Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Gbar_A08
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: 119882356
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.32
Warning! 2655529 characters in sequence are not A, C, G, or T
File 21 of 362
Found at i:6371956 original size:91 final size:91
Alignment explanation
Indices: 6371694--6371956 Score: 354
Period size: 91 Copynumber: 2.9 Consensus size: 91
6371684 TAATATATTG
* * * * *
6371694 ATTGATAGTTCAAGTATCACATT-GAACATTTTCAAAGTATAAGTACCTA-GTTGGACAATTTAT
1 ATTGATAGTTCAAGTACCACATTAG-ACATTTTCAAAGTATAGGTACC-ACATTGAACATTTTAT
6371757 GAAAGTACATGTATC-AATAAGACACAA
64 GAAAGTACATGTATCAAATAAGACACAA
* * * *
6371784 ATTGATAGTTCAAGTACCACATTAGAGATTTTCAAAGTATAGATATCACATT-AGACATATTATG
1 ATTGATAGTTCAAGTACCACATTAGACATTTTCAAAGTATAGGTACCACATTGA-ACATTTTATG
* *
6371848 AAAGTACATGTACCAAATAATACACAA
65 AAAGTACATGTATCAAATAAGACACAA
6371875 ATTGATAGTTCAAGTACCACATTAGACATTTTCAAAGTATAGGTACCACATTGAACATTTTATGA
1 ATTGATAGTTCAAGTACCACATTAGACATTTTCAAAGTATAGGTACCACATTGAACATTTTATGA
* *
6371940 AAGTATAAGTATCAAAT
66 AAGTACATGTATCAAAT
6371957 GTGACATTAT
Statistics
Matches: 150, Mismatches: 18, Indels: 9
0.85 0.10 0.05
Matches are distributed among these distances:
89 1 0.01
90 63 0.42
91 85 0.57
92 1 0.01
ACGTcount: A:0.42, C:0.14, G:0.13, T:0.31
Consensus pattern (91 bp):
ATTGATAGTTCAAGTACCACATTAGACATTTTCAAAGTATAGGTACCACATTGAACATTTTATGA
AAGTACATGTATCAAATAAGACACAA
Found at i:6374282 original size:24 final size:21
Alignment explanation
Indices: 6374238--6374287 Score: 55
Period size: 22 Copynumber: 2.2 Consensus size: 21
6374228 AAAAATATAT
*
6374238 ATATATATGTAATATACAAGAA
1 ATATATATATAATATACAAG-A
*
6374260 ATATATATATAATAGTATTAAGA
1 ATATATATATAATA-TA-CAAGA
6374283 ATATA
1 ATATA
6374288 AACATAAGAT
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
22 13 0.54
23 8 0.33
24 3 0.12
ACGTcount: A:0.54, C:0.02, G:0.08, T:0.36
Consensus pattern (21 bp):
ATATATATATAATATACAAGA
Found at i:6375148 original size:15 final size:16
Alignment explanation
Indices: 6375125--6375157 Score: 50
Period size: 15 Copynumber: 2.1 Consensus size: 16
6375115 AAGGTAAAAA
6375125 TTATATTTTTTTG-TT
1 TTATATTTTTTTGCTT
*
6375140 TTATTTTTTTTTGCTT
1 TTATATTTTTTTGCTT
6375156 TT
1 TT
6375158 TGCTTTTTAT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
15 12 0.75
16 4 0.25
ACGTcount: A:0.09, C:0.03, G:0.06, T:0.82
Consensus pattern (16 bp):
TTATATTTTTTTGCTT
Found at i:6375170 original size:22 final size:22
Alignment explanation
Indices: 6375132--6375193 Score: 63
Period size: 22 Copynumber: 2.8 Consensus size: 22
6375122 AAATTATATT
*
6375132 TTTTTGTTTTATTTTTTTTTGC
1 TTTTTGTTTTATATTTTTTTGC
*
6375154 TTTTTGCTTTT-TATTTTTTTGG
1 TTTTTG-TTTTATATTTTTTTGC
* *
6375176 TATTTGTTAATATATTTT
1 TTTTTGTT-TTATATTTT
6375194 ATGTGTATCT
Statistics
Matches: 33, Mismatches: 4, Indels: 5
0.79 0.10 0.12
Matches are distributed among these distances:
21 2 0.06
22 21 0.64
23 10 0.30
ACGTcount: A:0.11, C:0.03, G:0.10, T:0.76
Consensus pattern (22 bp):
TTTTTGTTTTATATTTTTTTGC
Found at i:6377645 original size:20 final size:19
Alignment explanation
Indices: 6377617--6377669 Score: 54
Period size: 20 Copynumber: 2.7 Consensus size: 19
6377607 AAAAAATTAA
* *
6377617 AATATATTTTTATACTTTTT
1 AATAAATTTTTA-AATTTTT
6377637 AATAAA-TTTTAAATTTTT
1 AATAAATTTTTAAATTTTT
*
6377655 ACTATAATTTTTAAA
1 AATA-AATTTTTAAA
6377670 ATTTAAAAAT
Statistics
Matches: 28, Mismatches: 3, Indels: 4
0.80 0.09 0.11
Matches are distributed among these distances:
18 9 0.32
19 7 0.25
20 12 0.43
ACGTcount: A:0.40, C:0.04, G:0.00, T:0.57
Consensus pattern (19 bp):
AATAAATTTTTAAATTTTT
Found at i:6379947 original size:27 final size:26
Alignment explanation
Indices: 6379903--6379960 Score: 64
Period size: 26 Copynumber: 2.2 Consensus size: 26
6379893 AATATTAAAT
*
6379903 TATTTATATAATTTTATTATATATTA
1 TATTTTTATAATTTTATTATATATTA
* * *
6379929 TATTTTTATGATTTGTATTTTTTATTA
1 TATTTTTATAATTT-TATTATATATTA
6379956 T-TTTT
1 TATTTT
6379961 AATGGTGTTT
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
26 16 0.59
27 11 0.41
ACGTcount: A:0.28, C:0.00, G:0.03, T:0.69
Consensus pattern (26 bp):
TATTTTTATAATTTTATTATATATTA
Found at i:6384853 original size:34 final size:34
Alignment explanation
Indices: 6384810--6384879 Score: 140
Period size: 34 Copynumber: 2.1 Consensus size: 34
6384800 TAGGAGTTTA
6384810 TTAGCTAGGTAGGGTACTAATCAGTCCAAGCTGG
1 TTAGCTAGGTAGGGTACTAATCAGTCCAAGCTGG
6384844 TTAGCTAGGTAGGGTACTAATCAGTCCAAGCTGG
1 TTAGCTAGGTAGGGTACTAATCAGTCCAAGCTGG
6384878 TT
1 TT
6384880 GACTTTTTTC
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
34 36 1.00
ACGTcount: A:0.26, C:0.17, G:0.29, T:0.29
Consensus pattern (34 bp):
TTAGCTAGGTAGGGTACTAATCAGTCCAAGCTGG
Found at i:6388311 original size:14 final size:15
Alignment explanation
Indices: 6388292--6388324 Score: 52
Period size: 14 Copynumber: 2.3 Consensus size: 15
6388282 AAATAAAGGG
6388292 CTTTTTCTTT-TTTT
1 CTTTTTCTTTATTTT
6388306 CTTTTTCTTTATTTT
1 CTTTTTCTTTATTTT
6388321 -TTTT
1 CTTTT
6388325 AACCTTTGAG
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
14 14 0.78
15 4 0.22
ACGTcount: A:0.03, C:0.12, G:0.00, T:0.85
Consensus pattern (15 bp):
CTTTTTCTTTATTTT
Found at i:6391542 original size:40 final size:40
Alignment explanation
Indices: 6391487--6391608 Score: 226
Period size: 40 Copynumber: 3.0 Consensus size: 40
6391477 TGTCGCACTT
*
6391487 TTCTATTTCAACCCTAGTATTCTTGCTCTAAGAATTTTAC
1 TTCTATTTCAACCCTAGTATTCTTGCTCTAAGGATTTTAC
6391527 TTCTATTTCAACCCTAGTATTCTTGCTCTAAGGATTTTAC
1 TTCTATTTCAACCCTAGTATTCTTGCTCTAAGGATTTTAC
*
6391567 TTCTATTTTAACCCTAGTATTCTTGCTCTAAGGATTTTAC
1 TTCTATTTCAACCCTAGTATTCTTGCTCTAAGGATTTTAC
6391607 TT
1 TT
6391609 TGCTCCATCA
Statistics
Matches: 80, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
40 80 1.00
ACGTcount: A:0.23, C:0.21, G:0.09, T:0.47
Consensus pattern (40 bp):
TTCTATTTCAACCCTAGTATTCTTGCTCTAAGGATTTTAC
Found at i:6401865 original size:30 final size:30
Alignment explanation
Indices: 6401806--6401868 Score: 81
Period size: 30 Copynumber: 2.1 Consensus size: 30
6401796 GTCTACATAC
* *
6401806 TTTATTTGATCAAATTTAACCCTTGTACTT
1 TTTAATTGATCAAATTTAACCCTTATACTT
* * *
6401836 TTTAATTGGTCAATTTTAATCCTTATACTT
1 TTTAATTGATCAAATTTAACCCTTATACTT
6401866 TTT
1 TTT
6401869 TTGAATTTTG
Statistics
Matches: 28, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
30 28 1.00
ACGTcount: A:0.25, C:0.14, G:0.06, T:0.54
Consensus pattern (30 bp):
TTTAATTGATCAAATTTAACCCTTATACTT
Found at i:6407792 original size:21 final size:20
Alignment explanation
Indices: 6407744--6407796 Score: 65
Period size: 20 Copynumber: 2.7 Consensus size: 20
6407734 GATGATATTT
*
6407744 TATA-ATTA-TTTAATTAGA
1 TATATATTATTTTAATGAGA
6407762 TATATATTATTTTAATGAGA
1 TATATATTATTTTAATGAGA
*
6407782 TATCTTATTATTTTA
1 TAT-ATATTATTTTA
6407797 TTATTATTTC
Statistics
Matches: 30, Mismatches: 2, Indels: 3
0.86 0.06 0.09
Matches are distributed among these distances:
18 4 0.13
19 4 0.13
20 12 0.40
21 10 0.33
ACGTcount: A:0.38, C:0.02, G:0.06, T:0.55
Consensus pattern (20 bp):
TATATATTATTTTAATGAGA
Found at i:6407800 original size:3 final size:3
Alignment explanation
Indices: 6407786--6407830 Score: 51
Period size: 3 Copynumber: 15.7 Consensus size: 3
6407776 ATGAGATATC
*
6407786 TTA TTA TT- TTA TTA TTA TT- TCA TTA TTA TT- TTA TTA TTAA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT-A TTA
6407829 TT
1 TT
6407831 TAGTATAAAA
Statistics
Matches: 36, Mismatches: 2, Indels: 8
0.78 0.04 0.17
Matches are distributed among these distances:
2 5 0.14
3 28 0.78
4 3 0.08
ACGTcount: A:0.29, C:0.02, G:0.00, T:0.69
Consensus pattern (3 bp):
TTA
Found at i:6407802 original size:11 final size:11
Alignment explanation
Indices: 6407786--6407824 Score: 69
Period size: 11 Copynumber: 3.5 Consensus size: 11
6407776 ATGAGATATC
6407786 TTATTATTTTA
1 TTATTATTTTA
*
6407797 TTATTATTTCA
1 TTATTATTTTA
6407808 TTATTATTTTA
1 TTATTATTTTA
6407819 TTATTA
1 TTATTA
6407825 ATTATTTAGT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
11 26 1.00
ACGTcount: A:0.28, C:0.03, G:0.00, T:0.69
Consensus pattern (11 bp):
TTATTATTTTA
Found at i:6410018 original size:23 final size:24
Alignment explanation
Indices: 6409978--6410028 Score: 68
Period size: 23 Copynumber: 2.2 Consensus size: 24
6409968 CCGATATATA
* *
6409978 GCTCTTCGTGAGCTTCCCGATAG-
1 GCTCTTCGTAAGCCTCCCGATAGT
*
6410001 GCTCTTTGTAAGCCTCCCGATAGT
1 GCTCTTCGTAAGCCTCCCGATAGT
6410025 GCTC
1 GCTC
6410029 GCTTGAACTT
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
23 20 0.83
24 4 0.17
ACGTcount: A:0.14, C:0.31, G:0.24, T:0.31
Consensus pattern (24 bp):
GCTCTTCGTAAGCCTCCCGATAGT
Found at i:6410041 original size:23 final size:23
Alignment explanation
Indices: 6409988--6410116 Score: 72
Period size: 23 Copynumber: 5.5 Consensus size: 23
6409978 GCTCTTCGTG
*
6409988 AGCTTCCCGATAGGCTCTTTGTA
1 AGCTTCCCGATAGGCTCCTTGTA
*
6410011 AGCCTCCCGATAGTGCTCGCTTG-A
1 AGCTTCCCGATAG-GCTC-CTTGTA
* *
6410035 A-CTTCCCGATATATGGCT-ATCTG-G
1 AGCTTCCCG--ATA-GGCTCCT-TGTA
* *
6410059 AGCTTCCCGGTAGGCT-CTTCGTG
1 AGCTTCCCGATAGGCTCCTT-GTA
* *
6410082 AGCTTTCCGATAGGCT-CTTCGTG
1 AGCTTCCCGATAGGCTCCTT-GTA
6410105 AGCTTCCCGATA
1 AGCTTCCCGATA
6410117 TGGTTCTTTG
Statistics
Matches: 87, Mismatches: 10, Indels: 18
0.76 0.09 0.16
Matches are distributed among these distances:
21 1 0.01
22 6 0.07
23 54 0.62
24 9 0.10
25 16 0.18
26 1 0.01
ACGTcount: A:0.16, C:0.29, G:0.24, T:0.31
Consensus pattern (23 bp):
AGCTTCCCGATAGGCTCCTTGTA
Found at i:6412100 original size:43 final size:43
Alignment explanation
Indices: 6412045--6412164 Score: 129
Period size: 42 Copynumber: 2.8 Consensus size: 43
6412035 AACAAGTACA
* * *
6412045 ATGCCGACGTCCCAAACGTGGTCTTACATGTAATTCA-ATATCG
1 ATGCCGATGTCCCAGACGTGGTCTTACATGTAAATCAGATA-CG
** *
6412088 ATGCCTCTGTCCCAGACAG-GGTCTTACACG-AAATCAGATACG
1 ATGCCGATGTCCCAGAC-GTGGTCTTACATGTAAATCAGATACG
* *
6412130 ATGCCGATGTCCCAGACATGGTCTTATATGTAAAT
1 ATGCCGATGTCCCAGACGTGGTCTTACATGTAAAT
6412165 ATTAATTGAG
Statistics
Matches: 62, Mismatches: 11, Indels: 8
0.77 0.14 0.10
Matches are distributed among these distances:
42 31 0.50
43 30 0.48
44 1 0.02
ACGTcount: A:0.28, C:0.25, G:0.20, T:0.27
Consensus pattern (43 bp):
ATGCCGATGTCCCAGACGTGGTCTTACATGTAAATCAGATACG
Found at i:6412188 original size:85 final size:86
Alignment explanation
Indices: 6412045--6412204 Score: 200
Period size: 85 Copynumber: 1.9 Consensus size: 86
6412035 AACAAGTACA
* * **
6412045 ATGCCGACGTCCCAAACGTGGTCTTACATGTAATTCAATATCGATGCCTCTGTCCCAGACAGGGT
