Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008061.1 Hibiscus syriacus cultivar Beakdansim tig00110556_pilon, whole genome shotgun sequence
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: 5800122
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 21 of 26
Found at i:4181044 original size:16 final size:15
Alignment explanation
Indices: 4181023--4181052 Score: 51
Period size: 16 Copynumber: 1.9 Consensus size: 15
4181013 TGAATTTTAG
4181023 TAATATATACTAATTT
1 TAATATATA-TAATTT
4181039 TAATATATATAATT
1 TAATATATATAATT
4181053 CAATTGAAGT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 5 0.36
16 9 0.64
ACGTcount: A:0.47, C:0.03, G:0.00, T:0.50
Consensus pattern (15 bp):
TAATATATATAATTT
Found at i:4187978 original size:28 final size:28
Alignment explanation
Indices: 4187938--4187993 Score: 112
Period size: 28 Copynumber: 2.0 Consensus size: 28
4187928 CTTTTACAGA
4187938 ATCGATCCCCTACAAGAATATGTGGAGC
1 ATCGATCCCCTACAAGAATATGTGGAGC
4187966 ATCGATCCCCTACAAGAATATGTGGAGC
1 ATCGATCCCCTACAAGAATATGTGGAGC
4187994 TCAGCATGTC
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 28 1.00
ACGTcount: A:0.32, C:0.25, G:0.21, T:0.21
Consensus pattern (28 bp):
ATCGATCCCCTACAAGAATATGTGGAGC
Found at i:4188607 original size:21 final size:20
Alignment explanation
Indices: 4188551--4188608 Score: 55
Period size: 20 Copynumber: 2.9 Consensus size: 20
4188541 GTTTTGCAAT
*
4188551 GAACCGGCTGAGAACCAGTA
1 GAACCGGCTGAGAACCGGTA
** *
4188571 GAACCGATTGAAAACCGGT-
1 GAACCGGCTGAGAACCGGTA
4188590 GTTAACCGGCTGAGAACCG
1 G--AACCGGCTGAGAACCG
4188609 ACAAAACCGG
Statistics
Matches: 29, Mismatches: 7, Indels: 3
0.74 0.18 0.08
Matches are distributed among these distances:
19 1 0.03
20 15 0.52
21 13 0.45
ACGTcount: A:0.33, C:0.24, G:0.29, T:0.14
Consensus pattern (20 bp):
GAACCGGCTGAGAACCGGTA
Found at i:4193151 original size:70 final size:70
Alignment explanation
Indices: 4193038--4193198 Score: 207
Period size: 70 Copynumber: 2.3 Consensus size: 70
4193028 AAATTAAATT
* * * * *
4193038 TTATATCATTTTTTGAATATTCTAAGTTAAAATATATTTATTATCTCTTTAATTTGAATATTAAT
1 TTATATC-TTTTTT-AATAATCTAAATTAAAAGATATTTATTATCTCTTTAATTTAAATATTAAC
4193103 AAAATAA
64 AAAATAA
*
4193110 TTATATCTTTTTTAATAGAT-TAAATTAAAAGATATTTATTATCTGTTTAATTTAAATATTAACA
1 TTATATCTTTTTTAATA-ATCTAAATTAAAAGATATTTATTATCTCTTTAATTTAAATATTAACA
*
4193174 GAATAA
65 AAATAA
* *
4193180 TTATATATTTTTGAATAAT
1 TTATATCTTTTTTAATAAT
4193199 TTTAAAATAT
Statistics
Matches: 79, Mismatches: 9, Indels: 5
0.85 0.10 0.05
Matches are distributed among these distances:
69 2 0.03
70 63 0.80
71 7 0.09
72 7 0.09
ACGTcount: A:0.41, C:0.04, G:0.05, T:0.50
Consensus pattern (70 bp):
TTATATCTTTTTTAATAATCTAAATTAAAAGATATTTATTATCTCTTTAATTTAAATATTAACAA
AATAA
Found at i:4193159 original size:35 final size:34
Alignment explanation
Indices: 4193064--4193171 Score: 96
Period size: 35 Copynumber: 3.1 Consensus size: 34
4193054 ATATTCTAAG
*
4193064 TTAAAATATATTTATTATCTCTTTAATTTGAATA
1 TTAAAAAATATTTATTATCTCTTTAATTTGAATA
* *
4193098 TTAATAAAATAATTA-TATCTTTTTTAATAGATT-AA-A
1 TTAA-AAAATATTTATTATC-TCTTTAAT---TTGAATA
* * *
4193134 TTAAAAGATATTTATTATCTGTTTAATTTAAATA
1 TTAAAAAATATTTATTATCTCTTTAATTTGAATA
4193168 TTAA
1 TTAA
4193172 CAGAATAATT
Statistics
Matches: 60, Mismatches: 6, Indels: 16
0.73 0.07 0.20
Matches are distributed among these distances:
32 2 0.03
33 2 0.03
34 13 0.22
35 30 0.50
36 9 0.15
37 2 0.03
38 2 0.03
ACGTcount: A:0.43, C:0.04, G:0.04, T:0.50
Consensus pattern (34 bp):
TTAAAAAATATTTATTATCTCTTTAATTTGAATA
Found at i:4194296 original size:29 final size:27
Alignment explanation
Indices: 4194239--4194354 Score: 115
Period size: 24 Copynumber: 4.5 Consensus size: 27
4194229 ATTTTAATTT
*
4194239 TAATATTAA-TTTTTAA-A-TAAATTA
1 TAATATTAATTTTTTAATATTATATTA
4194263 -AATATTAATTTTTTTAATATTATATTA
1 TAATATTAA-TTTTTTAATATTATATTA
*
4194290 TAGATATTAATTTTTTAA-A-TAAATTA
1 TA-ATATTAATTTTTTAATATTATATTA
4194316 -AATATT-A-TTTTTAATATTATATTA
1 TAATATTAATTTTTTAATATTATATTA
4194340 TAAATATTTAATTTT
1 T-AATA-TTAATTTT
4194355 ATATCATATA
Statistics
Matches: 76, Mismatches: 3, Indels: 21
0.76 0.03 0.21
Matches are distributed among these distances:
22 7 0.09
23 10 0.13
24 11 0.14
25 8 0.11
26 11 0.14
27 9 0.12
28 10 0.13
29 10 0.13
ACGTcount: A:0.44, C:0.00, G:0.01, T:0.55
Consensus pattern (27 bp):
TAATATTAATTTTTTAATATTATATTA
Found at i:4194347 original size:50 final size:52
Alignment explanation
Indices: 4194240--4194354 Score: 182
Period size: 50 Copynumber: 2.2 Consensus size: 52
4194230 TTTTAATTTT
4194240 AATATTAA-TTTTTAAATAAATTAAATATTAATTTTTTTAATATTATATTATA
1 AATATTAATTTTTTAAATAAATTAAATATTAA-TTTTTTAATATTATATTATA
*
4194292 GATATTAATTTTTTAAATAAATTAAATATT-A-TTTTTAATATTATATTATA
1 AATATTAATTTTTTAAATAAATTAAATATTAATTTTTTAATATTATATTATA
4194342 AATATTTAATTTT
1 AATA-TTAATTTT
4194355 ATATCATATA
Statistics
Matches: 59, Mismatches: 2, Indels: 5
0.89 0.03 0.08
Matches are distributed among these distances:
50 22 0.37
51 8 0.14
52 8 0.14
53 21 0.36
ACGTcount: A:0.44, C:0.00, G:0.01, T:0.55
Consensus pattern (52 bp):
AATATTAATTTTTTAAATAAATTAAATATTAATTTTTTAATATTATATTATA
Found at i:4194349 original size:21 final size:21
Alignment explanation
Indices: 4194325--4194400 Score: 63
Period size: 21 Copynumber: 3.7 Consensus size: 21
4194315 AAATATTATT
4194325 TTTAATATTATATTATAAATA
1 TTTAATATTATATTATAAATA
*
4194346 TTTAATTTTATATCATATAAATTA
1 TTTAATATTATAT--TATAAA-TA
4194370 TTT--TA-TATATTATTAAA-A
1 TTTAATATTATATTA-TAAATA
*
4194388 TTTTATATT-TATT
1 TTTAATATTATATT
4194401 TTAGTTATTT
Statistics
Matches: 46, Mismatches: 2, Indels: 15
0.73 0.03 0.24
Matches are distributed among these distances:
18 4 0.09
19 2 0.04
20 10 0.22
21 18 0.39
22 1 0.02
23 6 0.13
24 5 0.11
ACGTcount: A:0.41, C:0.01, G:0.00, T:0.58
Consensus pattern (21 bp):
TTTAATATTATATTATAAATA
Found at i:4194358 original size:26 final size:26
Alignment explanation
Indices: 4194274--4194363 Score: 82
Period size: 26 Copynumber: 3.5 Consensus size: 26
4194264 ATATTAATTT
*
4194274 TTTTAATATTATATTATAGATATTAA
1 TTTTAATATTATATTATAAATATTAA
* *
4194300 TTTTTTAA-A-TA-AAT-TAAATATTAT
1 --TTTTAATATTATATTATAAATATTAA
4194324 TTTTAATATTATATTATAAATATTTAA
1 TTTTAATATTATATTATAAATA-TTAA
*
4194351 TTTT-ATATCATAT
1 TTTTAATATTATAT
4194364 AAATTATTTT
Statistics
Matches: 51, Mismatches: 6, Indels: 12
0.74 0.09 0.17
Matches are distributed among these distances:
22 6 0.12
23 1 0.02
24 10 0.20
25 4 0.08
26 16 0.31
27 8 0.16
28 6 0.12
ACGTcount: A:0.42, C:0.01, G:0.01, T:0.56
Consensus pattern (26 bp):
TTTTAATATTATATTATAAATATTAA
Found at i:4194919 original size:31 final size:30
Alignment explanation
Indices: 4194868--4194926 Score: 82
Period size: 31 Copynumber: 1.9 Consensus size: 30
4194858 TAGTTGTATG
* * *
4194868 AATTATTTAAATTTAGTATTGTAAAACTAA
1 AATTATTTAAATTCACTATTGCAAAACTAA
4194898 AATTATTTAAATCTCACTATTGCAAAACT
1 AATTATTTAAAT-TCACTATTGCAAAACT
4194927 CTTTTAAGTT
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
30 12 0.48
31 13 0.52
ACGTcount: A:0.44, C:0.10, G:0.05, T:0.41
Consensus pattern (30 bp):
AATTATTTAAATTCACTATTGCAAAACTAA
Found at i:4195349 original size:11 final size:11
Alignment explanation
Indices: 4195333--4195367 Score: 63
Period size: 11 Copynumber: 3.3 Consensus size: 11
4195323 CGTATTACCA
4195333 CGACCACGACC
1 CGACCACGACC
4195344 CGACCACGACC
1 CGACCACGACC
4195355 CGACC-CGACC
1 CGACCACGACC
4195365 CGA
1 CGA
4195368 GACGGACGGC
Statistics
Matches: 24, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
10 8 0.33
11 16 0.67
ACGTcount: A:0.26, C:0.54, G:0.20, T:0.00
Consensus pattern (11 bp):
CGACCACGACC
Found at i:4195358 original size:5 final size:5
Alignment explanation
Indices: 4195333--4195367 Score: 52
Period size: 5 Copynumber: 6.6 Consensus size: 5
4195323 CGTATTACCA
4195333 CGACC ACGACC CGACC ACGACC CGACC CGACC CGA
1 CGACC -CGACC CGACC -CGACC CGACC CGACC CGA
4195368 GACGGACGGC
Statistics
Matches: 28, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
5 18 0.64
6 10 0.36
ACGTcount: A:0.26, C:0.54, G:0.20, T:0.00
Consensus pattern (5 bp):
CGACC
Found at i:4195844 original size:11 final size:11
Alignment explanation
Indices: 4195828--4195893 Score: 100
Period size: 11 Copynumber: 6.0 Consensus size: 11
4195818 GACTCTCGCG
4195828 CGGGTCGTGGT
1 CGGGTCGTGGT
4195839 CGGGTCGTGGT
1 CGGGTCGTGGT
4195850 CGGGTCG-GGT
1 CGGGTCGTGGT
4195860 CGTGGTCG-GGT
1 CG-GGTCGTGGT
4195871 CGGGTCGTGGT
1 CGGGTCGTGGT
4195882 CGTGGTCGTGGT
1 CG-GGTCGTGGT
4195894 AATACGTGTC
Statistics
Matches: 52, Mismatches: 0, Indels: 5
0.91 0.00 0.09
Matches are distributed among these distances:
10 10 0.19
11 33 0.63
12 9 0.17
ACGTcount: A:0.00, C:0.18, G:0.55, T:0.27
Consensus pattern (11 bp):
CGGGTCGTGGT
Found at i:4195850 original size:6 final size:6
Alignment explanation
Indices: 4195830--4195893 Score: 93
Period size: 6 Copynumber: 11.5 Consensus size: 6
4195820 CTCTCGCGCG
4195830 GGTCGT GGTCG- GGTCGT GGTCG- GGTCG- GGTCGT GGTCG- GGTCG-
1 GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT
4195873 GGTCGT GGTCGT GGTCGT GGT
1 GGTCGT GGTCGT GGTCGT GGT
4195894 AATACGTGTC
Statistics
Matches: 55, Mismatches: 0, Indels: 6
0.90 0.00 0.10
Matches are distributed among these distances:
5 25 0.45
6 30 0.55
ACGTcount: A:0.00, C:0.17, G:0.55, T:0.28
Consensus pattern (6 bp):
GGTCGT
Found at i:4195857 original size:16 final size:17
Alignment explanation
Indices: 4195830--4195889 Score: 106
Period size: 16 Copynumber: 3.6 Consensus size: 17
4195820 CTCTCGCGCG
4195830 GGTCGTGGTCGGGTCGT
1 GGTCGTGGTCGGGTCGT
4195847 GGTCG-GGTCGGGTCGT
1 GGTCGTGGTCGGGTCGT
4195863 GGTCG-GGTCGGGTCGT
1 GGTCGTGGTCGGGTCGT
4195879 GGTCGTGGTCG
1 GGTCGTGGTCG
4195890 TGGTAATACG
Statistics
Matches: 42, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
16 32 0.76
17 10 0.24
ACGTcount: A:0.00, C:0.18, G:0.55, T:0.27
Consensus pattern (17 bp):
GGTCGTGGTCGGGTCGT
Found at i:4199021 original size:15 final size:15
Alignment explanation
Indices: 4199001--4199031 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
4198991 CTTTGCTCCA
4199001 TTTCCAAAAACCCAC
1 TTTCCAAAAACCCAC
*
4199016 TTTCCAAAACCCCAC
1 TTTCCAAAAACCCAC
4199031 T
1 T
4199032 AAAGATGTTC
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.35, C:0.42, G:0.00, T:0.23
Consensus pattern (15 bp):
TTTCCAAAAACCCAC
Found at i:4214527 original size:37 final size:37
Alignment explanation
Indices: 4214454--4214528 Score: 91
Period size: 38 Copynumber: 2.0 Consensus size: 37
4214444 GTTGGAAAAT
* *
4214454 ATTTATATATTTTCTTTAAAAATTTTAAATTCATAAA
1 ATTTATATATTTTCTTTAAAAATTTGAAAATCATAAA
*
4214491 ATTTATATAATTTTTTTTACAAAA-TTGAAAAT-ATAAA
1 ATTTATAT-ATTTTCTTTA-AAAATTTGAAAATCATAAA
4214528 A
1 A
4214529 AGGTTTAATT
Statistics
Matches: 33, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
37 14 0.42
38 15 0.45
39 4 0.12
ACGTcount: A:0.47, C:0.04, G:0.01, T:0.48
Consensus pattern (37 bp):
ATTTATATATTTTCTTTAAAAATTTGAAAATCATAAA
Found at i:4215068 original size:23 final size:23
Alignment explanation
Indices: 4215010--4215068 Score: 57
Period size: 23 Copynumber: 2.6 Consensus size: 23
