Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: At_chr13
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: 91551117
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.32
Warning! 2824764 characters in sequence are not A, C, G, or T
File 123 of 276
Found at i:39524462 original size:41 final size:41
Alignment explanation
Indices: 39524389--39524648 Score: 450
Period size: 41 Copynumber: 6.4 Consensus size: 41
39524379 CGTTTTACCA
*
39524389 AAAACGCCGCTAAAAA-CAGAGCAATAGCGGCGCTTTTGGT
1 AAAACGCCGCTAAAAACCAGAGCATTAGCGGCGCTTTTGGT
39524429 AAAACGCCGCTAAAAACCAGAGCATTAGCGGCGCTTTTGGT
1 AAAACGCCGCTAAAAACCAGAGCATTAGCGGCGCTTTTGGT
**
39524470 AAAACGCCGCTAAAAACCAGAGCATTAGCAACGCTTTTGGT
1 AAAACGCCGCTAAAAACCAGAGCATTAGCGGCGCTTTTGGT
39524511 AAAACGCCGCTAAAAACCAGAGCATTAGCGGCGCTTTTGGT
1 AAAACGCCGCTAAAAACCAGAGCATTAGCGGCGCTTTTGGT
**
39524552 AAAACGCCGCTAAAAACCAGAGCATTAGCAACGCTTTTGGT
1 AAAACGCCGCTAAAAACCAGAGCATTAGCGGCGCTTTTGGT
* *
39524593 AAAACGCCACTAAAAACCAGAGCATTAGCGGCGCTTTTGGC
1 AAAACGCCGCTAAAAACCAGAGCATTAGCGGCGCTTTTGGT
39524634 AAAACGCCGCTAAAA
1 AAAACGCCGCTAAAA
39524649 GTCATATAAT
Statistics
Matches: 207, Mismatches: 12, Indels: 1
0.94 0.05 0.00
Matches are distributed among these distances:
40 16 0.08
41 191 0.92
ACGTcount: A:0.35, C:0.25, G:0.22, T:0.18
Consensus pattern (41 bp):
AAAACGCCGCTAAAAACCAGAGCATTAGCGGCGCTTTTGGT
Found at i:39524720 original size:47 final size:48
Alignment explanation
Indices: 39524653--39524784 Score: 122
Period size: 54 Copynumber: 2.6 Consensus size: 48
39524643 CTAAAAGTCA
* * * * *
39524653 TATAATCCTTAAAACCCTAAACCCCAAAAAAATA-ATAAACACTAATC
1 TATAACCCCTAAAACACTAAACCCCAAAAAAACACATAAACACTAAAC
* *
39524700 TATAACCCCTAGAACACTAAACCCCTAAATACTAAAAACACATGAACACTAAAC
1 TATAACCCCTAAAACACTAAACCCC---A-A--AAAAACACATAAACACTAAAC
* *
39524754 TATAACCCCTAAAACCCTAAACTCCAAAAAA
1 TATAACCCCTAAAACACTAAACCCCAAAAAA
39524785 CATCATATGG
Statistics
Matches: 68, Mismatches: 10, Indels: 13
0.75 0.11 0.14
Matches are distributed among these distances:
47 21 0.31
48 4 0.06
50 2 0.03
51 2 0.03
53 6 0.09
54 33 0.49
ACGTcount: A:0.52, C:0.29, G:0.02, T:0.18
Consensus pattern (48 bp):
TATAACCCCTAAAACACTAAACCCCAAAAAAACACATAAACACTAAAC
Found at i:39524723 original size:54 final size:53
Alignment explanation
Indices: 39524664--39524775 Score: 125
Period size: 54 Copynumber: 2.1 Consensus size: 53
39524654 ATAATCCTTA
* * *
39524664 AAACCCTAAACCCCAAAAAAATAATAAACACTAATCTATAACCCCTAGAACACT
1 AAACCCTAAACACCAAAAAAA-AATAAACACTAAACTATAACCCCTAAAACACT
* * * * * *
39524718 AAACCCCTAAATACTAAAAACACATGAACACTAAACTATAACCCCTAAAACCCT
1 AAA-CCCTAAACACCAAAAAAAAATAAACACTAAACTATAACCCCTAAAACACT
39524772 AAAC
1 AAAC
39524776 TCCAAAAAAC
Statistics
Matches: 48, Mismatches: 9, Indels: 3
0.80 0.15 0.05
Matches are distributed among these distances:
53 1 0.02
54 33 0.69
55 14 0.29
ACGTcount: A:0.52, C:0.30, G:0.02, T:0.16
Consensus pattern (53 bp):
AAACCCTAAACACCAAAAAAAAATAAACACTAAACTATAACCCCTAAAACACT
Found at i:39524735 original size:15 final size:16
Alignment explanation
Indices: 39524703--39524735 Score: 50
Period size: 15 Copynumber: 2.1 Consensus size: 16
39524693 ACTAATCTAT
39524703 AACCCCTAGAACACTA
1 AACCCCTAGAACACTA
*
39524719 AACCCCTA-AATACTA
1 AACCCCTAGAACACTA
39524734 AA
1 AA
39524736 AACACATGAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
15 8 0.50
16 8 0.50
ACGTcount: A:0.48, C:0.33, G:0.03, T:0.15
Consensus pattern (16 bp):
AACCCCTAGAACACTA
Found at i:39525831 original size:14 final size:14
Alignment explanation
Indices: 39525812--39525841 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
39525802 CTAATTTTTC
*
39525812 CCCCAAATCGAAAT
1 CCCCAAATCAAAAT
39525826 CCCCAAATCAAAAT
1 CCCCAAATCAAAAT
39525840 CC
1 CC
39525842 TTCCACCATT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.43, C:0.40, G:0.03, T:0.13
Consensus pattern (14 bp):
CCCCAAATCAAAAT
Found at i:39525926 original size:14 final size:14
Alignment explanation
Indices: 39525907--39525934 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
39525897 GCATTTCTTA
39525907 CTTCTCTAAATCTC
1 CTTCTCTAAATCTC
39525921 CTTCTCTAAATCTC
1 CTTCTCTAAATCTC
39525935 TATCCCTAAG
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:0.21, C:0.36, G:0.00, T:0.43
Consensus pattern (14 bp):
CTTCTCTAAATCTC
Found at i:39526319 original size:6 final size:6
Alignment explanation
Indices: 39526308--39526333 Score: 52
Period size: 6 Copynumber: 4.3 Consensus size: 6
39526298 GTGAATTTTT
39526308 TTTTGC TTTTGC TTTTGC TTTTGC TT
1 TTTTGC TTTTGC TTTTGC TTTTGC TT
39526334 CTGGTTATGC
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 20 1.00
ACGTcount: A:0.00, C:0.15, G:0.15, T:0.69
Consensus pattern (6 bp):
TTTTGC
Found at i:39537842 original size:28 final size:28
Alignment explanation
Indices: 39537766--39537843 Score: 83
Period size: 26 Copynumber: 2.9 Consensus size: 28
39537756 TAGTTTAAAT
* *
39537766 TTATTTATATCATAATA-TTTATTTTTTA
1 TTATTTATAT-ATAATAGTTTATATATTA
*
39537794 TT-TTT-TATAT-ATAGTAATATATATTA
1 TTATTTATATATAATAGT-TTATATATTA
39537820 TTATTTATATATAATAGTTTATAT
1 TTATTTATATATAATAGTTTATAT
39537844 TATATGAAAG
Statistics
Matches: 41, Mismatches: 4, Indels: 10
0.75 0.07 0.18
Matches are distributed among these distances:
24 3 0.07
25 3 0.07
26 12 0.29
27 6 0.15
28 12 0.29
29 5 0.12
ACGTcount: A:0.36, C:0.01, G:0.03, T:0.60
Consensus pattern (28 bp):
TTATTTATATATAATAGTTTATATATTA
Found at i:39537994 original size:30 final size:32
Alignment explanation
Indices: 39537960--39538025 Score: 91
Period size: 32 Copynumber: 2.1 Consensus size: 32
39537950 TAGATTAAAG
39537960 TTATTTAT-A-TTATATATATAATAATATATA
1 TTATTTATGATTTATATATATAATAATATATA
* * *
39537990 TTATTTATGATTTTTTTATATCATAATATATA
1 TTATTTATGATTTATATATATAATAATATATA
39538022 TTAT
1 TTAT
39538026 ATTAAAATGT
Statistics
Matches: 31, Mismatches: 3, Indels: 2
0.86 0.08 0.06
Matches are distributed among these distances:
30 8 0.26
31 1 0.03
32 22 0.71
ACGTcount: A:0.39, C:0.02, G:0.02, T:0.58
Consensus pattern (32 bp):
TTATTTATGATTTATATATATAATAATATATA
Found at i:39540472 original size:46 final size:46
Alignment explanation
Indices: 39540421--39540593 Score: 174
Period size: 46 Copynumber: 3.7 Consensus size: 46
39540411 TTGAGCATCC
*
39540421 GAACTCATTGAGTTGAGTCCGAGTTCACTTATGGATGTGAACGTCT
1 GAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGTGAACGTCT
* * * *
39540467 GAACTCGTTGAGTTGAGTTCGAGTTC-GTGA--GATGT-AACTAGGCATCC
1 GAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGTGAAC---G--TCT
* * * *
39540514 GAGCTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATGCCT
1 GAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGTGAACGTCT
* *
39540560 GAGCTCGTTGAGTTGAGTCCGAGTTCGCTTATGG
1 GAACTCGTTGAGTTGAGTCCGAGTTCACTTATGG
39540594 GCGAGTTACA
Statistics
Matches: 104, Mismatches: 14, Indels: 18
0.76 0.10 0.13
Matches are distributed among these distances:
42 3 0.03
43 5 0.05
45 3 0.03
46 58 0.56
47 26 0.25
48 3 0.03
50 4 0.04
51 2 0.02
ACGTcount: A:0.21, C:0.18, G:0.30, T:0.31
Consensus pattern (46 bp):
GAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGTGAACGTCT
Found at i:39540574 original size:93 final size:93
Alignment explanation
Indices: 39540415--39540586 Score: 281
Period size: 93 Copynumber: 1.8 Consensus size: 93
39540405 GGATATTTGA
* *
39540415 GCATCCGAACTCATTGAGTTGAGTCCGAGTTCACTTATGGATGTGAACGTCTGAACTCGTTGAGT
1 GCATCCGAACTCATTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCTGAACTCGTTGAGT
*
39540480 TGAGTTCGAGTTCGTGAGATGTAACTAG
66 TGAGTCCGAGTTCGTGAGATGTAACTAG
* * * *
39540508 GCATCCGAGCTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATGCCTGAGCTCGTTGAGT
1 GCATCCGAACTCATTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCTGAACTCGTTGAGT
39540573 TGAGTCCGAGTTCG
66 TGAGTCCGAGTTCG
39540587 CTTATGGGCG
Statistics
Matches: 72, Mismatches: 7, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
93 72 1.00
ACGTcount: A:0.21, C:0.19, G:0.30, T:0.30
Consensus pattern (93 bp):
GCATCCGAACTCATTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCTGAACTCGTTGAGT
TGAGTCCGAGTTCGTGAGATGTAACTAG
Found at i:39547079 original size:23 final size:24
Alignment explanation
Indices: 39547040--39547085 Score: 67
Period size: 23 Copynumber: 2.0 Consensus size: 24
39547030 TTTTTTAACA
* *
39547040 TTATTTCTTATTTTATATTTTTTG
1 TTATTTCTTACTTTATATCTTTTG
39547064 TTATTT-TTACTTTATATCTTTT
1 TTATTTCTTACTTTATATCTTTT
39547086 AATCTTATTT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
23 14 0.70
24 6 0.30
ACGTcount: A:0.17, C:0.07, G:0.02, T:0.74
Consensus pattern (24 bp):
TTATTTCTTACTTTATATCTTTTG
Found at i:39550753 original size:40 final size:40
Alignment explanation
Indices: 39550698--39550838 Score: 205
Period size: 40 Copynumber: 3.5 Consensus size: 40
39550688 TATTCGGATG
*
39550698 ATATCCGGGCTAAGTCCCGAAGGCATTTATGCTAGTGACT
1 ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCTAGTGACT
* *
39550738 ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCTAGCGACC
1 ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCTAGTGACT
*
39550778 ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTG-CT
1 ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCTAG-TGACT
* *
39550818 ATATCC-GGCTAAATCTCGAAG
1 ATATCCGGGCTAAGTCCCGAAG
39550839 ATACTTGGGT
Statistics
Matches: 92, Mismatches: 8, Indels: 3
0.89 0.08 0.03
Matches are distributed among these distances:
39 13 0.14
40 78 0.85
41 1 0.01
ACGTcount: A:0.24, C:0.24, G:0.26, T:0.26
Consensus pattern (40 bp):
ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCTAGTGACT
Found at i:39556212 original size:11 final size:11
Alignment explanation
Indices: 39556196--39556221 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
39556186 TACCAATAAT
39556196 ATAACATATTG
1 ATAACATATTG
39556207 ATAACATATTG
1 ATAACATATTG
39556218 ATAA
1 ATAA
39556222 ACCGTAATTT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.50, C:0.08, G:0.08, T:0.35
Consensus pattern (11 bp):
ATAACATATTG
Found at i:39564341 original size:5 final size:5
Alignment explanation
Indices: 39564331--39564381 Score: 75
Period size: 5 Copynumber: 9.6 Consensus size: 5
39564321 GAAAAAAATC
39564331 TTATT TTATTT TTATT TTATTT TTATT TTATT TTATT TTGATT TTATT
1 TTATT TTA-TT TTATT TTA-TT TTATT TTATT TTATT TT-ATT TTATT
39564379 TTA
1 TTA
39564382 AATTAGTTAA
Statistics
Matches: 43, Mismatches: 0, Indels: 6
0.88 0.00 0.12
Matches are distributed among these distances:
5 28 0.65
6 15 0.35
ACGTcount: A:0.20, C:0.00, G:0.02, T:0.78
Consensus pattern (5 bp):
TTATT
Found at i:39564345 original size:11 final size:10
Alignment explanation
Indices: 39564331--39564381 Score: 75
Period size: 11 Copynumber: 4.8 Consensus size: 10
39564321 GAAAAAAATC
39564331 TTATTTTATTT
1 TTATTTTA-TT
39564342 TTATTTTATTT
1 TTATTTTA-TT
39564353 TTATTTTATT
1 TTATTTTATT
39564363 TTATTTTGATT
1 TTATTTT-ATT
39564374 TTATTTTA
1 TTATTTTA
39564382 AATTAGTTAA
Statistics
Matches: 39, Mismatches: 0, Indels: 3
0.93 0.00 0.07
Matches are distributed among these distances:
