Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: At_chr1
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: 106989029
ACGTcount: A:0.31, C:0.17, G:0.17, T:0.31
Warning! 3754247 characters in sequence are not A, C, G, or T
File 118 of 322
Found at i:38476954 original size:22 final size:22
Alignment explanation
Indices: 38476929--38476980 Score: 54
Period size: 22 Copynumber: 2.4 Consensus size: 22
38476919 AACCATGAAC
* *
38476929 AATACTAAGA-CCCTAACTATAA
1 AATACTAA-ACCCCAAACTACAA
*
38476951 AATAATAAACCCCAAACTACAA
1 AATACTAAACCCCAAACTACAA
38476973 AAT-CTAAA
1 AATACTAAA
38476981 TCATAAACCC
Statistics
Matches: 25, Mismatches: 4, Indels: 3
0.78 0.12 0.09
Matches are distributed among these distances:
21 5 0.20
22 20 0.80
ACGTcount: A:0.56, C:0.23, G:0.02, T:0.19
Consensus pattern (22 bp):
AATACTAAACCCCAAACTACAA
Found at i:38476989 original size:28 final size:28
Alignment explanation
Indices: 38476950--38477007 Score: 82
Period size: 28 Copynumber: 2.1 Consensus size: 28
38476940 CCTAACTATA
38476950 AAATAATAAACCCCAAACTACAAAA-TCT
1 AAATAATAAACCCCAAACT-CAAAACTCT
* *
38476978 AAATCATAAACCCTAAACTCAAAACTCT
1 AAATAATAAACCCCAAACTCAAAACTCT
38477006 AA
1 AA
38477008 TCCCAAAATA
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
27 5 0.19
28 22 0.81
ACGTcount: A:0.55, C:0.26, G:0.00, T:0.19
Consensus pattern (28 bp):
AAATAATAAACCCCAAACTCAAAACTCT
Found at i:38478247 original size:17 final size:19
Alignment explanation
Indices: 38478205--38478248 Score: 56
Period size: 19 Copynumber: 2.4 Consensus size: 19
38478195 ACGAAATTTT
*
38478205 AATTAGTATTATGAGATAA
1 AATTATTATTATGAGATAA
*
38478224 AATTATTATTATTAGA-AA
1 AATTATTATTATGAGATAA
38478242 AA-TATTA
1 AATTATTA
38478249 CTGCATGTAT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
17 5 0.22
18 4 0.17
19 14 0.61
ACGTcount: A:0.50, C:0.00, G:0.09, T:0.41
Consensus pattern (19 bp):
AATTATTATTATGAGATAA
Found at i:38478358 original size:15 final size:14
Alignment explanation
Indices: 38478334--38478365 Score: 55
Period size: 15 Copynumber: 2.2 Consensus size: 14
38478324 TTAGATATAT
38478334 TTATAAAATTATTA
1 TTATAAAATTATTA
38478348 TTATAATAATTATTA
1 TTATAA-AATTATTA
38478363 TTA
1 TTA
38478366 GATATGGAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 6 0.35
15 11 0.65
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (14 bp):
TTATAAAATTATTA
Found at i:38484151 original size:113 final size:115
Alignment explanation
Indices: 38483945--38484196 Score: 339
Period size: 113 Copynumber: 2.2 Consensus size: 115
38483935 ATTACGGTGT
** * *
38483945 TTTTTAAAAAGCTTCGCTAATGCCACTAAAGCTCAGCAACAAAACGAGGTTGTTTTGCTCAACTT
1 TTTTTAAAAAGCACCGCTAATGCCACTAAAGCTCAACAACAAAACGACGTTGTTTTGCTCAACTT
** *
38484010 TTTTGCGGCGTTTTCTGAAAAGCACCGCTAATGCTCAATCTATTGCGGCA
66 TTTTAAGGCGTTTTCTGAAAAGCACCGCTAATGCTCAATCTATTGCGACA
* * *
38484060 TTTTTAAGAAGCGCCGCTAATGCCACTAAAGCTCAACAAC-AAACGACG-TGTTTTGCTTAACTT
1 TTTTTAAAAAGCACCGCTAATGCCACTAAAGCTCAACAACAAAACGACGTTGTTTTGCTCAACTT
** * *
38484123 TTTTAAGGCGTTTT-TCGAAAAGTGCCGCTAATGCTCGATCTATTGCGACG
66 TTTTAAGGCGTTTTCT-GAAAAGCACCGCTAATGCTCAATCTATTGCGACA
38484173 TTTTTCAAAAAGCACCGCTAATGC
1 TTTTT-AAAAAGCACCGCTAATGC
38484197 TCGACCTATA
Statistics
Matches: 120, Mismatches: 15, Indels: 5
0.86 0.11 0.04
Matches are distributed among these distances:
112 1 0.01
113 60 0.50
114 23 0.19
115 36 0.30
ACGTcount: A:0.28, C:0.23, G:0.18, T:0.31
Consensus pattern (115 bp):
TTTTTAAAAAGCACCGCTAATGCCACTAAAGCTCAACAACAAAACGACGTTGTTTTGCTCAACTT
TTTTAAGGCGTTTTCTGAAAAGCACCGCTAATGCTCAATCTATTGCGACA
Found at i:38484191 original size:40 final size:41
Alignment explanation
Indices: 38484131--38484233 Score: 120
Period size: 40 Copynumber: 2.5 Consensus size: 41
38484121 TTTTTTAAGG
* ** * *
38484131 CGTTTTTCGAAAAGTGCCGCTAATGCTCGATCTATTGCGA-
1 CGTTTTTCAAAAAGCACCGCTAATGCTCGACCTATAGCGAC
38484171 CGTTTTTCAAAAAGCACCGCTAATGCTCGACCTATAGCGAC
1 CGTTTTTCAAAAAGCACCGCTAATGCTCGACCTATAGCGAC
* *
38484212 CTTTGTTTCATAAA-CACCGCTA
1 CGTT-TTTCAAAAAGCACCGCTA
38484234 TAGCTCTAAC
Statistics
Matches: 54, Mismatches: 7, Indels: 3
0.84 0.11 0.05
Matches are distributed among these distances:
40 35 0.65
41 11 0.20
42 8 0.15
ACGTcount: A:0.26, C:0.26, G:0.17, T:0.30
Consensus pattern (41 bp):
CGTTTTTCAAAAAGCACCGCTAATGCTCGACCTATAGCGAC
Found at i:38484386 original size:19 final size:18
Alignment explanation
Indices: 38484362--38484409 Score: 62
Period size: 17 Copynumber: 2.7 Consensus size: 18
38484352 TCATGACTGC
38484362 AAAATAAATTAAGCAAAAT
1 AAAATAAATTAAG-AAAAT
*
38484381 AAAATAAATT-AGTAAAT
1 AAAATAAATTAAGAAAAT
*
38484398 AAAATATATTAA
1 AAAATAAATTAA
38484410 AGTTTAGCCT
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
17 13 0.50
18 3 0.12
19 10 0.38
ACGTcount: A:0.67, C:0.02, G:0.04, T:0.27
Consensus pattern (18 bp):
AAAATAAATTAAGAAAAT
Found at i:38487136 original size:6 final size:7
Alignment explanation
Indices: 38487118--38487142 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
38487108 TTGTGATGCT
38487118 ATTTTTA
1 ATTTTTA
38487125 ATTTTTA
1 ATTTTTA
38487132 ATTTTTA
1 ATTTTTA
38487139 ATTT
1 ATTT
38487143 AATAACTGCT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.28, C:0.00, G:0.00, T:0.72
Consensus pattern (7 bp):
ATTTTTA
Found at i:38489579 original size:25 final size:24
Alignment explanation
Indices: 38489551--38489618 Score: 57
Period size: 25 Copynumber: 2.8 Consensus size: 24
38489541 TTTTAAAATT
*
38489551 TATATGTAAAATATATTTATATGAA
1 TATAT-TAAAATATATTTACATGAA
* * *
38489576 TATAATTTAGATATATTTACATGTA
1 TAT-ATTAAAATATATTTACATGAA
*
38489601 TATA-TAATATATAATTTA
1 TATATTAAAATAT-ATTTA
38489619 TTTTTACCAA
Statistics
Matches: 35, Mismatches: 6, Indels: 5
0.76 0.13 0.11
Matches are distributed among these distances:
23 6 0.17
24 6 0.17
25 21 0.60
26 2 0.06
ACGTcount: A:0.46, C:0.01, G:0.06, T:0.47
Consensus pattern (24 bp):
TATATTAAAATATATTTACATGAA
Found at i:38507131 original size:16 final size:16
Alignment explanation
Indices: 38507110--38507141 Score: 64
Period size: 16 Copynumber: 2.0 Consensus size: 16
38507100 ATTTGATTCG
38507110 GTCCATACTTTTGCGA
1 GTCCATACTTTTGCGA
38507126 GTCCATACTTTTGCGA
1 GTCCATACTTTTGCGA
38507142 CTTTTTCACC
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.19, C:0.25, G:0.19, T:0.38
Consensus pattern (16 bp):
GTCCATACTTTTGCGA
Found at i:38511985 original size:5 final size:5
Alignment explanation
Indices: 38511970--38512185 Score: 423
Period size: 5 Copynumber: 43.0 Consensus size: 5
38511960 TTTCTTAACA
38511970 TATACT TATAT TATAT TATAT TATAT TATAT TATAT TATAT TATAT TATAT
1 TATA-T TATAT TATAT TATAT TATAT TATAT TATAT TATAT TATAT TATAT
38512021 TATAT TATAT TATAT TATAT TATAT TATAT TATAT TATAT TATAT TATAT
1 TATAT TATAT TATAT TATAT TATAT TATAT TATAT TATAT TATAT TATAT
38512071 TATAT TATAT TATAT TATAT TATAT TATAT TATAT TATAT TATAT TATAT
1 TATAT TATAT TATAT TATAT TATAT TATAT TATAT TATAT TATAT TATAT
38512121 TATAT TATAT TATAT TATAT TATAT TATAT TATAT TATAT TATAT TATAT
1 TATAT TATAT TATAT TATAT TATAT TATAT TATAT TATAT TATAT TATAT
38512171 TATAT TATAT TATAT
1 TATAT TATAT TATAT
38512186 ATAATAAAAC
Statistics
Matches: 210, Mismatches: 0, Indels: 1
1.00 0.00 0.00
Matches are distributed among these distances:
5 206 0.98
6 4 0.02
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (5 bp):
TATAT
Found at i:38512277 original size:17 final size:17
Alignment explanation
Indices: 38512265--38512300 Score: 54
Period size: 17 Copynumber: 2.0 Consensus size: 17
38512255 AGAGAAGGAA
38512265 AGAAAGAAAAGAAAAAG
1 AGAAAGAAAAGAAAAAG
38512282 AGAAAGAAAGGAGAAAAAG
1 AGAAAGAAA--AGAAAAAG
38512301 CTAGGGTTTT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 9 0.53
19 8 0.47
ACGTcount: A:0.72, C:0.00, G:0.28, T:0.00
Consensus pattern (17 bp):
AGAAAGAAAAGAAAAAG
Found at i:38512285 original size:25 final size:24
Alignment explanation
Indices: 38512219--38512298 Score: 72
Period size: 25 Copynumber: 3.2 Consensus size: 24
38512209 ATAAATAAAT
* *
38512219 AGAAATAGAAAAAGAG-AGCCAAAGC
1 AGAAA-AGAAAAAGAGAAG-GAAAGA
* *
38512244 AGAAATGAAACAGAGAAGGAAAGAA
1 AGAAAAGAAAAAGAGAAGGAAAG-A
* *
38512269 AGAAAAGAAAAAGAGAAAGAAAGG
1 AGAAAAGAAAAAGAGAAGGAAAGA
38512293 AGAAAA
1 AGAAAA
38512299 AGCTAGGGTT
Statistics
Matches: 45, Mismatches: 8, Indels: 5
0.78 0.14 0.09
Matches are distributed among these distances:
24 18 0.40
25 27 0.60
ACGTcount: A:0.66, C:0.05, G:0.26, T:0.03
Consensus pattern (24 bp):
AGAAAAGAAAAAGAGAAGGAAAGA
Found at i:38522003 original size:61 final size:61
Alignment explanation
Indices: 38521908--38522031 Score: 203
Period size: 61 Copynumber: 2.0 Consensus size: 61
38521898 GGTTTTGAAC
* * **
38521908 ACCTCTTAGTGATCCATATGAATATTGGAGTATTGTTAGAGTGTTACAATATGTGGTTCTT
1 ACCTCTTAGTGATCCACATGAATATCGGAGTATTGCCAGAGTGTTACAATATGTGGTTCTT
*
38521969 ACCTCTTAGTGATCCACATGAATATCGGAGTATTGCCAGAGTGTTACAATATGTGTTTCTT
1 ACCTCTTAGTGATCCACATGAATATCGGAGTATTGCCAGAGTGTTACAATATGTGGTTCTT
38522030 AC
1 AC
38522032 TCTACTTGAT
Statistics
Matches: 58, Mismatches: 5, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
61 58 1.00
ACGTcount: A:0.27, C:0.15, G:0.20, T:0.38
Consensus pattern (61 bp):
ACCTCTTAGTGATCCACATGAATATCGGAGTATTGCCAGAGTGTTACAATATGTGGTTCTT
Found at i:38526515 original size:17 final size:18
Alignment explanation
Indices: 38526476--38526517 Score: 50
Period size: 17 Copynumber: 2.3 Consensus size: 18
38526466 ATCATTTATT
* *
38526476 TTTTTAAAATTAAATTTAT
1 TTTTTAAAA-TAAATTGAG
38526495 TTTTTAAAA-AAATTGAG
1 TTTTTAAAATAAATTGAG
38526512 TTTTTA
1 TTTTTA
38526518 CAGAAAACAT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
17 12 0.57
19 9 0.43
ACGTcount: A:0.40, C:0.00, G:0.05, T:0.55
Consensus pattern (18 bp):
TTTTTAAAATAAATTGAG
Found at i:38537462 original size:74 final size:74
Alignment explanation
Indices: 38537341--38537634 Score: 579
Period size: 74 Copynumber: 4.0 Consensus size: 74
38537331 AAACGTTAAT
*
38537341 TTCTTTTCTAAGAGAGAGAGGAAAACAAAACTAATCAGATATTCCAAAATCCTCTTAATTCTCTC
1 TTCTTTTCTAAGAGGGAGAGGAAAACAAAACTAATCAGATATTCCAAAATCCTCTTAATTCTCTC
38537406 CACTACCTC
66 CACTACCTC
38537415 TTCTTTTCTAAGAGGGAGAGGAAAACAAAACTAATCAGATATTCCAAAATCCTCTTAATTCTCTC
1 TTCTTTTCTAAGAGGGAGAGGAAAACAAAACTAATCAGATATTCCAAAATCCTCTTAATTCTCTC
38537480 CACTACCTC
66 CACTACCTC
38537489 TTCTTTTCTAAGAGGGAGAGGAAAACAAAACTAATCAGATATTCCAAAATCCTCTTAATTCTCTC
1 TTCTTTTCTAAGAGGGAGAGGAAAACAAAACTAATCAGATATTCCAAAATCCTCTTAATTCTCTC
38537554 CACTACCTC
66 CACTACCTC
