Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: chr2
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: 41236440
ACGTcount: A:0.31, C:0.16, G:0.16, T:0.31
Warning! 2030548 characters in sequence are not A, C, G, or T
File 13 of 106
Found at i:6301746 original size:55 final size:54
Alignment explanation
Indices: 6301641--6301855 Score: 182
Period size: 55 Copynumber: 3.9 Consensus size: 54
6301631 CATAGCTTGA
* *
6301641 AACAATTAAATTTTTCAACATGGCA-AGTAAAAACTACATTTTTTAACATGGCATGT
1 AACAACTAAATTTTT-AACA-GACATA-TAAAAACTACATTTTTTAACATGGCATGT
* * * * *
6301697 AACAACTAAATTTTTAACACGACATATAATAACTACAGTTTTCAACATGGCGTAT
1 AACAACTAAATTTTTAACA-GACATATAAAAACTACATTTTTTAACATGGCATGT
* * ** * * *
6301752 AACAACTAAATCTTTAACATAGTGTGTAACAACTATATTTTTTAACATGGCATGT
1 AACAACTAAATTTTTAACAGA-CATATAAAAACTACATTTTTTAACATGGCATGT
* * * * *
6301807 AACAACTAAATTTTCAATATA-ATGTATAACAATTACATTTTTTAACATG
1 AACAACTAAATTTTTAACAGACA--TATAAAAACTACATTTTTTAACATG
6301856 ATGTGCAACA
Statistics
Matches: 129, Mismatches: 26, Indels: 9
0.79 0.16 0.05
Matches are distributed among these distances:
54 1 0.01
55 113 0.88
56 15 0.12
ACGTcount: A:0.41, C:0.15, G:0.09, T:0.35
Consensus pattern (54 bp):
AACAACTAAATTTTTAACAGACATATAAAAACTACATTTTTTAACATGGCATGT
Found at i:6301866 original size:55 final size:54
Alignment explanation
Indices: 6301675--6301917 Score: 208
Period size: 55 Copynumber: 4.4 Consensus size: 54
6301665 AAGTAAAAAC
* * * ** * *
6301675 TACATTTTTTAACATGGCATGTAACAACTAAATTTTTAACACGACATATAATAAC
1 TACATTTTTTAACATGGCATGTAACAACTAAATTTTCAATA-TATGTATAACAAT
* * * * * * *
6301730 TACAGTTTTCAACATGGCGTATAACAACTAAATCTTT-AACATAGTGTGTAACAAC
1 TACATTTTTTAACATGGCATGTAACAACTAAAT-TTTCAATATA-TGTATAACAAT
*
6301785 TATATTTTTTAACATGGCATGTAACAACTAAATTTTCAATATAATGTATAACAAT
1 TACATTTTTTAACATGGCATGTAACAACTAAATTTTCAATAT-ATGTATAACAAT
* *
6301840 TACATTTTTTAACAT-G-ATGTGCAACAATTAAAATTTCAATAT-TGCATATAACAAT
1 TACATTTTTTAACATGGCATGT--AACAACTAAATTTTCAATATATG--TATAACAAT
* *
6301895 TACA-TTTTTAACATAGCGTGTAA
1 TACATTTTTTAACATGGCATGTAA
6301918 TAATTATTTC
Statistics
Matches: 157, Mismatches: 21, Indels: 21
0.79 0.11 0.11
Matches are distributed among these distances:
53 6 0.04
54 17 0.11
55 127 0.81
56 7 0.04
ACGTcount: A:0.40, C:0.14, G:0.09, T:0.36
Consensus pattern (54 bp):
TACATTTTTTAACATGGCATGTAACAACTAAATTTTCAATATATGTATAACAAT
Found at i:6301892 original size:110 final size:111
Alignment explanation
Indices: 6301641--6301917 Score: 258
Period size: 110 Copynumber: 2.5 Consensus size: 111
6301631 CATAGCTTGA
* * * *
6301641 AACAATTAAATTTTTCAACATGGCA-AGTAAAAACTACATTTTTTAACATGGCATGTAACAACTA
1 AACAATTAAATATTTCAATATTGCATA-TAACAACTACATTTTTTAACATGGCATGTAACAACTA
* * * * *
6301705 AATTTTTAACACGACATATAATAACTACAGTTTTCAACATGGCGTAT
65 AATTTTCAACACAACATATAACAACTACAGTTTTCAACATGACGTAC
* * * * * *
6301752 AACAACTAAATCTTTAACATAGTG--TGTAACAACTATATTTTTTAACATGGCATGTAACAACTA
1 AACAATTAAATATTTCA-ATATTGCATATAACAACTACATTTTTTAACATGGCATGTAACAACTA
* * ** * * * * *
6301815 AATTTTCAATATAATGTATAACAATTACATTTTTTAACATGATGTGC
65 AATTTTCAACACAACATATAACAACTACAGTTTTCAACATGACGTAC
* * *
6301862 AACAATTAAA-ATTTCAATATTGCATATAACAATTACA-TTTTTAACATAGCGTGTAA
1 AACAATTAAATATTTCAATATTGCATATAACAACTACATTTTTTAACATGGCATGTAA
6301918 TAATTATTTC
Statistics
Matches: 130, Mismatches: 32, Indels: 10
0.76 0.19 0.06
Matches are distributed among these distances:
108 5 0.04
109 21 0.16
110 87 0.67
111 14 0.11
112 3 0.02
ACGTcount: A:0.42, C:0.14, G:0.09, T:0.35
Consensus pattern (111 bp):
AACAATTAAATATTTCAATATTGCATATAACAACTACATTTTTTAACATGGCATGTAACAACTAA
ATTTTCAACACAACATATAACAACTACAGTTTTCAACATGACGTAC
Found at i:6301985 original size:134 final size:137
Alignment explanation
Indices: 6301749--6301993 Score: 318
Period size: 134 Copynumber: 1.8 Consensus size: 137
6301739 CAACATGGCG
* * *
6301749 TATAACAACTAAATCTTTAACATAGTGTGTAACAACTATATTTTTTAACATGGCATGTAACAACT
1 TATAACAACTAAATCTTTAACATAGCGTGTAACAACTATATTTTCTAACATGGCACGTAACAACT
* *
6301814 AAATTTTCAATATAATGTATAACAATTACATTTTTTAACATGATGTGCAACAATTAAAATTTCAA
66 AAATTTTCAATATAACGTATAACAACTACATTTTTTAACATGATGTGCAACAATTAAAATTTCAA
6301879 TATTGCA
131 TATTGCA
* * * * **
6301886 TATAACAATTACATTTTTAACATAGCGTGTAATAA-T-TA-TTTCTAACATGGTGCGTAACAACT
1 TATAACAACTAAATCTTTAACATAGCGTGTAACAACTATATTTTCTAACATGGCACGTAACAACT
* * * *
6301948 AAATTTTAGAATATGACGTGTAA-TACTACATTTTTTAACATGATGT
66 AAATTTT-CAATATAACGTATAACAACTACATTTTTTAACATGATGT
6301994 TAACAACATT
Statistics
Matches: 92, Mismatches: 15, Indels: 5
0.82 0.13 0.04
Matches are distributed among these distances:
134 48 0.52
135 13 0.14
136 1 0.01
137 30 0.33
ACGTcount: A:0.40, C:0.13, G:0.10, T:0.38
Consensus pattern (137 bp):
TATAACAACTAAATCTTTAACATAGCGTGTAACAACTATATTTTCTAACATGGCACGTAACAACT
AAATTTTCAATATAACGTATAACAACTACATTTTTTAACATGATGTGCAACAATTAAAATTTCAA
TATTGCA
Found at i:6303585 original size:16 final size:17
Alignment explanation
Indices: 6303566--6303604 Score: 55
Period size: 16 Copynumber: 2.4 Consensus size: 17
6303556 CATGAAAATT
6303566 TATTAATTAATCAA-AA
1 TATTAATTAATCAATAA
*
6303582 TATTATTTAATCAATAA
1 TATTAATTAATCAATAA
6303599 -ATTAAT
1 TATTAAT
6303605 AATTTATTAA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
16 18 0.90
17 2 0.10
ACGTcount: A:0.51, C:0.05, G:0.00, T:0.44
Consensus pattern (17 bp):
TATTAATTAATCAATAA
Found at i:6317814 original size:61 final size:59
Alignment explanation
Indices: 6317720--6317836 Score: 216
Period size: 61 Copynumber: 1.9 Consensus size: 59
6317710 TCCATTTTTC
6317720 ATGTATCTCTCCCTCTCTCTCTCTCTCTCTCTATATATAGATATTGTGTATGTGTGNCTT
1 ATGTATCTCTCCCTCTCTCTCTCTCTCTCTCTATATATAGATATTGTGTATGTGTG-CTT
6317780 ATGTATCTCTCCCTCCTCTCTCTCTCTCTCTCTATATATAGATATTGTGTATGTGTG
1 ATGTATCTCTCCCT-CTCTCTCTCTCTCTCTCTATATATAGATATTGTGTATGTGTG
6317837 TTAACGAATT
Statistics
Matches: 56, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
60 14 0.25
61 42 0.75
ACGTcount: A:0.15, C:0.26, G:0.12, T:0.46
Consensus pattern (59 bp):
ATGTATCTCTCCCTCTCTCTCTCTCTCTCTCTATATATAGATATTGTGTATGTGTGCTT
Found at i:6321334 original size:14 final size:16
Alignment explanation
Indices: 6321297--6321336 Score: 57
Period size: 14 Copynumber: 2.6 Consensus size: 16
6321287 TTTTTTTATT
6321297 TTTATTAAGATTTTAG
1 TTTATTAAGATTTTAG
*
6321313 TATATTAA-ATTTTA-
1 TTTATTAAGATTTTAG
6321327 TTTATTAAGA
1 TTTATTAAGA
6321337 GGAAGATTTT
Statistics
Matches: 21, Mismatches: 2, Indels: 3
0.81 0.08 0.12
Matches are distributed among these distances:
14 7 0.33
15 7 0.33
16 7 0.33
ACGTcount: A:0.38, C:0.00, G:0.07, T:0.55
Consensus pattern (16 bp):
TTTATTAAGATTTTAG
Found at i:6321921 original size:19 final size:19
Alignment explanation
Indices: 6321897--6321934 Score: 60
Period size: 19 Copynumber: 2.0 Consensus size: 19
6321887 TTTTTAAAAA
6321897 AAAATTA-ATAAAAAATAAT
1 AAAATTATAT-AAAAATAAT
6321916 AAAATTATATAAAAATAAT
1 AAAATTATATAAAAATAAT
6321935 TATAAAAATT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
19 16 0.89
20 2 0.11
ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (19 bp):
AAAATTATATAAAAATAAT
Found at i:6322059 original size:20 final size:20
Alignment explanation
Indices: 6322036--6322089 Score: 65
Period size: 20 Copynumber: 2.6 Consensus size: 20
6322026 TTATGTGTCT
6322036 AATAAAAAATATT-TTTTAAA
1 AATAAAAAAT-TTATTTTAAA
*
6322056 AATAAAATATTTATTTTAAA
1 AATAAAAAATTTATTTTAAA
*
6322076 AATTAATAAATTTA
1 AA-TAAAAAATTTA
6322090 CGTGTAATTT
Statistics
Matches: 29, Mismatches: 3, Indels: 3
0.83 0.09 0.09
Matches are distributed among these distances:
19 2 0.07
20 18 0.62
21 9 0.31
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (20 bp):
AATAAAAAATTTATTTTAAA
Found at i:6323016 original size:17 final size:17
Alignment explanation
Indices: 6322994--6323026 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
6322984 TGATTTCTTC
6322994 TTTTTC-TTTCTATTTTG
1 TTTTTCGTTT-TATTTTG
6323011 TTTTTCGTTTTATTTT
1 TTTTTCGTTTTATTTT
6323027 CTATCGTTTT
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
17 12 0.80
18 3 0.20
ACGTcount: A:0.06, C:0.09, G:0.06, T:0.79
Consensus pattern (17 bp):
TTTTTCGTTTTATTTTG
Found at i:6332303 original size:23 final size:23
Alignment explanation
Indices: 6332203--6332304 Score: 123
Period size: 23 Copynumber: 4.4 Consensus size: 23
6332193 TAGGGTTTAA
* * *
6332203 CATTGCGTGATTGGTTTATATGT
1 CATTGCGTGACTGGTTGATAGGT
* * * *
6332226 TATTACGTGATTAGTTGATAGGT
1 CATTGCGTGACTGGTTGATAGGT
*
6332249 CATTGCATGACTGGTTGATAGGT
1 CATTGCGTGACTGGTTGATAGGT
6332272 CATTGCGTGACTGGTTGATAGGT
1 CATTGCGTGACTGGTTGATAGGT
*
6332295 CATTACGTGA
1 CATTGCGTGA
6332305 ATATTGTTCA
Statistics
Matches: 67, Mismatches: 12, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
23 67 1.00
ACGTcount: A:0.22, C:0.11, G:0.28, T:0.39
Consensus pattern (23 bp):
CATTGCGTGACTGGTTGATAGGT
Found at i:6332389 original size:23 final size:22
Alignment explanation
Indices: 6332362--6332439 Score: 68
Period size: 23 Copynumber: 3.5 Consensus size: 22
6332352 TTGTTCTTAG
*
6332362 CATTGCATGACTTGTTGATAGAT
1 CATTGCATGACTTATTGATAG-T
* * * *
6332385 CATTGCACGATTTAATGTTAGT
1 CATTGCATGACTTATTGATAGT
*
6332407 AATTGCATGACTTATTGATAAGGT
1 CATTGCATGACTTATTGAT-A-GT
6332431 -ATTGCATGA
1 CATTGCATGA
6332440 TTGTTTTCTG
Statistics
Matches: 43, Mismatches: 10, Indels: 4
0.75 0.18 0.07
Matches are distributed among these distances:
22 15 0.35
23 26 0.60
24 2 0.05
ACGTcount: A:0.29, C:0.12, G:0.21, T:0.38
Consensus pattern (22 bp):
CATTGCATGACTTATTGATAGT
Found at i:6336401 original size:55 final size:55
Alignment explanation
Indices: 6336317--6336472 Score: 213
Period size: 55 Copynumber: 2.8 Consensus size: 55
6336307 AACCACCGAC
* **
6336317 TCATCAGCTCATGTGCACACTCCCACACCGCACATAGCTGGAATTATGGTCCACCGG
1 TCATCAGCTCATGTG--CACTCCCACACCGCACATAGCTGGAATCATCATCCACCGG
* * *
6336374 TTATTAGCTCATGTGCACTCCCACACCGCACATAGCTGGAATCATCATCCATCGG
1 TCATCAGCTCATGTGCACTCCCACACCGCACATAGCTGGAATCATCATCCACCGG
* * *
6336429 TCATCAGCTCATGTGCACTCCCACACTGCATATTGCTGGAATCA
1 TCATCAGCTCATGTGCACTCCCACACCGCACATAGCTGGAATCA
6336473 CCCGTCATCA
Statistics
Matches: 88, Mismatches: 11, Indels: 2
0.87 0.11 0.02
Matches are distributed among these distances:
55 75 0.85
57 13 0.15
ACGTcount: A:0.25, C:0.33, G:0.17, T:0.24
Consensus pattern (55 bp):
TCATCAGCTCATGTGCACTCCCACACCGCACATAGCTGGAATCATCATCCACCGG
Found at i:6337331 original size:3 final size:3
Alignment explanation
Indices: 6337323--6337352 Score: 51
Period size: 3 Copynumber: 10.0 Consensus size: 3
6337313 TTGGAAGCAT
*
6337323 GAA GAA GAA GAA GAA GAA GAA GAA TAA GAA
1 GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA
6337353 AATGCTTTTT
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.67, C:0.00, G:0.30, T:0.03
Consensus pattern (3 bp):
GAA
Found at i:6338709 original size:22 final size:22
Alignment explanation
Indices: 6338646--6338702 Score: 62
Period size: 22 Copynumber: 2.6 Consensus size: 22
6338636 TAACGTCATG
*
6338646 CAATACATAATAA-CAAGTCACA
1 CAATACATAAAAATC-AGTCACA
*
6338668 CAATACATAAAAATCAGTCACG
1 CAATACATAAAAATCAGTCACA
* *
6338690 CAATGCTTAAAAA
1 CAATACATAAAAA
6338703 GTAGTCAAGA
Statistics
Matches: 30, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
22 29 0.97
23 1 0.03
ACGTcount: A:0.53, C:0.21, G:0.07, T:0.19
Consensus pattern (22 bp):
CAATACATAAAAATCAGTCACA
Found at i:6338903 original size:22 final size:22
Alignment explanation
Indices: 6338852--6338924 Score: 89
Period size: 22 Copynumber: 3.5 Consensus size: 22
6338842 TGGCCCAACG
*
6338852 TCACGCAATACAT-AACA--AC
1 TCACGCAATACATAAACACCAA
*
6338871 TCAAGCAATACATAAACACCAA
1 TCACGCAATACATAAACACCAA
*
6338893 TCACGCAATACATAAATACCAA
1 TCACGCAATACATAAACACCAA
*
6338915 TTACGCAATA
1 TCACGCAATA
6338925 TCTCAACACT
Statistics
Matches: 46, Mismatches: 5, Indels: 3
0.85 0.09 0.06
Matches are distributed among these distances:
19 12 0.26
20 4 0.09
22 30 0.65
ACGTcount: A:0.49, C:0.27, G:0.05, T:0.18
Consensus pattern (22 bp):
TCACGCAATACATAAACACCAA
Found at i:6339119 original size:22 final size:22
Alignment explanation
Indices: 6339086--6339151 Score: 105
Period size: 22 Copynumber: 3.0 Consensus size: 22
6339076 AATGAAACAC
*
6339086 ACAATGCCTAATATCCATTCAA
1 ACAATGCATAATATCCATTCAA
* *
6339108 GCTATGCATAATATCCATTCAA
1 ACAATGCATAATATCCATTCAA
6339130 ACAATGCATAATATCCATTCAA
1 ACAATGCATAATATCCATTCAA
6339152 TTAATGCCTA
Statistics
Matches: 39, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
22 39 1.00
ACGTcount: A:0.41, C:0.24, G:0.06, T:0.29
Consensus pattern (22 bp):
ACAATGCATAATATCCATTCAA
Found at i:6339983 original size:22 final size:22
Alignment explanation
Indices: 6339953--6340007 Score: 92
