Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: D05
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: 64368997
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 1610000 characters in sequence are not A, C, G, or T
File 42 of 208
Found at i:16172505 original size:46 final size:44
Alignment explanation
Indices: 16172455--16172580 Score: 105
Period size: 46 Copynumber: 2.8 Consensus size: 44
16172445 TTAAAAAAAT
16172455 ATAAATAATAATAAATAATAAATTTTATAAAAATT-ATTAAATTTTA
1 ATAAA-AATAATAAATAATAAATTTTATAAAAATTAATT--ATTTTA
* * *
16172501 ATAAAAAT-ATAAGA-AATTTAAAATTTATTAAAAATTAGATTTTTTTT
1 ATAAAAATAATAA-ATAA--TAAATTTTA-TAAAAATTA-ATTATTTTA
** *
16172548 ATAAAAATCGTAAAAAATAAATTTTATAAAAAT
1 ATAAAAATAATAAATAATAAATTTTATAAAAAT
16172581 AAAAAAAAGT
Statistics
Matches: 67, Mismatches: 5, Indels: 17
0.75 0.06 0.19
Matches are distributed among these distances:
44 6 0.09
45 11 0.16
46 21 0.31
47 21 0.31
48 5 0.07
49 3 0.04
ACGTcount: A:0.57, C:0.01, G:0.02, T:0.40
Consensus pattern (44 bp):
ATAAAAATAATAAATAATAAATTTTATAAAAATTAATTATTTTA
Found at i:16172520 original size:20 final size:19
Alignment explanation
Indices: 16172460--16172521 Score: 54
Period size: 20 Copynumber: 3.2 Consensus size: 19
16172450 AAAATATAAA
*
16172460 TAATAATAAATA-ATAAATT
1 TAATAA-AAATATAAAAATT
* * *
16172479 TTATAAAAATTATTAAATTT
1 TAATAAAAA-TATAAAAATT
16172499 TAATAAAAATATAAGAAATT
1 TAATAAAAATATAA-AAATT
16172519 TAA
1 TAA
16172522 AATTTATTAA
Statistics
Matches: 33, Mismatches: 7, Indels: 5
0.73 0.16 0.11
Matches are distributed among these distances:
18 3 0.09
19 11 0.33
20 19 0.58
ACGTcount: A:0.60, C:0.00, G:0.02, T:0.39
Consensus pattern (19 bp):
TAATAAAAATATAAAAATT
Found at i:16172902 original size:11 final size:11
Alignment explanation
Indices: 16172883--16172908 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
16172873 CGATTTTTAT
16172883 ATTTTTTTCTA
1 ATTTTTTTCTA
16172894 ATTTTTTTCTA
1 ATTTTTTTCTA
16172905 ATTT
1 ATTT
16172909 ATAATAATTT
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:0.19, C:0.08, G:0.00, T:0.73
Consensus pattern (11 bp):
ATTTTTTTCTA
Found at i:16173176 original size:91 final size:88
Alignment explanation
Indices: 16173004--16173178 Score: 208
Period size: 91 Copynumber: 2.0 Consensus size: 88
16172994 GAATAAAAGC
* * *
16173004 AAGGGATTAATTACTTTTTTTGAAAAAGTTTGAGGGTTTTTTGATACATTTTGAAAGTTCAAGTA
1 AAGGGATTAATTACTTTTTTTAAAAAAGTTTGAGCGTTTTTTGATACATTTTGAAAATTCAAGTA
*
16173069 CCCAATTGATTACAAAAAAGAGT
66 CCCAATTGAGTACAAAAAAGAGT
* * * * * *
16173092 AAGGGATTAGTTGCTTTTTTTAAAAAAGGTTTGAAGACTTTTTTTTATGCATTTTGAAAATTTAA
1 AAGGGATTAATTACTTTTTTTAAAAAA-GTTTG-AG-CGTTTTTTGATACATTTTGAAAATTCAA
*
16173157 GTACCCAAATT-AGTGCAAAAAA
63 GTACCC-AATTGAGTACAAAAAA
16173179 AGCAAGGCCT
Statistics
Matches: 72, Mismatches: 11, Indels: 5
0.82 0.12 0.06
Matches are distributed among these distances:
88 24 0.33
89 5 0.07
90 2 0.03
91 37 0.51
92 4 0.06
ACGTcount: A:0.37, C:0.08, G:0.17, T:0.38
Consensus pattern (88 bp):
AAGGGATTAATTACTTTTTTTAAAAAAGTTTGAGCGTTTTTTGATACATTTTGAAAATTCAAGTA
CCCAATTGAGTACAAAAAAGAGT
Found at i:16176321 original size:42 final size:42
Alignment explanation
Indices: 16176273--16176366 Score: 161
Period size: 42 Copynumber: 2.2 Consensus size: 42
16176263 CCGTGTGGCT
*
16176273 AGGCCGTGTGGCTCACACGGTCAAGAGACACACCCGTGTCTC
1 AGGCCGTGTGGCTCACACGGTCAAGAGACACACCCATGTCTC
**
16176315 AGGCCGTGTGGCTCACACGGTCAAGAGACATGCCCATGTCTC
1 AGGCCGTGTGGCTCACACGGTCAAGAGACACACCCATGTCTC
16176357 AGGCCGTGTG
1 AGGCCGTGTG
16176367 AGTATTCGAA
Statistics
Matches: 49, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
42 49 1.00
ACGTcount: A:0.20, C:0.31, G:0.31, T:0.18
Consensus pattern (42 bp):
AGGCCGTGTGGCTCACACGGTCAAGAGACACACCCATGTCTC
Found at i:16177410 original size:42 final size:42
Alignment explanation
Indices: 16177362--16177518 Score: 233
Period size: 42 Copynumber: 3.7 Consensus size: 42
16177352 GATCGAAAGC
*
16177362 TGAACAGAAGCTCATAAGAGCTGAACAGAAACTCATAAGAGT
1 TGAACAGAAGCTCGTAAGAGCTGAACAGAAACTCATAAGAGT
*
16177404 TGAACAGAAGTTCGTAAGAGCTGAACAGAAACTCATAAGAGT
1 TGAACAGAAGCTCGTAAGAGCTGAACAGAAACTCATAAGAGT
* * *
16177446 TGAACAAAAGCTCGTAAGAGCTGAACAGACACTCATATGAGT
1 TGAACAGAAGCTCGTAAGAGCTGAACAGAAACTCATAAGAGT
* * * *
16177488 TAAATAGAAGCTCGTAAGAGCTAAATAGAAA
1 TGAACAGAAGCTCGTAAGAGCTGAACAGAAA
16177519 GTAAAACATG
Statistics
Matches: 103, Mismatches: 12, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
42 103 1.00
ACGTcount: A:0.45, C:0.15, G:0.22, T:0.18
Consensus pattern (42 bp):
TGAACAGAAGCTCGTAAGAGCTGAACAGAAACTCATAAGAGT
Found at i:16177442 original size:63 final size:61
Alignment explanation
Indices: 16177345--16177474 Score: 181
Period size: 63 Copynumber: 2.1 Consensus size: 61
16177335 CTGATACGCC
* *
16177345 AACAGAAGATCGAAAGCTGAACAGAAGCTCATAAGAGCTGAACAGAAA-CTCATAAGAGTTG
1 AACAGAAGATCGAAAGCTGAACAGAAACTCATAAGAGCTGAACA-AAAGCTCATAAGAGCTG
* * *
16177406 AACAGAAGTTCGTAAGAGCTGAACAGAAACTCATAAGAGTTGAACAAAAGCTCGTAAGAGCTG
1 AACAGAAGATCG-AA-AGCTGAACAGAAACTCATAAGAGCTGAACAAAAGCTCATAAGAGCTG
16177469 AACAGA
1 AACAGA
16177475 CACTCATATG
Statistics
Matches: 61, Mismatches: 5, Indels: 4
0.87 0.07 0.06
Matches are distributed among these distances:
61 11 0.18
62 5 0.08
63 45 0.74
ACGTcount: A:0.45, C:0.16, G:0.23, T:0.15
Consensus pattern (61 bp):
AACAGAAGATCGAAAGCTGAACAGAAACTCATAAGAGCTGAACAAAAGCTCATAAGAGCTG
Found at i:16177517 original size:21 final size:21
Alignment explanation
Indices: 16177359--16177509 Score: 169
Period size: 21 Copynumber: 7.2 Consensus size: 21
16177349 GAAGATCGAA
16177359 AGCTGAACAGAAGCTCATAAG
1 AGCTGAACAGAAGCTCATAAG
*
16177380 AGCTGAACAGAAACTCATAAG
1 AGCTGAACAGAAGCTCATAAG
* * *
16177401 AGTTGAACAGAAGTTCGTAAG
1 AGCTGAACAGAAGCTCATAAG
*
16177422 AGCTGAACAGAAACTCATAAG
1 AGCTGAACAGAAGCTCATAAG
* * *
16177443 AGTTGAACAAAAGCTCGTAAG
1 AGCTGAACAGAAGCTCATAAG
*
16177464 AGCTGAACAGACA-CTCATATG
1 AGCTGAACAGA-AGCTCATAAG
* * * *
16177485 AGTTAAATAGAAGCTCGTAAG
1 AGCTGAACAGAAGCTCATAAG
16177506 AGCT
1 AGCT
16177510 AAATAGAAAG
Statistics
Matches: 105, Mismatches: 23, Indels: 4
0.80 0.17 0.03
Matches are distributed among these distances:
20 1 0.01
21 103 0.98
22 1 0.01
ACGTcount: A:0.42, C:0.17, G:0.23, T:0.19
Consensus pattern (21 bp):
AGCTGAACAGAAGCTCATAAG
Found at i:16187306 original size:238 final size:242
Alignment explanation
Indices: 16186879--16187358 Score: 752
Period size: 238 Copynumber: 2.0 Consensus size: 242
16186869 TTTAAGGGAT
*
16186879 TCATGAAATGCTACGACTTATGCACTACCACCTTCTACGACCGAGGTGGGTTACATTAGATGAAA
1 TCATGAAATGCTACGACTTATGCACTACCACCTTCTACGACCGAGATGGGTTACATTAGATGAAA
* * *
16186944 TTGAACACCTAAATGTATCTTCACTCACACAGTTGTTGGATTTGCAAGGAGCTGAAGAAAAATGC
66 TTGAACACCTAAATGTACCTTCACT-ACACAGTAGTTGGATTTGCAAGAAGCTGAAGAAAAATGC
* *
16187009 AGTTTTTTTTATGTCATCTAGGTTTTGGTTCACACAGCAGTCAAAATTCGCTAACTGTAGGCATC
130 AG-TTTTTTGATGTCATCTAGGTTTTGGTTCACACAGCACTCAAAATTCGCTAACTGTAGGCATC
16187074 TTGTGATGATAGACAGTGTAAAACTAACTGTCCACAAACTACACATACG
194 TTGTGATGATAGACAGTGTAAAACTAACTGTCCACAAACTACACATACG
* *
16187123 TCATGAAATGCTACGACTTATGCACTACCA-C-TCTACGACTGAGATGGGTTACGTTAGATGAAA
1 TCATGAAATGCTACGACTTATGCACTACCACCTTCTACGACCGAGATGGGTTACATTAGATGAAA
* * * *
16187186 TTGACCACCTAAATGTACCTTTACT-CGCAGTAGTTGGATTTGCAAGAAGCTGAAGAAAAATGGA
66 TTGAACACCTAAATGTACCTTCACTACACAGTAGTTGGATTTGCAAGAAGCTGAAGAAAAATGCA
* *
16187250 G-TTTTTGATGTCATCTAGGTTTTGGTTCACACAGCACTCAAAATTGGCTGACTGTAGGCATCTT
131 GTTTTTTGATGTCATCTAGGTTTTGGTTCACACAGCACTCAAAATTCGCTAACTGTAGGCATCTT
* * * *
16187314 TTGATGGTCGACAGTGTAAAACTAACTGTCCACAAACTACCCATA
196 GTGATGATAGACAGTGTAAAACTAACTGTCCACAAACTACACATA
16187359 GTTCATTATA
Statistics
Matches: 218, Mismatches: 18, Indels: 6
0.90 0.07 0.02
Matches are distributed among these distances:
238 100 0.46
240 36 0.17
242 51 0.23
243 1 0.00
244 30 0.14
ACGTcount: A:0.31, C:0.20, G:0.20, T:0.29
Consensus pattern (242 bp):
TCATGAAATGCTACGACTTATGCACTACCACCTTCTACGACCGAGATGGGTTACATTAGATGAAA
TTGAACACCTAAATGTACCTTCACTACACAGTAGTTGGATTTGCAAGAAGCTGAAGAAAAATGCA
GTTTTTTGATGTCATCTAGGTTTTGGTTCACACAGCACTCAAAATTCGCTAACTGTAGGCATCTT
GTGATGATAGACAGTGTAAAACTAACTGTCCACAAACTACACATACG
Found at i:16187721 original size:9 final size:9
Alignment explanation
Indices: 16187706--16187738 Score: 57
Period size: 9 Copynumber: 3.7 Consensus size: 9
16187696 TTGAATCTCT
16187706 CTTCTTCTG
1 CTTCTTCTG
*
16187715 TTTCTTCTG
1 CTTCTTCTG
16187724 CTTCTTCTG
1 CTTCTTCTG
16187733 CTTCTT
1 CTTCTT
16187739 TTTTTCCTCT
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
9 22 1.00
ACGTcount: A:0.00, C:0.30, G:0.09, T:0.61
Consensus pattern (9 bp):
CTTCTTCTG
Found at i:16194458 original size:23 final size:24
Alignment explanation
Indices: 16194426--16194470 Score: 65
Period size: 24 Copynumber: 1.9 Consensus size: 24
16194416 TTTGATCACC
*
16194426 TAAAAAATT-ATTTAAAAAAAACT
1 TAAAAAATTAATATAAAAAAAACT
*
16194449 TAAAAGATTAATATAAAAAAAA
1 TAAAAAATTAATATAAAAAAAA
16194471 GTATAAGCTA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
23 8 0.42
24 11 0.58
ACGTcount: A:0.69, C:0.02, G:0.02, T:0.27
Consensus pattern (24 bp):
TAAAAAATTAATATAAAAAAAACT
Found at i:16198839 original size:18 final size:17
Alignment explanation
Indices: 16198803--16198841 Score: 51
Period size: 18 Copynumber: 2.2 Consensus size: 17
16198793 TTTAAAAAAT
16198803 TTTAATTTCTTTATATC
1 TTTAATTTCTTTATATC
* *
16198820 TTTAATATTTTTTGTATC
1 TTTAAT-TTCTTTATATC
16198838 TTTA
1 TTTA
16198842 TTCTTGAAAA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
17 6 0.32
18 13 0.68
ACGTcount: A:0.23, C:0.08, G:0.03, T:0.67
Consensus pattern (17 bp):
TTTAATTTCTTTATATC
Found at i:16202514 original size:30 final size:31
Alignment explanation
Indices: 16202448--16202517 Score: 81
Period size: 30 Copynumber: 2.3 Consensus size: 31
16202438 TCCACCCTTA
* * * *
16202448 AAATATTTACACTATTGATCCTTCAACTTTT
1 AAATATTTACACTATTAACCCCTCAAATTTT
*
16202479 -CATATTTACACT-TTAACCCCTCAAATTTT
1 AAATATTTACACTATTAACCCCTCAAATTTT
16202508 AAATATTTAC
1 AAATATTTAC
16202518 TATTGGGCAA
Statistics
Matches: 32, Mismatches: 6, Indels: 3
0.78 0.15 0.07
Matches are distributed among these distances:
29 13 0.41
30 19 0.59
