCTGCTCCACTGCAACTTCAGGGAGATAAGACTGGATGCGATCTGCTCT
66 GATTGGTTTCTTTTGTCTGCTCCACTGCAACTTCAGGGAGATAAGATTGGATGCGATCTGCTCT
* * *
53289914 ACTGCAACTTCAGAGAGATAAGATATGTGGTTTTAATCTGCTCCACTGCAACTTTCGGGAGATAG
1 ACTGCAACTTCAGAGAGATAAGATCTGTGGTTTTAATCCGCTCCACTGCAACTTCCGGGAGATAG
* *
53289979 GATTGGTTTCTTTTGTCTGCTCCACTGCAACTTCAGGGAGATAAGACTT-GATACGATCTTCTCT
66 GATTGGTTTCTTTTGTCTGCTCCACTGCAACTTCAGGGAGATAAGA-TTGGATGCGATCTGCTCT
**
53290043 ACTGCAACTTCAGAGAGATAAGATCTGTGGTTTTAATCCGCTCCACTGCAACTTCAAGGAGATAG
1 ACTGCAACTTCAGAGAGATAAGATCTGTGGTTTTAATCCGCTCCACTGCAACTTCCGGGAGATAG
53290108 GA
66 GA
53290110 GTGGATGCGA
Statistics
Matches: 396, Mismatches: 56, Indels: 9
0.86 0.12 0.02
Matches are distributed among these distances:
129 304 0.77
130 1 0.00
133 4 0.01
134 86 0.22
135 1 0.00
ACGTcount: A:0.27, C:0.20, G:0.22, T:0.31
Consensus pattern (129 bp):
ACTGCAACTTCAGAGAGATAAGATCTGTGGTTTTAATCCGCTCCACTGCAACTTCCGGGAGATAG
GATTGGTTTCTTTTGTCTGCTCCACTGCAACTTCAGGGAGATAAGATTGGATGCGATCTGCTCT
Found at i:53290269 original size:50 final size:49
Alignment explanation
Indices: 53290192--53290573 Score: 239
Period size: 50 Copynumber: 7.7 Consensus size: 49
53290182 GCAATGTCAG
* *
53290192 GGGAAGCAAGATTCACCGTTGTAGCTTCAATCTGCTCCACTGCGAACTCA
1 GGGAAGTAAGATTCACCGTCGTAGCTTCAATCTGCTCCACTGC-AACTCA
* * ** ** * * *
53290242 GGGAGGTAAGATTCACCGTCGTGGCTTCAATCTTTTAAATTGCAATATCG
1 GGGAAGTAAGATTCACCGTCGTAGCTTCAATCTGCTCCACTGCAA-CTCA
* * * *
53290292 GGGAAGCAAGATTCACCGGCGTAGCTTCAATCTGCTCCACTGCACCGCCA
1 GGGAAGTAAGATTCACCGTCGTAGCTTCAATCTGCTCCACTGCAAC-TCA
* * ** ** * * *
53290342 GGGAAGTAAGATTCACCGTTGTGGCTTCAATCTTTTAAAATGCAATGTCGG
1 GGGAAGTAAGATTCACCGTCGTAGCTTCAATCTGCTCCACTGCAA-CTC-A
* * *
53290393 GGGAAGCAAGATTCACCGTCGTAGCTTCAATCTGCTCTACTGC-ACGCCA
1 GGGAAGTAAGATTCACCGTCGTAGCTTCAATCTGCTCCACTGCAAC-TCA
* * * ** * ** * * * **
53290442 AGGAAGTAAGATTCGCCGTTGCGGCTTTAATCTTTTCAATTGCAATGTTG
1 GGGAAGTAAGATTCACCGTCGTAGCTTCAATCTGCTCCACTGCAA-CTCA
* ** * *
53290492 GGGAA-CAAGATTCGTCGTTGTAGCTTCAATCTGTTCCACTGCACCAC-CA
1 GGGAAGTAAGATTCACCGTCGTAGCTTCAATCTGCTCCACTGCA--ACTCA
* *
53290541 GGGAAGTAAGATTCACCGTTGTGGCTTCAATCT
1 GGGAAGTAAGATTCACCGTCGTAGCTTCAATCT
53290574 TTTTAACCGT
Statistics
Matches: 243, Mismatches: 79, Indels: 20
0.71 0.23 0.06
Matches are distributed among these distances:
49 69 0.28
50 138 0.57
51 36 0.15
ACGTcount: A:0.25, C:0.24, G:0.24, T:0.27
Consensus pattern (49 bp):
GGGAAGTAAGATTCACCGTCGTAGCTTCAATCTGCTCCACTGCAACTCA
Found at i:53290316 original size:100 final size:101
Alignment explanation
Indices: 53290162--53290576 Score: 579
Period size: 100 Copynumber: 4.1 Consensus size: 101
53290152 CTGTGGTGTA
*
53290162 TGGCTTCAATCTTTTAAAATGCAATGTCAGGGGAAGCAAGATTCACCGTTGTAGCTTCAATCTGC
1 TGGCTTCAATCTTTTAAAATGCAATGTCAGGGGAAGCAAGATTCACCGTCGTAGCTTCAATCTGC
* * *
53290227 TCCACTGCGAAC-TCAGGGAGGTAAGATTCACCGTCG
66 TCCACTGC-AACGCCAGGGAAGTAAGATTCACCGTTG
* * *
53290263 TGGCTTCAATCTTTTAAATTGCAATATC-GGGGAAGCAAGATTCACCGGCGTAGCTTCAATCTGC
1 TGGCTTCAATCTTTTAAAATGCAATGTCAGGGGAAGCAAGATTCACCGTCGTAGCTTCAATCTGC
*
53290327 TCCACTGCACCGCCAGGGAAGTAAGATTCACCGTTG
66 TCCACTGCAACGCCAGGGAAGTAAGATTCACCGTTG
*
53290363 TGGCTTCAATCTTTTAAAATGCAATGTCGGGGGAAGCAAGATTCACCGTCGTAGCTTCAATCTGC
1 TGGCTTCAATCTTTTAAAATGCAATGTCAGGGGAAGCAAGATTCACCGTCGTAGCTTCAATCTGC
* * *
53290428 TCTACTGC-ACGCCAAGGAAGTAAGATTCGCCGTTG
66 TCCACTGCAACGCCAGGGAAGTAAGATTCACCGTTG
* * * * * ** * *
53290463 CGGCTTTAATCTTTTCAATTGCAATGT-TGGGGAA-CAAGATTCGTCGTTGTAGCTTCAATCTGT
1 TGGCTTCAATCTTTTAAAATGCAATGTCAGGGGAAGCAAGATTCACCGTCGTAGCTTCAATCTGC
* *
53290526 TCCACTGCACCACCAGGGAAGTAAGATTCACCGTTG
66 TCCACTGCAACGCCAGGGAAGTAAGATTCACCGTTG
53290562 TGGCTTCAATCTTTT
1 TGGCTTCAATCTTTT
53290577 TAACCGTAAT
Statistics
Matches: 280, Mismatches: 31, Indels: 8
0.88 0.10 0.03
Matches are distributed among these distances:
98 32 0.11
99 44 0.16
100 136 0.49
101 68 0.24
ACGTcount: A:0.25, C:0.23, G:0.23, T:0.29
Consensus pattern (101 bp):
TGGCTTCAATCTTTTAAAATGCAATGTCAGGGGAAGCAAGATTCACCGTCGTAGCTTCAATCTGC
TCCACTGCAACGCCAGGGAAGTAAGATTCACCGTTG
Found at i:53292889 original size:33 final size:33
Alignment explanation
Indices: 53292847--53293109 Score: 124
Period size: 42 Copynumber: 7.3 Consensus size: 33
53292837 CGGTGGATTT
*
53292847 AGCACTTAGCAACCACCAATGAGTCAGGGAATC
1 AGCACTTAGCAACCACCAATGAGTCGGGGAATC
* * *
53292880 AGCACTTAGCAACCCCTTTCACATTTAGGATACGGTGGGATC
1 AGCACTTAGCAACCAC---CA-A-TGA-G-T-CGG-GGAATC
* *
53292922 AGCACTTAGCAACCACCAGTGATTCGGGGAATC
1 AGCACTTAGCAACCACCAATGAGTCGGGGAATC
*
53292955 AGCACTTAGCAACC-CC--T-CG--GGGGAATC
1 AGCACTTAGCAACCACCAATGAGTCGGGGAATC
* *
53292982 AGCACTTAGCAACCCCCTTCACATTTAAGATACGGTGGAATC
1 AGCACTTAGCAA-CCAC--CA-A--TGAG-T-CGG-GGAATC
* *
53293024 AGCACTTAGCAACCCCTTTCACATTTAAGATACGGTGGAATC
1 AGCACTTAGCAACCAC---CA-A--TGAG-T-CGG-GGAATC
*
53293066 AGCACTTAGCAACCACCAATGAATCGGGGAATC
1 AGCACTTAGCAACCACCAATGAGTCGGGGAATC
*
53293099 AACACTTAGCA
1 AGCACTTAGCA
53293110 GCCCCTTGGG
Statistics
Matches: 189, Mismatches: 16, Indels: 50
0.74 0.06 0.20
Matches are distributed among these distances:
27 20 0.11
28 2 0.01
29 1 0.01
30 1 0.01
31 1 0.01
32 2 0.01
33 50 0.26
34 6 0.03
35 2 0.01
36 5 0.03
37 4 0.02
38 3 0.02
39 5 0.03
40 1 0.01
41 8 0.04
42 78 0.41
ACGTcount: A:0.32, C:0.28, G:0.20, T:0.21
Consensus pattern (33 bp):
AGCACTTAGCAACCACCAATGAGTCGGGGAATC
Found at i:53293035 original size:42 final size:42
Alignment explanation
Indices: 53292976--53293079 Score: 199
Period size: 42 Copynumber: 2.5 Consensus size: 42
53292966 ACCCCTCGGG
53292976 GGAATCAGCACTTAGCAACCCCCTTCACATTTAAGATACGGT
1 GGAATCAGCACTTAGCAACCCCCTTCACATTTAAGATACGGT
*
53293018 GGAATCAGCACTTAGCAACCCCTTTCACATTTAAGATACGGT
1 GGAATCAGCACTTAGCAACCCCCTTCACATTTAAGATACGGT
53293060 GGAATCAGCACTTAGCAACC
1 GGAATCAGCACTTAGCAACC
53293080 ACCAATGAAT
Statistics
Matches: 61, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
42 61 1.00
ACGTcount: A:0.32, C:0.28, G:0.17, T:0.23
Consensus pattern (42 bp):
GGAATCAGCACTTAGCAACCCCCTTCACATTTAAGATACGGT
Found at i:53293140 original size:144 final size:144
Alignment explanation
Indices: 53292874--53293143 Score: 461
Period size: 144 Copynumber: 1.9 Consensus size: 144
53292864 AATGAGTCAG
* *
53292874 GGAATCAGCACTTAGCAACCCCTTTCACATTTAGGATACGGTGGGATCAGCACTTAGCAACCACC
1 GGAATCAGCACTTAGCAACCCCTTTCACATTTAAGATACGGTGGAATCAGCACTTAGCAACCACC
* * *
53292939 AGTGATTCGGGGAATCAGCACTTAGCAACCCCTCGGGGGAATCAGCACTTAGCAACCCCCTTCAC
66 AATGAATCGGGGAATCAACACTTAGCAACCCCTCGGGGGAATCAGCACTTAGCAACCCCCTTCAC
53293004 ATTTAAGATACGGT
131 ATTTAAGATACGGT
53293018 GGAATCAGCACTTAGCAACCCCTTTCACATTTAAGATACGGTGGAATCAGCACTTAGCAACCACC
1 GGAATCAGCACTTAGCAACCCCTTTCACATTTAAGATACGGTGGAATCAGCACTTAGCAACCACC
* * *
53293083 AATGAATCGGGGAATCAACACTTAGCAGCCCCT-TGGGGAATCAGCACTTAGCAAACCCCTT
66 AATGAATCGGGGAATCAACACTTAGCAACCCCTCGGGGGAATCAGCACTTAGCAACCCCCTT
53293144 TATATTCAAA
Statistics
Matches: 118, Mismatches: 8, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
143 26 0.22
144 92 0.78
ACGTcount: A:0.30, C:0.29, G:0.20, T:0.21
Consensus pattern (144 bp):
GGAATCAGCACTTAGCAACCCCTTTCACATTTAAGATACGGTGGAATCAGCACTTAGCAACCACC
AATGAATCGGGGAATCAACACTTAGCAACCCCTCGGGGGAATCAGCACTTAGCAACCCCCTTCAC
ATTTAAGATACGGT
Found at i:53294649 original size:19 final size:18
Alignment explanation
Indices: 53294625--53294675 Score: 57
Period size: 19 Copynumber: 2.7 Consensus size: 18
53294615 GGTAGAGGTT
*
53294625 TTTTTTCTTTTTTATTTTC
1 TTTTTTCTTTTTT-TTTAC
*
53294644 TTTTTTGTTTTTTTTTAC
1 TTTTTTCTTTTTTTTTAC
*
53294662 TTTTATGCTTTTTT
1 TTTT-TTCTTTTTT
53294676 GCTTTTTTGC
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