1 ATGCCGACGTCCCAAACATGGTCTTACATGTAATTCAATATCGAGGCCTCTGTCCCAGACACAGT
6412110 C-TTACACGAAATCAGATACG
66 CTTTACACGAAATCAGATACG
* * * * *
6412130 ATGCCGATGTCCCAGACATGGTCTTATATGTAAATATTAAT-T-GAGGCCTGTGTCCCAGACACA
1 ATGCCGACGTCCCAAACATGGTCTTACATGT-AAT-TCAATATCGAGGCCTCTGTCCCAGACACA
6412193 GTCTTTACACGA
64 GTCTTTACACGA
6412205 TGTCTCAGAC
Statistics
Matches: 63, Mismatches: 9, Indels: 5
0.82 0.12 0.06
Matches are distributed among these distances:
85 47 0.75
86 12 0.19
87 4 0.06
ACGTcount: A:0.28, C:0.25, G:0.20, T:0.27
Consensus pattern (86 bp):
ATGCCGACGTCCCAAACATGGTCTTACATGTAATTCAATATCGAGGCCTCTGTCCCAGACACAGT
CTTTACACGAAATCAGATACG
Found at i:6414172 original size:86 final size:85
Alignment explanation
Indices: 6413949--6414319 Score: 241
Period size: 86 Copynumber: 4.3 Consensus size: 85
6413939 GATTTGAGCA
* * * * * ** *
6413949 CACACCTTTCAAGGGTATTGTCTGCTAAGTTAATAGTAGAATTTTTGCTAACCTCTTAATGCACT
1 CACACCCTACAAGAGTATTGCCCGCTAAGTTAATAGTAGAATCATTGCTAACCTCTCAATGCACT
*
6414014 TAACCAAATTTATTTGAA---G
66 T-AGCAAATTTATTT-AAGGCG
* ** ** * * * *
6414033 CACCCCCTATGAGAGTATTGTTCACTAAGTTAATAGCAGAACCACTGCTAACCTCTCAATGCACT
1 CACACCCTACAAGAGTATTGCCCGCTAAGTTAATAGTAGAATCATTGCTAACCTCTCAATGCACT
6414098 TAGTCAAATTTATTTAAGGCG
66 TAG-CAAATTTATTTAAGGCG
* * *
6414119 CACACCCTACAAGGGTA-TGACCCGCTAAGTCAATAGTAGAATCGTTGCTAACCTC-CTAA-GAC
1 CACACCCTACAAGAGTATTG-CCCGCTAAGTTAATAGTAGAATCATTGCTAACCTCTC-AATG-C
*
6414181 ACTTAGCAAAATTTATTTAAGGCA
63 ACTTAGC-AAATTTATTTAAGGCG
* ** * * ** * * * * * * *
6414205 CACACCTTATGAGGGTACTGCTAGTTAAGTTAATAGCAAAATCATTGTTAGCCTCTTAAGGCACT
1 CACACCCTACAAGAGTATTGCCCGCTAAGTTAATAGTAGAATCATTGCTAACCTCTCAATGCACT
* * *
6414270 TAGCTAAGTTTATTTAAAGCA
66 TAGC-AAATTTATTTAAGGCG
* * * *
6414291 CAAACCCTACGAGGGTATTGCCCACTAAG
1 CACACCCTACAAGAGTATTGCCCGCTAAG
6414320 CCAATAACAA
Statistics
Matches: 223, Mismatches: 53, Indels: 20
0.75 0.18 0.07
Matches are distributed among these distances:
83 3 0.01
84 62 0.28
85 5 0.02
86 150 0.67
87 3 0.01
ACGTcount: A:0.32, C:0.22, G:0.16, T:0.30
Consensus pattern (85 bp):
CACACCCTACAAGAGTATTGCCCGCTAAGTTAATAGTAGAATCATTGCTAACCTCTCAATGCACT
TAGCAAATTTATTTAAGGCG
Found at i:6414308 original size:172 final size:170
Alignment explanation
Indices: 6413958--6414390 Score: 426
Period size: 172 Copynumber: 2.5 Consensus size: 170
6413948 ACACACCTTT
* * * ** * * *
6413958 CAAGGGTATTGTCTGCTAAGTTAATAGTAGAATTTTTGCTAACCTCTTAATGCACTTAACCAAAT
1 CAAGGGTATTGCCCGCTAAGTCAATAGTAGAATCGTTGCTAACCTCCTAA-GCACTTAGCAAAAT
* * * * *
6414023 TTATTTGAA-GCAC-CCCCTATGAGAGTATTGTTCACTAAGTTAATAGCAGAACCACTGCTAACC
65 TTATTT-AAGGCACACACCTATGAGGGTACTGCTCACTAAGTTAATAGCAAAACCACTGCTAACC
* * * *
6414086 TCTCAATGCACTTAGTCAAATTTATTTAAGGCGCACACCCTA
129 TCTCAAGGCACTTAGTCAAATTTATTTAAAGCACAAACCCTA
6414128 CAAGGGTA-TGACCCGCTAAGTCAATAGTAGAATCGTTGCTAACCTCCTAAGACACTTAGCAAAA
1 CAAGGGTATTG-CCCGCTAAGTCAATAGTAGAATCGTTGCTAACCTCCTAAG-CACTTAGCAAAA
* * * * *
6414192 TTTATTTAAGGCACACACCTTATGAGGGTACTGCT-AGTTAAGTTAATAGCAAAATCATTGTTAG
64 TTTATTTAAGGCACACACC-TATGAGGGTACTGCTCA-CTAAGTTAATAGCAAAACCACTGCTAA
* *
6414256 CCTCTTAAGGCACTTAG-CTAAGTTTATTTAAAGCACAAACCCTA
127 CCTCTCAAGGCACTTAGTC-AAATTTATTTAAAGCACAAACCCTA
* * * ** * * * * * *
6414300 CGAGGGTATTGCCCACTAAGCCAATAACAAAATCGCTACTAGCCTTCTAAGCCACTTAGCGAAAT
1 CAAGGGTATTGCCCGCTAAGTCAATAGTAGAATCGTTGCTAACCTCCTAAG-CACTTAGCAAAAT
*
6414365 TTATTTAAGGCATACATCCTATGAGG
65 TTATTTAAGGCACACA-CCTATGAGG
6414391 ATATTACCCT
Statistics
Matches: 217, Mismatches: 37, Indels: 16
0.80 0.14 0.06
Matches are distributed among these distances:
169 5 0.02
170 62 0.29
171 5 0.02
172 141 0.65
173 4 0.02
ACGTcount: A:0.33, C:0.22, G:0.16, T:0.29
Consensus pattern (170 bp):
CAAGGGTATTGCCCGCTAAGTCAATAGTAGAATCGTTGCTAACCTCCTAAGCACTTAGCAAAATT
TATTTAAGGCACACACCTATGAGGGTACTGCTCACTAAGTTAATAGCAAAACCACTGCTAACCTC
TCAAGGCACTTAGTCAAATTTATTTAAAGCACAAACCCTA
Found at i:6414331 original size:86 final size:85
Alignment explanation
Indices: 6413993--6414390 Score: 295
Period size: 86 Copynumber: 4.7 Consensus size: 85
6413983 AGTAGAATTT
* * * * * **
6413993 TTGCTAACCTCTTAATGCACTTAACCAAATTTATTTGAA-GCAC-C-CCCTATGAGAGTATTGTT
1 TTGCTAACCTCTTAAGGCACTTAGCTAAATTTATTT-AAGGCACACACCCTACGAGGGTA-TGCC
* * *
6414055 CACTAAGTTAATAGCAGAACCA
64 CACTAAGTCAATAGCAAAATCA
* * * * *
6414077 CTGCTAACCTCTCAATGCACTTAG-TCAAATTTATTTAAGGCGCACACCCTACAAGGGTATGACC
1 TTGCTAACCTCTTAAGGCACTTAGCT-AAATTTATTTAAGGCACACACCCTACGAGGGTATG-CC
* * * *
6414141 CGCTAAGTCAATAGTAGAATCG
64 CACTAAGTCAATAGCAAAATCA
* * * * * *
6414163 TTGCTAACCTCCTAAGACACTTAGCAAAATTTATTTAAGGCACACACCTTATGAGGGTACTG-CT
1 TTGCTAACCTCTTAAGGCACTTAGCTAAATTTATTTAAGGCACACACCCTACGAGGGTA-TGCCC
* *
6414227 AGTTAAGTTAATAGCAAAATCA
65 A-CTAAGTCAATAGCAAAATCA
* * * * *
6414249 TTGTTAGCCTCTTAAGGCACTTAGCTAAGTTTATTTAAAGCACAAACCCTACGAGGGTATTGCCC
1 TTGCTAACCTCTTAAGGCACTTAGCTAAATTTATTTAAGGCACACACCCTACGAGGGTA-TGCCC
* * *
6414314 ACTAAGCCAATAACAAAATCG
65 ACTAAGTCAATAGCAAAATCA
* * * * * * * *
6414335 CTACTAGCCT-TCTAAGCCACTTAGCGAAATTTATTTAAGGCATACATCCTATGAGG
1 TTGCTAACCTCT-TAAGGCACTTAGCTAAATTTATTTAAGGCACACACCCTACGAGG
6414391 ATATTACCCT
Statistics
Matches: 244, Mismatches: 60, Indels: 18
0.76 0.19 0.06
Matches are distributed among these distances:
83 2 0.01
84 34 0.14
85 5 0.02
86 199 0.82
87 4 0.02
ACGTcount: A:0.33, C:0.23, G:0.16, T:0.28
Consensus pattern (85 bp):
TTGCTAACCTCTTAAGGCACTTAGCTAAATTTATTTAAGGCACACACCCTACGAGGGTATGCCCA
CTAAGTCAATAGCAAAATCA
Found at i:6419188 original size:79 final size:78
Alignment explanation
Indices: 6419002--6419227 Score: 326
Period size: 79 Copynumber: 2.9 Consensus size: 78
6418992 TTTATTCCTG
* *
6419002 ATTCACTATGGTAACTTAAGGTGGATAGGATTTAACCTGAAAAGGTAATCCTGATTCGCTACAGT
1 ATTCATTATGGTAACTTAAGGTGGATAGGATTTGACCTGAAAAGGTAATCCTGATTCGCTACAGT
* *
6419067 TACATGATATATG
66 TACACGATATATA
* * * *
6419080 ATTCATTATGGTAACCTAAGGTGGATAGGATTTGACCTGAAAAGGGTAATCCAGATTCGTTACGG
1 ATTCATTATGGTAACTTAAGGTGGATAGGATTTGACCTGAAAA-GGTAATCCTGATTCGCTACAG
6419145 TTACACGATATATA
65 TTACACGATATATA
* * * * *
6419159 ATTCCTTATGATAACTTAAGATGGGTAGGATTTGACCTGAAAAGGTAATCCTGATTCACTACAGT
1 ATTCATTATGGTAACTTAAGGTGGATAGGATTTGACCTGAAAAGGTAATCCTGATTCGCTACAGT
6419224 TACA
66 TACA
6419228 TGAGATGTGG
Statistics
Matches: 130, Mismatches: 17, Indels: 2
0.87 0.11 0.01
Matches are distributed among these distances:
78 62 0.48
79 68 0.52
ACGTcount: A:0.33, C:0.15, G:0.21, T:0.31
Consensus pattern (78 bp):
ATTCATTATGGTAACTTAAGGTGGATAGGATTTGACCTGAAAAGGTAATCCTGATTCGCTACAGT
TACACGATATATA
Found at i:6421004 original size:19 final size:19
Alignment explanation
Indices: 6420980--6421026 Score: 58
Period size: 19 Copynumber: 2.5 Consensus size: 19
6420970 AGAGAATACC
*
6420980 AAAAGAATGAAAAATAGAA
1 AAAAGAAAGAAAAATAGAA
* *
6420999 AAAAGAAAGGAAAATATAA
1 AAAAGAAAGAAAAATAGAA
*
6421018 AAAAAAAAG
1 AAAAGAAAG
6421027 TTGAAAAATG
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
19 24 1.00
ACGTcount: A:0.77, C:0.00, G:0.15, T:0.09
Consensus pattern (19 bp):
AAAAGAAAGAAAAATAGAA
Found at i:6421020 original size:20 final size:19
Alignment explanation
Indices: 6420988--6421040 Score: 56
Period size: 20 Copynumber: 2.7 Consensus size: 19
6420978 CCAAAAGAAT
6420988 GAAAAATAGAAAAAAGAAAG
1 GAAAAATAGAAAAAA-AAAG
6421008 GAAAATATA-AAAAAAAAAG
1 GAAAA-ATAGAAAAAAAAAG
6421027 TTGAAAAAT-GAAAA
1 --GAAAAATAGAAAA
6421041 TAAGAAATAA
Statistics
Matches: 29, Mismatches: 0, Indels: 8
0.78 0.00 0.22
Matches are distributed among these distances:
19 4 0.14
20 17 0.59
21 8 0.28
ACGTcount: A:0.74, C:0.00, G:0.15, T:0.11
Consensus pattern (19 bp):
GAAAAATAGAAAAAAAAAG
Found at i:6421040 original size:21 final size:20
Alignment explanation
Indices: 6420987--6421040 Score: 58
Period size: 21 Copynumber: 2.6 Consensus size: 20
6420977 ACCAAAAGAA
*
6420987 TGAAAAATAGAAAAAAGAAAG
1 TGAAAAAT-GAAAAAAAAAAG
6421008 -GAAAATAT-AAAAAAAAAAG
1 TGAAAA-ATGAAAAAAAAAAG
6421027 TTGAAAAATGAAAA
1 -TGAAAAATGAAAA
6421041 TAAGAAATAA
Statistics
Matches: 28, Mismatches: 1, Indels: 8
0.76 0.03 0.22
Matches are distributed among these distances:
19 10 0.36
20 7 0.25
21 11 0.39
ACGTcount: A:0.72, C:0.00, G:0.15, T:0.13
Consensus pattern (20 bp):
TGAAAAATGAAAAAAAAAAG
Found at i:6423012 original size:22 final size:23
Alignment explanation
Indices: 6422979--6423021 Score: 61
Period size: 22 Copynumber: 1.9 Consensus size: 23
6422969 AGTATATCTA
*
6422979 TTTTTCTATTTTCGTATTTAATT
1 TTTTTCTATTTTCGTACTTAATT
*
6423002 TTTTTCT-TTTTGGTACTTAA
1 TTTTTCTATTTTCGTACTTAA
6423022 ATATCAATTT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
22 11 0.61
23 7 0.39
ACGTcount: A:0.16, C:0.09, G:0.07, T:0.67
Consensus pattern (23 bp):
TTTTTCTATTTTCGTACTTAATT
Found at i:6423215 original size:15 final size:15
Alignment explanation
Indices: 6423156--6423226 Score: 57
Period size: 14 Copynumber: 5.0 Consensus size: 15
6423146 CAATTAGATT
6423156 TATTTAAA-ATTAAA
1 TATTTAAATATTAAA
*
6423170 T-TATTAAAT-GTAAA
1 TAT-TTAAATATTAAA
6423184 T-TTTAAA-A-TAGAA
1 TATTTAAATATTA-AA
6423197 TA-TTATAATATTAAA
1 TATTTA-AATATTAAA
6423212 TATTTAAATATTAAA
1 TATTTAAATATTAAA
6423227 AATACTATTG
Statistics
Matches: 47, Mismatches: 1, Indels: 17
0.72 0.02 0.26
Matches are distributed among these distances:
12 2 0.04
13 12 0.26
14 14 0.30
15 14 0.30
16 5 0.11
ACGTcount: A:0.54, C:0.00, G:0.03, T:0.44
Consensus pattern (15 bp):
TATTTAAATATTAAA
Found at i:6423453 original size:70 final size:72
Alignment explanation
Indices: 6423316--6423454 Score: 185
Period size: 71 Copynumber: 2.0 Consensus size: 72
6423306 CGGGTCTTTT
* * *
6423316 TTAATTTTTTTTTAATATTATATATATTATATGGATTAAAATATAAAAATTCATATATAATATAT
1 TTAATTTTTTTATAAAATTATATATATTATATGGATTAAAATATAAAAATTCAAATATAATATAT
6423381 AAAAAAA
66 AAAAAAA
* ** *
6423388 TTAATTTTTTTATAAAATTCTA-ATA-TATATAGTTTTAAAATTTAAAAATTCAAAT-TAATATA
1 TTAATTTTTTTATAAAATTATATATATTATAT-GGATTAAAATATAAAAATTCAAATATAATATA
6423450 TAAAA
65 TAAAA
6423455 TTGAAAATTG
Statistics
Matches: 59, Mismatches: 7, Indels: 4
0.84 0.10 0.06
Matches are distributed among these distances:
70 17 0.29
71 23 0.39
72 19 0.32
ACGTcount: A:0.50, C:0.02, G:0.02, T:0.46
Consensus pattern (72 bp):
TTAATTTTTTTATAAAATTATATATATTATATGGATTAAAATATAAAAATTCAAATATAATATAT
AAAAAAA
Found at i:6424429 original size:8 final size:9
Alignment explanation
Indices: 6424416--6424489 Score: 51
Period size: 9 Copynumber: 7.6 Consensus size: 9
6424406 TTCTTGTAAA
6424416 TTTTAT-TT
1 TTTTATATT
6424424 TTTTATATT
1 TTTTATATT
6424433 TTATATATACTT
1 TT-T-TATA-TT
*
6424445 TTTTGAAATT
1 TTTT-ATATT
6424455 TTTTATATAT
1 TTTTATAT-T
*
6424465 TTATTTTAATT
1 TT-TTAT-ATT
*
6424476 TTTCATATT
1 TTTTATATT
6424485 TTTTA