4215000 TTGTGACATG
4215010 TTTCTCTGCCTTTATAGCACGCT
1 TTTCTCTGCCTTTATAGCACGCT
* * * * *
4215033 TATCTCCGTCTTTGT-GTCACGTT
1 TTTCTCTGCCTTTATAG-CACGCT
4215056 TTTCTCTGCCTTT
1 TTTCTCTGCCTTT
4215069 TGGTAGCTTA
Statistics
Matches: 27, Mismatches: 8, Indels: 2
0.73 0.22 0.05
Matches are distributed among these distances:
22 1 0.04
23 26 0.96
ACGTcount: A:0.08, C:0.29, G:0.14, T:0.49
Consensus pattern (23 bp):
TTTCTCTGCCTTTATAGCACGCT
Found at i:4219241 original size:39 final size:39
Alignment explanation
Indices: 4219193--4219391 Score: 193
Period size: 39 Copynumber: 4.8 Consensus size: 39
4219183 ACAAGATTTC
*
4219193 AAAAGTAAATCCAATGATTTATTTCCTTTTACAAAATAGG
1 AAAA-TAAATCCAATGATTTATTTCTTTTTACAAAATAGG
* * *
4219233 AAAATAAATCCAACGATTTATTTCCTTTTACGAAATAGG
1 AAAATAAATCCAATGATTTATTTCTTTTTACAAAATAGG
* * *
4219272 AGAATAAATTAAACGATTTATTTCAATTTATTTCTTTTTACAAAATA-G
1 AAAATAAA-T---CCA---A--T-GATTTATTTCTTTTTACAAAATAGG
* *
4219320 AAAATAAATTCAATGATTTATTTTCTTTTTTCAAAATAGG
1 AAAATAAATCCAATGATTTA-TTTCTTTTTACAAAATAGG
*
4219360 AAAATAAATCCAACGATTTATTTCTTTTTACA
1 AAAATAAATCCAATGATTTATTTCTTTTTACA
4219392 TATCATAATC
Statistics
Matches: 131, Mismatches: 16, Indels: 25
0.76 0.09 0.15
Matches are distributed among these distances:
38 5 0.04
39 68 0.52
40 24 0.18
41 1 0.01
43 2 0.02
44 1 0.01
46 1 0.01
47 1 0.01
48 8 0.06
49 20 0.15
ACGTcount: A:0.41, C:0.12, G:0.08, T:0.40
Consensus pattern (39 bp):
AAAATAAATCCAATGATTTATTTCTTTTTACAAAATAGG
Found at i:4219314 original size:88 final size:88
Alignment explanation
Indices: 4219209--4219383 Score: 253
Period size: 88 Copynumber: 2.0 Consensus size: 88
4219199 AAATCCAATG
*
4219209 ATTTATTTCCTTTTACAAAATAGGAAAATAAATCCAACGATTTA-TTTCCTTTTACGAAATAGGA
1 ATTTATTTCCTTTTACAAAATA-GAAAATAAATCCAACGATTTATTTTCCTTTTACAAAATAGGA
* *
4219273 GAATAAATTAAACGATTTATTTCA
65 AAATAAATCAAACGATTTATTTCA
* * * * *
4219297 ATTTATTTCTTTTTACAAAATAGAAAATAAATTCAATGATTTATTTTCTTTTTTCAAAATAGGAA
1 ATTTATTTCCTTTTACAAAATAGAAAATAAATCCAACGATTTATTTTCCTTTTACAAAATAGGAA
*
4219362 AATAAATCCAACGATTTATTTC
66 AATAAATCAAACGATTTATTTC
4219384 TTTTTACATA
Statistics
Matches: 77, Mismatches: 9, Indels: 2
0.88 0.10 0.02
Matches are distributed among these distances:
87 19 0.25
88 58 0.75
ACGTcount: A:0.41, C:0.11, G:0.07, T:0.41
Consensus pattern (88 bp):
ATTTATTTCCTTTTACAAAATAGAAAATAAATCCAACGATTTATTTTCCTTTTACAAAATAGGAA
AATAAATCAAACGATTTATTTCA
Found at i:4219338 original size:48 final size:49
Alignment explanation
Indices: 4219248--4219342 Score: 138
Period size: 48 Copynumber: 2.0 Consensus size: 49
4219238 AAATCCAACG
* *
4219248 ATTTATTTCCTTTTACGAAATAGGAGAATAAATTAAACGATTTATTTCA
1 ATTTATTTCCTTTTACAAAATAGGAAAATAAATTAAACGATTTATTTCA
* * *
4219297 ATTTATTTCTTTTTACAAAATA-GAAAATAAATTCAATGATTTATTT
1 ATTTATTTCCTTTTACAAAATAGGAAAATAAATTAAACGATTTATTT
4219343 TCTTTTTTCA
Statistics
Matches: 41, Mismatches: 5, Indels: 1
0.87 0.11 0.02
Matches are distributed among these distances:
48 21 0.51
49 20 0.49
ACGTcount: A:0.40, C:0.08, G:0.07, T:0.44
Consensus pattern (49 bp):
ATTTATTTCCTTTTACAAAATAGGAAAATAAATTAAACGATTTATTTCA
Found at i:4219477 original size:39 final size:39
Alignment explanation
Indices: 4219428--4219502 Score: 105
Period size: 39 Copynumber: 1.9 Consensus size: 39
4219418 AAATCAATTT
*
4219428 AACGATTTATTTCCTTATACAAAACAGGAAAATAAACTC
1 AACGATTTATTTCCTTACACAAAACAGGAAAATAAACTC
* * * *
4219467 AACGTTTTATTTCCTTGCATAAAATAGGAAAATAAA
1 AACGATTTATTTCCTTACACAAAACAGGAAAATAAA
4219503 TCTTATACAA
Statistics
Matches: 31, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
39 31 1.00
ACGTcount: A:0.45, C:0.15, G:0.09, T:0.31
Consensus pattern (39 bp):
AACGATTTATTTCCTTACACAAAACAGGAAAATAAACTC
Found at i:4219808 original size:56 final size:58
Alignment explanation
Indices: 4219727--4219863 Score: 206
Period size: 56 Copynumber: 2.4 Consensus size: 58
4219717 TAAATGATAG
* * * *
4219727 AATCATTCACGATTCTAAAGAAAATAAATTCAATAATTTATTTTTCTTACAAAGTT-A
1 AATCATTCAAGATTCTCAAGGAAATAAATCCAATAATTTATTTTTCTTACAAAGTTAA
*
4219784 AATCATTTAAGATT-TCAAGGAAATAAATCCAATAATTTATTTTTCTTACAAAGTTAA
1 AATCATTCAAGATTCTCAAGGAAATAAATCCAATAATTTATTTTTCTTACAAAGTTAA
*
4219841 AATTATTCAAGATTCTCAAGGAA
1 AATCATTCAAGATTCTCAAGGAA
4219864 CAATTTTATT
Statistics
Matches: 71, Mismatches: 7, Indels: 3
0.88 0.09 0.04
Matches are distributed among these distances:
56 38 0.54
57 25 0.35
58 8 0.11
ACGTcount: A:0.44, C:0.12, G:0.07, T:0.37
Consensus pattern (58 bp):
AATCATTCAAGATTCTCAAGGAAATAAATCCAATAATTTATTTTTCTTACAAAGTTAA
Found at i:4220428 original size:14 final size:15
Alignment explanation
Indices: 4220409--4220441 Score: 50
Period size: 14 Copynumber: 2.3 Consensus size: 15
4220399 GTTATATGAT
4220409 AATAATACCAT-AAC
1 AATAATACCATGAAC
*
4220423 AATAATATCATGAAC
1 AATAATACCATGAAC
4220438 AATA
1 AATA
4220442 TCATAATCAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
14 10 0.59
15 7 0.41
ACGTcount: A:0.58, C:0.15, G:0.03, T:0.24
Consensus pattern (15 bp):
AATAATACCATGAAC
Found at i:4221827 original size:17 final size:17
Alignment explanation
Indices: 4221805--4221839 Score: 70
Period size: 17 Copynumber: 2.1 Consensus size: 17
4221795 TGCGATTAAC
4221805 TCTCTCGATAATCATCT
1 TCTCTCGATAATCATCT
4221822 TCTCTCGATAATCATCT
1 TCTCTCGATAATCATCT
4221839 T
1 T
4221840 TGGTCATCTC
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.23, C:0.29, G:0.06, T:0.43
Consensus pattern (17 bp):
TCTCTCGATAATCATCT
Found at i:4226561 original size:22 final size:21
Alignment explanation
Indices: 4226529--4226579 Score: 59
Period size: 22 Copynumber: 2.4 Consensus size: 21
4226519 TCATAATTAA
*
4226529 ATTTTTT-AAAATTATCAAAT
1 ATTTTTTAAAAATAATCAAAT
*
4226549 ATTTTTTAAAAAATAATTAAAT
1 ATTTTTT-AAAAATAATCAAAT
4226571 ATTTATTTA
1 ATTT-TTTA
4226580 TCAAATTTTG
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
20 7 0.27
22 16 0.62
23 3 0.12
ACGTcount: A:0.47, C:0.02, G:0.00, T:0.51
Consensus pattern (21 bp):
ATTTTTTAAAAATAATCAAAT
Found at i:4227422 original size:20 final size:20
Alignment explanation
Indices: 4227394--4227431 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
4227384 AATCATATTC
4227394 ACTGATAATCTTACATTCTT
1 ACTGATAATCTTACATTCTT
* *
4227414 ACTGGTAATCTTCCATTC
1 ACTGATAATCTTACATTC
4227432 CGTGAACTAA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.26, C:0.24, G:0.08, T:0.42
Consensus pattern (20 bp):
ACTGATAATCTTACATTCTT
Found at i:4229066 original size:43 final size:43
Alignment explanation
Indices: 4228991--4229320 Score: 309
Period size: 43 Copynumber: 7.7 Consensus size: 43
4228981 TAATTTTTCT
* * * *
4228991 CTTTATAATTGAAG-TCTTCAATTTTTGT-AATCTTATTTTTTAC
1 CTTTATAATTGAGGCTCCT-AATTTTT-TCAATCTCACTTTTTAC
* * * *
4229034 CTTCATAAATGAGG-TCTCTGATTTTTTCAATCTCACTTTTTAT
1 CTTTATAATTGAGGCTC-CTAATTTTTTCAATCTCACTTTTTAC
* * *
4229077 CTTTATAATTGAGAC-CTCTAATTTTCTTCAATCTCAC-TTCTAG
1 CTTTATAATTGAGGCTC-CTAATTTT-TTCAATCTCACTTTTTAC
* * *
4229120 CTTTATAATTGAAGTTCCTAATTTTTTTAATCTCACTTTTTAC
1 CTTTATAATTGAGGCTCCTAATTTTTTCAATCTCACTTTTTAC
* *
4229163 CTTTATAATTGAGGCTCCTGATTTTTTTAATCAT-ACTTTTTAC
1 CTTTATAATTGAGGCTCCTAATTTTTTCAATC-TCACTTTTTAC
* * * * *
4229206 ATTTATAATCGAGGCCCCTAATGTTTTCAATCTCA-TTTTATAT
1 CTTTATAATTGAGGCTCCTAATTTTTTCAATCTCACTTTT-TAC
* * *
4229249 CTTTATAATTGAAGCTCCTAGTTTTTT--ATCTTACTTTTTAC
1 CTTTATAATTGAGGCTCCTAATTTTTTCAATCTCACTTTTTAC
*
4229290 CTTTATAATCGAGGCTCCTAATTTTTTCAAT
1 CTTTATAATTGAGGCTCCTAATTTTTTCAAT
4229321 ATCAATGTAG
Statistics
Matches: 234, Mismatches: 41, Indels: 24
0.78 0.14 0.08
Matches are distributed among these distances:
41 31 0.13
42 20 0.09
43 169 0.72
44 14 0.06
ACGTcount: A:0.25, C:0.18, G:0.08, T:0.50
Consensus pattern (43 bp):
CTTTATAATTGAGGCTCCTAATTTTTTCAATCTCACTTTTTAC
Found at i:4229160 original size:129 final size:128
Alignment explanation
Indices: 4228991--4229320 Score: 395
Period size: 129 Copynumber: 2.6 Consensus size: 128
4228981 TAATTTTTCT
* * * *
4228991 CTTTATAATTGAAGTCTTCAATTTTTGTAATCTTATTTTTTACCTTCATAAATGAGG-TCTCTGA
1 CTTTATAATTGAAGTCCT-AATTTTTTTAATCTTACTTTTTACCTTTATAAATGAGGCTC-CTGA
* * * *
4229055 TTTTTTCAATC-TCACTTTTTATC-TTTATAATTGAGACCTCTAATTTTCTTCAATCTCA-CTTC
64 TTTTTTCAATCAT-ACTTTTTA-CATTTATAATCGAGACCCCTAATGTT-TTCAATCTCATCTTA
4229117 TAG
126 TAG
* *
4229120 CTTTATAATTGAAGTTCCTAATTTTTTTAATCTCACTTTTTACCTTTATAATTGAGGCTCCTGAT
1 CTTTATAATTGAAG-TCCTAATTTTTTTAATCTTACTTTTTACCTTTATAAATGAGGCTCCTGAT
* * * *
4229185 TTTTTTAATCATACTTTTTACATTTATAATCGAGGCCCCTAATGTTTTCAATCTCATTTTATAT
65 TTTTTCAATCATACTTTTTACATTTATAATCGAGACCCCTAATGTTTTCAATCTCATCTTATAG
* *
4229249 CTTTATAATTGAAGCTCCT-AGTTTTTT-ATCTTACTTTTTACCTTTAT-AATCGAGGCTCCTAA
1 CTTTATAATTGAAG-TCCTAATTTTTTTAATCTTACTTTTTACCTTTATAAAT-GAGGCTCCTGA
4229311 TTTTTTCAAT
64 TTTTTTCAAT
4229321 ATCAATGTAG
Statistics
Matches: 175, Mismatches: 20, Indels: 14
0.84 0.10 0.07
Matches are distributed among these distances:
126 2 0.01
127 38 0.22
128 18 0.10
129 111 0.63
130 6 0.03
ACGTcount: A:0.25, C:0.18, G:0.08, T:0.50
Consensus pattern (128 bp):
CTTTATAATTGAAGTCCTAATTTTTTTAATCTTACTTTTTACCTTTATAAATGAGGCTCCTGATT
TTTTCAATCATACTTTTTACATTTATAATCGAGACCCCTAATGTTTTCAATCTCATCTTATAG
Found at i:4229433 original size:75 final size:73
Alignment explanation
Indices: 4229354--4229528 Score: 171
Period size: 75 Copynumber: 2.3 Consensus size: 73
4229344 TCCATATATT
*
4229354 TTTTTATACATATATATTATATA-GTTTGCG-AA-TGTTTTTGAAATACATATAATATATATAT-
1 TTTTTATAAATATATATTATATATGTTTG-GAAACT-TTTTTGAAA-ACATAT-ATA-ATATATG
4229415 AATTTTGAAAACA
61 AATTTTGAAAACA
* *
4229428 GTTTTTGA-AAATATATATTATATAATTTTTGGAAAACTTTTTTGGAAACATATATAATATATGA
1 -TTTTT-ATAAATATATATTATAT-ATGTTTGG-AAACTTTTTTGAAAACATATATAATATATGA
*
4229492 TTTTTGAAAACA
62 ATTTTGAAAACA
* *
4229504 TTTTAATATATATATATATATATAT
1 TTTTTATAAATATATAT-TATATAT
4229529 ATATATTATA
Statistics
Matches: 85, Mismatches: 6, Indels: 18
0.78 0.06 0.17
Matches are distributed among these distances:
74 1 0.01
75 40 0.47
76 23 0.27
77 10 0.12
78 10 0.12
79 1 0.01
ACGTcount: A:0.41, C:0.04, G:0.08, T:0.47
Consensus pattern (73 bp):
TTTTTATAAATATATATTATATATGTTTGGAAACTTTTTTGAAAACATATATAATATATGAATTT
TGAAAACA
Found at i:4229451 original size:38 final size:39
Alignment explanation
Indices: 4229387--4229528 Score: 145
Period size: 37 Copynumber: 3.7 Consensus size: 39
4229377 GTTTGCGAAT
*
4229387 GTTTTTGAAATACATATAATATATATATAATTTTGAAAACA
1 GTTTTTGAAA-ACATAT-ATATATATATATTTTTGAAAACA
*
4229428 GTTTTTGAAAATATATAT-TATATA-ATTTTTGGAAAAC-
1 GTTTTTGAAAACATATATATATATATATTTTT-GAAAACA
* *
4229465 TTTTTTGGAAACATATATA-ATATATGATTTTTGAAAACA
1 GTTTTTGAAAACATATATATATATAT-ATTTTTGAAAACA
* *
4229504 --TTTT-AATATATATATATATATATAT
1 GTTTTTGAAAACATATATATATATATAT
4229529 ATATATTATA
Statistics
Matches: 87, Mismatches: 8, Indels: 17
0.78 0.07 0.15
Matches are distributed among these distances:
36 11 0.13
37 35 0.40
38 18 0.21
39 8 0.09
40 5 0.06
41 10 0.11
ACGTcount: A:0.43, C:0.04, G:0.08, T:0.46
Consensus pattern (39 bp):
GTTTTTGAAAACATATATATATATATATTTTTGAAAACA
Found at i:4229470 original size:37 final size:35
Alignment explanation
Indices: 4229405--4229525 Score: 122
Period size: 39 Copynumber: 3.3 Consensus size: 35
4229395 AATACATATA