38537563 TTCTTTTCTAAGAGGGAGAGGAAAACAAAACTAATCAGATATTCCAAAATCCTCTTAATTCTCTC
1 TTCTTTTCTAAGAGGGAGAGGAAAACAAAACTAATCAGATATTCCAAAATCCTCTTAATTCTCTC
38537628 CACTACC
66 CACTACC
38537635 CCACTCTTGA
Statistics
Matches: 219, Mismatches: 1, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
74 219 1.00
ACGTcount: A:0.36, C:0.24, G:0.11, T:0.30
Consensus pattern (74 bp):
TTCTTTTCTAAGAGGGAGAGGAAAACAAAACTAATCAGATATTCCAAAATCCTCTTAATTCTCTC
CACTACCTC
Found at i:38541068 original size:142 final size:142
Alignment explanation
Indices: 38540812--38541097 Score: 491
Period size: 142 Copynumber: 2.0 Consensus size: 142
38540802 TTGGTCTCGC
*
38540812 AAAGGGATTCAAACACAAGACCTTCAACAAACCAACACTCAACTTAACCACCAAACCAGTAGGCC
1 AAAGGGATTCAAACACAAGACCTTCAACAAACCAACACTCAACTTAACCACCAAACCAGTAGACC
* * * * *
38540877 CATTCTGATATGATTTTGCAAATAATTTAATATAAACTCACTGAGCAAGTATAATGCTTAAGTTA
66 CATTCTAATATGATTTTGCAAATAATTTAATATAAACCCACCGAGCAAGTATAACGCTTAAGTCA
38540942 GAAAAATACCAA
131 GAAAAATACCAA
* *
38540954 AAAGGGATTCAAACACAAGACCTTCAACAAACCAACACTCAATTTAACCACCAAACCAGTTGACC
1 AAAGGGATTCAAACACAAGACCTTCAACAAACCAACACTCAACTTAACCACCAAACCAGTAGACC
*
38541019 CATTCTAATATTATTTTGCAAATAATTTAATATAAACCCACCGAGCAAGTATAACGCTTAAGTCA
66 CATTCTAATATGATTTTGCAAATAATTTAATATAAACCCACCGAGCAAGTATAACGCTTAAGTCA
38541084 GAAAAATACCAA
131 GAAAAATACCAA
38541096 AA
1 AA
38541098 CTTACCAGAG
Statistics
Matches: 135, Mismatches: 9, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
142 135 1.00
ACGTcount: A:0.44, C:0.23, G:0.10, T:0.23
Consensus pattern (142 bp):
AAAGGGATTCAAACACAAGACCTTCAACAAACCAACACTCAACTTAACCACCAAACCAGTAGACC
CATTCTAATATGATTTTGCAAATAATTTAATATAAACCCACCGAGCAAGTATAACGCTTAAGTCA
GAAAAATACCAA
Found at i:38544553 original size:29 final size:29
Alignment explanation
Indices: 38544519--38544574 Score: 112
Period size: 29 Copynumber: 1.9 Consensus size: 29
38544509 TTATTTTTAT
38544519 TATTTTTATTTTTAAAAATAAATTTATAA
1 TATTTTTATTTTTAAAAATAAATTTATAA
38544548 TATTTTTATTTTTAAAAATAAATTTAT
1 TATTTTTATTTTTAAAAATAAATTTAT
38544575 GTATGCAAAT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 27 1.00
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (29 bp):
TATTTTTATTTTTAAAAATAAATTTATAA
Found at i:38548378 original size:20 final size:20
Alignment explanation
Indices: 38548349--38548393 Score: 72
Period size: 20 Copynumber: 2.2 Consensus size: 20
38548339 AGCACATGTA
*
38548349 TTCATAAAATTTTAGAATTT
1 TTCATAAAATTTTAGAACTT
*
38548369 TTCATCAAATTTTAGAACTT
1 TTCATAAAATTTTAGAACTT
38548389 TTCAT
1 TTCAT
38548394 TTTAGTCACT
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.36, C:0.11, G:0.04, T:0.49
Consensus pattern (20 bp):
TTCATAAAATTTTAGAACTT
Found at i:38552053 original size:3 final size:3
Alignment explanation
Indices: 38552040--38552072 Score: 57
Period size: 3 Copynumber: 10.7 Consensus size: 3
38552030 AATGCTAAAA
38552040 AAT ATAT AAT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT A-AT AAT AAT AAT AAT AAT AAT AAT AAT AA
38552073 ACTAATAAAC
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
3 26 0.90
4 3 0.10
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:38552207 original size:3 final size:3
Alignment explanation
Indices: 38552194--38552240 Score: 53
Period size: 3 Copynumber: 16.3 Consensus size: 3
38552184 ATATATATAG
* * *
38552194 ATA ATA A-A ATA ATA ATA ATG ATA ATA A-A ATG ATG ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
38552240 A
1 A
38552241 AGACACAAAA
Statistics
Matches: 38, Mismatches: 4, Indels: 4
0.83 0.09 0.09
Matches are distributed among these distances:
2 4 0.11
3 34 0.89
ACGTcount: A:0.64, C:0.00, G:0.06, T:0.30
Consensus pattern (3 bp):
ATA
Found at i:38552228 original size:14 final size:15
Alignment explanation
Indices: 38552201--38552240 Score: 64
Period size: 14 Copynumber: 2.7 Consensus size: 15
38552191 TAGATAATAA
38552201 AATAATAATAATGAT
1 AATAATAATAATGAT
*
38552216 AATAA-AATGATGAT
1 AATAATAATAATGAT
38552230 AATAATAATAA
1 AATAATAATAA
38552241 AGACACAAAA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
14 13 0.59
15 9 0.41
ACGTcount: A:0.62, C:0.00, G:0.07, T:0.30
Consensus pattern (15 bp):
AATAATAATAATGAT
Found at i:38552231 original size:23 final size:20
Alignment explanation
Indices: 38552193--38552241 Score: 71
Period size: 20 Copynumber: 2.5 Consensus size: 20
38552183 TATATATATA
38552193 GATAATAAAATAATAATAAT
1 GATAATAAAATAATAATAAT
* *
38552213 GATAATAAAATGATGATAAT
1 GATAATAAAATAATAATAAT
*
38552233 AATAATAAA
1 GATAATAAA
38552242 GACACAAAAA
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 26 1.00
ACGTcount: A:0.63, C:0.00, G:0.08, T:0.29
Consensus pattern (20 bp):
GATAATAAAATAATAATAAT
Found at i:38555370 original size:47 final size:47
Alignment explanation
Indices: 38555261--38555371 Score: 136
Period size: 47 Copynumber: 2.4 Consensus size: 47
38555251 CCGGGATAAG
* * *
38555261 CACATAGTGCTTCATCGGAATAAATCCGGAACTTTAACATTATAGTA
1 CACATAGTGCTTCATCGGAACAAATCCGAAACTTTAACAGTATAGTA
* * *
38555308 CACAAAGTACTTCATCGGAACAAATCCGAAACTTTAACAGTAGTCG-A
1 CACATAGTGCTTCATCGGAACAAATCCGAAACTTTAACAGTA-TAGTA
38555355 CACATAGTG-TCTCATCG
1 CACATAGTGCT-TCATCG
38555372 ACTCAATGTC
Statistics
Matches: 54, Mismatches: 8, Indels: 4
0.82 0.12 0.06
Matches are distributed among these distances:
46 1 0.02
47 51 0.94
48 2 0.04
ACGTcount: A:0.36, C:0.23, G:0.15, T:0.26
Consensus pattern (47 bp):
CACATAGTGCTTCATCGGAACAAATCCGAAACTTTAACAGTATAGTA
Found at i:38556143 original size:4 final size:4
Alignment explanation
Indices: 38556134--38556214 Score: 72
Period size: 4 Copynumber: 19.8 Consensus size: 4
38556124 CCCTTTTCTA
** * * * **
38556134 TTTC TTTC TTTC TTTC TTTC TTTC TTTC TCAC GTTTGC TCTC TGTA ACTC
1 TTTC TTTC TTTC TTTC TTTC TTTC TTTC TTTC -TTT-C TTTC TTTC TTTC
*
38556184 TTTC TATC TTTC TTTC TTTC TTTC TTTC TTT
1 TTTC TTTC TTTC TTTC TTTC TTTC TTTC TTT
38556215 TTAACTTACT
Statistics
Matches: 61, Mismatches: 14, Indels: 4
0.77 0.18 0.05
Matches are distributed among these distances:
4 57 0.93
5 3 0.05
6 1 0.02
ACGTcount: A:0.05, C:0.26, G:0.04, T:0.65
Consensus pattern (4 bp):
TTTC
Found at i:38562639 original size:47 final size:47
Alignment explanation
Indices: 38562530--38562640 Score: 145
Period size: 47 Copynumber: 2.4 Consensus size: 47
38562520 CCGGGATAAG
* *
38562530 CACATAGTGCTTCATCGGAATAAATCCGGAACTTTAACATTATAGTA
1 CACATAGTGCTTCATCGGAACAAATCCGGAACTTTAACAGTATAGTA
* * *
38562577 CACAAAGTACTTCATCGGAACAAATCCGGAACTTTAACAGTAGTCG-A
1 CACATAGTGCTTCATCGGAACAAATCCGGAACTTTAACAGTA-TAGTA
38562624 CACATAGTG-TCTCATCG
1 CACATAGTGCT-TCATCG
38562641 ACTCAATGTC
Statistics
Matches: 55, Mismatches: 7, Indels: 4
0.83 0.11 0.06
Matches are distributed among these distances:
46 1 0.02
47 52 0.95
48 2 0.04
ACGTcount: A:0.35, C:0.23, G:0.16, T:0.26
Consensus pattern (47 bp):
CACATAGTGCTTCATCGGAACAAATCCGGAACTTTAACAGTATAGTA
Found at i:38563412 original size:4 final size:4
Alignment explanation
Indices: 38563403--38563431 Score: 58
Period size: 4 Copynumber: 7.2 Consensus size: 4
38563393 CCCTTTTCTA
38563403 TTTC TTTC TTTC TTTC TTTC TTTC TTTC T
1 TTTC TTTC TTTC TTTC TTTC TTTC TTTC T
38563432 CACGTTTGCT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 25 1.00
ACGTcount: A:0.00, C:0.24, G:0.00, T:0.76
Consensus pattern (4 bp):
TTTC
Found at i:38565732 original size:192 final size:192
Alignment explanation
Indices: 38565387--38565792 Score: 627
Period size: 192 Copynumber: 2.1 Consensus size: 192
38565377 CAATTATTAA
*
38565387 AATTCCATGTACATGTAACATTTATACTGTATATCCTTATATCATATATATATATATGAACCATT
1 AATTCC-TGTACATGTAACATTTATACCGTATATCCTTATATC--A-ATATATATATGAACCATT
* * *
38565452 TCCATGTAAGTACCTATACTAGTTCGTATTGAACTTATATAATCTCATAATAACACTATGCCCAT
62 TCCATGTAAATACCTACACTAGTTCGTATTGAACTTATACAATCTCATAATAACACTATGCCCAT
**
38565517 TGAACCACTTAGAATCACGTTAGATACATG-GGTAGTACACATGAGGTGTACTGAACTGTAATCT
127 TGAACCACTTAGAATCACGTTAGAT--ATGCGGTAGTACACACAAGGTGTACTGAACTGTAATCT
38565581 GTC
190 GTC
*
38565584 AATTCCTGTACATGTAACATTTATACCGTATATCCTTATATC-ATATATATATGAACTATTTCCA
1 AATTCCTGTACATGTAACATTTATACCGTATATCCTTATATCAATATATATATGAACCATTTCCA
* * *
38565648 TGTAAATACTTGCACTAGTTCGTATTGAACTTATACAATCTCATAATAACACTATGCCCGTTGAA
66 TGTAAATACCTACACTAGTTCGTATTGAACTTATACAATCTCATAATAACACTATGCCCATTGAA
* *
38565713 CCACTTAGAATCTCGTTAGATATGCTGGTAGTACACACAAGGTGTATTGAACTGTAATCTGTC
131 CCACTTAGAATCACGTTAGATATGC-GGTAGTACACACAAGGTGTACTGAACTGTAATCTGTC
38565776 AATTCCTGTACATGTAA
1 AATTCCTGTACATGTAA
38565793 GCTCATACAA
Statistics
Matches: 195, Mismatches: 12, Indels: 9
0.90 0.06 0.04
Matches are distributed among these distances:
190 3 0.02
192 151 0.77
196 35 0.18
197 6 0.03
ACGTcount: A:0.33, C:0.19, G:0.13, T:0.35
Consensus pattern (192 bp):
AATTCCTGTACATGTAACATTTATACCGTATATCCTTATATCAATATATATATGAACCATTTCCA
TGTAAATACCTACACTAGTTCGTATTGAACTTATACAATCTCATAATAACACTATGCCCATTGAA
CCACTTAGAATCACGTTAGATATGCGGTAGTACACACAAGGTGTACTGAACTGTAATCTGTC
Found at i:38579445 original size:14 final size:14
Alignment explanation
Indices: 38579422--38579452 Score: 53
Period size: 14 Copynumber: 2.2 Consensus size: 14
38579412 TTAAGGTGAA
*
38579422 TTTTCTATTTTTAT
1 TTTTCAATTTTTAT
38579436 TTTTCAATTTTTAT
1 TTTTCAATTTTTAT
38579450 TTT
1 TTT
38579453 CGAATCTATT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.16, C:0.06, G:0.00, T:0.77
Consensus pattern (14 bp):
TTTTCAATTTTTAT
Found at i:38580323 original size:3 final size:3
Alignment explanation
Indices: 38580130--38580312 Score: 350
Period size: 3 Copynumber: 61.3 Consensus size: 3
38580120 AATACTCTTG
*
38580130 TTA TTG TTA -TA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
38580177 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
38580225 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
38580273 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
38580313 AATGTTATTA
Statistics
Matches: 177, Mismatches: 2, Indels: 2
0.98 0.01 0.01
Matches are distributed among these distances:
2 2 0.01
3 175 0.99
ACGTcount: A:0.33, C:0.00, G:0.01, T:0.67
Consensus pattern (3 bp):
TTA
Found at i:38584436 original size:48 final size:48
Alignment explanation
Indices: 38584360--38584457 Score: 169
Period size: 48 Copynumber: 2.0 Consensus size: 48
38584350 TGAAAGGATG
* * *
38584360 GAAAGAGTTCAGAGGGAATTACAGGAGCAGTTGGCCAAGTCGCAGCAA
1 GAAAGAGTGCAGAGGGAATTACAAGAGCAGTTGGCCAAGTCGCAACAA
38584408 GAAAGAGTGCAGAGGGAATTACAAGAGCAGTTGGCCAAGTCGCAACAA
1 GAAAGAGTGCAGAGGGAATTACAAGAGCAGTTGGCCAAGTCGCAACAA
38584456 GA
1 GA
38584458 GACAAGAGAT
