Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: D04
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: 56598092
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.32
Warning! 1600000 characters in sequence are not A, C, G, or T
File 158 of 185
Found at i:48622079 original size:9 final size:9
Alignment explanation
Indices: 48622065--48622090 Score: 52
Period size: 9 Copynumber: 2.9 Consensus size: 9
48622055 ATAAACTAGA
48622065 CTAATTTGT
1 CTAATTTGT
48622074 CTAATTTGT
1 CTAATTTGT
48622083 CTAATTTG
1 CTAATTTG
48622091 GTAAAGTCGA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 17 1.00
ACGTcount: A:0.23, C:0.12, G:0.12, T:0.54
Consensus pattern (9 bp):
CTAATTTGT
Found at i:48626832 original size:22 final size:22
Alignment explanation
Indices: 48626783--48626832 Score: 64
Period size: 22 Copynumber: 2.3 Consensus size: 22
48626773 AAGTTGGGTT
* *
48626783 CCACGTTGTGACGAGCCATTTC
1 CCACATTGTAACGAGCCATTTC
**
48626805 AAACATTGTAACGAGCCATTTC
1 CCACATTGTAACGAGCCATTTC
48626827 CCACAT
1 CCACAT
48626833 CGTGACATCG
Statistics
Matches: 22, Mismatches: 6, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.28, C:0.30, G:0.16, T:0.26
Consensus pattern (22 bp):
CCACATTGTAACGAGCCATTTC
Found at i:48634649 original size:18 final size:16
Alignment explanation
Indices: 48634627--48634674 Score: 51
Period size: 18 Copynumber: 2.8 Consensus size: 16
48634617 TTATCCATTT
48634627 TATTTAATTTATATAAA
1 TATTTAATTTATA-AAA
*
48634644 TAATTTAAAACTTATAAAA
1 T-ATTT--AATTTATAAAA
48634663 TATTTAATTTAT
1 TATTTAATTTAT
48634675 TTAATTTAAA
Statistics
Matches: 26, Mismatches: 2, Indels: 7
0.74 0.06 0.20
Matches are distributed among these distances:
16 6 0.23
17 1 0.04
18 8 0.31
19 4 0.15
20 7 0.27
ACGTcount: A:0.48, C:0.02, G:0.00, T:0.50
Consensus pattern (16 bp):
TATTTAATTTATAAAA
Found at i:48634707 original size:12 final size:13
Alignment explanation
Indices: 48634687--48634715 Score: 51
Period size: 12 Copynumber: 2.3 Consensus size: 13
48634677 AATTTAAAAT
48634687 TTATAAAAAGTAA
1 TTATAAAAAGTAA
48634700 TTAT-AAAAGTAA
1 TTATAAAAAGTAA
48634712 TTAT
1 TTAT
48634716 TCTATCTTTT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 12 0.75
13 4 0.25
ACGTcount: A:0.55, C:0.00, G:0.07, T:0.38
Consensus pattern (13 bp):
TTATAAAAAGTAA
Found at i:48634949 original size:9 final size:9
Alignment explanation
Indices: 48634935--48634989 Score: 58
Period size: 9 Copynumber: 6.1 Consensus size: 9
48634925 ATTATTTTCA
48634935 AATTTATAT
1 AATTTATAT
48634944 AATTTAATAT
1 AATTT-ATAT
*
48634954 TATTTATAT
1 AATTTATAT
* *
48634963 AAATAAT-T
1 AATTTATAT
*
48634971 AATTTATCT
1 AATTTATAT
48634980 AATTTATAT
1 AATTTATAT
48634989 A
1 A
48634990 GGGAAAAATA
Statistics
Matches: 37, Mismatches: 7, Indels: 4
0.77 0.15 0.08
Matches are distributed among these distances:
8 6 0.16
9 23 0.62
10 8 0.22
ACGTcount: A:0.45, C:0.02, G:0.00, T:0.53
Consensus pattern (9 bp):
AATTTATAT
Found at i:48636831 original size:31 final size:31
Alignment explanation
Indices: 48636795--48636857 Score: 74
Period size: 31 Copynumber: 2.0 Consensus size: 31
48636785 TAATAAAAGT
* *
48636795 AAAATTACACTTTAGCCCCTT-AAAATTATAA
1 AAAATT-CAATTTAACCCCTTAAAAATTATAA
* *
48636826 AAAATTCAATTTAATCCTTTAAAAATTATAA
1 AAAATTCAATTTAACCCCTTAAAAATTATAA
48636857 A
1 A
48636858 TATATAGACT
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
30 10 0.37
31 17 0.63
ACGTcount: A:0.49, C:0.14, G:0.02, T:0.35
Consensus pattern (31 bp):
AAAATTCAATTTAACCCCTTAAAAATTATAA
Found at i:48639139 original size:14 final size:14
Alignment explanation
Indices: 48639111--48639153 Score: 70
Period size: 14 Copynumber: 3.1 Consensus size: 14
48639101 TTGTTTAAAA
*
48639111 ATATTA-TAGTTTT
1 ATATTATTATTTTT
48639124 ATATTATTATTTTT
1 ATATTATTATTTTT
48639138 ATATTATTATTTTT
1 ATATTATTATTTTT
48639152 AT
1 AT
48639154 TAAATTTTCA
Statistics
Matches: 28, Mismatches: 1, Indels: 1
0.93 0.03 0.03
Matches are distributed among these distances:
13 6 0.21
14 22 0.79
ACGTcount: A:0.30, C:0.00, G:0.02, T:0.67
Consensus pattern (14 bp):
ATATTATTATTTTT
Found at i:48643108 original size:20 final size:20
Alignment explanation
Indices: 48643083--48643130 Score: 87
Period size: 20 Copynumber: 2.4 Consensus size: 20
48643073 GGTAAGTTGT
48643083 TGCATGTAACCATCTACATG
1 TGCATGTAACCATCTACATG
*
48643103 TGCATGTAACCATTTACATG
1 TGCATGTAACCATCTACATG
48643123 TGCATGTA
1 TGCATGTA
48643131 TGTGACAAGA
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 27 1.00
ACGTcount: A:0.29, C:0.21, G:0.17, T:0.33
Consensus pattern (20 bp):
TGCATGTAACCATCTACATG
Found at i:48645480 original size:3 final size:3
Alignment explanation
Indices: 48645472--48645532 Score: 77
Period size: 3 Copynumber: 20.3 Consensus size: 3
48645462 AGAATAACAT
* * * *
48645472 TAA TAA TAA TGA TGA TAA TGA TAA TAA TAG TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
*
48645520 CAA TAA TAA TAA T
1 TAA TAA TAA TAA T
48645533 CTAAGGTTTA
Statistics
Matches: 50, Mismatches: 8, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
3 50 1.00
ACGTcount: A:0.59, C:0.02, G:0.07, T:0.33
Consensus pattern (3 bp):
TAA
Found at i:48647363 original size:44 final size:44
Alignment explanation
Indices: 48647273--48647624 Score: 221
Period size: 44 Copynumber: 7.8 Consensus size: 44
48647263 TAATCCGCTT
* * ** * * * **
48647273 CACTGCAACTTCAAGGAGATAGGATTAATAGCTACAATCTATTC
1 CACTGCAACTTCAGGGAGATAAGATTGGTATCTTCAACCTGCTC
48647317 CACTGCAACTTCAGGGAGATAAGATTGGTATCTTCAACCTGCTC
1 CACTGCAACTTCAGGGAGATAAGATTGGTATCTTCAACCTGCTC
* * * **
48647361 CACTGTAACTTTAGGGAGATAAGGTTGGTTATCTTCAGTCTGCTC
1 CACTGCAACTTCAGGGAGATAAGATTGG-TATCTTCAACCTGCTC
* * * ** *
48647406 CATTGTAACTTCAGAGAGATAAGACTTGTTATAGTAGATTTAATCC-GAC-C
1 CACTGCAACTTCAGGGAGATAAGA-TTG-----GTATCTTCAA-CCTG-CTC
* * * *
48647456 TACTGCAACTTCAGAGG-TATAGGATT--TATCATTTTAATCC-GCTC
1 CACTGCAACTTCAG-GGAGATAAGATTGGTATC--TTCAA-CCTGCTC
* ** * *
48647500 CACTGCAACTTCAGGGAGATAGGATTAATAGCTTCAATCTGCTC
1 CACTGCAACTTCAGGGAGATAAGATTGGTATCTTCAACCTGCTC
* *
48647544 CACTACAACTTCAGGGAGATAAGATTGGTATCTTAAACCTGCTC
1 CACTGCAACTTCAGGGAGATAAGATTGGTATCTTCAACCTGCTC
* * * *
48647588 CACTGCAACTTTAGGAAGATAAGGTTTGTTATCTTCA
1 CACTGCAACTTCAGGGAGATAA-GATTGGTATCTTCA
48647625 TTCTTAATTT
Statistics
Matches: 241, Mismatches: 49, Indels: 35
0.74 0.15 0.11
Matches are distributed among these distances:
42 2 0.01
43 4 0.02
44 155 0.64
45 45 0.19
46 6 0.02
49 2 0.01
50 23 0.10
51 4 0.02
ACGTcount: A:0.30, C:0.20, G:0.19, T:0.31
Consensus pattern (44 bp):
CACTGCAACTTCAGGGAGATAAGATTGGTATCTTCAACCTGCTC
Found at i:48647565 original size:227 final size:227
Alignment explanation
Indices: 48647170--48647624 Score: 725
Period size: 227 Copynumber: 2.0 Consensus size: 227
48647160 TTGTGGTTTT
*
48647170 AGTCTGCTCCACTACAACTTCAAGGAGATAAGACTTTTTATGCTAGATTTAATCCGACCTACTGC
1 AGTCTGCTCCACTACAACTTCAAGGAGATAAGACTTGTTATGCTAGATTTAATCCGACCTACTGC
* * *
48647235 AATTTCAGAGGTATAGGATTCGTCATTTTAATCCGCTTCACTGCAACTTCAAGGAGATAGGATTA
66 AACTTCAGAGGTATAGGATTCATCATTTTAATCCGCTCCACTGCAACTTCAAGGAGATAGGATTA
* * *
48647300 ATAGCTACAATCTATTCCACTGCAACTTCAGGGAGATAAGATTGGTATCTTCAACCTGCTCCACT
131 ATAGCTACAATCTACTCCACTACAACTTCAGGGAGATAAGATTGGTATCTTAAACCTGCTCCACT
* *
48647365 GTAACTTTAGGGAGATAAGGTTGGTTATCTTC
196 GCAACTTTAGGAAGATAAGGTTGGTTATCTTC
* **
48647397 AGTCTGCTCCATTGTAACTTC-AGAGAGATAAGACTTGTTATAG-TAGATTTAATCCGACCTACT
1 AGTCTGCTCCACTACAACTTCAAG-GAGATAAGACTTGTTAT-GCTAGATTTAATCCGACCTACT
* *
48647460 GCAACTTCAGAGGTATAGGATTTATCATTTTAATCCGCTCCACTGCAACTTCAGGGAGATAGGAT
64 GCAACTTCAGAGGTATAGGATTCATCATTTTAATCCGCTCCACTGCAACTTCAAGGAGATAGGAT
* *
48647525 TAATAGCTTCAATCTGCTCCACTACAACTTCAGGGAGATAAGATTGGTATCTTAAACCTGCTCCA
129 TAATAGCTACAATCTACTCCACTACAACTTCAGGGAGATAAGATTGGTATCTTAAACCTGCTCCA
*
48647590 CTGCAACTTTAGGAAGATAAGGTTTGTTATCTTC
194 CTGCAACTTTAGGAAGATAAGGTTGGTTATCTTC
48647624 A
1 A
48647625 TTCTTAATTT
Statistics
Matches: 209, Mismatches: 17, Indels: 4
0.91 0.07 0.02
Matches are distributed among these distances:
226 2 0.01
227 206 0.99
228 1 0.00
ACGTcount: A:0.29, C:0.20, G:0.18, T:0.32
Consensus pattern (227 bp):
AGTCTGCTCCACTACAACTTCAAGGAGATAAGACTTGTTATGCTAGATTTAATCCGACCTACTGC
AACTTCAGAGGTATAGGATTCATCATTTTAATCCGCTCCACTGCAACTTCAAGGAGATAGGATTA
ATAGCTACAATCTACTCCACTACAACTTCAGGGAGATAAGATTGGTATCTTAAACCTGCTCCACT
GCAACTTTAGGAAGATAAGGTTGGTTATCTTC
Found at i:48647827 original size:51 final size:51
Alignment explanation
Indices: 48647743--48647856 Score: 156
Period size: 51 Copynumber: 2.2 Consensus size: 51
48647733 ATCCGCCCCA
* **
48647743 CTTCAGCTTTAATCTATTCCATTGCAATGCCAGGGAAATAAGATTCACTAC
1 CTTCAGCTTTAATCTATTCCACTGCAAAACCAGGGAAATAAGATTCACTAC
* * * **
48647794 CTTTAGCTTTAATCTGTTCCACTGCAAAACCAGGGCAATAAGATTCACTGT
1 CTTCAGCTTTAATCTATTCCACTGCAAAACCAGGGAAATAAGATTCACTAC
48647845 CTTCAGCTTTAA
1 CTTCAGCTTTAA
48647857 CGCTAGAGAG
Statistics
Matches: 54, Mismatches: 9, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
51 54 1.00
ACGTcount: A:0.30, C:0.24, G:0.14, T:0.32
Consensus pattern (51 bp):
CTTCAGCTTTAATCTATTCCACTGCAAAACCAGGGAAATAAGATTCACTAC
Found at i:48647839 original size:123 final size:123
Alignment explanation
Indices: 48647641--48648361 Score: 489
Period size: 123 Copynumber: 5.6 Consensus size: 123
48647631 ATTTGCTCCG
* * * * * *
48647641 CTGCAATGCCAGAGAAACAAGATTCGCTACCTTTAGCTTTAATCTATTCCACTGTAACGCCAATG
1 CTGCAACGCCAGGGAAACAAGATTCGCTACCTTTAGCTTTAATCTGTTCCACTGCAAAGCCAAGG
* *
48647706 AGATAGGATTCGCTACCTTTAGCATTAATCCGCCCCACTTCAGCTTTAATCTATTCCA
66 AGATAAGATTCGCTACCTTTAGCATTAATCCGCTCCACTTCAGCTTTAATCTATTCCA
* * * * * *
48647764 TTGCAATGCCAGGGAAATAAGATTCACTACCTTTAGCTTTAATCTGTTCCACTGCAAAACCAGGG
1 CTGCAACGCCAGGGAAACAAGATTCGCTACCTTTAGCTTTAATCTGTTCCACTGCAAAGCCAAGG
* * ** * * *
48647829 CA-ATAAGATTCACTGTCTTCAGCTTTAACGCTAGAGAGATAAGATTTGCTAC-CTTTAGATTTA
66 -AGATAAGATT--C-G-C-T-ACCTTT-A-GC-------ATTA-ATCCGCTCCACTTCAGCTTTA
* *
48647892 ATCTACTCCG
114 ATCTATTCCA
* * * * *
48647902 CTGCAACACCAGGGAAACAAGATTCTCTAACTTTAGCTTTAATCTGTTCCACTGTAATGCCAAGG
1 CTGCAACGCCAGGGAAACAAGATTCGCTACCTTTAGCTTTAATCTGTTCCACTGCAAAGCCAAGG
* * * * ** * *
48647967 AGATAGGATTCACTGCCTTCAGTTTTAATCCGCTGCACTTCAGTTTTAATCTATTCCA
66 AGATAAGATTCGCTACCTTTAGCATTAATCCGCTCCACTTCAGCTTTAATCTATTCCA
* * * * * * *
48648025 CTGCAATGCCAGGGAAACAATATTTGCTACCTTTAGCTTTAATTTGTTTCATTGCAAAGCCAGGG
1 CTGCAACGCCAGGGAAACAAGATTCGCTACCTTTAGCTTTAATCTGTTCCACTGCAAAGCCAAGG
* * * * *
48648090 AAATAAGATTCGTTGTCTTCAGCTTTAACGCTAGGGAGATAAGATTCGCTGC-CTTCAGCTTTAA
66 AGATAAGATTC---G-C-T-ACCTTT-A-GC-------ATTA-ATCCGCTCCACTTCAGCTTTAA
* *
48648154 TCTGCTT-CG
115 TCT-ATTCCA
* * * * * *
48648163 CTGCAACGCCAGGGAAACAAGATTCGCCACCTTTAGCTTTAATTTATTCCACTGTAATGCTAAGG
1 CTGCAACGCCAGGGAAACAAGATTCGCTACCTTTAGCTTTAATCTGTTCCACTGCAAAGCCAAGG
** ** * * * *
48648228 AGATGGGATTCATTGCCTTTAACTTTAATCCGCCCCACTTCAGCTTTAATCTATTCCA
66 AGATAAGATTCGCTACCTTTAGCATTAATCCGCTCCACTTCAGCTTTAATCTATTCCA
* *
48648286 CTGCAACGCCAAGGAAACAAGATTCGCTACCTTTAGCTTTAATCTGTTCCACTGCAACGCC-AGA
1 CTGCAACGCCAGGGAAACAAGATTCGCTACCTTTAGCTTTAATCTGTTCCACTGCAAAGCCAAG-
*
48648350 GAAATAAGATTC
65 GAGATAAGATTC
48648362 ACTGCCTTCA
Statistics
Matches: 452, Mismatches: 107, Indels: 78
0.71 0.17 0.12
Matches are distributed among these distances:
122 16 0.04
123 224 0.50
124 1 0.00
125 1 0.00
126 1 0.00
127 2 0.00
128 2 0.00
129 8 0.02
130 4 0.01
131 5 0.01
132 7 0.02
133 2 0.00
134 1 0.00
136 1 0.00
137 1 0.00
138 161 0.36
139 15 0.03
ACGTcount: A:0.28, C:0.24, G:0.17, T:0.31
Consensus pattern (123 bp):