Period size: 22 Copynumber: 2.5 Consensus size: 22
6339943 TAAAAATCAA
*
6339953 TCACACAATGCCTACAAACAAG
1 TCACGCAATGCCTACAAACAAG
*
6339975 TCACGCAATGCCTACAAACTAG
1 TCACGCAATGCCTACAAACAAG
6339997 TCACGCAATGC
1 TCACGCAATGC
6340008 AGAACCCACG
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
22 31 1.00
ACGTcount: A:0.38, C:0.33, G:0.13, T:0.16
Consensus pattern (22 bp):
TCACGCAATGCCTACAAACAAG
Found at i:6353563 original size:21 final size:23
Alignment explanation
Indices: 6353523--6353564 Score: 61
Period size: 21 Copynumber: 1.9 Consensus size: 23
6353513 GAGTAAATGA
*
6353523 TAAAAATATCTTTTATTAAAATT
1 TAAAAATATCTTTAATTAAAATT
6353546 TAAAAAT-T-TTTAATTAAAA
1 TAAAAATATCTTTAATTAAAA
6353565 AACAAAAATA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
21 10 0.56
22 1 0.06
23 7 0.39
ACGTcount: A:0.52, C:0.02, G:0.00, T:0.45
Consensus pattern (23 bp):
TAAAAATATCTTTAATTAAAATT
Found at i:6353719 original size:44 final size:46
Alignment explanation
Indices: 6353664--6353777 Score: 124
Period size: 47 Copynumber: 2.5 Consensus size: 46
6353654 ATCAAAATAA
* * *
6353664 CTTTTACTATAATTAAATAATATATT-CACCAAAATATAAACATAT
1 CTTTTATTATAATTAAATAATATATTGCACCAAAAGATAAACAAAT
* * ** **
6353709 -TTTTATTATAATTTAATAATATTTTTGCATTAAAAGATAATTAAAT
1 CTTTTATTATAATTAAATAATA-TATTGCACCAAAAGATAAACAAAT
6353755 CTTTTATTATAATTAAATAATAT
1 CTTTTATTATAATTAAATAATAT
6353778 TTAATATTAA
Statistics
Matches: 56, Mismatches: 10, Indels: 5
0.79 0.14 0.07
Matches are distributed among these distances:
44 19 0.34
45 3 0.05
46 14 0.25
47 20 0.36
ACGTcount: A:0.46, C:0.07, G:0.02, T:0.46
Consensus pattern (46 bp):
CTTTTATTATAATTAAATAATATATTGCACCAAAAGATAAACAAAT
Found at i:6353874 original size:10 final size:10
Alignment explanation
Indices: 6353859--6353933 Score: 57
Period size: 11 Copynumber: 7.5 Consensus size: 10
6353849 CATATTCAAA
6353859 AAATAATATT
1 AAATAATATT
6353869 AAATAATATTT
1 AAATAATA-TT
**
6353880 TTATAATATT
1 AAATAATATT
* *
6353890 -TATTATAGTT
1 AAATAATA-TT
*
6353900 AAATAACATT
1 AAATAATATT
6353910 -AAT-ATATT
1 AAATAATATT
6353918 AAATAATATTT
1 AAATAATA-TT
6353929 AAATA
1 AAATA
6353934 TTTTCATTTC
Statistics
Matches: 52, Mismatches: 7, Indels: 11
0.74 0.10 0.16
Matches are distributed among these distances:
8 4 0.08
9 12 0.23
10 17 0.33
11 19 0.37
ACGTcount: A:0.52, C:0.01, G:0.01, T:0.45
Consensus pattern (10 bp):
AAATAATATT
Found at i:6353934 original size:18 final size:18
Alignment explanation
Indices: 6353882--6353935 Score: 56
Period size: 18 Copynumber: 2.9 Consensus size: 18
6353872 TAATATTTTT
*
6353882 ATAATATTTATTATAGTTAA
1 ATAATATTTA-AATA-TTAA
*
6353902 ATAACA-TTAATATATTAA
1 ATAATATTTAA-ATATTAA
6353920 ATAATATTTAAATATT
1 ATAATATTTAAATATT
6353936 TTCATTTCTT
Statistics
Matches: 29, Mismatches: 3, Indels: 6
0.76 0.08 0.16
Matches are distributed among these distances:
18 14 0.48
19 10 0.34
20 5 0.17
ACGTcount: A:0.50, C:0.02, G:0.02, T:0.46
Consensus pattern (18 bp):
ATAATATTTAAATATTAA
Found at i:6354321 original size:13 final size:14
Alignment explanation
Indices: 6354300--6354332 Score: 50
Period size: 13 Copynumber: 2.4 Consensus size: 14
6354290 TTTAATTACA
*
6354300 TTTTATCTTT-TTT
1 TTTTCTCTTTCTTT
6354313 TTTTCTCTTTCTTT
1 TTTTCTCTTTCTTT
6354327 TTTTCT
1 TTTTCT
6354333 TTCCTCTCCA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
13 9 0.50
14 9 0.50
ACGTcount: A:0.03, C:0.15, G:0.00, T:0.82
Consensus pattern (14 bp):
TTTTCTCTTTCTTT
Found at i:6358331 original size:16 final size:17
Alignment explanation
Indices: 6358310--6358341 Score: 57
Period size: 16 Copynumber: 1.9 Consensus size: 17
6358300 ACTTTTTTTT
6358310 TAATGTAAAA-GAATGC
1 TAATGTAAAAGGAATGC
6358326 TAATGTAAAAGGAATG
1 TAATGTAAAAGGAATG
6358342 GGTTTGAAGA
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:0.50, C:0.03, G:0.22, T:0.25
Consensus pattern (17 bp):
TAATGTAAAAGGAATGC
Found at i:6358761 original size:30 final size:30
Alignment explanation
Indices: 6358722--6358796 Score: 84
Period size: 30 Copynumber: 2.5 Consensus size: 30
6358712 TATTTAACTC
* * *
6358722 AAAACAAAAATATAAAAATTTATTTG-ATTT
1 AAAATAAAAATATAAAAA-TTAATTGAATGT
6358752 AAAATAAAAATATTAAAAATTAATTGAATGT
1 AAAATAAAAATA-TAAAAATTAATTGAATGT
6358783 --AATAAAAATATAAA
1 AAAATAAAAATATAAA
6358797 GACCTATTCA
Statistics
Matches: 40, Mismatches: 3, Indels: 6
0.82 0.06 0.12
Matches are distributed among these distances:
28 4 0.10
29 10 0.25
30 17 0.43
31 9 0.22
ACGTcount: A:0.63, C:0.01, G:0.04, T:0.32
Consensus pattern (30 bp):
AAAATAAAAATATAAAAATTAATTGAATGT
Found at i:6378928 original size:2 final size:2
Alignment explanation
Indices: 6378921--6378950 Score: 53
Period size: 2 Copynumber: 15.5 Consensus size: 2
6378911 TAATTTACTA
6378921 AT AT AT AT AT AT AT AT AT AT AT AT A- AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
6378951 GAGTAAAAGC
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
1 1 0.04
2 26 0.96
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:6382066 original size:2 final size:2
Alignment explanation
Indices: 6382061--6382165 Score: 137
Period size: 2 Copynumber: 54.0 Consensus size: 2
6382051 TTGAAGAGAT
6382061 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
* * * *
6382103 TN TA TC TCA -A GA GA T- TA -A TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA T-A TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
6382143 -A TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA
6382166 GTAGAATTTC
Statistics
Matches: 93, Mismatches: 5, Indels: 10
0.86 0.05 0.09
Matches are distributed among these distances:
1 4 0.04
2 89 0.96
ACGTcount: A:0.49, C:0.02, G:0.02, T:0.47
Consensus pattern (2 bp):
TA
Found at i:6383081 original size:2 final size:2
Alignment explanation
Indices: 6383076--6383111 Score: 54
Period size: 2 Copynumber: 18.0 Consensus size: 2
6383066 TTTTTTTTAG
* *
6383076 AT AT AT AT AT AT AT AT AT AT AT AT AT GT AT GT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
6383112 GTGGATGTAT
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.44, C:0.00, G:0.06, T:0.50
Consensus pattern (2 bp):
AT
Found at i:6396351 original size:32 final size:32
Alignment explanation
Indices: 6396310--6396630 Score: 143
Period size: 32 Copynumber: 10.1 Consensus size: 32
6396300 CACTTGCAGA
6396310 TCTGGTGCCGCGCCAGCTGCCGCTCCTCTCTC
1 TCTGGTGCCGCGCCAGCTGCCGCTCCTCTCTC
* *
6396342 TCTGGTGCCGCGCCAGCCGCCGCTCCACTCTC
1 TCTGGTGCCGCGCCAGCTGCCGCTCCTCTCTC
* **
6396374 TCT--T-CC-C-CC-GTTCGGTGCTCCT-TC-C
1 TCTGGTGCCGCGCCAGCT-GCCGCTCCTCTCTC
* * * * * * * *
6396399 CCTCGCGCCAGATCTTCACTGTTGCTGCTCCCTTTCTC
1 TCTGGTGCC-G--C-GC-CAGCTGCCGCT-CCTCTCTC
6396437 TCTGGTGCCGCGCCAGCTGCCGCTCCTCTCTC
1 TCTGGTGCCGCGCCAGCTGCCGCTCCTCTCTC
*
6396469 TCTGGTGCCGCGCCAGCCGCCGCTCCTCTCTC
1 TCTGGTGCCGCGCCAGCTGCCGCTCCTCTCTC
* * **
6396501 TCT--T--C-CTCC-GTTCGATGCTCCT-TCT-
1 TCTGGTGCCGCGCCAGCT-GCCGCTCCTCTCTC
* * * * * * *
6396526 TCTCGCGCCAGATCTTCACTGTTGCTGCTCCCTTTCTC
1 TCTGGTGCC-G--C-GC-CAGCTGCCGCT-CCTCTCTC
*
6396564 TCTGGTGCCGCGCCAGCTGCCGTTCCTCTCTC
1 TCTGGTGCCGCGCCAGCTGCCGCTCCTCTCTC
* * *
6396596 TCTGTTGCCGCGCCAGCCGCCGCTTCTCTCTC
1 TCTGGTGCCGCGCCAGCTGCCGCTCCTCTCTC
6396628 TCT
1 TCT
6396631 TTCTCCGTTC
Statistics
Matches: 221, Mismatches: 38, Indels: 60
0.69 0.12 0.19
Matches are distributed among these distances:
25 6 0.03
26 7 0.03
27 18 0.08
28 4 0.02
29 3 0.01
30 2 0.01
32 113 0.51
33 16 0.07
34 5 0.02
35 14 0.06
36 12 0.05
37 7 0.03
38 14 0.06
ACGTcount: A:0.04, C:0.45, G:0.21, T:0.30
Consensus pattern (32 bp):
TCTGGTGCCGCGCCAGCTGCCGCTCCTCTCTC
Found at i:6396536 original size:127 final size:127
Alignment explanation
Indices: 6396310--6396689 Score: 634
Period size: 127 Copynumber: 3.0 Consensus size: 127
6396300 CACTTGCAGA
*
6396310 TCTGGTGCCGCGCCAGCTGCCGCTCCTCTCTCTCTGGTGCCGCGCCAGCCGCCGCTCCACTCTCT
1 TCTGGTGCCGCGCCAGCTGCCGCTCCTCTCTCTCTGGTGCCGCGCCAGCCGCCGCTCCTCTCTCT
*
6396375 CTTCCCCCGTTCGGTGCTCCTTCCCCTCGCGCCAGATCTTCACTGTTGCTGCTCCCTTTCTC
66 CTTCCTCCGTTCGGTGCTCCTTCCCCTCGCGCCAGATCTTCACTGTTGCTGCTCCCTTTCTC
6396437 TCTGGTGCCGCGCCAGCTGCCGCTCCTCTCTCTCTGGTGCCGCGCCAGCCGCCGCTCCTCTCTCT
1 TCTGGTGCCGCGCCAGCTGCCGCTCCTCTCTCTCTGGTGCCGCGCCAGCCGCCGCTCCTCTCTCT
* **
6396502 CTTCCTCCGTTCGATGCTCCTTCTTCTCGCGCCAGATCTTCACTGTTGCTGCTCCCTTTCTC
66 CTTCCTCCGTTCGGTGCTCCTTCCCCTCGCGCCAGATCTTCACTGTTGCTGCTCCCTTTCTC
* * *
6396564 TCTGGTGCCGCGCCAGCTGCCGTTCCTCTCTCTCTGTTGCCGCGCCAGCCGCCGCTTCTCTCTCT
1 TCTGGTGCCGCGCCAGCTGCCGCTCCTCTCTCTCTGGTGCCGCGCCAGCCGCCGCTCCTCTCTCT
* * * * *
6396629 CTTTCTCCGTTCGGTGCTCCTTCCCCTTTGCGCCAAATCCTCACTATTGCTGCTCCCTTTC
66 CTTCCTCCGTTCGGTGCTCCTTCCCC-TCGCGCCAGATCTTCACTGTTGCTGCTCCCTTTC
6396690 CTTTCCTCCT
Statistics
Matches: 236, Mismatches: 16, Indels: 1
0.93 0.06 0.00
Matches are distributed among these distances:
127 206 0.87
128 30 0.13
ACGTcount: A:0.05, C:0.44, G:0.19, T:0.31
Consensus pattern (127 bp):
TCTGGTGCCGCGCCAGCTGCCGCTCCTCTCTCTCTGGTGCCGCGCCAGCCGCCGCTCCTCTCTCT
CTTCCTCCGTTCGGTGCTCCTTCCCCTCGCGCCAGATCTTCACTGTTGCTGCTCCCTTTCTC
Found at i:6396873 original size:15 final size:14
Alignment explanation
Indices: 6396853--6396884 Score: 55
Period size: 15 Copynumber: 2.2 Consensus size: 14
6396843 CCTCTCTCCT
6396853 TTTTTCATTCTTTCA
1 TTTTTCATT-TTTCA
6396868 TTTTTCATTTTTCA
1 TTTTTCATTTTTCA
6396882 TTT
1 TTT
6396885 ATATATTTTT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 8 0.47
15 9 0.53
ACGTcount: A:0.12, C:0.16, G:0.00, T:0.72
Consensus pattern (14 bp):
TTTTTCATTTTTCA
Found at i:6396875 original size:7 final size:7
Alignment explanation
Indices: 6396853--6396884 Score: 55
Period size: 7 Copynumber: 4.4 Consensus size: 7
6396843 CCTCTCTCCT
6396853 TTTTTCA
1 TTTTTCA
6396860 TTCTTTCA
1 TT-TTTCA
6396868 TTTTTCA
1 TTTTTCA
6396875 TTTTTCA
1 TTTTTCA
6396882 TTT
1 TTT
6396885 ATATATTTTT
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
7 17 0.71
8 7 0.29
ACGTcount: A:0.12, C:0.16, G:0.00, T:0.72
Consensus pattern (7 bp):
TTTTTCA
Found at i:6401577 original size:12 final size:12
Alignment explanation
Indices: 6401560--6401590 Score: 53
Period size: 12 Copynumber: 2.6 Consensus size: 12
6401550 TATATAGTTA
*
6401560 ATAAAATAAAAT
1 ATAAAATAAAAG
6401572 ATAAAATAAAAG
1 ATAAAATAAAAG
6401584 ATAAAAT
1 ATAAAAT
6401591 TAACACTTAA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
12 18 1.00
ACGTcount: A:0.74, C:0.00, G:0.03, T:0.23
Consensus pattern (12 bp):
ATAAAATAAAAG
Found at i:6402117 original size:2 final size:2
Alignment explanation
Indices: 6402110--6402135 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
6402100 ATTAAATGTT
6402110 TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA
6402136 ATTTTTGTAA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:6405797 original size:2 final size:2
Alignment explanation
Indices: 6405790--6405827 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
6405780 AGTCAGTGTA
6405790 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
6405828 TTTAAAAAGC
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:6410119 original size:13 final size:13
Alignment explanation
Indices: 6410101--6410125 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
6410091 TTTCAAAAAA
6410101 TTTATAAAATCAT
1 TTTATAAAATCAT
6410114 TTTATAAAATCA
1 TTTATAAAATCA
6410126 CAATTTCTCT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.48, C:0.08, G:0.00, T:0.44
Consensus pattern (13 bp):
TTTATAAAATCAT
Found at i:6413688 original size:89 final size:89
Alignment explanation
Indices: 6413568--6413913 Score: 431
Period size: 89 Copynumber: 3.9 Consensus size: 89
6413558 GCCGTCAGTG
* * *
6413568 AAAGAAAGAAGTGAGAGAGAGAATATCTGGGTTCCTGTGCCGTCGATTCTAGAGAGAGCTGGGGC
1 AAAG-AAGAAGCGAGAGAGAGAAGATCTGGGTTCCTGTGCCGCCGATTCTAGAGAGAGCTGGGGC
*
6413633 TTCGGGCTTGTGTCGCCGGCTGAAA
65 TTCGGGCTTGTGTCACCGGCTGAAA
* * * * * *
6413658 AAATAAGAAGCGAGAGAGACAAGATGTGGGTTCCTGTGCCGCTGGTTCTAAAGAGAGCTGGGGCT
1 AAAGAAGAAGCGAGAGAGAGAAGATCTGGGTTCCTGTGCCGCCGATTCTAGAGAGAGCTGGGGCT
* * *
6413723 TCAGGCTTGTGTCACCGACTAAAA
66 TCGGGCTTGTGTCACCGGCTGAAA
* * * * ** * *
6413747 AAAGAAGAAGCGAGAGAGAGAAGATATGGGTTCCTATGTCGCCGGTTCTAGCTAGAGCTGGAGTT
1 AAAGAAGAAGCGAGAGAGAGAAGATCTGGGTTCCTGTGCCGCCGATTCTAGAGAGAGCTGGGGCT
* *
6413812 TCTGGCTTGTGTCATCGGCTGAAA
66 TCGGGCTTGTGTCACCGGCTGAAA
* * * * *
6413836 AAGGAAGAAGCGAGAGAGAGAAGATCTGGGTTTCTGTGCCGCCGATTTTAGAGAAAGTTGGGGCT
1 AAAGAAGAAGCGAGAGAGAGAAGATCTGGGTTCCTGTGCCGCCGATTCTAGAGAGAGCTGGGGCT
6413901 TCGGGCTTGTGTC
66 TCGGGCTTGTGTC
6413914 GTCGATTGGA
Statistics
Matches: 214, Mismatches: 42, Indels: 1
0.83 0.16 0.00
Matches are distributed among these distances:
89 211 0.99
90 3 0.01
ACGTcount: A:0.27, C:0.16, G:0.34, T:0.23
Consensus pattern (89 bp):
