Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: A03
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: 108673976
ACGTcount: A:0.31, C:0.17, G:0.16, T:0.31
Warning! 5040000 characters in sequence are not A, C, G, or T
File 12 of 333
Found at i:3163789 original size:25 final size:25
Alignment explanation
Indices: 3163760--3163810 Score: 102
Period size: 25 Copynumber: 2.0 Consensus size: 25
3163750 GAGTAGGAGT
3163760 TCACCTACGTGGTGAAGCGAACCCA
1 TCACCTACGTGGTGAAGCGAACCCA
3163785 TCACCTACGTGGTGAAGCGAACCCA
1 TCACCTACGTGGTGAAGCGAACCCA
3163810 T
1 T
3163811 GTAGGCGAAC
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 26 1.00
ACGTcount: A:0.27, C:0.31, G:0.24, T:0.18
Consensus pattern (25 bp):
TCACCTACGTGGTGAAGCGAACCCA
Found at i:3166382 original size:11 final size:12
Alignment explanation
Indices: 3166362--3166392 Score: 62
Period size: 12 Copynumber: 2.6 Consensus size: 12
3166352 ACATATATAT
3166362 ATATTTTTTTAA
1 ATATTTTTTTAA
3166374 ATATTTTTTTAA
1 ATATTTTTTTAA
3166386 ATATTTT
1 ATATTTT
3166393 ACTATACTCG
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 19 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (12 bp):
ATATTTTTTTAA
Found at i:3174945 original size:61 final size:62
Alignment explanation
Indices: 3174848--3175028 Score: 179
Period size: 62 Copynumber: 2.9 Consensus size: 62
3174838 TTAATATAGT
* * *
3174848 AACAAAATTAGCCCTCTAATGTATAC-ACATTCTATCATTTT-GATCCTAAATAT-AAAAAATTC
1 AACAAATTTAGCCCTC-AATGTTTACAAAATT-TATCATTTTAG-TCCTAAATATAAAAAAATTC
** ** *
3174910 AACAAATTTAGCCCTCAATGTTTACAAAATTTATCATTTTAGTTGTACTTCTAAAAAAATTC
1 AACAAATTTAGCCCTCAATGTTTACAAAATTTATCATTTTAGTCCTAAATATAAAAAAATTC
* ** * * * *
3174972 AATAAATTTAGCCCTCAACATTTATAAAATTTATCACTTTAGTCCTAACTCTAAAAA
1 AACAAATTTAGCCCTCAATGTTTACAAAATTTATCATTTTAGTCCTAAATATAAAAA
3175029 TAAAAAAATA
Statistics
Matches: 99, Mismatches: 17, Indels: 6
0.81 0.14 0.05
Matches are distributed among these distances:
61 22 0.22
62 77 0.78
ACGTcount: A:0.41, C:0.18, G:0.05, T:0.36
Consensus pattern (62 bp):
AACAAATTTAGCCCTCAATGTTTACAAAATTTATCATTTTAGTCCTAAATATAAAAAAATTC
Found at i:3176362 original size:2 final size:2
Alignment explanation
Indices: 3176355--3176416 Score: 115
Period size: 2 Copynumber: 31.0 Consensus size: 2
3176345 AGAATTTCAG
3176355 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
*
3176397 CT CT CT CT CT CT CT TT CT CT
1 CT CT CT CT CT CT CT CT CT CT
3176417 ATGTGTGTGT
Statistics
Matches: 58, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
2 58 1.00
ACGTcount: A:0.00, C:0.48, G:0.00, T:0.52
Consensus pattern (2 bp):
CT
Found at i:3177494 original size:103 final size:103
Alignment explanation
Indices: 3177315--3177522 Score: 416
Period size: 103 Copynumber: 2.0 Consensus size: 103
3177305 TACCACATTC
3177315 AACCTCAATTTATCTAAACCCCTTATCTTAGCCCATAATTAGATATATATTGTAATTAATAATAA
1 AACCTCAATTTATCTAAACCCCTTATCTTAGCCCATAATTAGATATATATTGTAATTAATAATAA
3177380 GTGTTGGTTGCAGTAATTAAACAAATTGCATTTTTAAA
66 GTGTTGGTTGCAGTAATTAAACAAATTGCATTTTTAAA
3177418 AACCTCAATTTATCTAAACCCCTTATCTTAGCCCATAATTAGATATATATTGTAATTAATAATAA
1 AACCTCAATTTATCTAAACCCCTTATCTTAGCCCATAATTAGATATATATTGTAATTAATAATAA
3177483 GTGTTGGTTGCAGTAATTAAACAAATTGCATTTTTAAA
66 GTGTTGGTTGCAGTAATTAAACAAATTGCATTTTTAAA
3177521 AA
1 AA
3177523 AGAATGCAGG
Statistics
Matches: 105, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
103 105 1.00
ACGTcount: A:0.38, C:0.14, G:0.10, T:0.38
Consensus pattern (103 bp):
AACCTCAATTTATCTAAACCCCTTATCTTAGCCCATAATTAGATATATATTGTAATTAATAATAA
GTGTTGGTTGCAGTAATTAAACAAATTGCATTTTTAAA
Found at i:3181986 original size:16 final size:16
Alignment explanation
Indices: 3181965--3182006 Score: 52
Period size: 15 Copynumber: 2.7 Consensus size: 16
3181955 TTATTAAATT
*
3181965 ATATATTTTAATTATA
1 ATATATTTTAATAATA
3181981 ATATA-TTTAATAATA
1 ATATATTTTAATAATA
3181996 AT-TATGTTTAA
1 ATATAT-TTTAA
3182007 ATATGATTAA
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
14 2 0.09
15 11 0.48
16 10 0.43
ACGTcount: A:0.45, C:0.00, G:0.02, T:0.52
Consensus pattern (16 bp):
ATATATTTTAATAATA
Found at i:3181991 original size:15 final size:15
Alignment explanation
Indices: 3181956--3181997 Score: 52
Period size: 15 Copynumber: 2.9 Consensus size: 15
3181946 TTAAGAATTT
*
3181956 TATTAAATTAT-ATA
1 TATTTAATTATAATA
3181970 T-TTTAATTATAATA
1 TATTTAATTATAATA
*
3181984 TATTTAATAATAAT
1 TATTTAATTATAAT
3181998 TATGTTTAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
13 8 0.33
14 5 0.21
15 11 0.46
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (15 bp):
TATTTAATTATAATA
Found at i:3182141 original size:157 final size:157
Alignment explanation
Indices: 3181940--3182256 Score: 555
Period size: 157 Copynumber: 2.0 Consensus size: 157
3181930 ATAAGAATAT
*
3181940 TAATTATTAAGAATTTTATTAAATTATATATTTTAATTATAATATATTTAATAATAATTATGTTT
1 TAATTATTAAGAATTTTATTAAATTATATATTTTAATTAAAATATATTTAATAATAATTATGTTT
* * *
3182005 AAATATGATTAAATTATTTATTATTGATATTAATAATCTTATTAAAATTTAAATAACAATAACAA
66 AAATATGATTAAAATATTTATTACTGATAATAATAATCTTATTAAAATTTAAATAACAATAACAA
*
3182070 TAATAATTTACCAAAACAAATTTCTGC
131 TAATAATTTACCAAAACAAATTTATGC
3182097 TAATTA-TAAGAATTTTATTAAATTATATATTATTAATTAAAATATATTTAATAATAATTATGTT
1 TAATTATTAAGAATTTTATTAAATTATATATT-TTAATTAAAATATATTTAATAATAATTATGTT
3182161 TAAATATGATTAAAATATTTATTACTGATAATAATAATCTTATTAAAATTTAAATAACAATAACA
65 TAAATATGATTAAAATATTTATTACTGATAATAATAATCTTATTAAAATTTAAATAACAATAACA
* *
3182226 ATAATCATTTACCAAAACAATTTTATGC
130 ATAATAATTTACCAAAACAAATTTATGC
3182254 TAA
1 TAA
3182257 GGGTATTCTA
Statistics
Matches: 152, Mismatches: 7, Indels: 2
0.94 0.04 0.01
Matches are distributed among these distances:
156 25 0.16
157 127 0.84
ACGTcount: A:0.48, C:0.05, G:0.03, T:0.44
Consensus pattern (157 bp):
TAATTATTAAGAATTTTATTAAATTATATATTTTAATTAAAATATATTTAATAATAATTATGTTT
AAATATGATTAAAATATTTATTACTGATAATAATAATCTTATTAAAATTTAAATAACAATAACAA
TAATAATTTACCAAAACAAATTTATGC
Found at i:3182373 original size:44 final size:45
Alignment explanation
Indices: 3182308--3182398 Score: 121
Period size: 45 Copynumber: 2.0 Consensus size: 45
3182298 ACCTCTATTC
* * *
3182308 CATTCAACCAAACACAAGATTA-CTATTACGCCTCTATTCCATTA
1 CATTCAACCAAACACAAGATTAGCTATTACACCTCTAATCCAATA
***
3182352 CATTCAACCAAACAGTGGATTAGCTATTACACCTCTAATCCAATA
1 CATTCAACCAAACACAAGATTAGCTATTACACCTCTAATCCAATA
3182397 CA
1 CA
3182399 CCTCTAATCC
Statistics
Matches: 40, Mismatches: 6, Indels: 1
0.85 0.13 0.02
Matches are distributed among these distances:
44 19 0.47
45 21 0.52
ACGTcount: A:0.37, C:0.29, G:0.07, T:0.27
Consensus pattern (45 bp):
CATTCAACCAAACACAAGATTAGCTATTACACCTCTAATCCAATA
Found at i:3182400 original size:16 final size:16
Alignment explanation
Indices: 3182379--3182430 Score: 104
Period size: 16 Copynumber: 3.2 Consensus size: 16
3182369 GATTAGCTAT
3182379 TACACCTCTAATCCAA
1 TACACCTCTAATCCAA
3182395 TACACCTCTAATCCAA
1 TACACCTCTAATCCAA
3182411 TACACCTCTAATCCAA
1 TACACCTCTAATCCAA
3182427 TACA
1 TACA
3182431 GCGAACCAAA
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 36 1.00
ACGTcount: A:0.38, C:0.37, G:0.00, T:0.25
Consensus pattern (16 bp):
TACACCTCTAATCCAA
Found at i:3189256 original size:26 final size:24
Alignment explanation
Indices: 3189212--3189261 Score: 73
Period size: 26 Copynumber: 2.0 Consensus size: 24
3189202 ATTTGTTTTA
*
3189212 ATATTTGTTTTTATGTTTTTAAAT
1 ATATTTGTTTTTATATTTTTAAAT
3189236 ATATTTGATTTATTATATTTTTAAAT
1 ATATTTG-TTT-TTATATTTTTAAAT
3189262 TTTTTTATTT
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
24 7 0.30
25 3 0.13
26 13 0.57
ACGTcount: A:0.30, C:0.00, G:0.06, T:0.64
Consensus pattern (24 bp):
ATATTTGTTTTTATATTTTTAAAT
Found at i:3204423 original size:21 final size:18
Alignment explanation
Indices: 3204386--3204420 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
3204376 GAAGAAAGAT
3204386 GGTGGGAAGAAAGATGAA
1 GGTGGGAAGAAAGATGAA
*
3204404 GGTGGGAAGAAGGATGA
1 GGTGGGAAGAAAGATGA
3204421 TGATAATAAA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.40, C:0.00, G:0.49, T:0.11
Consensus pattern (18 bp):
GGTGGGAAGAAAGATGAA
Found at i:3205831 original size:20 final size:21
Alignment explanation
Indices: 3205796--3205842 Score: 62
Period size: 20 Copynumber: 2.3 Consensus size: 21
3205786 AAGCTAATTT
* *
3205796 AAAATT-TAAAAGTTATTAA-
1 AAAATTATAAAAATTATAAAC
3205815 AAAATTATAAAAATTATAAAC
1 AAAATTATAAAAATTATAAAC
3205836 AAAATTA
1 AAAATTA
3205843 CTAATTTTTT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
19 6 0.25
20 11 0.46
21 7 0.29
ACGTcount: A:0.64, C:0.02, G:0.02, T:0.32
Consensus pattern (21 bp):
AAAATTATAAAAATTATAAAC
Found at i:3208355 original size:28 final size:28
Alignment explanation
Indices: 3208315--3208393 Score: 104
Period size: 28 Copynumber: 2.8 Consensus size: 28
3208305 GCAATCAAAT
* * *
3208315 ATGGTACTCAGTGTACGAAATATTGAGA
1 ATGGCACTTAGTGTGCGAAATATTGAGA
*
3208343 ATGGCACTTAGTGTGCGAGATATTGAGA
1 ATGGCACTTAGTGTGCGAAATATTGAGA
* *
3208371 ATGACACTTAGTGTGCAAAATAT
1 ATGGCACTTAGTGTGCGAAATAT
3208394 CGAATGATTC
Statistics
Matches: 44, Mismatches: 7, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
28 44 1.00
ACGTcount: A:0.34, C:0.11, G:0.25, T:0.29
Consensus pattern (28 bp):
ATGGCACTTAGTGTGCGAAATATTGAGA
Found at i:3211484 original size:30 final size:31
Alignment explanation
Indices: 3211440--3211513 Score: 89
Period size: 30 Copynumber: 2.4 Consensus size: 31
3211430 AGATGAGAGG
* *
3211440 TAATTTTATTTTATTTTATTTAA-TATTAATT
1 TAATTATATTTTA-TTTATATAATTATTAATT
* *
3211471 TAATTAT-TTTTATTTATATAATTTTTTATT
1 TAATTATATTTTATTTATATAATTATTAATT
3211501 TAATTATATTTTA
1 TAATTATATTTTA
3211514 ATGAGATAAT
Statistics
Matches: 37, Mismatches: 4, Indels: 4
0.82 0.09 0.09
Matches are distributed among these distances:
29 8 0.22
30 18 0.49
31 11 0.30
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (31 bp):
TAATTATATTTTATTTATATAATTATTAATT
Found at i:3211512 original size:15 final size:15
Alignment explanation
Indices: 3211440--3211513 Score: 62
Period size: 15 Copynumber: 4.9 Consensus size: 15
3211430 AGATGAGAGG
*
3211440 TAATTTTATTTTATT
1 TAATTATATTTTATT
* *
3211455 TTATT-TAATATTAATT
1 TAATTAT-AT-TTTATT
3211471 TAATTAT-TTTTATT
1 TAATTATATTTTATT
* *
3211485 TATATAATTTTTTATT
1 TA-ATTATATTTTATT
3211501 TAATTATATTTTA
1 TAATTATATTTTA
3211514 ATGAGATAAT
Statistics
Matches: 47, Mismatches: 7, Indels: 10
0.73 0.11 0.16
Matches are distributed among these distances:
14 8 0.17
15 20 0.43
16 18 0.38
17 1 0.02
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (15 bp):
TAATTATATTTTATT
Found at i:3211512 original size:16 final size:17
Alignment explanation
Indices: 3211475--3211512 Score: 53
Period size: 16 Copynumber: 2.4 Consensus size: 17
3211465 TTAATTTAAT
3211475 TATTTTTATTTATATAA
1 TATTTTTATTTATATAA
*
3211492 T-TTTTTATTTA-ATTA
1 TATTTTTATTTATATAA
3211507 TATTTT
1 TATTTT
3211513 AATGAGATAA
Statistics
Matches: 19, Mismatches: 1, Indels: 3