CTGCAACGCCAGGGAAACAAGATTCGCTACCTTTAGCTTTAATCTGTTCCACTGCAAAGCCAAGG
AGATAAGATTCGCTACCTTTAGCATTAATCCGCTCCACTTCAGCTTTAATCTATTCCA
Found at i:48647940 original size:87 final size:87
Alignment explanation
Indices: 48647780--48647943 Score: 211
Period size: 87 Copynumber: 1.9 Consensus size: 87
48647770 TGCCAGGGAA
* ** * * **
48647780 ATAAGATTCACTACCTTTAGCTTTAATCTGTTCCACTGCAAAACCAGGGCAATAAGATTCACTGT
1 ATAAGATTCACTACCTTTAGATTTAATCTACTCCACTGCAAAACCAGGGAAACAAGATTCACTAA
48647845 CTTCAGCTTTAACGCTAGAGAG
66 CTTCAGCTTTAACGCTAGAGAG
** * * *
48647867 ATAAGATTTGCTACCTTTAGATTTAATCTACTCCGCTGCAACACCAGGGAAACAAGATTCTCTAA
1 ATAAGATTCACTACCTTTAGATTTAATCTACTCCACTGCAAAACCAGGGAAACAAGATTCACTAA
*
48647932 CTTTAGCTTTAA
66 CTTCAGCTTTAA
48647944 TCTGTTCCAC
Statistics
Matches: 64, Mismatches: 13, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
87 64 1.00
ACGTcount: A:0.32, C:0.23, G:0.15, T:0.31
Consensus pattern (87 bp):
ATAAGATTCACTACCTTTAGATTTAATCTACTCCACTGCAAAACCAGGGAAACAAGATTCACTAA
CTTCAGCTTTAACGCTAGAGAG
Found at i:48648007 original size:21 final size:20
Alignment explanation
Indices: 48647979--48648017 Score: 69
Period size: 21 Copynumber: 1.9 Consensus size: 20
48647969 ATAGGATTCA
48647979 CTGCCTTCAGTTTTAATCCG
1 CTGCCTTCAGTTTTAATCCG
48647999 CTGCACTTCAGTTTTAATC
1 CTGC-CTTCAGTTTTAATC
48648018 TATTCCACTG
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
20 4 0.22
21 14 0.78
ACGTcount: A:0.18, C:0.28, G:0.13, T:0.41
Consensus pattern (20 bp):
CTGCCTTCAGTTTTAATCCG
Found at i:48648026 original size:21 final size:21
Alignment explanation
Indices: 48647983--48648026 Score: 52
Period size: 21 Copynumber: 2.1 Consensus size: 21
48647973 GATTCACTGC
* *
48647983 CTTCAGTTTTAATCCGCTGCA
1 CTTCAGTTTTAATCCACTCCA
* *
48648004 CTTCAGTTTTAATCTATTCCA
1 CTTCAGTTTTAATCCACTCCA
48648025 CT
1 CT
48648027 GCAATGCCAG
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.20, C:0.27, G:0.09, T:0.43
Consensus pattern (21 bp):
CTTCAGTTTTAATCCACTCCA
Found at i:48648097 original size:261 final size:261
Alignment explanation
Indices: 48647636--48648372 Score: 1060
Period size: 261 Copynumber: 2.8 Consensus size: 261
48647626 TCTTAATTTG
* * *
48647636 CTCCGCTGCAATGCCAGAGAAACAAGATTCGCTACCTTTAGCTTTAATCTATTCCACTGTAACGC
1 CTCCGCTGCAACGCCAGGGAAACAAGATTCGCTACCTTTAGCTTTAATCTATTCCACTGTAATGC
* * * * *
48647701 CAATGAGATAGGATTCGCTACCTTTAGCATTAATCCGCCCCACTTCAGCTTTAATCTATTCCATT
66 CAAGGAGATAGGATTCACTGCCTTTAGCTTTAATCCGCCCCACTTCAGCTTTAATCTATTCCACT
* * * *
48647766 GCAATGCCAGGGAAATAAGATTCACTACCTTTAGCTTTAATCTGTTCCACTGCAAAACCAGGGCA
131 GCAATGCCAGGGAAACAAGATTCGCTACCTTTAGCTTTAATCTGTTCCACTGCAAAGCCAGGGAA
* *
48647831 ATAAGATTCACTGTCTTCAGCTTTAACGCTAGAGAGATAAGATTTGCTACCTTTAGATTTAATCT
196 ATAAGATTCACTGTCTTCAGCTTTAACGCTAGAGAGATAAGATTCGCTACCTTCAGATTTAATCT
48647896 A
261 A
* * * *
48647897 CTCCGCTGCAACACCAGGGAAACAAGATTCTCTAACTTTAGCTTTAATCTGTTCCACTGTAATGC
1 CTCCGCTGCAACGCCAGGGAAACAAGATTCGCTACCTTTAGCTTTAATCTATTCCACTGTAATGC
* * ** *
48647962 CAAGGAGATAGGATTCACTGCCTTCAGTTTTAATCCGCTGCACTTCAGTTTTAATCTATTCCACT
66 CAAGGAGATAGGATTCACTGCCTTTAGCTTTAATCCGCCCCACTTCAGCTTTAATCTATTCCACT
* * * * *
48648027 GCAATGCCAGGGAAACAATATTTGCTACCTTTAGCTTTAATTTGTTTCATTGCAAAGCCAGGGAA
131 GCAATGCCAGGGAAACAAGATTCGCTACCTTTAGCTTTAATCTGTTCCACTGCAAAGCCAGGGAA
** * * *
48648092 ATAAGATTCGTTGTCTTCAGCTTTAACGCTAGGGAGATAAGATTCGCTGCCTTCAGCTTTAATCT
196 ATAAGATTCACTGTCTTCAGCTTTAACGCTAGAGAGATAAGATTCGCTACCTTCAGATTTAATCT
*
48648157 G
261 A
* * *
48648158 CTTCGCTGCAACGCCAGGGAAACAAGATTCGCCACCTTTAGCTTTAATTTATTCCACTGTAATGC
1 CTCCGCTGCAACGCCAGGGAAACAAGATTCGCTACCTTTAGCTTTAATCTATTCCACTGTAATGC
* * * *
48648223 TAAGGAGATGGGATTCATTGCCTTTAACTTTAATCCGCCCCACTTCAGCTTTAATCTATTCCACT
66 CAAGGAGATAGGATTCACTGCCTTTAGCTTTAATCCGCCCCACTTCAGCTTTAATCTATTCCACT
* * * *
48648288 GCAACGCCAAGGAAACAAGATTCGCTACCTTTAGCTTTAATCTGTTCCACTGCAACGCCAGAGAA
131 GCAATGCCAGGGAAACAAGATTCGCTACCTTTAGCTTTAATCTGTTCCACTGCAAAGCCAGGGAA
*
48648353 ATAAGATTCACTGCCTTCAG
196 ATAAGATTCACTGTCTTCAG
48648373 TCCGCTCCAC
Statistics
Matches: 414, Mismatches: 62, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
261 414 1.00
ACGTcount: A:0.28, C:0.25, G:0.17, T:0.31
Consensus pattern (261 bp):
CTCCGCTGCAACGCCAGGGAAACAAGATTCGCTACCTTTAGCTTTAATCTATTCCACTGTAATGC
CAAGGAGATAGGATTCACTGCCTTTAGCTTTAATCCGCCCCACTTCAGCTTTAATCTATTCCACT
GCAATGCCAGGGAAACAAGATTCGCTACCTTTAGCTTTAATCTGTTCCACTGCAAAGCCAGGGAA
ATAAGATTCACTGTCTTCAGCTTTAACGCTAGAGAGATAAGATTCGCTACCTTCAGATTTAATCT
A
Found at i:48648254 original size:138 final size:139
Alignment explanation
Indices: 48647997--48648371 Score: 331
Period size: 138 Copynumber: 2.8 Consensus size: 139
48647987 AGTTTTAATC
* * * * *
48647997 CGCTGCACTTCAGTTTTAATCTATTCCACTGCAATGCCAGGGAAACAATATTTGCTACCTTTAGC
1 CGCTGCACTTCAGCTTTAATCTATTCCACTGCAACGCCAGGGAAACAAGATTCGCCACCTTTAGC
* * * * * * *
48648062 TTTAATTTGTTTCATTGCAAAGCCAGGGAAATAAGATTCGTTGTCTTCAGCTTTAACGCTAGGGA
66 TTTAATTTATTCCACTGCAAAGCCAAGGAAATAAGATTCATTGCCTTCAACTTTAACGCTAGGGA
48648127 GATAAGATT
131 GATAAGATT
* *
48648136 CGCTGC-CTTCAGCTTTAATCTGCTT-CGCTGCAACGCCAGGGAAACAAGATTCGCCACCTTTAG
1 CGCTGCACTTCAGCTTTAATCT-ATTCCACTGCAACGCCAGGGAAACAAGATTCGCCACCTTTAG
* * * * ** *
48648199 CTTTAATTTATTCCACTGTAATGCTAAGGAGATGGGATTCATTGCCTTTAACTTTAATC-C----
65 CTTTAATTTATTCCACTGCAAAGCCAAGGAAATAAGATTCATTGCCTTCAACTTTAA-CGCTAGG
48648259 -------G---
129 GAGATAAGATT
* * *
48648260 C-C-CCACTTCAGCTTTAATCTATTCCACTGCAACGCCAAGGAAACAAGATTCGCTACCTTTAGC
1 CGCTGCACTTCAGCTTTAATCTATTCCACTGCAACGCCAGGGAAACAAGATTCGCCACCTTTAGC
* * * *
48648323 TTTAATCTGTTCCACTGCAACGCC-AGAGAAATAAGATTCACTGCCTTCA
66 TTTAATTTATTCCACTGCAAAGCCAAG-GAAATAAGATTCATTGCCTTCA
48648372 GTCCGCTCCA
Statistics
Matches: 195, Mismatches: 36, Indels: 26
0.76 0.14 0.10
Matches are distributed among these distances:
122 5 0.03
123 88 0.45
124 1 0.01
127 1 0.01
138 91 0.47
139 9 0.05
ACGTcount: A:0.27, C:0.25, G:0.17, T:0.31
Consensus pattern (139 bp):
CGCTGCACTTCAGCTTTAATCTATTCCACTGCAACGCCAGGGAAACAAGATTCGCCACCTTTAGC
TTTAATTTATTCCACTGCAAAGCCAAGGAAATAAGATTCATTGCCTTCAACTTTAACGCTAGGGA
GATAAGATT
Found at i:48649676 original size:15 final size:15
Alignment explanation
Indices: 48649653--48649684 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
48649643 TCACCTTGGC
48649653 TTCTCCTTTTTCTTT
1 TTCTCCTTTTTCTTT
*
48649668 TTCTTCTTTTTCTTT
1 TTCTCCTTTTTCTTT
48649683 TT
1 TT
48649685 TTTTTAAAAG
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:0.00, C:0.22, G:0.00, T:0.78
Consensus pattern (15 bp):
TTCTCCTTTTTCTTT
Found at i:48654559 original size:4 final size:4
Alignment explanation
Indices: 48654550--48654574 Score: 50
Period size: 4 Copynumber: 6.2 Consensus size: 4
48654540 CTAATGATAA
48654550 TAAT TAAT TAAT TAAT TAAT TAAT T
1 TAAT TAAT TAAT TAAT TAAT TAAT T
48654575 TAATAATAAC
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:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (4 bp):
TAAT
Found at i:48656811 original size:49 final size:48
Alignment explanation
Indices: 48656739--48656889 Score: 144
Period size: 49 Copynumber: 3.1 Consensus size: 48
48656729 GGGTGGTACA
* * *
48656739 AGTTGCTATCTAGATTGGCGTATGAGTTGGATGTCTGGTAGGGCATGTT
1 AGTTGCTAACCAGATTGGTGTATG-GTTGGATGTCTGGTAGGGCATGTT
* **
48656788 AGTTGCTAACCAGATTGGTGTATGTGCTTGG-TTTCCAGTAGGGCATGTT
1 AGTTGCTAACCAGATTGGTGTATG-G-TTGGATGTCTGGTAGGGCATGTT
* * * *
48656837 AGTTGCTAATCAGCTTGGTGCTATGGGT-GATGCCATCGGTAGGGCATGTT
1 AGTTGCTAACCAGATTGGTG-TATGGTTGGATGTC-T-GGTAGGGCATGTT
48656887 AGT
1 AGT
48656890 AGATAACTAT
Statistics
Matches: 83, Mismatches: 14, Indels: 9
0.78 0.13 0.08
Matches are distributed among these distances:
47 1 0.01
48 3 0.04
49 56 0.67
50 23 0.28
ACGTcount: A:0.19, C:0.13, G:0.33, T:0.35
Consensus pattern (48 bp):
AGTTGCTAACCAGATTGGTGTATGGTTGGATGTCTGGTAGGGCATGTT
Found at i:48658533 original size:25 final size:26
Alignment explanation
Indices: 48658479--48658534 Score: 80
Period size: 24 Copynumber: 2.2 Consensus size: 26
48658469 ACCTATTTCG
48658479 CTAATTAAAAAAAATGAAATAAAAAT
1 CTAATTAAAAAAAATGAAATAAAAAT
* *
48658505 -TAATT-AAAAAAATGAAATATACAT
1 CTAATTAAAAAAAATGAAATAAAAAT
48658529 CTAATT
1 CTAATT
48658535 TAGCCCAAAT
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
24 17 0.63
25 10 0.37
ACGTcount: A:0.62, C:0.05, G:0.04, T:0.29
Consensus pattern (26 bp):
CTAATTAAAAAAAATGAAATAAAAAT
Found at i:48662776 original size:16 final size:16
Alignment explanation
Indices: 48662755--48662788 Score: 68
Period size: 16 Copynumber: 2.1 Consensus size: 16
48662745 TTTTAGAGTA
48662755 AGAAACCTATTAGACC
1 AGAAACCTATTAGACC
48662771 AGAAACCTATTAGACC
1 AGAAACCTATTAGACC
48662787 AG
1 AG
48662789 TATGTCTTTG
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:0.44, C:0.24, G:0.15, T:0.18
Consensus pattern (16 bp):
AGAAACCTATTAGACC
Found at i:48677720 original size:68 final size:68
Alignment explanation
Indices: 48677588--48677721 Score: 162
Period size: 68 Copynumber: 2.0 Consensus size: 68
48677578 TTTTAATAGT
* * * *
48677588 TTAATATTAAATTAAATTTAATACTTATCTAAATAGTATTTTATTAATTTATTAATAAATTGATT
1 TTAATATTAAATTAAATTTAATACTTATCTAAATAATATTATATTAATTTAATAATAAAGTGATT
48677653 ATC
66 ATC
* * * ** *
48677656 TTAATATTTAATTTAATTTAATATTTATCTTGATAAATATTATATTAA-TTAATATTAAAGTGAT
1 TTAATATTAAATTAAATTTAATACTTATCTAAAT-AATATTATATTAATTTAATAATAAAGTGAT
48677720 TA
65 TA
48677722 AGTTTAATCA
Statistics
Matches: 55, Mismatches: 10, Indels: 2
0.82 0.15 0.03
Matches are distributed among these distances:
68 44 0.80
69 11 0.20
ACGTcount: A:0.43, C:0.03, G:0.04, T:0.51
Consensus pattern (68 bp):
TTAATATTAAATTAAATTTAATACTTATCTAAATAATATTATATTAATTTAATAATAAAGTGATT
ATC
Found at i:48679005 original size:29 final size:29
Alignment explanation
Indices: 48678949--48679023 Score: 82
Period size: 29 Copynumber: 2.6 Consensus size: 29
48678939 ACCGATACAT
*
48678949 AGTACCT-AATAA-TATAACACTGGCACAA
1 AGTACCTGAA-AACTATAACACTAGCACAA
* *
48678977 AGTGCCTGAAAACTATAACACTAGTACAA
1 AGTACCTGAAAACTATAACACTAGCACAA
* *
48679006 AGTACCTGATAAGTATAA
1 AGTACCTGAAAACTATAA
48679024 TCATCGGCAC
Statistics
Matches: 39, Mismatches: 6, Indels: 3
0.81 0.12 0.06
Matches are distributed among these distances:
28 8 0.21
29 31 0.79
ACGTcount: A:0.45, C:0.19, G:0.13, T:0.23
Consensus pattern (29 bp):
AGTACCTGAAAACTATAACACTAGCACAA
Found at i:48691272 original size:33 final size:33
Alignment explanation
Indices: 48691200--48691273 Score: 87
Period size: 33 Copynumber: 2.2 Consensus size: 33
48691190 ACTCACCTCG
* * * *
48691200 TGTTTACTGTCCTGATAGATTACCTCTATTTTG
1 TGTTTACTATCCTGATAGACTACCTCTATTCTA
*
48691233 TATTTACTAT-CTCGATAGACTACCTCTATTCTA
1 TGTTTACTATCCT-GATAGACTACCTCTATTCTA
48691266 TGTTTACT
1 TGTTTACT
48691274 GCCCTAGTGA
Statistics
Matches: 34, Mismatches: 6, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
32 2 0.06
33 32 0.94
ACGTcount: A:0.22, C:0.20, G:0.11, T:0.47
Consensus pattern (33 bp):
TGTTTACTATCCTGATAGACTACCTCTATTCTA
Found at i:48691330 original size:34 final size:33
Alignment explanation
Indices: 48691250--48691361 Score: 104
Period size: 33 Copynumber: 3.4 Consensus size: 33
48691240 TATCTCGATA
* * *
48691250 GACTACCTCTATTCTATGTTTACTG-CCCTA-G
1 GACTATCTCTATTCCATGTTTACTGTCCCAACG
* * *
48691281 TGAACTATCTTTATTCCATGTTTA-TTTCCCTTGACG
1 -G-ACTATCTCTATTCCATGTTTACTGTCCC--AACG
*
48691317 GACTATCTCTATTCCGTGTTTACTGTCCCAACG
1 GACTATCTCTATTCCATGTTTACTGTCCCAACG
48691350 GACTATCTCTAT
1 GACTATCTCTAT
48691362 GGATGTCATG
Statistics
Matches: 65, Mismatches: 9, Indels: 11
0.76 0.11 0.13
Matches are distributed among these distances:
32 2 0.03
33 36 0.55