18 8 0.30
19 19 0.70
ACGTcount: A:0.06, C:0.08, G:0.04, T:0.82
Consensus pattern (18 bp):
TTTTTTCTTTTTTTTTAC
Found at i:53294673 original size:18 final size:18
Alignment explanation
Indices: 53294633--53294675 Score: 50
Period size: 18 Copynumber: 2.3 Consensus size: 18
53294623 TTTTTTTTCT
* * *
53294633 TTTTTATTTTCTTTTTTGT
1 TTTTT-TTTACTTTTATGC
53294652 TTTTTTTTACTTTTATGC
1 TTTTTTTTACTTTTATGC
53294670 TTTTTT
1 TTTTTT
53294676 GCTTTTTTGC
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
18 16 0.76
19 5 0.24
ACGTcount: A:0.07, C:0.07, G:0.05, T:0.81
Consensus pattern (18 bp):
TTTTTTTTACTTTTATGC
Found at i:53294693 original size:10 final size:8
Alignment explanation
Indices: 53294654--53294692 Score: 51
Period size: 8 Copynumber: 4.8 Consensus size: 8
53294644 TTTTTTGTTT
*
53294654 TTTTTTAC
1 TTTTTTGC
*
53294662 TTTTATGC
1 TTTTTTGC
53294670 TTTTTTGC
1 TTTTTTGC
53294678 TTTTTTGC
1 TTTTTTGC
53294686 TCTTTTT
1 T-TTTTT
53294693 TTTGCCTCCA
Statistics
Matches: 27, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
8 22 0.81
9 5 0.19
ACGTcount: A:0.05, C:0.13, G:0.08, T:0.74
Consensus pattern (8 bp):
TTTTTTGC
Found at i:53303788 original size:25 final size:25
Alignment explanation
Indices: 53303760--53303849 Score: 110
Period size: 25 Copynumber: 3.6 Consensus size: 25
53303750 AAACGAGCAA
* *
53303760 TGAATTGGTATGCTCTCACGAGCTG
1 TGAATCGGTAAGCTCTCACGAGCTG
53303785 TGAATCGGTAAGCTCAT-ACGAGCTG
1 TGAATCGGTAAGCTC-TCACGAGCTG
* *
53303810 AGAATCGATAAGCTCTCACGAGCTG
1 TGAATCGGTAAGCTCTCACGAGCTG
**
53303835 CAAATCGGTAAGCTC
1 TGAATCGGTAAGCTC
53303850 ATACAAGCTG
Statistics
Matches: 56, Mismatches: 7, Indels: 4
0.84 0.10 0.06
Matches are distributed among these distances:
24 1 0.02
25 54 0.96
26 1 0.02
ACGTcount: A:0.28, C:0.22, G:0.26, T:0.24
Consensus pattern (25 bp):
TGAATCGGTAAGCTCTCACGAGCTG
Found at i:53303858 original size:25 final size:25
Alignment explanation
Indices: 53303777--53303859 Score: 107
Period size: 25 Copynumber: 3.3 Consensus size: 25
53303767 GTATGCTCTC
*
53303777 ACGAGCTGTGAATCGGTAAGCTCAT
1 ACGAGCTGAGAATCGGTAAGCTCAT
*
53303802 ACGAGCTGAGAATCGATAAGCTC-T
1 ACGAGCTGAGAATCGGTAAGCTCAT
53303826 CACGAGCTGCA-AATCGGTAAGCTCAT
1 -ACGAGCTG-AGAATCGGTAAGCTCAT
*
53303852 ACAAGCTG
1 ACGAGCTG
53303860 TGGTGTGTCA
Statistics
Matches: 51, Mismatches: 4, Indels: 6
0.84 0.07 0.10
Matches are distributed among these distances:
24 1 0.02
25 48 0.94
26 2 0.04
ACGTcount: A:0.31, C:0.23, G:0.25, T:0.20
Consensus pattern (25 bp):
ACGAGCTGAGAATCGGTAAGCTCAT
Found at i:53307236 original size:14 final size:15
Alignment explanation
Indices: 53307198--53307237 Score: 50
Period size: 14 Copynumber: 2.9 Consensus size: 15
53307188 AACAAAAAAT
53307198 CTAC-TAATATTAAA
1 CTACATAATATTAAA
*
53307212 CTACA-ACTATTAAA
1 CTACATAATATTAAA
53307226 CTA-ATAATATTA
1 CTACATAATATTA
53307238 TTATTCTAAT
Statistics
Matches: 22, Mismatches: 2, Indels: 4
0.79 0.07 0.14
Matches are distributed among these distances:
13 1 0.05
14 21 0.95
ACGTcount: A:0.50, C:0.15, G:0.00, T:0.35
Consensus pattern (15 bp):
CTACATAATATTAAA
Found at i:53307392 original size:7 final size:7
Alignment explanation
Indices: 53307380--53307410 Score: 53
Period size: 7 Copynumber: 4.3 Consensus size: 7
53307370 CAATAACAAT
53307380 AATAATA
1 AATAATA
53307387 AATAATA
1 AATAATA
53307394 AATAATA
1 AATAATA
53307401 AATAAATA
1 AAT-AATA
53307409 AA
1 AA
53307411 ATAAGAAGGG
Statistics
Matches: 23, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
7 17 0.74
8 6 0.26
ACGTcount: A:0.74, C:0.00, G:0.00, T:0.26
Consensus pattern (7 bp):
AATAATA
Found at i:53307754 original size:7 final size:7
Alignment explanation
Indices: 53307744--53307771 Score: 56
Period size: 7 Copynumber: 4.0 Consensus size: 7
53307734 AATGGAGCAA
53307744 CGAGGGG
1 CGAGGGG
53307751 CGAGGGG
1 CGAGGGG
53307758 CGAGGGG
1 CGAGGGG
53307765 CGAGGGG
1 CGAGGGG
53307772 AAAGGATAAG
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 21 1.00
ACGTcount: A:0.14, C:0.14, G:0.71, T:0.00
Consensus pattern (7 bp):
CGAGGGG
Found at i:53316851 original size:20 final size:20
Alignment explanation
Indices: 53316811--53316851 Score: 57
Period size: 20 Copynumber: 2.0 Consensus size: 20
53316801 AAACAAAAAT
*
53316811 ATTAAAAATATAAAAATTAA
1 ATTAAAAATATAAAAAATAA
53316831 ATTAAAAATA-AATAAAATAA
1 ATTAAAAATATAA-AAAATAA
53316851 A
1 A
53316852 AAATGGCTAA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
19 2 0.11
20 17 0.89
ACGTcount: A:0.73, C:0.00, G:0.00, T:0.27
Consensus pattern (20 bp):
ATTAAAAATATAAAAAATAA
Found at i:53327271 original size:19 final size:20
Alignment explanation
Indices: 53327249--53327288 Score: 55
Period size: 22 Copynumber: 1.9 Consensus size: 20
53327239 TTTTAAGTTT
53327249 TTTA-TTTTTAATTAATAAA
1 TTTATTTTTTAATTAATAAA
53327268 TTTATTGTTTTTAATTAATAA
1 TTTA-T-TTTTTAATTAATAA
53327289 TTATTTTATT
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
19 4 0.22
22 14 0.78
ACGTcount: A:0.38, C:0.00, G:0.03, T:0.60
Consensus pattern (20 bp):
TTTATTTTTTAATTAATAAA
Found at i:53328698 original size:3 final size:3
Alignment explanation
Indices: 53328685--53328718 Score: 61
Period size: 3 Copynumber: 11.7 Consensus size: 3
53328675 AAAGAAATTT
53328685 GAA GAA G-A GAA GAA GAA GAA GAA GAA GAA GAA GA
1 GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GA
53328719 GAGCGGGAAT
Statistics
Matches: 30, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
2 2 0.07
3 28 0.93
ACGTcount: A:0.65, C:0.00, G:0.35, T:0.00
Consensus pattern (3 bp):
GAA
Found at i:53330065 original size:17 final size:17
Alignment explanation
Indices: 53330051--53330094 Score: 70
Period size: 19 Copynumber: 2.5 Consensus size: 17
53330041 ATAATCTTCA
53330051 AAGATATGCAATCTTAG
1 AAGATATGCAATCTTAG
53330068 ATATGATATGCAATCTTAG
1 A-A-GATATGCAATCTTAG
53330087 AAGATATG
1 AAGATATG
53330095 ATTTTGTAAT
Statistics
Matches: 25, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
17 7 0.28
18 2 0.08
19 16 0.64
ACGTcount: A:0.41, C:0.09, G:0.18, T:0.32
Consensus pattern (17 bp):
AAGATATGCAATCTTAG
Found at i:53330113 original size:22 final size:22
Alignment explanation
Indices: 53330053--53330110 Score: 68
Period size: 19 Copynumber: 2.7 Consensus size: 22
53330043 AATCTTCAAA
53330053 GATATGCAATCTT---AGATAT
1 GATATGCAATCTTAGAAGATAT
53330072 GATATGCAATCTTAGAAGATAT
1 GATATGCAATCTTAGAAGATAT
* *
53330094 GATTTTGTAATCTTAGA
1 GA-TATGCAATCTTAGA
53330111 GATTTAATTT
Statistics
Matches: 33, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
19 13 0.39
22 8 0.24
23 12 0.36
ACGTcount: A:0.36, C:0.09, G:0.17, T:0.38
Consensus pattern (22 bp):
GATATGCAATCTTAGAAGATAT
Found at i:53331830 original size:3 final size:3
Alignment explanation
Indices: 53331824--53331894 Score: 56
Period size: 3 Copynumber: 23.3 Consensus size: 3
53331814 TTAATAATAA
* ** *
53331824 TAT TAT TAT TAT TAT TATT TAT TAA TCC TAT TAT TAT T-T GTAC TAT
1 TAT TAT TAT TAT TAT TA-T TAT TAT TAT TAT TAT TAT TAT -TAT TAT
*
53331870 TAT TGT TAT TAT TAT T-T TCAT TAT T
1 TAT TAT TAT TAT TAT TAT T-AT TAT T
53331895 TCTTCTTATC
Statistics
Matches: 54, Mismatches: 9, Indels: 10
0.74 0.12 0.14
Matches are distributed among these distances:
2 3 0.06
3 46 0.85
4 5 0.09
ACGTcount: A:0.28, C:0.06, G:0.03, T:0.63
Consensus pattern (3 bp):
TAT
Found at i:53337248 original size:41 final size:41
Alignment explanation
Indices: 53337203--53337285 Score: 166
Period size: 41 Copynumber: 2.0 Consensus size: 41
53337193 TCAGCGATAG
53337203 AGCAGTCGATTGTTAACTGACTGGTCGTAGGTTCGAATCCT
