Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Gbar_D05
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 63323194
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.32
Warning! 1953226 characters in sequence are not A, C, G, or T
File 185 of 199
Found at i:59024951 original size:28 final size:29
Alignment explanation
Indices: 59024915--59024982 Score: 79
Period size: 29 Copynumber: 2.3 Consensus size: 29
59024905 ATTATTTAAT
59024915 TAATAAATATCT-TTTACTT-AATAATAAA-
1 TAATAAATAT-TATTTACTTAAATAA-AAAG
59024943 TAATAAATAATTATTTACTTAAATAAAAAG
1 TAATAAAT-ATTATTTACTTAAATAAAAAG
59024973 TAATTAAATA
1 TAA-TAAATA
59024983 AATATATTAC
Statistics
Matches: 35, Mismatches: 0, Indels: 8
0.81 0.00 0.19
Matches are distributed among these distances:
28 9 0.26
29 12 0.34
30 9 0.26
31 5 0.14
ACGTcount: A:0.54, C:0.04, G:0.01, T:0.40
Consensus pattern (29 bp):
TAATAAATATTATTTACTTAAATAAAAAG
Found at i:59030765 original size:12 final size:12
Alignment explanation
Indices: 59030748--59030791 Score: 54
Period size: 12 Copynumber: 3.7 Consensus size: 12
59030738 ATGCCACACA
59030748 GCCGTGTGCTAG
1 GCCGTGTGCTAG
*
59030760 GCCGTGTGGTAG
1 GCCGTGTGCTAG
*
59030772 GCCATGTGCT-G
1 GCCGTGTGCTAG
59030783 GACCGTGTG
1 G-CCGTGTG
59030792 AGACACACGG
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
11 2 0.07
12 25 0.93
ACGTcount: A:0.09, C:0.23, G:0.43, T:0.25
Consensus pattern (12 bp):
GCCGTGTGCTAG
Found at i:59030810 original size:341 final size:341
Alignment explanation
Indices: 59030178--59030820 Score: 898
Period size: 341 Copynumber: 1.9 Consensus size: 341
59030168 CTGTTCGTCC
* * * ** * *
59030178 AGCGGTAAATGCTCTAATGTGTTCTTGGAGGGTTTAATTAGTTTGTTTGTTATCAATTTTTCTGA
1 AGCGGTAAATGCTCGAAAGTGTTCCTGGAGGGTTTAATTAGTTCATTTCTGATCAATTTTTCTGA
* * * **
59030243 TTAAGTTTCGCGAGTCGATACTAAAATTATTTATGTTAAGTGTCAATTTAGGTGTAGGAGTACTC
66 TTAAGTTTCGCGAATCGATACTAAAATTAGTTATGCTAACAGTCAATTTAGGTGTAGGAGTACTC
* *
59030308 GATTCTCGGTTTTATGTGAAAAAACCTCCAGGTGTGTAATAGAACTTTCAAAAACAACAAACAAC
131 GATTCTCGATTTTACGTGAAAAAACCTCCAGGTGTGTAATAGAACTTTCAAAAACAACAAACAAC
* *
59030373 GAAAGTCAAAAATTGGGGCTATCAATGCCACACAGCCGTGTGCTTGGCCGTGTGGTAGGCCATGT
196 GAAAGCCAAAAATTGGGGCTATCAATGCCACACAGCCGTGTGCTAGGCCGTGTGGTAGGCCATGT
*
59030438 GCTGGACCATGTGAGACACACGATTTGGGCCAATTT-GGCCGTATGAGCCATACAGGCTAGCTAA
261 GCTGGACCATGTGAGACACACGATCTGGGCC-ATTTGGGCCGTATGAGCCATACAGGCTAGCTAA
59030502 GTAGTTGTTGTTTGTTT
325 GTAGTTGTTGTTTGTTT
*
59030519 AGCGGTAAGTGCTCGAAAGTGTTCCTGGAGGGTTTAATTAGTTCATTTCTGATCAATTTTTCTGA
1 AGCGGTAAATGCTCGAAAGTGTTCCTGGAGGGTTTAATTAGTTCATTTCTGATCAATTTTTCTGA
* ** *
59030584 TTAAGTTTTGCGAATCGATACTAAAATTAGTTATGCTAACAGTTGATTTAGGTGTGGGAGTACTC
66 TTAAGTTTCGCGAATCGATACTAAAATTAGTTATGCTAACAGTCAATTTAGGTGTAGGAGTACTC
* * * * * * * * *
59030649 TATTCTTGATTTTACGCT-AGAAAACTTCCTGGTGTGTAAT-GAAAC-TTGAGAAAATAGCGAAC
131 GATTCTCGATTTTACG-TGAAAAAACCTCCAGGTGTGTAATAG-AACTTTCA-AAAACAACAAAC
* * *
59030711 GATGAAAGCCAAAAATTGGGGCTATCGATGCCACACAGCCGTGTGCTAGGCCGTGTGGTAGGCCA
193 AACGAAAGCCAAAAATTGGGGCTATCAATGCCACACAGCCGTGTGCTAGGCCGTGTGGTAGGCCA
* *
59030776 TGTGCTGGACCGTGTGAGACACACGGTCTGGGCCATTTGGGCCGT
258 TGTGCTGGACCATGTGAGACACACGATCTGGGCCATTTGGGCCGT
59030821 GTAGGCCACA
Statistics
Matches: 262, Mismatches: 36, Indels: 8
0.86 0.12 0.03
Matches are distributed among these distances:
340 8 0.03
341 253 0.97
342 1 0.00
ACGTcount: A:0.27, C:0.16, G:0.25, T:0.32
Consensus pattern (341 bp):
AGCGGTAAATGCTCGAAAGTGTTCCTGGAGGGTTTAATTAGTTCATTTCTGATCAATTTTTCTGA
TTAAGTTTCGCGAATCGATACTAAAATTAGTTATGCTAACAGTCAATTTAGGTGTAGGAGTACTC
GATTCTCGATTTTACGTGAAAAAACCTCCAGGTGTGTAATAGAACTTTCAAAAACAACAAACAAC
GAAAGCCAAAAATTGGGGCTATCAATGCCACACAGCCGTGTGCTAGGCCGTGTGGTAGGCCATGT
GCTGGACCATGTGAGACACACGATCTGGGCCATTTGGGCCGTATGAGCCATACAGGCTAGCTAAG
TAGTTGTTGTTTGTTT
Found at i:59033797 original size:16 final size:15
Alignment explanation
Indices: 59033778--59033826 Score: 55
Period size: 16 Copynumber: 3.3 Consensus size: 15
59033768 TTTGAAAAAA
59033778 AATAATGATAATTGTG
1 AATAATGATAATT-TG
*
59033794 AATAATGATACTTTG
1 AATAATGATAATTTG
* *
59033809 AATAGTCAT-ATTTG
1 AATAATGATAATTTG
59033823 AATA
1 AATA
59033827 TTTTAGGTAG
Statistics
Matches: 29, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
14 8 0.28
15 9 0.31
16 12 0.41
ACGTcount: A:0.43, C:0.04, G:0.14, T:0.39
Consensus pattern (15 bp):
AATAATGATAATTTG
Found at i:59033970 original size:3 final size:3
Alignment explanation
Indices: 59033962--59033999 Score: 67
Period size: 3 Copynumber: 12.7 Consensus size: 3
59033952 TAATTATGAG
*
59033962 TAA TAA TAA TAA TAA TAA TAC TAA TAA TAA TAA TAA TA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TA
59034000 GAAATCAAAT
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
3 33 1.00
ACGTcount: A:0.63, C:0.03, G:0.00, T:0.34
Consensus pattern (3 bp):
TAA
Found at i:59036623 original size:3 final size:3
Alignment explanation
Indices: 59036611--59036864 Score: 112
Period size: 3 Copynumber: 85.7 Consensus size: 3
59036601 ATACTACTAC
* *
59036611 TAT TAC TAT TAT TAT TAG TAT TAT TGA- TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT T-AT TAT TAT TAT TAT TAT TAT
** * * * * *
59036656 TAT TAT CCT TAC TAC TAT TAT TAG CAT TAT TAT CAT TAGT T-T TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA-T TAT TAT
* * * * ** * * *
59036701 TGT TAT T-T TAT TAC TAT TAA CAT TAT TAT TGG AAT TAT TAT TAA TGT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
* * * * * *
59036748 TAT TAC TAT TAT TAT T-T TTT TCT AAC TAT TAA TAT TAT T-T ATAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT -TAT
* * * * *
59036792 TAT TAT AAT TAC TAT TAT TAT T-T TCAT TAC CAC TAT TAT TA- TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT T-AT TAT TAT TAT TAT TAT TAT
**
59036836 T-T CTCG TA- TACT TAT TAT TAT TAT TAT TA
1 TAT -TAT TAT TA-T TAT TAT TAT TAT TAT TA
59036865 CCCTGTTGTT
Statistics
Matches: 182, Mismatches: 54, Indels: 30
0.68 0.20 0.11
Matches are distributed among these distances:
2 15 0.08
3 159 0.87
4 8 0.04
ACGTcount: A:0.31, C:0.08, G:0.04, T:0.57
Consensus pattern (3 bp):
TAT
Found at i:59042066 original size:14 final size:15
Alignment explanation
Indices: 59042040--59042072 Score: 50
Period size: 14 Copynumber: 2.3 Consensus size: 15
59042030 TACCAAATTG
59042040 GGAAGGACCTTATGT
1 GGAAGGACCTTATGT
*
59042055 GGAAGG-CCTTATTT
1 GGAAGGACCTTATGT
59042069 GGAA
1 GGAA
59042073 AAGCGTTGAT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
14 11 0.65
15 6 0.35
ACGTcount: A:0.27, C:0.12, G:0.33, T:0.27
Consensus pattern (15 bp):
GGAAGGACCTTATGT
Found at i:59043130 original size:44 final size:44
Alignment explanation
Indices: 59043064--59043548 Score: 365
Period size: 44 Copynumber: 10.8 Consensus size: 44
59043054 ATGGCAAATA
* * **
59043064 TTATCTCCCTGAAGCTGTAGTGGAGCAGATTGAAGCCACTAATC
1 TTATCTCCCTGAAGTTGCAGTGGAGCAGATTGAAGATACTAATC
* * *
59043108 TTATC-CCCTTGAAGTTACAGTGGGGCAGATTGAAGAGAC-AAGTC
1 TTATCTCCC-TGAAGTTGCAGTGGAGCAGATTGAAGATACTAA-TC
* * * * *
59043152 TTATCTCCCTGAAGTTGCAGTAGAGCTGACTGAAGATAGCAAACC
1 TTATCTCCCTGAAGTTGCAGTGGAGCAGATTGAAGATA-CTAATC
*
59043197 TTATCTCCCTGAAGTTGCAGTGGAGCAGGTTGAAGATA-TGAATC
1 TTATCTCCCTGAAGTTGCAGTGGAGCAGATTGAAGATACT-AATC
* * * * *
59043241 TTATCTCTCAGAAGTTGCAGTGGAGCAGACTGAAGATAGCAAACC
1 TTATCTCCCTGAAGTTGCAGTGGAGCAGATTGAAGATA-CTAATC
* * * *
59043286 TTATCTGCCGGAAGTTGCAGTGGAGCAGGTTAAAGATAC-AAGTC
1 TTATCTCCCTGAAGTTGCAGTGGAGCAGATTGAAGATACTAA-TC
* * *
59043330 TTATCTCCCTGAAGTTGCAATGGAGCAGACTGAAGATAGCAAATC
1 TTATCTCCCTGAAGTTGCAGTGGAGCAGATTGAAGATA-CTAATC
* * * * * *
59043375 TTATTTTCCTGAAGTGGCAGTGGAACAGATTAAAGCTATAAGTTATAGGTC
1 TTATCTCCCTGAAGTTGCAGTGGAGCAGATTGAAG--AT-A-CTA-A--TC
* * * * * * *
59043426 TTATCTCTCTGAAGTTGTAGTAGAGCAGA-T-CATAT-CAAACC
1 TTATCTCCCTGAAGTTGCAGTGGAGCAGATTGAAGATACTAATC
* * * * *
59043467 TTATCTCCCTGAAGTTGTAGTGGAGCAGGTTAAAAATAAATCAATC
1 TTATCTCCCTGAAGTTGCAGTGGAGCAGATTGAAGAT-ACT-AATC
*
59043513 TTATCTCCATGAAGTTG-AGTTGGAGCAGATTGAAGA
1 TTATCTCCCTGAAGTTGCAG-TGGAGCAGATTGAAGA
59043549 CCTTCTACAA
Statistics
Matches: 347, Mismatches: 71, Indels: 44
0.75 0.15 0.10
Matches are distributed among these distances:
41 27 0.08
42 1 0.00
43 11 0.03
44 131 0.38
45 107 0.31
46 36 0.10
47 4 0.01
48 3 0.01
49 2 0.01
50 1 0.00
51 24 0.07
ACGTcount: A:0.31, C:0.18, G:0.24, T:0.28
Consensus pattern (44 bp):
TTATCTCCCTGAAGTTGCAGTGGAGCAGATTGAAGATACTAATC
Found at i:59043219 original size:89 final size:89
Alignment explanation
Indices: 59043064--59043548 Score: 448
Period size: 89 Copynumber: 5.4 Consensus size: 89
59043054 ATGGCAAATA
* * * ** * * *
59043064 TTATCTCCCTGAAGCTGTAGTGGAGCAGATTGAAGCCA-CTAATCTTATC-CCCTTGAAGTTACA
1 TTATCTCCCTGAAGTTGCAGTGGAGCAGACTGAAGATAGCAAACCTTATCTCCC-TGAAGTTGCA
* * *
59043127 GTGGGGCAGATTGAAGAGACAAGTC
65 GTGGAGCAGGTTGAAGATACAAGTC
* *
59043152 TTATCTCCCTGAAGTTGCAGTAGAGCTGACTGAAGATAGCAAACCTTATCTCCCTGAAGTTGCAG
1 TTATCTCCCTGAAGTTGCAGTGGAGCAGACTGAAGATAGCAAACCTTATCTCCCTGAAGTTGCAG
*
59043217 TGGAGCAGGTTGAAGATATGAA-TC
66 TGGAGCAGGTTGAAGATA-CAAGTC
* * * *
59043241 TTATCTCTCAGAAGTTGCAGTGGAGCAGACTGAAGATAGCAAACCTTATCTGCCGGAAGTTGCAG
1 TTATCTCCCTGAAGTTGCAGTGGAGCAGACTGAAGATAGCAAACCTTATCTCCCTGAAGTTGCAG
*
59043306 TGGAGCAGGTTAAAGATACAAGTC
66 TGGAGCAGGTTGAAGATACAAGTC
* * * * *
59043330 TTATCTCCCTGAAGTTGCAATGGAGCAGACTGAAGATAGCAAATCTTATTTTCCTGAAGTGGCAG
1 TTATCTCCCTGAAGTTGCAGTGGAGCAGACTGAAGATAGCAAACCTTATCTCCCTGAAGTTGCAG
* * * *
59043395 TGGAACAGATTAAAGCTATAAGTTATAGGTC
66 TGGAGCAGGTTGAAG--AT-A--CA-A-GTC
* * * * * *
59043426 TTATCTCTCTGAAGTTGTAGTAGAGCAGA-T---CATATCAAACCTTATCTCCCTGAAGTTGTAG
1 TTATCTCCCTGAAGTTGCAGTGGAGCAGACTGAAGATAGCAAACCTTATCTCCCTGAAGTTGCAG
* *
59043487 TGGAGCAGGTTAAAAATAAATCAA-TC
66 TGGAGCAGGTTGAAGAT--A-CAAGTC
* *
59043513 TTATCTCCATGAAGTTG-AGTTGGAGCAGATTGAAGA
1 TTATCTCCCTGAAGTTGCAG-TGGAGCAGACTGAAGA
59043549 CCTTCTACAA
Statistics
Matches: 328, Mismatches: 52, Indels: 31
0.80 0.13 0.08
Matches are distributed among these distances:
86 2 0.01
87 25 0.08
88 34 0.10
89 185 0.56
90 9 0.03
91 5 0.02
92 37 0.11
94 1 0.00
95 2 0.01
96 28 0.09
ACGTcount: A:0.31, C:0.18, G:0.24, T:0.28
Consensus pattern (89 bp):
TTATCTCCCTGAAGTTGCAGTGGAGCAGACTGAAGATAGCAAACCTTATCTCCCTGAAGTTGCAG
TGGAGCAGGTTGAAGATACAAGTC
Found at i:59043243 original size:133 final size:133
Alignment explanation
Indices: 59043064--59043378 Score: 348
Period size: 133 Copynumber: 2.4 Consensus size: 133
59043054 ATGGCAAATA
* * ** *
59043064 TTATCTCCCTGAAGCTGTAGTGGAGCAGATTGAAGCCACTAATCTTATCCC-CTTGAAGTTACAG
1 TTATCTCCCTGAAGTTGCAGTGGAGCAGATTGAAGATACTAATCTTATCCCTC-AGAAGTTACAG
* * ** * * *
59043128 TGGGGCAGATTGAAGAGA-CAAGTCTTATCTCCCTGAAGTTGCAGTAGAGCTGACTGAAGATAGC
65 TGGAGCAGACTGAAGAGAGCAAACCTTATCTCCCGGAAGTTGCAGTAGAGCAGACTAAAGATA-C
59043192 AAACC
129 AAACC
* * *
59043197 TTATCTCCCTGAAGTTGCAGTGGAGCAGGTTGAAGATA-TGAATCTTATCTCTCAGAAGTTGCAG
1 TTATCTCCCTGAAGTTGCAGTGGAGCAGATTGAAGATACT-AATCTTATCCCTCAGAAGTTACAG
* * * **
59043261 TGGAGCAGACTGAAGATAGCAAACCTTATCTGCCGGAAGTTGCAGTGGAGCAGGTTAAAGATACA
65 TGGAGCAGACTGAAGAGAGCAAACCTTATCTCCCGGAAGTTGCAGTAGAGCAGACTAAAGATACA
**
59043326 AGTC
130 AACC
* * *
59043330 TTATCTCCCTGAAGTTGCAATGGAGCAGACTGAAGATAGCAAATCTTAT
1 TTATCTCCCTGAAGTTGCAGTGGAGCAGATTGAAGATA-CTAATCTTAT
59043379 TTTCCTGAAG
Statistics
Matches: 151, Mismatches: 26, Indels: 9
0.81 0.14 0.05
Matches are distributed among these distances:
132 1 0.01
133 106 0.70
134 44 0.29
ACGTcount: A:0.30, C:0.19, G:0.25, T:0.26
Consensus pattern (133 bp):
TTATCTCCCTGAAGTTGCAGTGGAGCAGATTGAAGATACTAATCTTATCCCTCAGAAGTTACAGT
GGAGCAGACTGAAGAGAGCAAACCTTATCTCCCGGAAGTTGCAGTAGAGCAGACTAAAGATACAA
ACC
Found at i:59045267 original size:3 final size:3