34 19 0.29
35 7 0.11
36 1 0.02
ACGTcount: A:0.20, C:0.27, G:0.12, T:0.41
Consensus pattern (33 bp):
GACTATCTCTATTCCATGTTTACTGTCCCAACG
Found at i:48691452 original size:63 final size:63
Alignment explanation
Indices: 48691371--48691522 Score: 234
Period size: 63 Copynumber: 2.4 Consensus size: 63
48691361 TGGATGTCAT
*
48691371 GGAGTCTTTCATCCATGGTTTTACA-TCGATTCACCATCTTGGCACACTATCTTTTAATGCCAC
1 GGAGTCTTTCATCCATGGTCTTACACT-GATTCACCATCTTGGCACACTATCTTTTAATGCCAC
* ** * *
48691434 GGAGTCTTTCATCCATGGTCTTACACTGATTCGCCATCTTGGTGCACTATCTTTTGATGCCAT
1 GGAGTCTTTCATCCATGGTCTTACACTGATTCACCATCTTGGCACACTATCTTTTAATGCCAC
48691497 GGAGTCTTTCATCCATGGTCTTACAC
1 GGAGTCTTTCATCCATGGTCTTACAC
48691523 CGTATACCTT
Statistics
Matches: 82, Mismatches: 6, Indels: 2
0.91 0.07 0.02
Matches are distributed among these distances:
63 81 0.99
64 1 0.01
ACGTcount: A:0.20, C:0.26, G:0.17, T:0.37
Consensus pattern (63 bp):
GGAGTCTTTCATCCATGGTCTTACACTGATTCACCATCTTGGCACACTATCTTTTAATGCCAC
Found at i:48702849 original size:57 final size:55
Alignment explanation
Indices: 48702785--48702912 Score: 166
Period size: 57 Copynumber: 2.3 Consensus size: 55
48702775 GAAATTCACT
* *
48702785 TGAAATTGATATAAACTTATTGATTAATGATAGAATATGACACTTAAATGAATTATG
1 TGAAATTG-TATAAACTTATGGATTAACGATAGAATATGACA-TTAAATGAATTATG
* * * *
48702842 TGAAATTGGTTTAAACTTATGGATTGACGATAGAATATGACATTGAATGAGTTATG
1 TGAAATT-GTATAAACTTATGGATTAACGATAGAATATGACATTAAATGAATTATG
48702898 TGAAATTCGTATAAA
1 TGAAATT-GTATAAA
48702913 TTGGTAATGT
Statistics
Matches: 62, Mismatches: 8, Indels: 3
0.85 0.11 0.04
Matches are distributed among these distances:
56 25 0.40
57 36 0.58
58 1 0.02
ACGTcount: A:0.41, C:0.05, G:0.18, T:0.36
Consensus pattern (55 bp):
TGAAATTGTATAAACTTATGGATTAACGATAGAATATGACATTAAATGAATTATG
Found at i:48718406 original size:47 final size:46
Alignment explanation
Indices: 48718241--48718512 Score: 269
Period size: 50 Copynumber: 5.7 Consensus size: 46
48718231 GTGAGTGTGC
* *
48718241 CAGTGTAAGACCATGTCTGGGACATGGCACCGGCACAGACTGAGGAGTG
1 CAGTGTAAGACCATGTCTGGGACATGGCATCGGCAC-GA--GATGAGTG
* * * *
48718290 CTAGTGTAAGACGATGTCTGGGACATGGCATCAGCACGGACAGAGGAGAG
1 C-AGTGTAAGACCATGTCTGGGACATGGCATCGGCAC-G--AGATGAGTG
*
48718340 TCAGTGTAAGACCATGTCTGGGACATGGCATCGGCTCGAGATGAGTG
1 -CAGTGTAAGACCATGTCTGGGACATGGCATCGGCACGAGATGAGTG
* * * *
48718387 ACAGTGTAAGACCATGTCTGGGACATGGCATCGACACCGATATGTGATCC
1 -CAGTGTAAGACCATGTCTGGGACATGGCATCGGCA-CGAGATGAG-T-G
* * *
48718437 CA-TGTAAGACCATGTCTGGGACATAGTATCGGCTCGAGATGAGTG
1 CAGTGTAAGACCATGTCTGGGACATGGCATCGGCACGAGATGAGTG
*
48718482 CTAGCT-TAAGACTATGTCTGGGACATGGCAT
1 C-AG-TGTAAGACCATGTCTGGGACATGGCAT
48718513 TGACACCGAT
Statistics
Matches: 187, Mismatches: 26, Indels: 22
0.80 0.11 0.09
Matches are distributed among these distances:
45 1 0.01
46 2 0.01
47 69 0.37
48 36 0.19
49 5 0.03
50 72 0.39
51 1 0.01
52 1 0.01
ACGTcount: A:0.27, C:0.20, G:0.32, T:0.21
Consensus pattern (46 bp):
CAGTGTAAGACCATGTCTGGGACATGGCATCGGCACGAGATGAGTG
Found at i:48718475 original size:95 final size:94
Alignment explanation
Indices: 48718244--48718544 Score: 358
Period size: 95 Copynumber: 3.1 Consensus size: 94
48718234 AGTGTGCCAG
* * * *
48718244 TGTAAGACCATGTCTGGGACATGGCACCGGCACAGACTGAGGAGTGCTAGTGTAAGACGATGTCT
1 TGTAAGACCATGTCTGGGACATGGCATCGGCTC-GA--GATGAGTGCTAGTGTAAGACCATGTCT
* * * *
48718309 GGGACATGGCATC-AGCACGGACAGAGGAGAGT-CA
63 GGGACATGGCATCGA-CACCG--ATATGTGA-TCCA
48718343 GTGTAAGACCATGTCTGGGACATGGCATCGGCTCGAGATGAGTGAC-AGTGTAAGACCATGTCTG
1 -TGTAAGACCATGTCTGGGACATGGCATCGGCTCGAGATGAGTG-CTAGTGTAAGACCATGTCTG
48718407 GGACATGGCATCGACACCGATATGTGATCCCA
64 GGACATGGCATCGACACCGATATGTGAT-CCA
* * *
48718439 TGTAAGACCATGTCTGGGACATAGTATCGGCTCGAGATGAGTGCTAGCT-TAAGACTATGTCTGG
1 TGTAAGACCATGTCTGGGACATGGCATCGGCTCGAGATGAGTGCTAG-TGTAAGACCATGTCTGG
*
48718503 GACATGGCATTGACACCGATATGTGATTCCA
65 GACATGGCATCGACACCGATATGTGA-TCCA
48718534 TGTAAGACCAT
1 TGTAAGACCAT
48718545 ATTTAGGATA
Statistics
Matches: 182, Mismatches: 12, Indels: 19
0.85 0.06 0.09
Matches are distributed among these distances:
94 2 0.01
95 101 0.55
96 4 0.02
97 40 0.22
98 2 0.01
99 2 0.01
100 31 0.17
ACGTcount: A:0.27, C:0.20, G:0.30, T:0.22
Consensus pattern (94 bp):
TGTAAGACCATGTCTGGGACATGGCATCGGCTCGAGATGAGTGCTAGTGTAAGACCATGTCTGGG
ACATGGCATCGACACCGATATGTGATCCA
Found at i:48724453 original size:27 final size:27
Alignment explanation
Indices: 48724389--48724453 Score: 103
Period size: 27 Copynumber: 2.4 Consensus size: 27
48724379 GGACATTGTG
* *
48724389 CATCACATGAGCCGCATATTCAACATC
1 CATCACATGGGCCACATATTCAACATC
48724416 CATCACATGGGCCACATATTCAACATC
1 CATCACATGGGCCACATATTCAACATC
*
48724443 CATCACGTGGG
1 CATCACATGGG
48724454 TCCAATGTTA
Statistics
Matches: 35, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
27 35 1.00
ACGTcount: A:0.31, C:0.32, G:0.15, T:0.22
Consensus pattern (27 bp):
CATCACATGGGCCACATATTCAACATC
Found at i:48739036 original size:29 final size:30
Alignment explanation
Indices: 48738983--48739082 Score: 76
Period size: 31 Copynumber: 3.3 Consensus size: 30
48738973 TACATTATTT
* *
48738983 TTTAATTTAATGTACAATTCTATATAT-AAAC
1 TTTAATTTAGTGT--AATTATATATATAAAAC
* *
48739014 TTTAATTTAGTGTAATTATATATGTAAAAG
1 TTTAATTTAGTGTAATTATATATATAAAAC
* ** * * *
48739044 TTTAATTGTGGTACAAATATATATTTGAAAC
1 TTTAATT-TAGTGTAATTATATATATAAAAC
48739075 TTTAATTT
1 TTTAATTT
48739083 TGATTTAATT
Statistics
Matches: 56, Mismatches: 11, Indels: 5
0.78 0.15 0.07
Matches are distributed among these distances:
29 10 0.18
30 11 0.20
31 35 0.62
ACGTcount: A:0.39, C:0.05, G:0.09, T:0.47
Consensus pattern (30 bp):
TTTAATTTAGTGTAATTATATATATAAAAC
Found at i:48743638 original size:20 final size:20
Alignment explanation
Indices: 48743613--48743650 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
48743603 GTATTTGCAT
* *
48743613 AAAAAAATATTAAAAAAAAC
1 AAAAAAAAAATAAAAAAAAC
48743633 AAAAAAAAAATAAAAAAA
1 AAAAAAAAAATAAAAAAA
48743651 GAAGAAGAAG
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.87, C:0.03, G:0.00, T:0.11
Consensus pattern (20 bp):
AAAAAAAAAATAAAAAAAAC
Found at i:48751464 original size:209 final size:208
Alignment explanation
Indices: 48751128--48751559 Score: 640
Period size: 209 Copynumber: 2.1 Consensus size: 208
48751118 GGCGGTTGTA
*
48751128 GAAAACGCCGCTATATCCTGCAATTAGCGGCGCTTAACTAAAAAACGCTGAAAATTTTTAAACCG
1 GAAAACGCCGCTATATCCTGCAATTAGCGGCGCTTAACTAAAAAACGCAGAAAATTTTTAAACCG
*
48751193 AAACGCAACGTTTCGTCTTGAGCTATAGCGCCATCAGCGGCGCTTACCCGAAAATGCCGCTATAT
66 AAACGCAACGTTTCGTCTTGAGCTATAGCGCCATCAGCGGCGCTTACCCGAAAACGCCGCTATAT
* *
48751258 ATTAGCTAGAAGC-GCCGTAAAAATTTTGACCAAAACGCATCGTTCCGGCTTGACCTATAGA-GC
131 ATCAGCT-GAAGCTG-C--AAAAATTTTGACCAAAACGCATCGTTCCAGCTTGACCTATAGAGGC
* *
48751321 GTTAGCGGCGCTTGCCT
192 ATTAGCGGCGCTTACCT
48751338 GAAAACGCCGCTATATCCCT-CAATTAGCGGCGCTTAACT-AAAAACGTCAGAAAA-TTTTAAAC
1 GAAAACGCCGCTATAT-CCTGCAATTAGCGGCGCTTAACTAAAAAACG-CAGAAAATTTTTAAAC
* * * *
48751400 CGAAATGCAACGTTTCGTCTTGAGCTATAGCGCCGTTAGCGGCGCTTACTCGAAAACGCCGCTAT
64 CGAAACGCAACGTTTCGTCTTGAGCTATAGCGCCATCAGCGGCGCTTACCCGAAAACGCCGCTAT
***
48751465 ATATCAGCTTTTGCTGCAAAAATTTTGACCAAAACGCATCGTTCCAGCTTGACCTATAGAGGCAT
129 ATATCAGCTGAAGCTGCAAAAATTTTGACCAAAACGCATCGTTCCAGCTTGACCTATAGAGGCAT
**
48751530 TAGCGGCGCTTATTT
194 TAGCGGCGCTTACCT
48751545 GAAAACGCCGCTATA
1 GAAAACGCCGCTATA
48751560 GAGCAACTTT
Statistics
Matches: 203, Mismatches: 15, Indels: 11
0.89 0.07 0.05
Matches are distributed among these distances:
206 42 0.21
207 30 0.15
208 3 0.01
209 84 0.41
210 41 0.20
211 3 0.01
ACGTcount: A:0.30, C:0.25, G:0.20, T:0.25
Consensus pattern (208 bp):
GAAAACGCCGCTATATCCTGCAATTAGCGGCGCTTAACTAAAAAACGCAGAAAATTTTTAAACCG
AAACGCAACGTTTCGTCTTGAGCTATAGCGCCATCAGCGGCGCTTACCCGAAAACGCCGCTATAT
ATCAGCTGAAGCTGCAAAAATTTTGACCAAAACGCATCGTTCCAGCTTGACCTATAGAGGCATTA
GCGGCGCTTACCT
Found at i:48752168 original size:7 final size:7
Alignment explanation
Indices: 48752156--48752218 Score: 54
Period size: 7 Copynumber: 9.0 Consensus size: 7
48752146 GTTAATTGAT
48752156 GGGTTTA
1 GGGTTTA
48752163 GGGTTTA
1 GGGTTTA
*
48752170 AGGTTTA
1 GGGTTTA
** *
48752177 CTGTTTG
1 GGGTTTA
*
48752184 GGGTTTG
1 GGGTTTA
48752191 GGGTTTA
1 GGGTTTA
*
48752198 AGGTTTA
1 GGGTTTA
**
48752205 TAGTTTA
1 GGGTTTA
48752212 GGGTTTA
1 GGGTTTA
48752219 AGATTTATGG
Statistics
Matches: 44, Mismatches: 12, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
7 44 1.00
ACGTcount: A:0.16, C:0.02, G:0.37, T:0.46
Consensus pattern (7 bp):
GGGTTTA
Found at i:48752210 original size:21 final size:21
Alignment explanation
Indices: 48752186--48752226 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
48752176 ACTGTTTGGG
* *
48752186 GTTTGGGGTTTAAGGTTTATA
1 GTTTAGGGTTTAAGATTTATA
48752207 GTTTAGGGTTTAAGATTTAT
1 GTTTAGGGTTTAAGATTTAT
48752227 GGTTAAGGCT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.22, C:0.00, G:0.29, T:0.49
Consensus pattern (21 bp):
GTTTAGGGTTTAAGATTTATA
Found at i:48752225 original size:28 final size:28
Alignment explanation
Indices: 48752156--48752218 Score: 92
Period size: 28 Copynumber: 2.2 Consensus size: 28
48752146 GTTAATTGAT
*
48752156 GGGTTTAGGGTTTAAGGTTTACTGTTTG
1 GGGTTTAGGGTTTAAGGTTTACTGTTTA
*
48752184 GGGTTTGGGGTTTAAGGTTTA-TAGTTTA
1 GGGTTTAGGGTTTAAGGTTTACT-GTTTA
48752212 GGGTTTA
1 GGGTTTA
48752219 AGATTTATGG
Statistics
Matches: 31, Mismatches: 3, Indels: 2
0.86 0.08 0.06
Matches are distributed among these distances:
27 1 0.03
28 30 0.97
ACGTcount: A:0.16, C:0.02, G:0.37, T:0.46
Consensus pattern (28 bp):
GGGTTTAGGGTTTAAGGTTTACTGTTTA
Found at i:48752374 original size:15 final size:15
Alignment explanation
Indices: 48752354--48752383 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
48752344 GCTTTTTTAG
*
48752354 AATATAAATGTAAAT
1 AATATAAATATAAAT
48752369 AATATAAATATAAAT
1 AATATAAATATAAAT
48752384 TATTATTTAA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.63, C:0.00, G:0.03, T:0.33
Consensus pattern (15 bp):
AATATAAATATAAAT
Found at i:48753183 original size:19 final size:20
Alignment explanation
Indices: 48753142--48753185 Score: 63
Period size: 19 Copynumber: 2.2 Consensus size: 20
48753132 AACTGTCATC
*
48753142 TCCCCTAAATCCCTAAAATT
1 TCCCCTAAATCCCTAAAAGT
*
48753162 TCCCCT-AATCCCTAACAGT
1 TCCCCTAAATCCCTAAAAGT
48753181 TCCCC
1 TCCCC
48753186 AAACCCAACG
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
19 16 0.73
20 6 0.27
ACGTcount: A:0.27, C:0.43, G:0.02, T:0.27
Consensus pattern (20 bp):
TCCCCTAAATCCCTAAAAGT
Found at i:48753552 original size:6 final size:6
Alignment explanation
Indices: 48753541--48753567 Score: 54
Period size: 6 Copynumber: 4.5 Consensus size: 6
48753531 GAAATTTATA
48753541 TATATG TATATG TATATG TATATG TAT
1 TATATG TATATG TATATG TATATG TAT
48753568 TAAAACTAAA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 21 1.00
ACGTcount: A:0.33, C:0.00, G:0.15, T:0.52
Consensus pattern (6 bp):
TATATG
Found at i:48760232 original size:21 final size:21
Alignment explanation
Indices: 48760208--48760247 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
48760198 ACATAAAGCT
48760208 GAGGCAGAAGCGAGAGAAGTG
1 GAGGCAGAAGCGAGAGAAGTG
* * *
48760229 GAGGCTGCAGCGAGGGAAG
1 GAGGCAGAAGCGAGAGAAG
48760248 CAGAGCAGAA
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 16 1.00
ACGTcount: A:0.33, C:0.12, G:0.50, T:0.05
Consensus pattern (21 bp):
GAGGCAGAAGCGAGAGAAGTG
Found at i:48760619 original size:43 final size:43
Alignment explanation
Indices: 48760571--48760714 Score: 125
Period size: 43 Copynumber: 3.3 Consensus size: 43
48760561 GCGTTTTACG