1 AGCAGTCGATTGTTAACTGACTGGTCGTAGGTTCGAATCCT
53337244 AGCAGTCGATTGTTAACTGACTGGTCGTAGGTTCGAATCCT
1 AGCAGTCGATTGTTAACTGACTGGTCGTAGGTTCGAATCCT
53337285 A
1 A
53337286 CTTGAGGAGA
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
41 42 1.00
ACGTcount: A:0.23, C:0.19, G:0.27, T:0.31
Consensus pattern (41 bp):
AGCAGTCGATTGTTAACTGACTGGTCGTAGGTTCGAATCCT
Found at i:53346719 original size:27 final size:27
Alignment explanation
Indices: 53346681--53346736 Score: 103
Period size: 27 Copynumber: 2.1 Consensus size: 27
53346671 ATCACTAACT
53346681 AATACTAATCTAACACTAATAGAATAG
1 AATACTAATCTAACACTAATAGAATAG
*
53346708 AATACTAATCTAATACTAATAGAATAG
1 AATACTAATCTAACACTAATAGAATAG
53346735 AA
1 AA
53346737 AAAATATAAT
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
27 28 1.00
ACGTcount: A:0.54, C:0.12, G:0.07, T:0.27
Consensus pattern (27 bp):
AATACTAATCTAACACTAATAGAATAG
Found at i:53350410 original size:16 final size:16
Alignment explanation
Indices: 53350389--53350421 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 16
53350379 TCTTATTGCT
*
53350389 TTGCTACTATAGAATA
1 TTGCTACTATAAAATA
53350405 TTGCTACTATAAAATA
1 TTGCTACTATAAAATA
53350421 T
1 T
53350422 AGAATACCGT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.39, C:0.12, G:0.09, T:0.39
Consensus pattern (16 bp):
TTGCTACTATAAAATA
Found at i:53352500 original size:33 final size:33
Alignment explanation
Indices: 53352463--53352531 Score: 129
Period size: 33 Copynumber: 2.1 Consensus size: 33
53352453 CATACATGTG
53352463 AATACGAATCCATTTTCCTTTTTCTCCGTAATC
1 AATACGAATCCATTTTCCTTTTTCTCCGTAATC
*
53352496 AATACGAATCCATTTTTCTTTTTCTCCGTAATC
1 AATACGAATCCATTTTCCTTTTTCTCCGTAATC
53352529 AAT
1 AAT
53352532 CTTCTCATTT
Statistics
Matches: 35, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
33 35 1.00
ACGTcount: A:0.26, C:0.25, G:0.06, T:0.43
Consensus pattern (33 bp):
AATACGAATCCATTTTCCTTTTTCTCCGTAATC
Found at i:53353752 original size:29 final size:29
Alignment explanation
Indices: 53353710--53353767 Score: 91
Period size: 29 Copynumber: 2.0 Consensus size: 29
53353700 GCAACCCATT
*
53353710 TTTATTATCATATCGAAA-TGCTATTCCTA
1 TTTATTATCATATCAAAACT-CTATTCCTA
53353739 TTTATTATCATATCAAAACTCTATTCCTA
1 TTTATTATCATATCAAAACTCTATTCCTA
53353768 ATAAAAGATA
Statistics
Matches: 27, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
29 26 0.96
30 1 0.04
ACGTcount: A:0.33, C:0.19, G:0.03, T:0.45
Consensus pattern (29 bp):
TTTATTATCATATCAAAACTCTATTCCTA
Found at i:53356248 original size:81 final size:81
Alignment explanation
Indices: 53356170--53356328 Score: 250
Period size: 81 Copynumber: 2.0 Consensus size: 81
53356160 TCCTTCCTTC
*
53356170 CCTCTTCTT-CTT-CTTTTTTTTTTCTCTTCTCCTTTCCTTTTCTTTCCTTCTTTTTCTTTCTTT
1 CCTCTTCTTACTTCCTTTTTTTTTTCTCTTCTCCTTTCCTTTTCTCTCCTTCTTTTTCTTTCTTT
53356233 CTTCTTCTCCTTTCCT
66 CTTCTTCTCCTTTCCT
* *
53356249 CTTCTTCTTATTTCCTTTTTTTTTTCTCTTCTCCTTTCCTTTTCTCTCCTTCTTTTTCTTTCTTT
1 CCTCTTCTTACTTCCTTTTTTTTTTCTCTTCTCCTTTCCTTTTCTCTCCTTCTTTTTCTTTCTTT
* *
53356314 CCTCTCCTTCCTTTC
66 CTTCTTC-TCCTTTC
53356329 TTTCTTTCCT
Statistics
Matches: 72, Mismatches: 5, Indels: 3
0.90 0.06 0.04
Matches are distributed among these distances:
79 8 0.11
80 2 0.03
81 55 0.76
82 7 0.10
ACGTcount: A:0.01, C:0.33, G:0.00, T:0.66
Consensus pattern (81 bp):
CCTCTTCTTACTTCCTTTTTTTTTTCTCTTCTCCTTTCCTTTTCTCTCCTTCTTTTTCTTTCTTT
CTTCTTCTCCTTTCCT
Found at i:53356289 original size:45 final size:46
Alignment explanation
Indices: 53356176--53356313 Score: 134
Period size: 45 Copynumber: 3.2 Consensus size: 46
53356166 CTTCCCTCTT
*
53356176 CTTCTTCTTT-TTTTTTTCT-CTTCTCCTTTCCT-T--TTC--TTTC
1 CTTCTT-TTTCTTTCTTTCTCCTTCTCCTTTCCTCTCCTTCTTTTTC
* *
53356216 CTTCTTTTTCTTTCTTTCTTCTTCTCCTTTCCTCTTCTTCTTATTTC
1 CTTCTTTTTCTTTCTTTCTCCTTCTCCTTTCCTCTCCTTCTT-TTTC
*
53356263 CTT-TTTTT-TTTCTCTTCTCCTT-TCCTTTTCTCTCCTTCTTTTTC
1 CTTCTTTTTCTTTCT-TTCTCCTTCTCCTTTCCTCTCCTTCTTTTTC
*
53356307 TTTCTTT
1 CTTCTTT
53356314 CCTCTCCTTC
Statistics
Matches: 83, Mismatches: 5, Indels: 15
0.81 0.05 0.15
Matches are distributed among these distances:
39 3 0.04
40 14 0.17
41 13 0.16
42 1 0.01
44 9 0.11
45 24 0.29
46 12 0.14
47 7 0.08
ACGTcount: A:0.01, C:0.30, G:0.00, T:0.69
Consensus pattern (46 bp):
CTTCTTTTTCTTTCTTTCTCCTTCTCCTTTCCTCTCCTTCTTTTTC
Found at i:53356330 original size:76 final size:74
Alignment explanation
Indices: 53356143--53356330 Score: 247
Period size: 81 Copynumber: 2.5 Consensus size: 74
53356133 TAAAAAATTA
* *
53356143 CCTT-TTTTTCTTTTTTTTCCT-TCCTTCC-CTCTTCTTCTTCTTTTTTTTTTCTCTTCTCCTTT
1 CCTTCTTTTTC-TTTCTTTCCTCTCCTTCCTTTCTTCTTCTTCTTTTTTTTTTCTCTTCTCCTTT
*
53356205 CCTTTTCTTT
65 CCTTTTCTCT
*
53356215 CCTTCTTTTTCTTTCTTTCTTCTTCTCCTTTCCTCTTCTTCTTATTTCCTTTTTTTTTTCTCTTC
1 CCTTCTTTTTCTTTCTTTC--C-TCTCC-TTCCT-TTCTTCTT-CTT-CTTTTTTTTTTCTCTTC
53356280 TCCTTTCCTTTTCTCT
59 TCCTTTCCTTTTCTCT
53356296 CCTTCTTTTTCTTTCTTTCCTCTCCTTCCTTTCTT
1 CCTTCTTTTTCTTTCTTTCCTCTCCTTCCTTTCTT
53356331 TCTTTCCTCT
Statistics
Matches: 102, Mismatches: 4, Indels: 16
0.84 0.03 0.13
Matches are distributed among these distances:
72 11 0.11
73 6 0.06
74 1 0.01
75 1 0.01
76 8 0.08
77 9 0.09
78 5 0.05
79 8 0.08
80 2 0.02
81 51 0.50
ACGTcount: A:0.01, C:0.32, G:0.00, T:0.67
Consensus pattern (74 bp):
CCTTCTTTTTCTTTCTTTCCTCTCCTTCCTTTCTTCTTCTTCTTTTTTTTTTCTCTTCTCCTTTC
CTTTTCTCT
Found at i:53356341 original size:45 final size:46
Alignment explanation
Indices: 53356282--53356368 Score: 115
Period size: 45 Copynumber: 1.9 Consensus size: 46
53356272 TTCTCTTCTC
* * * *
53356282 CTTTCCTTTTCTCTCCTTCTTTTTCTTTCTTT-CCTCTCCTTCCTTT
1 CTTTCCTTTCCTCTCATTC-CTTCCTTTCTTTCCCTCTCCTTCCTTT
53356328 CTTT-CTTTCCTCTCATTCCTTCCTTTCTTTCCCTCTCCTTC
1 CTTTCCTTTCCTCTCATTCCTTCCTTTCTTTCCCTCTCCTTC
53356369 TCCCCCCACC
Statistics
Matches: 36, Mismatches: 4, Indels: 3
0.84 0.09 0.07
Matches are distributed among these distances:
44 10 0.28
45 22 0.61
46 4 0.11
ACGTcount: A:0.01, C:0.40, G:0.00, T:0.59
Consensus pattern (46 bp):
CTTTCCTTTCCTCTCATTCCTTCCTTTCTTTCCCTCTCCTTCCTTT
Found at i:53356347 original size:26 final size:22
Alignment explanation
Indices: 53356282--53356368 Score: 111
Period size: 22 Copynumber: 3.8 Consensus size: 22
53356272 TTCTCTTCTC
* *
53356282 CTTTCCTTTTCTCTCCTTCTTTTT
1 CTTT-CTTTCCTCTCCTTC-CTTT
53356306 CTTTCTTTCCTCTCCTTCCTTT
1 CTTTCTTTCCTCTCCTTCCTTT
* *
53356328 CTTTCTTTCCTCTCATTCCTTC
1 CTTTCTTTCCTCTCCTTCCTTT
53356350 CTTTCTTTCCCTCTCCTTC
1 CTTTCTTT-CCTCTCCTTC
53356369 TCCCCCCACC
Statistics
Matches: 57, Mismatches: 5, Indels: 3
0.88 0.08 0.05
Matches are distributed among these distances:
22 31 0.54
23 22 0.39
24 4 0.07
ACGTcount: A:0.01, C:0.40, G:0.00, T:0.59
Consensus pattern (22 bp):
CTTTCTTTCCTCTCCTTCCTTT
Found at i:53356476 original size:27 final size:27
Alignment explanation
Indices: 53356398--53356468 Score: 115
Period size: 27 Copynumber: 2.6 Consensus size: 27
53356388 CCTATTATGG
*
53356398 CATTGGTGCCGCCAATGGTTTTGGCAC
1 CATTGGTGCCGCCAATGGCTTTGGCAC
*
53356425 CATTGGTGCCACCAATGGCTTTGGCAC
1 CATTGGTGCCGCCAATGGCTTTGGCAC
*
53356452 CTTTGGTGCCGCCAATG
1 CATTGGTGCCGCCAATG
53356469 CCATTGGCCT
Statistics
Matches: 40, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
27 40 1.00
ACGTcount: A:0.15, C:0.28, G:0.28, T:0.28
Consensus pattern (27 bp):
CATTGGTGCCGCCAATGGCTTTGGCAC
Found at i:53356590 original size:28 final size:30
Alignment explanation
Indices: 53356521--53356592 Score: 114
Period size: 30 Copynumber: 2.5 Consensus size: 30
53356511 TTGCATTTTT
53356521 TTAT-ATATTTTGGTAAATAATAAAAATAA
1 TTATAATATTTTGGTAAATAATAAAAATAA
*
53356550 TTATAATATTTTGGTAAATAAT-AAAA-AG