1 TTTTA
6424490 ATGTGTATAT
Statistics
Matches: 52, Mismatches: 6, Indels: 15
0.71 0.08 0.21
Matches are distributed among these distances:
8 6 0.12
9 14 0.27
10 13 0.25
11 13 0.25
12 6 0.12
ACGTcount: A:0.26, C:0.03, G:0.01, T:0.70
Consensus pattern (9 bp):
TTTTATATT
Found at i:6424478 original size:21 final size:20
Alignment explanation
Indices: 6424419--6424488 Score: 70
Period size: 22 Copynumber: 3.4 Consensus size: 20
6424409 TTGTAAATTT
*
6424419 TATTTTTTTATATTTTATATA
1 TATTTTTTTA-ATTTTTTATA
*
6424440 TACTTTTTTGAAATTTTTTATA
1 TA-TTTTTT-TAATTTTTTATA
*
6424462 TATTTATTTTAATTTTTCATA
1 TATTT-TTTTAATTTTTTATA
6424483 T-TTTTT
1 TATTTTT
6424489 AATGTGTATA
Statistics
Matches: 42, Mismatches: 4, Indels: 8
0.78 0.07 0.15
Matches are distributed among these distances:
19 2 0.05
20 3 0.07
21 16 0.38
22 20 0.48
23 1 0.02
ACGTcount: A:0.26, C:0.03, G:0.01, T:0.70
Consensus pattern (20 bp):
TATTTTTTTAATTTTTTATA
Found at i:6425828 original size:3 final size:3
Alignment explanation
Indices: 6425820--6425849 Score: 60
Period size: 3 Copynumber: 10.0 Consensus size: 3
6425810 TGGGGTTTTG
6425820 CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT
1 CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT
6425850 TCCCTTTAAT
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:0.00, C:0.33, G:0.00, T:0.67
Consensus pattern (3 bp):
CTT
Found at i:6429009 original size:12 final size:12
Alignment explanation
Indices: 6428992--6429016 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
6428982 ACAATTGAAA
6428992 AATATATTTTTT
1 AATATATTTTTT
6429004 AATATATTTTTT
1 AATATATTTTTT
6429016 A
1 A
6429017 TACAATATAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (12 bp):
AATATATTTTTT
Found at i:6437377 original size:30 final size:27
Alignment explanation
Indices: 6437301--6437369 Score: 66
Period size: 29 Copynumber: 2.4 Consensus size: 27
6437291 TCAAAACTTG
* *
6437301 AAAAATATAAAGACTGAAATTGACCAATT
1 AAAAATAT--AGACTAAAATTGACAAATT
*
6437330 AGAAAAGTATAGTCTAAAATTGATCAAATT
1 A-AAAA-TATAGACTAAAATTGA-CAAATT
6437360 AAAAATATAG
1 AAAAATATAG
6437370 GGACTAAATC
Statistics
Matches: 34, Mismatches: 3, Indels: 7
0.77 0.07 0.16
Matches are distributed among these distances:
28 5 0.15
29 16 0.47
30 10 0.29
31 3 0.09
ACGTcount: A:0.55, C:0.07, G:0.12, T:0.26
Consensus pattern (27 bp):
AAAAATATAGACTAAAATTGACAAATT
Found at i:6438536 original size:26 final size:24
Alignment explanation
Indices: 6438506--6438553 Score: 69
Period size: 26 Copynumber: 1.9 Consensus size: 24
6438496 ATAAAAAAAA
*
6438506 TTAAAAATATAATAAATCAAATATAT
1 TTAAAAACATAA-AAA-CAAATATAT
6438532 TTAAAAACATAAAAACAAATAT
1 TTAAAAACATAAAAACAAATAT
6438554 TAAAACAAAT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
24 7 0.33
25 3 0.14
26 11 0.52
ACGTcount: A:0.65, C:0.06, G:0.00, T:0.29
Consensus pattern (24 bp):
TTAAAAACATAAAAACAAATATAT
Found at i:6438565 original size:22 final size:21
Alignment explanation
Indices: 6438494--6438582 Score: 65
Period size: 21 Copynumber: 4.1 Consensus size: 21
6438484 TTATTTCATT
* *
6438494 AAATAAAAAAAAT-TAAAAAT
1 AAATAAAAAAAATATTAAAAC
*
6438514 ATAATAAATCAAATATATTTAAAA-
1 A-AATAAA--AAAAATA-TTAAAAC
*
6438538 ACATAAAAACAAATATTAAAAC
1 AAATAAAAA-AAATATTAAAAC
* *
6438560 AAATAAAAATAATACTAAAAC
1 AAATAAAAAAAATATTAAAAC
6438581 AA
1 AA
6438583 TTCTTAAAAC
Statistics
Matches: 55, Mismatches: 7, Indels: 13
0.73 0.09 0.17
Matches are distributed among these distances:
20 1 0.02
21 26 0.47
22 12 0.22
23 10 0.18
24 1 0.02
25 5 0.09
ACGTcount: A:0.71, C:0.07, G:0.00, T:0.22
Consensus pattern (21 bp):
AAATAAAAAAAATATTAAAAC
Found at i:6438623 original size:15 final size:15
Alignment explanation
Indices: 6438605--6438669 Score: 51
Period size: 16 Copynumber: 4.3 Consensus size: 15
6438595 TACACAAATT
*
6438605 AATAATATAATAAAA
1 AATAAAATAATAAAA
** *
6438620 AATAGTTATATTAAAA
1 AATA-AAATAATAAAA
* *
6438636 ATTTAAAATAATTAAA
1 A-ATAAAATAATAAAA
6438652 AATAAAATAA-AAAA
1 AATAAAATAATAAAA
6438666 AATA
1 AATA
6438670 TATTAATATA
Statistics
Matches: 39, Mismatches: 9, Indels: 5
0.74 0.17 0.09
Matches are distributed among these distances:
14 7 0.18
15 12 0.31
16 18 0.46
17 2 0.05
ACGTcount: A:0.69, C:0.00, G:0.02, T:0.29
Consensus pattern (15 bp):
AATAAAATAATAAAA
Found at i:6439280 original size:2 final size:2
Alignment explanation
Indices: 6439275--6439301 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
6439265 TTAAATTAGA
6439275 AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT A
6439302 AATAAAGATT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:6442835 original size:42 final size:42
Alignment explanation
Indices: 6442769--6442944 Score: 169
Period size: 42 Copynumber: 4.0 Consensus size: 42
6442759 TTTCGTTTTC
** * *
6442769 TCGATGCCATAGTTCAACTATGGTCTTACACATCTTCACATAA
1 TCGATGCCATAGCCCAGCTATGGTCTTACACATATTCACAT-A
* * *
6442812 T-GATGTCATAGCCCAGCTATGGTCTTACATATATTCATATA
1 TCGATGCCATAGCCCAGCTATGGTCTTACACATATTCACATA
6442853 TCGATGCCATAGCCCAGCTATGGTCTTACACGTAATCACATATCACATA
1 TCGATGCCATAGCCCAGCTATGGTCTTACAC---AT---AT-TCACATA
* *
6442902 TCGATGCCATAGCCCAGTTATGGTCGTACACGA-A-TCACATA
1 TCGATGCCATAGCCCAGCTATGGTCTTACAC-ATATTCACATA
6442943 TC
1 TC
6442945 TCACTGATGC
Statistics
Matches: 112, Mismatches: 13, Indels: 18
0.78 0.09 0.13
Matches are distributed among these distances:
41 11 0.10
42 59 0.53
43 2 0.02
45 2 0.02
47 1 0.01
48 2 0.02
49 35 0.31
ACGTcount: A:0.30, C:0.26, G:0.15, T:0.30
Consensus pattern (42 bp):
TCGATGCCATAGCCCAGCTATGGTCTTACACATATTCACATA
Found at i:6442913 original size:49 final size:48
Alignment explanation
Indices: 6442852--6443022 Score: 188
Period size: 47 Copynumber: 3.6 Consensus size: 48
6442842 ATATTCATAT
*
6442852 ATCGATGCCATAGCCCAGCTATGGTCTTACACGTAATCACATATCACA
1 ATCGATGCCATAGCCCAGATATGGTCTTACACGTAATCACATATCACA
* * *
6442900 TATCGATGCCATAGCCCAGTTATGGTCGTACACG-AATCACATATCTCA
1 -ATCGATGCCATAGCCCAGATATGGTCTTACACGTAATCACATATCACA
* * * * *
6442948 CT-GATGCCATATCCCAGATATGGTCTTATACAGT-AGCATATATCAC-
1 ATCGATGCCATAGCCCAGATATGGTCTTACAC-GTAATCACATATCACA
* * *
6442994 ACCGATGCCATATCCCAAATATGGTCTTA
1 ATCGATGCCATAGCCCAGATATGGTCTTA
6443023 TACGGAAATC
Statistics
Matches: 105, Mismatches: 14, Indels: 8
0.83 0.11 0.06
Matches are distributed among these distances:
46 25 0.24
47 36 0.34
48 13 0.12
49 31 0.30
ACGTcount: A:0.30, C:0.27, G:0.15, T:0.27
Consensus pattern (48 bp):
ATCGATGCCATAGCCCAGATATGGTCTTACACGTAATCACATATCACA
Found at i:6443004 original size:47 final size:46
Alignment explanation
Indices: 6442813--6443022 Score: 185
Period size: 47 Copynumber: 4.6 Consensus size: 46
6442803 TTCACATAAT
* * ** * *
6442813 GATGTCATAGCCCAGCTATGGTCTTACATATAT-TCATAT---ATC
1 GATGCCATAGCCCAGATATGGTCTTACACGTATCACATATCACACC
* *
6442855 GATGCCATAGCCCAGCTATGGTCTTACACGTAATCACATATCACATATC
1 GATGCCATAGCCCAGATATGGTCTTACACGT-ATCACATATCAC--ACC
* * * * *
6442904 GATGCCATAGCCCAGTTATGGTCGTACACGAATCACATATCTCACT
1 GATGCCATAGCCCAGATATGGTCTTACACGTATCACATATCACACC
* * * *
6442950 GATGCCATATCCCAGATATGGTCTTATACAGTAGCATATATCACACC
1 GATGCCATAGCCCAGATATGGTCTTACAC-GTATCACATATCACACC
* *
6442997 GATGCCATATCCCAAATATGGTCTTA
1 GATGCCATAGCCCAGATATGGTCTTA
6443023 TACGGAAATC
Statistics
Matches: 140, Mismatches: 20, Indels: 11
0.82 0.12 0.06
Matches are distributed among these distances:
42 28 0.20
43 2 0.01
44 5 0.04
46 26 0.19
47 37 0.26
48 11 0.08
49 31 0.22
ACGTcount: A:0.30, C:0.26, G:0.15, T:0.29
Consensus pattern (46 bp):
GATGCCATAGCCCAGATATGGTCTTACACGTATCACATATCACACC
Found at i:6443540 original size:18 final size:20
Alignment explanation
Indices: 6443498--6443534 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
6443488 ATATTTTATG
*
6443498 ATTA-TTTAATTAGATATAT
1 ATTATTTTAATGAGATATAT
6443517 ATTATTTTAATGAGATAT
1 ATTATTTTAATGAGATAT
6443535 TTTATTATTA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
19 4 0.25
20 12 0.75
ACGTcount: A:0.41, C:0.00, G:0.08, T:0.51
Consensus pattern (20 bp):
ATTATTTTAATGAGATATAT
Found at i:6445744 original size:46 final size:46
Alignment explanation
Indices: 6445692--6446002 Score: 415
Period size: 46 Copynumber: 6.7 Consensus size: 46
6445682 AGTGTGCTCT
6445692 CTGATATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAAC
1 CTGATATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAAC
* *
6445738 CTGATATGAAATGTGTAAGACCATGGTTGAAAGATATCATGGCAGC
1 CTGATATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAAC
* *
6445784 CTGATATGAAACGTGTAAGACCATGGTTGAAAGATACCATGGCAGC
1 CTGATATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAAC
6445830 CTGATATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAAC
1 CTGATATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAAC
* *** *** *
6445876 ATGACGGGAAATAAATAAGACCATGGTTGAAAGATACCATGGCAGC
1 CTGATATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAAC
* * **
6445922 GTGACATGAAATGAATAAGACCATGGTTGAAAGATACCATGGCAAC
1 CTGATATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAAC
* * ** * *
6445968 ATGACAAAAAAATGAGTAAGACCATAGTTGAAAGA
1 CTGA-TATGAAATGTGTAAGACCATGGTTGAAAGA
6446003 CATTATGGCA
Statistics
Matches: 239, Mismatches: 25, Indels: 1
0.90 0.09 0.00
Matches are distributed among these distances:
46 214 0.90
47 25 0.10
ACGTcount: A:0.40, C:0.14, G:0.24, T:0.22
Consensus pattern (46 bp):
CTGATATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAAC
Found at i:6446031 original size:92 final size:91
Alignment explanation
Indices: 6445707--6446035 Score: 264
Period size: 92 Copynumber: 3.6 Consensus size: 91
6445697 ATGAAATGTG
* * * * * ***
6445707 TAAGACCATGGTTGAAAGATACCATGGCAACCTGATATGAAATGTGTAAGACCATGGTTGAAAGA
1 TAAGACCATAGTTGAAAGACACCATGGCAGCATGACA-GAAATAAATAAGACCATGGTTGAAAGA
* * * * ** ****
6445772 TATCATGGCAGCCTGATATGAAACGTG
65 TACCATGGCAACATGACAAAAAATAAA
* * * * ***
6445799 TAAGACCATGGTTGAAAGATACCATGGCAGCCTGATATGAAATGTGTAAGACCATGGTTGAAAGA
1 TAAGACCATAGTTGAAAGACACCATGGCAGCATGACA-GAAATAAATAAGACCATGGTTGAAAGA
***
6445864 TACCATGGCAACATGACGGGAAATAAA
65 TACCATGGCAACATGACAAAAAATAAA
* * * *
6445891 TAAGACCATGGTTGAAAGATACCATGGCAGCGTGACATGAAATGAATAAGACCATGGTTGAAAGA
1 TAAGACCATAGTTGAAAGACACCATGGCAGCATGACA-GAAATAAATAAGACCATGGTTGAAAGA
* *
6445956 TACCATGGCAACATGACAAAAAAATGAG
65 TACCATGGCAACATGAC-AAAAAATAAA
** * *
6445984 TAAGACCATAGTTGAAAGACATTATGGCATCATGTCA-AAGATAAATAAGACC
1 TAAGACCATAGTTGAAAGACACCATGGCAGCATGACAGAA-ATAAATAAGACC
6446036 GTGGATGGGA
Statistics
Matches: 207, Mismatches: 28, Indels: 4
0.87 0.12 0.02
Matches are distributed among these distances:
91 2 0.01
92 170 0.82
93 35 0.17
ACGTcount: A:0.40, C:0.15, G:0.23, T:0.21
Consensus pattern (91 bp):