* *
48760571 AAAAGCGCCGCTAAAAGTC-GCCATCTATTA-CGGCGTTTTTGGA
1 AAAAGCGCCGCTAAAAGTCAG-CATCTA-TAGCGGCGATTGTGGA
* *
48760614 AAAAGCGCCGCTAAAAGTCAGGATCTATAGCGGCGATTGTGGG
1 AAAAGCGCCGCTAAAAGTCAGCATCTATAGCGGCGATTGTGGA
* * * * *
48760657 ATAAGCGCCGCTAAAGAG-CATG-ACCTTTAGCGGCGTTTGTGGG
1 AAAAGCGCCGCTAAA-AGTCA-GCATCTATAGCGGCGATTGTGGA
* *
48760700 ATAAGCGTCGCTAAA
1 AAAAGCGCCGCTAAA
48760715 GAACATGAGC
Statistics
Matches: 88, Mismatches: 9, Indels: 8
0.84 0.09 0.08
Matches are distributed among these distances:
42 2 0.02
43 82 0.93
44 4 0.05
ACGTcount: A:0.28, C:0.21, G:0.28, T:0.22
Consensus pattern (43 bp):
AAAAGCGCCGCTAAAAGTCAGCATCTATAGCGGCGATTGTGGA
Found at i:48760715 original size:43 final size:43
Alignment explanation
Indices: 48760601--48760866 Score: 302
Period size: 43 Copynumber: 6.2 Consensus size: 43
48760591 CCATCTATTA
* * * * * *
48760601 CGGCGTTTTTGGAAAAAGCGCCGCTAAA-AGTCAGGATCTATAG
1 CGGCGTTTGTGGGATAAGCGCCGCTAAAGAG-CATGACCTTTAG
*
48760644 CGGCGATTGTGGGATAAGCGCCGCTAAAGAGCATGACCTTTAG
1 CGGCGTTTGTGGGATAAGCGCCGCTAAAGAGCATGACCTTTAG
* * * *
48760687 CGGCGTTTGTGGGATAAGCGTCGCTAAAGAACATGAGCTTTAA
1 CGGCGTTTGTGGGATAAGCGCCGCTAAAGAGCATGACCTTTAG
* * *
48760730 CGGCATTTGTGGAATAAGTGCCGCTAAAGAGCATGACCTTTAG
1 CGGCGTTTGTGGGATAAGCGCCGCTAAAGAGCATGACCTTTAG
* * * * *
48760773 CGGCGTTTGTGGGATCAGCGCCGCTAAAGAACATAAGCTTTTG
1 CGGCGTTTGTGGGATAAGCGCCGCTAAAGAGCATGACCTTTAG
* *
48760816 CGGCGTTTGTGGGATAAGCACCGCTAAAG-GTCATGACCTTTAA
1 CGGCGTTTGTGGGATAAGCGCCGCTAAAGAG-CATGACCTTTAG
*
48760859 CGGTGTTT
1 CGGCGTTT
48760867 ATTTCTATAA
Statistics
Matches: 186, Mismatches: 35, Indels: 4
0.83 0.16 0.02
Matches are distributed among these distances:
43 184 0.99
44 2 0.01
ACGTcount: A:0.26, C:0.19, G:0.30, T:0.25
Consensus pattern (43 bp):
CGGCGTTTGTGGGATAAGCGCCGCTAAAGAGCATGACCTTTAG
Found at i:48760819 original size:129 final size:129
Alignment explanation
Indices: 48760600--48760861 Score: 346
Period size: 129 Copynumber: 2.0 Consensus size: 129
48760590 GCCATCTATT
* * *
48760600 ACGGCGTTTTTGGAAAAAGCGCCGCTAAAAGTCAGGATCTATAGCGGCGATTGTGGGATAAGCGC
1 ACGGCATTTGTGGAAAAAGCGCCGCTAAAAGTCAGGACCTATAGCGGCGATTGTGGGATAAGCGC
* * ** *
48760665 CGCTAAAGAGCATGACCTTTAGCGGCGTTTGTGGGATAAGCGTCGCTAAAGAACATGAGCTTTA
66 CGCTAAAGAACATAACCTTTAGCGGCGTTTGTGGGATAAGCACCGCTAAAGAACATGACCTTTA
* * * * * *
48760729 ACGGCATTTGTGGAATAAGTGCCGCTAAAGAG-CATGACCTTTAGCGGCGTTTGTGGGATCAGCG
1 ACGGCATTTGTGGAAAAAGCGCCGCTAAA-AGTCAGGACCTATAGCGGCGATTGTGGGATAAGCG
* * **
48760793 CCGCTAAAGAACATAAGCTTTTGCGGCGTTTGTGGGATAAGCACCGCTAAAGGTCATGACCTTTA
65 CCGCTAAAGAACATAACCTTTAGCGGCGTTTGTGGGATAAGCACCGCTAAAGAACATGACCTTTA
48760858 ACGG
1 ACGG
48760862 TGTTTATTTC
Statistics
Matches: 114, Mismatches: 18, Indels: 2
0.85 0.13 0.01
Matches are distributed among these distances:
129 112 0.98
130 2 0.02
ACGTcount: A:0.27, C:0.19, G:0.30, T:0.24
Consensus pattern (129 bp):
ACGGCATTTGTGGAAAAAGCGCCGCTAAAAGTCAGGACCTATAGCGGCGATTGTGGGATAAGCGC
CGCTAAAGAACATAACCTTTAGCGGCGTTTGTGGGATAAGCACCGCTAAAGAACATGACCTTTA
Found at i:48765581 original size:25 final size:27
Alignment explanation
Indices: 48765536--48765590 Score: 62
Period size: 25 Copynumber: 2.1 Consensus size: 27
48765526 ATGTAAAAAG
*
48765536 TAAAGAAATAATAAATAAATA-A-ATA
1 TAAAGAAAAAATAAATAAATATACATA
*
48765561 TAAAGAAAAAATAGAA-CAATATACATA
1 TAAAGAAAAAATA-AATAAATATACATA
48765588 TAA
1 TAA
48765591 GAATCTATAA
Statistics
Matches: 25, Mismatches: 2, Indels: 4
0.81 0.06 0.13
Matches are distributed among these distances:
25 16 0.64
26 3 0.12
27 6 0.24
ACGTcount: A:0.69, C:0.04, G:0.05, T:0.22
Consensus pattern (27 bp):
TAAAGAAAAAATAAATAAATATACATA
Found at i:48770459 original size:20 final size:20
Alignment explanation
Indices: 48770426--48770472 Score: 67
Period size: 20 Copynumber: 2.4 Consensus size: 20
48770416 ACTAAATATT
* * *
48770426 GATACGTGCCATTTTGTGTC
1 GATACCTGCAATTTTGTATC
48770446 GATACCTGCAATTTTGTATC
1 GATACCTGCAATTTTGTATC
48770466 GATACCT
1 GATACCT
48770473 ACTTTGATTT
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 24 1.00
ACGTcount: A:0.21, C:0.21, G:0.19, T:0.38
Consensus pattern (20 bp):
GATACCTGCAATTTTGTATC
Found at i:48772825 original size:51 final size:51
Alignment explanation
Indices: 48772765--48772872 Score: 171
Period size: 51 Copynumber: 2.1 Consensus size: 51
48772755 TTCTTTTTAG
48772765 ATATTGATATATTAACTCTTCTAGAGCTTTCAACTAATTTTGTACGACCAA
1 ATATTGATATATTAACTCTTCTAGAGCTTTCAACTAATTTTGTACGACCAA
* * ** *
48772816 ATATTGATATATTAACTTTTCTGGAGCTTTTGACTAATTTTGTACTACCAA
1 ATATTGATATATTAACTCTTCTAGAGCTTTCAACTAATTTTGTACGACCAA
48772867 ATATTG
1 ATATTG
48772873 GAATAATATT
Statistics
Matches: 52, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
51 52 1.00
ACGTcount: A:0.31, C:0.15, G:0.11, T:0.43
Consensus pattern (51 bp):
ATATTGATATATTAACTCTTCTAGAGCTTTCAACTAATTTTGTACGACCAA
Found at i:48780605 original size:150 final size:150
Alignment explanation
Indices: 48780334--48780621 Score: 567
Period size: 150 Copynumber: 1.9 Consensus size: 150
48780324 GAACCAATAT
48780334 TTTCTTGTAGCTTTTGATACTTGCAATTGATGCTTGGATTTTGTGTTAGAAAGATGCAGGCATAA
1 TTTCTTGTAGCTTTTGATACTTGCAATTGATGCTTGGATTTTGTGTTAGAAAGATGCAGGCATAA
*
48780399 ATCTATCTTATTTTATTTTAATTTTACAATATTGAAATTTACTGACTTGAAAAATGCTGTGGTTG
66 ATCTATCTTATTTTATTTTAATTTTACAATAGTGAAATTTACTGACTTGAAAAATGCTGTGGTTG
48780464 TAAAATTTATATGATGAACA
131 TAAAATTTATATGATGAACA
48780484 TTTCTTGTAGCTTTTGATACTTGCAATTGATGCTTGGATTTTGTGTTAGAAAGATGCAGGCATAA
1 TTTCTTGTAGCTTTTGATACTTGCAATTGATGCTTGGATTTTGTGTTAGAAAGATGCAGGCATAA
48780549 ATCTATCTTATTTTATTTTAATTTTACAATAGTGAAATTTACTGACTTGAAAAATGCTGTGGTTG
66 ATCTATCTTATTTTATTTTAATTTTACAATAGTGAAATTTACTGACTTGAAAAATGCTGTGGTTG
48780614 TAAAATTT
131 TAAAATTT
48780622 GGAATCTATC
Statistics
Matches: 137, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
150 137 1.00
ACGTcount: A:0.30, C:0.09, G:0.17, T:0.44
Consensus pattern (150 bp):
TTTCTTGTAGCTTTTGATACTTGCAATTGATGCTTGGATTTTGTGTTAGAAAGATGCAGGCATAA
ATCTATCTTATTTTATTTTAATTTTACAATAGTGAAATTTACTGACTTGAAAAATGCTGTGGTTG
TAAAATTTATATGATGAACA
Found at i:48784116 original size:3 final size:3
Alignment explanation
Indices: 48784110--48784139 Score: 53
Period size: 3 Copynumber: 10.3 Consensus size: 3
48784100 TTCTATGATT
48784110 TTA TTA TTA TTA TTA TTA TTA TTA TT- TTA T
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
48784140 AACATACATG
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
2 2 0.08
3 24 0.92
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (3 bp):
TTA
Found at i:48786205 original size:13 final size:13
Alignment explanation
Indices: 48786187--48786211 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
48786177 AAAGAGATTT
48786187 GTTTTCTAGTAAA
1 GTTTTCTAGTAAA
48786200 GTTTTCTAGTAA
1 GTTTTCTAGTAA
48786212 GAAATTGAAC
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:0.28, C:0.08, G:0.16, T:0.48
Consensus pattern (13 bp):
GTTTTCTAGTAAA
Found at i:48791785 original size:44 final size:43
Alignment explanation
Indices: 48791722--48792310 Score: 325
Period size: 44 Copynumber: 13.1 Consensus size: 43
48791712 GCAGGTTGAA
*
48791722 AAGAAAATAGATCTTGTCTTCATATATTGGCATGAAGTAGATCG
1 AAGAAAATAGATCTTGTCTTCATATAGTGGC-TGAAGTAGATCG
* * * *
48791766 AAGAAAGTAGATATTGTCTTCCCATACTGGTGGC-GAAGTAGATCA
1 AAGAAAATAGATCTTGTCTT--CATA-TAGTGGCTGAAGTAGATCG
* * *
48791811 AAGAAAATAGATCTTGTATTCATGTATTGGCGTGAAGTAGATCG
1 AAGAAAATAGATCTTGTCTTCATATAGTGGC-TGAAGTAGATCG
* *
48791855 AAGAAAACAGATCTTGTCTTCCCATACTGGTGGC-GAAGTAGATCG
1 AAGAAAATAGATCTTGTCTT--CATA-TAGTGGCTGAAGTAGATCG
* * * * *
48791900 AAGAAAACAAATCTTGTCTTCATGTACTGGCGTGAAGTAGATCA
1 AAGAAAATAGATCTTGTCTTCATATAGTGGC-TGAAGTAGATCG
* * *
48791944 AAGATAACAGATAACAGATTTTGTCTTCCCATACTGGTGGC-GAAGCAGATCG
1 AAG--AA-A-AT---AGATCTTGTCTT--CATA-TAGTGGCTGAAGTAGATCG
** * * *
48791996 AAGAAAGCAGATCTTGTCTTCATGTACTGGCGAGAAGTAGATC-
1 AAGAAAATAGATCTTGTCTTCATATAGTGGC-TGAAGTAGATCG
* ** * * * * **
48792039 AGAGATACCAAATCTTGCCTTCCCATACTGGTGGC-GAAGCAGATTA
1 A-AGAAAATAGATCTTGTCTT--CATA-TAGTGGCTGAAGTAGATCG
** * *
48792085 AAGAAAGCAGATCTTGTCTTCATGTACTGGCGTGAAGTAGATC-
1 AAGAAAATAGATCTTGTCTTCATATAGTGGC-TGAAGTAGATCG
* * * *
48792128 AA-AAATACCAGATCTTGCCTTC-TCATACCGGTGGC-AAAGTAGATCA
1 AAGAAA-A-TAGATCTTGTCTTCAT-ATA---GTGGCTGAAGTAGATCG
* * *
48792174 AAGAAAATAGATCTTGTCTTCATGTACTGGCGTGAAGTAGATCA
1 AAGAAAATAGATCTTGTCTTCATATAGTGGC-TGAAGTAGATCG
* ** *
48792218 AAGATACCAGATCTTGTCTTCCCATACTGGTGGC-GAAGTAGATCG
1 AAGAAAATAGATCTTGTCTT--CATA-TAGTGGCTGAAGTAGATCG
* * * *
48792263 AAGAAAATAGATCTTATCTTCATGTACTGGCGTGAAGTAGATCA
1 AAGAAAATAGATCTTGTCTTCATATAGTGGC-TGAAGTAGATCG
48792307 AAGA
1 AAGA
48792311 TAACAGGTCC
Statistics
Matches: 420, Mismatches: 80, Indels: 90
0.71 0.14 0.15
Matches are distributed among these distances:
42 32 0.08
43 19 0.05
44 147 0.35
45 140 0.33
46 20 0.05
47 28 0.07
48 1 0.00
49 1 0.00
50 2 0.00
51 10 0.02
52 12 0.03
53 3 0.01
54 5 0.01
ACGTcount: A:0.33, C:0.17, G:0.23, T:0.27
Consensus pattern (43 bp):
AAGAAAATAGATCTTGTCTTCATATAGTGGCTGAAGTAGATCG
Found at i:48791872 original size:89 final size:89
Alignment explanation
Indices: 48791721--48792328 Score: 779
Period size: 89 Copynumber: 6.8 Consensus size: 89
48791711 AGCAGGTTGA
* * * * *
48791721 AAAGAAAATAGATCTTGTCTTCATATATTGGCATGAAGTAGATCGAAGA-AAGTAGATATTGTCT
1 AAAGAAAATAGATCTTGTCTTCATGTACTGGCGTGAAGTAGATCGAAGATAA-CAGATCTTGTCT
48791785 TCCCATACTGGTGGCGAAGTAGATC
65 TCCCATACTGGTGGCGAAGTAGATC
* * *
48791810 AAAGAAAATAGATCTTGTATTCATGTATTGGCGTGAAGTAGATCGAAGAAAACAGATCTTGTCTT
1 AAAGAAAATAGATCTTGTCTTCATGTACTGGCGTGAAGTAGATCGAAGATAACAGATCTTGTCTT
48791875 CCCATACTGGTGGCGAAGTAGATC
66 CCCATACTGGTGGCGAAGTAGATC
* * * *
48791899 GAAGAAAACAAATCTTGTCTTCATGTACTGGCGTGAAGTAGATCAAAGATAACAGATAACAGATT
1 AAAGAAAATAGATCTTGTCTTCATGTACTGGCGTGAAGTAGATC---G---A-AGATAACAGATC
*
48791964 TTGTCTTCCCATACTGGTGGCGAAGCAGATC
59 TTGTCTTCCCATACTGGTGGCGAAGTAGATC
* ** * * * *
48791995 GAAGAAAGCAGATCTTGTCTTCATGTACTGGCGAGAAGTAGATC-AGAGATACCAAATCTTGCCT
1 AAAGAAAATAGATCTTGTCTTCATGTACTGGCGTGAAGTAGATCGA-AGATAACAGATCTTGTCT
* *
48792059 TCCCATACTGGTGGCGAAGCAGATT
65 TCCCATACTGGTGGCGAAGTAGATC
** * * * *
48792084 AAAGAAAGCAGATCTTGTCTTCATGTACTGGCGTGAAGTAGATCAAAAATACCAGATCTTGCCTT
1 AAAGAAAATAGATCTTGTCTTCATGTACTGGCGTGAAGTAGATCGAAGATAACAGATCTTGTCTT
* * *
48792149 CTCATACCGGTGGCAAAGTAGATC
66 CCCATACTGGTGGCGAAGTAGATC
* *
48792173 AAAGAAAATAGATCTTGTCTTCATGTACTGGCGTGAAGTAGATCAAAGATACCAGATCTTGTCTT
1 AAAGAAAATAGATCTTGTCTTCATGTACTGGCGTGAAGTAGATCGAAGATAACAGATCTTGTCTT
48792238 CCCATACTGGTGGCGAAGTAGATC
66 CCCATACTGGTGGCGAAGTAGATC
* * * * *
48792262 GAAGAAAATAGATCTTATCTTCATGTACTGGCGTGAAGTAGATCAAAGATAACAGGTCCTGTCTT
1 AAAGAAAATAGATCTTGTCTTCATGTACTGGCGTGAAGTAGATCGAAGATAACAGATCTTGTCTT
48792327 CC
66 CC
48792329 TATTTCGGTA
Statistics
Matches: 467, Mismatches: 43, Indels: 18
0.88 0.08 0.03
Matches are distributed among these distances:
89 381 0.82
90 3 0.01
92 1 0.00
95 1 0.00
96 81 0.17
ACGTcount: A:0.33, C:0.17, G:0.23, T:0.27
Consensus pattern (89 bp):
AAAGAAAATAGATCTTGTCTTCATGTACTGGCGTGAAGTAGATCGAAGATAACAGATCTTGTCTT
CCCATACTGGTGGCGAAGTAGATC
Found at i:48792409 original size:178 final size:176
Alignment explanation
Indices: 48791722--48792410 Score: 699
Period size: 178 Copynumber: 3.8 Consensus size: 176
48791712 GCAGGTTGAA
* * * * * * * *
48791722 AAGAAAATAGATCTTGTCTTCATATATTGGCATGAAGTAGATCGAAGA-AAGTAGATATTGTCTT
1 AAGAAAACAGATCTTGTCTTCATGTACTGGCGTGAAGTAGATCAAAGATAA-CAGGTCTTGTCTT
* * * * *
48791786 CCCA-TACTGGTGGCGAAGTAGATCAAAGAAAATAGATCTTGTATTCATGTATTGGCGTGAAGTA