ACGTcount: A:0.34, C:0.21, G:0.01, T:0.43
Consensus pattern (31 bp):
AAATATTTACACTATTAACCCCTCAAATTTT
Found at i:16206281 original size:23 final size:23
Alignment explanation
Indices: 16206232--16206281 Score: 57
Period size: 23 Copynumber: 2.2 Consensus size: 23
16206222 GTCCCTTGAT
* * *
16206232 TTTTTTTTGGGGGGTGGGAGGCT
1 TTTTCTTTGGGGGGTGGGAGCCA
16206255 TTTTCTTTGGTGGGGTGGG-GCCA
1 TTTTCTTTGG-GGGGTGGGAGCCA
16206278 TTTT
1 TTTT
16206282 TTGCAACCCT
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
23 15 0.65
24 8 0.35
ACGTcount: A:0.04, C:0.08, G:0.42, T:0.46
Consensus pattern (23 bp):
TTTTCTTTGGGGGGTGGGAGCCA
Found at i:16206281 original size:24 final size:24
Alignment explanation
Indices: 16206230--16206282 Score: 65
Period size: 24 Copynumber: 2.2 Consensus size: 24
16206220 ATGTCCCTTG
* *
16206230 ATTTTTTTTTGGGGGGTGGGAGGC
1 ATTTTTCTTTGGGGGGTGGGAGCC
16206254 -TTTTTCTTTGGTGGGGTGGG-GCC
1 ATTTTTCTTTGG-GGGGTGGGAGCC
16206277 ATTTTT
1 ATTTTT
16206283 TGCAACCCTA
Statistics
Matches: 25, Mismatches: 2, Indels: 4
0.81 0.06 0.13
Matches are distributed among these distances:
23 12 0.48
24 13 0.52
ACGTcount: A:0.06, C:0.08, G:0.40, T:0.47
Consensus pattern (24 bp):
ATTTTTCTTTGGGGGGTGGGAGCC
Found at i:16215197 original size:12 final size:12
Alignment explanation
Indices: 16215180--16215216 Score: 74
Period size: 12 Copynumber: 3.1 Consensus size: 12
16215170 ATGCCTTAAA
16215180 TTATGATATTAT
1 TTATGATATTAT
16215192 TTATGATATTAT
1 TTATGATATTAT
16215204 TTATGATATTAT
1 TTATGATATTAT
16215216 T
1 T
16215217 GGGAAGGACA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 25 1.00
ACGTcount: A:0.32, C:0.00, G:0.08, T:0.59
Consensus pattern (12 bp):
TTATGATATTAT
Found at i:16215406 original size:26 final size:27
Alignment explanation
Indices: 16215350--16215406 Score: 75
Period size: 26 Copynumber: 2.2 Consensus size: 27
16215340 TTATACAAAT
*
16215350 TAAATTCAAATTAATTAACTTCTGAAA
1 TAAATTCAAATTAATTAACTTATGAAA
16215377 -AAATATCAAATTAATT-ACTTAT-AAA
1 TAAAT-TCAAATTAATTAACTTATGAAA
16215402 TAAAT
1 TAAAT
16215407 CAGATAAAAA
Statistics
Matches: 27, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
25 3 0.11
26 13 0.48
27 11 0.41
ACGTcount: A:0.53, C:0.09, G:0.02, T:0.37
Consensus pattern (27 bp):
TAAATTCAAATTAATTAACTTATGAAA
Found at i:16221888 original size:19 final size:19
Alignment explanation
Indices: 16221864--16221908 Score: 90
Period size: 19 Copynumber: 2.4 Consensus size: 19
16221854 ACATTGTTTT
16221864 CAGAAGCCCGAAGGCTGAA
1 CAGAAGCCCGAAGGCTGAA
16221883 CAGAAGCCCGAAGGCTGAA
1 CAGAAGCCCGAAGGCTGAA
16221902 CAGAAGC
1 CAGAAGC
16221909 TCATGAGAGC
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 26 1.00
ACGTcount: A:0.38, C:0.27, G:0.31, T:0.04
Consensus pattern (19 bp):
CAGAAGCCCGAAGGCTGAA
Found at i:16224055 original size:11 final size:11
Alignment explanation
Indices: 16224039--16224082 Score: 52
Period size: 11 Copynumber: 3.8 Consensus size: 11
16224029 TATACTAACA
16224039 AAAATAATAAT
1 AAAATAATAAT
* *
16224050 AAAATATCTCATT
1 AAAATA-AT-AAT
16224063 AAAATAATAAT
1 AAAATAATAAT
16224074 AAAATAATA
1 AAAATAATA
16224083 TTTATCTAAT
Statistics
Matches: 27, Mismatches: 4, Indels: 4
0.77 0.11 0.11
Matches are distributed among these distances:
11 17 0.63
12 2 0.07
13 8 0.30
ACGTcount: A:0.66, C:0.05, G:0.00, T:0.30
Consensus pattern (11 bp):
AAAATAATAAT
Found at i:16224579 original size:16 final size:17
Alignment explanation
Indices: 16224552--16224583 Score: 57
Period size: 16 Copynumber: 1.9 Consensus size: 17
16224542 AACTATTTAT
16224552 TTAAAGATAATATTTTG
1 TTAAAGATAATATTTTG
16224569 TTAAA-ATAATATTTT
1 TTAAAGATAATATTTT
16224584 CCCTCTATTC
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 10 0.67
17 5 0.33
ACGTcount: A:0.44, C:0.00, G:0.06, T:0.50
Consensus pattern (17 bp):
TTAAAGATAATATTTTG
Found at i:16233661 original size:16 final size:16
Alignment explanation
Indices: 16233640--16233671 Score: 64
Period size: 16 Copynumber: 2.0 Consensus size: 16
16233630 TAACTCAGGA
16233640 GCTGCAGGAGTACATG
1 GCTGCAGGAGTACATG
16233656 GCTGCAGGAGTACATG
1 GCTGCAGGAGTACATG
16233672 TGTAACACCC
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:0.25, C:0.19, G:0.38, T:0.19
Consensus pattern (16 bp):
GCTGCAGGAGTACATG
Found at i:16235069 original size:103 final size:104
Alignment explanation
Indices: 16234890--16235154 Score: 417
Period size: 103 Copynumber: 2.6 Consensus size: 104
16234880 AACCGTTATT
* * * *
16234890 GGTGGATCTCGCACTTAGCACCACCACTTAATCGGGGAATCAGCACTTAGCAACCCCTTGGGGGA
1 GGTGGATATCGCACTTAGCACCACCAATGAATCGGGGAATCAGCACTTAGCAACCCCTCGGGGGA
** *
16234955 ATCAGCACATAGCAACCCCCTTT-TTATTTCAGAGATAC
66 ATCAGCACATAGCAACCCCCTTTCACATTTCAAAGATAC
16234993 GGTGGATATCGCACTTAGCACCACCAATGAA-CTGGGGAATCAGCACTTAGCAACCCCTCGGGGG
1 GGTGGATATCGCACTTAGCACCACCAATGAATC-GGGGAATCAGCACTTAGCAACCCCTCGGGGG
16235057 AATCAGCACATAGCAACCCCCTTTCACATTTCAAAGATAC
65 AATCAGCACATAGCAACCCCCTTTCACATTTCAAAGATAC
* **
16235097 GGTGGATATCGCACATAGCACCACCAATGAATCGGGGAATCAGCACACAGCAACCCCT
1 GGTGGATATCGCACTTAGCACCACCAATGAATCGGGGAATCAGCACTTAGCAACCCCT
16235155 TTATGTACAA
Statistics
Matches: 149, Mismatches: 10, Indels: 5
0.91 0.06 0.03
Matches are distributed among these distances:
102 1 0.01
103 82 0.55
104 65 0.44
105 1 0.01
ACGTcount: A:0.30, C:0.30, G:0.21, T:0.20
Consensus pattern (104 bp):
GGTGGATATCGCACTTAGCACCACCAATGAATCGGGGAATCAGCACTTAGCAACCCCTCGGGGGA
ATCAGCACATAGCAACCCCCTTTCACATTTCAAAGATAC
Found at i:16235515 original size:30 final size:29
Alignment explanation
Indices: 16235481--16235545 Score: 76
Period size: 30 Copynumber: 2.2 Consensus size: 29
16235471 TAATCCACCA
16235481 CCCAACTTTTTGAAAAATTACAATTTTGCC
1 CCCAAC-TTTTGAAAAATTACAATTTTGCC
* * * *
16235511 CCCAAACTTTTGCATAATTACACTTTTGTC
1 CCC-AACTTTTGAAAAATTACAATTTTGCC
16235541 CCCAA
1 CCCAA
16235546 GCTCGGAAAT
Statistics
Matches: 30, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
29 2 0.07
30 25 0.83
31 3 0.10
ACGTcount: A:0.31, C:0.28, G:0.06, T:0.35
Consensus pattern (29 bp):
CCCAACTTTTGAAAAATTACAATTTTGCC
Found at i:16235519 original size:31 final size:30
Alignment explanation
Indices: 16235488--16235545 Score: 80
Period size: 30 Copynumber: 1.9 Consensus size: 30
16235478 CCACCCAACT
16235488 TTTTGAAAAATTACAATTTTGCCCCCAAAC
1 TTTTGAAAAATTACAATTTTGCCCCCAAAC
* * * *
16235518 TTTTGCATAATTACACTTTTGTCCCCAA
1 TTTTGAAAAATTACAATTTTGCCCCCAA
16235546 GCTCGGAAAT
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
30 24 1.00
ACGTcount: A:0.31, C:0.24, G:0.07, T:0.38
Consensus pattern (30 bp):
TTTTGAAAAATTACAATTTTGCCCCCAAAC
Found at i:16247613 original size:51 final size:51
Alignment explanation
Indices: 16247498--16247659 Score: 245
Period size: 51 Copynumber: 3.2 Consensus size: 51
16247488 CGGATCACAT
* * * *
16247498 TTATCACTTGTCACTTGTCACTGCTCAGATAAGTGTAGCT-AAGCTACCAC
1 TTATCACTTGTCACTTATCACTGATCAGATAAGTGCAACTAAAGCTACCAC
* *
16247548 TTATCACTTGTCACTTATCACTGATTAGATAAGTGCAACTAAAGCTACCAT
1 TTATCACTTGTCACTTATCACTGATCAGATAAGTGCAACTAAAGCTACCAC
* *
16247599 TTGTCACTTGTCACTTATCACTAATCAGATAAGTGCAACTAAAGCTACCAC
1 TTATCACTTGTCACTTATCACTGATCAGATAAGTGCAACTAAAGCTACCAC
16247650 TTATCACTTG
1 TTATCACTTG
16247660 CTAAAGCTAC
Statistics
Matches: 100, Mismatches: 11, Indels: 1
0.89 0.10 0.01
Matches are distributed among these distances:
50 35 0.35
51 65 0.65
ACGTcount: A:0.30, C:0.24, G:0.13, T:0.33
Consensus pattern (51 bp):
TTATCACTTGTCACTTATCACTGATCAGATAAGTGCAACTAAAGCTACCAC
Found at i:16247667 original size:23 final size:23
Alignment explanation
Indices: 16247637--16247682 Score: 83
Period size: 23 Copynumber: 2.0 Consensus size: 23
16247627 ATAAGTGCAA
16247637 CTAAAGCTACCACTTATCACTTG
1 CTAAAGCTACCACTTATCACTTG
*
16247660 CTAAAGCTACCACTTATTACTTG
1 CTAAAGCTACCACTTATCACTTG
16247683 TCGCTTATCA
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
23 22 1.00
ACGTcount: A:0.30, C:0.28, G:0.09, T:0.33
Consensus pattern (23 bp):
CTAAAGCTACCACTTATCACTTG
Found at i:16247707 original size:74 final size:74
Alignment explanation
Indices: 16247586--16247733 Score: 233
Period size: 74 Copynumber: 2.0 Consensus size: 74
16247576 ATAAGTGCAA
* *
16247586 CTAAAGCTACCATTTGTCACTTGTCACTTATCACTAATCAGATAAGTGCAACTAAAGCTACCACT
1 CTAAAGCTACCACTTATCACTTGTCACTTATCACTAATCAGATAAGTGCAACTAAAGCTACCACT
16247651 TATCACTTG
66 TATCACTTG
* * * * *
16247660 CTAAAGCTACCACTTATTACTTGTCGCTTATCACTGATCAGATAAGTGTAGCTAAAGCTACCACT
1 CTAAAGCTACCACTTATCACTTGTCACTTATCACTAATCAGATAAGTGCAACTAAAGCTACCACT
16247725 TATCACTTG
66 TATCACTTG
16247734 TCGCTGATCA
Statistics
Matches: 67, Mismatches: 7, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
74 67 1.00
ACGTcount: A:0.31, C:0.25, G:0.12, T:0.32
Consensus pattern (74 bp):
CTAAAGCTACCACTTATCACTTGTCACTTATCACTAATCAGATAAGTGCAACTAAAGCTACCACT
TATCACTTG
Found at i:16247840 original size:17 final size:17
Alignment explanation
Indices: 16247818--16247850 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
16247808 TATTATCAAT
16247818 TCATCA-ACAAATATATC
1 TCATCATAC-AATATATC
16247835 TCATCATACAATATAT
1 TCATCATACAATATAT
16247851 AATTCATGAA
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
17 13 0.87
18 2 0.13
ACGTcount: A:0.45, C:0.21, G:0.00, T:0.33
Consensus pattern (17 bp):
TCATCATACAATATATC
Found at i:16257180 original size:12 final size:12
Alignment explanation
Indices: 16257163--16257201 Score: 71
Period size: 12 Copynumber: 3.3 Consensus size: 12
16257153 TGGAAGGGAT
16257163 CAAAATAACACA
1 CAAAATAACACA
16257175 CAAAATAACACA
1 CAAAATAACACA
16257187 C-AAATAACACA
1 CAAAATAACACA
16257198 CAAA
1 CAAA
16257202 TGTTTTCAAT
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
11 11 0.42
12 15 0.58
ACGTcount: A:0.67, C:0.26, G:0.00, T:0.08
Consensus pattern (12 bp):
CAAAATAACACA
Found at i:16257193 original size:11 final size:11
Alignment explanation
Indices: 16257165--16257202 Score: 67
Period size: 11 Copynumber: 3.4 Consensus size: 11
16257155 GAAGGGATCA
16257165 AAATAACACAC
1 AAATAACACAC
16257176 AAAATAACACAC
1 -AAATAACACAC
16257188 AAATAACACAC
1 AAATAACACAC
16257199 AAAT
1 AAAT
16257203 GTTTTCAATT
Statistics
Matches: 26, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
