Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008358.1 Hibiscus syriacus cultivar Beakdansim tig00111097_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: 729890
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 2 of 4
Found at i:145929 original size:30 final size:29
Alignment explanation
Indices: 145870--145936 Score: 73
Period size: 30 Copynumber: 2.2 Consensus size: 29
145860 GTTACGATAT
* *
145870 ATATTATTATTAAATTAAAAATTCTAAATA
1 ATATT-TTATAAAATTAAAAAATCTAAATA
145900 ATATTTTATAAAATATCAAAAAATC-AAATA
1 ATATTTTATAAAAT-T-AAAAAATCTAAATA
*
145930 ATTTTTT
1 ATATTTT
145937 GTGTAAATGA
Statistics
Matches: 32, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
29 8 0.25
30 17 0.53
31 7 0.22
ACGTcount: A:0.52, C:0.04, G:0.00, T:0.43
Consensus pattern (29 bp):
ATATTTTATAAAATTAAAAAATCTAAATA
Found at i:148446 original size:17 final size:17
Alignment explanation
Indices: 148424--148456 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
148414 AAGAGCAGTG
*
148424 TTACCTGCTACAAAATA
1 TTACCTGCTAAAAAATA
148441 TTACCTGCTAAAAAAT
1 TTACCTGCTAAAAAAT
148457 GTCACCAAAT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.42, C:0.21, G:0.06, T:0.30
Consensus pattern (17 bp):
TTACCTGCTAAAAAATA
Found at i:157054 original size:23 final size:23
Alignment explanation
Indices: 157010--157070 Score: 88
Period size: 23 Copynumber: 2.7 Consensus size: 23
157000 TAGTGCAGAT
*
157010 GGAATCGATACCCCC-TTGAAGG
1 GGAATCGATACCCCCTTTAAAGG
* *
157032 GGAACCGATTCCCCCTTTAAAGG
1 GGAATCGATACCCCCTTTAAAGG
157055 GGAATCGATACCCCCT
1 GGAATCGATACCCCCT
157071 GGGGTTCTGG
Statistics
Matches: 33, Mismatches: 5, Indels: 1
0.85 0.13 0.03
Matches are distributed among these distances:
22 13 0.39
23 20 0.61
ACGTcount: A:0.26, C:0.31, G:0.23, T:0.20
Consensus pattern (23 bp):
GGAATCGATACCCCCTTTAAAGG
Found at i:158682 original size:18 final size:18
Alignment explanation
Indices: 158659--158695 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
158649 CAACACGAGA
* *
158659 AACAAGCACGAGCAGAGG
1 AACAAGCACAACCAGAGG
158677 AACAAGCACAACCAGAGG
1 AACAAGCACAACCAGAGG
158695 A
1 A
158696 TCAAATGCCT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.49, C:0.24, G:0.27, T:0.00
Consensus pattern (18 bp):
AACAAGCACAACCAGAGG
Found at i:162047 original size:21 final size:20
Alignment explanation
Indices: 161980--162051 Score: 67
Period size: 21 Copynumber: 3.5 Consensus size: 20
161970 CGACAATCTC
* *
161980 ATACCCTAAACC-TATATCT
1 ATACCCTAAACCTTAAAACT
* *
161999 AAACCCTAAATCTTAAAACT
1 ATACCCTAAACCTTAAAACT
162019 -TAACCCCTAAACCTTAAACACT
1 AT-A-CCCTAAACCTTAAA-ACT
162041 ATACCCTAAAC
1 ATACCCTAAAC
162052 TATGATTCTT
Statistics
Matches: 42, Mismatches: 6, Indels: 8
0.75 0.11 0.14
Matches are distributed among these distances:
19 10 0.24
20 6 0.14
21 21 0.50
22 4 0.10
23 1 0.02
ACGTcount: A:0.43, C:0.32, G:0.00, T:0.25
Consensus pattern (20 bp):
ATACCCTAAACCTTAAAACT
Found at i:162246 original size:2 final size:2
Alignment explanation
Indices: 162241--162273 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
162231 TTCGTGTGTG
162241 TA TA TA TA 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 TA TA TA TA T
162274 TAAGAGATTT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:162542 original size:15 final size:15
Alignment explanation
Indices: 162477--162561 Score: 52
Period size: 15 Copynumber: 5.8 Consensus size: 15
162467 ATTTTATATA
162477 TATATATATATAATAT
1 TATATATATATAAT-T
* *
162493 TA-ATAAATTTAATT
1 TATATATATATAATT
* * **
162507 TAAAT-TA-AAAAAA
1 TATATATATATAATT
162520 TATATATATATAATAT
1 TATATATATATAAT-T
*
162536 T-TATATATTTAATT
1 TATATATATATAATT
*
162550 TAAATATATATA
1 TATATATATATA
162562 TTCGACCCGA
Statistics
Matches: 50, Mismatches: 14, Indels: 11
0.67 0.19 0.15
Matches are distributed among these distances:
13 6 0.12
14 8 0.16
15 33 0.66
16 3 0.06
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (15 bp):
TATATATATATAATT
Found at i:162705 original size:25 final size:25
Alignment explanation
Indices: 162668--162716 Score: 71
Period size: 25 Copynumber: 2.0 Consensus size: 25
162658 ATCACCGCAA
* * *
162668 TTTTTTAAGCGGGGACGAGTACGAG
1 TTTTTTAAACGGGAACGAGGACGAG
162693 TTTTTTAAACGGGAACGAGGACGA
1 TTTTTTAAACGGGAACGAGGACGA
162717 AGGACAAATC
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
25 21 1.00
ACGTcount: A:0.29, C:0.12, G:0.33, T:0.27
Consensus pattern (25 bp):
TTTTTTAAACGGGAACGAGGACGAG
Found at i:169335 original size:8 final size:8
Alignment explanation
Indices: 169324--169352 Score: 58
Period size: 8 Copynumber: 3.6 Consensus size: 8
169314 TTACAAACAT
169324 CAATCAAC
1 CAATCAAC
169332 CAATCAAC
1 CAATCAAC
169340 CAATCAAC
1 CAATCAAC
169348 CAATC
1 CAATC
169353 TGTTTTAGAT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 21 1.00
ACGTcount: A:0.48, C:0.38, G:0.00, T:0.14
Consensus pattern (8 bp):
CAATCAAC
Found at i:169563 original size:2 final size:2
Alignment explanation
Indices: 169556--169598 Score: 86
Period size: 2 Copynumber: 21.5 Consensus size: 2
169546 TTATAATGAT
169556 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
169598 T
1 T
169599 TATATATACA
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 41 1.00
ACGTcount: A:0.00, C:0.49, G:0.00, T:0.51
Consensus pattern (2 bp):
TC
Found at i:169937 original size:2 final size:2
Alignment explanation
Indices: 169926--169961 Score: 58
Period size: 2 Copynumber: 19.0 Consensus size: 2
169916 ACAACAGCAT
169926 TA TA -A TA TA TA TA TA TA TA TA TA TA TA TA TA T- TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
169962 AACGATACTC
Statistics
Matches: 32, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
1 2 0.06
2 30 0.94
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:171305 original size:13 final size:13
Alignment explanation
Indices: 171287--171316 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
171277 GATAATTTAG
171287 AATTTTTAAATTT
1 AATTTTTAAATTT
*
171300 AATTTTTAATTTT
1 AATTTTTAAATTT
171313 AATT
1 AATT
171317 ATTTTTTGTT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (13 bp):
AATTTTTAAATTT
Found at i:173415 original size:29 final size:30
Alignment explanation
Indices: 173370--173491 Score: 115
Period size: 30 Copynumber: 4.0 Consensus size: 30
173360 AAAATTTTAG
*
173370 TTAGTGACCAAAA-TATAAATTTTAAAAGT
1 TTAGGGACCAAAAGTATAAATTTTAAAAGT
* * *
173399 TTAGTGA-CTAAAGTATAAAGTTTGGAAAAGT
1 TTAGGGACCAAAAGTATAAA-TTT-TAAAAGT
** *
173430 TTAAGGGACCAAAAAG-GCAAATTTCAAAAGT
1 TT-AGGGACC-AAAAGTATAAATTTTAAAAGT
*
173461 TTAGGGACCAAAAGTATAATTTTTAAAAGT
1 TTAGGGACCAAAAGTATAAATTTTAAAAGT
173491 T
1 T
173492 AGGTTTTTGA
Statistics
Matches: 75, Mismatches: 11, Indels: 13
0.76 0.11 0.13
Matches are distributed among these distances:
28 4 0.05
29 18 0.24
30 22 0.29
31 16 0.21
32 7 0.09
33 4 0.05
34 4 0.05
ACGTcount: A:0.45, C:0.07, G:0.17, T:0.30
Consensus pattern (30 bp):
TTAGGGACCAAAAGTATAAATTTTAAAAGT
Found at i:173494 original size:29 final size:30
Alignment explanation
Indices: 173370--173491 Score: 99
Period size: 31 Copynumber: 4.0 Consensus size: 30
173360 AAAATTTTAG
* *
173370 TTAGTGACCAAAA-TATAAATTTTAAAAGT
1 TTAGGGACCAAAAGTATAATTTTTAAAAGT
* * **
173399 TTAGTGA-CTAAAGTATAAAGTTTGGAAAAGT
1 TTAGGGACCAAAAGTAT-AA-TTTTTAAAAGT
* *
173430 TTAAGGGACCAAAAAGGCA-AA-TTTCAAAAGT
1 TT-AGGGACC-AAAA-GTATAATTTTTAAAAGT
173461 TTAGGGACCAAAAGTATAATTTTTAAAAGT
1 TTAGGGACCAAAAGTATAATTTTTAAAAGT
173491 T
1 T
173492 AGGTTTTTGA
Statistics
Matches: 73, Mismatches: 11, Indels: 17
0.72 0.11 0.17
Matches are distributed among these distances:
28 6 0.08
29 16 0.22
30 19 0.26
31 20 0.27
32 4 0.05
33 3 0.04
34 3 0.04
35 2 0.03
ACGTcount: A:0.45, C:0.07, G:0.17, T:0.30
Consensus pattern (30 bp):
TTAGGGACCAAAAGTATAATTTTTAAAAGT
Found at i:178566 original size:90 final size:90
Alignment explanation
Indices: 178403--178580 Score: 302
Period size: 90 Copynumber: 2.0 Consensus size: 90
178393 TAATCCCGGA
* * * * *
178403 TATTTAATTTCAATTAATTAAATATAGATTTAATTAATTTGAAATAATAAAATCCCTGATATGAT
1 TATTAAATTCCAATTAATTAAATATAGATTTAATTAATTGGAAATAATAAAAACCCTAATATGAT
178468 TAGGGTAACTTGGATATAAAAGGAT
66 TAGGGTAACTTGGATATAAAAGGAT
178493 TATTAAATTCCAATTAATTAAATATAGATTTAATTAATTGGAAATAATAAAAACCCTAATATGAT
1 TATTAAATTCCAATTAATTAAATATAGATTTAATTAATTGGAAATAATAAAAACCCTAATATGAT
*
178558 TAGGGTAACTTGGCTATAAAAGG
66 TAGGGTAACTTGGATATAAAAGG
178581 GTGTGTTAGT
Statistics
Matches: 82, Mismatches: 6, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
90 82 1.00
ACGTcount: A:0.44, C:0.07, G:0.12, T:0.37
Consensus pattern (90 bp):
TATTAAATTCCAATTAATTAAATATAGATTTAATTAATTGGAAATAATAAAAACCCTAATATGAT
TAGGGTAACTTGGATATAAAAGGAT
Found at i:179670 original size:19 final size:20
Alignment explanation
Indices: 179628--179672 Score: 58
Period size: 19 Copynumber: 2.4 Consensus size: 20
179618 AGTATGGATT
179628 ATGAAAATGAAATGTAAAAG
1 ATGAAAATGAAATGTAAAAG
* *
179648 -TGAATATGAAA-GTGAAAG
1 ATGAAAATGAAATGTAAAAG
179666 ATGAAAA
1 ATGAAAA
179673 CGAGATATGA
Statistics
Matches: 21, Mismatches: 3, Indels: 3
0.78 0.11 0.11
Matches are distributed among these distances:
18 6 0.29
19 15 0.71
ACGTcount: A:0.58, C:0.00, G:0.22, T:0.20
Consensus pattern (20 bp):
ATGAAAATGAAATGTAAAAG
Found at i:179796 original size:23 final size:23
Alignment explanation
Indices: 179749--179835 Score: 86
Period size: 23 Copynumber: 3.8 Consensus size: 23
179739 AAAAATTACA
* *
179749 CCGAAGTG-CCACATGGAAATGTC
1 CCGAAG-GACCACATAGAAATATC
* * *
179772 CCGAAGGACCATATAGTATTATC
1 CCGAAGGACCACATAGAAATATC
* *
179795 CCGAAGGACCACGTAGAAATGTC
1 CCGAAGGACCACATAGAAATATC
*
179818 CCGAAGGACCACGTAGAA
1 CCGAAGGACCACATAGAA
179836 CCCTTGACTC
Statistics
Matches: 53, Mismatches: 10, Indels: 2
0.82 0.15 0.03
Matches are distributed among these distances:
22 1 0.02
23 52 0.98
ACGTcount: A:0.34, C:0.25, G:0.24, T:0.16
Consensus pattern (23 bp):
CCGAAGGACCACATAGAAATATC
Found at i:189314 original size:3 final size:3
Alignment explanation
Indices: 189299--189345 Score: 62
Period size: 3 Copynumber: 16.0 Consensus size: 3
189289 TTCATTTAAA
*
189299 TAT TAT T-T ATAT TAT TAT AAT TAT TAT TAT TAT TAT T-T TAT TAT
1 TAT TAT TAT -TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
189343 TAT
1 TAT
189346 AATACAGGCC