0.83 0.04 0.13
Matches are distributed among these distances:
15 4 0.21
16 14 0.74
17 1 0.05
ACGTcount: A:0.29, C:0.00, G:0.00, T:0.71
Consensus pattern (17 bp):
TATTTTTATTTATATAA
Found at i:3213411 original size:4 final size:4
Alignment explanation
Indices: 3213397--3213440 Score: 79
Period size: 4 Copynumber: 10.8 Consensus size: 4
3213387 ACTTTAAGTT
3213397 TTTC TTTTC TTTC TTTC TTTC TTTC TTTC TTTC TTTC TTTC TTT
1 TTTC -TTTC TTTC TTTC TTTC TTTC TTTC TTTC TTTC TTTC TTT
3213441 AATGGTGGAC
Statistics
Matches: 39, Mismatches: 0, Indels: 1
0.98 0.00 0.03
Matches are distributed among these distances:
4 35 0.90
5 4 0.10
ACGTcount: A:0.00, C:0.23, G:0.00, T:0.77
Consensus pattern (4 bp):
TTTC
Found at i:3213657 original size:24 final size:25
Alignment explanation
Indices: 3213610--3213657 Score: 62
Period size: 24 Copynumber: 2.0 Consensus size: 25
3213600 CATGGATAAA
* *
3213610 TTTGGTTAATTAATCATTTTGGTCT
1 TTTGGATAATTAATCATTTAGGTCT
*
3213635 TTTGGATAATT-ATTATTTAGGTC
1 TTTGGATAATTAATCATTTAGGTC
3213658 CCTAAGTATT
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
24 10 0.50
25 10 0.50
ACGTcount: A:0.23, C:0.06, G:0.17, T:0.54
Consensus pattern (25 bp):
TTTGGATAATTAATCATTTAGGTCT
Found at i:3215340 original size:19 final size:19
Alignment explanation
Indices: 3215316--3215353 Score: 76
Period size: 19 Copynumber: 2.0 Consensus size: 19
3215306 GAAATGAATA
3215316 ATTTCAGGCAAATAGGTTG
1 ATTTCAGGCAAATAGGTTG
3215335 ATTTCAGGCAAATAGGTTG
1 ATTTCAGGCAAATAGGTTG
3215354 GCAATCTCAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.32, C:0.11, G:0.26, T:0.32
Consensus pattern (19 bp):
ATTTCAGGCAAATAGGTTG
Found at i:3216557 original size:9 final size:8
Alignment explanation
Indices: 3216527--3216571 Score: 56
Period size: 8 Copynumber: 5.5 Consensus size: 8
3216517 AGAGGTTAAG
*
3216527 TTTTTTTC
1 TTTTTTTA
3216535 TTTTTCTTCA
1 TTTTT-TT-A
3216545 TTTTTTTA
1 TTTTTTTA
3216553 TTTTTTTA
1 TTTTTTTA
3216561 -TTTTTTA
1 TTTTTTTA
3216568 TTTT
1 TTTT
3216572 GAGTTGTATT
Statistics
Matches: 33, Mismatches: 1, Indels: 6
0.82 0.03 0.15
Matches are distributed among these distances:
7 7 0.21
8 17 0.52
9 4 0.12
10 5 0.15
ACGTcount: A:0.09, C:0.07, G:0.00, T:0.84
Consensus pattern (8 bp):
TTTTTTTA
Found at i:3222975 original size:50 final size:50
Alignment explanation
Indices: 3222900--3223001 Score: 204
Period size: 50 Copynumber: 2.0 Consensus size: 50
3222890 TTAAATTGGG
3222900 GTTTCATTTAGAACTCTACTCATTATGAGTAAATATATTCTTCTCTTTTA
1 GTTTCATTTAGAACTCTACTCATTATGAGTAAATATATTCTTCTCTTTTA
3222950 GTTTCATTTAGAACTCTACTCATTATGAGTAAATATATTCTTCTCTTTTA
1 GTTTCATTTAGAACTCTACTCATTATGAGTAAATATATTCTTCTCTTTTA
3223000 GT
1 GT
3223002 ATTCTTTTTT
Statistics
Matches: 52, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
50 52 1.00
ACGTcount: A:0.27, C:0.16, G:0.09, T:0.48
Consensus pattern (50 bp):
GTTTCATTTAGAACTCTACTCATTATGAGTAAATATATTCTTCTCTTTTA
Found at i:3234423 original size:23 final size:23
Alignment explanation
Indices: 3234396--3234441 Score: 65
Period size: 23 Copynumber: 2.0 Consensus size: 23
3234386 CATTCTTTTC
* *
3234396 TTTCTTTCTTTTTTTTTTTCATT
1 TTTCTTTCTTTTTATTTTCCATT
*
3234419 TTTCTTTGTTTTTATTTTCCATT
1 TTTCTTTCTTTTTATTTTCCATT
3234442 AAATCTGGGA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
23 20 1.00
ACGTcount: A:0.07, C:0.13, G:0.02, T:0.78
Consensus pattern (23 bp):
TTTCTTTCTTTTTATTTTCCATT
Found at i:3237864 original size:18 final size:19
Alignment explanation
Indices: 3237830--3237869 Score: 55
Period size: 18 Copynumber: 2.2 Consensus size: 19
3237820 TTCTTACTGT
* *
3237830 TTTAAATAATCATTATATA
1 TTTAAATAATAATTATAAA
3237849 TTTAAA-AATAATTATAAA
1 TTTAAATAATAATTATAAA
3237867 TTT
1 TTT
3237870 GATATAAATT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
18 13 0.68
19 6 0.32
ACGTcount: A:0.50, C:0.03, G:0.00, T:0.47
Consensus pattern (19 bp):
TTTAAATAATAATTATAAA
Found at i:3257055 original size:44 final size:44
Alignment explanation
Indices: 3256966--3257047 Score: 114
Period size: 44 Copynumber: 1.9 Consensus size: 44
3256956 GTACATTCAC
* *
3256966 GAACTCGACTCAACTCAACGAGTTCGACATTCGCATCCATAAGT
1 GAACTCGACTCAACTCAACGAGTTCGACATGCGCAACCATAAGT
* *
3257010 GAACTCGACTCAACTC-ACGAGTTCG-GATGCTCAACCAT
1 GAACTCGACTCAACTCAACGAGTTCGACATGCGCAACCAT
3257048 CCTAGTGACA
Statistics
Matches: 34, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
42 9 0.26
43 9 0.26
44 16 0.47
ACGTcount: A:0.30, C:0.30, G:0.17, T:0.22
Consensus pattern (44 bp):
GAACTCGACTCAACTCAACGAGTTCGACATGCGCAACCATAAGT
Found at i:3264415 original size:46 final size:45
Alignment explanation
Indices: 3264320--3264441 Score: 201
Period size: 46 Copynumber: 2.7 Consensus size: 45
3264310 AACCCGCCCC
* * *
3264320 TAAGTGAACTC-GACTCAACTCAACGAGCTCGGCGTTCGCATCCA
1 TAAGTGAACTCGGACTCAACTCAACGAGTTCGACATTCGCATCCA
3264364 TAAGTGAACTCGGACTCAACTCAACGAGTTCTGACATTCGCATCCA
1 TAAGTGAACTCGGACTCAACTCAACGAGTTC-GACATTCGCATCCA
3264410 TAAGTGAACTCGGACTCAACTCAACGAGTTCG
1 TAAGTGAACTCGGACTCAACTCAACGAGTTCG
3264442 GATGCTCAAC
Statistics
Matches: 73, Mismatches: 3, Indels: 3
0.92 0.04 0.04
Matches are distributed among these distances:
44 11 0.15
45 19 0.26
46 43 0.59
ACGTcount: A:0.30, C:0.29, G:0.20, T:0.22
Consensus pattern (45 bp):
TAAGTGAACTCGGACTCAACTCAACGAGTTCGACATTCGCATCCA
Found at i:3264462 original size:46 final size:45
Alignment explanation
Indices: 3264322--3264462 Score: 128
Period size: 46 Copynumber: 3.1 Consensus size: 45
3264312 CCCGCCCCTA
* * * *
3264322 AGTGAACTC-GACTCAACTCAACGAGCTCGG-CGTTC-GCATCCAT
1 AGTGAACTCGGACTCAACTCAACGAGTTCGGATGCTCACCATCC-T
* *** *
3264365 AAGTGAACTCGGACTCAACTCAACGAGTTCTGACATTC-GCATCCAT
1 -AGTGAACTCGGACTCAACTCAACGAGTTCGGATGCTCACCATCC-T
3264411 AAGTGAACTCGGACTCAACTCAACGAGTTCGGATGCTCAACCATCCT
1 -AGTGAACTCGGACTCAACTCAACGAGTTCGGATGCTC-ACCATCCT
3264458 AGTGA
1 AGTGA
3264463 CATGTCACTT
Statistics
Matches: 85, Mismatches: 8, Indels: 6
0.86 0.08 0.06
Matches are distributed among these distances:
44 9 0.11
45 19 0.22
46 51 0.60
47 1 0.01
48 5 0.06
ACGTcount: A:0.29, C:0.29, G:0.20, T:0.22
Consensus pattern (45 bp):
AGTGAACTCGGACTCAACTCAACGAGTTCGGATGCTCACCATCCT
Found at i:3267077 original size:44 final size:42
Alignment explanation
Indices: 3266920--3267083 Score: 170
Period size: 44 Copynumber: 3.7 Consensus size: 42
3266910 GGTTGAGCAT
*
3266920 CCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGAAATG
1 CCGAACTCGTTGAGTTGAGTCCGAGTTCA-TTATGGATG-GATG
* * *
3266964 TCCGAACTCGTTGAGTTGAGT-CGAGTTCGTGAGATGTAACTAGGCAT-
1 -CCGAACTCGTTGAGTTGAGTCCGAGTTCAT--TATG-GA-T-GG-ATG
3267011 CCGAACTCGTTGAGTTGAGTCCGAGTTCATTATGGATGCGATCG
1 CCGAACTCGTTGAGTTGAGTCCGAGTTCATTATGGATG-GAT-G
*
3267055 CCGAGCTCGTTGAGTTGAGTCCGAGTTCA
1 CCGAACTCGTTGAGTTGAGTCCGAGTTCA
3267084 CTTAGGGGGG
Statistics
Matches: 101, Mismatches: 8, Indels: 21
0.78 0.06 0.16
Matches are distributed among these distances:
42 3 0.03
43 3 0.03
44 36 0.36
45 26 0.26
46 21 0.21
47 9 0.09
48 3 0.03
ACGTcount: A:0.22, C:0.20, G:0.29, T:0.29
Consensus pattern (42 bp):
CCGAACTCGTTGAGTTGAGTCCGAGTTCATTATGGATGGATG
Found at i:3267080 original size:91 final size:91
Alignment explanation
Indices: 3266916--3267082 Score: 275
Period size: 91 Copynumber: 1.8 Consensus size: 91
3266906 GGATGGTTGA
3266916 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGAAATGTCCGAACTCGTTGAGTT
1 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGAAATGTCCGAACTCGTTGAGTT
3266981 GAGTCGAGTTCGTGAGATGTAACTAG
66 GAGTCGAGTTCGTGAGATGTAACTAG
** *
3267007 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCA-TTATGGATGCGATCG-CCGAGCTCGTTGAGT
1 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGAAAT-GTCCGAACTCGTTGAGT
3267070 TGAGTCCGAGTTC
65 TGAGT-CGAGTTC
3267083 ACTTAGGGGG
Statistics
Matches: 71, Mismatches: 3, Indels: 4
0.91 0.04 0.05
Matches are distributed among these distances:
90 30 0.42
91 41 0.58
ACGTcount: A:0.22, C:0.20, G:0.29, T:0.29
Consensus pattern (91 bp):
GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGAAATGTCCGAACTCGTTGAGTT
GAGTCGAGTTCGTGAGATGTAACTAG
Found at i:3267343 original size:19 final size:20
Alignment explanation
Indices: 3267306--3267343 Score: 53
Period size: 19 Copynumber: 1.9 Consensus size: 20
3267296 ATAAGGTGGT
3267306 AAGATGATGAATGATGTTTA
1 AAGATGATGAATGATGTTTA
3267326 AAGATG-TGATAT-ATGTTT
1 AAGATGATGA-ATGATGTTT
3267344 TGGTGGTACC
Statistics
Matches: 17, Mismatches: 0, Indels: 3
0.85 0.00 0.15
Matches are distributed among these distances:
19 9 0.53
20 8 0.47
ACGTcount: A:0.37, C:0.00, G:0.24, T:0.39
Consensus pattern (20 bp):
AAGATGATGAATGATGTTTA
Found at i:3273320 original size:47 final size:47
Alignment explanation
Indices: 3273202--3273370 Score: 229
Period size: 47 Copynumber: 3.6 Consensus size: 47
3273192 GGATGGTTGA
* * *
3273202 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAA--AT
1 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCA-TGA--GATGTAACTAG
*
3273250 G--TCCGAACTCGTTGAGTTGAGTCCGAGTTCGTGAGATGTAACTAG
1 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCATGAGATGTAACTAG
*
3273295 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCATGAAATGTAACTAG
1 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCATGAGATGTAACTAG
*
3273342 GCATCTGAACTCGTTGAGTTGAGTCCGAG
1 GCATCCGAACTCGTTGAGTTGAGTCCGAG
3273371 CTCACTTAGG
Statistics
Matches: 110, Mismatches: 7, Indels: 9
0.87 0.06 0.07
Matches are distributed among these distances:
43 6 0.05
45 4 0.04
46 29 0.26
47 70 0.64
48 1 0.01
ACGTcount: A:0.24, C:0.20, G:0.28, T:0.28
Consensus pattern (47 bp):
GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCATGAGATGTAACTAG
Found at i:3274908 original size:45 final size:45
Alignment explanation
Indices: 3274844--3275108 Score: 385
Period size: 45 Copynumber: 6.0 Consensus size: 45
3274834 TATCGTATAG
* * *
3274844 TACTATTCGGGCTTTTGAGCCTAGCAGACTATAATGCCGGTGATA
1 TACTATTCGGGCCTTTGAGCCTAGCAGGCTATAATGCCGGTGAGA
3274889 TACTATTCGGGCCTTTGAGCCTAGCAGGCTATAATGCCGGTGAGA
1 TACTATTCGGGCCTTTGAGCCTAGCAGGCTATAATGCCGGTGAGA
* *
3274934 TACTATTCGGGCCTTTGAGCCTAGCATGCTATAATACCGGTGAGA
1 TACTATTCGGGCCTTTGAGCCTAGCAGGCTATAATGCCGGTGAGA
3274979 TACTATTCGGGCCTTTGAGCCTAGCAGGCTATAATGCCGGTGAGA
1 TACTATTCGGGCCTTTGAGCCTAGCAGGCTATAATGCCGGTGAGA
* * *
3275024 TACTATTCTGGCCTTCGAGCCTAGCAGGCTATAATGCCGGTGAAA
1 TACTATTCGGGCCTTTGAGCCTAGCAGGCTATAATGCCGGTGAGA
* * * *
3275069 TGA-TA-TCGAG-CTTCGAGCCTAGCAGGC-AAAATGCTGGTGA
1 T-ACTATTCGGGCCTTTGAGCCTAGCAGGCTATAATGCCGGTGA
3275109 ATGAATTCGG
Statistics
Matches: 205, Mismatches: 14, Indels: 5
0.92 0.06 0.02
Matches are distributed among these distances:
42 11 0.05
43 17 0.08
44 3 0.01
45 173 0.84
46 1 0.00
ACGTcount: A:0.24, C:0.22, G:0.27, T:0.27
Consensus pattern (45 bp):
TACTATTCGGGCCTTTGAGCCTAGCAGGCTATAATGCCGGTGAGA
Found at i:3281996 original size:46 final size:46
Alignment explanation
Indices: 3281943--3282118 Score: 225
Period size: 46 Copynumber: 3.8 Consensus size: 46