10 10 0.26
11 29 0.74
ACGTcount: A:0.20, C:0.00, G:0.02, T:0.78
Consensus pattern (10 bp):
TTATTTTATT
Found at i:39564352 original size:16 final size:16
Alignment explanation
Indices: 39564334--39564381 Score: 78
Period size: 16 Copynumber: 2.9 Consensus size: 16
39564324 AAAAATCTTA
39564334 TTTTATTTTTATTTTAT
1 TTTTA-TTTTATTTTAT
39564351 TTTTATTTTATTTTAT
1 TTTTATTTTATTTTAT
*
39564367 TTTGATTTTATTTTA
1 TTTTATTTTATTTTA
39564382 AATTAGTTAA
Statistics
Matches: 30, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
16 25 0.83
17 5 0.17
ACGTcount: A:0.19, C:0.00, G:0.02, T:0.79
Consensus pattern (16 bp):
TTTTATTTTATTTTAT
Found at i:39577128 original size:37 final size:37
Alignment explanation
Indices: 39577078--39577156 Score: 97
Period size: 37 Copynumber: 2.1 Consensus size: 37
39577068 TTATTACGAA
* *
39577078 GTCTTACCCGGACATAA-TCTCCACACGAAGTTATCGG
1 GTCTTACCCGGACAAAATTC-CCACACGAAGTCATCGG
* * *
39577115 GTCTTACCTGGACAAAATTCCCACATGTAGTCATCGG
1 GTCTTACCCGGACAAAATTCCCACACGAAGTCATCGG
39577152 GTCTT
1 GTCTT
39577157 TAGAGCTCGG
Statistics
Matches: 36, Mismatches: 5, Indels: 2
0.84 0.12 0.05
Matches are distributed among these distances:
37 34 0.94
38 2 0.06
ACGTcount: A:0.25, C:0.28, G:0.19, T:0.28
Consensus pattern (37 bp):
GTCTTACCCGGACAAAATTCCCACACGAAGTCATCGG
Found at i:39577353 original size:47 final size:47
Alignment explanation
Indices: 39577275--39578186 Score: 1734
Period size: 47 Copynumber: 19.4 Consensus size: 47
39577265 CCCTTCGGGA
* * * * * * *
39577275 CTTATCACATTTATGCACTTTCACATCCATCACGTTGGCCACTCGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
* *
39577322 CCTGTCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
39577369 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
39577416 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
39577463 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
39577510 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
39577557 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
39577604 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
39577651 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
39577698 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
39577745 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
39577792 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
39577839 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
39577886 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
39577933 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
39577980 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
39578027 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
39578074 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
*
39578121 CTTATCACATATATACACTTTCACATTCATCACATCGGCTATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
39578168 CTTATCACATATATACACT
1 CTTATCACATATATACACT
39578187 GTCTTGGCTG
Statistics
Matches: 853, Mismatches: 12, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
47 853 1.00
ACGTcount: A:0.29, C:0.30, G:0.09, T:0.32
Consensus pattern (47 bp):
CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
Found at i:39588552 original size:41 final size:40
Alignment explanation
Indices: 39588472--39588556 Score: 98
Period size: 41 Copynumber: 2.1 Consensus size: 40
39588462 AGTTAAACTC
* ***
39588472 TATTTTTTAGTTTCCCACTTAAAATCTGATTATGGTAGGT
1 TATTTTTTAGTTTCCCACTTAAAATCTAATTAAAATAGGT
* * *
39588512 TATTTTATTATTTTCTCACTTAAACTCTAATTAAAATAGGT
1 TATTTT-TTAGTTTCCCACTTAAAATCTAATTAAAATAGGT
39588553 TATT
1 TATT
39588557 ATAATATTAT
Statistics
Matches: 37, Mismatches: 7, Indels: 1
0.82 0.16 0.02
Matches are distributed among these distances:
40 6 0.16
41 31 0.84
ACGTcount: A:0.29, C:0.12, G:0.09, T:0.49
Consensus pattern (40 bp):
TATTTTTTAGTTTCCCACTTAAAATCTAATTAAAATAGGT
Found at i:39591762 original size:13 final size:13
Alignment explanation
Indices: 39591744--39591768 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
39591734 CAAGTACCCA
39591744 ACCCAACCCAATT
1 ACCCAACCCAATT
39591757 ACCCAACCCAAT
1 ACCCAACCCAAT
39591769 CATAAAAATT
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:0.40, C:0.48, G:0.00, T:0.12
Consensus pattern (13 bp):
ACCCAACCCAATT
Found at i:39591860 original size:9 final size:9
Alignment explanation
Indices: 39591846--39591931 Score: 93
Period size: 9 Copynumber: 9.6 Consensus size: 9
39591836 TTCATACAAA
39591846 TAATTCGGT
1 TAATTCGGT
*
39591855 TAATTCAGT
1 TAATTCGGT
*
39591864 TAATTTGGT
1 TAATTCGGT
*
39591873 TAATTCGTT
1 TAATTCGGT
**
39591882 TAATTTAAG-
1 TAA-TTCGGT
39591891 TAATTCGGT
1 TAATTCGGT
39591900 TAATTCGGT
1 TAATTCGGT
*
39591909 TAATTCGAT
1 TAATTCGGT
*
39591918 TAATTCGAT
1 TAATTCGGT
39591927 TAATT
1 TAATT
39591932 TGATTACTTT
Statistics
Matches: 64, Mismatches: 11, Indels: 4
0.81 0.14 0.05
Matches are distributed among these distances:
8 3 0.05
9 59 0.92
10 2 0.03
ACGTcount: A:0.29, C:0.08, G:0.15, T:0.48
Consensus pattern (9 bp):
TAATTCGGT
Found at i:39591884 original size:27 final size:27
Alignment explanation
Indices: 39591846--39591931 Score: 104
Period size: 27 Copynumber: 3.2 Consensus size: 27
39591836 TTCATACAAA
*
39591846 TAATTCGGTTAATTCAGTTAATTTGGT
1 TAATTCGGTTAATTCAGTTAATTCGGT
* *
39591873 TAATTCGTTTAATTTAAG-TAATTCGGT
1 TAATTCGGTTAA-TTCAGTTAATTCGGT
*
39591900 TAATTCGGTTAATTC-GATTAATTCGAT
1 TAATTCGGTTAATTCAG-TTAATTCGGT
39591927 TAATT
1 TAATT
39591932 TGATTACTTT
Statistics
Matches: 50, Mismatches: 6, Indels: 6
0.81 0.10 0.10
Matches are distributed among these distances:
25 1 0.02
26 2 0.04
27 43 0.86
28 4 0.08
ACGTcount: A:0.29, C:0.08, G:0.15, T:0.48
Consensus pattern (27 bp):
TAATTCGGTTAATTCAGTTAATTCGGT
Found at i:39592273 original size:18 final size:18
Alignment explanation
Indices: 39592250--39592288 Score: 69
Period size: 18 Copynumber: 2.2 Consensus size: 18
39592240 AAAATTTTCA
39592250 TTTAAATTACTAAATTAT
1 TTTAAATTACTAAATTAT
*
39592268 TTTAAATTATTAAATTAT
1 TTTAAATTACTAAATTAT
39592286 TTT
1 TTT
39592289 TTTAAGTCCA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.41, C:0.03, G:0.00, T:0.56
Consensus pattern (18 bp):
TTTAAATTACTAAATTAT
Found at i:39598023 original size:46 final size:46
Alignment explanation
Indices: 39597943--39598303 Score: 396
Period size: 46 Copynumber: 8.2 Consensus size: 46
39597933 TCCCATCCAC
* * * * * *
39597943 GGTCTTATTTATCTT-TGACATGATGCCATAGTATCTTTCAACTAT
1 GGTCTTATTCATTTTCTGTCATGTTGCCATGGTATCTTTCAACCAT
*
39597988 GGTCTTACTCATTTTCTGTCATGTTGCCATGGTATCTTTCAACCAT
1 GGTCTTATTCATTTTCTGTCATGTTGCCATGGTATCTTTCAACCAT
* *
39598034 GGTCTTATTCATTTCCCGTCATGTTGCCATGGTATCTTTCAACCAT
1 GGTCTTATTCATTTTCTGTCATGTTGCCATGGTATCTTTCAACCAT
*
39598080 GG------TC---TTGTG-CA--TTGCCATGGTATCTTTCAACCAT
1 GGTCTTATTCATTTTCTGTCATGTTGCCATGGTATCTTTCAACCAT
* *
39598114 GGTCTTATTCA-TTCCCGTCATGTTGCCATGGTATCTTTCAACCAT
1 GGTCTTATTCATTTTCTGTCATGTTGCCATGGTATCTTTCAACCAT
* * *
39598159 GGTCTTGTTC-TTTTCATGTCACGTTACCATGGTATCTTTCAACCAT
1 GGTCTTATTCATTTTC-TGTCATGTTGCCATGGTATCTTTCAACCAT
* *
39598205 GGTCTTATTC-TTTTCATGTCACGTTGCCATGGTATTTTTCAACCAT
1 GGTCTTATTCATTTTC-TGTCATGTTGCCATGGTATCTTTCAACCAT
** *
39598251 GGTCTTACACA-TTTCATATCATGTTGCCATGGTATCTTTCAACCAT
1 GGTCTTATTCATTTTC-TGTCATGTTGCCATGGTATCTTTCAACCAT
39598297 GGTCTTA
1 GGTCTTA
39598304 CATATTTCCT
Statistics
Matches: 272, Mismatches: 29, Indels: 29
0.82 0.09 0.09
Matches are distributed among these distances:
34 25 0.09
36 2 0.01
37 2 0.01
40 4 0.01
42 2 0.01
43 2 0.01
45 47 0.17
46 188 0.69
ACGTcount: A:0.19, C:0.23, G:0.16, T:0.42
Consensus pattern (46 bp):
GGTCTTATTCATTTTCTGTCATGTTGCCATGGTATCTTTCAACCAT
Found at i:39598081 original size:16 final size:16
Alignment explanation
Indices: 39598060--39598116 Score: 55
Period size: 16 Copynumber: 3.4 Consensus size: 16
39598050 CGTCATGTTG
39598060 CCATGGTATCTTTCAA
1 CCATGGTATCTTTCAA
*
39598076 CCATGG--TCTTGTGCATTG
1 CCATGGTATCTT-T-CA--A
39598094 CCATGGTATCTTTCAA
1 CCATGGTATCTTTCAA
39598110 CCATGGT
1 CCATGGT
39598117 CTTATTCATT
Statistics
Matches: 33, Mismatches: 2, Indels: 12
0.70 0.04 0.26
Matches are distributed among these distances:
14 4 0.12
15 1 0.03
16 15 0.45
18 8 0.24
19 1 0.03
20 4 0.12
ACGTcount: A:0.19, C:0.25, G:0.19, T:0.37
Consensus pattern (16 bp):
CCATGGTATCTTTCAA
Found at i:39598160 original size:79 final size:80
Alignment explanation
Indices: 39598011--39598166 Score: 305
Period size: 79 Copynumber: 2.0 Consensus size: 80
39598001 TTCTGTCATG
39598011 TTGCCATGGTATCTTTCAACCATGGTCTTATTCATTTCCCGTCATGTTGCCATGGTATCTTTCAA
1 TTGCCATGGTATCTTTCAACCATGGTCTTATTCATTTCCCGTCATGTTGCCATGGTATCTTTCAA
39598076 CCATGGTCTTGTGCA
66 CCATGGTCTTGTGCA
39598091 TTGCCATGGTATCTTTCAACCATGGTCTTATTCA-TTCCCGTCATGTTGCCATGGTATCTTTCAA
1 TTGCCATGGTATCTTTCAACCATGGTCTTATTCATTTCCCGTCATGTTGCCATGGTATCTTTCAA
39598155 CCATGGTCTTGT
66 CCATGGTCTTGT
39598167 TCTTTTCATG
Statistics
Matches: 76, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
79 42 0.55
80 34 0.45
ACGTcount: A:0.17, C:0.25, G:0.17, T:0.40
Consensus pattern (80 bp):
TTGCCATGGTATCTTTCAACCATGGTCTTATTCATTTCCCGTCATGTTGCCATGGTATCTTTCAA
CCATGGTCTTGTGCA
Found at i:39600372 original size:11 final size:11
Alignment explanation
Indices: 39600356--39600407 Score: 59
Period size: 11 Copynumber: 4.5 Consensus size: 11
39600346 CTTTCTTTAT
39600356 ATAATAATAAA
1 ATAATAATAAA
39600367 ATAATAATAAA
1 ATAATAATAAA
* *
39600378 ATATCTTATTAAA
1 ATA--ATAATAAA
*
39600391 ATATTAATAAA
1 ATAATAATAAA
39600402 ATAATA
1 ATAATA
39600408 TTTATCTAAT
Statistics
Matches: 35, Mismatches: 4, Indels: 4
0.81 0.09 0.09
Matches are distributed among these distances:
11 26 0.74
13 9 0.26
ACGTcount: A:0.63, C:0.02, G:0.00, T:0.35
Consensus pattern (11 bp):
ATAATAATAAA
Found at i:39607689 original size:29 final size:30
Alignment explanation
Indices: 39607629--39607690 Score: 92
Period size: 29 Copynumber: 2.1 Consensus size: 30
39607619 TTTTATTTTA
*
39607629 TTGTTAATTTTCTTATTATTTTAAAGGTAT
1 TTGTTAATTTTCTTATTATTTTAAAGGCAT
39607659 TTGTTAATTTT-TTATTATTTTAGAA-GCAT
1 TTGTTAATTTTCTTATTATTTTA-AAGGCAT
39607688 TTG
1 TTG
39607691 CTTGTTAAGT
Statistics
Matches: 30, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
29 17 0.57
30 13 0.43
ACGTcount: A:0.26, C:0.03, G:0.11, T:0.60
Consensus pattern (30 bp):
TTGTTAATTTTCTTATTATTTTAAAGGCAT
Found at i:39609245 original size:18 final size:18
Alignment explanation
Indices: 39609213--39609258 Score: 58
Period size: 18 Copynumber: 2.6 Consensus size: 18
39609203 TTTTTAAGAT
* *
39609213 TATAATATA-ATATATTA
1 TATAATTTATATATATCA
*
39609230 TATTATTTATATATATCA
1 TATAATTTATATATATCA
39609248 TATAATTTATA
1 TATAATTTATA
39609259 ACATATAAAA
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
17 7 0.29
18 17 0.71
ACGTcount: A:0.46, C:0.02, G:0.00, T:0.52
Consensus pattern (18 bp):
TATAATTTATATATATCA
Found at i:39611876 original size:20 final size:20
Alignment explanation
Indices: 39611807--39611920 Score: 111
Period size: 20 Copynumber: 5.4 Consensus size: 20