Statistics
Matches: 47, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
48 47 1.00
ACGTcount: A:0.38, C:0.16, G:0.33, T:0.13
Consensus pattern (48 bp):
GAAAGAGTGCAGAGGGAATTACAAGAGCAGTTGGCCAAGTCGCAACAA
Found at i:38587678 original size:14 final size:14
Alignment explanation
Indices: 38587659--38587685 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
38587649 AGAAAACAAT
38587659 GAAAGAAGGATCAA
1 GAAAGAAGGATCAA
38587673 GAAAGAAGGATCA
1 GAAAGAAGGATCA
38587686 CAAGAACCTT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.56, C:0.07, G:0.30, T:0.07
Consensus pattern (14 bp):
GAAAGAAGGATCAA
Found at i:38592599 original size:88 final size:88
Alignment explanation
Indices: 38592452--38592613 Score: 218
Period size: 88 Copynumber: 1.8 Consensus size: 88
38592442 TTTTTATTTC
* * * * *** *
38592452 TCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGTCCCATGCCGAGGTATTTTTAA
1 TCAAAAATCAACTCAAATTACGAGAGGTGAGTTGAGCCTCAGCTCACACAACGAAGTATTTTTAA
38592517 ATTCTGTTTTCAAATTATGTTTT
66 ATTCTGTTTTCAAATTATGTTTT
*
38592540 TCAAAAATCAACTCAAATTACGAGAGGTGAGTTGAGCCTC-GACTCACACAATGAAGTATTTTTA
1 TCAAAAATCAACTCAAATTACGAGAGGTGAGTTGAGCCTCAG-CTCACACAACGAAGTATTTTTA
*
38592604 ATTTCTGTTT
65 AATTCTGTTT
38592614 CTTTCAAAAA
Statistics
Matches: 63, Mismatches: 10, Indels: 2
0.84 0.13 0.03
Matches are distributed among these distances:
87 1 0.02
88 62 0.98
ACGTcount: A:0.30, C:0.17, G:0.18, T:0.35
Consensus pattern (88 bp):
TCAAAAATCAACTCAAATTACGAGAGGTGAGTTGAGCCTCAGCTCACACAACGAAGTATTTTTAA
ATTCTGTTTTCAAATTATGTTTT
Found at i:38592683 original size:54 final size:54
Alignment explanation
Indices: 38592599--38592892 Score: 466
Period size: 54 Copynumber: 5.4 Consensus size: 54
38592589 AATGAAGTAT
*
38592599 TTTTAATTTCTGTTTCTTTCAAAAATCAACTCATATTGCGAAAGATGAGTTGAGCC
1 TTTTAATTTCTG-TT-TTTCAAAAATCAACTCATATTGCGAAAGGTGAGTTGAGCC
*
38592655 TTTTAATTTTTGTTTTTCAAAAATCAACTCATATTGC-AAGAGGTGAGTTGAGCC
1 TTTTAATTTCTGTTTTTCAAAAATCAACTCATATTGCGAA-AGGTGAGTTGAGCC
38592709 TTTTAATTTCTGTTTTTCAAAAATCAACTCATATTGC-AAGAGGTGAGTTGAGCC
1 TTTTAATTTCTGTTTTTCAAAAATCAACTCATATTGCGAA-AGGTGAGTTGAGCC
* *
38592763 TTTTAATTTCTATTTTTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCC
1 TTTTAATTTCTGTTTTTCAAAAATCAACTCATATTGCGAAAGGTGAGTTGAGCC
* * *
38592817 TTTTAATTTCTATTTTTCAAAAATCAACTCATATTGTGAGAGGTGAGTTGAGCC
1 TTTTAATTTCTGTTTTTCAAAAATCAACTCATATTGCGAAAGGTGAGTTGAGCC
*
38592871 CTTTAATTTCTGTTTTTCAAAA
1 TTTTAATTTCTGTTTTTCAAAA
38592893 TCTACTTTTC
Statistics
Matches: 228, Mismatches: 8, Indels: 6
0.94 0.03 0.02
Matches are distributed among these distances:
53 2 0.01
54 212 0.93
55 3 0.01
56 11 0.05
ACGTcount: A:0.30, C:0.14, G:0.15, T:0.41
Consensus pattern (54 bp):
TTTTAATTTCTGTTTTTCAAAAATCAACTCATATTGCGAAAGGTGAGTTGAGCC
Found at i:38594139 original size:14 final size:14
Alignment explanation
Indices: 38594120--38594150 Score: 62
Period size: 14 Copynumber: 2.2 Consensus size: 14
38594110 TTAAGGTGAA
38594120 TTTTCTATTTTTAT
1 TTTTCTATTTTTAT
38594134 TTTTCTATTTTTAT
1 TTTTCTATTTTTAT
38594148 TTT
1 TTT
38594151 CGAATCTATT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 17 1.00
ACGTcount: A:0.13, C:0.06, G:0.00, T:0.81
Consensus pattern (14 bp):
TTTTCTATTTTTAT
Found at i:38594848 original size:3 final size:3
Alignment explanation
Indices: 38594831--38594869 Score: 62
Period size: 3 Copynumber: 13.3 Consensus size: 3
38594821 AATACTCTTG
*
38594831 TTA TTG TTA -TA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
38594870 GCATTAGTTT
Statistics
Matches: 33, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
2 2 0.06
3 31 0.94
ACGTcount: A:0.31, C:0.00, G:0.03, T:0.67
Consensus pattern (3 bp):
TTA
Found at i:38595136 original size:27 final size:29
Alignment explanation
Indices: 38595104--38595170 Score: 77
Period size: 29 Copynumber: 2.4 Consensus size: 29
38595094 TTATTATTAT
*
38595104 TATTTTCTAATAC-TATATTATGT--GTA
1 TATTTTCTAATACGTATATTATGTACATA
* * *
38595130 TATTTTTTCACACGTATATTATGTACATA
1 TATTTTCTAATACGTATATTATGTACATA
38595159 TATTTTCTAATA
1 TATTTTCTAATA
38595171 TTTTACATAT
Statistics
Matches: 31, Mismatches: 7, Indels: 3
0.76 0.17 0.07
Matches are distributed among these distances:
26 10 0.32
27 10 0.32
29 11 0.35
ACGTcount: A:0.31, C:0.10, G:0.06, T:0.52
Consensus pattern (29 bp):
TATTTTCTAATACGTATATTATGTACATA
Found at i:38601179 original size:26 final size:26
Alignment explanation
Indices: 38601143--38601226 Score: 150
Period size: 26 Copynumber: 3.2 Consensus size: 26
38601133 CATGAAATTC
38601143 TTATCATGAAACATTTACCTAACCCA
1 TTATCATGAAACATTTACCTAACCCA
38601169 TTATCATGAAACATTTACCTAACCCA
1 TTATCATGAAACATTTACCTAACCCA
* *
38601195 TTATCATGGAACATTTACCTAACCTA
1 TTATCATGAAACATTTACCTAACCCA
38601221 TTATCA
1 TTATCA
38601227 ATTTGTATCA
Statistics
Matches: 56, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
26 56 1.00
ACGTcount: A:0.37, C:0.25, G:0.05, T:0.33
Consensus pattern (26 bp):
TTATCATGAAACATTTACCTAACCCA
Found at i:38604794 original size:8 final size:8
Alignment explanation
Indices: 38604780--38604810 Score: 53
Period size: 8 Copynumber: 3.9 Consensus size: 8
38604770 TATACAATAT
38604780 ATGAATTG
1 ATGAATTG
*
38604788 TTGAATTG
1 ATGAATTG
38604796 ATGAATTG
1 ATGAATTG
38604804 ATGAATT
1 ATGAATT
38604811 TGAAATAATT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
8 21 1.00
ACGTcount: A:0.35, C:0.00, G:0.23, T:0.42
Consensus pattern (8 bp):
ATGAATTG
Found at i:38605096 original size:20 final size:20
Alignment explanation
Indices: 38605071--38605113 Score: 77
Period size: 20 Copynumber: 2.1 Consensus size: 20
38605061 TAATTACTTG
*
38605071 TAAAAATATCATGGAATTGA
1 TAAAAATAGCATGGAATTGA
38605091 TAAAAATAGCATGGAATTGA
1 TAAAAATAGCATGGAATTGA
38605111 TAA
1 TAA
38605114 TGCTTATAAA
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.51, C:0.05, G:0.16, T:0.28
Consensus pattern (20 bp):
TAAAAATAGCATGGAATTGA
Found at i:38610466 original size:26 final size:27
Alignment explanation
Indices: 38610404--38610471 Score: 88
Period size: 26 Copynumber: 2.6 Consensus size: 27
38610394 AAGACCTCGT
*
38610404 TTTGTAAAATTA-CCAAAGTACCCCCAG
1 TTTGTAAAATTATCGAAAGTA-CCCCAG
38610431 TTTGTAAAATTATCGAAA-TA-CCCAGG
1 TTTGTAAAATTATCGAAAGTACCCCA-G
38610457 TTTGTAAAATTATCG
1 TTTGTAAAATTATCG
38610472 GATTTCCCTT
Statistics
Matches: 38, Mismatches: 1, Indels: 5
0.86 0.02 0.11
Matches are distributed among these distances:
25 4 0.11
26 16 0.42
27 14 0.37
28 4 0.11
ACGTcount: A:0.37, C:0.18, G:0.13, T:0.32
Consensus pattern (27 bp):
TTTGTAAAATTATCGAAAGTACCCCAG
Found at i:38610511 original size:27 final size:28
Alignment explanation
Indices: 38610433--38610520 Score: 85
Period size: 27 Copynumber: 3.3 Consensus size: 28
38610423 ACCCCCAGTT
* *
38610433 TGTAAAATTATCGAAATA-CCCAGGT-T
1 TGTAAAATTATCGAAATATCCCATGTAG
* * *
38610459 TGTAAAATTATCG-GATTTCCCTTGTAG
1 TGTAAAATTATCGAAATATCCCATGTAG
*
38610486 TGTAAAATTACCGAAATATCCC-TGTAG
1 TGTAAAATTATCGAAATATCCCATGTAG
*
38610513 GGTAAAAT
1 TGTAAAAT
38610521 GACTGTTTTG
Statistics
Matches: 50, Mismatches: 9, Indels: 5
0.78 0.14 0.08
Matches are distributed among these distances:
25 2 0.04
26 18 0.36
27 24 0.48
28 6 0.12
ACGTcount: A:0.35, C:0.15, G:0.17, T:0.33
Consensus pattern (28 bp):
TGTAAAATTATCGAAATATCCCATGTAG
Found at i:38610577 original size:9 final size:9
Alignment explanation
Indices: 38610563--38610589 Score: 54
Period size: 9 Copynumber: 3.0 Consensus size: 9
38610553 TGGACTATGA
38610563 ATTTGACTG
1 ATTTGACTG
38610572 ATTTGACTG
1 ATTTGACTG
38610581 ATTTGACTG
1 ATTTGACTG
38610590 TGATTGTACG
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 18 1.00
ACGTcount: A:0.22, C:0.11, G:0.22, T:0.44
Consensus pattern (9 bp):
ATTTGACTG
Found at i:38610719 original size:26 final size:26
Alignment explanation
Indices: 38610658--38610760 Score: 107
Period size: 27 Copynumber: 3.9 Consensus size: 26
38610648 AAGACCCTAT
* *
38610658 TTTGTAAAATTACCAAAATACCCCCAG
1 TTTGTAAAATTACCGAAATA-CCCAAG
*
38610685 TTTGTAAAATTATCGAAATACCCAAG
1 TTTGTAAAATTACCGAAATACCCAAG
* * * **
38610711 TTTGTAAAATTATCGGATTACCCTCG
1 TTTGTAAAATTACCGAAATACCCAAG
*
38610737 TAGTGTAAAATTACCGAAATACCC
1 T-TTGTAAAATTACCGAAATACCC
38610761 CTGTAGGGTA
Statistics
Matches: 64, Mismatches: 11, Indels: 2
0.83 0.14 0.03
Matches are distributed among these distances:
26 28 0.44
27 36 0.56
ACGTcount: A:0.38, C:0.20, G:0.12, T:0.30
Consensus pattern (26 bp):
TTTGTAAAATTACCGAAATACCCAAG
Found at i:38612844 original size:29 final size:27
Alignment explanation
Indices: 38612783--38612854 Score: 108
Period size: 27 Copynumber: 2.7 Consensus size: 27
38612773 AATGCCTTAT
38612783 TGGTGTGTTAGGGAGGATATACTATAC
1 TGGTGTGTTAGGGAGGATATACTATAC
* * *
38612810 TGGTGTGTTTGGGAGGCTATATTATAC
1 TGGTGTGTTAGGGAGGATATACTATAC
*
38612837 TGGTGTGTTATGGAGGAT
1 TGGTGTGTTAGGGAGGAT
38612855 TTATATTATT
Statistics
Matches: 39, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
27 39 1.00
ACGTcount: A:0.21, C:0.06, G:0.36, T:0.38
Consensus pattern (27 bp):
TGGTGTGTTAGGGAGGATATACTATAC
Found at i:38612859 original size:29 final size:27
Alignment explanation
Indices: 38612783--38612863 Score: 101
Period size: 27 Copynumber: 2.9 Consensus size: 27
38612773 AATGCCTTAT
* *
38612783 TGGTGTGTTAGGGAGGATATACTATAC
1 TGGTGTGTTATGGAGGATATATTATAC
*
38612810 TGGTGTGTT-TGGGAGGCTATATTATAC
1 TGGTGTGTTAT-GGAGGATATATTATAC
38612837 TGGTGTGTTATGGAGGATTTATATTAT
1 TGGTGTGTTATGGAGGA--TATATTAT
38612864 TCCGGGTGTG
Statistics
Matches: 46, Mismatches: 4, Indels: 6
0.82 0.07 0.11
Matches are distributed among these distances:
27 37 0.80
28 1 0.02
29 8 0.17
ACGTcount: A:0.22, C:0.05, G:0.32, T:0.41
Consensus pattern (27 bp):
TGGTGTGTTATGGAGGATATATTATAC
Found at i:38614971 original size:17 final size:19
Alignment explanation
Indices: 38614949--38614990 Score: 54
Period size: 18 Copynumber: 2.4 Consensus size: 19
38614939 TTACTCAAGC
*
38614949 TTTCAAAT-AAGA-AGGGT
1 TTTCAAATGAAAACAGGGT
38614966 TTTC-AATGAAAACAGGGT
1 TTTCAAATGAAAACAGGGT
38614984 TTTCAAA
1 TTTCAAA
38614991 AAACACTTCA
Statistics
Matches: 21, Mismatches: 1, Indels: 4
0.81 0.04 0.15
Matches are distributed among these distances:
16 3 0.14
17 7 0.33
18 9 0.43
19 2 0.10
ACGTcount: A:0.40, C:0.10, G:0.19, T:0.31
Consensus pattern (19 bp):
TTTCAAATGAAAACAGGGT
Found at i:38614995 original size:16 final size:17
Alignment explanation
Indices: 38614961--38614995 Score: 54
Period size: 18 Copynumber: 2.1 Consensus size: 17
38614951 TCAAATAAGA