3281933 TGGTTGAGCA
3281943 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
* * *
3281989 TCCGAACTCGTTGAGTTGAGTCCGAGTTC-GTGA--GATG-TAACTAGG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAA-T--G
3282034 CATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
1 --TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
* * *
3282082 CCCGAGCTCGTTGAGTTGAGTCCGAGTTCGCTTATGG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGG
3282119 GCGGGTTACA
Statistics
Matches: 112, Mismatches: 9, Indels: 18
0.81 0.06 0.13
Matches are distributed among these distances:
42 2 0.02
43 5 0.04
45 3 0.03
46 63 0.56
47 29 0.26
48 3 0.03
50 5 0.04
51 2 0.02
ACGTcount: A:0.20, C:0.20, G:0.30, T:0.30
Consensus pattern (46 bp):
TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
Found at i:3282099 original size:93 final size:93
Alignment explanation
Indices: 3281940--3282111 Score: 326
Period size: 93 Copynumber: 1.8 Consensus size: 93
3281930 GAATGGTTGA
*
3281940 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATGTCCGAACTCGTTGAGT
1 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATGCCCGAACTCGTTGAGT
3282005 TGAGTCCGAGTTCGTGAGATGTAACTAG
66 TGAGTCCGAGTTCGTGAGATGTAACTAG
*
3282033 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATGCCCGAGCTCGTTGAGT
1 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATGCCCGAACTCGTTGAGT
3282098 TGAGTCCGAGTTCG
66 TGAGTCCGAGTTCG
3282112 CTTATGGGCG
Statistics
Matches: 77, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
93 77 1.00
ACGTcount: A:0.21, C:0.21, G:0.30, T:0.28
Consensus pattern (93 bp):
GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATGCCCGAACTCGTTGAGT
TGAGTCCGAGTTCGTGAGATGTAACTAG
Found at i:3286697 original size:24 final size:24
Alignment explanation
Indices: 3286670--3286719 Score: 73
Period size: 24 Copynumber: 2.1 Consensus size: 24
3286660 CCATAGCTTT
* *
3286670 CCGATATGGTTCTTTGTGCACTTC
1 CCGATAAGGTTCTTTGTGAACTTC
*
3286694 CCGATAAGGTTTTTTGTGAACTTC
1 CCGATAAGGTTCTTTGTGAACTTC
3286718 CC
1 CC
3286720 AATTACGGCT
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
24 23 1.00
ACGTcount: A:0.16, C:0.24, G:0.20, T:0.40
Consensus pattern (24 bp):
CCGATAAGGTTCTTTGTGAACTTC
Found at i:3295677 original size:46 final size:46
Alignment explanation
Indices: 3295627--3295798 Score: 210
Period size: 46 Copynumber: 3.7 Consensus size: 46
3295617 TGGTTGAGCA
3295627 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
* * * *
3295673 TCCGAACTCGTTGAGTTGAGTCCGAGTTC-GTGA--AATG-TAACTAGG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAA-T--G
3295718 CATCC-AACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
1 --TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
* *
3295765 CCCGAGCTCGTTGAGTTGAGTCCGAGTTCACTTA
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTA
3295799 GGGGCGGGTT
Statistics
Matches: 106, Mismatches: 10, Indels: 20
0.78 0.07 0.15
Matches are distributed among these distances:
42 2 0.02
43 4 0.04
45 5 0.05
46 83 0.78
47 6 0.06
49 4 0.04
50 2 0.02
ACGTcount: A:0.22, C:0.21, G:0.27, T:0.30
Consensus pattern (46 bp):
TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
Found at i:3295788 original size:92 final size:93
Alignment explanation
Indices: 3295624--3295793 Score: 315
Period size: 92 Copynumber: 1.8 Consensus size: 93
3295614 GGATGGTTGA
*
3295624 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATGTCCGAACTCGTTGAGT
1 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATGCCCGAACTCGTTGAGT
3295689 TGAGTCCGAGTTCGTGAAATGTAACTAG
66 TGAGTCCGAGTTCGTGAAATGTAACTAG
*
3295717 GCATCC-AACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATGCCCGAGCTCGTTGAGT
1 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATGCCCGAACTCGTTGAGT
3295781 TGAGTCCGAGTTC
66 TGAGTCCGAGTTC
3295794 ACTTAGGGGC
Statistics
Matches: 75, Mismatches: 2, Indels: 1
0.96 0.03 0.01
Matches are distributed among these distances:
92 69 0.92
93 6 0.08
ACGTcount: A:0.22, C:0.21, G:0.28, T:0.29
Consensus pattern (93 bp):
GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATGCCCGAACTCGTTGAGT
TGAGTCCGAGTTCGTGAAATGTAACTAG
Found at i:3298352 original size:21 final size:20
Alignment explanation
Indices: 3298320--3298362 Score: 52
Period size: 20 Copynumber: 2.1 Consensus size: 20
3298310 AGATGACATG
*
3298320 AAATGTTTGTAATTGTTTTGT
1 AAATGTTTGTAA-TGCTTTGT
3298341 AAAT-TTTGGTAATGCTTTGT
1 AAATGTTT-GTAATGCTTTGT
3298361 AA
1 AA
3298363 CCCTGTTCTG
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
20 12 0.60
21 8 0.40
ACGTcount: A:0.28, C:0.02, G:0.19, T:0.51
Consensus pattern (20 bp):
AAATGTTTGTAATGCTTTGT
Found at i:3302224 original size:21 final size:20
Alignment explanation
Indices: 3302200--3302238 Score: 69
Period size: 21 Copynumber: 1.9 Consensus size: 20
3302190 GAGTATTTTG
3302200 ATGTTTGATGATAGATTATGA
1 ATGTTTGATGATAG-TTATGA
3302221 ATGTTTGATGATAGTTAT
1 ATGTTTGATGATAGTTAT
3302239 ACAAGTTTTG
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
20 4 0.22
21 14 0.78
ACGTcount: A:0.31, C:0.00, G:0.23, T:0.46
Consensus pattern (20 bp):
ATGTTTGATGATAGTTATGA
Found at i:3302248 original size:21 final size:21
Alignment explanation
Indices: 3302200--3302246 Score: 62
Period size: 21 Copynumber: 2.3 Consensus size: 21
3302190 GAGTATTTTG
*
3302200 ATGTTTGATGATAGATTATGA
1 ATGTTTGATGATAGATTATCA
3302221 ATGTTTGATGATAG-TTATACA
1 ATGTTTGATGATAGATTAT-CA
3302242 A-GTTT
1 ATGTTT
3302247 TGTAAAGTGA
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
20 8 0.33
21 16 0.67
ACGTcount: A:0.32, C:0.02, G:0.21, T:0.45
Consensus pattern (21 bp):
ATGTTTGATGATAGATTATCA
Found at i:3302386 original size:16 final size:16
Alignment explanation
Indices: 3302365--3302395 Score: 62
Period size: 16 Copynumber: 1.9 Consensus size: 16
3302355 ATTAAATTGC
3302365 ATGAATTTGTGATTTT
1 ATGAATTTGTGATTTT
3302381 ATGAATTTGTGATTT
1 ATGAATTTGTGATTT
3302396 GTAACTAATG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.26, C:0.00, G:0.19, T:0.55
Consensus pattern (16 bp):
ATGAATTTGTGATTTT
Found at i:3304630 original size:28 final size:28
Alignment explanation
Indices: 3304568--3304661 Score: 127
Period size: 28 Copynumber: 3.4 Consensus size: 28
3304558 TATTAAGTCT
*
3304568 GCACACTCAGTGCTATATAATC-AACTC
1 GCACACTTAGTGCTATATAATCAAACTC
3304595 GCACACTTAGTGCTATATAATCAAACTC
1 GCACACTTAGTGCTATATAATCAAACTC
* * * *
3304623 GCACACTTAGTGCTGTACAATTTAAACCC
1 GCACACTTAGTGCTATATAA-TCAAACTC
3304652 GCACACTTAG
1 GCACACTTAG
3304662 CGCCAATCTC
Statistics
Matches: 60, Mismatches: 5, Indels: 2
0.90 0.07 0.03
Matches are distributed among these distances:
27 21 0.35
28 23 0.38
29 16 0.27
ACGTcount: A:0.33, C:0.28, G:0.13, T:0.27
Consensus pattern (28 bp):
GCACACTTAGTGCTATATAATCAAACTC
Found at i:3307509 original size:6 final size:6
Alignment explanation
Indices: 3307479--3307621 Score: 105
Period size: 6 Copynumber: 23.3 Consensus size: 6
3307469 AAGAAAAATT
* * * *
3307479 ATCAGA A-CTAGA ATCAAA ATGAGA ATCAGA ATCAGA ATCAAA ATTAG-
1 ATCAGA ATC-AGA ATCAGA ATCAGA ATCAGA ATCAGA ATCAGA ATCAGA
* * * *
3307526 GTGACAGA ATCAAA ATCAAA ATCAGA ATCAGT ATCAGGTA A-CAGA ATCAGA
1 AT--CAGA ATCAGA ATCAGA ATCAGA ATCAGA ATCA-G-A ATCAGA ATCAGA
* *
3307577 ATCAGA ACCAGA ATCAGA ATCAGGTA A-CAGA ATTAGA ATCAGA AT
1 ATCAGA ATCAGA ATCAGA ATCA-G-A ATCAGA ATCAGA ATCAGA AT
3307622 GTGAATGCAA
Statistics
Matches: 108, Mismatches: 18, Indels: 22
0.73 0.12 0.15
Matches are distributed among these distances:
5 6 0.06
6 89 0.82
7 9 0.08
8 4 0.04
ACGTcount: A:0.50, C:0.15, G:0.17, T:0.18
Consensus pattern (6 bp):
ATCAGA
Found at i:3307552 original size:37 final size:37
Alignment explanation
Indices: 3307502--3307621 Score: 159
Period size: 37 Copynumber: 3.2 Consensus size: 37
3307492 TCAAAATGAG
* * *
3307502 AATCAGAATCAGAATCAAAATTAGGTGACAGAATCAA
1 AATCAGAATCAGAATCAGAATCAGGTAACAGAATCAA
* * *
3307539 AATCAAAATCAGAATCAGTATCAGGTAACAGAATCAG
1 AATCAGAATCAGAATCAGAATCAGGTAACAGAATCAA
* * *
3307576 AATCAGAACCAGAATCAGAATCAGGTAACAGAATTAG
1 AATCAGAATCAGAATCAGAATCAGGTAACAGAATCAA
3307613 AATCAGAAT
1 AATCAGAAT
3307622 GTGAATGCAA
Statistics
Matches: 72, Mismatches: 11, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
37 72 1.00
ACGTcount: A:0.50, C:0.15, G:0.17, T:0.18
Consensus pattern (37 bp):
AATCAGAATCAGAATCAGAATCAGGTAACAGAATCAA
Found at i:3307614 original size:19 final size:19
Alignment explanation
Indices: 3307511--3307618 Score: 107
Period size: 19 Copynumber: 5.8 Consensus size: 19
3307501 GAATCAGAAT
* * *
3307511 CAGAATCAAAATTAGGTGA
1 CAGAATCAGAATCAGGTAA
* *
3307530 CAGAATCAAAATCA--AAA
1 CAGAATCAGAATCAGGTAA
*
3307547 TCAGAATCAGTATCAGGTAA
1 -CAGAATCAGAATCAGGTAA
3307567 CAGAATCAGAATCA-G-AA
1 CAGAATCAGAATCAGGTAA
3307584 CCAGAATCAGAATCAGGTAA
1 -CAGAATCAGAATCAGGTAA
*
3307604 CAGAATTAGAATCAG
1 CAGAATCAGAATCAG
3307619 AATGTGAATG
Statistics
Matches: 75, Mismatches: 8, Indels: 12
0.79 0.08 0.13
Matches are distributed among these distances:
17 3 0.04
18 27 0.36
19 41 0.55
20 4 0.05
ACGTcount: A:0.49, C:0.16, G:0.18, T:0.18
Consensus pattern (19 bp):
CAGAATCAGAATCAGGTAA
Found at i:3314377 original size:27 final size:27
Alignment explanation
Indices: 3314371--3314423 Score: 81
Period size: 27 Copynumber: 2.0 Consensus size: 27
3314361 TATAGATATT
*
3314371 TGTGGCATAGCCACCAGAATCAGATAA
1 TGTGGCAAAGCCACCAGAATCAGATAA
*
3314398 TGTGGCAAAGCCACTAGAATC-GATAA
1 TGTGGCAAAGCCACCAGAATCAGATAA
3314424 CTGTAATAAC
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
26 5 0.21
27 19 0.79
ACGTcount: A:0.38, C:0.21, G:0.23, T:0.19
Consensus pattern (27 bp):
TGTGGCAAAGCCACCAGAATCAGATAA
Found at i:3314984 original size:27 final size:27
Alignment explanation
Indices: 3314954--3315284 Score: 466
Period size: 27 Copynumber: 12.3 Consensus size: 27
3314944 GGGGTAAAAT
* * * *
3314954 GGTAATTTTACCCCACAAGGGTA-TCTA
1 GGTAATTCTACCCTACAGGGGTATTC-C
*
3314981 GGTAATTCTACCCTACAGGGGTATTTC
1 GGTAATTCTACCCTACAGGGGTATTCC
*
3315008 GGTAATTCTACCCTACAGGGGTATTTC
1 GGTAATTCTACCCTACAGGGGTATTCC
3315035 GGTAATTCTACCCTACAGGGGTATTCC
1 GGTAATTCTACCCTACAGGGGTATTCC
3315062 GGTAATTCTACCCTACAGGGGTATTCC
1 GGTAATTCTACCCTACAGGGGTATTCC
*
3315089 GGTAATTCTACCCTACAGGGATATTCC
1 GGTAATTCTACCCTACAGGGGTATTCC
3315116 GGTAATTCTACCCTACAGGGGTATTCC
1 GGTAATTCTACCCTACAGGGGTATTCC
* * *
3315143 GATAATTCTACCCTATAGGGGTATTTC
1 GGTAATTCTACCCTACAGGGGTATTCC
* *
3315170 GGTAATTCTACCCTATAGGGGTATTTC
1 GGTAATTCTACCCTACAGGGGTATTCC
*
3315197 GGTAATTCTACCCTACAAGGGTATTCC
1 GGTAATTCTACCCTACAGGGGTATTCC
** *
3315224 GGTAATTCTACCCTACAAAGGTATTTC
1 GGTAATTCTACCCTACAGGGGTATTCC
* * *
3315251 AGTAATTCTACCCTACAAGGGTATTTC
1 GGTAATTCTACCCTACAGGGGTATTCC
*
3315278 GATAATT
1 GGTAATT
3315285 TCACAAATTA
Statistics
Matches: 282, Mismatches: 21, Indels: 2
0.92 0.07 0.01
Matches are distributed among these distances:
27 281 1.00
28 1 0.00
ACGTcount: A:0.25, C:0.23, G:0.20, T:0.32
Consensus pattern (27 bp):
