Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01000190.1 Hibiscus syriacus cultivar Beakdansim tig00000340_pilon, whole genome shotgun sequence
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: 14308945
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 18 of 62
Found at i:4193007 original size:20 final size:20
Alignment explanation
Indices: 4192982--4193115 Score: 124
Period size: 20 Copynumber: 6.6 Consensus size: 20
4192972 TAGTTGAAAA
4192982 TCGCGTTGCGATTTTCCATT
1 TCGCGTTGCGATTTTCCATT
* ** **
4193002 TCGCGTTGCGATAGTTGAAAA
1 TCGCGTTGCGAT-TTTCCATT
4193023 TCGCGTTGCGATTTTCCATT
1 TCGCGTTGCGATTTTCCATT
*
4193043 TCGCGTTGCGATTTTCTATT
1 TCGCGTTGCGATTTTCCATT
* * ** **
4193063 TCACGTTGCGATAGTTGAAAA
1 TCGCGTTGCGAT-TTTCCATT
* *
4193084 TCACATTGCGATTTTCCATT
1 TCGCGTTGCGATTTTCCATT
4193104 TCGCGTTGCGAT
1 TCGCGTTGCGAT
4193116 AGTCTACAGT
Statistics
Matches: 87, Mismatches: 25, Indels: 4
0.75 0.22 0.03
Matches are distributed among these distances:
20 58 0.67
21 29 0.33
ACGTcount: A:0.18, C:0.21, G:0.22, T:0.40
Consensus pattern (20 bp):
TCGCGTTGCGATTTTCCATT
Found at i:4193047 original size:61 final size:61
Alignment explanation
Indices: 4192982--4193115 Score: 232
Period size: 61 Copynumber: 2.2 Consensus size: 61
4192972 TAGTTGAAAA
* * *
4192982 TCGCGTTGCGATTTTCCATTTCGCGTTGCGATAGTTGAAAATCGCGTTGCGATTTTCCATT
1 TCGCGTTGCGATTTTCCATTTCACGTTGCGATAGTTGAAAATCACATTGCGATTTTCCATT
*
4193043 TCGCGTTGCGATTTTCTATTTCACGTTGCGATAGTTGAAAATCACATTGCGATTTTCCATT
1 TCGCGTTGCGATTTTCCATTTCACGTTGCGATAGTTGAAAATCACATTGCGATTTTCCATT
4193104 TCGCGTTGCGAT
1 TCGCGTTGCGAT
4193116 AGTCTACAGT
Statistics
Matches: 69, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
61 69 1.00
ACGTcount: A:0.18, C:0.21, G:0.22, T:0.40
Consensus pattern (61 bp):
TCGCGTTGCGATTTTCCATTTCACGTTGCGATAGTTGAAAATCACATTGCGATTTTCCATT
Found at i:4193152 original size:102 final size:101
Alignment explanation
Indices: 4192958--4193152 Score: 277
Period size: 102 Copynumber: 1.9 Consensus size: 101
4192948 TTCGCGTTGC
* * *
4192958 ATTTCTCGTTGCGATAGTTGAAAATCGCGTTGCGATTTTCCATTTCGCGTTGCGATAGTTGAAAA
1 ATTTCACGTTGCGATAGTTGAAAATCACATTGCGATTTTCCATTTCGCGTTGCGATAGTTGAAAA
*
4193023 TCGCGTTGCGATTTTCCATTTCGCGTTGCGATTTTCT
66 TCGCGTTGCGATTTTCCAATTC-CGTTGCGATTTTCT
*
4193060 ATTTCACGTTGCGATAGTTGAAAATCACATTGCGATTTTCCATTTCGCGTTGCGATAGTCT-ACA
1 ATTTCACGTTGCGATAGTTGAAAATCACATTGCGATTTTCCATTTCGCGTTGCGATAGT-TGAAA
* *
4193124 GTTGTCGTTGCGATTTTCCAAATT-CGTTG
65 ATCG-CGTTGCGATTTTCC-AATTCCGTTG
4193153 TGATAGTTAA
Statistics
Matches: 83, Mismatches: 7, Indels: 6
0.86 0.07 0.06
Matches are distributed among these distances:
102 65 0.78
103 15 0.18
104 3 0.04
ACGTcount: A:0.19, C:0.19, G:0.22, T:0.39
Consensus pattern (101 bp):
ATTTCACGTTGCGATAGTTGAAAATCACATTGCGATTTTCCATTTCGCGTTGCGATAGTTGAAAA
TCGCGTTGCGATTTTCCAATTCCGTTGCGATTTTCT
Found at i:4193247 original size:6 final size:6
Alignment explanation
Indices: 4193236--4193273 Score: 60
Period size: 6 Copynumber: 6.5 Consensus size: 6
4193226 GACACGTATT
*
4193236 ACCACG ACCACG ACCACG ACCACG ACCATG ACC-CG ACC
1 ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACC
4193274 CGAGACGAAC
Statistics
Matches: 30, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
5 4 0.13
6 26 0.87
ACGTcount: A:0.32, C:0.50, G:0.16, T:0.03
Consensus pattern (6 bp):
ACCACG
Found at i:4193888 original size:19 final size:19
Alignment explanation
Indices: 4193864--4193948 Score: 107
Period size: 19 Copynumber: 4.3 Consensus size: 19
4193854 TTAACTATCA
4193864 CAACGAATTTGGAAAATCG
1 CAACGAATTTGGAAAATCG
* * **
4193883 CAACGACAACTGTAGACTATCG
1 CAACG--AA-TTTGGAAAATCG
4193905 CAACGAATTTGGAAAATCG
1 CAACGAATTTGGAAAATCG
4193924 CAACGAATTTGGAAAATCG
1 CAACGAATTTGGAAAATCG
4193943 CAACGA
1 CAACGA
4193949 CAACTGCGAA
Statistics
Matches: 55, Mismatches: 8, Indels: 6
0.80 0.12 0.09
Matches are distributed among these distances:
19 38 0.69
20 2 0.04
21 2 0.04
22 13 0.24
ACGTcount: A:0.41, C:0.20, G:0.20, T:0.19
Consensus pattern (19 bp):
CAACGAATTTGGAAAATCG
Found at i:4193961 original size:28 final size:28
Alignment explanation
Indices: 4193927--4193982 Score: 112
Period size: 28 Copynumber: 2.0 Consensus size: 28
4193917 AAAATCGCAA
4193927 CGAATTTGGAAAATCGCAACGACAACTG
1 CGAATTTGGAAAATCGCAACGACAACTG
4193955 CGAATTTGGAAAATCGCAACGACAACTG
1 CGAATTTGGAAAATCGCAACGACAACTG
4193983 TAGACTATCG
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 28 1.00
ACGTcount: A:0.39, C:0.21, G:0.21, T:0.18
Consensus pattern (28 bp):
CGAATTTGGAAAATCGCAACGACAACTG
Found at i:4194678 original size:21 final size:21
Alignment explanation
Indices: 4194644--4194699 Score: 69
Period size: 21 Copynumber: 2.7 Consensus size: 21
4194634 TAGGGTTGCA
* *
4194644 CCGAAGTG-CCACATATTTGTC
1 CCGAA-TGACCACATAATTATC
*
4194665 CCGGATGACCACATAATTATC
1 CCGAATGACCACATAATTATC
4194686 CCGAATGACCACAT
1 CCGAATGACCACAT
4194700 GGACTCTTGA
Statistics
Matches: 30, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
20 2 0.07
21 28 0.93
ACGTcount: A:0.30, C:0.30, G:0.16, T:0.23
Consensus pattern (21 bp):
CCGAATGACCACATAATTATC
Found at i:4197141 original size:21 final size:21
Alignment explanation
Indices: 4197107--4197194 Score: 88
Period size: 21 Copynumber: 4.2 Consensus size: 21
4197097 TACATGAGTA
* *
4197107 CACCACAGCCATTTCAGATGG
1 CACCGCAGTCATTTCAGATGG
*
4197128 CACCGC-TTCAATTTCAGATGG
1 CACCGCAGTC-ATTTCAGATGG
*
4197149 CACCGCAGTCATTTCAGATGC
1 CACCGCAGTCATTTCAGATGG
* ** *
4197170 CACCACAGTCGGTTCAGATGC
1 CACCGCAGTCATTTCAGATGG
4197191 CACC
1 CACC
4197195 ATAACCGGTT
Statistics
Matches: 57, Mismatches: 8, Indels: 4
0.83 0.12 0.06
Matches are distributed among these distances:
20 1 0.02
21 54 0.95
22 2 0.04
ACGTcount: A:0.25, C:0.34, G:0.19, T:0.22
Consensus pattern (21 bp):
CACCGCAGTCATTTCAGATGG
Found at i:4197195 original size:21 final size:21
Alignment explanation
Indices: 4197140--4197217 Score: 84
Period size: 21 Copynumber: 3.7 Consensus size: 21
4197130 CCGCTTCAAT
* * **
4197140 TTCAGATGGCACCGCAGTCAT
1 TTCAGATGCCACCACAGTCGG
4197161 TTCAGATGCCACCACAGTCGG
1 TTCAGATGCCACCACAGTCGG
* **
4197182 TTCAGATGCCACCATAACCGG
1 TTCAGATGCCACCACAGTCGG
*
4197203 TTAAGATGCCACCAC
1 TTCAGATGCCACCAC
4197218 CGTGGGGTTT
Statistics
Matches: 48, Mismatches: 9, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 48 1.00
ACGTcount: A:0.27, C:0.32, G:0.21, T:0.21
Consensus pattern (21 bp):
TTCAGATGCCACCACAGTCGG
Found at i:4200127 original size:15 final size:15
Alignment explanation
Indices: 4200093--4200126 Score: 52
Period size: 14 Copynumber: 2.3 Consensus size: 15
4200083 TAAATACAAT
4200093 TAAAATATAAAGGAC
1 TAAAATATAAAGGAC
*
4200108 TAAAAT-TAAAGTAC
1 TAAAATATAAAGGAC
4200122 TAAAA
1 TAAAA
4200127 AAGGTAAAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
14 12 0.67
15 6 0.33
ACGTcount: A:0.62, C:0.06, G:0.09, T:0.24
Consensus pattern (15 bp):
TAAAATATAAAGGAC
Found at i:4200180 original size:14 final size:14
Alignment explanation
Indices: 4200161--4200197 Score: 56
Period size: 14 Copynumber: 2.6 Consensus size: 14
4200151 ATAAAATAGT
*
4200161 AAATTAAAGTAATG
1 AAATTAAAGGAATG
*
4200175 AAATTAAAGGACTG
1 AAATTAAAGGAATG
4200189 AAATTAAAG
1 AAATTAAAG
4200198 AAACAAAAAG
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.57, C:0.03, G:0.16, T:0.24
Consensus pattern (14 bp):
AAATTAAAGGAATG
Found at i:4200427 original size:30 final size:29
Alignment explanation
Indices: 4200381--4200450 Score: 77
Period size: 30 Copynumber: 2.4 Consensus size: 29
4200371 AAATAAATAA
*
4200381 AAAAGTTAGCAATTAGTAATTAGTGGTTAG
1 AAAAGTTAGCAATTAGTAATTAG-CGTTAG
** **
4200411 AAAAGTTAGCGGTTAGTGGTTAGCGTTAG
1 AAAAGTTAGCAATTAGTAATTAGCGTTAG
*
4200440 AAATGTTAGCA
1 AAAAGTTAGCA
4200451 GAATCTGGAT
Statistics
Matches: 33, Mismatches: 7, Indels: 1
0.80 0.17 0.02
Matches are distributed among these distances:
29 14 0.42
30 19 0.58
ACGTcount: A:0.36, C:0.06, G:0.27, T:0.31
Consensus pattern (29 bp):
AAAAGTTAGCAATTAGTAATTAGCGTTAG
Found at i:4203908 original size:33 final size:33
Alignment explanation
Indices: 4203866--4203933 Score: 127
Period size: 33 Copynumber: 2.1 Consensus size: 33
4203856 AAGAAGAAAA
*
4203866 TAAAAAGAAAATGGTATGCTGCAGGGTAGTTAG
1 TAAAAAGAAAATGGTATGATGCAGGGTAGTTAG
4203899 TAAAAAGAAAATGGTATGATGCAGGGTAGTTAG
1 TAAAAAGAAAATGGTATGATGCAGGGTAGTTAG
4203932 TA
1 TA
4203934 GTGGCGTTAC
Statistics
Matches: 34, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
33 34 1.00
ACGTcount: A:0.41, C:0.04, G:0.29, T:0.25
Consensus pattern (33 bp):
TAAAAAGAAAATGGTATGATGCAGGGTAGTTAG
Found at i:4210705 original size:33 final size:33
Alignment explanation
Indices: 4210638--4210707 Score: 81
Period size: 33 Copynumber: 2.1 Consensus size: 33
4210628 TTTTGTAAAC
* *
4210638 GGGAAAGATTCTAGTTAATCCCGTGAAAAGCTA
1 GGGAAAGATTCTAGTTAAGCCCGTGAAAAACTA
*
4210671 GGGAAATG-TTCTAGTTAAGCCTGCT-AAAAACTA
1 GGGAAA-GATTCTAGTTAAGCCCG-TGAAAAACTA
4210704 GGGA
1 GGGA
4210708 GTTTGTAAAG
Statistics
Matches: 32, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
33 30 0.94
34 2 0.06
ACGTcount: A:0.36, C:0.14, G:0.26, T:0.24
Consensus pattern (33 bp):
GGGAAAGATTCTAGTTAAGCCCGTGAAAAACTA
Found at i:4215350 original size:18 final size:19
Alignment explanation
Indices: 4215316--4215352 Score: 58
Period size: 19 Copynumber: 2.0 Consensus size: 19
4215306 TAACATTTTC
4215316 ATATATTTTCCAACAATTG
1 ATATATTTTCCAACAATTG
*
4215335 ATATATTTT-TAACAATTG
1 ATATATTTTCCAACAATTG
4215353 GTACCTTTTT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
18 8 0.47
19 9 0.53
ACGTcount: A:0.38, C:0.11, G:0.05, T:0.46
Consensus pattern (19 bp):
ATATATTTTCCAACAATTG
Found at i:4222620 original size:41 final size:41
Alignment explanation
Indices: 4222575--4222666 Score: 175
Period size: 41 Copynumber: 2.2 Consensus size: 41
4222565 GCCCCTAGGG
4222575 CGCGCCTTACGCCACGTAGGGGTATAGCACGGGGCAGGGGC
1 CGCGCCTTACGCCACGTAGGGGTATAGCACGGGGCAGGGGC
4222616 CGCGCCTTACGCCACGTAGGGGTATAGCACGGGGCAGGGGC