65 CCTATTAC-GGTGGCGAAGTAGATCGAAGAACAT--ATCTTGTCTTCATGTACTGGCGTGAAGTA
* *
48791850 GATCGAAGAAAACAGATCTTGTCTTCCCATACTGGTGGCGAAGTAGATCG
127 GATCGAAGATACCAGATCTTGTCTTCCCATACTGGTGGCGAAGTAGATCG
* *
48791900 AAGAAAACAAATCTTGTCTTCATGTACTGGCGTGAAGTAGATCAAAGATAACAGATAACAGATTT
1 AAGAAAACAGATCTTGTCTTCATGTACTGGCGTGAAGTAGATCAAAGATAACAG------G-TCT
* * * *
48791965 TGTCTTCCCA-TACTGGTGGCGAAGCAGATCGAAGAAAGCAGATCTTGTCTTCATGTACTGGCGA
59 TGTCTTCCTATTAC-GGTGGCGAAGTAGATCGAAG-AA-CATATCTTGTCTTCATGTACTGGCGT
* * * **
48792029 GAAGTAGATC-AGAGATACCAAATCTTGCCTTCCCATACTGGTGGCGAAGCAGATTA
121 GAAGTAGATCGA-AGATACCAGATCTTGTCTTCCCATACTGGTGGCGAAGTAGATCG
* * * * *
48792085 AAGAAAGCAGATCTTGTCTTCATGTACTGGCGTGAAGTAGATCAAAAATACCAGATCTTGCCTT-
1 AAGAAAACAGATCTTGTCTTCATGTACTGGCGTGAAGTAGATCAAAGATAACAGGTCTTGTCTTC
* * *
48792149 CTCA-TACCGGTGGCAAAGTAGATCAAAGAAAATAGATCTTGTCTTCATGTACTGGCGTGAAGTA
66 CT-ATTA-CGGTGGCGAAGTAGATCGAAGAACAT--ATCTTGTCTTCATGTACTGGCGTGAAGTA
*
48792213 GATCAAAGATACCAGATCTTGTCTTCCCATACTGGTGGCGAAGTAGATCG
127 GATCGAAGATACCAGATCTTGTCTTCCCATACTGGTGGCGAAGTAGATCG
* * *
48792263 AAGAAAATAGATCTTATCTTCATGTACTGGCGTGAAGTAGATCAAAGATAACAGGTCCTGTCTTC
1 AAGAAAACAGATCTTGTCTTCATGTACTGGCGTGAAGTAGATCAAAGATAACAGGTCTTGTCTTC
* * * * * *** *
48792328 CTATTTCGGTAGCGAAGTGGATCGAATATACATATTTTGTCTTCCCATACTGGTGGTGAAGTAGA
66 CTATTACGGTGGCGAAGTAGATCGAAGA-ACATATCTTGTCTTCATGTACTGG-CGTGAAGTAGA
*
48792393 TTGAAGATTA-CAGATCTT
129 TCGAAGA-TACCAGATCTT
48792411 ATCTCCCTAA
Statistics
Matches: 426, Mismatches: 64, Indels: 42
0.80 0.12 0.08
Matches are distributed among these distances:
176 1 0.00
177 19 0.04
178 239 0.56
179 12 0.03
184 1 0.00
185 151 0.35
186 2 0.00
187 1 0.00
ACGTcount: A:0.32, C:0.17, G:0.23, T:0.28
Consensus pattern (176 bp):
AAGAAAACAGATCTTGTCTTCATGTACTGGCGTGAAGTAGATCAAAGATAACAGGTCTTGTCTTC
CTATTACGGTGGCGAAGTAGATCGAAGAACATATCTTGTCTTCATGTACTGGCGTGAAGTAGATC
GAAGATACCAGATCTTGTCTTCCCATACTGGTGGCGAAGTAGATCG
Found at i:48792724 original size:11 final size:11
Alignment explanation
Indices: 48792708--48792787 Score: 69
Period size: 11 Copynumber: 7.4 Consensus size: 11
48792698 ATTTTTTTAA
48792708 TTTTAAAATAT
1 TTTTAAAATAT
48792719 TTTTAAAATACTT
1 TTTTAAAATA--T
**
48792732 TTTTTTAAT-T
1 TTTTAAAATAT
* *
48792742 TTTT---TTAA
1 TTTTAAAATAT
48792750 TTTTAAAATAT
1 TTTTAAAATAT
48792761 TTTTAAAATAT
1 TTTTAAAATAT
48792772 TTTTAAAATACT
1 TTTTAAAATA-T
48792784 TTTT
1 TTTT
48792788 TTTTAAAATT
Statistics
Matches: 56, Mismatches: 6, Indels: 13
0.75 0.08 0.17
Matches are distributed among these distances:
7 1 0.02
8 4 0.07
10 5 0.09
11 33 0.59
12 5 0.09
13 8 0.14
ACGTcount: A:0.36, C:0.03, G:0.00, T:0.61
Consensus pattern (11 bp):
TTTTAAAATAT
Found at i:48792758 original size:42 final size:41
Alignment explanation
Indices: 48792660--48792775 Score: 168
Period size: 42 Copynumber: 2.9 Consensus size: 41
48792650 ATAAATATTT
* * *
48792660 ATTTTTTAAATTTTAAAATATTTTTTACATAC---TTTTTA
1 ATTTTTTTAATTTTAAAATATTTTTAAAATACTTTTTTTTA
48792698 ATTTTTTTAATTTTAAAATATTTTTAAAATACTTTTTTTTA
1 ATTTTTTTAATTTTAAAATATTTTTAAAATACTTTTTTTTA
48792739 ATTTTTTTTAATTTTAAAATATTTTTAAAATA-TTTTT
1 A-TTTTTTTAATTTTAAAATATTTTTAAAATACTTTTT
48792776 AAAATACTTT
Statistics
Matches: 71, Mismatches: 3, Indels: 5
0.90 0.04 0.06
Matches are distributed among these distances:
38 29 0.41
41 12 0.17
42 30 0.42
ACGTcount: A:0.34, C:0.03, G:0.00, T:0.63
Consensus pattern (41 bp):
ATTTTTTTAATTTTAAAATATTTTTAAAATACTTTTTTTTA
Found at i:48792787 original size:42 final size:40
Alignment explanation
Indices: 48792659--48792806 Score: 166
Period size: 38 Copynumber: 3.8 Consensus size: 40
48792649 AATAAATATT
* * *
48792659 TATTTTTTAAATTTTAAAATATTTTTTACATACTTTTT-A
1 TATTTTTTTAATTTTAAAATATTTTTAAAATACTTTTTAA
48792698 -ATTTTTTTAATTTTAAAATATTTTTAAAATACTTTTTTTTAA
1 TATTTTTTTAATTTTAAAATATTTTTAAAATAC---TTTTTAA
48792740 T-TTTTTTTAATTTTAAAATATTTTTAAAATA-TTTTTAA
1 TATTTTTTTAATTTTAAAATATTTTTAAAATACTTTTTAA
* *
48792778 AATACTTTTT--TTTTAAAAT-TTTTTAAAAT
1 TAT-TTTTTTAATTTTAAAATATTTTTAAAAT
48792807 TTTAAAAATA
Statistics
Matches: 97, Mismatches: 5, Indels: 16
0.82 0.04 0.14
Matches are distributed among these distances:
37 10 0.10
38 45 0.46
39 1 0.01
40 5 0.05
41 5 0.05
42 31 0.32
ACGTcount: A:0.36, C:0.03, G:0.00, T:0.61
Consensus pattern (40 bp):
TATTTTTTTAATTTTAAAATATTTTTAAAATACTTTTTAA
Found at i:48792799 original size:11 final size:11
Alignment explanation
Indices: 48792708--48792809 Score: 52
Period size: 11 Copynumber: 9.1 Consensus size: 11
48792698 ATTTTTTTAA
*
48792708 TTTTAAAATAT
1 TTTTAAAATTT
48792719 TTTTAAAATACTT
1 TTTTAAAAT--TT
**
48792732 TTTTTTAATTT
1 TTTTAAAATTT
*
48792743 TTTT-TAA---
1 TTTTAAAATTT
*
48792750 TTTTAAAATAT
1 TTTTAAAATTT
48792761 TTTTAAAATATT
1 TTTTAAAAT-TT
*
48792773 TTTAAAATACTTTTT
1 TTTTAAA-A---TTT
48792788 TTTTAAAA-TT
1 TTTTAAAATTT
48792798 TTTTAAAATTT
1 TTTTAAAATTT
48792809 T
1 T
48792810 AAAAATAAAA
Statistics
Matches: 72, Mismatches: 7, Indels: 24
0.70 0.07 0.23
Matches are distributed among these distances:
7 4 0.06
8 2 0.03
10 13 0.18
11 27 0.38
12 7 0.10
13 9 0.12
14 1 0.01
15 8 0.11
16 1 0.01
ACGTcount: A:0.36, C:0.02, G:0.00, T:0.62
Consensus pattern (11 bp):
TTTTAAAATTT
Found at i:48795105 original size:12 final size:12
Alignment explanation
Indices: 48795088--48795112 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
48795078 GGTGTTCATT
48795088 CGGTTAACCGAC
1 CGGTTAACCGAC
48795100 CGGTTAACCGAC
1 CGGTTAACCGAC
48795112 C
1 C
48795113 CGAAATTACT
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:0.24, C:0.36, G:0.24, T:0.16
Consensus pattern (12 bp):
CGGTTAACCGAC
Found at i:48795278 original size:9 final size:9
Alignment explanation
Indices: 48795264--48795324 Score: 95
Period size: 9 Copynumber: 6.8 Consensus size: 9
48795254 TTTGGTTAAA
48795264 AATTACCCG
1 AATTACCCG
48795273 AATTACCCG
1 AATTACCCG
48795282 AATTACCCG
1 AATTACCCG
*
48795291 AATTAACCG
1 AATTACCCG
*
48795300 AATTAACCG
1 AATTACCCG
*
48795309 AATTAACCG
1 AATTACCCG
48795318 AATTACC
1 AATTACC
48795325 GAAAAATACC
Statistics
Matches: 50, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
9 50 1.00
ACGTcount: A:0.39, C:0.28, G:0.10, T:0.23
Consensus pattern (9 bp):
AATTACCCG
Found at i:48799576 original size:18 final size:18
Alignment explanation
Indices: 48799553--48799595 Score: 70
Period size: 18 Copynumber: 2.4 Consensus size: 18
48799543 TCTTTATATT
48799553 TATGGGTTG-GGAAGAGGC
1 TATGGGTTGAGG-AGAGGC
48799571 TATGGGTTGAGGAGAGGC
1 TATGGGTTGAGGAGAGGC
48799589 TATGGGT
1 TATGGGT
48799596 AGTTTTGTAT
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
18 22 0.92
19 2 0.08
ACGTcount: A:0.21, C:0.05, G:0.49, T:0.26
Consensus pattern (18 bp):
TATGGGTTGAGGAGAGGC
Found at i:48800272 original size:24 final size:23
Alignment explanation
Indices: 48800239--48800326 Score: 79
Period size: 24 Copynumber: 3.7 Consensus size: 23
48800229 TCATTAATAT
*
48800239 TGTTCGTGAACATGTTCAATTATA
1 TGTTCATGAACATGTTCAATTA-A
*
48800263 TGTTCATGAACATGTTCATTTAAA
1 TGTTCATGAACATGTTCAATT-AA
** * *
48800287 TGTTTGTGAACATATTCGATTAA
1 TGTTCATGAACATGTTCAATTAA
*
48800310 -GTTAAATGAACATGTTC
1 TGTT-CATGAACATGTTC
48800327 GTGGATATTA
Statistics
Matches: 52, Mismatches: 10, Indels: 5
0.78 0.15 0.07
Matches are distributed among these distances:
22 3 0.06
23 12 0.23
24 36 0.69
25 1 0.02
ACGTcount: A:0.32, C:0.11, G:0.16, T:0.41
Consensus pattern (23 bp):
TGTTCATGAACATGTTCAATTAA
Found at i:48815450 original size:34 final size:34
Alignment explanation
Indices: 48815389--48815456 Score: 84
Period size: 34 Copynumber: 2.0 Consensus size: 34
48815379 GCACAGTTGA
* *
48815389 ATAGTCTTGGGCCTAAACCCTTTTCAGTATCAGTG
1 ATAGTCTTGGGCCTAAACCCATCTCAGTA-CAGTG
* *
48815424 ATAGT-TTGGGCCTTAGCCCATCTCAGTACAGTG
1 ATAGTCTTGGGCCTAAACCCATCTCAGTACAGTG
48815457 TCAAAAATAC
Statistics
Matches: 29, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
33 5 0.17
34 19 0.66
35 5 0.17
ACGTcount: A:0.22, C:0.24, G:0.22, T:0.32
Consensus pattern (34 bp):
ATAGTCTTGGGCCTAAACCCATCTCAGTACAGTG
Found at i:48827591 original size:14 final size:14
Alignment explanation
Indices: 48827572--48827617 Score: 58
Period size: 14 Copynumber: 3.3 Consensus size: 14
48827562 GACTCGTTAA
48827572 TTTTATATAATTAT
1 TTTTATATAATTAT
48827586 TTTTATA-AATATAT
1 TTTTATATAAT-TAT
* *
48827600 TTTTACATAATTCT
1 TTTTATATAATTAT
48827614 TTTT
1 TTTT
48827618 TCAATCATAT
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
13 3 0.11
14 22 0.79
15 3 0.11
ACGTcount: A:0.33, C:0.04, G:0.00, T:0.63
Consensus pattern (14 bp):
TTTTATATAATTAT
Found at i:48832159 original size:22 final size:22
Alignment explanation
Indices: 48832133--48832178 Score: 58
Period size: 22 Copynumber: 2.1 Consensus size: 22
48832123 TTATTCTATG
48832133 AATTG-ATATATGTTTATAAATT
1 AATTGAATAT-TGTTTATAAATT
* *
48832155 AATTGAATATTTTTTCTAAATT
1 AATTGAATATTGTTTATAAATT
48832177 AA
1 AA
48832179 GATAAATTGT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
22 17 0.81
23 4 0.19
ACGTcount: A:0.41, C:0.02, G:0.07, T:0.50
Consensus pattern (22 bp):
AATTGAATATTGTTTATAAATT
Found at i:48834213 original size:43 final size:42
Alignment explanation
Indices: 48834125--48834351 Score: 239
Period size: 43 Copynumber: 5.4 Consensus size: 42
48834115 CTCGGTGGAT
**
48834125 TCAGCACTTAGCAACCACC-TTA-AATTCAGTGATACGGGGAA
1 TCAGCACTTAGCAACCACCTTTACAA-TCAAAGATACGGGGAA
*
48834166 TCAGCACATAGCAACC-CCTTTCACAATCAAAGATACGGTGGAA
1 TCAGCACTTAGCAACCACCTTT-ACAATCAAAGATACGG-GGAA
* * ** *
48834209 TCAGCACTTAGCAACCACCTTTATATTCAGTGATATGGGGAA
1 TCAGCACTTAGCAACCACCTTTACAATCAAAGATACGGGGAA
* * * *
48834251 TCAACACATAGCAACC-CATTTCACAATCAAATATACGGTGGAA
1 TCAGCACTTAGCAACCACCTTT-ACAATCAAAGATACGG-GGAA
* *
48834294 TCAGCACTTAGCAACCACCTTTAGAATCAATA-ATTCGGGGAA
1 TCAGCACTTAGCAACCACCTTTACAATCAA-AGATACGGGGAA
48834336 TCAGCACTTAGCAACC
1 TCAGCACTTAGCAACC
48834352 CCTCGGGGAA
Statistics
Matches: 154, Mismatches: 23, Indels: 17
0.79 0.12 0.09
Matches are distributed among these distances:
40 2 0.01
41 21 0.14
42 59 0.38
43 62 0.40
44 10 0.06
ACGTcount: A:0.36, C:0.26, G:0.16, T:0.22
Consensus pattern (42 bp):
TCAGCACTTAGCAACCACCTTTACAATCAAAGATACGGGGAA
Found at i:48834262 original size:85 final size:85
Alignment explanation
Indices: 48834117--48834354 Score: 356
Period size: 85 Copynumber: 2.8 Consensus size: 85
48834107 ATATTATCCT
* *
48834117 CGGTGGATTCAGCACTTAGCAACCACC-TTAAATTCAGTGATACGGGGAATCAGCACATAGCAAC
1 CGGTGGAATCAGCACTTAGCAACCACCTTTAAATTCAGTGATATGGGGAATCAGCACATAGCAAC
48834181 CCCTTTCACAATCAAAGATA
66 CCCTTTCACAATCAAAGATA
* *
48834201 CGGTGGAATCAGCACTTAGCAACCACCTTTATATTCAGTGATATGGGGAATCAACACATAGCAAC
1 CGGTGGAATCAGCACTTAGCAACCACCTTTAAATTCAGTGATATGGGGAATCAGCACATAGCAAC
* *
48834266 CCATTTCACAATCAAATATA
66 CCCTTTCACAATCAAAGATA
* * *
48834286 CGGTGGAATCAGCACTTAGCAACCACCTTTAGAA-TCAATAAT-TCGGGGAATCAGCACTTAGCA
1 CGGTGGAATCAGCACTTAGCAACCACCTTTA-AATTCAGTGATAT-GGGGAATCAGCACATAGCA
48834349 ACCCCT
64 ACCCCT
48834355 CGGGGAATCT
Statistics
Matches: 139, Mismatches: 12, Indels: 5
0.89 0.08 0.03
Matches are distributed among these distances:
84 27 0.19
85 111 0.80
86 1 0.01
ACGTcount: A:0.34, C:0.26, G:0.17, T:0.23
Consensus pattern (85 bp):
CGGTGGAATCAGCACTTAGCAACCACCTTTAAATTCAGTGATATGGGGAATCAGCACATAGCAAC
CCCTTTCACAATCAAAGATA
Found at i:48834357 original size:26 final size:26
Alignment explanation
Indices: 48834328--48834380 Score: 88
Period size: 26 Copynumber: 2.0 Consensus size: 26
48834318 AATCAATAAT
48834328 TCGGGGAATCAGCACTTAGCAACCCC
1 TCGGGGAATCAGCACTTAGCAACCCC
