Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: A08
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: 123748673
ACGTcount: A:0.31, C:0.17, G:0.17, T:0.31
Warning! 5630000 characters in sequence are not A, C, G, or T
File 12 of 373
Found at i:3497107 original size:21 final size:20
Alignment explanation
Indices: 3497081--3497119 Score: 60
Period size: 21 Copynumber: 1.9 Consensus size: 20
3497071 CGAGCCCAGA
*
3497081 AATAAATCCAAAAAGAAAAAT
1 AATAAACCCAAAAA-AAAAAT
3497102 AATAAACCCAAAAAAAAA
1 AATAAACCCAAAAAAAAA
3497120 CGAAGTCCAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 4 0.24
21 13 0.76
ACGTcount: A:0.74, C:0.13, G:0.03, T:0.10
Consensus pattern (20 bp):
AATAAACCCAAAAAAAAAAT
Found at i:3497252 original size:17 final size:19
Alignment explanation
Indices: 3497230--3497281 Score: 54
Period size: 19 Copynumber: 2.8 Consensus size: 19
3497220 ATGGAAATAT
*
3497230 AATCTT-CA-ATGATATGC
1 AATCTTACATATGATATGA
*
3497247 AATCTTAGATATGATATGA
1 AATCTTACATATGATATGA
**
3497266 AATCTTTGATATGATA
1 AATCTTACATATGATA
3497282 CAATCTTAGA
Statistics
Matches: 30, Mismatches: 3, Indels: 2
0.86 0.09 0.06
Matches are distributed among these distances:
17 6 0.20
18 1 0.03
19 23 0.77
ACGTcount: A:0.38, C:0.10, G:0.13, T:0.38
Consensus pattern (19 bp):
AATCTTACATATGATATGA
Found at i:3497262 original size:19 final size:19
Alignment explanation
Indices: 3497238--3497311 Score: 89
Period size: 19 Copynumber: 3.9 Consensus size: 19
3497228 ATAATCTTCA
3497238 ATGATATGCAATCTTAGAT
1 ATGATATGCAATCTTAGAT
* *
3497257 ATGATATGAAATCTTTGAT
1 ATGATATGCAATCTTAGAT
3497276 ATGATA--CAATCTTAGAT
1 ATGATATGCAATCTTAGAT
* *
3497293 ATGATTTTGTAATCTTAGA
1 ATGA-TATGCAATCTTAGA
3497312 AGATTTAATT
Statistics
Matches: 46, Mismatches: 6, Indels: 5
0.81 0.11 0.09
Matches are distributed among these distances:
17 13 0.28
18 1 0.02
19 23 0.50
20 9 0.20
ACGTcount: A:0.36, C:0.08, G:0.15, T:0.41
Consensus pattern (19 bp):
ATGATATGCAATCTTAGAT
Found at i:3499391 original size:118 final size:118
Alignment explanation
Indices: 3499235--3499472 Score: 467
Period size: 118 Copynumber: 2.0 Consensus size: 118
3499225 TTTGGGCCAG
*
3499235 TGTAAACATGGTGGCTTTTGTGACTTGAAAACTAAAAAATGTAGTTGTTTACCGGTGTTAGAGCA
1 TGTAAACATGGTGGCTTTTATGACTTGAAAACTAAAAAATGTAGTTGTTTACCGGTGTTAGAGCA
3499300 GCTACCATCTAACATTGCAACAAAGGTGGATGCTATGCAGCGATGACGGAAAC
66 GCTACCATCTAACATTGCAACAAAGGTGGATGCTATGCAGCGATGACGGAAAC
3499353 TGTAAACATGGTGGCTTTTATGACTTGAAAACTAAAAAATGTAGTTGTTTACCGGTGTTAGAGCA
1 TGTAAACATGGTGGCTTTTATGACTTGAAAACTAAAAAATGTAGTTGTTTACCGGTGTTAGAGCA
3499418 GCTACCATCTAACATTGCAACAAAGGTGGATGCTATGCAGCGATGACGGAAAC
66 GCTACCATCTAACATTGCAACAAAGGTGGATGCTATGCAGCGATGACGGAAAC
3499471 TG
1 TG
3499473 CAAAGGATTT
Statistics
Matches: 119, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
118 119 1.00
ACGTcount: A:0.32, C:0.16, G:0.24, T:0.27
Consensus pattern (118 bp):
TGTAAACATGGTGGCTTTTATGACTTGAAAACTAAAAAATGTAGTTGTTTACCGGTGTTAGAGCA
GCTACCATCTAACATTGCAACAAAGGTGGATGCTATGCAGCGATGACGGAAAC
Found at i:3500376 original size:20 final size:20
Alignment explanation
Indices: 3500351--3500396 Score: 92
Period size: 20 Copynumber: 2.3 Consensus size: 20
3500341 ATTTGCTTAT
3500351 TATTTAAGTAAATATTAATG
1 TATTTAAGTAAATATTAATG
3500371 TATTTAAGTAAATATTAATG
1 TATTTAAGTAAATATTAATG
3500391 TATTTA
1 TATTTA
3500397 TTATTATTAA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 26 1.00
ACGTcount: A:0.43, C:0.00, G:0.09, T:0.48
Consensus pattern (20 bp):
TATTTAAGTAAATATTAATG
Found at i:3500554 original size:15 final size:16
Alignment explanation
Indices: 3500513--3500547 Score: 54
Period size: 16 Copynumber: 2.2 Consensus size: 16
3500503 GTATATTTAC
*
3500513 TTATTATATAAGTATA
1 TTATTAAATAAGTATA
3500529 TTATTAAATAA-TATA
1 TTATTAAATAAGTATA
3500544 TTAT
1 TTAT
3500548 ATAATAAATA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
15 8 0.44
16 10 0.56
ACGTcount: A:0.46, C:0.00, G:0.03, T:0.51
Consensus pattern (16 bp):
TTATTAAATAAGTATA
Found at i:3502097 original size:18 final size:19
Alignment explanation
Indices: 3502055--3502122 Score: 86
Period size: 18 Copynumber: 3.7 Consensus size: 19
3502045 AAAGATCGAC
3502055 TGTTACTGAATAATTTAAT
1 TGTTACTGAATAATTTAAT
* *
3502074 TGTTACTGTAT-ATTTGAT
1 TGTTACTGAATAATTTAAT
* *
3502092 TTTTACTGAATAA-TTAAC
1 TGTTACTGAATAATTTAAT
3502110 TGTTACTGAATAA
1 TGTTACTGAATAA
3502123 CCGATCAATT
Statistics
Matches: 41, Mismatches: 7, Indels: 3
0.80 0.14 0.06
Matches are distributed among these distances:
18 30 0.73
19 11 0.27
ACGTcount: A:0.34, C:0.07, G:0.12, T:0.47
Consensus pattern (19 bp):
TGTTACTGAATAATTTAAT
Found at i:3506989 original size:458 final size:459
Alignment explanation
Indices: 3506155--3507001 Score: 1252
Period size: 458 Copynumber: 1.8 Consensus size: 459
3506145 TGCTAAAATG
** * * * * *
3506155 TTACCATTCTGACCTATTTCATATTGTGCCCATTAAAGCAGTCGAGGTAAGACTTGATTTGTCCT
1 TTACCATTCTGACCTATCGCATATTGTGCCCATCAAAGAAATCGAGGTAAGACCTAATTTGTCCT
* * * *
3506220 TTGAAGAAGAACACATTAGAATTATTTAAAAAGATGTGAAAGTTTTTATAAGGAAACAAATTCCA
66 TCGAAGAAGAACACATTAGAATTATTTAAAAAAATGTGAAAGTTCTGATAAGGAAACAAATTCCA
* * * * *
3506285 TTAGTAAAAGTGTTGTGGCAAAACCATGGTGTTGAGGACGTTACAAGGGAAATGGGAAGATTCAC
131 TTAGTAAAAGTGTTATGGCAAAACCATGGTGTTGAGGAAGCTACAAGGGAAATGAGAAGATCCAC
** * * * * * *
3506350 TCCGTCAACAATATCCCCACTTATTCGAAATAGGTAAAATTTCGAGGATAAAATTTCTTTAAGGA
196 TCCACCAAAAATATCCCCACTTATTCGAAAAAGGTAAAATTTCGAGGAAAAAAATTCCTTAAGAA
* *
3506415 GGGGAGAATTGTAACATCCCAAACAATAGGAGGTTAGATTCTTAGAAATTATCATGAATTGAATC
261 GGGGAGAATTCTAACATCCCAAACAATAGGAGGTTAGATTCTTAAAAATTATCATGAATTGAATC
* *
3506480 CTAGTCTAGTGGTTAAGAGCCTGGTAGAAAGTATAGAGAACCAAAGTTCAAGCCTCTTAAATTGA
326 CTAGTCTAGTGGTTAAGAGCCTGGTAGAAAGTATAGAGAACCAAAGTTCAAGACTCCTAAATTGA
3506545 ATTCAACTCTCCCCAATTCAACTAAAATTCTCATTTGTTATTTTAGCAAATAAAAACCATACTAA
391 ATTCAACTCTCCCCAATTCAACTAAAATTCTCATTTGTTATTTTAGCAAATAAAAACCATACTAA
3506610 GACA
456 GACA
* *
3506614 TTACCGTTCTGACCTATCGCATATTGTGCCCATCAAAGAAATTGAGGTAAGACCTAATTTGTCCT
1 TTACCATTCTGACCTATCGCATATTGTGCCCATCAAAGAAATCGAGGTAAGACCTAATTTGTCCT
* * *
3506679 TCGAAGAAGAACCCATTAGAATTCTTTAAAAAAATGTGAAAGTTCTGATAAGGAAACAAATTCTA
66 TCGAAGAAGAACACATTAGAATTATTTAAAAAAATGTGAAAGTTCTGATAAGGAAACAAATTCCA
* ** *
3506744 TTAGT-AAAGTGTTATGGCGAAACCATGGTGTTGAGGAAGCTACGTGGGAAAT-AGAAGATCCAT
131 TTAGTAAAAGTGTTATGGCAAAACCATGGTGTTGAGGAAGCTACAAGGGAAATGAGAAGATCCAC
3506807 TCCACCAAAAATATCCCCACTTATTCGAAAAAGGTAAAATTTCGA-GAAAAAGAATTCCTTAAGA
196 TCCACCAAAAATATCCCCACTTATTCGAAAAAGGTAAAATTTCGAGGAAAAA-AATTCCTTAAGA
* * * *
3506871 AGGGGGGAGTTCTAACA-CCCTACACAATAGGAGGTTAGATTCTTAAAAAATTATCATGAATTTA
260 AGGGGAGAATTCTAACATCCC-AAACAATAGGAGGTTAGATTCTT-AAAAATTATCATGAATTGA
* *
3506935 ATCCTAGTCTAGTGGTTAAGAGCTTGGTAGAAAGTATAGTGAACCAAAGTTCAAGACTCCTAAAT
323 ATCCTAGTCTAGTGGTTAAGAGCCTGGTAGAAAGTATAGAGAACCAAAGTTCAAGACTCCTAAAT
3507000 TG
388 TG
3507002 CACTTTTTCT
Statistics
Matches: 342, Mismatches: 43, Indels: 7
0.87 0.11 0.02
Matches are distributed among these distances:
456 8 0.02
457 94 0.27
458 121 0.35
459 119 0.35
ACGTcount: A:0.37, C:0.16, G:0.19, T:0.29
Consensus pattern (459 bp):
TTACCATTCTGACCTATCGCATATTGTGCCCATCAAAGAAATCGAGGTAAGACCTAATTTGTCCT
TCGAAGAAGAACACATTAGAATTATTTAAAAAAATGTGAAAGTTCTGATAAGGAAACAAATTCCA
TTAGTAAAAGTGTTATGGCAAAACCATGGTGTTGAGGAAGCTACAAGGGAAATGAGAAGATCCAC
TCCACCAAAAATATCCCCACTTATTCGAAAAAGGTAAAATTTCGAGGAAAAAAATTCCTTAAGAA
GGGGAGAATTCTAACATCCCAAACAATAGGAGGTTAGATTCTTAAAAATTATCATGAATTGAATC
CTAGTCTAGTGGTTAAGAGCCTGGTAGAAAGTATAGAGAACCAAAGTTCAAGACTCCTAAATTGA
ATTCAACTCTCCCCAATTCAACTAAAATTCTCATTTGTTATTTTAGCAAATAAAAACCATACTAA
GACA
Found at i:3511354 original size:16 final size:17
Alignment explanation
Indices: 3511323--3511356 Score: 61
Period size: 17 Copynumber: 2.1 Consensus size: 17
3511313 TTCATAAGTA
3511323 TATATCAATCATTTCAT
1 TATATCAATCATTTCAT
3511340 TATATCAAT-ATTTCAT
1 TATATCAATCATTTCAT
3511356 T
1 T
3511357 CTCCATCATT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 8 0.47
17 9 0.53
ACGTcount: A:0.35, C:0.15, G:0.00, T:0.50
Consensus pattern (17 bp):
TATATCAATCATTTCAT
Found at i:3511701 original size:46 final size:45
Alignment explanation
Indices: 3511636--3512095 Score: 479
Period size: 46 Copynumber: 9.9 Consensus size: 45
3511626 TTATCTTTGA
* * * * * *
3511636 CATGATGCCATAGTGTCTTTCAACTATGGTCTTACTCATTTTCTGT
1 CATGTTGCCATGGTATCTTTCAACCATGGTCTTACACA-TTTCTAT
* *** *
3511682 CAGGTTGCCATGGTATCTTTCAACCATGGTCTTGTTCATTTCATGT
1 CATGTTGCCATGGTATCTTTCAACCATGGTCTTACACATTTC-TAT
* ** * ** * **
3511728 TACATTGCCATGGTATCTTTCAACGATGGTCTTATTCATTCCCGT
1 CATGTTGCCATGGTATCTTTCAACCATGGTCTTACACATTTCTAT
* ** *
3511773 CATGTTGCCACGGTATCTTTCAGTCATGGTCTTACACATTTTATAT
1 CATGTTGCCATGGTATCTTTCAACCATGGTCTTACACA-TTTCTAT
* *
3511819 CCTGTTTCCATGGTATCTTTCAACCATGGTCTTACACATTTCATAT
1 CATGTTGCCATGGTATCTTTCAACCATGGTCTTACACATTTC-TAT
* *
3511865 CATGTTGCCATGGTATCTTTCAACCATAGTCTTACACATTTTATAT
1 CATGTTGCCATGGTATCTTTCAACCATGGTCTTACACA-TTTCTAT
*
3511911 CCTGTTGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATAT
1 CATGTTGCCATGGTATCTTTCAACCATGGTCTTACACATTTC-TAT
* *
3511957 CATGTTGCCATGGTGTCTTTCAACCATTGTCTTATGGTCTTACACATTTTATAT
1 CATGTTGCCATGGTATCTTTCAA-C-----C--ATGGTCTTACACA-TTTCTAT
* *
3512011 CATGTTGCCATGATGTCTTTCAACCATGGTCTTACACATTTCATAT
1 CATGTTGCCATGGTATCTTTCAACCATGGTCTTACACATTTC-TAT
3512057 CATGTTGCCATGGTATCTTTCAACCATGGTCTTACACAT
1 CATGTTGCCATGGTATCTTTCAACCATGGTCTTACACAT
3512096 ATCATTTCAG
Statistics
Matches: 352, Mismatches: 47, Indels: 30
0.82 0.11 0.07
Matches are distributed among these distances:
45 44 0.12
46 260 0.74
47 4 0.01
48 1 0.00
52 1 0.00
53 1 0.00
54 38 0.11
55 3 0.01
ACGTcount: A:0.22, C:0.23, G:0.14, T:0.41
Consensus pattern (45 bp):
CATGTTGCCATGGTATCTTTCAACCATGGTCTTACACATTTCTAT
Found at i:3511901 original size:92 final size:92
Alignment explanation
Indices: 3511641--3512095 Score: 547
