Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Gbar_D13
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: 60343961
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 596159 characters in sequence are not A, C, G, or T
File 140 of 204
Found at i:42822519 original size:36 final size:35
Alignment explanation
Indices: 42822471--42822539 Score: 86
Period size: 36 Copynumber: 1.9 Consensus size: 35
42822461 AGAAAACATG
* *
42822471 TAAGACCATGTTTGGAACATTGGTATCGTATATGTA
1 TAAGACCATGTTTGGAACAGTGGCATCG-ATATGTA
*
42822507 TAAGATCC-TGTTTGGGACAGTGGCATCGATATG
1 TAAGA-CCATGTTTGGAACAGTGGCATCGATATG
42822540 CATTAACATG
Statistics
Matches: 29, Mismatches: 3, Indels: 3
0.83 0.09 0.09
Matches are distributed among these distances:
35 5 0.17
36 22 0.76
37 2 0.07
ACGTcount: A:0.28, C:0.13, G:0.26, T:0.33
Consensus pattern (35 bp):
TAAGACCATGTTTGGAACAGTGGCATCGATATGTA
Found at i:42823878 original size:62 final size:59
Alignment explanation
Indices: 42823762--42823882 Score: 136
Period size: 62 Copynumber: 2.0 Consensus size: 59
42823752 TTGTACAAAC
* ****
42823762 TATTTTTATATTGTTTTATTTAATAAAATAAAAGTTGTTTTAAATATTTTAATAGTAAAT
1 TATTTTTATATTGTTTTATTTAATAAAATAAAAGTTATTTTAAATAAGACAATAG-AAAT
* *
42823822 TATTTTTATATT-TTATCCTATTTAATAAAATATAAGTTATTTTGAATAAGACAATAGAAAT
1 TATTTTTATATTGTT-T--TATTTAATAAAATAAAAGTTATTTTAAATAAGACAATAGAAAT
42823883 AATGCAACAT
Statistics
Matches: 51, Mismatches: 7, Indels: 5
0.81 0.11 0.08
Matches are distributed among these distances:
59 2 0.04
60 13 0.25
61 4 0.08
62 32 0.63
ACGTcount: A:0.41, C:0.02, G:0.07, T:0.50
Consensus pattern (59 bp):
TATTTTTATATTGTTTTATTTAATAAAATAAAAGTTATTTTAAATAAGACAATAGAAAT
Found at i:42827096 original size:123 final size:123
Alignment explanation
Indices: 42826865--42827100 Score: 332
Period size: 123 Copynumber: 1.9 Consensus size: 123
42826855 ACCAAACAAT
* * **
42826865 AACTACTGTAGAAAAAGAGCATCCACGTGGGAGCTTTTTTCAGTAATTTTGCTGACAGTGCATTT
1 AACTACTGTAGAAAAAGAACATCCACGTGGGAGATTTTTTCAGTAATTTTGCTGACAGTGCATCC
* **
42826930 TGCTTGAAGAGTTTTTGACACTAATTTTTTAGATTCGTCTTCTCAAAAATTTTTTAGG
66 TGCTTGAAGAGTTTTTGACACTAATTTTTCAGAACCGTCTTCTCAAAAATTTTTTAGG
**
42826988 AACTACTGTAGAAAAAGAATTTCCACGTGGGAGATTTTTTCAGTAATTTTGCTGACAGTGCATCC
1 AACTACTGTAGAAAAAGAACATCCACGTGGGAGATTTTTTCAGTAATTTTGCTGACAGTGCATCC
* * *
42827053 TGTTTGAAGCA-TTTTTGACA-TTATCTTTTCAGAACCGTTTTCTCAAAA
66 TGCTTGAAG-AGTTTTTGACACTAAT-TTTTCAGAACCGTCTTCTCAAAA
42827101 TTAATTTTTC
Statistics
Matches: 99, Mismatches: 12, Indels: 4
0.86 0.10 0.03
Matches are distributed among these distances:
122 3 0.03
123 95 0.96
124 1 0.01
ACGTcount: A:0.28, C:0.16, G:0.18, T:0.38
Consensus pattern (123 bp):
AACTACTGTAGAAAAAGAACATCCACGTGGGAGATTTTTTCAGTAATTTTGCTGACAGTGCATCC
TGCTTGAAGAGTTTTTGACACTAATTTTTCAGAACCGTCTTCTCAAAAATTTTTTAGG
Found at i:42827259 original size:34 final size:33
Alignment explanation
Indices: 42827218--42827345 Score: 141
Period size: 33 Copynumber: 3.8 Consensus size: 33
42827208 CACAAAATTA
*
42827218 TTTTTAAAAAAACTAAACCCTAATTTAATTAAT
1 TTTTTAAAAAATCTAAACCCTAATTTAATTAAT
* *
42827251 TTTCTT-AAAACTCTAAACCCTAATTTAATTTAT
1 TTT-TTAAAAAATCTAAACCCTAATTTAATTAAT
* * ***
42827284 TTATTTAAAACACCTAAAATGTAATTTAATTAAT
1 TT-TTTAAAAAATCTAAACCCTAATTTAATTAAT
*
42827318 TTTTTAAAAAACTCTAAACCTTAATTTA
1 TTTTTAAAAAA-TCTAAACCCTAATTTA
42827346 TTTTTTAAAA
Statistics
Matches: 76, Mismatches: 15, Indels: 7
0.78 0.15 0.07
Matches are distributed among these distances:
33 39 0.51
34 37 0.49
ACGTcount: A:0.44, C:0.13, G:0.01, T:0.42
Consensus pattern (33 bp):
TTTTTAAAAAATCTAAACCCTAATTTAATTAAT
Found at i:42827291 original size:67 final size:65
Alignment explanation
Indices: 42827220--42827352 Score: 169
Period size: 67 Copynumber: 2.0 Consensus size: 65
42827210 CAAAATTATT
*
42827220 TTTAAAAAAACTAAACCCTAATTTAATTAATTTTCTT-AAAACTCTAAACCCTAATTTAATTTAT
1 TTTAAAAAAACTAAAACCTAATTTAATTAATTTT-TTAAAAACTCTAAACCCTAATTT-ATTT-T
42827284 TTA
63 TTA
* * ** *
42827287 TTTAAAACACCTAAAATGTAATTTAATTAATTTTTTAAAAAACTCTAAACCTTAATTTATTTTTT
1 TTTAAAAAAACTAAAACCTAATTTAATTAATTTTTT-AAAAACTCTAAACCCTAATTTATTTTTT
42827352 A
65 A
42827353 AAATTTTTAA
Statistics
Matches: 58, Mismatches: 6, Indels: 5
0.84 0.09 0.07
Matches are distributed among these distances:
66 6 0.10
67 33 0.57
68 19 0.33
ACGTcount: A:0.43, C:0.13, G:0.01, T:0.44
Consensus pattern (65 bp):
TTTAAAAAAACTAAAACCTAATTTAATTAATTTTTTAAAAACTCTAAACCCTAATTTATTTTTTA
Found at i:42838781 original size:16 final size:16
Alignment explanation
Indices: 42838760--42838808 Score: 71
Period size: 16 Copynumber: 3.1 Consensus size: 16
42838750 CGCTGTATTG
42838760 GAATAGAGGCGTAATA
1 GAATAGAGGCGTAATA
* *
42838776 GAATAGAGGTGTAATG
1 GAATAGAGGCGTAATA
*
42838792 GAATAGAAGCGTAATA
1 GAATAGAGGCGTAATA
42838808 G
1 G
42838809 TATTTTTGTG
Statistics
Matches: 28, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
16 28 1.00
ACGTcount: A:0.43, C:0.04, G:0.33, T:0.20
Consensus pattern (16 bp):
GAATAGAGGCGTAATA
Found at i:42842514 original size:27 final size:27
Alignment explanation
Indices: 42842483--42842537 Score: 110
Period size: 27 Copynumber: 2.0 Consensus size: 27
42842473 TAATGGCTAA
42842483 TCCATTACACCCAACCAAACATGGTGT
1 TCCATTACACCCAACCAAACATGGTGT
42842510 TCCATTACACCCAACCAAACATGGTGT
1 TCCATTACACCCAACCAAACATGGTGT
42842537 T
1 T
42842538 AAATGGTAAT
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:0.33, C:0.33, G:0.11, T:0.24
Consensus pattern (27 bp):
TCCATTACACCCAACCAAACATGGTGT
Found at i:42844885 original size:11 final size:11
Alignment explanation
Indices: 42844871--42844896 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
42844861 AAATTAAAAA
42844871 AAAAGTATTTT
1 AAAAGTATTTT
42844882 AAAAGTATTTT
1 AAAAGTATTTT
42844893 AAAA
1 AAAA
42844897 TTAAAAAAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.54, C:0.00, G:0.08, T:0.38
Consensus pattern (11 bp):
AAAAGTATTTT
Found at i:42844920 original size:39 final size:40
Alignment explanation
Indices: 42844869--42844998 Score: 160
Period size: 39 Copynumber: 3.3 Consensus size: 40
42844859 AAAAATTAAA
*
42844869 AAAAAAGTATTTTAAAAGTATTTTAAAATTAAAAAAAATT
1 AAAAAAGTATTTTAAAAGTATTTTAAAATTTAAAAAAATT
* *
42844909 -AAAAAGTATTTTTTAAAA--ATTTAAAAATTTAAAAAATTT
1 AAAAAAGTA--TTTTAAAAGTATTTTAAAATTTAAAAAAATT
*
42844948 AAAAAAAGTATTTTAAAAGTATTTTAAAATTT-AAAAAATA
1 -AAAAAAGTATTTTAAAAGTATTTTAAAATTTAAAAAAATT
*
42844988 AAAAAATTATT
1 AAAAAAGTATT
42844999 ATATTTGGGC
Statistics
Matches: 77, Mismatches: 7, Indels: 13
0.79 0.07 0.13
Matches are distributed among these distances:
39 44 0.57
40 6 0.08
41 27 0.35
ACGTcount: A:0.59, C:0.00, G:0.04, T:0.37
Consensus pattern (40 bp):
AAAAAAGTATTTTAAAAGTATTTTAAAATTTAAAAAAATT
Found at i:42844923 original size:30 final size:28
Alignment explanation
Indices: 42844882--42844943 Score: 72
Period size: 30 Copynumber: 2.1 Consensus size: 28
42844872 AAAGTATTTT
42844882 AAAAGTATTTT-AAAATTAAAAAAAATTA
1 AAAAGTATTTTAAAAATT-AAAAAAATTA
* *
42844910 AAAAGTATTTTTTAAAAATTTAAAAATTTA
1 AAAAGTA--TTTTAAAAATTAAAAAAATTA
42844940 AAAA
1 AAAA
42844944 ATTTAAAAAA
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
28 7 0.24
30 16 0.55
31 6 0.21
ACGTcount: A:0.61, C:0.00, G:0.03, T:0.35
Consensus pattern (28 bp):
AAAAGTATTTTAAAAATTAAAAAAATTA
Found at i:42844942 original size:7 final size:8
Alignment explanation
Indices: 42844920--42844952 Score: 57
Period size: 8 Copynumber: 4.0 Consensus size: 8
42844910 AAAAGTATTT
42844920 TTTAAAAA
1 TTTAAAAA
42844928 TTTAAAAA
1 TTTAAAAA
42844936 TTTAAAAAA
1 TTT-AAAAA
42844945 TTTAAAAA
1 TTTAAAAA
42844953 AAGTATTTTA
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
8 16 0.67
9 8 0.33
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (8 bp):
TTTAAAAA
Found at i:42844943 original size:9 final size:9
Alignment explanation
Indices: 42844923--42844953 Score: 55
Period size: 9 Copynumber: 3.6 Consensus size: 9
42844913 AGTATTTTTT
42844923 AAAAATTT-
1 AAAAATTTA
42844931 AAAAATTTA
1 AAAAATTTA
42844940 AAAAATTTA
1 AAAAATTTA
42844949 AAAAA
1 AAAAA
42844954 AGTATTTTAA
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
8 8 0.36
9 14 0.64
ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (9 bp):
AAAAATTTA
Found at i:42844965 original size:11 final size:11
Alignment explanation
Indices: 42844951--42844976 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
42844941 AAAATTTAAA
42844951 AAAAGTATTTT
1 AAAAGTATTTT
42844962 AAAAGTATTTT
1 AAAAGTATTTT
42844973 AAAA
1 AAAA
42844977 TTTAAAAAAT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.54, C:0.00, G:0.08, T:0.38
Consensus pattern (11 bp):
AAAAGTATTTT
Found at i:42846260 original size:21 final size:21
Alignment explanation
Indices: 42846236--42846275 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
42846226 TTTAATATCT
*
42846236 AAGATTATATTTTTATTTGTA
1 AAGATTATATTTGTATTTGTA
42846257 AAGATTATATTTGTATTTG
1 AAGATTATATTTGTATTTG
42846276 AGTTTTAGGG
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.33, C:0.00, G:0.12, T:0.55
Consensus pattern (21 bp):
AAGATTATATTTGTATTTGTA
Found at i:42858686 original size:17 final size:19
Alignment explanation
Indices: 42858650--42858687 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 19
42858640 TATTATATAC
*
42858650 ATGTTTTATGTATATTTAA
1 ATGTTTAATGTATATTTAA
42858669 ATGTTTAAT-TAT-TTTAA
1 ATGTTTAATGTATATTTAA
42858686 AT
1 AT
42858688 CGAATATAAT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
17 7 0.39
18 3 0.17
19 8 0.44
ACGTcount: A:0.34, C:0.00, G:0.08, T:0.58
Consensus pattern (19 bp):
ATGTTTAATGTATATTTAA
Found at i:42861309 original size:27 final size:27
Alignment explanation
Indices: 42861279--42861339 Score: 68
Period size: 27 Copynumber: 2.3 Consensus size: 27
42861269 ATATAACCTC
* *
42861279 ATGTTTACCGTCTCAACAGACTATCCT
1 ATGTTTACCGTCCCAACAGACTACCCT
** * *
42861306 ATGTTTAGTGTCCCAGCGGACTACCCT
1 ATGTTTACCGTCCCAACAGACTACCCT
42861333 ATGTTTA
1 ATGTTTA
42861340 GTGTCTCGGT
Statistics
Matches: 28, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
27 28 1.00
ACGTcount: A:0.23, C:0.26, G:0.16, T:0.34
Consensus pattern (27 bp):
ATGTTTACCGTCCCAACAGACTACCCT
Found at i:42861478 original size:44 final size:45
Alignment explanation
Indices: 42861423--42861521 Score: 130