Statistics
Matches: 39, Mismatches: 2, Indels: 6
0.83 0.04 0.13
Matches are distributed among these distances:
2 3 0.08
3 35 0.90
4 1 0.03
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
TAT
Found at i:190777 original size:14 final size:14
Alignment explanation
Indices: 190737--190778 Score: 52
Period size: 14 Copynumber: 3.1 Consensus size: 14
190727 ATAAATAATA
*
190737 ATTTATTTTTCCAT
1 ATTTATTTTTCAAT
*
190751 AATTA-TTTT-AAT
1 ATTTATTTTTCAAT
190763 ATTTATTTTTCAAT
1 ATTTATTTTTCAAT
190777 AT
1 AT
190779 CGAAGAAAGG
Statistics
Matches: 23, Mismatches: 3, Indels: 4
0.77 0.10 0.13
Matches are distributed among these distances:
12 6 0.26
13 8 0.35
14 9 0.39
ACGTcount: A:0.31, C:0.07, G:0.00, T:0.62
Consensus pattern (14 bp):
ATTTATTTTTCAAT
Found at i:195993 original size:83 final size:84
Alignment explanation
Indices: 195894--196055 Score: 281
Period size: 83 Copynumber: 1.9 Consensus size: 84
195884 TTTTAGATAA
*
195894 AAATTGTATTTTGACAAAGTAAAGAAATATTTTAAATTAGACA-TAATTAGACAATTTATCTTAT
1 AAATTATATTTTGACAAAGTAAAGAAATATTTTAAATTAGACAGTAATTAGACAATTTATCTTAT
* *
195958 GATATTGAATAATGTAGAT
66 GATATAGAACAATGTAGAT
*
195977 AAATTATATTTTGACAAAGTAAAGAAATATTTTAAATTAGATAGTAATTAGACAATTTATCTTAT
1 AAATTATATTTTGACAAAGTAAAGAAATATTTTAAATTAGACAGTAATTAGACAATTTATCTTAT
196042 GATATAGAACAATG
66 GATATAGAACAATG
196056 AAGAATTGTC
Statistics
Matches: 74, Mismatches: 4, Indels: 1
0.94 0.05 0.01
Matches are distributed among these distances:
83 41 0.55
84 33 0.45
ACGTcount: A:0.46, C:0.05, G:0.12, T:0.38
Consensus pattern (84 bp):
AAATTATATTTTGACAAAGTAAAGAAATATTTTAAATTAGACAGTAATTAGACAATTTATCTTAT
GATATAGAACAATGTAGAT
Found at i:199170 original size:30 final size:31
Alignment explanation
Indices: 199131--199200 Score: 99
Period size: 30 Copynumber: 2.3 Consensus size: 31
199121 ATAAAATTTG
199131 AAAACGTTTAAGGACAAAAAAG-GTAATTTTC
1 AAAA-GTTTAAGGACAAAAAAGTGTAATTTTC
* *
199162 AAAAGTTTAAGGACCAAAAAGTGTAATTTTT
1 AAAAGTTTAAGGACAAAAAAGTGTAATTTTC
199193 AAAA-TTTA
1 AAAAGTTTA
199201 GGTTCTTGGC
Statistics
Matches: 36, Mismatches: 2, Indels: 3
0.88 0.05 0.07
Matches are distributed among these distances:
30 20 0.56
31 16 0.44
ACGTcount: A:0.49, C:0.07, G:0.14, T:0.30
Consensus pattern (31 bp):
AAAAGTTTAAGGACAAAAAAGTGTAATTTTC
Found at i:201897 original size:19 final size:18
Alignment explanation
Indices: 201873--201955 Score: 60
Period size: 19 Copynumber: 4.4 Consensus size: 18
201863 AATACATTGG
201873 GTTATGAA-CTTGAAAATAA
1 GTTATGAATC-TG-AAATAA
201892 GTTATGAATCTGAAATAA
1 GTTATGAATCTGAAATAA
* * * *
201910 GTTTTGAGTCCGAAAACAA
1 GTTATGAATCTG-AAATAA
* *
201929 GTTCTGAATCTGAGAATGA
1 GTTATGAATCTGA-AATAA
*
201948 GTTCTGAA
1 GTTATGAA
201956 ATGTGAAAGT
Statistics
Matches: 52, Mismatches: 9, Indels: 6
0.78 0.13 0.09
Matches are distributed among these distances:
18 16 0.31
19 35 0.67
20 1 0.02
ACGTcount: A:0.39, C:0.10, G:0.20, T:0.31
Consensus pattern (18 bp):
GTTATGAATCTGAAATAA
Found at i:202004 original size:25 final size:25
Alignment explanation
Indices: 201952--202027 Score: 84
Period size: 25 Copynumber: 3.0 Consensus size: 25
201942 GAATGAGTTC
* * *
201952 TGAAATGTGAAAGT-ATTATAAAAA
1 TGAAATGTGAAAATAAATATAAAAG
201976 TGAAATGTGAAAATAAATATAAAAG
1 TGAAATGTGAAAATAAATATAAAAG
*
202001 TGAAA-GATGAAAATAAGATATGAAAG
1 TGAAATG-TGAAAATAA-ATATAAAAG
202027 T
1 T
202028 TTTGTATTGT
Statistics
Matches: 45, Mismatches: 4, Indels: 4
0.85 0.08 0.08
Matches are distributed among these distances:
24 14 0.31
25 22 0.49
26 9 0.20
ACGTcount: A:0.57, C:0.00, G:0.18, T:0.25
Consensus pattern (25 bp):
TGAAATGTGAAAATAAATATAAAAG
Found at i:202078 original size:18 final size:18
Alignment explanation
Indices: 202055--202121 Score: 53
Period size: 18 Copynumber: 3.6 Consensus size: 18
202045 TGAAAAAGAA
202055 TATGATATGACTATTATG
1 TATGATATGACTATTATG
** *
202073 TATGATATTGTTTATCATGG
1 TATGATA-TGACTATTAT-G
* * *
202093 CTTTGATATGACTATTGTA
1 -TATGATATGACTATTATG
202112 TATGATATGA
1 TATGATATGA
202122 TTTTTCATGG
Statistics
Matches: 36, Mismatches: 10, Indels: 6
0.69 0.19 0.12
Matches are distributed among these distances:
18 16 0.44
19 7 0.19
20 7 0.19
21 6 0.17
ACGTcount: A:0.30, C:0.06, G:0.18, T:0.46
Consensus pattern (18 bp):
TATGATATGACTATTATG
Found at i:202105 original size:39 final size:39
Alignment explanation
Indices: 202057--202139 Score: 114
Period size: 39 Copynumber: 2.1 Consensus size: 39
202047 AAAAAGAATA
*
202057 TGATATGACTATTATGTATGATATTG-TTTATCATGGCTT
1 TGATATGACTATTATATATGATA-TGATTTATCATGGCTT
* * *
202096 TGATATGACTATTGTATATGATATGATTTTTCATGGTTT
1 TGATATGACTATTATATATGATATGATTTATCATGGCTT
202135 TGATA
1 TGATA
202140 AAATCATGAG
Statistics
Matches: 39, Mismatches: 4, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
38 2 0.05
39 37 0.95
ACGTcount: A:0.27, C:0.06, G:0.18, T:0.49
Consensus pattern (39 bp):
TGATATGACTATTATATATGATATGATTTATCATGGCTT
Found at i:202234 original size:18 final size:18
Alignment explanation
Indices: 202213--202247 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
202203 ATTAGTGTAT
202213 ACTATTATATATGATATG
1 ACTATTATATATGATATG
*
202231 ACTATTATGTATGATAT
1 ACTATTATATATGATAT
202248 TGTCTATAAT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.37, C:0.06, G:0.11, T:0.46
Consensus pattern (18 bp):
ACTATTATATATGATATG
Found at i:203233 original size:16 final size:15
Alignment explanation
Indices: 203191--203236 Score: 51
Period size: 16 Copynumber: 3.1 Consensus size: 15
203181 TCTAATACCG
*
203191 ATAAAA-TAAATTCT
1 ATAAAACTAAATTAT
203205 ATAAAAC-ATAATTGAT
1 ATAAAACTA-AATT-AT
203221 ATAAAACTAAATTAT
1 ATAAAACTAAATTAT
203236 A
1 A
203237 CTTCCATCAT
Statistics
Matches: 27, Mismatches: 1, Indels: 7
0.77 0.03 0.20
Matches are distributed among these distances:
14 7 0.26
15 7 0.26
16 12 0.44
17 1 0.04
ACGTcount: A:0.59, C:0.07, G:0.02, T:0.33
Consensus pattern (15 bp):
ATAAAACTAAATTAT
Found at i:205451 original size:13 final size:13
Alignment explanation
Indices: 205427--205486 Score: 59
Period size: 13 Copynumber: 4.7 Consensus size: 13
205417 AAGTATGTAT
*
205427 TATGAAAATGAAA
1 TATGAAAGTGAAA
*
205440 TGTGAAAGTG-AA
1 TATGAAAGTGAAA
*
205452 TATAAAAGTGAAA
1 TATGAAAGTGAAA
* * *
205465 GATGAAAATGAGA
1 TATGAAAGTGAAA
205478 TATGAAAGT
1 TATGAAAGT
205487 TTTGTATTGT
Statistics
Matches: 36, Mismatches: 10, Indels: 2
0.75 0.21 0.04
Matches are distributed among these distances:
12 10 0.28
13 26 0.72
ACGTcount: A:0.53, C:0.00, G:0.23, T:0.23
Consensus pattern (13 bp):
TATGAAAGTGAAA
Found at i:205659 original size:36 final size:36
Alignment explanation
Indices: 205618--205698 Score: 144
Period size: 36 Copynumber: 2.2 Consensus size: 36
205608 ATTTTCGAAC
*
205618 TAATTCGGTTAACCGACCGAATCGAATTAGTTCGAT
1 TAATTCGGTTAACCGACCGAATCAAATTAGTTCGAT
*
205654 TAATTCGGTTAACCGACCGAATCAAATTAGTTCGGT
1 TAATTCGGTTAACCGACCGAATCAAATTAGTTCGAT
205690 TAATTCGGT
1 TAATTCGGT
205699 CGACTACCTA
Statistics
Matches: 43, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
36 43 1.00
ACGTcount: A:0.30, C:0.19, G:0.20, T:0.32
Consensus pattern (36 bp):
TAATTCGGTTAACCGACCGAATCAAATTAGTTCGAT
Found at i:220300 original size:32 final size:33
Alignment explanation
Indices: 220230--220303 Score: 82
Period size: 32 Copynumber: 2.3 Consensus size: 33
220220 CCTAAGGTGG
*
220230 CCCTTGGGTAGGCTCCGAGGCCCCGAGAAACTT
1 CCCTTGGGTAGGCTCCGAGGCCCCAAGAAACTT
* **
220263 -TCTTGGGTAGGCTCTC-AGGCCCCAAGGCA-TT
1 CCCTTGGGTAGGCTC-CGAGGCCCCAAGAAACTT
220294 CCCTTGGGTA
1 CCCTTGGGTA
220304 AATCATGGGA
Statistics
Matches: 34, Mismatches: 5, Indels: 5
0.77 0.11 0.11
Matches are distributed among these distances:
31 2 0.06
32 31 0.91
33 1 0.03
ACGTcount: A:0.16, C:0.31, G:0.30, T:0.23
Consensus pattern (33 bp):
CCCTTGGGTAGGCTCCGAGGCCCCAAGAAACTT
Found at i:221600 original size:19 final size:19
Alignment explanation
Indices: 221576--221636 Score: 56
Period size: 19 Copynumber: 3.3 Consensus size: 19
221566 TGCATTGGGC
221576 TATGAACTTGAAAATAAGT
1 TATGAACTTGAAAATAAGT
* *
221595 TATGAA-TCTGAAATTAATT
1 TATGAACT-TGAAAATAAGT
*
221614 TATCAATCTTG--AATAAGT
1 TATGAA-CTTGAAAATAAGT
221632 TATGA
1 TATGA
221637 GTCCATAAAT
Statistics
Matches: 33, Mismatches: 6, Indels: 7
0.72 0.13 0.15
Matches are distributed among these distances:
18 10 0.30
19 20 0.61
20 2 0.06
21 1 0.03
ACGTcount: A:0.43, C:0.07, G:0.13, T:0.38
Consensus pattern (19 bp):
TATGAACTTGAAAATAAGT
Found at i:221704 original size:6 final size:6
Alignment explanation
Indices: 221693--221741 Score: 53
Period size: 6 Copynumber: 7.7 Consensus size: 6
221683 AATACGGATT
* *
221693 ATGAAA ATGAAA TATGAAA ATGAAT ATGAAA TTGAAA GATGAAA GATGA
1 ATGAAA ATGAAA -ATGAAA ATGAAA ATGAAA ATGAAA -ATGAAA -ATGA
221742 GATATGAAAG
Statistics
Matches: 37, Mismatches: 4, Indels: 3
0.84 0.09 0.07
Matches are distributed among these distances:
6 21 0.57
7 16 0.43
ACGTcount: A:0.57, C:0.00, G:0.20, T:0.22
Consensus pattern (6 bp):
ATGAAA
Found at i:221710 original size:13 final size:13
Alignment explanation
Indices: 221692--221750 Score: 75
Period size: 13 Copynumber: 4.5 Consensus size: 13
221682 AAATACGGAT
221692 TATGAAAATGAAA
1 TATGAAAATGAAA
221705 TATGAAAATG-AA
1 TATGAAAATGAAA
*
221717 TATGAAATTGAAA
1 TATGAAAATGAAA
* *
221730 GATGAAAGATGAGA
1 TATGAAA-ATGAAA
221744 TATGAAA
1 TATGAAA
221751 GTTTTGTATT
Statistics
Matches: 39, Mismatches: 5, Indels: 3
0.83 0.11 0.06
Matches are distributed among these distances:
12 11 0.28
13 18 0.46
14 10 0.26
ACGTcount: A:0.56, C:0.00, G:0.20, T:0.24
Consensus pattern (13 bp):
TATGAAAATGAAA
Found at i:221711 original size:7 final size:7
Alignment explanation
Indices: 221692--221750 Score: 63
Period size: 7 Copynumber: 9.0 Consensus size: 7
221682 AAATACGGAT
221692 TATGAAA
1 TATGAAA
221699 -ATGAAA
1 TATGAAA
221705 TATGAAA
1 TATGAAA
221712 -ATG-AA
1 TATGAAA
221717 TATGAAA
1 TATGAAA
221724 T-TGAAA
1 TATGAAA
*
221730 GATGAAA
1 TATGAAA
* *
221737 GATGAGA
1 TATGAAA
221744 TATGAAA
1 TATGAAA
221751 GTTTTGTATT
Statistics
Matches: 44, Mismatches: 4, Indels: 8
0.79 0.07 0.14
Matches are distributed among these distances:
5 2 0.05
6 17 0.39
7 25 0.57
ACGTcount: A:0.56, C:0.00, G:0.20, T:0.24
Consensus pattern (7 bp):
TATGAAA
Found at i:221728 original size:25 final size:27
