Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr01 ID=Chr01-JGI_221_v2.0
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: 55868233
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 983842 characters in sequence are not A, C, G, or T
File 28 of 187
Found at i:9167915 original size:3 final size:3
Alignment explanation
Indices: 9167907--9167946 Score: 80
Period size: 3 Copynumber: 13.3 Consensus size: 3
9167897 AGAAAAAATA
9167907 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A
9167947 TCAGCAAAAA
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 37 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:9169127 original size:45 final size:45
Alignment explanation
Indices: 9169078--9169321 Score: 233
Period size: 45 Copynumber: 5.4 Consensus size: 45
9169068 GTTCAATTAT
* * *
9169078 AACTTAAGGGAAATAAGATTCGTTATCTTTAATTTGCTCCACTGC
1 AACTTCAGGGAAATAAGATTCGCTATCTTTAATCTGCTCCACTGC
* * * * *
9169123 AACTTCAGGGAGATAAGGTTTGTAACTTAGCTTTAATCTGTTCCACTGC
1 AACTTCAGGGAAATAAGATTCG---C-TATCTTTAATCTGCTCCACTGC
* * *
9169172 AACTTCAGGGAAATAAGATTCACTATCTTCAATCTGCTCCATTGC
1 AACTTCAGGGAAATAAGATTCGCTATCTTTAATCTGCTCCACTGC
* * * *
9169217 AACTTCA-AGAAGATAAGATTTGCTATCTTCAATCTGCTCCACTAC
1 AACTTCAGGGAA-ATAAGATTCGCTATCTTTAATCTGCTCCACTGC
* * * *
9169262 AACTTCAGTGAGATAAGAATT-G-TAGCTTTAATCTGCTCCAGTGC
1 AACTTCAGGGAAATAAG-ATTCGCTATCTTTAATCTGCTCCACTGC
*
9169306 AACTTCAGGGAGATAA
1 AACTTCAGGGAAATAA
9169322 AATTGGTGCT
Statistics
Matches: 164, Mismatches: 28, Indels: 15
0.79 0.14 0.07
Matches are distributed among these distances:
44 36 0.22
45 85 0.52
46 6 0.04
49 37 0.23
ACGTcount: A:0.31, C:0.20, G:0.17, T:0.32
Consensus pattern (45 bp):
AACTTCAGGGAAATAAGATTCGCTATCTTTAATCTGCTCCACTGC
Found at i:9169186 original size:94 final size:93
Alignment explanation
Indices: 9169018--9169321 Score: 312
Period size: 94 Copynumber: 3.3 Consensus size: 93
9169008 TTTCAATTCA
* * * * * * * *
9169018 CTCCGCTGCAACTTCAGAGAGGTGAGACTTGTAACTTGTAGCTTTAATCTGTTCAATTATAACTT
1 CTCCACTGCAACTTCAGGGAGATAAGATTTGTAAC-T-TAGCTTTAATCTGTTCCACTACAACTT
* *
9169083 AAGGGAAATAAGATTCGTTATCTTTAATTTG
64 CAGGGAAATAAGATTCG-TATCTTTAATCTG
* *
9169114 CTCCACTGCAACTTCAGGGAGATAAGGTTTGTAACTTAGCTTTAATCTGTTCCACTGCAACTTCA
1 CTCCACTGCAACTTCAGGGAGATAAGATTTGTAACTTAGCTTTAATCTGTTCCACTACAACTTCA
* *
9169179 GGGAAATAAGATTCACTATCTTCAATCTG
66 GGGAAATAAGATTC-GTATCTTTAATCTG
* * * * * *
9169208 CTCCATTGCAACTTCAAGAAGATAAGATTTG---C-TATCTTCAATCTGCTCCACTACAACTTCA
1 CTCCACTGCAACTTCAGGGAGATAAGATTTGTAACTTAGCTTTAATCTGTTCCACTACAACTTCA
* * *
9169269 GTGAGATAAGAATT-GTAGCTTTAATCTG
66 GGGAAATAAG-ATTCGTATCTTTAATCTG
*
9169297 CTCCAGTGCAACTTCAGGGAGATAA
1 CTCCACTGCAACTTCAGGGAGATAA
9169322 AATTGGTGCT
Statistics
Matches: 176, Mismatches: 30, Indels: 11
0.81 0.14 0.05
Matches are distributed among these distances:
89 33 0.19
90 33 0.19
91 4 0.02
94 76 0.43
95 1 0.01
96 29 0.16
ACGTcount: A:0.30, C:0.20, G:0.17, T:0.33
Consensus pattern (93 bp):
CTCCACTGCAACTTCAGGGAGATAAGATTTGTAACTTAGCTTTAATCTGTTCCACTACAACTTCA
GGGAAATAAGATTCGTATCTTTAATCTG
Found at i:9176764 original size:3 final size:3
Alignment explanation
Indices: 9176756--9176810 Score: 110
Period size: 3 Copynumber: 18.3 Consensus size: 3
9176746 GCTAAAGCAT
9176756 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
9176804 TAA TAA T
1 TAA TAA T
9176811 GGGCATGTAA
Statistics
Matches: 52, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 52 1.00
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (3 bp):
TAA
Found at i:9176846 original size:15 final size:15
Alignment explanation
Indices: 9176826--9176855 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
9176816 TGTAAATAAA
9176826 TAAATAAATGAACAC
1 TAAATAAATGAACAC
9176841 TAAATAAATGAACAC
1 TAAATAAATGAACAC
9176856 CAAGTGAAGC
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.60, C:0.13, G:0.07, T:0.20
Consensus pattern (15 bp):
TAAATAAATGAACAC
Found at i:9176933 original size:23 final size:23
Alignment explanation
Indices: 9176903--9176947 Score: 90
Period size: 23 Copynumber: 2.0 Consensus size: 23
9176893 AAATTATAAA
9176903 ATATAAGAAAAATATATATGTAC
1 ATATAAGAAAAATATATATGTAC
9176926 ATATAAGAAAAATATATATGTA
1 ATATAAGAAAAATATATATGTA
9176948 TGTGAATTAT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 22 1.00
ACGTcount: A:0.58, C:0.02, G:0.09, T:0.31
Consensus pattern (23 bp):
ATATAAGAAAAATATATATGTAC
Found at i:9177149 original size:3 final size:3
Alignment explanation
Indices: 9177141--9177175 Score: 52
Period size: 3 Copynumber: 11.7 Consensus size: 3
9177131 ACGAGCAACC
* *
9177141 AAT AAT AAT AAT TAT AAT AAT AAT AAT CAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
9177176 AATCTAATTT
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
3 28 1.00
ACGTcount: A:0.63, C:0.03, G:0.00, T:0.34
Consensus pattern (3 bp):
AAT
Found at i:9178348 original size:17 final size:17
Alignment explanation
Indices: 9178326--9178359 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
9178316 GGGTCGTGCA
*
9178326 TTGTAATTGGGCTTGGG
1 TTGTAATTGGGCCTGGG
9178343 TTGTAATTGGGCCTGGG
1 TTGTAATTGGGCCTGGG
9178360 GTATTGGGTT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.12, C:0.09, G:0.41, T:0.38
Consensus pattern (17 bp):
TTGTAATTGGGCCTGGG
Found at i:9179016 original size:44 final size:44
Alignment explanation
Indices: 9178968--9179081 Score: 131
Period size: 44 Copynumber: 2.6 Consensus size: 44
9178958 TTTTAATCCA
* **
9178968 CTCCACTGCAACTTCAGGGATATAAGA-TTAGCAGCTTCAGTCTG
1 CTCCACTGCAACTTCAGGGAGATAAGACTT-GCAGCTTCAACCTG
* * * *
9179012 CTCCACTACAACTTTAGGGAGATAAGACTTGTAGTTTCAACCTG
1 CTCCACTGCAACTTCAGGGAGATAAGACTTGCAGCTTCAACCTG
* *
9179056 CCCCACTGCAACTTCAGGGGGATAAG
1 CTCCACTGCAACTTCAGGGAGATAAG
9179082 GTTTATGACT
Statistics
Matches: 58, Mismatches: 11, Indels: 2
0.82 0.15 0.03
Matches are distributed among these distances:
44 56 0.97
45 2 0.03
ACGTcount: A:0.28, C:0.25, G:0.21, T:0.25
Consensus pattern (44 bp):
CTCCACTGCAACTTCAGGGAGATAAGACTTGCAGCTTCAACCTG
Found at i:9179106 original size:44 final size:43
Alignment explanation
Indices: 9178968--9179110 Score: 121
Period size: 44 Copynumber: 3.3 Consensus size: 43
9178958 TTTTAATCCA
* *
9178968 CTCCACTGCAACTTCAGGGATATAA-GATTAGCAGCTT-CAGTCTG
1 CTCCACTGCAACTTCAGGGAGATAAGGTTTAG-A-CTTCCA-TCTG
* * * * * *
9179012 CTCCACTACAACTTTAGGGAGATAAGACTTGTAG-TTTCAACCTG
1 CTCCACTGCAACTTCAGGGAGATAAG-GTT-TAGACTTCCATCTG
* *
9179056 CCCCACTGCAACTTCAGGGGGATAAGGTTTATGACTTCCATCTG
1 CTCCACTGCAACTTCAGGGAGATAAGGTTTA-GACTTCCATCTG
9179100 CTCCACTGCAA
1 CTCCACTGCAA
9179111 TGCCAGGAAA
Statistics
Matches: 76, Mismatches: 17, Indels: 12
0.72 0.16 0.11
Matches are distributed among these distances:
42 2 0.03
43 3 0.04
44 66 0.87
45 1 0.01
46 1 0.01
47 3 0.04
ACGTcount: A:0.27, C:0.27, G:0.20, T:0.27
Consensus pattern (43 bp):
CTCCACTGCAACTTCAGGGAGATAAGGTTTAGACTTCCATCTG
Found at i:9179176 original size:50 final size:50
Alignment explanation
Indices: 9179104--9179706 Score: 445
Period size: 50 Copynumber: 12.1 Consensus size: 50
9179094 CATCTGCTCC
* * * *
9179104 ACTGCAATGCCAGGAAAACAAGATTCACTGTTGTAGCTTCAATCTGTTTA
1 ACTGCAATGTCAGGGAAGCAAGATTCACCGTTGTAGCTTCAATCTGTTTA
* *
9179154 ACTGCAATGTCGGGGAAGCAAGATTCACCGTTGTAGCTTCAATCTATTTA
1 ACTGCAATGTCAGGGAAGCAAGATTCACCGTTGTAGCTTCAATCTGTTTA
* * * * **
9179204 ACTGCAATATCGGGGAAGCAATATTCACCGTTGTAGGTTCAATCTGTTCC
1 ACTGCAATGTCAGGGAAGCAAGATTCACCGTTGTAGCTTCAATCTGTTTA
** * * * * *
9179254 ACTGCACCGCCAGGGAAGTAAGATTCATCGTTGTGGCTTCAATCTTTTTA
1 ACTGCAATGTCAGGGAAGCAAGATTCACCGTTGTAGCTTCAATCTGTTTA
* * * * * **
9179304 ATTGCAATTTCGGGGAAGCAAGATTCGCTGTTGTAGCTTCAATCTGTTCC
1 ACTGCAATGTCAGGGAAGCAAGATTCACCGTTGTAGCTTCAATCTGTTTA
* ** * * * * * * *
9179354 ACTGTACCGCCAAGGAAGTAAGATTCGCCGTTGTGGGTTCAATCTTTTTA
1 ACTGCAATGTCAGGGAAGCAAGATTCACCGTTGTAGCTTCAATCTGTTTA
* * * *
9179404 ATTGCAATGTCGGGGAAGCAAGATTCACCATTGTAGCTTCTATCTGTTCT-
1 ACTGCAATGTCAGGGAAGCAAGATTCACCGTTGTAGCTTCAATCTGTT-TA
* *** * ** * * *
9179454 GCTGCACCATCAGGGAAGTAAGATTTGCCATTGTGGCTTCAATCTTTTTA
1 ACTGCAATGTCAGGGAAGCAAGATTCACCGTTGTAGCTTCAATCTGTTTA
* ** * * * **
9179504 ATTATAATGTCGGGGAAGCAAGATTCACTGTTGTAGCTTCAATTTGTTCC
1 ACTGCAATGTCAGGGAAGCAAGATTCACCGTTGTAGCTTCAATCTGTTTA
* * * ** * * * * *
9179554 GCTGCACTGCCATAGAAGTAAGATTCGCCGTTGTGGCTTCAATATTTTTA
1 ACTGCAATGTCAGGGAAGCAAGATTCACCGTTGTAGCTTCAATCTGTTTA
* * * **
9179604 ATTGCAATGT-TGAGGAAGCAATATTCACCGTTGTAGCTTCAATCTGTTCC
1 ACTGCAATGTCAG-GGAAGCAAGATTCACCGTTGTAGCTTCAATCTGTTTA
** * * ** * *
9179654 ACTGCACCGCCAGGGAAGTAAGATTCGTCGTTGTGGCTTCAATCTTTTTA
1 ACTGCAATGTCAGGGAAGCAAGATTCACCGTTGTAGCTTCAATCTGTTTA
9179704 ACT
1 ACT
9179707 CCATTGATTT
Statistics
Matches: 406, Mismatches: 143, Indels: 8
0.73 0.26 0.01
Matches are distributed among these distances:
49 1 0.00
50 403 0.99
51 2 0.00
ACGTcount: A:0.25, C:0.20, G:0.22, T:0.33
Consensus pattern (50 bp):
ACTGCAATGTCAGGGAAGCAAGATTCACCGTTGTAGCTTCAATCTGTTTA
Found at i:9179277 original size:100 final size:100
Alignment explanation
Indices: 9179122--9179704 Score: 770
Period size: 100 Copynumber: 5.8 Consensus size: 100
9179112 GCCAGGAAAA
* ** ** * * * *
9179122 CAAGATTCACTGTTGTAGCTTCAATCTGTTTAACTGCAATGTCGGGGAAGCAAGATTCACCGTTG
1 CAAGATTCACCGTTGTAGCTTCAATCTGTTCCACTGCACCGCCAGGGAAGTAAGATTCGCCGTTG
* * * *
9179187 TAGCTTCAATCTATTTAACTGCAATATCGGGGAAG
66 TGGCTTCAATCTTTTTAATTGCAATGTCGGGGAAG
* * **
9179222 CAATATTCACCGTTGTAGGTTCAATCTGTTCCACTGCACCGCCAGGGAAGTAAGATTCATCGTTG
1 CAAGATTCACCGTTGTAGCTTCAATCTGTTCCACTGCACCGCCAGGGAAGTAAGATTCGCCGTTG
*
9179287 TGGCTTCAATCTTTTTAATTGCAATTTCGGGGAAG
66 TGGCTTCAATCTTTTTAATTGCAATGTCGGGGAAG
* * * *
9179322 CAAGATTCGCTGTTGTAGCTTCAATCTGTTCCACTGTACCGCCAAGGAAGTAAGATTCGCCGTTG
1 CAAGATTCACCGTTGTAGCTTCAATCTGTTCCACTGCACCGCCAGGGAAGTAAGATTCGCCGTTG
*
9179387 TGGGTTCAATCTTTTTAATTGCAATGTCGGGGAAG
66 TGGCTTCAATCTTTTTAATTGCAATGTCGGGGAAG
* * ** ** * *
9179422 CAAGATTCACCATTGTAGCTTCTATCTGTTCTGCTGCACCATCAGGGAAGTAAGATTTGCCATTG
1 CAAGATTCACCGTTGTAGCTTCAATCTGTTCCACTGCACCGCCAGGGAAGTAAGATTCGCCGTTG
**
9179487 TGGCTTCAATCTTTTTAATTATAATGTCGGGGAAG
66 TGGCTTCAATCTTTTTAATTGCAATGTCGGGGAAG
* * * * **
9179522 CAAGATTCACTGTTGTAGCTTCAATTTGTTCCGCTGCACTGCCATAGAAGTAAGATTCGCCGTTG
1 CAAGATTCACCGTTGTAGCTTCAATCTGTTCCACTGCACCGCCAGGGAAGTAAGATTCGCCGTTG
* * *
9179587 TGGCTTCAATATTTTTAATTGCAATGTTGAGGAAG
66 TGGCTTCAATCTTTTTAATTGCAATGTCGGGGAAG
* *
9179622 CAATATTCACCGTTGTAGCTTCAATCTGTTCCACTGCACCGCCAGGGAAGTAAGATTCGTCGTTG
1 CAAGATTCACCGTTGTAGCTTCAATCTGTTCCACTGCACCGCCAGGGAAGTAAGATTCGCCGTTG
9179687 TGGCTTCAATCTTTTTAA
66 TGGCTTCAATCTTTTTAA
9179705 CTCCATTGAT
Statistics