AAAGAAGAAGCGAGAGAGAGAAGATCTGGGTTCCTGTGCCGCCGATTCTAGAGAGAGCTGGGGCT
TCGGGCTTGTGTCACCGGCTGAAA
Found at i:6414906 original size:2 final size:2
Alignment explanation
Indices: 6414899--6414947 Score: 80
Period size: 2 Copynumber: 24.5 Consensus size: 2
6414889 NNNNNNTATC
* *
6414899 TA TA TA TA TT TA TA TA TA TA TA TA TA TA TA TA TA TA TA TT TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
6414941 TA TA TA T
1 TA TA TA T
6414948 TTTCTATAGC
Statistics
Matches: 43, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
2 43 1.00
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (2 bp):
TA
Found at i:6415810 original size:223 final size:223
Alignment explanation
Indices: 6415534--6416091 Score: 799
Period size: 223 Copynumber: 2.5 Consensus size: 223
6415524 TGCTCCAAAG
* *
6415534 GAAAA-TTTCATTGGAAATTCCGTTGGAAACTGTAAAAGATTGA-ACA--TTTTTTTTAAAGTTT
1 GAAAATTTTCGTTGGAAATTCCGTTGGAAACTGT-AAAGATT-ACACACGTTTTTTTT-TAGTTT
** * * *
6415595 AATA-TTCCAACTAATTTTCAATGAAAATTTTT-GTTAAAAATTCCGTTGGAAAAGATAAAGATA
63 AA-AGTTCCAACGGATTTTCAACG-AAATTTTTCGTTGAAAATTCCGTTGGAAAAAATAAAGATA
**
6415658 ACATAGGAAAAGTTTAGGGTTCCAACGAAAATTT-TCGTTGGAAATCTGTTGGAAATAATACAGT
126 ACATAGGAAAAGTTTAGGGTTCCAACGAAAATTTCT-GTTGGAAATCCATTGGAAATAATACAGT
*
6415722 GTCTTGAAGATGAAATTTCCAACAGATTTCCAAC
190 GTCTTGAAGATAAAATTTCCAACAGATTTCCAAC
* *
6415756 GAAAATTTTCGTTGGAAATTTCGTTGAAAACTGTAAAGATTACACACGTTTTTTTTTAGTTTAAA
1 GAAAATTTTCGTTGGAAATTCCGTTGGAAACTGTAAAGATTACACACGTTTTTTTTTAGTTTAAA
* * *
6415821 GTTCCAACGGAGTTCCAACGAAATTTTTCGTTGAAAATTCCGTTGGAAAAAATAAAGGTAACATA
66 GTTCCAACGGATTTTCAACGAAATTTTTCGTTGAAAATTCCGTTGGAAAAAATAAAGATAACATA
* * *
6415886 GGAAAAGTTTAGGGTTCCAATGGAAATTTCTGTTGGAAATCCATTGGAAATAATATAGTGTCTTG
131 GGAAAAGTTTAGGGTTCCAACGAAAATTTCTGTTGGAAATCCATTGGAAATAATACAGTGTCTTG
*
6415951 AAGATAAAATTTCCAACGGATTTCCAAC
196 AAGATAAAATTTCCAACAGATTTCCAAC
* * *
6415979 GAAAATTTTGGTTTGAAATTCCGTTGGAAACTGTAATGATTACACACGTTTTTTTTTAGTTTAAA
1 GAAAATTTTCGTTGGAAATTCCGTTGGAAACTGTAAAGATTACACACGTTTTTTTTTAGTTTAAA
*
6416044 GTTCCAACGGATTTTCAACGAAATTTTTCGCTGAAAA-TCCGTTGGAAA
66 GTTCCAACGGATTTTCAACGAAATTTTTCGTTGAAAATTCCGTTGGAAA
6416092 TATTAAACAG
Statistics
Matches: 302, Mismatches: 27, Indels: 14
0.88 0.08 0.04
Matches are distributed among these distances:
221 1 0.00
222 35 0.12
223 257 0.85
224 9 0.03
ACGTcount: A:0.36, C:0.12, G:0.17, T:0.34
Consensus pattern (223 bp):
GAAAATTTTCGTTGGAAATTCCGTTGGAAACTGTAAAGATTACACACGTTTTTTTTTAGTTTAAA
GTTCCAACGGATTTTCAACGAAATTTTTCGTTGAAAATTCCGTTGGAAAAAATAAAGATAACATA
GGAAAAGTTTAGGGTTCCAACGAAAATTTCTGTTGGAAATCCATTGGAAATAATACAGTGTCTTG
AAGATAAAATTTCCAACAGATTTCCAAC
Found at i:6418902 original size:856 final size:862
Alignment explanation
Indices: 6416719--6420498 Score: 4923
Period size: 856 Copynumber: 4.5 Consensus size: 862
6416709 AAAAAGAAAT
* * * *
6416719 AAGCGTAAATGAGAAGTTAAGGACTGATGTGGCAATTTTATGCTTACATGGTAGAGAATTGAATA
1 AAGCTTAAATGAGAAGTTAAGGACTGATGTGGCAATTATATGCTTAGATGGAAGAGAATTGAATA
** ** * * *
6416784 TTCATCTCCAAAAATAAGAATAGAATTGAATTA-TTCTATTTTGAGAATAAAGATTTTTTAATG-
66 CCCATCTCC-GGAATAAGAATAGAATTGAATGACCT-TATTTTGAGAATAAAGATTTTTTAGTGC
* * *
6416847 CCTATGAGAAAAATTTTCGTTTTATGTGGACGCAGCATATCTAGTTATTTTTTTAAAAGTAGTTT
129 CCT-TGAGAAAAATTTTC-CTTTATATGGACGCAGCATATCTAGTTATTTTTTTAAAGGTAGTTT
6416912 TTATTATCAAGTAACTGATCATAATCTAAAAGATAGTTTTATGACCTATTACATAATAAGAAGAA
192 TTATTATCAAGTAACTGATCATAATCTAAAAGATAGTTTTATGACCTATTACATAAT-A-AAGAA
* * * * *
6416977 AGATGAACCTTAGAATACACTA--G-T--G-CTAGGGGATATCTAGAACTTAAAAATAGTACACT
255 AGATGAA-CTCAAAATACACTAGTGCTAAGACTAGGGGATATCTAGCACTTAAAAACAATACACT
* * *
6417036 AATGCCC-ATCACTCGTCAAGACTTGGTTCTCCCCCCACAATCCAACATATATCATAATTTTCTT
319 AACGCCCTATCACTCGTCAAGACTTGGTTCTCCCCCCACAATCCAACGTATATCATGATTTTCTT
* *
6417100 ATTGCTGCGTTTGTTCGAATTGTTTGTTTGTGGATGTCTTTGTTCTATTTAGGT-GAAGAATTTT
384 ATTGTTGCGTCTGTTCGAATTGTTTGTTTGTGGATGTCTTTGTTCTATTTAGGTGGAA-AATTTT
* * * * * *
6417164 GTTTTGCTTGGTATTTTATTCCCTGCTATGAGAATATAATTCTCATTTTAATTTGTGGTTCATTA
448 GTTCTGCTGGGTATTTTATTCCCTACTATGAGAATACAATTCTTATTTTAATCTGTGGTTCATTA
* *
6417229 TTTTTTAAGACCATGGAGTTGTATTTTTATTAATGAATCTCTTGATGATTGAGAAAAGAAAAACT
513 TTTTTTAAGACAATGGAGTTGTATTTCTATTAATGAATCTCTTGATGATTGAGAAAAGAAAAACT
* * * *
6417294 GATATCAATTAAAATTTCTCATATATTAAATCCCCTA-TCAACTTTTTTGTGGAAAAGAATGTCC
578 GACATCAATTAAAATTTCTCATATATTAAATTCCCTACT-GACTTTTTTGT-GAAAAAAATGTCC
*
6417358 TCGTCAA-GCACGCTTTTGATTTTGAGGTTTAGGAGGAGCAATGGTCTACACACACCTCATTGGT
641 CCGT-AACGCACGCTTTTGATTTTGAGGTTTAGGAGGAGCAATGGTCTACACACACCTCATTGGT
* *
6417422 AGCCTA------AGATTTGTATGGAAAGGATAGGATTCTTGATGTAGCCAATAGGAAAC----TA
705 AGCCTAGGTGTGAGATTTGTATGGAAAGGATAGAATTCTTGATGTAGCCAATAAGAAACTAAGTA
* **
6417477 AGGACTTTGATAGTAAACAGATGGCATGTTGTTAATGGTTAGATTGTCATGTGCCCATCCAAATC
770 AGGACTTTGATAG----CAGATGGCATGTGGTTAATGGTTAGATTGTGGTGTGCCCATCCAAATC
6417542 ACAA-TT--TA--AT-AAT-A-G--GCAATTC
831 ACAATTTAATACCATCAATAAGGAAGCAATTC
* *
6417564 ATGCTTAAATGAGAAGTTAAGGACTGATGTGACAATTATATGCTTAGATGGAAGAGAATTGAATA
1 AAGCTTAAATGAGAAGTTAAGGACTGATGTGGCAATTATATGCTTAGATGGAAGAGAATTGAATA
* * * *
6417629 CCCATCTGCGGAAGAAGAATAGAATTGAATGACTTTATTTTGAGAATAAAGATTTTTTAGTGCCT
66 CCCATCTCCGGAATAAGAATAGAATTGAATGACCTTATTTTGAGAATAAAGATTTTTTAGTGCCC
* * * * *
6417694 TTAAGAAAAATTTTCGCTTTATATGGACGTAACATATTTAGTTA-TTTTTTAAAGGTCGTTTTTA
131 TTGAGAAAAATTTTC-CTTTATATGGACGCAGCATATCTAGTTATTTTTTTAAAGGTAGTTTTTA
* *
6417758 TTATCAAGTAACTGATCATAATCTAAAAG-TAGTTTTATGACCTATTATATAATAAGAAGAATGA
195 TTATCAAGTAACTGATCATAATCTAAAAGATAGTTTTATGACCTATTACATAAT-A-AAGAAAGA
* * *
6417822 TGAACCCAAAATACACTAGTGCTAAGACTGGGGGATATCTAGCACTTAAAAACAATACACTAACA
258 TGAACTCAAAATACACTAGTGCTAAGACTAGGGGATATCTAGCACTTAAAAACAATACACTAACG
* *
6417887 CCCTATCACTCGTCAAGACTTGGTTCTCCCCCCACAATCCTACGTATATCATGATTTTCTTATTA
323 CCCTATCACTCGTCAAGACTTGGTTCTCCCCCCACAATCCAACGTATATCATGATTTTCTTATTG
*
6417952 TTGCGTCTGTTCGAATTGTTTGTTTGTGGATGTCTTTGTTTTATTTAGGTGGAAAATTTTGTTCT
388 TTGCGTCTGTTCGAATTGTTTGTTTGTGGATGTCTTTGTTCTATTTAGGTGGAAAATTTTGTTCT
* * *
6418017 GTTGGGTGTTTTATTCCCTACTATGAGAATACAACTCTTATTTTAATCTGTGGTTCATTATTTTT
453 GCTGGGTATTTTATTCCCTACTATGAGAATACAATTCTTATTTTAATCTGTGGTTCATTATTTTT
* * * *
6418082 TAAGACAACGGAGTTGCATTTCTATTAATGAATCTCTTGATGATTAAGAAAAGAAAAATTGACAT
518 TAAGACAATGGAGTTGTATTTCTATTAATGAATCTCTTGATGATTGAGAAAAGAAAAACTGACAT
* * *
6418147 TAATTAAAATTTCTCATATATGAAATTCCCTA-TCGACTTTTTTGTGAAAAAAATGTCCTCGTAA
583 CAATTAAAATTTCTCATATATTAAATTCCCTACT-GACTTTTTTGTGAAAAAAATGTCCCCGTAA
* *
6418211 CGCATGCTTTTGATTTTGAGGTTTAGGAGGAGCAATGGTCTACACGCACCTCATTGGTAGCCTAG
647 CGCACGCTTTTGATTTTGAGGTTTAGGAGGAGCAATGGTCTACACACACCTCATTGGTAGCCTAG
* * *
6418276 GTGTGGGATTTGTATGGAAAGGATAGAATTCTTGATGTAGCCAATAAGAAACTTATTAAGGACTT
712 GTGTGAGATTTGTATGGAAAGGATAGAATTCTTGATGTAGCCAATAAGAAACTAAGTAAGGACTT
* *
6418341 TGATAGCAGATGGCATGTGGTTAATGGTTAGACTGTGGTGTGCCCATCCGAATCACAATTTAATA
777 TGATAGCAGATGGCATGTGGTTAATGGTTAGATTGTGGTGTGCCCATCCAAATCACAATTTAATA
* **
6418406 ACATTTATAAGGAAAGCAATTC
842 CCATCAATAAGG-AAGCAATTC
* *
6418428 AAGCTTAAATGAGAAGTTAAGGACTGATGTGGCAATTATATACTGAGATGGAAGAGAATTGAATA
1 AAGCTTAAATGAGAAGTTAAGGACTGATGTGGCAATTATATGCTTAGATGGAAGAGAATTGAATA
* * *
6418493 CCCATCTCCGGAATAAGAATAGAATAGAATGACCTTA-TTGGAGAATAAAGATTTTTT-TTGCCC
66 CCCATCTCCGGAATAAGAATAGAATTGAATGACCTTATTTTGAGAATAAAGATTTTTTAGTGCCC
** * *
6418556 TTGAGAAAAA-TTTCCACT-T-TGGACGCAGCATATTTAGTTATTTTTTTAAAAGTAGTTTTTAT
131 TTGAGAAAAATTTTCCTTTATATGGACGCAGCATATCTAGTTATTTTTTTAAAGGTAGTTTTTAT
* * *
6418618 TATCAAGTAACTGATCATAATCTAAAAGGTAGTTATATGACCTATTACATAAT-AAGAATGATGA
196 TATCAAGTAACTGATCATAATCTAAAAGATAGTTTTATGACCTATTACATAATAAAGAAAGATGA
*
6418682 ACTCAAAATACACTAGTGCTAAGACTAGGGGATATCTAGCACTTAAAAACAATACACTAACACCC
261 ACTCAAAATACACTAGTGCTAAGACTAGGGGATATCTAGCACTTAAAAACAATACACTAACGCCC
**
6418747 TATCACTCGTCAAGACTTGGTTCT-CCCCCACAATCCAACGTATATCATGATTTTCTTATTACTG
326 TATCACTCGTCAAGACTTGGTTCTCCCCCCACAATCCAACGTATATCATGATTTTCTTATTGTTG
* * * **
6418811 CGTCTGATCGGATTGTTTGTTTGTGGATGTCTTTCTTCTATTTAGGTGGGGAATTTTGTTCTGCT
391 CGTCTGTTCGAATTGTTTGTTTGTGGATGTCTTTGTTCTATTTAGGTGGAAAATTTTGTTCTGCT
* * * *
6418876 GGGTGTTTTATTCCCTACTATGAGAATACATTTCTTATTTTAATCCGTGGTTTATTATTTTTTAA
456 GGGTATTTTATTCCCTACTATGAGAATACAATTCTTATTTTAATCTGTGGTTCATTATTTTTTAA
* *
6418941 GACCATGGAGTTGTATTTCTATTAATGAATCTATTGATGATTGAGAAAAGAAAAACTGACATCAA
521 GACAATGGAGTTGTATTTCTATTAATGAATCTCTTGATGATTGAGAAAAGAAAAACTGACATCAA
* * * * * * * *
6419006 TTAAAATGTCTCAAACATTAAATTCCCTACTGACTTTTTTGTGGAAAAAATATCCCCGTCATGTA
586 TTAAAATTTCTCATATATTAAATTCCCTACTGACTTTTTTGTGAAAAAAATGTCCCCGTAACGCA
* * * * * *
6419071 CACTTTTGATTTTGAGGTTTAGAAGGAGAAATGGTCTATACACACCTCATTGGTAGCCTGGGTAT
651 CGCTTTTGATTTTGAGGTTTAGGAGGAGCAATGGTCTACACACACCTCATTGGTAGCCTAGGTGT
*
6419136 GAGATTTGTATGGAAAGGATAGAATTCTTGATGTAGCCAATAAGAAACTAAGTAACGAC-TT--T
716 GAGATTTGTATGGAAAGGATAGAATTCTTGATGTAGCCAATAAGAAACTAAGTAAGGACTTTGAT
*
6419198 ----GAT---A----G-TAA--G-TAGA------TG-G--CATCCAAATCACAATTTAATACCGT
781 AGCAGATGGCATGTGGTTAATGGTTAGATTGTGGTGTGCCCATCCAAATCACAATTTAATACCAT
*
6419239 CAATAACGCAAGCAATTC
846 CAATAA-GGAAGCAATTC
* * *
6419257 ATGCTTAAATGAGAAGTTAAGGATTGATGTGGCAATTATATACTTAGATGGAAGAGAATTGAATA
1 AAGCTTAAATGAGAAGTTAAGGACTGATGTGGCAATTATATGCTTAGATGGAAGAGAATTGAATA
* * * *
6419322 CCCATCTCCGAAATAAGAATAGAATTGAATGACCTTA-TTTGAGAATAAAGATTTTTAAGTGTCT
66 CCCATCTCCGGAATAAGAATAGAATTGAATGACCTTATTTTGAGAATAAAGATTTTTTAGTGCCC
* *
6419386 TTGAGAAAAATTTCCACTTTATATGGACGCAGCATATCTAATTATTTTTTTAAAGGTAGTTTTTA
131 TTGAGAAAAATTTTC-CTTTATATGGACGCAGCATATCTAGTTATTTTTTTAAAGGTAGTTTTTA
* * *
6419451 TTATCAAGTAACTGATTATAATCT-AAAGACAATTTTATGACCTATTACATAATAAGAAGAAAGA
195 TTATCAAGTAACTGATCATAATCTAAAAGATAGTTTTATGACCTATTACATAAT-A-AAGAAAGA
* * * * * * *
6419515 TGAACCCTAGAATATATTAGTGCTAAGACTGGGGGATATCTAACACTTGAAAACAATACACTAAC
258 TGAACTC-AAAATACACTAGTGCTAAGACTAGGGGATATCTAGCACTTAAAAACAATACACTAAC
*
6419580 GCCCCATCACTCGTCAAGACTTGGTTCTCCCCCCACAATCCAACGTATATCATGATTTTCTTATT
322 GCCCTATCACTCGTCAAGACTTGGTTCTCCCCCCACAATCCAACGTATATCATGATTTTCTTATT
* *
6419645 GTTGCGTCTGTTCAAATTGTTTGTCTGTGGATGTCTTTGTTCTATTTAGGTGG-AAATTTTGTTC
387 GTTGCGTCTGTTCGAATTGTTTGTTTGTGGATGTCTTTGTTCTATTTAGGTGGAAAATTTTGTTC
* * *
6419709 TACTGAGTATTTTATTCCCTGCTAT--G--------TC----------C-GTGGTTCATTATTTT
452 TGCTGGGTATTTTATTCCCTACTATGAGAATACAATTCTTATTTTAATCTGTGGTTCATTATTTT
* *
6419753 TTAAGACAATGAAGTTGTATTTCTATTAATGAATCTCTTGATGATTGAGAAAA-AAAAA-TTACA
517 TTAAGACAATGGAGTTGTATTTCTATTAATGAATCTCTTGATGATTGAGAAAAGAAAAACTGACA
* * * * * *
6419816 TCTATTAAAATTTCTCATATATTAAATTCTCTACTGACATTTTAGTGGAAAAAATGTCCCCGTTA
582 TCAATTAAAATTTCTCATATATTAAATTCCCTACTGACTTTTTTGTGAAAAAAATGTCCCCGTAA
* * *
6419881 CGCACGCTTTTGATTTTGAGGTTTAGGAAGAGCAATGGTCTACA-AGCACATCATTGGTAGCCTG
647 CGCACGCTTTTGATTTTGAGGTTTAGGAGGAGCAATGGTCTACACA-CACCTCATTGGTAGCCTA
* * * *
6419945 GGTGTGGGATTTGTATGGAAAGGATAGGATTCTTGATGTAGCCGATAAG-AACAAAGTAAGGACT
711 GGTGTGAGATTTGTATGGAAAGGATAGAATTCTTGATGTAGCCAATAAGAAACTAAGTAAGGACT
* * *
6420009 TTGATAGTAAGCAGATGGCATGTGGTTGATGGTTGGGTTGTGGTGTGCCCATCCAAATCACAATT
776 TTG--A-T-AGCAGATGGCATGTGGTTAATGGTTAGATTGTGGTGTGCCCATCCAAATCACAATT
* * * *
6420074 TAATACCGTCAATAAGGTAGGTAATTT
837 TAATACCATCAATAAGG-AAGCAATTC
* * *
6420101 AGGCTTAAATGAGAAGTTAAGGACTAATGTGGCAATTATATGCTTATATGGAAGAGAATTGAATA
1 AAGCTTAAATGAGAAGTTAAGGACTGATGTGGCAATTATATGCTTAGATGGAAGAGAATTGAATA
*
6420166 CCCATCTCTGGAATAAGAATAGAATTGAATGACCTTATTTTGAGAATAAAGATTTTTTAGTGCCC
66 CCCATCTCCGGAATAAGAATAGAATTGAATGACCTTATTTTGAGAATAAAGATTTTTTAGTGCCC
* *
6420231 TTGAGAAAAATTTTTGCTTTATATGGACGCGGCATATCTAGTTATTTTTTTAAAGGTAGTTTTTA
131 TTGAGAAAAA-TTTTCCTTTATATGGACGCAGCATATCTAGTTATTTTTTTAAAGGTAGTTTTTA
* *
6420296 TTATCAAGTAACTAATCATAATCTAAAAGATAGTTTTATGACCTATTACATAAAAGAAGAAAGAT
195 TTATCAAGTAACTGATCATAATCTAAAAGATAGTTTTATGACCTATTACATAATA-AAGAAAGAT
* * *
6420361 GAACCTCACAATACACTAGTGTTAAGA-TTGGGGATATCTAGCACTTAAAAACAATACACTAACG
259 GAA-CTCAAAATACACTAGTGCTAAGACTAGGGGATATCTAGCACTTAAAAACAATACACTAACG
6420425 CCCTATCACTCGTCAAGACTTGGTTCT-CCCCCACAATCCAACGTATATCATGATTTTCTTATTG
323 CCCTATCACTCGTCAAGACTTGGTTCTCCCCCCACAATCCAACGTATATCATGATTTTCTTATTG
6420489 TTGCGTCTGT
388 TTGCGTCTGT
6420499 GTCGTAATGT
Statistics
Matches: 2603, Mismatches: 249, Indels: 168
0.86 0.08 0.06
Matches are distributed among these distances:
813 13 0.00
814 161 0.06
815 5 0.00
816 64 0.02
817 1 0.00
819 1 0.00
824 3 0.00
827 3 0.00
829 150 0.06
830 14 0.01
831 5 0.00
832 6 0.00
833 26 0.01
834 63 0.02
835 3 0.00
836 13 0.00
837 108 0.04
838 86 0.03
839 1 0.00
841 16 0.01
842 39 0.01
843 96 0.04
844 275 0.11
845 202 0.08
846 35 0.01
847 112 0.04
848 270 0.10
849 6 0.00
853 92 0.04
854 2 0.00
855 2 0.00
856 382 0.15
857 114 0.04
858 21 0.01
859 50 0.02
860 25 0.01
861 5 0.00
862 13 0.00