1 CGCGCCTTACGCCACGTAGGGGTATAGCACGGGGCAGGGGC
*
4222657 CGTGCCTTAC
1 CGCGCCTTAC
4222667 CTTTAATTCT
Statistics
Matches: 50, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
41 50 1.00
ACGTcount: A:0.16, C:0.30, G:0.39, T:0.14
Consensus pattern (41 bp):
CGCGCCTTACGCCACGTAGGGGTATAGCACGGGGCAGGGGC
Found at i:4224445 original size:62 final size:63
Alignment explanation
Indices: 4224313--4224466 Score: 170
Period size: 62 Copynumber: 2.5 Consensus size: 63
4224303 CAGTGTGTAT
* * * ** * * * *
4224313 CGATGCACAGGGAGTGCATCGATGCACCCATTAAAATGGAAACATCGATTGCGATTGGTGCAT
1 CGATGCATAAGGAGTGCATCGATGCACCCACTAAAATACAAACATCGAATGAGATTGATGCAC
*
4224376 CGATGCATAAGGAGTGCATCGATGCATCCC-CT-AAATACAAACATCGAATGAGATTTATGCAC
1 CGATGCATAAGGAGTGCATCGATGCA-CCCACTAAAATACAAACATCGAATGAGATTGATGCAC
*
4224438 CGATGCAT-AGATAGTGCATCGATGCACCC
1 CGATGCATAAG-GAGTGCATCGATGCACCC
4224467 GTCTAGGGAT
Statistics
Matches: 78, Mismatches: 11, Indels: 6
0.82 0.12 0.06
Matches are distributed among these distances:
61 5 0.06
62 45 0.58
63 25 0.32
64 3 0.04
ACGTcount: A:0.32, C:0.23, G:0.23, T:0.22
Consensus pattern (63 bp):
CGATGCATAAGGAGTGCATCGATGCACCCACTAAAATACAAACATCGAATGAGATTGATGCAC
Found at i:4234441 original size:2 final size:2
Alignment explanation
Indices: 4234436--4234460 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
4234426 ACACACACGC
4234436 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 A
4234461 ATGAAGAAAT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:4235859 original size:53 final size:53
Alignment explanation
Indices: 4235767--4236075 Score: 422
Period size: 53 Copynumber: 5.8 Consensus size: 53
4235757 ATGATGTGTC
* **** *
4235767 CGCTCCCTCTTG-TTCAGGGATTAAGGAACTCGAACAATCTTCTAAAAATGGGTT
1 CGCTCCCTCTTGCTTCAGGGAGT-A-GAACTCGAACAATCTTCTGCCTACGGGTT
* ***
4235821 CGCTCCCTATTGCTTCAGGGAGTAGAACTCGAACAATCTTCTATTTACGGGTT
1 CGCTCCCTCTTGCTTCAGGGAGTAGAACTCGAACAATCTTCTGCCTACGGGTT
* *
4235874 CGCTCCCTCTTGCTTCAGGGAGTAAAACTCGAACAATCTTCTGCTTACGGGTT
1 CGCTCCCTCTTGCTTCAGGGAGTAGAACTCGAACAATCTTCTGCCTACGGGTT
* * * *
4235927 CACTCCCTCTTTCTTCAAGAAGTAGAACTCGAACAATCTTCTGCCTACGGGTT
1 CGCTCCCTCTTGCTTCAGGGAGTAGAACTCGAACAATCTTCTGCCTACGGGTT
* *
4235980 CTCTCCCTCTTGCTTCAGGGAGTAGAACTCGAACAATCTTCTGCCTATGGGTT
1 CGCTCCCTCTTGCTTCAGGGAGTAGAACTCGAACAATCTTCTGCCTACGGGTT
*
4236033 CGCTCCCTCTTGCTTCAGGGAGTATAACTCGAACAATCTTCTG
1 CGCTCCCTCTTGCTTCAGGGAGTAGAACTCGAACAATCTTCTG
4236076 GTGTGATTCT
Statistics
Matches: 231, Mismatches: 23, Indels: 3
0.90 0.09 0.01
Matches are distributed among these distances:
53 210 0.91
54 12 0.05
55 9 0.04
ACGTcount: A:0.23, C:0.27, G:0.19, T:0.31
Consensus pattern (53 bp):
CGCTCCCTCTTGCTTCAGGGAGTAGAACTCGAACAATCTTCTGCCTACGGGTT
Found at i:4236562 original size:42 final size:42
Alignment explanation
Indices: 4236497--4236881 Score: 664
Period size: 42 Copynumber: 9.2 Consensus size: 42
4236487 AAATCCTACC
*
4236497 CGAAAGACTTA-TGGATGACCCGAAGGATTTAATCATCATGCT
1 CGAAAGACTTACT-GATGGCCCGAAGGATTTAATCATCATGCT
* *
4236539 CGAAAGACTTACTGATGGTCCGAATGATTTAATCATCATGCT
1 CGAAAGACTTACTGATGGCCCGAAGGATTTAATCATCATGCT
* *
4236581 CGTAAGACTTACTGATGACCCGAAGGATTTAATCATCATGCT
1 CGAAAGACTTACTGATGGCCCGAAGGATTTAATCATCATGCT
4236623 CGAAAGACTTACTGATGGCCCGAAGGATTTAATCATCATGCT
1 CGAAAGACTTACTGATGGCCCGAAGGATTTAATCATCATGCT
*
4236665 CGAAAGACTTACTGATGACCCGAAGGATTTAATCATCATGCT
1 CGAAAGACTTACTGATGGCCCGAAGGATTTAATCATCATGCT
4236707 CGAAAGACTTACTGATGGCCCGAAGGATTTAATCATCATGCT
1 CGAAAGACTTACTGATGGCCCGAAGGATTTAATCATCATGCT
* *
4236749 CGAAAGACTTACTGATGACCCGAAGGATTTAATCATCATTCT
1 CGAAAGACTTACTGATGGCCCGAAGGATTTAATCATCATGCT
*
4236791 CGAAAGACTTACTGATGGCCTGAAGGATTTAATCATCATGCT
1 CGAAAGACTTACTGATGGCCCGAAGGATTTAATCATCATGCT
*
4236833 CAAAAGACTTACTGATGGCCCGAAGGATTTAATCATCATGCT
1 CGAAAGACTTACTGATGGCCCGAAGGATTTAATCATCATGCT
4236875 CGAAAGA
1 CGAAAGA
4236882 TTAAATCATC
Statistics
Matches: 323, Mismatches: 19, Indels: 2
0.94 0.06 0.01
Matches are distributed among these distances:
42 322 1.00
43 1 0.00
ACGTcount: A:0.32, C:0.21, G:0.20, T:0.27
Consensus pattern (42 bp):
CGAAAGACTTACTGATGGCCCGAAGGATTTAATCATCATGCT
Found at i:4236943 original size:42 final size:42
Alignment explanation
Indices: 4236886--4236996 Score: 195
Period size: 42 Copynumber: 2.6 Consensus size: 42
4236876 GAAAGATTAA
* *
4236886 ATCATCATGCTCGAAAGACTTATTGATGGCCCGAAGGATTTC
1 ATCATCATGCTCGAAAGACTTACTGATGGCCCGAAGGACTTC
4236928 ATCATCATGCTCGAAAGACTTACTGATGGCCCGAAGGACTTC
1 ATCATCATGCTCGAAAGACTTACTGATGGCCCGAAGGACTTC
*
4236970 ATCATCATGCTCAAAAGACTTACTGAT
1 ATCATCATGCTCGAAAGACTTACTGAT
4236997 TGCACTTACT
Statistics
Matches: 66, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
42 66 1.00
ACGTcount: A:0.31, C:0.23, G:0.19, T:0.27
Consensus pattern (42 bp):
ATCATCATGCTCGAAAGACTTACTGATGGCCCGAAGGACTTC
Found at i:4236967 original size:20 final size:20
Alignment explanation
Indices: 4236897--4236968 Score: 56
Period size: 20 Copynumber: 3.5 Consensus size: 20
4236887 TCATCATGCT
*
4236897 CGAAAGACTTATTGATGGCC
1 CGAAAGACTTACTGATGGCC
* * * *
4236917 CGAAGGATTTCATCATCAT-GCT
1 CGAAAGACTT-A-C-TGATGGCC
4236939 CGAAAGACTTACTGATGGCC
1 CGAAAGACTTACTGATGGCC
*
4236959 CGAAGGACTT
1 CGAAAGACTT
4236969 CATCATCATG
Statistics
Matches: 38, Mismatches: 10, Indels: 8
0.68 0.18 0.14
Matches are distributed among these distances:
19 3 0.08
20 20 0.53
21 2 0.05
22 10 0.26
23 3 0.08
ACGTcount: A:0.29, C:0.22, G:0.24, T:0.25
Consensus pattern (20 bp):
CGAAAGACTTACTGATGGCC
Found at i:4237635 original size:20 final size:17
Alignment explanation
Indices: 4237623--4237665 Score: 59
Period size: 17 Copynumber: 2.4 Consensus size: 17
4237613 TTTATCTTCT
4237623 TGTCTTCTCTTTTTTTTTC
1 TGTCTTCTC--TTTTTTTC
*
4237642 TGTATTCTCTTTTTTTC
1 TGTCTTCTCTTTTTTTC
4237659 TGTCTTC
1 TGTCTTC
4237666 ATTTTGGAGA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
17 14 0.64
19 8 0.36
ACGTcount: A:0.02, C:0.21, G:0.07, T:0.70
Consensus pattern (17 bp):
TGTCTTCTCTTTTTTTC
Found at i:4247705 original size:16 final size:16
Alignment explanation
Indices: 4247681--4247734 Score: 56
Period size: 16 Copynumber: 3.4 Consensus size: 16
4247671 TATATCTGCA
* *
4247681 AAAAAATTAAATAAGT
1 AAAATATTAAATAAAT
4247697 AAAATATTAAATAAAT
1 AAAATATTAAATAAAT
* * *
4247713 TAAATATAAAAT-ATT
1 AAAATATTAAATAAAT
4247728 AAAATAT
1 AAAATAT
4247735 AATAAAATAT
Statistics
Matches: 32, Mismatches: 6, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
15 8 0.25
16 24 0.75
ACGTcount: A:0.67, C:0.00, G:0.02, T:0.31
Consensus pattern (16 bp):
AAAATATTAAATAAAT
Found at i:4247712 original size:25 final size:23
Alignment explanation
Indices: 4247684--4247745 Score: 79
Period size: 25 Copynumber: 2.5 Consensus size: 23
4247674 ATCTGCAAAA
4247684 AAATTAAATAAGTAAAATATTAAAT
1 AAATTAAAT-A-TAAAATATTAAAT
4247709 AAATTAAATATAAAATATTAAAAT
1 AAATTAAATATAAAATATT-AAAT
*
4247733 ATAATAAAATATA
1 A-AATTAAATATA
4247746 CCTTAGAAGA
Statistics
Matches: 34, Mismatches: 1, Indels: 4
0.87 0.03 0.10
Matches are distributed among these distances:
23 9 0.26
24 6 0.18
25 19 0.56
ACGTcount: A:0.66, C:0.00, G:0.02, T:0.32
Consensus pattern (23 bp):
AAATTAAATATAAAATATTAAAT
Found at i:4247732 original size:15 final size:16
Alignment explanation
Indices: 4247683--4247740 Score: 54
Period size: 15 Copynumber: 3.9 Consensus size: 16
4247673 TATCTGCAAA
*
4247683 AAAAT-TAAAT-AAGT
1 AAAATATAAATAAATT
4247697 AAAATATTAAATAAATT
1 AAAATA-TAAATAAATT
*
4247714 -AAATATAAA-ATATT
1 AAAATATAAATAAATT
4247728 AAAATAT-AATAAA
1 AAAATATAAATAAA
4247741 ATATACCTTA
Statistics
Matches: 36, Mismatches: 3, Indels: 9
0.75 0.06 0.19
Matches are distributed among these distances:
14 11 0.31
15 12 0.33
16 10 0.28
17 3 0.08
ACGTcount: A:0.67, C:0.00, G:0.02, T:0.31
Consensus pattern (16 bp):
AAAATATAAATAAATT
Found at i:4249437 original size:58 final size:58
Alignment explanation
Indices: 4249347--4249458 Score: 152
Period size: 58 Copynumber: 1.9 Consensus size: 58
4249337 GATCATCGAC
* * * *
4249347 TATAAGATGTTGCTTTATTAAATCTCTTGACTATTAAAAGTTATAAAATGATCACAGT
1 TATAAGATGTTGCTTTATTAAATCACTCGACTATTAAAAATTACAAAATGATCACAGT
* * * *
4249405 TATAAGATGTTTCTTTTTTTAGTCACTCGACTATTAAAAATTACAAAATGATCA
1 TATAAGATGTTGCTTTATTAAATCACTCGACTATTAAAAATTACAAAATGATCA
4249459 TCTGACTACA
Statistics
Matches: 46, Mismatches: 8, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
58 46 1.00
ACGTcount: A:0.38, C:0.12, G:0.11, T:0.40
Consensus pattern (58 bp):
TATAAGATGTTGCTTTATTAAATCACTCGACTATTAAAAATTACAAAATGATCACAGT
Found at i:4251275 original size:21 final size:19
Alignment explanation
Indices: 4251220--4251277 Score: 64
Period size: 19 Copynumber: 2.9 Consensus size: 19
4251210 CAAGGGTTAT
4251220 ATGAGGTCCTTCGGGACATA
1 ATGA-GTCCTTCGGGACATA
*
4251240 A-GAGTTCCTTTGGGACATA
1 ATGAG-TCCTTCGGGACATA
4251259 CATGACGTCCTTCGGGACA
1 -ATGA-GTCCTTCGGGACA
4251278 AATTTCACAT
Statistics
Matches: 32, Mismatches: 2, Indels: 7
0.78 0.05 0.17
Matches are distributed among these distances:
18 1 0.03
19 15 0.47
20 2 0.06
21 13 0.41
22 1 0.03
ACGTcount: A:0.24, C:0.22, G:0.28, T:0.26
Consensus pattern (19 bp):
ATGAGTCCTTCGGGACATA
Found at i:4254782 original size:7 final size:7
Alignment explanation
Indices: 4254770--4254799 Score: 60
Period size: 7 Copynumber: 4.3 Consensus size: 7
4254760 AAAAGGGAAT
4254770 GAGGTGA
1 GAGGTGA
4254777 GAGGTGA
1 GAGGTGA
4254784 GAGGTGA
1 GAGGTGA
4254791 GAGGTGA
1 GAGGTGA
4254798 GA
1 GA
4254800 AGAGAGGGAG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 23 1.00
ACGTcount: A:0.30, C:0.00, G:0.57, T:0.13
Consensus pattern (7 bp):
GAGGTGA
Found at i:4258010 original size:21 final size:21
Alignment explanation
Indices: 4257981--4258022 Score: 75
Period size: 21 Copynumber: 2.0 Consensus size: 21
4257971 TTATGCATTC
4257981 TATCAATTTGATTCTAATTTT
1 TATCAATTTGATTCTAATTTT
*
4258002 TATCCATTTGATTCTAATTTT
1 TATCAATTTGATTCTAATTTT
4258023 AATTTTATTT
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:0.26, C:0.12, G:0.05, T:0.57