11 15 0.58
12 11 0.42
ACGTcount: A:0.66, C:0.24, G:0.00, T:0.11
Consensus pattern (11 bp):
AAATAACACAC
Found at i:16260127 original size:16 final size:16
Alignment explanation
Indices: 16260087--16260135 Score: 59
Period size: 16 Copynumber: 3.1 Consensus size: 16
16260077 TCACTTATGC
16260087 TTTA-AAAAATGAATAAT
1 TTTATAAAAAT-AAT-AT
16260104 TTT-T-AAAATAATAT
1 TTTATAAAAATAATAT
16260118 TTTATAAAAATAATAT
1 TTTATAAAAATAATAT
16260134 TT
1 TT
16260136 CATCCAGATA
Statistics
Matches: 29, Mismatches: 0, Indels: 7
0.81 0.00 0.19
Matches are distributed among these distances:
14 5 0.17
15 4 0.14
16 17 0.59
17 3 0.10
ACGTcount: A:0.53, C:0.00, G:0.02, T:0.45
Consensus pattern (16 bp):
TTTATAAAAATAATAT
Found at i:16262432 original size:2 final size:2
Alignment explanation
Indices: 16262425--16262454 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
16262415 AGGATGTATA
16262425 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG
1 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG
16262455 AGAGAGAGAG
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.00, C:0.00, G:0.50, T:0.50
Consensus pattern (2 bp):
TG
Found at i:16266938 original size:13 final size:12
Alignment explanation
Indices: 16266893--16266942 Score: 61
Period size: 11 Copynumber: 4.3 Consensus size: 12
16266883 ATTTTTTTAA
16266893 TTTTAAAAT-AT
1 TTTTAAAATAAT
16266904 TTTTAAAATAAT
1 TTTTAAAATAAT
*
16266916 TTTT-TAA-AAT
1 TTTTAAAATAAT
16266926 TTTTAAAATAAAT
1 TTTTAAAAT-AAT
16266939 TTTT
1 TTTT
16266943 GGTATTTATT
Statistics
Matches: 33, Mismatches: 2, Indels: 6
0.80 0.05 0.15
Matches are distributed among these distances:
10 7 0.21
11 13 0.39
12 6 0.18
13 7 0.21
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (12 bp):
TTTTAAAATAAT
Found at i:16266942 original size:22 final size:23
Alignment explanation
Indices: 16266891--16266942 Score: 79
Period size: 22 Copynumber: 2.3 Consensus size: 23
16266881 TTATTTTTTT
*
16266891 AATTTTAAAATATTTTTAAAATA
1 AATTTTTAAATATTTTTAAAATA
*
16266914 ATTTTTTAAA-ATTTTTAAAATA
1 AATTTTTAAATATTTTTAAAATA
16266936 AATTTTT
1 AATTTTT
16266943 GGTATTTATT
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
22 18 0.69
23 8 0.31
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (23 bp):
AATTTTTAAATATTTTTAAAATA
Found at i:16268761 original size:31 final size:31
Alignment explanation
Indices: 16268721--16268787 Score: 89
Period size: 31 Copynumber: 2.2 Consensus size: 31
16268711 TTATCAATCT
* *
16268721 AGTGGCTTAAATAAAAAATTTCAAATAGTTC
1 AGTGACTTAAATAAAAAATTTCAAATAATTC
* * *
16268752 AGTGACTTAAATGAAAATTTTCGAATAATTC
1 AGTGACTTAAATAAAAAATTTCAAATAATTC
16268783 AGTGA
1 AGTGA
16268788 TCATTATGTA
Statistics
Matches: 31, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
31 31 1.00
ACGTcount: A:0.43, C:0.09, G:0.15, T:0.33
Consensus pattern (31 bp):
AGTGACTTAAATAAAAAATTTCAAATAATTC
Found at i:16281524 original size:19 final size:19
Alignment explanation
Indices: 16281498--16281543 Score: 58
Period size: 20 Copynumber: 2.4 Consensus size: 19
16281488 AAGAACAAAT
16281498 GAGAAAAA-AAAGAGTCTGAC
1 GAGAAAAATAAA-AGT-TGAC
16281518 GAGAAAAATAAAAGTTGAC
1 GAGAAAAATAAAAGTTGAC
*
16281537 TAGAAAA
1 GAGAAAA
16281544 CAATTTTCTA
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
19 10 0.42
20 11 0.46
21 3 0.12
ACGTcount: A:0.59, C:0.07, G:0.22, T:0.13
Consensus pattern (19 bp):
GAGAAAAATAAAAGTTGAC
Found at i:16284678 original size:21 final size:22
Alignment explanation
Indices: 16284653--16284696 Score: 63
Period size: 21 Copynumber: 2.0 Consensus size: 22
16284643 ATCATCTAAC
*
16284653 TATTAAGATTTTCAA-TTTAAT
1 TATTAAAATTTTCAATTTTAAT
*
16284674 TATTAAAATTTTTAATTTTAAT
1 TATTAAAATTTTCAATTTTAAT
16284696 T
1 T
16284697 TTTTTAATTG
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
21 13 0.65
22 7 0.35
ACGTcount: A:0.39, C:0.02, G:0.02, T:0.57
Consensus pattern (22 bp):
TATTAAAATTTTCAATTTTAAT
Found at i:16284700 original size:15 final size:16
Alignment explanation
Indices: 16284668--16284705 Score: 51
Period size: 15 Copynumber: 2.4 Consensus size: 16
16284658 AGATTTTCAA
16284668 TTTAATTATTAAAATT
1 TTTAATTATTAAAATT
**
16284684 TTTAATT-TTAATTTT
1 TTTAATTATTAAAATT
16284699 TTTAATT
1 TTTAATT
16284706 GCTCTAGTGC
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
15 13 0.65
16 7 0.35
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (16 bp):
TTTAATTATTAAAATT
Found at i:16286971 original size:3 final size:3
Alignment explanation
Indices: 16286963--16286995 Score: 57
Period size: 3 Copynumber: 11.0 Consensus size: 3
16286953 CATTTTGACT
*
16286963 TTC TTC TTC TTC TTC TTG TTC TTC TTC TTC TTC
1 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC
16286996 CATTTTGTGT
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 28 1.00
ACGTcount: A:0.00, C:0.30, G:0.03, T:0.67
Consensus pattern (3 bp):
TTC
Found at i:16289817 original size:3 final size:3
Alignment explanation
Indices: 16289809--16289834 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
16289799 TTAGTCAAGT
16289809 TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TT
16289835 GCATTTTACA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (3 bp):
TTA
Found at i:16299669 original size:18 final size:18
Alignment explanation
Indices: 16299626--16299669 Score: 61
Period size: 18 Copynumber: 2.4 Consensus size: 18
16299616 AATTTTTATG
*
16299626 ATTGGGTTGGGTTGAGTA
1 ATTGGGTTGGGTTGAATA
*
16299644 ATTAGGTTGGGTTGAATA
1 ATTGGGTTGGGTTGAATA
*
16299662 CTTGGGTT
1 ATTGGGTT
16299670 TGAATTGGGT
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
18 22 1.00
ACGTcount: A:0.18, C:0.02, G:0.39, T:0.41
Consensus pattern (18 bp):
ATTGGGTTGGGTTGAATA
Found at i:16328827 original size:30 final size:30
Alignment explanation
Indices: 16328793--16328855 Score: 108
Period size: 30 Copynumber: 2.1 Consensus size: 30
16328783 ACTTAACAAG
16328793 CAAATGCCTCTAAAATAATAACAAAATTAA
1 CAAATGCCTCTAAAATAATAACAAAATTAA
* *
16328823 CAAATGTCTTTAAAATAATAACAAAATTAA
1 CAAATGCCTCTAAAATAATAACAAAATTAA
16328853 CAA
1 CAA
16328856 TAAAATAAGT
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
30 31 1.00
ACGTcount: A:0.57, C:0.14, G:0.03, T:0.25
Consensus pattern (30 bp):
CAAATGCCTCTAAAATAATAACAAAATTAA
Found at i:16334409 original size:19 final size:20
Alignment explanation
Indices: 16334387--16334428 Score: 59
Period size: 19 Copynumber: 2.1 Consensus size: 20
16334377 CCAATTTAAA
*
16334387 AAAAAAAAAGAACAA-CAAC
1 AAAAAAAAAGAAAAATCAAC
*
16334406 AAAAACAAAGAAAAATCAAC
1 AAAAAAAAAGAAAAATCAAC
16334426 AAA
1 AAA
16334429 GATGAAAGGA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
19 13 0.65
20 7 0.35
ACGTcount: A:0.79, C:0.14, G:0.05, T:0.02
Consensus pattern (20 bp):
AAAAAAAAAGAAAAATCAAC
Found at i:16347186 original size:27 final size:28
Alignment explanation
Indices: 16347156--16347224 Score: 69
Period size: 24 Copynumber: 2.7 Consensus size: 28
16347146 GTTAATTATC
16347156 CGAA-TTTGAACCAAATTAACCAATAAT
1 CGAACTTTGAACCAAATTAACCAATAAT
* *
16347183 CGAACTTTGAA--AAA--AATCATTAAT
1 CGAACTTTGAACCAAATTAACCAATAAT
*
16347207 CGAATTTTG-ACCAAATTA
1 CGAACTTTGAACCAAATTA
16347225 GATCGGTTAA
Statistics
Matches: 34, Mismatches: 3, Indels: 10
0.72 0.06 0.21
Matches are distributed among these distances:
23 1 0.03
24 16 0.47
25 3 0.09
26 3 0.09
27 5 0.15
28 6 0.18
ACGTcount: A:0.46, C:0.16, G:0.09, T:0.29
Consensus pattern (28 bp):
CGAACTTTGAACCAAATTAACCAATAAT
Found at i:16351782 original size:22 final size:22
Alignment explanation
Indices: 16351755--16351801 Score: 94
Period size: 22 Copynumber: 2.1 Consensus size: 22
16351745 TTAATAGCTT
16351755 TTTAGTTTCAGTGCATTTATAG
1 TTTAGTTTCAGTGCATTTATAG
16351777 TTTAGTTTCAGTGCATTTATAG
1 TTTAGTTTCAGTGCATTTATAG
16351799 TTT
1 TTT
16351802 TTCTTACTTT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 25 1.00
ACGTcount: A:0.21, C:0.09, G:0.17, T:0.53
Consensus pattern (22 bp):
TTTAGTTTCAGTGCATTTATAG
Found at i:16352288 original size:3 final size:3
Alignment explanation
Indices: 16352280--16352312 Score: 66
Period size: 3 Copynumber: 11.0 Consensus size: 3
16352270 ATTGATTACT
16352280 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
16352313 GCACTTCTGT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 30 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
TAA
Found at i:16353997 original size:24 final size:24
Alignment explanation
Indices: 16353909--16354090 Score: 80
Period size: 25 Copynumber: 7.3 Consensus size: 24
16353899 ACATAAACAA
* * * *
16353909 GAAGCTCTTTCGAGCCATAACACAG
1 GAAGCTCATACGAGCCATTA-ACGG
* *
16353934 GAAGCTCATGCAAGCCATGTAACGG
1 GAAGCTCATACGAGCCAT-TAACGG
*
16353959 GAAGCTC-TAGAGAGCCATTAACGG
1 GAAGCTCATA-CGAGCCATTAACGG
* * * *
16353983 GAATCTCATACGAGCCAATATCAGA
1 GAAGCTCATACGAGCCATTAAC-GG
* * * *
16354008 AAAGTTCA-AGCGAGCCAATATCGG
1 GAAGCTCATA-CGAGCCATTAACGG
* ** *
16354032 GAAGTTCCGAAGAGCCATTAATCGG
1 GAAGCTCATACGAGCCATTAA-CGG
* * *
16354057 GAAGCTCACAATGAGCCTTTAATCGG
1 GAAGCTCA-TACGAGCCATTAA-CGG
16354083 GAAGCTCA
1 GAAGCTCA
16354091 CGAAGAGCCA
Statistics
Matches: 122, Mismatches: 27, Indels: 15
0.74 0.16 0.09
Matches are distributed among these distances:
24 38 0.31
25 61 0.50
26 23 0.19
ACGTcount: A:0.34, C:0.23, G:0.24, T:0.19
Consensus pattern (24 bp):
GAAGCTCATACGAGCCATTAACGG
Found at i:16354078 original size:26 final size:26
Alignment explanation
Indices: 16354019--16354101 Score: 109
Period size: 26 Copynumber: 3.3 Consensus size: 26
16354009 AAGTTCAAGC
* *
16354019 GAGCCAAT-ATCGGGAAGTTC-CGAA
1 GAGCCATTAATCGGGAAGCTCACGAA
16354043 GAGCCATTAATCGGGAAGCTCAC-AA
1 GAGCCATTAATCGGGAAGCTCACGAA
*
16354068 TGAGCCTTTAATCGGGAAGCTCACGAA
1 -GAGCCATTAATCGGGAAGCTCACGAA
16354095 GAGCCAT
1 GAGCCAT
16354102 ATATCGAGAC
Statistics
Matches: 51, Mismatches: 4, Indels: 6
0.84 0.07 0.10
Matches are distributed among these distances:
24 7 0.14
25 13 0.25
26 29 0.57
27 2 0.04
ACGTcount: A:0.33, C:0.23, G:0.27, T:0.18
Consensus pattern (26 bp):
GAGCCATTAATCGGGAAGCTCACGAA
Found at i:16356828 original size:42 final size:42
Alignment explanation
Indices: 16356769--16356860 Score: 139