Period size: 92 Copynumber: 4.9 Consensus size: 92
3511631 TTTGACATGA
* * * * * *
3511641 TGCCATAGTGTCTTTCAACTATGGTCTTACTCATTTTC-TGTCAGGTTGCCATGGTATCTTTCAA
1 TGCCATGGTATCTTTCAACCATGGTCTTACACA-TTTCATATCATGTTGCCATGGTATCTTTCAA
*** * * * *
3511705 CCATGGTCTTGTTCATTTCATGTTAC-AT
65 CCATGGTCTTACACATTTTAT-ATCCTGT
* ** *** * **
3511733 TGCCATGGTATCTTTCAACGATGGTCTTATTCA-TTCCCGTCATGTTGCCACGGTATCTTTCAGT
1 TGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATATCATGTTGCCATGGTATCTTTCAAC
3511797 CATGGTCTTACACATTTTATATCCTGT
66 CATGGTCTTACACATTTTATATCCTGT
*
3511824 TTCCATGGTATCTTTCAACCATGGTCTTACACATTTCATATCATGTTGCCATGGTATCTTTCAAC
1 TGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATATCATGTTGCCATGGTATCTTTCAAC
*
3511889 CATAGTCTTACACATTTTATATCCTGT
66 CATGGTCTTACACATTTTATATCCTGT
*
3511916 TGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATATCATGTTGCCATGGTGTCTTTCAAC
1 TGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATATCATGTTGCCATGGTATCTTTCAA-
*
3511981 CATTGTCTTATGGTCTTACACATTTTATATCATGT
65 C-----C--ATGGTCTTACACATTTTATATCCTGT
* *
3512016 TGCCATGATGTCTTTCAACCATGGTCTTACACATTTCATATCATGTTGCCATGGTATCTTTCAAC
1 TGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATATCATGTTGCCATGGTATCTTTCAAC
3512081 CATGGTCTTACACAT
66 CATGGTCTTACACAT
3512096 ATCATTTCAG
Statistics
Matches: 318, Mismatches: 34, Indels: 22
0.85 0.09 0.06
Matches are distributed among these distances:
90 5 0.02
91 68 0.21
92 156 0.49
93 1 0.00
94 1 0.00
98 1 0.00
99 1 0.00
100 85 0.27
ACGTcount: A:0.21, C:0.23, G:0.14, T:0.41
Consensus pattern (92 bp):
TGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATATCATGTTGCCATGGTATCTTTCAAC
CATGGTCTTACACATTTTATATCCTGT
Found at i:3512018 original size:54 final size:53
Alignment explanation
Indices: 3511936--3512090 Score: 216
Period size: 54 Copynumber: 3.0 Consensus size: 53
3511926 TCTTTCAACC
3511936 ATGGTCTTACACATTTCATATCATGTTGCCATGGTGTCTTTCAACCATTGTCTT
1 ATGGTCTTACACATTTCATATCATGTTGCCATGGTGTCTTTCAACCA-TGTCTT
* *
3511990 ATGGTCTTACACATTTTATATCATGTTGCCATGATGTCTTTCAA-C----C--
1 ATGGTCTTACACATTTCATATCATGTTGCCATGGTGTCTTTCAACCATGTCTT
*
3512036 ATGGTCTTACACATTTCATATCATGTTGCCATGGTATCTTTCAACCATGGTCTT
1 ATGGTCTTACACATTTCATATCATGTTGCCATGGTGTCTTTCAACCAT-GTCTT
3512090 A
1 A
3512091 CACATATCAT
Statistics
Matches: 88, Mismatches: 5, Indels: 16
0.81 0.05 0.15
Matches are distributed among these distances:
46 41 0.47
47 1 0.01
48 1 0.01
52 1 0.01
53 1 0.01
54 43 0.49
ACGTcount: A:0.23, C:0.22, G:0.14, T:0.41
Consensus pattern (53 bp):
ATGGTCTTACACATTTCATATCATGTTGCCATGGTGTCTTTCAACCATGTCTT
Found at i:3512056 original size:192 final size:183
Alignment explanation
Indices: 3511636--3512100 Score: 567
Period size: 192 Copynumber: 2.5 Consensus size: 183
3511626 TTATCTTTGA
* * * * *
3511636 CATGATGCCAT-AGTGTCTTTCAACTATGGTCTTACTCATTTTC-TGTCAGGTTGCCATGGTATC
1 CATGTTGCCATGA-TGTCTTTCAACCATGGTCTTACACA-TTTCATATCATGTTGCCATGGTATC
*** * * **
3511699 TTTCAACCATGGTCTTGTTCATTTCATGTTACATTGCCATGGTATCTTTCAACGATGGTCTTATT
64 TTTCAACCATGGTCTTACACATTTCATGATACATTGCCATGGTATCTTTCAACCATGGTCTTACA
* *
3511764 CATTCCCGTCATGTTGCCACGGTATCTTTCAGTCATGGTCTTACACATTTTATAT
129 CATTCACATCATGTTGCCACGGTATCTTTCAGTCATGGTCTTACACATTTTATAT
* * * *
3511819 CCTGTTTCCATGGTATCTTTCAACCATGGTCTTACACATTTCATATCATGTTGCCATGGTATCTT
1 CATGTTGCCATGATGTCTTTCAACCATGGTCTTACACATTTCATATCATGTTGCCATGGTATCTT
* * * *
3511884 TCAACCATAGTCTTACACATTTTAT-ATCCTGTTGCCATGGTATCTTTCAACCATGGTCTTACAC
66 TCAACCATGGTCTTACACATTTCATGATAC-ATTGCCATGGTATCTTTCAACCATGGTCTTACAC
* * *
3511948 ATTTCATATCATGTTGCCATGGTGTCTTTCAACCATTGTCTTATGGTCTTACACATTTTATAT
130 A-TTCACATCATGTTGCCACGGTATCTTT----CA--GTC--ATGGTCTTACACATTTTATAT
3512011 CATGTTGCCATGATGTCTTTCAACCATGGTCTTACACATTTCATATCATGTTGCCATGGTATCTT
1 CATGTTGCCATGATGTCTTTCAACCATGGTCTTACACATTTCATATCATGTTGCCATGGTATCTT
*
3512076 TCAACCATGGTCTTACACATATCAT
66 TCAACCATGGTCTTACACATTTCAT
3512101 TTCAGAAAGC
Statistics
Matches: 238, Mismatches: 32, Indels: 15
0.84 0.11 0.05
Matches are distributed among these distances:
182 6 0.03
183 101 0.42
184 22 0.09
188 2 0.01
190 3 0.01
192 104 0.44
ACGTcount: A:0.22, C:0.23, G:0.14, T:0.41
Consensus pattern (183 bp):
CATGTTGCCATGATGTCTTTCAACCATGGTCTTACACATTTCATATCATGTTGCCATGGTATCTT
TCAACCATGGTCTTACACATTTCATGATACATTGCCATGGTATCTTTCAACCATGGTCTTACACA
TTCACATCATGTTGCCACGGTATCTTTCAGTCATGGTCTTACACATTTTATAT
Found at i:3512066 original size:100 final size:100
Alignment explanation
Indices: 3511893--3512090 Score: 351
Period size: 100 Copynumber: 2.0 Consensus size: 100
3511883 TTCAACCATA
* *
3511893 GTCTTACACATTTTATATCCTGTTGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATATC
1 GTCTTACACATTTTATATCATGTTGCCATGATATCTTTCAACCATGGTCTTACACATTTCATATC
* *
3511958 ATGTTGCCATGGTGTCTTTCAACCATTGTCTTATG
66 ATGTTGCCATGGTATCTTTCAACCATGGTCTTATG
*
3511993 GTCTTACACATTTTATATCATGTTGCCATGATGTCTTTCAACCATGGTCTTACACATTTCATATC
1 GTCTTACACATTTTATATCATGTTGCCATGATATCTTTCAACCATGGTCTTACACATTTCATATC
3512058 ATGTTGCCATGGTATCTTTCAACCATGGTCTTA
66 ATGTTGCCATGGTATCTTTCAACCATGGTCTTA
3512091 CACATATCAT
Statistics
Matches: 93, Mismatches: 5, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
100 93 1.00
ACGTcount: A:0.22, C:0.23, G:0.14, T:0.41
Consensus pattern (100 bp):
GTCTTACACATTTTATATCATGTTGCCATGATATCTTTCAACCATGGTCTTACACATTTCATATC
ATGTTGCCATGGTATCTTTCAACCATGGTCTTATG
Found at i:3514887 original size:39 final size:39
Alignment explanation
Indices: 3514828--3514928 Score: 148
Period size: 39 Copynumber: 2.6 Consensus size: 39
3514818 GCTCTGATGA
* *
3514828 GCTTCAGTTAACCTTCGGGCTTCCGTTTAGCACTTGTGT
1 GCTTCAGTTAGCCTTCGGGCTTCCGTTTAGCACTTATGT
* *
3514867 GCTTTAGTTAGCCTTCGGGCTTCCGTTTAGTACTTATGT
1 GCTTCAGTTAGCCTTCGGGCTTCCGTTTAGCACTTATGT
* *
3514906 GCTTCAGCTAGACTTCGGGCTTC
1 GCTTCAGTTAGCCTTCGGGCTTC
3514929 AAATCATGAT
Statistics
Matches: 55, Mismatches: 7, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
39 55 1.00
ACGTcount: A:0.13, C:0.25, G:0.24, T:0.39
Consensus pattern (39 bp):
GCTTCAGTTAGCCTTCGGGCTTCCGTTTAGCACTTATGT
Found at i:3515634 original size:13 final size:13
Alignment explanation
Indices: 3515611--3515644 Score: 50
Period size: 13 Copynumber: 2.5 Consensus size: 13
3515601 AGTTTTTTTT
*
3515611 AAATAATAATAATA
1 AAATAA-AATAAAA
3515625 AAATAAAATAAAA
1 AAATAAAATAAAA
3515638 AAATAAA
1 AAATAAA
3515645 TTCTAGAGTA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
13 13 0.68
14 6 0.32
ACGTcount: A:0.79, C:0.00, G:0.00, T:0.21
Consensus pattern (13 bp):
AAATAAAATAAAA
Found at i:3516111 original size:45 final size:45
Alignment explanation
Indices: 3516060--3516148 Score: 178
Period size: 45 Copynumber: 2.0 Consensus size: 45
3516050 GACAAGTAGT
3516060 GATGTTCCAATTTCCTTGATACGAGAACAAGAACTTAGAAACATA
1 GATGTTCCAATTTCCTTGATACGAGAACAAGAACTTAGAAACATA
3516105 GATGTTCCAATTTCCTTGATACGAGAACAAGAACTTAGAAACAT
1 GATGTTCCAATTTCCTTGATACGAGAACAAGAACTTAGAAACAT
3516149 GATTATTGGA
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
45 44 1.00
ACGTcount: A:0.39, C:0.18, G:0.16, T:0.27
Consensus pattern (45 bp):
GATGTTCCAATTTCCTTGATACGAGAACAAGAACTTAGAAACATA
Found at i:3531139 original size:18 final size:17
Alignment explanation
Indices: 3531106--3531144 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 17
3531096 TTGTATAAAT
3531106 TGTGAATTATATTTGATA
1 TGTGAATTATATTTGA-A
3531124 TGTGAATTA-ATATTGAA
1 TGTGAATTATAT-TTGAA
3531141 TGTG
1 TGTG
3531145 GAAGGAAAGT
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
17 7 0.35
18 13 0.65
ACGTcount: A:0.33, C:0.00, G:0.21, T:0.46
Consensus pattern (17 bp):
TGTGAATTATATTTGAA
Found at i:3531397 original size:23 final size:23
Alignment explanation
Indices: 3531370--3531467 Score: 162
Period size: 23 Copynumber: 4.3 Consensus size: 23
3531360 AGTGTTATTG
3531370 ATCAGTGGTAGCTTCGGCTACAT
1 ATCAGTGGTAGCTTCGGCTACAT
* *
3531393 TTCAGTGGTAGCTTTGGCTACAT
1 ATCAGTGGTAGCTTCGGCTACAT
*
3531416 -CCAGTGGTAGCTTCGGCTACAT
1 ATCAGTGGTAGCTTCGGCTACAT
3531438 ATCAGTGGTAGCTTCGGCTACAT
1 ATCAGTGGTAGCTTCGGCTACAT
3531461 ATCAGTG
1 ATCAGTG
3531468 TGGCACTTAT
Statistics
Matches: 69, Mismatches: 5, Indels: 2
0.91 0.07 0.03
Matches are distributed among these distances:
22 20 0.29
23 49 0.71
ACGTcount: A:0.20, C:0.21, G:0.27, T:0.32
Consensus pattern (23 bp):
ATCAGTGGTAGCTTCGGCTACAT
Found at i:3531436 original size:45 final size:45
Alignment explanation
Indices: 3531372--3531460 Score: 160
Period size: 45 Copynumber: 2.0 Consensus size: 45
3531362 TGTTATTGAT
* *
3531372 CAGTGGTAGCTTCGGCTACATTTCAGTGGTAGCTTTGGCTACATC
1 CAGTGGTAGCTTCGGCTACATATCAGTGGTAGCTTCGGCTACATC
3531417 CAGTGGTAGCTTCGGCTACATATCAGTGGTAGCTTCGGCTACAT
1 CAGTGGTAGCTTCGGCTACATATCAGTGGTAGCTTCGGCTACAT
3531461 ATCAGTGTGG
Statistics
Matches: 42, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
45 42 1.00
ACGTcount: A:0.19, C:0.22, G:0.27, T:0.31
Consensus pattern (45 bp):
CAGTGGTAGCTTCGGCTACATATCAGTGGTAGCTTCGGCTACATC
Found at i:3537193 original size:6 final size:6
Alignment explanation
Indices: 3537184--3537249 Score: 80
Period size: 6 Copynumber: 11.0 Consensus size: 6
3537174 GATGATGATG
* * *
3537184 TTTAAT TTTA-T TTTATT TTTATT TTTATT TTTATT TTCATT TCTATT
1 TTTATT TTTATT TTTATT TTTATT TTTATT TTTATT TTTATT TTTATT
*
3537231 TTTATT TTATGTT TTTATT
1 TTTATT TT-TATT TTTATT
3537250 AGTTTCACAT
Statistics
Matches: 52, Mismatches: 6, Indels: 4
0.84 0.10 0.06
Matches are distributed among these distances:
5 5 0.10
6 42 0.81
7 5 0.10
ACGTcount: A:0.18, C:0.03, G:0.02, T:0.77
Consensus pattern (6 bp):
TTTATT
Found at i:3538818 original size:112 final size:112
Alignment explanation
Indices: 3538621--3538847 Score: 454
Period size: 112 Copynumber: 2.0 Consensus size: 112
3538611 GAGTGCTTCA
3538621 TTTATTGTCCTTAAACACCTCGAGTGATTTGAGTGAATCTTTAGTAAGGATGTGAAACTCTGTGA
1 TTTATTGTCCTTAAACACCTCGAGTGATTTGAGTGAATCTTTAGTAAGGATGTGAAACTCTGTGA