* *
48834354 TCGGGGAATCTGCACTTAGCGACCCC
1 TCGGGGAATCAGCACTTAGCAACCCC
48834380 T
1 T
48834381 TTTTATCCAA
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
26 25 1.00
ACGTcount: A:0.23, C:0.34, G:0.25, T:0.19
Consensus pattern (26 bp):
TCGGGGAATCAGCACTTAGCAACCCC
Found at i:48837068 original size:42 final size:41
Alignment explanation
Indices: 48836914--48837069 Score: 158
Period size: 42 Copynumber: 3.7 Consensus size: 41
48836904 TATGTTATCG
*
48836914 TGTAAGACCACGTCTGGGACGTTGGCATCGAT-TTGAGATTTA
1 TGTAAGACCACGTCTGGGACGTTGGCATCGATATT--GATTCA
* * * *
48836956 TGTATAAGACCATGTCTGGGACATCGGCATC-ATATTTGATTTCG
1 TG--TAAGACCACGTCTGGGACGTTGGCATCGATA-TTGA-TTCA
48837000 TGTAAGACC-CTGTCTGGGACAG-TGGCATCGATATTGATTACA
1 TGTAAGACCAC-GTCTGGGAC-GTTGGCATCGATATTGATT-CA
48837042 TGTAAGACCACGTCTGGGACGTTGGCAT
1 TGTAAGACCACGTCTGGGACGTTGGCAT
48837070 TGTACGATTT
Statistics
Matches: 94, Mismatches: 9, Indels: 22
0.75 0.07 0.18
Matches are distributed among these distances:
41 3 0.03
42 53 0.56
43 8 0.09
44 28 0.30
45 2 0.02
ACGTcount: A:0.24, C:0.19, G:0.27, T:0.30
Consensus pattern (41 bp):
TGTAAGACCACGTCTGGGACGTTGGCATCGATATTGATTCA
Found at i:48844403 original size:42 final size:41
Alignment explanation
Indices: 48844249--48844404 Score: 158
Period size: 42 Copynumber: 3.7 Consensus size: 41
48844239 TATGTTATCG
*
48844249 TGTAAGACCACGTCTGGGACGTTGGCATCGAT-TTGAGATTTA
1 TGTAAGACCACGTCTGGGACGTTGGCATCGATATT--GATTCA
* * * *
48844291 TGTATAAGACCATGTCTGGGACATCGGCATC-ATATTTGATTTCG
1 TG--TAAGACCACGTCTGGGACGTTGGCATCGATA-TTGA-TTCA
48844335 TGTAAGACC-CTGTCTGGGACAG-TGGCATCGATATTGATTACA
1 TGTAAGACCAC-GTCTGGGAC-GTTGGCATCGATATTGATT-CA
48844377 TGTAAGACCACGTCTGGGACGTTGGCAT
1 TGTAAGACCACGTCTGGGACGTTGGCAT
48844405 TGTACGATTT
Statistics
Matches: 94, Mismatches: 9, Indels: 22
0.75 0.07 0.18
Matches are distributed among these distances:
41 3 0.03
42 53 0.56
43 8 0.09
44 28 0.30
45 2 0.02
ACGTcount: A:0.24, C:0.19, G:0.27, T:0.30
Consensus pattern (41 bp):
TGTAAGACCACGTCTGGGACGTTGGCATCGATATTGATTCA
Found at i:48850208 original size:7 final size:8
Alignment explanation
Indices: 48850184--48850212 Score: 51
Period size: 8 Copynumber: 3.8 Consensus size: 8
48850174 GTAGTGTTTG
48850184 ACATAAAC
1 ACATAAAC
48850192 ACATAAAC
1 ACATAAAC
48850200 ACA-AAAC
1 ACATAAAC
48850207 ACATAA
1 ACATAA
48850213 GGGAGACAGT
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
7 7 0.35
8 13 0.65
ACGTcount: A:0.66, C:0.24, G:0.00, T:0.10
Consensus pattern (8 bp):
ACATAAAC
Found at i:48858700 original size:19 final size:20
Alignment explanation
Indices: 48858660--48858704 Score: 65
Period size: 20 Copynumber: 2.3 Consensus size: 20
48858650 TCGTAATATT
* *
48858660 TTTTTTGTACTTTCTTATAA
1 TTTTTTATACTTTCTTAGAA
48858680 TTTTTTATACTTT-TTAGAA
1 TTTTTTATACTTTCTTAGAA
48858699 TTTTTT
1 TTTTTT
48858705 TGGTATACCC
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
19 11 0.48
20 12 0.52
ACGTcount: A:0.20, C:0.07, G:0.04, T:0.69
Consensus pattern (20 bp):
TTTTTTATACTTTCTTAGAA
Found at i:48859619 original size:20 final size:20
Alignment explanation
Indices: 48859571--48859744 Score: 88
Period size: 20 Copynumber: 8.7 Consensus size: 20
48859561 TAGTGCTTCC
*
48859571 TAATTTTTGGTATCCCCTCA
1 TAATTTTTGGTATTCCCTCA
* *
48859591 T-GTTATTTGGTATTCTCTCA
1 TAATT-TTTGGTATTCCCTCA
** *
48859611 TAATTTTTGACACTT-TCTCA
1 TAATTTTTGGTA-TTCCCTCA
* * *
48859631 TATTTTTTGGTATTCACTTA
1 TAATTTTTGGTATTCCCTCA
* *
48859651 CAATTTTTTGTATTCCCTCA
1 TAATTTTTGGTATTCCCTCA
** *
48859671 TGTTTTTTGGTATTCCCTTAA
1 TAATTTTTGGTATTCCC-TCA
* *
48859692 AAAATTTTGGTACTT-CCTCA
1 TAATTTTTGGTA-TTCCCTCA
* * *
48859712 -ACAATTTCGATACTT-CCTCA
1 TA-ATTTTTGGTA-TTCCCTCA
48859732 TAATTTTTGGTAT
1 TAATTTTTGGTAT
48859745 GGTCTCAGAA
Statistics
Matches: 115, Mismatches: 31, Indels: 17
0.71 0.19 0.10
Matches are distributed among these distances:
19 6 0.05
20 90 0.78
21 17 0.15
22 2 0.02
ACGTcount: A:0.22, C:0.18, G:0.10, T:0.50
Consensus pattern (20 bp):
TAATTTTTGGTATTCCCTCA
Found at i:48861504 original size:34 final size:35
Alignment explanation
Indices: 48861407--48861504 Score: 94
Period size: 34 Copynumber: 2.9 Consensus size: 35
48861397 GCATTTAATT
* * * *
48861407 ATGCTTTTAACAGAACAATATGA-TAGC-AATCAAT
1 ATGCTTATAACAGATCAAT-TCAGTAGCAAATCAAA
* * * *
48861441 ATGCCTATAATAGTTCAATACAGTAGCAAAT-AAA
1 ATGCTTATAACAGATCAATTCAGTAGCAAATCAAA
48861475 ATGCTTATAACAGATCAATTCAGTAGCAAA
1 ATGCTTATAACAGATCAATTCAGTAGCAAA
48861505 AGTCATGCTT
Statistics
Matches: 50, Mismatches: 12, Indels: 4
0.76 0.18 0.06
Matches are distributed among these distances:
33 1 0.02
34 46 0.92
35 3 0.06
ACGTcount: A:0.45, C:0.15, G:0.12, T:0.28
Consensus pattern (35 bp):
ATGCTTATAACAGATCAATTCAGTAGCAAATCAAA
Found at i:48861865 original size:28 final size:28
Alignment explanation
Indices: 48861838--48861956 Score: 139
Period size: 28 Copynumber: 4.2 Consensus size: 28
48861828 GGGGAAATTG
* * *
48861838 TAAAATCTAAAAAACATGGACAAAATTG
1 TAAAATCTAAAAAACATGGGCAAAACTA
* * *
48861866 TAAAAATCTAAAAAATAGGGGCAGAACTA
1 T-AAAATCTAAAAAACATGGGCAAAACTA
* *
48861895 TAAAATTTAAAAAATATGGGCAAAACTA
1 TAAAATCTAAAAAACATGGGCAAAACTA
* *
48861923 TAAAATCTAGAAAACATGGGCCAAACTA
1 TAAAATCTAAAAAACATGGGCAAAACTA
48861951 TAAAAT
1 TAAAAT
48861957 ATGGAAAATA
Statistics
Matches: 77, Mismatches: 13, Indels: 2
0.84 0.14 0.02
Matches are distributed among these distances:
28 55 0.71
29 22 0.29
ACGTcount: A:0.55, C:0.11, G:0.13, T:0.21
Consensus pattern (28 bp):
TAAAATCTAAAAAACATGGGCAAAACTA
Found at i:48861898 original size:29 final size:28
Alignment explanation
Indices: 48861804--48861956 Score: 123
Period size: 28 Copynumber: 5.5 Consensus size: 28
48861794 AAAAAAAAGA
** *
48861804 GCAAAACTATAAAAT-TTGAAATTAGGG
1 GCAAAACTATAAAATCTAAAAAATAGGG
* * * *
48861831 G--AAATTGTAAAATCTAAAAAACATGG
1 GCAAAACTATAAAATCTAAAAAATAGGG
* * *
48861857 ACAAAATTGTAAAAATCTAAAAAATAGGG
1 GCAAAACTAT-AAAATCTAAAAAATAGGG
* * *
48861886 GCAGAACTATAAAATTTAAAAAATATGG
1 GCAAAACTATAAAATCTAAAAAATAGGG
* * *
48861914 GCAAAACTATAAAATCTAGAAAACATGG
1 GCAAAACTATAAAATCTAAAAAATAGGG
*
48861942 GCCAAACTATAAAAT
1 GCAAAACTATAAAAT
48861957 ATGGAAAATA
Statistics
Matches: 101, Mismatches: 21, Indels: 7
0.78 0.16 0.05
Matches are distributed among these distances:
25 10 0.10
26 7 0.07
27 1 0.01
28 61 0.60
29 22 0.22
ACGTcount: A:0.54, C:0.10, G:0.14, T:0.22
Consensus pattern (28 bp):
GCAAAACTATAAAATCTAAAAAATAGGG
Found at i:48861950 original size:56 final size:57
Alignment explanation
Indices: 48861838--48861956 Score: 145
Period size: 57 Copynumber: 2.1 Consensus size: 57
48861828 GGGGAAATTG
* * *
48861838 TAAAATCTAAAAAACATGGACAAAATTGTAAAAATCTAAAAAATAGGGGCAGAACTA
1 TAAAATCTAAAAAACATGGACAAAACTATAAAAATCTAAAAAATAGGGCCAGAACTA
* * *
48861895 TAAAATTTAAAAAATATGGGCAAAACTAT-AAAATCTAGAAAACAT-GGGCCA-AACTA
1 TAAAATCTAAAAAACATGGACAAAACTATAAAAATCTA-AAAA-ATAGGGCCAGAACTA
48861951 TAAAAT
1 TAAAAT
48861957 ATGGAAAATA
Statistics
Matches: 54, Mismatches: 6, Indels: 5
0.83 0.09 0.08
Matches are distributed among these distances:
56 19 0.35
57 33 0.61
58 2 0.04
ACGTcount: A:0.55, C:0.11, G:0.13, T:0.21
Consensus pattern (57 bp):
TAAAATCTAAAAAACATGGACAAAACTATAAAAATCTAAAAAATAGGGCCAGAACTA
Found at i:48865636 original size:31 final size:31
Alignment explanation
Indices: 48865601--48865661 Score: 95
Period size: 31 Copynumber: 2.0 Consensus size: 31
48865591 ATGTGTATGG
48865601 TTAAATCAAAATTAAAGTTTCAAGTATATAT
1 TTAAATCAAAATTAAAGTTTCAAGTATATAT
* **
48865632 TTAAATCACAATTAGTGTTTCAAGTATATA
1 TTAAATCAAAATTAAAGTTTCAAGTATATA
48865662 ATTACACCAA
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
31 27 1.00
ACGTcount: A:0.44, C:0.08, G:0.08, T:0.39
Consensus pattern (31 bp):
TTAAATCAAAATTAAAGTTTCAAGTATATAT
Found at i:48875674 original size:19 final size:20
Alignment explanation
Indices: 48875645--48875691 Score: 78
Period size: 19 Copynumber: 2.4 Consensus size: 20
48875635 TAGTAAAATG
*
48875645 TTTTCTAGAAAATGATTTAT
1 TTTTCTAGAAAATGATTTAC
48875665 TTTTCT-GAAAATGATTTAC
1 TTTTCTAGAAAATGATTTAC
48875684 TTTTCTAG
1 TTTTCTAG
48875692 TATTTAGATG
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
19 18 0.72
20 7 0.28
ACGTcount: A:0.30, C:0.09, G:0.11, T:0.51
Consensus pattern (20 bp):
TTTTCTAGAAAATGATTTAC
Found at i:48877079 original size:32 final size:32
Alignment explanation
Indices: 48877043--48877122 Score: 90
Period size: 32 Copynumber: 2.5 Consensus size: 32
48877033 TGTCAATCAC
* *
48877043 TTCAATATCCAATAAGCTT-AAAACATAATAAA
1 TTCAATATCCAACAA-ATTCAAAACATAATAAA
* * *
48877075 TTCAATATCTAACAAATTCAAGACATAATAAT
1 TTCAATATCCAACAAATTCAAAACATAATAAA
*
48877107 TTCAAAATCCAACAAA
1 TTCAATATCCAACAAA
48877123 CTAAAATTTC
Statistics
Matches: 40, Mismatches: 7, Indels: 2
0.82 0.14 0.04
Matches are distributed among these distances:
31 2 0.05
32 38 0.95
ACGTcount: A:0.53, C:0.17, G:0.03, T:0.28
Consensus pattern (32 bp):
TTCAATATCCAACAAATTCAAAACATAATAAA
Found at i:48898261 original size:24 final size:25
Alignment explanation
Indices: 48898183--48898263 Score: 87
Period size: 25 Copynumber: 3.3 Consensus size: 25
48898173 TAAGTTTCTC
48898183 CGAGCTGAATAA-CGGTAAGCTCATA
1 CGAGCTGAA-AATCGGTAAGCTCATA
** *
48898208 CGAGCTGTGAATTGGTAAGCTC-TCA
1 CGAGCTGAAAATCGGTAAGCTCAT-A
*
48898233 AGAGCT-AAAATCGGTAAGCTCATA
1 CGAGCTGAAAATCGGTAAGCTCATA
48898257 CGAGCTG
1 CGAGCTG
48898264 TGGTGTGTCC
Statistics
Matches: 44, Mismatches: 8, Indels: 8
0.73 0.13 0.13
Matches are distributed among these distances:
24 21 0.48
25 23 0.52
ACGTcount: A:0.32, C:0.20, G:0.26, T:0.22
Consensus pattern (25 bp):
CGAGCTGAAAATCGGTAAGCTCATA
Found at i:48903869 original size:12 final size:12
Alignment explanation
Indices: 48903852--48903878 Score: 54
Period size: 12 Copynumber: 2.2 Consensus size: 12
48903842 ACACGCCCGA
48903852 GTGCTAGGCCGT
1 GTGCTAGGCCGT
48903864 GTGCTAGGCCGT
1 GTGCTAGGCCGT
48903876 GTG
1 GTG
48903879 TAAATTGGAG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 15 1.00
ACGTcount: A:0.07, C:0.22, G:0.44, T:0.26
Consensus pattern (12 bp):
GTGCTAGGCCGT
Found at i:48905121 original size:24 final size:24
Alignment explanation
Indices: 48905068--48905135 Score: 84
Period size: 24 Copynumber: 2.8 Consensus size: 24
48905058 GCTGAATAAC
* * *
48905068 GGTAAGCTTATACAAGCTGTGAATT
1 GGTAAGCTCATACGAGCTG-AAATT
48905093 GGTAAGCTC-TCACGAGCTGAAATT
1 GGTAAGCTCAT-ACGAGCTGAAATT
48905117 GGTAAGCTCATACGAGCTG
1 GGTAAGCTCATACGAGCTG
48905136 TGCTGTGTCC
Statistics
Matches: 38, Mismatches: 3, Indels: 5
0.83 0.07 0.11
Matches are distributed among these distances:
24 22 0.58
25 16 0.42
ACGTcount: A:0.29, C:0.18, G:0.26, T:0.26
Consensus pattern (24 bp):
GGTAAGCTCATACGAGCTGAAATT
Found at i:48908157 original size:2 final size:2
Alignment explanation
Indices: 48908150--48908176 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
48908140 GTGGAGCTTT
48908150 TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA T
48908177 TTATTTATTA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:48913235 original size:18 final size:18
Alignment explanation
Indices: 48913212--48913296 Score: 72
Period size: 18 Copynumber: 4.7 Consensus size: 18
48913202 ATATGTATTT
48913212 TTATTAA-TTTTTTATATA
1 TTATTAATTTTTTTA-ATA
48913230 TTATTAATATTTTTTGAAT-
1 TTATTAAT-TTTTTT-AATA
48913249 TT-TTGAATTTTTTTACATA
1 TTATT-AATTTTTTTA-ATA
*
48913268 -T-TTAATTTTTATAATA
1 TTATTAATTTTTTTAATA
48913284 TTTATTAATTTTT
1 -TTATTAATTTTT
48913297 AATAATTTTT
Statistics
Matches: 57, Mismatches: 1, Indels: 17
0.76 0.01 0.23