Period size: 44 Copynumber: 2.2 Consensus size: 45
42861413 ACACTTTCAT
* *
42861423 ATGATGCCATAGTGTCTTTCAGCTATG-GTCTTACACA-TTTTATC
1 ATGACGCCATAGTGTCTTTCAACTATGAG-CTTACACATTTTTATC
* * *
42861467 ATGGCGCCATAGTTTCTTTCAACTATGAGCTTACTCATTTTTATC
1 ATGACGCCATAGTGTCTTTCAACTATGAGCTTACACATTTTTATC
42861512 ATGACGCCAT
1 ATGACGCCAT
42861522 GACATATTTT
Statistics
Matches: 47, Mismatches: 6, Indels: 3
0.84 0.11 0.05
Matches are distributed among these distances:
44 30 0.64
45 17 0.36
ACGTcount: A:0.23, C:0.22, G:0.15, T:0.39
Consensus pattern (45 bp):
ATGACGCCATAGTGTCTTTCAACTATGAGCTTACACATTTTTATC
Found at i:42861538 original size:45 final size:45
Alignment explanation
Indices: 42861496--42861599 Score: 145
Period size: 45 Copynumber: 2.3 Consensus size: 45
42861486 CAACTATGAG
* * * *
42861496 CTTACTCATTTTTATCATGACGCCATGACATATTTTAGCTATGGT
1 CTTACTCATTTTTATCATAACACCATAACATATTTAAGCTATGGT
* *
42861541 CTTACTTATTTTTATCATAACACCATAACATCTTTAAGCTATGGT
1 CTTACTCATTTTTATCATAACACCATAACATATTTAAGCTATGGT
*
42861586 CTTATTCATTTTTA
1 CTTACTCATTTTTA
42861600 GGCATATAGC
Statistics
Matches: 51, Mismatches: 8, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
45 51 1.00
ACGTcount: A:0.27, C:0.19, G:0.09, T:0.45
Consensus pattern (45 bp):
CTTACTCATTTTTATCATAACACCATAACATATTTAAGCTATGGT
Found at i:42868582 original size:15 final size:15
Alignment explanation
Indices: 42868559--42868610 Score: 52
Period size: 15 Copynumber: 3.5 Consensus size: 15
42868549 CTAACTGAGC
* *
42868559 TTAAATTTTTATTAA
1 TTAAGTTTTAATTAA
*
42868574 TTAAGTTTTAACTAA
1 TTAAGTTTTAATTAA
* *
42868589 TTAA-ATTTGATTAA
1 TTAAGTTTTAATTAA
42868603 TTAAGTTT
1 TTAAGTTT
42868611 CTGTATATGT
Statistics
Matches: 29, Mismatches: 7, Indels: 2
0.76 0.18 0.05
Matches are distributed among these distances:
14 11 0.38
15 18 0.62
ACGTcount: A:0.38, C:0.02, G:0.06, T:0.54
Consensus pattern (15 bp):
TTAAGTTTTAATTAA
Found at i:42869247 original size:28 final size:29
Alignment explanation
Indices: 42869179--42869249 Score: 90
Period size: 29 Copynumber: 2.5 Consensus size: 29
42869169 CCTCGATACG
42869179 ATGTTAACTTGTGTGAACAAATTCATAAA
1 ATGTTAACTTGTGTGAACAAATTCATAAA
* * **
42869208 ATGTCAATTTGTGTGAGTAAATTCAT-AA
1 ATGTTAACTTGTGTGAACAAATTCATAAA
*
42869236 ATGTTAGCTTGTGT
1 ATGTTAACTTGTGT
42869250 AAGCAACCCT
Statistics
Matches: 35, Mismatches: 7, Indels: 1
0.81 0.16 0.02
Matches are distributed among these distances:
28 13 0.37
29 22 0.63
ACGTcount: A:0.34, C:0.08, G:0.18, T:0.39
Consensus pattern (29 bp):
ATGTTAACTTGTGTGAACAAATTCATAAA
Found at i:42870447 original size:36 final size:36
Alignment explanation
Indices: 42870398--42870471 Score: 121
Period size: 36 Copynumber: 2.1 Consensus size: 36
42870388 GTGGCCTAAC
*
42870398 GTCGTGACATGACAAACTATTTTGCGACGTCATGAT
1 GTCGTGACATGACAAACTACTTTGCGACGTCATGAT
* *
42870434 GTCGTGACGTGACAAACTACTTTGCGATGTCATGAT
1 GTCGTGACATGACAAACTACTTTGCGACGTCATGAT
42870470 GT
1 GT
42870472 GGAAATGATG
Statistics
Matches: 35, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
36 35 1.00
ACGTcount: A:0.26, C:0.19, G:0.24, T:0.31
Consensus pattern (36 bp):
GTCGTGACATGACAAACTACTTTGCGACGTCATGAT
Found at i:42871436 original size:19 final size:19
Alignment explanation
Indices: 42871396--42871437 Score: 50
Period size: 20 Copynumber: 2.2 Consensus size: 19
42871386 TATGTTAAAT
*
42871396 TAAAGTTAAATTAATAATAA
1 TAAAGTTAAA-TAATAAAAA
42871416 TAAAGTTAAA-ACATAAAAA
1 TAAAGTTAAATA-ATAAAAA
42871435 TAA
1 TAA
42871438 TGGTCATCTT
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
18 1 0.05
19 9 0.45
20 10 0.50
ACGTcount: A:0.64, C:0.02, G:0.05, T:0.29
Consensus pattern (19 bp):
TAAAGTTAAATAATAAAAA
Found at i:42885469 original size:13 final size:13
Alignment explanation
Indices: 42885451--42885475 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
42885441 ATTTAGTATT
42885451 TATATAATAAATG
1 TATATAATAAATG
42885464 TATATAATAAAT
1 TATATAATAAAT
42885476 ATATTTTTTA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.56, C:0.00, G:0.04, T:0.40
Consensus pattern (13 bp):
TATATAATAAATG
Found at i:42885530 original size:20 final size:21
Alignment explanation
Indices: 42885501--42885539 Score: 62
Period size: 20 Copynumber: 1.9 Consensus size: 21
42885491 TATTGTAAAG
42885501 TATTTGTAAAATAC-TTTTTT
1 TATTTGTAAAATACATTTTTT
*
42885521 TATTTTTAAAATACATTTT
1 TATTTGTAAAATACATTTT
42885540 CGGATATAAT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 13 0.76
21 4 0.24
ACGTcount: A:0.33, C:0.05, G:0.03, T:0.59
Consensus pattern (21 bp):
TATTTGTAAAATACATTTTTT
Found at i:42892473 original size:17 final size:18
Alignment explanation
Indices: 42892436--42892474 Score: 53
Period size: 17 Copynumber: 2.2 Consensus size: 18
42892426 TAAATTAATT
*
42892436 ATTTTATAAATACTTATA
1 ATTTTATAAATACTTAGA
*
42892454 ATTTTAT-AATTCTTAGA
1 ATTTTATAAATACTTAGA
42892471 ATTT
1 ATTT
42892475 CACTTCCGAG
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
17 12 0.63
18 7 0.37
ACGTcount: A:0.38, C:0.05, G:0.03, T:0.54
Consensus pattern (18 bp):
ATTTTATAAATACTTAGA
Found at i:42902174 original size:47 final size:47
Alignment explanation
Indices: 42902105--42902194 Score: 180
Period size: 47 Copynumber: 1.9 Consensus size: 47
42902095 ACTTGTTGGA
42902105 AGCTTAATCTATTTGACCATTACAAGGCCTGAAATTTCATACTTTGT
1 AGCTTAATCTATTTGACCATTACAAGGCCTGAAATTTCATACTTTGT
42902152 AGCTTAATCTATTTGACCATTACAAGGCCTGAAATTTCATACT
1 AGCTTAATCTATTTGACCATTACAAGGCCTGAAATTTCATACT
42902195 CTGTTAGTGT
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
47 43 1.00
ACGTcount: A:0.31, C:0.20, G:0.12, T:0.37
Consensus pattern (47 bp):
AGCTTAATCTATTTGACCATTACAAGGCCTGAAATTTCATACTTTGT
Found at i:42904306 original size:42 final size:42
Alignment explanation
Indices: 42904260--42904349 Score: 144
Period size: 42 Copynumber: 2.1 Consensus size: 42
42904250 TCTCAGGCCA
* *
42904260 TGTAACATTCGAAATAGGGACACACGGCCGTGTCCCAGCTCG
1 TGTAACATTCGAAATAGGGACACACGGCCGTCTCCCAGCCCG
* *
42904302 TGTAATATTCGAAATAGGGACACACGGTCGTCTCCCAGCCCG
1 TGTAACATTCGAAATAGGGACACACGGCCGTCTCCCAGCCCG
42904344 TGTAAC
1 TGTAAC
42904350 TCTCTGAATT
Statistics
Matches: 43, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
42 43 1.00
ACGTcount: A:0.27, C:0.28, G:0.24, T:0.21
Consensus pattern (42 bp):
TGTAACATTCGAAATAGGGACACACGGCCGTCTCCCAGCCCG
Found at i:42906487 original size:138 final size:137
Alignment explanation
Indices: 42906240--42906499 Score: 351
Period size: 138 Copynumber: 1.9 Consensus size: 137
42906230 ATGGGTATGT
* * * * * * *
42906240 TCACACAAGTTGACGGTCGGAATGTAGCTACACGATGCTGCTCACACAAGTTGATGAGTATCCGC
1 TCACACAAGCTGACGGTCAGAATGTAGCTACACAATGCTGCTCACACAAGCTAATAAGTATCCAC
* * * * * *
42906305 AACAAATGTTGAAACTCAGCTATCGGTAGGACATTCAGGACCAGCACCCTAAACATGGTAACATC
66 AAAAAATGTTCAAACTCAGCCATCGGTAGAACATTCAAGACCAGCACCCAAAACATGGTAACATC
42906370 GGTCTAC
131 GGTCTAC
* *
42906377 TCACACAAGCTGACGGTCAGAATGTAAGCTACACAATGTTGCTCACAGAAGCTAATAAGTATCCA
1 TCACACAAGCTGACGGTCAGAATGT-AGCTACACAATGCTGCTCACACAAGCTAATAAGTATCCA
*
42906442 CAAAAAATG-TCAAACCTCAGCCATCGGTAGAACATTTAAGACCAGCACCCAAAACATG
65 CAAAAAATGTTCAAA-CTCAGCCATCGGTAGAACATTCAAGACCAGCACCCAAAACATG
42906500 AAAACCCTAA
Statistics
Matches: 105, Mismatches: 16, Indels: 3
0.85 0.13 0.02
Matches are distributed among these distances:
137 27 0.26
138 78 0.74
ACGTcount: A:0.35, C:0.25, G:0.19, T:0.20
Consensus pattern (137 bp):
TCACACAAGCTGACGGTCAGAATGTAGCTACACAATGCTGCTCACACAAGCTAATAAGTATCCAC
AAAAAATGTTCAAACTCAGCCATCGGTAGAACATTCAAGACCAGCACCCAAAACATGGTAACATC
GGTCTAC
Found at i:42910455 original size:16 final size:17
Alignment explanation
Indices: 42910434--42910477 Score: 54
Period size: 18 Copynumber: 2.6 Consensus size: 17
42910424 TATATTTAGT
*
42910434 AATATAATTT-ATTACA
1 AATATAATTTCACTACA
*
42910450 AATATAATTATCACTCCA
1 AATATAATT-TCACTACA
42910468 AATATAATTT
1 AATATAATTT
42910478 TAACAATAAT
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
16 9 0.38
17 2 0.08
18 13 0.54
ACGTcount: A:0.48, C:0.11, G:0.00, T:0.41
Consensus pattern (17 bp):
AATATAATTTCACTACA
Found at i:42911274 original size:17 final size:17
Alignment explanation
Indices: 42911252--42911285 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
42911242 ACTTGAATAC
* *
42911252 AAATAAACATGATAATG
1 AAATAAAAATGAAAATG
42911269 AAATAAAAATGAAAATG
1 AAATAAAAATGAAAATG
42911286 GCCATTAATG
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.65, C:0.03, G:0.12, T:0.21
Consensus pattern (17 bp):
AAATAAAAATGAAAATG
Found at i:42911667 original size:22 final size:20
Alignment explanation
Indices: 42911619--42911667 Score: 53
Period size: 22 Copynumber: 2.4 Consensus size: 20
42911609 TTAAACACCT
42911619 TTTAAAAATAAAATAATCAA
1 TTTAAAAATAAAATAATCAA
* * *
42911639 ATGAAAAATTAAACATAATCAG
1 TTTAAAAA-TAAA-ATAATCAA
42911661 TTTAAAA
1 TTTAAAA
42911668 CATATTAAAA
Statistics
Matches: 22, Mismatches: 5, Indels: 2
0.76 0.17 0.07
Matches are distributed among these distances:
20 6 0.27
21 4 0.18
22 12 0.55
ACGTcount: A:0.61, C:0.06, G:0.04, T:0.29
Consensus pattern (20 bp):
TTTAAAAATAAAATAATCAA
Found at i:42914746 original size:17 final size:15
Alignment explanation
Indices: 42914716--42914767 Score: 50
Period size: 17 Copynumber: 3.2 Consensus size: 15
42914706 ACTACAAAAC
*
42914716 ATTTATTGTTAATAT
1 ATTTATTTTTAATAT
42914731 ATTTATAATTTTAATAAAT
1 ATTTAT--TTTTAAT--AT
*
42914750 ATTTATTTTTAAAAT
1 ATTTATTTTTAATAT
42914765 ATT
1 ATT
42914768 AATATTGAAA
Statistics
Matches: 31, Mismatches: 2, Indels: 8
0.76 0.05 0.20
Matches are distributed among these distances:
15 11 0.35
17 12 0.39
19 8 0.26
ACGTcount: A:0.40, C:0.00, G:0.02, T:0.58
Consensus pattern (15 bp):
ATTTATTTTTAATAT
Found at i:42914766 original size:15 final size:15
Alignment explanation
Indices: 42914711--42914767 Score: 51
Period size: 15 Copynumber: 3.5 Consensus size: 15
42914701 TTTATACTAC
* *
42914711 AAAACATTTATTGTT
1 AAAATATTTATTTTT
*
42914726 AATATATTTATAATTTT
1 AAAATATTTAT--TTTT
42914743 AATAAATATTTATTTTT
1 -A-AAATATTTATTTTT
42914760 AAAATATT
1 AAAATATT
42914768 AATATTGAAA
Statistics
Matches: 34, Mismatches: 4, Indels: 8
0.74 0.09 0.17
Matches are distributed among these distances:
15 16 0.47
16 1 0.03
17 7 0.21
18 1 0.03
19 9 0.26
ACGTcount: A:0.44, C:0.02, G:0.02, T:0.53
Consensus pattern (15 bp):
AAAATATTTATTTTT