Matches: 417, Mismatches: 66, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
100 417 1.00
ACGTcount: A:0.25, C:0.20, G:0.22, T:0.33
Consensus pattern (100 bp):
CAAGATTCACCGTTGTAGCTTCAATCTGTTCCACTGCACCGCCAGGGAAGTAAGATTCGCCGTTG
TGGCTTCAATCTTTTTAATTGCAATGTCGGGGAAG
Found at i:9181172 original size:49 final size:48
Alignment explanation
Indices: 9181097--9181236 Score: 158
Period size: 49 Copynumber: 2.9 Consensus size: 48
9181087 TCATATTTTA
* * *
9181097 TTTTTT-GGACTTAAAGCGCCCTTTGCGGGTTTTCACTTTGGTCTTTT
1 TTTTTTAGAACTTAAAGCGCCCGTTGCGGGTTTTCACTTTGGTCTCTT
* *
9181144 TTCTTTTAGAACTTAAGGCGTCCGTTGCGGGTTTTCACTTTGGTCTCTT
1 TT-TTTTAGAACTTAAAGCGCCCGTTGCGGGTTTTCACTTTGGTCTCTT
* * * *
9181193 TTTTTTAGGACTCAAAATAC-CCCTTTGCGGGTTTTCACTTTGGT
1 TTTTTTAGAACT-TAAA-GCGCCCGTTGCGGGTTTTCACTTTGGT
9181237 TCCTTTCTCT
Statistics
Matches: 78, Mismatches: 11, Indels: 6
0.82 0.12 0.06
Matches are distributed among these distances:
47 2 0.03
48 13 0.17
49 62 0.79
50 1 0.01
ACGTcount: A:0.14, C:0.20, G:0.21, T:0.46
Consensus pattern (48 bp):
TTTTTTAGAACTTAAAGCGCCCGTTGCGGGTTTTCACTTTGGTCTCTT
Found at i:9185901 original size:3 final size:3
Alignment explanation
Indices: 9185893--9185938 Score: 92
Period size: 3 Copynumber: 15.3 Consensus size: 3
9185883 AAGCATTAAA
9185893 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A
9185939 GGCATGTAAA
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 43 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:9186125 original size:12 final size:11
Alignment explanation
Indices: 9186071--9186126 Score: 51
Period size: 11 Copynumber: 5.1 Consensus size: 11
9186061 AATTTTAAAT
9186071 ATATATATATA
1 ATATATATATA
* *
9186082 ATATACATATT
1 ATATATATATA
* *
9186093 TTA-AAATATA
1 ATATATATATA
9186103 ATATATATATA
1 ATATATATATA
*
9186114 AGTATGTATATA
1 A-TATATATATA
9186126 A
1 A
9186127 AATTATGAAA
Statistics
Matches: 35, Mismatches: 8, Indels: 3
0.76 0.17 0.07
Matches are distributed among these distances:
10 7 0.20
11 18 0.51
12 10 0.29
ACGTcount: A:0.52, C:0.02, G:0.04, T:0.43
Consensus pattern (11 bp):
ATATATATATA
Found at i:9186255 original size:3 final size:3
Alignment explanation
Indices: 9186247--9186329 Score: 166
Period size: 3 Copynumber: 27.7 Consensus size: 3
9186237 ATGAGCAACC
9186247 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
9186295 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
9186330 CAACAACAAC
Statistics
Matches: 80, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 80 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:9187651 original size:25 final size:25
Alignment explanation
Indices: 9187623--9187754 Score: 94
Period size: 26 Copynumber: 5.3 Consensus size: 25
9187613 CTATTAACGG
*
9187623 GAAGCTCCAGATAGCCATATATCGA
1 GAAGCTCCAGAGAGCCATATATCGA
* * *
9187648 GAAGTTCAAGCGAGCC--ATATCGA
1 GAAGCTCCAGAGAGCCATATATCGA
*
9187671 GAAGCTCCAGAGAGCCAT-TAATCAA
1 GAAGCTCCAGAGAGCCATAT-ATCGA
* * *
9187696 GAAGCTTACAAAGAGCC-TTTAATCGA
1 GAAGC-TCCAGAGAGCCATAT-ATCGA
*
9187722 GAAGCT-CACGAAGAGTCATATATCGA
1 GAAGCTCCA-G-AGAGCCATATATCGA
*
9187748 GACGCTC
1 GAAGCTC
9187755 ATAAGAGTTG
Statistics
Matches: 83, Mismatches: 15, Indels: 16
0.73 0.13 0.14
Matches are distributed among these distances:
23 20 0.24
24 3 0.04
25 23 0.28
26 35 0.42
27 2 0.02
ACGTcount: A:0.36, C:0.23, G:0.22, T:0.19
Consensus pattern (25 bp):
GAAGCTCCAGAGAGCCATATATCGA
Found at i:9187671 original size:23 final size:23
Alignment explanation
Indices: 9187623--9187729 Score: 72
Period size: 25 Copynumber: 4.3 Consensus size: 23
9187613 CTATTAACGG
* *
9187623 GAAGCTCCAGATAGCCATATATCGA
1 GAAGCTCAAGAGAGCC--ATATCGA
* *
9187648 GAAGTTCAAGCGAGCCATATCGA
1 GAAGCTCAAGAGAGCCATATCGA
* *
9187671 GAAGCTCCAGAGAGCCATTAATCAA
1 GAAGCTCAAGAGAGCCA-T-ATCGA
*
9187696 GAAGCTTACAA-AGAGCCTTTAATCGA
1 GAAGC-T-CAAGAGAGCC-AT-ATCGA
9187722 GAAGCTCA
1 GAAGCTCA
9187730 CGAAGAGTCA
Statistics
Matches: 66, Mismatches: 11, Indels: 11
0.75 0.12 0.12
Matches are distributed among these distances:
23 21 0.32
24 3 0.05
25 22 0.33
26 18 0.27
27 2 0.03
ACGTcount: A:0.37, C:0.22, G:0.21, T:0.19
Consensus pattern (23 bp):
GAAGCTCAAGAGAGCCATATCGA
Found at i:9189139 original size:24 final size:24
Alignment explanation
Indices: 9189111--9189162 Score: 68
Period size: 24 Copynumber: 2.2 Consensus size: 24
9189101 TTAGTAAGTC
* *
9189111 AAATAAACTATGCTAATAAATGCT
1 AAATAAACTATACTAATAAATACT
* *
9189135 AAATATATTATACTAATAAATACT
1 AAATAAACTATACTAATAAATACT
9189159 AAAT
1 AAAT
9189163 CTTCTAGAAA
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.54, C:0.10, G:0.04, T:0.33
Consensus pattern (24 bp):
AAATAAACTATACTAATAAATACT
Found at i:9192323 original size:3 final size:3
Alignment explanation
Indices: 9192310--9192350 Score: 73
Period size: 3 Copynumber: 13.7 Consensus size: 3
9192300 TTGGTCTCTT
*
9192310 TTA TCA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
9192351 TATTTTTGTT
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
3 36 1.00
ACGTcount: A:0.32, C:0.02, G:0.00, T:0.66
Consensus pattern (3 bp):
TTA
Found at i:9192365 original size:14 final size:14
Alignment explanation
Indices: 9192346--9192372 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
9192336 ATTATTATTA
9192346 TTATTTATTTTTGT
1 TTATTTATTTTTGT
9192360 TTATTTATTTTTG
1 TTATTTATTTTTG
9192373 GTTTTGGGCC
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.15, C:0.00, G:0.07, T:0.78
Consensus pattern (14 bp):
TTATTTATTTTTGT
Found at i:9201993 original size:8 final size:8
Alignment explanation
Indices: 9201980--9202012 Score: 50
Period size: 8 Copynumber: 4.1 Consensus size: 8
9201970 TCTAAGTAGC
9201980 AAAAAAGA
1 AAAAAAGA
9201988 AAAAAAGA
1 AAAAAAGA
9201996 ACAAAAA-A
1 A-AAAAAGA
9202004 AAAAAAGA
1 AAAAAAGA
9202012 A
1 A
9202013 GAGAATTTTG
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
7 5 0.22
8 13 0.57
9 5 0.22
ACGTcount: A:0.88, C:0.03, G:0.09, T:0.00
Consensus pattern (8 bp):
AAAAAAGA
Found at i:9202006 original size:16 final size:17
Alignment explanation
Indices: 9201981--9202012 Score: 57
Period size: 16 Copynumber: 1.9 Consensus size: 17
9201971 CTAAGTAGCA
9201981 AAAAAGAAAAAAAGAAC
1 AAAAAGAAAAAAAGAAC
9201998 AAAAA-AAAAAAAGAA
1 AAAAAGAAAAAAAGAA
9202013 GAGAATTTTG
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:0.88, C:0.03, G:0.09, T:0.00
Consensus pattern (17 bp):
AAAAAGAAAAAAAGAAC
Found at i:9213129 original size:3 final size:3
Alignment explanation
Indices: 9213108--9213190 Score: 98
Period size: 3 Copynumber: 27.7 Consensus size: 3
9213098 TTTAGTCCCG
* * * *
9213108 TTA TTA TTT TTA TTT TTA TTA TTA TTA -AA CTAA TTA GTT- TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA -TTA TTA -TTA TTA TTA
9213153 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
9213191 TATATACATA
Statistics
Matches: 70, Mismatches: 6, Indels: 8
0.83 0.07 0.10
Matches are distributed among these distances:
2 3 0.04
3 63 0.90
4 4 0.06
ACGTcount: A:0.31, C:0.01, G:0.01, T:0.66
Consensus pattern (3 bp):
TTA
Found at i:9222715 original size:15 final size:16
Alignment explanation
Indices: 9222685--9222717 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
9222675 AAACAATATC
*
9222685 AAAAAATGAATACAAA
1 AAAAAACGAATACAAA
9222701 AAAAAACGAAT-CAAA
1 AAAAAACGAATACAAA
9222716 AA
1 AA
9222718 GAGAGAAAGA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
15 6 0.38
16 10 0.62
ACGTcount: A:0.76, C:0.09, G:0.06, T:0.09
Consensus pattern (16 bp):
AAAAAACGAATACAAA
Found at i:9228428 original size:28 final size:26
Alignment explanation
Indices: 9228389--9228462 Score: 76
Period size: 28 Copynumber: 2.7 Consensus size: 26
9228379 TTCAGATTCG
9228389 AAAAAAAAAGAAAAAAATCAAAGTCA
1 AAAAAAAAAGAAAAAAATCAAAGTCA
** *
9228415 AAAAAAAAGGAGAAATCAATCAAAGTTA
1 AAAAAAAA--AGAAAAAAATCAAAGTCA
9228443 AAATAAAAATATGAAAAAAA
1 AAA-AAAAA-A-GAAAAAAA
9228463 GAAAAAGAAA
Statistics
Matches: 38, Mismatches: 6, Indels: 5
0.78 0.12 0.10
Matches are distributed among these distances:
26 8 0.21
28 19 0.50
29 11 0.29
ACGTcount: A:0.73, C:0.05, G:0.09, T:0.12
Consensus pattern (26 bp):
AAAAAAAAAGAAAAAAATCAAAGTCA
Found at i:9228852 original size:13 final size:13
Alignment explanation
Indices: 9228828--9228861 Score: 52
Period size: 13 Copynumber: 2.7 Consensus size: 13
9228818 ATGGATTTCA
9228828 AAAAAATG-AAAT
1 AAAAAATGAAAAT
*
9228840 GAAAAATGAAAAT
1 AAAAAATGAAAAT
9228853 AAAAAATGA
1 AAAAAATGA
9228862 CGAAAAAGTA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
12 7 0.37
13 12 0.63
ACGTcount: A:0.74, C:0.00, G:0.12, T:0.15
Consensus pattern (13 bp):
AAAAAATGAAAAT
Found at i:9230184 original size:49 final size:49
Alignment explanation
Indices: 9230131--9230229 Score: 144
Period size: 49 Copynumber: 2.0 Consensus size: 49
9230121 CAGTGGAGCT
* *
9230131 GGTTAAAGATAGCAGATCTTGCCTTCCTGCATTAACAGTGAAGCAGATC
1 GGTTAAAGATAGCAGATCTTGCCTGCCTGCATTAACAGCGAAGCAGATC
* ** *
9230180 GGTTAAAGATAGTAGATCTTGCCTGCCTGTGTTAACAGCGAAGTAGATC
1 GGTTAAAGATAGCAGATCTTGCCTGCCTGCATTAACAGCGAAGCAGATC
9230229 G
1 G
9230230 AAAACAAAGC
Statistics
Matches: 44, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
49 44 1.00
ACGTcount: A:0.29, C:0.18, G:0.25, T:0.27
Consensus pattern (49 bp):
GGTTAAAGATAGCAGATCTTGCCTGCCTGCATTAACAGCGAAGCAGATC
Found at i:9230691 original size:25 final size:26
Alignment explanation
Indices: 9230663--9230711 Score: 64
Period size: 25 Copynumber: 1.9 Consensus size: 26
9230653 ATTACAATAA
* *
9230663 CCCTAACCCAAAA-TACTAGCCCAGG
1 CCCTAACCAAAAATTACAAGCCCAGG
*
9230688 CCCTAATCAAAAATTACAAGCCCA
1 CCCTAACCAAAAATTACAAGCCCA
9230712 AAAAACAAAC
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
25 11 0.55
26 9 0.45
ACGTcount: A:0.41, C:0.37, G:0.08, T:0.14
Consensus pattern (26 bp):
CCCTAACCAAAAATTACAAGCCCAGG
Found at i:9233382 original size:2 final size:2
Alignment explanation
Indices: 9233377--9233410 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
9233367 AAAAAAAAAA
9233377 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
9233411 TCATGTTATA
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:9235754 original size:2 final size:2
Alignment explanation
Indices: 9235747--9235775 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
9235737 CCATCATAGC
9235747 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
9235776 ATACCACAAC
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:9246014 original size:3 final size:3
Alignment explanation
Indices: 9246006--9246043 Score: 76
Period size: 3 Copynumber: 12.7 Consensus size: 3
9245996 TCCTTCAAAA
