Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Dt_chr11
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: 61124829
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 1263459 characters in sequence are not A, C, G, or T
File 45 of 205
Found at i:13298159 original size:101 final size:100
Alignment explanation
Indices: 13297975--13298219 Score: 382
Period size: 101 Copynumber: 2.4 Consensus size: 100
13297965 AAGGATGAAT
* * *
13297975 TGATGGATAAGACCATAACTGAGTTATGGCACTGTGAACGTAAGACTATGGTTGGACCATGGCAG
1 TGAT-GATAAGACCATAACTG-GTTATGGCACTATGAACGTAAGACTATGGTTGGACCATGACAA
*
13298040 TGTTTATATGTAAGACCATAGCTGGGCTATGGCATTC
64 TGTTTATATGTAAAACCATAGCTGGGCTATGGCATTC
13298077 TGATGATAAGACCATAACTAGGTTATGGCACTATGAACGTAAGACTATGGTTGGACCATGACAAT
1 TGATGATAAGACCATAACT-GGTTATGGCACTATGAACGTAAGACTATGGTTGGACCATGACAAT
* *
13298142 GTTTATATGTAAAACCATAGTTGGGCTATGGCATTT
65 GTTTATATGTAAAACCATAGCTGGGCTATGGCATTC
* *
13298178 TGATGATAAGACCATAACTGGGTTATGGCACTACGAATGTAA
1 TGATGATAAGACCATAACT-GGTTATGGCACTATGAACGTAA
13298220 ATGATGAATT
Statistics
Matches: 133, Mismatches: 9, Indels: 3
0.92 0.06 0.02
Matches are distributed among these distances:
101 128 0.96
102 5 0.04
ACGTcount: A:0.31, C:0.15, G:0.25, T:0.29
Consensus pattern (100 bp):
TGATGATAAGACCATAACTGGTTATGGCACTATGAACGTAAGACTATGGTTGGACCATGACAATG
TTTATATGTAAAACCATAGCTGGGCTATGGCATTC
Found at i:13298249 original size:24 final size:24
Alignment explanation
Indices: 13298213--13298263 Score: 75
Period size: 24 Copynumber: 2.1 Consensus size: 24
13298203 TGGCACTACG
*
13298213 AATGTAAATGATGAATTAATGGAA
1 AATGTAAAGGATGAATTAATGGAA
* *
13298237 AATGTAAAGGATGAATTGATGGCA
1 AATGTAAAGGATGAATTAATGGAA
13298261 AAT
1 AAT
13298264 TACCCAAGTA
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.47, C:0.02, G:0.24, T:0.27
Consensus pattern (24 bp):
AATGTAAAGGATGAATTAATGGAA
Found at i:13301773 original size:22 final size:21
Alignment explanation
Indices: 13301745--13301786 Score: 75
Period size: 22 Copynumber: 2.0 Consensus size: 21
13301735 AATATTTTAA
13301745 ATATAAATATTTATTTTATTTT
1 ATATAAATATTTA-TTTATTTT
13301767 ATATAAATATTTATTTATTT
1 ATATAAATATTTATTTATTT
13301787 ATGTTCATAT
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
21 7 0.35
22 13 0.65
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (21 bp):
ATATAAATATTTATTTATTTT
Found at i:13303518 original size:22 final size:22
Alignment explanation
Indices: 13303493--13303546 Score: 74
Period size: 22 Copynumber: 2.5 Consensus size: 22
13303483 CATTTTCCCA
*
13303493 TTCTCCCTTCTCTACACTTTCG
1 TTCTCCCTTCTCTACACTCTCG
*
13303515 TTCT-CCTTCCTCTATACTCTCG
1 TTCTCCCTT-CTCTACACTCTCG
13303537 TTCTCCCTTC
1 TTCTCCCTTC
13303547 CTCTCTACAC
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
21 4 0.14
22 20 0.71
23 4 0.14
ACGTcount: A:0.07, C:0.43, G:0.04, T:0.46
Consensus pattern (22 bp):
TTCTCCCTTCTCTACACTCTCG
Found at i:13304020 original size:14 final size:14
Alignment explanation
Indices: 13304003--13304031 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
13303993 GTTTGTTCTC
13304003 TTAAGAGGAAATGG
1 TTAAGAGGAAATGG
13304017 TTAAGAGGAAATGG
1 TTAAGAGGAAATGG
13304031 T
1 T
13304032 GGTGAGGTGT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.41, C:0.00, G:0.34, T:0.24
Consensus pattern (14 bp):
TTAAGAGGAAATGG
Found at i:13305401 original size:3 final size:3
Alignment explanation
Indices: 13305393--13305425 Score: 66
Period size: 3 Copynumber: 11.0 Consensus size: 3
13305383 TTAAATATTT
13305393 ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC
1 ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC
13305426 TCTTTTTGTT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 30 1.00
ACGTcount: A:0.33, C:0.33, G:0.00, T:0.33
Consensus pattern (3 bp):
ATC
Found at i:13307715 original size:32 final size:32
Alignment explanation
Indices: 13307672--13307732 Score: 95
Period size: 32 Copynumber: 1.9 Consensus size: 32
13307662 TTAGATATTG
* *
13307672 ATTATGTTTTAAGCTTGTTATATATTAAATTT
1 ATTATGATTTAAGCTTGTTAGATATTAAATTT
*
13307704 ATTATGATTTAAGCTTGTTGGATATTAAA
1 ATTATGATTTAAGCTTGTTAGATATTAAA
13307733 ATGATTGACA
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
32 26 1.00
ACGTcount: A:0.33, C:0.03, G:0.13, T:0.51
Consensus pattern (32 bp):
ATTATGATTTAAGCTTGTTAGATATTAAATTT
Found at i:13309121 original size:20 final size:20
Alignment explanation
Indices: 13309096--13309133 Score: 76
Period size: 20 Copynumber: 1.9 Consensus size: 20
13309086 ATATTTTCAG
13309096 TAAATCATTTTCCAGAAAAA
1 TAAATCATTTTCCAGAAAAA
13309116 TAAATCATTTTCCAGAAA
1 TAAATCATTTTCCAGAAA
13309134 TCATTTTTCA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.47, C:0.16, G:0.05, T:0.32
Consensus pattern (20 bp):
TAAATCATTTTCCAGAAAAA
Found at i:13309488 original size:12 final size:13
Alignment explanation
Indices: 13309471--13309499 Score: 58
Period size: 13 Copynumber: 2.2 Consensus size: 13
13309461 ATTCAAATAA
13309471 TTTTTTTGAATTT
1 TTTTTTTGAATTT
13309484 TTTTTTTGAATTT
1 TTTTTTTGAATTT
13309497 TTT
1 TTT
13309500 CCATTAAAAT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.14, C:0.00, G:0.07, T:0.79
Consensus pattern (13 bp):
TTTTTTTGAATTT
Found at i:13310118 original size:26 final size:26
Alignment explanation
Indices: 13310110--13310164 Score: 76
Period size: 26 Copynumber: 2.1 Consensus size: 26
13310100 CTTAATATTT
13310110 AAGTAAATATATATAATATAATAATA
1 AAGTAAATATATATAATATAATAATA
*
13310136 AAGTAAATATA-ATAAAATAAATAAGTA
1 AAGTAAATATATATAATAT-AATAA-TA
13310163 AA
1 AA
13310165 TGAAATAAAT
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
25 6 0.23
26 16 0.62
27 4 0.15
ACGTcount: A:0.65, C:0.00, G:0.05, T:0.29
Consensus pattern (26 bp):
AAGTAAATATATATAATATAATAATA
Found at i:13310148 original size:22 final size:22
Alignment explanation
Indices: 13310109--13310177 Score: 70
Period size: 22 Copynumber: 3.0 Consensus size: 22
13310099 ACTTAATATT
*
13310109 TAAGTAAATATATATAATATAATAA
1 TAAGTAAATATA-ATAAAAT-A-AA
13310134 TAAAGTAAATATAATAAAATAAA
1 T-AAGTAAATATAATAAAATAAA
13310157 TAAGTAAATGA-AAT-AAATAAA
1 TAAGTAAAT-ATAATAAAATAAA
13310178 GAAAATAGAA
Statistics
Matches: 41, Mismatches: 1, Indels: 8
0.82 0.02 0.16
Matches are distributed among these distances:
21 7 0.17
22 11 0.27
23 4 0.10
24 1 0.02
25 7 0.17
26 11 0.27
ACGTcount: A:0.65, C:0.00, G:0.06, T:0.29
Consensus pattern (22 bp):
TAAGTAAATATAATAAAATAAA
Found at i:13310170 original size:5 final size:4
Alignment explanation
Indices: 13310113--13310177 Score: 51
Period size: 4 Copynumber: 15.0 Consensus size: 4
13310103 AATATTTAAG
* *
13310113 TAAA TATA TATAA TATAA T-AA TAAA GTAAA TATAA TAAAA TAAA TAAG
1 TAAA TAAA TA-AA TA-AA TAAA TAAA -TAAA TA-AA T-AAA TAAA TAAA
13310161 TAAA TGAAA TAAA TAAA
1 TAAA T-AAA TAAA TAAA
13310178 GAAAATAGAA
Statistics
Matches: 51, Mismatches: 4, Indels: 12
0.76 0.06 0.18
Matches are distributed among these distances:
3 3 0.06
4 26 0.51
5 21 0.41
6 1 0.02
ACGTcount: A:0.66, C:0.00, G:0.05, T:0.29
Consensus pattern (4 bp):
TAAA
Found at i:13311191 original size:40 final size:40
Alignment explanation
Indices: 13311087--13311221 Score: 132
Period size: 40 Copynumber: 3.4 Consensus size: 40
13311077 CGAGTTGATA
* * * *
13311087 AGACACTGAGTGTCAATTTATTACTTCAGATATATTCGATG
1 AGACACTGGGTGTCAAATTATTACTTCAG-TTTATCCGATG
* * *
13311128 AGGCACTGGGTG-CGAA-T-TTACTTCAGTTTAGCCGATG
1 AGACACTGGGTGTCAAATTATTACTTCAGTTTATCCGATG
* **
13311165 AGACACTAGGTGTCAAATTATTACTTCAAATTATCCGATG
1 AGACACTGGGTGTCAAATTATTACTTCAGTTTATCCGATG
* *
13311205 AGGCACTGGGTGCCAAA
1 AGACACTGGGTGTCAAA
13311222 CTTGTGTGTT
Statistics
Matches: 75, Mismatches: 16, Indels: 7
0.77 0.16 0.07
Matches are distributed among these distances:
37 18 0.24
38 12 0.16
39 2 0.03
40 33 0.44
41 10 0.13
ACGTcount: A:0.30, C:0.18, G:0.22, T:0.30
Consensus pattern (40 bp):
AGACACTGGGTGTCAAATTATTACTTCAGTTTATCCGATG
Found at i:13318189 original size:41 final size:39
Alignment explanation
Indices: 13318142--13318255 Score: 126
Period size: 41 Copynumber: 2.9 Consensus size: 39
13318132 TTTGGCTTCG
13318142 AGTCGATGAGACATTGGGTGTCAATTTATTACTTCGGATAT
1 AGTCGATGAGACATTGGGTGTCAA-TTATTACTTCGG-TAT
* * * *
13318183 ATTCGATGAGGCATTGGGTG-CGAA-T-TTACTTCAGTTT
1 AGTCGATGAGACATTGGGTGTC-AATTATTACTTCGGTAT
*
13318220 AGCCGATGAGACATTGGGTGTCAAATTATTACTTCG
1 AGTCGATGAGACATTGGGTGTC-AATTATTACTTCG
13318256 AATTATCTGA
Statistics
Matches: 60, Mismatches: 9, Indels: 9
0.77 0.12 0.12
Matches are distributed among these distances:
37 19 0.32
38 11 0.18
39 2 0.03
40 8 0.13
41 20 0.33
ACGTcount: A:0.25, C:0.14, G:0.25, T:0.35
Consensus pattern (39 bp):
AGTCGATGAGACATTGGGTGTCAATTATTACTTCGGTAT
Found at i:13318268 original size:40 final size:40
Alignment explanation
Indices: 13318146--13318284 Score: 126
Period size: 40 Copynumber: 3.5 Consensus size: 40
13318136 GCTTCGAGTC
* *
13318146 GATGAGACATTGGGTGTCAATTTATTACTTCGGATATAT-T
1 GATGAGACATTGGGTGTCAAATTATTACTTCGAAT-TATCT
* * * * *
13318186 CGATGAGGCATTGGGTG-CGAA-T-TTACTTC-AGTTTAGCC
1 -GATGAGACATTGGGTGTCAAATTATTACTTCGA-ATTATCT
13318224 GATGAGACATTGGGTGTCAAATTATTACTTCGAATTATCT
1 GATGAGACATTGGGTGTCAAATTATTACTTCGAATTATCT
* * *
13318264 GATGAGGCACTGGGTGCCAAA
1 GATGAGACATTGGGTGTCAAA
13318285 CTGGTGTGTT
Statistics
Matches: 77, Mismatches: 15, Indels: 13
0.73 0.14 0.12
Matches are distributed among these distances:
37 17 0.22
38 11 0.14
39 2 0.03
40 31 0.40
41 16 0.21
ACGTcount: A:0.27, C:0.14, G:0.26, T:0.33
Consensus pattern (40 bp):
GATGAGACATTGGGTGTCAAATTATTACTTCGAATTATCT
Found at i:13326539 original size:22 final size:22
Alignment explanation
Indices: 13326512--13326554 Score: 70
Period size: 22 Copynumber: 2.0 Consensus size: 22
13326502 CAATCTAATT
13326512 TTTAAAT-AAGAAAATAAATATA
1 TTTAAATGAA-AAAATAAATATA
13326534 TTTAAATGAAAAAATAAATAT
1 TTTAAATGAAAAAATAAATAT
13326555 TAAATATATT
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
22 18 0.90
23 2 0.10
ACGTcount: A:0.63, C:0.00, G:0.05, T:0.33
Consensus pattern (22 bp):
TTTAAATGAAAAAATAAATATA
Found at i:13327940 original size:39 final size:39
Alignment explanation
Indices: 13327881--13327968 Score: 133
Period size: 39 Copynumber: 2.3 Consensus size: 39
13327871 ACTTAACGCC
* *
13327881 ATGCGAGCTCGATATACGAGCCCAATGTGCAAGCAT-GAT
1 ATGCAAGCTCGATACACGAGCCCAATGTGCAAGC-TCGAT
*
13327920 ATGCTAGCTCGATACACGAGCCCAATGTGCAAGCTCGAT
1 ATGCAAGCTCGATACACGAGCCCAATGTGCAAGCTCGAT
13327959 ATGCAAGCTC
1 ATGCAAGCTC
13327969 AATGTGTGAA
Statistics
Matches: 45, Mismatches: 3, Indels: 2
0.90 0.06 0.04
Matches are distributed among these distances:
38 1 0.02
39 44 0.98
ACGTcount: A:0.30, C:0.26, G:0.24, T:0.20
Consensus pattern (39 bp):