GGTAATTCTACCCTACAGGGGTATTCC
Found at i:3315340 original size:27 final size:27
Alignment explanation
Indices: 3315269--3315394 Score: 101
Period size: 27 Copynumber: 4.7 Consensus size: 27
3315259 TACCCTACAA
* * * **
3315269 GGGTATTTCGATAATTTCACAAATTAG
1 GGGTATTTTGGTAATTTTACAAACCAG
3315296 GGGTATTTTGGTAATTTTACAAACCAG
1 GGGTATTTTGGTAATTTTACAAACCAG
*** *
3315323 GGGTATTTTGGTAATTTTATTGATC-G
1 GGGTATTTTGGTAATTTTACAAACCAG
** *
3315349 AGGGTATTTTGGTAATTTTGTAAACCAA
1 -GGGTATTTTGGTAATTTTACAAACCAG
* **
3315377 AGGTATTTCAGTAATTTT
1 GGGTATTTTGGTAATTTT
3315395 GTAAATCGAG
Statistics
Matches: 80, Mismatches: 17, Indels: 4
0.79 0.17 0.04
Matches are distributed among these distances:
26 1 0.01
27 79 0.99
ACGTcount: A:0.29, C:0.08, G:0.21, T:0.42
Consensus pattern (27 bp):
GGGTATTTTGGTAATTTTACAAACCAG
Found at i:3315408 original size:27 final size:27
Alignment explanation
Indices: 3315296--3315802 Score: 214
Period size: 27 Copynumber: 18.9 Consensus size: 27
3315286 CACAAATTAG
* ** *
3315296 GGGTATTTTGGTAATTTTACAAA-CCA
1 GGGTATTTCGGTAATTTTGTAAATCGA
* * **
3315322 GGGGTATTTTGGTAATTTTATTGATCGA
1 -GGGTATTTCGGTAATTTTGTAAATCGA
* * *
3315350 GGGTATTTTGGTAATTTTGTAAACCAA
1 GGGTATTTCGGTAATTTTGTAAATCGA
* *
3315377 AGGTATTTCAGTAATTTTGTAAATCGA
1 GGGTATTTCGGTAATTTTGTAAATCGA
** *
3315404 GGGTAAAAT-GGTAATTCTGTAAATCGA
1 GGGT-ATTTCGGTAATTTTGTAAATCGA
*** * * *
3315431 GGGTAAGACGATAATTCTGTAAATCAA
1 GGGTATTTCGGTAATTTTGTAAATCGA
** * *
3315458 GGGTAAAAT-GGTAATTCTATAAATCGA
1 GGGT-ATTTCGGTAATTTTGTAAATCGA
*** *
3315485 GGGTAAAACGATAATTTTGTAAATCGA
1 GGGTATTTCGGTAATTTTGTAAATCGA
** * *
3315512 GGGTAAAAT-GGTAATTCTATAAATCGA
1 GGGT-ATTTCGGTAATTTTGTAAATCGA
** * *
3315539 GGGTAAAAT-GATAATTCTGTAAATCGA
1 GGGT-ATTTCGGTAATTTTGTAAATCGA
** * *
3315566 GGGTAAAAT-GGTAATTCTATCT-TA-C-A
1 GGGT-ATTTCGGTAATT-T-TGTAAATCGA
* * **
3315592 GAAGTATTTCAGTAATTTTACAAATCGA
1 G-GGTATTTCGGTAATTTTGTAAATCGA
* **
3315620 GGGTATTTCAGTAATTTTACAAATCGA
1 GGGTATTTCGGTAATTTTGTAAATCGA
** *
3315647 GGGTATTTTAGTAATTTTGCAAA-CTGA
1 GGGTATTTCGGTAATTTTGTAAATC-GA
** *
3315674 GGGTATTTCGGTAATTTTACAAATTGA
1 GGGTATTTCGGTAATTTTGTAAATCGA
* *
3315701 TGGTATTTCAGTAA-TTT-TACAATCGA
1 GGGTATTTCGGTAATTTTGTA-AATCGA
* * * *
3315727 CGGTATTTCGGTAATTTTATAAACCGG
1 GGGTATTTCGGTAATTTTGTAAATCGA
* * *
3315754 GGGTACTTT-GGTAATTTTATAACT-GG
1 GGGTA-TTTCGGTAATTTTGTAAATCGA
* *
3315780 GGGTATTTCTGTAATTTGGTAAA
1 GGGTATTTCGGTAATTTTGTAAA
3315803 CTAAAGTATT
Statistics
Matches: 389, Mismatches: 71, Indels: 41
0.78 0.14 0.08
Matches are distributed among these distances:
25 5 0.01
26 49 0.13
27 316 0.81
28 17 0.04
29 2 0.01
ACGTcount: A:0.33, C:0.09, G:0.22, T:0.36
Consensus pattern (27 bp):
GGGTATTTCGGTAATTTTGTAAATCGA
Found at i:3315430 original size:81 final size:81
Alignment explanation
Indices: 3315386--3315583 Score: 281
Period size: 81 Copynumber: 2.4 Consensus size: 81
3315376 AAGGTATTTC
* * * *
3315386 AGTAATTTTGTAAATCGAGGGTAAAATGGTAATTCTGTAAATCGAGGGTAAGACGATAATTCTGT
1 AGTAATTCTGTAAATCGAGGGTAAAATGGTAATTCTGTAAATCGAGGGTAAAATGGTAATTCTGT
3315451 AAATCAAGGGTAAAAT
66 AAATCAAGGGTAAAAT
* * * * * *
3315467 GGTAATTCTATAAATCGAGGGTAAAACGATAATTTTGTAAATCGAGGGTAAAATGGTAATTCTAT
1 AGTAATTCTGTAAATCGAGGGTAAAATGGTAATTCTGTAAATCGAGGGTAAAATGGTAATTCTGT
*
3315532 AAATCGAGGGTAAAAT
66 AAATCAAGGGTAAAAT
3315548 -GATAATTCTGTAAATCGAGGGTAAAATGGTAATTCT
1 AG-TAATTCTGTAAATCGAGGGTAAAATGGTAATTCT
3315584 ATCTTACAGA
Statistics
Matches: 101, Mismatches: 15, Indels: 2
0.86 0.13 0.02
Matches are distributed among these distances:
80 1 0.01
81 100 0.99
ACGTcount: A:0.39, C:0.08, G:0.23, T:0.30
Consensus pattern (81 bp):
AGTAATTCTGTAAATCGAGGGTAAAATGGTAATTCTGTAAATCGAGGGTAAAATGGTAATTCTGT
AAATCAAGGGTAAAAT
Found at i:3315651 original size:108 final size:108
Alignment explanation
Indices: 3315379--3315624 Score: 336
Period size: 108 Copynumber: 2.3 Consensus size: 108
3315369 TAAACCAAAG
* *
3315379 GTATTTCAGTAATTTTGTAAATCGAGGGTAAAATGGTAATTCTGTAAATCGAGGGTAAGACGATA
1 GTATTTCAGTAATTTTGTAAATCGAGGGTAAAATGGTAATTCTATAAATCGAGGGTAAAACGATA
*
3315444 ATTCTGTAAATCAAGGGTAAAATGGTAATTCTATAAATCGAGG
66 ATTCTGTAAATCAAGGGTAAAATGGTAATTCTATAAATCGAGA
*** *
3315487 GTAAAAC-GATAATTTTGTAAATCGAGGGTAAAATGGTAATTCTATAAATCGAGGGTAAAATGAT
1 GTATTTCAG-TAATTTTGTAAATCGAGGGTAAAATGGTAATTCTATAAATCGAGGGTAAAACGAT
* **
3315551 AATTCTGTAAATCGAGGGTAAAATGGTAATTCTAT-CTTAC-AGAA
65 AATTCTGTAAATCAAGGGTAAAATGGTAATTCTATAAAT-CGAG-A
**
3315595 GTATTTCAGTAATTTTACAAATCGAGGGTA
1 GTATTTCAGTAATTTTGTAAATCGAGGGTA
3315625 TTTCAGTAAT
Statistics
Matches: 119, Mismatches: 15, Indels: 8
0.84 0.11 0.06
Matches are distributed among these distances:
107 4 0.03
108 114 0.96
109 1 0.01
ACGTcount: A:0.38, C:0.09, G:0.22, T:0.32
Consensus pattern (108 bp):
GTATTTCAGTAATTTTGTAAATCGAGGGTAAAATGGTAATTCTATAAATCGAGGGTAAAACGATA
ATTCTGTAAATCAAGGGTAAAATGGTAATTCTATAAATCGAGA
Found at i:3315785 original size:53 final size:51
Alignment explanation
Indices: 3315595--3315796 Score: 199
Period size: 53 Copynumber: 3.8 Consensus size: 51
3315585 TCTTACAGAA
* *
3315595 GTATTTCAGTAATTTTACAAATCGAGGGTATTTCAGTAATTTTACAAATCGAGG
1 GTATTT-AGTAATTTTA-AACT-GAGGGTATTTCGGTAATTTTACAAATCGAGG
* *
3315649 GTATTTTAGTAATTTTGCAAACTGAGGGTATTTCGGTAATTTTACAAATTGATG
1 GTA-TTTAGTAATTTT--AAACTGAGGGTATTTCGGTAATTTTACAAATCGAGG
* * * *
3315703 GTATTTCAGTAATTTTACAA-TCGACGGTATTTCGGTAATTTTATAAACCGGGG
1 GTATTT-AGTAATTTTA-AACT-GAGGGTATTTCGGTAATTTTACAAATCGAGG
* * *
3315756 GTACTTTGGTAATTTTATAACTGGGGGTATTTCTGTAATTT
1 GTA-TTTAGTAATTTTA-AACTGAGGGTATTTCGGTAATTT
3315797 GGTAAACTAA
Statistics
Matches: 125, Mismatches: 15, Indels: 17
0.80 0.10 0.11
Matches are distributed among these distances:
52 2 0.02
53 60 0.48
54 56 0.45
55 6 0.05
56 1 0.01
ACGTcount: A:0.29, C:0.10, G:0.20, T:0.41
Consensus pattern (51 bp):
GTATTTAGTAATTTTAAACTGAGGGTATTTCGGTAATTTTACAAATCGAGG
Found at i:3319609 original size:22 final size:22
Alignment explanation
Indices: 3319584--3319706 Score: 67
Period size: 22 Copynumber: 5.3 Consensus size: 22
3319574 ACATACATAT
3319584 ATGTGATAAGGCCGAATGGCCA
1 ATGTGATAAGGCCGAATGGCCA
* *
3319606 ATGTGATGAATG-TGAACAT-G-CA
1 ATGTGAT-AAGGCCG-A-ATGGCCA
3319628 TATACGTGATAAGGCCGAATGGCCA
1 -AT--GTGATAAGGCCGAATGGCCA
* * *
3319653 ATGTGATGAATG-TGAACTTG-CA
1 ATGTGAT-AAGGCCGAA-TGGCCA
3319675 TATGTGTGATAAGGCCGAATGGCCA
1 -A--TGTGATAAGGCCGAATGGCCA
3319700 ATGTGAT
1 ATGTGAT
3319707 GAATGTGAAC
Statistics
Matches: 75, Mismatches: 10, Indels: 32
0.64 0.09 0.27
Matches are distributed among these distances:
22 26 0.35
23 15 0.20
24 15 0.20
25 19 0.25
ACGTcount: A:0.32, C:0.14, G:0.29, T:0.25
Consensus pattern (22 bp):
ATGTGATAAGGCCGAATGGCCA
Found at i:3319833 original size:141 final size:141
Alignment explanation
Indices: 3319563--3319843 Score: 422
Period size: 141 Copynumber: 2.0 Consensus size: 141
3319553 GATTTTATGA
3319563 GATGAATGTGAACATACATATATGTGATAAGGCCGAATGGCCAATGTGATGAATGTGAACATGCA
1 GATGAATGTGAACATACATATATGTGATAAGGCCGAATGGCCAATGTGATGAATGTGAACATGCA
* * * *
3319628 TATACGTGATAAGGCCGAATGGCCAATGTGATGAATGTGAACTTGCATATGTGTGATAAGGCCGA
66 TATACGTGATAAGGCAGAATGGCCAATGTGATGAACGTGAACTTACATATGTGTGAGAAGGCCGA
3319693 ATGGCCAATGT
131 ATGGCCAATGT
* *
3319704 GATGAATGTGAACATGCATATATGTGATAAGGCTGAATGGCCAATGTGATGAATGTGAACATGCA
1 GATGAATGTGAACATACATATATGTGATAAGGCCGAATGGCCAATGTGATGAATGTGAACATGCA
* * * * *
3319769 TATATGTGATAAGGTAGAATGGCCAATGTGATGAACGTGGAAGTGTATATATGTG-GCGAA-GCC
66 TATACGTGATAAGGCAGAATGGCCAATGTGATGAACGT-GAACT-TACATATGTGTGAGAAGGCC
*
3319832 GAATGGCTAATG
129 GAATGGCCAATG
3319844 CGAAATGTGT
Statistics
Matches: 126, Mismatches: 12, Indels: 4
0.89 0.08 0.03
Matches are distributed among these distances:
141 111 0.88
142 7 0.06
143 8 0.06
ACGTcount: A:0.33, C:0.12, G:0.29, T:0.26
Consensus pattern (141 bp):
GATGAATGTGAACATACATATATGTGATAAGGCCGAATGGCCAATGTGATGAATGTGAACATGCA
TATACGTGATAAGGCAGAATGGCCAATGTGATGAACGTGAACTTACATATGTGTGAGAAGGCCGA
ATGGCCAATGT
Found at i:3319838 original size:47 final size:47
Alignment explanation
Indices: 3319563--3319803 Score: 419
Period size: 47 Copynumber: 5.1 Consensus size: 47
3319553 GATTTTATGA
*
3319563 GATGAATGTGAACATACATATATGTGATAAGGCCGAATGGCCAATGT
1 GATGAATGTGAACATGCATATATGTGATAAGGCCGAATGGCCAATGT
*
3319610 GATGAATGTGAACATGCATATACGTGATAAGGCCGAATGGCCAATGT
1 GATGAATGTGAACATGCATATATGTGATAAGGCCGAATGGCCAATGT
* *
3319657 GATGAATGTGAACTTGCATATGTGTGATAAGGCCGAATGGCCAATGT
1 GATGAATGTGAACATGCATATATGTGATAAGGCCGAATGGCCAATGT
*
3319704 GATGAATGTGAACATGCATATATGTGATAAGGCTGAATGGCCAATGT
1 GATGAATGTGAACATGCATATATGTGATAAGGCCGAATGGCCAATGT
**
3319751 GATGAATGTGAACATGCATATATGTGATAAGGTAGAATGGCCAATGT
1 GATGAATGTGAACATGCATATATGTGATAAGGCCGAATGGCCAATGT
3319798 GATGAA
1 GATGAA
3319804 CGTGGAAGTG
Statistics
Matches: 184, Mismatches: 10, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
47 184 1.00
ACGTcount: A:0.34, C:0.12, G:0.28, T:0.26
Consensus pattern (47 bp):
GATGAATGTGAACATGCATATATGTGATAAGGCCGAATGGCCAATGT
Found at i:3319877 original size:46 final size:46
Alignment explanation
Indices: 3319827--3319953 Score: 218
Period size: 46 Copynumber: 2.8 Consensus size: 46
3319817 ATATGTGGCG
3319827 AAGCCGAATGGCTAATGCGAAATGTGTATGAGATGGATATGAGGTA
1 AAGCCGAATGGCTAATGCGAAATGTGTATGAGATGGATATGAGGTA
*
3319873 AAGCCGAATGGCTAATGCGAAACGTGTATGAGATGGATATGAGGTA
1 AAGCCGAATGGCTAATGCGAAATGTGTATGAGATGGATATGAGGTA
* * *
3319919 AAGCCGAATGGCTAATGTGAGATATGTATGAGATG
1 AAGCCGAATGGCTAATGCGAAATGTGTATGAGATG
3319954 TGTATATATA
Statistics
Matches: 76, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
46 76 1.00
ACGTcount: A:0.35, C:0.09, G:0.32, T:0.24
Consensus pattern (46 bp):
AAGCCGAATGGCTAATGCGAAATGTGTATGAGATGGATATGAGGTA
Found at i:3321052 original size:22 final size:23
Alignment explanation
Indices: 3321022--3321066 Score: 74
Period size: 22 Copynumber: 2.0 Consensus size: 23
3321012 ACCTGATCAG
*
3321022 AATATGACACAT-AAGTGCCTGA
1 AATACGACACATAAAGTGCCTGA
3321044 AATACGACACATAAAGTGCCTGA
1 AATACGACACATAAAGTGCCTGA
3321067 TCAGTAAAGC
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
22 11 0.52
23 10 0.48
ACGTcount: A:0.42, C:0.20, G:0.18, T:0.20
Consensus pattern (23 bp):
AATACGACACATAAAGTGCCTGA
Found at i:3321326 original size:28 final size:26
Alignment explanation
Indices: 3321257--3321374 Score: 131
Period size: 23 Copynumber: 4.6 Consensus size: 26
3321247 ATATGTCCAA
3321257 CCAAAACACACCAG---TATAATCCT
1 CCAAAACACACCAGATATATAATCCT
3321280 CCAAAACACACCAG---TATAATCCT
1 CCAAAACACACCAGATATATAATCCT
3321303 CCAAAACACACCAGTATCATATAATCCT
1 CCAAAACACACCAG-AT-ATATAATCCT
*
3321331 CCCAAACACACCAGAATAATATAATCCAT
1 CCAAAACACACCAG-AT-ATATAATCC-T
*
3321360 CCAAAACATACCAGA
1 CCAAAACACACCAGA
3321375 ATAGCACAAA
Statistics
Matches: 84, Mismatches: 5, Indels: 7
0.88 0.05 0.07
Matches are distributed among these distances:
23 37 0.44
28 34 0.40
29 13 0.15
ACGTcount: A:0.46, C:0.33, G:0.04, T:0.17
Consensus pattern (26 bp):
CCAAAACACACCAGATATATAATCCT