Period size: 42 Copynumber: 2.2 Consensus size: 42
16356759 CGTCCATACG
* * * *
16356769 GGCGTGTGTCTCATTCGTGTGTGACATATGGCCTAGCATATA
1 GGCGTGTGTCTCATTCGTGCGTGACACACGGCCTAGCACATA
16356811 GGCGTGTGTCTCATTCGTGCGTGACACACGGCCTAGCACATA
1 GGCGTGTGTCTCATTCGTGCGTGACACACGGCCTAGCACATA
*
16356853 GACGTGTG
1 GGCGTGTG
16356861 GTCTGGTCGT
Statistics
Matches: 45, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
42 45 1.00
ACGTcount: A:0.18, C:0.23, G:0.30, T:0.28
Consensus pattern (42 bp):
GGCGTGTGTCTCATTCGTGCGTGACACACGGCCTAGCACATA
Found at i:16357502 original size:14 final size:14
Alignment explanation
Indices: 16357483--16357523 Score: 82
Period size: 14 Copynumber: 2.9 Consensus size: 14
16357473 TAGGTGATAT
16357483 GTGTGAAAAATTTC
1 GTGTGAAAAATTTC
16357497 GTGTGAAAAATTTC
1 GTGTGAAAAATTTC
16357511 GTGTGAAAAATTT
1 GTGTGAAAAATTT
16357524 ATTGTTTATG
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 27 1.00
ACGTcount: A:0.37, C:0.05, G:0.22, T:0.37
Consensus pattern (14 bp):
GTGTGAAAAATTTC
Found at i:16357969 original size:19 final size:19
Alignment explanation
Indices: 16357941--16358003 Score: 54
Period size: 22 Copynumber: 3.1 Consensus size: 19
16357931 CCATGCCTCA
*
16357941 ATTTTAAAATTTTATTATG
1 ATTTTGAAATTTTATTATG
*
16357960 ATTTTGAAATGTGTCATTGATG
1 ATTTTGAAAT-T-TTATT-ATG
* *
16357982 ATTTTGTAAGTTTTGTTATG
1 ATTTTG-AAATTTTATTATG
16358002 AT
1 AT
16358004 AGTTGATGAA
Statistics
Matches: 35, Mismatches: 5, Indels: 7
0.74 0.11 0.15
Matches are distributed among these distances:
19 9 0.26
20 6 0.17
21 7 0.20
22 10 0.29
23 3 0.09
ACGTcount: A:0.29, C:0.02, G:0.16, T:0.54
Consensus pattern (19 bp):
ATTTTGAAATTTTATTATG
Found at i:16366347 original size:16 final size:16
Alignment explanation
Indices: 16366326--16366360 Score: 54
Period size: 16 Copynumber: 2.2 Consensus size: 16
16366316 AAAAATATCA
16366326 TCTTTTCTA-TTTTCTT
1 TCTTTT-TATTTTTCTT
16366342 TCTTTTTATTTTTCTT
1 TCTTTTTATTTTTCTT
16366358 TCT
1 TCT
16366361 AACCAATCAC
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
15 2 0.11
16 16 0.89
ACGTcount: A:0.06, C:0.17, G:0.00, T:0.77
Consensus pattern (16 bp):
TCTTTTTATTTTTCTT
Found at i:16369732 original size:76 final size:76
Alignment explanation
Indices: 16369606--16369757 Score: 295
Period size: 76 Copynumber: 2.0 Consensus size: 76
16369596 GCGAAACAGA
16369606 AAGAAATTTCTCCCAAGAATGAATTCACTTAAAACGATTGATTTGAAGGTTGTTTTTCTCGACAA
1 AAGAAATTTCTCCCAAGAATGAATTCACTTAAAACGATTGATTTGAAGGTTGTTTTTCTCGACAA
16369671 GATTTAAATGT
66 GATTTAAATGT
16369682 AAGAAATTTCTCCCAAGAATGAATTCACTTAAAACGATTGATTTGAAGGTTGTTTTTCTCGACAA
1 AAGAAATTTCTCCCAAGAATGAATTCACTTAAAACGATTGATTTGAAGGTTGTTTTTCTCGACAA
*
16369747 GATTTGAATGT
66 GATTTAAATGT
16369758 TCAAAACGTA
Statistics
Matches: 75, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
76 75 1.00
ACGTcount: A:0.35, C:0.13, G:0.16, T:0.36
Consensus pattern (76 bp):
AAGAAATTTCTCCCAAGAATGAATTCACTTAAAACGATTGATTTGAAGGTTGTTTTTCTCGACAA
GATTTAAATGT
Found at i:16371122 original size:3 final size:3
Alignment explanation
Indices: 16371114--16371138 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
16371104 ATACGAACAG
16371114 AGA AGA AGA AGA AGA AGA AGA AGA A
1 AGA AGA AGA AGA AGA AGA AGA AGA A
16371139 ACGAGGCGTT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.68, C:0.00, G:0.32, T:0.00
Consensus pattern (3 bp):
AGA
Found at i:16373275 original size:31 final size:32
Alignment explanation
Indices: 16373237--16373299 Score: 101
Period size: 32 Copynumber: 2.0 Consensus size: 32
16373227 ATCAGAACAA
*
16373237 GCAAGGCCT-GGGAAGGGCGAAGCCAAAAATT
1 GCAAGGCCTGGGGAAGGGCGAAGCAAAAAATT
*
16373268 GCAAGGCCTGGGGAAGGGTGAAGCAAAAAATT
1 GCAAGGCCTGGGGAAGGGCGAAGCAAAAAATT
16373300 TATTGTGTAA
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
31 9 0.31
32 20 0.69
ACGTcount: A:0.37, C:0.16, G:0.37, T:0.11
Consensus pattern (32 bp):
GCAAGGCCTGGGGAAGGGCGAAGCAAAAAATT
Found at i:16373889 original size:28 final size:28
Alignment explanation
Indices: 16373849--16373906 Score: 116
Period size: 28 Copynumber: 2.1 Consensus size: 28
16373839 AACAGATGAG
16373849 TTTGTGTCGGCACCCTGTAGAAGGAAAA
1 TTTGTGTCGGCACCCTGTAGAAGGAAAA
16373877 TTTGTGTCGGCACCCTGTAGAAGGAAAA
1 TTTGTGTCGGCACCCTGTAGAAGGAAAA
16373905 TT
1 TT
16373907 CTTGTTGATA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 30 1.00
ACGTcount: A:0.28, C:0.17, G:0.28, T:0.28
Consensus pattern (28 bp):
TTTGTGTCGGCACCCTGTAGAAGGAAAA
Found at i:16378107 original size:24 final size:25
Alignment explanation
Indices: 16378080--16378127 Score: 62
Period size: 24 Copynumber: 2.0 Consensus size: 25
16378070 AAGAGGAAAG
16378080 TTTAAAAAACATAAAA-GAAAAAAA
1 TTTAAAAAACATAAAACGAAAAAAA
** *
16378104 TTTAAATTACTTAAAACGAAAAAA
1 TTTAAAAAACATAAAACGAAAAAA
16378128 TATGGGGATC
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
24 13 0.65
25 7 0.35
ACGTcount: A:0.67, C:0.06, G:0.04, T:0.23
Consensus pattern (25 bp):
TTTAAAAAACATAAAACGAAAAAAA
Found at i:16387533 original size:18 final size:20
Alignment explanation
Indices: 16387512--16387549 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 20
16387502 TCATTGGAAT
16387512 ATTTAA-TA-TATTATTTTA
1 ATTTAACTACTATTATTTTA
16387530 ATTTAACTTACTATTATTTT
1 ATTTAAC-TACTATTATTTT
16387550 TATCATATCT
Statistics
Matches: 17, Mismatches: 0, Indels: 3
0.85 0.00 0.15
Matches are distributed among these distances:
18 6 0.35
20 2 0.12
21 9 0.53
ACGTcount: A:0.34, C:0.05, G:0.00, T:0.61
Consensus pattern (20 bp):
ATTTAACTACTATTATTTTA
Found at i:16388624 original size:43 final size:43
Alignment explanation
Indices: 16388397--16388598 Score: 323
Period size: 43 Copynumber: 4.7 Consensus size: 43
16388387 TTTTTAAAAA
*
16388397 AAACGCCGCTAAAGACCAAGACCTTTAGCGACGCTTCTCCCAC
1 AAACGCCGCTAAAGACCAAGACCTTTAGCGGCGCTTCTCCCAC
* *
16388440 CAACGCCGCTAAAGTCCAAGACCTTTAGCGGCGCTTCTCCCAC
1 AAACGCCGCTAAAGACCAAGACCTTTAGCGGCGCTTCTCCCAC
* *
16388483 AAACGCCGCTAAAGACCGAGACCTTTAGCGGCGCTTCTACCAC
1 AAACGCCGCTAAAGACCAAGACCTTTAGCGGCGCTTCTCCCAC
* *
16388526 AAACGCCGCTAAAGACCAAGACCTTTAGCGGCGCTTTTCCTAC
1 AAACGCCGCTAAAGACCAAGACCTTTAGCGGCGCTTCTCCCAC
* *
16388569 AAACGCTGCTAAAGACCATGACCTTTAGCG
1 AAACGCCGCTAAAGACCAAGACCTTTAGCG
16388599 ACGTTTTTGC
Statistics
Matches: 146, Mismatches: 13, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
43 146 1.00
ACGTcount: A:0.28, C:0.35, G:0.19, T:0.18
Consensus pattern (43 bp):
AAACGCCGCTAAAGACCAAGACCTTTAGCGGCGCTTCTCCCAC
Found at i:16388681 original size:22 final size:24
Alignment explanation
Indices: 16388655--16388698 Score: 65
Period size: 22 Copynumber: 1.9 Consensus size: 24
16388645 TTGTTTTAAT
16388655 TAAATAATAT-TTAT-TTTTATGA
1 TAAATAATATATTATGTTTTATGA
*
16388677 TAAATATTATATTATGTTTTAT
1 TAAATAATATATTATGTTTTAT
16388699 TTTTTAAATT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
22 9 0.47
23 4 0.21
24 6 0.32
ACGTcount: A:0.39, C:0.00, G:0.05, T:0.57
Consensus pattern (24 bp):
TAAATAATATATTATGTTTTATGA
Found at i:16392109 original size:11 final size:11
Alignment explanation
Indices: 16392093--16392117 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
16392083 GGAGAGCTTT
16392093 GGAGACGGAAA
1 GGAGACGGAAA
16392104 GGAGACGGAAA
1 GGAGACGGAAA
16392115 GGA
1 GGA
16392118 TCGAAGAACT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.44, C:0.08, G:0.48, T:0.00
Consensus pattern (11 bp):
GGAGACGGAAA
Found at i:16392994 original size:83 final size:81
Alignment explanation
Indices: 16392907--16393063 Score: 192
Period size: 81 Copynumber: 1.9 Consensus size: 81
16392897 AACCACAAAC
* *
16392907 CCCAA-ACCCTTAACTACTAACCTATAAACCTTATTTAATATATAAATTAAAAAACACTAATTAA
1 CCCAAGACCC-TAACCACTAACCCATAAACCTTATTT-A-ATATAAATTAAAAAACACTAATTAA
16392971 -TCTAAACCCTAAACCTTAT
63 CT-TAAACCCTAAACCTTAT
* * * * * *
16392990 CCCAAGTCCCTAACCCCTAACCCCTAAACCTTATTTAATATAGATTAAAACATACTAATTAACTT
1 CCCAAGACCCTAACCACTAACCCATAAACCTTATTTAATATAAATTAAAAAACACTAATTAACTT
16393055 AAACCCTAA
66 AAACCCTAA
16393064 GTCTTAACCT
Statistics
Matches: 64, Mismatches: 8, Indels: 6
0.82 0.10 0.08
Matches are distributed among these distances:
81 32 0.50
82 2 0.03
83 27 0.42
84 3 0.05
ACGTcount: A:0.43, C:0.27, G:0.01, T:0.29
Consensus pattern (81 bp):
CCCAAGACCCTAACCACTAACCCATAAACCTTATTTAATATAAATTAAAAAACACTAATTAACTT
AAACCCTAAACCTTAT
Found at i:16394418 original size:17 final size:17
Alignment explanation
Indices: 16394385--16394418 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
16394375 GTTTATAGTC
*
16394385 TTTATATTATGTTATTT
1 TTTATATTATGTAATTT
*
16394402 TTTATATTTTGTAATTT
1 TTTATATTATGTAATTT
16394419 AAAACACATA
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:0.24, C:0.00, G:0.06, T:0.71
Consensus pattern (17 bp):
TTTATATTATGTAATTT
Found at i:16398913 original size:73 final size:72
Alignment explanation
Indices: 16398836--16399009 Score: 170
Period size: 73 Copynumber: 2.4 Consensus size: 72
16398826 TGTATAATGA
* * *
16398836 GAAGCTCATAAGAGCCATAATCGGGAAGCTCATGCGAGCCAATAACGAGTAGCTCCAAATAGCCA
1 GAAGCTCATAAGAGCCATAATCGGGAAGCTCAAGCGAGCC-ATAACGAGAAGCTCCAAAGAGCCA
16398901 TTAATCAG
65 TTAATCAG
* * * * * * * **
16398909 GAAGCT-TTAGATAGACATATATCGGGAAGTTCAAGTGAGCCATATCGGGAAGCTCCGGAGAGCC
1 GAAGCTCATA-AGAGCCATA-ATCGGGAAGCTCAAGCGAGCCATAACGAGAAGCTCCAAAGAGCC
16398973 ATTAATCAG
64 ATTAATCAG
* *
16398982 GAAGCTCACGAAGAGCCATTTATCGGGA
1 GAAGCTCA-TAAGAGCCA-TAATCGGGA
16399010 CACTCATAAG
Statistics
Matches: 79, Mismatches: 17, Indels: 9
0.75 0.16 0.09
Matches are distributed among these distances:
72 2 0.03
73 45 0.57
74 30 0.38
75 2 0.03
ACGTcount: A:0.34, C:0.21, G:0.25, T:0.20
Consensus pattern (72 bp):
GAAGCTCATAAGAGCCATAATCGGGAAGCTCAAGCGAGCCATAACGAGAAGCTCCAAAGAGCCAT
TAATCAG
Found at i:16399015 original size:26 final size:26
Alignment explanation
Indices: 16398951--16399009 Score: 84
Period size: 26 Copynumber: 2.3 Consensus size: 26
16398941 AAGTGAGCCA
*
16398951 TATCGGGAAGCTC-CGGAGAGCCATT
1 TATCGGGAAGCTCACGAAGAGCCATT
* *
16398976 AATCAGGAAGCTCACGAAGAGCCATT
1 TATCGGGAAGCTCACGAAGAGCCATT
16399002 TATCGGGA
1 TATCGGGA
16399010 CACTCATAAG
Statistics
Matches: 28, Mismatches: 5, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
25 11 0.39