38614961 AGGGTTTTCAATGAAAAC
1 AGGGTTTTCAA-GAAAAC
38614979 AGGGTTTTCAA-AAAAC
1 AGGGTTTTCAAGAAAAC
38614995 A
1 A
38614996 CTTCAATGTG
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 6 0.35
18 11 0.65
ACGTcount: A:0.43, C:0.11, G:0.20, T:0.26
Consensus pattern (17 bp):
AGGGTTTTCAAGAAAAC
Found at i:38619916 original size:13 final size:14
Alignment explanation
Indices: 38619887--38619919 Score: 50
Period size: 13 Copynumber: 2.4 Consensus size: 14
38619877 TATGATTAGT
38619887 GTTAATTAGACTTA
1 GTTAATTAGACTTA
*
38619901 GTTAATTA-AGTTA
1 GTTAATTAGACTTA
38619914 GTTAAT
1 GTTAAT
38619920 ATTAATTATA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
13 10 0.56
14 8 0.44
ACGTcount: A:0.36, C:0.03, G:0.15, T:0.45
Consensus pattern (14 bp):
GTTAATTAGACTTA
Found at i:38620231 original size:46 final size:46
Alignment explanation
Indices: 38620138--38620239 Score: 134
Period size: 46 Copynumber: 2.2 Consensus size: 46
38620128 TTGATTTTCA
* * *
38620138 TAACATATGATTCAATACTAAAATTATTCCAAACTAATATGGTAAG
1 TAACATATGACTCAATACTAAAATCATTCCAAACTAATATGATAAG
* * *
38620184 TAATATATGACTCAATACTAAAATCATTCCCAACTAGTAT-ATCAAG
1 TAACATATGACTCAATACTAAAATCATTCCAAACTAATATGAT-AAG
38620230 TAACATATGA
1 TAACATATGA
38620240 TAAAAAATGT
Statistics
Matches: 48, Mismatches: 7, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
45 1 0.02
46 47 0.98
ACGTcount: A:0.45, C:0.16, G:0.08, T:0.31
Consensus pattern (46 bp):
TAACATATGACTCAATACTAAAATCATTCCAAACTAATATGATAAG
Found at i:38621291 original size:20 final size:17
Alignment explanation
Indices: 38621255--38621293 Score: 51
Period size: 20 Copynumber: 2.1 Consensus size: 17
38621245 TTTGAGAAGT
38621255 AACAAGAAAATAAAATA
1 AACAAGAAAATAAAATA
38621272 AACAAGTAAAATTGAAAATA
1 AACAAG-AAAA-T-AAAATA
38621292 AA
1 AA
38621294 GATGTATTAA
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
17 6 0.32
18 4 0.21
19 1 0.05
20 8 0.42
ACGTcount: A:0.72, C:0.05, G:0.08, T:0.15
Consensus pattern (17 bp):
AACAAGAAAATAAAATA
Found at i:38626089 original size:6 final size:6
Alignment explanation
Indices: 38626078--38626102 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
38626068 AGCAAGAGAG
38626078 AAAGAA AAAGAA AAAGAA AAAGAA A
1 AAAGAA AAAGAA AAAGAA AAAGAA A
38626103 GAGAGAGAAC
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.84, C:0.00, G:0.16, T:0.00
Consensus pattern (6 bp):
AAAGAA
Found at i:38626195 original size:2 final size:2
Alignment explanation
Indices: 38626188--38626215 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
38626178 GAAATCAAAA
38626188 AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG
38626216 CTAGTTAGGG
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:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
AG
Found at i:38628039 original size:18 final size:18
Alignment explanation
Indices: 38628016--38628050 Score: 70
Period size: 18 Copynumber: 1.9 Consensus size: 18
38628006 TTTATTTATT
38628016 TATTTTTAATTTTTAATA
1 TATTTTTAATTTTTAATA
38628034 TATTTTTAATTTTTAAT
1 TATTTTTAATTTTTAAT
38628051 TCTTTCTCTC
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (18 bp):
TATTTTTAATTTTTAATA
Found at i:38635099 original size:20 final size:19
Alignment explanation
Indices: 38635067--38635126 Score: 68
Period size: 20 Copynumber: 3.1 Consensus size: 19
38635057 AACATTATAT
38635067 TAAATTAAATATTAAGATAA
1 TAAATT-AATATTAAGATAA
*
38635087 TAATTTTAATATTAA-ATTAA
1 TAA-ATTAATATTAAGA-TAA
*
38635107 TAAATTACTATTAAGATAA
1 TAAATTAATATTAAGATAA
38635126 T
1 T
38635127 TAAGTTAAAT
Statistics
Matches: 34, Mismatches: 3, Indels: 7
0.77 0.07 0.16
Matches are distributed among these distances:
19 14 0.41
20 18 0.53
21 2 0.06
ACGTcount: A:0.53, C:0.02, G:0.03, T:0.42
Consensus pattern (19 bp):
TAAATTAATATTAAGATAA
Found at i:38635224 original size:117 final size:125
Alignment explanation
Indices: 38635091--38635328 Score: 334
Period size: 128 Copynumber: 1.9 Consensus size: 125
38635081 AGATAATAAT
38635091 TTTAATATTAAATTAATAAATTACTATTAAGAT-A-ATTAA-GTT-A-AAT-TT-AA-TATTAAA
1 TTTAATATTAAATTAATAAATTACTATTAAGATAAGATTAACGTTAATAATATTAAATTATTAAA
*
38635148 ATATTATTTTTTTTG-GAATAATTAATCTGAAATCAAATTCTC-GAGTAGAATCCAGTTCAC
66 ATATTATTATTTTTGAG-ATAATTAATCTGAAATCAAATTCTCTG-GTAGAATCCAGTTCAC
* *
38635208 TTTAATATTAAATTAATGAATTACTATTAAGATAAGTATTAACTTTAATTTAATATTAAATTATT
1 TTTAATATTAAATTAATAAATTACTATTAAGATAAG-ATTAACGTTAA--TAATATTAAATTATT
38635273 AAAATATTATTATTTTTGAGATAATTAATCTGAAATCAAATTCTCTGGTAGAATCC
63 AAAATATTATTATTTTTGAGATAATTAATCTGAAATCAAATTCTCTGGTAGAATCC
38635329 CAATAAGAGT
Statistics
Matches: 105, Mismatches: 3, Indels: 15
0.85 0.02 0.12
Matches are distributed among these distances:
117 32 0.30
118 1 0.01
120 5 0.05
121 2 0.02
122 1 0.01
125 3 0.03
126 2 0.02
127 2 0.02
128 55 0.52
129 2 0.02
ACGTcount: A:0.42, C:0.07, G:0.08, T:0.43
Consensus pattern (125 bp):
TTTAATATTAAATTAATAAATTACTATTAAGATAAGATTAACGTTAATAATATTAAATTATTAAA
ATATTATTATTTTTGAGATAATTAATCTGAAATCAAATTCTCTGGTAGAATCCAGTTCAC
Found at i:38639959 original size:21 final size:21
Alignment explanation
Indices: 38639933--38639973 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
38639923 ATCTGCTCAA
* *
38639933 ACTCCACCTGTTTTGGAGTAC
1 ACTCCACCTGCTGTGGAGTAC
38639954 ACTCCACCTGCTGTGGAGTA
1 ACTCCACCTGCTGTGGAGTA
38639974 TTGCTCGTCT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.20, C:0.29, G:0.22, T:0.29
Consensus pattern (21 bp):
ACTCCACCTGCTGTGGAGTAC
Found at i:38648612 original size:34 final size:34
Alignment explanation
Indices: 38648574--38648640 Score: 116
Period size: 34 Copynumber: 2.0 Consensus size: 34
38648564 ACATCTCTCA
*
38648574 ATAAACCCAGGAAAAAAACCCTTTTCCTCTCGTT
1 ATAAACCCAGAAAAAAAACCCTTTTCCTCTCGTT
*
38648608 ATAAACCCAGAAAAAAAACTCTTTTCCTCTCGT
1 ATAAACCCAGAAAAAAAACCCTTTTCCTCTCGT
38648641 AATGTATTAT
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
34 31 1.00
ACGTcount: A:0.37, C:0.28, G:0.07, T:0.27
Consensus pattern (34 bp):
ATAAACCCAGAAAAAAAACCCTTTTCCTCTCGTT
Found at i:38653443 original size:22 final size:23
Alignment explanation
Indices: 38653396--38653443 Score: 57
Period size: 21 Copynumber: 2.2 Consensus size: 23
38653386 TTTTTTTATT
* *
38653396 TTTA-TATATATTTTAAGATATA
1 TTTATTATATATTTTAAAAAATA
38653418 -TTATTATAT-TTTTAAAAAATA
1 TTTATTATATATTTTAAAAAATA
38653439 TTTAT
1 TTTAT
38653444 GTATTTATAT
Statistics
Matches: 22, Mismatches: 2, Indels: 4
0.79 0.07 0.14
Matches are distributed among these distances:
21 13 0.59
22 9 0.41
ACGTcount: A:0.42, C:0.00, G:0.02, T:0.56
Consensus pattern (23 bp):
TTTATTATATATTTTAAAAAATA
Found at i:38653839 original size:18 final size:20
Alignment explanation
Indices: 38653802--38653867 Score: 82
Period size: 19 Copynumber: 3.2 Consensus size: 20
38653792 TCTTTCAACA
38653802 AAAAATTCAAAATAATTTTT
1 AAAAATTCAAAATAATTTTT
38653822 -AAAATTCAAAAT-ATTTTT
1 AAAAATTCAAAATAATTTTT
*
38653840 AAAAATTCTAAAATTTATCTTTT
1 AAAAATTC-AAAA-TAAT-TTTT
38653863 AAAAA
1 AAAAA
38653868 ATATATAAAG
Statistics
Matches: 41, Mismatches: 0, Indels: 7
0.85 0.00 0.15
Matches are distributed among these distances:
18 6 0.15
19 19 0.46
20 4 0.10
21 1 0.02
22 2 0.05
23 9 0.22
ACGTcount: A:0.53, C:0.06, G:0.00, T:0.41
Consensus pattern (20 bp):
AAAAATTCAAAATAATTTTT
Found at i:38655139 original size:16 final size:15
Alignment explanation
Indices: 38655118--38655147 Score: 51
Period size: 15 Copynumber: 1.9 Consensus size: 15
38655108 AGAAAGGACA
38655118 AACAAAGAAAACAAAT
1 AACAAAG-AAACAAAT
38655134 AACAAAGAAACAAA
1 AACAAAGAAACAAA
38655148 AAATAGAAAT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 7 0.50
16 7 0.50
ACGTcount: A:0.77, C:0.13, G:0.07, T:0.03
Consensus pattern (15 bp):
AACAAAGAAACAAAT
Found at i:38656336 original size:27 final size:26
Alignment explanation
Indices: 38656207--38656775 Score: 170
Period size: 26 Copynumber: 22.3 Consensus size: 26
38656197 TTAAACTATT
38656207 TTATTTATTTTAAA---TTTTATATA
1 TTATTTATTTTAAATTGTTTTATATA
** * * *
38656230 TTAAACTGTTTTAAATTTTTTTAGATA
1 TT-ATTTATTTTAAATTGTTTTATATA
* *
38656257 -TA-TTATTTTAAATTATTTCATATA
1 TTATTTATTTTAAATTGTTTTATATA
* * * * *
38656281 CTATATACTTTAAATTGCTTTATACA
1 TTATTTATTTTAAATTGTTTTATATA
*
38656307 TTATTTATTTTAAATTTGTTTTATGTA
1 TTATTTATTTTAAA-TTGTTTTATATA
*
38656334 TTATTCATTTTAAATTGTTTTAT-TA
1 TTATTTATTTTAAATTGTTTTATATA
*
38656359 TTACTTTA----AAATT-TTTCATATA
1 TTA-TTTATTTTAAATTGTTTTATATA
** *
38656381 TTATCAATTTCAAA-T-TTTTATAT-
1 TTATTTATTTTAAATTGTTTTATATA
* *
38656404 GTA-TTA-TCT--ATT-TTTTATATA
1 TTATTTATTTTAAATTGTTTTATATA
** *
38656425 CCATTTATTTTTTAAGA-TGTTTTTTATA
1 TTATTTA--TTTTAA-ATTGTTTTATATA
* * *
38656453 TTACTTATTTTAAATTTCTTTTTACATA
1 TTATTTATTTTAAA-TT-GTTTTATATA
* * ** *
38656481 ATATTTATTTTAAACTCATTTATACA
1 TTATTTATTTTAAATTGTTTTATATA
* * *
38656507 TTATTTATCTTAAATTATTTTACATA
1 TTATTTATTTTAAATTGTTTTATATA
* *
38656533 TTATTTATTTTAAATTTTTTTCCCCTCGTATA
1 TTATTTATTTTAAA-TTGTTT----T-ATATA
* ****
38656565 TTATTTATTTCAAACTT-TCGCCTATA
1 TTATTTATTTTAAA-TTGTTTTATATA
** * *
38656591 TTACCTATTTTAAATTTTTTTTACATA
1 TTATTTATTTTAAA-TTGTTTTATATA
* * * *
38656618 TAATCTATTTTTAATTGTTTTGTATA
1 TTATTTATTTTAAATTGTTTTATATA
** * * * * *
38656644 TTGCTGATATTAAATTTCTTTTTTCACA
1 TTATTTATTTTAAA-TTGTTTTAT-ATA
**
38656672 TTATTTATTTTAAATTCATTTAT-TA
1 TTATTTATTTTAAATTGTTTTATATA
* * * *
38656697 TCA--T-TTTAAAATTTGTTTTACATT
1 TTATTTATTTTAAA-TTGTTTTATATA
* *
38656721 TTATTTATTTTAATTTGCTTTATA-A
1 TTATTTATTTTAAATTGTTTTATATA
* *
38656746 -T-TTT-TTTAAAATTGTTATATATA
1 TTATTTATTTTAAATTGTTTTATATA
38656769 TTATTTA
1 TTATTTA
38656776 ATTCATTTGT
Statistics
Matches: 388, Mismatches: 114, Indels: 85
0.66 0.19 0.14
Matches are distributed among these distances:
19 1 0.00
20 9 0.02
21 9 0.02
22 33 0.09
23 15 0.04
24 39 0.10
25 20 0.05
26 126 0.32
27 72 0.19
28 44 0.11
31 2 0.01
32 18 0.05
ACGTcount: A:0.30, C:0.08, G:0.03, T:0.59
Consensus pattern (26 bp):
TTATTTATTTTAAATTGTTTTATATA
Found at i:38656408 original size:26 final size:24
Alignment explanation
Indices: 38656306--38656417 Score: 83
Period size: 25 Copynumber: 4.6 Consensus size: 24
38656296 TGCTTTATAC
*
38656306 ATTATT-T-ATTTTAAATTTGTTTT
1 ATTATTATCATTTTAAATTT-TTAT
38656329 ATGTATTATTCATTTTAAATTGTTT-T
1 AT-TATTA-TCATTTTAAATT-TTTAT
*
38656355 ATTATTA-C-TTTAAAATTTTTCAT
1 ATTATTATCATTTTAAATTTTT-AT
*
38656378 A-TATTATCAATTTCAAATTTTTAT
1 ATTATTATC-ATTTTAAATTTTTAT
38656402 ATGTATTATCTATTTT
1 AT-TATTATC-ATTTT
38656418 TTATATACCA
Statistics
Matches: 73, Mismatches: 4, Indels: 21