9246006 AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AA
1 AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AA
9246044 AATAGAAACA
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 35 1.00
ACGTcount: A:0.68, C:0.00, G:0.32, T:0.00
Consensus pattern (3 bp):
AAG
Found at i:9246787 original size:21 final size:20
Alignment explanation
Indices: 9246758--9246798 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 20
9246748 ATGAATTAAG
9246758 TTCAAATAAGAATTTATATTT
1 TTCAAATAA-AATTTATATTT
* *
9246779 TTCATATAATATTTATATTT
1 TTCAAATAAAATTTATATTT
9246799 GGTAAAAGCA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
20 10 0.56
21 8 0.44
ACGTcount: A:0.39, C:0.05, G:0.02, T:0.54
Consensus pattern (20 bp):
TTCAAATAAAATTTATATTT
Found at i:9252405 original size:15 final size:15
Alignment explanation
Indices: 9252385--9252419 Score: 52
Period size: 15 Copynumber: 2.3 Consensus size: 15
9252375 TCTGGTCGTC
9252385 TGCCGCCGGCGACGG
1 TGCCGCCGGCGACGG
*
9252400 TGCCGCCGTCGACGG
1 TGCCGCCGGCGACGG
*
9252415 CGCCG
1 TGCCG
9252420 TCGTCCATGG
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.06, C:0.43, G:0.43, T:0.09
Consensus pattern (15 bp):
TGCCGCCGGCGACGG
Found at i:9252424 original size:15 final size:15
Alignment explanation
Indices: 9252386--9252424 Score: 51
Period size: 15 Copynumber: 2.6 Consensus size: 15
9252376 CTGGTCGTCT
* *
9252386 GCCGCCGGCGACGGT
1 GCCGCCGTCGACGGC
9252401 GCCGCCGTCGACGGC
1 GCCGCCGTCGACGGC
*
9252416 GCCGTCGTC
1 GCCGCCGTC
9252425 CATGGTGGCC
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
15 21 1.00
ACGTcount: A:0.05, C:0.44, G:0.41, T:0.10
Consensus pattern (15 bp):
GCCGCCGTCGACGGC
Found at i:9253663 original size:3 final size:3
Alignment explanation
Indices: 9253655--9253684 Score: 60
Period size: 3 Copynumber: 10.0 Consensus size: 3
9253645 TAAATAGGTA
9253655 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
9253685 TTGAAAGTAT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 27 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:9254615 original size:22 final size:23
Alignment explanation
Indices: 9254567--9254625 Score: 59
Period size: 24 Copynumber: 2.6 Consensus size: 23
9254557 AACACAACTT
* *
9254567 TAATTTCAAACATATATGAATAAA
1 TAATTACAAATATATAT-AATAAA
*
9254591 TAATTACAAATATATAT-ATATA
1 TAATTACAAATATATATAATAAA
*
9254613 TAAGTAC-AATATA
1 TAATTACAAATATA
9254626 CAAGTAAATT
Statistics
Matches: 31, Mismatches: 4, Indels: 3
0.82 0.11 0.08
Matches are distributed among these distances:
21 6 0.19
22 10 0.32
24 15 0.48
ACGTcount: A:0.54, C:0.07, G:0.03, T:0.36
Consensus pattern (23 bp):
TAATTACAAATATATATAATAAA
Found at i:9261417 original size:23 final size:24
Alignment explanation
Indices: 9261385--9261435 Score: 68
Period size: 24 Copynumber: 2.2 Consensus size: 24
9261375 GCTGTTCAAT
* * *
9261385 CCATCCCTCAA-CTAATACTCATG
1 CCATCACTCAACCCAATACTCATA
9261408 CCATCACTCAACCCAATACTCATA
1 CCATCACTCAACCCAATACTCATA
9261432 CCAT
1 CCAT
9261436 GGTCATACGT
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
23 10 0.42
24 14 0.58
ACGTcount: A:0.33, C:0.41, G:0.02, T:0.24
Consensus pattern (24 bp):
CCATCACTCAACCCAATACTCATA
Found at i:9264528 original size:21 final size:21
Alignment explanation
Indices: 9264486--9264528 Score: 52
Period size: 21 Copynumber: 2.0 Consensus size: 21
9264476 ACATGTTAAT
* *
9264486 TTTATCTTATTACAGAGTATA
1 TTTATCATATTACAGAATATA
9264507 TTTATCATATTACA-AATCATA
1 TTTATCATATTACAGAAT-ATA
9264528 T
1 T
9264529 ATAGCATGCG
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
20 2 0.11
21 17 0.89
ACGTcount: A:0.37, C:0.12, G:0.05, T:0.47
Consensus pattern (21 bp):
TTTATCATATTACAGAATATA
Found at i:9265709 original size:16 final size:17
Alignment explanation
Indices: 9265682--9265714 Score: 50
Period size: 16 Copynumber: 2.0 Consensus size: 17
9265672 TTAAGTTTTC
*
9265682 AATTTAAATTTAGAGTT
1 AATTTAAATTTAAAGTT
9265699 AATTT-AATTTAAAGTT
1 AATTTAAATTTAAAGTT
9265715 TTCAATTGAA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 10 0.67
17 5 0.33
ACGTcount: A:0.42, C:0.00, G:0.09, T:0.48
Consensus pattern (17 bp):
AATTTAAATTTAAAGTT
Found at i:9268521 original size:12 final size:12
Alignment explanation
Indices: 9268501--9268549 Score: 59
Period size: 12 Copynumber: 4.3 Consensus size: 12
9268491 AAATCCTTAT
9268501 AATAT-TATATA
1 AATATATATATA
*
9268512 TATATATATATA
1 AATATATATATA
9268524 AATA-A-ATATA
1 AATATATATATA
*
9268534 AATATAAATATA
1 AATATATATATA
9268546 AATA
1 AATA
9268550 CATACATGTA
Statistics
Matches: 33, Mismatches: 2, Indels: 5
0.82 0.05 0.12
Matches are distributed among these distances:
10 9 0.27
11 6 0.18
12 18 0.55
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (12 bp):
AATATATATATA
Found at i:9268532 original size:16 final size:16
Alignment explanation
Indices: 9268513--9268543 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
9268503 TATTATATAT
*
9268513 ATATATATATAAATAA
1 ATATAAATATAAATAA
9268529 ATATAAATATAAATA
1 ATATAAATATAAATA
9268544 TAAATACATA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (16 bp):
ATATAAATATAAATAA
Found at i:9268546 original size:6 final size:6
Alignment explanation
Indices: 9268506--9268549 Score: 54
Period size: 6 Copynumber: 7.3 Consensus size: 6
9268496 CTTATAATAT
* *
9268506 TATATA TATATA TATATAA -ATAAA TATAAA TATAAA TATAAA TA
1 TATAAA TATAAA TATA-AA TATAAA TATAAA TATAAA TATAAA TA
9268550 CATACATGTA
Statistics
Matches: 35, Mismatches: 1, Indels: 4
0.88 0.03 0.10
Matches are distributed among these distances:
5 2 0.06
6 32 0.91
7 1 0.03
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (6 bp):
TATAAA
Found at i:9270345 original size:47 final size:47
Alignment explanation
Indices: 9270276--9270369 Score: 179
Period size: 47 Copynumber: 2.0 Consensus size: 47
9270266 ATCTGAAGTC
9270276 AAAAAAATTATTTTAATATTATTTTGTGATCTACAACATGATAGTAT
1 AAAAAAATTATTTTAATATTATTTTGTGATCTACAACATGATAGTAT
*
9270323 AAAAAAGTTATTTTAATATTATTTTGTGATCTACAACATGATAGTAT
1 AAAAAAATTATTTTAATATTATTTTGTGATCTACAACATGATAGTAT
9270370 TATGGTATAA
Statistics
Matches: 46, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
47 46 1.00
ACGTcount: A:0.41, C:0.06, G:0.10, T:0.43
Consensus pattern (47 bp):
AAAAAAATTATTTTAATATTATTTTGTGATCTACAACATGATAGTAT
Found at i:9277671 original size:22 final size:21
Alignment explanation
Indices: 9277633--9277689 Score: 62
Period size: 23 Copynumber: 2.6 Consensus size: 21
9277623 ACTCAAAATT
9277633 ATATAATTTAAATAATA-AAA
1 ATATAATTTAAATAATATAAA
*
9277653 ATATATTTTAAAATAAATATAAA
1 ATATAATTT-AAAT-AATATAAA
*
9277676 ATGTAATTTCAAAT
1 ATATAATTT-AAAT
9277690 TTAATAAAAT
Statistics
Matches: 30, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
20 8 0.27
21 4 0.13
22 4 0.13
23 14 0.47
ACGTcount: A:0.58, C:0.02, G:0.02, T:0.39
Consensus pattern (21 bp):
ATATAATTTAAATAATATAAA
Found at i:9277684 original size:24 final size:21
Alignment explanation
Indices: 9277633--9277677 Score: 56
Period size: 20 Copynumber: 2.1 Consensus size: 21
9277623 ACTCAAAATT
*
9277633 ATATAATTT-AAATAATAAAA
1 ATATATTTTAAAATAATAAAA
9277653 ATATATTTTAAAATAAATATAAA
1 ATATATTTTAAAAT-AATA-AAA
9277676 AT
1 AT
9277678 GTAATTTCAA
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
20 8 0.38
21 4 0.19
22 4 0.19
23 5 0.24
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (21 bp):
ATATATTTTAAAATAATAAAA
Found at i:9279614 original size:20 final size:20
Alignment explanation
Indices: 9279569--9279621 Score: 70
Period size: 20 Copynumber: 2.6 Consensus size: 20
9279559 CCAGAACATG
*
9279569 ACAGAATAGAACAGAGCAGA
1 ACAGAATAGAACAGAGCAAA
**
9279589 GTAGAATAGAACAGAGCAAA
1 ACAGAATAGAACAGAGCAAA
*
9279609 ACAGAACAGAACA
1 ACAGAATAGAACA
9279622 TAACAGAGTA
Statistics
Matches: 27, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
20 27 1.00
ACGTcount: A:0.57, C:0.15, G:0.23, T:0.06
Consensus pattern (20 bp):
ACAGAATAGAACAGAGCAAA
Found at i:9279616 original size:5 final size:5
Alignment explanation
Indices: 9279560--9279628 Score: 50
Period size: 5 Copynumber: 13.8 Consensus size: 5
9279550 ACAAACCCAC
* * * * * * *
9279560 CAGAA CATG-A CAGAA TAGAA CAGAG CAGAG TAGAA TAGAA CAGAG CAAAA
1 CAGAA CA-GAA CAGAA CAGAA CAGAA CAGAA CAGAA CAGAA CAGAA CAGAA
*
9279610 CAGAA CAGAA CATAA CAGA
1 CAGAA CAGAA CAGAA CAGA
9279629 GTAGAGCAAA
Statistics
Matches: 50, Mismatches: 12, Indels: 4
0.76 0.18 0.06
Matches are distributed among these distances:
4 1 0.02
5 48 0.96
6 1 0.02
ACGTcount: A:0.55, C:0.16, G:0.22, T:0.07
Consensus pattern (5 bp):
CAGAA
Found at i:9279626 original size:15 final size:15
Alignment explanation
Indices: 9279596--9279648 Score: 52
Period size: 15 Copynumber: 3.5 Consensus size: 15
9279586 AGAGTAGAAT
*
9279596 AGAACAGAGCAAAAC
1 AGAACAGAACAAAAC
*
9279611 AGAACAGAACATAAC
1 AGAACAGAACAAAAC
** *
9279626 AGAGTAGAGCAAAAC
1 AGAACAGAACAAAAC
*
9279641 TGAACAGA
1 AGAACAGA
9279649 GCTACGCAGA
Statistics
Matches: 29, Mismatches: 9, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
15 29 1.00
ACGTcount: A:0.57, C:0.17, G:0.21, T:0.06
Consensus pattern (15 bp):
AGAACAGAACAAAAC
Found at i:9280835 original size:41 final size:41
Alignment explanation
Indices: 9280757--9280836 Score: 97
Period size: 41 Copynumber: 2.0 Consensus size: 41
9280747 GTACACAGCC
* * * **
9280757 GTGTGGCTCACACAACCTACTAGACGTCATGGTACACGACT
1 GTGTGGCTCACACAACCTACCACACGACATGACACACGACT
* *
9280798 GTGTGGCTCACACAACCTACCACATGACCTGACACACGA
1 GTGTGGCTCACACAACCTACCACACGACATGACACACGA
9280837 TCATGTGACG
Statistics
Matches: 32, Mismatches: 7, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
41 32 1.00
ACGTcount: A:0.29, C:0.33, G:0.20, T:0.19
Consensus pattern (41 bp):
GTGTGGCTCACACAACCTACCACACGACATGACACACGACT
Found at i:9292820 original size:6 final size:6
Alignment explanation
Indices: 9292809--9292846 Score: 76
Period size: 6 Copynumber: 6.3 Consensus size: 6
9292799 AAACAAATGA
9292809 AGTGAG AGTGAG AGTGAG AGTGAG AGTGAG AGTGAG AG
1 AGTGAG AGTGAG AGTGAG AGTGAG AGTGAG AGTGAG AG
9292847 ACTGAGTAAT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 32 1.00
ACGTcount: A:0.34, C:0.00, G:0.50, T:0.16
Consensus pattern (6 bp):
AGTGAG
Found at i:9292853 original size:18 final size:18
Alignment explanation
Indices: 9292813--9292853 Score: 55
Period size: 18 Copynumber: 2.3 Consensus size: 18
9292803 AAATGAAGTG
**
9292813 AGAGTGAGAGTGAGAGTG
1 AGAGTGAGAGTGAGAGAC
9292831 AGAGTGAGAGTGAGAGAC
1 AGAGTGAGAGTGAGAGAC
*
9292849 TGAGT
1 AGAGT
9292854 AATGGAGAAA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.34, C:0.02, G:0.46, T:0.17
Consensus pattern (18 bp):