39611797 TCATGGGGTG
39611807 CTTTGGTGGTATTCTGTTTAGC
1 CTTT-GTGGTATTCTG-TTAGC
*
39611829 CTTTGTAGCGTATTCTGGTTTGGC
1 CTTTGT-G-GTATTCT-G-TTAGC
*
39611853 CTTCGTGGTATTCTGTTAGC
1 CTTTGTGGTATTCTGTTAGC
* * *
39611873 CTTCGAGGTACTCTGTTAGC
1 CTTTGTGGTATTCTGTTAGC
* *
39611893 CTTTGCGGTACTCTGTTAGC
1 CTTTGTGGTATTCTGTTAGC
39611913 CTTTGTGG
1 CTTTGTGG
39611921 CATATTCCAT
Statistics
Matches: 81, Mismatches: 8, Indels: 8
0.84 0.08 0.08
Matches are distributed among these distances:
20 47 0.58
21 3 0.04
22 12 0.15
23 8 0.10
24 11 0.14
ACGTcount: A:0.10, C:0.19, G:0.27, T:0.44
Consensus pattern (20 bp):
CTTTGTGGTATTCTGTTAGC
Found at i:39613387 original size:44 final size:44
Alignment explanation
Indices: 39613322--39613405 Score: 107
Period size: 44 Copynumber: 1.9 Consensus size: 44
39613312 TTGATATCTC
* *
39613322 AAAGTCCATGGTTGTACCATGGAAATTAAGGAAGAATTGATGGA
1 AAAGTCCATGGTTATAACATGGAAATTAAGGAAGAATTGATGGA
* * *
39613366 AAAGTCCAT-GTTCATAACATGGCATTTAAGGAGGAATTGA
1 AAAGTCCATGGTT-ATAACATGGAAATTAAGGAAGAATTGA
39613406 CAGTTAAGGA
Statistics
Matches: 34, Mismatches: 5, Indels: 2
0.83 0.12 0.05
Matches are distributed among these distances:
43 3 0.09
44 31 0.91
ACGTcount: A:0.38, C:0.11, G:0.25, T:0.26
Consensus pattern (44 bp):
AAAGTCCATGGTTATAACATGGAAATTAAGGAAGAATTGATGGA
Found at i:39613593 original size:47 final size:47
Alignment explanation
Indices: 39613535--39613644 Score: 202
Period size: 47 Copynumber: 2.3 Consensus size: 47
39613525 TCAAGATGTG
*
39613535 ACCATGTAAGACCATGTTTGGAACATGGTATTTGGTAAGATAAGGAT
1 ACCATGTAAGACCATGTTTGGAACATGGCATTTGGTAAGATAAGGAT
39613582 ACCATGTAAGACCATGTTTGGAACATGGCATTTGGTAAGATAAGGAT
1 ACCATGTAAGACCATGTTTGGAACATGGCATTTGGTAAGATAAGGAT
*
39613629 ATCATGTAAGACCATG
1 ACCATGTAAGACCATG
39613645 CCAAGGCATG
Statistics
Matches: 61, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
47 61 1.00
ACGTcount: A:0.35, C:0.13, G:0.25, T:0.28
Consensus pattern (47 bp):
ACCATGTAAGACCATGTTTGGAACATGGCATTTGGTAAGATAAGGAT
Found at i:39613752 original size:55 final size:54
Alignment explanation
Indices: 39613623--39613815 Score: 237
Period size: 54 Copynumber: 3.6 Consensus size: 54
39613613 TTGGTAAGAT
* * * *
39613623 AAGGATATCATGTAAGACCATGCCAAGGCATGGCATTGATAAGTTCTATAAGGT
1 AAGGATACCATGTAAGACCATGCCAAGACATGGCATTGATGAGTTCTATAAGGC
* * *
39613677 AAGGAAATCATGTAAGACCATGTCAAGACATGGCATTGATGAGTTACTATAAGGC
1 AAGGATACCATGTAAGACCATGCCAAGACATGGCATTGATGAGTT-CTATAAGGC
* * * *
39613732 AAAGG-TCCCATGTAAGACCATGCCAGGGCATGGCATTGGTGAGTTC-ATAAGGC
1 -AAGGATACCATGTAAGACCATGCCAAGACATGGCATTGATGAGTTCTATAAGGC
* *
39613785 AAGGATACCACGTAAGACCATGTCAAGACAT
1 AAGGATACCATGTAAGACCATGCCAAGACAT
39613816 TGCAATGGTA
Statistics
Matches: 119, Mismatches: 17, Indels: 7
0.83 0.12 0.05
Matches are distributed among these distances:
52 4 0.03
53 28 0.24
54 42 0.35
55 41 0.34
56 4 0.03
ACGTcount: A:0.35, C:0.18, G:0.25, T:0.22
Consensus pattern (54 bp):
AAGGATACCATGTAAGACCATGCCAAGACATGGCATTGATGAGTTCTATAAGGC
Found at i:39613845 original size:108 final size:109
Alignment explanation
Indices: 39613631--39613841 Score: 273
Period size: 108 Copynumber: 2.0 Consensus size: 109
39613621 ATAAGGATAT
* * *
39613631 CATGTAAGACCATGCCAAGGCATGGCATTGATAAGTTCTATAAGGTAAGGAAATCATGTAAGACC
1 CATGTAAGACCATGCCAAGGCATGGCATTGATAAGTTCTATAAGGCAAGGAAACCACGTAAGACC
* * * * **
39613696 ATGTCAAGACATGGCATTGATGAGTTACTATAAGGCAAAGGTCC
66 ATGTCAAGACATGGCAATGATAAGTTACAAAAAGAAAAAGGTCC
* * * *
39613740 CATGTAAGACCATGCCAGGGCATGGCATTGGTGAGTTC-ATAAGGCAAGGATACCACGTAAGACC
1 CATGTAAGACCATGCCAAGGCATGGCATTGATAAGTTCTATAAGGCAAGGAAACCACGTAAGACC
* *
39613804 ATGTCAAGACATTGCAATGGTAAGTT-CAAAAAGAAAAA
66 ATGTCAAGACATGGCAATGATAAGTTACAAAAAGAAAAA
39613842 AGGTTCCCGA
Statistics
Matches: 87, Mismatches: 15, Indels: 2
0.84 0.14 0.02
Matches are distributed among these distances:
107 8 0.09
108 44 0.51
109 35 0.40
ACGTcount: A:0.37, C:0.17, G:0.24, T:0.22
Consensus pattern (109 bp):
CATGTAAGACCATGCCAAGGCATGGCATTGATAAGTTCTATAAGGCAAGGAAACCACGTAAGACC
ATGTCAAGACATGGCAATGATAAGTTACAAAAAGAAAAAGGTCC
Found at i:39617161 original size:3 final size:3
Alignment explanation
Indices: 39617148--39617249 Score: 56
Period size: 3 Copynumber: 34.0 Consensus size: 3
39617138 ATATTTAAAT
* *
39617148 ATA AAA ATA ATA AT- ATAA ATA ATA AT- ATA TATA AAA ATA ATA CATA
1 ATA ATA ATA ATA ATA AT-A ATA ATA ATA ATA -ATA ATA ATA ATA -ATA
* *
39617194 ATAA ATA ATA TGTA ATA ATA AT- ATAA ATA TATA AT- AGA AT- ATA A-A
1 AT-A ATA ATA -ATA ATA ATA ATA AT-A ATA -ATA ATA ATA ATA ATA ATA
39617239 ATA AT- ATA ATA
1 ATA ATA ATA ATA
39617250 TAGTAAAAAA
Statistics
Matches: 77, Mismatches: 8, Indels: 28
0.68 0.07 0.25
Matches are distributed among these distances:
2 13 0.17
3 46 0.60
4 18 0.23
ACGTcount: A:0.65, C:0.01, G:0.02, T:0.32
Consensus pattern (3 bp):
ATA
Found at i:39617196 original size:7 final size:7
Alignment explanation
Indices: 39617153--39617251 Score: 68
Period size: 7 Copynumber: 14.9 Consensus size: 7
39617143 TAAATATAAA
39617153 AATA-AT
1 AATATAT
39617159 AATATA-
1 AATATAT
39617165 AATA-AT
1 AATATAT
39617171 AATATAT
1 AATATAT
* *
39617178 ATAAAAAT
1 A-ATATAT
*
39617186 AATACAT
1 AATATAT
*
39617193 AATAAAT
1 AATATAT
*
39617200 AATATGT
1 AATATAT
39617207 AATA-AT
1 AATATAT
39617213 AATATA-
1 AATATAT
39617219 AATATAT
1 AATATAT
*
39617226 -A-ATAG
1 AATATAT
*
39617231 AATATAA
1 AATATAT
39617238 AATAATAT
1 AAT-ATAT
39617246 AATATA
1 AATATA
39617252 GTAAAAAACA
Statistics
Matches: 73, Mismatches: 11, Indels: 17
0.72 0.11 0.17
Matches are distributed among these distances:
5 4 0.05
6 25 0.34
7 33 0.45
8 11 0.15
ACGTcount: A:0.64, C:0.01, G:0.02, T:0.33
Consensus pattern (7 bp):
AATATAT
Found at i:39617247 original size:20 final size:18
Alignment explanation
Indices: 39617159--39617249 Score: 57
Period size: 16 Copynumber: 4.9 Consensus size: 18
39617149 TAAAAATAAT
39617159 AATATAAATA-ATAATA-
1 AATATAAATATATAATAG
*
39617175 TATATAAA-A-ATAATA-
1 AATATAAATATATAATAG
* *
39617190 CATAATAAATAATATGTAATAAT
1 AAT-ATAAAT-ATA--TAAT-AG
39617213 AATATAAATATATAATAG
1 AATATAAATATATAATAG
39617231 AATATAAAATAATATAATA
1 AATAT-AAAT-ATATAATA
39617250 TAGTAAAAAA
Statistics
Matches: 61, Mismatches: 4, Indels: 16
0.75 0.05 0.20
Matches are distributed among these distances:
15 9 0.15
16 12 0.20
18 7 0.11
19 9 0.15
20 8 0.13
21 7 0.11
22 7 0.11
23 2 0.03
ACGTcount: A:0.64, C:0.01, G:0.02, T:0.33
Consensus pattern (18 bp):
AATATAAATATATAATAG
Found at i:39617252 original size:22 final size:23
Alignment explanation
Indices: 39617155--39617255 Score: 73
Period size: 23 Copynumber: 4.1 Consensus size: 23
39617145 AATATAAAAA
*
39617155 TAATAATATAAATAATAATATATATAA
1 TAATAATA-AAAT-A-AATA-ATATAG
*
39617182 AAATAATACATAATAAATAATAT-G
1 TAATAATA-A-AATAAATAATATAG
*
39617206 TAATAATAATATAAATATATAATAG
1 TAATAATAAAATAAATA-AT-ATAG
39617231 -AAT-ATAAAATAATATAATATAG
1 TAATAATAAAATAA-ATAATATAG
39617253 TAA
1 TAA
39617256 AAAACATGAA
Statistics
Matches: 62, Mismatches: 6, Indels: 16
0.74 0.07 0.19
Matches are distributed among these distances:
22 11 0.18
23 15 0.24
24 15 0.24
25 5 0.08
26 4 0.06
27 9 0.15
28 3 0.05
ACGTcount: A:0.62, C:0.01, G:0.03, T:0.34
Consensus pattern (23 bp):
TAATAATAAAATAAATAATATAG
Found at i:39619328 original size:176 final size:174
Alignment explanation
Indices: 39618918--39619367 Score: 560
Period size: 176 Copynumber: 2.5 Consensus size: 174
39618908 CGTAAATACA
* * * *
39618918 TGAAAGCCAAATCTGCTGTGTCTTCGATTTGCTCCTTGTGAACATAAGGATGCCAAATCATCTTG
1 TGAAAGTCAAATCTGCTATGTCTTCGATTTGCTTCTTGTGAACATAA-GAAGCCAAATCATCTTG
* ** * * * *
39618983 GATCTGCTTCAGTA-AAATCATTTGAAGGTTAGATCTGCTATGTATCTGCTCTTCATTGAAATGG
65 GATCTACTTCAGTATAAA-CACCTGAAGGTTAGACCTGCTATGTACCTGCTCTCCATCGAAATGG
* * *
39619047 AGATGCGAGATCTGTTATCTTGGATCTGCTTTGGTGTGAGAACATC
129 AGATGCCAGATCTGTTATCTTGGATCTGCTTTGATGTGAAAACATC
* * * *
39619093 CGAAAGTCAAATCTGCTATGTCTTCGATTTGTTTCTTGTAAACACAAGAATGCCCAAATCATCTT
1 TGAAAGTCAAATCTGCTATGTCTTCGATTTGCTTCTTGTGAACATAAGAA-G-CCAAATCATCTT
* *
39619158 GGATCTACTTCAATATAAACACCTGAAGGTTAGACCTGCTATGTACCTGCTCTCCGTCGAAATGG
64 GGATCTACTTCAGTATAAACACCTGAAGGTTAGACCTGCTATGTACCTGCTCTCCATCGAAATGG
39619223 AGATGCCAGATCTGTTATCTTGGATCTGCTTTGATGTGAAAACATC
129 AGATGCCAGATCTGTTATCTTGGATCTGCTTTGATGTGAAAACATC
* * * *
39619269 TGAAAGTCAGATCTGCTATGTCTTCAATTTGCTTCTCGTCGAAGATAGAGAAGCCAAATCTTGTT
1 TGAAAGTCAAATCTGCTATGTCTTCGATTTGCTTCTTGT-GAACATA-AGAAGCCAAATC-----
* *
39619334 ATCTTGGATCTACTTCAGTGTAAACACGTGAAGG
59 ATCTTGGATCTACTTCAGTATAAACACCTGAAGG
39619368 CCAGATCTGT
Statistics
Matches: 234, Mismatches: 31, Indels: 14
0.84 0.11 0.05
Matches are distributed among these distances:
174 2 0.01
175 41 0.18
176 148 0.63
177 8 0.03
178 4 0.02
181 31 0.13
ACGTcount: A:0.27, C:0.19, G:0.20, T:0.33
Consensus pattern (174 bp):
TGAAAGTCAAATCTGCTATGTCTTCGATTTGCTTCTTGTGAACATAAGAAGCCAAATCATCTTGG
ATCTACTTCAGTATAAACACCTGAAGGTTAGACCTGCTATGTACCTGCTCTCCATCGAAATGGAG
ATGCCAGATCTGTTATCTTGGATCTGCTTTGATGTGAAAACATC
Found at i:39619373 original size:93 final size:93
Alignment explanation
Indices: 39619212--39619382 Score: 213
Period size: 93 Copynumber: 1.8 Consensus size: 93
39619202 ACCTGCTCTC
* * * * * *
39619212 CGTCGAAATGGAGATGCCAGATCTGTTATCTTGGATCTGCTTTGATGTGAAAACATCTGAAAGTC
1 CGTCGAAATAGAGAAGCCAAATCTGTTATCTTGGATCTACTTTCATGTGAAAACATCTGAAAGCC
39619277 AGATCTGCTATGTCTTCAATTTGCTTCT
66 AGATCTGCTATGTCTTCAATTTGCTTCT
* *
39619305 CGTCGAAGATAGAGAAGCCAAATCTTGTTATCTTGGATCTAC-TTCA-GTGTAAACA-CGTGAAG
1 CGTCGAA-ATAGAGAAGCCAAATC-TGTTATCTTGGATCTACTTTCATGTGAAAACATC-TGAAA
*
39619367 GCCAGATCTGTTATGT
63 GCCAGATCTGCTATGT
39619383 TTTGGTCTGT
Statistics
Matches: 66, Mismatches: 9, Indels: 6
0.81 0.11 0.07
Matches are distributed among these distances:
92 1 0.02
93 33 0.50
94 16 0.24
95 16 0.24
ACGTcount: A:0.27, C:0.18, G:0.22, T:0.33
Consensus pattern (93 bp):
CGTCGAAATAGAGAAGCCAAATCTGTTATCTTGGATCTACTTTCATGTGAAAACATCTGAAAGCC
AGATCTGCTATGTCTTCAATTTGCTTCT
Found at i:39630434 original size:40 final size:40
Alignment explanation
Indices: 39630376--39630589 Score: 256
Period size: 40 Copynumber: 5.4 Consensus size: 40
39630366 TGATAACCGA
** * * *
39630376 GCTAAGTCCCGAAGGCATTTGCGCTAGTGACTAGT-TCTGG
1 GCTAAGTCCCGAAGGCATTTGTACGAGTTACTA-TATCCGG
* *
39630416 GCCAAGTCCCGAAGGCATTTGTACGAGTTACTATATCCGA
1 GCTAAGTCCCGAAGGCATTTGTACGAGTTACTATATCCGG
39630456 GCTAAGTCCCGAAGGCATTTGTACGAGTTACTATATCCGG
1 GCTAAGTCCCGAAGGCATTTGTACGAGTTACTATATCCGG
* *
39630496 GCTAAGTCCCGAAGGCATTGGTGCGAGTTACTATATCCGG
1 GCTAAGTCCCGAAGGCATTTGTACGAGTTACTATATCCGG
* *
39630536 GCTATGTCCCGAAGGCATTCG-AGCGAG-TAGCTATATCC-G
1 GCTAAGTCCCGAAGGCATTTGTA-CGAGTTA-CTATATCCGG
* *
39630575 GTTAAATCCCGAAGG
1 GCTAAGTCCCGAAGG
39630590 TACTTGGCTT
Statistics
Matches: 154, Mismatches: 17, Indels: 7
0.87 0.10 0.04
Matches are distributed among these distances:
39 16 0.10
40 138 0.90
ACGTcount: A:0.24, C:0.23, G:0.27, T:0.25
Consensus pattern (40 bp):
GCTAAGTCCCGAAGGCATTTGTACGAGTTACTATATCCGG
Found at i:39641911 original size:24 final size:24
Alignment explanation