0.74 0.04 0.21
Matches are distributed among these distances:
21 3 0.04
22 13 0.18
23 6 0.08
24 7 0.10
25 16 0.22
26 15 0.21
27 12 0.16
28 1 0.01
ACGTcount: A:0.30, C:0.05, G:0.04, T:0.61
Consensus pattern (24 bp):
ATTATTATCATTTTAAATTTTTAT
Found at i:38656743 original size:49 final size:48
Alignment explanation
Indices: 38656671--38656775 Score: 122
Period size: 49 Copynumber: 2.2 Consensus size: 48
38656661 CTTTTTTCAC
* *
38656671 ATTATTTATTTTAAATTCATTTATTATCATTTTAAAATTTGTTTTACAT
1 ATTATTTATTTTAAATTCATTTATAATCATTTTAAAA-TTGTTATACAT
* * ** *
38656720 TTTATTTATTTTAATTTGC-TTTATAATTTTTTTAAAATTGTTATATAT
1 ATTATTTATTTTAAATT-CATTTATAATCATTTTAAAATTGTTATACAT
38656768 ATTATTTA
1 ATTATTTA
38656776 ATTCATTTGT
Statistics
Matches: 47, Mismatches: 8, Indels: 3
0.81 0.14 0.05
Matches are distributed among these distances:
48 16 0.34
49 30 0.64
50 1 0.02
ACGTcount: A:0.31, C:0.04, G:0.03, T:0.62
Consensus pattern (48 bp):
ATTATTTATTTTAAATTCATTTATAATCATTTTAAAATTGTTATACAT
Found at i:38673275 original size:18 final size:18
Alignment explanation
Indices: 38673254--38673290 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
38673244 GGTTCTCAAG
38673254 AATTAAAAAAATTCAAAA
1 AATTAAAAAAATTCAAAA
**
38673272 AATTAAAAATTTTCAAAA
1 AATTAAAAAAATTCAAAA
38673290 A
1 A
38673291 TTTATTTTAA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.68, C:0.05, G:0.00, T:0.27
Consensus pattern (18 bp):
AATTAAAAAAATTCAAAA
Found at i:38673291 original size:17 final size:17
Alignment explanation
Indices: 38673249--38673292 Score: 52
Period size: 18 Copynumber: 2.5 Consensus size: 17
38673239 TAAAAGGTTC
*
38673249 TCAAGAATTAAAAAAAT
1 TCAAAAATTAAAAAAAT
**
38673266 TCAAAAAATTAAAAATTT
1 TC-AAAAATTAAAAAAAT
38673284 TCAAAAATT
1 TCAAAAATT
38673293 TATTTTAAAA
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
17 9 0.39
18 14 0.61
ACGTcount: A:0.61, C:0.07, G:0.02, T:0.30
Consensus pattern (17 bp):
TCAAAAATTAAAAAAAT
Found at i:38676702 original size:306 final size:304
Alignment explanation
Indices: 38676149--38676742 Score: 752
Period size: 306 Copynumber: 1.9 Consensus size: 304
38676139 GATCACCTCC
* * * *
38676149 GATAAATAAGATTGGCCTTGACATCCAAGTCAATGTTAGGTTTAGTAATATCTTATTGTTTGGGA
1 GATAAATAAGATTGGCCTTGACATCCAAGTCAATATTAGATTTAGTAATATCTTATTATTTAGGA
* * *
38676214 ATTAAATTTCACATGTATGTGCACGAATTGTACTTTGACCTTGAGATCAAATCTAATTTATGGAT
66 ATCAAATTTCACATGTATGTGCACGAATCGTACTTTAACCTTGAGATCAAATCTAATTTATGGAT
** * * *
38676279 ATGCTTTTCAAAGAATCTTGGGCATAGGTTTTGTGGAGAATTAAATCCCACGAAAAACTTGACAC
131 ATGCTTTTCAAAGAATCTTGAACATAGATTTTGTAGAGAATTAAATCCCACAAAAAACTTGACAC
* * * *
38676344 CTATGAGTGTCGAGATTTACCTATAAAAAAGAGCATATATTGACAGATAATGAAAAAAAAAGTTT
196 CTATGAGTATCGAAATTTACCTATAAAAAACAGCATAGATTGACAGATAATG--AAAAAAAGTTT
* * *
38676409 TGAAAAAGAACTACAATGTTCTCCTCAAAACCATTAAGAGATTTTT
259 TAAAAAAGAACTACAATGTTCACCACAAAACCATTAAGAGATTTTT
** * **
38676455 GATAAATAAGATTGGCCTTGACATCCTGGTCGATATTAGATTTAGTCGTATCTTATTATTTAGGA
1 GATAAATAAGATTGGCCTTGACATCCAAGTCAATATTAGATTTAGTAATATCTTATTATTTAGGA
* * * *
38676520 ATCAAATTTCACATGTATGTGCACGAATCGTACTTTAACTTTGAGATCAAGTCTAATTTTTGTAT
66 ATCAAATTTCACATGTATGTGCACGAATCGTACTTTAACCTTGAGATCAAATCTAATTTATGGAT
** *
38676585 ATG-TTTTTTAAGAAATCTTGAATATAGATTTTGTAGAGAATTAAATCCCACAAAAAAC-TGAAC
131 ATGCTTTTCAAAG-AATCTTGAACATAGATTTTGTAGAGAATTAAATCCCACAAAAAACTTG-AC
* * *
38676648 ACCTATGAGTATCGAAATTTTTCCCTA-AAATGAAACTGCATCAGA-T-A-A-ATAATGAAAAAG
194 ACCTATGAGTATCGAAA--TTTACCTATAAA--AAACAGCAT-AGATTGACAGATAATGAAAAAA
38676708 AGTTTTAAAAAAGAACTACAATGTTCACCACAAAA
254 AGTTTTAAAAAAGAACTACAATGTTCACCACAAAA
38676743 TGTTGAATGT
Statistics
Matches: 247, Mismatches: 34, Indels: 16
0.83 0.11 0.05
Matches are distributed among these distances:
304 37 0.15
305 9 0.04
306 179 0.72
307 4 0.02
308 8 0.03
309 8 0.03
310 2 0.01
ACGTcount: A:0.38, C:0.14, G:0.16, T:0.33
Consensus pattern (304 bp):
GATAAATAAGATTGGCCTTGACATCCAAGTCAATATTAGATTTAGTAATATCTTATTATTTAGGA
ATCAAATTTCACATGTATGTGCACGAATCGTACTTTAACCTTGAGATCAAATCTAATTTATGGAT
ATGCTTTTCAAAGAATCTTGAACATAGATTTTGTAGAGAATTAAATCCCACAAAAAACTTGACAC
CTATGAGTATCGAAATTTACCTATAAAAAACAGCATAGATTGACAGATAATGAAAAAAAGTTTTA
AAAAAGAACTACAATGTTCACCACAAAACCATTAAGAGATTTTT
Found at i:38677003 original size:6 final size:6
Alignment explanation
Indices: 38676992--38677023 Score: 64
Period size: 6 Copynumber: 5.3 Consensus size: 6
38676982 TCCAAAAATA
38676992 ATTTAT ATTTAT ATTTAT ATTTAT ATTTAT AT
1 ATTTAT ATTTAT ATTTAT ATTTAT ATTTAT AT
38677024 AGCTTTAGGA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 26 1.00
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (6 bp):
ATTTAT
Found at i:38677463 original size:16 final size:16
Alignment explanation
Indices: 38677418--38677463 Score: 56
Period size: 16 Copynumber: 2.8 Consensus size: 16
38677408 GGGTTTGGGT
* * *
38677418 TAATTTTGATTTCAAG
1 TAATTTTAATTTAAAA
38677434 TAATTTTAAATTTAAAA
1 TAATTTT-AATTTAAAA
38677451 TAATTTTAATTTA
1 TAATTTTAATTTA
38677464 GGTTATTATT
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
16 13 0.50
17 13 0.50
ACGTcount: A:0.41, C:0.02, G:0.04, T:0.52
Consensus pattern (16 bp):
TAATTTTAATTTAAAA
Found at i:38679060 original size:76 final size:76
Alignment explanation
Indices: 38678934--38679082 Score: 298
Period size: 76 Copynumber: 2.0 Consensus size: 76
38678924 CGAACAAATA
38678934 CAATAACATAGAGTGGTTGGTTGATTTCCATGTGCTTGCTTAACTTCTAAATTAGGGATCTAATT
1 CAATAACATAGAGTGGTTGGTTGATTTCCATGTGCTTGCTTAACTTCTAAATTAGGGATCTAATT
38678999 CGTTATTAATG
66 CGTTATTAATG
38679010 CAATAACATAGAGTGGTTGGTTGATTTCCATGTGCTTGCTTAACTTCTAAATTAGGGATCTAATT
1 CAATAACATAGAGTGGTTGGTTGATTTCCATGTGCTTGCTTAACTTCTAAATTAGGGATCTAATT
38679075 CGTTATTA
66 CGTTATTA
38679083 CTTCTAAATT
Statistics
Matches: 73, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
76 73 1.00
ACGTcount: A:0.28, C:0.13, G:0.19, T:0.40
Consensus pattern (76 bp):
CAATAACATAGAGTGGTTGGTTGATTTCCATGTGCTTGCTTAACTTCTAAATTAGGGATCTAATT
CGTTATTAATG
Found at i:38690757 original size:40 final size:40
Alignment explanation
Indices: 38690713--38690799 Score: 129
Period size: 40 Copynumber: 2.2 Consensus size: 40
38690703 AAAATGAAAT
* * *
38690713 CGAAGGCATTTGTGCTAGCGACTATATCCGGGCTAAGTCC
1 CGAAGGCATTTATGCTAGCGACCATATCCGGGCTAAGACC
* *
38690753 CGAAGGCATTTATGCTAGTGACCATATTCGGGCTAAGACC
1 CGAAGGCATTTATGCTAGCGACCATATCCGGGCTAAGACC
38690793 CGAAGGC
1 CGAAGGC
38690800 CTTGTCCGAG
Statistics
Matches: 42, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
40 42 1.00
ACGTcount: A:0.25, C:0.24, G:0.28, T:0.23
Consensus pattern (40 bp):
CGAAGGCATTTATGCTAGCGACCATATCCGGGCTAAGACC
Found at i:38693640 original size:63 final size:62
Alignment explanation
Indices: 38693539--38693669 Score: 174
Period size: 63 Copynumber: 2.1 Consensus size: 62
38693529 ATCTTTGCTT
* *
38693539 ATTTGCAAATGAATTCATTTCTCATTTTCATTTTCATTTCCATTTT-GAGAAAACCACATTC
1 ATTTCCAAATGAATTCATTTCTCATTTTCATTTTCATTTCCATTTTGGAGAAAACCACAATC
* * ** *
38693600 ATTTCCAAATGATTTTATTTTCTCCATTTTCATTTTCATTTTGATTTTGGAGAAAACCATAATC
1 ATTTCCAAATGAATTCA-TTTCT-CATTTTCATTTTCATTTCCATTTTGGAGAAAACCACAATC
38693664 ATTTCC
1 ATTTCC
38693670 TGAATGTTTT
Statistics
Matches: 60, Mismatches: 7, Indels: 3
0.86 0.10 0.04
Matches are distributed among these distances:
61 14 0.23
62 5 0.08
63 22 0.37
64 19 0.32
ACGTcount: A:0.28, C:0.18, G:0.07, T:0.47
Consensus pattern (62 bp):
ATTTCCAAATGAATTCATTTCTCATTTTCATTTTCATTTCCATTTTGGAGAAAACCACAATC
Found at i:38695225 original size:22 final size:22
Alignment explanation
Indices: 38695197--38695241 Score: 90
Period size: 22 Copynumber: 2.0 Consensus size: 22
38695187 CAGCAACTTA
38695197 TCTCTCTCTCAAGTAAGTGATT
1 TCTCTCTCTCAAGTAAGTGATT
38695219 TCTCTCTCTCAAGTAAGTGATT
1 TCTCTCTCTCAAGTAAGTGATT
38695241 T
1 T
38695242 TGATAGTTTC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 23 1.00
ACGTcount: A:0.22, C:0.22, G:0.13, T:0.42
Consensus pattern (22 bp):
TCTCTCTCTCAAGTAAGTGATT
Found at i:38696054 original size:47 final size:45
Alignment explanation
Indices: 38695934--38696056 Score: 135
Period size: 47 Copynumber: 2.6 Consensus size: 45
38695924 AAGTTATCGT
*
38695934 GAGCTAGTGTAAGACATGTCTGGGACAT-GCATCGGTCACATTATGA
1 GAGCTAGTGTAAGACATGTCTGGGACATGGCATCAG--ACATTATGA
*
38695980 GAGCTAGTGTAAGACCATGTCTAGGACATGGCATCAG-CATTGA-GA
1 GAGCTAGTGTAAGA-CATGTCTGGGACATGGCATCAGACATT-ATGA
*
38696025 CGAAAGCTAGTGTAAGACTTGTCTGGGACATG
1 -G--AGCTAGTGTAAGACATGTCTGGGACATG
38696057 CATTGGCCTC
Statistics
Matches: 67, Mismatches: 4, Indels: 11
0.82 0.05 0.13
Matches are distributed among these distances:
45 6 0.09
46 16 0.24
47 26 0.39
48 19 0.28
ACGTcount: A:0.29, C:0.17, G:0.29, T:0.24
Consensus pattern (45 bp):
GAGCTAGTGTAAGACATGTCTGGGACATGGCATCAGACATTATGA
Found at i:38696060 original size:40 final size:36
Alignment explanation
Indices: 38696016--38696098 Score: 94
Period size: 36 Copynumber: 2.2 Consensus size: 36
38696006 CATGGCATCA
38696016 GCATTGAGACGAAAGCTAGTGTAAGACTTGTCTGGGACAT
1 GCATTG-GACGAAAG--A-TGTAAGACTTGTCTGGGACAT
* ***
38696056 GCATTGGCCTCGAGATGTAAGACTTGTCTGGGACAT
1 GCATTGGACGAAAGATGTAAGACTTGTCTGGGACAT
38696092 GCATTGG
1 GCATTGG
38696099 CCTCGAGATG
Statistics
Matches: 39, Mismatches: 4, Indels: 4
0.83 0.09 0.09
Matches are distributed among these distances:
36 28 0.72
37 1 0.03
39 4 0.10
40 6 0.15
ACGTcount: A:0.25, C:0.17, G:0.31, T:0.27
Consensus pattern (36 bp):
GCATTGGACGAAAGATGTAAGACTTGTCTGGGACAT
Found at i:38696076 original size:36 final size:36
Alignment explanation
Indices: 38696035--38696112 Score: 156
Period size: 36 Copynumber: 2.2 Consensus size: 36
38696025 CGAAAGCTAG
38696035 TGTAAGACTTGTCTGGGACATGCATTGGCCTCGAGA
1 TGTAAGACTTGTCTGGGACATGCATTGGCCTCGAGA
38696071 TGTAAGACTTGTCTGGGACATGCATTGGCCTCGAGA
1 TGTAAGACTTGTCTGGGACATGCATTGGCCTCGAGA
38696107 TGTAAG
1 TGTAAG
38696113 CTAGTGTAAG
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
36 42 1.00
ACGTcount: A:0.23, C:0.18, G:0.31, T:0.28
Consensus pattern (36 bp):
TGTAAGACTTGTCTGGGACATGCATTGGCCTCGAGA
Found at i:38698634 original size:19 final size:19
Alignment explanation
Indices: 38698591--38698634 Score: 61
Period size: 19 Copynumber: 2.3 Consensus size: 19
38698581 TACAAGCAAC
*
38698591 ACAACATTAATCCAAATAA
1 ACAACATTAATCCAAAAAA
*
38698610 ACAACATTAGTCCAAAAAA
1 ACAACATTAATCCAAAAAA
*
38698629 ATAACA
1 ACAACA
38698635 AAAAAATACA
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
19 22 1.00
ACGTcount: A:0.59, C:0.20, G:0.02, T:0.18
Consensus pattern (19 bp):
ACAACATTAATCCAAAAAA