1 TTATAATATTTTGGTAAATAATAAAAATAA
53356578 TTATAATATTTTGGT
1 TTATAATATTTTGGT
53356593 TATTTTTTTT
Statistics
Matches: 41, Mismatches: 1, Indels: 3
0.91 0.02 0.07
Matches are distributed among these distances:
28 16 0.39
29 8 0.20
30 17 0.41
ACGTcount: A:0.46, C:0.00, G:0.10, T:0.44
Consensus pattern (30 bp):
TTATAATATTTTGGTAAATAATAAAAATAA
Found at i:53357424 original size:6 final size:6
Alignment explanation
Indices: 53357363--53357422 Score: 95
Period size: 6 Copynumber: 10.2 Consensus size: 6
53357353 TCCAGATTTG
*
53357363 AGCACA AGCAAA AGCAAA AGCAAA AGCAAA AGCAAA AGCAAA AGCAAA
1 AGCAAA AGCAAA AGCAAA AGCAAA AGCAAA AGCAAA AGCAAA AGCAAA
*
53357411 A-CAAA ATCAAA A
1 AGCAAA AGCAAA A
53357423 TCGATTTAAC
Statistics
Matches: 52, Mismatches: 1, Indels: 2
0.95 0.02 0.04
Matches are distributed among these distances:
5 5 0.10
6 47 0.90
ACGTcount: A:0.67, C:0.18, G:0.13, T:0.02
Consensus pattern (6 bp):
AGCAAA
Found at i:53357507 original size:14 final size:14
Alignment explanation
Indices: 53357488--53357515 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
53357478 AGCAGAAATC
53357488 TGGAGAAAAGAAAA
1 TGGAGAAAAGAAAA
53357502 TGGAGAAAAGAAAA
1 TGGAGAAAAGAAAA
53357516 GAAATGTGAG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.64, C:0.00, G:0.29, T:0.07
Consensus pattern (14 bp):
TGGAGAAAAGAAAA
Found at i:53357513 original size:19 final size:18
Alignment explanation
Indices: 53357491--53357535 Score: 58
Period size: 19 Copynumber: 2.5 Consensus size: 18
53357481 AGAAATCTGG
53357491 AGAAAAGAAAATG-GAGAAA
1 AGAAAAGAAAATGTGAG--A
53357510 AGAAAAG-AAATGTGAGA
1 AGAAAAGAAAATGTGAGA
53357527 AGAAAAGAA
1 AGAAAAGAA
53357536 GCGTACCGTA
Statistics
Matches: 24, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
17 8 0.33
18 6 0.25
19 10 0.42
ACGTcount: A:0.67, C:0.00, G:0.27, T:0.07
Consensus pattern (18 bp):
AGAAAAGAAAATGTGAGA
Found at i:53361285 original size:31 final size:29
Alignment explanation
Indices: 53361250--53361326 Score: 91
Period size: 29 Copynumber: 2.6 Consensus size: 29
53361240 ATTAACGATC
*
53361250 AGTGACTAAAATGTTACAACACGATAACATA
1 AGTGACTAAAATGTAACAACAC-A-AACATA
* ***
53361281 AGTGACTAAAACGTAACATTTCAAACATA
1 AGTGACTAAAATGTAACAACACAAACATA
53361310 AGTGACTAAAATGTAAC
1 AGTGACTAAAATGTAAC
53361327 CTGAGGTAAA
Statistics
Matches: 40, Mismatches: 6, Indels: 2
0.83 0.12 0.04
Matches are distributed among these distances:
29 22 0.55
30 1 0.03
31 17 0.43
ACGTcount: A:0.48, C:0.16, G:0.13, T:0.23
Consensus pattern (29 bp):
AGTGACTAAAATGTAACAACACAAACATA
Found at i:53361538 original size:31 final size:29
Alignment explanation
Indices: 53361469--53361542 Score: 94
Period size: 29 Copynumber: 2.5 Consensus size: 29
53361459 AATAAATAAT
**
53361469 AACATAAGTGACTAAAATGTAACATTTCA
1 AACATAAGTGACTAAAATGTAACATGACA
*
53361498 AACATAAGTGACTAAAATGTAACCTGAGACA
1 AACATAAGTGACTAAAATGTAACAT--GACA
*
53361529 AACAAAAGTGACTA
1 AACATAAGTGACTA
53361543 TTTTGGTAGT
Statistics
Matches: 39, Mismatches: 4, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
29 24 0.62
31 15 0.38
ACGTcount: A:0.50, C:0.15, G:0.14, T:0.22
Consensus pattern (29 bp):
AACATAAGTGACTAAAATGTAACATGACA
Found at i:53361881 original size:58 final size:60
Alignment explanation
Indices: 53361785--53361905 Score: 140
Period size: 58 Copynumber: 2.0 Consensus size: 60
53361775 TATACATTTT
** *
53361785 GGTACTTGAACTTGGTTTCAAGGTTTAAATTAGCACCT-AAGGTT-TTTGGGTCCAATTA
1 GGTACTTGAACTTGGTTTCAAAATTCAAATTAGCACCTAAAGGTTATTTGGGTCCAATTA
* * * * *
53361843 GGTACTTGAACTTGGCTTT-AAAATTCAAATTGGTACCTAAAGTTTATTTTGGTCTAATTA
1 GGTACTTGAACTTGG-TTTCAAAATTCAAATTAGCACCTAAAGGTTATTTGGGTCCAATTA
53361903 GGT
1 GGT
53361906 GATTGGACTT
Statistics
Matches: 52, Mismatches: 8, Indels: 4
0.81 0.12 0.06
Matches are distributed among these distances:
58 29 0.56
59 8 0.15
60 15 0.29
ACGTcount: A:0.27, C:0.12, G:0.21, T:0.40
Consensus pattern (60 bp):
GGTACTTGAACTTGGTTTCAAAATTCAAATTAGCACCTAAAGGTTATTTGGGTCCAATTA
Found at i:53383291 original size:68 final size:68
Alignment explanation
Indices: 53383211--53383341 Score: 253
Period size: 68 Copynumber: 1.9 Consensus size: 68
53383201 ATATAAAAGT
53383211 ATGAAAATACAAAAGTATCACCATAATAATATTGATTATCATTTAAAAGAAATATGAAAATAAGT
1 ATGAAAATACAAAAGTATCACCATAATAATATTGATTATCATTTAAAAGAAATATGAAAATAAGT
53383276 CGC
66 CGC
*
53383279 ATGAAAATACAAAAGTATCACCATAATAATATTGATTATCATTTAAAAGAAATATGTAAATAA
1 ATGAAAATACAAAAGTATCACCATAATAATATTGATTATCATTTAAAAGAAATATGAAAATAA
53383342 ATCGTTTTCA
Statistics
Matches: 62, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
68 62 1.00
ACGTcount: A:0.53, C:0.09, G:0.09, T:0.29
Consensus pattern (68 bp):
ATGAAAATACAAAAGTATCACCATAATAATATTGATTATCATTTAAAAGAAATATGAAAATAAGT
CGC
Found at i:53383327 original size:34 final size:34
Alignment explanation
Indices: 53383221--53383327 Score: 83
Period size: 34 Copynumber: 3.1 Consensus size: 34
53383211 ATGAAAATAC
53383221 AAAAGTATCACCATAATAATATTGATTATCATTT
1 AAAAGTATCACCATAATAATATTGATTATCATTT
* ** * * * * ** **
53383255 AAAAGAAAT-ATGAAAATAA-GTCGCATGAAAATAC
1 AAAAG-TATCACCATAATAATATTG-ATTATCATTT
53383289 AAAAGTATCACCATAATAATATTGATTATCATTT
1 AAAAGTATCACCATAATAATATTGATTATCATTT
53383323 AAAAG
1 AAAAG
53383328 AAATATGTAA
Statistics
Matches: 47, Mismatches: 22, Indels: 8
0.61 0.29 0.10
Matches are distributed among these distances:
33 4 0.09
34 39 0.83
35 4 0.09
ACGTcount: A:0.50, C:0.10, G:0.09, T:0.30
Consensus pattern (34 bp):
AAAAGTATCACCATAATAATATTGATTATCATTT
Found at i:53383489 original size:24 final size:25
Alignment explanation
Indices: 53383454--53383503 Score: 68
Period size: 24 Copynumber: 2.0 Consensus size: 25
53383444 AAATTATGAT
*
53383454 TTAAAATAAAAAATAATT-ATAAAA
1 TTAAAATAAAAAAAAATTAATAAAA
53383478 TTAAAA-ACAAAAAAAATTAATAAAA
1 TTAAAATA-AAAAAAAATTAATAAAA
53383503 T
1 T
53383504 ATCTCAAATA
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
23 1 0.04
24 15 0.65
25 7 0.30
ACGTcount: A:0.72, C:0.02, G:0.00, T:0.26
Consensus pattern (25 bp):
TTAAAATAAAAAAAAATTAATAAAA
Found at i:53383490 original size:25 final size:25
Alignment explanation
Indices: 53383456--53383503 Score: 71
Period size: 25 Copynumber: 1.9 Consensus size: 25
53383446 ATTATGATTT
*
53383456 AAAATAAAAAATAATT-ATAAAATTA
1 AAAACAAAAAA-AATTAATAAAATTA
53383481 AAAACAAAAAAAATTAATAAAAT
1 AAAACAAAAAAAATTAATAAAAT
53383504 ATCTCAAATA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
24 4 0.19
25 17 0.81
ACGTcount: A:0.75, C:0.02, G:0.00, T:0.23
Consensus pattern (25 bp):
AAAACAAAAAAAATTAATAAAATTA
Found at i:53385398 original size:25 final size:26
Alignment explanation
Indices: 53385370--53385418 Score: 64
Period size: 26 Copynumber: 1.9 Consensus size: 26
53385360 AATTAGGCAA
*
53385370 AAAATA-ATAATGATTAAAAAAAGAG
1 AAAATAGATAATGACTAAAAAAAGAG
* *
53385395 AAAATAGGTTATGACTAAAAAAAG
1 AAAATAGATAATGACTAAAAAAAG
53385419 GGTATTAGAA
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
25 6 0.30
26 14 0.70
ACGTcount: A:0.63, C:0.02, G:0.14, T:0.20
Consensus pattern (26 bp):
AAAATAGATAATGACTAAAAAAAGAG
Found at i:53387110 original size:17 final size:16
Alignment explanation
Indices: 53387090--53387123 Score: 50
Period size: 17 Copynumber: 2.1 Consensus size: 16
53387080 ATATGAAGAT
53387090 AAAAAAAATCTTATGGG
1 AAAAAAAATCTTA-GGG
*
53387107 AAAAAAATTCTTAGGG
1 AAAAAAAATCTTAGGG
53387123 A
1 A
53387124 CGGAAAAAGA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 4 0.25
17 12 0.75
ACGTcount: A:0.53, C:0.06, G:0.18, T:0.24
Consensus pattern (16 bp):
AAAAAAAATCTTAGGG
Found at i:53389248 original size:24 final size:23