Found at i:3321376 original size:29 final size:28
Alignment explanation
Indices: 3321271--3321377 Score: 134
Period size: 28 Copynumber: 4.0 Consensus size: 28
3321261 AACACACCAG
3321271 TATAATCCTCCAAAACACACCAG-----
1 TATAATCCTCCAAAACACACCAGAATAA
* *
3321294 TATAATCCTCCAAAACACACCAGTATCA
1 TATAATCCTCCAAAACACACCAGAATAA
*
3321322 TATAATCCTCCCAAACACACCAGAATAA
1 TATAATCCTCCAAAACACACCAGAATAA
*
3321350 TATAATCCATCCAAAACATACCAGAATA
1 TATAATCC-TCCAAAACACACCAGAATA
3321378 GCACAAAGTG
Statistics
Matches: 73, Mismatches: 5, Indels: 6
0.87 0.06 0.07
Matches are distributed among these distances:
23 23 0.32
28 33 0.45
29 17 0.23
ACGTcount: A:0.46, C:0.31, G:0.04, T:0.20
Consensus pattern (28 bp):
TATAATCCTCCAAAACACACCAGAATAA
Found at i:3353503 original size:27 final size:27
Alignment explanation
Indices: 3353463--3353524 Score: 106
Period size: 27 Copynumber: 2.3 Consensus size: 27
3353453 CTGCTAGGGT
* *
3353463 TACTGAAATGGGCTAAGGCCTAATTGA
1 TACTGAAATAGGCTAAGGCCTAACTGA
3353490 TACTGAAATAGGCTAAGGCCTAACTGA
1 TACTGAAATAGGCTAAGGCCTAACTGA
3353517 TACTGAAA
1 TACTGAAA
3353525 GGGCTTAGTC
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
27 33 1.00
ACGTcount: A:0.37, C:0.16, G:0.23, T:0.24
Consensus pattern (27 bp):
TACTGAAATAGGCTAAGGCCTAACTGA
Found at i:3365220 original size:28 final size:28
Alignment explanation
Indices: 3365183--3365296 Score: 106
Period size: 28 Copynumber: 4.1 Consensus size: 28
3365173 CACATACCTA
* * *
3365183 TATATAGCCCATTAGGCCCAATCTA-TTT
1 TATATGGCCCATTAGGCACAATC-ACATT
3365211 TATATGGCCCATTAGGCACAATCACATT
1 TATATGGCCCATTAGGCACAATCACATT
* * *
3365239 TATGTGGCCCATTAAGCATAAATCACATT
1 TATATGGCCCATTAGGCA-CAATCACATT
* ** *
3365268 CATACAG-CCATTAGGCCCAATCACATT
1 TATATGGCCCATTAGGCACAATCACATT
3365295 TA
1 TA
3365297 CAGTTATACT
Statistics
Matches: 70, Mismatches: 14, Indels: 5
0.79 0.16 0.06
Matches are distributed among these distances:
27 11 0.16
28 47 0.67
29 12 0.17
ACGTcount: A:0.32, C:0.25, G:0.12, T:0.30
Consensus pattern (28 bp):
TATATGGCCCATTAGGCACAATCACATT
Found at i:3365545 original size:16 final size:16
Alignment explanation
Indices: 3365526--3365560 Score: 52
Period size: 16 Copynumber: 2.2 Consensus size: 16
3365516 CTTTTCGGCA
3365526 TTTCAGCATTTCAGCT
1 TTTCAGCATTTCAGCT
* *
3365542 TTTCGGCATTTCGGCT
1 TTTCAGCATTTCAGCT
3365558 TTT
1 TTT
3365561 TAAGATCTGC
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.11, C:0.23, G:0.17, T:0.49
Consensus pattern (16 bp):
TTTCAGCATTTCAGCT
Found at i:3365554 original size:8 final size:8
Alignment explanation
Indices: 3365518--3365556 Score: 51
Period size: 8 Copynumber: 4.9 Consensus size: 8
3365508 ACTTTTAGCT
3365518 TTTCGGCA
1 TTTCGGCA
*
3365526 TTTCAGCA
1 TTTCGGCA
* *
3365534 TTTCAGCT
1 TTTCGGCA
3365542 TTTCGGCA
1 TTTCGGCA
3365550 TTTCGGC
1 TTTCGGC
3365557 TTTTTAAGAT
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
8 27 1.00
ACGTcount: A:0.13, C:0.26, G:0.21, T:0.41
Consensus pattern (8 bp):
TTTCGGCA
Found at i:3375454 original size:40 final size:40
Alignment explanation
Indices: 3375371--3375633 Score: 318
Period size: 40 Copynumber: 6.6 Consensus size: 40
3375361 TTGAATGCTG
* * * * * *
3375371 TCCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGAATATA
1 TCCGGGTTAAGTCCCGAAGGCATTCGTGC-GAGTTATTAAA
* * * * *
3375411 TCCGGATTAAGAT-CCGAAGGCCTTTGTGCGAGATACTAAA
1 TCCGGGTTAAG-TCCCGAAGGCATTCGTGCGAGTTATTAAA
3375451 TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTATTAAA
1 TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTATTAAA
3375491 TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTATTAAA
1 TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTATTAAA
*
3375531 TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTGTTAAA
1 TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTATTAAA
* * *
3375571 TCCGGGTTATGTCCCGAAGGCATT-GTGTGAGTTACTAAAA
1 TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTA-TTAAA
* *
3375611 T-CGGGCTATGTCCCGAAGGCATT
1 TCCGGGTTAAGTCCCGAAGGCATT
3375634 TGAACGAGGA
Statistics
Matches: 201, Mismatches: 18, Indels: 9
0.88 0.08 0.04
Matches are distributed among these distances:
39 30 0.15
40 163 0.81
41 8 0.04
ACGTcount: A:0.25, C:0.20, G:0.28, T:0.27
Consensus pattern (40 bp):
TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTATTAAA
Found at i:3383382 original size:39 final size:37
Alignment explanation
Indices: 3383308--3383437 Score: 100
Period size: 39 Copynumber: 3.4 Consensus size: 37
3383298 CTGTCCGGGC
* *
3383308 TAAGTCCCGAAGG-CTTTGTGCAAGTGAATATATCCGGA
1 TAAGT-CCGAAGGCCTTTGTGCGAGT-AATAAATCCGGA
* *
3383346 TAAGATCCGAAGGCCTTTGTGCGAGATACTAAATCCGGGT
1 TAAG-TCCGAAGGCCTTTGTGCGAG-TAATAAATCC-GGA
* ** * *
3383386 TAAGTCCGAAGGCATTCATGCGAGTTATTAAATCCGGG
1 TAAGTCCGAAGGCCTTTGTGCGAG-TAATAAATCCGGA
*
3383424 TTAGTCCCGAAGGC
1 TAAGT-CCGAAGGC
3383438 TTCGGCGATT
Statistics
Matches: 76, Mismatches: 11, Indels: 9
0.79 0.11 0.09
Matches are distributed among these distances:
38 17 0.22
39 52 0.68
40 7 0.09
ACGTcount: A:0.28, C:0.20, G:0.27, T:0.25
Consensus pattern (37 bp):
TAAGTCCGAAGGCCTTTGTGCGAGTAATAAATCCGGA
Found at i:3383521 original size:39 final size:39
Alignment explanation
Indices: 3383352--3383550 Score: 211
Period size: 39 Copynumber: 5.3 Consensus size: 39
3383342 CGGATAAGAT
* * * *
3383352 CCGAAGGCCTTTGTGCGAGATACTAAATCCGGGTTAAGT-
1 CCGAAGGCATTCGTGCGAGTTATTAAATCCGGGTT-AGTC
*
3383391 CCGAAGGCATTCATGCGAGTTATTAAATCCGGGTTAGTC
1 CCGAAGGCATTCGTGCGAGTTATTAAATCCGGGTTAGTC
3383430 CCGAAGGC-TTCG-GCGA-TT-TT-AAT-C-GGTTAGTC
1 CCGAAGGCATTCGTGCGAGTTATTAAATCCGGGTTAGTC
*
3383462 CCGAAGGCATTCGTGCGAGTTGTTAAATCCGGGTTATGTC
1 CCGAAGGCATTCGTGCGAGTTATTAAATCCGGGTTA-GTC
* * * *
3383502 CCGAAGGCATT-GTGTGAGTTACTAAA-ACGGGCTATGTC
1 CCGAAGGCATTCGTGCGAGTTATTAAATCCGGGTTA-GTC
3383540 CCGAAGGCATT
1 CCGAAGGCATT
3383551 TGAACGAGGA
Statistics
Matches: 140, Mismatches: 11, Indels: 19
0.82 0.06 0.11
Matches are distributed among these distances:
32 16 0.11
33 5 0.04
34 7 0.05
35 4 0.03
36 4 0.03
37 7 0.05
38 28 0.20
39 55 0.39
40 14 0.10
ACGTcount: A:0.24, C:0.21, G:0.28, T:0.28
Consensus pattern (39 bp):
CCGAAGGCATTCGTGCGAGTTATTAAATCCGGGTTAGTC
Found at i:3383547 original size:38 final size:40
Alignment explanation
Indices: 3383459--3383550 Score: 125
Period size: 38 Copynumber: 2.4 Consensus size: 40
3383449 TAATCGGTTA
** * *
3383459 GTCCCGAAGGCATTCGTGCGAGTTGTTAAATCCGGGTTAT
1 GTCCCGAAGGCATTCGTGCGAGTTACTAAATACGGGCTAT
*
3383499 GTCCCGAAGGCATT-GTGTGAGTTACTAAA-ACGGGCTAT
1 GTCCCGAAGGCATTCGTGCGAGTTACTAAATACGGGCTAT
3383537 GTCCCGAAGGCATT
1 GTCCCGAAGGCATT
3383551 TGAACGAGGA
Statistics
Matches: 47, Mismatches: 5, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
38 21 0.45
39 12 0.26
40 14 0.30
ACGTcount: A:0.23, C:0.21, G:0.29, T:0.27
Consensus pattern (40 bp):
GTCCCGAAGGCATTCGTGCGAGTTACTAAATACGGGCTAT
Found at i:3401911 original size:103 final size:103
Alignment explanation
Indices: 3401752--3401953 Score: 395
Period size: 103 Copynumber: 2.0 Consensus size: 103
3401742 CACACAACAT
3401752 TTTTAGGTTGTGACATGTGGCACTGAGATGCCATAATCTATTCTTCCTATAAAAATATTTAAAAA
1 TTTTAGGTTGTGACATGTGGCACTGAGATGCCATAATCTATTCTTCCTATAAAAATATTTAAAAA
3401817 TTTAAAAGAAATATATAAAAATACTTAAAATTTAGCAC
66 TTTAAAAGAAATATATAAAAATACTTAAAATTTAGCAC
*
3401855 TTTTAGGTTGTGACATGTGGCACTGAGATGCCATAATCTATTCTTTCTATAAAAATATTTAAAAA
1 TTTTAGGTTGTGACATGTGGCACTGAGATGCCATAATCTATTCTTCCTATAAAAATATTTAAAAA
3401920 TTTAAAAGAAATATATAAAAATACTTAAAATTTA
66 TTTAAAAGAAATATATAAAAATACTTAAAATTTA
3401954 AGGAAACCTG
Statistics
Matches: 98, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
103 98 1.00
ACGTcount: A:0.42, C:0.10, G:0.11, T:0.36
Consensus pattern (103 bp):
TTTTAGGTTGTGACATGTGGCACTGAGATGCCATAATCTATTCTTCCTATAAAAATATTTAAAAA
TTTAAAAGAAATATATAAAAATACTTAAAATTTAGCAC
Found at i:3402350 original size:10 final size:10
Alignment explanation
Indices: 3402310--3402353 Score: 52
Period size: 10 Copynumber: 4.2 Consensus size: 10
3402300 GTTTATCAAC
*
3402310 ATTTAATTGT
1 ATTTAATTAT
*
3402320 GTTTAATTAT
1 ATTTAATTAT
3402330 AATTATAATTAT
1 -ATT-TAATTAT
3402342 ATTTAATTAT
1 ATTTAATTAT
3402352 AT
1 AT
3402354 GTGTTTGAGG
Statistics
Matches: 29, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
10 17 0.59
11 5 0.17
12 7 0.24
ACGTcount: A:0.39, C:0.00, G:0.05, T:0.57
Consensus pattern (10 bp):
ATTTAATTAT
Found at i:3402552 original size:27 final size:27
Alignment explanation
Indices: 3402514--3402568 Score: 110
Period size: 27 Copynumber: 2.0 Consensus size: 27
3402504 ATTAACCATT
3402514 TAACAGAGGTGACCAAAATAGAAACTA
1 TAACAGAGGTGACCAAAATAGAAACTA
3402541 TAACAGAGGTGACCAAAATAGAAACTA
1 TAACAGAGGTGACCAAAATAGAAACTA
3402568 T
1 T
3402569 CTAAAACATG
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 28 1.00
ACGTcount: A:0.51, C:0.15, G:0.18, T:0.16
Consensus pattern (27 bp):
TAACAGAGGTGACCAAAATAGAAACTA
Found at i:3402856 original size:4 final size:4
Alignment explanation
Indices: 3402840--3402874 Score: 61
Period size: 4 Copynumber: 8.8 Consensus size: 4
3402830 TTGGAAATGG
*
3402840 AATT AAGT AATT AATT AATT AATT AATT AATT AAT
1 AATT AATT AATT AATT AATT AATT AATT AATT AAT
3402875 ATTAGTACAT
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
4 29 1.00
ACGTcount: A:0.51, C:0.00, G:0.03, T:0.46
Consensus pattern (4 bp):
AATT
Found at i:3404377 original size:31 final size:31
Alignment explanation
Indices: 3404339--3404400 Score: 124
Period size: 31 Copynumber: 2.0 Consensus size: 31
3404329 GATATTATAC
3404339 ATACAAAGGTATTTTAATAATTATTCTAGGA
1 ATACAAAGGTATTTTAATAATTATTCTAGGA
3404370 ATACAAAGGTATTTTAATAATTATTCTAGGA
1 ATACAAAGGTATTTTAATAATTATTCTAGGA
3404401 CTAAGCGGGC
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
31 31 1.00
ACGTcount: A:0.42, C:0.06, G:0.13, T:0.39
Consensus pattern (31 bp):
ATACAAAGGTATTTTAATAATTATTCTAGGA
Found at i:3412569 original size:21 final size:21
Alignment explanation
Indices: 3412527--3412570 Score: 52
Period size: 21 Copynumber: 2.1 Consensus size: 21
3412517 CACATCGTTT
* *
3412527 CCTCCTCTTTCTCCGCCACCG
1 CCTCCTCTGTCTACGCCACCG
* *
3412548 CCTCCTCTGTCTACTCCGCCG
1 CCTCCTCTGTCTACGCCACCG
3412569 CC
1 CC
3412571 ACCGCCAGAG
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.05, C:0.57, G:0.11, T:0.27
Consensus pattern (21 bp):
CCTCCTCTGTCTACGCCACCG
Found at i:3416682 original size:22 final size:22
Alignment explanation
Indices: 3416638--3416692 Score: 58
Period size: 22 Copynumber: 2.5 Consensus size: 22
3416628 TTGGGTTTTC
* *
3416638 TTTGAAGAGAAAAATATTGGGT
1 TTTGAAGAGAAAAATAATAGGT
* *
3416660 TTTGATGAGAAAATTAATAGG-
1 TTTGAAGAGAAAAATAATAGGT
*
3416681 TTTGAAGGGAAA
1 TTTGAAGAGAAA
3416693 TTTGGGATCT
Statistics
Matches: 27, Mismatches: 6, Indels: 1
0.79 0.18 0.03
Matches are distributed among these distances:
21 10 0.37
22 17 0.63
ACGTcount: A:0.42, C:0.00, G:0.27, T:0.31
Consensus pattern (22 bp):
TTTGAAGAGAAAAATAATAGGT
Found at i:3418317 original size:18 final size:18