Consensus pattern (21 bp):
TATCAATTTGATTCTAATTTT
Found at i:4258481 original size:2 final size:2
Alignment explanation
Indices: 4258474--4258498 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
4258464 TTTCGAGTTA
4258474 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 A
4258499 AGATTATTAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:4258727 original size:2 final size:2
Alignment explanation
Indices: 4258722--4258764 Score: 70
Period size: 2 Copynumber: 22.0 Consensus size: 2
4258712 ATTTATTTAA
*
4258722 AT AT AT AT TT AT AT -T 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 AT AT
4258763 AT
1 AT
4258765 GAAATTATTA
Statistics
Matches: 38, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
1 1 0.03
2 37 0.97
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (2 bp):
AT
Found at i:4260169 original size:23 final size:23
Alignment explanation
Indices: 4260139--4260194 Score: 94
Period size: 23 Copynumber: 2.4 Consensus size: 23
4260129 ATATATTTTA
*
4260139 AAAAATTTATATATTTTTTTATT
1 AAAAATTTATATACTTTTTTATT
4260162 AAAAATTTATATACTTTTTTATT
1 AAAAATTTATATACTTTTTTATT
*
4260185 AAAAAATTAT
1 AAAAATTTAT
4260195 TTTCATCTCT
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
23 31 1.00
ACGTcount: A:0.45, C:0.02, G:0.00, T:0.54
Consensus pattern (23 bp):
AAAAATTTATATACTTTTTTATT
Found at i:4261849 original size:37 final size:35
Alignment explanation
Indices: 4261808--4261887 Score: 90
Period size: 37 Copynumber: 2.2 Consensus size: 35
4261798 AATTAATTTA
* *
4261808 TTAATTTTAGTATATTTATA-TTTATTTTGTATGCTT
1 TTAATTTTACT-TATTTACATTTTATTTTG-ATGCTT
*
4261844 GTTAATTATTTCTTATTTACATTTTATTTTGATGCTT
1 -TTAATT-TTACTTATTTACATTTTATTTTGATGCTT
4261881 TTAATTT
1 TTAATTT
4261888 ATTTTTCCAA
Statistics
Matches: 38, Mismatches: 3, Indels: 6
0.81 0.06 0.13
Matches are distributed among these distances:
35 1 0.03
36 6 0.16
37 19 0.50
38 12 0.32
ACGTcount: A:0.24, C:0.05, G:0.07, T:0.64
Consensus pattern (35 bp):
TTAATTTTACTTATTTACATTTTATTTTGATGCTT
Found at i:4261890 original size:37 final size:37
Alignment explanation
Indices: 4261820--4261891 Score: 103
Period size: 37 Copynumber: 1.9 Consensus size: 37
4261810 AATTTTAGTA
*
4261820 TATTTATATTTATTTTGTATGCTTGTTAATTATTTCT
1 TATTTACATTTATTTTGTATGCTTGTTAATTATTTCT
4261857 TATTTACATTTTATTTTG-ATGCTT-TTAATTTATTT
1 TATTTACA-TTTATTTTGTATGCTTGTTAA-TTATTT
4261892 TTCCAAGTTT
Statistics
Matches: 32, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
36 4 0.12
37 19 0.59
38 9 0.28
ACGTcount: A:0.22, C:0.06, G:0.07, T:0.65
Consensus pattern (37 bp):
TATTTACATTTATTTTGTATGCTTGTTAATTATTTCT
Found at i:4261915 original size:13 final size:13
Alignment explanation
Indices: 4261879--4261917 Score: 51
Period size: 14 Copynumber: 2.9 Consensus size: 13
4261869 ATTTTGATGC
4261879 TTTTAATTTATTT
1 TTTTAATTTATTT
**
4261892 TTCCAAGTTTATTT
1 TTTTAA-TTTATTT
4261906 TTTTAATTTATT
1 TTTTAATTTATT
4261918 AGATTTTAGG
Statistics
Matches: 21, Mismatches: 4, Indels: 2
0.78 0.15 0.07
Matches are distributed among these distances:
13 10 0.48
14 11 0.52
ACGTcount: A:0.23, C:0.05, G:0.03, T:0.69
Consensus pattern (13 bp):
TTTTAATTTATTT
Found at i:4262134 original size:2 final size:2
Alignment explanation
Indices: 4262071--4262122 Score: 104
Period size: 2 Copynumber: 26.0 Consensus size: 2
4262061 TTATTTTTAA
4262071 AT AT 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 AT AT
4262113 AT AT AT AT AT
1 AT AT AT AT AT
4262123 CATTTTATAT
Statistics
Matches: 50, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 50 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:4271075 original size:14 final size:14
Alignment explanation
Indices: 4271056--4271085 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
4271046 ATCACTAACA
*
4271056 CATATATTTCATAT
1 CATATAATTCATAT
4271070 CATATAATTCATAT
1 CATATAATTCATAT
4271084 CA
1 CA
4271086 CAAAACACAT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.40, C:0.17, G:0.00, T:0.43
Consensus pattern (14 bp):
CATATAATTCATAT
Found at i:4271304 original size:30 final size:30
Alignment explanation
Indices: 4271233--4271315 Score: 96
Period size: 30 Copynumber: 2.8 Consensus size: 30
4271223 CCCGAAGGAC
* * *
4271233 CTATTCAGAGGTCACAAAG-ACCCCGGTAA
1 CTATCCAGAGGTCACAAAGAACCTCGGCAA
*
4271262 CTATCCAGAGGTCATAAAGAACCTCGGCAA
1 CTATCCAGAGGTCACAAAGAACCTCGGCAA
* * *
4271292 CTGTCCATAGGTCCCAAAGAACCT
1 CTATCCAGAGGTCACAAAGAACCT
4271316 AGGTAAACTG
Statistics
Matches: 45, Mismatches: 8, Indels: 1
0.83 0.15 0.02
Matches are distributed among these distances:
29 17 0.38
30 28 0.62
ACGTcount: A:0.34, C:0.29, G:0.19, T:0.18
Consensus pattern (30 bp):
CTATCCAGAGGTCACAAAGAACCTCGGCAA
Found at i:4271373 original size:31 final size:31
Alignment explanation
Indices: 4271290--4271384 Score: 120
Period size: 31 Copynumber: 3.1 Consensus size: 31
4271280 GAACCTCGGC
* * * *
4271290 AACTGTCCATAGGTCCCAAAGAACCTAGGTA
1 AACTGTCCATATGTTCCATAGAACATAGGTA
* *
4271321 AACTGT-CATATATTCCTTAGAACATAGGTA
1 AACTGTCCATATGTTCCATAGAACATAGGTA
*
4271351 TACTGTCCATATGTTCCATAGAACATAGGTA
1 AACTGTCCATATGTTCCATAGAACATAGGTA
4271382 AAC
1 AAC
4271385 CCTCGACTCT
Statistics
Matches: 53, Mismatches: 10, Indels: 2
0.82 0.15 0.03
Matches are distributed among these distances:
30 23 0.43
31 30 0.57
ACGTcount: A:0.36, C:0.21, G:0.16, T:0.27
Consensus pattern (31 bp):
AACTGTCCATATGTTCCATAGAACATAGGTA
Found at i:4272119 original size:24 final size:20
Alignment explanation
Indices: 4272070--4272127 Score: 71
Period size: 20 Copynumber: 2.7 Consensus size: 20
4272060 TTCCCATTGA
*
4272070 AGTGCATCGGTGCATTCTAC
1 AGTGCATCGATGCATTCTAC
4272090 AGTGCATCGATGCATTCTTTAAC
1 AGTGCATCGATGCATTC--T-AC
4272113 AGGTGCATCGATGCA
1 A-GTGCATCGATGCA
4272128 CTACCATGCA
Statistics
Matches: 33, Mismatches: 1, Indels: 4
0.87 0.03 0.11
Matches are distributed among these distances:
20 16 0.48
22 1 0.03
23 3 0.09
24 13 0.39
ACGTcount: A:0.24, C:0.22, G:0.24, T:0.29
Consensus pattern (20 bp):
AGTGCATCGATGCATTCTAC
Found at i:4275716 original size:24 final size:23
Alignment explanation
Indices: 4275660--4275720 Score: 104
Period size: 23 Copynumber: 2.6 Consensus size: 23
4275650 TTCCCATTGA
*
4275660 AGTGCATCGGTGCATTCTTTAAC
1 AGTGCATCGATGCATTCTTTAAC
4275683 AGTGCATCGATGCATTCTTTAAC
1 AGTGCATCGATGCATTCTTTAAC
4275706 AGGTGCATCGATGCA
1 A-GTGCATCGATGCA
4275721 CTACCATGCA
Statistics
Matches: 36, Mismatches: 1, Indels: 1
0.95 0.03 0.03
Matches are distributed among these distances:
23 23 0.64
24 13 0.36
ACGTcount: A:0.25, C:0.21, G:0.23, T:0.31
Consensus pattern (23 bp):
AGTGCATCGATGCATTCTTTAAC
Found at i:4276953 original size:20 final size:20
Alignment explanation
Indices: 4276925--4276965 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 20
4276915 CGACAAATGT
* *
4276925 TAAAGGACAGGGAATATCTC
1 TAAAAGACAGGGAATACCTC
*
4276945 TAAAAGACATGGAATACCTC
1 TAAAAGACAGGGAATACCTC
4276965 T
1 T
4276966 GTAAAATATA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.41, C:0.17, G:0.20, T:0.22
Consensus pattern (20 bp):
TAAAAGACAGGGAATACCTC
Found at i:4282596 original size:20 final size:19
Alignment explanation
Indices: 4282535--4282597 Score: 58
Period size: 21 Copynumber: 3.3 Consensus size: 19
4282525 CAATTTAAGA
4282535 GTTCATAATGAGAAGAACT
1 GTTCATAATGAGAAGAACT
* *
4282554 CGTTCGATGAGGAGAAGAA--
1 -GTTC-ATAATGAGAAGAACT
*
4282573 GTTCCTAATGAGAAGAACTT
1 GTTCATAATGAGAAGAAC-T
4282593 GTTCA
1 GTTCA
4282598 ACCTTCGTTT
Statistics
Matches: 33, Mismatches: 6, Indels: 8
0.70 0.13 0.17
Matches are distributed among these distances:
17 10 0.30
18 4 0.12
20 8 0.24
21 11 0.33
ACGTcount: A:0.37, C:0.13, G:0.25, T:0.25
Consensus pattern (19 bp):
GTTCATAATGAGAAGAACT
Found at i:4282756 original size:44 final size:44
Alignment explanation
Indices: 4282703--4282812 Score: 148
Period size: 44 Copynumber: 2.5 Consensus size: 44
4282693 GAGGTTTAAA
* *
4282703 TCCATCACATAAGGAGTTGGATCAACATTACCACTTCGATCGAT
1 TCCATCACATAAGGAGTTGGATCAACATCACCACTTCCATCGAT
* * * * * *
4282747 TCTATCACATAAGGAGTTAGATCATCATCATCATTTCCTTCGAT
1 TCCATCACATAAGGAGTTGGATCAACATCACCACTTCCATCGAT
4282791 TCCATCACATAAGGAGTTGGAT
1 TCCATCACATAAGGAGTTGGAT
4282813 TAGTATGTTC
Statistics
Matches: 56, Mismatches: 10, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
44 56 1.00
ACGTcount: A:0.31, C:0.23, G:0.15, T:0.31
Consensus pattern (44 bp):
TCCATCACATAAGGAGTTGGATCAACATCACCACTTCCATCGAT
Found at i:4282935 original size:179 final size:180
Alignment explanation
Indices: 4282608--4282956 Score: 495
Period size: 179 Copynumber: 1.9 Consensus size: 180
4282598 ACCTTCGTTT
* * * *
4282608 GATTCTATCACATAAGGAGTTGGATCAACATCATCTCGCTCGAGATAGTTTCCCTTTAAACTCAG
1 GATTCCATCACATAAGGAGTTGGATCAACATCATCTCGCTCAAGATAGTTTCCCTTGAAACTCAA
* * * *
4282673 ACTTTAGTATCATTTCACTTGAGGTTTAAATCCATCACATAAGGAGTTGGATCAACATTACCACT
66 ACTTCAGTATCATTTCACTTGAGGTCTAAATCAATCACATAAGGAGTTGAATCAACATTACCACT
* *
4282738 TCGATCGATTCTATCACATAAGGAGTTAGATCATCATCATCATTTCCTTC
131 TCGATCGATTCCATCACATAAGGAGTTAGATCAGCATCATCATTTCCTTC
* ** **
4282788 GATTCCATCACATAAGGAGTTGGATTAGTATGTTCTCGCTCAAGATAGTTT-CCTTGAAACTCAA
1 GATTCCATCACATAAGGAGTTGGATCAACATCATCTCGCTCAAGATAGTTTCCCTTGAAACTCAA
* * *
4282852 ACTTCAGTATCATTTCACTTGATGTCTAAATCAATCACATAAGGAGTTGAATCATCATTATCACT
66 ACTTCAGTATCATTTCACTTGAGGTCTAAATCAATCACATAAGGAGTTGAATCAACATTACCACT
* *
4282917 TC-ACTTGATTCCATCACATAAGGAGTTGGATCAGCATCAT
131 TCGA-TCGATTCCATCACATAAGGAGTTAGATCAGCATCAT
4282957 TTCATAGAGA
Statistics
Matches: 148, Mismatches: 20, Indels: 3
0.87 0.12 0.02
Matches are distributed among these distances:
178 1 0.01
179 103 0.70
180 44 0.30
ACGTcount: A:0.31, C:0.21, G:0.15, T:0.33
Consensus pattern (180 bp):
GATTCCATCACATAAGGAGTTGGATCAACATCATCTCGCTCAAGATAGTTTCCCTTGAAACTCAA
ACTTCAGTATCATTTCACTTGAGGTCTAAATCAATCACATAAGGAGTTGAATCAACATTACCACT
TCGATCGATTCCATCACATAAGGAGTTAGATCAGCATCATCATTTCCTTC
Found at i:4285758 original size:39 final size:39
Alignment explanation
Indices: 4285705--4285819 Score: 144