Found at i:42917223 original size:20 final size:20
Alignment explanation
Indices: 42917195--42917246 Score: 59
Period size: 22 Copynumber: 2.5 Consensus size: 20
42917185 ATAAGGTCCA
*
42917195 TCTCAAGACAGAGTTCCTCG
1 TCTCGAGACAGAGTTCCTCG
**
42917215 TCTCGAGACAAAGAGTTCCTTT
1 TCTCGAGAC--AGAGTTCCTCG
42917237 TCTCGAGACA
1 TCTCGAGACA
42917247 CAACATTGAA
Statistics
Matches: 27, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
20 9 0.33
22 18 0.67
ACGTcount: A:0.27, C:0.27, G:0.19, T:0.27
Consensus pattern (20 bp):
TCTCGAGACAGAGTTCCTCG
Found at i:42917232 original size:22 final size:22
Alignment explanation
Indices: 42917204--42917246 Score: 68
Period size: 22 Copynumber: 2.0 Consensus size: 22
42917194 ATCTCAAGAC
42917204 AGAGTTCCTCGTCTCGAGACAA
1 AGAGTTCCTCGTCTCGAGACAA
**
42917226 AGAGTTCCTTTTCTCGAGACA
1 AGAGTTCCTCGTCTCGAGACA
42917247 CAACATTGAA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.26, C:0.26, G:0.21, T:0.28
Consensus pattern (22 bp):
AGAGTTCCTCGTCTCGAGACAA
Found at i:42918853 original size:6 final size:6
Alignment explanation
Indices: 42918817--42918851 Score: 52
Period size: 6 Copynumber: 5.8 Consensus size: 6
42918807 ATTTTCCGTA
* *
42918817 AAAATG AAAACG AAAATG AAAATG AAAATA AAAAT
1 AAAATG AAAATG AAAATG AAAATG AAAATG AAAAT
42918852 AACCTATGTT
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
6 26 1.00
ACGTcount: A:0.71, C:0.03, G:0.11, T:0.14
Consensus pattern (6 bp):
AAAATG
Found at i:42919380 original size:23 final size:23
Alignment explanation
Indices: 42919354--42919398 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 23
42919344 AGAAAATGTC
* *
42919354 ACAATAAAATTAACCAAAACGTT
1 ACAAAAAAATGAACCAAAACGTT
*
42919377 ACAAAAAAATGAACTAAAACGT
1 ACAAAAAAATGAACCAAAACGT
42919399 CAAAGAGAAA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.60, C:0.16, G:0.07, T:0.18
Consensus pattern (23 bp):
ACAAAAAAATGAACCAAAACGTT
Found at i:42923903 original size:7 final size:7
Alignment explanation
Indices: 42923891--42923920 Score: 51
Period size: 7 Copynumber: 4.3 Consensus size: 7
42923881 AAAAACCACC
*
42923891 TGGAAAT
1 TGGAAAA
42923898 TGGAAAA
1 TGGAAAA
42923905 TGGAAAA
1 TGGAAAA
42923912 TGGAAAA
1 TGGAAAA
42923919 TG
1 TG
42923921 AAGAACTGCC
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
7 22 1.00
ACGTcount: A:0.50, C:0.00, G:0.30, T:0.20
Consensus pattern (7 bp):
TGGAAAA
Found at i:42943267 original size:17 final size:17
Alignment explanation
Indices: 42943238--42943301 Score: 64
Period size: 17 Copynumber: 3.9 Consensus size: 17
42943228 AAATAATTAA
42943238 TAAA-TAATAAAATAAAT
1 TAAAGTAAT-AAATAAAT
42943255 TAAAGTAATAAATAAAT
1 TAAAGTAATAAATAAAT
*
42943272 TAAAG--A-AAATAAAA
1 TAAAGTAATAAATAAAT
* *
42943286 TAAAATAAAAAATAAA
1 TAAAGTAATAAATAAA
42943302 AATTCGGTTG
Statistics
Matches: 41, Mismatches: 2, Indels: 8
0.80 0.04 0.16
Matches are distributed among these distances:
14 11 0.27
15 1 0.02
16 1 0.02
17 24 0.59
18 4 0.10
ACGTcount: A:0.73, C:0.00, G:0.03, T:0.23
Consensus pattern (17 bp):
TAAAGTAATAAATAAAT
Found at i:42949023 original size:17 final size:17
Alignment explanation
Indices: 42949001--42949035 Score: 70
Period size: 17 Copynumber: 2.1 Consensus size: 17
42948991 CTTGGGTTCA
42949001 ATCCTCGGCTTTAGATG
1 ATCCTCGGCTTTAGATG
42949018 ATCCTCGGCTTTAGATG
1 ATCCTCGGCTTTAGATG
42949035 A
1 A
42949036 GCCATTTATA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.20, C:0.23, G:0.23, T:0.34
Consensus pattern (17 bp):
ATCCTCGGCTTTAGATG
Found at i:42950424 original size:16 final size:18
Alignment explanation
Indices: 42950400--42950442 Score: 54
Period size: 16 Copynumber: 2.5 Consensus size: 18
42950390 AAACCTTACT
*
42950400 AAGATAAAAACCCT-GTG
1 AAGAAAAAAACCCTAGTG
*
42950417 -AGAAAAAAATCCTAGTG
1 AAGAAAAAAACCCTAGTG
42950434 AAGAAAAAA
1 AAGAAAAAA
42950443 GAGTACACAT
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
16 11 0.50
17 3 0.14
18 8 0.36
ACGTcount: A:0.58, C:0.12, G:0.16, T:0.14
Consensus pattern (18 bp):
AAGAAAAAAACCCTAGTG
Found at i:42970067 original size:56 final size:51
Alignment explanation
Indices: 42970001--42970192 Score: 163
Period size: 50 Copynumber: 3.7 Consensus size: 51
42969991 GGAATGAGAC
* **
42970001 CCCATGTAAGACCATGTCTGGGACATGGCATTGGCATTATTGAGGTTATGAGAGGT
1 CCCACGTAAGACCATGTCTGGGACATGGCATTGGCA--ACCGA-G--ATGAGAGGT
* * * * *
42970057 CCTACGTAAGATCATGTATGGGACAAGGCGTTGGC-ACCGAGATGAGAGGT
1 CCCACGTAAGACCATGTCTGGGACATGGCATTGGCAACCGAGATGAGAGGT
* * * * **
42970107 CCCCCGTAAGACCATGTCTGGGACATAGCATGGGC-ACCGATATGAGAACT
1 CCCACGTAAGACCATGTCTGGGACATGGCATTGGCAACCGAGATGAGAGGT
* * * *
42970157 CCCATGTAAGACCATATCTGGGATATGACATTGGCA
1 CCCACGTAAGACCATGTCTGGGACATGGCATTGGCA
42970193 GTACAGGAAA
Statistics
Matches: 109, Mismatches: 26, Indels: 7
0.77 0.18 0.05
Matches are distributed among these distances:
50 76 0.70
52 1 0.01
53 3 0.03
56 29 0.27
ACGTcount: A:0.28, C:0.21, G:0.29, T:0.23
Consensus pattern (51 bp):
CCCACGTAAGACCATGTCTGGGACATGGCATTGGCAACCGAGATGAGAGGT
Found at i:42970468 original size:20 final size:20
Alignment explanation
Indices: 42970443--42970481 Score: 62
Period size: 20 Copynumber: 1.9 Consensus size: 20
42970433 TGAGTTATTT
42970443 AAGTAAGCA-AGTAAGTAAAC
1 AAGTAAG-AGAGTAAGTAAAC
42970463 AAGTAAGAGAGTAAGTAAA
1 AAGTAAGAGAGTAAGTAAA
42970482 GAAGAAAGTA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
19 1 0.06
20 17 0.94
ACGTcount: A:0.56, C:0.05, G:0.23, T:0.15
Consensus pattern (20 bp):
AAGTAAGAGAGTAAGTAAAC
Found at i:42975518 original size:20 final size:20
Alignment explanation
Indices: 42975493--42975531 Score: 62
Period size: 20 Copynumber: 1.9 Consensus size: 20
42975483 TACTTTCTTC
42975493 TTTACTTACTCT-CTTACTTG
1 TTTACTTACT-TGCTTACTTG
42975513 TTTACTTACTTGCTTACTT
1 TTTACTTACTTGCTTACTT
42975532 AAATAACTCA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
19 1 0.06
20 17 0.94
ACGTcount: A:0.15, C:0.23, G:0.05, T:0.56
Consensus pattern (20 bp):
TTTACTTACTTGCTTACTTG
Found at i:42975859 original size:49 final size:50
Alignment explanation
Indices: 42975740--42975926 Score: 202
Period size: 49 Copynumber: 3.8 Consensus size: 50
42975730 ACATGTCAAA
* ** * * *
42975740 GCCATGTCCCAGTCATGGTCTTACATGGGATGTTTCCTGTAC--TGCCAAT
1 GCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATAT-CGGTGCCAAT
* * **
42975789 GCCATATCCCAGATATGGTCTTACATGGGAGTTCTCATATCGGTGTCC-AT
1 GCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATATCGGTG-CCAAT
** *
42975839 GCCATGTCCCAGACAT-GTCTTACGGGGGACCTCTCATCTCGGTGCCAAT
1 GCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATATCGGTGCCAAT
*
42975888 GCCATGTCCCAGACATTGTCTTACATGGGACCTCTCATA
1 GCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATA
42975927 ACCTCAATAA
Statistics
Matches: 115, Mismatches: 18, Indels: 9
0.81 0.13 0.06
Matches are distributed among these distances:
48 3 0.03
49 73 0.63
50 37 0.32
51 2 0.02
ACGTcount: A:0.20, C:0.28, G:0.22, T:0.29
Consensus pattern (50 bp):
GCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATATCGGTGCCAAT
Found at i:42977956 original size:45 final size:45
Alignment explanation
Indices: 42977875--42978006 Score: 196
Period size: 45 Copynumber: 3.0 Consensus size: 45
42977865 AATCGTTACA
* * **
42977875 CGGTGG-ATCAGCACATAGC-ACCACCCTTATAATCAATTATATT
1 CGGTGGAATCAGCACATAGCAACCACCTTTATAATCAATGATACC
* *
42977918 CGGTGGAATCAGCACATAGCAACCACCTTTATAGTCAATGGTACC
1 CGGTGGAATCAGCACATAGCAACCACCTTTATAATCAATGATACC
42977963 CGGTGGAATCAGCACATAGCAACCACCTTTATAATCAATGATAC
1 CGGTGGAATCAGCACATAGCAACCACCTTTATAATCAATGATAC
42978007 TCAGTACACG
Statistics
Matches: 79, Mismatches: 8, Indels: 2
0.89 0.09 0.02
Matches are distributed among these distances:
43 6 0.08
44 13 0.16
45 60 0.76
ACGTcount: A:0.33, C:0.26, G:0.17, T:0.24
Consensus pattern (45 bp):
CGGTGGAATCAGCACATAGCAACCACCTTTATAATCAATGATACC
Found at i:42986318 original size:29 final size:29
Alignment explanation
Indices: 42986283--42986341 Score: 118
Period size: 29 Copynumber: 2.0 Consensus size: 29
42986273 CATTCTTTCG
42986283 CACACATTGAAGCTTGAGTTCATTTTTAT
1 CACACATTGAAGCTTGAGTTCATTTTTAT
42986312 CACACATTGAAGCTTGAGTTCATTTTTAT
1 CACACATTGAAGCTTGAGTTCATTTTTAT
42986341 C
1 C
42986342 CTTACACACC
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 30 1.00
ACGTcount: A:0.27, C:0.19, G:0.14, T:0.41
Consensus pattern (29 bp):
CACACATTGAAGCTTGAGTTCATTTTTAT
Found at i:42992445 original size:45 final size:45
Alignment explanation
Indices: 42992381--42992472 Score: 184
Period size: 45 Copynumber: 2.0 Consensus size: 45
42992371 GGTCCAGTTG
42992381 TGTATATTTGATTTTCCTTCAACTGCAATGCTGCAATATCCTCCT
1 TGTATATTTGATTTTCCTTCAACTGCAATGCTGCAATATCCTCCT
42992426 TGTATATTTGATTTTCCTTCAACTGCAATGCTGCAATATCCTCCT
1 TGTATATTTGATTTTCCTTCAACTGCAATGCTGCAATATCCTCCT
42992471 TG
1 TG
42992473 CTGCTAGAGC
Statistics
Matches: 47, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
45 47 1.00
ACGTcount: A:0.22, C:0.24, G:0.12, T:0.42
Consensus pattern (45 bp):
TGTATATTTGATTTTCCTTCAACTGCAATGCTGCAATATCCTCCT
Found at i:42993533 original size:2 final size:2
Alignment explanation
Indices: 42993526--42993553 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
42993516 CTCTAGCATC
42993526 GT GT GT GT GT GT GT GT GT GT GT GT GT GT
1 GT GT GT GT GT GT GT GT GT GT GT GT GT GT
42993554 CAACAGCAAA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.00, C:0.00, G:0.50, T:0.50
Consensus pattern (2 bp):
GT
Found at i:42995014 original size:44 final size:44
Alignment explanation
Indices: 42994965--42995053 Score: 169
Period size: 44 Copynumber: 2.0 Consensus size: 44
42994955 CTCCCATGAA
*
42994965 TGCAATATTGTACATTATAAGGAGATAAGAAAGACCTTTAAAAC
1 TGCAATATTGAACATTATAAGGAGATAAGAAAGACCTTTAAAAC
42995009 TGCAATATTGAACATTATAAGGAGATAAGAAAGACCTTTAAAAC
1 TGCAATATTGAACATTATAAGGAGATAAGAAAGACCTTTAAAAC
42995053 T
1 T
42995054 AAATAAAGAT
Statistics
Matches: 44, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
44 44 1.00
ACGTcount: A:0.46, C:0.11, G:0.16, T:0.27
Consensus pattern (44 bp):
TGCAATATTGAACATTATAAGGAGATAAGAAAGACCTTTAAAAC
Found at i:42998444 original size:25 final size:23
Alignment explanation
Indices: 42998416--42998461 Score: 65
Period size: 23 Copynumber: 1.9 Consensus size: 23
42998406 AATATAATAC
42998416 AAATACACAAATTCTTCTTCTTTTT