Indices: 39641884--39641932 Score: 64
Period size: 24 Copynumber: 2.0 Consensus size: 24
39641874 AAATAAGATA
*
39641884 AGTAATTAATT-AGGTAATAATAAT
1 AGTAA-TAATTGAGGTAATAAAAAT
*
39641908 AGTAATAATTGAGTTAATAAAAAT
1 AGTAATAATTGAGGTAATAAAAAT
39641932 A
1 A
39641933 TATTAGTAAG
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
23 5 0.23
24 17 0.77
ACGTcount: A:0.53, C:0.00, G:0.12, T:0.35
Consensus pattern (24 bp):
AGTAATAATTGAGGTAATAAAAAT
Found at i:39651981 original size:12 final size:12
Alignment explanation
Indices: 39651966--39652001 Score: 58
Period size: 12 Copynumber: 3.2 Consensus size: 12
39651956 TTAGAAAACT
39651966 AATAAGAAGATA
1 AATAAGAAGATA
39651978 AATAA-AA-ATA
1 AATAAGAAGATA
39651988 AATAAGAAGATA
1 AATAAGAAGATA
39652000 AA
1 AA
39652002 GTGATTACAA
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
10 8 0.36
11 4 0.18
12 10 0.45
ACGTcount: A:0.72, C:0.00, G:0.11, T:0.17
Consensus pattern (12 bp):
AATAAGAAGATA
Found at i:39653799 original size:30 final size:30
Alignment explanation
Indices: 39653743--39653801 Score: 75
Period size: 30 Copynumber: 2.0 Consensus size: 30
39653733 AATCGAAAAC
* * *
39653743 AAATAAAATAAATAAGAGTAATAAATAAAT
1 AAATAAAATAAATAAAAATAAGAAATAAAT
39653773 AAATAAAAT-AATAAAAAATAAGAAATAAA
1 AAATAAAATAAAT-AAAAATAAGAAATAAA
39653802 CCAAACAATG
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
29 3 0.12
30 22 0.88
ACGTcount: A:0.75, C:0.00, G:0.05, T:0.20
Consensus pattern (30 bp):
AAATAAAATAAATAAAAATAAGAAATAAAT
Found at i:39659952 original size:22 final size:23
Alignment explanation
Indices: 39659926--39659981 Score: 80
Period size: 22 Copynumber: 2.5 Consensus size: 23
39659916 TATATTTAGG
* *
39659926 GAGAAAATACAATGGTTTA-GAA
1 GAGAAAATACAATAGTTAAGGAA
39659948 GAGAAAATACAATAGTTAAGGAA
1 GAGAAAATACAATAGTTAAGGAA
39659971 -AGAAAATACAA
1 GAGAAAATACAA
39659982 GACTATAAGA
Statistics
Matches: 31, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
22 28 0.90
23 3 0.10
ACGTcount: A:0.57, C:0.05, G:0.20, T:0.18
Consensus pattern (23 bp):
GAGAAAATACAATAGTTAAGGAA
Found at i:39659993 original size:22 final size:21
Alignment explanation
Indices: 39659927--39659993 Score: 55
Period size: 22 Copynumber: 3.0 Consensus size: 21
39659917 ATATTTAGGG
* *
39659927 AGAAAATACAATG-GTTTAGAA
1 AGAAAATACAA-GACTTAAGAA
* *
39659948 GAGAAAATACAATAGTTAAGGAA
1 -AGAAAATACAAGACTTAA-GAA
39659971 AGAAAATACAAGACTATAAGAA
1 AGAAAATACAAGACT-TAAGAA
39659993 A
1 A
39659994 TCTAAATCAT
Statistics
Matches: 38, Mismatches: 4, Indels: 6
0.79 0.08 0.12
Matches are distributed among these distances:
22 32 0.84
23 6 0.16
ACGTcount: A:0.58, C:0.06, G:0.18, T:0.18
Consensus pattern (21 bp):
AGAAAATACAAGACTTAAGAA
Found at i:39662663 original size:12 final size:12
Alignment explanation
Indices: 39662646--39662692 Score: 53
Period size: 12 Copynumber: 4.0 Consensus size: 12
39662636 TAAAGGCATC
39662646 AGAACTCCATAT
1 AGAACTCCATAT
*
39662658 AGAACT-CA-AA
1 AGAACTCCATAT
*
39662668 AGGAACTCCAAAT
1 A-GAACTCCATAT
39662681 AGAACTCCATAT
1 AGAACTCCATAT
39662693 TTAATCCCCA
Statistics
Matches: 29, Mismatches: 3, Indels: 6
0.76 0.08 0.16
Matches are distributed among these distances:
10 2 0.07
11 7 0.24
12 18 0.62
13 2 0.07
ACGTcount: A:0.47, C:0.23, G:0.11, T:0.19
Consensus pattern (12 bp):
AGAACTCCATAT
Found at i:39664182 original size:43 final size:42
Alignment explanation
Indices: 39663990--39664172 Score: 204
Period size: 43 Copynumber: 4.3 Consensus size: 42
39663980 TTATGTGGAA
* * * * *
39663990 AAACACCGTTATAGAACATGACCATTAGTAGCACTTTTCCCAC
1 AAACGCCGCTATAGAACATGACCTTTAGCAGC-GTTTTCCCAC
* *
39664033 AAACGCCGATATAGAACATGACCTTTAACAGCGCTTTTCCCAC
1 AAACGCCGCTATAGAACATGACCTTTAGCAGCG-TTTTCCCAC
* * * *
39664076 AAACGCCGCTATAGAGCATAACCTTTAGCAGCGCTTTCCCTAA
1 AAACGCCGCTATAGAACATGACCTTTAGCAGCGTTTTCCC-AC
* * *
39664119 AAATGCCACTATAGAACATGACCTTTAGCGGCGTTTTCCCCAC
1 AAACGCCGCTATAGAACATGACCTTTAGCAGCGTTTT-CCCAC
39664162 AAACGCCGCTA
1 AAACGCCGCTA
39664173 AAGGTCATGA
Statistics
Matches: 116, Mismatches: 21, Indels: 6
0.81 0.15 0.04
Matches are distributed among these distances:
42 6 0.05
43 107 0.92
44 3 0.03
ACGTcount: A:0.32, C:0.30, G:0.15, T:0.23
Consensus pattern (42 bp):
AAACGCCGCTATAGAACATGACCTTTAGCAGCGTTTTCCCAC
Found at i:39665633 original size:33 final size:33
Alignment explanation
Indices: 39665577--39665651 Score: 82
Period size: 33 Copynumber: 2.3 Consensus size: 33
39665567 CAAGTTGTCG
*
39665577 AATAAGACCATAGCCGGGCTATGGCA-ATCGAAT
1 AATAAGACCATAACCGGGCTATGGCATAT-GAAT
** *
39665610 AATAAGACCATAATTGGGTTATGGCATATGAAT
1 AATAAGACCATAACCGGGCTATGGCATATGAAT
*
39665643 GA-AAGACCA
1 AATAAGACCA
39665652 CGGCAGGACC
Statistics
Matches: 36, Mismatches: 5, Indels: 3
0.82 0.11 0.07
Matches are distributed among these distances:
32 7 0.19
33 27 0.75
34 2 0.06
ACGTcount: A:0.40, C:0.16, G:0.23, T:0.21
Consensus pattern (33 bp):
AATAAGACCATAACCGGGCTATGGCATATGAAT
Found at i:39669642 original size:35 final size:35
Alignment explanation
Indices: 39669596--39669667 Score: 135
Period size: 35 Copynumber: 2.1 Consensus size: 35
39669586 TAAAATAAAT
*
39669596 ATGATATCATCCTATTTCCCATTTCTTCTTTATTG
1 ATGATATCATCCTATTTCCCATTTCTTATTTATTG
39669631 ATGATATCATCCTATTTCCCATTTCTTATTTATTG
1 ATGATATCATCCTATTTCCCATTTCTTATTTATTG
39669666 AT
1 AT
39669668 TTTTTAGCCA
Statistics
Matches: 36, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
35 36 1.00
ACGTcount: A:0.22, C:0.21, G:0.06, T:0.51
Consensus pattern (35 bp):
ATGATATCATCCTATTTCCCATTTCTTATTTATTG
Found at i:39670627 original size:46 final size:45
Alignment explanation
Indices: 39670574--39670692 Score: 143
Period size: 46 Copynumber: 2.6 Consensus size: 45
39670564 GAGTGCTAGA
* *
39670574 GTAAGACATGTCTGGGACATGCATCAGCCT-CGAGACGTAAGTTAGT
1 GTAAGACATGTCTGGGACATGCATCAGACTACGAGACGT--GTCAGT
*
39670620 GTAAGACATGTCTGGGACATGCATC-GACTACGAGATGTGTCAGT
1 GTAAGACATGTCTGGGACATGCATCAGACTACGAGACGTGTCAGT
* *
39670664 GTAAGACCATTTTTGGGACATGGCATCAG
1 GTAAGA-CATGTCTGGGACAT-GCATCAG
39670693 GACAGATATG
Statistics
Matches: 64, Mismatches: 5, Indels: 7
0.84 0.07 0.09
Matches are distributed among these distances:
44 11 0.17
45 15 0.23
46 37 0.58
47 1 0.02
ACGTcount: A:0.28, C:0.18, G:0.29, T:0.25
Consensus pattern (45 bp):
GTAAGACATGTCTGGGACATGCATCAGACTACGAGACGTGTCAGT
Found at i:39685146 original size:23 final size:23
Alignment explanation
Indices: 39685083--39685160 Score: 79
Period size: 23 Copynumber: 3.3 Consensus size: 23
39685073 GGACTCACAG
39685083 CAGCTCG-AATGAGCTTACCGATATAT
1 CAGCTCGTAA-GAGCTTACCG-T-T-T
* *
39685109 TAGCTCGTAAGAGCTTACTGTTT
1 CAGCTCGTAAGAGCTTACCGTTT
39685132 CAGCTCGTCAA-AGCTTACCGTTT
1 CAGCTCGT-AAGAGCTTACCGTTT
39685155 CAGCTC
1 CAGCTC
39685161 AATAGAGCTT
Statistics
Matches: 46, Mismatches: 4, Indels: 7
0.81 0.07 0.12
Matches are distributed among these distances:
23 25 0.54
24 3 0.07
25 1 0.02
26 15 0.33
27 2 0.04
ACGTcount: A:0.24, C:0.26, G:0.19, T:0.31
Consensus pattern (23 bp):
CAGCTCGTAAGAGCTTACCGTTT
Found at i:39685169 original size:23 final size:23
Alignment explanation
Indices: 39685118--39685171 Score: 65
Period size: 23 Copynumber: 2.3 Consensus size: 23
39685108 TTAGCTCGTA
* *
39685118 AGAGCTTACTGTTTCAGCTCGTC
1 AGAGCTTACCGTTTCAGCTCATC
*
39685141 AAAGCTTACCGTTTCAGCTCAAT-
1 AGAGCTTACCGTTTCAGCTC-ATC
39685164 AGAGCTTA
1 AGAGCTTA
39685172 GTGTCCATCA
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
23 25 0.96
24 1 0.04
ACGTcount: A:0.26, C:0.24, G:0.19, T:0.31
Consensus pattern (23 bp):
AGAGCTTACCGTTTCAGCTCATC
Found at i:39685336 original size:20 final size:20
Alignment explanation
Indices: 39685311--39685351 Score: 73
Period size: 20 Copynumber: 2.0 Consensus size: 20
39685301 CAATGAGCAT
39685311 AAATATTGTTTATATAGATG
1 AAATATTGTTTATATAGATG
*
39685331 AAATATTGTTTATATGGATG
1 AAATATTGTTTATATAGATG
39685351 A
1 A
39685352 GCCATTGTTT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.39, C:0.00, G:0.17, T:0.44
Consensus pattern (20 bp):
AAATATTGTTTATATAGATG
Found at i:39685358 original size:20 final size:20
Alignment explanation
Indices: 39685315--39685361 Score: 58
Period size: 20 Copynumber: 2.4 Consensus size: 20
39685305 GAGCATAAAT
*
39685315 ATTGTTTATATAGATGAAAT
1 ATTGTTTATATAGATGAAAC
* **
39685335 ATTGTTTATATGGATGAGCC
1 ATTGTTTATATAGATGAAAC
39685355 ATTGTTT
1 ATTGTTT
39685362 GCAAATGGAT
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.30, C:0.04, G:0.19, T:0.47
Consensus pattern (20 bp):
ATTGTTTATATAGATGAAAC
Found at i:39686315 original size:43 final size:44
Alignment explanation
Indices: 39686235--39686319 Score: 136
Period size: 43 Copynumber: 1.9 Consensus size: 44
39686225 ATGAAGTCAG
39686235 TATGCTCCACACGATCTCACACACGAGCGTGTGACCGACCATCAA
1 TATGCTCCACACGATCT-ACACACGAGCGTGTGACCGACCATCAA
* *
39686280 TATGCTCCACACGGTCT-CACACGGGCGTGTGACCGACCAT
1 TATGCTCCACACGATCTACACACGAGCGTGTGACCGACCAT
39686320 GTGGTACAAG
Statistics
Matches: 38, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
43 22 0.58
45 16 0.42
ACGTcount: A:0.25, C:0.35, G:0.21, T:0.19
Consensus pattern (44 bp):
TATGCTCCACACGATCTACACACGAGCGTGTGACCGACCATCAA
Found at i:39687919 original size:23 final size:23
Alignment explanation
Indices: 39687888--39687959 Score: 58
Period size: 23 Copynumber: 3.2 Consensus size: 23
39687878 CATTCGAACT
* * * *
39687888 TAAAACACATCATTCAAATATCA
1 TAAATCACAACATTCAAACACCA
*
39687911 TAAATCACAACTTTCAAACACCA
1 TAAATCACAACATTCAAACACCA
* * *
39687934 TAAATTACAGCATT-TAACACC-
1 TAAATCACAACATTCAAACACCA
39687955 TAAAT
1 TAAAT
39687960 TTTCAGCTTA
Statistics
Matches: 40, Mismatches: 9, Indels: 2
0.78 0.18 0.04
Matches are distributed among these distances:
21 5 0.12
22 6 0.15
23 29 0.73
ACGTcount: A:0.49, C:0.24, G:0.01, T:0.26
Consensus pattern (23 bp):
TAAATCACAACATTCAAACACCA
Found at i:39688860 original size:21 final size:21
Alignment explanation
Indices: 39688823--39688862 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
39688813 ATTTCAGCAT
*
39688823 TTGAACATCATCTATTTACCA
1 TTGAACATCATCAATTTACCA
39688844 TTGAGACATCAT-AATTTAC
1 TTGA-ACATCATCAATTTAC
39688863 AATATGTAGC
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
21 10 0.59
22 7 0.41
ACGTcount: A:0.35, C:0.20, G:0.07, T:0.38
Consensus pattern (21 bp):
TTGAACATCATCAATTTACCA
Found at i:39690919 original size:22 final size:23
Alignment explanation
Indices: 39690893--39690943 Score: 72
Period size: 22 Copynumber: 2.3 Consensus size: 23
39690883 CTCTCCTATT
*
39690893 AATATAAATA-ATATATTAGATG
1 AATATAAATAGATATATCAGATG
39690915 AATAT-AATAGATATATCAGATG
1 AATATAAATAGATATATCAGATG
39690937 AAT-TAAA
1 AATATAAA
39690944 AAATTTAAAT
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
21 5 0.19
22 21 0.81
ACGTcount: A:0.55, C:0.02, G:0.10, T:0.33
Consensus pattern (23 bp):
AATATAAATAGATATATCAGATG
Found at i:39695016 original size:20 final size:20
Alignment explanation
Indices: 39694993--39695073 Score: 72
Period size: 21 Copynumber: 4.0 Consensus size: 20
39694983 GAATCAAGTT
39694993 AAACAATAAAGAATCGATTC
1 AAACAATAAAGAATCGATTC