ATGCAAGCTCGATACACGAGCCCAATGTGCAAGCTCGAT
Found at i:13330759 original size:47 final size:47
Alignment explanation
Indices: 13330707--13330799 Score: 168
Period size: 47 Copynumber: 2.0 Consensus size: 47
13330697 GCAACGATAC
* *
13330707 TATTTGTATAAAAAGTAAGCAAAAGCATTGATTTTTCTTGTTAATTT
1 TATTTGTATAAAAAGTAAGCAAAAACATTAATTTTTCTTGTTAATTT
13330754 TATTTGTATAAAAAGTAAGCAAAAACATTAATTTTTCTTGTTAATT
1 TATTTGTATAAAAAGTAAGCAAAAACATTAATTTTTCTTGTTAATT
13330800 ATTTTTTACA
Statistics
Matches: 44, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
47 44 1.00
ACGTcount: A:0.39, C:0.06, G:0.11, T:0.44
Consensus pattern (47 bp):
TATTTGTATAAAAAGTAAGCAAAAACATTAATTTTTCTTGTTAATTT
Found at i:13333112 original size:32 final size:32
Alignment explanation
Indices: 13333071--13333153 Score: 116
Period size: 32 Copynumber: 2.6 Consensus size: 32
13333061 AAACATGTGG
* *
13333071 TTTTATGAAATGATAACAAA-TATCAGCTTTC-A
1 TTTTGTGAAATGATAACAAATTA-CAAC-TTCAA
13333103 TTTTGTGAAATGATAACAAATTACAACTTCAA
1 TTTTGTGAAATGATAACAAATTACAACTTCAA
13333135 TTTTGTGAAATGATAACAA
1 TTTTGTGAAATGATAACAA
13333154 TGGGAAACCC
Statistics
Matches: 47, Mismatches: 2, Indels: 4
0.89 0.04 0.08
Matches are distributed among these distances:
31 3 0.06
32 42 0.89
33 2 0.04
ACGTcount: A:0.42, C:0.11, G:0.11, T:0.36
Consensus pattern (32 bp):
TTTTGTGAAATGATAACAAATTACAACTTCAA
Found at i:13333218 original size:17 final size:18
Alignment explanation
Indices: 13333192--13333232 Score: 57
Period size: 18 Copynumber: 2.3 Consensus size: 18
13333182 CGTTAACCAT
*
13333192 AAACCTTAAC-ACACTAA
1 AAACCCTAACAACACTAA
*
13333209 AAACCCTAACAACCCTAA
1 AAACCCTAACAACACTAA
13333227 AAACCC
1 AAACCC
13333233 ATAAATAACA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
17 9 0.43
18 12 0.57
ACGTcount: A:0.51, C:0.37, G:0.00, T:0.12
Consensus pattern (18 bp):
AAACCCTAACAACACTAA
Found at i:13333691 original size:22 final size:21
Alignment explanation
Indices: 13333660--13333702 Score: 68
Period size: 22 Copynumber: 2.0 Consensus size: 21
13333650 TTATTTTAAT
*
13333660 TAAAATGGTTAAATTAAAATA
1 TAAAATGGTTAAAATAAAATA
13333681 TAAAAGTGGTTAAAATAAAATA
1 TAAAA-TGGTTAAAATAAAATA
13333703 AATCATATTT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
21 5 0.25
22 15 0.75
ACGTcount: A:0.58, C:0.00, G:0.12, T:0.30
Consensus pattern (21 bp):
TAAAATGGTTAAAATAAAATA
Found at i:13347198 original size:40 final size:40
Alignment explanation
Indices: 13347115--13347457 Score: 467
Period size: 40 Copynumber: 8.6 Consensus size: 40
13347105 TTGAATGCTG
* * * * * *
13347115 TCCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGAATATA
1 TCCGGGTTAAGTCCCGAAGGCATTCGTGC-GAGTTATTAAA
* * * * *
13347155 TCCGGATTAAGAT-CCGAAGGCCTTTGTGCGAGATACTAAA
1 TCCGGGTTAAG-TCCCGAAGGCATTCGTGCGAGTTATTAAA
13347195 TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTATTAAA
1 TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTATTAAA
13347235 TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTATTAAA
1 TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTATTAAA
*
13347275 TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTGTTAAA
1 TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTATTAAA
*
13347315 TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTGTTAAA
1 TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTATTAAA
*
13347355 TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTGTTAAA
1 TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTATTAAA
* * *
13347395 TCCGGGTTATGTCCCGAAGGCATT-GTGTGAGTTACTAAA
1 TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTATTAAA
* * *
13347434 ACCGGGCTATGTCCCGAAGGCATT
1 TCCGGGTTAAGTCCCGAAGGCATT
13347458 TGAACGAGGA
Statistics
Matches: 281, Mismatches: 19, Indels: 7
0.92 0.06 0.02
Matches are distributed among these distances:
39 35 0.12
40 238 0.85
41 8 0.03
ACGTcount: A:0.24, C:0.20, G:0.28, T:0.27
Consensus pattern (40 bp):
TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTATTAAA
Found at i:13355262 original size:80 final size:79
Alignment explanation
Indices: 13355178--13355349 Score: 220
Period size: 79 Copynumber: 2.2 Consensus size: 79
13355168 GGACTAAGAT
*
13355178 CCGAAGGCATTTGTGCGAGATA-CAAATTCCGGGTTAAGCCCCGAAGGCCTTTGTGCGAGATACT
1 CCGAAGGCATTTGTGCGAGATATCAAA-TCCGGGTTAAGCCCCGAAGG-CATTGTGCGAGATACT
* *
13355242 AAATCCGGGTTAAGTC
64 AAAACCGGGCTAAGTC
* * * * * * *
13355258 CCGAAGGCATTCGTGCGAGTTATTAAATCCGGGTTATGTCCCGAAGGCATTGTGTGAGTTACTAA
1 CCGAAGGCATTTGTGCGAGATATCAAATCCGGGTTAAGCCCCGAAGGCATTGTGCGAGATACTAA
*
13355323 AACCGGGCTATGTC
66 AACCGGGCTAAGTC
13355337 CCGAAGGCATTTG
1 CCGAAGGCATTTG
13355350 AACGAGGAGC
Statistics
Matches: 79, Mismatches: 12, Indels: 3
0.84 0.13 0.03
Matches are distributed among these distances:
79 38 0.48
80 38 0.48
81 3 0.04
ACGTcount: A:0.25, C:0.22, G:0.28, T:0.26
Consensus pattern (79 bp):
CCGAAGGCATTTGTGCGAGATATCAAATCCGGGTTAAGCCCCGAAGGCATTGTGCGAGATACTAA
AACCGGGCTAAGTC
Found at i:13355329 original size:39 final size:39
Alignment explanation
Indices: 13355125--13355347 Score: 209
Period size: 40 Copynumber: 5.6 Consensus size: 39
13355115 TTGAATGCTG
* * * * *
13355125 TCCGGGCTAAGTCCCGAAGGCTTTGTGCTA-AGTGAATATA
1 TCCGGGTTAAGTCCCGAAGGCATTGTGCGAGA-T-ACTAAA
**
13355165 TCCGGACTAAGAT-CCGAAGGCATTTGTGCGAGATAC-AAA
1 TCCGGGTTAAG-TCCCGAAGGCA-TTGTGCGAGATACTAAA
* *
13355204 TTCCGGGTTAAGCCCCGAAGGCCTTTGTGCGAGATACTAAA
1 -TCCGGGTTAAGTCCCGAAGG-CATTGTGCGAGATACTAAA
* *
13355245 TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTATTAAA
1 TCCGGGTTAAGTCCCGAAGGCATT-GTGCGAGATACTAAA
* * *
13355285 TCCGGGTTATGTCCCGAAGGCATTGTGTGAGTTACTAAA
1 TCCGGGTTAAGTCCCGAAGGCATTGTGCGAGATACTAAA
* * *
13355324 ACCGGGCTATGTCCCGAAGGCATT
1 TCCGGGTTAAGTCCCGAAGGCATT
13355348 TGAACGAGGA
Statistics
Matches: 157, Mismatches: 18, Indels: 17
0.82 0.09 0.09
Matches are distributed among these distances:
39 40 0.25
40 103 0.66
41 13 0.08
42 1 0.01
ACGTcount: A:0.26, C:0.22, G:0.27, T:0.26
Consensus pattern (39 bp):
TCCGGGTTAAGTCCCGAAGGCATTGTGCGAGATACTAAA
Found at i:13355367 original size:79 final size:80
Alignment explanation
Indices: 13355205--13355382 Score: 191
Period size: 79 Copynumber: 2.2 Consensus size: 80
13355195 AGATACAAAT
* * * *
13355205 TCCGGGTTAAGCCCCGAAGGCCTTTGTGCGAGATACTAAATCCGGGTTAAGTCCCGAAGGCATTC
1 TCCGGGTTAAGTCCCGAAGGCCATTGTGCGAGATACTAAAACCGGGCTAAGTCCCGAAGGCATTC
** * *
13355270 GTGCGAGTTATTAAA
66 GAACGAGTGACTAAA
* * * * *
13355285 TCCGGGTTATGTCCCGAAGG-CATTGTGTGAGTTACTAAAACCGGGCTATGTCCCGAAGGCATTT
1 TCCGGGTTAAGTCCCGAAGGCCATTGTGCGAGATACTAAAACCGGGCTAAGTCCCGAAGGCATTC
*
13355349 GAACGAG-GAGCTATA
66 GAACGAGTGA-CTAAA
*
13355364 TCC-GGTTAAATCCCGAAGG
1 TCCGGGTTAAGTCCCGAAGG
13355383 TACGTGATTT
Statistics
Matches: 81, Mismatches: 16, Indels: 4
0.80 0.16 0.04
Matches are distributed among these distances:
78 15 0.19
79 48 0.59
80 18 0.22
ACGTcount: A:0.25, C:0.22, G:0.28, T:0.25
Consensus pattern (80 bp):
TCCGGGTTAAGTCCCGAAGGCCATTGTGCGAGATACTAAAACCGGGCTAAGTCCCGAAGGCATTC
GAACGAGTGACTAAA
Found at i:13357894 original size:17 final size:18
Alignment explanation
Indices: 13357853--13357895 Score: 54
Period size: 17 Copynumber: 2.5 Consensus size: 18
13357843 TAAAAATTGA
*
13357853 ATTCCAATAGCTATAAGG
1 ATTCAAATAGCTATAAGG
*
13357871 ATT-AAATAGCTAT-GGG
1 ATTCAAATAGCTATAAGG
13357887 ATTCAAATA
1 ATTCAAATA
13357896 TAGAGGTCCT
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
16 5 0.23
17 14 0.64
18 3 0.14
ACGTcount: A:0.42, C:0.12, G:0.16, T:0.30
Consensus pattern (18 bp):
ATTCAAATAGCTATAAGG
Found at i:13364835 original size:26 final size:25
Alignment explanation
Indices: 13364795--13364848 Score: 72
Period size: 26 Copynumber: 2.1 Consensus size: 25
13364785 TCTCATTTTT
* * *
13364795 TTTCTTTTCTTTTCTTCTTTCTTTC
1 TTTCTTTTCGTTTCTTCTCTATTTC
13364820 TTTCTATTTCGTTTCTTCTCTATTTC
1 TTTCT-TTTCGTTTCTTCTCTATTTC
13364846 TTT
1 TTT
13364849 TTCTTGTTTT
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
25 5 0.20
26 20 0.80
ACGTcount: A:0.04, C:0.22, G:0.02, T:0.72
Consensus pattern (25 bp):
TTTCTTTTCGTTTCTTCTCTATTTC
Found at i:13384804 original size:28 final size:28
Alignment explanation
Indices: 13384741--13384894 Score: 220
Period size: 28 Copynumber: 5.5 Consensus size: 28
13384731 ATATTAAGTC
*
13384741 CGCACACTCAGTGCTATATAATC-AACT
1 CGCACACTTAGTGCTATATAATCAAACT
*
13384768 TGCACACTTAGTGCTATATAATCAAACT
1 CGCACACTTAGTGCTATATAATCAAACT
*
13384796 CGCACACTTAGTGCTACATAATCAAACT
1 CGCACACTTAGTGCTATATAATCAAACT
*
13384824 TGCACACTTAGTGCTATATAATCAAACT
1 CGCACACTTAGTGCTATATAATCAAACT
* * * *
13384852 CGCACACTTAGTGCTGTACAATTTAAACC
1 CGCACACTTAGTGCTATATAA-TCAAACT
13384881 CGCACACTTAGTGC
1 CGCACACTTAGTGC
13384895 CAATCTCATG
Statistics
Matches: 114, Mismatches: 11, Indels: 2
0.90 0.09 0.02
Matches are distributed among these distances:
27 21 0.18
28 74 0.65
29 19 0.17
ACGTcount: A:0.33, C:0.27, G:0.12, T:0.28
Consensus pattern (28 bp):
CGCACACTTAGTGCTATATAATCAAACT
Found at i:13386692 original size:14 final size:13
Alignment explanation
Indices: 13386671--13386711 Score: 57
Period size: 14 Copynumber: 3.2 Consensus size: 13
13386661 TATTAGGATA
13386671 ATTATTAGATTTT
1 ATTATTAGATTTT
13386684 ATTATTTAGATTTT
1 ATTA-TTAGATTTT
*
13386698 ATT-TTAGCTTTT
1 ATTATTAGATTTT
13386710 AT
1 AT
13386712 CTCCATTTAT
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
12 10 0.38
13 4 0.15
14 12 0.46
ACGTcount: A:0.27, C:0.02, G:0.07, T:0.63
Consensus pattern (13 bp):
ATTATTAGATTTT
Found at i:13386734 original size:10 final size:10
Alignment explanation
Indices: 13386716--13386764 Score: 64
Period size: 10 Copynumber: 5.0 Consensus size: 10
13386706 TTTTATCTCC
13386716 ATTTATCTTT
1 ATTTATCTTT
13386726 ATTTATCTTT
1 ATTTATCTTT
**
13386736 AAAT-TCTTT
1 ATTTATCTTT
*
13386745 ATTTATCTGT
1 ATTTATCTTT
13386755 ATTTATCTTT
1 ATTTATCTTT
13386765 TAGAATTTAA
Statistics
Matches: 32, Mismatches: 6, Indels: 2
0.80 0.15 0.05
Matches are distributed among these distances:
9 7 0.22
10 25 0.78
ACGTcount: A:0.22, C:0.10, G:0.02, T:0.65
Consensus pattern (10 bp):
ATTTATCTTT
Found at i:13387515 original size:17 final size:18
Alignment explanation
Indices: 13387484--13387517 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
13387474 TATTCTCTAT
*
13387484 TTTAATTTTCGCAATTTA
1 TTTAATTTTCACAATTTA
13387502 TTTAA-TTTCACAATTT
1 TTTAATTTTCACAATTT
13387518 CAATCAACTT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 10 0.67
18 5 0.33
ACGTcount: A:0.29, C:0.12, G:0.03, T:0.56
Consensus pattern (18 bp):
TTTAATTTTCACAATTTA
Found at i:13388233 original size:33 final size:33
Alignment explanation
Indices: 13388187--13388263 Score: 127
Period size: 33 Copynumber: 2.3 Consensus size: 33
13388177 GTGAATAACA