TAAGACCATAGTTGAAAGACACCATGGCAGCATGACAGAAATAAATAAGACCATGGTTGAAAGAT
ACCATGGCAACATGACAAAAAATAAA
Found at i:6446667 original size:31 final size:31
Alignment explanation
Indices: 6446624--6446772 Score: 217
Period size: 31 Copynumber: 4.8 Consensus size: 31
6446614 TGTTACACTT
* *
6446624 GTAGCCGAAGCTACCACTATTCACTGATCAA
1 GTAGCCGAAGCTACCACTTTTCACTGATCAG
* *
6446655 GTAGCCGGAGCTACCATTTTTCACTGATCAG
1 GTAGCCGAAGCTACCACTTTTCACTGATCAG
** *
6446686 GTAATCGGAGCTACCACTTTTCACTGATCAG
1 GTAGCCGAAGCTACCACTTTTCACTGATCAG
* *
6446717 GCAGCAGAAGCTACCACTTTTCACTGATCAG
1 GTAGCCGAAGCTACCACTTTTCACTGATCAG
6446748 GTAGCCGAAGCTACCACTTTTCACT
1 GTAGCCGAAGCTACCACTTTTCACT
6446773 TGTCATTTGT
Statistics
Matches: 104, Mismatches: 14, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
31 104 1.00
ACGTcount: A:0.27, C:0.28, G:0.19, T:0.26
Consensus pattern (31 bp):
GTAGCCGAAGCTACCACTTTTCACTGATCAG
Found at i:6446854 original size:50 final size:51
Alignment explanation
Indices: 6446748--6446876 Score: 197
Period size: 50 Copynumber: 2.5 Consensus size: 51
6446738 CACTGATCAG
* * * *
6446748 GTAGCCGAAGCTACCACTTTTCACTTGTCATTTGTCCTTGATCAGATAATT
1 GTAGCCGAAGCTATCACTTATCACTTGTCACTTGTCCTTGATCAGATAAGT
* *
6446799 GTAGCCGAAGCTATCACTTATCACTT-TCACTTGTCTTTGATTAGATAAGT
1 GTAGCCGAAGCTATCACTTATCACTTGTCACTTGTCCTTGATCAGATAAGT
6446849 GTAGCCGAAGCTATCACTTATCACTTGT
1 GTAGCCGAAGCTATCACTTATCACTTGT
6446877 TGCCATGGTC
Statistics
Matches: 71, Mismatches: 6, Indels: 2
0.90 0.08 0.03
Matches are distributed among these distances:
50 46 0.65
51 25 0.35
ACGTcount: A:0.25, C:0.22, G:0.16, T:0.36
Consensus pattern (51 bp):
GTAGCCGAAGCTATCACTTATCACTTGTCACTTGTCCTTGATCAGATAAGT
Found at i:6450839 original size:20 final size:21
Alignment explanation
Indices: 6450800--6450840 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
6450790 TTTTGTAACG
*
6450800 AAACAGTATAAATGATATACA
1 AAACAATATAAATGATATACA
*
6450821 AAACAATATATAT-ATATACA
1 AAACAATATAAATGATATACA
6450841 CGAATAAATA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
20 7 0.39
21 11 0.61
ACGTcount: A:0.59, C:0.10, G:0.05, T:0.27
Consensus pattern (21 bp):
AAACAATATAAATGATATACA
Found at i:6450908 original size:23 final size:21
Alignment explanation
Indices: 6450878--6450920 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 21
6450868 ATAGCTTAAT
6450878 ATAAATAATATATACAAAAATA
1 ATAAATAATATATA-AAAAATA
*
6450900 ATAATATAATATTTAAAAAAT
1 ATAA-ATAATATATAAAAAAT
6450921 GCTCATAAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
22 10 0.53
23 9 0.47
ACGTcount: A:0.65, C:0.02, G:0.00, T:0.33
Consensus pattern (21 bp):
ATAAATAATATATAAAAAATA
Found at i:6450982 original size:14 final size:14
Alignment explanation
Indices: 6450958--6450995 Score: 51
Period size: 14 Copynumber: 2.6 Consensus size: 14
6450948 ATAATGAAAC
6450958 AGAATGAAAATATACA
1 AGAA-GAAAATA-ACA
6450974 A-AAGAAAATAACA
1 AGAAGAAAATAACA
6450987 AGAAGAAAA
1 AGAAGAAAA
6450996 AATTAAAATA
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
13 4 0.19
14 14 0.67
15 2 0.10
16 1 0.05
ACGTcount: A:0.71, C:0.05, G:0.13, T:0.11
Consensus pattern (14 bp):
AGAAGAAAATAACA
Found at i:6452742 original size:34 final size:34
Alignment explanation
Indices: 6452699--6452766 Score: 136
Period size: 34 Copynumber: 2.0 Consensus size: 34
6452689 AGAATCAAGT
6452699 AAGAAATTTTCAGGTTTTCGAATTGAATTATTCA
1 AAGAAATTTTCAGGTTTTCGAATTGAATTATTCA
6452733 AAGAAATTTTCAGGTTTTCGAATTGAATTATTCA
1 AAGAAATTTTCAGGTTTTCGAATTGAATTATTCA
6452767 GCTACCTCTT
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
34 34 1.00
ACGTcount: A:0.35, C:0.09, G:0.15, T:0.41
Consensus pattern (34 bp):
AAGAAATTTTCAGGTTTTCGAATTGAATTATTCA
Found at i:6457022 original size:17 final size:18
Alignment explanation
Indices: 6457000--6457034 Score: 63
Period size: 17 Copynumber: 2.0 Consensus size: 18
6456990 TCATTATATT
6457000 AAAAATATATAT-TTTTA
1 AAAAATATATATATTTTA
6457017 AAAAATATATATATTTTA
1 AAAAATATATATATTTTA
6457035 TATTTCAAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 12 0.71
18 5 0.29
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (18 bp):
AAAAATATATATATTTTA
Found at i:6458294 original size:31 final size:31
Alignment explanation
Indices: 6458258--6458317 Score: 77
Period size: 31 Copynumber: 1.9 Consensus size: 31
6458248 AAATTTTTCC
*
6458258 TAAAAATAAT-TTAAAAATTACTATAAATTAT
1 TAAAAATAATGTTAAAAATT-CAATAAATTAT
* *
6458289 TAAAAATTATGTTGAAAATTCAATAAATT
1 TAAAAATAATGTTAAAAATTCAATAAATT
6458318 TAGCCCTCAA
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
31 17 0.68
32 8 0.32
ACGTcount: A:0.55, C:0.03, G:0.03, T:0.38
Consensus pattern (31 bp):
TAAAAATAATGTTAAAAATTCAATAAATTAT
Found at i:6458411 original size:61 final size:61
Alignment explanation
Indices: 6458303--6458427 Score: 151
Period size: 61 Copynumber: 2.0 Consensus size: 61
6458293 AATTATGTTG
** * * * * *
6458303 AAAATTCAATAAATTTAGCCCTCAATGTTTACAAATTTTTTAATTTTAATTATAATTCTAA
1 AAAATTCAATAAATTTAGCCCTCAAAATTTACAAAATCTGTAATTTTAATCATAACTCTAA
* ** *
6458364 AAAATTCAATAAATTTGGCCCTCAAAATTTACAAAATCTGTCGTTTTAATCCTAACTCTAA
1 AAAATTCAATAAATTTAGCCCTCAAAATTTACAAAATCTGTAATTTTAATCATAACTCTAA
6458425 AAA
1 AAA
6458428 TTTTAAAAAA
Statistics
Matches: 53, Mismatches: 11, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
61 53 1.00
ACGTcount: A:0.42, C:0.15, G:0.05, T:0.38
Consensus pattern (61 bp):
AAAATTCAATAAATTTAGCCCTCAAAATTTACAAAATCTGTAATTTTAATCATAACTCTAA
Found at i:6459876 original size:23 final size:23
Alignment explanation
Indices: 6459831--6459876 Score: 56
Period size: 23 Copynumber: 2.0 Consensus size: 23
6459821 TTTTTTTTAA
* * *
6459831 AGATTTTTTTATGTAAATTTTTT
1 AGATTTGTTTACGTAAATATTTT
*
6459854 AGATTTGTTTACGTATATATTTT
1 AGATTTGTTTACGTAAATATTTT
6459877 GAACGTTTAG
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.26, C:0.02, G:0.11, T:0.61
Consensus pattern (23 bp):
AGATTTGTTTACGTAAATATTTT
Found at i:6459954 original size:20 final size:20
Alignment explanation
Indices: 6459917--6459960 Score: 54
Period size: 20 Copynumber: 2.2 Consensus size: 20
6459907 TATTCATAAA
*
6459917 AATATTTTCACATAATTTTT
1 AATATTTTCACATAATTTTC
*
6459937 AATATTTTTA-ATATATTTTC
1 AATATTTTCACATA-ATTTTC
6459957 AATA
1 AATA
6459961 ATCTATATTT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
19 3 0.14
20 18 0.86
ACGTcount: A:0.39, C:0.07, G:0.00, T:0.55
Consensus pattern (20 bp):
AATATTTTCACATAATTTTC
Found at i:6461432 original size:21 final size:21
Alignment explanation
Indices: 6461407--6461448 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
6461397 ATTATTTGAG
*
6461407 TTATTCGA-ATTATAACTCAAA
1 TTATTCGATATT-GAACTCAAA
6461428 TTATTCGATATTGAACTCAAA
1 TTATTCGATATTGAACTCAAA
6461449 ACTCGAATAA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
21 16 0.84
22 3 0.16
ACGTcount: A:0.40, C:0.14, G:0.07, T:0.38
Consensus pattern (21 bp):
TTATTCGATATTGAACTCAAA
Found at i:6463448 original size:15 final size:15
Alignment explanation
Indices: 6463428--6463457 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
6463418 CTAGGGCTAA
6463428 ATTGAACTGGGTTTT
1 ATTGAACTGGGTTTT
6463443 ATTGAACTGGGTTTT
1 ATTGAACTGGGTTTT
6463458 GTAAATATTC
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.20, C:0.07, G:0.27, T:0.47
Consensus pattern (15 bp):
ATTGAACTGGGTTTT
Found at i:6471756 original size:25 final size:26
Alignment explanation
Indices: 6471702--6471757 Score: 62
Period size: 28 Copynumber: 2.2 Consensus size: 26
6471692 CGAATTTGAC
* *
6471702 ATTTTTTTCTAATGTGGTACATGTGTT
1 ATTTTTTTCTAATCTAGTACA-GTGTT
6471729 ATTTTTTGTCTAATCTAGTACA-TG-T
1 ATTTTTT-TCTAATCTAGTACAGTGTT
6471754 ATTT
1 ATTT
6471758 GACAAAAATT
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
25 5 0.19
26 2 0.08
27 7 0.27
28 12 0.46
ACGTcount: A:0.21, C:0.09, G:0.14, T:0.55
Consensus pattern (26 bp):
ATTTTTTTCTAATCTAGTACAGTGTT
Found at i:6474316 original size:19 final size:20
Alignment explanation
Indices: 6474282--6474320 Score: 62
Period size: 19 Copynumber: 2.0 Consensus size: 20
6474272 AAGAAATTTG
*
6474282 TCTAATATGATTAAAAATAT
1 TCTAAAATGATTAAAAATAT
6474302 TCTAAAATG-TTAAAAATAT
1 TCTAAAATGATTAAAAATAT
6474321 ACATGTTCGA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
19 10 0.56
20 8 0.44
ACGTcount: A:0.51, C:0.05, G:0.05, T:0.38
Consensus pattern (20 bp):
TCTAAAATGATTAAAAATAT
Found at i:6478919 original size:34 final size:34
Alignment explanation
Indices: 6478872--6478952 Score: 108
Period size: 34 Copynumber: 2.4 Consensus size: 34
6478862 CGGTCCGCCG
* * * *
6478872 ACACGGCTATGTAACCCCTTTACATGGTCTACCC
1 ACACGACTGTGTAACCCCTTTACACGGTCTAACC
**
6478906 ACACGACTGTGTAAGTCCTTTACACGGTCTAACC
1 ACACGACTGTGTAACCCCTTTACACGGTCTAACC
6478940 ACACGACTGTGTA
1 ACACGACTGTGTA
6478953 CCTTTATTTT
Statistics
Matches: 41, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
34 41 1.00
ACGTcount: A:0.26, C:0.31, G:0.17, T:0.26
Consensus pattern (34 bp):
ACACGACTGTGTAACCCCTTTACACGGTCTAACC
Found at i:6483906 original size:48 final size:48
Alignment explanation
Indices: 6483834--6483928 Score: 120
Period size: 48 Copynumber: 2.0 Consensus size: 48
6483824 ACGTAGGAAG
* * *
6483834 TAGTCGACAATTTATCTACCCGACT-AGTGGTTCATCCATAATGTATTT
1 TAGTCGACAATTTATCTACACGACTGA-TGGTTCATCCACAATATATTT
* * *
6483882 TAGTCGGCAGTTTATCTATACGACTGATGGTTCATCCACAATATATT
1 TAGTCGACAATTTATCTACACGACTGATGGTTCATCCACAATATATT
6483929 GGCAAAATTT
Statistics
Matches: 40, Mismatches: 6, Indels: 2
0.83 0.12 0.04
Matches are distributed among these distances:
48 39 0.98
49 1 0.03
ACGTcount: A:0.27, C:0.20, G:0.16, T:0.37
Consensus pattern (48 bp):
TAGTCGACAATTTATCTACACGACTGATGGTTCATCCACAATATATTT
Found at i:6492342 original size:31 final size:30
Alignment explanation
Indices: 6492301--6492378 Score: 138
Period size: 31 Copynumber: 2.6 Consensus size: 30
6492291 GAAAAGCTCC
*
6492301 TGAAGATTATAGCTTTTCAGGGCATTCCAT
1 TGAAGTTTATAGCTTTTCAGGGCATTCCAT
6492331 TGAAGTTTTATAGCTTTTCAGGGCATTCCAT
1 TGAAG-TTTATAGCTTTTCAGGGCATTCCAT
6492362 TGAAGTTTATAGCTTTT
1 TGAAGTTTATAGCTTTT
6492379 AATCCTTGGG
Statistics
Matches: 46, Mismatches: 1, Indels: 2
0.94 0.02 0.04
Matches are distributed among these distances:
30 17 0.37
31 29 0.63
ACGTcount: A:0.24, C:0.14, G:0.19, T:0.42
Consensus pattern (30 bp):
TGAAGTTTATAGCTTTTCAGGGCATTCCAT
Found at i:6496664 original size:23 final size:23
Alignment explanation
Indices: 6496620--6496664 Score: 56
Period size: 23 Copynumber: 2.0 Consensus size: 23
6496610 AAGAAATTAT
**
6496620 AAAATTTTATTAAAAACTAAAAG
1 AAAATTTTATTAAAAAAAAAAAG
6496643 AAAATTTTA-TAAAATAAAAAAA
1 AAAATTTTATTAAAA-AAAAAAA
6496665 TCAATAAACA
