Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Gbar_D05
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: 63323194
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.32
Warning! 1953226 characters in sequence are not A, C, G, or T
File 118 of 199
Found at i:39294220 original size:46 final size:46
Alignment explanation
Indices: 39294160--39294274 Score: 194
Period size: 46 Copynumber: 2.5 Consensus size: 46
39294150 CCACACTGTT
* *
39294160 ATGTAGCCAAAGCTACCACTGATATGTAGTCGTAGCTACCACTGAA
1 ATGTAGCCGAAGCTACCACTGATATGTAGCCGTAGCTACCACTGAA
39294206 ATGTAGCCGAAGCTACCACTGATATGTAGCCGTAGCTACCACTGAA
1 ATGTAGCCGAAGCTACCACTGATATGTAGCCGTAGCTACCACTGAA
* *
39294252 TTGTAGCTGAAGCTACCACTGAT
1 ATGTAGCCGAAGCTACCACTGAT
39294275 CAATAACACT
Statistics
Matches: 65, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
46 65 1.00
ACGTcount: A:0.30, C:0.24, G:0.21, T:0.24
Consensus pattern (46 bp):
ATGTAGCCGAAGCTACCACTGATATGTAGCCGTAGCTACCACTGAA
Found at i:39294514 original size:18 final size:17
Alignment explanation
Indices: 39294488--39294526 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 17
39294478 ATTTTCCTTC
39294488 CACATTC-AATATTAATT
1 CACATTCAAATA-TAATT
39294505 CACATATCAAATATAATT
1 CACAT-TCAAATATAATT
39294523 CACA
1 CACA
39294527 ATTTATAAAA
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
17 5 0.25
18 11 0.55
19 4 0.20
ACGTcount: A:0.46, C:0.21, G:0.00, T:0.33
Consensus pattern (17 bp):
CACATTCAAATATAATT
Found at i:39295623 original size:18 final size:17
Alignment explanation
Indices: 39295590--39295623 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
39295580 TTTTCCTTGC
*
39295590 TATTTTTTACTCTTTTT
1 TATTTTTTACTATTTTT
39295607 TATTTTTTCACTATTTT
1 TATTTTTT-ACTATTTT
39295624 ATTACAATTT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 8 0.53
18 7 0.47
ACGTcount: A:0.15, C:0.12, G:0.00, T:0.74
Consensus pattern (17 bp):
TATTTTTTACTATTTTT
Found at i:39297615 original size:13 final size:13
Alignment explanation
Indices: 39297599--39297629 Score: 62
Period size: 13 Copynumber: 2.4 Consensus size: 13
39297589 AAAATATTAA
39297599 TTAAAAATCAAAT
1 TTAAAAATCAAAT
39297612 TTAAAAATCAAAT
1 TTAAAAATCAAAT
39297625 TTAAA
1 TTAAA
39297630 CTATTTATAG
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 18 1.00
ACGTcount: A:0.61, C:0.06, G:0.00, T:0.32
Consensus pattern (13 bp):
TTAAAAATCAAAT
Found at i:39305089 original size:13 final size:13
Alignment explanation
Indices: 39305068--39305103 Score: 54
Period size: 13 Copynumber: 2.8 Consensus size: 13
39305058 TAGAGAGAAC
39305068 AAAATAAAAAATA
1 AAAATAAAAAATA
* *
39305081 TATATAAAAAATA
1 AAAATAAAAAATA
39305094 AAAATAAAAA
1 AAAATAAAAA
39305104 CAGAATTATA
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
13 19 1.00
ACGTcount: A:0.81, C:0.00, G:0.00, T:0.19
Consensus pattern (13 bp):
AAAATAAAAAATA
Found at i:39310708 original size:20 final size:20
Alignment explanation
Indices: 39310683--39310721 Score: 69
Period size: 20 Copynumber: 1.9 Consensus size: 20
39310673 TCTTGAAGAA
39310683 CTTTAACAATCTAGATGTAC
1 CTTTAACAATCTAGATGTAC
*
39310703 CTTTAACAATCTGGATGTA
1 CTTTAACAATCTAGATGTA
39310722 GATGCATTAA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.33, C:0.18, G:0.13, T:0.36
Consensus pattern (20 bp):
CTTTAACAATCTAGATGTAC
Found at i:39310949 original size:30 final size:29
Alignment explanation
Indices: 39310855--39310950 Score: 86
Period size: 29 Copynumber: 3.2 Consensus size: 29
39310845 ACACCAACAG
* * *
39310855 TCACTCAACTTTGATTATAATAACAAAACAA
1 TCACTAAACTTTGA--AAAATAACAAACCAA
* * *
39310886 TCATTAAACTTTGAAAATTTAC-AACTCAA
1 TCACTAAACTTTGAAAAATAACAAAC-CAA
*
39310915 TCACTAAACTTTAGAAAAATAACAAACCAG
1 TCACTAAACTTT-GAAAAATAACAAACCAA
39310945 TCACTA
1 TCACTA
39310951 GCAACCATCT
Statistics
Matches: 52, Mismatches: 10, Indels: 7
0.75 0.14 0.10
Matches are distributed among these distances:
28 2 0.04
29 19 0.37
30 16 0.31
31 15 0.29
ACGTcount: A:0.48, C:0.20, G:0.04, T:0.28
Consensus pattern (29 bp):
TCACTAAACTTTGAAAAATAACAAACCAA
Found at i:39311061 original size:3 final size:3
Alignment explanation
Indices: 39311042--39311136 Score: 52
Period size: 3 Copynumber: 32.3 Consensus size: 3
39311032 GTTGGGCAGT
* * * * * *
39311042 AGA AGA AAA AGA A-A AGA AGA ATAA AGA AGA AGA AAA AGA GGA GGG
1 AGA AGA AGA AGA AGA AGA AGA A-GA AGA AGA AGA AGA AGA AGA AGA
* * * * * *
39311087 AGA GGA GGA AG- AGG AGA ACA ATA AGA AGA AAA AGA AGA AGA AGA A-A
1 AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA
39311133 AGA A
1 AGA A
39311137 TAAATGGATA
Statistics
Matches: 70, Mismatches: 18, Indels: 8
0.73 0.19 0.08
Matches are distributed among these distances:
2 6 0.09
3 62 0.89
4 2 0.03
ACGTcount: A:0.65, C:0.01, G:0.32, T:0.02
Consensus pattern (3 bp):
AGA
Found at i:39312120 original size:21 final size:21
Alignment explanation
Indices: 39312084--39312126 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
39312074 ATCTTGAGGT
* *
39312084 AACTTCTTGTTGAGTTAGGGC
1 AACTTCTTGATAAGTTAGGGC
*
39312105 AACTTCTTGATAAGTTGGGGC
1 AACTTCTTGATAAGTTAGGGC
39312126 A
1 A
39312127 GCCGCTTGGT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.23, C:0.14, G:0.28, T:0.35
Consensus pattern (21 bp):
AACTTCTTGATAAGTTAGGGC
Found at i:39315291 original size:35 final size:35
Alignment explanation
Indices: 39315245--39315318 Score: 112
Period size: 35 Copynumber: 2.1 Consensus size: 35
39315235 CATGGCAGAC
* *
39315245 AATAACTAAAGAAATCCAAACCTGCCATACACTTT
1 AATAACCAAAGAAATCCAAACCTGCCATACACATT
* *
39315280 AATAACCAAAGAAATCCAAACTTGTCATACACATT
1 AATAACCAAAGAAATCCAAACCTGCCATACACATT
39315315 AATA
1 AATA
39315319 CAAACAATAA
Statistics
Matches: 35, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
35 35 1.00
ACGTcount: A:0.49, C:0.23, G:0.05, T:0.23
Consensus pattern (35 bp):
AATAACCAAAGAAATCCAAACCTGCCATACACATT
Found at i:39316538 original size:23 final size:23
Alignment explanation
Indices: 39316511--39316576 Score: 82
Period size: 23 Copynumber: 2.9 Consensus size: 23
39316501 ATATTTAAGT
39316511 ATATTTTATTTATAATTTTTTGA
1 ATATTTTATTTATAATTTTTTGA
* * *
39316534 ATATTTTATTAATTATTTTTATGC
1 ATATTTTATTTATAATTTTT-TGA
39316558 AT-TTTTATTT-TAATTTTTT
1 ATATTTTATTTATAATTTTTT
39316577 TAAAAAAATC
Statistics
Matches: 37, Mismatches: 5, Indels: 4
0.80 0.11 0.09
Matches are distributed among these distances:
21 1 0.03
22 7 0.19
23 25 0.68
24 4 0.11
ACGTcount: A:0.27, C:0.02, G:0.03, T:0.68
Consensus pattern (23 bp):
ATATTTTATTTATAATTTTTTGA
Found at i:39328030 original size:9 final size:9
Alignment explanation
Indices: 39328006--39328039 Score: 50
Period size: 9 Copynumber: 3.8 Consensus size: 9
39327996 TTGGGTTAAG
39328006 AAATTAATT
1 AAATTAATT
* *
39328015 TAGTTAATT
1 AAATTAATT
39328024 AAATTAATT
1 AAATTAATT
39328033 AAATTAA
1 AAATTAA
39328040 ATTGTTTAAA
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
9 21 1.00
ACGTcount: A:0.53, C:0.00, G:0.03, T:0.44
Consensus pattern (9 bp):
AAATTAATT
Found at i:39329478 original size:85 final size:85
Alignment explanation
Indices: 39329335--39329505 Score: 333
Period size: 85 Copynumber: 2.0 Consensus size: 85
39329325 CCCACACTCA
*
39329335 AAGCGGTTCGTGGTTTGAAAATAAAGAAAAAGGTCATTTAGTAGAAATTTGGGATCGACTTAACC
1 AAGCGGTTCGTGGTTCGAAAATAAAGAAAAAGGTCATTTAGTAGAAATTTGGGATCGACTTAACC
39329400 ACCTCATACAAAGCACATGT
66 ACCTCATACAAAGCACATGT
39329420 AAGCGGTTCGTGGTTCGAAAATAAAGAAAAAGGTCATTTAGTAGAAATTTGGGATCGACTTAACC
1 AAGCGGTTCGTGGTTCGAAAATAAAGAAAAAGGTCATTTAGTAGAAATTTGGGATCGACTTAACC
39329485 ACCTCATACAAAGCACATGT
66 ACCTCATACAAAGCACATGT
39329505 A
1 A
39329506 TAATTTTGGT
Statistics
Matches: 85, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
85 85 1.00
ACGTcount: A:0.38, C:0.16, G:0.21, T:0.25
Consensus pattern (85 bp):
AAGCGGTTCGTGGTTCGAAAATAAAGAAAAAGGTCATTTAGTAGAAATTTGGGATCGACTTAACC
ACCTCATACAAAGCACATGT
Found at i:39330689 original size:26 final size:26
Alignment explanation
Indices: 39330653--39330702 Score: 82
Period size: 26 Copynumber: 1.9 Consensus size: 26
39330643 CTCTCCTTGA
*
39330653 TTTTTTTAATTTTGATAGGGTTAGGG
1 TTTTATTAATTTTGATAGGGTTAGGG
*
39330679 TTTTATTAATTTTGTTAGGGTTAG
1 TTTTATTAATTTTGATAGGGTTAG
39330703 TGTTAAGGCA
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
26 22 1.00
ACGTcount: A:0.20, C:0.00, G:0.24, T:0.56
Consensus pattern (26 bp):
TTTTATTAATTTTGATAGGGTTAGGG
Found at i:39336209 original size:20 final size:20
Alignment explanation
Indices: 39336186--39336243 Score: 55
Period size: 22 Copynumber: 2.8 Consensus size: 20
39336176 TGATTTAAAA
39336186 AATTTATATAATAATATTTG
1 AATTTATATAATAATATTTG
*
39336206 AATTGATAAGTTAAT-ATATTTG
1 AATTTAT-A--TAATAATATTTG
*
39336228 AATTATATTTAATAAT
1 AATT-TATATAATAAT
39336244 TCAAATAAAA
Statistics
Matches: 30, Mismatches: 3, Indels: 9
0.71 0.07 0.21
Matches are distributed among these distances:
20 10 0.33
21 3 0.10
22 11 0.37
23 6 0.20
ACGTcount: A:0.45, C:0.00, G:0.07, T:0.48
Consensus pattern (20 bp):
AATTTATATAATAATATTTG
Found at i:39336220 original size:23 final size:21
Alignment explanation
Indices: 39336194--39336243 Score: 66
Period size: 22 Copynumber: 2.3 Consensus size: 21
39336184 AAAATTTATA
39336194 TAATAATATTTGAATTGATAAGT
1 TAATAATATTTGAATT-AT-AGT
*
39336217 TAAT-ATATTTGAATTATATT
1 TAATAATATTTGAATTATAGT
39336237 TAATAAT
1 TAATAAT
39336244 TCAAATAAAA
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
20 6 0.24
21 4 0.16
22 11 0.44
23 4 0.16
ACGTcount: A:0.44, C:0.00, G:0.08, T:0.48
Consensus pattern (21 bp):
TAATAATATTTGAATTATAGT
Found at i:39336380 original size:15 final size:16
Alignment explanation
Indices: 39336357--39336389 Score: 50
Period size: 15 Copynumber: 2.1 Consensus size: 16
39336347 GAACTTAAAA
39336357 TAAAATCAAATT-ATT
1 TAAAATCAAATTAATT
*
39336372 TAAACTCAAATTAATT
1 TAAAATCAAATTAATT
39336388 TA
1 TA
39336390 TTTCATTTTA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
15 11 0.69
16 5 0.31
ACGTcount: A:0.52, C:0.09, G:0.00, T:0.39
Consensus pattern (16 bp):
TAAAATCAAATTAATT
Found at i:39337860 original size:26 final size:27
Alignment explanation
Indices: 39337826--39337882 Score: 89
Period size: 27 Copynumber: 2.1 Consensus size: 27
39337816 AAAAGGTTGT
39337826 GAATGCACAG-AAAACCGTCACAGGTG
1 GAATGCACAGCAAAACCGTCACAGGTG
* *
39337852 GAATTCACAGCAAAACCGTCACAGTTG
1 GAATGCACAGCAAAACCGTCACAGGTG
39337879 GAAT
1 GAAT
39337883 CTGCTATGGA
Statistics
Matches: 28, Mismatches: 2, Indels: 1
0.90 0.06 0.03
Matches are distributed among these distances:
26 9 0.32
27 19 0.68
ACGTcount: A:0.39, C:0.23, G:0.23, T:0.16
Consensus pattern (27 bp):
GAATGCACAGCAAAACCGTCACAGGTG
Found at i:39339654 original size:29 final size:29
Alignment explanation
Indices: 39339622--39339682 Score: 95
Period size: 29 Copynumber: 2.1 Consensus size: 29
39339612 TTGTCGCTGC
* *
39339622 CACACGGCCGTGTGCCAGGTCGTGTGTGA
1 CACACGGCCGTGTGACAGGCCGTGTGTGA
*
39339651 CACACGGCCGTGTGATAGGCCGTGTGTGA
1 CACACGGCCGTGTGACAGGCCGTGTGTGA
39339680 CAC
1 CAC
39339683 TGTATTGAGC