*
13388187 CAGTATCAGTATAGTCTGGGCCAAAGCCCTATT
1 CAGTATCAATATAGTCTGGGCCAAAGCCCTATT
*
13388220 CAGTATCAATATAGTTTGGGCCAAAGCCCTATT
1 CAGTATCAATATAGTCTGGGCCAAAGCCCTATT
*
13388253 CAGTAACAATA
1 CAGTATCAATA
13388264 CAGTAGATGT
Statistics
Matches: 41, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
33 41 1.00
ACGTcount: A:0.32, C:0.22, G:0.18, T:0.27
Consensus pattern (33 bp):
CAGTATCAATATAGTCTGGGCCAAAGCCCTATT
Found at i:13388454 original size:27 final size:27
Alignment explanation
Indices: 13388424--13388476 Score: 79
Period size: 27 Copynumber: 2.0 Consensus size: 27
13388414 CTGCCAGAAA
13388424 CAGTAAATGTCGCAAAGCCACCAGTAT
1 CAGTAAATGTCGCAAAGCCACCAGTAT
* * *
13388451 CAGTAATTGTGGCATAGCCACCAGTA
1 CAGTAAATGTCGCAAAGCCACCAGTA
13388477 ACGGCGAATG
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
27 23 1.00
ACGTcount: A:0.34, C:0.25, G:0.21, T:0.21
Consensus pattern (27 bp):
CAGTAAATGTCGCAAAGCCACCAGTAT
Found at i:13388674 original size:27 final size:27
Alignment explanation
Indices: 13388644--13388775 Score: 117
Period size: 27 Copynumber: 4.9 Consensus size: 27
13388634 GGGCATAATT
* *
13388644 GTCATTTTACCATACAAGGGTATTACG
1 GTCATTTTACCCTACAGGGGTATTACG
*
13388671 GTCACTCTT-CCCTACAGGGGCT-TTACG
1 GTCA-TTTTACCCTACAGGGG-TATTACG
*
13388698 GTCATTTTACCCTACAGGGGCATTACG
1 GTCATTTTACCCTACAGGGGTATTACG
* * ***
13388725 GTCTTTTTA-CCTATTAGGGGTATTTTA
1 GTCATTTTACCCTA-CAGGGGTATTACG
* *
13388752 GTCATTTCACCCTACAAGGGTATT
1 GTCATTTTACCCTACAGGGGTATT
13388776 TTGGTAAATC
Statistics
Matches: 84, Mismatches: 15, Indels: 12
0.76 0.14 0.11
Matches are distributed among these distances:
26 7 0.08
27 69 0.82
28 8 0.10
ACGTcount: A:0.22, C:0.23, G:0.20, T:0.36
Consensus pattern (27 bp):
GTCATTTTACCCTACAGGGGTATTACG
Found at i:13388796 original size:27 final size:27
Alignment explanation
Indices: 13388766--13388831 Score: 78
Period size: 27 Copynumber: 2.4 Consensus size: 27
13388756 TTTCACCCTA
**
13388766 CAAGGGTATTTTGGTAAATCTACAAAC
1 CAAGGGTATTTCAGTAAATCTACAAAC
* * *
13388793 CAAGGGTATTTCAGTAATTTTGCAAAC
1 CAAGGGTATTTCAGTAAATCTACAAAC
*
13388820 CAATGGTATTTC
1 CAAGGGTATTTC
13388832 TATAATTTTT
Statistics
Matches: 33, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
27 33 1.00
ACGTcount: A:0.33, C:0.15, G:0.18, T:0.33
Consensus pattern (27 bp):
CAAGGGTATTTCAGTAAATCTACAAAC
Found at i:13388837 original size:27 final size:27
Alignment explanation
Indices: 13388788--13389020 Score: 174
Period size: 27 Copynumber: 8.6 Consensus size: 27
13388778 GGTAAATCTA
*
13388788 CAAACCAAGGGTATTTC-AGTAATTTTG
1 CAAATCAAGGGTATTTCTA-TAATTTTG
* *
13388815 CAAACCAATGGTATTTCTATAATTTTTG
1 CAAATCAAGGGTATTTCTATAA-TTTTG
13388843 -AAAGTCAA-GGTATTTCTATAATTTTG
1 CAAA-TCAAGGGTATTTCTATAATTTTG
* * *
13388869 TAAATCAGGGGTATTTCTGTAATTTT-
1 CAAATCAAGGGTATTTCTATAATTTTG
* * * *
13388895 CTAAATCAATGGTATTT-TGGTAACTTTA
1 C-AAATCAAGGGTATTTCT-ATAATTTTG
* *
13388923 CAAATCGAGGGTATTT-TAGTAATTTTA
1 CAAATCAAGGGTATTTCTA-TAATTTTG
* * * * *
13388950 CAAGTTAGGGGTATTTCGATAATTTTA
1 CAAATCAAGGGTATTTCTATAATTTTG
**
13388977 CAGGTCAAGGGTATTTCTATAATTTTG
1 CAAATCAAGGGTATTTCTATAATTTTG
*
13389004 TAAA-CGAAGGGTATTTC
1 CAAATC-AAGGGTATTTC
13389021 AGTGATTCTA
Statistics
Matches: 170, Mismatches: 25, Indels: 22
0.78 0.12 0.10
Matches are distributed among these distances:
26 10 0.06
27 149 0.88
28 11 0.06
ACGTcount: A:0.31, C:0.10, G:0.18, T:0.40
Consensus pattern (27 bp):
CAAATCAAGGGTATTTCTATAATTTTG
Found at i:13391650 original size:33 final size:33
Alignment explanation
Indices: 13391613--13391686 Score: 87
Period size: 33 Copynumber: 2.2 Consensus size: 33
13391603 GTATACGTGC
* * *
13391613 AAGACCATAGCTGGGCTATGGCATCCTG-ATGAT
1 AAGACCATAACTGAGCTATGGCATCATGAATG-T
* *
13391646 AAGACCATAACTGAGTTATGGCATTATGAATGT
1 AAGACCATAACTGAGCTATGGCATCATGAATGT
13391679 AAGACCAT
1 AAGACCAT
13391687 GGTAAGGCCA
Statistics
Matches: 35, Mismatches: 5, Indels: 2
0.83 0.12 0.05
Matches are distributed among these distances:
33 32 0.91
34 3 0.09
ACGTcount: A:0.34, C:0.18, G:0.23, T:0.26
Consensus pattern (33 bp):
AAGACCATAACTGAGCTATGGCATCATGAATGT
Found at i:13391698 original size:105 final size:105
Alignment explanation
Indices: 13391508--13391698 Score: 269
Period size: 105 Copynumber: 1.8 Consensus size: 105
13391498 GTTTGAATGT
* ** *
13391508 AAGACCATAGTTGGGCTATGGCATTTTAATGAAAAGACCATAACTGGGTTATGGCACCTTGAACG
1 AAGACCATAGCTGGGCTATGGCATCCTAATGAAAAGACCATAACTGAGTTATGGCACCTTGAACG
*
13391573 TAAGACCATGGTTGGACCATGACACTATATGTATACGTGC
66 TAAGACCATGGTAGGACCATGACACTATATGTATACGTGC
* * * *
13391613 AAGACCATAGCTGGGCTATGGCATCCTGATGATAAGACCATAACTGAGTTATGGCA-TTATGAAT
1 AAGACCATAGCTGGGCTATGGCATCCTAATGAAAAGACCATAACTGAGTTATGGCACCT-TGAAC
13391677 GTAAGACCATGGTAAGG-CCATG
65 GTAAGACCATGGT-AGGACCATG
13391699 GCAACTGTGT
Statistics
Matches: 75, Mismatches: 9, Indels: 4
0.85 0.10 0.05
Matches are distributed among these distances:
104 1 0.01
105 72 0.96
106 2 0.03
ACGTcount: A:0.32, C:0.18, G:0.25, T:0.26
Consensus pattern (105 bp):
AAGACCATAGCTGGGCTATGGCATCCTAATGAAAAGACCATAACTGAGTTATGGCACCTTGAACG
TAAGACCATGGTAGGACCATGACACTATATGTATACGTGC
Found at i:13396771 original size:17 final size:17
Alignment explanation
Indices: 13396749--13396784 Score: 72
Period size: 17 Copynumber: 2.1 Consensus size: 17
13396739 CAATTAGAGG
13396749 AAAGATAATAAAAATAA
1 AAAGATAATAAAAATAA
13396766 AAAGATAATAAAAATAA
1 AAAGATAATAAAAATAA
13396783 AA
1 AA
13396785 CCCTTTTTTA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.78, C:0.00, G:0.06, T:0.17
Consensus pattern (17 bp):
AAAGATAATAAAAATAA
Found at i:13399742 original size:32 final size:27
Alignment explanation
Indices: 13399675--13399730 Score: 103
Period size: 27 Copynumber: 2.1 Consensus size: 27
13399665 ACAATACTCT
*
13399675 ATCGCTAAAAATAGAACTAGAAGAGAA
1 ATCGCCAAAAATAGAACTAGAAGAGAA
13399702 ATCGCCAAAAATAGAACTAGAAGAGAA
1 ATCGCCAAAAATAGAACTAGAAGAGAA
13399729 AT
1 AT
13399731 TAAACCTCCA
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
27 28 1.00
ACGTcount: A:0.55, C:0.12, G:0.18, T:0.14
Consensus pattern (27 bp):
ATCGCCAAAAATAGAACTAGAAGAGAA
Found at i:13403000 original size:61 final size:60
Alignment explanation
Indices: 13402902--13403076 Score: 182
Period size: 60 Copynumber: 2.9 Consensus size: 60
13402892 TCAAGCTTTA
* *
13402902 CTGGGCCCA-AGCCCTATTCAGAAATCAGAGT-TAACTGGGCCTTAGCCCATATCAATATTAAT
1 CTGGG-CCATAGCCCTATT-A-CAATCAGAGTAT-ACTGGGCCTTAGCCCATATCAATATAAAT
* *
13402964 CTGGGCCATAGCCC-CTTACAGTATCAGAGTATACTGGGCC-TAGCCCATATCAGTATAAAT
1 CTGGGCCATAGCCCTATTACA--ATCAGAGTATACTGGGCCTTAGCCCATATCAATATAAAT
* *
13403024 CTTGGCCATAGCCCTATTACAAGTC-GAGATATATTGGGCCTTA-CCCATATCAA
1 CTGGGCCATAGCCCTATTACAA-TCAGAG-TATACTGGGCCTTAGCCCATATCAA
13403077 CACAGTTGGG
Statistics
Matches: 97, Mismatches: 8, Indels: 18
0.79 0.07 0.15
Matches are distributed among these distances:
59 5 0.05
60 53 0.55
61 28 0.29
62 11 0.11
ACGTcount: A:0.29, C:0.26, G:0.18, T:0.26
Consensus pattern (60 bp):
CTGGGCCATAGCCCTATTACAATCAGAGTATACTGGGCCTTAGCCCATATCAATATAAAT
Found at i:13403037 original size:28 final size:28
Alignment explanation
Indices: 13402936--13403037 Score: 91
Period size: 28 Copynumber: 3.5 Consensus size: 28
13402926 TCAGAGTTAA
* * *
13402936 CTGGGCCTTAGCCCATATCAATATTAAT
1 CTGGGCCATAGCCCATATCAGTATAAAT
*
13402964 CTGGGCCATAGCCCCT-TACAGTATCAGAGTAT
1 CTGGGCCATAGCCCATAT-CAGTAT-A-A--AT
13402996 ACTGGGCC-TAGCCCATATCAGTATAAAT
1 -CTGGGCCATAGCCCATATCAGTATAAAT
*
13403024 CTTGGCCATAGCCC
1 CTGGGCCATAGCCC
13403038 TATTACAAGT
Statistics
Matches: 60, Mismatches: 6, Indels: 16
0.73 0.07 0.20
Matches are distributed among these distances:
27 7 0.12
28 27 0.45
30 2 0.03
31 1 0.02
32 15 0.25
33 8 0.13
ACGTcount: A:0.26, C:0.28, G:0.19, T:0.26
Consensus pattern (28 bp):
CTGGGCCATAGCCCATATCAGTATAAAT
Found at i:13403109 original size:19 final size:20
Alignment explanation
Indices: 13403067--13403109 Score: 61
Period size: 20 Copynumber: 2.2 Consensus size: 20
13403057 TTGGGCCTTA
13403067 CCCATATCAACACAGTTGGG
1 CCCATATCAACACAGTTGGG
* *
13403087 CCCATTTCAATACAGTT-GG
1 CCCATATCAACACAGTTGGG
13403106 CCCA
1 CCCA
13403110 CAACAAAACA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
19 6 0.29
20 15 0.71
ACGTcount: A:0.28, C:0.33, G:0.16, T:0.23
Consensus pattern (20 bp):
CCCATATCAACACAGTTGGG
Found at i:13404286 original size:19 final size:18
Alignment explanation
Indices: 13404249--13404292 Score: 54
Period size: 19 Copynumber: 2.4 Consensus size: 18
13404239 ATACATACAG
13404249 TAAT-ATTTTTCTAATAA
1 TAATAATTTTTCTAATAA
*
13404266 TAATAATTTTATCTTATAA
1 TAATAATTTT-TCTAATAA
*
13404285 TACTAATT
1 TAATAATT
13404293 AAAATTTCAT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
17 4 0.17
18 5 0.22
19 14 0.61
ACGTcount: A:0.41, C:0.07, G:0.00, T:0.52
Consensus pattern (18 bp):
TAATAATTTTTCTAATAA
Found at i:13408704 original size:15 final size:15
Alignment explanation
Indices: 13408672--13408700 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
13408662 TTATTTTGTG
13408672 TTTATTATGTGTGAA
1 TTTATTATGTGTGAA
13408687 TTTA-TATGTGTGAA
1 TTTATTATGTGTGAA
13408701 ATTTTCGTGC
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 10 0.71
15 4 0.29
ACGTcount: A:0.28, C:0.00, G:0.21, T:0.52
Consensus pattern (15 bp):
TTTATTATGTGTGAA
Found at i:13412413 original size:68 final size:68
Alignment explanation
Indices: 13412295--13412588 Score: 356
Period size: 68 Copynumber: 4.3 Consensus size: 68
13412285 TGGCCGTAGT
* * * * * * *
13412295 CTAGCCATAGTCTTACACAGTATGAACCCATGTTTAATGTCCTGGAGGACTCTATATATTGCCAT
1 CTAGCTATGGTCTTACACATTATAAACCCATGTTTACTATCCTGGAGGACTCTATATGTTGCCAT
13412360 AGC
66 AGC
* *
13412363 CTAGTTATGGTCTTACACATTATAAACCCATGTTTACTATCCT-GATGGACTCTATATGTTGCTA
1 CTAGCTATGGTCTTACACATTATAAACCCATGTTTACTATCCTGGA-GGACTCTATATGTTGCCA
13412427 TAGC
65 TAGC
* * * * *
13412431 CTAGCTATGGTCTCACACATTATAAACCTATGTTTACTGTCCTGGAAGACTCTATATGTTTCCAT
1 CTAGCTATGGTCTTACACATTATAAACCCATGTTTACTATCCTGGAGGACTCTATATGTTGCCAT
13412496 AGC
66 AGC
* * * * * *
13412499 CTAGCTATGGTTTTACATATTATAAACCCATGTTTACTATCTTGGCGAACTCTTTATGTTGCCAT
1 CTAGCTATGGTCTTACACATTATAAACCCATGTTTACTATCCTGGAGGACTCTATATGTTGCCAT
*
13412564 AGT
66 AGC
* * *
13412567 TTAGCAATGGTCTTACATATTA
1 CTAGCTATGGTCTTACACATTA
13412589 AACCTCTCTC
Statistics
Matches: 193, Mismatches: 31, Indels: 4
0.85 0.14 0.02
Matches are distributed among these distances:
67 2 0.01
68 189 0.98
69 2 0.01
ACGTcount: A:0.27, C:0.21, G:0.15, T:0.37
Consensus pattern (68 bp):
CTAGCTATGGTCTTACACATTATAAACCCATGTTTACTATCCTGGAGGACTCTATATGTTGCCAT
AGC
Found at i:13414495 original size:23 final size:23
Alignment explanation
Indices: 13414465--13414545 Score: 65
Period size: 23 Copynumber: 3.3 Consensus size: 23