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
22 5 0.26
23 14 0.74
ACGTcount: A:0.67, C:0.02, G:0.02, T:0.29
Consensus pattern (23 bp):
AAAATTTTATTAAAAAAAAAAAG
Found at i:6499196 original size:17 final size:16
Alignment explanation
Indices: 6499171--6499226 Score: 53
Period size: 16 Copynumber: 3.4 Consensus size: 16
6499161 ATAACTTAAG
6499171 AAAATTAATATAAAATCT
1 AAAA-TAATATAAAAT-T
*
6499189 AAAATAATA-ATAATT
1 AAAATAATATAAAATT
*
6499204 AAAAATAA-ATAAACTT
1 -AAAATAATATAAAATT
6499220 AAAATAA
1 AAAATAA
6499227 AATTTCCTAT
Statistics
Matches: 33, Mismatches: 3, Indels: 7
0.77 0.07 0.16
Matches are distributed among these distances:
15 9 0.27
16 15 0.45
17 5 0.15
18 4 0.12
ACGTcount: A:0.68, C:0.04, G:0.00, T:0.29
Consensus pattern (16 bp):
AAAATAATATAAAATT
Found at i:6503341 original size:29 final size:29
Alignment explanation
Indices: 6503285--6503342 Score: 98
Period size: 29 Copynumber: 2.0 Consensus size: 29
6503275 ACATAGACAT
*
6503285 GCTTTAGTAAAAAGCACTGACAATGACGC
1 GCTTTAGTAAAAAGCACTGACAAGGACGC
*
6503314 GCTTTAGTAAAAAGCACTGACGAGGACGC
1 GCTTTAGTAAAAAGCACTGACAAGGACGC
6503343 ATTTTTGGTT
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
29 27 1.00
ACGTcount: A:0.36, C:0.21, G:0.24, T:0.19
Consensus pattern (29 bp):
GCTTTAGTAAAAAGCACTGACAAGGACGC
Found at i:6505579 original size:15 final size:16
Alignment explanation
Indices: 6505559--6505588 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
6505549 TGGAATTATT
6505559 ATTTTAAT-TAATATC
1 ATTTTAATATAATATC
6505574 ATTTTAATATAATAT
1 ATTTTAATATAATAT
6505589 GTTGTTGTTA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 8 0.57
16 6 0.43
ACGTcount: A:0.43, C:0.03, G:0.00, T:0.53
Consensus pattern (16 bp):
ATTTTAATATAATATC
Found at i:6506045 original size:22 final size:22
Alignment explanation
Indices: 6506020--6506076 Score: 55
Period size: 21 Copynumber: 2.7 Consensus size: 22
6506010 AAACCATCAT
*
6506020 TTTTAAAAAAAATTAATAAATA
1 TTTTAAAAAAAATTAAAAAATA
* *
6506042 TTTTATAAAATA-TAAAAAATA
1 TTTTAAAAAAAATTAAAAAATA
* *
6506063 -ATTAATAAAAATTA
1 TTTTAAAAAAAATTA
6506077 CACGTGAAAT
Statistics
Matches: 27, Mismatches: 7, Indels: 3
0.73 0.19 0.08
Matches are distributed among these distances:
20 7 0.26
21 10 0.37
22 10 0.37
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (22 bp):
TTTTAAAAAAAATTAAAAAATA
Found at i:6506738 original size:54 final size:57
Alignment explanation
Indices: 6506665--6506945 Score: 270
Period size: 54 Copynumber: 4.8 Consensus size: 57
6506655 GGGTTTAGAA
6506665 AAAAATTAAATTAGGGTATTATGTTTTTAATTGTTTAGGGTTTTAG-GA-T-TTAGG
1 AAAAATTAAATTAGGGTATTATGTTTTTAATTGTTTAGGGTTTTAGTGATTGTTAGG
* * *
6506719 AAAAATTAAATTAGAGTATTATGTTTTTAATTGTTTAGGGTTTTA--AAAT-TTAGG
1 AAAAATTAAATTAGGGTATTATGTTTTTAATTGTTTAGGGTTTTAGTGATTGTTAGG
* * * *
6506773 AAAATTTAAATTAAGGTATTATG-TTTTAATTGTTTAGGATTTTAGCGTTTTATTAGGGTTAGG
1 AAAAATTAAATTAGGGTATTATGTTTTTAATTGTTTAGGGTTTTA--G--TGATT---GTTAGG
* * * *
6506836 AAAAATTATATTAGGGTATTAGGTTTTTAATTATTTAAGGTTTTATGGTTTGATTAGAGGTTAGG
1 AAAAATTAAATTAGGGTATTATGTTTTTAATTGTTTAGGGTTTTA--G--TGATT----GTTAGG
*
6506901 AAAAATTAAATTAGGGTATTAGGTTTTTAATTGTTTAGGGTTTTA
1 AAAAATTAAATTAGGGTATTATGTTTTTAATTGTTTAGGGTTTTA
6506946 TGGTTTAATT
Statistics
Matches: 191, Mismatches: 23, Indels: 15
0.83 0.10 0.07
Matches are distributed among these distances:
53 21 0.11
54 70 0.37
59 2 0.01
63 24 0.13
64 25 0.13
65 49 0.26
ACGTcount: A:0.32, C:0.00, G:0.21, T:0.47
Consensus pattern (57 bp):
AAAAATTAAATTAGGGTATTATGTTTTTAATTGTTTAGGGTTTTAGTGATTGTTAGG
Found at i:6506868 original size:25 final size:25
Alignment explanation
Indices: 6506839--6506886 Score: 62
Period size: 25 Copynumber: 1.9 Consensus size: 25
6506829 GGTTAGGAAA
*
6506839 AATTATATTAGGGTATTA-GGTTTTT
1 AATTAT-TTAAGGTATTATGGTTTTT
*
6506864 AATTATTTAAGGTTTTATGGTTT
1 AATTATTTAAGGTATTATGGTTT
6506887 GATTAGAGGT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
24 9 0.45
25 11 0.55
ACGTcount: A:0.27, C:0.00, G:0.19, T:0.54
Consensus pattern (25 bp):
AATTATTTAAGGTATTATGGTTTTT
Found at i:6506914 original size:65 final size:64
Alignment explanation
Indices: 6506768--6506951 Score: 257
Period size: 65 Copynumber: 2.9 Consensus size: 64
6506758 GTTTTAAAAT
* * * *
6506768 TTAGGAAAATTTAAATTAAGGTATTATG-TTTTAATTGTTT-AGGATTTTA-GCGTTTTATTAGG
1 TTAGGAAAAATTAAATTAGGGTATTAGGTTTTTAATTGTTTAAGG-TTTTATG-GTTTGATTAGG
6506830 G
64 G
* *
6506831 TTAGGAAAAATTATATTAGGGTATTAGGTTTTTAATTATTTAAGGTTTTATGGTTTGATTAGAGG
1 TTAGGAAAAATTAAATTAGGGTATTAGGTTTTTAATTGTTTAAGGTTTTATGGTTTGATTAG-GG
*
6506896 TTAGGAAAAATTAAATTAGGGTATTAGGTTTTTAATTGTTTAGGGTTTTATGGTTT
1 TTAGGAAAAATTAAATTAGGGTATTAGGTTTTTAATTGTTTAAGGTTTTATGGTTT
6506952 AATTTTTTAA
Statistics
Matches: 108, Mismatches: 9, Indels: 6
0.88 0.07 0.05
Matches are distributed among these distances:
63 24 0.22
64 25 0.23
65 59 0.55
ACGTcount: A:0.30, C:0.01, G:0.22, T:0.47
Consensus pattern (64 bp):
TTAGGAAAAATTAAATTAGGGTATTAGGTTTTTAATTGTTTAAGGTTTTATGGTTTGATTAGGG
Found at i:6507099 original size:59 final size:59
Alignment explanation
Indices: 6507018--6507221 Score: 327
Period size: 59 Copynumber: 3.4 Consensus size: 59
6507008 TACAGTCACT
* * *
6507018 AATATATTTATACAAAACTATTCAAAAGAAATTCTATTTTATTAAATGAAACAATATAAA
1 AATA-ATTTGTACAAAAATATTCAAAAGAACTTCTATTTTATTAAATGAAACAATATAAA
* * *
6507078 AATAATTTGTACAAAAATATTCAGAAGAACTTCTATTTTATTAAATGAAAAAATATTAA
1 AATAATTTGTACAAAAATATTCAAAAGAACTTCTATTTTATTAAATGAAACAATATAAA
*
6507137 AATAATTTGTACAAAAATATTCAAAAGGACTTCTATTTTATTAAATGAAACAATATAAA
1 AATAATTTGTACAAAAATATTCAAAAGAACTTCTATTTTATTAAATGAAACAATATAAA
*
6507196 AATAATTTGTACAAAAATATTAAAAA
1 AATAATTTGTACAAAAATATTCAAAA
6507222 ATAAATCAAG
Statistics
Matches: 133, Mismatches: 11, Indels: 1
0.92 0.08 0.01
Matches are distributed among these distances:
59 129 0.97
60 4 0.03
ACGTcount: A:0.53, C:0.07, G:0.05, T:0.34
Consensus pattern (59 bp):
AATAATTTGTACAAAAATATTCAAAAGAACTTCTATTTTATTAAATGAAACAATATAAA
Found at i:6510228 original size:22 final size:21
Alignment explanation
Indices: 6510203--6510243 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
6510193 TTAATTAATT
*
6510203 TTTATATATATTTTTAAAAATA
1 TTTATATA-ATTTTAAAAAATA
*
6510225 TTTATTTAATTTTAAAAAA
1 TTTATATAATTTTAAAAAA
6510244 AAAAAGTCAA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 10 0.59
22 7 0.41
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (21 bp):
TTTATATAATTTTAAAAAATA
Found at i:6514489 original size:160 final size:160
Alignment explanation
Indices: 6514225--6514544 Score: 640
Period size: 160 Copynumber: 2.0 Consensus size: 160
6514215 TTCCAATAAA
6514225 AACATTGTATTAAAGAATGAAAATAAGCATGAACATGATGGTACACGTACAACATAGGCCCTCAT
1 AACATTGTATTAAAGAATGAAAATAAGCATGAACATGATGGTACACGTACAACATAGGCCCTCAT
6514290 TTAAAAAGTCTGACCCAAGCCAAACCCGTGTGTGAAAGGGACAGGCATAGAGAACTTACTTGCAT
66 TTAAAAAGTCTGACCCAAGCCAAACCCGTGTGTGAAAGGGACAGGCATAGAGAACTTACTTGCAT
6514355 GGTTGTTGTGATACTCATGCCGCCATCTTC
131 GGTTGTTGTGATACTCATGCCGCCATCTTC
6514385 AACATTGTATTAAAGAATGAAAATAAGCATGAACATGATGGTACACGTACAACATAGGCCCTCAT
1 AACATTGTATTAAAGAATGAAAATAAGCATGAACATGATGGTACACGTACAACATAGGCCCTCAT
6514450 TTAAAAAGTCTGACCCAAGCCAAACCCGTGTGTGAAAGGGACAGGCATAGAGAACTTACTTGCAT
66 TTAAAAAGTCTGACCCAAGCCAAACCCGTGTGTGAAAGGGACAGGCATAGAGAACTTACTTGCAT
6514515 GGTTGTTGTGATACTCATGCCGCCATCTTC
131 GGTTGTTGTGATACTCATGCCGCCATCTTC
6514545 TTCAGGGCGA
Statistics
Matches: 160, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
160 160 1.00
ACGTcount: A:0.34, C:0.21, G:0.21, T:0.24
Consensus pattern (160 bp):
AACATTGTATTAAAGAATGAAAATAAGCATGAACATGATGGTACACGTACAACATAGGCCCTCAT
TTAAAAAGTCTGACCCAAGCCAAACCCGTGTGTGAAAGGGACAGGCATAGAGAACTTACTTGCAT
GGTTGTTGTGATACTCATGCCGCCATCTTC
Found at i:6516898 original size:5 final size:5
Alignment explanation
Indices: 6516882--6516947 Score: 57
Period size: 5 Copynumber: 13.6 Consensus size: 5
6516872 ATTATTTACC
* * * *
6516882 TATAT CTATAT TATAT TTTAT TACAT AATAT T-TAT TATAT TATTT TATAT
1 TATAT -TATAT TATAT TATAT TATAT TATAT TATAT TATAT TATAT TATAT
*
6516932 TTTA- T-TAT TATAT TAT
1 TATAT TATAT TATAT TAT
6516948 TTTACACTTT
Statistics
Matches: 48, Mismatches: 9, Indels: 7
0.75 0.14 0.11
Matches are distributed among these distances:
3 2 0.04
4 6 0.12
5 35 0.73
6 5 0.10
ACGTcount: A:0.35, C:0.03, G:0.00, T:0.62
Consensus pattern (5 bp):
TATAT
Found at i:6516940 original size:8 final size:8
Alignment explanation
Indices: 6516913--6516951 Score: 53
Period size: 8 Copynumber: 5.0 Consensus size: 8
6516903 TACATAATAT
*
6516913 TTATTATA
1 TTATTTTA
6516921 TTATTTTA
1 TTATTTTA
6516929 -TATTTTA
1 TTATTTTA
*
6516936 TTATTATA
1 TTATTTTA
6516944 TTATTTTA
1 TTATTTTA
6516952 CACTTTAATA
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
7 7 0.26
8 20 0.74
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (8 bp):
TTATTTTA
Found at i:6516943 original size:23 final size:23
Alignment explanation
Indices: 6516913--6516983 Score: 83
Period size: 23 Copynumber: 3.1 Consensus size: 23
6516903 TACATAATAT
6516913 TTATTATATTATTTTATATTTTA
1 TTATTATATTATTTTATATTTTA
* *
6516936 TTATTATATTATTTTACACTTTA
1 TTATTATATTATTTTATATTTTA
* *
6516959 ATA-TATGTTA-TTTATATTATTA
1 TTATTATATTATTTTATATT-TTA
6516981 TTA
1 TTA
6516984 CATCATATTT
Statistics
Matches: 40, Mismatches: 7, Indels: 3
0.80 0.14 0.06
Matches are distributed among these distances:
21 6 0.15
22 11 0.28
23 23 0.57
ACGTcount: A:0.32, C:0.03, G:0.01, T:0.63
Consensus pattern (23 bp):
TTATTATATTATTTTATATTTTA
Found at i:6517549 original size:18 final size:18
Alignment explanation
Indices: 6517526--6517562 Score: 74
Period size: 18 Copynumber: 2.1 Consensus size: 18
6517516 TGTTGTTATG
6517526 TAACTAAGATTTGCTATA
1 TAACTAAGATTTGCTATA
6517544 TAACTAAGATTTGCTATA
1 TAACTAAGATTTGCTATA
6517562 T
1 T
6517563 TTATGTATGT
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:0.38, C:0.11, G:0.11, T:0.41
Consensus pattern (18 bp):
TAACTAAGATTTGCTATA
Found at i:6523977 original size:33 final size:33
Alignment explanation
Indices: 6523940--6524017 Score: 88
Period size: 33 Copynumber: 2.4 Consensus size: 33
6523930 TGGCCTTGCC
* *
6523940 ATGGTCTTACACTCGTAG-TGCCATAACCCAGTT
1 ATGGTCTTACACTC-AAGATGCCATAACCCAGCT
**
6523973 ATGGTCTTATCA-TCAAGATGCCATGGCCCAGCT
1 ATGGTCTTA-CACTCAAGATGCCATAACCCAGCT
6524006 ATGGTCTTACAC
1 ATGGTCTTACAC
6524018 GTATTCATAT
Statistics
Matches: 38, Mismatches: 4, Indels: 6
0.79 0.08 0.12
Matches are distributed among these distances:
32 4 0.11
33 32 0.84
34 2 0.05
ACGTcount: A:0.24, C:0.27, G:0.19, T:0.29
Consensus pattern (33 bp):
ATGGTCTTACACTCAAGATGCCATAACCCAGCT
Found at i:6527617 original size:30 final size:30