Alignment explanation
Indices: 59045019--59045244 Score: 122
Period size: 3 Copynumber: 75.0 Consensus size: 3
59045009 ATACTACTAC
* * *
59045019 TAT TAC TAT TAT TAT TAG TAT TAT TGA- TAT TAT TAT TAA TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT T-AT TAT TAT TAT TAT TAT TAT
** * * * *
59045064 TAT TAT TAT TAT CCT TAC TAT TAT TAT TAG CAT TAT TAT CAT TAGT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA-T
* * * *
59045110 T-T TAT TGT TAT T-T TAT TAC TAT TAA CAT TAT TAT TGGAGT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T--A-T TAT TAT
* ** * * * * *
59045156 TAA TGC TAT TAC TAT TAT T-T TTT TCT TAC TAT TAA TAT TAT T-T ATAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT -TAT
* * * *
59045203 TAT TAT AAT TAC TAT TAT TAT T-T TCAT TAC CAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT T-AT TAT TAT TAT TAT TAT
59045245 ATTTCTCGTA
Statistics
Matches: 163, Mismatches: 47, Indels: 26
0.69 0.20 0.11
Matches are distributed among these distances:
2 10 0.06
3 143 0.88
4 7 0.04
5 1 0.01
6 2 0.01
ACGTcount: A:0.31, C:0.07, G:0.04, T:0.58
Consensus pattern (3 bp):
TAT
Found at i:59048719 original size:24 final size:24
Alignment explanation
Indices: 59048691--59048748 Score: 89
Period size: 24 Copynumber: 2.4 Consensus size: 24
59048681 TTTTTAGAAG
* *
59048691 ATTTAGTATTTATTAGTATAATAT
1 ATTTAGCATTTACTAGTATAATAT
59048715 ATTTAGCATTTACTAGTATAATAT
1 ATTTAGCATTTACTAGTATAATAT
*
59048739 ATTTAACATT
1 ATTTAGCATT
59048749 GATTGGAATT
Statistics
Matches: 31, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
24 31 1.00
ACGTcount: A:0.38, C:0.05, G:0.07, T:0.50
Consensus pattern (24 bp):
ATTTAGCATTTACTAGTATAATAT
Found at i:59052201 original size:29 final size:29
Alignment explanation
Indices: 59052169--59052227 Score: 91
Period size: 29 Copynumber: 2.0 Consensus size: 29
59052159 TTGTGGAAGA
** *
59052169 GGTGGAGAACTTGTTCATTGAGAGTTCGT
1 GGTGGAGAACTTACTCATTGAGAATTCGT
59052198 GGTGGAGAACTTACTCATTGAGAATTCGT
1 GGTGGAGAACTTACTCATTGAGAATTCGT
59052227 G
1 G
59052228 TCAAGGTGGA
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
29 27 1.00
ACGTcount: A:0.24, C:0.12, G:0.32, T:0.32
Consensus pattern (29 bp):
GGTGGAGAACTTACTCATTGAGAATTCGT
Found at i:59052381 original size:24 final size:24
Alignment explanation
Indices: 59052318--59052369 Score: 79
Period size: 24 Copynumber: 2.2 Consensus size: 24
59052308 TTTCTAGAAG
*
59052318 ATTTAGTATTTATTAG-TGTAATAT
1 ATTTAGCATTTATTAGCT-TAATAT
59052342 ATTTAGCATTTATTAGCTTAATAT
1 ATTTAGCATTTATTAGCTTAATAT
59052366 ATTT
1 ATTT
59052370 GACATTTTTT
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
24 25 0.96
25 1 0.04
ACGTcount: A:0.33, C:0.04, G:0.10, T:0.54
Consensus pattern (24 bp):
ATTTAGCATTTATTAGCTTAATAT
Found at i:59054788 original size:15 final size:16
Alignment explanation
Indices: 59054768--59054797 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
59054758 ATTCAAGATC
59054768 AATTTA-CTTGTTTGA
1 AATTTATCTTGTTTGA
59054783 AATTTATCTTGTTTG
1 AATTTATCTTGTTTG
59054798 CATGATTGAA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 6 0.43
16 8 0.57
ACGTcount: A:0.23, C:0.07, G:0.13, T:0.57
Consensus pattern (16 bp):
AATTTATCTTGTTTGA
Found at i:59055263 original size:17 final size:17
Alignment explanation
Indices: 59055231--59055263 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
59055221 ATGGAAATTG
59055231 TGTATTATTTTGTTAAA
1 TGTATTATTTTGTTAAA
59055248 TGTATATATTTT-TTAA
1 TGTAT-TATTTTGTTAA
59055264 CTTATATGGA
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
17 9 0.60
18 6 0.40
ACGTcount: A:0.30, C:0.00, G:0.09, T:0.61
Consensus pattern (17 bp):
TGTATTATTTTGTTAAA
Found at i:59055571 original size:19 final size:18
Alignment explanation
Indices: 59055549--59055625 Score: 66
Period size: 19 Copynumber: 4.2 Consensus size: 18
59055539 TGCACTTTGT
59055549 TGCCAGAAATGCGCTTATG
1 TGCCA-AAATGCGCTTATG
* * *
59055568 TGCCAATATGC-ATTTTG
1 TGCCAAAATGCGCTTATG
*
59055585 TGCCAAGAATGTGCTTATG
1 TGCCAA-AATGCGCTTATG
* *
59055604 CGCCAAAATGCACTTCATG
1 TGCCAAAATGCGCTT-ATG
59055623 TGC
1 TGC
59055626 TAGGATTCAC
Statistics
Matches: 44, Mismatches: 11, Indels: 6
0.72 0.18 0.10
Matches are distributed among these distances:
17 10 0.23
18 15 0.34
19 19 0.43
ACGTcount: A:0.26, C:0.22, G:0.22, T:0.30
Consensus pattern (18 bp):
TGCCAAAATGCGCTTATG
Found at i:59055601 original size:36 final size:37
Alignment explanation
Indices: 59055537--59055618 Score: 105
Period size: 36 Copynumber: 2.2 Consensus size: 37
59055527 TGTATAGGTG
*
59055537 TATGCACTTTGTTGCCAGAAATGCGCTTATGTGCCAA
1 TATGCACTTTGTTGCCAGAAATGCGCTTATGCGCCAA
* *
59055574 TATGCATTTTG-TGCCA-AGAATGTGCTTATGCGCCAA
1 TATGCACTTTGTTGCCAGA-AATGCGCTTATGCGCCAA
*
59055610 AATGCACTT
1 TATGCACTT
59055619 CATGTGCTAG
Statistics
Matches: 39, Mismatches: 5, Indels: 3
0.83 0.11 0.06
Matches are distributed among these distances:
35 1 0.03
36 28 0.72
37 10 0.26
ACGTcount: A:0.26, C:0.21, G:0.21, T:0.33
Consensus pattern (37 bp):
TATGCACTTTGTTGCCAGAAATGCGCTTATGCGCCAA
Found at i:59060168 original size:40 final size:41
Alignment explanation
Indices: 59060024--59060176 Score: 254
Period size: 41 Copynumber: 3.8 Consensus size: 41
59060014 TTATATAAAA
* * *
59060024 CACCGGCATAAAGCCTGCTAGGCACAAAGCCCGATACATTT
1 CACCGGCATAGAGCCTGCTAGGCATAAAGCCTGATACATTT
*
59060065 CACCGGCACAGAGCCTGCTAGGCATAAAGCCTGATACATTT
1 CACCGGCATAGAGCCTGCTAGGCATAAAGCCTGATACATTT
59060106 CACCGGCATAGAGCCTGCTAGGCATAAAGCCTGATACATTT
1 CACCGGCATAGAGCCTGCTAGGCATAAAGCCTGATACATTT
*
59060147 CACC-GAATAGAGCCTGCTAGGCATAAAGCC
1 CACCGGCATAGAGCCTGCTAGGCATAAAGCC
59060177 CGAACTTACA
Statistics
Matches: 106, Mismatches: 6, Indels: 1
0.94 0.05 0.01
Matches are distributed among these distances:
40 25 0.24
41 81 0.76
ACGTcount: A:0.31, C:0.29, G:0.22, T:0.18
Consensus pattern (41 bp):
CACCGGCATAGAGCCTGCTAGGCATAAAGCCTGATACATTT
Found at i:59060387 original size:47 final size:47
Alignment explanation
Indices: 59060284--59060418 Score: 162
Period size: 47 Copynumber: 2.8 Consensus size: 47
59060274 TAACTTCAAA
* * * *
59060284 TAATTTATTTCAATGCATAACAAGTATATATATGCATTCAGCCATAGTT
1 TAATTCATTTCAATGCATAACAA-T-TATATATACATTCAGCTATAGAT
** *
59060333 TAATTCATTTCTCTGCATAACAATTACATATACATTCAGCTATAGAT
1 TAATTCATTTCAATGCATAACAATTATATATACATTCAGCTATAGAT
*
59060380 TAATTCATTTCAATGTATAACAAATATATATATACATTC
1 TAATTCATTTCAATGCATAAC-AAT-TATATATACATTC
59060419 GGCCATAACC
Statistics
Matches: 73, Mismatches: 11, Indels: 4
0.83 0.12 0.05
Matches are distributed among these distances:
47 37 0.51
48 4 0.05
49 32 0.44
ACGTcount: A:0.39, C:0.16, G:0.07, T:0.39
Consensus pattern (47 bp):
TAATTCATTTCAATGCATAACAATTATATATACATTCAGCTATAGAT
Found at i:59060512 original size:47 final size:47
Alignment explanation
Indices: 59060443--59060737 Score: 194
Period size: 47 Copynumber: 5.9 Consensus size: 47
59060433 TAATTTCAAA
* * *
59060443 TAATTTATTTCAATGCATAACAAATATATATAGATTCGGCCATAGCT
1 TAATTCATTTCAATGCATAACAAATATATATAAATTCGGCCATAGAT
** * * * *
59060490 TAATTCATTTCTCTGCATAACAATTACATATAAATTCAGCTATAGAT
1 TAATTCATTTCAATGCATAACAAATATATATAAATTCGGCCATAGAT
* *
59060537 TAATTCATTTCAATGTATAACAAATATATATATACATTCGGCCATAACCTAT
1 TAATTCATTTCAATGCATAACAAATATATATA-A-ATTCGGCCAT-A--GAT
* * * * * * *
59060589 GTAATTTCAAATAATTTATTTCAACTCATAACAAATATATATACATTCGGCCATAGCT
1 -TAA-TTC--AT--TTCAATGC-A-TAACAA-ATATATATA-A-ATTCGGCCATAGAT
** * * * * * *
59060647 TAATTCATTTCTCTGCATAACAATTACATATACATTCAGCTATAGTT
1 TAATTCATTTCAATGCATAACAAATATATATAAATTCGGCCATAGAT
* *
59060694 TAATTCATTTCAATGTATAACAAATATATATACATTCGGCCATA
1 TAATTCATTTCAATGCATAACAAATATATATAAATTCGGCCATA
59060738 ACCTATGTAA
Statistics
Matches: 188, Mismatches: 46, Indels: 28
0.72 0.18 0.11
Matches are distributed among these distances:
47 113 0.60
48 1 0.01
49 14 0.07
50 5 0.03
51 1 0.01
52 6 0.03
53 3 0.02
54 5 0.03
56 5 0.03
57 3 0.02
58 5 0.03
59 1 0.01
60 5 0.03
61 21 0.11
ACGTcount: A:0.39, C:0.17, G:0.07, T:0.37
Consensus pattern (47 bp):
TAATTCATTTCAATGCATAACAAATATATATAAATTCGGCCATAGAT
Found at i:59060778 original size:155 final size:157
Alignment explanation
Indices: 59060248--59060815 Score: 982
Period size: 157 Copynumber: 3.6 Consensus size: 157
59060238 AACAATTCAC
* * * *
59060248 TATAT-TACATTTGGCCATAGCTTATGTAACTTCAAATAATTTATTTCAATGCATAACAAGTATA
1 TATATATACATTCGGCCATAACCTATGTAATTTCAAATAATTTATTTCAATGCATAACAA--ATA
* * *
59060312 TATATGCATTCAGCCATAGTTTAATTCATTTCTCTGCATAACAATTACATATACATTCAGCTATA
64 TATATACATTCGGCCATAGCTTAATTCATTTCTCTGCATAACAATTACATATACATTCAGCTATA
59060377 GATTAATTCATTTCAATGTATAACAAATA
129 GATTAATTCATTTCAATGTATAACAAATA
59060406 TATATATACATTCGGCCATAACCTATGTAATTTCAAATAATTTATTTCAATGCATAACAAATATA
1 TATATATACATTCGGCCATAACCTATGTAATTTCAAATAATTTATTTCAATGCATAACAAATATA
* *
59060471 TATAGATTCGGCCATAGCTTAATTCATTTCTCTGCATAACAATTACATATAAATTCAGCTATAGA
66 TATACATTCGGCCATAGCTTAATTCATTTCTCTGCATAACAATTACATATACATTCAGCTATAGA
59060536 TTAATTCATTTCAATGTATAACAAATA
131 TTAATTCATTTCAATGTATAACAAATA
59060563 TATATATACATTCGGCCATAACCTATGTAATTTCAAATAATTTATTTCAACT-CATAACAAATAT
1 TATATATACATTCGGCCATAACCTATGTAATTTCAAATAATTTATTTCAA-TGCATAACAAATAT
59060627 ATATACATTCGGCCATAGCTTAATTCATTTCTCTGCATAACAATTACATATACATTCAGCTATAG
65 ATATACATTCGGCCATAGCTTAATTCATTTCTCTGCATAACAATTACATATACATTCAGCTATAG
*
59060692 TTTAATTCATTTCAATGTATAAC-AA-A
130 ATTAATTCATTTCAATGTATAACAAATA
59060718 TATATATACATTCGGCCATAACCTATGTAATTTCAAATAATTTATTTCAATGCATAACAAATATA
1 TATATATACATTCGGCCATAACCTATGTAATTTCAAATAATTTATTTCAATGCATAACAAATATA
*
59060783 TATACATTCGACCATAGCTTAATTCATTTCTCT
66 TATACATTCGGCCATAGCTTAATTCATTTCTCT
59060816 CAGATGTCGT
Statistics
Matches: 394, Mismatches: 13, Indels: 9
0.95 0.03 0.02
Matches are distributed among these distances:
154 1 0.00
155 96 0.24
156 2 0.01
157 239 0.61
158 6 0.02
159 50 0.13
ACGTcount: A:0.38, C:0.17, G:0.07, T:0.38
Consensus pattern (157 bp):
TATATATACATTCGGCCATAACCTATGTAATTTCAAATAATTTATTTCAATGCATAACAAATATA
TATACATTCGGCCATAGCTTAATTCATTTCTCTGCATAACAATTACATATACATTCAGCTATAGA
TTAATTCATTTCAATGTATAACAAATA
Found at i:59061765 original size:57 final size:59
Alignment explanation
Indices: 59061690--59061804 Score: 164
Period size: 57 Copynumber: 1.9 Consensus size: 59
59061680 GCTAAATCCA
* *
59061690 TTTTCCACATATTCTTCGGGAGGGTTATATC-A-A-GATCACCCGTCCGGGCTAGAGCT
1 TTTTCCACATATTATTCGGGAGGGCTATATCGATAGGATCACCCGTCCGGGCTAGAGCT
59061746 TTTTCACACATATTATTCGGGAGGGCTATATCAGGATAGGATCACCCGTCCGGGCTAGA
1 TTTTC-CACATATTATTCGGGAGGGCTATATC--GATAGGATCACCCGTCCGGGCTAGA
59061805 TCCTTTTTAC
Statistics
Matches: 51, Mismatches: 2, Indels: 6
0.86 0.03 0.10
Matches are distributed among these distances:
56 5 0.10
57 24 0.47
60 1 0.02
61 1 0.02
62 20 0.39
ACGTcount: A:0.23, C:0.23, G:0.24, T:0.29
Consensus pattern (59 bp):
TTTTCCACATATTATTCGGGAGGGCTATATCGATAGGATCACCCGTCCGGGCTAGAGCT
Found at i:59063412 original size:8 final size:8
Alignment explanation
Indices: 59063399--59063423 Score: 50
Period size: 8 Copynumber: 3.1 Consensus size: 8
59063389 ATATATACTA
59063399 AATAAAAT
1 AATAAAAT
59063407 AATAAAAT
1 AATAAAAT
59063415 AATAAAAT
1 AATAAAAT
59063423 A
1 A
59063424 TCTTTTAAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 17 1.00
ACGTcount: A:0.76, C:0.00, G:0.00, T:0.24
Consensus pattern (8 bp):
AATAAAAT
Found at i:59066294 original size:19 final size:18
Alignment explanation
Indices: 59066266--59066309 Score: 52
Period size: 19 Copynumber: 2.4 Consensus size: 18
59066256 ATTGATTAGT
**
59066266 TTAATTAATTTTTTAAAA
1 TTAATTAATTAATTAAAA
59066284 TTAATTTAATTAATTAAAA
1 TTAA-TTAATTAATTAAAA
*
59066303 TTTATTA
1 TTAATTA
59066310 TGAAATAAAA
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