Alignment explanation
Indices: 3418294--3418345 Score: 86
Period size: 18 Copynumber: 2.9 Consensus size: 18
3418284 AAAATGCGAG
*
3418294 AAATGATGTTTACATTTC
1 AAATGATGTTCACATTTC
*
3418312 AAATGATATTCACATTTC
1 AAATGATGTTCACATTTC
3418330 AAATGATGTTCACATT
1 AAATGATGTTCACATT
3418346 GATGAAAATG
Statistics
Matches: 31, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
18 31 1.00
ACGTcount: A:0.37, C:0.13, G:0.10, T:0.40
Consensus pattern (18 bp):
AAATGATGTTCACATTTC
Found at i:3420913 original size:26 final size:26
Alignment explanation
Indices: 3420861--3420913 Score: 61
Period size: 26 Copynumber: 2.0 Consensus size: 26
3420851 CTTAAATCAA
* * *
3420861 ACTTTTCAAAAATACTTTTCTACAGC
1 ACTTTTCAAAAACACTTTTCAAAAGC
* *
3420887 ACTTTTCTAAAACATTTTTCAAAAGC
1 ACTTTTCAAAAACACTTTTCAAAAGC
3420913 A
1 A
3420914 ATACTAAACT
Statistics
Matches: 22, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
26 22 1.00
ACGTcount: A:0.38, C:0.21, G:0.04, T:0.38
Consensus pattern (26 bp):
ACTTTTCAAAAACACTTTTCAAAAGC
Found at i:3424355 original size:6 final size:6
Alignment explanation
Indices: 3424346--3424388 Score: 86
Period size: 6 Copynumber: 7.2 Consensus size: 6
3424336 AGAAACAGAA
3424346 GAGTTG GAGTTG GAGTTG GAGTTG GAGTTG GAGTTG GAGTTG G
1 GAGTTG GAGTTG GAGTTG GAGTTG GAGTTG GAGTTG GAGTTG G
3424389 TTATGATTAG
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 37 1.00
ACGTcount: A:0.16, C:0.00, G:0.51, T:0.33
Consensus pattern (6 bp):
GAGTTG
Found at i:3431906 original size:26 final size:26
Alignment explanation
Indices: 3431877--3432062 Score: 300
Period size: 26 Copynumber: 7.2 Consensus size: 26
3431867 TGGTACAAAT
3431877 TGATAATGGGTTAGGTAAATGTTCCA
1 TGATAATGGGTTAGGTAAATGTTCCA
* *
3431903 TGATAATGGATTAGGTAAATATTCCA
1 TGATAATGGGTTAGGTAAATGTTCCA
3431929 TGATAATGGGTTAGGTAAATGTTCCA
1 TGATAATGGGTTAGGTAAATGTTCCA
* * * *
3431955 TGATAATTGATTAGGTAAATATTTCA
1 TGATAATGGGTTAGGTAAATGTTCCA
3431981 TGATAATGGGTTAGGTAAATGTTCCA
1 TGATAATGGGTTAGGTAAATGTTCCA
*
3432007 TGATAATGGCTTAGGTAAATGTTCCA
1 TGATAATGGGTTAGGTAAATGTTCCA
*
3432033 TGATAATGGTTTAGGTAAATGTTCCA
1 TGATAATGGGTTAGGTAAATGTTCCA
3432059 TGAT
1 TGAT
3432063 GGGCATTTCA
Statistics
Matches: 146, Mismatches: 14, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
26 146 1.00
ACGTcount: A:0.33, C:0.08, G:0.23, T:0.37
Consensus pattern (26 bp):
TGATAATGGGTTAGGTAAATGTTCCA
Found at i:3439024 original size:26 final size:26
Alignment explanation
Indices: 3438995--3439155 Score: 227
Period size: 26 Copynumber: 6.2 Consensus size: 26
3438985 TGGTACAAAT
3438995 TGATAAT-GAGTTAGGTAAATGTTCCA
1 TGATAATGGA-TTAGGTAAATGTTCCA
*
3439021 TGATAAATGGATTAGGTAAATATTCCA
1 TGAT-AATGGATTAGGTAAATGTTCCA
3439048 TGATAATTGG-TTAGGTAAATGTTCCA
1 TGATAA-TGGATTAGGTAAATGTTCCA
* *
3439074 TGGTAATGGATTAGGTAAATATTCCA
1 TGATAATGGATTAGGTAAATGTTCCA
*
3439100 TGATAATGGGTTAGGTAAATGTTCCA
1 TGATAATGGATTAGGTAAATGTTCCA
* *
3439126 TGATAATGGTTTAGGTAAATGTTCCG
1 TGATAATGGATTAGGTAAATGTTCCA
3439152 TGAT
1 TGAT
3439156 GGGCATTTCA
Statistics
Matches: 122, Mismatches: 9, Indels: 8
0.88 0.06 0.06
Matches are distributed among these distances:
25 3 0.02
26 92 0.75
27 25 0.20
28 2 0.02
ACGTcount: A:0.33, C:0.07, G:0.24, T:0.36
Consensus pattern (26 bp):
TGATAATGGATTAGGTAAATGTTCCA
Found at i:3439103 original size:52 final size:52
Alignment explanation
Indices: 3438995--3439155 Score: 252
Period size: 52 Copynumber: 3.1 Consensus size: 52
3438985 TGGTACAAAT
3438995 TGATAA-TGAGTTAGGTAAATGTTCCATGATAAATGGATTAGGTAAATATTCCA
1 TGATAATTG-GTTAGGTAAATGTTCCATGAT-AATGGATTAGGTAAATATTCCA
*
3439048 TGATAATTGGTTAGGTAAATGTTCCATGGTAATGGATTAGGTAAATATTCCA
1 TGATAATTGGTTAGGTAAATGTTCCATGATAATGGATTAGGTAAATATTCCA
* * * *
3439100 TGATAATGGGTTAGGTAAATGTTCCATGATAATGGTTTAGGTAAATGTTCCG
1 TGATAATTGGTTAGGTAAATGTTCCATGATAATGGATTAGGTAAATATTCCA
3439152 TGAT
1 TGAT
3439156 GGGCATTTCA
Statistics
Matches: 101, Mismatches: 6, Indels: 3
0.92 0.05 0.03
Matches are distributed among these distances:
52 73 0.72
53 26 0.26
54 2 0.02
ACGTcount: A:0.33, C:0.07, G:0.24, T:0.36
Consensus pattern (52 bp):
TGATAATTGGTTAGGTAAATGTTCCATGATAATGGATTAGGTAAATATTCCA
Found at i:3445131 original size:6 final size:6
Alignment explanation
Indices: 3445120--3445152 Score: 57
Period size: 6 Copynumber: 5.5 Consensus size: 6
3445110 TTCTGAGAAT
*
3445120 GATAGG GATAGG GATAGG GATAGG GACAGG GAT
1 GATAGG GATAGG GATAGG GATAGG GATAGG GAT
3445153 GGAGTAATTT
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
6 25 1.00
ACGTcount: A:0.33, C:0.03, G:0.48, T:0.15
Consensus pattern (6 bp):
GATAGG
Found at i:3453522 original size:16 final size:18
Alignment explanation
Indices: 3453488--3453528 Score: 50
Period size: 19 Copynumber: 2.3 Consensus size: 18
3453478 ATGTTTTTTT
3453488 ATATATATTATTATGTTAA
1 ATATATATTA-TATGTTAA
3453507 ATATATATTA-AT-TTAA
1 ATATATATTATATGTTAA
*
3453523 AAATAT
1 ATATAT
3453529 CAACTAATTT
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
16 9 0.43
17 2 0.10
19 10 0.48
ACGTcount: A:0.49, C:0.00, G:0.02, T:0.49
Consensus pattern (18 bp):
ATATATATTATATGTTAA
Found at i:3453712 original size:15 final size:15
Alignment explanation
Indices: 3453692--3453752 Score: 54
Period size: 13 Copynumber: 4.1 Consensus size: 15
3453682 GAATATATAA
3453692 AAATAATTATATTTG
1 AAATAATTATATTTG
3453707 AAATAA-T-TATTTG
1 AAATAATTATATTTG
* * **
3453720 AAATATTTCACATATAA
1 AAATAATT-ATAT-TTG
3453737 AAATAATTATATTTG
1 AAATAATTATATTTG
3453752 A
1 A
3453753 GATATTTTAT
Statistics
Matches: 34, Mismatches: 8, Indels: 8
0.68 0.16 0.16
Matches are distributed among these distances:
13 11 0.32
14 2 0.06
15 8 0.24
16 5 0.15
17 8 0.24
ACGTcount: A:0.49, C:0.03, G:0.05, T:0.43
Consensus pattern (15 bp):
AAATAATTATATTTG
Found at i:3453741 original size:30 final size:32
Alignment explanation
Indices: 3453707--3453769 Score: 85
Period size: 32 Copynumber: 2.0 Consensus size: 32
3453697 ATTATATTTG
3453707 AAATAA-T-TATTTGAAATATTTCACATATAA
1 AAATAATTATATTTGAAATATTTCACATATAA
* * *
3453737 AAATAATTATATTTGAGATATTTTATATATAA
1 AAATAATTATATTTGAAATATTTCACATATAA
3453769 A
1 A
3453770 TTTAAAATAG
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
30 6 0.21
31 1 0.04
32 21 0.75
ACGTcount: A:0.49, C:0.03, G:0.05, T:0.43
Consensus pattern (32 bp):
AAATAATTATATTTGAAATATTTCACATATAA
Found at i:3466316 original size:16 final size:17
Alignment explanation
Indices: 3466288--3466320 Score: 59
Period size: 16 Copynumber: 2.0 Consensus size: 17
3466278 AAATAGATTT
3466288 TTAATTAAAAATTTTAA
1 TTAATTAAAAATTTTAA
3466305 TTAATT-AAAATTTTAA
1 TTAATTAAAAATTTTAA
3466321 ACCTAAACCT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 10 0.62
17 6 0.38
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (17 bp):
TTAATTAAAAATTTTAA
Found at i:3468383 original size:28 final size:28
Alignment explanation
Indices: 3468352--3468408 Score: 105
Period size: 28 Copynumber: 2.0 Consensus size: 28
3468342 AAAATTATTG
3468352 ATGAAAATAGAAATGGTTAGCATTAATA
1 ATGAAAATAGAAATGGTTAGCATTAATA
*
3468380 ATGAAAATAGAGATGGTTAGCATTAATA
1 ATGAAAATAGAAATGGTTAGCATTAATA
3468408 A
1 A
3468409 GTTGGAATTA
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
28 28 1.00
ACGTcount: A:0.49, C:0.04, G:0.19, T:0.28
Consensus pattern (28 bp):
ATGAAAATAGAAATGGTTAGCATTAATA
Found at i:3469232 original size:30 final size:30
Alignment explanation
Indices: 3469166--3469232 Score: 73
Period size: 30 Copynumber: 2.2 Consensus size: 30
3469156 AACTTAAATG
* **
3469166 AAAACTTTTTTGTAGTTCAGTAACCAAATT
1 AAAACTTTTTTGTAGTTAAGTAACCAAACA
**
3469196 GTAACTTTTTT-TAGTTAAGTAACCAAAACA
1 AAAACTTTTTTGTAGTTAAGTAACC-AAACA
3469226 AAAACTT
1 AAAACTT
3469233 ATCAATAATT
Statistics
Matches: 29, Mismatches: 7, Indels: 2
0.76 0.18 0.05
Matches are distributed among these distances:
29 12 0.41
30 17 0.59
ACGTcount: A:0.40, C:0.13, G:0.09, T:0.37
Consensus pattern (30 bp):
AAAACTTTTTTGTAGTTAAGTAACCAAACA
Found at i:3470304 original size:48 final size:48
Alignment explanation
Indices: 3470249--3470346 Score: 196
Period size: 48 Copynumber: 2.0 Consensus size: 48
3470239 AGGTTGGTAG
3470249 AATCCTAGTTGAAGTGGTAGAATACAAATAATATTATTTTAATAGAAA
1 AATCCTAGTTGAAGTGGTAGAATACAAATAATATTATTTTAATAGAAA
3470297 AATCCTAGTTGAAGTGGTAGAATACAAATAATATTATTTTAATAGAAA
1 AATCCTAGTTGAAGTGGTAGAATACAAATAATATTATTTTAATAGAAA
3470345 AA
1 AA
3470347 ATCTCTAACT
Statistics
Matches: 50, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
48 50 1.00
ACGTcount: A:0.47, C:0.06, G:0.14, T:0.33
Consensus pattern (48 bp):
AATCCTAGTTGAAGTGGTAGAATACAAATAATATTATTTTAATAGAAA
Found at i:3472345 original size:23 final size:23
Alignment explanation
Indices: 3472319--3472439 Score: 88
Period size: 23 Copynumber: 5.2 Consensus size: 23
3472309 ATTTTAGGTG
3472319 TTTGTCTTCCACAATTTTAAGGA
1 TTTGTCTTCCACAATTTTAAGGA
* * *
3472342 TTTGT-TTAGCTAAAATTTTAGGTGA
1 TTTGTCTT--CCACAATTTTAAG-GA
*
3472367 -TTGTCTTCCATAATTTTAAGGA
1 TTTGTCTTCCACAATTTTAAGGA
** *
3472389 TTTGTTCGGCTA-AATTTT-AGGCA
1 TTTG-TCTTCCACAATTTTAAGG-A
* *
3472412 TTTTTCTTCCACAATTTTAAGGG
1 TTTGTCTTCCACAATTTTAAGGA
3472435 TTTGT
1 TTTGT
3472440 TTCTCTTTTA
Statistics
Matches: 74, Mismatches: 15, Indels: 18
0.69 0.14 0.17
Matches are distributed among these distances:
22 11 0.15
23 38 0.51
24 21 0.28
25 4 0.05
ACGTcount: A:0.24, C:0.12, G:0.17, T:0.47
Consensus pattern (23 bp):
TTTGTCTTCCACAATTTTAAGGA
Found at i:3472372 original size:47 final size:46
Alignment explanation
Indices: 3472304--3472441 Score: 188
Period size: 47 Copynumber: 3.0 Consensus size: 46
3472294 TGCAGGTTAG
*
3472304 GCTAAATTTTAGGTGTTTGTCTTCCACAATTTTAAGGATTTGTTTA
1 GCTAAATTTTAGGTGATTGTCTTCCACAATTTTAAGGATTTGTTTA
* **
3472350 GCTAAAATTTTAGGTGATTGTCTTCCATAATTTTAAGGATTTGTTCG
1 GCT-AAATTTTAGGTGATTGTCTTCCACAATTTTAAGGATTTGTTTA
* * *
3472397 GCTAAATTTTAGG-CATTTTTCTTCCACAATTTTAAGGGTTTGTTT
1 GCTAAATTTTAGGTGA-TTGTCTTCCACAATTTTAAGGATTTGTTT
3472442 CTCTTTTATC
Statistics
Matches: 81, Mismatches: 9, Indels: 4
0.86 0.10 0.04
Matches are distributed among these distances:
45 1 0.01
46 38 0.47
47 42 0.52
ACGTcount: A:0.24, C:0.12, G:0.17, T:0.47
Consensus pattern (46 bp):
GCTAAATTTTAGGTGATTGTCTTCCACAATTTTAAGGATTTGTTTA
Found at i:3473815 original size:9 final size:9
Alignment explanation
Indices: 3473801--3473835 Score: 52
Period size: 9 Copynumber: 3.9 Consensus size: 9
3473791 TTATTTATCC
3473801 AATTAATTA
1 AATTAATTA
*
3473810 AATTAATTG
1 AATTAATTA
*
3473819 AATTAACTA
1 AATTAATTA
3473828 AATTAATT
1 AATTAATT
3473836 TCTTAATTAA
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
9 22 1.00
ACGTcount: A:0.51, C:0.03, G:0.03, T:0.43
Consensus pattern (9 bp):
AATTAATTA
Found at i:3473822 original size:18 final size:18
Alignment explanation
Indices: 3473801--3473835 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
3473791 TTATTTATCC
*
3473801 AATTAATTAAATTAATTG
1 AATTAACTAAATTAATTG