Alignment explanation
Indices: 6527581--6527640 Score: 111
Period size: 30 Copynumber: 2.0 Consensus size: 30
6527571 ATTCTAGAGA
6527581 TAGAGAACTTAACCCATGAACCCGTCTCGT
1 TAGAGAACTTAACCCATGAACCCGTCTCGT
*
6527611 TAGAGAACTTAACCTATGAACCCGTCTCGT
1 TAGAGAACTTAACCCATGAACCCGTCTCGT
6527641 GGGTTCTATA
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
30 29 1.00
ACGTcount: A:0.30, C:0.28, G:0.17, T:0.25
Consensus pattern (30 bp):
TAGAGAACTTAACCCATGAACCCGTCTCGT
Found at i:6531827 original size:13 final size:13
Alignment explanation
Indices: 6531809--6531844 Score: 51
Period size: 11 Copynumber: 3.0 Consensus size: 13
6531799 CTGCCCGCCC
6531809 ATATTAATTTTTT
1 ATATTAATTTTTT
6531822 ATATT-A-TTTTT
1 ATATTAATTTTTT
6531833 ATA-TAATTTTTT
1 ATATTAATTTTTT
6531845 TTAAAAAATA
Statistics
Matches: 21, Mismatches: 0, Indels: 5
0.81 0.00 0.19
Matches are distributed among these distances:
10 1 0.05
11 9 0.43
12 6 0.29
13 5 0.24
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (13 bp):
ATATTAATTTTTT
Found at i:6532093 original size:22 final size:23
Alignment explanation
Indices: 6532068--6532111 Score: 72
Period size: 22 Copynumber: 2.0 Consensus size: 23
6532058 AAATGGTAGC
*
6532068 AAAATAATGAAAAAA-CAACAAG
1 AAAATAATAAAAAAAGCAACAAG
6532090 AAAATAATAAAAAAAGCAACAA
1 AAAATAATAAAAAAAGCAACAA
6532112 TTTTTTTGTT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
22 14 0.70
23 6 0.30
ACGTcount: A:0.75, C:0.09, G:0.07, T:0.09
Consensus pattern (23 bp):
AAAATAATAAAAAAAGCAACAAG
Found at i:6532777 original size:73 final size:72
Alignment explanation
Indices: 6532619--6532780 Score: 234
Period size: 73 Copynumber: 2.2 Consensus size: 72
6532609 ATCTATACCC
* * *
6532619 TTCTCCCTCTTTTTCTTTCTCATGTCTGAAGCATCTTCTTATTTTCATTCTTCTTCCCATTTCCC
1 TTCTCCCTCTTTTTCATTCTCACGTCTGAAGCATCTTCTTATTTTCATTCTTCTACCCATTTCCC
*
6532684 TCCAACC
66 TCCAACA
* * *
6532691 TTCTCTCTCTTTTTCATTCTCACGTCTGAAGCATCTTCTTTTTTTTCATTCTTCTACCTATTTCC
1 TTCTCCCTCTTTTTCATTCTCACGTCTGAAGCATCTTC-TTATTTTCATTCTTCTACCCATTTCC
* *
6532756 TTCTAACA
65 CTCCAACA
6532764 TTCTCCCTCTTTTTCAT
1 TTCTCCCTCTTTTTCAT
6532781 GCTTCTATCC
Statistics
Matches: 79, Mismatches: 10, Indels: 1
0.88 0.11 0.01
Matches are distributed among these distances:
72 35 0.44
73 44 0.56
ACGTcount: A:0.13, C:0.32, G:0.04, T:0.51
Consensus pattern (72 bp):
TTCTCCCTCTTTTTCATTCTCACGTCTGAAGCATCTTCTTATTTTCATTCTTCTACCCATTTCCC
TCCAACA
Found at i:6535778 original size:33 final size:33
Alignment explanation
Indices: 6535739--6535805 Score: 116
Period size: 33 Copynumber: 2.0 Consensus size: 33
6535729 AACTCTTGTT
6535739 TCCATCATGGATGTTTGAACTTGATCAAATTGG
1 TCCATCATGGATGTTTGAACTTGATCAAATTGG
* *
6535772 TCCATCATGGATGTTTGGATTTGATCAAATTGG
1 TCCATCATGGATGTTTGAACTTGATCAAATTGG
6535805 T
1 T
6535806 TGGTTTAATC
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
33 32 1.00
ACGTcount: A:0.25, C:0.13, G:0.22, T:0.39
Consensus pattern (33 bp):
TCCATCATGGATGTTTGAACTTGATCAAATTGG
Found at i:6535884 original size:43 final size:43
Alignment explanation
Indices: 6535823--6535908 Score: 154
Period size: 43 Copynumber: 2.0 Consensus size: 43
6535813 ATCAGGAATT
6535823 GGTTGGGTATAAAGTTGGAAAAGACATCAAATTGGTTGCCTTA
1 GGTTGGGTATAAAGTTGGAAAAGACATCAAATTGGTTGCCTTA
* *
6535866 GGTTGGGTATCAAGTTGGAAAAGGCATCAAATTGGTTGCCTTA
1 GGTTGGGTATAAAGTTGGAAAAGACATCAAATTGGTTGCCTTA
6535909 TTGATTCGTA
Statistics
Matches: 41, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
43 41 1.00
ACGTcount: A:0.30, C:0.10, G:0.29, T:0.30
Consensus pattern (43 bp):
GGTTGGGTATAAAGTTGGAAAAGACATCAAATTGGTTGCCTTA
Found at i:6536337 original size:17 final size:17
Alignment explanation
Indices: 6536317--6536349 Score: 66
Period size: 17 Copynumber: 1.9 Consensus size: 17
6536307 ATTAAGAATG
6536317 TTATTAAATTATATTTT
1 TTATTAAATTATATTTT
6536334 TTATTAAATTATATTT
1 TTATTAAATTATATTT
6536350 AATAATAATT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (17 bp):
TTATTAAATTATATTTT
Found at i:6536616 original size:16 final size:16
Alignment explanation
Indices: 6536595--6536665 Score: 106
Period size: 16 Copynumber: 4.4 Consensus size: 16
6536585 TAAATTACTG
*
6536595 ATTACAGCTCTATTCC
1 ATTACAGCTCTATTCA
6536611 ATTACAGCTCTATTCA
1 ATTACAGCTCTATTCA
*
6536627 ATTATAGCTCTATTCA
1 ATTACAGCTCTATTCA
* *
6536643 ATTACATCCCTATTCA
1 ATTACAGCTCTATTCA
6536659 ATTACAG
1 ATTACAG
6536666 TGAACCAAAA
Statistics
Matches: 49, Mismatches: 6, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 49 1.00
ACGTcount: A:0.31, C:0.25, G:0.06, T:0.38
Consensus pattern (16 bp):
ATTACAGCTCTATTCA
Found at i:6537438 original size:8 final size:8
Alignment explanation
Indices: 6537425--6537451 Score: 54
Period size: 8 Copynumber: 3.4 Consensus size: 8
6537415 AAGTAGATAT
6537425 AATTTTTA
1 AATTTTTA
6537433 AATTTTTA
1 AATTTTTA
6537441 AATTTTTA
1 AATTTTTA
6537449 AAT
1 AAT
6537452 GTTATATGTT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 19 1.00
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (8 bp):
AATTTTTA
Found at i:6537569 original size:17 final size:19
Alignment explanation
Indices: 6537542--6537580 Score: 55
Period size: 18 Copynumber: 2.2 Consensus size: 19
6537532 TAAATAAAAA
*
6537542 TTTACTTTTAA-ATTATTT
1 TTTACTTTTAAGATAATTT
6537560 TTTA-TTTTAAGATAATTT
1 TTTACTTTTAAGATAATTT
6537578 TTT
1 TTT
6537581 TAATGAAACC
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
17 6 0.32
18 13 0.68
ACGTcount: A:0.28, C:0.03, G:0.03, T:0.67
Consensus pattern (19 bp):
TTTACTTTTAAGATAATTT
Found at i:6538173 original size:11 final size:11
Alignment explanation
Indices: 6538159--6538194 Score: 56
Period size: 11 Copynumber: 3.4 Consensus size: 11
6538149 TTTCTACGTT
6538159 TTTTGTTTTTG
1 TTTTGTTTTTG
6538170 TTTTG-TTTTG
1 TTTTGTTTTTG
*
6538180 TTTTTTTTTTG
1 TTTTGTTTTTG
6538191 TTTT
1 TTTT
6538195 TGGTAAATCT
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
10 9 0.39
11 14 0.61
ACGTcount: A:0.00, C:0.00, G:0.14, T:0.86
Consensus pattern (11 bp):
TTTTGTTTTTG
Found at i:6538178 original size:16 final size:16
Alignment explanation
Indices: 6538159--6538194 Score: 63
Period size: 16 Copynumber: 2.2 Consensus size: 16
6538149 TTTCTACGTT
6538159 TTTTGTTTTTGTTTTG
1 TTTTGTTTTTGTTTTG
*
6538175 TTTTGTTTTTTTTTTG
1 TTTTGTTTTTGTTTTG
6538191 TTTT
1 TTTT
6538195 TGGTAAATCT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
16 19 1.00
ACGTcount: A:0.00, C:0.00, G:0.14, T:0.86
Consensus pattern (16 bp):
TTTTGTTTTTGTTTTG
Found at i:6538453 original size:15 final size:15
Alignment explanation
Indices: 6538433--6538468 Score: 54
Period size: 15 Copynumber: 2.4 Consensus size: 15
6538423 TTTAATTCTT
*
6538433 TATAAATTATAAAAA
1 TATAAACTATAAAAA
6538448 TATAAACTATAAAAA
1 TATAAACTATAAAAA
*
6538463 TTTAAA
1 TATAAA
6538469 ATTTCATCCC
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
15 19 1.00
ACGTcount: A:0.64, C:0.03, G:0.00, T:0.33
Consensus pattern (15 bp):
TATAAACTATAAAAA
Found at i:6548409 original size:10 final size:9
Alignment explanation
Indices: 6548362--6548576 Score: 80
Period size: 10 Copynumber: 22.7 Consensus size: 9
6548352 ATTTGACAAA
*
6548362 AAAAATGAT
1 AAAAATTAT
6548371 AAAAA-T-T
1 AAAAATTAT
*
6548378 AAAAATCAAT
1 AAAAAT-TAT
**
6548388 AAAGGTTAT
1 AAAAATTAT
6548397 AAAAATTATT
1 AAAAATTA-T
**
6548407 AAATTTTAAT
1 AAAAATT-AT
6548417 AATAAAATATAT
1 -A-AAAAT-TAT
6548429 AAAATATT-T
1 AAAA-ATTAT
*
6548438 AAAACTTACT
1 AAAAATTA-T
*
6548448 AAAAATTAG
1 AAAAATTAT
*
6548457 AAAAAATAT
1 AAAAATTAT
*
6548466 AAAAATCAT
1 AAAAATTAT
*
6548475 AAAAAATTGT
1 -AAAAATTAT
*
6548485 AAAATTTTAT
1 AAAA-ATTAT
*
6548495 AAAAATCAT
1 AAAAATTAT
6548504 AAAATATTAT
1 AAAA-ATTAT
6548514 -AAAATATAT
1 AAAAAT-TAT
* *
6548523 AGAAATGTAG
1 AAAAAT-TAT
*
6548533 AAAAAATAT
1 AAAAATTAT
*
6548542 -AAAATTTT
1 AAAAATTAT
* *
6548550 ATAAAGTCAT
1 A-AAAATTAT
6548560 AAGAAAATTAT
1 -A-AAAATTAT
6548571 AAAAAT
1 AAAAAT
6548577 ATGTAAAGAA
Statistics
Matches: 148, Mismatches: 39, Indels: 38
0.66 0.17 0.17
Matches are distributed among these distances:
7 6 0.04
8 10 0.07
9 56 0.38
10 58 0.39
11 12 0.08
12 5 0.03
13 1 0.01
ACGTcount: A:0.61, C:0.03, G:0.05, T:0.31
Consensus pattern (9 bp):
AAAAATTAT
Found at i:6548470 original size:19 final size:19
Alignment explanation
Indices: 6548448--6548545 Score: 58
Period size: 19 Copynumber: 5.2 Consensus size: 19
6548438 AAAACTTACT
6548448 AAAAATTAGAAAAAATAT-
1 AAAAATTAGAAAAAATATA
* * *
6548466 AAAAATCATAAAAAATTGTA
1 AAAAATTAGAAAAAA-TATA
** *
6548486 AAATTTTA-TAAAAATCATA
1 AAAAATTAGAAAAAAT-ATA
* * *
6548505 AAATATTATAAAATATAT-
1 AAAAATTAGAAAAAATATA
*
6548523 AGAAATGTAGAAAAAATATA
1 AAAAAT-TAGAAAAAATATA
6548543 AAA
1 AAA
6548546 TTTTATAAAG
Statistics
Matches: 58, Mismatches: 16, Indels: 10
0.69 0.19 0.12
Matches are distributed among these distances:
18 18 0.31
19 28 0.48
20 12 0.21
ACGTcount: A:0.65, C:0.02, G:0.05, T:0.28
Consensus pattern (19 bp):
AAAAATTAGAAAAAATATA
Found at i:6548480 original size:29 final size:29
Alignment explanation
Indices: 6548448--6548528 Score: 87
Period size: 29 Copynumber: 2.9 Consensus size: 29
6548438 AAAACTTACT
6548448 AAAAATTAG-AAAA-AATATAAAAATCATA
1 AAAAATT-GTAAAATAATATAAAAATCATA
**
6548476 AAAAATTGTAAAATTTTATAAAAATCATA
1 AAAAATTGTAAAATAATATAAAAATCATA
* * *
6548505 AAATATTATAAAAT-ATATAGAAAT
1 AAAAATTGTAAAATAATATAAAAAT
6548529 GTAGAAAAAA
Statistics
Matches: 45, Mismatches: 6, Indels: 4
0.82 0.11 0.07
Matches are distributed among these distances:
27 1 0.02
28 19 0.42
29 25 0.56
ACGTcount: A:0.64, C:0.02, G:0.04, T:0.30
Consensus pattern (29 bp):
AAAAATTGTAAAATAATATAAAAATCATA
Found at i:6548571 original size:29 final size:28
Alignment explanation
Indices: 6548471--6548574 Score: 104
Period size: 29 Copynumber: 3.6 Consensus size: 28
6548461 AATATAAAAA
* *
6548471 TCATAAAAAATTGTAAAATTTTATAAAAA
1 TCATAAAAAATTATAAAATTTTAT-AAAG
* * *
6548500 TCATAAAATATTATAAAATATATAGAAATG
1 TCATAAAAAATTATAAAAT-TTTATAAA-G
*
6548530 T-AGAAAAAA-TATAAAATTTTATAAAG
1 TCATAAAAAATTATAAAATTTTATAAAG
6548556 TCATAAGAAAATTATAAAA
1 TCATAA-AAAATTATAAAA
6548575 ATATGTAAAG
Statistics
Matches: 60, Mismatches: 10, Indels: 10
0.75 0.12 0.12
Matches are distributed among these distances:
26 2 0.03
27 9 0.15
28 12 0.20
29 33 0.55
30 4 0.07
ACGTcount: A:0.60, C:0.03, G:0.06, T:0.32
Consensus pattern (28 bp):
TCATAAAAAATTATAAAATTTTATAAAG
Found at i:6548575 original size:38 final size:39
Alignment explanation
Indices: 6548418--6548575 Score: 113
Period size: 38 Copynumber: 4.2 Consensus size: 39
6548408 AATTTTAATA
*
6548418 ATAAAATAT-ATAAAATATT-TAAAACT-TACTA-AAAATT