Alignment explanation
Indices: 53389221--53389298 Score: 68
Period size: 24 Copynumber: 3.2 Consensus size: 23
53389211 GTCCCATTGT
*
53389221 TAGCTCTCATGAGCATCCCGTTAA
1 TAGCTCTC-TGAGCTTCCCGTTAA
* *
53389245 TAGCCCTCTCGAGCTTCCCATTATA
1 TAGCTCTCT-GAGCTTCCCGTTA-A
*
53389270 TAGTTCT-TGCGAGCTTCCCGTTAA
1 TAGCTCTCT--GAGCTTCCCGTTAA
53389294 TAGCT
1 TAGCT
53389299 TTTCGGAGCA
Statistics
Matches: 44, Mismatches: 7, Indels: 6
0.77 0.12 0.11
Matches are distributed among these distances:
23 1 0.02
24 24 0.55
25 19 0.43
ACGTcount: A:0.21, C:0.29, G:0.17, T:0.33
Consensus pattern (23 bp):
TAGCTCTCTGAGCTTCCCGTTAA
Found at i:53389307 original size:24 final size:24
Alignment explanation
Indices: 53389231--53389313 Score: 64
Period size: 24 Copynumber: 3.4 Consensus size: 24
53389221 TAGCTCTCAT
* *
53389231 GAGCATCCCGTTAATAGCCCTCTC-
1 GAGCATCCCGTTAATAG-CTTTTCG
* *
53389255 GAGCTTCCCATTATATAG-TTCTT-G
1 GAGCATCCCGTTA-ATAGCTT-TTCG
*
53389279 CGAGCTTCCCGTTAATAGCTTTTCG
1 -GAGCATCCCGTTAATAGCTTTTCG
53389304 GAGCATCCCG
1 GAGCATCCCG
53389314 ATTGGTTGTG
Statistics
Matches: 47, Mismatches: 6, Indels: 12
0.72 0.09 0.18
Matches are distributed among these distances:
23 1 0.02
24 27 0.57
25 19 0.40
ACGTcount: A:0.19, C:0.30, G:0.19, T:0.31
Consensus pattern (24 bp):
GAGCATCCCGTTAATAGCTTTTCG
Found at i:53389405 original size:26 final size:26
Alignment explanation
Indices: 53389376--53389447 Score: 76
Period size: 25 Copynumber: 2.8 Consensus size: 26
53389366 CCTATTATAT
53389376 GGCTCTTCGTGAGCTTTCCGATTAAA
1 GGCTCTTCGTGAGCTTTCCGATTAAA
* * *
53389402 GGCTCTTTGTGAGC-TTCCCATTAAT
1 GGCTCTTCGTGAGCTTTCCGATTAAA
* * *
53389427 GACTCTCCG-GAGCTTCCCGAT
1 GGCTCTTCGTGAGCTTTCCGAT
53389448 ATGGCTCGCT
Statistics
Matches: 37, Mismatches: 8, Indels: 3
0.77 0.17 0.06
Matches are distributed among these distances:
24 4 0.11
25 20 0.54
26 13 0.35
ACGTcount: A:0.17, C:0.28, G:0.22, T:0.33
Consensus pattern (26 bp):
GGCTCTTCGTGAGCTTTCCGATTAAA
Found at i:53389432 original size:25 final size:25
Alignment explanation
Indices: 53389359--53389444 Score: 84
Period size: 26 Copynumber: 3.4 Consensus size: 25
53389349 ACAGCTCTTA
* *
53389359 TGAGCGTCCTATTATATGGCTCTTCG
1 TGAGCTTCCCATTA-ATGGCTCTTCG
* * *
53389385 TGAGCTTTCCGATTAAAGGCTCTTTG
1 TGAGC-TTCCCATTAATGGCTCTTCG
* *
53389411 TGAGCTTCCCATTAATGACTCTCCG
1 TGAGCTTCCCATTAATGGCTCTTCG
53389436 -GAGCTTCCC
1 TGAGCTTCCC
53389445 GATATGGCTC
Statistics
Matches: 50, Mismatches: 9, Indels: 4
0.79 0.14 0.06
Matches are distributed among these distances:
24 9 0.18
25 15 0.30
26 19 0.38
27 7 0.14
ACGTcount: A:0.17, C:0.27, G:0.21, T:0.35
Consensus pattern (25 bp):
TGAGCTTCCCATTAATGGCTCTTCG
Found at i:53391986 original size:33 final size:34
Alignment explanation
Indices: 53391914--53392037 Score: 86
Period size: 33 Copynumber: 3.9 Consensus size: 34
53391904 TCCACATAAC
* * ** *
53391914 AGAGATAG-TCGGTTGGGACAGTAAGCACAGAAC
1 AGAGATAGTTCGGTTGGGACAATAAACATGGAAT
*
53391947 ATAGATAGTTC-GTTGGGACAATAAACATGGAAT
1 AGAGATAGTTCGGTTGGGACAATAAACATGGAAT
* * * *
53391980 AGAGATA-ATCTGTTAGGACAATTAACATGG-AT
1 AGAGATAGTTCGGTTGGGACAATAAACATGGAAT
*
53392012 --A-A-AG-TCCGTTGGGACAATAAACATGG
1 AGAGATAGTTCGGTTGGGACAATAAACATGG
53392038 GATAAGTTCG
Statistics
Matches: 75, Mismatches: 13, Indels: 11
0.76 0.13 0.11
Matches are distributed among these distances:
28 20 0.27
29 1 0.01
30 1 0.01
32 4 0.05
33 47 0.63
34 2 0.03
ACGTcount: A:0.39, C:0.12, G:0.27, T:0.23
Consensus pattern (34 bp):
AGAGATAGTTCGGTTGGGACAATAAACATGGAAT
Found at i:53392044 original size:28 final size:28
Alignment explanation
Indices: 53391957--53392044 Score: 79
Period size: 28 Copynumber: 3.0 Consensus size: 28
53391947 ATAGATAGTT
*
53391957 CGTTGGGACAATAAACATGGAATAGAGATAATC
1 CGTTGGGACAATAAACATGGGATA-AG----TC
* * *
53391990 TGTTAGGACAATTAACAT-GGATAAAGTC
1 CGTTGGGACAATAAACATGGGAT-AAGTC
53392018 CGTTGGGACAATAAACATGGGATAAGT
1 CGTTGGGACAATAAACATGGGATAAGT
53392045 TCGACGAGAT
Statistics
Matches: 46, Mismatches: 7, Indels: 9
0.74 0.11 0.15
Matches are distributed among these distances:
28 21 0.46
29 4 0.09
32 5 0.11
33 16 0.35
ACGTcount: A:0.40, C:0.11, G:0.25, T:0.24
Consensus pattern (28 bp):
CGTTGGGACAATAAACATGGGATAAGTC
Found at i:53392755 original size:18 final size:18
Alignment explanation
Indices: 53392729--53392764 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
53392719 ATTTGATTTG
*
53392729 ACTCGAATAACTCAATTA
1 ACTCAAATAACTCAATTA
*
53392747 ACTCAAATAACTCGATTA
1 ACTCAAATAACTCAATTA
53392765 GTTTAACTCA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.44, C:0.22, G:0.06, T:0.28
Consensus pattern (18 bp):
ACTCAAATAACTCAATTA
Found at i:53392978 original size:37 final size:37
Alignment explanation
Indices: 53392936--53393016 Score: 153
Period size: 37 Copynumber: 2.2 Consensus size: 37
53392926 GGTTCTCCAT
53392936 CATAAACCATCATCTTAATGCCTCTTTAGACCACTTA
1 CATAAACCATCATCTTAATGCCTCTTTAGACCACTTA
53392973 CATAAACCATCATCTTAATGCCTCTTTAGACCACTTA
1 CATAAACCATCATCTTAATGCCTCTTTAGACCACTTA
53393010 CAGTAAA
1 CA-TAAA
53393017 AACCACAATT
Statistics
Matches: 43, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
37 39 0.91
38 4 0.09
ACGTcount: A:0.35, C:0.28, G:0.06, T:0.31
Consensus pattern (37 bp):
CATAAACCATCATCTTAATGCCTCTTTAGACCACTTA
Found at i:53395526 original size:42 final size:40
Alignment explanation
Indices: 53395452--53395539 Score: 104
Period size: 41 Copynumber: 2.1 Consensus size: 40
53395442 TTGATTATTC
* *
53395452 TAAAAATTTTAGATTAAATAACGTTAATAACAATAAAACTA
1 TAAAAAGTTTAGATTAAATAACGTTAATAACAA-AAAAATA
* ** *
53395493 TTAAAAGTTTAGATTAAATAAATTTTATTAACAAAAAAATA
1 TAAAAAGTTTAGATTAAAT-AACGTTAATAACAAAAAAATA
53395534 TAAAAA
1 TAAAAA
53395540 TTGAAAATTG
Statistics
Matches: 39, Mismatches: 7, Indels: 2
0.81 0.15 0.04
Matches are distributed among these distances:
41 28 0.72
42 11 0.28
ACGTcount: A:0.58, C:0.05, G:0.05, T:0.33
Consensus pattern (40 bp):
TAAAAAGTTTAGATTAAATAACGTTAATAACAAAAAAATA
Found at i:53404602 original size:43 final size:43
Alignment explanation
Indices: 53404524--53404605 Score: 103
Period size: 43 Copynumber: 1.9 Consensus size: 43
53404514 TTCTGATAAA
* ***
53404524 TGTTTTCGTGTAAGACCACTTCTGGGACGTTGGCATCGACTTG
1 TGTTTTCGTGTAAGACCACTTCCGGGACAACGGCATCGACTTG
*
53404567 TGTTTTTGTGTAAGACC-CTGTCCGGGACAACGGCATCGA
1 TGTTTTCGTGTAAGACCACT-TCCGGGACAACGGCATCGA
53404606 TCAGTGATTA
Statistics
Matches: 33, Mismatches: 5, Indels: 2
0.82 0.12 0.05
Matches are distributed among these distances:
42 2 0.06
43 31 0.94
ACGTcount: A:0.18, C:0.22, G:0.28, T:0.32
Consensus pattern (43 bp):
TGTTTTCGTGTAAGACCACTTCCGGGACAACGGCATCGACTTG
Found at i:53408342 original size:21 final size:21
Alignment explanation
Indices: 53408318--53408501 Score: 118
Period size: 21 Copynumber: 8.8 Consensus size: 21
53408308 CCGTTTAGCT
*
53408318 CTTAAGAGCTTCTGTTTAACC
1 CTTATGAGCTTCTGTTTAACC
* * * * *
53408339 CTTATGGGTTTCTATTTAGCT
1 CTTATGAGCTTCTGTTTAACC
*
53408360 CTTTTGAGCTTCTGTTTAACC
1 CTTATGAGCTTCTGTTTAACC
* * * * *
53408381 CTTATGGGTTTCTATTTAGCT
1 CTTATGAGCTTCTGTTTAACC
*
53408402 CTTTTGAGCTTCTGTTTAACC
1 CTTATGAGCTTCTGTTTAACC
* * * * * *
53408423 CTTATGGGTTTCTATTCAGCT
1 CTTATGAGCTTCTGTTTAACC
* * *
53408444 CTTACGAGCTTTTGTTCAACC
1 CTTATGAGCTTCTGTTTAACC
* * *
53408465 CTTATGGGTTTCTG-TTAAGCT
1 CTTATGAGCTTCTGTTTAA-CC
*
53408486 CTCATGAGCTTCTGTT
1 CTTATGAGCTTCTGTT
53408502 CAGCTTTCGA
Statistics
Matches: 114, Mismatches: 47, Indels: 3
0.70 0.29 0.02
Matches are distributed among these distances:
20 3 0.03
21 110 0.96
22 1 0.01
ACGTcount: A:0.16, C:0.21, G:0.17, T:0.46