1 AAATACAC--ATTCTTCTTCTTTTT
*
42998441 AAATACACATTCTTTTTCTTT
1 AAATACACATTCTTCTTCTTT
42998462 CTTTCTTTTT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
23 12 0.60
25 8 0.40
ACGTcount: A:0.30, C:0.20, G:0.00, T:0.50
Consensus pattern (23 bp):
AAATACACATTCTTCTTCTTTTT
Found at i:43006534 original size:17 final size:16
Alignment explanation
Indices: 43006500--43006530 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
43006490 AAACGCTTTC
43006500 AGCTAGAAGTCTTTTA
1 AGCTAGAAGTCTTTTA
*
43006516 AGCTAGAAGTATTTT
1 AGCTAGAAGTCTTTT
43006531 TAAGTGATTT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.32, C:0.10, G:0.19, T:0.39
Consensus pattern (16 bp):
AGCTAGAAGTCTTTTA
Found at i:43006729 original size:17 final size:17
Alignment explanation
Indices: 43006707--43006745 Score: 53
Period size: 17 Copynumber: 2.3 Consensus size: 17
43006697 TTGACTCTAT
*
43006707 TTTTAT-TTTCTAGTTTA
1 TTTTATATTT-TAGTATA
43006724 TTTTATATTTTAGTATA
1 TTTTATATTTTAGTATA
43006741 TTTTA
1 TTTTA
43006746 CATCTAAATT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
17 17 0.85
18 3 0.15
ACGTcount: A:0.23, C:0.03, G:0.05, T:0.69
Consensus pattern (17 bp):
TTTTATATTTTAGTATA
Found at i:43007678 original size:28 final size:28
Alignment explanation
Indices: 43007636--43007691 Score: 94
Period size: 28 Copynumber: 2.0 Consensus size: 28
43007626 TCCAACAAGA
**
43007636 AGTGTTTTTTTGCAAATCACCTGAAAAC
1 AGTGTTTTTCCGCAAATCACCTGAAAAC
43007664 AGTGTTTTTCCGCAAATCACCTGAAAAC
1 AGTGTTTTTCCGCAAATCACCTGAAAAC
43007692 TTGTAAAATT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
28 26 1.00
ACGTcount: A:0.32, C:0.21, G:0.14, T:0.32
Consensus pattern (28 bp):
AGTGTTTTTCCGCAAATCACCTGAAAAC
Found at i:43008793 original size:18 final size:18
Alignment explanation
Indices: 43008770--43008805 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
43008760 AGTGTTTCAT
*
43008770 AAGCTATATCACAAATAC
1 AAGCTACATCACAAATAC
43008788 AAGCTACATCACAAATAC
1 AAGCTACATCACAAATAC
43008806 CTCTTTATTA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.50, C:0.25, G:0.06, T:0.19
Consensus pattern (18 bp):
AAGCTACATCACAAATAC
Found at i:43009061 original size:13 final size:13
Alignment explanation
Indices: 43009045--43009070 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
43009035 TAAAAAAATT
43009045 AATTCAAAATTTA
1 AATTCAAAATTTA
43009058 AATTCAAAATTTA
1 AATTCAAAATTTA
43009071 TTGAGACAAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.54, C:0.08, G:0.00, T:0.38
Consensus pattern (13 bp):
AATTCAAAATTTA
Found at i:43011290 original size:21 final size:21
Alignment explanation
Indices: 43011264--43011306 Score: 77
Period size: 21 Copynumber: 2.0 Consensus size: 21
43011254 ATAAGAATAA
43011264 ACTATGGATAAATGAGTGTAT
1 ACTATGGATAAATGAGTGTAT
*
43011285 ACTATGGATAAATGGGTGTAT
1 ACTATGGATAAATGAGTGTAT
43011306 A
1 A
43011307 TGTAATATAG
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.37, C:0.05, G:0.26, T:0.33
Consensus pattern (21 bp):
ACTATGGATAAATGAGTGTAT
Found at i:43015452 original size:41 final size:41
Alignment explanation
Indices: 43015407--43015491 Score: 143
Period size: 41 Copynumber: 2.1 Consensus size: 41
43015397 TAGCAGAATC
*
43015407 CCAGACAATTGGATGTAACATTTCACTATAGAATAAAGCCA
1 CCAGACAATTGGATATAACATTTCACTATAGAATAAAGCCA
* *
43015448 CCAGACATTTGGATATAACGTTTCACTATAGAATAAAGCCA
1 CCAGACAATTGGATATAACATTTCACTATAGAATAAAGCCA
43015489 CCA
1 CCA
43015492 TCTAGAACAA
Statistics
Matches: 41, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
41 41 1.00
ACGTcount: A:0.40, C:0.21, G:0.14, T:0.25
Consensus pattern (41 bp):
CCAGACAATTGGATATAACATTTCACTATAGAATAAAGCCA
Found at i:43016442 original size:14 final size:14
Alignment explanation
Indices: 43016423--43016459 Score: 65
Period size: 14 Copynumber: 2.6 Consensus size: 14
43016413 AAAAGGTCTA
43016423 GTTGAACCGCATTG
1 GTTGAACCGCATTG
*
43016437 GTTGAATCGCATTG
1 GTTGAACCGCATTG
43016451 GTTGAACCG
1 GTTGAACCG
43016460 AATCTAGTGA
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.22, C:0.19, G:0.30, T:0.30
Consensus pattern (14 bp):
GTTGAACCGCATTG
Found at i:43024291 original size:21 final size:21
Alignment explanation
Indices: 43024221--43024291 Score: 54
Period size: 21 Copynumber: 3.2 Consensus size: 21
43024211 TGATTATTAC
43024221 AATAAATTGTTATATTAGCTT
1 AATAAATTGTTATATTAGCTT
* * * **
43024242 AAT-AATGACGTGAAATGTATTTCT
1 AATAAAT--TGTTATAT-TAGCT-T
43024266 AATAAATTGTTATATTAGCTT
1 AATAAATTGTTATATTAGCTT
43024287 AATAA
1 AATAA
43024292 TGACATGAAA
Statistics
Matches: 35, Mismatches: 10, Indels: 10
0.64 0.18 0.18
Matches are distributed among these distances:
20 3 0.09
21 9 0.26
22 8 0.23
23 8 0.23
24 4 0.11
25 3 0.09
ACGTcount: A:0.41, C:0.06, G:0.11, T:0.42
Consensus pattern (21 bp):
AATAAATTGTTATATTAGCTT
Found at i:43024329 original size:44 final size:45
Alignment explanation
Indices: 43024221--43024360 Score: 264
Period size: 45 Copynumber: 3.1 Consensus size: 45
43024211 TGATTATTAC
*
43024221 AATAAATTGTTATATTAGCTTAATAATGACGTGAAATGTATTTCT
1 AATAAATTGTTATATTAGCTTAATAATGACATGAAATGTATTTCT
43024266 AATAAATTGTTATATTAGCTTAATAATGACATGAAATGTATTTC-
1 AATAAATTGTTATATTAGCTTAATAATGACATGAAATGTATTTCT
43024310 AATAAATTGTTATATTAGCTTAATAATGACATGAAATGTATTTCT
1 AATAAATTGTTATATTAGCTTAATAATGACATGAAATGTATTTCT
43024355 AATAAA
1 AATAAA
43024361 GCATGCGAAT
Statistics
Matches: 93, Mismatches: 1, Indels: 2
0.97 0.01 0.02
Matches are distributed among these distances:
44 44 0.47
45 49 0.53
ACGTcount: A:0.41, C:0.06, G:0.11, T:0.41
Consensus pattern (45 bp):
AATAAATTGTTATATTAGCTTAATAATGACATGAAATGTATTTCT
Found at i:43025428 original size:18 final size:19
Alignment explanation
Indices: 43025405--43025443 Score: 62
Period size: 18 Copynumber: 2.1 Consensus size: 19
43025395 ATTGTCGAAC
43025405 AATAATTAAA-TATGATAA
1 AATAATTAAATTATGATAA
*
43025423 AATAATTAAATTATGTTAA
1 AATAATTAAATTATGATAA
43025442 AA
1 AA
43025444 ATATGAACAT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
18 10 0.53
19 9 0.47
ACGTcount: A:0.59, C:0.00, G:0.05, T:0.36
Consensus pattern (19 bp):
AATAATTAAATTATGATAA
Found at i:43030897 original size:3 final size:3
Alignment explanation
Indices: 43030889--43030918 Score: 60
Period size: 3 Copynumber: 10.0 Consensus size: 3
43030879 TCCATTTTCC
43030889 TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT
1 TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT
43030919 AACTTTCATC
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):
TCT
Found at i:43046796 original size:25 final size:23
Alignment explanation
Indices: 43046738--43046801 Score: 65
Period size: 25 Copynumber: 2.7 Consensus size: 23
43046728 CCGTTATTAT
* *
43046738 CTCTCATGAGCATTTCGATATTGG
1 CTCTCATGAGC-TTCCAATATTGG
* *
43046762 CACTCTTGAGCTTCCTAATATATGG
1 CTCTCATGAGCTTCC-AATAT-TGG
43046787 CTCTCATGAGCTTCC
1 CTCTCATGAGCTTCC
43046802 CATTAGTAGC
Statistics
Matches: 32, Mismatches: 6, Indels: 3
0.78 0.15 0.07
Matches are distributed among these distances:
23 3 0.09
24 13 0.41
25 16 0.50
ACGTcount: A:0.20, C:0.27, G:0.17, T:0.36
Consensus pattern (23 bp):
CTCTCATGAGCTTCCAATATTGG
Found at i:43046978 original size:24 final size:25
Alignment explanation
Indices: 43046923--43046982 Score: 77
Period size: 24 Copynumber: 2.4 Consensus size: 25
43046913 AAGGCCCTTT
*
43046923 CATGAGCTTCCTAATTAATGGCTCT
1 CATGAGCTTCCTAATTAATGGCTCG
** *
43046948 CCGGAGCTTCCTAA-TATTGGCTCG
1 CATGAGCTTCCTAATTAATGGCTCG
43046972 CATGAGCTTCC
1 CATGAGCTTCC
43046983 CGATTATCGC
Statistics
Matches: 29, Mismatches: 6, Indels: 1
0.81 0.17 0.03
Matches are distributed among these distances:
24 17 0.59
25 12 0.41
ACGTcount: A:0.20, C:0.28, G:0.20, T:0.32
Consensus pattern (25 bp):
CATGAGCTTCCTAATTAATGGCTCG
Found at i:43047036 original size:25 final size:25
Alignment explanation
Indices: 43047004--43047065 Score: 63
Period size: 25 Copynumber: 2.5 Consensus size: 25
43046994 CTTATAAGCT
* * *
43047004 TTCT-GTTACATGGCTCACATGAGC
1 TTCTCGTTACATGGATCAAAAGAGC
*
43047028 TTCTCGTTATATGGATCAAAAGAGC
1 TTCTCGTTACATGGATCAAAAGAGC
*
43047053 TTCCCGTTTACAT
1 TTCTCG-TTACAT
43047066 TCTTGTATAA
Statistics
Matches: 30, Mismatches: 6, Indels: 2
0.79 0.16 0.05
Matches are distributed among these distances:
24 4 0.13
25 21 0.70
26 5 0.17
ACGTcount: A:0.24, C:0.23, G:0.18, T:0.35
Consensus pattern (25 bp):
TTCTCGTTACATGGATCAAAAGAGC
Found at i:43051109 original size:50 final size:50
Alignment explanation
Indices: 43051005--43051194 Score: 209
Period size: 50 Copynumber: 3.7 Consensus size: 50
43050995 AAAGAGATCT
* *
43051005 CATGTAAGACCATGTCTGGGACATGGCATTGGCATCATTGAGATTATGAGAGGTCT
1 CATGTAAGACCATGTCTGGGACATGGCATTGGCA-C--CGAG---ATGAGAGGTCC
*
43051061 CATGTAAGACCATGTCTGGGACATGGCGTTGGCACCGAGATGAGAGGTCC
1 CATGTAAGACCATGTCTGGGACATGGCATTGGCACCGAGATGAGAGGTCC
** * * * **
43051111 CCCGTAAGACCATGTCTGGGACATGGCATGGGCACCTATATGAGAACTCC
1 CATGTAAGACCATGTCTGGGACATGGCATTGGCACCGAGATGAGAGGTCC
* * *
43051161 CATGTAAGACCATATCTGGGATATGGCACTGGCA
1 CATGTAAGACCATGTCTGGGACATGGCATTGGCA
43051195 GTACAAGAAA
Statistics
Matches: 117, Mismatches: 17, Indels: 6
0.84 0.12 0.04
Matches are distributed among these distances:
50 80 0.68
53 3 0.03
55 1 0.01
56 33 0.28
ACGTcount: A:0.26, C:0.22, G:0.29, T:0.23
Consensus pattern (50 bp):
CATGTAAGACCATGTCTGGGACATGGCATTGGCACCGAGATGAGAGGTCC
Found at i:43051194 original size:100 final size:104
Alignment explanation
Indices: 43051008--43051194 Score: 247
Period size: 100 Copynumber: 1.8 Consensus size: 104
43050998 GAGATCTCAT
* * ** *
43051008 GTAAGACCATGTCTGGGACATGGCATTGGCATCATTGAGATTATGAGAGGTCTCATGTAAGACCA
1 GTAAGACCATGTCTGGGACATGGCATGGGCATCACT--GATTATGAGAACTCCCATGTAAGACCA
* **
43051073 TGTCTGGGACATGGCGTTGGCACCGAGATGAGAGGTCCCCC
64 TATCTGGGACATGGCACTGGCACCGAGATGAGAGGTCCCCC
43051114 GTAAGACCATGTCTGGGACATGGCATGGGCA-C-CT-A-TATGAGAACTCCCATGTAAGACCATA
1 GTAAGACCATGTCTGGGACATGGCATGGGCATCACTGATTATGAGAACTCCCATGTAAGACCATA
*
43051175 TCTGGGATATGGCACTGGCA
66 TCTGGGACATGGCACTGGCA
43051195 GTACAAGAAA
Statistics
Matches: 72, Mismatches: 9, Indels: 6
0.83 0.10 0.07
Matches are distributed among these distances:
100 39 0.54
101 1 0.01
104 1 0.01
105 1 0.01
106 30 0.42
ACGTcount: A:0.26, C:0.21, G:0.29, T:0.23
Consensus pattern (104 bp):
GTAAGACCATGTCTGGGACATGGCATGGGCATCACTGATTATGAGAACTCCCATGTAAGACCATA