Found at i:38698696 original size:19 final size:19
Alignment explanation
Indices: 38698672--38698708 Score: 65
Period size: 19 Copynumber: 1.9 Consensus size: 19
38698662 CATAAGTAAA
*
38698672 AGTCGAAGTAAGCAACATG
1 AGTCGAAGTAAACAACATG
38698691 AGTCGAAGTAAACAACAT
1 AGTCGAAGTAAACAACAT
38698709 TATAATAATA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.46, C:0.16, G:0.22, T:0.16
Consensus pattern (19 bp):
AGTCGAAGTAAACAACATG
Found at i:38702043 original size:37 final size:37
Alignment explanation
Indices: 38701981--38702064 Score: 141
Period size: 37 Copynumber: 2.2 Consensus size: 37
38701971 ATCATATGAG
*
38701981 AATTTACTAATTACAACTTGAACCAGTAATACAAAATT
1 AATTAACT-ATTACAACTTGAACCAGTAATACAAAATT
*
38702019 AATTAACTATTACAACTTGGACCAGTAATACAAAATT
1 AATTAACTATTACAACTTGAACCAGTAATACAAAATT
38702056 AATTAACTA
1 AATTAACTA
38702065 AGTTTTAAAA
Statistics
Matches: 44, Mismatches: 2, Indels: 1
0.94 0.04 0.02
Matches are distributed among these distances:
37 37 0.84
38 7 0.16
ACGTcount: A:0.48, C:0.15, G:0.06, T:0.31
Consensus pattern (37 bp):
AATTAACTATTACAACTTGAACCAGTAATACAAAATT
Found at i:38708633 original size:46 final size:46
Alignment explanation
Indices: 38708459--38708679 Score: 204
Period size: 46 Copynumber: 4.8 Consensus size: 46
38708449 AAGTTATCGT
* * * *
38708459 GAGCTAGTGTAAGACATGTTTGGGACATGCATCGGCCAC-ATTATGA
1 GAGCTAGTGTAAGACATGTCTGGGACATGCATCGACCTCGA-GATGA
* * * *
38708505 GAGCTAGTGTAAGACTATGTCTGGGACATGGCA-CCAGCATTGAGACGA
1 GAGCTAGTGTAAGAC-ATGTCTGGGACAT-GCATCGA-CCTCGAGATGA
*
38708553 GAGCTAGTGTAAGACATGTCTGAGACATGCATCGACCTCGAGATGTA
1 GAGCTAGTGTAAGACATGTCTGGGACATGCATCGACCTCGAGATG-A
* *
38708600 -AGCTAGTGTAAGACATGTTTGGGACATGTATCGA-CTACGAGAT--
1 GAGCTAGTGTAAGACATGTCTGGGACATGCATCGACCT-CGAGATGA
* *
38708643 -AGTTAGTGTAAGACTATGTCTGGAACATGGCATCGAC
1 GAGCTAGTGTAAGAC-ATGTCTGGGACAT-GCATCGAC
38708680 ATTCTACCCC
Statistics
Matches: 145, Mismatches: 20, Indels: 20
0.78 0.11 0.11
Matches are distributed among these distances:
43 13 0.09
44 11 0.08
45 8 0.06
46 62 0.43
47 28 0.19
48 22 0.15
49 1 0.01
ACGTcount: A:0.29, C:0.17, G:0.29, T:0.25
Consensus pattern (46 bp):
GAGCTAGTGTAAGACATGTCTGGGACATGCATCGACCTCGAGATGA
Found at i:38727654 original size:40 final size:40
Alignment explanation
Indices: 38727610--38727700 Score: 155
Period size: 40 Copynumber: 2.3 Consensus size: 40
38727600 TGACTAAATC
38727610 GTAATAAATTGGACTAAATCAAATAGAACTAAGAACTTAA
1 GTAATAAATTGGACTAAATCAAATAGAACTAAGAACTTAA
* * *
38727650 GTAATAAATTGGACTAAATCGAATATAACTAAGAACTTAG
1 GTAATAAATTGGACTAAATCAAATAGAACTAAGAACTTAA
38727690 GTAATAAATTG
1 GTAATAAATTG
38727701 AACCAAGGAC
Statistics
Matches: 48, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
40 48 1.00
ACGTcount: A:0.49, C:0.09, G:0.14, T:0.27
Consensus pattern (40 bp):
GTAATAAATTGGACTAAATCAAATAGAACTAAGAACTTAA
Found at i:38730426 original size:26 final size:26
Alignment explanation
Indices: 38730392--38730445 Score: 81
Period size: 26 Copynumber: 2.1 Consensus size: 26
38730382 TTCTTTCTAC
* *
38730392 TTGTGGTAGCCTGGAGACCTTATTCT
1 TTGTAGTAGCCTAGAGACCTTATTCT
*
38730418 TTGTAGTAGCTTAGAGACCTTATTCT
1 TTGTAGTAGCCTAGAGACCTTATTCT
38730444 TT
1 TT
38730446 CCTCTCTTAG
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
26 25 1.00
ACGTcount: A:0.19, C:0.17, G:0.22, T:0.43
Consensus pattern (26 bp):
TTGTAGTAGCCTAGAGACCTTATTCT
Found at i:38734648 original size:5 final size:5
Alignment explanation
Indices: 38734633--38734662 Score: 51
Period size: 5 Copynumber: 5.8 Consensus size: 5
38734623 AACAAGTGTG
38734633 TAAAA TAAAAA TAAAA TAAAA TAAAA TAAA
1 TAAAA T-AAAA TAAAA TAAAA TAAAA TAAA
38734663 GAACACACAG
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
5 19 0.79
6 5 0.21
ACGTcount: A:0.80, C:0.00, G:0.00, T:0.20
Consensus pattern (5 bp):
TAAAA
Found at i:38735927 original size:5 final size:5
Alignment explanation
Indices: 38735917--38735961 Score: 72
Period size: 5 Copynumber: 8.6 Consensus size: 5
38735907 AACATATGTG
38735917 AAAAT AAAAT AAAAT AAAAT AAAAAAT AAAAT AAAAT AAAAT AAA
1 AAAAT AAAAT AAAAT AAAAT --AAAAT AAAAT AAAAT AAAAT AAA
38735962 GAACACACAG
Statistics
Matches: 38, Mismatches: 0, Indels: 4
0.90 0.00 0.10
Matches are distributed among these distances:
5 33 0.87
7 5 0.13
ACGTcount: A:0.82, C:0.00, G:0.00, T:0.18
Consensus pattern (5 bp):
AAAAT
Found at i:38735943 original size:22 final size:22
Alignment explanation
Indices: 38735917--38735961 Score: 90
Period size: 22 Copynumber: 2.0 Consensus size: 22
38735907 AACATATGTG
38735917 AAAATAAAATAAAATAAAATAA
1 AAAATAAAATAAAATAAAATAA
38735939 AAAATAAAATAAAATAAAATAA
1 AAAATAAAATAAAATAAAATAA
38735961 A
1 A
38735962 GAACACACAG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 23 1.00
ACGTcount: A:0.82, C:0.00, G:0.00, T:0.18
Consensus pattern (22 bp):
AAAATAAAATAAAATAAAATAA
Found at i:38735944 original size:17 final size:17
Alignment explanation
Indices: 38735922--38735957 Score: 72
Period size: 17 Copynumber: 2.1 Consensus size: 17
38735912 ATGTGAAAAT
38735922 AAAATAAAATAAAATAA
1 AAAATAAAATAAAATAA
38735939 AAAATAAAATAAAATAA
1 AAAATAAAATAAAATAA
38735956 AA
1 AA
38735958 TAAAGAACAC
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:0.83, C:0.00, G:0.00, T:0.17
Consensus pattern (17 bp):
AAAATAAAATAAAATAA
Found at i:38741516 original size:15 final size:16
Alignment explanation
Indices: 38741498--38741530 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
38741488 GAAAAAGACC
38741498 ATTAAT-AAATTAAAA
1 ATTAATGAAATTAAAA
*
38741513 ATTAATGTAATTAAAA
1 ATTAATGAAATTAAAA
38741529 AT
1 AT
38741531 ATTTAATTAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
15 6 0.38
16 10 0.62
ACGTcount: A:0.61, C:0.00, G:0.03, T:0.36
Consensus pattern (16 bp):
ATTAATGAAATTAAAA
Found at i:38741538 original size:23 final size:25
Alignment explanation
Indices: 38741512--38741562 Score: 70
Period size: 25 Copynumber: 2.1 Consensus size: 25
38741502 ATAAATTAAA
*
38741512 AATTAATGTAA-T-TAAAAATATTT
1 AATTAATGTAATTATAAAAATAATT
*
38741535 AATTAATTTAATTATAAAAATAATT
1 AATTAATGTAATTATAAAAATAATT
38741560 AAT
1 AAT
38741563 ATTAAAATTC
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
23 10 0.42
24 1 0.04
25 13 0.54
ACGTcount: A:0.55, C:0.00, G:0.02, T:0.43
Consensus pattern (25 bp):
AATTAATGTAATTATAAAAATAATT
Found at i:38748200 original size:18 final size:19
Alignment explanation
Indices: 38748154--38748210 Score: 64
Period size: 19 Copynumber: 2.9 Consensus size: 19
38748144 TATAGTTTTC
38748154 CATTAAAAATATATAAAAAAAT
1 CATTAAAAATAT-T--AAAAAT
38748176 CATT-AAAATGATTAAAAAT
1 CATTAAAAAT-ATTAAAAAT
38748195 CA-TAAAAATATTAAAA
1 CATTAAAAATATTAAAA
38748211 TTTATATAAT
Statistics
Matches: 33, Mismatches: 0, Indels: 8
0.80 0.00 0.20
Matches are distributed among these distances:
18 8 0.24
19 13 0.39
21 6 0.18
22 6 0.18
ACGTcount: A:0.65, C:0.05, G:0.02, T:0.28
Consensus pattern (19 bp):
CATTAAAAATATTAAAAAT
Found at i:38748221 original size:17 final size:19
Alignment explanation
Indices: 38748201--38748235 Score: 56
Period size: 17 Copynumber: 1.9 Consensus size: 19
38748191 AAATCATAAA
38748201 AATATTA-AAAT-TTATAT
1 AATATTATAAATATTATAT
38748218 AATATTATAAATATTATA
1 AATATTATAAATATTATA
38748236 AAAGTTCTAA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 7 0.44
18 4 0.25
19 5 0.31
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (19 bp):
AATATTATAAATATTATAT
Found at i:38748232 original size:9 final size:9
Alignment explanation
Indices: 38748200--38748237 Score: 53
Period size: 9 Copynumber: 4.3 Consensus size: 9
38748190 AAAATCATAA
38748200 AAATATTA-
1 AAATATTAT
38748208 AAAT-TTAT
1 AAATATTAT
38748216 ATAATATTAT
1 A-AATATTAT
38748226 AAATATTAT
1 AAATATTAT
38748235 AAA
1 AAA
38748238 AGTTCTAATA
Statistics
Matches: 27, Mismatches: 0, Indels: 5
0.84 0.00 0.16
Matches are distributed among these distances:
7 3 0.11
8 5 0.19
9 14 0.52
10 5 0.19
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (9 bp):
AAATATTAT
Found at i:38748237 original size:28 final size:28
Alignment explanation
Indices: 38748206--38748317 Score: 81
Period size: 29 Copynumber: 3.9 Consensus size: 28
38748196 ATAAAAATAT
38748206 TAAAATTTATATAATATTATAAATATTA
1 TAAAATTTATATAATATTATAAATATTA
*
38748234 TAAAAGTTCTA-ATAA-ATTATAAATTTTTA
1 TAAAA-TT-TATATAATATTATAAA-TATTA
* * *
38748263 TAAAATTAATAAAACATATT-TAAAATAGT-
1 TAAAATTTAT-ATA-ATATTAT-AAATATTA
38748292 TAAAATTT-TATAATAAATTATAAATA
1 TAAAATTTATATAAT--ATTATAAATA
38748318 AATAATAAAT
Statistics
Matches: 66, Mismatches: 7, Indels: 22
0.69 0.07 0.23
Matches are distributed among these distances:
26 2 0.03
27 3 0.05
28 24 0.36
29 25 0.38
30 6 0.09
31 6 0.09
ACGTcount: A:0.54, C:0.02, G:0.02, T:0.42
Consensus pattern (28 bp):
TAAAATTTATATAATATTATAAATATTA
Found at i:38748319 original size:11 final size:11
Alignment explanation
Indices: 38748299--38748339 Score: 50
Period size: 11 Copynumber: 3.9 Consensus size: 11
38748289 AGTTAAAATT
38748299 TTAT-AATAAA
1 TTATAAATAAA
38748309 TTATAAATAAA
1 TTATAAATAAA
*
38748320 TAATAAAT-AA
1 TTATAAATAAA
*
38748330 TTACAAATAA
1 TTATAAATAA
38748340 TAGAAATTTT
Statistics
Matches: 26, Mismatches: 3, Indels: 3
0.81 0.09 0.09
Matches are distributed among these distances:
10 12 0.46
11 14 0.54
ACGTcount: A:0.63, C:0.02, G:0.00, T:0.34
Consensus pattern (11 bp):
TTATAAATAAA
Found at i:38749190 original size:9 final size:9
Alignment explanation
Indices: 38749126--38749367 Score: 132
Period size: 9 Copynumber: 25.3 Consensus size: 9
38749116 TATAACTTTA
38749126 TTTATAATT
1 TTTATAATT
*
38749135 TATTAGAACTT
1 T-TTATAA-TT
* *
38749146 ATTATGATTT
1 TTTAT-AATT
*
38749156 TTTATAAGT
1 TTTATAATT
38749165 TTTATAATT
1 TTTATAATT
* *
38749174 AATGATAATT
1 -TTTATAATT
38749184 TTTATAATT
1 TTTATAATT
*
38749193 TGTATGATGATT
1 T-T-T-ATAATT
38749205 TATTATAACTT
1 T-TTATAA-TT
*
38749216 TTTAGAATT
1 TTTATAATT
*
38749225 TTTATAAGCT
1 TTTATAA-TT
*
38749235 TTTATAATA
1 TTTATAATT
38749244 TTTATAAGTT
1 TTTATAA-TT
*
38749254 TTGATGAATT
1 TTTAT-AATT
*
38749264 CTTTATAAGT
1 -TTTATAATT
38749274 TTTA-AATAT
1 TTTATAAT-T
38749283 TTTA-AATAT
1 TTTATAAT-T
38749292 TTT-TCAATT
1 TTTAT-AATT
*
38749301 TTTATTATT
1 TTTATAATT
*
38749310 TTTATTATT
1 TTTATAATT
38749319 TTTATAATT
1 TTTATAATT
*
38749328 TATTAGAATT
1 T-TTATAATT
38749338 TTTATAAGTT
1 TTTATAA-TT
** *
38749348 TACATGATT
1 TTTATAATT
38749357 TTTA-AATT
1 TTTATAATT
38749365 TTT
1 TTT
38749368 TATGTATTTT
Statistics
Matches: 180, Mismatches: 35, Indels: 37