3473819 AATTAACTAAATTAATT
1 AATTAACTAAATTAATT
3473836 TCTTAATTAA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.51, C:0.03, G:0.03, T:0.43
Consensus pattern (18 bp):
AATTAACTAAATTAATTG
Found at i:3474815 original size:17 final size:17
Alignment explanation
Indices: 3474793--3474828 Score: 72
Period size: 17 Copynumber: 2.1 Consensus size: 17
3474783 GACTTAAAAG
3474793 TAACAATGTTAACTTTT
1 TAACAATGTTAACTTTT
3474810 TAACAATGTTAACTTTT
1 TAACAATGTTAACTTTT
3474827 TA
1 TA
3474829 GTGTTTAATT
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:0.36, C:0.11, G:0.06, T:0.47
Consensus pattern (17 bp):
TAACAATGTTAACTTTT
Found at i:3486065 original size:13 final size:13
Alignment explanation
Indices: 3486047--3486073 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
3486037 ATGAGAGTAC
3486047 TTTTAGGAAACCT
1 TTTTAGGAAACCT
3486060 TTTTAGGAAACCT
1 TTTTAGGAAACCT
3486073 T
1 T
3486074 ATCAAGAGAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.30, C:0.15, G:0.15, T:0.41
Consensus pattern (13 bp):
TTTTAGGAAACCT
Found at i:3486626 original size:40 final size:40
Alignment explanation
Indices: 3486581--3486656 Score: 100
Period size: 40 Copynumber: 1.9 Consensus size: 40
3486571 TTACACCATG
* *
3486581 TGGGGATAGAATCGACCCA-CCTAACCTTACACACCAAGTA
1 TGGGGATAGAATCAACCCATCC-AACCCTACACACCAAGTA
**
3486621 TGGGGATTTAATCAACCCATCCAACCCTACACACCA
1 TGGGGATAGAATCAACCCATCCAACCCTACACACCA
3486657 TAAGGTACCG
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
40 29 0.94
41 2 0.06
ACGTcount: A:0.34, C:0.33, G:0.14, T:0.18
Consensus pattern (40 bp):
TGGGGATAGAATCAACCCATCCAACCCTACACACCAAGTA
Found at i:3488182 original size:2 final size:2
Alignment explanation
Indices: 3488175--3488433 Score: 218
Period size: 2 Copynumber: 131.0 Consensus size: 2
3488165 AAATTATTCT
* * * * *
3488175 TC TC TC TC TC TC TC TC TC TC TC CC AC TC TC TC CC TC CC TT TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
* * * * * * *
3488217 TT TC TC T- TC -C TC CC TC -C CC TC CC TC TC CC TC CC TT TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
* * * * * * * *
3488256 CC CC TC TC TC TC TC CC TC TC CC AC TC TC CC AC TC TC CC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
3488298 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
* * * *
3488340 TC TC TC CC CC TC TC TC CC TC TC TC CC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
* * * * * *
3488382 TC TC TC CC TC TC CC CC TT TC TC CC TC TC TC TC TC TC TC TC CC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
*
3488424 CC TC TC TC TC
1 TC TC TC TC TC
3488434 CCTCACACAC
Statistics
Matches: 204, Mismatches: 50, Indels: 6
0.78 0.19 0.02
Matches are distributed among these distances:
1 3 0.01
2 201 0.99
ACGTcount: A:0.01, C:0.58, G:0.00, T:0.41
Consensus pattern (2 bp):
TC
Found at i:3489493 original size:38 final size:38
Alignment explanation
Indices: 3489366--3489495 Score: 93
Period size: 38 Copynumber: 3.2 Consensus size: 38
3489356 ACAAAGAGCA
3489366 AATTAATTAACATAATTAGCAAAAATAAACCTTTGCAC
1 AATTAATTAACATAATTAGCAAAAATAAACCTTTGCAC
* * * * ***
3489404 AAATACA-TATCATAACTTCAACAACCAAATAATTCAACAAAG-AGC
1 AATTA-ATTAACATAA-TT-AGCAA--AAATAA---ACCTTTGCA-C
3489449 AAATTAATTAACATAATTAGCAAAAATAAACCTTTGCAC
1 -AATTAATTAACATAATTAGCAAAAATAAACCTTTGCAC
3489488 AATTAATT
1 AATTAATT
3489496 TAGGCAAAAG
Statistics
Matches: 66, Mismatches: 14, Indels: 24
0.63 0.13 0.23
Matches are distributed among these distances:
38 19 0.29
39 7 0.11
40 5 0.08
42 12 0.18
44 5 0.08
45 7 0.11
46 11 0.17
ACGTcount: A:0.52, C:0.17, G:0.05, T:0.27
Consensus pattern (38 bp):
AATTAATTAACATAATTAGCAAAAATAAACCTTTGCAC
Found at i:3490827 original size:53 final size:54
Alignment explanation
Indices: 3490724--3490839 Score: 132
Period size: 54 Copynumber: 2.1 Consensus size: 54
3490714 GCAGAAAAGA
*
3490724 AAAAAATAAATCATGGAAGAAAATTATAAATTTTAATATAACTTTTTGAA-TTTT
1 AAAAAATTAATCATGGAAGAAAATTATAAATTTTAATAT-ACTTTTTGAATTTTT
* *
3490778 AAAAAATTAATC-TCGGAAGAAATTTAT-AATTTGTAATAT-TTTTTATGAATTTTT
1 AAAAAATTAATCAT-GGAAGAAAATTATAAATTT-TAATATACTTTT-TGAATTTTT
*
3490832 AAATAATT
1 AAAAAATT
3490840 GTAATAATTT
Statistics
Matches: 54, Mismatches: 4, Indels: 8
0.82 0.06 0.12
Matches are distributed among these distances:
52 4 0.07
53 10 0.19
54 40 0.74
ACGTcount: A:0.47, C:0.03, G:0.08, T:0.42
Consensus pattern (54 bp):
AAAAAATTAATCATGGAAGAAAATTATAAATTTTAATATACTTTTTGAATTTTT
Found at i:3493226 original size:54 final size:54
Alignment explanation
Indices: 3493144--3493252 Score: 218
Period size: 54 Copynumber: 2.0 Consensus size: 54
3493134 TTGTCGGAAC
3493144 ATATCCATTCGATATTTGACAACGGATAAGCATAAAACCATCTAAACAAAAACA
1 ATATCCATTCGATATTTGACAACGGATAAGCATAAAACCATCTAAACAAAAACA
3493198 ATATCCATTCGATATTTGACAACGGATAAGCATAAAACCATCTAAACAAAAACA
1 ATATCCATTCGATATTTGACAACGGATAAGCATAAAACCATCTAAACAAAAACA
3493252 A
1 A
3493253 GTCAAGCCAA
Statistics
Matches: 55, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
54 55 1.00
ACGTcount: A:0.49, C:0.20, G:0.09, T:0.22
Consensus pattern (54 bp):
ATATCCATTCGATATTTGACAACGGATAAGCATAAAACCATCTAAACAAAAACA
Found at i:3495908 original size:52 final size:54
Alignment explanation
Indices: 3495851--3495954 Score: 149
Period size: 56 Copynumber: 1.9 Consensus size: 54
3495841 AACTCCTAAG
**
3495851 GAACCCTAGGTGTGA-C-AGTATTCTTTCTTCTTGGTTGTTTGATACATGTAAA
1 GAACCCTAGGTGTGACCTAGTATTCTTTCTTCTTGGTTCATTGATACATGTAAA
*
3495903 GAACCCTAGGTGTGACCCTTGGTATTCTTTCTTCTTGGTTCATTGATACATG
1 GAACCCTAGGTGTGA-CC-TAGTATTCTTTCTTCTTGGTTCATTGATACATG
3495955 GAAGAAACCT
Statistics
Matches: 45, Mismatches: 3, Indels: 4
0.87 0.06 0.08
Matches are distributed among these distances:
52 15 0.33
54 1 0.02
56 29 0.64
ACGTcount: A:0.20, C:0.18, G:0.21, T:0.40
Consensus pattern (54 bp):
GAACCCTAGGTGTGACCTAGTATTCTTTCTTCTTGGTTCATTGATACATGTAAA
Found at i:3496686 original size:3 final size:3
Alignment explanation
Indices: 3496678--3496703 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
3496668 AGACAAGGTG
3496678 ATA ATA ATA ATA ATA ATA ATA ATA AT
1 ATA ATA ATA ATA ATA ATA ATA ATA AT
3496704 GAAAACAACA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (3 bp):
ATA
Found at i:3513506 original size:4 final size:4
Alignment explanation
Indices: 3513497--3513521 Score: 50
Period size: 4 Copynumber: 6.2 Consensus size: 4
3513487 CAAAAATAAA
3513497 ATTT ATTT ATTT ATTT ATTT ATTT A
1 ATTT ATTT ATTT ATTT ATTT ATTT A
3513522 ATAGAAAACC
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 21 1.00
ACGTcount: A:0.28, C:0.00, G:0.00, T:0.72
Consensus pattern (4 bp):
ATTT
Found at i:3513682 original size:24 final size:23
Alignment explanation
Indices: 3513646--3513696 Score: 61
Period size: 24 Copynumber: 2.2 Consensus size: 23
3513636 TTTTTAATAT
3513646 TATTAGATAATCATATCATTTTTC-
1 TATTAGATAATCAT-T-ATTTTTCA
3513670 TATTA-ATATATCATTATTTTTCA
1 TATTAGATA-ATCATTATTTTTCA
3513693 TATT
1 TATT
3513697 TATGAAATTA
Statistics
Matches: 25, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
22 7 0.28
23 8 0.32
24 10 0.40
ACGTcount: A:0.33, C:0.10, G:0.02, T:0.55
Consensus pattern (23 bp):
TATTAGATAATCATTATTTTTCA
Found at i:3513763 original size:18 final size:18
Alignment explanation
Indices: 3513742--3513777 Score: 72
Period size: 18 Copynumber: 2.0 Consensus size: 18
3513732 GTACCAAAAA
3513742 ATATTAATAATTTAAGTT
1 ATATTAATAATTTAAGTT
3513760 ATATTAATAATTTAAGTT
1 ATATTAATAATTTAAGTT
3513778 TAATATAAAT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.44, C:0.00, G:0.06, T:0.50
Consensus pattern (18 bp):
ATATTAATAATTTAAGTT
Found at i:3540038 original size:10 final size:10
Alignment explanation
Indices: 3540014--3540047 Score: 50
Period size: 10 Copynumber: 3.3 Consensus size: 10
3540004 GAAACAAAAT
*
3540014 AAAAAATTTA
1 AAAAAATTGA
3540024 GAAAAAATTGA
1 -AAAAAATTGA
3540035 AAAAAATTGA
1 AAAAAATTGA
3540045 AAA
1 AAA
3540048 CAGAAGTCAT
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
10 13 0.59
11 9 0.41
ACGTcount: A:0.71, C:0.00, G:0.09, T:0.21
Consensus pattern (10 bp):
AAAAAATTGA
Found at i:3542170 original size:16 final size:16
Alignment explanation
Indices: 3542149--3542181 Score: 66
Period size: 16 Copynumber: 2.1 Consensus size: 16
3542139 ATTCGAATTC
3542149 AACGAGAAAAGTCGCA
1 AACGAGAAAAGTCGCA
3542165 AACGAGAAAAGTCGCA
1 AACGAGAAAAGTCGCA
3542181 A
1 A
3542182 CCTAGTAAGT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.52, C:0.18, G:0.24, T:0.06
Consensus pattern (16 bp):
AACGAGAAAAGTCGCA
Found at i:3543047 original size:22 final size:21
Alignment explanation
Indices: 3543017--3543082 Score: 64
Period size: 19 Copynumber: 3.2 Consensus size: 21
3543007 TACAAATTAA
3543017 ATCTCCAAGATTACAAGATCAT
1 ATCTCCAAGATTAC-AGATCAT
* * *
3543039 ATCTTCAAGATTGCATATCAT
1 ATCTCCAAGATTACAGATCAT
* *
3543060 ATCT--AGGATTACATATCAT
1 ATCTCCAAGATTACAGATCAT
3543079 ATCT
1 ATCT
3543083 AAGATTGTAT
Statistics
Matches: 39, Mismatches: 5, Indels: 3
0.83 0.11 0.06
Matches are distributed among these distances:
19 17 0.44
21 10 0.26
22 12 0.31
ACGTcount: A:0.36, C:0.20, G:0.09, T:0.35
Consensus pattern (21 bp):
ATCTCCAAGATTACAGATCAT
Found at i:3543074 original size:19 final size:19
Alignment explanation
Indices: 3543034--3543185 Score: 215
Period size: 19 Copynumber: 8.2 Consensus size: 19
3543024 AGATTACAAG
3543034 ATCATATCTTCAAGATTGCAT
1 ATCATATC-T-AAGATTGCAT
* *
3543055 ATCATATCTAGGATTACAT
1 ATCATATCTAAGATTGCAT
3543074 ATCATATCTAAGATTG--T
1 ATCATATCTAAGATTGCAT
3543091 ATCATATCTAAGATTGCA-
1 ATCATATCTAAGATTGCAT
*
3543109 ATCATATCTAATATTGCAT
1 ATCATATCTAAGATTGCAT
*
3543128 ATCATATCTAATATTG--T
1 ATCATATCTAAGATTGCAT
3543145 ATCATATCTAAGATTGCAT
1 ATCATATCTAAGATTGCAT
3543164 ATCATATCTAAGATTGCAT
1 ATCATATCTAAGATTGCAT
3543183 ATC
1 ATC
3543186 CTTAAAGATT
Statistics
Matches: 120, Mismatches: 6, Indels: 12
0.87 0.04 0.09
Matches are distributed among these distances:
17 33 0.28
18 17 0.14
19 61 0.51
20 1 0.01
21 8 0.07
ACGTcount: A:0.36, C:0.16, G:0.09, T:0.39
Consensus pattern (19 bp):
ATCATATCTAAGATTGCAT
Found at i:3543098 original size:36 final size:37
Alignment explanation
Indices: 3543023--3543185 Score: 181
Period size: 36 Copynumber: 4.4 Consensus size: 37
3543013 TTAAATCTCC
*
3543023 AAGATTACAAGATCATATCTTCAAGATTGCATATCATATCT
1 AAGATTAC-ATATCATATC-T-AAGATTG-ATATCATATCT
*
3543064 AGGATTACATATCATATCTAAGATTG-TATCATATCT
1 AAGATTACATATCATATCTAAGATTGATATCATATCT
* *
3543100 AAGATTGCA-ATCATATCTAATATTGCATATCATATCT
1 AAGATTACATATCATATCTAAGATTG-ATATCATATCT
* *
3543137 AATATT--GTATCATATCTAAGATTGCATATCATATCT
1 AAGATTACATATCATATCTAAGATTG-ATATCATATCT
*
3543173 AAGATTGCATATC
1 AAGATTACATATC
3543186 CTTAAAGATT
Statistics
Matches: 107, Mismatches: 10, Indels: 13
0.82 0.08 0.10
Matches are distributed among these distances:
35 15 0.14
36 49 0.46
37 15 0.14
38 11 0.10
39 1 0.01
40 9 0.08
41 7 0.07
ACGTcount: A:0.37, C:0.15, G:0.10, T:0.37
Consensus pattern (37 bp):