TCTGGGACATGGCACTGGCACCGAGATGAGAGGTCCCCC
Found at i:43051228 original size:49 final size:50
Alignment explanation
Indices: 43051005--43051233 Score: 167
Period size: 50 Copynumber: 4.5 Consensus size: 50
43050995 AAAGAGATCT
* * * ** *
43051005 CATGTAAGACCATGTCTGGGACATGGCATTGGCATCATTGAGATTATGAGAGGTCT
1 CATGTAAGACCATGTCTGGGACATGGCATGGGCA-C-CT-ACA--A-GAGAACTCC
* * * * * **
43051061 CATGTAAGACCATGTCTGGGACATGGCGTTGGCACCGAGATGAGAGGTCC
1 CATGTAAGACCATGTCTGGGACATGGCATGGGCACCTACAAGAGAACTCC
** * *
43051111 CCCGTAAGACCATGTCTGGGACATGGCATGGGCACCTATATGAGAACTCC
1 CATGTAAGACCATGTCTGGGACATGGCATGGGCACCTACAAGAGAACTCC
* * *
43051161 CATGTAAGACCATATCTGGGATATGGCACT-GGCA-GTACAAGA-AACATCC
1 CATGTAAGACCATGTCTGGGACATGGCA-TGGGCACCTACAAGAGAAC-TCC
* *
43051210 TATGTAAGACTATGTCTGGGACAT
1 CATGTAAGACCATGTCTGGGACAT
43051234 AGCTTTCTCA
Statistics
Matches: 147, Mismatches: 24, Indels: 11
0.81 0.13 0.06
Matches are distributed among these distances:
48 3 0.02
49 28 0.19
50 78 0.53
51 1 0.01
53 3 0.02
55 1 0.01
56 33 0.22
ACGTcount: A:0.28, C:0.21, G:0.28, T:0.24
Consensus pattern (50 bp):
CATGTAAGACCATGTCTGGGACATGGCATGGGCACCTACAAGAGAACTCC
Found at i:43058158 original size:79 final size:78
Alignment explanation
Indices: 43058021--43058231 Score: 210
Period size: 79 Copynumber: 2.7 Consensus size: 78
43058011 TTGTATGATT
* *
43058021 GCACATACGTGCCCCTATTTGTACTTCAGTACCCTTGAATGCACATACGTGCCCTGTTTGTACTT
1 GCACATACGTG-CCCTATTTGTACTTCAGCACCCCTGAATGCACATACGTGCCCTGTTTGTACTT
* *
43058086 TGATACCCCTGAAC
65 CGATACACCTGAAC
* * **
43058100 GCACATACGTGCCCTGTCTT-TACTTC-GACACCCCTGATTGCACATGTGTGCCCATGTTTGTAC
1 GCACATACGTGCCCTAT-TTGTACTTCAG-CACCCCTGAATGCACATACGTGCCC-TGTTTGTAC
* **
43058163 TTCGGTACACCTGATT
63 TTCGATACACCTGAAC
* * * * **
43058179 GCACATACGTGCCCCTATATGTACTTCGGTACCCCTGAACGCATTTACGTGCC
1 GCACATACGTG-CCCTATTTGTACTTCAGCACCCCTGAATGCACATACGTGCC
43058232 TTAACTGTAC
Statistics
Matches: 106, Mismatches: 20, Indels: 11
0.77 0.15 0.08
Matches are distributed among these distances:
77 1 0.01
78 31 0.29
79 45 0.42
80 28 0.26
81 1 0.01
ACGTcount: A:0.20, C:0.31, G:0.18, T:0.31
Consensus pattern (78 bp):
GCACATACGTGCCCTATTTGTACTTCAGCACCCCTGAATGCACATACGTGCCCTGTTTGTACTTC
GATACACCTGAAC
Found at i:43058176 original size:40 final size:39
Alignment explanation
Indices: 43058016--43058216 Score: 224
Period size: 39 Copynumber: 5.1 Consensus size: 39
43058006 AATATTTGTA
* * *
43058016 TGATTGCACATACGTGCCCCTATTTGTACTTCAGTACCCT
1 TGATTGCACATACGTG-CCCTGTTTGTACTTCGGTACCCC
* * *
43058056 TGAATGCACATACGTGCCCTGTTTGTACTTTGATACCCC
1 TGATTGCACATACGTGCCCTGTTTGTACTTCGGTACCCC
** **
43058095 TGAACGCACATACGTGCCCTGTCTT-TACTTCGACACCCC
1 TGATTGCACATACGTGCCCTGT-TTGTACTTCGGTACCCC
** *
43058134 TGATTGCACATGTGTGCCCATGTTTGTACTTCGGTACACC
1 TGATTGCACATACGTGCCC-TGTTTGTACTTCGGTACCCC
* *
43058174 TGATTGCACATACGTGCCCCTATATGTACTTCGGTACCCC
1 TGATTGCACATACGTG-CCCTGTTTGTACTTCGGTACCCC
43058214 TGA
1 TGA
43058217 ACGCATTTAC
Statistics
Matches: 136, Mismatches: 21, Indels: 8
0.82 0.13 0.05
Matches are distributed among these distances:
39 68 0.50
40 65 0.48
41 3 0.02
ACGTcount: A:0.20, C:0.30, G:0.18, T:0.32
Consensus pattern (39 bp):
TGATTGCACATACGTGCCCTGTTTGTACTTCGGTACCCC
Found at i:43058228 original size:40 final size:40
Alignment explanation
Indices: 43058020--43058231 Score: 223
Period size: 40 Copynumber: 5.3 Consensus size: 40
43058010 TTTGTATGAT
* * *
43058020 TGCACATACGTGCCCCTATTTGTACTTCAGTACCCTTGAA
1 TGCACATACGTGCCCCTGTTTGTACTTCGGTACCCCTGAA
* *
43058060 TGCACATACGTG-CCCTGTTTGTACTTTGATACCCCTGAA
1 TGCACATACGTGCCCCTGTTTGTACTTCGGTACCCCTGAA
* ** *
43058099 CGCACATACGTG-CCCTGTCTT-TACTTCGACACCCCTGAT
1 TGCACATACGTGCCCCTGT-TTGTACTTCGGTACCCCTGAA
** * * *
43058138 TGCACATGTGTGCCCATGTTTGTACTTCGGTACACCTGAT
1 TGCACATACGTGCCCCTGTTTGTACTTCGGTACCCCTGAA
* *
43058178 TGCACATACGTGCCCCTATATGTACTTCGGTACCCCTGAA
1 TGCACATACGTGCCCCTGTTTGTACTTCGGTACCCCTGAA
* **
43058218 CGCATTTACGTGCC
1 TGCACATACGTGCC
43058232 TTAACTGTAC
Statistics
Matches: 143, Mismatches: 26, Indels: 6
0.82 0.15 0.03
Matches are distributed among these distances:
39 65 0.45
40 78 0.55
ACGTcount: A:0.20, C:0.31, G:0.18, T:0.31
Consensus pattern (40 bp):
TGCACATACGTGCCCCTGTTTGTACTTCGGTACCCCTGAA
Found at i:43059972 original size:16 final size:17
Alignment explanation
Indices: 43059951--43059989 Score: 53
Period size: 17 Copynumber: 2.3 Consensus size: 17
43059941 TAGAAATTTC
43059951 TATAAT-TTCTATTTTT
1 TATAATATTCTATTTTT
*
43059967 TATAATATTTTATTTTT
1 TATAATATTCTATTTTT
43059984 TCATAA
1 T-ATAA
43059990 AATATTAATA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
16 6 0.30
17 10 0.50
18 4 0.20
ACGTcount: A:0.31, C:0.05, G:0.00, T:0.64
Consensus pattern (17 bp):
TATAATATTCTATTTTT
Found at i:43061277 original size:81 final size:82
Alignment explanation
Indices: 43061126--43061278 Score: 218
Period size: 81 Copynumber: 1.9 Consensus size: 82
43061116 TTTTTCTTGG
**
43061126 TTTTTGTTAAAATAAAAAGACTAAAATACCCTCAAATAATATGACTCATTTTAATTACGAAGGGA
1 TTTTTGTTAAAATAAAAAGACTAAAATACCCTCAAATAATATGACTCATTTTAATTACGAAAAGA
*
43061191 TATTTTCGTAATTTCCT
66 CATTTTCGTAATTTCCT
* * * * * *
43061208 TTTTTGTTAAAATGAAAATATTAAAATA-CTTCAAATAATATGACTCATTTTAATTATGAAAATA
1 TTTTTGTTAAAATAAAAAGACTAAAATACCCTCAAATAATATGACTCATTTTAATTACGAAAAGA
43061272 CATTTTC
66 CATTTTC
43061279 TTAAATTTTT
Statistics
Matches: 62, Mismatches: 9, Indels: 1
0.86 0.12 0.01
Matches are distributed among these distances:
81 37 0.60
82 25 0.40
ACGTcount: A:0.41, C:0.11, G:0.08, T:0.40
Consensus pattern (82 bp):
TTTTTGTTAAAATAAAAAGACTAAAATACCCTCAAATAATATGACTCATTTTAATTACGAAAAGA
CATTTTCGTAATTTCCT
Found at i:43061958 original size:22 final size:22
Alignment explanation
Indices: 43061914--43061958 Score: 54
Period size: 22 Copynumber: 2.0 Consensus size: 22
43061904 TTATGTTGAT
* *
43061914 TCATAGAGCTGATTTCTAGGGA
1 TCATAGAACTGATTTCTAAGGA
* *
43061936 TCATAGAATTGATTTGTAAGGA
1 TCATAGAACTGATTTCTAAGGA
43061958 T
1 T
43061959 TTGGTTTATT
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.31, C:0.09, G:0.24, T:0.36
Consensus pattern (22 bp):
TCATAGAACTGATTTCTAAGGA
Found at i:43061972 original size:23 final size:23
Alignment explanation
Indices: 43061943--43061996 Score: 90
Period size: 23 Copynumber: 2.3 Consensus size: 23
43061933 GGATCATAGA
*
43061943 ATTGATTTGTAAGGATTTGGTTT
1 ATTGATTTGCAAGGATTTGGTTT
43061966 ATTGATTTGCAAGGATTTGGTTT
1 ATTGATTTGCAAGGATTTGGTTT
*
43061989 ATTTATTT
1 ATTGATTT
43061997 CTTTCCTTCT
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
23 29 1.00
ACGTcount: A:0.22, C:0.02, G:0.22, T:0.54
Consensus pattern (23 bp):
ATTGATTTGCAAGGATTTGGTTT
Found at i:43066090 original size:22 final size:22
Alignment explanation
Indices: 43066062--43066106 Score: 72
Period size: 22 Copynumber: 2.0 Consensus size: 22
43066052 ACAGTTAGAT
*
43066062 TCATAGAGCTGATTTGTAGGGA
1 TCATAGAACTGATTTGTAGGGA
*
43066084 TCATAGAATTGATTTGTAGGGA
1 TCATAGAACTGATTTGTAGGGA
43066106 T
1 T
43066107 TTTTTTCTGA
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.29, C:0.07, G:0.29, T:0.36
Consensus pattern (22 bp):
TCATAGAACTGATTTGTAGGGA
Found at i:43066250 original size:6 final size:6
Alignment explanation
Indices: 43066239--43066367 Score: 249
Period size: 6 Copynumber: 21.5 Consensus size: 6
43066229 TGCTAATATT
43066239 TATACA TATACA TATACA TATACA TATACA TATACA TATACA TATACA
1 TATACA TATACA TATACA TATACA TATACA TATACA TATACA TATACA
*
43066287 TATACA TATATA TATACA TATACA TATACA TATACA TATACA TATACA
1 TATACA TATACA TATACA TATACA TATACA TATACA TATACA TATACA
43066335 TATACA TATACA TATACA TATACA TATACA TAT
1 TATACA TATACA TATACA TATACA TATACA TAT
43066368 GTTGGAATCC
Statistics
Matches: 121, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
6 121 1.00
ACGTcount: A:0.50, C:0.16, G:0.00, T:0.35
Consensus pattern (6 bp):
TATACA
Found at i:43066408 original size:32 final size:32
Alignment explanation
Indices: 43066367--43066429 Score: 117
Period size: 32 Copynumber: 2.0 Consensus size: 32
43066357 CATATACATA
43066367 TGTTGGAATCCCTATAATTAAGGATAGAAATT
1 TGTTGGAATCCCTATAATTAAGGATAGAAATT
*
43066399 TGTTGGAATCCCTATAATTAATGATAGAAAT
1 TGTTGGAATCCCTATAATTAAGGATAGAAAT
43066430 CTTACCTTAT
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
32 30 1.00
ACGTcount: A:0.38, C:0.10, G:0.17, T:0.35
Consensus pattern (32 bp):
TGTTGGAATCCCTATAATTAAGGATAGAAATT
Found at i:43071057 original size:32 final size:32
Alignment explanation
Indices: 43071016--43071080 Score: 130
Period size: 32 Copynumber: 2.0 Consensus size: 32
43071006 TTGAGGGGAG
43071016 TGTTGGAATCCCTATAATTAAGGATAGAAATC
1 TGTTGGAATCCCTATAATTAAGGATAGAAATC
43071048 TGTTGGAATCCCTATAATTAAGGATAGAAATC
1 TGTTGGAATCCCTATAATTAAGGATAGAAATC
43071080 T
1 T
43071081 TACCTTATTA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
32 33 1.00
ACGTcount: A:0.37, C:0.12, G:0.18, T:0.32
Consensus pattern (32 bp):
TGTTGGAATCCCTATAATTAAGGATAGAAATC
Found at i:43074786 original size:33 final size:33
Alignment explanation
Indices: 43074740--43074809 Score: 133
Period size: 33 Copynumber: 2.2 Consensus size: 33
43074730 ATTAGAAAAA
43074740 TTAA-CCAAAATGGTTACTTAGATGTTGAACCC
1 TTAATCCAAAATGGTTACTTAGATGTTGAACCC
43074772 TTAATCCAAAATGGTTACTTAGATGTTGAACCC
1 TTAATCCAAAATGGTTACTTAGATGTTGAACCC
43074805 TTAAT
1 TTAAT
43074810 GGATTGTTGA
Statistics
Matches: 37, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
32 4 0.11
33 33 0.89
ACGTcount: A:0.34, C:0.17, G:0.14, T:0.34
Consensus pattern (33 bp):
TTAATCCAAAATGGTTACTTAGATGTTGAACCC
Found at i:43079549 original size:18 final size:17
Alignment explanation
Indices: 43079521--43079555 Score: 52
Period size: 18 Copynumber: 2.0 Consensus size: 17
43079511 ATTATTAAGA
*
43079521 ATTTTATTAAATTATAT
1 ATTTTATTAAAATATAT
43079538 ATTTTAATTAAAATATAT
1 ATTTT-ATTAAAATATAT
43079556 TTAATAATAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 5 0.31
18 11 0.69
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (17 bp):
ATTTTATTAAAATATAT
Found at i:43079704 original size:157 final size:157
Alignment explanation
Indices: 43079509--43079825 Score: 607
Period size: 157 Copynumber: 2.0 Consensus size: 157
43079499 ATAAGAATAT
43079509 TAATTATTAAGAATTTTATTAAATTATATATTTTAATTAAAATATATTTAATAATAATTATGTTT