0.71 0.14 0.15
Matches are distributed among these distances:
8 8 0.04
9 85 0.47
10 66 0.37
11 14 0.08
12 7 0.04
ACGTcount: A:0.33, C:0.02, G:0.07, T:0.58
Consensus pattern (9 bp):
TTTATAATT
Found at i:38749231 original size:19 final size:18
Alignment explanation
Indices: 38749126--38749344 Score: 118
Period size: 19 Copynumber: 11.4 Consensus size: 18
38749116 TATAACTTTA
38749126 TTTATAATTTATTAGAACTT
1 TTTATAATTT-TTAGAA-TT
* * * *
38749146 ATTATGATTTTTTATAAGT
1 TTTAT-AATTTTTAGAATT
* * *
38749165 TTTATAATTAATGATAATT
1 TTTATAATT-TTTAGAATT
*
38749184 TTTATAATTTGTATGATGATT
1 TTTATAATTTTTA-GA--ATT
38749205 TATTATAACTTTTTAGAATT
1 T-TTATAA-TTTTTAGAATT
* * *
38749225 TTTATAAGCTTTTATAATA
1 TTTATAA-TTTTTAGAATT
*
38749244 TTTATAAGTTTTGATGAATT
1 TTTATAA-TTTTTA-GAATT
*
38749264 CTTTATAAGTTTTA-AATAT
1 -TTTATAATTTTTAGAAT-T
**
38749283 TTTA-AATATTTTTCAATT
1 TTTATAAT-TTTTAGAATT
* **
38749301 TTTATTATTTTTATTATT
1 TTTATAATTTTTAGAATT
38749319 TTTATAATTTATTAGAATT
1 TTTATAATTT-TTAGAATT
38749338 TTTATAA
1 TTTATAA
38749345 GTTTACATGA
Statistics
Matches: 152, Mismatches: 33, Indels: 29
0.71 0.15 0.14
Matches are distributed among these distances:
17 2 0.01
18 36 0.24
19 66 0.43
20 20 0.13
21 15 0.10
22 8 0.05
23 5 0.03
ACGTcount: A:0.34, C:0.02, G:0.06, T:0.58
Consensus pattern (18 bp):
TTTATAATTTTTAGAATT
Found at i:38749270 original size:21 final size:19
Alignment explanation
Indices: 38749180--38749386 Score: 105
Period size: 19 Copynumber: 10.8 Consensus size: 19
38749170 AATTAATGAT
38749180 AATTTTTATAA-TTTGTATG
1 AATTTTTATAAGTTT-TATG
*
38749199 ATGATTTATTATAACTTTT-TAG
1 A--ATTT-TTATAAGTTTTAT-G
38749221 AATTTTTATAAGCTTTTAT-
1 AATTTTTATAAG-TTTTATG
*
38749240 AATATTTATAAGTTTTGATG
1 AATTTTTATAAGTTTT-ATG
38749260 AATTCTTTATAAGTTTTA--
1 AATT-TTTATAAGTTTTATG
* *
38749278 AATATTTTA-AA-TATTTTTC
1 AAT-TTTTATAAGT-TTTATG
* *
38749297 AATTTTTATTATTTTTAT-
1 AATTTTTATAAGTTTTATG
* *
38749315 TATTTTTATAATTTATTA-G
1 AATTTTTATAAGTT-TTATG
*
38749334 AATTTTTATAAGTTTACATG
1 AATTTTTATAAGTTT-TATG
*
38749354 -ATTTTTA-AATTTTTTATG
1 AATTTTTATAA-GTTTTATG
* *
38749372 TA-TTTTATAAATTTT
1 AATTTTTATAAGTTTT
38749387 TTTAAAAAGT
Statistics
Matches: 151, Mismatches: 14, Indels: 47
0.71 0.07 0.22
Matches are distributed among these distances:
16 1 0.01
17 5 0.03
18 43 0.28
19 58 0.38
20 14 0.09
21 18 0.12
22 9 0.06
23 3 0.02
ACGTcount: A:0.32, C:0.02, G:0.06, T:0.59
Consensus pattern (19 bp):
AATTTTTATAAGTTTTATG
Found at i:38749282 original size:38 final size:38
Alignment explanation
Indices: 38749207--38749345 Score: 108
Period size: 37 Copynumber: 3.7 Consensus size: 38
38749197 TGATGATTTA
*
38749207 TTATAACTTTTTAGAATTTTTATAAGCTTTTATAATAT
1 TTATAACTTTTGAGAATTTTTATAAGCTTTTATAATAT
*
38749245 TTATAAGTTTTGATGAATTCTTTATAAG-TTTTA-AATAT
1 TTATAACTTTTGA-GAATT-TTTATAAGCTTTTATAATAT
* *** * * * *
38749283 TT-TAAATATTTTTCAATTTTTATTA-TTTTTATTATTT
1 TTATAACT-TTTGAGAATTTTTATAAGCTTTTATAATAT
*
38749320 TTATAA-TTTATTAGAATTTTTATAAG
1 TTATAACTTT-TGAGAATTTTTATAAG
38749346 TTTACATGAT
Statistics
Matches: 81, Mismatches: 12, Indels: 16
0.74 0.11 0.15
Matches are distributed among these distances:
36 13 0.16
37 26 0.32
38 24 0.30
39 10 0.12
40 8 0.10
ACGTcount: A:0.33, C:0.03, G:0.06, T:0.58
Consensus pattern (38 bp):
TTATAACTTTTGAGAATTTTTATAAGCTTTTATAATAT
Found at i:38753870 original size:12 final size:12
Alignment explanation
Indices: 38753853--38753878 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
38753843 TTTCCTGATT
38753853 TTGCCTTACCAA
1 TTGCCTTACCAA
38753865 TTGCCTTACCAA
1 TTGCCTTACCAA
38753877 TT
1 TT
38753879 CAACAGGCAC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.23, C:0.31, G:0.08, T:0.38
Consensus pattern (12 bp):
TTGCCTTACCAA
Found at i:38759326 original size:102 final size:102
Alignment explanation
Indices: 38759183--38759840 Score: 1021
Period size: 102 Copynumber: 6.6 Consensus size: 102
38759173 TTCTCTTCAC
38759183 CTTCTACCTCAT-C--CTTCTTCTTTTCTTTCTTCTTCTCCTTTGCCTCTTTGTCTTTCTTCTTT
1 CTTCTACCTCATCCTTCTTCTTCTTTTCTTTCTTCTTCTCCTTTGCCTCTTTGTCTTTCTTCTTT
*
38759245 TCTTTCTTTCCCTCTTCTGATTCTTCATCTTCATCTT
66 TCTTTCTTTCCCTCTTCTAATTCTTCATCTTCATCTT
38759282 CTTCTACCTCATCCTTCTTCTTCTTTTCTTTCTTCTTCTCCTTTGCCTCTTTGTCTTTCTTCTTT
1 CTTCTACCTCATCCTTCTTCTTCTTTTCTTTCTTCTTCTCCTTTGCCTCTTTGTCTTTCTTCTTT
*
38759347 TCTTTCTTTCCCTCTTCTGATTCTTCATCTTCATCTT
66 TCTTTCTTTCCCTCTTCTAATTCTTCATCTTCATCTT
38759384 CTTCTACCTCATCCTTCTTCTTCTTTTCTTTCTTCTTCTCCTTTGCCTCTTTGTCTTTCTTCTTT
1 CTTCTACCTCATCCTTCTTCTTCTTTTCTTTCTTCTTCTCCTTTGCCTCTTTGTCTTTCTTCTTT
38759449 TCTTTCTTTCCCTCTTCTAATTCTTCATCTTCA---T
66 TCTTTCTTTCCCTCTTCTAATTCTTCATCTTCATCTT
* *
38759483 CTTCTACCTCATCCTTGTTCTTCTTTTCTTTCTTCTTCTCCTTTGCTTCTTTGTCTTTCTTCTTT
1 CTTCTACCTCATCCTTCTTCTTCTTTTCTTTCTTCTTCTCCTTTGCCTCTTTGTCTTTCTTCTTT
*
38759548 TCTTTTTTTCCCTCTTCTAATTC-T--TCTTCATCTT
66 TCTTTCTTTCCCTCTTCTAATTCTTCATCTTCATCTT
*
38759582 CTTCTACCTCATCCTTCTT-TTC-TTTC-TTCTTC-TCT--TTTGCCTCTTTGTCTTTCTCCTTT
1 CTTCTACCTCATCCTTCTTCTTCTTTTCTTTCTTCTTCTCCTTTGCCTCTTTGTCTTTCTTCTTT
38759641 TCTTTCTTTCCCTCTTCTAATTCTTCATCTTCATC-T
66 TCTTTCTTTCCCTCTTCTAATTCTTCATCTTCATCTT
* * * *
38759677 C--CTACATCATCCTTCTTCTTCTTCTCTTTCTTCTTTTCCTTTGCTTCTTTGTCTTTCTTCTTT
1 CTTCTACCTCATCCTTCTTCTTCTTTTCTTTCTTCTTCTCCTTTGCCTCTTTGTCTTTCTTCTTT
* *
38759740 TCTTTCTTTCCCTCTTCTATTTCTTCATCTTCATCTC
66 TCTTTCTTTCCCTCTTCTAATTCTTCATCTTCATCTT
* * * * *
38759777 CTTCTACTTTATCCTTATTCTTTTCTTTC-TTCTTCTCCTCCTTTGCCTCTTTGTCTTTCTTCTT
1 CTTCTACCTCATCCTTCTTCTTCT-TTTCTTTCTTCTTCTCCTTTGCCTCTTTGTCTTTCTTCTT
38759841 CTCTGTCTCT
Statistics
Matches: 517, Mismatches: 23, Indels: 35
0.90 0.04 0.06
Matches are distributed among these distances:
93 59 0.11
94 4 0.01
95 8 0.02
96 26 0.05
97 6 0.01
98 4 0.01
99 173 0.33
100 2 0.00
102 232 0.45
103 3 0.01
ACGTcount: A:0.05, C:0.33, G:0.03, T:0.59
Consensus pattern (102 bp):
CTTCTACCTCATCCTTCTTCTTCTTTTCTTTCTTCTTCTCCTTTGCCTCTTTGTCTTTCTTCTTT
TCTTTCTTTCCCTCTTCTAATTCTTCATCTTCATCTT
Found at i:38759690 original size:192 final size:195
Alignment explanation
Indices: 38759183--38759840 Score: 1000
Period size: 192 Copynumber: 3.3 Consensus size: 195
38759173 TTCTCTTCAC
38759183 CTTCTACCTCATCCTTCTTCTTTTCTTTCTTCTTCTC-CTTTGCCTCTTTGTCTTTCTTCTTTTC
1 CTTCTACCTCAT-C--CTTCTTTTCTTTCTTCTTCTCTCTTTGCCTCTTTGTCTTTCTTCTTTTC
*
38759247 TTTCTTTCCCTCTTCTGATTCTTCATCTTCATCTTCTTCTACCTCATCCTTCTTCTTCTTTTCTT
63 TTTCTTTCCCTCTTCTAATTCTTCATCTTCATC-TC--CTACCTCATCCTTCTTCTTCTTTTCTT
* *
38759312 TCTTCTTCTCCTTTGCCTCTTTGTCTTTCTTCTTTTCTTTCTTTCCCTCTTCTGATTCTTCATCT
125 TCTTCTTCTCCTTTGCTTCTTTGTCTTTCTTCTTTTCTTTCTTTCCCTCTTCTAATTCTT-ATCT
38759377 TCATCTT
189 TCATCTT
38759384 CTTCTACCTCATCCTTCTTCTTCTTTTCTTTCTTCTTCTCCTTTGCCTCTTTGTCTTTCTTCTTT
1 CTTCTACCTCATCCTTCTT-TTC-TTTC-TTCTTC-TCT-CTTTGCCTCTTTGTCTTTCTTCTTT
* *
38759449 TCTTTCTTTCCCTCTTCTAATTCTTCATCTTCATCTTCTACCTCATCCTTGTTCTTCTTTTCTTT
61 TCTTTCTTTCCCTCTTCTAATTCTTCATCTTCATCTCCTACCTCATCCTTCTTCTTCTTTTCTTT
*
38759514 CTTCTTCTCCTTTGCTTCTTTGTCTTTCTTCTTTTCTTTTTTTCCCTCTTCTAATTC-T-TCTTC
126 CTTCTTCTCCTTTGCTTCTTTGTCTTTCTTCTTTTCTTTCTTTCCCTCTTCTAATTCTTATCTTC
38759577 ATCTT
191 ATCTT
*
38759582 CTTCTACCTCATCCTTCTTTTCTTTCTTCTTCTCT-TTTGCCTCTTTGTCTTTCTCCTTTTCTTT
1 CTTCTACCTCATCCTTCTTTTCTTTCTTCTTCTCTCTTTGCCTCTTTGTCTTTCTTCTTTTCTTT
* *
38759646 CTTTCCCTCTTCTAATTCTTCATCTTCATCTCCTACATCATCCTTCTTCTTCTTCTCTTTCTTCT
66 CTTTCCCTCTTCTAATTCTTCATCTTCATCTCCTACCTCATCCTTCTTCTTCTTTTCTTTCTTCT
* *
38759711 TTTCCTTTGCTTCTTTGTCTTTCTTCTTTTCTTTCTTTCCCTCTTCTATTTCTTCATCTTCATCT
131 TCTCCTTTGCTTCTTTGTCTTTCTTCTTTTCTTTCTTTCCCTCTTCTAATTCTT-ATCTTCATCT
*
38759776 C
195 T
* *
38759777 CTTCTACTTTATCCTTATTCTTTTCTTTCTTCTTCTCCTCCTTTGCCTCTTTGTCTTTCTTCTT
1 CTTCTACCTCATCC---TTCTTTTCTTTCTTCTTCT-CT-CTTTGCCTCTTTGTCTTTCTTCTT
38759841 CTCTGTCTCT
Statistics
Matches: 424, Mismatches: 18, Indels: 30
0.90 0.04 0.06
Matches are distributed among these distances:
192 138 0.33
193 1 0.00
194 3 0.01
195 27 0.06
196 4 0.01
197 3 0.01
198 54 0.13
199 5 0.01
200 6 0.01
201 121 0.29
202 2 0.00
203 1 0.00
204 59 0.14
ACGTcount: A:0.05, C:0.33, G:0.03, T:0.59
Consensus pattern (195 bp):
CTTCTACCTCATCCTTCTTTTCTTTCTTCTTCTCTCTTTGCCTCTTTGTCTTTCTTCTTTTCTTT
CTTTCCCTCTTCTAATTCTTCATCTTCATCTCCTACCTCATCCTTCTTCTTCTTTTCTTTCTTCT
TCTCCTTTGCTTCTTTGTCTTTCTTCTTTTCTTTCTTTCCCTCTTCTAATTCTTATCTTCATCTT
Found at i:38760083 original size:18 final size:17
Alignment explanation
Indices: 38760060--38760108 Score: 53
Period size: 18 Copynumber: 2.8 Consensus size: 17
38760050 TCTCCTTATG
* *
38760060 CTTCTTTTCTTTTTTCTT
1 CTTCTTCTCTTCTTTC-T
38760078 CTTCTTCTCTTCTTTCT
1 CTTCTTCTCTTCTTTCT
*
38760095 CTTCATCATCTTCT
1 CTTCTTC-TCTTCT
38760109 ACCACCTCTT
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
17 7 0.26
18 20 0.74
ACGTcount: A:0.04, C:0.31, G:0.00, T:0.65
Consensus pattern (17 bp):
CTTCTTCTCTTCTTTCT
Found at i:38764795 original size:3 final size:3
Alignment explanation
Indices: 38764753--38765083 Score: 133
Period size: 3 Copynumber: 108.7 Consensus size: 3
38764743 ATTTAATATA
* * * *
38764753 TAT TAT TACT TAC TAT T-T TAC TAT TAT TGT CTAA TA- TAT TAT TAT
1 TAT TAT TA-T TAT TAT TAT TAT TAT TAT TAT -TAT TAT TAT TAT TAT
* * * * * * *
38764798 TGT CAC TAT TAT TAT TAC T-T TAC TAT TGT AATT TAT GGTAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA-T TAT --TAT TAT TAT
* * * *
38764845 TAT TAT TAT TAT TAT TAT TAT TAT TAGT GACC TAT TAC TAT TCT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TA-T TA-T TAT TAT TAT TAT TAT
* * * * * *
38764892 TAG CA- TAC TAT TAT T-T CCTAT T-T TA- TAT TAT TAT TGT TAT CAA
1 TAT TAT TAT TAT TAT TAT --TAT TAT TAT TAT TAT TAT TAT TAT TAT
* * * **
38764935 CAT ATAT TAT TAT CAT TAAT GTAT TGT TAT TCCC TAT TAT TAT TAT TAT
1 TAT -TAT TAT TAT TAT T-AT -TAT TAT TAT T-AT TAT TAT TAT TAT TAT
* * * * * * * *
38764984 TAT TAT TAC TAT TAT AAA TAT TCT TAT TAT TAC TAC TAT TTT TAT TCCT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T-AT
* *
38765033 T-T TAT TATT TAT TAT CAA TA- TAT TAT TAT TAT TAT TAT TAT T-T
1 TAT TAT TA-T TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
38765076 TAT TAT TA
1 TAT TAT TA
38765084 CTACTACTAA
Statistics
Matches: 240, Mismatches: 64, Indels: 48
0.68 0.18 0.14
Matches are distributed among these distances:
2 17 0.07
3 196 0.82
4 22 0.09
5 5 0.02
ACGTcount: A:0.31, C:0.09, G:0.03, T:0.57
Consensus pattern (3 bp):
TAT
Found at i:38765066 original size:20 final size:20
Alignment explanation
Indices: 38765034--38765083 Score: 64