26 17 0.61
ACGTcount: A:0.31, C:0.22, G:0.29, T:0.19
Consensus pattern (26 bp):
TATCGGGAAGCTCACGAAGAGCCATT
Found at i:16399117 original size:25 final size:25
Alignment explanation
Indices: 16399083--16399146 Score: 83
Period size: 25 Copynumber: 2.6 Consensus size: 25
16399073 GAAGAGCTAT
* * *
16399083 TAACGGGAAGCTCGTAATAACCATA
1 TAACGAGAAGCTCGCAAGAACCATA
*
16399108 TAACGAGAAGCTTGCAAGAACCATA
1 TAACGAGAAGCTCGCAAGAACCATA
*
16399133 TAACGAGGAGCTCG
1 TAACGAGAAGCTCG
16399147 AGAGGGCCAA
Statistics
Matches: 33, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
25 33 1.00
ACGTcount: A:0.39, C:0.20, G:0.23, T:0.17
Consensus pattern (25 bp):
TAACGAGAAGCTCGCAAGAACCATA
Found at i:16403758 original size:20 final size:20
Alignment explanation
Indices: 16403721--16403759 Score: 55
Period size: 18 Copynumber: 2.0 Consensus size: 20
16403711 AGTCTATATA
*
16403721 TATATGTATATTTATTTTTT
1 TATATGTACATTTATTTTTT
16403741 TATATGTACA--TATTTTTT
1 TATATGTACATTTATTTTTT
16403759 T
1 T
16403760 CAACTAATAT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
18 9 0.50
20 9 0.50
ACGTcount: A:0.26, C:0.03, G:0.05, T:0.67
Consensus pattern (20 bp):
TATATGTACATTTATTTTTT
Found at i:16404610 original size:9 final size:9
Alignment explanation
Indices: 16404595--16404654 Score: 93
Period size: 9 Copynumber: 6.7 Consensus size: 9
16404585 GTATTTTTCA
16404595 GTAATTCGG
1 GTAATTCGG
*
16404604 TTAATTCGG
1 GTAATTCGG
*
16404613 TTAATTCGG
1 GTAATTCGG
16404622 GTAATTCGG
1 GTAATTCGG
16404631 GTAATTCGG
1 GTAATTCGG
*
16404640 GTAATTCGA
1 GTAATTCGG
16404649 GTAATT
1 GTAATT
16404655 TTTAACCAAA
Statistics
Matches: 48, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
9 48 1.00
ACGTcount: A:0.25, C:0.10, G:0.27, T:0.38
Consensus pattern (9 bp):
GTAATTCGG
Found at i:16404831 original size:12 final size:12
Alignment explanation
Indices: 16404814--16404838 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
16404804 AGTAATTTCG
16404814 GGTCGGTTAACC
1 GGTCGGTTAACC
16404826 GGTCGGTTAACC
1 GGTCGGTTAACC
16404838 G
1 G
16404839 AATGAACACC
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.16, C:0.24, G:0.36, T:0.24
Consensus pattern (12 bp):
GGTCGGTTAACC
Found at i:16409363 original size:43 final size:41
Alignment explanation
Indices: 16409295--16409375 Score: 108
Period size: 43 Copynumber: 1.9 Consensus size: 41
16409285 AAAACACATA
* *
16409295 TATCACATACAATGCCATATCCCAAATATGGTCTTACATGT
1 TATCACATACAATGCCATATCCCAAACAGGGTCTTACATGT
* *
16409336 TATCACATATCGATGCCTGTATCCCAAACAGGGTCTTACA
1 TATCACATA-CAATGCC-ATATCCCAAACAGGGTCTTACA
16409376 CGAATCATAT
Statistics
Matches: 34, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
41 9 0.26
42 6 0.18
43 19 0.56
ACGTcount: A:0.32, C:0.26, G:0.12, T:0.30
Consensus pattern (41 bp):
TATCACATACAATGCCATATCCCAAACAGGGTCTTACATGT
Found at i:16409449 original size:43 final size:43
Alignment explanation
Indices: 16409322--16409466 Score: 145
Period size: 43 Copynumber: 3.4 Consensus size: 43
16409312 TATCCCAAAT
* * * ** * * *
16409322 ATGGTCTTACATGTTATCACATATCGATGCCTGTATCCCAAAC
1 ATGGTCTTACACGTAATCTCATATCGATGCCAATGTCCTAGAC
* *
16409365 AGGGTCTTACACG-AA--TCATATACGGTGCCAATGT-CTCAGAC
1 ATGGTCTTACACGTAATCTCATAT-CGATGCCAATGTCCT-AGAC
16409406 ATGGTCTTACACGTAATCTCATATCGATGCCAATGTCCTAGAC
1 ATGGTCTTACACGTAATCTCATATCGATGCCAATGTCCTAGAC
*
16409449 ATGGTCTTACACGAAATC
1 ATGGTCTTACACGTAATC
16409467 ACACCTCAAA
Statistics
Matches: 83, Mismatches: 13, Indels: 12
0.77 0.12 0.11
Matches are distributed among these distances:
40 6 0.07
41 23 0.28
42 3 0.04
43 43 0.52
44 8 0.10
ACGTcount: A:0.29, C:0.25, G:0.17, T:0.29
Consensus pattern (43 bp):
ATGGTCTTACACGTAATCTCATATCGATGCCAATGTCCTAGAC
Found at i:16410986 original size:102 final size:102
Alignment explanation
Indices: 16410854--16411055 Score: 325
Period size: 102 Copynumber: 2.0 Consensus size: 102
16410844 CCAATGAGTA
* * * *
16410854 GGGGAATCAGCACTTAGCGACCTCTTTCACATTTAAGATACGGTGGGATCAGCACTTAGAAACCA
1 GGGGAATCAGCACTTAGCAACCCCCTTCACATTTAAGATACGGTGGAATCAGCACTTAGAAACCA
* *
16410919 CCAATGATTCGGGGAATTAGA-ACTTAGCAACCCCTCG
66 CCAATGAGTCGGGGAATCA-ACACTTAGCAACCCCTCG
*
16410956 GGGGAATCAGCACTTAGCAACCCCCTTCACATTTAAGATACGGTGGAATCAGCACTTAGCAACCA
1 GGGGAATCAGCACTTAGCAACCCCCTTCACATTTAAGATACGGTGGAATCAGCACTTAGAAACCA
16411021 CCAATGAGTCGGGGAATCAACACTTAGCAACCCCT
66 CCAATGAGTCGGGGAATCAACACTTAGCAACCCCT
16411056 TTCACATTTA
Statistics
Matches: 92, Mismatches: 7, Indels: 2
0.91 0.07 0.02
Matches are distributed among these distances:
101 1 0.01
102 91 0.99
ACGTcount: A:0.31, C:0.27, G:0.21, T:0.21
Consensus pattern (102 bp):
GGGGAATCAGCACTTAGCAACCCCCTTCACATTTAAGATACGGTGGAATCAGCACTTAGAAACCA
CCAATGAGTCGGGGAATCAACACTTAGCAACCCCTCG
Found at i:16411017 original size:42 final size:42
Alignment explanation
Indices: 16410958--16411094 Score: 175
Period size: 42 Copynumber: 3.5 Consensus size: 42
16410948 ACCCCTCGGG
16410958 GGAATCAGCACTTAGCAACCCCCTTCACATTTAAGATACGGT
1 GGAATCAGCACTTAGCAACCCCCTTCACATTTAAGATACGGT
* *
16411000 GGAATCAGCACTTAGCAA-CCAC--CA-A--TGAG-T-CGG-
1 GGAATCAGCACTTAGCAACCCCCTTCACATTTAAGATACGGT
* *
16411033 GGAATCAACACTTAGCAACCCCTTTCACATTTAAGATACGGT
1 GGAATCAGCACTTAGCAACCCCCTTCACATTTAAGATACGGT
16411075 GGAATCAGCACTTAGCAACC
1 GGAATCAGCACTTAGCAACC
16411095 ACCAACGAAT
Statistics
Matches: 79, Mismatches: 7, Indels: 18
0.76 0.07 0.17
Matches are distributed among these distances:
33 17 0.22
34 5 0.06
35 1 0.01
36 5 0.06
37 1 0.01
38 1 0.01
39 5 0.06
40 1 0.01
41 6 0.08
42 37 0.47
ACGTcount: A:0.33, C:0.28, G:0.18, T:0.21
Consensus pattern (42 bp):
GGAATCAGCACTTAGCAACCCCCTTCACATTTAAGATACGGT
Found at i:16411048 original size:75 final size:75
Alignment explanation
Indices: 16410956--16411132 Score: 318
Period size: 75 Copynumber: 2.4 Consensus size: 75
16410946 CAACCCCTCG
16410956 GGGGAATCAGCACTTAGCAACCCCCTTCACATTTAAGATACGGTGGAATCAGCACTTAGCAACCA
1 GGGGAATCAGCACTTAGCAACCCCCTTCACATTTAAGATACGGTGGAATCAGCACTTAGCAACCA
* *
16411021 CCAATGAGTC
66 CCAACGAATC
* *
16411031 GGGGAATCAACACTTAGCAACCCCTTTCACATTTAAGATACGGTGGAATCAGCACTTAGCAACCA
1 GGGGAATCAGCACTTAGCAACCCCCTTCACATTTAAGATACGGTGGAATCAGCACTTAGCAACCA
16411096 CCAACGAATC
66 CCAACGAATC
16411106 GGGGAATCAGCACTTAGCAACCCCCTT
1 GGGGAATCAGCACTTAGCAACCCCCTT
16411133 TATATTCAAT
Statistics
Matches: 96, Mismatches: 6, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
75 96 1.00
ACGTcount: A:0.32, C:0.29, G:0.19, T:0.20
Consensus pattern (75 bp):
GGGGAATCAGCACTTAGCAACCCCCTTCACATTTAAGATACGGTGGAATCAGCACTTAGCAACCA
CCAACGAATC
Found at i:16411492 original size:30 final size:30
Alignment explanation
Indices: 16411458--16411515 Score: 80
Period size: 30 Copynumber: 1.9 Consensus size: 30
16411448 TAGTCCTCCA
*
16411458 CCCAAATTTTTGAAAAATTACAATTTTGCC
1 CCCAAACTTTTGAAAAATTACAATTTTGCC
* * *
16411488 CCCAAACTTTTGAATATTTACACTTTTG
1 CCCAAACTTTTGAAAAATTACAATTTTG
16411516 TCCCTAAGCT
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
30 24 1.00
ACGTcount: A:0.33, C:0.21, G:0.07, T:0.40
Consensus pattern (30 bp):
CCCAAACTTTTGAAAAATTACAATTTTGCC
Found at i:16413149 original size:10 final size:10
Alignment explanation
Indices: 16413134--16413159 Score: 52
Period size: 10 Copynumber: 2.6 Consensus size: 10
16413124 AATTTATTTT
16413134 AAAAATTAAA
1 AAAAATTAAA
16413144 AAAAATTAAA
1 AAAAATTAAA
16413154 AAAAAT
1 AAAAAT
16413160 AAATATATTT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 16 1.00
ACGTcount: A:0.81, C:0.00, G:0.00, T:0.19
Consensus pattern (10 bp):
AAAAATTAAA
Found at i:16416253 original size:45 final size:46
Alignment explanation
Indices: 16416186--16416309 Score: 200
Period size: 46 Copynumber: 2.8 Consensus size: 46
16416176 CATATGACCT
*
16416186 CTTATCAC-TTGTC-CTTGATCAGATAAGTGTAGCT-AGGCTACCA
1 CTTATCACTTTGTCACTTGATCAGATAAGTGTAGCTGAAGCTACCA
*
16416229 CTTATCACTTTGCCACTTGATCAGATAAGTGTAGCTGAAGCTACCA
1 CTTATCACTTTGTCACTTGATCAGATAAGTGTAGCTGAAGCTACCA
*
16416275 CTTATCACTTTATCACTTGATCAGATAAGTGTAGC
1 CTTATCACTTTGTCACTTGATCAGATAAGTGTAGC
16416310 CACTTATCAC
Statistics
Matches: 74, Mismatches: 4, Indels: 3
0.91 0.05 0.04
Matches are distributed among these distances:
43 8 0.11
44 4 0.05
45 21 0.28
46 41 0.55
ACGTcount: A:0.27, C:0.23, G:0.17, T:0.33
Consensus pattern (46 bp):
CTTATCACTTTGTCACTTGATCAGATAAGTGTAGCTGAAGCTACCA
Found at i:16416292 original size:46 final size:45
Alignment explanation
Indices: 16416186--16416381 Score: 203
Period size: 37 Copynumber: 4.7 Consensus size: 45
16416176 CATATGACCT
*
16416186 CTTATCAC-TTGTC-CTTGATCAGATAAGTGTAGCTAGGCTACCA
1 CTTATCACTTTGTCACTTGATCAGATAAGTGTAGCTAAGCTACCA
*
16416229 CTTATCACTTTGCCACTTGATCAGATAAGTGTAGCTGAAGCTACCA
1 CTTATCACTTTGTCACTTGATCAGATAAGTGTAGCT-AAGCTACCA
*
16416275 CTTATCACTTTATCACTTGATCAGATAA--GT-G-T-AG---CCA
1 CTTATCACTTTGTCACTTGATCAGATAAGTGTAGCTAAGCTACCA
*
16416312 CTTATCACTTTGTCTCTTGATCAGATAA--GT-G-T-A---ACCA
1 CTTATCACTTTGTCACTTGATCAGATAAGTGTAGCTAAGCTACCA
**
16416349 CTTATCACTTTGTTTCTTGATCAGATAAGTGTA
1 CTTATCACTTTGTCACTTGATCAGATAAGTGTA
16416382 ACCACTTATC
Statistics
Matches: 139, Mismatches: 7, Indels: 17
0.85 0.04 0.10
Matches are distributed among these distances:
37 64 0.46
39 2 0.01
40 2 0.01
42 1 0.01
43 9 0.06
44 6 0.04
45 21 0.15
46 34 0.24
ACGTcount: A:0.27, C:0.21, G:0.16, T:0.36
Consensus pattern (45 bp):
CTTATCACTTTGTCACTTGATCAGATAAGTGTAGCTAAGCTACCA
Found at i:16416313 original size:37 final size:37
Alignment explanation
Indices: 16416271--16416410 Score: 235
Period size: 37 Copynumber: 3.8 Consensus size: 37
16416261 AGCTGAAGCT
* *
16416271 ACCACTTATCACTTTATCACTTGATCAGATAAGTGTA
1 ACCACTTATCACTTTGTCTCTTGATCAGATAAGTGTA
*
16416308 GCCACTTATCACTTTGTCTCTTGATCAGATAAGTGTA
1 ACCACTTATCACTTTGTCTCTTGATCAGATAAGTGTA
*
16416345 ACCACTTATCACTTTGTTTCTTGATCAGATAAGTGTA
1 ACCACTTATCACTTTGTCTCTTGATCAGATAAGTGTA
*
16416382 ACCACTTATCACTTTGTTTCTTGATCAGA
1 ACCACTTATCACTTTGTCTCTTGATCAGA
16416411 AGTACTCAAA
Statistics
Matches: 98, Mismatches: 5, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
37 98 1.00
ACGTcount: A:0.27, C:0.21, G:0.13, T:0.39
Consensus pattern (37 bp):
ACCACTTATCACTTTGTCTCTTGATCAGATAAGTGTA
Found at i:16417763 original size:26 final size:26