Matches are distributed among these distances:
16 3 0.05
17 10 0.18
18 21 0.37
19 14 0.25
20 8 0.14
21 1 0.02
ACGTcount: A:0.31, C:0.01, G:0.02, T:0.66
Consensus pattern (18 bp):
TTATTAATTTTTTTAATA
Found at i:48913276 original size:16 final size:16
Alignment explanation
Indices: 48913254--48913287 Score: 50
Period size: 17 Copynumber: 2.1 Consensus size: 16
48913244 TGAATTTTTG
*
48913254 AATTTTTTTACATATTT
1 AATTTTTATA-ATATTT
48913271 AATTTTTATAATATTT
1 AATTTTTATAATATTT
48913287 A
1 A
48913288 TTAATTTTTA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 7 0.44
17 9 0.56
ACGTcount: A:0.35, C:0.03, G:0.00, T:0.62
Consensus pattern (16 bp):
AATTTTTATAATATTT
Found at i:48913289 original size:20 final size:21
Alignment explanation
Indices: 48913266--48913308 Score: 63
Period size: 20 Copynumber: 2.1 Consensus size: 21
48913256 TTTTTTTACA
48913266 TATTTAATTTTT-ATAATATT
1 TATTTAATTTTTAATAATATT
*
48913286 TA-TTAATTTTTAATAATTTT
1 TATTTAATTTTTAATAATATT
48913306 TAT
1 TAT
48913309 AATTTAAAAA
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
19 9 0.45
20 11 0.55
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (21 bp):
TATTTAATTTTTAATAATATT
Found at i:48913294 original size:36 final size:39
Alignment explanation
Indices: 48913210--48913296 Score: 96
Period size: 38 Copynumber: 2.4 Consensus size: 39
48913200 AGATATGTAT
* *
48913210 TTTTATTAA-TTTTTTATATATTATTAATATTTTTTGAA
1 TTTTATTAATTTTTTTACATATTATTAATATTTTATGAA
*
48913248 TTTT-TGAATTTTTTTACATA-T-TTAAT-TTTTAT-AA
1 TTTTATTAATTTTTTTACATATTATTAATATTTTATGAA
48913282 TATTTATTAATTTTT
1 T-TTTATTAATTTTT
48913297 AATAATTTTT
Statistics
Matches: 42, Mismatches: 4, Indels: 8
0.78 0.07 0.15
Matches are distributed among these distances:
34 3 0.07
35 8 0.19
36 13 0.31
37 4 0.10
38 14 0.33
ACGTcount: A:0.30, C:0.01, G:0.02, T:0.67
Consensus pattern (39 bp):
TTTTATTAATTTTTTTACATATTATTAATATTTTATGAA
Found at i:48913297 original size:10 final size:9
Alignment explanation
Indices: 48913270--48913313 Score: 61
Period size: 9 Copynumber: 4.7 Consensus size: 9
48913260 TTTACATATT
48913270 TAATTTTTA
1 TAATTTTTA
*
48913279 TAATATTTA
1 TAATTTTTA
48913288 TTAATTTTTAA
1 -TAATTTTT-A
48913299 TAATTTTTA
1 TAATTTTTA
48913308 TAATTT
1 TAATTT
48913314 AAAAAAAAGT
Statistics
Matches: 31, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
9 15 0.48
10 15 0.48
11 1 0.03
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (9 bp):
TAATTTTTA
Found at i:48913394 original size:32 final size:32
Alignment explanation
Indices: 48913339--48913400 Score: 79
Period size: 32 Copynumber: 1.9 Consensus size: 32
48913329 ACTCATCTTG
*
48913339 AATGAATCTAGACAAACGGTTGTCAAGATTTA
1 AATGAATCTAGACAAACGATTGTCAAGATTTA
* ** *
48913371 AATGAATCTGGACAAATTATTGTCCAGATT
1 AATGAATCTAGACAAACGATTGTCAAGATT
48913401 CATTCTAGAT
Statistics
Matches: 25, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
32 25 1.00
ACGTcount: A:0.39, C:0.13, G:0.18, T:0.31
Consensus pattern (32 bp):
AATGAATCTAGACAAACGATTGTCAAGATTTA
Found at i:48914739 original size:17 final size:16
Alignment explanation
Indices: 48914717--48914773 Score: 53
Period size: 17 Copynumber: 3.4 Consensus size: 16
48914707 ATAGATTAAT
48914717 TTATATTTTATATATCA
1 TTATATTTTAT-TATCA
**
48914734 TTATATTAAATTAATCA
1 TTATATTTTATT-ATCA
*
48914751 -AATATTTTATGTATCA
1 TTATATTTTAT-TATCA
48914767 TTATATT
1 TTATATT
48914774 AAATTATTTA
Statistics
Matches: 31, Mismatches: 6, Indels: 6
0.72 0.14 0.14
Matches are distributed among these distances:
16 12 0.39
17 19 0.61
ACGTcount: A:0.39, C:0.05, G:0.02, T:0.54
Consensus pattern (16 bp):
TTATATTTTATTATCA
Found at i:48914757 original size:33 final size:33
Alignment explanation
Indices: 48914719--48914808 Score: 121
Period size: 33 Copynumber: 2.8 Consensus size: 33
48914709 AGATTAATTT
48914719 ATATTTTATATATCATTATATTAAATTAATCAA
1 ATATTTTATATATCATTATATTAAATTAATCAA
* * *
48914752 ATATTTTATGTATCATTATATTAAATTATTTAA
1 ATATTTTATATATCATTATATTAAATTAATCAA
* *
48914785 ATA--TAATTTATCATTATATTAAAT
1 ATATTTTATATATCATTATATTAAAT
48914809 CATTTAAATT
Statistics
Matches: 52, Mismatches: 5, Indels: 2
0.88 0.08 0.03
Matches are distributed among these distances:
31 19 0.37
33 33 0.63
ACGTcount: A:0.43, C:0.04, G:0.01, T:0.51
Consensus pattern (33 bp):
ATATTTTATATATCATTATATTAAATTAATCAA
Found at i:48914800 original size:31 final size:32
Alignment explanation
Indices: 48914729--48914817 Score: 117
Period size: 31 Copynumber: 2.8 Consensus size: 32
48914719 ATATTTTATA
* * *
48914729 TATCATTATATTAAATTAATCAAATATTTTATG
1 TATCATTATATTAAATTATTTAAATA-TTAATG
*
48914762 TATCATTATATTAAATTATTTAAATA-TAATT
1 TATCATTATATTAAATTATTTAAATATTAATG
*
48914793 TATCATTATATTAAATCATTTAAAT
1 TATCATTATATTAAATTATTTAAAT
48914818 TTAGTTCATT
Statistics
Matches: 51, Mismatches: 5, Indels: 2
0.88 0.09 0.03
Matches are distributed among these distances:
31 27 0.53
33 24 0.47
ACGTcount: A:0.44, C:0.06, G:0.01, T:0.49
Consensus pattern (32 bp):
TATCATTATATTAAATTATTTAAATATTAATG
Found at i:48919789 original size:14 final size:15
Alignment explanation
Indices: 48919753--48919790 Score: 60
Period size: 15 Copynumber: 2.6 Consensus size: 15
48919743 TAAAAATTAA
48919753 AAAAATTAAATGATG
1 AAAAATTAAATGATG
*
48919768 AGAAATTAAATGAT-
1 AAAAATTAAATGATG
48919782 AAAAATTAA
1 AAAAATTAA
48919791 GTATTCAAAA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
14 8 0.38
15 13 0.62
ACGTcount: A:0.63, C:0.00, G:0.11, T:0.26
Consensus pattern (15 bp):
AAAAATTAAATGATG
Found at i:48932575 original size:16 final size:15
Alignment explanation
Indices: 48932537--48932586 Score: 55
Period size: 16 Copynumber: 3.1 Consensus size: 15
48932527 ATTAATTTCT
*
48932537 TAAAAAATTCAAAACA
1 TAAAAAATTTAAAA-A
48932553 TATAAAAATATTAAAAA
1 TA-AAAAAT-TTAAAAA
48932570 TAAAAAATTTTAAAAA
1 TAAAAAA-TTTAAAAA
48932586 T
1 T
48932587 TTTAATTAAT
Statistics
Matches: 30, Mismatches: 1, Indels: 6
0.81 0.03 0.16
Matches are distributed among these distances:
16 15 0.50
17 10 0.33
18 5 0.17
ACGTcount: A:0.68, C:0.04, G:0.00, T:0.28
Consensus pattern (15 bp):
TAAAAAATTTAAAAA
Found at i:48934041 original size:6 final size:6
Alignment explanation
Indices: 48934032--48934059 Score: 56
Period size: 6 Copynumber: 4.7 Consensus size: 6
48934022 ATTGAGGTTG
48934032 AAAACA AAAACA AAAACA AAAACA AAAA
1 AAAACA AAAACA AAAACA AAAACA AAAA
48934060 AATTGGCGGG
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 22 1.00
ACGTcount: A:0.86, C:0.14, G:0.00, T:0.00
Consensus pattern (6 bp):
AAAACA
Found at i:48934164 original size:17 final size:18
Alignment explanation
Indices: 48934142--48934184 Score: 54
Period size: 17 Copynumber: 2.5 Consensus size: 18
48934132 TTTTATTGTT
*
48934142 TATTATAAT-AATTTTTA
1 TATTATAATAAATGTTTA
48934159 TATTAT-ATAAATGTTTA
1 TATTATAATAAATGTTTA
*
48934176 TATTTTAAT
1 TATTATAAT
48934185 TTATTGTTAA
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
16 2 0.09
17 18 0.82
18 2 0.09
ACGTcount: A:0.40, C:0.00, G:0.02, T:0.58
Consensus pattern (18 bp):
TATTATAATAAATGTTTA
Found at i:48934362 original size:144 final size:146
Alignment explanation
Indices: 48934192--48934497 Score: 451
Period size: 144 Copynumber: 2.1 Consensus size: 146
48934182 AATTTATTGT
48934192 TAATTTTTAGATTTAATATTTAAGATTATATTTTTGTTTGTAAAGATTATATTTGTGTTTAA-TG
1 TAATTTTTAGATTTAATATTTAAGATTATATTTTTGTTTGTAAAGATTATATTTGTGTTTAAGT-
48934256 TGTAGGGATAGA-TTAAAATA-TTTCTAATGTA-TG-TTTCTTGAGTTTGTAATAATAATTTGTA
65 TGTAGGGATAGACTT-AAATAGTTT-TAATGTATTGTTTTCTTGAGTTTGTAATAATAATTTGTA
48934317 TATTATAAAATTTTACATA
128 TATTATAAAATTTTACATA
* *
48934336 TAATATTTAGATTTAATTTTTAAGATTATATTTTTGTTTGTAAAGATTATATTTGTGTTTAAGTT
1 TAATTTTTAGATTTAATATTTAAGATTATATTTTTGTTTGTAAAGATTATATTTGTGTTTAAGTT
** * *
48934401 GTAGGGATAGACTTGGATAGTTTTAATGTATTGTTTTTTTTTTAGTTTGTAATAATAATTTGTAT
66 GTAGGGATAGACTTAAATAGTTTTAATGTATTG--TTTTCTTGAGTTTGTAATAATAATTTGTAT
* *
48934466 ATTATAATATTTTACATT
129 ATTATAAAATTTTACATA
48934484 TAATTTTTAAGATT
1 TAATTTTT-AGATT
48934498 ATAAAAAATT
Statistics
Matches: 145, Mismatches: 9, Indels: 11
0.88 0.05 0.07
Matches are distributed among these distances:
144 82 0.57
145 8 0.06
148 50 0.34
149 5 0.03
ACGTcount: A:0.32, C:0.02, G:0.13, T:0.53
Consensus pattern (146 bp):
TAATTTTTAGATTTAATATTTAAGATTATATTTTTGTTTGTAAAGATTATATTTGTGTTTAAGTT
GTAGGGATAGACTTAAATAGTTTTAATGTATTGTTTTCTTGAGTTTGTAATAATAATTTGTATAT
TATAAAATTTTACATA
Found at i:48938210 original size:23 final size:22
Alignment explanation
Indices: 48938172--48938232 Score: 61
Period size: 21 Copynumber: 2.6 Consensus size: 22
48938162 TATAAAATAA
*
48938172 ATTAAAAATAATATATATCGGCTTCT
1 ATTAAAAA-AATATATA---GCTCCT
*
48938198 ATTACAAAAATAT-TAGCTCCT
1 ATTAAAAAAATATATAGCTCCT
48938219 ATTAAAAAAATATA
1 ATTAAAAAAATATA
48938233 GCAACAAAAA
Statistics
Matches: 31, Mismatches: 3, Indels: 6
0.77 0.08 0.15
Matches are distributed among these distances:
21 17 0.55
24 2 0.06
25 5 0.16
26 7 0.23
ACGTcount: A:0.49, C:0.11, G:0.05, T:0.34
Consensus pattern (22 bp):
ATTAAAAAAATATATAGCTCCT
Found at i:48938530 original size:29 final size:29
Alignment explanation
Indices: 48938485--48938548 Score: 76
Period size: 29 Copynumber: 2.2 Consensus size: 29
48938475 TTTTTAACTC
*
48938485 TTTTTTTTCTCCCCTTCTAC-TAAACAGA
1 TTTTTTTTCTCCCCTTCAACATAAACAGA
* * *
48938513 TTATTTTTTCTTCTCTTCAACATAAATAGA
1 TT-TTTTTTCTCCCCTTCAACATAAACAGA
48938543 TTTTTT
1 TTTTTT
48938549 GCTGAGGGAG
Statistics
Matches: 30, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
28 2 0.07
29 19 0.63
30 9 0.30
ACGTcount: A:0.23, C:0.20, G:0.03, T:0.53
Consensus pattern (29 bp):
TTTTTTTTCTCCCCTTCAACATAAACAGA
Found at i:48939082 original size:26 final size:26
Alignment explanation
Indices: 48939036--48939099 Score: 78
Period size: 27 Copynumber: 2.4 Consensus size: 26
48939026 CAGCTCATTC
48939036 CGTAATTAATTTTCCATATCCCA-TTT
1 CGTAATTAATTTTCCA-ATCCCATTTT
*
48939062 CTGTAATTAATTTTCTC-ATCCTATTTT
1 C-GTAATTAATTTTC-CAATCCCATTTT
48939089 CGTAATTAATT
1 CGTAATTAATT
48939100 AAATTTTTAT
Statistics
Matches: 34, Mismatches: 1, Indels: 6
0.83 0.02 0.15
Matches are distributed among these distances:
26 16 0.47
27 17 0.50
28 1 0.03
ACGTcount: A:0.27, C:0.19, G:0.05, T:0.50
Consensus pattern (26 bp):
CGTAATTAATTTTCCAATCCCATTTT
Found at i:48939089 original size:27 final size:25
Alignment explanation
Indices: 48939031--48939099 Score: 77
Period size: 26 Copynumber: 2.6 Consensus size: 25
48939021 ACAAGCAGCT
*
48939031 CATTCCGTAATTAATTTTCCATATCC
1 CATTTCGTAATTAATTTTCCA-ATCC
48939057 CATTTCTGTAATTAATTTTCTC-ATCC
1 CATTTC-GTAATTAATTTTC-CAATCC
*
48939083 TATTTTCGTAATTAATT
1 CA-TTTCGTAATTAATT
48939100 AAATTTTTAT
Statistics
Matches: 38, Mismatches: 2, Indels: 6
0.83 0.04 0.13
Matches are distributed among these distances:
26 20 0.53
27 17 0.45
28 1 0.03
ACGTcount: A:0.26, C:0.20, G:0.04, T:0.49
Consensus pattern (25 bp):
CATTTCGTAATTAATTTTCCAATCC
Found at i:48943932 original size:87 final size:87
Alignment explanation
Indices: 48943808--48943994 Score: 236
Period size: 87 Copynumber: 2.1 Consensus size: 87
48943798 ACTGAATTTT
* * * *
48943808 AAGGAATA-CCTTTGTGGCAAAACTTAGGAAAGGTAAGCCAATGTGGTGAACCTTTGAAAGGAAA
1 AAGGAA-AGCCTTTATGGAAAAACTTAGGAAAGATAAGCCAATGTAGTGAACCTTTGAAAGGAAA
* **
48943872 TGCCTCTATGTTAAAACTCTGGA
65 TACCTCTATGGAAAAACTCTGGA
*
48943895 CAA-GAAAGCCTTTATGGAAAAACTTA-GAAACGATAAGCCTATGTAGTGAACCTTTGAAAGGAA
1 -AAGGAAAGCCTTTATGGAAAAACTTAGGAAA-GATAAGCCAATGTAGTGAACCTTTGAAAGGAA
* *
48943958 ATACCTTTATGGAAAAACTTTGGA
64 ATACCTCTATGGAAAAACTCTGGA