4229405 ATATA-TATATAA-TTTTGAAAACAGTTTTTGAAAAT
1 ATATATTATATAATTTTTGAAAAC--TTTTTGAAAAT
4229440 ATATATTATATAATTTTTGGAAAACTTTTTTGGAAACAT
1 ATATATTATATAATTTTT-GAAAAC-TTTTT-GAAA-AT
* * * *
4229479 ATATAATATATGATTTTTGAAAACATTTT-AATAT
1 ATATATTATATAATTTTTGAAAACTTTTTGAAAAT
4229513 ATATATATATATA
1 ATATAT-TATATA
4229526 TATATATATT
Statistics
Matches: 73, Mismatches: 7, Indels: 12
0.79 0.08 0.13
Matches are distributed among these distances:
34 7 0.10
35 12 0.16
36 7 0.10
37 13 0.18
38 16 0.22
39 18 0.25
ACGTcount: A:0.44, C:0.03, G:0.07, T:0.45
Consensus pattern (35 bp):
ATATATTATATAATTTTTGAAAACTTTTTGAAAAT
Found at i:4229510 original size:25 final size:26
Alignment explanation
Indices: 4229466--4229554 Score: 76
Period size: 26 Copynumber: 3.5 Consensus size: 26
4229456 TTGGAAAACT
*
4229466 TTTTTGGAAACATATATAATATATGA
1 TTTTTGAAAACATATATAATATATGA
*
4229492 TTTTTGAAAACAT-TTTAATATAT-A
1 TTTTTGAAAACATATATAATATATGA
* * * * * *
4229516 TATAT-ATATATATATATATTATATAA
1 TTTTTGA-AAACATATATAATATATGA
4229542 TTTTTGAAAACAT
1 TTTTTGAAAACAT
4229555 TTTGAAAATA
Statistics
Matches: 47, Mismatches: 12, Indels: 8
0.70 0.18 0.12
Matches are distributed among these distances:
23 1 0.02
24 8 0.17
25 17 0.36
26 20 0.43
27 1 0.02
ACGTcount: A:0.44, C:0.03, G:0.06, T:0.47
Consensus pattern (26 bp):
TTTTTGAAAACATATATAATATATGA
Found at i:4229516 original size:2 final size:2
Alignment explanation
Indices: 4229509--4229540 Score: 57
Period size: 2 Copynumber: 16.5 Consensus size: 2
4229499 AAACATTTTA
4229509 AT AT AT AT AT AT AT AT AT AT AT AT AT -T AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
4229541 ATTTTTGAAA
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 28 0.97
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:4229539 original size:50 final size:50
Alignment explanation
Indices: 4229477--4229575 Score: 155
Period size: 50 Copynumber: 2.0 Consensus size: 50
4229467 TTTTGGAAAC
* *
4229477 ATATATAATATATGATTTTTGAAAACATTTT-AATATATATATATATATAT
1 ATATATAATATATAATTTTTGAAAACATTTTGAAAATATATAT-TATATAT
*
4229527 ATATATATTATATAATTTTTGAAAACATTTTGAAAATATATATTATATA
1 ATATATAATATATAATTTTTGAAAACATTTTGAAAATATATATTATATA
4229576 GTTTTGAAAT
Statistics
Matches: 45, Mismatches: 3, Indels: 2
0.90 0.06 0.04
Matches are distributed among these distances:
50 35 0.78
51 10 0.22
ACGTcount: A:0.46, C:0.02, G:0.04, T:0.47
Consensus pattern (50 bp):
ATATATAATATATAATTTTTGAAAACATTTTGAAAATATATATTATATAT
Found at i:4229546 original size:89 final size:83
Alignment explanation
Indices: 4229438--4229607 Score: 234
Period size: 89 Copynumber: 2.0 Consensus size: 83
4229428 GTTTTTGAAA
* *
4229438 ATATATATTATATAATTTTTGGAAAACTTTTTTGGAAACATATATAATATATGATTTTTGAAAAC
1 ATATATATTATATAATTTTT-GAAAAC-ATTTT-GAAA-ATATATAATATAT-AGTTTTGAAAAC
4229503 A-TTTTAATATATATATATATATAT
61 ATTTTTAA-ATATA-ATATATATAT
* *
4229527 ATATATATTATATAATTTTTGAAAACATTTTGAAAATATATATTATATAGTTTTGAAATCATTTT
1 ATATATATTATATAATTTTTGAAAACATTTTGAAAATATATAATATATAGTTTTGAAAACATTTT
4229592 TAAATATAATATATAT
66 TAAATATAATATATAT
4229608 TAAAAAAAAC
Statistics
Matches: 76, Mismatches: 4, Indels: 8
0.86 0.05 0.09
Matches are distributed among these distances:
83 8 0.11
84 16 0.21
85 18 0.24
86 4 0.05
87 4 0.05
88 6 0.08
89 20 0.26
ACGTcount: A:0.44, C:0.03, G:0.06, T:0.48
Consensus pattern (83 bp):
ATATATATTATATAATTTTTGAAAACATTTTGAAAATATATAATATATAGTTTTGAAAACATTTT
TAAATATAATATATATAT
Found at i:4229567 original size:35 final size:35
Alignment explanation
Indices: 4229527--4229725 Score: 164
Period size: 34 Copynumber: 5.9 Consensus size: 35
4229517 ATATATATAT
4229527 ATATATATTATATAATTTTTGAAAACATTTTGAAA
1 ATATATATTATATAATTTTTGAAAACATTTTGAAA
* * *
4229562 ATATATATTATAT-AGTTTTGAAATCATTTT-TAA
1 ATATATATTATATAATTTTTGAAAACATTTTGAAA
****
4229595 ATATA-A-TATAT-ATTAAAAAAAACATTTTTGAAA
1 ATATATATTATATAATTTTTGAAAACA-TTTTGAAA
* * *
4229628 ACATGTAATATATAA-TTTT-AAAACATTTTTGAAA
1 ATATATATTATATAATTTTTGAAAACA-TTTTGAAA
* * *
4229662 AT-TATATAATATAATTTTTGAAAATATTTT-TAA
1 ATATATATTATATAATTTTTGAAAACATTTTGAAA
* * * *
4229695 ATATATAATATATAGTTTTTAAAAATATTTT
1 ATATATATTATATAATTTTTGAAAACATTTT
4229726 TTATATATTA
Statistics
Matches: 131, Mismatches: 25, Indels: 17
0.76 0.14 0.10
Matches are distributed among these distances:
31 12 0.09
32 5 0.04
33 25 0.19
34 64 0.49
35 24 0.18
36 1 0.01
ACGTcount: A:0.47, C:0.03, G:0.05, T:0.46
Consensus pattern (35 bp):
ATATATATTATATAATTTTTGAAAACATTTTGAAA
Found at i:4229738 original size:7 final size:7
Alignment explanation
Indices: 4229726--4229762 Score: 51
Period size: 7 Copynumber: 5.6 Consensus size: 7
4229716 AAAATATTTT
4229726 TTATATA
1 TTATATA
4229733 TTATATA
1 TTATATA
*
4229740 TTATATT
1 TTATATA
4229747 TTAT-TA
1 TTATATA
4229753 TTAT-TA
1 TTATATA
4229759 TTAT
1 TTAT
4229763 TCTTTTAATT
Statistics
Matches: 28, Mismatches: 2, Indels: 1
0.90 0.06 0.03
Matches are distributed among these distances:
6 11 0.39
7 17 0.61
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (7 bp):
TTATATA
Found at i:4229740 original size:33 final size:34
Alignment explanation
Indices: 4229527--4229749 Score: 133
Period size: 34 Copynumber: 6.6 Consensus size: 34
4229517 ATATATATAT
* * * *
4229527 ATATATATTATATAATTTTTGAAAACATTTTGAAA
1 ATATATAATATATAATTTTTAAAAATATTTT-TAA
* * *
4229562 ATATATATTATAT-AGTTTT-GAAATCATTTTT-A
1 ATATATAATATATAATTTTTAAAAAT-ATTTTTAA
*** *
4229594 A-ATATAATATAT-ATTAAAAAAAACATTTTTGAAA
1 ATATATAATATATAATTTTTAAAAATATTTTT--AA
* * *
4229628 ACATGTAATATATAA-TTTTAAAACAT-TTTTGAA
1 ATATATAATATATAATTTTTAAAA-ATATTTTTAA
*
4229661 A-AT-TATATAATATAATTTTTGAAAATATTTTTAA
1 ATATATA-AT-ATATAATTTTTAAAAATATTTTTAA
* *
4229695 ATATATAATATATAGTTTTTAAAAATATTTTT-T
1 ATATATAATATATAATTTTTAAAAATATTTTTAA
* *
4229728 ATATATTATATATTATATTTTA
1 ATATATAATATATAAT-TTTTA
4229750 TTATTATTAT
Statistics
Matches: 148, Mismatches: 25, Indels: 31
0.73 0.12 0.15
Matches are distributed among these distances:
31 20 0.14
32 9 0.06
33 27 0.18
34 52 0.35
35 36 0.24
36 4 0.03
ACGTcount: A:0.46, C:0.02, G:0.04, T:0.48
Consensus pattern (34 bp):
ATATATAATATATAATTTTTAAAAATATTTTTAA
Found at i:4229743 original size:14 final size:13
Alignment explanation
Indices: 4229726--4229778 Score: 56
Period size: 12 Copynumber: 4.2 Consensus size: 13
4229716 AAAATATTTT
4229726 TTATATATTATATA
1 TTATATATTAT-TA
*
4229740 TTATATTTTATTA
1 TTATATATTATTA
*
4229753 TTAT-TATTATTC
1 TTATATATTATTA
*
4229765 TTTTA-ATTATTA
1 TTATATATTATTA
4229777 TT
1 TT
4229779 TTTTCTTATT
Statistics
Matches: 33, Mismatches: 5, Indels: 4
0.79 0.12 0.10
Matches are distributed among these distances:
12 17 0.52
13 6 0.18
14 10 0.30
ACGTcount: A:0.32, C:0.02, G:0.00, T:0.66
Consensus pattern (13 bp):
TTATATATTATTA
Found at i:4229780 original size:12 final size:11
Alignment explanation
Indices: 4229720--4229789 Score: 53
Period size: 10 Copynumber: 6.7 Consensus size: 11
4229710 TTTTTAAAAA
4229720 TATT-TTTTAT
1 TATTATTTTAT
*
4229730 ATATTA-TATAT
1 -TATTATTTTAT
4229741 TA-TATTTTAT
1 TATTATTTTAT
4229751 TATTA--TTAT
1 TATTATTTTAT
*
4229760 TATTCTTTTAAT
1 TATTATTTT-AT
4229772 TATTATTTT-T
1 TATTATTTTAT
*
4229782 TCTTATTT
1 TATTATTT
4229790 ATTTATTTCT
Statistics
Matches: 48, Mismatches: 5, Indels: 13
0.73 0.08 0.20
Matches are distributed among these distances:
9 10 0.21
10 16 0.33
11 12 0.25
12 10 0.21
ACGTcount: A:0.27, C:0.03, G:0.00, T:0.70
Consensus pattern (11 bp):
TATTATTTTAT
Found at i:4229790 original size:21 final size:22
Alignment explanation
Indices: 4229726--4229796 Score: 67
Period size: 21 Copynumber: 3.2 Consensus size: 22
4229716 AAAATATTTT
* *
4229726 TTATATATTATATATTATATTTTA
1 TTAT-TATTAT-TATTCTATTTAA
4229750 TTATTATTATTATTCT-TTTAA
1 TTATTATTATTATTCTATTTAA
*
4229771 TTATTATT-TT-TTCTTATTTAT
1 TTATTATTATTATTC-TATTTAA
4229792 TTATT
1 TTATT
4229797 TCTTTTTGTT
Statistics
Matches: 42, Mismatches: 3, Indels: 7
0.81 0.06 0.13
Matches are distributed among these distances:
19 3 0.07
20 3 0.07
21 21 0.50
22 5 0.12
23 6 0.14
24 4 0.10
ACGTcount: A:0.28, C:0.03, G:0.00, T:0.69
Consensus pattern (22 bp):
TTATTATTATTATTCTATTTAA
Found at i:4229800 original size:34 final size:31
Alignment explanation
Indices: 4229739--4229802 Score: 76
Period size: 31 Copynumber: 2.0 Consensus size: 31
4229729 TATATTATAT
4229739 ATTATATTTTATTATTATTATTATTCTTTTA
1 ATTATATTTTATTATTATTATTATTCTTTTA
*
4229770 ATTATTATTTT-TTCTTATTTATTTATTTCTTTT
1 ATTA-TATTTTATTATTA-TTA-TTA-TTCTTTT
4229803 TGTTTTTCTG
Statistics
Matches: 28, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
31 9 0.32
32 9 0.32
33 3 0.11
34 7 0.25
ACGTcount: A:0.23, C:0.05, G:0.00, T:0.72
Consensus pattern (31 bp):
ATTATATTTTATTATTATTATTATTCTTTTA
Found at i:4230528 original size:10 final size:10
Alignment explanation
Indices: 4230513--4230547 Score: 70
Period size: 10 Copynumber: 3.5 Consensus size: 10
4230503 TTAGGTTTGC
4230513 TCGGCCACCG
1 TCGGCCACCG
4230523 TCGGCCACCG
1 TCGGCCACCG
4230533 TCGGCCACCG
1 TCGGCCACCG
4230543 TCGGC
1 TCGGC
4230548 GATAGCCGGC
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 25 1.00
ACGTcount: A:0.09, C:0.49, G:0.31, T:0.11
Consensus pattern (10 bp):
TCGGCCACCG
Found at i:4230557 original size:20 final size:20
Alignment explanation
Indices: 4230514--4230557 Score: 52
Period size: 20 Copynumber: 2.2 Consensus size: 20
4230504 TAGGTTTGCT
* *
4230514 CGGCCACCGTCGGCCACCGT
1 CGGCCACCGTCGGCCACAGC
* *
4230534 CGGCCACCGTCGGCGATAGC
1 CGGCCACCGTCGGCCACAGC
4230554 CGGC
1 CGGC
4230558 ACGGTGGCCG
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.11, C:0.45, G:0.34, T:0.09
Consensus pattern (20 bp):
CGGCCACCGTCGGCCACAGC
Found at i:4232805 original size:19 final size:19
Alignment explanation
Indices: 4232771--4232815 Score: 74
Period size: 19 Copynumber: 2.4 Consensus size: 19
4232761 ATTTAGACAT
4232771 TTTGCA-TTTCTTATTTTC
1 TTTGCATTTTCTTATTTTC
*
4232789 TTTGCATTTTGTTATTTTC
1 TTTGCATTTTCTTATTTTC
4232808 TTTGCATT
1 TTTGCATT
4232816 CACATTAACT
Statistics
Matches: 25, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
18 6 0.24
19 19 0.76
ACGTcount: A:0.11, C:0.13, G:0.09, T:0.67
Consensus pattern (19 bp):
TTTGCATTTTCTTATTTTC
Found at i:4237191 original size:164 final size:164
Alignment explanation
Indices: 4236157--4237165 Score: 1639
Period size: 164 Copynumber: 6.1 Consensus size: 164
4236147 CTCAAGGCTG
** * * *
4236157 GAAGGGTTATCTGTGACCAAAAGACCTTTGAGTTCGACTACGCTCAGCTCCAAGGCACATCATTT
1 GAAGGGTTATCTGCCAACAAAAGACCTTCGAGTTCGACTACGCTCAGCTCTAAGGCACATCATTT
*
4236222 GCAGCATAGCTTAAGTCGAGGAA-GGCTATCTGCCAAAGACCTTCGAGTTCGATTACACTCAGC-
66 GCAGCATAGCTTAAGTCGA-GAAGGGCTATCTGCCAAAGACC-CCGAGTTCGATTACACTCAGCT
* * * *
4236285 TCTGAGGGCATATCATTTGCAGCACAACTTAAGTCTA
129 TC-GAGGGCACATCATTTGCAGTATAACTTAAGTCAA
4236322 GAAGGGTTGA-CTGCCAACAAAAGACCTTCGAGTTCGACTACGCTCAGCTCTAAGGCACATCATT
1 GAAGGGTT-ATCTGCCAACAAAAGACCTTCGAGTTCGACTACGCTCAGCTCTAAGGCACATCATT
4236386 TGCAGCATAGCTTAAGTCGAGAAGGGCTATCTGCCAAAGACCCCGAGTTCGATTACACTCAGCTT
65 TGCAGCATAGCTTAAGTCGAGAAGGGCTATCTGCCAAAGACCCCGAGTTCGATTACACTCAGCTT
4236451 CGAGGGCACATCATTTGCAGTATAACTTAAGTCAA
130 CGAGGGCACATCATTTGCAGTATAACTTAAGTCAA