Period size: 20 Copynumber: 2.5 Consensus size: 20
38765024 TTTATTCCTT
38765034 TTATTATTTATTATCAATATA
1 TTATTA-TTATTATCAATATA
* * *
38765055 TTATTATTATTATTATTATT
1 TTATTATTATTATCAATATA
38765075 TTATTATTA
1 TTATTATTA
38765084 CTACTACTAA
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
20 20 0.77
21 6 0.23
ACGTcount: A:0.34, C:0.02, G:0.00, T:0.64
Consensus pattern (20 bp):
TTATTATTATTATCAATATA
Found at i:38765143 original size:3 final size:3
Alignment explanation
Indices: 38765135--38765191 Score: 51
Period size: 3 Copynumber: 18.0 Consensus size: 3
38765125 TTATTTAACA
* * *
38765135 TAT TAT TAT TAT TAAT TTT TAT TAT CAT TAT TAC TAT CGTAT TAT TAT
1 TAT TAT TAT TAT T-AT TAT TAT TAT TAT TAT TAT TAT --TAT TAT TAT
*
38765183 TAC TAT TAT
1 TAT TAT TAT
38765192 ATTTTCATTT
Statistics
Matches: 43, Mismatches: 8, Indels: 6
0.75 0.14 0.11
Matches are distributed among these distances:
3 37 0.86
4 3 0.07
5 3 0.07
ACGTcount: A:0.32, C:0.07, G:0.02, T:0.60
Consensus pattern (3 bp):
TAT
Found at i:38765194 original size:17 final size:17
Alignment explanation
Indices: 38765138--38765194 Score: 51
Period size: 17 Copynumber: 3.2 Consensus size: 17
38765128 TTTAACATAT
* *
38765138 TATTATTATTAATTTTTA
1 TATTATTATT-ACTATTA
* **
38765156 TTATCATTATTACTATCG
1 -TATTATTATTACTATTA
38765174 TATTATTATTACTATTA
1 TATTATTATTACTATTA
38765191 TATT
1 TATT
38765195 TTCATTTATA
Statistics
Matches: 30, Mismatches: 8, Indels: 2
0.75 0.20 0.05
Matches are distributed among these distances:
17 18 0.60
18 3 0.10
19 9 0.30
ACGTcount: A:0.32, C:0.07, G:0.02, T:0.60
Consensus pattern (17 bp):
TATTATTATTACTATTA
Found at i:38769365 original size:6 final size:6
Alignment explanation
Indices: 38769354--38769378 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
38769344 ATTTTATAAT
38769354 TTTTTA TTTTTA TTTTTA TTTTTA T
1 TTTTTA TTTTTA TTTTTA TTTTTA T
38769379 CAATTTTTAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.16, C:0.00, G:0.00, T:0.84
Consensus pattern (6 bp):
TTTTTA
Found at i:38786189 original size:14 final size:14
Alignment explanation
Indices: 38786170--38786196 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
38786160 TATTAAGGCA
38786170 ATAATTAAGAACAC
1 ATAATTAAGAACAC
38786184 ATAATTAAGAACA
1 ATAATTAAGAACA
38786197 AGAACAAGTA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.59, C:0.11, G:0.07, T:0.22
Consensus pattern (14 bp):
ATAATTAAGAACAC
Found at i:38788423 original size:8 final size:8
Alignment explanation
Indices: 38788405--38788463 Score: 57
Period size: 8 Copynumber: 7.2 Consensus size: 8
38788395 AATAAAGTTC
38788405 AAAATAAA
1 AAAATAAA
*
38788413 AAAAAACAA
1 AAAATA-AA
38788422 AAAATAAA
1 AAAATAAA
38788430 AAAATAAA
1 AAAATAAA
38788438 AATAA-AAA
1 AA-AATAAA
* * *
38788446 TAAAGATA
1 AAAATAAA
38788454 AAAATAAA
1 AAAATAAA
38788462 AA
1 AA
38788464 TAAACATAAA
Statistics
Matches: 41, Mismatches: 7, Indels: 6
0.76 0.13 0.11
Matches are distributed among these distances:
7 2 0.05
8 30 0.73
9 9 0.22
ACGTcount: A:0.85, C:0.02, G:0.02, T:0.12
Consensus pattern (8 bp):
AAAATAAA
Found at i:38788430 original size:6 final size:6
Alignment explanation
Indices: 38788405--38788479 Score: 82
Period size: 6 Copynumber: 12.3 Consensus size: 6
38788395 AATAAAGTTC
*
38788405 AAAATA AAAA-A AAACA-A AAAATAAA AAAATA AAAATA AAAATA AAGATA
1 AAAATA AAAATA AAA-ATA AAAAT--A AAAATA AAAATA AAAATA AAAATA
* *
38788454 AAAATA AAAATA AACATA AAGATA AA
1 AAAATA AAAATA AAAATA AAAATA AA
38788480 TGGACTCAAT
Statistics
Matches: 61, Mismatches: 4, Indels: 8
0.84 0.05 0.11
Matches are distributed among these distances:
5 5 0.08
6 50 0.82
8 6 0.10
ACGTcount: A:0.81, C:0.03, G:0.03, T:0.13
Consensus pattern (6 bp):
AAAATA
Found at i:38790152 original size:3 final size:3
Alignment explanation
Indices: 38790144--38790204 Score: 70
Period size: 3 Copynumber: 19.7 Consensus size: 3
38790134 AACAAAAGAC
**
38790144 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT -AT GGACC AAT AAT AGAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT --AAT AAT AAT A-AT
38790191 AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AA
38790205 CAAAGAAAAA
Statistics
Matches: 50, Mismatches: 4, Indels: 8
0.81 0.06 0.13
Matches are distributed among these distances:
2 2 0.04
3 45 0.90
4 3 0.06
ACGTcount: A:0.62, C:0.03, G:0.05, T:0.30
Consensus pattern (3 bp):
AAT
Found at i:38794869 original size:24 final size:24
Alignment explanation
Indices: 38794837--38794885 Score: 98
Period size: 24 Copynumber: 2.0 Consensus size: 24
38794827 GGTTGGTAGC
38794837 TTGTTTTGAAGAATAGCTGAACAT
1 TTGTTTTGAAGAATAGCTGAACAT
38794861 TTGTTTTGAAGAATAGCTGAACAT
1 TTGTTTTGAAGAATAGCTGAACAT
38794885 T
1 T
38794886 CCTTGTTGAG
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.33, C:0.08, G:0.20, T:0.39
Consensus pattern (24 bp):
TTGTTTTGAAGAATAGCTGAACAT
Found at i:38797372 original size:14 final size:14
Alignment explanation
Indices: 38797353--38797379 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
38797343 TATTAAGGCA
38797353 ATAATTAAGAACAC
1 ATAATTAAGAACAC
38797367 ATAATTAAGAACA
1 ATAATTAAGAACA
38797380 AGAACAAGTA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.59, C:0.11, G:0.07, T:0.22
Consensus pattern (14 bp):
ATAATTAAGAACAC
Found at i:38800255 original size:6 final size:6
Alignment explanation
Indices: 38800240--38800278 Score: 69
Period size: 6 Copynumber: 6.5 Consensus size: 6
38800230 GCAAATGGAT
*
38800240 CATTTC CATTTT CATTTC CATTTC CATTTC CATTTC CAT
1 CATTTC CATTTC CATTTC CATTTC CATTTC CATTTC CAT
38800279 ATTTGGAAAC
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
6 31 1.00
ACGTcount: A:0.18, C:0.31, G:0.00, T:0.51
Consensus pattern (6 bp):
CATTTC
Found at i:38802782 original size:11 final size:12
Alignment explanation
Indices: 38802754--38802781 Score: 56
Period size: 12 Copynumber: 2.3 Consensus size: 12
38802744 TTATACATCT
38802754 TTTTTCTTTTTA
1 TTTTTCTTTTTA
38802766 TTTTTCTTTTTA
1 TTTTTCTTTTTA
38802778 TTTT
1 TTTT
38802782 CCTTCTTCTT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 16 1.00
ACGTcount: A:0.07, C:0.07, G:0.00, T:0.86
Consensus pattern (12 bp):
TTTTTCTTTTTA
Found at i:38807628 original size:40 final size:40
Alignment explanation
Indices: 38807539--38807641 Score: 118
Period size: 40 Copynumber: 2.6 Consensus size: 40
38807529 AGATAGACCG
* *
38807539 AACACACCAAACAGAAGCTCATAAGAGCTGATCCAACCAA
1 AACACGCCAAACAGAAGCTCATAAGAGCAGATCCAACCAA
* * * * **
38807579 AATATGCCAAACAGAAGCTCATAAGAGCAGGTCCACCCGC
1 AACACGCCAAACAGAAGCTCATAAGAGCAGATCCAACCAA
*
38807619 AACACGCC-AATAGAAGCTCATAA
1 AACACGCCAAACAGAAGCTCATAA
38807642 AAGCTTAACA
Statistics
Matches: 52, Mismatches: 11, Indels: 1
0.81 0.17 0.02
Matches are distributed among these distances:
39 14 0.27
40 38 0.73
ACGTcount: A:0.44, C:0.29, G:0.16, T:0.12
Consensus pattern (40 bp):
AACACGCCAAACAGAAGCTCATAAGAGCAGATCCAACCAA
Found at i:38809276 original size:17 final size:16
Alignment explanation
Indices: 38809254--38809299 Score: 58
Period size: 17 Copynumber: 2.9 Consensus size: 16
38809244 TAATTTTAAG
*
38809254 AAAAATCTATAAAATAT
1 AAAAATATATAAAAT-T
*
38809271 AAAAATATATACAATT
1 AAAAATATATAAAATT
38809287 -AAAATATATAAAA
1 AAAAATATATAAAA
38809300 AGCTTATAAT
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
15 12 0.46
16 1 0.04
17 13 0.50
ACGTcount: A:0.67, C:0.04, G:0.00, T:0.28
Consensus pattern (16 bp):
AAAAATATATAAAATT
Found at i:38809719 original size:11 final size:11
Alignment explanation
Indices: 38809692--38809730 Score: 53
Period size: 11 Copynumber: 3.5 Consensus size: 11
38809682 ATTTAAAACT
*
38809692 TTTAAAA-TAA
1 TTTAAAATTTA
38809702 TTATAAAATTTA
1 TT-TAAAATTTA
38809714 TTTAAAATTTA
1 TTTAAAATTTA
38809725 TTTAAA
1 TTTAAA
38809731 TTATTCTTAA
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
10 2 0.08
11 20 0.77
12 4 0.15
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (11 bp):
TTTAAAATTTA
Found at i:38811756 original size:39 final size:39
Alignment explanation
Indices: 38811702--38811942 Score: 243
Period size: 39 Copynumber: 6.5 Consensus size: 39
38811692 ATTACACTAA
* *
38811702 CACACAGCCTACTAGGCACATAGACCGAATAATCACCGG
1 CACACAGCCTGCTAGGCACATAGCCCGAATAATCACCGG
* ** *
38811741 CACACAGCCTGCTAGGCACATTGCTTGAATAATCATCGG
1 CACACAGCCTGCTAGGCACATAGCCCGAATAATCACCGG
* * *
38811780 CACACAGCTTACTAGGCACATAGCCCGAATAATCACCAG
1 CACACAGCCTGCTAGGCACATAGCCCGAATAATCACCGG
*
38811819 CATACAGCCTGCTAGGCACATAGCCCG---AAT------
1 CACACAGCCTGCTAGGCACATAGCCCGAATAATCACCGG
* * * * *
38811849 -A-ACAGCTTGCTAGGTACATAGCTCGAATAATCACTGA
1 CACACAGCCTGCTAGGCACATAGCCCGAATAATCACCGG
* *
38811886 CACACAACCTGCTAGGCACATAGCCCGAATAATCACCAG
1 CACACAGCCTGCTAGGCACATAGCCCGAATAATCACCGG
*
38811925 CATACAGCCTGCTAGGCA
1 CACACAGCCTGCTAGGCA
38811943 TATAATCTGA
Statistics
Matches: 163, Mismatches: 28, Indels: 22
0.77 0.13 0.10
Matches are distributed among these distances:
28 21 0.13
29 1 0.01
31 3 0.02
36 3 0.02
38 1 0.01
39 134 0.82
ACGTcount: A:0.33, C:0.31, G:0.18, T:0.17
Consensus pattern (39 bp):
CACACAGCCTGCTAGGCACATAGCCCGAATAATCACCGG
Found at i:38811862 original size:28 final size:28
Alignment explanation
Indices: 38811822--38811878 Score: 87
Period size: 28 Copynumber: 2.0 Consensus size: 28
38811812 TCACCAGCAT
38811822 ACAGCCTGCTAGGCACATAGCCCGAATA
1 ACAGCCTGCTAGGCACATAGCCCGAATA
* * *
38811850 ACAGCTTGCTAGGTACATAGCTCGAATA
1 ACAGCCTGCTAGGCACATAGCCCGAATA
38811878 A
1 A
38811879 TCACTGACAC
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
28 26 1.00
ACGTcount: A:0.33, C:0.26, G:0.21, T:0.19
Consensus pattern (28 bp):
ACAGCCTGCTAGGCACATAGCCCGAATA
Found at i:38811897 original size:67 final size:67
Alignment explanation
Indices: 38811783--38811917 Score: 200
Period size: 67 Copynumber: 2.0 Consensus size: 67
38811773 TCATCGGCAC
* *
38811783 ACAGCTTACTAGGCACATAGCCCGAATAATCACCAGCATACAGCCTGCTAGGCACATAGCCCGAA
1 ACAGCTTACTAGGCACATAGCCCGAATAATCACCAGCACACAACCTGCTAGGCACATAGCCCGAA
38811848 TA
66 TA
* * * *
38811850 ACAGCTTGCTAGGTACATAGCTCGAATAATCA-CTGACACACAACCTGCTAGGCACATAGCCCGA
1 ACAGCTTACTAGGCACATAGCCCGAATAATCACCAG-CACACAACCTGCTAGGCACATAGCCCGA
38811914 ATA
65 ATA
38811917 A
1 A
38811918 TCACCAGCAT
Statistics
Matches: 61, Mismatches: 6, Indels: 2
0.88 0.09 0.03
Matches are distributed among these distances:
66 2 0.03
67 59 0.97
ACGTcount: A:0.35, C:0.30, G:0.18, T:0.18
Consensus pattern (67 bp):
ACAGCTTACTAGGCACATAGCCCGAATAATCACCAGCACACAACCTGCTAGGCACATAGCCCGAA
TA
Done.