Alignment explanation
Indices: 16417733--16417805 Score: 76
Period size: 26 Copynumber: 2.8 Consensus size: 26
16417723 GCAACTCTTA
*
16417733 TGAGCGTCCCG-TTATATGGCTCTTCG
1 TGAGCGTCCCGATTA-AAGGCTCTTCG
* *
16417759 TGAGCTTCCCGATTAAAGGCTCTTTG
1 TGAGCGTCCCGATTAAAGGCTCTTCG
* * *
16417785 TGAGCTTCCTGATTAATGGCT
1 TGAGCGTCCCGATTAAAGGCT
16417806 TTCCGGAGCT
Statistics
Matches: 41, Mismatches: 5, Indels: 2
0.85 0.10 0.04
Matches are distributed among these distances:
26 38 0.93
27 3 0.07
ACGTcount: A:0.16, C:0.23, G:0.25, T:0.36
Consensus pattern (26 bp):
TGAGCGTCCCGATTAAAGGCTCTTCG
Found at i:16420016 original size:21 final size:21
Alignment explanation
Indices: 16419992--16420171 Score: 121
Period size: 21 Copynumber: 8.6 Consensus size: 21
16419982 GAAGCCCGAA
* * *
16419992 AGCTGAACATAAGCTCATAAG
1 AGCTGAACAGAAACCCATAAG
*
16420013 AGCTAAACAGAAACCCATAAG
1 AGCTGAACAGAAACCCATAAG
* * * **
16420034 GGTTGAACAGAAGCTTATAAG
1 AGCTGAACAGAAACCCATAAG
*
16420055 AGCTGAATAGAAACCCATAAG
1 AGCTGAACAGAAACCCATAAG
16420076 AGCTGAACAGAAA-CCATAAG
1 AGCTGAACAGAAACCCATAAG
* * * * *
16420096 GGTTGAATAGAAGCTCGA-AAG
1 AGCTGAACAGAAAC-CCATAAG
* * *
16420117 AGTTGAACAGAAACTCATATG
1 AGCTGAACAGAAACCCATAAG
* * * * *
16420138 AGTTAAATAGAAACTCGTAAG
1 AGCTGAACAGAAACCCATAAG
*
16420159 AGCTAAACAGAAA
1 AGCTGAACAGAAA
16420172 GTAAAACATA
Statistics
Matches: 122, Mismatches: 34, Indels: 6
0.75 0.21 0.04
Matches are distributed among these distances:
20 17 0.14
21 103 0.84
22 2 0.02
ACGTcount: A:0.46, C:0.16, G:0.21, T:0.17
Consensus pattern (21 bp):
AGCTGAACAGAAACCCATAAG
Found at i:16420048 original size:42 final size:42
Alignment explanation
Indices: 16419992--16420170 Score: 146
Period size: 42 Copynumber: 4.3 Consensus size: 42
16419982 GAAGCCCGAA
*
16419992 AGCTGAACATAAGCTCATAAGAGCTAAACAGAAACCCATAAG
1 AGCTGAACAGAAGCTCATAAGAGCTAAACAGAAACCCATAAG
* * * * *
16420034 GGTTGAACAGAAGCTTATAAGAGCTGAATAGAAACCCATAAG
1 AGCTGAACAGAAGCTCATAAGAGCTAAACAGAAACCCATAAG
* * * * * * *
16420076 AGCTGAACAGAAAC-CATAAGGGTTGAATAGAAGCTCGA-AAG
1 AGCTGAACAGAAGCTCATAAGAGCTAAACAGAAAC-CCATAAG
* * * * * * *
16420117 AGTTGAACAGAAACTCATATGAGTTAAATAGAAACTCGTAAG
1 AGCTGAACAGAAGCTCATAAGAGCTAAACAGAAACCCATAAG
*
16420159 AGCTAAACAGAA
1 AGCTGAACAGAA
16420171 AGTAAAACAT
Statistics
Matches: 110, Mismatches: 24, Indels: 6
0.79 0.17 0.04
Matches are distributed among these distances:
41 32 0.29
42 78 0.71
ACGTcount: A:0.46, C:0.16, G:0.21, T:0.17
Consensus pattern (42 bp):
AGCTGAACAGAAGCTCATAAGAGCTAAACAGAAACCCATAAG
Found at i:16420129 original size:62 final size:63
Alignment explanation
Indices: 16419992--16420151 Score: 189
Period size: 62 Copynumber: 2.6 Consensus size: 63
16419982 GAAGCCCGAA
* * * *
16419992 AGCTGAACATAAGCTCATAAGAGCTAAACAGAAACCCATAAGGGTTGAACAGAAGCTTATAAG
1 AGCTGAACAGAAACCCATAAGAGCTAAACAGAAACCCATAAGGGTTGAACAGAAGCTGATAAG
* * *
16420055 AGCTGAATAGAAACCCATAAGAGCTGAACAGAAA-CCATAAGGGTTGAATAGAAGCTCGA-AAG
1 AGCTGAACAGAAACCCATAAGAGCTAAACAGAAACCCATAAGGGTTGAACAGAAGCT-GATAAG
* * * * *
16420117 AGTTGAACAGAAACTCATATGAGTTAAATAGAAAC
1 AGCTGAACAGAAACCCATAAGAGCTAAACAGAAAC
16420152 TCGTAAGAGC
Statistics
Matches: 81, Mismatches: 14, Indels: 4
0.82 0.14 0.04
Matches are distributed among these distances:
62 51 0.63
63 30 0.37
ACGTcount: A:0.46, C:0.16, G:0.21, T:0.17
Consensus pattern (63 bp):
AGCTGAACAGAAACCCATAAGAGCTAAACAGAAACCCATAAGGGTTGAACAGAAGCTGATAAG
Found at i:16423274 original size:40 final size:40
Alignment explanation
Indices: 16423214--16423293 Score: 142
Period size: 40 Copynumber: 2.0 Consensus size: 40
16423204 TATACTCAAC
* *
16423214 GCACTAACTTTCAACTCATTAACTATTTGAGCTCAGGTTT
1 GCACCAACTTTCAACTCATTAACTATTTGAGCTCAAGTTT
16423254 GCACCAACTTTCAACTCATTAACTATTTGAGCTCAAGTTT
1 GCACCAACTTTCAACTCATTAACTATTTGAGCTCAAGTTT
16423294 TGTAACACCC
Statistics
Matches: 38, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
40 38 1.00
ACGTcount: A:0.29, C:0.24, G:0.11, T:0.36
Consensus pattern (40 bp):
GCACCAACTTTCAACTCATTAACTATTTGAGCTCAAGTTT
Found at i:16424643 original size:45 final size:46
Alignment explanation
Indices: 16424576--16424699 Score: 200
Period size: 46 Copynumber: 2.8 Consensus size: 46
16424566 CATATGACCT
*
16424576 CTTATCAC-TTGTC-CTTGATCAGATAAGTGTAGCT-AGGCTACCA
1 CTTATCACTTTGTCACTTGATCAGATAAGTGTAGCTGAAGCTACCA
*
16424619 CTTATCACTTTGCCACTTGATCAGATAAGTGTAGCTGAAGCTACCA
1 CTTATCACTTTGTCACTTGATCAGATAAGTGTAGCTGAAGCTACCA
*
16424665 CTTATCACTTTATCACTTGATCAGATAAGTGTAGC
1 CTTATCACTTTGTCACTTGATCAGATAAGTGTAGC
16424700 CACTTATCAC
Statistics
Matches: 74, Mismatches: 4, Indels: 3
0.91 0.05 0.04
Matches are distributed among these distances:
43 8 0.11
44 4 0.05
45 21 0.28
46 41 0.55
ACGTcount: A:0.27, C:0.23, G:0.17, T:0.33
Consensus pattern (46 bp):
CTTATCACTTTGTCACTTGATCAGATAAGTGTAGCTGAAGCTACCA
Found at i:16424682 original size:46 final size:45
Alignment explanation
Indices: 16424576--16424810 Score: 207
Period size: 37 Copynumber: 5.8 Consensus size: 45
16424566 CATATGACCT
*
16424576 CTTATCAC-TTGTC-CTTGATCAGATAAGTGTAGCTAGGCTACCA
1 CTTATCACTTTGTCACTTGATCAGATAAGTGTAGCTAAGCTACCA
*
16424619 CTTATCACTTTGCCACTTGATCAGATAAGTGTAGCTGAAGCTACCA
1 CTTATCACTTTGTCACTTGATCAGATAAGTGTAGCT-AAGCTACCA
*
16424665 CTTATCACTTTATCACTTGATCAGATAA--GT-G-T-AG---CCA
1 CTTATCACTTTGTCACTTGATCAGATAAGTGTAGCTAAGCTACCA
*
16424702 CTTATCACTTTGTCTCTTGATCAGATAA--GT-G-T-A---ACCA
1 CTTATCACTTTGTCACTTGATCAGATAAGTGTAGCTAAGCTACCA
**
16424739 CTTATCACTTTGTTTCTTGATCAGATAA--GT-G-T-A---ACCA
1 CTTATCACTTTGTCACTTGATCAGATAAGTGTAGCTAAGCTACCA
**
16424776 CTTATCACTTTGTTTCTTGATCAGATAAGTGTAGC
1 CTTATCACTTTGTCACTTGATCAGATAAGTGTAGC
16424811 CACTTATCAC
Statistics
Matches: 177, Mismatches: 7, Indels: 18
0.88 0.03 0.09
Matches are distributed among these distances:
37 101 0.57
39 2 0.01
40 3 0.02
42 1 0.01
43 9 0.05
44 6 0.03
45 21 0.12
46 34 0.19
ACGTcount: A:0.27, C:0.21, G:0.16, T:0.36
Consensus pattern (45 bp):
CTTATCACTTTGTCACTTGATCAGATAAGTGTAGCTAAGCTACCA
Found at i:16424703 original size:37 final size:37
Alignment explanation
Indices: 16424661--16424837 Score: 282
Period size: 37 Copynumber: 4.8 Consensus size: 37
16424651 AGCTGAAGCT
* *
16424661 ACCACTTATCACTTTATCACTTGATCAGATAAGTGTA
1 ACCACTTATCACTTTGTCTCTTGATCAGATAAGTGTA
*
16424698 GCCACTTATCACTTTGTCTCTTGATCAGATAAGTGTA
1 ACCACTTATCACTTTGTCTCTTGATCAGATAAGTGTA
*
16424735 ACCACTTATCACTTTGTTTCTTGATCAGATAAGTGTA
1 ACCACTTATCACTTTGTCTCTTGATCAGATAAGTGTA
*
16424772 ACCACTTATCACTTTGTTTCTTGATCAGATAAGTGTA
1 ACCACTTATCACTTTGTCTCTTGATCAGATAAGTGTA
* * *
16424809 GCCACTTATCACTTTGTTTATTGATCAGA
1 ACCACTTATCACTTTGTCTCTTGATCAGA
16424838 AGTACTCAAA
Statistics
Matches: 133, Mismatches: 7, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
37 133 1.00
ACGTcount: A:0.27, C:0.20, G:0.14, T:0.39
Consensus pattern (37 bp):
ACCACTTATCACTTTGTCTCTTGATCAGATAAGTGTA
Found at i:16426202 original size:26 final size:26
Alignment explanation
Indices: 16426173--16426226 Score: 108
Period size: 26 Copynumber: 2.1 Consensus size: 26
16426163 CAAAATATAT
16426173 AAGTCACACATACAAAACCCATCATC
1 AAGTCACACATACAAAACCCATCATC
16426199 AAGTCACACATACAAAACCCATCATC
1 AAGTCACACATACAAAACCCATCATC
16426225 AA
1 AA
16426227 TGTAGGTATG
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 28 1.00
ACGTcount: A:0.48, C:0.33, G:0.04, T:0.15
Consensus pattern (26 bp):
AAGTCACACATACAAAACCCATCATC
Found at i:16430946 original size:25 final size:25
Alignment explanation
Indices: 16430918--16430970 Score: 63
Period size: 25 Copynumber: 2.1 Consensus size: 25
16430908 GTCAACAAGT
*
16430918 AATTTAAAAATTA-AAAAATATTCAA
1 AATTTAAAAACTATAAAAA-ATTCAA
* *
16430943 AATTTTAAAACTATAAAAAGTTCAA
1 AATTTAAAAACTATAAAAAATTCAA
16430968 AAT
1 AAT
16430971 AACTAGCATG
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
25 19 0.79
26 5 0.21
ACGTcount: A:0.60, C:0.06, G:0.02, T:0.32
Consensus pattern (25 bp):
AATTTAAAAACTATAAAAAATTCAA
Found at i:16434391 original size:44 final size:44
Alignment explanation
Indices: 16434315--16434398 Score: 116
Period size: 44 Copynumber: 1.9 Consensus size: 44
16434305 TAGAGTGTGG
* *
16434315 AATGCCATGTTATCTTAAGAAAAACGGTATCAAATTTATCACGA
1 AATGCCATATTATCTTAAGAAAAACGGTATCAAAATTATCACGA
* *
16434359 AATGTCATATTAT-TTAAGGAAAAATGGTATCAAAATTATC
1 AATGCCATATTATCTTAA-GAAAAACGGTATCAAAATTATC
16434399 GCTTGATCCA
Statistics
Matches: 35, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
43 4 0.11
44 31 0.89
ACGTcount: A:0.43, C:0.12, G:0.13, T:0.32
Consensus pattern (44 bp):
AATGCCATATTATCTTAAGAAAAACGGTATCAAAATTATCACGA
Found at i:16448245 original size:17 final size:17
Alignment explanation
Indices: 16448223--16448285 Score: 54
Period size: 17 Copynumber: 3.4 Consensus size: 17
16448213 TTTAGAGTTC
16448223 TAATTGTATACAACTTT
1 TAATTGTATACAACTTT
* * *
16448240 TAATTGTGTAATCTTAGAGTTC
1 TAATTGTAT-A-C--A-ACTTT
16448262 TAATTGTATACAACTTT
1 TAATTGTATACAACTTT
16448279 TAATTGT
1 TAATTGT
16448286 GTAATCTTAG
Statistics
Matches: 35, Mismatches: 6, Indels: 10
0.69 0.12 0.20
Matches are distributed among these distances:
17 18 0.51
18 2 0.06
19 1 0.03
20 1 0.03
21 2 0.06
22 11 0.31
ACGTcount: A:0.32, C:0.10, G:0.11, T:0.48
Consensus pattern (17 bp):
TAATTGTATACAACTTT
Found at i:16448261 original size:39 final size:39
Alignment explanation
Indices: 16448207--16448312 Score: 194
Period size: 39 Copynumber: 2.7 Consensus size: 39
16448197 GATATGATTA
*
16448207 TGTAATTTTAGAGTTCTAATTGTATACAACTTTTAATTG
1 TGTAATCTTAGAGTTCTAATTGTATACAACTTTTAATTG
16448246 TGTAATCTTAGAGTTCTAATTGTATACAACTTTTAATTG
1 TGTAATCTTAGAGTTCTAATTGTATACAACTTTTAATTG
*
16448285 TGTAATCTTAGAGTTTTAATTGTATACA
1 TGTAATCTTAGAGTTCTAATTGTATACA
16448313 GGAGGCTCAA
Statistics
Matches: 65, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
39 65 1.00
ACGTcount: A:0.31, C:0.08, G:0.13, T:0.47
Consensus pattern (39 bp):
TGTAATCTTAGAGTTCTAATTGTATACAACTTTTAATTG
Found at i:16448266 original size:22 final size:22
Alignment explanation
Indices: 16448237--16448307 Score: 80
Period size: 22 Copynumber: 3.5 Consensus size: 22
16448227 TGTATACAAC
16448237 TTTTAATTGTGTAATCTTAGAG
1 TTTTAATTGTGTAATCTTAGAG
* * *
16448259 TTCTAATTGTAT-A-C--A-AC