18 7 0.32
19 15 0.68
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (18 bp):
TTAATTAATTAATTAAAA
Found at i:59075317 original size:42 final size:42
Alignment explanation
Indices: 59075251--59075393 Score: 164
Period size: 42 Copynumber: 3.4 Consensus size: 42
59075241 GTATATGGCC
* * *
59075251 TTGGATATGGCATTGAAGATGGGAACCAGTTAGGTACAGCCA
1 TTGGATATGGCATTGGAGAAGGGAACCAGTTAGGTACAGGCA
* *
59075293 TTGGATATGGCATTGGAGAAGGGAACCGGGTAGGTACAGGCA
1 TTGGATATGGCATTGGAGAAGGGAACCAGTTAGGTACAGGCA
* * **
59075335 TTGGAAATGGCA-TGG-GAAGTGGGAACCAGTTAGGAATGGGCA
1 TTGGATATGGCATTGGAGAA--GGGAACCAGTTAGGTACAGGCA
*
59075377 TTGGGTATGGCATTGGA
1 TTGGATATGGCATTGGA
59075394 AATGGGGGTC
Statistics
Matches: 84, Mismatches: 13, Indels: 6
0.82 0.13 0.06
Matches are distributed among these distances:
40 3 0.04
41 3 0.04
42 75 0.89
43 3 0.04
ACGTcount: A:0.29, C:0.11, G:0.38, T:0.22
Consensus pattern (42 bp):
TTGGATATGGCATTGGAGAAGGGAACCAGTTAGGTACAGGCA
Found at i:59075412 original size:42 final size:42
Alignment explanation
Indices: 59075365--59075489 Score: 103
Period size: 42 Copynumber: 3.0 Consensus size: 42
59075355 GGGAACCAGT
59075365 TAGGAATGGGCATTGGGTATGGCATTGGAAATGGGGGTCA-A
1 TAGGAATGGGCATTGGGTATGGCATTGGAAATGGGGGTCAGA
* * * * * ***
59075406 TCAGGAAAT-AGCA-TGGGATTTGGTATCGGAAATGCGAACCAGA
1 T-AGG-AATGGGCATTGGG-TATGGCATTGGAAATGGGGGTCAGA
* * *
59075449 TGGGAATGGGTATCGGGTATGGCATTGGAAATGGGGGTCAG
1 TAGGAATGGGCATTGGGTATGGCATTGGAAATGGGGGTCAG
59075490 GCCGGAAATA
Statistics
Matches: 59, Mismatches: 19, Indels: 11
0.66 0.21 0.12
Matches are distributed among these distances:
41 8 0.14
42 43 0.73
43 8 0.14
ACGTcount: A:0.28, C:0.10, G:0.39, T:0.23
Consensus pattern (42 bp):
TAGGAATGGGCATTGGGTATGGCATTGGAAATGGGGGTCAGA
Found at i:59075576 original size:42 final size:42
Alignment explanation
Indices: 59075517--59075620 Score: 145
Period size: 42 Copynumber: 2.5 Consensus size: 42
59075507 ATATGGCATA
** *
59075517 GGATATGGCGCTGGAAATGGGAACCAGTTAGGAACTGGTATC
1 GGATATGGTACTGGAAATGGGAACCAGTTAGGAACCGGTATC
* *
59075559 GGATATGGTATTGGAAATGGGAACCAGTTAGGAACCGGTATT
1 GGATATGGTACTGGAAATGGGAACCAGTTAGGAACCGGTATC
* *
59075601 GGATTTGGTACCGGAAATGG
1 GGATATGGTACTGGAAATGG
59075621 AGGTCAGTCA
Statistics
Matches: 54, Mismatches: 8, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
42 54 1.00
ACGTcount: A:0.29, C:0.12, G:0.36, T:0.24
Consensus pattern (42 bp):
GGATATGGTACTGGAAATGGGAACCAGTTAGGAACCGGTATC
Found at i:59077735 original size:13 final size:13
Alignment explanation
Indices: 59077719--59077745 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
59077709 AAAGAAAAAG
59077719 AAAAAAGGATTCA
1 AAAAAAGGATTCA
59077732 AAAAAAGGATTCA
1 AAAAAAGGATTCA
59077745 A
1 A
59077746 GAAGAAATAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.63, C:0.07, G:0.15, T:0.15
Consensus pattern (13 bp):
AAAAAAGGATTCA
Found at i:59078011 original size:13 final size:12
Alignment explanation
Indices: 59077994--59078022 Score: 58
Period size: 12 Copynumber: 2.4 Consensus size: 12
59077984 AGAGTAGAGA
59077994 GTTTTTTTTTTT
1 GTTTTTTTTTTT
59078006 GTTTTTTTTTTT
1 GTTTTTTTTTTT
59078018 GTTTT
1 GTTTT
59078023 AAAGAATGGA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 17 1.00
ACGTcount: A:0.00, C:0.00, G:0.10, T:0.90
Consensus pattern (12 bp):
GTTTTTTTTTTT
Found at i:59082847 original size:18 final size:18
Alignment explanation
Indices: 59082794--59082847 Score: 72
Period size: 18 Copynumber: 2.9 Consensus size: 18
59082784 TAACACCTAA
* *
59082794 ACCCAATCCAAACCCAAGT
1 ACCCAA-CCCAACCCAATT
*
59082813 ATCCAACCCAACCCAATT
1 ACCCAACCCAACCCAATT
59082831 ACCCAACCCAACCCAAT
1 ACCCAACCCAACCCAAT
59082848 CATAAAAATT
Statistics
Matches: 31, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
18 26 0.84
19 5 0.16
ACGTcount: A:0.41, C:0.46, G:0.02, T:0.11
Consensus pattern (18 bp):
ACCCAACCCAACCCAATT
Found at i:59083073 original size:9 final size:9
Alignment explanation
Indices: 59082993--59083077 Score: 102
Period size: 9 Copynumber: 9.4 Consensus size: 9
59082983 TTAGTGATTC
59082993 AATTCGGTT
1 AATTCGGTT
59083002 AATTCTGG-T
1 AATTC-GGTT
*
59083011 AATTCGGGT
1 AATTCGGTT
59083020 AATTCAGG-T
1 AATTC-GGTT
59083029 AATTCGGTT
1 AATTCGGTT
*
59083038 AATTCGGGT
1 AATTCGGTT
*
59083047 AATTCTGTT
1 AATTCGGTT
59083056 AATTCGGTT
1 AATTCGGTT
*
59083065 AATTAGGTT
1 AATTCGGTT
59083074 AATT
1 AATT
59083078 TAGTTAATTT
Statistics
Matches: 67, Mismatches: 5, Indels: 8
0.84 0.06 0.10
Matches are distributed among these distances:
8 4 0.06
9 59 0.88
10 4 0.06
ACGTcount: A:0.26, C:0.09, G:0.22, T:0.42
Consensus pattern (9 bp):
AATTCGGTT
Found at i:59089444 original size:27 final size:27
Alignment explanation
Indices: 59089369--59089433 Score: 112
Period size: 27 Copynumber: 2.4 Consensus size: 27
59089359 AAAAACTTTT
* *
59089369 CTTTCATATTACACCACAAAGGTGTTC
1 CTTTCATATTGCGCCACAAAGGTGTTC
59089396 CTTTCATATTGCGCCACAAAGGTGTTC
1 CTTTCATATTGCGCCACAAAGGTGTTC
59089423 CTTTCATATTG
1 CTTTCATATTG
59089434 TGTCATAAAG
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
27 36 1.00
ACGTcount: A:0.25, C:0.25, G:0.14, T:0.37
Consensus pattern (27 bp):
CTTTCATATTGCGCCACAAAGGTGTTC
Found at i:59091881 original size:13 final size:13
Alignment explanation
Indices: 59091860--59091925 Score: 82
Period size: 13 Copynumber: 5.1 Consensus size: 13
59091850 AGTATAGCAA
59091860 TGCTTTTGAAAAG
1 TGCTTTTGAAAAG
*
59091873 TGTTTTTGAAAAG
1 TGCTTTTGAAAAG
*
59091886 TG-TTGTGGAAAAG
1 TGCTT-TTGAAAAG
59091899 TGCTTTT-AAGAAG
1 TGCTTTTGAA-AAG
59091912 TGCTTTTGAAAAG
1 TGCTTTTGAAAAG
59091925 T
1 T
59091926 TTGGTTTAAA
Statistics
Matches: 46, Mismatches: 3, Indels: 8
0.81 0.05 0.14
Matches are distributed among these distances:
12 4 0.09
13 38 0.83
14 4 0.09
ACGTcount: A:0.30, C:0.05, G:0.26, T:0.39
Consensus pattern (13 bp):
TGCTTTTGAAAAG
Found at i:59092500 original size:18 final size:18
Alignment explanation
Indices: 59092477--59092524 Score: 96
Period size: 18 Copynumber: 2.7 Consensus size: 18
59092467 CTTTTCTTCT
59092477 AAAAGTGCTTTTGGAGTC
1 AAAAGTGCTTTTGGAGTC
59092495 AAAAGTGCTTTTGGAGTC
1 AAAAGTGCTTTTGGAGTC
59092513 AAAAGTGCTTTT
1 AAAAGTGCTTTT
59092525 TTTAAGCAAT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 30 1.00
ACGTcount: A:0.29, C:0.10, G:0.25, T:0.35
Consensus pattern (18 bp):
AAAAGTGCTTTTGGAGTC
Found at i:59095258 original size:12 final size:12
Alignment explanation
Indices: 59095241--59095265 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
59095231 CGTTCGACCC
59095241 TTGTTTTTGACA
1 TTGTTTTTGACA
59095253 TTGTTTTTGACA
1 TTGTTTTTGACA
59095265 T
1 T
59095266 AATCAAACAA
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:0.16, C:0.08, G:0.16, T:0.60
Consensus pattern (12 bp):
TTGTTTTTGACA
Found at i:59100873 original size:19 final size:20
Alignment explanation
Indices: 59100839--59100881 Score: 56
Period size: 20 Copynumber: 2.2 Consensus size: 20
59100829 GTTTGTGGGG
59100839 TTTT-TTTAAAATATTT-TA
1 TTTTATTTAAAATATTTATA
59100857 TTTTATTTATAAA-ATTTATA
1 TTTTATTTA-AAATATTTATA
59100877 TTTTA
1 TTTTA
59100882 ATAAATAAAT
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
18 4 0.18
19 8 0.36
20 10 0.45
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (20 bp):
TTTTATTTAAAATATTTATA
Found at i:59101002 original size:13 final size:14
Alignment explanation
Indices: 59100979--59101009 Score: 55
Period size: 13 Copynumber: 2.3 Consensus size: 14
59100969 TCTAAATACT
59100979 TTTTAATTTTTGAA
1 TTTTAATTTTTGAA
59100993 TTTT-ATTTTTGAA
1 TTTTAATTTTTGAA
59101006 TTTT
1 TTTT
59101010 TCAGAATCAA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 13 0.76
14 4 0.24
ACGTcount: A:0.23, C:0.00, G:0.06, T:0.71
Consensus pattern (14 bp):
TTTTAATTTTTGAA
Found at i:59106739 original size:3 final size:3
Alignment explanation
Indices: 59106731--59106768 Score: 76
Period size: 3 Copynumber: 12.7 Consensus size: 3
59106721 TTTTATCCCT
59106731 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
59106769 TCTATCATTT
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 35 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:59109455 original size:58 final size:58
Alignment explanation
Indices: 59109365--59109481 Score: 234
Period size: 58 Copynumber: 2.0 Consensus size: 58
59109355 ATACTTAGGA
59109365 TATGGGGATCTGTTGGATATACCCTCTACTTGTATCAAGACAGTATAGGTCGAGGCAG
1 TATGGGGATCTGTTGGATATACCCTCTACTTGTATCAAGACAGTATAGGTCGAGGCAG
59109423 TATGGGGATCTGTTGGATATACCCTCTACTTGTATCAAGACAGTATAGGTCGAGGCAG
1 TATGGGGATCTGTTGGATATACCCTCTACTTGTATCAAGACAGTATAGGTCGAGGCAG
59109481 T
1 T
59109482 TTGTATCGAC
Statistics
Matches: 59, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
58 59 1.00
ACGTcount: A:0.26, C:0.17, G:0.27, T:0.30
Consensus pattern (58 bp):
TATGGGGATCTGTTGGATATACCCTCTACTTGTATCAAGACAGTATAGGTCGAGGCAG
Found at i:59113792 original size:33 final size:33
Alignment explanation
Indices: 59113747--59113818 Score: 126
Period size: 33 Copynumber: 2.2 Consensus size: 33
59113737 AAATACCTTC
59113747 AAGAAAGAGTCGAGGCACCAATGCTGATGGACA
1 AAGAAAGAGTCGAGGCACCAATGCTGATGGACA
* *
59113780 AAGAAAGGGTCGAGGCACCAATGCTGATGGATA
1 AAGAAAGAGTCGAGGCACCAATGCTGATGGACA
59113813 AAGAAA
1 AAGAAA
59113819 ACCACTTTGG
Statistics
Matches: 37, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
33 37 1.00
ACGTcount: A:0.42, C:0.15, G:0.31, T:0.12
Consensus pattern (33 bp):
AAGAAAGAGTCGAGGCACCAATGCTGATGGACA
Found at i:59117283 original size:294 final size:294
Alignment explanation
Indices: 59116753--59117338 Score: 1091
Period size: 294 Copynumber: 2.0 Consensus size: 294
59116743 AACGACCAAG
* *
59116753 CAAATCATGAGATTCGAATATTATTGGTCCACAATGGAAGGGGATTGTATTAGTTATGCCAACAG
1 CAAATCATGAGATTCAAATATTATTGGTCCACAATAGAAGGGGATTGTATTAGTTATGCCAACAG
59116818 ATTTCATAAATGCCAAATTTATGGAGACAAAATTCATGTACCTCATTCACTTCTTCACATTACAA
66 ATTTCATAAATGCCAAATTTATGGAGACAAAATTCATGTACCTCATTCACTTCTTCACATTACAA
59116883 CTTCTCCATGTCCTTTCTCTATGTAGGGCATGAATGTTATTGGGTCGATCTCGCCAAAAGCTTTC
131 CTTCTCCATGTCCTTTCTCTATGTAGGGCATGAATGTTATTGGGTCGATCTCGCCAAAAGCTTTC
* *
59116948 AATGGGCATCGATTAATCTTTGTGGTCATCAACTGCTTCACCAAGTGGGTAGAAAACACTTCTTA
196 AATGGGCATCGATTAATCTTTATGGTCATCAACTACTTCACCAAGTGGGTAGAAAACACTTCTTA
59117013 CACTAATGTCACGAAGACGATAATCAATAAATGC
261 CACTAATGTCACGAAGACGATAATCAATAAATGC
*
59117047 CAAATCATGAGATTCAAATATTATTGGTCCACAATAGAAGGGGATTGTATTAGTTATGCCAAGAG
1 CAAATCATGAGATTCAAATATTATTGGTCCACAATAGAAGGGGATTGTATTAGTTATGCCAACAG
59117112 ATTTCATAAATGCCAAATTTATGGAGACAAAATTCATGTACCTCATTCACTTCTTCACATTACAA
66 ATTTCATAAATGCCAAATTTATGGAGACAAAATTCATGTACCTCATTCACTTCTTCACATTACAA
* * *
59117177 CTTGTCCATGTCCTTTCTCTATGTAGGGCATGGATGTTATTGGGTTGATCTCGCCAAAAGCTTTC
131 CTTCTCCATGTCCTTTCTCTATGTAGGGCATGAATGTTATTGGGTCGATCTCGCCAAAAGCTTTC
*
59117242 AATGGGCATCGATTCATCTTTATGGTCATCAACTACTTCACCAAGTGGGTAGAAAACACTTCTTA
196 AATGGGCATCGATTAATCTTTATGGTCATCAACTACTTCACCAAGTGGGTAGAAAACACTTCTTA
59117307 CACTAATGTCACGAAGACGATAATCAATAAAT
261 CACTAATGTCACGAAGACGATAATCAATAAAT
59117339 TCTTGAAGAA
Statistics
Matches: 283, Mismatches: 9, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
294 283 1.00
ACGTcount: A:0.32, C:0.20, G:0.17, T:0.32
Consensus pattern (294 bp):
CAAATCATGAGATTCAAATATTATTGGTCCACAATAGAAGGGGATTGTATTAGTTATGCCAACAG
ATTTCATAAATGCCAAATTTATGGAGACAAAATTCATGTACCTCATTCACTTCTTCACATTACAA
CTTCTCCATGTCCTTTCTCTATGTAGGGCATGAATGTTATTGGGTCGATCTCGCCAAAAGCTTTC
AATGGGCATCGATTAATCTTTATGGTCATCAACTACTTCACCAAGTGGGTAGAAAACACTTCTTA
CACTAATGTCACGAAGACGATAATCAATAAATGC
Found at i:59118318 original size:88 final size:88
Alignment explanation
Indices: 59118213--59118392 Score: 261
Period size: 88 Copynumber: 2.0 Consensus size: 88