Alignment explanation
Indices: 221692--221750 Score: 86
Period size: 25 Copynumber: 2.3 Consensus size: 27
221682 AAATACGGAT
*
221692 TATGAAAATGAAATATGAAA-ATGA-A
1 TATGAAAATGAAAGATGAAAGATGAGA
*
221717 TATGAAATTGAAAGATGAAAGATGAGA
1 TATGAAAATGAAAGATGAAAGATGAGA
221744 TATGAAA
1 TATGAAA
221751 GTTTTGTATT
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
25 18 0.60
26 4 0.13
27 8 0.27
ACGTcount: A:0.56, C:0.00, G:0.20, T:0.24
Consensus pattern (27 bp):
TATGAAAATGAAAGATGAAAGATGAGA
Found at i:226389 original size:32 final size:32
Alignment explanation
Indices: 226344--226425 Score: 119
Period size: 32 Copynumber: 2.6 Consensus size: 32
226334 CTAGTTAGGG
*
226344 TGCATTCAAATAATGCACAGAACAATCAGATT
1 TGCATTCAGATAATGCACAGAACAATCAGATT
* * *
226376 TGCATTCAGATAATGCACAGTACAGTCAGGTT
1 TGCATTCAGATAATGCACAGAACAATCAGATT
*
226408 TGCATTTAGATAATGCAC
1 TGCATTCAGATAATGCAC
226426 GGAGTATCAG
Statistics
Matches: 45, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
32 45 1.00
ACGTcount: A:0.37, C:0.18, G:0.17, T:0.28
Consensus pattern (32 bp):
TGCATTCAGATAATGCACAGAACAATCAGATT
Found at i:230366 original size:19 final size:19
Alignment explanation
Indices: 230339--230406 Score: 61
Period size: 19 Copynumber: 3.6 Consensus size: 19
230329 TAATATACTC
230339 AATTATATTATAATAATAT
1 AATTATATTATAATAATAT
* *
230358 AATTTTATTTTAATAATATGT
1 AATTATATTATAATAATA--T
*
230379 AA-TAAATTATTAATAA-A-
1 AATTATATTA-TAATAATAT
230396 AATTATATTAT
1 AATTATATTAT
230407 TTATTAATTT
Statistics
Matches: 39, Mismatches: 6, Indels: 10
0.71 0.11 0.18
Matches are distributed among these distances:
17 3 0.08
18 6 0.15
19 16 0.41
20 5 0.13
21 9 0.23
ACGTcount: A:0.50, C:0.00, G:0.01, T:0.49
Consensus pattern (19 bp):
AATTATATTATAATAATAT
Found at i:234287 original size:219 final size:218
Alignment explanation
Indices: 233892--234397 Score: 547
Period size: 219 Copynumber: 2.4 Consensus size: 218
233882 ATGTCTTCAC
* * *
233892 CATAAACTATGATCCAACAACATCAAATTACGCATACTCACTTCGCACATATACATATATTTTCA
1 CATAAACTACGATCCAACAACATCAAATTACACATACTCACTTAGCACATATACATATATTTTCA
* * * * *
233957 AGAGGTATCTATTTTTACTAAGCAAATTTTATATGTACTAAGAAATCTTAGCACATAATACATAT
66 AGAGATATCTATTTTTACCAAGCAAATTTTATATATACTAAGAAATATTAGCACATAATACACAT
* **
234022 ATTTAATGCTATTCGGTCACATAAATAAGACTCTTTAATATGTGGTAACAAACTACGATAGGTAT
131 ATTTAATACTATTCAATCACATAAATAAGACTCTTTAATATGTGGTAACAAACTACGAT-GGTAT
234087 AGCGACATATTTATATATATATAT
195 AGCGACATATTTATATATATATAT
* * * *
234111 CATAAATTACGATCCAACAACATCAAATTTCACATGCTCATTTAGCACATATACATATATTTTCA
1 CATAAACTACGATCCAACAACATCAAATTACACATACTCACTTAGCACATATACATATATTTTCA
*
234176 A-ACGATATCTATTTTTACCAAG-AAGATTTTATATATGCTAAGAAATATTAGCACATAATACAC
66 AGA-GATATCTATTTTTACCAAGCAA-ATTTTATATATACTAAGAAATATTAGCACATAATACAC
* * ** * * *
234239 ATATTTAGTACTATTCAATTAGGTAAA-AAGGACT-TTTCATTCTGTGGTAATAAACTACGATGG
129 ATATTTAATACTATTCAATCACATAAATAA-GACTCTTT-AATATGTGGTAACAAACTACGATGG
* * * * * *
234302 --TACCGAAACATCT-T-TATGTATAC
192 TATAGCGACATATTTATATATATATAT
* * * *
234325 CAT----T-C-ATCCAACAACATCAAATTACACATATTCACTTAGTACAAATACATATATTTCCA
1 CATAAACTACGATCCAACAACATCAAATTACACATACTCACTTAGCACATATACATATATTTTCA
*
234384 A-ATGGTATCTATTT
66 AGA-GATATCTATTT
234398 CTACTAATCA
Statistics
Matches: 245, Mismatches: 38, Indels: 19
0.81 0.13 0.06
Matches are distributed among these distances:
208 59 0.24
209 1 0.00
210 1 0.00
214 10 0.04
215 1 0.00
216 9 0.04
218 10 0.04
219 154 0.63
ACGTcount: A:0.39, C:0.17, G:0.09, T:0.34
Consensus pattern (218 bp):
CATAAACTACGATCCAACAACATCAAATTACACATACTCACTTAGCACATATACATATATTTTCA
AGAGATATCTATTTTTACCAAGCAAATTTTATATATACTAAGAAATATTAGCACATAATACACAT
ATTTAATACTATTCAATCACATAAATAAGACTCTTTAATATGTGGTAACAAACTACGATGGTATA
GCGACATATTTATATATATATAT
Found at i:240926 original size:130 final size:134
Alignment explanation
Indices: 240689--240951 Score: 498
Period size: 130 Copynumber: 2.0 Consensus size: 134
240679 GAGAAGATTT
240689 TCATCTGACCGAGCATCTCTCCTTGAGGAGTGTCGATCCTATTCGTTAAGGAGAAAGATGGGTCG
1 TCATCTGACCGAGCATCTCTCCTTGAGGAGTGTCGATCCTATTCGTTAAGGAGAAAGATGGGTCG
240754 AAGAGGTTGTGCATCGACTACAGGCAGTTAAATAAGTTGACCATCAAGAAACGTTACCCACTCCC
66 AAGAGGTTGTGCATCGACTACAGGCAGTTAAATAAGTTGACCATCAAGAAACGTTACCCACTCCC
240819 CAGG
131 CAGG
240823 TCATCTGACCGAGCATCTCTCCTTGA-G-G-GTCGATCCTATTCGTTAAGGAGAAAGATGGGTCG
1 TCATCTGACCGAGCATCTCTCCTTGAGGAGTGTCGATCCTATTCGTTAAGGAGAAAGATGGGTCG
240885 -AGAGGTTGTGCATCGACTACAGGCAGTTAAATAAGTTGACCATCAAGAAACGTTACCCACTCCC
66 AAGAGGTTGTGCATCGACTACAGGCAGTTAAATAAGTTGACCATCAAGAAACGTTACCCACTCCC
240949 CAG
131 CAG
240952 TATAAATGAC
Statistics
Matches: 129, Mismatches: 0, Indels: 4
0.97 0.00 0.03
Matches are distributed among these distances:
130 67 0.52
131 34 0.26
132 1 0.01
133 1 0.01
134 26 0.20
ACGTcount: A:0.28, C:0.24, G:0.24, T:0.24
Consensus pattern (134 bp):
TCATCTGACCGAGCATCTCTCCTTGAGGAGTGTCGATCCTATTCGTTAAGGAGAAAGATGGGTCG
AAGAGGTTGTGCATCGACTACAGGCAGTTAAATAAGTTGACCATCAAGAAACGTTACCCACTCCC
CAGG
Found at i:246370 original size:14 final size:14
Alignment explanation
Indices: 246350--246383 Score: 52
Period size: 14 Copynumber: 2.5 Consensus size: 14
246340 AAAATGAATT
*
246350 ACATTTTCT-GAAA
1 ACATTTTTTGGAAA
246363 ACATTTTTTGGAAA
1 ACATTTTTTGGAAA
246377 ACATTTT
1 ACATTTT
246384 ATGGTGTTTG
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
13 8 0.42
14 11 0.58
ACGTcount: A:0.35, C:0.12, G:0.09, T:0.44
Consensus pattern (14 bp):
ACATTTTTTGGAAA
Found at i:246707 original size:27 final size:28
Alignment explanation
Indices: 246662--246723 Score: 74
Period size: 27 Copynumber: 2.2 Consensus size: 28
246652 TCATTAGATA
246662 ATTATATCAATATTAAATACA-TAAATAAT
1 ATTAT-TCAATATTAAATA-ATTAAATAAT
* *
246691 ATTATTCATTATT-AATAATTTAATAAT
1 ATTATTCAATATTAAATAATTAAATAAT
246718 ATTATT
1 ATTATT
246724 TCTATGAAAT
Statistics
Matches: 30, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
26 1 0.03
27 17 0.57
28 7 0.23
29 5 0.17
ACGTcount: A:0.48, C:0.05, G:0.00, T:0.47
Consensus pattern (28 bp):
ATTATTCAATATTAAATAATTAAATAAT
Found at i:246902 original size:14 final size:13
Alignment explanation
Indices: 246883--246922 Score: 55
Period size: 14 Copynumber: 3.0 Consensus size: 13
246873 TTTAATGATT
246883 AATATTTTGATTAA
1 AATATTTT-ATTAA
246897 AATATTATTATTAA
1 AATATT-TTATTAA
246911 AATATTTT-TTAA
1 AATATTTTATTAA
246923 TGTTAAATTC
Statistics
Matches: 25, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
12 4 0.16
13 2 0.08
14 17 0.68
15 2 0.08
ACGTcount: A:0.45, C:0.00, G:0.03, T:0.53
Consensus pattern (13 bp):
AATATTTTATTAA
Found at i:247122 original size:13 final size:14
Alignment explanation
Indices: 247104--247133 Score: 53
Period size: 13 Copynumber: 2.2 Consensus size: 14
247094 GAAAATAAGA
247104 AAAATATTTTC-TG
1 AAAATATTTTCGTG
247117 AAAATATTTTCGTG
1 AAAATATTTTCGTG
247131 AAA
1 AAA
247134 CAAACAGACC
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 11 0.69
14 5 0.31
ACGTcount: A:0.43, C:0.07, G:0.10, T:0.40
Consensus pattern (14 bp):
AAAATATTTTCGTG
Found at i:259898 original size:16 final size:16
Alignment explanation
Indices: 259877--259917 Score: 73
Period size: 16 Copynumber: 2.6 Consensus size: 16
259867 GCTTGGTAGG
259877 AAAGAAAAGTGGGGGC
1 AAAGAAAAGTGGGGGC
*
259893 AAAGAAAAGTGGGGGG
1 AAAGAAAAGTGGGGGC
259909 AAAGAAAAG
1 AAAGAAAAG
259918 GAGGGATGTG
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
16 24 1.00
ACGTcount: A:0.51, C:0.02, G:0.41, T:0.05
Consensus pattern (16 bp):
AAAGAAAAGTGGGGGC
Found at i:273374 original size:2 final size:2
Alignment explanation
Indices: 273367--273392 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
273357 TCGTCATCTA
273367 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
273393 TAAAATCATG
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:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:273925 original size:29 final size:29
Alignment explanation
Indices: 273893--273968 Score: 82
Period size: 29 Copynumber: 2.6 Consensus size: 29
273883 CTTTTTCATT
*
273893 TAAGTACCTAAAATATTTTTTTATCAAAA
1 TAAGTACCTAAAATATTTTTATATCAAAA
* * *
273922 TAAGTACTTAAAAGTA-TTTTATGTCAAGA
1 TAAGTACCTAAAA-TATTTTTATATCAAAA
* *
273951 TAGGTACCTAAATTATTT
1 TAAGTACCTAAAATATTT
273969 AATTTTTTTC
Statistics
Matches: 38, Mismatches: 7, Indels: 4
0.78 0.14 0.08
Matches are distributed among these distances:
28 2 0.05
29 34 0.89
30 2 0.05
ACGTcount: A:0.41, C:0.09, G:0.09, T:0.41
Consensus pattern (29 bp):
TAAGTACCTAAAATATTTTTATATCAAAA
Found at i:275193 original size:16 final size:16
Alignment explanation
Indices: 275172--275202 Score: 62
Period size: 16 Copynumber: 1.9 Consensus size: 16
275162 AATAATAAAT
275172 GAACATAAACGAACAC
1 GAACATAAACGAACAC
275188 GAACATAAACGAACA
1 GAACATAAACGAACA
275203 ATTTTTTTTT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.58, C:0.23, G:0.13, T:0.06
Consensus pattern (16 bp):
GAACATAAACGAACAC
Found at i:275282 original size:10 final size:10
Alignment explanation
Indices: 275267--275297 Score: 62
Period size: 10 Copynumber: 3.1 Consensus size: 10
275257 CATTTAATAA
275267 ATAAACGAAC
1 ATAAACGAAC
275277 ATAAACGAAC
1 ATAAACGAAC
275287 ATAAACGAAC
1 ATAAACGAAC
275297 A
1 A
275298 CGAACATAAC
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 21 1.00
ACGTcount: A:0.61, C:0.19, G:0.10, T:0.10
Consensus pattern (10 bp):
ATAAACGAAC
Found at i:275302 original size:16 final size:16
Alignment explanation
Indices: 275281--275356 Score: 127
Period size: 16 Copynumber: 4.8 Consensus size: 16
275271 ACGAACATAA
275281 ACGAACATAAACGAAC
1 ACGAACATAAACGAAC
275297 ACGAACAT-AACGAAC
1 ACGAACATAAACGAAC
*
275312 ACGAATATAAACGAAC
1 ACGAACATAAACGAAC
*
275328 ACGAACATAAATGAAC
1 ACGAACATAAACGAAC
275344 ACGAACATAAACG
1 ACGAACATAAACG
275357 TTGGAGACCC
Statistics
Matches: 55, Mismatches: 4, Indels: 2
0.90 0.07 0.03
Matches are distributed among these distances:
15 14 0.25
16 41 0.75
ACGTcount: A:0.55, C:0.22, G:0.13, T:0.09
Consensus pattern (16 bp):
ACGAACATAAACGAAC
Found at i:275322 original size:31 final size:32
Alignment explanation
Indices: 275281--275356 Score: 127
Period size: 31 Copynumber: 2.4 Consensus size: 32
275271 ACGAACATAA
275281 ACGAACATAAACGAACACGAACAT-AACGAAC
1 ACGAACATAAACGAACACGAACATAAACGAAC
* *
275312 ACGAATATAAACGAACACGAACATAAATGAAC