13414455 GAATTAATTC
13414465 TAACAATTCAATCTTCCTATCAT
1 TAACAATTCAATCTTCCTATCAT
* * ** *
13414488 TAACAATT-TATTTTTATGAATTAATT
1 TAACAATTCAATCTTCCT--A-TCA-T
13414514 CTAACAATTCAATCTTCCTATCAT
1 -TAACAATTCAATCTTCCTATCAT
13414538 TAACAATT
1 TAACAATT
13414546 TTTAAGAAAG
Statistics
Matches: 42, Mismatches: 10, Indels: 12
0.66 0.16 0.19
Matches are distributed among these distances:
22 5 0.12
23 16 0.38
24 2 0.05
25 4 0.10
26 2 0.05
27 8 0.19
28 5 0.12
ACGTcount: A:0.37, C:0.19, G:0.01, T:0.43
Consensus pattern (23 bp):
TAACAATTCAATCTTCCTATCAT
Found at i:13414526 original size:50 final size:50
Alignment explanation
Indices: 13414451--13414546 Score: 192
Period size: 50 Copynumber: 1.9 Consensus size: 50
13414441 TTCTAAATCA
13414451 TTATGAATTAATTCTAACAATTCAATCTTCCTATCATTAACAATTTATTT
1 TTATGAATTAATTCTAACAATTCAATCTTCCTATCATTAACAATTTATTT
13414501 TTATGAATTAATTCTAACAATTCAATCTTCCTATCATTAACAATTT
1 TTATGAATTAATTCTAACAATTCAATCTTCCTATCATTAACAATTT
13414547 TTAAGAAAGG
Statistics
Matches: 46, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
50 46 1.00
ACGTcount: A:0.36, C:0.17, G:0.02, T:0.45
Consensus pattern (50 bp):
TTATGAATTAATTCTAACAATTCAATCTTCCTATCATTAACAATTTATTT
Found at i:13415420 original size:30 final size:31
Alignment explanation
Indices: 13415364--13415424 Score: 88
Period size: 32 Copynumber: 2.0 Consensus size: 31
13415354 AACAAGTAAG
13415364 TGCCTCTAAAATAATAAAAAAAAATTAACAAA
1 TGCCTCTAAAATAAT-AAAAAAAATTAACAAA
* *
13415396 TGCCTTTAAAATAAT-AACAAAATTAACAA
1 TGCCTCTAAAATAATAAAAAAAATTAACAA
13415425 GAAAATAAGT
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
30 13 0.48
32 14 0.52
ACGTcount: A:0.59, C:0.13, G:0.03, T:0.25
Consensus pattern (31 bp):
TGCCTCTAAAATAATAAAAAAAATTAACAAA
Found at i:13415722 original size:26 final size:26
Alignment explanation
Indices: 13415693--13415742 Score: 82
Period size: 26 Copynumber: 1.9 Consensus size: 26
13415683 TTTTGGGCGG
* *
13415693 GCCTTCGGGCTGGGCCGAGTAGCCGA
1 GCCTTCGGGCCGGGCCAAGTAGCCGA
13415719 GCCTTCGGGCCGGGCCAAGTAGCC
1 GCCTTCGGGCCGGGCCAAGTAGCC
13415743 CGGCCCATGA
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
26 22 1.00
ACGTcount: A:0.12, C:0.34, G:0.40, T:0.14
Consensus pattern (26 bp):
GCCTTCGGGCCGGGCCAAGTAGCCGA
Found at i:13417736 original size:21 final size:22
Alignment explanation
Indices: 13417707--13417747 Score: 57
Period size: 21 Copynumber: 1.9 Consensus size: 22
13417697 TACAAATTTT
13417707 ATTTATCTAACAACAAACATAC
1 ATTTATCTAACAACAAACATAC
* *
13417729 ATTT-TCTATCATCAAACAT
1 ATTTATCTAACAACAAACAT
13417748 CAAAATAAAC
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 13 0.76
22 4 0.24
ACGTcount: A:0.44, C:0.22, G:0.00, T:0.34
Consensus pattern (22 bp):
ATTTATCTAACAACAAACATAC
Found at i:13420727 original size:28 final size:27
Alignment explanation
Indices: 13420670--13420821 Score: 232
Period size: 27 Copynumber: 5.6 Consensus size: 27
13420660 TAAATTGTGC
*
13420670 AGCACTAAGTGTGCGAATTGACTATGT
1 AGCACTAAGTGTGCGAGTTGACTATGT
13420697 AGCACTAAGTGTGCGAGTTTGACTATGT
1 AGCACTAAGTGTGCGAG-TTGACTATGT
13420725 AGCACTAAGTGTGCGAGTTGACTATGT
1 AGCACTAAGTGTGCGAGTTGACTATGT
* *
13420752 AGCACTAAGTGCGCGAGTTTGATTATGT
1 AGCACTAAGTGTGCGAG-TTGACTATGT
* *
13420780 AGCACTAAGTGTGCGAGTTGATTATAT
1 AGCACTAAGTGTGCGAGTTGACTATGT
*
13420807 AGCACTGAGTGTGCG
1 AGCACTAAGTGTGCG
13420822 GACTTAATAT
Statistics
Matches: 117, Mismatches: 6, Indels: 4
0.92 0.05 0.03
Matches are distributed among these distances:
27 65 0.56
28 52 0.44
ACGTcount: A:0.26, C:0.14, G:0.29, T:0.30
Consensus pattern (27 bp):
AGCACTAAGTGTGCGAGTTGACTATGT
Found at i:13420734 original size:55 final size:55
Alignment explanation
Indices: 13420670--13420821 Score: 250
Period size: 55 Copynumber: 2.8 Consensus size: 55
13420660 TAAATTGTGC
*
13420670 AGCACTAAGTGTGCGAATTGACTATGTAGCACTAAGTGTGCGAGTTTGACTATGT
1 AGCACTAAGTGTGCGAGTTGACTATGTAGCACTAAGTGTGCGAGTTTGACTATGT
* *
13420725 AGCACTAAGTGTGCGAGTTGACTATGTAGCACTAAGTGCGCGAGTTTGATTATGT
1 AGCACTAAGTGTGCGAGTTGACTATGTAGCACTAAGTGTGCGAGTTTGACTATGT
* * *
13420780 AGCACTAAGTGTGCGAGTTGATTATATAGCACTGAGTGTGCG
1 AGCACTAAGTGTGCGAGTTGACTATGTAGCACTAAGTGTGCG
13420822 GACTTAATAT
Statistics
Matches: 90, Mismatches: 7, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
55 90 1.00
ACGTcount: A:0.26, C:0.14, G:0.29, T:0.30
Consensus pattern (55 bp):
AGCACTAAGTGTGCGAGTTGACTATGTAGCACTAAGTGTGCGAGTTTGACTATGT
Found at i:13433384 original size:19 final size:19
Alignment explanation
Indices: 13433360--13433405 Score: 67
Period size: 19 Copynumber: 2.4 Consensus size: 19
13433350 GTGAAAGTTT
13433360 AATGCAAATG-ATGCAATG
1 AATGCAAATGTATGCAATG
*
13433378 CAATGCAAATGTATGGAATG
1 -AATGCAAATGTATGCAATG
13433398 AATGCAAA
1 AATGCAAA
13433406 AGAAAGGAAG
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
19 18 0.72
20 7 0.28
ACGTcount: A:0.46, C:0.11, G:0.22, T:0.22
Consensus pattern (19 bp):
AATGCAAATGTATGCAATG
Found at i:13435653 original size:26 final size:24
Alignment explanation
Indices: 13435624--13435730 Score: 76
Period size: 26 Copynumber: 4.2 Consensus size: 24
13435614 ATACATTATA
13435624 AAATAAAGTATAAATCAATTTGAAAT
1 AAATAAA-TATAAATCAATTT-AAAT
* *
13435650 AAATAATTTATAAAACAATTTAAAGT
1 AAATAA-ATATAAATCAATTTAAA-T
13435676 AAATAATATATAAAAT-AATTTTAAA-
1 AAATAA-ATAT-AAATCAA-TTTAAAT
* * *
13435701 AAAT-AATACAAAACGAATTAAAAT
1 AAATAAATATAAATC-AATTTAAAT
13435725 AAATAA
1 AAATAA
13435731 TATGGTAAAA
Statistics
Matches: 66, Mismatches: 7, Indels: 17
0.73 0.08 0.19
Matches are distributed among these distances:
22 3 0.05
23 8 0.12
24 7 0.11
25 8 0.12
26 31 0.47
27 9 0.14
ACGTcount: A:0.63, C:0.04, G:0.04, T:0.30
Consensus pattern (24 bp):
AAATAAATATAAATCAATTTAAAT
Found at i:13437635 original size:22 final size:20
Alignment explanation
Indices: 13437587--13437646 Score: 68
Period size: 21 Copynumber: 2.9 Consensus size: 20
13437577 GTCGTGTTGC
*
13437587 ATTTTTTTAATGTTTTATTTT
1 ATTTTTTGAAT-TTTTATTTT
13437608 ATTTTTTTGAATTTTTCCATTTT
1 A-TTTTTTGAATTTTT--ATTTT
13437631 A-TTTTTGAATTTTTAT
1 ATTTTTTGAATTTTTAT
13437647 ACTTCTTTAT
Statistics
Matches: 35, Mismatches: 1, Indels: 8
0.80 0.02 0.18
Matches are distributed among these distances:
19 2 0.06
21 18 0.51
22 9 0.26
23 6 0.17
ACGTcount: A:0.20, C:0.03, G:0.05, T:0.72
Consensus pattern (20 bp):
ATTTTTTGAATTTTTATTTT
Found at i:13443095 original size:3 final size:3
Alignment explanation
Indices: 13443087--13443163 Score: 68
Period size: 3 Copynumber: 26.0 Consensus size: 3
13443077 ATAAGTAAAG
* * *
13443087 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATG ATG ATG ATA ATA A-A
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
* * * *
13443134 TATA GTA ATG ATA ATA GTA AGA AT- ATA ATA
1 -ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
13443164 TATAGTATTA
Statistics
Matches: 61, Mismatches: 10, Indels: 6
0.79 0.13 0.08
Matches are distributed among these distances:
2 3 0.05
3 57 0.93
4 1 0.02
ACGTcount: A:0.58, C:0.00, G:0.09, T:0.32
Consensus pattern (3 bp):
ATA
Found at i:13445036 original size:18 final size:15
Alignment explanation
Indices: 13445007--13445060 Score: 54
Period size: 18 Copynumber: 3.2 Consensus size: 15
13444997 ATGGGGTTAA
13445007 GGGTTAGTTGGGTTTT
1 GGGTT-GTTGGGTTTT
13445023 GGGCTTCTGTTGGGTTTAGT
1 GGG--T-TGTTGGGTTT--T
13445043 GGGTTGTTGGGTTTT
1 GGGTTGTTGGGTTTT
13445058 GGG
1 GGG
13445061 GCTAGGGTTT
Statistics
Matches: 33, Mismatches: 0, Indels: 11
0.75 0.00 0.25
Matches are distributed among these distances:
15 4 0.12
16 3 0.09
17 10 0.30
18 11 0.33
19 1 0.03
20 4 0.12
ACGTcount: A:0.04, C:0.04, G:0.46, T:0.46
Consensus pattern (15 bp):
GGGTTGTTGGGTTTT
Found at i:13446729 original size:14 final size:14
Alignment explanation
Indices: 13446710--13446739 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
13446700 AGTGCTTGTG
13446710 TAACTTTATTTAAT
1 TAACTTTATTTAAT
*
13446724 TAACTTTATTTCAT
1 TAACTTTATTTAAT
13446738 TA
1 TA
13446740 TTAATAATTA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.33, C:0.10, G:0.00, T:0.57
Consensus pattern (14 bp):
TAACTTTATTTAAT
Found at i:13452398 original size:37 final size:37
Alignment explanation
Indices: 13452339--13452447 Score: 173
Period size: 37 Copynumber: 2.9 Consensus size: 37
13452329 AGCTCAGACG
* *
13452339 AAATCTCCACACGAAGTTATCGGGTCTTACCCGGACA
1 AAATCTCCACACGTAGTCATCGGGTCTTACCCGGACA
*
13452376 AAATCTCCACACGTAGTCATCGGGTCTTACCCGAACA
1 AAATCTCCACACGTAGTCATCGGGTCTTACCCGGACA
* *
13452413 TAATCTCCACACGTAGTCATCGGGTCTTACTCGGA
1 AAATCTCCACACGTAGTCATCGGGTCTTACCCGGA
13452448 ATATATTTCC
Statistics
Matches: 66, Mismatches: 6, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
37 66 1.00
ACGTcount: A:0.28, C:0.30, G:0.18, T:0.24
Consensus pattern (37 bp):
AAATCTCCACACGTAGTCATCGGGTCTTACCCGGACA
Found at i:13452743 original size:47 final size:47
Alignment explanation
Indices: 13452652--13452796 Score: 222
Period size: 47 Copynumber: 3.1 Consensus size: 47
13452642 TATATATATT
* * *
13452652 TCACATTGACCATTCGGCTTTA-C-CACATATGCATGTTCATATTCA
1 TCACATTGGCCATTCGGCCTTATCACACATATGCATGTTCACATTCA
* *
13452697 CCACATTGGCCATTCGGCCTTATCACACATATGCATGCTCACATTCA
1 TCACATTGGCCATTCGGCCTTATCACACATATGCATGTTCACATTCA
*
13452744 TCACATTGGCCATTCGGCCTTATCACATATATGCATGTTCACATTCA
1 TCACATTGGCCATTCGGCCTTATCACACATATGCATGTTCACATTCA
13452791 TCACAT
1 TCACAT
13452797 AAAATCCTAA
Statistics
Matches: 90, Mismatches: 8, Indels: 2
0.90 0.08 0.02
Matches are distributed among these distances:
45 19 0.21
46 1 0.01
47 70 0.78
ACGTcount: A:0.26, C:0.30, G:0.12, T:0.32
Consensus pattern (47 bp):
TCACATTGGCCATTCGGCCTTATCACACATATGCATGTTCACATTCA
Found at i:13453997 original size:25 final size:25
Alignment explanation
Indices: 13453940--13453991 Score: 104
Period size: 25 Copynumber: 2.1 Consensus size: 25
13453930 AGCTTAAGTA
13453940 AAACAATAGATTTGCTTAAGTACTT
1 AAACAATAGATTTGCTTAAGTACTT
13453965 AAACAATAGATTTGCTTAAGTACTT
1 AAACAATAGATTTGCTTAAGTACTT
13453990 AA
1 AA
13453992 GTAATATTAT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 27 1.00
ACGTcount: A:0.42, C:0.12, G:0.12, T:0.35
Consensus pattern (25 bp):
AAACAATAGATTTGCTTAAGTACTT
Found at i:13467139 original size:35 final size:35
Alignment explanation
Indices: 13467093--13467165 Score: 130
Period size: 35 Copynumber: 2.1 Consensus size: 35
13467083 AGATATAGGG
13467093 TTTGTGTACCCAAAAAAAT-AAACTTATTTGGAAAA
1 TTTGTGTACCCAAAAAAATGAAA-TTATTTGGAAAA
13467128 TTTGTGTACCCAAAAAAATGAAATTATTTGGAAAA
1 TTTGTGTACCCAAAAAAATGAAATTATTTGGAAAA
13467163 TTT
1 TTT
13467166 TGCAAGAAGC
Statistics
Matches: 37, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
35 34 0.92
36 3 0.08
ACGTcount: A:0.44, C:0.10, G:0.12, T:0.34