59118203 TACTATAGCG
* * *
59118213 AATCTTATTTTTCTGAAGTTGCAGTGGAGCAGATTAAAGCTACAAATCTAATCTCCCTGAAATTA
1 AATCTTATTCTCCTGAAGTTGCAGTGGAACAGATTAAAGCTACAAATCTAATCTCCCTGAAATTA
*
59118278 CAATGGAGTAGATTGAAGCTACA
66 CAATGGAGTAGATTGAAGCAACA
* * * * *
59118301 AATCTTATTCTCCTGAAGTTGTAGTGGAATAGATTAAAGCTACAAATTTAATCTCCCTGAAGTTG
1 AATCTTATTCTCCTGAAGTTGCAGTGGAACAGATTAAAGCTACAAATCTAATCTCCCTGAAATTA
* *
59118366 TAGTGGAGTAGATTGAAGCAACA
66 CAATGGAGTAGATTGAAGCAACA
59118389 AATC
1 AATC
59118393 CTATACCTAT
Statistics
Matches: 81, Mismatches: 11, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
88 81 1.00
ACGTcount: A:0.35, C:0.15, G:0.19, T:0.31
Consensus pattern (88 bp):
AATCTTATTCTCCTGAAGTTGCAGTGGAACAGATTAAAGCTACAAATCTAATCTCCCTGAAATTA
CAATGGAGTAGATTGAAGCAACA
Found at i:59118406 original size:44 final size:44
Alignment explanation
Indices: 59118224--59118409 Score: 164
Period size: 44 Copynumber: 4.2 Consensus size: 44
59118214 ATCTTATTTT
* * * *
59118224 TCTGAAGTTGCAGTGGAGCAGATTAAAGCTACAAATCTAAT-CTC
1 TCTGAAGTTGTAGTGGAGTAGATTGAAGCTACAAATCTTATAC-C
* * ** * *
59118268 CCTGAAATTACAATGGAGTAGATTGAAGCTACAAATCTTAT-TC
1 TCTGAAGTTGTAGTGGAGTAGATTGAAGCTACAAATCTTATACC
* *
59118311 TCCTGAAGTTGTAGTGGAATAGATTAAAGCTACAAAT-TTA-ATCTC
1 T-CTGAAGTTGTAGTGGAGTAGATTGAAGCTACAAATCTTATA-C-C
* * *
59118356 CCTGAAGTTGTAGTGGAGTAGATTGAAGCAACAAATCCTATACC
1 TCTGAAGTTGTAGTGGAGTAGATTGAAGCTACAAATCTTATACC
*
59118400 TATGAAGTTG
1 TCTGAAGTTG
59118410 GCAATGGGTA
Statistics
Matches: 113, Mismatches: 23, Indels: 12
0.76 0.16 0.08
Matches are distributed among these distances:
43 4 0.04
44 104 0.92
45 4 0.04
46 1 0.01
ACGTcount: A:0.35, C:0.16, G:0.20, T:0.30
Consensus pattern (44 bp):
TCTGAAGTTGTAGTGGAGTAGATTGAAGCTACAAATCTTATACC
Found at i:59118625 original size:138 final size:137
Alignment explanation
Indices: 59118299--59118630 Score: 409
Period size: 139 Copynumber: 2.4 Consensus size: 137
59118289 ATTGAAGCTA
*
59118299 CAAATCTTATTCTCCTGAAGTTGTAGTGGAATAGATTAAAGCTACAAAT-TTAATCTCCCTGAAG
1 CAAATCTTA-TCTCCTGAAGTTGCAGTGGAATAGA-TAAAGCTACAAATCTT-ATCTCCCTGAAG
** * *
59118363 TTGTAGTGGAGTAGATTGAAGCAACAAATCCTATACCTATGAAGTTGGCAATGGGTAAGATTAAA
63 TTGTAGTCAAGCAGATTGAAGCAACAAATCCCATACCTATGAAGTTGGCAATGGGTAAGATTAAA
59118428 TCTACCATAG
128 TCTACCATAG
** * *
59118438 CAAATCTTATCTCCCTGAAGTTGCAGTAAAACAAGATAAAGCTACAAATCTTATGTCCCTGAAGT
1 CAAATCTTATCT-CCTGAAGTTGCAGTGGAA-TAGATAAAGCTACAAATCTTATCTCCCTGAAGT
** * * *
59118503 TGTAGTCAAGCAGATTGAAGTGACAAATCCCATACCTCTGAAGTT-GCAGTGGGT-CGAATTAAA
64 TGTAGTCAAGCAGATTGAAGCAACAAATCCCATACCTATGAAGTTGGCAATGGGTAAG-ATTAAA
*
59118566 TTTACCATAG
128 TCTACCATAG
* * *
59118576 CAAATATTATCTCCTTGAAGTTGCAGTGGAATGAGATGAAGATACAAATCTTATC
1 CAAATCTTATCTCC-TGAAGTTGCAGTGGAAT-AGATAAAGCTACAAATCTTATC
59118631 CATCTCTGAG
Statistics
Matches: 165, Mismatches: 22, Indels: 13
0.82 0.11 0.06
Matches are distributed among these distances:
137 3 0.02
138 70 0.42
139 87 0.53
140 5 0.03
ACGTcount: A:0.35, C:0.17, G:0.19, T:0.29
Consensus pattern (137 bp):
CAAATCTTATCTCCTGAAGTTGCAGTGGAATAGATAAAGCTACAAATCTTATCTCCCTGAAGTTG
TAGTCAAGCAGATTGAAGCAACAAATCCCATACCTATGAAGTTGGCAATGGGTAAGATTAAATCT
ACCATAG
Found at i:59121232 original size:22 final size:23
Alignment explanation
Indices: 59121207--59121257 Score: 68
Period size: 24 Copynumber: 2.2 Consensus size: 23
59121197 AAAAGTGATA
*
59121207 TAATTATCATGT-AAACATTAAC
1 TAATTATCATATAAAACATTAAC
*
59121229 TAATTTTCATATAGAAACATTAAC
1 TAATTATCATATA-AAACATTAAC
59121253 TAATT
1 TAATT
59121258 GCCACAACAT
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
22 10 0.40
24 15 0.60
ACGTcount: A:0.45, C:0.12, G:0.04, T:0.39
Consensus pattern (23 bp):
TAATTATCATATAAAACATTAAC
Found at i:59131233 original size:163 final size:163
Alignment explanation
Indices: 59130963--59131288 Score: 643
Period size: 163 Copynumber: 2.0 Consensus size: 163
59130953 GACAATAACC
*
59130963 AAAAAAAGAAAAAGAAAAAATAAAGAAAAATGAGAGAAGAGAATAACAAGGATGAAGAAAAAGGA
1 AAAAAAAAAAAAAGAAAAAATAAAGAAAAATGAGAGAAGAGAATAACAAGGATGAAGAAAAAGGA
59131028 GTTAATGCCAACATAATTTTAACTTCTACAAAAAAATGAAATCAGTACTATAGAGAAGTTCAAAA
66 GTTAATGCCAACATAATTTTAACTTCTACAAAAAAATGAAATCAGTACTATAGAGAAGTTCAAAA
59131093 ATATATTCCCTAATGGACAGACCAAGATTCGAA
131 ATATATTCCCTAATGGACAGACCAAGATTCGAA
59131126 AAAAAAAAAAAAAGAAAAAATAAAGAAAAATGAGAGAAGAGAATAACAAGGATGAAGAAAAAGGA
1 AAAAAAAAAAAAAGAAAAAATAAAGAAAAATGAGAGAAGAGAATAACAAGGATGAAGAAAAAGGA
59131191 GTTAATGCCAACATAATTTTAACTTCTACAAAAAAATGAAATCAGTACTATAGAGAAGTTCAAAA
66 GTTAATGCCAACATAATTTTAACTTCTACAAAAAAATGAAATCAGTACTATAGAGAAGTTCAAAA
59131256 ATATATTCCCTAATGGACAGACCAAGATTCGAA
131 ATATATTCCCTAATGGACAGACCAAGATTCGAA
59131289 TACAGGACTA
Statistics
Matches: 162, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
163 162 1.00
ACGTcount: A:0.56, C:0.10, G:0.16, T:0.18
Consensus pattern (163 bp):
AAAAAAAAAAAAAGAAAAAATAAAGAAAAATGAGAGAAGAGAATAACAAGGATGAAGAAAAAGGA
GTTAATGCCAACATAATTTTAACTTCTACAAAAAAATGAAATCAGTACTATAGAGAAGTTCAAAA
ATATATTCCCTAATGGACAGACCAAGATTCGAA
Found at i:59139523 original size:162 final size:162
Alignment explanation
Indices: 59139282--59139634 Score: 546
Period size: 162 Copynumber: 2.2 Consensus size: 162
59139272 CAATTGGGAA
* * * *
59139282 CAGCTCTTTATCCTCAGAGTTTGCAATTGCCCAAGACTATTAGCAACACACATTGGGAAGAGAAA
1 CAGCTCTCTATCTTCAGAGTTTGCAATTTCCCAAGACTATTAGCAACACACACTGGGAAGAGAAA
* * *
59139347 TTTCAACTTATTGC-ATTCAGTGACTTGTACTTCCCTTAGGCATTGGAAGCTTGTGGTTGATACT
66 TTTCAACTTATTGCAATT-AGTGACTTGTAATTCCCTTAGGCATTGGAAGATTATGGTTGATACT
*
59139411 TGTGAGTCTTGGATTATTTCTTCCATTCCAAAG
130 TGTGAGTCTTGAATTATTTCTTCCATTCCAAAG
** *
59139444 TGGCTCTCTATCTTCAGAGTTTGCAATTTCTCAAGACTATTAGCAACACACACTGGGAAGAGAAA
1 CAGCTCTCTATCTTCAGAGTTTGCAATTTCCCAAGACTATTAGCAACACACACTGGGAAGAGAAA
* *
59139509 TTTCAATTTATTGCAATTTGTGACTTGTAATTCCCTTAGGCATTGGAAGATTATGGTTGATACTT
66 TTTCAACTTATTGCAATTAGTGACTTGTAATTCCCTTAGGCATTGGAAGATTATGGTTGATACTT
59139574 GTGAGTCTTGAATTATTTCTTCCATTCCAAAG
131 GTGAGTCTTGAATTATTTCTTCCATTCCAAAG
** *
59139606 CAATTCTGTATCTTCAGAGTTTGCAATTT
1 CAGCTCTCTATCTTCAGAGTTTGCAATTT
59139635 GGGCGCATTT
Statistics
Matches: 172, Mismatches: 18, Indels: 2
0.90 0.09 0.01
Matches are distributed among these distances:
162 169 0.98
163 3 0.02
ACGTcount: A:0.27, C:0.19, G:0.18, T:0.37
Consensus pattern (162 bp):
CAGCTCTCTATCTTCAGAGTTTGCAATTTCCCAAGACTATTAGCAACACACACTGGGAAGAGAAA
TTTCAACTTATTGCAATTAGTGACTTGTAATTCCCTTAGGCATTGGAAGATTATGGTTGATACTT
GTGAGTCTTGAATTATTTCTTCCATTCCAAAG
Found at i:59151743 original size:21 final size:23
Alignment explanation
Indices: 59151696--59151745 Score: 68
Period size: 24 Copynumber: 2.2 Consensus size: 23
59151686 AACAATATTG
59151696 ATATTAAATAAAAAAACTATATTA
1 ATATTAAATAAAAAAACTATA-TA
*
59151720 ATATTAAATAAAAATAC-ATA-A
1 ATATTAAATAAAAAAACTATATA
59151741 ATATT
1 ATATT
59151746 TTCAACTTAT
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
21 6 0.24
23 3 0.12
24 16 0.64
ACGTcount: A:0.62, C:0.04, G:0.00, T:0.34
Consensus pattern (23 bp):
ATATTAAATAAAAAAACTATATA
Found at i:59152046 original size:28 final size:28
Alignment explanation
Indices: 59151984--59152040 Score: 114
Period size: 28 Copynumber: 2.0 Consensus size: 28
59151974 ATTTATCCTT
59151984 TGTTTTTAAAGATATGGATTAATTCACA
1 TGTTTTTAAAGATATGGATTAATTCACA
59152012 TGTTTTTAAAGATATGGATTAATTCACA
1 TGTTTTTAAAGATATGGATTAATTCACA
59152040 T
1 T
59152041 TCTTTTGGGT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 29 1.00
ACGTcount: A:0.35, C:0.07, G:0.14, T:0.44
Consensus pattern (28 bp):
TGTTTTTAAAGATATGGATTAATTCACA
Found at i:59162677 original size:16 final size:16
Alignment explanation
Indices: 59162656--59162686 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
59162646 CCAACTATAA
*
59162656 CTCCAATGACTATTTT
1 CTCCAACGACTATTTT
59162672 CTCCAACGACTATTT
1 CTCCAACGACTATTT
59162687 AATTAGTCAT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.26, C:0.29, G:0.06, T:0.39
Consensus pattern (16 bp):
CTCCAACGACTATTTT
Found at i:59163774 original size:28 final size:28
Alignment explanation
Indices: 59163734--59163794 Score: 113
Period size: 28 Copynumber: 2.2 Consensus size: 28
59163724 ATCAGTTTTT
59163734 ACTAACTCATATAGCTTTCTGAAAATAA
1 ACTAACTCATATAGCTTTCTGAAAATAA
*
59163762 ACTAACTTATATAGCTTTCTGAAAATAA
1 ACTAACTCATATAGCTTTCTGAAAATAA
59163790 ACTAA
1 ACTAA
59163795 GTTTTCTTCT
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
28 32 1.00
ACGTcount: A:0.44, C:0.16, G:0.07, T:0.33
Consensus pattern (28 bp):
ACTAACTCATATAGCTTTCTGAAAATAA
Found at i:59163809 original size:22 final size:24
Alignment explanation
Indices: 59163778--59163822 Score: 67
Period size: 22 Copynumber: 2.0 Consensus size: 24
59163768 TTATATAGCT
*
59163778 TTCTGAAAATAAACTAA-GTTTTC
1 TTCTGAAAATAAACAAATGTTTTC
59163801 TTCT-AAAATAAACAAATGTTTT
1 TTCTGAAAATAAACAAATGTTTT
59163823 AAAATCAACC
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
22 11 0.55
23 9 0.45
ACGTcount: A:0.42, C:0.11, G:0.07, T:0.40
Consensus pattern (24 bp):
TTCTGAAAATAAACAAATGTTTTC
Found at i:59164429 original size:29 final size:29
Alignment explanation
Indices: 59164359--59164434 Score: 89
Period size: 29 Copynumber: 2.6 Consensus size: 29
59164349 ATAAATATTT
* *
59164359 TTTTATTTTTTTATTTTTTAAAAGTAATAA
1 TTTTATTTTATTA-TTTTTAAAAATAATAA
* * *
59164389 TATTAATATATTATTTTTAAAAATAATAA
1 TTTTATTTTATTATTTTTAAAAATAATAA
*
59164418 TTTTATTTTATTGTTTT
1 TTTTATTTTATTATTTT
59164435 AATATTTCAT
Statistics
Matches: 37, Mismatches: 9, Indels: 1
0.79 0.19 0.02
Matches are distributed among these distances:
29 28 0.76
30 9 0.24
ACGTcount: A:0.36, C:0.00, G:0.03, T:0.62
Consensus pattern (29 bp):
TTTTATTTTATTATTTTTAAAAATAATAA
Found at i:59165381 original size:40 final size:39
Alignment explanation
Indices: 59165337--59165472 Score: 137
Period size: 40 Copynumber: 3.4 Consensus size: 39
59165327 GTTTGGACAA
* *
59165337 AAAACGCTGCTAAAAATAAAGCATTAGCGGCGCTTTAAAT
1 AAAACGCCGCTAAAAAT-AAGCATTAGCGGCGCTTTAAAG
** * *
59165377 AAAACGCCGCTAAAGACCAAGCATTAGCGGCGCTTTCAGG
1 AAAACGCCGCTAAA-AATAAGCATTAGCGGCGCTTTAAAG
* * * ***
59165417 AAAACGCCGCCAAAAATGAGCATTAGCGGCGTTTTTTTG
1 AAAACGCCGCTAAAAATAAGCATTAGCGGCGCTTTAAAG
59165456 AAAAACGCCGCTAAAAA
1 -AAAACGCCGCTAAAAA
59165473 CCTAAGCCTC
Statistics
Matches: 79, Mismatches: 15, Indels: 4
0.81 0.15 0.04
Matches are distributed among these distances:
39 18 0.23
40 60 0.76
41 1 0.01
ACGTcount: A:0.38, C:0.22, G:0.21, T:0.19
Consensus pattern (39 bp):
AAAACGCCGCTAAAAATAAGCATTAGCGGCGCTTTAAAG
Found at i:59165950 original size:13 final size:13
Alignment explanation
Indices: 59165934--59165979 Score: 58
Period size: 13 Copynumber: 3.5 Consensus size: 13
59165924 TTGTGATTTA
*
59165934 AGGGTTAAGGTTT
1 AGGGTTAGGGTTT
59165947 AGGGGTTAGGGATTT
1 A-GGGTTAGGG-TTT
59165962 -GGGTTAGGGTTT
1 AGGGTTAGGGTTT
59165974 AGGGTT
1 AGGGTT
59165980 TAGATTAATT
Statistics
Matches: 29, Mismatches: 1, Indels: 6
0.81 0.03 0.17
Matches are distributed among these distances:
12 3 0.10
13 15 0.52
14 8 0.28
15 3 0.10
ACGTcount: A:0.17, C:0.00, G:0.46, T:0.37
Consensus pattern (13 bp):
AGGGTTAGGGTTT
Found at i:59165980 original size:7 final size:7
Alignment explanation
Indices: 59165942--59165982 Score: 50
Period size: 7 Copynumber: 6.0 Consensus size: 7
59165932 TAAGGGTTAA
59165942 GGTTTAG
1 GGTTTAG
*
59165949 GGGTTAG
1 GGTTTAG
59165956 GGATTT-G
1 GG-TTTAG
59165963 GG-TTAG
1 GGTTTAG
59165969 GGTTTAG
1 GGTTTAG
59165976 GGTTTAG
1 GGTTTAG
59165983 ATTAATTAGT
Statistics
Matches: 29, Mismatches: 2, Indels: 6
0.78 0.05 0.16
Matches are distributed among these distances:
5 2 0.07
6 3 0.10
7 22 0.76
8 2 0.07
ACGTcount: A:0.15, C:0.00, G:0.46, T:0.39