1 TAATTATTAAGAATTTTATTAAATTATATATTTTAATTAAAATATATTTAATAATAATTATGTTT
*
43079574 AAATATGATTAAATTATTTATTATTGATATTAATAATCTTATTAAAATTTAAATAACAATAACAA
66 AAATATGATTAAATTATTTATTATTGATAATAATAATCTTATTAAAATTTAAATAACAATAACAA
*
43079639 TAATAATTTACCAAAACAAATTTCTGC
131 TAATAATTTACCAAAACAAATTTATGC
43079666 TAATTATTAAGAATTTTATTAAATTATATATTTTAATTAAAATATATTTAATAATAATTATGTTT
1 TAATTATTAAGAATTTTATTAAATTATATATTTTAATTAAAATATATTTAATAATAATTATGTTT
43079731 AAATATGATTAAATTATTTATTATTGATAATAATAATCTTATTAAAATTTAAATAACAATAACAA
66 AAATATGATTAAATTATTTATTATTGATAATAATAATCTTATTAAAATTTAAATAACAATAACAA
*
43079796 TAATCATTTACCAAAACAAATTTATGC
131 TAATAATTTACCAAAACAAATTTATGC
43079823 TAA
1 TAA
43079826 GGGTATTCTA
Statistics
Matches: 157, Mismatches: 3, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
157 157 1.00
ACGTcount: A:0.48, C:0.05, G:0.03, T:0.44
Consensus pattern (157 bp):
TAATTATTAAGAATTTTATTAAATTATATATTTTAATTAAAATATATTTAATAATAATTATGTTT
AAATATGATTAAATTATTTATTATTGATAATAATAATCTTATTAAAATTTAAATAACAATAACAA
TAATAATTTACCAAAACAAATTTATGC
Found at i:43079706 original size:18 final size:17
Alignment explanation
Indices: 43079678--43079712 Score: 52
Period size: 18 Copynumber: 2.0 Consensus size: 17
43079668 ATTATTAAGA
*
43079678 ATTTTATTAAATTATAT
1 ATTTTATTAAAATATAT
43079695 ATTTTAATTAAAATATAT
1 ATTTT-ATTAAAATATAT
43079713 TTAATAATAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 5 0.31
18 11 0.69
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (17 bp):
ATTTTATTAAAATATAT
Found at i:43079746 original size:75 final size:75
Alignment explanation
Indices: 43079510--43079748 Score: 200
Period size: 75 Copynumber: 3.1 Consensus size: 75
43079500 TAAGAATATT
43079510 AATTATTAAGAATTTTATTAAATTATATATTTTAATTAAAATATATTTAATAATAATTATGTTTA
1 AATTATTAAGAATTTTATTAAATTATATATTTTAATTAAAATATATTTAATAATAATTATGTTTA
43079575 AATATGATTA
66 AATATGATTA
* ** * * * * *
43079585 AATTATTTATTATTGATATTAATAATCTTATTAAAATTTAAATAACAATA-A--CAATAATAATT
1 AATTATTAAGAATT-TTATT-A-AA--TTA-TATATTTTAATTAA-AATATATTTAATAATAATT
**** * * *
43079647 -TACCAAAACAAAT-TTCTGCT
59 AT-GTTTAA-ATATGAT-T--A
43079667 AATTATTAAGAATTTTATTAAATTATATATTTTAATTAAAATATATTTAATAATAATTATGTTTA
1 AATTATTAAGAATTTTATTAAATTATATATTTTAATTAAAATATATTTAATAATAATTATGTTTA
43079732 AATATGATTA
66 AATATGATTA
43079742 AATTATT
1 AATTATT
43079749 TATTATTGAT
Statistics
Matches: 117, Mismatches: 30, Indels: 34
0.65 0.17 0.19
Matches are distributed among these distances:
75 22 0.19
76 16 0.14
77 8 0.07
78 16 0.14
79 16 0.14
80 8 0.07
81 16 0.14
82 15 0.13
ACGTcount: A:0.47, C:0.03, G:0.03, T:0.46
Consensus pattern (75 bp):
AATTATTAAGAATTTTATTAAATTATATATTTTAATTAAAATATATTTAATAATAATTATGTTTA
AATATGATTA
Found at i:43079903 original size:39 final size:40
Alignment explanation
Indices: 43079860--43079964 Score: 113
Period size: 44 Copynumber: 2.5 Consensus size: 40
43079850 TTCCATTATG
43079860 CTATTACACCTCTATTCCATTCAACCAAACACAAGA-TTA
1 CTATTACACCTCTATTCCATTCAACCAAACACAAGATTTA
* *** *
43079899 CTATTACGCCTCTATTCCATTACATTCAACCAAACAGTTGATTTG
1 CTATTACACCTCTATT-C----CATTCAACCAAACACAAGATTTA
43079944 CTATTACACCTCTATTCCATT
1 CTATTACACCTCTATTCCATT
43079965 ACACCTCTAT
Statistics
Matches: 54, Mismatches: 6, Indels: 11
0.76 0.08 0.15
Matches are distributed among these distances:
39 15 0.28
40 5 0.09
44 17 0.31
45 17 0.31
ACGTcount: A:0.31, C:0.30, G:0.05, T:0.34
Consensus pattern (40 bp):
CTATTACACCTCTATTCCATTCAACCAAACACAAGATTTA
Found at i:43079958 original size:45 final size:44
Alignment explanation
Indices: 43079858--43079967 Score: 131
Period size: 45 Copynumber: 2.6 Consensus size: 44
43079848 TTTTCCATTA
43079858 TGCTATTACACCTCTATT-C----CATTCAACCAAACACAAGAT
1 TGCTATTACACCTCTATTCCATTACATTCAACCAAACACAAGAT
* * ***
43079897 TACTATTACGCCTCTATTCCATTACATTCAACCAAACAGTTGATT
1 TGCTATTACACCTCTATTCCATTACATTCAACCAAACACAAGA-T
43079942 TGCTATTACACCTCTATTCCATTACA
1 TGCTATTACACCTCTATTCCATTACA
43079968 CCTCTATTCC
Statistics
Matches: 58, Mismatches: 7, Indels: 6
0.82 0.10 0.08
Matches are distributed among these distances:
39 16 0.28
40 1 0.02
44 16 0.28
45 25 0.43
ACGTcount: A:0.32, C:0.29, G:0.05, T:0.34
Consensus pattern (44 bp):
TGCTATTACACCTCTATTCCATTACATTCAACCAAACACAAGAT
Found at i:43079967 original size:16 final size:16
Alignment explanation
Indices: 43079946--43080015 Score: 104
Period size: 16 Copynumber: 4.4 Consensus size: 16
43079936 TTGATTTGCT
*
43079946 ATTACACCTCTATTCC
1 ATTACACCTCTAATCC
*
43079962 ATTACACCTCTATTCC
1 ATTACACCTCTAATCC
43079978 ATTACACCTCTAATCC
1 ATTACACCTCTAATCC
*
43079994 AATACACCTCTAATCC
1 ATTACACCTCTAATCC
*
43080010 AATACA
1 ATTACA
43080016 GCGAACCAAA
Statistics
Matches: 52, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
16 52 1.00
ACGTcount: A:0.33, C:0.36, G:0.00, T:0.31
Consensus pattern (16 bp):
ATTACACCTCTAATCC
Found at i:43085984 original size:31 final size:30
Alignment explanation
Indices: 43085946--43086007 Score: 79
Period size: 31 Copynumber: 2.0 Consensus size: 30
43085936 TGTCAAAATT
* **
43085946 AAAATATATAGATTAAATATCAAATTTAAAC
1 AAAATATAGAGACCAAAT-TCAAATTTAAAC
*
43085977 AAAATATAGAGACCAAATTGAAATTTAAAC
1 AAAATATAGAGACCAAATTCAAATTTAAAC
43086007 A
1 A
43086008 TTCTTGTAAT
Statistics
Matches: 27, Mismatches: 4, Indels: 1
0.84 0.12 0.03
Matches are distributed among these distances:
30 12 0.44
31 15 0.56
ACGTcount: A:0.58, C:0.08, G:0.06, T:0.27
Consensus pattern (30 bp):
AAAATATAGAGACCAAATTCAAATTTAAAC
Found at i:43087944 original size:6 final size:6
Alignment explanation
Indices: 43087935--43087960 Score: 52
Period size: 6 Copynumber: 4.3 Consensus size: 6
43087925 TTATGTTCTA
43087935 TTTATT TTTATT TTTATT TTTATT TT
1 TTTATT TTTATT TTTATT TTTATT TT
43087961 CCTTCATCAA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 20 1.00
ACGTcount: A:0.15, C:0.00, G:0.00, T:0.85
Consensus pattern (6 bp):
TTTATT
Found at i:43098935 original size:13 final size:13
Alignment explanation
Indices: 43098917--43098943 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
43098907 GGCATTTATA
43098917 TTGAAACAAAATG
1 TTGAAACAAAATG
43098930 TTGAAACAAAATG
1 TTGAAACAAAATG
43098943 T
1 T
43098944 GGCATCGTGT
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:0.52, C:0.07, G:0.15, T:0.26
Consensus pattern (13 bp):
TTGAAACAAAATG
Found at i:43102213 original size:41 final size:41
Alignment explanation
Indices: 43102178--43102284 Score: 151
Period size: 43 Copynumber: 2.6 Consensus size: 41
43102168 ACCGGCACTT
* *
43102178 AGCCTGCTAGACGTAAAGTCTGGTATGTTTCACCGGTGTATCA
1 AGCCTGCTAGACGTAATGTCTGGTATGTTTCACC-G-GCATCA
*
43102221 AGCCTACTAGACGTAATGTCTGGTATGTTTCACCGGCATCA
1 AGCCTGCTAGACGTAATGTCTGGTATGTTTCACCGGCATCA
* *
43102262 AGCCTGTTAAACGTAATGTCTGG
1 AGCCTGCTAGACGTAATGTCTGG
43102285 ATTACATCAC
Statistics
Matches: 58, Mismatches: 6, Indels: 2
0.88 0.09 0.03
Matches are distributed among these distances:
41 25 0.43
42 1 0.02
43 32 0.55
ACGTcount: A:0.24, C:0.21, G:0.24, T:0.30
Consensus pattern (41 bp):
AGCCTGCTAGACGTAATGTCTGGTATGTTTCACCGGCATCA
Found at i:43111659 original size:9 final size:10
Alignment explanation
Indices: 43111637--43111673 Score: 65
Period size: 10 Copynumber: 3.6 Consensus size: 10
43111627 TTATATACTC
43111637 TTTAGAATTTT
1 TTTA-AATTTT
43111648 TTTAAATTTT
1 TTTAAATTTT
43111658 TTTAAATTTT
1 TTTAAATTTT
43111668 TTTAAA
1 TTTAAA
43111674 AAATATAAAT
Statistics
Matches: 26, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
10 22 0.85
11 4 0.15
ACGTcount: A:0.32, C:0.00, G:0.03, T:0.65
Consensus pattern (10 bp):
TTTAAATTTT
Found at i:43112960 original size:19 final size:19
Alignment explanation
Indices: 43112928--43112965 Score: 58
Period size: 19 Copynumber: 2.0 Consensus size: 19
43112918 AATGAAGAGT
*
43112928 TTTGTTAGTAATTTTGTTA
1 TTTGTAAGTAATTTTGTTA
*
43112947 TTTGTAAGTTATTTTGTTA
1 TTTGTAAGTAATTTTGTTA
43112966 GGTTATTAAT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.21, C:0.00, G:0.16, T:0.63
Consensus pattern (19 bp):
TTTGTAAGTAATTTTGTTA
Found at i:43115985 original size:443 final size:443
Alignment explanation
Indices: 43115159--43116044 Score: 1655
Period size: 443 Copynumber: 2.0 Consensus size: 443
43115149 TCGGCCACAT
43115159 TCTACAGGTTGGCTACCTTGATGCGAAGAATGGGGCAGTACCAAGTCAACCAGATGGAGGCGGGA
1 TCTACAGGTTGGCTACCTTGATGCGAAGAATGGGGCAGTACCAAGTCAACCAGATGGAGGCGGGA
*
43115224 CACGTGTTTGTCAAACATGTCAGGAATGCTATGGTTGCAAATCAGCGGATGGCGAGGTCGATGAA
66 CACGTGTTTGTCAAACATGTCAGGAATGCTATGGTTGCAAATCAGCGGATGGCGAGGTCGACGAA
*
43115289 TGTAGAAGTATATTCACGACGTAATGAAGCATTTTAAGTTACAGATACCATTGGTTATCAACCCG
131 TGTAGAAGTATATTCACGACGTAATGAAACATTTTAAGTTACAGATACCATTGGTTATCAACCCG
43115354 ATATACCACCTAGGTCCTATGGAGTTGATCTCTAAAACAGACGGTGCGATTGTAGGAGGTTCCAG
196 ATATACCACCTAGGTCCTATGGAGTTGATCTCTAAAACAGACGGTGCGATTGTAGGAGGTTCCAG
*
43115419 ACACTTCATTATTCCTGTGAACATGTCGTGGCAACTTGTGGTAAAGTCTTGCTCAATAGTGAACA
261 ACACTTCATTATTCCTGTGAACATGTCGTGGCAACTTGTGCTAAAGTCTTGCTCAATAGTGAACA
*
43115484 ATTTATTGATGAAGTGTACACCCTCAAACGCACGTTGCGTGTATGGGAGAACGAGTTCCCTGTGC
326 ATTTATTGATGAAGTGTACACCCTCAAACGCACGTTGCGTGTATGGGAGAACGAGTTCCCCGTGC
*
43115549 TACCTGACCTATCTACATGGGAGGTACCTCCGATGACTTTCGAGCTTGACCTA
391 TACCTGACCTATCTACATGGGAGGTACCTCCGACGACTTTCGAGCTTGACCTA
*
43115602 TCTACAGGTTGGCTACCTTGATGCGAAGAATGGGGCAGTACCAAGTCAACCAGATGGAGGTGGGA
1 TCTACAGGTTGGCTACCTTGATGCGAAGAATGGGGCAGTACCAAGTCAACCAGATGGAGGCGGGA
43115667 CACGTGTTTGTCAAACATGTCAGGAATGCTATGGTTGCAAATCAGCGGATGGCGAGGTCGACGAA
66 CACGTGTTTGTCAAACATGTCAGGAATGCTATGGTTGCAAATCAGCGGATGGCGAGGTCGACGAA
* **
43115732 TGTAGAAGTATATTCACGACGTAATGAAACATTTTGAGTTACAGATACCATTGGTTATTGACCCG
131 TGTAGAAGTATATTCACGACGTAATGAAACATTTTAAGTTACAGATACCATTGGTTATCAACCCG
*
43115797 GTATACCACCTAGGTCCTATGGAGTTGATCTCTAAAACAGACGGTGCGATTGTAGGAGGTTCCAG
196 ATATACCACCTAGGTCCTATGGAGTTGATCTCTAAAACAGACGGTGCGATTGTAGGAGGTTCCAG
*
43115862 ACACTTCATTATTCCTGTGAACATGTCGTGGCAGCTTGTGCTAAAGTCTTGCTCAATAGTGAACA
261 ACACTTCATTATTCCTGTGAACATGTCGTGGCAACTTGTGCTAAAGTCTTGCTCAATAGTGAACA
43115927 ATTTATTGATGAAGTGTACACCCTCAAACGCACGTTGCGTGTATGGGAGAACGAGTTCCCCGTGC
326 ATTTATTGATGAAGTGTACACCCTCAAACGCACGTTGCGTGTATGGGAGAACGAGTTCCCCGTGC
* *
43115992 TACCTGACCTATCTACATGGGAGGTGCCTCCGACGACTTTCGAGCTTGTCCTA
391 TACCTGACCTATCTACATGGGAGGTACCTCCGACGACTTTCGAGCTTGACCTA
43116045 GACAAAAGGT
Statistics