4236486 GAAGGGTTATCTGCCAACAAAAGACCTTCGAGTTCGACTACGCTCAGCTCTAAGGCACATCATTT
1 GAAGGGTTATCTGCCAACAAAAGACCTTCGAGTTCGACTACGCTCAGCTCTAAGGCACATCATTT
4236551 GCAGCATAGCTTAAGTCGAGAAGGGCTATCTGCCAAAGACCCCGAGTTCGATTACACTCAGCTTC
66 GCAGCATAGCTTAAGTCGAGAAGGGCTATCTGCCAAAGACCCCGAGTTCGATTACACTCAGCTTC
4236616 GAGGGCACATCATTTGCAGTATAACTTAAGTCAA
131 GAGGGCACATCATTTGCAGTATAACTTAAGTCAA
4236650 GAAGGGTTATCTGCCAACAAAAGACCTTCGAGTTCGACTACGCTCAGCTCTAAGGCACATCATTT
1 GAAGGGTTATCTGCCAACAAAAGACCTTCGAGTTCGACTACGCTCAGCTCTAAGGCACATCATTT
*
4236715 GCAGCATAGCTTAAGTCGAGAAGGGCTATCTGCCAAAGACCCCGAGTTCAATTACACTCAGCTTC
66 GCAGCATAGCTTAAGTCGAGAAGGGCTATCTGCCAAAGACCCCGAGTTCGATTACACTCAGCTTC
*
4236780 GATGGCACATCATTTGCAGTATAACTTAAGTCAA
131 GAGGGCACATCATTTGCAGTATAACTTAAGTCAA
4236814 GAAGGGTTATCTGCCAACAAAAGACCTTCGAGTTCGACTACGCTCAGCTCTAAGGCACATCATTT
1 GAAGGGTTATCTGCCAACAAAAGACCTTCGAGTTCGACTACGCTCAGCTCTAAGGCACATCATTT
4236879 GCAGCATAGCTTAAGTCGAGAAGGGCTATCTGCCAAAGACCCCGAGTTCGATTACACTCAGCTTC
66 GCAGCATAGCTTAAGTCGAGAAGGGCTATCTGCCAAAGACCCCGAGTTCGATTACACTCAGCTTC
*
4236944 GAGGGTACATCATTTGCAGTATAACTTAAGTCAA
131 GAGGGCACATCATTTGCAGTATAACTTAAGTCAA
* *
4236978 TAAGGGTTATCTGCCAACAAAAGACCTTCGAGTTCGACTACGCTCAGCTCCAAGGCACATCATTT
1 GAAGGGTTATCTGCCAACAAAAGACCTTCGAGTTCGACTACGCTCAGCTCTAAGGCACATCATTT
* * * ** * * *
4237043 GCAGCGTAGCTTAAGTCGAGAAGGGTTATCTGCTAAAGACCTTTGAGTTCGATTATATTCAACTT
66 GCAGCATAGCTTAAGTCGAGAAGGGCTATCTGCCAAAGACC-CCGAGTTCGATTACACTCAGCTT
* * * * * * * *
4237108 AGA-GGCAAATCAAGCTTACAGAATAGCTCAAGGCAA
130 CGAGGGCACATC-A-TTTGCAGTATAACTTAAGTCAA
*
4237144 GAAGGGTTATCTGCCAATAAAA
1 GAAGGGTTATCTGCCAACAAAA
4237166 TTGTTGAGTT
Statistics
Matches: 801, Mismatches: 36, Indels: 13
0.94 0.04 0.02
Matches are distributed among these distances:
163 1 0.00
164 645 0.81
165 118 0.15
166 37 0.05
ACGTcount: A:0.30, C:0.24, G:0.21, T:0.24
Consensus pattern (164 bp):
GAAGGGTTATCTGCCAACAAAAGACCTTCGAGTTCGACTACGCTCAGCTCTAAGGCACATCATTT
GCAGCATAGCTTAAGTCGAGAAGGGCTATCTGCCAAAGACCCCGAGTTCGATTACACTCAGCTTC
GAGGGCACATCATTTGCAGTATAACTTAAGTCAA
Found at i:4237795 original size:38 final size:38
Alignment explanation
Indices: 4237705--4237872 Score: 143
Period size: 37 Copynumber: 4.5 Consensus size: 38
4237695 ATTTTTTTAT
* ** *
4237705 ACATATATAT-TATATA-GTTTGCGAATGTTTTTGAAA
1 ACATATATATATATATATTTTTGAAAACGTTTTTGAAA
*
4237741 TACATATAATATATATATAATTTTGAAAACGGTTTTTGAAA
1 -ACATAT-ATATATATATATTTTTGAAAAC-GTTTTTGAAA
* * *
4237782 ATATATAT-TATATA-ATTTTTGGAAAACTTTTTTGGAA
1 ACATATATATATATATATTTTT-GAAAACGTTTTTGAAA
* *
4237819 ACATATATA-ATATATGATTTTTGAAAAC-ATTTT-AAT
1 ACATATATATATATAT-ATTTTTGAAAACGTTTTTGAAA
*
4237855 ATATATATATATATATAT
1 ACATATATATATATATAT
4237873 ATATATAATT
Statistics
Matches: 109, Mismatches: 13, Indels: 19
0.77 0.09 0.13
Matches are distributed among these distances:
36 11 0.10
37 41 0.38
38 22 0.20
39 14 0.13
40 11 0.10
41 10 0.09
ACGTcount: A:0.42, C:0.04, G:0.09, T:0.45
Consensus pattern (38 bp):
ACATATATATATATATATTTTTGAAAACGTTTTTGAAA
Found at i:4237854 original size:25 final size:26
Alignment explanation
Indices: 4237810--4237858 Score: 73
Period size: 26 Copynumber: 1.9 Consensus size: 26
4237800 TTGGAAAACT
*
4237810 TTTTTGGAAACATATATAATATATGA
1 TTTTTGAAAACATATATAATATATGA
*
4237836 TTTTTGAAAACAT-TTTAATATAT
1 TTTTTGAAAACATATATAATATAT
4237859 ATATATATAT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
25 9 0.43
26 12 0.57
ACGTcount: A:0.41, C:0.04, G:0.08, T:0.47
Consensus pattern (26 bp):
TTTTTGAAAACATATATAATATATGA
Found at i:4237860 original size:2 final size:2
Alignment explanation
Indices: 4237853--4237879 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
4237843 AAACATTTTA
4237853 AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT A
4237880 ATTTTTGAAA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:4237884 original size:45 final size:44
Alignment explanation
Indices: 4237821--4237914 Score: 136
Period size: 45 Copynumber: 2.1 Consensus size: 44
4237811 TTTTGGAAAC
* *
4237821 ATATATAATATATGATTTTTGAAAACATTTT-AATATATATATAT
1 ATATATAATATATAATTTTTGAAAACATTTTCAAAATATATAT-T
*
4237865 ATATATATATATATAATTTTTGAAAACATTTTCAAAATGTATATT
1 ATATATA-ATATATAATTTTTGAAAACATTTTCAAAATATATATT
4237910 ATATA
1 ATATA
4237915 GTTTTGAAAT
Statistics
Matches: 45, Mismatches: 3, Indels: 3
0.88 0.06 0.06
Matches are distributed among these distances:
44 7 0.16
45 29 0.64
46 9 0.20
ACGTcount: A:0.46, C:0.03, G:0.04, T:0.47
Consensus pattern (44 bp):
ATATATAATATATAATTTTTGAAAACATTTTCAAAATATATATT
Found at i:4237908 original size:34 final size:33
Alignment explanation
Indices: 4237867--4238082 Score: 129
Period size: 34 Copynumber: 6.4 Consensus size: 33
4237857 ATATATATAT
4237867 ATATATATATATAATTTTTGAAAACATTTTCAAA
1 ATATATATATATAATTTTTGAAAACATTTT-AAA
* * * *
4237901 ATGTATAT-TATATAGTTTTGAAATCATTTTTAA
1 ATATATATATATA-ATTTTTGAAAACATTTTAAA
****
4237934 ATATA-ATATAT-ATTAAAAAAAACATTTTTGAAA
1 ATATATATATATAATTTTTGAAAACA-TTTT-AAA
* *
4237967 ACATGTAATATATAA-TTTT-AAAACATTTTTGAAA
1 ATATAT-ATATATAATTTTTGAAAACA-TTTT-AAA
* * *
4238001 AT-TATATAATATAATTTTGGAAAATATTTTTAA
1 ATATATAT-ATATAATTTTTGAAAACATTTTAAA
* * * * *
4238034 ATATATAATATATAGTTTTTAAAAATATTTTTTAT
1 ATATAT-ATATATAATTTTTGAAAACA-TTTTAAA
4238069 ATATTATATATATA
1 ATA-TATATATATA
4238083 TTATTATTAT
Statistics
Matches: 142, Mismatches: 26, Indels: 27
0.73 0.13 0.14
Matches are distributed among these distances:
31 7 0.05
32 8 0.06
33 30 0.21
34 63 0.44
35 30 0.21
36 4 0.03
ACGTcount: A:0.46, C:0.03, G:0.05, T:0.46
Consensus pattern (33 bp):
ATATATATATATAATTTTTGAAAACATTTTAAA
Found at i:4238867 original size:10 final size:10
Alignment explanation
Indices: 4238852--4238886 Score: 70
Period size: 10 Copynumber: 3.5 Consensus size: 10
4238842 TTAGGTTTGC
4238852 TCGGCCACCG
1 TCGGCCACCG
4238862 TCGGCCACCG
1 TCGGCCACCG
4238872 TCGGCCACCG
1 TCGGCCACCG
4238882 TCGGC
1 TCGGC
4238887 GATAGCCGGC
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 25 1.00
ACGTcount: A:0.09, C:0.49, G:0.31, T:0.11
Consensus pattern (10 bp):
TCGGCCACCG
Found at i:4238896 original size:20 final size:20
Alignment explanation
Indices: 4238853--4238896 Score: 52
Period size: 20 Copynumber: 2.2 Consensus size: 20
4238843 TAGGTTTGCT
* *
4238853 CGGCCACCGTCGGCCACCGT
1 CGGCCACCGTCGGCCACAGC
* *
4238873 CGGCCACCGTCGGCGATAGC
1 CGGCCACCGTCGGCCACAGC
4238893 CGGC
1 CGGC
4238897 ACGGTGGCCG
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.11, C:0.45, G:0.34, T:0.09
Consensus pattern (20 bp):
CGGCCACCGTCGGCCACAGC
Found at i:4239817 original size:43 final size:42
Alignment explanation
Indices: 4239747--4240082 Score: 200
Period size: 43 Copynumber: 7.8 Consensus size: 42
4239737 GACAACCAAT
**
4239747 TTTTACCTTTATAATTG-AGACATCTAATTTTTTCAATCTCAC
1 TTTTACCTTTATAATTGAAG-CCCCTAATTTTTTCAATCTCAC
* *
4239789 TTTCTACCTTTATAATTGAAGCCCCTAA-TTTTTCTATTCTCAT
1 TTT-TACCTTTATAATTGAAGCCCCTAATTTTTTC-AATCTCAC
*
4239832 TTCTTACCTGTATAATTG-AGACTCCC-AATTCTTTTCAACTTCTC-C
1 TT-TTACCTTTATAATTGAAG-C-CCCTAATT-TTTTCAA--TCTCAC
* * * * *
4239877 TTTTATCTTTATAATTGAAGCCCTTAATTTTTTTTATTCTCATTT
1 TTTTACCTTTATAATTGAAGCCCCTAA-TTTTTTCAATCTCA--C
* ** * *
4239922 TTTTACATTTATAATTG-AGATTCTTAATTTTTTAAATCTCATC
1 TTTTACCTTTATAATTGAAG-CCCCTAATTTTTTCAATCTCA-C
* * * *** * *
4239965 TTTTACTTTTATAACTGAGGTTTCTAATTTTTTTTAATCTCTC
1 TTTTACCTTTATAATTGAAGCCCCTAA-TTTTTTCAATCTCAC
* * * *
4240008 TTTCTACCTTTATAATTAAAGTCCCTAATTTTTT-AATCACGCC
1 TTT-TACCTTTATAATTGAAGCCCCTAATTTTTTCAATCTC-AC
* * *
4240051 TTTTAACTTTATAATTGAGGCTCCTAATTTTT
1 TTTTACCTTTATAATTGAAGCCCCTAATTTTT
4240083 AAATCCAACT
Statistics
Matches: 233, Mismatches: 40, Indels: 42
0.74 0.13 0.13
Matches are distributed among these distances:
42 44 0.19
43 80 0.34
44 74 0.32
45 31 0.13
46 4 0.02
ACGTcount: A:0.25, C:0.18, G:0.06, T:0.51
Consensus pattern (42 bp):
TTTTACCTTTATAATTGAAGCCCCTAATTTTTTCAATCTCAC
Found at i:4239894 original size:87 final size:86
Alignment explanation
Indices: 4239745--4240082 Score: 259
Period size: 86 Copynumber: 3.9 Consensus size: 86
4239735 GCGACAACCA
*
4239745 ATTTTTACCTTTATAATTGAGACATCTAATTTTTTCAATCTCACTTTCTACCTTTATAATTGAAG
1 ATTTTTACCTTTATAATTGAGACATCCAATTTTTTCAATCTCACTTTCTACCTTTATAATTGAAG
4239810 CCCCTAA-TTTTTCTATTCTC
66 CCCCTAATTTTTTCTATTCTC
* *
4239830 ATTTCTTACCTGTATAATTGAGAC-TCCCAATTCTTTTCAACTTCTC-CTTT-TATCTTTATAAT
1 ATTT-TTACCTTTATAATTGAGACAT-CCAATT-TTTTCAA--TCTCACTTTCTACCTTTATAAT
* *
4239892 TGAAGCCCTTAATTTTTTTTATTCTC
61 TGAAGCCCCTAATTTTTTCTATTCTC
* * * * * *
4239918 ATTTTTTTACATTTATAATTGAGA-TTCTTAATTTTTTAAATCTCATCTTT-TACTTTTATAACT
1 A--TTTTTACCTTTATAATTGAGACATC-CAATTTTTTCAATCTCA-CTTTCTACCTTTATAATT
* *** *
4239981 GAGGTTTCTAATTTTTTTTAATCTCTC
62 GAAGCCCCTAATTTTTTCT-AT-TCTC
* * * *
4240008 -TTTCTACCTTTATAATT-A-A-AGTCCCTAATTTTTT-AATCACGCCTTT-TAACTTTATAATT
1 ATTTTTACCTTTATAATTGAGACA-T-CC-AATTTTTTCAATCTC-ACTTTCTACCTTTATAATT
* *
4240067 GAGGCTCCTAATTTTT
62 GAAGCCCCTAATTTTT
4240083 AAATCCAACT
Statistics
Matches: 207, Mismatches: 28, Indels: 35
0.77 0.10 0.13
Matches are distributed among these distances:
85 6 0.03
86 62 0.30
87 53 0.26
88 52 0.25
89 27 0.13
90 7 0.03
ACGTcount: A:0.25, C:0.18, G:0.06, T:0.51
Consensus pattern (86 bp):
ATTTTTACCTTTATAATTGAGACATCCAATTTTTTCAATCTCACTTTCTACCTTTATAATTGAAG
CCCCTAATTTTTTCTATTCTC
Found at i:4239933 original size:45 final size:45
Alignment explanation
Indices: 4239746--4240041 Score: 120
Period size: 44 Copynumber: 6.8 Consensus size: 45
4239736 CGACAACCAA
* * * *
4239746 TTTTTACCTTTATAATTGAGA-CATCTAA-TTTTTTCAATCTCA-C
1 TTTTTACATTTATAATTGAGACCCT-TAATTTTTTTTAATCTCATT
* * * * *
4239789 TTTCTACCTTTATAATTGA-AGCCCCTAA-TTTTTCTATTCTCA-T
1 TTTTTACATTTATAATTGAGA-CCCTTAATTTTTTTTAATCTCATT
* * * * * * *
4239832 TTCTTACCTGTATAATTGAGACTCC-CAATTCTTTTCAA-CTTC-TC
1 TTTTTACATTTATAATTGAGAC-CCTTAATTTTTTTTAATC-TCATT
* *
4239876 CTTTTATC-TTTATAATTGA-AGCCCTTAATTTTTTTTATTCTCATT
1 TTTTTA-CATTTATAATTGAGA-CCCTTAATTTTTTTTAATCTCATT
** *
4239921 TTTTTACATTTATAATTGAGATTCTTAA-TTTTTTAAATCTCA-T
1 TTTTTACATTTATAATTGAGACCCTTAATTTTTTTTAATCTCATT
* * * *** *
4239964 CTTTTACTTTTATAACTGAG-GTTTCTAATTTTTTTTAATCTC-TC
1 TTTTTACATTTATAATTGAGACCCT-TAATTTTTTTTAATCTCATT
* * * *
4240008 TTTCTACCTTTATAATTAAAGTCCC-TAATTTTTT
1 TTTTTACATTTATAATT-GAGACCCTTAATTTTTT
4240042 AATCACGCCT
Statistics
Matches: 190, Mismatches: 44, Indels: 37
0.70 0.16 0.14
Matches are distributed among these distances:
42 3 0.02
43 76 0.40
44 84 0.44
45 26 0.14
46 1 0.01
ACGTcount: A:0.25, C:0.18, G:0.05, T:0.52
Consensus pattern (45 bp):
TTTTTACATTTATAATTGAGACCCTTAATTTTTTTTAATCTCATT
Found at i:4239997 original size:44 final size:44
Alignment explanation
Indices: 4239899--4240022 Score: 137
Period size: 44 Copynumber: 2.8 Consensus size: 44
4239889 AATTGAAGCC
* * *
4239899 CTTAATTTTTTTTATTCTCATTTTTTTACATTTATAATTGAGATT
1 CTTAATTTTTTTTAATCTCA-TCTTTTACATTTATAACTGAGATT
* * *
4239944 CTTAA-TTTTTTAAATCTCATCTTTTACTTTTATAACTGAGGTT
1 CTTAATTTTTTTTAATCTCATCTTTTACATTTATAACTGAGATT
*
4239987 -TCTAATTTTTTTTAATCTC-TCTTTCTACCTTTATAA
1 CT-TAATTTTTTTTAATCTCATCTTT-TACATTTATAA
4240023 TTAAAGTCCC
Statistics
Matches: 68, Mismatches: 8, Indels: 7
0.82 0.10 0.08