Consensus pattern (35 bp):
TTTGTGTACCCAAAAAAATGAAATTATTTGGAAAA
Found at i:13473836 original size:6 final size:6
Alignment explanation
Indices: 13473819--13473859 Score: 64
Period size: 6 Copynumber: 6.8 Consensus size: 6
13473809 AAGAGAAAAA
* *
13473819 AAAACT AGAACT AAAACT AAAACT AAAAAT AAAACT AAAAC
1 AAAACT AAAACT AAAACT AAAACT AAAACT AAAACT AAAAC
13473860 CGTATCTATA
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
6 31 1.00
ACGTcount: A:0.68, C:0.15, G:0.02, T:0.15
Consensus pattern (6 bp):
AAAACT
Found at i:13479370 original size:19 final size:20
Alignment explanation
Indices: 13479346--13479384 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 20
13479336 TTCTCAGGGG
13479346 CTTGGGCCG-TAATGGGCCA
1 CTTGGGCCGATAATGGGCCA
*
13479365 CTTGGGTCGACTAATGGGCC
1 CTTGGGCCGA-TAATGGGCC
13479385 TTGGGCCATT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 8 0.47
21 9 0.53
ACGTcount: A:0.15, C:0.26, G:0.36, T:0.23
Consensus pattern (20 bp):
CTTGGGCCGATAATGGGCCA
Found at i:13489913 original size:39 final size:39
Alignment explanation
Indices: 13489864--13489941 Score: 120
Period size: 39 Copynumber: 2.0 Consensus size: 39
13489854 CAGCGATGGT
* *
13489864 GTTTGCACTAAAGATTTGGAGGCATTATTTATATAGGGA
1 GTTTGAACTAAAAATTTGGAGGCATTATTTATATAGGGA
* *
13489903 GTTTGAACTAAAAATTTGGAGGCATTATTTGTATGGGGA
1 GTTTGAACTAAAAATTTGGAGGCATTATTTATATAGGGA
13489942 AAGAACGATT
Statistics
Matches: 35, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
39 35 1.00
ACGTcount: A:0.31, C:0.06, G:0.27, T:0.36
Consensus pattern (39 bp):
GTTTGAACTAAAAATTTGGAGGCATTATTTATATAGGGA
Found at i:13493547 original size:27 final size:26
Alignment explanation
Indices: 13493517--13493590 Score: 69
Period size: 27 Copynumber: 2.8 Consensus size: 26
13493507 AAGTACTGTA
*
13493517 CTAGTGGCTTTGCCACATTTTGCCGAT
1 CTAGTGGCTTTGCCACATTTTGAC-AT
* * *
13493544 CTAGAGGCCTTGCCATGCATTCTGACAT
1 CTAGTGGCTTTGCCA--CATTTTGACAT
*
13493572 -TAGTGGCTATGCCACATTT
1 CTAGTGGCTTTGCCACATTT
13493591 ATTACTACAA
Statistics
Matches: 37, Mismatches: 8, Indels: 6
0.73 0.16 0.12
Matches are distributed among these distances:
25 4 0.11
27 24 0.65
28 2 0.05
29 7 0.19
ACGTcount: A:0.19, C:0.26, G:0.22, T:0.34
Consensus pattern (26 bp):
CTAGTGGCTTTGCCACATTTTGACAT
Found at i:13493817 original size:33 final size:33
Alignment explanation
Indices: 13493743--13493819 Score: 102
Period size: 33 Copynumber: 2.3 Consensus size: 33
13493733 TGTGTGCTGG
** *
13493743 ATTACTGTATAGGGCTTAGGCCCAGACTGTATT
1 ATTACTGTATAGGGCCAAGGCCCAGACTGTACT
*
13493776 GTTACTGTATAGGGCCAAGGCCCAGACTGTTACT
1 ATTACTGTATAGGGCCAAGGCCCAGACTG-TACT
13493810 ATT-CTGTATA
1 ATTACTGTATA
13493820 ATGACTGTAA
Statistics
Matches: 38, Mismatches: 5, Indels: 2
0.84 0.11 0.04
Matches are distributed among these distances:
33 33 0.87
34 5 0.13
ACGTcount: A:0.25, C:0.19, G:0.23, T:0.32
Consensus pattern (33 bp):
ATTACTGTATAGGGCCAAGGCCCAGACTGTACT
Found at i:13495765 original size:30 final size:31
Alignment explanation
Indices: 13495729--13495792 Score: 94
Period size: 31 Copynumber: 2.1 Consensus size: 31
13495719 ACTTATTTTA
*
13495729 TTGTTAAATTTTTT-ATTATTTTAAAGGCGT
1 TTGTTAAATTTTTTAATTATTTTAAAGGCAT
* *
13495759 TTGTTAATTTTTTTAATTATTTTAGAGGCAT
1 TTGTTAAATTTTTTAATTATTTTAAAGGCAT
13495790 TTG
1 TTG
13495793 CTTGTTAAGT
Statistics
Matches: 30, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
30 13 0.43
31 17 0.57
ACGTcount: A:0.25, C:0.03, G:0.14, T:0.58
Consensus pattern (31 bp):
TTGTTAAATTTTTTAATTATTTTAAAGGCAT
Found at i:13495940 original size:10 final size:11
Alignment explanation
Indices: 13495914--13495947 Score: 50
Period size: 11 Copynumber: 3.0 Consensus size: 11
13495904 TATATATATT
13495914 TAAAAATAACA
1 TAAAAATAACA
*
13495925 TAAAAATAATA
1 TAAAAATAACA
13495936 TAAAAATTAACA
1 TAAAAA-TAACA
13495948 CGGGCGGGTC
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
11 16 0.80
12 4 0.20
ACGTcount: A:0.71, C:0.06, G:0.00, T:0.24
Consensus pattern (11 bp):
TAAAAATAACA
Found at i:13506683 original size:39 final size:40
Alignment explanation
Indices: 13506588--13506810 Score: 266
Period size: 39 Copynumber: 5.7 Consensus size: 40
13506578 TTGAATGATG
*
13506588 TCCGGGCTAAGTCCCGAAGGC--TTGTGCTA-AGTGAC-AAT
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGA-T-ACTAAT
*
13506626 ATCCGGACTAAGAT-CCGAAGGCATTTGTGCGAGATACTAAT
1 -TCCGGGCTAAG-TCCCGAAGGCATTTGTGCGAGATACTAAT
13506667 TCCGGGCTAAG-CCCGAAGGCATTTGTGCGAGATACTAAT
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGATACTAAT
* *
13506706 TCCGGGCTAAG-CCCGAAGGCATTTGTGCGAGTTACTAAA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGATACTAAT
*
13506745 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGA-ATTACT-AT
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGA-TACTAAT
* *
13506784 AACCGGGCTATGTCCCGAAGGCATTTG
1 -TCCGGGCTAAGTCCCGAAGGCATTTG
13506811 AACGAGGAGC
Statistics
Matches: 164, Mismatches: 11, Indels: 17
0.85 0.06 0.09
Matches are distributed among these distances:
39 93 0.57
40 59 0.36
41 11 0.07
42 1 0.01
ACGTcount: A:0.26, C:0.22, G:0.27, T:0.25
Consensus pattern (40 bp):
TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGATACTAAT
Found at i:13506774 original size:79 final size:81
Alignment explanation
Indices: 13506588--13506810 Score: 282
Period size: 79 Copynumber: 2.8 Consensus size: 81
13506578 TTGAATGATG
* * *
13506588 TCCGGGCTAAGTCCCGAAGGC--TTGTGCTAAGTGAC-AATATCCGGACTAAGATCCGAAGGCAT
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAAGT-ACTAATATCCGGGCTAAGACCCGAAGGCAT
*
13506650 TTGTGCGAGATACTAAT
65 TTGTGCGAGATACTAAA
13506667 TCCGGGCTAAG-CCCGAAGGCATTTGTGCG-AGATACTAAT-TCCGGGCTAAG-CCCGAAGGCAT
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAAG-TACTAATATCCGGGCTAAGACCCGAAGGCAT
*
13506728 TTGTGCGAGTTACTAAA
65 TTGTGCGAGATACTAAA
* * * * *
13506745 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAATTACT-ATAACCGGGCTATGTCCCGAAGGCATT
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAAGTACTAATATCCGGGCTAAGACCCGAAGGCATT
13506809 TG
66 TG
13506811 AACGAGGAGC
Statistics
Matches: 127, Mismatches: 9, Indels: 15
0.84 0.06 0.10
Matches are distributed among these distances:
78 46 0.36
79 56 0.44
80 25 0.20
ACGTcount: A:0.26, C:0.22, G:0.27, T:0.25
Consensus pattern (81 bp):
TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAAGTACTAATATCCGGGCTAAGACCCGAAGGCATT
TGTGCGAGATACTAAA
Found at i:13506832 original size:79 final size:79
Alignment explanation
Indices: 13506588--13506843 Score: 217
Period size: 79 Copynumber: 3.3 Consensus size: 79
13506578 TTGAATGATG
* * * *
13506588 TCCGGGCTAAGTCCCGAAGGC--TTGTGCTA-AGTGAC-AATATCCGGACTAAGATCCGAAGGCA
1 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGA-T-ACTAATA-CCGGGCTAAG-CCCGAAGGCA
** *
13506649 TTTGTGCGAGAT-ACTAAT
62 TTTGAACGAG-TGACTAAA
* *
13506667 TCCGGGCTAAG-CCCGAAGGCATTTGTGCGAGATACTAATTCCGGGCTAAGCCCGAAGGCATTTG
1 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGATACTAATACCGGGCTAAGCCCGAAGGCATTTG
** *
13506731 TGCGAGTTACTAAA
66 AACGAGTGACTAAA
*
13506745 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGA-ATTACT-ATAACCGGGCTATGTCCCGAAGGCAT
1 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGA-TACTAAT-ACCGGGCTAAG-CCCGAAGGCAT
*
13506808 TTGAACGAG-GAGCTATA
63 TTGAACGAGTGA-CTAAA
* *
13506825 TCC-GGTTAAATTCCGAAGG
1 TCCGGGTTAAGTCCCGAAGG
13506844 TACGTGATTT
Statistics
Matches: 153, Mismatches: 14, Indels: 20
0.82 0.07 0.11
Matches are distributed among these distances:
77 1 0.01
78 46 0.30
79 69 0.45
80 36 0.24
81 1 0.01
ACGTcount: A:0.27, C:0.22, G:0.27, T:0.24
Consensus pattern (79 bp):
TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGATACTAATACCGGGCTAAGCCCGAAGGCATTTG
AACGAGTGACTAAA
Found at i:13509445 original size:14 final size:14
Alignment explanation
Indices: 13509426--13509455 Score: 60
Period size: 14 Copynumber: 2.1 Consensus size: 14
13509416 ATTATGACCC
13509426 ATGTATTCGAATTT
1 ATGTATTCGAATTT
13509440 ATGTATTCGAATTT
1 ATGTATTCGAATTT
13509454 AT
1 AT
13509456 AATAAGTGAA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.30, C:0.07, G:0.13, T:0.50
Consensus pattern (14 bp):
ATGTATTCGAATTT
Found at i:13510397 original size:39 final size:39
Alignment explanation
Indices: 13510338--13510415 Score: 129
Period size: 39 Copynumber: 2.0 Consensus size: 39
13510328 CAAGTGTACA
* *
13510338 TAGTCGTTATCAAGTCATAAGTAAGTATCGAGTTATCGT
1 TAGTCGTAATCAAGTAATAAGTAAGTATCGAGTTATCGT
*
13510377 TAGTCGTAATCAAGTAATAAGTAAGTCTCGAGTTATCGT
1 TAGTCGTAATCAAGTAATAAGTAAGTATCGAGTTATCGT
13510416 CTCCACAGGG
Statistics
Matches: 36, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
39 36 1.00
ACGTcount: A:0.32, C:0.13, G:0.21, T:0.35
Consensus pattern (39 bp):
TAGTCGTAATCAAGTAATAAGTAAGTATCGAGTTATCGT
Found at i:13515699 original size:6 final size:6
Alignment explanation
Indices: 13515681--13515737 Score: 55
Period size: 6 Copynumber: 9.3 Consensus size: 6
13515671 AAGAAACATT
* *
13515681 ATCAGA A-CTAGA ATCAGA ATCAGA ATCAGT ATCAGGTA A-CAGA ATCAAA
1 ATCAGA ATC-AGA ATCAGA ATCAGA ATCAGA ATCA-G-A ATCAGA ATCAGA
13515730 ATCAGA AT
1 ATCAGA AT
13515738 GTGAATGCAA
Statistics
Matches: 42, Mismatches: 4, Indels: 10
0.75 0.07 0.18
Matches are distributed among these distances:
5 3 0.07
6 34 0.81
7 4 0.10
8 1 0.02
ACGTcount: A:0.49, C:0.16, G:0.16, T:0.19
Consensus pattern (6 bp):
ATCAGA
Found at i:13515953 original size:27 final size:27
Alignment explanation
Indices: 13515854--13515955 Score: 111
Period size: 27 Copynumber: 3.8 Consensus size: 27
13515844 CAGCATGGCT
** *
13515854 ACCAGAA-CAGATATTGTGATAGAGTC
1 ACCAGAATCAGATATTGTGGCAGAGCC
*
13515880 ACCAG-ATACAGATATTTTGGCAGAGCC
1 ACCAGAAT-CAGATATTGTGGCAGAGCC
*
13515907 ACCAGAA-CAGATATTTGTGGCATAGCC
1 ACCAGAATCAGATA-TTGTGGCAGAGCC
*
13515934 ACCAGAATCAGATAATGTGGCA
1 ACCAGAATCAGATATTGTGGCA
13515956 ATGCCACTTA
Statistics
Matches: 64, Mismatches: 7, Indels: 9
0.80 0.09 0.11
Matches are distributed among these distances:
25 1 0.02
26 11 0.17
27 45 0.70
28 7 0.11
ACGTcount: A:0.36, C:0.20, G:0.23, T:0.22
Consensus pattern (27 bp):
ACCAGAATCAGATATTGTGGCAGAGCC
Found at i:13515962 original size:54 final size:53
Alignment explanation
Indices: 13515854--13515955 Score: 125
Period size: 54 Copynumber: 1.9 Consensus size: 53
13515844 CAGCATGGCT
* * * *
13515854 ACCAGAACAGATATTGTGATAGAGTCACCAGATACAGATATTTTGGCAGAGCC
1 ACCAGAACAGATATTGTGACAGAGCCACCAGATACAGATAATGTGGCAGAGCC
* *
13515907 ACCAGAACAGATATTTGTGGCATAGCCACCAGA-ATCAGATAATGTGGCA
1 ACCAGAACAGATA-TTGTGACAGAGCCACCAGATA-CAGATAATGTGGCA
13515956 ATGCCACTTA
Statistics
Matches: 41, Mismatches: 6, Indels: 3
0.82 0.12 0.06
Matches are distributed among these distances:
53 14 0.34
54 27 0.66
ACGTcount: A:0.36, C:0.20, G:0.23, T:0.22
Consensus pattern (53 bp):
ACCAGAACAGATATTGTGACAGAGCCACCAGATACAGATAATGTGGCAGAGCC
Found at i:13516553 original size:27 final size:27
Alignment explanation
Indices: 13516523--13516753 Score: 284
Period size: 27 Copynumber: 8.6 Consensus size: 27
13516513 ACCCCAATAA
13516523 GGTATCTT-GGTAATTCTACCCTACAGG
1 GGTAT-TTCGGTAATTCTACCCTACAGG
* * * *
13516550 GGTATTTCGATAATTATACCTTACAGA
1 GGTATTTCGGTAATTCTACCCTACAGG
** *
13516577 GGTATTTCAATAATTCTACCCTAGAGG
1 GGTATTTCGGTAATTCTACCCTACAGG
*
13516604 GGTATTTCGATAATTCTACCCTACAGG
1 GGTATTTCGGTAATTCTACCCTACAGG
* * *
13516631 GGTATTTCAGTAATTCTACCATATAGG
1 GGTATTTCGGTAATTCTACCCTACAGG
* *
13516658 GGTATTTTGGTAATTCTACCCTATAGG
1 GGTATTTCGGTAATTCTACCCTACAGG
*
13516685 GGTATTTCGGTAATTCTACCTTACAGG
1 GGTATTTCGGTAATTCTACCCTACAGG
*
13516712 GGTATTTCGGTAATTCTACCCTATAGG
1 GGTATTTCGGTAATTCTACCCTACAGG
* * *
13516739 GTTGTTTTGGTAATT
1 GGTATTTCGGTAATT
13516754 TTGTAAATCA
Statistics
Matches: 177, Mismatches: 26, Indels: 2
0.86 0.13 0.01
Matches are distributed among these distances:
26 2 0.01
27 175 0.99
ACGTcount: A:0.25, C:0.17, G:0.20, T:0.38
Consensus pattern (27 bp):
GGTATTTCGGTAATTCTACCCTACAGG
Found at i:13516777 original size:81 final size:81
Alignment explanation
Indices: 13516531--13516780 Score: 207
Period size: 81 Copynumber: 3.1 Consensus size: 81
13516521 AAGGTATCTT
* * * * ***
13516531 GGTAATTCTACCCTACAGGGGTATTTC-GATAATTATACCTTACAGAGGTATTTCAATAATTCTA
1 GGTAATTCTACCCTACAGGGGTATTTCAG-TAATTCTACCATATAGGGGTATTTTGGTAATTCTA
** * * ***
13516595 CCCTAGAGGGGTATTTC
65 CCAAATAAGGGTAAAAC
*
13516612 GATAATTCTACCCTACAGGGGTATTTCAGTAATTCTACCATATAGGGGTATTTTGGTAATTCTAC
1 GGTAATTCTACCCTACAGGGGTATTTCAGTAATTCTACCATATAGGGGTATTTTGGTAATTCTAC
** * ***
13516677 CCTATAGGGGTATTTC
66 CAAATAAGGGTAAAAC
* * * * * **
13516693 GGTAATTCTACCTTACAGGGGTATTTCGGTAATTCTACCCTATAGGGTTGTTTTGGTAATT-TTG
1 GGTAATTCTACCCTACAGGGGTATTTCAGTAATTCTACCATATAGGGGTATTTTGGTAATTCTAC
*
13516757 TAAATCAAGGGTAAAAC
66 CAAAT-AAGGGTAAAAC
13516774 GGTAATT
1 GGTAATT
13516781 TTGTAAATCG
Statistics
Matches: 143, Mismatches: 24, Indels: 4
0.84 0.14 0.02
Matches are distributed among these distances:
80 3 0.02
81 139 0.97
82 1 0.01
ACGTcount: A:0.27, C:0.16, G:0.20, T:0.36
Consensus pattern (81 bp):
GGTAATTCTACCCTACAGGGGTATTTCAGTAATTCTACCATATAGGGGTATTTTGGTAATTCTAC
CAAATAAGGGTAAAAC
Found at i:13516804 original size:27 final size:27
Alignment explanation
Indices: 13516774--13516995 Score: 189
Period size: 27 Copynumber: 8.3 Consensus size: 27
13516764 AGGGTAAAAC
* ** *
13516774 GGTAATTTTGTAAATCGGGGGTACTTT
1 GGTAATTTTGCAAATCAAGGGTATTTT
* * *
13516801 GGTAATTTTACAAGTCAAAGGTATTTT
1 GGTAATTTTGCAAATCAAGGGTATTTT
* * *
13516828 AGTAATTTTACAAATC-AGGGTATTTC
1 GGTAATTTTGCAAATCAAGGGTATTTT
* *
13516854 AGTAATTTTGCAAATCGAA-GGTATTTC
1 GGTAATTTTGCAAATC-AAGGGTATTTT
**
13516881 GGTAATTTTGCAAATCGGGGGTATTTT
1 GGTAATTTTGCAAATCAAGGGTATTTT
* * *
13516908 GGTAATTTTACAAATTAGGGGTATTTT
1 GGTAATTTTGCAAATCAAGGGTATTTT
* * *
13516935 GGTAATTTTACAAA-CCAGGGTATTTC
1 GGTAATTTTGCAAATCAAGGGTATTTT
** * * *
13516961 AATAATTTTGCTAATCGAGTGTATTTT
1 GGTAATTTTGCAAATCAAGGGTATTTT
13516988 GGTAATTT
1 GGTAATTT
13516996 GGTAAACTAA
Statistics
Matches: 159, Mismatches: 32, Indels: 8
0.80 0.16 0.04
Matches are distributed among these distances:
26 41 0.26
27 117 0.74
28 1 0.01
ACGTcount: A:0.29, C:0.09, G:0.21, T:0.41
Consensus pattern (27 bp):
GGTAATTTTGCAAATCAAGGGTATTTT
Found at i:13516885 original size:80 final size:81
Alignment explanation
Indices: 13516775--13516948 Score: 208
Period size: 80 Copynumber: 2.2 Consensus size: 81
13516765 GGGTAAAACG
* ** *
13516775 GTAATTTTGTAAATCGGGGGTACTTTGGTAATTTTACAAGTCAAAGGTATTTTAGTAATTTTACA
1 GTAATTTTGCAAATCGAAGGTACTTTGGTAATTTTACAAATCAAAGGTATTTTAGTAATTTTACA
13516840 AATCA-GGGTATTTCA
66 AATCAGGGGTATTTCA
* *** *
13516855 GTAATTTTGCAAATCGAAGGTA-TTTCGGTAATTTTGCAAATCGGGGGTATTTTGGTAATTTTAC
1 GTAATTTTGCAAATCGAAGGTACTTT-GGTAATTTTACAAATCAAAGGTATTTTAGTAATTTTAC
* **
13516919 AAATTAGGGGTATTTTG
65 AAATCAGGGGTATTTCA
*
13516936 GTAATTTTACAAA
1 GTAATTTTGCAAA
13516949 CCAGGGTATT
Statistics
Matches: 79, Mismatches: 13, Indels: 3
0.83 0.14 0.03
Matches are distributed among these distances:
79 3 0.04
80 56 0.71
81 20 0.25
ACGTcount: A:0.30, C:0.08, G:0.21, T:0.40
Consensus pattern (81 bp):
GTAATTTTGCAAATCGAAGGTACTTTGGTAATTTTACAAATCAAAGGTATTTTAGTAATTTTACA
AATCAGGGGTATTTCA
Found at i:13516897 original size:107 final size:107
Alignment explanation
Indices: 13516773--13516995 Score: 331
Period size: 107 Copynumber: 2.1 Consensus size: 107
13516763 AAGGGTAAAA
* *
13516773 CGGTAATTTTGTAAATCGGGGGTACTTTGGTAATTTTACAAGTCAAAGGTATTTTAGTAATTTTA
1 CGGTAATTTTGCAAATCGGGGGTACTTTGGTAATTTTACAAATCAAAGGTATTTTAGTAATTTTA
* *
13516838 CAAATCAGGGTATTTCAGTAATTTTGCAAATCGAAG-GTATTT
66 CAAACCAGGGTATTTCAATAATTTTGCAAATCG-AGTGTATTT
* * ** *
13516880 CGGTAATTTTGCAAATCGGGGGTATTTTGGTAATTTTACAAATTAGGGGTATTTTGGTAATTTTA
1 CGGTAATTTTGCAAATCGGGGGTACTTTGGTAATTTTACAAATCAAAGGTATTTTAGTAATTTTA
*
13516945 CAAACCAGGGTATTTCAATAATTTTGCTAATCGAGTGTATTT
66 CAAACCAGGGTATTTCAATAATTTTGCAAATCGAGTGTATTT
*
13516987 TGGTAATTT
1 CGGTAATTT
13516996 GGTAAACTAA
Statistics
Matches: 104, Mismatches: 11, Indels: 2
0.89 0.09 0.02
Matches are distributed among these distances:
106 2 0.02
107 102 0.98
ACGTcount: A:0.29, C:0.09, G:0.21, T:0.41
Consensus pattern (107 bp):
CGGTAATTTTGCAAATCGGGGGTACTTTGGTAATTTTACAAATCAAAGGTATTTTAGTAATTTTA
CAAACCAGGGTATTTCAATAATTTTGCAAATCGAGTGTATTT
Found at i:13516957 original size:80 final size:80
Alignment explanation
Indices: 13516820--13516995 Score: 228
Period size: 80 Copynumber: 2.2 Consensus size: 80
13516810 ACAAGTCAAA
* * * **
13516820 GGTATTTTAGTAATTTTACAAATCAGGGTATTTCAGTAATTTTGCAAATCGAAGGTATTTCGGTA
1 GGTATTTTGGTAATTTTACAAATCAGGGTATTTCAGTAATTTTACAAATCCAAGGTATTTCAATA
*
13516885 ATTTTGCAAATCGGG
66 ATTTTGCAAATCGAG
* ** *
13516900 GGTATTTTGGTAATTTTACAAATTAGGGGTATTTTGGTAATTTTACAAA-CCAGGGTATTTCAAT
1 GGTATTTTGGTAATTTTACAAATCA-GGGTATTTCAGTAATTTTACAAATCCAAGGTATTTCAAT
*
13516964 AATTTTGCTAATCGAG
65 AATTTTGCAAATCGAG
*
13516980 TGTATTTTGGTAATTT
1 GGTATTTTGGTAATTT
13516996 GGTAAACTAA
Statistics
Matches: 83, Mismatches: 12, Indels: 2
0.86 0.12 0.02
Matches are distributed among these distances:
80 63 0.76
81 20 0.24
ACGTcount: A:0.29, C:0.09, G:0.20, T:0.42
Consensus pattern (80 bp):
GGTATTTTGGTAATTTTACAAATCAGGGTATTTCAGTAATTTTACAAATCCAAGGTATTTCAATA
ATTTTGCAAATCGAG
Found at i:13519054 original size:21 final size:20
Alignment explanation
Indices: 13519016--13519055 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 20
13519006 ATACTTAGTA
*
13519016 AAAGGTATCATACTTTTTGG
1 AAAGGTATCATACATTTTGG
*
13519036 AAAGGTATTGATACATTTTG
1 AAAGGTA-TCATACATTTTG
13519056 TAATTGATTG
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 7 0.41
21 10 0.59
ACGTcount: A:0.33, C:0.07, G:0.20, T:0.40
Consensus pattern (20 bp):
AAAGGTATCATACATTTTGG
Found at i:13520377 original size:18 final size:18
Alignment explanation
Indices: 13520343--13520402 Score: 59
Period size: 18 Copynumber: 3.3 Consensus size: 18
13520333 AATCGGTTAA
* *
13520343 TCAGTAATATTCATTTAT
1 TCAGTAACAGTCATTTAT
* *
13520361 TCAGTATCAGTCGTTTAT
1 TCAGTAACAGTCATTTAT
*
13520379 TCTA-TAACAGTCAATTAT
1 TC-AGTAACAGTCATTTAT
13520397 TCAGTA
1 TCAGTA
13520403 GCAGACAGTC
Statistics
Matches: 33, Mismatches: 7, Indels: 4
0.75 0.16 0.09
Matches are distributed among these distances:
17 1 0.03
18 31 0.94
19 1 0.03
ACGTcount: A:0.32, C:0.15, G:0.10, T:0.43
Consensus pattern (18 bp):
TCAGTAACAGTCATTTAT
Found at i:13520938 original size:37 final size:37
Alignment explanation
Indices: 13520889--13520960 Score: 85
Period size: 37 Copynumber: 1.9 Consensus size: 37
13520879 TTCAATTTTC
*
13520889 CACTCAATATTCA-CATATTCTATTCAATATCAATAAT
1 CACTCAATATTCATCAAATTCTATTCAAT-TCAATAAT
* *
13520926 CACT-AATAATTCATGAAATTTTATTCAATTCAATA
1 CACTCAAT-ATTCATCAAATTCTATTCAATTCAATA
13520961 CCATAATAAT
Statistics
Matches: 30, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
36 3 0.10
37 15 0.50
38 12 0.40
ACGTcount: A:0.42, C:0.18, G:0.01, T:0.39
Consensus pattern (37 bp):
CACTCAATATTCATCAAATTCTATTCAATTCAATAAT
Found at i:13520971 original size:3 final size:3
Alignment explanation
Indices: 13520963--13520992 Score: 60
Period size: 3 Copynumber: 10.0 Consensus size: 3
13520953 ATTCAATACC
13520963 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
13520993 GTACTTATGT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 27 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:13522856 original size:20 final size:20
Alignment explanation
Indices: 13522790--13522856 Score: 98
Period size: 20 Copynumber: 3.4 Consensus size: 20
13522780 ATTTTGATAA
*
13522790 ACATGGTATGTATGATATGC
1 ACATGATATGTATGATATGC
*
13522810 ACATGACATGTATGATATGC
1 ACATGATATGTATGATATGC
*
13522830 ACCTGATATGTATGATATGC
1 ACATGATATGTATGATATGC
*
13522850 ACGTGAT
1 ACATGAT
13522857 GTAATCATAA
Statistics
Matches: 42, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 42 1.00
ACGTcount: A:0.31, C:0.13, G:0.22, T:0.33
Consensus pattern (20 bp):
ACATGATATGTATGATATGC
Found at i:13522937 original size:23 final size:23
Alignment explanation
Indices: 13522907--13523073 Score: 253
Period size: 23 Copynumber: 7.1 Consensus size: 23
13522897 AGGAAGTGAA
13522907 AAAGGGCTTATGCCCCAGTTATT
1 AAAGGGCTTATGCCCCAGTTATT
*
13522930 AAAGGGCTTGTGCCCCAGTTATT
1 AAAGGGCTTATGCCCCAGTTATT
*
13522953 AAAGGGCTTATGCCCCAGTTATCA
1 AAAGGGCTTATGCCCCAGTTAT-T
*
13522977 AAAGGGCTTATGCCCCAGTTATCA
1 AAAGGGCTTATGCCCCAGTTAT-T
*
13523001 AAAGGGCTTACGCCCCAGTTATT
1 AAAGGGCTTATGCCCCAGTTATT
*
13523024 AAAGGGCTTATGCCCCAGTTATAA
1 AAAGGGCTTATGCCCCAGTTAT-T
*
13523048 AAAGGGCTTTTGCCCCAGTTATT
1 AAAGGGCTTATGCCCCAGTTATT
13523071 AAA
1 AAA
13523074 AGAGGCTAGG
Statistics
Matches: 133, Mismatches: 9, Indels: 4
0.91 0.06 0.03
Matches are distributed among these distances:
23 67 0.50
24 66 0.50
ACGTcount: A:0.28, C:0.23, G:0.22, T:0.28
Consensus pattern (23 bp):
AAAGGGCTTATGCCCCAGTTATT
Found at i:13522985 original size:24 final size:23
Alignment explanation
Indices: 13522906--13523095 Score: 256
Period size: 24 Copynumber: 8.0 Consensus size: 23
13522896 GAGGAAGTGA
13522906 AAAAGGGCTTATGCCCCAGTTAT
1 AAAAGGGCTTATGCCCCAGTTAT
* *
13522929 TAAAGGGCTTGTGCCCCAGTTAT
1 AAAAGGGCTTATGCCCCAGTTAT
*
13522952 TAAAGGGCTTATGCCCCAGTTAT
1 AAAAGGGCTTATGCCCCAGTTAT
13522975 CAAAAGGGCTTATGCCCCAGTTAT
1 -AAAAGGGCTTATGCCCCAGTTAT
*
13522999 CAAAAGGGCTTACGCCCCAGTTAT
1 -AAAAGGGCTTATGCCCCAGTTAT
*
13523023 TAAAGGGCTTATGCCCCAGTTAT
1 AAAAGGGCTTATGCCCCAGTTAT
*
13523046 AAAAAGGGCTTTTGCCCCAGTTATT