* * *
39695013 AAACAATAATGAATCAAGTTT
1 AAACAATAAAGAATCGA-TTC
* * *
39695034 AAACAATGAACAATTGATTC
1 AAACAATAAAGAATCGATTC
* *
39695054 AAAGAAGCAAAGAATCGATT
1 AAACAA-TAAAGAATCGATT
39695074 TAAAACAACA
Statistics
Matches: 45, Mismatches: 14, Indels: 3
0.73 0.23 0.05
Matches are distributed among these distances:
20 22 0.49
21 23 0.51
ACGTcount: A:0.53, C:0.12, G:0.12, T:0.22
Consensus pattern (20 bp):
AAACAATAAAGAATCGATTC
Found at i:39695076 original size:41 final size:41
Alignment explanation
Indices: 39694991--39695122 Score: 113
Period size: 45 Copynumber: 3.1 Consensus size: 41
39694981 TTGAATCAAG
* * * * * *
39694991 TTAAACAATAAAGAATCGATTCAAACAA-TAATGAATCAAGT
1 TTAAACAATAAACAATTGATTCAAAGAAGCAAAGAATCGA-T
*
39695032 TTAAACAATGAACAATTGATTCAAAGAAGCAAAGAATCGAT
1 TTAAACAATAAACAATTGATTCAAAGAAGCAAAGAATCGAT
* * * *
39695073 TTAAAACAACAATCATGAATTGATTCAAAGAAGCAAATAATTGAT
1 TT-AAACAATAA--A-CAATTGATTCAAAGAAGCAAAGAATCGAT
39695118 TTAAA
1 TTAAA
39695123 ACAACAATAA
Statistics
Matches: 74, Mismatches: 12, Indels: 7
0.80 0.13 0.08
Matches are distributed among these distances:
41 27 0.36
42 15 0.20
44 4 0.05
45 28 0.38
ACGTcount: A:0.52, C:0.11, G:0.11, T:0.25
Consensus pattern (41 bp):
TTAAACAATAAACAATTGATTCAAAGAAGCAAAGAATCGAT
Found at i:39695097 original size:45 final size:45
Alignment explanation
Indices: 39695045--39695213 Score: 202
Period size: 45 Copynumber: 3.8 Consensus size: 45
39695035 AACAATGAAC
* *
39695045 AATTGATTCAAAGAAGCAAAGAATCGATTTAAAACAACAATCATG
1 AATTGATTCAAAGAAGCAAATAATCGATTTAAAACAACAATAATG
*
39695090 AATTGATTCAAAGAAGCAAATAATTGATTTAAAACAACAATAATG
1 AATTGATTCAAAGAAGCAAATAATCGATTTAAAACAACAATAATG
** * *
39695135 AATCAATTCAAAAAAGCAAATAATCAATTTAAAACAACAA-AA--
1 AATTGATTCAAAGAAGCAAATAATCGATTTAAAACAACAATAATG
* * **
39695177 AATCT-ATTCAAAGAAGAAAAAAATTAATTTAAAACAA
1 AAT-TGATTCAAAGAAGCAAATAATCGATTTAAAACAA
39695214 GAAATTTAGT
Statistics
Matches: 110, Mismatches: 13, Indels: 5
0.86 0.10 0.04
Matches are distributed among these distances:
42 31 0.28
44 2 0.02
45 77 0.70
ACGTcount: A:0.57, C:0.11, G:0.08, T:0.23
Consensus pattern (45 bp):
AATTGATTCAAAGAAGCAAATAATCGATTTAAAACAACAATAATG
Found at i:39695116 original size:21 final size:21
Alignment explanation
Indices: 39695045--39695118 Score: 69
Period size: 21 Copynumber: 3.4 Consensus size: 21
39695035 AACAATGAAC
*
39695045 AATTGATTCAAAGAAGCAAAG
1 AATTGATTCAAAGAAGCAAAT
* * *
39695066 AATCGATTTAAA-ACAACAATCAT
1 AATTGATTCAAAGA-AGCAA--AT
39695089 GAATTGATTCAAAGAAGCAAAT
1 -AATTGATTCAAAGAAGCAAAT
39695111 AATTGATT
1 AATTGATT
39695119 TAAAACAACA
Statistics
Matches: 41, Mismatches: 7, Indels: 10
0.71 0.12 0.17
Matches are distributed among these distances:
20 1 0.02
21 22 0.54
22 2 0.05
23 1 0.02
24 14 0.34
25 1 0.02
ACGTcount: A:0.50, C:0.11, G:0.14, T:0.26
Consensus pattern (21 bp):
AATTGATTCAAAGAAGCAAAT
Found at i:39695154 original size:90 final size:87
Alignment explanation
Indices: 39695050--39695213 Score: 222
Period size: 87 Copynumber: 1.9 Consensus size: 87
39695040 TGAACAATTG
* * * * *
39695050 ATTCAAAGAAGCAAAGAATCGATTTAAAACAACAATCATGAAT-TGATTCAAAGAAGCAAATAAT
1 ATTCAAAAAAGCAAAGAATCAATTTAAAACAACAA--A-AAATCT-ATTCAAAGAAGAAAAAAAT
*
39695114 TGATTTAAAACAACAATAATGAATCA
62 TAATTTAAAACAACAATAATGAATCA
*
39695140 ATTCAAAAAAGCAAATAATCAATTTAAAACAACAAAAAATCTATTCAAAGAAGAAAAAAATTAAT
1 ATTCAAAAAAGCAAAGAATCAATTTAAAACAACAAAAAATCTATTCAAAGAAGAAAAAAATTAAT
39695205 TTAAAACAA
66 TTAAAACAA
39695214 GAAATTTAGT
Statistics
Matches: 66, Mismatches: 7, Indels: 5
0.85 0.09 0.06
Matches are distributed among these distances:
87 32 0.48
88 2 0.03
90 32 0.48
ACGTcount: A:0.58, C:0.12, G:0.08, T:0.23
Consensus pattern (87 bp):
ATTCAAAAAAGCAAAGAATCAATTTAAAACAACAAAAAATCTATTCAAAGAAGAAAAAAATTAAT
TTAAAACAACAATAATGAATCA
Found at i:39695159 original size:21 final size:21
Alignment explanation
Indices: 39695106--39695188 Score: 69
Period size: 21 Copynumber: 3.8 Consensus size: 21
39695096 TTCAAAGAAG
** *
39695106 CAAATAATTGATTTAAAACAA
1 CAAATAATCAATTCAAAACAA
39695127 CAATAATGAATCAATTCAAAA-AA
1 C-A-AAT-AATCAATTCAAAACAA
*
39695150 GCAAATAATCAATTTAAAACAA
1 -CAAATAATCAATTCAAAACAA
* *
39695172 CAAAAAATCTATTCAAA
1 CAAATAATCAATTCAAA
39695189 GAAGAAAAAA
Statistics
Matches: 50, Mismatches: 7, Indels: 10
0.75 0.10 0.15
Matches are distributed among these distances:
21 27 0.54
22 6 0.12
23 6 0.12
24 11 0.22
ACGTcount: A:0.59, C:0.13, G:0.04, T:0.24
Consensus pattern (21 bp):
CAAATAATCAATTCAAAACAA
Found at i:39696260 original size:50 final size:50
Alignment explanation
Indices: 39696175--39696271 Score: 122
Period size: 50 Copynumber: 1.9 Consensus size: 50
39696165 GCGGATGTAA
* * * *
39696175 AGCCTTCAGGCTTGGAACTTGGTGCCCAGAAATGTTTTTGGAGGGATGAT
1 AGCCTTCAGGCTAGGAACTTGCTGCCAAGAAATGTTCTTGGAGGGATGAT
* ** *
39696225 AGCCTTCAGGCTAGGCACTTGCTGCCAAGGCATGTTCTTGGATGGAT
1 AGCCTTCAGGCTAGGAACTTGCTGCCAAGAAATGTTCTTGGAGGGAT
39696272 TAGCTCGTTG
Statistics
Matches: 39, Mismatches: 8, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
50 39 1.00
ACGTcount: A:0.21, C:0.20, G:0.31, T:0.29
Consensus pattern (50 bp):
AGCCTTCAGGCTAGGAACTTGCTGCCAAGAAATGTTCTTGGAGGGATGAT
Found at i:39697897 original size:24 final size:27
Alignment explanation
Indices: 39697850--39697901 Score: 74
Period size: 24 Copynumber: 2.0 Consensus size: 27
39697840 AACCGAGGTA
39697850 AGTTCGTATGTTAAATAAGCTTTAATAT
1 AGTTCGTATGTTAAAT-AGCTTTAATAT
39697878 AGTT-GTAT-TTAAAT-GCTTTAATAT
1 AGTTCGTATGTTAAATAGCTTTAATAT
39697902 TGCATGAACT
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
24 10 0.42
26 6 0.25
27 4 0.17
28 4 0.17
ACGTcount: A:0.35, C:0.06, G:0.13, T:0.46
Consensus pattern (27 bp):
AGTTCGTATGTTAAATAGCTTTAATAT
Found at i:39701888 original size:15 final size:14
Alignment explanation
Indices: 39701864--39701894 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 14
39701854 TGTTTTTGTC
39701864 TTCTTTTTTTCTTT
1 TTCTTTTTTTCTTT
39701878 TTCTATTTTTTCTTT
1 TTCT-TTTTTTCTTT
39701893 TT
1 TT
39701895 TCCTTTATTT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 4 0.25
15 12 0.75
ACGTcount: A:0.03, C:0.13, G:0.00, T:0.84
Consensus pattern (14 bp):
TTCTTTTTTTCTTT
Found at i:39724245 original size:112 final size:112
Alignment explanation
Indices: 39724032--39724247 Score: 389
Period size: 112 Copynumber: 1.9 Consensus size: 112
39724022 CGTAAATTTC
* *
39724032 TCTAAACTCAAACTTGGAAAGTGATAAGGTTTTGTTTCCAAAACAGCATTAGGGAAACTAGTTGA
1 TCTAAACTCAAACTTGGAAAGTGATAAGGTTTTGTTTCCAAAACAACATTAGAGAAACTAGTTGA
* *
39724097 TAATGTGTCACTATGATTGCATATTTCAAGTTAAAAAAAAAACCCGA
66 TAATGTGTCACAATGACTGCATATTTCAAGTTAAAAAAAAAACCCGA
39724144 TCTAAACTCAAACTTGGAAAGTGATAAGGTTTTGTTTCCAAAACAACATTAGAGAAACTAGTTGA
1 TCTAAACTCAAACTTGGAAAGTGATAAGGTTTTGTTTCCAAAACAACATTAGAGAAACTAGTTGA
39724209 TAATGTGTC-CAATGACTGCATATTTCAAGTTAAAAAAAA
66 TAATGTGTCACAATGACTGCATATTTCAAGTTAAAAAAAA
39724248 CCCCCAGAAA
Statistics
Matches: 100, Mismatches: 4, Indels: 1
0.95 0.04 0.01
Matches are distributed among these distances:
111 28 0.28
112 72 0.72
ACGTcount: A:0.40, C:0.14, G:0.16, T:0.30
Consensus pattern (112 bp):
TCTAAACTCAAACTTGGAAAGTGATAAGGTTTTGTTTCCAAAACAACATTAGAGAAACTAGTTGA
TAATGTGTCACAATGACTGCATATTTCAAGTTAAAAAAAAAACCCGA
Found at i:39725052 original size:81 final size:81
Alignment explanation
Indices: 39724917--39725072 Score: 285
Period size: 81 Copynumber: 1.9 Consensus size: 81
39724907 TGACAGGGTC
*
39724917 GGATCACATTATCAAGTAGGTTACTATCCTTGTATATACATACATCATCTAATTATATAGTTTTA
1 GGATCACATTATCAAGTAGGTTACTATCCTTGTATATACATACATCATCTAATTATATAATTTTA
*
39724982 TTCATTTCAGCATGTT
66 TCCATTTCAGCATGTT
*
39724998 GGATCACATTATCAAGTAGGTTCCTATCCTTGTATATACATACATCATCTAATTATATAATTTTA
1 GGATCACATTATCAAGTAGGTTACTATCCTTGTATATACATACATCATCTAATTATATAATTTTA
39725063 TCCATTTCAG
66 TCCATTTCAG
39725073 TATGCTATTG
Statistics
Matches: 72, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
81 72 1.00
ACGTcount: A:0.31, C:0.17, G:0.10, T:0.41
Consensus pattern (81 bp):
GGATCACATTATCAAGTAGGTTACTATCCTTGTATATACATACATCATCTAATTATATAATTTTA
TCCATTTCAGCATGTT
Found at i:39729730 original size:28 final size:29
Alignment explanation
Indices: 39729696--39729750 Score: 85
Period size: 29 Copynumber: 1.9 Consensus size: 29
39729686 TAATAGAAAT
39729696 ACTGATA-TCATGGCCCGAAGCCAAATCA
1 ACTGATATTCATGGCCCGAAGCCAAATCA
* *
39729724 ACTGATATTTATGGTCCGAAGCCAAAT
1 ACTGATATTCATGGCCCGAAGCCAAAT
39729751 TGGTATAACT
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
28 7 0.29
29 17 0.71
ACGTcount: A:0.35, C:0.24, G:0.18, T:0.24
Consensus pattern (29 bp):
ACTGATATTCATGGCCCGAAGCCAAATCA
Found at i:39732282 original size:26 final size:26
Alignment explanation
Indices: 39732224--39732276 Score: 97
Period size: 26 Copynumber: 2.0 Consensus size: 26
39732214 GGGCTTGGCT
39732224 CTAACATCACTCATAAGAAGAAGTTA
1 CTAACATCACTCATAAGAAGAAGTTA
*
39732250 CTAACATCACTCATGAGAAGAAGTTA
1 CTAACATCACTCATAAGAAGAAGTTA
39732276 C
1 C
39732277 AGACATATGA
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
26 26 1.00
ACGTcount: A:0.43, C:0.21, G:0.13, T:0.23
Consensus pattern (26 bp):
CTAACATCACTCATAAGAAGAAGTTA
Found at i:39737587 original size:40 final size:40
Alignment explanation
Indices: 39737525--39737742 Score: 316
Period size: 40 Copynumber: 5.5 Consensus size: 40
39737515 AAGCCAAGTA
* * * *
39737525 CCTTCGGGATTTA-ACCGGATATAGCTACTCGCTCGAATG
1 CCTTCGGGACTTAGCCCGGATATAGCTACTCGCACAAATG
* *
39737564 CCTTCGGGACATAGCCCGGATATAG-TAACTCGCACCAATG
1 CCTTCGGGACTTAGCCCGGATATAGCT-ACTCGCACAAATG
* *
39737604 CCTTCGGGACTTAGCCCGGATATAGCAACTCACACAAATG
1 CCTTCGGGACTTAGCCCGGATATAGCTACTCGCACAAATG
*
39737644 CCTTCGGGACTTAGCCCGGATATAGCAACTCGCACAAATG
1 CCTTCGGGACTTAGCCCGGATATAGCTACTCGCACAAATG
39737684 CCTTCGGGACTTAGCCCGGATATAG-TAACTCGCACAAATG
1 CCTTCGGGACTTAGCCCGGATATAGCT-ACTCGCACAAATG
39737724 CCTTCGGGACTTAGCCCGG
1 CCTTCGGGACTTAGCCCGG
39737743 TTATCATCCA
Statistics
Matches: 164, Mismatches: 11, Indels: 7
0.90 0.06 0.04
Matches are distributed among these distances:
39 12 0.07
40 152 0.93
ACGTcount: A:0.26, C:0.29, G:0.23, T:0.22
Consensus pattern (40 bp):
CCTTCGGGACTTAGCCCGGATATAGCTACTCGCACAAATG
Found at i:39739915 original size:34 final size:34
Alignment explanation
Indices: 39739872--39739937 Score: 123
Period size: 34 Copynumber: 1.9 Consensus size: 34
39739862 TTTCGCATAC
39739872 TTAGTGCCATCTCAAATAACCGAGCCTAAGTCAG
1 TTAGTGCCATCTCAAATAACCGAGCCTAAGTCAG
*
39739906 TTAGTGCCATCTCAAATAACCGATCCTAAGTC
1 TTAGTGCCATCTCAAATAACCGAGCCTAAGTC
39739938 GGTATCGCAC
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
34 31 1.00
ACGTcount: A:0.32, C:0.27, G:0.15, T:0.26
Consensus pattern (34 bp):
TTAGTGCCATCTCAAATAACCGAGCCTAAGTCAG
Found at i:39740011 original size:30 final size:29
Alignment explanation
Indices: 39739972--39740029 Score: 98
Period size: 30 Copynumber: 2.0 Consensus size: 29
39739962 ATAGCCGAAG
*
39739972 CTAGTTAAATCGCACACTTAGTGCCAAAT
1 CTAGTTAAATCACACACTTAGTGCCAAAT
39740001 CTAGTTTAAATCACACACTTAGTGCCAAA
1 CTAG-TTAAATCACACACTTAGTGCCAAA