Matches are distributed among these distances:
42 1 0.01
43 28 0.41
44 34 0.50
45 5 0.07
ACGTcount: A:0.24, C:0.14, G:0.04, T:0.58
Consensus pattern (44 bp):
CTTAATTTTTTTTAATCTCATCTTTTACATTTATAACTGAGATT
Found at i:4240830 original size:2 final size:2
Alignment explanation
Indices: 4240825--4240859 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
4240815 GTTAGAGAGC
4240825 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
4240860 GGGCAGTTTT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:4240883 original size:25 final size:25
Alignment explanation
Indices: 4240850--4240900 Score: 102
Period size: 25 Copynumber: 2.0 Consensus size: 25
4240840 TATATATATA
4240850 TATATATATAGGGCAGTTTTAACTT
1 TATATATATAGGGCAGTTTTAACTT
4240875 TATATATATAGGGCAGTTTTAACTT
1 TATATATATAGGGCAGTTTTAACTT
4240900 T
1 T
4240901 TTTGCGCGGT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 26 1.00
ACGTcount: A:0.31, C:0.08, G:0.16, T:0.45
Consensus pattern (25 bp):
TATATATATAGGGCAGTTTTAACTT
Found at i:4248520 original size:15 final size:15
Alignment explanation
Indices: 4248500--4248533 Score: 59
Period size: 15 Copynumber: 2.3 Consensus size: 15
4248490 AGATTTTATT
4248500 ATTAATTTACAATAA
1 ATTAATTTACAATAA
*
4248515 ATTAATTTATAATAA
1 ATTAATTTACAATAA
4248530 ATTA
1 ATTA
4248534 TTTTTAAAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.53, C:0.03, G:0.00, T:0.44
Consensus pattern (15 bp):
ATTAATTTACAATAA
Found at i:4250302 original size:67 final size:67
Alignment explanation
Indices: 4250176--4250309 Score: 180
Period size: 67 Copynumber: 2.0 Consensus size: 67
4250166 TCTTAGGCCT
* * * *
4250176 ATAAAGAATTATCAGTCAGTGCTGAACCTATTCAAGGAATTACCAGCAGCGACTAAACCTGCCAG
1 ATAAAGAATTACCAGTCAGTGCTGAACCTATACAAGGAATTACCAACAACGACTAAACCTGCCAG
4250241 AG
66 AG
* * * *
4250243 ATAAGGAATTACCAGTC-GATGCTGAACCTATACATGGAATTACCAACAACGATTGAACCTGCCA
1 ATAAAGAATTACCAGTCAG-TGCTGAACCTATACAAGGAATTACCAACAACGACTAAACCTGCCA
4250307 GAG
65 GAG
4250310 TCTTCATACC
Statistics
Matches: 58, Mismatches: 8, Indels: 2
0.85 0.12 0.03
Matches are distributed among these distances:
66 1 0.02
67 57 0.98
ACGTcount: A:0.37, C:0.22, G:0.19, T:0.21
Consensus pattern (67 bp):
ATAAAGAATTACCAGTCAGTGCTGAACCTATACAAGGAATTACCAACAACGACTAAACCTGCCAG
AG
Found at i:4253355 original size:25 final size:25
Alignment explanation
Indices: 4253318--4253367 Score: 82
Period size: 25 Copynumber: 2.0 Consensus size: 25
4253308 TCTATCTATC
4253318 GATATGTTCAGTCTAAGATAAAGCT
1 GATATGTTCAGTCTAAGATAAAGCT
* *
4253343 GATATGTTTAGTCTAATATAAAGCT
1 GATATGTTCAGTCTAAGATAAAGCT
4253368 TTTTTTATGT
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
25 23 1.00
ACGTcount: A:0.36, C:0.10, G:0.18, T:0.36
Consensus pattern (25 bp):
GATATGTTCAGTCTAAGATAAAGCT
Found at i:4274831 original size:9 final size:10
Alignment explanation
Indices: 4274802--4274833 Score: 55
Period size: 10 Copynumber: 3.2 Consensus size: 10
4274792 TGTTTAGATT
*
4274802 AATAATAAAA
1 AATATTAAAA
4274812 AATATTAAAA
1 AATATTAAAA
4274822 AATATTAAAA
1 AATATTAAAA
4274832 AA
1 AA
4274834 AACCAATTAT
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
10 21 1.00
ACGTcount: A:0.75, C:0.00, G:0.00, T:0.25
Consensus pattern (10 bp):
AATATTAAAA
Found at i:4275584 original size:22 final size:22
Alignment explanation
Indices: 4275559--4275606 Score: 62
Period size: 22 Copynumber: 2.2 Consensus size: 22
4275549 TCATTCCATG
* *
4275559 TTTTTTCTG-TATTTTGATAGT
1 TTTTTTTTGTTATTTTCATAGT
*
4275580 TTTTTTTTGTTCTTTTCATAGT
1 TTTTTTTTGTTATTTTCATAGT
4275602 TTTTT
1 TTTTT
4275607 CACTTAATTT
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
21 8 0.35
22 15 0.65
ACGTcount: A:0.10, C:0.06, G:0.10, T:0.73
Consensus pattern (22 bp):
TTTTTTTTGTTATTTTCATAGT
Found at i:4277226 original size:2 final size:2
Alignment explanation
Indices: 4277219--4277248 Score: 51
Period size: 2 Copynumber: 15.0 Consensus size: 2
4277209 TGGTTTCTAG
*
4277219 TA TA TA TA TA TA TA TA TA TA TA TA TT TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
4277249 ATCAAATATT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (2 bp):
TA
Found at i:4283028 original size:2 final size:2
Alignment explanation
Indices: 4283021--4283045 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
4283011 ATTCCATTAC
4283021 TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA T
4283046 GAGTGAGTTC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:4285800 original size:16 final size:17
Alignment explanation
Indices: 4285779--4285811 Score: 50
Period size: 16 Copynumber: 2.0 Consensus size: 17
4285769 TAAAAGTTAA
4285779 ATTAATTATT-AAAAAT
1 ATTAATTATTGAAAAAT
*
4285795 ATTAATTTTTGAAAAAT
1 ATTAATTATTGAAAAAT
4285812 GTCAAATCTT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 9 0.60
17 6 0.40
ACGTcount: A:0.52, C:0.00, G:0.03, T:0.45
Consensus pattern (17 bp):
ATTAATTATTGAAAAAT
Found at i:4290417 original size:20 final size:20
Alignment explanation
Indices: 4290392--4290438 Score: 85
Period size: 20 Copynumber: 2.4 Consensus size: 20
4290382 TATTCCCTGA
*
4290392 TAATCTTTTATTCTCACTGG
1 TAATCTTTTATTCCCACTGG
4290412 TAATCTTTTATTCCCACTGG
1 TAATCTTTTATTCCCACTGG
4290432 TAATCTT
1 TAATCTT
4290439 ACATCACTTG
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 26 1.00
ACGTcount: A:0.21, C:0.21, G:0.09, T:0.49
Consensus pattern (20 bp):
TAATCTTTTATTCCCACTGG
Found at i:4294238 original size:31 final size:31
Alignment explanation
Indices: 4294200--4294262 Score: 126
Period size: 31 Copynumber: 2.0 Consensus size: 31
4294190 AAATTATATG
4294200 AAAAATTGATGAAATACCCACAAAGAAATGA
1 AAAAATTGATGAAATACCCACAAAGAAATGA
4294231 AAAAATTGATGAAATACCCACAAAGAAATGA
1 AAAAATTGATGAAATACCCACAAAGAAATGA
4294262 A
1 A
4294263 GGAAAAAGAA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
31 32 1.00
ACGTcount: A:0.59, C:0.13, G:0.13, T:0.16
Consensus pattern (31 bp):
AAAAATTGATGAAATACCCACAAAGAAATGA
Found at i:4298510 original size:21 final size:21
Alignment explanation
Indices: 4298481--4298521 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
4298471 TTCTAAAACA
* *
4298481 TAAATATATTTTCGAAAGTCC
1 TAAAAATATTTTAGAAAGTCC
4298502 TAAAAATATTTTAGAAAGTC
1 TAAAAATATTTTAGAAAGTC
4298522 AGGAGTTTAA
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:0.44, C:0.10, G:0.10, T:0.37
Consensus pattern (21 bp):
TAAAAATATTTTAGAAAGTCC
Found at i:4300996 original size:27 final size:27
Alignment explanation
Indices: 4300933--4301036 Score: 104
Period size: 27 Copynumber: 3.8 Consensus size: 27
4300923 ACTACTTGGG
* *
4300933 GCTCTTAATTTTTATGTTTATAATT-A
1 GCTCCTAATTTTTATATTTATAATTGA
4300959 GACTCCTTAATTTTTATATTTATAATTGA
1 G-CTCC-TAATTTTTATATTTATAATTGA
* * * *
4300988 GGTTCTAATTTCTGTATTT-TAATTGAA
1 GCTCCTAATTTTTATATTTATAATTG-A
*
4301015 CCTCCTAATTTTTATATTTATA
1 GCTCCTAATTTTTATATTTATA
4301037 GTTGTGGCCT
Statistics
Matches: 62, Mismatches: 11, Indels: 8
0.77 0.14 0.10
Matches are distributed among these distances:
26 7 0.11
27 30 0.48
28 23 0.37
29 2 0.03
ACGTcount: A:0.28, C:0.11, G:0.08, T:0.54
Consensus pattern (27 bp):
GCTCCTAATTTTTATATTTATAATTGA
Found at i:4301034 original size:26 final size:25
Alignment explanation
Indices: 4300938--4301034 Score: 63
Period size: 28 Copynumber: 3.6 Consensus size: 25
4300928 TTGGGGCTCT
*
4300938 TAATTTTTATGTTTATAATTAGA-CTCC
1 TAATTTTTAT-ATT-TAATT-GACCTCC
** *
4300965 TTAATTTTTATATTTATAATTGAGGTTC
1 -TAATTTTTATA-TT-TAATTGACCTCC
4300993 TAATTTCTGTAT-TTTAATTGAACCTCC
1 TAATTT-T-TATATTTAATTG-ACCTCC
4301020 TAATTTTTATATTTA
1 TAATTTTTATATTTA
4301035 TAGTTGTGGC
Statistics
Matches: 57, Mismatches: 6, Indels: 14
0.74 0.08 0.18
Matches are distributed among these distances:
25 3 0.05
26 11 0.19
27 19 0.33
28 21 0.37
29 3 0.05
ACGTcount: A:0.29, C:0.09, G:0.07, T:0.55
Consensus pattern (25 bp):
TAATTTTTATATTTAATTGACCTCC
Found at i:4304046 original size:43 final size:43
Alignment explanation
Indices: 4303985--4304071 Score: 174
Period size: 43 Copynumber: 2.0 Consensus size: 43
4303975 ACACACCTCT
4303985 ATACCAAGAAAGAAATTAAGAGAACCAAGGTCCTTCAACGCAA
1 ATACCAAGAAAGAAATTAAGAGAACCAAGGTCCTTCAACGCAA
4304028 ATACCAAGAAAGAAATTAAGAGAACCAAGGTCCTTCAACGCAA
1 ATACCAAGAAAGAAATTAAGAGAACCAAGGTCCTTCAACGCAA
4304071 A
1 A
4304072 ACGAGTGTTC
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
43 44 1.00
ACGTcount: A:0.49, C:0.21, G:0.16, T:0.14
Consensus pattern (43 bp):
ATACCAAGAAAGAAATTAAGAGAACCAAGGTCCTTCAACGCAA
Found at i:4305785 original size:30 final size:30
Alignment explanation
Indices: 4305751--4305818 Score: 109
Period size: 30 Copynumber: 2.3 Consensus size: 30
4305741 TGGCAGATGT
*
4305751 GTTGATGGAGCAGGTACTAGTGGAACACAC
1 GTTGATGGAGCAGGCACTAGTGGAACACAC
* *
4305781 GTTGATGGAGCAGGCACTGGTGGAACGCAC
1 GTTGATGGAGCAGGCACTAGTGGAACACAC
4305811 GTTGATGG
1 GTTGATGG
4305819 GACTTGCAGT
Statistics
Matches: 35, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
30 35 1.00
ACGTcount: A:0.25, C:0.16, G:0.38, T:0.21
Consensus pattern (30 bp):
GTTGATGGAGCAGGCACTAGTGGAACACAC
Found at i:4319951 original size:21 final size:20
Alignment explanation
Indices: 4319865--4320022 Score: 86
Period size: 21 Copynumber: 7.8 Consensus size: 20
4319855 AAATGACCAA
**
4319865 CAAAATCGCAACGCGA-AAT
1 CAAAATCGCAACGCGATTTT
* ***
4319884 AAAAATCGCAACGCGATCCC
1 CAAAATCGCAACGCGATTTT
* ** *
4319904 CAGAATCGCAAATC-AGTTTC
1 CAAAATCGCAACGCGA-TTTT
4319924 CAAAATCGCAACGCGATTCTT
1 CAAAATCGCAACGCGATT-TT
* * * *
4319945 GAAAATCGCAATGCGATAGTA
1 CAAAATCGCAACGCGAT-TTT
* **
4319966 CAAATTCGCATTGCGATTTT
1 CAAAATCGCAACGCGATTTT
* *
4319986 CCAAAATCGCAACGCGAATAT
1 -CAAAATCGCAACGCGATTTT
*
4320007 GAAAATCGCAACGCGA
1 CAAAATCGCAACGCGA
4320023 ACACATAAAT
Statistics
Matches: 104, Mismatches: 29, Indels: 11
0.72 0.20 0.08
Matches are distributed among these distances:
19 16 0.15
20 41 0.39
21 47 0.45
ACGTcount: A:0.39, C:0.25, G:0.17, T:0.19
Consensus pattern (20 bp):
CAAAATCGCAACGCGATTTT
Found at i:4320051 original size:20 final size:20
Alignment explanation
Indices: 4319989--4320218 Score: 225
Period size: 20 Copynumber: 11.5 Consensus size: 20
4319979 CGATTTTCCA
* ** *
4319989 AAATCGCAACGCGAATATGA
1 AAATCGCAACGCGTATCCGT
* *
4320009 AAATCGCAACGCG-AACACAT
1 AAATCGCAACGCGTATC-CGT
4320029 AAATCGCAACGCGTATCCGT
1 AAATCGCAACGCGTATCCGT
*
4320049 AAATCGCAACGTGTATCCGT
1 AAATCGCAACGCGTATCCGT
**
4320069 AAATCGCAACGCGTATGGGT
1 AAATCGCAACGCGTATCCGT
*
4320089 AAATCGCAATGCGTATCCGT
1 AAATCGCAACGCGTATCCGT
*
4320109 ATATCGCAACGCGTATCCGT
1 AAATCGCAACGCGTATCCGT
*
4320129 AAATCGCAACG-ATAATCCGT
1 AAATCGCAACGCGT-ATCCGT
* * * *
4320149 AAATCGCAGCGAGAATCTGT
1 AAATCGCAACGCGTATCCGT
*
4320169 AAATCGCAACG-ATAATCCGT
1 AAATCGCAACGCGT-ATCCGT
*
4320189 AAATCGCAACG-ATAATCCGT
1 AAATCGCAACGCGT-ATCCGT
*
4320209 AAATCACAAC
1 AAATCGCAAC
4320219 ACTGAAATTT
Statistics
Matches: 178, Mismatches: 27, Indels: 10
0.83 0.13 0.05
Matches are distributed among these distances:
19 2 0.01
20 174 0.98
21 2 0.01
ACGTcount: A:0.37, C:0.25, G:0.19, T:0.20
Consensus pattern (20 bp):
AAATCGCAACGCGTATCCGT
Found at i:4320940 original size:24 final size:24
Alignment explanation
Indices: 4320901--4320947 Score: 69