3538686 CATTTTGAATCAAAGGTAATTACTTAAACAAGGGGAGACACCTATGT
66 CATTTTGAATCAAAGGTAATTACTTAAACAAGGGGAGACACCTATGT
3538733 TTTATTGTCCTTAAACACCTCGAGTGATTTGAGTGAATCTTTAGTAAGGATGTGAAACTCTGTGA
1 TTTATTGTCCTTAAACACCTCGAGTGATTTGAGTGAATCTTTAGTAAGGATGTGAAACTCTGTGA
3538798 CATTTTGAATCAAAGGTAATTACTTAAACAAGGGGAGACACCTATGT
66 CATTTTGAATCAAAGGTAATTACTTAAACAAGGGGAGACACCTATGT
3538845 TTT
1 TTT
3538848 CTTGATAAAA
Statistics
Matches: 115, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
112 115 1.00
ACGTcount: A:0.32, C:0.14, G:0.20, T:0.34
Consensus pattern (112 bp):
TTTATTGTCCTTAAACACCTCGAGTGATTTGAGTGAATCTTTAGTAAGGATGTGAAACTCTGTGA
CATTTTGAATCAAAGGTAATTACTTAAACAAGGGGAGACACCTATGT
Found at i:3543257 original size:14 final size:14
Alignment explanation
Indices: 3543238--3543264 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
3543228 TATCAAAACG
3543238 ATAATTAAGAACAC
1 ATAATTAAGAACAC
3543252 ATAATTAAGAACA
1 ATAATTAAGAACA
3543265 AGTCAAATAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.59, C:0.11, G:0.07, T:0.22
Consensus pattern (14 bp):
ATAATTAAGAACAC
Found at i:3546309 original size:39 final size:39
Alignment explanation
Indices: 3546261--3546361 Score: 148
Period size: 39 Copynumber: 2.6 Consensus size: 39
3546251 AGCTCGATGA
* *
3546261 GCTTCAGTTAGCCTTCGGGCTTCCGTTTAGCACTTGTGT
1 GCTTCAGTTAGCCTTCGGGCTTCCATTTAGCACTTATGT
* *
3546300 GCTTTAGTTAGCCTTCAGGCTTCCATTTAGCACTTATGT
1 GCTTCAGTTAGCCTTCGGGCTTCCATTTAGCACTTATGT
* *
3546339 GCTTCAGCTAGACTTCGGGCTTC
1 GCTTCAGTTAGCCTTCGGGCTTC
3546362 AAATCATGAT
Statistics
Matches: 54, Mismatches: 8, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
39 54 1.00
ACGTcount: A:0.14, C:0.26, G:0.23, T:0.38
Consensus pattern (39 bp):
GCTTCAGTTAGCCTTCGGGCTTCCATTTAGCACTTATGT
Found at i:3546343 original size:21 final size:21
Alignment explanation
Indices: 3546279--3546343 Score: 57
Period size: 19 Copynumber: 3.2 Consensus size: 21
3546269 TAGCCTTCGG
* *
3546279 GCTTCCGTTTAGCACTTGTGT
1 GCTTCCATTTAGCACTTATGT
* *
3546300 GCTT-TAGTTAGC-CTTCA-G-
1 GCTTCCATTTAGCACTT-ATGT
3546318 GCTTCCATTTAGCACTTATGT
1 GCTTCCATTTAGCACTTATGT
3546339 GCTTC
1 GCTTC
3546344 AGCTAGACTT
Statistics
Matches: 33, Mismatches: 6, Indels: 10
0.67 0.12 0.20
Matches are distributed among these distances:
18 4 0.12
19 11 0.33
20 9 0.27
21 9 0.27
ACGTcount: A:0.14, C:0.25, G:0.20, T:0.42
Consensus pattern (21 bp):
GCTTCCATTTAGCACTTATGT
Found at i:3551233 original size:19 final size:17
Alignment explanation
Indices: 3551203--3551245 Score: 50
Period size: 19 Copynumber: 2.4 Consensus size: 17
3551193 AAAAAACAGA
3551203 AAAAACAAAATAAAAAC
1 AAAAACAAAATAAAAAC
*
3551220 AAAAACATATAATAATAAC
1 AAAAACA-A-AATAAAAAC
3551239 AATAAAC
1 AA-AAAC
3551246 CCATAACAAA
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
17 7 0.32
18 1 0.05
19 10 0.45
20 4 0.18
ACGTcount: A:0.74, C:0.12, G:0.00, T:0.14
Consensus pattern (17 bp):
AAAAACAAAATAAAAAC
Found at i:3553973 original size:50 final size:49
Alignment explanation
Indices: 3553857--3553986 Score: 170
Period size: 50 Copynumber: 2.6 Consensus size: 49
3553847 TCTGGTAGCA
* * **
3553857 TAGTAGCCTGCACTTAGTACTACACATGCGACCAACAATCTGGTACACG
1 TAGTAGCCTGCACTTAGTACTACACACGTGACCAACAATCTAATACACG
* * * *
3553906 TAGTAGCCTGCATTTAGTATTACACACGTGACCTCACCATCTAATACACG
1 TAGTAGCCTGCACTTAGTACTACACACGTGACC-AACAATCTAATACACG
*
3553956 TAGTAGCTTGCACTTAGTACTACACACGTGA
1 TAGTAGCCTGCACTTAGTACTACACACGTGA
3553987 TTACAGTTTT
Statistics
Matches: 69, Mismatches: 11, Indels: 1
0.85 0.14 0.01
Matches are distributed among these distances:
49 29 0.42
50 40 0.58
ACGTcount: A:0.30, C:0.27, G:0.17, T:0.26
Consensus pattern (49 bp):
TAGTAGCCTGCACTTAGTACTACACACGTGACCAACAATCTAATACACG
Found at i:3557196 original size:24 final size:25
Alignment explanation
Indices: 3557150--3557196 Score: 69
Period size: 25 Copynumber: 1.9 Consensus size: 25
3557140 CTATAGAGAA
*
3557150 CTAATTTGATTATCTTTTTGTACAT
1 CTAATTTGATTATCTTTTAGTACAT
*
3557175 CTAATTTGATTGT-TTTTAGTAC
1 CTAATTTGATTATCTTTTAGTAC
3557197 TTATATTTTT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
24 8 0.40
25 12 0.60
ACGTcount: A:0.23, C:0.11, G:0.11, T:0.55
Consensus pattern (25 bp):
CTAATTTGATTATCTTTTAGTACAT
Found at i:3560816 original size:28 final size:28
Alignment explanation
Indices: 3560763--3560837 Score: 107
Period size: 28 Copynumber: 2.7 Consensus size: 28
3560753 AGGGTAATTT
*
3560763 TTTTTAATATGAATATTAATATAAAAATA
1 TTTTTAA-ATTAATATTAATATAAAAATA
3560792 -TTTTAAATTAATATTAATATAAAAATA
1 TTTTTAAATTAATATTAATATAAAAATA
* *
3560819 TTTTTAATTTAATTTTAAT
1 TTTTTAAATTAATATTAAT
3560838 GAGGTGGTGA
Statistics
Matches: 42, Mismatches: 3, Indels: 3
0.88 0.06 0.06
Matches are distributed among these distances:
27 20 0.48
28 22 0.52
ACGTcount: A:0.48, C:0.00, G:0.01, T:0.51
Consensus pattern (28 bp):
TTTTTAAATTAATATTAATATAAAAATA
Found at i:3561116 original size:48 final size:51
Alignment explanation
Indices: 3561045--3561149 Score: 164
Period size: 48 Copynumber: 2.1 Consensus size: 51
3561035 GCTTTTGTCC
3561045 TTTTATGTGACAAGATAGAAATATAAATACATCT-TCAATAATATAAAACTT
1 TTTTATGTGACAAGATAGAAATATAAATACATCTCT-AATAATATAAAACTT
*
3561096 TTTTAT-TGA-AA-ATAGAAATATAAATACATCTCTACTAATATAAAACTT
1 TTTTATGTGACAAGATAGAAATATAAATACATCTCTAATAATATAAAACTT
3561144 TTTTAT
1 TTTTAT
3561150 CGAGTTTGGT
Statistics
Matches: 52, Mismatches: 1, Indels: 5
0.90 0.02 0.09
Matches are distributed among these distances:
48 40 0.77
49 3 0.06
50 3 0.06
51 6 0.12
ACGTcount: A:0.46, C:0.10, G:0.06, T:0.39
Consensus pattern (51 bp):
TTTTATGTGACAAGATAGAAATATAAATACATCTCTAATAATATAAAACTT
Found at i:3572781 original size:16 final size:17
Alignment explanation
Indices: 3572762--3572799 Score: 51
Period size: 16 Copynumber: 2.3 Consensus size: 17
3572752 TGGAATTTAA
*
3572762 TTTATGTATTT-TTCTT
1 TTTATGAATTTATTCTT
*
3572778 TTTATGAATTTATTTTT
1 TTTATGAATTTATTCTT
3572795 TTTAT
1 TTTAT
3572800 TGTTTAAATT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
16 10 0.53
17 9 0.47
ACGTcount: A:0.18, C:0.03, G:0.05, T:0.74
Consensus pattern (17 bp):
TTTATGAATTTATTCTT
Found at i:3572805 original size:24 final size:24
Alignment explanation
Indices: 3572760--3572805 Score: 58
Period size: 24 Copynumber: 1.9 Consensus size: 24
3572750 TTTGGAATTT
*
3572760 AATTTATGTATTTTTCTTTTTATG
1 AATTTATGTATTTTTATTTTTATG
*
3572784 AATTTAT-TTTTTTTATTGTTTA
1 AATTTATGTATTTTTATT-TTTA
3572806 AATTTTAAAT
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
23 8 0.42
24 11 0.58
ACGTcount: A:0.22, C:0.02, G:0.07, T:0.70
Consensus pattern (24 bp):
AATTTATGTATTTTTATTTTTATG
Found at i:3572826 original size:20 final size:21
Alignment explanation
Indices: 3572801--3572839 Score: 55
Period size: 20 Copynumber: 1.9 Consensus size: 21
3572791 TTTTTTTATT
3572801 GTTTAAATT-TTAA-ATTTTAA
1 GTTT-AATTATTAATATTTTAA
3572821 GTTTAATTATTAATATTTT
1 GTTTAATTATTAATATTTT
3572840 TAAATTTTTT
Statistics
Matches: 17, Mismatches: 0, Indels: 3
0.85 0.00 0.15
Matches are distributed among these distances:
19 4 0.24
20 8 0.47
21 5 0.29
ACGTcount: A:0.36, C:0.00, G:0.05, T:0.59
Consensus pattern (21 bp):
GTTTAATTATTAATATTTTAA
Found at i:3573417 original size:21 final size:24
Alignment explanation
Indices: 3573393--3573441 Score: 61
Period size: 21 Copynumber: 2.2 Consensus size: 24
3573383 AATTTTCTTG
*
3573393 TTTTATT-TTAAAA-TTTAATT-A
1 TTTTATTGTGAAAATTTTAATTAA
3573414 TTTT-TTGTGAAAATTTTAATTAA
1 TTTTATTGTGAAAATTTTAATTAA
3573437 TTTTA
1 TTTTA
3573442 AACATTTTAG
Statistics
Matches: 23, Mismatches: 1, Indels: 5
0.79 0.03 0.17
Matches are distributed among these distances:
20 2 0.09
21 9 0.39
22 7 0.30
23 5 0.22
ACGTcount: A:0.35, C:0.00, G:0.04, T:0.61
Consensus pattern (24 bp):
TTTTATTGTGAAAATTTTAATTAA
Found at i:3580699 original size:30 final size:29
Alignment explanation
Indices: 3580663--3580723 Score: 113
Period size: 30 Copynumber: 2.1 Consensus size: 29
3580653 AAACGGAAGT
3580663 TTTGGCACTAAGTGTGCGATTTAAACTAGC
1 TTTGGCACTAAGTGTGCGATTT-AACTAGC
3580693 TTTGGCACTAAGTGTGCGATTTAACTAGC
1 TTTGGCACTAAGTGTGCGATTTAACTAGC
3580722 TT
1 TT
3580724 CGGCTACTTG
Statistics
Matches: 31, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
29 9 0.29
30 22 0.71
ACGTcount: A:0.25, C:0.16, G:0.23, T:0.36
Consensus pattern (29 bp):
TTTGGCACTAAGTGTGCGATTTAACTAGC
Found at i:3595165 original size:19 final size:20
Alignment explanation
Indices: 3595127--3595166 Score: 55
Period size: 19 Copynumber: 2.0 Consensus size: 20
3595117 GCAATAATAT
* *
3595127 TTTTTAATTTTTATATTTTA
1 TTTTTAATTTTTAAAATTTA
3595147 TTTTT-ATTTTTAAAATTTA
1 TTTTTAATTTTTAAAATTTA
3595166 T
1 T
3595167 AATTATATAT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
19 13 0.72
20 5 0.28
ACGTcount: A:0.28, C:0.00, G:0.00, T:0.72
Consensus pattern (20 bp):
TTTTTAATTTTTAAAATTTA
Found at i:3595338 original size:21 final size:22
Alignment explanation
Indices: 3595312--3595352 Score: 66
Period size: 21 Copynumber: 1.9 Consensus size: 22
3595302 GGCTATGTGG
*
3595312 TCGCTCAAC-ATTGGTCAACCC
1 TCGCTCAACGACTGGTCAACCC
3595333 TCGCTCAACGACTGGTCAAC
1 TCGCTCAACGACTGGTCAAC
3595353 AATCGGCCAA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 9 0.50
22 9 0.50
ACGTcount: A:0.24, C:0.37, G:0.17, T:0.22
Consensus pattern (22 bp):
TCGCTCAACGACTGGTCAACCC
Found at i:3595941 original size:40 final size:40
Alignment explanation
Indices: 3595897--3595973 Score: 136
Period size: 40 Copynumber: 1.9 Consensus size: 40
3595887 TTGATAATGG
*
3595897 GTTAGGTAAATGTTCCATGATAATGGATTAGGTAAATATT
1 GTTAGGTAAATGTTCCATGATAATGGATTAAGTAAATATT
*
3595937 GTTAGGTAAATGTTCCATGATAATGGTTTAAGTAAAT
1 GTTAGGTAAATGTTCCATGATAATGGATTAAGTAAAT
3595974 GTTCCATGAT
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
40 35 1.00
ACGTcount: A:0.35, C:0.05, G:0.22, T:0.38
Consensus pattern (40 bp):
GTTAGGTAAATGTTCCATGATAATGGATTAAGTAAATATT