Matches: 430, Mismatches: 13, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
443 430 1.00
ACGTcount: A:0.27, C:0.21, G:0.26, T:0.27
Consensus pattern (443 bp):
TCTACAGGTTGGCTACCTTGATGCGAAGAATGGGGCAGTACCAAGTCAACCAGATGGAGGCGGGA
CACGTGTTTGTCAAACATGTCAGGAATGCTATGGTTGCAAATCAGCGGATGGCGAGGTCGACGAA
TGTAGAAGTATATTCACGACGTAATGAAACATTTTAAGTTACAGATACCATTGGTTATCAACCCG
ATATACCACCTAGGTCCTATGGAGTTGATCTCTAAAACAGACGGTGCGATTGTAGGAGGTTCCAG
ACACTTCATTATTCCTGTGAACATGTCGTGGCAACTTGTGCTAAAGTCTTGCTCAATAGTGAACA
ATTTATTGATGAAGTGTACACCCTCAAACGCACGTTGCGTGTATGGGAGAACGAGTTCCCCGTGC
TACCTGACCTATCTACATGGGAGGTACCTCCGACGACTTTCGAGCTTGACCTA
Found at i:43116511 original size:74 final size:75
Alignment explanation
Indices: 43116390--43116576 Score: 278
Period size: 74 Copynumber: 2.6 Consensus size: 75
43116380 TTACGTAAAT
* *
43116390 AATACAAAGTTT-ATTATTTAAATTACAAAAACCCCTAAAATTAATAACTGAAATGGC-AAAAAA
1 AATACAAA-TTTGATTATTTAAATTACAAAAATCCCTAAAATTAATAACTAAAATGGCAAAAAAA
43116453 GTCATTACATA
65 GTCATTACATA
*
43116464 AATACAAATTTGACTATTTAAATTACAAAAATCCCTAAAATTAATAACTAAAATGGCAAAAAAAG
1 AATACAAATTTGATTATTTAAATTACAAAAATCCCTAAAATTAATAACTAAAATGGCAAAAAAAG
43116529 TCATTACATA
66 TCATTACATA
* *
43116539 AATACAAA---G-TTATTTAAATTACAAAACTGCCTAAAATT
1 AATACAAATTTGATTATTTAAATTACAAAAATCCCTAAAATT
43116577 GATGGTTTGA
Statistics
Matches: 105, Mismatches: 6, Indels: 7
0.89 0.05 0.06
Matches are distributed among these distances:
71 26 0.25
72 1 0.01
73 3 0.03
74 50 0.48
75 25 0.24
ACGTcount: A:0.52, C:0.13, G:0.06, T:0.29
Consensus pattern (75 bp):
AATACAAATTTGATTATTTAAATTACAAAAATCCCTAAAATTAATAACTAAAATGGCAAAAAAAG
TCATTACATA
Found at i:43118975 original size:104 final size:101
Alignment explanation
Indices: 43118838--43119230 Score: 465
Period size: 104 Copynumber: 3.9 Consensus size: 101
43118828 TAAAATTACA
*
43118838 TTATAAAAAATTTACATTAATGAAAAATCACAAAACACTAAACTAAACACTAACAATTTATGTAA
1 TTAT-AAAAA-TTACATTAATAAAAAATCACAAAACACTAAACTAAACACTAACAATTTA--TAA
43118903 CCTAATCATAAATTACTAACAAAATAACTATAAAATTATTT
62 CCTAATCATAAATTACTAACAAAATAACTATAAAA-TATTT
* * * * **
43118944 TTTTAAAAATTACATTATTAAAAAATTACAAAACCCTAAACTAAACACTAACAATTTATAAAATA
1 TTATAAAAATTACATTAATAAAAAATCACAAAACACTAAACTAAACACTAACAATTTATAACCTA
* * *
43119009 ATCATAAATTATTAACAAAATAACTATAACAT-TTA
66 ATCATAAATTACTAACAAAATAACTATAAAATATTT
** * * * * *
43119044 AAAAAAAAATTACATTACTGATAAATCACAAAACAC---A--AAACACTAATAATTTATAACCTA
1 TTATAAAAATTACATTAATAAAAAATCACAAAACACTAAACTAAACACTAACAATTTATAACCTA
43119104 ATCATAAATTACTAACAAAATAACTATAAAATTATTT
66 ATCATAAATTACTAACAAAATAACTATAAAA-TATTT
* * * * * *
43119141 TTTTAAAATTTACATTACTAAAAAATCACAAAACACAAAACACGAAACATTAACAATTTATAACC
1 TTATAAAAATTACATTAATAAAAAATCACAAAACAC-TAA-ACTAAACACTAACAATTTATAACC
43119206 TAATCATAAATTACTAACAAAATAA
64 TAATCATAAATTACTAACAAAATAA
43119231 TTAACAAAAT
Statistics
Matches: 244, Mismatches: 34, Indels: 20
0.82 0.11 0.07
Matches are distributed among these distances:
95 49 0.20
96 1 0.00
97 32 0.13
100 29 0.12
101 1 0.00
102 35 0.14
104 89 0.36
105 5 0.02
106 3 0.01
ACGTcount: A:0.55, C:0.15, G:0.01, T:0.29
Consensus pattern (101 bp):
TTATAAAAATTACATTAATAAAAAATCACAAAACACTAAACTAAACACTAACAATTTATAACCTA
ATCATAAATTACTAACAAAATAACTATAAAATATTT
Found at i:43119319 original size:92 final size:95
Alignment explanation
Indices: 43119146--43119324 Score: 247
Period size: 92 Copynumber: 1.9 Consensus size: 95
43119136 TATTTTTTTA
* * * *
43119146 AAATTTACATTACTAAAAAATCACAAAACACAAAACACGAAACATTAACAATTTATAACCTAATC
1 AAATTTACATTAATAAAAAATCACAAAACACAAAACACGAAACATCAACAATTTAGAACATAATC
43119211 ATAAATTACTAACAAAATAATTAACAAAAT
66 ATAAATTACTAACAAAATAATTAACAAAAT
* * * *
43119241 AAATTTACATTAATAAAAAATCACAAAATAC-TAA-ACTAAACA-CAACAATTTGGAACATAATC
1 AAATTTACATTAATAAAAAATCACAAAACACAAAACACGAAACATCAACAATTTAGAACATAATC
* *
43119303 CTAAATTACTACCAAAATAATT
66 ATAAATTACTAACAAAATAATT
43119325 TTAAACTAAT
Statistics
Matches: 74, Mismatches: 10, Indels: 3
0.85 0.11 0.03
Matches are distributed among these distances:
92 36 0.49
93 7 0.09
94 2 0.03
95 29 0.39
ACGTcount: A:0.56, C:0.17, G:0.02, T:0.25
Consensus pattern (95 bp):
AAATTTACATTAATAAAAAATCACAAAACACAAAACACGAAACATCAACAATTTAGAACATAATC
ATAAATTACTAACAAAATAATTAACAAAAT
Found at i:43119851 original size:21 final size:20
Alignment explanation
Indices: 43119829--43119865 Score: 67
Period size: 19 Copynumber: 1.9 Consensus size: 20
43119819 CCCGGTATAT
43119829 ATATATTTTT-TAAAAAATA
1 ATATATTTTTATAAAAAATA
43119848 ATATATTTTTATAAAAAA
1 ATATATTTTTATAAAAAA
43119866 ATTATTATAA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
19 10 0.59
20 7 0.41
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (20 bp):
ATATATTTTTATAAAAAATA
Found at i:43123177 original size:167 final size:167
Alignment explanation
Indices: 43122901--43123236 Score: 672
Period size: 167 Copynumber: 2.0 Consensus size: 167
43122891 GTGAACATTC
43122901 ATATAACATGAAGTTTGTTTCCCTCTTGGTAGCCGTGCTGCATTTCAAGTGCTCCACATTTACAT
1 ATATAACATGAAGTTTGTTTCCCTCTTGGTAGCCGTGCTGCATTTCAAGTGCTCCACATTTACAT
43122966 TAGAATTAGATAAGGATAAATTCTTCAGCTGAGTGTTTCGGATATAAACATCCTGTTAATAATAA
66 TAGAATTAGATAAGGATAAATTCTTCAGCTGAGTGTTTCGGATATAAACATCCTGTTAATAATAA
43123031 AATTTTAGTAATGGCAATTGGTATTTTCTCCTGTTTG
131 AATTTTAGTAATGGCAATTGGTATTTTCTCCTGTTTG
43123068 ATATAACATGAAGTTTGTTTCCCTCTTGGTAGCCGTGCTGCATTTCAAGTGCTCCACATTTACAT
1 ATATAACATGAAGTTTGTTTCCCTCTTGGTAGCCGTGCTGCATTTCAAGTGCTCCACATTTACAT
43123133 TAGAATTAGATAAGGATAAATTCTTCAGCTGAGTGTTTCGGATATAAACATCCTGTTAATAATAA
66 TAGAATTAGATAAGGATAAATTCTTCAGCTGAGTGTTTCGGATATAAACATCCTGTTAATAATAA
43123198 AATTTTAGTAATGGCAATTGGTATTTTCTCCTGTTTG
131 AATTTTAGTAATGGCAATTGGTATTTTCTCCTGTTTG
43123235 AT
1 AT
43123237 TCTGAATGTG
Statistics
Matches: 169, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
167 169 1.00
ACGTcount: A:0.29, C:0.15, G:0.17, T:0.38
Consensus pattern (167 bp):
ATATAACATGAAGTTTGTTTCCCTCTTGGTAGCCGTGCTGCATTTCAAGTGCTCCACATTTACAT
TAGAATTAGATAAGGATAAATTCTTCAGCTGAGTGTTTCGGATATAAACATCCTGTTAATAATAA
AATTTTAGTAATGGCAATTGGTATTTTCTCCTGTTTG
Found at i:43129685 original size:51 final size:51
Alignment explanation
Indices: 43129609--43129713 Score: 183
Period size: 51 Copynumber: 2.1 Consensus size: 51
43129599 TCAGAAGCTA
* * *
43129609 GCACAATAAAGGGAGTATGCAGGAAAAGGGTGCATGTGTGAAAATAGTAGT
1 GCACAATAAAGAGAGTATGCAGGAAAAGGGTACATGTGTGAAAATAATAGT
43129660 GCACAATAAAGAGAGTATGCAGGAAAAGGGTACATGTGTGAAAATAATAGT
1 GCACAATAAAGAGAGTATGCAGGAAAAGGGTACATGTGTGAAAATAATAGT
43129711 GCA
1 GCA
43129714 AGTTGTATGA
Statistics
Matches: 51, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
51 51 1.00
ACGTcount: A:0.42, C:0.09, G:0.30, T:0.19
Consensus pattern (51 bp):
GCACAATAAAGAGAGTATGCAGGAAAAGGGTACATGTGTGAAAATAATAGT
Found at i:43138384 original size:14 final size:15
Alignment explanation
Indices: 43138350--43138387 Score: 51
Period size: 15 Copynumber: 2.6 Consensus size: 15
43138340 GGTTTTTGTA
43138350 ATAATAAAATAAAAG
1 ATAATAAAATAAAAG
* *
43138365 ATAATAACATAAAGG
1 ATAATAAAATAAAAG
43138380 A-AATAAAA
1 ATAATAAAA
43138388 GTTCAAAAGA
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
14 6 0.30
15 14 0.70
ACGTcount: A:0.71, C:0.03, G:0.08, T:0.18
Consensus pattern (15 bp):
ATAATAAAATAAAAG
Found at i:43139822 original size:38 final size:38
Alignment explanation
Indices: 43139780--43139861 Score: 110
Period size: 38 Copynumber: 2.2 Consensus size: 38
43139770 ATCAAGTGCG
* *
43139780 GCGACAATTCTAAACGCAATTTGGAATTAACCCATGCA
1 GCGACAATTCTAAACACAATCTGGAATTAACCCATGCA
** **
43139818 GCGACAATTCTGGACACAATCTGGAATTAACTTATGCA
1 GCGACAATTCTAAACACAATCTGGAATTAACCCATGCA
43139856 GCGACA
1 GCGACA
43139862 TTAATATAAT
Statistics
Matches: 38, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
38 38 1.00
ACGTcount: A:0.35, C:0.23, G:0.18, T:0.23
Consensus pattern (38 bp):
GCGACAATTCTAAACACAATCTGGAATTAACCCATGCA
Found at i:43142896 original size:23 final size:22
Alignment explanation
Indices: 43142853--43142896 Score: 54
Period size: 23 Copynumber: 1.9 Consensus size: 22
43142843 GTCTAAGTCG
43142853 ATATTCAATTCAATTCCACACCT
1 ATATTCAATTCAATT-CACACCT
43142876 ATATTCATTATTCAATT-ACAC
1 ATATTCA--ATTCAATTCACAC
43142897 TTAGTCAATT
Statistics
Matches: 19, Mismatches: 0, Indels: 4
0.83 0.00 0.17
Matches are distributed among these distances:
23 11 0.58
25 8 0.42
ACGTcount: A:0.36, C:0.25, G:0.00, T:0.39
Consensus pattern (22 bp):
ATATTCAATTCAATTCACACCT
Found at i:43143098 original size:51 final size:51
Alignment explanation
Indices: 43143037--43143176 Score: 183
Period size: 51 Copynumber: 2.7 Consensus size: 51
43143027 TGTTCGGTTG
* *
43143037 ACATAGTAGCCTGCACATAGTACTACACATGTGACCATTACCATCTGATAT
1 ACATAGTAGCCTGCACATAGTACTACACATGTGACCATAACCATCCGATAT
* * * * * *
43143088 ACGTAGTAGCCTACACATAGTACTACACAAGTGATCGA-AACTATCCGGTAT
1 ACATAGTAGCCTGCACATAGTACTACACATGTGA-CCATAACCATCCGATAT
*
43143139 GCATAGTAGCCTGCACATAGTACTACACATGTGACCAT
1 ACATAGTAGCCTGCACATAGTACTACACATGTGACCAT
43143177 CACTTTCACT
Statistics
Matches: 74, Mismatches: 13, Indels: 4
0.81 0.14 0.04
Matches are distributed among these distances:
50 2 0.03
51 70 0.95
52 2 0.03
ACGTcount: A:0.34, C:0.25, G:0.16, T:0.25
Consensus pattern (51 bp):
ACATAGTAGCCTGCACATAGTACTACACATGTGACCATAACCATCCGATAT
Found at i:43144480 original size:21 final size:21
Alignment explanation
Indices: 43144454--43144499 Score: 65
Period size: 21 Copynumber: 2.2 Consensus size: 21
43144444 TTCTCATTTT
*
43144454 CAACAACCTCCTCTTCTTCAA
1 CAACAACCTCCTCTTCTGCAA
* *
43144475 CAACAACTTTCTCTTCTGCAA
1 CAACAACCTCCTCTTCTGCAA
43144496 CAAC
1 CAAC
43144500 TTCTGTTTCT
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.30, C:0.39, G:0.02, T:0.28
Consensus pattern (21 bp):
CAACAACCTCCTCTTCTGCAA
Found at i:43158833 original size:13 final size:13
Alignment explanation
Indices: 43158815--43158850 Score: 72
Period size: 13 Copynumber: 2.8 Consensus size: 13
43158805 GACTAAATGA
43158815 ATCCACATAGTTT
1 ATCCACATAGTTT
43158828 ATCCACATAGTTT
1 ATCCACATAGTTT
43158841 ATCCACATAG
1 ATCCACATAG
43158851 CCGAGTGGTA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 23 1.00
ACGTcount: A:0.33, C:0.25, G:0.08, T:0.33
Consensus pattern (13 bp):
ATCCACATAGTTT
Found at i:43159272 original size:16 final size:15
Alignment explanation
Indices: 43159251--43159280 Score: 51
Period size: 16 Copynumber: 1.9 Consensus size: 15