1 ATAAAAAATCATAAAATATTATAAAA-TATA-TAGAAAATT
* * *
6548455 AGAAAAAAT-ATAAAA-ATCATAAAA-A-ATTGTAAAATT
1 ATAAAAAATCATAAAATATTATAAAATATATAG-AAAATT
*
6548491 TTATAAAAATCATAAAATATTATAAAATATATAG-AAATGT
1 ATA-AAAAATCATAAAATATTATAAAATATATAGAAAAT-T
* * *
6548531 AGAAAAAAT-ATAAAATTTTATAAAGTCATA-AGAAAATT
1 ATAAAAAATCATAAAATATTATAAAAT-ATATAGAAAATT
6548569 ATAAAAA
1 ATAAAAA
6548576 TATGTAAAGA
Statistics
Matches: 96, Mismatches: 13, Indels: 23
0.73 0.10 0.17
Matches are distributed among these distances:
34 1 0.01
35 1 0.01
36 9 0.09
37 24 0.25
38 30 0.31
39 25 0.26
40 3 0.03
41 3 0.03
ACGTcount: A:0.62, C:0.03, G:0.04, T:0.30
Consensus pattern (39 bp):
ATAAAAAATCATAAAATATTATAAAATATATAGAAAATT
Found at i:6548608 original size:20 final size:21
Alignment explanation
Indices: 6548560--6548617 Score: 59
Period size: 19 Copynumber: 2.8 Consensus size: 21
6548550 ATAAAGTCAT
6548560 AAGAAAATTATAAAAATATGTA
1 AAGAAAA-TATAAAAATATGTA
6548582 AAG-AAATAT-AAAAT-TCGTA
1 AAGAAAATATAAAAATAT-GTA
*
6548601 AAGAAAATTACAAAAAT
1 AAGAAAA-TATAAAAAT
6548618 TATCGTACCA
Statistics
Matches: 31, Mismatches: 1, Indels: 8
0.77 0.03 0.20
Matches are distributed among these distances:
18 1 0.03
19 11 0.35
20 6 0.19
21 5 0.16
22 8 0.26
ACGTcount: A:0.64, C:0.03, G:0.09, T:0.24
Consensus pattern (21 bp):
AAGAAAATATAAAAATATGTA
Found at i:6551377 original size:244 final size:247
Alignment explanation
Indices: 6550876--6551483 Score: 836
Period size: 244 Copynumber: 2.5 Consensus size: 247
6550866 ATTGTCAGAA
* * * * *
6550876 ATTGCTCAAGGTAAT-GATGATCCAAGATGAATGCCCT-TTCGTTTACCACTGCCTGCCATATAG
1 ATTGCTCAAGG--ATGGA-GATCCAAGATGAATGCACTATTGGCTT-CAATTGCCTGCCATATAG
* *
6550939 TGTTGTGTATGTATTCATAAAGTAGTTAATTTGAAAGGAAAAGAAATACATAAATTTGTTTTTCT
62 TGTTATGTATGTATTCATAAAGTAGTTAATTTGAAAGGAAAAGAAATACATAAACTTGTTTTTCT
* * * * *
6551004 TTTTTACCAAATACACATCTAGCAATTGCGGCTGTTTATGCTTCTTTCCCTGTAGAACCTGCAAC
127 TTTTTACCAAATACAAATCTAGCAATTGCGACTGTTAATGCTTATTTCCCAGTAGAACCTGCAAC
**
6551069 GTTTAAAATACTGGATTGTAAGCTCAAACATTATATGTTATAAACCTAGGAAAGAG
192 GTTTAAAATACTGGATCCTAAGCTCAAACATTATATGTTATAAACCTAGGAAAGAG
* *
6551125 ATTGCTCAAGG-T-GTGATCCAAGATGAATGCAGTATTGGCTTCAATTGCCTGCCATATAGTGTT
1 ATTGCTCAAGGATGGAGATCCAAGATGAATGCACTATTGGCTTCAATTGCCTGCCATATAGTGTT
6551188 ATGTATGTATTCATAAAGTAGTTAATTTGAAAGGAAAAGAAATACATAAACTTG-TTTTCTTTTT
66 ATGTATGTATTCATAAAGTAGTTAATTTGAAAGGAAAAGAAATACATAAACTTGTTTTTCTTTTT
*** * * *
6551252 TACCTTTTTCAAATTTTGCAATTGCGACTGGTTAAT-CTTATTGT-CCAGCT-GAACCTGCAACG
131 TACCAAATACAAATCTAGCAATTGCGACT-GTTAATGCTTATT-TCCCAG-TAGAACCTGCAACG
*
6551314 TTTAAAATATTGGATCCTAAGCTCAAACATTATATGTTATAAACCTAGGAAAGAG
193 TTTAAAATACTGGATCCTAAGCTCAAACATTATATGTTATAAACCTAGGAAAGAG
* * *
6551369 ATTGCTCAAGGTAATGGAGATCCAAGATGAATGCCCTATTGGCTTCCATTGGCTGCCATATAGTG
1 ATTGCTCAAGG--ATGGAGATCCAAGATGAATGCACTATTGGCTTCAATTGCCTGCCATATAGTG
*
6551434 TTATGTATGTATTCATAAAGTAGTTAATTTGAAAGGAAAAGAGATACATA
64 TTATGTATGTATTCATAAAGTAGTTAATTTGAAAGGAAAAGAAATACATA
6551484 TCTCTGCAAA
Statistics
Matches: 322, Mismatches: 29, Indels: 17
0.88 0.08 0.05
Matches are distributed among these distances:
244 114 0.35
245 96 0.30
246 7 0.02
247 1 0.00
248 93 0.29
249 11 0.03
ACGTcount: A:0.33, C:0.15, G:0.18, T:0.34
Consensus pattern (247 bp):
ATTGCTCAAGGATGGAGATCCAAGATGAATGCACTATTGGCTTCAATTGCCTGCCATATAGTGTT
ATGTATGTATTCATAAAGTAGTTAATTTGAAAGGAAAAGAAATACATAAACTTGTTTTTCTTTTT
TACCAAATACAAATCTAGCAATTGCGACTGTTAATGCTTATTTCCCAGTAGAACCTGCAACGTTT
AAAATACTGGATCCTAAGCTCAAACATTATATGTTATAAACCTAGGAAAGAG
Found at i:6556287 original size:239 final size:239
Alignment explanation
Indices: 6555868--6556483 Score: 1124
Period size: 239 Copynumber: 2.6 Consensus size: 239
6555858 GTATTATGTA
*
6555868 ATCCGTCACCGGAACAGGGTTACAAGATGTTACCGATGTTTACGGAATAGTTACACAAAATTCCA
1 ATCCGTCACCGGAACAGGGTTACAAGATGTTACCGATGTTTACGGAATAATTACACAAAATTCCA
* *
6555933 TTATTTACTTATATTCACATCAAAGCTGTCCACTCGAATCATAGTCACTAAATTATTAATATCTT
66 TTAATTACTTATATTCACATCAAAGCTGTCCACTCGAGTCATAGTCACTAAATTATTAATATCTT
6555998 GAGCTACTGATGCACAAGGATGTACATATCATAGCAACAAAAGGCATCACAGGTCAGAGGATAGT
131 GAGCTACTGATGCACAAGGATGTACATATCATAGCAACAAAAGGCATCACAGGTCAGAGGATAGT
*
6556063 AACAACCAGTTTTGCATACGTATTATGTAACACCTCTAACCCAC
196 AACAACCAGTTTTACATACGTATTATGTAACACCTCTAACCCAC
*
6556107 ATCCGTCACCGGAACAGGGTTACAAGATGTTATCGATGTTTACGGAATAATTACACAAAATTCCA
1 ATCCGTCACCGGAACAGGGTTACAAGATGTTACCGATGTTTACGGAATAATTACACAAAATTCCA
6556172 TTAATTACTTATATTCACATCAAAGCTGTCCACTCGAGTCATAGTCACTAAATTATTAATATCTT
66 TTAATTACTTATATTCACATCAAAGCTGTCCACTCGAGTCATAGTCACTAAATTATTAATATCTT
*
6556237 GAGCTACTGATGCACAAGGATGTACATATCATAGCAACAAAAGGCATCACAGTTCAGAGGATAGT
131 GAGCTACTGATGCACAAGGATGTACATATCATAGCAACAAAAGGCATCACAGGTCAGAGGATAGT
*
6556302 AACAACCGGTTTTACATACGTATTATGTAACACCTCTAACCCAC
196 AACAACCAGTTTTACATACGTATTATGTAACACCTCTAACCCAC
* *
6556346 ATCCGTCACCGGAACAGGGTTACAAGTTGTTACCGAAGTTTACGGAATAATTACACAAAAATTCC
1 ATCCGTCACCGGAACAGGGTTACAAGATGTTACCGATGTTTACGGAATAATTACAC-AAAATTCC
* *
6556411 ATTAATTACTTATATTCACATCAAAACTGTCCACTCGAGTCATACTCACTAAATTATTAATATCT
65 ATTAATTACTTATATTCACATCAAAGCTGTCCACTCGAGTCATAGTCACTAAATTATTAATATCT
6556476 TGAGCTAC
130 TGAGCTAC
6556484 GGAACTCAAA
Statistics
Matches: 364, Mismatches: 12, Indels: 1
0.97 0.03 0.00
Matches are distributed among these distances:
239 285 0.78
240 79 0.22
ACGTcount: A:0.35, C:0.22, G:0.15, T:0.28
Consensus pattern (239 bp):
ATCCGTCACCGGAACAGGGTTACAAGATGTTACCGATGTTTACGGAATAATTACACAAAATTCCA
TTAATTACTTATATTCACATCAAAGCTGTCCACTCGAGTCATAGTCACTAAATTATTAATATCTT
GAGCTACTGATGCACAAGGATGTACATATCATAGCAACAAAAGGCATCACAGGTCAGAGGATAGT
AACAACCAGTTTTACATACGTATTATGTAACACCTCTAACCCAC
Found at i:6557555 original size:35 final size:35
Alignment explanation
Indices: 6557438--6557596 Score: 159
Period size: 35 Copynumber: 4.7 Consensus size: 35
6557428 TCCTCATTGA
* * * *
6557438 AATATCATACCTACATTTTACAACTCGGTATGGAA
1 AATACCATACCTACATTTCACAACTCAGTATGGAT
* * **
6557473 AATGCCATACCTACGTTTCTTAACTCAGTATGGAT
1 AATACCATACCTACATTTCACAACTCAGTATGGAT
* *
6557508 AATA-C---CGT--ATTTCACAACTCAGTATGGTT
1 AATACCATACCTACATTTCACAACTCAGTATGGAT
*
6557537 AATACCATACCTACATTTCACAATTCAGTATGGAT
1 AATACCATACCTACATTTCACAACTCAGTATGGAT
* *
6557572 GATACCATACCTACGTTTCACAACT
1 AATACCATACCTACATTTCACAACT
6557597 TTGCCATGGA
Statistics
Matches: 98, Mismatches: 20, Indels: 12
0.75 0.15 0.09
Matches are distributed among these distances:
29 21 0.21
30 1 0.01
31 2 0.02
33 2 0.02
34 1 0.01
35 71 0.72
ACGTcount: A:0.33, C:0.23, G:0.11, T:0.32
Consensus pattern (35 bp):
AATACCATACCTACATTTCACAACTCAGTATGGAT
Found at i:6557565 original size:64 final size:64
Alignment explanation
Indices: 6557452--6557577 Score: 162
Period size: 64 Copynumber: 2.0 Consensus size: 64
6557442 TCATACCTAC
* * * * **
6557452 ATTTTACAACTCGGTATGGAAAATGCCATACCTACGTTTCTTAACTCAGTATGGATAATACCGT
1 ATTTCACAACTCAGTATGGAAAATACCATACCTACATTTCACAACTCAGTATGGATAATACCGT
** * *
6557516 ATTTCACAACTCAGTATGGTTAATACCATACCTACATTTCACAATTCAGTATGGATGATACC
1 ATTTCACAACTCAGTATGGAAAATACCATACCTACATTTCACAACTCAGTATGGATAATACC
6557578 ATACCTACGT
Statistics
Matches: 52, Mismatches: 10, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
64 52 1.00
ACGTcount: A:0.33, C:0.21, G:0.13, T:0.33
Consensus pattern (64 bp):
ATTTCACAACTCAGTATGGAAAATACCATACCTACATTTCACAACTCAGTATGGATAATACCGT
Found at i:6560758 original size:42 final size:42
Alignment explanation
Indices: 6560672--6560768 Score: 103
Period size: 42 Copynumber: 2.3 Consensus size: 42
6560662 AGTTAACTCA
*
6560672 TATGAG-TTTTAGTTTAACCCTATTAGGTTTCCATCCAGCTCT
1 TATGAGCTTTT-GTTTAACCCTATTAGGTTTCCATCCAGCACT
**
6560714 TATGAGCTTTTGTTTAA-CCT-TTACGGGTTTCCATTTAGCACT
1 TATGAGCTTTTGTTTAACCCTATTA--GGTTTCCATCCAGCACT
6560756 TATGTA-CTTTTGT
1 TATG-AGCTTTTGT
6560769 GCAGCCTTTG
Statistics
Matches: 48, Mismatches: 3, Indels: 8
0.81 0.05 0.14
Matches are distributed among these distances:
40 3 0.06
41 3 0.06
42 37 0.77
43 5 0.10
ACGTcount: A:0.20, C:0.19, G:0.15, T:0.46
Consensus pattern (42 bp):
TATGAGCTTTTGTTTAACCCTATTAGGTTTCCATCCAGCACT
Found at i:6563720 original size:17 final size:18
Alignment explanation
Indices: 6563698--6563731 Score: 61
Period size: 17 Copynumber: 1.9 Consensus size: 18
6563688 ATTCAAATTG
6563698 AAATTGCG-AAATTAAAT
1 AAATTGCGAAAATTAAAT
6563715 AAATTGCGAAAATTAAA
1 AAATTGCGAAAATTAAA
6563732 ATGGAGAATA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 8 0.50
18 8 0.50
ACGTcount: A:0.56, C:0.06, G:0.12, T:0.26
Consensus pattern (18 bp):
AAATTGCGAAAATTAAAT
Found at i:6565647 original size:46 final size:45
Alignment explanation
Indices: 6565597--6565772 Score: 144
Period size: 46 Copynumber: 3.8 Consensus size: 45
6565587 TGATTGAGCA
6565597 TCCGAACTCATTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
1 TCCGAACTCATTGAGTTGAGTCCGAGTTCACTTATGGATG-GAATG
* * * * *
6565643 TCCGAACTCGTTGAGTTGAGTCCGAGTTC-GTGA--AATGTAACTAGG
1 TCCGAACTCATTGAGTTGAGTCCGAGTTCACTTATGGATGGAA-T--G
* * * *
6565688 CATCCGAACTCGTTGAGTTGAGTCTGAGTTCACCTATGGATGTGAACG
1 --TCCGAACTCATTGAGTTGAGTCCGAGTTCACTTATGGATG-GAATG
* * *
6565736 -CCCAAGCTCATTGAATTGAGTCCGAGTTCGCTTATGG
1 TCCGAA-CTCATTGAGTTGAGTCCGAGTTCACTTATGG
6565773 GCGGGTTACA
Statistics
Matches: 102, Mismatches: 18, Indels: 20
0.73 0.13 0.14
Matches are distributed among these distances:
42 2 0.02
43 4 0.04
45 7 0.07
46 54 0.53
47 28 0.27
48 2 0.02
50 3 0.03
51 2 0.02
ACGTcount: A:0.23, C:0.20, G:0.27, T:0.30
Consensus pattern (45 bp):
TCCGAACTCATTGAGTTGAGTCCGAGTTCACTTATGGATGGAATG
Found at i:6565755 original size:93 final size:93
Alignment explanation
Indices: 6565594--6565765 Score: 256
Period size: 93 Copynumber: 1.8 Consensus size: 93
6565584 GGATGATTGA
* * * * *
6565594 GCATCCGAACTCATTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATGTCCGAACTCGTTGAGT
1 GCATCCGAACTCATTGAGTTGAGTCCGAGTTCACCTATGGATGCGAACGTCCCAACTCATTGAAT
6565659 TGAGTCCGAGTTCGTGAAATGTAACTAG
66 TGAGTCCGAGTTCGTGAAATGTAACTAG
* * *
6565687 GCATCCGAACTCGTTGAGTTGAGTCTGAGTTCACCTATGGATGTGAACG-CCCAAGCTCATTGAA
1 GCATCCGAACTCATTGAGTTGAGTCCGAGTTCACCTATGGATGCGAACGTCCCAA-CTCATTGAA
6565751 TTGAGTCCGAGTTCG
65 TTGAGTCCGAGTTCG
6565766 CTTATGGGCG
Statistics
Matches: 70, Mismatches: 8, Indels: 2
0.88 0.10 0.03
Matches are distributed among these distances:
92 4 0.06
93 66 0.94
ACGTcount: A:0.24, C:0.21, G:0.27, T:0.28
Consensus pattern (93 bp):
GCATCCGAACTCATTGAGTTGAGTCCGAGTTCACCTATGGATGCGAACGTCCCAACTCATTGAAT
TGAGTCCGAGTTCGTGAAATGTAACTAG
Found at i:6566702 original size:10 final size:10
Alignment explanation
Indices: 6566687--6566732 Score: 60
Period size: 10 Copynumber: 4.6 Consensus size: 10
6566677 ATAGTAAAAT
6566687 ATAAATACAA-
1 ATAAATA-AAG