1 -AAAAGGGCTTATGCCCCAGTTA-T
*
13523071 AAAAGAGGC-TAGGCCTCCAGTTAT
1 AAAAG-GGCTTATGCC-CCAGTTAT
13523095 A
1 A
13523096 TGATAAAGCA
Statistics
Matches: 151, Mismatches: 11, Indels: 9
0.88 0.06 0.05
Matches are distributed among these distances:
23 64 0.42
24 76 0.50
25 11 0.07
ACGTcount: A:0.28, C:0.23, G:0.22, T:0.27
Consensus pattern (23 bp):
AAAAGGGCTTATGCCCCAGTTAT
Found at i:13523028 original size:47 final size:46
Alignment explanation
Indices: 13522906--13523095 Score: 265
Period size: 47 Copynumber: 4.0 Consensus size: 46
13522896 GAGGAAGTGA
*
13522906 AAAAGGGCTTATGCCCCAGTTATTAAAGGGCTTGTGCCCCAGTTAT
1 AAAAGGGCTTATGCCCCAGTTATTAAAGGGCTTATGCCCCAGTTAT
* *
13522952 TAAAGGGCTTATGCCCCAGTTATCAAAAGGGCTTATGCCCCAGTTAT
1 AAAAGGGCTTATGCCCCAGTTAT-TAAAGGGCTTATGCCCCAGTTAT
*
13522999 CAAAAGGGCTTACGCCCCAGTTATTAAAGGGCTTATGCCCCAGTTAT
1 -AAAAGGGCTTATGCCCCAGTTATTAAAGGGCTTATGCCCCAGTTAT
* *
13523046 AAAAAGGGCTTTTGCCCCAGTTATTAAAAGAGGC-TAGGCCTCCAGTTAT
1 -AAAAGGGCTTATGCCCCAGTTATT-AAAG-GGCTTATGCC-CCAGTTAT
13523095 A
1 A
13523096 TGATAAAGCA
Statistics
Matches: 129, Mismatches: 10, Indels: 8
0.88 0.07 0.05
Matches are distributed among these distances:
46 22 0.17
47 65 0.50
48 31 0.24
49 11 0.09
ACGTcount: A:0.28, C:0.23, G:0.22, T:0.27
Consensus pattern (46 bp):
AAAAGGGCTTATGCCCCAGTTATTAAAGGGCTTATGCCCCAGTTAT
Found at i:13524699 original size:16 final size:15
Alignment explanation
Indices: 13524677--13524715 Score: 51
Period size: 16 Copynumber: 2.5 Consensus size: 15
13524667 CTTTTTCTCC
13524677 TTCTTTCTCCACTGT
1 TTCTTTCTCCACTGT
* *
13524692 TTCATTTCTTCTCTGT
1 TTC-TTTCTCCACTGT
13524708 TTCTTTCT
1 TTCTTTCT
13524716 ATTCTTTTTC
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
15 8 0.38
16 13 0.62
ACGTcount: A:0.05, C:0.28, G:0.05, T:0.62
Consensus pattern (15 bp):
TTCTTTCTCCACTGT
Found at i:13526017 original size:35 final size:35
Alignment explanation
Indices: 13525971--13526042 Score: 135
Period size: 35 Copynumber: 2.1 Consensus size: 35
13525961 TATCTATTCC
*
13525971 TTTTCTTGCTGCATCCAATCAAATGCTATGAAGTT
1 TTTTCTTGCTGCATCCAATCAAATACTATGAAGTT
13526006 TTTTCTTGCTGCATCCAATCAAATACTATGAAGTT
1 TTTTCTTGCTGCATCCAATCAAATACTATGAAGTT
13526041 TT
1 TT
13526043 ACATTCACAA
Statistics
Matches: 36, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
35 36 1.00
ACGTcount: A:0.26, C:0.19, G:0.12, T:0.42
Consensus pattern (35 bp):
TTTTCTTGCTGCATCCAATCAAATACTATGAAGTT
Found at i:13527913 original size:25 final size:25
Alignment explanation
Indices: 13527885--13527962 Score: 72
Period size: 25 Copynumber: 3.2 Consensus size: 25
13527875 CTCGGCCCTG
13527885 TCACATATATACACTTTCACATTCA
1 TCACATATATACACTTTCACATTCA
*** *** *
13527910 TCACAT-TGGCCA-TTAGGCCTT-A
1 TCACATATATACACTTTCACATTCA
13527932 TCACATATATACACTTTCACATTCA
1 TCACATATATACACTTTCACATTCA
13527957 TCACAT
1 TCACAT
13527963 CGGCTATTAG
Statistics
Matches: 36, Mismatches: 14, Indels: 6
0.64 0.25 0.11
Matches are distributed among these distances:
22 7 0.19
23 8 0.22
24 8 0.22
25 13 0.36
ACGTcount: A:0.32, C:0.28, G:0.05, T:0.35
Consensus pattern (25 bp):
TCACATATATACACTTTCACATTCA
Found at i:13528064 original size:49 final size:47
Alignment explanation
Indices: 13527834--13528269 Score: 590
Period size: 47 Copynumber: 9.4 Consensus size: 47
13527824 CCCTTCGGGA
* * * * * *
13527834 CTTATCACATTTATACACTTTCACATCCATCACGTTGGCCACTCGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
* * *
13527881 CCTGTCACATATATACACTTTCACATTCATCACATTGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
*
13527928 CTTATCACATATATACACTTTCACATTCATCACATCGGCTATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
13527975 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
* *
13528022 CTTATCACATATATGTACACTTTCACATTCATCACATTGGCCATTCGGC
1 CTTATCACATATA--TACACTTTCACATTCATCACATCGGCCATTAGGC
*
13528071 CTTATCAC----AT--ACTTTCACATTCATCACATCGGCTATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
*
13528112 CTTATCACATATATACACTTTCACATTAATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
* *
13528159 CTTATCACATATATATACACTTTCACATTCATCACATTGGCCATTCGGC
1 CTTATCAC--ATATATACACTTTCACATTCATCACATCGGCCATTAGGC
*
13528208 CTTATCAC----AT--ACTTTCACATTCATCACATCGGCTATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
*
13528249 CTTATCTCATATATACACTTT
1 CTTATCACATATATACACTTT
13528270 ATCTTGGCCG
Statistics
Matches: 347, Mismatches: 26, Indels: 32
0.86 0.06 0.08
Matches are distributed among these distances:
41 71 0.20
43 3 0.01
45 5 0.01
47 184 0.53
49 84 0.24
ACGTcount: A:0.28, C:0.29, G:0.09, T:0.34
Consensus pattern (47 bp):
CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
Found at i:13528086 original size:41 final size:41
Alignment explanation
Indices: 13528040--13528259 Score: 242
Period size: 41 Copynumber: 5.0 Consensus size: 41
13528030 ATATATGTAC
* *
13528040 ACTTTCACATTCATCACATTGGCCATTCGGCCTTATCACAT
1 ACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACAT
*
13528081 ACTTTCACATTCATCACATCGGCTATTAGGCCTTATCACATATAT
1 ACTTTCACATTCATCACATCGGCCATTAGGCCTTATCAC----AT
*
13528126 ACACTTTCACATTAATCACATCGGCCATTAGGCCTTATCACATATATAT
1 --ACTTTCACATTCATCACATCGGCCATTAGGCCTTATCAC------AT
* *
13528175 ACACTTTCACATTCATCACATTGGCCATTCGGCCTTATCACAT
1 --ACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACAT
* *
13528218 ACTTTCACATTCATCACATCGGCTATTAGGCCTTATCTCAT
1 ACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACAT
13528259 A
1 A
13528260 TATACACTTT
Statistics
Matches: 159, Mismatches: 12, Indels: 16
0.85 0.06 0.09
Matches are distributed among these distances:
41 74 0.47
43 2 0.01
45 2 0.01
47 37 0.23
49 44 0.28
ACGTcount: A:0.28, C:0.29, G:0.09, T:0.34
Consensus pattern (41 bp):
ACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACAT
Found at i:13528125 original size:137 final size:136
Alignment explanation
Indices: 13527834--13528269 Score: 694
Period size: 137 Copynumber: 3.2 Consensus size: 136
13527824 CCCTTCGGGA
* * * * * * * *
13527834 CTTATCACATTTATACACTTTCACATCCATCACGTTGGCCACTCGGCCCTGTCACATATA-TACA
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATTACA
*
13527898 CTTTCACATTCATCACATTGGCCATTAGGCCTTATCACATATATACACTTTCACATTCATCACAT
66 CTTTCACATTCATCACATTGGCCATTCGGCCTTATCAC----AT--ACTTTCACATTCATCACAT
13527963 CGGCTATTAGGC
125 CGGCTATTAGGC
13527975 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATGTAC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATAT-TAC
13528040 ACTTTCACATTCATCACATTGGCCATTCGGCCTTATCACATACTTTCACATTCATCACATCGGCT
65 ACTTTCACATTCATCACATTGGCCATTCGGCCTTATCACATACTTTCACATTCATCACATCGGCT
13528105 ATTAGGC
130 ATTAGGC
*
13528112 CTTATCACATATATACACTTTCACATTAATCACATCGGCCATTAGGCCTTATCACATATATATAC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATAT-TAC
13528177 ACTTTCACATTCATCACATTGGCCATTCGGCCTTATCACATACTTTCACATTCATCACATCGGCT
65 ACTTTCACATTCATCACATTGGCCATTCGGCCTTATCACATACTTTCACATTCATCACATCGGCT
13528242 ATTAGGC
130 ATTAGGC
*
13528249 CTTATCTCATATATACACTTT
1 CTTATCACATATATACACTTT
13528270 ATCTTGGCCG
Statistics
Matches: 281, Mismatches: 12, Indels: 8
0.93 0.04 0.03
Matches are distributed among these distances:
137 186 0.66
139 2 0.01
141 52 0.19
143 41 0.15
ACGTcount: A:0.28, C:0.29, G:0.09, T:0.34
Consensus pattern (136 bp):
CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATTACA
CTTTCACATTCATCACATTGGCCATTCGGCCTTATCACATACTTTCACATTCATCACATCGGCTA
TTAGGC
Found at i:13531931 original size:27 final size:27
Alignment explanation
Indices: 13531883--13532041 Score: 175
Period size: 27 Copynumber: 5.9 Consensus size: 27
13531873 GCGAGGCTGC
* *
13531883 CAGATATTGTGAC-GAGGTCACCAGATA
1 CAGATATTGTGGCAGA-GCCACCAGATA
13531910 CAGATATTGTGGCAGAGCCACCAGA-A
1 CAGATATTGTGGCAGAGCCACCAGATA
13531936 CAGATATATGTGGCAGAGCCACCAGAT-
1 CAGATAT-TGTGGCAGAGCCACCAGATA
* * * *
13531963 CAGATAATTATGGCATAGCCACTAG-GA
1 CAGAT-ATTGTGGCAGAGCCACCAGATA
13531990 CAGATATATGTGGCAGAGCCACCAGAT-
1 CAGATAT-TGTGGCAGAGCCACCAGATA
*
13532017 CAGATAATTGTGGCATAGCCACCAG
1 CAGAT-ATTGTGGCAGAGCCACCAG
13532042 GACGCTTCCT
Statistics
Matches: 113, Mismatches: 11, Indels: 16
0.81 0.08 0.11
Matches are distributed among these distances:
26 10 0.09
27 97 0.86
28 6 0.05
ACGTcount: A:0.34, C:0.21, G:0.25, T:0.19
Consensus pattern (27 bp):
CAGATATTGTGGCAGAGCCACCAGATA
Found at i:13532044 original size:54 final size:54
Alignment explanation
Indices: 13531901--13532044 Score: 236
Period size: 54 Copynumber: 2.7 Consensus size: 54
13531891 GTGACGAGGT
* *
13531901 CACCAGATACAGAT-ATTGTGGCAGAGCCACCAGAACAGATATATGTGGCAGAGC
1 CACCAGAT-CAGATAATTGTGGCATAGCCACCAGGACAGATATATGTGGCAGAGC
* *
13531955 CACCAGATCAGATAATTATGGCATAGCCACTAGGACAGATATATGTGGCAGAGC
1 CACCAGATCAGATAATTGTGGCATAGCCACCAGGACAGATATATGTGGCAGAGC
13532009 CACCAGATCAGATAATTGTGGCATAGCCACCAGGAC
1 CACCAGATCAGATAATTGTGGCATAGCCACCAGGAC
13532045 GCTTCCTCCA
Statistics
Matches: 83, Mismatches: 6, Indels: 2
0.91 0.07 0.02
Matches are distributed among these distances:
53 5 0.06
54 78 0.94
ACGTcount: A:0.35, C:0.23, G:0.24, T:0.18
Consensus pattern (54 bp):
CACCAGATCAGATAATTGTGGCATAGCCACCAGGACAGATATATGTGGCAGAGC
Found at i:13532444 original size:8 final size:8
Alignment explanation
Indices: 13532431--13532456 Score: 52
Period size: 8 Copynumber: 3.2 Consensus size: 8
13532421 CTCAAAATAC
13532431 CGGCATTT
1 CGGCATTT
13532439 CGGCATTT
1 CGGCATTT
13532447 CGGCATTT
1 CGGCATTT
13532455 CG
1 CG
13532457 ACTTTTCGAC
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 18 1.00
ACGTcount: A:0.12, C:0.27, G:0.27, T:0.35
Consensus pattern (8 bp):
CGGCATTT
Found at i:13532463 original size:16 final size:16
Alignment explanation
Indices: 13532431--13532464 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
13532421 CTCAAAATAC
*
13532431 CGGCATTTCGGCATTT
1 CGGCATTTCGACATTT
*
13532447 CGGCATTTCGACTTTT
1 CGGCATTTCGACATTT
13532463 CG
1 CG
13532465 ACTTGTGCCG
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.12, C:0.26, G:0.24, T:0.38
Consensus pattern (16 bp):
CGGCATTTCGACATTT
Found at i:13537044 original size:18 final size:18
Alignment explanation
Indices: 13537009--13537079 Score: 63
Period size: 18 Copynumber: 3.9 Consensus size: 18
13536999 CAGTCAACAA
* * *
13537009 TAATAATCAGTTAATCAG
1 TAATAGTCATTTATTCAG
*
13537027 TAATATTCATTTATTCAG
1 TAATAGTCATTTATTCAG
* *
13537045 T-ATCAGTCGTTTATTCTG
1 TAAT-AGTCATTTATTCAG
*
13537063 TAATAGTCAATTATTCA
1 TAATAGTCATTTATTCA
13537080 ATAGTAGATA
Statistics
Matches: 42, Mismatches: 9, Indels: 4
0.76 0.16 0.07
Matches are distributed among these distances:
17 2 0.05
18 38 0.90
19 2 0.05
ACGTcount: A:0.34, C:0.13, G:0.10, T:0.44
Consensus pattern (18 bp):
TAATAGTCATTTATTCAG
Found at i:13538321 original size:16 final size:15