Consensus pattern (7 bp):
GGTTTAG
Found at i:59166049 original size:7 final size:7
Alignment explanation
Indices: 59166039--59166127 Score: 88
Period size: 7 Copynumber: 12.7 Consensus size: 7
59166029 TAGTAGTTAT
59166039 GGGTTTG
1 GGGTTTG
59166046 GGGTTTG
1 GGGTTTG
* *
59166053 GGATTTA
1 GGGTTTG
59166060 GGGTTTG
1 GGGTTTG
*
59166067 GGGTTTA
1 GGGTTTG
*
59166074 GGGTTAG
1 GGGTTTG
*
59166081 AGGTTTG
1 GGGTTTG
59166088 GGGTTTG
1 GGGTTTG
* *
59166095 TGATTTG
1 GGGTTTG
*
59166102 GGATTTG
1 GGGTTTG
*
59166109 GGGTTAG
1 GGGTTTG
*
59166116 GGGTTAG
1 GGGTTTG
59166123 GGGTT
1 GGGTT
59166128 AAGGGTTAGA
Statistics
Matches: 67, Mismatches: 15, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
7 67 1.00
ACGTcount: A:0.10, C:0.00, G:0.49, T:0.40
Consensus pattern (7 bp):
GGGTTTG
Found at i:59166049 original size:21 final size:20
Alignment explanation
Indices: 59166018--59166115 Score: 65
Period size: 21 Copynumber: 4.7 Consensus size: 20
59166008 TATTAAATAA
59166018 GGTTTAGGGGTTAGTAGTTATG
1 GGTTT-GGGGTTAGTAGTTA-G
* * *
59166040 GGTTTGGGGTTTGGGATTTAG
1 GGTTTGGGG-TTAGTAGTTAG
*
59166061 GGTTTGGGGTTTAG-GGTTAG
1 GGTTTGGGG-TTAGTAGTTAG
* *
59166081 AGGTTTGGGGTTTGT-GATTTG
1 -GGTTTGGGGTTAGTAG-TTAG
59166102 GGATTTGGGGTTAG
1 GG-TTTGGGGTTAG
59166116 GGGTTAGGGG
Statistics
Matches: 62, Mismatches: 9, Indels: 11
0.76 0.11 0.13
Matches are distributed among these distances:
20 10 0.16
21 40 0.65
22 12 0.19
ACGTcount: A:0.12, C:0.00, G:0.46, T:0.42
Consensus pattern (20 bp):
GGTTTGGGGTTAGTAGTTAG
Found at i:59166120 original size:42 final size:42
Alignment explanation
Indices: 59166040--59166127 Score: 126
Period size: 42 Copynumber: 2.1 Consensus size: 42
59166030 AGTAGTTATG
59166040 GGTTTGGGGTTTGGGATTTAGGGTTTGGGGTTTAGGGTTAGA
1 GGTTTGGGGTTTGGGATTTAGGGTTTGGGGTTTAGGGTTAGA
* *
59166082 GGTTTGGGGTTTGTGATTT-GGGATTTGGGG-TTAGGGGTTAGG
1 GGTTTGGGGTTTGGGATTTAGGG-TTTGGGGTTTA-GGGTTAGA
59166124 GGTT
1 GGTT
59166128 AAGGGTTAGA
Statistics
Matches: 42, Mismatches: 2, Indels: 4
0.88 0.04 0.08
Matches are distributed among these distances:
41 6 0.14
42 36 0.86
ACGTcount: A:0.10, C:0.00, G:0.49, T:0.41
Consensus pattern (42 bp):
GGTTTGGGGTTTGGGATTTAGGGTTTGGGGTTTAGGGTTAGA
Found at i:59166128 original size:7 final size:7
Alignment explanation
Indices: 59166021--59166142 Score: 59
Period size: 7 Copynumber: 17.4 Consensus size: 7
59166011 TAAATAAGGT
59166021 TTAGGGG
1 TTAGGGG
**
59166028 TTAGTAG
1 TTAGGGG
*
59166035 TTATGGG
1 TTAGGGG
*
59166042 TTTGGGG
1 TTAGGGG
* *
59166049 TTTGGGAT
1 TTAGGG-G
59166057 TTA-GGG
1 TTAGGGG
*
59166063 TTTGGGG
1 TTAGGGG
59166070 TTTA-GGG
1 -TTAGGGG
*
59166077 TTAGAGG
1 TTAGGGG
*
59166084 TTTGGGG
1 TTAGGGG
* * *
59166091 TTTGTGA
1 TTAGGGG
* *
59166098 TTTGGGA
1 TTAGGGG
*
59166105 TTTGGGG
1 TTAGGGG
59166112 TTAGGGG
1 TTAGGGG
59166119 TTAGGGG
1 TTAGGGG
*
59166126 TTAAGGG
1 TTAGGGG
*
59166133 TTAGAGG
1 TTAGGGG
59166140 TTA
1 TTA
59166143 AGAGTTAGTG
Statistics
Matches: 88, Mismatches: 23, Indels: 8
0.74 0.19 0.07
Matches are distributed among these distances:
6 5 0.06
7 79 0.90
8 4 0.05
ACGTcount: A:0.15, C:0.00, G:0.46, T:0.39
Consensus pattern (7 bp):
TTAGGGG
Found at i:59166143 original size:14 final size:14
Alignment explanation
Indices: 59166110--59166150 Score: 55
Period size: 14 Copynumber: 2.9 Consensus size: 14
59166100 TGGGATTTGG
* *
59166110 GGTTAGGGGTTAGG
1 GGTTAAGGGTTAGA
59166124 GGTTAAGGGTTAGA
1 GGTTAAGGGTTAGA
*
59166138 GGTTAAGAGTTAG
1 GGTTAAGGGTTAG
59166151 TGATTTAAGG
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
14 24 1.00
ACGTcount: A:0.24, C:0.00, G:0.46, T:0.29
Consensus pattern (14 bp):
GGTTAAGGGTTAGA
Found at i:59166149 original size:21 final size:21
Alignment explanation
Indices: 59166109--59166149 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
59166099 TTGGGATTTG
* * *
59166109 GGGTTAGGGGTTAGGGGTTAA
1 GGGTTAGAGGTTAAGAGTTAA
59166130 GGGTTAGAGGTTAAGAGTTA
1 GGGTTAGAGGTTAAGAGTTA
59166150 GTGATTTAAG
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.24, C:0.00, G:0.46, T:0.29
Consensus pattern (21 bp):
GGGTTAGAGGTTAAGAGTTAA
Found at i:59166456 original size:7 final size:7
Alignment explanation
Indices: 59166446--59166527 Score: 58
Period size: 7 Copynumber: 11.7 Consensus size: 7
59166436 TAGTAGTTAT
59166446 GGGTTTG
1 GGGTTTG
59166453 GGGTTTG
1 GGGTTTG
*
59166460 GGGTTTA
1 GGGTTTG
*
59166467 AGGTTTG
1 GGGTTTG
* *
59166474 GTGTTTA
1 GGGTTTG
*
59166481 GGGTTAG
1 GGGTTTG
**
59166488 ATGTTTG
1 GGGTTTG
59166495 GGGTTAT-
1 GGGTT-TG
59166502 GGGTTTG
1 GGGTTTG
* *
59166509 GGATTTA
1 GGGTTTG
*
59166516 GGGTTAG
1 GGGTTTG
59166523 GGGTT
1 GGGTT
59166528 AGAGATTAAG
Statistics
Matches: 54, Mismatches: 19, Indels: 4
0.70 0.25 0.05
Matches are distributed among these distances:
6 1 0.02
7 52 0.96
8 1 0.02
ACGTcount: A:0.11, C:0.00, G:0.46, T:0.43
Consensus pattern (7 bp):
GGGTTTG
Found at i:59166471 original size:21 final size:21
Alignment explanation
Indices: 59166447--59166531 Score: 68
Period size: 21 Copynumber: 4.0 Consensus size: 21
59166437 AGTAGTTATG
59166447 GGTTTGGGGTTTGGGGTTTA-A
1 GGTTTGGGGTTTGGGG-TTAGA
* *
59166468 GGTTTGGTGTTTAGGGTTAGA
1 GGTTTGGGGTTTGGGGTTAGA
* *
59166489 TGTTTGGGGTTAT-GGGTTTG-
1 GGTTTGGGGTT-TGGGGTTAGA
* *
59166509 GGATTTAGGGTTAGGGGTTAGA
1 GG-TTTGGGGTTTGGGGTTAGA
59166531 G
1 G
59166532 ATTAAGAGTT
Statistics
Matches: 50, Mismatches: 9, Indels: 9
0.74 0.13 0.13
Matches are distributed among these distances:
20 4 0.08
21 44 0.88
22 2 0.04
ACGTcount: A:0.13, C:0.00, G:0.46, T:0.41
Consensus pattern (21 bp):
GGTTTGGGGTTTGGGGTTAGA
Found at i:59166494 original size:35 final size:35
Alignment explanation
Indices: 59166455--59166522 Score: 95
Period size: 35 Copynumber: 1.9 Consensus size: 35
59166445 TGGGTTTGGG
59166455 GTTTGGGGTT-TAAGGTTTGGTG-TTTAGGGTTAGAT
1 GTTTGGGGTTAT-AGGTTTGG-GATTTAGGGTTAGAT
*
59166490 GTTTGGGGTTATGGGTTTGGGATTTAGGGTTAG
1 GTTTGGGGTTATAGGTTTGGGATTTAGGGTTAG
59166523 GGGTTAGAGA
Statistics
Matches: 30, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
34 1 0.03
35 28 0.93
36 1 0.03
ACGTcount: A:0.13, C:0.00, G:0.43, T:0.44
Consensus pattern (35 bp):
GTTTGGGGTTATAGGTTTGGGATTTAGGGTTAGAT
Found at i:59166534 original size:21 final size:21
Alignment explanation
Indices: 59166481--59166543 Score: 56
Period size: 21 Copynumber: 3.0 Consensus size: 21
59166471 TTGGTGTTTA
* *
59166481 GGGTTAGATG-TTTGGGGTTAT
1 GGGTTAGA-GATTTAGGGTTAG
* *
59166502 GGGTTTGGGATTTAGGGTTAG
1 GGGTTAGAGATTTAGGGTTAG
* *
59166523 GGGTTAGAGATTAAGAGTTAG
1 GGGTTAGAGATTTAGGGTTAG
59166544 TGATTTAAGG
Statistics
Matches: 33, Mismatches: 8, Indels: 2
0.77 0.19 0.05
Matches are distributed among these distances:
20 1 0.03
21 32 0.97
ACGTcount: A:0.21, C:0.00, G:0.43, T:0.37
Consensus pattern (21 bp):
GGGTTAGAGATTTAGGGTTAG
Found at i:59166963 original size:5 final size:5
Alignment explanation
Indices: 59166953--59166984 Score: 64
Period size: 5 Copynumber: 6.4 Consensus size: 5
59166943 AAAACCAATC
59166953 AATAT AATAT AATAT AATAT AATAT AATAT AA
1 AATAT AATAT AATAT AATAT AATAT AATAT AA
59166985 AAATAATTAT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 27 1.00
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (5 bp):
AATAT
Found at i:59170861 original size:43 final size:43
Alignment explanation
Indices: 59170796--59170977 Score: 258
Period size: 43 Copynumber: 4.3 Consensus size: 43
59170786 ATGGCACTTT
* **
59170796 TAGCGGCGTTTGTGAAAAAAGCGCCGCTAAAAGTTATGATCTA
1 TAGCGGCGTTTGTGAGAAAAGCGCCGCTAAAAGTCCTGATCTA
* * *
59170839 TAGCGGCGTTCGTGAGAGAAGCGTCGCTAAAAGTCCTGATCTA
1 TAGCGGCGTTTGTGAGAAAAGCGCCGCTAAAAGTCCTGATCTA
* *
59170882 TAGCGGCGTTTGTGGGAAAAGCGCCGCTAAAGGTCCTGATCTA
1 TAGCGGCGTTTGTGAGAAAAGCGCCGCTAAAAGTCCTGATCTA
* * *
59170925 TAGCGGCGTTTGTG-GGAAAGCGCCGCTAAAGGTCTTGATCTA
1 TAGCGGCGTTTGTGAGAAAAGCGCCGCTAAAAGTCCTGATCTA
59170967 TAGCGGCGTTT
1 TAGCGGCGTTT
59170978 ATTTCTAAAA
Statistics
Matches: 126, Mismatches: 13, Indels: 1
0.90 0.09 0.01
Matches are distributed among these distances:
42 37 0.29
43 89 0.71
ACGTcount: A:0.25, C:0.19, G:0.31, T:0.25
Consensus pattern (43 bp):
TAGCGGCGTTTGTGAGAAAAGCGCCGCTAAAAGTCCTGATCTA
Found at i:59170993 original size:86 final size:86
Alignment explanation
Indices: 59170796--59170999 Score: 250
Period size: 86 Copynumber: 2.4 Consensus size: 86
59170786 ATGGCACTTT
* * *
59170796 TAGCGGCGTTTGTG-AAAAAAGCGCCGCTAAAAGTTATGATCTATAGCGGCGTTCGTGAGAGAAG
1 TAGCGGCGTTTGTGCGAAAAA-CGCCGCTAAAGGTCATGATCTATAGCGGCGTTCGTGAGAGAAG
*
59170860 CGTCGCTAAAAGTCCTGATCTA
65 CGCCGCTAAAAGTCCTGATCTA
* * * * *
59170882 TAGCGGCGTTTGTGGGAAAAGCGCCGCTAAAGGTCCTGATCTATAGCGGCGTTTGTGGGA-AAGC
1 TAGCGGCGTTTGTGCGAAAAACGCCGCTAAAGGTCATGATCTATAGCGGCGTTCGTGAGAGAAGC
* *
59170946 GCCGCTAAAGGTCTTGATCTA
66 GCCGCTAAAAGTCCTGATCTA
* * *
59170967 TAGCGGCGTTTATTTCTAAAAACGCCGCTAAAG
1 TAGCGGCGTTT-GTGCGAAAAACGCCGCTAAAG
59171000 TTTGCGGCAC
Statistics
Matches: 101, Mismatches: 15, Indels: 4
0.84 0.12 0.03
Matches are distributed among these distances:
85 33 0.33
86 64 0.63
87 4 0.04
ACGTcount: A:0.26, C:0.20, G:0.29, T:0.25
Consensus pattern (86 bp):
TAGCGGCGTTTGTGCGAAAAACGCCGCTAAAGGTCATGATCTATAGCGGCGTTCGTGAGAGAAGC
GCCGCTAAAAGTCCTGATCTA
Found at i:59176316 original size:41 final size:41
Alignment explanation
Indices: 59176266--59176354 Score: 151
Period size: 41 Copynumber: 2.2 Consensus size: 41
59176256 CAAAAATCAC
* *
59176266 CTAATTACATCAAGTACATTAAAAACTTAGTTCAAATCTAA
1 CTAAGTACATCAAGTACATTAAAAACTTACTTCAAATCTAA
*
59176307 CTAAGTACATCAAGTACATTAACAACTTACTTCAAATCTAA
1 CTAAGTACATCAAGTACATTAAAAACTTACTTCAAATCTAA
59176348 CTAAGTA
1 CTAAGTA
59176355 GCAAAACATT
Statistics
Matches: 45, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
41 45 1.00
ACGTcount: A:0.45, C:0.19, G:0.06, T:0.30
Consensus pattern (41 bp):
CTAAGTACATCAAGTACATTAAAAACTTACTTCAAATCTAA
Found at i:59176341 original size:22 final size:22
Alignment explanation
Indices: 59176270--59176341 Score: 53
Period size: 22 Copynumber: 3.4 Consensus size: 22
59176260 AATCACCTAA
*
59176270 TTACATCAAGTACATTAAAAAC
1 TTACATCAAGTACATTAACAAC
** *
59176292 TTAGTTCAAAT-C--TAACTAA-
1 TTACATCAAGTACATTAAC-AAC
*
59176311 GTACATCAAGTACATTAACAAC
1 TTACATCAAGTACATTAACAAC
*
59176333 TTACTTCAA
1 TTACATCAA
59176342 ATCTAACTAA
Statistics
Matches: 35, Mismatches: 10, Indels: 10
0.64 0.18 0.18
Matches are distributed among these distances:
19 10 0.29
20 3 0.09
21 3 0.09
22 19 0.54
ACGTcount: A:0.44, C:0.19, G:0.06, T:0.31
Consensus pattern (22 bp):
TTACATCAAGTACATTAACAAC
Found at i:59176656 original size:14 final size:13
Alignment explanation
Indices: 59176628--59176653 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
59176618 GTGAGCAATT
59176628 TAAAAAAATTCAA
1 TAAAAAAATTCAA
59176641 TAAAAAAATTCAA
1 TAAAAAAATTCAA
59176654 ATAGTTATGA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.69, C:0.08, G:0.00, T:0.23
Consensus pattern (13 bp):
TAAAAAAATTCAA
Found at i:59183124 original size:7 final size:7
Alignment explanation
Indices: 59183112--59183144 Score: 50
Period size: 7 Copynumber: 4.7 Consensus size: 7
59183102 TTGATTTATT
59183112 TTTTTTA
1 TTTTTTA
59183119 TTTTTT-
1 TTTTTTA
59183125 TATTTTTA
1 T-TTTTTA
59183133 TTTTTTA
1 TTTTTTA
59183140 TTTTT
1 TTTTT
59183145 CCCAAAACTC
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
6 1 0.04
7 22 0.92
8 1 0.04
ACGTcount: A:0.12, C:0.00, G:0.00, T:0.88
Consensus pattern (7 bp):
TTTTTTA
Found at i:59183132 original size:14 final size:13
Alignment explanation
Indices: 59183113--59183144 Score: 55
Period size: 13 Copynumber: 2.4 Consensus size: 13
59183103 TGATTTATTT
59183113 TTTTTATTTTTTTA