Found at i:3597524 original size:26 final size:25
Alignment explanation
Indices: 3597472--3597524 Score: 63
Period size: 26 Copynumber: 2.0 Consensus size: 25
3597462 TTTACAGTTT
3597472 TACCCCTAGTAGATAAATTACCGAAA
1 TACCCCTAG-AGATAAATTACCGAAA
*
3597498 TACCCCTAG-GATTAAATTGACCTAAA
1 TACCCCTAGAGA-TAAATT-ACCGAAA
3597524 T
1 T
3597525 GCATGTTTGA
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
24 2 0.08
25 6 0.25
26 16 0.67
ACGTcount: A:0.40, C:0.23, G:0.11, T:0.26
Consensus pattern (25 bp):
TACCCCTAGAGATAAATTACCGAAA
Found at i:3602872 original size:40 final size:40
Alignment explanation
Indices: 3602828--3602904 Score: 145
Period size: 40 Copynumber: 1.9 Consensus size: 40
3602818 TTGATAATGG
3602828 GTTAGGTAAATGTTCCATGATAATGGATTAGGTAAATATT
1 GTTAGGTAAATGTTCCATGATAATGGATTAGGTAAATATT
*
3602868 GTTAGGTAAATGTTCCATGATAATGGTTTAGGTAAAT
1 GTTAGGTAAATGTTCCATGATAATGGATTAGGTAAAT
3602905 GTTCCATGAT
Statistics
Matches: 36, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
40 36 1.00
ACGTcount: A:0.34, C:0.05, G:0.23, T:0.38
Consensus pattern (40 bp):
GTTAGGTAAATGTTCCATGATAATGGATTAGGTAAATATT
Found at i:3618554 original size:40 final size:40
Alignment explanation
Indices: 3618510--3618586 Score: 145
Period size: 40 Copynumber: 1.9 Consensus size: 40
3618500 TTGATAATGG
3618510 GTTAGGTAAATGTTCCATGATAATGGATTAGGTAAATATT
1 GTTAGGTAAATGTTCCATGATAATGGATTAGGTAAATATT
*
3618550 GTTAGGTAAATGTTCCATGATAATGGTTTAGGTAAAT
1 GTTAGGTAAATGTTCCATGATAATGGATTAGGTAAAT
3618587 GTTCCATGAT
Statistics
Matches: 36, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
40 36 1.00
ACGTcount: A:0.34, C:0.05, G:0.23, T:0.38
Consensus pattern (40 bp):
GTTAGGTAAATGTTCCATGATAATGGATTAGGTAAATATT
Found at i:3633130 original size:36 final size:35
Alignment explanation
Indices: 3633077--3633151 Score: 82
Period size: 36 Copynumber: 2.1 Consensus size: 35
3633067 AAATAAAATG
*
3633077 TTTATAATTTTTATTTATAATTTAGCA-TAAATATAA
1 TTTATAATTTATATTTATAATTT-G-ATTAAATATAA
*
3633113 TTTAT-ATTTATATTTTATTATTTGATTTAAATATAA
1 TTTATAATTTATA-TTTATAATTTGA-TTAAATATAA
3633149 TTT
1 TTT
3633152 GTAGCGACGT
Statistics
Matches: 34, Mismatches: 2, Indels: 6
0.81 0.05 0.14
Matches are distributed among these distances:
34 1 0.03
35 7 0.21
36 26 0.76
ACGTcount: A:0.37, C:0.01, G:0.03, T:0.59
Consensus pattern (35 bp):
TTTATAATTTATATTTATAATTTGATTAAATATAA
Found at i:3634488 original size:23 final size:23
Alignment explanation
Indices: 3634470--3634523 Score: 67
Period size: 23 Copynumber: 2.4 Consensus size: 23
3634460 GGTATACACG
3634470 TACATAATAAAAATATATACTAA
1 TACATAATAAAAATATATACTAA
* **
3634493 TACATAATAATAATA-ATGGTAA
1 TACATAATAAAAATATATACTAA
3634515 TAC-TAATAA
1 TACATAATAA
3634524 TACTAATAAT
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
21 6 0.21
22 8 0.29
23 14 0.50
ACGTcount: A:0.57, C:0.07, G:0.04, T:0.31
Consensus pattern (23 bp):
TACATAATAAAAATATATACTAA
Found at i:3634504 original size:3 final size:3
Alignment explanation
Indices: 3634473--3634543 Score: 54
Period size: 3 Copynumber: 23.3 Consensus size: 3
3634463 ATACACGTAC
* * * * *
3634473 ATA ATA AAA ATA TATA CTA ATA CATA ATA ATA ATA ATG GTA ATA CTA
1 ATA ATA ATA ATA -ATA ATA ATA -ATA ATA ATA ATA ATA ATA ATA ATA
* *
3634520 ATA ATA CTA ATA AT- ATA AAA ATA A
1 ATA ATA ATA ATA ATA ATA ATA ATA A
3634544 CAAGGATATT
Statistics
Matches: 51, Mismatches: 14, Indels: 6
0.72 0.20 0.08
Matches are distributed among these distances:
2 2 0.04
3 43 0.84
4 6 0.12
ACGTcount: A:0.61, C:0.06, G:0.03, T:0.31
Consensus pattern (3 bp):
ATA
Found at i:3635036 original size:18 final size:18
Alignment explanation
Indices: 3635009--3635045 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
3634999 AAGAAAAAAA
*
3635009 AGAAGAGAGAGGGAAGAG
1 AGAAGAGAGAGAGAAGAG
*
3635027 AGAAGGGAGAGAGAAGAG
1 AGAAGAGAGAGAGAAGAG
3635045 A
1 A
3635046 CGGGAATCCG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.51, C:0.00, G:0.49, T:0.00
Consensus pattern (18 bp):
AGAAGAGAGAGAGAAGAG
Found at i:3635041 original size:11 final size:12
Alignment explanation
Indices: 3635010--3635042 Score: 52
Period size: 11 Copynumber: 2.9 Consensus size: 12
3635000 AGAAAAAAAA
3635010 GAAGAGAG-AGG
1 GAAGAGAGAAGG
3635021 GAAGAGAGAAGG
1 GAAGAGAGAAGG
3635033 G-AGAGAGAAG
1 GAAGAGAGAAG
3635043 AGACGGGAAT
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
11 17 0.81
12 4 0.19
ACGTcount: A:0.48, C:0.00, G:0.52, T:0.00
Consensus pattern (12 bp):
GAAGAGAGAAGG
Found at i:3635160 original size:11 final size:11
Alignment explanation
Indices: 3635142--3635171 Score: 53
Period size: 10 Copynumber: 2.8 Consensus size: 11
3635132 AGGTAAAAAA
3635142 TATTTTTTTT-
1 TATTTTTTTTC
3635152 TATTTTTTTTC
1 TATTTTTTTTC
3635163 TATTTTTTT
1 TATTTTTTT
3635172 ATGCTTAATA
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
10 10 0.53
11 9 0.47
ACGTcount: A:0.10, C:0.03, G:0.00, T:0.87
Consensus pattern (11 bp):
TATTTTTTTTC
Found at i:3636951 original size:51 final size:51
Alignment explanation
Indices: 3636896--3636996 Score: 184
Period size: 51 Copynumber: 2.0 Consensus size: 51
3636886 TTTTAAAAAT
3636896 TGTAAAGCGTTACAAATAAAAATTGATGGACTAAATTCTAAATGTGTAAAC
1 TGTAAAGCGTTACAAATAAAAATTGATGGACTAAATTCTAAATGTGTAAAC
* *
3636947 TGTAAAGTGTTACAAATAAAAATTGATGTACTAAATTCTAAATGTGTAAA
1 TGTAAAGCGTTACAAATAAAAATTGATGGACTAAATTCTAAATGTGTAAA
3636997 AAGTATATAG
Statistics
Matches: 48, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
51 48 1.00
ACGTcount: A:0.46, C:0.08, G:0.15, T:0.32
Consensus pattern (51 bp):
TGTAAAGCGTTACAAATAAAAATTGATGGACTAAATTCTAAATGTGTAAAC
Found at i:3652519 original size:30 final size:31
Alignment explanation
Indices: 3652483--3652542 Score: 88
Period size: 32 Copynumber: 1.9 Consensus size: 31
3652473 AAAAAAAATC
3652483 TTATAATTTTA-AATTTTTTA-TAAATTTTGT
1 TTATAATTTTAGAATTTTTTACT-AATTTTGT
3652513 TTATAATTTTAGTAATTTTTTACTAATTTT
1 TTATAATTTTAG-AATTTTTTACTAATTTT
3652543 AAAATTTTAA
Statistics
Matches: 27, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
30 11 0.41
32 15 0.56
33 1 0.04
ACGTcount: A:0.32, C:0.02, G:0.03, T:0.63
Consensus pattern (31 bp):
TTATAATTTTAGAATTTTTTACTAATTTTGT
Found at i:3654712 original size:26 final size:24
Alignment explanation
Indices: 3654682--3654729 Score: 69
Period size: 26 Copynumber: 1.9 Consensus size: 24
3654672 AATAAAAAAA
*
3654682 TTAAAAATATAATAAATCAAATATAT
1 TTAAAAACATAA-AAA-CAAATATAT
3654708 TTAAAAACATAAAAACAAATAT
1 TTAAAAACATAAAAACAAATAT
3654730 TAAAACAAAT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
24 7 0.33
25 3 0.14
26 11 0.52
ACGTcount: A:0.65, C:0.06, G:0.00, T:0.29
Consensus pattern (24 bp):
TTAAAAACATAAAAACAAATATAT
Found at i:3654749 original size:21 final size:21
Alignment explanation
Indices: 3654700--3654758 Score: 59
Period size: 21 Copynumber: 2.8 Consensus size: 21
3654690 ATAATAAATC
*
3654700 AAAT-ATATTTAAAA-ACATAA
1 AAATAATA-TTAAAACAAATAA
*
3654720 AAACAAATATTAAAACAAATAA
1 AAA-TAATATTAAAACAAATAA
*
3654742 AAATAATACTAAAACAA
1 AAATAATATTAAAACAA
3654759 TTCTTAAAAC
Statistics
Matches: 32, Mismatches: 4, Indels: 5
0.78 0.10 0.12
Matches are distributed among these distances:
20 3 0.09
21 18 0.56
22 11 0.34
ACGTcount: A:0.69, C:0.08, G:0.00, T:0.22
Consensus pattern (21 bp):
AAATAATATTAAAACAAATAA
Found at i:3655808 original size:16 final size:16
Alignment explanation
Indices: 3655787--3655835 Score: 61
Period size: 16 Copynumber: 3.2 Consensus size: 16
3655777 ATATTTAGTC
3655787 ATATAATAAATTATTA
1 ATATAATAAATTATTA
3655803 ATATAAT---TTATTA
1 ATATAATAAATTATTA
3655816 A-ATAATAAATTATTTA
1 ATATAATAAATTA-TTA
3655832 ATAT
1 ATAT
3655836 TTCAATTTTA
Statistics
Matches: 28, Mismatches: 0, Indels: 9
0.76 0.00 0.24
Matches are distributed among these distances:
12 5 0.18
13 7 0.25
15 3 0.11
16 11 0.39
17 2 0.07
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (16 bp):
ATATAATAAATTATTA
Found at i:3655821 original size:28 final size:28
Alignment explanation
Indices: 3655789--3655875 Score: 88
Period size: 28 Copynumber: 2.9 Consensus size: 28
3655779 ATTTAGTCAT
3655789 ATAATAAATTATTAATATAATTTATTAA
1 ATAATAAATTATTAATATAATTTATTAA
*
3655817 ATAATAAATTATTTAATATTTCAATTTTATTTTA
1 ATAATAAATTA-TTAATA--T-AA-TTTA-TTAA
3655851 ATAATAAATT-TTAA-ATAATATTATT
1 ATAATAAATTATTAATATAAT-TTATT
3655876 CACATATTAT
Statistics
Matches: 51, Mismatches: 1, Indels: 15
0.76 0.01 0.22
Matches are distributed among these distances:
27 3 0.06
28 16 0.31
29 7 0.14
31 2 0.04
32 6 0.12
33 4 0.08
34 13 0.25
ACGTcount: A:0.48, C:0.01, G:0.00, T:0.51
Consensus pattern (28 bp):
ATAATAAATTATTAATATAATTTATTAA
Found at i:3655923 original size:15 final size:15
Alignment explanation
Indices: 3655889--3655959 Score: 65
Period size: 15 Copynumber: 4.6 Consensus size: 15
3655879 ATATTATTGG
3655889 AAATA-TTTAAT-AT
1 AAATATTTTAATAAT
*
3655902 TAATATTTTAATAAT
1 AAATATTTTAATAAT
*
3655917 AAATATTTATTACAATTAT
1 AAATA-TT-TT--AATAAT
*
3655936 AAATATATTAATAAT
1 AAATATTTTAATAAT
3655951 AAATATTTT
1 AAATATTTT
3655960 GTAGTATAAA
Statistics
Matches: 46, Mismatches: 6, Indels: 10
0.74 0.10 0.16
Matches are distributed among these distances:
13 4 0.09
14 6 0.13
15 19 0.41
16 2 0.04
17 4 0.09
18 1 0.02
19 10 0.22
ACGTcount: A:0.51, C:0.01, G:0.00, T:0.48
Consensus pattern (15 bp):
AAATATTTTAATAAT
Found at i:3656657 original size:15 final size:15
Alignment explanation
Indices: 3656637--3656669 Score: 66
Period size: 15 Copynumber: 2.2 Consensus size: 15
3656627 CTCCTTACTA
3656637 AGTTACATCTCTTTT
1 AGTTACATCTCTTTT
3656652 AGTTACATCTCTTTT
1 AGTTACATCTCTTTT
3656667 AGT
1 AGT
3656670 GTTATTTAAG
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.21, C:0.18, G:0.09, T:0.52
Consensus pattern (15 bp):
AGTTACATCTCTTTT
Found at i:3658811 original size:18 final size:18
Alignment explanation