863 19 0.01
864 101 0.04
ACGTcount: A:0.33, C:0.14, G:0.18, T:0.35
Consensus pattern (862 bp):
AAGCTTAAATGAGAAGTTAAGGACTGATGTGGCAATTATATGCTTAGATGGAAGAGAATTGAATA
CCCATCTCCGGAATAAGAATAGAATTGAATGACCTTATTTTGAGAATAAAGATTTTTTAGTGCCC
TTGAGAAAAATTTTCCTTTATATGGACGCAGCATATCTAGTTATTTTTTTAAAGGTAGTTTTTAT
TATCAAGTAACTGATCATAATCTAAAAGATAGTTTTATGACCTATTACATAATAAAGAAAGATGA
ACTCAAAATACACTAGTGCTAAGACTAGGGGATATCTAGCACTTAAAAACAATACACTAACGCCC
TATCACTCGTCAAGACTTGGTTCTCCCCCCACAATCCAACGTATATCATGATTTTCTTATTGTTG
CGTCTGTTCGAATTGTTTGTTTGTGGATGTCTTTGTTCTATTTAGGTGGAAAATTTTGTTCTGCT
GGGTATTTTATTCCCTACTATGAGAATACAATTCTTATTTTAATCTGTGGTTCATTATTTTTTAA
GACAATGGAGTTGTATTTCTATTAATGAATCTCTTGATGATTGAGAAAAGAAAAACTGACATCAA
TTAAAATTTCTCATATATTAAATTCCCTACTGACTTTTTTGTGAAAAAAATGTCCCCGTAACGCA
CGCTTTTGATTTTGAGGTTTAGGAGGAGCAATGGTCTACACACACCTCATTGGTAGCCTAGGTGT
GAGATTTGTATGGAAAGGATAGAATTCTTGATGTAGCCAATAAGAAACTAAGTAAGGACTTTGAT
AGCAGATGGCATGTGGTTAATGGTTAGATTGTGGTGTGCCCATCCAAATCACAATTTAATACCAT
CAATAAGGAAGCAATTC
Found at i:6421362 original size:21 final size:24
Alignment explanation
Indices: 6421338--6421394 Score: 59
Period size: 24 Copynumber: 2.4 Consensus size: 24
6421328 TTTTTTTGTC
6421338 ATTTTTTATTATTT-A-ATTAT-T
1 ATTTTTTATTATTTCATATTATAT
6421359 ATTTTCATT-TTATTTCATATTATCAT
1 ATTTT--TTATTATTTCATATTAT-AT
6421385 ATTTTTTATT
1 ATTTTTTATT
6421395 TTTTTTATTC
Statistics
Matches: 29, Mismatches: 0, Indels: 10
0.74 0.00 0.26
Matches are distributed among these distances:
21 5 0.17
22 6 0.21
23 3 0.10
24 7 0.24
25 2 0.07
26 6 0.21
ACGTcount: A:0.26, C:0.05, G:0.00, T:0.68
Consensus pattern (24 bp):
ATTTTTTATTATTTCATATTATAT
Found at i:6421419 original size:30 final size:32
Alignment explanation
Indices: 6421357--6421423 Score: 86
Period size: 30 Copynumber: 2.1 Consensus size: 32
6421347 TATTTAATTA
6421357 TTATTTTCATTTTATTTCATATTATCATATTTT
1 TTATTTT-ATTTTATTTCATATTATCATATTTT
*
6421390 TTATTTT-TTTTATTCTCCTA-TAT-ATATTTT
1 TTATTTTATTTTATT-TCATATTATCATATTTT
6421420 TTAT
1 TTAT
6421424 ATTCTAAGTT
Statistics
Matches: 32, Mismatches: 1, Indels: 5
0.84 0.03 0.13
Matches are distributed among these distances:
30 11 0.34
31 10 0.31
32 4 0.12
33 7 0.22
ACGTcount: A:0.22, C:0.09, G:0.00, T:0.69
Consensus pattern (32 bp):
TTATTTTATTTTATTTCATATTATCATATTTT
Found at i:6421669 original size:11 final size:11
Alignment explanation
Indices: 6421655--6421679 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
6421645 TTCTTCTTTT
6421655 TTTATTTATTA
1 TTTATTTATTA
6421666 TTTATTTATTA
1 TTTATTTATTA
6421677 TTT
1 TTT
6421680 TTTTGAATGA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.24, C:0.00, G:0.00, T:0.76
Consensus pattern (11 bp):
TTTATTTATTA
Found at i:6424467 original size:73 final size:74
Alignment explanation
Indices: 6424347--6424501 Score: 224
Period size: 73 Copynumber: 2.1 Consensus size: 74
6424337 AACTTCTATT
* * * **
6424347 TATTTCTTGACATTGGAAACTTCGTTTGGTTATTCTCTTCGAGGTTTGGTAGGTTTTACATTTAT
1 TATTTTTTAACATGGGAAACTTCGAGTGGTTATTCTCTTCGAGGTTTGGTAGGTTTTACATTTAT
6424412 TCTC-TTCA
66 TCTCTTTCA
* *
6424420 TATTTTTTAACATGGGAAACTTCGAGTGTTTATTCTCTTC-AGAGTTTGGTGGGTTTTACATTTA
1 TATTTTTTAACATGGGAAACTTCGAGTGGTTATTCTCTTCGAG-GTTTGGTAGGTTTTACATTTA
6424484 TTCTCTTTCA
65 TTCTCTTTCA
6424494 TATTTTTT
1 TATTTTTT
6424502 TTTTTCTGAT
Statistics
Matches: 73, Mismatches: 7, Indels: 3
0.88 0.08 0.04
Matches are distributed among these distances:
72 2 0.03
73 59 0.81
74 12 0.16
ACGTcount: A:0.19, C:0.14, G:0.17, T:0.51
Consensus pattern (74 bp):
TATTTTTTAACATGGGAAACTTCGAGTGGTTATTCTCTTCGAGGTTTGGTAGGTTTTACATTTAT
TCTCTTTCA
Found at i:6424749 original size:27 final size:27
Alignment explanation
Indices: 6424697--6424749 Score: 63
Period size: 27 Copynumber: 2.0 Consensus size: 27
6424687 TTTTTCATAA
* *
6424697 CTTGACTTAAGAAACTTCTGTTGATTT
1 CTTGACATAAGAAACTTCTGTGGATTT
*
6424724 CTTGACATGAGAAACTT-TGTCGGATT
1 CTTGACATAAGAAACTTCTGT-GGATT
6424750 ACTCTCTTTG
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
26 3 0.14
27 19 0.86
ACGTcount: A:0.26, C:0.15, G:0.19, T:0.40
Consensus pattern (27 bp):
CTTGACATAAGAAACTTCTGTGGATTT
Found at i:6430818 original size:2 final size:2
Alignment explanation
Indices: 6430806--6430849 Score: 63
Period size: 2 Copynumber: 22.5 Consensus size: 2
6430796 AAATAAATAA
* *
6430806 AT AT TT AT AT AT AT AT TT AT AT AT AT AT AT -T AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
6430847 AT A
1 AT A
6430850 ATTCACTTCA
Statistics
Matches: 37, Mismatches: 4, Indels: 2
0.86 0.09 0.05
Matches are distributed among these distances:
1 1 0.03
2 36 0.97
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (2 bp):
AT
Found at i:6435412 original size:10 final size:10
Alignment explanation
Indices: 6435397--6435453 Score: 57
Period size: 10 Copynumber: 5.8 Consensus size: 10
6435387 TTGTGAAATT
*
6435397 ATTATTTAAA
1 ATTATTAAAA
6435407 ATTATTAAAA
1 ATTATTAAAA
*
6435417 ATTA-TAAAT
1 ATTATTAAAA
6435426 ATT-TTAAATAA
1 ATTATT-AA-AA
6435437 ATTA-TAAAA
1 ATTATTAAAA
6435446 ATTATTAA
1 ATTATTAA
6435454 TATGTTAATT
Statistics
Matches: 39, Mismatches: 3, Indels: 10
0.75 0.06 0.19
Matches are distributed among these distances:
9 14 0.36
10 20 0.51
11 5 0.13
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (10 bp):
ATTATTAAAA
Found at i:6435455 original size:20 final size:20
Alignment explanation
Indices: 6435404--6435455 Score: 72
Period size: 20 Copynumber: 2.6 Consensus size: 20
6435394 ATTATTATTT
6435404 AAAATTATTAA-AAATTATA
1 AAAATTATTAATAAATTATA
*
6435423 AATATT-TTAAATAAATTATA
1 AAAATTATT-AATAAATTATA
6435443 AAAATTATTAATA
1 AAAATTATTAATA
6435456 TGTTAATTCT
Statistics
Matches: 28, Mismatches: 2, Indels: 5
0.80 0.06 0.14
Matches are distributed among these distances:
18 2 0.07
19 7 0.25
20 17 0.61
21 2 0.07
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (20 bp):
AAAATTATTAATAAATTATA
Found at i:6435487 original size:10 final size:10
Alignment explanation
Indices: 6435396--6435492 Score: 51
Period size: 9 Copynumber: 9.5 Consensus size: 10
6435386 TTTGTGAAAT
6435396 TATTATTTAAA
1 TATTA-TTAAA
6435407 -ATTATTAAA
1 TATTATTAAA
*
6435416 AATTA-TAAA
1 TATTATTAAA
6435425 TATT-TTAAA
1 TATTATTAAA
6435434 TAAATTA-TAAA
1 T--ATTATTAAA
*
6435445 AATTATTAATA
1 TATTATTAA-A
* *
6435456 TGTTAATTCTAA
1 TATT-ATT-AAA
*
6435468 -ATTATAAAA
1 TATTATTAAA
6435477 TATTATTAAA
1 TATTATTAAA
6435487 TGATTA
1 T-ATTA
6435493 ATGAATTATT
Statistics
Matches: 66, Mismatches: 9, Indels: 22
0.68 0.09 0.23
Matches are distributed among these distances:
9 23 0.35
10 22 0.33
11 16 0.24
12 4 0.06
13 1 0.02
ACGTcount: A:0.52, C:0.01, G:0.02, T:0.45
Consensus pattern (10 bp):
TATTATTAAA
Found at i:6435494 original size:32 final size:31
Alignment explanation
Indices: 6435405--6435494 Score: 105
Period size: 29 Copynumber: 2.9 Consensus size: 31
6435395 TTATTATTTA
* * *
6435405 AAATTATTAAAAATTATAAATATTTTAA--AT
1 AAATTA-TAAAAATTATTAATATGTTAATTCT
6435435 AAATTATAAAAATTATTAATATGTTAATTCT
1 AAATTATAAAAATTATTAATATGTTAATTCT
6435466 AAATTATAAAATATTATTAA-ATGATTAAT
1 AAATTATAAAA-ATTATTAATATG-TTAAT
6435495 GAATTATTAT
Statistics
Matches: 53, Mismatches: 3, Indels: 6
0.85 0.05 0.10
Matches are distributed among these distances:
29 19 0.36
30 6 0.11
31 15 0.28
32 13 0.25
ACGTcount: A:0.53, C:0.01, G:0.02, T:0.43
Consensus pattern (31 bp):
AAATTATAAAAATTATTAATATGTTAATTCT
Found at i:6435520 original size:34 final size:34
Alignment explanation
Indices: 6435473--6435547 Score: 91
Period size: 34 Copynumber: 2.2 Consensus size: 34
6435463 TCTAAATTAT
*
6435473 AAAATATTATTAAATGATTAATGAA-TTATTA-TGA
1 AAAATATTATTAAATGAATAAT-AATTTATTACT-A
* *
6435507 AAAATATTTTTAAATTAATAATAATTTATTACTA
1 AAAATATTATTAAATGAATAATAATTTATTACTA
6435541 AAAATAT
1 AAAATAT
6435548 AGTTAATTAA
Statistics
Matches: 36, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
33 2 0.06
34 33 0.92
35 1 0.03
ACGTcount: A:0.52, C:0.01, G:0.04, T:0.43
Consensus pattern (34 bp):
AAAATATTATTAAATGAATAATAATTTATTACTA
Found at i:6449679 original size:18 final size:18
Alignment explanation
Indices: 6449623--6449670 Score: 53
Period size: 19 Copynumber: 2.6 Consensus size: 18
6449613 ACCATATTAA
*
6449623 TATACATAAAAAATT-ATT
1 TATAAATAAAAAATTCA-T
*
6449641 TAAAAAATAAAAAATTCAT
1 T-ATAAATAAAAAATTCAT
6449660 TATAAATAAAA
1 TATAAATAAAA
6449671 CTATTATTAA
Statistics
Matches: 25, Mismatches: 3, Indels: 4
0.78 0.09 0.12
Matches are distributed among these distances:
18 10 0.40
19 14 0.56
20 1 0.04
ACGTcount: A:0.65, C:0.04, G:0.00, T:0.31
Consensus pattern (18 bp):
TATAAATAAAAAATTCAT
Found at i:6452114 original size:33 final size:34
Alignment explanation
Indices: 6452046--6452118 Score: 87
Period size: 33 Copynumber: 2.2 Consensus size: 34
6452036 AAATGGTAAA
6452046 ATGTCACATAATCATATCATTATATCATATCAAC
1 ATGTCACATAATCATATCATTATATCATATCAAC
* * * *
6452080 ATGTCGCATTATCATCT-ATTATAAT-ATATTAAC
1 ATGTCACATAATCATATCATTAT-ATCATATCAAC
6452113 ATGTCA
1 ATGTCA
6452119 TGTTAGCATC
Statistics
Matches: 33, Mismatches: 5, Indels: 3
0.80 0.12 0.07
Matches are distributed among these distances:
33 17 0.52
34 16 0.48
ACGTcount: A:0.38, C:0.18, G:0.05, T:0.38
Consensus pattern (34 bp):
ATGTCACATAATCATATCATTATATCATATCAAC
Found at i:6457338 original size:22 final size:22
Alignment explanation
Indices: 6457313--6457391 Score: 72
Period size: 22 Copynumber: 3.5 Consensus size: 22
6457303 ATAAAAAATC
6457313 TAAATTTATAAA-ATTAATATTT
1 TAAA-TTATAAATATTAATATTT
* *
6457335 TAAATTAAAAATATTAATATTG
1 TAAATTATAAATATTAATATTT
* *
6457357 TAATATTTTAATTATAATAATATTT
1 TAA-ATTATAA--ATATTAATATTT
6457382 T-AATTATAAA
1 TAAATTATAAA
6457392 ATAAAAATAT
Statistics
Matches: 46, Mismatches: 7, Indels: 9
0.74 0.11 0.15
Matches are distributed among these distances:
21 7 0.15
22 16 0.35
23 11 0.24
24 1 0.02
25 11 0.24
ACGTcount: A:0.51, C:0.00, G:0.01, T:0.48
Consensus pattern (22 bp):
TAAATTATAAATATTAATATTT
Found at i:6457379 original size:17 final size:17
Alignment explanation
Indices: 6457357--6457394 Score: 69
Period size: 17 Copynumber: 2.3 Consensus size: 17
6457347 ATTAATATTG
6457357 TAATATTTTAATTATAA
1 TAATATTTTAATTATAA
6457374 TAATATTTTAATTATAA
1 TAATATTTTAATTATAA
6457391 -AATA
1 TAATA
6457395 AAAATATTAA
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
16 4 0.19
17 17 0.81
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (17 bp):
TAATATTTTAATTATAA
Found at i:6457395 original size:22 final size:22
Alignment explanation
Indices: 6457318--6457402 Score: 68
Period size: 22 Copynumber: 3.8 Consensus size: 22
6457308 AAATCTAAAT
6457318 TTATAAAAT--TAATATTTTAAA
1 TTATAAAATAATAATATTTT-AA
* *
6457339 TTA-AAAATATTAATATTGTAATA
1 TTATAAAATAATAATATT-TTA-A
* *
6457362 TTTTAATTATAATAATATTTTAA
1 TTATAA-AATAATAATATTTTAA
*
6457385 TTATAAAATAAAAATATT
1 TTATAAAATAATAATATT
6457403 AATATTTTAA
Statistics
Matches: 50, Mismatches: 8, Indels: 11
0.72 0.12 0.16
Matches are distributed among these distances:
20 5 0.10
21 3 0.06
22 18 0.36
23 10 0.20
24 4 0.08
25 10 0.20
ACGTcount: A:0.52, C:0.00, G:0.01, T:0.47
Consensus pattern (22 bp):
TTATAAAATAATAATATTTTAA
Found at i:6457417 original size:18 final size:17
Alignment explanation
Indices: 6457394--6457430 Score: 65
Period size: 18 Copynumber: 2.1 Consensus size: 17
6457384 ATTATAAAAT
6457394 AAAAATATTAATATTTTA
1 AAAAATATTAAT-TTTTA
6457412 AAAAATATTAATTTTTA
1 AAAAATATTAATTTTTA
6457429 AA
1 AA
6457431 TCATTAAGTG
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
17 7 0.37
18 12 0.63
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (17 bp):
AAAAATATTAATTTTTA
Found at i:6457842 original size:26 final size:27
Alignment explanation
Indices: 6457799--6457849 Score: 68
Period size: 26 Copynumber: 1.9 Consensus size: 27
6457789 TTTTATAATG
**
6457799 TTAATGATTAAATTAT-AAATAAAATA
1 TTAATGATTAAAAAATAAAATAAAATA
*
6457825 TTAATGTTTAAAAAATAAAATAAAA
1 TTAATGATTAAAAAATAAAATAAAA
6457850 ATAAATTATA
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
26 13 0.62
27 8 0.38
ACGTcount: A:0.61, C:0.00, G:0.04, T:0.35
Consensus pattern (27 bp):
TTAATGATTAAAAAATAAAATAAAATA
Found at i:6458451 original size:28 final size:30
Alignment explanation
Indices: 6458381--6458489 Score: 122
Period size: 30 Copynumber: 3.8 Consensus size: 30
6458371 ATTAAATATT
* * *
6458381 AATAATAAAAACTTATTTAGTTCAAAATAA
1 AATAATAAAAATTTATTTAATTTAAAATAA
6458411 AA-ATATAAAAATTTATTTAATTTAAAAT-A
1 AATA-ATAAAAATTTATTTAATTTAAAATAA
* *
6458440 AAT-ATAAAAA-TTAATTAA-ATAAAATAA
1 AATAATAAAAATTTATTTAATTTAAAATAA
6458467 AATAATAAAAATTTATTT-ATTTA
1 AATAATAAAAATTTATTTAATTTA
6458490 CTTTAATAAT
Statistics
Matches: 66, Mismatches: 7, Indels: 13
0.77 0.08 0.15