1 TTTTAATTGTGTAATCTTAGAG
16448276 TTTTAATTGTGTAATCTTAGAG
1 TTTTAATTGTGTAATCTTAGAG
16448298 TTTTAATTGT
1 TTTTAATTGT
16448308 ATACAGGAGG
Statistics
Matches: 38, Mismatches: 6, Indels: 10
0.70 0.11 0.19
Matches are distributed among these distances:
17 11 0.29
18 2 0.05
19 1 0.03
20 1 0.03
21 2 0.05
22 21 0.55
ACGTcount: A:0.28, C:0.07, G:0.14, T:0.51
Consensus pattern (22 bp):
TTTTAATTGTGTAATCTTAGAG
Found at i:16448597 original size:48 final size:49
Alignment explanation
Indices: 16448504--16448597 Score: 127
Period size: 48 Copynumber: 1.9 Consensus size: 49
16448494 GAGAATTTTA
* * * ***
16448504 TTGAATCTTTTATCGTTGCGAGATTAGGCTGATTTAGGTGTTTTTATTG
1 TTGAATCCTTTATCATTGCAAGATTAGGCTGATTTAGGCACTTTTATTG
16448553 TTGAATCCTTTATCATTGCAAG-TTAGGCTGATTTAGGCACTTTTA
1 TTGAATCCTTTATCATTGCAAGATTAGGCTGATTTAGGCACTTTTA
16448598 AATAAAGAAA
Statistics
Matches: 39, Mismatches: 6, Indels: 1
0.85 0.13 0.02
Matches are distributed among these distances:
48 20 0.51
49 19 0.49
ACGTcount: A:0.21, C:0.12, G:0.21, T:0.46
Consensus pattern (49 bp):
TTGAATCCTTTATCATTGCAAGATTAGGCTGATTTAGGCACTTTTATTG
Found at i:16454459 original size:20 final size:19
Alignment explanation
Indices: 16454433--16454477 Score: 81
Period size: 20 Copynumber: 2.3 Consensus size: 19
16454423 TTATTTTTAA
16454433 ATTTTTTTAATTTTAAAAT
1 ATTTTTTTAATTTTAAAAT
16454452 ACTTTTTTTAATTTTAAAAT
1 A-TTTTTTTAATTTTAAAAT
16454472 ATTTTT
1 ATTTTT
16454478 AAAATATGTT
Statistics
Matches: 25, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
19 6 0.24
20 19 0.76
ACGTcount: A:0.33, C:0.02, G:0.00, T:0.64
Consensus pattern (19 bp):
ATTTTTTTAATTTTAAAAT
Found at i:16454520 original size:30 final size:30
Alignment explanation
Indices: 16454425--16454520 Score: 104
Period size: 31 Copynumber: 3.2 Consensus size: 30
16454415 AAATATATTT
* *
16454425 ATTTTTAAATTTTTTTAA-TTTTAAAATAC
1 ATTTTTTAATTTTTTTAATTTTTAAAATAA
* *** *
16454454 TTTTTTTAATTTTAAAATATTTTTAAAATAT
1 ATTTTTTAATTTTTTTA-ATTTTTAAAATAA
*
16454485 GTTTTTTAATTTTTTTAATTTTTAAAATAA
1 ATTTTTTAATTTTTTTAATTTTTAAAATAA
16454515 ATTTTT
1 ATTTTT
16454521 GGTATTTTAT
Statistics
Matches: 53, Mismatches: 12, Indels: 3
0.78 0.18 0.04
Matches are distributed among these distances:
29 12 0.23
30 18 0.34
31 23 0.43
ACGTcount: A:0.35, C:0.01, G:0.01, T:0.62
Consensus pattern (30 bp):
ATTTTTTAATTTTTTTAATTTTTAAAATAA
Found at i:16455247 original size:26 final size:26
Alignment explanation
Indices: 16455210--16455325 Score: 143
Period size: 26 Copynumber: 4.7 Consensus size: 26
16455200 GCACACATTA
*
16455210 GCTCTTT-TGAGCTTCCTGATTAAAG
1 GCTCTTTGTGAGCTTCCTGATTAATG
*
16455235 GCTTTTTGTGAGCTTCCTGATTAATG
1 GCTCTTTGTGAGCTTCCTGATTAATG
16455261 GCTCTTTGTGAGCTTCCTGATTAATG
1 GCTCTTTGTGAGCTTCCTGATTAATG
** *
16455287 GCTCTCCG-GAGCTTCCCGA-T-ATG
1 GCTCTTTGTGAGCTTCCTGATTAATG
*
16455310 GCTCTCTG-GAGCTTCC
1 GCTCTTTGTGAGCTTCC
16455326 CGATATGGCT
Statistics
Matches: 83, Mismatches: 7, Indels: 4
0.88 0.07 0.04
Matches are distributed among these distances:
23 18 0.22
24 1 0.01
25 16 0.19
26 48 0.58
ACGTcount: A:0.15, C:0.24, G:0.23, T:0.38
Consensus pattern (26 bp):
GCTCTTTGTGAGCTTCCTGATTAATG
Found at i:16455314 original size:23 final size:23
Alignment explanation
Indices: 16455270--16455336 Score: 98
Period size: 23 Copynumber: 2.8 Consensus size: 23
16455260 GGCTCTTTGT
*
16455270 GAGCTTCCTGATTAATGGCTCTCCG
1 GAGCTTCCCGA-T-ATGGCTCTCCG
*
16455295 GAGCTTCCCGATATGGCTCTCTG
1 GAGCTTCCCGATATGGCTCTCCG
16455318 GAGCTTCCCGATATGGCTC
1 GAGCTTCCCGATATGGCTC
16455337 GCTTGAACTT
Statistics
Matches: 40, Mismatches: 2, Indels: 2
0.91 0.05 0.05
Matches are distributed among these distances:
23 29 0.73
24 1 0.03
25 10 0.25
ACGTcount: A:0.15, C:0.30, G:0.25, T:0.30
Consensus pattern (23 bp):
GAGCTTCCCGATATGGCTCTCCG
Found at i:16455347 original size:23 final size:23
Alignment explanation
Indices: 16455284--16455354 Score: 79
Period size: 23 Copynumber: 3.1 Consensus size: 23
16455274 TTCCTGATTA
* * *
16455284 ATGGCTCTCCGGAGCTTCCCGAT
1 ATGGCTCGCTGGAACTTCCCGAT
* *
16455307 ATGGCTCTCTGGAGCTTCCCGAT
1 ATGGCTCGCTGGAACTTCCCGAT
* *
16455330 ATGGCTCGCTTGAACTTCCTGAT
1 ATGGCTCGCTGGAACTTCCCGAT
16455353 AT
1 AT
16455355 AGGGCTATCT
Statistics
Matches: 43, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
23 43 1.00
ACGTcount: A:0.15, C:0.30, G:0.24, T:0.31
Consensus pattern (23 bp):
ATGGCTCGCTGGAACTTCCCGAT
Found at i:16458382 original size:15 final size:15
Alignment explanation
Indices: 16458346--16458385 Score: 62
Period size: 15 Copynumber: 2.7 Consensus size: 15
16458336 AACTTAGATT
* *
16458346 ATTATTATTACTATT
1 ATTATTGTTACTATC
16458361 ATTATTGTTACTATC
1 ATTATTGTTACTATC
16458376 ATTATTGTTA
1 ATTATTGTTA
16458386 TTTATATTAT
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
15 23 1.00
ACGTcount: A:0.30, C:0.07, G:0.05, T:0.57
Consensus pattern (15 bp):
ATTATTGTTACTATC
Found at i:16458394 original size:15 final size:14
Alignment explanation
Indices: 16458345--16458395 Score: 57
Period size: 15 Copynumber: 3.4 Consensus size: 14
16458335 AAACTTAGAT
*
16458345 TATTATTATTACTA
1 TATTATTGTTACTA
16458359 TTATTATTGTTACTA
1 -TATTATTGTTACTA
*
16458374 TCATTATTGTTATTTA
1 T-ATTATTGTTA-CTA
16458390 TATTAT
1 TATTAT
16458396 CGTTTTCATC
Statistics
Matches: 32, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
14 1 0.03
15 28 0.88
16 3 0.09
ACGTcount: A:0.29, C:0.06, G:0.04, T:0.61
Consensus pattern (14 bp):
TATTATTGTTACTA
Found at i:16470207 original size:24 final size:24
Alignment explanation
Indices: 16470162--16470208 Score: 60
Period size: 24 Copynumber: 2.0 Consensus size: 24
16470152 GGTGCCAATG
*
16470162 AATAAAATAATAATAATTTTTTTT
1 AATAAAATAATAATAATATTTTTT
*
16470186 AATAAAAT-ATAAATTATATTTTT
1 AATAAAATAAT-AATAATATTTTT
16470209 CCAGGTTAGT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
23 2 0.10
24 18 0.90
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (24 bp):
AATAAAATAATAATAATATTTTTT
Found at i:16470293 original size:27 final size:27
Alignment explanation
Indices: 16470263--16470338 Score: 82
Period size: 27 Copynumber: 2.8 Consensus size: 27
16470253 TTTGGAAGGC
* * *
16470263 GCCTATTTGGGAGGTGCTAATGGTGGT
1 GCCTATTTAGGAGGCGCCAATGGTGGT
* *
16470290 GCCTATGTAGTAGGCGCCAATGGTGGT
1 GCCTATTTAGGAGGCGCCAATGGTGGT
*
16470317 GCC-ATATTAGAAGGCGCCAATG
1 GCCTAT-TTAGGAGGCGCCAATG
16470339 CTGTGATTTT
Statistics
Matches: 41, Mismatches: 7, Indels: 2
0.82 0.14 0.04
Matches are distributed among these distances:
26 2 0.05
27 39 0.95
ACGTcount: A:0.21, C:0.17, G:0.36, T:0.26
Consensus pattern (27 bp):
GCCTATTTAGGAGGCGCCAATGGTGGT
Found at i:16470439 original size:17 final size:17
Alignment explanation
Indices: 16470400--16470444 Score: 56
Period size: 17 Copynumber: 2.6 Consensus size: 17
16470390 AAAACGGAAG
*
16470400 AAAGAAG-AAGGAAGGA
1 AAAGAAGAAAAGAAGGA
*
16470416 AGCAGAAGAAAAGAAGGA
1 A-AAGAAGAAAAGAAGGA
16470434 AAAGAAGAAAA
1 AAAGAAGAAAA
16470445 AAAGTAGGTA
Statistics
Matches: 24, Mismatches: 3, Indels: 3
0.80 0.10 0.10
Matches are distributed among these distances:
16 1 0.04
17 14 0.58
18 9 0.38
ACGTcount: A:0.67, C:0.02, G:0.31, T:0.00
Consensus pattern (17 bp):
AAAGAAGAAAAGAAGGA
Found at i:16472807 original size:38 final size:38
Alignment explanation
Indices: 16472764--16472845 Score: 146
Period size: 38 Copynumber: 2.2 Consensus size: 38
16472754 AAAAAGTCAG
16472764 TTATAATTAAACTTTTAATAAAATGATTTTTAATTTAT
1 TTATAATTAAACTTTTAATAAAATGATTTTTAATTTAT
* *
16472802 TTATAATTAAACTTTTAATGAAATGATTTTTAATTTTT
1 TTATAATTAAACTTTTAATAAAATGATTTTTAATTTAT
16472840 TTATAA
1 TTATAA
16472846 ACTTTATATG
Statistics
Matches: 42, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
38 42 1.00
ACGTcount: A:0.40, C:0.02, G:0.04, T:0.54
Consensus pattern (38 bp):
TTATAATTAAACTTTTAATAAAATGATTTTTAATTTAT
Found at i:16473027 original size:8 final size:8
Alignment explanation
Indices: 16473014--16473077 Score: 56
Period size: 8 Copynumber: 7.4 Consensus size: 8
16473004 TCATACAAAA
16473014 ATTACAAT
1 ATTACAAT
16473022 ATTACAAT
1 ATTACAAT
* * *
16473030 ATATCCCCAC
1 AT-T-ACAAT
16473040 ATTACAAT
1 ATTACAAT
16473048 ATTCATACAAT
1 A-T--TACAAT
16473059 ATTACAAT
1 ATTACAAT
16473067 ATTACAAT
1 ATTACAAT
16473075 ATT
1 ATT
16473078 CATACAAAAA
Statistics
Matches: 45, Mismatches: 6, Indels: 10
0.74 0.10 0.16
Matches are distributed among these distances:
8 30 0.67
9 3 0.07
10 5 0.11
11 7 0.16
ACGTcount: A:0.45, C:0.19, G:0.00, T:0.36
Consensus pattern (8 bp):
ATTACAAT
Found at i:16473116 original size:19 final size:19
Alignment explanation
Indices: 16473116--16473491 Score: 165
Period size: 19 Copynumber: 19.2 Consensus size: 19
16473106 AAATTATAAT
*
16473116 ATTACAATATTCATACAAC
1 ATTACAATATTCATACAAA
*
16473135 ATTACAATATTCATAAAAAA
1 ATTACAATATTCAT-ACAAA
*
16473155 ATTATAATATTCATACAAA
1 ATTACAATATTCATACAAA
*
16473174 ATTACAATA-T--TACAAT
1 ATTACAATATTCATACAAA
*
16473190 ATT-C-ATA--CA-AAAAA
1 ATTACAATATTCATACAAA
*
16473204 ATTGCAATATTCATACAAAATTATAA
1 ATTACAATATTCATAC------A-AA
16473230 TATTACAATATTCATACAAA
1 -ATTACAATATTCATACAAA
** *
16473250 AAAATAATATTCATACAAA
1 ATTACAATATTCATACAAA
*
16473269 ATTACAA-AAT--TACAATA
1 ATTACAATATTCATACAA-A
* * * *
16473286 TTCATACAAAACT-ATA-ATATT
1 AT--TACAATATTCATACA-A-A
16473307 ATTACAATATTCATACAAAAA
1 ATTACAATATTCATAC--AAA
*
16473328 ATTTATAATATTCATACAAA
1 A-TTACAATATTCATACAAA
16473348 ATTACAATATTCATACAAAA
1 ATTACAATATTCATAC-AAA
* * *
16473368 ATTACTA-ATCCAAAACTATAA
1 ATTACAATATTC-ATAC-A-AA
*
16473389 A-TACAAATTTAATT-ATAAAATA
1 ATTAC-AA--T-ATTCATACAA-A
*
16473411 ATTACAATATTCATACAAC
1 ATTACAATATTCATACAAA
*
16473430 ATTACAATATTCATAAAAAA
1 ATTACAATATTCAT-ACAAA
*
16473450 ATTATAATATTCATACAAAA
1 ATTACAATATTCATAC-AAA
*
16473470 ATTTA-AAAATTCATACAAA
1 A-TTACAATATTCATACAAA
16473489 ATT
1 ATT
16473492 CTAATCTAAA
Statistics
Matches: 275, Mismatches: 41, Indels: 83
0.69 0.10 0.21
Matches are distributed among these distances:
14 9 0.03
15 2 0.01
16 16 0.06
17 2 0.01
18 7 0.03
19 98 0.36
20 80 0.29
21 15 0.05
22 20 0.07
23 6 0.02
25 3 0.01
26 2 0.01
27 15 0.05
ACGTcount: A:0.54, C:0.13, G:0.00, T:0.33
Consensus pattern (19 bp):
ATTACAATATTCATACAAA