Alignment explanation
Indices: 13538299--13538337 Score: 51
Period size: 16 Copynumber: 2.5 Consensus size: 15
13538289 CTTTTTCTCC
13538299 TTCTTTCTCCCCTGT
1 TTCTTTCTCCCCTGT
* *
13538314 TTCATTTCTTCTCTGT
1 TTC-TTTCTCCCCTGT
13538330 TTCTTTCT
1 TTCTTTCT
13538338 ATTCTTTTTC
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
15 8 0.38
16 13 0.62
ACGTcount: A:0.03, C:0.31, G:0.05, T:0.62
Consensus pattern (15 bp):
TTCTTTCTCCCCTGT
Found at i:13538413 original size:11 final size:11
Alignment explanation
Indices: 13538388--13538429 Score: 52
Period size: 9 Copynumber: 3.8 Consensus size: 11
13538378 TATATAATAA
13538388 TAATAATAA--
1 TAATAATAACT
13538397 TAATAATAACT
1 TAATAATAACT
13538408 TAATAATATACT
1 TAATAATA-ACT
13538420 TATATAATAA
1 TA-ATAATAA
13538430 GTAAATATAC
Statistics
Matches: 29, Mismatches: 0, Indels: 5
0.85 0.00 0.15
Matches are distributed among these distances:
9 9 0.31
11 8 0.28
12 6 0.21
13 6 0.21
ACGTcount: A:0.57, C:0.05, G:0.00, T:0.38
Consensus pattern (11 bp):
TAATAATAACT
Found at i:13538429 original size:3 final size:3
Alignment explanation
Indices: 13538381--13538415 Score: 52
Period size: 3 Copynumber: 11.0 Consensus size: 3
13538371 TTATATATAT
13538381 ATA ATA ATA ATA ATA ATA ATA ATA ACTTA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA A--TA ATA ATA
13538416 TACTTATATA
Statistics
Matches: 30, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
3 27 0.90
5 3 0.10
ACGTcount: A:0.63, C:0.03, G:0.00, T:0.34
Consensus pattern (3 bp):
ATA
Found at i:13550612 original size:27 final size:28
Alignment explanation
Indices: 13550528--13550625 Score: 135
Period size: 27 Copynumber: 3.5 Consensus size: 28
13550518 CATGAGATTG
* * * *
13550528 GCACTAAGTGTGCGGGTTTAAATTGTACA
1 GCACTAAGTGTGCGAGTTT-GATTATATA
13550557 GCACTAAGTGTGCGAGTTTGATTATATA
1 GCACTAAGTGTGCGAGTTTGATTATATA
13550585 GCACTAAGTGTGCGAG-TTGATTATATA
1 GCACTAAGTGTGCGAGTTTGATTATATA
*
13550612 GCACTGAGTGTGCG
1 GCACTAAGTGTGCG
13550626 GACTTAATAT
Statistics
Matches: 64, Mismatches: 5, Indels: 2
0.90 0.07 0.03
Matches are distributed among these distances:
27 24 0.38
28 22 0.34
29 18 0.28
ACGTcount: A:0.27, C:0.13, G:0.29, T:0.32
Consensus pattern (28 bp):
GCACTAAGTGTGCGAGTTTGATTATATA
Found at i:13550636 original size:27 final size:27
Alignment explanation
Indices: 13550556--13550638 Score: 96
Period size: 27 Copynumber: 3.0 Consensus size: 27
13550546 TAAATTGTAC
* *
13550556 AGCACTAAGTGTGCGAGTTTGATTATAT
1 AGCACTAAGTGTGCGA-CTTGAATATAT
* *
13550584 AGCACTAAGTGTGCGAGTTGATTATAT
1 AGCACTAAGTGTGCGACTTGAATATAT
*
13550611 AGCACTGAGTGTGCGGACTT-AATATAT
1 AGCACTAAGTGTGC-GACTTGAATATAT
13550638 A
1 A
13550639 TTTTTGAATC
Statistics
Matches: 50, Mismatches: 4, Indels: 3
0.88 0.07 0.05
Matches are distributed among these distances:
27 30 0.60
28 20 0.40
ACGTcount: A:0.30, C:0.12, G:0.25, T:0.33
Consensus pattern (27 bp):
AGCACTAAGTGTGCGACTTGAATATAT
Found at i:13550639 original size:29 final size:27
Alignment explanation
Indices: 13550528--13550639 Score: 98
Period size: 28 Copynumber: 4.0 Consensus size: 27
13550518 CATGAGATTG
** * *
13550528 GCACTAAGTGTGCGGGTTTAAATTGTACA
1 GCACTAAGTGTGC-GACTT-AATTATATA
* *
13550557 GCACTAAGTGTGCGAGTTTGATTATATA
1 GCACTAAGTGTGCGA-CTTAATTATATA
* *
13550585 GCACTAAGTGTGCGAGTTGATTATATA
1 GCACTAAGTGTGCGACTTAATTATATA
*
13550612 GCACTGAGTGTGCGGACTTAATATATAT
1 GCACTAAGTGTGC-GACTTAAT-TATAT
13550640 TTTTGAATCA
Statistics
Matches: 72, Mismatches: 8, Indels: 6
0.84 0.09 0.07
Matches are distributed among these distances:
27 23 0.32
28 28 0.39
29 21 0.29
ACGTcount: A:0.29, C:0.12, G:0.26, T:0.33
Consensus pattern (27 bp):
GCACTAAGTGTGCGACTTAATTATATA
Found at i:13558717 original size:27 final size:28
Alignment explanation
Indices: 13558633--13558730 Score: 135
Period size: 27 Copynumber: 3.5 Consensus size: 28
13558623 CATGAGATTG
* * * *
13558633 GCACTAAGTGTGCGGGTTTAAATTGTACA
1 GCACTAAGTGTGCGAGTTT-GATTATATA
13558662 GCACTAAGTGTGCGAGTTTGATTATATA
1 GCACTAAGTGTGCGAGTTTGATTATATA
13558690 GCACTAAGTGTGCGAG-TTGATTATATA
1 GCACTAAGTGTGCGAGTTTGATTATATA
*
13558717 GCACTGAGTGTGCG
1 GCACTAAGTGTGCG
13558731 GACTTAATAT
Statistics
Matches: 64, Mismatches: 5, Indels: 2
0.90 0.07 0.03
Matches are distributed among these distances:
27 24 0.38
28 22 0.34
29 18 0.28
ACGTcount: A:0.27, C:0.13, G:0.29, T:0.32
Consensus pattern (28 bp):
GCACTAAGTGTGCGAGTTTGATTATATA
Found at i:13558741 original size:27 final size:27
Alignment explanation
Indices: 13558661--13558743 Score: 96
Period size: 27 Copynumber: 3.0 Consensus size: 27
13558651 TAAATTGTAC
* *
13558661 AGCACTAAGTGTGCGAGTTTGATTATAT
1 AGCACTAAGTGTGCGA-CTTGAATATAT
* *
13558689 AGCACTAAGTGTGCGAGTTGATTATAT
1 AGCACTAAGTGTGCGACTTGAATATAT
*
13558716 AGCACTGAGTGTGCGGACTT-AATATAT
1 AGCACTAAGTGTGC-GACTTGAATATAT
13558743 A
1 A
13558744 TTTTTGAATC
Statistics
Matches: 50, Mismatches: 4, Indels: 3
0.88 0.07 0.05
Matches are distributed among these distances:
27 30 0.60
28 20 0.40
ACGTcount: A:0.30, C:0.12, G:0.25, T:0.33
Consensus pattern (27 bp):
AGCACTAAGTGTGCGACTTGAATATAT
Found at i:13558744 original size:29 final size:27
Alignment explanation
Indices: 13558633--13558744 Score: 98
Period size: 28 Copynumber: 4.0 Consensus size: 27
13558623 CATGAGATTG
** * *
13558633 GCACTAAGTGTGCGGGTTTAAATTGTACA
1 GCACTAAGTGTGC-GACTT-AATTATATA
* *
13558662 GCACTAAGTGTGCGAGTTTGATTATATA
1 GCACTAAGTGTGCGA-CTTAATTATATA
* *
13558690 GCACTAAGTGTGCGAGTTGATTATATA
1 GCACTAAGTGTGCGACTTAATTATATA
*
13558717 GCACTGAGTGTGCGGACTTAATATATAT
1 GCACTAAGTGTGC-GACTTAAT-TATAT
13558745 TTTTGAATCA
Statistics
Matches: 72, Mismatches: 8, Indels: 6
0.84 0.09 0.07
Matches are distributed among these distances:
27 23 0.32
28 28 0.39
29 21 0.29
ACGTcount: A:0.29, C:0.12, G:0.26, T:0.33
Consensus pattern (27 bp):
GCACTAAGTGTGCGACTTAATTATATA
Found at i:13560204 original size:29 final size:29
Alignment explanation
Indices: 13560149--13560235 Score: 106
Period size: 29 Copynumber: 3.0 Consensus size: 29
13560139 GTGAGCATGA
* * *
13560149 ATATGAATGTGA-CTGGGCCTAACAGGCC
1 ATATAAATGTGATTTGGGCCTAATAGGCC
13560177 ATATAAATGTGATTTGGGCCTAATAGGCC
1 ATATAAATGTGATTTGGGCCTAATAGGCC
* *
13560206 ATATACA-GATGATTTGGGCCTAATGGGCC
1 ATATAAATG-TGATTTGGGCCTAATAGGCC
13560235 A
1 A
13560236 GATACAGGTA
Statistics
Matches: 52, Mismatches: 5, Indels: 3
0.87 0.08 0.05
Matches are distributed among these distances:
28 12 0.23
29 40 0.77
ACGTcount: A:0.30, C:0.17, G:0.26, T:0.26
Consensus pattern (29 bp):
ATATAAATGTGATTTGGGCCTAATAGGCC
Found at i:13568562 original size:43 final size:43
Alignment explanation
Indices: 13568513--13568663 Score: 169
Period size: 43 Copynumber: 3.5 Consensus size: 43
13568503 GATTACCGAG
* * *
13568513 ATGTGATTACATGTAAGACCATGTCTGGGACGTTGGCATTGTGT
1 ATGTGATTACGTGTAAGACCATGTCTGGGACATTGGCATCGT-T
13568557 -TGTGATTACGTGTAAGACCATGTCTGGGACATTGGCATCGTT
1 ATGTGATTACGTGTAAGACCATGTCTGGGACATTGGCATCGTT
* * * * * *
13568599 ATATGATTTCGTGTAAGACCATGTTTGGGAAATTAGCATCGAT
1 ATGTGATTACGTGTAAGACCATGTCTGGGACATTGGCATCGTT
* * * *
13568642 ATGTTATAACATGCAAGACCAT
1 ATGTGATTACGTGTAAGACCAT
13568664 ATCTAGGATA
Statistics
Matches: 91, Mismatches: 15, Indels: 3
0.83 0.14 0.03
Matches are distributed among these distances:
42 1 0.01
43 90 0.99
ACGTcount: A:0.27, C:0.15, G:0.25, T:0.33
Consensus pattern (43 bp):
ATGTGATTACGTGTAAGACCATGTCTGGGACATTGGCATCGTT
Found at i:13569162 original size:61 final size:61
Alignment explanation
Indices: 13569067--13569188 Score: 235
Period size: 61 Copynumber: 2.0 Consensus size: 61
13569057 TAGTTTTGGA
*
13569067 TGCATGTAAATATGGTATATGGCATGTATAGGCTAGTAATATGATGATATGTGTAACGCCC
1 TGCATGTAAATATGGTATATGGCATGTATAGGCTAGTAATATGATGATATGGGTAACGCCC
13569128 TGCATGTAAATATGGTATATGGCATGTATAGGCTAGTAATATGATGATATGGGTAACGCCC
1 TGCATGTAAATATGGTATATGGCATGTATAGGCTAGTAATATGATGATATGGGTAACGCCC
13569189 CAAATCTTTA
Statistics
Matches: 60, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
61 60 1.00
ACGTcount: A:0.31, C:0.11, G:0.25, T:0.32
Consensus pattern (61 bp):
TGCATGTAAATATGGTATATGGCATGTATAGGCTAGTAATATGATGATATGGGTAACGCCC
Found at i:13570083 original size:8 final size:8
Alignment explanation
Indices: 13570070--13570107 Score: 60
Period size: 8 Copynumber: 4.9 Consensus size: 8
13570060 CTAAATACCG
13570070 TTCTTCTC
1 TTCTTCTC
13570078 TTCTTCTC
1 TTCTTCTC
*
13570086 ATCTTCTC
1 TTCTTCTC
13570094 TTCTTCTC
1 TTCTTCTC
13570102 TT-TTCT
1 TTCTTCT
13570108 GTGCTTGACT
Statistics
Matches: 28, Mismatches: 2, Indels: 1
0.90 0.06 0.03
Matches are distributed among these distances:
7 4 0.14
8 24 0.86
ACGTcount: A:0.03, C:0.34, G:0.00, T:0.63
Consensus pattern (8 bp):
TTCTTCTC
Found at i:13573006 original size:12 final size:12
Alignment explanation
Indices: 13572989--13573014 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
13572979 AAATTATTCT
13572989 TTGTTATTATTA
1 TTGTTATTATTA
13573001 TTGTTATTATTA
1 TTGTTATTATTA
13573013 TT
1 TT
13573015 ATTTATTTTT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.23, C:0.00, G:0.08, T:0.69
Consensus pattern (12 bp):
TTGTTATTATTA
Found at i:13573350 original size:36 final size:36
Alignment explanation
Indices: 13573303--13573372 Score: 122
Period size: 36 Copynumber: 1.9 Consensus size: 36
13573293 ATGCCTAAAA
*
13573303 GCCTAGCTATCATTTCATTCTTCTTCATCTTCTTAT
1 GCCTAGCTATCATTTCATTCTTCCTCATCTTCTTAT
*
13573339 GCCTAGCTATCATTTCCTTCTTCCTCATCTTCTT
1 GCCTAGCTATCATTTCATTCTTCCTCATCTTCTT
13573373 TCTCCACTGA
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
36 32 1.00
ACGTcount: A:0.14, C:0.31, G:0.06, T:0.49
Consensus pattern (36 bp):
GCCTAGCTATCATTTCATTCTTCCTCATCTTCTTAT
Found at i:13573471 original size:12 final size:12
Alignment explanation
Indices: 13573454--13573490 Score: 74
Period size: 12 Copynumber: 3.1 Consensus size: 12
13573444 GTGTAAGTGA
13573454 TCTTGATGATTT
1 TCTTGATGATTT
13573466 TCTTGATGATTT
1 TCTTGATGATTT
13573478 TCTTGATGATTT
1 TCTTGATGATTT
13573490 T
1 T
13573491 TACATTTTTA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 25 1.00
ACGTcount: A:0.16, C:0.08, G:0.16, T:0.59
Consensus pattern (12 bp):
TCTTGATGATTT
Found at i:13573845 original size:30 final size:30
Alignment explanation
Indices: 13573806--13573866 Score: 86
Period size: 30 Copynumber: 2.0 Consensus size: 30
13573796 ATCGATTTTC
* * *
13573806 AGGCATAGGGGTAAAATGGTTATTTTGCCA
1 AGGCATAGGGGCAAAATGGTCATTTTACCA
*
13573836 AGGCCTAGGGGCAAAATGGTCATTTTACCA
1 AGGCATAGGGGCAAAATGGTCATTTTACCA
13573866 A
1 A
13573867 AGTTGTGAAT
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
30 27 1.00
ACGTcount: A:0.31, C:0.15, G:0.28, T:0.26
Consensus pattern (30 bp):
AGGCATAGGGGCAAAATGGTCATTTTACCA
Done.