Indices: 3658788--3658823 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
3658778 ACTCACTTCT
3658788 CCTTCGCCTCCGCCTCCG
1 CCTTCGCCTCCGCCTCCG
* *
3658806 CCTTCGTCTCCGTCTCCG
1 CCTTCGCCTCCGCCTCCG
3658824 TCGGATTCGG
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:0.00, C:0.56, G:0.17, T:0.28
Consensus pattern (18 bp):
CCTTCGCCTCCGCCTCCG
Found at i:3663189 original size:98 final size:98
Alignment explanation
Indices: 3663020--3663217 Score: 378
Period size: 98 Copynumber: 2.0 Consensus size: 98
3663010 TGAAAATTAC
*
3663020 TATAAAGTGCTTAATTTTTGTGATATTTTTCTCTTTGTCTTCTCTTTTCAAATGCTTGTAATCTT
1 TATAAAGTGCTTAATTTTTGTGATATTTTTCTCTCTGTCTTCTCTTTTCAAATGCTTGTAATCTT
3663085 GCAAACTCTGTAATGCTGTATGGTCACATCAGT
66 GCAAACTCTGTAATGCTGTATGGTCACATCAGT
3663118 TATAAAGTGCTTAATTTTTGTGATATTTTTCTCTCTGTCTTCTCTTTTCAAATGCTTGTAATCTT
1 TATAAAGTGCTTAATTTTTGTGATATTTTTCTCTCTGTCTTCTCTTTTCAAATGCTTGTAATCTT
*
3663183 GCAAACTCTGTAATGCTGTATGGTCAGATCAGT
66 GCAAACTCTGTAATGCTGTATGGTCACATCAGT
3663216 TA
1 TA
3663218 GAATGCTTTA
Statistics
Matches: 98, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
98 98 1.00
ACGTcount: A:0.23, C:0.16, G:0.15, T:0.46
Consensus pattern (98 bp):
TATAAAGTGCTTAATTTTTGTGATATTTTTCTCTCTGTCTTCTCTTTTCAAATGCTTGTAATCTT
GCAAACTCTGTAATGCTGTATGGTCACATCAGT
Found at i:3665163 original size:17 final size:18
Alignment explanation
Indices: 3665129--3665174 Score: 64
Period size: 17 Copynumber: 2.8 Consensus size: 18
3665119 CCGTTATGTC
3665129 CGCGACCGCGA-C--AAA
1 CGCGACCGCGACCGAAAA
3665144 CGCGA-CGCGACCGAAAA
1 CGCGACCGCGACCGAAAA
3665161 CGCGACCGCGACCG
1 CGCGACCGCGACCG
3665175 CAATTTAAAT
Statistics
Matches: 27, Mismatches: 0, Indels: 5
0.84 0.00 0.16
Matches are distributed among these distances:
14 5 0.19
15 6 0.22
17 8 0.30
18 8 0.30
ACGTcount: A:0.28, C:0.41, G:0.30, T:0.00
Consensus pattern (18 bp):
CGCGACCGCGACCGAAAA
Found at i:3679739 original size:26 final size:26
Alignment explanation
Indices: 3679710--3679760 Score: 75
Period size: 26 Copynumber: 2.0 Consensus size: 26
3679700 CCCTAAGTAT
* *
3679710 AGTTAGTATTATATTTCAAAAATAAA
1 AGTTAATATTATATTCCAAAAATAAA
*
3679736 AGTTAATGTTATATTCCAAAAATAA
1 AGTTAATATTATATTCCAAAAATAA
3679761 GAAAATAGAA
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
26 22 1.00
ACGTcount: A:0.49, C:0.06, G:0.08, T:0.37
Consensus pattern (26 bp):
AGTTAATATTATATTCCAAAAATAAA
Found at i:3686801 original size:92 final size:89
Alignment explanation
Indices: 3686692--3686869 Score: 275
Period size: 92 Copynumber: 2.0 Consensus size: 89
3686682 ATCTCCATTA
*
3686692 CCCAATCTCTCATTGGAATTTTATTAAAAATTTATATTGATATATTAATAATATTATTAAATAAT
1 CCCAATCTCTCATTGGAATTTTATTAAAAATTTATAGTGATATATTAATAATATTATTAAATAAT
3686757 AATTAAAAAATGAAATTAAAATTGCTG
66 AA-T--AAAATGAAATTAAAATTGCTG
* * ** *
3686784 CCCACTCTCTCATTGGAATTTTATTAAATATTTATAGTGATATATTAATTTTATTATTAGATAAT
1 CCCAATCTCTCATTGGAATTTTATTAAAAATTTATAGTGATATATTAATAATATTATTAAATAAT
3686849 AATAAAATGAAATTAAAATTG
66 AATAAAATGAAATTAAAATTG
3686870 TACCAGGGCA
Statistics
Matches: 80, Mismatches: 6, Indels: 3
0.90 0.07 0.03
Matches are distributed among these distances:
89 18 0.22
91 1 0.01
92 61 0.76
ACGTcount: A:0.43, C:0.08, G:0.07, T:0.42
Consensus pattern (89 bp):
CCCAATCTCTCATTGGAATTTTATTAAAAATTTATAGTGATATATTAATAATATTATTAAATAAT
AATAAAATGAAATTAAAATTGCTG
Found at i:3691639 original size:175 final size:176
Alignment explanation
Indices: 3691337--3691688 Score: 616
Period size: 175 Copynumber: 2.0 Consensus size: 176
3691327 ACTATCATTC
*
3691337 AGGAGGTTGGGATTGAGAAAACCTGATATCTTGTTCGTGAGCTTGGGAAGATCTAATATTTGATT
1 AGGAGATTGGGATTGAGAAAACCTGATATCTTGTTCGTGAGCTTGGGAAGATCTAATATTTGATT
* * * * *
3691402 TTTCTCCACTATTAACAAAAGGTTAAGGAACTGATTGATCATTATTGCTTTTTGTTACCCTTTTT
66 TTTCTCCACTAATAACAAAAGGTTAAAGAACTGATTGATCATAATTGCTTTCTGTCACCCTTTTT
*
3691467 TCGAAAAAAGATTCGGTCTTTTTGTTGACCATTATTTAATCTGAAA
131 TCGAAAAAAGATTCGGTCTTTTTGTTGACCATAATTTAATCTGAAA
3691513 AGGAGATTGGGATTGAGAAAACCTGATATCTTGTTCGTGAGCTT-GGAAGATCTAATATTTGATT
1 AGGAGATTGGGATTGAGAAAACCTGATATCTTGTTCGTGAGCTTGGGAAGATCTAATATTTGATT
*
3691577 TTTCTCCACTAATAACAAAAGGTTAAAGAACTGATTGATCGTAATTGCTTTCTGTCACCCTTTTT
66 TTTCTCCACTAATAACAAAAGGTTAAAGAACTGATTGATCATAATTGCTTTCTGTCACCCTTTTT
*
3691642 TCGAAAAATGATTCGGTCTTTTTGTTGACCATAATTTAATCTGAAA
131 TCGAAAAAAGATTCGGTCTTTTTGTTGACCATAATTTAATCTGAAA
3691688 A
1 A
3691689 ACCTGAAGAC
Statistics
Matches: 167, Mismatches: 9, Indels: 1
0.94 0.05 0.01
Matches are distributed among these distances:
175 124 0.74
176 43 0.26
ACGTcount: A:0.30, C:0.14, G:0.19, T:0.38
Consensus pattern (176 bp):
AGGAGATTGGGATTGAGAAAACCTGATATCTTGTTCGTGAGCTTGGGAAGATCTAATATTTGATT
TTTCTCCACTAATAACAAAAGGTTAAAGAACTGATTGATCATAATTGCTTTCTGTCACCCTTTTT
TCGAAAAAAGATTCGGTCTTTTTGTTGACCATAATTTAATCTGAAA
Found at i:3692838 original size:15 final size:15
Alignment explanation
Indices: 3692787--3692838 Score: 50
Period size: 15 Copynumber: 3.2 Consensus size: 15
3692777 ATTCAATATT
*
3692787 AATATCTTAATAATA
1 AATATATTAATAATA
*
3692802 AATATTTATTACAGTTATA
1 AATA--TATTA-A-TAATA
3692821 AATATATTAATAATA
1 AATATATTAATAATA
3692836 AAT
1 AAT
3692839 GTTTTGTAGT
Statistics
Matches: 30, Mismatches: 3, Indels: 8
0.73 0.07 0.20
Matches are distributed among these distances:
15 11 0.37
16 1 0.03
17 9 0.30
18 1 0.03
19 8 0.27
ACGTcount: A:0.52, C:0.04, G:0.02, T:0.42
Consensus pattern (15 bp):
AATATATTAATAATA
Found at i:3708562 original size:49 final size:48
Alignment explanation
Indices: 3708508--3708604 Score: 133
Period size: 48 Copynumber: 2.0 Consensus size: 48
3708498 ATAAAGAGGG
* * *
3708508 TTTAAAATAAATAATATATAAAATAGTTT-AACTACATAATGTATATAAA
1 TTTAAAATAAATAATATAT-AAA-AGTTTAAAATAAATAACGTATATAAA
*
3708557 TTTAAAATAAATAATATGTAAAAGTTTAAAATAAATAACGTATATAAA
1 TTTAAAATAAATAATATATAAAAGTTTAAAATAAATAACGTATATAAA
3708605 AAGAAAATCA
Statistics
Matches: 43, Mismatches: 4, Indels: 3
0.86 0.08 0.06
Matches are distributed among these distances:
47 5 0.12
48 20 0.47
49 18 0.42
ACGTcount: A:0.57, C:0.03, G:0.05, T:0.35
Consensus pattern (48 bp):
TTTAAAATAAATAATATATAAAAGTTTAAAATAAATAACGTATATAAA
Found at i:3708584 original size:24 final size:24
Alignment explanation
Indices: 3708456--3708605 Score: 103
Period size: 24 Copynumber: 6.2 Consensus size: 24
3708446 ATTATATAAA
* * * *
3708456 AAAAATTTAAAATAAACAATGTAG
1 AAAAGTTTAAAATAAATAATATAT
*
3708480 AACAA-TTTAAAATAACTAATA-A-
1 AA-AAGTTTAAAATAAATAATATAT
**
3708502 AGAGGGTTTAAAATAAATAATATAT
1 A-AAAGTTTAAAATAAATAATATAT
* * *
3708527 AAAATAGTTT-AACTACATAATGTAT
1 -AAA-AGTTTAAAATAAATAATATAT
*
3708552 ATAAA-TTTAAAATAAATAATATGT
1 A-AAAGTTTAAAATAAATAATATAT
3708576 AAAAGTTTAAAATAAATAACGTATAT
1 AAAAGTTTAAAATAAATAA--TATAT
3708602 AAAA
1 AAAA
3708606 AGAAAATCAT
Statistics
Matches: 98, Mismatches: 16, Indels: 22
0.72 0.12 0.16
Matches are distributed among these distances:
22 1 0.01
23 23 0.23
24 44 0.45
25 17 0.17
26 13 0.13
ACGTcount: A:0.58, C:0.04, G:0.07, T:0.31
Consensus pattern (24 bp):
AAAAGTTTAAAATAAATAATATAT
Found at i:3718529 original size:29 final size:29
Alignment explanation
Indices: 3718466--3718537 Score: 92
Period size: 29 Copynumber: 2.5 Consensus size: 29
3718456 ATTCACAATA
* *
3718466 AATTGAGCCTTCAACATCTATTTTCATGC
1 AATTGACCCTTCAACATCTATTTTCATCC
*
3718495 ATTTGAACCCTTCAA-ATCTATTTTCATCC
1 AATTG-ACCCTTCAACATCTATTTTCATCC
*
3718524 AATTGAGCCTTCAA
1 AATTGACCCTTCAA
3718538 TCTGACAATT
Statistics
Matches: 37, Mismatches: 5, Indels: 3
0.82 0.11 0.07
Matches are distributed among these distances:
28 8 0.22
29 21 0.57
30 8 0.22
ACGTcount: A:0.29, C:0.25, G:0.08, T:0.38
Consensus pattern (29 bp):
AATTGACCCTTCAACATCTATTTTCATCC
Found at i:3721995 original size:39 final size:39
Alignment explanation
Indices: 3721951--3722062 Score: 206
Period size: 39 Copynumber: 2.9 Consensus size: 39
3721941 ATTTTAACCG
* *
3721951 GACAAAACATAATACACATACCAATTCCTTCACACTAAA
1 GACAAAACATAAAACACATACCAATTCCTTCACACCAAA
3721990 GACAAAACATAAAACACATACCAATTCCTTCACACCAAA
1 GACAAAACATAAAACACATACCAATTCCTTCACACCAAA
3722029 GACAAAACATAAAACACATACCAATTCCTTCACA
1 GACAAAACATAAAACACATACCAATTCCTTCACA
3722063 TCACTCATGT
Statistics
Matches: 71, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
39 71 1.00
ACGTcount: A:0.50, C:0.29, G:0.03, T:0.18
Consensus pattern (39 bp):
GACAAAACATAAAACACATACCAATTCCTTCACACCAAA
Found at i:3729176 original size:15 final size:15
Alignment explanation
Indices: 3729156--3729189 Score: 59
Period size: 15 Copynumber: 2.3 Consensus size: 15
3729146 AACCTTCTGA
3729156 TGATTCTCTACCAAT
1 TGATTCTCTACCAAT
*
3729171 TGATTCTCTACCAGT
1 TGATTCTCTACCAAT
3729186 TGAT
1 TGAT
3729190 GCAATGGAAT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.24, C:0.24, G:0.12, T:0.41
Consensus pattern (15 bp):
TGATTCTCTACCAAT
Found at i:3738304 original size:28 final size:28
Alignment explanation
Indices: 3738250--3738310 Score: 70
Period size: 28 Copynumber: 2.2 Consensus size: 28
3738240 AAAATTTTAT
* *
3738250 TATAAAAATATTTTATATATTATAAAAA
1 TATAAAAATATTTCATATATTAAAAAAA
* *
3738278 TATAAAAATATATTCATTTA-TAAAAAAT
1 TATAAAAATAT-TTCATATATTAAAAAAA
3738306 TATAA
1 TATAA
3738311 TAGAGTATGA
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
28 22 0.79
29 6 0.21
ACGTcount: A:0.57, C:0.02, G:0.00, T:0.41
Consensus pattern (28 bp):
TATAAAAATATTTCATATATTAAAAAAA
Found at i:3739274 original size:23 final size:23
Alignment explanation
Indices: 3739244--3739290 Score: 76
Period size: 23 Copynumber: 2.0 Consensus size: 23
3739234 TGAATATATT
* *
3739244 ATTACATGCGTAAATTTTACGGA
1 ATTACATGCATAAATTTTAAGGA
3739267 ATTACATGCATAAATTTTAAGGA
1 ATTACATGCATAAATTTTAAGGA
3739290 A
1 A
3739291 AAAATATATT
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
23 22 1.00
ACGTcount: A:0.40, C:0.11, G:0.15, T:0.34
Consensus pattern (23 bp):
ATTACATGCATAAATTTTAAGGA
Found at i:3755968 original size:7 final size:7
Alignment explanation