AAGATTACATATCATATCTAAGATTGATATCATATCT
Found at i:3543117 original size:54 final size:55
Alignment explanation
Indices: 3543034--3543185 Score: 243
Period size: 54 Copynumber: 2.7 Consensus size: 55
3543024 AGATTACAAG
* *
3543034 ATCATATCTTCAAGATTGCATATCATATCTAGGATTACATATCATATCTAAGATTGT
1 ATCATATC-T-AAGATTGCATATCATATCTAAGATTGCATATCATATCTAAGATTGT
* *
3543091 ATCATATCTAAGATTGCA-ATCATATCTAATATTGCATATCATATCTAATATTGT
1 ATCATATCTAAGATTGCATATCATATCTAAGATTGCATATCATATCTAAGATTGT
3543145 ATCATATCTAAGATTGCATATCATATCTAAGATTGCATATC
1 ATCATATCTAAGATTGCATATCATATCTAAGATTGCATATC
3543186 CTTAAAGATT
Statistics
Matches: 89, Mismatches: 5, Indels: 4
0.91 0.05 0.04
Matches are distributed among these distances:
54 50 0.56
55 30 0.34
56 1 0.01
57 8 0.09
ACGTcount: A:0.36, C:0.16, G:0.09, T:0.39
Consensus pattern (55 bp):
ATCATATCTAAGATTGCATATCATATCTAAGATTGCATATCATATCTAAGATTGT
Found at i:3543131 original size:73 final size:74
Alignment explanation
Indices: 3543034--3543181 Score: 212
Period size: 73 Copynumber: 2.0 Consensus size: 74
3543024 AGATTACAAG
*
3543034 ATCATATCTTCAAGATTGCATATCATATCTAGGATTACATATCATATCTAAGATTG-TATCATAT
1 ATCATATCTTCAAGATTGCATATCATATCTAAGATT--ATATCATATCTAAGATTGATATCATAT
3543098 CTAAGATTGCA
64 CTAAGATTGCA
* * *
3543109 ATCATATC-T-AATATTGCATATCATATCTAATATTGTATCATATCTAAGATTGCATATCATATC
1 ATCATATCTTCAAGATTGCATATCATATCTAAGATTATATCATATCTAAGATTG-ATATCATATC
3543172 TAAGATTGCA
65 TAAGATTGCA
3543182 TATCCTTAAA
Statistics
Matches: 67, Mismatches: 4, Indels: 6
0.87 0.05 0.08
Matches are distributed among these distances:
71 17 0.25
73 41 0.61
74 1 0.01
75 8 0.12
ACGTcount: A:0.36, C:0.16, G:0.09, T:0.39
Consensus pattern (74 bp):
ATCATATCTTCAAGATTGCATATCATATCTAAGATTATATCATATCTAAGATTGATATCATATCT
AAGATTGCA
Found at i:3544381 original size:79 final size:79
Alignment explanation
Indices: 3544250--3544406 Score: 233
Period size: 79 Copynumber: 2.0 Consensus size: 79
3544240 ATCAGACGTG
* * * * *
3544250 CCCATATACAGATAAAACATATCAGAACATTCTAGTTGCACATATAATTAATAGATCAAAACATG
1 CCCATATACAAATAAAACAGATCAAAACATACTAATTGCACATATAATTAATAGATCAAAACATG
*
3544315 TTATTGGCATATTA
66 CTATTGGCATATTA
* *
3544329 CCCATATGCAAATAAAACAGATCAAAACATACTAATTGCACATATAGTTAATAGATCAAAACATG
1 CCCATATACAAATAAAACAGATCAAAACATACTAATTGCACATATAATTAATAGATCAAAACATG
*
3544394 CTATTGGTATATT
66 CTATTGGCATATT
3544407 CGACCATTAC
Statistics
Matches: 69, Mismatches: 9, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
79 69 1.00
ACGTcount: A:0.44, C:0.17, G:0.10, T:0.29
Consensus pattern (79 bp):
CCCATATACAAATAAAACAGATCAAAACATACTAATTGCACATATAATTAATAGATCAAAACATG
CTATTGGCATATTA
Found at i:3547690 original size:16 final size:15
Alignment explanation
Indices: 3547669--3547700 Score: 55
Period size: 16 Copynumber: 2.1 Consensus size: 15
3547659 TAGGGTGTGA
3547669 AATTATTTAATTGAAT
1 AATTATTTAATT-AAT
3547685 AATTATTTAATTAAT
1 AATTATTTAATTAAT
3547700 A
1 A
3547701 TTCAAAATAA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 4 0.25
16 12 0.75
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.50
Consensus pattern (15 bp):
AATTATTTAATTAAT
Found at i:3555864 original size:22 final size:23
Alignment explanation
Indices: 3555838--3555881 Score: 81
Period size: 22 Copynumber: 2.0 Consensus size: 23
3555828 CCTGATCAAA
3555838 ATACGACACAT-AAGTGCCTGAC
1 ATACGACACATAAAGTGCCTGAC
3555860 ATACGACACATAAAGTGCCTGA
1 ATACGACACATAAAGTGCCTGA
3555882 TCAGTAAAGC
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
22 11 0.52
23 10 0.48
ACGTcount: A:0.39, C:0.25, G:0.18, T:0.18
Consensus pattern (23 bp):
ATACGACACATAAAGTGCCTGAC
Found at i:3556123 original size:28 final size:29
Alignment explanation
Indices: 3556072--3556146 Score: 98
Period size: 28 Copynumber: 2.6 Consensus size: 29
3556062 AAATGTCTAA
* * *
3556072 CCAAAACACACCAGTATCAGATAATCC-T
1 CCAAAACACACCAGAATAATATAATCCAT
* *
3556100 CCCAAACACACTAGAATAATATAATCCAT
1 CCAAAACACACCAGAATAATATAATCCAT
3556129 CCAAAACACACCAGAATA
1 CCAAAACACACCAGAATA
3556147 GCACAAAGTG
Statistics
Matches: 39, Mismatches: 7, Indels: 1
0.83 0.15 0.02
Matches are distributed among these distances:
28 22 0.56
29 17 0.44
ACGTcount: A:0.48, C:0.31, G:0.05, T:0.16
Consensus pattern (29 bp):
CCAAAACACACCAGAATAATATAATCCAT
Found at i:3567206 original size:75 final size:73
Alignment explanation
Indices: 3567118--3567289 Score: 199
Period size: 75 Copynumber: 2.4 Consensus size: 73
3567108 GGTTTTCCTC
** * * * ** *
3567118 ATTGAAATACCATACCTACATTTTTCAACTCGGTATGGGA-AATGCTATACCTACATTTCTTAAC
1 ATTGAAATACCATACCTACATTTCACAACTCAGTAT-GGATAATACCATACCTACATTTCACAAA
3567182 TCAGTATGG
65 TCAGTATGG
* *
3567191 ATTTGATAATACCATACCTATATTTCACAGCTCAGTATGGATAATACCATACCTACATTTCACAA
1 A-TTGA-AATACCATACCTACATTTCACAACTCAGTATGGATAATACCATACCTACATTTCACAA
3567256 ATCAGTATGG
64 ATCAGTATGG
3567266 A-TG--ATACCATACCTACATTTCACA
1 ATTGAAATACCATACCTACATTTCACA
3567290 CTTTTCCATG
Statistics
Matches: 85, Mismatches: 11, Indels: 9
0.81 0.10 0.09
Matches are distributed among these distances:
70 20 0.24
73 3 0.04
74 7 0.08
75 55 0.65
ACGTcount: A:0.34, C:0.22, G:0.11, T:0.33
Consensus pattern (73 bp):
ATTGAAATACCATACCTACATTTCACAACTCAGTATGGATAATACCATACCTACATTTCACAAAT
CAGTATGG
Found at i:3567225 original size:40 final size:38
Alignment explanation
Indices: 3567123--3567289 Score: 163
Period size: 35 Copynumber: 4.6 Consensus size: 38
3567113 TCCTCATTGA
** *
3567123 AATACCATACCTACATTTTTCAACTCGGTATGG--GA-
1 AATACCATACCTACATTTCACAACTCAGTATGGATGAT
* * **
3567158 AATGCTATACCTACATTTCTTAACTCAGTATGGATTTGAT
1 AATACCATACCTACATTTCACAACTCAGTATGGA--TGAT
* *
3567198 AATACCATACCTATATTTCACAGCTCAGTAT-G--GAT
1 AATACCATACCTACATTTCACAACTCAGTATGGATGAT
*
3567233 AATACCATACCTACATTTCACAAATCAGTATGGATG--
1 AATACCATACCTACATTTCACAACTCAGTATGGATGAT
3567269 -ATACCATACCTACATTTCACA
1 AATACCATACCTACATTTCACA
3567290 CTTTTCCATG
Statistics
Matches: 110, Mismatches: 14, Indels: 16
0.79 0.10 0.11
Matches are distributed among these distances:
35 80 0.73
36 1 0.01
38 1 0.01
39 3 0.03
40 25 0.23
ACGTcount: A:0.34, C:0.23, G:0.11, T:0.32
Consensus pattern (38 bp):
AATACCATACCTACATTTCACAACTCAGTATGGATGAT
Found at i:3570305 original size:46 final size:46
Alignment explanation
Indices: 3570245--3570472 Score: 314
Period size: 46 Copynumber: 5.0 Consensus size: 46
3570235 TTTGACATGA
* * * * ** * *
3570245 TGCCATAGTGTCTTTCAACTATGGTCTTACTCATTTTC-TGCCATGT
1 TGCCATGGTATCTTTCAACCATGGTCTTACACA-TTTCATATCAGGC
* *** * *
3570291 TGCCATGATATCTTTCAACCATGGTCTTGTTCATTTCATATCACGT
1 TGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATATCAGGC
3570337 TGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATATCAGGC
1 TGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATATCAGGC
3570383 TGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATATCAGGC
1 TGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATATCAGGC
3570429 TGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATATCAG
1 TGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATATCAG
3570473 AGAGCACACT
Statistics
Matches: 166, Mismatches: 15, Indels: 2
0.91 0.08 0.01
Matches are distributed among these distances:
45 4 0.02
46 162 0.98
ACGTcount: A:0.22, C:0.25, G:0.14, T:0.38
Consensus pattern (46 bp):
TGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATATCAGGC
Found at i:3589051 original size:465 final size:467
Alignment explanation
Indices: 3588179--3589107 Score: 1718
Period size: 465 Copynumber: 2.0 Consensus size: 467
3588169 TAGTTTCTTG
3588179 AGGGTTAAGTTGAGGGTTAATAATAAAATTTTATTTGCAAAAGTCCATTTTATATATGTTGTAAC
1 AGGGTTAAGTTGAGGGTTAATAATAAAATTTTATTTGCAAAAGTCCATTTTATATATGTTGTAAC
*
3588244 ATATTTACAACTTTTCTGATTATTATCTTTGAATTAATAAAGAGGTCTGGAGACTTTCTATAACT
66 ATATTTACAACTTTTCTGATTATTATCTTTGAATTAATAAAGAGGCCTGGAGACTTTCTATAACT
* * *
3588309 CTTAATTTTTCTAGAGTTTCAAATTCTTTTCTTATTCGTTTTACAGCCTTAATTATTTCAATTAT
131 CTTAAGTTTTCTAGAGTTTCAAATTCTTTGCTTATTCGTTTTACAGCCATAATTATTTCAATTAT
3588374 GGTTGTTTTCTTCCCTAAACCATATCAATTTTGGCATTAGAACTTAATTAGATCCTACGGTTGCT
196 GGTTGTTTTCTTCCCTAAACCATATCAATTTTGGCATTAGAACTTAATTAGATCCTACGGTTGCT
*
3588439 ATTAAGCCATGGTTGGACATAGTGGATATTAAGGAAGCGGAAGTCAAGGTCAAGAGACAATATTG
261 ATTAAGCCATGGTTGGACATAGTAGATATTAAGGAAGCGGAAGTCAAGGTCAAGAGACAATATTG
*
3588504 ACTGCAATACAAAGTGATATTAAAGAATTGTCGCATGCAATTTATGCTACATTGCGACAAGAGCC
326 ACTGCAATACAAAGTGATATTAAAGAATTGTCGCATGCAATTTATGCTACATTGCGACAAGAACC
*
3588569 AGTGGGAGTCCAGATGGA-ATTCTGGAAGGTGCCCACAATTGTGTATGCCTTAGAATTAAATAGG
391 AGTGGGAGTCCAGATGGAGATTCTGGAAGGTGCCCACAATTGTGTAAGCCTTAGAATTAAATAGG
3588633 GTGGAATTATAT
456 GTGGAATTATAT
3588645 AGGGTTAAGTTGAGGGTTAATAATAAAATTTTATTTGCAAAAGTCCATTTTATATATGTTGTAAC
1 AGGGTTAAGTTGAGGGTTAATAATAAAATTTTATTTGCAAAAGTCCATTTTATATATGTTGTAAC
* *
3588710 ATATTTTCAACTTTTCTGATTATTATCTTTGAATTAATAAAGAGGCCTGGAGAGTTTCTATAACT
66 ATATTTACAACTTTTCTGATTATTATCTTTGAATTAATAAAGAGGCCTGGAGACTTTCTATAACT
*
3588775 C-TAAGTTTTCTAGAGTTTCAAATTCTTTGCTTATTCGTTTTACAGCCATAATTCTTTCAATTAT
131 CTTAAGTTTTCTAGAGTTTCAAATTCTTTGCTTATTCGTTTTACAGCCATAATTATTTCAATTAT
*
3588839 GGTTGTTTTCTTCTCTAAACCATATCAATTTTGGCATTAGAACTTAATTAGATCCTACGGTTGCT
196 GGTTGTTTTCTTCCCTAAACCATATCAATTTTGGCATTAGAACTTAATTAGATCCTACGGTTGCT
*
3588904 ATTAAGCCATGGTTGGACATGGTAGATATTAAGGAAGCGGAAGTCAAGGTCAAGAGACAATATTG
261 ATTAAGCCATGGTTGGACATAGTAGATATTAAGGAAGCGGAAGTCAAGGTCAAGAGACAATATTG
*
3588969 ACTGCAATACGAAGTGATATTAAAGAATTGTCGCATGCAATTTATGCTACATTGCGACAAGAACC
326 ACTGCAATACAAAGTGATATTAAAGAATTGTCGCATGCAATTTATGCTACATTGCGACAAGAACC
*
3589034 AGTGGGAGTCCAGATGGAGATTCTGGAAGGTGCCCACAATTGTGTAAGCCTTTGAATTAAATAGG
391 AGTGGGAGTCCAGATGGAGATTCTGGAAGGTGCCCACAATTGTGTAAGCCTTAGAATTAAATAGG
3589099 GTGGAATTA
456 GTGGAATTA
3589108 AGATCAAAGT
Statistics
Matches: 448, Mismatches: 14, Indels: 2
0.97 0.03 0.00
Matches are distributed among these distances:
465 267 0.60
466 181 0.40
ACGTcount: A:0.31, C:0.14, G:0.19, T:0.36
Consensus pattern (467 bp):
AGGGTTAAGTTGAGGGTTAATAATAAAATTTTATTTGCAAAAGTCCATTTTATATATGTTGTAAC
ATATTTACAACTTTTCTGATTATTATCTTTGAATTAATAAAGAGGCCTGGAGACTTTCTATAACT
CTTAAGTTTTCTAGAGTTTCAAATTCTTTGCTTATTCGTTTTACAGCCATAATTATTTCAATTAT
GGTTGTTTTCTTCCCTAAACCATATCAATTTTGGCATTAGAACTTAATTAGATCCTACGGTTGCT
ATTAAGCCATGGTTGGACATAGTAGATATTAAGGAAGCGGAAGTCAAGGTCAAGAGACAATATTG
ACTGCAATACAAAGTGATATTAAAGAATTGTCGCATGCAATTTATGCTACATTGCGACAAGAACC
AGTGGGAGTCCAGATGGAGATTCTGGAAGGTGCCCACAATTGTGTAAGCCTTAGAATTAAATAGG
GTGGAATTATAT
Found at i:3595868 original size:33 final size:31
Alignment explanation
Indices: 3595843--3595901 Score: 84
Period size: 31 Copynumber: 1.9 Consensus size: 31
3595833 ATATCATCAT
* *
3595843 ATACAAA-AATGAGAGTACAAACCATATTGA
1 ATACAAATAATGAAAGTACAAACCATATTCA
*
3595873 ATTCAAATAATGAAAGTACAAACCATATT
1 ATACAAATAATGAAAGTACAAACCATATT
3595902 AGCCACTCAT
Statistics
Matches: 26, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
30 6 0.23
31 20 0.77
ACGTcount: A:0.53, C:0.14, G:0.10, T:0.24
Consensus pattern (31 bp):
ATACAAATAATGAAAGTACAAACCATATTCA
Done.