Period size: 38 Copynumber: 3.0 Consensus size: 39
4285695 CATAAAATGA
4285705 GGTAA-GATTTACCCTGTGGAAAAAGTAGAGGAGCCTGC
1 GGTAAGGATTTACCCTGTGGAAAAAGTAGAGGAGCCTGC
* * * *
4285743 GGTAAGGACTTACCCTGT-GCAAAAGTAGAGGAGCTTGT
1 GGTAAGGATTTACCCTGTGGAAAAAGTAGAGGAGCCTGC
* * **
4285781 AGTAAGGATTTACCCTGTGCAAAAAACAGAGGAGCCTGC
1 GGTAAGGATTTACCCTGTGGAAAAAGTAGAGGAGCCTGC
4285820 AGCAAGGTCT
Statistics
Matches: 63, Mismatches: 12, Indels: 3
0.81 0.15 0.04
Matches are distributed among these distances:
38 38 0.60
39 25 0.40
ACGTcount: A:0.32, C:0.17, G:0.30, T:0.21
Consensus pattern (39 bp):
GGTAAGGATTTACCCTGTGGAAAAAGTAGAGGAGCCTGC
Found at i:4289532 original size:14 final size:14
Alignment explanation
Indices: 4289513--4289542 Score: 60
Period size: 14 Copynumber: 2.1 Consensus size: 14
4289503 ACCTTGAATT
4289513 CAACCTTATTTCTG
1 CAACCTTATTTCTG
4289527 CAACCTTATTTCTG
1 CAACCTTATTTCTG
4289541 CA
1 CA
4289543 TTGATTGAGA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.23, C:0.30, G:0.07, T:0.40
Consensus pattern (14 bp):
CAACCTTATTTCTG
Found at i:4295538 original size:28 final size:28
Alignment explanation
Indices: 4295507--4295562 Score: 71
Period size: 28 Copynumber: 2.0 Consensus size: 28
4295497 GAAAATAATG
4295507 TAAC-AAAGAAAAGGAAAAGAAAA-AAAAA
1 TAACAAAAG-AAAGGAAAA-AAAACAAAAA
*
4295535 TAACAAAAGAAAGTAAAAAAAACAAAAA
1 TAACAAAAGAAAGGAAAAAAAACAAAAA
4295563 CAAAAAATCA
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
27 4 0.16
28 17 0.68
29 4 0.16
ACGTcount: A:0.79, C:0.05, G:0.11, T:0.05
Consensus pattern (28 bp):
TAACAAAAGAAAGGAAAAAAAACAAAAA
Found at i:4295558 original size:19 final size:18
Alignment explanation
Indices: 4295521--4295561 Score: 57
Period size: 18 Copynumber: 2.2 Consensus size: 18
4295511 AAAGAAAAGG
4295521 AAAAGAAAAAAAAATAAC
1 AAAAGAAAAAAAAATAAC
4295539 AAAAGAAAGTAAAAAA-AAC
1 AAAAGAAA--AAAAAATAAC
4295558 AAAA
1 AAAA
4295562 ACAAAAAATC
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
18 8 0.38
19 7 0.33
20 6 0.29
ACGTcount: A:0.83, C:0.05, G:0.07, T:0.05
Consensus pattern (18 bp):
AAAAGAAAAAAAAATAAC
Found at i:4295592 original size:17 final size:17
Alignment explanation
Indices: 4295549--4295598 Score: 50
Period size: 17 Copynumber: 2.9 Consensus size: 17
4295539 AAAAGAAAGT
*
4295549 AAAAAAA-ACAAA-AAC
1 AAAAAAATAAAAATAAC
4295564 AAAAAATCATAAAAATAAC
1 AAAAAA--ATAAAAATAAC
*
4295583 AAAAAAATAATAATAA
1 AAAAAAATAAAAATAA
4295599 TATGTAGCGC
Statistics
Matches: 29, Mismatches: 2, Indels: 6
0.78 0.05 0.16
Matches are distributed among these distances:
15 6 0.21
17 10 0.34
18 4 0.14
19 9 0.31
ACGTcount: A:0.80, C:0.08, G:0.00, T:0.12
Consensus pattern (17 bp):
AAAAAAATAAAAATAAC
Found at i:4306523 original size:30 final size:31
Alignment explanation
Indices: 4306487--4306549 Score: 119
Period size: 31 Copynumber: 2.1 Consensus size: 31
4306477 GGAATGCTTT
4306487 TGCTTGA-TTTTTTTTATGTAAATCAGAAAA
1 TGCTTGATTTTTTTTTATGTAAATCAGAAAA
4306517 TGCTTGATTTTTTTTTATGTAAATCAGAAAA
1 TGCTTGATTTTTTTTTATGTAAATCAGAAAA
4306548 TG
1 TG
4306550 GAAATGGGTT
Statistics
Matches: 32, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
30 7 0.22
31 25 0.78
ACGTcount: A:0.32, C:0.06, G:0.14, T:0.48
Consensus pattern (31 bp):
TGCTTGATTTTTTTTTATGTAAATCAGAAAA
Found at i:4312068 original size:57 final size:58
Alignment explanation
Indices: 4312002--4312111 Score: 170
Period size: 58 Copynumber: 1.9 Consensus size: 58
4311992 ATCCCCAACT
* *
4312002 ATAGTATAATG-TTTATT-AGGTCTCTTGACTATTAAAAGTTATAAAATGGTCCTAATC
1 ATAGTATAATGCTTTATTGA-ATCTCTTGACTATTAAAAGTTACAAAATGGTCCTAATC
*
4312059 ATAGTATAATGCTTTATTGAATCTCTTGACTATTAAACGTTACAAAATGGTCC
1 ATAGTATAATGCTTTATTGAATCTCTTGACTATTAAAAGTTACAAAATGGTCC
4312112 CCCGATCATA
Statistics
Matches: 48, Mismatches: 3, Indels: 3
0.89 0.06 0.06
Matches are distributed among these distances:
57 11 0.23
58 36 0.75
59 1 0.02
ACGTcount: A:0.35, C:0.13, G:0.14, T:0.39
Consensus pattern (58 bp):
ATAGTATAATGCTTTATTGAATCTCTTGACTATTAAAAGTTACAAAATGGTCCTAATC
Found at i:4314971 original size:3 final size:3
Alignment explanation
Indices: 4314963--4315007 Score: 81
Period size: 3 Copynumber: 15.0 Consensus size: 3
4314953 GAGATATGAG
*
4314963 ATA ATA ATA ATA ATA ATA ATA ATA ATA GTA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
4315008 TAAAAAATGA
Statistics
Matches: 40, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
3 40 1.00
ACGTcount: A:0.64, C:0.00, G:0.02, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:4315774 original size:34 final size:32
Alignment explanation
Indices: 4315712--4315782 Score: 88
Period size: 34 Copynumber: 2.2 Consensus size: 32
4315702 ACCTTACAAC
* *
4315712 TCCCTAGTTTTTCCGGGCTAAACTAGAACATT
1 TCCCTAGTTTTACCGGGATAAACTAGAACATT
* *
4315744 TCCCTAGCTTTTACACGGGATAAGCTAGAACCTT
1 TCCCTAG-TTTTAC-CGGGATAAACTAGAACATT
4315778 TCCCT
1 TCCCT
4315783 TTACAAAAGG
Statistics
Matches: 33, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
32 7 0.21
33 5 0.15
34 21 0.64
ACGTcount: A:0.24, C:0.28, G:0.15, T:0.32
Consensus pattern (32 bp):
TCCCTAGTTTTACCGGGATAAACTAGAACATT
Found at i:4316268 original size:21 final size:20
Alignment explanation
Indices: 4316201--4316297 Score: 81
Period size: 21 Copynumber: 4.7 Consensus size: 20
4316191 GATGTTTGAG
*
4316201 TGCATGGATGCA-TGCATGA
1 TGCATGGATGCACTGCAGGA
* *
4316220 TGCATCGATGCATTAGTGCAGG-
1 TGCATGGATGC---ACTGCAGGA
4316242 TGCATGGATGCACTGCAGGGA
1 TGCATGGATGCACTGCA-GGA
* *
4316263 TGCATGGATTCACTGCAGGGG
1 TGCATGGATGCACTGCA-GGA
*
4316284 TGCATGAATGCACT
1 TGCATGGATGCACT
4316298 TTGACACCCT
Statistics
Matches: 64, Mismatches: 8, Indels: 10
0.78 0.10 0.12
Matches are distributed among these distances:
19 15 0.23
20 2 0.03
21 31 0.48
22 11 0.17
23 5 0.08
ACGTcount: A:0.24, C:0.19, G:0.33, T:0.25
Consensus pattern (20 bp):
TGCATGGATGCACTGCAGGA
Found at i:4316398 original size:29 final size:29
Alignment explanation
Indices: 4316377--4316434 Score: 91
Period size: 30 Copynumber: 2.0 Consensus size: 29
4316367 AAACTTTGAA
4316377 TAAATTCAATT-AAGTCCAAAAACATTTTG
1 TAAATTCAATTCAAGTCCAAAAACA-TTTG
4316406 TAAATTCAATTCAAGTCCAAAAACCATTT
1 TAAATTCAATTCAAGTCCAAAAA-CATTT
4316435 TGCCTTAAAT
Statistics
Matches: 27, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
29 11 0.41
30 14 0.52
31 2 0.07
ACGTcount: A:0.45, C:0.17, G:0.05, T:0.33
Consensus pattern (29 bp):
TAAATTCAATTCAAGTCCAAAAACATTTG
Found at i:4316424 original size:30 final size:30
Alignment explanation
Indices: 4316377--4316436 Score: 104
Period size: 29 Copynumber: 2.0 Consensus size: 30
4316367 AAACTTTGAA
4316377 TAAATTCAATTAAGTCCAAAAA-CATTTTG
1 TAAATTCAATTAAGTCCAAAAACCATTTTG
4316406 TAAATTCAATTCAAGTCCAAAAACCATTTTG
1 TAAATTCAATT-AAGTCCAAAAACCATTTTG
4316437 CCTTAAATTG
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
29 11 0.38
30 11 0.38
31 7 0.24
ACGTcount: A:0.43, C:0.17, G:0.07, T:0.33
Consensus pattern (30 bp):
TAAATTCAATTAAGTCCAAAAACCATTTTG
Found at i:4319502 original size:20 final size:22
Alignment explanation
Indices: 4319477--4319516 Score: 66
Period size: 21 Copynumber: 1.9 Consensus size: 22
4319467 TGTTGTATAT
4319477 AGCCG-TTGGGGATG-TTTTGG
1 AGCCGTTTGGGGATGATTTTGG
4319497 AGCCGTTTGGGGATGATTTT
1 AGCCGTTTGGGGATGATTTT
4319517 TCTACTAAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 5 0.28
21 9 0.50
22 4 0.22
ACGTcount: A:0.12, C:0.10, G:0.40, T:0.38
Consensus pattern (22 bp):
AGCCGTTTGGGGATGATTTTGG
Found at i:4319572 original size:21 final size:21
Alignment explanation
Indices: 4319546--4319594 Score: 98
Period size: 21 Copynumber: 2.3 Consensus size: 21
4319536 CATAACATGA
4319546 TGCATCGGTGCACTATCAAGT
1 TGCATCGGTGCACTATCAAGT
4319567 TGCATCGGTGCACTATCAAGT
1 TGCATCGGTGCACTATCAAGT
4319588 TGCATCG
1 TGCATCG
4319595 ATACCCCTTC
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 28 1.00
ACGTcount: A:0.22, C:0.24, G:0.24, T:0.29
Consensus pattern (21 bp):
TGCATCGGTGCACTATCAAGT
Found at i:4319690 original size:20 final size:20
Alignment explanation
Indices: 4319667--4319713 Score: 85
Period size: 20 Copynumber: 2.4 Consensus size: 20
4319657 ATTCATGGCA
4319667 CGATGCATGGCAGAATGCAT
1 CGATGCATGGCAGAATGCAT
*
4319687 CGATGCATGGCAGGATGCAT
1 CGATGCATGGCAGAATGCAT
4319707 CGATGCA
1 CGATGCA
4319714 CTAAGTGCAT
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 26 1.00
ACGTcount: A:0.28, C:0.21, G:0.32, T:0.19
Consensus pattern (20 bp):
CGATGCATGGCAGAATGCAT
Found at i:4319804 original size:21 final size:21
Alignment explanation
Indices: 4319778--4319833 Score: 94
Period size: 21 Copynumber: 2.7 Consensus size: 21
4319768 TTAGTGCAGG
*
4319778 TGCATGGATGCACTGCAGGGA
1 TGCATGGATGCACTACAGGGA
*
4319799 TGCATGGATGCACTACAGGGG
1 TGCATGGATGCACTACAGGGA
4319820 TGCATGGATGCACT
1 TGCATGGATGCACT
4319834 TTGACACCCT
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
21 33 1.00
ACGTcount: A:0.23, C:0.20, G:0.36, T:0.21
Consensus pattern (21 bp):
TGCATGGATGCACTACAGGGA
Found at i:4319934 original size:29 final size:29
Alignment explanation
Indices: 4319913--4319970 Score: 91
Period size: 30 Copynumber: 2.0 Consensus size: 29
4319903 AAACTTTGAA
4319913 TAAATTCAATT-AAGTCCAAAAACATTTTG
1 TAAATTCAATTCAAGTCCAAAAACA-TTTG
4319942 TAAATTCAATTCAAGTCCAAAAACCATTT
1 TAAATTCAATTCAAGTCCAAAAA-CATTT
4319971 TGCCTTAAAT
Statistics
Matches: 27, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
29 11 0.41
30 14 0.52
31 2 0.07
ACGTcount: A:0.45, C:0.17, G:0.05, T:0.33
Consensus pattern (29 bp):
TAAATTCAATTCAAGTCCAAAAACATTTG
Found at i:4319960 original size:30 final size:30
Alignment explanation
Indices: 4319913--4319972 Score: 104
Period size: 29 Copynumber: 2.0 Consensus size: 30
4319903 AAACTTTGAA
4319913 TAAATTCAATTAAGTCCAAAAA-CATTTTG
1 TAAATTCAATTAAGTCCAAAAACCATTTTG
4319942 TAAATTCAATTCAAGTCCAAAAACCATTTTG
1 TAAATTCAATT-AAGTCCAAAAACCATTTTG
4319973 CCTTAAATTG
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
29 11 0.38
30 11 0.38
31 7 0.24