Period size: 24 Copynumber: 2.0 Consensus size: 24
4320891 AAATTTGGTC
4320901 TTGGTCAATATCCGGACTTTGATA
1 TTGGTCAATATCCGGACTTTGATA
*
4320925 TTGGTCAATA-CACGGATTTTGAT
1 TTGGTCAATATC-CGGACTTTGAT
4320948 GATGTTTCAG
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
23 1 0.05
24 20 0.95
ACGTcount: A:0.26, C:0.15, G:0.21, T:0.38
Consensus pattern (24 bp):
TTGGTCAATATCCGGACTTTGATA
Found at i:4323480 original size:33 final size:34
Alignment explanation
Indices: 4323429--4323637 Score: 202
Period size: 33 Copynumber: 6.1 Consensus size: 34
4323419 CGGAAATTAC
*
4323429 AATCGCAACGA-GAGAATCGCAATGCGAAATGAA
1 AATCGCAACGATGAAAATCGCAATGCGAAATGAA
*
4323462 AATCCCAAC-ATGAAAATCGCAATGCGGAAATGAA
1 AATCGCAACGATGAAAATCGCAATGC-GAAATGAA
*
4323496 AATCGCAACGA-GAGAATCGCAATGCGAAATGAA
1 AATCGCAACGATGAAAATCGCAATGCGAAATGAA
* *
4323529 AATCGCAATGCGAAATGAAAAGCGCAA--CG--A-GAG
1 AATCGCAA--CG--ATGAAAATCGCAATGCGAAATGAA
4323562 AATCGCAATGCGAAATGAAAATCGCAATGCGAAAATGAA
1 AATCGCAA--CG--ATGAAAATCGCAATGCG-AAATGAA
* *
4323601 AATCGCAACGA-GAGAATCGCAATGCGAAATTAA
1 AATCGCAACGATGAAAATCGCAATGCGAAATGAA
4323634 AATC
1 AATC
4323638 ACATTGCGAT
Statistics
Matches: 151, Mismatches: 11, Indels: 28
0.79 0.06 0.15
Matches are distributed among these distances:
32 1 0.01
33 75 0.50
34 44 0.29
35 6 0.04
36 2 0.01
37 3 0.02
38 10 0.07
39 10 0.07
ACGTcount: A:0.46, C:0.18, G:0.22, T:0.13
Consensus pattern (34 bp):
AATCGCAACGATGAAAATCGCAATGCGAAATGAA
Found at i:4323646 original size:53 final size:53
Alignment explanation
Indices: 4323471--4323646 Score: 300
Period size: 53 Copynumber: 3.3 Consensus size: 53
4323461 AAATCCCAAC
*
4323471 ATGAAAATCGCAATGCGGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAA
1 ATGAAAATCGCAATGCGAAAATGAAAATCGCAACGAGAGAATCGCAATGCGAA
*
4323524 ATGAAAATCGCAATGCG-AAATGAAAAGCGCAACGAGAGAATCGCAATGCGAA
1 ATGAAAATCGCAATGCGAAAATGAAAATCGCAACGAGAGAATCGCAATGCGAA
4323576 ATGAAAATCGCAATGCGAAAATGAAAATCGCAACGAGAGAATCGCAATGCGAA
1 ATGAAAATCGCAATGCGAAAATGAAAATCGCAACGAGAGAATCGCAATGCGAA
* * *
4323629 ATTAAAATCACATTGCGA
1 ATGAAAATCGCAATGCGA
4323647 TTCTCTCGTT
Statistics
Matches: 117, Mismatches: 5, Indels: 2
0.94 0.04 0.02
Matches are distributed among these distances:
52 51 0.44
53 66 0.56
ACGTcount: A:0.46, C:0.17, G:0.23, T:0.14
Consensus pattern (53 bp):
ATGAAAATCGCAATGCGAAAATGAAAATCGCAACGAGAGAATCGCAATGCGAA
Found at i:4323680 original size:53 final size:52
Alignment explanation
Indices: 4323617--4323732 Score: 160
Period size: 53 Copynumber: 2.2 Consensus size: 52
4323607 AACGAGAGAA
*
4323617 TCGCAATGCGAAATTAAAATCACATTGCGATTCTCTCGTTGCGATTTTCATT
1 TCGCATTGCGAAATTAAAATCACATTGCGATTCTCTCGTTGCGATTTTCATT
** * ** *
4323669 TCCGCATTGCGATTTTCATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATT
1 T-CGCATTGCGAAATTAAAATCACATTGCGATTCTCTCGTTGCGATTTTCATT
4323722 TCGCATTGCGA
1 TCGCATTGCGA
4323733 TTTTCATTTC
Statistics
Matches: 56, Mismatches: 7, Indels: 2
0.86 0.11 0.03
Matches are distributed among these distances:
52 11 0.20
53 45 0.80
ACGTcount: A:0.20, C:0.23, G:0.17, T:0.40
Consensus pattern (52 bp):
TCGCATTGCGAAATTAAAATCACATTGCGATTCTCTCGTTGCGATTTTCATT
Found at i:4323749 original size:52 final size:53
Alignment explanation
Indices: 4323639--4323752 Score: 221
Period size: 53 Copynumber: 2.2 Consensus size: 53
4323629 ATTAAAATCA
4323639 CATTGCGATTCTCTCGTTGCGATTTTCATTTCCGCATTGCGATTTTCATTTCG
1 CATTGCGATTCTCTCGTTGCGATTTTCATTTCCGCATTGCGATTTTCATTTCG
4323692 CATTGCGATTCTCTCGTTGCGATTTTCATTT-CGCATTGCGATTTTCATTTCG
1 CATTGCGATTCTCTCGTTGCGATTTTCATTTCCGCATTGCGATTTTCATTTCG
4323744 CATTGCGAT
1 CATTGCGAT
4323753 AGTCATTTTT
Statistics
Matches: 61, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
52 30 0.49
53 31 0.51
ACGTcount: A:0.14, C:0.24, G:0.18, T:0.45
Consensus pattern (53 bp):
CATTGCGATTCTCTCGTTGCGATTTTCATTTCCGCATTGCGATTTTCATTTCG
Found at i:4323760 original size:19 final size:19
Alignment explanation
Indices: 4323655--4323752 Score: 143
Period size: 19 Copynumber: 5.4 Consensus size: 19
4323645 GATTCTCTCG
4323655 TTGCGATTTTCATTTCCGCA
1 TTGCGATTTTCATTT-CGCA
4323675 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
*
4323694 TTGCGA--TTC-TCTCG--
1 TTGCGATTTTCATTTCGCA
4323708 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
4323727 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
4323746 TTGCGAT
1 TTGCGAT
4323753 AGTCATTTTT
Statistics
Matches: 71, Mismatches: 2, Indels: 11
0.85 0.02 0.13
Matches are distributed among these distances:
14 6 0.08
16 7 0.10
17 7 0.10
19 36 0.51
20 15 0.21
ACGTcount: A:0.14, C:0.22, G:0.17, T:0.46
Consensus pattern (19 bp):
TTGCGATTTTCATTTCGCA
Found at i:4323878 original size:14 final size:14
Alignment explanation
Indices: 4323859--4323895 Score: 65
Period size: 14 Copynumber: 2.6 Consensus size: 14
4323849 CATCAATTAC
4323859 ACAAATCAACTTTT
1 ACAAATCAACTTTT
*
4323873 ACAAATCATCTTTT
1 ACAAATCAACTTTT
4323887 ACAAATCAA
1 ACAAATCAA
4323896 TTAAACAATC
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.46, C:0.22, G:0.00, T:0.32
Consensus pattern (14 bp):
ACAAATCAACTTTT
Found at i:4325862 original size:19 final size:19
Alignment explanation
Indices: 4325820--4325992 Score: 168
Period size: 19 Copynumber: 9.6 Consensus size: 19
4325810 TAGTTTACTT
* *
4325820 TCGCAACACGAAACTTAAAA
1 TCGCAACGCGAAA-TGAAAA
*
4325840 TCGCAACGCGAAATGATAA
1 TCGCAACGCGAAATGAAAA
* **
4325859 TCGCAACGAGAAACCAAAA
1 TCGCAACGCGAAATGAAAA
**
4325878 TCGCAACGCGAAACCAAAA
1 TCGCAACGCGAAATGAAAA
4325897 TCGCAACGCGAAATGAAAA
1 TCGCAACGCGAAATGAAAA
*
4325916 TCGCAA--CGACA-G--AA
1 TCGCAACGCGAAATGAAAA
*
4325930 TCGCAATGCGAAATGAAAA
1 TCGCAACGCGAAATGAAAA
4325949 TCGCAA--CGAAA-G--AA
1 TCGCAACGCGAAATGAAAA
4325963 TCGCAACGCGAAATGAAAA
1 TCGCAACGCGAAATGAAAA
*
4325982 TCGCAATGCGA
1 TCGCAACGCGA
4325993 TTTTGGTTTC
Statistics
Matches: 130, Mismatches: 13, Indels: 21
0.79 0.08 0.13
Matches are distributed among these distances:
14 16 0.12
16 11 0.08
17 11 0.08
19 80 0.62
20 12 0.09
ACGTcount: A:0.46, C:0.24, G:0.19, T:0.11
Consensus pattern (19 bp):
TCGCAACGCGAAATGAAAA
Found at i:4325933 original size:14 final size:14
Alignment explanation
Indices: 4325914--4325970 Score: 60
Period size: 14 Copynumber: 3.7 Consensus size: 14
4325904 GCGAAATGAA
*
4325914 AATCGCAACGACAG
1 AATCGCAACGAAAG
4325928 AATCGCAATGCGAAATG
1 AATCGCAA--CGAAA-G
4325945 AAAATCGCAACGAAAG
1 --AATCGCAACGAAAG
4325961 AATCGCAACG
1 AATCGCAACG
4325971 CGAAATGAAA
Statistics
Matches: 37, Mismatches: 1, Indels: 10
0.77 0.02 0.21
Matches are distributed among these distances:
14 18 0.49
16 5 0.14
17 6 0.16
19 8 0.22
ACGTcount: A:0.46, C:0.23, G:0.21, T:0.11
Consensus pattern (14 bp):
AATCGCAACGAAAG
Found at i:4325941 original size:33 final size:33
Alignment explanation
Indices: 4325895--4325987 Score: 168
Period size: 33 Copynumber: 2.8 Consensus size: 33
4325885 GCGAAACCAA
*
4325895 AATCGCAACGCGAAATGAAAATCGCAACGACAG
1 AATCGCAACGCGAAATGAAAATCGCAACGAAAG
*
4325928 AATCGCAATGCGAAATGAAAATCGCAACGAAAG
1 AATCGCAACGCGAAATGAAAATCGCAACGAAAG
4325961 AATCGCAACGCGAAATGAAAATCGCAA
1 AATCGCAACGCGAAATGAAAATCGCAA
4325988 TGCGATTTTG
Statistics
Matches: 57, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
33 57 1.00
ACGTcount: A:0.47, C:0.22, G:0.20, T:0.11
Consensus pattern (33 bp):
AATCGCAACGCGAAATGAAAATCGCAACGAAAG
Found at i:4326004 original size:19 final size:19
Alignment explanation
Indices: 4325988--4326083 Score: 103
Period size: 19 Copynumber: 5.3 Consensus size: 19
4325978 AAAATCGCAA
4325988 TGCGATTTTGGTTTCGCGT
1 TGCGATTTTGGTTTCGCGT
*
4326007 TGCGATTCT-G--T--CGT
1 TGCGATTTTGGTTTCGCGT
**
4326021 TGCGATTTTCATTTCGCGT
1 TGCGATTTTGGTTTCGCGT
4326040 TGCGATTTTGGTTTCGCGT
1 TGCGATTTTGGTTTCGCGT
* *
4326059 TGCGATTTTAAGTTTCGTGT
1 TGCGATTTT-GGTTTCGCGT
4326079 TGCGA
1 TGCGA
4326084 AAGTAAACTA
Statistics
Matches: 64, Mismatches: 7, Indels: 11
0.78 0.09 0.13
Matches are distributed among these distances:
14 11 0.17
16 1 0.02
17 1 0.02
18 1 0.02
19 37 0.58
20 13 0.20
ACGTcount: A:0.09, C:0.17, G:0.28, T:0.46
Consensus pattern (19 bp):
TGCGATTTTGGTTTCGCGT
Found at i:4326247 original size:93 final size:93
Alignment explanation
Indices: 4326131--4326967 Score: 1621
Period size: 93 Copynumber: 9.1 Consensus size: 93
4326121 ATGGATTGCA
4326131 TTAC-TTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTT
1 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTT
4326195 TAGCAGAATTGGCAGCAACCGAACAAAT
66 TAGCAGAATTGGCAGCAACCGAACAAAT
4326223 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTT-AAGAATACACAGTT
1 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTT
4326287 TAGCAGAATTGGCAGCAACCGAACAAAT
66 TAGCAGAATTGGCAGCAACCGAACAAAT
4326315 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTT
1 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTT
4326380 TAGCAGAATTGGCAGCAACCGAACAAAT
66 TAGCAGAATTGGCAGCAACCGAACAAAT
4326408 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTT
1 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTT
4326473 TAGCAGAATTGGCAGCAACCGAACAAA-
66 TAGCAGAATTGGCAGCAACCGAACAAAT
4326500 TTACTTTCAACCAAAAGACAAAACAAAGAC-AATACTATTTCACAGTGTTAAAGAATACACAGTT
1 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTT
4326564 TAGCAGAATTGGCAGCAACCGAACAAAT
66 TAGCAGAATTGGCAGCAACCGAACAAAT
4326592 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTT
1 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTT
4326657 TAGCAGAATTGGCAGCAACCGAACAAAT
66 TAGCAGAATTGGCAGCAACCGAACAAAT
4326685 TTACTTT-AACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTT
1 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTT
4326749 TAGCAGAATTGGCAGCAACCGAACAAAT
66 TAGCAGAATTGGCAGCAACCGAACAAAT
*
4326777 TTACTTTTAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTT
1 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTT
4326842 TAGCAGAATTGGCAGCAACCGAACAAAT
66 TAGCAGAATTGGCAGCAACCGAACAAAT
4326870 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTT
1 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTT
*
4326935 TAGCAGAATTGGCAGCAACCGAATAAAT
66 TAGCAGAATTGGCAGCAACCGAACAAAT
4326963 TTACT
1 TTACT
4326968 AAGCAATCTA
Statistics
Matches: 738, Mismatches: 2, Indels: 9
0.99 0.00 0.01
Matches are distributed among these distances:
91 61 0.08
92 248 0.34
93 429 0.58
ACGTcount: A:0.46, C:0.19, G:0.13, T:0.22
Consensus pattern (93 bp):
TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTT
TAGCAGAATTGGCAGCAACCGAACAAAT
Found at i:4326447 original size:185 final size:186
Alignment explanation
Indices: 4326131--4326967 Score: 1621
Period size: 185 Copynumber: 4.5 Consensus size: 186
4326121 ATGGATTGCA
4326131 TTAC-TTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTT
1 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTT
4326195 TAGCAGAATTGGCAGCAACCGAACAAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACT
66 TAGCAGAATTGGCAGCAACCGAACAAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACT
4326260 ATTTCACAGTGTT-AAGAATACACAGTTTAGCAGAATTGGCAGCAACCGAACAAAT
131 ATTTCACAGTGTTAAAGAATACACAGTTTAGCAGAATTGGCAGCAACCGAACAAAT
4326315 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTT
1 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTT
4326380 TAGCAGAATTGGCAGCAACCGAACAAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACT
66 TAGCAGAATTGGCAGCAACCGAACAAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACT
4326445 ATTTCACAGTGTTAAAGAATACACAGTTTAGCAGAATTGGCAGCAACCGAACAAA-
131 ATTTCACAGTGTTAAAGAATACACAGTTTAGCAGAATTGGCAGCAACCGAACAAAT
4326500 TTACTTTCAACCAAAAGACAAAACAAAGAC-AATACTATTTCACAGTGTTAAAGAATACACAGTT
1 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTT
4326564 TAGCAGAATTGGCAGCAACCGAACAAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACT
66 TAGCAGAATTGGCAGCAACCGAACAAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACT
4326629 ATTTCACAGTGTTAAAGAATACACAGTTTAGCAGAATTGGCAGCAACCGAACAAAT
131 ATTTCACAGTGTTAAAGAATACACAGTTTAGCAGAATTGGCAGCAACCGAACAAAT
4326685 TTACTTT-AACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTT
1 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTT
*
4326749 TAGCAGAATTGGCAGCAACCGAACAAATTTACTTTTAACCAAAAGACAAAACAAAGACAAATACT
66 TAGCAGAATTGGCAGCAACCGAACAAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACT
4326814 ATTTCACAGTGTTAAAGAATACACAGTTTAGCAGAATTGGCAGCAACCGAACAAAT
131 ATTTCACAGTGTTAAAGAATACACAGTTTAGCAGAATTGGCAGCAACCGAACAAAT
4326870 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTT
1 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTT
*
4326935 TAGCAGAATTGGCAGCAACCGAATAAATTTACT
66 TAGCAGAATTGGCAGCAACCGAACAAATTTACT
4326968 AAGCAATCTA
Statistics
Matches: 646, Mismatches: 2, Indels: 8
0.98 0.00 0.01
Matches are distributed among these distances:
184 180 0.28
185 336 0.52
186 130 0.20
ACGTcount: A:0.46, C:0.19, G:0.13, T:0.22
Consensus pattern (186 bp):
TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTT
TAGCAGAATTGGCAGCAACCGAACAAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACT
ATTTCACAGTGTTAAAGAATACACAGTTTAGCAGAATTGGCAGCAACCGAACAAAT
Found at i:4328699 original size:20 final size:20
Alignment explanation
Indices: 4328668--4328764 Score: 100
Period size: 20 Copynumber: 5.2 Consensus size: 20
4328658 TTTTGGTTGA
4328668 AATGAAAATCGCAACGAGAG
1 AATGAAAATCGCAACGAGAG
***
4328688 AATGACTGTCGCAACGAGAG
1 AATGAAAATCGCAACGAGAG
4328708 AAATGAAAATCGCAAC--GAG
1 -AATGAAAATCGCAACGAGAG
*
4328727 -A-G--AATCGCAACGCGA-
1 AATGAAAATCGCAACGAGAG
4328742 AATGAAAATCGCAACGAGAG
1 AATGAAAATCGCAACGAGAG
4328762 AAT
1 AAT
4328765 CGCAACGCGA
Statistics
Matches: 62, Mismatches: 7, Indels: 16
0.73 0.08 0.19
Matches are distributed among these distances:
14 9 0.15
16 4 0.06
17 2 0.03
19 15 0.24
20 20 0.32
21 12 0.19
ACGTcount: A:0.46, C:0.18, G:0.25, T:0.11
Consensus pattern (20 bp):
AATGAAAATCGCAACGAGAG
Found at i:4328720 original size:21 final size:21
Alignment explanation
Indices: 4328666--4328730 Score: 96
Period size: 21 Copynumber: 3.1 Consensus size: 21
4328656 TCTTTTGGTT
4328666 GAAATGAAAATCGCAACGAGA
1 GAAATGAAAATCGCAACGAGA
***
4328687 G-AATGACTGTCGCAACGAGA
1 GAAATGAAAATCGCAACGAGA
4328707 GAAATGAAAATCGCAACGAGA
1 GAAATGAAAATCGCAACGAGA
4328728 GAA
1 GAA
4328731 TCGCAACGCG
Statistics
Matches: 37, Mismatches: 6, Indels: 2
0.82 0.13 0.04
Matches are distributed among these distances:
20 17 0.46
21 20 0.54
ACGTcount: A:0.48, C:0.15, G:0.26, T:0.11
Consensus pattern (21 bp):
GAAATGAAAATCGCAACGAGA
Found at i:4328734 original size:14 final size:14
Alignment explanation
Indices: 4328715--4328771 Score: 60
Period size: 14 Copynumber: 3.7 Consensus size: 14
4328705 GAGAAATGAA
4328715 AATCGCAACGAGAG
1 AATCGCAACGAGAG
*
4328729 AATCGCAACGCGAAATGAA
1 AATCGCAA--CG--A-GAG
4328748 AATCGCAACGAGAG
1 AATCGCAACGAGAG
4328762 AATCGCAACG
1 AATCGCAACG
4328772 CGAAATGAAA
Statistics
Matches: 36, Mismatches: 2, Indels: 10
0.75 0.04 0.21
Matches are distributed among these distances:
14 20 0.56
15 1 0.03
16 2 0.06
17 2 0.06
18 1 0.03
19 10 0.28
ACGTcount: A:0.44, C:0.23, G:0.25, T:0.09
Consensus pattern (14 bp):
AATCGCAACGAGAG
Found at i:4328747 original size:33 final size:33
Alignment explanation
Indices: 4328666--4328788 Score: 156
Period size: 33 Copynumber: 3.5 Consensus size: 33
4328656 TCTTTTGGTT
*
4328666 GAAATGAAAATCGCAACGAGAGAATGACTGTCGCAACGAGA
1 GAAATGAAAATCGCAACGAGAG-A--A---TCGCAAC--GC
4328707 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
1 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
4328740 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
1 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
*
4328773 GAAATGAAAATTGCAA
1 GAAATGAAAATCGCAA
4328789 TGCGATTTTG
Statistics
Matches: 80, Mismatches: 2, Indels: 8
0.89 0.02 0.09
Matches are distributed among these distances:
33 49 0.61
35 7 0.09
38 1 0.01
40 1 0.01
41 22 0.28
ACGTcount: A:0.46, C:0.18, G:0.24, T:0.11
Consensus pattern (33 bp):
GAAATGAAAATCGCAACGAGAGAATCGCAACGC
Found at i:4328824 original size:14 final size:14
Alignment explanation
Indices: 4328805--4328861 Score: 60
Period size: 14 Copynumber: 3.7 Consensus size: 14
4328795 TTTGGTTTCA
4328805 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
*
4328819 CGTTGCGATTTTCATTTCG
1 CGTTGCGA--TTC---TCT
4328838 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
4328852 CGTTGCGATT
1 CGTTGCGATT
4328862 TTCATTTCTC
Statistics
Matches: 36, Mismatches: 2, Indels: 10
0.75 0.04 0.21
Matches are distributed among these distances:
14 20 0.56
16 3 0.08
17 3 0.08
19 10 0.28
ACGTcount: A:0.09, C:0.25, G:0.23, T:0.44
Consensus pattern (14 bp):
CGTTGCGATTCTCT
Found at i:4328842 original size:33 final size:33
Alignment explanation
Indices: 4328789--4328869 Score: 135
Period size: 33 Copynumber: 2.5 Consensus size: 33
4328779 AAAATTGCAA
**
4328789 TGCGATTTTGGTTTCACGTTGCGATTCTCTCGT
1 TGCGATTTTCATTTCACGTTGCGATTCTCTCGT
*
4328822 TGCGATTTTCATTTCGCGTTGCGATTCTCTCGT
1 TGCGATTTTCATTTCACGTTGCGATTCTCTCGT
4328855 TGCGATTTTCATTTC
1 TGCGATTTTCATTTC
4328870 TCTCGTTGCG
Statistics
Matches: 45, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
33 45 1.00
ACGTcount: A:0.10, C:0.22, G:0.21, T:0.47
Consensus pattern (33 bp):
TGCGATTTTCATTTCACGTTGCGATTCTCTCGT
Found at i:4328872 original size:21 final size:21
Alignment explanation
Indices: 4328846--4328921 Score: 109
Period size: 21 Copynumber: 3.7 Consensus size: 21
4328836 CGCGTTGCGA
4328846 TTCTCTCGTTGCGATTTTCAT
1 TTCTCTCGTTGCGATTTTCAT
***
4328867 TTCTCTCGTTGCGACAGTCA-
1 TTCTCTCGTTGCGATTTTCAT
4328887 TTCTCTCGTTGCGATTTTCAT
1 TTCTCTCGTTGCGATTTTCAT
*
4328908 TTATCTCGTTGCGA
1 TTCTCTCGTTGCGA
4328922 CTCTTCTGCA
Statistics
Matches: 47, Mismatches: 7, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
20 17 0.36
21 30 0.64
ACGTcount: A:0.12, C:0.25, G:0.17, T:0.46
Consensus pattern (21 bp):
TTCTCTCGTTGCGATTTTCAT
Found at i:4328902 original size:41 final size:41
Alignment explanation
Indices: 4328845--4328922 Score: 147
Period size: 41 Copynumber: 1.9 Consensus size: 41
4328835 TCGCGTTGCG
*
4328845 ATTCTCTCGTTGCGATTTTCATTTCTCTCGTTGCGACAGTC
1 ATTCTCTCGTTGCGATTTTCATTTATCTCGTTGCGACAGTC
4328886 ATTCTCTCGTTGCGATTTTCATTTATCTCGTTGCGAC
1 ATTCTCTCGTTGCGATTTTCATTTATCTCGTTGCGAC
4328923 TCTTCTGCAA
Statistics
Matches: 36, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
41 36 1.00
ACGTcount: A:0.13, C:0.26, G:0.17, T:0.45
Consensus pattern (41 bp):
ATTCTCTCGTTGCGATTTTCATTTATCTCGTTGCGACAGTC
Found at i:4329043 original size:33 final size:33
Alignment explanation
Indices: 4329001--4329071 Score: 115
Period size: 33 Copynumber: 2.2 Consensus size: 33
4328991 AATACTAACT
*
4329001 TGAAAATCGCAACGAGAGAATAGCAACGCGAAA
1 TGAAAATCGCAACGACAGAATAGCAACGCGAAA
* *
4329034 TGAAAATCGCAACGACAGAATCGTAACGCGAAA
1 TGAAAATCGCAACGACAGAATAGCAACGCGAAA
4329067 TGAAA
1 TGAAA
4329072 TCTAAGTGAA
Statistics
Matches: 35, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
33 35 1.00
ACGTcount: A:0.48, C:0.18, G:0.23, T:0.11
Consensus pattern (33 bp):
TGAAAATCGCAACGACAGAATAGCAACGCGAAA
Found at i:4329305 original size:22 final size:22
Alignment explanation
Indices: 4329253--4329307 Score: 74
Period size: 22 Copynumber: 2.5 Consensus size: 22
4329243 TGGTTGTGAG
**
4329253 GGATTTCGCCGGAGATGGGGAC
1 GGATTTCTTCGGAGATGGGGAC
**
4329275 GGAAATCTTCGGAGATGGGGAC
1 GGATTTCTTCGGAGATGGGGAC
4329297 GGATTTCTTCG
1 GGATTTCTTCG
4329308 CCGTAGAGAG
Statistics
Matches: 27, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
22 27 1.00
ACGTcount: A:0.20, C:0.16, G:0.40, T:0.24
Consensus pattern (22 bp):
GGATTTCTTCGGAGATGGGGAC
Found at i:4329479 original size:20 final size:20
Alignment explanation
Indices: 4329454--4329647 Score: 221
Period size: 20 Copynumber: 9.7 Consensus size: 20
4329444 CTTTAAATAT
4329454 CGCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
* *
4329474 CGCGTTGCGATTTTATGTATTA
1 CGCGTTGCGA-TTTACGGA-TA
*
4329496 -TCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
*
4329515 CGCGTTGCGATATACGGATA
1 CGCGTTGCGATTTACGGATA
* **
4329535 CGCATTGCGATTTACCCATA
1 CGCGTTGCGATTTACGGATA
4329555 CGCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
*
4329575 CACGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
* *
4329595 CGCGTTGCGATTTATGTG-TT
1 CGCGTTGCGATTTACG-GATA
* ** *
4329615 CGCGTTGCGATTTTCATATT
1 CGCGTTGCGATTTACGGATA
4329635 CGCGTTGCGATTT
1 CGCGTTGCGATTT
4329648 TGGAAAATCG
Statistics
Matches: 147, Mismatches: 22, Indels: 10
0.82 0.12 0.06
Matches are distributed among these distances:
19 2 0.01
20 128 0.87
21 15 0.10
22 2 0.01
ACGTcount: A:0.19, C:0.20, G:0.26, T:0.36
Consensus pattern (20 bp):
CGCGTTGCGATTTACGGATA
Found at i:4329641 original size:60 final size:60
Alignment explanation
Indices: 4329454--4329647 Score: 253
Period size: 60 Copynumber: 3.2 Consensus size: 60
4329444 CTTTAAATAT
**
4329454 CGCGTTGCGATTTACGGATACGCGTTGCGATTTTATGTATTATCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATACGCGTTGCGA-TTTATGTATTCGCGTTGCGATTTACGGATA
* * *** *
4329515 CGCGTTGCGATATACGGATACGCATTGCGATTTACCCATACGCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATACGCGTTGCGATTTATGTATTCGCGTTGCGATTTACGGATA
* * * ** *
4329575 CACGTTGCGATTTACGGATACGCGTTGCGATTTATGTGTTCGCGTTGCGATTTTCATATT
1 CGCGTTGCGATTTACGGATACGCGTTGCGATTTATGTATTCGCGTTGCGATTTACGGATA
4329635 CGCGTTGCGATTT
1 CGCGTTGCGATTT
4329648 TGGAAAATCG
Statistics
Matches: 112, Mismatches: 21, Indels: 1
0.84 0.16 0.01
Matches are distributed among these distances:
60 84 0.75
61 28 0.25
ACGTcount: A:0.19, C:0.20, G:0.26, T:0.36
Consensus pattern (60 bp):
CGCGTTGCGATTTACGGATACGCGTTGCGATTTATGTATTCGCGTTGCGATTTACGGATA
Found at i:4329664 original size:21 final size:21
Alignment explanation
Indices: 4329634--4329716 Score: 78
Period size: 21 Copynumber: 4.0 Consensus size: 21
4329624 ATTTTCATAT
*
4329634 TCGCGTTGCGATTTTGGAAAA
1 TCGCATTGCGATTTTGGAAAA
* * * **
4329655 TCGCAATGCGAATTTGTACTA
1 TCGCATTGCGATTTTGGAAAA
*
4329676 TCGCATTGCGATTTT-CAAGAA
1 TCGCATTGCGATTTTGGAA-AA
*
4329697 TCGCGTTGCGATTTTGGAAA
1 TCGCATTGCGATTTTGGAAA
4329717 CTGATTTGCG
Statistics
Matches: 47, Mismatches: 13, Indels: 4
0.73 0.20 0.06
Matches are distributed among these distances:
20 1 0.02
21 44 0.94
22 2 0.04
ACGTcount: A:0.25, C:0.17, G:0.24, T:0.34
Consensus pattern (21 bp):
TCGCATTGCGATTTTGGAAAA