AGAGTGAGAGTGAGAGAC
Found at i:9294922 original size:25 final size:29
Alignment explanation
Indices: 9294887--9294972 Score: 117
Period size: 30 Copynumber: 3.0 Consensus size: 29
9294877 AATATTTATG
9294887 GAAAGTCAAAGATATGGGTATC-AA-A-T
1 GAAAGTCAAAGATATGGGTATCAAATATT
9294913 -AAAGTCAAAGATATGGGTATCAAATATT
1 GAAAGTCAAAGATATGGGTATCAAATATT
*
9294941 GGAAAGTCAAAGATATGGGTATCGAGATATT
1 -GAAAGTCAAAGATATGGGTATC-AAATATT
9294972 G
1 G
9294973 GCATAAGAAA
Statistics
Matches: 53, Mismatches: 1, Indels: 8
0.85 0.02 0.13
Matches are distributed among these distances:
25 21 0.40
26 2 0.04
27 1 0.02
28 1 0.02
30 22 0.42
31 6 0.11
ACGTcount: A:0.43, C:0.07, G:0.24, T:0.26
Consensus pattern (29 bp):
GAAAGTCAAAGATATGGGTATCAAATATT
Found at i:9294949 original size:30 final size:30
Alignment explanation
Indices: 9294885--9294973 Score: 125
Period size: 25 Copynumber: 3.1 Consensus size: 30
9294875 TCAATATTTA
9294885 TGGAAAGTCAAAGATATGGGTATC-AA-A-
1 TGGAAAGTCAAAGATATGGGTATCAAATAT
9294912 T--AAAGTCAAAGATATGGGTATCAAATAT
1 TGGAAAGTCAAAGATATGGGTATCAAATAT
*
9294940 TGGAAAGTCAAAGATATGGGTATCGAGATAT
1 TGGAAAGTCAAAGATATGGGTATC-AAATAT
9294971 TGG
1 TGG
9294974 CATAAGAAAT
Statistics
Matches: 55, Mismatches: 1, Indels: 8
0.86 0.02 0.12
Matches are distributed among these distances:
25 21 0.38
26 2 0.04
27 2 0.04
28 1 0.02
30 21 0.38
31 8 0.15
ACGTcount: A:0.42, C:0.07, G:0.26, T:0.26
Consensus pattern (30 bp):
TGGAAAGTCAAAGATATGGGTATCAAATAT
Found at i:9299595 original size:15 final size:15
Alignment explanation
Indices: 9299575--9299621 Score: 51
Period size: 15 Copynumber: 3.1 Consensus size: 15
9299565 TCAAATAAAG
9299575 TCAAATATATGGGTA
1 TCAAATATATGGGTA
**
9299590 TCAAATAT-TGGAAA
1 TCAAATATATGGGTA
*
9299604 GTCAAAGATATGGGTA
1 -TCAAATATATGGGTA
9299620 TC
1 TC
9299622 GAGATATTGA
Statistics
Matches: 25, Mismatches: 5, Indels: 4
0.74 0.15 0.12
Matches are distributed among these distances:
14 4 0.16
15 17 0.68
16 4 0.16
ACGTcount: A:0.40, C:0.09, G:0.21, T:0.30
Consensus pattern (15 bp):
TCAAATATATGGGTA
Found at i:9299607 original size:30 final size:30
Alignment explanation
Indices: 9299543--9299630 Score: 114
Period size: 25 Copynumber: 3.1 Consensus size: 30
9299533 TCCATATTTA
9299543 TGGAAAGTCAAAGATATGGGTATC-AA-A-
1 TGGAAAGTCAAAGATATGGGTATCAAATAT
*
9299570 T--AAAGTCAAATATATGGGTATCAAATAT
1 TGGAAAGTCAAAGATATGGGTATCAAATAT
*
9299598 TGGAAAGTCAAAGATATGGGTATCGAGATAT
1 TGGAAAGTCAAAGATATGGGTATC-AAATAT
9299629 TG
1 TG
9299631 ACATAAGAAA
Statistics
Matches: 52, Mismatches: 3, Indels: 8
0.83 0.05 0.13
Matches are distributed among these distances:
25 20 0.38
26 2 0.04
27 2 0.04
28 1 0.02
30 20 0.38
31 7 0.13
ACGTcount: A:0.42, C:0.07, G:0.24, T:0.27
Consensus pattern (30 bp):
TGGAAAGTCAAAGATATGGGTATCAAATAT
Found at i:9299783 original size:2 final size:2
Alignment explanation
Indices: 9299776--9299810 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
9299766 AAGGCATTGT
9299776 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
9299811 TTGTAAATTT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.00, C:0.49, G:0.00, T:0.51
Consensus pattern (2 bp):
TC
Found at i:9304277 original size:7 final size:6
Alignment explanation
Indices: 9304269--9304300 Score: 55
Period size: 6 Copynumber: 5.2 Consensus size: 6
9304259 TTTAAAATTA
9304269 AAAAAT AAAAAT AAAAAT AAAAAT AAAGAAT A
1 AAAAAT AAAAAT AAAAAT AAAAAT AAA-AAT A
9304301 TATTTATTAC
Statistics
Matches: 25, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
6 21 0.84
7 4 0.16
ACGTcount: A:0.81, C:0.00, G:0.03, T:0.16
Consensus pattern (6 bp):
AAAAAT
Found at i:9304283 original size:13 final size:13
Alignment explanation
Indices: 9304261--9304300 Score: 55
Period size: 12 Copynumber: 3.2 Consensus size: 13
9304251 TAAAGTATTT
*
9304261 TAAAATTAAAAAA
1 TAAAAATAAAAAA
9304274 TAAAAAT-AAAAA
1 TAAAAATAAAAAA
*
9304286 TAAAAATAAAGAA
1 TAAAAATAAAAAA
9304299 TA
1 TA
9304301 TATTTATTAC
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
12 12 0.50
13 12 0.50
ACGTcount: A:0.78, C:0.00, G:0.03, T:0.20
Consensus pattern (13 bp):
TAAAAATAAAAAA
Found at i:9304847 original size:27 final size:27
Alignment explanation
Indices: 9304796--9304849 Score: 72
Period size: 27 Copynumber: 2.0 Consensus size: 27
9304786 GAAATGCAGG
*
9304796 GACTAGTTGAGCCTATCTGACAGGCGC
1 GACTAGTTGAGCCTAACTGACAGGCGC
* * *
9304823 GACTAGTTGTGCCTAACTTAGAGGCGC
1 GACTAGTTGAGCCTAACTGACAGGCGC
9304850 AAATGGTGGA
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
27 23 1.00
ACGTcount: A:0.22, C:0.24, G:0.30, T:0.24
Consensus pattern (27 bp):
GACTAGTTGAGCCTAACTGACAGGCGC
Found at i:9309147 original size:56 final size:56
Alignment explanation
Indices: 9309074--9309186 Score: 208
Period size: 56 Copynumber: 2.0 Consensus size: 56
9309064 CCAATTGCTC
9309074 ATATCACATCACCTTTTCATTTGTCAACTTTCTCCACTCCACCTCCTGTCCTACGT
1 ATATCACATCACCTTTTCATTTGTCAACTTTCTCCACTCCACCTCCTGTCCTACGT
* *
9309130 ATATCACATCACTTTTTCATTTGTCAACTTTCTCCACTCCACCTCCTGTCCTCCGT
1 ATATCACATCACCTTTTCATTTGTCAACTTTCTCCACTCCACCTCCTGTCCTACGT
9309186 A
1 A
9309187 CAACTCTGCC
Statistics
Matches: 55, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
56 55 1.00
ACGTcount: A:0.19, C:0.37, G:0.05, T:0.38
Consensus pattern (56 bp):
ATATCACATCACCTTTTCATTTGTCAACTTTCTCCACTCCACCTCCTGTCCTACGT
Found at i:9314638 original size:20 final size:19
Alignment explanation
Indices: 9314613--9314711 Score: 65
Period size: 20 Copynumber: 4.9 Consensus size: 19
9314603 GCTTGTACGA
9314613 GATTGCACTTCGGTGCCTCT
1 GATTGCACTT-GGTGCCTCT
* * * *
9314633 GATTGCGCATTTGTACCCCT
1 GATTGCAC-TTGGTGCCTCT
* *
9314653 GTTTGCACTTTGGTGCCTTT
1 GATTGCAC-TTGGTGCCTCT
*
9314673 GATTGCACATTGATGCCTCT
1 GATTGCAC-TTGGTGCCTCT
*
9314693 -ATTTGCACTACGGTGCCTC
1 GA-TTGCACT-TGGTGCCTC
9314712 CGTTTGGCAT
Statistics
Matches: 59, Mismatches: 17, Indels: 6
0.72 0.21 0.07
Matches are distributed among these distances:
19 2 0.03
20 55 0.93
21 2 0.03
ACGTcount: A:0.13, C:0.27, G:0.22, T:0.37
Consensus pattern (19 bp):
GATTGCACTTGGTGCCTCT
Found at i:9314660 original size:40 final size:40
Alignment explanation
Indices: 9314615--9314711 Score: 115
Period size: 40 Copynumber: 2.4 Consensus size: 40
9314605 TTGTACGAGA
* *
9314615 TTGCACTTCGGTGCCTCTGATTGCGCATTTG-TACCCCTGT
1 TTGCACTTCGGTGCCTCTGATTGCACA-TTGATACCCCTAT
* * * *
9314655 TTGCACTTTGGTGCCTTTGATTGCACATTGATGCCTCTAT
1 TTGCACTTCGGTGCCTCTGATTGCACATTGATACCCCTAT
*
9314695 TTGCACTACGGTGCCTC
1 TTGCACTTCGGTGCCTC
9314712 CGTTTGGCAT
Statistics
Matches: 47, Mismatches: 9, Indels: 2
0.81 0.16 0.03
Matches are distributed among these distances:
39 3 0.06
40 44 0.94
ACGTcount: A:0.12, C:0.28, G:0.22, T:0.38
Consensus pattern (40 bp):
TTGCACTTCGGTGCCTCTGATTGCACATTGATACCCCTAT
Found at i:9318930 original size:66 final size:65
Alignment explanation
Indices: 9318822--9318946 Score: 153
Period size: 66 Copynumber: 1.9 Consensus size: 65
9318812 CTATAGTTGA
* *
9318822 AGTTCGTCATATTTTCTGCTTGCCTCTGCTTCCCTCGCTGCTGCATCCGCTTTAAGTTGTAGCTG
1 AGTTCGTCATATTTTCT-CTTGCCTCTACTTCCCTCGATGCTGCATCCGCTTTAAGTTGTAGCTG
9318887 G
65 G
* * * **
9318888 AGTTCTTCATATTTTCT-TTGAGCCTCTACTTCTCTCGATGCTGCCTTTGCTTTAAGTTG
1 AGTTCGTCATATTTTCTCTT--GCCTCTACTTCCCTCGATGCTGCATCCGCTTTAAGTTG
9318947 AGCAATTTGC
Statistics
Matches: 50, Mismatches: 7, Indels: 4
0.82 0.11 0.07
Matches are distributed among these distances:
64 2 0.04
66 48 0.96
ACGTcount: A:0.12, C:0.26, G:0.18, T:0.43
Consensus pattern (65 bp):
AGTTCGTCATATTTTCTCTTGCCTCTACTTCCCTCGATGCTGCATCCGCTTTAAGTTGTAGCTGG
Found at i:9328765 original size:43 final size:43
Alignment explanation
Indices: 9328704--9328818 Score: 169
Period size: 43 Copynumber: 2.7 Consensus size: 43
9328694 TTTTTGATAA
*
9328704 GTGTTTTCGTGTAAGACCACGTCTGGGACGTTAGTATCGACTT
1 GTGTTTTCGTGTAAGACCACGTCTGGGACGTTAGAATCGACTT
* * *
9328747 GTGTTTTCGTGTAAGACCACGTCTAGGATGTTGGAATCGACTT
1 GTGTTTTCGTGTAAGACCACGTCTGGGACGTTAGAATCGACTT
*
9328790 GTGTTTTTGTGTAAGACC-CTGTCTGGGAC
1 GTGTTTTCGTGTAAGACCAC-GTCTGGGAC
9328819 AGTGGCATTG
Statistics
Matches: 64, Mismatches: 7, Indels: 2
0.88 0.10 0.03
Matches are distributed among these distances:
42 1 0.02
43 63 0.98
ACGTcount: A:0.18, C:0.17, G:0.29, T:0.36
Consensus pattern (43 bp):
GTGTTTTCGTGTAAGACCACGTCTGGGACGTTAGAATCGACTT
Found at i:9338716 original size:43 final size:43
Alignment explanation
Indices: 9338655--9338818 Score: 210
Period size: 43 Copynumber: 3.8 Consensus size: 43
9338645 TTTTTGGTAA
*
9338655 GTATTTTCATGTAAGACCACGTCTAGGACGATGGCATCGATTT
1 GTATTTTCATGTAAGACCACGTCTGGGACGATGGCATCGATTT
* * *
9338698 GTATTTTCGTGTAAGACCACGTCTGAGACAATGGCATCGATTT
1 GTATTTTCATGTAAGACCACGTCTGGGACGATGGCATCGATTT
9338741 GTATTTTCGA-GTAAGACC-CTGTCTGGGAC-AGTGGCATCGATTT
1 GTATTTTC-ATGTAAGACCAC-GTCTGGGACGA-TGGCATCGATTT
* *
9338784 GCGA-TTACATGTAAGACCACGTCTGGGACGATGGC
1 G-TATTTTCATGTAAGACCACGTCTGGGACGATGGC
9338819 GTTGTATGAA
Statistics
Matches: 106, Mismatches: 8, Indels: 14
0.83 0.06 0.11
Matches are distributed among these distances:
42 3 0.03
43 100 0.94
44 3 0.03
ACGTcount: A:0.24, C:0.20, G:0.26, T:0.30
Consensus pattern (43 bp):
GTATTTTCATGTAAGACCACGTCTGGGACGATGGCATCGATTT
Found at i:9342872 original size:24 final size:26
Alignment explanation
Indices: 9342829--9342891 Score: 67
Period size: 24 Copynumber: 2.5 Consensus size: 26
9342819 AATATGAAAT
* * *
9342829 ATAAAAAATATATATTTATA-ATA-A
1 ATAAAAAGTATGTATGTATATATATA
*
9342853 ATAAAAAGTATGTATGTATATATATT
1 ATAAAAAGTATGTATGTATATATATA
9342879 ATAAAAATGTATG
1 ATAAAAA-GTATG
9342892 AAACAATTTG
Statistics
Matches: 32, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
24 17 0.53
25 3 0.09
26 7 0.22
27 5 0.16
ACGTcount: A:0.54, C:0.00, G:0.08, T:0.38
Consensus pattern (26 bp):
ATAAAAAGTATGTATGTATATATATA
Found at i:9342952 original size:15 final size:16
Alignment explanation
Indices: 9342932--9342964 Score: 59
Period size: 15 Copynumber: 2.1 Consensus size: 16
9342922 TTTGACATAG
9342932 ATAATAATATATA-AA
1 ATAATAATATATATAA
9342947 ATAATAATATATATAA
1 ATAATAATATATATAA
9342963 AT
1 AT
9342965 TTAAACCAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 13 0.76
16 4 0.24
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (16 bp):
ATAATAATATATATAA
Found at i:9343647 original size:8 final size:8
Alignment explanation
Indices: 9343634--9343667 Score: 52
Period size: 8 Copynumber: 4.2 Consensus size: 8
9343624 AAACAAAAGT
9343634 AAAAATAA
1 AAAAATAA
9343642 AAAAATAA
1 AAAAATAA
9343650 AAAAATAA
1 AAAAATAA
9343658 ACAAAA-AA
1 A-AAAATAA
9343666 AA
1 AA
9343668 GGTTTTGGAA
Statistics