Found at i:16473178 original size:115 final size:118
Alignment explanation
Indices: 16472994--16473358 Score: 450
Period size: 115 Copynumber: 3.0 Consensus size: 118
16472984 TTATAAAATA
* * * * * *
16472994 ATTACAATATTCATACAAAAATTACAATATTACAATATATCCCCACATTACAATATTCATACAAT
1 ATTACAATATTCATACAAAAA-AACAATATT-C-ATAAAT-ACAAAATTACAATATTCATACAAA
*
16473059 ATTACAATATTACAATATTCATACAAAAAAATTGCAATATTCATGCAAAATTATAAT
62 ATTACAATATTACAATATTCATACAAAAAAATTGCAATATTCATACAAAATTATAAT
* ** *
16473116 ATTACAATATTCATACAACATTACAATATTCAT-AA-A-AAAATTATAATATTCATACAAAATTA
1 ATTACAATATTCATACAAAAAAACAATATTCATAAATACAAAATTACAATATTCATACAAAATTA
16473178 CAATATTACAATATTCATACAAAAAAATTGCAATATTCATACAAAATTATAAT
66 CAATATTACAATATTCATACAAAAAAATTGCAATATTCATACAAAATTATAAT
*
16473231 ATTACAATATTCATACAAAAAAATAATATTCATACAAAATTACAAAATTACAATATTCATACAAA
1 ATTACAATATTCATACAAAAAAACAATATTCAT---AAA-TACAAAATTACAATATTCATACAAA
* ** *
16473296 ACTATA-ATATTATTACAATATTCATACAAAAAATTTATAATATTCATACAAAATTACAAT
62 A-T-TACA-A-TATTACAATATTCATACAAAAAAATTGCAATATTCATACAAAATTATAAT
16473356 ATT
1 ATT
16473359 CATACAAAAA
Statistics
Matches: 214, Mismatches: 18, Indels: 19
0.85 0.07 0.08
Matches are distributed among these distances:
115 103 0.48
118 1 0.00
119 4 0.02
120 1 0.00
121 10 0.05
122 41 0.19
123 2 0.01
124 3 0.01
125 49 0.23
ACGTcount: A:0.52, C:0.14, G:0.01, T:0.33
Consensus pattern (118 bp):
ATTACAATATTCATACAAAAAAACAATATTCATAAATACAAAATTACAATATTCATACAAAATTA
CAATATTACAATATTCATACAAAAAAATTGCAATATTCATACAAAATTATAAT
Found at i:16473205 original size:30 final size:27
Alignment explanation
Indices: 16473040--16473358 Score: 239
Period size: 27 Copynumber: 13.1 Consensus size: 27
16473030 ATATCCCCAC
*
16473040 ATTACAATATTCATACAATATTACAAT
1 ATTACAATATTCATACAAAATTACAAT
16473067 ATTACAATATTCATAC-AAA--A-AA-
1 ATTACAATATTCATACAAAATTACAAT
* * *
16473089 ATTGCAATATTCATGCAAAATTATAAT
1 ATTACAATATTCATACAAAATTACAAT
*
16473116 ATTACAATATTCATACAACATTACAAT
1 ATTACAATATTCATACAAAATTACAAT
*
16473143 ATT-C-ATA---A-A-AAAATT--AT-
1 ATTACAATATTCATACAAAATTACAAT
16473160 -----AATATTCATACAAAATTACAAT
1 ATTACAATATTCATACAAAATTACAAT
16473182 ATTACAATATTCATAC-AAA--A-AA-
1 ATTACAATATTCATACAAAATTACAAT
* *
16473204 ATTGCAATATTCATACAAAATTATAAT
1 ATTACAATATTCATACAAAATTACAAT
16473231 ATTACAATATTCATAC-AAA--A-AA-
1 ATTACAATATTCATACAAAATTACAAT
*
16473253 A-T--AATATTCATACAAAATTACAAA
1 ATTACAATATTCATACAAAATTACAAT
16473277 ATTACAATATTCATACAAAACTATA-ATATT
1 ATTACAATATTCATACAAAA-T-TACA-A-T
16473307 ATTACAATATTCATAC-AAA--A-AAT
1 ATTACAATATTCATACAAAATTACAAT
*
16473330 -TTATAATATTCATACAAAATTACAAT
1 ATTACAATATTCATACAAAATTACAAT
16473356 ATT
1 ATT
16473359 CATACAAAAA
Statistics
Matches: 237, Mismatches: 14, Indels: 82
0.71 0.04 0.25
Matches are distributed among these distances:
14 3 0.01
17 1 0.00
18 2 0.01
19 17 0.07
20 8 0.03
21 3 0.01
22 46 0.19
23 18 0.08
24 5 0.02
25 9 0.04
26 16 0.07
27 85 0.36
28 2 0.01
29 6 0.03
30 16 0.07
ACGTcount: A:0.53, C:0.13, G:0.01, T:0.34
Consensus pattern (27 bp):
ATTACAATATTCATACAAAATTACAAT
Found at i:16473221 original size:49 final size:47
Alignment explanation
Indices: 16473129--16473296 Score: 259
Period size: 49 Copynumber: 3.6 Consensus size: 47
16473119 ACAATATTCA
* *
16473129 TACAACATTACAATATTCATA-AAAAAATTATAATATTCATACAAAAT
1 TACAATATTACAATATTCATACAAAAAAAT-TAATATTCATACAAAAT
16473176 TACAATATTACAATATTCATACAAAAAAATTGCAATATTCATACAAAAT
1 TACAATATTACAATATTCATACAAAAAAATT--AATATTCATACAAAAT
*
16473225 TATAATATTACAATATTCATACAAAAAAA-TAATATTCATACAAAAT
1 TACAATATTACAATATTCATACAAAAAAATTAATATTCATACAAAAT
*
16473271 TACAAAATTACAATATTCATACAAAA
1 TACAATATTACAATATTCATACAAAA
16473297 CTATAATATT
Statistics
Matches: 113, Mismatches: 5, Indels: 7
0.90 0.04 0.06
Matches are distributed among these distances:
46 40 0.35
47 21 0.19
48 8 0.07
49 44 0.39
ACGTcount: A:0.55, C:0.13, G:0.01, T:0.31
Consensus pattern (47 bp):
TACAATATTACAATATTCATACAAAAAAATTAATATTCATACAAAAT
Found at i:16473337 original size:22 final size:21
Alignment explanation
Indices: 16473307--16473489 Score: 143
Period size: 20 Copynumber: 9.0 Consensus size: 21
16473297 CTATAATATT
16473307 ATTACAATATTCATACAAAAA
1 ATTACAATATTCATACAAAAA
*
16473328 ATTTATAATATTCATAC--AAA
1 A-TTACAATATTCATACAAAAA
16473348 ATTACAATATTCATAC-AAAA
1 ATTACAATATTCATACAAAAA
* * * * *
16473368 ATTACTA-ATCCAAAACTATAA
1 ATTACAATATTC-ATACAAAAA
* *
16473389 A-TACAA-ATTTAATTATAAAATA
1 ATTACAATA-TTCA-TACAAAA-A
*
16473411 ATTACAATATTCATAC--AAC
1 ATTACAATATTCATACAAAAA
16473430 ATTACAATATTCATA-AAAAA
1 ATTACAATATTCATACAAAAA
*
16473450 ATTATAATATTCATACAAAAA
1 ATTACAATATTCATACAAAAA
* *
16473471 TTTA-AAAATTCATACAAAA
1 ATTACAATATTCATACAAAA
16473490 TTCTAATCTA
Statistics
Matches: 130, Mismatches: 20, Indels: 25
0.74 0.11 0.14
Matches are distributed among these distances:
19 32 0.25
20 54 0.42
21 17 0.13
22 18 0.14
23 8 0.06
24 1 0.01
ACGTcount: A:0.55, C:0.13, G:0.00, T:0.32
Consensus pattern (21 bp):
ATTACAATATTCATACAAAAA
Found at i:16473679 original size:14 final size:14
Alignment explanation
Indices: 16473660--16473689 Score: 60
Period size: 14 Copynumber: 2.1 Consensus size: 14
16473650 TTTTTTTCTT
16473660 TCTTCTTCTCCTTC
1 TCTTCTTCTCCTTC
16473674 TCTTCTTCTCCTTC
1 TCTTCTTCTCCTTC
16473688 TC
1 TC
16473690 CTTTCTCTCT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.00, C:0.43, G:0.00, T:0.57
Consensus pattern (14 bp):
TCTTCTTCTCCTTC
Found at i:16473700 original size:20 final size:20
Alignment explanation
Indices: 16473659--16473697 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
16473649 TTTTTTTTCT
*
16473659 TTCTTCTTCTCCTTCTCTTC
1 TTCTCCTTCTCCTTCTCTTC
16473679 TTCTCCTTCTCCTTTCTCT
1 TTCTCCTTCTCC-TTCTCT
16473698 CTTTTTTTTT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 11 0.65
21 6 0.35
ACGTcount: A:0.00, C:0.41, G:0.00, T:0.59
Consensus pattern (20 bp):
TTCTCCTTCTCCTTCTCTTC
Found at i:16473900 original size:13 final size:13
Alignment explanation
Indices: 16473882--16473907 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
16473872 CACCCGACTC
16473882 GACCCGTATTTTT
1 GACCCGTATTTTT
16473895 GACCCGTATTTTT
1 GACCCGTATTTTT
16473908 TTCAAAAAAA
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:0.15, C:0.23, G:0.15, T:0.46
Consensus pattern (13 bp):
GACCCGTATTTTT
Found at i:16478159 original size:92 final size:92
Alignment explanation
Indices: 16478002--16478284 Score: 530
Period size: 92 Copynumber: 3.1 Consensus size: 92
16477992 AATTTTGCAT
* *
16478002 ATAGGTTCAAACAAAATGCATACTTGTTGTTTAAATTATAGCTTATATGCATACTTTGATACAAA
1 ATAGGTTCAAACAAAATGCATACTTGCTGTTTAAATTGTAGCTTATATGCATACTTTGATACAAA
16478067 TAGGTTTATATTTTATTAAATATACAA
66 TAGGTTTATATTTTATTAAATATACAA
*
16478094 ATAGGTTCAAACAAAATGCATACTTGCTGTCTAAATTGTAGCTTATATGCATACTTTGATACAAA
1 ATAGGTTCAAACAAAATGCATACTTGCTGTTTAAATTGTAGCTTATATGCATACTTTGATACAAA
16478159 TAGGTTTATATTTTATTAAATATACAA
66 TAGGTTTATATTTTATTAAATATACAA
16478186 ATAGGTTCAAACAAAATGCATACTTGCTGTTTAAATTGTAGCTTATATGCATACTTTGATACAAA
1 ATAGGTTCAAACAAAATGCATACTTGCTGTTTAAATTGTAGCTTATATGCATACTTTGATACAAA
*
16478251 TAGGTTCATATTTTATTAAATATACAA
66 TAGGTTTATATTTTATTAAATATACAA
16478278 ATAGGTT
1 ATAGGTT
16478285 AAAAATTGTA
Statistics
Matches: 186, Mismatches: 5, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
92 186 1.00
ACGTcount: A:0.38, C:0.11, G:0.12, T:0.39
Consensus pattern (92 bp):
ATAGGTTCAAACAAAATGCATACTTGCTGTTTAAATTGTAGCTTATATGCATACTTTGATACAAA
TAGGTTTATATTTTATTAAATATACAA
Found at i:16478799 original size:17 final size:19
Alignment explanation
Indices: 16478759--16478799 Score: 50
Period size: 20 Copynumber: 2.2 Consensus size: 19
16478749 TTAATGAAAT
*
16478759 CTATTACAGTGAATAAAAAT
1 CTATTACAGT-AATAAAAAC
16478779 CTATTACAGT-A-AAAAAC
1 CTATTACAGTAATAAAAAC
16478796 CTAT
1 CTAT
16478800 GAGGACCGAA
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
17 9 0.45
18 1 0.05
20 10 0.50
ACGTcount: A:0.49, C:0.15, G:0.07, T:0.29
Consensus pattern (19 bp):
CTATTACAGTAATAAAAAC
Found at i:16480807 original size:20 final size:20
Alignment explanation
Indices: 16480782--16480821 Score: 62
Period size: 20 Copynumber: 2.0 Consensus size: 20
16480772 CGTGAAATGA
*
16480782 TTTCTGAAAAATATTTTACT
1 TTTCTGAAAAATAATTTACT
*
16480802 TTTCTGTAAAATAATTTACT
1 TTTCTGAAAAATAATTTACT
16480822 AAAAAATATT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.35, C:0.10, G:0.05, T:0.50
Consensus pattern (20 bp):
TTTCTGAAAAATAATTTACT
Found at i:16483368 original size:12 final size:12
Alignment explanation
Indices: 16483351--16483379 Score: 58
Period size: 12 Copynumber: 2.4 Consensus size: 12
16483341 CAAATCAAGC
16483351 GAGAACGAAAGG
1 GAGAACGAAAGG
16483363 GAGAACGAAAGG
1 GAGAACGAAAGG
16483375 GAGAA
1 GAGAA
16483380 GGGAGAACGA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 17 1.00
ACGTcount: A:0.52, C:0.07, G:0.41, T:0.00
Consensus pattern (12 bp):
GAGAACGAAAGG
Found at i:16483709 original size:30 final size:32
Alignment explanation
Indices: 16483654--16483729 Score: 93
Period size: 30 Copynumber: 2.4 Consensus size: 32
16483644 CTAAAAACTT
* *
16483654 AAACATAAATATATATATTTTTTAAACATAAA
1 AAACATAAATATATATATATTTTAAAAATAAA
*
16483686 AAACTTAAAT-TAT-TATATTTTAAAAATAAA
1 AAACATAAATATATATATATTTTAAAAATAAA
* *
16483716 AAAAATATATATAT
1 AAACATAAATATAT
16483730 TTAATATATT
Statistics
Matches: 37, Mismatches: 6, Indels: 3
0.80 0.13 0.07
Matches are distributed among these distances:
30 22 0.59
31 6 0.16
32 9 0.24
ACGTcount: A:0.58, C:0.04, G:0.00, T:0.38
Consensus pattern (32 bp):
AAACATAAATATATATATATTTTAAAAATAAA
Found at i:16484666 original size:30 final size:31
Alignment explanation
Indices: 16484632--16484699 Score: 84
Period size: 30 Copynumber: 2.2 Consensus size: 31
16484622 TTGCCCAAGA
** * **
16484632 GTAAATACTCAAAATTTGAGGGGTTAA-AGT
1 GTAAATACAAAAAATTTGAAGGGCCAATAGT
16484662 GTAAATACAAAAAATTTGAAGGGCCAATAGT
1 GTAAATACAAAAAATTTGAAGGGCCAATAGT
16484693 GTAAATA
1 GTAAATA
16484700 TTTTAAGGGT
Statistics
Matches: 32, Mismatches: 5, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
30 22 0.69
31 10 0.31
ACGTcount: A:0.46, C:0.07, G:0.21, T:0.26
Consensus pattern (31 bp):
GTAAATACAAAAAATTTGAAGGGCCAATAGT
Done.