Matches are distributed among these distances:
26 6 0.09
27 11 0.17
28 15 0.23
29 11 0.17
30 23 0.35
ACGTcount: A:0.60, C:0.02, G:0.01, T:0.38
Consensus pattern (30 bp):
AATAATAAAAATTTATTTAATTTAAAATAA
Found at i:6467182 original size:6 final size:6
Alignment explanation
Indices: 6467174--6467203 Score: 51
Period size: 6 Copynumber: 5.0 Consensus size: 6
6467164 GAAATTGCCT
*
6467174 AGCCCT AGCCCC AGCCCC AGCCCC AGCCCC
1 AGCCCC AGCCCC AGCCCC AGCCCC AGCCCC
6467204 TATGATTTTG
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
6 23 1.00
ACGTcount: A:0.17, C:0.63, G:0.17, T:0.03
Consensus pattern (6 bp):
AGCCCC
Found at i:6468697 original size:27 final size:27
Alignment explanation
Indices: 6468675--6468795 Score: 163
Period size: 27 Copynumber: 4.5 Consensus size: 27
6468665 TTAGAAATTG
* *
6468675 ATGGATACCTTTATTCATAAGAAGT-A
1 ATGGATACCTTTATTCACAAAAAGTGA
* *
6468701 GATAGATACCTTTACTCACAAAAAGTGA
1 -ATGGATACCTTTATTCACAAAAAGTGA
*
6468729 ATGGATATCTTTATTCACAAAAAGTGA
1 ATGGATACCTTTATTCACAAAAAGTGA
*
6468756 ATGGATATCTTTATTCACAAAAAGTGA
1 ATGGATACCTTTATTCACAAAAAGTGA
*
6468783 ATGGATACATTTA
1 ATGGATACCTTTA
6468796 CCCACTAGAA
Statistics
Matches: 84, Mismatches: 9, Indels: 2
0.88 0.09 0.02
Matches are distributed among these distances:
27 83 0.99
28 1 0.01
ACGTcount: A:0.40, C:0.12, G:0.15, T:0.32
Consensus pattern (27 bp):
ATGGATACCTTTATTCACAAAAAGTGA
Found at i:6471939 original size:16 final size:16
Alignment explanation
Indices: 6471918--6471955 Score: 58
Period size: 16 Copynumber: 2.4 Consensus size: 16
6471908 GATATTTATA
*
6471918 TGATCTATACAAAGCT
1 TGATCTACACAAAGCT
6471934 TGATCTACACAAAGCT
1 TGATCTACACAAAGCT
*
6471950 CGATCT
1 TGATCT
6471956 TAGACAAATT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
16 20 1.00
ACGTcount: A:0.34, C:0.24, G:0.13, T:0.29
Consensus pattern (16 bp):
TGATCTACACAAAGCT
Found at i:6473085 original size:19 final size:19
Alignment explanation
Indices: 6473061--6473097 Score: 65
Period size: 19 Copynumber: 1.9 Consensus size: 19
6473051 AAATTATTGC
*
6473061 TTTCATATCGTGGCAATCG
1 TTTCATATCATGGCAATCG
6473080 TTTCATATCATGGCAATC
1 TTTCATATCATGGCAATC
6473098 TTAACATACC
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.24, C:0.22, G:0.16, T:0.38
Consensus pattern (19 bp):
TTTCATATCATGGCAATCG
Found at i:6480905 original size:266 final size:266
Alignment explanation
Indices: 6480424--6480957 Score: 978
Period size: 266 Copynumber: 2.0 Consensus size: 266
6480414 AAATGAGAAA
6480424 TCATACACATTCCTATTTTCATGTTATCAAAAATTTTGCTTTCCCTTCAGAAAAGTTGTACACCA
1 TCATACACATTCCTATTTTCATGTTATCAAAAATTTTGCTTTCCCTTCAGAAAAGTTGTACACCA
*
6480489 TGATTTAACTCAAACCGAAAATCAGTATAAAACTTTACCAGGTTCACTGCAGCAGTTTCCTTTAC
66 CGATTTAACTCAAACCGAAAATCAGTATAAAACTTTACCAGGTTCACTGCAGCAGTTTCCTTTAC
*
6480554 CTCTGCTACTCGTACAGGTTTTATTTCTTTCTGCAGCGTGCTAGGCTCTCTGTCCTTTGACTACA
131 CTCTGCTACTCGTACAGGTTTTATTTCTTTCTGCAGCATGCTAGGCTCTCTGTCCTTTGACTACA
*
6480619 TTGCGAAGCAGAAGGATTAGATCTTAGGAAGATTTATAAACTTGTAATTTTACACTATAACAACC
196 TTGCGAAGCAGAAGGATTAGATCTTAGGAAGATTTATAAACTTGTAATTTTACACTACAACAACC
6480684 TTTTCT
261 TTTTCT
* *
6480690 TCATACGCATTCCTATTTTCATGTTATCAAAAATTTTGCTTTCCCTTCAGAAAAGTTGTACATCA
1 TCATACACATTCCTATTTTCATGTTATCAAAAATTTTGCTTTCCCTTCAGAAAAGTTGTACACCA
*
6480755 CGATTTAACTCAAACCGAAAATCAGTATAAAACTTTACCAGGTTCACTGCAGCAGTTTCCTTTTC
66 CGATTTAACTCAAACCGAAAATCAGTATAAAACTTTACCAGGTTCACTGCAGCAGTTTCCTTTAC
* *
6480820 CTGTGTTACTCGTACAGGTTTTATTTCTTTCTGCAGCATGCTAGGCTCTCTGTCCTTTGACTACA
131 CTCTGCTACTCGTACAGGTTTTATTTCTTTCTGCAGCATGCTAGGCTCTCTGTCCTTTGACTACA
* *
6480885 TTGTGAAGCAGAAGGATTAGATCTTAGGAAGATTTATAAACTTGTAATTTTACACTACGACAACC
196 TTGCGAAGCAGAAGGATTAGATCTTAGGAAGATTTATAAACTTGTAATTTTACACTACAACAACC
6480950 TTTTCT
261 TTTTCT
6480956 TC
1 TC
6480958 GATAGTCATT
Statistics
Matches: 258, Mismatches: 10, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
266 258 1.00
ACGTcount: A:0.28, C:0.22, G:0.14, T:0.37
Consensus pattern (266 bp):
TCATACACATTCCTATTTTCATGTTATCAAAAATTTTGCTTTCCCTTCAGAAAAGTTGTACACCA
CGATTTAACTCAAACCGAAAATCAGTATAAAACTTTACCAGGTTCACTGCAGCAGTTTCCTTTAC
CTCTGCTACTCGTACAGGTTTTATTTCTTTCTGCAGCATGCTAGGCTCTCTGTCCTTTGACTACA
TTGCGAAGCAGAAGGATTAGATCTTAGGAAGATTTATAAACTTGTAATTTTACACTACAACAACC
TTTTCT
Found at i:6483782 original size:17 final size:17
Alignment explanation
Indices: 6483760--6483793 Score: 52
Period size: 17 Copynumber: 2.0 Consensus size: 17
6483750 TTACATTATT
6483760 AATTTG-GATATACAAAA
1 AATTTGTGA-ATACAAAA
6483777 AATTTGTGAATACAAAA
1 AATTTGTGAATACAAAA
6483794 TAAAATTGTA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 14 0.88
18 2 0.12
ACGTcount: A:0.53, C:0.06, G:0.12, T:0.29
Consensus pattern (17 bp):
AATTTGTGAATACAAAA
Found at i:6492318 original size:2 final size:2
Alignment explanation
Indices: 6492311--6492337 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
6492301 TGAAATTTGT
6492311 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 T
6492338 TTAATTTTAA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:6522630 original size:185 final size:184
Alignment explanation
Indices: 6522315--6522687 Score: 674
Period size: 185 Copynumber: 2.0 Consensus size: 184
6522305 GCATCCTAAC
6522315 AGACAAAAGCAAATTTGAAGTGCACTTACAAAACTGGGGAACAAACAATAAAAGTGCATTGGAGA
1 AGACAAAAGCAAATTTGAAGTGCACTTACAAAACTGGGGAACAAACAATAAAAGTGCATTGGAGA
* * * *
6522380 TGAGATAGTTCCTAATTTACCGGCTTAAGGAAAGCTTGCACACTTGTTGAATGCTACTGTAATCT
66 TGAGATAGTTCCTAATTTACCAGCTCAAGGAAAGCTTGCACACTTGTAGAATGCTACTATAATCT
*
6522445 TTATTTATTTATCTTCTTAGTACCTCATCTCCAGGGCATACAATTAACTATTTTA
131 TTATTTATTTATCTTCTTAGTACCTCATCTCCAGAGCATACAATTAACTA-TTTA
* *
6522500 AGACAAAAGCAAATTTGAAGTGCGCTTACAAAACTGGGGAACAAACAATAGAAGTGCATTGGAGA
1 AGACAAAAGCAAATTTGAAGTGCACTTACAAAACTGGGGAACAAACAATAAAAGTGCATTGGAGA
6522565 TGAGATAGTTCCTAATTTACCAGCTCAAGGAAAGCTTGCACACTTGTAGAATGCTACTATAATCT
66 TGAGATAGTTCCTAATTTACCAGCTCAAGGAAAGCTTGCACACTTGTAGAATGCTACTATAATCT
6522630 TTATTTATTTATCTTCTTAGTACCTCATCTCCAGAGCATACAATTAACTATTTA
131 TTATTTATTTATCTTCTTAGTACCTCATCTCCAGAGCATACAATTAACTATTTA
6522684 AGAC
1 AGAC
6522688 CCTGAATCGA
Statistics
Matches: 181, Mismatches: 7, Indels: 1
0.96 0.04 0.01
Matches are distributed among these distances:
184 8 0.04
185 173 0.96
ACGTcount: A:0.35, C:0.18, G:0.17, T:0.30
Consensus pattern (184 bp):
AGACAAAAGCAAATTTGAAGTGCACTTACAAAACTGGGGAACAAACAATAAAAGTGCATTGGAGA
TGAGATAGTTCCTAATTTACCAGCTCAAGGAAAGCTTGCACACTTGTAGAATGCTACTATAATCT
TTATTTATTTATCTTCTTAGTACCTCATCTCCAGAGCATACAATTAACTATTTA
Found at i:6536264 original size:35 final size:35
Alignment explanation
Indices: 6536223--6536289 Score: 116
Period size: 35 Copynumber: 1.9 Consensus size: 35
6536213 GAAAAACACA
*
6536223 CTTTAAGGAATGACTTTTAGGACTTTCATTACTTT
1 CTTTAAGCAATGACTTTTAGGACTTTCATTACTTT
*
6536258 CTTTAAGCAATGACTTTTAGGACTTTCTTTAC
1 CTTTAAGCAATGACTTTTAGGACTTTCATTAC
6536290 AGTTGACTTG
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
35 30 1.00
ACGTcount: A:0.25, C:0.16, G:0.13, T:0.45
Consensus pattern (35 bp):
CTTTAAGCAATGACTTTTAGGACTTTCATTACTTT
Found at i:6538714 original size:36 final size:36
Alignment explanation
Indices: 6538667--6538792 Score: 191
Period size: 36 Copynumber: 3.5 Consensus size: 36
6538657 CCTCCTGAGA
6538667 AACAACATCAATAGGTCTACGCAAGGAGCCCTGTGG
1 AACAACATCAATAGGTCTACGCAAGGAGCCCTGTGG
*
6538703 AACAACATCAATATGTCTACGCAAGGAGCCCTGTGG
1 AACAACATCAATAGGTCTACGCAAGGAGCCCTGTGG
** *
6538739 AACAACATCAATAGGTCTGTGCAATG-GCTCCTGTGG
1 AACAACATCAATAGGTCTACGCAAGGAGC-CCTGTGG
*
6538775 AACAACCTCAATAGGTCT
1 AACAACATCAATAGGTCT
6538793 GTGCAAAGTC
Statistics
Matches: 83, Mismatches: 6, Indels: 2
0.91 0.07 0.02
Matches are distributed among these distances:
35 2 0.02
36 81 0.98
ACGTcount: A:0.33, C:0.25, G:0.22, T:0.21
Consensus pattern (36 bp):
AACAACATCAATAGGTCTACGCAAGGAGCCCTGTGG
Found at i:6538793 original size:36 final size:36
Alignment explanation
Indices: 6538653--6538848 Score: 180
Period size: 36 Copynumber: 5.4 Consensus size: 36
6538643 CAGATCAGGT
* * * *
6538653 AAAGCCTCCTGAGAAACAACATCAATAGGTCTACGC
1 AAAGGCTCCTGTGGAACAACATCAATAGGTCTGCGC
* * *
6538689 AAGGAGC-CCTGTGGAACAACATCAATATGTCTACGC
1 AAAG-GCTCCTGTGGAACAACATCAATAGGTCTGCGC
* *
6538725 AAGGAGC-CCTGTGGAACAACATCAATAGGTCTGTGC
1 AAAG-GCTCCTGTGGAACAACATCAATAGGTCTGCGC
* * *
6538761 AATGGCTCCTGTGGAACAACCTCAATAGGTCTGTGC
1 AAAGGCTCCTGTGGAACAACATCAATAGGTCTGCGC
* * ** * *
6538797 AAAGTCTCCTGGGGAAGTACCTCAATAGCTCTGCGC
1 AAAGGCTCCTGTGGAACAACATCAATAGGTCTGCGC
* *
6538833 AAAGTCTCCTGAGGAA
1 AAAGGCTCCTGTGGAA
6538849 GTAAGTCAAT
Statistics
Matches: 140, Mismatches: 18, Indels: 4
0.86 0.11 0.02
Matches are distributed among these distances:
35 2 0.01
36 137 0.98
37 1 0.01
ACGTcount: A:0.31, C:0.25, G:0.23, T:0.20
Consensus pattern (36 bp):
AAAGGCTCCTGTGGAACAACATCAATAGGTCTGCGC
Found at i:6538933 original size:36 final size:36
Alignment explanation
Indices: 6538746--6538933 Score: 193
Period size: 36 Copynumber: 5.2 Consensus size: 36
6538736 TGGAACAACA
* * * * *
6538746 TCAATAGGTCTGTGCAATGGCTCCTGTGGAA-CAACC
1 TCAATAGGCCTGTGCAAAGTCTCCTGAGGAAGTAA-C
* * *
6538782 TCAATAGGTCTGTGCAAAGTCTCCTGGGGAAGTACC
1 TCAATAGGCCTGTGCAAAGTCTCCTGAGGAAGTAAC
* *
6538818 TCAATA-GCTCTGCGCAAAGTCTCCTGAGGAAGTAAG
1 TCAATAGGC-CTGTGCAAAGTCTCCTGAGGAAGTAAC
* * * * *
6538854 TCAATAGGCCTGTACAAAGTGTCCTGGGGAAATAAG
1 TCAATAGGCCTGTGCAAAGTCTCCTGAGGAAGTAAC
6538890 TCAATAGGCCT-TCGCAAAGTCTCCTGAGGAAGTAAC
1 TCAATAGGCCTGT-GCAAAGTCTCCTGAGGAAGTAAC
6538926 TCAATAGG
1 TCAATAGG
6538934 TTTATGCCAA
Statistics
Matches: 128, Mismatches: 20, Indels: 8
0.82 0.13 0.05
Matches are distributed among these distances:
35 2 0.02
36 123 0.96
37 3 0.02
ACGTcount: A:0.29, C:0.22, G:0.26, T:0.23
Consensus pattern (36 bp):
TCAATAGGCCTGTGCAAAGTCTCCTGAGGAAGTAAC
Found at i:6545575 original size:21 final size:21
Alignment explanation
Indices: 6545549--6545590 Score: 75
Period size: 21 Copynumber: 2.0 Consensus size: 21
6545539 GTTGGACTGG
*
6545549 AGTTACTTACACCATGATTTT
1 AGTTACTTAAACCATGATTTT
6545570 AGTTACTTAAACCATGATTTT
1 AGTTACTTAAACCATGATTTT
6545591 GGTGGTCACA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.31, C:0.17, G:0.10, T:0.43
Consensus pattern (21 bp):
AGTTACTTAAACCATGATTTT
Found at i:6547175 original size:4 final size:4
Alignment explanation
Indices: 6547168--6547193 Score: 52
Period size: 4 Copynumber: 6.5 Consensus size: 4
6547158 ATATACATAC
6547168 ATGT ATGT ATGT ATGT ATGT ATGT AT
1 ATGT ATGT ATGT ATGT ATGT ATGT AT
6547194 ATGTTTGTAT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 22 1.00
ACGTcount: A:0.27, C:0.00, G:0.23, T:0.50
Consensus pattern (4 bp):
ATGT
Found at i:6549490 original size:15 final size:15
Alignment explanation
Indices: 6549470--6549515 Score: 74
Period size: 15 Copynumber: 3.1 Consensus size: 15
6549460 ACATCAGATC
*
6549470 CATCATCTGCATCAT
1 CATCATCTTCATCAT
6549485 CATCATCTTCATCAT
1 CATCATCTTCATCAT
*
6549500 CACCATCTTCATCAT
1 CATCATCTTCATCAT
6549515 C
1 C
6549516 TTCAGTACTC
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 29 1.00
ACGTcount: A:0.26, C:0.37, G:0.02, T:0.35
Consensus pattern (15 bp):
CATCATCTTCATCAT
Found at i:6553685 original size:23 final size:23
Alignment explanation
Indices: 6553655--6553709 Score: 110
Period size: 23 Copynumber: 2.4 Consensus size: 23
6553645 CTAGTTAGAC
6553655 TAGGATAAGATTCCTAATTATAT
1 TAGGATAAGATTCCTAATTATAT
6553678 TAGGATAAGATTCCTAATTATAT
1 TAGGATAAGATTCCTAATTATAT
6553701 TAGGATAAG
1 TAGGATAAG
6553710 GTTATTGTAT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 32 1.00
ACGTcount: A:0.40, C:0.07, G:0.16, T:0.36
Consensus pattern (23 bp):
TAGGATAAGATTCCTAATTATAT
Found at i:6555335 original size:21 final size:21
Alignment explanation
Indices: 6555301--6555340 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
6555291 TCATCAAATT
6555301 CAGAATGTCTGCAACTCATTAA
1 CAGAATGTCTGCAAC-CATTAA
*
6555323 CAGAA-GTTTGCAACCATT
1 CAGAATGTCTGCAACCATT
6555341 GCATTTAACA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 4 0.24
21 8 0.47
22 5 0.29
ACGTcount: A:0.35, C:0.23, G:0.15, T:0.28
Consensus pattern (21 bp):
CAGAATGTCTGCAACCATTAA
Found at i:6565282 original size:24 final size:24
Alignment explanation
Indices: 6565235--6565282 Score: 60
Period size: 24 Copynumber: 2.0 Consensus size: 24
6565225 ATATTCTATG
* *
6565235 TATAAAAATCTGTGACACACCATA
1 TATAAAAACCTGTGACAAACCATA
* *
6565259 TATAAAAACCTGTGATAAATCATA
1 TATAAAAACCTGTGACAAACCATA
6565283 ATTAGCGTGT
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
24 20 1.00
ACGTcount: A:0.48, C:0.17, G:0.08, T:0.27
Consensus pattern (24 bp):
TATAAAAACCTGTGACAAACCATA
Found at i:6565310 original size:69 final size:69