Consensus pattern (21 bp):
CTTATGAGCTTCTGTTTAACC
Found at i:53408503 original size:42 final size:42
Alignment explanation
Indices: 53408311--53408501 Score: 292
Period size: 42 Copynumber: 4.5 Consensus size: 42
53408301 TTACTTTCCG
*
53408311 TTTAGCTCTTAAGAGCTTCTGTTTAACCCTTATGGGTTTCTA
1 TTTAGCTCTTATGAGCTTCTGTTTAACCCTTATGGGTTTCTA
*
53408353 TTTAGCTCTTTTGAGCTTCTGTTTAACCCTTATGGGTTTCTA
1 TTTAGCTCTTATGAGCTTCTGTTTAACCCTTATGGGTTTCTA
*
53408395 TTTAGCTCTTTTGAGCTTCTGTTTAACCCTTATGGGTTTCTA
1 TTTAGCTCTTATGAGCTTCTGTTTAACCCTTATGGGTTTCTA
* * * * *
53408437 TTCAGCTCTTACGAGCTTTTGTTCAACCCTTATGGGTTTCTG
1 TTTAGCTCTTATGAGCTTCTGTTTAACCCTTATGGGTTTCTA
* *
53408479 TTAAGCTCTCATGAGCTTCTGTT
1 TTTAGCTCTTATGAGCTTCTGTT
53408502 CAGCTTTCGA
Statistics
Matches: 137, Mismatches: 12, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
42 137 1.00
ACGTcount: A:0.16, C:0.20, G:0.17, T:0.47
Consensus pattern (42 bp):
TTTAGCTCTTATGAGCTTCTGTTTAACCCTTATGGGTTTCTA
Found at i:53413064 original size:26 final size:26
Alignment explanation
Indices: 53413035--53413094 Score: 86
Period size: 26 Copynumber: 2.3 Consensus size: 26
53413025 TTCCCCCAGC
53413035 AAAATTTTGATGATTTTA-CTCCTAGT
1 AAAATTTTGATGATTTTACCT-CTAGT
* *
53413061 AAAATTTTGATGATTTTGCCTCTGGT
1 AAAATTTTGATGATTTTACCTCTAGT
53413087 AAAATTTT
1 AAAATTTT
53413095 TAGAAAATAA
Statistics
Matches: 31, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
26 29 0.94
27 2 0.06
ACGTcount: A:0.30, C:0.10, G:0.13, T:0.47
Consensus pattern (26 bp):
AAAATTTTGATGATTTTACCTCTAGT
Found at i:53419749 original size:13 final size:14
Alignment explanation
Indices: 53419724--53419752 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
53419714 CTTTGTTGTT
53419724 TGTTTTTCTTTATG
1 TGTTTTTCTTTATG
53419738 TGTTTTTC-TTATG
1 TGTTTTTCTTTATG
53419751 TG
1 TG
53419753 CAACAAATTA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 7 0.47
14 8 0.53
ACGTcount: A:0.07, C:0.07, G:0.17, T:0.69
Consensus pattern (14 bp):
TGTTTTTCTTTATG
Found at i:53422010 original size:11 final size:11
Alignment explanation
Indices: 53421994--53422044 Score: 61
Period size: 10 Copynumber: 4.8 Consensus size: 11
53421984 TTTAGGTTTA
*
53421994 GTTTTCTCGAG
1 GTTTTCTCTAG
*
53422005 GTTTTCTTTA-
1 GTTTTCTCTAG
53422015 GTTTTCTCTAG
1 GTTTTCTCTAG
*
53422026 GTTTTCTTTA-
1 GTTTTCTCTAG
53422036 GTTTTCTCT
1 GTTTTCTCT
53422045 GTACTTTTCT
Statistics
Matches: 34, Mismatches: 5, Indels: 3
0.81 0.12 0.07
Matches are distributed among these distances:
10 17 0.50
11 17 0.50
ACGTcount: A:0.08, C:0.16, G:0.16, T:0.61
Consensus pattern (11 bp):
GTTTTCTCTAG
Found at i:53422044 original size:21 final size:21
Alignment explanation
Indices: 53421990--53422044 Score: 101
Period size: 21 Copynumber: 2.6 Consensus size: 21
53421980 TAGTTTTAGG
*
53421990 TTTAGTTTTCTCGAGGTTTTC
1 TTTAGTTTTCTCTAGGTTTTC
53422011 TTTAGTTTTCTCTAGGTTTTC
1 TTTAGTTTTCTCTAGGTTTTC
53422032 TTTAGTTTTCTCT
1 TTTAGTTTTCTCT
53422045 GTACTTTTCT
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
21 33 1.00
ACGTcount: A:0.09, C:0.15, G:0.15, T:0.62
Consensus pattern (21 bp):
TTTAGTTTTCTCTAGGTTTTC
Found at i:53427153 original size:24 final size:24
Alignment explanation
Indices: 53427132--53427188 Score: 96
Period size: 24 Copynumber: 2.4 Consensus size: 24
53427122 AAGATTTAGT
*
53427132 ATTTATTAGTATAATATATTTAAC
1 ATTTATTAGCATAATATATTTAAC
*
53427156 ATTTATTAGCATAATATATTTGAC
1 ATTTATTAGCATAATATATTTAAC
53427180 ATTTATTAG
1 ATTTATTAG
53427189 AAATAGATTT
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
24 31 1.00
ACGTcount: A:0.39, C:0.05, G:0.07, T:0.49
Consensus pattern (24 bp):
ATTTATTAGCATAATATATTTAAC
Found at i:53431436 original size:23 final size:23
Alignment explanation
Indices: 53431410--53431455 Score: 65
Period size: 23 Copynumber: 2.0 Consensus size: 23
53431400 TTCTAGAAGA
* * *
53431410 TTTAGTATTTATTGGTATAATAT
1 TTTAGCATTTATTAGCATAATAT
53431433 TTTAGCATTTATTAGCATAATAT
1 TTTAGCATTTATTAGCATAATAT
53431456 ATTTGACATT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
23 20 1.00
ACGTcount: A:0.33, C:0.04, G:0.11, T:0.52
Consensus pattern (23 bp):
TTTAGCATTTATTAGCATAATAT
Found at i:53431470 original size:24 final size:23
Alignment explanation
Indices: 53431426--53431470 Score: 56
Period size: 24 Copynumber: 1.9 Consensus size: 23
53431416 ATTTATTGGT
*
53431426 ATAATATTTTAGCATTTATTAGC
1 ATAATATTTTAGCATTGATTAGC
53431449 ATAATATATTT-GACATTGATTA
1 ATAATAT-TTTAG-CATTGATTA
53431471 AAATTAGGTT
Statistics
Matches: 19, Mismatches: 1, Indels: 3
0.83 0.04 0.13
Matches are distributed among these distances:
23 8 0.42
24 11 0.58
ACGTcount: A:0.38, C:0.07, G:0.09, T:0.47
Consensus pattern (23 bp):
ATAATATTTTAGCATTGATTAGC
Found at i:53439616 original size:9 final size:9
Alignment explanation
Indices: 53439602--53439638 Score: 58
Period size: 9 Copynumber: 4.1 Consensus size: 9
53439592 TATAATTTGA
53439602 TATTCGAAT
1 TATTCGAAT
53439611 TATTCGAAT
1 TATTCGAAT
53439620 TATTC-AAGT
1 TATTCGAA-T
53439629 TATTCGAAT
1 TATTCGAAT
53439638 T
1 T
53439639 CGAAAACTCA
Statistics
Matches: 26, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
8 2 0.08
9 22 0.85
10 2 0.08
ACGTcount: A:0.32, C:0.11, G:0.11, T:0.46
Consensus pattern (9 bp):
TATTCGAAT
Found at i:53439855 original size:25 final size:24
Alignment explanation
Indices: 53439805--53439855 Score: 59
Period size: 25 Copynumber: 2.1 Consensus size: 24
53439795 CTATATCACT
* *
53439805 TTTTCTATTTTTTTTCCTTTTTCC
1 TTTTCTATTTTTTTTCCTCTTCCC
53439829 TTTTCT-TTTATTCTTTCCTCTTCCC
1 TTTTCTATTT-TT-TTTCCTCTTCCC
53439854 TT
1 TT
53439856 CCCTTCCCAT
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
23 3 0.13
24 8 0.35
25 12 0.52
ACGTcount: A:0.04, C:0.25, G:0.00, T:0.71
Consensus pattern (24 bp):
TTTTCTATTTTTTTTCCTCTTCCC
Found at i:53441333 original size:15 final size:15
Alignment explanation
Indices: 53441313--53441342 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
53441303 GGAACATCAG
53441313 AAAAAATATAAATAA
1 AAAAAATATAAATAA
53441328 AAAAAATATAAATAA
1 AAAAAATATAAATAA
53441343 TTTTTAAAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.80, C:0.00, G:0.00, T:0.20
Consensus pattern (15 bp):
AAAAAATATAAATAA
Found at i:53441382 original size:22 final size:22
Alignment explanation
Indices: 53441340--53441380 Score: 66
Period size: 21 Copynumber: 1.9 Consensus size: 22
53441330 AAAATATAAA
53441340 TAATTTTTAAAAATATTTTTAT
1 TAATTTTTAAAAATATTTTTAT
*
53441362 TAATTTTT-AATATATTTTT
1 TAATTTTTAAAAATATTTTT
53441381 TAGATTATGA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 10 0.56
22 8 0.44
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (22 bp):
TAATTTTTAAAAATATTTTTAT
Found at i:53443871 original size:3 final size:3
Alignment explanation
Indices: 53443863--53443928 Score: 123
Period size: 3 Copynumber: 22.0 Consensus size: 3
53443853 ACCCAATCTC
53443863 CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT
1 CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT
*
53443911 CTT CTT CTT CTT CAT CTT
1 CTT CTT CTT CTT CTT CTT
53443929 TATCTACATT
Statistics
Matches: 61, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
3 61 1.00
ACGTcount: A:0.02, C:0.33, G:0.00, T:0.65
Consensus pattern (3 bp):
CTT
Found at i:53447312 original size:19 final size:19
Alignment explanation
Indices: 53447288--53447355 Score: 75
Period size: 19 Copynumber: 3.5 Consensus size: 19
53447278 CTTCAAGGAC
*
53447288 ATGCAATCTTATATATGAT
1 ATGCAATCTTAGATATGAT
*
53447307 ATGCAA-ATTAGATATGATAT
1 ATGCAATCTTAGATATG--AT
*
53447327 ATGCAATCTTGGATATGAT