48943982 AAGGAAAGCCTTT
1 AAGGAAAGCCTTT
48943995 GTGGCGAGTA
Statistics
Matches: 86, Mismatches: 10, Indels: 7
0.83 0.10 0.07
Matches are distributed among these distances:
86 7 0.08
87 77 0.90
88 2 0.02
ACGTcount: A:0.39, C:0.14, G:0.22, T:0.25
Consensus pattern (87 bp):
AAGGAAAGCCTTTATGGAAAAACTTAGGAAAGATAAGCCAATGTAGTGAACCTTTGAAAGGAAAT
ACCTCTATGGAAAAACTCTGGA
Found at i:48943993 original size:29 final size:28
Alignment explanation
Indices: 48943859--48943994 Score: 94
Period size: 29 Copynumber: 4.7 Consensus size: 28
48943849 TGTGGTGAAC
* **
48943859 CTTTGAAAGGAAATGCCTCTATGTTAAAA
1 CTTTGAAAGGAAA-GCCTTTATGGAAAAA
*
48943888 CTCTGGACAA-GAAAGCCTTTATGGAAAAA
1 CT-TTGA-AAGGAAAGCCTTTATGGAAAAA
* * * * * ** *
48943917 CTTAGAAACGATAAGCCTATGTAGTGAAC
1 CTTTGAAAGGA-AAGCCTTTATGGAAAAA
*
48943946 CTTTGAAAGGAAATACCTTTATGGAAAAA
1 CTTTGAAAGGAAA-GCCTTTATGGAAAAA
48943975 CTTTGGAAAGGAAAGCCTTT
1 CTTT-GAAAGGAAAGCCTTT
48943995 GTGGCGAGTA
Statistics
Matches: 80, Mismatches: 21, Indels: 12
0.71 0.19 0.11
Matches are distributed among these distances:
27 2 0.03
28 7 0.09
29 53 0.66
30 16 0.20
31 2 0.03
ACGTcount: A:0.39, C:0.15, G:0.20, T:0.26
Consensus pattern (28 bp):
CTTTGAAAGGAAAGCCTTTATGGAAAAA
Found at i:48945745 original size:26 final size:26
Alignment explanation
Indices: 48945709--48945770 Score: 81
Period size: 26 Copynumber: 2.4 Consensus size: 26
48945699 TTCAAATTCA
48945709 GGAATGCTCATACAAGCACATAAACG
1 GGAATGCTCATACAAGCACATAAACG
* * * *
48945735 GGAATGCTCATACGAGTACATTAATG
1 GGAATGCTCATACAAGCACATAAACG
48945761 GGAA-GCTCAT
1 GGAATGCTCAT
48945771 GTGAGCTATG
Statistics
Matches: 32, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
25 6 0.19
26 26 0.81
ACGTcount: A:0.37, C:0.19, G:0.23, T:0.21
Consensus pattern (26 bp):
GGAATGCTCATACAAGCACATAAACG
Found at i:48945801 original size:25 final size:25
Alignment explanation
Indices: 48945734--48945801 Score: 77
Period size: 25 Copynumber: 2.7 Consensus size: 25
48945724 GCACATAAAC
48945734 GGGAATGCTCATACGAG-TACATTAAT
1 GGGAA-GCTCATACGAGCTA-ATTAAT
**
48945760 GGGAAGCTCATGTGAGCT-ATGTAAT
1 GGGAAGCTCATACGAGCTAAT-TAAT
48945785 GGGAAGCTCATACGAGC
1 GGGAAGCTCATACGAGC
48945802 CAATATCGAG
Statistics
Matches: 36, Mismatches: 4, Indels: 5
0.80 0.09 0.11
Matches are distributed among these distances:
24 2 0.06
25 28 0.78
26 6 0.17
ACGTcount: A:0.31, C:0.16, G:0.29, T:0.24
Consensus pattern (25 bp):
GGGAAGCTCATACGAGCTAATTAAT
Found at i:48945837 original size:23 final size:24
Alignment explanation
Indices: 48945734--48945840 Score: 65
Period size: 25 Copynumber: 4.4 Consensus size: 24
48945724 GCACATAAAC
* * *
48945734 GGGAATGCTCATACGAGTACATTAAT
1 GGGAA-GCTCATACGAG-CCAATATT
** * * *
48945760 GGGAAGCTCATGTGAGCTATGTAAT
1 GGGAAGCTCATACGAGCCA-ATATT
*
48945785 GGGAAGCTCATACGAGCCAATATC
1 GGGAAGCTCATACGAGCCAATATT
* *
48945809 GAGAAGTTCA-AGCGAG-CAATATT
1 GGGAAGCTCATA-CGAGCCAATATT
48945832 GGGAAGCTC
1 GGGAAGCTC
48945841 CGAAGAGCCA
Statistics
Matches: 63, Mismatches: 16, Indels: 7
0.73 0.19 0.08
Matches are distributed among these distances:
23 14 0.22
24 15 0.24
25 29 0.46
26 5 0.08
ACGTcount: A:0.33, C:0.17, G:0.28, T:0.22
Consensus pattern (24 bp):
GGGAAGCTCATACGAGCCAATATT
Found at i:48945863 original size:25 final size:25
Alignment explanation
Indices: 48945835--48945902 Score: 82
Period size: 26 Copynumber: 2.7 Consensus size: 25
48945825 CAATATTGGG
*
48945835 AAGCTCCGAAGAGCCATTAATCGGA
1 AAGCTCCGAAGAGCCATTAAACGGA
* * *
48945860 AAGCTCATGAAGAGCCTTTAAACGGT
1 AAGCTC-CGAAGAGCCATTAAACGGA
*
48945886 AAGCTCCGAAAAGCCAT
1 AAGCTCCGAAGAGCCAT
48945903 ATATCGGGAC
Statistics
Matches: 35, Mismatches: 7, Indels: 2
0.80 0.16 0.05
Matches are distributed among these distances:
25 14 0.40
26 21 0.60
ACGTcount: A:0.37, C:0.24, G:0.22, T:0.18
Consensus pattern (25 bp):
AAGCTCCGAAGAGCCATTAAACGGA
Found at i:48951732 original size:21 final size:20
Alignment explanation
Indices: 48951706--48951746 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 20
48951696 CTCTAAACCT
*
48951706 TAAACCTCAATCTCCAAGCCC
1 TAAACCT-AAACTCCAAGCCC
*
48951727 TAAACCTAAACTCTAAGCCC
1 TAAACCTAAACTCCAAGCCC
48951747 AAATCACAAA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
20 11 0.61
21 7 0.39
ACGTcount: A:0.37, C:0.39, G:0.05, T:0.20
Consensus pattern (20 bp):
TAAACCTAAACTCCAAGCCC
Found at i:48952302 original size:134 final size:131
Alignment explanation
Indices: 48952095--48952506 Score: 438
Period size: 133 Copynumber: 3.1 Consensus size: 131
48952085 GAACCGTTTC
* * * * *
48952095 CGGCGTTTTTAACATTTCGCCACTAAAG-CATAAAAAGGAAACAACAAAACGGTACCGTTTTGCT
1 CGGCGTTTTTTACAATGCGCCACTAAAGAAAT-AAAATGAAACAACAAAACGGTA-CGTTTTGCT
* *
48952159 CAAAATTTTTCCTCAAATTAGATTTCTTTACCGGCGTTTCTCCAATAACGCCACTATATCCCAAT
64 CAAATTTTTTCCTCAAATTAGATTTCTTTACCGGCGTTTCTCCAA-AACGCCGCTATAT-CCAAT
*
48952224 ATTTG
127 TTTTG
* * *
48952229 CGGCGTTTTTTACAATGCGCCACTAAGGAAATAAAATGAAGCAATAAAACGGTAGCGTTTTG-TC
1 CGGCGTTTTTTACAATGCGCCACTAAAGAAATAAAATGAAACAACAAAACGGTA-CGTTTTGCT-
* * * * *
48952293 CAAATTTTTTCCTCAAATTAGATATCTTTATCGGCGTTTC-CCTGAAAACGCCGCT-GATGCATT
64 CAAATTTTTTCCTCAAATTAGATTTCTTTACCGGCGTTTCTCC--AAAACGCCGCTATATCCAAT
*
48952356 CTTTTC
127 -TTTTG
* * *
48952362 CGACGTTTTTTAAAATGCGCCACTAAAGAAATAAAATGAAACAACAAAACGGTACTGTTTTACTC
1 CGGCGTTTTTTACAATGCGCCACTAAAGAAATAAAATGAAACAACAAAACGGTAC-GTTTTGCTC
* * * * *
48952427 AGATTTTTTCTTCAAATTTG-TTATCGTTACCGGCGTTTCTCAGAAAACGCCGCTATATTCCAAT
65 AAATTTTTTCCTCAAATTAGATT-TCTTTACCGGCGTTTCTC-CAAAACGCCGCTATA-TCCAA-
48952491 TTTTTG
126 TTTTTG
48952497 CGGCGTTTTT
1 CGGCGTTTTT
48952507 GGGGAAGCGC
Statistics
Matches: 229, Mismatches: 36, Indels: 25
0.79 0.12 0.09
Matches are distributed among these distances:
132 5 0.02
133 105 0.46
134 98 0.43
135 20 0.09
136 1 0.00
ACGTcount: A:0.30, C:0.21, G:0.15, T:0.33
Consensus pattern (131 bp):
CGGCGTTTTTTACAATGCGCCACTAAAGAAATAAAATGAAACAACAAAACGGTACGTTTTGCTCA
AATTTTTTCCTCAAATTAGATTTCTTTACCGGCGTTTCTCCAAAACGCCGCTATATCCAATTTTT
G
Found at i:48953410 original size:27 final size:29
Alignment explanation
Indices: 48953322--48953419 Score: 82
Period size: 28 Copynumber: 3.5 Consensus size: 29
48953312 AATGGTTGAA
* *
48953322 ATTATATTTATATTGAAGAATATATTATAA-
1 ATTATATTTATATT-AAAAAT-TATTAAAAT
**
48953352 ATTA-AAAT-TATTAAAAATTATTAAAAT
1 ATTATATTTATATTAAAAATTATTAAAAT
*
48953379 -TT-TATTTATATTAAGAAATTGTTAAAA-
1 ATTATATTTATATTAA-AAATTATTAAAAT
48953406 ATTATATTTATATT
1 ATTATATTTATATT
48953420 GATTAATAAA
Statistics
Matches: 55, Mismatches: 7, Indels: 13
0.73 0.09 0.17
Matches are distributed among these distances:
26 11 0.20
27 11 0.20
28 17 0.31
29 12 0.22
30 4 0.07
ACGTcount: A:0.48, C:0.00, G:0.04, T:0.48
Consensus pattern (29 bp):
ATTATATTTATATTAAAAATTATTAAAAT
Found at i:48953434 original size:23 final size:21
Alignment explanation
Indices: 48953396--48953442 Score: 58
Period size: 23 Copynumber: 2.1 Consensus size: 21
48953386 ATATTAAGAA
* *
48953396 ATTGTTAAAAATTATATTTAT
1 ATTGTTAAAAAATATATTAAT
48953417 ATTGATTAATAAAATATATTAAT
1 ATTG-TTAA-AAAATATATTAAT
48953440 ATT
1 ATT
48953443 AAACTATGAT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
21 4 0.18
22 4 0.18
23 14 0.64
ACGTcount: A:0.47, C:0.00, G:0.04, T:0.49
Consensus pattern (21 bp):
ATTGTTAAAAAATATATTAAT
Found at i:48955669 original size:17 final size:17
Alignment explanation
Indices: 48955630--48955665 Score: 58
Period size: 16 Copynumber: 2.2 Consensus size: 17
48955620 CAAAAATTTG
48955630 AAAGA-AAAAGAAAGAA
1 AAAGAGAAAAGAAAGAA
48955646 AAAGAGAAAAG-AAGAA
1 AAAGAGAAAAGAAAGAA
48955662 AAAG
1 AAAG
48955666 GAGATGTACG
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
16 14 0.74
17 5 0.26
ACGTcount: A:0.78, C:0.00, G:0.22, T:0.00
Consensus pattern (17 bp):
AAAGAGAAAAGAAAGAA
Found at i:48956039 original size:20 final size:20
Alignment explanation
Indices: 48956003--48956040 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
48955993 GTGGAATTTG
*
48956003 TATGAAAATATAGAATTAAA
1 TATGAAAATATAAAATTAAA
48956023 TATGAAGAATA-AAAATTA
1 TATGAA-AATATAAAATTA
48956041 GCCTCGATTT
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:0.00, G:0.11, T:0.29
Consensus pattern (20 bp):
TATGAAAATATAAAATTAAA
Found at i:48960046 original size:9 final size:9
Alignment explanation
Indices: 48960026--48960101 Score: 84
Period size: 9 Copynumber: 8.4 Consensus size: 9
48960016 TTTGGTTAAA
*
48960026 AATTCACCG
1 AATTAACCG
*
48960035 AATTAACTG
1 AATTAACCG
48960044 AATT-ACCTG
1 AATTAACC-G
48960053 AATTAACCG
1 AATTAACCG
*
48960062 GATT-ACTCG
1 AATTAAC-CG
*
48960071 AATTACCCG
1 AATTAACCG
48960080 AATTAACCG
1 AATTAACCG
48960089 AATTAACCG
1 AATTAACCG
48960098 AATT
1 AATT
48960102 GAATAACTAC
Statistics
Matches: 56, Mismatches: 7, Indels: 8
0.79 0.10 0.11
Matches are distributed among these distances:
8 4 0.07
9 48 0.86
10 4 0.07
ACGTcount: A:0.38, C:0.22, G:0.12, T:0.28
Consensus pattern (9 bp):
AATTAACCG
Found at i:48960066 original size:27 final size:27
Alignment explanation
Indices: 48960026--48960101 Score: 100
Period size: 27 Copynumber: 2.8 Consensus size: 27
48960016 TTTGGTTAAA
* *
48960026 AATTCACCGAATTAACTGAATTACCTG
1 AATTAACCGAATTAACTGAATTACCCG
*
48960053 AATTAACCGGATT-ACTCGAATTACCCG
1 AATTAACCGAATTAACT-GAATTACCCG
*
48960080 AATTAACCGAATTAACCGAATT
1 AATTAACCGAATTAACTGAATT
48960102 GAATAACTAC
Statistics
Matches: 42, Mismatches: 5, Indels: 4
0.82 0.10 0.08
Matches are distributed among these distances:
26 3 0.07
27 37 0.88
28 2 0.05
ACGTcount: A:0.38, C:0.22, G:0.12, T:0.28
Consensus pattern (27 bp):
AATTAACCGAATTAACTGAATTACCCG
Found at i:48960197 original size:6 final size:6
Alignment explanation
Indices: 48960141--48960181 Score: 82
Period size: 6 Copynumber: 6.8 Consensus size: 6
48960131 ACTTTTAGAC
48960141 TTTAGT TTTAGT TTTAGT TTTAGT TTTAGT TTTAGT TTTAG
1 TTTAGT TTTAGT TTTAGT TTTAGT TTTAGT TTTAGT TTTAG
48960182 AATTTTATTT
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 35 1.00
ACGTcount: A:0.17, C:0.00, G:0.17, T:0.66
Consensus pattern (6 bp):
TTTAGT
Found at i:48960205 original size:20 final size:20
Alignment explanation
Indices: 48960146--48960194 Score: 75
Period size: 18 Copynumber: 2.5 Consensus size: 20
48960136 TAGACTTTAG
48960146 TTTTAGTTTTAGTTTTAG--
1 TTTTAGTTTTAGTTTTAGAA
48960164 TTTTAGTTTTAGTTTTAGAA
1 TTTTAGTTTTAGTTTTAGAA
*
48960184 TTTTATTTTTA
1 TTTTAGTTTTA
48960195 TTTATTAAAT
Statistics
Matches: 28, Mismatches: 1, Indels: 2
0.90 0.03 0.06
Matches are distributed among these distances:
18 18 0.64
20 10 0.36
ACGTcount: A:0.20, C:0.00, G:0.12, T:0.67
Consensus pattern (20 bp):
TTTTAGTTTTAGTTTTAGAA
Found at i:48960276 original size:29 final size:28
Alignment explanation
Indices: 48960223--48960278 Score: 69
Period size: 29 Copynumber: 2.0 Consensus size: 28
48960213 ATTTTTATGA
* *
48960223 TTGGGTTGGGTTGGGTTGGGTTGAATAC
1 TTGGGTTGGATTGGGTTAGGTTGAATAC
48960251 TTGGGTTTGGATTGGGTTTAGG-TGAATA
1 TTGGG-TTGGATTGGG-TTAGGTTGAATA
48960279 GTGGGCCTAT
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
28 5 0.21
29 15 0.62
30 4 0.17
ACGTcount: A:0.14, C:0.02, G:0.43, T:0.41
Consensus pattern (28 bp):
TTGGGTTGGATTGGGTTAGGTTGAATAC
Found at i:48960971 original size:12 final size:12
Alignment explanation
Indices: 48960954--48960979 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
48960944 TATTATTTAT
48960954 TTAAATAATTAA
1 TTAAATAATTAA
48960966 TTAAATAATTAA
1 TTAAATAATTAA
48960978 TT
1 TT
48960980 TTCCTAATTA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (12 bp):
TTAAATAATTAA
Done.