1 TTTTTA-TTTTTTA
59183127 TTTTTATTTTTTA
1 TTTTTATTTTTTA
59183140 TTTTT
1 TTTTT
59183145 CCCAAAACTC
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
13 12 0.67
14 6 0.33
ACGTcount: A:0.12, C:0.00, G:0.00, T:0.88
Consensus pattern (13 bp):
TTTTTATTTTTTA
Found at i:59184368 original size:21 final size:19
Alignment explanation
Indices: 59184327--59184368 Score: 57
Period size: 19 Copynumber: 2.1 Consensus size: 19
59184317 CAACATAACA
*
59184327 AAACATCTCATTTCCATAT
1 AAACATCTCATTTCAATAT
59184346 AAACATCTCATTTTCGAATAT
1 AAACATCTCA-TTTC-AATAT
59184367 AA
1 AA
59184369 TCTCATATAC
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
19 10 0.50
20 4 0.20
21 6 0.30
ACGTcount: A:0.40, C:0.21, G:0.02, T:0.36
Consensus pattern (19 bp):
AAACATCTCATTTCAATAT
Found at i:59186151 original size:26 final size:25
Alignment explanation
Indices: 59186105--59186158 Score: 65
Period size: 25 Copynumber: 2.1 Consensus size: 25
59186095 ATAATCAAGA
59186105 ATATAATAATAAAGCATTTAAATCAT
1 ATATAATAATAAAGCATTTAAA-CAT
* *
59186131 ATATAAT-ATAATGCTTATTAAACAT
1 ATATAATAATAAAGCAT-TTAAACAT
59186156 ATA
1 ATA
59186159 AACTTACCTC
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
25 13 0.52
26 12 0.48
ACGTcount: A:0.52, C:0.07, G:0.04, T:0.37
Consensus pattern (25 bp):
ATATAATAATAAAGCATTTAAACAT
Found at i:59189212 original size:5 final size:6
Alignment explanation
Indices: 59189196--59189220 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
59189186 TTTTTCGGTG
59189196 GAAAAA GAAAAA GAAAAA GAAAAA G
1 GAAAAA GAAAAA GAAAAA GAAAAA G
59189221 CAAGAAAGGA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.80, C:0.00, G:0.20, T:0.00
Consensus pattern (6 bp):
GAAAAA
Found at i:59191552 original size:34 final size:35
Alignment explanation
Indices: 59191478--59191552 Score: 107
Period size: 35 Copynumber: 2.2 Consensus size: 35
59191468 GCTTTGTTGA
* * *
59191478 ATGAGCTCAGGTGAGTTTTAATCTGTCTTGGCATG
1 ATGAACTCAGGTGAGTTCTAATCTGTCTTGACATG
*
59191513 ATGAACTCAGGTGAGTTCTAATCTG-CTTTACATG
1 ATGAACTCAGGTGAGTTCTAATCTGTCTTGACATG
59191547 ATGAAC
1 ATGAAC
59191553 CAAGCTCATG
Statistics
Matches: 36, Mismatches: 4, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
34 13 0.36
35 23 0.64
ACGTcount: A:0.25, C:0.16, G:0.24, T:0.35
Consensus pattern (35 bp):
ATGAACTCAGGTGAGTTCTAATCTGTCTTGACATG
Found at i:59196141 original size:32 final size:32
Alignment explanation
Indices: 59196105--59196176 Score: 81
Period size: 32 Copynumber: 2.2 Consensus size: 32
59196095 GTTGCTATAT
* *
59196105 TTAAAAATTTAACATTTTAGTTGATATTTTCA
1 TTAAAAATTTAACATTTTAGTCGACATTTTCA
** * * *
59196137 TTAAAAGCTTAACGTTTTAGTCGGCATTTTTA
1 TTAAAAATTTAACATTTTAGTCGACATTTTCA
59196169 TTAAAAAT
1 TTAAAAAT
59196177 GATGGTCAAA
Statistics
Matches: 31, Mismatches: 9, Indels: 0
0.77 0.22 0.00
Matches are distributed among these distances:
32 31 1.00
ACGTcount: A:0.36, C:0.08, G:0.10, T:0.46
Consensus pattern (32 bp):
TTAAAAATTTAACATTTTAGTCGACATTTTCA
Found at i:59201557 original size:2 final size:2
Alignment explanation
Indices: 59201550--59201596 Score: 94
Period size: 2 Copynumber: 23.5 Consensus size: 2
59201540 TTTCCTAATT
59201550 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
59201592 AG AG A
1 AG AG A
59201597 TGAAATTAAT
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 45 1.00
ACGTcount: A:0.51, C:0.00, G:0.49, T:0.00
Consensus pattern (2 bp):
AG
Found at i:59203793 original size:20 final size:20
Alignment explanation
Indices: 59203768--59203806 Score: 62
Period size: 20 Copynumber: 1.9 Consensus size: 20
59203758 AAAAGTAATG
59203768 TAGTTTTAG-TTTAATTTTTT
1 TAGTTTT-GTTTTAATTTTTT
59203788 TAGTTTTGTTTTAATTTTT
1 TAGTTTTGTTTTAATTTTT
59203807 GTTGAAGTCG
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
19 1 0.06
20 17 0.94
ACGTcount: A:0.18, C:0.00, G:0.10, T:0.72
Consensus pattern (20 bp):
TAGTTTTGTTTTAATTTTTT
Found at i:59204295 original size:29 final size:27
Alignment explanation
Indices: 59204232--59204302 Score: 74
Period size: 28 Copynumber: 2.6 Consensus size: 27
59204222 AATTATTTGT
*
59204232 AAATTTAATTATACATGAAATATTTTAA
1 AAATTTAAATATA-ATGAAATATTTTAA
*
59204260 AATTTTAAATATAAT-AAATAATATTTAA
1 AAATTTAAATATAATGAAAT-AT-TTTAA
59204288 ATAATTT-AATATAAT
1 A-AATTTAAATATAAT
59204303 TATATATAAA
Statistics
Matches: 37, Mismatches: 3, Indels: 6
0.80 0.07 0.13
Matches are distributed among these distances:
26 4 0.11
27 4 0.11
28 25 0.68
29 4 0.11
ACGTcount: A:0.54, C:0.01, G:0.01, T:0.44
Consensus pattern (27 bp):
AAATTTAAATATAATGAAATATTTTAA
Found at i:59206161 original size:18 final size:18
Alignment explanation
Indices: 59206138--59206174 Score: 74
Period size: 18 Copynumber: 2.1 Consensus size: 18
59206128 AACTTAAATA
59206138 TTTTTATATTTTAATATC
1 TTTTTATATTTTAATATC
59206156 TTTTTATATTTTAATATC
1 TTTTTATATTTTAATATC
59206174 T
1 T
59206175 CAAAGAAATG
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.27, C:0.05, G:0.00, T:0.68
Consensus pattern (18 bp):
TTTTTATATTTTAATATC
Found at i:59206404 original size:32 final size:32
Alignment explanation
Indices: 59206368--59206429 Score: 88
Period size: 32 Copynumber: 1.9 Consensus size: 32
59206358 AGCCCGGGTT
* *
59206368 AAATAAATACCAAAAAATTATTTTAAAAATTA
1 AAATAAAAACCAAAAAAGTATTTTAAAAATTA
**
59206400 AAATAAAAATTAAAAAAGTATTTTAAAAAT
1 AAATAAAAACCAAAAAAGTATTTTAAAAAT
59206430 ATTTTAAAAT
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
32 26 1.00
ACGTcount: A:0.65, C:0.03, G:0.02, T:0.31
Consensus pattern (32 bp):
AAATAAAAACCAAAAAAGTATTTTAAAAATTA
Found at i:59206461 original size:40 final size:39
Alignment explanation
Indices: 59206397--59206533 Score: 185
Period size: 40 Copynumber: 3.5 Consensus size: 39
59206387 ATTTTAAAAA
59206397 TTAAAA-T-AAAAATT-AAAAAAGTATTTTAAAAATATT
1 TTAAAATTAAAAAATTAAAAAAAGTATTTTAAAAATATT
*
59206433 TTAAAATTAAACAAATTAAAAAAAGTATTTTAAAAAAATT
1 TTAAAATTAAA-AAATTAAAAAAAGTATTTTAAAAATATT
*
59206473 TTAAAATTAAAAAAATTTTAAAAAAAGTATTTTAAAAGTATT
1 TTAAAATT-AAAAAA--TTAAAAAAAGTATTTTAAAAATATT
59206515 TTAAAA-TAAAAAA-TAAAAA
1 TTAAAATTAAAAAATTAAAAA
59206534 TATTTATTAT
Statistics
Matches: 91, Mismatches: 3, Indels: 13
0.85 0.03 0.12
Matches are distributed among these distances:
36 6 0.07
37 7 0.08
38 2 0.02
39 5 0.05
40 38 0.42
41 4 0.04
42 29 0.32
ACGTcount: A:0.63, C:0.01, G:0.03, T:0.34
Consensus pattern (39 bp):
TTAAAATTAAAAAATTAAAAAAAGTATTTTAAAAATATT
Found at i:59206482 original size:17 final size:17
Alignment explanation
Indices: 59206462--59206495 Score: 68
Period size: 17 Copynumber: 2.0 Consensus size: 17
59206452 AAAAAGTATT
59206462 TTAAAAAAATTTTAAAA
1 TTAAAAAAATTTTAAAA
59206479 TTAAAAAAATTTTAAAA
1 TTAAAAAAATTTTAAAA
59206496 AAAGTATTTT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (17 bp):
TTAAAAAAATTTTAAAA
Found at i:59206483 original size:31 final size:30
Alignment explanation
Indices: 59206445--59206509 Score: 87
Period size: 31 Copynumber: 2.1 Consensus size: 30
59206435 AAAATTAAAC
*
59206445 AAATTAAAAAAAGTATTTTAAAAAA-ATTTTA
1 AAATTAAAAAAA-T-TTTAAAAAAAGATTTTA
59206476 AAATTAAAAAAATTTTAAAAAAAGTATTTTA
1 AAATTAAAAAAATTTTAAAAAAAG-ATTTTA
59206507 AAA
1 AAA
59206510 GTATTTTAAA
Statistics
Matches: 31, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
29 9 0.29
30 1 0.03
31 21 0.68
ACGTcount: A:0.63, C:0.00, G:0.03, T:0.34
Consensus pattern (30 bp):
AAATTAAAAAAATTTTAAAAAAAGATTTTA
Found at i:59206509 original size:11 final size:11
Alignment explanation
Indices: 59206495--59206520 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
59206485 AAATTTTAAA
59206495 AAAAGTATTTT
1 AAAAGTATTTT
59206506 AAAAGTATTTT
1 AAAAGTATTTT
59206517 AAAA
1 AAAA
59206521 TAAAAAATAA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.54, C:0.00, G:0.08, T:0.38
Consensus pattern (11 bp):
AAAAGTATTTT
Found at i:59211621 original size:19 final size:20
Alignment explanation
Indices: 59211597--59211638 Score: 59
Period size: 19 Copynumber: 2.1 Consensus size: 20
59211587 AATTTTTTTT
59211597 ATTTTAAAAAAAACTC-AAA
1 ATTTTAAAAAAAACTCTAAA
* *
59211616 ATTTTAAGAAAAAGTCTAAA
1 ATTTTAAAAAAAACTCTAAA
59211636 ATT
1 ATT
59211639 ACTCCCCCAT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
19 14 0.70
20 6 0.30
ACGTcount: A:0.57, C:0.07, G:0.05, T:0.31
Consensus pattern (20 bp):
ATTTTAAAAAAAACTCTAAA
Found at i:59222686 original size:65 final size:66
Alignment explanation
Indices: 59222602--59222741 Score: 192
Period size: 66 Copynumber: 2.1 Consensus size: 66
59222592 GGATCTCTAT
* *
59222602 CACACCAAATAGACTCATAGAGCCAAACATGT-CCCATAAGTGAAGAATAAAACTAACACTCTCC
1 CACACC-AATAGACTCATAGAGCCAAACATATCCCCAAAAGTGAAGAATAAAACTAACACTCTCC
59222666 AA
65 AA
* * * ** *
59222668 CACACCAATTGACTCATAGAGTCGAACATATCCCCAAAAGTGAAGCTTAAAGCTAACACTCTCCA
1 CACACCAATAGACTCATAGAGCCAAACATATCCCCAAAAGTGAAGAATAAAACTAACACTCTCCA
59222733 A
66 A
59222734 CACACCAA
1 CACACCAA
59222742 ACATGTATTG
Statistics
Matches: 65, Mismatches: 8, Indels: 2
0.87 0.11 0.03
Matches are distributed among these distances:
65 21 0.32
66 44 0.68
ACGTcount: A:0.43, C:0.29, G:0.11, T:0.17
Consensus pattern (66 bp):
CACACCAATAGACTCATAGAGCCAAACATATCCCCAAAAGTGAAGAATAAAACTAACACTCTCCA
A
Found at i:59225929 original size:20 final size:20
Alignment explanation
Indices: 59225904--59225959 Score: 59
Period size: 20 Copynumber: 3.0 Consensus size: 20
59225894 CTCTCAAATG
59225904 TGAGCATTAATATCTCATAA
1 TGAGCATTAATATCTCATAA
**
59225924 TGAGC----A-ATCTTGTAA
1 TGAGCATTAATATCTCATAA
59225939 TGAGCATTAATATCTCATAA
1 TGAGCATTAATATCTCATAA
59225959 T
1 T
59225960 TTTCTGAATC
Statistics
Matches: 27, Mismatches: 4, Indels: 10
0.66 0.10 0.24
Matches are distributed among these distances:
15 12 0.44
16 1 0.04
19 1 0.04
20 13 0.48
ACGTcount: A:0.38, C:0.14, G:0.12, T:0.36
Consensus pattern (20 bp):
TGAGCATTAATATCTCATAA
Found at i:59232308 original size:14 final size:14
Alignment explanation
Indices: 59232289--59232336 Score: 62
Period size: 14 Copynumber: 3.4 Consensus size: 14
59232279 TCTATTTCTT
59232289 TTATTTTTTTAATA
1 TTATTTTTTTAATA
*
59232303 TTATTTTATTAA-A
1 TTATTTTTTTAATA
*
59232316 TGTAATTTTTTAATA
1 T-TATTTTTTTAATA
59232331 TTATTT
1 TTATTT
59232337 ACAAAATTAA
Statistics
Matches: 28, Mismatches: 4, Indels: 4
0.78 0.11 0.11
Matches are distributed among these distances:
13 2 0.07
14 24 0.86
15 2 0.07
ACGTcount: A:0.31, C:0.00, G:0.02, T:0.67
Consensus pattern (14 bp):
TTATTTTTTTAATA
Found at i:59238462 original size:3 final size:3
Alignment explanation
Indices: 59238454--59238487 Score: 68
Period size: 3 Copynumber: 11.3 Consensus size: 3
59238444 CAAGAACCAA
59238454 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A
59238488 GGTCCTTTTT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 31 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:59238947 original size:6 final size:6
Alignment explanation
Indices: 59238936--59238963 Score: 56
Period size: 6 Copynumber: 4.7 Consensus size: 6
59238926 TTTTAGTTTA
59238936 ATTGGT ATTGGT ATTGGT ATTGGT ATTG
1 ATTGGT ATTGGT ATTGGT ATTGGT ATTG
59238964 TTGCTAGTAT
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:0.18, C:0.00, G:0.32, T:0.50
Consensus pattern (6 bp):
ATTGGT
Found at i:59240263 original size:79 final size:80
Alignment explanation
Indices: 59240164--59240331 Score: 275
Period size: 79 Copynumber: 2.1 Consensus size: 80
59240154 GAATTTATCT
* * * *
59240164 ATTTTTAAATTAAAATTAAATTATAATTTTTACGATAGTAAAATTGTAATTTTATCGTTTTAATA
1 ATTTTTAAAATAAAATTAAATTATAAATTTTACGATAGTAAAATTATAATTTTATCATTTTAATA
*
59240229 ACCTAAATTTTTATA
66 ACCTAAATCTTTATA
*
59240244 ATTTTTAAAAT-AAATTAAATTATAAATTTTATGATAGTAAAATTATAATTTTATCATTTTAATA