1 ACGAACATAAACGAACACGAACATAAACGAAC
275344 ACGAACATAAACG
1 ACGAACATAAACG
275357 TTGGAGACCC
Statistics
Matches: 41, Mismatches: 3, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
31 23 0.56
32 18 0.44
ACGTcount: A:0.55, C:0.22, G:0.13, T:0.09
Consensus pattern (32 bp):
ACGAACATAAACGAACACGAACATAAACGAAC
Found at i:276292 original size:14 final size:14
Alignment explanation
Indices: 276275--276330 Score: 66
Period size: 14 Copynumber: 4.3 Consensus size: 14
276265 AATGAGCATA
276275 AACGAACATAACCG
1 AACGAACATAACCG
276289 AACGAACAT-A---
1 AACGAACATAACCG
276299 AACGAACATAACCG
1 AACGAACATAACCG
* *
276313 AATGAACATAACTG
1 AACGAACATAACCG
276327 AACG
1 AACG
276331 TTCACGAACG
Statistics
Matches: 35, Mismatches: 3, Indels: 8
0.76 0.07 0.17
Matches are distributed among these distances:
10 9 0.26
11 1 0.03
13 1 0.03
14 24 0.69
ACGTcount: A:0.52, C:0.23, G:0.14, T:0.11
Consensus pattern (14 bp):
AACGAACATAACCG
Found at i:276329 original size:24 final size:24
Alignment explanation
Indices: 276265--276323 Score: 100
Period size: 24 Copynumber: 2.5 Consensus size: 24
276255 AACATAAATA
*
276265 AATGAGCATAAACGAACATAACCG
1 AATGAACATAAACGAACATAACCG
*
276289 AACGAACATAAACGAACATAACCG
1 AATGAACATAAACGAACATAACCG
276313 AATGAACATAA
1 AATGAACATAA
276324 CTGAACGTTC
Statistics
Matches: 32, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
24 32 1.00
ACGTcount: A:0.54, C:0.20, G:0.14, T:0.12
Consensus pattern (24 bp):
AATGAACATAAACGAACATAACCG
Found at i:280514 original size:90 final size:89
Alignment explanation
Indices: 280361--280533 Score: 292
Period size: 90 Copynumber: 1.9 Consensus size: 89
280351 TAACGCACCA
* * *
280361 TTTTATAGCCAAGTTATCCTAATCATATTAGGGTTTTTATTATTTCAAATTAATTAAATCTATAT
1 TTTTATAGCCAAGTTACCCTAATCATATTAAGGATTTTATTATTTCAAATTAATTAAATCTATAT
*
280426 TTAATTAATTAGAATTTAATAATCC
66 TTAATTAATT-GAAATTAATAATCC
*
280451 TTTTATATCCAAGTTACCCTAATCATATTAAGGATTTTATTATTTCAAATTAATTAAATCTATAT
1 TTTTATAGCCAAGTTACCCTAATCATATTAAGGATTTTATTATTTCAAATTAATTAAATCTATAT
280516 TTAATTAATTGAAATTAA
66 TTAATTAATTGAAATTAA
280534 ATATTAAGGA
Statistics
Matches: 78, Mismatches: 5, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
89 7 0.09
90 71 0.91
ACGTcount: A:0.38, C:0.10, G:0.06, T:0.46
Consensus pattern (89 bp):
TTTTATAGCCAAGTTACCCTAATCATATTAAGGATTTTATTATTTCAAATTAATTAAATCTATAT
TTAATTAATTGAAATTAATAATCC
Found at i:290446 original size:21 final size:22
Alignment explanation
Indices: 290420--290469 Score: 75
Period size: 21 Copynumber: 2.3 Consensus size: 22
290410 AAATGTGTAG
* *
290420 CGATGCACTGCTACAGT-GCAT
1 CGATGCACCGCTACAGTAACAT
290441 CGATGCACCGCTACAGTAACAT
1 CGATGCACCGCTACAGTAACAT
290463 CGATGCA
1 CGATGCA
290470 TGCAGTAACA
Statistics
Matches: 26, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
21 16 0.62
22 10 0.38
ACGTcount: A:0.28, C:0.30, G:0.22, T:0.20
Consensus pattern (22 bp):
CGATGCACCGCTACAGTAACAT
Found at i:291204 original size:58 final size:59
Alignment explanation
Indices: 291021--291348 Score: 285
Period size: 58 Copynumber: 5.6 Consensus size: 59
291011 ATACCATTAG
* * * ** *
291021 TATGATTTCCTTATC-TTTGTAGCACCCTTAGTGCTTTATCTGGAAATCCATACACTCAA
1 TATGATTTCCTTACCATTT-TAGCACACTAAGTGCTCCATATGGAAATCCATACACTCAA
* * * ***
291080 TAT-AATTCACTTACCATTTTAGCACA-TAAAATGC-CCTATCTGGAAATCCATATTTTCAA
1 TATGATTTC-CTTACCATTTTAGCACACT-AAGTGCTCC-ATATGGAAATCCATACACTCAA
* * * * *
291139 TACGATTTCCTTATCA-TTTAGCACACTCAGTGCTCCATATGGAAATCTATACACTCAG
1 TATGATTTCCTTACCATTTTAGCACACTAAGTGCTCCATATGGAAATCCATACACTCAA
* * *** *
291197 TATGATTTCCTTACCATTTTTAGCACA-TAAAATGC-CCTATATGAAAATCCATATTTTAAA
1 TATGATTTCCTTACCA-TTTTAGCACACT-AAGTGCTCC-ATATGGAAATCCATACACTCAA
* * * *
291257 TATGATTTCCTTATCA-TTTAGCACACTTAGTGCTCCATATGGAAATCTATACACTCAG
1 TATGATTTCCTTACCATTTTAGCACACTAAGTGCTCCATATGGAAATCCATACACTCAA
*
291315 TATGATTTCCTTACCATTTTAGCACACAAAGTGC
1 TATGATTTCCTTACCATTTTAGCACACTAAGTGC
291349 CATTCGGTAA
Statistics
Matches: 210, Mismatches: 45, Indels: 28
0.74 0.16 0.10
Matches are distributed among these distances:
58 91 0.43
59 69 0.33
60 50 0.24
ACGTcount: A:0.31, C:0.23, G:0.10, T:0.36
Consensus pattern (59 bp):
TATGATTTCCTTACCATTTTAGCACACTAAGTGCTCCATATGGAAATCCATACACTCAA
Found at i:291210 original size:117 final size:117
Alignment explanation
Indices: 291024--291349 Score: 483
Period size: 118 Copynumber: 2.8 Consensus size: 117
291014 CCATTAGTAT
* * ** * * * *
291024 GATTTCCTTATCTTTGTAGCACCCTTAGTGCTTTATCTGGAAATCCATACACTCAATAT-AATTC
1 GATTTCCTTATCATT-TAGCACACTTAGTGCTCCATATGGAAATCTATACACTCAGTATGATTTC
* * *
291088 ACTTACCATTTTAGCACATAAAATGCCCTATCTGGAAATCCATATTTTCAATAC
65 -CTTACCATTTTAGCACATAAAATGCCCTATATGAAAATCCATATTTTAAATAC
*
291142 GATTTCCTTATCATTTAGCACACTCAGTGCTCCATATGGAAATCTATACACTCAGTATGATTTCC
1 GATTTCCTTATCATTTAGCACACTTAGTGCTCCATATGGAAATCTATACACTCAGTATGATTTCC
*
291207 TTACCATTTTTAGCACATAAAATGCCCTATATGAAAATCCATATTTTAAATAT
66 TTACCA-TTTTAGCACATAAAATGCCCTATATGAAAATCCATATTTTAAATAC
291260 GATTTCCTTATCATTTAGCACACTTAGTGCTCCATATGGAAATCTATACACTCAGTATGATTTCC
1 GATTTCCTTATCATTTAGCACACTTAGTGCTCCATATGGAAATCTATACACTCAGTATGATTTCC
* *
291325 TTACCATTTTAGCACACAAAGTGCC
66 TTACCATTTTAGCACATAAAATGCC
291350 ATTCGGTAAT
Statistics
Matches: 190, Mismatches: 16, Indels: 5
0.90 0.08 0.02
Matches are distributed among these distances:
117 60 0.32
118 130 0.68
ACGTcount: A:0.31, C:0.23, G:0.10, T:0.36
Consensus pattern (117 bp):
GATTTCCTTATCATTTAGCACACTTAGTGCTCCATATGGAAATCTATACACTCAGTATGATTTCC
TTACCATTTTAGCACATAAAATGCCCTATATGAAAATCCATATTTTAAATAC
Found at i:297929 original size:59 final size:58
Alignment explanation
Indices: 297766--298184 Score: 229
Period size: 59 Copynumber: 7.1 Consensus size: 58
297756 CCTTTTAATA
* * * * * *
297766 TTAGCACTCTCAGTGCTCTATCTGGAAGAT-CATACACTTAGTATG-CTTCCATTTTCATT
1 TTAGCACCCTAAGTGCTCTATCTGGAA-ATCCATACACTCAATATGATTTCC-TTATC-TT
* * * * * * * *
297825 TTTGCACACGAAGTGCCCTAT-TCGAAAATCCATAC-CATTAGTATGATATCCTTATCTT
1 TTAGCACCCTAAGTGCTCTATCT-GGAAATCCATACAC-TCAATATGATTTCCTTATCTT
* * * *
297883 TGTAGCACCCTTAGTGCTTTATCTGGAAATCCATACACTCAATATGATTCCCTTACCATT
1 T-TAGCACCCTAAGTGCTCTATCTGGAAATCCATACACTCAATATGATTTCCTTATC-TT
* * * * *** *
297943 TTAGCA-CATAAAATTCCCTATCTGGAAATCCATATTTTCAATATGATTTCCTTATCAT
1 TTAGCACCCT-AAGTGCTCTATCTGGAAATCCATACACTCAATATGATTTCCTTATCTT
* * * * * * *
298001 TTAGCACACTCAGTGCTCCATATGGAAATCTATACACTCAGTATGATTTCCTTACCATTT
1 TTAGCACCCTAAGTGCTCTATCTGGAAATCCATACACTCAATATGATTTCCTTATC--TT
* * * * * *** * *
298061 TTAGCA-CATAAAATGCCCTATATGAAAATCCATATTTTTAATATGATTTCCTTATCAT
1 TTAGCACCCT-AAGTGCTCTATCTGGAAATCCATACACTCAATATGATTTCCTTATCTT
* * * * * * * *
298119 TTAGCACACTTAGTGCTCCATATGGAAATCTATACACTCAGTATGTTTTCCTTACCATT
1 TTAGCACCCTAAGTGCTCTATCTGGAAATCCATACACTCAATATGATTTCCTTATC-TT
298178 TTAGCAC
1 TTAGCAC
298185 ACAAAGTGTC
Statistics
Matches: 266, Mismatches: 79, Indels: 30
0.71 0.21 0.08
Matches are distributed among these distances:
58 90 0.34
59 127 0.48
60 49 0.18
ACGTcount: A:0.29, C:0.23, G:0.11, T:0.37
Consensus pattern (58 bp):
TTAGCACCCTAAGTGCTCTATCTGGAAATCCATACACTCAATATGATTTCCTTATCTT
Found at i:297950 original size:118 final size:116
Alignment explanation
Indices: 297752--298189 Score: 468
Period size: 118 Copynumber: 3.7 Consensus size: 116
297742 AATTCATGTA
* * * * * * *
297752 ATTTCCTTTTAATATTAGCACTCTCAGTGCTCTATCTGGAAGAT-CATACACTTAGTATGCTTCC
1 ATTTCCTTATCAT-TTAGCACACTCAGTGCTCCATATGGAA-ATCCATACACTCAGTATGATTCC
* ** * * * ** *
297816 ATTTTCATTTTTGCACACGAAGTGCCCTATTCGAAAATCCATACCATTAGTATG
64 CTTACCATTTTAGCACACAAAATGCCCTATTCGAAAATCCATA-TTTTAATATG
* * * * ** * *
297870 ATATCCTTATCTTTGTAGCACCCTTAGTGCTTTATCTGGAAATCCATACACTCAATATGATTCCC
1 ATTTCCTTATCATT-TAGCACACTCAGTGCTCCATATGGAAATCCATACACTCAGTATGATTCCC
* * *
297935 TTACCATTTTAGCACATAAAATTCCCTA-TCTGGAAATCCATATTTTCAATATG
65 TTACCATTTTAGCACACAAAATGCCCTATTC-GAAAATCCATATTTT-AATATG
* *
297988 ATTTCCTTATCATTTAGCACACTCAGTGCTCCATATGGAAATCTATACACTCAGTATGATTTCCT
1 ATTTCCTTATCATTTAGCACACTCAGTGCTCCATATGGAAATCCATACACTCAGTATGATTCCCT
*
298053 TACCATTTTTAGCACATAAAATGCCCTATAT-GAAAATCCATATTTTTAATATG
66 TACCA-TTTTAGCACACAAAATGCCCTAT-TCGAAAATCCATA-TTTTAATATG
* * * *
298106 ATTTCCTTATCATTTAGCACACTTAGTGCTCCATATGGAAATCTATACACTCAGTATGTTTTCCT
1 ATTTCCTTATCATTTAGCACACTCAGTGCTCCATATGGAAATCCATACACTCAGTATGATTCCCT
298171 TACCATTTTAGCACACAAA
66 TACCATTTTAGCACACAAA
298190 GTGTCATTCG
Statistics
Matches: 275, Mismatches: 37, Indels: 17
0.84 0.11 0.05
Matches are distributed among these distances:
117 68 0.25
118 202 0.73
119 4 0.01
120 1 0.00
ACGTcount: A:0.30, C:0.23, G:0.10, T:0.37
Consensus pattern (116 bp):
ATTTCCTTATCATTTAGCACACTCAGTGCTCCATATGGAAATCCATACACTCAGTATGATTCCCT
TACCATTTTAGCACACAAAATGCCCTATTCGAAAATCCATATTTTAATATG
Found at i:298090 original size:60 final size:59
Alignment explanation
Indices: 297906--298186 Score: 277
Period size: 58 Copynumber: 4.8 Consensus size: 59
297896 GTGCTTTATC
* * *
297906 TGGAAATCCATACACTCAATATGATTCCCTTACCATTTTAGCACA-TAAAATTC-CCTATC
1 TGGAAATCCATACACTCAATATGATTTCCTTACCATTTTAGCACACT-AAATGCTCC-ATA
*** * * *
297965 TGGAAATCCATATTTTCAATATGATTTCCTTATCA-TTTAGCACACTCAGTGCTCCATA
1 TGGAAATCCATACACTCAATATGATTTCCTTACCATTTTAGCACACTAAATGCTCCATA
* *
298023 TGGAAATCTATACACTCAGTATGATTTCCTTACCATTTTTAGCACA-TAAAATGC-CCTATA
1 TGGAAATCCATACACTCAATATGATTTCCTTACCA-TTTTAGCACACT-AAATGCTCC-ATA
* *** * * * *
298083 TGAAAATCCATATTTTTAATATGATTTCCTTATCA-TTTAGCACACTTAGTGCTCCATA
1 TGGAAATCCATACACTCAATATGATTTCCTTACCATTTTAGCACACTAAATGCTCCATA
* * *
298141 TGGAAATCTATACACTCAGTATGTTTTCCTTACCATTTTAGCACAC
1 TGGAAATCCATACACTCAATATGATTTCCTTACCATTTTAGCACAC
298187 AAAGTGTCAT
Statistics
Matches: 177, Mismatches: 36, Indels: 18
0.77 0.16 0.08
Matches are distributed among these distances:
58 85 0.48
59 49 0.28
60 43 0.24
ACGTcount: A:0.31, C:0.23, G:0.09, T:0.37
Consensus pattern (59 bp):
TGGAAATCCATACACTCAATATGATTTCCTTACCATTTTAGCACACTAAATGCTCCATA
Found at i:298174 original size:235 final size:236
Alignment explanation
Indices: 297752--298185 Score: 563
Period size: 235 Copynumber: 1.8 Consensus size: 236
297742 AATTCATGTA
* * * * *
297752 ATTTCCTTTTAATATTAGCACTCTCAGTGCTCTATCTGGAAGATCATACACTTAGTATGCTTCCA
1 ATTTCCTTATAATATTAGCACACTCAGTGCTCCATATGGAAGATCATACACTCAGTATGCTTCCA