ACGTcount: A:0.43, C:0.17, G:0.07, T:0.33
Consensus pattern (30 bp):
TAAATTCAATTAAGTCCAAAAACCATTTTG
Found at i:4320174 original size:44 final size:44
Alignment explanation
Indices: 4320124--4320219 Score: 174
Period size: 44 Copynumber: 2.2 Consensus size: 44
4320114 GTTAAGCTCT
4320124 CCCTTTTTCATTAAGAAAATAAATTTTTCAAACCAAACTTCTCC
1 CCCTTTTTCATTAAGAAAATAAATTTTTCAAACCAAACTTCTCC
* *
4320168 CCCTTTTTCATTAAGAAATTGAATTTTTCAAACCAAACTTCTCC
1 CCCTTTTTCATTAAGAAAATAAATTTTTCAAACCAAACTTCTCC
4320212 CCCTTTTT
1 CCCTTTTT
4320220 GTTATATAAA
Statistics
Matches: 50, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
44 50 1.00
ACGTcount: A:0.31, C:0.26, G:0.03, T:0.40
Consensus pattern (44 bp):
CCCTTTTTCATTAAGAAAATAAATTTTTCAAACCAAACTTCTCC
Found at i:4321324 original size:18 final size:18
Alignment explanation
Indices: 4321259--4321324 Score: 55
Period size: 18 Copynumber: 3.6 Consensus size: 18
4321249 TGAAAGCTCT
*
4321259 AAATTATTTTTCAAAATTC
1 AAATTATCTTTCAAAA-TC
**
4321278 ATTTTAAT-TTTCAAAATC
1 AAATT-ATCTTTCAAAATC
*
4321296 AACTT-TGCTTTCAAAATC
1 AAATTAT-CTTTCAAAATC
4321314 AAATTATCTTT
1 AAATTATCTTT
4321325 AATTTGAGTT
Statistics
Matches: 38, Mismatches: 5, Indels: 9
0.73 0.10 0.17
Matches are distributed among these distances:
16 1 0.03
18 23 0.61
19 12 0.32
20 2 0.05
ACGTcount: A:0.38, C:0.14, G:0.02, T:0.47
Consensus pattern (18 bp):
AAATTATCTTTCAAAATC
Found at i:4323357 original size:21 final size:20
Alignment explanation
Indices: 4323289--4323386 Score: 90
Period size: 21 Copynumber: 4.7 Consensus size: 20
4323279 GATGTTTGAG
* *
4323289 TGCATGGATGCATTGCATGA
1 TGCATGGATGCACTGCAGGA
* *
4323309 TGCATCGATGCATTAGTGCAGG-
1 TGCATGGATGC---ACTGCAGGA
4323331 TGCATGGATGCACTGCAGGGA
1 TGCATGGATGCACTGCA-GGA
* *
4323352 TGCATGGATGCACTACAGGGG
1 TGCATGGATGCACTGCA-GGA
4323373 TGCATGGATGCACT
1 TGCATGGATGCACT
4323387 TTGACACCCT
Statistics
Matches: 66, Mismatches: 7, Indels: 9
0.80 0.09 0.11
Matches are distributed among these distances:
19 5 0.08
20 12 0.18
21 33 0.50
22 10 0.15
23 6 0.09
ACGTcount: A:0.23, C:0.18, G:0.34, T:0.24
Consensus pattern (20 bp):
TGCATGGATGCACTGCAGGA
Found at i:4323375 original size:42 final size:42
Alignment explanation
Indices: 4323288--4323386 Score: 119
Period size: 42 Copynumber: 2.4 Consensus size: 42
4323278 CGATGTTTGA
* * * **
4323288 GTGCATGGATGCATTGCATGATGCATCGATGCATTAGTGCAG
1 GTGCATGGATGCACTGCAGGATGCATCGATGCACTACAGCAG
* *
4323330 GTGCATGGATGCACTGCAGGGATGCATGGATGCACTACAG-GG
1 GTGCATGGATGCACTGCA-GGATGCATCGATGCACTACAGCAG
4323372 GTGCATGGATGCACT
1 GTGCATGGATGCACT
4323387 TTGACACCCT
Statistics
Matches: 49, Mismatches: 7, Indels: 2
0.84 0.12 0.03
Matches are distributed among these distances:
42 33 0.67
43 16 0.33
ACGTcount: A:0.23, C:0.18, G:0.34, T:0.24
Consensus pattern (42 bp):
GTGCATGGATGCACTGCAGGATGCATCGATGCACTACAGCAG
Found at i:4323487 original size:29 final size:30
Alignment explanation
Indices: 4323455--4323522 Score: 93
Period size: 29 Copynumber: 2.3 Consensus size: 30
4323445 GAAACCTTTT
4323455 AAAACATTGAATAAATTCAATT-AAGTCCA
1 AAAACATTGAATAAATTCAATTCAAGTCCA
***
4323484 AAAACATTTTGTAAATTCAATTCAAGTCCA
1 AAAACATTGAATAAATTCAATTCAAGTCCA
4323514 AAAATCATT
1 AAAA-CATT
4323523 TTGCCTTAAA
Statistics
Matches: 34, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
29 19 0.56
30 11 0.32
31 4 0.12
ACGTcount: A:0.49, C:0.15, G:0.06, T:0.31
Consensus pattern (30 bp):
AAAACATTGAATAAATTCAATTCAAGTCCA
Found at i:4323513 original size:30 final size:30
Alignment explanation
Indices: 4323466--4323525 Score: 104
Period size: 29 Copynumber: 2.0 Consensus size: 30
4323456 AAACATTGAA
4323466 TAAATTCAATTAAGTCCAAAAA-CATTTTG
1 TAAATTCAATTAAGTCCAAAAATCATTTTG
4323495 TAAATTCAATTCAAGTCCAAAAATCATTTTG
1 TAAATTCAATT-AAGTCCAAAAATCATTTTG
4323526 CCTTAAATTG
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
29 11 0.38
30 11 0.38
31 7 0.24
ACGTcount: A:0.43, C:0.15, G:0.07, T:0.35
Consensus pattern (30 bp):
TAAATTCAATTAAGTCCAAAAATCATTTTG
Found at i:4324284 original size:3 final size:3
Alignment explanation
Indices: 4324276--4324386 Score: 186
Period size: 3 Copynumber: 37.0 Consensus size: 3
4324266 GTTTTGTTTG
4324276 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
* * *
4324324 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAG TAA TGA TAA TAA TAA TTA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
*
4324372 TTA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA
4324387 ATATATATAG
Statistics
Matches: 102, Mismatches: 6, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
3 102 1.00
ACGTcount: A:0.63, C:0.00, G:0.02, T:0.35
Consensus pattern (3 bp):
TAA
Found at i:4326525 original size:18 final size:18
Alignment explanation
Indices: 4326502--4326560 Score: 64
Period size: 20 Copynumber: 3.1 Consensus size: 18
4326492 TTTCTTATTC
4326502 TAAAATATTTTTTATTAA
1 TAAAATATTTTTTATTAA
*
4326520 TAAAATATTCTTTTTGAATAA
1 TAAAATA-T-TTTTT-ATTAA
*
4326541 CTTAAATATTTTTTATTAA
1 -TAAAATATTTTTTATTAA
4326560 T
1 T
4326561 CTAGGTAAGT
Statistics
Matches: 34, Mismatches: 3, Indels: 8
0.76 0.07 0.18
Matches are distributed among these distances:
18 8 0.24
19 5 0.15
20 10 0.29
21 5 0.15
22 6 0.18
ACGTcount: A:0.41, C:0.03, G:0.02, T:0.54
Consensus pattern (18 bp):
TAAAATATTTTTTATTAA
Found at i:4329599 original size:6 final size:6
Alignment explanation
Indices: 4329592--4329637 Score: 65
Period size: 6 Copynumber: 7.5 Consensus size: 6
4329582 TACTTTCTAA
* *
4329592 AAACAA AAACAA AAAGCAT AAACAT AAACAT AAACAT AAACAT AAA
1 AAACAT AAACAT AAA-CAT AAACAT AAACAT AAACAT AAACAT AAA
4329638 TTTTTTTCTT
Statistics
Matches: 38, Mismatches: 1, Indels: 2
0.93 0.02 0.05
Matches are distributed among these distances:
6 33 0.87
7 5 0.13
ACGTcount: A:0.72, C:0.15, G:0.02, T:0.11
Consensus pattern (6 bp):
AAACAT
Found at i:4329631 original size:18 final size:19
Alignment explanation
Indices: 4329592--4329637 Score: 67
Period size: 19 Copynumber: 2.5 Consensus size: 19
4329582 TACTTTCTAA
*
4329592 AAACAAAAACAAAAAGCAT
1 AAACATAAACAAAAAGCAT
*
4329611 AAACATAAACATAAA-CAT
1 AAACATAAACAAAAAGCAT
4329629 AAACATAAA
1 AAACATAAA
4329638 TTTTTTTCTT
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
18 12 0.48
19 13 0.52
ACGTcount: A:0.72, C:0.15, G:0.02, T:0.11
Consensus pattern (19 bp):
AAACATAAACAAAAAGCAT
Found at i:4330623 original size:30 final size:31
Alignment explanation
Indices: 4330566--4330625 Score: 95
Period size: 31 Copynumber: 2.0 Consensus size: 31
4330556 GGGTCGAATC
*
4330566 GGGTTAGGTTCGGATTTTACCCCCAAAAAAG
1 GGGTTAGGTTCAGATTTTACCCCCAAAAAAG
*
4330597 GGGTTAGGTTCAGATTTTA-TCCCAAAAAA
1 GGGTTAGGTTCAGATTTTACCCCCAAAAAA
4330626 TTGGGTCGGT
Statistics
Matches: 27, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
30 9 0.33
31 18 0.67
ACGTcount: A:0.32, C:0.17, G:0.23, T:0.28
Consensus pattern (31 bp):
GGGTTAGGTTCAGATTTTACCCCCAAAAAAG
Found at i:4334828 original size:19 final size:20
Alignment explanation
Indices: 4334782--4334829 Score: 64
Period size: 20 Copynumber: 2.5 Consensus size: 20
4334772 GAATAAAAGG
4334782 TTGTTAG-GAATGTTAGAAA
1 TTGTTAGAGAATGTTAGAAA
*
4334801 TCAGTTAGAGAA-GTTAGAAA
1 T-TGTTAGAGAATGTTAGAAA
4334821 TTGTTAGAG
1 TTGTTAGAG
4334830 GATTAGTTAG
Statistics
Matches: 25, Mismatches: 2, Indels: 4
0.81 0.06 0.13
Matches are distributed among these distances:
19 8 0.32
20 14 0.56
21 3 0.12
ACGTcount: A:0.38, C:0.02, G:0.27, T:0.33
Consensus pattern (20 bp):
TTGTTAGAGAATGTTAGAAA
Found at i:4335280 original size:13 final size:13
Alignment explanation
Indices: 4335262--4335286 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
4335252 TTCTCCAAAT
4335262 GAGTTTTTTCAAC
1 GAGTTTTTTCAAC
4335275 GAGTTTTTTCAA
1 GAGTTTTTTCAA
4335287 TGCAAAAGTA
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:0.24, C:0.12, G:0.16, T:0.48
Consensus pattern (13 bp):
GAGTTTTTTCAAC
Found at i:4341778 original size:12 final size:12
Alignment explanation
Indices: 4341761--4341785 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
4341751 GAATAGCTGC
4341761 TTTTTGTTTTTT
1 TTTTTGTTTTTT
4341773 TTTTTGTTTTTT
1 TTTTTGTTTTTT
4341785 T
1 T
4341786 GGTTTTTTTT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.00, C:0.00, G:0.08, T:0.92
Consensus pattern (12 bp):
TTTTTGTTTTTT
Found at i:4342664 original size:13 final size:12
Alignment explanation
Indices: 4342644--4342678 Score: 52
Period size: 12 Copynumber: 2.9 Consensus size: 12
4342634 GCTTAATCGG
4342644 AAAAAAAAATAA
1 AAAAAAAAATAA
*
4342656 AAGAAAAAATAA
1 AAAAAAAAATAA
*
4342668 AAATAAAAATA
1 AAAAAAAAATA
4342679 TAACGGAATT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
12 20 1.00
ACGTcount: A:0.86, C:0.00, G:0.03, T:0.11
Consensus pattern (12 bp):
AAAAAAAAATAA
Found at i:4348221 original size:23 final size:21
Alignment explanation
Indices: 4348185--4348237 Score: 63
Period size: 23 Copynumber: 2.4 Consensus size: 21
4348175 GGGATTTTAG
4348185 TAAAAGATAATAAAGTGAATAAA
1 TAAAAGATAATAAAGT-AA-AAA
4348208 TAAAAG-TAATTAAAGTAAAAA
1 TAAAAGATAA-TAAAGTAAAAA
4348229 TAAGAAGAT
1 TAA-AAGAT
4348238 GAAGATTGTG
Statistics
Matches: 27, Mismatches: 0, Indels: 6
0.82 0.00 0.18
Matches are distributed among these distances:
21 6 0.22
22 8 0.30
23 13 0.48
ACGTcount: A:0.64, C:0.00, G:0.13, T:0.23
Consensus pattern (21 bp):
TAAAAGATAATAAAGTAAAAA
Found at i:4350591 original size:56 final size:56
Alignment explanation
Indices: 4350523--4350635 Score: 201
Period size: 56 Copynumber: 2.0 Consensus size: 56
4350513 TGTGGAGTGC
*
4350523 ACACTTGTTTGAATTTATTCTGATTTG-ATCTGTTATGTGGTGGTTTTGTAACTGCT
1 ACACTTATTTGAATTTATTCTGATTTGAAT-TGTTATGTGGTGGTTTTGTAACTGCT
4350579 ACACTTATTTGAATTTATTCTGATTTGAATTGTTATGTGGTGGTTTTGTAACTGCT
1 ACACTTATTTGAATTTATTCTGATTTGAATTGTTATGTGGTGGTTTTGTAACTGCT
4350635 A
1 A
4350636 ATTTTAGTTT
Statistics
Matches: 55, Mismatches: 1, Indels: 2
0.95 0.02 0.03
Matches are distributed among these distances:
56 53 0.96
57 2 0.04
ACGTcount: A:0.20, C:0.10, G:0.20, T:0.50