Matches: 25, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
7 1 0.04
8 20 0.80
9 4 0.16
ACGTcount: A:0.88, C:0.03, G:0.00, T:0.09
Consensus pattern (8 bp):
AAAAATAA
Found at i:9343655 original size:16 final size:16
Alignment explanation
Indices: 9343624--9343667 Score: 54
Period size: 16 Copynumber: 2.8 Consensus size: 16
9343614 ACATTAGAAA
**
9343624 AAACAAAAGTAAAAAT
1 AAACAAAAAAAAAAAT
9343640 AAA-AAAATAAAAAAAT
1 AAACAAAA-AAAAAAAT
9343656 AAACAAAAAAAA
1 AAACAAAAAAAA
9343668 GGTTTTGGAA
Statistics
Matches: 24, Mismatches: 2, Indels: 4
0.80 0.07 0.13
Matches are distributed among these distances:
15 4 0.17
16 16 0.67
17 4 0.17
ACGTcount: A:0.84, C:0.05, G:0.02, T:0.09
Consensus pattern (16 bp):
AAACAAAAAAAAAAAT
Found at i:9344659 original size:128 final size:128
Alignment explanation
Indices: 9344414--9345444 Score: 1587
Period size: 128 Copynumber: 8.0 Consensus size: 128
9344404 GGATTCATCA
* * ** * * **
9344414 TTTTAATCCGCTCCACTGCAACTTCAAGGAGATAGGATTAGTAGCTTCAGTCTGCTCCACTGCAA
1 TTTTAATCCGCTCCACTGCAACTTCAGGGAGATAGGATTGGTTTCTTCTGTCTGCTCCACTACTG
* * * *
9344479 CTTCAGGGAGATAAGACTCGATGCGATCTGCTCTACTGCAACTTTAGAGAGATAAAATCTGTGG
66 CTT-AGGGAGATAAGACTTGATGCGATCTGCTCTACTGTAACTTCAGAGAGATAAGATCTGTGG
* *
9344543 TTTTAATCCGCTCCACTGCAACTTCAGGGAGATATGATTGATTTCTTCTGTCTGCTCCACTACTG
1 TTTTAATCCGCTCCACTGCAACTTCAGGGAGATAGGATTGGTTTCTTCTGTCTGCTCCACTACTG
*
9344608 CTTAGGGAGATAAGACTTAATGCGATCTGCTCTACTGTAACTTCAGAGAGATAAGATCTGTGG
66 CTTAGGGAGATAAGACTTGATGCGATCTGCTCTACTGTAACTTCAGAGAGATAAGATCTGTGG
* *
9344671 ATTTAATCCTCTCCACTGCAACTTCAGGGAGATAGGATTGGTTTCTTCTGTCTGCTCCACTACTG
1 TTTTAATCCGCTCCACTGCAACTTCAGGGAGATAGGATTGGTTTCTTCTGTCTGCTCCACTACTG
* *
9344736 CTTAGGGAGATAAGACTTGATGCGATCTACTCTACTGTAACTTCAGAGAGATACGATCTGTGG
66 CTTAGGGAGATAAGACTTGATGCGATCTGCTCTACTGTAACTTCAGAGAGATAAGATCTGTGG
* * * * *
9344799 TTTTAATCCGCTCCACTGTAAATTTAGGGAGATAGGTTTGGTTTCTTCTGTCTGCTCCACT-GTA
1 TTTTAATCCGCTCCACTGCAACTTCAGGGAGATAGGATTGGTTTCTTCTGTCTGCTCCACTACT-
* * * * *
9344863 ACTTCAGGGAGATAAGACTAGATGCGATTTGCTCTACTGTAACTTCAAAGAGATAAGATCTATGG
65 GCTT-AGGGAGATAAGACTTGATGCGATCTGCTCTACTGTAACTTCAGAGAGATAAGATCTGTGG
* *
9344928 TTTTAATCCGCTCCACTGCAACTTTAGGGAGATAGGATTGGTTTCTTCTGTCTTCTCCACTACTG
1 TTTTAATCCGCTCCACTGCAACTTCAGGGAGATAGGATTGGTTTCTTCTGTCTGCTCCACTACTG
* * *
9344993 CTTAGGGAGATAAGACTTGATGCGATTTGCTCTACTGCAACTTTAGAGAGATAAGATCTGTGG
66 CTTAGGGAGATAAGACTTGATGCGATCTGCTCTACTGTAACTTCAGAGAGATAAGATCTGTGG
* * *
9345056 TTTTAATCTGCTCCACTGCAACTTCAGGGAGATAGGATTAGTTTCTTCTGTCTGCTCCACTACTT
1 TTTTAATCCGCTCCACTGCAACTTCAGGGAGATAGGATTGGTTTCTTCTGTCTGCTCCACTACTG
* *
9345121 TTTAGGGAGATAAGACTTGATGCGATCTGCTCTACTATAACTTCAGAGAGATAAGATCTGTGG
66 CTTAGGGAGATAAGACTTGATGCGATCTGCTCTACTGTAACTTCAGAGAGATAAGATCTGTGG
* *
9345184 TTTTAATCTGCTCCACTGCAACTTCAGAGAGATAGGATTGGTTTCTTCTGTCTGCTCCACTACTG
1 TTTTAATCCGCTCCACTGCAACTTCAGGGAGATAGGATTGGTTTCTTCTGTCTGCTCCACTACTG
* *
9345249 CTTAGGGAGATAAGACTTGATGCGATCTGCTCTACTGTAACTTCAGAAAGATAAGATTTGTGG
66 CTTAGGGAGATAAGACTTGATGCGATCTGCTCTACTGTAACTTCAGAGAGATAAGATCTGTGG
* *
9345312 TTTTAATCCGCTCCACTGCAACTTTAGGGAGATAGGATTGGTTCCTTCTGTCTGCTCCACTACTG
1 TTTTAATCCGCTCCACTGCAACTTCAGGGAGATAGGATTGGTTTCTTCTGTCTGCTCCACTACTG
* * * *
9345377 TTTAGGGAGATAAGATTTGATGCGATCTACTCTACTGCAACTTCAGAGAGATAAGATCTGTGG
66 CTTAGGGAGATAAGACTTGATGCGATCTGCTCTACTGTAACTTCAGAGAGATAAGATCTGTGG
9345440 TTTTA
1 TTTTA
9345445 CTGATCTGTA
Statistics
Matches: 825, Mismatches: 74, Indels: 7
0.91 0.08 0.01
Matches are distributed among these distances:
127 1 0.00
128 651 0.79
129 172 0.21
130 1 0.00
ACGTcount: A:0.25, C:0.20, G:0.22, T:0.33
Consensus pattern (128 bp):
TTTTAATCCGCTCCACTGCAACTTCAGGGAGATAGGATTGGTTTCTTCTGTCTGCTCCACTACTG
CTTAGGGAGATAAGACTTGATGCGATCTGCTCTACTGTAACTTCAGAGAGATAAGATCTGTGG
Found at i:9345102 original size:385 final size:385
Alignment explanation
Indices: 9344414--9345444 Score: 1629
Period size: 385 Copynumber: 2.7 Consensus size: 385
9344404 GGATTCATCA
* * ** * *
9344414 TTTTAATCCGCTCCACTGCAACTTCAAGGAGATAGGATTAGTAGCTTCAGTCTGCTCCACTGCAA
1 TTTTAATCCGCTCCACTGCAACTTCAGGGAGATAGGATTGGTTTCTTCTGTCTGCTCCACTGTAA
* * * * *
9344479 CTTCAGGGAGATAAGACTCGATGCGATCTGCTCTACTGCAACTTTAGAGAGATAAAATCTGTGGT
66 CTTCAGGGAGATAAGACTAGATGCGATCTGCTCTACTGTAACTTCAAAGAGATAAGATCTGTGGT
* * *
9344544 TTTAATCCGCTCCACTGCAACTTCAGGGAGATATGATTGATTTCTTCTGTCTGCTCCACTACTGC
131 TTTAATCCGCTCCACTGCAACTTTAGGGAGATAGGATTGGTTTCTTCTGTCTGCTCCACTACTGC
* * *
9344609 TTAGGGAGATAAGACTTAATGCGATCTGCTCTACTGTAACTTCAGAGAGATAAGATCTGTGGATT
196 TTAGGGAGATAAGACTTGATGCGATCTGCTCTACTGCAACTTCAGAGAGATAAGATCTGTGGTTT
*
9344674 TAATCCTCTCCACTGCAACTTCAGGGAGATAGGATTGGTTTCTTCTGTCTGCTCCACTACTGCTT
261 TAATCCTCTCCACTGCAACTTCAGGGAGATAGGATTAGTTTCTTCTGTCTGCTCCACTACTGCTT
* *
9344739 AGGGAGATAAGACTTGATGCGATCTACTCTACTGTAACTTCAGAGAGATACGATCTGTGG
326 AGGGAGATAAGACTTGATGCGATCTACTCTACTATAACTTCAGAGAGATAAGATCTGTGG
* * * *
9344799 TTTTAATCCGCTCCACTGTAAATTTAGGGAGATAGGTTTGGTTTCTTCTGTCTGCTCCACTGTAA
1 TTTTAATCCGCTCCACTGCAACTTCAGGGAGATAGGATTGGTTTCTTCTGTCTGCTCCACTGTAA
* *
9344864 CTTCAGGGAGATAAGACTAGATGCGATTTGCTCTACTGTAACTTCAAAGAGATAAGATCTATGGT
66 CTTCAGGGAGATAAGACTAGATGCGATCTGCTCTACTGTAACTTCAAAGAGATAAGATCTGTGGT
*
9344929 TTTAATCCGCTCCACTGCAACTTTAGGGAGATAGGATTGGTTTCTTCTGTCTTCTCCACTACTGC
131 TTTAATCCGCTCCACTGCAACTTTAGGGAGATAGGATTGGTTTCTTCTGTCTGCTCCACTACTGC
* *
9344994 TTAGGGAGATAAGACTTGATGCGATTTGCTCTACTGCAACTTTAGAGAGATAAGATCTGTGGTTT
196 TTAGGGAGATAAGACTTGATGCGATCTGCTCTACTGCAACTTCAGAGAGATAAGATCTGTGGTTT
**
9345059 TAAT-CTGCTCCACTGCAACTTCAGGGAGATAGGATTAGTTTCTTCTGTCTGCTCCACTACTTTT
261 TAATCCT-CTCCACTGCAACTTCAGGGAGATAGGATTAGTTTCTTCTGTCTGCTCCACTACTGCT
*
9345123 TAGGGAGATAAGACTTGATGCGATCTGCTCTACTATAACTTCAGAGAGATAAGATCTGTGG
325 TAGGGAGATAAGACTTGATGCGATCTACTCTACTATAACTTCAGAGAGATAAGATCTGTGG
* * *
9345184 TTTTAATCTGCTCCACTGCAACTTCAGAGAGATAGGATTGGTTTCTTCTGTCTGCTCCACTACT-
1 TTTTAATCCGCTCCACTGCAACTTCAGGGAGATAGGATTGGTTTCTTCTGTCTGCTCCACT-GTA
* * *
9345248 GCTT-AGGGAGATAAGACTTGATGCGATCTGCTCTACTGTAACTTCAGAA-AGATAAGATTTGTG
65 ACTTCAGGGAGATAAGACTAGATGCGATCTGCTCTACTGTAACTTCA-AAGAGATAAGATCTGTG
*
9345311 GTTTTAATCCGCTCCACTGCAACTTTAGGGAGATAGGATTGGTTCCTTCTGTCTGCTCCACTACT
129 GTTTTAATCCGCTCCACTGCAACTTTAGGGAGATAGGATTGGTTTCTTCTGTCTGCTCCACTACT
* * *
9345376 GTTTAGGGAGATAAGATTTGATGCGATCTACTCTACTGCAACTTCAGAGAGATAAGATCTGTGGT
194 GCTTAGGGAGATAAGACTTGATGCGATCTGCTCTACTGCAACTTCAGAGAGATAAGATCTGTGGT
9345441 TTTA
259 TTTA
9345445 CTGATCTGTA
Statistics
Matches: 592, Mismatches: 51, Indels: 7
0.91 0.08 0.01
Matches are distributed among these distances:
384 181 0.31
385 410 0.69
386 1 0.00
ACGTcount: A:0.25, C:0.20, G:0.22, T:0.33
Consensus pattern (385 bp):
TTTTAATCCGCTCCACTGCAACTTCAGGGAGATAGGATTGGTTTCTTCTGTCTGCTCCACTGTAA
CTTCAGGGAGATAAGACTAGATGCGATCTGCTCTACTGTAACTTCAAAGAGATAAGATCTGTGGT
TTTAATCCGCTCCACTGCAACTTTAGGGAGATAGGATTGGTTTCTTCTGTCTGCTCCACTACTGC
TTAGGGAGATAAGACTTGATGCGATCTGCTCTACTGCAACTTCAGAGAGATAAGATCTGTGGTTT
TAATCCTCTCCACTGCAACTTCAGGGAGATAGGATTAGTTTCTTCTGTCTGCTCCACTACTGCTT
AGGGAGATAAGACTTGATGCGATCTACTCTACTATAACTTCAGAGAGATAAGATCTGTGG
Found at i:9345369 original size:44 final size:45
Alignment explanation
Indices: 9344423--9345391 Score: 207
Period size: 44 Copynumber: 22.6 Consensus size: 45
9344413 ATTTTAATCC
* * * * ** *
9344423 GCTCCACTGCAACTTCAAGGAGATAGGA-TTAGTAGCTTCAGTCT
1 GCTCCACTGCAACTTTAGGGAGATAAGACTTGGTTCCTTCTGTCT
* * * * **
9344467 GCTCCACTGCAACTTCAGGGAGATAAGACTCGATGCGATCTG-CT
1 GCTCCACTGCAACTTTAGGGAGATAAGACTTGGTTCCTTCTGTCT
* * ** *
9344511 -CT--ACTGCAACTTTAGAGAGATAAAATCTGTGGTT--TT-AATCC
1 GCTCCACTGCAACTTTAGGGAGATAAGA-CT-TGGTTCCTTCTGTCT
* * * *
9344552 GCTCCACTGCAACTTCAGGGAGATATGA-TTGATTTCTTCTGTCT
1 GCTCCACTGCAACTTTAGGGAGATAAGACTTGGTTCCTTCTGTCT
* ** ** * **
9344596 GCTCCACTACTGC-TTAGGGAGATAAGACTTAATGCGATCTG-CT
1 GCTCCACTGCAACTTTAGGGAGATAAGACTTGGTTCCTTCTGTCT
* * * ** *
9344639 -CT--ACTGTAACTTCAGAGAGATAAGATCTGTGGATT--TAAT-CCT
1 GCTCCACTGCAACTTTAGGGAGATAAGA-CT-TGG-TTCCTTCTGTCT
* * *
9344681 -CTCCACTGCAACTTCAGGGAGATAGGA-TTGGTTTCTTCTGTCT
1 GCTCCACTGCAACTTTAGGGAGATAAGACTTGGTTCCTTCTGTCT
* ** * * ** *
9344724 GCTCCACTACTGC-TTAGGGAGATAAGACTTGATGCGATCT-ACT
1 GCTCCACTGCAACTTTAGGGAGATAAGACTTGGTTCCTTCTGTCT
* * * * ** *
9344767 -CT--ACTGTAACTTCAGAGAGATACGATCTGTGGTT--TT-AATCC
1 GCTCCACTGCAACTTTAGGGAGATAAGA-CT-TGGTTCCTTCTGTCT
* * ** *
9344808 GCTCCACTGTAAATTTAGGGAGAT-AGGTTTGGTTTCTTCTGTCT
1 GCTCCACTGCAACTTTAGGGAGATAAGACTTGGTTCCTTCTGTCT
* * * * * *
9344852 GCTCCACTGTAACTTCAGGGAGATAAGACTAGATGCGATT-TG-CT
1 GCTCCACTGCAACTTTAGGGAGATAAGACTTGGTTC-CTTCTGTCT
* * ** ** *
9344896 -CT--ACTGTAACTTCAAAGAGATAAGATCTATGGTT--TT-AATCC
1 GCTCCACTGCAACTTTAGGGAGATAAGA-CT-TGGTTCCTTCTGTCT
* *
9344937 GCTCCACTGCAACTTTAGGGAGATAGGA-TTGGTTTCTTCTGTCT
1 GCTCCACTGCAACTTTAGGGAGATAAGACTTGGTTCCTTCTGTCT
* * ** * * *
9344981 TCTCCACTACTGC-TTAGGGAGATAAGACTTGATGCGATT-TG-CT
1 GCTCCACTGCAACTTTAGGGAGATAAGACTTGGTTC-CTTCTGTCT
* **
9345024 -CT--ACTGCAACTTTAGAGAGATAAGATCTGTGGTT--TT-AATCT
1 GCTCCACTGCAACTTTAGGGAGATAAGA-CT-TGGTTCCTTCTGTCT
* * * *
9345065 GCTCCACTGCAACTTCAGGGAGATAGGA-TTAGTTTCTTCTGTCT
1 GCTCCACTGCAACTTTAGGGAGATAAGACTTGGTTCCTTCTGTCT
* ** * * **
9345109 GCTCCACTAC-TTTTTAGGGAGATAAGACTTGATGCGATCTG-CT
1 GCTCCACTGCAACTTTAGGGAGATAAGACTTGGTTCCTTCTGTCT
** * * **
9345152 -CT--ACTATAACTTCAGAGAGATAAGATCTGTGGTT--TT-AATCT
1 GCTCCACTGCAACTTTAGGGAGATAAGA-CT-TGGTTCCTTCTGTCT
* * * *
9345193 GCTCCACTGCAACTTCAGAGAGATAGGA-TTGGTTTCTTCTGTCT
1 GCTCCACTGCAACTTTAGGGAGATAAGACTTGGTTCCTTCTGTCT
* ** * * **
9345237 GCTCCACTACTGC-TTAGGGAGATAAGACTTGATGCGATCTG-CT
1 GCTCCACTGCAACTTTAGGGAGATAAGACTTGGTTCCTTCTGTCT
* * ** * ** *
9345280 -CT--ACTGTAACTTCAGAAAGATAAGATTTGTGGTT--TT-AATCC
1 GCTCCACTGCAACTTTAGGGAGATAAGA-CT-TGGTTCCTTCTGTCT
*
9345321 GCTCCACTGCAACTTTAGGGAGATAGGA-TTGGTTCCTTCTGTCT
1 GCTCCACTGCAACTTTAGGGAGATAAGACTTGGTTCCTTCTGTCT
* **
9345365 GCTCCACTAC-TGTTTAGGGAGATAAGA
1 GCTCCACTGCAACTTTAGGGAGATAAGA
9345392 TTTGATGCGA
Statistics
Matches: 647, Mismatches: 200, Indels: 157
0.64 0.20 0.16
Matches are distributed among these distances:
40 27 0.04
41 144 0.22
42 49 0.08
43 121 0.19
44 290 0.45
45 14 0.02
46 2 0.00
ACGTcount: A:0.25, C:0.20, G:0.22, T:0.33
Consensus pattern (45 bp):
GCTCCACTGCAACTTTAGGGAGATAAGACTTGGTTCCTTCTGTCT
Found at i:9346741 original size:16 final size:16
Alignment explanation
Indices: 9346720--9346753 Score: 68
Period size: 16 Copynumber: 2.1 Consensus size: 16
9346710 AGCCAATATG
9346720 TTGCCACGGCAGAGAT
1 TTGCCACGGCAGAGAT
9346736 TTGCCACGGCAGAGAT
1 TTGCCACGGCAGAGAT
9346752 TT
1 TT
9346754 TTTTTTTTAC
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.24, C:0.24, G:0.29, T:0.24