** * * * *
297817 TTTTCATTTTTGCACACGAAGTGCCCTATTCGAAAATCCATACCATTAGTATGATATCCTTATCT
66 TTACCATTTTTGCACACAAAATGCCCTATTCGAAAATCCATACCATTAATATGATATCCTTATCA
* ** *
297882 TTGTAGCACCCTTAGTGCTTTATCTGGAAATCCATACACTCAATATGATTCCCTTACCATTTTAG
131 TTGTAGCACACTTAGTGCTCCATATGGAAATCCATACACTCAATATGATTCCCTTACCATTTTAG
297947 CACATAAAATTCCCTATCTGGAAATCCATATTTTCAATATG
196 CACATAAAATTCCCTATCTGGAAATCCATATTTTCAATATG
* *
297988 ATTTCCTTATCAT-TTAGCACACTCAGTGCTCCATATGGAA-ATCTATACACTCAGTATGATTTC
1 ATTTCCTTATAATATTAGCACACTCAGTGCTCCATATGGAAGATC-ATACACTCAGTATG-CTTC
* *** *
298051 C-TTACCATTTTTAGCACATAAAATGCCCTATAT-GAAAATCCATATTTTTAATATGATTTCCTT
64 CATTACCATTTTT-GCACACAAAATGCCCTAT-TCGAAAATCCATACCATTAATATGATATCCTT
* * * *
298114 ATCATT-TAGCACACTTAGTGCTCCATATGGAAATCTATACACTCAGTATGTTTTCCTTACCATT
127 ATCATTGTAGCACACTTAGTGCTCCATATGGAAATCCATACACTCAATATGATTCCCTTACCATT
298178 TTAGCACA
192 TTAGCACA
298186 CAAAGTGTCA
Statistics
Matches: 168, Mismatches: 26, Indels: 9
0.83 0.13 0.04
Matches are distributed among these distances:
234 3 0.02
235 104 0.62
236 60 0.36
237 1 0.01
ACGTcount: A:0.29, C:0.23, G:0.10, T:0.38
Consensus pattern (236 bp):
ATTTCCTTATAATATTAGCACACTCAGTGCTCCATATGGAAGATCATACACTCAGTATGCTTCCA
TTACCATTTTTGCACACAAAATGCCCTATTCGAAAATCCATACCATTAATATGATATCCTTATCA
TTGTAGCACACTTAGTGCTCCATATGGAAATCCATACACTCAATATGATTCCCTTACCATTTTAG
CACATAAAATTCCCTATCTGGAAATCCATATTTTCAATATG
Found at i:300978 original size:32 final size:32
Alignment explanation
Indices: 300935--301018 Score: 105
Period size: 32 Copynumber: 2.6 Consensus size: 32
300925 CTAGTTAAGG
* * * **
300935 TGCATTAAGATAATGCACAATATCGTTATGTT
1 TGCATTCAGATAATGCACAATATAGTCAAATT
*
300967 TGCATTCAGATAATGCACGATATAGTCAAATT
1 TGCATTCAGATAATGCACAATATAGTCAAATT
*
300999 TTCATTCAGATAATGCACAA
1 TGCATTCAGATAATGCACAA
301019 GAATATTAGT
Statistics
Matches: 44, Mismatches: 8, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
32 44 1.00
ACGTcount: A:0.37, C:0.15, G:0.14, T:0.33
Consensus pattern (32 bp):
TGCATTCAGATAATGCACAATATAGTCAAATT
Found at i:301792 original size:21 final size:19
Alignment explanation
Indices: 301767--301806 Score: 53
Period size: 21 Copynumber: 2.0 Consensus size: 19
301757 ATATGTTATG
*
301767 GTAAAGTTATATTTTAGTAAT
1 GTAAAGATA-ATTTT-GTAAT
301788 GTAAAGATAATTTTGTAAT
1 GTAAAGATAATTTTGTAAT
301807 TAGGTAGTTT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
19 5 0.28
20 5 0.28
21 8 0.44
ACGTcount: A:0.40, C:0.00, G:0.15, T:0.45
Consensus pattern (19 bp):
GTAAAGATAATTTTGTAAT
Found at i:302773 original size:10 final size:10
Alignment explanation
Indices: 302758--302785 Score: 56
Period size: 10 Copynumber: 2.8 Consensus size: 10
302748 AATGTGATAC
302758 ATCAGATCGA
1 ATCAGATCGA
302768 ATCAGATCGA
1 ATCAGATCGA
302778 ATCAGATC
1 ATCAGATC
302786 ATCTGTATAA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 18 1.00
ACGTcount: A:0.39, C:0.21, G:0.18, T:0.21
Consensus pattern (10 bp):
ATCAGATCGA
Found at i:303497 original size:179 final size:180
Alignment explanation
Indices: 303189--303523 Score: 514
Period size: 179 Copynumber: 1.9 Consensus size: 180
303179 ATAAAATAAC
* *
303189 AATTTAACTGTTCATTTTATAAAAATAAAATGCAAGTTTCATAAAAGAAAAAAGAGGGAACAAAA
1 AATTTAACTGTTCATCTTATAAAAATAAAATGCAAGTTTCATAAAAGAAAAAACAGGGAACAAAA
* *
303254 TGATTAAACAAATAAGGGTAATTATAGATTTAATATCTAAACTATCAATTTTGATACATTTTAAT
66 AGATTAAACAAATAAGGGTAATTATAGATTTAATATCTAAACTATCAATTTTAATACATTTTAAT
*
303319 A-CTTAAACTTTGAATTTTTTTAAAATCATATACTTACAAAAAATAGTAAT
131 ATC-TAAACTTTGAATATTTTTAAAATCATATACTTACAAAAAATAGTAAT
* * *
303369 AATTTAAGTGTTCATCTTATAAAAATAAAATGTAAGTTTCAT-AAAGAAAGAACAGGGAACAAAA
1 AATTTAACTGTTCATCTTATAAAAATAAAATGCAAGTTTCATAAAAGAAAAAACAGGGAACAAAA
* * * *
303433 AGATT-AATAAATAAGGGTAAATTATAGATTTAGTATCTAAACTATCAATTTTAATTCGTTTTAA
66 AGATTAAACAAATAAGGGT-AATTATAGATTTAATATCTAAACTATCAATTTTAATACATTTTAA
*
303497 TATCTAAACTTTTAATATTTTTAAAAT
130 TATCTAAACTTTGAATATTTTTAAAAT
303524 TATGCCTAAA
Statistics
Matches: 140, Mismatches: 13, Indels: 5
0.89 0.08 0.03
Matches are distributed among these distances:
178 12 0.09
179 88 0.63
180 40 0.29
ACGTcount: A:0.47, C:0.08, G:0.10, T:0.36
Consensus pattern (180 bp):
AATTTAACTGTTCATCTTATAAAAATAAAATGCAAGTTTCATAAAAGAAAAAACAGGGAACAAAA
AGATTAAACAAATAAGGGTAATTATAGATTTAATATCTAAACTATCAATTTTAATACATTTTAAT
ATCTAAACTTTGAATATTTTTAAAATCATATACTTACAAAAAATAGTAAT
Found at i:303721 original size:35 final size:36
Alignment explanation
Indices: 303670--303738 Score: 88
Period size: 36 Copynumber: 1.9 Consensus size: 36
303660 CGGTATAGTA
*
303670 TTAAAATAAAATAAAAA-CTAAATATTAAATATAATT
1 TTAAAATAAAATAAAAATCTAAATAGTAAA-ATAATT
* *
303706 TTAAAA-AAACTAAAAATTTAAATAGTAAAATAA
1 TTAAAATAAAATAAAAATCTAAATAGTAAAATAA
303739 ATCAAAAATA
Statistics
Matches: 29, Mismatches: 3, Indels: 3
0.83 0.09 0.09
Matches are distributed among these distances:
35 13 0.45
36 16 0.55
ACGTcount: A:0.65, C:0.03, G:0.01, T:0.30
Consensus pattern (36 bp):
TTAAAATAAAATAAAAATCTAAATAGTAAAATAATT
Found at i:303739 original size:29 final size:28
Alignment explanation
Indices: 303674--303739 Score: 64
Period size: 28 Copynumber: 2.3 Consensus size: 28
303664 ATAGTATTAA
*
303674 AATAA-AATAAAAACTAAATATTAAATAT
1 AATAATAA-AAAAACTAAAAATTAAATAT
**
303702 AATTTTAAAAAAACTAAAAATTTAAATAGT
1 AATAATAAAAAAACTAAAAA-TTAAATA-T
303732 AA-AATAAA
1 AATAATAAA
303740 TCAAAAATAA
Statistics
Matches: 30, Mismatches: 5, Indels: 5
0.75 0.12 0.12
Matches are distributed among these distances:
28 14 0.47
29 13 0.43
30 3 0.10
ACGTcount: A:0.67, C:0.03, G:0.02, T:0.29
Consensus pattern (28 bp):
AATAATAAAAAAACTAAAAATTAAATAT
Found at i:304368 original size:2 final size:2
Alignment explanation
Indices: 304361--304387 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
304351 TGCGAGTTAG
304361 TC TC TC TC TC TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC TC T
304388 GTATATATAT
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:0.00, C:0.48, G:0.00, T:0.52
Consensus pattern (2 bp):
TC
Found at i:306491 original size:42 final size:42
Alignment explanation
Indices: 306365--306469 Score: 158
Period size: 42 Copynumber: 2.5 Consensus size: 42
306355 TGCTTTGTCC
* *
306365 TGCCCACTCTTC-TGTCAAGTTTCCAAGTGAGAAGTCTAGAAA
1 TGCCCACTCTTCAT-CCAAGTTTCCAAGTGAGAACTCTAGAAA
**
306407 AACCCACTCTTCATCCAAGTTTCCAAGTGAGAACTCTAGAAA
1 TGCCCACTCTTCATCCAAGTTTCCAAGTGAGAACTCTAGAAA
306449 TGCCCACTCTTCATCCAAGTT
1 TGCCCACTCTTCATCCAAGTT
306470 CTTGAATGAT
Statistics
Matches: 56, Mismatches: 6, Indels: 2
0.88 0.09 0.03
Matches are distributed among these distances:
42 55 0.98
43 1 0.02
ACGTcount: A:0.30, C:0.29, G:0.14, T:0.28
Consensus pattern (42 bp):
TGCCCACTCTTCATCCAAGTTTCCAAGTGAGAACTCTAGAAA
Found at i:307112 original size:20 final size:18
Alignment explanation
Indices: 307087--307127 Score: 55
Period size: 18 Copynumber: 2.2 Consensus size: 18
307077 ATATAGATAA
*
307087 ATAATTAATATATTATTTTT
1 ATAATT-ATA-ATAATTTTT
307107 ATAATTATAATAATTTTT
1 ATAATTATAATAATTTTT
307125 ATA
1 ATA
307128 TAATTTGAAA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
18 11 0.55
19 3 0.15
20 6 0.30
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (18 bp):
ATAATTATAATAATTTTT
Found at i:307129 original size:20 final size:22
Alignment explanation
Indices: 307092--307132 Score: 59
Period size: 20 Copynumber: 2.0 Consensus size: 22
307082 GATAAATAAT
*
307092 TAATATATTATTTTTATAATTA
1 TAATATATTATTTATATAATTA
307114 TAATA-ATT-TTTATATAATT
1 TAATATATTATTTATATAATT
307133 TGAAATATAA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 10 0.56
21 3 0.17
22 5 0.28
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (22 bp):
TAATATATTATTTATATAATTA
Found at i:307334 original size:20 final size:20
Alignment explanation
Indices: 307295--307334 Score: 62
Period size: 20 Copynumber: 2.0 Consensus size: 20
307285 TGTGAAATGC
*
307295 TTTGGAAGGTAAGGTATTGT
1 TTTGGAAGGTAAGATATTGT
*
307315 TTTGGAAGGTAAGATTTTGT
1 TTTGGAAGGTAAGATATTGT
307335 AAATGGTAGA
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:0.25, C:0.00, G:0.33, T:0.42
Consensus pattern (20 bp):
TTTGGAAGGTAAGATATTGT
Found at i:309485 original size:15 final size:15
Alignment explanation
Indices: 309467--309522 Score: 58
Period size: 15 Copynumber: 3.6 Consensus size: 15
309457 TAACCGGTTT
309467 CGGTTTTAAAAAAAC
1 CGGTTTTAAAAAAAC
*
309482 CGGTTTTTTTAAAAAAC
1 CGG--TTTTAAAAAAAC
* *
309499 TGGTTATAAAAAAAC
1 CGGTTTTAAAAAAAC
*
309514 CGATTTTAA
1 CGGTTTTAA
309523 TATTCCAGAT
Statistics
Matches: 32, Mismatches: 7, Indels: 4
0.74 0.16 0.09
Matches are distributed among these distances:
15 19 0.59
17 13 0.41
ACGTcount: A:0.43, C:0.11, G:0.12, T:0.34
Consensus pattern (15 bp):
CGGTTTTAAAAAAAC
Found at i:309495 original size:17 final size:17
Alignment explanation
Indices: 309470--309520 Score: 52
Period size: 17 Copynumber: 3.1 Consensus size: 17
309460 CCGGTTTCGG
309470 TTTTAAAAAAACCGGTT
1 TTTTAAAAAAACCGGTT
* *
309487 TTTTTAAAAAACTGG--
1 TTTTAAAAAAACCGGTT
* *
309502 TTATAAAAAAACCGATT
1 TTTTAAAAAAACCGGTT
309519 TT
1 TT
309521 AATATTCCAG
Statistics
Matches: 26, Mismatches: 6, Indels: 4
0.72 0.17 0.11
Matches are distributed among these distances:
15 11 0.42
17 15 0.58
ACGTcount: A:0.43, C:0.10, G:0.10, T:0.37
Consensus pattern (17 bp):
TTTTAAAAAAACCGGTT
Found at i:309939 original size:13 final size:13
Alignment explanation
Indices: 309918--309972 Score: 58
Period size: 13 Copynumber: 4.2 Consensus size: 13
309908 AAGTTCGATA
*
309918 AATTTAAATACTT
1 AATTGAAATACTT
309931 AATTGAAATACTT
1 AATTGAAATACTT
* *
309944 AATT-AACTCAACAT
1 AATTGAAAT--ACTT
309958 AATTGAAATACTT
1 AATTGAAATACTT
309971 AA
1 AA
309973 ATACTTCCAA
Statistics
Matches: 34, Mismatches: 5, Indels: 6
0.76 0.11 0.13
Matches are distributed among these distances:
12 3 0.09
13 21 0.62
14 7 0.21
15 3 0.09
ACGTcount: A:0.49, C:0.11, G:0.04, T:0.36
Consensus pattern (13 bp):
AATTGAAATACTT
Found at i:310054 original size:32 final size:33
Alignment explanation
Indices: 309958--310056 Score: 164
Period size: 33 Copynumber: 3.0 Consensus size: 33
309948 AACTCAACAT
* * *
309958 AATTGAAATACTTAAATACTTCCAAGTTTGATA
1 AATTCAAATACTTAAAAACTTCCAAGTTCGATA
309991 AATTCAAATACTTAAAAACTTCCAAGTTCGATA
1 AATTCAAATACTTAAAAACTTCCAAGTTCGATA
310024 AATTCAAATACTTAAAAACTT-CAAGTTCGATA