Found at i:4329707 original size:42 final size:43
Alignment explanation
Indices: 4329614--4329712 Score: 100
Period size: 42 Copynumber: 2.4 Consensus size: 43
4329604 ATTTATGTGT
* *
4329614 TCGCGTTGCG-ATTT-TCATATTCGCGTTGCGATTTTGGAAAA
1 TCGCGTTGCGAATTTGTCATATTCGCATTGCGATTTTGCAAAA
**
4329655 TCGCAATGCGAATTTGT-ACTA-TCGCATTGCGATTTT-CAAGAA
1 TCGCGTTGCGAATTTGTCA-TATTCGCATTGCGATTTTGCAA-AA
*
4329697 TCGCGTTGCGATTTTG
1 TCGCGTTGCGAATTTG
4329713 GAAACTGATT
Statistics
Matches: 47, Mismatches: 7, Indels: 7
0.77 0.11 0.11
Matches are distributed among these distances:
41 10 0.21
42 34 0.72
43 3 0.06
ACGTcount: A:0.21, C:0.18, G:0.23, T:0.37
Consensus pattern (43 bp):
TCGCGTTGCGAATTTGTCATATTCGCATTGCGATTTTGCAAAA
Found at i:4334336 original size:19 final size:20
Alignment explanation
Indices: 4334304--4334342 Score: 62
Period size: 19 Copynumber: 2.0 Consensus size: 20
4334294 GAACCGGCTG
4334304 AAAACCGGAAAAAATCGGGA
1 AAAACCGGAAAAAATCGGGA
*
4334324 AAAACCGG-GAAAATCGGGA
1 AAAACCGGAAAAAATCGGGA
4334343 TTTTAATTTT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
19 10 0.56
20 8 0.44
ACGTcount: A:0.51, C:0.15, G:0.28, T:0.05
Consensus pattern (20 bp):
AAAACCGGAAAAAATCGGGA
Found at i:4339028 original size:6 final size:6
Alignment explanation
Indices: 4339013--4339068 Score: 51
Period size: 6 Copynumber: 9.2 Consensus size: 6
4339003 CCGTCTCGTC
* ** *
4339013 TCGTGA TCGTGG TCGTGG TCGTGG TCGTCA TC-TCGTC TCGTGG TCGTGG
1 TCGTGG TCGTGG TCGTGG TCGTGG TCGTGG TCGT-G-G TCGTGG TCGTGG
4339062 TCGTGG T
1 TCGTGG T
4339069 AATACGTGTC
Statistics
Matches: 41, Mismatches: 6, Indels: 6
0.77 0.11 0.11
Matches are distributed among these distances:
5 1 0.02
6 36 0.88
7 3 0.07
8 1 0.02
ACGTcount: A:0.04, C:0.21, G:0.39, T:0.36
Consensus pattern (6 bp):
TCGTGG
Found at i:4364182 original size:22 final size:22
Alignment explanation
Indices: 4364157--4364201 Score: 65
Period size: 23 Copynumber: 2.0 Consensus size: 22
4364147 AAATGATAAA
4364157 AATTCAT-GTACCCGATTATCCG
1 AATTCATGGTACCCGATTA-CCG
*
4364179 AATTCTTGGTACCCGATTACCG
1 AATTCATGGTACCCGATTACCG
4364201 A
1 A
4364202 GTACCCGTAA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
22 10 0.48
23 11 0.52
ACGTcount: A:0.27, C:0.27, G:0.16, T:0.31
Consensus pattern (22 bp):
AATTCATGGTACCCGATTACCG
Found at i:4366404 original size:2 final size:2
Alignment explanation
Indices: 4366397--4366422 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
4366387 AGGAGGGGAC
4366397 GT GT GT GT GT GT GT GT GT GT GT GT GT
1 GT GT GT GT GT GT GT GT GT GT GT GT GT
4366423 AGAGAGAGAG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.00, C:0.00, G:0.50, T:0.50
Consensus pattern (2 bp):
GT
Found at i:4374068 original size:2 final size:2
Alignment explanation
Indices: 4374056--4374085 Score: 51
Period size: 2 Copynumber: 15.0 Consensus size: 2
4374046 TATTACCTTG
*
4374056 TA TA TA CA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
4374086 AACCATTGGA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.03, G:0.00, T:0.47
Consensus pattern (2 bp):
TA
Found at i:4375307 original size:2 final size:2
Alignment explanation
Indices: 4375300--4375355 Score: 112
Period size: 2 Copynumber: 28.0 Consensus size: 2
4375290 GTAATCATGA
4375300 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
4375342 AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT
4375356 CAGCACCAGC
Statistics
Matches: 54, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 54 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:4379610 original size:23 final size:22
Alignment explanation
Indices: 4379554--4379612 Score: 59
Period size: 23 Copynumber: 2.6 Consensus size: 22
4379544 TCATATAATA
*
4379554 AAAAATTATGTATATTTAAATT
1 AAAAATTATGTAAATTTAAATT
*
4379576 --AAATTGAGTGTAAATTTTAACTT
1 AAAAATT-A-TGTAAA-TTTAAATT
4379599 AAAAATTATGTAAA
1 AAAAATTATGTAAA
4379613 ATAAAACCCT
Statistics
Matches: 30, Mismatches: 2, Indels: 9
0.73 0.05 0.22
Matches are distributed among these distances:
20 5 0.17
21 1 0.03
22 5 0.17
23 13 0.43
24 1 0.03
25 5 0.17
ACGTcount: A:0.49, C:0.02, G:0.08, T:0.41
Consensus pattern (22 bp):
AAAAATTATGTAAATTTAAATT
Found at i:4380502 original size:8 final size:9
Alignment explanation
Indices: 4380471--4380510 Score: 50
Period size: 8 Copynumber: 4.7 Consensus size: 9
4380461 TTCTATTTTA
4380471 ATTTTAATT
1 ATTTTAATT
4380480 ATTGTTAA-T
1 ATT-TTAATT
4380489 ATTTTAATT
1 ATTTTAATT
4380498 A-TTTAATT
1 ATTTTAATT
4380506 -TTTTA
1 ATTTTA
4380511 GTATTAATTT
Statistics
Matches: 28, Mismatches: 0, Indels: 7
0.80 0.00 0.20
Matches are distributed among these distances:
8 15 0.54
9 9 0.32
10 4 0.14
ACGTcount: A:0.33, C:0.00, G:0.03, T:0.65
Consensus pattern (9 bp):
ATTTTAATT
Found at i:4382337 original size:3 final size:3
Alignment explanation
Indices: 4382331--4382356 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
4382321 ATGATGATGA
4382331 TGG TGG TGG TGG TGG TGG TGG TGG TG
1 TGG TGG TGG TGG TGG TGG TGG TGG TG
4382357 ATGATGATGA
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:0.00, C:0.00, G:0.65, T:0.35
Consensus pattern (3 bp):
TGG
Found at i:4390700 original size:44 final size:44
Alignment explanation
Indices: 4390637--4390720 Score: 150
Period size: 44 Copynumber: 1.9 Consensus size: 44
4390627 GCTGTTCAGC
*
4390637 TTCAACTACTTGTTTTATTTCTCTTACCCTTACTTTTGTTTAAA
1 TTCAACTACTTGTTTTATTTCTCTTACCCTCACTTTTGTTTAAA
*
4390681 TTCAACTACTTGTTTTATTTCTTTTACCCTCACTTTTGTT
1 TTCAACTACTTGTTTTATTTCTCTTACCCTCACTTTTGTT
4390721 GAATTTGACT
Statistics
Matches: 38, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
44 38 1.00
ACGTcount: A:0.18, C:0.21, G:0.05, T:0.56
Consensus pattern (44 bp):
TTCAACTACTTGTTTTATTTCTCTTACCCTCACTTTTGTTTAAA
Found at i:4393322 original size:12 final size:12
Alignment explanation
Indices: 4393305--4393337 Score: 57
Period size: 12 Copynumber: 2.8 Consensus size: 12
4393295 TTCACCATCA
*
4393305 TCATCGGCTGGC
1 TCATCGACTGGC
4393317 TCATCGACTGGC
1 TCATCGACTGGC
4393329 TCATCGACT
1 TCATCGACT
4393338 TAGTTGAGGG
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
12 20 1.00
ACGTcount: A:0.15, C:0.33, G:0.24, T:0.27
Consensus pattern (12 bp):
TCATCGACTGGC
Found at i:4398341 original size:4 final size:4
Alignment explanation
Indices: 4398332--4398509 Score: 121
Period size: 4 Copynumber: 42.2 Consensus size: 4
4398322 CATGAGGTCT
4398332 CTCC CTCC CTCC CTCCC ACTCC CTCC C-CC TCTCC CTCTC TCTCC CTCTC
1 CTCC CTCC CTCC CT-CC -CTCC CTCC CTCC -CTCC CTC-C -CTCC CTC-C
* * * * *
4398381 C-CT CTCC CTCC CTCC CACC CTCC CTCT CTCT CTCC CTCTC C-CT CTCC
1 CTCC CTCC CTCC CTCC CTCC CTCC CTCC CTCC CTCC CTC-C CTCC CTCC
* * *
4398428 CTCC CTCC CTCC CTCT CTCT CTCC CTCTC TCTCC CTCC ATTTCC CTCC
1 CTCC CTCC CTCC CTCC CTCC CTCC CTC-C -CTCC CTCC --CTCC CTCC
* *
4398476 CTCC CTCC CACC CCCC CTCTC TCTCC C-CC CTCC C
1 CTCC CTCC CTCC CTCC CTC-C -CTCC CTCC CTCC C
4398510 CCTCTCCAAC
Statistics
Matches: 142, Mismatches: 15, Indels: 34
0.74 0.08 0.18
Matches are distributed among these distances:
3 7 0.05
4 105 0.74
5 16 0.11
6 14 0.10
ACGTcount: A:0.02, C:0.69, G:0.00, T:0.29
Consensus pattern (4 bp):
CTCC
Found at i:4398406 original size:44 final size:43
Alignment explanation
Indices: 4398336--4398516 Score: 176
Period size: 40 Copynumber: 4.1 Consensus size: 43
4398326 AGGTCTCTCC
4398336 CTCCCTCCCTCCCACTCCCTCCCCCTCTCCCTCTCTCTCCCTCTCCCT
1 CTCCCTCCCTCCCA--CCCT--CCC-CTCCCTCTCTCTCCCTCTCCCT
4398384 CTCCCTCCCTCCCACCCT-CCCT--CTCTCTCTCCCTCTCCCT
1 CTCCCTCCCTCCCACCCTCCCCTCCCTCTCTCTCCCTCTCCCT
* *
4398424 CTCCCTCCCTCCCTCCCTCTCTCTCTCCCTCTCTCTCCCTCCATTTCC-
1 CTCCCTCCCTCCCACCCTC-C-C-CTCCCTCTCTCTCCCT-C--TCCCT
* * *
4398472 CTCCCTCCCTCCCACCC-CCCCTCTCTCTC-CCCCCTCCCCCT
1 CTCCCTCCCTCCCACCCTCCCCTCCCTCTCTCTCCCTCTCCCT
4398513 CTCC
1 CTCC
4398517 AACTTTGTTT
Statistics
Matches: 116, Mismatches: 7, Indels: 27
0.77 0.05 0.18
Matches are distributed among these distances:
40 37 0.32
41 4 0.03
42 4 0.03
43 8 0.07
44 10 0.09
45 1 0.01
46 17 0.15
47 2 0.02
48 30 0.26
49 3 0.03
ACGTcount: A:0.02, C:0.69, G:0.00, T:0.29
Consensus pattern (43 bp):
CTCCCTCCCTCCCACCCTCCCCTCCCTCTCTCTCCCTCTCCCT
Found at i:4398473 original size:36 final size:35
Alignment explanation
Indices: 4398332--4398515 Score: 173
Period size: 36 Copynumber: 5.3 Consensus size: 35
4398322 CATGAGGTCT
* * *
4398332 CTCCCTCCCTCCCTCCCACTCC-CTCCC-CCTCTCC
1 CTCCCTCTCTCTCTCCCTCTCCTCTCCCTCC-CTCC
* * *
4398366 CTCTCTCTCCCTCTCCCTCTCC-CTCCCTCCCACC
1 CTCCCTCTCTCTCTCCCTCTCCTCTCCCTCCCTCC
4398400 CTCCCTCTCTCTCTCCCTCTCCCTCTCCCTCCCTCC
1 CTCCCTCTCTCTCTCCCTCT-CCTCTCCCTCCCTCC
*
4398436 CTCCCTCTCTCTCTCCCTCT-CTCTCCCTCCATTTCC
1 CTCCCTCTCTCTCTCCCTCTCCTCTCCCTCC--CTCC
* * * * *
4398472 CTCCCTCCCTCCCACCC-CCCCTCTCTCTCCC-CC
1 CTCCCTCTCTCTCTCCCTCTCCTCTCCCTCCCTCC
*
4398505 CTCCCCCTCTC
1 CTCCCTCTCTC
4398516 CAACTTTGTT
Statistics
Matches: 126, Mismatches: 18, Indels: 13
0.80 0.11 0.08
Matches are distributed among these distances:
33 11 0.09
34 53 0.42
35 5 0.04
36 57 0.45
ACGTcount: A:0.02, C:0.68, G:0.00, T:0.29
Consensus pattern (35 bp):
CTCCCTCTCTCTCTCCCTCTCCTCTCCCTCCCTCC
Found at i:4398473 original size:40 final size:38
Alignment explanation
Indices: 4398329--4398509 Score: 185
Period size: 38 Copynumber: 4.8 Consensus size: 38
4398319 TTACATGAGG
* *
4398329 TCTCTCCCTCCCTCCCTC-CCACTCCCTCCC-CCTCTCCC
1 TCTCTCTCTCCCTCTCTCTCC-CTCCCTCCCTCC-CTCCC
* *
4398367 TCTCTCTC-CCTCTCCCTCTCCCTCCCTCCCACCCTCCC
1 TCTCTCTCTCC-CTCTCTCTCCCTCCCTCCCTCCCTCCC
*
4398405 TCTCTCTCTCCCTCTC-C-CTCTCCCTCCCTCCCTCCC
1 TCTCTCTCTCCCTCTCTCTCCCTCCCTCCCTCCCTCCC
*
4398441 TCTCTCTCTCCCTCTCTCTCCCTCCATTTCCCTCCCTCCC
1 TCTCTCTCTCCCTCTCTCTCCCTCC--CTCCCTCCCTCCC
* * * *
4398481 TCCCACCCCCCCTCTCTCTCCC-CCCTCCC
1 TCTCTCTCTCCCTCTCTCTCCCTCCCTCCC
4398510 CCTCTCCAAC
Statistics
Matches: 124, Mismatches: 11, Indels: 17
0.82 0.07 0.11
Matches are distributed among these distances:
36 33 0.27
37 8 0.06
38 45 0.36
39 8 0.06
40 30 0.24
ACGTcount: A:0.02, C:0.68, G:0.00, T:0.30
Consensus pattern (38 bp):
TCTCTCTCTCCCTCTCTCTCCCTCCCTCCCTCCCTCCC
Found at i:4398473 original size:56 final size:54
Alignment explanation
Indices: 4398329--4398509 Score: 146
Period size: 60 Copynumber: 3.3 Consensus size: 54
4398319 TTACATGAGG
* *
4398329 TCTCTCCCTCCCTCCCTCCCA-CTCCCTCCCCCTCTCCCTCTCTCTCCCTCTCCCTCTCCC
1 TCTCTCCCTCCCTCCCT-CCATTTCCCTCTCCCTCTCCCTC-C-CT-CC-CTCCCTCT--C
* *
4398389 TCCCTCCCACCCTCCCTCTC-TCTCTCCCTCTCCCTCTCCCTCCCTCCCTCCCTCTC
1 TCTCTCCCTCCCTCCCTC-CAT-T-TCCCTCTCCCTCTCCCTCCCTCCCTCCCTCTC
*
4398445 TCTCTCCCTCTCTCTCCCTCCATTT-CC-CT-CC-CTCCCTCCCACCC-CCC-CTC
1 TCTCTCCCTC-C-CTCCCTCCATTTCCCTCTCCCTCTCCCTCCCTCCCTCCCTCTC
4398495 TCTCTCCC-CCCTCCC
1 TCTCTCCCTCCCTCCC
4398510 CCTCTCCAAC
Statistics
Matches: 107, Mismatches: 7, Indels: 27
0.76 0.05 0.19
Matches are distributed among these distances:
47 5 0.05
48 1 0.01
49 1 0.01
50 11 0.10
51 3 0.03
52 12 0.11
53 2 0.02
54 2 0.02
55 2 0.02
56 10 0.09
57 3 0.03
58 16 0.15
59 3 0.03
60 18 0.17
61 1 0.01
62 17 0.16
ACGTcount: A:0.02, C:0.68, G:0.00, T:0.30
Consensus pattern (54 bp):
TCTCTCCCTCCCTCCCTCCATTTCCCTCTCCCTCTCCCTCCCTCCCTCCCTCTC
Done.