39740030 ACTTCCGTTT
Statistics
Matches: 27, Mismatches: 1, Indels: 1
0.93 0.03 0.03
Matches are distributed among these distances:
29 4 0.15
30 23 0.85
ACGTcount: A:0.36, C:0.24, G:0.12, T:0.28
Consensus pattern (29 bp):
CTAGTTAAATCACACACTTAGTGCCAAAT
Found at i:39751125 original size:30 final size:29
Alignment explanation
Indices: 39751091--39751149 Score: 82
Period size: 29 Copynumber: 2.0 Consensus size: 29
39751081 GAATTAGATT
* *
39751091 AAATCAAAATTTCTTGTATAAAATTGCACA
1 AAATCAAAATTT-ATATATAAAATTGCACA
*
39751121 AAATCAAAGTTTATATATAAAATTGCACA
1 AAATCAAAATTTATATATAAAATTGCACA
39751150 TTAAACAAAA
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
29 15 0.58
30 11 0.42
ACGTcount: A:0.49, C:0.12, G:0.07, T:0.32
Consensus pattern (29 bp):
AAATCAAAATTTATATATAAAATTGCACA
Found at i:39751911 original size:27 final size:24
Alignment explanation
Indices: 39751855--39751912 Score: 71
Period size: 25 Copynumber: 2.2 Consensus size: 24
39751845 AAAATATAAA
*
39751855 AAAATATAAAATATTTTTATAATT
1 AAAATTTAAAATATTTTTATAATT
39751879 ATAAATTTAAAATATATTTTATACACTT
1 A-AAATTTAAAATAT-TTTTATA-A-TT
39751907 AAAATT
1 AAAATT
39751913 GAAAGTGCAT
Statistics
Matches: 29, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
24 1 0.03
25 12 0.41
26 7 0.24
27 6 0.21
28 3 0.10
ACGTcount: A:0.52, C:0.03, G:0.00, T:0.45
Consensus pattern (24 bp):
AAAATTTAAAATATTTTTATAATT
Found at i:39757170 original size:49 final size:49
Alignment explanation
Indices: 39757079--39757204 Score: 146
Period size: 49 Copynumber: 2.6 Consensus size: 49
39757069 ATCAAAGTTG
* * * *
39757079 ATGCCATGTCCCAGACAGGTCTTACGCTAACTTTTATATATCGAG-GCCG
1 ATGCCATGTCCCAGACAGGTCTTACACTAACTCTCATATATCG-GTGCCA
** * * *
39757128 ATGCTGTGTCCCAGACAGGTCTTACACTAGCTCTCATCTATCGGTGTCA
1 ATGCCATGTCCCAGACAGGTCTTACACTAACTCTCATATATCGGTGCCA
*
39757177 ATGCCATGTCCCAGATAGGTCTTACACT
1 ATGCCATGTCCCAGACAGGTCTTACACT
39757205 GACACACAAC
Statistics
Matches: 64, Mismatches: 12, Indels: 2
0.82 0.15 0.03
Matches are distributed among these distances:
48 1 0.02
49 63 0.98
ACGTcount: A:0.23, C:0.28, G:0.20, T:0.29
Consensus pattern (49 bp):
ATGCCATGTCCCAGACAGGTCTTACACTAACTCTCATATATCGGTGCCA
Found at i:39765873 original size:42 final size:42
Alignment explanation
Indices: 39765834--39766021 Score: 268
Period size: 42 Copynumber: 4.4 Consensus size: 42
39765824 GGCACACGGT
39765834 CGTGTCTCTGCCCGTGTGTCACACACGGCCTAGACACACGCC
1 CGTGTCTCTGCCCGTGTGTCACACACGGCCTAGACACACGCC
* * ** * **
39765876 CGTGTCTTTACCTATGCGTCACACACGGCCTAGACACATACC
1 CGTGTCTCTGCCCGTGTGTCACACACGGCCTAGACACACGCC
* *
39765918 CGTGTCTCTGCCCGTGTGTCACACACAGCCTAGACACATGCC
1 CGTGTCTCTGCCCGTGTGTCACACACGGCCTAGACACACGCC
*
39765960 CATGTCTCTGCCCGTGTGTCACACACGGCCTAGACACACGCC
1 CGTGTCTCTGCCCGTGTGTCACACACGGCCTAGACACACGCC
39766002 CGTGTGTCTCTGCCCGTGTG
1 C--GTGTCTCTGCCCGTGTG
39766022 GACAATATAA
Statistics
Matches: 126, Mismatches: 18, Indels: 2
0.86 0.12 0.01
Matches are distributed among these distances:
42 110 0.87
44 16 0.13
ACGTcount: A:0.18, C:0.38, G:0.22, T:0.22
Consensus pattern (42 bp):
CGTGTCTCTGCCCGTGTGTCACACACGGCCTAGACACACGCC
Found at i:39766813 original size:47 final size:48
Alignment explanation
Indices: 39766744--39766910 Score: 144
Period size: 49 Copynumber: 3.4 Consensus size: 48
39766734 TGATGCCGAT
** *
39766744 GCCATGTCCCGGACATGCTCTTACACTGGCTCATC-CATCAAGTCGAG
1 GCCATGTCCCAAACATGGTCTTACACTGGCTCATCACATCAAGTCGAG
* * * * *
39766791 GCCATGTCCCAAACATGGTCTTACACTGACT-ATCGAAATCGAGGCTGAC
1 GCCATGTCCCAAACATGGTCTTACACTGGCTCATC-ACATCAAGTC-GAG
* * *
39766840 GCCATGTCTCAAACATGGTCTTACACTAGCTC-TCACAT-ATCCGTGACGAG
1 GCCATGTCCCAAACATGGTCTTACACTGGCTCATCACATCA--AGT--CGAG
*
39766890 GCCATGTCCCAGACATGGTCT
1 GCCATGTCCCAAACATGGTCT
39766911 CGACGAGGCC
Statistics
Matches: 94, Mismatches: 18, Indels: 13
0.75 0.14 0.10
Matches are distributed among these distances:
46 3 0.03
47 27 0.29
48 9 0.10
49 33 0.35
50 21 0.22
51 1 0.01
ACGTcount: A:0.25, C:0.31, G:0.20, T:0.24
Consensus pattern (48 bp):
GCCATGTCCCAAACATGGTCTTACACTGGCTCATCACATCAAGTCGAG
Found at i:39766916 original size:28 final size:28
Alignment explanation
Indices: 39766884--39766938 Score: 110
Period size: 28 Copynumber: 2.0 Consensus size: 28
39766874 ACATATCCGT
39766884 GACGAGGCCATGTCCCAGACATGGTCTC
1 GACGAGGCCATGTCCCAGACATGGTCTC
39766912 GACGAGGCCATGTCCCAGACATGGTCT
1 GACGAGGCCATGTCCCAGACATGGTCT
39766939 TACACTGAAA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 27 1.00
ACGTcount: A:0.22, C:0.31, G:0.29, T:0.18
Consensus pattern (28 bp):
GACGAGGCCATGTCCCAGACATGGTCTC
Found at i:39766990 original size:48 final size:45
Alignment explanation
Indices: 39766919--39767036 Score: 150
Period size: 48 Copynumber: 2.6 Consensus size: 45
39766909 CTCGACGAGG
*
39766919 CCATGTCCCAGACATGGTCTTACACTGAAACCTCTATACGT-GCCGAT
1 CCATGTCCCAGACATGGTCTTACACTGAAACATCT-T--GTAGCCGAT
*
39766966 CCCATGTCCCAGACATGGTCTTACACTGACACATCTTGTAGCCGAT
1 -CCATGTCCCAGACATGGTCTTACACTGAAACATCTTGTAGCCGAT
* *
39767012 GCATGTCCAAGACAT-GTCTTACACT
1 CCATGTCCCAGACATGGTCTTACACT
39767037 AGCTTACATC
Statistics
Matches: 65, Mismatches: 4, Indels: 6
0.87 0.05 0.08
Matches are distributed among these distances:
44 10 0.15
45 15 0.23
46 6 0.09
47 1 0.02
48 33 0.51
ACGTcount: A:0.25, C:0.31, G:0.17, T:0.26
Consensus pattern (45 bp):
CCATGTCCCAGACATGGTCTTACACTGAAACATCTTGTAGCCGAT
Found at i:39776684 original size:96 final size:94
Alignment explanation
Indices: 39776489--39776755 Score: 247
Period size: 96 Copynumber: 2.8 Consensus size: 94
39776479 TGATGCCAAT
* * *
39776489 GCCATGTCCCAGACATGGT-TTACACTAGCTCATCCATCA-A--GTCGATACCATGTCCCAGACA
1 GCCATGTCCCAGACATGGTCTTACACTAGCTC-T-CATAATATGGCCGAT-GCATGTCCCAGACA
* * * ** ** *
39776550 TGGTCTTACATTGGCTATTGAAATCGAGGCCGAC
63 T-GTCTTACACTAGCTCTTG-TCTTAATGCCGAC
* * * *
39776584 GCCATGTCTCAGACATGGTCTTACACTAGCTCTTACAT-ATCTGTGCCGATGCTTGTCCCAGGCA
1 GCCATGTCCCAGACATGGTCTTACACTAGCTC-T-CATAATATG-GCCGATGCATGTCCCAGACA
* *
39776648 TGTTTTACACTAGCTCTTGTCTTAATGCCGAT
63 TGTCTTACACTAGCTCTTGTCTTAATGCCGAC
* * *
39776680 GCCATGTCCCAGACATGGTCTTACACTGGGTCTCATAATATGGCCGATGCATGTTCCAGACATGT
1 GCCATGTCCCAGACATGGTCTTACACTAGCTCTCATAATATGGCCGATGCATGTCCCAGACATGT
39776745 CTTACACTAGC
66 CTTACACTAGC
39776756 ACACAAAAAA
Statistics
Matches: 140, Mismatches: 26, Indels: 13
0.78 0.15 0.07
Matches are distributed among these distances:
94 33 0.24
95 24 0.17
96 52 0.37
97 14 0.10
98 12 0.09
99 5 0.04
ACGTcount: A:0.23, C:0.28, G:0.20, T:0.29
Consensus pattern (94 bp):
GCCATGTCCCAGACATGGTCTTACACTAGCTCTCATAATATGGCCGATGCATGTCCCAGACATGT
CTTACACTAGCTCTTGTCTTAATGCCGAC
Found at i:39782129 original size:6 final size:6
Alignment explanation
Indices: 39782110--39782148 Score: 60
Period size: 6 Copynumber: 6.3 Consensus size: 6
39782100 TGTTAATGAA
*
39782110 TTCATT TCTCATT TTCATT TTCATT TTCATT TCCATT TT
1 TTCATT T-TCATT TTCATT TTCATT TTCATT TTCATT TT
39782149 GAGAAAACCA
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
6 24 0.80
7 6 0.20
ACGTcount: A:0.15, C:0.21, G:0.00, T:0.64
Consensus pattern (6 bp):
TTCATT
Found at i:39782195 original size:57 final size:59
Alignment explanation
Indices: 39782131--39782251 Score: 158
Period size: 58 Copynumber: 2.1 Consensus size: 59
39782121 TTTTCATTTT
*
39782131 CATTTTCATTTCCATTTT-GAGAAAACCACATTAATTT-TCAAATG-ATTCCATTTTCTC
1 CATTTTCATTTCCATTTTGGAGAAAACCACAATAATTTCTCAAATGTATTCCA-TTTCTC
* * * * *
39782188 TATTTTCATTTTCATTTTGGAGAAAACCATAATAATTTCTTAAATGTTTTCCATTTCTC
1 CATTTTCATTTCCATTTTGGAGAAAACCACAATAATTTCTCAAATGTATTCCATTTCTC
39782247 CATTT
1 CATTT
39782252 CTATTCATTC
Statistics
Matches: 54, Mismatches: 7, Indels: 4
0.83 0.11 0.06
Matches are distributed among these distances:
57 16 0.30
58 17 0.31
59 16 0.30
60 5 0.09
ACGTcount: A:0.29, C:0.18, G:0.06, T:0.47
Consensus pattern (59 bp):
CATTTTCATTTCCATTTTGGAGAAAACCACAATAATTTCTCAAATGTATTCCATTTCTC
Found at i:39785021 original size:27 final size:27
Alignment explanation
Indices: 39784991--39785044 Score: 90
Period size: 27 Copynumber: 2.0 Consensus size: 27
39784981 GCATGTAGAG
39784991 AACCAAGCATTGCAGAACTCTCTCTCT
1 AACCAAGCATTGCAGAACTCTCTCTCT
* *
39785018 AACCAAGTATTGTAGAACTCTCTCTCT
1 AACCAAGCATTGCAGAACTCTCTCTCT
39785045 TTCTCTTTGT
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
27 25 1.00
ACGTcount: A:0.30, C:0.30, G:0.11, T:0.30
Consensus pattern (27 bp):
AACCAAGCATTGCAGAACTCTCTCTCT
Found at i:39788124 original size:24 final size:24
Alignment explanation
Indices: 39788092--39788140 Score: 98
Period size: 24 Copynumber: 2.0 Consensus size: 24
39788082 AAAGTAATAG
39788092 CCAGTCCCCATTCCCATGGTCGGC
1 CCAGTCCCCATTCCCATGGTCGGC
39788116 CCAGTCCCCATTCCCATGGTCGGC
1 CCAGTCCCCATTCCCATGGTCGGC
39788140 C
1 C
39788141 ATGCTTGGTG
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.12, C:0.47, G:0.20, T:0.20
Consensus pattern (24 bp):
CCAGTCCCCATTCCCATGGTCGGC
Found at i:39790978 original size:58 final size:58
Alignment explanation
Indices: 39790877--39791015 Score: 140
Period size: 58 Copynumber: 2.4 Consensus size: 58
39790867 ATATCACATT
* * * * * *
39790877 TCAGGATTACCAGTTCAGGATAAATCCTTTATGTAACGTATGCTCAGAAAAGGCTCA-A
1 TCAGGATTACCAGTCCAGGCTAAACCCTATATGTAACATATGCTC-GAAAAGGATCATA
* * * * *
39790935 TTAGGATTACCAGTCCAGGCTAAACCCTA-ATTGTAGCATATGCTCGAGAGGGATTATA
1 TCAGGATTACCAGTCCAGGCTAAACCCTATA-TGTAACATATGCTCGAAAAGGATCATA
39790993 TCAGGATTACCA-TCCAGGCTAAA
1 TCAGGATTACCAGTCCAGGCTAAA
39791016 TCCTTTCTAT
Statistics
Matches: 67, Mismatches: 12, Indels: 5
0.80 0.14 0.06
Matches are distributed among these distances:
57 19 0.28
58 48 0.72
ACGTcount: A:0.33, C:0.20, G:0.20, T:0.27
Consensus pattern (58 bp):
TCAGGATTACCAGTCCAGGCTAAACCCTATATGTAACATATGCTCGAAAAGGATCATA
Found at i:39802582 original size:39 final size:39
Alignment explanation
Indices: 39802522--39802605 Score: 123
Period size: 39 Copynumber: 2.2 Consensus size: 39
39802512 ACGATAGGGG
39802522 CCTTCACGTGTCTAACACCACACACTAAACTTTTTTCAT
1 CCTTCACGTGTCTAACACCACACACTAAACTTTTTTCAT
* * * *
39802561 CCTTCACGTGTCTACCGCCACACATTACACTTTTTTCAT
1 CCTTCACGTGTCTAACACCACACACTAAACTTTTTTCAT
*
39802600 TCTTCA
1 CCTTCA
39802606 TTGTATTAAC
Statistics
Matches: 40, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
39 40 1.00
ACGTcount: A:0.24, C:0.35, G:0.06, T:0.36
Consensus pattern (39 bp):
CCTTCACGTGTCTAACACCACACACTAAACTTTTTTCAT
Found at i:39802754 original size:15 final size:15
Alignment explanation
Indices: 39802734--39802765 Score: 64
Period size: 15 Copynumber: 2.1 Consensus size: 15
39802724 CAAATTTGAA
39802734 AACCTCGTGAAATCG
1 AACCTCGTGAAATCG
39802749 AACCTCGTGAAATCG
1 AACCTCGTGAAATCG
39802764 AA
1 AA
39802766 TCGTCTTCCA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.38, C:0.25, G:0.19, T:0.19
Consensus pattern (15 bp):
AACCTCGTGAAATCG
Found at i:39811409 original size:26 final size:26
Alignment explanation
Indices: 39811380--39811487 Score: 180
Period size: 26 Copynumber: 4.2 Consensus size: 26
39811370 TGGTACAAAT
*
39811380 TGATAATGGGTTAGGTAAATGTTCCA
1 TGATAATGGGTTAGGTAAATATTCCA
*