1 AATTCAAATACTTAAAAACTTCCAAGTTCGATA
310056 A
1 A
310057 TTGAAACAAA
Statistics
Matches: 63, Mismatches: 3, Indels: 1
0.94 0.04 0.01
Matches are distributed among these distances:
32 12 0.19
33 51 0.81
ACGTcount: A:0.45, C:0.15, G:0.07, T:0.32
Consensus pattern (33 bp):
AATTCAAATACTTAAAAACTTCCAAGTTCGATA
Found at i:310075 original size:21 final size:21
Alignment explanation
Indices: 310051--310090 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
310041 ACTTCAAGTT
310051 CGATAATTGAAACAAAGTTTA
1 CGATAATTGAAACAAAGTTTA
*
310072 CGATAATTGAAATAAAGTT
1 CGATAATTGAAACAAAGTT
310091 ATAAAATAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.47, C:0.07, G:0.15, T:0.30
Consensus pattern (21 bp):
CGATAATTGAAACAAAGTTTA
Found at i:312406 original size:11 final size:12
Alignment explanation
Indices: 312385--312415 Score: 53
Period size: 12 Copynumber: 2.6 Consensus size: 12
312375 TCCGGATAAA
312385 AACCGGTTTTTT
1 AACCGGTTTTTT
312397 AACCGGTTTTTT
1 AACCGGTTTTTT
*
312409 ATCCGGT
1 AACCGGT
312416 AAAAAAACCG
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
12 18 1.00
ACGTcount: A:0.16, C:0.19, G:0.19, T:0.45
Consensus pattern (12 bp):
AACCGGTTTTTT
Found at i:315831 original size:2 final size:2
Alignment explanation
Indices: 315824--315855 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
315814 AGAAGAAGTT
315824 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
315856 AAAGGGCTTT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
GA
Found at i:324240 original size:35 final size:34
Alignment explanation
Indices: 324201--324345 Score: 139
Period size: 35 Copynumber: 4.1 Consensus size: 34
324191 TCCATTCTAG
*
324201 TTGAATTGAAAGTACGATAACTCATTCCGTTCGAC
1 TTGAATTGAAAGTACGAT-ACTCCTTCCGTTCGAC
* *
324236 TTGAATTTG-AAGTGCGATGCTTCCTTCCGTTCGAC
1 TTGAA-TTGAAAGTACGATAC-TCCTTCCGTTCGAC
* *
324271 TTGAATCGAAAGTACGATGCCTCCTTCCGTTCGAC
1 TTGAATTGAAAGTACGAT-ACTCCTTCCGTTCGAC
* * * * * *
324306 TTGAATCGGAAGTGCGATGCTTCTTTTCGTTCGAC
1 TTGAATTGAAAGTACGATAC-TCCTTCCGTTCGAC
324341 TTGAA
1 TTGAA
324346 CCGATGCAAA
Statistics
Matches: 94, Mismatches: 11, Indels: 10
0.82 0.10 0.09
Matches are distributed among these distances:
34 4 0.04
35 86 0.91
36 4 0.04
ACGTcount: A:0.23, C:0.22, G:0.21, T:0.34
Consensus pattern (34 bp):
TTGAATTGAAAGTACGATACTCCTTCCGTTCGAC
Found at i:324318 original size:70 final size:70
Alignment explanation
Indices: 324201--324345 Score: 218
Period size: 70 Copynumber: 2.1 Consensus size: 70
324191 TCCATTCTAG
* **
324201 TTGAATTGAAAGTACGATAACTCATTCCGTTCGACTTGAATTTGAAGTGCGATGCTTCCTTCCGT
1 TTGAATCGAAAGTACGATAACTCATTCCGTTCGACTTGAATCGGAAGTGCGATGCTTCCTTCCGT
324266 TCGAC
66 TCGAC
** * * *
324271 TTGAATCGAAAGTACGATGCCTCCTTCCGTTCGACTTGAATCGGAAGTGCGATGCTTCTTTTCGT
1 TTGAATCGAAAGTACGATAACTCATTCCGTTCGACTTGAATCGGAAGTGCGATGCTTCCTTCCGT
324336 TCGAC
66 TCGAC
324341 TTGAA
1 TTGAA
324346 CCGATGCAAA
Statistics
Matches: 67, Mismatches: 8, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
70 67 1.00
ACGTcount: A:0.23, C:0.22, G:0.21, T:0.34
Consensus pattern (70 bp):
TTGAATCGAAAGTACGATAACTCATTCCGTTCGACTTGAATCGGAAGTGCGATGCTTCCTTCCGT
TCGAC
Found at i:328941 original size:42 final size:42
Alignment explanation
Indices: 328864--329053 Score: 254
Period size: 42 Copynumber: 4.5 Consensus size: 42
328854 TGTTAACCTG
* * * * *
328864 TGCACAAAGCAGAGGAGCCTAGGAAAACTGTAAGGCTTACCCT
1 TGCACACAGCAAAGGAACCT-GGGAAACTATAAGGCTTACCCT
* * * *
328907 TGCACACAGTAAAAGAACATGGGAAACTATAAGGCTTACCAT
1 TGCACACAGCAAAGGAACCTGGGAAACTATAAGGCTTACCCT
* *
328949 TGCACATAGCAAAGGAACCTTGGAAACTATAAGGCTTACCCT
1 TGCACACAGCAAAGGAACCTGGGAAACTATAAGGCTTACCCT
* *
328991 TGCACACAACAAAGGAACCTGGGAAACTGTAAGGCTTACCCT
1 TGCACACAGCAAAGGAACCTGGGAAACTATAAGGCTTACCCT
329033 TGCACACAGCAAAGGAACCTG
1 TGCACACAGCAAAGGAACCTG
329054 AAATACTTCC
Statistics
Matches: 127, Mismatches: 20, Indels: 1
0.86 0.14 0.01
Matches are distributed among these distances:
42 113 0.89
43 14 0.11
ACGTcount: A:0.37, C:0.24, G:0.22, T:0.17
Consensus pattern (42 bp):
TGCACACAGCAAAGGAACCTGGGAAACTATAAGGCTTACCCT
Found at i:331368 original size:13 final size:13
Alignment explanation
Indices: 331350--331380 Score: 62
Period size: 13 Copynumber: 2.4 Consensus size: 13
331340 TAGCTAAGAT
331350 TCTGACTGGTTCC
1 TCTGACTGGTTCC
331363 TCTGACTGGTTCC
1 TCTGACTGGTTCC
331376 TCTGA
1 TCTGA
331381 ATAGGTCATA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 18 1.00
ACGTcount: A:0.10, C:0.29, G:0.23, T:0.39
Consensus pattern (13 bp):
TCTGACTGGTTCC
Found at i:338832 original size:184 final size:183
Alignment explanation
Indices: 338538--339011 Score: 454
Period size: 184 Copynumber: 2.6 Consensus size: 183
338528 TAAAAATCAT
* * * *
338538 AATTTAGTCA-TTTTTATGCTTTATTAATATAATATTAGATTAATTATTCAAAATAGT-GTAATA
1 AATTTAATCATTTTTTATGATTTATTAATATAATATTAAATTAATTTTTCAAAATAGTAG-AATA
* * *** * * ** *
338601 TATCTCCGTTCTATAGGTTTTATTTTTCAGTTTTGCTCAAGGTTTATAGTTAAGAATTCCTAATT
65 TATTTTCGTTCTATAGGCCCTATTTTTCAGTTTTGATCAAAGTTTATAACTAAGAACTCCTAATT
* ** *
338666 TTTTTA-TTTTATAAAAAAATCCATAGTTTTTTGCTTTTATAACTAAGATCACAC
130 TTTTTAGTTTTATAAAAAAATCCATACTTTTTACCTTTTATAAC-AAGAGCACAC
* *
338720 AATTTAATCATTTTTCTATGATTTATTAATCTAAAATTAAATTAATTTTTCAAAATAGTAGAATA
1 AATTTAATCATTTTT-TATGATTTATTAATATAATATTAAATTAATTTTTCAAAATAGTAGAATA
* * * **
338785 TATTTTTGTTTTATAGGCCCTA-TTTTGAGTTTTCGATCAAAGTTTATAACTAAGGGCTCCTAAT
65 TATTTTCGTTCTATAGGCCCTATTTTTCAGTTTT-GATCAAAGTTTATAACTAAGAACTCCTAAT
** * * * * * *
338849 TTTTTTAGTTTTATAAAATTATCCCTACTTTTTACCTTTTATAGCGAGGGCTCAT
129 TTTTTTAGTTTTATAAAAAAATCCATACTTTTTACCTTTTATAACAAGAGCACAC
* * * *
338904 AGTTCAATTATTTTTTTATGATTTATTAATATAATATTAAATTAATTATTT-AAAATAATAGAAT
1 AATTTAATCA-TTTTTTATGATTTATTAATATAATATTAAATTAATT-TTTCAAAATAGTAGAAT
* * * * * * *
338968 CTATTTTCATTCTATATGACCTATATTTAAGTTTTAGCTCAAAG
64 ATATTTTCGTTCTATAGGCCCTATTTTTCAGTTTT-GATCAAAG
339012 CTCTGAAAAT
Statistics
Matches: 235, Mismatches: 49, Indels: 13
0.79 0.16 0.04
Matches are distributed among these distances:
182 9 0.04
183 14 0.06
184 157 0.67
185 55 0.23
ACGTcount: A:0.33, C:0.10, G:0.09, T:0.47
Consensus pattern (183 bp):
AATTTAATCATTTTTTATGATTTATTAATATAATATTAAATTAATTTTTCAAAATAGTAGAATAT
ATTTTCGTTCTATAGGCCCTATTTTTCAGTTTTGATCAAAGTTTATAACTAAGAACTCCTAATTT
TTTTAGTTTTATAAAAAAATCCATACTTTTTACCTTTTATAACAAGAGCACAC
Found at i:340929 original size:27 final size:29
Alignment explanation
Indices: 340884--340939 Score: 89
Period size: 28 Copynumber: 2.0 Consensus size: 29
340874 AAATATCTAA
*
340884 ATTATTTTACGAATATTTTTA-GATATAT
1 ATTATTTTACGAATATTTTCAGGATATAT
340912 ATTATTTTA-GAATATTTTCAGGATATAT
1 ATTATTTTACGAATATTTTCAGGATATAT
340940 CTCGTAAATG
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
27 10 0.38
28 16 0.62
ACGTcount: A:0.36, C:0.04, G:0.09, T:0.52
Consensus pattern (29 bp):
ATTATTTTACGAATATTTTCAGGATATAT
Found at i:341865 original size:2 final size:2
Alignment explanation
Indices: 341860--341895 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
341850 CTTTGACTTA
341860 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
341896 TGATATTATG
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:341943 original size:21 final size:21
Alignment explanation
Indices: 341888--341943 Score: 67
Period size: 21 Copynumber: 2.6 Consensus size: 21
341878 ATATATATAT
*
341888 ATATATATTGATATTATGTTTG
1 ATATATATTAAT-TTATGTTTG
* *
341910 ATATTTATAAATTTATGTTTG
1 ATATATATTAATTTATGTTTG
*
341931 GTATATATTAATT
1 ATATATATTAATT
341944 AATTTAAATA
Statistics
Matches: 28, Mismatches: 6, Indels: 1
0.80 0.17 0.03
Matches are distributed among these distances:
21 19 0.68
22 9 0.32
ACGTcount: A:0.34, C:0.00, G:0.11, T:0.55
Consensus pattern (21 bp):
ATATATATTAATTTATGTTTG
Found at i:346544 original size:158 final size:158
Alignment explanation
Indices: 346256--346572 Score: 634
Period size: 158 Copynumber: 2.0 Consensus size: 158
346246 TACAATTGAA
346256 GGCAGTTCGTAATGGAGGTTAGTTTCATCTGCTTATGTGTTTCGTCTTGTCTTTTTCTTGTTCAA
1 GGCAGTTCGTAATGGAGGTTAGTTTCATCTGCTTATGTGTTTCGTCTTGTCTTTTTCTTGTTCAA
346321 ACATCTAGATCCACTCATTAGTTACAAAATTGTAACCTCCAAAATCACTCACCTTATCATTTGCC
66 ACATCTAGATCCACTCATTAGTTACAAAATTGTAACCTCCAAAATCACTCACCTTATCATTTGCC
346386 AGTTAGTACGCTTACTCAATTCTTGGTG
131 AGTTAGTACGCTTACTCAATTCTTGGTG
346414 GGCAGTTCGTAATGGAGGTTAGTTTCATCTGCTTATGTGTTTCGTCTTGTCTTTTTCTTGTTCAA
1 GGCAGTTCGTAATGGAGGTTAGTTTCATCTGCTTATGTGTTTCGTCTTGTCTTTTTCTTGTTCAA
346479 ACATCTAGATCCACTCATTAGTTACAAAATTGTAACCTCCAAAATCACTCACCTTATCATTTGCC
66 ACATCTAGATCCACTCATTAGTTACAAAATTGTAACCTCCAAAATCACTCACCTTATCATTTGCC
346544 AGTTAGTACGCTTACTCAATTCTTGGTG
131 AGTTAGTACGCTTACTCAATTCTTGGTG
346572 G
1 G
346573 TAAGTTTATT
Statistics
Matches: 159, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
158 159 1.00
ACGTcount: A:0.23, C:0.21, G:0.16, T:0.39
Consensus pattern (158 bp):
GGCAGTTCGTAATGGAGGTTAGTTTCATCTGCTTATGTGTTTCGTCTTGTCTTTTTCTTGTTCAA
ACATCTAGATCCACTCATTAGTTACAAAATTGTAACCTCCAAAATCACTCACCTTATCATTTGCC
AGTTAGTACGCTTACTCAATTCTTGGTG
Found at i:351427 original size:12 final size:12
Alignment explanation
Indices: 351410--351434 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
351400 TAGGTGACCA
351410 TTTTATAATTTT
1 TTTTATAATTTT
351422 TTTTATAATTTT
1 TTTTATAATTTT
351434 T
1 T
351435 ATAGTCGATA
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:0.24, C:0.00, G:0.00, T:0.76
Consensus pattern (12 bp):
TTTTATAATTTT
Found at i:352364 original size:16 final size:16
Alignment explanation
Indices: 352343--352375 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 16
352333 GGTCAAAGAC
*
352343 TCGGTCTAGGCATAGT
1 TCGGTCTAGGCACAGT
352359 TCGGTCTAGGCACAGT
1 TCGGTCTAGGCACAGT
352375 T
1 T
352376 TGGTTCAGGC
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.18, C:0.21, G:0.30, T:0.30
Consensus pattern (16 bp):
TCGGTCTAGGCACAGT
Found at i:356527 original size:24 final size:24
Alignment explanation
Indices: 356500--356548 Score: 98
Period size: 24 Copynumber: 2.0 Consensus size: 24
356490 TGCATGACAT
356500 TGTACATAGATGTTTTATACATCA
1 TGTACATAGATGTTTTATACATCA
356524 TGTACATAGATGTTTTATACATCA
1 TGTACATAGATGTTTTATACATCA
356548 T
1 T
356549 CAGGAAGACT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.33, C:0.12, G:0.12, T:0.43
Consensus pattern (24 bp):