Indices: 3755956--3755980 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
3755946 ATTTGACAAA
3755956 AAAAAAC
1 AAAAAAC
3755963 AAAAAAC
1 AAAAAAC
3755970 AAAAAAC
1 AAAAAAC
3755977 AAAA
1 AAAA
3755981 CAAAACATGC
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:0.88, C:0.12, G:0.00, T:0.00
Consensus pattern (7 bp):
AAAAAAC
Found at i:3755987 original size:17 final size:17
Alignment explanation
Indices: 3755951--3755985 Score: 52
Period size: 19 Copynumber: 1.9 Consensus size: 17
3755941 TATACATTTG
3755951 ACAAAAAAAAACAAAAA
1 ACAAAAAAAAACAAAAA
3755968 ACAAAAAACAAAACAAAA
1 AC-AAAAA-AAAACAAAA
3755986 CATGCAGGAA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 2 0.12
18 5 0.31
19 9 0.56
ACGTcount: A:0.86, C:0.14, G:0.00, T:0.00
Consensus pattern (17 bp):
ACAAAAAAAAACAAAAA
Found at i:3761788 original size:6 final size:6
Alignment explanation
Indices: 3761730--3761785 Score: 94
Period size: 6 Copynumber: 9.3 Consensus size: 6
3761720 AATGGTGAAA
*
3761730 GGCAAT GGCAAT GGCAAT GGCAAT GGCAAT GGCAAT GGCAAT GGGAAT
1 GGCAAT GGCAAT GGCAAT GGCAAT GGCAAT GGCAAT GGCAAT GGCAAT
*
3761778 GGGAAT GG
1 GGCAAT GG
3761786 GAAAGGTTAT
Statistics
Matches: 49, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
6 49 1.00
ACGTcount: A:0.32, C:0.12, G:0.39, T:0.16
Consensus pattern (6 bp):
GGCAAT
Found at i:3773027 original size:24 final size:25
Alignment explanation
Indices: 3772995--3773045 Score: 95
Period size: 24 Copynumber: 2.1 Consensus size: 25
3772985 TAAATACAAT
3772995 GTAATGCAAGCCTAAGAAGATG-AA
1 GTAATGCAAGCCTAAGAAGATGTAA
3773019 GTAATGCAAGCCTAAGAAGATGTAA
1 GTAATGCAAGCCTAAGAAGATGTAA
3773044 GT
1 GT
3773046 TCAAGCCAGA
Statistics
Matches: 26, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
24 22 0.85
25 4 0.15
ACGTcount: A:0.43, C:0.12, G:0.25, T:0.20
Consensus pattern (25 bp):
GTAATGCAAGCCTAAGAAGATGTAA
Found at i:3773043 original size:21 final size:21
Alignment explanation
Indices: 3772993--3773052 Score: 75
Period size: 24 Copynumber: 2.7 Consensus size: 21
3772983 CATAAATACA
3772993 ATGTAATGCAAGCCTAAGAAG
1 ATGTAATGCAAGCCTAAGAAG
3773014 ATGAAGTAATGCAAGCCTAAGAAG
1 AT---GTAATGCAAGCCTAAGAAG
*
3773038 ATGTAAGTTCAAGCC
1 ATGTAA-TGCAAGCC
3773053 AGATGACCTC
Statistics
Matches: 34, Mismatches: 1, Indels: 7
0.81 0.02 0.17
Matches are distributed among these distances:
21 6 0.18
22 7 0.21
24 21 0.62
ACGTcount: A:0.42, C:0.15, G:0.23, T:0.20
Consensus pattern (21 bp):
ATGTAATGCAAGCCTAAGAAG
Found at i:3774312 original size:13 final size:13
Alignment explanation
Indices: 3774294--3774321 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
3774284 AAAAATTCCG
3774294 AAATCTGTACACA
1 AAATCTGTACACA
3774307 AAATCTGTACACA
1 AAATCTGTACACA
3774320 AA
1 AA
3774322 CTACAAAAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.50, C:0.21, G:0.07, T:0.21
Consensus pattern (13 bp):
AAATCTGTACACA
Found at i:3781537 original size:12 final size:12
Alignment explanation
Indices: 3781520--3781549 Score: 51
Period size: 12 Copynumber: 2.5 Consensus size: 12
3781510 TTTAAATTAT
3781520 GAAAGAGAACTC
1 GAAAGAGAACTC
*
3781532 GAAAGAGAACTT
1 GAAAGAGAACTC
3781544 GAAAGA
1 GAAAGA
3781550 TAAAAATCAA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
12 17 1.00
ACGTcount: A:0.53, C:0.10, G:0.27, T:0.10
Consensus pattern (12 bp):
GAAAGAGAACTC
Found at i:3782601 original size:34 final size:34
Alignment explanation
Indices: 3782558--3782623 Score: 132
Period size: 34 Copynumber: 1.9 Consensus size: 34
3782548 GAATCTATGA
3782558 TACCATTAGGGTTAGCTAGCTCAAGTATCCAGCT
1 TACCATTAGGGTTAGCTAGCTCAAGTATCCAGCT
3782592 TACCATTAGGGTTAGCTAGCTCAAGTATCCAG
1 TACCATTAGGGTTAGCTAGCTCAAGTATCCAG
3782624 TAACACATGA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
34 32 1.00
ACGTcount: A:0.27, C:0.23, G:0.21, T:0.29
Consensus pattern (34 bp):
TACCATTAGGGTTAGCTAGCTCAAGTATCCAGCT
Found at i:3787876 original size:16 final size:15
Alignment explanation
Indices: 3787851--3787884 Score: 50
Period size: 16 Copynumber: 2.2 Consensus size: 15
3787841 ACTTTTGTAG
*
3787851 TATATATATATTTTA
1 TATATATATAATTTA
3787866 TATATTATATAATTTA
1 TATA-TATATAATTTA
3787882 TAT
1 TAT
3787885 CACATAAAAT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
15 4 0.24
16 13 0.76
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (15 bp):
TATATATATAATTTA
Found at i:3790283 original size:20 final size:20
Alignment explanation
Indices: 3790258--3790309 Score: 68
Period size: 20 Copynumber: 2.5 Consensus size: 20
3790248 AACGCAAACG
** *
3790258 GAAAAAGATGAGTAAACCTA
1 GAAAAAGAAAAGTAAAACTA
3790278 GAAAAAGAAAAGTAAAACTA
1 GAAAAAGAAAAGTAAAACTA
3790298 GAAAAATGAAAA
1 GAAAAA-GAAAA
3790310 ACCGAATATG
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
20 23 0.82
21 5 0.18
ACGTcount: A:0.65, C:0.06, G:0.17, T:0.12
Consensus pattern (20 bp):
GAAAAAGAAAAGTAAAACTA
Found at i:3797090 original size:21 final size:20
Alignment explanation
Indices: 3797066--3797114 Score: 55
Period size: 20 Copynumber: 2.5 Consensus size: 20
3797056 ATAAGCATTA
*
3797066 AAATAAATAAAAAATTGTATT
1 AAAT-AATAAAAAATTGAATT
* *
3797087 AAATTATTAAAAATTGAATT
1 AAATAATAAAAAATTGAATT
3797107 AAA-AATAA
1 AAATAATAA
3797115 CATAAACTTT
Statistics
Matches: 23, Mismatches: 5, Indels: 2
0.77 0.17 0.07
Matches are distributed among these distances:
19 3 0.13
20 16 0.70
21 4 0.17
ACGTcount: A:0.63, C:0.00, G:0.04, T:0.33
Consensus pattern (20 bp):
AAATAATAAAAAATTGAATT
Found at i:3803303 original size:3 final size:3
Alignment explanation
Indices: 3803295--3803328 Score: 68
Period size: 3 Copynumber: 11.3 Consensus size: 3
3803285 TCTATCCTTT
3803295 TCC TCC TCC TCC TCC TCC TCC TCC TCC TCC TCC T
1 TCC TCC TCC TCC TCC TCC TCC TCC TCC TCC TCC T
3803329 TTTCTTCTTA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 31 1.00
ACGTcount: A:0.00, C:0.65, G:0.00, T:0.35
Consensus pattern (3 bp):
TCC
Found at i:3803557 original size:11 final size:10
Alignment explanation
Indices: 3803540--3803598 Score: 68
Period size: 10 Copynumber: 6.0 Consensus size: 10
3803530 ATATTTTTTA
3803540 TAAAAAATAT
1 TAAAAAATAT
3803550 TAAAAAA-AT
1 TAAAAAATAT
* *
3803559 TATAAAATTT
1 TAAAAAATAT
3803569 ATAAAAAATA-
1 -TAAAAAATAT
*
3803579 GAAAAAATAT
1 TAAAAAATAT
3803589 TAAAAAATAT
1 TAAAAAATAT
3803599 AAACTTATAA
Statistics
Matches: 40, Mismatches: 6, Indels: 6
0.77 0.12 0.12
Matches are distributed among these distances:
9 16 0.40
10 17 0.43
11 7 0.17
ACGTcount: A:0.69, C:0.00, G:0.02, T:0.29
Consensus pattern (10 bp):
TAAAAAATAT
Found at i:3803570 original size:30 final size:30
Alignment explanation
Indices: 3803536--3803596 Score: 88
Period size: 30 Copynumber: 2.0 Consensus size: 30
3803526 TCTAATATTT
* *
3803536 TTTATAAAAAATATTAAAAAA-ATTATAAAA
1 TTTATAAAAAATA-GAAAAAATATTAAAAAA
3803566 TTTATAAAAAATAGAAAAAATATTAAAAAA
1 TTTATAAAAAATAGAAAAAATATTAAAAAA
3803596 T
1 T
3803597 ATAAACTTAT
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
29 6 0.21
30 22 0.79
ACGTcount: A:0.67, C:0.00, G:0.02, T:0.31
Consensus pattern (30 bp):
TTTATAAAAAATAGAAAAAATATTAAAAAA
Found at i:3803574 original size:19 final size:18
Alignment explanation
Indices: 3803543--3803667 Score: 76
Period size: 19 Copynumber: 6.7 Consensus size: 18
3803533 TTTTTTATAA
3803543 AAAATATTA-AAAAAATTAT
1 AAAAT-TTATAAAAAA-TAT
*
3803562 AAAATTTATAAAAAATAG
1 AAAATTTATAAAAAATAT
**
3803580 AAAAAATATTAAAAAATAT
1 AAAATTTA-TAAAAAATAT
* *
3803599 -AAACTTATAAAAATTAT
1 AAAATTTATAAAAAATAT
* * *
3803616 AAAA-ATATATATAATAGT
1 AAAATTTATAAAAAATA-T
*
3803634 ATAAATATTATAATAAATAT
1 A-AAAT-TTATAAAAAATAT
*
3803654 AATAAATTATAAAA
1 AA-AATTTATAAAA
3803668 TTAATAAAAA
Statistics
Matches: 81, Mismatches: 17, Indels: 16
0.71 0.15 0.14
Matches are distributed among these distances:
17 17 0.21
18 21 0.26
19 31 0.38
20 4 0.05
21 8 0.10
ACGTcount: A:0.66, C:0.01, G:0.02, T:0.32
Consensus pattern (18 bp):
AAAATTTATAAAAAATAT
Found at i:3803601 original size:9 final size:9
Alignment explanation
Indices: 3803538--3803685 Score: 84
Period size: 9 Copynumber: 15.7 Consensus size: 9
3803528 TAATATTTTT
3803538 TATAAAAAA
1 TATAAAAAA
3803547 TATTAAAAAAA
1 TA-T-AAAAAA
**
3803558 TTATAAAATT
1 -TATAAAAAA
3803568 TATAAAAAA
1 TATAAAAAA
*
3803577 TAGAAAAAA
1 TATAAAAAA
3803586 TATTAAAAAA
1 TA-TAAAAAA
**
3803596 TAT-AAACT
1 TATAAAAAA
*
3803604 TATAAAAAT
1 TATAAAAAA
3803613 TATAAAAATA
1 TATAAAAA-A
* *
3803623 TATATAATAG
1 TATA-AAAAA
* *
3803633 TATAAATAT
1 TATAAAAAA
*
3803642 TATAATAAA
1 TATAAAAAA
*
3803651 TATAATAAAT
1 TATAA-AAAA
3803661 TATAAAATTAA
1 TATAAAA--AA
3803672 TA-AAAAAA
1 TATAAAAAA
*
3803680 TTTAAA
1 TATAAA
3803686 TTTTATAAAA
Statistics
Matches: 108, Mismatches: 20, Indels: 22
0.72 0.13 0.15
Matches are distributed among these distances:
8 9 0.08
9 52 0.48
10 32 0.30
11 13 0.12
12 2 0.02
ACGTcount: A:0.66, C:0.01, G:0.01, T:0.32
Consensus pattern (9 bp):
TATAAAAAA
Found at i:3803685 original size:19 final size:20
Alignment explanation
Indices: 3803550--3803696 Score: 63
Period size: 19 Copynumber: 7.3 Consensus size: 20
3803540 TAAAAAATAT
*
3803550 TAAAAAAATTATAAAATTTA
1 TAAAAAAATTATAAAATTAA
** *
3803570 TAAAAAATAGAAAAAATATTAA
1 TAAAAAA-ATTATAAA-ATTAA
*
3803592 AAAATATAAACTTATAAAAATT-A
1 TAAA-A-AAA-TTAT-AAAATTAA
* * *
3803615 TAAAAATA-TATATAA-TAG
1 TAAAAAAATTATAAAATTAA
* * *
3803633 TATAAATATTAT--AATAAA
1 TAAAAAAATTATAAAATTAA
*
3803651 TATAATAAATTATAAAATTAA
1 TA-AAAAAATTATAAAATTAA
* *
3803672 TAAAAAAATT-TAAATTTTA
1 TAAAAAAATTATAAAATTAA
3803691 TAAAAA
1 TAAAAA
3803697 CGTATTAAAA
Statistics
Matches: 93, Mismatches: 22, Indels: 25
0.66 0.16 0.18
Matches are distributed among these distances:
17 3 0.03
18 13 0.14
19 26 0.28
20 14 0.15
21 14 0.15
22 8 0.09
23 6 0.06
24 6 0.06
25 3 0.03
ACGTcount: A:0.65, C:0.01, G:0.01, T:0.33
Consensus pattern (20 bp):
TAAAAAAATTATAAAATTAA