Alignment explanation
Indices: 6565190--6565448 Score: 252
Period size: 69 Copynumber: 3.8 Consensus size: 69
6565180 ACACGTAATG
* * * * * *
6565190 TACAAAAATCTGTAACAAGTTATGGTTAGCGTGTTATAT-TCTATGTATAAAAATCTGTGACACA
1 TACAAAAACCTGTGACAAGTCATGGTTAGCGTGTGACATGTC-ATGTACAAAAATCTGTGACACA
6565254 CCATA
65 CCATA
* * * ** * * **
6565259 TATAAAAACCTGTGATAAATCATAATTAGCGTGTGACATGTCATGTATAAAAATATGTGACACGT
1 TACAAAAACCTGTGACAAGTCATGGTTAGCGTGTGACATGTCATGTACAAAAATCTGTGACACAC
*
6565324 CATC
66 CATA
* * * * * *
6565328 TACAAAAATCTGTGACAAGTCATGGTTAGTGTGTAATATGTCATGTACAAAAA-CATATGACATA
1 TACAAAAACCTGTGACAAGTCATGGTTAGCGTGTGACATGTCATGTACAAAAATC-TGTGACACA
*
6565392 CCATG
65 CCATA
* * *
6565397 TACAAAAACCTGTGACAAGTCATGGTTAGGGTGTGACACGGCATGTACAAAA
1 TACAAAAACCTGTGACAAGTCATGGTTAGCGTGTGACATGTCATGTACAAAA
6565449 GCTTGTGACA
Statistics
Matches: 152, Mismatches: 36, Indels: 4
0.79 0.19 0.02
Matches are distributed among these distances:
69 150 0.99
70 2 0.01
ACGTcount: A:0.38, C:0.15, G:0.18, T:0.29
Consensus pattern (69 bp):
TACAAAAACCTGTGACAAGTCATGGTTAGCGTGTGACATGTCATGTACAAAAATCTGTGACACAC
CATA
Found at i:6565317 original size:24 final size:24
Alignment explanation
Indices: 6565290--6565351 Score: 79
Period size: 24 Copynumber: 2.6 Consensus size: 24
6565280 ATAATTAGCG
* *
6565290 TGTGACATGTCATGTATAAAAATA
1 TGTGACAAGTCATGTACAAAAATA
* * *
6565314 TGTGACACGTCATCTACAAAAATC
1 TGTGACAAGTCATGTACAAAAATA
6565338 TGTGACAAGTCATG
1 TGTGACAAGTCATG
6565352 GTTAGTGTGT
Statistics
Matches: 32, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
24 32 1.00
ACGTcount: A:0.37, C:0.16, G:0.18, T:0.29
Consensus pattern (24 bp):
TGTGACAAGTCATGTACAAAAATA
Found at i:6565420 original size:24 final size:25
Alignment explanation
Indices: 6565367--6565420 Score: 67
Period size: 24 Copynumber: 2.2 Consensus size: 25
6565357 TGTGTAATAT
6565367 GTCATGTACAAAAACATATGACATA
1 GTCATGTACAAAAACATATGACATA
* * *
6565392 -CCATGTACAAAAACCTGTGACA-A
1 GTCATGTACAAAAACATATGACATA
6565415 GTCATG
1 GTCATG
6565421 GTTAGGGTGT
Statistics
Matches: 24, Mismatches: 4, Indels: 3
0.77 0.13 0.10
Matches are distributed among these distances:
23 1 0.04
24 23 0.96
ACGTcount: A:0.43, C:0.20, G:0.15, T:0.22
Consensus pattern (25 bp):
GTCATGTACAAAAACATATGACATA
Found at i:6565442 original size:45 final size:45
Alignment explanation
Indices: 6565392--6565549 Score: 217
Period size: 45 Copynumber: 3.5 Consensus size: 45
6565382 ATATGACATA
* *
6565392 CCATGTACAAAAACCTGTGACAAGTCATGGTTAGGGTGTGACACG
1 CCATGTACAAAAGCCTGTGACAAGTCATGGTTAGCGTGTGACACG
* * * *
6565437 GCATGTACAAAAGCTTGTGACAAGTCATGGTTAGCGTGTTATACG
1 CCATGTACAAAAGCCTGTGACAAGTCATGGTTAGCGTGTGACACG
* * *
6565482 TCATGTACAAAAGCCTATGACAAGTCATGGTTAACGTGTGACACG
1 CCATGTACAAAAGCCTGTGACAAGTCATGGTTAGCGTGTGACACG
* *
6565527 CCATATACAAAAGGCTGTGACAA
1 CCATGTACAAAAGCCTGTGACAA
6565550 ACTATGTATA
Statistics
Matches: 97, Mismatches: 16, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
45 97 1.00
ACGTcount: A:0.33, C:0.19, G:0.24, T:0.24
Consensus pattern (45 bp):
CCATGTACAAAAGCCTGTGACAAGTCATGGTTAGCGTGTGACACG
Found at i:6565458 original size:138 final size:138
Alignment explanation
Indices: 6565175--6565448 Score: 336
Period size: 138 Copynumber: 2.0 Consensus size: 138
6565165 ACACGCTATG
* * * * * *
6565175 ATGTTACACGTAATGTACAAAAATCTGTAACAAGTTATGGTTAGCGTGTTATATTCTATGTATAA
1 ATGTGACACGTCATCTACAAAAATCTGTAACAAGTCATGGTTAGCGTGTAATATTCTATGTACAA
* * * * *
6565240 AAATCTGTGACACACCATATATAAAAACCTGTGATAAATCATAATTAGCGTGTGACATGTCATGT
66 AAATCTATGACACACCATATACAAAAACCTGTGACAAATCATAATTAGCGTGTGACACGGCATGT
*
6565305 ATAAAAAT
131 ACAAAAAT
* *
6565313 ATGTGACACGTCATCTACAAAAATCTGTGACAAGTCATGGTTAGTGTGTAATATGTC-ATGTACA
1 ATGTGACACGTCATCTACAAAAATCTGTAACAAGTCATGGTTAGCGTGTAATAT-TCTATGTACA
* * * ** *
6565377 AAAA-CATATGACATACCATGTACAAAAACCTGTGACAAGTCATGGTTAGGGTGTGACACGGCAT
65 AAAATC-TATGACACACCATATACAAAAACCTGTGACAAATCATAATTAGCGTGTGACACGGCAT
6565441 GTACAAAA
129 GTACAAAA
6565449 GCTTGTGACA
Statistics
Matches: 114, Mismatches: 20, Indels: 4
0.83 0.14 0.03
Matches are distributed among these distances:
137 1 0.01
138 111 0.97
139 2 0.02
ACGTcount: A:0.38, C:0.15, G:0.18, T:0.29
Consensus pattern (138 bp):
ATGTGACACGTCATCTACAAAAATCTGTAACAAGTCATGGTTAGCGTGTAATATTCTATGTACAA
AAATCTATGACACACCATATACAAAAACCTGTGACAAATCATAATTAGCGTGTGACACGGCATGT
ACAAAAAT
Found at i:6566025 original size:9 final size:10
Alignment explanation
Indices: 6566001--6566029 Score: 51
Period size: 9 Copynumber: 3.0 Consensus size: 10
6565991 TTATCAAGTC
6566001 ATAATTAAAT
1 ATAATTAAAT
6566011 ATAATTAAA-
1 ATAATTAAAT
6566020 ATAATTAAAT
1 ATAATTAAAT
6566030 TTATTTTGAT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
9 9 0.50
10 9 0.50
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (10 bp):
ATAATTAAAT
Found at i:6599586 original size:681 final size:681
Alignment explanation
Indices: 6598202--6599534 Score: 2019
Period size: 681 Copynumber: 2.0 Consensus size: 681
6598192 AGCCTGATGT
* * * * *
6598202 ATGTTCAAGTGTGTATGAGACTTGACATAGCTTTTTGCAAAAAGTCTTTTGAGAAGATATTTATC
1 ATGTTCAAGAGTGTATGAAACGTGACATAGCTTTCTGCAAAAAGTCTTTTAAGAAGATATTTATC
* *
6598267 TAATCACGATAAAGAGGCTATCTGGTTGAGAAATCTCATTAAAAATTGTCTATAGTTAACTCTAA
66 TAATCACGATAAAGAGGCTATCTGGTTGAGAAATCTCATTAAAAATTGTCAATAGTTAACTATAA
*
6598332 TGCTAGACCAAATATAGTTGTACTATGATAACGTTGCAACATTTTTGTTCACTAACAATAGGGGT
131 TGCTAGACCAAATATAGTTGTACTATGATAACGTTGCAACATTTTTGTTCACTAACAATAGAGGT
*
6598397 ATCACAAGGGGCTAAGCCTATAGAGATAAAATATTTGACACTTAAAAAACTTGTGAAAAAAGATT
196 ATCACAAGGGGCTAAGCCTATAGAGATAAAATATTTGACACTTAAAAAACCTGTGAAAAAAGATT
** *
6598462 ACGTTAAAGCAAAGCATATCAGAACTGATGAAATAATAGTTGATCCTCTAATTAAGAGACGCCTT
261 AAATTAAAGCAAAGCATATCAGAACTGATGAAATAATAGTTGATCCTCTAACT-A-AGACGCCTT
*
6598527 GTCAATTTCAAGAAATACATTTTGACATAGATATTGTAGAGTCTTTTGATGTACTTGGTTAGTGA
324 GCCAATTTCAAGAAATACATTTTGACATAGATATTGTAGAGTCTTTTGATGTACTTGGTTAGTGA
* * ** *
6598592 GAGGATTTGACATTATTTTATACTTTATGCTTAATTTTTTTGGCATACATTGATGATGATGTATA
389 GAGGATTTAACATTATTTTACACTTTACACTTAATTTTTTTGGCATACATCGATGATGATGTATA
* * *
6598657 TGAATTTAATATTAAGAGTAATTATTCAATGATATAAGTCATAAAGTGTTTATGTATGTATGCAT
454 TGAATTTAATATTAAGAGTAATTACTCAATGATATAACTCATAAAGTGTTTATGTATGTATACAT
* *
6598722 TTTTGCATATGTGCAGAATTAATAAATATGTTAGTCTCAAGTATAGGCTAGGACATATTTGATAG
519 TTTTGCATATGTGAAGAATTAATAAATATGTCAGTCTCAAGTATAGGCTAGGACATATTTGATAG
* * * * * **
6598787 CTCTAACGAAATATCTTTCTCATATAAAGCATATCTTGAGATATGTAAGACATCTATGAAAGTGA
584 CCCTAACAAAATATCATTCTCATATAAAGCATATCTTGAGATATGTAAGACAACTATCAAAAAGA
* * * * **
6598852 AGCTATACGCTAATGCAACAGGGAGCCAAAAATGT
649 A-CAATACGCTAATGAAACAAGAAG-CAAAAATCA
* * *
6598887 ATGTTCAAGTGTGTATGAAACGTGACATTGC-TTCTGCAATAAGTCTTTTAAGAAGATATTTATC
1 ATGTTCAAGAGTGTATGAAACGTGACATAGCTTTCTGCAAAAAGTCTTTTAAGAAGATATTTATC
*
6598951 TAATC-CTGATAAAGAGGCTATCTGGTTGAGAAATCTCATTAAAAATTGTCAATAGTTGACTATA
66 TAATCAC-GATAAAGAGGCTATCTGGTTGAGAAATCTCATTAAAAATTGTCAATAGTTAACTATA
* ** * *
6599015 TTGCTAGACCAAATATAGTTGTTGTATGATAATGTTGCAACATTTTTGTTCACTAATAATAGAGG
130 ATGCTAGACCAAATATAGTTGTACTATGATAACGTTGCAACATTTTTGTTCACTAACAATAGAGG
*
6599080 TATCACACA-GGGCTAAGCCTATAGAGATAAAATATTTGACACTTAAAACACCTGTGAAAAAAGA
195 TATCACA-AGGGGCTAAGCCTATAGAGATAAAATATTTGACACTTAAAAAACCTGTGAAAAAAGA
** * * *
6599144 TTAAATTTCAGTAAAGCATATTAGAACTGATGAAATAATAGTTGATCCTCTAACT-AGATGCCTT
259 TTAAATTAAAGCAAAGCATATCAGAACTGATGAAATAATAGTTGATCCTCTAACTAAGACGCCTT
* *
6599208 GCCAATTTCAAGAAATACATTTTGACATAGATATTGTAGAGTCTTTTGATGTGCTTGGTTAGTGG
324 GCCAATTTCAAGAAATACATTTTGACATAGATATTGTAGAGTCTTTTGATGTACTTGGTTAGTGA
* *
6599273 GAGGATTTAACATTATTTTACACTTTACACTTAATTTTTTTGGCCTACATCGATGATGATGTATT
389 GAGGATTTAACATTATTTTACACTTTACACTTAATTTTTTTGGCATACATCGATGATGATGTATA
6599338 TGAATTTAATATTAAGAGTAATTACTCAATGATATAACTCATAAAGTGTTTATGTATGTATACAT
454 TGAATTTAATATTAAGAGTAATTACTCAATGATATAACTCATAAAGTGTTTATGTATGTATACAT
* *
6599403 TTTTGCATATGTGAAGACTTAATAAATATGTCAGTCTTAAGTATAGGCTAGGACATATTTGATAG
519 TTTTGCATATGTGAAGAATTAATAAATATGTCAGTCTCAAGTATAGGCTAGGACATATTTGATAG
* **
6599468 CCCTAACAAAATATCATTCTCATATAGAGTTTATCTTGAGATATGTAAGACAAAC-ATACAAAAA
584 CCCTAACAAAATATCATTCTCATATAAAGCATATCTTGAGATATGTAAGAC-AACTAT-CAAAAA
6599532 GAA
647 GAA
6599535 AATTTTCTAA
Statistics
Matches: 592, Mismatches: 52, Indels: 11
0.90 0.08 0.02
Matches are distributed among these distances:
681 298 0.50
682 8 0.01
683 1 0.00
684 256 0.43
685 29 0.05
ACGTcount: A:0.36, C:0.12, G:0.17, T:0.35
Consensus pattern (681 bp):
ATGTTCAAGAGTGTATGAAACGTGACATAGCTTTCTGCAAAAAGTCTTTTAAGAAGATATTTATC
TAATCACGATAAAGAGGCTATCTGGTTGAGAAATCTCATTAAAAATTGTCAATAGTTAACTATAA
TGCTAGACCAAATATAGTTGTACTATGATAACGTTGCAACATTTTTGTTCACTAACAATAGAGGT
ATCACAAGGGGCTAAGCCTATAGAGATAAAATATTTGACACTTAAAAAACCTGTGAAAAAAGATT
AAATTAAAGCAAAGCATATCAGAACTGATGAAATAATAGTTGATCCTCTAACTAAGACGCCTTGC
CAATTTCAAGAAATACATTTTGACATAGATATTGTAGAGTCTTTTGATGTACTTGGTTAGTGAGA
GGATTTAACATTATTTTACACTTTACACTTAATTTTTTTGGCATACATCGATGATGATGTATATG
AATTTAATATTAAGAGTAATTACTCAATGATATAACTCATAAAGTGTTTATGTATGTATACATTT
TTGCATATGTGAAGAATTAATAAATATGTCAGTCTCAAGTATAGGCTAGGACATATTTGATAGCC
CTAACAAAATATCATTCTCATATAAAGCATATCTTGAGATATGTAAGACAACTATCAAAAAGAAC
AATACGCTAATGAAACAAGAAGCAAAAATCA
Found at i:6601961 original size:2 final size:2
Alignment explanation
Indices: 6601954--6601983 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
6601944 TACAACTTGA
6601954 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
6601984 GCTTAATATG
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:6608376 original size:13 final size:13
Alignment explanation
Indices: 6608360--6608412 Score: 52
Period size: 13 Copynumber: 3.9 Consensus size: 13
6608350 TTTATTTTTA
6608360 AAAATTATAAATT
1 AAAATTATAAATT
6608373 AAAACTTATAAAATT
1 AAAA-TTAT-AAATT
** *
6608388 AATTTTTTAAATT
1 AAAATTATAAATT
*
6608401 AAAATTAAAAAT
1 AAAATTATAAAT
6608413 ATTAATATTT
Statistics
Matches: 31, Mismatches: 7, Indels: 4
0.74 0.17 0.10
Matches are distributed among these distances:
13 17 0.55
14 7 0.23
15 7 0.23
ACGTcount: A:0.58, C:0.02, G:0.00, T:0.40
Consensus pattern (13 bp):
AAAATTATAAATT
Found at i:6608376 original size:14 final size:15
Alignment explanation
Indices: 6608357--6608389 Score: 50
Period size: 14 Copynumber: 2.3 Consensus size: 15
6608347 TTATTTATTT
6608357 TTAAAAATTAT-AAA
1 TTAAAAATTATAAAA
*
6608371 TTAAAACTTATAAAA
1 TTAAAAATTATAAAA
6608386 TTAA
1 TTAA
6608390 TTTTTTAAAT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
14 10 0.59
15 7 0.41
ACGTcount: A:0.61, C:0.03, G:0.00, T:0.36
Consensus pattern (15 bp):
TTAAAAATTATAAAA
Found at i:6608466 original size:38 final size:37
Alignment explanation
Indices: 6608391--6608467 Score: 104
Period size: 37 Copynumber: 2.1 Consensus size: 37
6608381 TAAAATTAAT
*
6608391 TTTTTAAATTAAAATTAAAAATATTAATATTTCAATA
1 TTTTTAAATTAAAATTAAAAATATTAATATTTAAATA
6608428 TTTTTAAATTATAAA-TAAAAA-ATTAATATTTTAAAATA
1 TTTTTAAATTA-AAATTAAAAATATTAATA-TTT-AAATA
6608466 TT
1 TT
6608468 AATTTTTAAA
Statistics
Matches: 36, Mismatches: 1, Indels: 5
0.86 0.02 0.12
Matches are distributed among these distances:
36 7 0.19
37 20 0.56
38 9 0.25
ACGTcount: A:0.52, C:0.01, G:0.00, T:0.47
Consensus pattern (37 bp):
TTTTTAAATTAAAATTAAAAATATTAATATTTAAATA
Found at i:6608474 original size:15 final size:16
Alignment explanation
Indices: 6608443--6608484 Score: 59
Period size: 15 Copynumber: 2.7 Consensus size: 16
6608433 AAATTATAAA
*
6608443 TAAAAAATTAATATTT
1 TAAAATATTAATATTT
6608459 TAAAATATTAAT-TTT
1 TAAAATATTAATATTT
*
6608474 TAAATTATTAA
1 TAAAATATTAA
6608485 GTGAAATTTA
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
15 13 0.54
16 11 0.46
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (16 bp):
TAAAATATTAATATTT
Found at i:6608791 original size:17 final size:18
Alignment explanation
Indices: 6608769--6608815 Score: 51
Period size: 17 Copynumber: 2.6 Consensus size: 18
6608759 AACAATTATC
6608769 AATATTTTAATCAT-AAT
1 AATATTTTAATCATAAAT
* *
6608786 AATATTTAAATTATAAAT
1 AATATTTTAATCATAAAT
*
6608804 AAAATATTTAAT
1 AATAT-TTTAAT
6608816 ATTTAATATT
Statistics
Matches: 24, Mismatches: 4, Indels: 2
0.80 0.13 0.07
Matches are distributed among these distances:
17 12 0.50
18 7 0.29
19 5 0.21
ACGTcount: A:0.53, C:0.02, G:0.00, T:0.45
Consensus pattern (18 bp):
AATATTTTAATCATAAAT
Found at i:6608865 original size:153 final size:152
Alignment explanation
Indices: 6608558--6608841 Score: 353
Period size: 153 Copynumber: 1.8 Consensus size: 152
6608548 AGGTTCAAGT
* *
6608558 TTTAATTATAAATTATAAAAA-AATAATATTTAAAATTTAAAAATAAATTGAAAATATCAATATT
1 TTTAATT-TATATTATAAAAATAATAATATTTAAAATTTAAAAATAAATTAAAAATATCAATATT
* * * * ***
6608622 TTAATCATAATAATATTAAAATTATACATAAAGTATTAATATATAAATTATCAATTATTGTTATT