TGTACATAGATGTTTTATACATCA
Found at i:362767 original size:21 final size:21
Alignment explanation
Indices: 362742--362801 Score: 93
Period size: 21 Copynumber: 2.9 Consensus size: 21
362732 CGAGGGTTAT
*
362742 AGTGGTCCTTCGAGACAATAC
1 AGTGGTCCTTCGGGACAATAC
*
362763 AGTGGTCTTTCGGGACAATAC
1 AGTGGTCCTTCGGGACAATAC
*
362784 AGTAGTCCTTCGGGACAA
1 AGTGGTCCTTCGGGACAA
362802 ATTTCATATG
Statistics
Matches: 35, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 35 1.00
ACGTcount: A:0.27, C:0.22, G:0.27, T:0.25
Consensus pattern (21 bp):
AGTGGTCCTTCGGGACAATAC
Found at i:364389 original size:13 final size:12
Alignment explanation
Indices: 364356--364422 Score: 64
Period size: 14 Copynumber: 5.1 Consensus size: 12
364346 TTTAAGCATC
364356 TCTCATTTTTTTCT
1 TCTC-TTTTTTT-T
364370 TCTTCTTTTCTTTT
1 TC-TCTTTT-TTTT
364384 TCTCTTTTTTTT
1 TCTCTTTTTTTT
364396 T-TCTTTTTTTT
1 TCTCTTTTTTTT
364407 CTCTCTCTCTTTTTT
1 -TCTCT-T-TTTTTT
364422 T
1 T
364423 TAGCTCTTAT
Statistics
Matches: 47, Mismatches: 0, Indels: 12
0.80 0.00 0.20
Matches are distributed among these distances:
11 10 0.21
12 6 0.13
13 9 0.19
14 11 0.23
15 11 0.23
ACGTcount: A:0.01, C:0.21, G:0.00, T:0.78
Consensus pattern (12 bp):
TCTCTTTTTTTT
Found at i:364406 original size:28 final size:30
Alignment explanation
Indices: 364361--364423 Score: 94
Period size: 28 Copynumber: 2.2 Consensus size: 30
364351 GCATCTCTCA
* *
364361 TTTTTTTCTTCTTCTTTTCTTTTTCTCTTT
1 TTTTTTTCTTCTTCTTTTCTCTCTCTCTTT
364391 TTTTTTTCTT-TT-TTTTCTCTCTCTCTTT
1 TTTTTTTCTTCTTCTTTTCTCTCTCTCTTT
364419 TTTTT
1 TTTTT
364424 AGCTCTTATA
Statistics
Matches: 31, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
28 19 0.61
29 2 0.06
30 10 0.32
ACGTcount: A:0.00, C:0.19, G:0.00, T:0.81
Consensus pattern (30 bp):
TTTTTTTCTTCTTCTTTTCTCTCTCTCTTT
Found at i:364905 original size:14 final size:14
Alignment explanation
Indices: 364886--364915 Score: 60
Period size: 14 Copynumber: 2.1 Consensus size: 14
364876 TTAACTGTCG
364886 ATAATCTATGCATA
1 ATAATCTATGCATA
364900 ATAATCTATGCATA
1 ATAATCTATGCATA
364914 AT
1 AT
364916 CGCATAGATC
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:0.43, C:0.13, G:0.07, T:0.37
Consensus pattern (14 bp):
ATAATCTATGCATA
Found at i:367138 original size:13 final size:13
Alignment explanation
Indices: 367120--367145 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
367110 CATAATCCCA
367120 AGATAATAATATC
1 AGATAATAATATC
367133 AGATAATAATATC
1 AGATAATAATATC
367146 TTTATAATCA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.54, C:0.08, G:0.08, T:0.31
Consensus pattern (13 bp):
AGATAATAATATC
Found at i:367843 original size:24 final size:24
Alignment explanation
Indices: 367811--367859 Score: 98
Period size: 24 Copynumber: 2.0 Consensus size: 24
367801 AGTCTTCCTG
367811 ATGATGTATAAAACATCTATGTAC
1 ATGATGTATAAAACATCTATGTAC
367835 ATGATGTATAAAACATCTATGTAC
1 ATGATGTATAAAACATCTATGTAC
367859 A
1 A
367860 ATGTCATGCA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.43, C:0.12, G:0.12, T:0.33
Consensus pattern (24 bp):
ATGATGTATAAAACATCTATGTAC
Found at i:371696 original size:78 final size:78
Alignment explanation
Indices: 371567--371719 Score: 261
Period size: 78 Copynumber: 2.0 Consensus size: 78
371557 TAAATCCCAT
* * *
371567 CTTAATACTTAAACTCCAAAATCAACACACTTTCCAGAATTTCCATAATTATTCTAACTCACCCA
1 CTTAATACTTAAACTCCAAAATCAACAAACTTTCCAAAATTTCCAGAATTATTCTAACTCACCCA
*
371632 AATGATACTTCAA
66 AATAATACTTCAA
*
371645 CTTAATACTTAAACTCCAAAATCAACAAACTTTCCAAAATTTTCAGAATTATTCTAACTCACCCA
1 CTTAATACTTAAACTCCAAAATCAACAAACTTTCCAAAATTTCCAGAATTATTCTAACTCACCCA
371710 AATAATACTT
66 AATAATACTT
371720 TTACATTTAA
Statistics
Matches: 70, Mismatches: 5, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
78 70 1.00
ACGTcount: A:0.41, C:0.25, G:0.02, T:0.31
Consensus pattern (78 bp):
CTTAATACTTAAACTCCAAAATCAACAAACTTTCCAAAATTTCCAGAATTATTCTAACTCACCCA
AATAATACTTCAA
Found at i:374481 original size:16 final size:16
Alignment explanation
Indices: 374460--374491 Score: 64
Period size: 16 Copynumber: 2.0 Consensus size: 16
374450 GATCCTGTAT
374460 TTATGGGTTTGTATCG
1 TTATGGGTTTGTATCG
374476 TTATGGGTTTGTATCG
1 TTATGGGTTTGTATCG
374492 AATGGTTGCG
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:0.12, C:0.06, G:0.31, T:0.50
Consensus pattern (16 bp):
TTATGGGTTTGTATCG
Found at i:376069 original size:33 final size:33
Alignment explanation
Indices: 376021--376083 Score: 90
Period size: 33 Copynumber: 1.9 Consensus size: 33
376011 TAATTTGATT
* *
376021 TCATTTCTTACATCAATTTAGTTAAGTGAAGAG
1 TCATTGCTTAAATCAATTTAGTTAAGTGAAGAG
* *
376054 TCATTGCTTAAATCAATTTATTTAGGTGAA
1 TCATTGCTTAAATCAATTTAGTTAAGTGAA
376084 AATTAGGTAT
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
33 26 1.00
ACGTcount: A:0.33, C:0.11, G:0.14, T:0.41
Consensus pattern (33 bp):
TCATTGCTTAAATCAATTTAGTTAAGTGAAGAG
Found at i:376600 original size:21 final size:21
Alignment explanation
Indices: 376576--376615 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
376566 TCTTTCCTAT
* *
376576 TTTTTTAATTCATTTATTATA
1 TTTTGTAATTCATCTATTATA
376597 TTTTGTAATTCATCTATTA
1 TTTTGTAATTCATCTATTA
376616 ATTCCTTAGG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.28, C:0.07, G:0.03, T:0.62
Consensus pattern (21 bp):
TTTTGTAATTCATCTATTATA
Found at i:379061 original size:13 final size:14
Alignment explanation
Indices: 379017--379064 Score: 53
Period size: 15 Copynumber: 3.4 Consensus size: 14
379007 AATACTAATA
*
379017 ATAATAATTAAATAT
1 ATAA-AATTAAACAT
*
379032 ATTAAAAATAAACAT
1 A-TAAAATTAAACAT
379047 ATAAAATTAAA-AT
1 ATAAAATTAAACAT
379060 ATAAA
1 ATAAA
379065 TAAACAATGA
Statistics
Matches: 29, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
13 7 0.24
14 9 0.31
15 10 0.34
16 3 0.10
ACGTcount: A:0.67, C:0.02, G:0.00, T:0.31
Consensus pattern (14 bp):
ATAAAATTAAACAT
Found at i:379099 original size:17 final size:19
Alignment explanation
Indices: 379077--379120 Score: 67
Period size: 16 Copynumber: 2.5 Consensus size: 19
379067 AACAATGACT
379077 AAAATAAATAAAA-TT-TA
1 AAAATAAATAAAACTTGTA
379094 AAAAT-AATAAAACTTGTA
1 AAAATAAATAAAACTTGTA
379112 AAAATAAAT
1 AAAATAAAT
379121 GAAAGTAGTG
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
16 7 0.29
17 7 0.29
18 7 0.29
19 3 0.12
ACGTcount: A:0.68, C:0.02, G:0.02, T:0.27
Consensus pattern (19 bp):
AAAATAAATAAAACTTGTA
Found at i:380483 original size:3 final size:3
Alignment explanation
Indices: 380475--380545 Score: 117
Period size: 3 Copynumber: 24.0 Consensus size: 3
380465 AATATTTATT
380475 TAA TAA TAA TAA TAA T-A TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
**
380522 TAA TAA TTT TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA
380546 AATGAAATGA
Statistics
Matches: 63, Mismatches: 4, Indels: 2
0.91 0.06 0.03
Matches are distributed among these distances:
2 2 0.03
3 61 0.97
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (3 bp):
TAA
Found at i:380764 original size:45 final size:45
Alignment explanation
Indices: 380700--381444 Score: 1337
Period size: 45 Copynumber: 16.6 Consensus size: 45
380690 AGAGGTCCTA
380700 AAAACATCATGCACTGAAGGGCTTACAGATGACCCGAAGGTTTTG
1 AAAACATCATGCACTGAAGGGCTTACAGATGACCCGAAGGTTTTG
380745 AAAACATCATGCACTGAAGGGCTTACAGATGACCCGAAGGTTTTG
1 AAAACATCATGCACTGAAGGGCTTACAGATGACCCGAAGGTTTTG
380790 AAAACATCATGCACTGAAGGGCTTACAGATGACCCGAAGGTTTTG
1 AAAACATCATGCACTGAAGGGCTTACAGATGACCCGAAGGTTTTG
*
380835 AAAACATCATGCACTGAAGGGCTTACAGATGACCCGAAGGTTTTA
1 AAAACATCATGCACTGAAGGGCTTACAGATGACCCGAAGGTTTTG
* * *
380880 AAAACATCATGCACTGAAGGTCTTACAGATGGCTCGAAGGTTTTG
1 AAAACATCATGCACTGAAGGGCTTACAGATGACCCGAAGGTTTTG
* *
380925 ATAACATCATACACTGAAGGGCTTACAGATGACCCGAAGGTTTTG
1 AAAACATCATGCACTGAAGGGCTTACAGATGACCCGAAGGTTTTG
* *
380970 AAAACATCATGCATTGAAGGGCTTACAGATGACCTGAAGGTTTTG
1 AAAACATCATGCACTGAAGGGCTTACAGATGACCCGAAGGTTTTG
381015 AAAACATCATGCACTGAAGGGCTTACAGATGACCCGAAGGTTTTG
1 AAAACATCATGCACTGAAGGGCTTACAGATGACCCGAAGGTTTTG
*
381060 ATAACATCATGCACTGAAGGGCTTACAGATGACCCGAAGGTTTTG
1 AAAACATCATGCACTGAAGGGCTTACAGATGACCCGAAGGTTTTG
381105 AAAACATCATGCACTGAAGGGCTTACAGATGACCCGAAGGTTTTG
1 AAAACATCATGCACTGAAGGGCTTACAGATGACCCGAAGGTTTTG
* * *
381150 AAAACAACATGCACTGAAGGTCTTACAGATGGCCCGAAGGTTTTG
1 AAAACATCATGCACTGAAGGGCTTACAGATGACCCGAAGGTTTTG
* *
381195 AAAACATCATGCACTGAAGGTCTTACAGATGGCCCGAAGGTTTTG
1 AAAACATCATGCACTGAAGGGCTTACAGATGACCCGAAGGTTTTG
381240 AAAACATCATGCACTGAAGGGCTTACAGATGACCCGAAGGTTTTG
1 AAAACATCATGCACTGAAGGGCTTACAGATGACCCGAAGGTTTTG
* *
381285 ATAACATCATGAACTGAAGGGCTTACAGATGACCCGAAGGTTTTG
1 AAAACATCATGCACTGAAGGGCTTACAGATGACCCGAAGGTTTTG
381330 AAAACATCATGCACTGAAGGGCTTACAGATGACCCGAAGGTTTTG
1 AAAACATCATGCACTGAAGGGCTTACAGATGACCCGAAGGTTTTG
381375 AAAACATCATGCACTGAAGGGCTTACAGATGACCCGAAGGTTTTG
1 AAAACATCATGCACTGAAGGGCTTACAGATGACCCGAAGGTTTTG
*
381420 AAAACATCATGCACTGAAGGTCTTA
1 AAAACATCATGCACTGAAGGGCTTA
381445 TGTATGGCCC
Statistics
Matches: 671, Mismatches: 29, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
45 671 1.00
ACGTcount: A:0.33, C:0.19, G:0.24, T:0.23
Consensus pattern (45 bp):
AAAACATCATGCACTGAAGGGCTTACAGATGACCCGAAGGTTTTG
Found at i:381190 original size:20 final size:20
Alignment explanation
Indices: 381165--381235 Score: 54
Period size: 20 Copynumber: 3.3 Consensus size: 20
381155 AACATGCACT
381165 GAAGGTCTTACAGATGGCCC
1 GAAGGTCTTACAGATGGCCC
* * *
381185 GAAGGTTTTGAAAACATCAT-GCACT
1 GAAGGTCTT----ACA-GATGGC-CC
381210 GAAGGTCTTACAGATGGCCC
1 GAAGGTCTTACAGATGGCCC
381230 GAAGGT
1 GAAGGT
381236 TTTGAAAACA
Statistics
Matches: 38, Mismatches: 6, Indels: 14
0.66 0.10 0.24
Matches are distributed among these distances:
20 17 0.45
21 5 0.13
24 5 0.13
25 11 0.29
ACGTcount: A:0.30, C:0.20, G:0.28, T:0.23
Consensus pattern (20 bp):
GAAGGTCTTACAGATGGCCC
Found at i:382136 original size:22 final size:22
Alignment explanation
Indices: 382123--382167 Score: 81
Period size: 22 Copynumber: 2.0 Consensus size: 22
382113 TTTGTAAAGA
382123 GAATCTATCATCTTTGAAGAAT
1 GAATCTATCATCTTTGAAGAAT
*
382145 GAATCTATCATCTTTAAAGAAT
1 GAATCTATCATCTTTGAAGAAT
382167 G
1 G
382168 TAGATGTAGA
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.38, C:0.13, G:0.13, T:0.36
Consensus pattern (22 bp):
GAATCTATCATCTTTGAAGAAT
Found at i:386554 original size:17 final size:16