Consensus pattern (56 bp):
ACACTTATTTGAATTTATTCTGATTTGAATTGTTATGTGGTGGTTTTGTAACTGCT
Found at i:4352962 original size:26 final size:26
Alignment explanation
Indices: 4352932--4352986 Score: 83
Period size: 26 Copynumber: 2.1 Consensus size: 26
4352922 TCTGGTTGGT
* *
4352932 CTGGGCCGGTTCTGGTTTGTTTGTAA
1 CTGGGCCGGTCCAGGTTTGTTTGTAA
*
4352958 CTGGGCCGGTCCAGTTTTGTTTGTAA
1 CTGGGCCGGTCCAGGTTTGTTTGTAA
4352984 CTG
1 CTG
4352987 TTTGTAAATA
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
26 26 1.00
ACGTcount: A:0.09, C:0.18, G:0.33, T:0.40
Consensus pattern (26 bp):
CTGGGCCGGTCCAGGTTTGTTTGTAA
Found at i:4353001 original size:3 final size:3
Alignment explanation
Indices: 4352993--4353048 Score: 78
Period size: 3 Copynumber: 18.7 Consensus size: 3
4352983 ACTGTTTGTA
* *
4352993 AAT AAT AAT TAT AAT -AT AAT AAT AAT ATTT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT A-AT AAT AAT AAT AAT AAT
4353038 AAT AAT AAT AA
1 AAT AAT AAT AA
4353049 AATTAGTGTT
Statistics
Matches: 47, Mismatches: 4, Indels: 4
0.85 0.07 0.07
Matches are distributed among these distances:
2 2 0.04
3 43 0.91
4 2 0.04
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (3 bp):
AAT
Found at i:4353600 original size:226 final size:226
Alignment explanation
Indices: 4353184--4353817 Score: 1157
Period size: 226 Copynumber: 2.8 Consensus size: 226
4353174 GAGGTCTTAA
* * * *
4353184 AAACATCATGCACTGCATGACTTACAGATGATCCC-AAGGTTTTGAAAACATCAAAAAGCTCCTG
1 AAACATCATGCACTGAAGGACTTACAGATGA-CCCGAAGGCTTTGAAAACATCAAAAAGCTCCCG
4353248 AAGGCTTTTTGGAAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGCTTTGAAAACATCA
65 AAGGCTTTTTGGAAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGCTTTGAAAACATCA
4353313 AAAAGCTCCCGAAGGC-TTTTGGAAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGCTT
130 AAAAGCT-CCGAAGGCTTTTTGGAAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGCTT
4353377 TGAAAACATCAAAAAGCTCCCGAAGGCTTTTTGG
194 TGAAAACATCAAAAAGCT-CCGAAGGCTTTTTGG
*
4353411 ATACATCATGCACTGAAGGAC-TACAGATGACCCGAAGGCTTTGAAAACATCAAAAAGCTCCCGA
1 AAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGCTTTGAAAACATCAAAAAGCTCCCGA
4353475 AGGCTTTTTGGAAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGCTTTGAAAACATCAA
66 AGGCTTTTTGGAAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGCTTTGAAAACATCAA
*
4353540 AAAGCTCCGAAGGCTTTTTGGAAACATCATGCACTGAAAGACTTACAGATGACCCGAAGGCTTTG
131 AAAGCTCCGAAGGCTTTTTGGAAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGCTTTG
4353605 AAAACATCAAAAAGCTCCGAAGGCTTTTTGG
196 AAAACATCAAAAAGCTCCGAAGGCTTTTTGG
*
4353636 AAACATCATGCACTGAAGGGCTTACAGATGACCCGAAGGCTTTGAAAACATCAAAAAGCTCCCGA
1 AAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGCTTTGAAAACATCAAAAAGCTCCCGA
4353701 AGGCTTTTTGGAAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGCTTTGAAAACATCAA
66 AGGCTTTTTGGAAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGCTTTGAAAACATCAA
4353766 AAAGCTCCGAAGGCTTTTTGGAAACATCATGCACTGAAGGACTTACAGATGA
131 AAAGCTCCGAAGGCTTTTTGGAAACATCATGCACTGAAGGACTTACAGATGA
4353818 GGGAAATAGT
Statistics
Matches: 395, Mismatches: 9, Indels: 7
0.96 0.02 0.02
Matches are distributed among these distances:
225 45 0.11
226 332 0.84
227 18 0.05
ACGTcount: A:0.36, C:0.22, G:0.21, T:0.22
Consensus pattern (226 bp):
AAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGCTTTGAAAACATCAAAAAGCTCCCGA
AGGCTTTTTGGAAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGCTTTGAAAACATCAA
AAAGCTCCGAAGGCTTTTTGGAAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGCTTTG
AAAACATCAAAAAGCTCCGAAGGCTTTTTGG
Found at i:4353843 original size:75 final size:76
Alignment explanation
Indices: 4353184--4353817 Score: 1154
Period size: 75 Copynumber: 8.4 Consensus size: 76
4353174 GAGGTCTTAA
* * * *
4353184 AAACATCATGCACTGCATGACTTACAGATGATCCC-AAGGTTTTGAAAACATCAAAAAGCTCCTG
1 AAACATCATGCACTGAAGGACTTACAGATGA-CCCGAAGGCTTTGAAAACATCAAAAAGCTCCCG
4353248 AAGGCTTTTTGG
65 AAGGCTTTTTGG
4353260 AAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGCTTTGAAAACATCAAAAAGCTCCCGA
1 AAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGCTTTGAAAACATCAAAAAGCTCCCGA
4353325 AGGC-TTTTGG
66 AGGCTTTTTGG
4353335 AAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGCTTTGAAAACATCAAAAAGCTCCCGA
1 AAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGCTTTGAAAACATCAAAAAGCTCCCGA
4353400 AGGCTTTTTGG
66 AGGCTTTTTGG
*
4353411 ATACATCATGCACTGAAGGAC-TACAGATGACCCGAAGGCTTTGAAAACATCAAAAAGCTCCCGA
1 AAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGCTTTGAAAACATCAAAAAGCTCCCGA
4353475 AGGCTTTTTGG
66 AGGCTTTTTGG
4353486 AAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGCTTTGAAAACATCAAAAAGCT-CCGA
1 AAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGCTTTGAAAACATCAAAAAGCTCCCGA
4353550 AGGCTTTTTGG
66 AGGCTTTTTGG
*
4353561 AAACATCATGCACTGAAAGACTTACAGATGACCCGAAGGCTTTGAAAACATCAAAAAGCT-CCGA
1 AAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGCTTTGAAAACATCAAAAAGCTCCCGA
4353625 AGGCTTTTTGG
66 AGGCTTTTTGG
*
4353636 AAACATCATGCACTGAAGGGCTTACAGATGACCCGAAGGCTTTGAAAACATCAAAAAGCTCCCGA
1 AAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGCTTTGAAAACATCAAAAAGCTCCCGA
4353701 AGGCTTTTTGG
66 AGGCTTTTTGG
4353712 AAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGCTTTGAAAACATCAAAAAGCT-CCGA
1 AAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGCTTTGAAAACATCAAAAAGCTCCCGA
4353776 AGGCTTTTTGG
66 AGGCTTTTTGG
4353787 AAACATCATGCACTGAAGGACTTACAGATGA
1 AAACATCATGCACTGAAGGACTTACAGATGA
4353818 GGGAAATAGT
Statistics
Matches: 544, Mismatches: 10, Indels: 9
0.97 0.02 0.02
Matches are distributed among these distances:
75 345 0.63
76 199 0.37
ACGTcount: A:0.36, C:0.22, G:0.21, T:0.22
Consensus pattern (76 bp):
AAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGCTTTGAAAACATCAAAAAGCTCCCGA
AGGCTTTTTGG
Found at i:4353843 original size:151 final size:152
Alignment explanation
Indices: 4353184--4353817 Score: 1154
Period size: 151 Copynumber: 4.2 Consensus size: 152
4353174 GAGGTCTTAA
* * * *
4353184 AAACATCATGCACTGCATGACTTACAGATGATCCC-AAGGTTTTGAAAACATCAAAAAGCTCCTG
1 AAACATCATGCACTGAAGGACTTACAGATGA-CCCGAAGGCTTTGAAAACATCAAAAAGCTCCCG
4353248 AAGGCTTTTTGGAAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGCTTTGAAAACATCA
65 AAGGCTTTTTGGAAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGCTTTGAAAACATCA
4353313 AAAAGCTCCCGAAGGC-TTTTGG
130 AAAAGCTCCCGAAGGCTTTTTGG
4353335 AAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGCTTTGAAAACATCAAAAAGCTCCCGA
1 AAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGCTTTGAAAACATCAAAAAGCTCCCGA
*
4353400 AGGCTTTTTGGATACATCATGCACTGAAGGAC-TACAGATGACCCGAAGGCTTTGAAAACATCAA
66 AGGCTTTTTGGAAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGCTTTGAAAACATCAA
4353464 AAAGCTCCCGAAGGCTTTTTGG
131 AAAGCTCCCGAAGGCTTTTTGG
4353486 AAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGCTTTGAAAACATCAAAAAGCT-CCGA
1 AAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGCTTTGAAAACATCAAAAAGCTCCCGA
*
4353550 AGGCTTTTTGGAAACATCATGCACTGAAAGACTTACAGATGACCCGAAGGCTTTGAAAACATCAA
66 AGGCTTTTTGGAAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGCTTTGAAAACATCAA
4353615 AAAGCT-CCGAAGGCTTTTTGG
131 AAAGCTCCCGAAGGCTTTTTGG
*
4353636 AAACATCATGCACTGAAGGGCTTACAGATGACCCGAAGGCTTTGAAAACATCAAAAAGCTCCCGA
1 AAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGCTTTGAAAACATCAAAAAGCTCCCGA
4353701 AGGCTTTTTGGAAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGCTTTGAAAACATCAA
66 AGGCTTTTTGGAAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGCTTTGAAAACATCAA
4353766 AAAGCT-CCGAAGGCTTTTTGG
131 AAAGCTCCCGAAGGCTTTTTGG
4353787 AAACATCATGCACTGAAGGACTTACAGATGA
1 AAACATCATGCACTGAAGGACTTACAGATGA
4353818 GGGAAATAGT
Statistics
Matches: 469, Mismatches: 10, Indels: 8
0.96 0.02 0.02
Matches are distributed among these distances:
150 158 0.34
151 311 0.66
ACGTcount: A:0.36, C:0.22, G:0.21, T:0.22
Consensus pattern (152 bp):
AAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGCTTTGAAAACATCAAAAAGCTCCCGA
AGGCTTTTTGGAAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGCTTTGAAAACATCAA
AAAGCTCCCGAAGGCTTTTTGG
Found at i:4354539 original size:22 final size:22
Alignment explanation
Indices: 4354488--4354539 Score: 77
Period size: 22 Copynumber: 2.4 Consensus size: 22
4354478 CATAAAGTTT
** *
4354488 TCATCTTCGAAAAGAGAATCTG
1 TCATCTTTAAAAAGAGAATCTA
4354510 TCATCTTTAAAAAGAGAATCTA
1 TCATCTTTAAAAAGAGAATCTA
4354532 TCATCTTT
1 TCATCTTT
4354540 GAAGAATGTA
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 27 1.00
ACGTcount: A:0.37, C:0.17, G:0.12, T:0.35
Consensus pattern (22 bp):
TCATCTTTAAAAAGAGAATCTA
Found at i:4354992 original size:55 final size:53
Alignment explanation
Indices: 4354909--4355024 Score: 171
Period size: 55 Copynumber: 2.2 Consensus size: 53
4354899 AGAATAACAG
* *
4354909 GTTCGTAAAACATTGACAGTGCATTCAT-CTTTTCCTGTGGCTTCTGCTCAGAT
1 GTTCGTAAAACATTGACAATACATTCATCCTTTT-CTGTGGCTTCTGCTCAGAT
*
4354962 GTTCGTAAAACATTTTGACAATACATTCATCCTTTTTTGTGGCTTCTGCTCAGAT
1 GTTCGTAAAACA--TTGACAATACATTCATCCTTTTCTGTGGCTTCTGCTCAGAT
4355017 GTTCGTAA
1 GTTCGTAA
4355025 TCATTGAAGT
Statistics
Matches: 57, Mismatches: 3, Indels: 4
0.89 0.05 0.06
Matches are distributed among these distances:
53 12 0.21
55 40 0.70
56 5 0.09
ACGTcount: A:0.22, C:0.21, G:0.17, T:0.40
Consensus pattern (53 bp):
GTTCGTAAAACATTGACAATACATTCATCCTTTTCTGTGGCTTCTGCTCAGAT
Found at i:4357432 original size:148 final size:148
Alignment explanation
Indices: 4357164--4357467 Score: 599
Period size: 148 Copynumber: 2.1 Consensus size: 148
4357154 ATGATCATGC
*
4357164 AGTTCATCTTTTAATTCCAATGATCGGTTCTGGGGTTCCTACCGAATCAGATCAGATAACTCAAA
1 AGTTCATATTTTAATTCCAATGATCGGTTCTGGGGTTCCTACCGAATCAGATCAGATAACTCAAA
4357229 GAACACTTCCAGAAGATGCTATTGAGTCTCCTTATTTCTACTATGAGCAAAATTCATCTTTCAAA
66 GAACACTTCCAGAAGATGCTATTGAGTCTCCTTATTTCTACTATGAGCAAAATTCATCTTTCAAA
4357294 TCCAATGATTGATTTTGG
131 TCCAATGATTGATTTTGG