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
29 29 1.00
ACGTcount: A:0.16, C:0.28, G:0.36, T:0.20
Consensus pattern (29 bp):
CACACGGCCGTGTGACAGGCCGTGTGTGA
Found at i:39343032 original size:23 final size:23
Alignment explanation
Indices: 39343001--39343051 Score: 75
Period size: 23 Copynumber: 2.2 Consensus size: 23
39342991 ACGTACTTTC
* *
39343001 TTACTGTAGTAATTTTCGGGGTA
1 TTACAGTAGTAATTTTCGGGATA
*
39343024 TTACAGTAGTAATTTTTGGGATA
1 TTACAGTAGTAATTTTCGGGATA
39343047 TTACA
1 TTACA
39343052 CGTATGTTCT
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
23 25 1.00
ACGTcount: A:0.27, C:0.08, G:0.22, T:0.43
Consensus pattern (23 bp):
TTACAGTAGTAATTTTCGGGATA
Found at i:39344777 original size:43 final size:43
Alignment explanation
Indices: 39344729--39344822 Score: 143
Period size: 43 Copynumber: 2.2 Consensus size: 43
39344719 GCGTCCCTAA
39344729 CTTTAGCGGCGATTTTAAAAAAAACGCCGCTAAAGACCAGGAC
1 CTTTAGCGGCGATTTTAAAAAAAACGCCGCTAAAGACCAGGAC
* *** *
39344772 CTTTAGCGGCGCTTTTTTCACAAACGCCGCTAAAGACCAGGAC
1 CTTTAGCGGCGATTTTAAAAAAAACGCCGCTAAAGACCAGGAC
39344815 CTTTAGCG
1 CTTTAGCG
39344823 TCGCTTCTTC
Statistics
Matches: 46, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
43 46 1.00
ACGTcount: A:0.30, C:0.27, G:0.21, T:0.22
Consensus pattern (43 bp):
CTTTAGCGGCGATTTTAAAAAAAACGCCGCTAAAGACCAGGAC
Found at i:39344847 original size:42 final size:43
Alignment explanation
Indices: 39344750--39344847 Score: 162
Period size: 43 Copynumber: 2.3 Consensus size: 43
39344740 ATTTTAAAAA
*
39344750 AAACGCCGCTAAAGACCAGGACCTTTAGCGGCGCTTTTTTCAC
1 AAACGCCGCTAAAGACCAGGACCTTTAGCGGCGCTTTCTTCAC
*
39344793 AAACGCCGCTAAAGACCAGGACCTTTAGCGTCGC-TTCTTCAC
1 AAACGCCGCTAAAGACCAGGACCTTTAGCGGCGCTTTCTTCAC
*
39344835 AAACGCCACTAAA
1 AAACGCCGCTAAA
39344848 AGCATAACTT
Statistics
Matches: 52, Mismatches: 3, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
42 19 0.37
43 33 0.63
ACGTcount: A:0.30, C:0.32, G:0.18, T:0.20
Consensus pattern (43 bp):
AAACGCCGCTAAAGACCAGGACCTTTAGCGGCGCTTTCTTCAC
Found at i:39346676 original size:5 final size:5
Alignment explanation
Indices: 39346632--39346658 Score: 54
Period size: 5 Copynumber: 5.4 Consensus size: 5
39346622 GATTCTTGTT
39346632 TTTTA TTTTA TTTTA TTTTA TTTTA TT
1 TTTTA TTTTA TTTTA TTTTA TTTTA TT
39346659 GGTAAAATAT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 22 1.00
ACGTcount: A:0.19, C:0.00, G:0.00, T:0.81
Consensus pattern (5 bp):
TTTTA
Found at i:39347940 original size:32 final size:33
Alignment explanation
Indices: 39347885--39347949 Score: 114
Period size: 32 Copynumber: 2.0 Consensus size: 33
39347875 CATTATAAGC
*
39347885 AAAACCCAGAAAACATAACAAATTACAAATAAA
1 AAAACACAGAAAACATAACAAATTACAAATAAA
39347918 AAAACACAGAAAA-ATAACAAATTACAAATAAA
1 AAAACACAGAAAACATAACAAATTACAAATAAA
39347950 CAAATTCCAG
Statistics
Matches: 31, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
32 19 0.61
33 12 0.39
ACGTcount: A:0.69, C:0.15, G:0.03, T:0.12
Consensus pattern (33 bp):
AAAACACAGAAAACATAACAAATTACAAATAAA
Found at i:39349453 original size:159 final size:158
Alignment explanation
Indices: 39349263--39349576 Score: 556
Period size: 159 Copynumber: 2.0 Consensus size: 158
39349253 AAAAAATTAA
*
39349263 ATTTCTGTAGCGAAACGGCACGTTTTGAAAAAATTTAATACTTACTTGCGGCGTTTTTCGTCCAA
1 ATTTCTGTAGCGAAACGGCACGTTTTGAAAAAATTTAATACATACTTGCGGCGTTTTTCGTCCAA
* *
39349328 ACGCCGCTATTGTTTACCTTTTGTGGCGTTTTTCTCATAAACGCCGCTAATGATTAATTTTTTTC
66 ACGCCGCTATTGTTTACCTTTTGCGGCGTTTTTCTCATAAACGCCGCTAATGATT-ACTTTTTTC
*
39349393 ACAATTTTATATTTAATTATTATATATAC
130 ACAATTTTATATTAAATTATTATATATAC
* *
39349422 ATTTTTGTAGCGAAACGGCACGTTTTGAAAAAATTTAATACATATTTGCGGCGTTTTTCGTCCAA
1 ATTTCTGTAGCGAAACGGCACGTTTTGAAAAAATTTAATACATACTTGCGGCGTTTTTCGTCCAA
*
39349487 ATGCCGCTATTGTTTACCTTTTGCGGCGTTTTTCTCATAAACGCCGCTAATGATTACTTTTTTCA
66 ACGCCGCTATTGTTTACCTTTTGCGGCGTTTTTCTCATAAACGCCGCTAATGATTACTTTTTTCA
39349552 CAATTTTATATTAAATTATTATATA
131 CAATTTTATATTAAATTATTATATA
39349577 ATTCATATCA
Statistics
Matches: 148, Mismatches: 7, Indels: 1
0.95 0.04 0.01
Matches are distributed among these distances:
158 33 0.22
159 115 0.78
ACGTcount: A:0.27, C:0.17, G:0.14, T:0.42
Consensus pattern (158 bp):
ATTTCTGTAGCGAAACGGCACGTTTTGAAAAAATTTAATACATACTTGCGGCGTTTTTCGTCCAA
ACGCCGCTATTGTTTACCTTTTGCGGCGTTTTTCTCATAAACGCCGCTAATGATTACTTTTTTCA
CAATTTTATATTAAATTATTATATATAC
Found at i:39350149 original size:7 final size:7
Alignment explanation
Indices: 39350110--39350229 Score: 66
Period size: 7 Copynumber: 17.0 Consensus size: 7
39350100 ACTAATTAAT
*
39350110 CTAAACT
1 CTAAACC
39350117 CTAAACC
1 CTAAACC
39350124 CT-AACC
1 CTAAACC
* *
39350130 CTTATCTC
1 CTAAAC-C
*
39350138 TTAAACC
1 CTAAACC
*
39350145 CTAAATC
1 CTAAACC
* *
39350152 ATAAAAC
1 CTAAACC
*
39350159 ATAAACC
1 CTAAACC
39350166 CTAAACC
1 CTAAACC
39350173 CTAAACTC
1 CTAAAC-C
*
39350181 CTAACCC
1 CTAAACC
39350188 CT-AACC
1 CTAAACC
*
39350194 CTTACACC
1 C-TAAACC
*
39350202 TTAAACC
1 CTAAACC
*
39350209 C-CAACC
1 CTAAACC
39350215 CTTAAACC
1 C-TAAACC
*
39350223 ATAAACC
1 CTAAACC
39350230 TTAACTCATA
Statistics
Matches: 86, Mismatches: 20, Indels: 14
0.72 0.17 0.12
Matches are distributed among these distances:
6 15 0.17
7 54 0.63
8 17 0.20
ACGTcount: A:0.40, C:0.38, G:0.00, T:0.22
Consensus pattern (7 bp):
CTAAACC
Found at i:39351041 original size:41 final size:41
Alignment explanation
Indices: 39350996--39351115 Score: 177
Period size: 41 Copynumber: 2.9 Consensus size: 41
39350986 AGGATTGTAA
39350996 TGATCATTAGCGGCGCTTTCCCAAAAACGCCGCTAAAGCCC
1 TGATCATTAGCGGCGCTTTCCCAAAAACGCCGCTAAAGCCC
* *
39351037 TGATCATTAGCGACGCTTTCCCAAAAATGCCGCTAAAGCCC
1 TGATCATTAGCGGCGCTTTCCCAAAAACGCCGCTAAAGCCC
* ** *
39351078 TAATCATTAGTTGCGCTTTCTCAAAAAACGCCGCTAAA
1 TGATCATTAGCGGCGCTTTC-CCAAAAACGCCGCTAAA
39351116 ACCCCGAAAG
Statistics
Matches: 70, Mismatches: 8, Indels: 1
0.89 0.10 0.01
Matches are distributed among these distances:
41 55 0.79
42 15 0.21
ACGTcount: A:0.30, C:0.30, G:0.17, T:0.23
Consensus pattern (41 bp):
TGATCATTAGCGGCGCTTTCCCAAAAACGCCGCTAAAGCCC
Found at i:39353946 original size:20 final size:20
Alignment explanation
Indices: 39353923--39353966 Score: 72
Period size: 20 Copynumber: 2.2 Consensus size: 20
39353913 TTAATAGTAT
39353923 TTTATTA-ATTTAATATTAAA
1 TTTATTATA-TTAATATTAAA
39353943 TTTATTATATTAATATTAAA
1 TTTATTATATTAATATTAAA
39353963 TTTA
1 TTTA
39353967 ATTTAATATT
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
20 22 0.96
21 1 0.04
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (20 bp):
TTTATTATATTAATATTAAA
Found at i:39353948 original size:25 final size:25
Alignment explanation
Indices: 39353920--39353971 Score: 70
Period size: 25 Copynumber: 2.1 Consensus size: 25
39353910 ATCTTAATAG
*
39353920 TATTTTATTAAT-TTAATATTAAATT
1 TATTATATTAATATTAA-ATTAAATT
*
39353945 TATTATATTAATATTAAATTTAATT
1 TATTATATTAATATTAAATTAAATT
39353970 TA
1 TA
39353972 ATATTTATCT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
25 20 0.83
26 4 0.17
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (25 bp):
TATTATATTAATATTAAATTAAATT
Found at i:39354021 original size:68 final size:66
Alignment explanation
Indices: 39353884--39354069 Score: 163
Period size: 68 Copynumber: 2.8 Consensus size: 66
39353874 TTTAATAGAT
* *
39353884 TTAATATCATATTAAATTTAATATTTATCTTAATAGTATTTTATTAATTTAATATTAAATTTATT
1 TTAATATCAAATTAAATTTAATATTTATCTTAATAGTATTCTATTAATTTAATA-TAAATTTA-T
39353949 ATA
64 ATA
* * * *
39353952 TTAATATTAAATTTAATTTAATATTTATCTTGTAGATAATTATTCTATTAATTTAATA-AGATTT
1 TTAATATCAAATTAAATTTAATATTTATC-T-TA-AT-AGTATTCTATTAATTTAATATAAATTT
39354016 A-ATA
62 ATATA
* * * *
39354020 TTAA-AT----TT-AATCTAACATTTATCTTGATAAGTATTATATTAATTTAATAT
1 TTAATATCAAATTAAATTTAATATTTATCTTAAT-AGTATTCTATTAATTTAATAT
39354070 TAAAGTGATT
Statistics
Matches: 102, Mismatches: 11, Indels: 18
0.78 0.08 0.14
Matches are distributed among these distances:
59 21 0.21
60 1 0.01
61 1 0.01
62 13 0.13
63 2 0.02
67 2 0.02
68 33 0.32
69 1 0.01
70 8 0.08
71 2 0.02
72 18 0.18
ACGTcount: A:0.41, C:0.04, G:0.03, T:0.52
Consensus pattern (66 bp):
TTAATATCAAATTAAATTTAATATTTATCTTAATAGTATTCTATTAATTTAATATAAATTTATAT
A
Found at i:39354027 original size:62 final size:59
Alignment explanation
Indices: 39353952--39354068 Score: 171
Period size: 62 Copynumber: 1.9 Consensus size: 59
39353942 ATTTATTATA
* * * *
39353952 TTAATATTAAATTTAATTTAATATTTATCTTGTAGATAATTATTCTATTAATTTAATAAGAT
1 TTAATATTAAATTTAATCTAACATTTATC-T-T-GATAAGTATTATATTAATTTAATAAGAT
39354014 TTAATATTAAATTTAATCTAACATTTATCTTGATAAGTATTATATTAATTTAATA
1 TTAATATTAAATTTAATCTAACATTTATCTTGATAAGTATTATATTAATTTAATA
39354069 TTAAAGTGAT
Statistics
Matches: 51, Mismatches: 4, Indels: 3
0.88 0.07 0.05
Matches are distributed among these distances:
59 22 0.43
60 1 0.02
61 1 0.02
62 27 0.53
ACGTcount: A:0.41, C:0.04, G:0.04, T:0.50
Consensus pattern (59 bp):
TTAATATTAAATTTAATCTAACATTTATCTTGATAAGTATTATATTAATTTAATAAGAT
Found at i:39364021 original size:82 final size:82
Alignment explanation
Indices: 39363884--39364046 Score: 290
Period size: 82 Copynumber: 2.0 Consensus size: 82
39363874 TAGGCCACTT
*
39363884 ATTAAGTAAGACTAGAAATACATGGCAATGCTCAAATAAGTTGATATGAGATATCATACTTATTT
1 ATTAAGTAAGACTAGAAATACATGGCAATGCTCAAATAAGTTGATATAAGATATCATACTTATTT
*
39363949 GTTTATTGTAGTTTACG
66 GTTTATTATAGTTTACG
* *
39363966 ATTAAGTAAGACTAGAAATACATGGCAATGCTCGAATAAGTTGATATAAGATATCATGCTTATTT
1 ATTAAGTAAGACTAGAAATACATGGCAATGCTCAAATAAGTTGATATAAGATATCATACTTATTT
39364031 GTTTATTATAGTTTAC
66 GTTTATTATAGTTTAC
39364047 TCGAGATATC
Statistics
Matches: 77, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
82 77 1.00
ACGTcount: A:0.37, C:0.10, G:0.17, T:0.37
Consensus pattern (82 bp):
ATTAAGTAAGACTAGAAATACATGGCAATGCTCAAATAAGTTGATATAAGATATCATACTTATTT
GTTTATTATAGTTTACG
Found at i:39366827 original size:15 final size:15
Alignment explanation
Indices: 39366808--39366837 Score: 51
Period size: 15 Copynumber: 1.9 Consensus size: 15
39366798 AAAAAATATT
39366808 AAAAAGAAAAAGAAAG
1 AAAAA-AAAAAGAAAG
39366824 AAAAAAAAAAGAAA
1 AAAAAAAAAAGAAA
39366838 ACAAACCAAA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 9 0.64
16 5 0.36
ACGTcount: A:0.87, C:0.00, G:0.13, T:0.00
Consensus pattern (15 bp):
AAAAAAAAAAGAAAG
Found at i:39367871 original size:92 final size:86
Alignment explanation
Indices: 39367741--39367945 Score: 266
Period size: 92 Copynumber: 2.3 Consensus size: 86
39367731 AGGCTCTACT
** * * *
39367741 CTTTTTTTTGCACTCAATTAGGTACTTAAACTTTCAAAATGTATCAAAAAGGCCCTCAAACTTTT
1 CTTTTTTTTGCACTCAATT-GGTACTTAAACTGCCAAAATGCATCAAAAAGACCCTCAAAATTTT
39367806 TCAAAAAAAGCAATTAAGCCCCTG
65 TC--AAAAAGCAATTAAGCCCCTG
*
39367830 CTTTTTTTTTTGGCACTCAATTGGGTACTTGAACTGCCAAAATGCATCAAAAAGACCCTCAAAAT
1 C--TTTTTTTT-GCACTCAATT-GGTACTTAAACTGCCAAAATGCATCAAAAAGACCCTCAAAAT
* *
39367895 TTTTCAGAAAGCAATTAAGTCCCTG
62 TTTTCAAAAAGCAATTAAGCCCCTG
*
39367920 CTTTCTTTTGCACTCAATTGGTACTT
1 CTTTTTTTTGCACTCAATTGGTACTT
39367946 TAACAGTTGA
Statistics
Matches: 103, Mismatches: 10, Indels: 9
0.84 0.08 0.07
Matches are distributed among these distances:
86 7 0.07
87 10 0.10
88 7 0.07
89 1 0.01
90 19 0.18
91 8 0.08
92 51 0.50
ACGTcount: A:0.32, C:0.21, G:0.12, T:0.35
Consensus pattern (86 bp):
CTTTTTTTTGCACTCAATTGGTACTTAAACTGCCAAAATGCATCAAAAAGACCCTCAAAATTTTT
CAAAAAGCAATTAAGCCCCTG
Found at i:39368043 original size:60 final size:61
Alignment explanation
Indices: 39367947--39368067 Score: 174
Period size: 60 Copynumber: 2.0 Consensus size: 61
39367937 TTGGTACTTT
* * * *
39367947 AACAGTTGACCGTTAAAGTTAATTGCCCTAATTTTTTTTAGTTAAAGCCA-CACGTGTCAC
1 AACAGTTGACCGTTAAAGTTAACTGCCCTAAGTTTTTTCAGTTAAAGCCATCACATGTCAC
*
39368007 AACAGTTGACTGTTAAAGTTAACTGCTCCT-AGTTTTTTCAGTTAAAGCCATCACATGTCAC
1 AACAGTTGACCGTTAAAGTTAACTGC-CCTAAGTTTTTTCAGTTAAAGCCATCACATGTCAC
39368068 GACCACAGCG
Statistics
Matches: 54, Mismatches: 5, Indels: 3
0.87 0.08 0.05
Matches are distributed among these distances:
60 42 0.78
61 12 0.22
ACGTcount: A:0.30, C:0.21, G:0.15, T:0.35
Consensus pattern (61 bp):
AACAGTTGACCGTTAAAGTTAACTGCCCTAAGTTTTTTCAGTTAAAGCCATCACATGTCAC
Found at i:39368238 original size:29 final size:28
Alignment explanation
Indices: 39368204--39368296 Score: 96
Period size: 29 Copynumber: 3.2 Consensus size: 28
39368194 TAAAAGAGTG
*
39368204 TAAAATTTTATATAAATAGTAATAAATTA
1 TAAAATTTTATA-AAATAGTAAAAAATTA
* * *
39368233 TAAAATATATAGAAATATAGAAAAAAATTA
1 TAAAAT-TTTATAAA-ATAGTAAAAAATTA
* *
39368263 TAAAATTTTATAAAGTCGTAAGAAAATTA
1 TAAAATTTTATAAAATAGTAA-AAAATTA
39368292 TAAAA
1 TAAAA
39368297 ATGTAAAAAA
Statistics
Matches: 52, Mismatches: 9, Indels: 6
0.78 0.13 0.09
Matches are distributed among these distances:
28 4 0.08
29 26 0.50
30 22 0.42
ACGTcount: A:0.59, C:0.01, G:0.06, T:0.33
Consensus pattern (28 bp):
TAAAATTTTATAAAATAGTAAAAAATTA
Found at i:39368321 original size:20 final size:19
Alignment explanation
Indices: 39368280--39368338 Score: 73
Period size: 19 Copynumber: 3.0 Consensus size: 19
39368270 TTATAAAGTC
* *
39368280 GTAAGAAAATTATAAAAAT
1 GTAAAAAAAATATAAAAAT
*
39368299 GTAAAAAAAATATAAAATTT
1 GTAAAAAAAATATAAAA-AT
39368319 GTAAAAAAAATTATAAAAAT
1 GTAAAAAAAA-TATAAAAAT
39368339 TATCGTACCA
Statistics
Matches: 34, Mismatches: 4, Indels: 3
0.83 0.10 0.07
Matches are distributed among these distances:
19 15 0.44
20 12 0.35
21 7 0.21
ACGTcount: A:0.66, C:0.00, G:0.07, T:0.27
Consensus pattern (19 bp):
GTAAAAAAAATATAAAAAT
Found at i:39368546 original size:19 final size:19
Alignment explanation
Indices: 39368513--39368596 Score: 80
Period size: 19 Copynumber: 4.3 Consensus size: 19
39368503 AAAGGGGAAT
*
39368513 TTTTTTATG-TATTTTATAG
1 TTTTTTATGAT-TTTTATAA
39368532 TTTTTTATGATTTTTATAA
1 TTTTTTATGATTTTTATAA
** ** *
39368551 AATTTTACAATTTTTTTATA
1 TTTTTTATGATTTTTATA-A
39368571 TTTTGTTATGATTTTTATAA
1 TTTT-TTATGATTTTTATAA
39368591 TTTTTT
1 TTTTTT
39368597 TTCTAATTTT
Statistics
Matches: 51, Mismatches: 11, Indels: 6
0.75 0.16 0.09
Matches are distributed among these distances:
19 31 0.61
20 9 0.18
21 11 0.22
ACGTcount: A:0.25, C:0.01, G:0.06, T:0.68
Consensus pattern (19 bp):
TTTTTTATGATTTTTATAA
Found at i:39368556 original size:21 final size:21
Alignment explanation
Indices: 39368532--39368617 Score: 61
Period size: 21 Copynumber: 4.1 Consensus size: 21
39368522 TATTTTATAG
*
39368532 TTTTTTATGATTTTTATAAAA
1 TTTTTTATAATTTTTATAAAA
* * *
39368553 --TTTTACAATTTTT-TTATA
1 TTTTTTATAATTTTTATAAAA
* **
39368571 TTTTGTTATGATTTTTATAATT
1 TTTT-TTATAATTTTTATAAAA
*
39368593 TTTTTTCTAATTTTTAATAAAA
1 TTTTTTATAATTTTT-ATAAAA
39368615 TTT
1 TTT
39368618 AAATATTTGT
Statistics
Matches: 48, Mismatches: 12, Indels: 9
0.70 0.17 0.13
Matches are distributed among these distances:
18 3 0.06
19 11 0.23
20 2 0.04
21 18 0.38
22 14 0.29
ACGTcount: A:0.29, C:0.02, G:0.03, T:0.65
Consensus pattern (21 bp):
TTTTTTATAATTTTTATAAAA
Found at i:39368574 original size:9 final size:10
Alignment explanation
Indices: 39368524--39368596 Score: 53
Period size: 10 Copynumber: 7.4 Consensus size: 10
39368514 TTTTTATGTA
*
39368524 TTTTATAGTT
1 TTTTATAATT
*
39368534 TTTTATGA-T
1 TTTTATAATT
**
39368543 TTTTATAAAA
1 TTTTATAATT
*
39368553 TTTTACAATT
1 TTTTATAATT
39368563 TTTT-TATATT
1 TTTTATA-ATT
*
39368573 TTGTTATGA-T
1 TT-TTATAATT
39368583 TTTTATAATT
1 TTTTATAATT
39368593 TTTT
1 TTTT
39368597 TTCTAATTTT
Statistics
Matches: 48, Mismatches: 10, Indels: 10
0.71 0.15 0.15
Matches are distributed among these distances:
9 14 0.29
10 30 0.62
11 3 0.06
12 1 0.02
ACGTcount: A:0.26, C:0.01, G:0.05, T:0.67
Consensus pattern (10 bp):
TTTTATAATT
Found at i:39369242 original size:45 final size:45
Alignment explanation
Indices: 39369174--39369264 Score: 164
Period size: 45 Copynumber: 2.0 Consensus size: 45
39369164 TTCCTTTTTC
*
39369174 TGTTGTTAGTTTCTTTCGATTTTGAATCAAGGTGGTTGAATTGTT
1 TGTTGTAAGTTTCTTTCGATTTTGAATCAAGGTGGTTGAATTGTT
*
39369219 TGTTGTAAGTTTCTTTCGGTTTTGAATCAAGGTGGTTGAATTGTT
1 TGTTGTAAGTTTCTTTCGATTTTGAATCAAGGTGGTTGAATTGTT
39369264 T
1 T
39369265 TCGAAGTATT
Statistics
Matches: 44, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
45 44 1.00
ACGTcount: A:0.18, C:0.07, G:0.25, T:0.51
Consensus pattern (45 bp):
TGTTGTAAGTTTCTTTCGATTTTGAATCAAGGTGGTTGAATTGTT
Found at i:39369826 original size:98 final size:98
Alignment explanation
Indices: 39369655--39369832 Score: 239
Period size: 98 Copynumber: 1.8 Consensus size: 98
39369645 GGGATTTAAG
* * * *
39369655 CAGACCGTGTGTTGTGGTCGTATGTAGCACACGATCGTGTGGGATTATGTAGCCTATGTGGCTAG
1 CAGACCGTGCGTTGTGGTCGTATGTAGCACACGATCGTGTGGGATTATGTAGCCCACGTGACTAG
39369720 GCTATGTGAGACATTCGGCCGTGTGAGTCATTA
66 GCTATGTGAGACATTCGGCCGTGTGAGTCATTA
* * * * * * *
39369753 CAGACCGTGCGTTGTGGTCGTGTGTAGCACACGGTTGTGTGGGATTGTGTAGCCCGCGTGATTGG
1 CAGACCGTGCGTTGTGGTCGTATGTAGCACACGATCGTGTGGGATTATGTAGCCCACGTGACTAG
* *
39369818 GCTGTGTGAGTCATT
66 GCTATGTGAGACATT
39369833 ACAAACCATG
Statistics
Matches: 67, Mismatches: 13, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
98 67 1.00
ACGTcount: A:0.16, C:0.17, G:0.35, T:0.31
Consensus pattern (98 bp):
CAGACCGTGCGTTGTGGTCGTATGTAGCACACGATCGTGTGGGATTATGTAGCCCACGTGACTAG
GCTATGTGAGACATTCGGCCGTGTGAGTCATTA
Found at i:39371914 original size:127 final size:125
Alignment explanation
Indices: 39371696--39371978 Score: 374
Period size: 127 Copynumber: 2.2 Consensus size: 125
39371686 TTTTTTTGAG
** **
39371696 TTGACGTTTCTGGTCAAATAGTATAAAATCGCTTCTACCAGGATGCTATCAGAGAAGAAATTGTG
1 TTGACGTTTCTGAACAAATAGTATAAAATCGCTGATACCAGGATGCTATCAGAGAAGAAATTGTG
*** *
39371761 AAATCGTGCCCTCGTGGACGCCATTTCGGC-ACAGTTGGTCATGTCA-GAAATAATTTTTTTT
66 AAATAACGCCCTCGTGGACGCCATTTC-GCTACAGTTGGTCATGT-AGGAAATAA-TTATTTT
* *
39371822 TTTACGTTTTCTGAACAAATAGTATAAAATCGCTGATACCAGGATGCTAT-ATGAGAAGATATTG
1 TTGACG-TTTCTGAACAAATAGTATAAAATCGCTGATACCAGGATGCTATCA-GAGAAGAAATTG
*
39371886 TGAAATAACGCCCTCGTGGACGCGATTTCGCTACAGTTGGTCATGTAGGAAATAATTATTTT
64 TGAAATAACGCCCTCGTGGACGCCATTTCGCTACAGTTGGTCATGTAGGAAATAATTATTTT
* * *
39371948 TTGACGTTTCTGAGCAAATAGTGTCAAATCG
1 TTGACGTTTCTGAACAAATAGTATAAAATCG
39371979 TGCCCTCGTG
Statistics
Matches: 138, Mismatches: 15, Indels: 9
0.85 0.09 0.06
Matches are distributed among these distances:
125 22 0.16
126 20 0.14
127 96 0.70
ACGTcount: A:0.30, C:0.17, G:0.21, T:0.33
Consensus pattern (125 bp):
TTGACGTTTCTGAACAAATAGTATAAAATCGCTGATACCAGGATGCTATCAGAGAAGAAATTGTG
AAATAACGCCCTCGTGGACGCCATTTCGCTACAGTTGGTCATGTAGGAAATAATTATTTT
Found at i:39374072 original size:14 final size:15
Alignment explanation
Indices: 39374055--39374087 Score: 50
Period size: 15 Copynumber: 2.3 Consensus size: 15
39374045 AATATTTATC
39374055 TAAAAATA-CATAAA
1 TAAAAATATCATAAA
*
39374069 TAAAAATATCTTAAA
1 TAAAAATATCATAAA
39374084 TAAA
1 TAAA
39374088 GTTTAAAATT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
14 8 0.47
15 9 0.53
ACGTcount: A:0.67, C:0.06, G:0.00, T:0.27
Consensus pattern (15 bp):
TAAAAATATCATAAA
Found at i:39374210 original size:20 final size:18
Alignment explanation
Indices: 39374179--39374228 Score: 57
Period size: 20 Copynumber: 2.7 Consensus size: 18
39374169 GCCATTGTTG
**
39374179 AAAATA-TTAAAAATTTA
1 AAAATATTTAAAAAAATA
39374196 AAAATTATTTTAAAAAAATA
1 AAAA-TA-TTTAAAAAAATA
39374216 AAAATATTTAAAA
1 AAAATATTTAAAA
39374229 TTTTCTTTAA
Statistics
Matches: 28, Mismatches: 2, Indels: 5
0.80 0.06 0.14
Matches are distributed among these distances:
17 4 0.14
18 9 0.32
19 2 0.07
20 13 0.46
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (18 bp):
AAAATATTTAAAAAAATA
Found at i:39374249 original size:29 final size:30
Alignment explanation
Indices: 39374187--39374244 Score: 84
Period size: 30 Copynumber: 2.0 Consensus size: 30
39374177 TGAAAATATT
39374187 AAAA-ATTTAAAAATTATTTTAAAAAAATA
1 AAAATATTTAAAAATTATTTTAAAAAAATA
*
39374216 AAAATATTT-AAAATTTTCTTTAAAAAAAT
1 AAAATATTTAAAAATTAT-TTTAAAAAAAT
39374245 GAAATTGAAT
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
29 11 0.42
30 15 0.58
ACGTcount: A:0.60, C:0.02, G:0.00, T:0.38
Consensus pattern (30 bp):
AAAATATTTAAAAATTATTTTAAAAAAATA
Found at i:39374353 original size:52 final size:52
Alignment explanation
Indices: 39374281--39374380 Score: 146
Period size: 52 Copynumber: 1.9 Consensus size: 52
39374271 TATGGAGTTG
* * * *
39374281 AGAGATTTTTTGAAGGAAATTGTGAGGATTTTGGAAGGAATTTAAGAGTTTA
1 AGAGAATTTTGGAAGGAAATTGAGAGAATTTTGGAAGGAATTTAAGAGTTTA
* *
39374333 AGAGAATTTTGGAAGGAAATTGAGAGAATTTTTGAAGGAATTTGAGAG
1 AGAGAATTTTGGAAGGAAATTGAGAGAATTTTGGAAGGAATTTAAGAG
39374381 AATTTTTGAA
Statistics
Matches: 42, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
52 42 1.00
ACGTcount: A:0.37, C:0.00, G:0.30, T:0.33
Consensus pattern (52 bp):
AGAGAATTTTGGAAGGAAATTGAGAGAATTTTGGAAGGAATTTAAGAGTTTA
Found at i:39374360 original size:22 final size:22
Alignment explanation
Indices: 39374333--39374401 Score: 111
Period size: 22 Copynumber: 3.1 Consensus size: 22
39374323 TAAGAGTTTA
*
39374333 AGAGAATTTTGGAAGGAAATTG
1 AGAGAATTTTTGAAGGAAATTG
*
39374355 AGAGAATTTTTGAAGGAATTTG
1 AGAGAATTTTTGAAGGAAATTG
*
39374377 AGAGAATTTTTGAATGAAATTG
1 AGAGAATTTTTGAAGGAAATTG
39374399 AGA
1 AGA
39374402 TGGGATTTGT
Statistics
Matches: 43, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 43 1.00
ACGTcount: A:0.41, C:0.00, G:0.28, T:0.32
Consensus pattern (22 bp):
AGAGAATTTTTGAAGGAAATTG
Found at i:39374848 original size:20 final size:20
Alignment explanation
Indices: 39374825--39374870 Score: 60
Period size: 19 Copynumber: 2.4 Consensus size: 20
39374815 TTAATTTTAC
*
39374825 TTTAAATTT-TTTTTGAAAAT
1 TTTAAATTTATTATT-AAAAT
39374845 TTT-AATTTATTATTAAAAT
1 TTTAAATTTATTATTAAAAT
39374864 TTTAAAT
1 TTTAAAT
39374871 CTAAAATTTT
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
19 13 0.57
20 10 0.43
ACGTcount: A:0.39, C:0.00, G:0.02, T:0.59
Consensus pattern (20 bp):
TTTAAATTTATTATTAAAAT
Found at i:39374861 original size:31 final size:31
Alignment explanation
Indices: 39374804--39374866 Score: 92
Period size: 31 Copynumber: 2.0 Consensus size: 31
39374794 TCTCCAAAGC
*
39374804 TTTTGAAAATTTTAATTTTACTTTAAATTTT
1 TTTTGAAAATTTTAATTTTACTTTAAAATTT
*
39374835 TTTTGAAAATTTTAA-TTTATTATTAAAATTT