43159241 TTTATTTTTA
43159251 TTTTTATTGTTATTTG
1 TTTTTATT-TTATTTG
43159267 TTTTTATTTTATTT
1 TTTTTATTTTATTT
43159281 TCCAAACTTA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 6 0.43
16 8 0.57
ACGTcount: A:0.13, C:0.00, G:0.07, T:0.80
Consensus pattern (15 bp):
TTTTTATTTTATTTG
Found at i:43159313 original size:22 final size:22
Alignment explanation
Indices: 43159246--43159331 Score: 68
Period size: 22 Copynumber: 3.6 Consensus size: 22
43159236 CTATCTTTAT
43159246 TTTTATTTTTATTGTTATT-TGT-
1 TTTTA-TTTTATT-TTATTATGTA
43159268 TTTTATTTTATTTTCCAAACTTATGTA
1 TTTTATTTTATTTT----A-TTATGTA
*
43159295 TTTTATTTTATTTTATTATGCA
1 TTTTATTTTATTTTATTATGTA
*
43159317 CTTTATTATTATTTT
1 TTTTATT-TTATTTT
43159332 TTCGAATTTT
Statistics
Matches: 54, Mismatches: 2, Indels: 15
0.76 0.03 0.21
Matches are distributed among these distances:
20 2 0.04
21 7 0.13
22 17 0.31
23 8 0.15
24 1 0.02
25 2 0.04
26 3 0.06
27 14 0.26
ACGTcount: A:0.21, C:0.06, G:0.05, T:0.69
Consensus pattern (22 bp):
TTTTATTTTATTTTATTATGTA
Found at i:43161577 original size:49 final size:49
Alignment explanation
Indices: 43161516--43161624 Score: 166
Period size: 49 Copynumber: 2.2 Consensus size: 49
43161506 GGGCTGAATG
* * *
43161516 ATTCCACGTGGCCATACCACACGGTCATGTGATCC-ACATAGGTTGAACT
1 ATTCCACATGGCCATACCACACGGTCATGTGA-CCAACACAGGTTGAACC
*
43161565 ATTCCACATGGCCATACCACACGGTCGTGTGACCAACACAGGTTGAACC
1 ATTCCACATGGCCATACCACACGGTCATGTGACCAACACAGGTTGAACC
43161614 ATTCCACATGG
1 ATTCCACATGG
43161625 TCGTTGACCT
Statistics
Matches: 55, Mismatches: 4, Indels: 2
0.90 0.07 0.03
Matches are distributed among these distances:
48 2 0.04
49 53 0.96
ACGTcount: A:0.28, C:0.30, G:0.20, T:0.22
Consensus pattern (49 bp):
ATTCCACATGGCCATACCACACGGTCATGTGACCAACACAGGTTGAACC
Found at i:43164918 original size:13 final size:14
Alignment explanation
Indices: 43164897--43164938 Score: 52
Period size: 13 Copynumber: 3.1 Consensus size: 14
43164887 TTTCAAAATG
*
43164897 GAAATAATAAA-AA
1 GAAAAAATAAATAA
43164910 GAAAAAATAAATAA
1 GAAAAAATAAATAA
*
43164924 -ATAAAATAAATAA
1 GAAAAAATAAATAA
43164937 GA
1 GA
43164939 CCTTAACATG
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
13 22 0.88
14 3 0.12
ACGTcount: A:0.76, C:0.00, G:0.07, T:0.17
Consensus pattern (14 bp):
GAAAAAATAAATAA
Found at i:43166049 original size:147 final size:146
Alignment explanation
Indices: 43165723--43166281 Score: 678
Period size: 147 Copynumber: 3.7 Consensus size: 146
43165713 CAAAATAGTT
* * * * *
43165723 AAAAAATAAAAAATTATTCTAAAATTTTAAATTTTCATTTAAAATGATTTAAAAAACATATTTTT
1 AAAAAATAAAAATTTATTTTAAAATTTTAAATTTTCCTTTAAAATGACTAAAAAAACATATTTTT
* *
43165788 ATTTTTCAAAATCTAAAATTTCTCTCTTTTTTTTTAAAAAAAAACACTGTTTTTCTTAAAGATTA
66 ATTTTTCAAAATCTAAACTTTCTC-C----TTTTT-AAAAAAAACACTATTTTTCTTAAAGATTA
43165853 AAGCTTTTATTTTGAAGTAGTTTGAA
125 AAG-TTTTATTTT--A-TAGTTTGAA
* * * *
43165879 AAAAAATCAAAACTTTGTTTTAAACA-TTTAAACTTTCCTTTAAAATGACTTAAAAAAACAAATT
1 AAAAAAT-AAAAATTTATTTTAAA-ATTTTAAATTTTCCTTTAAAATGAC-TAAAAAAACATATT
*
43165943 TATATTTTTCAAAATCTAAACTTTCTCCTTTTTAAAAAAAACACTATTTTTCTTAAAGATTAAAG
63 TTTATTTTTCAAAATCTAAACTTTCTCCTTTTTAAAAAAAACACTATTTTTCTTAAAGATTAAAG
43166008 TTTTATTTTATAGTTTG-A
128 TTTTATTTTATAGTTTGAA
* *
43166026 AAAAAATAAAAACTTTGTTTTAAAATTTTAAAATTTCCTTTAAAATGACTAACAAAAACATATTT
1 AAAAAATAAAAA-TTTATTTTAAAATTTTAAATTTTCCTTTAAAATGACTAA-AAAAACATATTT
*
43166091 TTATTTTTCAAAATCTAAACTTTCTCC-TTTTAAAAAAAACCACAATTTTTCTTAAAGATTAAAA
64 TTATTTTTCAAAATCTAAACTTTCTCCTTTTTAAAAAAAA-CACTATTTTTCTTAAAGATT-AAA
* *
43166155 CTTTTACTTTAAAATAG-TTGAAA
127 GTTTTA-TTT--TATAGTTTG-AA
*
43166178 AAAAAATCAAAAATTTATTTTAAAATTTTAAATTTTCCTTTAAAATAACTAAAAAAACATATTTT
1 AAAAAAT-AAAAATTTATTTTAAAATTTTAAATTTTCCTTTAAAATGACTAAAAAAACATATTTT
* * * *
43166243 TACTTGTT-AAAATCTAAATTTTCTCGTTTTAAAAAAAAA
65 TA-TTTTTCAAAATCTAAACTTTCTCCTTTTTAAAAAAAA
43166282 TTTCCCAAAA
Statistics
Matches: 361, Mismatches: 26, Indels: 36
0.85 0.06 0.09
Matches are distributed among these distances:
146 20 0.06
147 97 0.27
148 15 0.04
149 4 0.01
150 3 0.01
151 44 0.12
152 90 0.25
153 10 0.03
156 7 0.02
157 33 0.09
158 38 0.11
ACGTcount: A:0.44, C:0.10, G:0.04, T:0.42
Consensus pattern (146 bp):
AAAAAATAAAAATTTATTTTAAAATTTTAAATTTTCCTTTAAAATGACTAAAAAAACATATTTTT
ATTTTTCAAAATCTAAACTTTCTCCTTTTTAAAAAAAACACTATTTTTCTTAAAGATTAAAGTTT
TATTTTATAGTTTGAA
Found at i:43166217 original size:299 final size:298
Alignment explanation
Indices: 43165723--43166281 Score: 768
Period size: 299 Copynumber: 1.9 Consensus size: 298
43165713 CAAAATAGTT
* * *
43165723 AAAAAATAAAAAATTATTCTAAAATTTTAAATTTTCATTTAAAATGATTTAAAAAACATATTTTT
1 AAAAAATAAAAAATTATTCTAAAATTTTAAAATTTCATTTAAAATGACTAAAAAAACATATTTTT
**
43165788 ATTTTTCAAAATCTAAAATTTCTCTCTTTTTTTTTAAAAAAAAACACTGTTTTTCTTAAAGATTA
66 ATTTTTCAAAATCTAAAATTTCTCTC----TTTTTAAAAAAAAACACAATTTTTCTTAAAGATTA
* * * * * *
43165853 AAGCTTTTATTTTGAAGTAGTTTGAAAAAAAATCAAAACTTTGTTTTAAACATTTAAACTTTCCT
127 AAACTTTTACTTTAAAATAGTTTGAAAAAAAATCAAAAATTTATTTTAAACATTTAAACTTTCCT
* * *
43165918 TTAAAATGACTTAAAAAAACAAATTTATA-TTTTTCAAAATCTAAACTTTCTCCTTTTTAAAAAA
192 TTAAAATAAC-TAAAAAAACAAATTTATACTTGTT-AAAATCTAAACTTTCTCCTTTTAAAAAAA
43165982 AACACTATTTTTCTTAAAGATTAAAGTTTTATTTTATAGTTTGA
255 AACACTATTTTTCTTAAAGATTAAAGTTTTATTTTATAGTTTGA
* * * *
43166026 AAAAAATAAAAACTTTGTTTTAAAATTTTAAAATTTCCTTTAAAATGACTAACAAAAACATATTT
1 AAAAAATAAAAA-ATTATTCTAAAATTTTAAAATTTCATTTAAAATGACTAA-AAAAACATATTT
* *
43166091 TTATTTTTCAAAATCTAAACTTTCTC-C-TTTTAAAAAAAACCACAATTTTTCTTAAAGATTAAA
64 TTATTTTTCAAAATCTAAAATTTCTCTCTTTTTAAAAAAAAACACAATTTTTCTTAAAGATTAAA
*
43166154 ACTTTTACTTTAAAATAG-TTGAAAAAAAAATCAAAAATTTATTTTAAA-ATTTTAAATTTTCCT
129 ACTTTTACTTTAAAATAGTTTG-AAAAAAAATCAAAAATTTATTTTAAACA-TTTAAACTTTCCT
* * * *
43166217 TTAAAATAACTAAAAAAACATATTTTTACTTGTTAAAATCTAAATTTTCTCGTTTTAAAAAAAAA
192 TTAAAATAACTAAAAAAACAAATTTATACTTGTTAAAATCTAAACTTTCTCCTTTTAAAAAAAAA
43166282 TTTCCCAAAA
Statistics
Matches: 226, Mismatches: 25, Indels: 15
0.85 0.09 0.06
Matches are distributed among these distances:
298 48 0.21
299 96 0.42
303 12 0.05
304 33 0.15
305 37 0.16
ACGTcount: A:0.44, C:0.10, G:0.04, T:0.42
Consensus pattern (298 bp):
AAAAAATAAAAAATTATTCTAAAATTTTAAAATTTCATTTAAAATGACTAAAAAAACATATTTTT
ATTTTTCAAAATCTAAAATTTCTCTCTTTTTAAAAAAAAACACAATTTTTCTTAAAGATTAAAAC
TTTTACTTTAAAATAGTTTGAAAAAAAATCAAAAATTTATTTTAAACATTTAAACTTTCCTTTAA
AATAACTAAAAAAACAAATTTATACTTGTTAAAATCTAAACTTTCTCCTTTTAAAAAAAAACACT
ATTTTTCTTAAAGATTAAAGTTTTATTTTATAGTTTGA
Found at i:43170332 original size:20 final size:20
Alignment explanation
Indices: 43170309--43170349 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 20
43170299 TGAAAAACAC
43170309 ATATAAAAATGAAAAATAAA
1 ATATAAAAATGAAAAATAAA
** *
43170329 ATATGCAAATGAAAAGTAAA
1 ATATAAAAATGAAAAATAAA
43170349 A
1 A
43170350 ACAAAAGCTT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.68, C:0.02, G:0.10, T:0.20
Consensus pattern (20 bp):
ATATAAAAATGAAAAATAAA
Found at i:43178235 original size:8 final size:8
Alignment explanation
Indices: 43178222--43178249 Score: 56
Period size: 8 Copynumber: 3.5 Consensus size: 8
43178212 GATTTTTAAA
43178222 TATTATTT
1 TATTATTT
43178230 TATTATTT
1 TATTATTT
43178238 TATTATTT
1 TATTATTT
43178246 TATT
1 TATT
43178250 GTTTAGTATA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 20 1.00
ACGTcount: A:0.25, C:0.00, G:0.00, T:0.75
Consensus pattern (8 bp):
TATTATTT
Found at i:43186179 original size:13 final size:13
Alignment explanation
Indices: 43186161--43186186 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
43186151 AATTTTAAAA
43186161 ATTTTAAAAATTT
1 ATTTTAAAAATTT
43186174 ATTTTAAAAATTT
1 ATTTTAAAAATTT
43186187 TTAAAACACT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (13 bp):
ATTTTAAAAATTT
Found at i:43188410 original size:14 final size:14
Alignment explanation
Indices: 43188391--43188424 Score: 68
Period size: 14 Copynumber: 2.4 Consensus size: 14
43188381 TATTGTAAAA
43188391 AAAATTTTGATTTT
1 AAAATTTTGATTTT
43188405 AAAATTTTGATTTT
1 AAAATTTTGATTTT
43188419 AAAATT
1 AAAATT
43188425 CAATGAATAA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.41, C:0.00, G:0.06, T:0.53
Consensus pattern (14 bp):
AAAATTTTGATTTT
Found at i:43192201 original size:45 final size:45
Alignment explanation
Indices: 43192097--43192227 Score: 138
Period size: 45 Copynumber: 2.9 Consensus size: 45
43192087 GCTATACACC
* * * *
43192097 TAAAAATAAGTAAGACCATAGTTGAAAGATGCTATGGTATCACGA
1 TAAAAATGAGTAAGACTATAGTTGAAAGATGCTATGGCATCACAA
* * * * * *
43192142 TATAATTGAGTAAGACTATGGTTGAACGATGCTATGACATCATAA
1 TAAAAATGAGTAAGACTATAGTTGAAAGATGCTATGGCATCACAA
* *
43192187 TAAAAATGACTAAGA-TCATAGTTGAAAGACGCTATGGCATC
1 TAAAAATGAGTAAGACT-ATAGTTGAAAGATGCTATGGCATC
43192228 CTAGCAGCCC
Statistics
Matches: 68, Mismatches: 17, Indels: 2
0.78 0.20 0.02
Matches are distributed among these distances:
44 1 0.01
45 67 0.99
ACGTcount: A:0.41, C:0.12, G:0.20, T:0.27
Consensus pattern (45 bp):
TAAAAATGAGTAAGACTATAGTTGAAAGATGCTATGGCATCACAA
Found at i:43192348 original size:27 final size:27
Alignment explanation
Indices: 43192318--43192407 Score: 90
Period size: 27 Copynumber: 3.3 Consensus size: 27
43192308 CTGATGGGAA
*
43192318 ATTAAACATGAGATAGTCCGATAGGAC
1 ATTAAACATGAGATAGTCCGACAGGAC
* * ** *
43192345 ATTAAACATGGGATAGTTCGACAAAAT
1 ATTAAACATGAGATAGTCCGACAGGAC
** *
43192372 ATTAAACACAAGATAGTCTGACAGGAC
1 ATTAAACATGAGATAGTCCGACAGGAC
*
43192399 ACTAAACAT
1 ATTAAACAT
43192408 AGAGCGGTCA
Statistics
Matches: 47, Mismatches: 16, Indels: 0
0.75 0.25 0.00
Matches are distributed among these distances:
27 47 1.00
ACGTcount: A:0.44, C:0.16, G:0.18, T:0.22
Consensus pattern (27 bp):
ATTAAACATGAGATAGTCCGACAGGAC
Found at i:43205999 original size:24 final size:23
Alignment explanation
Indices: 43205946--43205999 Score: 67
Period size: 24 Copynumber: 2.3 Consensus size: 23
43205936 TCAAAGTATA
43205946 AAAAT-ATTATATTAAATGAAAT
1 AAAATAATTATATTAAATGAAAT
43205968 AAACATAATTATATTAATAAT-AAAT
1 AAA-ATAATTATATT-A-AATGAAAT
43205993 AAAATAA
1 AAAATAA
43206000 AAACCTCCCA
Statistics
Matches: 28, Mismatches: 0, Indels: 6
0.82 0.00 0.18
Matches are distributed among these distances:
22 3 0.11
23 2 0.07
24 12 0.43
25 8 0.29
26 3 0.11
ACGTcount: A:0.63, C:0.02, G:0.02, T:0.33
Consensus pattern (23 bp):
AAAATAATTATATTAAATGAAAT
Done.