4357312 AGTTCATATTTTAATTCCAATGATCGGTTCTGGGGTTCCTACCGAATCAGATCAGATAACTCAAA
1 AGTTCATATTTTAATTCCAATGATCGGTTCTGGGGTTCCTACCGAATCAGATCAGATAACTCAAA
4357377 GAACACTTCCAGAAGATGCTATTGAGTCTCCTTATTTCTACTATGAGCAAAATTCATCTTTCAAA
66 GAACACTTCCAGAAGATGCTATTGAGTCTCCTTATTTCTACTATGAGCAAAATTCATCTTTCAAA
4357442 TCCAATGATTGATTTTGG
131 TCCAATGATTGATTTTGG
4357460 AGTTCATA
1 AGTTCATA
4357468 CCAAATCAGA
Statistics
Matches: 155, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
148 155 1.00
ACGTcount: A:0.30, C:0.20, G:0.15, T:0.35
Consensus pattern (148 bp):
AGTTCATATTTTAATTCCAATGATCGGTTCTGGGGTTCCTACCGAATCAGATCAGATAACTCAAA
GAACACTTCCAGAAGATGCTATTGAGTCTCCTTATTTCTACTATGAGCAAAATTCATCTTTCAAA
TCCAATGATTGATTTTGG
Found at i:4357576 original size:93 final size:93
Alignment explanation
Indices: 4357417--4357700 Score: 421
Period size: 94 Copynumber: 3.0 Consensus size: 93
4357407 CTTATTTCTA
* * * * *
4357417 CTATGAGCAAAATTCATCTTTCAAATCCAATGATTGATT-T-TGGAGTTCATACCAAATCAGATC
1 CTATGAGC-ACATTCATCTTCCAAATTCAATGATTGATTCTGTGG-TTTCATACCAAACCAGATC
4357480 AGATAACTCAAAGAACACTTCCAGAAGATG
64 AGATAACTCAAAGAACACTTCCAGAAGATG
4357510 CTATGAGCACATTCATCTTCCAAATTCAATGATTGATTCTGTGGTTTCATACCAAACCAGATCAG
1 CTATGAGCACATTCATCTTCCAAATTCAATGATTGATTCTGTGGTTTCATACCAAACCAGATCAG
*
4357575 ATAACTCAAAGAACACTTCCCAAAAGATG
66 ATAACTCAAAGAACACTT-CCAGAAGATG
* * *
4357604 ATGTGAGCACATTCATCTTCCAAATTCAATGATT-AGTTCTGTGGTTTCATACCAAACCCGATCA
1 CTATGAGCACATTCATCTTCCAAATTCAATGATTGA-TTCTGTGGTTTCATACCAAACCAGATCA
*
4357668 GATAACTCAAAGAACACTTCCAGAAGATA
65 GATAACTCAAAGAACACTTCCAGAAGATG
4357697 CTAT
1 CTAT
4357701 TGGGTCTTCT
Statistics
Matches: 174, Mismatches: 13, Indels: 8
0.89 0.07 0.04
Matches are distributed among these distances:
92 27 0.16
93 57 0.33
94 90 0.52
ACGTcount: A:0.37, C:0.22, G:0.13, T:0.28
Consensus pattern (93 bp):
CTATGAGCACATTCATCTTCCAAATTCAATGATTGATTCTGTGGTTTCATACCAAACCAGATCAG
ATAACTCAAAGAACACTTCCAGAAGATG
Found at i:4366122 original size:12 final size:13
Alignment explanation
Indices: 4366095--4366120 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
4366085 GTTCTCTTTC
4366095 TCTGTTTTTTTTT
1 TCTGTTTTTTTTT
4366108 TCTGTTTTTTTTT
1 TCTGTTTTTTTTT
4366121 CTCTCCCCTT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.00, C:0.08, G:0.08, T:0.85
Consensus pattern (13 bp):
TCTGTTTTTTTTT
Found at i:4366432 original size:26 final size:26
Alignment explanation
Indices: 4366402--4366456 Score: 83
Period size: 26 Copynumber: 2.1 Consensus size: 26
4366392 TCTGGTTGGT
* *
4366402 CTGGGCCGGTTCTGGTTTGTTTGTAA
1 CTGGGCCGGTCCAGGTTTGTTTGTAA
*
4366428 CTGGGCCGGTCCAGTTTTGTTTGTAA
1 CTGGGCCGGTCCAGGTTTGTTTGTAA
4366454 CTG
1 CTG
4366457 TTTGTAAATA
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
26 26 1.00
ACGTcount: A:0.09, C:0.18, G:0.33, T:0.40
Consensus pattern (26 bp):
CTGGGCCGGTCCAGGTTTGTTTGTAA
Found at i:4366471 original size:3 final size:3
Alignment explanation
Indices: 4366463--4366545 Score: 80
Period size: 3 Copynumber: 27.7 Consensus size: 3
4366453 ACTGTTTGTA
* *
4366463 AAT AAT AAT TAT AAT -AT AA- ATAT AAT AAT AAT ATTT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT A-AT AAT AAT AAT A-AT AAT AAT AAT
** **
4366508 AAT AAT AAT TTT AAT TTT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
4366546 AAAATTAGTG
Statistics
Matches: 64, Mismatches: 12, Indels: 8
0.76 0.14 0.10
Matches are distributed among these distances:
2 3 0.05
3 58 0.91
4 3 0.05
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (3 bp):
AAT
Found at i:4379846 original size:20 final size:20
Alignment explanation
Indices: 4379821--4379858 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
4379811 TTTGGTTCAC
4379821 GGAATGTAAGATTACCAGTG
1 GGAATGTAAGATTACCAGTG
*
4379841 GGAATGTAGGATTACCAG
1 GGAATGTAAGATTACCAG
4379859 GGAATAGGAA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.34, C:0.11, G:0.32, T:0.24
Consensus pattern (20 bp):
GGAATGTAAGATTACCAGTG
Found at i:4380085 original size:34 final size:36
Alignment explanation
Indices: 4380015--4380085 Score: 85
Period size: 34 Copynumber: 2.0 Consensus size: 36
4380005 GTTGGAAAAT
* *
4380015 ATTTATATATTTTCTTTAAAAAATTTAAATTCATAA
1 ATTTATATATTTTCTTTAAAAAATTAAAAATCATAA
*
4380051 ATTTATATA-TTT-TTTACAAAATTGAAAAAT-ATAA
1 ATTTATATATTTTCTTTAAAAAATT-AAAAATCATAA
4380085 A
1 A
4380086 AAGGTTTAAT
Statistics
Matches: 31, Mismatches: 3, Indels: 4
0.82 0.08 0.11
Matches are distributed among these distances:
34 15 0.48
35 7 0.23
36 9 0.29
ACGTcount: A:0.48, C:0.04, G:0.01, T:0.46
Consensus pattern (36 bp):
ATTTATATATTTTCTTTAAAAAATTAAAAATCATAA
Found at i:4381137 original size:51 final size:51
Alignment explanation
Indices: 4381060--4381159 Score: 139
Period size: 51 Copynumber: 1.9 Consensus size: 51
4381050 TTAAAAAATC
*
4381060 ATAAAAATATAATTAAACTTTGTCAAACAT-AATTAAACATAAATTTTAATT
1 ATAAAAATATAATTAAACTTTATCAAACATAAATTAAACAT-AATTTTAATT
* * *
4381111 ATAAAAATATAATTAAATTTTATCAAATATAAAATTAAATATAATTTTA
1 ATAAAAATATAATTAAACTTTATCAAACAT-AAATTAAACATAATTTTA
4381160 CAAAAAAAAA
Statistics
Matches: 43, Mismatches: 4, Indels: 3
0.86 0.08 0.06
Matches are distributed among these distances:
51 27 0.63
52 7 0.16
53 9 0.21
ACGTcount: A:0.55, C:0.05, G:0.01, T:0.39
Consensus pattern (51 bp):
ATAAAAATATAATTAAACTTTATCAAACATAAATTAAACATAATTTTAATT
Found at i:4381168 original size:51 final size:50
Alignment explanation
Indices: 4381062--4381170 Score: 121
Period size: 51 Copynumber: 2.1 Consensus size: 50
4381052 AAAAAATCAT
* *
4381062 AAAAATATAATTAAACTTTGTCAAACATAATTAAACATAAATTTTAATTAT
1 AAAAATATAATTAAACTTTATCAAACATAATTAAACATAAATTTTAA-TAA
* * * *
4381113 AAAAATATAATTAAATTTTATCAAATATAAAATTAAATAT-AATTTTACAAAA
1 AAAAATATAATTAAACTTTATCAAACAT--AATTAAACATAAATTTTA-ATAA
4381165 AAAAAT
1 AAAAAT
4381171 CTTAAAGAAA
Statistics
Matches: 49, Mismatches: 6, Indels: 5
0.82 0.10 0.08
Matches are distributed among these distances:
51 25 0.51
52 14 0.29
53 10 0.20
ACGTcount: A:0.58, C:0.06, G:0.01, T:0.36
Consensus pattern (50 bp):
AAAAATATAATTAAACTTTATCAAACATAATTAAACATAAATTTTAATAA
Found at i:4382948 original size:29 final size:31
Alignment explanation
Indices: 4382899--4382963 Score: 75
Period size: 29 Copynumber: 2.1 Consensus size: 31
4382889 AATTAATTAC
4382899 AAAATAAAATATTAGACATA-TATTTTA-AT
1 AAAATAAAATATTAGACATATTATTTTACAT
4382928 AAAATAAAATAATTTA-A-ATATTTATTTTACAT
1 AAAATAAAAT-A-TTAGACATA-TTATTTTACAT
4382960 AAAA
1 AAAA
4382964 GGCCAAATAC
Statistics
Matches: 31, Mismatches: 0, Indels: 7
0.82 0.00 0.18
Matches are distributed among these distances:
29 13 0.42
30 2 0.06
31 10 0.32
32 6 0.19
ACGTcount: A:0.57, C:0.03, G:0.02, T:0.38
Consensus pattern (31 bp):
AAAATAAAATATTAGACATATTATTTTACAT
Found at i:4385394 original size:21 final size:21
Alignment explanation
Indices: 4385343--4385394 Score: 52
Period size: 21 Copynumber: 2.5 Consensus size: 21
4385333 GTTGGAAGAT
*
4385343 ATTTTTTTAACTTTTTTTTAA
1 ATTTTTTTAACTTATTTTTAA
**
4385364 ATTTGATTAACTTAATTTTT-A
1 ATTTTTTTAACTT-ATTTTTAA
*
4385385 TTTTTTTTAA
1 ATTTTTTTAA
4385395 TCTTTTTCTA
Statistics
Matches: 24, Mismatches: 6, Indels: 2
0.75 0.19 0.06
Matches are distributed among these distances:
21 19 0.79
22 5 0.21
ACGTcount: A:0.27, C:0.04, G:0.02, T:0.67
Consensus pattern (21 bp):
ATTTTTTTAACTTATTTTTAA
Found at i:4391056 original size:12 final size:12
Alignment explanation
Indices: 4391039--4391068 Score: 51
Period size: 12 Copynumber: 2.5 Consensus size: 12
4391029 TAAAATCTTC
4391039 TTTTTCTCTCTA
1 TTTTTCTCTCTA
*
4391051 TTTTTCTCTTTA
1 TTTTTCTCTCTA
4391063 TTTTTC
1 TTTTTC
4391069 GCATACTTTT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
12 17 1.00
ACGTcount: A:0.07, C:0.20, G:0.00, T:0.73
Consensus pattern (12 bp):
TTTTTCTCTCTA
Found at i:4399432 original size:19 final size:19
Alignment explanation
Indices: 4399403--4399452 Score: 66
Period size: 19 Copynumber: 2.6 Consensus size: 19
4399393 AATCTCTTTA
*
4399403 ATTTGTTTATTTAATTATT
1 ATTTTTTTATTTAATTATT
*
4399422 -TTTCTTTTATTTAATTCTT
1 ATTT-TTTTATTTAATTATT
4399441 ATTTTTTTATTT
1 ATTTTTTTATTT
4399453 TAAAAACAAC
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
18 3 0.11
19 21 0.78
20 3 0.11
ACGTcount: A:0.20, C:0.04, G:0.02, T:0.74
Consensus pattern (19 bp):
ATTTTTTTATTTAATTATT
Found at i:4399522 original size:19 final size:21
Alignment explanation
Indices: 4399486--4399531 Score: 60
Period size: 19 Copynumber: 2.3 Consensus size: 21
4399476 CTTTTATATT
4399486 TATTATTATTACTATTTTTTA
1 TATTATTATTACTATTTTTTA
*
4399507 TATTATT-TTTCT-TTTTTTA
1 TATTATTATTACTATTTTTTA
*
4399526 TTTTAT
1 TATTAT
4399532 AATATATCTT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
19 12 0.52
20 4 0.17
21 7 0.30
ACGTcount: A:0.22, C:0.04, G:0.00, T:0.74
Consensus pattern (21 bp):
TATTATTATTACTATTTTTTA
Found at i:4405487 original size:19 final size:21
Alignment explanation
Indices: 4405441--4405492 Score: 72
Period size: 19 Copynumber: 2.5 Consensus size: 21
4405431 GAATTTTTTG
*
4405441 TATCTCAAAAATTTGATATATC
1 TATC-CAAAAACTTGATATATC
4405463 TATCCAAAAACTTGAT-TAT-
1 TATCCAAAAACTTGATATATC
4405482 TATCCAAAAAC
1 TATCCAAAAAC
4405493 CCTCTCTCAA
Statistics
Matches: 29, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
19 11 0.38
20 3 0.10
21 11 0.38
22 4 0.14
ACGTcount: A:0.44, C:0.17, G:0.04, T:0.35
Consensus pattern (21 bp):
TATCCAAAAACTTGATATATC
Found at i:4405924 original size:2 final size:2
Alignment explanation
Indices: 4405912--4405942 Score: 53
Period size: 2 Copynumber: 15.5 Consensus size: 2
4405902 AGCAAGCAGC
*
4405912 AT AT GT 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 AT A
4405943 GAAACTGATC
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.03, T:0.48
Consensus pattern (2 bp):
AT
Found at i:4412018 original size:25 final size:25
Alignment explanation
Indices: 4411983--4412041 Score: 93
Period size: 25 Copynumber: 2.4 Consensus size: 25
4411973 AAAGAATGAT
*
4411983 GAGTGTTAATTACTTGTTCGCATGG
1 GAGTGTCAATTACTTGTTCGCATGG