1 TTTTGAAAATTTTAATTTTACT-TTAAAATTT
39374866 T
1 T
39374867 AAATCTAAAA
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
30 5 0.17
31 24 0.83
ACGTcount: A:0.35, C:0.02, G:0.03, T:0.60
Consensus pattern (31 bp):
TTTTGAAAATTTTAATTTTACTTTAAAATTT
Found at i:39376732 original size:29 final size:29
Alignment explanation
Indices: 39376686--39376756 Score: 97
Period size: 29 Copynumber: 2.4 Consensus size: 29
39376676 TTAGACCATG
* *
39376686 GACCTTGGACCCTAGATCTTGAAACCCTA
1 GACCATGGACCCTAGATCCTGAAACCCTA
* * *
39376715 GACCATGGACTCTGGATCCTGAAACCTTA
1 GACCATGGACCCTAGATCCTGAAACCCTA
39376744 GACCATGGACCCT
1 GACCATGGACCCT
39376757 CGACCTTGAA
Statistics
Matches: 36, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
29 36 1.00
ACGTcount: A:0.27, C:0.31, G:0.20, T:0.23
Consensus pattern (29 bp):
GACCATGGACCCTAGATCCTGAAACCCTA
Found at i:39376766 original size:29 final size:29
Alignment explanation
Indices: 39376686--39376766 Score: 92
Period size: 29 Copynumber: 2.8 Consensus size: 29
39376676 TTAGACCATG
* *
39376686 GACCTTGGACCCTAGATCTTGAAACCCTA
1 GACCATGGACCCTAGACCTTGAAACCCTA
* * *
39376715 GACCATGGACTCTGGATCC-TGAAACCTTA
1 GACCATGGACCCTAGA-CCTTGAAACCCTA
*
39376744 GACCATGGACCCTCGACCTTGAA
1 GACCATGGACCCTAGACCTTGAA
39376767 CTAGGGTCTA
Statistics
Matches: 43, Mismatches: 7, Indels: 4
0.80 0.13 0.07
Matches are distributed among these distances:
28 2 0.05
29 40 0.93
30 1 0.02
ACGTcount: A:0.27, C:0.31, G:0.20, T:0.22
Consensus pattern (29 bp):
GACCATGGACCCTAGACCTTGAAACCCTA
Found at i:39376831 original size:28 final size:27
Alignment explanation
Indices: 39376767--39376836 Score: 79
Period size: 28 Copynumber: 2.6 Consensus size: 27
39376757 CGACCTTGAA
* *
39376767 CTAGGGTCTAGGGTTCAAGTTTAGGGT
1 CTAGGGTCCAAGGTTCAAGTTTAGGGT
* *
39376794 -TCAGGATCCATGGTTCAAGATTTAGGGT
1 CT-AGGGTCCAAGGTTCAAG-TTTAGGGT
39376822 CTAGGGTCCAAGGTT
1 CTAGGGTCCAAGGTT
39376837 TAAGGTCGAG
Statistics
Matches: 35, Mismatches: 5, Indels: 5
0.78 0.11 0.11
Matches are distributed among these distances:
26 1 0.03
27 14 0.40
28 19 0.54
29 1 0.03
ACGTcount: A:0.21, C:0.14, G:0.33, T:0.31
Consensus pattern (27 bp):
CTAGGGTCCAAGGTTCAAGTTTAGGGT
Found at i:39387711 original size:43 final size:42
Alignment explanation
Indices: 39387644--39387795 Score: 205
Period size: 43 Copynumber: 3.5 Consensus size: 42
39387634 GGCAGCGTTT
* *
39387644 TTTTTCACATAAATGCCGCTAAAGAACATGACCTTTAGTGACGC
1 TTTTTCAC--AAACGCCGCTAAAGAACATGACCTTTAGCGACGC
* *
39387688 TTTTATCACAAACGCCGCTAAAGATCATGACCTTTAGCGGCGCC
1 TTTT-TCACAAACGCCGCTAAAGAACATGACCTTTAGCGACG-C
*
39387732 TTTTTCACAAACGCCGCTAAAGAACATGACCTTTAGCGACGTT
1 TTTTTCACAAACGCCGCTAAAGAACATGACCTTTAGCGACG-C
*
39387775 TTTTTCACAAACACCGCTAAA
1 TTTTTCACAAACGCCGCTAAA
39387796 AGTACCGTTC
Statistics
Matches: 97, Mismatches: 9, Indels: 5
0.87 0.08 0.05
Matches are distributed among these distances:
43 84 0.87
44 9 0.09
45 4 0.04
ACGTcount: A:0.31, C:0.26, G:0.15, T:0.28
Consensus pattern (42 bp):
TTTTTCACAAACGCCGCTAAAGAACATGACCTTTAGCGACGC
Found at i:39391898 original size:12 final size:12
Alignment explanation
Indices: 39391883--39391908 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
39391873 ATCATCCTCT
39391883 TCATCAGATTCA
1 TCATCAGATTCA
39391895 TCATCAGATTCA
1 TCATCAGATTCA
39391907 TC
1 TC
39391909 CATCGATCTT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.31, C:0.27, G:0.08, T:0.35
Consensus pattern (12 bp):
TCATCAGATTCA
Found at i:39393641 original size:9 final size:9
Alignment explanation
Indices: 39393627--39393740 Score: 106
Period size: 9 Copynumber: 12.1 Consensus size: 9
39393617 TAAGTATAAA
39393627 TAAGTTATG
1 TAAGTTATG
39393636 TAAGTTATG
1 TAAGTTATG
* *
39393645 ATATGATATATA
1 -TAAG-T-TATG
39393657 TAAGTTAT-
1 TAAGTTATG
*
39393665 TGAGTTATG
1 TAAGTTATG
39393674 TAAGTTATG
1 TAAGTTATG
39393683 TGAA-TTATG
1 T-AAGTTATG
39393692 TAAGTTATG
1 TAAGTTATG
* *
39393701 ATATGATATATA
1 -TAAG-T-TATG
39393713 TAAGTTATG
1 TAAGTTATG
39393722 TAAGTTATG
1 TAAGTTATG
39393731 TAAGTTATG
1 TAAGTTATG
39393740 T
1 T
39393741 GAGTAATGAA
Statistics
Matches: 87, Mismatches: 9, Indels: 18
0.76 0.08 0.16
Matches are distributed among these distances:
8 9 0.10
9 54 0.62
10 10 0.11
11 8 0.09
12 6 0.07
ACGTcount: A:0.36, C:0.00, G:0.19, T:0.45
Consensus pattern (9 bp):
TAAGTTATG
Found at i:39393662 original size:30 final size:30
Alignment explanation
Indices: 39393621--39393730 Score: 140
Period size: 30 Copynumber: 3.8 Consensus size: 30
39393611 TATTTATAAG
*
39393621 TATAAATAAGTTATGTAAGTTATGATATGA
1 TATATATAAGTTATGTAAGTTATGATATGA
* *
39393651 TATATATAAGTTAT-TGAGTTATG-TAAG-
1 TATATATAAGTTATGTAAGTTATGATATGA
*
39393678 T-TATGTGAA-TTATGTAAGTTATGATATGA
1 TATATAT-AAGTTATGTAAGTTATGATATGA
39393707 TATATATAAGTTATGTAAGTTATG
1 TATATATAAGTTATGTAAGTTATG
39393731 TAAGTTATGT
Statistics
Matches: 67, Mismatches: 7, Indels: 12
0.78 0.08 0.14
Matches are distributed among these distances:
26 8 0.12
27 11 0.16
28 6 0.09
29 11 0.16
30 31 0.46
ACGTcount: A:0.38, C:0.00, G:0.18, T:0.44
Consensus pattern (30 bp):
TATATATAAGTTATGTAAGTTATGATATGA
Found at i:39393692 original size:56 final size:57
Alignment explanation
Indices: 39393631--39393742 Score: 208
Period size: 56 Copynumber: 2.0 Consensus size: 57
39393621 TATAAATAAG
*
39393631 TTATGTAAGTTATGATATGATATATATAAGTTAT-TGAGTTATGTAAGTTATGTGAA
1 TTATGTAAGTTATGATATGATATATATAAGTTATGTAAGTTATGTAAGTTATGTGAA
39393687 TTATGTAAGTTATGATATGATATATATAAGTTATGTAAGTTATGTAAGTTATGTGA
1 TTATGTAAGTTATGATATGATATATATAAGTTATGTAAGTTATGTAAGTTATGTGA
39393743 GTAATGAATT
Statistics
Matches: 54, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
56 34 0.63
57 20 0.37
ACGTcount: A:0.36, C:0.00, G:0.20, T:0.45
Consensus pattern (57 bp):
TTATGTAAGTTATGATATGATATATATAAGTTATGTAAGTTATGTAAGTTATGTGAA
Found at i:39393878 original size:120 final size:120
Alignment explanation
Indices: 39393732--39394330 Score: 991
Period size: 120 Copynumber: 5.0 Consensus size: 120
39393722 TAAGTTATGT
* *
39393732 AAGTTATGTGAGTAATGAATTTGAAATATAGGTTACATATCCATACTAATATATGTTATATATTA
1 AAGTTAT-T-AGTAATGAATTTGAAATATAGGTTATATATCCATACTAATATAGGTTATATATTA
* *
39393797 AAAATATAGGTTTTAATAATTAAAATATAATATTTATAATTATGTATAAAATTTAAA
64 AAAATATAGGTTTTAATATTTAAAATATAATATTTATAATTATGTTTAAAATTTAAA
*
39393854 AAGTTATTAGTAATGAATTTGAAATATAGGTAATATATCCATACTAATATAGGTTATATATTAAA
1 AAGTTATTAGTAATGAATTTGAAATATAGGTTATATATCCATACTAATATAGGTTATATATTAAA
* *
39393919 AATATAGGTTTTAATATTTAAAATATAATATTTATAATTATGTATAAAATTGAAA
66 AATATAGGTTTTAATATTTAAAATATAATATTTATAATTATGTTTAAAATTTAAA
** * *
39393974 ATTTTATTAGTAATGAATTTGAAATATAGGTAATATATTCATACTAATATAGGTTATATATTAAA
1 AAGTTATTAGTAATGAATTTGAAATATAGGTTATATATCCATACTAATATAGGTTATATATTAAA
* **
39394039 AATATAGGTTTTAATATTTAAAATATAAAATAAATAATTATGTTTAAAATTTAAA
66 AATATAGGTTTTAATATTTAAAATATAATATTTATAATTATGTTTAAAATTTAAA
*
39394094 AAGTTATTAGTAATGAATTTGAAATATAGGTTATATATCCATACTAATATACGTTATATATTAAA
1 AAGTTATTAGTAATGAATTTGAAATATAGGTTATATATCCATACTAATATAGGTTATATATTAAA
* *
39394159 AATATAGGTTTTAATATTTAAAATATAATATTTTTAATTATTTTTAAAATTTAAA
66 AATATAGGTTTTAATATTTAAAATATAATATTTATAATTATGTTTAAAATTTAAA
39394214 AAGTTATTAGTAATGAATTTGAAATATAGGTTATATATCCATACTTAATATAGGTTATATATTAA
1 AAGTTATTAGTAATGAATTTGAAATATAGGTTATATATCCATAC-TAATATAGGTTATATATTAA
* * *
39394279 AAATATAGGTTTTAATATTTAAAATATAATATATGTAATTATTTTTAAAATT
65 AAATATAGGTTTTAATATTTAAAATATAATATTTATAATTATGTTTAAAATT
39394331 GCATAGGAAT
Statistics
Matches: 450, Mismatches: 26, Indels: 3
0.94 0.05 0.01
Matches are distributed among these distances:
120 373 0.83
121 70 0.16
122 7 0.02
ACGTcount: A:0.46, C:0.03, G:0.09, T:0.43
Consensus pattern (120 bp):
AAGTTATTAGTAATGAATTTGAAATATAGGTTATATATCCATACTAATATAGGTTATATATTAAA
AATATAGGTTTTAATATTTAAAATATAATATTTATAATTATGTTTAAAATTTAAA
Found at i:39393924 original size:20 final size:21
Alignment explanation
Indices: 39393899--39393945 Score: 69
Period size: 21 Copynumber: 2.3 Consensus size: 21
39393889 TATCCATACT
39393899 AATATAGGTTAT-ATATTAAA
1 AATATAGGTTATAATATTAAA
* *
39393919 AATATAGGTTTTAATATTTAA
1 AATATAGGTTATAATATTAAA
39393940 AATATA
1 AATATA
39393946 ATATTTATAA
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
20 11 0.46
21 13 0.54
ACGTcount: A:0.49, C:0.00, G:0.09, T:0.43
Consensus pattern (21 bp):
AATATAGGTTATAATATTAAA
Found at i:39394061 original size:21 final size:20
Alignment explanation
Indices: 39393995--39394065 Score: 70
Period size: 23 Copynumber: 3.4 Consensus size: 20
39393985 AATGAATTTG
*
39393995 AAATATAGGTAATATATTCATA
1 AAATATAGGTTATATATT-A-A
*
39394017 CTAATATAGGTTATATATTAA
1 -AAATATAGGTTATATATTAA
* *
39394038 AAATATAGGTTTTAATATTTA
1 AAATATAGGTTAT-ATATTAA
39394059 AAATATA
1 AAATATA
39394066 AAATAAATAA
Statistics
Matches: 42, Mismatches: 5, Indels: 4
0.82 0.10 0.08
Matches are distributed among these distances:
20 11 0.26
21 14 0.33
22 1 0.02
23 16 0.38
ACGTcount: A:0.48, C:0.03, G:0.08, T:0.41
Consensus pattern (20 bp):
AAATATAGGTTATATATTAA
Found at i:39394285 original size:20 final size:21
Alignment explanation
Indices: 39394260--39394306 Score: 69
Period size: 21 Copynumber: 2.3 Consensus size: 21
39394250 ATCCATACTT
39394260 AATATAGGTTAT-ATATTAAA
1 AATATAGGTTATAATATTAAA
* *
39394280 AATATAGGTTTTAATATTTAA
1 AATATAGGTTATAATATTAAA
39394301 AATATA
1 AATATA
39394307 ATATATGTAA
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
20 11 0.46
21 13 0.54
ACGTcount: A:0.49, C:0.00, G:0.09, T:0.43
Consensus pattern (21 bp):
AATATAGGTTATAATATTAAA
Found at i:39396801 original size:30 final size:30
Alignment explanation
Indices: 39396765--39396821 Score: 98
Period size: 30 Copynumber: 1.9 Consensus size: 30
39396755 CAAAAGTAAT
39396765 TAAATCCTAAAA-CCATAAAACCCTAAATCC
1 TAAATCCTAAAACCCAT-AAACCCTAAATCC
39396795 TAAATCCTAAAACCCATAAACCCTAAA
1 TAAATCCTAAAACCCATAAACCCTAAA
39396822 CCATAAACAC
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
30 22 0.85
31 4 0.15
ACGTcount: A:0.51, C:0.30, G:0.00, T:0.19
Consensus pattern (30 bp):
TAAATCCTAAAACCCATAAACCCTAAATCC
Found at i:39396821 original size:7 final size:7
Alignment explanation
Indices: 39396782--39396863 Score: 67
Period size: 7 Copynumber: 11.4 Consensus size: 7
39396772 TAAAACCATA
39396782 AAACCCT
1 AAACCCT
*
39396789 AAATCCT
1 AAACCCT
*
39396796 AAATCCT
1 AAACCCT
39396803 AAAACCCAT
1 -AAACCC-T
39396812 AAACCCT
1 AAACCCT
*
39396819 AAACCAT
1 AAACCCT
*
39396826 AAACACT
1 AAACCCT
* *
39396833 ATACCTT
1 AAACCCT
*
39396840 AAACCAT
1 AAACCCT
39396847 AAACACC-
1 AAAC-CCT
39396854 AAACCCT
1 AAACCCT
39396861 AAA
1 AAA
39396864 ACCTTAAACT
Statistics
Matches: 60, Mismatches: 11, Indels: 8
0.76 0.14 0.10
Matches are distributed among these distances:
6 2 0.03
7 45 0.75
8 12 0.20
9 1 0.02
ACGTcount: A:0.50, C:0.33, G:0.00, T:0.17
Consensus pattern (7 bp):
AAACCCT
Found at i:39396863 original size:21 final size:21
Alignment explanation
Indices: 39396812--39396872 Score: 77
Period size: 21 Copynumber: 2.9 Consensus size: 21
39396802 TAAAACCCAT
*
39396812 AAACCCTAAACCATAAACACT
1 AAACCCTAAACCATAAACACC