6566697 ATAAATAAAG
1 ATAAATAAAG
6566707 ATAAATAAAG
1 ATAAATAAAG
6566717 ATAAATGAAA-
1 ATAAAT-AAAG
6566727 ATAAAT
1 ATAAAT
6566733 CTTAAAATTA
Statistics
Matches: 34, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
9 2 0.06
10 29 0.85
11 3 0.09
ACGTcount: A:0.70, C:0.02, G:0.07, T:0.22
Consensus pattern (10 bp):
ATAAATAAAG
Found at i:6567523 original size:96 final size:96
Alignment explanation
Indices: 6567394--6567583 Score: 283
Period size: 96 Copynumber: 2.0 Consensus size: 96
6567384 TTTAAATTTA
* * * *
6567394 TTTATTTTTACTTAGGAATATATTGAACCTTTTGACGCGAAGAGAGATGACAGTCAAACACCTCA
1 TTTATTTTTACTTAAGAACATATCGAACCTTTTGACGCGAAGAGAGATGACAGCCAAACACCTCA
*
6567459 CCCCGATTACTCAGCCTAACACACTCTTAATT
66 -CCCGATTACTCAGCCCAACACACTCTTAATT
*
6567491 TTTATTTTT-CTTAAGAACATATCGAACCTTTTGACGTGAAGAGAGATGACAGCCAAACACCTCA
1 TTTATTTTTACTTAAGAACATATCGAACCTTTTGACGCGAAGAGAGATGACAGCCAAACACCTCA
* * *
6567555 CCCGGTTACTCAGCCCAACATATTCTTAA
66 CCCGATTACTCAGCCCAACACACTCTTAA
6567584 AAATTAATTC
Statistics
Matches: 84, Mismatches: 9, Indels: 2
0.88 0.09 0.02
Matches are distributed among these distances:
95 25 0.30
96 50 0.60
97 9 0.11
ACGTcount: A:0.32, C:0.24, G:0.14, T:0.30
Consensus pattern (96 bp):
TTTATTTTTACTTAAGAACATATCGAACCTTTTGACGCGAAGAGAGATGACAGCCAAACACCTCA
CCCGATTACTCAGCCCAACACACTCTTAATT
Found at i:6568241 original size:18 final size:18
Alignment explanation
Indices: 6568218--6568320 Score: 71
Period size: 18 Copynumber: 5.4 Consensus size: 18
6568208 ACATCGTGAT
6568218 CTGAAGCCCGAAGTCTAA
1 CTGAAGCCCGAAGTCTAA
** *
6568236 CTGAAGCACATAAATGCTAAA
1 CTGAAGC-CCGAAGT-CT-AA
* *
6568257 CGGAAGCCCGAAGGCTAA
1 CTGAAGCCCGAAGTCTAA
**
6568275 CTGAAGCACATAAGTGCTAAA
1 CTGAAGC-CCGAAGT-CT-AA
* *
6568296 CGGAAGCCCGAAGGCTAA
1 CTGAAGCCCGAAGTCTAA
6568314 CTGAAGC
1 CTGAAGC
6568321 TCACCAGAGC
Statistics
Matches: 62, Mismatches: 17, Indels: 12
0.68 0.19 0.13
Matches are distributed among these distances:
18 23 0.37
19 12 0.19
20 11 0.18
21 16 0.26
ACGTcount: A:0.38, C:0.24, G:0.24, T:0.14
Consensus pattern (18 bp):
CTGAAGCCCGAAGTCTAA
Found at i:6568262 original size:21 final size:21
Alignment explanation
Indices: 6568238--6568302 Score: 64
Period size: 21 Copynumber: 3.2 Consensus size: 21
6568228 AAGTCTAACT
6568238 GAAGCACATAAATGCTAAACG
1 GAAGCACATAAATGCTAAACG
** * *
6568259 GAAGC-C-CGAAGGCT-AACT
1 GAAGCACATAAATGCTAAACG
*
6568277 GAAGCACATAAGTGCTAAACG
1 GAAGCACATAAATGCTAAACG
6568298 GAAGC
1 GAAGC
6568303 CCGAAGGCTA
Statistics
Matches: 32, Mismatches: 9, Indels: 6
0.68 0.19 0.13
Matches are distributed among these distances:
18 8 0.25
19 6 0.19
20 5 0.16
21 13 0.41
ACGTcount: A:0.42, C:0.22, G:0.25, T:0.12
Consensus pattern (21 bp):
GAAGCACATAAATGCTAAACG
Found at i:6568275 original size:39 final size:39
Alignment explanation
Indices: 6568220--6568320 Score: 184
Period size: 39 Copynumber: 2.6 Consensus size: 39
6568210 ATCGTGATCT
*
6568220 GAAGCCCGAAGTCTAACTGAAGCACATAAATGCTAAACG
1 GAAGCCCGAAGGCTAACTGAAGCACATAAATGCTAAACG
*
6568259 GAAGCCCGAAGGCTAACTGAAGCACATAAGTGCTAAACG
1 GAAGCCCGAAGGCTAACTGAAGCACATAAATGCTAAACG
6568298 GAAGCCCGAAGGCTAACTGAAGC
1 GAAGCCCGAAGGCTAACTGAAGC
6568321 TCACCAGAGC
Statistics
Matches: 60, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
39 60 1.00
ACGTcount: A:0.39, C:0.24, G:0.25, T:0.13
Consensus pattern (39 bp):
GAAGCCCGAAGGCTAACTGAAGCACATAAATGCTAAACG
Found at i:6568762 original size:21 final size:22
Alignment explanation
Indices: 6568722--6568762 Score: 57
Period size: 21 Copynumber: 1.9 Consensus size: 22
6568712 TTCCAAATAA
* *
6568722 AACATTATATCGTTTCTAATTC
1 AACATTATATCGATTATAATTC
6568744 AACATT-TATCGATTATAAT
1 AACATTATATCGATTATAAT
6568763 CGGGCATGTG
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 11 0.65
22 6 0.35
ACGTcount: A:0.37, C:0.15, G:0.05, T:0.44
Consensus pattern (22 bp):
AACATTATATCGATTATAATTC
Found at i:6571583 original size:5 final size:5
Alignment explanation
Indices: 6571573--6571681 Score: 82
Period size: 5 Copynumber: 21.6 Consensus size: 5
6571563 TTAATATCCA
* * *
6571573 AAAAT AAAAT AATAA- ATAAT AAAAT AAAGT AAAAT AAAAT AAAAAT ACTAAT
1 AAAAT AAAAT AA-AAT AAAAT AAAAT AAAAT AAAAT AAAAT -AAAAT A-AAAT
* * * *
6571625 AAAAT AAAAT GAAAT AAAAT AATAA- ACAAT AAAATT AAGA- AAAGT AAAA-
1 AAAAT AAAAT AAAAT AAAAT AA-AAT AAAAT AAAA-T AAAAT AAAAT AAAAT
6571674 AAAAT AAA
1 AAAAT AAA
6571682 GGTTGGGTTG
Statistics
Matches: 81, Mismatches: 14, Indels: 18
0.72 0.12 0.16
Matches are distributed among these distances:
4 10 0.12
5 54 0.67
6 17 0.21
ACGTcount: A:0.74, C:0.02, G:0.04, T:0.20
Consensus pattern (5 bp):
AAAAT
Found at i:6571625 original size:27 final size:28
Alignment explanation
Indices: 6571573--6571650 Score: 97
Period size: 27 Copynumber: 2.8 Consensus size: 28
6571563 TTAATATCCA
*
6571573 AAAATAAAATAATAAATAATAAAATAAAGT
1 AAAATAAAATAA-AAATAAT-AAATAAAAT
*
6571603 AAAATAAAATAAAAATACT-AATAAAAT
1 AAAATAAAATAAAAATAATAAATAAAAT
*
6571630 AAAATGAAAT-AAAATAATAAA
1 AAAATAAAATAAAAATAATAAA
6571651 CAATAAAATT
Statistics
Matches: 43, Mismatches: 4, Indels: 5
0.83 0.08 0.10
Matches are distributed among these distances:
26 7 0.16
27 18 0.42
29 6 0.14
30 12 0.28
ACGTcount: A:0.74, C:0.01, G:0.03, T:0.22
Consensus pattern (28 bp):
AAAATAAAATAAAAATAATAAATAAAAT
Found at i:6574683 original size:17 final size:18
Alignment explanation
Indices: 6574661--6574694 Score: 61
Period size: 17 Copynumber: 1.9 Consensus size: 18
6574651 AGTCAAATTG
6574661 AAATTGCG-AAATTAAAT
1 AAATTGCGAAAATTAAAT
6574678 AAATTGCGAAAATTAAA
1 AAATTGCGAAAATTAAA
6574695 ATGGAGAATA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 8 0.50
18 8 0.50
ACGTcount: A:0.56, C:0.06, G:0.12, T:0.26
Consensus pattern (18 bp):
AAATTGCGAAAATTAAAT
Found at i:6575427 original size:10 final size:10
Alignment explanation
Indices: 6575408--6575457 Score: 68
Period size: 10 Copynumber: 5.0 Consensus size: 10
6575398 TTAAATACTA
6575408 AAAGATAAAT
1 AAAGATAAAT
6575418 ACAA-ATAAAT
1 A-AAGATAAAT
6575428 AAAGATAAAT
1 AAAGATAAAT
6575438 AAAGATAAAT
1 AAAGATAAAT
6575448 GAAA-ATAAAT
1 -AAAGATAAAT
6575458 CCTAAAATTA
Statistics
Matches: 37, Mismatches: 0, Indels: 6
0.86 0.00 0.14
Matches are distributed among these distances:
9 2 0.05
10 30 0.81
11 5 0.14
ACGTcount: A:0.70, C:0.02, G:0.08, T:0.20
Consensus pattern (10 bp):
AAAGATAAAT
Found at i:6577073 original size:12 final size:12
Alignment explanation
Indices: 6577056--6577087 Score: 50
Period size: 11 Copynumber: 2.8 Consensus size: 12
6577046 CAGCCTGCTC
6577056 ATATTAATTTTT
1 ATATTAATTTTT
6577068 ATATT-ATTTTT
1 ATATTAATTTTT
6577079 ATA-TAATTT
1 ATATTAATTT
6577088 AAAAAATATA
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
10 1 0.05
11 13 0.68
12 5 0.26
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (12 bp):
ATATTAATTTTT
Found at i:6577338 original size:11 final size:10
Alignment explanation
Indices: 6577308--6577373 Score: 53
Period size: 10 Copynumber: 6.6 Consensus size: 10
6577298 TGTGAAATGG
*
6577308 TAGCAAAATA
1 TAGCAAAAAA
* *
6577318 GAGAAAAAAA
1 TAGCAAAAAA
6577328 TAGCAAGAAAA
1 TAGCAA-AAAA
**
6577339 TAATAAAAAA
1 TAGCAAAAAA
6577349 TAGCAAAAAA
1 TAGCAAAAAA
* *
6577359 AAGTAAAAAA
1 TAGCAAAAAA
6577369 -AGCAA
1 TAGCAA
6577374 CAATTTTTTT
Statistics
Matches: 43, Mismatches: 12, Indels: 3
0.74 0.21 0.05
Matches are distributed among these distances:
9 4 0.09
10 31 0.72
11 8 0.19
ACGTcount: A:0.71, C:0.06, G:0.12, T:0.11
Consensus pattern (10 bp):
TAGCAAAAAA
Found at i:6577348 original size:21 final size:20
Alignment explanation
Indices: 6577308--6577373 Score: 73
Period size: 20 Copynumber: 3.3 Consensus size: 20
6577298 TGTGAAATGG
* * *
6577308 TAGCAAAATAGAGAAAAAAA
1 TAGCAAAAAAAAGTAAAAAA
6577328 TAGCAAGAAAATAA-TAAAAAA
1 TAGCAA-AAAA-AAGTAAAAAA
6577349 TAGCAAAAAAAAGTAAAAAA
1 TAGCAAAAAAAAGTAAAAAA
6577369 -AGCAA
1 TAGCAA
6577374 CAATTTTTTT
Statistics
Matches: 40, Mismatches: 3, Indels: 7
0.80 0.06 0.14
Matches are distributed among these distances:
19 7 0.17
20 17 0.43
21 15 0.38
22 1 0.03
ACGTcount: A:0.71, C:0.06, G:0.12, T:0.11
Consensus pattern (20 bp):
TAGCAAAAAAAAGTAAAAAA
Found at i:6578502 original size:17 final size:19
Alignment explanation
Indices: 6578475--6578513 Score: 55
Period size: 18 Copynumber: 2.2 Consensus size: 19
6578465 TAAATAAAAA
*
6578475 TTTACTTTTAA-ATTATTT
1 TTTACTTTTAAGATAATTT
6578493 TTTA-TTTTAAGATAATTT
1 TTTACTTTTAAGATAATTT
6578511 TTT
1 TTT
6578514 TAATGAAACC
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
17 6 0.32
18 13 0.68
ACGTcount: A:0.28, C:0.03, G:0.03, T:0.67
Consensus pattern (19 bp):
TTTACTTTTAAGATAATTT
Found at i:6578762 original size:18 final size:17
Alignment explanation
Indices: 6578700--6578765 Score: 59
Period size: 17 Copynumber: 3.9 Consensus size: 17
6578690 CAAATAAAAT
6578700 AAATAGATATTTAAA--A
1 AAATAGA-ATTTAAATTA
6578716 AAATTA-AATTTAAATTA
1 AAA-TAGAATTTAAATTA
*
6578733 AAATAGATTTTATAATT-
1 AAATAGAATTTA-AATTA
6578750 AAATAGTAATTTAAAT
1 AAATAG-AATTTAAAT
6578766 CAAATTTAGA
Statistics
Matches: 42, Mismatches: 2, Indels: 11
0.76 0.04 0.20
Matches are distributed among these distances:
15 7 0.17
16 6 0.14
17 20 0.48
18 9 0.21
ACGTcount: A:0.56, C:0.00, G:0.05, T:0.39
Consensus pattern (17 bp):
AAATAGAATTTAAATTA
Found at i:6578770 original size:17 final size:16
Alignment explanation
Indices: 6578696--6578770 Score: 57
Period size: 17 Copynumber: 4.6 Consensus size: 16
6578686 TAAACAAATA
6578696 AAAT-AAATAGATATTT
1 AAATAAAATAGA-ATTT
6578712 AAA-AAAATTA-AATTT
1 AAATAAAA-TAGAATTT
*
6578727 AAATTAAAATAGATTTT
1 AAA-TAAAATAGAATTT
*
6578744 ATAATTAAATAGTAATTT
1 A-AATAAAATAG-AATTT
*
6578762 AAATCAAAT
1 AAATAAAAT
6578771 TTAGAAAAAA
Statistics
Matches: 48, Mismatches: 4, Indels: 13
0.74 0.06 0.20
Matches are distributed among these distances:
15 7 0.15
16 9 0.19
17 25 0.52
18 7 0.15
ACGTcount: A:0.57, C:0.01, G:0.04, T:0.37
Consensus pattern (16 bp):
AAATAAAATAGAATTT
Found at i:6579776 original size:23 final size:23
Alignment explanation
Indices: 6579741--6579834 Score: 134
Period size: 23 Copynumber: 4.1 Consensus size: 23
6579731 AAGTTAGAAG
6579741 AGTGAAGAGACTTGAATATGAAA
1 AGTGAAGAGACTTGAATATGAAA
* * *
6579764 AGTGAAAAAACTTGAATATGAAT
1 AGTGAAGAGACTTGAATATGAAA
*
6579787 AGTGAAGAGACTTGAAGATGAAA
1 AGTGAAGAGACTTGAATATGAAA
* *
6579810 AGTTAAGAGGCTTGAATATGAAA
1 AGTGAAGAGACTTGAATATGAAA
6579833 AG
1 AG
6579835 ATACACACAT
Statistics
Matches: 61, Mismatches: 10, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 61 1.00
ACGTcount: A:0.48, C:0.04, G:0.26, T:0.22
Consensus pattern (23 bp):
AGTGAAGAGACTTGAATATGAAA
Done.