Found at i:3804520 original size:30 final size:30
Alignment explanation
Indices: 3804486--3804548 Score: 74
Period size: 30 Copynumber: 2.1 Consensus size: 30
3804476 ATAATTAAAA
* *
3804486 ATAAA-ATTATTAAGATTGATATAATATAAT
1 ATAAATATTATTAAAATT-ATAAAATATAAT
* *
3804516 ATAAATATTTTTAAAATTTTAAAATATAAT
1 ATAAATATTATTAAAATTATAAAATATAAT
3804546 ATA
1 ATA
3804549 GGCGGGTTAA
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
30 18 0.64
31 10 0.36
ACGTcount: A:0.54, C:0.00, G:0.03, T:0.43
Consensus pattern (30 bp):
ATAAATATTATTAAAATTATAAAATATAAT
Found at i:3812508 original size:35 final size:36
Alignment explanation
Indices: 3812444--3812529 Score: 129
Period size: 35 Copynumber: 2.4 Consensus size: 36
3812434 GTGGCATTTT
3812444 ATATTTTTAAAAATTTACTTATAAAAATAAAAAAAATG
1 ATATTTTTAAAAA--TACTTATAAAAATAAAAAAAATG
*
3812482 ATATTTTTAAAAA-ATTTATAAAAATAAAAAAAATG
1 ATATTTTTAAAAATACTTATAAAAATAAAAAAAATG
*
3812517 ATAATTTTAAAAA
1 ATATTTTTAAAAA
3812530 CGTATTAAAA
Statistics
Matches: 46, Mismatches: 2, Indels: 3
0.90 0.04 0.06
Matches are distributed among these distances:
35 33 0.72
38 13 0.28
ACGTcount: A:0.60, C:0.01, G:0.02, T:0.36
Consensus pattern (36 bp):
ATATTTTTAAAAATACTTATAAAAATAAAAAAAATG
Found at i:3812527 original size:18 final size:18
Alignment explanation
Indices: 3812471--3812529 Score: 57
Period size: 18 Copynumber: 3.3 Consensus size: 18
3812461 CTTATAAAAA
3812471 TAAAAAAAATGAT-ATTT
1 TAAAAAAAATGATAATTT
* * * ***
3812488 TTAAAAAATTTATAAAAA
1 TAAAAAAAATGATAATTT
3812506 TAAAAAAAATGATAATTT
1 TAAAAAAAATGATAATTT
3812524 TAAAAA
1 TAAAAA
3812530 CGTATTAAAA
Statistics
Matches: 29, Mismatches: 12, Indels: 1
0.69 0.29 0.02
Matches are distributed among these distances:
17 10 0.34
18 19 0.66
ACGTcount: A:0.64, C:0.00, G:0.03, T:0.32
Consensus pattern (18 bp):
TAAAAAAAATGATAATTT
Found at i:3812528 original size:17 final size:17
Alignment explanation
Indices: 3812473--3812529 Score: 51
Period size: 17 Copynumber: 3.3 Consensus size: 17
3812463 TATAAAAATA
*
3812473 AAAAAAATGATATTTTT
1 AAAAAAATGATAATTTT
* * ** *
3812490 AAAAAATTTATAAAAATA
1 AAAAAAATGAT-AATTTT
3812508 AAAAAAATGATAATTTT
1 AAAAAAATGATAATTTT
3812525 AAAAA
1 AAAAA
3812530 CGTATTAAAA
Statistics
Matches: 28, Mismatches: 11, Indels: 2
0.68 0.27 0.05
Matches are distributed among these distances:
17 17 0.61
18 11 0.39
ACGTcount: A:0.65, C:0.00, G:0.04, T:0.32
Consensus pattern (17 bp):
AAAAAAATGATAATTTT
Found at i:3814989 original size:11 final size:11
Alignment explanation
Indices: 3814975--3815004 Score: 51
Period size: 11 Copynumber: 2.7 Consensus size: 11
3814965 AAGTAAAATT
3814975 AGAAAAAAAAA
1 AGAAAAAAAAA
*
3814986 AGAAAGAAAAA
1 AGAAAAAAAAA
3814997 AGAAAAAA
1 AGAAAAAA
3815005 GAAATAGTGA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
11 17 1.00
ACGTcount: A:0.87, C:0.00, G:0.13, T:0.00
Consensus pattern (11 bp):
AGAAAAAAAAA
Found at i:3814995 original size:14 final size:14
Alignment explanation
Indices: 3814975--3815008 Score: 50
Period size: 15 Copynumber: 2.4 Consensus size: 14
3814965 AAGTAAAATT
*
3814975 AGAAAAAAAAAAGAA
1 AGAAAAAAGAAA-AA
3814990 AGAAAAAAGAAAAA
1 AGAAAAAAGAAAAA
3815004 AGAAA
1 AGAAA
3815009 TAGTGAATGA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
14 7 0.39
15 11 0.61
ACGTcount: A:0.85, C:0.00, G:0.15, T:0.00
Consensus pattern (14 bp):
AGAAAAAAGAAAAA
Found at i:3815000 original size:7 final size:7
Alignment explanation
Indices: 3814975--3815008 Score: 50
Period size: 7 Copynumber: 4.7 Consensus size: 7
3814965 AAGTAAAATT
3814975 AGAAAAA
1 AGAAAAA
*
3814982 AAAAAGAA
1 AGAAA-AA
3814990 AGAAAAA
1 AGAAAAA
3814997 AGAAAAA
1 AGAAAAA
3815004 AGAAA
1 AGAAA
3815009 TAGTGAATGA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
7 18 0.75
8 6 0.25
ACGTcount: A:0.85, C:0.00, G:0.15, T:0.00
Consensus pattern (7 bp):
AGAAAAA
Found at i:3815443 original size:2 final size:2
Alignment explanation
Indices: 3815436--3815470 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
3815426 ATATGCAAAG
3815436 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
3815471 TTATGATTAG
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:3829769 original size:3 final size:3
Alignment explanation
Indices: 3829761--3829791 Score: 53
Period size: 3 Copynumber: 10.3 Consensus size: 3
3829751 GAATGCAATT
*
3829761 TTC TTC TTC TTC TTC TTC TTC TTC TTT TTC T
1 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC T
3829792 GAGCATTCTT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.00, C:0.29, G:0.00, T:0.71
Consensus pattern (3 bp):
TTC
Found at i:3832065 original size:11 final size:12
Alignment explanation
Indices: 3832050--3832081 Score: 57
Period size: 11 Copynumber: 2.8 Consensus size: 12
3832040 GTAATTATTC
3832050 TATAAATAAAAA
1 TATAAATAAAAA
3832062 -ATAAATAAAAA
1 TATAAATAAAAA
3832073 TATAAATAA
1 TATAAATAA
3832082 TATATTTAAG
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
11 11 0.58
12 8 0.42
ACGTcount: A:0.75, C:0.00, G:0.00, T:0.25
Consensus pattern (12 bp):
TATAAATAAAAA
Found at i:3832100 original size:21 final size:22
Alignment explanation
Indices: 3832074--3832123 Score: 59
Period size: 22 Copynumber: 2.3 Consensus size: 22
3832064 AAATAAAAAT
*
3832074 ATAAATAATAT-ATTTAAGAAC-
1 ATAAATAATATAATTCAAG-ACG
*
3832095 ATAAATAGTATAATTCAAGACG
1 ATAAATAATATAATTCAAGACG
3832117 ATAAATA
1 ATAAATA
3832124 TCACAAATAA
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
21 12 0.48
22 13 0.52
ACGTcount: A:0.56, C:0.06, G:0.08, T:0.30
Consensus pattern (22 bp):
ATAAATAATATAATTCAAGACG
Found at i:3838713 original size:36 final size:36
Alignment explanation
Indices: 3838661--3838733 Score: 137
Period size: 36 Copynumber: 2.0 Consensus size: 36
3838651 TGCTTACTTG
*
3838661 TTATGATATATGTAAACATAGTCTATTTTATAATAT
1 TTATGATATATATAAACATAGTCTATTTTATAATAT
3838697 TTATGATATATATAAACATAGTCTATTTTATAATAT
1 TTATGATATATATAAACATAGTCTATTTTATAATAT
3838733 T
1 T
3838734 GGTTGGCTTC
Statistics
Matches: 36, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
36 36 1.00
ACGTcount: A:0.40, C:0.05, G:0.07, T:0.48
Consensus pattern (36 bp):
TTATGATATATATAAACATAGTCTATTTTATAATAT
Found at i:3846578 original size:21 final size:21
Alignment explanation
Indices: 3846552--3846592 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
3846542 AGACGAGCAA
* *
3846552 TACTCCACAGCAGGTGGAGTG
1 TACTCCAAAACAGGTGGAGTG
3846573 TACTCCAAAACAGGTGGAGT
1 TACTCCAAAACAGGTGGAGT
3846593 TAAAGCAGAT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.29, C:0.22, G:0.29, T:0.20
Consensus pattern (21 bp):
TACTCCAAAACAGGTGGAGTG
Found at i:3852059 original size:3 final size:3
Alignment explanation
Indices: 3852053--3852077 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
3852043 AAAATTTATT
3852053 ATA ATA ATA ATA ATA ATA ATA ATA A
1 ATA ATA ATA ATA ATA ATA ATA ATA A
3852078 ATCTACTATA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
ATA
Found at i:3859125 original size:21 final size:21
Alignment explanation
Indices: 3859078--3859123 Score: 58
Period size: 21 Copynumber: 2.2 Consensus size: 21
3859068 TTTTAATTTT
* *
3859078 AAAATTTTTAAAAATATAATA
1 AAAAATTTAAAAAATATAATA
*
3859099 ATAAATTTAAAAAATAT-ATA
1 AAAAATTTAAAAAATATAATA
3859119 AAAAA
1 AAAAA
3859124 ATATAATAGT
Statistics
Matches: 21, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
20 7 0.33
21 14 0.67
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (21 bp):
AAAAATTTAAAAAATATAATA
Found at i:3859394 original size:14 final size:15
Alignment explanation
Indices: 3859377--3859417 Score: 57
Period size: 17 Copynumber: 2.7 Consensus size: 15
3859367 TTAATCATTT
3859377 TAAAATTATAAAT-A
1 TAAAATTATAAATAA
3859391 TAAAATTATTAAAATAA
1 TAAAATTA-T-AAATAA
3859408 TAAAATTATA
1 TAAAATTATA
3859418 TTTTTATTAT
Statistics
Matches: 24, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
14 8 0.33
15 2 0.08
16 5 0.21
17 9 0.38
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (15 bp):
TAAAATTATAAATAA
Found at i:3862503 original size:8 final size:8
Alignment explanation
Indices: 3862490--3862515 Score: 52
Period size: 8 Copynumber: 3.2 Consensus size: 8
3862480 ATTATACTTG
3862490 AATTTTAA
1 AATTTTAA
3862498 AATTTTAA
1 AATTTTAA
3862506 AATTTTAA
1 AATTTTAA
3862514 AA
1 AA
3862516 ATAGAGGGAT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 18 1.00
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (8 bp):
AATTTTAA
Found at i:3866797 original size:29 final size:29
Alignment explanation
Indices: 3866754--3866817 Score: 76
Period size: 29 Copynumber: 2.2 Consensus size: 29
3866744 TTGATAATAT
* *
3866754 TTGATTCTTTTTAATAGTATATGA-ACTAAA
1 TTGA-TCTATTTAATAATATA-GAGACTAAA
*
3866784 TTGATCTATTTAATAATATAGAGACTAAT
1 TTGATCTATTTAATAATATAGAGACTAAA
3866813 TTGAT
1 TTGAT
3866818 AGAAATATTC
Statistics
Matches: 30, Mismatches: 3, Indels: 3
0.83 0.08 0.08
Matches are distributed among these distances:
28 2 0.07
29 24 0.80
30 4 0.13
ACGTcount: A:0.38, C:0.06, G:0.11, T:0.45
Consensus pattern (29 bp):
TTGATCTATTTAATAATATAGAGACTAAA
Found at i:3875368 original size:14 final size:14
Alignment explanation
Indices: 3875349--3875388 Score: 53
Period size: 14 Copynumber: 2.9 Consensus size: 14
3875339 TTGATTGGCA
3875349 GTAAAATGTTTTCC
1 GTAAAATGTTTTCC
* *
3875363 GTAAAATGATTTCT
1 GTAAAATGTTTTCC
*
3875377 GAAAAATGTTTT
1 GTAAAATGTTTT
3875389 ACTTTTCTGT
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
14 22 1.00
ACGTcount: A:0.35, C:0.07, G:0.15, T:0.42
Consensus pattern (14 bp):
GTAAAATGTTTTCC
Found at i:3880732 original size:7 final size:7
Alignment explanation
Indices: 3880720--3880746 Score: 54
Period size: 7 Copynumber: 3.9 Consensus size: 7
3880710 GGACTAGAAA
3880720 ATTAATT
1 ATTAATT
3880727 ATTAATT
1 ATTAATT
3880734 ATTAATT
1 ATTAATT
3880741 ATTAAT
1 ATTAAT