* *
39396833 ATACCTTAAACCATAAACACC
1 AAACCCTAAACCATAAACACC
*
39396854 AAACCCTAAAACCTTAAAC
1 AAACCCT-AAACCATAAAC
39396873 TTCTAAGTCT
Statistics
Matches: 33, Mismatches: 6, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
21 23 0.70
22 10 0.30
ACGTcount: A:0.51, C:0.33, G:0.00, T:0.16
Consensus pattern (21 bp):
AAACCCTAAACCATAAACACC
Found at i:39397342 original size:115 final size:115
Alignment explanation
Indices: 39397105--39397350 Score: 309
Period size: 115 Copynumber: 2.1 Consensus size: 115
39397095 GGTATTTTTA
* * *
39397105 TCAAAAA-CGCCGTTAATGCCACTAAAGCTCAACAACAAACGACGTCGTTTTCTCAAATTTTTTG
1 TCAAAAAGCGCCGCTAATGCCACTAAAGCTCAACAAAAAACGAAGTCGTTTTCTCAAATTTTTTG
* * * * *
39397169 CGATGTTTCTAAAAACATGCCGCTAATGCTTGATCTATTGCGGAGTTTGT
66 CGATATTTCTAAAAAAACGCCGCTAATGCTTGATCTATAGCGGAGTTTGC
* *
39397219 TGAAAAAGCGCCGCTAATGCCACTAATGCTCAACAAAAAACGAAGTCGTTTTGCTCAAATTTTTT
1 TCAAAAAGCGCCGCTAATGCCACTAAAGCTCAACAAAAAACGAAGTCGTTTT-CTCAAATTTTTT
* * * *
39397284 GCGGTATTT-TACAAAAAACGCCGCTAATTCTTTATCTATAGCGGCGTTT-C
65 GCGATATTTCTA-AAAAAACGCCGCTAATGCTTGATCTATAGCGGAGTTTGC
* *
39397334 TCAGAAAGCACCGCTAA
1 TCAAAAAGCGCCGCTAA
39397351 AACTCAATCT
Statistics
Matches: 112, Mismatches: 17, Indels: 5
0.84 0.13 0.04
Matches are distributed among these distances:
114 6 0.05
115 56 0.50
116 50 0.45
ACGTcount: A:0.31, C:0.22, G:0.17, T:0.30
Consensus pattern (115 bp):
TCAAAAAGCGCCGCTAATGCCACTAAAGCTCAACAAAAAACGAAGTCGTTTTCTCAAATTTTTTG
CGATATTTCTAAAAAAACGCCGCTAATGCTTGATCTATAGCGGAGTTTGC
Found at i:39397388 original size:40 final size:40
Alignment explanation
Indices: 39397317--39397411 Score: 118
Period size: 40 Copynumber: 2.4 Consensus size: 40
39397307 CTAATTCTTT
*
39397317 ATCTATAGCGGCGTTTCTCAGAAAGCACCGCTAAAACTCA
1 ATCTATTGCGGCGTTTCTCAGAAAGCACCGCTAAAACTCA
** * ** *
39397357 ATCTATTGCGGCGTTTCTCAGTTAGCGCCGCTAATGCTCG
1 ATCTATTGCGGCGTTTCTCAGAAAGCACCGCTAAAACTCA
*
39397397 ATCTATTGTGGCGTT
1 ATCTATTGCGGCGTT
39397412 CTTTAAAAGG
Statistics
Matches: 47, Mismatches: 8, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
40 47 1.00
ACGTcount: A:0.22, C:0.25, G:0.22, T:0.31
Consensus pattern (40 bp):
ATCTATTGCGGCGTTTCTCAGAAAGCACCGCTAAAACTCA
Found at i:39397462 original size:195 final size:196
Alignment explanation
Indices: 39397187--39397567 Score: 559
Period size: 195 Copynumber: 1.9 Consensus size: 196
39397177 CTAAAAACAT
* * * * *
39397187 GCCGCTAATGCTTGATCTATTGCGGAGTTTGTTGAAAAAGCGCCGCTAATGCCACTAATGCTCAA
1 GCCGCTAATGCTCGATCTATTGCGGAGTTTGTTGAAAAAGCGCCACTAAAGCCAATAAAGCTCAA
* * *
39397252 CAAAAAACGAAGTCGTTTTGCTCAAATTTTTTGCGGTATTTTACAAAAAACGCCGCTAATTCTTT
66 CAAAAAACAAAGTCGTTTTGCTCAAATTTTTTGCGGCATTTTACAAAAAACGCCGCTAATTCTTG
39397317 ATCTATAGCGGCGTTTCTCAGAAAGCACCGCTAAAACTCAATCTATTGCGGCGTTTCTCAGTTAG
131 ATCTATAGCGGCGTTTCTCAGAAAGCACCGCTAAAACTCAATCTATTGCGGCGTTTCTCAGTTAG
39397382 C
196 C
* * *
39397383 GCCGCTAATGCTCGATCTATTGTGGCGTTCT-TT-AAAAGGCGCCACTAAAGCCAATAAAGCTCA
1 GCCGCTAATGCTCGATCTATTGCGGAGTT-TGTTGAAAAAGCGCCACTAAAGCCAATAAAGCTCA
* * * *
39397446 ACAAAAAACAAAGTCGTTTTGCTCAACTTTTTTGCGGCGTTTTACATAAAGCGCCGCTAATTCTT
65 ACAAAAAACAAAGTCGTTTTGCTCAAATTTTTTGCGGCATTTTACAAAAAACGCCGCTAATTCTT
* * * * *
39397511 GATCTATAGCGGCGTTTCTCAGAAAGCGCTGCTAAAGCTCGATCTATTGCGGTGTTT
130 GATCTATAGCGGCGTTTCTCAGAAAGCACCGCTAAAACTCAATCTATTGCGGCGTTT
39397568 TTTAAAAAGC
Statistics
Matches: 164, Mismatches: 20, Indels: 3
0.88 0.11 0.02
Matches are distributed among these distances:
195 135 0.82
196 28 0.17
197 1 0.01
ACGTcount: A:0.27, C:0.23, G:0.20, T:0.30
Consensus pattern (196 bp):
GCCGCTAATGCTCGATCTATTGCGGAGTTTGTTGAAAAAGCGCCACTAAAGCCAATAAAGCTCAA
CAAAAAACAAAGTCGTTTTGCTCAAATTTTTTGCGGCATTTTACAAAAAACGCCGCTAATTCTTG
ATCTATAGCGGCGTTTCTCAGAAAGCACCGCTAAAACTCAATCTATTGCGGCGTTTCTCAGTTAG
C
Found at i:39397497 original size:155 final size:155
Alignment explanation
Indices: 39397357--39397726 Score: 555
Period size: 155 Copynumber: 2.4 Consensus size: 155
39397347 CTAAAACTCA
** * * *
39397357 ATCTATTGCGGCGTTTCTCAGTTAGCGCCGCTAATGCTCGATCTATTGTGGCGTTCTTTAAAAGG
1 ATCTATTGCGGCGTTTCTCAGAAAGCGCCGCTAAAGCTCGATCTATTGCGGCGTTCTTTAAAAAG
39397422 CGCCACTAAAGCCAATAAAGCTCAACAAAAAACAAAGTCGTTTTGCTCAACTTTTTTGCGGCGTT
66 CGCCACTAAAGCCAATAAAGCTCAACAAAAAACAAAGTCGTTTTGCTCAACTTTTTTGCGGCGTT
39397487 TTACATAAAGCGCCGCTAATTCTTG
131 TTACATAAAGCGCCGCTAATTCTTG
* * * *
39397512 ATCTATAGCGGCGTTTCTCAGAAAGCGCTGCTAAAGCTCGATCTATTGCGGTGTTTTTTAAAAAG
1 ATCTATTGCGGCGTTTCTCAGAAAGCGCCGCTAAAGCTCGATCTATTGCGGCGTTCTTTAAAAAG
* *
39397577 CGCCACTAAAGCCAATAAAGCTCAACAAAAAACGAAGTCGTTTTGCTCAACTTTTTTGCGGTGTT
66 CGCCACTAAAGCCAATAAAGCTCAACAAAAAACAAAGTCGTTTTGCTCAACTTTTTTGCGGCGTT
39397642 TTACATAAAGCGCCGCTAATTCTTG
131 TTACATAAAGCGCCGCTAATTCTTG
* * * * * *
39397667 ATCTATTGCGGCGCTTTTTGA-AAAGCACCGCTAATA-CTTGATCTTTTGCGGCGTTTTTTA
1 ATCTATTGCGGCG-TTTCTCAGAAAGCGCCGCTAA-AGCTCGATCTATTGCGGCGTTCTTTA
39397727 TTCAAACACC
Statistics
Matches: 194, Mismatches: 19, Indels: 4
0.89 0.09 0.02
Matches are distributed among these distances:
155 188 0.97
156 6 0.03
ACGTcount: A:0.26, C:0.22, G:0.19, T:0.32
Consensus pattern (155 bp):
ATCTATTGCGGCGTTTCTCAGAAAGCGCCGCTAAAGCTCGATCTATTGCGGCGTTCTTTAAAAAG
CGCCACTAAAGCCAATAAAGCTCAACAAAAAACAAAGTCGTTTTGCTCAACTTTTTTGCGGCGTT
TTACATAAAGCGCCGCTAATTCTTG
Found at i:39397555 original size:40 final size:40
Alignment explanation
Indices: 39397479--39397588 Score: 105
Period size: 40 Copynumber: 2.8 Consensus size: 40
39397469 CAACTTTTTT
* ** *
39397479 GCGGCGTTTTACATAAAGCGCCGCTAATTCTTGATCTATA
1 GCGGCGTTTTACAGAAAGCGCCGCTAAAGCTCGATCTATA
* *
39397519 GCGGCGTTTCT-CAGAAAGCGCTGCTAAAGCTCGATCTATT
1 GCGGCGTTT-TACAGAAAGCGCCGCTAAAGCTCGATCTATA
* ** * *
39397559 GCGGTGTTTTTTAAAAAGCGCCACTAAAGC
1 GCGGCGTTTTACAGAAAGCGCCGCTAAAGC
39397589 CAATAAAGCT
Statistics
Matches: 57, Mismatches: 11, Indels: 4
0.79 0.15 0.06
Matches are distributed among these distances:
39 1 0.02
40 55 0.96
41 1 0.02
ACGTcount: A:0.25, C:0.23, G:0.23, T:0.29
Consensus pattern (40 bp):
GCGGCGTTTTACAGAAAGCGCCGCTAAAGCTCGATCTATA
Found at i:39397692 original size:40 final size:40
Alignment explanation
Indices: 39397648--39397725 Score: 120
Period size: 40 Copynumber: 1.9 Consensus size: 40
39397638 TGTTTTACAT
* *
39397648 AAAGCGCCGCTAATTCTTGATCTATTGCGGCGCTTTTTGA
1 AAAGCACCGCTAATACTTGATCTATTGCGGCGCTTTTTGA
* *
39397688 AAAGCACCGCTAATACTTGATCTTTTGCGGCGTTTTTT
1 AAAGCACCGCTAATACTTGATCTATTGCGGCGCTTTTT
39397726 ATTCAAACAC
Statistics
Matches: 34, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
40 34 1.00
ACGTcount: A:0.21, C:0.22, G:0.21, T:0.37
Consensus pattern (40 bp):
AAAGCACCGCTAATACTTGATCTATTGCGGCGCTTTTTGA
Found at i:39405951 original size:23 final size:23
Alignment explanation
Indices: 39405925--39405968 Score: 63
Period size: 23 Copynumber: 1.9 Consensus size: 23
39405915 AAAATGGAAA
39405925 GAAATAATATATAT-AAATAATCT
1 GAAA-AATATATATGAAATAATCT
*
39405948 GAAAAATATATGTGAAATAAT
1 GAAAAATATATATGAAATAAT
39405969 TAAATGTATA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
22 8 0.42
23 11 0.58
ACGTcount: A:0.57, C:0.02, G:0.09, T:0.32
Consensus pattern (23 bp):
GAAAAATATATATGAAATAATCT
Found at i:39408758 original size:50 final size:50
Alignment explanation
Indices: 39408655--39408748 Score: 122
Period size: 50 Copynumber: 1.9 Consensus size: 50
39408645 ATATATATAT
*
39408655 TTATGAAAATAAAATACATATATAGACATGTATATAGATATGTATAAAAA
1 TTATGAAAATAAAATACATATATAGACATGTATATAGATATATATAAAAA
* **
39408705 TTATGAAATATAAAA-ATATATATAGGTATGTATAT-G-TATATATA
1 TTATGAAA-ATAAAATACATATATAGACATGTATATAGATATATATA
39408749 GATAGATTAT
Statistics
Matches: 39, Mismatches: 4, Indels: 4
0.83 0.09 0.09
Matches are distributed among these distances:
48 7 0.18
49 1 0.03
50 25 0.64
51 6 0.15
ACGTcount: A:0.51, C:0.02, G:0.11, T:0.36
Consensus pattern (50 bp):
TTATGAAAATAAAATACATATATAGACATGTATATAGATATATATAAAAA
Found at i:39410369 original size:44 final size:44
Alignment explanation
Indices: 39410316--39410434 Score: 114
Period size: 45 Copynumber: 2.7 Consensus size: 44
39410306 TTATCATTTT
* * *
39410316 AATCCGCTCCAGTACAACTTCAGGGAGATAGGATTAG-TAGCTTA
1 AATCTGCTCCACTGCAACTTCAGGGAGATAGG-TTAGTTAGCTTA
* * * * * *
39410360 AATCTGCTCCATTGCAAATTCAGGTAGATAAGGTTTGTTATCTTC
1 AATCTGCTCCACTGCAACTTCAGGGAGAT-AGGTTAGTTAGCTTA
* *
39410405 AGTCTGCTCTACTGCAACTTCAGGGAGATA
1 AATCTGCTCCACTGCAACTTCAGGGAGATA
39410435 AAACTTGTCA
Statistics
Matches: 60, Mismatches: 13, Indels: 4
0.78 0.17 0.05
Matches are distributed among these distances:
44 28 0.47
45 32 0.53
ACGTcount: A:0.29, C:0.20, G:0.21, T:0.30
Consensus pattern (44 bp):
AATCTGCTCCACTGCAACTTCAGGGAGATAGGTTAGTTAGCTTA
Found at i:39410609 original size:129 final size:129
Alignment explanation
Indices: 39410401--39410831 Score: 515
Period size: 129 Copynumber: 3.3 Consensus size: 129
39410391 GGTTTGTTAT
* * * * * * * *
39410401 CTTCAGTCTGCTCTACTGCAACTTCAGGGAGATAAAACTTGTCATGGTGTGATCCGCTCTATTGC
1 CTTCAATCTACTCCACTGCAACTTCAGGGAGATAAGA-TTG----GATGCGATCTGCTCTACTGC
** * * * * * *
39410466 AACTTTAGAGAGATAAGATCTGTCATTTTAATTCGCTTCACTGTAACTTCAGGAAGATATGA-TT
61 AACTTTAGAGAGATAAGATCTGTGGTTTTAATACACTCCACTGCAACTTCAGGAAGATAGGACTA
**
39410530 GATTT
126 G-TAA
*
39410535 CTTCAATCTACTCCACTGCAACTTTAGGGAGATAAGATTGGATGCGATCTGCTCTACTGCAACTT
1 CTTCAATCTACTCCACTGCAACTTCAGGGAGATAAGATTGGATGCGATCTGCTCTACTGCAACTT
*
39410600 TAGATAGATAAGATCTGTGGTTTTAATACACTCCACTGCAACTTCA-GAGAGATAGGACTAGTAA
66 TAGAGAGATAAGATCTGTGGTTTTAATACACTCCACTGCAACTTCAGGA-AGATAGGACTAGTAA
*
39410664 CTTCAATCTACTCCACTGCAACTTCAGGGAGATAAGATTGGATGCAATCTGCTCTACTGCAACTT
1 CTTCAATCTACTCCACTGCAACTTCAGGGAGATAAGATTGGATGCGATCTGCTCTACTGCAACTT
* * * * * *
39410729 CAAAGAGATAAGATCTATGGTTTTAATCCACTCCACTGCAACTTTAGGGAGATAGGACTAGTAA
66 TAGAGAGATAAGATCTGTGGTTTTAATACACTCCACTGCAACTTCAGGAAGATAGGACTAGTAA
* * *
39410793 CTTCAATCTGCTCCACTACAACTTCAGGGAAATAAGATT
1 CTTCAATCTACTCCACTGCAACTTCAGGGAGATAAGATT
39410832 TGTTGGCTTT
Statistics
Matches: 262, Mismatches: 32, Indels: 11
0.86 0.10 0.04
Matches are distributed among these distances:
128 2 0.01
129 222 0.85
130 3 0.01
133 3 0.01
134 32 0.12
ACGTcount: A:0.30, C:0.21, G:0.19, T:0.31
Consensus pattern (129 bp):
CTTCAATCTACTCCACTGCAACTTCAGGGAGATAAGATTGGATGCGATCTGCTCTACTGCAACTT
TAGAGAGATAAGATCTGTGGTTTTAATACACTCCACTGCAACTTCAGGAAGATAGGACTAGTAA
Found at i:39410643 original size:44 final size:43
Alignment explanation
Indices: 39410536--39410874 Score: 240
Period size: 44 Copynumber: 7.8 Consensus size: 43
39410526 GATTGATTTC
* * *
39410536 TTCAATCTACTCCACTGCAACTTTAGGGAGATAAGA-T-TGGA
1 TTCAATCTACTCCACTGCAACTTCAGAGAGATAAGACTGTGGT
* * * * * *
39410577 TGCGATCTGCTCTACTGCAACTTTAGATAGATAAGATCTGTGGT
1 TTCAATCTACTCCACTGCAACTTCAGAGAGATAAGA-CTGTGGT
* * ***
39410621 TTTAATAC-ACTCCACTGCAACTTCAGAGAGATAGGACTAGTAAC
1 TTCAAT-CTACTCCACTGCAACTTCAGAGAGATAAGACT-GTGGT
* *
39410665 TTCAATCTACTCCACTGCAACTTCAGGGAGATAAGA-T-TGGA
1 TTCAATCTACTCCACTGCAACTTCAGAGAGATAAGACTGTGGT
* * * * *
39410706 TGCAATCTGCTCTACTGCAACTTCAAAGAGATAAGATCTATGGT
1 TTCAATCTACTCCACTGCAACTTCAGAGAGATAAGA-CTGTGGT
* * * * * ***