65 TTAATCATAATAATATTAAAATTATAAATAAAATATTAATATATAAATTATAAATGATAACTATT
6608687 TAAAAATTAAAATAATAATAAAAA
130 TAAAAATTAAAATAAT-ATAAAAA
*
6608711 TTTAATTTATATTATAAAAATAAT-AT-TTTAAAA-TTACAAAATTAATTAAACAATTATCAATA
1 TTTAATTTATATTATAAAAATAATAATATTTAAAATTTA-AAAATAAATTAAA-AA-TATCAATA
* *
6608773 TTTTAATCATAATAATATTTAAATTATAAATAAAATATTTAATATTTAATATT-TAAATGATCAA
63 TTTTAATCATAATAATATTAAAATTATAAATAAAATA-TTAATATATAA-ATTATAAATGAT-AA
6608837 CTATT
125 CTATT
6608842 AATATATTAA
Statistics
Matches: 112, Mismatches: 12, Indels: 12
0.82 0.09 0.09
Matches are distributed among these distances:
150 3 0.03
151 18 0.16
152 16 0.14
153 52 0.46
154 16 0.14
155 7 0.06
ACGTcount: A:0.54, C:0.04, G:0.01, T:0.42
Consensus pattern (152 bp):
TTTAATTTATATTATAAAAATAATAATATTTAAAATTTAAAAATAAATTAAAAATATCAATATTT
TAATCATAATAATATTAAAATTATAAATAAAATATTAATATATAAATTATAAATGATAACTATTT
AAAAATTAAAATAATATAAAAA
Found at i:6609046 original size:129 final size:130
Alignment explanation
Indices: 6608813--6609046 Score: 278
Period size: 129 Copynumber: 1.8 Consensus size: 130
6608803 TAAAATATTT
* *
6608813 AATATTTAATATTTAAATGATCAACTATTAATATATTAAATTAATTCTAAATTATTAATATTTAA
1 AATATTTAATATTTAAATGATCAACTATTAATATATTAAATAAATTATAAATTATTAATATTTAA
* * * * * *
6608878 AAATAAATTAAAATTTTAATTATGTTATAAAATANTTTTAATATTAATGATTAAAGTATAAAGAA
66 AAATAAATTAAAATGTAAATAATATAATAAAATATTTTTAATATTAATGATTAAAGTATAAAGAA
* * * * * *
6608943 AATA-TTAATATTTAAACT-ATTAATTTTTAATATTTTAAATAAATTATACATTATTAATGTTT-
1 AATATTTAATATTTAAA-TGATCAACTATTAATATATTAAATAAATTATAAATTATTAATATTTA
*
6609005 AAAATAAAATTAAAA-GTAAATAATCATAATAACATATTTTTA
65 AAAAT-AAATTAAAATGTAAATAAT-ATAATAAAATATTTTTA
6609047 TTTATAATTT
Statistics
Matches: 86, Mismatches: 15, Indels: 7
0.80 0.14 0.06
Matches are distributed among these distances:
128 11 0.13
129 70 0.81
130 5 0.06
ACGTcount: A:0.50, C:0.03, G:0.03, T:0.44
Consensus pattern (130 bp):
AATATTTAATATTTAAATGATCAACTATTAATATATTAAATAAATTATAAATTATTAATATTTAA
AAATAAATTAAAATGTAAATAATATAATAAAATATTTTTAATATTAATGATTAAAGTATAAAGAA
Found at i:6609081 original size:16 final size:16
Alignment explanation
Indices: 6609044--6609099 Score: 78
Period size: 16 Copynumber: 3.6 Consensus size: 16
6609034 TAACATATTT
* *
6609044 TTATTTATAATTTAAA
1 TTATTAATATTTTAAA
6609060 -TATTAATATTTTAAA
1 TTATTAATATTTTAAA
6609075 TTATTAATATTTTAAA
1 TTATTAATATTTTAAA
*
6609091 TTATAAATA
1 TTATTAATA
6609100 AAATATTTAT
Statistics
Matches: 36, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
15 13 0.36
16 23 0.64
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (16 bp):
TTATTAATATTTTAAA
Found at i:6609119 original size:21 final size:21
Alignment explanation
Indices: 6609032--6609125 Score: 64
Period size: 21 Copynumber: 4.4 Consensus size: 21
6609022 AAATAATCAT
* * *
6609032 AATAACATATTTTTATTTATA
1 AATAAAATATTTATATTTAAA
* * * *
6609053 ATTTAAATATTAATATTTTAA
1 AATAAAATATTTATATTTAAA
* * * *
6609074 ATTATTAATATTT-TAAATTATA
1 AATA-AAATATTTAT-ATTTAAA
6609096 AATAAAATATTTATATTTAAA
1 AATAAAATATTTATATTTAAA
6609117 AATAAAATA
1 AATAAAATA
6609126 AAATTAAATA
Statistics
Matches: 53, Mismatches: 17, Indels: 6
0.70 0.22 0.08
Matches are distributed among these distances:
21 39 0.74
22 14 0.26
ACGTcount: A:0.51, C:0.01, G:0.00, T:0.48
Consensus pattern (21 bp):
AATAAAATATTTATATTTAAA
Found at i:6616017 original size:31 final size:30
Alignment explanation
Indices: 6615981--6616039 Score: 75
Period size: 30 Copynumber: 1.9 Consensus size: 30
6615971 TTTAAGAATC
6615981 GAATGAATAAAACAT-TAATTTTTAAAAATAT
1 GAATG-ATAAAA-ATGTAATTTTTAAAAATAT
* *
6616012 GAATGATTAAAATGTAATTTTTCAAAAT
1 GAATGATAAAAATGTAATTTTTAAAAAT
6616040 TAAAAATAAA
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
29 2 0.08
30 18 0.72
31 5 0.20
ACGTcount: A:0.51, C:0.03, G:0.08, T:0.37
Consensus pattern (30 bp):
GAATGATAAAAATGTAATTTTTAAAAATAT
Found at i:6616394 original size:6 final size:6
Alignment explanation
Indices: 6616383--6616409 Score: 54
Period size: 6 Copynumber: 4.5 Consensus size: 6
6616373 AAAATGACAC
6616383 CCCCTT CCCCTT CCCCTT CCCCTT CCC
1 CCCCTT CCCCTT CCCCTT CCCCTT CCC
6616410 TTTCAATTGT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 21 1.00
ACGTcount: A:0.00, C:0.70, G:0.00, T:0.30
Consensus pattern (6 bp):
CCCCTT
Found at i:6632292 original size:18 final size:17
Alignment explanation
Indices: 6632250--6632362 Score: 60
Period size: 18 Copynumber: 6.8 Consensus size: 17
6632240 ACCAAAAGTG
*
6632250 CCTGAGTTG-CC-AAAG
1 CCTGAGTTGCCCAAAAT
*
6632265 CCTGAATTGCCCAAAACT
1 CCTGAGTTGCCCAAAA-T
6632283 CCTGAGTTG-CCAAAAGT
1 CCTGAGTTGCCCAAAA-T
* * *
6632300 GCCAGAGCTG-CC-AAAG
1 -CCTGAGTTGCCCAAAAT
* *
6632316 CCTGAATTGCCCAAAGTT
1 CCTGAGTTGCCCAAA-AT
*
6632334 CCTGAGTTG-CC-AAAG
1 CCTGAGTTGCCCAAAAT
*
6632349 CCTGAGTTACCCAA
1 CCTGAGTTGCCCAA
6632363 GTTGCCTGAA
Statistics
Matches: 73, Mismatches: 16, Indels: 16
0.70 0.15 0.15
Matches are distributed among these distances:
15 22 0.30
16 8 0.11
17 18 0.25
18 25 0.34
ACGTcount: A:0.29, C:0.29, G:0.21, T:0.20
Consensus pattern (17 bp):
CCTGAGTTGCCCAAAAT
Found at i:6632317 original size:51 final size:51
Alignment explanation
Indices: 6632241--6632347 Score: 178
Period size: 51 Copynumber: 2.1 Consensus size: 51
6632231 GCCAGAAATA
* *
6632241 CCAAAAGTGCCTGAGTTGCCAAAGCCTGAATTGCCCAAAACTCCTGAGTTG
1 CCAAAAGTGCCAGAGCTGCCAAAGCCTGAATTGCCCAAAACTCCTGAGTTG
**
6632292 CCAAAAGTGCCAGAGCTGCCAAAGCCTGAATTGCCCAAAGTTCCTGAGTTG
1 CCAAAAGTGCCAGAGCTGCCAAAGCCTGAATTGCCCAAAACTCCTGAGTTG
6632343 CCAAA
1 CCAAA
6632348 GCCTGAGTTA
Statistics
Matches: 52, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
51 52 1.00
ACGTcount: A:0.31, C:0.28, G:0.21, T:0.20
Consensus pattern (51 bp):
CCAAAAGTGCCAGAGCTGCCAAAGCCTGAATTGCCCAAAACTCCTGAGTTG
Found at i:6632320 original size:33 final size:33
Alignment explanation
Indices: 6632283--6632596 Score: 301
Period size: 33 Copynumber: 9.3 Consensus size: 33
6632273 GCCCAAAACT
* * *
6632283 CCTGAGTTGCCAAAAGTGCCAGAGCTGCCAAAG
1 CCTGAATTGCCAAAAGTTCCAGAGTTGCCAAAG
* *
6632316 CCTGAATTGCCCAAAGTTCCTGAGTTGCCAAAG
1 CCTGAATTGCCAAAAGTTCCAGAGTTGCCAAAG
* * * * * * *
6632349 CCTGAGTTACC-CAAGTTGCCTGAATTGCAAAAA
1 CCTGAATTGCCAAAAGTT-CCAGAGTTGCCAAAG
** **
6632382 CCTGAAGAAG-TGAAAGTTCCAGAGTTGCCCAAAG
1 CCTGAA-TTGCCAAAAGTTCCAGAGTTG-CCAAAG
*
6632416 CTCCTGAATTGCCAAAAGTTCCGGAGTTGCCAAAG
1 --CCTGAATTGCCAAAAGTTCCAGAGTTGCCAAAG
* *
6632451 CCTGAATCGCCCAAAGTTCCAGAGTTGCCCAAAG
1 CCTGAATTGCCAAAAGTTCCAGAGTTG-CCAAAG
*
6632485 CTCCTGAATTGCCAAAAGTTCCGGAGTTGCCAAAG
1 --CCTGAATTGCCAAAAGTTCCAGAGTTGCCAAAG
* * *
6632520 CCTGAATCGCCCAAAGTTCCAGAGTTGCCAAAA
1 CCTGAATTGCCAAAAGTTCCAGAGTTGCCAAAG
* *
6632553 CCTGAATTGCCTAAAGTTCCAGAGTTACCAAAG
1 CCTGAATTGCCAAAAGTTCCAGAGTTGCCAAAG
6632586 CCT-AAGTTGCC
1 CCTGAA-TTGCC
6632597 CAAGCCAGAA
Statistics
Matches: 230, Mismatches: 40, Indels: 22
0.79 0.14 0.08
Matches are distributed among these distances:
32 7 0.03
33 151 0.66
34 15 0.07
35 13 0.06
36 44 0.19
ACGTcount: A:0.31, C:0.27, G:0.22, T:0.21
Consensus pattern (33 bp):
CCTGAATTGCCAAAAGTTCCAGAGTTGCCAAAG
Found at i:6632338 original size:69 final size:69
Alignment explanation
Indices: 6632271--6632599 Score: 352
Period size: 69 Copynumber: 4.9 Consensus size: 69
6632261 AAAGCCTGAA
* * *
6632271 TTGCCCAAAACTCCTGAGTTGCCAAAAGTGCCAGAGCTGCCAAAGCCTGAATTGCCCAAAGTTCC
1 TTGCCCAAAACTCCTGAATTGCCAAAAGTTCCAGAGTTGCCAAAGCCTGAATTGCCCAAAGTTCC
*
6632336 TGAG
66 AGAG
* * * * * * * * ** **
6632340 TTG-CC-AAA-GCCTGAGTTACC-CAAGTTGCCTGAATTGCAAAAACCTGAAGAAG-TGAAAGTT
1 TTGCCCAAAACTCCTGAATTGCCAAAAGTT-CCAGAGTTGCCAAAGCCTGAA-TTGCCCAAAGTT
6632400 CCAGAG
64 CCAGAG
* * *
6632406 TTGCCCAAAGCTCCTGAATTGCCAAAAGTTCCGGAGTTGCCAAAGCCTGAATCGCCCAAAGTTCC
1 TTGCCCAAAACTCCTGAATTGCCAAAAGTTCCAGAGTTGCCAAAGCCTGAATTGCCCAAAGTTCC
6632471 AGAG
66 AGAG
* * *
6632475 TTGCCCAAAGCTCCTGAATTGCCAAAAGTTCCGGAGTTGCCAAAGCCTGAATCGCCCAAAGTTCC
1 TTGCCCAAAACTCCTGAATTGCCAAAAGTTCCAGAGTTGCCAAAGCCTGAATTGCCCAAAGTTCC
6632540 AGAG
66 AGAG
* *
6632544 TTG-CCAAAA--CCTGAATTGCCTAAAGTTCCAGAGTTACCAAAGCCT-AAGTTGCCCAA
1 TTGCCCAAAACTCCTGAATTGCCAAAAGTTCCAGAGTTGCCAAAGCCTGAA-TTGCCCAA
6632600 GCCAGAACTA
Statistics
Matches: 220, Mismatches: 32, Indels: 19
0.81 0.12 0.07
Matches are distributed among these distances:
65 6 0.03
66 80 0.36
67 6 0.03
68 10 0.05
69 113 0.51
70 5 0.02
ACGTcount: A:0.31, C:0.27, G:0.21, T:0.21
Consensus pattern (69 bp):
TTGCCCAAAACTCCTGAATTGCCAAAAGTTCCAGAGTTGCCAAAGCCTGAATTGCCCAAAGTTCC
AGAG
Found at i:6632370 original size:51 final size:49
Alignment explanation
Indices: 6632249--6632557 Score: 155
Period size: 51 Copynumber: 6.1 Consensus size: 49
6632239 TACCAAAAGT
* * **
6632249 GCCTGAGTTGCCAA-AGCCTGAATTGCCCAAAACTCCTGAGTTGCCAAAA
1 GCCTGAGTTCCCAAGTGCCTGAATTGCCCAAAGTTCCTGAGTTGCC-AAA
* * * *
6632298 GTGCCAGAGCTGCCAA-AGCCTGAATTGCCCAAAGTTCCTGAGTTGCCAAA
1 --GCCTGAGTTCCCAAGTGCCTGAATTGCCCAAAGTTCCTGAGTTGCCAAA
** ** **
6632348 GCCTGAGTTACCCAAGTTGCCTGAATTG--CAAA-AACCTGAAGAAGTGAAA
1 GCCTGAGTT-CCCAAG-TGCCTGAATTGCCCAAAGTTCCTG-AGTTGCCAAA
* * *
6632397 GTTCCAGAGTTGCCCAAAGCT-CCTGAATTGCCAAAAGTTCCGGAGTTGCCAAA
1 G--CCTGAGTT-CCC-AAG-TGCCTGAATTGCCCAAAGTTCCTGAGTTGCCAAA
* * * * * * *
6632450 GCCTGAATCGCCCAAAGTTCCAGAGTTGCCCAAAGCTCCTGAATTGCCAAAA
1 GCCTGAGT-TCCC-AAGTGCCTGAATTGCCCAAAGTTCCTGAGTTGCC-AAA
* * * * *
6632502 GTTCCGGAGTTGCCAA-AGCCTGAATCGCCCAAAGTTCCAGAGTTGCCAAA
1 G--CCTGAGTTCCCAAGTGCCTGAATTGCCCAAAGTTCCTGAGTTGCCAAA
*
6632552 ACCTGA
1 GCCTGA
6632558 ATTGCCTAAA
Statistics
Matches: 195, Mismatches: 48, Indels: 33
0.71 0.17 0.12
Matches are distributed among these distances:
48 15 0.08
49 15 0.08
50 7 0.04
51 128 0.66
52 10 0.05
53 12 0.06
54 8 0.04
ACGTcount: A:0.30, C:0.27, G:0.22, T:0.20
Consensus pattern (49 bp):
GCCTGAGTTCCCAAGTGCCTGAATTGCCCAAAGTTCCTGAGTTGCCAAA
Found at i:6632427 original size:18 final size:18
Alignment explanation
Indices: 6632394--6632572 Score: 133
Period size: 18 Copynumber: 10.4 Consensus size: 18
6632384 TGAAGAAGTG
* *
6632394 AAAGTTCCAGAGTTGCCC
1 AAAGTTCCTGAATTGCCC
* *
6632412 AAAGCTCCTGAATTGCCA
1 AAAGTTCCTGAATTGCCC
* *
6632430 AAAGTTCCGGAGTTG-CC
1 AAAGTTCCTGAATTGCCC
*
6632447 AAAG--CCTGAATCGCCC
1 AAAGTTCCTGAATTGCCC
* *
6632463 AAAGTTCCAGAGTTGCCC
1 AAAGTTCCTGAATTGCCC
* *
6632481 AAAGCTCCTGAATTGCCA
1 AAAGTTCCTGAATTGCCC
* *
6632499 AAAGTTCCGGAGTTG-CC
1 AAAGTTCCTGAATTGCCC
*
6632516 AAAG--CCTGAATCGCCC
1 AAAGTTCCTGAATTGCCC
* *
6632532 AAAGTTCCAGAGTTG-CC
1 AAAGTTCCTGAATTGCCC
* *
6632549 AAA--ACCTGAATTGCCT
1 AAAGTTCCTGAATTGCCC
6632565 AAAGTTCC
1 AAAGTTCC
6632573 AGAGTTACCA
Statistics
Matches: 119, Mismatches: 33, Indels: 18
0.70 0.19 0.11
Matches are distributed among these distances:
15 19 0.16
16 16 0.13
17 15 0.13
18 69 0.58
ACGTcount: A:0.30, C:0.28, G:0.21, T:0.21
Consensus pattern (18 bp):
AAAGTTCCTGAATTGCCC
Found at i:6634017 original size:49 final size:49
Alignment explanation
Indices: 6633903--6634017 Score: 121
Period size: 49 Copynumber: 2.3 Consensus size: 49
6633893 AGGCATTAAG
6633903 TTATTTGTTTAAAATCTTAGCTATTTGTTTTTCTCTTGACAATAATACAA
1 TTATTTGTTTAAAAT-TTAGCTATTTGTTTTTCTCTTGACAATAATACAA
* * * *
6633953 TT-GTTGTTTACAATTTCAAG-TATTTGTTCTTT-T-TTGAGAATAATATAA
1 TTATTTGTTTAAAATTT--AGCTATTTGTT-TTTCTCTTGACAATAATACAA
*
6634001 TTATTTTTTTAAAATTT
1 TTATTTGTTTAAAATTT
6634018 TTTTTCAAAT
Statistics
Matches: 54, Mismatches: 7, Indels: 9
0.77 0.10 0.13
Matches are distributed among these distances:
48 17 0.31
49 30 0.56
50 7 0.13
ACGTcount: A:0.30, C:0.08, G:0.09, T:0.54
Consensus pattern (49 bp):
TTATTTGTTTAAAATTTAGCTATTTGTTTTTCTCTTGACAATAATACAA
Found at i:6636413 original size:33 final size:33
Alignment explanation
Indices: 6636376--6636536 Score: 214
Period size: 33 Copynumber: 4.9 Consensus size: 33
6636366 ACCGAAAGTG
6636376 CCTGAGTTGCCAAAGCCTGAATTGCCCAAAACT
1 CCTGAGTTGCCAAAGCCTGAATTGCCCAAAACT
* **
6636409 CCTGAGTTGCCAAAGCCTGAATTCCCCAAAGTT
1 CCTGAGTTGCCAAAGCCTGAATTGCCCAAAACT
*
6636442 CCTGAGTTGCCTAAGCCTGAATTGCCCAAAACT
1 CCTGAGTTGCCAAAGCCTGAATTGCCCAAAACT
* * * **
6636475 TCTGAGTTGCCAAAGTCTGAATTGCCCATAGTT
1 CCTGAGTTGCCAAAGCCTGAATTGCCCAAAACT
* * *
6636508 CCTGAGTCGCCAAAGCCTGAGTTACCCAA
1 CCTGAGTTGCCAAAGCCTGAATTGCCCAA
6636537 GTTGTCTGAA
Statistics
Matches: 109, Mismatches: 19, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
33 109 1.00
ACGTcount: A:0.27, C:0.29, G:0.19, T:0.24
Consensus pattern (33 bp):
CCTGAGTTGCCAAAGCCTGAATTGCCCAAAACT
Found at i:6636418 original size:18 final size:17
Alignment explanation
Indices: 6636391--6636502 Score: 65
Period size: 15 Copynumber: 6.8 Consensus size: 17
6636381 GTTGCCAAAG
6636391 CCTGAATTGCCCAAAACT
1 CCTGAATTGCCCAAAA-T
* *