4412008 GAGTGTCAATTACTTGTTCGCATGG
1 GAGTGTCAATTACTTGTTCGCATGG
4412033 GTA-TGTCAA
1 G-AGTGTCAA
4412042 AAGCTATTTT
Statistics
Matches: 32, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
25 31 0.97
26 1 0.03
ACGTcount: A:0.22, C:0.14, G:0.27, T:0.37
Consensus pattern (25 bp):
GAGTGTCAATTACTTGTTCGCATGG
Found at i:4413128 original size:13 final size:13
Alignment explanation
Indices: 4413110--4413147 Score: 51
Period size: 13 Copynumber: 2.8 Consensus size: 13
4413100 TTGAATTAAA
4413110 TAATAATAAAAAT
1 TAATAATAAAAAT
4413123 TAATAA-AATAAAT
1 TAATAATAA-AAAT
4413136 TAAGTAATAAAA
1 TAA-TAATAAAA
4413148 GGTAAATAAT
Statistics
Matches: 22, Mismatches: 0, Indels: 5
0.81 0.00 0.19
Matches are distributed among these distances:
12 2 0.09
13 13 0.59
14 5 0.23
15 2 0.09
ACGTcount: A:0.68, C:0.00, G:0.03, T:0.29
Consensus pattern (13 bp):
TAATAATAAAAAT
Found at i:4413318 original size:12 final size:12
Alignment explanation
Indices: 4413303--4413327 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
4413293 CATCACTCTT
4413303 ATCATCATCACC
1 ATCATCATCACC
4413315 ATCATCATCACC
1 ATCATCATCACC
4413327 A
1 A
4413328 GCACCACCAC
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.36, C:0.40, G:0.00, T:0.24
Consensus pattern (12 bp):
ATCATCATCACC
Found at i:4414467 original size:21 final size:20
Alignment explanation
Indices: 4414429--4414467 Score: 51
Period size: 21 Copynumber: 1.9 Consensus size: 20
4414419 GAAATAATTT
* *
4414429 TTATTATATACTAGATAAGA
1 TTATTATATACGAAATAAGA
4414449 TTATTAATATACGAAATAA
1 TTATT-ATATACGAAATAA
4414468 ATATTGTAAT
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
20 5 0.31
21 11 0.69
ACGTcount: A:0.49, C:0.05, G:0.08, T:0.38
Consensus pattern (20 bp):
TTATTATATACGAAATAAGA
Found at i:4415502 original size:10 final size:10
Alignment explanation
Indices: 4415483--4415525 Score: 52
Period size: 10 Copynumber: 4.3 Consensus size: 10
4415473 TTGAGCTTTA
*
4415483 AGAGGGTTTG
1 AGAGGATTTG
4415493 AGATGG-TTTG
1 AGA-GGATTTG
4415503 AGAGGATTTG
1 AGAGGATTTG
*
4415513 ATAGGATTTG
1 AGAGGATTTG
4415523 AGA
1 AGA
4415526 TTTTGGTGTT
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
9 2 0.07
10 25 0.86
11 2 0.07
ACGTcount: A:0.28, C:0.00, G:0.40, T:0.33
Consensus pattern (10 bp):
AGAGGATTTG
Found at i:4418183 original size:189 final size:191
Alignment explanation
Indices: 4417861--4418252 Score: 511
Period size: 189 Copynumber: 2.1 Consensus size: 191
4417851 TACAGTTCGT
* * * *** *
4417861 ATATAGCGGCGTTTTTTAATAAACGCTACAATAGAATAATACTTTGGCGGTGTTTTTGTAAAAAA
1 ATATAGCGGCGTGTTTTAATAAACGCCACAACAGAATAATACTACAGCGGCGTTTTTGTAAAAAA
* * * *
4417926 ACACTGCAATAGGGTTCATATATAGAGGCATTTTGGTAACAAACGCCACAAATAATTTGAAATTT
66 ACACTGCAAGAGGGTTAACATATAGAGACATTTTGGTAACAAACGCCACAAATAATTTGAAATTT
*
4417991 AGTGTCGTTTTATCAAAAAACGCCGCAAATGTTTTTTATTTAAACGCCATTAACTTTAGAC
131 AGTGGCGTTTTATCAAAAAACGCCGCAAATGTTTTTTATTTAAACGCCATTAACTTTAGAC
* * *
4418052 ATATAGCGGCGTGTTTTAATAAACGCCGCAACAGATTAATACTACAGCGGCG-TTTTG-ACAAAA
1 ATATAGCGGCGTGTTTTAATAAACGCCACAACAGAATAATACTACAGCGGCGTTTTTGTAAAAAA
* * * *** * *
4418115 ACGGC-GCAAGAGGGTTAACATATAGCGACGTTTTGGTAACAAACGGTGCAAATAATTTGTACTT
66 AC-ACTGCAAGAGGGTTAACATATAGAGACATTTTGGTAACAAACGCCACAAATAATTTGAAATT
* * *
4418179 TAGTGGCGTTTTGTCAAAAAATGCCGCAAATGTTTTTTATTTGAACGCCATTAACTTTAGAC
130 TAGTGGCGTTTTATCAAAAAACGCCGCAAATGTTTTTTATTTAAACGCCATTAACTTTAGAC
*
4418241 ATATGGCGGCGT
1 ATATAGCGGCGT
4418253 AAACGCCGCA
Statistics
Matches: 173, Mismatches: 27, Indels: 4
0.85 0.13 0.02
Matches are distributed among these distances:
189 124 0.72
190 6 0.03
191 43 0.25
ACGTcount: A:0.33, C:0.16, G:0.19, T:0.31
Consensus pattern (191 bp):
ATATAGCGGCGTGTTTTAATAAACGCCACAACAGAATAATACTACAGCGGCGTTTTTGTAAAAAA
ACACTGCAAGAGGGTTAACATATAGAGACATTTTGGTAACAAACGCCACAAATAATTTGAAATTT
AGTGGCGTTTTATCAAAAAACGCCGCAAATGTTTTTTATTTAAACGCCATTAACTTTAGAC
Found at i:4419885 original size:14 final size:14
Alignment explanation
Indices: 4419866--4419892 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
4419856 TTTAATCAGA
4419866 TTGCTTCTCATAAT
1 TTGCTTCTCATAAT
4419880 TTGCTTCTCATAA
1 TTGCTTCTCATAA
4419893 GTTTCTGTAC
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:0.22, C:0.22, G:0.07, T:0.48
Consensus pattern (14 bp):
TTGCTTCTCATAAT
Found at i:4427747 original size:43 final size:44
Alignment explanation
Indices: 4427602--4427785 Score: 169
Period size: 43 Copynumber: 4.2 Consensus size: 44
4427592 TTTTTGTTAC
* * * * * * *
4427602 AAACGCCACTATATACCA-ACCTTTACCGTCGTCTATATACT-A
1 AAACGCCGCTATATACCAGATCTTTAGCGGCGTTTGTATCCTAA
* * *
4427644 AAACGCCGCTATATACCAGACCATCAGCGGCGTTTGTATCCTAA
1 AAACGCCGCTATATACCAGATCTTTAGCGGCGTTTGTATCCTAA
* * * *
4427688 AAACGTCGTTATATACCAGATCTTTATCTGCGTTT-TATCCTAA
1 AAACGCCGCTATATACCAGATCTTTAGCGGCGTTTGTATCCTAA
* * *
4427731 AAACGCCGCTACATACCAAATTTTTAGCGGCGTTTGTA-CACTAA
1 AAACGCCGCTATATACCAGATCTTTAGCGGCGTTTGTATC-CTAA
*
4427775 AAACCCCGCTA
1 AAACGCCGCTA
4427786 AATGTCAAAA
Statistics
Matches: 115, Mismatches: 23, Indels: 6
0.80 0.16 0.04
Matches are distributed among these distances:
42 17 0.15
43 53 0.46
44 45 0.39
ACGTcount: A:0.31, C:0.28, G:0.13, T:0.28
Consensus pattern (44 bp):
AAACGCCGCTATATACCAGATCTTTAGCGGCGTTTGTATCCTAA
Found at i:4427784 original size:44 final size:44
Alignment explanation
Indices: 4427643--4427785 Score: 146
Period size: 44 Copynumber: 3.3 Consensus size: 44
4427633 TCTATATACT
* * * * *
4427643 AAAACGCCGCTATATACCAGACCATCAGCGGCGTTTGTATCCTA
1 AAAACGCCGCTACATACCAAATCTTTAGCGGCGTTTGTATCCTA
* * * * * *
4427687 AAAACGTCGTTATATACCAGATCTTTATCTGCGTTT-TATCCTA
1 AAAACGCCGCTACATACCAAATCTTTAGCGGCGTTTGTATCCTA
*
4427730 AAAACGCCGCTACATACCAAATTTTTAGCGGCGTTTGTA-CACTA
1 AAAACGCCGCTACATACCAAATCTTTAGCGGCGTTTGTATC-CTA
*
4427774 AAAACCCCGCTA
1 AAAACGCCGCTA
4427786 AATGTCAAAA
Statistics
Matches: 82, Mismatches: 15, Indels: 4
0.81 0.15 0.04
Matches are distributed among these distances:
43 37 0.45
44 45 0.55
ACGTcount: A:0.31, C:0.27, G:0.15, T:0.28
Consensus pattern (44 bp):
AAAACGCCGCTACATACCAAATCTTTAGCGGCGTTTGTATCCTA
Found at i:4427863 original size:43 final size:43
Alignment explanation
Indices: 4427775--4427873 Score: 117
Period size: 43 Copynumber: 2.3 Consensus size: 43
4427765 TGTACACTAA
* * * ***
4427775 AAACCCCGCTAAATGTCAAAACCTATTGTGGCGTTTGTCTTAC
1 AAACGCCGCTAAATGTCAAAACCTATTGCGGCGTTTATAAGAC
* * *
4427818 AAATGTCGCTAACTGTCAAAACCTATTGCGGCGTTTATAAGAC
1 AAACGCCGCTAAATGTCAAAACCTATTGCGGCGTTTATAAGAC
4427861 AAACGCCGCTAAA
1 AAACGCCGCTAAA
4427874 GATCAGAACT
Statistics
Matches: 44, Mismatches: 12, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
43 44 1.00
ACGTcount: A:0.32, C:0.24, G:0.17, T:0.26
Consensus pattern (43 bp):
AAACGCCGCTAAATGTCAAAACCTATTGCGGCGTTTATAAGAC
Found at i:4429677 original size:19 final size:21
Alignment explanation
Indices: 4429634--4429677 Score: 56
Period size: 19 Copynumber: 2.1 Consensus size: 21
4429624 TTAAAAATAT
*
4429634 TAAAAAATATTAATGTTTTATA
1 TAAAAAATA-TAATGTTTTAAA
4429656 TAAAAAATA-AAT-TTTTAAA
1 TAAAAAATATAATGTTTTAAA
4429675 TAA
1 TAA
4429678 TTTTTTTTAT
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
19 9 0.43
20 3 0.14
22 9 0.43
ACGTcount: A:0.57, C:0.00, G:0.02, T:0.41
Consensus pattern (21 bp):
TAAAAAATATAATGTTTTAAA
Found at i:4433950 original size:14 final size:15
Alignment explanation
Indices: 4433933--4433964 Score: 57
Period size: 15 Copynumber: 2.2 Consensus size: 15
4433923 AAATAAATAT
4433933 TTAA-ATTAAAAAAA
1 TTAATATTAAAAAAA
4433947 TTAATATTAAAAAAA
1 TTAATATTAAAAAAA
4433962 TTA
1 TTA
4433965 TGTTAGTTGA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 4 0.24
15 13 0.76
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (15 bp):
TTAATATTAAAAAAA
Found at i:4434693 original size:17 final size:18
Alignment explanation
Indices: 4434665--4434712 Score: 71
Period size: 17 Copynumber: 2.7 Consensus size: 18
4434655 GTTGGTTCGC
*
4434665 GGAATAAGATTATCAGTG
1 GGAATAAGATTACCAGTG
4434683 GGAAT-AGATTACCAGTG
1 GGAATAAGATTACCAGTG
*
4434700 AGAATAAGATTAC
1 GGAATAAGATTAC
4434713 TGAGAATATT
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
17 15 0.56
18 12 0.44
ACGTcount: A:0.42, C:0.08, G:0.25, T:0.25
Consensus pattern (18 bp):
GGAATAAGATTACCAGTG
Found at i:4435713 original size:54 final size:54
Alignment explanation
Indices: 4435647--4435755 Score: 150
Period size: 54 Copynumber: 2.0 Consensus size: 54
4435637 AGGGTGCATC
* *
4435647 GCATCAAGTGCATTCGATGTTTCA-AAATAGCCAT-GGTGCATCGATGCATGGCTG
1 GCATCAAATGCATTCGATGTTTCATAAA-AGCC-TCAGTGCATCGATGCATGGCTG
* *
4435701 GCATCAAATGCATTCGATGTTTCATAAAATCCTCAGTGCATCGGTGCATGGCTG
1 GCATCAAATGCATTCGATGTTTCATAAAAGCCTCAGTGCATCGATGCATGGCTG
4435755 G
1 G
4435756 TGCATCGATC
Statistics
Matches: 49, Mismatches: 4, Indels: 4
0.86 0.07 0.07
Matches are distributed among these distances:
53 1 0.02
54 45 0.92
55 3 0.06
ACGTcount: A:0.26, C:0.21, G:0.25, T:0.28
Consensus pattern (54 bp):
GCATCAAATGCATTCGATGTTTCATAAAAGCCTCAGTGCATCGATGCATGGCTG
Found at i:4442046 original size:25 final size:25
Alignment explanation
Indices: 4442018--4442072 Score: 110
Period size: 25 Copynumber: 2.2 Consensus size: 25
4442008 AACCTTTAAA
4442018 TGAGTGAGGCTCTGATACCAATTGT
1 TGAGTGAGGCTCTGATACCAATTGT
4442043 TGAGTGAGGCTCTGATACCAATTGT
1 TGAGTGAGGCTCTGATACCAATTGT
4442068 TGAGT
1 TGAGT
4442073 TAATCGATTG
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 30 1.00
ACGTcount: A:0.24, C:0.15, G:0.29, T:0.33
Consensus pattern (25 bp):
TGAGTGAGGCTCTGATACCAATTGT
Found at i:4444938 original size:22 final size:22
Alignment explanation
Indices: 4444887--4444931 Score: 72
Period size: 22 Copynumber: 2.0 Consensus size: 22
4444877 CAAATCTCAA
*
4444887 CCAAACCCACCCGGTTTTGGCC
1 CCAAACCCACCCGATTTTGGCC
*
4444909 CCAAACCCACCTGATTTTGGCC
1 CCAAACCCACCCGATTTTGGCC
4444931 C
1 C
4444932 AAGACCCGAA
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.20, C:0.44, G:0.16, T:0.20
Consensus pattern (22 bp):
CCAAACCCACCCGATTTTGGCC
Done.