39410750 TTTAATCCACTCCACTGCAACTTTAGGGAGATAGGACTAGTAAC
1 TTCAATCTACTCCACTGCAACTTCAGAGAGATAAGACT-GTGGT
* * * * *
39410794 TTCAATCTGCTCCACTACAACTTCAGGGAAATAAGATTTGTTGGCT
1 TTCAATCTACTCCACTGCAACTTCAGAGAGATAAGA-CTG-TGG-T
* *
39410840 TT-AATCTTCTCCACTGCAACTTCAGGGAGATAAGA
1 TTCAATCTACTCCACTGCAACTTCAGAGAGATAAGA
39410875 ATTGTCATCT
Statistics
Matches: 228, Mismatches: 57, Indels: 22
0.74 0.19 0.07
Matches are distributed among these distances:
41 62 0.27
43 8 0.04
44 123 0.54
45 33 0.14
46 2 0.01
ACGTcount: A:0.31, C:0.21, G:0.19, T:0.29
Consensus pattern (43 bp):
TTCAATCTACTCCACTGCAACTTCAGAGAGATAAGACTGTGGT
Found at i:39410723 original size:85 final size:88
Alignment explanation
Indices: 39410630--39410874 Score: 273
Period size: 85 Copynumber: 2.8 Consensus size: 88
39410620 TTTTAATACA
* ** *
39410630 CTCCACTGCAACTTCAGAGAGATAGGACTAGTAACTTCAATCTACTCCACTGCAACTTCAGGGAG
1 CTCCACTGCAACTTCAGAGAGATAAGACTAGTGGCTTTAATCTACTCCACTGCAACTTCAGGGAG
* *
39410695 ATAAGA-TTG-GA-TGCAATCTG
66 ATAAGACTAGTAACTGCAATCTG
* * * * *
39410715 CTCTACTGCAACTTCAAAGAGATAAGATCTA-TGGTTTTAATCCACTCCACTGCAACTTTAGGGA
1 CTCCACTGCAACTTCAGAGAGATAAGA-CTAGTGGCTTTAATCTACTCCACTGCAACTTCAGGGA
* *
39410779 GATAGGACTAGTAACTTCAATCTG
65 GATAAGACTAGTAACTGCAATCTG
* * * * * *
39410803 CTCCACTACAACTTCAGGGAAATAAGATTTGTTGGCTTTAATCTTCTCCACTGCAACTTCAGGGA
1 CTCCACTGCAACTTCAGAGAGATAAGACTAG-TGGCTTTAATCTACTCCACTGCAACTTCAGGGA
39410868 GATAAGA
65 GATAAGA
39410875 ATTGTCATCT
Statistics
Matches: 129, Mismatches: 25, Indels: 8
0.80 0.15 0.05
Matches are distributed among these distances:
85 57 0.44
86 5 0.04
87 2 0.02
88 30 0.23
89 35 0.27
ACGTcount: A:0.31, C:0.22, G:0.18, T:0.28
Consensus pattern (88 bp):
CTCCACTGCAACTTCAGAGAGATAAGACTAGTGGCTTTAATCTACTCCACTGCAACTTCAGGGAG
ATAAGACTAGTAACTGCAATCTG
Found at i:39411105 original size:45 final size:45
Alignment explanation
Indices: 39411040--39411527 Score: 454
Period size: 45 Copynumber: 11.0 Consensus size: 45
39411030 AACTATGGTG
* * *
39411040 TCTTTGATCTGCTTCACTGTCAGTACAAGAAGGCAAGATCTGCTA
1 TCTTCGATCTGCTTCGCTGTCAGTACAGGAAGGCAAGATCTGCTA
* * * * *
39411085 TCTTC-AGTCTGCTCCGCTGTCAGTACAGTAAGGCAAG-GCTGGTG
1 TCTTCGA-TCTGCTTCGCTGTCAGTACAGGAAGGCAAGATCTGCTA
* * * * *
39411129 TCTTCGAT-TATCTTCGCTGCCGGTACATGAAGGCATGATCTGCTA
1 TCTTCGATCT-GCTTCGCTGTCAGTACAGGAAGGCAAGATCTGCTA
* * * * * * *
39411174 TCTTCAATCTGCTCCGCTGTCAATATAGGAATG-AAG-GCTAG-TG
1 TCTTCGATCTGCTTCGCTGTCAGTACAGGAAGGCAAGATCT-GCTA
* * *
39411217 TCTTCGATCTGCTTCGCTGCCAGTACAGGAAGGCAAAATTTGCTA
1 TCTTCGATCTGCTTCGCTGTCAGTACAGGAAGGCAAGATCTGCTA
* * * * *
39411262 TCTTC-AGTCTGCTCCGCTATCAGTACAGGAAGGCAAG-GCTGATG
1 TCTTCGA-TCTGCTTCGCTGTCAGTACAGGAAGGCAAGATCTGCTA
39411306 TCTTCGATCTGCTTCGCTGTCAGTACAGGAAGGCAAGATCTGCTA
1 TCTTCGATCTGCTTCGCTGTCAGTACAGGAAGGCAAGATCTGCTA
* * * * * *
39411351 TCTTCGATCTACTTTGCTGCCAATACAAGAAGACAAGATCTGCTA
1 TCTTCGATCTGCTTCGCTGTCAGTACAGGAAGGCAAGATCTGCTA
* ** * * * *
39411396 TCTTCGATCTACTTCGCTACCAATATAGGAAGACAAGATCTTCTA
1 TCTTCGATCTGCTTCGCTGTCAGTACAGGAAGGCAAGATCTGCTA
* * * * *
39411441 TCTTCAATCTGCTCCGCTGTTAGTACAGGAAGGCAAG-GCTGGTA
1 TCTTCGATCTGCTTCGCTGTCAGTACAGGAAGGCAAGATCTGCTA
*
39411485 TCTTCGATCTGCTTCGCTGCCAGTACAGGAAGGCAAGATCTGC
1 TCTTCGATCTGCTTCGCTGTCAGTACAGGAAGGCAAGATCTGC
39411528 AACTTCATTG
Statistics
Matches: 348, Mismatches: 82, Indels: 26
0.76 0.18 0.06
Matches are distributed among these distances:
43 31 0.09
44 111 0.32
45 205 0.59
46 1 0.00
ACGTcount: A:0.24, C:0.24, G:0.23, T:0.29
Consensus pattern (45 bp):
TCTTCGATCTGCTTCGCTGTCAGTACAGGAAGGCAAGATCTGCTA
Found at i:39411186 original size:89 final size:89
Alignment explanation
Indices: 39411035--39411527 Score: 603
Period size: 89 Copynumber: 5.5 Consensus size: 89
39411025 CTGCAAACTA
* * * * *
39411035 TGGTGTCTTTGATCTGCTTCACTGTCAGTACAAGAAGGCAAGATCTGCTATCTTCAGTCTGCTCC
1 TGGTGTCTTCGATCTGCTTCGCTGCCAGTACAGGAAGGCAAGATCTGCTATCTTCAATCTGCTCC
*
39411100 GCTGTCAGTACAGTAAGGCAAGGC
66 GCTGTCAGTACAGGAAGGCAAGGC
* * * *
39411124 TGGTGTCTTCGAT-TATCTTCGCTGCCGGTACATGAAGGCATGATCTGCTATCTTCAATCTGCTC
1 TGGTGTCTTCGATCT-GCTTCGCTGCCAGTACAGGAAGGCAAGATCTGCTATCTTCAATCTGCTC
* * *
39411188 CGCTGTCAATATAGGAATG-AAGGC
65 CGCTGTCAGTACAGGAAGGCAAGGC
* * * *
39411212 TAGTGTCTTCGATCTGCTTCGCTGCCAGTACAGGAAGGCAAAATTTGCTATCTTCAGTCTGCTCC
1 TGGTGTCTTCGATCTGCTTCGCTGCCAGTACAGGAAGGCAAGATCTGCTATCTTCAATCTGCTCC
*
39411277 GCTATCAGTACAGGAAGGCAAGGC
66 GCTGTCAGTACAGGAAGGCAAGGC
* * * * **
39411301 TGATGTCTTCGATCTGCTTCGCTGTCAGTACAGGAAGGCAAGATCTGCTATCTTCGATCTACTTT
1 TGGTGTCTTCGATCTGCTTCGCTGCCAGTACAGGAAGGCAAGATCTGCTATCTTCAATCTGCTCC
* * * * *
39411366 GCTGCCAATACAAGAAGACAAGATC
66 GCTGTCAGTACAGGAAGGCAAG-GC
* * * * * * * *
39411391 TGCTATCTTCGATCTACTTCGCTACCAATATAGGAAGACAAGATCTTCTATCTTCAATCTGCTCC
1 TGGTGTCTTCGATCTGCTTCGCTGCCAGTACAGGAAGGCAAGATCTGCTATCTTCAATCTGCTCC
*
39411456 GCTGTTAGTACAGGAAGGCAAGGC
66 GCTGTCAGTACAGGAAGGCAAGGC
*
39411480 TGGTATCTTCGATCTGCTTCGCTGCCAGTACAGGAAGGCAAGATCTGC
1 TGGTGTCTTCGATCTGCTTCGCTGCCAGTACAGGAAGGCAAGATCTGC
39411528 AACTTCATTG
Statistics
Matches: 334, Mismatches: 66, Indels: 8
0.82 0.16 0.02
Matches are distributed among these distances:
88 75 0.22
89 189 0.57
90 70 0.21
ACGTcount: A:0.24, C:0.24, G:0.23, T:0.29
Consensus pattern (89 bp):
TGGTGTCTTCGATCTGCTTCGCTGCCAGTACAGGAAGGCAAGATCTGCTATCTTCAATCTGCTCC
GCTGTCAGTACAGGAAGGCAAGGC
Found at i:39411340 original size:177 final size:177
Alignment explanation
Indices: 39411037--39411527 Score: 621
Period size: 177 Copynumber: 2.8 Consensus size: 177
39411027 GCAAACTATG
* * * * *
39411037 GTGTCTTTGATCTGCTTCACTGTCAGTACAAGAAGGCAAGATCTGCTATCTTCAGTCTGCTCCGC
1 GTGTCTTCGATCTGCTTCGCTGCCAGTACAGGAAGGCAAGATTTGCTATCTTCAGTCTGCTCCGC
* * * * *
39411102 TGTCAGTACAGTAAGGCAAGGCTGGTGTCTTCGAT-TATCTTCGCTGCCGGTACATGAAGGCATG
66 TGTCAGTACAGGAAGGCAAGGCTGGTGTCTTCGATCT-GCTTCGCTGCCAGTACAGGAAGGCAAG
* * * *
39411166 ATCTGCTATCTTCAATCTGCTCCGCTGTCAATATAGGAATG-AAG-GCT
130 ATCTGCTATCTTCAATCTACTCCGCTGCCAATACAAGAA-GAAAGAGCT
*
39411213 AGTGTCTTCGATCTGCTTCGCTGCCAGTACAGGAAGGCAAAATTTGCTATCTTCAGTCTGCTCCG
1 -GTGTCTTCGATCTGCTTCGCTGCCAGTACAGGAAGGCAAGATTTGCTATCTTCAGTCTGCTCCG
* * *
39411278 CTATCAGTACAGGAAGGCAAGGCTGATGTCTTCGATCTGCTTCGCTGTCAGTACAGGAAGGCAAG
65 CTGTCAGTACAGGAAGGCAAGGCTGGTGTCTTCGATCTGCTTCGCTGCCAGTACAGGAAGGCAAG
* ** *
39411343 ATCTGCTATCTTCGATCTACTTTGCTGCCAATACAAGAAGACAAGATCT
130 ATCTGCTATCTTCAATCTACTCCGCTGCCAATACAAGAAGA-AAGAGCT
* * * * * * *
39411392 GCTATCTTCGATCTACTTCGCTACCAATATAGGAAGACAAGATCTT-CTATCTTCAATCTGCTCC
1 G-TGTCTTCGATCTGCTTCGCTGCCAGTACAGGAAGGCAAGAT-TTGCTATCTTCAGTCTGCTCC
* *
39411456 GCTGTTAGTACAGGAAGGCAAGGCTGGTATCTTCGATCTGCTTCGCTGCCAGTACAGGAAGGCAA
64 GCTGTCAGTACAGGAAGGCAAGGCTGGTGTCTTCGATCTGCTTCGCTGCCAGTACAGGAAGGCAA
39411521 GATCTGC
129 GATCTGC
39411528 AACTTCATTG
Statistics
Matches: 273, Mismatches: 35, Indels: 10
0.86 0.11 0.03
Matches are distributed among these distances:
176 1 0.00
177 145 0.53
178 5 0.02
179 120 0.44
180 2 0.01
ACGTcount: A:0.24, C:0.24, G:0.23, T:0.29
Consensus pattern (177 bp):
GTGTCTTCGATCTGCTTCGCTGCCAGTACAGGAAGGCAAGATTTGCTATCTTCAGTCTGCTCCGC
TGTCAGTACAGGAAGGCAAGGCTGGTGTCTTCGATCTGCTTCGCTGCCAGTACAGGAAGGCAAGA
TCTGCTATCTTCAATCTACTCCGCTGCCAATACAAGAAGAAAGAGCT
Found at i:39412631 original size:7 final size:7
Alignment explanation
Indices: 39412619--39412688 Score: 70
Period size: 7 Copynumber: 9.7 Consensus size: 7
39412609 TGGCCTCTCC
39412619 TTTTTCT
1 TTTTTCT
39412626 TTTTTCT
1 TTTTTCT
*
39412633 TTTCTCTTT
1 TTT-T-TCT
39412642 TTCTTTCT
1 TT-TTTCT
39412650 TTTTTCT
1 TTTTTCT
*
39412657 TCTTT-T
1 TTTTTCT
*
39412663 TCTTTCT
1 TTTTTCT
*
39412670 TTTTCCT
1 TTTTTCT
39412677 TTTTTCT
1 TTTTTCT
39412684 TTTTT
1 TTTTT
39412689 TTCTCTATTT
Statistics
Matches: 53, Mismatches: 6, Indels: 8
0.79 0.09 0.12
Matches are distributed among these distances:
6 6 0.11
7 36 0.68
8 5 0.09
9 5 0.09
10 1 0.02
ACGTcount: A:0.00, C:0.19, G:0.00, T:0.81
Consensus pattern (7 bp):
TTTTTCT
Found at i:39412641 original size:20 final size:19
Alignment explanation
Indices: 39412618--39412709 Score: 102
Period size: 20 Copynumber: 4.9 Consensus size: 19
39412608 TTGGCCTCTC
*
39412618 CTTTTTCTTTTTTCTTTTCT
1 CTTTTTCTTTCTT-TTTTCT
39412638 CTTTTTCTTTCTTTTTTCTT
1 CTTTTTCTTTCTTTTTTC-T
*
39412658 CTTTTTCTTTCTTTTTCCT
1 CTTTTTCTTTCTTTTTTCT
39412677 -TTTTTC-TT-TTTTTTCT
1 CTTTTTCTTTCTTTTTTCT
*
39412693 CTATTTT-TTTATTTTTT
1 CT-TTTTCTTTCTTTTTT
39412710 ATTGAATCTG
Statistics
Matches: 64, Mismatches: 3, Indels: 11
0.82 0.04 0.14
Matches are distributed among these distances:
16 7 0.11
17 3 0.05
18 12 0.19
19 12 0.19
20 30 0.47
ACGTcount: A:0.02, C:0.17, G:0.00, T:0.80
Consensus pattern (19 bp):
CTTTTTCTTTCTTTTTTCT
Found at i:39412648 original size:24 final size:23
Alignment explanation
Indices: 39412621--39412692 Score: 89
Period size: 24 Copynumber: 3.2 Consensus size: 23
39412611 GCCTCTCCTT
39412621 TTTCTTTTTTCTTTTCTCTTTTTC
1 TTTCTTTTTTCTTTT-TCTTTTTC
39412645 TTTCTTTTTTC---TTCTTTTTC
1 TTTCTTTTTTCTTTTTCTTTTTC
*
39412665 TTTCTTTTTCCTTTTTTCTTTTT-
1 TTTCTTTTTTC-TTTTTCTTTTTC
39412688 TTTCT
1 TTTCT
39412693 CTATTTTTTT
Statistics
Matches: 43, Mismatches: 1, Indels: 9
0.81 0.02 0.17
Matches are distributed among these distances:
20 18 0.42
21 1 0.02
23 5 0.12
24 19 0.44
ACGTcount: A:0.00, C:0.19, G:0.00, T:0.81
Consensus pattern (23 bp):
TTTCTTTTTTCTTTTTCTTTTTC
Found at i:39412678 original size:27 final size:25
Alignment explanation
Indices: 39412618--39412689 Score: 94
Period size: 26 Copynumber: 2.8 Consensus size: 25
39412608 TTGGCCTCTC
*
39412618 CTTTTTCTTTTTTC-TTTTCTCTTT
1 CTTTTTCTTTTTTCTTTTTTTCTTT
39412642 -TTCTTTCTTTTTTCTTCTTTTTCTTT
1 CTT-TTTCTTTTTTCTT-TTTTTCTTT
39412668 CTTTTTCCTTTTTTCTTTTTTT
1 CTTTTT-CTTTTTTCTTTTTTT
39412690 TCTCTATTTT
Statistics
Matches: 42, Mismatches: 1, Indels: 8
0.82 0.02 0.16
Matches are distributed among these distances:
23 2 0.05
24 11 0.26
25 1 0.02
26 16 0.38
27 12 0.29
ACGTcount: A:0.00, C:0.19, G:0.00, T:0.81
Consensus pattern (25 bp):
CTTTTTCTTTTTTCTTTTTTTCTTT
Found at i:39412690 original size:27 final size:29
Alignment explanation
Indices: 39412614--39412709 Score: 92
Period size: 27 Copynumber: 3.3 Consensus size: 29
39412604 TACCTTGGCC
*
39412614 TCTCCTTTTTCTTTTTTCTT-TTCTCTTTT
1 TCTCTTTTTTCTTTTTT-TTCTTCTCTTTT
*
39412643 TCTTTCTTTTTTCTTCTTTTTCTT-TCTTTT
1 TC--TCTTTTTTCTTTTTTTTCTTCTCTTTT
*
39412673 TC-CTTTTTTCTTTTTTTTC-TCTATTTT
1 TCTCTTTTTTCTTTTTTTTCTTCTCTTTT
* *
39412700 TTTATTTTTT
1 TCTCTTTTTT
39412710 ATTGAATCTG
Statistics
Matches: 56, Mismatches: 6, Indels: 11
0.77 0.08 0.15
Matches are distributed among these distances:
26 1 0.02
27 22 0.39
28 6 0.11
29 2 0.04
30 10 0.18
31 15 0.27
ACGTcount: A:0.02, C:0.19, G:0.00, T:0.79
Consensus pattern (29 bp):
TCTCTTTTTTCTTTTTTTTCTTCTCTTTT
Found at i:39412699 original size:10 final size:9
Alignment explanation
Indices: 39412632--39412700 Score: 61
Period size: 9 Copynumber: 7.4 Consensus size: 9
39412622 TTCTTTTTTC
39412632 TTTTCTCTT
1 TTTTCTCTT
*
39412641 TTTCTTTCTT
1 TTT-TCTCTT
39412651 TTTTCT-TCT
1 TTTTCTCT-T
*