3880747 CAACAGTCAT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 20 1.00
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (7 bp):
ATTAATT
Found at i:3892955 original size:19 final size:20
Alignment explanation
Indices: 3892923--3892973 Score: 68
Period size: 19 Copynumber: 2.5 Consensus size: 20
3892913 AATCAAATTA
*
3892923 TTTAATTAATTTAAGTTTGAT
1 TTTAATT-ATTTAAGTTTAAT
*
3892944 TTTAA-TATTTAATTTTAAT
1 TTTAATTATTTAAGTTTAAT
3892963 TTTAATTATTT
1 TTTAATTATTT
3892974 GTATTAGAAT
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
19 16 0.59
20 6 0.22
21 5 0.19
ACGTcount: A:0.33, C:0.00, G:0.04, T:0.63
Consensus pattern (20 bp):
TTTAATTATTTAAGTTTAAT
Found at i:3892962 original size:6 final size:6
Alignment explanation
Indices: 3892928--3892969 Score: 50
Period size: 6 Copynumber: 7.0 Consensus size: 6
3892918 AATTATTTAA
* *
3892928 TTAA-T TTAAGT TTGATT TTAATAT TTAATT TTAATT TTAATT
1 TTAATT TTAATT TTAATT TTAAT-T TTAATT TTAATT TTAATT
3892970 ATTTGTATTA
Statistics
Matches: 32, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
5 4 0.12
6 22 0.69
7 6 0.19
ACGTcount: A:0.33, C:0.00, G:0.05, T:0.62
Consensus pattern (6 bp):
TTAATT
Found at i:3900504 original size:41 final size:38
Alignment explanation
Indices: 3900459--3900558 Score: 119
Period size: 39 Copynumber: 2.5 Consensus size: 38
3900449 CGTGGTATTT
**
3900459 TTAGCGGCGTTTGAATGAAAAACCCCACTAACGATCGAGCA
1 TTAGCGGCGTTT-AA--AAAAACCCCACTAAAAATCGAGCA
* *
3900500 TTAGCGGCGCTTTAAAAAAACGCCTCTAAAAATCGAGCA
1 TTAGCGGCG-TTTAAAAAAACCCCACTAAAAATCGAGCA
3900539 TTAGCGGCGTTTTAAAAAAA
1 TTAGCGGCG-TTTAAAAAAA
3900559 AAGCCGCAAA
Statistics
Matches: 53, Mismatches: 5, Indels: 4
0.85 0.08 0.06
Matches are distributed among these distances:
39 39 0.74
41 11 0.21
42 3 0.06
ACGTcount: A:0.37, C:0.21, G:0.20, T:0.22
Consensus pattern (38 bp):
TTAGCGGCGTTTAAAAAAACCCCACTAAAAATCGAGCA
Found at i:3900570 original size:39 final size:39
Alignment explanation
Indices: 3900492--3900571 Score: 117
Period size: 39 Copynumber: 2.1 Consensus size: 39
3900482 CCCACTAACG
* *
3900492 ATCGAGCATTAGCGGCGCTTTAAAAAAACGCCTCTAAAA
1 ATCGAGCATTAGCGGCGCTTTAAAAAAAAGCCGCTAAAA
*
3900531 ATCGAGCATTAGCGGCGTTTTAAAAAAAAAGCCGC-AAAA
1 ATCGAGCATTAGCGGCGCTTT-AAAAAAAAGCCGCTAAAA
3900570 AT
1 AT
3900572 TAAAGTAGGA
Statistics
Matches: 37, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
39 26 0.70
40 11 0.30
ACGTcount: A:0.41, C:0.20, G:0.19, T:0.20
Consensus pattern (39 bp):
ATCGAGCATTAGCGGCGCTTTAAAAAAAAGCCGCTAAAA
Found at i:3900680 original size:41 final size:41
Alignment explanation
Indices: 3900629--3900907 Score: 436
Period size: 41 Copynumber: 6.8 Consensus size: 41
3900619 GCGTTATTCC
* *
3900629 AAAAGCGCCGCTAATGCTCATATCTATAGCGGCGCTTATTG
1 AAAAACGCCGCTAATGCTCAGATCTATAGCGGCGCTTATTG
*
3900670 AAAAACGCCGCTAATGCTCAAATCTATAGCGGCGCTTATTG
1 AAAAACGCCGCTAATGCTCAGATCTATAGCGGCGCTTATTG
* * *
3900711 AAAAGCGCAGCTAATGCTCATATCTATAGCGGCGCTTATTG
1 AAAAACGCCGCTAATGCTCAGATCTATAGCGGCGCTTATTG
* *
3900752 AAAAACGCCGCGAATGCTCAGATCTATAGCGGCGCTTATTT
1 AAAAACGCCGCTAATGCTCAGATCTATAGCGGCGCTTATTG
*
3900793 AAAAACGCCGCTAATGCTCAGATCTATAGCGGCGCTTATTT
1 AAAAACGCCGCTAATGCTCAGATCTATAGCGGCGCTTATTG
3900834 AAAAACGCCGCTAATGCTCAGATCTATAGCGGCGGCTT-TTG
1 AAAAACGCCGCTAATGCTCAGATCTATAGCGGC-GCTTATTG
* *
3900875 AAAAACGTCGCTAATGCTC-GATTTATAGCGGCG
1 AAAAACGCCGCTAATGCTCAGATCTATAGCGGCG
3900908 TTTTTTCAAA
Statistics
Matches: 223, Mismatches: 14, Indels: 4
0.93 0.06 0.02
Matches are distributed among these distances:
39 1 0.00
40 12 0.05
41 206 0.92
42 4 0.02
ACGTcount: A:0.29, C:0.24, G:0.22, T:0.25
Consensus pattern (41 bp):
AAAAACGCCGCTAATGCTCAGATCTATAGCGGCGCTTATTG
Found at i:3901210 original size:7 final size:7
Alignment explanation
Indices: 3901198--3901346 Score: 57
Period size: 7 Copynumber: 20.3 Consensus size: 7
3901188 TATAGTTCAA
3901198 GGTTTAT
1 GGTTTAT
*
3901205 GGTTTAG
1 GGTTTAT
*
3901212 GGTATAT
1 GGTTTAT
* *
3901219 AGTTTAA
1 GGTTTAT
3901226 GGTTTAT
1 GGTTTAT
3901233 GGTTTATGAT
1 GG-TT-T-AT
*
3901243 GAGTTAAT
1 G-GTTTAT
** *
3901251 ATTTTAA
1 GGTTTAT
3901258 GGTTTAT
1 GGTTTAT
**
3901265 GAATTAT
1 GGTTTAT
*
3901272 GGGTTTAG
1 -GGTTTAT
*
3901280 GGTTTAA
1 GGTTTAT
*
3901287 GGTTTAGG
1 GGTTTA-T
3901295 GGTTTAT
1 GGTTTAT
3901302 GGTTTAT
1 GGTTTAT
*
3901309 GAGTTAAT
1 G-GTTTAT
* * *
3901317 -ATCTCAA
1 GGT-TTAT
3901324 GGTTTAT
1 GGTTTAT
3901331 GGTTTAT
1 GGTTTAT
*
3901338 GGATTAT
1 GGTTTAT
3901345 GG
1 GG
3901347 ACTTAGGAAT
Statistics
Matches: 101, Mismatches: 32, Indels: 18
0.67 0.21 0.12
Matches are distributed among these distances:
6 1 0.01
7 73 0.72
8 20 0.20
9 1 0.01
10 5 0.05
11 1 0.01
ACGTcount: A:0.24, C:0.01, G:0.28, T:0.46
Consensus pattern (7 bp):
GGTTTAT
Found at i:3901278 original size:22 final size:22
Alignment explanation
Indices: 3901253--3901310 Score: 62
Period size: 22 Copynumber: 2.6 Consensus size: 22
3901243 GAGTTAATAT
*
3901253 TTTAAGGTTTATGAATTATGGG
1 TTTAAGGTTTATGAATTAGGGG
* * **
3901275 TTTAGGGTTTAAGGTTTAGGGG
1 TTTAAGGTTTATGAATTAGGGG
*
3901297 TTTATGGTTTATGA
1 TTTAAGGTTTATGA
3901311 GTTAATATCT
Statistics
Matches: 28, Mismatches: 8, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
22 28 1.00
ACGTcount: A:0.22, C:0.00, G:0.31, T:0.47
Consensus pattern (22 bp):
TTTAAGGTTTATGAATTAGGGG
Found at i:3901297 original size:15 final size:14
Alignment explanation
Indices: 3901273--3901307 Score: 52
Period size: 15 Copynumber: 2.4 Consensus size: 14
3901263 ATGAATTATG
3901273 GGTTTAGGGTTTAA
1 GGTTTAGGGTTTAA
*
3901287 GGTTTAGGGGTTTAT
1 GGTTTA-GGGTTTAA
3901302 GGTTTA
1 GGTTTA
3901308 TGAGTTAATA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
14 6 0.32
15 13 0.68
ACGTcount: A:0.17, C:0.00, G:0.37, T:0.46
Consensus pattern (14 bp):
GGTTTAGGGTTTAA
Found at i:3901442 original size:44 final size:43
Alignment explanation
Indices: 3901356--3901447 Score: 107
Period size: 44 Copynumber: 2.1 Consensus size: 43
3901346 GACTTAGGAA
* * *
3901356 TTATGATTTATGGTTCAAGGGTTGAGGTTTAGAGATTTAGGGT
1 TTATGATTTAGGGTTAAAGGGTTGAGGTTTAGAGATTAAGGGT
3901399 TTATGATTTAGGGGTTAAAGGG-TGAGGGTTTAGA-AGTTAAGGGT
1 TTATGATTTA-GGGTTAAAGGGTTGA-GGTTTAGAGA-TTAAGGGT
*
3901443 CTATG
1 TTATG
3901448 GGTTAAGGGT
Statistics
Matches: 42, Mismatches: 4, Indels: 5
0.82 0.08 0.10
Matches are distributed among these distances:
43 14 0.33
44 28 0.67
ACGTcount: A:0.25, C:0.02, G:0.35, T:0.38
Consensus pattern (43 bp):
TTATGATTTAGGGTTAAAGGGTTGAGGTTTAGAGATTAAGGGT
Found at i:3901745 original size:16 final size:16
Alignment explanation
Indices: 3901692--3901745 Score: 57
Period size: 16 Copynumber: 3.8 Consensus size: 16
3901682 ATATTAAATA
*
3901692 ATTTCAAATTTTAAAG
1 ATTTCAAATTTTCAAG
3901708 ATTTCAAATTTTC-A-
1 ATTTCAAATTTTCAAG
3901722 A--T--AATTTTCAAG
1 ATTTCAAATTTTCAAG
3901734 ATTTCAAATTTT
1 ATTTCAAATTTT
3901746 ATCTAATTCT
Statistics
Matches: 31, Mismatches: 1, Indels: 12
0.70 0.02 0.27
Matches are distributed among these distances:
10 7 0.23
11 1 0.03
12 2 0.06
14 2 0.06
15 1 0.03
16 18 0.58
ACGTcount: A:0.39, C:0.09, G:0.04, T:0.48
Consensus pattern (16 bp):
ATTTCAAATTTTCAAG
Found at i:3901951 original size:15 final size:16
Alignment explanation
Indices: 3901920--3901952 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
3901910 ATAAGTGATT
*
3901920 TTTTTAATTTATATTA
1 TTTTTAAATTATATTA
3901936 TTTTTAAATTAT-TTA
1 TTTTTAAATTATATTA
3901951 TT
1 TT
3901953 AAATAATTTT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
15 5 0.31
16 11 0.69
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (16 bp):
TTTTTAAATTATATTA
Found at i:3903078 original size:14 final size:15
Alignment explanation
Indices: 3903059--3903088 Score: 53
Period size: 14 Copynumber: 2.1 Consensus size: 15
3903049 TGTGTTTATA
3903059 TAAATACAT-AATTC
1 TAAATACATAAATTC
3903073 TAAATACATAAATTC
1 TAAATACATAAATTC
3903088 T
1 T
3903089 GAAGTTTGTG
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 9 0.60
15 6 0.40
ACGTcount: A:0.50, C:0.13, G:0.00, T:0.37
Consensus pattern (15 bp):
TAAATACATAAATTC
Found at i:3906625 original size:40 final size:40
Alignment explanation
Indices: 3906534--3906703 Score: 198
Period size: 40 Copynumber: 4.3 Consensus size: 40
3906524 TCCTCGTTCA
* * * *
3906534 AATGCCTTCGGGACATAGCCCGGTTTTAGTAACTCACAC-
1 AATGCCTTCGGGACTTAACCCGGATTTAATAACTCACACG
* * * *
3906573 CATGCCTTCGGGACGTAACCCGGATTTAACAACTCGCACG
1 AATGCCTTCGGGACTTAACCCGGATTTAATAACTCACACG
*
3906613 AATGCCTTCGGGACTTAACCCGGCTTTAATAACTCACACG
1 AATGCCTTCGGGACTTAACCCGGATTTAATAACTCACACG
* * * * *
3906653 AATGCCCTCGGGACTTAACCCGGATTTAGTATCTCGCACA
1 AATGCCTTCGGGACTTAACCCGGATTTAATAACTCACACG
*
3906693 AAGGCCTTCGG
1 AATGCCTTCGG
3906704 ATCTTAGTCC
Statistics
Matches: 110, Mismatches: 20, Indels: 1
0.84 0.15 0.01
Matches are distributed among these distances:
39 32 0.29
40 78 0.71
ACGTcount: A:0.25, C:0.30, G:0.21, T:0.24
Consensus pattern (40 bp):
AATGCCTTCGGGACTTAACCCGGATTTAATAACTCACACG
Found at i:3906635 original size:79 final size:80
Alignment explanation
Indices: 3906532--3906703 Score: 229
Period size: 80 Copynumber: 2.2 Consensus size: 80
3906522 GCTCCTCGTT
* * * * *
3906532 CAAATGCCTTCGGGACATAGCCCGGTTTTAGTAACTCACAC-CATGCCTTCGGGACGTAACCCGG
1 CAAATGCCTTCGGGACATAACCCGGCTTTAATAACTCACACGAATGCCCTCGGGACGTAACCCGG
3906596 ATTTAACAACTCGCA
66 ATTTAACAACTCGCA
* * *
3906611 CGAATGCCTTCGGGACTTAACCCGGCTTTAATAACTCACACGAATGCCCTCGGGACTTAACCCGG
1 CAAATGCCTTCGGGACATAACCCGGCTTTAATAACTCACACGAATGCCCTCGGGACGTAACCCGG
** *
3906676 ATTTAGTATCTCGCA
66 ATTTAACAACTCGCA
*
3906691 CAAAGGCCTTCGG
1 CAAATGCCTTCGG
3906704 ATCTTAGTCC
Statistics
Matches: 79, Mismatches: 13, Indels: 1
0.85 0.14 0.01
Matches are distributed among these distances:
79 36 0.46
80 43 0.54
ACGTcount: A:0.26, C:0.30, G:0.21, T:0.23
Consensus pattern (80 bp):
CAAATGCCTTCGGGACATAACCCGGCTTTAATAACTCACACGAATGCCCTCGGGACGTAACCCGG
ATTTAACAACTCGCA
Done.