1 ATTTTTAAAATAAAATTAAATTATAAATTTTACGATAGTAAAATTATAATTTTATCATTTTAATA
59240308 ACCTAAATCTTTATA
66 ACCTAAATCTTTATA
59240323 ATTTTTAAA
1 ATTTTTAAA
59240332 GGATTAAATC
Statistics
Matches: 82, Mismatches: 6, Indels: 1
0.92 0.07 0.01
Matches are distributed among these distances:
79 72 0.88
80 10 0.12
ACGTcount: A:0.43, C:0.05, G:0.04, T:0.48
Consensus pattern (80 bp):
ATTTTTAAAATAAAATTAAATTATAAATTTTACGATAGTAAAATTATAATTTTATCATTTTAATA
ACCTAAATCTTTATA
Found at i:59242713 original size:31 final size:32
Alignment explanation
Indices: 59242662--59242722 Score: 79
Period size: 31 Copynumber: 1.9 Consensus size: 32
59242652 TTATAAAATT
* * * *
59242662 AATGATACATTATATTTAAA-TAATTTAATAA
1 AATGATACATAAAATATAAATTAATCTAATAA
59242693 AATGATACATAAAATATAAATTAATCTAAT
1 AATGATACATAAAATATAAATTAATCTAAT
59242723 TTTTTATATA
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
31 17 0.68
32 8 0.32
ACGTcount: A:0.54, C:0.05, G:0.03, T:0.38
Consensus pattern (32 bp):
AATGATACATAAAATATAAATTAATCTAATAA
Found at i:59247128 original size:27 final size:24
Alignment explanation
Indices: 59247098--59247157 Score: 66
Period size: 24 Copynumber: 2.4 Consensus size: 24
59247088 GAAAACAAGA
59247098 TTTAAAATCAACTATATACAAAATAAT
1 TTTAAAAT--ACTATATACAAAA-AAT
* **
59247125 TTTAAAATATTATATATGAAAAAT
1 TTTAAAATACTATATACAAAAAAT
59247149 TTTAAAATA
1 TTTAAAATA
59247158 AATAATAACA
Statistics
Matches: 30, Mismatches: 3, Indels: 3
0.83 0.08 0.08
Matches are distributed among these distances:
24 12 0.40
25 10 0.33
27 8 0.27
ACGTcount: A:0.55, C:0.05, G:0.02, T:0.38
Consensus pattern (24 bp):
TTTAAAATACTATATACAAAAAAT
Found at i:59249170 original size:82 final size:82
Alignment explanation
Indices: 59249068--59250331 Score: 1736
Period size: 82 Copynumber: 15.4 Consensus size: 82
59249058 TGTGTTTTTA
* * * *
59249068 GTCTGCTCCACTACTGCTTAGGGAGATAAGACTGGATGTGATCTACTCCACTATTGCTTAGGTGA
1 GTCTGCTCCACTATTGCTTAGGGAGATAAGACTTGATGCGATCTGCTCCACTATTGCTTAGG-GA
59249133 -ATAAGATCTGTGGTTCT
65 GATAAGATCTGTGGTTCT
* * * *
59249150 GTCTACTCCACTATTGCTTAGGGACATAAGACTTGGTGCGATCTGCTCCACTACTGCTTAGGGAG
1 GTCTGCTCCACTATTGCTTAGGGAGATAAGACTTGATGCGATCTGCTCCACTATTGCTTAGGGAG
* *
59249215 ATAATATCTATGGTTCT
66 ATAAGATCTGTGGTTCT
* * *
59249232 GTCTGCCCCACTATTTCTTAGAGAGATAAGACTTGATGCGATCTGCTCCACTATTGCTTAGGGAG
1 GTCTGCTCCACTATTGCTTAGGGAGATAAGACTTGATGCGATCTGCTCCACTATTGCTTAGGGAG
59249297 ATAAGATCTGTGGTTCT
66 ATAAGATCTGTGGTTCT
* *
59249314 GTCTGCTCCACTATTGCTTAGGGAGATAAGACTTGATGCGATCTGCTCCACTACTGTTTAGGGAG
1 GTCTGCTCCACTATTGCTTAGGGAGATAAGACTTGATGCGATCTGCTCCACTATTGCTTAGGGAG
59249379 ATAAGATCTGTGGTTCT
66 ATAAGATCTGTGGTTCT
* *
59249396 GTCTGCTCCACTACTGCTTAGGGAGATAAGACTTGATGCGATCTGCTCCACTACTGCTTAGGGAG
1 GTCTGCTCCACTATTGCTTAGGGAGATAAGACTTGATGCGATCTGCTCCACTATTGCTTAGGGAG
59249461 ATAAGATCTGTGGTTCT
66 ATAAGATCTGTGGTTCT
* * *
59249478 ATCTGCTCCACTACTGCTTAGGGAGATAAGACTTGATGCGATCCGCTCCACTATTGCTTAGGGAG
1 GTCTGCTCCACTATTGCTTAGGGAGATAAGACTTGATGCGATCTGCTCCACTATTGCTTAGGGAG
59249543 ATAAGATCTGTGGTTCT
66 ATAAGATCTGTGGTTCT
*
59249560 GTCTGCTCCACTATTGCTTAGGGAGATAAGACTTGATGCAATCTGCTCCACTATTGCTTAGGGAG
1 GTCTGCTCCACTATTGCTTAGGGAGATAAGACTTGATGCGATCTGCTCCACTATTGCTTAGGGAG
*
59249625 ATAAGATCTATGGTTCT
66 ATAAGATCTGTGGTTCT
* *
59249642 GTCTGCTCCACTATTGCTTAGGGAGGTAAGAC-TGATGCGATCTGCTCCACTACTGCTTAGGGAG
1 GTCTGCTCCACTATTGCTTAGGGAGATAAGACTTGATGCGATCTGCTCCACTATTGCTTAGGGAG
*
59249706 ATAAGGTCTGTGGTTCT
66 ATAAGATCTGTGGTTCT
* * *
59249723 GTCTACTCCACTATTACTTAGGGAGATAAGACTTGATGCGATCTGCTCCACTACTGCTTAGGGAG
1 GTCTGCTCCACTATTGCTTAGGGAGATAAGACTTGATGCGATCTGCTCCACTATTGCTTAGGGAG
59249788 ATAAGATCTGTGGTTCT
66 ATAAGATCTGTGGTTCT
59249805 GTCTGCTCCACTATTGCTTAGGGAGATAAGACTTGATGCGATCTGCTCCACTATTGCTTAGGGAG
1 GTCTGCTCCACTATTGCTTAGGGAGATAAGACTTGATGCGATCTGCTCCACTATTGCTTAGGGAG
59249870 ATAAGATCTGTGGTTCT
66 ATAAGATCTGTGGTTCT
*
59249887 GTCTGCTCCACTATTGCTTAGGGTGATAAGACTTGATGCGATCTGCTCCACTATTGCTTAGGGAG
1 GTCTGCTCCACTATTGCTTAGGGAGATAAGACTTGATGCGATCTGCTCCACTATTGCTTAGGGAG
*
59249952 ATAAGATCTG-GTTTCTTTT
66 ATAAGATCTGTGGTTC---T
* *
59249971 GTCTACTCCACTAATGCTTAGGGAGATAAGACTTGATGCGATCTGCTCCACTATTGCTTAGGGAG
1 GTCTGCTCCACTATTGCTTAGGGAGATAAGACTTGATGCGATCTGCTCCACTATTGCTTAGGGAG
* *
59250036 ATAAGA-CT-TGATGC-
66 ATAAGATCTGTGGTTCT
* * * *
59250050 GATCTTCTCTACTATTGCTTAGGGAGATAAGATCTGTGGTTCTG-TCTGCTCCACTATTGCTTAG
1 G-TCTGCTCCACTATTGCTTAGGGAGATAAGA-CT-TGATGC-GATCTGCTCCACTATTGCTTAG
* *
59250114 GGAGATAAGA-CT-TGATGC-
62 GGAGATAAGATCTGTGGTTCT
* * * * *
59250132 GATCTGCTCCACTATTGCTTAGGGAGATAAGATCTGGTTTCTTTTG-TCTGCTCCACTACTACTT
1 G-TCTGCTCCACTATTGCTTAGGGAGATAAGA-CTTGATGC----GATCTGCTCCACTATTGCTT
* *
59250196 AGGGAGATAAGA-CT-TGATGC-
60 AGGGAGATAAGATCTGTGGTTCT
* * *
59250216 GATCTGCTCCACTATTGCTTAGGGAGATAAGATCTGGTTTCTTTTG-TCTGCTCCACTATTGCTT
1 G-TCTGCTCCACTATTGCTTAGGGAGATAAGA-CTTGATGC----GATCTGCTCCACTATTGCTT
* *
59250280 AGGGAGATAAGA-CT-T-GATGT
60 AGGGAGATAAGATCTGTGGTTCT
*
59250300 GATCTGCTCCACTACTGCTTAGGGAGATAAGA
1 G-TCTGCTCCACTATTGCTTAGGGAGATAAGA
59250332 TCTGGTTTCT
Statistics
Matches: 1097, Mismatches: 71, Indels: 26
0.92 0.06 0.02
Matches are distributed among these distances:
79 1 0.00
80 27 0.02
81 86 0.08
82 762 0.69
83 6 0.01
84 215 0.20
ACGTcount: A:0.23, C:0.20, G:0.24, T:0.33
Consensus pattern (82 bp):
GTCTGCTCCACTATTGCTTAGGGAGATAAGACTTGATGCGATCTGCTCCACTATTGCTTAGGGAG
ATAAGATCTGTGGTTCT
Found at i:59250510 original size:50 final size:50
Alignment explanation
Indices: 59250352--59250930 Score: 274
Period size: 50 Copynumber: 11.6 Consensus size: 50
59250342 ATTTGCTAGA
* * * * *
59250352 GAAGTGAGATTCGCTGTTGTGGCTTCAATCTCTTT-AATTGCAATGTCGGG
1 GAAGTAAGATTCGCCGTTGTAGCTTCAATCT-TTTAAATTGTAATGTCAGG
* * ** ** * * * *
59250402 GAA-CAAGATTCGTCGTTGTAGCTTCAATCTGATCCACTG-CATCGACAAG
1 GAAGTAAGATTCGCCGTTGTAGCTTCAATCTTTTAAATTGTAAT-GTCAGG
* * ** *
59250451 AAAGTAAGATTCGCTGTTGCGGCTTCAATCTTTTAAATTGTAATATCAGG
1 GAAGTAAGATTCGCCGTTGTAGCTTCAATCTTTTAAATTGTAATGTCAGG
* * * ** ** * * * *
59250501 GAAGCAAGATTCGCCGTCGTAGCTTTAATCTGCTGCACTGTACTGCCAGA
1 GAAGTAAGATTCGCCGTTGTAGCTTCAATCTTTTAAATTGTAATGTCAGG
* * * * *
59250551 GAAGTGAGATTCGCCGTTGTGGCTCCAATCTCTTT-AATTGCAATGTCGGG
1 GAAGTAAGATTCGCCGTTGTAGCTTCAATCT-TTTAAATTGTAATGTCAGG
** ** * * * *
59250601 GAA-TAAGATTCGCCGTTGTAGCTTCAATCTGATCCACTG-CATCGCCAAG
1 GAAGTAAGATTCGCCGTTGTAGCTTCAATCTTTTAAATTGTAAT-GTCAGG
* ** * * * *
59250650 AAAGTAAGATTCGCCGTTGCGGCATCAATCTTTTAAATTGCAATATCAAG
1 GAAGTAAGATTCGCCGTTGTAGCTTCAATCTTTTAAATTGTAATGTCAGG
* * * * * ** * * * * *
59250700 AAAGCAAGATTCGCCATCGTAGCTTTAATCTGCTACACTGTACTGCCAGA
1 GAAGTAAGATTCGCCGTTGTAGCTTCAATCTTTTAAATTGTAATGTCAGG
* * ** *
59250750 GAAGTGAGATTCGTCGTTGCGGCTTCAATCTTTTAAATTGTAATGT-TGAG
1 GAAGTAAGATTCGCCGTTGTAGCTTCAATCTTTTAAATTGTAATGTCAG-G
* * * ***** * * * *
59250800 GAAGCAAGATTCGCTGTTGTAGCTTTAATCTGCCCCACTG-CATCGCCATG
1 GAAGTAAGATTCGCCGTTGTAGCTTCAATCTTTTAAATTGTAAT-GTCAGG
** * * *
59250850 GAAGTAAGATTCGTTGTTGCAGCTTCAATTTTTTAAATTGTAATGTCGGG
1 GAAGTAAGATTCGCCGTTGTAGCTTCAATCTTTTAAATTGTAATGTCAGG
*
59250900 GAAGCAAGATTCGCCGTTGTAGCTTCAATCT
1 GAAGTAAGATTCGCCGTTGTAGCTTCAATCT
59250931 GTTCCACAAT
Statistics
Matches: 363, Mismatches: 153, Indels: 26
0.67 0.28 0.05
Matches are distributed among these distances:
48 6 0.02
49 65 0.18
50 285 0.79
51 7 0.02
ACGTcount: A:0.26, C:0.20, G:0.23, T:0.31
Consensus pattern (50 bp):
GAAGTAAGATTCGCCGTTGTAGCTTCAATCTTTTAAATTGTAATGTCAGG
Found at i:59250563 original size:100 final size:100
Alignment explanation
Indices: 59250349--59250937 Score: 667
Period size: 100 Copynumber: 5.9 Consensus size: 100
59250339 TCTATTTGCT
* *
59250349 AGAGAAGTGAGATTCGCTGTTGTGGCTTCAATCTCTTT-AATTGCAATGTCGGGGAA-CAAGATT
1 AGAGAAGTAAGATTCGCTGTTGCGGCTTCAATCT-TTTAAATTGCAATGTCGGGGAAGCAAGATT
* * *
59250412 CGTCGTTGTAGCTTCAATCTGATCCACTGCATCGAC
65 CGCCGTTGTAGCTTCAATCTGCTCCACTGCATCGCC
* * *
59250448 A-AGAAAGTAAGATTCGCTGTTGCGGCTTCAATCTTTTAAATTGTAATATCAGGGAAGCAAGATT
1 AGAG-AAGTAAGATTCGCTGTTGCGGCTTCAATCTTTTAAATTGCAATGTCGGGGAAGCAAGATT
* * * *
59250512 CGCCGTCGTAGCTTTAATCTGCTGCACTGTA-CTGCC
65 CGCCGTTGTAGCTTCAATCTGCTCCACTGCATC-GCC
* * * * *
59250548 AGAGAAGTGAGATTCGCCGTTGTGGCTCCAATCTCTTT-AATTGCAATGTCGGGGAA-TAAGATT
1 AGAGAAGTAAGATTCGCTGTTGCGGCTTCAATCT-TTTAAATTGCAATGTCGGGGAAGCAAGATT
*
59250611 CGCCGTTGTAGCTTCAATCTGATCCACTGCATCGCC
65 CGCCGTTGTAGCTTCAATCTGCTCCACTGCATCGCC
* * * ** *
59250647 A-AGAAAGTAAGATTCGCCGTTGCGGCATCAATCTTTTAAATTGCAATATCAAGAAAGCAAGATT
1 AGAG-AAGTAAGATTCGCTGTTGCGGCTTCAATCTTTTAAATTGCAATGTCGGGGAAGCAAGATT
* * * * *
59250711 CGCCATCGTAGCTTTAATCTGCTACACTGTA-CTGCC
65 CGCCGTTGTAGCTTCAATCTGCTCCACTGCATC-GCC
* * * *
59250747 AGAGAAGTGAGATTCG-TCGTTGCGGCTTCAATCTTTTAAATTGTAATGTTGAGGAAGCAAGATT
1 AGAGAAGTAAGATTCGCT-GTTGCGGCTTCAATCTTTTAAATTGCAATGTCGGGGAAGCAAGATT
* * *
59250811 CGCTGTTGTAGCTTTAATCTGCCCCACTGCATCGCC
65 CGCCGTTGTAGCTTCAATCTGCTCCACTGCATCGCC
* * * *
59250847 ATG-GAAGTAAGATTCGTTGTTGCAGCTTCAATTTTTTAAATTGTAATGTCGGGGAAGCAAGATT
1 A-GAGAAGTAAGATTCGCTGTTGCGGCTTCAATCTTTTAAATTGCAATGTCGGGGAAGCAAGATT
*
59250911 CGCCGTTGTAGCTTCAATCTGTTCCAC
65 CGCCGTTGTAGCTTCAATCTGCTCCAC
59250938 AATATAGGAA
Statistics
Matches: 411, Mismatches: 63, Indels: 31
0.81 0.12 0.06
Matches are distributed among these distances:
98 10 0.02
99 122 0.30
100 269 0.65
101 10 0.02
ACGTcount: A:0.26, C:0.20, G:0.23, T:0.31
Consensus pattern (100 bp):
AGAGAAGTAAGATTCGCTGTTGCGGCTTCAATCTTTTAAATTGCAATGTCGGGGAAGCAAGATTC
GCCGTTGTAGCTTCAATCTGCTCCACTGCATCGCC
Found at i:59250689 original size:199 final size:199
Alignment explanation
Indices: 59250349--59250931 Score: 871
Period size: 199 Copynumber: 2.9 Consensus size: 199
59250339 TCTATTTGCT
*
59250349 AGAGAAGTGAGATTCGCTGTTGTGGCTTCAATCTCTTTAATTGCAATGTCGGGGAACAAGATTCG
1 AGAGAAGTGAGATTCGCCGTTGTGGCTTCAATCTCTTTAATTGCAATGTCGGGGAACAAGATTCG
* *
59250414 TCGTTGTAGCTTCAATCTGATCCACTGCATCGACAAGAAAGTAAGATTCGCTGTTGCGGCTTCAA
66 CCGTTGTAGCTTCAATCTGATCCACTGCATCGCCAAGAAAGTAAGATTCGCTGTTGCGGCTTCAA
*
59250479 TCTTTTAAATTGTAATATCAGGGAAGCAAGATTCGCCGTCGTAGCTTTAATCTGCTGCACTGTAC
131 TCTTTTAAATTGTAATATCAGGGAAGCAAGATTCGCCGTCGTAGCTTTAATCTGCTACACTGTAC
59250544 TGCC
196 TGCC
* *
59250548 AGAGAAGTGAGATTCGCCGTTGTGGCTCCAATCTCTTTAATTGCAATGTCGGGGAATAAGATTCG
1 AGAGAAGTGAGATTCGCCGTTGTGGCTTCAATCTCTTTAATTGCAATGTCGGGGAACAAGATTCG
* *
59250613 CCGTTGTAGCTTCAATCTGATCCACTGCATCGCCAAGAAAGTAAGATTCGCCGTTGCGGCATCAA
66 CCGTTGTAGCTTCAATCTGATCCACTGCATCGCCAAGAAAGTAAGATTCGCTGTTGCGGCTTCAA
* * * *
59250678 TCTTTTAAATTGCAATATCAAGAAAGCAAGATTCGCCATCGTAGCTTTAATCTGCTACACTGTAC
131 TCTTTTAAATTGTAATATCAGGGAAGCAAGATTCGCCGTCGTAGCTTTAATCTGCTACACTGTAC
59250743 TGCC
196 TGCC
* * * * *
59250747 AGAGAAGTGAGATTCGTCGTTGCGGCTTCAATCT-TTTAAATTGTAATGTTGAGGAAGCAAGATT
1 AGAGAAGTGAGATTCGCCGTTGTGGCTTCAATCTCTTT-AATTGCAATGTCGGGGAA-CAAGATT
* * ** * * * *
59250811 CGCTGTTGTAGCTTTAATCTGCCCCACTGCATCGCCATGGAAGTAAGATTCGTTGTTGCAGCTTC
64 CGCCGTTGTAGCTTCAATCTGATCCACTGCATCGCCAAGAAAGTAAGATTCGCTGTTGCGGCTTC
* * * * *
59250876 AATTTTTTAAATTGTAATGTCGGGGAAGCAAGATTCGCCGTTGTAGCTTCAATCTG
129 AATCTTTTAAATTGTAATATCAGGGAAGCAAGATTCGCCGTCGTAGCTTTAATCTG
59250932 TTCCACAATA
Statistics
Matches: 344, Mismatches: 38, Indels: 3
0.89 0.10 0.01
Matches are distributed among these distances:
198 3 0.01
199 233 0.68
200 108 0.31
ACGTcount: A:0.26, C:0.20, G:0.23, T:0.31
Consensus pattern (199 bp):
AGAGAAGTGAGATTCGCCGTTGTGGCTTCAATCTCTTTAATTGCAATGTCGGGGAACAAGATTCG
CCGTTGTAGCTTCAATCTGATCCACTGCATCGCCAAGAAAGTAAGATTCGCTGTTGCGGCTTCAA
TCTTTTAAATTGTAATATCAGGGAAGCAAGATTCGCCGTCGTAGCTTTAATCTGCTACACTGTAC
TGCC
Found at i:59251101 original size:132 final size:132
Alignment explanation
Indices: 59250937--59251363 Score: 624
Period size: 125 Copynumber: 3.3 Consensus size: 132