39811406 TGATAATGGATTAGGTAAATATTCCA
1 TGATAATGGGTTAGGTAAATATTCCA
39811432 TGATAATGGGTTAGGTAAATATTCCA
1 TGATAATGGGTTAGGTAAATATTCCA
* *
39811458 TGATAATGGTTTAGGTAAATGTTCCA
1 TGATAATGGGTTAGGTAAATATTCCA
39811484 TGAT
1 TGAT
39811488 GGGCATTTCA
Statistics
Matches: 77, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
26 77 1.00
ACGTcount: A:0.33, C:0.07, G:0.23, T:0.36
Consensus pattern (26 bp):
TGATAATGGGTTAGGTAAATATTCCA
Found at i:39816600 original size:13 final size:13
Alignment explanation
Indices: 39816584--39816616 Score: 57
Period size: 13 Copynumber: 2.5 Consensus size: 13
39816574 TCTTACACAG
39816584 GCGTGTCACACGA
1 GCGTGTCACACGA
*
39816597 GCGTGTCACACGG
1 GCGTGTCACACGA
39816610 GCGTGTC
1 GCGTGTC
39816617 CCTGTCAAGC
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
13 19 1.00
ACGTcount: A:0.15, C:0.30, G:0.36, T:0.18
Consensus pattern (13 bp):
GCGTGTCACACGA
Found at i:39821177 original size:15 final size:15
Alignment explanation
Indices: 39821157--39821186 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
39821147 CAACACTTGT
39821157 GCCGAAACCACAAAA
1 GCCGAAACCACAAAA
*
39821172 GCCGAAACCTCAAAA
1 GCCGAAACCACAAAA
39821187 AATACATTAG
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.50, C:0.33, G:0.13, T:0.03
Consensus pattern (15 bp):
GCCGAAACCACAAAA
Found at i:39822787 original size:98 final size:98
Alignment explanation
Indices: 39822618--39822812 Score: 390
Period size: 98 Copynumber: 2.0 Consensus size: 98
39822608 CTATTACAGC
39822618 AAGGTCGCTCATTCCCAAGCCAAGTACCTTCGGGATTTAACCGGATATAGCTACTCGCTCGAATG
1 AAGGTCGCTCATTCCCAAGCCAAGTACCTTCGGGATTTAACCGGATATAGCTACTCGCTCGAATG
39822683 CCTTCGGGACATAGCCCGGATATAGTAATTCGT
66 CCTTCGGGACATAGCCCGGATATAGTAATTCGT
39822716 AAGGTCGCTCATTCCCAAGCCAAGTACCTTCGGGATTTAACCGGATATAGCTACTCGCTCGAATG
1 AAGGTCGCTCATTCCCAAGCCAAGTACCTTCGGGATTTAACCGGATATAGCTACTCGCTCGAATG
39822781 CCTTCGGGACATAGCCCGGATATAGTAATTCG
66 CCTTCGGGACATAGCCCGGATATAGTAATTCG
39822813 CACCAATGCC
Statistics
Matches: 97, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
98 97 1.00
ACGTcount: A:0.26, C:0.27, G:0.23, T:0.25
Consensus pattern (98 bp):
AAGGTCGCTCATTCCCAAGCCAAGTACCTTCGGGATTTAACCGGATATAGCTACTCGCTCGAATG
CCTTCGGGACATAGCCCGGATATAGTAATTCGT
Found at i:39822804 original size:40 final size:40
Alignment explanation
Indices: 39822742--39822959 Score: 298
Period size: 40 Copynumber: 5.5 Consensus size: 40
39822732 AAGCCAAGTA
* * * *
39822742 CCTTCGGGATTTA-ACCGGATATAGCT-ACTCGCTCGAATG
1 CCTTCGGGACTTAGCCCGGATATAG-TAACTCGCACAAATG
* * *
39822781 CCTTCGGGACATAGCCCGGATATAGTAATTCGCACCAATG
1 CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATG
*
39822821 CCTTCGGGACTTAGCCCGGATATAGTAACTCGTACAAATG
1 CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATG
39822861 CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATG
1 CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATG
* * *
39822901 CCTTCGGGACTTAGCCCGGA-ACTAGTCACTAGCGCAAATG
1 CCTTCGGGACTTAGCCCGGATA-TAGTAACTCGCACAAATG
39822941 CCTTCGGGACTTAGCCCGG
1 CCTTCGGGACTTAGCCCGG
39822960 TTATCATCCA
Statistics
Matches: 162, Mismatches: 14, Indels: 5
0.90 0.08 0.03
Matches are distributed among these distances:
39 13 0.08
40 149 0.92
ACGTcount: A:0.25, C:0.28, G:0.24, T:0.23
Consensus pattern (40 bp):
CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATG
Found at i:39826441 original size:43 final size:43
Alignment explanation
Indices: 39826394--39826509 Score: 187
Period size: 43 Copynumber: 2.7 Consensus size: 43
39826384 TAAAGGTCAT
39826394 GCTTTCCCCACAAACGCCGCTAAAAGTCATGACCTATAGCGAC
1 GCTTTCCCCACAAACGCCGCTAAAAGTCATGACCTATAGCGAC
* * * *
39826437 GCTTTCCCCACAAATGCCGCTATAAGTCATGACCTTTAGCGGC
1 GCTTTCCCCACAAACGCCGCTAAAAGTCATGACCTATAGCGAC
*
39826480 GCTTTCCCCAAAAACGCCGCTAAAAGTCAT
1 GCTTTCCCCACAAACGCCGCTAAAAGTCAT
39826510 TAAATTTTTA
Statistics
Matches: 66, Mismatches: 7, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
43 66 1.00
ACGTcount: A:0.28, C:0.34, G:0.16, T:0.22
Consensus pattern (43 bp):
GCTTTCCCCACAAACGCCGCTAAAAGTCATGACCTATAGCGAC
Found at i:39830741 original size:38 final size:40
Alignment explanation
Indices: 39830691--39830773 Score: 125
Period size: 41 Copynumber: 2.1 Consensus size: 40
39830681 AAATAATGGC
* *
39830691 TTTTTGTGGCG-T-TCTTAAAAACGCCACTGTAGCTTAAT
1 TTTTTGCGGCGTTATCTTAAAAACGCCACTATAGCTTAAT
39830729 TTTTTGCGGCGTTTATCTTAAAAACGCCACTATAGCTTAAT
1 TTTTTGCGGCG-TTATCTTAAAAACGCCACTATAGCTTAAT
39830770 TTTT
1 TTTT
39830774 ATGGCGTTTT
Statistics
Matches: 40, Mismatches: 2, Indels: 3
0.89 0.04 0.07
Matches are distributed among these distances:
38 10 0.25
40 1 0.03
41 29 0.73
ACGTcount: A:0.24, C:0.18, G:0.16, T:0.42
Consensus pattern (40 bp):
TTTTTGCGGCGTTATCTTAAAAACGCCACTATAGCTTAAT
Found at i:39830968 original size:6 final size:7
Alignment explanation
Indices: 39830946--39830976 Score: 53
Period size: 7 Copynumber: 4.4 Consensus size: 7
39830936 ATTTAAGTTC
*
39830946 TTTATTT
1 TTTAATT
39830953 TTTAATT
1 TTTAATT
39830960 TTTAATT
1 TTTAATT
39830967 TTTAATT
1 TTTAATT
39830974 TTT
1 TTT
39830977 TGAATATTTT
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
7 23 1.00
ACGTcount: A:0.23, C:0.00, G:0.00, T:0.77
Consensus pattern (7 bp):
TTTAATT
Found at i:39831001 original size:8 final size:8
Alignment explanation
Indices: 39830949--39831001 Score: 54
Period size: 8 Copynumber: 6.4 Consensus size: 8
39830939 TAAGTTCTTT
*
39830949 ATTTTTTA
1 ATTTTTAA
39830957 ATTTTT-A
1 ATTTTTAA
39830964 ATTTTTAA
1 ATTTTTAA
*
39830972 TTTTTTGAA
1 ATTTTT-AA
39830981 TATTTTTATA
1 -ATTTTTA-A
39830991 ATTTTTAA
1 ATTTTTAA
39830999 ATT
1 ATT
39831002 ATCATATAAA
Statistics
Matches: 39, Mismatches: 2, Indels: 8
0.80 0.04 0.16
Matches are distributed among these distances:
7 7 0.18
8 16 0.41
9 10 0.26
10 6 0.15
ACGTcount: A:0.30, C:0.00, G:0.02, T:0.68
Consensus pattern (8 bp):
ATTTTTAA
Found at i:39831704 original size:21 final size:22
Alignment explanation
Indices: 39831680--39831724 Score: 65
Period size: 21 Copynumber: 2.1 Consensus size: 22
39831670 ATTAACTTTG
* *
39831680 AACCCTTAACTC-TTAACCCCT
1 AACCCTTAAATCATAAACCCCT
39831701 AACCCTTAAATCATAAACCCCT
1 AACCCTTAAATCATAAACCCCT
39831723 AA
1 AA
39831725 AGCTTAAACC
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
21 11 0.52
22 10 0.48
ACGTcount: A:0.38, C:0.38, G:0.00, T:0.24
Consensus pattern (22 bp):
AACCCTTAAATCATAAACCCCT
Found at i:39831780 original size:15 final size:15
Alignment explanation
Indices: 39831749--39831790 Score: 50
Period size: 15 Copynumber: 2.9 Consensus size: 15
39831739 CCCTTAAACT
* *
39831749 ATAAACCATAAA-AC
1 ATAATCCATAAACCC
*
39831763 ATAATCCCTAAACCC
1 ATAATCCATAAACCC
39831778 ATAATCCATAAAC
1 ATAATCCATAAAC
39831791 TTTAAAATAG
Statistics
Matches: 23, Mismatches: 4, Indels: 1
0.82 0.14 0.04
Matches are distributed among these distances:
14 10 0.43
15 13 0.57
ACGTcount: A:0.52, C:0.29, G:0.00, T:0.19
Consensus pattern (15 bp):
ATAATCCATAAACCC
Found at i:39832369 original size:40 final size:40
Alignment explanation
Indices: 39832319--39832414 Score: 120
Period size: 40 Copynumber: 2.4 Consensus size: 40
39832309 GGCTTTTTCT
* * *
39832319 AAAAAGCGCCGCTAATGCTTGATCTTCAGCAGCGTTTTGC
1 AAAAAACGCCGCTAATGCTCGATCTTCAGCAGCATTTTGC
* * *
39832359 AAAAAACGCCGCTAATGCTCGATCTTTAGCGGCATTTTTC
1 AAAAAACGCCGCTAATGCTCGATCTTCAGCAGCATTTTGC
*
39832399 ATTAAAACGCCGCTAA
1 A-AAAAACGCCGCTAA
39832415 AAACGCCGCT
Statistics
Matches: 48, Mismatches: 7, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
40 35 0.73
41 13 0.27
ACGTcount: A:0.29, C:0.25, G:0.19, T:0.27
Consensus pattern (40 bp):
AAAAAACGCCGCTAATGCTCGATCTTCAGCAGCATTTTGC
Found at i:39832419 original size:12 final size:12
Alignment explanation
Indices: 39832402--39832430 Score: 58
Period size: 12 Copynumber: 2.4 Consensus size: 12
39832392 ATTTTTCATT
39832402 AAAACGCCGCTA
1 AAAACGCCGCTA
39832414 AAAACGCCGCTA
1 AAAACGCCGCTA
39832426 AAAAC
1 AAAAC
39832431 CTGTTTTGGT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 17 1.00
ACGTcount: A:0.48, C:0.31, G:0.14, T:0.07
Consensus pattern (12 bp):
AAAACGCCGCTA
Found at i:39843336 original size:43 final size:43
Alignment explanation
Indices: 39843286--39843478 Score: 237
Period size: 43 Copynumber: 4.5 Consensus size: 43
39843276 TATCCTATAT
* * *
39843286 ATGGTCTTACATGTTATCA-AATATCGATGCCACTGTCCCAGAC
1 ATGGTCTTACATGTAATCACAATA-CAATGCCAATGTCCCAGAC
* * *** * * *
39843329 AAGGTCTTATACAAAATCA-TATAGCGATGCCAATGTCTCAGAC
1 ATGGTCTTACATGTAATCACAATA-CAATGCCAATGTCCCAGAC
39843372 ATGGTCTTACATGTAATCACAATACAATGCCAATGTCCCAGAC
1 ATGGTCTTACATGTAATCACAATACAATGCCAATGTCCCAGAC
* *
39843415 ATGGTCTTACACGTAATCACAACACAATGCCAATGTCCCAGAC
1 ATGGTCTTACATGTAATCACAATACAATGCCAATGTCCCAGAC
39843458 ATGGTCTTACATGTAATCACA
1 ATGGTCTTACATGTAATCACA
39843479 TCTAGGTAAT
Statistics
Matches: 128, Mismatches: 21, Indels: 2
0.85 0.14 0.01
Matches are distributed among these distances:
43 125 0.98
44 3 0.02
ACGTcount: A:0.34, C:0.25, G:0.15, T:0.26
Consensus pattern (43 bp):
ATGGTCTTACATGTAATCACAATACAATGCCAATGTCCCAGAC
Found at i:39845544 original size:38 final size:38
Alignment explanation
Indices: 39845495--39845572 Score: 156
Period size: 38 Copynumber: 2.1 Consensus size: 38
39845485 GAATAAGAGA
39845495 AAACAATGGAAGGAATAGTGCAAGGCCATCACTCTCAG
1 AAACAATGGAAGGAATAGTGCAAGGCCATCACTCTCAG
39845533 AAACAATGGAAGGAATAGTGCAAGGCCATCACTCTCAG
1 AAACAATGGAAGGAATAGTGCAAGGCCATCACTCTCAG
39845571 AA
1 AA
39845573 GTGGGACACA
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
38 40 1.00
ACGTcount: A:0.41, C:0.21, G:0.23, T:0.15
Consensus pattern (38 bp):
AAACAATGGAAGGAATAGTGCAAGGCCATCACTCTCAG
Found at i:39846641 original size:36 final size:36
Alignment explanation
Indices: 39846594--39846685 Score: 139
Period size: 36 Copynumber: 2.6 Consensus size: 36
39846584 GAATCTTTGG
* * * *
39846594 ATTTAAAATATGCATATTTGAAACCTTTACTGTAAT
1 ATTTAAAATATGCATATTTGAAACATTTACCGCAAC
*
39846630 ATTTAAAATATGCATATTTGAAACATTTGCCGCAAC
1 ATTTAAAATATGCATATTTGAAACATTTACCGCAAC
39846666 ATTTAAAATATGCATATTTG
1 ATTTAAAATATGCATATTTG
39846686 GGAGACAACA
Statistics
Matches: 51, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
36 51 1.00
ACGTcount: A:0.39, C:0.12, G:0.10, T:0.39
Consensus pattern (36 bp):
ATTTAAAATATGCATATTTGAAACATTTACCGCAAC
Found at i:39857875 original size:14 final size:13
Alignment explanation
Indices: 39857855--39857886 Score: 55
Period size: 14 Copynumber: 2.4 Consensus size: 13
39857845 AATATTTGAC
39857855 TTGTTCTTAATTA
1 TTGTTCTTAATTA
39857868 TGTGTTCTTAATTA
1 T-TGTTCTTAATTA
39857882 TTGTT
1 TTGTT
39857887 TTCATATTCC
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
13 5 0.28
14 13 0.72
ACGTcount: A:0.19, C:0.06, G:0.12, T:0.62
Consensus pattern (13 bp):
TTGTTCTTAATTA
Found at i:39861710 original size:55 final size:55
Alignment explanation
Indices: 39861583--39861714 Score: 156
Period size: 55 Copynumber: 2.4 Consensus size: 55
39861573 CCAAACCAAT
* * * * *
39861583 ACGGGCGTGCGACACGTCCGTGTTCTGAAACCGTGGGCAAACCTATCAATTTAGC