Consensus pattern (16 bp):
TTGCCACGGCAGAGAT
Found at i:9351730 original size:56 final size:57
Alignment explanation
Indices: 9351613--9351730 Score: 125
Period size: 56 Copynumber: 2.1 Consensus size: 57
9351603 GAAAATGAAT
* * * *
9351613 AAAATTATAAAAACATAAAAAGATATATAAGTATGTATATATATATATATGTACATT
1 AAAATTATAAAAACATAAAAAGATATATAAGTATATATATATATATATATGAAAATA
** * *
9351670 AAAATTAT-AAAGTATAAAAATATATATAAGTATATAT-TA-ATAAGTTTATGAAAATA
1 AAAATTATAAAAACATAAAAAGATATATAAGTATATATATATAT-A-TATATGAAAATA
9351726 AAAAT
1 AAAAT
9351731 GCATATATAG
Statistics
Matches: 51, Mismatches: 8, Indels: 5
0.80 0.12 0.08
Matches are distributed among these distances:
54 2 0.04
55 3 0.06
56 38 0.75
57 8 0.16
ACGTcount: A:0.57, C:0.02, G:0.07, T:0.35
Consensus pattern (57 bp):
AAAATTATAAAAACATAAAAAGATATATAAGTATATATATATATATATATGAAAATA
Found at i:9351998 original size:15 final size:16
Alignment explanation
Indices: 9351978--9352010 Score: 59
Period size: 15 Copynumber: 2.1 Consensus size: 16
9351968 TTTGACATAG
9351978 ATAATAATATATA-AA
1 ATAATAATATATATAA
9351993 ATAATAATATATATAA
1 ATAATAATATATATAA
9352009 AT
1 AT
9352011 TTAAACCAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 13 0.76
16 4 0.24
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (16 bp):
ATAATAATATATATAA
Found at i:9355971 original size:15 final size:17
Alignment explanation
Indices: 9355951--9355997 Score: 55
Period size: 16 Copynumber: 2.9 Consensus size: 17
9355941 TATTTAAAAT
9355951 TAAAAAAT-AAA-TTTA
1 TAAAAAATAAAATTTTA
*
9355966 TAAAAATTAAAATTTTA
1 TAAAAAATAAAATTTTA
*
9355983 T-AAAACTAAAATTTT
1 TAAAAAATAAAATTTT
9355998 CTGAAAAACA
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
15 7 0.25
16 16 0.57
17 5 0.18
ACGTcount: A:0.60, C:0.02, G:0.00, T:0.38
Consensus pattern (17 bp):
TAAAAAATAAAATTTTA
Found at i:9355978 original size:16 final size:16
Alignment explanation
Indices: 9355944--9355996 Score: 53
Period size: 16 Copynumber: 3.6 Consensus size: 16
9355934 TAAAAATTAT
9355944 TTAAAA-TTA-AAAAA
1 TTAAAATTTATAAAAA
9355958 -T-AAATTTATAAAAA
1 TTAAAATTTATAAAAA
9355972 TTAAAATTT-TATAAAA
1 TTAAAATTTATA-AAAA
*
9355988 CTAAAATTT
1 TTAAAATTT
9355997 TCTGAAAAAC
Statistics
Matches: 33, Mismatches: 1, Indels: 8
0.79 0.02 0.19
Matches are distributed among these distances:
12 3 0.09
13 4 0.12
14 5 0.15
15 3 0.09
16 18 0.55
ACGTcount: A:0.60, C:0.02, G:0.00, T:0.38
Consensus pattern (16 bp):
TTAAAATTTATAAAAA
Found at i:9355997 original size:16 final size:17
Alignment explanation
Indices: 9355962--9356010 Score: 57
Period size: 16 Copynumber: 2.9 Consensus size: 17
9355952 AAAAAATAAA
*
9355962 TTTATAAAAATTAAAAT
1 TTTATAAAAACTAAAAT
9355979 TTTAT-AAAACTAAAAT
1 TTTATAAAAACTAAAAT
*
9355995 TTTCTGAAAAAC-AAAA
1 TTTAT-AAAAACTAAAA
9356011 AAAATAAGGA
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
16 14 0.50
17 9 0.32
18 5 0.18
ACGTcount: A:0.57, C:0.06, G:0.02, T:0.35
Consensus pattern (17 bp):
TTTATAAAAACTAAAAT
Found at i:9374072 original size:27 final size:27
Alignment explanation
Indices: 9374023--9374074 Score: 70
Period size: 27 Copynumber: 1.9 Consensus size: 27
9374013 ATTTTATCGG
* *
9374023 GGGTAAAATTGTCACAATTTTACTAAA
1 GGGTAAAATTATCACAATATTACTAAA
9374050 GGGTAAAATTATCGA-AATATTACTA
1 GGGTAAAATTATC-ACAATATTACTA
9374075 GAGTAAAATT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
27 21 0.95
28 1 0.05
ACGTcount: A:0.42, C:0.10, G:0.15, T:0.33
Consensus pattern (27 bp):
GGGTAAAATTATCACAATATTACTAAA
Found at i:9377930 original size:31 final size:31
Alignment explanation
Indices: 9377875--9377935 Score: 79
Period size: 31 Copynumber: 2.0 Consensus size: 31
9377865 AAAAAATGAG
* *
9377875 CCCACACAGCCTACCTAATCTGCCCGTGTGT
1 CCCACACAGCCTACCAAATCTGCCCATGTGT
*
9377906 CCCACACGGCCTACCCAAAT-TGCCCATGTG
1 CCCACACAGCCTA-CCAAATCTGCCCATGTG
9377936 CTTCACACGG
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
31 21 0.81
32 5 0.19
ACGTcount: A:0.21, C:0.43, G:0.16, T:0.20
Consensus pattern (31 bp):
CCCACACAGCCTACCAAATCTGCCCATGTGT
Found at i:9382711 original size:13 final size:14
Alignment explanation
Indices: 9382677--9382716 Score: 50
Period size: 14 Copynumber: 3.1 Consensus size: 14
9382667 AAAGTTACTA
9382677 AAATACAAAAA-A-
1 AAATACAAAAAGAG
9382689 AAATAC-AAAAGAG
1 AAATACAAAAAGAG
*
9382702 AAATATAAAAAGAG
1 AAATACAAAAAGAG
9382716 A
1 A
9382717 GCACCACTTT
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
11 4 0.17
12 7 0.29
13 5 0.21
14 8 0.33
ACGTcount: A:0.75, C:0.05, G:0.10, T:0.10
Consensus pattern (14 bp):
AAATACAAAAAGAG
Found at i:9383191 original size:89 final size:90
Alignment explanation
Indices: 9383063--9383268 Score: 301
Period size: 89 Copynumber: 2.3 Consensus size: 90
9383053 ACTTAAAAAA
* *
9383063 AAAAAAAGCAATTAAGCCCCT-CTTTTTTTTTGCACTCAATTGAGCAGTTGAACTTTCAAAATGC
1 AAAAAAAGCAATTAAGCCCCTACTTTTTGTTTGCACTCAATTGAGCACTTGAACTTTCAAAATGC
**
9383127 ATCAAAAATGCCCTCAAACCTTTTC
66 ATCAAAAAAACCCTCAAACCTTTTC
* *
9383152 AAAAAAA-CAATTAAGCCCCTACTTTTTGTTTGCACTCAATTGGGTACTTGAACTTTCAAAATGC
1 AAAAAAAGCAATTAAGCCCCTACTTTTTGTTTGCACTCAATTGAGCACTTGAACTTTCAAAATGC
* *
9383216 ATCAAAAAAACCCTCAAACTTTTTT
66 ATCAAAAAAACCCTCAAACCTTTTC
*
9383241 AGAAAAAAGCAATTAATCCCCTA-TTTTT
1 A-AAAAAAGCAATTAAGCCCCTACTTTTT
9383269 ATTAAAAATT
Statistics
Matches: 105, Mismatches: 9, Indels: 5
0.88 0.08 0.04
Matches are distributed among these distances:
88 13 0.12
89 68 0.65
90 11 0.10
91 13 0.12
ACGTcount: A:0.37, C:0.22, G:0.09, T:0.32
Consensus pattern (90 bp):
AAAAAAAGCAATTAAGCCCCTACTTTTTGTTTGCACTCAATTGAGCACTTGAACTTTCAAAATGC
ATCAAAAAAACCCTCAAACCTTTTC
Found at i:9383285 original size:10 final size:10
Alignment explanation
Indices: 9383267--9383419 Score: 75
Period size: 10 Copynumber: 16.8 Consensus size: 10
9383257 TCCCCTATTT
*
9383267 TTATTAAAAA
1 TTATAAAAAA
9383277 TTATAAAAAA
1 TTATAAAAAA
9383287 TTATAAAAAA
1 TTATAAAAAA
*
9383297 TTA-AAATAA
1 TTATAAAAAA
*
9383306 --AT-AAAAC
1 TTATAAAAAA
* *
9383313 CTAT-AAATA
1 TTATAAAAAA
9383322 TTAT--AAAA
1 TTATAAAAAA
* *
9383330 TTTTAATAAA
1 TTATAAAAAA
*
9383340 -TAT-TAAAA
1 TTATAAAAAA
* *
9383348 -TATTAAAAT
1 TTATAAAAAA
*
9383357 TTAGAAAAAA
1 TTATAAAAAA
9383367 -TAT-AAAAA
1 TTATAAAAAA
*
9383375 TCATAAAAAA
1 TTATAAAAAA
*
9383385 TTATAAAATA
1 TTATAAAAAA
*
9383395 -TAT-AGAAA
1 TTATAAAAAA
9383403 -TATAAAAAA
1 TTATAAAAAA
9383412 TTATAAAA
1 TTATAAAA
9383420 TTTTATAAAG
Statistics
Matches: 107, Mismatches: 25, Indels: 22
0.69 0.16 0.14
Matches are distributed among these distances:
7 4 0.04
8 23 0.21
9 29 0.27
10 51 0.48
ACGTcount: A:0.65, C:0.02, G:0.01, T:0.32
Consensus pattern (10 bp):
TTATAAAAAA
Found at i:9383299 original size:27 final size:26
Alignment explanation
Indices: 9383268--9383456 Score: 130
Period size: 27 Copynumber: 7.0 Consensus size: 26
9383258 CCCCTATTTT
9383268 TATTAAAAATTATAAAAAATTATAAAA
1 TATTAAAAATTATAAAAAA-TATAAAA
* * **
9383295 AATT-AAAATAAATAAAACCTAT-AAA
1 TATTAAAAAT-TATAAAAAATATAAAA
* *
9383320 TATTATAAAATTTTAATAAATATTAAAA
1 TATTA-AAAATTATAAAAAATA-TAAAA
* *
9383348 TATTAAAATTTAGAAAAAATATAAAAA
1 TATTAAAAATTATAAAAAATAT-AAAA
* *
9383375 TCATAAAAAATTATAAAATATATAGAAA
1 T-ATTAAAAATTATAAAAAATATA-AAA
* ** *
9383403 TATAAAAAATTATAAAATTTTATAAAG
1 TATTAAAAATTATAAAA-AATATAAAA
* *
9383430 TCATTAGAAAATTATACAAAATGTAAA
1 T-ATTA-AAAATTATAAAAAATATAAA
9383457 GAAATATAAA
Statistics
Matches: 126, Mismatches: 25, Indels: 21
0.73 0.15 0.12
Matches are distributed among these distances:
25 6 0.05
26 15 0.12
27 52 0.41
28 42 0.33
29 11 0.09
ACGTcount: A:0.62, C:0.03, G:0.03, T:0.32
Consensus pattern (26 bp):
TATTAAAAATTATAAAAAATATAAAA
Found at i:9383695 original size:17 final size:19
Alignment explanation
Indices: 9383675--9383710 Score: 58
Period size: 19 Copynumber: 2.0 Consensus size: 19
9383665 AAAAAAAATT
9383675 ATAA-TTTT-TAAAATTTA
1 ATAATTTTTCTAAAATTTA
9383692 ATAATTTTTCTAAAATTTA
1 ATAATTTTTCTAAAATTTA
9383711 TTATTTATTA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 4 0.24
18 4 0.24
19 9 0.53
ACGTcount: A:0.44, C:0.03, G:0.00, T:0.53
Consensus pattern (19 bp):
ATAATTTTTCTAAAATTTA
Found at i:9383901 original size:87 final size:87
Alignment explanation
Indices: 9383757--9383972 Score: 285
Period size: 87 Copynumber: 2.5 Consensus size: 87
9383747 ATAAAAGCAT
* *
9383757 GGGCTTAATTG-ATTTTTTGAAAAATTTTGAGGGTCTTTTTGATGCATTTTGAAAGTTTAAGTAC
1 GGGCTTAATTGCATTTTTTGAAAAAGTTTGAGGG-CTTTTTGATACATTTTGAAAGTTTAAGTAC
*
9383821 CCAATTAAGTG-AAAAAAATAG-
65 CCAATTAAGTGAAAAAAAAAAGA
* * *
9383842 GGGCTTAATTGCTTTTTTTTGAACAAGTTTGAGGGCCTTTTTGATACATTTTGAAAGTTTAAGTG
1 GGGCTTAATTGC-ATTTTTTGAAAAAGTTTGAGGG-CTTTTTGATACATTTTGAAAGTTTAAGTA
*
9383907 CTCAATTAAGTGCAAAAAAAAAAGAA
64 CCCAATTAAGTG-AAAAAAAAAAG-A
* *
9383933 GGGCTTAATTACCTTTTTTGAAAAAGTTTGAGGGCTTTTT
1 GGGCTTAATTGCATTTTTTGAAAAAGTTTGAGGGCTTTTT
9383973 ATATCCTTAA
Statistics
Matches: 114, Mismatches: 11, Indels: 8
0.86 0.08 0.06
Matches are distributed among these distances:
85 11 0.10
87 57 0.50
89 15 0.13
90 20 0.18
91 11 0.10
ACGTcount: A:0.32, C:0.09, G:0.20, T:0.39
Consensus pattern (87 bp):
GGGCTTAATTGCATTTTTTGAAAAAGTTTGAGGGCTTTTTGATACATTTTGAAAGTTTAAGTACC
CAATTAAGTGAAAAAAAAAAGA
Found at i:9387371 original size:19 final size:20
Alignment explanation
Indices: 9387331--9387374 Score: 56
Period size: 19 Copynumber: 2.3 Consensus size: 20
9387321 ATCTCTTTAG
* *
9387331 GCATT-CATTTCATGCATTT
1 GCATTACATTGCATGCATAT
9387350 GCATTACATTGCAT-CATAT
1 GCATTACATTGCATGCATAT
9387369 GCATTA
1 GCATTA
9387375 AACACCTCTA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
19 15 0.68
20 7 0.32
ACGTcount: A:0.27, C:0.20, G:0.11, T:0.41
Consensus pattern (20 bp):
GCATTACATTGCATGCATAT
Found at i:9389328 original size:21 final size:21
Alignment explanation
Indices: 9389304--9389349 Score: 56
Period size: 21 Copynumber: 2.2 Consensus size: 21
9389294 TCAAATTTTT
*
9389304 TTCTGCCAAATTATTCATTCA
1 TTCTGCCAAATTATTCATACA
** *
9389325 TTCTTTCATATTATTCATACA
1 TTCTGCCAAATTATTCATACA
9389346 TTCT
1 TTCT
9389350 TTTGTATATT
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.26, C:0.22, G:0.02, T:0.50
Consensus pattern (21 bp):
TTCTGCCAAATTATTCATACA
Found at i:9390166 original size:44 final size:45
Alignment explanation
Indices: 9390082--9390166 Score: 118
Period size: 45 Copynumber: 1.9 Consensus size: 45
9390072 AAAAGGTGGG
* * *
9390082 ACCAAGGTGAAAGCCTACAAAGGGCGCTTTGAGTCAAAAAAAAAA
1 ACCAAGGTGAAACCCTACAAAGGGAGCCTTGAGTCAAAAAAAAAA
* *
9390127 ACCAGGGTGAAACCCTACAAGGGGAGCCTTGAG-CAAAAAA
1 ACCAAGGTGAAACCCTACAAAGGGAGCCTTGAGTCAAAAAA
9390167 TGGAGAGGCT
Statistics
Matches: 35, Mismatches: 5, Indels: 1