1 ATGCAATCTTAGATATGAT
*
53447346 ATGTAATCTT
1 ATGCAATCTT
53447356 GGAAGATATG
Statistics
Matches: 41, Mismatches: 5, Indels: 6
0.79 0.10 0.12
Matches are distributed among these distances:
18 8 0.20
19 17 0.41
20 8 0.20
21 8 0.20
ACGTcount: A:0.37, C:0.09, G:0.15, T:0.40
Consensus pattern (19 bp):
ATGCAATCTTAGATATGAT
Found at i:53447328 original size:20 final size:21
Alignment explanation
Indices: 53447288--53447347 Score: 63
Period size: 21 Copynumber: 3.0 Consensus size: 21
53447278 CTTCAAGGAC
* *
53447288 ATGCAATCTTATATATG--AT
1 ATGCAATATTAGATATGATAT
53447307 ATGCAA-ATTAGATATGATAT
1 ATGCAATATTAGATATGATAT
* *
53447327 ATGCAATCTTGGATATGATAT
1 ATGCAATATTAGATATGATAT
53447348 GTAATCTTGG
Statistics
Matches: 34, Mismatches: 4, Indels: 4
0.81 0.10 0.10
Matches are distributed among these distances:
18 8 0.24
19 6 0.18
20 8 0.24
21 12 0.35
ACGTcount: A:0.38, C:0.08, G:0.15, T:0.38
Consensus pattern (21 bp):
ATGCAATATTAGATATGATAT
Found at i:53447391 original size:22 final size:23
Alignment explanation
Indices: 53447347--53447391 Score: 56
Period size: 23 Copynumber: 2.0 Consensus size: 23
53447337 GGATATGATA
* *
53447347 TGTAATCTTGGAAGATATGATTT
1 TGTAATCTTAGAAGATATAATTT
*
53447370 TGTAATCTTAG-AGATTTAATTT
1 TGTAATCTTAGAAGATATAATTT
53447392 GTAGATACCC
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
22 9 0.47
23 10 0.53
ACGTcount: A:0.31, C:0.04, G:0.18, T:0.47
Consensus pattern (23 bp):
TGTAATCTTAGAAGATATAATTT
Found at i:53451188 original size:20 final size:19
Alignment explanation
Indices: 53451158--53451244 Score: 74
Period size: 20 Copynumber: 4.6 Consensus size: 19
53451148 ATCAACTATG
53451158 ATTAAACTTAATCATTTTAAT
1 ATTAAA-TTAATCA-TTTAAT
* *
53451179 ATTAAATTAATGA-TAAAT
1 ATTAAATTAATCATTTAAT
* *
53451197 ATTAGACTAA--ATTTAAT
1 ATTAAATTAATCATTTAAT
53451214 ATTAAGA-TAATCACTTTAAT
1 ATTAA-ATTAATCA-TTTAAT
53451234 ATTAAATTAAT
1 ATTAAATTAAT
53451245 AAAATACTAT
Statistics
Matches: 54, Mismatches: 6, Indels: 13
0.74 0.08 0.18
Matches are distributed among these distances:
16 1 0.02
17 11 0.20
18 13 0.24
19 2 0.04
20 21 0.39
21 6 0.11
ACGTcount: A:0.48, C:0.06, G:0.03, T:0.43
Consensus pattern (19 bp):
ATTAAATTAATCATTTAAT
Found at i:53467938 original size:7 final size:7
Alignment explanation
Indices: 53467928--53467957 Score: 51
Period size: 7 Copynumber: 4.3 Consensus size: 7
53467918 TGAGAGATGG
*
53467928 GAGGGTT
1 GAGGGAT
53467935 GAGGGAT
1 GAGGGAT
53467942 GAGGGAT
1 GAGGGAT
53467949 GAGGGAT
1 GAGGGAT
53467956 GA
1 GA
53467958 TTGAAAAAGT
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
7 22 1.00
ACGTcount: A:0.27, C:0.00, G:0.57, T:0.17
Consensus pattern (7 bp):
GAGGGAT
Found at i:53469583 original size:12 final size:12
Alignment explanation
Indices: 53469558--53469590 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
53469548 TTTATCAACA
53469558 TAAATATTAAAT
1 TAAATATTAAAT
53469570 TAAAT-TTAATAT
1 TAAATATTAA-AT
53469582 TAAATATTA
1 TAAATATTA
53469591 TTAAAATAAT
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
11 4 0.21
12 12 0.63
13 3 0.16
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (12 bp):
TAAATATTAAAT
Found at i:53469671 original size:20 final size:18
Alignment explanation
Indices: 53469621--53469672 Score: 63
Period size: 20 Copynumber: 2.8 Consensus size: 18
53469611 CTACAAGATA
53469621 AATATTAAATTAA-ATTT
1 AATATTAAATTAATATTT
53469638 AATATTAAGA-TAATCACTTT
1 AATATTAA-ATTAAT-A-TTT
53469658 AATATTAAATTAATA
1 AATATTAAATTAATA
53469673 AAATATTACT
Statistics
Matches: 30, Mismatches: 0, Indels: 8
0.79 0.00 0.21
Matches are distributed among these distances:
17 11 0.37
18 1 0.03
19 3 0.10
20 15 0.50
ACGTcount: A:0.52, C:0.04, G:0.02, T:0.42
Consensus pattern (18 bp):
AATATTAAATTAATATTT
Found at i:53475032 original size:51 final size:52
Alignment explanation
Indices: 53474962--53475065 Score: 183
Period size: 51 Copynumber: 2.0 Consensus size: 52
53474952 TCTAAATTTG
*
53474962 ATTTGATTTGATTTCGTTAATGGTAAACTATAAAAGAAAGA-TTGAGTTAAA
1 ATTTGATTTGATTTCGTTAATGGTAAACGATAAAAGAAAGATTTGAGTTAAA
*
53475013 ATTTGATTTGATTTGGTTAATGGTAAACGATAAAAGAAAGATTTGAGTTAAA
1 ATTTGATTTGATTTCGTTAATGGTAAACGATAAAAGAAAGATTTGAGTTAAA
53475065 A
1 A
53475066 GAAAATTATT
Statistics
Matches: 50, Mismatches: 2, Indels: 1
0.94 0.04 0.02
Matches are distributed among these distances:
51 39 0.78
52 11 0.22
ACGTcount: A:0.41, C:0.03, G:0.19, T:0.37
Consensus pattern (52 bp):
ATTTGATTTGATTTCGTTAATGGTAAACGATAAAAGAAAGATTTGAGTTAAA
Found at i:53483535 original size:25 final size:26
Alignment explanation
Indices: 53483492--53483562 Score: 99
Period size: 25 Copynumber: 2.8 Consensus size: 26
53483482 ATTTTCTCGA
53483492 AATTTTACCAGGGGTAAAATCATCAT
1 AATTTTACCAGGGGTAAAATCATCAT
* *
53483518 AATTTTACC-GGGGTAAAATCGTTAT
1 AATTTTACCAGGGGTAAAATCATCAT
* *
53483543 AATTTTATCAAGGGTAAAAT
1 AATTTTACCAGGGGTAAAAT
53483563 TGGGATTAGA
Statistics
Matches: 40, Mismatches: 4, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
25 22 0.55
26 18 0.45
ACGTcount: A:0.38, C:0.11, G:0.17, T:0.34
Consensus pattern (26 bp):
AATTTTACCAGGGGTAAAATCATCAT
Found at i:53509445 original size:20 final size:20
Alignment explanation
Indices: 53509420--53509461 Score: 84
Period size: 20 Copynumber: 2.1 Consensus size: 20
53509410 TATCAGTTAA
53509420 ATCCATCACATGTGTTATCT
1 ATCCATCACATGTGTTATCT
53509440 ATCCATCACATGTGTTATCT
1 ATCCATCACATGTGTTATCT
53509460 AT
1 AT
53509462 GGATGAAATT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.26, C:0.24, G:0.10, T:0.40
Consensus pattern (20 bp):
ATCCATCACATGTGTTATCT
Found at i:53513892 original size:39 final size:40
Alignment explanation
Indices: 53513775--53513998 Score: 260
Period size: 40 Copynumber: 5.7 Consensus size: 40
53513765 GCTACTCGTT
* *
53513775 CAAATGCCTTCGGGACATAGCCCGG-TTATAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAACCCGGATT-TAGTAACTCGCA
*
53513815 CAATTGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
* * *
53513855 CAAATGCCTTCGGG-CTTAGCCCGGAATTAGTATCTCGCA
1 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
53513894 CAAATGCCTTC-GGACTTAACCCGGATTTAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
** * * * *
53513933 CAAATGCCTTC-GGATCTTAGTCCGGATATGGTCACTTAGCA
1 CAAATGCCTTCGGGA-CTTAACCCGGATTTAGTAAC-TCGCA
* *
53513974 CAAA-GCCTTCGGGACTCAGCCCGGA
1 CAAATGCCTTCGGGACTTAACCCGGA
53513999 CATCATTCAA
Statistics
Matches: 161, Mismatches: 18, Indels: 10
0.85 0.10 0.05
Matches are distributed among these distances:
38 2 0.01
39 69 0.43
40 77 0.48
41 13 0.08
ACGTcount: A:0.25, C:0.28, G:0.22, T:0.25
Consensus pattern (40 bp):
CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
Found at i:53513935 original size:78 final size:80
Alignment explanation
Indices: 53513775--53513998 Score: 287
Period size: 79 Copynumber: 2.8 Consensus size: 80
53513765 GCTACTCGTT
* *
53513775 CAAATGCCTTCGGGACATAGCCCGGTTATAGTAACTCGCACAATTGCCTTCGGGACTTAACCCGG
1 CAAATGCCTTCGGGACATAGCCCGGATATAGTAACTCGCACAAATGCCTTCGGGACTTAACCCGG
53513840 ATTTAGTAACTCGCA
66 ATTTAGTAACTCGCA
* *
53513855 CAAATGCCTTCGGG-CTTAGCCCGGA-ATTAGTATCTCGCACAAATGCCTTC-GGACTTAACCCG
1 CAAATGCCTTCGGGACATAGCCCGGATA-TAGTAACTCGCACAAATGCCTTCGGGACTTAACCCG
53513917 GATTTAGTAACTCGCA
65 GATTTAGTAACTCGCA
* * * * * * *
53513933 CAAATGCCTTC-GGATCTTAGTCCGGATATGGTCACTTAGCACAAA-GCCTTCGGGACTCAGCCC
1 CAAATGCCTTCGGGA-CATAGCCCGGATATAGTAAC-TCGCACAAATGCCTTCGGGACTTAACCC
53513996 GGA
64 GGA
53513999 CATCATTCAA
Statistics
Matches: 127, Mismatches: 11, Indels: 12
0.85 0.07 0.08
Matches are distributed among these distances:
77 2 0.02
78 40 0.31
79 50 0.39