6636409 CCTGAGTTG-CC-AAAG
1 CCTGAATTGCCCAAAAT
* *
6636424 CCTGAATTCCCCAAAGTT
1 CCTGAATTGCCCAAA-AT
* * *
6636442 CCTGAGTTG-CC-TAAG
1 CCTGAATTGCCCAAAAT
6636457 CCTGAATTGCCCAAAACT
1 CCTGAATTGCCCAAAA-T
* * *
6636475 TCTGAGTTG-CCAAAGT
1 CCTGAATTGCCCAAAAT
6636491 -CTGAATTGCCCA
1 CCTGAATTGCCCA
6636503 TAGTTCCTGA
Statistics
Matches: 69, Mismatches: 18, Indels: 16
0.67 0.17 0.16
Matches are distributed among these distances:
15 22 0.32
16 12 0.17
17 13 0.19
18 22 0.32
ACGTcount: A:0.28, C:0.29, G:0.18, T:0.25
Consensus pattern (17 bp):
CCTGAATTGCCCAAAAT
Found at i:6636461 original size:66 final size:66
Alignment explanation
Indices: 6636370--6636536 Score: 253
Period size: 66 Copynumber: 2.5 Consensus size: 66
6636360 AGAAATACCG
*
6636370 AAAGTGCCTGAGTTGCCAAAGCCTGAATTGCCCAAAACTCCTGAGTTGCCAAAGCCTGAATTCCC
1 AAAGTTCCTGAGTTGCCAAAGCCTGAATTGCCCAAAACTCCTGAGTTGCCAAAGCCTGAATTCCC
6636435 C
66 C
* * * *
6636436 AAAGTTCCTGAGTTGCCTAAGCCTGAATTGCCCAAAACTTCTGAGTTGCCAAAGTCTGAATTGCC
1 AAAGTTCCTGAGTTGCCAAAGCCTGAATTGCCCAAAACTCCTGAGTTGCCAAAGCCTGAATTCCC
6636501 C
66 C
* * * *
6636502 ATAGTTCCTGAGTCGCCAAAGCCTGAGTTACCCAA
1 AAAGTTCCTGAGTTGCCAAAGCCTGAATTGCCCAA
6636537 GTTGTCTGAA
Statistics
Matches: 91, Mismatches: 10, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
66 91 1.00
ACGTcount: A:0.28, C:0.28, G:0.20, T:0.24
Consensus pattern (66 bp):
AAAGTTCCTGAGTTGCCAAAGCCTGAATTGCCCAAAACTCCTGAGTTGCCAAAGCCTGAATTCCC
C
Found at i:6636560 original size:99 final size:99
Alignment explanation
Indices: 6636377--6636561 Score: 246
Period size: 99 Copynumber: 1.9 Consensus size: 99
6636367 CCGAAAGTGC
* *
6636377 CTGAGTTGCCAAAGCCTGAATTGCCCAAAACTCCTGAGTTGCCAAAGCCTGAATTCCCCAAAGTT
1 CTGAGTTGCCAAAGCCTGAATTGCCCAAAACTCCTGAGTCGCCAAAGCCTGAATTACCCAAAGTT
* ** *
6636442 CCTGAGTTGCCTAAGCCTGAATTGCCCAAAACTT
66 CCTGAATTGCAAAAACCTGAATTGCCCAAAACTT
* * ** *
6636476 CTGAGTTGCCAAAGTCTGAATTGCCCATAGTTCCTGAGTCGCCAAAGCCTGAGTTACCC-AAGTT
1 CTGAGTTGCCAAAGCCTGAATTGCCCAAAACTCCTGAGTCGCCAAAGCCTGAATTACCCAAAGTT
*
6636540 GTCTGAATTGCAAAAACCTGAA
66 -CCTGAATTGCAAAAACCTGAA
6636562 GAAGTAAAAG
Statistics
Matches: 73, Mismatches: 12, Indels: 2
0.84 0.14 0.02
Matches are distributed among these distances:
98 5 0.07
99 68 0.93
ACGTcount: A:0.29, C:0.27, G:0.19, T:0.25
Consensus pattern (99 bp):
CTGAGTTGCCAAAGCCTGAATTGCCCAAAACTCCTGAGTCGCCAAAGCCTGAATTACCCAAAGTT
CCTGAATTGCAAAAACCTGAATTGCCCAAAACTT
Found at i:6636623 original size:51 final size:50
Alignment explanation
Indices: 6636568--6636673 Score: 133
Period size: 51 Copynumber: 2.1 Consensus size: 50
6636558 TGAAGAAGTA
* * * *
6636568 AAAGCTCCAGAGTTTCCA-ACTCCTGAATTGCCTACAGTTCCAGAGTTGCCC
1 AAAGCTCCAGAGTTGCCAGA-GCCTGAATTGCCAAAAGTTCCAGAGTTG-CC
* *
6636619 AAAGCTCCTGAGTTGCCAGAGCCTGAATTGCCAAAAGTTCCTGAGTTGCC
1 AAAGCTCCAGAGTTGCCAGAGCCTGAATTGCCAAAAGTTCCAGAGTTGCC
6636669 AAAGC
1 AAAGC
6636674 CTGAATTGCC
Statistics
Matches: 48, Mismatches: 6, Indels: 3
0.84 0.11 0.05
Matches are distributed among these distances:
50 7 0.15
51 40 0.83
52 1 0.02
ACGTcount: A:0.27, C:0.28, G:0.21, T:0.24
Consensus pattern (50 bp):
AAAGCTCCAGAGTTGCCAGAGCCTGAATTGCCAAAAGTTCCAGAGTTGCC
Found at i:6636631 original size:18 final size:18
Alignment explanation
Indices: 6636587--6636673 Score: 65
Period size: 18 Copynumber: 5.1 Consensus size: 18
6636577 GAGTTTCCAA
* * *
6636587 CTCCTGAATTGCCTACAG
1 CTCCTGAGTTGCCCAAAG
* *
6636605 TTCCAGAGTTGCCCAAAG
1 CTCCTGAGTTGCCCAAAG
*
6636623 CTCCTGAGTTG-CCAGAG
1 CTCCTGAGTTGCCCAAAG
* *
6636640 --CCTGAATTGCCAAAAG
1 CTCCTGAGTTGCCCAAAG
*
6636656 TTCCTGAGTTG-CCAAAG
1 CTCCTGAGTTGCCCAAAG
6636673 C
1 C
6636674 CTGAATTGCC
Statistics
Matches: 52, Mismatches: 14, Indels: 7
0.71 0.19 0.10
Matches are distributed among these distances:
15 8 0.15
16 4 0.08
17 10 0.19
18 30 0.58
ACGTcount: A:0.25, C:0.29, G:0.22, T:0.24
Consensus pattern (18 bp):
CTCCTGAGTTGCCCAAAG
Found at i:6636649 original size:15 final size:15
Alignment explanation
Indices: 6636625--6636683 Score: 64
Period size: 15 Copynumber: 3.7 Consensus size: 15
6636615 GCCCAAAGCT
* *
6636625 CCTGAGTTGCCAGAG
1 CCTGAATTGCCAAAG
6636640 CCTGAATTGCCAAAAG
1 CCTGAATTGCC-AAAG
*
6636656 TTCCTGAGTTGCCAAAG
1 --CCTGAATTGCCAAAG
6636673 CCTGAATTGCC
1 CCTGAATTGCC
6636684 TAAGTTGCCT
Statistics
Matches: 37, Mismatches: 4, Indels: 6
0.79 0.09 0.13
Matches are distributed among these distances:
15 20 0.54
16 3 0.08
17 4 0.11
18 10 0.27
ACGTcount: A:0.25, C:0.27, G:0.24, T:0.24
Consensus pattern (15 bp):
CCTGAATTGCCAAAG
Found at i:6636702 original size:66 final size:66
Alignment explanation
Indices: 6636655--6636976 Score: 455
Period size: 66 Copynumber: 4.9 Consensus size: 66
6636645 ATTGCCAAAA
* * *
6636655 GTTCCTGAGTTGCCAAAGCCTGAATTGCCTAAGTTGCCTGACATGCCAAAACCTGAAGAACCCAA
1 GTTCCTGAGTTACCAAAGCCTGAGTTGCCTAAGCTGCCTGACATGCCAAAACCTGAAGAACCCAA
6636720 G
66 G
6636721 GTTCCTGAGTTACCAAAGCCTGAGTTGCCTAAGCTGCCTGACATGCCAAAACCTGAAGAACCCAA
1 GTTCCTGAGTTACCAAAGCCTGAGTTGCCTAAGCTGCCTGACATGCCAAAACCTGAAGAACCCAA
6636786 G
66 G
* * *
6636787 GTTCCTGAGTTACCAAAGCCTGAGTTGCCTACGCTGCCTGACCTGCCAAAACCCGAAGAACCCAA
1 GTTCCTGAGTTACCAAAGCCTGAGTTGCCTAAGCTGCCTGACATGCCAAAACCTGAAGAACCCAA
6636852 G
66 G
* *
6636853 GTTCCTGAGTTACCAAAGCCTGAGTTGCCTAAGCTGCCTGACCTGCCAAAACCCGAAGAACCCAA
1 GTTCCTGAGTTACCAAAGCCTGAGTTGCCTAAGCTGCCTGACATGCCAAAACCTGAAGAACCCAA
*
6636918 A
66 G
* * * * * ** * * * * *
6636919 GTACCGGAGTTGCCCAAGCCAGAACTACCCAAGTTGCCTGACTTGCCAAACCCTGAAG
1 GTTCCTGAGTTACCAAAGCCTGAGTTGCCTAAGCTGCCTGACATGCCAAAACCTGAAG
6636977 CGCCAAAGGA
Statistics
Matches: 235, Mismatches: 21, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
66 235 1.00
ACGTcount: A:0.29, C:0.31, G:0.21, T:0.19
Consensus pattern (66 bp):
GTTCCTGAGTTACCAAAGCCTGAGTTGCCTAAGCTGCCTGACATGCCAAAACCTGAAGAACCCAA
G
Found at i:6636743 original size:150 final size:150
Alignment explanation
Indices: 6636463--6636751 Score: 364
Period size: 150 Copynumber: 1.9 Consensus size: 150
6636453 TAAGCCTGAA
* * * *
6636463 TTGCCCAAAACTTCTGAGTTGCCAAAGTCTGAATTGCCCATAGTTCCTGAGTCGCCAAAGCCTGA
1 TTGCCCAAAACTCCTGAGTTGCCAAAGCCTGAATTGCCAAAAGTTCCTGAGTCGCCAAAGCCTGA
* * ** * **
6636528 GTTACCCAAGTTGTCTGAATTGCAAAAACCTGAAGAAGTAAAAGCTCCAGAGTTTCCAACTCCTG
66 ATTACCCAAGTTGCCTGAATTGCAAAAACCTGAAGAACCAAAAGCTCCAGAGTTACCAAAGCCTG
6636593 AATTGCCTACAGTTCCAGAG
131 AATTGCCTACAGTTCCAGAG
* * *
6636613 TTGCCCAAAGCTCCTGAGTTGCCAGAGCCTGAATTGCCAAAAGTTCCTGAGTTGCCAAAGCCTGA
1 TTGCCCAAAACTCCTGAGTTGCCAAAGCCTGAATTGCCAAAAGTTCCTGAGTCGCCAAAGCCTGA
* * * * * * *
6636678 ATTGCCTAAGTTGCCTGACA-TGCCAAAACCTGAAGAACCCAAGGTTCCTGAGTTACCAAAGCCT
66 ATTACCCAAGTTGCCTGA-ATTGCAAAAACCTGAAGAACCAAAAGCTCCAGAGTTACCAAAGCCT
*
6636742 GAGTTGCCTA
130 GAATTGCCTA
6636752 AGCTGCCTGA
Statistics
Matches: 116, Mismatches: 22, Indels: 2
0.83 0.16 0.01
Matches are distributed among these distances:
150 115 0.99
151 1 0.01
ACGTcount: A:0.29, C:0.26, G:0.20, T:0.24
Consensus pattern (150 bp):
TTGCCCAAAACTCCTGAGTTGCCAAAGCCTGAATTGCCAAAAGTTCCTGAGTCGCCAAAGCCTGA
ATTACCCAAGTTGCCTGAATTGCAAAAACCTGAAGAACCAAAAGCTCCAGAGTTACCAAAGCCTG
AATTGCCTACAGTTCCAGAG
Found at i:6636817 original size:216 final size:216
Alignment explanation
Indices: 6636397--6636818 Score: 501
Period size: 216 Copynumber: 2.0 Consensus size: 216
6636387 AAAGCCTGAA
* *
6636397 TTGCCCAAAACTCCTGAGTTGCCAAAGCCTGAATTCCCCAAAGTTCCTGAGTTGCCTAAGCCTGA
1 TTGCCCAAAACTCCTGAGTTGCCAAAGCCTGAATTCCCAAAAGTTCCTGAGTTGCCAAAGCCTGA
** ** *** *
6636462 ATTGCCCAAAACTTCTGAGTTGCCAAAGTCTGAATTGCCCATAGTTCCTGAGTCGCCAAAGCCTG
66 ATTGCCCAAAACTTCTGACATGCCAAAACCTGAAGAACCCATAGTTCCTGAGTCACCAAAGCCTG
* * ** * **
6636527 AGTTACCCAAGTTGTCTGAATTGCAAAAACCTGAAGAAGTAAAAGCTCCAGAGTTTCCAACTCCT
131 AGTTACCCAAGCTGCCTGAATTGCAAAAACCTGAAGAACCAAAAGCTCCAGAGTTACCAAAGCCT
6636592 GAATTGCCTACAGTTCCAGAG
196 GAATTGCCTACAGTTCCAGAG
* * *
6636613 TTGCCCAAAGCTCCTGAGTTGCCAGAGCCTGAATTGCCAAAAGTTCCTGAGTTGCCAAAGCCTGA
1 TTGCCCAAAACTCCTGAGTTGCCAAAGCCTGAATTCCCAAAAGTTCCTGAGTTGCCAAAGCCTGA
* * *
6636678 ATTG-CC-TAAGTTGCCTGACATGCCAAAACCTGAAGAACCCA-AGGTTCCTGAGTTACCAAAGC
66 ATTGCCCAAAACTT--CTGACATGCCAAAACCTGAAGAACCCATA-GTTCCTGAGTCACCAAAGC
* * * * * * *
6636740 CTGAGTTGCCTAAGCTGCCTGACA-TGCCAAAACCTGAAGAACCCAAGGTTCCTGAGTTACCAAA
128 CTGAGTTACCCAAGCTGCCTGA-ATTGCAAAAACCTGAAGAACCAAAAGCTCCAGAGTTACCAAA
*
6636804 GCCTGAGTTGCCTAC
192 GCCTGAATTGCCTAC
6636819 GCTGCCTGAC
Statistics
Matches: 171, Mismatches: 31, Indels: 8
0.81 0.15 0.04
Matches are distributed among these distances:
214 4 0.02
215 3 0.02
216 163 0.95
217 1 0.01
ACGTcount: A:0.29, C:0.27, G:0.20, T:0.23
Consensus pattern (216 bp):
TTGCCCAAAACTCCTGAGTTGCCAAAGCCTGAATTCCCAAAAGTTCCTGAGTTGCCAAAGCCTGA
ATTGCCCAAAACTTCTGACATGCCAAAACCTGAAGAACCCATAGTTCCTGAGTCACCAAAGCCTG
AGTTACCCAAGCTGCCTGAATTGCAAAAACCTGAAGAACCAAAAGCTCCAGAGTTACCAAAGCCT
GAATTGCCTACAGTTCCAGAG
Found at i:6636902 original size:33 final size:33
Alignment explanation
Indices: 6636610--6636902 Score: 155
Period size: 33 Copynumber: 8.9 Consensus size: 33
6636600 TACAGTTCCA
* * *
6636610 GAGTTGCCCAAAGCT-CCTGAGTTGCCAGAGCCT
1 GAGTTG-CCTAAGCTGCCTGACTTGCCAAAGCCT
* * * *
6636643 GAATTGCCAAAAG-TTCCTGAGTTGCCAAAGCCT
1 GAGTTGCC-TAAGCTGCCTGACTTGCCAAAGCCT
* * * *
6636676 GAATTGCCTAAGTTGCCTGACATGCCAAAACCT
1 GAGTTGCCTAAGCTGCCTGACTTGCCAAAGCCT
** * * * * *
6636709 GAAG-AACCCAAGGTTCCTGAGTTACCAAAGCCT
1 G-AGTTGCCTAAGCTGCCTGACTTGCCAAAGCCT
* *
6636742 GAGTTGCCTAAGCTGCCTGACATGCCAAAACCT
1 GAGTTGCCTAAGCTGCCTGACTTGCCAAAGCCT
** * * * * *
6636775 GAAG-AACCCAAGGTTCCTGAGTTACCAAAGCCT
1 G-AGTTGCCTAAGCTGCCTGACTTGCCAAAGCCT
* * * *
6636808 GAGTTGCCTACGCTGCCTGACCTGCCAAAACCC
1 GAGTTGCCTAAGCTGCCTGACTTGCCAAAGCCT
** * * * * *
6636841 GAAG-AACCCAAGGTTCCTGAGTTACCAAAGCCT
1 G-AGTTGCCTAAGCTGCCTGACTTGCCAAAGCCT
*
6636874 GAGTTGCCTAAGCTGCCTGACCTGCCAAA
1 GAGTTGCCTAAGCTGCCTGACTTGCCAAA
6636903 ACCCGAAGAA
Statistics
Matches: 186, Mismatches: 65, Indels: 18
0.69 0.24 0.07
Matches are distributed among these distances:
32 12 0.06
33 169 0.91
34 5 0.03
ACGTcount: A:0.28, C:0.29, G:0.22, T:0.20
Consensus pattern (33 bp):
GAGTTGCCTAAGCTGCCTGACTTGCCAAAGCCT
Found at i:6640391 original size:33 final size:33
Alignment explanation
Indices: 6640372--6640449 Score: 111
Period size: 33 Copynumber: 2.4 Consensus size: 33
6640362 TACATGAGTT
*
6640372 GCCAAAGCCAGAGGTGCCTAAAGCAACTGAATC
1 GCCAAAGCCAGAGGTGCCTAAATCAACTGAATC
** * *
6640405 GCCAAAGCCAGAGGTGCCTAAATGGACTAAATG
1 GCCAAAGCCAGAGGTGCCTAAATCAACTGAATC
6640438 GCCAAAGCCAGA
1 GCCAAAGCCAGA
6640450 AGAACCTAAG
Statistics
Matches: 40, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
33 40 1.00
ACGTcount: A:0.37, C:0.26, G:0.26, T:0.12
Consensus pattern (33 bp):
GCCAAAGCCAGAGGTGCCTAAATCAACTGAATC
Found at i:6641997 original size:17 final size:17
Alignment explanation
Indices: 6641969--6642002 Score: 52
Period size: 17 Copynumber: 2.0 Consensus size: 17
6641959 CAAATATTTG
6641969 AACTTCATAATCATAATT
1 AACTTCATAATC-TAATT
6641987 AACTT-ATAATCTAATT
1 AACTTCATAATCTAATT
6642003 GGTACCTCGA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 5 0.31
17 6 0.38
18 5 0.31
ACGTcount: A:0.44, C:0.15, G:0.00, T:0.41
Consensus pattern (17 bp):
AACTTCATAATCTAATT
Found at i:6643245 original size:15 final size:17
Alignment explanation
Indices: 6643225--6643266 Score: 52
Period size: 18 Copynumber: 2.5 Consensus size: 17
6643215 ACCTGAATTT
6643225 CCAGAATTG-CCAAA-G
1 CCAGAATTGCCCAAATG
*
6643240 CCAGAACTGCCCAAATTG
1 CCAGAATTGCCCAAA-TG
6643258 CCAGAATTG
1 CCAGAATTG
6643267 TTTAAGCACT
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
15 8 0.36
16 5 0.23
18 9 0.41
ACGTcount: A:0.36, C:0.29, G:0.19, T:0.17
Consensus pattern (17 bp):
CCAGAATTGCCCAAATG
Found at i:6643436 original size:2 final size:2
Alignment explanation
Indices: 6643429--6643462 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
6643419 TCTAAATTAC
6643429 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
6643463 GTGTGTGTGT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:6643516 original size:2 final size:2
Alignment explanation
Indices: 6643509--6643540 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
6643499 ACNNNNNNNN
6643509 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
6643541 GTGTGTGTGT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:6645556 original size:13 final size:13
Alignment explanation
Indices: 6645538--6645567 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
6645528 GCATAAATTA
6645538 AAAATAAATAAAT
1 AAAATAAATAAAT
*
6645551 AAAATAAATAATT
1 AAAATAAATAAAT
6645564 AAAA
1 AAAA
6645568 GCTAAAAACA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.77, C:0.00, G:0.00, T:0.23
Consensus pattern (13 bp):
AAAATAAATAAAT
Done.