39412660 TTTTCTTTCT
1 TTTTCTCT-T
39412670 TTTTC-CTT
1 TTTTCTCTT
*
39412678 TTTTCTTTT
1 TTTTCTCTT
39412687 TTTTCTCTAT
1 TTTTCTCT-T
39412697 TTTT
1 TTTT
39412701 TTATTTTTTA
Statistics
Matches: 50, Mismatches: 5, Indels: 9
0.78 0.08 0.14
Matches are distributed among these distances:
8 7 0.14
9 22 0.44
10 21 0.42
ACGTcount: A:0.01, C:0.19, G:0.00, T:0.80
Consensus pattern (9 bp):
TTTTCTCTT
Found at i:39412701 original size:11 final size:9
Alignment explanation
Indices: 39412619--39412692 Score: 62
Period size: 9 Copynumber: 7.8 Consensus size: 9
39412609 TGGCCTCTCC
39412619 TTTTTCTTT
1 TTTTTCTTT
39412628 TTTCTT-TTCT
1 TTT-TTCTT-T
39412638 CTTTTTCTTTCT
1 -TTTTTC-TT-T
*
39412650 TTTTTCTTC
1 TTTTTCTTT
39412659 TTTTTCTTT
1 TTTTTCTTT
*
39412668 CTTTTTC-CT
1 -TTTTTCTTT
39412677 TTTTTCTTT
1 TTTTTCTTT
39412686 TTTTTCT
1 TTTTTCT
39412693 CTATTTTTTT
Statistics
Matches: 54, Mismatches: 4, Indels: 14
0.75 0.06 0.19
Matches are distributed among these distances:
8 6 0.11
9 22 0.41
10 13 0.24
11 9 0.17
12 4 0.07
ACGTcount: A:0.00, C:0.19, G:0.00, T:0.81
Consensus pattern (9 bp):
TTTTTCTTT
Found at i:39412707 original size:17 final size:17
Alignment explanation
Indices: 39412625--39412707 Score: 69
Period size: 18 Copynumber: 4.6 Consensus size: 17
39412615 CTCCTTTTTC
39412625 TTTTTTCTTTTCTCTTT
1 TTTTTTCTTTTCTCTTT
*
39412642 TTCTTTCTTTTTTCTTCTTT
1 TT-TTT-TCTTTTC-TCTTT
*
39412662 TTCTTTCTTTT-TCCTTT
1 TTTTTTCTTTTCT-CTTT
* *
39412679 TTTCTTTTTTTTCTCTAT
1 TTT-TTTCTTTTCTCTTT
*
39412697 TTTTTTATTTT
1 TTTTTTCTTTT
39412708 TTATTGAATC
Statistics
Matches: 53, Mismatches: 7, Indels: 12
0.74 0.10 0.17
Matches are distributed among these distances:
16 1 0.02
17 15 0.28
18 21 0.40
19 9 0.17
20 7 0.13
ACGTcount: A:0.02, C:0.17, G:0.00, T:0.81
Consensus pattern (17 bp):
TTTTTTCTTTTCTCTTT
Found at i:39418564 original size:25 final size:25
Alignment explanation
Indices: 39418535--39418586 Score: 86
Period size: 25 Copynumber: 2.1 Consensus size: 25
39418525 CCTATTTAAG
39418535 CTAAAAAATTTTCAAAAATTTCATT
1 CTAAAAAATTTTCAAAAATTTCATT
**
39418560 CTAAAATTTTTTCAAAAATTTCATT
1 CTAAAAAATTTTCAAAAATTTCATT
39418585 CT
1 CT
39418587 TCCCACTTTT
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
25 25 1.00
ACGTcount: A:0.42, C:0.13, G:0.00, T:0.44
Consensus pattern (25 bp):
CTAAAAAATTTTCAAAAATTTCATT
Found at i:39418567 original size:13 final size:13
Alignment explanation
Indices: 39418549--39418586 Score: 51
Period size: 12 Copynumber: 3.0 Consensus size: 13
39418539 AAAATTTTCA
39418549 AAAATTTCATTCT
1 AAAATTTCATTCT
* *
39418562 AAAATTT-TTTCA
1 AAAATTTCATTCT
39418574 AAAATTTCATTCT
1 AAAATTTCATTCT
39418587 TCCCACTTTT
Statistics
Matches: 20, Mismatches: 4, Indels: 2
0.77 0.15 0.08
Matches are distributed among these distances:
12 10 0.50
13 10 0.50
ACGTcount: A:0.39, C:0.13, G:0.00, T:0.47
Consensus pattern (13 bp):
AAAATTTCATTCT
Found at i:39418882 original size:16 final size:17
Alignment explanation
Indices: 39418857--39418888 Score: 57
Period size: 16 Copynumber: 1.9 Consensus size: 17
39418847 AAACTTCTGC
39418857 TTTTTATTTCTTTTTTA
1 TTTTTATTTCTTTTTTA
39418874 TTTTT-TTTCTTTTTT
1 TTTTTATTTCTTTTTT
39418889 CCAAAATCTC
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 10 0.67
17 5 0.33
ACGTcount: A:0.06, C:0.06, G:0.00, T:0.88
Consensus pattern (17 bp):
TTTTTATTTCTTTTTTA
Found at i:39419752 original size:33 final size:32
Alignment explanation
Indices: 39419689--39419752 Score: 83
Period size: 33 Copynumber: 2.0 Consensus size: 32
39419679 TTGTTTTCTT
* * * *
39419689 TTGTTGTTTTTTACTATTTTGTTGCTATTTTC
1 TTGTTGTTTTTCACTATTTTGCTACAATTTTC
39419721 TTGTTGTTTTCTCACTATTTTGCTACAATTTT
1 TTGTTGTTTT-TCACTATTTTGCTACAATTTT
39419753 ATTATTATGT
Statistics
Matches: 27, Mismatches: 4, Indels: 1
0.84 0.12 0.03
Matches are distributed among these distances:
32 10 0.37
33 17 0.63
ACGTcount: A:0.12, C:0.12, G:0.11, T:0.64
Consensus pattern (32 bp):
TTGTTGTTTTTCACTATTTTGCTACAATTTTC
Found at i:39421800 original size:13 final size:14
Alignment explanation
Indices: 39421784--39421816 Score: 50
Period size: 14 Copynumber: 2.4 Consensus size: 14
39421774 AATAAATATA
39421784 TATTTTTT-ATTTT
1 TATTTTTTAATTTT
39421797 TATTTTTTAATTTT
1 TATTTTTTAATTTT
*
39421811 AATTTT
1 TATTTT
39421817 AAAATACTTT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
13 8 0.44
14 10 0.56
ACGTcount: A:0.21, C:0.00, G:0.00, T:0.79
Consensus pattern (14 bp):
TATTTTTTAATTTT
Found at i:39421877 original size:26 final size:28
Alignment explanation
Indices: 39421824--39421888 Score: 80
Period size: 26 Copynumber: 2.4 Consensus size: 28
39421814 TTTAAAATAC
* *
39421824 TTTTAAAATAAATTTTTTTATTTTTTTAT
1 TTTTAAAAT-AATTTTTTTATATATTTAT
39421853 TTTTAAAATAA-TTTTTTA-ATATTTAT
1 TTTTAAAATAATTTTTTTATATATTTAT
*
39421879 TTTAAAAATA
1 TTTTAAAATA
39421889 GGCCGGGCCG
Statistics
Matches: 33, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
26 15 0.45
27 7 0.21
28 2 0.06
29 9 0.27
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (28 bp):
TTTTAAAATAATTTTTTTATATATTTAT
Found at i:39432093 original size:16 final size:18
Alignment explanation
Indices: 39432054--39432095 Score: 54
Period size: 18 Copynumber: 2.5 Consensus size: 18
39432044 AAAGTTTATA
39432054 ATATTT-TATATTATGTT
1 ATATTTATATATTATGTT
*
39432071 ATTTTTATATATTATG-T
1 ATATTTATATATTATGTT
39432088 A-ATTTATA
1 ATATTTATA
39432096 ACATATTAAA
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
16 6 0.27
17 7 0.32
18 9 0.41
ACGTcount: A:0.33, C:0.00, G:0.05, T:0.62
Consensus pattern (18 bp):
ATATTTATATATTATGTT
Found at i:39432216 original size:15 final size:15
Alignment explanation
Indices: 39432196--39432245 Score: 55
Period size: 15 Copynumber: 3.2 Consensus size: 15
39432186 AATAAATATA
39432196 AAATATAAAATTATT
1 AAATATAAAATTATT
* *
39432211 AAATATAAAAATAAT
1 AAATATAAAATTATT
*
39432226 ACAATATAAATATTTTT
1 A-AATATAAA-ATTATT
39432243 AAA
1 AAA
39432246 AAAATTAAAA
Statistics
Matches: 28, Mismatches: 5, Indels: 3
0.78 0.14 0.08
Matches are distributed among these distances:
15 14 0.50
16 10 0.36
17 4 0.14
ACGTcount: A:0.62, C:0.02, G:0.00, T:0.36
Consensus pattern (15 bp):
AAATATAAAATTATT
Found at i:39432221 original size:16 final size:16
Alignment explanation
Indices: 39432196--39432245 Score: 50
Period size: 16 Copynumber: 3.2 Consensus size: 16
39432186 AATAAATATA
39432196 AAATAT-AAAATTATT
1 AAATATAAAAATTATT
*
39432211 AAATATAAAAA-TAAT
1 AAATATAAAAATTATT
* *
39432226 ACAATATAAATATTTTT
1 A-AATATAAAAATTATT
39432243 AAA
1 AAA
39432246 AAAATTAAAA
Statistics
Matches: 28, Mismatches: 4, Indels: 5
0.76 0.11 0.14
Matches are distributed among these distances:
15 10 0.36
16 15 0.54
17 3 0.11
ACGTcount: A:0.62, C:0.02, G:0.00, T:0.36
Consensus pattern (16 bp):
AAATATAAAAATTATT
Found at i:39432235 original size:22 final size:21
Alignment explanation
Indices: 39432187--39432238 Score: 61
Period size: 22 Copynumber: 2.4 Consensus size: 21
39432177 AAAAATTTCA
*
39432187 ATAAATATAAAATATAAAATT
1 ATAAATATAAAATATAAAAAT
39432208 ATTAAATATAAAA-ATAATACAAT
1 A-TAAATATAAAATATAA-A-AAT
39432231 ATAAATAT
1 ATAAATAT
39432239 TTTTAAAAAA
Statistics
Matches: 27, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
21 5 0.19
22 19 0.70
23 3 0.11
ACGTcount: A:0.65, C:0.02, G:0.00, T:0.33
Consensus pattern (21 bp):
ATAAATATAAAATATAAAAAT
Found at i:39435765 original size:29 final size:29
Alignment explanation
Indices: 39435703--39435785 Score: 91
Period size: 29 Copynumber: 2.8 Consensus size: 29
39435693 GCAAAATAAT
* *
39435703 AAATATTAATAATATTTATAAAAATATAGAA
1 AAATATTTA-AAT-TTTATAAAAATTTAGAA
39435734 AAATATTTAAATTTTACTAAAAATTTAG-A
1 AAATATTTAAATTTTA-TAAAAATTTAGAA
39435763 AAAT-TTTAAAATTTT-TAAAAATT
1 AAATATTT-AAATTTTATAAAAATT
39435786 ATAAAATTAC
Statistics
Matches: 48, Mismatches: 2, Indels: 8
0.83 0.03 0.14
Matches are distributed among these distances:
27 8 0.17
28 3 0.06
29 16 0.33
30 13 0.27
31 8 0.17
ACGTcount: A:0.55, C:0.01, G:0.02, T:0.41
Consensus pattern (29 bp):
AAATATTTAAATTTTATAAAAATTTAGAA
Found at i:39435772 original size:18 final size:18
Alignment explanation
Indices: 39435733--39435792 Score: 59
Period size: 18 Copynumber: 3.3 Consensus size: 18
39435723 AAAATATAGA
**
39435733 AAAATATTTAAATTTTACT
1 AAAATATTTAAAAATTA-T
*
39435752 AAAA-ATTTAGAAAATTTT
1 AAAATATTTA-AAAATTAT
*
39435770 AAAATTTTTAAAAATTAT
1 AAAATATTTAAAAATTAT
39435788 AAAAT
1 AAAAT
39435793 TACGATAAAA
Statistics
Matches: 34, Mismatches: 5, Indels: 5
0.77 0.11 0.11
Matches are distributed among these distances:
18 22 0.65
19 12 0.35
ACGTcount: A:0.55, C:0.02, G:0.02, T:0.42
Consensus pattern (18 bp):
AAAATATTTAAAAATTAT
Found at i:39435925 original size:10 final size:9
Alignment explanation
Indices: 39435893--39435991 Score: 60
Period size: 9 Copynumber: 10.4 Consensus size: 9
39435883 CACATGGTGT
*
39435893 AAAATGATA
1 AAAATTATA
*
39435902 AAAATTTATT
1 AAAA-TTATA
39435912 AAAATTAATAA
1 AAAATT-AT-A
*
39435923 AAAATCATA
1 AAAATTATA
*
39435932 AAAGTTAT-
1 AAAATTATA
39435940 AAAATATATTA
1 AAAAT-TA-TA
39435951 CAAAA-TATA
1 -AAAATTATA
39435960 AAAA-TATA
1 AAAATTATA
*
39435968 GAAAATTATTT
1 -AAAATTA-TA
39435979 AAAATTATA
1 AAAATTATA
39435988 AAAA
1 AAAA
39435992 AATATGTAGA
Statistics
Matches: 71, Mismatches: 9, Indels: 20
0.71 0.09 0.20
Matches are distributed among these distances:
8 12 0.17
9 26 0.37
10 23 0.32
11 6 0.08
12 4 0.06
ACGTcount: A:0.64, C:0.02, G:0.03, T:0.31
Consensus pattern (9 bp):
AAAATTATA
Found at i:39435977 original size:28 final size:27
Alignment explanation
Indices: 39435893--39435991 Score: 83
Period size: 28 Copynumber: 3.5 Consensus size: 27
39435883 CACATGGTGT
* *
39435893 AAAATGATAAAAATTTATTAAAATTAATAA
1 AAAATCATAAAAA-TTA-TAAAATT-ATTA
*
39435923 AAAATCATAAAAGTTATAAAATATATTA
1 AAAATCATAAAAATTATAAAAT-TATTA
* *
39435951 CAAAAT-ATAAAAATATAGAAAATTATTT
1 -AAAATCATAAAAAT-TATAAAATTATTA
*
39435979 AAAATTATAAAAA
1 AAAATCATAAAAA
39435992 AATATGTAGA
Statistics
Matches: 59, Mismatches: 6, Indels: 10
0.79 0.08 0.13
Matches are distributed among these distances:
27 5 0.08
28 27 0.46
29 16 0.27
30 11 0.19
ACGTcount: A:0.64, C:0.02, G:0.03, T:0.31
Consensus pattern (27 bp):
AAAATCATAAAAATTATAAAATTATTA
Found at i:39435992 original size:10 final size:10
Alignment explanation
Indices: 39435893--39435992 Score: 50
Period size: 10 Copynumber: 10.4 Consensus size: 10
39435883 CACATGGTGT
*
39435893 AAAATGATAA
1 AAAATTATAA
* *
39435903 AAATTTAT-T
1 AAAATTATAA
39435912 AAAATTAATAA
1 AAAATT-ATAA
*
39435923 AAAATCAT-A
1 AAAATTATAA
*
39435932 AAAGTTATAA
1 AAAATTATAA
* *
39435942 AATA-TATTAC
1 AAAATTA-TAA
39435952 AAAA-TAT-A
1 AAAATTATAA
*
39435960 AAAA-TATAG
1 AAAATTATAA
**
39435969 AAAATTATTT
1 AAAATTATAA
39435979 AAAATTATAA
1 AAAATTATAA
39435989 AAAA
1 AAAA
39435993 ATATGTAGAA
Statistics
Matches: 66, Mismatches: 18, Indels: 12
0.69 0.19 0.12
Matches are distributed among these distances:
8 7 0.11
9 19 0.29
10 35 0.53
11 5 0.08
ACGTcount: A:0.64, C:0.02, G:0.03, T:0.31