59250927 ATCTGTTCCA
* * * *
59250937 CAATATAGGAAGACAGGACCTGCTATCTTCGATCTACTTCACGCCAATACATGAAGAAAAGATTT
1 CAATATAGGAAGACAGGACCTGCTATCTTCGATCTACTTCACGCCAACACAGGAAGACAAGATCT
* * * * *
59251002 GCTTTCTTGGATCTACTTCGCCACCAGTATGGGAAGACAAGATCTGCATCTTCGATCCACTTCCT
66 ACTTTCTTCGATCTACTCCACCACCAATATGGGAAGACAAGATCTGCATCTTCGATCCACTTCCT
59251067 AC
131 AC
* *
59251069 CAATATAAGAAGACAGGACCTGCTATCTTCGA--T-C-T---GCCAACATAGGAAGACAAGATCT
1 CAATATAGGAAGACAGGACCTGCTATCTTCGATCTACTTCACGCCAACACAGGAAGACAAGATCT
59251127 ACTTTCTTCGATCTACTCCACCACCAATATGGGAAGACAAGATCTGCATCTTCGATCCACTTCCT
66 ACTTTCTTCGATCTACTCCACCACCAATATGGGAAGACAAGATCTGCATCTTCGATCCACTTCCT
59251192 AC
131 AC
59251194 CAATATAGGAAGACAGGACCTGCTATCTTCGATCTACTTCACTGCCAACACAGGAAGACAAGATC
1 CAATATAGGAAGACAGGACCTGCTATCTTCGATCTACTTCAC-GCCAACACAGGAAGACAAGATC
*
59251259 TACTTT-TTTGATCTACTCCACCACCAATATGGGAAGACAAGATCTGCATCCTT-GATCCACTTC
65 TACTTTCTTCGATCTACTCCACCACCAATATGGGAAGACAAGATCTGCAT-CTTCGATCCACTTC
59251322 CTAC
129 CTAC
* *
59251326 CAATATAGGAAGACAAGG-TCTGC-ATCTTCGATCCACTT
1 CAATATAGGAAGAC-AGGACCTGCTATCTTCGATCTACTT
59251364 TCTACCAATA
Statistics
Matches: 269, Mismatches: 16, Indels: 21
0.88 0.05 0.07
Matches are distributed among these distances:
125 111 0.41
127 1 0.00
128 2 0.01
129 2 0.01
130 1 0.00
131 14 0.05
132 105 0.39
133 33 0.12
ACGTcount: A:0.31, C:0.27, G:0.16, T:0.26
Consensus pattern (132 bp):
CAATATAGGAAGACAGGACCTGCTATCTTCGATCTACTTCACGCCAACACAGGAAGACAAGATCT
ACTTTCTTCGATCTACTCCACCACCAATATGGGAAGACAAGATCTGCATCTTCGATCCACTTCCT
AC
Found at i:59251683 original size:15 final size:15
Alignment explanation
Indices: 59251643--59251683 Score: 64
Period size: 16 Copynumber: 2.7 Consensus size: 15
59251633 TAACTAGATG
59251643 TGTATGAATGATATT
1 TGTATGAATGATATT
*
59251658 TGCATTGAATGATATT
1 TGTA-TGAATGATATT
59251674 TGTATGAATG
1 TGTATGAATG
59251684 CAGAATGTCA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
15 9 0.39
16 14 0.61
ACGTcount: A:0.32, C:0.02, G:0.22, T:0.44
Consensus pattern (15 bp):
TGTATGAATGATATT
Found at i:59252143 original size:109 final size:103
Alignment explanation
Indices: 59251986--59252177 Score: 260
Period size: 109 Copynumber: 1.8 Consensus size: 103
59251976 GAAAAATGCT
*
59251986 TGAAAAAGATTATCAAAATAAATGAAATTTTGTTGAGAGCAAAGCTCTAAACAAACAAATCAATC
1 TGAAAAAGATTATCAAAATAAATGAAATTTTGTTAAGAGCAAAGCTCTAAACAAACAAATCAATC
59252051 AAGACAGAAAATTTTGCTGAGATACGAGATGTATAAGA
66 AAGACAGAAAATTTTGCTGAGATACGAGATGTATAAGA
**
59252089 TGAAAAAGATTATCACAATGGATAAGATGGAAA-TTTGTTAAGAGCAAAAGCTCTAAATGAACAA
1 TGAAAAAGATTATCA-AA---ATAA-AT-GAAATTTTGTTAAGAGC-AAAGCTCTAAACAAACAA
* * *
59252153 ATTAATCAAGATAGCAAATTTTGCT
59 ATCAATCAAGACAGAAAATTTTGCT
59252178 AGAATAAAAA
Statistics
Matches: 76, Mismatches: 6, Indels: 8
0.84 0.07 0.09
Matches are distributed among these distances:
103 15 0.20
104 2 0.03
107 4 0.05
108 13 0.17
109 42 0.55
ACGTcount: A:0.47, C:0.10, G:0.17, T:0.26
Consensus pattern (103 bp):
TGAAAAAGATTATCAAAATAAATGAAATTTTGTTAAGAGCAAAGCTCTAAACAAACAAATCAATC
AAGACAGAAAATTTTGCTGAGATACGAGATGTATAAGA
Found at i:59252219 original size:45 final size:47
Alignment explanation
Indices: 59252151--59252238 Score: 117
Period size: 45 Copynumber: 1.9 Consensus size: 47
59252141 CTAAATGAAC
* *
59252151 AAATTAATCAAGATAGCAAATTTTG-CTAGAATA-AAAAATGAGAAT
1 AAATTAATCAAGATAGCAAATTTTGTCAAAAATACAAAAATGAGAAT
* **
59252196 AAATTAATCAAGATGGCGTATTTTGTCAAAAATACAAAAATGA
1 AAATTAATCAAGATAGCAAATTTTGTCAAAAATACAAAAATGA
59252239 ATAAAATGGA
Statistics
Matches: 36, Mismatches: 5, Indels: 2
0.84 0.12 0.05
Matches are distributed among these distances:
45 22 0.61
46 6 0.17
47 8 0.22
ACGTcount: A:0.51, C:0.08, G:0.14, T:0.27
Consensus pattern (47 bp):
AAATTAATCAAGATAGCAAATTTTGTCAAAAATACAAAAATGAGAAT
Found at i:59252241 original size:45 final size:43
Alignment explanation
Indices: 59252143--59252243 Score: 112
Period size: 45 Copynumber: 2.3 Consensus size: 43
59252133 CAAAAGCTCT
* * *
59252143 AAATGAACAAATTAATCAAGATAGCAAATTTTGCTAGAATAAA
1 AAATGAATAAATTAATCAAGATAGCAAATTTTGCAAAAATAAA
* **
59252186 AAATGAGAATAAATTAATCAAGATGGCGTATTTTGTCAAAAATACAA
1 AAAT--GAATAAATTAATCAAGATAGCAAATTTTG-CAAAAATA-AA
59252233 AAATGAATAAA
1 AAATGAATAAA
59252244 ATGGAAATAG
Statistics
Matches: 48, Mismatches: 6, Indels: 6
0.80 0.10 0.10
Matches are distributed among these distances:
43 4 0.08
45 32 0.67
46 6 0.12
47 6 0.12
ACGTcount: A:0.53, C:0.08, G:0.13, T:0.26
Consensus pattern (43 bp):
AAATGAATAAATTAATCAAGATAGCAAATTTTGCAAAAATAAA
Found at i:59252532 original size:12 final size:11
Alignment explanation
Indices: 59252515--59252557 Score: 52
Period size: 12 Copynumber: 3.8 Consensus size: 11
59252505 CCTCTCCTTT
59252515 TTCTTTTTGTTA
1 TTCTTTTT-TTA
*
59252527 TTCTTTTCTT-
1 TTCTTTTTTTA
59252537 TTCTTTTTTTA
1 TTCTTTTTTTA
59252548 TTTCTTTTTT
1 -TTCTTTTTT
59252558 CAAGTGAAGT
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
10 9 0.33
11 2 0.07
12 16 0.59
ACGTcount: A:0.05, C:0.12, G:0.02, T:0.81
Consensus pattern (11 bp):
TTCTTTTTTTA
Found at i:59252538 original size:22 final size:22
Alignment explanation
Indices: 59252513--59252555 Score: 70
Period size: 22 Copynumber: 2.0 Consensus size: 22
59252503 GGCCTCTCCT
59252513 TTTTCTTTTTGTTA-TTCTTTTC
1 TTTTCTTTTT-TTATTTCTTTTC
59252535 TTTTCTTTTTTTATTTCTTTT
1 TTTTCTTTTTTTATTTCTTTT
59252556 TTCAAGTGAA
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
21 3 0.15
22 17 0.85
ACGTcount: A:0.05, C:0.12, G:0.02, T:0.81
Consensus pattern (22 bp):
TTTTCTTTTTTTATTTCTTTTC
Found at i:59253034 original size:14 final size:13
Alignment explanation
Indices: 59253017--59253055 Score: 53
Period size: 14 Copynumber: 2.9 Consensus size: 13
59253007 TGTTCTCTTT
59253017 TTTTTGTTTTTGTG
1 TTTTTGTTTTTG-G
59253031 TTTTTGGTTTTTGG
1 TTTTT-GTTTTTGG
59253045 TTTTT-TTTTTG
1 TTTTTGTTTTTG
59253056 CCTTTTTCTT
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
12 6 0.25
14 11 0.46
15 7 0.29
ACGTcount: A:0.00, C:0.00, G:0.21, T:0.79
Consensus pattern (13 bp):
TTTTTGTTTTTGG
Found at i:59253040 original size:15 final size:14
Alignment explanation
Indices: 59253016--59253049 Score: 50
Period size: 15 Copynumber: 2.4 Consensus size: 14
59253006 TTGTTCTCTT
*
59253016 TTTTTTGTTTTTGTG
1 TTTTTGGTTTTTG-G
59253031 TTTTTGGTTTTTGG
1 TTTTTGGTTTTTGG
59253045 TTTTT
1 TTTTT
59253050 TTTTTGCCTT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
14 6 0.33
15 12 0.67
ACGTcount: A:0.00, C:0.00, G:0.21, T:0.79
Consensus pattern (14 bp):
TTTTTGGTTTTTGG
Found at i:59253050 original size:8 final size:7
Alignment explanation
Indices: 59253016--59253049 Score: 50
Period size: 7 Copynumber: 4.7 Consensus size: 7
59253006 TTGTTCTCTT
*
59253016 TTTTTTG
1 TTTTTGG
59253023 TTTTTGTG
1 TTTTTG-G
59253031 TTTTTGG
1 TTTTTGG
59253038 TTTTTGG
1 TTTTTGG
59253045 TTTTT
1 TTTTT
59253050 TTTTTGCCTT
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
7 18 0.72
8 7 0.28
ACGTcount: A:0.00, C:0.00, G:0.21, T:0.79
Consensus pattern (7 bp):
TTTTTGG
Found at i:59254523 original size:62 final size:62
Alignment explanation
Indices: 59254338--59254524 Score: 302
Period size: 62 Copynumber: 3.0 Consensus size: 62
59254328 CTAAACTCGA
* * * * *
59254338 CGTACTTTTGGATTTTAAGAAATTTACTGTATGCAATGAAACGTAATGTTGATGCATGAATA
1 CGTATTTTTGGATTTTAAGAAATTTATTGCATGCAATGAAATGTAATGTTGATGCATGAATG
*
59254400 CGTATTTTTGGATTTTAAGAAATTTATTGCATGCAATGAAATTTAATGTTGATGCATGAATG
1 CGTATTTTTGGATTTTAAGAAATTTATTGCATGCAATGAAATGTAATGTTGATGCATGAATG
* *
59254462 CGTATTTTTGGATTTTAGGAAATTTATTGCATGCGATGAAATGTAATGTTGATGCATGAATG
1 CGTATTTTTGGATTTTAAGAAATTTATTGCATGCAATGAAATGTAATGTTGATGCATGAATG
59254524 C
1 C
59254525 AAAAAAGAGA
Statistics
Matches: 116, Mismatches: 9, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
62 116 1.00
ACGTcount: A:0.32, C:0.08, G:0.21, T:0.40
Consensus pattern (62 bp):
CGTATTTTTGGATTTTAAGAAATTTATTGCATGCAATGAAATGTAATGTTGATGCATGAATG
Found at i:59257601 original size:8 final size:8
Alignment explanation
Indices: 59257585--59257616 Score: 50
Period size: 7 Copynumber: 4.2 Consensus size: 8
59257575 CAAAGAACGC
59257585 AAAAA-AA
1 AAAAATAA
59257592 AAAAAT-A
1 AAAAATAA
59257599 AAAAATAA
1 AAAAATAA
59257607 AAAAATAA
1 AAAAATAA
59257615 AA
1 AA
59257617 GGGAAGTCCC
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
7 12 0.52
8 11 0.48
ACGTcount: A:0.91, C:0.00, G:0.00, T:0.09
Consensus pattern (8 bp):
AAAAATAA
Found at i:59257608 original size:15 final size:14
Alignment explanation
Indices: 59257585--59257616 Score: 55
Period size: 15 Copynumber: 2.2 Consensus size: 14
59257575 CAAAGAACGC
59257585 AAAAAAAAAAAATA
1 AAAAAAAAAAAATA
59257599 AAAAATAAAAAAATA
1 AAAAA-AAAAAAATA
59257614 AAA
1 AAA
59257617 GGGAAGTCCC
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 5 0.29
15 12 0.71
ACGTcount: A:0.91, C:0.00, G:0.00, T:0.09
Consensus pattern (14 bp):
AAAAAAAAAAAATA
Found at i:59259102 original size:20 final size:20
Alignment explanation
Indices: 59259079--59259119 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 20
59259069 TTAAATTAAA
*
59259079 ATTAATTATAAATAATTTTT
1 ATTAATTATAAATAATATTT
* *
59259099 ATTAATTTTTAATAATATTT
1 ATTAATTATAAATAATATTT
59259119 A
1 A
59259120 ATATTTTCTA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (20 bp):
ATTAATTATAAATAATATTT
Found at i:59259104 original size:10 final size:10
Alignment explanation
Indices: 59259089--59259157 Score: 56
Period size: 10 Copynumber: 7.0 Consensus size: 10
59259079 ATTAATTATA
59259089 AATAATTTTT
1 AATAATTTTT
*
59259099 ATTAATTTTT
1 AATAATTTTT
*
59259109 AATAATATTT
1 AATAATTTTT
59259119 AAT-ATTTTCT
1 AATAATTTT-T
*
59259129 -AT-ATTTTA
1 AATAATTTTT
59259137 AATAATTATTT
1 AATAATT-TTT
59259148 -ATAAATTTTT
1 AAT-AATTTTT
59259158 TGAACAACCA
Statistics
Matches: 48, Mismatches: 6, Indels: 10
0.75 0.09 0.16
Matches are distributed among these distances:
9 13 0.27
10 29 0.60
11 6 0.12
ACGTcount: A:0.39, C:0.01, G:0.00, T:0.59
Consensus pattern (10 bp):
AATAATTTTT
Found at i:59259851 original size:17 final size:17
Alignment explanation
Indices: 59259837--59259871 Score: 63
Period size: 16 Copynumber: 2.1 Consensus size: 17
59259827 TATTTTTTTA
59259837 TTTTTCTTCTTTTTTCT
1 TTTTTCTTCTTTTTTCT
59259854 TTTTTCTTC-TTTTTCT
1 TTTTTCTTCTTTTTTCT
59259870 TT
1 TT
59259872 CCTTCTTTGT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
16 9 0.50
17 9 0.50
ACGTcount: A:0.00, C:0.17, G:0.00, T:0.83
Consensus pattern (17 bp):
TTTTTCTTCTTTTTTCT
Found at i:59259852 original size:10 final size:10
Alignment explanation
Indices: 59259837--59259891 Score: 51
Period size: 10 Copynumber: 5.3 Consensus size: 10
59259827 TATTTTTTTA
59259837 TTTTTCTTCT
1 TTTTTCTTCT
59259847 TTTTTCTT-T
1 TTTTTCTTCT
59259856 TTTCTTCTT-T
1 TTT-TTCTTCT
59259866 TTCTTTCCTTCT
1 TT-TTT-CTTCT
*
59259878 TTGTTCTTCCT
1 TTTTTCTT-CT
59259889 TTT
1 TTT
59259892 CAAACCCTAA
Statistics
Matches: 38, Mismatches: 2, Indels: 9
0.78 0.04 0.18
Matches are distributed among these distances:
9 4 0.11
10 21 0.55
11 10 0.26
12 3 0.08
ACGTcount: A:0.00, C:0.22, G:0.02, T:0.76
Consensus pattern (10 bp):
TTTTTCTTCT
Found at i:59259877 original size:17 final size:17
Alignment explanation
Indices: 59259830--59259878 Score: 57
Period size: 16 Copynumber: 2.9 Consensus size: 17
59259820 GTTTATTTAT
*
59259830 TTTTTTATTT-TTCTTC
1 TTTTTTCTTTCTTCTTC
*
59259846 TTTTTTCTTTTTTCTTC
1 TTTTTTCTTTCTTCTTC
59259863 -TTTTTCTTTCCTTCTT
1 TTTTTTCTTT-CTTCTT
59259879 TGTTCTTCCT
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
16 18 0.62
17 11 0.38
ACGTcount: A:0.02, C:0.18, G:0.00, T:0.80
Consensus pattern (17 bp):
TTTTTTCTTTCTTCTTC
Done.