0.85 0.12 0.02
Matches are distributed among these distances:
44 7 0.20
45 28 0.80
ACGTcount: A:0.44, C:0.20, G:0.25, T:0.12
Consensus pattern (45 bp):
ACCAAGGTGAAACCCTACAAAGGGAGCCTTGAGTCAAAAAAAAAA
Found at i:9391726 original size:43 final size:43
Alignment explanation
Indices: 9391657--9391739 Score: 105
Period size: 43 Copynumber: 1.9 Consensus size: 43
9391647 CAAAGATGGT
** *
9391657 GAATTTTACCTCCCTGAGGTTGCAGTGGAGTACATTGAAGCCA
1 GAATTTTACCTCCCTGAGCATGCAGTGGAATACATTGAAGCCA
* *
9391700 GAATTTCTACTTCCCTGAGCAT-CAGTGGAATAGATTGAAG
1 GAATTT-TACCTCCCTGAGCATGCAGTGGAATACATTGAAG
9391740 ATTTCAGATC
Statistics
Matches: 34, Mismatches: 5, Indels: 2
0.83 0.12 0.05
Matches are distributed among these distances:
43 22 0.65
44 12 0.35
ACGTcount: A:0.28, C:0.19, G:0.24, T:0.29
Consensus pattern (43 bp):
GAATTTTACCTCCCTGAGCATGCAGTGGAATACATTGAAGCCA
Found at i:9391840 original size:132 final size:132
Alignment explanation
Indices: 9391468--9392398 Score: 1131
Period size: 132 Copynumber: 7.0 Consensus size: 132
9391458 GTGGAGCAGG
* * * *
9391468 TTGAAGATTTCAGATCTTGCCTTCCT--GCATAGACAGCGGAGCAGATCAAAGATGGTGGATTTT
1 TTGAAGATTTCAGATCTTGCCTCCCTAAGC--AG-TAGTGGAGCAGATCAAAGATGGCGGATTTT
** *
9391531 ACCTCCCTGAAGTTGCAGTGGAGTACATTGAAGCCAAAAATTCTACTTCCCTGGGCAGCAGTGGA
63 ACCTCCCTGTGGTTGCAGTGGAGTACATTGAAGCCAATAATTCTACTTCCCTGGGCAGCAGTGGA
9391596 ATAGA
128 ATAGA
* * * * * * *
9391601 TTAAAGATTTCAGATTTTGCCTTCCT--GCATAGACAGCGGAGCAGATCAAAGATGGTGAATTTT
1 TTGAAGATTTCAGATCTTGCCTCCCTAAGC--AG-TAGTGGAGCAGATCAAAGATGGCGGATTTT
* * * *
9391664 ACCTCCCTGAGGTTGCAGTGGAGTACATTGAAGCCAGA-ATTTCTACTTCCCTGAGCATCAGTGG
63 ACCTCCCTGTGGTTGCAGTGGAGTACATTGAAGCCA-ATAATTCTACTTCCCTGGGCAGCAGTGG
9391728 AATAGA
127 AATAGA
* * * *
9391734 TTGAAGATTTCAGATCTTGTCTCCTTAAGCAGTAGTGGGGCAGATCAAATATGGCGGATTTTACC
1 TTGAAGATTTCAGATCTTGCCTCCCTAAGCAGTAGTGGAGCAGATCAAAGATGGCGGATTTTACC
* * *
9391799 T-CCTCGTGGTTACAGTGGAGTACATTGAAGCCAATAATTCTACTTCCCTGAGCAGCAGCGGAAT
66 TCCCT-GTGGTTGCAGTGGAGTACATTGAAGCCAATAATTCTACTTCCCTGGGCAGCAGTGGAAT
9391863 AGA
130 AGA
** * * ** * * *
9391866 TTGAAGATTGAAGATCCTGCCTCCCTAAACAACAGCGGAGCGGATCAAAGATGGCGAATTTTACC
1 TTGAAGATTTCAGATCTTGCCTCCCTAAGCAGTAGTGGAGCAGATCAAAGATGGCGGATTTTACC
* * * * **
9391931 TCCCTGTAGCTACAGTGGAGTACATTGAAGCCAGTAATTCTACTTCCCTGGGCAGCAGCAGAATA
66 TCCCTGTGGTTGCAGTGGAGTACATTGAAGCCAATAATTCTACTTCCCTGGGCAGCAGTGGAATA
9391996 GA
131 GA
* * * *
9391998 TTGAAGATTTCAGGTCTTGCCTCCCTTAGCAGTAGTGGAGCAGGTCAAAGATGGCAGATTTTACC
1 TTGAAGATTTCAGATCTTGCCTCCCTAAGCAGTAGTGGAGCAGATCAAAGATGGCGGATTTTACC
* *
9392063 TCCCTGTGGTTACAGTGGAGTACATTGAAGCTAGA-AATTCTACTTCCCTGGGCAGCAGTGGAAT
66 TCCCTGTGGTTGCAGTGGAGTACATTGAAGCCA-ATAATTCTACTTCCCTGGGCAGCAGTGGAAT
9392127 AGA
130 AGA
* * *
9392130 TTGAAGATTTCAGATCTTGACTCCCTAAGCAGTAGTGGAGCAGATCAAAGATGGTGAATTTTACC
1 TTGAAGATTTCAGATCTTGCCTCCCTAAGCAGTAGTGGAGCAGATCAAAGATGGCGGATTTTACC
* * * *
9392195 TCCCTGAGGTTGCAGTGGAGTATATTGAAGCCAATAATTCTA-TCTCCCTGGGCGGCAATGGAAT
66 TCCCTGTGGTTGCAGTGGAGTACATTGAAGCCAATAATTCTACT-TCCCTGGGCAGCAGTGGAAT
9392259 AGA
130 AGA
* * *
9392262 TTGAAGATTACAGATTTTGCCTCCCTAAGCAGTAGTGGAGCAGATCGAAGATGGCGGATTTTACC
1 TTGAAGATTTCAGATCTTGCCTCCCTAAGCAGTAGTGGAGCAGATCAAAGATGGCGGATTTTACC
** * * * * * * *
9392327 TCCCTGAAGTTGCAGTGGAGTATATTGAAGCCAGTAATTCTACCTCCCCGGTCGGCAGTGGAATC
66 TCCCTGTGGTTGCAGTGGAGTACATTGAAGCCAATAATTCTACTTCCCTGGGCAGCAGTGGAATA
9392392 GA
131 GA
9392394 TTGAA
1 TTGAA
9392399 AAAGCAGATC
Statistics
Matches: 702, Mismatches: 86, Indels: 21
0.87 0.11 0.03
Matches are distributed among these distances:
131 6 0.01
132 543 0.77
133 150 0.21
134 1 0.00
135 2 0.00
ACGTcount: A:0.28, C:0.20, G:0.25, T:0.27
Consensus pattern (132 bp):
TTGAAGATTTCAGATCTTGCCTCCCTAAGCAGTAGTGGAGCAGATCAAAGATGGCGGATTTTACC
TCCCTGTGGTTGCAGTGGAGTACATTGAAGCCAATAATTCTACTTCCCTGGGCAGCAGTGGAATA
GA
Found at i:9395962 original size:109 final size:107
Alignment explanation
Indices: 9395770--9395981 Score: 302
Period size: 109 Copynumber: 2.0 Consensus size: 107
9395760 AAATTCAAGA
* *
9395770 GGATATTTGGCAATTTGGTTAAACGAGAAATTGAAACCCAGCACCTTAGGGCACGTTCCTCGAAT
1 GGATATTTAGCAATTTGGTTAAACGAGAAATCGAAACCCAGCACCTTAGGGCACGTTCCTCGAAT
*
9395835 TTTCAAACGCAAAACATTGCC-TAATTTTG-AATTTTTTGAAG
66 TTCCAAACGCAAAACATTGCCAT-ATTTTGAAATTTTTTGAAG
* * * * *
9395876 GGATATTTAGCTATTTGGTTGAACGAGAAAAATCGACACCCAGCACCTTAGGGCATGTTTTCTCG
1 GGATATTTAGCAATTTGGTTAAACGAG--AAATCGAAACCCAGCACCTTAGGGCACG-TTCCTCG
9395941 AATTTCCAAACGCAAAACATTGCCATATTTTGAAATTTTTT
63 AATTTCCAAACGCAAAACATTGCCATATTTTGAAATTTTTT
9395982 CTTTTTTGAA
Statistics
Matches: 93, Mismatches: 8, Indels: 6
0.87 0.07 0.06
Matches are distributed among these distances:
106 24 0.26
108 25 0.27
109 35 0.38
110 9 0.10
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32
Consensus pattern (107 bp):
GGATATTTAGCAATTTGGTTAAACGAGAAATCGAAACCCAGCACCTTAGGGCACGTTCCTCGAAT
TTCCAAACGCAAAACATTGCCATATTTTGAAATTTTTTGAAG
Found at i:9396212 original size:18 final size:16
Alignment explanation
Indices: 9396191--9396243 Score: 52
Period size: 18 Copynumber: 3.1 Consensus size: 16
9396181 CAATAACAAC
9396191 AAATAATGAAAATAAATA
1 AAATAAT-AAAATAAA-A
*
9396209 AAATTATCAAAATAAAA
1 AAATAAT-AAAATAAAA
*
9396226 ATAAAAATAAAATAAAA
1 A-AATAATAAAATAAAA
9396243 A
1 A
9396244 TAAAATTTAT
Statistics
Matches: 30, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
17 12 0.40
18 18 0.60
ACGTcount: A:0.75, C:0.02, G:0.02, T:0.21
Consensus pattern (16 bp):
AAATAATAAAATAAAA
Found at i:9396228 original size:6 final size:6
Alignment explanation
Indices: 9396217--9396248 Score: 57
Period size: 6 Copynumber: 5.5 Consensus size: 6
9396207 TAAAATTATC
9396217 AAAATA AAAATA AAAAT- AAAATA AAAATA AAA
1 AAAATA AAAATA AAAATA AAAATA AAAATA AAA
9396249 TTTATGTATA
Statistics
Matches: 25, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
5 5 0.20
6 20 0.80
ACGTcount: A:0.84, C:0.00, G:0.00, T:0.16
Consensus pattern (6 bp):
AAAATA
Found at i:9396237 original size:11 final size:11
Alignment explanation
Indices: 9396217--9396249 Score: 57
Period size: 11 Copynumber: 2.9 Consensus size: 11
9396207 TAAAATTATC
9396217 AAAATAAAAATA
1 AAAAT-AAAATA
9396229 AAAATAAAATA
1 AAAATAAAATA
9396240 AAAATAAAAT
1 AAAATAAAAT
9396250 TTATGTATAT
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
11 16 0.76
12 5 0.24
ACGTcount: A:0.82, C:0.00, G:0.00, T:0.18
Consensus pattern (11 bp):
AAAATAAAATA
Found at i:9400345 original size:29 final size:30
Alignment explanation
Indices: 9400313--9400369 Score: 89
Period size: 29 Copynumber: 1.9 Consensus size: 30
9400303 TAGTTTGATG
9400313 TGCAATTATATACAT-GAACTTTGATTTTA
1 TGCAATTATATACATGGAACTTTGATTTTA
* *
9400342 TGCAATTTTATACATGGAATTTTGATTT
1 TGCAATTATATACATGGAACTTTGATTT
9400370 GATCCAACTT
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
29 14 0.56
30 11 0.44
ACGTcount: A:0.32, C:0.09, G:0.12, T:0.47
Consensus pattern (30 bp):
TGCAATTATATACATGGAACTTTGATTTTA
Found at i:9402189 original size:20 final size:20
Alignment explanation
Indices: 9402153--9402190 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
9402143 ATTTGGTTCG
*
9402153 TAAATAAATAATTAAAGTAT
1 TAAATAAATAATCAAAGTAT
9402173 TAAATAATATAA-CAAAGT
1 TAAATAA-ATAATCAAAGT
9402191 TTTATTGTAC
Statistics
Matches: 16, Mismatches: 1, Indels: 2
0.84 0.05 0.11
Matches are distributed among these distances:
20 12 0.75
21 4 0.25
ACGTcount: A:0.61, C:0.03, G:0.05, T:0.32
Consensus pattern (20 bp):
TAAATAAATAATCAAAGTAT
Found at i:9402934 original size:40 final size:40
Alignment explanation
Indices: 9402879--9403026 Score: 206
Period size: 40 Copynumber: 3.7 Consensus size: 40
9402869 AGCTTTAGTG
9402879 GCATTAGCGGCGCTTTTTGAAAAACGCCACTATAGATCGA
1 GCATTAGCGGCGCTTTTTGAAAAACGCCACTATAGATCGA
* * * * *
9402919 GCATTAGTGGTGCTTTTTTAAAAATGTCACTATAGATCGA
1 GCATTAGCGGCGCTTTTTGAAAAACGCCACTATAGATCGA
* * *
9402959 GCATTAGCGGCGCTTTTTTAAAAACACTACTATAGATCGA
1 GCATTAGCGGCGCTTTTTGAAAAACGCCACTATAGATCGA
* *
9402999 CCATTAGCTGCGCTTTTTGAAAAACGCC
1 GCATTAGCGGCGCTTTTTGAAAAACGCC
9403027 GCAAAATATT
Statistics
Matches: 92, Mismatches: 16, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
40 92 1.00
ACGTcount: A:0.30, C:0.20, G:0.20, T:0.30
Consensus pattern (40 bp):
GCATTAGCGGCGCTTTTTGAAAAACGCCACTATAGATCGA
Found at i:9403075 original size:137 final size:137
Alignment explanation
Indices: 9402919--9403169 Score: 369
Period size: 137 Copynumber: 1.8 Consensus size: 137
9402909 TATAGATCGA
* *
9402919 GCATTAGTGGTGCTTTTTTAAAAATGTCACTATAGATCGAGCATTAGCGGCGCTTTTTTAAAAAC
1 GCATTAGTGGTGCTTTTTTAAAAACGTCACTATAGATCGAGCATTAGCGGCGCTTTTTGAAAAAC
*
9402984 ACTACTATAGATCGACCATTAGCTG-CGCTTTTTGAAAAACGCCGCAAAATATTAAGCATAACAC
66 ACCACTATAGATCGACCATTAGC-GACGCTTTTTGAAAAACGCCGCAAAATATTAAGCATAACAC
9403048 CGTTAGTG
130 CGTTAGTG
* * *
9403056 GCATTAGTGGTGTTTTTTTAAAAACGTCGCTATAGATCGAGCATTAGCGGCGCTTTTTGAGAAAC
1 GCATTAGTGGTGCTTTTTTAAAAACGTCACTATAGATCGAGCATTAGCGGCGCTTTTTGAAAAAC
* * * * * * *
9403121 GCCGCTATTGATTGAGCATTAGCGACGCTTTTTGAAAAATGCTGCAAAA
66 ACCACTATAGATCGACCATTAGCGACGCTTTTTGAAAAACGCCGCAAAA
9403170 AATTCAATAA
Statistics
Matches: 100, Mismatches: 13, Indels: 2
0.87 0.11 0.02
Matches are distributed among these distances:
136 1 0.01
137 99 0.99
ACGTcount: A:0.30, C:0.18, G:0.21, T:0.31
Consensus pattern (137 bp):
GCATTAGTGGTGCTTTTTTAAAAACGTCACTATAGATCGAGCATTAGCGGCGCTTTTTGAAAAAC
ACCACTATAGATCGACCATTAGCGACGCTTTTTGAAAAACGCCGCAAAATATTAAGCATAACACC
GTTAGTG
Found at i:9403113 original size:40 final size:40
Alignment explanation
Indices: 9403069--9403159 Score: 128
Period size: 40 Copynumber: 2.3 Consensus size: 40
9403059 TTAGTGGTGT
* * *
9403069 TTTTTTAAAAACGTCGCTATAGATCGAGCATTAGCGGCGC
1 TTTTTGAAAAACGCCGCTATAGATCGAGCATTAGCGACGC
* * *
9403109 TTTTTGAGAAACGCCGCTATTGATTGAGCATTAGCGACGC
1 TTTTTGAAAAACGCCGCTATAGATCGAGCATTAGCGACGC
9403149 TTTTTGAAAAA
1 TTTTTGAAAAA
9403160 TGCTGCAAAA
Statistics
Matches: 44, Mismatches: 7, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
40 44 1.00
ACGTcount: A:0.29, C:0.18, G:0.22, T:0.32
Consensus pattern (40 bp):
TTTTTGAAAAACGCCGCTATAGATCGAGCATTAGCGACGC
Found at i:9407737 original size:16 final size:16
Alignment explanation
Indices: 9407697--9407735 Score: 64
Period size: 15 Copynumber: 2.6 Consensus size: 16
9407687 AAAGCTTCTC
9407697 CAAAATTTTAAGTTTT
1 CAAAATTTTAAGTTTT
9407713 CAAAA-TTTAAGTTTT
1 CAAAATTTTAAGTTTT
9407728 -AAAATTTT
1 CAAAATTTT
9407736 TATTACAAAT
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
14 4 0.18
15 13 0.59
16 5 0.23
ACGTcount: A:0.41, C:0.05, G:0.05, T:0.49
Consensus pattern (16 bp):
CAAAATTTTAAGTTTT