Alignment explanation
Indices: 386532--386581 Score: 64
Period size: 17 Copynumber: 3.0 Consensus size: 16
386522 CTTGATTAAA
386532 TTTTTTCCCTTTTTTCT
1 TTTTTTCCCTTTTTT-T
386549 TTTTTTCCCTTCTTTTT
1 TTTTTTCCCTT-TTTTT
* *
386566 TTTTCTCTCTTTTTTT
1 TTTTTTCCCTTTTTTT
386582 ACTTCAATTG
Statistics
Matches: 30, Mismatches: 2, Indels: 3
0.86 0.06 0.09
Matches are distributed among these distances:
16 5 0.17
17 21 0.70
18 4 0.13
ACGTcount: A:0.00, C:0.22, G:0.00, T:0.78
Consensus pattern (16 bp):
TTTTTTCCCTTTTTTT
Found at i:391940 original size:2 final size:2
Alignment explanation
Indices: 391935--391972 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
391925 TGTGTGTGTG
391935 TA TA TA TA TA TA TA TA 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 TA TA TA TA
391973 AAAGATATTT
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:393513 original size:22 final size:22
Alignment explanation
Indices: 393488--393538 Score: 75
Period size: 22 Copynumber: 2.3 Consensus size: 22
393478 TATATCAAAT
*
393488 GCGGTTGTTCATCTTCCCAGAG
1 GCGGCTGTTCATCTTCCCAGAG
*
393510 GCGGCTGTTCATCTTCCCAGCG
1 GCGGCTGTTCATCTTCCCAGAG
*
393532 GCTGCTG
1 GCGGCTG
393539 GGTGCATGGG
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 26 1.00
ACGTcount: A:0.10, C:0.31, G:0.29, T:0.29
Consensus pattern (22 bp):
GCGGCTGTTCATCTTCCCAGAG
Found at i:393692 original size:3 final size:3
Alignment explanation
Indices: 393684--393743 Score: 77
Period size: 3 Copynumber: 20.0 Consensus size: 3
393674 AATATTTATT
*
393684 TAA TAA TAA TAA TAA TAA T-A TAA TATA TAA TAT TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TA-A TAA TAA TAA TAA TAA TAA
**
393729 TAA TTT TAA TAA TAA
1 TAA TAA TAA TAA TAA
393744 AAATTTCAAT
Statistics
Matches: 49, Mismatches: 6, Indels: 4
0.83 0.10 0.07
Matches are distributed among these distances:
2 2 0.04
3 44 0.90
4 3 0.06
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (3 bp):
TAA
Found at i:396269 original size:213 final size:213
Alignment explanation
Indices: 395896--396325 Score: 754
Period size: 213 Copynumber: 2.0 Consensus size: 213
395886 GAAAATCGAC
395896 GCAAGAGCAAGAAAGACAGACAAGTAAATCTACAACAAGCAGAAGTGTTGAGAACGATGAGAGGG
1 GCAAGAGCAAGAAAGACAGACAAGTAAATCTACAACAAGCAGAAGTGTTGAGAACGATGAGAGGG
395961 AGGTGAACAGAACGTGGCCAAAGCAACAATCACAAACATGGTAGATCAAAGTCGAGAAGCAAAAA
66 AGGTGAACAGAACGTGGCCAAAGCAACAATCACAAACATGGTAGATCAAAGTCGAGAAGCAAAAA
* *
396026 GAATTTAAAGTGCTACAACTGTGAAAAGAATGATCACTTGAAGAAGGATTGTTGGAGTCTAGGTA
131 GAATTTAAAGTGCTACAACTATGAAAAGAATGATCACTTAAAGAAGGATTGTTGGAGTCTAGGTA
396091 AAAACTCCAATCCACAAG
196 AAAACTCCAATCCACAAG
396109 GCAAGAGCAAGAAAGACAGACAAGTAAATCTACAACAAGCAGAAGTGTTGAGAACGATGAGAGGG
1 GCAAGAGCAAGAAAGACAGACAAGTAAATCTACAACAAGCAGAAGTGTTGAGAACGATGAGAGGG
* * * *
396174 AGGTGACCAGAACGTGGCCAAAGTAGCAGTCACAAACATGGTAGATCAAAGTCGAGAAGCAAAAA
66 AGGTGAACAGAACGTGGCCAAAGCAACAATCACAAACATGGTAGATCAAAGTCGAGAAGCAAAAA
* *
396239 GAATTTTAAA-TGCTACAACTATGGAAAGAATGGTCACTTAAAGAAGGATTGTTGGAGTCTAGGT
131 GAA-TTTAAAGTGCTACAACTATGAAAAGAATGATCACTTAAAGAAGGATTGTTGGAGTCTAGGT
* *
396303 AAAAACTTCAATCTACAAG
195 AAAAACTCCAATCCACAAG
396322 GCAA
1 GCAA
396326 TACCACAAAC
Statistics
Matches: 206, Mismatches: 10, Indels: 2
0.94 0.05 0.01
Matches are distributed among these distances:
213 200 0.97
214 6 0.03
ACGTcount: A:0.43, C:0.15, G:0.25, T:0.17
Consensus pattern (213 bp):
GCAAGAGCAAGAAAGACAGACAAGTAAATCTACAACAAGCAGAAGTGTTGAGAACGATGAGAGGG
AGGTGAACAGAACGTGGCCAAAGCAACAATCACAAACATGGTAGATCAAAGTCGAGAAGCAAAAA
GAATTTAAAGTGCTACAACTATGAAAAGAATGATCACTTAAAGAAGGATTGTTGGAGTCTAGGTA
AAAACTCCAATCCACAAG
Found at i:401986 original size:30 final size:31
Alignment explanation
Indices: 401952--402009 Score: 82
Period size: 31 Copynumber: 1.9 Consensus size: 31
401942 AAAATTTGGG
* *
401952 GACC-ATTCTATAATTTTTGAAAAGTTGAGA
1 GACCAATTCGATAATTTTAGAAAAGTTGAGA
*
401982 GACCAATTCGATAATTTTAGAAATGTTG
1 GACCAATTCGATAATTTTAGAAAAGTTG
402010 TGAATGATTG
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
30 4 0.17
31 20 0.83
ACGTcount: A:0.36, C:0.10, G:0.17, T:0.36
Consensus pattern (31 bp):
GACCAATTCGATAATTTTAGAAAAGTTGAGA
Found at i:408525 original size:81 final size:81
Alignment explanation
Indices: 408385--408571 Score: 332
Period size: 81 Copynumber: 2.4 Consensus size: 81
408375 CCATGTGCTA
408385 AATAT-TTACTGGCTCCTCTTCATATGATAAATCTAGTGAATCTCAATTTTCTCCGGTGTAATCA
1 AATATCTTACTGGCTCCTCTTCATATGATAAATCTAGTGAATCTCAATTTTCTCCGGTGTAATCA
408449 CAGTGAAGATCTGATC
66 CAGTGAAGATCTGATC
408465 AATATCTTACTGGCTCCTCTTCATATGATAAATCTAGTGAATCTCAATTTTCTCCGGTGTAATCA
1 AATATCTTACTGGCTCCTCTTCATATGATAAATCTAGTGAATCTCAATTTTCTCCGGTGTAATCA
408530 CAGTGAAGATCTGATC
66 CAGTGAAGATCTGATC
408546 AATATC-T--T--CTCCTCTTCATATGATAA
1 AATATCTTACTGGCTCCTCTTCATATGATAA
408572 TCATCTTCGA
Statistics
Matches: 106, Mismatches: 0, Indels: 6
0.95 0.00 0.05
Matches are distributed among these distances:
76 18 0.17
78 1 0.01
80 6 0.06
81 81 0.76
ACGTcount: A:0.29, C:0.21, G:0.13, T:0.37
Consensus pattern (81 bp):
AATATCTTACTGGCTCCTCTTCATATGATAAATCTAGTGAATCTCAATTTTCTCCGGTGTAATCA
CAGTGAAGATCTGATC
Found at i:411909 original size:31 final size:30
Alignment explanation
Indices: 411874--412050 Score: 151
Period size: 31 Copynumber: 5.7 Consensus size: 30
411864 GAGTATCTTG
*
411874 GGGCCTGAGAGCCTACCCAAGAAAGTTCTCA
1 GGGCC-GAGAGCCTACCCAAGAAAGATCTCA
*
411905 GGGCC-ACGAGGCCTATCCAAGAAAGATCTCA
1 GGGCCGA-GA-GCCTACCCAAGAAAGATCTCA
* * *
411936 GGGCCACAGGGCCTACCCAAGAATGATCTCA
1 GGGCC-GAGAGCCTACCCAAGAAAGATCTCA
* * *
411967 GGGCC-ACGGGGCCTACCCAAGAAAAATCCCA
1 GGGCCGA--GAGCCTACCCAAGAAAGATCTCA
* * * *
411998 AGGCCGCTGAGCCTACCCAAGAATGATCTCG
1 GGGCCG-AGAGCCTACCCAAGAAAGATCTCA
*
412029 GGGTCGCAGAGCCTACCCAAGA
1 GGGCCG-AGAGCCTACCCAAGA
412051 GTCACATTAG
Statistics
Matches: 120, Mismatches: 18, Indels: 16
0.78 0.12 0.10
Matches are distributed among these distances:
29 2 0.02
30 2 0.02
31 114 0.95
32 1 0.01
33 1 0.01
ACGTcount: A:0.29, C:0.32, G:0.27, T:0.12
Consensus pattern (30 bp):
GGGCCGAGAGCCTACCCAAGAAAGATCTCA
Found at i:411971 original size:62 final size:62
Alignment explanation
Indices: 411881--412050 Score: 209
Period size: 62 Copynumber: 2.7 Consensus size: 62
411871 TTGGGGCCTG
* * * * * *
411881 AGAGCCTACCCAAGAAAGTTCTCAGGGCCACGAGGCCTATCCAAGAAAGATCTCAGGGCCAC
1 AGAGCCTACCCAAGAATGATCTCAGGGCCACGAGGCCTACCCAAGAAAAATCCCAAGGCCAC
* * *
411943 AGGGCCTACCCAAGAATGATCTCAGGGCCACGGGGCCTACCCAAGAAAAATCCCAAGGCCGC
1 AGAGCCTACCCAAGAATGATCTCAGGGCCACGAGGCCTACCCAAGAAAAATCCCAAGGCCAC
* *
412005 TGAGCCTACCCAAGAATGATCTCGGGGTCGCA-GA-GCCTACCCAAGA
1 AGAGCCTACCCAAGAATGATCTCAGGG-C-CACGAGGCCTACCCAAGA
412051 GTCACATTAG
Statistics
Matches: 93, Mismatches: 13, Indels: 4
0.85 0.12 0.04
Matches are distributed among these distances:
62 89 0.96
63 2 0.02
64 2 0.02
ACGTcount: A:0.31, C:0.32, G:0.25, T:0.12
Consensus pattern (62 bp):
AGAGCCTACCCAAGAATGATCTCAGGGCCACGAGGCCTACCCAAGAAAAATCCCAAGGCCAC
Found at i:418077 original size:20 final size:20
Alignment explanation
Indices: 418041--418078 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
418031 ATCCTATTCC
**
418041 CTGGTAATCTTTTATTCCCA
1 CTGGTAATCTTACATTCCCA
418061 CTGGTAATCTTACATTCC
1 CTGGTAATCTTACATTCC
418079 GTGAACCAAA
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:0.21, C:0.26, G:0.11, T:0.42
Consensus pattern (20 bp):
CTGGTAATCTTACATTCCCA
Found at i:423044 original size:12 final size:11
Alignment explanation
Indices: 423000--423117 Score: 57
Period size: 12 Copynumber: 10.5 Consensus size: 11
422990 TACATGAATG
423000 TTTT-ATCTGA
1 TTTTGATCTGA
*
423010 TTTTCGATTTGAA
1 TTTT-GATCTG-A
* *
423023 TTCTGTTCTGA
1 TTTTGATCTGA
423034 TTTCTGATCTGA
1 TTT-TGATCTGA
*
423046 -ATT-A--TGA
1 TTTTGATCTGA
*
423053 TTTTTATCTGAA
1 TTTTGATCTG-A
*
423065 TTTTGTTCTGA
1 TTTTGATCTGA
423076 TTTCTGATCTGGA
1 TTT-TGATCT-GA
*
423089 TTTTGTTCTGA
1 TTTTGATCTGA
*
423100 TATATGATCTGAA
1 T-TTTGATCTG-A
423113 TTTTG
1 TTTTG
423118 TTTTGATTTC
Statistics
Matches: 80, Mismatches: 15, Indels: 24
0.67 0.13 0.20
Matches are distributed among these distances:
7 3 0.04
8 2 0.03
9 2 0.03
10 5 0.06
11 13 0.16
12 44 0.55
13 11 0.14
ACGTcount: A:0.19, C:0.10, G:0.16, T:0.54
Consensus pattern (11 bp):
TTTTGATCTGA
Found at i:423046 original size:24 final size:24
Alignment explanation
Indices: 423005--423128 Score: 118
Period size: 24 Copynumber: 5.4 Consensus size: 24
422995 GAATGTTTTA
* *
423005 TCTGATTT-TCGATTTGAATTCTGT
1 TCTGATTTCT-GATCTGAATTTTGT
423029 TCTGATTTCTGATCTGAA-----T
1 TCTGATTTCTGATCTGAATTTTGT
* *
423048 TATGATTT-TTATCTGAATTTTGT
1 TCTGATTTCTGATCTGAATTTTGT
*
423071 TCTGATTTCTGATCTGGATTTTGT
1 TCTGATTTCTGATCTGAATTTTGT
* *
423095 TCTGATATATGATCTGAATTTTGT
1 TCTGATTTCTGATCTGAATTTTGT
*
423119 TTTGATTTCT
1 TCTGATTTCT
423129 TATATCTCCG
Statistics
Matches: 81, Mismatches: 12, Indels: 14
0.76 0.11 0.13
Matches are distributed among these distances:
18 8 0.10
19 8 0.10
23 8 0.10
24 56 0.69
25 1 0.01
ACGTcount: A:0.19, C:0.10, G:0.16, T:0.55
Consensus pattern (24 bp):
TCTGATTTCTGATCTGAATTTTGT
Found at i:423055 original size:19 final size:18
Alignment explanation
Indices: 423031--423066 Score: 54
Period size: 18 Copynumber: 1.9 Consensus size: 18
423021 AATTCTGTTC
423031 TGATTTCTGATCTGAATTA
1 TGATTT-TGATCTGAATTA
*
423050 TGATTTTTATCTGAATT
1 TGATTTTGATCTGAATT
423067 TTGTTCTGAT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 10 0.62
19 6 0.38
ACGTcount: A:0.25, C:0.08, G:0.14, T:0.53
Consensus pattern (18 bp):
TGATTTTGATCTGAATTA
Found at i:423081 original size:54 final size:54
Alignment explanation
Indices: 423000--423107 Score: 125
Period size: 54 Copynumber: 2.0 Consensus size: 54
422990 TACATGAATG
*
423000 TTTTATCTGATTTTCGATTTGAATTCTGTTCT-GATTTCTGATCTGA-ATTATGAT
1 TTTTATCTGATTTTCGATTTGAATTCTGATCTGGATTT-TGATCTGATA-TATGAT
* *
423054 TTTTATCTGAATTTT-G-TTCTGATTTCTGATCTGGATTTTGTTCTGATATATGAT
1 TTTTATCTG-ATTTTCGATT-TGAATTCTGATCTGGATTTTGATCTGATATATGAT
423108 CTGAATTTTG
Statistics
Matches: 47, Mismatches: 3, Indels: 8
0.81 0.05 0.14
Matches are distributed among these distances:
53 2 0.04
54 34 0.72
55 11 0.23
ACGTcount: A:0.19, C:0.10, G:0.16, T:0.55
Consensus pattern (54 bp):
TTTTATCTGATTTTCGATTTGAATTCTGATCTGGATTTTGATCTGATATATGAT
Done.