80 35 0.28
ACGTcount: A:0.25, C:0.28, G:0.22, T:0.25
Consensus pattern (80 bp):
CAAATGCCTTCGGGACATAGCCCGGATATAGTAACTCGCACAAATGCCTTCGGGACTTAACCCGG
ATTTAGTAACTCGCA
Found at i:53513958 original size:118 final size:120
Alignment explanation
Indices: 53513775--53513998 Score: 296
Period size: 118 Copynumber: 1.9 Consensus size: 120
53513765 GCTACTCGTT
* *
53513775 CAAATGCCTTCGGGACATAGCCCGGTTATAGTAACTCGCACAATTGCCTTCGGGACTTAACCCGG
1 CAAATGCCTTCGGGACATAACCCGGTTATAGTAACTCGCACAAATGCCTTCGGGACTTAACCCGG
* * *
53513840 ATTTAGTAAC-TCGCACAAATGCCTTCGGG-CTTAGCCCGGAATTAGTATCTCGCA
66 ATATAGTAACTTAGCACAAA-GCCTTCGGGACTCAGCCCGGAATTAGTATCTCGCA
* **
53513894 CAAATGCCTTC-GGACTTAACCCGGATT-TAGTAACTCGCACAAATGCCTTC-GGATCTTAGTCC
1 CAAATGCCTTCGGGACATAACCCGG-TTATAGTAACTCGCACAAATGCCTTCGGGA-CTTAACCC
* *
53513956 GGATATGGTCACTTAGCACAAAGCCTTCGGGACTCAGCCCGGA
64 GGATATAGTAACTTAGCACAAAGCCTTCGGGACTCAGCCCGGA
53513999 CATCATTCAA
Statistics
Matches: 91, Mismatches: 10, Indels: 8
0.83 0.09 0.07
Matches are distributed among these distances:
117 3 0.03
118 57 0.63
119 31 0.34
ACGTcount: A:0.25, C:0.28, G:0.22, T:0.25
Consensus pattern (120 bp):
CAAATGCCTTCGGGACATAACCCGGTTATAGTAACTCGCACAAATGCCTTCGGGACTTAACCCGG
ATATAGTAACTTAGCACAAAGCCTTCGGGACTCAGCCCGGAATTAGTATCTCGCA
Found at i:53515811 original size:29 final size:31
Alignment explanation
Indices: 53515779--53515838 Score: 70
Period size: 29 Copynumber: 2.0 Consensus size: 31
53515769 ATGTGAAAAG
* *
53515779 AAAGTGCAGGAAAACCA-TAAAG-ATGGAAA
1 AAAGAGCAAGAAAACCATTAAAGTATGGAAA
* *
53515808 AAAGAGCAAGAAAGCTATTAAAGTATGGAAA
1 AAAGAGCAAGAAAACCATTAAAGTATGGAAA
53515839 CCCAATTCCA
Statistics
Matches: 25, Mismatches: 4, Indels: 2
0.81 0.13 0.06
Matches are distributed among these distances:
29 13 0.52
30 5 0.20
31 7 0.28
ACGTcount: A:0.55, C:0.08, G:0.23, T:0.13
Consensus pattern (31 bp):
AAAGAGCAAGAAAACCATTAAAGTATGGAAA
Found at i:53516999 original size:10 final size:10
Alignment explanation
Indices: 53516984--53517008 Score: 50
Period size: 10 Copynumber: 2.5 Consensus size: 10
53516974 TTAGTAACTA
53516984 TATTTTATAT
1 TATTTTATAT
53516994 TATTTTATAT
1 TATTTTATAT
53517004 TATTT
1 TATTT
53517009 ATTTGTTAAT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 15 1.00
ACGTcount: A:0.28, C:0.00, G:0.00, T:0.72
Consensus pattern (10 bp):
TATTTTATAT
Found at i:53517315 original size:19 final size:19
Alignment explanation
Indices: 53517291--53517338 Score: 96
Period size: 19 Copynumber: 2.5 Consensus size: 19
53517281 ATTTTCAGGA
53517291 TCCACACGGGCTGGGCATT
1 TCCACACGGGCTGGGCATT
53517310 TCCACACGGGCTGGGCATT
1 TCCACACGGGCTGGGCATT
53517329 TCCACACGGG
1 TCCACACGGG
53517339 TTGGCCACAC
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 29 1.00
ACGTcount: A:0.17, C:0.33, G:0.31, T:0.19
Consensus pattern (19 bp):
TCCACACGGGCTGGGCATT
Found at i:53517366 original size:30 final size:30
Alignment explanation
Indices: 53517330--53517447 Score: 146
Period size: 30 Copynumber: 3.9 Consensus size: 30
53517320 CTGGGCATTT
* * *
53517330 CCACACGGGTTGGCCACACGCCCGTGTGAG
1 CCACACGGGCTAGACACACGCCCGTGTGAG
* *
53517360 CCACACGGGCTGGACATACGCCCGTGTGAG
1 CCACACGGGCTAGACACACGCCCGTGTGAG
* * *
53517390 CCATACGGACTAGACACACACCCGTGTGAG
1 CCACACGGGCTAGACACACGCCCGTGTGAG
* *
53517420 CCACACGGGCTAGCCACACGCCCATGTG
1 CCACACGGGCTAGACACACGCCCGTGTG
53517448 CTAGCCTGTG
Statistics
Matches: 75, Mismatches: 13, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
30 75 1.00
ACGTcount: A:0.22, C:0.36, G:0.29, T:0.13
Consensus pattern (30 bp):
CCACACGGGCTAGACACACGCCCGTGTGAG
Found at i:53525283 original size:3 final size:3
Alignment explanation
Indices: 53525275--53525303 Score: 58
Period size: 3 Copynumber: 9.7 Consensus size: 3
53525265 TAATACAAAA
53525275 AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
53525304 AAGTAGAGGC
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (3 bp):
AAT
Found at i:53528555 original size:22 final size:22
Alignment explanation
Indices: 53528515--53528557 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 22
53528505 TAATAATAAA
* *
53528515 TTTTAATTGATATTTTTAATTT
1 TTTTAATTGATAATGTTAATTT
*
53528537 TTTTAATTTATAATGTTAATT
1 TTTTAATTGATAATGTTAATT
53528558 AAAAGTATAC
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.30, C:0.00, G:0.05, T:0.65
Consensus pattern (22 bp):
TTTTAATTGATAATGTTAATTT
Found at i:53529652 original size:13 final size:13
Alignment explanation
Indices: 53529634--53529658 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
53529624 TTAAAAATAA
53529634 AATTAACTAAATT
1 AATTAACTAAATT
53529647 AATTAACTAAAT
1 AATTAACTAAAT
53529659 AACACGACAA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.56, C:0.08, G:0.00, T:0.36
Consensus pattern (13 bp):
AATTAACTAAATT
Found at i:53530500 original size:17 final size:17
Alignment explanation
Indices: 53530478--53530511 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
53530468 ACACGGTCTG
*
53530478 GCATATGGCCATGTGGC
1 GCATATGGCCATATGGC
53530495 GCATATGGCCATATGGC
1 GCATATGGCCATATGGC
53530512 AGACGTGTGG
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.21, C:0.24, G:0.32, T:0.24
Consensus pattern (17 bp):
GCATATGGCCATATGGC
Found at i:53534716 original size:104 final size:104
Alignment explanation
Indices: 53534536--53534740 Score: 356
Period size: 104 Copynumber: 2.0 Consensus size: 104
53534526 TATCCAACAG
* * *
53534536 CTCCCGAATATTGGTTTCAGAACTTTGCCCTCTTTCCCATGTAAACTAGGGTCATTTGAAGCCCA
1 CTCCCGAATATTGGTTTCAGAACTCTACCCTCTTTCCCATATAAACTAGGGTCATTTGAAGCCCA
*
53534601 GATTAGCTAACGAGCAGTCATCCAAATCCTGACGAATTA
66 GATTAGCTAACGAGCAGTCATCCAAAGCCTGACGAATTA
* *
53534640 CTCCCGAATATTGGTTTCAGAGCTCTACCCTCTTTCCCATATATACTAGGGTCATTTGAAGCCCA
1 CTCCCGAATATTGGTTTCAGAACTCTACCCTCTTTCCCATATAAACTAGGGTCATTTGAAGCCCA
53534705 GATTAGCTAACGAGCAGTCATCCAAAGCCTGACGAA
66 GATTAGCTAACGAGCAGTCATCCAAAGCCTGACGAA
53534741 ATTCTTCTAT
Statistics
Matches: 95, Mismatches: 6, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
104 95 1.00
ACGTcount: A:0.28, C:0.27, G:0.18, T:0.28
Consensus pattern (104 bp):
CTCCCGAATATTGGTTTCAGAACTCTACCCTCTTTCCCATATAAACTAGGGTCATTTGAAGCCCA
GATTAGCTAACGAGCAGTCATCCAAAGCCTGACGAATTA
Found at i:53537824 original size:17 final size:20
Alignment explanation
Indices: 53537802--53537848 Score: 55
Period size: 21 Copynumber: 2.5 Consensus size: 20
53537792 TTCAATTTCA
53537802 AATAAAAA-ATT-T-TAAAT
1 AATAAAAATATTATATAAAT
53537819 AATAAATAATATTATATAAAT
1 AATAAA-AATATTATATAAAT
*
53537840 AGTAAAAAT
1 AATAAAAAT
53537849 TAACTATATT
Statistics
Matches: 25, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
17 6 0.24
18 2 0.08
19 3 0.12
20 4 0.16
21 10 0.40
ACGTcount: A:0.64, C:0.00, G:0.02, T:0.34
Consensus pattern (20 bp):
AATAAAAATATTATATAAAT
Found at i:53541452 original size:15 final size:15
Alignment explanation
Indices: 53541432--53541461 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
53541422 CATGCAAATT
53541432 AGAAAAGAAAGAAAA
1 AGAAAAGAAAGAAAA
53541447 AGAAAAGAAAGAAAA
1 AGAAAAGAAAGAAAA
53541462 GAGAGAAAGG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.80, C:0.00, G:0.20, T:0.00
Consensus pattern (15 bp):
AGAAAAGAAAGAAAA
Found at i:53542860 original size:7 final size:7
Alignment explanation
Indices: 53542848--53542872 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
53542838 GGGTCACTGG
53542848 TTCTCTC
1 TTCTCTC
53542855 TTCTCTC
1 TTCTCTC
53542862 TTCTCTC
1 TTCTCTC
53542869 TTCT
1 TTCT
53542873 TAGATCTCTA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.00, C:0.40, G:0.00, T:0.60
Consensus pattern (7 bp):
TTCTCTC
Done.