Found at i:9411419 original size:19 final size:18
Alignment explanation
Indices: 9411397--9411446 Score: 57
Period size: 18 Copynumber: 2.8 Consensus size: 18
9411387 ATCAAAACTC
9411397 GTTTCTCCAAAGTTTTAAA
1 GTTTCTCCAAA-TTTTAAA
* *
9411416 GTTTCTCCGAATTTTTAA
1 GTTTCTCCAAATTTTAAA
*
9411434 GTTT-TCAAAATTT
1 GTTTCTCCAAATTT
9411447 AAGTTTTAAA
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
17 7 0.26
18 10 0.37
19 10 0.37
ACGTcount: A:0.28, C:0.14, G:0.10, T:0.48
Consensus pattern (18 bp):
GTTTCTCCAAATTTTAAA
Found at i:9411459 original size:14 final size:15
Alignment explanation
Indices: 9411429--9411460 Score: 57
Period size: 15 Copynumber: 2.2 Consensus size: 15
9411419 TCTCCGAATT
9411429 TTTAAGTTTTCAAAA
1 TTTAAGTTTTCAAAA
9411444 TTTAAGTTTT-AAAA
1 TTTAAGTTTTCAAAA
9411458 TTT
1 TTT
9411461 TTATTACAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 7 0.41
15 10 0.59
ACGTcount: A:0.38, C:0.03, G:0.06, T:0.53
Consensus pattern (15 bp):
TTTAAGTTTTCAAAA
Found at i:9413245 original size:15 final size:15
Alignment explanation
Indices: 9413221--9413252 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
9413211 TATGCATGCA
*
9413221 AAATATAAAAGACAT
1 AAATACAAAAGACAT
9413236 AAATACAAAAGACAT
1 AAATACAAAAGACAT
9413251 AA
1 AA
9413253 TAGTGAAATG
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.69, C:0.09, G:0.06, T:0.16
Consensus pattern (15 bp):
AAATACAAAAGACAT
Found at i:9413282 original size:4 final size:4
Alignment explanation
Indices: 9413273--9413297 Score: 50
Period size: 4 Copynumber: 6.2 Consensus size: 4
9413263 TGAAGTTAAC
9413273 TTTA TTTA TTTA TTTA TTTA TTTA T
1 TTTA TTTA TTTA TTTA TTTA TTTA T
9413298 CGTTCAAATA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 21 1.00
ACGTcount: A:0.24, C:0.00, G:0.00, T:0.76
Consensus pattern (4 bp):
TTTA
Found at i:9415303 original size:40 final size:40
Alignment explanation
Indices: 9415259--9415367 Score: 157
Period size: 40 Copynumber: 2.8 Consensus size: 40
9415249 GTTTGGATAA
*
9415259 AAAAATGCCGCTAAAAATCGAGCACTAGCGGCGCTTTATG
1 AAAAATGCCGCTAAAAATCGAGCATTAGCGGCGCTTTATG
* * * *
9415299 AAAAACGCCGCTAAAGATCGAGCATTTGCGGCGCTTTTTG
1 AAAAATGCCGCTAAAAATCGAGCATTAGCGGCGCTTTATG
*
9415339 GAAAATGCCGCTAAAAAT-GAGCATTAGCG
1 AAAAATGCCGCTAAAAATCGAGCATTAGCG
9415368 ATGTTTTTCT
Statistics
Matches: 60, Mismatches: 9, Indels: 1
0.86 0.13 0.01
Matches are distributed among these distances:
39 10 0.17
40 50 0.83
ACGTcount: A:0.34, C:0.21, G:0.24, T:0.21
Consensus pattern (40 bp):
AAAAATGCCGCTAAAAATCGAGCATTAGCGGCGCTTTATG
Found at i:9415384 original size:40 final size:39
Alignment explanation
Indices: 9415258--9415395 Score: 125
Period size: 40 Copynumber: 3.5 Consensus size: 39
9415248 CGTTTGGATA
* *
9415258 AAAAAATGCCGCTAAAAATCGAGCACTAGCGGCGCTTTAT
1 AAAAAATGCCGCTAAAAATCGAGCATTAGCGGCG-TTTTT
* * * *
9415298 GAAAAACGCCGCTAAAGATCGAGCATTTGCGGCGCTTTTT
1 AAAAAATGCCGCTAAAAATCGAGCATTAGCGGCG-TTTTT
** **
9415338 GGAAAATGCCGCTAAAAAT-GAGCATTAGCGATGTTTTTCT
1 AAAAAATGCCGCTAAAAATCGAGCATTAGCGGCG-TTTT-T
* *
9415378 AAAAAATACCGCAAAAAA
1 AAAAAATGCCGCTAAAAA
9415396 CCTAAGCCCA
Statistics
Matches: 80, Mismatches: 17, Indels: 2
0.81 0.17 0.02
Matches are distributed among these distances:
39 15 0.19
40 65 0.81
ACGTcount: A:0.38, C:0.20, G:0.20, T:0.22
Consensus pattern (39 bp):
AAAAAATGCCGCTAAAAATCGAGCATTAGCGGCGTTTTT
Found at i:9415489 original size:41 final size:41
Alignment explanation
Indices: 9415429--9415583 Score: 195
Period size: 41 Copynumber: 3.8 Consensus size: 41
9415419 CTGACTTTCG
** *
9415429 GGGCTTTAGCAGCGTTTTTGAAAAAGCGCCGCTAATGCTTA
1 GGGCTTTAGTGGCGGTTTTGAAAAAGCGCCGCTAATGCTTA
* *
9415470 GTGCTTTAGTGGCGGTTTTGAAAAAGTGCCGCTAATGCTTA
1 GGGCTTTAGTGGCGGTTTTGAAAAAGCGCCGCTAATGCTTA
* **
9415511 GGGCTTTAGTGGC-GTTTTCCAAAAAGCGCCGCTAATGCTCG
1 GGGCTTTAGTGGCGGTTTT-GAAAAAGCGCCGCTAATGCTTA
** *
9415552 GGGCTTTAGCAGCGTTTTTGAAAAAGCGCCGC
1 GGGCTTTAGTGGCGGTTTTGAAAAAGCGCCGC
9415584 AAAAAACATT
Statistics
Matches: 98, Mismatches: 14, Indels: 4
0.84 0.12 0.03
Matches are distributed among these distances:
40 5 0.05
41 89 0.91
42 4 0.04
ACGTcount: A:0.22, C:0.20, G:0.29, T:0.29
Consensus pattern (41 bp):
GGGCTTTAGTGGCGGTTTTGAAAAAGCGCCGCTAATGCTTA
Found at i:9416058 original size:15 final size:14
Alignment explanation
Indices: 9415956--9416088 Score: 58
Period size: 14 Copynumber: 9.3 Consensus size: 14
9415946 TATTTTAAGA
9415956 TTTAAGGATTATA-GG
1 TTTAAGG-TT-TAGGG
* *
9415971 TTTAAGGGTTATGG
1 TTTAAGGTTTAGGG
* *
9415985 TTTATGGTTTATGG
1 TTTAAGGTTTAGGG
* * *
9415999 TATAAAGG-CTGGGG
1 T-TTAAGGTTTAGGG
*
9416013 TTTAAGGTTCAGAGG
1 TTTAAGGTTTAG-GG
* *
9416028 -TTATGTGTTAAGGG
1 TTTAAG-GTTTAGGG
9416042 TTTAAGGTTTTAGGG
1 TTTAAGG-TTTAGGG
* *
9416057 TTTTAGGGTTTA-GA
1 -TTTAAGGTTTAGGG
*
9416071 TTTATGGTTTAGGG
1 TTTAAGGTTTAGGG
9416085 TTTA
1 TTTA
9416089 GATTAACTAG
Statistics
Matches: 89, Mismatches: 20, Indels: 19
0.70 0.16 0.15
Matches are distributed among these distances:
13 17 0.19
14 34 0.38
15 32 0.36
16 6 0.07
ACGTcount: A:0.23, C:0.02, G:0.32, T:0.44
Consensus pattern (14 bp):
TTTAAGGTTTAGGG
Found at i:9416089 original size:7 final size:7
Alignment explanation
Indices: 9416038--9416089 Score: 52
Period size: 7 Copynumber: 7.3 Consensus size: 7
9416028 TTATGTGTTA
9416038 AGGGTTT
1 AGGGTTT
*
9416045 AAGGTTTT
1 -AGGGTTT
9416053 AGGGTTTT
1 AGGG-TTT
9416061 AGGGTTT
1 AGGGTTT
*
9416068 A-GATTT
1 AGGGTTT
*
9416074 ATGGTTT
1 AGGGTTT
9416081 AGGGTTT
1 AGGGTTT
9416088 AG
1 AG
9416090 ATTAACTAGT
Statistics
Matches: 37, Mismatches: 5, Indels: 5
0.79 0.11 0.11
Matches are distributed among these distances:
6 5 0.14
7 19 0.51
8 13 0.35
ACGTcount: A:0.19, C:0.00, G:0.35, T:0.46
Consensus pattern (7 bp):
AGGGTTT
Found at i:9417573 original size:43 final size:43
Alignment explanation
Indices: 9417524--9417664 Score: 160
Period size: 43 Copynumber: 3.3 Consensus size: 43
9417514 TCATAAACGT
* *
9417524 CGCTAAAGAACGGTACTTTTAGCGGCGTTTGTGATAAAAGCGC
1 CGCTAAAGATCAGTACTTTTAGCGGCGTTTGTGATAAAAGCGC
* * * *
9417567 CGCTAAAGATCATGTTC-TATAGTGGCGTTTGTGATAAAAGCGT
1 CGCTAAAGATCA-GTACTTTTAGCGGCGTTTGTGATAAAAGCGC
* *
9417610 CGCTAAAGGTCATTA-TCTTTAGCGGCGTTTGTGATAAAAGCGC
1 CGCTAAAGATCAGTACT-TTTAGCGGCGTTTGTGATAAAAGCGC
**
9417653 CATTAAAGATCA
1 CGCTAAAGATCA
9417665 TGCCCAAAAG
Statistics
Matches: 80, Mismatches: 15, Indels: 6
0.79 0.15 0.06
Matches are distributed among these distances:
42 1 0.01
43 76 0.95
44 3 0.04
ACGTcount: A:0.29, C:0.17, G:0.25, T:0.29
Consensus pattern (43 bp):
CGCTAAAGATCAGTACTTTTAGCGGCGTTTGTGATAAAAGCGC
Found at i:9419156 original size:22 final size:21
Alignment explanation
Indices: 9419130--9419178 Score: 71
Period size: 22 Copynumber: 2.2 Consensus size: 21
9419120 AATCCGAATT
9419130 TTAAACTTTTAAAAATAAACAA
1 TTAAACTTTTAAAAATAAA-AA
*
9419152 TTAAATTTTTAAAAATAAAAA
1 TTAAACTTTTAAAAATAAAAA
9419173 TATAAA
1 T-TAAA
9419179 AATTAAATTC
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
21 3 0.12
22 22 0.88
ACGTcount: A:0.61, C:0.04, G:0.00, T:0.35
Consensus pattern (21 bp):
TTAAACTTTTAAAAATAAAAA
Found at i:9420894 original size:15 final size:15
Alignment explanation
Indices: 9420869--9420903 Score: 54
Period size: 15 Copynumber: 2.4 Consensus size: 15
9420859 AACTCTATTT
*
9420869 TAATT-ATATTAGGA
1 TAATTAATATTAAGA
9420883 TAATTAATATTAAGA
1 TAATTAATATTAAGA
9420898 TAATTA
1 TAATTA
9420904 TTAAGGATTA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
14 5 0.26
15 14 0.74
ACGTcount: A:0.49, C:0.00, G:0.09, T:0.43
Consensus pattern (15 bp):
TAATTAATATTAAGA
Found at i:9420919 original size:18 final size:17
Alignment explanation
Indices: 9420907--9420939 Score: 50
Period size: 18 Copynumber: 1.9 Consensus size: 17
9420897 ATAATTATTA
9420907 AGGA-TTATTTAATTTT
1 AGGATTTATTTAATTTT
9420923 AGGATTTTATTTAATTT
1 AGGA-TTTATTTAATTT
9420940 ATATTTATTT
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 4 0.27
18 11 0.73
ACGTcount: A:0.30, C:0.00, G:0.12, T:0.58
Consensus pattern (17 bp):
AGGATTTATTTAATTTT
Found at i:9423138 original size:13 final size:13
Alignment explanation
Indices: 9423122--9423148 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
9423112 CAATGCGTGA
9423122 CTTCAATGTGAGG
1 CTTCAATGTGAGG
9423135 CTTCAATGTGAGG
1 CTTCAATGTGAGG
9423148 C
1 C
9423149 AATATAAAGC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.22, C:0.19, G:0.30, T:0.30
Consensus pattern (13 bp):
CTTCAATGTGAGG
Found at i:9428399 original size:26 final size:27
Alignment explanation
Indices: 9428370--9428420 Score: 86
Period size: 26 Copynumber: 1.9 Consensus size: 27
9428360 TATTTGCAAT
9428370 AATTAGCTATTTTT-TATAAATATTAA
1 AATTAGCTATTTTTCTATAAATATTAA
*
9428396 AATTAGCTTTTTTTCTATAAATATT
1 AATTAGCTATTTTTCTATAAATATT
9428421 TTAAAATAGC
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
26 13 0.57
27 10 0.43
ACGTcount: A:0.37, C:0.06, G:0.04, T:0.53
Consensus pattern (27 bp):
AATTAGCTATTTTTCTATAAATATTAA
Found at i:9446787 original size:21 final size:22
Alignment explanation
Indices: 9446736--9446790 Score: 60
Period size: 21 Copynumber: 2.6 Consensus size: 22
9446726 AATTGTATAA
* * *
9446736 TCATAAATTAATATAATATAAT
1 TCATAATTTAATTTAATAAAAT
*
9446758 T-ATATTTTAATTTAA-AAAAT
1 TCATAATTTAATTTAATAAAAT
9446778 TCATAATTTAATT
1 TCATAATTTAATT
9446791 CAATTCTAAA
Statistics
Matches: 27, Mismatches: 5, Indels: 3
0.77 0.14 0.09
Matches are distributed among these distances:
20 5 0.19
21 21 0.78
22 1 0.04
ACGTcount: A:0.49, C:0.04, G:0.00, T:0.47
Consensus pattern (22 bp):
TCATAATTTAATTTAATAAAAT
Found at i:9451317 original size:22 final size:22
Alignment explanation
Indices: 9451291--9451351 Score: 95
Period size: 22 Copynumber: 2.8 Consensus size: 22
9451281 TTGGTTGGGC
* * *
9451291 CCCTTTTTGTATTTTTCATTTT
1 CCCTTTCTCTATTTTCCATTTT
9451313 CCCTTTCTCTATTTTCCATTTT
1 CCCTTTCTCTATTTTCCATTTT
9451335 CCCTTTCTCTATTTTCC
1 CCCTTTCTCTATTTTCC
9451352 TTCTCCATTG
Statistics
Matches: 36, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
22 36 1.00
ACGTcount: A:0.08, C:0.30, G:0.02, T:0.61
Consensus pattern (22 bp):
CCCTTTCTCTATTTTCCATTTT
Found at i:9459678 original size:17 final size:18
Alignment explanation
Indices: 9459646--9459681 Score: 56
Period size: 17 Copynumber: 2.1 Consensus size: 18
9459636 TACCTATCCT
*
9459646 GCCCGTGTGATTTCACAC
1 GCCCGTATGATTTCACAC
9459664 GCCCGTATG-TTTCACAC
1 GCCCGTATGATTTCACAC
9459681 G
1 G
9459682 ACCTTCCTGG
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
17 9 0.53
18 8 0.47
ACGTcount: A:0.17, C:0.33, G:0.22, T:0.28
Consensus pattern (18 bp):
GCCCGTATGATTTCACAC
Done.