1 ACGGGTGTGTGACACGCCCGTGTTCTAAAACCGTAGGCAAACCTATCAATTTAGC
*** * * *
39861638 ACGGGTGTGTCTTACGCCCGTGTTTTAAAACCGTAGGCTAACCTGTCAATTTAGC
1 ACGGGTGTGTGACACGCCCGTGTTCTAAAACCGTAGGCAAACCTATCAATTTAGC
*
39861693 ACGGGTGTTTGACACGCCCGTG
1 ACGGGTGTGTGACACGCCCGTG
39861715 CCTAGCCCTC
Statistics
Matches: 62, Mismatches: 15, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
55 62 1.00
ACGTcount: A:0.21, C:0.26, G:0.27, T:0.26
Consensus pattern (55 bp):
ACGGGTGTGTGACACGCCCGTGTTCTAAAACCGTAGGCAAACCTATCAATTTAGC
Found at i:39865252 original size:46 final size:47
Alignment explanation
Indices: 39865202--39865377 Score: 193
Period size: 46 Copynumber: 3.8 Consensus size: 47
39865192 TGGTTGAGCA
*
39865202 TCCGAACTTGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAA-TG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACTG
* * * *
39865248 TCCGAACTCGTTGAGTTGAGTCCGAGTTC-GTGA--AATG-TAACTAGG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACT--G
39865293 CATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACT-
1 --TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACTG
* * * *
39865341 CCCGAGCTCATTGAGTTGAGTTCGAGTTCACTTATGG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGG
39865378 GCGGGTTACA
Statistics
Matches: 108, Mismatches: 13, Indels: 18
0.78 0.09 0.13
Matches are distributed among these distances:
42 2 0.02
43 4 0.04
45 3 0.03
46 61 0.56
47 29 0.27
48 2 0.02
50 3 0.03
51 4 0.04
ACGTcount: A:0.22, C:0.20, G:0.27, T:0.31
Consensus pattern (47 bp):
TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACTG
Found at i:39865358 original size:93 final size:93
Alignment explanation
Indices: 39865199--39865369 Score: 281
Period size: 93 Copynumber: 1.8 Consensus size: 93
39865189 GGATGGTTGA
* * *
39865199 GCATCCGAACTTGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATGTCCGAACTCGTTGAGT
1 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATGCCCGAACTCATTGAGT
39865264 TGAGTCCGAGTTCGTGAAATGTAACTAG
66 TGAGTCCGAGTTCGTGAAATGTAACTAG
*
39865292 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACT-CCCGAGCTCATTGAG
1 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAA-TGCCCGAACTCATTGAG
*
39865356 TTGAGTTCGAGTTC
65 TTGAGTCCGAGTTC
39865370 ACTTATGGGC
Statistics
Matches: 72, Mismatches: 5, Indels: 2
0.91 0.06 0.03
Matches are distributed among these distances:
93 71 0.99
94 1 0.01
ACGTcount: A:0.22, C:0.20, G:0.27, T:0.30
Consensus pattern (93 bp):
GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATGCCCGAACTCATTGAGT
TGAGTCCGAGTTCGTGAAATGTAACTAG
Found at i:39880495 original size:34 final size:34
Alignment explanation
Indices: 39880424--39880495 Score: 81
Period size: 34 Copynumber: 2.1 Consensus size: 34
39880414 GAGTACCGAA
** * * *
39880424 TGAAGAGCGGCGTGTGTTTCATATGTGGTTATTT
1 TGAAGAGCGGCGCATGTTTCAGATGCGGTTATCT
* *
39880458 TGAAGAGCGGTGCATGTTTCAGATGCGGTTCTCT
1 TGAAGAGCGGCGCATGTTTCAGATGCGGTTATCT
39880492 TGAA
1 TGAA
39880496 CACTTCCTTA
Statistics
Matches: 31, Mismatches: 7, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
34 31 1.00
ACGTcount: A:0.19, C:0.12, G:0.32, T:0.36
Consensus pattern (34 bp):
TGAAGAGCGGCGCATGTTTCAGATGCGGTTATCT
Found at i:39881033 original size:32 final size:32
Alignment explanation
Indices: 39880991--39881054 Score: 110
Period size: 32 Copynumber: 2.0 Consensus size: 32
39880981 TTGGTTAGCC
* *
39880991 CTACATGATGTAATTGTGAATTGTGGTAGTAA
1 CTACACGATGTAATTGTAAATTGTGGTAGTAA
39881023 CTACACGATGTAATTGTAAATTGTGGTAGTAA
1 CTACACGATGTAATTGTAAATTGTGGTAGTAA
39881055 GTATATTGAA
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
32 30 1.00
ACGTcount: A:0.33, C:0.08, G:0.23, T:0.36
Consensus pattern (32 bp):
CTACACGATGTAATTGTAAATTGTGGTAGTAA
Found at i:39882985 original size:29 final size:28
Alignment explanation
Indices: 39882938--39883065 Score: 148
Period size: 28 Copynumber: 4.5 Consensus size: 28
39882928 CATGAGATTG
* * **
39882938 GCACTAAGTATGCGGGTTTAAATTGCATA
1 GCACTAAGTGTGCGAGTTT-AATTATATA
* *
39882967 GCACTAAGTGTGCAAGTTTGATTATATA
1 GCACTAAGTGTGCGAGTTTAATTATATA
* *
39882995 GCACTAAGTGTGCGAGTTTGATTATGTAA
1 GCACTAAGTGTGCGAGTTTAATTATAT-A
*
39883024 GCACTAAGTGTGCGAGTTTGATTATATA
1 GCACTAAGTGTGCGAGTTTAATTATATA
*
39883052 ACACTAAGTGTGCG
1 GCACTAAGTGTGCG
39883066 GACTTACTAT
Statistics
Matches: 88, Mismatches: 10, Indels: 3
0.87 0.10 0.03
Matches are distributed among these distances:
28 45 0.51
29 43 0.49
ACGTcount: A:0.30, C:0.12, G:0.25, T:0.33
Consensus pattern (28 bp):
GCACTAAGTGTGCGAGTTTAATTATATA
Found at i:39883004 original size:28 final size:28
Alignment explanation
Indices: 39882964--39883065 Score: 168
Period size: 28 Copynumber: 3.6 Consensus size: 28
39882954 TTTAAATTGC
*
39882964 ATAGCACTAAGTGTGCAAGTTTGATTAT
1 ATAGCACTAAGTGTGCGAGTTTGATTAT
39882992 ATAGCACTAAGTGTGCGAGTTTGATTAT
1 ATAGCACTAAGTGTGCGAGTTTGATTAT
*
39883020 GTAAGCACTAAGTGTGCGAGTTTGATTAT
1 AT-AGCACTAAGTGTGCGAGTTTGATTAT
*
39883049 ATAACACTAAGTGTGCG
1 ATAGCACTAAGTGTGCG
39883066 GACTTACTAT
Statistics
Matches: 69, Mismatches: 4, Indels: 2
0.92 0.05 0.03
Matches are distributed among these distances:
28 42 0.61
29 27 0.39
ACGTcount: A:0.30, C:0.12, G:0.25, T:0.33
Consensus pattern (28 bp):
ATAGCACTAAGTGTGCGAGTTTGATTAT
Found at i:39895716 original size:54 final size:54
Alignment explanation
Indices: 39895647--39896550 Score: 1808
Period size: 54 Copynumber: 16.7 Consensus size: 54
39895637 TTGGTTTTCA
39895647 GCACTAAGTGTGCGGGCAATAAGTGTTCACGGTTGTGAGACGGTTGTGAGATTG
1 GCACTAAGTGTGCGGGCAATAAGTGTTCACGGTTGTGAGACGGTTGTGAGATTG
39895701 GCACTAAGTGTGCGGGCAATAAGTGTTCACGGTTGTGAGACGGTTGTGAGATTG
1 GCACTAAGTGTGCGGGCAATAAGTGTTCACGGTTGTGAGACGGTTGTGAGATTG
39895755 GCACTAAGTGTGCGGGCAATAAGTGTTCACGGTTGTGAGACGGTTGTGAGATTG
1 GCACTAAGTGTGCGGGCAATAAGTGTTCACGGTTGTGAGACGGTTGTGAGATTG
39895809 GCACTAAGTGTGCGGGCAATAAGTGTTCACGGTTGTGAGACGGTTGTGAGATTG
1 GCACTAAGTGTGCGGGCAATAAGTGTTCACGGTTGTGAGACGGTTGTGAGATTG
39895863 GCACTAAGTGTGCGGGCAATAAGTGTTCACGGTTGTGAGACGGTTGTGAGATTG
1 GCACTAAGTGTGCGGGCAATAAGTGTTCACGGTTGTGAGACGGTTGTGAGATTG
39895917 GCACTAAGTGTGCGGGCAATAAGTGTTCACGGTTGTGAGACGGTTGTGAGATTG
1 GCACTAAGTGTGCGGGCAATAAGTGTTCACGGTTGTGAGACGGTTGTGAGATTG
39895971 GCACTAAGTGTGCGGGCAATAAGTGTTCACGGTTGTGAGACGGTTGTGAGATTG
1 GCACTAAGTGTGCGGGCAATAAGTGTTCACGGTTGTGAGACGGTTGTGAGATTG
39896025 GCACTAAGTGTGCGGGCAATAAGTGTTCACGGTTGTGAGACGGTTGTGAGATTG
1 GCACTAAGTGTGCGGGCAATAAGTGTTCACGGTTGTGAGACGGTTGTGAGATTG
39896079 GCACTAAGTGTGCGGGCAATAAGTGTTCACGGTTGTGAGACGGTTGTGAGATTG
1 GCACTAAGTGTGCGGGCAATAAGTGTTCACGGTTGTGAGACGGTTGTGAGATTG
39896133 GCACTAAGTGTGCGGGCAATAAGTGTTCACGGTTGTGAGACGGTTGTGAGATTG
1 GCACTAAGTGTGCGGGCAATAAGTGTTCACGGTTGTGAGACGGTTGTGAGATTG
39896187 GCACTAAGTGTGCGGGCAATAAGTGTTCACGGTTGTGAGACGGTTGTGAGATTG
1 GCACTAAGTGTGCGGGCAATAAGTGTTCACGGTTGTGAGACGGTTGTGAGATTG
39896241 GCACTAAGTGTGCGGGCAATAAGTGTTCACGGTTGTGAGACGGTTGTGAGATTG
1 GCACTAAGTGTGCGGGCAATAAGTGTTCACGGTTGTGAGACGGTTGTGAGATTG
39896295 GCACTAAGTGTGCGGGCAATAAGTGTTCACGGTTGTGAGACGGTTGTGAGATTG
1 GCACTAAGTGTGCGGGCAATAAGTGTTCACGGTTGTGAGACGGTTGTGAGATTG
39896349 GCACTAAGTGTGCGGGCAATAAGTGTTCACGGTTGTGAGACGGTTGTGAGATTG
1 GCACTAAGTGTGCGGGCAATAAGTGTTCACGGTTGTGAGACGGTTGTGAGATTG
39896403 GCACTAAGTGTGCGGGCAATAAGTGTTCACGGTTGTGAGACGGTTGTGAGATTG
1 GCACTAAGTGTGCGGGCAATAAGTGTTCACGGTTGTGAGACGGTTGTGAGATTG
39896457 GCACTAAGTGTGCGGGCAATAAGTGTTCACGGTTGTGAGACGGTTGTGAGATTG
1 GCACTAAGTGTGCGGGCAATAAGTGTTCACGGTTGTGAGACGGTTGTGAGATTG
39896511 GCACTAAGTGTGCGGGCAATAAGTGTTCACGGTTGTGAGA
1 GCACTAAGTGTGCGGGCAATAAGTGTTCACGGTTGTGAGA
39896551 TTGGCACTAA
Statistics
Matches: 850, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
54 850 1.00
ACGTcount: A:0.22, C:0.13, G:0.37, T:0.28
Consensus pattern (54 bp):
GCACTAAGTGTGCGGGCAATAAGTGTTCACGGTTGTGAGACGGTTGTGAGATTG
Found at i:39896587 original size:29 final size:29
Alignment explanation
Indices: 39896552--39896625 Score: 105
Period size: 29 Copynumber: 2.6 Consensus size: 29
39896542 GTTGTGAGAT
* *
39896552 TGGCACTAAGTGTGCGGGCTTGAAA-TGCA
1 TGGCACTAAGTGTGCGAG-TTGAAAGTACA
*
39896581 TGGCACTAAGTGTGCGAGTTTAAAGTACA
1 TGGCACTAAGTGTGCGAGTTGAAAGTACA
39896610 TGGCACTAAGTGTGCG
1 TGGCACTAAGTGTGCG
39896626 TGGTTGATTA
Statistics
Matches: 41, Mismatches: 3, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
28 5 0.12
29 36 0.88
ACGTcount: A:0.26, C:0.16, G:0.32, T:0.26
Consensus pattern (29 bp):
TGGCACTAAGTGTGCGAGTTGAAAGTACA
Found at i:39896994 original size:40 final size:39
Alignment explanation
Indices: 39896935--39897152 Score: 183
Period size: 40 Copynumber: 5.5 Consensus size: 39
39896925 TTGAATGATG
*
39896935 TCCGGGCTAAGTCCTGAAGGC-TTTGTGCTAAGTGACCATA
1 TCCGGGCTAAGTCC-GAAGGCATTTGTGCT-AGTGACTATA
* * *
39896975 TCCGGACTAAGATCCGAAGGCATTTGTGCGAGTTACTA-A
1 TCCGGGCTAAG-TCCGAAGGCATTTGTGCTAGTGACTATA
* * * *
39897014 TTCCGGGCTAAGCCCGAAGGCATTGGTGCTAGTTACTAAA
1 -TCCGGGCTAAGTCCGAAGGCATTTGTGCTAGTGACTATA
* **
39897054 TCCGGGCTAAGTTCCGAAGAGCATTCGTGCTAGTGA-GGTA
1 TCCGGGCTAAG-TCCGAAG-GCATTTGTGCTAGTGACTATA
* * * *
39897094 TCCGGACTAAGTTCCGAAGAGCATTCGTGCTGGTG-TTATA
1 TCCGGGCTAAG-TCCGAAG-GCATTTGTGCTAGTGACTATA
*
39897134 TCCGGGCTAGGTCCCGAAG
1 TCCGGGCTAAGT-CCGAAG
39897153 AGCAATCATG
Statistics
Matches: 150, Mismatches: 20, Indels: 16
0.81 0.11 0.09
Matches are distributed among these distances:
39 36 0.24
40 90 0.60
41 24 0.16
ACGTcount: A:0.23, C:0.22, G:0.29, T:0.26
Consensus pattern (39 bp):
TCCGGGCTAAGTCCGAAGGCATTTGTGCTAGTGACTATA
Found at i:39897070 original size:79 final size:81
Alignment explanation
Indices: 39896935--39897083 Score: 196
Period size: 79 Copynumber: 1.9 Consensus size: 81
39896925 TTGAATGATG
* * *
39896935 TCCGGGCTAAGTCCTGAAGGCTTTGTGCTAAGTGACCATATCCGGACTAAGATCCGAAG-GCATT
1 TCCGGGCTAAGTCCCGAAGGCTTGGTGCTAAGTGACCAAATCCGGACTAAGATCCGAAGAGCATT
*
39896999 TGTGCGAGTTACTAAT
66 CGTGCGAGTTACTAAT
* * * *
39897015 TCCGGGCTAAG-CCCGAAGGCATTGGTGCT-AGTTACTAAATCCGGGCTAAGTTCCGAAGAGCAT
1 TCCGGGCTAAGTCCCGAAGGC-TTGGTGCTAAGTGACCAAATCCGGACTAAGATCCGAAGAGCAT
39897078 TCGTGC
65 TCGTGC
39897084 TAGTGAGGTA
Statistics
Matches: 59, Mismatches: 8, Indels: 4
0.83 0.11 0.06
Matches are distributed among these distances:
79 32 0.54
80 27 0.46
ACGTcount: A:0.24, C:0.23, G:0.28, T:0.26
Consensus pattern (81 bp):
TCCGGGCTAAGTCCCGAAGGCTTGGTGCTAAGTGACCAAATCCGGACTAAGATCCGAAGAGCATT
CGTGCGAGTTACTAAT
Found at i:39897165 original size:40 final size:40
Alignment explanation
Indices: 39897053--39897169 Score: 153
Period size: 40 Copynumber: 2.9 Consensus size: 40
39897043 TAGTTACTAA
* *
39897053 ATCCGGGCTAAGTTCCGAAGAGCATTCGTGCTAGTGAGGT
1 ATCCGGGCTAAGTTCCGAAGAGCATTCGTGCTGGTGAGAT
* **
39897093 ATCCGGACTAAGTTCCGAAGAGCATTCGTGCTGGTGTTAT
1 ATCCGGGCTAAGTTCCGAAGAGCATTCGTGCTGGTGAGAT
* * * *
39897133 ATCCGGGCTAGGTCCCGAAGAGCAATCATGCTGGTGA
1 ATCCGGGCTAAGTTCCGAAGAGCATTCGTGCTGGTGA
39897170 CGTGTATTCG
Statistics
Matches: 66, Mismatches: 11, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
40 66 1.00
ACGTcount: A:0.23, C:0.21, G:0.31, T:0.25
Consensus pattern (40 bp):
ATCCGGGCTAAGTTCCGAAGAGCATTCGTGCTGGTGAGAT
Done.