Consensus pattern (10 bp):
AAAATTATAA
Found at i:39435992 original size:20 final size:20
Alignment explanation
Indices: 39435958--39436006 Score: 53
Period size: 20 Copynumber: 2.4 Consensus size: 20
39435948 TTACAAAATA
* * * *
39435958 TAAAAATATAGAAAATTATT
1 TAAAATTATAAAAAAATATG
39435978 TAAAATTATAAAAAAATATG
1 TAAAATTATAAAAAAATATG
39435998 TAGAAATTA
1 TA-AAATTA
39436007 GTCTTAGTTT
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
20 18 0.75
21 6 0.25
ACGTcount: A:0.61, C:0.00, G:0.06, T:0.33
Consensus pattern (20 bp):
TAAAATTATAAAAAAATATG
Found at i:39442298 original size:45 final size:44
Alignment explanation
Indices: 39442209--39442301 Score: 127
Period size: 44 Copynumber: 2.1 Consensus size: 44
39442199 ATTACAACAT
*
39442209 CATTCCATTCAACCAAACACAAGAATACTATTATAGTTCTATTC
1 CATTCCATTCAACCAAACACAAGAATACTATTATAGCTCTATTC
*
39442253 CATTCCATTCAACCAAACA-ATTGAATTACTATTAT-GCCTCTATTC
1 CATTCCATTCAACCAAACACA-AGAA-TACTATTATAG-CTCTATTC
39442298 CATT
1 CATT
39442302 ACAGCTCTAT
Statistics
Matches: 44, Mismatches: 2, Indels: 5
0.86 0.04 0.10
Matches are distributed among these distances:
43 1 0.02
44 23 0.52
45 20 0.45
ACGTcount: A:0.35, C:0.26, G:0.04, T:0.34
Consensus pattern (44 bp):
CATTCCATTCAACCAAACACAAGAATACTATTATAGCTCTATTC
Found at i:39442309 original size:16 final size:16
Alignment explanation
Indices: 39442290--39442322 Score: 66
Period size: 16 Copynumber: 2.1 Consensus size: 16
39442280 ACTATTATGC
39442290 CTCTATTCCATTACAG
1 CTCTATTCCATTACAG
39442306 CTCTATTCCATTACAG
1 CTCTATTCCATTACAG
39442322 C
1 C
39442323 GAACCAAACG
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.24, C:0.33, G:0.06, T:0.36
Consensus pattern (16 bp):
CTCTATTCCATTACAG
Found at i:39445559 original size:14 final size:14
Alignment explanation
Indices: 39445540--39445571 Score: 50
Period size: 13 Copynumber: 2.4 Consensus size: 14
39445530 ATTATGTTAG
39445540 AATTAAAAACACAT
1 AATTAAAAACACAT
39445554 AATT-AAAACACAT
1 AATTAAAAACACAT
39445567 -ATTAA
1 AATTAA
39445572 TGATATTCAA
Statistics
Matches: 17, Mismatches: 0, Indels: 3
0.85 0.00 0.15
Matches are distributed among these distances:
12 3 0.18
13 10 0.59
14 4 0.24
ACGTcount: A:0.62, C:0.12, G:0.00, T:0.25
Consensus pattern (14 bp):
AATTAAAAACACAT
Found at i:39445654 original size:39 final size:39
Alignment explanation
Indices: 39445550--39445656 Score: 180
Period size: 39 Copynumber: 2.8 Consensus size: 39
39445540 AATTAAAAAC
*
39445550 ACATAATTAAA-ACACATATTAATGATATTCAAACTAAG
1 ACATAATTAAAGACACATATTAATGATGTTCAAACTAAG
*
39445588 ACATAATTAAAGACACATATTAATGATGTTCAAGCTAAG
1 ACATAATTAAAGACACATATTAATGATGTTCAAACTAAG
*
39445627 ACATAATTAAAGACTCATATTAATGATGTT
1 ACATAATTAAAGACACATATTAATGATGTT
39445657 TACACTAATA
Statistics
Matches: 65, Mismatches: 3, Indels: 1
0.94 0.04 0.01
Matches are distributed among these distances:
38 11 0.17
39 54 0.83
ACGTcount: A:0.48, C:0.12, G:0.09, T:0.31
Consensus pattern (39 bp):
ACATAATTAAAGACACATATTAATGATGTTCAAACTAAG
Found at i:39448835 original size:33 final size:31
Alignment explanation
Indices: 39448777--39448839 Score: 83
Period size: 31 Copynumber: 2.0 Consensus size: 31
39448767 TTTGCCTCAT
*
39448777 TTTTTCCTTTCTTTTTTTCTATTTTCTTTTC
1 TTTTTCCTTTCTTTTTTTCCATTTTCTTTTC
39448808 TTTTT-CTTTCTTATTTTTCCACTTTTTCTTTT
1 TTTTTCCTTTCTT-TTTTTCCA--TTTTCTTTT
39448840 GCTCTCATTT
Statistics
Matches: 28, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
30 7 0.25
31 12 0.43
33 9 0.32
ACGTcount: A:0.05, C:0.19, G:0.00, T:0.76
Consensus pattern (31 bp):
TTTTTCCTTTCTTTTTTTCCATTTTCTTTTC
Found at i:39451041 original size:14 final size:14
Alignment explanation
Indices: 39451022--39451053 Score: 50
Period size: 13 Copynumber: 2.4 Consensus size: 14
39451012 ATTATGTTAG
39451022 AATTAAAAACACAT
1 AATTAAAAACACAT
39451036 AATT-AAAACACAT
1 AATTAAAAACACAT
39451049 -ATTAA
1 AATTAA
39451054 TGATATTAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 3
0.85 0.00 0.15
Matches are distributed among these distances:
12 3 0.18
13 10 0.59
14 4 0.24
ACGTcount: A:0.62, C:0.12, G:0.00, T:0.25
Consensus pattern (14 bp):
AATTAAAAACACAT
Found at i:39451091 original size:39 final size:38
Alignment explanation
Indices: 39451032--39451146 Score: 142
Period size: 39 Copynumber: 3.0 Consensus size: 38
39451022 AATTAAAAAC
39451032 ACATAATTAAAACACATATTAATGATATT-AAACCTAAG
1 ACATAATTAAAACACATATTAATGATATTCAAA-CTAAG
* * *
39451070 ACATATTTAAAGACACATATTAATTATGTTCAAACTAAG
1 ACATAATTAAA-ACACATATTAATGATATTCAAACTAAG
* * *
39451109 ACATAATTAAATACTCATATTCATGATGTTCAAACTAA
1 ACATAATTAAA-ACACATATTAATGATATTCAAACTAA
39451147 AATAACTAAA
Statistics
Matches: 67, Mismatches: 8, Indels: 3
0.86 0.10 0.04
Matches are distributed among these distances:
38 10 0.15
39 54 0.81
40 3 0.04
ACGTcount: A:0.48, C:0.14, G:0.06, T:0.32
Consensus pattern (38 bp):
ACATAATTAAAACACATATTAATGATATTCAAACTAAG
Found at i:39456038 original size:33 final size:34
Alignment explanation
Indices: 39455965--39456034 Score: 117
Period size: 33 Copynumber: 2.1 Consensus size: 34
39455955 GATTTAAACA
39455965 AATTAATTACTAACACTTATTTAAGCTGAACTAC
1 AATTAATTACTAACACTTATTTAAGCTGAACTAC
*
39455999 AATTAATT-CTAACACTTATTTGAGCTGAACTA-
1 AATTAATTACTAACACTTATTTAAGCTGAACTAC
39456031 AATT
1 AATT
39456035 TAATAAACTA
Statistics
Matches: 35, Mismatches: 1, Indels: 2
0.92 0.03 0.05
Matches are distributed among these distances:
32 4 0.11
33 23 0.66
34 8 0.23
ACGTcount: A:0.40, C:0.16, G:0.07, T:0.37
Consensus pattern (34 bp):
AATTAATTACTAACACTTATTTAAGCTGAACTAC
Found at i:39457831 original size:18 final size:18
Alignment explanation
Indices: 39457808--39457846 Score: 62
Period size: 18 Copynumber: 2.2 Consensus size: 18
39457798 CTCTTTTTGC
39457808 TCTTTTTC-ATTCTCTTTT
1 TCTTTTTCGATT-TCTTTT
39457826 TCTTTTTCGATTTCTTTT
1 TCTTTTTCGATTTCTTTT
39457844 TCT
1 TCT
39457847 ATCTTCCTTT
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
18 17 0.85
19 3 0.15
ACGTcount: A:0.05, C:0.21, G:0.03, T:0.72
Consensus pattern (18 bp):
TCTTTTTCGATTTCTTTT
Found at i:39461097 original size:32 final size:32
Alignment explanation
Indices: 39461049--39461145 Score: 103
Period size: 32 Copynumber: 3.1 Consensus size: 32
39461039 CTAAAAGAAC
* *
39461049 ATTTGGTATTTGAATTTGTTATTTTTTTCTTA
1 ATTTGGTACTTAAATTTGTTATTTTTTTCTTA
*
39461081 ATTTGGTACTTAAA-TT-TT-TTTTTATC-TA
1 ATTTGGTACTTAAATTTGTTATTTTTTTCTTA
* **
39461109 ATTTGGTACTCAAATTTGACATTTTTTTTCTTA
1 ATTTGGTACTTAAATTTGTTA-TTTTTTTCTTA
39461142 ATTT
1 ATTT
39461146 AGTATCTAAA
Statistics
Matches: 53, Mismatches: 7, Indels: 9
0.77 0.10 0.13
Matches are distributed among these distances:
28 15 0.28
29 9 0.17
30 2 0.04
31 2 0.04
32 19 0.36
33 6 0.11
ACGTcount: A:0.23, C:0.07, G:0.09, T:0.61
Consensus pattern (32 bp):
ATTTGGTACTTAAATTTGTTATTTTTTTCTTA
Found at i:39461144 original size:33 final size:32
Alignment explanation
Indices: 39461070--39461176 Score: 107
Period size: 28 Copynumber: 3.4 Consensus size: 32
39461060 GAATTTGTTA
*
39461070 TTTTTTTCTTAATTTGGTACTTAAATTT---T
1 TTTTTTTCTTAATTTGGTACTCAAATTTGACT
*
39461099 TTTTTATC-TAATTTGGTACTCAAATTTGACAT
1 TTTTTTTCTTAATTTGGTACTCAAATTTGAC-T
* *
39461131 TTTTTTTCTTAATTTAGTA-TCTAAAGTTGACGTT
1 TTTTTTTCTTAATTTGGTACTC-AAATTTGAC--T
39461165 TTTTTTTCTTAA
1 TTTTTTTCTTAA
39461177 GTTGATACAT
Statistics
Matches: 65, Mismatches: 6, Indels: 9
0.81 0.08 0.11
Matches are distributed among these distances:
28 18 0.28
29 7 0.11
32 10 0.15
33 17 0.26
34 13 0.20
ACGTcount: A:0.23, C:0.09, G:0.08, T:0.59
Consensus pattern (32 bp):
TTTTTTTCTTAATTTGGTACTCAAATTTGACT
Found at i:39461168 original size:34 final size:33
Alignment explanation
Indices: 39461070--39461176 Score: 100
Period size: 33 Copynumber: 3.4 Consensus size: 33
39461060 GAATTTGTTA
* *
39461070 TTTTTTTCTTAATTTGGTACTTAAA-TT---TT
1 TTTTTTTCTTAATTTAGTACTCAAAGTTGACTT
* * * *
39461099 TTTTTATC-TAATTTGGTACTCAAATTTGACAT
1 TTTTTTTCTTAATTTAGTACTCAAAGTTGACTT
39461131 TTTTTTTCTTAATTTAGTA-TCTAAAGTTGACGTT
1 TTTTTTTCTTAATTTAGTACTC-AAAGTTGAC-TT
39461165 TTTTTTTCTTAA
1 TTTTTTTCTTAA
39461177 GTTGATACAT
Statistics
Matches: 64, Mismatches: 7, Indels: 9
0.80 0.09 0.11
Matches are distributed among these distances:
28 15 0.23
29 9 0.14
32 10 0.16
33 17 0.27
34 13 0.20
ACGTcount: A:0.23, C:0.09, G:0.08, T:0.59
Consensus pattern (33 bp):
TTTTTTTCTTAATTTAGTACTCAAAGTTGACTT
Found at i:39461175 original size:95 final size:94
Alignment explanation
Indices: 39461070--39461247 Score: 227
Period size: 96 Copynumber: 1.9 Consensus size: 94
39461060 GAATTTGTTA
* * * *** *
39461070 TTTTTTTCTTAATTTGGTACTTAA-ATTTTTTTTTATCTAATTTGGTA-CTCAAATTTGACATTT
1 TTTTTTTCTTAAGTTGATACATAATATTTTTTGGGATCTAATTTGGTACCT-AAATTTGAC--TC
39461133 TTTTTCTTAATTT-AGTATCTAAAGTTGACGTT
63 TTTTTCTTAATTTGA-TATCTAAAGTTGACGTT
*
39461165 TTTTTTTCTTAAGTTGATACATAATATTTTTTGGGATTTAATTTGGTACCTAAATTTGACTCTTT
1 TTTTTTTCTTAAGTTGATACATAATATTTTTTGGGATCTAATTTGGTACCTAAATTTGACTCTTT
39461230 TTCTTAATTTGATATCTA
66 TTCTTAATTTGATATCTA
39461248 TTTTTTTTTC
Statistics
Matches: 72, Mismatches: 8, Indels: 7
0.83 0.09 0.08
Matches are distributed among these distances:
94 20 0.28
95 22 0.31
96 28 0.39
97 2 0.03
ACGTcount: A:0.25, C:0.10, G:0.10, T:0.56
Consensus pattern (94 bp):
TTTTTTTCTTAAGTTGATACATAATATTTTTTGGGATCTAATTTGGTACCTAAATTTGACTCTTT
TTCTTAATTTGATATCTAAAGTTGACGTT
Found at i:39463280 original size:39 final size:40
Alignment explanation
Indices: 39463193--39463282 Score: 164
Period size: 40 Copynumber: 2.3 Consensus size: 40
39463183 CTTAGATTGC
39463193 AAAGTCAAATATCTAAAGTTATTATTATAAAAAAAAAACG
1 AAAGTCAAATATCTAAAGTTATTATTATAAAAAAAAAACG
39463233 AAAGTCAAATATCTAAAGTTATTATTATAAAAAAAAAACG
1 AAAGTCAAATATCTAAAGTTATTATTATAAAAAAAAAACG
*
39463273 -AATTCAAATA
1 AAAGTCAAATA
39463283 ATAAAGATAT
Statistics
Matches: 49, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
39 9 0.18
40 40 0.82
ACGTcount: A:0.58, C:0.08, G:0.07, T:0.28
Consensus pattern (40 bp):
AAAGTCAAATATCTAAAGTTATTATTATAAAAAAAAAACG
Found at i:39470316 original size:29 final size:29
Alignment explanation
Indices: 39470283--39470341 Score: 118
Period size: 29 Copynumber: 2.0 Consensus size: 29
39470273 CACATTTGAG
39470283 TGCCAAAGTAGTCTTGGCTAAATTCAATC
1 TGCCAAAGTAGTCTTGGCTAAATTCAATC
39470312 TGCCAAAGTAGTCTTGGCTAAATTCAATC
1 TGCCAAAGTAGTCTTGGCTAAATTCAATC
39470341 T
1 T
39470342 TCTGAACCCT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 30 1.00
ACGTcount: A:0.31, C:0.20, G:0.17, T:0.32
Consensus pattern (29 bp):
TGCCAAAGTAGTCTTGGCTAAATTCAATC
Found at i:39476133 original size:30 final size:30
Alignment explanation
Indices: 39476097--39476153 Score: 105
Period size: 30 Copynumber: 1.9 Consensus size: 30
39476087 AGTGTCAGCT
*
39476097 AACCTAGGGTTGAGGATGACGACAACCTTA
1 AACCTAGGGTTGAGGATGACAACAACCTTA
39476127 AACCTAGGGTTGAGGATGACAACAACC
1 AACCTAGGGTTGAGGATGACAACAACC
39476154 CTAACTCTAT
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
30 26 1.00
ACGTcount: A:0.35, C:0.21, G:0.26, T:0.18
Consensus pattern (30 bp):
AACCTAGGGTTGAGGATGACAACAACCTTA
Done.